Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_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: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:2016386 original size:32 final size:32
Alignment explanation
Indices: 2016339--2016429 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
2016329 TTTATTATTG
* *
2016339 TATTTGTATGGATTGATTTATTTTAAATAATT
1 TATTAGTATGAATTGATTTATTTTAAATAATT
2016371 TATTAGTATGAATTGATTTATTTTAAATAATT
1 TATTAGTATGAATTGATTTATTTTAAATAATT
2016403 TATTAGTATGAATTGATTTATTTTAAA
1 TATTAGTATGAATTGATTTATTTTAAA
2016430 ATATAGATTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
TATTAGTATGAATTGATTTATTTTAAATAATT
Found at i:2016391 original size:18 final size:18
Alignment explanation
Indices: 2016368--2016424 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
2016358 ATTTTAAATA
2016368 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
2016386 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
2016400 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
2016418 ATTTATT
1 ATTTATT
2016425 TTAAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 2 0.06
17 1 0.03
18 17 0.55
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:2019420 original size:15 final size:15
Alignment explanation
Indices: 2019400--2019430 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2019390 TCACTTAATC
*
2019400 CTGTTAATTTTCTAA
1 CTGTTAACTTTCTAA
2019415 CTGTTAACTTTCTAA
1 CTGTTAACTTTCTAA
2019430 C
1 C
2019431 GTGACAGCTT
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:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (15 bp):
CTGTTAACTTTCTAA
Found at i:2020753 original size:29 final size:29
Alignment explanation
Indices: 2020717--2020774 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2020707 CCCTAAAAAT
2020717 AATAATATTATATT-AT-TATTATTAATATA
1 AATAATATTA-ATTAATATATTA-TAATATA
2020746 AATAATATTAATTAATATATTATAATATA
1 AATAATATTAATTAATATATTATAATATA
2020775 TAAAAACGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 3 0.11
29 19 0.70
30 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AATAATATTAATTAATATATTATAATATA
Found at i:2025390 original size:19 final size:19
Alignment explanation
Indices: 2025366--2025403 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2025356 TGTATAAAAC
*
2025366 ATCAACACTATATTTTTTT
1 ATCAACACTACATTTTTTT
2025385 ATCAACACTACATTTTTTT
1 ATCAACACTACATTTTTTT
2025404 TACTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (19 bp):
ATCAACACTACATTTTTTT
Found at i:2026202 original size:17 final size:18
Alignment explanation
Indices: 2026165--2026205 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2026155 ATATTATGTA
*
2026165 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2026183 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2026200 TTTACT
1 TTTACT
2026206 AATATAATTC
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:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2027898 original size:18 final size:18
Alignment explanation
Indices: 2027875--2027914 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2027865 ACAGCAGCCA
*
2027875 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
2027893 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
2027911 CCGC
1 CCGC
2027915 CATCGCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.23
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:2028261 original size:3 final size:3
Alignment explanation
Indices: 2028253--2028296 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2028243 ACCTACTCAG
* * * *
2028253 GAC GAC GAC GAC GAC GAT GGC GAT GAC GAC GAC GAC AAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
2028297 TGATGACAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.34, T:0.05
Consensus pattern (3 bp):
GAC
Found at i:2028297 original size:21 final size:21
Alignment explanation
Indices: 2028256--2028299 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2028246 TACTCAGGAC
* * *
2028256 GACGACGACGACGATGGCGAT
1 GACGACGACGACAACGACGAT
2028277 GACGACGACGACAACGACGAT
1 GACGACGACGACAACGACGAT
2028298 GA
1 GA
2028300 TGACAACTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.34, T:0.07
Consensus pattern (21 bp):
GACGACGACGACAACGACGAT
Found at i:2033576 original size:21 final size:21
Alignment explanation
Indices: 2033551--2033613 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
2033541 GTACAACAGG
2033551 AACCATCAGTATGGTGGCCAA
1 AACCATCAGTATGGTGGCCAA
* * * *
2033572 AACCAAT-TGTATGATGGTCAT
1 AACC-ATCAGTATGGTGGCCAA
*
2033593 AACCAGCAGTATGGTGGCCAA
1 AACCATCAGTATGGTGGCCAA
2033614 TCTGGAGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (21 bp):
AACCATCAGTATGGTGGCCAA
Found at i:2035252 original size:45 final size:45
Alignment explanation
Indices: 2035167--2035258 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
2035157 CGCTTCCTGC
* * * *
2035167 AGAGGAAGTGTCTCGGGCTCAGCAGTTGATGGGAAATGTCGTGCA
1 AGAGAAAGTGTCTCAGGCTCAGCAGTCGATGGGAAATGTCGTACA
* *
2035212 AGAGAAAGTGTCTCAGGCTCAGTAGTCGAT-GGAAGGTGTCGTACA
1 AGAGAAAGTGTCTCAGGCTCAGCAGTCGATGGGAA-ATGTCGTACA
2035257 AG
1 AG
2035259 GTATGGCGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 4 0.10
45 36 0.90
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (45 bp):
AGAGAAAGTGTCTCAGGCTCAGCAGTCGATGGGAAATGTCGTACA
Found at i:2050908 original size:31 final size:31
Alignment explanation
Indices: 2050872--2050931 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2050862 CTCGTGCTGA
* *
2050872 CCATATCTTAATTAAATTAAAATGAAAGTGG
1 CCATATCTTAATAAAATAAAAATGAAAGTGG
2050903 CCATATCTTAATAAAATAAAAATGAAAGT
1 CCATATCTTAATAAAATAAAAATGAAAGT
2050932 AACCATCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (31 bp):
CCATATCTTAATAAAATAAAAATGAAAGTGG
Found at i:2050943 original size:31 final size:31
Alignment explanation
Indices: 2050871--2050943 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
2050861 ACTCGTGCTG
* * *
2050871 ACCATATCTTAATTAAATTAAAATGAAAGTG
1 ACCATATCTTAATAAAATAAAAATGAAAGTA
*
2050902 GCCATATCTTAATAAAATAAAAATGAAAGTA
1 ACCATATCTTAATAAAATAAAAATGAAAGTA
*
2050933 ACCATCTCTTA
1 ACCATATCTTA
2050944 TGTTTTTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (31 bp):
ACCATATCTTAATAAAATAAAAATGAAAGTA
Found at i:2053514 original size:16 final size:16
Alignment explanation
Indices: 2053493--2053525 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2053483 GCCTGGATCC
2053493 ACTGATTGTTGTATTT
1 ACTGATTGTTGTATTT
2053509 ACTGATTGTTGTATTT
1 ACTGATTGTTGTATTT
2053525 A
1 A
2053526 TGCTAAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (16 bp):
ACTGATTGTTGTATTT
Found at i:2053804 original size:20 final size:20
Alignment explanation
Indices: 2053776--2053831 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2053766 TATGACCTAA
*
2053776 AGTAGCGATACTCTTGAAAG
1 AGTATCGATACTCTTGAAAG
2053796 AGTATCGATACTCTTGAAAG
1 AGTATCGATACTCTTGAAAG
2053816 AGTATCGATACTCTTG
1 AGTATCGATACTCTTG
2053832 CCCATAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTCTTGAAAG
Found at i:2055513 original size:2 final size:2
Alignment explanation
Indices: 2055508--2055560 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
2055498 TATGACATAC
2055508 AT AT AT AT A- AT A- AT AT AT AT AT AT A- AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2055546 A- AA AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT A
2055561 ATAGAGTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
1 6 0.14
2 38 0.86
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2055514 original size:18 final size:18
Alignment explanation
Indices: 2055491--2055537 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2055481 GGGATTAATC
*
2055491 TATATAATATGACATACA
1 TATATAATATAACATACA
* *
2055509 TATAT-ATAATAATATATA
1 TATATAAT-ATAACATACA
2055527 TATATAATATA
1 TATATAATATA
2055538 TAATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (18 bp):
TATATAATATAACATACA
Found at i:2055527 original size:16 final size:16
Alignment explanation
Indices: 2055508--2055563 Score: 84
Period size: 14 Copynumber: 3.8 Consensus size: 16
2055498 TATGACATAC
2055508 ATATATATAATAATAT
1 ATATATATAATAATAT
2055524 ATATATATAAT-ATAT
1 ATATATATAATAATAT
2055539 A-ATATATAA-AATAT
1 ATATATATAATAATAT
2055553 AT-TATATAATA
1 ATATATATAATA
2055564 GAGTATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 20 0.54
15 6 0.16
16 11 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATATAATAATAT
Found at i:2063316 original size:38 final size:37
Alignment explanation
