Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 14
Found at i:775817 original size:21 final size:21
Alignment explanation
Indices: 775792--775842 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
775782 TATTTTCATT
*
775792 TTATTATTACTCTATATAT-A
1 TTATTATTACTATATATATCA
*
775812 TATATT-TATACTATATCTATCA
1 T-TATTAT-TACTATATATATCA
775834 TTATTATTA
1 TTATTATTA
775843 TTTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATTATTACTATATATATCA
Found at i:775984 original size:28 final size:30
Alignment explanation
Indices: 775940--776020 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
775930 TGTATTTAGC
775940 TATATTTTT-TCATGTATTTTATT-GTAT-
1 TATATTTTTCTCATGTATTTTATTAGTATA
*
775967 TATATTTTTCTCATGTATATTT-TTATTATA
1 TATATTTTTCTCATGTAT-TTTATTAGTATA
*
775997 TATATTTTTACTTAT-TATTTTATT
1 TATATTTTT-CTCATGTATTTTATT
776021 TGATTATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
27 9 0.20
28 10 0.22
29 9 0.20
30 14 0.30
31 4 0.09
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.67
Consensus pattern (30 bp):
TATATTTTTCTCATGTATTTTATTAGTATA
Found at i:775985 original size:15 final size:14
Alignment explanation
Indices: 775940--776005 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 14
775930 TGTATTTAGC
775940 TATATTTTTTCATG
1 TATATTTTTTCATG
775954 TAT-TTTATTGT-AT-
1 TATATTT-TT-TCATG
775967 TATATTTTTCTCATG
1 TATATTTTT-TCATG
* *
775982 TATATTTTTATTATA
1 TATATTTTT-TCATG
775997 TATATTTTT
1 TATATTTTT
776006 ACTTATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
13 9 0.21
14 12 0.28
15 22 0.51
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (14 bp):
TATATTTTTTCATG
Found at i:775993 original size:26 final size:27
Alignment explanation
Indices: 775899--775997 Score: 98
Period size: 27 Copynumber: 3.6 Consensus size: 27
775889 TTTATCCATT
*
775899 TATATTATATT-TTTTATTATTTCTCAT-
1 TATATTAT-TTATTATATT-TTTCTCATG
*
775926 TATATGTATTTAGCTATATTTTT-TCATG
1 TATAT-TATTTA-TTATATTTTTCTCATG
*
775954 TATTTTATTGTATTATATTTTTCTCATG
1 TATATTATT-TATTATATTTTTCTCATG
775982 TATATT-TTTATTATAT
1 TATATTATTTATTATAT
775998 ATATTTTTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
26 8 0.13
27 26 0.43
28 22 0.36
29 5 0.08
ACGTcount: A:0.25, C:0.06, G:0.05, T:0.64
Consensus pattern (27 bp):
TATATTATTTATTATATTTTTCTCATG
Found at i:776006 original size:15 final size:15
Alignment explanation
Indices: 775956--776011 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
775946 TTTTCATGTA
*
775956 TTTTATTGTATTATAT
1 TTTTATTATA-TATAT
* * *
775972 TTTTCTCATGTATAT
1 TTTTATTATATATAT
775987 TTTTATTATATATAT
1 TTTTATTATATATAT
776002 TTTTACTTAT
1 TTTTA-TTAT
776012 TATTTTATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (15 bp):
TTTTATTATATATAT
Found at i:776015 original size:13 final size:15
Alignment explanation
Indices: 775967--776017 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
775957 TTTATTGTAT
*
775967 TATATTTTT-CTCATG
1 TATATTTTTACT-ATA
*
775982 TATATTTTTATTATA
1 TATATTTTTACTATA
775997 TATATTTTTACT-TA
1 TATATTTTTACTATA
776011 T-TATTTT
1 TATATTTT
776018 ATTTGATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 6 0.19
14 3 0.09
15 22 0.69
16 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (15 bp):
TATATTTTTACTATA
Found at i:776270 original size:24 final size:23
Alignment explanation
Indices: 776234--776325 Score: 66
Period size: 23 Copynumber: 4.0 Consensus size: 23
776224 CTTGTTTCAT
* *
776234 TTATTTACTTATTTTACTTCTTG
1 TTATTTTCTTATTTTACTTCTTC
* * *
776257 TTATTTTGCTTA-TTTAGTTTTTT
1 TTATTTT-CTTATTTTACTTCTTC
776280 TTATTTTC-TATTTTATCTTCATTC
1 TTATTTTCTTATTTTA-CTTC-TTC
776304 TTA-TTTCATTTATTTTA-TTCTT
1 TTATTTTC--TTATTTTACTTCTT
776326 TTTACCTTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
21 2 0.04
22 5 0.09
23 29 0.53
24 12 0.22
26 7 0.13
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.70
Consensus pattern (23 bp):
TTATTTTCTTATTTTACTTCTTC
Found at i:786976 original size:78 final size:78
Alignment explanation
Indices: 786860--787011 Score: 180
Period size: 78 Copynumber: 1.9 Consensus size: 78
786850 AGTATTTCGC
* * * * ***
786860 TTAGGATGAAAACCCGAAAGGGCATCTTAAGTCGAAAAAAGGGGGAAAAAGAAAAAAAAAGAA-A
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAAAGGAAAAA-AAAAAAAAAGAACA
786924 AAAAGAAAAAACGT
65 AAAAGAAAAAACGT
* * * * *
786938 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAAAGGAAAAAAGAGAAAAAGAACAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAAAGGAAAAAAAAAAAAAAGAACAA
787003 AAAGAAAAA
66 AAAGAAAAA
787012 GAAAAATAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
77 10 0.16
78 51 0.84
ACGTcount: A:0.59, C:0.10, G:0.22, T:0.09
Consensus pattern (78 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAAAGGAAAAAAAAAAAAAAGAACAA
AAAGAAAAAACGT
Found at i:787008 original size:15 final size:14
Alignment explanation
Indices: 786971--787017 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
786961 GCCCTAAATT
*
786971 AAAAAA-AAAAGGA
1 AAAAAAGAAAAAGA
786984 AAAAAGAGAAAAAGA
1 AAAAA-AGAAAAAGA
786999 ACAAAAAGAAAAAGA
1 A-AAAAAGAAAAAGA
787014 AAAA
1 AAAA
787018 TAAGGTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.17
14 4 0.13
15 17 0.57
16 4 0.13
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:789075 original size:23 final size:24
Alignment explanation
Indices: 789036--789081 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
789026 TGTATATGTT
789036 AATGTGATATTATTTATAGTATAC
1 AATGTGATATTATTTATAGTATAC
*
789060 AATGT-ATATGTA-TTATATTATA
1 AATGTGATAT-TATTTATAGTATA
789082 AATACATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (24 bp):
AATGTGATATTATTTATAGTATAC
Found at i:789086 original size:27 final size:25
Alignment explanation
Indices: 789043--789095 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
789033 GTTAATGTGA
*
789043 TATTATTTATAGTATACAATGTATATG
1 TATTATTTATAGAATAC-ATGT-TATG
789070 TATTATATTATA-AATACATGTTATG
1 TATTAT-TTATAGAATACATGTTATG
789095 T
1 T
789096 TACATACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 10 0.42
28 5 0.21
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (25 bp):
TATTATTTATAGAATACATGTTATG
Found at i:790365 original size:2 final size:2
Alignment explanation
Indices: 790353--790397 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
790343 TTATTATTAC
*
790353 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
790395 TA T
1 TA T
790398 CTATCATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:790435 original size:19 final size:21
Alignment explanation
Indices: 790411--790455 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
790401 TCATTATTAT
*
790411 TATTTAATTA-TAT-TTTTTC
1 TATTTAATTACTATATTTCTC
*
790430 TATTTATTTACTATATTTCTC
1 TATTTAATTACTATATTTCTC
790451 TATTT
1 TATTT
790456 TTGGTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 3 0.14
21 10 0.45
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTAATTACTATATTTCTC
Found at i:790514 original size:27 final size:25
Alignment explanation
Indices: 790476--790574 Score: 85
Period size: 27 Copynumber: 3.8 Consensus size: 25
790466 ATCCATTTAT
790476 ATTATATT-TTTATTATTATTTTCTC
1 ATTATATTATTTATTA-TATTTTCTC
* *
790501 ATTATATGTATTTAGCTATATTTTTTC
1 ATTATAT-TATTTA-TTATATTTTCTC
*
790528 ATGTATTTTATTGTATTATATTTTTCTC
1 AT-TATATTATT-TATTATA-TTTTCTC
*
790556 ATGTACATT-TTTATTATAT
1 AT-TATATTATTTATTATAT
790575 ATATTTTTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
25 8 0.13
26 8 0.13
27 24 0.39
28 21 0.34
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (25 bp):
ATTATATTATTTATTATATTTTCTC
Found at i:790678 original size:25 final size:27
Alignment explanation
Indices: 790611--790684 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 27
790601 TTATAATACA
*
790611 TATTTATTTGTTT-TTTATTCTTTAGC
1 TATTTATTTATTTATTTATTCTTTAGC
*
790637 TA-TTA-TTACTTTCATTT-TT-TTTAGT
1 TATTTATTTA-TTT-ATTTATTCTTTAGC
790662 TATTTATTTATTTATTTA-TCTTT
1 TATTTATTTATTTATTTATTCTTT
790685 TCTTTTCTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
24 2 0.05
25 18 0.46
26 13 0.33
27 6 0.15
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (27 bp):
TATTTATTTATTTATTTATTCTTTAGC
Found at i:790859 original size:24 final size:22
Alignment explanation
Indices: 790817--790915 Score: 78
Period size: 24 Copynumber: 4.4 Consensus size: 22
790807 AGCTTCCTTG
* *
790817 TTTCATTTATTTACTTATTTTA
1 TTTCTTTTATTTTCTTATTTTA
**
790839 TTTCTTGTTATTTTGCTTATTTGG
1 TTTCTT-TTATTTT-CTTATTTTA
790863 TTT-TTTTATTTTC-TATTTTA
1 TTTCTTTTATTTTCTTATTTTA
*
790883 TCTTCATTCTTATTTCCTTTATTTTA
1 T-TTC-TT-TTATTTTC-TTATTTTA
790909 -TTCTTTT
1 TTTCTTTT
790916 TACCTTACTC
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
20 6 0.10
21 3 0.05
22 14 0.23
23 12 0.19
24 20 0.32
26 7 0.11
ACGTcount: A:0.14, C:0.11, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTCTTTTATTTTCTTATTTTA
Found at i:794537 original size:31 final size:31
Alignment explanation
Indices: 794499--794562 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
794489 AATACAGTCT
*
794499 CCCAACATTTAGTCCATTTGCATTATGATCC
1 CCCAACATTTAGTCCATTTGCAATATGATCC
** *
794530 CCCAACATTTAGTCTGTTTGCAATATGGTCC
1 CCCAACATTTAGTCCATTTGCAATATGATCC
794561 CC
1 CC
794563 GACCGTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (31 bp):
CCCAACATTTAGTCCATTTGCAATATGATCC
Found at i:796574 original size:31 final size:31
Alignment explanation
Indices: 796500--796567 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
796490 TCAAACAGTC
* * *
796500 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGAAAACAGACTAAATATTA
*
