Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 24 of 26
Found at i:10371241 original size:85 final size:85
Alignment explanation
Indices: 10370930--10371288 Score: 325
Period size: 86 Copynumber: 4.1 Consensus size: 85
10370920 TCCTCCCAAG
* *
10370930 TTCAATGAATTTTTACATCAATAAAAATTACTC-TCGATATTAAATACATTTATAT-TA-TAAGC
1 TTCAATGAATTTTTACATGAATAAAAATTACTCTTAG-TATTAAA-A-A--TAT-TCTAGTAA--
** *
10370992 TTAATTTTACCTAATTATTTCATCAG-GAG
58 -TAATTTTAATTAATTATTTCAT-AGTGAA
* * * * * *
10371021 TTCAATGAATTTTTACAT-CATAAAAATTACCCTCAGTATTAAAAATATTTTAATATTAATTTT-
1 TTCAATGAATTTTTACATGAATAAAAATTACTCTTAGTATTAAAAATATTCTAGTAATAATTTTA
*
10371084 ATCTAATTATTTCATCGTGAA
66 AT-TAATTATTTCATAGTGAA
* * * * **
10371105 TTCAATCAAATTTTACACGGTATAAAAATTACTCTTAGTATTAGGAATATTCTAGTAATAATTTT
1 TTCAATGAATTTTTACA-TGAATAAAAATTACTCTTAGTATTAAAAATATTCTAGTAATAATTTT
*
10371170 AATTATTTATTTCATAGTGAA
65 AATTAATTATTTCATAGTGAA
* * *
10371191 TTCAATTAATTTTTGCATGAATAAAAATTACTCTTAATATTAAAAATATTCTAGAGTAATAATTT
1 TTCAATGAATTTTTACATGAATAAAAATTACTCTTAGTATTAAAAATATTCT--AGTAATAATTT
* * *
10371256 TAACTAATTATTTCATCGTGAG
64 TAATTAATTATTTCATAGTGAA
10371278 TTCAATGAATT
1 TTCAATGAATT
10371289 CTCATGTGTA
Statistics
Matches: 223, Mismatches: 35, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
83 1 0.00
84 36 0.16
85 31 0.14
86 72 0.32
87 43 0.19
88 1 0.00
89 1 0.00
90 19 0.09
91 19 0.09
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (85 bp):
TTCAATGAATTTTTACATGAATAAAAATTACTCTTAGTATTAAAAATATTCTAGTAATAATTTTA
ATTAATTATTTCATAGTGAA
Found at i:10371302 original size:87 final size:86
Alignment explanation
Indices: 10370993--10371303 Score: 326
Period size: 86 Copynumber: 3.6 Consensus size: 86
10370983 ATTATAAGCT
* * * * * * *
10370993 TAATTTTACCTAATTATTTCATCAG-GAGTTCAATGAATTTTTACAT-CATAAAAATTACCCTCA
1 TAATTTTAACTAATTATTTCATC-GTGAATTCAATGAATTTTCACGTGTATAAAAATTACTCTTA
* *
10371056 GTATTAAAAATATTTTAA-TAT
65 GTATTAAAAATATTCTAAGTAA
* *
10371077 TAATTTTATCTAATTATTTCATCGTGAATTCAATCAAATTTTACACG-GTATAAAAATTACTCTT
1 TAATTTTAACTAATTATTTCATCGTGAATTCAAT-GAATTTT-CACGTGTATAAAAATTACTCTT
**
10371141 AGTATTAGGAATATTCT-AGTAA
64 AGTATTAAAAATATTCTAAGTAA
* * * * ** * * *
10371163 TAATTTTAATTATTTATTTCATAGTGAATTCAATTAATTTTTGCATGAATAAAAATTACTCTTAA
1 TAATTTTAACTAATTATTTCATCGTGAATTCAATGAATTTTCACGTGTATAAAAATTACTCTTAG
10371228 TATTAAAAATATTCTAGAGTAA
66 TATTAAAAATATTCTA-AGTAA
* * *
10371250 TAATTTTAACTAATTATTTCATCGTGAGTTCAATGAATTCTCATGTGTATAAAA
1 TAATTTTAACTAATTATTTCATCGTGAATTCAATGAATTTTCACGTGTATAAAA
10371304 GTTCAAATAA
Statistics
Matches: 184, Mismatches: 35, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
83 1 0.01
84 31 0.17
85 43 0.23
86 61 0.33
87 48 0.26
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.43
Consensus pattern (86 bp):
TAATTTTAACTAATTATTTCATCGTGAATTCAATGAATTTTCACGTGTATAAAAATTACTCTTAG
TATTAAAAATATTCTAAGTAA
Found at i:10385410 original size:22 final size:23
Alignment explanation
Indices: 10385377--10385420 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
10385367 TTTCATTTTT
*
10385377 TTAACTTTAATTT-TTTTATAAA
1 TTAACTTTAATTTCATTTATAAA
10385399 TTAA-TTTAAATTTCATTTATAA
1 TTAACTTT-AATTTCATTTATAA
10385421 TATACATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 9 0.47
23 7 0.37
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAACTTTAATTTCATTTATAAA
Found at i:10386559 original size:29 final size:29
Alignment explanation
Indices: 10386523--10386578 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
10386513 TTTTATTTTC
* *
10386523 TTTTATATTGAAATTAGTTTAATTGATTT
1 TTTTATATTAAAATTAGTTCAATTGATTT
10386552 TTTTATATTAAAATTAGTTCAATTGAT
1 TTTTATATTAAAATTAGTTCAATTGAT
10386579 ATTTAGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (29 bp):
TTTTATATTAAAATTAGTTCAATTGATTT
Found at i:10392862 original size:2 final size:2
Alignment explanation
Indices: 10392857--10392883 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10392847 AGCAAGATGG
10392857 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10392884 ACACTTGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10404797 original size:38 final size:39
Alignment explanation
Indices: 10404726--10404800 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
10404716 GGTAAAAGGT
* * *
10404726 GTTTCTTTCATAACTAAAGTGATATTTTGTGATTAAGAA
1 GTTTCCTTCACAACTAAAGTGACATTTTGTGATTAAGAA
*
10404765 GTTTCCTTCACAATTAAAGT-ACATTTTGTGATTAAG
1 GTTTCCTTCACAACTAAAGTGACATTTTGTGATTAAG
10404801 TGATATAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 15 0.47
39 17 0.53
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (39 bp):
GTTTCCTTCACAACTAAAGTGACATTTTGTGATTAAGAA
Found at i:10408673 original size:27 final size:27
Alignment explanation
Indices: 10408635--10408688 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
10408625 GTAGCACAAG
*
10408635 TTCACACATTAGCAGGGAACCATGTAC
1 TTCACACATTAGCAGGGAACCAGGTAC
10408662 TTCACACATTAGCAGGGAACCAGGTAC
1 TTCACACATTAGCAGGGAACCAGGTAC
10408689 ATGCCCTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (27 bp):
TTCACACATTAGCAGGGAACCAGGTAC
Found at i:10409109 original size:23 final size:24
Alignment explanation
Indices: 10409064--10409111 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
10409054 TTAGTTTTTT
* * *
10409064 TTTTTTAAAATATTCGAATTCATA
1 TTTTTTAAAATAATCAAAATCATA
10409088 TTTTTTAAAATAAT-AAAATCATA
1 TTTTTTAAAATAATCAAAATCATA
10409111 T
1 T
10409112 ATTAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTTTAAAATAATCAAAATCATA
Found at i:10413085 original size:68 final size:68
Alignment explanation
Indices: 10412976--10413115 Score: 273
Period size: 68 Copynumber: 2.1 Consensus size: 68
10412966 CCATCAATTT
10412976 TGATAAGATTAAAAATTTTCACTAAAGTGAAGAATAGTCAAAATCTCATTTTGATTAGTTAGACC
1 TGATAAGATTAAAAATTTTCACTAAAGTGAAGAATAGTCAAAATCTCATTTTGATTAGTTAGACC
10413041 AAA
66 AAA
10413044 TGATAAGATTAAAAATTTTCACTAAAGTGAAGAATAGTCAAAATCTCATTTTGATTAGTTAGACC
1 TGATAAGATTAAAAATTTTCACTAAAGTGAAGAATAGTCAAAATCTCATTTTGATTAGTTAGACC
10413109 AAA
66 AAA
10413112 -GATA
1 TGATA
10413116 CAAAAACTTC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 4 0.06
68 68 0.94
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (68 bp):
TGATAAGATTAAAAATTTTCACTAAAGTGAAGAATAGTCAAAATCTCATTTTGATTAGTTAGACC
AAA
Found at i:10413429 original size:29 final size:27
Alignment explanation
Indices: 10413366--10413448 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 27
10413356 ATTTTTAATA
*
10413366 AAAAT-AAAAAAAATTCT-AATCTAAAT
1 AAAATAAAAAAAAATTTTAAAT-TAAAT
*
10413392 AAAATAAAAAAAAATTTTAAATTAATT
1 AAAATAAAAAAAAATTTTAAATTAAAT
**
10413419 AAAATTAAAAAAAATAAATTAAATTAAAT
1 AAAA-TAAAAAAAA-ATTTTAAATTAAAT
10413448 A
1 A
10413449 CAATTTCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.10
27 19 0.40
28 12 0.25
29 12 0.25
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATAAAAAAAAATTTTAAATTAAAT
Found at i:10413453 original size:29 final size:27
Alignment explanation
Indices: 10413371--10413453 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 27
10413361 TAATAAAAAT
* *
10413371 AAAAAAAATTCTAATCTAAATAAAATAAA
1 AAAAAAAATT-AAAT-TAAATAAATTAAA
** *
10413400 AAAAAATTTTAAATTAATTAAAATTAAA
1 AAAAAAAATTAAATTAAAT-AAATTAAA
10413428 AAAAATAAATTAAATTAAATACAATT
1 AAAAA-AAATTAAATTAAATA-AATT
10413454 TCAAACGCTC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.09
28 16 0.37
29 23 0.53
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAAAAATTAAATTAAATAAATTAAA
Found at i:10419521 original size:2 final size:2
Alignment explanation
Indices: 10419509--10419545 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
10419499 GCAGTCAAAC
