Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 50 of 333
Found at i:14411283 original size:44 final size:43
Alignment explanation
Indices: 14411229--14411360 Score: 103
Period size: 44 Copynumber: 3.0 Consensus size: 43
14411219 AATAGTAAAA
*
14411229 AATATGAAAAAAAATATAAATAGCAAAATAAAAATAAAAATAAT
1 AATATAAAAAAAAATATAAATAG-AAAATAAAAATAAAAATAAT
14411273 AATATAAAAAATTAAA-A-AAATTA-AAACATAAAAAATTAAAAAT-AT
1 AATATAAAAAA--AAATATAAA-TAGAAA-AT-AAAAA-TAAAAATAAT
* * *
14411318 AAGTATAAGAATAAAT-TAATTAGTAAAATAAAAATAAATAATA
1 AA-TATAAAAAAAAATATAAATAG-AAAATAAAAATAAA-AATA
14411361 TAACAATTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
43 7 0.10
44 28 0.39
45 16 0.23
46 20 0.28
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (43 bp):
AATATAAAAAAAAATATAAATAGAAAATAAAAATAAAAATAAT
Found at i:14411290 original size:9 final size:8
Alignment explanation
Indices: 14411277--14411314 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
14411267 AATAATAATA
14411277 TAAAAAAT
1 TAAAAAAT
14411285 TAAAAAAAT
1 T-AAAAAAT
*
14411294 TAAAACA-
1 TAAAAAAT
14411301 TAAAAAAT
1 TAAAAAAT
14411309 TAAAAA
1 TAAAAA
14411315 TATAAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 12 0.46
9 8 0.31
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (8 bp):
TAAAAAAT
Found at i:14411291 original size:24 final size:23
Alignment explanation
Indices: 14411264--14411319 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
14411254 AAATAAAAAT
*
14411264 AAAAATAATAATATAAAAAATTAA
1 AAAAATAA-AACATAAAAAATTAA
14411288 AAAAATTAAAACATAAAAAATTAA
1 AAAAA-TAAAACATAAAAAATTAA
*
14411312 AAATATAA
1 AAAAATAA
14411320 GTATAAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 3 0.10
24 23 0.79
25 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAATAAAACATAAAAAATTAA
Found at i:14411361 original size:44 final size:42
Alignment explanation
Indices: 14411253--14411363 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 42
14411243 TATAAATAGC
14411253 AAAATAAAAATAAAAATAATAATATAAAAAATTAAAAAAATTA
1 AAAATAAAAATAAAAAT-ATAATATAAAAAATTAAAAAAATTA
* **
14411296 AAACATAAAAAATTAAAAATATAAGTAT-AAGAA-TAAATTAATTA
1 AAA-AT-AAAAA-TAAAAATATAA-TATAAAAAATTAAAAAAATTA
14411340 GTAAAATAAAAATAAATAATATAA
1 --AAAATAAAAATAAA-AATATAA
14411364 CAATTAATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
43 7 0.12
44 23 0.40
45 15 0.26
46 13 0.22
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (42 bp):
AAAATAAAAATAAAAATATAATATAAAAAATTAAAAAAATTA
Found at i:14411363 original size:38 final size:36
Alignment explanation
Indices: 14411300--14411387 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 36
14411290 AAATTAAAAC
* *
14411300 ATAAA-AAATTAAAAATATAAGTATAAGAATAAATTA
1 ATAAATAAAATAAAAATATAAGTATAACAATAAA-TA
* * *
14411336 ATTAGTAAAATAAAAATAAATAA-TATAACAATTAATA
1 ATAAATAAAATAAAAAT--ATAAGTATAACAATAAATA
14411373 ATAAATAAAATAAAA
1 ATAAATAAAATAAAA
14411388 TTGGGGTGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
36 3 0.07
37 25 0.60
38 10 0.24
39 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.27
Consensus pattern (36 bp):
ATAAATAAAATAAAAATATAAGTATAACAATAAATA
Found at i:14427299 original size:2 final size:2
Alignment explanation
Indices: 14427294--14427328 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14427284 AACATATATA
14427294 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
14427329 TTGGTGTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:14431424 original size:11 final size:11
Alignment explanation
Indices: 14431408--14431466 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
14431398 CTTTATATAC
14431408 TAATAAAATAA
1 TAATAAAATAA
14431419 TAATAAAATAA
1 TAATAAAATAA
*
14431430 TAATAAAATATCT
1 TAATAAAATA--A
* *
14431443 TATTAAAATAT
1 TAATAAAATAA
14431454 TAATAAAATAA
1 TAATAAAATAA
14431465 TA
1 TA
14431467 TTTATCTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 33 0.79
13 9 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:14434738 original size:46 final size:46
Alignment explanation
Indices: 14434469--14434738 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
14434459 TTTGACATGA
* * * * ** *
14434469 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGCCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** *
14434515 TGCCATGGTATCTTTCAACCATGGTATTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * *
14434561 TCCCATGGTATCTTTCAACCATGGTCTTA-TCATTT-ATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
14434605 TGCCATGGTATCTTTCAACCAT-GTCTTACA-ATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * *
14434649 TGCCATGGTATATTTCAACCATGGTCTTAAACAATTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
14434695 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
14434739 AGAGCACACT
Statistics
Matches: 200, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
43 10 0.05
44 59 0.29
45 17 0.09
46 114 0.57
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:14436871 original size:27 final size:27
Alignment explanation
Indices: 14436805--14436882 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
14436795 TCTTTATATA
14436805 CTAATAAAATAATAAAAAAATATCTTAT
1 CTAAT-AAATAATAAAAAAATATCTTAT
*
14436833 -TAA-AATATTAATAAAATAATAT-TTAT
1 CTAATAA-A-TAATAAAAAAATATCTTAT
* *
14436859 CTAATTAAATAATTATAAAATATC
1 CTAA-TAAATAATAAAAAAATATC
14436883 AAAATATCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 30 0.75
28 1 0.03
29 2 0.05
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (27 bp):
CTAATAAATAATAAAAAAATATCTTAT
Found at i:14438910 original size:2 final size:2
Alignment explanation
Indices: 14438903--14438929 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14438893 ATGCTAGCTT
14438903 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 T
14438930 TAAGTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14447866 original size:41 final size:42
Alignment explanation
Indices: 14447788--14447866 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
14447778 AATACTCGAT
**
14447788 ATCTCGCACACTAAGTGCCAATACATAGTTGAAGCTATTATA
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTATTATA
*
14447830 ATCTCGCACACTAAGTGCC-TTACATAGCCGAAGCTAT
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTAT
14447867 CTCGGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (42 bp):
ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTATTATA
Found at i:14448196 original size:20 final size:20
Alignment explanation
Indices: 14448166--14448204 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
14448156 TGCTTTAAAA
14448166 CACATTTTCAC-TTTTTCCC
1 CACATTTTCACATTTTTCCC
14448185 CACATATTTCACATTTTTCC
1 CACAT-TTTCACATTTTTCC
14448205 TAATTTAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (20 bp):
CACATTTTCACATTTTTCCC
Found at i:14449091 original size:2 final size:2
Alignment explanation
Indices: 14449084--14449118 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14449074 ATGCTAGCTT
14449084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14449119 TAATTTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14452473 original size:18 final size:19
Alignment explanation
Indices: 14452450--14452486 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
14452440 CATTCAAACA
14452450 CCAGAAAAGT-AATCATTT
1 CCAGAAAAGTAAATCATTT
14452468 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
14452487 TTCAGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:14454049 original size:3 final size:3
Alignment explanation
Indices: 14454041--14454070 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
14454031 TTGCATGGAA
14454041 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14454071 CCAATCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:14456560 original size:24 final size:21
Alignment explanation
Indices: 14456525--14456571 Score: 51
Period size: 24 Copynumber: 2.1 Consensus size: 21
14456515 AAGGATAAAG
14456525 AAACAAACAAGATCATAAAACAAA
1 AAACAAACAAGA-CA-AAAA-AAA
14456549 AAACATAA-AAGACAAAAAAAA
1 AAACA-AACAAGACAAAAAAAA
14456570 AA
1 AA
14456572 CCGACAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 5 0.23
22 4 0.18
23 2 0.09
24 9 0.41
25 2 0.09
ACGTcount: A:0.77, C:0.13, G:0.04, T:0.06
Consensus pattern (21 bp):
AAACAAACAAGACAAAAAAAA
Found at i:14457375 original size:19 final size:18
Alignment explanation
Indices: 14457348--14457383 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
14457338 GGTTTAAGTA
14457348 TTAAATTAAATATTAAAG
1 TTAAATTAAATATTAAAG
