Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 5 of 93
Found at i:2241345 original size:20 final size:20
Alignment explanation
Indices: 2241307--2241360 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
2241297 TTTCTCTCCT
2241307 TTTGGCTTTTTTTGCTTTTTTTG
1 TTTGG-TTTTTTT--TTTTTTTG
2241330 TTGTGGTTTTTTTTTTTTTTG
1 TT-TGGTTTTTTTTTTTTTTG
2241351 TTTGGTTTTT
1 TTTGGTTTTT
2241361 GATTGTGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.27
21 10 0.33
23 9 0.30
24 3 0.10
ACGTcount: A:0.00, C:0.04, G:0.19, T:0.78
Consensus pattern (20 bp):
TTTGGTTTTTTTTTTTTTTG
Found at i:2243767 original size:15 final size:15
Alignment explanation
Indices: 2243712--2243766 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
2243702 CTTTACAATA
*
2243712 TAATGTGATTACAAG
1 TAATATGATTACAAG
2243727 TAATATGATTACAAG
1 TAATATGATTACAAG
*
2243742 TAATATGATTGCAAG
1 TAATATGATTACAAG
* *
2243757 CAATGTGATT
1 TAATATGATT
2243767 GTAGGGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TAATATGATTACAAG
Found at i:2244012 original size:60 final size:60
Alignment explanation
Indices: 2243948--2244066 Score: 136
Period size: 60 Copynumber: 2.0 Consensus size: 60
2243938 TTATTAATTT
*
2243948 TTAT-ATGATATCATCTCTTAAATAT-ATTTTTA-ATGTCATATATTTTATTTTTATTTCTTA
1 TTATAATGATAT-ATCTCTTAAATATAATTTTTATAT-T-ATATATTTTATTTTAATTTCTTA
** * * *
2244008 TTATAATTTTATATTTTTTTAATATAATTTTTATATTATATATTTTATTTTAATTTCTT
1 TTATAATGATATATCTCTTAAATATAATTTTTATATTATATATTTTATTTTAATTTCTT
2244067 TTACCTATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
60 35 0.70
61 13 0.26
62 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (60 bp):
TTATAATGATATATCTCTTAAATATAATTTTTATATTATATATTTTATTTTAATTTCTTA
Found at i:2244021 original size:31 final size:29
Alignment explanation
Indices: 2243985--2244146 Score: 93
Period size: 30 Copynumber: 5.5 Consensus size: 29
2243975 TTTTAATGTC
2243985 ATATATTTTATTTTTATTTCTTATTATAATT
1 ATATATTTTATTTTTATTTCTT-TTAT-ATT
* * *
2244016 TTATATTTT-TTTAATATAAT-TTTTATATT
1 ATATATTTTATTT-TTAT-TTCTTTTATATT
*
2244045 ATATATTTTATTTTAATTTCTTTTACCTA-T
1 ATATATTTTATTTTTATTTCTTTTA--TATT
** * * *
2244075 AT-TATATAAATTTTAATTTCTTATATTTT
1 ATATAT-TTTATTTTTATTTCTTTTATATT
* *
2244104 ATTTTATTTTATTTTT-TGAT-TTTTATATT
1 A-TATATTTTATTTTTAT-TTCTTTTATATT
*
2244133 ATACATTTTATTTT
1 ATATATTTTATTTT
2244147 AATGTTTTTT
Statistics
Matches: 101, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
28 13 0.13
29 32 0.32
30 37 0.37
31 18 0.18
32 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (29 bp):
ATATATTTTATTTTTATTTCTTTTATATT
Found at i:2244117 original size:24 final size:25
Alignment explanation
Indices: 2244084--2244134 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
2244074 TATTATATAA
*
2244084 ATTTTAATTTCTT-ATATTTTATTTT
1 ATTTTAATTTCTTGAT-TTTTATATT
*
2244109 ATTTT-ATTTTTTGATTTTTATATT
1 ATTTTAATTTCTTGATTTTTATATT
2244133 AT
1 AT
2244135 ACATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (25 bp):
ATTTTAATTTCTTGATTTTTATATT
Found at i:2244167 original size:33 final size:33
Alignment explanation
Indices: 2244104--2244168 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2244094 CTTATATTTT
*
2244104 ATTTTATTTTATTTTTTGATTTTTATATTATAC
1 ATTTTATTTTATTTTTTGATTTTTAGATTATAC
*
2244137 ATTTTATTTTAATGTTTTTTA-TTTT-GATTATA
1 ATTTTATTTT-AT-TTTTTGATTTTTAGATTATA
2244169 ACGTTACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 16 0.57
34 6 0.21
35 6 0.21
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.69
Consensus pattern (33 bp):
ATTTTATTTTATTTTTTGATTTTTAGATTATAC
Found at i:2253234 original size:15 final size:15
Alignment explanation
Indices: 2253202--2253231 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2253192 TAGTAATGTC
2253202 ATAATTAAAATAATA
1 ATAATTAAAATAATA
2253217 ATAATTAAAA-AATA
1 ATAATTAAAATAATA
2253231 A
1 A
2253232 ATACATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAATTAAAATAATA
Found at i:2254352 original size:25 final size:27
Alignment explanation
Indices: 2254294--2254352 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
2254284 TGGTTGGAAA
* *
2254294 TTAAAAATTAAAAAAAAATTATATCTG
1 TTAAAAATTAAAAAAAAATTACATCCG
* *
2254321 CTGAAAA-T-AAAAAAAATTACATCCG
1 TTAAAAATTAAAAAAAAATTACATCCG
2254346 TTAAAAA
1 TTAAAAA
2254353 AGATCAATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 20 0.77
26 1 0.04
27 5 0.19
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (27 bp):
TTAAAAATTAAAAAAAAATTACATCCG
Found at i:2282001 original size:21 final size:19
Alignment explanation
Indices: 2281976--2282023 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
2281966 TCAGGTTGTT
2281976 TCTTTTTTTTCAATTCTTTTC
1 TCTTTTTTTTC--TTCTTTTC
*
2281997 TCTTTTTCTTCTTCTTTTC
1 TCTTTTTTTTCTTCTTTTC
2282016 TCGTTTTT
1 TC-TTTTT
2282024 AGTGTGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 5 0.20
21 10 0.40
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (19 bp):
TCTTTTTTTTCTTCTTTTC
Found at i:2292800 original size:2 final size:2
Alignment explanation
Indices: 2292793--2292826 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2292783 ATGCAAAGAC
2292793 AG AG AG AG AG AG AG AG AG AG A- AG -G AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2292827 TGAAACCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2295216 original size:2 final size:2
Alignment explanation
Indices: 2295211--2295246 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2295201 TAAGTAGAAA
2295211 AG AG AG AG AG AG A- 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 AG AG AG AG AG AG A
2295247 AAGGAGGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2299913 original size:45 final size:45
Alignment explanation
Indices: 2299847--2299940 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
2299837 ATTCGAGGAG
* * *
2299847 CATACCTATGTTTTACCAGTAACAATATAAAGTTACGAAAATATA
1 CATACCTATGTTTTACAAGTAACAATATAAAATTACGAAAATACA
*
2299892 CATACCTATGTTTTGCAAGTAACAATATAAAATTACGAAAATACA
1 CATACCTATGTTTTACAAGTAACAATATAAAATTACGAAAATACA
2299937 CATA
1 CATA
2299941 AAGAAGCTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (45 bp):
CATACCTATGTTTTACAAGTAACAATATAAAATTACGAAAATACA
Found at i:2321490 original size:2 final size:2
Alignment explanation
Indices: 2321483--2321509 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2321473 TATTAAAACC
2321483 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 A
2321510 CTACTATTAN
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2356424 original size:2 final size:2
Alignment explanation
Indices: 2356419--2356450 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2356409 TATGATGCAA
2356419 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
2356451 TAAGAGCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2365005 original size:12 final size:12
Alignment explanation
Indices: 2364987--2365018 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2364977 CATTTGCAAG
2364987 CTAATAATAATA
1 CTAATAATAATA
*
2364999 GTAATAATAATA
1 CTAATAATAATA
2365011 CTAATAAT
1 CTAATAAT
2365019 CATGATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (12 bp):
CTAATAATAATA
Found at i:2388387 original size:34 final size:34
Alignment explanation
Indices: 2388349--2388416 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2388339 ATTAAATTAA
2388349 TTATATATAGTACATTCTAATATTTCATCACGAT
1 TTATATATAGTACATTCTAATATTTCATCACGAT
2388383 TTATATATAGTACATTCTAATATTTCATCACGAT
1 TTATATATAGTACATTCTAATATTTCATCACGAT
2388417 GAGAGGATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (34 bp):
TTATATATAGTACATTCTAATATTTCATCACGAT
Found at i:2392683 original size:20 final size:19
Alignment explanation
Indices: 2392643--2392683 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2392633 ATAAAGTTTT
*
2392643 ATTTAAATTTTATTAATTA
1 ATTTAAATTTTATTAAATA
*
2392662 ATTTAAATTCTTTTTAAATA
1 ATTTAAATT-TTATTAAATA
2392682 AT
1 AT
2392684 ATTTTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAATTTTATTAAATA
Found at i:2396342 original size:22 final size:24
Alignment explanation
Indices: 2396303--2396350 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2396293 AATAGCTTAA
* *
2396303 AGAGAAGAAGGAACAAAACAAAAG
1 AGAGAAGAAGGAAAAAAAAAAAAG
*
2396327 AGAGAA-AAGAAAAAAAAAAAAAG
1 AGAGAAGAAGGAAAAAAAAAAAAG
2396350 A
1 A
2396351 AATGAAAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.75, C:0.04, G:0.21, T:0.00
Consensus pattern (24 bp):
AGAGAAGAAGGAAAAAAAAAAAAG
Found at i:2406711 original size:3 final size:3
Alignment explanation
Indices: 2406703--2406736 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2406693 AAATGAAACT
* *
2406703 GAA GAA GAA GAA GAA GAA GAA GAG GAA GAG GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2406737 GGAACGAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2420068 original size:80 final size:80
Alignment explanation
Indices: 2419913--2420068 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 80
2419903 CGTATCGATG
* * *
2419913 TGTCTGTATGCTACTTTTAGATCCTTTTAAGCCAACTCCGTGAGTCCAAACCTTTAAGCAAAAGG
1 TGTCCGTATCCTACTTTTAGATCATTTTAAGCCAACTCCGTGAGTCCAAACCTTTAAGCAAAAGG