Indices: 2063262--2063359 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 37
2063252 TCGTATAAAT
*
2063262 TGTGTCCCAAAGGACCTATCATCCCGAAGGATGTCATC
1 TGTGTCCCAAA-GACCTATCATCCCGAAGGATGTAATC
* *
2063300 TGTGTCCCGAAAGACCTGTCATCCCGAATGATGTAATC
1 TGTGTCCC-AAAGACCTATCATCCCGAAGGATGTAATC
*
2063338 TGTGTCCCATAGGACCTATCAT
1 TGTGTCCCA-AAGACCTATCAT
2063360 ATGTCTTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
37 1 0.02
38 49 0.92
39 3 0.06
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (37 bp):
TGTGTCCCAAAGACCTATCATCCCGAAGGATGTAATC
Found at i:2066745 original size:3 final size:3
Alignment explanation
Indices: 2066732--2066762 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2066722 AATAACAGCA
2066732 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2066763 AAAAGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2068452 original size:35 final size:35
Alignment explanation
Indices: 2068406--2068477 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
2068396 CTGTAACCAA
2068406 TTATATAATTAAAAAGTGATGTATTAAGTGATAGT
1 TTATATAATTAAAAAGTGATGTATTAAGTGATAGT
*
2068441 TTATATAATTAAAAAGTGATTTATTAAGTGATAGT
1 TTATATAATTAAAAAGTGATGTATTAAGTGATAGT
2068476 TT
1 TT
2068478 GAGTGGTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (35 bp):
TTATATAATTAAAAAGTGATGTATTAAGTGATAGT
Found at i:2068800 original size:15 final size:15
Alignment explanation
Indices: 2068780--2068811 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2068770 TCCTGTTTCT
2068780 AAGATATATTTAAAA
1 AAGATATATTTAAAA
2068795 AAGATATATTTAAAA
1 AAGATATATTTAAAA
2068810 AA
1 AA
2068812 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
AAGATATATTTAAAA
Found at i:2077834 original size:20 final size:20
Alignment explanation
Indices: 2077797--2077839 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2077787 TTTGTTTTTA
*
2077797 TTTTTTAATATTTTAAT-AT
1 TTTTTTAATATTTGAATAAT
*
2077816 TTTTTTGAATGTTTGAATAAT
1 TTTTTT-AATATTTGAATAAT
2077837 TTT
1 TTT
2077840 ATATTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 9 0.45
21 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTTTAATATTTGAATAAT
Found at i:2079366 original size:32 final size:31
Alignment explanation
Indices: 2079281--2079366 Score: 84
Period size: 37 Copynumber: 2.6 Consensus size: 31
2079271 TTGTATAATA
2079281 TTAC-AAATTATAAAATATTTATATATTTTCT
1 TTACAAAATTA-AAAATATTTATATATTTTCT
* *
2079312 TTAAAAAATTAAATTCATAATATTTATATAATTTTTT
1 TTACAAAATT-AA---A-AATATTTATAT-ATTTTCT
2079349 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
2079367 AAAAAAGGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
31 3 0.07
32 11 0.24
33 2 0.04
35 1 0.02
36 13 0.29
37 15 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATATATTTTCT
Found at i:2083203 original size:20 final size:20
Alignment explanation
Indices: 2083173--2083228 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
2083163 GTAGTGCTCG
2083173 ACTCG-TGCTCGTTAAGAAA
1 ACTCGTTGCTCGTTAAGAAA
*
2083192 GCTCGTTGCTCGTTAAGAAA
1 ACTCGTTGCTCGTTAAGAAA
2083212 ACTCGTTGCTCGTTAAG
1 ACTCGTTGCTCGTTAAG
2083229 CTCGTTACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 4 0.12
20 30 0.88
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (20 bp):
ACTCGTTGCTCGTTAAGAAA
Found at i:2083233 original size:9 final size:9
Alignment explanation
Indices: 2083219--2083264 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
2083209 AAAACTCGTT
2083219 GCTCGTTAA
1 GCTCGTTAA
2083228 GCTCGTT-A
1 GCTCGTTAA
2083236 -CTCGTTAA
1 GCTCGTTAA
2083244 GCTCGTT-A
1 GCTCGTTAA
2083252 -CTCGTTAA
1 GCTCGTTAA
2083260 GCTCG
1 GCTCG
2083265 ATGCTCATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 12 0.36
8 4 0.12
9 17 0.52
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (9 bp):
GCTCGTTAA
Found at i:2083234 original size:16 final size:16
Alignment explanation
Indices: 2083190--2083270 Score: 99
Period size: 16 Copynumber: 4.8 Consensus size: 16
2083180 CTCGTTAAGA
2083190 AAGCTCGTTGCTCGTT
1 AAGCTCGTTGCTCGTT
2083206 AAGAAAACTCGTTGCTCGTT
1 AAG----CTCGTTGCTCGTT
*
2083226 AAGCTCGTTACTCGTT
1 AAGCTCGTTGCTCGTT
*
2083242 AAGCTCGTTACTCGTT
1 AAGCTCGTTGCTCGTT
*
2083258 AAGCTCGATGCTC
1 AAGCTCGTTGCTC
2083271 ATTGCTCGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
16 42 0.72
20 16 0.28
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (16 bp):
AAGCTCGTTGCTCGTT
Found at i:2084765 original size:12 final size:12
Alignment explanation
Indices: 2084748--2084772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2084738 GCTTTGGTGG
2084748 AGAAAAAGAAGA
1 AGAAAAAGAAGA
2084760 AGAAAAAGAAGA
1 AGAAAAAGAAGA
2084772 A
1 A
2084773 CGAGGCTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAGA
Found at i:2087400 original size:2 final size:2
Alignment explanation
Indices: 2087393--2087455 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
2087383 GAGTGAGTTG
2087393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2087435 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2087456 ATCAATCAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2087710 original size:25 final size:25
Alignment explanation
Indices: 2087676--2087726 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
2087666 ACTAAAAGTC
*
2087676 TGCAGTCTGC-AAGAATAAGACT-ATT
1 TGCAGACTGCTAA-AATAA-ACTGATT
2087701 TGCAGACTGCTAAAATAAACTGATT
1 TGCAGACTGCTAAAATAAACTGATT
2087726 T
1 T
2087727 TTTAAACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 3 0.13
25 18 0.78
26 2 0.09
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (25 bp):
TGCAGACTGCTAAAATAAACTGATT
Found at i:2087777 original size:31 final size:31
Alignment explanation
Indices: 2087741--2087799 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2087731 AACTTAAAAG
*
2087741 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
2087772 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2087800 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2087849 original size:22 final size:22
Alignment explanation
Indices: 2087823--2088112 Score: 336
Period size: 22 Copynumber: 13.2 Consensus size: 22
2087813 ATAATAATTT
* *
2087823 TTTTAAAATAAATAAATCTATA
1 TTTTAAAATAAATCAATCCATA
2087845 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
2087867 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
2087889 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* ** *
2087911 TTTTGAAATAAAAT-TTTCTATA
1 TTTTAAAAT-AAATCAATCCATA
2087933 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
2087955 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
2087977 TTTTAAAATAAATCAAAT-CATA
1 TTTTAAAATAAATC-AATCCATA
*
2087999 TTTCAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
2088021 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
2088043 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2088065 TTTTAAAATAAATCAATCCACA
1 TTTTAAAATAAATCAATCCATA
*
2088087 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
2088109 TTTT
1 TTTT
2088113 TCCCGCAGAC
Statistics
Matches: 226, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
21 15 0.07
22 198 0.88
23 13 0.06
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:2089747 original size:23 final size:24
Alignment explanation
Indices: 2089708--2089760 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
2089698 AAAAACCTAG
* *
2089708 ACCGGTTTTTTTACCGGATAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
2089732 ACCGGTTTTTAT-CCGGAAAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
2089755 ACCGGT
1 ACCGGT
2089761 CTGGGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (24 bp):
ACCGGTTTTTATACCGGAAAAAAA
Found at i:2092061 original size:21 final size:21
Alignment explanation
Indices: 2092037--2092076 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2092027 TTTATTTTAT
2092037 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2092058 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2092077 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2092124 original size:33 final size:33
Alignment explanation
Indices: 2092071--2092169 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2092061 TTTGTTTCAA
2092071 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2092103 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2092136 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2092169 T
1 T
2092170 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2092198 original size:13 final size:13
Alignment explanation