14457366 TTAAATTTAAATATTAAA
1 TTAAA-TTAAATATTAAA
14457384 TACTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTAAATTAAATATTAAAG
Found at i:14458942 original size:299 final size:299
Alignment explanation
Indices: 14458553--14459195 Score: 785
Period size: 299 Copynumber: 2.1 Consensus size: 299
14458543 CTTTATTTTA
* * * ** *
14458553 ATATTTTAATATATTTTAATTTTATTATTCACATTTTATTA-CTTACATCAATTGTATATCAATA
1 ATATTTTAACAT-TTTT-ATTTTAATATGCACAAGTTAATATCTT-CATCAATTGTATATCAATA
14458617 CTTACTATTTATTAAGTGTTTTATTGAGTTGGTGGC-TCCCTCAACCAAGTCACCAACTCGGCTA
63 CTTACTATTTATTAAGTGTTTTATTGAGTTGGTGGCAT-CCTCAACCAAGTCACCAACTCGGCTA
* * * * *
14458681 GGAAATTACGAAAATGTCATTCCATAATTAAAATAAGTTATATTATTTGAGGGTAGTTTAATCTT
127 GGAAATTACGAAAATATCATTCCATAATTAAAA-AAGCTATACTATTCGAAGGTAGTTTAATCTT
* *
14458746 TTCATTTTAAGAAAAAAC-AATTAAAATATGCAGATGGTAGGATTTAAATCCGCGCCAATTAGA-
191 TTCATTTTAA-AAAAAACTAATTAAAATATGAAGATGGTAGGATTTAAATCCGCGCAAATTAGAT
* * * *
14458809 A-AAAAATCCTTAAATTTACCATTCAACCAAAGCTTCA-TTTTAAT
255 AGAAAAAT-ATTAAATTTACCACTAAACCAAAGCTTCATTTTTAAC
*
14458853 ATATTTTAGACATTTTTATTTTAATATGCGCAAGTTAATATCTTCATCAATTGTATATCAATACT
1 ATATTTTA-ACATTTTTATTTTAATATGCACAAGTTAATATCTTCATCAATTGTATATCAATACT
* * * * *
14458918 TACTATTTATTAAGTGTTTTATTGAGTTGGTGTCATCCTCAATCGAGTGACCAACTCGGTTAGGA
65 TACTATTTATTAAGTGTTTTATTGAGTTGGTGGCATCCTCAACCAAGTCACCAACTCGGCTAGGA
* * * * * * *
14458983 AATTATGGAAATATCCTTCCCTCATTAAAAAAGCTATACTATTCGAAGGTATTTTAGTCTTTTCA
130 AATTACGAAAATATCATTCCATAATTAAAAAAGCTATACTATTCGAAGGTAGTTTAATCTTTTCA
* * * * *
14459048 TTTTAACAAAAACTAATTAAAATATGAATATGGTGGGATTTGAATCCGCGCAAATTAGATTAGTA
195 TTTTAAAAAAAACTAATTAAAATATGAAGATGGTAGGATTTAAATCCGCGCAAATTAGA-TAGAA
* ** * *
14459113 AAATATTAAATTTATCACTAAACCAAATTTTTATTTTTGAC
259 AAATATTAAATTTACCACTAAACCAAAGCTTCATTTTTAAC
* *
14459154 ATATTTTATCATTTTTATTTTAATATGCACAAGTTATTATCT
1 ATATTTTAACATTTTTATTTTAATATGCACAAGTTAATATCT
14459196 CTATTAGTTG
Statistics
Matches: 292, Mismatches: 43, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
297 6 0.02
298 75 0.26
299 120 0.41
300 70 0.24
301 21 0.07
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (299 bp):
ATATTTTAACATTTTTATTTTAATATGCACAAGTTAATATCTTCATCAATTGTATATCAATACTT
ACTATTTATTAAGTGTTTTATTGAGTTGGTGGCATCCTCAACCAAGTCACCAACTCGGCTAGGAA
ATTACGAAAATATCATTCCATAATTAAAAAAGCTATACTATTCGAAGGTAGTTTAATCTTTTCAT
TTTAAAAAAAACTAATTAAAATATGAAGATGGTAGGATTTAAATCCGCGCAAATTAGATAGAAAA
ATATTAAATTTACCACTAAACCAAAGCTTCATTTTTAAC
Found at i:14459411 original size:19 final size:19
Alignment explanation
Indices: 14459387--14459427 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
14459377 GTTTCAGGAG
14459387 CCATACGGGCTGGGCCATT
1 CCATACGGGCTGGGCCATT
14459406 CCATACGGGCTGGGCCATT
1 CCATACGGGCTGGGCCATT
14459425 CCA
1 CCA
14459428 CACAGGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.34, G:0.29, T:0.20
Consensus pattern (19 bp):
CCATACGGGCTGGGCCATT
Found at i:14459435 original size:19 final size:19
Alignment explanation
Indices: 14459394--14459435 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
14459384 GAGCCATACG
* *
14459394 GGCTGGGCCATTCCATACG
1 GGCTGGGCCATTCCACACA
14459413 GGCTGGGCCATTCCACACA
1 GGCTGGGCCATTCCACACA
14459432 GGCT
1 GGCT
14459436 AGACACACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (19 bp):
GGCTGGGCCATTCCACACA
Found at i:14459481 original size:29 final size:30
Alignment explanation
Indices: 14459425--14459481 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
14459415 CTGGGCCATT
* * *
14459425 CCACACAGGCTAGACACACGGCCGTGTGAG
1 CCACACAAGCTAGACACACGACCATGTGAG
*
14459455 CCACACAAGCTA-CCACACGACCATGTG
1 CCACACAAGCTAGACACACGACCATGTG
14459482 CCAAACCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.30, C:0.37, G:0.23, T:0.11
Consensus pattern (30 bp):
CCACACAAGCTAGACACACGACCATGTGAG
Found at i:14460591 original size:20 final size:19
Alignment explanation
Indices: 14460543--14460603 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
14460533 AGGAAAACTT
14460543 TATTTTTA--TTAATTTAA
1 TATTTTTATTTTAATTTAA
* *
14460560 TATTTTTATTTTATTTTAG
1 TATTTTTATTTTAATTTAA
*
14460579 TATTTTTGTTTTTAATTTAA
1 TATTTTT-ATTTTAATTTAA
14460599 T-TTTT
1 TATTTT
14460604 ACATTCTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 8 0.22
19 18 0.50
20 10 0.28
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TATTTTTATTTTAATTTAA
Found at i:14461082 original size:22 final size:23
Alignment explanation
Indices: 14461057--14461102 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
14461047 CAACCAAACC
14461057 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
14461079 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
14461102 A
1 A
14461103 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:14461108 original size:23 final size:23
Alignment explanation
Indices: 14461064--14461108 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
14461054 ACCAATTCAA
*
14461064 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
14461087 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
14461109 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:14462628 original size:106 final size:106
Alignment explanation
Indices: 14462442--14462637 Score: 383
Period size: 106 Copynumber: 1.8 Consensus size: 106
14462432 TCTTCACTAA
14462442 AAATTAATTATCTCTTCATAAAAAATTCGAATGATGTTTTCGTTTGTTTCTATTGAAAATAGACT
1 AAATTAATTATCTCTTCATAAAAAATTCGAATGATGTTTTCGTTTGTTTCTATTGAAAATAGACT
14462507 CATTCAAGATCCTATGCATATAAATAATAATGAAATTATAG
66 CATTCAAGATCCTATGCATATAAATAATAATGAAATTATAG
14462548 AAATTAATTATCTCTTCATAAAAAATTCGAATGATGTTTTCGTTTGTTTCTATTGAAAATAGACT
1 AAATTAATTATCTCTTCATAAAAAATTCGAATGATGTTTTCGTTTGTTTCTATTGAAAATAGACT
*
14462613 CATTCAAGATTCTATGCATATAAAT
66 CATTCAAGATCCTATGCATATAAAT
14462638 TTAAGCCCCT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (106 bp):
AAATTAATTATCTCTTCATAAAAAATTCGAATGATGTTTTCGTTTGTTTCTATTGAAAATAGACT
CATTCAAGATCCTATGCATATAAATAATAATGAAATTATAG
Found at i:14468136 original size:25 final size:25
Alignment explanation
Indices: 14468065--14468125 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
14468055 ACGAGAGACA
14468065 AACGGTAAGCTCATCCGAGCTGAAT
1 AACGGTAAGCTCATCCGAGCTGAAT
* * *
14468090 ATCGGTAAGCTCCTCCGAGCTGGAT
1 AACGGTAAGCTCATCCGAGCTGAAT
14468115 AACGGTAAGCT
1 AACGGTAAGCT
14468126 TATGCAAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (25 bp):
AACGGTAAGCTCATCCGAGCTGAAT
Found at i:14470609 original size:169 final size:169
Alignment explanation
Indices: 14470330--14470670 Score: 673
Period size: 169 Copynumber: 2.0 Consensus size: 169
14470320 ATCTGGATAC
14470330 AGAGTCGGAAATATGATGTTTCATTACGGGTCATTGATACATCTGTTTCCATTTATTGTACAATT
1 AGAGTCGGAAATATGATGTTTCATTACGGGTCATTGATACATCTGTTTCCATTTATTGTACAATT
14470395 AATTACTTCTGAAATGAACAAACATAATACCATTTTGAGCTTCGTGCAAAATTTTTTGTATCAGC
66 AATTACTTCTGAAATGAACAAACATAATACCATTTTGAGCTTCGTGCAAAATTTTTTGTATCAGC
*
14470460 TCTGGACTTTTGAGTACACTAAATATATTTCTGAATAAT
131 TCTGGACTTTTCAGTACACTAAATATATTTCTGAATAAT
14470499 AGAGTCGGAAATATGATGTTTCATTACGGGTCATTGATACATCTGTTTCCATTTATTGTACAATT
1 AGAGTCGGAAATATGATGTTTCATTACGGGTCATTGATACATCTGTTTCCATTTATTGTACAATT
14470564 AATTACTTCTGAAATGAACAAACATAATACCATTTTGAGCTTCGTGCAAAATTTTTTGTATCAGC
66 AATTACTTCTGAAATGAACAAACATAATACCATTTTGAGCTTCGTGCAAAATTTTTTGTATCAGC
14470629 TCTGGACTTTTCAGTACACTAAATATATTTCTGAATAAT
131 TCTGGACTTTTCAGTACACTAAATATATTTCTGAATAAT
14470668 AGA
1 AGA
14470671 CAATCATTGT
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 171 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (169 bp):
AGAGTCGGAAATATGATGTTTCATTACGGGTCATTGATACATCTGTTTCCATTTATTGTACAATT
AATTACTTCTGAAATGAACAAACATAATACCATTTTGAGCTTCGTGCAAAATTTTTTGTATCAGC
TCTGGACTTTTCAGTACACTAAATATATTTCTGAATAAT
Found at i:14471564 original size:34 final size:34
Alignment explanation
Indices: 14471515--14471582 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
14471505 TGAAGCAGAA
*
14471515 GTATCGTCCACCGTATACACTTTTAGTAATGTCT
1 GTATCGTCCACCGTATACACTTTTACTAATGTCT
* *
14471549 GTATCTTCCATCGTATACACTTTTACTAATGTCT
1 GTATCGTCCACCGTATACACTTTTACTAATGTCT
14471583 ATCCTTTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (34 bp):
GTATCGTCCACCGTATACACTTTTACTAATGTCT
Found at i:14474646 original size:25 final size:25
Alignment explanation
Indices: 14474612--14474670 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
14474602 AGCGATAAAC
*
14474612 GGTAAGCTCATTCGAGCTGAATATT
1 GGTAAGCTCATCCGAGCTGAATATT
*
14474637 GGTAAGCTCATCCGATCTGAATATT