10419509 TA TA T- 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
10419546 GCTCAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10420186 original size:17 final size:16
Alignment explanation
Indices: 10420155--10420195 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
10420145 ACCTTATCAA
10420155 ATTGTATAACATTTTT
1 ATTGTATAACATTTTT
10420171 ATTGTATTAAC-TTTTT
1 ATTGTA-TAACATTTTT
10420187 CATT-TATAA
1 -ATTGTATAA
10420196 AAGAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.13
16 13 0.57
17 7 0.30
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (16 bp):
ATTGTATAACATTTTT
Found at i:10423699 original size:33 final size:33
Alignment explanation
Indices: 10423657--10423725 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
10423647 ATTTTAAAAG
* *
10423657 ATGGATTTTATTAGCCATACATTCGATATGACA
1 ATGGATTTTAATAGCCATACATTCCATATGACA
*
10423690 ATGGATTTTAATAGCCATACATTCCATATGTCA
1 ATGGATTTTAATAGCCATACATTCCATATGACA
10423723 ATG
1 ATG
10423726 TTGTAATTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (33 bp):
ATGGATTTTAATAGCCATACATTCCATATGACA
Found at i:10442916 original size:6 final size:6
Alignment explanation
Indices: 10442905--10442933 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
10442895 AAACATTATT
10442905 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
10442934 CTTCAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (6 bp):
TTCTTG
Found at i:10448012 original size:21 final size:21
Alignment explanation
Indices: 10447973--10448012 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10447963 AACAGAAAAC
*
10447973 TTTCTTCTCATTTTCGTTTCT
1 TTTCTTCTAATTTTCGTTTCT
10447994 TTTCTTC-AATTTTCTGTTT
1 TTTCTTCTAATTTTC-GTTT
10448013 GTATCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.07, C:0.20, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTCTTCTAATTTTCGTTTCT
Found at i:10458992 original size:334 final size:353
Alignment explanation
Indices: 10458548--10459221 Score: 865
Period size: 334 Copynumber: 2.0 Consensus size: 353
10458538 AATATTTTAA
* *
10458548 TATATATAATAGTAATTATAGTCCTTATAAATGAATCTAATATATATATATAAAGTATATATATT
1 TATATATAATAGTAATTATAGTCCTTATAAATGAATC-AACATATATATATAAACTATATATATT
* * * *
10458613 AAAAGACATTACAAGTTAATTAATAATTATAATTTCATTAATTAATTTAATTAACTATA-GAGGT
65 AAAAGACATTACAAGTTAAATAATAATAATAATTTCATGAATTAATTTAATTAACTATATG-GAT
* * ** * *
10458677 TTG-TCTTTAAT-TACATAAAATTAAAAAAATA-AC-TAAGTTTTAGAACTATTCTAATCTCACA
129 TTGTTC-TTAATAT-CATAAAATTAAAAAAAAACACTTAAATTCCAAAACTATTCTAATCTCAAA
* *
10458738 A-CTTTTCTTT-AG-GT-T-TA-TATAAGTTTATATAAATAAAG-T-T-T-TATATAT-T-ATAA
192 AGCTTTT-TTTAAGTATATATATTATAAGATTATATAAATAAAGATATATATATATATATGATAA
* * * * *
10458791 TTAATAATTTTATAAGTTATAA-TTTTGTAATGTTAATACAAAATATAAAGTAAATATGTTTATA
256 TTAATAATTTTATAAGTCATAATTTTTGTAATGCTAATACAAAACAGAAAGTAAATATATTTATA
10458855 -TATAAAGTATATATATACTACAAAAATTTAGTG
321 TTA-AAAGTATATATATACTACAAAAATTTAGTG
* * *
10458888 TATATATAATAGTAATTATATTTCTTATAAATTAA-C-ACA-A-A-ATATAAACTATATATATTA
1 TATATATAATAGTAATTATAGTCCTTATAAATGAATCAACATATATATATAAACTATATATATTA
** *
10458948 AAAGACATTACAAGTTAAATAATAATAATGGTTTCATGAATTAATTTAATTAATTATATGGATTT
66 AAAGACATTACAAGTTAAATAATAATAATAATTTCATGAATTAATTTAATTAACTATATGGATTT
*
10459013 GTTCTTAATATCATGAAATTAAAAAAAAACACTTAAATTCCAAAACTATTCTAATCTCAAAAGCT
131 GTTCTTAATATCATAAAATTAAAAAAAAACACTTAAATTCCAAAACTATTCTAATCTCAAAAGCT
*
10459078 TTTTTTAAGTATATATATTATAAGATTATATAAATAATGCTATATATATATATATATGATAATTA
196 TTTTTTAAGTATATATATTATAAGATTATATAAATAAAG--ATATATATATATATATGATAATTA
10459143 ATAATTTTATAAGTCATAATTTTTGTAATGCTAATACAAAACAGAAAGTAAATATATTTATATTA
259 ATAATTTTATAAGTCATAATTTTTGTAATGCTAATACAAAACAGAAAGTAAATATATTTATATTA
10459208 AAAGTATATATATA
324 AAAGTATATATATA
10459222 TATATAATAG
Statistics
Matches: 286, Mismatches: 27, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
334 96 0.34
335 7 0.02
336 28 0.10
337 9 0.03
338 1 0.00
339 2 0.01
340 34 0.12
341 19 0.07
344 1 0.00
345 1 0.00
346 1 0.00
347 7 0.02
348 1 0.00
349 25 0.09
350 52 0.18
351 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (353 bp):
TATATATAATAGTAATTATAGTCCTTATAAATGAATCAACATATATATATAAACTATATATATTA
AAAGACATTACAAGTTAAATAATAATAATAATTTCATGAATTAATTTAATTAACTATATGGATTT
GTTCTTAATATCATAAAATTAAAAAAAAACACTTAAATTCCAAAACTATTCTAATCTCAAAAGCT
TTTTTTAAGTATATATATTATAAGATTATATAAATAAAGATATATATATATATATGATAATTAAT
AATTTTATAAGTCATAATTTTTGTAATGCTAATACAAAACAGAAAGTAAATATATTTATATTAAA
AGTATATATATACTACAAAAATTTAGTG
Found at i:10459211 original size:21 final size:20
Alignment explanation
Indices: 10459187--10459241 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
10459177 TACAAAACAG
10459187 AAAGTAAATATATTTATATTA
1 AAAGTAAATATATTTATA-TA
* *
10459208 AAAGTATATATATATATATA
1 AAAGTAAATATATTTATATA
* *
10459228 ATAGTAATTATATT
1 AAAGTAAATATATT
10459242 CCTTTATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAGTAAATATATTTATATA
Found at i:10460933 original size:2 final size:2
Alignment explanation
Indices: 10460926--10460956 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10460916 CAGTGCGGCC
10460926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10460957 ATACAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10462875 original size:22 final size:23
Alignment explanation
Indices: 10462842--10462921 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 23
10462832 GTTTTGGTAG
*
10462842 TTTTT-GAGCATTACGTGGCTAA
1 TTTTTAGAGCATTACGTGACTAA
* *
10462864 TTTTTAGA-CATTACATGACTGA
1 TTTTTAGAGCATTACGTGACTAA
* * *
10462886 -CTTT-GAACATTACGTAACTAA
1 TTTTTAGAGCATTACGTGACTAA
*
10462907 TTTTTAGATCATTAC
1 TTTTTAGAGCATTAC
10462922 ATAATTAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 2 0.04
21 14 0.31
22 19 0.42
23 10 0.22
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (23 bp):
TTTTTAGAGCATTACGTGACTAA
Found at i:10463128 original size:22 final size:22
Alignment explanation
Indices: 10463050--10463129 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
10463040 TTAAACATTA
* *
10463050 CTTAAAAATCAATAACGTAATG
1 CTTAAAAACCAATCACGTAATG
* * *
10463072 CTTAAAAACTAA-CTATGCAATG
1 CTTAAAAACCAATC-ACGTAATG
*
10463094 CCT-AAAACCAATCACGTAATG
1 CTTAAAAACCAATCACGTAATG
10463115 CTTAAAAACCAATCA
1 CTTAAAAACCAATCA
10463130 TTGAGTGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
21 15 0.33
22 30 0.67
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.24
Consensus pattern (22 bp):
CTTAAAAACCAATCACGTAATG
Found at i:10466632 original size:14 final size:14
Alignment explanation
Indices: 10466613--10466639 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10466603 AATCCACAAG
10466613 ATATAAATGCAATC
1 ATATAAATGCAATC
10466627 ATATAAATGCAAT
1 ATATAAATGCAAT
10466640 AATCCAAACA
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:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (14 bp):
ATATAAATGCAATC
Found at i:10472139 original size:71 final size:70
Alignment explanation
Indices: 10472023--10472156 Score: 198
Period size: 71 Copynumber: 1.9 Consensus size: 70
10472013 TTGTATCATA
* *
10472023 TTACACGGATTGAGTTTGGAAAGCTCTAGTCTATCAATGCCTCAATTGTTCATGTTTTCCCTAAT
1 TTACACGGATTGACTTTGGAAAGCTCTAGTCAATCAATGCCTCAATTGTTCA-GTTTTCCCTAAT
10472088 ACTATG
65 ACTATG
* * *
10472094 TTACACGGATTGACTTTGG-AAGACTTTAGTCAATTAGTGCCTCAATTGTTCAGTTTTCCCTAA
1 TTACACGGATTGACTTTGGAAAG-CTCTAGTCAATCAATGCCTCAATTGTTCAGTTTTCCCTAA
10472157 AGTGTAGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
70 14 0.25
71 43 0.75
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (70 bp):
TTACACGGATTGACTTTGGAAAGCTCTAGTCAATCAATGCCTCAATTGTTCAGTTTTCCCTAATA
CTATG
Found at i:10473542 original size:30 final size:30