** *
2419978 GGAGTTAGACACACA
66 AAAGTCAGACACACA
* ** *
2419993 TGTCCGTATCCTACTTTTGGATCATTTTAAGCTGACTCTGTGAGTCCATAA-CTTTAAGCAAAAG
1 TGTCCGTATCCTACTTTTAGATCATTTTAAGCCAACTCCGTGAGTCCA-AACCTTTAAGCAAAAG
2420057 GCAAAG-CAGACA
65 G-AAAGTCAGACA
2420069 TGCAGATACC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
80 60 0.94
81 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (80 bp):
TGTCCGTATCCTACTTTTAGATCATTTTAAGCCAACTCCGTGAGTCCAAACCTTTAAGCAAAAGG
AAAGTCAGACACACA
Found at i:2425577 original size:20 final size:21
Alignment explanation
Indices: 2425539--2425577 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2425529 TAGCATCTTA
*
2425539 TTCTCTTTTTAGTTGTTTTAT
1 TTCTCTTTTTAGTTCTTTTAT
*
2425560 TTCTC-TTTTATTTCTTTT
1 TTCTCTTTTTAGTTCTTTT
2425578 GCTTCTTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (21 bp):
TTCTCTTTTTAGTTCTTTTAT
Found at i:2439893 original size:65 final size:65
Alignment explanation
Indices: 2439810--2439939 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
2439800 AAAAAAACTC
*
2439810 TTTCGCTGAACACATAAGTTCTGTCATTAGTCACTT-ATTAGTATTTCTATCAAAAAGATAATTT
1 TTTCGCTGAACACATAAGTTCTGTCATTAGTCA-TTCATTAATATTTCTATCAAAAAGATAATTT
2439874 T
65 T
2439875 TTTCGCTGAACACATAAGTTCTGTCATTAGTCATTCATTAATATTTCTATCAAAAAGATAATTTT
1 TTTCGCTGAACACATAAGTTCTGTCATTAGTCATTCATTAATATTTCTATCAAAAAGATAATTTT
2439940 ACTCATTATT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 2 0.03
65 61 0.97
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (65 bp):
TTTCGCTGAACACATAAGTTCTGTCATTAGTCATTCATTAATATTTCTATCAAAAAGATAATTTT
Found at i:2443834 original size:67 final size:67
Alignment explanation
Indices: 2443726--2443858 Score: 266
Period size: 67 Copynumber: 2.0 Consensus size: 67
2443716 TTAAAAATAT
2443726 GTGCAGCTAGAGACAGCTTAAAAAGACATTGCTGGCAAAGTCTTGACAAAATCAAATTTTAACTT
1 GTGCAGCTAGAGACAGCTTAAAAAGACATTGCTGGCAAAGTCTTGACAAAATCAAATTTTAACTT
2443791 AC
66 AC
2443793 GTGCAGCTAGAGACAGCTTAAAAAGACATTGCTGGCAAAGTCTTGACAAAATCAAATTTTAACTT
1 GTGCAGCTAGAGACAGCTTAAAAAGACATTGCTGGCAAAGTCTTGACAAAATCAAATTTTAACTT
2443858 A
66 A
2443859 GGTAAAGGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (67 bp):
GTGCAGCTAGAGACAGCTTAAAAAGACATTGCTGGCAAAGTCTTGACAAAATCAAATTTTAACTT
AC
Found at i:2453068 original size:27 final size:28
Alignment explanation
Indices: 2453038--2453112 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
2453028 ATCTTATATA
2453038 AATATTTATTTTATTATGGTTGATAAT-
1 AATATTTATTTTATTATGGTTGATAATG
* *
2453065 AATAGTGATTGATTTTGTTATGGTTGATGATG
1 AATA-T--TT-ATTTTATTATGGTTGATAATG
*
2453097 AAT-TTTATTTTTTTAT
1 AATATTTATTTTATTAT
2453113 TATAATTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
27 13 0.32
28 3 0.08
30 3 0.08
31 18 0.45
32 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (28 bp):
AATATTTATTTTATTATGGTTGATAATG
Found at i:2453687 original size:27 final size:27
Alignment explanation
Indices: 2453656--2453720 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
2453646 CGATTCAGTT
*
2453656 TTTTTTAAATTTAATCAATTCTAGTTAA
1 TTTTTTAAATATAATCAATT-TAGTTAA
* * * *
2453684 TTTTTTAAAAATATTTAATTTATTTAA
1 TTTTTTAAATATAATCAATTTAGTTAA
2453711 -TTTTTAAATA
1 TTTTTTAAATA
2453721 CGTGTGACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 9 0.29
27 6 0.19
28 16 0.52
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTTAAATATAATCAATTTAGTTAA
Found at i:2458342 original size:34 final size:33
Alignment explanation
Indices: 2458304--2458435 Score: 104
Period size: 34 Copynumber: 3.9 Consensus size: 33
2458294 ATAATCTAAA
2458304 ATTTAATTAAAATATTAATAATTAATAATTNTTT
1 ATTTAATTAAAATATTAATAATTAATAATT-TTT
* * * *
2458338 ATTTAATTTAAATATT-ATTATGATTAATTTTT
1 ATTTAATTAAAATATTAATAATTAATAATTTTT
* ** * * * * *
2458370 ATTTTATTTTATTTTTAAAATATTAATAATTGATA
1 ATTTAATTAAAATATTAATA-ATTAATAATT-TTT
* *
2458405 ATTTATTTAAAATATTAATAATTGATAATTT
1 ATTTAATTAAAATATTAATAATTAATAATTT
2458436 AAATATTAAT
Statistics
Matches: 72, Mismatches: 23, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
32 15 0.21
33 11 0.15
34 32 0.44
35 14 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
ATTTAATTAAAATATTAATAATTAATAATTTTT
Found at i:2458355 original size:101 final size:100
Alignment explanation
Indices: 2458249--2458435 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 100
2458239 AAACACTTTT
*
2458249 TATTATTTAT-ATGACA-TTTTATTTTATTAGATTTTTTAAATATTAATAATCT-AAAATTTAAT
1 TATTA-TTATGATGA-ATTTTTATTTTATTAGATTTTTAAAATATTAATAAT-TGAAAATTTAAT
2458311 TAAAATATTAATAATTAATAATTNTTTATTTAATTTAAA
63 TAAAATATTAATAATTAATAATT-TTTATTTAATTTAAA
* ** * *
2458350 TATTATTATGATTAATTTTTATTTTATTTTATTTTTAAAATATTAATAATTGATAATTTATTTAA
1 TATTATTATGATGAATTTTTATTTTATTAGATTTTTAAAATATTAATAATTGAAAATTTAATTAA
*
2458415 AATATTAATAATTGATAATTT
66 AATATTAATAATTAATAATTT
2458436 AAATATTAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
100 7 0.09
101 69 0.91
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (100 bp):
TATTATTATGATGAATTTTTATTTTATTAGATTTTTAAAATATTAATAATTGAAAATTTAATTAA
AATATTAATAATTAATAATTTTTATTTAATTTAAA
Found at i:2458396 original size:74 final size:72
Alignment explanation
Indices: 2458310--2458549 Score: 183
Period size: 74 Copynumber: 3.2 Consensus size: 72
2458300 TAAAATTTAA
*
2458310 TTAAAATATTAATAATTAATAATTNTTTATTTAATTTAAATATTATTATGATTAATTTTTATTTT
1 TTAAAATATTAATAATTAATAATT-TTTATTTAATTTAAATATTATAATGATTAA-TTTTATTTT
2458375 ATTTTATTT
64 ATTTTATTT
*
2458384 TTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAAT-TTA-AAT-ATTAAT
1 TTAAAATATTAATAATTAATAA-TT-TTT---AT-TTAAT--TT-A-AATATTATAATGATTAAT
* *
2458446 ATTTATTTATAATTTAATTA
56 -TTTATTT-T-ATTTTATTT
* * * * *
2458466 TT-ATATTTTAA-AA-TATTAATATTTTATTTAATTTAAATATTATGATGATCAA--TTATTTTA
1 TTAAAATATTAATAATTAATAAT-TTTTATTTAATTTAAATATTATAATGATTAATTTTATTTTA
2458526 TTTTATTT
65 TTTTATTT
*
2458534 TTGAAA-ATTAATAATT
1 TTAAAATATTAATAATT
2458550 GATTATTTAT
Statistics
Matches: 132, Mismatches: 15, Indels: 42
0.70 0.08 0.22
Matches are distributed among these distances:
68 13 0.10
69 5 0.04
70 10 0.08
71 4 0.03
72 4 0.03
73 4 0.03
74 26 0.20
75 7 0.05
78 6 0.05
79 11 0.08
80 14 0.11
81 12 0.09
82 13 0.10
83 3 0.02
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (72 bp):
TTAAAATATTAATAATTAATAATTTTTATTTAATTTAAATATTATAATGATTAATTTTATTTTAT
TTTATTT
Found at i:2458416 original size:27 final size:27
Alignment explanation
Indices: 2458383--2458436 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2458373 TTATTTTATT
2458383 TTTAAAATATTAATAATTGATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
2458410 TTTAAAATATTAATAATTGATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
2458437 AATATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTAAAATATTAATAATTGATAATTTA
Found at i:2458462 original size:18 final size:18
Alignment explanation
Indices: 2458405--2458496 Score: 78
Period size: 22 Copynumber: 4.6 Consensus size: 18
2458395 ATAATTGATA
2458405 ATTTATTTAAAATATTAAT
1 ATTTATTT-AAATATTAAT
2458424 AATTGATAATTTAAATATTAAT
1 -ATT--T-ATTTAAATATTAAT
2458446 ATTTATTTATAAT-TTAATT
1 ATTTATTTA-AATATTAA-T
2458465 ATTATATTTTAAAATATTAAT
1 ATT-TA-TTT-AAATATTAAT
2458486 ATTTTATTTAA
1 A-TTTATTTAA
2458497 TTTAAATATT
Statistics
Matches: 62, Mismatches: 0, Indels: 21
0.75 0.00 0.25
Matches are distributed among these distances:
18 9 0.15
19 10 0.16
20 8 0.13
21 13 0.21
22 18 0.29
23 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
ATTTATTTAAATATTAAT
Found at i:2458484 original size:22 final size:21
Alignment explanation
Indices: 2458410--2458494 Score: 88
Period size: 21 Copynumber: 4.1 Consensus size: 21
2458400 TGATAATTTA
*
2458410 TTTAAAATATTAATAATTGATAA
1 TTTAAAATATTAAT-ATT-ATAT
2458433 TTT-AAATATTAATATT-TA-
1 TTTAAAATATTAATATTATAT
*
2458451 TTTATAAT-TTAATTATTATAT
1 TTTAAAATATTAA-TATTATAT
*
2458472 TTTAAAATATTAATATTTTAT
1 TTTAAAATATTAATATTATAT
2458493 TT
1 TT
2458495 AATTTAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
18 7 0.13
19 9 0.17
20 2 0.04
21 19 0.35
22 14 0.26
23 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTAAAATATTAATATTATAT
Found at i:2458498 original size:39 final size:39
Alignment explanation
Indices: 2458405--2458508 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 39
2458395 ATAATTGATA
* *
2458405 ATTTATTTAAAATATTAATAATTGATAATTTAAATATTAAT
1 ATTTATTTATAAT-TTAATTATT-ATAATTTAAATATTAAT
*
2458446 ATTTATTTATAATTTAATTATTATATTTTAAAATATTAAT
1 ATTTATTTATAATTTAATTATTATAATTT-AAATATTAAT
*
2458486 ATTT-TATT-TAATTTAAATATTAT
1 ATTTAT-TTATAATTTAATTATTAT
2458509 GATGATCAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
39 21 0.37
40 24 0.42
41 12 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
ATTTATTTATAATTTAATTATTATAATTTAAATATTAAT
Found at i:2458535 original size:150 final size:150
Alignment explanation
Indices: 2458335--2458618 Score: 448
Period size: 150 Copynumber: 1.9 Consensus size: 150
2458325 TTAATAATTN
* *
2458335 TTTATTTAATTTAAATATTATTATGATTAATTTTTATTTTATTTTATTTTTAAAATATTAATAAT
1 TTTATTTAATTTAAATATTATGATGATCAA--TTTATTTTATTTTATTTTTAAAA-ATTAATAAT
*
2458400 TGATAATTTATTT-AAAATATTAATAATTGATAATTTAAATATTAATA-TTTATTTATAATTTAA