1 GGTAAGCTCATCCGAGCTGAATATT
14474662 GGTAAGCTC
1 GGTAAGCTC
14474671 TTCCAAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (25 bp):
GGTAAGCTCATCCGAGCTGAATATT
Found at i:14476777 original size:46 final size:44
Alignment explanation
Indices: 14476675--14476779 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 44
14476665 TATTTTTATA
*
14476675 TTATTTTTTTCTTTTTTGTTTCTATTTTATTATGCACTGTTCTT
1 TTATTTTTTTCTTTGTTGTTTCTATTTTATTATGCACTGTTCTT
* *
14476719 TTATTGTTTTTTCGTTTGTT-TTTCTATTTTATTAT-CGCTTTATCTT
1 TTA-T-TTTTTTC-TTTGTTGTTTCTATTTTATTATGCACTGT-TCTT
14476765 CTTATTTATTTTCTT
1 -TTATTT-TTTTCTT
14476780 ATTAGTTTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
44 3 0.06
45 9 0.17
46 32 0.62
47 8 0.15
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.70
Consensus pattern (44 bp):
TTATTTTTTTCTTTGTTGTTTCTATTTTATTATGCACTGTTCTT
Found at i:14477663 original size:21 final size:20
Alignment explanation
Indices: 14477635--14477692 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
14477625 TTTTTGTTCT
14477635 AAAA-AAAGAATAAAAAATCG
1 AAAAGAAAGAATAAAAAA-CG
*
14477655 AAAAGAAAGAA-AAAAAAGG
1 AAAAGAAAGAATAAAAAACG
14477674 AAAAGGAAA-ACATAAAAAA
1 AAAA-GAAAGA-ATAAAAAA
14477693 GAGAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 6 0.18
20 15 0.45
21 12 0.36
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAAGAAAGAATAAAAAACG
Found at i:14480517 original size:25 final size:25
Alignment explanation
Indices: 14480489--14480538 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
14480479 CGAAAAGTGT
14480489 GATTTTTGGATTTCGATTCTGTAAA
1 GATTTTTGGATTTCGATTCTGTAAA
14480514 GATTTTTGGATTTCGATTCTGTAAA
1 GATTTTTGGATTTCGATTCTGTAAA
14480539 CTAGACTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (25 bp):
GATTTTTGGATTTCGATTCTGTAAA
Found at i:14482568 original size:13 final size:13
Alignment explanation
Indices: 14482550--14482576 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14482540 GCTTTTAATT
14482550 TGGATTTGGCATC
1 TGGATTTGGCATC
14482563 TGGATTTGGCATC
1 TGGATTTGGCATC
14482576 T
1 T
14482577 ACCTAGGATG
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:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (13 bp):
TGGATTTGGCATC
Found at i:14486962 original size:26 final size:26
Alignment explanation
Indices: 14486931--14487038 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
14486921 TGAAATGCCC
*
14486931 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
14486957 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
14486983 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
14487009 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
14487035 ATCA
1 ATCA
14487039 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:14493341 original size:14 final size:14
Alignment explanation
Indices: 14493324--14493350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14493314 GTGTCTATAA
14493324 TTTAAAATTTAGGG
1 TTTAAAATTTAGGG
14493338 TTTAAAATTTAGG
1 TTTAAAATTTAGG
14493351 ATTCATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (14 bp):
TTTAAAATTTAGGG
Found at i:14493388 original size:15 final size:15
Alignment explanation
Indices: 14493357--14493391 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
14493347 TAGGATTCAT
**
14493357 GATTTCAAGATTTAA
1 GATTTCAAGATACAA
14493372 GATTTCAAGATACAA
1 GATTTCAAGATACAA
14493387 GATTT
1 GATTT
14493392 AGAGCTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (15 bp):
GATTTCAAGATACAA
Found at i:14494992 original size:23 final size:23
Alignment explanation
Indices: 14494948--14494992 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
14494938 TTGTATTAAA
**
14494948 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAAAATAAATATG
*
14494971 ATTAAAAATAAAAAATATATAT
1 ATTAAAAATAAAAAATAAATAT
14494993 TTAGTATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTAAAAATAAAAAATAAATATG
Found at i:14496088 original size:27 final size:26
Alignment explanation
Indices: 14496069--14496124 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
14496059 TTTTATTATT
14496069 TTTAAGAATAAAACTAATTTTACGAC
1 TTTAAGAATAAAACTAATTTTACGAC
**
14496095 TTTATTAATAAAACTAATTTTACGAC
1 TTTAAGAATAAAACTAATTTTACGAC
14496121 TTTA
1 TTTA
14496125 TTCATAGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (26 bp):
TTTAAGAATAAAACTAATTTTACGAC
Found at i:14496104 original size:26 final size:26
Alignment explanation
Indices: 14496075--14496126 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
14496065 TATTTTTAAG
14496075 AATAAAACTAATTTTACGACTTTATT
1 AATAAAACTAATTTTACGACTTTATT
14496101 AATAAAACTAATTTTACGACTTTATT
1 AATAAAACTAATTTTACGACTTTATT
14496127 CATAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (26 bp):
AATAAAACTAATTTTACGACTTTATT
Found at i:14498484 original size:2 final size:2
Alignment explanation
Indices: 14498477--14498501 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14498467 ATTGCTCCAT
14498477 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
14498502 TTTTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:14499615 original size:9 final size:9
Alignment explanation
Indices: 14499601--14499648 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
14499591 AATCGAATCG
14499601 AGTTATTCA
1 AGTTATTCA
14499610 AGTTATTCGA
1 AGTTATTC-A
14499620 A-TTATTCA
1 AGTTATTCA
*
14499628 ACTTATTCGA
1 AGTTATTC-A
14499638 A-TTATTCA
1 AGTTATTCA
14499646 AGT
1 AGT
14499649 CAACTCGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.11
9 27 0.77
10 4 0.11
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (9 bp):
AGTTATTCA
Found at i:14499624 original size:18 final size:18
Alignment explanation
Indices: 14499598--14499648 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
14499588 GTTAATCGAA
*
14499598 TCGAGTTATTCAAGTTAT
1 TCGAATTATTCAAGTTAT
*
14499616 TCGAATTATTCAACTTAT
1 TCGAATTATTCAAGTTAT
14499634 TCGAATTATTCAAGT
1 TCGAATTATTCAAGT
14499649 CAACTCGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (18 bp):
TCGAATTATTCAAGTTAT
Found at i:14501850 original size:27 final size:30
Alignment explanation
Indices: 14501774--14501850 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 30
14501764 TTTAAAAGTT
* *
14501774 AATTT-TTTTAGATCCCTTAAAAGTTGATA
1 AATTTCTTTTTGACCCCTTAAAAGTTGATA
* *
14501803 AATTTCTTTTTTACCCTTTAAAAGTT-A-A
1 AATTTCTTTTTGACCCCTTAAAAGTTGATA
14501831 AA-TTC-TTTTGAGCCCCTTAA
1 AATTTCTTTTTGA-CCCCTTAA
14501851 CAACTGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
26 5 0.12
27 10 0.25
28 3 0.08
29 6 0.15
30 16 0.40
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (30 bp):
AATTTCTTTTTGACCCCTTAAAAGTTGATA
Found at i:14503749 original size:27 final size:27
Alignment explanation
Indices: 14503691--14503751 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
14503681 CATTTTATTG
* *
14503691 GTTTTTTTAATATAATTTAGTTTTAGAT
1 GTTTTTTAAATATAATTTA-TTTTAAAT
14503719 -TTTTTTAAATATAATTT-TTTTAAATT
1 GTTTTTTAAATATAATTTATTTTAAA-T
14503745 GTTTTTT
1 GTTTTTT
14503752 TTCCTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 6 0.21
26 1 0.03
27 22 0.76
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (27 bp):
GTTTTTTAAATATAATTTATTTTAAAT
Found at i:14506437 original size:21 final size:19
Alignment explanation
Indices: 14506413--14506453 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
14506403 GCAGGGGAAG
14506413 GAAAGAAAGAAAAAGAGAAAA
1 GAAAG-AAGAAAAA-AGAAAA
*
14506434 GAAAGAAGAAAGAAGAAAA
1 GAAAGAAGAAAAAAGAAAA
14506453 G
1 G
14506454 GAAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
GAAAGAAGAAAAAAGAAAA
Found at i:14508967 original size:46 final size:46
Alignment explanation
Indices: 14508900--14509220 Score: 437
Period size: 46 Copynumber: 7.0 Consensus size: 46
14508890 GCTCTCTGAA
* *
14508900 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
14508946 ATGAAATGTGTAAGACCATGGTTGAAAGATAACATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
14508992 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
14509038 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
14509084 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* ** *
14509130 AGGAAAATGAATAAGACCATGGTTGAAAGATACTATGGCAACATGAC
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * * * *
14509177 A-GAAAACGAGTAAAACTATAGTTGAAAGATACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
14509221 TCGAAGATAA
Statistics
Matches: 258, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 215 0.83
47 43 0.17
