Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 2 of 150
Found at i:378190 original size:8 final size:8
Alignment explanation
Indices: 378159--378190 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
378149 TCAATGTCAT
378159 AAAAAAAG
1 AAAAAAAG
378167 CAAAAAAAG
1 -AAAAAAAG
378176 AAAAAAAG
1 AAAAAAAG
378184 AAAAAAA
1 AAAAAAA
378191 CTATACCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:378385 original size:29 final size:29
Alignment explanation
Indices: 378351--378443 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
378341 GAATAGTTAA
378351 TGACCATTTTGTAACTTTTCATAGTTGGG
1 TGACCATTTTGTAACTTTTCATAGTTGGG
***** *
378380 TGACCAAAAAAATAA-TTTTACTAATAGTTAGG
1 TGACC-ATTTTGTAACTTTT-C--ATAGTTGGG
* *
378412 TGATCATTTTGTAACTTTTCATAATTGGG
1 TGACCATTTTGTAACTTTTCATAGTTGGG
378441 TGA
1 TGA
378444 TTAAAAAAGA
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
29 19 0.42
30 5 0.11
31 5 0.11
32 16 0.36
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (29 bp):
TGACCATTTTGTAACTTTTCATAGTTGGG
Found at i:379841 original size:16 final size:17
Alignment explanation
Indices: 379812--379851 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
379802 CGTTTGGTTT
379812 GCTGTAATCGAATA-AA
1 GCTGTAATCGAATAGAA
379828 GCTGTAAT-GAAATAGAA
1 GCTGTAATCG-AATAGAA
379845 -CTGTAAT
1 GCTGTAAT
379852 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.05
16 19 0.86
17 2 0.09
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (17 bp):
GCTGTAATCGAATAGAA
Found at i:380206 original size:17 final size:18
Alignment explanation
Indices: 380076--380198 Score: 76
Period size: 18 Copynumber: 6.9 Consensus size: 18
380066 TTATTATTAA
380076 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
380094 ATATAATTTAATAAAACT
1 ATATAATTTAATAAAAAT
* ****
380112 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
*
380131 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * **
380149 -CATAATAT-ATAGTTAAT
1 ATATAATTTAATA-AAAAT
380166 A-ATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
380183 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
380199 TTCTTAATAT
Statistics
Matches: 76, Mismatches: 20, Indels: 18
0.67 0.18 0.16
Matches are distributed among these distances:
15 1 0.01
16 4 0.05
17 19 0.25
18 38 0.50
19 8 0.11
20 3 0.04
21 3 0.04
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:380238 original size:88 final size:89
Alignment explanation
Indices: 380078--380247 Score: 315
Period size: 89 Copynumber: 1.9 Consensus size: 89
380068 ATTATTAAAT
380078 ATAATTTAATAAAAATATATAATTTAATAAAACTCTTAATATTAAATATTCTTATATGAATTTAC
1 ATAATTTAATAAAAATATATAATTTAATAAAACTCTTAATATTAAATATTCTTATATGAATTTAC
380143 TAAAATCATAATATATAGTTAATA
66 TAAAATCATAATATATAGTTAATA
* *
380167 ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTAC
1 ATAATTTAATAAAAATATATAATTTAATAAAACTCTTAATATTAAATATTCTTATATGAATTTAC
380231 TAAAATCATAATATATA
66 TAAAATCATAATATATA
380248 ATACTATAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
88 39 0.49
89 40 0.51
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (89 bp):
ATAATTTAATAAAAATATATAATTTAATAAAACTCTTAATATTAAATATTCTTATATGAATTTAC
TAAAATCATAATATATAGTTAATA
Found at i:383276 original size:15 final size:15
Alignment explanation
Indices: 383253--383283 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
383243 TGAAAATGAC
383253 CTAAAATTTGCAAAT
1 CTAAAATTTGCAAAT
*
383268 CTAACATTTGCAAAT
1 CTAAAATTTGCAAAT
383283 C
1 C
383284 AGCTGTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
CTAAAATTTGCAAAT
Found at i:384168 original size:23 final size:23
Alignment explanation
Indices: 384100--384168 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
384090 TTAATTTTAA
*
384100 ATTAA-ATAAAATTTTAAAATTT
1 ATTAATATAAAATTATAAAATTT
*
384122 AATT-ATA-AAAATATCTAAAA--T
1 -ATTAATATAAAAT-TATAAAATTT
384143 ATTAATATAAAATTATAAAATTT
1 ATTAATATAAAATTATAAAATTT
384166 ATT
1 ATT
384169 TTTCTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
20 3 0.08
21 10 0.26
22 11 0.29
23 14 0.37
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTAATATAAAATTATAAAATTT
Found at i:384980 original size:24 final size:25
Alignment explanation
Indices: 384944--385004 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
384934 ATAAAAAATA
384944 ACCAAAATATTAT-CTTTTTTATTT
1 ACCAAAATATTATACTTTTTTATTT
* *
384968 ACCAAAATGTTATAAATTTTTTTATTT
1 ACCAAAATATTAT--ACTTTTTTATTT
384995 ACCAAAATAT
1 ACCAAAATAT
385005 ACAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.39
27 19 0.61
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (25 bp):
ACCAAAATATTATACTTTTTTATTT
Found at i:385408 original size:20 final size:20
Alignment explanation
Indices: 385374--385411 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
385364 ATTTTATTAT
*
385374 TAAAGTAAATATATTTTACC
1 TAAAGTAAAGATATTTTACC
*
385394 TAAAGTAAAGCTATTTTA
1 TAAAGTAAAGATATTTTA
385412 AAAAGTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
TAAAGTAAAGATATTTTACC
Found at i:387976 original size:50 final size:50
Alignment explanation
Indices: 387870--388110 Score: 277
Period size: 50 Copynumber: 4.7 Consensus size: 50
387860 CATGCCAAAA
* * ** * * *
387870 CCATGTCCCAGAAATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGGTGCCAATG
*
387921 CCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAATG
* *
387971 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCTC-ATG
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGC-CAATG
* *
388021 TCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCAATG
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG-TGCCAATG
* *
388077 CCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCT
388111 TTACCCAAAT
Statistics
Matches: 164, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
50 94 0.57
51 27 0.16
53 2 0.01
54 1 0.01
55 3 0.02
56 37 0.23
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAATG
Found at i:388051 original size:100 final size:104
Alignment explanation
Indices: 387861--388110 Score: 328
Period size: 100 Copynumber: 2.4 Consensus size: 104
387851 TGATAATAAC
** * ** * *
387861 ATGCCAAAACCATGTCCCAGAAATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
387926 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
387963 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCTCATGTCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
388027 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
388068 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
388111 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
100 48 0.37
101 34 0.26
103 3 0.02
104 1 0.01
105 2 0.02
106 41 0.32
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (104 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:388126 original size:106 final size:100
Alignment explanation
Indices: 387917--388110 Score: 271
Period size: 106 Copynumber: 1.9 Consensus size: 100
387907 TGTTGGTGCC
* *
387917 CATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAG
1 CATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAATGCCATGTCCCAG
* **
387982 ACATGGTCTTACATGGGACCTCTCGTCTCGGTGCT
66 ACATGGTCTTACATGGGACCTCTCGTCCCAATGCT
*
388017 CATGTCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCAATGCCATG
1 CATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-AGG-TGCCAATGCCATG
*
388082 TCCCAGACATGGTCTTACATGGGATCTCT
60 TCCCAGACATGGTCTTACATGGGACCTCT
388111 TTACCCAAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
100 37 0.44
103 3 0.04
104 1 0.01
105 2 0.02
106 41 0.49
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (100 bp):
CATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAATGCCATGTCCCAG
ACATGGTCTTACATGGGACCTCTCGTCCCAATGCT
Found at i:389896 original size:27 final size:27
Alignment explanation
Indices: 389835--389896 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
389825 TTTAGTCCTA
*
389835 TGCCGCCAATCTCTTTGCCACCTTTGG
1 TGCCGCCAATCACTTTGCCACCTTTGG
*
389862 T-CAGGCCAATCACTTTGCCACCTTTGG
1 TGC-CGCCAATCACTTTGCCACCTTTGG
389889 TGCCGCCA
1 TGCCGCCA
389897 CAGGTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.15, C:0.37, G:0.19, T:0.29
Consensus pattern (27 bp):
TGCCGCCAATCACTTTGCCACCTTTGG
Found at i:389918 original size:16 final size:17
Alignment explanation
Indices: 389897--389928 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
389887 GGTGCCGCCA
389897 CAGGTTTTT-TTTTTTG
1 CAGGTTTTTGTTTTTTG
389913 CAGGTTTTTGTTTTTT
1 CAGGTTTTTGTTTTTT
389929 TTGGTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.06, C:0.06, G:0.19, T:0.69
Consensus pattern (17 bp):
CAGGTTTTTGTTTTTTG
Found at i:390739 original size:57 final size:56
Alignment explanation
Indices: 390632--390741 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 56
390622 ACCAAATCGA
* **
390632 ACAAAAAAAAAAGGTACCAAATTAGGGGAAAAAATGTCAAGTTTGGATACCAACTTGG
1 ACAAAAAAAAAAGGTACCAAATTA--GGAAAAAATATCAAGTTCAGATACCAACTTGG
*
390690 ACAAAAAAAAATTAGGTACCAAATTA-GAAAAAATATCAAGTTCATATACCAA
1 ACAAAAAAAAA--AGGTACCAAATTAGGAAAAAATATCAAGTTCAGATACCAA
390742 ATGTTATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 22 0.48
58 11 0.24
60 13 0.28
ACGTcount: A:0.53, C:0.13, G:0.15, T:0.20
Consensus pattern (56 bp):
ACAAAAAAAAAAGGTACCAAATTAGGAAAAAATATCAAGTTCAGATACCAACTTGG
Found at i:393710 original size:15 final size:15
Alignment explanation
Indices: 393685--393722 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
393675 CTAAACTTAT
*
393685 TTATATAAATTAGTAA
1 TTATTTAAATTA-TAA
393701 TT-TTTAAATTATAA
1 TTATTTAAATTATAA
393715 TTATTTAA
1 TTATTTAA
393723 TATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 5 0.25
15 13 0.65
16 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATTTAAATTATAA
Found at i:394219 original size:31 final size:31
Alignment explanation
Indices: 394183--394261 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
394173 AAAAAACAAA
* *
394183 CAAACTCATGTACCAAACTGAATATTGATG-
1 CAAACTCATGTACCAAACTGAATATTAAAGT
* * *
394213 CTAAACTCAAGTACCGATCTGAATATTAAAGT
1 C-AAACTCATGTACCAAACTGAATATTAAAGT
394245 CAAACTCATGTACCAAA
1 CAAACTCATGTACCAAA
394262 TCGAGAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (31 bp):
CAAACTCATGTACCAAACTGAATATTAAAGT