63 TGATAATTTATTTAAAAATATTAATAATAGATAATTTAAATATTAATATTTTA-TT-TAATTTAA
*
2458463 TTATTATATTTTAAAATATTAATAT
126 ATATTATATTTTAAAATATTAATAT
*
2458488 TTTATTTAATTTAAATATTATGATGATCAA-TTATTTTATTTTATTTTTGAAAATTAATAATTGA
1 TTTATTTAATTTAAATATTATGATGATCAATTTATTTTATTTTATTTTTAAAAATTAATAATTGA
*
2458552 TTATTTATTTAAAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTAATTTAAATATT
66 TAATTTATTTAAAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTAATTTAAATATT
2458617 AT
131 AT
2458619 TATGACTAAT
Statistics
Matches: 123, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
149 35 0.28
150 56 0.46
151 4 0.03
153 28 0.23
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (150 bp):
TTTATTTAATTTAAATATTATGATGATCAATTTATTTTATTTTATTTTTAAAAATTAATAATTGA
TAATTTATTTAAAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTAATTTAAATATT
ATATTTTAAAATATTAATAT
Found at i:2458603 original size:110 final size:108
Alignment explanation
Indices: 2458446--2458835 Score: 399
Period size: 106 Copynumber: 3.6 Consensus size: 108
2458436 AAATATTAAT
* *
2458446 ATTTATTTATAAT-TTAATTATT-ATATTTTAAAATATTAATATTTTATTTAATTTAAATATTAT
1 ATTTATTTA-AATATTAATAATTGATAATTT-AAATATTAATATTTTATTTAATTTAAATATTAT
* * *
2458509 GATGATCAATTATTTTATTTTATTTTTGAAA-ATTAATAATTGATT
64 TATGATC-ATTATTTTATTTTATTTTTTAAATATTAATAATTGATA
*
2458554 ATTTATTTAAAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTAATTTAAATATTAT
1 ATTTATTT--AAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTAT
* *
2458619 TATGA-C--TAATTT-TTTTATTTTTTAAATATTAATAATTGGTA
64 TATGATCATTATTTTATTTTATTTTTTAAATATTAATAATTGATA
* * *
2458660 ATTTATTTAAATATTAATAATTGATGATTTAATTATTAATATTGTTTATCTAATTTAAATGA-TA
1 ATTTATTTAAATATTAATAATTGATAATTTAAATATTAATA-T-TTTATTTAATTTAAAT-ATTA
* * * ** *
2458724 TTATGTTTATTTATTTTTAATTTATTTTGTTTTTAAATAGGAATAATTTATA
63 TTATGATCA-TTA-TTTT-A-TT-TTAT-TTTTTAAATATTAATAATTGATA
2458776 ATTTATTT---TATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTT-AATATTA
1 ATTTATTTAAATATTAATAATTGATAATTTAAATATTAATATTTTA-TT-TAATTTAAATATTA
2458836 ATATTTTATT
Statistics
Matches: 238, Mismatches: 23, Indels: 38
0.80 0.08 0.13
Matches are distributed among these distances:
104 30 0.13
105 14 0.06
106 47 0.20
107 1 0.00
108 8 0.03
109 4 0.02
110 47 0.20
111 14 0.06
112 7 0.03
113 34 0.14
114 2 0.01
115 3 0.01
116 27 0.11
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (108 bp):
ATTTATTTAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTA
TGATCATTATTTTATTTTATTTTTTAAATATTAATAATTGATA
Found at i:2458664 original size:22 final size:24
Alignment explanation
Indices: 2458639--2458700 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 24
2458629 TTTTTTATTT
*
2458639 TTTAAATATTAATAATTGGTAATTTA
1 TTTAAATATTAATAATTGATAA--TA
*
2458665 TTTAAATATTAATAATTGAT--GA
1 TTTAAATATTAATAATTGATAATA
*
2458687 TTTAATTATTAATA
1 TTTAAATATTAATA
2458701 TTGTTTATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 14 0.42
26 19 0.58
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (24 bp):
TTTAAATATTAATAATTGATAATA
Found at i:2458689 original size:26 final size:26
Alignment explanation
Indices: 2458635--2458690 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
2458625 TAATTTTTTT
*
2458635 ATTT-TTTAAATATTAATAATTGGTA
1 ATTTATTTAAATATTAATAATTGATA
*
2458660 ATTTATTTAAATATTAATAATTGATG
1 ATTTATTTAAATATTAATAATTGATA
2458686 ATTTA
1 ATTTA
2458691 ATTATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:2458713 original size:21 final size:22
Alignment explanation
Indices: 2458661--2458714 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2458651 TAATTGGTAA
*
2458661 TTTATTTAAATATTAATAATTG
1 TTTATTTAATTATTAATAATTG
* *
2458683 ATGATTTAATTATTAAT-ATTG
1 TTTATTTAATTATTAATAATTG
*
2458704 TTTATCTAATT
1 TTTATTTAATT
2458715 TAAATGATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTATTTAATTATTAATAATTG
Found at i:2458837 original size:25 final size:26
Alignment explanation
Indices: 2458796--2458845 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
2458786 TTAATAATTG
2458796 ATAATTTAAATATTAATATTTTATTT
1 ATAATTTAAATATTAATATTTTATTT
2458822 ATAATTT-AATATTAATATTTTATT
1 ATAATTTAAATATTAATATTTTATT
2458846 AAAAGTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATAATTTAAATATTAATATTTTATTT
Found at i:2461098 original size:27 final size:27
Alignment explanation
Indices: 2461050--2461126 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 27
2461040 ATGACGTGTG
2461050 ATAATTAAATTTTTCAATATAACATGTA
1 ATAATTAAATTTTT-AATATAACATGTA
* **
2461078 ATAACTAAATTTTTAATATAATGTGTA
1 ATAATTAAATTTTTAATATAACATGTA
* *
2461105 ACAATTATATTTTTTAATATAA
1 ATAATTA-AATTTTTAATATAA
2461127 GGTGTAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 16 0.38
28 26 0.62
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (27 bp):
ATAATTAAATTTTTAATATAACATGTA
Found at i:2461101 original size:25 final size:28
Alignment explanation
Indices: 2461050--2461126 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
2461040 ATGACGTGTG
*
2461050 ATAATTAAATTTTTCAATATAACATGTA
1 ATAACTAAATTTTTCAATATAACATGTA
**
2461078 ATAACTAAATTTTT-AATATAATGTGTA
1 ATAACTAAATTTTTCAATATAACATGTA
* * * *
2461105 ACAATTATATTTTTTAATATAA
1 ATAACTAAATTTTTCAATATAA
2461127 GGTGTAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 22 0.52
28 20 0.48
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (28 bp):
ATAACTAAATTTTTCAATATAACATGTA
Found at i:2461131 original size:28 final size:27
Alignment explanation
Indices: 2461043--2461133 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
2461033 TTTTATCATG
* * *
2461043 ACGTGTGATAATTAAATTTTTCAATATA
1 ACGTGTAACAATT-AATTTTTTAATATA
* * * *
2461071 ACATGTAATAACTAAATTTTTAATATA
1 ACGTGTAACAATTAATTTTTTAATATA
*
2461098 ATGTGTAACAATTATATTTTTTAATATA
1 ACGTGTAACAATTA-ATTTTTTAATATA
*
2461126 AGGTGTAA
1 ACGTGTAA
2461134 TTTTTTAACT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 22 0.43
28 29 0.57
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (27 bp):
ACGTGTAACAATTAATTTTTTAATATA
Found at i:2461216 original size:27 final size:26
Alignment explanation
Indices: 2461147--2461220 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
2461137 TTTAACTTAG
* *
2461147 TATGTAGTAATTATATTTTTCAACATT
1 TATGTAATAATTA-AATTTTCAACATT
* * *
2461174 AAGTGTAACAAGTAAATTTTCAACATAT
1 TA-TGTAATAATTAAATTTTCAACAT-T
2461202 TATGTAATAATTAAATTTT
1 TATGTAATAATTAAATTTT
2461221 TAATATGACA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 27 0.73
28 10 0.27
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (26 bp):
TATGTAATAATTAAATTTTCAACATT
Found at i:2463709 original size:24 final size:24
Alignment explanation
Indices: 2463670--2463718 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2463660 CATGAACCTC
*
2463670 TCTTCTATCTTCTCCTCTTCTTTT
1 TCTTCTATCTTCTCCTATTCTTTT
*
2463694 TCTTCT-TCTTCGTCCTATTTTTTT
1 TCTTCTATCTTC-TCCTATTCTTTT
2463718 T
1 T
2463719 GACCACTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.04, C:0.29, G:0.02, T:0.65
Consensus pattern (24 bp):
TCTTCTATCTTCTCCTATTCTTTT
Found at i:2463922 original size:38 final size:38
Alignment explanation
Indices: 2463853--2463934 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
2463843 AGAGGAAGTC
* *
2463853 TTCAGT-TCAGTTTGGGTTTTTTGAGGGTTTTTATCAG
1 TTCAGTCTCAGTTTGGGTTTTTTGAGGATTTTTAACAG
* *
2463890 TTCAGTCTCATTTTGGGTTTTTTTTA-GATTTTTAACAG
1 TTCAGTCTCAGTTTGGG-TTTTTTGAGGATTTTTAACAG
2463928 TTCAGTC
1 TTCAGTC
2463935 AGAGACGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 6 0.15
38 26 0.67
39 7 0.18
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.52
Consensus pattern (38 bp):
TTCAGTCTCAGTTTGGGTTTTTTGAGGATTTTTAACAG
Found at i:2465151 original size:11 final size:11
Alignment explanation
Indices: 2465131--2465159 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2465121 AAATATTAAA
2465131 ATATTATTATT
1 ATATTATTATT
2465142 ATATTATTATT
1 ATATTATTATT
2465153 -TATTATT
1 ATATTATT
2465160 TTAAGGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATATTATTATT
Found at i:2478264 original size:26 final size:27
Alignment explanation
Indices: 2478218--2478271 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
2478208 CAAGCGCATG
* *
2478218 TGTTAAAAAAAGTATTGTTACATGTCA
1 TGTTAAAAAAAGTATTATTACACGTCA
2478245 TGTTGAAAAAAA-TA-TATTACACGTCA
1 TGTT-AAAAAAAGTATTATTACACGTCA
2478271 T
1 T
2478272 ATTTAAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.46
27 6 0.25
28 7 0.29
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (27 bp):
TGTTAAAAAAAGTATTATTACACGTCA
Found at i:2478448 original size:15 final size:15
Alignment explanation
Indices: 2478428--2478461 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2478418 CACGTCATAC
2478428 TTAAGATGTTTA-ATT
1 TTAAGA-GTTTATATT
2478443 TTAAGAGTTTATATT
1 TTAAGAGTTTATATT
2478458 TTAA
1 TTAA
2478462 TAAAATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TTAAGAGTTTATATT
Found at i:2478448 original size:154 final size:151
Alignment explanation
Indices: 2478244--2478526 Score: 363
Period size: 154 Copynumber: 1.9 Consensus size: 151
2478234 GTTACATGTC
* * *