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:14510459 original size:10 final size:10
Alignment explanation
Indices: 14510440--14510489 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
14510430 TCAAATTCTA
14510440 AAAGATAAAT
1 AAAGATAAAT
14510450 ACAA-ATAAAT
1 A-AAGATAAAT
*
14510460 AAAGATAATT
1 AAAGATAAAT
14510470 AAAGATAAAT
1 AAAGATAAAT
*
14510480 AAATATAAAT
1 AAAGATAAAT
14510490 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:14512881 original size:6 final size:6
Alignment explanation
Indices: 14512870--14512899 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
14512860 TTTCTTCTAG
14512870 CACCTC CACCTC CACCTC CACCTC CACCTC
1 CACCTC CACCTC CACCTC CACCTC CACCTC
14512900 TAGACGCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CACCTC
Found at i:14514509 original size:20 final size:20
Alignment explanation
Indices: 14514477--14514514 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
14514467 TGTTTCACAT
14514477 TCATATAACTAATATTTATA
1 TCATATAACTAATATTTATA
*
14514497 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
14514515 ACTTAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATA
Found at i:14519736 original size:33 final size:32
Alignment explanation
Indices: 14519698--14519781 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 32
14519688 CCATGTCAAT
* *
14519698 ATTTAAATGTAAGACCATAGCTA-ATCTATGGC
1 ATTTTAATGTAAGACCATAACTAGAT-TATGGC
* *
14519730 ATTTTAATGAAAAGACCATAACTAGGTTATGGC
1 ATTTTAATG-TAAGACCATAACTAGATTATGGC
* *
14519763 ATCTTGAACGTAAGACCAT
1 AT-TTTAATGTAAGACCAT
14519782 GGTTGGACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
32 8 0.19
33 28 0.67
34 6 0.14
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (32 bp):
ATTTTAATGTAAGACCATAACTAGATTATGGC
Found at i:14519853 original size:103 final size:101
Alignment explanation
Indices: 14519676--14519886 Score: 255
Period size: 103 Copynumber: 2.1 Consensus size: 101
14519666 GACAGATAAA
* * **
14519676 ACCATGGTTGGACCATGTCAATATTTAAATGTAAGACCATAGCTAATCTATGGCATTTTAATGAA
1 ACCATGGTTGGACCATGTCAATATTTAAATGTAAGACCATAGCTAAGCTATGACATCCTAATGAA
*
14519741 AAGACCATAACTAGGTTATGGCATCT-TGAACGTAAG
66 AAGACCATAACTAGGTTATGGCA-CTACGAACGTAAG
** ** *
14519777 ACCATGGTTGGACCATGGT-AGTATATTTATGTGTAAGACCATAGCTGGGCTATGACATCCTGAT
1 ACCATGGTTGGACCAT-GTCA--ATATTTAAATGTAAGACCATAGCTAAGCTATGACATCCTAAT
** *
14519841 GGTAAGACCATAACTAGGTTATGGCACTACGAATGTAAG
63 GAAAAGACCATAACTAGGTTATGGCACTACGAACGTAAG
14519880 ACCATGG
1 ACCATGG
14519887 AAAGGCCATC
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
101 17 0.18
102 4 0.04
103 72 0.77
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (101 bp):
ACCATGGTTGGACCATGTCAATATTTAAATGTAAGACCATAGCTAAGCTATGACATCCTAATGAA
AAGACCATAACTAGGTTATGGCACTACGAACGTAAG
Found at i:14521314 original size:44 final size:44
Alignment explanation
Indices: 14521251--14521338 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
14521241 TATGTTGAGA
14521251 AAATATAACTGATGAGGACTTGTTAAAGAAAACATTTTCAACCT
1 AAATATAACTGATGAGGACTTGTTAAAGAAAACATTTTCAACCT
14521295 AAATATAACTGATGAGGACTTGTTAAAGAAAACATTTTCAACCT
1 AAATATAACTGATGAGGACTTGTTAAAGAAAACATTTTCAACCT
14521339 TTCATGCTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (44 bp):
AAATATAACTGATGAGGACTTGTTAAAGAAAACATTTTCAACCT
Found at i:14524130 original size:24 final size:25
Alignment explanation
Indices: 14524015--14524132 Score: 87
Period size: 25 Copynumber: 4.7 Consensus size: 25
14524005 TTCATATTCA
* *
14524015 GGAATGCTCATACGA-CCACATAAATG
1 GGAA-GCTCATACGAGCCATAT-AACG
* ** *
14524041 GGAAGCTCTTTTGAGCCATATAATG
1 GGAAGCTCATACGAGCCATATAACG
* ** *
14524066 GGAAACTCATGTGAGCCATGTAACG
1 GGAAGCTCATACGAGCCATATAACG
** *
14524091 GGAAGCTCCGAAGAGCCAT-TAACG
1 GGAAGCTCATACGAGCCATATAACG
14524115 GGAAGCTCATACGAGCCA
1 GGAAGCTCATACGAGCCA
14524133 ATATTGAGAA
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
24 20 0.27
25 45 0.61
26 9 0.12
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
GGAAGCTCATACGAGCCATATAACG
Found at i:14524143 original size:24 final size:24
Alignment explanation
Indices: 14524116--14524170 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
14524106 CCATTAACGG
*
14524116 GAAGCTCATA-CGAGCCAATATTGA
1 GAAGCTCA-AGCGACCCAATATTGA
* *
14524140 GAAGTTCAAGCGACCCAATATTGG
1 GAAGCTCAAGCGACCCAATATTGA
14524164 GAAGCTC
1 GAAGCTC
14524171 CGAAGAGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (24 bp):
GAAGCTCAAGCGACCCAATATTGA
Found at i:14543471 original size:21 final size:20
Alignment explanation
Indices: 14543437--14543475 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
14543427 CTAAGATGTC
*
14543437 AATTGGATTGAATTGAATGCG
1 AATTGGATTAAATT-AATGCG
*
14543458 AATTGTATTAAATTAATG
1 AATTGGATTAAATTAATG
14543476 TTAAATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (20 bp):
AATTGGATTAAATTAATGCG
Found at i:14543864 original size:24 final size:24
Alignment explanation
Indices: 14543837--14543891 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
14543827 TGGTTCTTGC
*
14543837 GAGCTTCCCATTAATAGCTCTTCA
1 GAGCATCCCATTAATAGCTCTTCA
** *
14543861 GAGCATCCTGTTAATAGCTCTTCG
1 GAGCATCCCATTAATAGCTCTTCA
14543885 GAGCATC
1 GAGCATC
14543892 TCGTTTGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (24 bp):
GAGCATCCCATTAATAGCTCTTCA
Found at i:14544138 original size:74 final size:73
Alignment explanation
Indices: 14544060--14544236 Score: 191
Period size: 74 Copynumber: 2.4 Consensus size: 73
14544050 TCTGATATTA
* *
14544060 GCTCATATGAGCTTCCTTTTAATGGTTCTC-TGGAGCTTTCCGTTACATGGCTCACATAAGCTTT
1 GCTCATATGAGCTTCCTTTTAATGGTTCTCAT-GAG-TTTCCATTACATGGCTCACATAAGCTTC
14544124 CCATTACATG
64 CCATTACATG
** * * *
14544134 GCTCATATGAGCTTCCCATTACATGGCTCACATGAGTTTCCATTACATGGCTCACATGAGCTTCC
1 GCTCATATGAGCTTCCTTTTA-ATGGTTCTCATGAGTTTCCATTACATGGCTCACATAAGCTTCC
* *
14544199 CGTTATATG
65 CATTACATG
*
14544208 GCTCGA-AAGAGCTTCCTGTTT-AT-GTTCTC
1 GCTC-ATATGAGCTTCCT-TTTAATGGTTCTC
14544237 GTAAGAGCAT
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
72 4 0.05
73 2 0.02
74 65 0.76
75 13 0.15
76 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (73 bp):
GCTCATATGAGCTTCCTTTTAATGGTTCTCATGAGTTTCCATTACATGGCTCACATAAGCTTCCC
ATTACATG
Found at i:14544181 original size:24 final size:25
Alignment explanation
Indices: 14544092--14544211 Score: 170
Period size: 25 Copynumber: 4.8 Consensus size: 25
14544082 TGGTTCTCTG
*
14544092 GAGCTTTCCGTTACATGGCTCACAT
1 GAGCTTTCCATTACATGGCTCACAT
* *
14544117 AAGCTTTCCATTACATGGCTCATAT
1 GAGCTTTCCATTACATGGCTCACAT
*
14544142 GAGCTTCCCATTACATGGCTCACAT
1 GAGCTTTCCATTACATGGCTCACAT
14544167 GAG-TTTCCATTACATGGCTCACAT
1 GAGCTTTCCATTACATGGCTCACAT
* * *
14544191 GAGCTTCCCGTTATATGGCTC
1 GAGCTTTCCATTACATGGCTC
14544212 GAAAGAGCTT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
24 23 0.27
25 61 0.73
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (25 bp):
GAGCTTTCCATTACATGGCTCACAT
Found at i:14544193 original size:49 final size:50
Alignment explanation
Indices: 14544092--14544211 Score: 188
Period size: 49 Copynumber: 2.4 Consensus size: 50
14544082 TGGTTCTCTG
* *
14544092 GAGCTTTCCGTTACATGGCTCACATAAGCTTTCCATTACATGGCTCATAT
1 GAGCTTCCCGTTACATGGCTCACATAAGCTTTCCATTACATGGCTCACAT
* *
14544142 GAGCTTCCCATTACATGGCTCACATGAG-TTTCCATTACATGGCTCACAT
1 GAGCTTCCCGTTACATGGCTCACATAAGCTTTCCATTACATGGCTCACAT
*
14544191 GAGCTTCCCGTTATATGGCTC
1 GAGCTTCCCGTTACATGGCTC
14544212 GAAAGAGCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
49 39 0.61
50 25 0.39
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (50 bp):
GAGCTTCCCGTTACATGGCTCACATAAGCTTTCCATTACATGGCTCACAT
Found at i:14544219 original size:25 final size:25
Alignment explanation
Indices: 14544191--14544249 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
14544181 TGGCTCACAT
14544191 GAGCTTCCCGTTATATG-GCTCGAAA
1 GAGCTTCCCGTT-TATGTGCTCGAAA
* * *
14544216 GAGCTTCCTGTTTATGTTCTCGTAA
1 GAGCTTCCCGTTTATGTGCTCGAAA
14544241 GAGCATTCC
1 GAGC-TTCC
14544250 TAAATATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 21 0.72
26 4 0.14
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTTATGTGCTCGAAA
Found at i:14556841 original size:19 final size:20
Alignment explanation
Indices: 14556817--14556854 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
14556807 GGTACCACCG
14556817 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
14556836 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
14556855 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:14557250 original size:46 final size:47
