Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold393
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: 702984
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 4 of 6
Found at i:408784 original size:17 final size:18
Alignment explanation
Indices: 408476--408784 Score: 80
Period size: 17 Copynumber: 16.8 Consensus size: 18
408466 TATTAAATAT
*
408476 TATTATTAGAATATTTAATA
1 TATTATTA-AATA-TTATTA
408496 TATTATTAAATATTATTA
1 TATTATTAAATATTATTA
* *
408514 GA-TATTTACTATATTATTTA
1 TATTA-TTA-AATATTA-TTA
* * * *
408534 GAGTATTTTAATA--A-AA
1 TATTA-TTAAATATTATTA
* *
408550 TATTATCAAATA-TAAT-
1 TATTATTAAATATTATTA
408566 TATTATTAAATATTA-TA
1 TATTATTAAATATTATTA
* *
408583 -AATATATAAATTTTATTA
1 TATTAT-TAAATATTATTA
*
408601 TATTATTAAAATATTATAAA
1 TATTATT-AAATATTAT-TA
408621 GTAATT-TTAATATATTATTAA
1 -T-ATTATTAA-ATATTATT-A
*
408642 TAATCTTATCAAAATATTAATT-
1 T-A--TTAT-TAAATATT-ATTA
*
408664 TATTATT-AATATTTTTACA
1 TATTATTAAATATTATT--A
**
408683 TATGTTATTTGATATT-TTA
1 TA--TTATTAAATATTATTA
408702 -A-TATTAACAT-TTA-TA
1 TATTATTAA-ATATTATTA
* * *
408717 TATT-TTACATCTTTTTTA
1 TATTATTAAAT-ATTATTA
408735 TATTATTAAATATT-TTA
1 TATTATTAAATATTATTA
*
408752 TATTTTTAATATATTATTA
1 TATTATTAA-ATATTATTA
408771 T-TTATTAAATATTA
1 TATTATTAAATATTA
408785 ATAAAATATT
Statistics
Matches: 221, Mismatches: 30, Indels: 79
0.67 0.09 0.24
Matches are distributed among these distances:
15 15 0.07
16 29 0.13
17 38 0.17
18 33 0.15
19 38 0.17
20 22 0.10
21 24 0.11
22 11 0.05
23 6 0.03
24 5 0.02
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (18 bp):
TATTATTAAATATTATTA
Found at i:408819 original size:25 final size:24
Alignment explanation
Indices: 408730--408821 Score: 68
Period size: 25 Copynumber: 3.8 Consensus size: 24
408720 TTTACATCTT
*
408730 TTTTATATTATTAAATATT-TTATAT
1 TTTTATA-TATTAAATATTATTA-AA
*
408755 TTTTAATATATT-ATTATTTATTAAA
1 TTTT-ATATATTAAATA-TTATTAAA
*
408780 TATTA-ATA--AAATATTATTAAA
1 TTTTATATATTAAATATTATTAAA
*
408801 TTTTATATGATTAATTATTAT
1 TTTTATAT-ATTAAATATTAT
408822 CATATGAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
21 12 0.23
22 5 0.09
23 4 0.08
24 4 0.08
25 22 0.42
26 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TTTTATATATTAAATATTATTAAA
Found at i:408980 original size:14 final size:15
Alignment explanation
Indices: 408961--408992 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
408951 TTTAAATAGA
408961 TTTTAAA-ATATTAT
1 TTTTAAATATATTAT
408975 TTTTAAATATATTAT
1 TTTTAAATATATTAT
408990 TTT
1 TTT
408993 AATGTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAATATATTAT
Found at i:408993 original size:14 final size:13
Alignment explanation
Indices: 408960--408994 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
408950 ATTTAAATAG
408960 ATTTTAAAATATT
1 ATTTTAAAATATT
408973 ATTTTTAAATATATT
1 A-TTTTAAA-ATATT
408988 ATTTTAA
1 ATTTTAA
408995 TGTTATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 13 0.65
15 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTTAAAATATT
Found at i:411235 original size:19 final size:19
Alignment explanation
Indices: 411211--411254 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
411201 TCGATTAGTT
*
411211 AATTACGTAAGCCATGGTG
1 AATTACGTAAGCCAAGGTG
* *
411230 AATTACTTAAGCCAAGGTT
1 AATTACGTAAGCCAAGGTG
411249 AATTAC
1 AATTAC
411255 ACCCTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
AATTACGTAAGCCAAGGTG
Found at i:411926 original size:13 final size:13
Alignment explanation
Indices: 411908--411936 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
411898 TTTGATTGTA
411908 TTATGTTAATAAG
1 TTATGTTAATAAG
411921 TTATGTTAATAAG
1 TTATGTTAATAAG
411934 TTA
1 TTA
411937 CATTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
TTATGTTAATAAG
Found at i:411946 original size:22 final size:22
Alignment explanation
Indices: 411921--411969 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
411911 TGTTAATAAG
411921 TTATGTTAATAAGTTACATTTA
1 TTATGTTAATAAGTTACATTTA
*
411943 TTATGTTAATAAGTTACGTTTA
1 TTATGTTAATAAGTTACATTTA
411965 TTATG
1 TTATG
411970 ATTACAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (22 bp):
TTATGTTAATAAGTTACATTTA
Found at i:412663 original size:70 final size:70
Alignment explanation
Indices: 412583--412727 Score: 272
Period size: 70 Copynumber: 2.1 Consensus size: 70
412573 GCTTATTAAC
* *
412583 AGAAAAGATTGAAGAGTGCTGCACTGACCAAGTCCTTCAGTGACCAATAGCATAATGAAAATCTT
1 AGAAAAGATTGAAGAGTGCTGCACTGACCAAGTCCTTCAGTGAACAACAGCATAATGAAAATCTT
412648 ATCCA
66 ATCCA
412653 AGAAAAGATTGAAGAGTGCTGCACTGACCAAGTCCTTCAGTGAACAACAGCATAATGAAAATCTT
1 AGAAAAGATTGAAGAGTGCTGCACTGACCAAGTCCTTCAGTGAACAACAGCATAATGAAAATCTT
412718 ATCCA
66 ATCCA
412723 AGAAA
1 AGAAA
412728 CTAGCATAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (70 bp):
AGAAAAGATTGAAGAGTGCTGCACTGACCAAGTCCTTCAGTGAACAACAGCATAATGAAAATCTT
ATCCA
Found at i:414670 original size:5 final size:5
Alignment explanation
Indices: 414652--414724 Score: 82
Period size: 5 Copynumber: 15.0 Consensus size: 5
414642 ACATAAATAT
* *
414652 TATTA TATT- T-TTA TATTA TATTA TATTA TATT- TTTTA TTTTA -ATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
414698 TTATTA TATTA TATTTA TATTA TATTA
1 -TATTA TATTA TA-TTA TATTA TATTA
414725 ATTTAAATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
3 2 0.03
4 8 0.13
5 41 0.68
6 9 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:414700 original size:31 final size:29
Alignment explanation
Indices: 414660--414727 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
414650 ATTATTATAT
414660 TTTTATATTA-TATTATATTATATTTTTTA
1 TTTTA-ATTATTATTATATTATATTTTTTA
414689 TTTTAATTATTATTATATTATATTTATATTA
1 TTTTAATTATTATTATATTATATTT-T-TTA
*
414720 TATTAATT
1 TTTTAATT
414728 TAAATATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 4 0.11
29 20 0.57
30 1 0.03
31 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTAATTATTATTATATTATATTTTTTA
Found at i:414702 original size:24 final size:25
Alignment explanation
Indices: 414649--414724 Score: 104
Period size: 24 Copynumber: 3.1 Consensus size: 25
414639 GTTACATAAA
414649 TATTATTATA-TTTTTATATTATAT
1 TATTATTATATTTTTTATATTATAT
*
414673 TA-TATTATATTTTTTATTTTA-AT
1 TATTATTATATTTTTTATATTATAT
414696 TATTATTATATTATATTTATATTATAT
1 TATTATTATATT-T-TTTATATTATAT
414723 TA
1 TA
414725 ATTTAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.24
24 21 0.47
25 1 0.02
26 8 0.18
27 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TATTATTATATTTTTTATATTATAT
Found at i:415032 original size:23 final size:22
Alignment explanation
Indices: 415006--415052 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
414996 AATTTAATAA
415006 AATAAAAAATAAAAATATTATTT
1 AATAAAAAATAAAAATATT-TTT
* **
415029 AATATAAAATTTAAATATTTTT
1 AATAAAAAATAAAAATATTTTT
415051 AA
1 AA
415053 CTAATTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAAAAAATAAAAATATTTTT
Found at i:415846 original size:15 final size:15
Alignment explanation
Indices: 415826--415874 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
415816 CAAAAAGTTA
415826 AAAAATTTAAACTCG
1 AAAAATTTAAACTCG
*
415841 AAAAATTTAAATTCG
1 AAAAATTTAAACTCG
* *
415856 AAATAGTCTAAACTCG
1 AAA-AATTTAAACTCG
415872 AAA
1 AAA
415875 TAACTCGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (15 bp):
AAAAATTTAAACTCG
Found at i:415872 original size:16 final size:16
Alignment explanation
Indices: 415833--415890 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
415823 TTAAAAAATT
*
415833 TAAACTCGAAA-AATT
1 TAAACTCGAAATAATC
* *
415848 TAAATTCGAAATAGTC
1 TAAACTCGAAATAATC
415864 TAAACTCGAAATAA-C
1 TAAACTCGAAATAATC
*
415879 TCGAACTCGAAA
1 T-AAACTCGAAA
415891 GAACTTAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 12 0.34
16 23 0.66
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.24
Consensus pattern (16 bp):
TAAACTCGAAATAATC
Found at i:416156 original size:36 final size:36
Alignment explanation
Indices: 416090--416161 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
416080 AATAAAATAC
* * *
416090 TAAAAACTTAATTTATATTATGAAATAGTAATTTAT
1 TAAAAACTAAATTTATATTATGAAAAAGTAAATTAT
* *
416126 TAAAAAGTAAATTATATCTTAT-AAAAAGTAAATTAT
1 TAAAAACTAAATT-TATATTATGAAAAAGTAAATTAT
416162 ATGATGAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 23 0.77
37 7 0.23
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (36 bp):
TAAAAACTAAATTTATATTATGAAAAAGTAAATTAT
Found at i:416976 original size:2 final size:2
Alignment explanation
Indices: 416969--417017 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
416959 CTTTATCTAA
416969 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
417011 AT AT AT A
1 AT AT AT A
417018 ACTCTGATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:419242 original size:43 final size:42
Alignment explanation
Indices: 419181--419322 Score: 230
Period size: 43 Copynumber: 3.3 Consensus size: 42
419171 TGAACAAATG
*
419181 TATCGATGCATGAAACTGGCAGTAGCTATCCTACCACTATTTA
1 TATCGATACATGAAACTGGCAGTAGCTA-CCTACCACTATTTA
*
419224 TATCGATACATGAAACTGGTAGTAGCTACTCTACCACTATTTA
1 TATCGATACATGAAACTGGCAGTAGCTAC-CTACCACTATTTA
*
419267 TATTGATACATGAAACTGGCAGTAGCTACCCTACCACTATTTA
1 TATCGATACATGAAACTGGCAGTAGCTA-CCTACCACTATTTA
419310 TATCGATACATGA
1 TATCGATACATGA
419323 CACAATGTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
42 1 0.01
43 90 0.98
44 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (42 bp):
TATCGATACATGAAACTGGCAGTAGCTACCTACCACTATTTA
Found at i:419342 original size:13 final size:13
Alignment explanation
Indices: 419324--419350 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
419314 GATACATGAC
419324 ACAATGTATCGAT
1 ACAATGTATCGAT
419337 ACAATGTATCGAT
1 ACAATGTATCGAT
419350 A
1 A
419351 TATGAAGAAT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:419365 original size:33 final size:33
Alignment explanation
Indices: 419310--419372 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
419300 CCACTATTTA
419310 TATCGATACATGACACAATGTATCGATACAATG
1 TATCGATACATGACACAATGTATCGATACAATG
* *
419343 TATCGATATATGA-AGAATTGTATCGATACA
1 TATCGATACATGACACAA-TGTATCGATACA