796531 GGGGACCATATTGAAAACGGACTAAATATTA
1 GGGGACCATATTGAAAACAGACTAAATATTA
796562 GGGGAC
1 GGGGAC
796568 TGTATTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTGAAAACAGACTAAATATTA
Found at i:799452 original size:35 final size:35
Alignment explanation
Indices: 799369--799558 Score: 193
Period size: 35 Copynumber: 5.4 Consensus size: 35
799359 AAACATATAC
* ***
799369 ATATATA-TATATAATTTTTAAAACGATTTTAAAAA
1 ATATATAGTATATAGTTTTTAAAGTAATTTT-AAAA
* *
799404 ACATATAGTATATAGTTTTTAAAGTAATTTTGAAA
1 ATATATAGTATATAGTTTTTAAAGTAATTTTAAAA
*
799439 ATATATAGTATATAGTTTTTAAAGTAATTTTGAAA
1 ATATATAGTATATAGTTTTTAAAGTAATTTTAAAA
* * * ****
799474 ACATATAATATATGGTTTTTTAAAACGGTTTTAAAA
1 ATATATAGTATATAG-TTTTTAAAGTAATTTTAAAA
* *
799510 AGTATATAGTATATAGGTTTTAAAGTAAGTTTAAAA
1 A-TATATAGTATATAGTTTTTAAAGTAATTTTAAAA
*
799546 ATATATAGCATAT
1 ATATATAGTATAT
799559 TTTATTATTA
Statistics
Matches: 127, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
35 66 0.52
36 50 0.39
37 11 0.09
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (35 bp):
ATATATAGTATATAGTTTTTAAAGTAATTTTAAAA
Found at i:802875 original size:37 final size:37
Alignment explanation
Indices: 802820--802893 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
802810 GAAGATAGAA
802820 AACTATAGTTCTATCAATTTACAACTCAGGTAAATTT
1 AACTATAGTTCTATCAATTTACAACTCAGGTAAATTT
* * *
802857 AACTGTAGTTCTATCAATTTACAGCTTAGGTAAATTT
1 AACTATAGTTCTATCAATTTACAACTCAGGTAAATTT
802894 CCAAACCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (37 bp):
AACTATAGTTCTATCAATTTACAACTCAGGTAAATTT
Found at i:803854 original size:69 final size:70
Alignment explanation
Indices: 803743--803889 Score: 251
Period size: 69 Copynumber: 2.1 Consensus size: 70
803733 CACAATCATT
* *
803743 AATTATATTCTAAACCCCAAAATCCAAAATACTTTAATTACATTCTAAACCTC-AATTCCAAAAT
1 AATTACATTCTAAACCCCAAAATCCAAAATACTTCAATTACATTCTAAACCTCAAATTCCAAAAT
803807 ACTTC
66 ACTTC
* *
803812 AATTACATTCTAAACCTCAAATTCCAAAATACTTCAATTACATTCTAAACCTCAAATTCCAAAAT
1 AATTACATTCTAAACCCCAAAATCCAAAATACTTCAATTACATTCTAAACCTCAAATTCCAAAAT
803877 ACTTC
66 ACTTC
803882 AATTACAT
1 AATTACAT
803890 GGCCAACCCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
69 49 0.67
70 24 0.33
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (70 bp):
AATTACATTCTAAACCCCAAAATCCAAAATACTTCAATTACATTCTAAACCTCAAATTCCAAAAT
ACTTC
Found at i:803905 original size:35 final size:35
Alignment explanation
Indices: 803743--803889 Score: 251
Period size: 35 Copynumber: 4.2 Consensus size: 35
803733 CACAATCATT
* * * *
803743 AATTATATTCTAAACCCCAAAATCCAAAATACTTT
1 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
803778 AATTACATTCTAAACCTC-AATTCCAAAATACTTC
1 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
803812 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
1 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
803847 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
1 AATTACATTCTAAACCTCAAATTCCAAAATACTTC
803882 AATTACAT
1 AATTACAT
803890 GGCCAACCCC
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
34 32 0.30
35 75 0.70
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
AATTACATTCTAAACCTCAAATTCCAAAATACTTC
Found at i:804261 original size:147 final size:148
Alignment explanation
Indices: 804068--804359 Score: 433
Period size: 147 Copynumber: 2.0 Consensus size: 148
804058 AAATACTCAA
***** *
804068 TTCAGTTTATAAAATAGTTGACTCGAATTTTTTTCGATTTGAGTTTATAACATTCAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCGAAAAAAATTCGATTTGAGTTTATAAAATTCAAATCAAGTC
* * * * *
804133 GAATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATAT
66 GAATTGAATTAAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAT
804198 TATTTGATTCTAATTCAG
131 TATTTGATTCTAATTCAG
* * *
804216 TTCAGTTTATAAAATAGTTTACTC-AAAAAAATTCGATTTGAGTTTATAAAATTTAAATCAATTC
1 TTCAGTTTATAAAATAGTTGACTCGAAAAAAATTCGATTTGAGTTTATAAAATTCAAATCAAGTC
*
804280 GATTTGAATTAAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAT
66 GAATTGAATTAAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAT
*
804345 TATTTTATTCTAATT
131 TATTTGATTCTAATT
804360 TAAATAGTTT
Statistics
Matches: 128, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
147 105 0.82
148 23 0.18
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (148 bp):
TTCAGTTTATAAAATAGTTGACTCGAAAAAAATTCGATTTGAGTTTATAAAATTCAAATCAAGTC
GAATTGAATTAAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAT
TATTTGATTCTAATTCAG
Found at i:804876 original size:35 final size:34
Alignment explanation
Indices: 804836--804932 Score: 122
Period size: 35 Copynumber: 2.8 Consensus size: 34
804826 GAATGTATTA
** * *
804836 TGAATTTGGGGTTGGGCATGTAATTGAAGTATTT
1 TGAATTTGGGGTTTAGAATGTAATTGAAGCATTT
* *
804870 TAGAATTTGAGGTTTCGAATGTAATTGAAGCATTT
1 T-GAATTTGGGGTTTAGAATGTAATTGAAGCATTT
804905 TGAAATTTGGGGTTTAGAATGTAATTGA
1 TG-AATTTGGGGTTTAGAATGTAATTGA
804933 TGACTATATT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.04
35 52 0.96
ACGTcount: A:0.29, C:0.03, G:0.28, T:0.40
Consensus pattern (34 bp):
TGAATTTGGGGTTTAGAATGTAATTGAAGCATTT
Found at i:806035 original size:15 final size:15
Alignment explanation
Indices: 806015--806056 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
806005 TTTTAATCAC
806015 TTAACTATTGTCTAT
1 TTAACTATTGTCTAT
806030 TTAACTATTGAT-TAT
1 TTAACTATTG-TCTAT
*
806045 TAAACTATTGTC
1 TTAACTATTGTC
806057 AATCAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (15 bp):
TTAACTATTGTCTAT
Found at i:809577 original size:51 final size:51
Alignment explanation
Indices: 809501--809603 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
809491 CTATCTGAAG
809501 TTTGTAAGGTATACGAATTTGAGTTT-CCCCCATAGGTAATGACAAAGACCC
1 TTTGTAAGGTATACGAATTTGAGTTTCCCCCCATAGGTAATGAC-AAGACCC
809552 TTTGTAAGGTATACGAATTTGAGTTTCCCCCCATAGGTAATGACAAGACCC
1 TTTGTAAGGTATACGAATTTGAGTTTCCCCCCATAGGTAATGACAAGACCC
809603 T
1 T
809604 GATGAGGTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 34 0.67
52 17 0.33
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (51 bp):
TTTGTAAGGTATACGAATTTGAGTTTCCCCCCATAGGTAATGACAAGACCC
Found at i:810095 original size:12 final size:12
Alignment explanation
Indices: 810078--810109 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
810068 CTCGCTGTCA
810078 TCATCGTCGTCG
1 TCATCGTCGTCG
810090 TCATCGTCGTCG
1 TCATCGTCGTCG
*
810102 TCGTCGTC
1 TCATCGTC
810110 CTGAGCAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.34, G:0.25, T:0.34
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:812528 original size:17 final size:18
Alignment explanation
Indices: 812485--812525 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
812475 GAATTATATT
812485 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
812502 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
812520 ATTAAA
1 AGTAAA
812526 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:812604 original size:10 final size:10
Alignment explanation
Indices: 812567--812607 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
812557 CTTAAACAGA
*
812567 GAGAGTATTT
1 GAGAGAATTT
*
812577 GAGAGAAATT
1 GAGAGAATTT
812587 GAGAGAATTT
1 GAGAGAATTT
812597 GAGAGAATTT
1 GAGAGAATTT
812607 G
1 G
812608 GTGTGATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:816225 original size:21 final size:21
Alignment explanation
Indices: 816199--816244 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
816189 CCACTTCGTT
816199 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
816220 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
816241 TCTT
1 TCTT
816245 CTTATCTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.24, G:0.11, T:0.54
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:821124 original size:16 final size:16
Alignment explanation
Indices: 821078--821137 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
821068 TGTAAATGAT
*
821078 CTGACTTGTTATTTGAC
1 CTGACTTGATATTT-AC
821095 CTGA-TATGATATTTAC
1 CTGACT-TGATATTTAC
*
821111 CTGACTTGACATTTAC
1 CTGACTTGATATTTAC
*
821127 TTGACTT-ATAT
1 CTGACTTGATAT
821138 ATCACCATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 3 0.08
16 22 0.59
17 12 0.32
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (16 bp):
CTGACTTGATATTTAC
Found at i:821309 original size:28 final size:28
Alignment explanation
Indices: 821278--821415 Score: 80
Period size: 28 Copynumber: 5.1 Consensus size: 28
821268 ATATATTTAA
821278 TATATTTATTA-TGATAATTAATATACTT
1 TATATTTATTACTGAT-ATTAATATACTT
* * * *
821306 TATAATTAATACTTATATTTATATACTT
1 TATATTTATTACTGATATTAATATACTT
*
821334 TA-A--TACTT--T-ATATTTA-ATACTT
1 TATATTTA-TTACTGATATTAATATACTT
*
821356 TATA-TTATATACTTTAGTACTT-ATATACTT
1 TATATTTAT-TAC-TGA-TA-TTAATATACTT
* *
821386 TATATTTAATACTTATATTAATATACTT
1 TATATTTATTACTGATATTAATATACTT
821414 TA
1 TA
821416 ATACTTATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 28
0.73 0.05 0.23
Matches are distributed among these distances:
22 8 0.09
23 9 0.10
24 4 0.04
25 2 0.02
26 1 0.01
27 4 0.04
28 35 0.39
29 9 0.10
30 15 0.17
31 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (28 bp):
TATATTTATTACTGATATTAATATACTT
Found at i:821319 original size:14 final size:14
Alignment explanation
Indices: 821300--821408 Score: 76
Period size: 14 Copynumber: 8.2 Consensus size: 14
821290 GATAATTAAT
821300 ATACTTTATAATTA
1 ATACTTTATAATTA
821314 ATAC-TTAT-ATT-
1 ATACTTTATAATTA
*
821325 -TA---TATACTTTA
1 ATACTTTATAAT-TA
*
821336 ATACTTTATATTTA
1 ATACTTTATAATTA
821350 ATACTTTAT-ATTA
1 ATACTTTATAATTA
*
821363 TATACTTTAGTACTTA
1 -ATACTTTA-TAATTA
*
821379 TATACTTTATATTTA
1 -ATACTTTATAATTA