Alignment explanation
Indices: 14557079--14557251 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 47
14557069 AACCCGCCCC
* * * *
14557079 TAAGTGAACTCAGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
* * *
14557125 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-ATTTGCATCCA
* * *
14557173 TCA-CGAACTAGGACTCAACTCAACGAGTTCGGA-CATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
14557218 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
14557252 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 56 0.53
47 30 0.29
48 3 0.03
49 2 0.02
50 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
Found at i:14557270 original size:46 final size:45
Alignment explanation
Indices: 14557129--14557270 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 45
14557119 CATCCATAAA
14557129 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AG
* * * * *
14557176 CGAACTAGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-AAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTAG
14557222 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAG
14557268 TGA
1 TGA
14557271 CATGTCACTT
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 32 0.42
47 30 0.39
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAG
Found at i:14558846 original size:24 final size:25
Alignment explanation
Indices: 14558800--14558849 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
14558790 TCTTATCATG
* *
14558800 TCAATATCCATTTTCATGCATTTCA
1 TCAATAGCCATTTTCATACATTTCA
*
14558825 TCAATAGCCA-TTTCATATATTTCA
1 TCAATAGCCATTTTCATACATTTCA
14558849 T
1 T
14558850 TTCTATATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (25 bp):
TCAATAGCCATTTTCATACATTTCA
Found at i:14559642 original size:18 final size:17
Alignment explanation
Indices: 14559621--14559696 Score: 82
Period size: 17 Copynumber: 4.4 Consensus size: 17
14559611 ACATTTGAAA
*
14559621 TCACTTTCAATGTCAATT
1 TCACTTTCAAT-TCAAAT
14559639 TCACTTTCAATTCAAAT
1 TCACTTTCAATTCAAAT
**
14559656 TCAAAATTCAATTC-AAT
1 TC-ACTTTCAATTCAAAT
* *
14559673 TCTCATTCAATTCAAAT
1 TCACTTTCAATTCAAAT
14559690 TCACTTT
1 TCACTTT
14559697 TCCACTTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
16 9 0.18
17 20 0.41
18 20 0.41
ACGTcount: A:0.34, C:0.22, G:0.01, T:0.42
Consensus pattern (17 bp):
TCACTTTCAATTCAAAT
Found at i:14559658 original size:11 final size:11
Alignment explanation
Indices: 14559644--14559692 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
14559634 CAATTTCACT
14559644 TTCAATTCAAA
1 TTCAATTCAAA
14559655 TTCAAAATTC-AA
1 TTC--AATTCAAA
**
14559667 TTCAATTCTCA
1 TTCAATTCAAA
14559678 TTCAATTCAAA
1 TTCAATTCAAA
14559689 TTCA
1 TTCA
14559693 CTTTTCCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 5 0.16
13 5 0.16
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (11 bp):
TTCAATTCAAA
Found at i:14560016 original size:70 final size:76
Alignment explanation
Indices: 14559861--14560036 Score: 195
Period size: 70 Copynumber: 2.3 Consensus size: 76
14559851 TTTCCAATCA
* * *
14559861 AATTCAAATCACTAATTACTTTTCAATCAATATACATTTCAAATACTCACATATTTTCTTCACTC
1 AATTCAAATCACT-ATTAATTTCCAATCAATATACATTTCAAATACTCACATA---TATTCACTC
14559926 AATTCAATTTGATTC
62 AATTCAATTTGATTC
* * *
14559941 AATTCAAATCACTCTTAGTTTCCAATCAATATAC-TTTCAAATATTCACATA-ATTCA-T-AATT
1 AATTCAAATCACTATTAATTTCCAATCAATATACATTTCAAATACTCACATATATTCACTCAATT
14560002 CAA-TT-ACTT-
66 CAATTTGA-TTC
*
14560011 AATTCAAATCACTTTTAATTTCCAAT
1 AATTCAAATCACTATTAATTTCCAAT
14560037 TTGTTCACGT
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
70 25 0.28
71 4 0.05
72 7 0.08
73 1 0.01
74 4 0.05
78 16 0.18
79 18 0.20
80 13 0.15
ACGTcount: A:0.38, C:0.20, G:0.01, T:0.41
Consensus pattern (76 bp):
AATTCAAATCACTATTAATTTCCAATCAATATACATTTCAAATACTCACATATATTCACTCAATT
CAATTTGATTC
Found at i:14560357 original size:30 final size:30
Alignment explanation
Indices: 14560306--14560364 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
14560296 ATTAATACAA
*
14560306 TATTAATTTTTATCTATTAAATTGAATTTC
1 TATTAATTTTTATCTATTAAATTCAATTTC
14560336 TATTCAATTTTCTA-CT-TTAAATTCAATTT
1 TATT-AATTTT-TATCTATTAAATTCAATTT
14560365 AATCTTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 16 0.62
31 8 0.31
32 2 0.08
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (30 bp):
TATTAATTTTTATCTATTAAATTCAATTTC
Found at i:14560880 original size:3 final size:3
Alignment explanation
Indices: 14560862--14560913 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
14560852 ATATGTTTGT
* * *
14560862 TAA TAA TAT TAG TAA TAA TAA TACA TTA TAA TAA TAA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
14560906 TAA TAA TA
1 TAA TAA TA
14560914 TTTAATTCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:14560895 original size:16 final size:16
Alignment explanation
Indices: 14560869--14560913 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
14560859 TGTTAATAAT
14560869 ATTAGTAATAATAATAC
1 ATTA-TAATAATAATAC
*
14560886 ATTATAATAATAATAT
1 ATTATAATAATAATAC
*
14560902 AATATAATAATA
1 ATTATAATAATA
14560914 TTTAATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
ATTATAATAATAATAC
Found at i:14561425 original size:12 final size:12
Alignment explanation
Indices: 14561367--14561429 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
14561357 TTTTTATTTC
14561367 ATAA-TATAATA
1 ATAATTATAATA
14561378 AT-ATTAATAATA
1 ATAATT-ATAATA
*
14561390 ATATTTA-AATAA
1 ATAATTATAAT-A
* **
14561402 AAAACCATAATA
1 ATAATTATAATA
14561414 ATAATTATAATA
1 ATAATTATAATA
14561426 ATAA
1 ATAA
14561430 ATTGATAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 27 0.69
13 5 0.13
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATTATAATA
Found at i:14562055 original size:2 final size:2
Alignment explanation
Indices: 14562048--14562081 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
14562038 AGACCATTTG
*
14562048 CA CA CA CA CA CA CA CA CA CA CA CA CA CT CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
14562082 GAGACATATA
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:0.50, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:14564565 original size:14 final size:14
Alignment explanation
Indices: 14564548--14564577 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14564538 TGAGAGCCAG
14564548 TGTAAGACCATGTT
1 TGTAAGACCATGTT
14564562 TGTAAGACCATGTT
1 TGTAAGACCATGTT
14564576 TG
1 TG
14564578 GAACATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (14 bp):
TGTAAGACCATGTT
Found at i:14564576 original size:62 final size:62
Alignment explanation
Indices: 14564500--14564624 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
14564490 TGTGTGCTAG
*
14564500 TGTAAGACCATGTTTGGAACATGGCATCGGCCATATTATGAGAGCCAGTGTAAGACCATGTT
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTT
14564562 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTT
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTT
14564624 T
1 T
14564625 TGAACATAGC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (62 bp):
TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTT
Found at i:14564637 original size:48 final size:48
Alignment explanation
Indices: 14564562--14564878 Score: 306
Period size: 48 Copynumber: 6.6 Consensus size: 48
14564552 AGACCATGTT
14564562 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAG
* * * *
14564610 TGTAAGACCATGTTTTGAACATAGCATCAGCCACATTATGAGAGCTAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAG
* **
14564658 TGTAAGACCATGTTTGGAACATGGCATCGGCAATGTTATG-GA-CCTAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCC-AG
* * * **
14564705 TGTAAGACCATGTTTGCAACATGACATC-GCAATGTTATGAGAGCCAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAG
* * * *
14564752 TGTAAGACCATGTCTGGGACATGGCATTGG---CATTGAGGTGAGAGCTAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATT-A--TGAGAGCCAG
* * * * * * * *
14564800 TGTAAAACCATGTCTGGGACATAGCGTCGGCCACGA-CATGTGAGCTAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCCAC-ATTATGAGAGCCAG
* *
14564848 TGTAAGACCATGTCTGGGACATGGCATCGGC
1 TGTAAGACCATGTTTGGAACATGGCATCGGC
14564879 AATTTACCCT
Statistics
Matches: 228, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
45 2 0.01
46 13 0.06
47 57 0.25
48 153 0.67
50 1 0.00
51 1 0.00
52 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAG
Found at i:14564830 original size:142 final size:143
Alignment explanation
Indices: 14564562--14564880 Score: 349
Period size: 142 Copynumber: 2.2 Consensus size: 143
