Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 8 of 230
Found at i:2481211 original size:30 final size:29
Alignment explanation
Indices: 2481177--2481245 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
2481167 ATTAGACCTG
*
2481177 AATTTTGAAATCTGAAAAGTA-AAGAGACTA
1 AATTTTGAAATAT-AAAAGTATAAGAG-CTA
*
2481207 AATTTTTGAAA-ATAAAAGTATATGAGCTA
1 AA-TTTTGAAATATAAAAGTATAAGAGCTA
2481236 AATTTT-AAAT
1 AATTTTGAAAT
2481246 TTGTAAAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 3 0.09
28 4 0.12
29 12 0.35
30 7 0.21
31 8 0.24
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (29 bp):
AATTTTGAAATATAAAAGTATAAGAGCTA
Found at i:2483990 original size:21 final size:21
Alignment explanation
Indices: 2483961--2484002 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2483951 TTCAAGTTTT
2483961 TGTTCTTGAGGTCTAGAGACA
1 TGTTCTTGAGGTCTAGAGACA
* * *
2483982 TGTTTTTGATGTCTCGAGACA
1 TGTTCTTGAGGTCTAGAGACA
2484003 CATGTCCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
TGTTCTTGAGGTCTAGAGACA
Found at i:2494998 original size:91 final size:91
Alignment explanation
Indices: 2494875--2495082 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
2494865 CTGATTTTAG
* *
2494875 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
2494940 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
2494967 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
2495032 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
2495058 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
2495083 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:2495051 original size:26 final size:28
Alignment explanation
Indices: 2494997--2495057 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2494987 TATTATCAAG
* *
2494997 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
2495025 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
2495051 AATTATA
1 AATTATA
2495058 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:2495057 original size:44 final size:43
Alignment explanation
Indices: 2494915--2495057 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
2494905 GAATTTTATG
* *
2494915 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
2494959 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
2495006 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
2495050 AAATTATA
1 AAATTATA
2495058 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:2495175 original size:59 final size:57
Alignment explanation
Indices: 2495109--2495297 Score: 161
Period size: 59 Copynumber: 3.2 Consensus size: 57
2495099 ATTTTATTAA
2495109 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** *
2495168 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTATAAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATT-TAAATTATTTTTATAGT
* * * *
2495229 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
2495288 ATCATATATT
1 ATCATATATT
2495298 ATGATTTCAG
Statistics
Matches: 101, Mismatches: 15, Indels: 28
0.70 0.10 0.19
Matches are distributed among these distances:
54 16 0.16
55 6 0.06
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 5 0.05
66 18 0.18
67 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:2495206 original size:66 final size:63
Alignment explanation
Indices: 2495136--2495334 Score: 184
Period size: 66 Copynumber: 3.2 Consensus size: 63
2495126 AAATATATTT
2495136 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
2495201 G
63 G
* * * * **
2495202 AATATTAATTATTATAAATT-TTATTA-A--ATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATT-TAAATTATTTTTATAGTATCATATATTATGATTTAGTAAATTCATATAAG
* *
2495256 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
2495321 G
63 G
*
2495322 AATATTGATTATT
1 AATATTAATTATT
2495335 AAGAATTTTA
Statistics
Matches: 103, Mismatches: 16, Indels: 29
0.70 0.11 0.20
Matches are distributed among these distances:
54 16 0.16
55 6 0.06
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 6 0.06
66 28 0.27
67 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTAGTAAATTCATATAAG
Found at i:2495220 original size:120 final size:120
Alignment explanation
Indices: 2495087--2495396 Score: 498
Period size: 120 Copynumber: 2.6 Consensus size: 120
2495077 TTATTAGTTA
* * * *
2495087 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTC
1 TAATTATTATAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-
* *
2495151 AAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
65 AAATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
2495207 TAATTATTATAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
1 TAATTATTATAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
*
2495272 ATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
66 AATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
*
2495327 TGATTATTA-AGAATTTTATTATAATTATATATTTTAATTATAATATATTTAATAATAATTATGT
1 TAATTATTATA-AATTTTATTA-AATTATATATTTTAATTATAATATATTTAATAATAATTATG-
2495391 TTAAAT
63 TTAAAT
2495397 ATGATTAAAT
Statistics
Matches: 177, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
119 1 0.01
120 128 0.72
121 43 0.24
122 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (120 bp):
TAATTATTATAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
AATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
Found at i:2495258 original size:15 final size:15
Alignment explanation
Indices: 2495223--2495274 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2495213 TTATAAATTT
*
2495223 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2495237 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2495251 TATTTAATAATAAT-
1 TATTTAATTATAATA
2495265 TATGTTAATT
1 TAT-TTAATT
2495275 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2495360 original size:18 final size:18
Alignment explanation
Indices: 2495339--2495374 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2495329 ATTATTAAGA
2495339 ATTTT-ATTATAATTATAT
1 ATTTTAATTATAA-TATAT
2495357 ATTTTAATTATAATATAT
1 ATTTTAATTATAATATAT
2495375 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTAATTATAATATAT
Found at i:2495364 original size:13 final size:14
Alignment explanation
Indices: 2495343--2495385 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2495333 TTAAGAATTT
*
2495343 TATTATAATTAT-A
1 TATTTTAATTATAA
2495356 TATTTTAATTATAA
1 TATTTTAATTATAA
*
2495370 TATATTTAATAATAA
1 TAT-TTTAATTATAA
2495385 T
1 T
2495386 TATGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTTAATTATAA
Found at i:2495374 original size:16 final size:16
Alignment explanation
Indices: 2495347--2495394 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2495337 GAATTTTATT
*
2495347 ATAATTATATATTTTA
1 ATAATAATATATTTTA
*
2495363 ATTATAATATA-TTTA
1 ATAATAATATATTTTA
2495378 ATAATAAT-TATGTTTA
1 ATAATAATATAT-TTTA
2495394 A
1 A
2495395 ATATGATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATAATAATATATTTTA
Found at i:2495379 original size:15 final size:15
Alignment explanation
Indices: 2495343--2495385 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2495333 TTAAGAATTT
2495343 TATTATAATTAT-ATA
1 TATT-TAATTATAATA
2495358 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2495372 TATTTAATAATAAT
1 TATTTAATTATAAT
2495386 TATGTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2495650 original size:16 final size:16
Alignment explanation
Indices: 2495608--2495653 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
2495598 TTGATTTGAT
2495608 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
2495624 ATTAAATCTCTATTCC
1 ATTACACCTCTATTCC
*
2495640 ATTACGCCTCTATT
1 ATTACACCTCTATT
2495654 ACAATACAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:2496273 original size:112 final size:111
Alignment explanation
Indices: 2496077--2496298 Score: 340
Period size: 112 Copynumber: 2.0 Consensus size: 111
2496067 TATTCTGTTA
* * *
2496077 AATTAGGGTTACATGTGACTGGATTTGGGGGAATTTTTTTAATTTCTGCTGGGTTTAAGGTTTCT
1 AATTAGGGTTACAGGTGACTGGATTTGGGGAAATTTTTTTAATTTCTGCTAGGTTTAAGGTTTCT
2496142 AAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
66 AAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
* * *
2496188 AATTAGGGTTACAGGTGACTGTCGATTT-GGGAAATTTTTTTACTTTCTGTTAGGTTTAGGGTTT
1 AATTAGGGTTACAGGTGACTG--GATTTGGGGAAATTTTTTTAATTTCTGCTAGGTTTAAGGTTT
*
2496252 CTAAG-CTTCTTTGTTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
64 CTAAGTC-TCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
2496299 TTAGAGCTGT
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
111 21 0.21
112 75 0.74
113 5 0.05
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.45
Consensus pattern (111 bp):
AATTAGGGTTACAGGTGACTGGATTTGGGGAAATTTTTTTAATTTCTGCTAGGTTTAAGGTTTCT
AAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
Found at i:2498598 original size:16 final size:16
Alignment explanation
Indices: 2498577--2498645 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
2498567 TTTGGTTCGC
2498577 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2498593 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2498609 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
2498626 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2498642 TGTA