Found at i:399335 original size:32 final size:32
Alignment explanation
Indices: 399281--399346 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
399271 CTTGCTTGAA
*
399281 GACGAAATACGGTTCTTTTCGTGACTTGTTGC
1 GACGAAATACGCTTCTTTTCGTGACTTGTTGC
*
399313 GACGAAATATGCTT-TTTCTCGTGACTTGTTGC
1 GACGAAATACGCTTCTTT-TCGTGACTTGTTGC
399345 GA
1 GA
399347 AATGAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (32 bp):
GACGAAATACGCTTCTTTTCGTGACTTGTTGC
Found at i:410083 original size:2 final size:2
Alignment explanation
Indices: 410066--410105 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
410056 TCTCTACTGA
* *
410066 AT AT GT AT AT AC 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
410106 TAGTTCTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:417432 original size:28 final size:28
Alignment explanation
Indices: 417400--417456 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
417390 CAAGAAAAGA
417400 TAAATTCAAACTCTAGTAACGATATTAT
1 TAAATTCAAACTCTAGTAACGATATTAT
417428 TAAATTCAAACTCTAGTAACGATATTAT
1 TAAATTCAAACTCTAGTAACGATATTAT
417456 T
1 T
417457 GAGAAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (28 bp):
TAAATTCAAACTCTAGTAACGATATTAT
Found at i:423671 original size:72 final size:72
Alignment explanation
Indices: 423585--423728 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
423575 AACTGCTCCG
*
423585 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGGCTCAAGCTCAAGTAG
1 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGTAG
423650 GAATGCA
66 GAATGCA
* *
423657 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAATCAAGCTCAGCCTCAAGCTCAAGTAG
1 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGTAG
423722 GAATGCA
66 GAATGCA
423729 TATGAAACAC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (72 bp):
AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGTAG
GAATGCA
Found at i:426769 original size:3 final size:3
Alignment explanation
Indices: 426761--426786 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
426751 CGTTCTTTAC
426761 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
426787 ATATATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:428984 original size:30 final size:31
Alignment explanation
Indices: 428924--428988 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 31
428914 ACTTAACAAC
428924 CAAATGCCTCTAAAATAATAAAAAAAAATTAA
1 CAAATGCCTCTAAAATAAT-AAAAAAAATTAA
* *
428956 CAAATGCCTTTAAAATAAT-AACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAAATTAA
428986 CAA
1 CAA
428989 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 13 0.42
32 18 0.58
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.23
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAAAAAAAATTAA
Found at i:434887 original size:27 final size:27
Alignment explanation
Indices: 434857--434918 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
434847 CCTATCAGGT
*
434857 AGGCGTCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
* *
434884 AGGCACCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
434911 AGGCGCCA
1 AGGCGCCA
434919 TTACTAGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.32, T:0.16
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:435104 original size:21 final size:21
Alignment explanation
Indices: 435080--435122 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
435070 AATAAACACC
435080 AAAAAAT-TTTTAAAAATAAA
1 AAAAAATATTTTAAAAATAAA
*
435100 AAAAAGTATTTTAAAAATAAA
1 AAAAAATATTTTAAAAATAAA
435121 AA
1 AA
435123 TTAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAAATATTTTAAAAATAAA
Found at i:435411 original size:19 final size:19
Alignment explanation
Indices: 435389--435426 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
435379 AATTTAATTT
*
435389 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
435408 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
435427 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:435556 original size:27 final size:27
Alignment explanation
Indices: 435525--435596 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
435515 TACCGACATT
* *
435525 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
435552 CAATATTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
*
435579 CAATATTCATATAAAATT
1 CAATATTCATACAAAATT
435597 GCAATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:435669 original size:22 final size:24
Alignment explanation
Indices: 435636--435807 Score: 148
Period size: 27 Copynumber: 7.1 Consensus size: 24
435626 ATAAATTATC
*
435636 TATATTTAGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
435660 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
*
435684 TATAATTTTGTATGAATATTGCAAT
1 TAT-ATTTTGTATGAATATTGTAAT
435709 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
435733 TATAATTTTGTATGAATATTGTAATGT
1 TAT-ATTTTGTATGAATATTGTAA--T
*
435760 CGGTATATATTG--T-AATATTGTAA-
1 ---TATATTTTGTATGAATATTGTAAT
435783 T-T-TTTTGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
435805 TAT
1 TAT
435808 TTTATAATTA
Statistics
Matches: 123, Mismatches: 5, Indels: 41
0.73 0.03 0.24
Matches are distributed among these distances:
18 4 0.03
19 1 0.01
20 2 0.02
21 10 0.08
22 33 0.27
23 4 0.03
24 8 0.07
25 6 0.05
26 12 0.10
27 35 0.28
29 5 0.04
30 3 0.02
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (24 bp):
TATATTTTGTATGAATATTGTAAT
Found at i:435698 original size:49 final size:49
Alignment explanation
Indices: 435639--435810 Score: 235
Period size: 49 Copynumber: 3.6 Consensus size: 49
435629 AATTATCTAT
*
435639 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
435688 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
* ** *
435737 ATTTTGTATGAATATTGTAA--TGTCGGTAT--ATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
435782 ATTTTTTGTATGAATATTGTAATTATTTT
1 A--TTTTGTATGAATATTGTAATTTTTTT
435811 ATAATTAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
45 16 0.15
47 25 0.23
49 67 0.62
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:435833 original size:22 final size:21
Alignment explanation
Indices: 435808--435880 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
435798 TTGTAATTAT
435808 TTTATAATTAATTTGTTAGTAA
1 TTTATAATTAA-TTGTTAGTAA
**
435830 TTTAGGATT-A-TGTTA-TAAA
1 TTTATAATTAATTGTTAGT-AA
* *
435849 TTTATTAGTAACTTGTTAGTAA
1 TTTATAATTAA-TTGTTAGTAA
435871 TTTAGTAATT
1 TTTA-TAATT
435881 TATTACTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 11
0.68 0.12 0.20
Matches are distributed among these distances:
18 1 0.03
19 13 0.34
20 1 0.03
21 1 0.03
22 18 0.47
23 4 0.11
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (21 bp):
TTTATAATTAATTGTTAGTAA
Found at i:436143 original size:27 final size:28
Alignment explanation
Indices: 436105--436181 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
436095 CCGGCCCGGC
*
436105 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
436132 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
436159 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
436182 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:436253 original size:29 final size:30
Alignment explanation
Indices: 436220--436276 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
436210 TACTAACCCG
*
436220 AAAAAGTATAAAATTA-TATTTTATTCAAA
1 AAAAAATATAAAATTATTATTTTATTCAAA
* **
436249 AAAAAATTTATTATTATTATTTTATTCA
1 AAAAAATATAAAATTATTATTTTATTCA
436277 TTGGCGCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (30 bp):
AAAAAATATAAAATTATTATTTTATTCAAA
Found at i:437833 original size:40 final size:42
Alignment explanation
Indices: 437756--437833 Score: 99
Period size: 39 Copynumber: 1.9 Consensus size: 42
437746 GAACCAATTT
* * *
437756 AAATTATATATTTAAATAGTTTATTTGAATTTAAAATTCAAC
1 AAATTAAATATTTAAATAGATTATTTGAAATTAAAATTCAAC
437798 AAATTAAAT-TTTAAATA-ATTA-TTGAAATTAGAAATT
1 AAATTAAATATTTAAATAGATTATTTGAAATTA-AAATT
437834 TATTTTCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 8 0.25
40 8 0.25
41 8 0.25
42 8 0.25
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (42 bp):
AAATTAAATATTTAAATAGATTATTTGAAATTAAAATTCAAC
Found at i:438853 original size:24 final size:24
Alignment explanation
Indices: 438825--438877 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
438815 TTAGTAGGTC
* * *
438825 AAATAAACTGTGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
438849 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
438873 AAATA
1 AAATA
438878 TTCTAGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:439518 original size:13 final size:13
Alignment explanation
Indices: 439491--439532 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
439481 CAGAACTCAA
439491 GTTTA-AGTTCAAG
1 GTTTAGAGTTC-AG
439504 GTTTAGA-TTCGAG
1 GTTTAGAGTTC-AG
439517 GTTTAGAGTTCAG
1 GTTTAGAGTTCAG
439530 GTT
1 GTT
439533 CGGGTTCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.40
Consensus pattern (13 bp):
GTTTAGAGTTCAG
Found at i:442462 original size:22 final size:20
Alignment explanation
Indices: 442443--442505 Score: 78
Period size: 18 Copynumber: 3.3 Consensus size: 20
442433 TAATAAATAC
442443 TAAAAATTTATTTTAAAAAT
1 TAAAAATTTATTTTAAAAAT
**
442463 TAAAAAAATATTTT-AAAAT
1 TAAAAATTTATTTTAAAAAT
*
442482 TAAAAA-ATATTTT-AAAAT
1 TAAAAATTTATTTTAAAAAT
442500 TAAAAA
1 TAAAAA
442506 AATAAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 18 0.44
19 11 0.27
20 12 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATTTATTTTAAAAAT
Found at i:442480 original size:19 final size:19
Alignment explanation
Indices: 442451--442509 Score: 102
Period size: 18 Copynumber: 3.1 Consensus size: 19
442441 ACTAAAAATT
442451 TATTTTAAAAATTAAAAAAA
1 TATTTT-AAAATTAAAAAAA
442471 TATTTTAAAATT-AAAAAA
1 TATTTTAAAATTAAAAAAA
442489 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
442508 TA
1 TA
442510 AATATATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.47
19 14 0.37
20 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATTTTAAAATTAAAAAAA
Found at i:444798 original size:9 final size:9
Alignment explanation
Indices: 444784--444859 Score: 125
Period size: 9 Copynumber: 8.4 Consensus size: 9
444774 TTTGGTTAAA
444784 AATTAACCG
1 AATTAACCG
*