821394 ATAC-TTAT-ATTA
1 ATACTTTATAATTA
821406 ATA
1 ATA
821409 TACTTTAATA
Statistics
Matches: 79, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
8 3 0.04
9 1 0.01
10 3 0.04
12 11 0.14
13 11 0.14
14 27 0.34
15 11 0.14
16 12 0.15
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (14 bp):
ATACTTTATAATTA
Found at i:821341 original size:36 final size:36
Alignment explanation
Indices: 821300--821426 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 36
821290 GATAATTAAT
*
821300 ATACTTTATAATTAATACTTATATTTATATACTTTA
1 ATACTTTATATTTAATACTTATATTTATATACTTTA
*
821336 ATACTTTATATTTAATACTTTATATTATATACTTTAGTACTTA
1 ATACTTTATATTTAATAC-TTATATT-TATA---TACT--TTA
*
821379 TATACTTTATATTTAATACTTATATTAATATACTTTA
1 -ATACTTTATATTTAATACTTATATTTATATACTTTA
821416 ATAC-TTATATT
1 ATACTTTATATT
821427 CAAACACTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
35 7 0.09
36 21 0.27
37 10 0.13
38 4 0.05
39 3 0.04
41 3 0.04
42 3 0.04
43 10 0.13
44 18 0.23
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.54
Consensus pattern (36 bp):
ATACTTTATATTTAATACTTATATTTATATACTTTA
Found at i:821384 original size:44 final size:44
Alignment explanation
Indices: 821319--821425 Score: 157
Period size: 44 Copynumber: 2.4 Consensus size: 44
821309 AATTAATACT
821319 TATA-TTTATATACTT-TAATACTTTATATTTAATACTTTATATT-A
1 TATACTTTA-ATACTTAT-ATACTTTATATTTAATAC-TTATATTAA
*
821363 TATACTTTAGTACTTATATACTTTATATTTAATACTTATATTAA
1 TATACTTTAATACTTATATACTTTATATTTAATACTTATATTAA
821407 TATACTTTAATACTTATAT
1 TATACTTTAATACTTATAT
821426 TCAAACACTT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
43 7 0.12
44 46 0.79
45 5 0.09
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.54
Consensus pattern (44 bp):
TATACTTTAATACTTATATACTTTATATTTAATACTTATATTAA
Found at i:821416 original size:22 final size:21
Alignment explanation
Indices: 821342--821469 Score: 102
Period size: 22 Copynumber: 5.9 Consensus size: 21
821332 TTTAATACTT
821342 TATATTTAATACTTTATATT-A
1 TATATTTAATAC-TTATATTAA
* *
821363 TATACTTTAGTACTTATA-TACTT
1 TATA-TTTAATACTTATATTA--A
821386 TATATTTAATACTTATATTAA
1 TATATTTAATACTTATATTAA
821407 TATACTTTAATACTTATATTCAA
1 TATA-TTTAATACTTATATT-AA
* *
821430 -ACACTTTATTACTCTATATT-A
1 TATA-TTTAATACT-TATATTAA
*
821451 TATATTTTATACTTTATAT
1 TATATTTAATAC-TTATAT
821470 ATAAAGTAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.01
21 25 0.28
22 48 0.55
23 14 0.16
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (21 bp):
TATATTTAATACTTATATTAA
Found at i:821424 original size:14 final size:14
Alignment explanation
Indices: 821311--821424 Score: 58
Period size: 14 Copynumber: 7.9 Consensus size: 14
821301 TACTTTATAA
821311 TTAATACTTATA-T
1 TTAATACTTATACT
821324 TTATATACTTTAATACT
1 TTA-ATAC-TT-ATACT
*
821341 TT-ATATTTAATACT
1 TTAATACTT-ATACT
*
821355 TT-ATATTATATACT
1 TTAATACT-TATACT
*
821369 TTAGTACTTATATACT
1 TTAATAC-T-TATACT
*
821385 TT-ATATTTAATACT
1 TTAATACTT-ATACT
* *
821399 TATATTA-ATATACT
1 T-TAATACTTATACT
821413 TTAATACTTATA
1 TTAATACTTATA
821425 TTCAAACACT
Statistics
Matches: 81, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.10
14 43 0.53
15 12 0.15
16 15 0.19
17 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.54
Consensus pattern (14 bp):
TTAATACTTATACT
Found at i:821454 original size:44 final size:43
Alignment explanation
Indices: 821345--821474 Score: 131
Period size: 44 Copynumber: 3.0 Consensus size: 43
821335 AATACTTTAT
* ** *
821345 ATTTAATACTTTATATTATATACTTTAGTACTTATATACTTTAT
1 ATTTAATAC-TTATATTATATACTTTAATACTTATATACTAAAC
*
821389 ATTTAATACTTATATTAATATACTTTAATACTTATATTC-AAAC
1 ATTTAATACTTATATT-ATATACTTTAATACTTATATACTAAAC
* *
821432 ACTTTATTACTCTATATTATATA-TTTTATACTTTATATA-TAAA
1 A-TTTAATACT-TATATTATATACTTTAATAC-TTATATACTAAA
821475 GTAAACATGA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
43 16 0.22
44 51 0.70
45 6 0.08
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.52
Consensus pattern (43 bp):
ATTTAATACTTATATTATATACTTTAATACTTATATACTAAAC
Found at i:821537 original size:7 final size:7
Alignment explanation
Indices: 821525--821580 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
821515 CAACACTTTA
821525 TATACTT
1 TATACTT
821532 TATACTT
1 TATACTT
821539 TATA-TT
1 TATACTT
* *
821545 AAACACTT
1 -TATACTT
821553 TATTACTT
1 TA-TACTT
821561 TATA-TT
1 TATACTT
821567 ATATACTT
1 -TATACTT
821575 TATACT
1 TATACT
821581 AAGATGACAC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
6 4 0.10
7 26 0.65
8 10 0.25
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (7 bp):
TATACTT
Found at i:821562 original size:22 final size:22
Alignment explanation
Indices: 821528--821577 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
821518 CACTTTATAT
821528 ACTTTA-TACTTTATATTAAAC
1 ACTTTATTACTTTATATTAAAC
* *
821549 ACTTTATTACTTTATATTATAT
1 ACTTTATTACTTTATATTAAAC
821571 ACTTTAT
1 ACTTTAT
821578 ACTAAGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (22 bp):
ACTTTATTACTTTATATTAAAC
Found at i:821780 original size:17 final size:18
Alignment explanation
Indices: 821758--821808 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
821748 TTAAAAATTA
821758 AATAAAT-ATTTAAACAT
1 AATAAATCATTTAAACAT
*
821775 AATAAATCCTTTAAACAT
1 AATAAATCATTTAAACAT
*
821793 AATAAATCCTTTAAAC
1 AATAAATCATTTAAAC
821809 TTTTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 7 0.22
18 25 0.78
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCATTTAAACAT
Found at i:821789 original size:18 final size:18
Alignment explanation
Indices: 821766--821808 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
821756 TAAATAAATA
821766 TTTAAACATAATAAATCC
1 TTTAAACATAATAAATCC
821784 TTTAAACATAATAAATCC
1 TTTAAACATAATAAATCC
821802 TTTAAAC
1 TTTAAAC
821809 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAACATAATAAATCC
Found at i:822622 original size:16 final size:16
Alignment explanation
Indices: 822601--822631 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
822591 TCCAGGCAGG
822601 CAACTAATATTGGCGC
1 CAACTAATATTGGCGC
822617 CAACTAATATTGGCG
1 CAACTAATATTGGCG
822632 GGTGATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (16 bp):
CAACTAATATTGGCGC
Found at i:823898 original size:15 final size:15
Alignment explanation
Indices: 823880--823912 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
823870 ATTAATATTT
823880 TATCTATTTGTATAA
1 TATCTATTTGTATAA
823895 TATCTATTTGTATAA
1 TATCTATTTGTATAA
823910 TAT
1 TAT
823913 ACACTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (15 bp):
TATCTATTTGTATAA
Found at i:824684 original size:7 final size:7
Alignment explanation
Indices: 824672--824750 Score: 115
Period size: 7 Copynumber: 11.3 Consensus size: 7
824662 AATACCTATA
824672 TTAGGGT
1 TTAGGGT
824679 TTAGGGT
1 TTAGGGT
*
824686 TTAAGGT
1 TTAGGGT
824693 TTAGGGT
1 TTAGGGT
824700 TTAGGGT
1 TTAGGGT
824707 TTAGGGT
1 TTAGGGT
**
824714 TTATGATT
1 TTA-GGGT
824722 TTA-GGT
1 TTAGGGT
824728 TTAGGGT
1 TTAGGGT
824735 TTAGGGT
1 TTAGGGT
824742 TTAGGGT
1 TTAGGGT
824749 TT
1 TT
824751 CTATAAACTA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
6 4 0.06
7 55 0.86
8 5 0.08
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:824855 original size:16 final size:15
Alignment explanation
Indices: 824824--824860 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
824814 TAATTTACTT
*
824824 TATATAGTTTATATA
1 TATATAGTTAATATA
824839 TATATAGGTTAATATA
1 TATATA-GTTAATATA
824855 TATATA
1 TATATA
824861 TATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (15 bp):
TATATAGTTAATATA
Found at i:824858 original size:20 final size:20
Alignment explanation
Indices: 824833--824895 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
824823 TTATATAGTT
*
824833 TATATATATATAGGTTAATA
1 TATATATATATAGGTTTATA
824853 TATATATATATA-GTTTATA
1 TATATATATATAGGTTTATA
*
824872 TATACTATACAT-GGTTTATA
1 TATA-TATATATAGGTTTATA
824892 TATA
1 TATA
824896 CATTAGAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.26
20 29 0.74
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (20 bp):
TATATATATATAGGTTTATA
Found at i:825405 original size:2 final size:2
Alignment explanation
Indices: 825400--825503 Score: 102
Period size: 2 Copynumber: 51.0 Consensus size: 2
825390 TTATATAGTT
* *
825400 TA TA TA TA TA TT TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
825442 -A TA TA TA TA CA CTA TA TA CA TA CA TA CA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
825484 TA TA GTT TA TA TA TA CTA TA
1 TA TA -TA TA TA TA TA -TA TA
825504 CATGGTTTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
1 1 0.01
2 79 0.94
3 4 0.05
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:825870 original size:20 final size:20
Alignment explanation
Indices: 825818--825886 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
825808 TAAATCTCAA
* *
825818 TTCTCAATTTTCCTCCAAAT
1 TTCTCAATTTCCCTCTAAAT
*
825838 TT-T-TATATTCCCTCTAAAT
1 TTCTCAAT-TTCCCTCTAAAT
825857 TTCTCAATTTCCCTCTAAA-
1 TTCTCAATTTCCCTCTAAAT
825876 TTCTCAATTTC
1 TTCTCAATTTC
825887 TCTATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.05
19 24 0.57
20 14 0.33
21 2 0.05
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.48
Consensus pattern (20 bp):
TTCTCAATTTCCCTCTAAAT
Found at i:826006 original size:2 final size:2
Alignment explanation
Indices: 825999--826039 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
825989 ACTTTGAATA
825999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
826039 A
1 A
826040 GTTTATAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:826081 original size:22 final size:22