1 TGTA
2498646 ATAGCAAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:2498623 original size:33 final size:32
Alignment explanation
Indices: 2498577--2498645 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
2498567 TTTGGTTCGC
2498577 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
2498609 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
2498642 TGTA
1 TGTA
2498646 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:2498901 original size:16 final size:16
Alignment explanation
Indices: 2498861--2498915 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
2498851 TTAATCATAT
*
2498861 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
2498877 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
2498892 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
2498910 -TAAAAT
1 TTAAAAT
2498916 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:2498908 original size:18 final size:17
Alignment explanation
Indices: 2498881--2498915 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2498871 TTTTTATTAA
*
2498881 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2498899 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2498916 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2499025 original size:120 final size:114
Alignment explanation
Indices: 2498829--2499516 Score: 672
Period size: 120 Copynumber: 5.8 Consensus size: 114
2498819 TAATAAGATT
* * *
2498829 ATTATTATCAATAATAAATAATTT--AATCAT-ATTTAAACATAATTTTTATTAAATATATTTTA
1 ATTATTAT-AACAATAAATAATTTAAAAT-ATAATTTAAA-ATAATTATTATTAAATATAATTTA
* * *
2498891 ATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATT-TGT-TTTGGTAA
63 ATAAAAATATATAATTTAATAAAATTCTTAAT-ATTA--A-ATATTCT-TATAT-G-AA
* *
2498948 ATTATTATTAACAATAAATAATTTAAAAGATAATTTAACATAATTATTATTAAATATAATTTAAT
1 ATTATTA-TAACAATAAATAATTTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
2499013 AAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
65 AAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
* * * * *
2499063 TTTAATAAAATTATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAATATAAT
1 ATT-AT--TATAACAATAAATAAT--T-TAAAATATAATTTAAAATAATTATTATTAAATATAAT
* *
2499128 TTAATAGAAATATATAATTTAATAAAATTCTTAATATTTAAATATTCTTAAATGAA
60 TTAATAAAAATATATAATTTAATAAAATTCTTAATA-TTAAATATTCTTATATGAA
* * * *
2499184 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAATATAAT
1 ATTATTATAA-C--AATAAATAAT--T-TAAAATATAATTTAAAATAATTATTATTAAATATAAT
* *
2499249 TTAACAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAA
60 TTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
* * * *
2499304 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAAATATA
1 ATTATTATAA-C--AATAAATAAT--T-TAAAATATAATTTAAAATAATTATTATT--AAATATA
*
2499369 ATTTAGTAAAAATATATAATTTAATAAAATTCTTTAATATTAAATATTC-T-TA-GAA
58 ATTTAATAAAAATATATAATTTAATAAAATTC-TTAATATTAAATATTCTTATATGAA
* * * * * *
2499424 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAATTAATTATTTTTAAATATAAT
1 ATTATTATAA-C--AATAAATAAT--T-TAAAATATAATTTAAAATAATTATTATTAAATATAAT
*
2499489 TTAATAAAAATATATAATTTAATCAAAT
60 TTAATAAAAATATATAATTTAATAAAAT
2499517 CATTATATTC
Statistics
Matches: 519, Mismatches: 31, Indels: 39
0.88 0.05 0.07
Matches are distributed among these distances:
115 4 0.01
116 8 0.02
117 15 0.03
118 38 0.07
119 26 0.05
120 259 0.50
121 115 0.22
122 38 0.07
123 16 0.03
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (114 bp):
ATTATTATAACAATAAATAATTTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATA
AAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
Found at i:2499076 original size:19 final size:18
Alignment explanation
Indices: 2499001--2499156 Score: 77
Period size: 18 Copynumber: 8.0 Consensus size: 18
2498991 TTATTATTAA
*
2499001 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAATT
2499019 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
* ***
2499037 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAATT
2499056 ATATGAATTTAATAAAATT
1 ATAT-AATTTAATAAAATT
* *
2499075 ATA-ATATATAATACTATAA-A
1 ATATA-ATTTAATA--A-AATT
2499095 ATATAATTTAAAATAATTATTATT
1 ATATAATTT--AATAA--A--ATT
2499119 AAATATAATTTAATAGAAA-T
1 --ATATAATTTAATA-AAATT
2499139 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
2499157 CTTAATATTT
Statistics
Matches: 106, Mismatches: 13, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
17 8 0.08
18 41 0.39
19 16 0.15
20 12 0.11
21 9 0.08
22 4 0.04
23 2 0.02
24 4 0.04
25 1 0.01
26 9 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAATT
Found at i:2499109 original size:22 final size:23
Alignment explanation
Indices: 2499067--2499109 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2499057 TATGAATTTA
*
2499067 ATAAAATTATAATATATAATACT
1 ATAAAATTATAATATAAAATACT
*
2499090 ATAAAA-TATAATTTAAAATA
1 ATAAAATTATAATATAAAATA
2499110 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAATTATAATATAAAATACT
Found at i:2499282 original size:241 final size:239
Alignment explanation
Indices: 2498971--2499516 Score: 934
Period size: 241 Copynumber: 2.3 Consensus size: 239
2498961 ATAAATAATT
* *
2498971 TAAAAGATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
* *
2499036 TCTTAATATTAAATATTCTTATATGAATTTAATAAAATTATAATATATAATACTATAAAATATAA
66 TCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
*
2499101 TTTAAAATAATTATTATT-AAATATAATTTAATAGAAATATATAATTTAATAAAATTC-TTAATA
131 TTTAAAATAATTATTATTAAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTTAATA
2499164 TTTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
196 -TTAAATATTCTT--A-GAATTTACTAAAATCATAATATATAATACTA
*
2499212 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
*
2499277 TCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 TCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
*
2499342 TTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATATAATTTAATAAAATTCTTTAAT
131 TTTAAAATAATTATTATT-AAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTTAAT
2499407 ATTAAATATTCTTAGAATTTACTAAAATCATAATATATAATACTA
195 ATTAAATATTCTTAGAATTTACTAAAATCATAATATATAATACTA
* * *
2499452 TAAAATATAATTTAAATTAATTATTTTTAAATATAATTTAATAAAAATATATAATTTAATCAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
2499517 CATTATATTC
Statistics
Matches: 290, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
240 92 0.32
241 143 0.49
243 49 0.17
244 6 0.02
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (239 bp):
TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
TCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
TTTAAAATAATTATTATTAAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTTAATA
TTAAATATTCTTAGAATTTACTAAAATCATAATATATAATACTA
Found at i:2499379 original size:15 final size:16
Alignment explanation
Indices: 2499333--2499397 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 16
2499323 ATAATACTAT
2499333 AAAATATAATTTAA-A
1 AAAATATAATTTAATA
* *
2499348 ATAAT-T-A-TTATTA
1 AAAATATAATTTAATA
*
2499361 AAAATATAATTTAGTAA
1 AAAATATAATTTAAT-A
2499378 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
2499395 AAA
1 AAA
2499398 TTCTTTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 2 0.05
15 5 0.13
16 4 0.10
17 8 0.21
18 11 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:2499385 original size:18 final size:17
Alignment explanation
Indices: 2499360--2499397 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2499350 AATTATTATT
*
2499360 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
2499377 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
2499395 AAA
1 AAA
2499398 TTCTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:2504104 original size:159 final size:160
Alignment explanation
Indices: 2503784--2504297 Score: 603
Period size: 159 Copynumber: 3.2 Consensus size: 160
2503774 TGTTCTTTGG
* * * * *
2503784 CTTGCTGCTCTAGTGATCCTCATATAATATTTTATCTTAGCCAT-GATTGTAAATCATAATCCTT
1 CTTGCTGGTCTAGTGAACCTCATATAAT-TTTTATCATAGCC-TGGATTGTTAATCATACTCCTT
* *** * * * *
2503848 CATCAAATTATACCCAGTGAAGCTTCTTCTTTATCGTCTCCTTTCAAAGCTTTT-TTTATTGCCT
64 CATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCTTTTCTTTATTGCCT
* * * *
2503912 TAGAATTTTTATGTT-TGTCATGTTATTTATGA
129 TAGAATTTATATGTTCTATCATATT-GTTATGA
* *
2503944 CTTTCTGGTCTAGTGAACCTCATATAATTTTTATAATAGCCTGGATTGTTAATCATACTCCTTCA
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTATCATAGCCTGGATTGTTAATCATACTCCTTCA
* * * *
2504009 TTAAAGTATACTTTTTGAAGCTTTTTCTTTATTGCCTCCGTTT-GAAGCTTTTCTTTCTTGCCTT
66 TCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCC-TTTCGAAGCTTTTCTTTATTGCCTT
2504073 AGAATTTATATGTTCTATCATATTGTT-TGA
130 AGAATTTATATGTTCTATCATATTGTTATGA
* ** * * *
2504103 CTTGCTGATCTAGTTTACCTCAGATAATTTTTATCATAGCCAGGATT-TTAGTCATACT-CTGTC
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTATCATAGCCTGGATTGTTAATCATACTCCT-TC
*
2504166 ATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCGTTTCTTTATTGCCTT
65 ATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCTTTTCTTTATTGCCTT
*
2504231 AGAATTTATATTTTCTATCATATTGTTTATGA
130 AGAATTTATATGTTCTATCATATTG-TTATGA
* * *
2504263 CTTGCT-GTCTAGCGAACCACATATATATATTTATC
1 CTTGCTGGTCTAGTGAACCTCATATA-ATTTTTATC
2504298 TTAATTCTTA
