Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3572271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 44823 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:2840324 original size:2 final size:2
Alignment explanation
Indices: 2840317--2840345 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2840307 TTTGACCTTT
2840317 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2840346 CAAAGCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2843922 original size:13 final size:13
Alignment explanation
Indices: 2843904--2843930 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2843894 GAAGTATTAA
2843904 GAGGGGGGGGGGG
1 GAGGGGGGGGGGG
2843917 GAGGGGGGGGGGG
1 GAGGGGGGGGGGG
2843930 G
1 G
2843931 GGCAATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.93, T:0.00
Consensus pattern (13 bp):
GAGGGGGGGGGGG
Found at i:2846952 original size:20 final size:18
Alignment explanation
Indices: 2846919--2846973 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 18
2846909 TGATATCATA
2846919 AAAATTTATTAATTAATT
1 AAAATTTATTAATTAATT
*
2846937 AAAA--TATTATTTAATT
1 AAAATTTATTAATTAATT
*
2846953 AATAATTTATTAATTTATT
1 AA-AATTTATTAATTAATT
2846972 AA
1 AA
2846974 TTTATACATC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
18 4 0.13
19 12 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTTATTAATTAATT
Found at i:2846976 original size:8 final size:8
Alignment explanation
Indices: 2846921--2846978 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
2846911 ATATCATAAA
2846921 AATTTATT
1 AATTTATT
*
2846929 AATTAATT
1 AATTTATT
2846937 AAAATATTATTT
1 --AAT-TTA-TT
*
2846949 AA-TTAAT
1 AATTTATT
2846956 AATTTATT
1 AATTTATT
2846964 AATTTATT
1 AATTTATT
2846972 AATTTAT
1 AATTTAT
2846979 ACATCAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 3 0.07
8 29 0.71
10 5 0.12
11 2 0.05
12 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
AATTTATT
Found at i:2853154 original size:33 final size:33
Alignment explanation
Indices: 2853080--2853154 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
2853070 GCTGATATGG
*
2853080 TATATTAACATATCATAATTAATAATAATGTAA
1 TATATTAATATATCATAATTAATAATAATGTAA
* * * * *
2853113 TATGTTAATATATTATAATTAATGATGATGTGA
1 TATATTAATATATCATAATTAATAATAATGTAA
2853146 TATATTAAT
1 TATATTAAT
2853155 TTAACATGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (33 bp):
TATATTAATATATCATAATTAATAATAATGTAA
Found at i:2859559 original size:3 final size:3
Alignment explanation
Indices: 2859553--2859586 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2859543 TGATGATGAT
2859553 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2859587 TTGAGCCTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2869587 original size:2 final size:2
Alignment explanation
Indices: 2869580--2869604 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2869570 AAAGGAAAAC
2869580 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2869605 TTTACTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2870774 original size:31 final size:31
Alignment explanation
Indices: 2870709--2870782 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 31
2870699 GTAATACTTA
*
2870709 TTAAAATTTATTATTTTTTATAAATATGATT
1 TTAAAATTTATTATTTTTTATAAATATGAAT
*
2870740 TTAAAATTTAATTTATTTTTTATGAAT-T-AAT
1 TTAAAATTT-A-TTATTTTTTATAAATATGAAT
*
2870771 TT-AATTTTATTA
1 TTAAAATTTATTA
2870783 ATAATATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 3 0.08
29 1 0.03
30 5 0.13
31 13 0.34
32 2 0.05
33 14 0.37
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
TTAAAATTTATTATTTTTTATAAATATGAAT
Found at i:2910334 original size:45 final size:45
Alignment explanation
Indices: 2910270--2910357 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
2910260 ATTGATCATA
*
2910270 TATTCTTATTGGGTAATTCTAATACTACTTTGAGTATGTCATCTT
1 TATTCTTATTGGGTAATTCTAATACTACTTTGAGCATGTCATCTT
2910315 TATTCTTATTGGGTAATTCTAATACTACTTTGAGCATGTCATC
1 TATTCTTATTGGGTAATTCTAATACTACTTTGAGCATGTCATC
2910358 CTTTGCGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (45 bp):
TATTCTTATTGGGTAATTCTAATACTACTTTGAGCATGTCATCTT
Found at i:2917953 original size:38 final size:39
Alignment explanation
Indices: 2917875--2917959 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 39
2917865 ATTGACAATA
* * * * *
2917875 CTTCTTCTCTT-GGGGTGTTTTGAATACTATTTGTAGTG
1 CTTCTTCTTTTGGGGGTGTTCTGAATACTACTTCTAATG
*
2917913 CTT-TTCTTTTGGGGGTGTTCTGAATTCTACTTCTAATG
1 CTTCTTCTTTTGGGGGTGTTCTGAATACTACTTCTAATG
2917951 CTTCTTCTT
1 CTTCTTCTT
2917960 CTATCAAGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
37 6 0.15
38 28 0.72
39 5 0.13
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (39 bp):
CTTCTTCTTTTGGGGGTGTTCTGAATACTACTTCTAATG
Found at i:2918539 original size:162 final size:162
Alignment explanation
Indices: 2918272--2918597 Score: 580
Period size: 162 Copynumber: 2.0 Consensus size: 162
2918262 TTCAAGTCTT
*
2918272 GTTGTAACATTTGAAGCTTTTGGAGCATACAAAGTAGAAGGTGAATTTTGACCTTTTAAAAGCAA
1 GTTGTAACATTTGAAGCTTTTGGAGCATACAAAGTAGAAGGTGAATCTTGACCTTTTAAAAGCAA
* *
2918337 AATCGTGAACAAAGCTATTATGGATACGTTGGGCAATGCCTTAAAGATTGCTTCCTCCCTATGCT
66 AATCATGAACAAAGCTATTATGGATACATTGGGCAATGCCTTAAAGATTGCTTCCTCCCTATGCT
* *
2918402 TAGACATTTCTTTCAAAGAATCGTAGAAGATG
131 TAGACATTTCCTTCAAAGAATCGCAGAAGATG
*
2918434 GTTGTAACATTTGAAGCTTTTGGAGCATACAAAGTAGAAGGTGAATCTTGACCTTTTAAAAGCGA
1 GTTGTAACATTTGAAGCTTTTGGAGCATACAAAGTAGAAGGTGAATCTTGACCTTTTAAAAGCAA
*
2918499 AATTATGAACAAAGCTATTATGGATACATTGGGCAATGCCTTAAAGATTGCTTCCTCCCTATGCT
66 AATCATGAACAAAGCTATTATGGATACATTGGGCAATGCCTTAAAGATTGCTTCCTCCCTATGCT
*
2918564 TAGACATTTCCTTCAAAGAATTGCAGAAGATG
131 TAGACATTTCCTTCAAAGAATCGCAGAAGATG
2918596 GT
1 GT
2918598 GCATCTCTTG
Statistics
Matches: 156, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 156 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (162 bp):
GTTGTAACATTTGAAGCTTTTGGAGCATACAAAGTAGAAGGTGAATCTTGACCTTTTAAAAGCAA
AATCATGAACAAAGCTATTATGGATACATTGGGCAATGCCTTAAAGATTGCTTCCTCCCTATGCT
TAGACATTTCCTTCAAAGAATCGCAGAAGATG
Found at i:2923247 original size:28 final size:28
Alignment explanation
Indices: 2923164--2923324 Score: 160
Period size: 29 Copynumber: 5.5 Consensus size: 28
2923154 CAGATTTAAC
*
2923164 ATGTTTGTTTTAATTTAGACAAGAAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
2923192 ATGTTTGATCTTAATTTAGACAAGAAAAT
1 ATGTTTG-TCTTAATTTAGACAAGAAAAT
* *
2923221 ATGTTTGTCTTAATTTAAGATAAAAAAATT
1 ATGTTTGTCTTAATTT-AGACAAGAAAA-T
* * *
2923251 ATTTTTTGTCTTAATCTAGACGAGAAAAT
1 A-TGTTTGTCTTAATTTAGACAAGAAAAT
* * * *
2923280 ATATTTGTCTCAATTTTGATAAGATTAAAT
1 ATGTTTGTCTTAATTTAGACAAGA--AAAT
* *
2923310 ATTTTTATCTTAATT
1 ATGTTTGTCTTAATT
2923325 AAAGATCAGA
Statistics
Matches: 110, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
28 33 0.30
29 38 0.35
30 26 0.24
31 13 0.12
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAT
Found at i:2923277 original size:59 final size:57
Alignment explanation
Indices: 2923164--2923295 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 57
2923154 CAGATTTAAC
* * *
2923164 ATGTTTGTTTTAATTTAGACAAGAAAATATGTTTGATCTTAATTTAGACAAGAAAAT
1 ATGTTTGTCTTAATTTAGACAAAAAAATATGTTTGATCTTAATCTAGACAAGAAAAT
* * *
2923221 ATGTTTGTCTTAATTTAAGATAAAAAAATTATTTTTTG-TCTTAATCTAGACGAGAAAAT
1 ATGTTTGTCTTAATTT-AGACAAAAAAA-TA-TGTTTGATCTTAATCTAGACAAGAAAAT
* *
2923280 ATATTTGTCTCAATTT
1 ATGTTTGTCTTAATTT
2923296 TGATAAGATT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 15 0.23
58 9 0.14
59 35 0.55
60 5 0.08
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (57 bp):
ATGTTTGTCTTAATTTAGACAAAAAAATATGTTTGATCTTAATCTAGACAAGAAAAT
Found at i:2927727 original size:348 final size:347
Alignment explanation
Indices: 2927081--2927763 Score: 851
Period size: 348 Copynumber: 2.0 Consensus size: 347
2927071 TCGCTATTAA
* ** * * * ** *
2927081 ATTGTTTGAATTTCATGCTGGTGTAATCTTTGGTATATGGCTTGGCTACTATTTTGGCAAGATAT
1 ATTGTTTGAATTTCAGGCAAGTGTAATCCTTGGGATATGGCTTGACTACTACCTTGGCAAGATAA
* * * * *
2927146 GGTAGTTTCAAGTCAAACTCTGAGAAGTTGAGGCTTTTATTCTTTTGATCGAGTAATTTCTCAAG
66 GGTAGTTT-AAGTCAAACTCTAAGAAGTTGAGGCTGTTATTCTTCTAATCGAGTAACTTCTCAAG
* * * *
2927211 TTCTTCCTTCATAACAAAACTTTGAGCCCCGGTTGAATAAGTTGTGGTGATAGGACTTCCAAGAA
130 TTCTTCCTTCATAACAAAACTTTGAGCACCGGTTGAAGAAGTTGTGGTAACAGGACTTCCAAGAA
** * *
2927276 TTGCAGGATTAGTGGTATTGAGGAATAGGACGGTCGTGCTCTTTCCATTTCCTCCATTTTCATTC
195 TTAAAGGATTAGTGGTATTGAGGAATAGGACAGTCATGCTCTTTCCATTTCCTCCATTTTCATT-
* * *
2927341 ATGTTGTTGACCATGCTAGCGACATTTTTACTATTATGGGTTGGCATTAGTTAAGGTTGAGAAGT
259 ATGTTGTTGACCATGCTAACAACATTTTTACCATTATGGGTTGGCATTAGTTAAGGTTGAGAAGT
2927406 TGTGGCAATTGACGATACAAACTG
324 TGTGGCAATTGACGATACAAACTG
*
2927430 ATTGTTTGAATTTCGGGCAAGTGTAATCCTTGGGATATGGCTTGACTACTACCTTGGCAAGATAA
1 ATTGTTTGAATTTCAGGCAAGTGTAATCCTTGGGATATGGCTTGACTACTACCTTGGCAAGATAA
*
2927495 GGTAGCTTT-AGTCAAACTCTAAGACGTTGAGGCTGTTATTCTTCTAATCGAGTAACTTCTCAAG
66 GGTAG-TTTAAGTCAAACTCTAAGAAGTTGAGGCTGTTATTCTTCTAATCGAGTAACTTCTCAAG
