Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold119
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: 3173904
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 20
Found at i:2271179 original size:28 final size:28
Alignment explanation
Indices: 2271127--2271181 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2271117 TTTTTTCATA
* *
2271127 ATCGGGGGTACTCCAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCTATTATTTC
2271155 ATCGGGGATACTCCAA-CCTCATTATTT
1 ATCGGGGATACTCCAACCCT-ATTATTT
2271182 TTGAGGGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTATTATTTC
Found at i:2271220 original size:109 final size:107
Alignment explanation
Indices: 2270972--2271282 Score: 308
Period size: 109 Copynumber: 2.9 Consensus size: 107
2270962 CCGCAATCGA
* * * * *
2270972 GGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATTTT-TCACAACTGGGGATACTCCAAC
1 GGATACTCCAACCCCGACTTTATATCCAAAAATACCAATTTTCT-ATAA-TGGGGATACTCCAAC
** *
2271035 CCCATTATTTAATCGGGGATACTCCAACCCCATTATTTCCGAGG
64 CCTGTTATTTCATCGGGGATACTCCAACCCCATTATTTCCGAGG
* *** * *
2271079 GGATACTCCAACCCCGGCTTTATATCCAAAAATATTGATTTTTTCATAATCGGGGGTACTCCAAC
1 GGATACTCCAACCCCGACTTTATATCCAAAAATACCAATTTTCT-ATAAT-GGGGATACTCCAAC
* **
2271144 CCTGTTATTTCATCGGGGATACTCCAACCTCATTATTTTTGAGG
64 CCTGTTATTTCATCGGGGATACTCCAACCCCATTATTTCCGAGG
* * * * *
2271188 GGATACTCTAACCCCGATTTTATTTTTC-AAAATACCAATTTTCTATAATGAGGGATACTCTAAC
1 GGATACTCCAACCCCGACTTTA-TATCCAAAAATACCAATTTTCTATAATG-GGGATACTCCAAC
*
2271252 CTTGTTATTTC--CGAAGGGATACTCCAACCCC
64 CCTGTTATTTCATCG--GGGATACTCCAACCCC
2271283 GATTTTATTT
Statistics
Matches: 168, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
106 2 0.01
107 24 0.14
108 52 0.31
109 87 0.52
110 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (107 bp):
GGATACTCCAACCCCGACTTTATATCCAAAAATACCAATTTTCTATAATGGGGATACTCCAACCC
TGTTATTTCATCGGGGATACTCCAACCCCATTATTTCCGAGG
Found at i:2271310 original size:80 final size:79
Alignment explanation
Indices: 2271159--2271331 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 79
2271149 TATTTCATCG
** * * *
2271159 GGGATACTCCAACCTCATTATTTTTGAGGGGATACTCTAACCCCGATTTTATTTTTCAAAATACC
1 GGGATACTCCAACCTCATTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCTCAAAATACC
*
2271224 AATTTTCTATAATGA
66 AATTTTC-ATAATCA
* ** **
2271239 GGGATACTCTAACCTTGTTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCT-GGAATACC
1 GGGATACTCCAACCTCATTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCTCAAAATACC
*
2271303 GATTTTTCATAATCA
66 -AATTTTCATAATCA
*
2271318 GGGATACTTCAACC
1 GGGATACTCCAACC
2271332 CCGTTGTTAT
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 24 0.31
80 54 0.69
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (79 bp):
GGGATACTCCAACCTCATTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCTCAAAATACC
AATTTTCATAATCA
Found at i:2278189 original size:10 final size:10
Alignment explanation
Indices: 2278174--2278240 Score: 68
Period size: 11 Copynumber: 6.7 Consensus size: 10
2278164 TCCCATTAAC
2278174 AAAAAAACAA
1 AAAAAAACAA
2278184 AAAAAAAC--
1 AAAAAAACAA
*
2278192 -AAAAAGCAA
1 AAAAAAACAA
2278201 AAAAACAACAA
1 AAAAA-AACAA
2278212 AAAAAAACAA
1 AAAAAAACAA
*
2278222 AGAAAAAAGAGA
1 A-AAAAAACA-A
2278234 AAAAAAA
1 AAAAAAA
2278241 AAGAACCTAC
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.12
10 18 0.38
11 22 0.46
12 2 0.04
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:2278194 original size:18 final size:19
Alignment explanation
Indices: 2278171--2278216 Score: 69
Period size: 17 Copynumber: 2.5 Consensus size: 19
2278161 GCATCCCATT
2278171 AACAAAAAAACAAAAAAA-