Statistics
Matches: 302, Mismatches: 43, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
157 5 0.02
158 93 0.31
159 127 0.42
160 70 0.23
161 7 0.02
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (160 bp):
CTTGCTGGTCTAGTGAACCTCATATAATTTTTATCATAGCCTGGATTGTTAATCATACTCCTTCA
TCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCTTTTCTTTATTGCCTTA
GAATTTATATGTTCTATCATATTGTTATGA
Found at i:2532283 original size:160 final size:160
Alignment explanation
Indices: 2531985--2532582 Score: 604
Period size: 160 Copynumber: 3.7 Consensus size: 160
2531975 AGTTAACTTT
* ** * *
2531985 GAAAGGAGACAATAAAG-AAAAGCTCCATTAGGCATACTTTGATG-A--AGTATGATCAACAATC
1 GAAAGGAGACAATAAAGAAAAAGCTTCAAAAGGTATACTTTGATGAAGGAGTATGATTAACAATC
** * * * *
2532046 CCAGCTAAGAATTAAGATAAATATATATATGTGGTTCGCTAGACAGCAAGTCATAAACAATATGA
66 CTGGCTATG-A-T-A-A-AAA-AT-TATATGAGGTACACTAGACAGCAAGTCA-AAACAATATGA
* *
2532111 TAGAAAATATAAATTCTAAGGCAATAAAGAAACGCTTC
123 TAGAACATATAAATTCTAAGGCAATAAAGAAAAGCTTC
* * *
2532149 GAAAGGAGTCAATAAAGAAAAAGCTTCAAAAGGTATACTTTGATGACA-GAGTATGACTAAAAAT
1 GAAAGGAGACAATAAAGAAAAAGCTTCAAAAGGTATACTTTGATGA-AGGAGTATGATTAACAAT
* *
2532213 CCTGGCTATGATAAAAAATTATCTGAGGTAAACTAGATCAGCAAGTC-AAACAATATGATAGAAC
65 CCTGGCTATGATAAAAAATTATATGAGGTACACTAGA-CAGCAAGTCAAAACAATATGATAGAAC
*
2532277 ATATAAATTCTAAGGCAAGAAAGAAAAGCTTC
129 ATATAAATTCTAAGGCAATAAAGAAAAGCTTC
* * *
2532309 -AAACGGAGGCAATAAAGAAAAAGCTTCAAAAAGTATACTTTAATGAAGGAGTATGATTAACAAT
1 GAAA-GGAGACAATAAAGAAAAAGCTTCAAAAGGTATACTTTGATGAAGGAGTATGATTAACAAT
* * * * * * *
2532373 CCAGGCTATTATAAAAAATTATATGAGGTTCACTAGACCAGAAAGTCATAAATAACATGACA-AA
65 CCTGGCTATGATAAAAAATTATATGAGGTACACTAGA-CAGCAAGTCA-AAACAATATGATAGAA
* *
2532437 CATAAAAATTCTAAGGCAATAAA-AAAAGCTTT
128 CATATAAATTCTAAGGCAATAAAGAAAAGCTTC
* * *** * * *
2532469 GAAAGGAGACGATAAAGAAGAAGCTTCACTGGGTATAATTTGATGAAGGATTATGATTTACAATC
1 GAAAGGAGACAATAAAGAAAAAGCTTCAAAAGGTATACTTTGATGAAGGAGTATGATTAACAATC
* * * *
2532534 ATGGCTAAGATAAAATATTATATGAGG-ATCACTAGAGCAGCAAGCCAAA
66 CTGGCTATGATAAAAAATTATATGAGGTA-CACTAGA-CAGCAAGTCAAA
2532583 GAACAACATG
Statistics
Matches: 366, Mismatches: 57, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
159 6 0.02
160 234 0.64
161 39 0.11
162 21 0.06
163 3 0.01
164 17 0.05
165 24 0.07
166 1 0.00
167 2 0.01
168 19 0.05
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (160 bp):
GAAAGGAGACAATAAAGAAAAAGCTTCAAAAGGTATACTTTGATGAAGGAGTATGATTAACAATC
CTGGCTATGATAAAAAATTATATGAGGTACACTAGACAGCAAGTCAAAACAATATGATAGAACAT
ATAAATTCTAAGGCAATAAAGAAAAGCTTC
Found at i:2536985 original size:18 final size:17
Alignment explanation
Indices: 2536964--2537001 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2536954 TATTAAAGAA
*
2536964 TTTTATTAAATTATATAT
1 TTTTACTAAATTATAT-T
2536982 TTTTACTAAATTATATT
1 TTTTACTAAATTATATT
2536999 TTT
1 TTT
2537002 AATAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTACTAAATTATATT
Found at i:2537026 original size:120 final size:118
Alignment explanation
Indices: 2536845--2537496 Score: 871
Period size: 120 Copynumber: 5.5 Consensus size: 118
2536835 GAATATAATG
* * *
2536845 ATTTGATTAAATTATATATTTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATATTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
2536910 TAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTAATATTAAAGA
66 TAGTATTATATATTATGATTTTAGTAAATTCTTAAGAATATTTAATATT-AAGA
*
2536963 ATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTTTAAATTATATTT
1 ATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTTAAATTATATTT
2537028 TATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGA
64 TATAGTATTATATATTATGATTTTAGTAAATTC--TTAAGAATATTTAATATTAAGA
*
2537085 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
2537150 TAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAAATATTAAGA
66 TAGTATTATATATTATGATTTTAGTAAATTC--TTAAGAATATTT-AATATTAAGA
*
2537206 ATTTTATT-AATTATATATTTCTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
* *
2537270 TAGTATTATATATTATAATTTTATTAAATTCATATAAGAATATTTAATATTAAGA
66 TAGTATTATATATTATGATTTTAGTAAATTC-T-TAAGAATATTTAATATTAAGA
* *
2537325 ATTTTATTAAATTATATATTTTTATT-AATTATATTT-ATAATAATTATGTT-AATTATCTTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
* * * ** * *
2537387 -ATTATT-TATTGTTAATAATAATTTACCAAA-AC---A-AATTTCTGCTAATTATTAAGA
66 TAGTATTATA-TATT-ATGAT--TTTAGTAAATTCTTAAGAATAT-T--TAA-TATTAAGA
* *
2537441 ATTTTATTAAATTATATATTTTAATTAAA-TATATTTAATAAAAATTATGTTTAAAT
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT-TTTAAAT
2537497 ATGATTAAAT
Statistics
Matches: 491, Mismatches: 23, Indels: 39
0.89 0.04 0.07
Matches are distributed among these distances:
112 4 0.01
113 2 0.00
115 5 0.01
116 48 0.10
117 28 0.06
118 48 0.10
119 39 0.08
120 246 0.50
121 18 0.04
122 36 0.07
123 17 0.03
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (118 bp):
ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
TAGTATTATATATTATGATTTTAGTAAATTCTTAAGAATATTTAATATTAAGA
Found at i:2537232 original size:17 final size:17
Alignment explanation
Indices: 2537206--2537358 Score: 56
Period size: 17 Copynumber: 9.0 Consensus size: 17
2537196 AATATTAAGA
2537206 ATTTTATT-AATTATAT
1 ATTTTATTAAATTATAT
2537222 ATTTCTATTAAA-T-TAT
1 ATTT-TATTAAATTATAT
* *
2537238 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
2537252 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* *
2537271 AGTATTA-TATATTATA-
1 A-TTTTATTAAATTATAT
2537287 ATTTTATTAAATTCATAT
1 ATTTTATTAAATT-ATAT
*** *
2537305 AAGAATATTTAATATTA-AGA
1 -ATTTTA-TTAA-ATTATA-T
2537325 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
2537342 ATTTTTATT-AATTATAT
1 A-TTTTATTAAATTATAT
2537359 TTATAATAAT
Statistics
Matches: 100, Mismatches: 18, Indels: 37
0.65 0.12 0.24
Matches are distributed among these distances:
13 2 0.02
14 5 0.05
15 10 0.10
16 14 0.14
17 31 0.31
18 18 0.18
19 9 0.09
20 8 0.08
21 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:2537237 original size:18 final size:16
Alignment explanation
Indices: 2537206--2537283 Score: 53
Period size: 15 Copynumber: 5.2 Consensus size: 16
2537196 AATATTAAGA
2537206 ATTTTATTAATTATAT
1 ATTTTATTAATTATAT
*
2537222 ATTTCTATTAAAT-TAT
1 ATTT-TATTAATTATAT
* *
2537238 A-TTTAATAATAAT-T
1 ATTTTATTAATTATAT
2537252 ATTTTA--AATTATAT
1 ATTTTATTAATTATAT
*
2537266 -TTTATAGT-ATTATAT
1 ATTT-TATTAATTATAT
2537281 ATT
1 ATT
2537284 ATAATTTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 8 0.16
14 10 0.20
15 14 0.29
16 10 0.20
17 7 0.14
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
ATTTTATTAATTATAT
Found at i:2537276 original size:22 final size:23
Alignment explanation
Indices: 2537251--2537293 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2537241 TAATAATAAT
*
2537251 TATTTTAAATTAT-ATTTTATAG
1 TATTATAAATTATAATTTTATAG
*
2537273 TATTATATATTATAATTTTAT
1 TATTATAAATTATAATTTTAT
2537294 TAAATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTATAAATTATAATTTTATAG
Found at i:2537380 original size:24 final size:26
Alignment explanation
Indices: 2537349--2537411 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
2537339 TATATTTTTA
2537349 TTAATTATATTTATAA-TAATTA-TG
1 TTAATTATATTTATAATTAATTATTG
* *
2537373 TTAATTATCTTT-TAATTATTTATTG
1 TTAATTATATTTATAATTAATTATTG
*
2537398 TTAATAATAATTTA
1 TTAATTAT-ATTTA
2537412 CCAAAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 3 0.10
24 16 0.52
25 9 0.29
26 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (26 bp):
TTAATTATATTTATAATTAATTATTG
Found at i:2537461 original size:17 final size:17
Alignment explanation
Indices: 2537441--2537474 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2537431 ATTATTAAGA
2537441 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
2537458 ATTTTAATTAAATATAT
1 ATTTTAATTAAATATAT
2537475 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:2537730 original size:16 final size:16
Alignment explanation
Indices: 2537709--2537777 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
2537699 GATTTGCTAT
2537709 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2537725 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
2537742 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2537758 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2537774 TACA
1 TACA
2537778 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2537751 original size:33 final size:32
Alignment explanation
Indices: 2537709--2537777 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
2537699 GATTTGCTAT
2537709 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
2537742 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
2537774 TACA
1 TACA
2537778 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:2540181 original size:112 final size:111
Alignment explanation
Indices: 2540056--2540277 Score: 340
Period size: 112 Copynumber: 2.0 Consensus size: 111
2540046 ACAGCTCTAA
*
2540056 AACCCTAGAAATATTATACCACTGGAATTGAAAACAAAGA-AGCTTAGAAACCCTAAACCTAACA
1 AACCCTAGAAATATTATACCACTGGAATTGAAAACAAAGAGA-CTTAGAAACCCTAAACCCAACA
* *
2540120 GAAAGTAAAAAAATT-TCCCAAATCGACAGTCACCTGTAACCCTAATTC
65 GAAAGTAAAAAAATTCCCCCAAATC--CAGTCACATGTAACCCTAATTC
* * *