** * * * * * *
2927559 TTCTTCCTTTGTAACAAAGCTTTGAGCACTGGTTTAAGGAGTTGTTGTAACAGGA-TTCCCAATA
130 TTCTTCCTTCATAACAAAACTTTGAGCACCGGTTGAAGAAGTTGTGGTAACAGGACTT-CCAAGA
* *
2927623 A-TAAAGGGATTGGTGGTATTGAGGAATAGGTCAGTCATGCT-TTCTCCATTTCCTCCA-TTTCT
194 ATTAAA-GGATTAGTGGTATTGAGGAATAGGACAGTCATGCTCTT-TCCATTTCCTCCATTTTC-
* * *
2927685 ATT-TGTAATGTTGACCACTTC-AACAACATTTTCT-CCATTATGGGTTGGCATTGGTTGAGGTT
256 ATTATGT--TGTTGACCA-TGCTAACAACATTTT-TACCATTATGGGTTGGCATTAGTTAAGGTT
2927747 GAGAAGTTGTGGCAATT
317 GAGAAGTTGTGGCAATT
2927764 AAGGATGTAA
Statistics
Matches: 285, Mismatches: 40, Indels: 19
0.83 0.12 0.06
Matches are distributed among these distances:
346 3 0.01
347 10 0.04
348 206 0.72
349 63 0.22
350 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (347 bp):
ATTGTTTGAATTTCAGGCAAGTGTAATCCTTGGGATATGGCTTGACTACTACCTTGGCAAGATAA
GGTAGTTTAAGTCAAACTCTAAGAAGTTGAGGCTGTTATTCTTCTAATCGAGTAACTTCTCAAGT
TCTTCCTTCATAACAAAACTTTGAGCACCGGTTGAAGAAGTTGTGGTAACAGGACTTCCAAGAAT
TAAAGGATTAGTGGTATTGAGGAATAGGACAGTCATGCTCTTTCCATTTCCTCCATTTTCATTAT
GTTGTTGACCATGCTAACAACATTTTTACCATTATGGGTTGGCATTAGTTAAGGTTGAGAAGTTG
TGGCAATTGACGATACAAACTG
Found at i:2929277 original size:22 final size:22
Alignment explanation
Indices: 2929249--2929307 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
2929239 CTGCACAGAA
2929249 GTATCGATACTTCCATAGGAGG
1 GTATCGATACTTCCATAGGAGG
2929271 GTATCGATACTTCCATAGGAGG
1 GTATCGATACTTCCATAGGAGG
*
2929293 GTATCGAAACTTCCA
1 GTATCGATACTTCCA
2929308 AGATAGAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (22 bp):
GTATCGATACTTCCATAGGAGG
Found at i:2940796 original size:18 final size:18
Alignment explanation
Indices: 2940781--2940818 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2940771 GCATCAACTC
*
2940781 CAACATCAAGAACAACCT
1 CAACAACAAGAACAACCT
*
2940799 CAACAACAAGAATAACCT
1 CAACAACAAGAACAACCT
2940817 CA
1 CA
2940819 GTGTTGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.32, G:0.05, T:0.11
Consensus pattern (18 bp):
CAACAACAAGAACAACCT
Found at i:2943212 original size:21 final size:21
Alignment explanation
Indices: 2943170--2943225 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
2943160 ACTTTTAAGA
*
2943170 ATATATATAATAAAAAGTTAT
1 ATATATATAATAAAAAGATAT
*
2943191 ATATATGTAATATAAAA-ATAT
1 ATATATATAATA-AAAAGATAT
*
2943212 A-ATAAATAAATAAA
1 ATATATAT-AATAAA
2943226 TAAAACTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
ATATATATAATAAAAAGATAT
Found at i:2943274 original size:11 final size:11
Alignment explanation
Indices: 2943253--2943321 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
2943243 CTAAAACTTC
*
2943253 AAATAAAAATA
1 AAATAATAATA
*
2943264 ACATAATAATA
1 AAATAATAATA
2943275 AAATAATTAA-A
1 AAATAA-TAATA
* *
2943286 AAATTATAATT
1 AAATAATAATA
*
2943297 ACA-AA-AATA
1 AAATAATAATA
2943306 AAATAA-AATA
1 AAATAATAATA
2943316 AAATAA
1 AAATAA
2943322 ATCTATTGCG
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 5 0.11
10 16 0.35
11 22 0.48
12 3 0.07
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAATAATA
Found at i:2944525 original size:35 final size:35
Alignment explanation
Indices: 2944471--2944593 Score: 129
Period size: 35 Copynumber: 3.5 Consensus size: 35
2944461 TATTATACAG
* ** ** *
2944471 AGAACAACAAAAATGAGTGAAGTACTACTTCACGT
1 AGAACAACTAAAACAAGTGAAGTGTTACTTCATGT
* *
2944506 AGAACAACTAAAACAAGTGAAGTGTTAGTTCATGC
1 AGAACAACTAAAACAAGTGAAGTGTTACTTCATGT
* * * *
2944541 AGAATAAATAGAACAAGTGAAATGTTACTTCATGT
1 AGAACAACTAAAACAAGTGAAGTGTTACTTCATGT
*
2944576 AGAACAACTAAAATAAGT
1 AGAACAACTAAAACAAGT
2944594 AAAGCATTAC
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (35 bp):
AGAACAACTAAAACAAGTGAAGTGTTACTTCATGT
Found at i:2947353 original size:40 final size:40
Alignment explanation
Indices: 2947304--2947387 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
2947294 TAAATAATTC
2947304 ATAT-AAGATTATTTCATTTTTTCAAAAATATTGTCTTTG
1 ATATAAAGATTATTTCATTTTTTCAAAAATATTGTCTTTG
2947343 ATATAAAGATTATTTCATTTTTTCAAAAATATTGTCTTTG
1 ATATAAAGATTATTTCATTTTTTCAAAAATATTGTCTTTG
2947383 ATATA
1 ATATA
2947388 TTTATATCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 4 0.09
40 40 0.91
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (40 bp):
ATATAAAGATTATTTCATTTTTTCAAAAATATTGTCTTTG
Found at i:2956657 original size:51 final size:51
Alignment explanation
Indices: 2956602--2956698 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
2956592 TTTATTTTCG
2956602 ATGGTAAAATTA-TCTATCCACTTTTAGTGGTAAAATTATTCTTAGATTCTA
1 ATGGTAAAATTATTC-ATCCACTTTTAGTGGTAAAATTATTCTTAGATTCTA
* *
2956653 ATGGTAAAATTATTCATCTACTTTTGGTGGTAAAATTATTCTTAGA
1 ATGGTAAAATTATTCATCCACTTTTAGTGGTAAAATTATTCTTAGA
2956699 ATAATGATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
51 41 0.95
52 2 0.05
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (51 bp):
ATGGTAAAATTATTCATCCACTTTTAGTGGTAAAATTATTCTTAGATTCTA
Found at i:2956692 original size:26 final size:26
Alignment explanation
Indices: 2956603--2956693 Score: 98
Period size: 26 Copynumber: 3.5 Consensus size: 26
2956593 TTATTTTCGA
*
2956603 TGGTAAAATTA-TCTATCCACTTTTAG
1 TGGTAAAATTATTC-ATCTACTTTTAG
* * *
2956629 TGGTAAAATTATTC-T-TAGATTCTAA
1 TGGTAAAATTATTCATCTA-CTTTTAG
*
2956654 TGGTAAAATTATTCATCTACTTTTGG
1 TGGTAAAATTATTCATCTACTTTTAG
2956680 TGGTAAAATTATTC
1 TGGTAAAATTATTC
2956694 TTAGAATAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
24 1 0.02
25 19 0.36
26 29 0.55
27 4 0.08
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (26 bp):
TGGTAAAATTATTCATCTACTTTTAG
Found at i:2957026 original size:20 final size:21
Alignment explanation
Indices: 2956975--2957015 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2956965 ATTAGCTAAA
2956975 ATAAAAAATCAAAGACCAACC
1 ATAAAAAATCAAAGACCAACC
2956996 ATAAAAAATCAAAGACCAAC
1 ATAAAAAATCAAAGACCAAC
2957016 TATTGAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.63, C:0.22, G:0.05, T:0.10
Consensus pattern (21 bp):
ATAAAAAATCAAAGACCAACC
Found at i:2958484 original size:30 final size:30
Alignment explanation
Indices: 2958448--2958511 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
2958438 AATCAAACCC
*
2958448 TTATACTTTTATTTTATA-TCAAATAAGTTT
1 TTATACTTTTATTTTA-AGTCAAATAAGTCT
2958478 TTATACTTTTATTTTAAGTCAAATAAGTCT
1 TTATACTTTTATTTTAAGTCAAATAAGTCT
2958508 TTAT
1 TTAT
2958512 GATTAATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.55
Consensus pattern (30 bp):
TTATACTTTTATTTTAAGTCAAATAAGTCT
Found at i:2958830 original size:30 final size:30
Alignment explanation
Indices: 2958771--2958834 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
2958761 AATCATTAAT
*
2958771 TATAAGAATTTATTTGATTCAAAATAAAAA
1 TATAAGAATTTATTTGATGCAAAATAAAAA
*
2958801 TATAAGAATTTGA-TTGAATGCAATAAAAAAAA
1 TATAAGAATTT-ATTTG-ATGCAA-AATAAAAA
2958833 TA
1 TA
2958835 AACGCTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 14 0.48
31 6 0.21
32 9 0.31
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (30 bp):
TATAAGAATTTATTTGATGCAAAATAAAAA
Found at i:2962078 original size:16 final size:16
Alignment explanation
Indices: 2962057--2962089 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2962047 GAACGCTTAC
2962057 ATTCATATACAGATAT
1 ATTCATATACAGATAT
*
2962073 ATTCATATACATATAT
1 ATTCATATACAGATAT
2962089 A
1 A
2962090 CATTTGTATA
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:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTCATATACAGATAT
Found at i:2965416 original size:21 final size:22
Alignment explanation
Indices: 2965391--2965434 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2965381 AAGTGATTAA
2965391 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
2965412 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2965434 T
1 T
2965435 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2966190 original size:19 final size:19
Alignment explanation
Indices: 2966166--2966202 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2966156 AAGATCATAA
2966166 ATCTCTAACTATTAGTTTT
1 ATCTCTAACTATTAGTTTT
2966185 ATCTCTAACTATTAGTTT
1 ATCTCTAACTATTAGTTT
2966203 CTCTCTTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (19 bp):
ATCTCTAACTATTAGTTTT
Found at i:2969989 original size:2 final size:2
Alignment explanation
Indices: 2969982--2970033 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2969972 TTCTACTAGA
2969982 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
2970024 AT AT AT AT AT
1 AT AT AT AT AT
2970034 TTCTGGAGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2979062 original size:15 final size:15
Alignment explanation
Indices: 2979042--2979073 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2979032 TTAAGTTATA
2979042 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
2979057 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
2979072 AT
1 AT
2979074 AATATAAGAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:2979173 original size:20 final size:20
Alignment explanation
Indices: 2979148--2979242 Score: 54