1 AACAAAAAAACAAAAAAAC
*
2278189 AAC-AAAAAGCAAAAAAAC
1 AACAAAAAAACAAAAAAAC
2278207 AACAAAAAAA
1 AACAAAAAAA
2278217 AACAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 13 0.54
18 6 0.25
19 5 0.21
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (19 bp):
AACAAAAAAACAAAAAAAC
Found at i:2278207 original size:25 final size:25
Alignment explanation
Indices: 2278173--2278242 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
2278163 ATCCCATTAA
2278173 CAAAAAAACAAAAAAAAACAA-AAAG
1 CAAAAAAACAAAAAAAAA-AACAAAG
2278198 CAAAAAAACAACAAAAAAAAACAAAG
1 CAAAAAAACAA-AAAAAAAAACAAAG
*
2278224 -AAAAAAGAGAAAAAAAAAA
1 CAAAAAA-ACAAAAAAAAAA
2278243 GAACCTACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
25 27 0.66
26 14 0.34
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (25 bp):
CAAAAAAACAAAAAAAAAAACAAAG
Found at i:2278229 original size:33 final size:34
Alignment explanation
Indices: 2278171--2278239 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
2278161 GCATCCCATT
2278171 AACAAAAAAACAAAAAAAAACAAAAAG-CAAAAA
1 AACAAAAAAACAAAAAAAAACAAAAAGACAAAAA
* *
2278204 AACAACAAAAA-AAAACAAAGA-AAAAAGAGAAAAA
1 AACAA-AAAAACAAAA-AAAAACAAAAAGACAAAAA
2278238 AA
1 AA
2278240 AAAGAACCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (34 bp):
AACAAAAAAACAAAAAAAAACAAAAAGACAAAAA
Found at i:2278243 original size:13 final size:13
Alignment explanation
Indices: 2278182--2278244 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
2278172 ACAAAAAAAC
2278182 AAAAAAAA-ACAA
1 AAAAAAAAGACAA
*
2278194 AAAGCAAAAAAACAA
1 AAA--AAAAAGACAA
2278209 CAAAAAAAA-ACAA
1 -AAAAAAAAGACAA
* *
2278222 AGAAAAAAGAGAA
1 AAAAAAAAGACAA
2278235 AAAAAAAAGA
1 AAAAAAAAGA
2278245 ACCTACTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
12 10 0.23
13 16 0.37
14 10 0.23
15 4 0.09
16 3 0.07
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGACAA
Found at i:2279304 original size:55 final size:56
Alignment explanation
Indices: 2279228--2279693 Score: 541
Period size: 55 Copynumber: 8.3 Consensus size: 56
2279218 TTCACTTTTT
* *
2279228 AGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCC
* * * *
2279283 AGTCCTCAAAGAGCAGGATGCCTTTTCTTTTTAAAGCTCACACAAGTTGGTGGAACCTT-TC
1 AGTCCTCAAAGAGCAGGACGCC-TTTC-----AAAGCCCACACAAGTTGGTGGCACCTTCCC
* * *
2279344 AGTCCTCAAAGAGCAAGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCC
* *
2279399 AGCCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCC
* * *
2279454 AGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCC
* * *
2279509 AGTCCTCAAAGAGCAGGACCCCTTTCAAATCCCACACAAGTTGGTGGCACCTT-TC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCC
* * * ** ***
2279564 AGTCCTCAAAGAGCAAGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCCC
* * * *
2279621 AGTCCTCAAAGAGCAAGATGCCTTTTAAAGCCCACACAAGTTGGTCGCA-CTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCC
* *
2279676 AATCCTCAAAGAGTAGGA
1 AGTCCTCAAAGAGCAGGA
2279694 AGCTCTCTCC
Statistics
Matches: 362, Mismatches: 38, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
54 3 0.01
55 255 0.70
56 7 0.02
57 47 0.13
60 4 0.01
61 43 0.12
62 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (56 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCC
Found at i:2279559 original size:165 final size:164
Alignment explanation
Indices: 2279231--2279693 Score: 604
Period size: 165 Copynumber: 2.8 Consensus size: 164
2279221 ACTTTTTAGT
* *
2279231 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAG
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
* * *
2279296 CAGGATGCCTTTTCTTTTTAAAGCTCACACAAGTTGGTGGAACCTTT-CAGTCCTCAAAGAGCAA