Alignment explanation
Indices: 826039--826081 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
826029 ATTATATTAT
*
826039 AGTTTATAAACTATATTTTTAG
1 AGTTTATAAACTATATGTTTAG
*
826061 AGTTTATACA-TATATAGTTTA
1 AGTTTATAAACTATAT-GTTTA
826082 CATTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (22 bp):
AGTTTATAAACTATATGTTTAG
Found at i:826160 original size:18 final size:19
Alignment explanation
Indices: 826139--826174 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
826129 TATAATAATT
826139 ATATAGTTTATA-ATATAA
1 ATATAGTTTATATATATAA
826157 ATATAGTTTATATATATA
1 ATATAGTTTATATATATA
826175 GTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATAGTTTATATATATAA
Found at i:826185 original size:30 final size:30
Alignment explanation
Indices: 826138--826203 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
826128 TTATAATAAT
826138 TATATAGTTTATAATATAAA-TATAGTTTATA
1 TATATAGTTTATAATATAAACTATA--TTATA
826169 TATATAGTTTAT-ATATAAACCTATATTATA
1 TATATAGTTTATAATATAAA-CTATATTATA
826199 TATAT
1 TATAT
826204 TATATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
30 17 0.52
31 12 0.36
32 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (30 bp):
TATATAGTTTATAATATAAACTATATTATA
Found at i:827887 original size:16 final size:16
Alignment explanation
Indices: 827866--827904 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
827856 GGTATTACCC
827866 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
827882 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
827898 GACCTGT
1 GACCTGT
827905 AAATGATCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:828359 original size:21 final size:21
Alignment explanation
Indices: 828332--828379 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
828322 TTCATATTAT
**
828332 GGTTTATGGTTTAGTGTTTAG
1 GGTTTATGGTTTAAAGTTTAG
*
828353 TGTTTATGGTTTAAAGTTTAG
1 GGTTTATGGTTTAAAGTTTAG
828374 GGTTTA
1 GGTTTA
828380 GGATTTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (21 bp):
GGTTTATGGTTTAAAGTTTAG
Found at i:828889 original size:21 final size:20
Alignment explanation
Indices: 828865--828936 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
828855 GTCATTTACA
828865 TTAGGGTTTATGGTTTAGTGT
1 TTAGGGTTTATGGTTTA-TGT
* * *
828886 TTAGTGTTCATGGTTTAAAGT
1 TTAGGGTTTATGGTTT-ATGT
* * *
828907 TTATGATTTAGGGTTTATGAT
1 TTAGGGTTTATGGTTTATG-T
828928 TTAGGGTTT
1 TTAGGGTTT
828937 CTATAAACTA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.92
22 1 0.03
ACGTcount: A:0.19, C:0.01, G:0.28, T:0.51
Consensus pattern (20 bp):
TTAGGGTTTATGGTTTATGT
Found at i:828931 original size:14 final size:14
Alignment explanation
Indices: 828905--828936 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
828895 ATGGTTTAAA
828905 GTTTATGATTTAGG
1 GTTTATGATTTAGG
828919 GTTTATGATTTAGG
1 GTTTATGATTTAGG
828933 GTTT
1 GTTT
828937 CTATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (14 bp):
GTTTATGATTTAGG
Found at i:828985 original size:17 final size:17
Alignment explanation
Indices: 828963--829001 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
828953 TAATATACTT
828963 TATATAGTTTATATATA
1 TATATAGTTTATATATA
828980 TATATAGTTTATATATA
1 TATATAGTTTATATATA
828997 T-TATA
1 TATATA
829002 CATGGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:829001 original size:9 final size:9
Alignment explanation
Indices: 828955--828994 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
828945 TATATAAGTA
*
828955 ATATACTTT
1 ATATAGTTT
828964 ATATAGTTT
1 ATATAGTTT
*
828973 ATATA-TAT
1 ATATAGTTT
828981 ATATAGTTT
1 ATATAGTTT
828990 ATATA
1 ATATA
828995 TATTATACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (9 bp):
ATATAGTTT
Found at i:829311 original size:504 final size:496
Alignment explanation
Indices: 828466--829366 Score: 1342
Period size: 504 Copynumber: 1.8 Consensus size: 496
828456 TTTATATAGT
828466 TTTATATATATACTATACATATATAGTTTATATATACTATACATGGTTTATACATACATATTATA
1 TTTATATATATACTATACATATATAGTTTATATATACTATACATGGTTTATACATACATATTATA
*
828531 TAAAACTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAAT
66 TAAAACTATTTAATAAAATTATTTAAATGTAAATCATATAAAACATGATTAATTAGGTGTTAAAT
*
828596 AATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTTAT
131 AATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCAT
* ** *
828661 TTGCATGATTAGTATTTTAGTTACATGTTAGGTTAATTCACATTAATAGTCCATTTATTTTGTTA
196 TTGCATAATTAGTATTTTAACTACATGTTAGGTTAATTCACATTAATACTCCATTTATTTTGTTA
* * * ***
828726 TTATGAATAAGTAATAATAAAACTAAAAAATAAGTCCATTTACAATAATGCTAGTCCATTTGTAA
261 TTATGAATAAGTAATAATAAAACCAAAAAATAAGTACATTTACAATAATGCTAATCCATTAACAA
*
828791 TAGTATACACAGGCCCAATACATAAACT-CACTCTTTTATTACAAATATATATGCATTAGTGCTA
326 TAGTATACACAGGCCCAATACAT-AACTCCACTCTTTTATTACAAATATATAAGCATTAGTGCTA
828855 GT-CATTTACATTAGGGTTTATGGTTTAGTGTTTAGTGTTCATGGTTTAAAGTTTATGATTTAGG
390 GTCCATTTACATTAGGGTTTATGGTTTAGTGTTTAGTGTTCATGGTTTAAAGTTTATGATTTAGG
828919 GTTTATGATTTAGGGTTTCTATAAACTATATAAGTAATATAC
455 GTTTATGATTTAGGGTTTCTATAAACTATATAAGTAATATAC
* * *
828961 TTTATATAGTTTA-TATATATATATAGTTTATATATATTATACATGGTTTATACATACATATTAT
1 TTTATATA-TATACTATACATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
*
829025 ATAAAATTATTTAATAAAATTAATAATATTATTTAAATGTAAATCATATAAAACATGATTAATTA
65 ATAAAACTA-TT--T--AA-T-A-AA-ATTATTTAAATGTAAATCATATAAAACATGATTAATTA
* * *
829090 TGTGTTAAATAATTAGTATGTCACATTGCATGTTATATGGTTTATAAATAGTAGTACATGTCATA
121 GGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATA
* *
829155 TTAATTTCATTTGCATAATTAGTATTTTAACTGCATGTTATGTTAATTCACATTAATAACT-CAT
186 TTAATTTCATTTGCATAATTAGTATTTTAACTACATGTTAGGTTAATTCACATTAAT-ACTCCAT
* * * ** * *
829219 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTATATTTGTAATAGTGTTAA
250 TTATTTTGTTATTATGAATAAGTAATAATAAAACCAAAAAATAAGTACATTTACAATAATGCTAA
* * * * * *
829284 TCCATTAACATTAGTTTACATAGGCCCAATACATAAGTCCACTCTTTTATTATAAATATATAAGT
315 TCCATTAACAATAGTATACACAGGCCCAATACATAACTCCACTCTTTTATTACAAATATATAAGC
*
829349 ATTAGTGTTAGTCCATTT
380 ATTAGTGCTAGTCCATTT
829367 CGAAAAATGA
Statistics
Matches: 357, Mismatches: 36, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
495 65 0.18
496 5 0.01
498 1 0.00
500 2 0.01
501 1 0.00
502 1 0.00
503 5 0.01
504 270 0.76
505 7 0.02
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (496 bp):
TTTATATATATACTATACATATATAGTTTATATATACTATACATGGTTTATACATACATATTATA
TAAAACTATTTAATAAAATTATTTAAATGTAAATCATATAAAACATGATTAATTAGGTGTTAAAT
AATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCAT
TTGCATAATTAGTATTTTAACTACATGTTAGGTTAATTCACATTAATACTCCATTTATTTTGTTA
TTATGAATAAGTAATAATAAAACCAAAAAATAAGTACATTTACAATAATGCTAATCCATTAACAA
TAGTATACACAGGCCCAATACATAACTCCACTCTTTTATTACAAATATATAAGCATTAGTGCTAG
TCCATTTACATTAGGGTTTATGGTTTAGTGTTTAGTGTTCATGGTTTAAAGTTTATGATTTAGGG
TTTATGATTTAGGGTTTCTATAAACTATATAAGTAATATAC
Found at i:829747 original size:30 final size:31
Alignment explanation
Indices: 829682--829747 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
829672 GAAAAAAATT
829682 AATATGATTACTTTTTAAATGTAATTAAAAA
1 AATATGATTACTTTTTAAATGTAATTAAAAA
* *
829713 AATATGATTACTTTTTAAATGTTA-TAATAA
1 AATATGATTACTTTTTAAATGTAATTAAAAA
829743 AATAT
1 AATAT
829748 TTATTATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (31 bp):
AATATGATTACTTTTTAAATGTAATTAAAAA
Found at i:829869 original size:21 final size:23
Alignment explanation
Indices: 829835--829878 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
829825 TAATGCAAAG
829835 GAAAATTAATATAGTTT-ATTTA
1 GAAAATTAATATAGTTTAATTTA
829857 GAAAATT-ATATAGTTTAATTTA
1 GAAAATTAATATAGTTTAATTTA
829879 TATAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (23 bp):
GAAAATTAATATAGTTTAATTTA
Found at i:830337 original size:2 final size:2
Alignment explanation
Indices: 830326--830452 Score: 58
Period size: 2 Copynumber: 66.0 Consensus size: 2
830316 ATAATATTTC
* *
830326 TA TA -A TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
830364 TA GT- TA TA CA TA CA TA TA TA TA CTA TA T- TA -A TA TA -A TT TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
830404 TA AA CTA TA TA T- TT TA TA TA GTT TA TA TA CA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
830447 TA TA TA
1 TA TA TA
830453 GAAAATTAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 30
0.66 0.12 0.21
Matches are distributed among these distances:
1 10 0.11
2 77 0.83
3 6 0.06
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:830428 original size:25 final size:27
Alignment explanation
Indices: 830379--830450 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 27
830369 ATACATACAT
830379 ATATATACTATATTAATATAATTTATAAAC
1 ATATATA-TATA-T-ATATAATTTATAAAC
* * *
830409 -TATATAT-TTTATATAGTTTATATAC
1 ATATATATATATATATAATTTATAAAC
830434 ATATATATATATATATA
1 ATATATATATATATATA
830451 TAGAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 13 0.36
26 8 0.22
27 8 0.22
28 1 0.03
29 6 0.17
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (27 bp):
ATATATATATATATATAATTTATAAAC
Found at i:830692 original size:20 final size:19
Alignment explanation
Indices: 830638--830716 Score: 81
Period size: 19 Copynumber: 4.1 Consensus size: 19
830628 AATAAAATCT
* *
830638 AATTATCAATTTCCCTCCAA
1 AATTTTCAATTTCCCT-CTA
*
830658 AATTTTCTA-TTCCCTCTA
1 AATTTTCAATTTCCCTCTA
830676 AATTTCTCAATTTCCCTCTA
1 AATTT-TCAATTTCCCTCTA
*
830696 AATTATT-AATTTCCCTATA
1 AATT-TTCAATTTCCCTCTA
830715 AA
1 AA
830717 AAAATTTCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
18 7 0.14
19 22 0.43
20 21 0.41
21 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTTCAATTTCCCTCTA
Found at i:830792 original size:2 final size:2
Alignment explanation
Indices: 830785--830929 Score: 51
Period size: 2 Copynumber: 74.5 Consensus size: 2
830775 ATAATGTATG
* *
830785 TA TA TA TA TA TA TA T- TA -A TA TA AA T- TA TA GTA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
830825 TA GTT TA CA TA TA TA GTT TA TA TA TA GT- TCA TA TA AA CA TA -A
1 TA -TA TA TA TA TA TA -TA TA TA TA TA -TA T-A TA TA TA TA TA TA
* *
830867 TT TA TA TA T- TA AA T- TA TA TA -A T- TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
830904 GTT TA TA TA AA CT- TA TA TA TA TA TA T
1 -TA TA TA TA TA -TA TA TA TA TA TA TA T
830930 TTTTTTCAAA
Statistics
Matches: 104, Mismatches: 21, Indels: 36
0.65 0.13 0.22
Matches are distributed among these distances:
1 11 0.11
2 86 0.83
3 7 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:830828 original size:13 final size:13
Alignment explanation
Indices: 830785--830841 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
830775 ATAATGTATG
*
830785 TATATA-TATATA
1 TATATAGTATACA
* *
830797 TAT-TAATATAAA
1 TATATAGTATACA
830809 T-TATAGTATACA
1 TATATAGTATACA
*
830821 TATATAGTTTACA
1 TATATAGTATACA
830834 TATATAGT
1 TATATAGT
830842 TTATATATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 3 0.08
12 17 0.45
13 18 0.47
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (13 bp):
TATATAGTATACA
Found at i:830842 original size:13 final size:13
Alignment explanation
Indices: 830810--830853 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
830800 TAATATAAAT
*
830810 TATAGTATACATA
1 TATAGTTTACATA
830823 TATAGTTTACATA
1 TATAGTTTACATA
830836 TATAGTTT--ATA
1 TATAGTTTACATA
830847 TATAGTT
1 TATAGTT
830854 CATATAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 10 0.33
13 20 0.67
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (13 bp):
TATAGTTTACATA
Found at i:830858 original size:11 final size:11
Alignment explanation
Indices: 830819--830859 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
830809 TTATAGTATA
830819 CATATATAGTTT
1 CATATATAG-TT
830831 ACATATATAGTT
1 -CATATATAGTT
*
830843 TATATATAGTT
1 CATATATAGTT
830854 CATATA
1 CATATA
830860 AACATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 15 0.58
12 2 0.08
13 9 0.35
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (11 bp):
CATATATAGTT
Found at i:834345 original size:19 final size:19
Alignment explanation
Indices: 834318--834354 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
834308 ATGACTAACA
* *
834318 AAATTGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
834337 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
834355 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:834814 original size:22 final size:22
Alignment explanation
Indices: 834789--834839 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
834779 CTACGGTAAC
834789 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
834811 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
834833 ATCCGTC
1 ATCCGTC
834840 TATCTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:835220 original size:20 final size:20
Alignment explanation
Indices: 835195--835282 Score: 97
Period size: 20 Copynumber: 4.5 Consensus size: 20
835185 AGGATCGCAA
835195 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
835215 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
** * *
835235 CGATTTTC-ATTTCACGTTG
1 CGATAGTCAAATTCGCGTTG
*
835254 CGATAGTCAAATTCGCGTTA
1 CGATAGTCAAATTCGCGTTG
835274 CGATAGTCA
1 CGATAGTCA
835283 TTTACGTGTT
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.26
20 40 0.74
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:835284 original size:39 final size:39
Alignment explanation
Indices: 835194--835289 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 39
835184 GAGGATCGCA
* * ** *
835194 ACGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTT
1 ACGATAGTC-ATTTCACGTTGCGATAGTCAAATTCGCGTT
* **
835234 GCGATTTTCATTTCACGTTGCGATAGTCAAATTCGCGTT
1 ACGATAGTCATTTCACGTTGCGATAGTCAAATTCGCGTT
835273 ACGATAGTCATTT-ACGT
1 ACGATAGTCATTTCACGT
835290 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 4 0.09
39 35 0.78
40 6 0.13
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (39 bp):
ACGATAGTCATTTCACGTTGCGATAGTCAAATTCGCGTT
Found at i:835297 original size:20 final size:20
Alignment explanation
Indices: 835211--835317 Score: 85
Period size: 20 Copynumber: 5.4 Consensus size: 20
835201 TCAAATTCGC
*
835211 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTACGT
**
835231 GTTGCGATTTTCATTTCAC--
1 GTTGCGATAGTCATTT-ACGT
* *
835250 GTTGCGATAGTCAAATT-CGC
1 GTTGCGATAGTC-ATTTACGT
*
835270 GTTACGATAGTCATTTACGT
1 GTTGCGATAGTCATTTACGT
** *
835290 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTACGT
*
835310 GGTGCGAT
1 GTTGCGAT
835318 TTTAAGTTTC
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 13 0.19
20 53 0.78
21 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (20 bp):
GTTGCGATAGTCATTTACGT
Found at i:835327 original size:20 final size:20
Alignment explanation
Indices: 835287--835327 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
835277 TAGTCATTTA
* * *
835287 CGTGTTGCGATTTTCATTTT
1 CGTGGTGCGATTTTAAGTTT
835307 CGTGGTGCGATTTTAAGTTT
1 CGTGGTGCGATTTTAAGTTT
835327 C
1 C
835328 AGAAACTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (20 bp):
CGTGGTGCGATTTTAAGTTT
Found at i:837313 original size:33 final size:34
Alignment explanation
Indices: 837258--837333 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
837248 GAATTTGACT
* *
837258 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCACAATGCGAAAATAAAA
* *
837291 ATCGCAACGTGAAAATCACAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCACAATGCGAAAATAAAA
837325 ATCGCAACG
1 ATCGCAACG
837334 CGAATTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCACAATGCGAAAATAAAA
Found at i:837323 original size:20 final size:20
Alignment explanation
Indices: 837300--837337 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
837290 AATCGCAACG
*
837300 TGAAAATCACAATGCGAAAA
1 TGAAAATCACAACGCGAAAA
*
837320 TGAAAATCGCAACGCGAA
1 TGAAAATCACAACGCGAA
837338 TTTAGTTTCG
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:0.50, C:0.18, G:0.18, T:0.13
Consensus pattern (20 bp):
TGAAAATCACAACGCGAAAA
Found at i:837355 original size:19 final size:19
Alignment explanation
Indices: 837333--837375 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
837323 AAATCGCAAC
837333 GCGA-ATTTAGTTTCGCATT
1 GCGATATTTA-TTTCGCATT
*
837352 GCGATTTTTATTTCGCATT
1 GCGATATTTATTTCGCATT
837371 GCGAT
1 GCGAT
837376 TATCCCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATATTTATTTCGCATT
Found at i:837376 original size:19 final size:20
Alignment explanation
Indices: 837338--837376 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
837328 GCAACGCGAA
837338 TTTAGTTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
837358 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
837377 ATCCCGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:837406 original size:20 final size:20
Alignment explanation
Indices: 837381--837469 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
837371 GCGATTATCC
837381 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
837401 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
837421 CGTTGCGATAGTC-ATTTCTG
1 CGTTGCGATAGTCAAATTC-G
* **
837441 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
837461 CGTTGCGAT
1 CGTTGCGAT
837470 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.06
20 55 0.87
21 4 0.06
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:837479 original size:20 final size:19
Alignment explanation
Indices: 837456--837498 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
837446 TGATAGTCAT
837456 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTT-AG
*
837476 TTTCGTGTTGCGATTTTAG
1 TTTCGCGTTGCGATTTTAG
837495 TTTC
1 TTTC
837499 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.51
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTAG
Found at i:839233 original size:14 final size:14
Alignment explanation
Indices: 839214--839262 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
839204 TCTTGTTTAA
*
839214 TTGATTTCTAAAAG
1 TTGATTTATAAAAG
*
839228 TTGATTTGTAAAAG
1 TTGATTTATAAAAG
839242 TTGATTTATAAAAG
1 TTGATTTATAAAAG
839256 TTGATTT
1 TTGATTT
839263 GTTTAATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (14 bp):
TTGATTTATAAAAG
Found at i:839279 original size:41 final size:40
Alignment explanation
Indices: 839228--839357 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 40
839218 TTTCTAAAAG
*
839228 TTGATTTGTAAAAGTTGATTTATAAAAGTTGATTTGTTTAA
1 TTGATGTGTAAAAGTTGATTT-TAAAAGTTGATTTGTTTAA
* * *
839269 TTGATGTGTAAAA---AATTCTT---ATTTGTACTTGTTTAA
1 TTGATGTGTAAAAGTTGATT-TTAAAAGTTG-ATTTGTTTAA
*
839305 TTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAA
1 TTGATGTGTAAAAGTTGATTT-TAAAAGTTGATTTGTTTAA
839346 TTGATGTGTAAA
1 TTGATGTGTAAA
839358 TAATTCTTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
35 4 0.06
36 21 0.30
38 5 0.07
39 5 0.07
41 32 0.45
42 4 0.06
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (40 bp):
TTGATGTGTAAAAGTTGATTTTAAAAGTTGATTTGTTTAA
Found at i:839282 original size:28 final size:26
Alignment explanation
Indices: 839206--839282 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 26
839196 CATTTTTTTC
*
839206 TTGTTTAATTGATTTCTAAAAGTTGAT
1 TTGTTTAATTGATTT-AAAAAGTTGAT
**
839233 TTGTAAAAGTTGATTTATAAAAGTTGAT
1 TTGTTTAA-TTGATTTA-AAAAGTTGAT