444793 AATTAACCA
1 AATTAACCG
444802 AATTAACCG
1 AATTAACCG
444811 AATTAACCG
1 AATTAACCG
444820 AATTAACCG
1 AATTAACCG
444829 AATTAACCG
1 AATTAACCG
*
444838 AATTACCCG
1 AATTAACCG
*
444847 AATTAACCT
1 AATTAACCG
444856 AATT
1 AATT
444860 GAATCATACA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:446428 original size:19 final size:20
Alignment explanation
Indices: 446394--446435 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
446384 AATTTTTAAT
446394 TTTATTGTATATTATAATAA
1 TTTATTGTATATTATAATAA
* *
446414 TTTATTTTA-ATTATAATTA
1 TTTATTGTATATTATAATAA
446433 TTT
1 TTT
446436 GAATGTATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATTGTATATTATAATAA
Found at i:449422 original size:329 final size:329
Alignment explanation
Indices: 448824--449475 Score: 1286
Period size: 329 Copynumber: 2.0 Consensus size: 329
448814 GAAAGCGGAC
*
448824 TTTAACAGAAGCAGAATTCCTTTAATCACTTAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
1 TTTAACAGAAGCAGAATTCCTTTAATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
448889 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
66 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
448954 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
131 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
449019 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
196 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
449084 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAAGT
261 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAAGT
449149 TTTT
326 TTTT
*
449153 TTTAACAGAAGCAGAATTCCTTTGATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
1 TTTAACAGAAGCAGAATTCCTTTAATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
449218 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
66 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
449283 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
131 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
449348 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
196 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
449413 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAA
261 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAA
449476 TTTATTATAT
Statistics
Matches: 321, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
329 321 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (329 bp):
TTTAACAGAAGCAGAATTCCTTTAATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAAGT
TTTT
Found at i:452675 original size:39 final size:39
Alignment explanation
Indices: 452616--452694 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
452606 TTCTTATATT
452616 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
1 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
* *
452655 AAAATTCGAATCTAGTAGTCTTGAGTTTTAAGGTGTTCA
1 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
452694 A
1 A
452695 GAAAATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (39 bp):
AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
Found at i:457543 original size:4 final size:4
Alignment explanation
Indices: 457534--457564 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
457524 TTAAAACTTC
457534 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
457565 CCTGCAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:459616 original size:3 final size:3
Alignment explanation
Indices: 459610--459644 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
459600 ATTGTCTGGT
459610 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
459645 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:461028 original size:2 final size:2
Alignment explanation
Indices: 461021--461054 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
461011 TAACTCTTTA
461021 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
461055 TTAGGTTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:467000 original size:4 final size:4
Alignment explanation
Indices: 466991--467047 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
466981 TTAAAACTTC
466991 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
467039 ATGT ATGT A
1 ATGT ATGT A
467048 CCTGCAAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:468849 original size:37 final size:37
Alignment explanation
Indices: 468762--468849 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 37
468752 TTTTTTATGT
* * *
468762 AAAACAAATTTAAAAAATATAATATATCAAATACATTA
1 AAAATAAA-TTAAAAAATATAATATATCAAACAAATTA
*
468800 AAAAT--ATT--AAAATA-AATATTTCCAAACAAATTA
1 AAAATAAATTAAAAAATATAATATAT-CAAACAAATTA
468833 AAAATAAATTAAAAAAT
1 AAAATAAATTAAAAAAT
468850 TATTTATACT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
32 6 0.15
33 20 0.49
35 5 0.12
36 1 0.02
37 5 0.12
38 4 0.10
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (37 bp):
AAAATAAATTAAAAAATATAATATATCAAACAAATTA
Found at i:470586 original size:13 final size:13
Alignment explanation
Indices: 470568--470601 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
470558 TTTAAATTAA
*
470568 ACTTTTCAAAAGT
1 ACTTTTCAAAAAT
470581 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
470594 ACTTTTCA
1 ACTTTTCA
470602 CAATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:474805 original size:280 final size:282
Alignment explanation
Indices: 473987--474847 Score: 732
Period size: 280 Copynumber: 3.0 Consensus size: 282
473977 GGAATGTTGC
* * *
473987 TTGAAAATGAAACCTAGCTTGTACTAAAGCTGCATGTAAATTTGA-ACTGGAGACTGGAACAAA-
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTT-ACACTGGAGAATGGAACAAAG
* * * ** * *
474050 AGATCATGCAAGTTATATAGTGGG-A-ATCATTTAACAGATTATGAAGCTTATATCTTCAATGAG
65 A-ATCATGCAAGTTATATAATGGGAATATCATCTAA-TGATCGTGAAGCTTACATCTTC--TGAC
* * * ****** * * *
474113 T-TTTTTATTCATTAGTTACAGTGAAAGAGTCCCTGTTTCACTTCGATTTGTTCTTGCTGCACAT
126 TGTCTTT-TT-ATTAGTAACAGTGAAGGAGGGAAACTCTAACTTCAATTTGTTCTTGCTGCACAT
* * * * ** ** **
474177 TGGTTCTAGGCCTGCTTGTGTTCTTTCACTACAGTTTAGCTTCTTTCT-TTGTATT-AGCTAGAA
189 TGGTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTATTTGTATTGGCTTCCCCT-GTG
** * * *
474240 T-CT-AGTGAAA-TTGCATTTTGCCCATGGTGAAATGTT
253 TGCTCA-T-AAACTAACA-CTTGCTC-T--TGCAA---T
* *
474276 GCTTGAACATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACTCTGGAGAATGGAACAAA
1 --TTGAAAATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACACTGGAGAATGGAACAAA
474341 GAATCATGCAAGTTATATAATGGGAAATATCATCTAATGGATCGTGAAGCTTACATCTTCTGACT
64 GAATCATGCAAGTTATATAATGGG-AATATCATCTAAT-GATCGTGAAGCTTACATCTTCTGACT
* * * * *
474406 TTCTTTTTAATTAGTAACATTGGAGGAGGGACACTTTAACTTCAATTTGTTCTTGCTGCACATTG
127 GTCTTTTT-ATTAGTAACAGTGAAGGAGGGAAACTCTAACTTCAATTTGTTCTTGCTGCACATTG
* * *
474471 GTTCTAGGTCTGCTTGTGTTCTTTCACTAGTGGTTAGCTTCTTTGTATTGGCTTCCCCTGTGTGC
191 GTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTATTTGTATTGGCTTCCCCTGTGTGC
474536 TCATAAACTAACACTTGCTCTTGCAAT
256 TCATAAACTAACACTTGCTCTTGCAAT
* * * *
474563 TTGAAAATGAAACCTAGCTTGTACTAAAGCTGCATGTTAATTTGCACTGGAGAATGGAACAAAGA
1 TTGAAAATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACACTGGAGAATGGAACAAAGA
*
474628 ATCATGCAAGTTATATAAT-GG-A-ATCATTTAAT-ATACTGTGAAGCTTACATCTT-TGA-TGA
66 ATCATGCAAGTTATATAATGGGAATATCATCTAATGAT-C-GTGAAGCTTACATCTTCTGACT--
* * * ** *
474687 GTGTATTTT-TTAGTATCAGTGAAGGAGGGATAAC-CTCACTTGTATTTGTTCTTGTTGCACATT
127 GTCT-TTTTATTAGTAACAGTGAAGGAGGGA-AACTCTAACTTCAATTTGTTCTTGCTGCACATT
** ** * *
474750 GGTTCTCTGCCTGCTTGTGTTCTTTTGCTACTGTTTAGCTTATTTGTATTGGCTTCCCCTTTGTG
190 GGTTCTAGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTATTTGTATTGGCTTCCCCTGTGTG
* * * *
474815 TTCATAAACTGACACTTTCTCTTGTAAT
255 CTCATAAACTAACACTTGCTCTTGCAAT
474843 TTGAA
1 TTGAA
474848 GATTAAGAGA
Statistics
Matches: 480, Mismatches: 72, Indels: 47
0.80 0.12 0.08
Matches are distributed among these distances:
279 3 0.01
280 131 0.27
281 29 0.06
282 5 0.01
284 2 0.00
285 78 0.16
287 1 0.00
290 5 0.01
291 77 0.16
292 94 0.20
293 20 0.04
294 34 0.07
295 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (282 bp):
TTGAAAATGAAACCTAACTTGTACCAAAGCTGCATGTAAATTTACACTGGAGAATGGAACAAAGA
ATCATGCAAGTTATATAATGGGAATATCATCTAATGATCGTGAAGCTTACATCTTCTGACTGTCT
TTTTATTAGTAACAGTGAAGGAGGGAAACTCTAACTTCAATTTGTTCTTGCTGCACATTGGTTCT
AGGCCTGCTTGTGTTCTTTCACTACTGGTTAGCTTATTTGTATTGGCTTCCCCTGTGTGCTCATA
AACTAACACTTGCTCTTGCAAT
Found at i:474916 original size:21 final size:22
Alignment explanation
Indices: 474873--474935 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
474863 AGAGAAGGCC
*
474873 AAGAAGGA-AAGGAAGAAAGAA
1 AAGAAGGAGAAGAAAGAAAGAA
474894 AAGAAGGAGAAGAAAG--AGAA
1 AAGAAGGAGAAGAAAGAAAGAA
474914 AA-AACGGGAGAAGAAAGAAAGA
1 AAGAA--GGAGAAGAAAGAAAGA
474936 GATAAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 19 0.53
22 6 0.17
23 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (22 bp):
AAGAAGGAGAAGAAAGAAAGAA
Found at i:476976 original size:125 final size:125
Alignment explanation
Indices: 476672--477023 Score: 451
Period size: 126 Copynumber: 2.8 Consensus size: 125
476662 TAATTTCGAG
** * * * *
476672 TTGACGTTTCTGATAAAATAATATAAAATCGCCTCTAGCAAGATGGTCTTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * * *
476737 AAATTGCGCCCTAGTGAACGCGCTTTTGTTATAGTAGGTTACAGAAGAAATAATTATTTTT
66 AAATTGCGCCCTCGT-AGCGCACTTTTGCTACAGTAGGTTACAGAAGAAATAAATATTTTT
*
476798 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
476863 AAATTGCGGCCTCGTCAGCGCACTTTTGCTACAGTAGG-T-CATGTAAGAAATAAAT-TTTTT
66 AAATTGCGCCCTCGT-AGCGCACTTTTGCTACAGTAGGTTACA-G-AAGAAATAAATATTTTT
* * *
476923 TTGACGTTTCTGAGCAAATAATATAAAATCACTTATAGCAGGATGCTATTTGAGAAGAATTTTTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
476988 AAATCGCGCCCTCGTGGACGCGA-TTTTGCTACAGTA
66 AAATTGCGCCCTCGTAG-CGC-ACTTTTGCTACAGTA
477024 ACATGTTTGG
Statistics
Matches: 200, Mismatches: 22, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
124 3 0.01
125 97 0.49
126 100 0.50
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATTGCGCCCTCGTAGCGCACTTTTGCTACAGTAGGTTACAGAAGAAATAAATATTTTT
Found at i:480194 original size:23 final size:23
Alignment explanation
Indices: 480164--480499 Score: 361
Period size: 23 Copynumber: 14.7 Consensus size: 23
480154 CATTACGTTA