66 CAGGATGCC-TTTC-----AAAGCCCACACAAGTTGGTGG--CATTTCCAGTCCTCAAAGAGCAG
**
2279360 GATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGC
123 GACCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGC
* *
2279402 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAG
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
*
2279467 CAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTCCTAGTCCTCAAAGAGCAGGACCCCT
66 CAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTCC-AGTCCTCAAAGAGCAGGACCCCT
* *
2279532 TTCAAATCCCACACAAGTTGGTGGCACCTTTCAGT
130 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGC
* * * **
2279567 CCTCAAAGAGCAAGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAG
1 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA--CTTCCTAGTCCTCAAAG
* * * * * *
2279632 AGCAAGATGCCTTTTAAAGCCCACACAAGTTGGTCGCACTTCCCAATCCTCAAAGAGTAGGA
64 AGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTCCAGTCCTCAAAGAGCAGGA
2279694 AGCTCTCTCC
Statistics
Matches: 261, Mismatches: 26, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
163 4 0.02
164 1 0.00
165 116 0.44
167 63 0.24
168 4 0.02
170 4 0.02
171 69 0.26
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (164 bp):
CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
CAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTCCAGTCCTCAAAGAGCAGGACCCCTT
TCAAAGCCCACACAAGTTGGTGGCACCTTTCAGC
Found at i:2279795 original size:28 final size:28
Alignment explanation
Indices: 2279714--2279797 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
2279704 TTTCGCCCTT
*
2279714 TAGTCCTCAAAGAGCAGGACGCCTTTTA
1 TAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * ** **
2279742 AAGCCCACACA-AGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGC-CTTTTC
2279770 TAGTCCTCAAAGAGCAGGACGCCTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTC
2279798 CTGTTAAAGC
Statistics
Matches: 37, Mismatches: 17, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
27 6 0.16
28 25 0.68
29 6 0.16
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (28 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTC
Found at i:2279894 original size:211 final size:205
Alignment explanation
Indices: 2279508--2279913 Score: 553
Period size: 211 Copynumber: 1.9 Consensus size: 205
2279498 TGGCATTTCC
*
2279508 TAGTCCTCAAAGAGCAGGACCCCTTTCAAATCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* *
2279573 AGAGCAAGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAGAGCAAG
66 AGAGCAAGACACCTTTTAAAGCCCACACAAGTGGGTGGCA-TTTTTTCAGTCCTCAAAGAGCAAG
* * ** *
2279638 ATGCCTTTTAAAGCCCACACAAGTTGGTCGCACTTCCCAATCCTCAAAGAGTAGGAAGCTCTCTC
130 ACGCCTTTCAAAGCCCACACAAGTCAGTCGCACTTCCCAATCCTCAAAGAGCAGGAAGCTCTCTC
2279703 CTTTCGCCCTT
195 CTTTCGCCCTT
* * *
2279714 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCA
1 TAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCA
* * *
2279779 AAGAGCAGGACGCCTTTTCCTGTTAAAGCCTACACAAGTGGGTGGCA-TTTTTCAGTCCTCAAAG
65 AAGAGCAAGACACC---T--T-TTAAAGCCCACACAAGTGGGTGGCATTTTTTCAGTCCTCAAAG
* * * * *
2279843 AGCAGGACGCCTTTCAAAGCCCACACAAGTCAGTGGCATTTTCCAATCCTCAAAGAGCAGGATGC
124 AGCAAGACGCCTTTCAAAGCCCACACAAGTCAGTCGCACTTCCCAATCCTCAAAGAGCAGGAAGC
*
2279908 TTTCTC
189 TCTCTC
2279914 TTTGCAAAGC
Statistics
Matches: 173, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
206 52 0.30
207 20 0.12
210 1 0.01
211 76 0.44
212 1 0.01
213 23 0.13
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (205 bp):
TAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
AGAGCAAGACACCTTTTAAAGCCCACACAAGTGGGTGGCATTTTTTCAGTCCTCAAAGAGCAAGA