Alignment explanation
Indices: 10473508--10473564 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10473498 AATAAGCCCT
10473508 TTAATTTTTATTTT-AAGCTAAATAAACATC
1 TTAATTTTTATTTTGAA-CTAAATAAACATC
*
10473538 TTAATTTTTATTTTGAATTAAATAAAC
1 TTAATTTTTATTTTGAACTAAATAAAC
10473565 CCTTTTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (30 bp):
TTAATTTTTATTTTGAACTAAATAAACATC
Found at i:10493382 original size:25 final size:25
Alignment explanation
Indices: 10493346--10493404 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
10493336 TGATTTCAGG
10493346 CCACCAGCCTAAGATGCTGCTGATA
1 CCACCAGCCTAAGATGCTGCTGATA
* *
10493371 CCACCAGGCTAAGATGCTGCTGATG
1 CCACCAGCCTAAGATGCTGCTGATA
*
10493396 CCGCCAGCC
1 CCACCAGCC
10493405 ATGAACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.17
Consensus pattern (25 bp):
CCACCAGCCTAAGATGCTGCTGATA
Found at i:10496164 original size:2 final size:2
Alignment explanation
Indices: 10496157--10496203 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
10496147 ATAAATCAGA
10496157 TC TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC TC TC TC T- TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10496197 TC TC TC T
1 TC TC TC T
10496204 ATGCATTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:10496183 original size:17 final size:17
Alignment explanation
Indices: 10496157--10496203 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
10496147 ATAAATCAGA
10496157 TCTC-TCTCTCTCTCTC
1 TCTCTTCTCTCTCTCTC
10496173 TCTCTTCTCTCTCTCTC
1 TCTCTTCTCTCTCTCTC
10496190 TCTCTTCTCTCTCT
1 TCTCTTCTCTCTCT
10496204 ATGCATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (17 bp):
TCTCTTCTCTCTCTCTC
Found at i:10520253 original size:2 final size:2
Alignment explanation
Indices: 10520246--10520288 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10520236 GTGTGAAGGA
10520246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10520288 A
1 A
10520289 AGCATTGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10532635 original size:2 final size:2
Alignment explanation
Indices: 10532628--10532661 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10532618 GGGAACTTAA
10532628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10532662 TGGCATAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10549154 original size:2 final size:2
Alignment explanation
Indices: 10549147--10549177 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10549137 CTTAAAATTT
10549147 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
10549178 TATTGAATTA
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:10559086 original size:2 final size:2
Alignment explanation
Indices: 10559079--10559103 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10559069 TTCTAATTCA
10559079 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10559104 ATTTTAAGCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10563515 original size:2 final size:2
Alignment explanation
Indices: 10563510--10563539 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10563500 ATAGAGAGAA
10563510 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
10563540 TAAGAAATAG
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):
AT
Found at i:10570307 original size:19 final size:20
Alignment explanation
Indices: 10570271--10570308 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
10570261 AGACAAAACT
*
10570271 CAAAAATATATATATATTTG
1 CAAAAATATACATATATTTG
*
10570291 CAAAAA-ATACATTTATTT
1 CAAAAATATACATATATTT
10570309 TTTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (20 bp):
CAAAAATATACATATATTTG
Found at i:10584990 original size:33 final size:33
Alignment explanation
Indices: 10584953--10585019 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
10584943 TGATCATATA
* *
10584953 ATTAT-ATCATATTGATATATTATATTATTATTT
1 ATTATAAT-ATATTAATATATTATATTAATATTT
*
10584986 ATTATAATATGTTAATATATTATATTAATATTT
1 ATTATAATATATTAATATATTATATTAATATTT
10585019 A
1 A
10585020 AAATATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (33 bp):
ATTATAATATATTAATATATTATATTAATATTT
Found at i:10585013 original size:13 final size:12
Alignment explanation
Indices: 10584955--10585017 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 12
10584945 ATCATATAAT
*
10584955 TATATCATATTGA
1 TATATTATATT-A
10584968 TATATTATATTA
1 TATATTATATTA
10584980 T-TATT-TATTA
1 TATATTATATTA
*
10584990 TA-A-TATGTTAA
1 TATATTATATT-A
10585001 TATATTATATTA
1 TATATTATATTA
10585013 -ATATT
1 TATATT
10585018 TAAAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 1 0.02
10 10 0.24
11 12 0.29
12 4 0.10
13 15 0.36
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATTATATTA
Found at i:10590979 original size:19 final size:16
Alignment explanation
Indices: 10590945--10590975 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10590935 TTAATTGATA
10590945 TTATTATTGCATGCTT
1 TTATTATTGCATGCTT
10590961 TTATTATTGCATGCT
1 TTATTATTGCATGCT
10590976 GCTTGCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (16 bp):
TTATTATTGCATGCTT
Found at i:10594157 original size:2 final size:2
Alignment explanation
Indices: 10594150--10594185 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10594140 ATGCACAGCT
*
10594150 GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10594186 ATCTGGAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10601026 original size:20 final size:20
Alignment explanation
Indices: 10601001--10601038 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10600991 CACTGAATGT
10601001 TTTATTTTTTATATTAAAAA
1 TTTATTTTTTATATTAAAAA
10601021 TTTATTTTTTATATTAAA
1 TTTATTTTTTATATTAAA
10601039 CAATATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTTTTTATATTAAAAA
Found at i:10601058 original size:23 final size:20
Alignment explanation
Indices: 10601008--10601086 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 20
10600998 TGTTTTATTT
* *
10601008 TTTATATTAAAAATTTATTT
1 TTTATATTAAAAATTTAATA
10601028 TTTATATTAAACAATATTGAATA
1 TTTATATTAAA-AAT-TT-AATA
10601051 TTTATATTATAAAAAATTTAA-A
1 TTTATA-T-T-AAAAATTTAATA
* *
10601073 TTTAAATTTAAAAT
1 TTTATATTAAAAAT
10601087 ATATTAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 5 0.10
20 12 0.24
21 4 0.08
22 8 0.16
23 10 0.20
24 3 0.06
25 4 0.08
26 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
TTTATATTAAAAATTTAATA
Found at i:10601093 original size:22 final size:23
Alignment explanation
Indices: 10601035--10601094 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
10601025 TTTTTTATAT
* *
10601035 TAAACAATATTGAATATTTATATTA
1 TAAAAAATATT-AA-ATTTAAATTA
10601060 TAAAAAAT-TTAAATTTAAATT-
1 TAAAAAATATTAAATTTAAATTA
*
10601081 TAAAATATATTAAA
1 TAAAAAATATTAAA
10601095 ATCAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 7 0.23
22 13 0.42
23 2 0.06
24 2 0.06
25 7 0.23
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAAAAATATTAAATTTAAATTA
Found at i:10602626 original size:2 final size:2
Alignment explanation
Indices: 10602619--10602651 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
10602609 ACAATTCTTC
*
10602619 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10602652 GTATGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:10605661 original size:20 final size:20
Alignment explanation
Indices: 10605636--10605677 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
10605626 TGATGATAAG
10605636 TAGCCATATACGGATTTACC
1 TAGCCATATACGGATTTACC
*
10605656 TAGCCATATATGGATTTACC
1 TAGCCATATACGGATTTACC
10605676 TA
1 TA
10605678 CCAGGCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
TAGCCATATACGGATTTACC