2478244 ATGTTGAAAAAAATATATTACACGTCATATTTAAGGGATTAAACTCTAAGAGTTTATATCTTAGT
1 ATGTTGAAAAAAAAATATTACACGTCATACTTAAGGGATTAAACTCTAAGAGTTTATATCTTAAT
* * * * * *
2478309 GAAATATAAAGATAGAGATCAAGTTACACC-CTATGTTTAAAAAATAATGTTGTTACAGGTTATG
66 AAAATACAAAGATAGAAACCAAGTTACACCTC-ATG-TTAAAAAA-AAAGTTGTTACAGGTCATG
2478373 TTCAAAAAAATATTATTACACACA
128 TTCAAAAAAATATTATTACACACA
* * * * *
2478397 ATGTTGAAAAAAAAATTATTACACGTCATACTTAAGATG-TTTAATTTTAAGAGTTTATATTTTA
1 ATGTTGAAAAAAAAA-TATTACACGTCATACTTAAG-GGATTAAACTCTAAGAGTTTATATCTTA
**
2478461 ATAAAATACAAAGATAGAAACCAAGTTACATTTCATGTTAAAAAAAAAGTTGTTACAGGTCATGT
64 ATAAAATACAAAGATAGAAACCAAGTTACACCTCATGTTAAAAAAAAAGTTGTTACAGGTCATGT
2478526 T
129 T
2478527 TAAGGTGTTT
Statistics
Matches: 111, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
152 19 0.17
153 22 0.20
154 68 0.61
155 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (151 bp):
ATGTTGAAAAAAAAATATTACACGTCATACTTAAGGGATTAAACTCTAAGAGTTTATATCTTAAT
AAAATACAAAGATAGAAACCAAGTTACACCTCATGTTAAAAAAAAAGTTGTTACAGGTCATGTTC
AAAAAAATATTATTACACACA
Found at i:2478505 original size:98 final size:98
Alignment explanation
Indices: 2478397--2478614 Score: 294
Period size: 98 Copynumber: 2.2 Consensus size: 98
2478387 ATTACACACA
* * *
2478397 ATGTTGAAAAAAAAATTATTACACGTCATACTTAAGATGTTTAATTTTAAGAGTTTATATTT-TA
1 ATGTTAAAAAAAAAATTATTACACGTCATACTTAAGATGTTTAACTCTAAGAGTTTAT-TTTCTA
*
2478461 ATAAAATACAAAGATAGAAACCAAGTTACATTTC
65 ATAAAATACAAAGATAGAAACCAAGTTACATGTC
* * * ** *
2478495 ATGTTAAAAAAAAAGTTGTTACAGGTCATGTTTAAGGTGTTTAACTCTAAGAGTTTATTTTCTAA
1 ATGTTAAAAAAAAAATTATTACACGTCATACTTAAGATGTTTAACTCTAAGAGTTTATTTTCTAA
* * *
2478560 TGAAATACAAATATAGAGACCAAGTTACATGTC
66 TAAAATACAAAGATAGAAACCAAGTTACATGTC
2478593 ATGTTAAAAAAAATAATTATTA
1 ATGTTAAAAAAAA-AATTATTA
2478615 TACACCATGT
Statistics
Matches: 103, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
97 3 0.03
98 94 0.91
99 6 0.06
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (98 bp):
ATGTTAAAAAAAAAATTATTACACGTCATACTTAAGATGTTTAACTCTAAGAGTTTATTTTCTAA
TAAAATACAAAGATAGAAACCAAGTTACATGTC
Found at i:2478675 original size:99 final size:98
Alignment explanation
Indices: 2478397--2478696 Score: 287
Period size: 98 Copynumber: 3.1 Consensus size: 98
2478387 ATTACACACA
* ** ** * ** * **
2478397 ATGTTGAAAAAAAAATTATTACACGTCATACTT-AAGATGTTTAATTTTAAGAGTTTATATTTTA
1 ATGTTAAAAAAAAAATTATTACACACCATGTTTAAAG-TGTTTAACTCCAAAAGTTTATATTCGA
* * *
2478461 ATAAAATACAAAGATAGAAACCAAGTTACATTTC
65 ATGAAATACAAAGATAGAGACCAAGTTACATGTC
* * *** * * * * *
2478495 ATGTTAAAAAAAAAGTTGTTACAGGTCATGTTTAAGGTGTTTAACTCTAAGAGTTTATTTTCTAA
1 ATGTTAAAAAAAAAATTATTACACACCATGTTTAAAGTGTTTAACTCCAAAAGTTTATATTCGAA
*
2478560 TGAAATACAAATATAGAGACCAAGTTACATGTC
66 TGAAATACAAAGATAGAGACCAAGTTACATGTC
*
2478593 ATGTTAAAAAAAATAATTATTATACACCATGTTTAAAGTGTTTAACTCCAAAAGTTTATATTCGA
1 ATGTTAAAAAAAA-AATTATTACACACCATGTTTAAAGTGTTTAACTCCAAAAGTTTATATTCGA
* * * ** *
2478658 GTGAATTACACAGATAGAGATTAAGTTACATGTT
65 ATGAAATACAAAGATAGAGACCAAGTTACATGTC
2478692 ATGTT
1 ATGTT
2478697 TAAACCATGT
Statistics
Matches: 167, Mismatches: 33, Indels: 3
0.82 0.16 0.01
Matches are distributed among these distances:
98 93 0.56
99 74 0.44
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (98 bp):
ATGTTAAAAAAAAAATTATTACACACCATGTTTAAAGTGTTTAACTCCAAAAGTTTATATTCGAA
TGAAATACAAAGATAGAGACCAAGTTACATGTC
Found at i:2480225 original size:266 final size:266
Alignment explanation
Indices: 2479745--2480267 Score: 1028
Period size: 266 Copynumber: 2.0 Consensus size: 266
2479735 ATATAAATAA
*
2479745 AAATTGTTTTGAAATTAAGTACATGCAAAAAGATATTAAAGCCGCTTTATTTTTTCTTTTAATAG
1 AAATTATTTTGAAATTAAGTACATGCAAAAAGATATTAAAGCCGCTTTATTTTTTCTTTTAATAG
2479810 TTTAGTTAAATTAATTAATGCTGATCATATGCAGGACCACAAGAGGAAAAGAAAAAGAGGGAAAG
66 TTTAGTTAAATTAATTAATGCTGATCATATGCAGGACCACAAGAGGAAAAGAAAAAGAGGGAAAG
*
2479875 GAGTTTAGTTGATTAAACAAGATGCAAGCTCTGAAAGTAATTAAGATTAAAAATGGCGGCTGCTC
131 GAGTTTAGTTGATTAAACAAGATGCAAGCTCTGAAAGTAATTAAGATTAAAAATGGCGGCCGCTC
2479940 CACATGGGTGGTGGTGGTCGATCTTACTTTCTTTTTTTTTTTTAATATCAGAAACAATTTATATA
196 CACATGGGTGGTGGTGGTCGATCTTACTTTCTTTTTTTTTTTTAATATCAGAAACAATTTATATA
2480005 TGTAAC
261 TGTAAC
2480011 AAATTATTTTGAAATTAAGTACATGCAAAAAGATATTAAAGCCGCTTTATTTTTTCTTTTAATAG
1 AAATTATTTTGAAATTAAGTACATGCAAAAAGATATTAAAGCCGCTTTATTTTTTCTTTTAATAG
2480076 TTTAGTTAAATTAATTAATGCTGATCATATGCAGGACCACAAGAGGAAAAGAAAAAGAGGGAAAG
66 TTTAGTTAAATTAATTAATGCTGATCATATGCAGGACCACAAGAGGAAAAGAAAAAGAGGGAAAG
2480141 GAGTTTAGTTGATTAAACAAGATGCAAGCTCTGAAAGTAATTAAGATTAAAAATGGCGGCCGCTC
131 GAGTTTAGTTGATTAAACAAGATGCAAGCTCTGAAAGTAATTAAGATTAAAAATGGCGGCCGCTC
2480206 CACATGGGTGGTGGTGGTCGATCTTACTTTCTTTTTTTTTTTTAATATCAGAAACAATTTAT
196 CACATGGGTGGTGGTGGTCGATCTTACTTTCTTTTTTTTTTTTAATATCAGAAACAATTTAT
2480268 TAAGATGATT
Statistics
Matches: 255, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 255 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (266 bp):
AAATTATTTTGAAATTAAGTACATGCAAAAAGATATTAAAGCCGCTTTATTTTTTCTTTTAATAG
TTTAGTTAAATTAATTAATGCTGATCATATGCAGGACCACAAGAGGAAAAGAAAAAGAGGGAAAG
GAGTTTAGTTGATTAAACAAGATGCAAGCTCTGAAAGTAATTAAGATTAAAAATGGCGGCCGCTC
CACATGGGTGGTGGTGGTCGATCTTACTTTCTTTTTTTTTTTTAATATCAGAAACAATTTATATA
TGTAAC
Found at i:2482993 original size:2 final size:2
Alignment explanation
Indices: 2482986--2483014 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2482976 ATAGCTTTGA
2482986 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2483015 CAGAGNTAAT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2483072 original size:2 final size:2
Alignment explanation
Indices: 2483065--2483093 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2483055 GAATTTGGTA
2483065 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2483094 CAGGGGGGTG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2484673 original size:13 final size:13
Alignment explanation
Indices: 2484655--2484684 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2484645 ACATTTCTAC
2484655 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
*
2484668 TTCTTCTTCTTTT
1 TTCTTCTTCTTCT
2484681 TTCT
1 TTCT
2484685 AAGGAGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCTTCTTCTTCT
Found at i:2486992 original size:24 final size:23
Alignment explanation
Indices: 2486944--2486994 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
2486934 TCTTCCTCCT
**
2486944 TTCCCTCTTTCTCTCAGCCGTTC
1 TTCCCTCTTTCTCTCAGCCACTC
*
2486967 TTCCCTTCTTTCTCTCCGCCACTC
1 TTCCC-TCTTTCTCTCAGCCACTC
2486991 TTCC
1 TTCC
2486995 ACTGTTTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.04, C:0.47, G:0.06, T:0.43
Consensus pattern (23 bp):
TTCCCTCTTTCTCTCAGCCACTC
Found at i:2487291 original size:60 final size:60
Alignment explanation
Indices: 2487224--2487353 Score: 251
Period size: 60 Copynumber: 2.2 Consensus size: 60
2487214 GTTGGGTTAG
2487224 GGGTGTGAGTCAACGACACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
1 GGGTGTGAGTCAACGACACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
*
2487284 GGGTGTGAGTCAACGACACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGTTGGGATTT
1 GGGTGTGAGTCAACGACACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
2487344 GGGTGTGAGT
1 GGGTGTGAGT
2487354 AGCTGTTTGG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.18, C:0.13, G:0.37, T:0.32
Consensus pattern (60 bp):
GGGTGTGAGTCAACGACACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
Found at i:2493043 original size:20 final size:20
Alignment explanation
Indices: 2493018--2493059 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2493008 TTTTTAGAAA
2493018 AAAATGATTCATAATATATG
1 AAAATGATTCATAATATATG
*
2493038 AAAATGATTTATAATATATG
1 AAAATGATTCATAATATATG
2493058 AA
1 AA
2493060 GAATTGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAATGATTCATAATATATG
Found at i:2502838 original size:26 final size:29
Alignment explanation
Indices: 2502801--2502856 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 29
2502791 GCTGTTTTTT
2502801 ACTTGTTTTCTTAGTTT-TTA-TC-TACAG
1 ACTTGTTTTCTT-GTTTATTATTCGTACAG
2502828 ACTT-TTTTCTTGTTTATTATTCGTACAG
1 ACTTGTTTTCTTGTTTATTATTCGTACAG
2502856 A
1 A
2502857 AAATAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 4 0.15
26 10 0.38
27 6 0.23
28 6 0.23
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (29 bp):
ACTTGTTTTCTTGTTTATTATTCGTACAG
Found at i:2527583 original size:4 final size:4
Alignment explanation
Indices: 2527568--2527630 Score: 67
Period size: 4 Copynumber: 16.2 Consensus size: 4
2527558 CAACAATAAG
* * * * *
2527568 ACAT ATAT ACAT ACAT AC-- ACAT ATAT ATAT ATAC ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2527614 ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT A
2527631 TATATAAGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
4 49 0.96
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.29
Consensus pattern (4 bp):
ACAT
Found at i:2531366 original size:16 final size:17
Alignment explanation
Indices: 2531340--2531371 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2531330 GATCAAATAA
2531340 AATTCAAAATTTTAATC
1 AATTCAAAATTTTAATC
2531357 AATT-AAAATTTTAAT
1 AATTCAAAATTTTAAT