2540168 AACCCTAGAAATATTATACCACTGGAATTGAAAATAAAGAGACTTAGAAACCTTAAACCCAGCAG
1 AACCCTAGAAATATTATACCACTGGAATTGAAAACAAAGAGACTTAGAAACCCTAAACCCAACAG
*
2540233 AAATTAAAAAAATTCCCCCAAATCCAGTCACATGTAACCCTAATT
66 AAAGTAAAAAAATTCCCCCAAATCCAGTCACATGTAACCCTAATT
2540278 AACAGAATAC
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
111 20 0.20
112 72 0.71
113 9 0.09
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.21
Consensus pattern (111 bp):
AACCCTAGAAATATTATACCACTGGAATTGAAAACAAAGAGACTTAGAAACCCTAAACCCAACAG
AAAGTAAAAAAATTCCCCCAAATCCAGTCACATGTAACCCTAATTC
Found at i:2540716 original size:16 final size:16
Alignment explanation
Indices: 2540695--2540740 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
2540685 GCTGTATTGT
*
2540695 AATAGAGGCGTAATGG
1 AATAGAGGTGTAATGG
* *
2540711 AATAGAGATTTAATGG
1 AATAGAGGTGTAATGG
2540727 AATAGAGGTGTAAT
1 AATAGAGGTGTAAT
2540741 ATCAAATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.26
Consensus pattern (16 bp):
AATAGAGGTGTAATGG
Found at i:2540985 original size:15 final size:15
Alignment explanation
Indices: 2540961--2541003 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2540951 TTTAAACATA
*
2540961 ATTATTATTAAATAT
1 ATTATAATTAAATAT
2540976 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
2540990 A-TATAATTATAATA
1 ATTATAATTA-AATA
2541004 AAATTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 5 0.20
15 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:2540989 original size:16 final size:16
Alignment explanation
Indices: 2540952--2540993 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2540942 TTAATCATAT
*
2540952 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
2540968 TT-AAATATATTATAA
1 TTAAAATATATTATAA
2540983 TTAAAATATAT
1 TTAAAATATAT
2540994 AATTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:2540993 original size:18 final size:18
Alignment explanation
Indices: 2540972--2541007 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2540962 TTATTATTAA
2540972 ATAT-ATTATAATTAAAAT
1 ATATAATTATAA-TAAAAT
2540990 ATATAATTATAATAAAAT
1 ATATAATTATAATAAAAT
2541008 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAATTATAATAAAAT
Found at i:2540996 original size:13 final size:14
Alignment explanation
Indices: 2540961--2541003 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2540951 TTTAAACATA
*
2540961 ATTATTATTAAATAT
1 ATTATAATTAAA-AT
2540976 ATTATAATTAAAAT
1 ATTATAATTAAAAT
*
2540990 A-TATAATTATAAT
1 ATTATAATTAAAAT
2541003 A
1 A
2541004 AAATTCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAATTAAAAT
Found at i:2541103 original size:23 final size:23
Alignment explanation
Indices: 2541077--2541150 Score: 78
Period size: 23 Copynumber: 3.1 Consensus size: 23
2541067 TATAATTAAC
2541077 ATAAATTATTAAATATATTATTT
1 ATAAATTATTAAATATATTATTT
* *
2541100 ATAATATT-TAAAATATATAATTT
1 ATAA-ATTATTAAATATATTATTT
*
2541123 AATAAAATTATATAAATATATTAATT
1 -AT-AAATTAT-TAAATATATTATTT
2541149 AT
1 AT
2541151 TCATAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 17 0.41
24 8 0.20
25 5 0.12
26 11 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAATTATTAAATATATTATTT
Found at i:2541265 original size:16 final size:16
Alignment explanation
Indices: 2541230--2541280 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
2541220 ATTTTAAATT
2541230 TAAAATT-AT-ATTTAA
1 TAAAATTAATAATTT-A
2541245 TAAAATTAATAATTTA
1 TAAAATTAATAATTTA
* *
2541261 TAAAAATAAATATTTTA
1 T-AAAATTAATAATTTA
2541278 TAA
1 TAA
2541281 GAAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.23
16 6 0.19
17 18 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATTAATAATTTA
Found at i:2552171 original size:20 final size:20
Alignment explanation
Indices: 2552117--2552179 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
2552107 TTAGATAGAT
*
2552117 ATTTTTATTTAA--TTTTGAA
1 ATTTTTATATAATTTTTTG-A
*
2552136 ATTTTTTTATAATTTTTTGA
1 ATTTTTATATAATTTTTTGA
* *
2552156 ATTTTTATAT-GTTTTTTTA
1 ATTTTTATATAATTTTTTGA
2552175 ATTTT
1 ATTTT
2552180 AAGAGCTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 22 0.59
20 10 0.27
21 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
ATTTTTATATAATTTTTTGA
Found at i:2552527 original size:23 final size:23
Alignment explanation
Indices: 2552497--2552542 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2552487 CTGTAGAATG
2552497 ACCAAAATGCAAT-TCGAAGTATA
1 ACCAAAATGCAATCT-GAAGTATA
2552520 ACCAAAATGCAATCTGAAGTATA
1 ACCAAAATGCAATCTGAAGTATA
2552543 GTTTAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
ACCAAAATGCAATCTGAAGTATA
Found at i:2554539 original size:31 final size:31
Alignment explanation
Indices: 2554469--2554528 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2554459 AAAAATTACA
*
2554469 ATTC-AGTCACTAAACTAATCTAAAGTTTTC
1 ATTCAAGTCACTAAACTAATCAAAAGTTTTC
* *
2554499 ATTCAAGTCACTGAACTATTCAAAAGTTTT
1 ATTCAAGTCACTAAACTAATCAAAAGTTTT
2554529 TACTTAAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (31 bp):
ATTCAAGTCACTAAACTAATCAAAAGTTTTC
Found at i:2561073 original size:19 final size:19
Alignment explanation
Indices: 2561046--2561087 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2561036 TAATATATGG
*
2561046 ATTTGATATCTGAATTT-AT
1 ATTTAATAT-TGAATTTAAT
*
2561065 ATTTAATATTTAATTTAAT
1 ATTTAATATTGAATTTAAT
2561084 ATTT
1 ATTT
2561088 TAGTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTTAATATTGAATTTAAT
Found at i:2561080 original size:12 final size:13
Alignment explanation
Indices: 2561059--2561096 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
2561049 TGATATCTGA
2561059 ATTTATATTTAAT
1 ATTTATATTTAAT
2561072 ATTTA-ATTTAAT
1 ATTTATATTTAAT
2561084 ATTT-TAGTTTAAT
1 ATTTATA-TTTAAT
2561097 TTTGTACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
ATTTATATTTAAT
Found at i:2576108 original size:18 final size:18
Alignment explanation
Indices: 2576087--2576146 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
2576077 GATCAAACAT
2576087 ATATATTATAAAATTAAA
1 ATATATTATAAAATTAAA
*
2576105 ATATA-TATATATATTAAA
1 ATATATTATA-AAATTAAA
*
2576123 ATAT-TTAGTAAAATTTAA
1 ATATATTA-TAAAATTAAA
2576141 ATATAT
1 ATATAT
2576147 GAAATAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 4 0.11
18 28 0.80
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATATTATAAAATTAAA
Found at i:2583542 original size:22 final size:24
Alignment explanation
Indices: 2583507--2583555 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2583497 ATGATGAAAT
2583507 AAATAATAATATAT-TAGATTTAA
1 AAATAATAATATATATAGATTTAA
2583530 AAATAA-AATATATAATAGATTTAA
1 AAATAATAATATAT-ATAGATTTAA
2583554 AA
1 AA
2583556 CATCAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAATAATATATATAGATTTAA
Found at i:2586838 original size:50 final size:50
Alignment explanation
Indices: 2586763--2587010 Score: 343
Period size: 50 Copynumber: 4.8 Consensus size: 50
2586753 GATAATAACA
* *
2586763 TGCCAAAGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
2586813 TGCCAACGCCATGTCCCAGTCATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
2586863 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
2586913 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
2586968 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
2587011 TTACCCAAAT
Statistics
Matches: 178, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
50 134 0.75
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.22
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:2587126 original size:13 final size:13
Alignment explanation
Indices: 2587105--2587148 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
2587095 GCTTGGATCA
*
2587105 TCATCAAATAAAT
1 TCATAAAATAAAT
2587118 TCATAAAATAAAT
1 TCATAAAATAAAT
2587131 TCATAAAATAAAT
1 TCATAAAATAAAT
2587144 TCATA
1 TCATA
2587149 GTTGCTGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:2587396 original size:30 final size:30
Alignment explanation
Indices: 2587361--2587418 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2587351 CCTCGACTCT
*
2587361 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
2587391 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
2587419 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:2594598 original size:88 final size:89
Alignment explanation
Indices: 2594416--2594608 Score: 201
Period size: 88 Copynumber: 2.2 Consensus size: 89
2594406 TTCAGACTTT
* * * * * * * *
2594416 AATATAAGAACATTTGCCAAGTCTAGGAACTAACTTGAAATAAAAAAAAGTCAAGCTTCAATGTG
1 AATATAAGAACAATTACCCAGT-TAGGTATTAACTTGAAACAAAAAAAAGTCAAGCCTCAACGTG
*
2594481 AGGACAATCGCCTAATTCAAGCCCC
65 AGGACAATCACCTAATTCAAGCCCC
* * *
2594506 AATATAGGAAGAATTACCCAGTTAGGTATTAACTTGAAACAAAAAAGA-TCAAGCCTCAACGTG-
1 AATATAAGAACAATTACCCAGTTAGGTATTAACTTGAAACAAAAAAAAGTCAAGCCTCAACGTGA
* * * * *
2594569 GAGACAATTACCTAGTTCAGGTCCG
66 G-GACAATCACCTAATTCAAGCCCC
2594594 AATATAAGAACAATT
1 AATATAAGAACAATT
2594609 GTCGACTTAC
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
87 1 0.01
88 43 0.52
89 22 0.27
90 17 0.20
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (89 bp):
AATATAAGAACAATTACCCAGTTAGGTATTAACTTGAAACAAAAAAAAGTCAAGCCTCAACGTGA
GGACAATCACCTAATTCAAGCCCC
Found at i:2601645 original size:12 final size:12
Alignment explanation