Found at i:10608831 original size:66 final size:66
Alignment explanation
Indices: 10608732--10608867 Score: 209
Period size: 66 Copynumber: 2.1 Consensus size: 66
10608722 CCACTAGAAC
*
10608732 GGGTCCAAACGGGACCACTGGCAAGAGGTACTTGGGCTTTCTATGCTCAATTTTTACACCTAGTT
1 GGGTCCAAACGGGACCACTGGCAAGAGGGACTTGGGCTTTCTATGCTCAATTTTTACACCTAGTT
10608797 T
66 T
* * ** * *
10608798 GGGTCCAAATGGGACCACTTGCTTGAGGGACTTGGGCTTTCTATGTTCCATTTTTACACCTAGTT
1 GGGTCCAAACGGGACCACTGGCAAGAGGGACTTGGGCTTTCTATGCTCAATTTTTACACCTAGTT
10608863 T
66 T
10608864 GGGT
1 GGGT
10608868 AGCTGTTAGC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (66 bp):
GGGTCCAAACGGGACCACTGGCAAGAGGGACTTGGGCTTTCTATGCTCAATTTTTACACCTAGTT
T
Found at i:10612325 original size:10 final size:10
Alignment explanation
Indices: 10612310--10612339 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
10612300 AAAAAAATAA
10612310 TTTTATTAAT
1 TTTTATTAAT
10612320 TTTTATT-AT
1 TTTTATTAAT
10612329 TTTTATTAAT
1 TTTTATTAAT
10612339 T
1 T
10612340 AAAAAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATTAAT
Found at i:10614071 original size:15 final size:18
Alignment explanation
Indices: 10614033--10614072 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
10614023 ATATTTTATA
10614033 ATTTTAATAGTATTGAAT
1 ATTTTAATAGTATTGAAT
*
10614051 AATTTAA-A-TATT-AAT
1 ATTTTAATAGTATTGAAT
10614066 ATTTTAA
1 ATTTTAA
10614073 GTTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 1 0.05
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTAATAGTATTGAAT
Found at i:10615007 original size:20 final size:21
Alignment explanation
Indices: 10614984--10615038 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
10614974 TTATTTTACT
* *
10614984 TAAACTTAAAAT-ATTAAATA
1 TAAAATTAAAATCATAAAATA
10615004 TAAAATTAAAATGCATAAAATA
1 TAAAATTAAAAT-CATAAAATA
*
10615026 TAAATATTTAAAT
1 TAAA-ATTAAAAT
10615039 ACGATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
22 11 0.38
23 7 0.24
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAATTAAAATCATAAAATA
Found at i:10615620 original size:23 final size:24
Alignment explanation
Indices: 10615580--10615625 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
10615570 TCAAATATGT
* * *
10615580 AAAAATAATAATATAAATTAAAAG
1 AAAAATAATAAAAAAAATAAAAAG
10615604 AAAAA-AATAAAAAAAATAAAAA
1 AAAAATAATAAAAAAAATAAAAA
10615626 TTGAGTGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (24 bp):
AAAAATAATAAAAAAAATAAAAAG
Found at i:10617709 original size:17 final size:17
Alignment explanation
Indices: 10617689--10617733 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
10617679 TTGAAAACAC
10617689 GTTAACTTTTTAAAAGA
1 GTTAACTTTTTAAAAGA
*
10617706 GTTAATTTTTTAAAAGA
1 GTTAACTTTTTAAAAGA
*
10617723 GTTGACTTTTT
1 GTTAACTTTTT
10617734 CTTAGATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (17 bp):
GTTAACTTTTTAAAAGA
Found at i:10629447 original size:24 final size:24
Alignment explanation
Indices: 10629401--10629457 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 24
10629391 CTATTTATAA
*
10629401 ATAGGATGGTAGAAAATATTTTTC
1 ATAGGATGGCAGAAAATATTTTTC
10629425 ATAGTGATGGCAGAAAATATTTTTC
1 ATAG-GATGGCAGAAAATATTTTTC
*
10629450 ACAGGATG
1 ATAGGATG
10629458 ATCCAAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.27
25 22 0.73
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (24 bp):
ATAGGATGGCAGAAAATATTTTTC
Found at i:10630056 original size:14 final size:14
Alignment explanation
Indices: 10630037--10630063 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10630027 GTAATGTTAT
10630037 AATTAAAATAAAAA
1 AATTAAAATAAAAA
10630051 AATTAAAATAAAA
1 AATTAAAATAAAA
10630064 TATAACATAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATTAAAATAAAAA
Found at i:10630123 original size:55 final size:56
Alignment explanation
Indices: 10630040--10630168 Score: 138
Period size: 55 Copynumber: 2.3 Consensus size: 56
10630030 ATGTTATAAT
* *
10630040 TAAAATA-AAAAAATTAAAATAAAATATAACATAAG-AATTAGAAACTAAAATTAAA
1 TAAAATATAAAAAATTAAAATAAAATATAACATAAGTAA-AAGAAACTAAAATAAAA
* ** * * *
10630095 TAAAATATAAGAAATTAAAAT-TTATATAATATATGTAAAAGAAATTAAAATAAAA
1 TAAAATATAAAAAATTAAAATAAAATATAACATAAGTAAAAGAAACTAAAATAAAA
10630150 TATATAATATAAAAAATTA
1 TA-A-AATATAAAAAATTA
10630169 TATTAAAGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
55 33 0.54
56 15 0.25
57 13 0.21
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (56 bp):
TAAAATATAAAAAATTAAAATAAAATATAACATAAGTAAAAGAAACTAAAATAAAA
Found at i:10635623 original size:21 final size:21
Alignment explanation
Indices: 10635599--10635639 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10635589 AATTCAGTAC
10635599 TGTTT-TAATCAAAAGTCTTGA
1 TGTTTGTAAT-AAAAGTCTTGA
*
10635620 TGTTTGTTATAAAAGTCTTG
1 TGTTTGTAATAAAAGTCTTG
10635640 TGTCTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (21 bp):
TGTTTGTAATAAAAGTCTTGA
Found at i:10676242 original size:26 final size:25
Alignment explanation
Indices: 10676193--10676242 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
10676183 ATCTAAACTC
**
10676193 AAATCTTATTATTTATAAGGTACCT
1 AAATCTTATTATTTATAAAATACCT
*
10676218 AAATTTTATTATTTTATAAAATACC
1 AAATCTTATTA-TTTATAAAATACC
10676243 CGAATCCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (25 bp):
AAATCTTATTATTTATAAAATACCT
Found at i:10688095 original size:16 final size:16
Alignment explanation
Indices: 10688065--10688109 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
10688055 AATACGAATG
10688065 ATTTTA-TGATGATTAA
1 ATTTTATTGAT-ATTAA
10688081 GA-TTTATTGATATTAA
1 -ATTTTATTGATATTAA
10688097 ATTTTATT-ATATT
1 ATTTTATTGATATT
10688110 TGATAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.23
16 15 0.58
17 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
ATTTTATTGATATTAA
Found at i:10688223 original size:17 final size:18
Alignment explanation
Indices: 10688187--10688224 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
10688177 ATATTTTAAT
* *
10688187 TTAATCATGGTAATCGTG
1 TTAATCATGGTAAACATG
10688205 TTAATCAT-GTAAACATG
1 TTAATCATGGTAAACATG
10688222 TTA
1 TTA
10688225 TAATTGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (18 bp):
TTAATCATGGTAAACATG
Found at i:10689007 original size:15 final size:14
Alignment explanation
Indices: 10688982--10689019 Score: 67
Period size: 15 Copynumber: 2.6 Consensus size: 14
10688972 CATGGTTTTA
10688982 AATAAAAAAATAAT
1 AATAAAAAAATAAT
10688996 AATAACAAAAATAAT
1 AATAA-AAAAATAAT
10689011 AATAAAAAA
1 AATAAAAAA
10689020 TTTTAAGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (14 bp):
AATAAAAAAATAAT
Found at i:10689231 original size:21 final size:21
Alignment explanation
Indices: 10689202--10689241 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
10689192 TATTCTTTGG
10689202 AGGGAATGAGCTATATGGGGA
1 AGGGAATGAGCTATATGGGGA
*
10689223 AGGGGATGAGCTATATGGG
1 AGGGAATGAGCTATATGGG
10689242 ACATGAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.45, T:0.20
Consensus pattern (21 bp):
AGGGAATGAGCTATATGGGGA
Found at i:10700685 original size:25 final size:25
Alignment explanation
Indices: 10700634--10700685 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
10700624 TTTATATTCT
* *
10700634 ATTTGATATATTGTTATTTGTATAA
1 ATTTGATATATTATTATTTGAATAA
*
10700659 ATTTTATATATTATTA-TTGAATCAA
1 ATTTGATATATTATTATTTGAAT-AA
10700684 AT
1 AT
10700686 GTTGTTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (25 bp):
ATTTGATATATTATTATTTGAATAA
Found at i:10707157 original size:9 final size:9
Alignment explanation
Indices: 10707135--10707187 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
10707125 CCTCTCCTCA
10707135 ATAATTTTT
1 ATAATTTTT
10707144 A-AATTTTT