CGCCTTTCAAAGCCCACACAAGTCAGTCGCACTTCCCAATCCTCAAAGAGCAGGAAGCTCTCTCC
TTTCGCCCTT
Found at i:2279951 original size:116 final size:117
Alignment explanation
Indices: 2279715--2279972 Score: 344
Period size: 116 Copynumber: 2.2 Consensus size: 117
2279705 TTCGCCCTTT
* ** * *
2279715 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCAGTGGCACTTTTCCAATCCTCAA
** *
2279780 AGAGCAGGACGCCTTTTCCTGTTAAAGCCTACACAAGTGGGTGGCATTTTTC
66 AGAGCAGGACGCCTTTTCCTGTTAAAGCCTACACAAGTGGGTGGCACCTTCC
2279832 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCAGTGGCA-TTTTCCAATCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCAGTGGCACTTTTCCAATCCTCAA
* * *
2279896 AGAGCAGGATG-C-TTTCTCT-TTGCAAAGCCTATACAAGTTGGTGGCACCTTCC
66 AGAGCAGGACGCCTTTTC-CTGTT--AAAGCCTACACAAGTGGGTGGCACCTTCC
* *
2279948 AGTCCTCAAAAAGCAGGATGCCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTT
2279973 TTTTTTTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
114 6 0.05
115 3 0.02
116 70 0.56
117 46 0.37
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (117 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCAGTGGCACTTTTCCAATCCTCAA
AGAGCAGGACGCCTTTTCCTGTTAAAGCCTACACAAGTGGGTGGCACCTTCC
Found at i:2279954 original size:61 final size:60
Alignment explanation
Indices: 2279715--2280030 Score: 296
Period size: 61 Copynumber: 5.3 Consensus size: 60
2279705 TTCGCCCTTT
*
2279715 AGTCCTCAAAGAGCAGGACGC---CT-TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCTTTCTCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCC
* * * *
2279771 AGTCCTCAAAGAGCAGGACGCCTTT-TCCTGTT-AAAGCCTACACAAGTGGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACG-CTTTCT-CT-TTCAAAGCCCACACAAGTTGGTGGCACTTTCC
** *
2279832 AGTCCTCAAAGAGCAGGACG----C-CTTTCAAAGCCCACACAAGTCAGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTCTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * * *
2279887 AATCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCTATACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTCTCTTT-CAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * * * **
2279948 AGTCCTCAAAAAGCAGGATGCCTTTTTTTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACG-C-TTTCTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
*
2280010 AGTCCTCAAAGAGCAGAACGC
1 AGTCCTCAAAGAGCAGGACGC
2280031 ACTTTATTTT
Statistics
Matches: 213, Mismatches: 30, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
54 2 0.01
55 45 0.21
56 20 0.09
57 1 0.00
59 2 0.01
60 4 0.02
61 67 0.31
62 65 0.31
63 7 0.03
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCTTTCTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:2280014 original size:62 final size:61
Alignment explanation
Indices: 2279736--2280025 Score: 294
Period size: 62 Copynumber: 4.8 Consensus size: 61
2279726 AGCAGGACGC
*
2279736 CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTT-T
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGATG-CTTTCT
* * * * *
2279797 CCTGTT-AAAGCCTACACAAGTGGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA--C--GC-
1 -CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
** *
2279853 C-TTTCAAAGCCCACACAAGTCAGTGGCA-TTTTCCAATCCTCAAAGAGCAGGATGCTTTCT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGATGCTTTCT
* * * * * * *
2279913 CTTTGCAAAGCCTATACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGATGCCTTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG-CTTTCT
* * *
2279975 TTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAG
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAG
2280026 AACGCACTTT
Statistics
Matches: 187, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