Indices: 2601628--2601652 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2601618 AGGCTCGAGG
2601628 CAAGCCAAATCT
1 CAAGCCAAATCT
2601640 CAAGCCAAATCT
1 CAAGCCAAATCT
2601652 C
1 C
2601653 GACACCCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CAAGCCAAATCT
Found at i:2608929 original size:51 final size:51
Alignment explanation
Indices: 2608862--2608983 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
2608852 CTTTGTTATC
* * * *
2608862 TGATCAGTGACGAGTGATAAGTGATTGTTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAG
* *
2608913 TGATAAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAG
* *
2608964 GGACAAGTGACAAGTGATAA
1 TGATAAGTGACAAGTGATAA
2608984 ATGTGATCCC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (51 bp):
TGATAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAG
Found at i:2611836 original size:11 final size:11
Alignment explanation
Indices: 2611820--2611844 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2611810 TCTATCTTGG
2611820 TACCTCTATGT
1 TACCTCTATGT
2611831 TACCTCTATGT
1 TACCTCTATGT
2611842 TAC
1 TAC
2611845 GTTCACCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.28, G:0.08, T:0.44
Consensus pattern (11 bp):
TACCTCTATGT
Found at i:2614971 original size:16 final size:16
Alignment explanation
Indices: 2614952--2614983 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2614942 AAAAACCCAA
2614952 AAAGAAAAAAAAATGG
1 AAAGAAAAAAAAATGG
*
2614968 AAAGAAAAAAAGATGG
1 AAAGAAAAAAAAATGG
2614984 TAACAGCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAAAAATGG
Found at i:2619267 original size:22 final size:22
Alignment explanation
Indices: 2619227--2619269 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2619217 TATCCAAACA
*
2619227 ATAATAACAAAATCCTAGCAAT
1 ATAATAACAAAATCATAGCAAT
* *
2619249 ATAATAGCAAAATGATAGCAA
1 ATAATAACAAAATCATAGCAA
2619270 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATCATAGCAAT
Found at i:2619929 original size:24 final size:24
Alignment explanation
Indices: 2619884--2619929 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2619874 GAGTGATTTA
* *
2619884 TAAAAAAAATATAAATTCAAATAT
1 TAAAAAAAATAGAAAATCAAATAT
2619908 TAAAATAAAATAGAAAAT-AAAT
1 TAAAA-AAAATAGAAAATCAAAT
2619930 TAAATTGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
TAAAAAAAATAGAAAATCAAATAT
Found at i:2620020 original size:18 final size:18
Alignment explanation
Indices: 2619999--2620041 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2619989 AAGAAAAAGG
2619999 AAATCAAAATTAAAAAAA
1 AAATCAAAATTAAAAAAA
* * *
2620017 AAATAAAAATTGAGAAAA
1 AAATCAAAATTAAAAAAA
*
2620035 TAATCAA
1 AAATCAA
2620042 GGAAGGTCAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATCAAAATTAAAAAAA
Found at i:2620788 original size:21 final size:21
Alignment explanation
Indices: 2620762--2620805 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2620752 GAAATTTTGA
2620762 ATCGATTTAATATATTAT-TAT
1 ATCGATTTAA-ATATTATATAT
2620783 ATCGATTTAAATATTATATAT
1 ATCGATTTAAATATTATATAT
2620804 AT
1 AT
2620806 TAATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
ATCGATTTAAATATTATATAT
Found at i:2621949 original size:15 final size:16
Alignment explanation
Indices: 2621929--2621971 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2621919 TAAATAATAA
2621929 AATTTATTATTTTT-T
1 AATTTATTATTTTTAT
*
2621944 AATTTAATATTTTTAT
1 AATTTATTATTTTTAT
*
2621960 ATATTTTTTATT
1 A-ATTTATTATT
2621972 AAAATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
AATTTATTATTTTTAT
Found at i:2621951 original size:25 final size:23
Alignment explanation
Indices: 2621909--2621969 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
2621899 AATCAGTCCA
2621909 TATTATTTTTTAAATAATAAAATT
1 TATTATTTTTTAAATAAT-AAATT
* **
2621933 TATTATTTTTTAATTTAATATTTT
1 TATTATTTTTTAA-ATAATAAATT
2621957 TATATATTTTTTA
1 TAT-TATTTTTTA
2621970 TTAAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.59
25 13 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTTTTTAAATAATAAATT
Found at i:2621982 original size:22 final size:24
Alignment explanation
Indices: 2621912--2621986 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 24
2621902 CAGTCCATAT
*
2621912 TATTTTTTAAATAATAAAA-TTTAT-
1 TATTTTTT-AAT-TTAAAATTTTATA
*
2621936 TATTTTTTAATTTAATATTTTTATA
1 TATTTTTTAATTTAA-AATTTTATA
2621961 TATTTTTT-A-TTAAAATTTTATA
1 TATTTTTTAATTTAAAATTTTATA
2621983 TATT
1 TATT
2621987 ATCATCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
22 15 0.33
23 8 0.18
24 14 0.31
25 8 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTTTAATTTAAAATTTTATA
Found at i:2622045 original size:18 final size:18
Alignment explanation
Indices: 2622014--2622056 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2622004 TTACATTATA
* *
2622014 ATAATAT-TATAAATTAT
1 ATAATATATAAAAATAAT
*
2622031 GTAATATATAAAAATAAT
1 ATAATATATAAAAATAAT
2622049 ATAATATA
1 ATAATATA
2622057 AAATATTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAATATATAAAAATAAT
Found at i:2633826 original size:22 final size:22
Alignment explanation
Indices: 2633801--2633844 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2633791 ATATATATAT
2633801 ATAGAATTTCAAGCCCAATCAA
1 ATAGAATTTCAAGCCCAATCAA
2633823 ATAGAATTTCAAGCCCAATCAA
1 ATAGAATTTCAAGCCCAATCAA
2633845 TCATGTTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAGAATTTCAAGCCCAATCAA
Found at i:2634217 original size:6 final size:6
Alignment explanation
Indices: 2634208--2634254 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
2634198 AATAATAAAT
* *
2634208 TTAATA TTAATA TTAATA TTAA-A TAAATA TAAATA TAATAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA T--TAATA TTAA
2634255 ATAAATCTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
8 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
TTAATA
Found at i:2634242 original size:10 final size:12
Alignment explanation
Indices: 2634195--2634247 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
2634185 TTTAAAAAAT
*
2634195 TATAATAATAAA
1 TATAATATTAAA
*
2634207 TTTAATATT-AA
1 TATAATATTAAA
2634218 TATTAATATTAAA
1 TA-TAATATTAAA
2634231 TA-AATA-TAAA
1 TATAATATTAAA
2634241 TATAATA
1 TATAATA
2634248 ATATTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 6 0.17
11 11 0.31
12 14 0.40
13 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATAATATTAAA
Found at i:2634242 original size:17 final size:18
Alignment explanation
Indices: 2634202--2634247 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2634192 AATTATAATA
*
2634202 ATAAAT-TTAATATTAAT
1 ATAAATATTAATATAAAT
*
2634219 ATTAATATTAA-ATAAAT
1 ATAAATATTAATATAAAT
2634236 ATAAATA-TAATA
1 ATAAATATTAATA
2634248 ATATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.12
17 17 0.71
18 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAATATTAATATAAAT
Found at i:2634255 original size:25 final size:24
Alignment explanation
Indices: 2634191--2634260 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
2634181 ATATTTTAAA
* *
2634191 AAAT-TATAATAATAAATTTAATAT
1 AAATATATAATATTAAA-TAAATAT
*
2634215 TAATAT-TAATATTAAATAAATAT
1 AAATATATAATATTAAATAAATAT
2634238 AAATATAATAATATTAAATAAAT
1 AAATAT-ATAATATTAAATAAAT
2634261 CTACCAAGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 11 0.28
24 12 0.31
25 16 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATATATAATATTAAATAAATAT
Found at i:2636120 original size:30 final size:28
Alignment explanation
Indices: 2636053--2636122 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2636043 TCCTCATAAA
*
2636053 TTGAAAATTTAGTCTCTATACTTTTATT
1 TTGAAAATTTAATCTCTATACTTTTATT
* *
2636081 TCT-AGAAATTTAATCTCTTTATTTTTTATAT
1 T-TGA-AAATTTAATCTCTATA-CTTTTAT-T
2636112 TTGAAAATTTA
1 TTGAAAATTTA
2636123 TGTCTAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 2 0.06
29 15 0.44
30 14 0.41
31 3 0.09
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (28 bp):
TTGAAAATTTAATCTCTATACTTTTATT
Found at i:2638589 original size:436 final size:436
Alignment explanation
Indices: 2637777--2638654 Score: 1702
Period size: 436 Copynumber: 2.0 Consensus size: 436
2637767 CCTTCTGTAC
2637777 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
1 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
2637842 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
66 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
*
2637907 AATTTAAATGGGTTTGGGCTAGATTCTATTGAGCTCGCAAACTAAGCTCGCGGGATACTCAGTAA
131 AATTTAAATGGGTTTGGGCTAGATTCTATTGAGCTCGCAAACTAAGCTCGCGGGATACACAGTAA
2637972 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
196 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
2638037 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
261 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
2638102 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
326 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
*
2638167 AGACCATATAAACACGTGTTCGGTTTAGAGTAGGATACGTGTCTAT
391 AGACCATATAAACACGTGTTCGGTTTAGAGTAGGATACGTATCTAT
*
2638213 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAGC
1 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
2638278 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