Period size: 18 Copynumber: 5.3 Consensus size: 20
2979138 AAAACAAATT
2979148 AAAATAAAATATATAATATA
1 AAAATAAAATATATAATATA
2979168 AAAAT---ATATAT--TA-A
1 AAAATAAAATATATAATATA
2979182 AAAAT-AAA-A-A-AATATA
1 AAAATAAAATATATAATATA
* * *
2979198 AAATTATAATA-ATAA-ATG
1 AAAATAAAATATATAATATA
2979216 AAAATAAAATATATGACAT-TA
1 AAAATAAAATATAT-A-ATATA
2979237 AAAATA
1 AAAATA
2979243 TATTTAAGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 23
0.66 0.07 0.27
Matches are distributed among these distances:
14 7 0.12
15 5 0.09
16 6 0.11
17 8 0.14
18 13 0.23
19 4 0.07
20 6 0.11
21 8 0.14
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAATAAAATATATAATATA
Found at i:2979429 original size:113 final size:113
Alignment explanation
Indices: 2979197--2979411 Score: 385
Period size: 113 Copynumber: 1.9 Consensus size: 113
2979187 AAAAAAATAT
* *
2979197 AAAATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATTTAAGATATCATATTA
1 AAAATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATCTAAGAGATCATATTA
2979262 TATAAAAATTAATAATAAAAAATATAAATAGATTAAAAATATATATAA
66 TATAAAAATTAATAATAAAAAATATAAATAGATTAAAAATATATATAA
* *
2979310 AAAATTATAATAATAAATGAAAATAAAATATATGATATTAAAAATATATCTAAGAGATGATATTA
1 AAAATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATCTAAGAGATCATATTA
*
2979375 TATAAAAATTAATAATAAAAAATATAAATATATTAAA
66 TATAAAAATTAATAATAAAAAATATAAATAGATTAAA
2979412 CTTGTATTTT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 97 1.00
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (113 bp):
AAAATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATCTAAGAGATCATATTA
TATAAAAATTAATAATAAAAAATATAAATAGATTAAAAATATATATAA
Found at i:2979567 original size:15 final size:15
Alignment explanation
Indices: 2979547--2979605 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
2979537 TTATTTTTTC
2979547 TGCAATCACATTGCT
1 TGCAATCACATTGCT
* *
2979562 TGCAATCATATTACT
1 TGCAATCACATTGCT
2979577 TGCAATCACATTGGC-
1 TGCAATCACATT-GCT
*
2979592 TGTAATCACATTGC
1 TGCAATCACATTGC
2979606 ATTGTAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
14 2 0.05
15 35 0.92
16 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (15 bp):
TGCAATCACATTGCT
Found at i:2982905 original size:15 final size:16
Alignment explanation
Indices: 2982887--2982916 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2982877 AATACCATGT
2982887 TCATCAAT-AACTTCA
1 TCATCAATCAACTTCA
2982902 TCATCAATCAACTTC
1 TCATCAATCAACTTC
2982917 TTGGTGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (16 bp):
TCATCAATCAACTTCA
Found at i:2987533 original size:12 final size:12
Alignment explanation
Indices: 2987518--2987565 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
2987508 AGAGATTTTT
2987518 GAGGCAGCAAGA
1 GAGGCAGCAAGA
2987530 GAGGCAGCAAGA
1 GAGGCAGCAAGA
2987542 GAGGCAGCAA-A
1 GAGGCAGCAAGA
2987553 GGAGGCAGCAAGA
1 -GAGGCAGCAAGA
2987566 ACTATTAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:2990244 original size:29 final size:29
Alignment explanation
Indices: 2990212--2990272 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2990202 TACCTTCCTA
*
2990212 TCTTTACAATTTCA-TCTTTTCTTTCTCTC
1 TCTTTACAATTTCAGTCTCTT-TTTCTCTC
* *
2990241 TCTTTATAATTTTAGTCTCTTTTTCTCTC
1 TCTTTACAATTTCAGTCTCTTTTTCTCTC
2990270 TCT
1 TCT
2990273 CACCAAGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.13, C:0.25, G:0.02, T:0.61
Consensus pattern (29 bp):
TCTTTACAATTTCAGTCTCTTTTTCTCTC
Found at i:3011308 original size:50 final size:51
Alignment explanation
Indices: 3011251--3011367 Score: 157
Period size: 50 Copynumber: 2.3 Consensus size: 51
3011241 ACTGAATAAG
* *
3011251 TTAATGTCAGTTTTATATTATCAAGTTAAAAACAAAAACAGTCAAAA-AAA
1 TTAATGTCAGTTTTATACTATCAAATTAAAAACAAAAACAGTCAAAAGAAA
* * * *
3011301 TTAATGTCAGGTTTATACTATCAAATTTAAAAGAAAAACAGTCAAAAGAAG
1 TTAATGTCAGTTTTATACTATCAAATTAAAAACAAAAACAGTCAAAAGAAA
*
3011352 TTGA-GTCAGTTTTATA
1 TTAATGTCAGTTTTATA
3011368 ACAAAATGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 53 0.91
51 5 0.09
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (51 bp):
TTAATGTCAGTTTTATACTATCAAATTAAAAACAAAAACAGTCAAAAGAAA
Found at i:3022894 original size:21 final size:20
Alignment explanation
Indices: 3022864--3022905 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
3022854 TGGTGTACAT
3022864 TGTATTAATATATTAT-TATA
1 TGTATTAATATA-TATGTATA
3022884 TGTAGTTAATATATATGTATA
1 TGTA-TTAATATATATGTATA
3022905 T
1 T
3022906 AGAATATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
TGTATTAATATATATGTATA
Found at i:3025228 original size:31 final size:29
Alignment explanation
Indices: 3025168--3025228 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
3025158 TATTAAATAA
* *
3025168 ATATTTTTATTAATTATCTTAATTTTTAT
1 ATATTTTTATTAATTATATTAATTATTAT
3025197 ATATTTTTAATATAATTA-ATTATATTATTAT
1 ATATTTTT-AT-TAATTATATTA-ATTATTAT
3025228 A
1 A
3025229 AAATTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 8 0.30
30 5 0.19
31 14 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATTTTTATTAATTATATTAATTATTAT
Found at i:3025785 original size:35 final size:35
Alignment explanation
Indices: 3025722--3025820 Score: 94
Period size: 35 Copynumber: 2.8 Consensus size: 35
3025712 GAATAACCAC
* * *
3025722 AATAAGTGAAA-TACTATTTTACATAGAACAAATAA
1 AATAAGTGAAACT-CTACTTCACACAGAACAAATAA
* * * * *
3025757 AATAAGTG-AAGTGTTACTTCACACAGAACTATTAG
1 AATAAGTGAAACT-CTACTTCACACAGAACAAATAA
3025792 AATAAGTGAAACTCTACTTCACACAGAAC
1 AATAAGTGAAACTCTACTTCACACAGAAC
3025821 GATTATAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 2 0.04
35 47 0.90
36 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (35 bp):
AATAAGTGAAACTCTACTTCACACAGAACAAATAA
Found at i:3027490 original size:2 final size:2
Alignment explanation
Indices: 3027483--3027517 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3027473 TAGAATTATC
3027483 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
3027518 CACACACACA
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:3050643 original size:20 final size:20
Alignment explanation
Indices: 3050603--3050650 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3050593 ATATATATAT
* **
3050603 ATATATATATATATCTTACC
1 ATATATATATAAATCAAACC
3050623 ATATATATATAAATCAAACC
1 ATATATATATAAATCAAACC
3050643 ATCATATA
1 AT-ATATA
3050651 CGTATCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATATATAAATCAAACC
Found at i:3053056 original size:2 final size:2
Alignment explanation
Indices: 3053049--3053075 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3053039 TGACATAATT
3053049 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3053076 TGTGACATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3055427 original size:15 final size:16
Alignment explanation
Indices: 3055399--3055428 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3055389 CAACTTGAAG
3055399 AATAAAATAATTATTA
1 AATAAAATAATTATTA
3055415 AATAAAA-AATTATT
1 AATAAAATAATTATT
3055429 TGGAGAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAAATAATTATTA
Found at i:3055692 original size:21 final size:21
Alignment explanation
Indices: 3055668--3055733 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
3055658 GATTAAAATT
3055668 ATAGAAAATAAAATCTACATA
1 ATAGAAAATAAAATCTACATA
* *
3055689 ATAGAGAAAGGAAAAACATGACA-A
1 ATAGA-AAA-TAAAATC-T-ACATA
* *
3055713 GTAGAAGATAAAATCTACATA
1 ATAGAAAATAAAATCTACATA
3055734 TGATATAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
20 3 0.09
21 7 0.21
22 8 0.24
23 7 0.21
24 6 0.18
25 3 0.09
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (21 bp):
ATAGAAAATAAAATCTACATA
Found at i:3057911 original size:24 final size:24
Alignment explanation
Indices: 3057884--3057935 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3057874 AAAGGAAAAG
* * *
3057884 AAAAACAACAAGAAAAAAAAGTGA
1 AAAAACAAAAAAAAAAAAAAGAGA
**
3057908 AAAATGAAAAAAAAAAAAAAGAGA
1 AAAAACAAAAAAAAAAAAAAGAGA
3057932 AAAA
1 AAAA
3057936 TAAATGAGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.04
Consensus pattern (24 bp):
AAAAACAAAAAAAAAAAAAAGAGA
Found at i:3059114 original size:16 final size:17
Alignment explanation
Indices: 3059090--3059127 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
3059080 AATTTTACAC
*
3059090 AATAATTAAAT-ATATA
1 AATAGTTAAATAATATA
3059106 AATAGTTAAATAATATA
1 AATAGTTAAATAATATA
3059123 AATAG
1 AATAG
3059128 AAAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AATAGTTAAATAATATA
Found at i:3061924 original size:15 final size:16
Alignment explanation
Indices: 3061902--3061946 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
3061892 ACATTACAAT
3061902 GCAATGTGATTACAGA
1 GCAATGTGATTACAGA
* *
3061918 -TAATGTGATTGCA-A
1 GCAATGTGATTACAGA
3061932 GCAATGTGATTACAG
1 GCAATGTGATTACAG
3061947 GGAAAATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (16 bp):
GCAATGTGATTACAGA
Found at i:3062128 original size:28 final size:28
Alignment explanation
Indices: 3062097--3062328 Score: 71