54 6 0.03
55 39 0.21
57 1 0.01
58 1 0.01
59 1 0.01
60 1 0.01
61 59 0.32
62 79 0.42
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (61 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
Found at i:2280073 original size:42 final size:41
Alignment explanation
Indices: 2280006--2280174 Score: 130
Period size: 42 Copynumber: 3.9 Consensus size: 41
2279996 TGGTGGCACT
* *
2280006 TTTTAGTCCTCAAAGAGCAGAACGCACTTT-ATTTTCCTCTTTC
1 TTTT-GTCCTCAAAGAGTAGGACGCA-TTTCATTTTCCT-TTTC
* *
2280049 TTTTGTCCTTAAAGAGTAGGACGCATTTCGTTTTCCTTTTC
1 TTTTGTCCTCAAAGAGTAGGACGCATTTCATTTTCCTTTTC
*
2280090 TCCTTTGTCCTCAAAGAGTAGGA--CATGTTCCATTCCCTTCTTTTTTCC
1 T--TTTGTCCTCAAAGAGTAGGACGCAT-TT-CATT---TTC-CTTTT-C
* * *
2280138 TTTTATCCTCAAAGAGCAGGACGCACTTCA-TTTCCTT
1 TTTTGTCCTCAAAGAGTAGGACGCATTTCATTTTCCTT
2280175 CTTTTCCTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 26
0.74 0.08 0.19
Matches are distributed among these distances:
41 13 0.13
42 30 0.29
43 26 0.25
45 1 0.01
46 23 0.22
47 6 0.06
48 4 0.04
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (41 bp):
TTTTGTCCTCAAAGAGTAGGACGCATTTCATTTTCCTTTTC
Found at i:2280175 original size:46 final size:44
Alignment explanation
Indices: 2280006--2280204 Score: 151
Period size: 46 Copynumber: 4.5 Consensus size: 44
2279996 TGGTGGCACT
* *
2280006 TTTTAGTCCTCAAAGAGCAGAACGCACTTTATTTTCC-TC-TTT-C
1 TTTTA-TCCTCAAAGAGCAGGACGCACTTCA-TTTCCTTCTTTTCC
* * * * * *
2280049 TTTTGTCCTTAAAGAGTAGGACGCATTTCGTTTTCCTT-TTCTCC
1 TTTTATCCTCAAAGAGCAGGACGCACTTC-ATTTCCTTCTTTTCC
* * * *
2280093 -TTTGTCCTCAAAGAGTAGGA--CATGTTCCATTCCCTTCTTTTTTCC
1 TTTTATCCTCAAAGAGCAGGACGCA-CTT-CATTTCCTTC--TTTTCC
2280138 TTTTATCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCC
1 TTTTATCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCC
*
2280182 TTTCTAGTCCTTAAAGAGCAGGA
1 TTT-TA-TCCTCAAAGAGCAGGA
2280205 AACATTTTGT
Statistics
Matches: 124, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
41 2 0.02
42 32 0.26
43 27 0.22
44 10 0.08
45 7 0.06
46 42 0.34
47 2 0.02
48 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (44 bp):
TTTTATCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCC
Found at i:2280226 original size:46 final size:43
Alignment explanation
Indices: 2280129--2280230 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 43
2280119 CCATTCCCTT
**
2280129 CTTTTTTCCTTTTATCCTCAAAGAGCAGGACGCACTTCATTTC
1 CTTTTTTCCTTTTATCCTCAAAGAGCAGGAAACACTTCATTTC
* * **
2280172 CTTCTTTTCCTTTCTAGTCCTTAAAGAGCAGGAAACATTTTGTTTTC
1 CTT-TTTTCCTTT-TA-TCCTCAAAGAGCAGGAAACA-CTTCATTTC
2280219 CTTTTTTCCTTT
1 CTTTTTTCCTTT
2280231 GTCCTCGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.06
44 9 0.18
45 2 0.04
46 26 0.53
47 9 0.18
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.46
Consensus pattern (43 bp):
CTTTTTTCCTTTTATCCTCAAAGAGCAGGAAACACTTCATTTC
Found at i:2280350 original size:40 final size:38
Alignment explanation
Indices: 2280257--2280351 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 38
2280247 ACGTACTCTT
* **
2280257 TTTCACTTTGTCCTCAAGAAGCAAGACACTTTCTTTTTT
1 TTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCTTCTCA
*
2280296 TTTCCTTTGTCCTCAAGGAGCAAGAC-CTATTTCATTCTCA
1 TTTCCTTTGTCCTCAAGAAGCAAGACAC--TTTC-TTCTCA
2280336 TTTCCTTTGTCCTCAA
1 TTTCCTTTGTCCTCAA
2280352 AAAGTGGGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 1 0.02
38 21 0.43
39 8 0.16
40 19 0.39
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (38 bp):
TTTCCTTTGTCCTCAAGAAGCAAGACACTTTCTTCTCA
Found at i:2280962 original size:20 final size:20
Alignment explanation