1 ATAATTTTT
10707152 ATAATTTATTT
1 ATAA-TT-TTT
*
10707163 ATAATTTTA
1 ATAATTTTT
*
10707172 AAAATTTTT
1 ATAATTTTT
10707181 ATAATTT
1 ATAATTT
10707188 CATCCCTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 8 0.22
9 18 0.49
10 4 0.11
11 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:10707244 original size:63 final size:61
Alignment explanation
Indices: 10707132--10707331 Score: 199
Period size: 63 Copynumber: 3.2 Consensus size: 61
10707122 CCCCCTCTCC
* * * *
10707132 TCAATAATTTTTAAATTTTTATAATTTATTTATAATTTTAAAAATTTTTATAATTTCATCCCT
1 TCAATAATTTTTAAAATTTTATAATTTTTTTAT-TTTTTAGAAA-TTTTATAATTTCATCCCT
*
10707195 TCAATAATTTTTAAAATTTTATAATTTGCTTTTATTTTTTAGAAATTTTATAATTTCATCCAT
1 TCAATAATTTTTAAAATTTTATAATTT--TTTTATTTTTTAGAAATTTTATAATTTCATCCCT
* * * * * *
10707258 AT-AAAAAGTTTAAAAATTTT-TAACATATTTTTATTTTTTTGAAATTTTATAATTTGA-CCCT
1 -TCAATAATTTTTAAAATTTTAT-A-ATTTTTTTATTTTTTAGAAATTTTATAATTTCATCCCT
*
10707319 TATAATAATTTTT
1 T-CAATAATTTTT
10707332 TGTTTAGTGA
Statistics
Matches: 115, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
60 1 0.01
61 3 0.03
62 35 0.30
63 59 0.51
64 12 0.10
65 5 0.04
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (61 bp):
TCAATAATTTTTAAAATTTTATAATTTTTTTATTTTTTAGAAATTTTATAATTTCATCCCT
Found at i:10713200 original size:3 final size:3
Alignment explanation
Indices: 10713192--10713217 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10713182 TCCATACATC
10713192 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
10713218 ATGATGGTAA
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:10716950 original size:7 final size:8
Alignment explanation
Indices: 10716921--10716947 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
10716911 GATTGGCTCG
10716921 ATTTAAAA
1 ATTTAAAA
10716929 ATTTAAAA
1 ATTTAAAA
10716937 ATTTAAAA
1 ATTTAAAA
10716945 ATT
1 ATT
10716948 AAATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTTAAAA
Found at i:10718964 original size:17 final size:19
Alignment explanation
Indices: 10718942--10718979 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
10718932 CAAGTATAAA
10718942 TGTTTGA-GTT-TTAAGTT
1 TGTTTGACGTTATTAAGTT
10718959 TGTTTGACGTTCATTAAGTT
1 TGTTTGACGTT-ATTAAGTT
10718979 T
1 T
10718980 TAATAATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
20 8 0.44
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.55
Consensus pattern (19 bp):
TGTTTGACGTTATTAAGTT
Found at i:10725446 original size:3 final size:3
Alignment explanation
Indices: 10725438--10725465 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10725428 GTTCTTGCCT
10725438 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
10725466 CTCCGGGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:10731660 original size:2 final size:2
Alignment explanation
Indices: 10731653--10731679 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10731643 ACATACATAC
10731653 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10731680 ATTTTGAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10738151 original size:2 final size:2
Alignment explanation
Indices: 10738140--10738180 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10738130 GCACGCATTA
10738140 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10738181 TACATCTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10743716 original size:93 final size:93
Alignment explanation
Indices: 10743483--10743728 Score: 332
Period size: 93 Copynumber: 2.6 Consensus size: 93
10743473 GGACTGCTGT
* * *
10743483 TTGGTGAAGGCAGTAGCATCAACGCTGCAGCGTTGGGAGTGTGGCGCTGCAGCGTTGATGCCATT
1 TTGGTGAAGGCAGTAGCATCAACGTTGCAGCGTTGGGAGTGCGGCGCTGCAGCGTTGATGCCACT
10743548 GCTTGGTGCATGTCCCAGCGCTATCCCC
66 GCTTGGTGCATGTCCCAGCGCTATCCCC
* **** * * * *
10743576 TTGGTGAAGGCAGTAGCATCAATGTTGCAGCG-CCACACTCCCAGCGCTGCAGCATTGATGCCAC
1 TTGGTGAAGGCAGTAGCATCAACGTTGCAGCGTTGGGAGT-GCGGCGCTGCAGCGTTGATGCCAC
* *
10743640 TGCTTGGTGCATGTCCTAGCGCTGTCCCC
65 TGCTTGGTGCATGTCCCAGCGCTATCCCC
* *
10743669 TTGGTGAAAGCAGTAGCATCAACGTTGCAGCGTTGGGAGTGCGGCGCTACAGCGTTGATG
1 TTGGTGAAGGCAGTAGCATCAACGTTGCAGCGTTGGGAGTGCGGCGCTGCAGCGTTGATG
10743729 GTTTTTTTGC
Statistics
Matches: 126, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
92 2 0.02
93 122 0.97
94 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (93 bp):
TTGGTGAAGGCAGTAGCATCAACGTTGCAGCGTTGGGAGTGCGGCGCTGCAGCGTTGATGCCACT
GCTTGGTGCATGTCCCAGCGCTATCCCC
Found at i:10751856 original size:29 final size:29
Alignment explanation
Indices: 10751793--10751880 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
10751783 TACTTGAAAC
* * *
10751793 CATTTTCATTTG-CAAAAAAGAAAAAAAAAT
1 CATTTTCATTTGAC-AAATA-AAAAATATAT
* *
10751823 TATTTTCATTTTACAAATAAAAAATATAT
1 CATTTTCATTTGACAAATAAAAAATATAT
* * *
10751852 CATTTTTATTTGAGAAATAAAAATTATAT
1 CATTTTCATTTGACAAATAAAAAATATAT
10751881 TAGTAAATAA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 32 0.68
30 14 0.30
31 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (29 bp):
CATTTTCATTTGACAAATAAAAAATATAT
Found at i:10753888 original size:2 final size:2
Alignment explanation
Indices: 10753881--10753910 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10753871 TTTTAATCTG
10753881 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
10753911 TCGCTTCAGC
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):
AT
Found at i:10766168 original size:29 final size:25
Alignment explanation
Indices: 10766136--10766202 Score: 64
Period size: 29 Copynumber: 2.5 Consensus size: 25
10766126 ATTTAAAAAA
10766136 ATTTAAATAAATTGTTATTATTTTATTAT
1 ATTTAAATAAATT-TTA-TA-TTT-TTAT
*
10766165 ATTTAATTAATATTTTATATTTTTAT
1 ATTTAAATAA-ATTTTATATTTTTAT
10766191 -TTTAAATCAAAT
1 ATTTAAAT-AAAT
10766203 AAGCTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
25 8 0.24
26 6 0.18
27 3 0.09
28 2 0.06
29 12 0.35
30 3 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (25 bp):
ATTTAAATAAATTTTATATTTTTAT
Found at i:10771988 original size:2 final size:2
Alignment explanation
Indices: 10771981--10772014 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10771971 GGATATAATT
10771981 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
10772015 AACACATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10776048 original size:123 final size:122
Alignment explanation
Indices: 10775809--10776177 Score: 506
Period size: 123 Copynumber: 3.0 Consensus size: 122
10775799 AATATGGTAG
* * *
10775809 GACCTTAGGAAATGATAAGAGGAAATTCTACTGCATCATTGAGGTTTTGAATTATCTATATAAAA
1 GACCTTAGGAAATGATAAGAGGAAATTCAACTGCATCATTGAGGTTTTGAATGATCTAT-T-TAA
** *
10775874 ACAATCCCTGTGATTCTCTGTATACCATGGAGTCAAGTGCTGCTGTTTCCTTGAGATAA
64 ACAATCCCTGTGATTCTCTGTATGGCATAGAGTCAAGTGCTGCTGTTTCCTTGAGATAA
* * * *
10775933 GACCCTAGGAAATGATAAGAGGAAATTCCACTGCACCATTGAGGTTTTGAATGATCTGTTTCAAA
1 GACCTTAGGAAATGATAAGAGGAAATTCAACTGCATCATTGAGGTTTTGAATGATCTATTT-AAA
* *
10775998 CAATCCCTCTGATTCTCTGTATGGCATAGTGTCAAGTGCTGCTGTTTCCTTGAGATAA
65 CAATCCCTGTGATTCTCTGTATGGCATAGAGTCAAGTGCTGCTGTTTCCTTGAGATAA
* * *
10776056 GACCTTATGAAATGATAAAAGGAAATTCAACTGCATCATTGAGGTTTTGAATGATCTAATATAAA
1 GACCTTAGGAAATGATAAGAGGAAATTCAACTGCATCATTGAGGTTTTGAATGATCT-ATTTAAA
* * * *
10776121 GCAATCCATGTGATTCTCTGTATAGG-ATAGAGTCAAGTACTGTTGCTTCCTTGAGAT
65 -CAATCCCTGTGATTCTCTGTAT-GGCATAGAGTCAAGTGCTGCTGTTTCCTTGAGAT
10776178 TTCCACAATA
Statistics
Matches: 217, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
123 112 0.52
124 103 0.47
125 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (122 bp):
GACCTTAGGAAATGATAAGAGGAAATTCAACTGCATCATTGAGGTTTTGAATGATCTATTTAAAC
AATCCCTGTGATTCTCTGTATGGCATAGAGTCAAGTGCTGCTGTTTCCTTGAGATAA