Indices: 2092155--2092209 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2092145 TTGGAAGTAT
2092155 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2092168 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2092182 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2092195 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2092208 TT
1 TT
2092210 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2092616 original size:15 final size:15
Alignment explanation
Indices: 2092591--2092645 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
2092581 ATCTGGAATA
*
2092591 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2092606 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
**
2092621 AAAAAAACCGGTTTTT
1 -TTAAAACCGGTTTTT
2092637 TTAAAACCG
1 TTAAAACCG
2092646 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2092642 original size:16 final size:16
Alignment explanation
Indices: 2092593--2092642 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
2092583 CTGGAATATT
*
2092593 AAAATCGGTTTTTTT-
1 AAAACCGGTTTTTTTA
* **
2092608 ATAACCGGTTTTTAAA
1 AAAACCGGTTTTTTTA
2092624 AAAACCGGTTTTTTTA
1 AAAACCGGTTTTTTTA
2092640 AAA
1 AAA
2092643 CCGAAACCGG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (16 bp):
AAAACCGGTTTTTTTA
Found at i:2094052 original size:85 final size:84
Alignment explanation
Indices: 2093891--2094053 Score: 190
Period size: 85 Copynumber: 1.9 Consensus size: 84
2093881 ATGACGCACG
* * *
2093891 TTTATGACGCGCATTTATGACGATCATTGCACGTCATTGAAGCCCCCGTCATAAATGAAGATGAC
1 TTTATGACGCGCATTTATGACGATCATTGCACGTCATTGAAGCACACGTCATAAA-GAAGATCAC
2093956 ACACATTTGTGTGTCATAAA
65 ACACATTTGTGTGTCATAAA
* ** *
2093976 TTTATGACGCGCATTTATGAC-TTACATTGCGTGTCATTGAAGCACATGTCACT-AA-AA-ATCA
1 TTTATGACGCGCATTTATGACGAT-CATTGCACGTCATTGAAGCACACGTCA-TAAAGAAGATCA
*
2094037 CGACACATTCGTGTGTC
64 C-ACACATTTGTGTGTC
2094054 GTGATTGTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
82 4 0.06
83 16 0.24
84 1 0.01
85 45 0.67
86 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (84 bp):
TTTATGACGCGCATTTATGACGATCATTGCACGTCATTGAAGCACACGTCATAAAGAAGATCACA
CACATTTGTGTGTCATAAA
Found at i:2098502 original size:15 final size:15
Alignment explanation
Indices: 2098482--2098522 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
2098472 CCTTCCTTAA
*
2098482 GGTATCGGTACCCTT
1 GGTATCGATACCCTT
2098497 GGTATCGATACCCTT
1 GGTATCGATACCCTT
*
2098512 GGTATTGATAC
1 GGTATCGATAC
2098523 TGTTCTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (15 bp):
GGTATCGATACCCTT
Found at i:2106086 original size:30 final size:30
Alignment explanation
Indices: 2106052--2106116 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
2106042 CACAAATCGG
2106052 TCACTAACGTTATCGTTTGTTACAAAATGA
1 TCACTAACGTTATCGTTTGTTACAAAATGA
2106082 TCACTAACGTTATCGTTTGTTACAAAATGA
1 TCACTAACGTTATCGTTTGTTACAAAATGA
2106112 TCACT
1 TCACT
2106117 TGATGTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (30 bp):
TCACTAACGTTATCGTTTGTTACAAAATGA
Found at i:2108927 original size:22 final size:19
Alignment explanation
Indices: 2108864--2108912 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
2108854 GCGATTTTGA
2108864 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
2108883 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
2108902 AAAATGTGTTG
1 AAAATGTGTTG
2108913 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:2109225 original size:6 final size:6
Alignment explanation
Indices: 2109216--2109240 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2109206 TGCCGCCGTC
2109216 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
2109241 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:2111830 original size:58 final size:57
Alignment explanation
Indices: 2111729--2111943 Score: 245
Period size: 58 Copynumber: 3.7 Consensus size: 57
2111719 ACTTTGTAAG
* * * **
2111729 GAAAATAAATTGCTGAATTTATTTTCTTGAGAATCGTGGATGATTCTATCCTTTAAAAA
1 GAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTAT--TTTAAAAA
* * * *
2111788 G-AAATAAATTGTTAAATTTATTTTCTTAATAATTTTAAATGATTCTATTTTGTAAAA
1 GAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTT-AAAAA
** * *
2111845 GTTAATAAATTGTTAAATTTATTTTCTTGAGAATCTAAAATGATTCTATTTTATTAAA
1 GAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTA-AAAA
*
2111903 GAAAATAAAATT-TTAAATTTATTTTCTTGGGAATCTTAAAT
1 GAAAAT-AAATTGTTAAATTTATTTTCTTGAGAATCTTAAAT
2111944 AAAGAAATAA
Statistics
Matches: 132, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
56 3 0.02
57 5 0.04
58 118 0.89
59 6 0.05
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (57 bp):
GAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTAAAAA
Found at i:2111942 original size:116 final size:115
Alignment explanation
Indices: 2111732--2111943 Score: 277
Period size: 116 Copynumber: 1.8 Consensus size: 115
2111722 TTGTAAGGAA
* **
2111732 AATAAATTGCTGAATTTATTTTCTTGAGAATCGTGGATGATTCTATCCTTTAAAAAGAAATAAAT
1 AATAAATTGCTAAATTTATTTTCTTGAGAATCGTAAATGATTCTAT-CTTTAAAAAGAAATAAAT
* *
2111797 TGTTAAATTTATTTTCTTAATAATTTTAAATGATTCTATTTTGTAAAAGTT
65 TGTTAAATTTATTTTCTTAAGAATCTTAAATGATTCTATTTTGTAAAAGTT
* *
2111848 AATAAATTGTTAAATTTATTTTCTTGAGAATC-TAAAATGATTCTAT-TTTATTAAAGAAAATAA
1 AATAAATTGCTAAATTTATTTTCTTGAGAATCGT-AAATGATTCTATCTTTA-AAAAG-AAAT-A
**
2111911 AATT-TTAAATTTATTTTCTTGGGAATCTTAAAT
62 AATTGTTAAATTTATTTTCTTAAGAATCTTAAAT
2111944 AAAGAAATAA
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
114 4 0.05
115 5 0.06
116 69 0.83
117 5 0.06
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (115 bp):
AATAAATTGCTAAATTTATTTTCTTGAGAATCGTAAATGATTCTATCTTTAAAAAGAAATAAATT
GTTAAATTTATTTTCTTAAGAATCTTAAATGATTCTATTTTGTAAAAGTT
Found at i:2112344 original size:82 final size:83
Alignment explanation
Indices: 2112232--2112383 Score: 225
Period size: 82 Copynumber: 1.8 Consensus size: 83
2112222 TATTTTCCTA
* *
2112232 TTTTGTAAAAAGAAAATAAATCATTGGATTTAGTTTCCTAATTTGTAAGAGGAAATAAATTGAAA
1 TTTTGTAAAAAGAAAATAAATCATTGGATTTAGTTTCCTAATTTGTAAAAAGAAATAAATTGAAA
2112297 CAAATCTTTATTTTATTG
66 CAAATCTTTATTTTATTG
* * * * * *
2112315 TTTTGT-AAAAGAAAATAAATCGTTTGATTTATTTTTCTATTTTGTAAAAATAAATAAATTGAAA
1 TTTTGTAAAAAGAAAATAAATCATTGGATTTAGTTTCCTAATTTGTAAAAAGAAATAAATTGAAA
2112379 CAAAT
66 CAAAT
2112384 TGTTTGATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
82 55 0.90
83 6 0.10
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (83 bp):
TTTTGTAAAAAGAAAATAAATCATTGGATTTAGTTTCCTAATTTGTAAAAAGAAATAAATTGAAA
CAAATCTTTATTTTATTG
Found at i:2112358 original size:39 final size:39
Alignment explanation
Indices: 2112199--2112373 Score: 136
Period size: 39 Copynumber: 4.4 Consensus size: 39
2112189 AAATTTGAAA
*
2112199 AAAAGGAAATAAATCGTTAAATTTATTTTCCTATTTTGT
1 AAAAGAAAATAAATCGTTAAATTTATTTTCCTATTTTGT
* ** * *
2112238 AAAAAGAAAATAAATCATTGGATTTAGTTTCCTAATTTGT
1 -AAAAGAAAATAAATCGTTAAATTTATTTTCCTATTTTGT
* * * ** ** *
2112278 AAGAGGAAATAAATTGAAACAAATCTTTATTTTATTGTTTTGT
1 AAAAGAAAATAAATCG--TTAAA--TTTATTTTCCTATTTTGT
** *
2112321 AAAAGAAAATAAATCGTTTGATTTATTTTTCTATTTTGT
1 AAAAGAAAATAAATCGTTAAATTTATTTTCCTATTTTGT
2112360 AAAA-ATAAATAAAT
1 AAAAGA-AAATAAAT
2112374 TGAAACAAAT
Statistics
Matches: 101, Mismatches: 29, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
38 1 0.01
39 39 0.39
40 33 0.33
41 2 0.02
43 26 0.26
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (39 bp):
AAAAGAAAATAAATCGTTAAATTTATTTTCCTATTTTGT
Found at i:2112392 original size:49 final size:49
Alignment explanation
Indices: 2112331--2112426 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
2112321 AAAAGAAAAT
*
2112331 AAATCGTTTGATTTATTTTTCTATTTTGTAAAAATAAATAAATTGAAAC
1 AAATCGTTTGATTTATTTTTCTATTTTGTAAAAAGAAATAAATTGAAAC
* * * *
2112380 AAATTGTTTGATTTATTTTTCTGTTTTTTAAAAGGAAATAAATTGAA
1 AAATCGTTTGATTTATTTTTCTATTTTGTAAAAAGAAATAAATTGAA
2112427 TTTATTTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (49 bp):
AAATCGTTTGATTTATTTTTCTATTTTGTAAAAAGAAATAAATTGAAAC
Found at i:2119417 original size:2 final size:2
Alignment explanation
Indices: 2119410--2119444 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2119400 TTGGAATGGA
2119410 AT 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 AT A
2119445 AATGAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2124740 original size:20 final size:20
Alignment explanation
Indices: 2124712--2124749 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2124702 TTATACATTT
2124712 AAAACATAAATAAAACAATC
1 AAAACATAAATAAAACAATC
*
2124732 AAAAGATAAATAAAACAA
1 AAAACATAAATAAAACAA