419373 TTGCCTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (33 bp):
TATCGATACATGACACAATGTATCGATACAATG
Found at i:420135 original size:13 final size:13
Alignment explanation
Indices: 420117--420142 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
420107 TACACCAAGT
420117 ATGTATCGATACA
1 ATGTATCGATACA
420130 ATGTATCGATACA
1 ATGTATCGATACA
420143 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:420140 original size:32 final size:33
Alignment explanation
Indices: 420099--420162 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
420089 TAGCCAAACT
* **
420099 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
420131 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
420163 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:424123 original size:13 final size:13
Alignment explanation
Indices: 424105--424142 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
424095 CATTTTTCTT
424105 TGTATCGATACAA
1 TGTATCGATACAA
*
424118 TGTATCGATACAC
1 TGTATCGATACAA
424131 TGTATCGATACA
1 TGTATCGATACA
424143 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:426697 original size:32 final size:33
Alignment explanation
Indices: 426659--426722 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
426649 TAGCCAAACT
* **
426659 TGTATCAATACACCAAGTA-TGTATCGATACAA
1 TGTATCAATACACAAAAAATTGTATCGATACAA
426691 TGTATCAATACACAAAAAATTGTATCGATACA
1 TGTATCAATACACAAAAAATTGTATCGATACA
426723 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACAAAAAATTGTATCGATACAA
Found at i:431003 original size:19 final size:20
Alignment explanation
Indices: 430958--431009 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
430948 TTATAAGCCA
*
430958 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
430978 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
430998 -TGTATCGATACA
1 ATGTATCGATACA
431010 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:431098 original size:20 final size:21
Alignment explanation
Indices: 431051--431103 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
431041 GCCAATGACC
**
431051 TGTATCGATACATTTTTTACA
1 TGTATCGATACATTTGGTACA
*
431072 AGTATCGATACATTTGGT-CA
1 TGTATCGATACATTTGGTACA
431092 TGTATCGATACA
1 TGTATCGATACA
431104 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTGGTACA
Found at i:431109 original size:13 final size:13
Alignment explanation
Indices: 431091--431121 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
431081 ACATTTGGTC
431091 ATGTATCGATACA
1 ATGTATCGATACA
*
431104 ATGTATCGATACT
1 ATGTATCGATACA
431117 ATGTA
1 ATGTA
431122 ATCTGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:432324 original size:28 final size:27
Alignment explanation
Indices: 432290--432359 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
432280 AATAAAGTCG
** *
432290 GGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGTTGGAGTATCCCCGAGGAAATAAC
*
432317 GGGATTGGAGTATCCCCGATGAAATAAC
1 GGG-TTGGAGTATCCCCGAGGAAATAAC
432345 GAGGTTGGAGTATCC
1 G-GGTTGGAGTATCC
432360 TCGATTATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.08
28 32 0.86
29 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:432345 original size:107 final size:107
Alignment explanation
Indices: 432209--432413 Score: 288
Period size: 107 Copynumber: 1.9 Consensus size: 107
432199 AAAAAAAAAT
*
432209 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
1 CGGGATTGGAGTATCCC-TCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
* * *
432273 TTTTGGGAATAAAGTCGGGGTTGGAGTATCCCCTCGGAAGTAA
65 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAGTAA
* * ***
432316 CGGGATTGGAGTATCCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTATGAGAAATTGGTA
1 CGGGATTGGAGTATCCCTCGA--AAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATA
432380 TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
64 TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
432414 GATTAAAGGA
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
105 3 0.03
107 53 0.62
108 30 0.35
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (107 bp):
CGGGATTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATATT
TTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAGTAA
Found at i:432417 original size:52 final size:52
Alignment explanation
Indices: 432348--432517 Score: 161
Period size: 52 Copynumber: 3.3 Consensus size: 52
432338 AAATAACGAG
* *
432348 GTTGGAGTATCCTCGATTATGAGAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAGAAATTGGTATTTTTGGAAATAAAACCGGA
* ** *
432400 GTTGGAGTATCCCCGATTA-AAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTATGA-G-AAATTGGTATTTTTGGAAATAAAACC-GGA
* * * * *
432453 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAGAAATTGGTATTTTTG-GAAATAAAACCGGA
432504 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
432518 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
51 4 0.04
52 77 0.80
53 14 0.15
54 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAGAAATTGGTATTTTTGGAAATAAAACCGGA
Found at i:432563 original size:27 final size:27
Alignment explanation
Indices: 432525--432602 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
432515 CCCTCAGAAA
432525 TAACGGGGTTGGAGTATCCCCGATGAT
1 TAACGGGGTTGGAGTATCCCCGATGAT
*
432552 TAACAGGGTTGGAGTATCCCCGATGAT
1 TAACGGGGTTGGAGTATCCCCGATGAT
432579 TAACGGGGTTGGAGTATCCCCGAT
1 TAACGGGGTTGGAGTATCCCCGAT
432603 TGTGAAGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (27 bp):
TAACGGGGTTGGAGTATCCCCGATGAT
Found at i:432686 original size:51 final size:53
Alignment explanation
Indices: 432590--432692 Score: 140
Period size: 51 Copynumber: 2.0 Consensus size: 53
432580 AACGGGGTTG
* * *
432590 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
432644 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGT
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGT
432693 CGAAATATCC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 20 0.44
52 2 0.04
53 8 0.18
54 15 0.33
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:435092 original size:13 final size:13
Alignment explanation
Indices: 435074--435099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
435064 ACAAAGATCC
435074 ATGTATCGATACA
1 ATGTATCGATACA
435087 ATGTATCGATACA
1 ATGTATCGATACA
435100 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:435111 original size:33 final size:33
Alignment explanation
Indices: 435053--435119 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
435043 AAAATTTCCA
*** *
435053 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
*
435086 AATGTATCGATACACAGAAAAATGTATCAATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
435119 A
1 A
435120 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCAATAC
Found at i:435163 original size:19 final size:18
Alignment explanation
Indices: 435139--435206 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
435129 CAGTAGCTAA
435139 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
435158 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
435173 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
435190 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
435207 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:435179 original size:13 final size:13
Alignment explanation
Indices: 435161--435185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
435151 ACAATACTTA
435161 TGTATCGATACAT
1 TGTATCGATACAT
435174 TGTATCGATACA
1 TGTATCGATACA
435186 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:435181 original size:32 final size:32
Alignment explanation
Indices: 435142--435204 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
435132 TAGCTAATTA
*
435142 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
435174 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
435205 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:435268 original size:21 final size:21
Alignment explanation
Indices: 435242--435319 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
435232 GTTGGGACCC
435242 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
435263 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
435283 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
435304 TGTATCGATACATTTG
1 TGTATCGATACATTTG
435320 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:435306 original size:41 final size:40
Alignment explanation
Indices: 435242--435323 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
435232 GTTGGGACCC
* *
435242 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
435283 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
435323 T
1 T
435324 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:436157 original size:55 final size:55
Alignment explanation
Indices: 436062--436856 Score: 1072
Period size: 55 Copynumber: 14.3 Consensus size: 55
436052 ATAAAGTGTA
* * * * * * *
436062 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
436117 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
436172 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTGAAA-ATAAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGT-----G
** * *
436231 CATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 --TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
436288 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
436343 TCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
436398 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
436453 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTAGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
436509 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
436564 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGAGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
436619 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
436674 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
436729 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
436784 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
436839 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