480164 AGGTTAGGGTTTTTAATTGAATTAGGTT
1 AGGTTAGGGTTTTTAATT-AA--A--TT
480192 AGGGTTAGGGTTTTTAA-TAAA--
1 A-GGTTAGGGTTTTTAATTAAATT
*
480213 GGGTTTAGGGTTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
*
480237 AGGCTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
480260 AGGTTAGGGTTTTTAATT-AA--
1 AGGTTAGGGTTTTTAATTAAATT
* *
480280 GGGTTTAGGGTTTTTAATTACATT
1 AGG-TTAGGGTTTTTAATTAAATT
*
480304 AGGCTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
480327 AGGCTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
480350 AAGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
480373 AGGTTAGGGTTTTTAATTTAA--
1 AGGTTAGGGTTTTTAATTAAATT
* *
480394 GGGTTTAGGGTTTTTAATTGAATT
1 AGG-TTAGGGTTTTTAATTAAATT
480418 AGGTTAGGGTTTTTAATT-AA--
1 AGGTTAGGGTTTTTAATTAAATT
* *
480438 GGGTTTAGGGCTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
***
480462 AGGTTAGGGTTTAGGATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
480485 AGGCTAGGGTTTTTA
1 AGGTTAGGGTTTTTA
480500 TTACATGTCA
Statistics
Matches: 265, Mismatches: 27, Indels: 37
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.02
21 44 0.17
22 28 0.11
23 159 0.60
24 8 0.03
25 1 0.00
27 2 0.01
28 2 0.01
29 15 0.06
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.45
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:480250 original size:44 final size:44
Alignment explanation
Indices: 480165--480473 Score: 333
Period size: 44 Copynumber: 6.8 Consensus size: 44
480155 ATTACGTTAA
480165 GGTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAA-TAAAG
1 GGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAAG
* *
480214 GGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAA--G
*
480261 GGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATTACATTA-
1 GGTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTA-A--AG
* * *
480305 GGCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAA--G
* *
480351 AGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAAG
*
480395 GGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTTTTAATT-AAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAAG
*
480439 GGTTTAGGGCTTTTAATTAAATTAGGTTAGGGTTT
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
480474 AGGATTAAAT
Statistics
Matches: 229, Mismatches: 16, Indels: 35
0.82 0.06 0.12
Matches are distributed among these distances:
43 3 0.01
44 82 0.36
45 50 0.22
46 69 0.30
47 6 0.03
49 4 0.02
50 15 0.07
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (44 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAAG
Found at i:480276 original size:67 final size:67
Alignment explanation
Indices: 480194--480473 Score: 333
Period size: 67 Copynumber: 4.2 Consensus size: 67
480184 ATTAGGTTAG
480194 GGTTAGGGTTTTTAA-TAAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
1 GGTTAGGGTTTTTAATTAAAGGG-TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
480258 TTA
65 TTA
*
480261 GGTTAGGGTTTTTAATT-AAGGGTTTAGGGTTTTTAATTACATTAGGCTAGGGTTTTTAATTAAA
1 GGTTAGGGTTTTTAATTAAAGGG-TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
480325 TTA
65 TTA
* ** * *
480328 GGCTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTA
1 GGTTAGGGTTTTTAATTAAA--GGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAA
*
480393 A--G
64 ATTA
* * *
480395 GGTTTAGGGTTTTTAATTGAATTA-GGTTAGGGTTTTTAATT-AA--GGGTTTAGGGCTTTTAAT
1 GG-TTAGGGTTTTTAATT-AA--AGGGTTAGGGTTTTTAATTAAATTAGG-CTAGGGTTTTTAAT
480456 TAAATTA
61 TAAATTA
480463 GGTTAGGGTTT
1 GGTTAGGGTTT
480474 AGGATTAAAT
Statistics
Matches: 188, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
65 2 0.01
66 16 0.09
67 93 0.49
68 35 0.19
69 40 0.21
70 1 0.01
71 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.46
Consensus pattern (67 bp):
GGTTAGGGTTTTTAATTAAAGGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAAT
TA
Found at i:480325 original size:90 final size:90
Alignment explanation
Indices: 480194--480473 Score: 335
Period size: 90 Copynumber: 3.1 Consensus size: 90
480184 ATTAGGTTAG
*
480194 GGTTAGGGTTTTTAA--TAAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAA
1 GGTTAGGGTTTTTAATTTAAA-GGTCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAA
* *
480257 ATTAGGTTAGGGTTTTTAATT-AA-G
65 ATTAAGTTAGGGTTTTTAATTAAATA
480281 GGTTTAGGGTTTTTAA-TTACATTAGG-CTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAAT
1 GG-TTAGGGTTTTTAATTTA-A--AGGTCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAAT
480344 TAAATTAAGTTAGGGTTTTTAATTAAATTA
62 TAAATTAAGTTAGGGTTTTTAATTAAA-TA
* * * *
480374 GGTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTTTTAATT-AA
1 GGTTAGGGTTTTTAATTTAAAGGTCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
** *
480438 --GGGTTTAGGGCTTTTAATTAAATTA
66 TTAAG-TTAGGGTTTTTAATTAAA-TA
480463 GGTTAGGGTTT
1 GGTTAGGGTTT
480474 AGGATTAAAT
Statistics
Matches: 172, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
87 2 0.01
88 14 0.08
89 33 0.19
90 64 0.37
91 39 0.23
92 15 0.09
93 5 0.03
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.46
Consensus pattern (90 bp):
GGTTAGGGTTTTTAATTTAAAGGTCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
TTAAGTTAGGGTTTTTAATTAAATA
Found at i:480405 original size:158 final size:156
Alignment explanation
Indices: 480195--480499 Score: 452
Period size: 158 Copynumber: 1.9 Consensus size: 156
480185 TTAGGTTAGG
*
480195 GTTAGGGTTTTTAATAAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATT
1 GTTAGGGTTTTTAATAAAAGGTTTAGGGTTTTTAATTAAA-TAGGCTAGGGTTTTTAATTAAATT
* * **
480260 AGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTACATTAGGCTAGGGTTTTTAATTAAA
65 AGGTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAA
480325 TTAGGCTAGGGTTTTTAATTAAATTAA
130 TTAGGCTAGGGTTTTTAATTAAATTAA
* * * *
480352 GTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTTAA-GGGTTTAGGGTTTTTAATTGA
1 GTTAGGGTTTTTAA-TAAA--AGGTTTAGGGTTTTTAATTAAATAGG-CTAGGGTTTTTAATTAA
* *
480415 ATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTAGGATT
62 ATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGCTAGGGTTTAGAATT
480480 AAATTAGGCTAGGGTTTTTA
127 AAATTAGGCTAGGGTTTTTA
480500 TTACATGTCA
Statistics
Matches: 133, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
157 16 0.12
158 98 0.74
159 17 0.13
160 2 0.02
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.46
Consensus pattern (156 bp):
GTTAGGGTTTTTAATAAAAGGTTTAGGGTTTTTAATTAAATAGGCTAGGGTTTTTAATTAAATTA
GGTTAGGGTTTTTAATTAAGGGTTTAGGGCTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAAT
TAGGCTAGGGTTTTTAATTAAATTAA
Found at i:480581 original size:44 final size:44
Alignment explanation
Indices: 480518--480644 Score: 146
Period size: 53 Copynumber: 2.7 Consensus size: 44
480508 CATAAACTTC
* *
480518 TATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATTTA
1 TATTTTTTTACATAAAATAATATCAAAATAACTCAAAAAATTTA
*
480562 TATTTTTTTACATAAAATAATATCAAAATATTCAAAATAACTCAAAAATTTTA
1 TATTTTTTTACAT---A-AA-AT---AATA-TCAAAATAACTCAAAAAATTTA
480615 TATTTTTTTACATAAAATAATATCAAAATA
1 TATTTTTTTACATAAAATAATATCAAAATA
480645 TTCAAAATAT
Statistics
Matches: 71, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
44 20 0.28
45 4 0.06
48 4 0.06
49 4 0.06
50 1 0.01
52 4 0.06
53 34 0.48
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.39
Consensus pattern (44 bp):
TATTTTTTTACATAAAATAATATCAAAATAACTCAAAAAATTTA
Found at i:480615 original size:53 final size:53
Alignment explanation
Indices: 480536--480653 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
480526 TACATCAAAT
480536 AATA-TCAAAATAACTCAAAAAATTTATATTTTTTTACATAAAATAATATCAA
1 AATATTCAAAATAACTCAAAAAATTTATATTTTTTTACATAAAATAATATCAA
*
480588 AATATTCAAAATAACTCAAAAATTTTATATTTTTTTACATAAAATAATATCAA
1 AATATTCAAAATAACTCAAAAAATTTATATTTTTTTACATAAAATAATATCAA
480641 AATATTCAAAATA
1 AATATTCAAAATA
480654 TTTGTACAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 4 0.06
53 60 0.94
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (53 bp):
AATATTCAAAATAACTCAAAAAATTTATATTTTTTTACATAAAATAATATCAA
Found at i:482968 original size:51 final size:51
Alignment explanation
Indices: 482912--483034 Score: 203
Period size: 51 Copynumber: 2.4 Consensus size: 51
482902 TATTTTAAAA
* *
482912 AAGGAAATTGAGAAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
*
482963 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
*
483014 AAGGAAATTGAG-AGGAATTGA
1 AAGGAAATTGAGAAGAAATTGA
483035 GAGGAAATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 7 0.10
51 60 0.90
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (51 bp):
AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
Found at i:486113 original size:102 final size:101
Alignment explanation
Indices: 485930--486130 Score: 312
Period size: 102 Copynumber: 2.0 Consensus size: 101
485920 ACATTACCTT
*
485930 TCAAGACCCCCCTATCCGGTAGCTACATTGGACTTAAATAAACCCGAAGTTTAGCCAAATTAGAC
1 TCAAGACCCCCCTATCCGGTAGCTACATTGAACTTAAATAAACCCGAAGTTTAGCCAAATTAGAC
* **
485995 CCTTACGAAAGCAAGCTCTCCTAGTGGTATTTTCAA
66 CCTTAAGAAAGCAAGCTCTCCTACCGGTATTTTCAA
* * * * *
486031 TCAAGACTCCCCCTATCTGGTAGCTACGTTGAACTTAACTAAACCCGGAGTTTAGCCGAATTAGA
1 TCAAGAC-CCCCCTATCCGGTAGCTACATTGAACTTAAATAAACCCGAAGTTTAGCCAAATTAGA
486096 CCCTTAAGAAAGCAAGCTCTCCTACCGGTATTTTC
65 CCCTTAAGAAAGCAAGCTCTCCTACCGGTATTTTC
486131 TCCACTCCTA
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 7 0.08
102 83 0.92
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (101 bp):
TCAAGACCCCCCTATCCGGTAGCTACATTGAACTTAAATAAACCCGAAGTTTAGCCAAATTAGAC
CCTTAAGAAAGCAAGCTCTCCTACCGGTATTTTCAA
Found at i:491912 original size:30 final size:31
Alignment explanation
Indices: 491876--491942 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
491866 ATTAAATCGT
*
491876 AATTTTTATAATTTTTAAAAGA-TTAAATTA-
1 AATTTTTA-AATTTTTAAAAGAGTTAAACTAC
* *
491906 AATTTTTAATTTTTTAAATGAGTTAAACTAC
1 AATTTTTAAATTTTTAAAAGAGTTAAACTAC
491937 AATTTT
1 AATTTT
491943 ACTTTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.34
30 15 0.47
31 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (31 bp):
AATTTTTAAATTTTTAAAAGAGTTAAACTAC
Found at i:493319 original size:34 final size:35
Alignment explanation
Indices: 493261--493327 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