Period size: 28 Copynumber: 8.2 Consensus size: 28
3062087 ATAAGTTTAA
3062097 TATATTTATATTTTTTATTATTAATTTT
1 TATATTTATATTTTTTATTATTAATTTT
** * *
3062125 TATA--TATATTCATTCTTAAATATATTTT
1 TATATTTATATTTTTTATT-ATTA-ATTTT
* *
3062153 TAAATATCATATATTTTTTATTTATT-ATTAT
1 T--ATAT-TTATATTTTTTA-TTATTAATTTT
* * *
3062184 AATATTT-TA-TATTTATTTTTAA----
1 TATATTTATATTTTTTATTATTAATTTT
3062206 TATATTTATA-TTTTTA-TATT-ATTTT
1 TATATTTATATTTTTTATTATTAATTTT
* * *
3062231 TATATAATATCATTTCTTAATA-T-ATTTT
1 TATAT-TTAT-ATTTTTTATTATTAATTTT
* *
3062259 TA-ATTCATATATTTTATTTTTATTTATTATTT
1 TATATT--TATATTTT-TTATTA-TTAAT-TTT
3062291 TATATTTATATTTATTTATATATTTATATTTT
1 TATATTTATATTT-TTTAT-TA-TTA-ATTTT
*
3062323 TTTATT
1 TATATT
3062329 AATTTTATTA
Statistics
Matches: 149, Mismatches: 26, Indels: 54
0.65 0.11 0.24
Matches are distributed among these distances:
21 1 0.01
22 9 0.06
23 7 0.05
25 9 0.06
26 19 0.13
27 12 0.08
28 31 0.21
29 6 0.04
30 4 0.03
31 15 0.10
32 20 0.13
33 14 0.09
34 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (28 bp):
TATATTTATATTTTTTATTATTAATTTT
Found at i:3062193 original size:20 final size:19
Alignment explanation
Indices: 3062167--3062518 Score: 77
Period size: 20 Copynumber: 17.2 Consensus size: 19
3062157 TATCATATAT
3062167 TTTTTATTTATTATTATAATA
1 TTTTTATTTATT-TT-TAATA
3062188 TTTTATATTTATTTTTAATA
1 TTTT-TATTTATTTTTAATA
*
3062208 TATTTA--TATTTTTATATTA
1 TTTTTATTTATTTTTA-A-TA
3062227 TTTTTATATAATATCATTTCTTAATATA
1 -TTTT-TAT--T-T-ATTT-TT-A-ATA
*
3062255 TTTTTAATTCATATATTT--TA
1 TTTTT-ATT--TATTTTTAATA
*
3062275 TTTTTATTTATTATTTTATA
1 TTTTTATTTATT-TTTAATA
* *
3062295 TTTATATTTATTTAT-ATA
1 TTTTTATTTATTTTTAATA
* *
3062313 TTTATATTTTTTTATTAAT-
1 TTTTTATTTATTT-TTAATA
*
3062332 TTTATTAATATCATTTCTTAAATA
1 TTT-TT-AT-TTATTT-TT-AATA
*
3062356 TTTTTAATGTCATATATTT--TA
1 TTTTT-AT-T--TATTTTTAATA
3062377 -TTTTATTTATTATTATAATA
1 TTTTTATTTATT-TT-TAATA
* *
3062397 TTTATATTT-TATTTATATA
1 TTTTTATTTATTTTTA-ATA
* *
3062416 TTTATATTTTATTATTAAT-
1 TTTTTA-TTTATTTTTAATA
* * *
3062435 TTATAATATATTTTTATATA
1 TTTTTATTTATTTTTA-ATA
*
3062455 TTTTTAATGTCATATATTT--TA
1 TTTTT-AT-T--TATTTTTAATA
*
3062476 -TTTTATTT-TATTATAATA
1 TTTTTATTTAT-TTTTAATA
3062494 TTATTTATTTTATTTTTAATA
1 TT-TTTA-TTTATTTTTAATA
3062515 TTTT
1 TTTT
3062519 ATATATATAT
Statistics
Matches: 251, Mismatches: 32, Indels: 97
0.66 0.08 0.26
Matches are distributed among these distances:
15 1 0.00
16 6 0.02
17 13 0.05
18 34 0.14
19 34 0.14
20 59 0.24
21 39 0.16
22 15 0.06
23 9 0.04
24 13 0.05
25 7 0.03
26 4 0.02
27 10 0.04
28 4 0.02
29 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTTATTTATTTTTAATA
Found at i:3062356 original size:103 final size:104
Alignment explanation
Indices: 3062096--3062606 Score: 564
Period size: 103 Copynumber: 5.0 Consensus size: 104
3062086 TATAAGTTTA
*
3062096 ATATATTTATATTTTTTATTATTAATTTT-TATATATATTCA-TTCTTAAATATATTTTTAAATA
1 ATATATTTATA-TTTTT-TTATTAATTTTATATA-ATA-TCATTTCTT-AATATATTTTT-AATG
* *
3062159 TCATATATTTTTTATTTATTATTATAATATTTTATA-TT-TATTT-TTA
60 TCATATA--TTTTATTT-TTATT-TATTATTTTATATTTATATTTATTT
* *
3062205 ATATATTTATATTTTTATATTATTTTTATATAATATCATTTCTTAATATATTTTTAAT-TCATAT
1 ATATATTTATATTTTTTTATTAATTTTATATAATATCATTTCTTAATATATTTTTAATGTCATAT
3062269 ATTTTATTTTTATTTATTATTTTATATTTATATTTATTT
66 ATTTTATTTTTATTTATTATTTTATATTTATATTTATTT
3062308 ATATATTTATATTTTTTTATTAATTTTAT-TAATATCATTTCTTAA-ATATTTTTAATGTCATAT
1 ATATATTTATATTTTTTTATTAATTTTATATAATATCATTTCTTAATATATTTTTAATGTCATAT
*
3062371 ATTTTA-TTTTATTTATTATTATAATATTTATATTTTATTT
66 ATTTTATTTTTATTTATTATT-TTATATTTATA-TTTATTT
*
3062411 ATATATTTATATTTTATTATTAA--TT-TATAATAT-ATTT-TT-ATATATTTTTAATGTCATAT
1 ATATATTTATATTTTTTTATTAATTTTATATAATATCATTTCTTAATATATTTTTAATGTCATAT
**
3062470 ATTTTA-TTTTATTTTATTATAATATTATTTAT-TTTATTT
66 ATTTTATTTTTA-TTTATTATTTTA-TATTTATATTTATTT
* * * * *
3062509 TTAATATTT-TATATATATATTATTTTTATATAATATCATTAT-TTAA-ATATATTTT-ATGTCA
1 AT-ATATTTATATTTTTTTATTAATTTTATATAATATCATT-TCTTAATATAT-TTTTAATGTCA
*
3062570 TATATTTTATTTTTATTTATT-TTATA-ATTTTATATTT
63 TATATTTTATTTTTATTTATTATTTTATA-TTTATATTT
3062607 TTTCAGTTCT
Statistics
Matches: 361, Mismatches: 18, Indels: 53
0.84 0.04 0.12
Matches are distributed among these distances:
98 18 0.05
99 38 0.11
100 34 0.09
101 53 0.15
102 61 0.17
103 86 0.24
104 17 0.05
105 3 0.01
106 14 0.04
107 17 0.05
108 9 0.02
109 11 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (104 bp):
ATATATTTATATTTTTTTATTAATTTTATATAATATCATTTCTTAATATATTTTTAATGTCATAT
ATTTTATTTTTATTTATTATTTTATATTTATATTTATTT
Found at i:3062380 original size:5 final size:5
Alignment explanation
Indices: 3062370--3062509 Score: 51
Period size: 5 Copynumber: 28.2 Consensus size: 5
3062360 TAATGTCATA
** *
3062370 TATTT TATTT TA-TT TATTAT TATAA TATTT ATATTT TA-TT TA-TA TATTT
1 TATTT TATTT TATTT TATT-T TATTT TATTT -TATTT TATTT TATTT TATTT
* ** * * * *
3062419 ATATTT TATTAT TAATT TATAA TATATT T-TTA TATAT T-TTT AATGT
1 -TATTT TATT-T TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT
* * * *
3062465 CA-TA TATTT TATTT TATTT TATTAT AATAT TA-TT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATT-T TATTT TATTT TATTT TATTT T
3062510 TAATATTTTA
Statistics
Matches: 96, Mismatches: 27, Indels: 24
0.65 0.18 0.16
Matches are distributed among these distances:
4 19 0.20
5 55 0.57
6 22 0.23
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (5 bp):
TATTT
Found at i:3062549 original size:19 final size:17
Alignment explanation
Indices: 3062147--3062585 Score: 64
Period size: 16 Copynumber: 26.5 Consensus size: 17
3062137 TTCTTAAATA
*
3062147 TATTTTTAAATATCATA-
1 TATTTTTATATAT-ATAT
3062164 TATTTTT-TAT-T-TAT
1 TATTTTTATATATATAT
* * *
3062178 TATTATAATATTTTATATT
1 TATTTTTATA-TATATA-T
3062197 TATTTTTA-ATATAT-T
1 TATTTTTATATATATAT
*
3062212 TA-TATT-T-T-TATAT
1 TATTTTTATATATATAT
3062225 TATTTTTATATA-ATAT
1 TATTTTTATATATATAT
*
3062241 CATTTCTTA-ATATAT-T
1 TATTT-TTATATATATAT
*
3062257 T-TTAATTCATATAT-T-T
1 TATT--TTTATATATATAT
3062273 TA-TTTT-TAT-T-TAT
1 TATTTTTATATATATAT
*
3062286 TA-TTTTATATTTATATT
1 TATTTTTATATATATA-T
* *
3062303 TATTTATATATTTATAT
1 TATTTTTATATATATAT
*
3062320 T-TTTTTAT-TA-ATTT
1 TATTTTTATATATATAT
** * * *
3062334 TATTAATATCATTTCTTAAA
1 TATTTTTAT-ATAT-AT-AT
*
3062354 TATTTTTAATGTCATATAT
1 TATTTTT-ATAT-ATATAT
* *
3062373 TTTATTTTATTTAT-TAT
1 TAT-TTTTATATATATAT
** * *
3062390 TA-TAATATTTATATTT
1 TATTTTTATATATATAT
* *
3062406 TATTTATATATTTATAT
1 TATTTTTATATATATAT
* *
3062423 T-TTATTATTAATTTATAAT
1 TATTTTTA-T-ATATAT-AT
*
3062442 ATATTTTTATATAT-TTT
1 -TATTTTTATATATATAT
* * * *
3062459 TAATGTCATATATTTTAT
1 TATTTTTATATA-TATAT
*
3062477 TTTATTTTAT-TATAATAT
1 TAT-TTTTATATAT-ATAT
* * * *
3062495 TATTTATTTTATTTTTAA
1 TATTT-TTATATATATAT
3062513 TA-TTTTATATATATAT
1 TATTTTTATATATATAT
3062529 TATTTTTATATA-ATAT
1 TATTTTTATATATATAT
* * *
3062545 CATTATTTAAATATATTT
1 TATT-TTTATATATATAT
* *
3062563 TA-TGTCATATAT-T-T
1 TATTTTTATATATATAT
3062577 TATTTTTAT
1 TATTTTTAT
3062586 TTATTTTATA
Statistics
Matches: 302, Mismatches: 70, Indels: 102
0.64 0.15 0.22
Matches are distributed among these distances:
12 5 0.02
13 16 0.05
14 23 0.08
15 29 0.10
16 70 0.23
17 68 0.23
18 45 0.15
19 25 0.08
20 13 0.04
21 8 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (17 bp):
TATTTTTATATATATAT
Found at i:3062601 original size:8 final size:7
Alignment explanation
Indices: 3062556--3062743 Score: 56
Period size: 7 Copynumber: 26.9 Consensus size: 7
3062546 ATTATTTAAA
3062556 TATATTT
1 TATATTT
* **
3062563 TATGTCA
1 TATATTT
3062570 TATATTT
1 TATATTT
3062577 TAT-TTT
1 TATATTT
3062583 TATTTATTT
1 TA--TATTT
3062592 TATAATTT
1 TAT-ATTT
3062600 TATATTT
1 TATATTT
*
3062607 TTTCAGTTCT
1 TAT-A-TT-T
* *
3062617 T-TAATA
1 TATATTT
*
3062623 TATTTTT
1 TATATTT
*
3062630 TATATTA
1 TATATTT
3062637 TATATTT
1 TATATTT
3062644 TAT-TTT
1 TATATTT
3062650 TAT-TTGT
1 TATATT-T
* **
3062657 TTTACCT
1 TATATTT
*
3062664 TAT-TATA
1 TATAT-TT
*
3062671 TAAATGTT
1 TATAT-TT
* *
3062679 AATTTTT
1 TATATTT
3062686 TATATTT
1 TATATTT
3062693 TATTTATTT
1 TA--TATTT
3062702 TA-ATTT
1 TATATTT
3062708 T-TA-TT
1 TATATTT
*
3062713 TATATTA
1 TATATTT
3062720 TATA-TT
1 TATATTT
3062726 T-TATTT
1 TATATTT
3062732 TA-ATTT
1 TATATTT
3062738 TATATT
1 TATATT
3062744 ATTAATATTA
Statistics
Matches: 129, Mismatches: 32, Indels: 40
0.64 0.16 0.20
Matches are distributed among these distances:
5 5 0.04
6 33 0.26
7 60 0.47
8 14 0.11
9 15 0.12
10 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:3062625 original size:103 final size:101
Alignment explanation
Indices: 3062096--3062609 Score: 492
Period size: 101 Copynumber: 5.0 Consensus size: 101
3062086 TATAAGTTTA
* * *
3062096 ATATATTTATATTTTTTATTATTAATTTTTATAT-ATATTCATTCTTAAATATATTTTTAAATAT
1 ATATATTTATA-TATTTA-TATT-ATTTTTATATAATA-TCATTTTTAAATATA-TTTT-AATGT
*
3062160 CATATATTTT-TTATTTA-TTATTATA-ATATTTTATATTTATTTTT
60 CATATATTTTATT-TTTATTTATTTTATA-ATTTTATA--T-TTTTT
*