436857 AAAAAGCGGA
Statistics
Matches: 667, Mismatches: 49, Indels: 48
0.87 0.06 0.06
Matches are distributed among these distances:
54 20 0.03
55 533 0.80
56 65 0.10
57 2 0.00
59 1 0.00
61 45 0.07
62 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:436196 original size:26 final size:26
Alignment explanation
Indices: 436108--436197 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
436098 GTGTGGGCTT
* *
436108 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
436134 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
436161 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
436189 TGAAAGGTG
1 TGAAAGGTG
436198 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:437878 original size:13 final size:14
Alignment explanation
Indices: 437862--437894 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
437852 TGTTTTTTTG
437862 TTTTTTTT-CCTTT
1 TTTTTTTTGCCTTT
437875 TTTTTTTTGCCTTT
1 TTTTTTTTGCCTTT
437889 TTTTTT
1 TTTTTT
437895 GAAGAGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTTTTTTGCCTTT
Found at i:437890 original size:15 final size:15
Alignment explanation
Indices: 437856--437894 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
437846 TTGTTTTGTT
*
437856 TTTTTGTTTTTTTTCC
1 TTTTT-TTTTTTTGCC
437872 -TTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
437886 TTTTTTTTT
1 TTTTTTTTT
437895 GAAGAGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:450434 original size:81 final size:79
Alignment explanation
Indices: 450299--450499 Score: 217
Period size: 79 Copynumber: 2.5 Consensus size: 79
450289 ATAACGAGGG
* * ** * *
450299 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTA
450362 GAAAAAAAAAAATCGGGA
64 G--AAAAAAAAATCGGGA
* *
450380 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
* * * *
450445 GAATAAAGTCGGGG
66 AAAAAAAATCGGGA
* * *
450459 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
450500 GATGAAATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
79 48 0.47
80 7 0.07
81 48 0.47
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
AAAAAAAATCGGGA
Found at i:450488 original size:28 final size:28
Alignment explanation
Indices: 450454--450525 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
450444 GGAATAAAGT
** *
450454 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
450482 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
450510 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
450526 TCGATTATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:450583 original size:52 final size:52
Alignment explanation
Indices: 450514--450683 Score: 161
Period size: 52 Copynumber: 3.3 Consensus size: 52
450504 AAATAACGAG
* *
450514 GTTGGAGTATCCTCGATTATGAGAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAGAAATTGGTATTTTTGGAAATAAAACCGGA
* ** *
450566 GTTGGAGTATCCCCGATTA-AAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTATGA-G-AAATTGGTATTTTTGGAAATAAAACC-GGA
* * * * *
450619 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAGAAATTGGTATTTTTG-GAAATAAAACCGGA
450670 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
450684 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
51 4 0.04
52 77 0.80
53 14 0.15
54 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAGAAATTGGTATTTTTGGAAATAAAACCGGA
Found at i:450766 original size:27 final size:27
Alignment explanation
Indices: 450691--450768 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
450681 CCCTCAGAAA
*
450691 TAACGGGGTTGGAGTATCCCCAATGAT
1 TAACGGGGTTGGAGTATCCCCGATGAT
450718 TAACGGGGTTGGAGTATCCCCGATGAT
1 TAACGGGGTTGGAGTATCCCCGATGAT
450745 TAACGGGGTTGGAGTATCCCCGAT
1 TAACGGGGTTGGAGTATCCCCGAT
450769 TGTGAAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (27 bp):
TAACGGGGTTGGAGTATCCCCGATGAT
Found at i:450852 original size:51 final size:53
Alignment explanation
Indices: 450756--450874 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
450746 AACGGGGTTG
* * * *
450756 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTCA
*
450810 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTCG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTCA
*
450861 GAATATCCCCGATT
1 GAGTATCCCCGATT
450875 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.31
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTCA
Found at i:453259 original size:13 final size:13
Alignment explanation
Indices: 453241--453266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
453231 ACAAAGATCC
453241 ATGTATCGATACA
1 ATGTATCGATACA
453254 ATGTATCGATACA
1 ATGTATCGATACA
453267 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:453262 original size:33 final size:33
Alignment explanation
Indices: 453220--453286 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
453210 AAAATTTCCA
***
453220 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
453253 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
453286 A
1 A
453287 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:453330 original size:19 final size:18
Alignment explanation
Indices: 453306--453373 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
453296 CAGTAGCTAA
453306 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
453325 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
453340 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
453357 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
453374 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:453346 original size:13 final size:13
Alignment explanation
Indices: 453328--453352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
453318 ACAATACTTA
453328 TGTATCGATACAT
1 TGTATCGATACAT
453341 TGTATCGATACA
1 TGTATCGATACA
453353 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:453350 original size:32 final size:32
Alignment explanation
Indices: 453309--453371 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
453299 TAGCTAATTA
*
453309 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
453341 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
453372 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:453435 original size:21 final size:21
Alignment explanation
Indices: 453409--453486 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
453399 GTTGGGACCC
453409 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
453430 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
453450 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
453471 TGTATCGATACATTTG
1 TGTATCGATACATTTG
453487 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:453473 original size:41 final size:40
Alignment explanation
Indices: 453409--453490 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
453399 GTTGGGACCC
* *
453409 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
453450 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
453490 T
1 T
453491 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:454322 original size:55 final size:55
Alignment explanation
Indices: 454227--455131 Score: 1251
Period size: 55 Copynumber: 16.3 Consensus size: 55
454217 ATAAAGTGTA
* * * * * * *
454227 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
454282 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
454337 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTGAAA-ATAAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGT-----G
** * *
454396 CATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 --TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
454453 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
454508 TCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
454563 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
454618 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
454674 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
454729 TCCTGCTCTTTAAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
454784 TCCTGCTCTTTGAGGACTGAAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
454839 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
454894 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
454949 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
455004 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
455059 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGACGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
455114 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
455132 AAAAAGCGGA
Statistics
Matches: 771, Mismatches: 51, Indels: 56
0.88 0.06 0.06
Matches are distributed among these distances:
54 26 0.03
55 624 0.81
56 72 0.09
57 2 0.00
59 1 0.00
61 45 0.06
62 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:454361 original size:26 final size:26
Alignment explanation
Indices: 454273--454362 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
454263 GTGTGGGCTT
* *
454273 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
454299 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
454326 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
454354 TGAAAGGTG
1 TGAAAGGTG
454363 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:456144 original size:17 final size:17
Alignment explanation
Indices: 456098--456170 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 17
456088 CTTAAGTAGG
*
456098 TTTTTTCTTTTCTCTCTTT
1 TTTTTTTTTTTC-CT-TTT
* * *
456117 TTCTTTGTTTT-GTTTT
1 TTTTTTTTTTTCCTTTT
456133 TTTGTTTTTTTTCC--TT
1 TTT-TTTTTTTTCCTTTT
*
456149 TTTTTTTTTTGCCTTTT
1 TTTTTTTTTTTCCTTTT
456166 TTTTT
1 TTTTT
456171 GAAGAGAAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
15 9 0.21
16 10 0.23
17 15 0.35
19 9 0.21
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTCCTTTT
Found at i:456163 original size:15 final size:15
Alignment explanation
Indices: 456131--456170 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
456121 TTGTTTTGTT
*
456131 TTTTTGTTTTTTTTCC
1 TTTTT-TTTTTTTGCC
456147 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
456162 TTTTTTTTT
1 TTTTTTTTT
456171 GAAGAGAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:457898 original size:13 final size:13