493251 CAAACACCAG
493261 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
493296 AAAATATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
493328 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:496061 original size:31 final size:32
Alignment explanation
Indices: 496025--496095 Score: 101
Period size: 31 Copynumber: 2.2 Consensus size: 32
496015 TTATAAAATG
496025 GTCACTAAACTATTTGAAAGT-TTTCA-TTTAA
1 GTCACTAAACTATTTGAAAGTCTTT-ATTTTAA
*
496056 GTCACTGAACTATTTGAAAGTCTTTATTTTTAA
1 GTCACTAAACTATTTGAAAGTCTTTA-TTTTAA
496089 GTCACTA
1 GTCACTA
496096 GGTTGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 21 0.60
32 3 0.09
33 11 0.31
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (32 bp):
GTCACTAAACTATTTGAAAGTCTTTATTTTAA
Found at i:497957 original size:4 final size:4
Alignment explanation
Indices: 497945--497990 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
497935 AGGCAGGAAG
497945 GTAT G-AT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
497991 GGTGGTCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:509762 original size:146 final size:145
Alignment explanation
Indices: 509536--509890 Score: 570
Period size: 146 Copynumber: 2.4 Consensus size: 145
509526 ACTAATTCCA
* * * * * * *
509536 AAATTAGAGCATAATAGAAGGG-CCAAAATCAGAACTTGA-CCCTGGTTTTAACCATGGATGAGC
1 AAATTTGAGCATAACAG-AGGGACCAAAACCAGAATTTGACCCCTAGTTTCAGCCATGGATGAGC
* *
509599 AAACTACTATTTGATTGGAATTCTAACGATATTTTGATTAACTAAAGGAAAAGAATCATGCCAAA
65 AAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAAA
509664 TTATAAACACAACCCC
130 TTATAAACACAACCCC
509680 AAATTTGAGCATAACAGAGGGACCAAAACCAGAATTTGACCCGCTAGTTTCAGCCATGGATGAGC
1 AAATTTGAGCATAACAGAGGGACCAAAACCAGAATTTGACCC-CTAGTTTCAGCCATGGATGAGC
509745 AAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAAA
65 AAAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAAA
*
509810 TTATAAGCACAACCCC
130 TTATAAACACAACCCC
*
509826 AAATTTGAGCATAACAGAGGGACCAAAACCAGAATTTGACCCTCTAGTTTCGGCCATGGATGAGC
1 AAATTTGAGCATAACAGAGGGACCAAAACCAGAATTTGACCC-CTAGTTTCAGCCATGGATGAGC
509891 TGAGAAAAAG
Statistics
Matches: 196, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
143 4 0.02
144 30 0.15
145 2 0.01
146 160 0.82
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (145 bp):
AAATTTGAGCATAACAGAGGGACCAAAACCAGAATTTGACCCCTAGTTTCAGCCATGGATGAGCA
AAATACTATTTGATTGGAATTCTAACGATATTTTGATCAACTAAAGGAAAAGAATCATGCCAAAT
TATAAACACAACCCC
Found at i:512651 original size:2 final size:2
Alignment explanation
Indices: 512644--512672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
512634 CTAAATATGA
512644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
512673 ATAAAAATGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:516760 original size:20 final size:20
Alignment explanation
Indices: 516735--516775 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
516725 TTCGTGTTAC
516735 TTGTTCAAGTCATTTCAAGT
1 TTGTTCAAGTCATTTCAAGT
516755 TTGTTCAAGTCATTTCAAGT
1 TTGTTCAAGTCATTTCAAGT
516775 T
1 T
516776 CAAGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGTTCAAGTCATTTCAAGT
Found at i:516778 original size:16 final size:17
Alignment explanation
Indices: 516736--516780 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
516726 TCGTGTTACT
516736 TGTTCAAGTCATTTCAA
1 TGTTCAAGTCATTTCAA
516753 GTTTGTTCAAGTCATTTCAA
1 ---TGTTCAAGTCATTTCAA
516773 -GTTCAAGT
1 TGTTCAAGT
516781 TTTTTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.32
20 17 0.68
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (17 bp):
TGTTCAAGTCATTTCAA
Found at i:516985 original size:29 final size:29
Alignment explanation
Indices: 516943--517001 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
516933 GGGTTAAAAT
516943 TGAAAACTATACATATATGGTCTCCATGG
1 TGAAAACTATACATATATGGTCTCCATGG
516972 TGAAAACTATACATATATGGTCTCCATGG
1 TGAAAACTATACATATATGGTCTCCATGG
517001 T
1 T
517002 ACATGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (29 bp):
TGAAAACTATACATATATGGTCTCCATGG
Found at i:520196 original size:13 final size:14
Alignment explanation
Indices: 520170--520217 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
520160 CCCATTATCC
520170 AAAACAAAAGGAAAA-
1 AAAAC-AAA-GAAAAG
520185 AAAACAAAGAAAAG
1 AAAACAAAGAAAAG
*
520199 AAAA-AAAGAAATG
1 AAAACAAAGAAAAG
520212 AAAACA
1 AAAACA
520218 TAAAAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 17 0.57
14 8 0.27
15 5 0.17
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAACAAAGAAAAG
Found at i:520214 original size:18 final size:17
Alignment explanation
Indices: 520182--520225 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
520172 AACAAAAGGA
* *
520182 AAAAAAACAAAGAAAAG
1 AAAAAAAGAAAGAAAAC
520199 AAAAAAAGAAATGAAAAC
1 AAAAAAAGAAA-GAAAAC
520217 ATAAAAAAG
1 A-AAAAAAG
520226 TAACATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAAGAAAGAAAAC
Found at i:521133 original size:66 final size:65
Alignment explanation
Indices: 521025--521195 Score: 207
Period size: 66 Copynumber: 2.6 Consensus size: 65
521015 AGGAGGAGAA
* * **
521025 GGATCTGAGTAACCGTTATGGCCGCTAACGGAATATTCAAAAGACGGTGCCGTTGGCGCAAAAGA
1 GGATCTGAGTAACCGTTATGG-TGCTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGA
521090 C
65 C
* * *
521091 GGATCTGAGTAACCGTTATGGTGACTGACGGAATATTGAAAAGACTCAGCCGTTGGTGCAAAAGA
1 GGATCTGAGTAACCGTTATGGTG-CTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGA
521156 C
65 C
* *** *
521157 GGAGCTGAGTGGTCGTTACGGTGTCTAACGGAATATTGA
1 GGATCTGAGTAACCGTTATGGTG-CTAACGGAATATTGA
521196 GGATAGTCCG
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 1 0.01
66 89 0.99
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (65 bp):
GGATCTGAGTAACCGTTATGGTGCTAACGGAATATTGAAAAGACGCAGCCGTTGGCGCAAAAGAC
Found at i:524336 original size:29 final size:29
Alignment explanation
Indices: 524293--524348 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
524283 GTTGAGATTT
*
524293 TGTCAATTTAGTCCTTATACTAATAAATG
1 TGTCAATTTAATCCTTATACTAATAAATG
*
524322 TGTCAATTTAATCCTTATACTATTAAA
1 TGTCAATTTAATCCTTATACTAATAAA
524349 AGAAATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (29 bp):
TGTCAATTTAATCCTTATACTAATAAATG
Found at i:526216 original size:77 final size:76
Alignment explanation
Indices: 526133--526278 Score: 204
Period size: 76 Copynumber: 1.9 Consensus size: 76
526123 CTCATAGAAA
*
526133 GGCTTCTCAAATATCGTACATC-AGATTTCAAATTATGTTTTTATTACTTTATTTTCTTTTCAAG
1 GGCTTCTCAAATAT-GTACATCAAG-TTTCAAATTATGTTTTTATTACTTTATTTTATTTTCAAG
526197 CAATATATATAAG
64 CAATATATATAAG
* * * * * *
526210 GGCTTCTTAAATGTTTATATCAAGTTTCAAATTATGTTTTTATTATTTTCTTTTATTTTCAAGCA
1 GGCTTCTCAAATATGTACATCAAGTTTCAAATTATGTTTTTATTACTTTATTTTATTTTCAAGCA
526275 ATAT
66 ATAT
526279 TTGATTCAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
76 47 0.77
77 14 0.23
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (76 bp):
GGCTTCTCAAATATGTACATCAAGTTTCAAATTATGTTTTTATTACTTTATTTTATTTTCAAGCA
ATATATATAAG
Found at i:527335 original size:24 final size:24
Alignment explanation
Indices: 527307--527357 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
527297 AAAACAAAGA
*
527307 TTAAAACATACGCAAAACCGGGAC
1 TTAAAACATACCCAAAACCGGGAC
527331 TTAAAACATACCCAAAACCGGGAC
1 TTAAAACATACCCAAAACCGGGAC
527355 TTA
1 TTA
527358 CATGATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.16
Consensus pattern (24 bp):
TTAAAACATACCCAAAACCGGGAC
Found at i:532636 original size:95 final size:95
Alignment explanation
Indices: 532473--532648 Score: 316
Period size: 95 Copynumber: 1.9 Consensus size: 95
532463 AAAGTGTGAG
* *
532473 ATTTGGATAAGGAATCACTGCATAATCGTGAGACTGTTTGGGTTAAGCAGTCAACGCATGTATCA
1 ATTTGGATAAGGAATCACTGCATAATCGTGAGACTGTTTGGGTCAAGCAGTCAACACATGTATCA
*
532538 CTCGCTTTCTTAATAAGCTTGGTTTGCTTC
66 CTCGATTTCTTAATAAGCTTGGTTTGCTTC
*
532568 ATTTGGATAAGGAATCACTGCATAATCGTGAGATTGTTTGGGTCAAGCAGTCAACACATGTATCA
1 ATTTGGATAAGGAATCACTGCATAATCGTGAGACTGTTTGGGTCAAGCAGTCAACACATGTATCA
532633 CTCGATTTCTTAATAA
66 CTCGATTTCTTAATAA
532649 TCGAGGGATT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (95 bp):
ATTTGGATAAGGAATCACTGCATAATCGTGAGACTGTTTGGGTCAAGCAGTCAACACATGTATCA
CTCGATTTCTTAATAAGCTTGGTTTGCTTC
Found at i:538050 original size:174 final size:170
Alignment explanation
Indices: 537743--538135 Score: 533
Period size: 174 Copynumber: 2.3 Consensus size: 170
537733 AGACAAAATG
*
537743 GCCATTCGAGTCATGTTTTCCATCACCAAATGCCATCATGTCACAATAAGGACTAGTTCTAGCAA
1 GCCATTCGAGT-ATGTTTTCCACCACCAAATGCCATCATGTCACAATAAGGACTAGTTCTAGCAA
*
537808 AGTAAAACAATAAGGTAAGTCAGGTCAAGATCCTTATCTTTGCAATAAAGGAGAGAAATGCTGAC
65 AGTAAAACAATAAGGTAAGTCAGGTCAAGATCCTTATCTTTGCAAGAAAGGAGAGAAATGCTGAC
*
537873 AAAATATGTCTTCATTAGATGCTAC-AAGGATAATAAGACCA
130 AAAATATGTCTTCATGAGATGCTACAAAGG-TAATAAGACCA
* * * *
537914 GCCATTCGAGTGATGTTTTTCACCACCAAATGCCATCACGTCACAAT-AGGCCTAGTTCTAGCTA
1 GCCATTCGAGT-ATGTTTTCCACCACCAAATGCCATCATGTCACAATAAGGACTAGTTCTAGCAA
537978 AGT-AAACAATAAGGTACGGTATGTCAGGTCAAGATCCTTATCTTTGCAAGAAAGGAGAGAAATG
65 AGTAAAACAATAAGGTA----A-GTCAGGTCAAGATCCTTATCTTTGCAAGAAAGGAGAGAAATG
* * **
538042 -TAGACAAAATATGTCTTCATGATATGGTACAAAGGTAATAAGACTG
125 CT-GACAAAATATGTCTTCATGAGATGCTACAAAGGTAATAAGACCA
* * *
538088 GCCATTCTAGTATCGTTTGCCACCACCAAAATGCCATCATGCCACAAT
1 GCCATTCGAGTAT-GTTTTCCACCACC-AAATGCCATCATGTCACAAT
538136 TGCCCACGTA
Statistics
Matches: 196, Mismatches: 17, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
169 13 0.07
170 18 0.09
171 43 0.22
173 4 0.02
174 96 0.49
175 22 0.11
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (170 bp):
GCCATTCGAGTATGTTTTCCACCACCAAATGCCATCATGTCACAATAAGGACTAGTTCTAGCAAA
GTAAAACAATAAGGTAAGTCAGGTCAAGATCCTTATCTTTGCAAGAAAGGAGAGAAATGCTGACA
AAATATGTCTTCATGAGATGCTACAAAGGTAATAAGACCA
Found at i:544412 original size:164 final size:164
Alignment explanation
Indices: 543948--544563 Score: 844
Period size: 164 Copynumber: 3.7 Consensus size: 164
543938 ATGCAATTCT
* * * * *
543948 TTACATTTATTCG-TGAGGACTCGAAACTTGCCCATCACATGAGTATGACAGAGACTTTAGCTCC
1 TTACATTTATT-GATGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCC
* *
544012 AGTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACTTATGTCTAAGTTTTATGTA
65 GGTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTTTATGTA
*
544077 TATGCAACTTTTTCTAATGTGTAACGTTGATTTTC
130 TATGCAACTTTTTCTAATGTGTAACGCTGATTTTC
* * *
544112 TTACATTTATTGATGAATACTCGAAACATGTCGGTTACATGAGCATGACAGAG-CTTTAGCTCCG
1 TTACATTTATTGATGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCCG
544176 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTTTATGTAT
66 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTTTATGTAT
* *
544241 ATGCAACTTGTTCTAATGTGTAACACTGATTTTC
131 ATGCAACTTTTTCTAATGTGTAACGCTGATTTTC
* *
544275 TTACATTTATTGACGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGTTCCG
1 TTACATTTATTGATGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCCG
* * *
544340 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTTAAGGTATGTCTAAGTTATATGTAT
66 GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTTTATGTAT
544405 ATGCAACTTTTTCTAATGTGTAACGCTGATTTTC
131 ATGCAACTTTTTCTAATGTGTAACGCTGATTTTC
* * * * * *
544439 CTACCTTTATTAAAGAGTACTCGAAACTTGTCCGTCCGTTGCATGAGAATGGA-AGAGACTTTAG
1 TTACATTTATTGATGAGTACTCGAAAC-T-T--GTCCGTTACATGAGCAT-GACAGAGACTTTAG
* * * * * * * * *
544503 CTCCGGCATCTTGCCGTCC-TAGACTCAAAACTTACGTCCTTACATCAACATACGTCTAAGT
61 CTCCGGTATCATG-TGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGT
544564 CGTCAACGTT
Statistics
Matches: 403, Mismatches: 41, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
163 155 0.38
164 170 0.42
165 1 0.00
166 1 0.00
168 71 0.18
169 5 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (164 bp):
TTACATTTATTGATGAGTACTCGAAACTTGTCCGTTACATGAGCATGACAGAGACTTTAGCTCCG
GTATCATGTGGCCTTAGGCTCAAAACTTCCGTCCTTACGTCAACGTATGTCTAAGTTTTATGTAT
ATGCAACTTTTTCTAATGTGTAACGCTGATTTTC
Found at i:549246 original size:32 final size:29
Alignment explanation
Indices: 549179--549249 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
549169 TGGCAAAATT
549179 AAACTTATTAT-ATAATTTTTTAATTAAA
1 AAACTTATTATAATAATTTTTTAATTAAA
* *
549207 AAA-TTATTATAATTATTTTTTATTTCTATAA
1 AAACTTATTATAATAATTTTTTA-AT-TA-AA
549238 AAACTTATTATA
1 AAACTTATTATA
549250 TATTTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 7 0.19
28 13 0.36
29 1 0.03
30 2 0.06
31 5 0.14
32 8 0.22
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (29 bp):
AAACTTATTATAATAATTTTTTAATTAAA
Found at i:549255 original size:28 final size:27
Alignment explanation
Indices: 549179--549266 Score: 79
Period size: 32 Copynumber: 3.0 Consensus size: 27
549169 TGGCAAAATT
* *
549179 AAACTTATTATATAATTT-TTTAATTAA
1 AAACTTATTATATATTTTATTTTA-TAA
*
549206 AAAATTATTATAATTATTTTTTATTTCTATAA
1 AAACTTATTAT-A-TA--TTTTATTT-TATAA
549238 AAACTTATTATATATTTTAATTTTATAA
1 AAACTTATTATATATTTT-ATTTTATAA
549266 A
1 A
549267 TATTTTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
27 10 0.20
28 11 0.22
29 6 0.12
30 2 0.04
31 4 0.08
32 16 0.32
33 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
AAACTTATTATATATTTTATTTTATAA
Found at i:549892 original size:11 final size:11
Alignment explanation
Indices: 549873--549916 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
549863 AACACCGAAC
*
549873 TTTTTGGGTAA
1 TTTTCGGGTAA
549884 TTTTCGGGTAA
1 TTTTCGGGTAA
549895 --TTCGGGTAA
1 TTTTCGGGTAA
*
549904 TTTTTGGGTAA
1 TTTTCGGGTAA
549915 TT
1 TT
549917 CAGTTAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.31
11 20 0.69
ACGTcount: A:0.18, C:0.05, G:0.27, T:0.50
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:549900 original size:9 final size:9
Alignment explanation
Indices: 549886--549960 Score: 71
Period size: 9 Copynumber: 8.2 Consensus size: 9
549876 TTGGGTAATT
549886 TTCGGGTAA
1 TTCGGGTAA
549895 TTCGGGTAA
1 TTCGGGTAA
*
549904 TTTTTGGGTAA
1 --TTCGGGTAA
* *
549915 TTCAGTTAA
1 TTCGGGTAA
**
549924 TTCGATTAA
1 TTCGGGTAA
*
549933 TTCGGTTAA
1 TTCGGGTAA
549942 -TCGGGTAA
1 TTCGGGTAA
549950 TTCGGGTAA
1 TTCGGGTAA
549959 TT
1 TT
549961 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
8 7 0.13
9 40 0.73
11 8 0.15
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.41
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:549903 original size:20 final size:20
Alignment explanation
Indices: 549878--549962 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
549868 CGAACTTTTT
549878 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
*
549898 GGGTAATTTTTGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
* * **
549918 AGTTAA--TTCGATTAATTC
1 GGGTAATTTTCGGGTAATTC
*
549936 GGTTAA---TCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
549953 GGGTAATTTT
1 GGGTAATTTT
549963 TAACCAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
17 14 0.27
18 14 0.27
20 24 0.46
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (20 bp):
GGGTAATTTTCGGGTAATTC
Found at i:555277 original size:47 final size:46
Alignment explanation
Indices: 555214--555307 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 46
555204 GTCACCAAAC
* * ** *
555214 TATGAAAAGTTACAAAATAGTCATTCAACTATTTAATTTTGTCTTT
1 TATGAAAAATTACAAAATAATCACCCAACTATTCAATTTTGTCTTT
555260 TATGAAAAAATTACAAAATAATCACCCAACTATTCAATTTTGTCTTT
1 TATG-AAAAATTACAAAATAATCACCCAACTATTCAATTTTGTCTTT
555307 T
1 T
555308 CTAGTCACCA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 4 0.10
47 38 0.90
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.40
Consensus pattern (46 bp):
TATGAAAAATTACAAAATAATCACCCAACTATTCAATTTTGTCTTT
Found at i:558734 original size:2 final size:2
Alignment explanation
Indices: 558727--558764 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
558717 AGCTGACATC
558727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
558765 AAATAGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:560566 original size:14 final size:15
Alignment explanation
Indices: 560547--560587 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
560537 AATAAAAAAC
560547 ATATTAAATATTA-A
1 ATATTAAATATTATA
*
560561 ATATTAAAATAATATA
1 ATATT-AAATATTATA
560577 ATA-TAAATATT
1 ATATTAAATATT
560588 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.48
15 8 0.35
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTAAATATTATA
Found at i:561120 original size:30 final size:31
Alignment explanation
Indices: 561058--561131 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
561048 AATATATATA
* *
561058 ATGACAATAAAATATACTTATATTTAATAAAT
1 ATGA-AATAAAATATAATGATATTTAATAAAT
561090 ATGAAATAAAA-ATAATGATATTTTAA-AAAT
1 ATGAAATAAAATATAATGATA-TTTAATAAAT
**
561120 AAAAAATAAAAT
1 ATGAAATAAAAT
561132 GTACGGATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 20 0.56
31 12 0.33
32 4 0.11
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (31 bp):
ATGAAATAAAATATAATGATATTTAATAAAT
Found at i:565382 original size:17 final size:17
Alignment explanation
Indices: 565360--565403 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
565350 TCCGAACATA
*
565360 TATTTGTAATTATATTG
1 TATTTGTAATTATATTC
565377 TATTTGTGAA-TATATTC
1 TATTTGT-AATTATATTC
565394 TATTTGTAAT
1 TATTTGTAAT
565404 AATAAAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (17 bp):
TATTTGTAATTATATTC
Found at i:568582 original size:16 final size:16
Alignment explanation
Indices: 568542--568582 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
568532 TTTTTCCTTA
568542 AAATTTAAAAATAAAT
1 AAATTTAAAAATAAAT
568558 -AA-TTATAAAATAAAAT
1 AAATTTA-AAAAT-AAAT
568574 AAATTTAAA
1 AAATTTAAA
568583 TTTAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.14
15 7 0.33
16 4 0.19
17 4 0.19
18 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTTAAAAATAAAT
Found at i:569380 original size:13 final size:13
Alignment explanation
Indices: 569362--569390 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
569352 ACATAAAAAA
569362 ATTATTTTATTTT
1 ATTATTTTATTTT
569375 ATTATTTTATTTT
1 ATTATTTTATTTT
569388 ATT
1 ATT
569391 TTTCTACCTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTATTTTATTTT
Found at i:570289 original size:11 final size:11
Alignment explanation
Indices: 570269--570298 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
570259 ACAACAGCAA
570269 CAAAATAATAG
1 CAAAATAATAG
*
570280 CAATATAATAG
1 CAAAATAATAG
570291 CAAAATAA
1 CAAAATAA
570299 CAATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:575304 original size:8 final size:8
Alignment explanation
Indices: 575291--575454 Score: 247
Period size: 8 Copynumber: 20.5 Consensus size: 8
575281 TGCCATGTCA
*
575291 TATGTATG
1 TATGTGTG
*
575299 TATGTATG
1 TATGTGTG
*
575307 TATGTATG
1 TATGTGTG
*
575315 TATGTATG
1 TATGTGTG
575323 TATGTGTG
1 TATGTGTG
575331 TATGTGTG
1 TATGTGTG
575339 TATGTGTG
1 TATGTGTG
575347 TATGTGTG
1 TATGTGTG
575355 TATGTGTG
1 TATGTGTG
575363 TATGTGTG
1 TATGTGTG
575371 TATGTGTG
1 TATGTGTG
575379 TATGTGTG
1 TATGTGTG
575387 TATGTGTG
1 TATGTGTG
575395 TATGTGTG
1 TATGTGTG
575403 TATGTGTG
1 TATGTGTG
*
575411 TATGTATG
1 TATGTGTG
*
575419 TATGTATG
1 TATGTGTG
*
575427 TATGTATG
1 TATGTGTG
*
575435 TATGTATG
1 TATGTGTG
*
575443 TATGTATG
1 TATGTGTG
575451 TATG
1 TATG
575455 ATGCATTAGA
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
8 154 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (8 bp):
TATGTGTG
Found at i:575654 original size:4 final size:4
Alignment explanation
Indices: 575647--575686 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
575637 GCAGTCATTC
* * *
575647 ATGT ATGT ATGT ATGT ATGT ATGT GTGT TTGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
575687 TTATTGATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.20, C:0.03, G:0.28, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:582542 original size:21 final size:21
Alignment explanation
Indices: 582516--582557 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
582506 CTTTTTAAGT
582516 TAAGGGGGTAAAATACAATAC
1 TAAGGGGGTAAAATACAATAC
582537 TAAGGGGGTAAAATACAATAC
1 TAAGGGGGTAAAATACAATAC
582558 AACTTTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.19
Consensus pattern (21 bp):
TAAGGGGGTAAAATACAATAC
Found at i:585559 original size:2 final size:2
Alignment explanation
Indices: 585554--585589 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
585544 ACCCACAACA
585554 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
585590 TTCGAAAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:590293 original size:21 final size:19