3062204 AATATATTTATATTTTTATATTATTTTTATATAATATCATTTCTT-AATATATTTTTAAT-TCAT
1 -ATATATTTATATATTTATATTATTTTTATATAATATCATTT-TTAAATATA-TTTTAATGTCAT
*
3062267 ATATTTTATTTTTATTTATTATT-TTATATTTATATTTATTT
63 ATATTTTATTTTTATTTATT-TTATAAT-TTTATATTT-TTT
* * *
3062308 ATATATTTATATTTTTTTATTAATTTTAT-TAATATCATTTCTTAAATAT-TTTTAATGTCATAT
1 ATATATTTATATATTTATATTATTTTTATATAATATCATTT-TTAAATATATTTTAATGTCATAT
3062371 ATTTTA-TTTTATTTATTATTATAATATTTATATTTTATT
65 ATTTTATTTTTATTTATT-TTATAAT-TTTATATTTT-TT
* *
3062410 -TATATATT-TATATTT-TATTATTAATT-TATAATAT-ATTTTTATATAT-TTTTAATGTCATA
1 ATATAT-TTATATATTTATATTATT-TTTATATAATATCATTTTTAAATATATTTTAATGTCATA
* *
3062469 TATTTTA-TTTTATTT-TATTATAATATTATTTATTTTATTT
64 TATTTTATTTTTATTTATTTTATAAT-TT-TATA-TTT-TTT
* *
3062509 TTAATATTT-TATATATATATTATTTTTATATAATATCATTATTTAAATATATTTT-ATGTCATA
1 AT-ATATTTATATATTTATATTATTTTTATATAATATCATT-TTTAAATATATTTTAATGTCATA
3062572 TATTTTATTTTTATTTATTTTATAATTTTATATTTTTT
64 TATTTTATTTTTATTTATTTTATAATTTTATATTTTTT
3062610 CAGTTCTTTA
Statistics
Matches: 361, Mismatches: 17, Indels: 62
0.82 0.04 0.14
Matches are distributed among these distances:
97 10 0.03
98 4 0.01
99 40 0.11
100 23 0.06
101 63 0.17
102 49 0.14
103 60 0.17
104 33 0.09
105 20 0.06
106 33 0.09
107 9 0.02
108 6 0.02
109 11 0.03
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (101 bp):
ATATATTTATATATTTATATTATTTTTATATAATATCATTTTTAAATATATTTTAATGTCATATA
TTTTATTTTTATTTATTTTATAATTTTATATTTTTT
Found at i:3062746 original size:34 final size:34
Alignment explanation
Indices: 3062677--3062755 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
3062667 TATATAAATG
* * *
3062677 TTAATTTTTTATATTTTATTTATTTTAATTTTTA
1 TTAATATTATATATTTTATTTATTTTAATTATTA
*
3062711 TTTATATTATATATTTTATTTTAATTTT-A-TATTA
1 TTAATATTATATATTTTA-TTT-ATTTTAATTATTA
3062745 TTAATATTATA
1 TTAATATTATA
3062756 AAATATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
34 29 0.76
35 4 0.11
36 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (34 bp):
TTAATATTATATATTTTATTTATTTTAATTATTA
Found at i:3074679 original size:23 final size:23
Alignment explanation
Indices: 3074653--3074716 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
3074643 CAAATTATAA
*
3074653 CATGACGTGTAACAATTTTTCAT
1 CATGACGTGTAATAATTTTTCAT
* *
3074676 CATGATGTGTAATAGTTTTTTCAT
1 CATGACGTGTAATA-ATTTTTCAT
* *
3074700 TATGACATGTAATAATT
1 CATGACGTGTAATAATT
3074717 AAAAATTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (23 bp):
CATGACGTGTAATAATTTTTCAT
Found at i:3074767 original size:27 final size:27
Alignment explanation
Indices: 3074701--3074942 Score: 177
Period size: 27 Copynumber: 8.9 Consensus size: 27
3074691 TTTTTTCATT
* * *
3074701 ATGACATGTAATAATTAAAAATTTCAAC
1 ATGACTTGTAACAATT-AAATTTTCAAC
* * *
3074729 CTGACGTGTAACAATTAAATTTTTAAC
1 ATGACTTGTAACAATTAAATTTTCAAC
** *
3074756 ATGACTTGTAACAATTACTTTTTTCAAT
1 ATGACTTGTAACAATTA-AATTTTCAAC
* *
3074784 ATGA-TATATAACAATTAAATTTTCAAT
1 ATGACT-TGTAACAATTAAATTTTCAAC
*
3074811 ATGA-TGTGTAACAACTAAATTTTCAAC
1 ATGACT-TGTAACAATTAAATTTTCAAC
* * * *
3074838 ATGACGTATAATAATTAAATCTTCAAC
1 ATGACTTGTAACAATTAAATTTTCAAC
* * * * *
3074865 ATAACATGTAATAATTACATTTTTCAAT
1 ATGACTTGTAACAATTA-AATTTTCAAC
* * *
3074893 AT-AGTATATAACAATTATATTTTCAAC
1 ATGACT-TGTAACAATTAAATTTTCAAC
3074920 ATGACGTT-TAACAATTAAATTTT
1 ATGAC-TTGTAACAATTAAATTTT
3074943 AAAACATAGT
Statistics
Matches: 169, Mismatches: 38, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
27 115 0.68
28 53 0.31
29 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (27 bp):
ATGACTTGTAACAATTAAATTTTCAAC
Found at i:3074772 original size:55 final size:55
Alignment explanation
Indices: 3074701--3074942 Score: 204
Period size: 55 Copynumber: 4.4 Consensus size: 55
3074691 TTTTTTCATT
* * * * *
3074701 ATGACATGTAATAATTAAAAATTTCAACCTGACGTGTAACAATTAAATTTTTAAC
1 ATGACATGTAACAATTAAAATTTTCAACATGACGTATAACAATTAAATTTTCAAC
* *** * ** *
3074756 ATGACTTGTAACAATTACTTTTTTCAATATGATATATAACAATTAAATTTTCAAT
1 ATGACATGTAACAATTAAAATTTTCAACATGACGTATAACAATTAAATTTTCAAC
** * * *
3074811 ATGATGTGTAACAACT-AAATTTTCAACATGACGTATAATAATTAAATCTTCAAC
1 ATGACATGTAACAATTAAAATTTTCAACATGACGTATAACAATTAAATTTTCAAC
* * * * * *
3074865 ATAACATGTAATAATTACATTTTTCAATAT-A-GTATATAACAATTATATTTTCAAC
1 ATGACATGTAACAATTAAAATTTTCAACATGACG--TATAACAATTAAATTTTCAAC
* *
3074920 ATGACGTTTAACAATT-AAATTTT
1 ATGACATGTAACAATTAAAATTTT
3074943 AAAACATAGT
Statistics
Matches: 142, Mismatches: 42, Indels: 7
0.74 0.22 0.04
Matches are distributed among these distances:
53 1 0.01
54 46 0.32
55 95 0.67
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (55 bp):
ATGACATGTAACAATTAAAATTTTCAACATGACGTATAACAATTAAATTTTCAAC
Found at i:3074855 original size:109 final size:109
Alignment explanation
Indices: 3074722--3074942 Score: 300
Period size: 109 Copynumber: 2.0 Consensus size: 109
3074712 TAATTAAAAA
* * * * * * *
3074722 TTTCAACCTGACGTGTAACAATTAAATTTTTAACATGACTTGTAACAATTACTTTTTTCAATAT-
1 TTTCAACATGACGTATAACAATTAAATCTTCAACATAACATGTAACAATTACATTTTTCAATATA
* *
3074786 GATATATAACAATTAAATTTTCAATATGATGTGTAACAACTAAAT
66 G-TATATAACAATTAAATTTTCAACATGACGTGTAACAACTAAAT
* *
3074831 TTTCAACATGACGTATAATAATTAAATCTTCAACATAACATGTAATAATTACATTTTTCAATATA
1 TTTCAACATGACGTATAACAATTAAATCTTCAACATAACATGTAACAATTACATTTTTCAATATA
* * *
3074896 GTATATAACAATTATATTTTCAACATGACGTTTAACAATTAAAT
66 GTATATAACAATTAAATTTTCAACATGACGTGTAACAACTAAAT
3074940 TTT
1 TTT
3074943 AAAACATAGT
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 96 0.99
110 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.40
Consensus pattern (109 bp):
TTTCAACATGACGTATAACAATTAAATCTTCAACATAACATGTAACAATTACATTTTTCAATATA
GTATATAACAATTAAATTTTCAACATGACGTGTAACAACTAAAT
Found at i:3074889 original size:82 final size:81
Alignment explanation
Indices: 3074704--3074939 Score: 231
Period size: 82 Copynumber: 2.9 Consensus size: 81
3074694 TTTCATTATG
* ** * * * *
3074704 ACATGTAATAATTAAAAATTTCAACCTGACGTGTAACAATTAAATTTTTAACATGACTTGTAACA
1 ACATGTAATAATT-AAATTTTCAATATGATGTGTAACAATTAAATTTTCAACATGACGTATAACA
** * * *
3074769 ATTACTTTTTTCAATATG
65 ATTA-AATCTTCAACATA
* * * * *
3074787 ATATATAACAATTAAATTTTCAATATGATGTGTAACAACTAAATTTTCAACATGACGTATAATAA
1 ACATGTAATAATTAAATTTTCAATATGATGTGTAACAATTAAATTTTCAACATGACGTATAACAA
3074852 TTAAATCTTCAACATA
66 TTAAATCTTCAACATA
* * * * *
3074868 ACATGTAATAATTACATTTTTCAATAT-AGTATATAACAATTATATTTTCAACATGACGTTTAAC
1 ACATGTAATAATTA-AATTTTCAATATGA-TGTGTAACAATTAAATTTTCAACATGACGTATAAC
3074932 AATTAAAT
64 AATTAAAT
3074940 TTTAAAACAT
Statistics
Matches: 124, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
81 20 0.16
82 94 0.76
83 10 0.08
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (81 bp):
ACATGTAATAATTAAATTTTCAATATGATGTGTAACAATTAAATTTTCAACATGACGTATAACAA
TTAAATCTTCAACATA
Found at i:3074954 original size:55 final size:54
Alignment explanation
Indices: 3074737--3074942 Score: 209
Period size: 55 Copynumber: 3.8 Consensus size: 54
3074727 ACCTGACGTG
* * ** *
3074737 TAACAATTAAATTTTTAACATGACTTGTAACAATTACTTTTTTCAATATGATATA
1 TAACAATTAAATTTTCAACATGACGTGTAACAATTAAATTTTTCAACATG-TATA
* * *
3074792 TAACAATTAAATTTTCAATATGATGTGTAACAACTAAA-TTTTCAACATG-ACGTA
1 TAACAATTAAATTTTCAACATGACGTGTAACAATTAAATTTTTCAACATGTA--TA
* * * * * * *
3074846 TAATAATTAAATCTTCAACATAACATGTAATAATTACATTTTTCAATATAGTATA
1 TAACAATTAAATTTTCAACATGACGTGTAACAATTAAATTTTTCAACAT-GTATA
* *
3074901 TAACAATTATATTTTCAACATGACGTTTAACAATTAAATTTT
1 TAACAATTAAATTTTCAACATGACGTGTAACAATTAAATTTT
3074943 AAAACATAGT
Statistics
Matches: 120, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
52 1 0.01
54 41 0.34
55 76 0.63
56 1 0.01
57 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (54 bp):
TAACAATTAAATTTTCAACATGACGTGTAACAATTAAATTTTTCAACATGTATA
Found at i:3089570 original size:20 final size:21
Alignment explanation
Indices: 3089541--3089600 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
3089531 TTTGTTTTTA
3089541 ATTA-ATTTTTATAATTAT-T
1 ATTATATTTTTATAATTATCT
3089560 ATTATATTTTTAT-ATTATCT
1 ATTATATTTTTATAATTATCT
*
3089580 TTTATCATTTGTTACTAATTA
1 ATTAT-ATTT-TTA-TAATTA
3089601 AAAACAAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 9 0.26
20 13 0.38
21 4 0.12
22 3 0.09
23 1 0.03
24 4 0.12
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATATTTTTATAATTATCT
Found at i:3089576 original size:19 final size:19
Alignment explanation
Indices: 3089541--3089577 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3089531 TTTGTTTTTA
3089541 ATTAATTTTTATAATTATT
1 ATTAATTTTTATAATTATT
3089560 ATTATATTTTTAT-ATTAT
1 ATTA-ATTTTTATAATTAT
3089578 CTTTTATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTAATTTTTATAATTATT
Found at i:3090181 original size:23 final size:23
Alignment explanation
Indices: 3090150--3090195 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3090140 AAAAAAATTA
* * *
3090150 AAAAATATATTTTTATTAATTTT
1 AAAAATATAATTATATAAATTTT
*
3090173 AAAATTATAATTATATAAATTTT
1 AAAAATATAATTATATAAATTTT