Alignment explanation
Indices: 457880--457905 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
457870 ACAAAGATCC
457880 ATGTATCGATACA
1 ATGTATCGATACA
457893 ATGTATCGATACA
1 ATGTATCGATACA
457906 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:457901 original size:33 final size:33
Alignment explanation
Indices: 457859--457925 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
457849 AAAATTTCCA
***
457859 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
457892 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
457925 A
1 A
457926 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:457969 original size:19 final size:18
Alignment explanation
Indices: 457945--458012 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
457935 CAGTAGCTAA
457945 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
457964 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
457979 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
457996 TTATGTATCAATACAAA
1 TTATGTATCGATACAAA
458013 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:457985 original size:13 final size:13
Alignment explanation
Indices: 457967--457991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
457957 ACAATACTTA
457967 TGTATCGATACAT
1 TGTATCGATACAT
457980 TGTATCGATACA
1 TGTATCGATACA
457992 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:457989 original size:32 final size:32
Alignment explanation
Indices: 457948--458010 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
457938 TAGCTAATTA
* *
457948 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCAATACAT
457980 TGTATCGATACAAAACTTATGTATCAATACA
1 TGTATCGATACAAAACTTATGTATCAATACA
458011 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCAATACAT
Found at i:458091 original size:20 final size:20
Alignment explanation
Indices: 458048--458149 Score: 152
Period size: 20 Copynumber: 5.0 Consensus size: 20
458038 GTTGGGACCC
458048 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGT-GAA
458069 TGTATCGATACATTTGTGAA
1 TGTATCGATACATTTGTGAA
458089 TGTATCGATACATTTGTGAA
1 TGTATCGATACATTTGTGAA
***
458109 TGTATCGATACATTCTACAAA
1 TGTATCGATACATT-TGTGAA
458130 TGTATCGATACATTTG-GAA
1 TGTATCGATACATTTGTGAA
458149 T
1 T
458150 TTTTTTTTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
19 3 0.04
20 38 0.51
21 34 0.45
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTGTGAA
Found at i:458105 original size:41 final size:41
Alignment explanation
Indices: 458048--458149 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
458038 GTTGGGACCC
***
458048 TGTATCGATACATTTGTAGAATGTATCGATACATT-TGTGAA
1 TGTATCGATACATTTGT-GAATGTATCGATACATTCTACAAA
458089 TGTATCGATACATTTGTGAATGTATCGATACATTCTACAAA
1 TGTATCGATACATTTGTGAATGTATCGATACATTCTACAAA
458130 TGTATCGATACATTTG-GAAT
1 TGTATCGATACATTTGTGAAT
458150 TTTTTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 21 0.37
41 36 0.63
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (41 bp):
TGTATCGATACATTTGTGAATGTATCGATACATTCTACAAA
Found at i:458911 original size:22 final size:21
Alignment explanation
Indices: 458869--458912 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
458859 TTTTTTTTTC
* *
458869 TCTCCCCTTTAATCAAAAATT
1 TCTCCCCCTTAATAAAAAATT
*
458890 TCTCCCCCTTAGTAAAATAATT
1 TCTCCCCCTTAATAAAA-AATT
458912 T
1 T
458913 AACAATTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAAAATT
Found at i:460319 original size:20 final size:21
Alignment explanation
Indices: 460289--460332 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
460279 GCTGCTAGTG
* *
460289 TGGGGGTTGCCGGTTGTGACC
1 TGGGGGTTGCCGGTCGCGACC
460310 TGGGGG-TGCCGGTCGCGACC
1 TGGGGGTTGCCGGTCGCGACC
460330 TGG
1 TGG
460333 TGAGTGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.05, C:0.23, G:0.50, T:0.23
Consensus pattern (21 bp):
TGGGGGTTGCCGGTCGCGACC
Found at i:460792 original size:13 final size:13
Alignment explanation
Indices: 460774--460811 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
460764 ATAAACCCTT
*
460774 TGTATCGATACAC
1 TGTATCGATACAA
460787 TGTATCGATACAA
1 TGTATCGATACAA
*
460800 TGAATCGATACA
1 TGTATCGATACA
460812 GAGAATGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:466952 original size:13 final size:13
Alignment explanation
Indices: 466934--466959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
466924 CATTTTGGGA
466934 TGTATCGATACAT
1 TGTATCGATACAT
466947 TGTATCGATACAT
1 TGTATCGATACAT
466960 CTTGTGTATC
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:466956 original size:33 final size:30
Alignment explanation
Indices: 466914--466975 Score: 88
Period size: 33 Copynumber: 2.0 Consensus size: 30
466904 TACAAGCCAA
*
466914 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTT--G-TGTATCGATACAT
466947 TGTATCGATACATCTTGTGTATCGATACA
1 TGTATCGATACATCTTGTGTATCGATACA
466976 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 12 0.43
31 1 0.04
33 15 0.54
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (30 bp):
TGTATCGATACATCTTGTGTATCGATACAT
Found at i:466969 original size:17 final size:16
Alignment explanation
Indices: 466914--466975 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
466904 TACAAGCCAA
466914 TGTATCGATACATTTTGGG
1 TGTATCGATACA-TTT--G
466933 ATGTATCGATACA--T-
1 -TGTATCGATACATTTG
466947 TGTATCGATACATCTTG
1 TGTATCGATACAT-TTG
466964 TGTATCGATACA
1 TGTATCGATACA
466976 AACAGTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.32
16 1 0.03
17 13 0.34
20 12 0.32
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (16 bp):
TGTATCGATACATTTG
Found at i:467064 original size:20 final size:21
Alignment explanation
Indices: 467017--467068 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
467007 GCCAATGACC
*
467017 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
467038 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
467058 TGTATCGATAC
1 TGTATCGATAC
467069 TGTGCAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:478772 original size:8 final size:7
Alignment explanation
Indices: 478753--478804 Score: 50
Period size: 8 Copynumber: 6.9 Consensus size: 7
478743 TTTTTTTTAA
478753 AAAAAAC
1 AAAAAAC
478760 AAAAACAAC
1 -AAAA-AAC
478769 AAAAAAC
1 AAAAAAC
478776 AAAAAAAC
1 -AAAAAAC
*
478784 AAAAAAA
1 AAAAAAC
*
478791 ACAAAAAG
1 A-AAAAAC
478799 AAAAAA
1 AAAAAA
478805 AGAGAATCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
7 15 0.38
8 21 0.54
9 3 0.08
ACGTcount: A:0.87, C:0.12, G:0.02, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:478774 original size:16 final size:15
Alignment explanation
Indices: 478753--478804 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
478743 TTTTTTTTAA
478753 AAAAAACAAAAACAAC
1 AAAAAACAAAAA-AAC
478769 AAAAAACAAAAAAAC
1 AAAAAACAAAAAAAC
*
478784 AAAAAA-AACAAAAAG
1 AAAAAACAA-AAAAAC
478799 AAAAAA
1 AAAAAA
478805 AGAGAATCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 2 0.06
15 20 0.59
16 12 0.35
ACGTcount: A:0.87, C:0.12, G:0.02, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:478784 original size:24 final size:23
Alignment explanation
Indices: 478752--478805 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
478742 CTTTTTTTTA
*
478752 AAAAAAACAAAAACAACAAAAAAC
1 AAAAAAACAAAAAAAAC-AAAAAC
*
478776 AAAAAAACAAAAAAAACAAAAAG
1 AAAAAAACAAAAAAAACAAAAAC
478799 AAAAAAA
1 AAAAAAA
478806 GAGAATCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAAAAACAAAAAAAACAAAAAC
Found at i:478807 original size:8 final size:8
Alignment explanation
Indices: 478752--478797 Score: 67
Period size: 8 Copynumber: 5.6 Consensus size: 8
478742 CTTTTTTTTA
478752 AAAAAAAC
1 AAAAAAAC
478760 AAAAACAAC
1 AAAAA-AAC
478769 -AAAAAAC
1 AAAAAAAC
478776 AAAAAAAC
1 AAAAAAAC
478784 AAAAAAAAC
1 -AAAAAAAC
478793 AAAAA
1 AAAAA
478798 GAAAAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.09
8 21 0.60
9 11 0.31
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:480011 original size:54 final size:54
Alignment explanation
Indices: 479874--480130 Score: 190
Period size: 61 Copynumber: 4.5 Consensus size: 54
479864 CTCCTTTCAC
* * * **
479874 CCTTTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCTCACACAAGTTGGTGGCA
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCCGGTGGCA
* * * * *
479928 CCTTTCATTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACATAAGCCGGTGGCG
1 CC-TTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCCGGTGGCA
* **
479983 CCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGCCGGTGGCA
* * * * **
480043 CTTTTCAGTCCTCAAAGAGTAGGATGCTTTCTTTTTGCAAAGCCCATACAAGTTGGTGGCA
1 C-CTTCAGTCCTCAAAGAGCAGGACGC---C--TTT-CAAAGCCCACACAAGCCGGTGGCA
* *
480104 CTTTCTAGTCCTCAAAGAGTAGGACGC
1 CCTTC-AGTCCTCAAAGAGCAGGACGC
480131 TCTCTCCTTT
Statistics
Matches: 164, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
54 26 0.16
55 45 0.27
60 24 0.15
61 64 0.39
64 1 0.01
65 2 0.01
66 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (54 bp):
CCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCCGGTGGCA
Found at i:480085 original size:61 final size:60
Alignment explanation
Indices: 479901--480378 Score: 406
Period size: 61 Copynumber: 7.8 Consensus size: 60
479891 GTAGGACGCC
* * *
479901 TTTCAAAGCTCACACAAGTTGGTGGCACCTTTCATTCCTCAAAGAGCAGGATGC---C-T
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTT
* ** * * * * *
479957 TTT-AAAGCCCACATAAGCCGGTGGCGC-CTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG-CTT-TCTT
*
480017 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAGGATGCTTTCTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTT
* * *
480076 TTTGCAAAGCCCATACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGTAGGACGCTCTCTCCTT
1 TTT-CAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGA-------TGCTT
480140 TCACCTT
57 T---CTT
* * * * * * *
480147 TTTCTTTTAAAGCCCACATAAGCTAGTGGCAC-CTTCAGTCCTCAAAGAGTAGGACGCCTTCTTT
1 TTTC----AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTC-TT
* * *
480211 TTTTAAAGCTCACACAAGTTGGTGGCACTTTTCGGTCCTCAAAGAGCAGGATGCTTTCTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTT
*
480271 TTTGCAAAGCCCACACAAGTT-GTGGCA-TCTTTCAGTCCTCAAAGGGCAGGACAT-CTTT-TCT
1 TTT-CAAAGCCCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCAGG--ATGCTTTCT-T
*
480332 TTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGC
480379 GGGACACACT
Statistics
Matches: 345, Mismatches: 44, Indels: 61
0.77 0.10 0.14
Matches are distributed among these distances:
54 20 0.06
55 20 0.06
56 3 0.01
59 8 0.02
60 98 0.28
61 131 0.38
62 3 0.01
63 1 0.00
64 5 0.01
66 3 0.01
68 5 0.01
70 1 0.00
71 6 0.02
73 18 0.05
74 23 0.07
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (60 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTT
Found at i:480209 original size:134 final size:135
Alignment explanation
Indices: 480015--480383 Score: 387
Period size: 121 Copynumber: 2.8 Consensus size: 135
480005 ACGCCTTCTC
* * * * *
480015 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAGGATGCTTTCTTTTTG
1 CTTTTAAAGCCCACACAAGCTAGTGGCACTCTTCAGTCCTCAAAGAGTAGGACGCCTTCTTTTTG
* *
480080 CAAAGCCCATACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGTAGGACGCTCTCTCCTTTCAC
66 CAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCAC
480144 CTTTTT
130 CTTTTT
* *
480150 CTTTTAAAGCCCACATAAGCTAGTGGCAC-CTTCAGTCCTCAAAGAGTAGGACGCCTTCTTTTTT
1 CTTTTAAAGCCCACACAAGCTAGTGGCACTCTTCAGTCCTCAAAGAGTAGGACGCCTTCTTTTTG
* * * *
480214 TAAAGCTCACACAAGTTGGTGGCACTTTTCGGTCCTCAAAGAGCAGGATGCT-T-T-C--T----
66 CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACC
*
480270 TTTTG
131 TTTTT
* * * **
480275 C----AAAGCCCACACAAG-TTGTGGCA-TCTTTCAGTCCTCAAAGGGCAGGACATCTT-TTCTT
1 CTTTTAAAGCCCACACAAGCTAGTGGCACTC-TTCAGTCCTCAAAGAGTAGGACGCCTTCTT-TT
* * *
480333 TTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCGGGAC
64 TGCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
480384 ACACTTCCTT
Statistics
Matches: 204, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
120 10 0.05
121 83 0.41
125 5 0.02
129 1 0.00
131 1 0.00
132 1 0.00
133 1 0.00
134 72 0.35
135 30 0.15
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (135 bp):
CTTTTAAAGCCCACACAAGCTAGTGGCACTCTTCAGTCCTCAAAGAGTAGGACGCCTTCTTTTTG
CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACC
TTTTT
Found at i:480217 original size:60 final size:60
Alignment explanation
Indices: 480143--480383 Score: 265
Period size: 60 Copynumber: 4.0 Consensus size: 60
480133 TCTCCTTTCA
* * * * * *
480143 CCTTTTTCTTTTAAAGCCCACATAAGCTAGTGGCAC-CTTCAGTCCTCAAAGAGTAGGACG
1 CCTTTTT-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
* * * *
480203 CCTTCTTTTTTTAAAGCTCACACAAGTTGGTGGCACTTTTCGGTCCTCAAAGAGCAGGATG
1 CCTT-TTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
* *
480264 -CTTTCTTTTTGCAAAGCCCACACAAGTT-GTGGCA-TCTTTCAGTCCTCAAAGGGCAGGACA
1 CCTTT-TTTTT-CAAAGCCCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCAGGACG
* * *
480324 TCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCGGGAC
1 CCTTTT-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
480384 ACACTTCCTT
Statistics
Matches: 155, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
59 2 0.01
60 79 0.51
61 73 0.47
62 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (60 bp):
CCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
Found at i:480291 original size:195 final size:194
Alignment explanation
Indices: 479955--480314 Score: 596
Period size: 195 Copynumber: 1.9 Consensus size: 194
479945 AGCAGGATGC
* *
479955 CTTTTAAAGCCCACATAAGCCGGTGGCGCCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTT
1 CTTTTAAAGCCCACATAAGCCAGTGGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTT
*
480020 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAGGATGCTTTCTTTTTGCAAAG
66 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAG
*
480085 CCCATACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGTAGGACGCTCTCTCCTTTCACCTTTT
131 CCCACACAAGTT-GTGGCATCTTTC-AGTCCTCAAAGAGTAGGACGCTCTCTCCTTTCACCTTTT
480149 T
194 T
* * * **
480150 CTTTTAAAGCCCACATAAGCTAGTGGCACCTTCAGTCCTCAAAGAGTAGGACGCCTTCTTTTTTT
1 CTTTTAAAGCCCACATAAGCCAGTGGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTT
* *
480215 AAAGCTCACACAAGTTGGTGGCACTTTTCGGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAG
66 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAG
480280 CCCACACAAGTTGTGGCATCTTTCAGTCCTCAAAG
131 CCCACACAAGTTGTGGCATCTTTCAGTCCTCAAAG
480315 GGCAGGACAT
Statistics
Matches: 153, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
194 17 0.11
195 136 0.89
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (194 bp):
CTTTTAAAGCCCACATAAGCCAGTGGCACCTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTT
AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAG
CCCACACAAGTTGTGGCATCTTTCAGTCCTCAAAGAGTAGGACGCTCTCTCCTTTCACCTTTTT
Found at i:481361 original size:20 final size:21
Alignment explanation
Indices: 481336--481378 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
481326 TACCAAGGAA
* *
481336 ATGTATCGCTATATTAT-TCG
1 ATGTATCGATACATTATATCG
481356 ATGTATCGATACATTATATCG
1 ATGTATCGATACATTATATCG
481377 AT
1 AT
481379 ACATCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATTATATCG
Found at i:483835 original size:51 final size:49
Alignment explanation
Indices: 483776--483914 Score: 143
Period size: 52 Copynumber: 2.7 Consensus size: 49
483766 CCGGTTTCAT
* ** *
483776 TTTCAAAACATCAATTTTTCTCAATCGGGGATACTCCAACTTTGATTTTA
1 TTTCAAAACACCAATTTTTC-CAATCGGGGATACTCCAACTCCGATTCTA
* *
483826 TTTCTAAAACACCCATTTCTCCATAATCGGGGATACTCCAACTCCGATTCTA
1 TTTC-AAAACACCAATTTTTCC--AATCGGGGATACTCCAACTCCGATTCTA
* * *
483878 TTTCCAAAACACCGACTATTCACAATCGGGGATACTC
1 TTT-CAAAACACCAATTTTTC-CAATCGGGGATACTC
483915 TAACCCCATT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
50 5 0.07
51 27 0.36
52 40 0.54
53 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (49 bp):
TTTCAAAACACCAATTTTTCCAATCGGGGATACTCCAACTCCGATTCTA
Found at i:483965 original size:79 final size:76
Alignment explanation
Indices: 483854--484075 Score: 288
Period size: 75 Copynumber: 2.9 Consensus size: 76
483844 CTCCATAATC
* *
483854 GGGGATACTCCAA-CTCCGATTCTATTTCCAAAACACCGACTATTCACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCT-CGATTTTATTTCCAAAACACC-A-TATTCACAATCGGGGATACTCCAA
483918 CCCCATTATTTCTGA
63 CCCCATTA-TTCTGA
* * **
483933 GGGGATACTCCAACCTCGATTTTATTTCCAAAACATCAAATTTTC-ATCGGGGATACTCCAACCC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCATATTCACAATCGGGGATACTCCAACCC
*
483997 CGTTATTCTGA
66 CATTATTCTGA
*
484008 GGGGATACTCCAACCTCGATTTTATTTCTAAAACACCA-ATTCCACACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCATATT---CACAATCGGGGATACTCCAA
484072 CCCC
63 CCCC
484076 GGCTTTACTT
Statistics
Matches: 127, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
74 3 0.02
75 42 0.33
76 22 0.17
77 5 0.04
78 21 0.17
79 32 0.25
80 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.27
Consensus pattern (76 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCATATTCACAATCGGGGATACTCCAACCC
CATTATTCTGA
Found at i:484164 original size:205 final size:206
Alignment explanation
Indices: 483802--484172 Score: 448
Period size: 205 Copynumber: 1.8 Consensus size: 206
483792 TTTCTCAATC
* * * *
483802 GGGGATACTCCAACTTTGATTTTATTTCTAAAACACCCATTTCTCCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAACACCCAATTCTCCACAATCGGGGATACTCCAA
* * * * *
483867 CTCCGATTCTATTTCCAAAACACCGACTATTCACAATCGGGGATACTCTAACCCCATTATTTCTG
66 CCCCGATTCTACTTCCAAAACACCGAATATTCACAATCGGGAATACTCCAACCCCATTATTTCTG
* *
483932 AGGGGATACTCCAACCTCGATTTTATTTCCAAAACATCAAATTTTCATCGGGGATACTCCAACCC
131 AGGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAAATTTTCATCGGGGATACTCCAACCC
483997 CGTTATTCTGA
196 CGTTATTCTGA
484008 GGGGATACTCCAACCTCGATTTTATTTCTAAAACA-CCAATTC-CACACAATCGGGGATACTCCA
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAACACCCAATTCTC-CACAATCGGGGATACTCCA
* * * ** * * * **
484071 ACCCCGGCTT-TACTTCTAAAATA-TTAATTTCTCATAATCGGGAATACTCCAATCCTGTTATTT
65 ACCCC-GATTCTACTTCCAAAACACCGAATAT-TCACAATCGGGAATACTCCAACCCCATTATTT
* *
484134 -TCGA-GGGAGTACTCTAACCCCAATTTTATTTCTAAAACA
128 CT-GAGGGGA-TACTCCAACCCCAATTTTATTTCCAAAACA
484173 CCAATTCTCC
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
204 9 0.07
205 92 0.67
206 36 0.26
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (206 bp):
GGGGATACTCCAACCTCGATTTTATTTCTAAAACACCCAATTCTCCACAATCGGGGATACTCCAA
CCCCGATTCTACTTCCAAAACACCGAATATTCACAATCGGGAATACTCCAACCCCATTATTTCTG
AGGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAAATTTTCATCGGGGATACTCCAACCC
CGTTATTCTGA
Found at i:484208 original size:51 final size:51
Alignment explanation
Indices: 484137--484249 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 51
484127 GTTATTTTCG
*
484137 AGGGAGTACTCTAACCCCAATTTTA-TTTCTAAAACACCAATTCTCCACAATC
1 AGGGA-TACTCTAACCCCAATTTTATTTTC-AAAACACAAATTCTCCACAATC
* * * *
484189 GGGGATACTCTAACTCCAATTTTATTTTCAAAACACAAATTTTTCACAATC
1 AGGGATACTCTAACCCCAATTTTATTTTCAAAACACAAATTCTCCACAATC
*
484240 AGAGATACTC
1 AGGGATACTC
484250 CAGCTCTGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 45 0.85
52 8 0.15
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (51 bp):
AGGGATACTCTAACCCCAATTTTATTTTCAAAACACAAATTCTCCACAATC
Found at i:484230 original size:130 final size:126
Alignment explanation
Indices: 483933--484284 Score: 331
Period size: 130 Copynumber: 2.7 Consensus size: 126
483923 TTATTTCTGA
* *
483933 GGGGATACTCCAACCTCGATTTTATTTCCAAAACATCAAATTTTC--ATCGGGGATACTCCAACC
1 GGGGATACTCCAACC-CGATTTTATTTTCAAAACA-CAAATTTTCAAATCGGGAATACTCCAACC
* *
483996 CCGTTATTCTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACCAATTCCACACAATC
64 CCGTTATTCTGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTCCACACAATC
** * * **
484059 GGGGATACTCCAACCCCGGCTTTA-CTTCTAAAATATTAATTTCTCATAATCGGGAATACTCCAA
1 GGGGATACTCCAA-CCCGATTTTATTTTC-AAAACACAAATTT-TCA-AATCGGGAATACTCCAA
* * * *
484123 TCCTGTTATTTTCGA-GGGAGTACTCTAACCCCAATTTTATTTCTAAAACACCAATTCTC-CACA
62 CCCCGTTATTCT-GAGGGGA-TACTCCAACCCCAATTTTATTTCTAAAACACCAATTC-CACACA
484186 ATC
124 ATC
* * * *