839261 TTGTTTAATTGATGTGTAAAAA
1 TTGTTTAATTGAT-T-TAAAAA
839283 ATTCTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
27 11 0.27
28 28 0.68
29 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (26 bp):
TTGTTTAATTGATTTAAAAAGTTGAT
Found at i:839308 original size:36 final size:36
Alignment explanation
Indices: 839261--839386 Score: 112
Period size: 36 Copynumber: 3.4 Consensus size: 36
839251 AAAAGTTGAT
839261 TTGTTTAATTGATGTGTAAAAAATTCTTATTTGTAC
1 TTGTTTAATTGATGTGTAAAAAATTCTTATTTGTAC
* * * *
839297 TTGTTTAATTGATTTGTAAAAGTTGATT-TGTAAAAGTTG-AT
1 TTGTTTAATTGATGTGTAAAA---AATTCT-T---ATTTGTAC
* *
839338 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTTAATTGATGTGTAAAAAATTCTTATTTGTAC
*
839374 TTATTTAATTGAT
1 TTGTTTAATTGAT
839387 TGAAATGTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
35 4 0.06
36 32 0.46
38 5 0.07
39 5 0.07
41 20 0.29
42 4 0.06
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (36 bp):
TTGTTTAATTGATGTGTAAAAAATTCTTATTTGTAC
Found at i:839324 original size:14 final size:14
Alignment explanation
Indices: 839305--839341 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
839295 ACTTGTTTAA
839305 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
839319 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
839333 TTGATTTGT
1 TTGATTTGT
839342 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:839355 original size:77 final size:77
Alignment explanation
Indices: 839228--839408 Score: 290
Period size: 77 Copynumber: 2.3 Consensus size: 77
839218 TTTCTAAAAG
*
839228 TTGATTTGTAAAAGTTGATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAAAAATTCTTATTT
1 TTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAAAAATTCTTATTT
*
839293 GTACTTGTTTAA
66 GTACTTATTTAA
*
839305 TTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTT
1 TTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAAAAATTCTTATTT
*
839370 GTGCTTATTTAA
66 GTACTTATTTAA
839382 TTGATTGAAATGTAAAAGTTGATTTGT
1 TTGATT----TGTAAAAGTTGATTTGT
839409 TGAGTTCAAT
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
77 79 0.82
81 17 0.18
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.49
Consensus pattern (77 bp):
TTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAAAAATTCTTATTT
GTACTTATTTAA
Found at i:839486 original size:20 final size:20
Alignment explanation
Indices: 839461--839504 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
839451 AGGTACACTT
*
839461 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
839481 TCGCAACGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
839501 TCGC
1 TCGC
839505 GTTGTGATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.41, C:0.32, G:0.16, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:839636 original size:54 final size:54
Alignment explanation
Indices: 839578--839680 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
839568 ATCAAATTCA
* *
839578 CGTTGCGATAGTCAAATTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* *
839632 CGTTGCGATAGTCATATTCGCATTGCGATAGTCAAATTCGTGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGAT
839681 AGTCAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:839636 original size:74 final size:74
Alignment explanation
Indices: 839558--839742 Score: 289
Period size: 74 Copynumber: 2.5 Consensus size: 74
839548 GTCAAATTCT
* * * *
839558 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTTGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTA
839623 CGATTTTTG
66 CGATTTTTG
* * *
839632 CGTTGCGATAGTCATATTCGCATTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTA
839697 CGATTTTTG
66 CGATTTTTG
* *
839706 AGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
839743 GAATGTGTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 100 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTA
CGATTTTTG
Found at i:839636 original size:94 final size:94
Alignment explanation
Indices: 839496--839700 Score: 270
Period size: 94 Copynumber: 2.2 Consensus size: 94
839486 ACGCGAAAGC
* * * * * *
839496 CAAAATCGCGTTGTGATAGTCTATTACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCTCGT
1 CAAATTCGCGTTGCGATAGTCAATTACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATTCGCAT
839561 TGCGATAATCAAATTCACGTTGCGATAGT
66 TGCGATAATCAAATTCACGTTGCGATAGT
* *
839590 CAAATTTGCGTTGCGATAGTCAAATT-CGCGTTGCGATTTT-TGCGTTGCGATAGTCATATTCGC
1 CAAATTCGCGTTGCGATAGTC-AATTACGCGTTGCGATTTTCT-CGTTGCGATAGTCAAATTCGC
* **
839653 ATTGCGATAGTCAAATTCGTGTTGCGATAGT
64 ATTGCGATAATCAAATTCACGTTGCGATAGT
*
839684 CAAATTCGCGTTACGAT
1 CAAATTCGCGTTGCGAT
839701 TTTTGAGTTG
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
93 1 0.01
94 92 0.96
95 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (94 bp):
CAAATTCGCGTTGCGATAGTCAATTACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATTCGCAT
TGCGATAATCAAATTCACGTTGCGATAGT
Found at i:839732 original size:20 final size:20
Alignment explanation
Indices: 839538--839742 Score: 218
Period size: 20 Copynumber: 10.8 Consensus size: 20
839528 GCGATTTTCT
*
839538 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
* *
839558 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
839578 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
839598 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
839618 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
839632 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
839652 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
839672 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
839692 CGTTACGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
839706 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
839726 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
839743 GAATGTGTAA
Statistics
Matches: 153, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
14 22 0.14
16 2 0.01
18 2 0.01
20 127 0.83
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:839965 original size:140 final size:140
Alignment explanation
Indices: 839713--839995 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
839703 TTGAGTTGCG
*
839713 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGAAAACAACTGAACAGATCA
*
839778 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
66 TAGAAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
839843 AATACACATA
131 AATACACATA
* *
839853 ATAGTCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGAAAACAACTGAATAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGAAAACAACTGAACAGATCA
*
839918 TAGAAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGAAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
839983 AATACACATA
131 AATACACATA
839993 ATA
1 ATA
839996 CAACGTTTGC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGAAAACAACTGAACAGATCA
TAGAAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:842122 original size:14 final size:14
Alignment explanation
Indices: 842103--842129 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
842093 TCCCGTGGTA
842103 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
842117 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
842130 TTTCTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:842135 original size:12 final size:13
Alignment explanation
Indices: 842104--842136 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
842094 CCCGTGGTAT
842104 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
842117 TTTTCTTCGGGGA-
1 -TTTCTTCGGGGAC
842130 TTTCTTC
1 TTTCTTC
842137 TTTTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:843202 original size:20 final size:20
Alignment explanation
Indices: 843155--843202 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
843145 GAAATTCAGT
*
843155 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
843175 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
843195 GTTGCGAT
1 GTTGCGAT
843203 TTACAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:843715 original size:79 final size:80
Alignment explanation
Indices: 843621--843844 Score: 335
Period size: 79 Copynumber: 2.8 Consensus size: 80
843611 GTAATATGTT
* * *
843621 TTTAATATTTTCGGTAAAGCGTTACCTAAAATATTA-TTTTTTCTACCGAAAATATTAATATTGG
1 TTTAATATTTCCGGTAAAGCGTTACCTAAAACATTATTTTTTTCTACCGAAAATGTTAATATTGG
*
843685 ACGCTACCTAAAATG
66 ACGCTACCTAAAATA
* *
843700 TTTAACATTTCCGGTAAAGAGTTACCTAAAACATTATTTTTTTCTACCGAAAATGTT-ATATTGG
1 TTTAATATTTCCGGTAAAGCGTTACCTAAAACATTATTTTTTTCTACCGAAAATGTTAATATTGG
843764 ACGCTACCTAAAATA
66 ACGCTACCTAAAATA
* * * *
843779 TTTTATATTTCCGGTAAAACATTACTTAAAACATTATTTTTTTTCTACCGAAAATGTTAATATTG
1 TTTAATATTTCCGGTAAAGCGTTACCTAAAACATTA-TTTTTTTCTACCGAAAATGTTAATATTG
843844 G
65 G
843845 GTTCTACCGT
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 83 0.64
80 40 0.31
81 7 0.05
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (80 bp):
TTTAATATTTCCGGTAAAGCGTTACCTAAAACATTATTTTTTTCTACCGAAAATGTTAATATTGG
ACGCTACCTAAAATA
Found at i:850023 original size:39 final size:39
Alignment explanation
Indices: 849980--850061 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
849970 TAATTTTGAA
849980 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTT
1 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTT
850019 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTT
1 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTT
850058 ATTT
1 ATTT
850062 CATGCATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (39 bp):
ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTT
Found at i:850232 original size:120 final size:120
Alignment explanation