Alignment explanation
Indices: 590251--590307 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
590241 TTATTATCCT
590251 GAACCCTAA-CCTAGAACTC
1 GAACCCTAACCCT-GAACTC
590270 GAACCCTAGACCCTGAACCTC
1 GAACCCTA-ACCCTGAA-CTC
*
590291 GAACCCCAAACCCTGAA
1 GAA-CCCTAACCCTGAA
590308 TCCCAAACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.24
20 4 0.12
21 17 0.52
22 4 0.12
ACGTcount: A:0.35, C:0.40, G:0.12, T:0.12
Consensus pattern (19 bp):
GAACCCTAACCCTGAACTC
Found at i:590500 original size:21 final size:19
Alignment explanation
Indices: 590458--590514 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
590448 GTATTATCCT
590458 GAACCCTAA-CCTAGAACTC
1 GAACCCTAACCCT-GAACTC
590477 GAACCCTAGACCCTGAACCTC
1 GAACCCTA-ACCCTGAA-CTC
*
590498 GAACCCCAAACCCTGAA
1 GAA-CCCTAACCCTGAA
590515 TCCCAAACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.24
20 4 0.12
21 17 0.52
22 4 0.12
ACGTcount: A:0.35, C:0.40, G:0.12, T:0.12
Consensus pattern (19 bp):
GAACCCTAACCCTGAACTC
Found at i:590597 original size:207 final size:206
Alignment explanation
Indices: 590242--590658 Score: 762
Period size: 207 Copynumber: 2.0 Consensus size: 206
590232 TTGGTAATTT
590242 TATTATCCTGAACCCTAACCTAGAACTCGAACCCTAGACCCTGAACCTCGAACCCCAAACCCTGA
1 TATTATCCTGAACCCTAACCTAGAACTCGAACCCTAGACCCTGAACCTCGAACCCCAAACCCTGA
590307 ATCCCAAACCTTGAACTCGAACCACGCTTAAGGCCCAAGGTTAAGGATAATTTTTTTTACCAAAA
66 ATCCCAAACCTTGAACTCGAACCACGCTTAAGGCCCAAGGTTAAGGATAATTTTTTTTACCAAAA
* *
590372 TTATTGAAATGTCATTAAATAATTGGAAAAAGACCATAAATAATGTGATGGGAATGATCCATCAA
131 TGATTGAAATGTCATTAAATAATTGAAAAAAGACCATAAATAATGTGATGGGAATGATCCATCAA
590437 ACAATTTCTCGG
196 ACAATTTCTC-G
590449 TATTATCCTGAACCCTAACCTAGAACTCGAACCCTAGACCCTGAACCTCGAACCCCAAACCCTGA
1 TATTATCCTGAACCCTAACCTAGAACTCGAACCCTAGACCCTGAACCTCGAACCCCAAACCCTGA
*
590514 ATCCCAAACCTTGAACTCGAACCACGCTTAAGGCCCAAGGTTCAGGATAATTTTTTTTACCAAAA
66 ATCCCAAACCTTGAACTCGAACCACGCTTAAGGCCCAAGGTTAAGGATAATTTTTTTTACCAAAA
* * * *
590579 TGATTGAAATGTCATTAAATAATTGAAAAAAGACCATAGATAATGTGGTGGGAATGGTCCATCAG
131 TGATTGAAATGTCATTAAATAATTGAAAAAAGACCATAAATAATGTGATGGGAATGATCCATCAA
590644 ACAATTTCTCG
196 ACAATTTCTCG
590655 TATT
1 TATT
590659 GAAGGGATTG
Statistics
Matches: 203, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
206 5 0.02
207 198 0.98
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (206 bp):
TATTATCCTGAACCCTAACCTAGAACTCGAACCCTAGACCCTGAACCTCGAACCCCAAACCCTGA
ATCCCAAACCTTGAACTCGAACCACGCTTAAGGCCCAAGGTTAAGGATAATTTTTTTTACCAAAA
TGATTGAAATGTCATTAAATAATTGAAAAAAGACCATAAATAATGTGATGGGAATGATCCATCAA
ACAATTTCTCG
Found at i:597001 original size:3 final size:3
Alignment explanation
Indices: 596993--597024 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
596983 AAGAGAAGGT
596993 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
597025 GCATTGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:616337 original size:22 final size:21
Alignment explanation
Indices: 616302--616343 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
616292 TTATTTTCTA
*
616302 TTTTAAATATAAAACATTTAT
1 TTTTAAATATAAAAAATTTAT
*
616323 TTTTACATCATAAAAAATTTA
1 TTTTAAAT-ATAAAAAATTTA
616344 AATTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTAAATATAAAAAATTTAT
Found at i:629209 original size:6 final size:6
Alignment explanation
Indices: 629200--629230 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
629190 AACTCATTCT
*
629200 CACCGC CACCGC CACCGC CATCGC CACCGC C
1 CACCGC CACCGC CACCGC CACCGC CACCGC C
629231 TCTAGGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.65, G:0.16, T:0.03
Consensus pattern (6 bp):
CACCGC
Found at i:634029 original size:3 final size:3
Alignment explanation
Indices: 634023--634048 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
634013 GGCAACGACA
634023 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
634049 GGAGAACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:635665 original size:139 final size:141
Alignment explanation
Indices: 635408--635865 Score: 604
Period size: 139 Copynumber: 3.2 Consensus size: 141
635398 CTCTAGCAGA
* * * * *
635408 AAGGGCGCAAAGCCAAGCTAAAACCCTTAAATTGTCTTGCATTCGAAAGAGGTTTTTT-TGTATG
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-AAGAGTTTTTTTGTGTGTG
* ** * *
635472 -TCTCTCATTCGAAAGGGTTTAAGACATTTTTGTAGTAGAGCTAAATTCACTAGGCAATGGCACA
65 TTCTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACA
635536 ACTAGTGTTGTT
130 ACTAGTGTTGTT
* *
635548 AAAGGTGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-A-A-TTTTTTTGTGTGTGT
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAGAGTTTTTTTGTGTGTGT
*
635610 CTCTCTCATTTGAAAGGGTTCGAGATATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACA
66 -TCTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACA
*
635675 ACTGGTGTTGTT
130 ACTAGTGTTGTT
* * * *
635687 AAGGGAGCAAAGCCGAGCTAGAATCCTAATATTGTCTTGCATTCGAAAGGATTTCTTTCTTGTGT
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-AA-GAGTT-TTT-TTGTGT
* * * *
635752 GTGTT-TCTCACTTGAAAGGGTTCGGGACATTTTTGTACTAAAGCTAAATTCATTAGGCAATGTC
62 GTGTTCTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTC
635816 ACAACTAGTGTTGTT
127 ACAACTAGTGTTGTT
* *
635831 AAGGGCGCAAAGCCGAGCTAGAACCCTTATATTGT
1 AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGT
635866 TTTGGATTTG
Statistics
Matches: 281, Mismatches: 27, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
136 6 0.02
137 6 0.02
138 1 0.00
139 109 0.39
140 41 0.15
141 1 0.00
143 1 0.00
144 102 0.36
145 4 0.01
146 10 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (141 bp):
AAGGGAGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAGAGTTTTTTTGTGTGTGT
TCTCTCATTTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACAA
CTAGTGTTGTT
Found at i:635899 original size:144 final size:142
Alignment explanation
Indices: 635408--635899 Score: 613
Period size: 144 Copynumber: 3.5 Consensus size: 142
635398 CTCTAGCAGA
* *
635408 AAGGGCGCAAAGCCAAGCTAAAACCCTTAAATTGTCTTGCATTCGAAAGAGG--TTTTTTTGTA-
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAG-GGTTTTTTTTTGTAT
** * *
635470 -TGTCTCTCATTCGAAAGGGTTTAAGACATTTTTGTAGTAGAGCTAAATTCACTAGGCAATGGCA
65 GTGTCTCTCATT-GAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCA
635534 CAACTAGTGTTGTT
129 CAACTAGTGTTGTT
* * * *
635548 AAAGGTGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCG-AA---TTTTTTTGTGTGTG
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAGGGTTTTTTTTTGTATG
* *
635609 TCTCTCTCATTTGAAAGGGTTCGAGATATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCAC
66 TGTCTCTCA-TTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCAC
*
635674 AACTGGTGTTGTT
130 AACTAGTGTTGTT
* * * * * * *
635687 AAGGGAGCAAAGCCGAGCTAGAATCCTAATATTGTCTTGCATTCGAAAGGATTTCTTTCTTGTGT
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAGGGTTT-TTTTTTGTAT
* * * *
635752 GTGTTTCTCACTTGAAAGGGTTCGGGACATTTTTGTACTAAAGCTAAATTCATTAGGCAATGTCA
65 GTGTCTCTCA-TTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCA
635817 CAACTAGTGTTGTT
129 CAACTAGTGTTGTT
* * * * *
635831 AAGGGCGCAAAGCCGAGCTAGAACCCTTATATTGTTTTGGATTTGAAAGGGTTTTTTCTTTTTAT
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAGGGTTTTTT-TTTGTAT
635896 GTGT
65 GTGT
635900 GTTTCTCATT
Statistics
Matches: 303, Mismatches: 38, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
137 8 0.03
139 110 0.36
140 45 0.15
143 6 0.02
144 134 0.44
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (142 bp):
AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAGGGTTTTTTTTTGTATG
TGTCTCTCATTGAAAGGGTTCGAGACATTTTTGTACTAGAGCTAAATTCACTAGGCAATGTCACA
ACTAGTGTTGTT
Found at i:637692 original size:4 final size:4
Alignment explanation
Indices: 637683--637763 Score: 76
Period size: 4 Copynumber: 20.8 Consensus size: 4
637673 GAAAAGGTAA
* * * *
637683 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT GTGT GTGT GTTT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
637731 ATGC ATGC ATGC ATGT ATG- -TGT GTGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
637764 CATGCGTGTG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.03
4 66 0.97
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:640427 original size:22 final size:21
Alignment explanation
Indices: 640378--640428 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
640368 ATAAGCATAG
640378 AATTATTTAAAATTTAAAATAT
1 AATT-TTTAAAATTTAAAATAT
* *
640400 ATATTTTTAAATTTTAAAATTT
1 A-ATTTTTAAAATTTAAAATAT
640422 CAATTTT
1 -AATTTT
640429 GATTAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTTAAAATTTAAAATAT
Found at i:646367 original size:138 final size:136
Alignment explanation
Indices: 646112--646359 Score: 297
Period size: 138 Copynumber: 1.8 Consensus size: 136
646102 AACGGTTAAC
* *
646112 GATAGTTTAGGGATGTATTTAGAATGATTTAAAGTTTATGGAATAATTTAGAATGAGAGCCATAG
1 GATAGTTTAGGGATGTAATTAGAATGATTTAAAGTTTATGGAACAATTTAGAAT-AGAGCCATAG
* * * ** * *
646177 TTTGAGGATGTTTTGTGCAATTAACTCTTAAATTAATGATTTAGTAATGAAATAACCTTATTAAT
65 TTTGAGGACGTTTAGTGCAATTAACACTTAAATTAACCA-TAAGAAATGAAATAACCTTATTAAT
646242 ATAACATT
129 ATAACATT
* * *
646250 GATAGTTTCA-GGATGTAATTAGAATGTTTTAAAAGTTTA-GGACCAATTTAGAAT-GAGTCATA
1 GATAGTTT-AGGGATGTAATTAGAATGATTT-AAAGTTTATGGAACAATTTAGAATAGAGCCATA
*
646312 GTTTGGGGACGTTTAGTGCAATTAACACATTAAATTAACCCA-AAGAAA
64 GTTTGAGGACGTTTAGTGCAATTAACAC-TTAAATTAA-CCATAAGAAA
646360 ATTGAAATTT
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
136 35 0.38
137 9 0.10
138 40 0.43
139 9 0.10
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (136 bp):
GATAGTTTAGGGATGTAATTAGAATGATTTAAAGTTTATGGAACAATTTAGAATAGAGCCATAGT
TTGAGGACGTTTAGTGCAATTAACACTTAAATTAACCATAAGAAATGAAATAACCTTATTAATAT
AACATT
Found at i:652723 original size:21 final size:22
Alignment explanation
Indices: 652690--652731 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
652680 TTTTTTAAAA
* *
652690 TTAAATACCAAATTTAATTAAT
1 TTAAATACAAAATTAAATTAAT
652712 TTAAATA-AAAATTAAATTAA
1 TTAAATACAAAATTAAATTAA
652732 CAAAAGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAATACAAAATTAAATTAAT
Found at i:652914 original size:29 final size:30
Alignment explanation
Indices: 652869--652930 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