Found at i:10777073 original size:19 final size:19
Alignment explanation
Indices: 10777049--10777086 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
10777039 CTAAGCACTG
10777049 TAATTTCCAATATTTTGAA
1 TAATTTCCAATATTTTGAA
*
10777068 TAATTTCCTATATTTTGAA
1 TAATTTCCAATATTTTGAA
10777087 AATGTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
TAATTTCCAATATTTTGAA
Found at i:10777977 original size:2 final size:2
Alignment explanation
Indices: 10777970--10777998 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10777960 CTTCTCCCCT
10777970 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 G
10777999 TGTAAAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10782911 original size:2 final size:2
Alignment explanation
Indices: 10782904--10782940 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
10782894 NNNNNNNNNN
* *
10782904 TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10782941 CTGTGTGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:10789906 original size:2 final size:2
Alignment explanation
Indices: 10789894--10789958 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
10789884 AACATCCAGA
* *
10789894 CT CT CT GT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10789936 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
10789959 ATATGCATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:10796551 original size:15 final size:15
Alignment explanation
Indices: 10796531--10796560 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10796521 AGTTGATGTG
10796531 CATTGATATGTCAGA
1 CATTGATATGTCAGA
*
10796546 CATTGATCTGTCAGA
1 CATTGATATGTCAGA
10796561 ATTCAGCTAG
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:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (15 bp):
CATTGATATGTCAGA
Found at i:10797803 original size:24 final size:23
Alignment explanation
Indices: 10797776--10797837 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
10797766 GTTTCACATC
*
10797776 AATTTATAAAATATTATTCATTTT
1 AATTTATAAAATATTA-TAATTTT
* * *
10797800 AATTTATTATATTTTATAATTTT
1 AATTTATAAAATATTATAATTTT
* *
10797823 ATTTTAAAAAATATT
1 AATTTATAAAATATT
10797838 TTATAAATTA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AATTTATAAAATATTATAATTTT
Found at i:10799346 original size:1 final size:1
Alignment explanation
Indices: 10799342--10799398 Score: 96
Period size: 1 Copynumber: 57.0 Consensus size: 1
10799332 TACCCCCTCT
* *
10799342 CCCCCCACCCCCCCCCCCCCCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
10799399 TAATGGAGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.02, C:0.96, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:10799367 original size:24 final size:23
Alignment explanation
Indices: 10799334--10799398 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
10799324 GAAAGCCTTA
*
10799334 CCCCCTCTCCCCCCACCCCCCCCC
1 CCCCCCCTCCCCCC-CCCCCCCCC
10799358 CCCCCCCTCCCCCCCCCCCCCCC
1 CCCCCCCTCCCCCCCCCCCCCCC
10799381 CCCCCCC-CCCCCCCCCCC
1 CCCCCCCTCCCCCCCCCCC
10799399 TAATGGAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 11 0.28
23 16 0.40
24 13 0.32
ACGTcount: A:0.02, C:0.94, G:0.00, T:0.05
Consensus pattern (23 bp):
CCCCCCCTCCCCCCCCCCCCCCC
Found at i:10799371 original size:26 final size:25
Alignment explanation
Indices: 10799334--10799398 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
10799324 GAAAGCCTTA
*
10799334 CCCCCTCTCCCCCCACCCCCCCCCCC
1 CCCCCTC-CCCCCCCCCCCCCCCCCC
10799360 CCCCCTCCCCCCCCCCCCCCCCCCC
1 CCCCCTCCCCCCCCCCCCCCCCCCC
10799385 CCCCC-CCCCCCCCC
1 CCCCCTCCCCCCCCC
10799399 TAATGGAGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 9 0.24
25 22 0.58
26 7 0.18
ACGTcount: A:0.02, C:0.94, G:0.00, T:0.05
Consensus pattern (25 bp):
CCCCCTCCCCCCCCCCCCCCCCCCC
Found at i:10809823 original size:3 final size:3
Alignment explanation
Indices: 10809815--10809852 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
10809805 GCGGTGCTGA
10809815 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
10809853 ACGGTGGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:10815324 original size:72 final size:71
Alignment explanation
Indices: 10815142--10815324 Score: 215
Period size: 72 Copynumber: 2.5 Consensus size: 71
10815132 CGAAATAGAC
* *
10815142 AATCGAAACCTCAACCTTTTCAATCAATAATCAAATACCCAAATCAGAAAAGTAGGGAAAAACCC
1 AATCAAAACCTCAA-CTTTTCAATCAATAATCAAA-A-CCAAATCAGAAAAGTAGGCAAAAACCC
* *
10815207 CAAACTGGT
63 CAAACAGAT
* * * *
10815216 AATCAAAACCTCAACTTTAACAATCAATAATTAAAACCAAATCAGAAAAGTA-GCCAAAACCTCA
1 AATCAAAACCTCAACTTT-TCAATCAATAATCAAAACCAAATCAGAAAAGTAGGCAAAAACCCCA
10815280 AACCAGAT
65 AA-CAGAT
* *
10815288 AATCAAAATCTCAACTTTGTCAATCAATAACCAAAAC
1 AATCAAAACCTCAACTTT-TCAATCAATAATCAAAAC
10815325 ACAGTCAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
71 11 0.12
72 51 0.54
73 5 0.05
74 27 0.29
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (71 bp):
AATCAAAACCTCAACTTTTCAATCAATAATCAAAACCAAATCAGAAAAGTAGGCAAAAACCCCAA
ACAGAT
Found at i:10825687 original size:2 final size:2
Alignment explanation
Indices: 10825680--10825707 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10825670 TGTTTGTATC
10825680 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10825708 AAAGCCAAAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10829888 original size:18 final size:18
Alignment explanation
Indices: 10829854--10829887 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10829844 TTTATTTTGA
*
10829854 TATTATTTATTATAAAAT
1 TATTATTTATTAAAAAAT
10829872 TATTATTT-TTAAAAAA
1 TATTATTTATTAAAAAA
10829888 AAATTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATTTATTAAAAAAT
Found at i:10834051 original size:8 final size:8
Alignment explanation
Indices: 10834031--10834059 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
10834021 TATCTGTTGG
10834031 CTATTTG-
1 CTATTTGT
10834038 CTATTTGT
1 CTATTTGT
10834046 CTATTTGT
1 CTATTTGT
10834054 CTATTT
1 CTATTT
10834060 TTGCTTGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (8 bp):
CTATTTGT
Found at i:10834383 original size:103 final size:103
Alignment explanation
Indices: 10834260--10834464 Score: 347
Period size: 103 Copynumber: 2.0 Consensus size: 103
10834250 TGTCTATGTT
* * *
10834260 TTTTCTTATATTCCACTCTGCTAAGATCTTTAAGCCATTTTCTGGTTCACGGAGCTCCCTGAATG
1 TTTTCTTATATCCCACTCTGCTAAGATCTTTAAGCCATTATCTGGTTCACGGAACTCCCTGAATG
10834325 TCTATGTATATGTTACTCTTAAAAGAATGGGATATATG
66 TCTATGTATATGTTACTCTTAAAAGAATGGGATATATG
* *
10834363 TTTTCTTGTATCCCACTCTGCTAAGATCTTTAAGCCATTATCTGGTTCACTGAACTCCCTGAATG
1 TTTTCTTATATCCCACTCTGCTAAGATCTTTAAGCCATTATCTGGTTCACGGAACTCCCTGAATG
* *
10834428 TCTATGTCTATGTTACTCTTTAAAGAATGGGATATAT
66 TCTATGTATATGTTACTCTTAAAAGAATGGGATATAT
10834465 ATTTATTGAT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (103 bp):
TTTTCTTATATCCCACTCTGCTAAGATCTTTAAGCCATTATCTGGTTCACGGAACTCCCTGAATG
TCTATGTATATGTTACTCTTAAAAGAATGGGATATATG
Found at i:10841856 original size:17 final size:18
Alignment explanation
Indices: 10841834--10841868 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10841824 AGAACTGGCT
10841834 ACAAT-AATGATTAAACA
1 ACAATAAATGATTAAACA
10841851 ACAATAAATGATTAAACA
1 ACAATAAATGATTAAACA
10841869 TCCTTCCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (18 bp):
ACAATAAATGATTAAACA
Found at i:10847140 original size:32 final size:32
Alignment explanation
Indices: 10847103--10847177 Score: 150
Period size: 32 Copynumber: 2.3 Consensus size: 32
10847093 GCCGAACATG
10847103 TTGGCCCAAGCCAAATATGGGCTATGGTAACA
1 TTGGCCCAAGCCAAATATGGGCTATGGTAACA
10847135 TTGGCCCAAGCCAAATATGGGCTATGGTAACA
1 TTGGCCCAAGCCAAATATGGGCTATGGTAACA
10847167 TTGGCCCAAGC