2124750 ACTCATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAACATAAATAAAACAATC
Found at i:2126006 original size:28 final size:28
Alignment explanation
Indices: 2125974--2126028 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2125964 AATAGACTGA
2125974 AATAAATACAACATACAAATTAGAAACC
1 AATAAATACAACATACAAATTAGAAACC
*
2126002 AATAAATACAAGATACAAATTAGAAAC
1 AATAAATACAACATACAAATTAGAAAC
2126029 TGATTAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.62, C:0.15, G:0.05, T:0.18
Consensus pattern (28 bp):
AATAAATACAACATACAAATTAGAAACC
Found at i:2128157 original size:12 final size:13
Alignment explanation
Indices: 2128139--2128188 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
2128129 GTATGAATAC
2128139 CCGGGT-ATCGGG
1 CCGGGTAATCGGG
*
2128151 TCGGGT-ATCGGG
1 CCGGGTAATCGGG
2128163 CCGGGTAATCGGG
1 CCGGGTAATCGGG
2128176 CCGGGTAATCGGG
1 CCGGGTAATCGGG
2128189 TAATCGGGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 16 0.46
13 19 0.54
ACGTcount: A:0.12, C:0.22, G:0.48, T:0.18
Consensus pattern (13 bp):
CCGGGTAATCGGG
Found at i:2128180 original size:25 final size:25
Alignment explanation
Indices: 2128139--2128188 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2128129 GTATGAATAC
*
2128139 CCGGGTATCGGGTCGGGT-ATCGGG
1 CCGGGTATCGGGCCGGGTAATCGGG
2128163 CCGGGTAATCGGGCCGGGTAATCGGG
1 CCGGGT-ATCGGGCCGGGTAATCGGG
2128189 TAATCGGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.26
25 11 0.48
26 6 0.26
ACGTcount: A:0.12, C:0.22, G:0.48, T:0.18
Consensus pattern (25 bp):
CCGGGTATCGGGCCGGGTAATCGGG
Found at i:2132415 original size:3 final size:3
Alignment explanation
Indices: 2132387--2132463 Score: 75
Period size: 3 Copynumber: 24.7 Consensus size: 3
2132377 TTGGGTTTTG
* *
2132387 TAA TAT TAA TAAA TAAA TATA TAA TAA TAA TATA TTA TAA TAA TAA TAA
1 TAA TAA TAA T-AA T-AA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* *
2132436 T-A TAA TAA TTA TAA TGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2132464 TAAATAACGT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 2 0.03
3 48 0.77
4 12 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2132446 original size:23 final size:24
Alignment explanation
Indices: 2132402--2132460 Score: 84
Period size: 23 Copynumber: 2.4 Consensus size: 24
2132392 TTAATAAATA
2132402 AATATATAATAATAATATATTATAAT
1 AATA-ATAAT-ATAATATATTATAAT
2132428 AATAATAATATAATA-ATTATAAT
1 AATAATAATATAATATATTATAAT
*
2132451 GATAATAATA
1 AATAATAATA
2132461 ATATAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 17 0.53
24 6 0.19
25 5 0.16
26 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AATAATAATATAATATATTATAAT
Found at i:2132935 original size:112 final size:113
Alignment explanation
Indices: 2132689--2133973 Score: 1562
Period size: 109 Copynumber: 11.7 Consensus size: 113
2132679 TAGAGTCATT
* ** *
2132689 CAAAAGGTTGAATAAGCTCTTCT-ATTATGAAC-T-TTC-T--TTCTTCAGATGAGTTTTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * * * * * **
2132748 TTATGAACTTTCTCT-GTAAAGTTGATCTATTAAGTGATGAATTCAAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* * * *
2132795 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2132859 TTATGAACTCTAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
2132907 CAAAAGGTTGAACAAATTC-TCTAATTATGAACTTCTTCTTCCTTC-TCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2132970 TTATGAACTCGAACTGG-AAAGCTGATCCATCAAGTGATGGA-TTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
2133016 CAAAAGGTTGAACAAA-TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
2133080 TTA-G-ACTCGAACTGGAAAAGTTGATCC--CAAGTGATGGATTTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
2133124 CAAAAGGTTGAACAAATTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * ** ** * *
2133186 TTATGAACTCGAACTGGCACTGCTGATCCATTGAGTGATGAATTTAAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* * *
2133234 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCTTCTTCTTCAGATGAGTTCTTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC--CTTCTTCAGATGAGTTCTTCT
* * * *
2133299 CATTATGAACTCTAACT-GAAATA--TGATCCACCGA-TGGATGAATTTAAG
64 CATTATGAACTCTAACTGGAAA-AGCTGATCCATCAAGT-GATGGATTTGAG
* *
2133347 CAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTTTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
2133410 TTATGAACTCTAACT-GAAAATGTTGATCCATTGAA-TGATGGATTTAAG
66 TTATGAACTCTAACTGGAAAA-GCTGATCCA-TCAAGTGATGGATTTGAG
* * *
2133458 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * *
2133523 TTATGAACTTTTTCTGGAGAAGCTGA-CCATCAAATGATGGATTTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* *
2133570 CAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATGA-TTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * *
2133633 TTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* *
2133681 C-AAAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** *
2133744 TTATGAACT-TTTCTGGCAAAGCT-ATCCATC-AGTGATGGATTTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
2133789 CAAAAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
2133852 TTA-GAACT-T-TCTGGCAAAGCTAATCCATCAAGTGATGGA-TTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
2133896 CCAAAAGGTTGAACAAAATTCTTCTCATTATG-ATTTCTTCTTCCTTCTTC--ATGAGTTCTTCT
1 -CAAAAGGTTGAAC-AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
2133958 CATTATGAACACTAAC
64 CATTATGAACTCTAAC
2133974 GACACTGTGA
Statistics
Matches: 1062, Mismatches: 72, Indels: 85
0.87 0.06 0.07
Matches are distributed among these distances:
105 15 0.01
106 59 0.06
107 31 0.03
108 138 0.13
109 198 0.19
110 178 0.17
111 141 0.13
112 178 0.17
113 81 0.08
114 6 0.01
115 37 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
Found at i:2133511 original size:24 final size:23
Alignment explanation
Indices: 2133476--2133520 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2133466 TGAACAAGTT
2133476 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
2133500 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
2133521 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:2134434 original size:21 final size:20
Alignment explanation
Indices: 2134395--2134511 Score: 137
Period size: 21 Copynumber: 5.7 Consensus size: 20
2134385 ATTAAAGCTT
*
2134395 TCATCTTTGAAGAGAATCTA
1 TCATCTTTAAAGAGAATCTA
*
2134415 TCATCTTTAAAAGCGAATCTA
1 TCATCTTT-AAAGAGAATCTA
*
2134436 TCATCTTT-GAGAGAGATCTA
1 TCATCTTTAAAGAGA-ATCTA
2134456 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTT--AAAGAGAATCTA
*
2134478 TCATCTTTGAAGAGAGATCTA
1 TCATCTTTAAAGAGA-ATCTA
*
2134499 TCATCTTTGAAGA
1 TCATCTTTAAAGA
2134512 ATGTAGATGT
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.05
20 27 0.32
21 36 0.42
22 13 0.15
23 5 0.06
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
TCATCTTTAAAGAGAATCTA
Found at i:2134441 original size:41 final size:43
Alignment explanation
Indices: 2134395--2134509 Score: 200
Period size: 41 Copynumber: 2.7 Consensus size: 43
2134385 ATTAAAGCTT
*
2134395 TCATCTTTGAAGAGA-ATCTATCATCTTT-AAAAGCGAATCTA
1 TCATCTTTGAAGAGAGATCTATCATCTTTGAAAAGAGAATCTA
2134436 TCATCTTTG-AGAGAGATCTATCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGATCTATCATCTTTGAAAAGAGAATCTA
2134478 TCATCTTTGAAGAGAGATCTATCATCTTTGAA
1 TCATCTTTGAAGAGAGATCTATCATCTTTGAA
2134510 GAATGTAGAT
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
40 5 0.07
41 22 0.31
42 21 0.30
43 22 0.31
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (43 bp):
TCATCTTTGAAGAGAGATCTATCATCTTTGAAAAGAGAATCTA
Found at i:2139279 original size:16 final size:16
Alignment explanation
Indices: 2139260--2139302 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2139250 AATTTTTTTC
*
2139260 TTTTTCTTTTTTGTTT
1 TTTTTCTTTTTTATTT
* *
2139276 TTTTTCTATTTCATTT
1 TTTTTCTTTTTTATTT
2139292 TTTTT-TTTTTT
1 TTTTTCTTTTTT
2139303 TCCCTCTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (16 bp):
TTTTTCTTTTTTATTT
Found at i:2139280 original size:22 final size:23
Alignment explanation
Indices: 2139252--2139304 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2139242 CTTGATTTAA
*
2139252 TTTTTTTCTTTTTC-TTTTTTGT
1 TTTTTTTCTATTTCATTTTTTGT
*
2139274 TTTTTTTCTATTTCATTTTTTTT
1 TTTTTTTCTATTTCATTTTTTGT
2139297 TTTTTTTC
1 TTTTTTTC
2139305 CCTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.04, C:0.09, G:0.02, T:0.85
Consensus pattern (23 bp):
TTTTTTTCTATTTCATTTTTTGT
Found at i:2139643 original size:2 final size:2
Alignment explanation
Indices: 2139636--2139705 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
2139626 GGGGACAACA