14564552 AGACCATGTT
* * * * *
14564562 TGTAAGACCATGTTTGGAACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTTTTG
1 TGTAAGACCATGTTTGCAACATGACATCGGCAACATTATGAGAGCCAGTGTAAGACCATGTCTGG
* * * *
14564627 AACATAGCATCAGCCACATTATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCAAT
66 AACATAGCATCAG-CACATTATGAGAGCTAGTGTAAAACCATGTCTGGAACATAGCATCGGCAAC
**
14564692 GTTATG-GACCTAG
130 GACATGTGACCTAG
**
14564705 TGTAAGACCATGTTTGCAACATGACATC-GCAATGTTATGAGAGCCAGTGTAAGACCATGTCTGG
1 TGTAAGACCATGTTTGCAACATGACATCGGCAACATTATGAGAGCCAGTGTAAGACCATGTCTGG
* * * * * * *
14564769 GACATGGCAT-TG-GCATTGAGGTGAGAGCTAGTGTAAAACCATGTCTGGGACATAGCGTCGGCC
66 AACATAGCATCAGCACATT-A--TGAGAGCTAGTGTAAAACCATGTCTGGAACATAGCATCGGCA
*
14564832 ACGACATGTGAGCTAG
128 ACGACATGTGACCTAG
* ** *
14564848 TGTAAGACCATGTCTGGGACATGGCATCGGCAA
1 TGTAAGACCATGTTTGCAACATGACATCGGCAA
14564881 TTTACCCTCT
Statistics
Matches: 146, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
139 4 0.03
140 1 0.01
141 1 0.01
142 80 0.55
143 56 0.38
144 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (143 bp):
TGTAAGACCATGTTTGCAACATGACATCGGCAACATTATGAGAGCCAGTGTAAGACCATGTCTGG
AACATAGCATCAGCACATTATGAGAGCTAGTGTAAAACCATGTCTGGAACATAGCATCGGCAACG
ACATGTGACCTAG
Found at i:14567058 original size:43 final size:41
Alignment explanation
Indices: 14567010--14567164 Score: 170
Period size: 43 Copynumber: 3.7 Consensus size: 41
14567000 TGTTTTCTCA
* *
14567010 TGTAAGACCACATCTGGGATGTTGGCATTCATATGTGATTACG
1 TGTAAGACCACGTCTGGGAAGTTGGCA-TCATATGTGATT-CG
* * * *
14567053 TGTAAGACCATGTCTGGGAAATTGGCATCGTATTTGATTCG
1 TGTAAGACCACGTCTGGGAAGTTGGCATCATATGTGATTCG
*
14567094 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTGCA
1 TGTAAGACCAC-GTCTGGGA-AGTTGGCATC-ATATGTGATT-CG
*
14567137 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGAAGTTGGCAT
14567165 TGTATGATAT
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
41 26 0.28
42 20 0.21
43 47 0.50
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGAAGTTGGCATCATATGTGATTCG
Found at i:14570690 original size:33 final size:33
Alignment explanation
Indices: 14570653--14570727 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
14570643 ATCTCAGTAA
* * *
14570653 ACTTACTCTGTTCCATTTTTACTACCCCGACAG
1 ACTTACTCTGTTCCATGTTTACTAACCCAACAG
* *
14570686 ACTTACTCTGTTCCGTGTTTACTAACGCAACAG
1 ACTTACTCTGTTCCATGTTTACTAACCCAACAG
14570719 ACTTACTCT
1 ACTTACTCT
14570728 ATGGATGCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.36
Consensus pattern (33 bp):
ACTTACTCTGTTCCATGTTTACTAACCCAACAG
Found at i:14572209 original size:19 final size:20
Alignment explanation
Indices: 14572185--14572232 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
14572175 GCAGAAGCTT
*
14572185 AGGAAAACCG-TCACGTTTA
1 AGGAAAACCGTTCACATTTA
* *
14572204 AGGAAAACAGTTCACATTTT
1 AGGAAAACCGTTCACATTTA
14572224 AGGAAAACC
1 AGGAAAACC
14572233 TTGTTTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
AGGAAAACCGTTCACATTTA
Found at i:14573217 original size:22 final size:22
Alignment explanation
Indices: 14573192--14573240 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
14573182 GCCCGTGGCC
* *
14573192 CACACGGCTACACTCCAGTGGT
1 CACACGGCTACACTCAAGTCGT
14573214 CACACGGCTACACTCAAGTCGT
1 CACACGGCTACACTCAAGTCGT
14573236 CACAC
1 CACAC
14573241 AGCCATGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.16
Consensus pattern (22 bp):
CACACGGCTACACTCAAGTCGT
Found at i:14587560 original size:70 final size:70
Alignment explanation
Indices: 14587447--14587581 Score: 243
Period size: 70 Copynumber: 1.9 Consensus size: 70
14587437 TGAACAATAT
* *
14587447 TTTATAAAGGTATCGATATGAATTGACTTGTTTCCAAAATTTTGAAAATGGCAAAATGTCAAAAC
1 TTTATAAAGGTATCGATATGAATTGACTTGTGTCCAAAATTTTGAAAATGGCAAAATGCCAAAAC
14587512 GATAC
66 GATAC
*
14587517 TTTATAAAGGTATCGATATGAATTGACTTGTGTCCAAAATTTTGAAAATGGCAGAATGCCAAAAC
1 TTTATAAAGGTATCGATATGAATTGACTTGTGTCCAAAATTTTGAAAATGGCAAAATGCCAAAAC
14587582 TATATCGATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (70 bp):
TTTATAAAGGTATCGATATGAATTGACTTGTGTCCAAAATTTTGAAAATGGCAAAATGCCAAAAC
GATAC
Found at i:14588887 original size:55 final size:55
Alignment explanation
Indices: 14588809--14588994 Score: 255
Period size: 55 Copynumber: 3.4 Consensus size: 55
14588799 CGTGCCCTTA
* * * * * *
14588809 GCCCATGTGCAACACTGACTTTAAAACACGGTCATGGCGTATGCCCGTGTGGCTT
1 GCCCGTGTACAACACTGACTTTAATACACGGCCATGGCGCATGCCCGTGTGGCCT
* * *
14588864 GCCCGTGTACAACACTGAATTTAATACACGGCCATGGTGCACGCCCGTGTGGCCT
1 GCCCGTGTACAACACTGACTTTAATACACGGCCATGGCGCATGCCCGTGTGGCCT
* * *
14588919 GCCCGTGTACAATACTGACTTTAATACAAGGCCATGGCACATGCCCGTGTGGCCT
1 GCCCGTGTACAACACTGACTTTAATACACGGCCATGGCGCATGCCCGTGTGGCCT
*
14588974 GCCCGTGTACAACAATGACTT
1 GCCCGTGTACAACACTGACTT
14588995 AAAATTTGAA
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 114 1.00
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (55 bp):
GCCCGTGTACAACACTGACTTTAATACACGGCCATGGCGCATGCCCGTGTGGCCT
Found at i:14596774 original size:62 final size:62
Alignment explanation
Indices: 14596698--14596900 Score: 379
Period size: 62 Copynumber: 3.3 Consensus size: 62
14596688 ATATATATCA
14596698 GACATTAAAGCATAAAGTAAACAGTACATAAAGTAAGAATACTACTGATATTAGACATTATTT
1 GACA-TAAAGCATAAAGTAAACAGTACATAAAGTAAGAATACTACTGATATTAGACATTATTT
*
14596761 GACATAAAGCATAAAGTAAACAGTACATAAAGTAAGAATAGTACTGATATTAGACATTATTT
1 GACATAAAGCATAAAGTAAACAGTACATAAAGTAAGAATACTACTGATATTAGACATTATTT
14596823 GACATAAAGCATAAAGTAAACAGTACATAAAGTAAGAATACTACTGATATTAGACATTATTT
1 GACATAAAGCATAAAGTAAACAGTACATAAAGTAAGAATACTACTGATATTAGACATTATTT
*
14596885 GACATAAAGCAAAAAG
1 GACATAAAGCATAAAG
14596901 CTCTTTAATT
Statistics
Matches: 137, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
62 133 0.97
63 4 0.03
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (62 bp):
GACATAAAGCATAAAGTAAACAGTACATAAAGTAAGAATACTACTGATATTAGACATTATTT
Found at i:14606698 original size:27 final size:27
Alignment explanation
Indices: 14606594--14606851 Score: 285
Period size: 27 Copynumber: 9.7 Consensus size: 27
14606584 TACATCACGT
* * ** *
14606594 AGGGATAAATCAGTCATCTTACCATAAA
1 AGGGA-AAAACAGTCATTTTACCCCATA
* * * ** *
14606622 AGGGCAAAATAGTCATCTTACCATAAA
1 AGGGAAAAACAGTCATTTTACCCCATA
* *
14606649 AGGGCAAAACATTCATTTTACCCCATA
1 AGGGAAAAACAGTCATTTTACCCCATA
14606676 AGGGAAAAACAGTCATTTTACCCCATA
1 AGGGAAAAACAGTCATTTTACCCCATA
* *
14606703 AGGG--CAACAGCCATTTTACCCCATA
1 AGGGAAAAACAGTCATTTTACCCCATA
*
14606728 AGGG--CAACAGTCATTTTACCCCATA
1 AGGGAAAAACAGTCATTTTACCCCATA
14606753 AGGGAAAAACAGTCATTTTACCCCATA
1 AGGGAAAAACAGTCATTTTACCCCATA
*
14606780 AGGGAAAAATAGTCATTTTACCCCATA
1 AGGGAAAAACAGTCATTTTACCCCATA
*
14606807 AGGG--CAACAGTCATTTTACCCCATA
1 AGGGAAAAACAGTCATTTTACCCCATA
* *
14606832 AGGGTAAAATAGTCATTTTA
1 AGGGAAAAACAGTCATTTTA
14606852 TCAATTTGAG
Statistics
Matches: 206, Mismatches: 20, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
25 70 0.34
27 132 0.64
28 4 0.02
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (27 bp):
AGGGAAAAACAGTCATTTTACCCCATA
Found at i:14606794 original size:104 final size:104
Alignment explanation
Indices: 14606648--14606835 Score: 340
Period size: 104 Copynumber: 1.8 Consensus size: 104
14606638 CTTACCATAA
* *
14606648 AAGGGCAAAACATTCATTTTACCCCATAAGGGAAAAACAGTCATTTTACCCCATAAGGGCAACAG
1 AAGGGAAAAACAGTCATTTTACCCCATAAGGGAAAAACAGTCATTTTACCCCATAAGGGCAACAG
14606713 CCATTTTACCCCATAAGGGCAACAGTCATTTTACCCCAT
66 CCATTTTACCCCATAAGGGCAACAGTCATTTTACCCCAT
*
14606752 AAGGGAAAAACAGTCATTTTACCCCATAAGGGAAAAATAGTCATTTTACCCCATAAGGGCAACAG
1 AAGGGAAAAACAGTCATTTTACCCCATAAGGGAAAAACAGTCATTTTACCCCATAAGGGCAACAG
*
14606817 TCATTTTACCCCATAAGGG
66 CCATTTTACCCCATAAGGG
14606836 TAAAATAGTC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 80 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (104 bp):
AAGGGAAAAACAGTCATTTTACCCCATAAGGGAAAAACAGTCATTTTACCCCATAAGGGCAACAG
CCATTTTACCCCATAAGGGCAACAGTCATTTTACCCCAT
Found at i:14606841 original size:52 final size:52
Alignment explanation
Indices: 14606621--14606851 Score: 304
Period size: 52 Copynumber: 4.4 Consensus size: 52
14606611 CTTACCATAA
* * ** * *
14606621 AAGGGCAAAATAGTCATCTTACCATAAAAGGGCAAAACATTCATTTTACCCCAT
1 AAGGGAAAAATAGTCATTTTACCCCATAAGGGC--AACAGTCATTTTACCCCAT
* *
14606675 AAGGGAAAAACAGTCATTTTACCCCATAAGGGCAACAGCCATTTTACCCCAT
1 AAGGGAAAAATAGTCATTTTACCCCATAAGGGCAACAGTCATTTTACCCCAT
* * *
14606727 AAGGG--CAACAGTCATTTTACCCCATAAGGGAAAAACAGTCATTTTACCCCAT
1 AAGGGAAAAATAGTCATTTTACCCCATAAGGG--CAACAGTCATTTTACCCCAT