1 TTGGCCCAAGC
10847178 AATATTGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.21
Consensus pattern (32 bp):
TTGGCCCAAGCCAAATATGGGCTATGGTAACA
Found at i:10848897 original size:25 final size:25
Alignment explanation
Indices: 10848861--10848918 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
10848851 TTTTATTTTT
* * *
10848861 TAAT-TTTGATTTTTTATTAAAATA
1 TAATATTTAATTTATTAGTAAAATA
*
10848885 TAATATTTAATTTATTAGTAATATA
1 TAATATTTAATTTATTAGTAAAATA
*
10848910 TAAAATTTA
1 TAATATTTA
10848919 TACACCGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (25 bp):
TAATATTTAATTTATTAGTAAAATA
Found at i:10849346 original size:19 final size:19
Alignment explanation
Indices: 10849319--10849394 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 19
10849309 ACTCGTGGGA
*
10849319 GCCGGAGGGGGCGGGCAGG
1 GCCGCAGGGGGCGGGCAGG
*
10849338 GCCGCAGGGGGGACCGGACTCATGGG
1 GCCGCA-GGGGG--CGG--GCA--GG
*
10849364 AGCCGGAGGGGGCGGGCAGG
1 -GCCGCAGGGGGCGGGCAGG
10849384 GCCGCAGGGGG
1 GCCGCAGGGGG
10849395 GAATCGGGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 16
0.68 0.08 0.25
Matches are distributed among these distances:
19 15 0.34
20 7 0.16
22 5 0.11
24 5 0.11
26 7 0.16
27 5 0.11
ACGTcount: A:0.13, C:0.24, G:0.61, T:0.03
Consensus pattern (19 bp):
GCCGCAGGGGGCGGGCAGG
Found at i:10849429 original size:94 final size:96
Alignment explanation
Indices: 10849265--10849438 Score: 241
Period size: 94 Copynumber: 1.8 Consensus size: 96
10849255 AAAGACTCGT
*
10849265 GGAGCCGGAGGAGGGGGGGCATGGGCCGCAAGGGGGAACGCGGGACTCGTGGGAGCCGGAGGGGG
1 GGAGCCGGAGGAGGGCGGGCATGGGCCGCAAGGGGGAACGCGGGACTCGTGGGAGCCGGAGGGGG
10849330 CGGGCAGGGCCGCAGGGGGGACCGGACTCATG
66 CGGGCAGGG-CGCAGGGGGGACCGGACTCATG
* * *
10849362 GGAGCCGGAGG-GGGCGGGCA-GGGCCGCAGGGGGGAA-TCGGGACTCGTGGGA-CTGTG-GGAG
1 GGAGCCGGAGGAGGGCGGGCATGGGCCGCAAGGGGGAACGCGGGACTCGTGGGAGCCG-GAGG-G
*
10849422 GGGGGGCAGGGCGCAGG
64 GGCGGGCAGGGCGCAGG
10849439 CACTCCCAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
93 10 0.14
94 26 0.37
95 15 0.21
96 8 0.11
97 11 0.16
ACGTcount: A:0.16, C:0.20, G:0.59, T:0.06
Consensus pattern (96 bp):
GGAGCCGGAGGAGGGCGGGCATGGGCCGCAAGGGGGAACGCGGGACTCGTGGGAGCCGGAGGGGG
CGGGCAGGGCGCAGGGGGGACCGGACTCATG
Found at i:10849433 original size:48 final size:47
Alignment explanation
Indices: 10849258--10849412 Score: 215
Period size: 46 Copynumber: 3.2 Consensus size: 47
10849248 TCATCCAAAA
* *
10849258 GACTCGT-GGAGCCGGAGGAGGGGGGGCATGGGCCGCAAGGGGGAACGCGG
1 GACTCGTGGGAGCCGGAGG-GGGCGGGCA-GGGCCGCAGGGGGGAA--CGG
*
10849308 GACTCGTGGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGG-ACCG
1 GACTCGTGGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGGAACGG
*
10849354 GACTCATGGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGGAATCGG
1 GACTCGTGGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGGAA-CGG
10849402 GACTCGTGGGA
1 GACTCGTGGGA
10849413 CTGTGGGAGG
Statistics
Matches: 96, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
46 43 0.45
47 1 0.01
48 13 0.14
49 13 0.14
50 15 0.16
51 11 0.11
ACGTcount: A:0.16, C:0.21, G:0.56, T:0.06
Consensus pattern (47 bp):
GACTCGTGGGAGCCGGAGGGGGCGGGCAGGGCCGCAGGGGGGAACGG
Found at i:10860017 original size:27 final size:27
Alignment explanation
Indices: 10859973--10860027 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
10859963 AAAGCCGGTG
*
10859973 CAGCAGCAGCCACCCCAGCGTTAAACC
1 CAGCAGCAGCAACCCCAGCGTTAAACC
* * *
10860000 CAGCAGCAGCAACTCCAGGGTTGAACC
1 CAGCAGCAGCAACCCCAGCGTTAAACC
10860027 C
1 C
10860028 CACTGCAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.40, G:0.22, T:0.09
Consensus pattern (27 bp):
CAGCAGCAGCAACCCCAGCGTTAAACC
Found at i:10860971 original size:15 final size:15
Alignment explanation
Indices: 10860951--10860993 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10860941 TGGTTTTCAG
10860951 CTTCTTCGTCATCGT
1 CTTCTTCGTCATCGT
*
10860966 CTTCTTCGTTC-TCTT
1 CTTCTTCG-TCATCGT
*
10860981 CTTCTTCCTCATC
1 CTTCTTCGTCATC
10860994 CTCCTCTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.05, C:0.37, G:0.07, T:0.51
Consensus pattern (15 bp):
CTTCTTCGTCATCGT
Found at i:10861002 original size:21 final size:21
Alignment explanation
Indices: 10860976--10861029 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
10860966 CTTCTTCGTT
*
10860976 CTCTTCTTCTTCCTCATCCTC
1 CTCTTCTTCTTCCTCAACCTC
* * *
10860997 CTCTTCCTCTTCTTCAACTTC
1 CTCTTCTTCTTCCTCAACCTC
*
10861018 CTCTTCTACTTC
1 CTCTTCTTCTTC
10861030 TTCTTCTACT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.07, C:0.44, G:0.00, T:0.48
Consensus pattern (21 bp):
CTCTTCTTCTTCCTCAACCTC
Found at i:10861028 original size:12 final size:12
Alignment explanation
Indices: 10861007--10861053 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
10860997 CTCTTCCTCT
10861007 TCTTCAACTTCC
1 TCTTCAACTTCC
* *
10861019 TCTTCTACTTCT
1 TCTTCAACTTCC
*
10861031 TCTTCTACTTCC
1 TCTTCAACTTCC
10861043 TCTTCAACTTC
1 TCTTCAACTTC
10861054 TTGTAGCTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.13, C:0.38, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTTCAACTTCC
Found at i:10861045 original size:24 final size:24
Alignment explanation
Indices: 10860974--10861055 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
10860964 GTCTTCTTCG
*
10860974 TTCT-CTTCTTCTTCCT-CATCCTC
1 TTCTACTTCTTCTT-CTACTTCCTC
* * * *
10860997 CTCTTCCTCTTCTTCAACTTCCTC
1 TTCTACTTCTTCTTCTACTTCCTC
10861021 TTCTACTTCTTCTTCTACTTCCTC
1 TTCTACTTCTTCTTCTACTTCCTC
*
10861045 TTCAACTTCTT
1 TTCTACTTCTT
10861056 GTAGCTGCTG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 4 0.08
24 44 0.92
ACGTcount: A:0.09, C:0.40, G:0.00, T:0.51
Consensus pattern (24 bp):
TTCTACTTCTTCTTCTACTTCCTC
Found at i:10861432 original size:19 final size:20
Alignment explanation
Indices: 10861410--10861447 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10861400 TTTAAGCCCG
10861410 TTTT-AAATATTTATTTTTC
1 TTTTGAAATATTTATTTTTC
* *
10861429 TTTTGAATTATTTCTTTTT
1 TTTTGAAATATTTATTTTT
10861448 TGAATGGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTGAAATATTTATTTTTC
Found at i:10861441 original size:16 final size:16
Alignment explanation
Indices: 10861420--10861452 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10861410 TTTTAAATAT
10861420 TTATTT-TTCTTTTGAA
1 TTATTTCTT-TTTTGAA
10861436 TTATTTCTTTTTTGAA
1 TTATTTCTTTTTTGAA
10861452 T
1 T
10861453 GGGTCACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (16 bp):
TTATTTCTTTTTTGAA
Found at i:10874323 original size:11 final size:10
Alignment explanation
Indices: 10874297--10874330 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
10874287 AGCATATCTC
10874297 ATTTTTTAAA
1 ATTTTTTAAA
10874307 A-TTTTTAAA
1 ATTTTTTAAA
10874316 ATTATTTTAAA
1 ATT-TTTTAAA
10874327 ATTT
1 ATTT
10874331 GAAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.41
10 3 0.14
11 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:10876483 original size:22 final size:24
Alignment explanation
Indices: 10876458--10876501 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
10876448 ATATATCAAA
10876458 ATATTAAT-T-ATAAAAATAATAT
1 ATATTAATATAATAAAAATAATAT
10876480 ATATTAATATAATAAAAATAAT
1 ATATTAATATAATAAAAATAAT
10876502 TACACAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATTAATATAATAAAAATAATAT
Found at i:10876503 original size:18 final size:18
Alignment explanation
Indices: 10876443--10876503 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
10876433 TAATTATTTT
*
10876443 TTAATATATATCAAAAT-A
1 TTAATATA-ATAAAAATAA
*
10876461 TTAATTATAAAAATAATATATA
1 TTAA-TATAATAA-AA-ATA-A
10876483 TTAATATAATAAAAATAA
1 TTAATATAATAAAAATAA