2139636 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2139677 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
2139706 AAGGATAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2142592 original size:13 final size:13
Alignment explanation
Indices: 2142548--2142603 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
2142538 AGCAAACATA
* *
2142548 AAAATACAAATGC
1 AAAATGCAAATGT
2142561 AAAGATGCCAAATGT
1 AAA-ATG-CAAATGT
*
2142576 -AAATGCAATTGT
1 AAAATGCAAATGT
*
2142588 AAAATGTAAATGT
1 AAAATGCAAATGT
2142601 AAA
1 AAA
2142604 TTATTTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 6 0.17
13 19 0.54
14 4 0.11
15 6 0.17
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (13 bp):
AAAATGCAAATGT
Found at i:2144289 original size:21 final size:21
Alignment explanation
Indices: 2144252--2144291 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2144242 AATACCTGAA
*
2144252 AAAAATATTAACAAAAAATAT
1 AAAAATAATAACAAAAAATAT
2144273 AAAAATAATAA-ATAAAAAT
1 AAAAATAATAACA-AAAAAT
2144292 TTTGAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATAATAACAAAAAATAT
Found at i:2146396 original size:3 final size:3
Alignment explanation
Indices: 2146382--2146455 Score: 71
Period size: 3 Copynumber: 24.7 Consensus size: 3
2146372 TTGAGTTTTG
* * * *
2146382 TAA TAT TAA TAA TAA T-A TATA TAA TAA TAA TAA TTA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
2146427 TAA TAA TAA -ATA TAA TGA TAA TAA TAA TA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA
2146456 TAAATAACGT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 3 0.05
3 54 0.89
4 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2146412 original size:21 final size:21
Alignment explanation
Indices: 2146382--2146462 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
2146372 TTGAGTTTTG
*
2146382 TAATATTAATAATAATATATA
1 TAATAATAATAATAATATATA
2146403 TAATAATAATAAT--TAT-TA
1 TAATAATAATAATAATATATA
*
2146421 T--T-ATAATAATAATAAATA
1 TAATAATAATAATAATATATA
* *
2146439 TAATGATAATAATAATATAAA
1 TAATAATAATAATAATATATA
2146460 TAA
1 TAA
2146463 CGTTTAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.16
16 1 0.02
17 2 0.04
18 6 0.12
19 3 0.06
20 1 0.02
21 29 0.58
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (21 bp):
TAATAATAATAATAATATATA
Found at i:2151685 original size:20 final size:21
Alignment explanation
Indices: 2151656--2151695 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2151646 TGATAGAACG
*
2151656 CTACTTAAAATATT-ATTTTT
1 CTACTGAAAATATTAATTTTT
2151676 CTACTGAAAATATTAATTTT
1 CTACTGAAAATATTAATTTT
2151696 GTTACCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
CTACTGAAAATATTAATTTTT
Found at i:2159139 original size:13 final size:13
Alignment explanation
Indices: 2159121--2159145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2159111 CGGCAACAGC
2159121 TGGTTTGACATGA
1 TGGTTTGACATGA
2159134 TGGTTTGACATG
1 TGGTTTGACATG
2159146 TACCTCGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.32, T:0.40
Consensus pattern (13 bp):
TGGTTTGACATGA
Found at i:2160225 original size:66 final size:66
Alignment explanation
Indices: 2160143--2160275 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
2160133 TACTTCATGT
2160143 TACTTCTAAATCTATCCTCGATTTCGTCAATGTGCAATTGAATTGCAAGAGTTCTCACGAATTTG
1 TACTTCTAAATCTATCCTCGATTTCGTCAATGTGCAATTGAATTGCAAGAGTTCTCACGAATTTG
2160208 C
66 C
2160209 TACTTCTAAATCTATCCTCGATTTCGTCAATGTGCAATTGAATTGCAAGAGTTCTCACGAATTTG
1 TACTTCTAAATCTATCCTCGATTTCGTCAATGTGCAATTGAATTGCAAGAGTTCTCACGAATTTG
2160274 C
66 C
2160275 T
1 T
2160276 GATCAAAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (66 bp):
TACTTCTAAATCTATCCTCGATTTCGTCAATGTGCAATTGAATTGCAAGAGTTCTCACGAATTTG
C
Found at i:2167067 original size:15 final size:15
Alignment explanation
Indices: 2167047--2167075 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2167037 AGGAAACAAA
2167047 ACATGGGCGGCTATG
1 ACATGGGCGGCTATG
2167062 ACATGGGCGGCTAT
1 ACATGGGCGGCTAT
2167076 CAAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (15 bp):
ACATGGGCGGCTATG
Found at i:2169999 original size:42 final size:42
Alignment explanation
Indices: 2169940--2170035 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
2169930 TTTGGGAGCC
* * *
2169940 GGAACTGGAATCGGAACCTGTTGC-ACCGGTTCCTAAAAAATG
1 GGAACCGGAACCGGAACCTGTT-CAACCGGTCCCTAAAAAATG
* *
2169982 GGAACCGGAACCGGAACCTGTTCAACCGGTCCCTAGAAATTG
1 GGAACCGGAACCGGAACCTGTTCAACCGGTCCCTAAAAAATG
2170024 GGAACCGGAACC
1 GGAACCGGAACC
2170036 TGTAGGTACC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (42 bp):
GGAACCGGAACCGGAACCTGTTCAACCGGTCCCTAAAAAATG
Found at i:2170064 original size:13 final size:13
Alignment explanation
Indices: 2170046--2170077 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2170036 TGTAGGTACC
2170046 GGTACCGGTTCCA
1 GGTACCGGTTCCA
2170059 GGTACCGGTTCCA
1 GGTACCGGTTCCA
2170072 GGTACC
1 GGTACC
2170078 CTGTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (13 bp):
GGTACCGGTTCCA
Found at i:2175987 original size:30 final size:30
Alignment explanation
Indices: 2175951--2176009 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2175941 TATATTTAGG
2175951 ACCTATGAGAAAGATATG-TCAATATCAAGC
1 ACCTATGAGAAAGATATGCT-AATATCAAGC
2175981 ACCTATGAGAAAGATATGCTAATATCAAG
1 ACCTATGAGAAAGATATGCTAATATCAAG
2176010 AACGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (30 bp):
ACCTATGAGAAAGATATGCTAATATCAAGC
Found at i:2176515 original size:64 final size:65
Alignment explanation
Indices: 2176385--2176522 Score: 224
Period size: 64 Copynumber: 2.1 Consensus size: 65
2176375 GAATGCAGTA
2176385 GAAGGCAAATAAATAGAATAACATCACATAATATAATATTTATTTAGAGTGGCAGATTCACATGT
1 GAAGGCAAATAAATAGAATAACATCAC---A-ATAATATTTATTTAGAGTGGCAGATTCACATGT
2176450 ATCC
62 ATCC
*
2176454 GAAGGCAAATAAATAGAATAACATCAC-ATAATATTTATTTAGAGTGGCGGATTCACATGTATCC
1 GAAGGCAAATAAATAGAATAACATCACAATAATATTTATTTAGAGTGGCAGATTCACATGTATCC
2176518 GAAGG
1 GAAGG
2176523 TGGGCACGTG
Statistics
Matches: 68, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
64 41 0.60
69 27 0.40
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (65 bp):
GAAGGCAAATAAATAGAATAACATCACAATAATATTTATTTAGAGTGGCAGATTCACATGTATCC
Found at i:2182057 original size:6 final size:6
Alignment explanation
Indices: 2182046--2182074 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2182036 CTTGAGCTGA
2182046 TTCTGG TTCTGG TTCTGG TTCTGG TTCTG
1 TTCTGG TTCTGG TTCTGG TTCTGG TTCTG
2182075 ACTCTACCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.31, T:0.52
Consensus pattern (6 bp):
TTCTGG
Found at i:2193734 original size:2 final size:2
Alignment explanation
Indices: 2193727--2193763 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2193717 TAGTTTTTAA
2193727 AT AT 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 AT AT A
2193764 ATGGTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2194463 original size:2 final size:2
Alignment explanation
Indices: 2194456--2194480 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2194446 TGAACAAAAT
2194456 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2194481 TGAAATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2199831 original size:9 final size:9
Alignment explanation
Indices: 2199817--2199885 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
2199807 CCGGTTTTCA
2199817 ACCGGTTTG
1 ACCGGTTTG
*
2199826 ACCGGTTTCA
1 ACCGGTTT-G
*
2199836 ACCGGTTCG
1 ACCGGTTTG
2199845 AACCGGTTTG
1 -ACCGGTTTG
*
2199855 ACCGGTCTG
1 ACCGGTTTG
2199864 AACCGGTTTG
1 -ACCGGTTTG
*
2199874 ACCGGTCTG
1 ACCGGTTTG
2199883 ACC
1 ACC
2199886 CGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 27 0.54
10 23 0.46
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2199836 original size:19 final size:18
Alignment explanation
Indices: 2199796--2199885 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 18
2199786 GGCTGCTGGA
* *
2199796 AACCGATTTAACCGGTTTT
1 AACCGGTTTGACCGG-TTT
2199815 CAACCGGTTTGACCGGTTT
1 -AACCGGTTTGACCGGTTT
*
2199834 CAACCGGTTCGAACCGGTTT
1 -AACCGGTTTG-ACCGGTTT
* *
2199854 GACCGGTCTGAACCGGTTT
1 AACCGGTTTG-ACCGGTTT
* *
2199873 GACCGGTCTGACC
1 AACCGGTTTGACC
2199886 CGACCCGACC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
18 3 0.05
19 39 0.62
20 21 0.33
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.28
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTT
Found at i:2199841 original size:10 final size:9
Alignment explanation
Indices: 2199796--2199879 Score: 69
Period size: 10 Copynumber: 8.8 Consensus size: 9