Indices: 2280937--2281006 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 20
2280927 TTTTCATAAT
*
2280937 TTGTATTGATACATTATTCA
1 TTGTATCGATACATTATTCA
2280957 TTGTATC---A-A-T--TCA
1 TTGTATCGATACATTATTCA
**
2280970 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTATTCA
2280990 TTGTATCGATACATTAT
1 TTGTATCGATACATTAT
2281007 ATCAATACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
13 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
20 24 0.60
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:2280970 original size:13 final size:13
Alignment explanation
Indices: 2280952--2280976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2280942 TTGATACATT
2280952 ATTCATTGTATCA
1 ATTCATTGTATCA
2280965 ATTCATTGTATC
1 ATTCATTGTATC
2280977 GATACATTGC
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTCATTGTATCA
Found at i:2280984 original size:13 final size:13
Alignment explanation
Indices: 2280955--2281018 Score: 50
Period size: 13 Copynumber: 5.4 Consensus size: 13
2280945 ATACATTATT
*
2280955 CATTGTATCAATT
1 CATTGTATCAATA
*
2280968 CATTGTATCGATA
1 CATTGTATCAATA
2280981 CATTG---C--T-
1 CATTGTATCAATA
*
2280988 CATTGTATCGATA
1 CATTGTATCAATA
*
2281001 CATTATATCAATA
1 CATTGTATCAATA
2281014 CATTG
1 CATTG
2281019 CTCATTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
7 5 0.12
8 1 0.03
10 2 0.05
12 1 0.03
13 31 0.77
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:2281015 original size:33 final size:33
Alignment explanation
Indices: 2280945--2281037 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
2280935 ATTTGTATTG
** * * * *
2280945 ATACATTATTCATTGTATCAATTCATTGTATCG
1 ATACATTGCTCATTGTATCGATACATTATATCA
2280978 ATACATTGCTCATTGTATCGATACATTATATCA
1 ATACATTGCTCATTGTATCGATACATTATATCA
*
2281011 ATACATTGCTCATTATATCGATACATT
1 ATACATTGCTCATTGTATCGATACATT
2281038 TTACAATGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (33 bp):
ATACATTGCTCATTGTATCGATACATTATATCA
Found at i:2283437 original size:51 final size:51
Alignment explanation
Indices: 2283361--2283525 Score: 156
Period size: 51 Copynumber: 3.3 Consensus size: 51
2283351 TTTCATCTCG
* * * ** **
2283361 GGGATACTCCAA-TCCCGGTTCTATTTCCAAAACATTAATTTTTCTTAATC-
1 GGGATACTCCAACT-CCGATTTTATTTCCAAAACATCAATTTACCGCAATCA
* * * *
2283411 GAGGATACTCCAACTCCGATTTTATTTCTAAAGCCTCGATTTACCGCAATCA
1 G-GGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTACCGCAATCA
* * * *
2283463 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTT-TCACAATTA
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTACCGCAATCA
2283513 GGGATACTCCAAC
1 GGGATACTCCAAC
2283526 CCCGTTATTT
Statistics
Matches: 93, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 20 0.22
51 71 0.76
52 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTACCGCAATCA
Found at i:2283545 original size:28 final size:27
Alignment explanation
Indices: 2283513--2283583 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
2283503 TTCACAATTA
*
2283513 GGGATACTCCAACCCCGTTA-TTTCATCG
1 GGGATACTCCAACCCCATTATTTTCA--G
*
2283541 GGGATACTCCAATCCCATTATTTTCGAG
1 GGGATACTCCAACCCCATTATTTTC-AG
2283569 GGGATACTCCAACCC
1 GGGATACTCCAACCC
2283584 TGGCTTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 33 0.87
29 4 0.11
30 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (27 bp):
GGGATACTCCAACCCCATTATTTTCAG
Found at i:2283659 original size:28 final size:28
Alignment explanation
Indices: 2283621--2283694 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
2283611 TTTCATAATC
2283621 AGGGG-TACTCCAACCCCGTTATTTCAT-
1 AGGGGATACTCCAACCCCGTTATTT-ATG
* * *
2283648 CGGGGATACTCCAATCCCGTTATTTTTG