66 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
*
2638343 AATTTAAATGGGTTTGGGCTAGATTCTATTGAGCTCGCAAACTAAGCTCGCGGGGTACACAGTAA
131 AATTTAAATGGGTTTGGGCTAGATTCTATTGAGCTCGCAAACTAAGCTCGCGGGATACACAGTAA
*
2638408 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCTCAACTAGAGTCACTTTATGACTCTC
196 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
*
2638473 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATTGATCCAAAAACCCAAATGG
261 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
2638538 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
326 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
2638603 AGACCATATAAACACGTGTTCGGTTTAGAGTAGGATACGTATCTAT
391 AGACCATATAAACACGTGTTCGGTTTAGAGTAGGATACGTATCTAT
2638649 ATACAT
1 ATACAT
2638655 GAAACCTACC
Statistics
Matches: 436, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
436 436 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (436 bp):
ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
AATTTAAATGGGTTTGGGCTAGATTCTATTGAGCTCGCAAACTAAGCTCGCGGGATACACAGTAA
GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
AGACCATATAAACACGTGTTCGGTTTAGAGTAGGATACGTATCTAT
Found at i:2641902 original size:8 final size:7
Alignment explanation
Indices: 2641869--2641893 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2641859 TTATAATTTG
2641869 TTTTGAA
1 TTTTGAA
2641876 TTTTGAA
1 TTTTGAA
2641883 TTTTGAA
1 TTTTGAA
2641890 TTTT
1 TTTT
2641894 TGTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTGAA
Found at i:2648241 original size:112 final size:112
Alignment explanation
Indices: 2648116--2648339 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
2648106 TCAAAGTAAG
2648116 ATTTCAGCAAAAGTGATTGATCCGTACAAAAATTCAACAAGGCAACAATCAAACATAACACAGCT
1 ATTTCAGCAAAAGTGATTGATCCGTACAAAAATTCAACAAGGCAACAATCAAACATAACACAGCT
2648181 CAATTCATATCCTTAAATCTAAAAATATTGGTCAAAGTACTATAGAA
66 CAATTCATATCCTTAAATCTAAAAATATTGGTCAAAGTACTATAGAA
2648228 ATTTCAGCAAAAGTGATTGATCCGTACAAAAATTCAACAAGGCAACAATCAAACATAACACAGCT
1 ATTTCAGCAAAAGTGATTGATCCGTACAAAAATTCAACAAGGCAACAATCAAACATAACACAGCT
2648293 CAATTCATATCCTTAAATCTAAAAATATTGGTCAAAGTACTATAGAA
66 CAATTCATATCCTTAAATCTAAAAATATTGGTCAAAGTACTATAGAA
2648340 GCCCTTGTAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.25
Consensus pattern (112 bp):
ATTTCAGCAAAAGTGATTGATCCGTACAAAAATTCAACAAGGCAACAATCAAACATAACACAGCT
CAATTCATATCCTTAAATCTAAAAATATTGGTCAAAGTACTATAGAA
Found at i:2671285 original size:23 final size:23
Alignment explanation
Indices: 2671259--2671302 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2671249 TTTTGGCCTT
2671259 AATTCTAAAAATTTA-ACAAATTC
1 AATT-TAAAAATTTACACAAATTC
* *
2671282 AATTTCAACATTTACACAAAT
1 AATTTAAAAATTTACACAAAT
2671303 GTTGTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (23 bp):
AATTTAAAAATTTACACAAATTC
Found at i:2674239 original size:4 final size:4
Alignment explanation
Indices: 2674230--2674258 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2674220 TTATTAGGAA
2674230 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
2674259 TACACTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:2678702 original size:13 final size:13
Alignment explanation
Indices: 2678684--2678708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2678674 GATTTCTAAA
2678684 TTATATTAAATTT
1 TTATATTAAATTT
2678697 TTATATTAAATT
1 TTATATTAAATT
2678709 ACTGAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATTAAATTT
Found at i:2678770 original size:6 final size:6
Alignment explanation
Indices: 2678759--2678786 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2678749 TTGTCTAAAA
2678759 AATTTG AATTTG AATTTG AATTTG AATT
1 AATTTG AATTTG AATTTG AATTTG AATT
2678787 GTCTAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
AATTTG
Found at i:2683020 original size:23 final size:23
Alignment explanation
Indices: 2682993--2683037 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2682983 CCCGTTACAC
2682993 GGCTCTTAGTAAGCTTCCCGATA
1 GGCTCTTAGTAAGCTTCCCGATA
* * *
2683016 GGCTCTTCGTGAGCTTCTCGAT
1 GGCTCTTAGTAAGCTTCCCGAT
2683038 TAAATGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (23 bp):
GGCTCTTAGTAAGCTTCCCGATA
Found at i:2685386 original size:13 final size:14
Alignment explanation
Indices: 2685365--2685403 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
2685355 TCTTTGATTT
2685365 ATTATTTTATTTTA
1 ATTATTTTATTTTA
*
2685379 GTTA-TTTATTTTA
1 ATTATTTTATTTTA
2685392 ATTATTTTATTT
1 ATTATTTTATTT
2685404 GACTTCGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
ATTATTTTATTTTA
Found at i:2697213 original size:40 final size:41
Alignment explanation
Indices: 2697061--2697218 Score: 165
Period size: 41 Copynumber: 3.9 Consensus size: 41
2697051 GGCGCTAATG
* * * * * * *
2697061 GAAAAACGTCGCAATAGGTAAAGCAGTAGTGGGGTTTACGA
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* *
2697102 GAAAAATGCCACAAAAGGTCAAGCAGTAGCGGCATTTATGA
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* * ** *
2697143 AAAAAACGCCTTAAAAAGTCAAGCAGTAGCGGCGTTTATGA
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* *
2697184 GAAAAATACCGCAAAAGGT-AAGCAATAGCGGCGTT
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTT
2697219 AAAAAACATC
Statistics
Matches: 95, Mismatches: 22, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
40 15 0.16
41 80 0.84
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.18
Consensus pattern (41 bp):
GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
Found at i:2697336 original size:37 final size:36
Alignment explanation
Indices: 2697277--2697361 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 36
2697267 CTTAAACCAT
* * *
2697277 AATCCCAAAATCCATT-ATTTTTTCCCCTAAAAGTCAG
1 AATCCCCAAATCCATTAATTTTTTCCCCT-AAA-TAAA
* *
2697314 AATCCCCAAATCCCTTAATTTTTTTCCCTAAATAAA
1 AATCCCCAAATCCATTAATTTTTTCCCCTAAATAAA
2697350 AATCCCCAAATC
1 AATCCCCAAATC
2697362 GAAATCTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 14 0.33
37 17 0.40
38 11 0.26
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.32
Consensus pattern (36 bp):
AATCCCCAAATCCATTAATTTTTTCCCCTAAATAAA
Found at i:2698853 original size:92 final size:92
Alignment explanation
Indices: 2698694--2698890 Score: 331
Period size: 92 Copynumber: 2.1 Consensus size: 92
2698684 ATGGTTGTTT
* * * *
2698694 AAACCGATTCAATCGGTAGAGGTACCAATCTAGAGAGAGGCATCAAACTTATTGACTTGCAAACT
1 AAACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAACT
*
2698759 GGTACGAGCTGGTAGAACTAGACTAAA
66 GGTACGAGCTAGTAGAACTAGACTAAA
*
2698786 AAACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAGCT
1 AAACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAACT
2698851 GGTACGAGCTAGTAGAACTAGACTAAA
66 GGTACGAGCTAGTAGAACTAGACTAAA
*
2698878 AAATCGATTGAAC
1 AAACCGATTGAAC
2698891 GCAATTTTTA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 98 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (92 bp):
AAACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAACT
GGTACGAGCTAGTAGAACTAGACTAAA
Found at i:2705431 original size:85 final size:85
Alignment explanation
Indices: 2705288--2705455 Score: 300
Period size: 85 Copynumber: 2.0 Consensus size: 85
2705278 GTCACTTCAC
* *
2705288 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCTTTGGGCCTTCTTTAGACATGTTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2705353 AGCTTGAACAATGATAGACT
66 AGCTTGAACAATGATAGACT
* *
2705373 TTAATCGCTAAAACCTAGTACTTCTGTTTATGTCTGATCCCTTGGGCCTTCTTTAGACATGCTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2705438 AGCTTGAACAATGATAGA
66 AGCTTGAACAATGATAGA
2705456 ATTGGGCTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (85 bp):
TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
AGCTTGAACAATGATAGACT
Found at i:2715809 original size:30 final size:30
Alignment explanation
Indices: 2715769--2715855 Score: 167
Period size: 30 Copynumber: 2.9 Consensus size: 30
2715759 GAATATAAAC
2715769 TATA-TTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACA
2715798 TATATTTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACA
2715828 TATATTTTTTTATTTTTAAAATACACTA
1 TATATTTTTTTATTTTTAAAATACACTA
2715856 ATACAGTGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 4 0.07
30 53 0.93
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (30 bp):
TATATTTTTTTATTTTTAAAATACACTACA
Found at i:2718414 original size:22 final size:22
Alignment explanation
Indices: 2718389--2718442 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
2718379 AGCAAAAAAG
*
2718389 AGGGGAGAAACCATCAAGAACA
1 AGGGGAGAAACCAGCAAGAACA
*
2718411 A-GGGAGAAACCAGCAAGAACG
1 AGGGGAGAAACCAGCAAGAACA
2718432 AGGGGAGAAAC
1 AGGGGAGAAAC
2718443 TGCTGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.48, C:0.17, G:0.33, T:0.02
Consensus pattern (22 bp):
AGGGGAGAAACCAGCAAGAACA
Found at i:2718965 original size:23 final size:23
Alignment explanation
Indices: 2718922--2718966 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2718912 GTATATGCAA
*
2718922 TTTAATATTTTTATTCTTTATAT
1 TTTAATATTTTTATTCATTATAT
2718945 TTTAATATTATTTATT-ATTATA
1 TTTAATATT-TTTATTCATTATA
2718967 AATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATATTTTTATTCATTATAT
Found at i:2719443 original size:22 final size:21