2199786 GGCTGCTGGA
*
2199796 AACCGATTT
1 AACCGGTTT
2199805 AACCGGTTTT
1 AACCGG-TTT
2199815 CAACCGGTTT
1 -AACCGGTTT
*
2199825 GACCGGTTT
1 AACCGGTTT
*
2199834 CAACCGGTTCG
1 -AACCGGTT-T
2199845 AACCGGTTT
1 AACCGGTTT
* *
2199854 GACCGGTCTG
1 AACCGGT-TT
2199864 AACCGGTTT
1 AACCGGTTT
*
2199873 GACCGGT
1 AACCGGT
2199880 CTGACCCGAC
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
9 26 0.43
10 28 0.47
11 6 0.10
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:2199848 original size:29 final size:29
Alignment explanation
Indices: 2199816--2199885 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
2199806 ACCGGTTTTC
*
2199816 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
* *
2199845 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
*
2199874 -ACCGGTCTGACC
1 AACCGGTTTGACC
2199886 CGACCCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 11 0.30
29 26 0.70
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.26
Consensus pattern (29 bp):
AACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:2199903 original size:17 final size:17
Alignment explanation
Indices: 2199881--2199919 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2199871 TTGACCGGTC
2199881 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2199898 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2199915 TGACC
1 TGACC
2199920 GTTGATCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:2203149 original size:23 final size:23
Alignment explanation
Indices: 2203119--2203178 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
2203109 ATTATTATAT
2203119 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
2203142 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
2203165 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
2203179 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2209606 original size:16 final size:16
Alignment explanation
Indices: 2209585--2209617 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2209575 TACATCTCAT
*
2209585 TTTGAAAGTTTGAGAG
1 TTTGAAAGATTGAGAG
2209601 TTTGAAAGATTGAGAG
1 TTTGAAAGATTGAGAG
2209617 T
1 T
2209618 CTTATATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (16 bp):
TTTGAAAGATTGAGAG
Found at i:2210073 original size:14 final size:14
Alignment explanation
Indices: 2210049--2210082 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2210039 TAGCTGGAGT
2210049 AATAATGGAAGGGG
1 AATAATGGAAGGGG
* *
2210063 GATAATTGAAGGGG
1 AATAATGGAAGGGG
2210077 AATAAT
1 AATAAT
2210083 AGTTCAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (14 bp):
AATAATGGAAGGGG
Found at i:2213028 original size:23 final size:24
Alignment explanation
Indices: 2213002--2213048 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2212992 CTTTACACTT
*
2213002 GTCCAA-ATTTGACCTTTCTTTAA
1 GTCCAACATGTGACCTTTCTTTAA
*
2213025 GTCCAACTATGTGCCCTTTCTTTA
1 GTCCAAC-ATGTGACCTTTCTTTA
2213049 TAAAAGACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
25 14 0.70
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.43
Consensus pattern (24 bp):
GTCCAACATGTGACCTTTCTTTAA
Found at i:2230829 original size:55 final size:55
Alignment explanation
Indices: 2230735--2230844 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
2230725 ACTGATCAAA
2230735 CCCACCGAAGTGTACCAACAACCATCCGTTTGCATTTAGCTTGATTTGGAGCTTC
1 CCCACCGAAGTGTACCAACAACCATCCGTTTGCATTTAGCTTGATTTGGAGCTTC
2230790 CCCA-CGAAGTGTACCAACAACCATCCGATTTGCATTTAGCTTGATTTGGAGCTTC
1 CCCACCGAAGTGTACCAACAACCATCCG-TTTGCATTTAGCTTGATTTGGAGCTTC
2230845 TTGTCCATGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 23 0.43
55 31 0.57
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (55 bp):
CCCACCGAAGTGTACCAACAACCATCCGTTTGCATTTAGCTTGATTTGGAGCTTC
Found at i:2232818 original size:51 final size:50
Alignment explanation
Indices: 2232758--2232863 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 50
2232748 TATGAAGTCT
2232758 TAGAATTGTATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATTATA
1 TAGAATTGTATTTAGAACATATTGAAATTTGAGTATGATTCTTGAA-TATA
2232809 TAGAATTGTATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATATA
1 TAGAATTGTATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATATA
2232859 T-GAAT
1 TAGAAT
2232864 GATAGGATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 4 0.07
50 5 0.09
51 46 0.84
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (50 bp):
TAGAATTGTATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATATA
Found at i:2233631 original size:21 final size:22
Alignment explanation
Indices: 2233589--2233670 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
2233579 TCGAGGGTAT
2233589 AGTAGTCCTTCGGGACGTATCC
1 AGTAGTCCTTCGGGACGTATCC
2233611 AGTAGTCCTTCGGGA-GTATCC
1 AGTAGTCCTTCGGGACGTATCC
* **
2233632 AGTAGTCCTACAGGGACGTATAT
1 AGTAGTCCTTC-GGGACGTATCC
* *
2233655 AGTGGTCCTTTGGGAC
1 AGTAGTCCTTCGGGAC
2233671 ATAATAGTCC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 16 0.31
22 24 0.46
23 12 0.23
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (22 bp):
AGTAGTCCTTCGGGACGTATCC
Found at i:2241369 original size:22 final size:22
Alignment explanation
Indices: 2241341--2241403 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
2241331 TCGAGGGTAT
*
2241341 AGTAGTCCTTCGGGACATATCC
1 AGTAGTCCTTCGGGACATATAC
* * * *
2241363 AGTAGTCCTACAGGACGTATAT
1 AGTAGTCCTTCGGGACATATAC
* *
2241385 AGTGGTCATTCGGGACATA
1 AGTAGTCCTTCGGGACATA
2241404 ATAGTCCTTC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (22 bp):
AGTAGTCCTTCGGGACATATAC
Found at i:2249018 original size:21 final size:22
Alignment explanation
Indices: 2248989--2249032 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2248979 TTACTGAATG
2248989 TCATACTGT-CAAA-TCCATATT
1 TCATACTGTACAAATTCC-TATT
*
2249010 TCATTCTGTACAAATTCCTATT
1 TCATACTGTACAAATTCCTATT
2249032 T
1 T
2249033 TAAAATGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 9 0.45
23 3 0.15
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (22 bp):
TCATACTGTACAAATTCCTATT
Found at i:2254435 original size:15 final size:16
Alignment explanation
Indices: 2254404--2254437 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2254394 TTCTTCGATA
*
2254404 TTAAAATAATTTATTT
1 TTAAAATAATATATTT
2254420 TTAAAATAA-ATATTT
1 TTAAAATAATATATTT
2254435 TTA
1 TTA
2254438 TTATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAATAATATATTT
Found at i:2255319 original size:15 final size:15
Alignment explanation
Indices: 2255295--2255326 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2255285 CCTCGGTAAG
2255295 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
*
2255310 TTTCTTTTCTTTCTT
1 TTTCTCTTCTTTCTT
2255325 TT
1 TT
2255327 CTGCTGCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:2255842 original size:3 final size:3
Alignment explanation
Indices: 2255834--2255908 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
2255824 TTAATATATT
* *
2255834 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2255882 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2255909 ATCAATATGG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2256366 original size:112 final size:113
Alignment explanation
Indices: 2256233--2256658 Score: 660
Period size: 112 Copynumber: 3.8 Consensus size: 113
2256223 ATAGAATTAT
* * *
2256233 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2256298 ATTATGAAC-TTCTCTGGAAAAGCTGCTCCTTCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
2256345 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * * * * **
2256410 CTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
* *
2256461 ACAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2256525 ATTATGAACTTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
2256573 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2256638 ATTATGAACTTTCTCTGGAAA
66 ATTATGAACTTTCTCTGGAAA
2256659 TGTCAATCCA
Statistics
Matches: 281, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
111 2 0.01
112 103 0.37
113 78 0.28
115 66 0.23
116 30 0.11
117 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
Found at i:2257722 original size:82 final size:82
Alignment explanation
Indices: 2257471--2258060 Score: 1066
Period size: 82 Copynumber: 7.2 Consensus size: 82
2257461 CTTATTTCTA
* * * *
2257471 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCCAACCAGATTAGATAACTCAAA
1 CTATGAGCACATTCATCTT-CAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAA
2257536 GAACACTTCCAGAAGATG
65 GAACACTTCCAGAAGATG
* *