2531372 TTATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTCAAAATTTTAATC
Found at i:2541272 original size:117 final size:114
Alignment explanation
Indices: 2541108--2541428 Score: 340
Period size: 117 Copynumber: 2.8 Consensus size: 114
2541098 AAAAGAAACC
* * * * * *
2541108 TTCTTATAATAATTATTCGTACAAATTTTTTTATTTTTATTTTAATATTTATGTTATTGTAATTC
1 TTCTTAAAATAATTATACGTATAAA-TTATTTA-TTTT-TTTTAATATTTAAGTTACTGTAATT-
* * *
2541173 ACTTGATCACATCTTTTGAATTCGAATTTTAAAAGAAGTCA-ATTATTTAAATT
62 ACTTGATCACATCTCTTGAATTCGAATTTCAAAAGAAGT-AGATCATTTAAATT
* * * ** * *
2541226 TTTTTATAATAATTATACTTATACTTTATTTATTTTTGTTTAAATATATAAATTACTGTAATTTA
1 TTCTTAAAATAATTATACGTATAAATTATTTATTTTT-TTT-AATATTTAAGTTACTGTAA-TTA
* * * *
2541291 TTTGGTCACATCTCTTGAATTTGAATTTCAAAAGAAGTAGGTCATTTAAATT
63 CTTGATCACATCTCTTGAATTCGAATTTCAAAAGAAGTAGATCATTTAAATT
* *
2541343 TTCTTAAAATAATTATACGTATAAATTA-ATATTTTTTTTACTATTTAAGTTACTGTAACTTACT
1 TTCTTAAAATAATTATACGTATAAATTATTTATTTTTTTTAATATTTAAGTTACTGTAA-TTACT
*
2541407 TGCTCACATCTCTTGAATTCGA
65 TGATCACATCTCTTGAATTCGA
2541429 TCATTTAAAT
Statistics
Matches: 168, Mismatches: 31, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
114 40 0.24
115 4 0.02
116 15 0.09
117 88 0.52
118 21 0.12
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (114 bp):
TTCTTAAAATAATTATACGTATAAATTATTTATTTTTTTTAATATTTAAGTTACTGTAATTACTT
GATCACATCTCTTGAATTCGAATTTCAAAAGAAGTAGATCATTTAAATT
Found at i:2542828 original size:110 final size:111
Alignment explanation
Indices: 2542618--2542843 Score: 393
Period size: 110 Copynumber: 2.0 Consensus size: 111
2542608 ATTAGTATTG
2542618 GAAT-GCTGATCTCATCCCATAACGTGCCAGTCGATTTCATTCTCCACTTTTTTTTTTTCCTTTT
1 GAATAGCTGATCTCATCCCATAACGTGCCAGTCGATTTCATTCTCCAC-TTTTTTTTTTCCTTTT
*
2542682 ATTTCCATGTCGTGCTTTATTTTTCCTGGTTTATTTCTATGGAAGCA
65 ATTTCCATATCGTGCTTTATTTTTCCTGGTTTATTTCTATGGAAGCA
* *
2542729 GAATAGCTGATCTTATCCCATAAGGTGCCAGTCGATTTCATTCTCCAC-TTTTTTTTTCCTTTTA
1 GAATAGCTGATCTCATCCCATAACGTGCCAGTCGATTTCATTCTCCACTTTTTTTTTTCCTTTTA
*
2542793 TTTCCATATCGTGCTTTGTTTTTCCTGGTTTATTTCTATGGAAGCA
66 TTTCCATATCGTGCTTTATTTTTCCTGGTTTATTTCTATGGAAGCA
2542839 GAATA
1 GAATA
2542844 TTTGTTAGAA
Statistics
Matches: 110, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
110 65 0.59
111 4 0.04
112 41 0.37
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (111 bp):
GAATAGCTGATCTCATCCCATAACGTGCCAGTCGATTTCATTCTCCACTTTTTTTTTTCCTTTTA
TTTCCATATCGTGCTTTATTTTTCCTGGTTTATTTCTATGGAAGCA
Found at i:2548579 original size:161 final size:163
Alignment explanation
Indices: 2548339--2548650 Score: 547
Period size: 161 Copynumber: 1.9 Consensus size: 163
2548329 AATAATTATC
2548339 CATTTTGACAAATCTTTTTTCTCTATAGTTATTGACAAATGCCATATTCATGAAATTGATGGCAA
1 CATTTTGACAAATCTTTTTTCTCTATAGTTATTGACAAATGCCATATTCATGAAATTGATGGCAA
* * * *
2548404 GTAAAGTAAGACACTCTATTTATTTTTAATTAAATACCTTTTACATGCTTTTGTAATTATAATAA
66 GCAAAGTAAGACACTCTATTTATTTTTAATTAAATACCCTATACATACTTTTGTAATTATAATAA
2548469 TAACTATACATGTGATGCTCATTGTCACATAAT
131 TAACTATACATGTGATGCTCATTGTCACATAAT
* *
2548502 CATTTTGACAAAT-TTTTTTCTCTATATTTATTGACAAATGCCATATTTATG-AATTGATGGCAA
1 CATTTTGACAAATCTTTTTTCTCTATAGTTATTGACAAATGCCATATTCATGAAATTGATGGCAA
2548565 GCAAAGTAAGACACTCTATTTATTTTTAATTAAATACCCTATACATACTTTTGTAATTATAATAA
66 GCAAAGTAAGACACTCTATTTATTTTTAATTAAATACCCTATACATACTTTTGTAATTATAATAA
*
2548630 TAAGTATACATGTGATGCTCA
131 TAACTATACATGTGATGCTCA
2548651 ACTAGCTTCA
Statistics
Matches: 142, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
161 93 0.65
162 36 0.25
163 13 0.09
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (163 bp):
CATTTTGACAAATCTTTTTTCTCTATAGTTATTGACAAATGCCATATTCATGAAATTGATGGCAA
GCAAAGTAAGACACTCTATTTATTTTTAATTAAATACCCTATACATACTTTTGTAATTATAATAA
TAACTATACATGTGATGCTCATTGTCACATAAT
Found at i:2553801 original size:1 final size:1
Alignment explanation
Indices: 2553795--2553824 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2553785 CATTAACGTT
*
2553795 GGGGGGGGGGGGGGGGGGGGGGGGNGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2553825 CGGTGCGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:2560678 original size:2 final size:2
Alignment explanation
Indices: 2560671--2560697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2560661 ATGATCGCCA
2560671 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2560698 GATAGGATAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2568863 original size:5 final size:5
Alignment explanation
Indices: 2568847--2568887 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
2568837 ACCCGGCTTC
2568847 TCTCT T-TCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TC
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TC
2568888 ATATGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTCT
Found at i:2574378 original size:21 final size:21
Alignment explanation
Indices: 2574339--2574387 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2574329 ACAAGAAATT
*
2574339 TATAAA-TATAATGTAATATA
1 TATAAATTAAAATGTAATATA
*
2574359 TATAAATTAAAATTTAATATA
1 TATAAATTAAAATGTAATATA
*
2574380 -AAAAATTA
1 TATAAATTA
2574388 TTATTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TATAAATTAAAATGTAATATA
Found at i:2576349 original size:29 final size:30
Alignment explanation
Indices: 2576316--2576383 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
2576306 CGTTCTTTGG
*
2576316 GAGATTATTTCGGATGATG-CCATCGACAA
1 GAGATTACTTCGGATGATGTCCATCGACAA
* * * *
2576345 GAGATTACTTCGGGTGATGTCGATCGTCCA
1 GAGATTACTTCGGATGATGTCCATCGACAA
2576375 GAGATTACT
1 GAGATTACT
2576384 CTGATCGATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (30 bp):
GAGATTACTTCGGATGATGTCCATCGACAA
Found at i:2577704 original size:20 final size:18
Alignment explanation
Indices: 2577676--2577718 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2577666 TTTATAATTC
*
2577676 ATAAGGAAGTAAATTATTTG
1 ATAAAGAAG-AAATTA-TTG
*
2577696 ATAAAGAAGATATTATTG
1 ATAAAGAAGAAATTATTG
2577714 ATAAA
1 ATAAA
2577719 TTGATATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (18 bp):
ATAAAGAAGAAATTATTG
Found at i:2578738 original size:20 final size:18
Alignment explanation
Indices: 2578698--2578767 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 18
2578688 TTATTATTAA
2578698 TTATTATTTTCATTT-TATT
1 TTATT-TTTT-ATTTCTATT
2578717 TTATTTTTTATTATCATATT
1 TTATTTTTTATT-TC-TATT
* *
2578737 TTCTATTTTATTTCTAATT
1 TTATTTTTTATTTCT-ATT
2578756 GTTATTTTTTAT
1 -TTATTTTTTAT
2578768 ACTTTACATT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 3 0.07
18 6 0.14
19 10 0.24
20 23 0.55
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.71
Consensus pattern (18 bp):
TTATTTTTTATTTCTATT
Found at i:2578883 original size:20 final size:20
Alignment explanation
Indices: 2578858--2578926 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 20
2578848 AGTGACAAAA
*
2578858 ATTTTATATTTTTTTATTTT
1 ATTTTATATTTTTATATTTT
2578878 ATTTTATATTTTTATATTTTGT
1 ATTTTATATTTTTATA-TTT-T
*
2578900 ATATATATATTTCTTATATTTCT
1 AT-TTTATATTT-TTATATTT-T
2578923 ATTT
1 ATTT
2578927 ATTTCACGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 15 0.37
21 3 0.07
22 4 0.10
23 14 0.34
24 5 0.12
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (20 bp):
ATTTTATATTTTTATATTTT
Found at i:2579259 original size:15 final size:14
Alignment explanation
Indices: 2579239--2579276 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2579229 TATTTTGTAT
*
2579239 TTTTTCTTTATTTA
1 TTTTTCTTTATATA
2579253 CTTTTTCTTTATATA
1 -TTTTTCTTTATATA
2579268 TTTTT-TTTA
1 TTTTTCTTTA
2579277 AGATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
15 13 0.59
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTCTTTATATA
Found at i:2579615 original size:14 final size:15
Alignment explanation
Indices: 2579589--2579620 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2579579 AGTTTTTATT
2579589 TTTATATTATATATA
1 TTTATATTATATATA
2579604 TTTATA-TATATATA
1 TTTATATTATATATA
2579618 TTT
1 TTT
2579621 GCATTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATATTATATATA
Found at i:2580246 original size:62 final size:62
Alignment explanation
Indices: 2580136--2580258 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
2580126 CTCTCCTTTC
**** *
2580136 TCTCTACCGCCTGCCAACTCCCTCTCTATCCTGCGTTGGCGTCATTTCTTCCCTCTTTACCT
1 TCTCTACCGCCTGCCAACTCCCTCTCTATCCTGCACCAGCGTCATTTCTTCCCTCTCTACCT
* *
2580198 TCTCTACCG-CTGGCCAACTCCCTCTCTATCCTGCACCAGTGTCCTTTCTTCCCTCTCTACC
1 TCTCTACCGCCT-GCCAACTCCCTCTCTATCCTGCACCAGCGTCATTTCTTCCCTCTCTACC
2580259 GCCAGCCAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
61 2 0.04
62 51 0.96
ACGTcount: A:0.11, C:0.44, G:0.11, T:0.35
Consensus pattern (62 bp):
TCTCTACCGCCTGCCAACTCCCTCTCTATCCTGCACCAGCGTCATTTCTTCCCTCTCTACCT
Found at i:2580295 original size:53 final size:54
Alignment explanation
Indices: 2580198--2580313 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 54
2580188 CTCTTTACCT
** * *
2580198 TCTCTACCGCTGGCCAACTCCCTCTCTATCCTGCACCAGTGTCCTT-TCTTCCC
1 TCTCTACCGCCAGCCAACTCCCTATCTATCCTGCACCAGCGTCCTTCTCTTCCC
* * *
2580251 TCTCTACCGCCAGCCAACTCCCTATCTATCCTGCGCC-GACGTCCTTCTTTTCCT