484189 GGGGATACTCTAACTCCAATTTTATTTTCAAAACACAAATTTTTCACAATC-AGAGATACTCCAG
1 GGGGATACTCCAAC-CCGATTTTATTTTCAAAACACAAA-TTTTCA-AATCGGGA-ATACTCCAA
* * *
484253 CTCTGTTATTTCAT-CGGGGATACTCCAACCCC
62 CCCCGTTA-TTC-TGAGGGGATACTCCAACCCC
484285 GTTATTTCTG
Statistics
Matches: 180, Mismatches: 30, Indels: 28
0.76 0.13 0.12
Matches are distributed among these distances:
125 7 0.04
126 26 0.14
127 2 0.01
129 31 0.17
130 100 0.56
131 13 0.07
132 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (126 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAACACAAATTTTCAAATCGGGAATACTCCAACCCC
GTTATTCTGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTCCACACAATC
Found at i:488322 original size:16 final size:17
Alignment explanation
Indices: 488296--488334 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
488286 AAAGGCTTTC
*
488296 AAAAT-TTTTAATTGA-
1 AAAATGTTTTAATAGAG
488311 AAAATGTTTTAATAGAG
1 AAAATGTTTTAATAGAG
488328 AAAATGT
1 AAAATGT
488335 AGATAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 9 0.43
17 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (17 bp):
AAAATGTTTTAATAGAG
Found at i:488882 original size:122 final size:123
Alignment explanation
Indices: 488699--488933 Score: 337
Period size: 122 Copynumber: 1.9 Consensus size: 123
488689 TTCTTTTTAC
* * * * * *
488699 TTTATAATTTATTTATTGATTTCATATTTTATGCTATGTATATACATTTAACATATTTAATA-TT
1 TTTATAATTTATTTATTGATTCCATACTTTAGGCCATGTATATACACTTAAAATATTTAATATTT
* *** * *
488763 TATTATAATTATATATCGGTCTCCACTTTTAATTTTATTATAATTAATCTTCTTATAA
66 TATTATAATAATATATAAATCTCCAATTTTAATTTTATTAGAATTAATCTTCTTATAA
488821 TTTATAATTTATTTATTGATTCCATACTTTAGGCCATGTATATACACTTAAAATATTTAATATTT
1 TTTATAATTTATTTATTGATTCCATACTTTAGGCCATGTATATACACTTAAAATATTTAATATTT
* *
488886 TATTATAATAATATATAAATTTTCAATTTTAATTTTATTAGAATTAAT
66 TATTATAATAATATATAAATCTCCAATTTTAATTTTATTAGAATTAAT
488934 TTTATAGTAA
Statistics
Matches: 98, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
122 56 0.57
123 42 0.43
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (123 bp):
TTTATAATTTATTTATTGATTCCATACTTTAGGCCATGTATATACACTTAAAATATTTAATATTT
TATTATAATAATATATAAATCTCCAATTTTAATTTTATTAGAATTAATCTTCTTATAA
Found at i:489038 original size:23 final size:23
Alignment explanation
Indices: 489008--489054 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
488998 TCTCCTAATT
489008 TGTTATTTCATTGAAGAAAAATG
1 TGTTATTTCATTGAAGAAAAATG
489031 TGTTATTTCATTGAAGAAAAATG
1 TGTTATTTCATTGAAGAAAAATG
489054 T
1 T
489055 ACAATCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (23 bp):
TGTTATTTCATTGAAGAAAAATG
Found at i:489064 original size:24 final size:23
Alignment explanation
Indices: 489012--489066 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
489002 CTAATTTGTT
***
489012 ATTTCATTGAAGAAAAATGTGTT
1 ATTTCATTGAAGAAAAATGTACA
489035 ATTTCATTGAAGAAAAATGTACA
1 ATTTCATTGAAGAAAAATGTACA
489058 ATCTTCATT
1 AT-TTCATT
489067 ATATAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (23 bp):
ATTTCATTGAAGAAAAATGTACA
Found at i:489179 original size:39 final size:38
Alignment explanation
Indices: 489077--489179 Score: 136
Period size: 39 Copynumber: 2.7 Consensus size: 38
489067 ATATAAATTC
* *
489077 AAAAGAAATTTATGTTAATTGCTGAAAATAAGGGAAAA
1 AAAAGAAATTTATGCTAATTGTTGAAAATAAGGGAAAA
* *
489115 AAAAGAAATTTATGCTAAGTATTGAAAAT-AGGGAAAAAA
1 AAAAGAAATTTATGCTAATTGTTGAAAATAAGGG--AAAA
*
489154 AAAAGAAATTGATGCTAATTGTTGAA
1 AAAAGAAATTTATGCTAATTGTTGAA
489180 CAAAGAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 4 0.07
38 25 0.45
39 27 0.48
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.26
Consensus pattern (38 bp):
AAAAGAAATTTATGCTAATTGTTGAAAATAAGGGAAAA
Found at i:489411 original size:21 final size:22
Alignment explanation
Indices: 489371--489422 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
489361 AAGAATAAAA
489371 ATTTAATTAGTTTAAAAATTAT
1 ATTTAATTAGTTTAAAAATTAT
489393 ATTTAATTA--TTATAAAATTAT
1 ATTTAATTAGTTTA-AAAATTAT
489414 ATTATAATT
1 ATT-TAATT
489423 TAAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.11
21 11 0.39
22 14 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTAATTAGTTTAAAAATTAT
Found at i:489431 original size:21 final size:21
Alignment explanation
Indices: 489385--489435 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
489375 AATTAGTTTA
*
489385 AAAATTATATTTAATTATTAT
1 AAAATTATATTTAATTATAAT
489406 AAAATTATATTATAATT-TAAAT
1 AAAATTATATT-TAATTAT-AAT
489428 AAATATTA
1 AAA-ATTA
489436 AATATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 12 0.46
22 10 0.38
23 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTATATTTAATTATAAT
Found at i:489474 original size:37 final size:38
Alignment explanation
Indices: 489387--489475 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 38
489377 TTAGTTTAAA
*
489387 AATTATA-TTTAATTATTATAAAATTATATTATAATTT
1 AATTATATTTTAAATATTATAAAATTATATTATAATTT
* * * * * *
489424 AAATAAATATTAAATATTTTAAATTTAT-TTTTAATTT
1 AATTATATTTTAAATATTATAAAATTATATTATAATTT
489461 AATTATATTTTAAAT
1 AATTATATTTTAAAT
489476 TTGAGATAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
37 25 0.61
38 16 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (38 bp):
AATTATATTTTAAATATTATAAAATTATATTATAATTT
Found at i:490822 original size:2 final size:2
Alignment explanation
Indices: 490815--490843 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
490805 AAGAATCATT
490815 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
490844 GACACAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492358 original size:21 final size:23
Alignment explanation
Indices: 492332--492384 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
492322 CAAATTTAAT
492332 TAAAAAT-TTT-ATCAAATCAAA
1 TAAAAATATTTAATCAAATCAAA
492353 TAAAAATAAATTTAAATCAAATCAAA
1 TAAAAAT--ATTT-AATCAAATCAAA
492379 TAAAAA
1 TAAAAA
492385 AAAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.26
24 3 0.11
26 17 0.63
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAAATATTTAATCAAATCAAA
Found at i:493404 original size:10 final size:10
Alignment explanation
Indices: 493391--493420 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
493381 TATAATTGTT
*
493391 TAAATATATA
1 TAAATATAAA
493401 TAAATATAAA
1 TAAATATAAA
493411 TAAATATAAA
1 TAAATATAAA
493421 CGATAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAATATAAA
Found at i:494753 original size:13 final size:13
Alignment explanation
Indices: 494735--494760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
494725 AATTTTCTGA
494735 TGTATCGATACAT
1 TGTATCGATACAT
494748 TGTATCGATACAT
1 TGTATCGATACAT
494761 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:495486 original size:39 final size:40
Alignment explanation
Indices: 495401--495486 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 40
495391 TTTTCTTTTC
* **
495401 TTTCTCCCTTAATCAAAATAATTTTAACAAATTCGTACAT
1 TTTCCCCCTTAATCAAAATAATTTTAACAAATTCACACAT
* * * *
495441 TCTCCCCCTTAAT-AAAGTAATTTTAGCAAATTCACGCAT
1 TTTCCCCCTTAATCAAAATAATTTTAACAAATTCACACAT
495480 TTTCCCC
1 TTTCCCC
495487 TTTTATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (40 bp):
TTTCCCCCTTAATCAAAATAATTTTAACAAATTCACACAT
Found at i:497186 original size:21 final size:21
Alignment explanation
Indices: 497162--497208 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
497152 TTTGAAGCTG
497162 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
497182 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
497203 ATTTTG
1 ATTTTG
497209 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:501287 original size:22 final size:20
Alignment explanation
Indices: 501238--501289 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
501228 ATCATGCAAG
501238 TTTTTATTTTTCTTAGCTAAT
1 TTTTTA-TTTTCTTAGCTAAT
**
501259 TCATTATTTTCATTAGCTAAAT
1 TTTTTATTTTC-TTAGCT-AAT
501281 TTTTTATTT
1 TTTTTATTT
501290 CAACTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 10 0.40
22 10 0.40
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTCTTAGCTAAT
Found at i:503436 original size:13 final size:13
Alignment explanation
Indices: 503418--503443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
503408 AATTTTCTGA
503418 TGTATCGATACAT
1 TGTATCGATACAT
503431 TGTATCGATACAT
1 TGTATCGATACAT
503444 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:505235 original size:156 final size:156
Alignment explanation
Indices: 504945--505235 Score: 329
Period size: 156 Copynumber: 1.9 Consensus size: 156
504935 GTCCCTAGGG
* *
504945 GATACCTTCGATATAAAAGTACCCCATACCCCTAAAGGACCAAAATAAGATTTTAAAAGGGATGA
1 GATACCTTCGACATAAAAGTACCCCATACCCCTAAAGGACCAAAATAAGATTTAAAAAGGGATGA
* ** ** * *** * **
505010 ACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGACCCGATGATGACCTAGGAGTTAGTTCTT
66 ACCTATCCTAAATATCTACCTTCGACATAAAAACGGACCCGATGACAACCTAGCAAACAGTGCAA
505075 AAAAAATTACGAAAATGCCCTTAGAA
131 AAAAAATTACGAAAATGCCCTTAGAA
* ** **
505101 GATACCTTCGACATAATAGTACCTGATACCCCTAAAGGACTTGAAA-AAGA-TTAAAAATGGGAT
1 GATACCTTCGACATAAAAGTACCCCATACCCCTAAAGGAC-CAAAATAAGATTTAAAAA-GGGAT
*
505164 GAACCTATCCT-AATATCTACTTTCGACATAAAAACGGACCCGATGACAACCTAAGCCAAACA-T
64 GAACCTATCCTAAATATCTACCTTCGACATAAAAACGGACCCGATGACAACCT-AG-CAAACAGT
*
505227 GGAAAAAAA
127 GCAAAAAAA
505236 TCCTTATCAA
Statistics
Matches: 110, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
155 41 0.37
156 64 0.58
157 5 0.05
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (156 bp):
GATACCTTCGACATAAAAGTACCCCATACCCCTAAAGGACCAAAATAAGATTTAAAAAGGGATGA
ACCTATCCTAAATATCTACCTTCGACATAAAAACGGACCCGATGACAACCTAGCAAACAGTGCAA
AAAAAATTACGAAAATGCCCTTAGAA
Found at i:506205 original size:14 final size:15
Alignment explanation
Indices: 506182--506211 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
506172 AACAATAACT
506182 AAATTATAAAAATTA
1 AAATTATAAAAATTA
506197 AAATT-TAAAAATTA
1 AAATTATAAAAATTA
506211 A
1 A
506212 CATAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATAAAAATTA
Found at i:506358 original size:7 final size:8
Alignment explanation
Indices: 506344--506378 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
506334 TTATTATACG