2257554 CTATGAGTACATTCATCTTCAAATTCAATGATTGATTCTGTC-AACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
2257618 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
2257635 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
2257700 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
2257717 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
2257782 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
2257799 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
2257864 AACACTTCCAGAAGATGG
66 AACACTTCCAGAAGAT-G
2257882 C---GAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
2257944 AACACTT-CAGAAGATG
66 AACACTTCCAGAAGATG
2257960 CTATGAGCACATTCATCTTCAAATTC-ATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
2258024 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
2258041 CTATGAGCACATTCATCTTC
1 CTATGAGCACATTCATCTTC
2258061 CAGTTAAGGT
Statistics
Matches: 494, Mismatches: 7, Indels: 14
0.96 0.01 0.03
Matches are distributed among these distances:
78 2 0.00
79 8 0.02
80 113 0.23
81 129 0.26
82 223 0.45
83 19 0.04
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (82 bp):
CTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATG
Found at i:2258750 original size:16 final size:17
Alignment explanation
Indices: 2258710--2258753 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
2258700 TTCATAGAAG
*
2258710 AATAAATTGAATTTCCA
1 AATAAATTGAATCTCCA
2258727 AA-ATAATTGAATCT-CA
1 AATA-AATTGAATCTCCA
2258743 AATAAATTGAA
1 AATAAATTGAA
2258754 CTTGAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (17 bp):
AATAAATTGAATCTCCA
Found at i:2259095 original size:10 final size:10
Alignment explanation
Indices: 2259081--2259117 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2259071 TTGACCCACC
2259081 CTTTTTTCTTT
1 CTTTTTT-TTT
*
2259092 TTTTTTTTTT
1 CTTTTTTTTT
2259102 CTTTTTTTTT
1 CTTTTTTTTT
2259112 CTTTTT
1 CTTTTT
2259118 CTTCAAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:2259101 original size:14 final size:14
Alignment explanation
Indices: 2259082--2259116 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
2259072 TGACCCACCC
2259082 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
2259096 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
2259110 TTCTTTT
1 TT-TTTT
2259117 TCTTCAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTCTTTTTTT
Found at i:2259108 original size:16 final size:16
Alignment explanation
Indices: 2259083--2259120 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
2259073 GACCCACCCT
2259083 TTTTTC-TTTTTTTT-
1 TTTTTCTTTTTTTTTC
2259097 TTTTTCTTTTTTTTTC
1 TTTTTCTTTTTTTTTC
2259113 TTTTTCTT
1 TTTTTCTT
2259121 CAAGCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 8 0.36
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:2269743 original size:19 final size:19
Alignment explanation
Indices: 2269699--2269765 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
2269689 CAGAAAAATA
*
2269699 AATAATGAAATAAATACTT
1 AATAATAAAATAAATACTT
2269718 ACA-AATAAAATGAAATA-TT
1 A-ATAATAAAAT-AAATACTT
*
2269737 AATAATATATATAAATACTAT
1 AATAATA-AAATAAATACT-T
*
2269758 AAAAATAA
1 AATAATAA
2269766 TATGTATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
18 1 0.03
19 20 0.51
20 11 0.28
21 7 0.18
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAATAAAATAAATACTT
Found at i:2269764 original size:24 final size:22
Alignment explanation
Indices: 2269737--2269794 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
2269727 ATGAAATATT
2269737 AATAATATATATAAATACTATAAA
1 AATAATAT-TATAAATA-TATAAA
2269761 AATAATATGTAT--ATATATAAA
1 AATAATAT-TATAAATATATAAA
2269782 AA-AA-ATTATAAAT
1 AATAATATTATAAAT
2269795 TAAATATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 3 0.10
19 2 0.06
20 4 0.13
21 8 0.26
22 3 0.10
24 11 0.35
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AATAATATTATAAATATATAAA
Found at i:2271875 original size:3 final size:3
Alignment explanation
Indices: 2271867--2271950 Score: 141
Period size: 3 Copynumber: 28.0 Consensus size: 3
2271857 TTAATATATT
* *
2271867 TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2271915 TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2271951 ATCAATATGG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2272720 original size:17 final size:17
Alignment explanation
Indices: 2272700--2272763 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
2272690 ATTATTTTAA
2272700 TATTTAAATTTAAAATT
1 TATTTAAATTTAAAATT
*
2272717 TATTT-AATTTTAAA-T
1 TATTTAAATTTAAAATT
* *
2272732 TATATAAA-TT-AATTT
1 TATTTAAATTTAAAATT
*
2272747 TATTATTAATTTAAAAT
1 TATT-TAAATTTAAAAT
2272764 CTTTATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
14 2 0.06
15 11 0.31
16 13 0.36
17 7 0.19
18 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTAAATTTAAAATT
Found at i:2272747 original size:50 final size:49
Alignment explanation
Indices: 2272671--2272819 Score: 135
Period size: 50 Copynumber: 3.0 Consensus size: 49
2272661 AAAATCTATC
* *
2272671 AATTATTAATTTATATTTAATT-ATTTTAATATTTAAATTTAAAATTTATTT
1 AATT-TTAAATTATA-TAAATTAATTTTAATATTT-AATTTAAAATTTATTT
* *
2272722 AATTTTAAATTATATAAATTAATTTTATTA-TTAATTTAAAATCTTTATAT
1 AATTTTAAATTATATAAATTAATTTTAATATTTAATTTAAAA--TTTATTT
* * * *
2272772 AATTTCAAATTATTATAAAAATAATTTTTACATTTAA--TAAAATTTATT
1 AATTTTAAATTA-TAT-AAATTAATTTTAATATTTAATTTAAAATTTATT
2272820 ATTTAAATAT
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
48 9 0.11
49 12 0.15
50 34 0.41
51 12 0.15
52 11 0.13
53 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (49 bp):
AATTTTAAATTATATAAATTAATTTTAATATTTAATTTAAAATTTATTT
Found at i:2272787 original size:18 final size:18
Alignment explanation
Indices: 2272706--2272788 Score: 63
Period size: 18 Copynumber: 4.9 Consensus size: 18
2272696 TTAATATTTA
*
2272706 AATTTAAAA-T-TTATTT
1 AATTTAAAATTATTATAT
*
2272722 AATTTTAAATTA-TATA-
1 AATTTAAAATTATTATAT
**
2272738 AA-TTAATTTTATTAT-T
1 AATTTAAAATTATTATAT
2272754 AATTTAAAATCT-TTATAT
1 AATTTAAAAT-TATTATAT
*
2272772 AATTTCAAATTATTATA
1 AATTTAAAATTATTATA
2272789 AAAATAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
15 6 0.12
16 15 0.29
17 14 0.27
18 16 0.31
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTAAAATTATTATAT
Found at i:2272838 original size:23 final size:23
Alignment explanation
Indices: 2272811--2272880 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
2272801 ACATTTAATA
2272811 AAATTTATTATTTAAATATTATT
1 AAATTTATTATTTAAATATTATT
* * * *
2272834 TAATTTAATATTTTATTATT-TT
1 AAATTTATTATTTAAATATTATT
*
2272856 AAATTAATTA--TAAATATTATT
1 AAATTTATTATTTAAATATTATT
2272877 AAAT
1 AAAT
2272881 AAATAAATTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 6 0.16
21 6 0.16
22 9 0.24
23 16 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTTATTATTTAAATATTATT
Found at i:2272854 original size:15 final size:16
Alignment explanation
Indices: 2272814--2272859 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2272804 TTTAATAAAA
2272814 TTTATTATTTAAATAT
1 TTTATTATTTAAATAT
*
2272830 TATT-TAATTT-AATAT
1 T-TTATTATTTAAATAT
2272845 TTTATTATTTTAAAT
1 TTTATTA-TTTAAAT
2272860 TAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
16 9 0.38
17 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATTATTTAAATAT
Found at i:2272878 original size:21 final size:22
Alignment explanation
Indices: 2272823--2272894 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 22
2272813 ATTTATTATT
* *
2272823 TAAATATTATTTAATTTAATATT
1 TAAATATTA-TTAAATTAATATA
* *
2272846 TTATTATT-TTAAATTAAT-TA
1 TAAATATTATTAAATTAATATA
* *
2272866 TAAATATTATTAAATAAATAAA
1 TAAATATTATTAAATTAATATA
2272888 TTAAATA
1 -TAAATA
2272895 ATATAACATT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 7 0.18
21 18 0.47
22 1 0.03
23 12 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATATTATTAAATTAATATA
Found at i:2280604 original size:46 final size:46
Alignment explanation
Indices: 2280535--2280640 Score: 151
Period size: 46 Copynumber: 2.3 Consensus size: 46
2280525 TATTCACTAC
2280535 TTCAACTACTTTTCAGAGATCATTTATTGCAGTAATAATGCATCAT
1 TTCAACTACTTTTCAGAGATCATTTATTGCAGTAATAATGCATCAT
* * *
2280581 TTCAATTATTTTTCAGATG-TCATTTATTGCAGTAATAATGCATCGT
1 TTCAACTACTTTTCAGA-GATCATTTATTGCAGTAATAATGCATCAT
* *
2280627 TTCAGCTACATTTC
1 TTCAACTACTTTTC
2280641 GGATGCCATT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 51 0.98
47 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (46 bp):
TTCAACTACTTTTCAGAGATCATTTATTGCAGTAATAATGCATCAT