1 TCTCTACCGCCAGCCAACTCCCTATCTATCCTGCACCAG-CGTCCTTCTCTTCCC
2580305 TCTCTACCG
1 TCTCTACCG
2580314 TCGGTCGGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.02
53 39 0.72
54 14 0.26
ACGTcount: A:0.12, C:0.45, G:0.11, T:0.32
Consensus pattern (54 bp):
TCTCTACCGCCAGCCAACTCCCTATCTATCCTGCACCAGCGTCCTTCTCTTCCC
Found at i:2581077 original size:2 final size:2
Alignment explanation
Indices: 2581070--2581104 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2581060 TTTAGTGTCT
2581070 AC AC AC AC AC AC AC AC AC AC -C AC -C AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2581105 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2585171 original size:2 final size:2
Alignment explanation
Indices: 2585160--2585192 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2585150 CTGTTCTCGT
2585160 TC TC -C TC TC TC TC TC TC TC TC T- TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2585193 GTGGTTCGGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2585180 original size:17 final size:17
Alignment explanation
Indices: 2585160--2585192 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2585150 CTGTTCTCGT
2585160 TCTCCTCTCTCTCTCTC
1 TCTCCTCTCTCTCTCTC
*
2585177 TCTCTTCTCTCTCTCT
1 TCTCCTCTCTCTCTCT
2585193 GTGGTTCGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (17 bp):
TCTCCTCTCTCTCTCTC
Found at i:2595201 original size:16 final size:15
Alignment explanation
Indices: 2595175--2595204 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2595165 TTGAAGATTG
2595175 TTTTAATTTAATTTT
1 TTTTAATTTAATTTT
2595190 TTTTATATTTAATTT
1 TTTTA-ATTTAATTT
2595205 AAGACGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTAATTTAATTTT
Found at i:2599000 original size:12 final size:11
Alignment explanation
Indices: 2598985--2599019 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
2598975 TCTTCTGGAA
2598985 TTTCTTTCTTCT
1 TTTC-TTCTTCT
2598997 TTTCTTCTTCT
1 TTTCTTCTTCT
2599008 TCTTCTTCTTCT
1 T-TTCTTCTTCT
2599020 CGTTCCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTCTTCTTCT
Found at i:2599004 original size:3 final size:3
Alignment explanation
Indices: 2598990--2599019 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2598980 TGGAATTTCT
2598990 TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2599020 CGTTCCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:2600474 original size:19 final size:18
Alignment explanation
Indices: 2600452--2600506 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 18
2600442 TTTTAATTAA
2600452 AATTTTAAATAAATATATT
1 AATTTTAAATAAATAT-TT
*
2600471 AATTTTTAAAATAGATATTT
1 AA-TTTT-AAATAAATATTT
2600491 -ATTTTAAA-AAATATTT
1 AATTTTAAATAAATATTT
2600507 TTATTGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 4 0.12
19 3 0.09
20 6 0.19
21 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTTTAAATAAATATTT
Found at i:2600509 original size:18 final size:18
Alignment explanation
Indices: 2600453--2600511 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2600443 TTTAATTAAA
*
2600453 ATTTTAAATAAATATATTA
1 ATTTTAAA-AAATATATTT
* *
2600472 ATTTTTAAAATAGATATTT
1 A-TTTTAAAAAATATATTT
*
2600491 ATTTTAAAAAATATTTTT
1 ATTTTAAAAAATATATTT
2600509 ATT
1 ATT
2600512 GAATACATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 17 0.52
19 9 0.27
20 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTTAAAAAATATATTT
Found at i:2605661 original size:3 final size:3
Alignment explanation
Indices: 2605648--2605680 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2605638 GAGATAGAAT
2605648 ATC AT- ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
2605681 CTGACCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:2608518 original size:15 final size:16
Alignment explanation
Indices: 2608493--2608525 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2608483 TATTAAGAAG
2608493 AATTAATAATAAATTT
1 AATTAATAATAAATTT
*
2608509 AATT-ATAATATATTT
1 AATTAATAATAAATTT
2608524 AA
1 AA
2608526 AATATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATAATAAATTT
Found at i:2608529 original size:26 final size:25
Alignment explanation
Indices: 2608495--2608545 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
2608485 TTAAGAAGAA
2608495 TTAATAATAAATTTAATTATAATATAT
1 TTAATAATAAA-TTAATT-TAATATAT
* *
2608522 TTAA-AATATATTAATTTATTATAT
1 TTAATAATAAATTAATTTAATATAT
2608546 GTATGTATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 5 0.23
27 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAATAATAAATTAATTTAATATAT
Found at i:2608606 original size:18 final size:19
Alignment explanation
Indices: 2608580--2608617 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2608570 ACAATTTAAT
*
2608580 TTTAGTTATATATAT-TTA
1 TTTAGTTATAAATATGTTA
*
2608598 TTTATTTATAAATATGTTA
1 TTTAGTTATAAATATGTTA
2608617 T
1 T
2608618 AGTTATTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTAGTTATAAATATGTTA
Found at i:2608689 original size:2 final size:2
Alignment explanation
Indices: 2608684--2608743 Score: 56
Period size: 2 Copynumber: 31.5 Consensus size: 2
2608674 GTATAAACAT
* * *
2608684 TA TA TA TA TA TA TA TA TA TT TA -A TT TA TA CA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2608723 NT- TA TA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA T
2608744 TTAATTTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
1 4 0.09
2 42 0.89
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2608728 original size:41 final size:41
Alignment explanation
Indices: 2608682--2608769 Score: 160
Period size: 41 Copynumber: 2.1 Consensus size: 41
2608672 TTGTATAAAC
2608682 ATTATATATATATATATATATTTAATTTATACAT-AATATT
1 ATTATATATATATATATATATTTAATTTATACATAAATATT
2608722 ANTTATATATATATATATATATTTAATTTATACATAAATATT
1 A-TTATATATATATATATATATTTAATTTATACATAAATATT
2608764 ATTATA
1 ATTATA
2608770 ACTTATAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
40 1 0.02
41 38 0.83
42 7 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.51
Consensus pattern (41 bp):
ATTATATATATATATATATATTTAATTTATACATAAATATT
Found at i:2609023 original size:216 final size:216
Alignment explanation
Indices: 2608777--2609184 Score: 558
Period size: 216 Copynumber: 1.9 Consensus size: 216
2608767 ATAACTTATA
* * *
2608777 ATTTATATGATTACATTTAATAACTTTATTAATTGTCACCC-AAGTTTTTATAACATATTGTTTA
1 ATTTATATGATTACACTTAATAACTTTATTAATTATCACCCTAA-TTTTTATAACATATTATTTA
* * *
2608841 TAATTAGTTATTATTTATATAAACTTTGATATAAAACA-T-TA-TA-A-CTTATAAGTTGTGTCA
65 AAATTAGTTATTATTTATATAAACTTTGATATAAAA-ATTATATTATATCATATAAGTTATGTCA
*
2608901 TTAATTTCATATATACATAATAAAATAATATATTATATATATACATATACTTAATTTATACATAA
129 TTAATTTCAT-T-T--ATAATAAAATAATATATTATATATATACATATACTTAATCTATACATAA
2608966 GCAATATTGTAATTTATAATATACTTT
190 GCAATATTGTAATTTATAATATACTTT
* * *
2608993 ATTTATATGATTGCACTTAATAATTTTATTAGTTATCACCCTAATTTTTATAACATATTATTTAA
1 ATTTATATGATTACACTTAATAACTTTATTAATTATCACCCTAATTTTTATAACATATTATTTAA
*
2609058 AATTAGTTATTATTTATATAAACTTTGATATAAAAATTAAAATATTATATCATATAAGTTATTTC
66 AATTAGTTATTATTTATATAAACTTTGATATAAAAATT---ATATTATATCATATAAGTTATGTC
* * * *
2609123 ATTAATTTCATTTATAATAAAGTAATATATTATATATATACATTTATTTAATCTATCCATAA
128 ATTAATTTCATTTATAATAAAATAATATATTATATATATACATATACTTAATCTATACATAA
2609185 TTTGTATATA
Statistics
Matches: 168, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
215 1 0.01
216 91 0.54
217 2 0.01
219 44 0.26
220 2 0.01
221 3 0.02
222 2 0.01
223 23 0.14
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (216 bp):
ATTTATATGATTACACTTAATAACTTTATTAATTATCACCCTAATTTTTATAACATATTATTTAA
AATTAGTTATTATTTATATAAACTTTGATATAAAAATTATATTATATCATATAAGTTATGTCATT
AATTTCATTTATAATAAAATAATATATTATATATATACATATACTTAATCTATACATAAGCAATA
TTGTAATTTATAATATACTTT
Found at i:2613833 original size:3 final size:3
Alignment explanation
Indices: 2613825--2613868 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2613815 TTTTCTCATG
2613825 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2613869 TGTGAGCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2617076 original size:81 final size:79
Alignment explanation
Indices: 2616935--2617087 Score: 234
Period size: 81 Copynumber: 1.9 Consensus size: 79
2616925 TTTTTCTTAT
* * *
2616935 AGAGAAAACTCAAATTTTAAAATTATTTTTCTTATTTTTCTTTTTTCTTATAAAGTAAAAGATTC
1 AGAGAAAACTCAAATTTTAAAATTATTTTTCATATTTTTATTTTTTCTTATAAAGTAAAAGATGC
2617000 ATTGCTTAACTACA
66 ATTGCTTAACTACA
* * *
2617014 AGAGTAAACTCAAATTTTGAAATTATTTTTCATAGTTTTTTATTTTTTTTTATAAAGTAAAAGAT
1 AGAGAAAACTCAAATTTTAAAATTATTTTTCATA--TTTTTATTTTTTCTTATAAAGTAAAAGAT
2617079 GCATTGCTT
64 GCATTGCTT
2617088 TTAAAGAGTA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 31 0.47
81 35 0.53
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.47
Consensus pattern (79 bp):
AGAGAAAACTCAAATTTTAAAATTATTTTTCATATTTTTATTTTTTCTTATAAAGTAAAAGATGC
ATTGCTTAACTACA
Found at i:2620710 original size:19 final size:19
Alignment explanation
Indices: 2620667--2620710 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
2620657 ATATTTTATT
2620667 ATATTAAAAATATATAAAA
1 ATATTAAAAATATATAAAA
2620686 AT-TTAAAAA-ATATAAAA
1 ATATTAAAAATATATAAAA
2620703 ATAATTAA
1 AT-ATTAA