3090196 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAAATATAATTATATAAATTTT
Found at i:3104879 original size:3 final size:3
Alignment explanation
Indices: 3104871--3104901 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3104861 TGTTTGTTTG
3104871 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3104902 CAAAAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3109312 original size:2 final size:2
Alignment explanation
Indices: 3109301--3109335 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3109291 TTTTATTCTG
3109301 AT AT -T 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
3109336 TGGTACGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3111384 original size:2 final size:2
Alignment explanation
Indices: 3111377--3111412 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3111367 CAAAAGAACT
3111377 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3111413 GAGGGGGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3111421 original size:1 final size:1
Alignment explanation
Indices: 3111415--3111517 Score: 170
Period size: 1 Copynumber: 103.0 Consensus size: 1
3111405 AGAGAGAGGA
* *
3111415 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGTGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
* *
3111480 GGGTGGGGGGGGGGTGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3111518 AAAAGGGTGA
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.00, C:0.01, G:0.96, T:0.03
Consensus pattern (1 bp):
G
Found at i:3123353 original size:38 final size:38
Alignment explanation
Indices: 3123294--3123380 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
3123284 ATAAAAGATA
* *
3123294 ACAAGGTTTCATATTACAAACAGAAATTGCATTCAACT
1 ACAATGTTTCATATTACAAACAAAAATTGCATTCAACT
* * *
3123332 ATAATGTTTCATCTTATAAACAAAAATTGCATTCAACT
1 ACAATGTTTCATATTACAAACAAAAATTGCATTCAACT
3123370 ACAATGTTTCA
1 ACAATGTTTCA
3123381 AGATTTCCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (38 bp):
ACAATGTTTCATATTACAAACAAAAATTGCATTCAACT
Found at i:3129602 original size:23 final size:23
Alignment explanation
Indices: 3129576--3129619 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3129566 AAAAAATAAA
*
3129576 AATATAAAAATTTA-ATTAAATAT
1 AATA-AAAAATATATATTAAATAT
3129599 AATAAAAAATATATATTAAAT
1 AATAAAAAATATATATTAAAT
3129620 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAAAAAATATATATTAAATAT
Found at i:3129613 original size:32 final size:32
Alignment explanation
Indices: 3129547--3129629 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
3129537 ATTGTTAGTC
* *
3129547 ATAAAAATTTATTTAATTTAAAAAATAAAAAT
1 ATAAAAATTTATTAAATATAAAAAATAAAAAT
* *
3129579 ATAAAAATTTAATTAAATATAATAAA-AAATAT
1 ATAAAAATTT-ATTAAATATAAAAAATAAAAAT
* *
3129611 ATATTAAATTTTTTAAATA
1 ATA-AAAATTTATTAAATA
3129630 ATTAAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAAAATTTATTAAATATAAAAAATAAAAAT
Found at i:3129639 original size:18 final size:18
Alignment explanation
Indices: 3129616--3129651 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3129606 AATATATATT
* *
3129616 AAATTTTTTAAATAATTA
1 AAATTTTTAAAAAAATTA
3129634 AAATTTTTAAAAAAATTA
1 AAATTTTTAAAAAAATTA
3129652 TATTATGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTTTAAAAAAATTA
Found at i:3135860 original size:123 final size:123
Alignment explanation
Indices: 3135703--3135953 Score: 484
Period size: 123 Copynumber: 2.0 Consensus size: 123
3135693 TTGGGTTTGA
*
3135703 TGGGCAAATTTTCTTTTTCATTTGCTTGTGGATGTATCAGTCGAGAGAACATGCCCAATTCCAAT
1 TGGGTAAATTTTCTTTTTCATTTGCTTGTGGATGTATCAGTCGAGAGAACATGCCCAATTCCAAT
3135768 TCCTTGGAATGACCCGATGCAACGCAAAGGCTGAGAAGTGCTTGCTTTAAGCGAAAGC
66 TCCTTGGAATGACCCGATGCAACGCAAAGGCTGAGAAGTGCTTGCTTTAAGCGAAAGC
3135826 TGGGTAAATTTTCTTTTTCATTTGCTTGTGGATGTATCAGTCGAGAGAACATGCCCAATTCCAAT
1 TGGGTAAATTTTCTTTTTCATTTGCTTGTGGATGTATCAGTCGAGAGAACATGCCCAATTCCAAT
*
3135891 TCCTTGTAATGACCCGATGCAACGCAAAGGCTGAGAAGTGCTTGCTTTAAGCGAAAGC
66 TCCTTGGAATGACCCGATGCAACGCAAAGGCTGAGAAGTGCTTGCTTTAAGCGAAAGC
3135949 TGGGT
1 TGGGT
3135954 CTCTTACAGC
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (123 bp):
TGGGTAAATTTTCTTTTTCATTTGCTTGTGGATGTATCAGTCGAGAGAACATGCCCAATTCCAAT
TCCTTGGAATGACCCGATGCAACGCAAAGGCTGAGAAGTGCTTGCTTTAAGCGAAAGC
Found at i:3142199 original size:14 final size:14
Alignment explanation
Indices: 3142182--3142210 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3142172 TATTCTGTAA
3142182 GATTTATATTTGAT
1 GATTTATATTTGAT
3142196 GATTTATATTTGAT
1 GATTTATATTTGAT
3142210 G
1 G
3142211 TATCGAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (14 bp):
GATTTATATTTGAT
Found at i:3142331 original size:18 final size:18
Alignment explanation
Indices: 3142308--3142356 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3142298 ATTTAACTAT
*
3142308 TAATAATTAAAAAGTTTA
1 TAATAAATAAAAAGTTTA
* *
3142326 TAATAAATAATAATTTTA
1 TAATAAATAAAAAGTTTA
3142344 T-ATAACATAAAAA
1 TAATAA-ATAAAAA
3142357 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
TAATAAATAAAAAGTTTA
Found at i:3150175 original size:35 final size:35
Alignment explanation
Indices: 3150114--3150182 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
3150104 GTAACATTTG
3150114 TCTTGAGGTGAAGTGCAACATGCCTTTAAACTCGA
1 TCTTGAGGTGAAGTGCAACATGCCTTTAAACTCGA
* *
3150149 TCTTGAGGTG-AGATGCATCATTCCTTTAAACTCG
1 TCTTGAGGTGAAG-TGCAACATGCCTTTAAACTCG
3150183 TTGAATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (35 bp):
TCTTGAGGTGAAGTGCAACATGCCTTTAAACTCGA
Found at i:3157631 original size:17 final size:18
Alignment explanation
Indices: 3157605--3157638 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3157595 ATTTTTTATT
3157605 TAAAAGTTATTT-AAATA
1 TAAAAGTTATTTCAAATA
*
3157622 TAAAATTTATTTCAAAT
1 TAAAAGTTATTTCAAAT
3157639 TTATTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAAAGTTATTTCAAATA
Found at i:3159307 original size:3 final size:3
Alignment explanation
Indices: 3159301--3159326 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3159291 TATTATTATT
3159301 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
3159327 TATCTCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:3161627 original size:61 final size:61
Alignment explanation
Indices: 3161359--3161903 Score: 465
Period size: 60 Copynumber: 9.0 Consensus size: 61
3161349 AAGTCAAAGT
* * * ** * *
3161359 TCTTAAACTTAATCTAGCCTTGATTTATCT-AACAACA-AGTTCGATTTAAAAAGTTTGGAAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAA-AACAGA-TTCGATTTAAAAATTTTGAAAC
* * * * * *
3161420 TCTTAGACTTAATTTAGACTCGACCTATCTCAAAATAGATTCAATTT-GATATTTTGAAAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAAC
* * * * ** * * *
3161480 TTTTAGACTTAATCTAGGCTCAACTTATCTGAAAGTAGATTCGATTT-GATATTTTCAAAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAAC
* * *
3161540 TCCTAGACTTAATCTAGGCTCAACCTATCTCAAAACAGATTCGATTTAAAAAGTTTGAAAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAAC
* *
3161601 TCTTAGACTTAATCTAGGCTCGACCTATCTCATAACA-AGTTCGATGTAAAAAATTTTGAAAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGA-TTCGAT-TTAAAAATTTTGAAAC
* * * ** * * * *
3161663 TCCTAAACTTAATCTAGGCTCAAATTATCTCAAAATAGATTCAATTTAAAAAGTTTGGAAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAAC
* * * * * * **
3161724 TCCTAGACTTAATTTAGGCTCGAACTATCTCAAAACAGATTCGATTT-GATATGTTGGGAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAAC
* * * * * * *
3161784 TCTTAGACTTAATCTGGGCTCGACTTATCTTAAAATAGATTCAATTT-GATATTTTGAAAC
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAAC
* * ** *** * *
3161844 TCATAGACTTAATTTAGGCTTAACCTATCTTGTAACAGGTTTGATTTAAAAATTTTGAAA
1 TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAA
3161904 TTCTCTCATG
Statistics
Matches: 394, Mismatches: 83, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
60 194 0.49
61 147 0.37
62 52 0.13
63 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (61 bp):
TCTTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTTTGAAAC
Found at i:3177502 original size:49 final size:49
Alignment explanation
Indices: 3177418--3177517 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 49
3177408 ATTTGCCATT
* * * * *
3177418 TACTTTTCTTGCATACTAAGTAGGTTTAGGTCTAGTTAGCTATTATAAA
1 TACTTTACTTGCACACTAAGTAAGTGTAGGCCTAGTTAGCTATTATAAA
*
3177467 TACTTTACTTGCACA-TCAAGTAAGTGTAGGCCTAGTTGGCTATTATAAA
1 TACTTTACTTGCACACT-AAGTAAGTGTAGGCCTAGTTAGCTATTATAAA
3177516 TA
1 TA
3177518 ACCCCTATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.98
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (49 bp):
TACTTTACTTGCACACTAAGTAAGTGTAGGCCTAGTTAGCTATTATAAA
Found at i:3189523 original size:15 final size:15
Alignment explanation
Indices: 3189501--3189544 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
3189491 TGTTATTTTC
3189501 CCTGCAATCACATTA
1 CCTGCAATCACATTA
*
3189516 CTTGCAATCACATTA
1 CCTGCAATCACATTA
*
3189531 CCTGTAATCACATT
1 CCTGCAATCACATT
3189545 GCATTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:3192842 original size:14 final size:16
Alignment explanation