Alignment explanation
Indices: 2719399--2719443 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2719389 CATGTAATTC
*
2719399 ATAAAAATTTAAAATAAATAA
1 ATAAAAATTTAAAATAAACAA
*
2719420 ATAAAAATTTAAAAATCAACAA
1 ATAAAAATTT-AAAATAAACAA
2719442 AT
1 AT
2719444 TCCAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAAAATTTAAAATAAACAA
Found at i:2726298 original size:83 final size:83
Alignment explanation
Indices: 2726167--2726352 Score: 259
Period size: 83 Copynumber: 2.2 Consensus size: 83
2726157 CTATATGCAT
* * * *
2726167 AGTACAAG-ACTAGTAATTTAGTTTAATCAAATGGATTTAAGCATTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTA-AAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACT
* *
2726231 AAAATTTCAAATTTTGAAA
65 AAAATTTAAAAATTTGAAA
* *
2726250 AGTAGAGGAACTAAAATTGAGTTTAATCAAACGGATTTAA-CTACTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGC-ACTACTATTTTGGGTTAGGACT
2726314 AAAATTTAAAAATTTGAAA
65 AAAATTTAAAAATTTGAAA
*
2726333 AGTACAATAACTAAAATTGA
1 AGTACAAGAACTAAAATTGA
2726353 CTAATTCGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 85 0.94
84 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (83 bp):
AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACTA
AAATTTAAAAATTTGAAA
Found at i:2747589 original size:11 final size:11
Alignment explanation
Indices: 2747570--2747613 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
2747560 AACACCAAAC
*
2747570 TTTTTGGGTAA
1 TTTTCGGGTAA
2747581 TTTTCGGGTAA
1 TTTTCGGGTAA
2747592 --TTCGGGTAA
1 TTTTCGGGTAA
2747601 TTTTCGGGTAA
1 TTTTCGGGTAA
2747612 TT
1 TT
2747614 CGGTTAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:2747597 original size:9 final size:9
Alignment explanation
Indices: 2747583--2747655 Score: 85
Period size: 9 Copynumber: 8.0 Consensus size: 9
2747573 TTGGGTAATT
2747583 TTCGGGTAA
1 TTCGGGTAA
2747592 TTCGGGTAA
1 TTCGGGTAA
2747601 TTTTCGGGTAA
1 --TTCGGGTAA
*
2747612 TTCGGTTAA
1 TTCGGGTAA
*
2747621 TTCGGTTAA
1 TTCGGGTAA
**
2747630 TTCGATTAA
1 TTCGGGTAA
2747639 -TCGGGTAA
1 TTCGGGTAA
2747647 TTCGGGTAA
1 TTCGGGTAA
2747656 ATTTTAACCA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
8 6 0.11
9 42 0.74
11 9 0.16
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.38
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:2747600 original size:20 final size:20
Alignment explanation
Indices: 2747575--2747660 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
2747565 CAAACTTTTT
2747575 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
2747595 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
* *
2747615 GGTTAA--TTCGGTTAATTC
1 GGGTAATTTTCGGGTAATTC
**
2747633 GATTAA---TCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
2747650 GGGTAAATTTT
1 GGGT-AATTTT
2747661 AACCAAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
17 12 0.21
18 18 0.32
20 25 0.45
21 1 0.02
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (20 bp):
GGGTAATTTTCGGGTAATTC
Found at i:2747778 original size:30 final size:30
Alignment explanation
Indices: 2747720--2747780 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2747710 TTATTAACCG
***
2747720 AAAAAAATTCGGTTCGGTTAATTTTTAAAA
1 AAAAAAATTCGGTTCGGTTAACGGTTAAAA
2747750 AAAAAAATTCGGTTCGGTTAACGGTTAAAA
1 AAAAAAATTCGGTTCGGTTAACGGTTAAAA
2747780 A
1 A
2747781 TTTTGGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (30 bp):
AAAAAAATTCGGTTCGGTTAACGGTTAAAA
Found at i:2748130 original size:11 final size:11
Alignment explanation
Indices: 2748114--2748139 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2748104 ATTTTTTTAT
2748114 TTTTAAAATAC
1 TTTTAAAATAC
2748125 TTTTAAAATAC
1 TTTTAAAATAC
2748136 TTTT
1 TTTT
2748140 TTTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:2748142 original size:39 final size:40
Alignment explanation
Indices: 2748099--2748206 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 40
2748089 ATAATAAATA
2748099 TTTTT-ATTTTTTTATTTTTAAAATACTTTTAAAATACTTTTT
1 TTTTTAATTTTTTTATTTTTAAAATA-TTTTAAAATAC--TTT
* *
2748141 TTTTTAATTTTTTTAATTTT--AAT-TTTTTAAATAC-TT
1 TTTTTAATTTTTTTATTTTTAAAATATTTTAAAATACTTT
2748177 TTTTTAATTTTAATTTTAATTTTTAAAATA
1 TTTTTAA-TTT--TTTT-ATTTTTAAAATA
2748207 AATTTTTGGT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 9 0.16
37 3 0.05
39 14 0.25
40 5 0.09
41 3 0.05
42 8 0.15
43 13 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (40 bp):
TTTTTAATTTTTTTATTTTTAAAATATTTTAAAATACTTT
Found at i:2748154 original size:15 final size:15
Alignment explanation
Indices: 2748142--2748193 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
2748132 ATACTTTTTT
2748142 TTTTAATTTTTTTAA
1 TTTTAATTTTTTTAA
2748157 TTTTAA-TTTTTTAA
1 TTTTAATTTTTTTAA
* *
2748171 --ATACTTTTTTTAA
1 TTTTAATTTTTTTAA
2748184 TTTTAATTTT
1 TTTTAATTTT
2748194 AATTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 2 0.07
13 8 0.27
14 8 0.27
15 12 0.40
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATTTTTTTAA
Found at i:2748166 original size:27 final size:27
Alignment explanation
Indices: 2748136--2748202 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
2748126 TTTAAAATAC
2748136 TTTTTTTTTTAATTTTTTTAATTTTAA
1 TTTTTTTTTTAATTTTTTTAATTTTAA
*** *
2748163 TTTTTTAAATACTTTTTTTAATTTTAA
1 TTTTTTTTTTAATTTTTTTAATTTTAA
*
2748190 TTTTAATTTTTAA
1 TTTT-TTTTTTAA
2748203 AATAAATTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTTTTTTTAATTTTTTTAATTTTAA
Found at i:2748213 original size:33 final size:33
Alignment explanation
Indices: 2748151--2748213 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2748141 TTTTTAATTT
* **
2748151 TTTTAATTTTAATTTTTTAAATACTTTTTTTAA
1 TTTTAATTTTAATTTTTAAAATAAATTTTTTAA
2748184 TTTTAATTTTAATTTTTAAAATAAATTTTT
1 TTTTAATTTTAATTTTTAAAATAAATTTTT
2748214 GGTATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTTAATTTTAATTTTTAAAATAAATTTTTTAA
Found at i:2759526 original size:30 final size:31
Alignment explanation
Indices: 2759455--2759527 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
2759445 TTAAATTAGT
* *
2759455 AAATT-TAAAAATATATTTTAATTTCTTTAA
1 AAATTATAAAAATATAGTTTAATATCTTTAA
*
2759485 AAA-TA-AGAAAATTTAGTTTAATAT-TTTAA
1 AAATTATA-AAAATATAGTTTAATATCTTTAA
2759514 AAATTATAAAAATA
1 AAATTATAAAAATA
2759528 GAATATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
29 10 0.29
30 24 0.69
31 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (31 bp):
AAATTATAAAAATATAGTTTAATATCTTTAA
Found at i:2759632 original size:29 final size:33
Alignment explanation
Indices: 2759600--2759663 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 33
2759590 TAATGTTAAA
* *
2759600 TATTTTATTTAGTT-AT-TAAA-TAATA-TATT
1 TATTTTATGTAATTAATATAAAGTAATATTATT
2759629 TATTTTATGTAATTAATATAAAGTAATATTATT
1 TATTTTATGTAATTAATATAAAGTAATATTATT
2759662 TA
1 TA
2759664 ATGTTGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.41
30 2 0.07
31 4 0.14
32 5 0.17
33 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (33 bp):
TATTTTATGTAATTAATATAAAGTAATATTATT
Found at i:2759635 original size:25 final size:25
Alignment explanation
Indices: 2759598--2759649 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2759588 TTTAATGTTA
*
2759598 AATATTTTATTTA-GTTATTAA-AT
1 AATATTTTATTTATGTAATTAATAT
2759621 AATATATTTATTTTATGTAATTAATAT
1 AATAT-TTTA-TTTATGTAATTAATAT
2759648 AA
1 AA
2759650 AGTAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 4 0.17
26 7 0.29
27 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
AATATTTTATTTATGTAATTAATAT
Found at i:2766541 original size:18 final size:18
Alignment explanation
Indices: 2766520--2766675 Score: 89
Period size: 18 Copynumber: 9.0 Consensus size: 18
2766510 ATATTAAGAA
2766520 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
2766538 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
* *
2766553 -TTTAAT-AATAAT-TAT
1 TTTTATTAAATTATATAT
* *
2766568 TTTAAATTATATTATATAT
1 TTT-TATTAAATTATATAT
* * *
2766587 TATTA-TATATTAT-GA-
1 TTTTATTAAATTATATAT
*
2766602 TTTTATTAAATTCATATAA
1 TTTTATTAAATT-ATATAT
*** * *
2766621 GAATATTTAATATTA-AAAA
1 TTTTA-TTAA-ATTATATAT
2766640 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
2766658 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
2766676 AATAATAATT
Statistics
Matches: 103, Mismatches: 21, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 5 0.05
16 12 0.12
17 17 0.17
18 40 0.39
19 12 0.12
20 5 0.05
21 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:2766543 original size:47 final size:48
Alignment explanation
Indices: 2766492--2766595 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 48
2766482 TTTTATTAAA
*
2766492 TTTATATAAGA-ATATTTAATATTAAGAATTTT-ATTAAATTATATATT
1 TTTATATAA-ATATATTTAATAATAAGAATTTTAATTAAATTATATATT
** *
2766539 TTTAT-TAAATTATATTTAATAATAATTATTTTAAATTATATTATATATT
1 TTTATATAAA-TATATTTAATAATAAGAATTTT-AATTAAATTATATATT
*
2766588 ATTATATA
1 TTTATATA
2766596 TTATGATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
45 1 0.02
46 3 0.06
47 23 0.49
49 18 0.38
50 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (48 bp):
TTTATATAAATATATTTAATAATAAGAATTTTAATTAAATTATATATT
Found at i:2766592 original size:120 final size:120
Alignment explanation
Indices: 2766455--2766935 Score: 782