2620711 TAATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.43
18 7 0.30
19 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATTAAAAATATATAAAA
Found at i:2620715 original size:27 final size:27
Alignment explanation
Indices: 2620671--2620723 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2620661 TTTATTATAT
2620671 TAAAAATATATAAAAATTTAA-AAAATA
1 TAAAAATATATAAAAA-TTAATAAAATA
*
2620698 TAAAAATA-ATTAATAATTAATAAAAT
1 TAAAAATATA-TAAAAATTAATAAAAT
2620724 TATCTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
TAAAAATATATAAAAATTAATAAAATA
Found at i:2627913 original size:18 final size:18
Alignment explanation
Indices: 2627892--2627948 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 18
2627882 TTTAATTTTT
2627892 AATTATATTTTTATAAAA
1 AATTATATTTTTATAAAA
2627910 AATTATTAATTTTTA-AAATA
1 AATTA-T-ATTTTTATAAA-A
2627930 AA-TAT-TTTATT-TAAAA
1 AATTATATTT-TTATAAAA
2627946 AAT
1 AAT
2627949 ATTTTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
16 6 0.18
17 5 0.15
18 6 0.18
19 6 0.18
20 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTATATTTTTATAAAA
Found at i:2627935 original size:19 final size:21
Alignment explanation
Indices: 2627893--2627941 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2627883 TTAATTTTTA
2627893 ATTATATTTTTATAAAAAATT
1 ATTATATTTTTATAAAAAATT
2627914 ATTA-ATTTTTA-AAATAAA-T
1 ATTATATTTTTATAAA-AAATT
*
2627933 ATTTTATTT
1 ATTATATTT
2627942 AAAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.28
20 14 0.56
21 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATATTTTTATAAAAAATT
Found at i:2627955 original size:18 final size:18
Alignment explanation
Indices: 2627921--2627953 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2627911 ATTATTAATT
2627921 TTTAAAATAAATATTTTA
1 TTTAAAATAAATATTTTA
2627939 TTT-AAA-AAATATTTT
1 TTTAAAATAAATATTTT
2627954 TTTGTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
17 3 0.20
18 3 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTAAAATAAATATTTTA
Found at i:2629092 original size:21 final size:22
Alignment explanation
Indices: 2629068--2629122 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
2629058 NNNNNATTTA
*
2629068 AATTAGATAAACAA-TATTAAT
1 AATTAAATAAACAATTATTAAT
* *
2629089 AATTAAATCATCAATTATTAAT
1 AATTAAATAAACAATTATTAAT
*
2629111 ATTTTAAATAAA
1 A-ATTAAATAAA
2629123 TTACCAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 11 0.42
22 8 0.31
23 7 0.27
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (22 bp):
AATTAAATAAACAATTATTAAT
Found at i:2629218 original size:109 final size:111
Alignment explanation
Indices: 2629063--2629346 Score: 360
Period size: 114 Copynumber: 2.5 Consensus size: 111
2629053 NNNNNNNNNN
* * * *
2629063 ATTTAAATTAGATAAACAATATTAATAATTAAATCATCAATTATTAATATTTTAAATAAATTACC
1 ATTTAAATTAAAT-AA-AATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATAACC
*
2629128 AATTATTAATATTT-AA-AAAATAAAATATAA-AATTAATCATAATAAT
64 AATTATTAAT-TTTAAATAAAATAAAATAAAATAATTAATCATAATAAT
* *
2629174 ATTTAAATTAAATAAAATATTAATATTTAAATTATCTATTATTAATATTTTAAATAAATAATCAA
1 ATTTAAATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATAACCAA
* *
2629239 TTATTAATTTTCAAAAATAAAATAAAATAAAATAATTGATCATCATAAT
66 TTATTAATTTT---AAATAAAATAAAATAAAATAATTAATCATAATAAT
* * * * *
2629288 ATTTAAATAAAATAAAATATTAATATTTAAAATATAAATAATTAA-ATTATAAATAAATA
1 ATTTAAATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATA
2629347 TTAATATTAA
Statistics
Matches: 152, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
108 3 0.02
109 53 0.35
110 2 0.01
111 12 0.08
112 2 0.01
113 26 0.17
114 54 0.36
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (111 bp):
ATTTAAATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATAACCAA
TTATTAATTTTAAATAAAATAAAATAAAATAATTAATCATAATAAT
Found at i:2629320 original size:15 final size:14
Alignment explanation
Indices: 2629300--2629474 Score: 59
Period size: 15 Copynumber: 12.9 Consensus size: 14
2629290 TTAAATAAAA
2629300 TAAAATATTAATATT
1 TAAAATATTAATA-T
*
2629315 TAAAATATAAATAAT
1 TAAAATATTAAT-AT
*
2629330 TAAATTA-TAA-A-
1 TAAAATATTAATAT
2629341 T-AAATATTAATAT
1 TAAAATATTAATAT
*
2629354 TAAAATTATCAATTAT
1 TAAAA-TATTAA-TAT
* *
2629370 TAATATTTTAA-A-
1 TAAAATATTAATAT
* *
2629382 TAAATTATCAATTAT
1 TAAAATATTAA-TAT
* * * *
2629397 TAATATTTTAAAAA
1 TAAAATATTAATAT
*
2629411 TAAAATA--AAAAT
1 TAAAATATTAATAT
* *
2629423 TAATCATAATAATAT
1 TAA-AATATTAATAT
*
2629438 T-TAA-ATTAA-AT
1 TAAAATATTAATAT
2629449 T-AAATATTAATATT
1 TAAAATATTAATA-T
*
2629463 TAAATTATTAAT
1 TAAAATATTAAT
2629475 TATTCATATT
Statistics
Matches: 115, Mismatches: 28, Indels: 34
0.65 0.16 0.19
Matches are distributed among these distances:
10 4 0.03
11 9 0.08
12 25 0.22
13 7 0.06
14 14 0.12
15 48 0.42
16 8 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATATTAATAT
Found at i:2629331 original size:22 final size:20
Alignment explanation
Indices: 2629295--2629376 Score: 89
Period size: 22 Copynumber: 4.0 Consensus size: 20
2629285 AATATTTAAA
2629295 TAAAATA-AAATATTAATATT
1 TAAAATATAAATATTAATA-T
2629315 TAAAATATAAATAATTAA-AT
1 TAAAATATAAAT-ATTAATAT
*
2629335 TATAA-ATAAATATTAATAT
1 TAAAATATAAATATTAATAT
*
2629354 TAAAATTATCAATTATTAATAT
1 TAAAA-TAT-AAATATTAATAT
2629376 T
1 T
2629377 TTAAATAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.09
19 12 0.23
20 12 0.23
21 7 0.13
22 17 0.32
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATATAAATATTAATAT
Found at i:2629345 original size:19 final size:18
Alignment explanation
Indices: 2629295--2629359 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 18
2629285 AATATTTAAA
2629295 TAAAATAAAATATTAATATT
1 TAAAAT-AAATATTAATA-T
2629315 TAAAATATAAATAATTAA-AT
1 T-AAA-ATAAAT-ATTAATAT
2629335 TATAAATAAATATTAATAT
1 TA-AAATAAATATTAATAT
2629354 TAAAAT
1 TAAAAT
2629360 TATCAATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
18 9 0.22
19 11 0.28
20 5 0.12
21 8 0.20
22 7 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATAAATATTAATAT
Found at i:2629351 original size:40 final size:40
Alignment explanation
Indices: 2629285--2629386 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 40
2629275 TGATCATCAT
*
2629285 AATATTTAAA-TA-AAATAAAATATTAATATTTAAAA-TATA
1 AATAATTAAATTATAAAT-AAATATTAATA-TTAAAATTATA
*
2629324 AATAATTAAATTATAAATAAATATTAATATTAAAATTATC
1 AATAATTAAATTATAAATAAATATTAATATTAAAATTATA
* *
2629364 AATTATTAATATTTTAAATAAAT
1 AATAATTAA-ATTATAAATAAAT
2629387 TATCAATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
39 15 0.27
40 24 0.44
41 16 0.29
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (40 bp):
AATAATTAAATTATAAATAAATATTAATATTAAAATTATA
Found at i:2629371 original size:154 final size:147
Alignment explanation
Indices: 2629134--2629466 Score: 419
Period size: 154 Copynumber: 2.2 Consensus size: 147
2629124 TACCAATTAT
* * *
2629134 TAATATTT-AA-AAAATAAAATA-TAA-AATTAATCATAATAATATTTAAATTAAATAAAATATT
1 TAATATTTAAATAAAATAAAATATTAATATTTAA-AATAATAATAATTAAATTAAATAAAATATT
* *
2629195 AATATTTAAATTATCTATTATTAATATTTTAAATAAATAATCAATTATTAAT-TTTCAAAAATAA
65 AATATTAAAATTATCAATTATTAATATTTTAAATAAATAATCAATTATTAATATTT----AA-AA
* *
2629259 AATAAAATAAAATAATTGATCATCA
125 AATAAAAT-AAA-AATTAATCATAA
2629284 TAATATTTAAATAAAATAAAATATTAATATTTAAAAT-ATAAATAATTAAATTATAA-ATAAATA
1 TAATATTTAAATAAAATAAAATATTAATATTTAAAATAAT-AATAATTAAATTA-AATA-AAATA
* *
2629347 TTAATATTAAAATTATCAATTATTAATATTTTAAATAAATTATCAATTATTAATATTTTAAAAAT
63 TTAATATTAAAATTATCAATTATTAATATTTTAAATAAATAATCAATTATTAATATTTAAAAAAT
2629412 AAAATAAAAATTAATCATAA
128 AAAATAAAAATTAATCATAA
* *
2629432 TAATATTTAAATTAAATTAAATATTAATATTTAAA
1 TAATATTTAAATAAAATAAAATATTAATATTTAAA
2629467 TTATTAATTA
Statistics
Matches: 164, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
148 43 0.26
149 3 0.02
150 18 0.11
151 3 0.02
152 13 0.08
153 18 0.11
154 63 0.38
155 3 0.02
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (147 bp):
TAATATTTAAATAAAATAAAATATTAATATTTAAAATAATAATAATTAAATTAAATAAAATATTA
ATATTAAAATTATCAATTATTAATATTTTAAATAAATAATCAATTATTAATATTTAAAAAATAAA
ATAAAAATTAATCATAA
Found at i:2629392 original size:27 final size:26
Alignment explanation
Indices: 2629356--2629520 Score: 110
Period size: 27 Copynumber: 6.2 Consensus size: 26
2629346 ATTAATATTA
2629356 AAATTATCAATTATTAATATTTTAAAT
1 AAATTAT-AATTATTAATATTTTAAAT
2629383 AAATTATCAATTATTAATATTTTAAAAAT
1 AAATTAT-AATTATTAATATTTT--AAAT
* *
2629412 AAAATAAAAATTAATCATAATAATATTTAAATT
1 -AAATTATAATT-AT--TAAT-AT-TTTAAA-T
2629445 AAATTA-AA-TATTAATA-TTTAAAT
1 AAATTATAATTATTAATATTTTAAAT
* * *
2629468 -TA-T-TAATTATTCATATTTTAATT
1 AAATTATAATTATTAATATTTTAAAT
* *
2629491 AAATTCTAGATTATTAATA-TTTAAAA
1 AAATTATA-ATTATTAATATTTTAAAT
2629517 AAAT
1 AAAT
2629521 CTAATAAAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 33
0.72 0.06 0.21
Matches are distributed among these distances:
21 3 0.03
22 8 0.07
23 7 0.06
24 7 0.06
25 1 0.01
26 12 0.11
27 36 0.32
29 10 0.09
30 8 0.07
31 2 0.02
32 12 0.11
33 3 0.03
34 3 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.45
Consensus pattern (26 bp):
AAATTATAATTATTAATATTTTAAAT
Found at i:2629478 original size:22 final size:23