14606779 AAGGGAAAAATAGTCATTTTACCCCATAAGGGCAACAGTCATTTTACCCCAT
1 AAGGGAAAAATAGTCATTTTACCCCATAAGGGCAACAGTCATTTTACCCCAT
*
14606831 AAGGGTAAAATAGTCATTTTA
1 AAGGGAAAAATAGTCATTTTA
14606852 TCAATTTGAG
Statistics
Matches: 158, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
50 24 0.15
52 84 0.53
54 50 0.32
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
AAGGGAAAAATAGTCATTTTACCCCATAAGGGCAACAGTCATTTTACCCCAT
Found at i:14609512 original size:17 final size:17
Alignment explanation
Indices: 14609475--14609518 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
14609465 GGAGGATTTG
*
14609475 ATAAAATAAAATTAAAAA
1 ATAAAAT-AAGTTAAAAA
* *
14609493 ATATAATAAGTTAAAGA
1 ATAAAATAAGTTAAAAA
14609510 ATAAAATAA
1 ATAAAATAA
14609519 ACATAAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (17 bp):
ATAAAATAAGTTAAAAA
Found at i:14610442 original size:32 final size:32
Alignment explanation
Indices: 14610406--14610472 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
14610396 TGTATATGAT
14610406 TATGTTAAAAGGTTAAGAAATATATGAATTAC
1 TATGTTAAAAGGTTAAGAAATATATGAATTAC
* *
14610438 TATGTTACAAGGTTAAGAAGTATATGAATTAC
1 TATGTTAAAAGGTTAAGAAATATATGAATTAC
14610470 TAT
1 TAT
14610473 TCGATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.36
Consensus pattern (32 bp):
TATGTTAAAAGGTTAAGAAATATATGAATTAC
Found at i:14612029 original size:17 final size:17
Alignment explanation
Indices: 14612007--14612041 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
14611997 TGAATATTTG
14612007 AAGGATTTATTTATGAT
1 AAGGATTTATTTATGAT
14612024 AAGGATTTATTTATGAT
1 AAGGATTTATTTATGAT
14612041 A
1 A
14612042 TGCTTGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
AAGGATTTATTTATGAT
Found at i:14614304 original size:18 final size:18
Alignment explanation
Indices: 14614278--14614324 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
14614268 ACTCACATCT
*
14614278 TATTCTCTCAAATCTTTC
1 TATTCTCTCAAATATTTC
*
14614296 TATTTTCTCAAATATTTC
1 TATTCTCTCAAATATTTC
14614314 TATTCTCTCAA
1 TATTCTCTCAA
14614325 CTCTCTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTCTCTCAAATATTTC
Found at i:14627044 original size:19 final size:20
Alignment explanation
Indices: 14627007--14627064 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
14626997 TCCAGATGAT
* * *
14627007 TTTTTATTATTAATTTTATG
1 TTTTTAATATAAATATTATG
14627027 TTTTTAATA-AAATATTATG
1 TTTTTAATATAAATATTATG
* *
14627046 TTTTTTATATAATTATTAT
1 TTTTTAATATAAATATTAT
14627065 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTAATATAAATATTATG
Found at i:14629247 original size:3 final size:3
Alignment explanation
Indices: 14629241--14629284 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
14629231 GAAGGAAAAA
14629241 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAGG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG A
14629285 TTTGTGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:14646714 original size:20 final size:21
Alignment explanation
Indices: 14646679--14646719 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
14646669 TTTGCTTTCC
*
14646679 GTTAAGCTCTTATGAGCTTCA
1 GTTAAGCTCATATGAGCTTCA
*
14646700 GTTAA-CTCATATGAGTTTCA
1 GTTAAGCTCATATGAGCTTCA
14646720 TTTCAACCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
GTTAAGCTCATATGAGCTTCA
Found at i:14647294 original size:2 final size:2
Alignment explanation
Indices: 14647287--14647324 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14647277 ATGGCAATTA
14647287 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
14647325 AGTATATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:14656831 original size:21 final size:19
Alignment explanation
Indices: 14656791--14656844 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
14656781 AATGTATGAT
14656791 TTAAAATTAATAATATGTAAAA
1 TTAAAA-TAA-AATATGT-AAA
14656813 TTAAAATAAAATAATGTAAA
1 TTAAAATAAAAT-ATGTAAA
14656833 TTATAAATAAAA
1 TTA-AAATAAAA
14656845 AACAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.30
21 15 0.50
22 6 0.20
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
TTAAAATAAAATATGTAAA
Found at i:14659137 original size:32 final size:32
Alignment explanation
Indices: 14659101--14659166 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
14659091 ATTATTCAAC
*
14659101 TTTAAAAAATTTCTATTTATGTCACTGAACTA
1 TTTAAAAAATTTCTATTTAAGTCACTGAACTA
*** * *
14659133 TTTAAATTTTTTTTATTTAAGTCACTGAGCTA
1 TTTAAAAAATTTCTATTTAAGTCACTGAACTA
14659165 TT
1 TT
14659167 AATTTTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (32 bp):
TTTAAAAAATTTCTATTTAAGTCACTGAACTA
Found at i:14659175 original size:32 final size:32
Alignment explanation
Indices: 14659114--14659175 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
14659104 AAAAAATTTC
*
14659114 TATTTATGTCACTGAACTATTTAAATTTTTTT
1 TATTTAAGTCACTGAACTATTTAAATTTTTTT
*
14659146 TATTTAAGTCACTGAGCTA-TT-AATTTTTTT
1 TATTTAAGTCACTGAACTATTTAAATTTTTTT
14659176 AAAAAAAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 9 0.32
31 2 0.07
32 17 0.61
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (32 bp):
TATTTAAGTCACTGAACTATTTAAATTTTTTT
Found at i:14665806 original size:22 final size:22
Alignment explanation
Indices: 14665781--14665828 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
14665771 ACAAAACCCC
*
14665781 TGTCAACAAGCTCTTGCAACTG
1 TGTCAACAAGCTCTTACAACTG
***
14665803 TGTCTTTAAGCTCTTACAACTG
1 TGTCAACAAGCTCTTACAACTG
14665825 TGTC
1 TGTC
14665829 TTTAACTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (22 bp):
TGTCAACAAGCTCTTACAACTG
Found at i:14665829 original size:22 final size:22
Alignment explanation
Indices: 14665788--14665838 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
14665778 CCCTGTCAAC
*
14665788 AAGCTCTTGCAACTGTGTCTTT
1 AAGCTCTTACAACTGTGTCTTT
14665810 AAGCTCTTACAACTGTGTCTTT
1 AAGCTCTTACAACTGTGTCTTT
14665832 AA-CTCTT
1 AAGCTCTT
14665839 TTAATTCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (22 bp):
AAGCTCTTACAACTGTGTCTTT
Found at i:14670673 original size:35 final size:35
Alignment explanation
Indices: 14670622--14670693 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
14670612 TACTAGTTTG
14670622 TACCACAAGACACCTTATGTACACATGCCACAAAC
1 TACCACAAGACACCTTATGTACACATGCCACAAAC
*
14670657 TACCGCAAGACACCTTATGTACACATGCCACAAAC
1 TACCACAAGACACCTTATGTACACATGCCACAAAC
14670692 TA
1 TA
14670694 TGACACTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (35 bp):
TACCACAAGACACCTTATGTACACATGCCACAAAC
Found at i:14674835 original size:27 final size:27
Alignment explanation
Indices: 14674805--14674869 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
14674795 CCTAAAGATG
*
14674805 AAATAAAAATAGTATT-AAAGAGAAATA
1 AAATAAAAATAAT-TTAAAAGAGAAATA
*
14674832 AAATGAAAAATAATTTAAAAAGATAAATA
1 AAAT-AAAAATAATTT-AAAAGAGAAATA
14674861 AAGATAAAA
1 AA-ATAAAA
14674870 GTAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.19
28 8 0.25
29 16 0.50
30 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (27 bp):
AAATAAAAATAATTTAAAAGAGAAATA
Found at i:14676223 original size:29 final size:30
Alignment explanation
Indices: 14676191--14676247 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
14676181 GCCATGAATA
* *
14676191 TAATTAAAATAACAA-ATTCAACCAAAAAC
1 TAATGAAAATAACAAGACTCAACCAAAAAC
* *
14676220 TAATGACATTAACAAGACTCAACCAAAA
1 TAATGAAAATAACAAGACTCAACCAAAA
14676248 GTAATCGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.58, C:0.19, G:0.04, T:0.19
Consensus pattern (30 bp):
TAATGAAAATAACAAGACTCAACCAAAAAC
Found at i:14685947 original size:16 final size:15
Alignment explanation
Indices: 14685926--14685956 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
14685916 AGAAATGAGT
14685926 ATTAATTTATAATTTA
1 ATTAATTT-TAATTTA
14685942 ATTAATTTTAATTTA
1 ATTAATTTTAATTTA
14685957 TTCCCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTAATTTTAATTTA
Found at i:14692090 original size:18 final size:18
Alignment explanation
Indices: 14692067--14692101 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
14692057 CCTATCCAAT
14692067 ATACCTATCAGAAGTACC
1 ATACCTATCAGAAGTACC
14692085 ATACCTATCAGAAGTAC
1 ATACCTATCAGAAGTAC
14692102 TTCAATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (18 bp):
ATACCTATCAGAAGTACC
Found at i:14692732 original size:35 final size:35
Alignment explanation
Indices: 14692636--14692782 Score: 154
Period size: 35 Copynumber: 4.1 Consensus size: 35
14692626 GTCCAACCAC
* * *
14692636 AACACACCAGATGCTCATATGAGCTTA-TCC-CTCAAA