Indices: 850019--850237 Score: 438
Period size: 120 Copynumber: 1.8 Consensus size: 120
850009 AACACCATTT
850019 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTTATTTCATGCATGAAAAAGTTTTGAAA
1 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTTATTTCATGCATGAAAAAGTTTTGAAA
850084 TTTTGAAGGTTGGGAAACACATGTATTCCATGCATGAGAAAATATTAATTTTGAA
66 TTTTGAAGGTTGGGAAACACATGTATTCCATGCATGAGAAAATATTAATTTTGAA
850139 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTTATTTCATGCATGAAAAAGTTTTGAAA
1 ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTTATTTCATGCATGAAAAAGTTTTGAAA
850204 TTTTGAAGGTTGGGAAACACATGTATTCCATGCA
66 TTTTGAAGGTTGGGAAACACATGTATTCCATGCA
850238 GGGGCGGATG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 99 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (120 bp):
ATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATTTATTTCATGCATGAAAAAGTTTTGAAA
TTTTGAAGGTTGGGAAACACATGTATTCCATGCATGAGAAAATATTAATTTTGAA
Found at i:850715 original size:2 final size:2
Alignment explanation
Indices: 850708--850747 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
850698 TGAGCAGGGC
850708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
850748 CTGTACCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:851439 original size:634 final size:636
Alignment explanation
Indices: 850112--851597 Score: 2692
Period size: 661 Copynumber: 2.3 Consensus size: 636
850102 ACATGTATTC
850112 CATGCATGAGAAAATATTAATTTTGAAATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATT
1 CATGCATGAGAAAATATTAATTTTGAAATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATT
850177 TATTTCATGCATGAAAAAGTTTTGAAATTTTGAAGGTTGGGAAACACATGTATTCCATGCAGGGG
66 TATTTCATGCATGAAAAAGTTTTGAAATTTTGAAGGTTGGGAAACACATGTATTCCATGCAGGGG
850242 CGGATGCACTAAGCCTCCTA-GGGTCAAGTGCATCTCCATTATTTAGAGAAAAAAACAATGAATC
131 CGGATGCACTAAGCCTCCTAGGGGTCAAGTGCATCTCCATTATTTAGAGAAAAAAACAATGAATC
850306 GTAAAATACTTCAAATAAAATCTATTCACACTTACTTCATTGTTTCCTTCAACAACTTGACTTGA
196 GTAAAATACTTCAAATAAAATCTATTCACACTTACTTCATTGTTTCCTTCAACAACTTGACTTGA
850371 AAAAAATCCTTCTATCTTTTCTGTCTTATGTAAAAAAATTTGACATATTAAGTAAATAATTTCAT
261 AAAAAATCCTTCTATCTTTTCTGTCTTATGTAAAAAAATTTGACATATTAAGTAAATAATTTCAT
850436 ACAAAATAAAAAAATTAAACAAATAATTTCACATTTACTCAAAAAAAATAAGAGAGAAAACATAT
326 ACAAAATAAAAAAATTAAACAAATAATTTCACATTTACTCAAAAAAAATAAGAGAGAAAACATAT
850501 CAAATCAGCAGGTCAGGAAAAATGCATCAAATGAACACTCAAATCTTTTACACTTCACCAATTGA
391 CAAATCAGCAGGTCAGGAAAAATGCATCAAATGAACACTCAAATCTTTTACACTTCACCAATTGA
850566 TTCTCTCTTCTTAATGATCATTCTCGGATTCATTCCTATATGTTTATTGATGGAAAAATAATTTT
456 TTCTCTCTTCTTAATGATCATTCTCGGATTCATTCCTATATGTTTATTGATGGAAAAATAATTTT
*
850631 TTTTCCAACAACTTGTTGTGCGAGGGTATGAATTATATATGACATGATTCAATATAATTGTACCT
521 TTTTCCAACAACTTGTTGTGCGAGGGTATGAATTATATAGGACATGATTCAATATAATTGTACCT
850696 AATGAGCAGGGCATATATATATATATATATATATATATATATATATATATATCTGTACCTATAGC
586 AATGAGCAGGGC------------------------A-ATATATATATATATCTGTACCTATAGC
850761 TCTGCACGGAA
626 TCTGCACGGAA
*
850772 CATGCATGAGAAAATATTAATTTTGAAATTTTGAGCACAATGCGTCTTGGTTGGGAAACACCATT
1 CATGCATGAGAAAATATTAATTTTGAAATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATT
850837 TATTTCATGCATGAAAAAGTTTTGAAATTTTGAAGGTTGGGAAACACATGTATTCCATGCAGGGG
66 TATTTCATGCATGAAAAAGTTTTGAAATTTTGAAGGTTGGGAAACACATGTATTCCATGCAGGGG
*
850902 CAGATGCACTAAGCCTCCTAGGGGTCAAGTGCATCTCCATTATTTAGAGAAAAAAACAATGAATC
131 CGGATGCACTAAGCCTCCTAGGGGTCAAGTGCATCTCCATTATTTAGAGAAAAAAACAATGAATC
850967 GTAAAATACTTCAAATAAAATCTATTCACACTTACTTCATTGTTTCCTTCAACAACTTGACTTGA
196 GTAAAATACTTCAAATAAAATCTATTCACACTTACTTCATTGTTTCCTTCAACAACTTGACTTGA
851032 AAAAAATCCTTCTATCTTTTCTGTCTTATGTAAAAAAATTTGACATATTAAGTAAATAATTTCAT
261 AAAAAATCCTTCTATCTTTTCTGTCTTATGTAAAAAAATTTGACATATTAAGTAAATAATTTCAT
851097 ACAAAATAAAAAAATTAAACAAATAATTTCACATTTACTCAAAAAAAATAAGAGAGAAAACATAT
326 ACAAAATAAAAAAATTAAACAAATAATTTCACATTTACTCAAAAAAAATAAGAGAGAAAACATAT
851162 CAAATCAGCAGGTCAGGAAAAATGCATCAAATGAACACTCAAATCTTTTACACTTCACCAATTGA
391 CAAATCAGCAGGTCAGGAAAAATGCATCAAATGAACACTCAAATCTTTTACACTTCACCAATTGA
851227 TTCTCTCTTCTTAATGATCATTCTCGGATTCATTCCTATATGTTTATTGATGGAAAAATAA-TTT
456 TTCTCTCTTCTTAATGATCATTCTCGGATTCATTCCTATATGTTTATTGATGGAAAAATAATTTT
851291 TTTTCCAACAACTTGTTGTGCGAGGGTATGAATTATATAGGACATGATTCAATATAATTGTACCT
521 TTTTCCAACAACTTGTTGTGCGAGGGTATGAATTATATAGGACATGATTCAATATAATTGTACCT
851356 AATGAGCAGGGC-ATATATATATATATCTGTACCTATAGCTCTGCACGGAA
586 AATGAGCAGGGCAATATATATATATATCTGTACCTATAGCTCTGCACGGAA
851406 CATGCATGAGAAAATATTAATTTTGAAATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATT
1 CATGCATGAGAAAATATTAATTTTGAAATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATT
851471 TATTTCATGCATGAAAAAGTTTTGAAATTTTGAAGGTTGGGAAACACATGTATTCCATGCAGGGG
66 TATTTCATGCATGAAAAAGTTTTGAAATTTTGAAGGTTGGGAAACACATGTATTCCATGCAGGGG
851536 CGGATGCACTAAGCCTCCTAGGGGTCAAGTGCATCTCCATTATTTAGAGAAAAAAA-AATGAA
131 CGGATGCACTAAGCCTCCTAGGGGTCAAGTGCATCTCCATTATTTAGAGAAAAAAACAATGAA
851598 ATTTAGTATA
Statistics
Matches: 820, Mismatches: 5, Indels: 29
0.96 0.01 0.03
Matches are distributed among these distances:
633 6 0.01
634 222 0.27
660 227 0.28
661 365 0.45
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (636 bp):
CATGCATGAGAAAATATTAATTTTGAAATTTTGAACACAATGCGTCTTGGTTGGGAAACACCATT
TATTTCATGCATGAAAAAGTTTTGAAATTTTGAAGGTTGGGAAACACATGTATTCCATGCAGGGG
CGGATGCACTAAGCCTCCTAGGGGTCAAGTGCATCTCCATTATTTAGAGAAAAAAACAATGAATC
GTAAAATACTTCAAATAAAATCTATTCACACTTACTTCATTGTTTCCTTCAACAACTTGACTTGA
AAAAAATCCTTCTATCTTTTCTGTCTTATGTAAAAAAATTTGACATATTAAGTAAATAATTTCAT
ACAAAATAAAAAAATTAAACAAATAATTTCACATTTACTCAAAAAAAATAAGAGAGAAAACATAT
CAAATCAGCAGGTCAGGAAAAATGCATCAAATGAACACTCAAATCTTTTACACTTCACCAATTGA
TTCTCTCTTCTTAATGATCATTCTCGGATTCATTCCTATATGTTTATTGATGGAAAAATAATTTT
TTTTCCAACAACTTGTTGTGCGAGGGTATGAATTATATAGGACATGATTCAATATAATTGTACCT
AATGAGCAGGGCAATATATATATATATCTGTACCTATAGCTCTGCACGGAA
Found at i:858319 original size:2 final size:2
Alignment explanation
Indices: 858312--858353 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
858302 AAAGCACACC
858312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
858354 GGATGGTCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:863009 original size:32 final size:32
Alignment explanation
Indices: 862973--863042 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
862963 GTATTAATTG
* *
862973 ATTTCTTTCCTTTTGTTTGTGTACATTAACTA
1 ATTTCTTTCCTTTTGTTTATGTACACTAACTA
*
863005 ATTTCTTTCCTTTTGTTTATGTACACTAACTT
1 ATTTCTTTCCTTTTGTTTATGTACACTAACTA
863037 ATTTCT
1 ATTTCT
863043 CTTGATTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.19, C:0.17, G:0.07, T:0.57
Consensus pattern (32 bp):
ATTTCTTTCCTTTTGTTTATGTACACTAACTA
Found at i:866479 original size:30 final size:30
Alignment explanation
Indices: 866445--866504 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
866435 AGTTGATAAG
866445 GTCAAAACAAATGAAGCATATAGAAGAATA
1 GTCAAAACAAATGAAGCATATAGAAGAATA
866475 GTCAAAACAAATGAAGCATATAGAAGAATA
1 GTCAAAACAAATGAAGCATATAGAAGAATA
866505 CCTGAGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.17
Consensus pattern (30 bp):
GTCAAAACAAATGAAGCATATAGAAGAATA
Found at i:867635 original size:2 final size:2
Alignment explanation
Indices: 867628--867660 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
867618 TGTTTACCAA
867628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
867661 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:869090 original size:66 final size:65
Alignment explanation
Indices: 868965--869104 Score: 160
Period size: 66 Copynumber: 2.1 Consensus size: 65
868955 GGTTTTCTAA
* ** **
868965 AAACAAAATTTTGTTTCTTTGAGACATTTTCTTTTTAAGAAAAATATTTGAGTTTGTTTCTTTGG
1 AAACAAAATTTTGTCTCTTTGAGACAACTTCTTTTTAAGAAAAATATTTGAGTCGGTTTCTTTGG
869030 AAACAAAATTTTGTCTCTTTTGAGACAACTTC-TTTT-A-AAAAATCATCTCTGAGTCGGTTTCT
1 AAACAAAATTTTGTCTC-TTTGAGACAACTTCTTTTTAAGAAAAAT-AT-T-TGAGTCGGTTTCT
*
869092 TTTG
62 TTGG
869096 AAACCAAAA
1 AAA-CAAAA
869105 CCCTGATGGC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
63 6 0.09
64 3 0.05
65 21 0.33
66 29 0.45
67 5 0.08
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (65 bp):
AAACAAAATTTTGTCTCTTTGAGACAACTTCTTTTTAAGAAAAATATTTGAGTCGGTTTCTTTGG
Found at i:871856 original size:57 final size:56
Alignment explanation
Indices: 871757--871929 Score: 191
Period size: 57 Copynumber: 3.2 Consensus size: 56
871747 CTCAGTTTCA
* * * *
871757 GAAATTCGCGTTGCGATAGTTA-TGTTTACCTATATCGATAATTAGCATTGCAAATTT
1 GAAAATCGC-TTGCGATAG-TACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
* *
871814 GAAAATCGCATTGCGATAGTACTGTTTACTTATATCGGTAATTAGCGTTGTGAATTT
1 GAAAATCGC-TTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
*
871871 GAAAAT--C-T----TAGTACTGTTTACCTATATCGGTAATTAACGTTGCGAATTT
1 GAAAATCGCTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
871920 GGAAAATCGC
1 -GAAAATCGC
871930 GTTGTGATTT
Statistics
Matches: 102, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
49 38 0.37
50 6 0.06
52 1 0.01
53 1 0.01
55 1 0.01
56 2 0.02
57 53 0.52
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (56 bp):
GAAAATCGCTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
Found at i:871902 original size:49 final size:50
Alignment explanation
Indices: 871830--871927 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 50
871820 CGCATTGCGA
* * *
871830 TAGTACTGTTTACTTATATCGGTAATTAGCGTTGTGAATTT-GAAAATCT
1 TAGTACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTGGAAAATCT
871879 TAGTACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTGGAAAATC
1 TAGTACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTGGAAAATC
871928 GCGTTGTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 38 0.84
50 7 0.16
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (50 bp):
TAGTACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTGGAAAATCT
Found at i:872572 original size:13 final size:13
Alignment explanation
Indices: 872554--872586 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
872544 AATCACCTTG
872554 TATGCCTCACTAT
1 TATGCCTCACTAT
872567 TATGCCTCACTAT
1 TATGCCTCACTAT
872580 TATGCCT
1 TATGCCT
872587 TATTGCAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.39
Consensus pattern (13 bp):
TATGCCTCACTAT
Found at i:876421 original size:15 final size:15
Alignment explanation
Indices: 876401--876431 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
876391 CAACGTGTGG
876401 TCCACCAGTACATAC
1 TCCACCAGTACATAC
*
876416 TCCACCAGTGCATAC
1 TCCACCAGTACATAC
876431 T
1 T
876432 TTATCTGCGC
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:0.29, C:0.39, G:0.10, T:0.23
Consensus pattern (15 bp):
TCCACCAGTACATAC
Found at i:886090 original size:151 final size:151
Alignment explanation
Indices: 885816--886118 Score: 606
Period size: 151 Copynumber: 2.0 Consensus size: 151
885806 CCATGTCAAC
885816 AGCTTCAAAGTTAGTTTCTTGGTGATCCTACAAATTACAGAAAATGCATAATTAACAATTACTGG
1 AGCTTCAAAGTTAGTTTCTTGGTGATCCTACAAATTACAGAAAATGCATAATTAACAATTACTGG
885881 CTTTGATGTTTATGACGTGCTTGATGCACCCAATATTTAATGTCACAAACGGTTTTGAGGTTAAT
66 CTTTGATGTTTATGACGTGCTTGATGCACCCAATATTTAATGTCACAAACGGTTTTGAGGTTAAT
885946 GATAATGAATATTGATGAGTG
131 GATAATGAATATTGATGAGTG
885967 AGCTTCAAAGTTAGTTTCTTGGTGATCCTACAAATTACAGAAAATGCATAATTAACAATTACTGG
1 AGCTTCAAAGTTAGTTTCTTGGTGATCCTACAAATTACAGAAAATGCATAATTAACAATTACTGG
886032 CTTTGATGTTTATGACGTGCTTGATGCACCCAATATTTAATGTCACAAACGGTTTTGAGGTTAAT
66 CTTTGATGTTTATGACGTGCTTGATGCACCCAATATTTAATGTCACAAACGGTTTTGAGGTTAAT
886097 GATAATGAATATTGATGAGTG
131 GATAATGAATATTGATGAGTG
886118 A
1 A
886119 TTTAAATAGT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 152 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (151 bp):
AGCTTCAAAGTTAGTTTCTTGGTGATCCTACAAATTACAGAAAATGCATAATTAACAATTACTGG
CTTTGATGTTTATGACGTGCTTGATGCACCCAATATTTAATGTCACAAACGGTTTTGAGGTTAAT
GATAATGAATATTGATGAGTG
Found at i:890158 original size:11 final size:11
Alignment explanation
Indices: 890142--890182 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
890132 CGTTTGCTTA
890142 ATTTTTATTTT
1 ATTTTTATTTT
*
890153 ATTTTTAGTTT
1 ATTTTTATTTT
*
890164 AATTTTA-TTT
1 ATTTTTATTTT
890174 ATTTTTATT
1 ATTTTTATT
890183 GTAGATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:890194 original size:21 final size:21
Alignment explanation
Indices: 890139--890180 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
890129 TTTCGTTTGC
890139 TTAATTTTTATTTTATTTTTAGT
1 TTAA-TTTTA-TTTATTTTTAGT
890162 TTAATTTTATTTATTTTTA
1 TTAATTTTATTTATTTTTA
890181 TTGTAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTAATTTTATTTATTTTTAGT
Found at i:891510 original size:211 final size:212
Alignment explanation
Indices: 890881--891697 Score: 1196
Period size: 211 Copynumber: 3.8 Consensus size: 212
890871 ATTTAATAAT
*
890881 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAC-A-ACACA-T-ATAAG
* *
890946 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAACTATAC
62 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATAC
* * * * * * *
891011 CCATTTAAAAAGTTATGGGCCAATTAAAAAAATATAATTAAGTAATAAGCATGGATCAATTTCAT
127 TCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
891076 ATGCAAATAAAATTTGGAGGAC
191 ATGCAAATAAAATTTGGAGGAC
*
891098 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACTTTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA---T-ATAAG
*
891163 GGATCAAATCGAAATAATTTTAAATTGTGATGTTAAAATTAATACAAAAAAGTACTAAATTATAC
62 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATAC
* * *
891228 ACATTTTAAAAGTTATGGGTCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
127 TCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
891293 TGCAAATAAAATTTGGAGGAC
192 TGCAAATAAAATTTGGAGGAC
* *
891314 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATATATTAAACAACACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATATAAGGGAT
* * * *
891377 CAAATCAAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAAAAGTATTAAATTATAGTCA
66 CAAATCGAAATAATTTTAAATTGTGAGGTTAAAATTAATAC-AAAAAAGTACTAAATTATACTCA
* * *
891442 TTTAAAAAGTTATGAGCCAATTTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGGTGC
130 TTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGC
891507 AAATAAAATTTGGAGGAC
195 AAATAAAATTTGGAGGAC
* *
891525 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATAAAACAACACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATATAAGGGAT
* * * *
891588 CGAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATA-TTCTAAATTATACTCA
66 CAAATCGAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAA-AGTACTAAATTATACTCA
* *
891652 TTTAAAAAGTTATGGACCAA-TTAATAAATAGAAATAAGTAACAAGT
130 TTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
891698 TGAGAAAAAA
Statistics
Matches: 557, Mismatches: 38, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
209 4 0.01
210 99 0.18
211 199 0.36
215 5 0.01
216 109 0.20
217 141 0.25
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (212 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATATAAGGGAT
CAAATCGAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATACTCAT
TTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCA
AATAAAATTTGGAGGAC
Found at i:891728 original size:2 final size:2
Alignment explanation
Indices: 891723--891813 Score: 67
Period size: 2 Copynumber: 43.0 Consensus size: 2
891713 AAAACAACTA
* *
891723 AT AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* * * *
891766 AT AA AGT AT AT GT AT CAT AT AT AT AA ACT AT AT AGT TT AT AT AT
1 AT AT A-T AT AT AT AT -AT AT AT AT AT A-T AT AT A-T AT AT AT AT
891810 AT AT
1 AT AT
891814 TATGTATAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
1 1 0.01
2 62 0.89
3 7 0.10
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:891789 original size:22 final size:22
Alignment explanation
Indices: 891739--891812 Score: 91
Period size: 22 Copynumber: 3.4 Consensus size: 22
891729 ATATATATAT
891739 ATATAATATAAACTATATAGTT-
1 ATAT-ATATAAACTATATAGTTC
*
891761 -TATATATAAAGTATAT-GTATC
1 ATATATATAAACTATATAGT-TC
*
891782 ATATATATAAACTATATAGTTT
1 ATATATATAAACTATATAGTTC
891804 ATATATATA
1 ATATATATA
891813 TTATGTATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 3 0.07
22 25 0.56
23 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (22 bp):
ATATATATAAACTATATAGTTC
Found at i:891790 original size:42 final size:40
Alignment explanation
Indices: 891723--891837 Score: 148
Period size: 42 Copynumber: 2.9 Consensus size: 40
891713 AAAACAACTA
* *
891723 ATATATATATATATATATATA-ATATAAACTATATAGTTT
1 ATATATAAATATATGTATATATATATAAACTATATAGTTT
891762 ATATATAAAGTATATGTATCATATATATAAACTATATAGTTT
1 ATATATAAA-TATATGTAT-ATATATATAAACTATATAGTTT
*
891804 ATATATATAT-TATGTATA-A-AGTATAAACTATATA
1 ATATATAAATATATGTATATATA-TATAAACTATATA
891838 TACCATGTAT
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
37 1 0.01
38 14 0.20
39 9 0.13
40 15 0.22
41 4 0.06
42 26 0.38
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (40 bp):
ATATATAAATATATGTATATATATATAAACTATATAGTTT
Found at i:891952 original size:20 final size:20
Alignment explanation
Indices: 891730--891954 Score: 91
Period size: 20 Copynumber: 10.7 Consensus size: 20
891720 CTAATATATA
*
891730 TATATATATATATAATATAAAC
1 TATATA-ATTTAT-ATATAAAC
* *
891752 TATATAGTTTATATATAAAG
1 TATATAATTTATATATAAAC
* *
891772 TATATGTATCATATATATAAAC
1 TATAT-AAT-TTATATATAAAC
* *
891794 TATATAGTTTATATATATA-
1 TATATAATTTATATATAAAC
* * *
891813 T-TAT-GTATAAAGTATAAAC
1 TATATAATTTATA-TATAAAC
*
891832 TATATATACCATGTATAAACTATAATAC
1 --TATATA--AT-T-TATA-TATAA-AC
* *
891860 TATATAGTTTATATATGAAC
1 TATATAATTTATATATAAAC
* *
891880 TAT-TGAA-CTATATAGAAAC
1 TATAT-AATTTATATATAAAC
* * *
891899 TACATAGTTTATATATAAAT
1 TATATAATTTATATATAAAC
*
891919 TATATATGAATTATATATAAAC
1 TATATA--ATTTATATATAAAC
*
891941 TATACAATTTATAT
1 TATATAATTTATAT
891955 TTATATATTA
Statistics
Matches: 150, Mismatches: 35, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
17 5 0.03
18 8 0.05
19 14 0.09
20 49 0.33
21 11 0.07
22 43 0.29
23 1 0.01
24 1 0.01
25 1 0.01
26 6 0.04
27 9 0.06
28 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (20 bp):
TATATAATTTATATATAAAC
Found at i:891952 original size:42 final size:43
Alignment explanation
Indices: 891883--891981 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 43
891873 TATGAACTAT
* * * *
891883 TGAACTATATAGAAACTACATAGTTTATA-TATAAATTATATA
1 TGAATTATATATAAACTACACAATTTATATTATAAATTATATA
* * *
891925 TGAATTATATATAAACTATACAATTTATATTTATATATTATGTA
1 TGAATTATATATAAACTACACAATTTATA-TTATAAATTATATA
*
891969 T-AATTATAAATAA
1 TGAATTATATATAA
891982 TATATATTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 24 0.51
43 11 0.23
44 12 0.26
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (43 bp):
TGAATTATATATAAACTACACAATTTATATTATAAATTATATA
Found at i:891970 original size:17 final size:17
Alignment explanation
Indices: 891950--892003 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
891940 CTATACAATT
* *
891950 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
891967 TATAATTATAAATAATA
1 TATATTTATAAATTATA
891984 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
892002 TA
1 TA
892004 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Done.