10876501 TTA
1 TTA
10876504 CACAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 10 0.29
19 9 0.26
20 4 0.11
21 7 0.20
22 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATATAATAAAAATAA
Found at i:10876515 original size:21 final size:23
Alignment explanation
Indices: 10876463--10876516 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
10876453 TCAAAATATT
* *
10876463 AATTATAAAAATAATATATATTA
1 AATTATAAAAATAATATACATCA
*
10876486 ATATAATAAAAATAAT-TACA-CA
1 A-ATTATAAAAATAATATACATCA
10876508 AATTATAAA
1 AATTATAAA
10876517 CTAAATTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.27
22 2 0.08
23 4 0.15
24 13 0.50
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AATTATAAAAATAATATACATCA
Found at i:10883160 original size:21 final size:21
Alignment explanation
Indices: 10883122--10883175 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
10883112 TTTAGGAATT
* *
10883122 TATATTT-TTAATTCAAAAAA
1 TATATTTATTAAATAAAAAAA
10883142 TATATTTATTAAATAAAAAAA
1 TATATTTATTAAATAAAAAAA
10883163 -ATTATTTA-TAAAT
1 TA-TATTTATTAAAT
10883176 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATTTATTAAATAAAAAAA
Found at i:10883181 original size:20 final size:22
Alignment explanation
Indices: 10883122--10883181 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
10883112 TTTAGGAATT
*
10883122 TATATTT-TT-AATTCAAAAAA
1 TATATTTATTAAATTAAAAAAA
*
10883142 TATATTTATTAAATAAAAAAAA
1 TATATTTATTAAATTAAAAAAA
*
10883164 T-TATTTA-TAAATTTAAAA
1 TATATTTATTAAATTAAAAA
10883182 TTTATCTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 16 0.47
21 8 0.24
22 10 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATTTATTAAATTAAAAAAA
Found at i:10883181 original size:21 final size:22
Alignment explanation
Indices: 10883136--10883175 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10883126 TTTTTAATTC
10883136 AAAAAATATATTTATTAAATAA
1 AAAAAATATATTTATTAAATAA
10883158 AAAAAAT-TATTTA-TAAAT
1 AAAAAATATATTTATTAAAT
10883176 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAAATATATTTATTAAATAA
Found at i:10894565 original size:21 final size:21
Alignment explanation
Indices: 10894535--10894584 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
10894525 AACATAAATA
*
10894535 TCAT-AATTCATAGATGCAAG
1 TCATAAATTCATAGACGCAAG
10894555 TCATAAATTCATAGACGCAAG
1 TCATAAATTCATAGACGCAAG
10894576 TCATAAATT
1 TCATAAATT
10894585 ATCGATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (21 bp):
TCATAAATTCATAGACGCAAG
Found at i:10909065 original size:23 final size:21
Alignment explanation
Indices: 10909038--10909081 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
10909028 AATTTTAAAA
10909038 TATCTAAAAATATTTAAAATTTT
1 TATCTAAAAAT-TTT-AAATTTT
**
10909061 TATCTTTAAATTTTAAATTTT
1 TATCTAAAAATTTTAAATTTT
10909082 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATCTAAAAATTTTAAATTTT
Found at i:10919191 original size:2 final size:2
Alignment explanation
Indices: 10919178--10919221 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
10919168 TGATTCATGA
*
10919178 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10919220 AT
1 AT
10919222 GAAAGAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10923821 original size:4 final size:4
Alignment explanation
Indices: 10923812--10923837 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
10923802 TTCTTTTTAT
10923812 GGAG GGAG GGAG GGAG GGAG GGAG GG
1 GGAG GGAG GGAG GGAG GGAG GGAG GG
10923838 GGGTCCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:10931095 original size:25 final size:26
Alignment explanation
Indices: 10931046--10931096 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
10931036 CTCTATATAA
**
10931046 ATAATTAAGGGTTTTTTTTCTCACTT
1 ATAATTAAGGGTTTTGCTTCTCACTT
*
10931072 ATAATTATGGGTTTTGCTTC-CACTT
1 ATAATTAAGGGTTTTGCTTCTCACTT
10931097 GATGATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (26 bp):
ATAATTAAGGGTTTTGCTTCTCACTT
Found at i:10962323 original size:20 final size:21
Alignment explanation
Indices: 10962288--10962326 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10962278 AAACAAAATC
10962288 AGTGGTTAAATAAATTAATTA
1 AGTGGTTAAATAAATTAATTA
*
10962309 AGTGG-TAATTAAATTAAT
1 AGTGGTTAAATAAATTAAT
10962327 AAAAACTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (21 bp):
AGTGGTTAAATAAATTAATTA
Found at i:10962509 original size:6 final size:6
Alignment explanation
Indices: 10962473--10962508 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
10962463 AAAGGCAAAG
* *
10962473 CCTCTC CCTCTC CCTCTC CGTCTC CCTCTC TCTCTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
10962509 TATCTCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.61, G:0.03, T:0.36
Consensus pattern (6 bp):
CCTCTC
Found at i:10962514 original size:18 final size:18
Alignment explanation
Indices: 10962475--10962514 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10962465 AGGCAAAGCC
*
10962475 TCTCCCTCTCCCTCTCCG
1 TCTCCCTCTCCCTCTCCA
* *
10962493 TCTCCCTCTCTCTCTCTA
1 TCTCCCTCTCCCTCTCCA
10962511 TCTC
1 TCTC
10962515 TTTCCCTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.55, G:0.03, T:0.40
Consensus pattern (18 bp):
TCTCCCTCTCCCTCTCCA
Found at i:10965867 original size:27 final size:26
Alignment explanation
Indices: 10965810--10965902 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 26
10965800 GTCCAGCACC
10965810 ATCTGCAGTATCCTCTCAGCCACCAGC-
1 ATCTGCAGT-TCCTCTCAGCCACCA-CA
* *
10965837 ATCTGCAGTTCCTACGCAGCCAGCACA
1 ATCTGCAGTTCCT-CTCAGCCACCACA
***
10965864 ATCTGTTCTTCCTGCTCAGCCACCACA
1 ATCTGCAGTTCCT-CTCAGCCACCACA
*
10965891 ATCTGCCGTTCC
1 ATCTGCAGTTCC
10965903 CCCTCAGCAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.09
27 48 0.91
ACGTcount: A:0.20, C:0.40, G:0.15, T:0.25
Consensus pattern (26 bp):
ATCTGCAGTTCCTCTCAGCCACCACA
Found at i:10983308 original size:18 final size:19
Alignment explanation
Indices: 10983261--10983311 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
10983251 ATGGATATTT
10983261 TTATTATTAAATTAAATAAAA
1 TTATTATT-AATT-AATAAAA
*
10983282 TT-TTA-TAATTAAT-TAA
1 TTATTATTAATTAATAAAA
10983298 TTATTATTAATTAA
1 TTATTATTAATTAA
10983312 AACACTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
18 11 0.41
19 1 0.04
20 3 0.11
21 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTATTAATTAATAAAA
Found at i:10990875 original size:18 final size:20
Alignment explanation
Indices: 10990845--10990902 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
10990835 TCAATTTTTT
10990845 TAAAAAATAATTAAAATTGA
1 TAAAAAATAATTAAAATTGA
*
10990865 T-AAAAAT-ATTATAAAAT-A
1 TAAAAAATAATTA-AAATTGA
10990883 TAAAAAATAATTAAAATTGA
1 TAAAAAATAATTAAAATTGA
10990903 CTTATGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 20 0.62
20 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAAAAATAATTAAAATTGA
Found at i:10997039 original size:29 final size:29
Alignment explanation
Indices: 10996997--10997056 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
10996987 CTGAAATTGC
10996997 ATGTTAGATCTATATCTTGCATTAGGGCA
1 ATGTTAGATCTATATCTTGCATTAGGGCA
10997026 ATGTTAGATCTATATCTTGCATTAGGGCA
1 ATGTTAGATCTATATCTTGCATTAGGGCA
10997055 AT
1 AT
10997057 TTTACTGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (29 bp):
ATGTTAGATCTATATCTTGCATTAGGGCA
Found at i:11011635 original size:11 final size:12
Alignment explanation
Indices: 11011608--11011633 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11011598 TAAAAAGGTT
11011608 TTTATTTTTTGA
1 TTTATTTTTTGA
11011620 TTTATTTTTTGA
1 TTTATTTTTTGA
11011632 TT
1 TT
11011634 ATGGCGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTATTTTTTGA
Done.