Indices: 3192823--3192854 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3192813 AGTAGCACTG
3192823 ATGTATT-TTTTA-AA
1 ATGTATTATTTTATAA
3192837 ATGTATTATTTTATAA
1 ATGTATTATTTTATAA
3192853 AT
1 AT
3192855 TTAGTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATGTATTATTTTATAA
Found at i:3200253 original size:22 final size:22
Alignment explanation
Indices: 3200225--3200274 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3200215 TTAGCACCCA
3200225 CTCACCTTGAATGGTGGGATTT
1 CTCACCTTGAATGGTGGGATTT
3200247 CTCACCTTGAATGGTGGGATTT
1 CTCACCTTGAATGGTGGGATTT
3200269 CTCACC
1 CTCACC
3200275 AATATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (22 bp):
CTCACCTTGAATGGTGGGATTT
Found at i:3223748 original size:18 final size:18
Alignment explanation
Indices: 3223725--3223760 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3223715 CTTCAATATG
*
3223725 GACCACGTGAAAAGTTTC
1 GACCACATGAAAAGTTTC
*
3223743 GACCACATTAAAAGTTTC
1 GACCACATGAAAAGTTTC
3223761 AAATCTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (18 bp):
GACCACATGAAAAGTTTC
Found at i:3237815 original size:14 final size:14
Alignment explanation
Indices: 3237796--3237831 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3237786 TATCTGTTGG
3237796 AAATAAAAATAAAT
1 AAATAAAAATAAAT
*
3237810 AAATAAAATTAAAT
1 AAATAAAAATAAAT
3237824 AAA-AAAAA
1 AAATAAAAA
3237832 AGAGTCACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:3256174 original size:2 final size:2
Alignment explanation
Indices: 3256160--3256192 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3256150 CACACACATG
3256160 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3256193 CTATTCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3266478 original size:7 final size:7
Alignment explanation
Indices: 3266466--3266493 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3266456 CTGGAGAGAT
3266466 TAGGGAG
1 TAGGGAG
3266473 TAGGGAG
1 TAGGGAG
3266480 TAGGGAG
1 TAGGGAG
3266487 TAGGGAG
1 TAGGGAG
3266494 GAGGCACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
TAGGGAG
Found at i:3268168 original size:26 final size:27
Alignment explanation
Indices: 3268117--3268169 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3268107 TCAAAAGAAA
*
3268117 AAATATCAAATAAAAATATAAAAATTT
1 AAATATCAAAGAAAAATATAAAAATTT
* *
3268144 AAATCTCAAAGAAAAA-ATAATAATTT
1 AAATATCAAAGAAAAATATAAAAATTT
3268170 TGTCACGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (27 bp):
AAATATCAAAGAAAAATATAAAAATTT
Found at i:3271885 original size:16 final size:16
Alignment explanation
Indices: 3271861--3271894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3271851 ACTATGCAGG
3271861 TGATCTTGGTGGGGCA
1 TGATCTTGGTGGGGCA
* *
3271877 TGATTTTGGTGGTGCA
1 TGATCTTGGTGGGGCA
3271893 TG
1 TG
3271895 TGTATCCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (16 bp):
TGATCTTGGTGGGGCA
Found at i:3292580 original size:2 final size:2
Alignment explanation
Indices: 3292575--3292605 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3292565 GCATGTTTGT
3292575 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3292606 GGCGAGCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3299927 original size:2 final size:2
Alignment explanation
Indices: 3299922--3299964 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3299912 GTGTGTGTGT
*
3299922 GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3299964 G
1 G
3299965 TGAGGGTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3300621 original size:3 final size:3
Alignment explanation
Indices: 3300613--3300643 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3300603 ATTCTTGTTT
3300613 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3300644 CATTTTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3305518 original size:3 final size:3
Alignment explanation
Indices: 3305512--3305548 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3305502 CGATGATGAA
*
3305512 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3305549 CATATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3318162 original size:34 final size:33
Alignment explanation
Indices: 3318090--3318175 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 33
3318080 GTTTCATATC
* *
3318090 AAAATAAAAGAAAAAATTATGACTGTTAGAAATT
1 AAAATAAAA-AAAAAATTATGACGGTTAGAAATA
3318124 AAAATCAAAAAAAAAATTAT-ATCGGTT-GAAAATA
1 AAAAT-AAAAAAAAAATTATGA-CGGTTAG-AAATA
3318158 AAAATAAATAAATAAAAT
1 AAAATAAA-AAA-AAAAT
3318176 AAAATAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
33 5 0.11
34 31 0.69
35 9 0.20
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.24
Consensus pattern (33 bp):
AAAATAAAAAAAAAATTATGACGGTTAGAAATA
Found at i:3318172 original size:14 final size:15
Alignment explanation
Indices: 3318153--3318188 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3318143 TATCGGTTGA
3318153 AAATAAAAAT-AAAT
1 AAATAAAAATAAAAT
3318167 AAAT-AAAATAAAAT
1 AAATAAAAATAAAAT
3318181 AAA-AAAAA
1 AAATAAAAA
3318189 GTTTATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:3334583 original size:2 final size:2
Alignment explanation
Indices: 3334576--3334618 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3334566 CTTTTAAGAT
* *
3334576 TA TA TA TA TA TA TA TA TA TG TA CA TA TA T- TA -A 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
3334616 TA T
1 TA T
3334619 TTTTGAGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3338460 original size:30 final size:30
Alignment explanation
Indices: 3338403--3338460 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3338393 GACCTTCTAG
* *
3338403 TGTGTGGCCCTCTGGTATGAGGCCTTTTAA
1 TGTGTGGCCCTCTCGTATAAGGCCTTTTAA
* * *
3338433 TGTGTGGTCCTTTCGTATAAGGTCTTTT
1 TGTGTGGCCCTCTCGTATAAGGCCTTTT
3338461 GGTGTGCAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (30 bp):
TGTGTGGCCCTCTCGTATAAGGCCTTTTAA
Found at i:3340181 original size:35 final size:35
Alignment explanation
Indices: 3340141--3340212 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
3340131 CAAGCATTCA
* *
3340141 TTTTCAAGCATCTATACTTGGGATTTCATTCAAGT
1 TTTTCAAGCATCTATACTTAGAATTTCATTCAAGT
*
3340176 TTTTCAAGCATCTATAGTTAGAATTTCATTCAAGT
1 TTTTCAAGCATCTATACTTAGAATTTCATTCAAGT
3340211 TT
1 TT
3340213 CCATATCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (35 bp):
TTTTCAAGCATCTATACTTAGAATTTCATTCAAGT
Found at i:3340295 original size:22 final size:23
Alignment explanation
Indices: 3340267--3340319 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
3340257 CTAGATGTAT
*
3340267 TAACAAGACT-TGACAAGGCACG
1 TAACAAGACTGTGACAAGACACG
*
3340289 TAACAAGA-TGTGACAAGACATG
1 TAACAAGACTGTGACAAGACACG
3340311 TAACAAGAC
1 TAACAAGAC
3340320 CCATAATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (23 bp):
TAACAAGACTGTGACAAGACACG
Found at i:3342476 original size:22 final size:22
Alignment explanation
Indices: 3342441--3342489 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
3342431 TATTGTAGAT
3342441 TGGAA-AAATCAAGAAAAAAAA
1 TGGAAGAAATCAAGAAAAAAAA
* * *
3342462 TGGAAGAAATTAAGAAAAGAGA
1 TGGAAGAAATCAAGAAAAAAAA
3342484 TGGAAG
1 TGGAAG
3342490 GAGTGAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.12
Consensus pattern (22 bp):
TGGAAGAAATCAAGAAAAAAAA
Found at i:3343271 original size:22 final size:23
Alignment explanation
Indices: 3343243--3343291 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
3343233 CGTGACTAGT
*
3343243 ATTGCGTAACTTGTT-GTAAGGC
1 ATTGCGTAACTAGTTGGTAAGGC
*
3343265 ATTGCGTGACTAGTTGGTAAGGC
1 ATTGCGTAACTAGTTGGTAAGGC
3343288 ATTG
1 ATTG
3343292 TGTGACTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (23 bp):
ATTGCGTAACTAGTTGGTAAGGC
Found at i:3343288 original size:23 final size:22
Alignment explanation
Indices: 3343243--3343299 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
3343233 CGTGACTAGT
* *
3343243 ATTGCGTAACTTGTTGTAAGGC
1 ATTGCGTGACTAGTTGTAAGGC
3343265 ATTGCGTGACTAGTTGGTAAGGC
1 ATTGCGTGACTAGTT-GTAAGGC
*
3343288 ATTGTGTGACTA
1 ATTGCGTGACTA
3343300 AGGTATTGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (22 bp):
ATTGCGTGACTAGTTGTAAGGC
Found at i:3343344 original size:21 final size:21
Alignment explanation
Indices: 3343319--3343371 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3343309 TTAAAAATCA
3343319 ATCACGTAATACATAAAACT-
1 ATCACGTAATACATAAAACTG
* *
3343339 AGTCACGTAATGCCTAAAACTG
1 A-TCACGTAATACATAAAACTG
3343361 ATCACGTAATA
1 ATCACGTAATA
3343372 TCTAAAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (21 bp):
ATCACGTAATACATAAAACTG
Found at i:3343376 original size:21 final size:19
Alignment explanation
Indices: 3343319--3343378 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
3343309 TTAAAAATCA
3343319 ATCACGTAATACATAAAACT
1 ATCACGTAATAC-TAAAACT
*
3343339 AGTCACGTAATGCCTAAAACT
1 A-TCACGTAAT-ACTAAAACT
3343360 GATCACGTAATATCTAAAA
1 -ATCACGTAATA-CTAAAA
3343379 ACCAGTCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 31 0.91
22 2 0.06