1 AGGGGATACTCCAACCCCGTTATTTATG
2283676 AGGGGATACTCCAACCCCG
1 AGGGGATACTCCAACCCCG
2283695 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
27 5 0.12
28 35 0.88
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (28 bp):
AGGGGATACTCCAACCCCGTTATTTATG
Found at i:2283701 original size:109 final size:106
Alignment explanation
Indices: 2283463--2283741 Score: 344
Period size: 109 Copynumber: 2.6 Consensus size: 106
2283453 ACCGCAATCA
* * *
2283463 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCACAATTAGGGATACTCCAACCC
1 GGGATACTCCAACCCCGATTTTATATCCAAAACACCAATTTTCACAATCAGGGATACTCCAACCC
2283528 CGTTATTTCATCGGGGATACTCCAATCCCATTATTTTCGAG
66 CGTTATTTCATCGGGGATACTCCAATCCCATTATTTTCGAG
* ** * ** * * *
2283569 GGGATACTCCAACCCTGGCTTTATATCCAAAAATATTGATTTTTTCATAATCAGGGGTACTCCAA
1 GGGATACTCCAACCCCGATTTTATATCC-AAAACA-CCA-ATTTTCACAATCAGGGATACTCCAA
* *
2283634 CCCCGTTATTTCATCGGGGATACTCCAATCCCGTTATTTTTGAG
63 CCCCGTTATTTCATCGGGGATACTCCAATCCCATTATTTTCGAG
* * * *
2283678 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATC-GAGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATATCCAAAACACCAA-TTTTCACAATCAG-GGATACTCCAAC
2283742 TCTAATTTTA
Statistics
Matches: 145, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
106 24 0.17
107 28 0.19
108 7 0.05
109 86 0.59
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (106 bp):
GGGATACTCCAACCCCGATTTTATATCCAAAACACCAATTTTCACAATCAGGGATACTCCAACCC
CGTTATTTCATCGGGGATACTCCAATCCCATTATTTTCGAG
Found at i:2283739 original size:51 final size:50
Alignment explanation
Indices: 2283678--2283839 Score: 173
Period size: 51 Copynumber: 3.2 Consensus size: 50
2283668 TATTTTTGAG
* *
2283678 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTTCATAATC
* ** * * *
2283728 GAGGATACTCCAACTCTAATTTTATTTCCAAAATATTGATTTCTCATAATC
1 G-GGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTTCATAATC
* ** *
2283779 GGAGATACTGCAACCCCGACCTTATTTCT-AAATCATCGATTTTTCACAATC
1 GG-GATACTCCAACCCCGATTTTATTTCTAAAAT-ATCGATTTTTCATAATC
2283830 GGGGATACTC
1 -GGGATACTC
2283840 TAATCTCGTT
Statistics
Matches: 89, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
50 6 0.07
51 81 0.91
52 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTTCATAATC
Found at i:2283914 original size:79 final size:80
Alignment explanation
Indices: 2283803--2283963 Score: 211
Period size: 79 Copynumber: 2.0 Consensus size: 80
2283793 CCCGACCTTA
* * * *
2283803 TTTCTAAATCATCGATTTTTCACAATCGGGGATACTCTAA-TCTCGTTATTTTCGAAGGGATACT
1 TTTCCAAATCATCGATTTTTCACAATCAGGGATACTCCAACCCT-GTTATTTTCGAAGGGATACT
*
2283867 CTAACCCCAATTTTAT
65 CCAACCCCAATTTTAT
* *
2283883 TTTCCAAAT-ATCGATTTTCTC-TAATCAGGGATACTCCAACCCTGTTATTTTCGAGGGGATACT
1 TTTCCAAATCATCGATTTT-TCACAATCAGGGATACTCCAACCCTGTTATTTTCGAAGGGATACT
*
2283946 CCAACCCCAGTTTTAT
65 CCAACCCCAATTTTAT
2283962 TT
1 TT
2283964 CTGGAACACC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
79 59 0.83
80 12 0.17
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (80 bp):
TTTCCAAATCATCGATTTTTCACAATCAGGGATACTCCAACCCTGTTATTTTCGAAGGGATACTC
CAACCCCAATTTTAT
Found at i:2284009 original size:79 final size:79
Alignment explanation
Indices: 2283815--2284010 Score: 204
Period size: 79 Copynumber: 2.5 Consensus size: 79
2283805 TCTAAATCAT
* * *
2283815 CGATTTTTCACAATCGGGGATAC-TCTAA-TCTCGTTATTTTCGAAGGGATACTCTAACCCCAAT
1 CGATTTTCCATAATCGGGGATACTTC-AACTC-CGTTATTTTCGAAGGGATACTCCAACCCCAAT
* *
2283878 TTTATTTTCCAAATAT
64 TTTATTTTCCAAACAC
* * * *
2283894 CGATTTTCTC-TAATCAGGGATACTCCAAC-CCTGTTATTTTCGAGGGGATACTCCAACCCCAGT
1 CGATTTTC-CATAATCGGGGATACTTCAACTCC-GTTATTTTCGAAGGGATACTCCAACCCCAAT