Alignment explanation
Indices: 2629432--2629515 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 23
2629422 TTAATCATAA
*
2629432 TAATATTTAAATTAAATTAAATAT
1 TAATATTTAAATT-AATTAATTAT
2629456 TAATATTTAAATT-ATTAATTAT
1 TAATATTTAAATTAATTAATTAT
* *
2629478 TCATATTTTAATTAAATTCTAGATTAT
1 TAATATTTAAATT-AA-T-TA-ATTAT
2629505 TAATATTTAAA
1 TAATATTTAAA
2629516 AAAATCTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 19 0.38
24 14 0.28
25 1 0.02
26 2 0.04
27 14 0.28
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (23 bp):
TAATATTTAAATTAATTAATTAT
Found at i:2652677 original size:2 final size:2
Alignment explanation
Indices: 2652670--2652761 Score: 94
Period size: 2 Copynumber: 44.5 Consensus size: 2
2652660 GCATAAATTA
* *
2652670 AT AT AT AT AA AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
2652713 TT TT GAG AG AT GNT 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
2652757 AT AT A
1 AT AT A
2652762 GTTTTTAGGG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
2 75 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2652681 original size:14 final size:15
Alignment explanation
Indices: 2652662--2652708 Score: 71
Period size: 14 Copynumber: 3.2 Consensus size: 15
2652652 ACTCAAGTGC
2652662 ATAAATTA-ATATAT
1 ATAAATTATATATAT
2652676 ATAAA-TATATATAT
1 ATAAATTATATATAT
2652690 ATAAATATATATATAT
1 ATAAAT-TATATATAT
2652706 ATA
1 ATA
2652709 TAGTTTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.07
14 16 0.53
16 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATTATATATAT
Found at i:2661015 original size:15 final size:15
Alignment explanation
Indices: 2660995--2661026 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2660985 CATTGATGAA
2660995 GATGAGGAGGAGGAG
1 GATGAGGAGGAGGAG
2661010 GATGAGGAGGAGGAG
1 GATGAGGAGGAGGAG
2661025 GA
1 GA
2661027 AGACGATGAA
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:0.34, C:0.00, G:0.59, T:0.06
Consensus pattern (15 bp):
GATGAGGAGGAGGAG
Found at i:2685465 original size:16 final size:17
Alignment explanation
Indices: 2685434--2685477 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2685424 GAAACAATTT
2685434 AATTTTTTTAATTTTAA
1 AATTTTTTTAATTTTAA
2685451 AATTTTTTTAA-TTTAA
1 AATTTTTTTAATTTTAA
**
2685467 TTTTTTTTTAA
1 AATTTTTTTAA
2685478 CGATATCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTTTTTAATTTTAA
Found at i:2685886 original size:2 final size:2
Alignment explanation
Indices: 2685879--2685918 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2685869 TAGTGTTAAA
2685879 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
2685919 TCTTACTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2687101 original size:30 final size:30
Alignment explanation
Indices: 2687025--2687111 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
2687015 ATATTTTTAA
*
2687025 ATATTTTTTTCAATTT-AGTCACTCGATATCTT
1 ATATTTTTTTCAATTTAATTC-CT--ATATCTT
* *
2687057 A-ATTTTGTTGAATTTAATTCCTATA-CTAT
1 ATATTTTTTTCAATTTAATTCCTATATCT-T
*
2687086 ATATTTTTTTCAATTTAATCCCTATA
1 ATATTTTTTTCAATTTAATTCCTATA
2687112 ACGTGATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 2 0.04
29 5 0.11
30 21 0.46
31 14 0.30
32 4 0.09
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.53
Consensus pattern (30 bp):
ATATTTTTTTCAATTTAATTCCTATATCTT
Found at i:2688732 original size:86 final size:84
Alignment explanation
Indices: 2688625--2688862 Score: 260
Period size: 86 Copynumber: 2.9 Consensus size: 84
2688615 AGCGTCCATA
* * * *
2688625 TTTATATTCTTTTCAGAATTTCTTTACTTGTTTATGAGATTAAAATACTCTATTTATTTATTTTT
1 TTTATACTCTTTTCAGGATTTC-TTA-TTGTTTATGAGATTGAAACACTCTATTTATTTATTTTT
** *
2688690 GAAATGCTTG-CTATGCTCACG
64 GAAACACTTGTC-ATGCCCACG
* *
2688711 TTTATACTCTTTTCAGGATTTCTCTATT-TATTCAGGAAATTGAAACACTCTATTTATTTATTTT
1 TTTATACTCTTTTCAGGATTTCT-TATTGT-TT-ATGAGATTGAAACACTCTATTTATTTATTTT
* *
2688775 CGAAACACTTGTCATGCCCATG
63 TGAAACACTTGTCATGCCCACG
2688797 TTTATACTCTTTTCA-GA------ATTGTTTATGAGATTGAAACACTCTATTTATTTATTTTTGA
1 TTTATACTCTTTTCAGGATTTCTTATTGTTTATGAGATTGAAACACTCTATTTATTTATTTTTGA
2688855 AACACTTG
66 AACACTTG
2688863 ATATAACATT
Statistics
Matches: 133, Mismatches: 14, Indels: 19
0.80 0.08 0.11
Matches are distributed among these distances:
77 39 0.29
78 5 0.04
79 1 0.01
84 1 0.01
85 7 0.05
86 79 0.59
87 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.48
Consensus pattern (84 bp):
TTTATACTCTTTTCAGGATTTCTTATTGTTTATGAGATTGAAACACTCTATTTATTTATTTTTGA
AACACTTGTCATGCCCACG
Found at i:2707400 original size:147 final size:147
Alignment explanation
Indices: 2707131--2707430 Score: 476
Period size: 147 Copynumber: 2.0 Consensus size: 147
2707121 TCTCACAATC
* * *
2707131 TTATTTTTCTCATTTCGTTTTCGTATAAATAGCTATTTAGATCTTACTGGTTTTACACCATTTGG
1 TTATTTTTCTCATTTCGTTTTCGCATAAATAGCCATTTAGATCCTACTGGTTTTACACCATTTGG
* * * *
2707196 TGTATAAACTACAAGTCTAAAAATTTCATGTTTTTCAGGTGAATTCAATTTCATTTTGATTGCGT
66 TGTATAAACTACAAGTCCAAAAAATTCACGTTTTTCAGATGAATTCAATTTCATTTTGATTGCGT
2707261 CTTTCCACATTAGCCAA
131 CTTTCCACATTAGCCAA
2707278 TTATTTTTCTCATTTCGTTTTCGCATAAATAGCCATTTAGATCCTACTGGTTTTACACCATTTGG
1 TTATTTTTCTCATTTCGTTTTCGCATAAATAGCCATTTAGATCCTACTGGTTTTACACCATTTGG
* * *
2707343 TGTATAGACTACAAGTCCAAAAAATTCACGTTTTGTTA-ATGAATTCAATTTCGTTTTGATTGCG
66 TGTATAAACTACAAGTCCAAAAAATTCACGTTTT-TCAGATGAATTCAATTTCATTTTGATTGCG
*
2707407 TCTTTCCATATTAGCCAA
130 TCTTTCCACATTAGCCAA
*
2707425 TCATTT
1 TTATTT
2707431 CTATGCTCCA
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
147 138 0.99
148 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.44
Consensus pattern (147 bp):
TTATTTTTCTCATTTCGTTTTCGCATAAATAGCCATTTAGATCCTACTGGTTTTACACCATTTGG
TGTATAAACTACAAGTCCAAAAAATTCACGTTTTTCAGATGAATTCAATTTCATTTTGATTGCGT
CTTTCCACATTAGCCAA
Found at i:2709669 original size:27 final size:27
Alignment explanation
Indices: 2709630--2709738 Score: 130
Period size: 27 Copynumber: 4.0 Consensus size: 27
2709620 GGTTAAGGTA
* * *
2709630 TCTATCCAATTCTAATAGATAAAGTTC
1 TCTATCCACTTCTAGTGGATAAAGTTC
*
2709657 TCTATCCACTTCTAGTGGATAAAGTTA
1 TCTATCCACTTCTAGTGGATAAAGTTC
* *
2709684 TCTATCCATTTCTTGTGGATAAAGTTC
1 TCTATCCACTTCTAGTGGATAAAGTTC
* *
2709711 T-TCATCCACTTCTGGTGGGTAAAGTTC
1 TCT-ATCCACTTCTAGTGGATAAAGTTC
2709738 T
1 T
2709739 TCATCTACTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 70 0.99
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (27 bp):
TCTATCCACTTCTAGTGGATAAAGTTC
Found at i:2709710 original size:54 final size:54
Alignment explanation
Indices: 2709628--2709736 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
2709618 TGGGTTAAGG
2709628 TATCTATCCAATTCTAATAGATAAAGTTC-TCTATCCACTTCTAGTGGATAAAGT
1 TATCTATCCAATTCTAATAGATAAAGTTCTTC-ATCCACTTCTAGTGGATAAAGT
* ** * * *
2709682 TATCTATCCATTTCTTGTGGATAAAGTTCTTCATCCACTTCTGGTGGGTAAAGT
1 TATCTATCCAATTCTAATAGATAAAGTTCTTCATCCACTTCTAGTGGATAAAGT
2709736 T
1 T
2709737 CTTCATCTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 46 0.96
55 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (54 bp):
TATCTATCCAATTCTAATAGATAAAGTTCTTCATCCACTTCTAGTGGATAAAGT
Found at i:2709739 original size:27 final size:28
Alignment explanation
Indices: 2709647--2709763 Score: 134
Period size: 27 Copynumber: 4.3 Consensus size: 28
2709637 AATTCTAATA
*
2709647 GATAAAGTTC-TCTATCCACTTCTAGTG
1 GATAAAGTTCTTCTATCCACTTCTGGTG
* * *
2709674 GATAAAGTT-ATCTATCCATTTCTTGTG
1 GATAAAGTTCTTCTATCCACTTCTGGTG
2709701 GATAAAGTTCTTC-ATCCACTTCTGGTG
1 GATAAAGTTCTTCTATCCACTTCTGGTG
* * * *
2709728 GGTAAAGTTCTTC-ATCTACTTATGGTA
1 GATAAAGTTCTTCTATCCACTTCTGGTG
2709755 GATAAAGTT
1 GATAAAGTT
2709764 ATCAATGATA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 76 0.97
28 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (28 bp):
GATAAAGTTCTTCTATCCACTTCTGGTG
Found at i:2711484 original size:19 final size:18
Alignment explanation
Indices: 2711462--2711504 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
2711452 TATGTAAATT
*
2711462 AAATAAATATTCAGTTATA
1 AAATAAATATTCAATTA-A
2711481 AAATAAATATTCAATTAA
1 AAATAAATATTCAATTAA
2711499 AAATAA
1 AAATAA
2711505 TAATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATAAATATTCAATTAA
Found at i:2711506 original size:17 final size:17
Alignment explanation
Indices: 2711444--2711506 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
2711434 TTAGGTAGAT
*
2711444 AAAATATATATGTAAATTA
1 AAAATA-ATAT-TCAATTA
* *
2711463 AATA-AATATTCAGTTA
1 AAAATAATATTCAATTA
2711479 TAAAATAAATATTCAATTA
1 -AAAAT-AATATTCAATTA
2711498 AAAATAATA
1 AAAATAATA
2711507 ATAATAATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
16 5 0.14
17 11 0.31
18 6 0.17
19 14 0.39
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATAATATTCAATTA
Found at i:2711515 original size:26 final size:27
Alignment explanation
Indices: 2711478--2711531 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
2711468 ATATTCAGTT
*
2711478 ATAAAATAAATATTCAATTAAAA-ATA
1 ATAAAATAAATAGTCAATTAAAATATA
2711504 ATAATAAT-AATAGTCAATTAAAATATA
1 ATAA-AATAAATAGTCAATTAAAATATA
2711531 A
1 A
2711532 AGAATAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (27 bp):
ATAAAATAAATAGTCAATTAAAATATA
Done.