506344 TAAAAAAA
1 TAAAAAAA
506352 TAAAAAAA
1 TAAAAAAA
506360 TAAAAAAA
1 TAAAAAAA
506368 T-AAAAAA
1 TAAAAAAA
506375 TAAA
1 TAAA
506379 TTGATCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:506363 original size:16 final size:15
Alignment explanation
Indices: 506344--506378 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
506334 TTATTATACG
506344 TAAAAAAATAAAAAAA
1 TAAAAAAAT-AAAAAA
506360 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
506375 TAAA
1 TAAA
506379 TTGATCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:509049 original size:26 final size:26
Alignment explanation
Indices: 509013--509087 Score: 114
Period size: 26 Copynumber: 2.9 Consensus size: 26
509003 TAAAAATAAG
* *
509013 ATTGATAAAGTTCAACTTTATTTGAT
1 ATTGATAAAGTTCAACTTTATCTGAA
*
509039 ATTGACAAAGTTCAACTTTATCTGAA
1 ATTGATAAAGTTCAACTTTATCTGAA
*
509065 ATTAATAAAGTTCAACTTTATCT
1 ATTGATAAAGTTCAACTTTATCT
509088 AGGATTCTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (26 bp):
ATTGATAAAGTTCAACTTTATCTGAA
Found at i:515096 original size:16 final size:17
Alignment explanation
Indices: 515077--515129 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
515067 AAAAAAAGTC
*
515077 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCAAAA
515093 AAAATG-AAAAG-AAAA
1 AAAATGCAAAAGCAAAA
515108 AAAATGCAAAAGCAAAA
1 AAAATGCAAAAGCAAAA
515125 TAAAA
1 -AAAA
515130 AAAGGAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 9 0.28
16 14 0.44
17 5 0.16
18 4 0.12
ACGTcount: A:0.74, C:0.09, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAATGCAAAAGCAAAA
Found at i:515131 original size:20 final size:21
Alignment explanation
Indices: 515106--515154 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
515096 ATGAAAAGAA
515106 AAAAAATGCAA-AAGC-AAAAT
1 AAAAAATGCAACAA-CAAAAAT
* *
515126 AAAAAAAGGAACAACAAAAAT
1 AAAAAATGCAACAACAAAAAT
515147 AAAAAATG
1 AAAAAATG
515155 AGGACATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.08
Consensus pattern (21 bp):
AAAAAATGCAACAACAAAAAT
Found at i:516535 original size:27 final size:28
Alignment explanation
Indices: 516464--516846 Score: 591
Period size: 27 Copynumber: 13.9 Consensus size: 28
516454 GTGGCATTTT
* * *
516464 TTTTAAAGTCCATAACTCCTTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
516492 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
516520 TTTT-AAGTCCACAACTCTGTGGCACTC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
516547 TTTTAAAGTTCACAACTCCGTGGCGCCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
516575 TTTT-AAGTCCACAATTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
516602 TTTTTAAAGTCCACAACTCCGTGGCACCC
1 -TTTTAAAGTCCACAACTCCGTGGCACCC
*
516631 TTTT-AAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
516658 TTTT-AAGTCCATAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
516685 TTTT-AAGTCCACAACTCCGTGCCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
516712 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
516740 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
516768 TTTTAAAGTCCACAACTTCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
516796 TTTT-AAGTCCACAACTCCGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
516823 TTTT-AAGTCCACAACTCCGTGGCA
1 TTTTAAAGTCCACAACTCCGTGGCA
516847 ACACCCATTT
Statistics
Matches: 329, Mismatches: 22, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
27 166 0.50
28 141 0.43
29 22 0.07
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (28 bp):
TTTTAAAGTCCACAACTCCGTGGCACCC
Found at i:516677 original size:165 final size:165
Alignment explanation
Indices: 516464--516846 Score: 608
Period size: 165 Copynumber: 2.3 Consensus size: 165
516454 GTGGCATTTT
* *
516464 TTTTAAAGTCCATAACTCCT-TGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 TTTT-AAGTCCACAACT-CTGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGT
* * * * * *
516528 CCACAACTCTGTGGCACTCTTTTAAAGTTCACAACTCCGTGGCGCCCTTTT-AAGTCCACAATTC
63 CCACAACTCCGTGCCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTC
516592 CGTGGCACCCTTTTTAAAGTCCACAACTCCGTGGCACCC
128 CGTGGCACCC-TTTTAAAGTCCACAACTCCGTGGCACCC
*
516631 TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCATAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
516696 CAACTCCGTGCCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
66 CAACTCCGTGCCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
*
516761 GGCACCCTTTTAAAGTCCACAACTTCGTGGCACCC
131 GGCACCCTTTTAAAGTCCACAACTCCGTGGCACCC
* *
516796 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCA
1 TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA
516847 ACACCCATTT
Statistics
Matches: 201, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
165 153 0.76
166 44 0.22
167 4 0.02
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (165 bp):
TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCGTGCCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
GGCACCCTTTTAAAGTCCACAACTCCGTGGCACCC
Found at i:516690 original size:138 final size:139
Alignment explanation
Indices: 516463--516846 Score: 614
Period size: 138 Copynumber: 2.8 Consensus size: 139
516453 AGTGGCATTT
* * * *
516463 TTTTTAAAGTCCATAACTCCTTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 TTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGT
* * * * *
516528 CCACAACTCTGTGGCACTCTTTTAAAGTTCACAACTCCGTGGCGCCCTTTT-AAGTCCACAATTC
66 CCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTC
516592 CGTGGCACCC
130 CGTGGCACCC
516602 TTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGT
1 TTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGT
* *
516666 CCATAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGCCACCCTTTTAAAGTCCACAACTCC
66 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCC
516731 GTGGCACCC
131 GTGGCACCC
516740 -TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT-TCGTGGCACCCTTTTAAG
1 TTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCT-GTGGCACCCTTTTAAG
*
516803 TCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCA
65 TCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA
516847 ACACCCATTT
Statistics
Matches: 228, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
137 57 0.25
138 141 0.62
139 30 0.13
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (139 bp):
TTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGT
CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCC
GTGGCACCC
Found at i:516891 original size:32 final size:32
Alignment explanation
Indices: 516852--518333 Score: 1231
Period size: 32 Copynumber: 48.7 Consensus size: 32
516842 TGGCAACACC
*
516852 CATTTCAAAGCCCATACAAGTCGGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
*
516884 CATTTCAAAGCCCACACAAGTTGGTGGCAAC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
516915 CTATTTCAAAGTCCACACAAGTTGGTGGCAACC
1 C-ATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
516948 CATTTTAAAGCCCACACAAGTTGGTGGCAAGT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
516980 CATTTGAAAGCCCACACAAGTTGGTGGCAAGT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
517012 TATTTAAAAGCCCACACAAGTCGGTGGCAACC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
517044 CATTTTAAAGCCCACACAAGTTGGTGGCAAGT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517076 TATTTAAAAGCCCACACAAGTCGGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
517108 TATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
*
517140 CATTTCAAAGCCCACACAAGTCAGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517172 CATTTGAAAGCCCACACAAGTTGGTGGCAAC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517203 CTATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 C-ATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517236 CATTTCAAAGCCCACACAAGTTGGTGGCAAGT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517268 CATTTGAAAGCCCACACAAGTCGGTGGCAAGT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
*
517300 CATTTCAAAGCCCATACAAGTCGGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
517332 CATTTTAAAGCCCACATAAGTCAGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517364 CATTTCAAAGCCCACACAAGTCAGTGGCAACC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517396 CATTTCAAAGACCACACAAGTCGGTGGAAAC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
*
517427 CTATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-ATTTCAAAGCCCACACAAGTCGGTGGCAACT
*
517460 CATTTCAAAG-CC-CATAAGTCGGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517488 CTTTTCAAAG-CC-CACAAGTCAGTGGC-AC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517516 CCTTTCAAAG-CC-CACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* ** **
517544 CCTTTTTAAG-CC-CACAAGTTAGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517574 CATTTCAAAGCCCACGC--GTCGGTGGCAACC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517604 CATTTCAAAGCCCACACAAAGTTGGTGGCAACC
1 CATTTCAAAGCCCACAC-AAGTCGGTGGCAACT
*
517637 CATTTCAAAGCCCACACAAGTCGGTGGAAAC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
*
517668 CTATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-ATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517701 CATTTCAAA-CCC-CATAAGTCGGTAGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517729 CTTTTCAAAG-CC-CACAAGTCAGTGGC-AC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517757 CCTTTCAAAG-CC-CACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* ** **
517785 CGTTTTTAAG-CC-CACAAGTTAGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517815 CATTTCAAAGCCCACGC--GTCGGTGGCAACC
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
517845 CATTTCAAAGCCCACACAAAGTTGGTGGCAACC
1 CATTTCAAAGCCCACAC-AAGTCGGTGGCAACT
* *
517878 CATTTTAAAGCCCACACAAGTCAGTGGCAAC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
*** * *
517909 CTATTTCAAAGCCCATGTAAGTCGATGGCAACC
1 C-ATTTCAAAGCCCACACAAGTCGGTGGCAACT
517942 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
*
517970 C-TTTCCAAAG-CC-CACAAGTCAGTGGC-AC-
1 CATTT-CAAAGCCCACACAAGTCGGTGGCAACT
* *
517998 CCTTTCAAAG-CC-CACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