Found at i:2280632 original size:272 final size:271
Alignment explanation
Indices: 2280130--2280653 Score: 587
Period size: 272 Copynumber: 1.9 Consensus size: 271
2280120 ATAATTGAAG
* *
2280130 AAAACGGGTGAAAATAATGTTGCATTATCATCTTCTGCAACTTCTCAGTGATATATCAACTTAAA
1 AAAACGGGTGAAAATAATGTTGCATTATCATCTTCTGCAACTTCTCAATGATATATCAACTCAAA
* * * * **
2280195 TTAGAAAACTTTTCAATGTTGAATTGTCACTTCAAATCATAAAAAATGTGTATTTTAACCAGGTC
66 TCAGAAAACTTTCCAATATTAAATTGTCACTTCAAATCATAAAAAAAATGTATTTTAACCAGGTC
* * * ** * *
2280260 AAATTATTTAATGCTTCAGCTACTTTTTAGAGGTCATTTATTGCACCATTTCAACTACTTCTCAG
131 -AACTATTCAATACTTCAGAGACTTTTTAGAGGTCATATAATGCACCATTTCAACTACTTCTCAG
* * *
2280325 AGGTCGTTTATTGCGGCAAGAATGCACTATTTCAGCTACTTTTCAGAGGCCATTTAATGAAAATT
195 AGGTCATTTATTGCAGCAAGAATGCACTATTTCAGCTACATTTCAGAGGCCATTTAATGAAAATT
2280390 CAAACTATTCAA
260 CAAACTATTCAA
* * *
2280402 AAAACGGGTGAAAATAGTGTTGCATTATCATCTTTTGCAACTTCTCAATGGTATAT-AACTCAAA
1 AAAACGGGTGAAAATAATGTTGCATTATCATCTTCTGCAACTTCTCAATGATATATCAACTCAAA
* * * *
2280466 TCATAAAACTTTCCAGTATTAAATTGTCACTTCAAATCATAAAAAAAATGTATTTTAACTA-TTC
66 TCAGAAAACTTTCCAATATTAAATTGTCACTTCAAATCATAAAAAAAATGTATTTTAACCAGGTC
* * *
2280530 -ACTACTTCAACTACTTTTCAGAGATCATTTATT-GCA-GT-A-ATAATGCATCATTTCAATTAT
131 AACTA-TTCAA-TAC--TTCAGAGA-C-TTT-TTAG-AGGTCATATAATGCACCATTTCAACTAC
* * * * * * *
2280590 TTTTCAGATGTCATTTATTGCAGTAATAATGCA-TCGTTTCAGCTACATTTCGGATGCCATTTAA
188 TTCTCAGAGGTCATTTATTGCAGCAAGAATGCACT-ATTTCAGCTACATTTCAGAGGCCATTTAA
2280654 GGCATAATTC
Statistics
Matches: 208, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
268 3 0.01
269 4 0.02
270 4 0.02
271 60 0.29
272 126 0.61
273 2 0.01
274 6 0.03
275 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (271 bp):
AAAACGGGTGAAAATAATGTTGCATTATCATCTTCTGCAACTTCTCAATGATATATCAACTCAAA
TCAGAAAACTTTCCAATATTAAATTGTCACTTCAAATCATAAAAAAAATGTATTTTAACCAGGTC
AACTATTCAATACTTCAGAGACTTTTTAGAGGTCATATAATGCACCATTTCAACTACTTCTCAGA
GGTCATTTATTGCAGCAAGAATGCACTATTTCAGCTACATTTCAGAGGCCATTTAATGAAAATTC
AAACTATTCAA
Found at i:2280651 original size:46 final size:46
Alignment explanation
Indices: 2280535--2280652 Score: 139
Period size: 46 Copynumber: 2.6 Consensus size: 46
2280525 TATTCACTAC
* *
2280535 TTCAACTACTTTTCAGA-GATCATTTATTGCAGTAATAATGCATCAT
1 TTCAACTACATTTCAGATG-CCATTTATTGCAGTAATAATGCATCAT
* ** * *
2280581 TTCAATTATTTTTCAGATGTCATTTATTGCAGTAATAATGCATCGT
1 TTCAACTACATTTCAGATGCCATTTATTGCAGTAATAATGCATCAT
* *
2280627 TTCAGCTACATTTCGGATGCCATTTA
1 TTCAACTACATTTCAGATGCCATTTA
2280653 AGGCATAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 61 0.98
47 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (46 bp):
TTCAACTACATTTCAGATGCCATTTATTGCAGTAATAATGCATCAT
Found at i:2284163 original size:19 final size:20
Alignment explanation
Indices: 2284136--2284188 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
2284126 AACGCGATTT
* *
2284136 AGAAAATCGCAACGTTGAAA
1 AGAAAATCGCAACGGTCAAA
2284156 AG-AAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTCAAA
2284175 AGAAAATCGCAACG
1 AGAAAATCGCAACG
2284189 CGATATTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTCAAA
Found at i:2284234 original size:20 final size:20
Alignment explanation
Indices: 2284220--2284380 Score: 184
Period size: 20 Copynumber: 7.8 Consensus size: 20
2284210 ACGATTAAGA
2284220 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2284240 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
2284262 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
2284282 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2284302 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
2284324 GAATCGCGTTGCGATT-TTAT
1 GAATCGCGTTGCGATTCTT-G
*
2284344 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2284364 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
2284381 CTTCTTTTCA
Statistics
Matches: 125, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.02
20 66 0.53
21 11 0.09
22 46 0.37
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.35
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:2284257 original size:42 final size:41
Alignment explanation
Indices: 2284220--2284380 Score: 177
Period size: 42 Copynumber: 3.9 Consensus size: 41
2284210 ACGATTAAGA
*
2284220 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCGATTCTAG
* *
2284262 GAATCGCGTTGCGATTTTCTG-A-ATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTT-GGAAGATCGCGTTGCGATTCTAG
* * *
2284302 GAAGATCGCGTTGCGATTTT--ATGAATCGCGTTGCGATTTTAT
1 G-A-ATCGCGTTGCGATTTTGGAAG-ATCGCGTTGCGATTCTAG
*
2284344 GAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGAT
1 GAATCGCGTTGCGATT-TTGGAAGATCGCGTTGCGAT
2284381 CTTCTTTTCA
Statistics
Matches: 103, Mismatches: 7, Indels: 18
0.80 0.05 0.14
Matches are distributed among these distances:
40 32 0.31
41 7 0.07
42 62 0.60
43 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.35
Consensus pattern (41 bp):
GAATCGCGTTGCGATTTTGGAAGATCGCGTTGCGATTCTAG
Found at i:2284396 original size:62 final size:61
Alignment explanation
Indices: 2284220--2284439 Score: 275
Period size: 62 Copynumber: 3.6 Consensus size: 61
2284210 ACGATTAAGA
**
2284220 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA-TCTTATAATCGCGTTGCGATTTTCT
* *
2284282 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCGTTGCGATTTTAT
1 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTAT-AATCGCGTTGCGATTTTCT
* * ** * *
2284344 GAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTTTCAACGTTGCGCTTTTCT
1 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTATAATC-GCGTTGCGATTTTCT
* * *
2284406 AAATCGCGTTGCGGTT-TT-G-ATATCGCGTTGCGAT
1 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
2284440 TTTGTTGGTC
Statistics
Matches: 140, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
59 14 0.10
60 1 0.01
61 7 0.05
62 118 0.84
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (61 bp):
GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTATAATCGCGTTGCGATTTTCT
Found at i:2284415 original size:20 final size:20
Alignment explanation
Indices: 2284221--2284442 Score: 153
Period size: 20 Copynumber: 10.8 Consensus size: 20
2284211 CGATTAAGAG
**
2284221 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
**
2284242 AGATCGCGTTGCGATTCTT-GG
1 A-ATCGCGTTGCGATT-TTCTA
*
2284263 AATCGCGTTGCGATTTTCTG
1 AATCGCGTTGCGATTTTCTA
**
2284283 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
* *
2284304 AGATCGCGTTGCGATTTTATG
1 A-ATCGCGTTGCGATTTTCTA
* *
2284325 AATCGCGTTGCGATTTTATG
1 AATCGCGTTGCGATTTTCTA
* **
2284345 AATCGCATTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
*
2284366 AGATCGCGTTGCGATCTTCT-
1 A-ATCGCGTTGCGATTTTCTA
** * *
2284386 TTTCAACGTTGCGCTTTTCTA
1 AATC-GCGTTGCGATTTTCTA
* *
2284407 AATCGCGTTGCGGTTTT-GA
1 AATCGCGTTGCGATTTTCTA
*
2284426 TATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
2284443 GTTGGTCATT
Statistics
Matches: 165, Mismatches: 28, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
19 20 0.12
20 86 0.52
21 16 0.10
22 43 0.26
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCTA
Found at i:2287615 original size:18 final size:18
Alignment explanation
Indices: 2287592--2287636 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2287582 AGAAAGAGAT
*
2287592 GGGGACAAAGAGTCGCAG
1 GGGGACAAAGAGACGCAG
2287610 GGGGACAAAGAGACGCAG
1 GGGGACAAAGAGACGCAG
*
2287628 GGAGACAAA
1 GGGGACAAA
2287637 CAAGTGCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.42, T:0.02
Consensus pattern (18 bp):
GGGGACAAAGAGACGCAG
Found at i:2288258 original size:32 final size:32
Alignment explanation
Indices: 2288214--2288283 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
2288204 GGGTCGGTTT
* *
2288214 AATATCAGATCGATTAGA-TTTCGGATCGGATC
1 AATATCAAATCGATT-GATTTTCGAATCGGATC
*
2288246 AATATCAAATCGATTGATTTTCGAATCGGGTC
1 AATATCAAATCGATTGATTTTCGAATCGGATC
2288278 AATATC
1 AATATC
2288284 GGATCAGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (32 bp):
AATATCAAATCGATTGATTTTCGAATCGGATC
Found at i:2288587 original size:16 final size:16
Alignment explanation
Indices: 2288568--2288628 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
2288558 GTTTGAGTTA
2288568 TTTTCGGTTCGGATTG-
1 TTTT-GGTTCGGATTGC
*
2288584 TTTTGAGTTCGAATTGC
1 TTTTG-GTTCGGATTGC
* * *
2288601 TTTTGATTCGGGTTGT
1 TTTTGGTTCGGATTGC
2288617 TTTTCGGTTCGG
1 TTTT-GGTTCGG
2288629 GTCAAATTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 1 0.03
16 24 0.67
17 11 0.31
ACGTcount: A:0.08, C:0.11, G:0.30, T:0.51
Consensus pattern (16 bp):
TTTTGGTTCGGATTGC
Done.