652859 TTATTTCTAA
652869 TAAAAAAAATAATTTTTCATATAATATTTT
1 TAAAAAAAATAATTTTTCATATAATATTTT
*
652899 TAAAAAAAATAATTTTT-ATATATTATTTT
1 TAAAAAAAATAATTTTTCATATAATATTTT
652928 TAA
1 TAA
652931 GTTATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAAAAAATAATTTTTCATATAATATTTT
Found at i:655253 original size:10 final size:11
Alignment explanation
Indices: 655233--655258 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
655223 ACATTTAAGC
655233 AAAAACAAAAA
1 AAAAACAAAAA
655244 AAAAACAAAAA
1 AAAAACAAAAA
655255 AAAA
1 AAAA
655259 GTTGCTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:655637 original size:2 final size:2
Alignment explanation
Indices: 655632--655664 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
655622 ATGTTACGTC
655632 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
655665 ATGTAAATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:669162 original size:137 final size:138
Alignment explanation
Indices: 668916--669190 Score: 498
Period size: 137 Copynumber: 2.0 Consensus size: 138
668906 GTTCATGGAT
668916 TGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTA
1 TGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTA
* *
668981 AGAATGTGAAAGCATCTTCGGCTTGAATGAATGTTTTTGGATACTTTTCT-CATATCTAGTGAGT
66 AGAATGTGAAAGCATCTTCGGCTTGAATGAAGGTTTTTGGATACTTCTCTCCATATCTAGTGAGT
669045 TGATGAAC
131 TGATGAAC
*
669053 TGCCATTGATGAATTTATTTGATTCTTTTGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTA
1 TGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTA
* *
669118 AGGATGTGAAAGCATCTTCGGCTTGAATGAAGGTTTTTGGATACTTCTCTCCATATCTAGTGGGT
66 AGAATGTGAAAGCATCTTCGGCTTGAATGAAGGTTTTTGGATACTTCTCTCCATATCTAGTGAGT
669183 TGATGAAC
131 TGATGAAC
669191 ACGATTTGAT
Statistics
Matches: 132, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
137 111 0.84
138 21 0.16
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41
Consensus pattern (138 bp):
TGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTACTTGTA
AGAATGTGAAAGCATCTTCGGCTTGAATGAAGGTTTTTGGATACTTCTCTCCATATCTAGTGAGT
TGATGAAC
Found at i:669317 original size:160 final size:159
Alignment explanation
Indices: 669047--669398 Score: 560
Period size: 160 Copynumber: 2.2 Consensus size: 159
669037 TAGTGAGTTG
* *
669047 ATGAACTGCCATTGATGAATTTATTTGATTCTTTTGTTGATTTAAAGCTTGTGAAAATTAGTGTA
1 ATGAATTGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTA
* **
669112 CTTGTAAGGATGTGAAAGCATCTTCGGCTTGAATGAAGGTTTTTGGATACTTCTCTCCATATCTA
66 CTTGTAAGAATGTGAAAGCATCTTCGGCTCAAATGAAGGTTTTTGGATACTTCTCT-CATATCTA
* *
669177 GTGGGTTGATGAACACGATTTGATATGTTT
130 GTGAGTTGATGAACACAATTTGATATGTTT
* *
669207 GTGGATTGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTA
1 ATGAATTGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTA
* *
669272 CTTGTAAGAATGTGAAAGCGTCTTCGGCTCAAATGAATGTTTTTGGATACTTCTCTCATATCTAG
66 CTTGTAAGAATGTGAAAGCATCTTCGGCTCAAATGAAGGTTTTTGGATACTTCTCTCATATCTAG
669337 TGAGTTGATGAACACAATTTGATATGTTT
131 TGAGTTGATGAACACAATTTGATATGTTT
* * *
669366 ATGAATTGACATTTGATGAATTGATTTGGTTCT
1 ATGAATTGCCA-TTGATGAATTTATTTGATTCT
669399 GATTGTATTG
Statistics
Matches: 175, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
159 44 0.25
160 131 0.75
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (159 bp):
ATGAATTGCCATTGATGAATTTATTTGATTCTTTCGTTGATTTAAAGCTTGTGAAAATTAGTGTA
CTTGTAAGAATGTGAAAGCATCTTCGGCTCAAATGAAGGTTTTTGGATACTTCTCTCATATCTAG
TGAGTTGATGAACACAATTTGATATGTTT
Found at i:670426 original size:17 final size:18
Alignment explanation
Indices: 670395--670429 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
670385 GTTCGGAAAA
670395 TGTTTTACGAAAAAAATT
1 TGTTTTACGAAAAAAATT
670413 TGTTTTAC-AAAAAAATT
1 TGTTTTACGAAAAAAATT
670430 ACTTTGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
TGTTTTACGAAAAAAATT
Found at i:671473 original size:31 final size:31
Alignment explanation
Indices: 671428--671559 Score: 99
Period size: 31 Copynumber: 4.4 Consensus size: 31
671418 GTCATATACC
*
671428 ATTTGATACCTGAGTTTAGCTTCAATGTTCA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
* * * *
671459 ATTTGGTACTTGAGTTTGGCTTCCATGTTTA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
* * ** ****
671490 ATTTGGCAGCTGAGTTT-TTTTC--CCCCCA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
* * *
671518 ATTTGGTACCTGAGATTGGCATCAATGTTCA
1 ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
671549 ATTTGGTACCT
1 ATTTGGTACCT
671560 AGATCAAACG
Statistics
Matches: 73, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
28 15 0.21
29 2 0.03
30 3 0.04
31 53 0.73
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (31 bp):
ATTTGGTACCTGAGTTTAGCTTCAATGTTCA
Found at i:671790 original size:31 final size:31
Alignment explanation
Indices: 671755--671852 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
671745 CAAATTGAAG
*
671755 CCAAATTGAACATTAAAGCTAAATTCAGGTA
1 CCAAATTGAACATTAAAGCCAAATTCAGGTA
**
671786 CCAAATTGAACATGGAAGCCAAATTCAGGTA
1 CCAAATTGAACATTAAAGCCAAATTCAGGTA
* * * *
671817 CCAAATTGAACATTGAA-CCAAACTCAAGTG
1 CCAAATTGAACATTAAAGCCAAATTCAGGTA
671847 CCAAAT
1 CCAAAT
671853 AGTATGTAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 16 0.27
31 44 0.73
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.21
Consensus pattern (31 bp):
CCAAATTGAACATTAAAGCCAAATTCAGGTA
Found at i:685557 original size:166 final size:165
Alignment explanation
Indices: 685250--685684 Score: 597
Period size: 166 Copynumber: 2.6 Consensus size: 165
685240 GGTTAAATTT
* * * *
685250 TAAAATATATTTCATGATCAACGAGTTACTTTTTTGAAGGCC-ACCCGCGAGGATTTAAGGTTTA
1 TAAAACATATTTCATGATCAACGAATTACTTCTTTGAAGACCAACCCG-G-GGATTTAAGGTTTA
* * * *
685314 GCAACCATGTGATTCCATCATGCATGCATTAAGGAGAGAGAGATAATTACTCACTTCATCCTTTA
64 GCAATCATGTGATTCCATCATGCATGCATTACGTAGAGACAGATAATTACTCACTTCATCCTTTA
* * * *
685379 TTTACATGGTTGAGGGTTAAATCTTCACCTATGAGAC
129 TTCACATGGTTGAGGGTTAAATCTCCACCTATAAAAC
* * *
685416 TAAAACATATTTTATGATTAACGAATTACTTCTTTGAAGACCATCCACGGGGATTTAAGGTTTAG
1 TAAAACATATTTCATGATCAACGAATTACTTCTTTGAAGACCAACC-CGGGGATTTAAGGTTTAG
*
685481 CAATCATGTGATTCCATCATGCATGCATTACGTAGAGACAGATAATTACTCACTTTATCCTTTAT
65 CAATCATGTGATTCCATCATGCATGCATTACGTAGAGACAGATAATTACTCACTTCATCCTTTAT
* *
685546 TCACGTGGTTGAGGGTTCAATCTCCACCTATAAAAC
130 TCACATGGTTGAGGGTTAAATCTCCACCTATAAAAC
* * *
685582 TGAAACATATTTCATGATCAACGAATTACTTCTTTGAATA-CAACCCGCGGAAGTTTAAGGTTTA
1 TAAAACATATTTCATGATCAACGAATTACTTCTTTGAAGACCAACCCG-GGGA-TTTAAGGTTTA
*
685646 GTC-ATCATGTGATTCCATCATGTATGCATTACGTAGAGA
64 G-CAATCATGTGATTCCATCATGCATGCATTACGTAGAGA
685685 GATGCTTGAA
Statistics
Matches: 239, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
164 2 0.01
165 7 0.03
166 224 0.94
167 4 0.02
168 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (165 bp):
TAAAACATATTTCATGATCAACGAATTACTTCTTTGAAGACCAACCCGGGGATTTAAGGTTTAGC
AATCATGTGATTCCATCATGCATGCATTACGTAGAGACAGATAATTACTCACTTCATCCTTTATT
CACATGGTTGAGGGTTAAATCTCCACCTATAAAAC
Found at i:687577 original size:2 final size:2
Alignment explanation
Indices: 687570--687608 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
687560 CTAATGTAAC
* *
687570 AT AT AT AT AT AT AT AT GT AT AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
687609 GATGGGGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:691648 original size:3 final size:3
Alignment explanation
Indices: 691640--691668 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
691630 CAGTCCTTGC
691640 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
691669 CTCCCCACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:692374 original size:283 final size:278
Alignment explanation
Indices: 691884--692405 Score: 704
Period size: 283 Copynumber: 1.9 Consensus size: 278
691874 CTTTTATTAC
* *
691884 AATACACACTTTGGGTTGTGTTTTTTTTAGCTGTTTAATTGGTCTCCCATGTTTGATTTTCTACT
1 AATACACACTTTGGGTTGTGTTTTTTTTAGCTGTTTAATCGGTCTCCCATGTTTGACTTTCTACT
* *
691949 GGTTTATTGTATTCTTCTTTGTCGCAAGCACAATTCTTTTTTTCTCCATGATTGATGCTTTATGC
66 GGTTTATTGTATTCTTCTTTGTAGCAAGCACAATTCTTTTTTTCTCCAAGATTGATGCTTTATGC
* * *
692014 TGTCTTTTTTTGTTTTAAAAAATATGGGTATTTTTTATTTTTAAGTATTGTAATCTTGTTTAGAA
131 TG-CTTTTTTTGTTTTAAAAAATATGGGTATTTTTGATTTTTAAGCATTGTAACCTTGTTTAGAA
* * *
692079 TTTTGGTTTCTTACATTGTTCTAGATTGTCCTGG-AAAATGGTACCTGTGATGAAAAGGTTGGTT
195 TTTAGATTTCTTACATTGTTCTAGATTGTCCAGGAAAAATGGTACCTGTGATGAAAAGGTTGGTT
692143 CTTTTGATTTCTTTATGTT
260 CTTTTGATTTCTTTATGTT
692162 AATACACACTTTGGGTTGTGTTTTTCTTTAGCTGTTTAATCGGTC-CCTCATGTTTG-CTTT-T-
1 AATACACACTTTGGGTTGTGTTTTT-TTTAGCTGTTTAATCGGTCTCC-CATGTTTGACTTTCTA
* *
692223 CTGGTTTATTGTGTTCTTCTTTGTAGCAAAGCACAATAAATACCCTTCTTTTCTTCTTCAAGATT
64 CTGGTTTATTGTATTCTTCTTTGTAGC-AAGCACAAT---T---C-T-TTTT-TTCTCCAAGATT
* *
692288 GAT-CTTTTATGCTG-TTTTTTT-TTTTAAAAAA-AGTGGGT-TTATTTGATTTTTATGCGTTGT
119 GATGC-TTTATGCTGCTTTTTTTGTTTTAAAAAATA-TGGGTATT-TTTGATTTTTAAGCATTGT
692348 AACCTTGTTTAGAATTTAGATTTCTTACATTGTTCTAGATTGTCCAGGAAAAATGGTA
181 AACCTTGTTTAGAATTTAGATTTCTTACATTGTTCTAGATTGTCCAGGAAAAATGGTA
692406 GTACCTCCTG
Statistics
Matches: 214, Mismatches: 14, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
276 25 0.12
277 10 0.05
278 30 0.14
279 26 0.12
280 1 0.00
282 3 0.01
283 75 0.35
284 17 0.08
285 5 0.02
286 22 0.10
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (278 bp):
AATACACACTTTGGGTTGTGTTTTTTTTAGCTGTTTAATCGGTCTCCCATGTTTGACTTTCTACT
GGTTTATTGTATTCTTCTTTGTAGCAAGCACAATTCTTTTTTTCTCCAAGATTGATGCTTTATGC
TGCTTTTTTTGTTTTAAAAAATATGGGTATTTTTGATTTTTAAGCATTGTAACCTTGTTTAGAAT
TTAGATTTCTTACATTGTTCTAGATTGTCCAGGAAAAATGGTACCTGTGATGAAAAGGTTGGTTC
TTTTGATTTCTTTATGTT
Found at i:693787 original size:51 final size:52
Alignment explanation
Indices: 693728--693830 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 52
693718 CATTTAGCAC
*
693728 GTGCAATATCACGCCTTTGTCTCGATGCATGAAAAAGACATAA-ACCTTATA
1 GTGCAATATCACGCCTTTGTCTCGATGCATAAAAAAGACATAATACCTTATA
* * * *
693779 GTGCAATATCATGCCTTTGTTTCGATGTATAAAAAAGATATAATACCTTATA
1 GTGCAATATCACGCCTTTGTCTCGATGCATAAAAAAGACATAATACCTTATA
693831 TGATGATTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 38 0.83
52 8 0.17
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (52 bp):
GTGCAATATCACGCCTTTGTCTCGATGCATAAAAAAGACATAATACCTTATA
Done.