1 AACACACC-GATGCTCATAAGAGC-TAGTCCAATC-GA
* * * *
14692672 AACACACTGGATACTAATAAGAGCTAGTCTAATCGA
1 AACACAC-CGATGCTCATAAGAGCTAGTCCAATCGA
14692708 AACACACCGATGCTCATAAGAGCTAGTCCAATCGA
1 AACACACCGATGCTCATAAGAGCTAGTCCAATCGA
* * *
14692743 AACACGCCGATGCTCATAAGATCTAGTCCAACCGA
1 AACACACCGATGCTCATAAGAGCTAGTCCAATCGA
14692778 AACAC
1 AACAC
14692783 GCTAAACAGA
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
35 63 0.67
36 29 0.31
37 2 0.02
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (35 bp):
AACACACCGATGCTCATAAGAGCTAGTCCAATCGA
Found at i:14692783 original size:35 final size:35
Alignment explanation
Indices: 14692688--14692784 Score: 158
Period size: 35 Copynumber: 2.8 Consensus size: 35
14692678 CTGGATACTA
* *
14692688 ATAAGAGCTAGTCTAATCGAAACACACCGATGCTC
1 ATAAGAGCTAGTCCAATCGAAACACGCCGATGCTC
14692723 ATAAGAGCTAGTCCAATCGAAACACGCCGATGCTC
1 ATAAGAGCTAGTCCAATCGAAACACGCCGATGCTC
* *
14692758 ATAAGATCTAGTCCAACCGAAACACGC
1 ATAAGAGCTAGTCCAATCGAAACACGC
14692785 TAAACAGAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.18
Consensus pattern (35 bp):
ATAAGAGCTAGTCCAATCGAAACACGCCGATGCTC
Found at i:14693887 original size:62 final size:62
Alignment explanation
Indices: 14693812--14693935 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
14693802 GTTAGTGTTA
14693812 GGCAATATTTTACCTCTTTTTTTTAATTTAGTCCTTTTTATTTAATTAACTATCTAAATGGT
1 GGCAATATTTTACCTCTTTTTTTTAATTTAGTCCTTTTTATTTAATTAACTATCTAAATGGT
14693874 GGCAATATTTTACCTCTTTTTTTTAATTTAGTCCTTTTTATTTAATTAACTATCTAAATGGT
1 GGCAATATTTTACCTCTTTTTTTTAATTTAGTCCTTTTTATTTAATTAACTATCTAAATGGT
14693936 AATATTTCCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (62 bp):
GGCAATATTTTACCTCTTTTTTTTAATTTAGTCCTTTTTATTTAATTAACTATCTAAATGGT
Found at i:14702501 original size:7 final size:7
Alignment explanation
Indices: 14702489--14702530 Score: 66
Period size: 7 Copynumber: 5.7 Consensus size: 7
14702479 GGTATTCTAC
14702489 TTTTTCT
1 TTTTTCT
14702496 TTTTTCT
1 TTTTTCT
14702503 TTTTTCT
1 TTTTTCT
14702510 TTGTTTCTT
1 TT-TTTC-T
14702519 TTTTTCT
1 TTTTTCT
14702526 TTTTT
1 TTTTT
14702531 AGAATCTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 22 0.67
8 8 0.24
9 3 0.09
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:14702506 original size:8 final size:8
Alignment explanation
Indices: 14702489--14702530 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
14702479 GGTATTCTAC
14702489 TTTTTC-T
1 TTTTTCTT
14702496 TTTTTC-T
1 TTTTTCTT
14702503 TTTTTCTT
1 TTTTTCTT
*
14702511 TGTTTCTT
1 TTTTTCTT
14702519 TTTTTCTT
1 TTTTTCTT
14702527 TTTT
1 TTTT
14702531 AGAATCTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 13 0.41
8 19 0.59
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:14705450 original size:59 final size:57
Alignment explanation
Indices: 14705384--14705572 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
14705374 ATTTTATTAA
14705384 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
14705443 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
14705504 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
14705563 ATCATATATT
1 ATCATATATT
14705573 ATTATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:14705481 original size:66 final size:64
Alignment explanation
Indices: 14705411--14705609 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
14705401 AAATATATTT
*
14705411 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
14705476 G
64 G
* * * * **
14705477 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
* *
14705531 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
14705596 G
64 G
*
14705597 AATATTGATTATT
1 AATATTAATTATT
14705610 AAGAATTTTA
Statistics
Matches: 102, Mismatches: 17, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 9 0.09
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.26
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
Found at i:14705503 original size:120 final size:120
Alignment explanation
Indices: 14705373--14705670 Score: 483
Period size: 120 Copynumber: 2.5 Consensus size: 120
14705363 AATTATTTTA
* * *
14705373 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATCATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
14705437 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
14705493 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
14705558 ATAGTATCATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
14705613 AATTTTATTAAATTC-TATATTTTAATTATAATATATCTAATAATAATTATGTTTAAAT
1 AATTTTATTAAA-TCATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
14705671 ATGATTAAAT
Statistics
Matches: 165, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
120 157 0.95
121 8 0.05
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:14705513 original size:61 final size:61
Alignment explanation
Indices: 14705446--14705633 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
14705436 TTATAGTATC
*
14705446 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
14705507 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATTATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
14705565 C
61 T
*
14705566 ATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
*
14705627 CTATATT
1 ATATATT
14705634 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 17 0.18
61 24 0.25
62 7 0.07
63 11 0.11
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:14705533 original size:15 final size:15
Alignment explanation
Indices: 14705498--14705549 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
14705488 TTAAGAATTT
*
14705498 TATTAAATTAT-ATA
1 TATTTAATTATAATA
14705512 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
14705526 TATTTAATAATAAT-
1 TATTTAATTATAATA
14705540 TATGTTAATT
1 TAT-TTAATT
14705550 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:14705908 original size:16 final size:16
Alignment explanation
Indices: 14705884--14705935 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
14705874 GATTTGCTAT
14705884 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
14705900 TACAACTCTAATCCAA
1 TACACCTCTAATCCAA
14705916 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
14705932 TACA
1 TACA
14705936 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:14713631 original size:9 final size:9
Alignment explanation
Indices: 14713617--14713645 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
14713607 GTTAGCGTAC
14713617 ATGTTTGAA
1 ATGTTTGAA
14713626 ATGTTTGAA
1 ATGTTTGAA
14713635 ATGTTTGAA
1 ATGTTTGAA
14713644 AT
1 AT
14713646 AGGTGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
ATGTTTGAA
Found at i:14713787 original size:13 final size:13
Alignment explanation
Indices: 14713769--14713794 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14713759 TGTTGGGAAT
14713769 TAATGTGTATGCA
1 TAATGTGTATGCA
14713782 TAATGTGTATGCA
1 TAATGTGTATGCA
14713795 ACGAACAAGT
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:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TAATGTGTATGCA
Found at i:14720715 original size:19 final size:19
Alignment explanation
Indices: 14720691--14720749 Score: 109
Period size: 19 Copynumber: 3.1 Consensus size: 19
14720681 CTTAAAGAGC
14720691 TCGTATGAAAGCAATTTAA
1 TCGTATGAAAGCAATTTAA
14720710 TCGTATGAAAGCAATTTAA
1 TCGTATGAAAGCAATTTAA
*
14720729 TCATATGAAAGCAATTTAA
1 TCGTATGAAAGCAATTTAA
14720748 TC
1 TC
14720750 ATGTTTTTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (19 bp):
TCGTATGAAAGCAATTTAA
Found at i:14727852 original size:56 final size:56
Alignment explanation
Indices: 14727766--14727878 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
14727756 TGTGAAATCG
14727766 ACTTAATAAACATTTCCTTGTCACCTTGAGAAAGCATTGGAACATTCCAATTTTAT
1 ACTTAATAAACATTTCCTTGTCACCTTGAGAAAGCATTGGAACATTCCAATTTTAT
14727822 ACTTAATAAACATTTCCTTGTCACCTTGAGAAAGCATTGGAACATTCCAATTTTAT
1 ACTTAATAAACATTTCCTTGTCACCTTGAGAAAGCATTGGAACATTCCAATTTTAT
14727878 A
1 A
14727879 TCCTACTATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (56 bp):
ACTTAATAAACATTTCCTTGTCACCTTGAGAAAGCATTGGAACATTCCAATTTTAT
Found at i:14728867 original size:27 final size:27
Alignment explanation
Indices: 14728837--14728890 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
14728827 ATATATAATT
*
14728837 ATTA-TAAAATAATTAAATTGTACTTAA
1 ATTATTAAAATAATAAAATT-TACTTAA
* *
14728864 ATTATTAACATGATAAAATTTACTTAA
1 ATTATTAAAATAATAAAATTTACTTAA
14728891 TTCTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (27 bp):
ATTATTAAAATAATAAAATTTACTTAA
Done.