518026 CCTTTCCAAG-CC-CACAAGTTGGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * *
518056 --TTTCAAAGCCTACGC--GTCAGTGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
** **
518084 --TTTCAAAG-CC-CATGAGTTAGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * * *
518110 CCTTCCAAAG-CC-CACAAGTCAGTAG-AA-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
518138 CCTTTCAAAG-CC-CACAAGTCAGTGGC-A-T
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * * * *
518166 CCTTTCAATG-TC-CACAAGTCAGTTGC-AC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* ** *
518194 CCTTTCAAAG-CC-CACAAGTTAGTGGC-GC-
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* *
518222 CATTTCAAAG-CC-TACAAGTCAGTGGC-ACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * * *
518251 CTTTTCAAAG-CC-CACAAGCCAGTGGTAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * * *
518281 CTTTTAAAAGCCCACACGAGTCGATGGCAACT
1 CATTTCAAAGCCCACACAAGTCGGTGGCAACT
* * * *
518313 CTTTTCGAAGCTCACAAAAGT
1 CATTTCAAAGCCCACACAAGT
518334 TAGTAGCACC
Statistics
Matches: 1247, Mismatches: 155, Indels: 96
0.83 0.10 0.06
Matches are distributed among these distances:
26 2 0.00
27 5 0.00
28 361 0.29
29 32 0.03
30 118 0.09
31 18 0.01
32 649 0.52
33 62 0.05
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (32 bp):
CATTTCAAAGCCCACACAAGTCGGTGGCAACT
Found at i:517501 original size:28 final size:28
Alignment explanation
Indices: 516484--518296 Score: 709
Period size: 32 Copynumber: 60.8 Consensus size: 28
516474 CATAACTCCT
* * *
516484 TGGCACTCTTTT-AAAGTCCACAACTCCG
1 TGGCAC-CTTTTCAAAGCCCACAAGTCAG
* * *
516512 TGGCACCCTTTT--AAGTCCACAACTCTG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
** * *
516539 TGGCACTCTTTT-AAAGTTCACAACTCCG
1 TGGCAC-CTTTTCAAAGCCCACAAGTCAG
* * * *
516567 TGGCGCCCTTTT--AAGTCCACAATTCCG
1 TGGC-ACCTTTTCAAAGCCCACAAGTCAG
* * * *
516594 TGGCACCCTTTTTAAAGTCCACAACTCCG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * *
516623 TGGCACCCTTTT--AAGTCCACAACTCTG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * * *
516650 TGGCACCCTTTT--AAGTCCATAACTCCG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * *
516677 TGGCACCCTTTT--AAGTCCACAACTCCG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * * *
516704 TGCCACCCTTTT-AAAGTCCACAACTCCG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * *
516732 TGGCACCCTTTT-AAAGTCCACAACTCCG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* *
516760 TGGCACCCTTTT-AAAGTCCACAACTTC-G
1 TGGCA-CCTTTTCAAAGCCCACAA-GTCAG
* * *
516788 TGGCACCCTTTT--AAGTCCACAACTCCG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * *
516815 TGGCATCCTTTT--AAGTCCACAACTCCG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* *
516842 TGGCAACACCCATTTCAAAGCCCATACAAGTCGG
1 TGG---CA-CCTTTTCAAAGCCC--ACAAGTCAG
* **
516876 TGGCAACTCATTTCAAAGCCCACACAAGTTGG
1 TGGC-AC-CTTTTCAAAG-CC-CACAAGTCAG
**
516908 TGGCAACCTATTTCAAAGTCCACACAAGTTGG
1 TGGC-ACCT-TTTCAAAG-CC-CACAAGTCAG
**
516940 TGGCAACCCATTTT-AAAGCCCACACAAGTTGG
1 TGGC-A-CC-TTTTCAAAG-CC-CACAAGTCAG
* * * **
516972 TGGCAAGTCATTTGAAAGCCCACACAAGTTGG
1 TGGC-A-CCTTTTCAAAG-CC-CACAAGTCAG
** * *
517004 TGGCAAGTTATTTAAAAGCCCACACAAGTCGG
1 TGGC-ACCT-TTTCAAAG-CC-CACAAGTCAG
**
517036 TGGCAACCCATTTT-AAAGCCCACACAAGTTGG
1 TGGC-A-CC-TTTTCAAAG-CC-CACAAGTCAG
** * *
517068 TGGCAAGTTATTTAAAAGCCCACACAAGTCGG
1 TGGC-ACCT-TTTCAAAG-CC-CACAAGTCAG
* **
517100 TGGCAACTTATTTCAAAGCCCACACAAGTTGG
1 TGGC-ACCT-TTTCAAAG-CC-CACAAGTCAG
*
517132 TGGCAACCCATTTCAAAGCCCACACAAGTCAG
1 TGGC-A-CCTTTTCAAAG-CC-CACAAGTCAG
* * **
517164 TGGCAACTCATTTGAAAGCCCACACAAGTTGG
1 TGGC-AC-CTTTTCAAAG-CC-CACAAGTCAG
**
517196 TGGCAACCTATTTCAAAGCCCACACAAGTTGG
1 TGGC-ACCT-TTTCAAAG-CC-CACAAGTCAG
* **
517228 TGGCAACCCATTTCAAAGCCCACACAAGTTGG
1 TGGC-A-CCTTTTCAAAG-CC-CACAAGTCAG
* * * *
517260 TGGCAAGTCATTTGAAAGCCCACACAAGTCGG
1 TGGC-A-CCTTTTCAAAG-CC-CACAAGTCAG
* * *
517292 TGGCAAGTCATTTCAAAGCCCATACAAGTCGG
1 TGGC-A-CCTTTTCAAAGCCC--ACAAGTCAG
517324 TGGCAACTCATTTT-AAAGCCCACATAAGTCAG
1 TGGC-AC-C-TTTTCAAAGCCCAC--AAGTCAG
*
517356 TGGCAACTCATTTCAAAGCCCACACAAGTCAG
1 TGGC-AC-CTTTTCAAAG-CC-CACAAGTCAG
* *
517388 TGGCAACCCATTTCAAAGACCACACAAGTCGG
1 TGGC-A-CCTTTTCAAAG-CC-CACAAGTCAG
* *
517420 TGGAAACCTATTTCAAAGCCCACACAAGTCGG
1 TGG-CACCT-TTTCAAAG-CC-CACAAGTCAG
* * *
517452 TGGCAACCCATTTCAAAGCCCATAAGTCGG
1 TGGC-A-CCTTTTCAAAGCCCACAAGTCAG
*
517482 TGGCATCTTTTCAAAGCCCACAAGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
*
517510 TGGCACCCTTTCAAAGCCCACAAGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
* *
517538 TGGCATCCTTTT-TAAGCCCACAAGTTAG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* ** *
517566 TGGCAACTCATTTCAAAGCCCACGCGTCGG
1 TGGC-AC-CTTTTCAAAGCCCACAAGTCAG
* **
517596 TGGCAACCCATTTCAAAGCCCACACAAAGTTGG
1 TGGC-A-CCTTTTCAAAG-CC-CAC-AAGTCAG
* *
517629 TGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 TGGC-A-CCTTTTCAAAG-CC-CACAAGTCAG
* *
517661 TGGAAACCTATTTCAAAGCCCACACAAGTCGG
1 TGG-CACCT-TTTCAAAG-CC-CACAAGTCAG
* * * *
517693 TGGCAACCCATTTCAAACCCCATAAGTCGG
1 TGGC-A-CCTTTTCAAAGCCCACAAGTCAG
* *
517723 TAGCATCTTTTCAAAGCCCACAAGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
*
517751 TGGCACCCTTTCAAAGCCCACAAGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
* * *
517779 TGGCATCGTTTT-TAAGCCCACAAGTTAG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* ** *
517807 TGGCAACTCATTTCAAAGCCCACGCGTCGG
1 TGGC-AC-CTTTTCAAAGCCCACAAGTCAG
* **
517837 TGGCAACCCATTTCAAAGCCCACACAAAGTTGG
1 TGGC-A-CCTTTTCAAAG-CC-CAC-AAGTCAG
517870 TGGCAACCCATTTT-AAAGCCCACACAAGTCAG
1 TGGC-A-CC-TTTTCAAAG-CC-CACAAGTCAG
*
517902 TGGCAACCTATTTCAAAGCCCATGTAAGTC-G
1 TGGC-ACCT-TTTCAAAGCCCA--CAAGTCAG
* *
517933 ATGGCAACCCATTTCAAAGCCCACAAGTCGG
1 -TGGC-A-CCTTTTCAAAGCCCACAAGTCAG
* *
517964 TGGCATCTTTCCAAAGCCCACAAGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
*
517992 TGGCACCCTTTCAAAGCCCACAAGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
* **
518020 TGGCATCC-TTTCCAAGCCCACAAGTTGG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * **
518048 TGGCAACTTTTCAAAGCCTACGCGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
* ** *
518076 TGGCAACTTTTCAAAGCCCATGAGTTAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
*
518104 TGGCATCC-TTCCAAAGCCCACAAGTCAG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* *
518132 TAGAATCC-TTTCAAAGCCCACAAGTCAG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* *
518160 TGGCATCC-TTTCAATGTCCACAAGTCAG
1 TGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * *
518188 TTGCACCCTTTCAAAGCCCACAAGTTAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
* * *
518216 TGGCGCCATTTCAAAGCCTACAAGTCAG
1 TGGCACCTTTTCAAAGCCCACAAGTCAG
*
518244 TGGCACTCTTTTCAAAGCCCACAAGCCAG
1 TGGCAC-CTTTTCAAAGCCCACAAGTCAG
* *
518273 TGGTAACTCTTTTAAAAGCCCACA
1 TGG-CAC-CTTTTCAAAGCCCACA
518297 CGAGTCGATG
Statistics
Matches: 1531, Mismatches: 172, Indels: 162
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.00
27 166 0.11
28 474 0.31
29 76 0.05
30 120 0.08
31 39 0.03
32 556 0.36
33 78 0.05
34 19 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TGGCACCTTTTCAAAGCCCACAAGTCAG
Found at i:518581 original size:47 final size:48
Alignment explanation
Indices: 518465--518643 Score: 261
Period size: 48 Copynumber: 3.8 Consensus size: 48
518455 GGCACCTTTA
* *
518465 TTAGCTCAATGTCACTGGCCTTGAATTAGCACATTGTCCACATTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
*
518513 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCA-TTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
* **
518560 TTAGCTCAATGTCGCTAGCCTTGAATTAGCACATTGTTTACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
* * **
518608 TTAGCTCGATGTCGTTGGCCTTGAATGGGCACATTG
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTG
518644 GCACCCCTCT
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 42 0.36
48 76 0.64
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
Found at i:518594 original size:95 final size:95
Alignment explanation
Indices: 518465--518643 Score: 277
Period size: 95 Copynumber: 1.9 Consensus size: 95
518455 GGCACCTTTA
*
518465 TTAGCTCAATGTCACTGGCCTTGAATTAGCACATTGTCCACATTTCCCTTAGCTCAATGTCGCTG
1 TTAGCTCAATGTCACTAGCCTTGAATTAGCACATTGTCCACATTTCCCTTAGCTCAATGTCGCTG
518530 GCCTTGAATCAGCACATTGTCCATTTTCCC
66 GCCTTGAATCAGCACATTGTCCATTTTCCC
* ** * * *
518560 TTAGCTCAATGTCGCTAGCCTTGAATTAGCACATTGTTTACTTTTCCCTTAGCTCGATGTCGTTG
1 TTAGCTCAATGTCACTAGCCTTGAATTAGCACATTGTCCACATTTCCCTTAGCTCAATGTCGCTG
**
518625 GCCTTGAATGGGCACATTG
66 GCCTTGAATCAGCACATTG
518644 GCACCCCTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 75 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (95 bp):
TTAGCTCAATGTCACTAGCCTTGAATTAGCACATTGTCCACATTTCCCTTAGCTCAATGTCGCTG
GCCTTGAATCAGCACATTGTCCATTTTCCC
Found at i:525611 original size:21 final size:20
Alignment explanation
Indices: 525587--525633 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
525577 TTCTATAATT
*
525587 TGTATCAATACAAGAAGTGAA
1 TGTATCAATAC-AGAACTGAA
* *
525608 TGTATCGATACATAACTGAA
1 TGTATCAATACAGAACTGAA
525628 TGTATC
1 TGTATC
525634 GATATTGGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCAATACAGAACTGAA
Found at i:528187 original size:27 final size:26
Alignment explanation
Indices: 528133--528188 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
528123 AATCCTTTCC
*
528133 TTTCGAGGGGATACTCTAACCCTATT
1 TTTCGAGGGGATACTCTAACCCCATT
*
528159 TTTCTGAGGGGATACTCTAACCCCGTT
1 TTTC-GAGGGGATACTCTAACCCCATT
528186 TTT
1 TTT
528189 AAACTTGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (26 bp):
TTTCGAGGGGATACTCTAACCCCATT
Found at i:533339 original size:13 final size:13
Alignment explanation
Indices: 533316--533358 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
533306 TTTAAACTAT
533316 TTAAA-AATAAAA
1 TTAAATAATAAAA
533328 TTAAATAATAAAA
1 TTAAATAATAAAA
**
533341 TCCAATAA-AAAA
1 TTAAATAATAAAA
533353 TTAAAT
1 TTAAAT
533359 TTAATCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 13 0.50
13 13 0.50
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (13 bp):
TTAAATAATAAAA
Done.