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (19 bp):
ATCACGTAATACTAAAACT
Found at i:3344221 original size:19 final size:20
Alignment explanation
Indices: 3344190--3344227 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3344180 AGTCATGTCA
3344190 AAAATTGATAAAAAATAATT
1 AAAATTGATAAAAAATAATT
3344210 AAAATT-ATAAAAAATAAT
1 AAAATTGATAAAAAATAAT
3344228 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATTGATAAAAAATAATT
Found at i:3347400 original size:24 final size:23
Alignment explanation
Indices: 3347373--3347417 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
3347363 GCTTCTATAC
*
3347373 AAAATCATTTAAATAAATATAAAT
1 AAAAACATTTAAATAAA-ATAAAT
* *
3347397 AAAAACTTTTTAATAAAATAA
1 AAAAACATTTAAATAAAATAA
3347418 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAACATTTAAATAAAATAAAT
Found at i:3352463 original size:18 final size:18
Alignment explanation
Indices: 3352442--3352480 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3352432 ATTTTTAATA
3352442 ATTAATAATTAATAA-ATT
1 ATTAATAATTAA-AATATT
*
3352460 ATTATTAATTAAAATATT
1 ATTAATAATTAAAATATT
3352478 ATT
1 ATT
3352481 TATTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAATAATTAAAATATT
Found at i:3378611 original size:23 final size:23
Alignment explanation
Indices: 3378583--3378644 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
3378573 ACTAGTTGAT
3378583 AGGCATTGCATGACTTGTTAGTA
1 AGGCATTGCATGACTTGTTAGTA
* *
3378606 AGGCATTGCGTGACTAGTTAGTA
1 AGGCATTGCATGACTTGTTAGTA
**
3378629 AGGCATTATATGACTT
1 AGGCATTGCATGACTT
3378645 AGGTATTACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (23 bp):
AGGCATTGCATGACTTGTTAGTA
Found at i:3378717 original size:21 final size:22
Alignment explanation
Indices: 3378655--3378726 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
3378645 AGGTATTACT
*
3378655 TAAAAATTAGTCACGTAATACC
1 TAAAAATTAGTCACGTAATGCC
* *
3378677 TAAAAATTAGTCATGCAATGCC
1 TAAAAATTAGTCACGTAATGCC
* **
3378699 T-AAAACTAGTCACGTAATGTT
1 TAAAAATTAGTCACGTAATGCC
3378720 TAAAAAT
1 TAAAAAT
3378727 CAATCATGTA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 16 0.40
22 24 0.60
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.29
Consensus pattern (22 bp):
TAAAAATTAGTCACGTAATGCC
Found at i:3383065 original size:29 final size:28
Alignment explanation
Indices: 3383009--3383065 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
3382999 ACATATAGAT
*
3383009 GAAAAATCATCAATATTTAATTTTATAA
1 GAAAAATCATCAATATTTAATTTGATAA
*
3383037 GAAAAAT-ATCAATTATTTTACTTTGATAA
1 GAAAAATCATCAA-TA-TTTAATTTGATAA
3383066 TTAAGATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 9 0.36
29 11 0.44
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (28 bp):
GAAAAATCATCAATATTTAATTTGATAA
Found at i:3388862 original size:12 final size:12
Alignment explanation
Indices: 3388839--3388877 Score: 62
Period size: 11 Copynumber: 3.2 Consensus size: 12
3388829 CCCTATTTAC
3388839 TTTTTCAGCTTTT
1 TTTTTCA-CTTTT
3388852 TTTTTCAC-TTT
1 TTTTTCACTTTT
3388863 TTTTTCACTTTT
1 TTTTTCACTTTT
3388875 TTT
1 TTT
3388878 ATTTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.44
12 7 0.28
13 7 0.28
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTTCACTTTT
Found at i:3390338 original size:12 final size:12
Alignment explanation
Indices: 3390299--3390334 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
3390289 TTTCGTTGAA
3390299 AATTTCTAATGG
1 AATTTCTAATGG
3390311 -ATTTCTAATGG
1 AATTTCTAATGG
3390322 AATTTC-AATGG
1 AATTTCTAATGG
3390333 AA
1 AA
3390335 ATTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (12 bp):
AATTTCTAATGG
Found at i:3390920 original size:19 final size:20
Alignment explanation
Indices: 3390896--3390940 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
3390886 CTACTAATAG
3390896 TTTATTAGTAA-TTA-TAACT
1 TTTATTAGTAACTTATTAA-T
3390915 TTTATTAGTAACTTATTAAT
1 TTTATTAGTAACTTATTAAT
3390935 TTTATT
1 TTTATT
3390941 TATATGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.46
20 10 0.42
21 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTATTAGTAACTTATTAAT
Found at i:3393620 original size:32 final size:32
Alignment explanation
Indices: 3393579--3393675 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 32
3393569 AAAGTCATTG
*
3393579 ACTACTATTAAAATCAAATCTCTGAATCTTTC
1 ACTACTATTAAAATCAAATCTCTGAATATTTC
*
3393611 ACTACTATT-AAAT-AAA--T-TGAAAGAGTTTC
1 ACTACTATTAAAATCAAATCTCTG-AATA-TTTC
* *
3393640 ACTACTATTAAAATCAAATCGCTAAATATTTC
1 ACTACTATTAAAATCAAATCTCTGAATATTTC
3393672 ACTA
1 ACTA
3393676 GAGTTATGGC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
27 2 0.04
28 3 0.06
29 13 0.25
30 7 0.13
31 7 0.13
32 17 0.32
33 3 0.06
34 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (32 bp):
ACTACTATTAAAATCAAATCTCTGAATATTTC
Found at i:3394400 original size:54 final size:55
Alignment explanation
Indices: 3394317--3394437 Score: 147
Period size: 54 Copynumber: 2.2 Consensus size: 55
3394307 TTTTTCAACA
** * * * *
3394317 AAAAATTCCATTAGAAATTTCTTATGAAATTTCGTTGGAAATGCT-TTACC-ATTG
1 AAAAATTCCATTAGAAATTTCCGACGAAATTCCGTTAGAAATGCTCTT-CCAATAG
* *
3394371 AAAAATTTCGTTAGAAATTTCCGACGAAATTCCGTTAGAAATGCTCTTCCAATAG
1 AAAAATTCCATTAGAAATTTCCGACGAAATTCCGTTAGAAATGCTCTTCCAATAG
3394426 AAAAATTCCATT
1 AAAAATTCCATT
3394438 GGCAATTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 40 0.73
55 15 0.27
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (55 bp):
AAAAATTCCATTAGAAATTTCCGACGAAATTCCGTTAGAAATGCTCTTCCAATAG
Found at i:3396233 original size:14 final size:13
Alignment explanation
Indices: 3396210--3396257 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3396200 TATTTCTATT
*
3396210 TAAATTTAAAATA
1 TAAATATAAAATA
3396223 CTAAATATAAAACTA
1 -TAAATATAAAA-TA
*
3396238 TAATGTATAAAATA
1 TAA-ATATAAAATA
3396252 TAAATA
1 TAAATA
3396258 GTTAAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 18 0.62
15 9 0.31
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (13 bp):
TAAATATAAAATA
Found at i:3396319 original size:17 final size:16
Alignment explanation
Indices: 3396245--3396323 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 16
3396235 CTATAATGTA
3396245 TAAA-ATATAAATAGT
1 TAAATATATAAATAGT
3396260 TAAATATGAT--ATA--
1 TAAATAT-ATAAATAGT
* *
3396273 TAAGATTTCATATAATGGT
1 TAA-ATAT-ATA-AATAGT
3396292 TAAATATATAAATAGT
1 TAAATATATAAATAGT
3396308 TAAATAATATAAATAG
1 TAAAT-ATATAAATAG
3396324 AAAAAAGATA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 3 0.06
14 5 0.10
15 7 0.14
16 12 0.24
17 17 0.34
18 3 0.06
19 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (16 bp):
TAAATATATAAATAGT
Found at i:3399433 original size:15 final size:14
Alignment explanation
Indices: 3399408--3399452 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
3399398 ATAAAAAATT
3399408 AATATTTAATTTTAA
1 AATA-TTAATTTTAA
3399423 AATCATTAA-TTTAA
1 AAT-ATTAATTTTAA
3399437 AATATTAATATTTAA
1 AATATTAAT-TTTAA
3399452 A
1 A
3399453 TTATACAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 13 0.48
16 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTAATTTTAA
Found at i:3403504 original size:197 final size:197
Alignment explanation
Indices: 3403181--3403685 Score: 530
Period size: 197 Copynumber: 2.6 Consensus size: 197
3403171 TACTCAAGAT
* * * * * * ** * * *
3403181 CCACCTCATCTCTTACTAATTTGTTTGCTATACTCTCGTTGCACTAACTCCTACTAATGTGGTAT
1 CCACCCCATCTCTTACTAATATATATGCTATACCCTCATTAAACTATCTCTTACAAATGTGGTAT
* *
3403246 GCTATACTCTCATTACACTATTTCTTTAGCCATCTTTTACTTATGTGGTAAGCAATACTCTCATT
66 GCTATACTCTCATTACACTATCTCTTTAGCCATCTTTTACTAATGTGGTAAGCAATACTCTCATT
*** * * * *
3403311 GCACTACCCTTACACTGGTCT-GGTATTTTGCATCTCTCATGAAGGTCC-ATGTTTATATGCACA
131 GCACTACCCTTACACCAATCTGGGT-CTTCGCATCTCTCATGAAGG-CCAATGCTTATATACACA
*
3403374 AATC
194 AAGC
* * **
3403378 CCACTCCATCTCTTATTAATATATATGCTATACTTTCATTAAACTATCTCTTACAAATGTGGTAT
1 CCACCCCATCTCTTACTAATATATATGCTATACCCTCATTAAACTATCTCTTACAAATGTGGTAT
** * * * *
3403443 GCTATACT-TGTGTTGCACTATCTCTTTAGCCATCTTTTACTAATGTGGTATGCAGTACTCTCGT
66 GCTATACTCT-CATTACACTATCTCTTTAGCCATCTTTTACTAATGTGGTAAGCAATACTCTCAT
* * * * *
3403507 TGCACTACCCTTATACCAATTTGGGTCTTCGTATCTCTCATGAAGGCCAATGCTTGTATACTCAA
130 TGCACTACCCTTACACCAATCTGGGTCTTCGCATCTCTCATGAAGGCCAATGCTTATATACACAA
*
3403572 GGC
195 AGC
* * ** **
3403575 TCACCCCATCTCTTGCTAATATATATGCTATACCCTCATTGCACTATCTCTTATTAATGTGGTAT
1 CCACCCCATCTCTTACTAATATATATGCTATACCCTCATTAAACTATCTCTTACAAATGTGGTAT
* * ** *
3403640 GCTATACTCTCATTAGATTATCTAGTTAGCCATCTCTTACTAATGT
66 GCTATACTCTCATTACACTATCTCTTTAGCCATCTTTTACTAATGT
3403686 AGTATGCTAT
Statistics
Matches: 251, Mismatches: 53, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
196 3 0.01
197 244 0.97
198 4 0.02
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (197 bp):
CCACCCCATCTCTTACTAATATATATGCTATACCCTCATTAAACTATCTCTTACAAATGTGGTAT
GCTATACTCTCATTACACTATCTCTTTAGCCATCTTTTACTAATGTGGTAAGCAATACTCTCATT
GCACTACCCTTACACCAATCTGGGTCTTCGCATCTCTCATGAAGGCCAATGCTTATATACACAAA
GC
Done.