Period size: 120 Copynumber: 4.0 Consensus size: 120
2766445 ATTATTAATC
* *
2766455 TATATTATATAGTATTATATATTATGATTTTATTAAATTTATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
2766520 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * *
2766575 TATATTATATATTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAAAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
2766640 TTTTATTAAATTATATATTTTTATTAAATTATATATAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* *
2766695 TATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
2766760 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAA
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * * * * * *
2766815 TATATTTTATAGTATCATATATTATTATTTTAGTAAATTCAGATAAAAATATTGATTATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
2766880 TTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATG-TTAAAT
2766936 ATGATTAAAT
Statistics
Matches: 338, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
120 333 0.99
121 5 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
Found at i:2766695 original size:44 final size:44
Alignment explanation
Indices: 2766645--2766822 Score: 118
Period size: 44 Copynumber: 4.4 Consensus size: 44
2766635 AAAAATTTTA
2766645 TTAAATTATATATTTTTATTAAATTATATATAATAATAATTATG
1 TTAAATTATATATTTTTATTAAATTATATATAATAATAATTATG
* * * * *
2766689 TTAAATTATAT-TTTATAGT--ATTATATATTATGAT-TTTA-G
1 TTAAATTATATATTTTTATTAAATTATATATAATAATAATTATG
* * * * * *
2766728 -AAAATTCATATA-----A-GAATATT-TA-ATATTAAGAATTTTA
1 TTAAATT-ATATATTTTTATTAA-ATTATATATAATAATAATTATG
*
2766765 TTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATG
1 TTAAATTATATATTTTTATTAAATTATATATAATAATAATTATG
2766809 TTAAA--ATATATTTT
1 TTAAATTATATATTTT
2766823 ATAGTATCAT
Statistics
Matches: 97, Mismatches: 21, Indels: 34
0.64 0.14 0.22
Matches are distributed among these distances:
35 5 0.05
36 4 0.04
37 8 0.08
38 10 0.10
39 5 0.05
40 3 0.03
41 13 0.13
42 13 0.13
43 10 0.10
44 26 0.27
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (44 bp):
TTAAATTATATATTTTTATTAAATTATATATAATAATAATTATG
Found at i:2766907 original size:18 final size:17
Alignment explanation
Indices: 2766879--2766913 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2766869 ATTATTAAGA
*
2766879 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2766896 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2766914 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2767191 original size:16 final size:16
Alignment explanation
Indices: 2767149--2767200 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
2767139 GATTTGCTAT
*
2767149 TACACCTCT-ATTCTAT
1 TACACCTCTAATTC-AA
*
2767165 TATACCTCTAATTCAA
1 TACACCTCTAATTCAA
2767181 TACACCTCTAATTCAA
1 TACACCTCTAATTCAA
2767197 TACA
1 TACA
2767201 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 28 0.88
17 4 0.12
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (16 bp):
TACACCTCTAATTCAA
Found at i:2767449 original size:7 final size:7
Alignment explanation
Indices: 2767437--2767461 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2767427 AGTAAATCAA
2767437 TTTTGGG
1 TTTTGGG
2767444 TTTTGGG
1 TTTTGGG
2767451 TTTTGGG
1 TTTTGGG
2767458 TTTT
1 TTTT
2767462 TGCTTCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (7 bp):
TTTTGGG
Found at i:2776829 original size:21 final size:22
Alignment explanation
Indices: 2776800--2776846 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
2776790 CAGAAGGAGT
*
2776800 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
2776822 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
2776843 GAGT
1 GAGT
2776847 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:2783452 original size:27 final size:30
Alignment explanation
Indices: 2783393--2783454 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
2783383 ATAATTTGAT
*
2783393 AATCAACTGAGTCCTTAATTGAAAATAAGC
1 AATCAACTGAGTCCCTAATTGAAAATAAGC
2783423 AATCAACTGAGTCCCT-A-T-AAAATAAGC
1 AATCAACTGAGTCCCTAATTGAAAATAAGC
2783450 AATCA
1 AATCA
2783455 GTTCAATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 14 0.45
28 1 0.03
29 1 0.03
30 15 0.48
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.24
Consensus pattern (30 bp):
AATCAACTGAGTCCCTAATTGAAAATAAGC
Found at i:2784249 original size:23 final size:23
Alignment explanation
Indices: 2784223--2784282 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
2784213 ATCGGATGAA
2784223 ATTTAAAAAAAAATCAA-ATCATT
1 ATTTAAAAAAAAAT-AATATCATT
*
2784246 ATTTAAAATAAAAATAATATTATT
1 ATTTAAAA-AAAAATAATATCATT
*
2784270 -TTTAATAAAAAAT
1 ATTTAAAAAAAAAT
2784283 TATGATTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 6 0.18
23 16 0.48
24 11 0.33
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTTAAAAAAAAATAATATCATT
Found at i:2784267 original size:21 final size:23
Alignment explanation
Indices: 2784223--2784280 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
2784213 ATCGGATGAA
2784223 ATTTAAAA-AAAAATCAAATCATT
1 ATTTAAAATAAAAAT-AAATCATT
2784246 ATTTAAAATAAAAAT-AAT-ATT
1 ATTTAAAATAAAAATAAATCATT
**
2784267 ATTTTTAATAAAAA
1 ATTTAAAATAAAAA
2784281 ATTATGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 15 0.47
22 3 0.09
23 8 0.25
24 6 0.19
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTTAAAATAAAAATAAATCATT
Found at i:2785605 original size:22 final size:24
Alignment explanation
Indices: 2785580--2785625 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2785570 GGCCGGATTC
2785580 CCCTTC-CCCCTCCCT-TCTCTCT
1 CCCTTCTCCCCTCCCTCTCTCTCT
* *
2785602 CCCTTCTCTCTTCCCTCTCTCTCT
1 CCCTTCTCCCCTCCCTCTCTCTCT
2785626 TCTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 7 0.35
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (24 bp):
CCCTTCTCCCCTCCCTCTCTCTCT
Found at i:2785622 original size:13 final size:12
Alignment explanation
Indices: 2785590--2785627 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
2785580 CCCTTCCCCC
2785590 TCCCTTCTCTC-
1 TCCCTTCTCTCT
2785601 TCCCTTCTCTCT
1 TCCCTTCTCTCT
2785613 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
2785626 TC
1 TC
2785628 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:2786119 original size:3 final size:3
Alignment explanation
Indices: 2786095--2786165 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
2786085 AATATCCTTG
* * * *
2786095 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2786142 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
2786166 GTACGCGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2786162 original size:23 final size:22
Alignment explanation
Indices: 2786107--2786168 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
2786097 ATTTTTATAT
*
2786107 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
2786128 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
2786150 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
2786169 CGCGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:2786175 original size:23 final size:23
Alignment explanation
Indices: 2786131--2786176 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2786121 GTATTACTAT
**
2786131 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
2786154 TATTTTTATTATGTACGCGTATA
1 TATTATTATTATGTACGAGTATA
2786177 CATGTATATA
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:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:2797799 original size:44 final size:44
Alignment explanation
Indices: 2797732--2798240 Score: 354
Period size: 44 Copynumber: 11.7 Consensus size: 44
2797722 AAAAAATTTC
* *
2797732 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
** * *
2797776 AGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGATAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * * *
2797820 TA-ATCCTATCTCCTTGAGATTACAATGGAGCGGATT--A-A-A-
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * * * *
2797859 AGATCTTATCTCTCTGA-AGTTACAGTAGAGAAGA-TCACA-TCAG
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA-AGACAG
* * * ** *
2797902 -G-TCTTATTTCCCTGAGGTTACAGTGGAGTAGA-CCAGAGA-ATTCC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGA-AGACA---G
* *
2797946 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
*
2797990 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
** * * * * * *
2798033 CTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGA-TCAAAATGAT
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGA-CAG
* ** * *
2798077 AGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAA-AAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---G
* *
2798123 AGATCTTATCTCCCTGAGATTACAATGGAGCAGATTGAAGATAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * *
2798167 TA-ATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAG
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * *
2798211 TA-ATCCTATCTGCCTGAGATTACAGCGGAG
1 -AGATCTTATCTCCCTGAGATTACAGTGGAG
2798241 TGGATTAAAA
Statistics
Matches: 372, Mismatches: 66, Indels: 54
0.76 0.13 0.11
Matches are distributed among these distances:
38 3 0.01
39 23 0.06
40 1 0.00
41 31 0.08
42 7 0.02
43 30 0.08
44 201 0.54
45 6 0.02
46 66 0.18
47 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
Done.