**
2283957 TTTA-TTTCTGGAACAC
64 TTTATTTTC-CAAACAC
*
2283973 CGATTTTCCATAATCGGGGATACTTCAGCTCCGTTATT
1 CGATTTTCCATAATCGGGGATACTTCAACTCCGTTATT
2284011 ATCTCCAACC
Statistics
Matches: 96, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
78 6 0.06
79 86 0.90
80 4 0.04
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (79 bp):
CGATTTTCCATAATCGGGGATACTTCAACTCCGTTATTTTCGAAGGGATACTCCAACCCCAATTT
TATTTTCCAAACAC
Found at i:2285997 original size:20 final size:21
Alignment explanation
Indices: 2285972--2286025 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
2285962 ATTTGGGACA
**
2285972 ATGTATCGATACAATT-TGTT
1 ATGTATCGATACAATTGTGCC
2285992 ATGTATCGATAC-ATTGTGCC
1 ATGTATCGATACAATTGTGCC
2286012 ATGTATCGATACAA
1 ATGTATCGATACAA
2286026 ATAGTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (21 bp):
ATGTATCGATACAATTGTGCC
Found at i:2288620 original size:13 final size:13
Alignment explanation
Indices: 2288602--2288685 Score: 76
Period size: 13 Copynumber: 7.1 Consensus size: 13
2288592 TAGTAACCCA
2288602 TGTATCGATACAT
1 TGTATCGATACAT
* *
2288615 TGTATCAATACAA
1 TGTATCGATACAT
2288628 TGTATCGATACA-
1 TGTATCGATACAT
*
2288640 ---A-AGA-ACAT
1 TGTATCGATACAT
*
2288648 TGTATCAATACAT
1 TGTATCGATACAT
2288661 TGTAT-GA-ACAT
1 TGTATCGATACAT
2288672 TGTATCGATACAT
1 TGTATCGATACAT
2288685 T
1 T
2288686 TGGGTTTTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
7 3 0.05
8 2 0.04
9 1 0.02
11 10 0.18
12 4 0.07
13 36 0.64
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2288653 original size:20 final size:21
Alignment explanation
Indices: 2288628--2288684 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 21
2288618 ATCAATACAA
2288628 TGTATCGATACA-AAGAACAT
1 TGTATCGATACATAAGAACAT
* *
2288648 TGTATCAATACATTGTATGAACAT
1 TGTATCGATACA---TAAGAACAT
2288672 TGTATCGATACAT
1 TGTATCGATACAT
2288685 TTGGGTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 11 0.37
21 1 0.03
24 18 0.60
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATAAGAACAT
Found at i:2293478 original size:20 final size:21
Alignment explanation
Indices: 2293453--2293505 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2293443 TACAAGCCAA
* *
2293453 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
*
2293473 TGTATCGTTAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
2293493 TGTATCGATACAA
1 TGTATCGATACAA
2293506 GTTTGGCTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:2293510 original size:19 final size:19
Alignment explanation
Indices: 2293453--2293511 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
2293443 TACAAGCCAA
* *
2293453 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
*
2293473 TGTATCGTTACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
2293493 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
2293512 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 6 0.18
20 26 0.79
21 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:2295616 original size:21 final size:20
Alignment explanation
Indices: 2295587--2295629 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2295577 GGCTAGTATG
* *
2295587 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCAACCT
*
2295608 GGGAGTGCCGGTCGCAACCT
1 GGGACTGCCGGTCGCAACCT
2295628 GG
1 GG
2295630 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCAACCT
Found at i:2296088 original size:13 final size:13
Alignment explanation
Indices: 2296070--2296108 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2296060 ATAATCCCCC
*
2296070 TGTATCGATACAG
1 TGTATCGATACAA
2296083 TGTATCGATACAA
1 TGTATCGATACAA
2296096 TGTATCGATACAA
1 TGTATCGATACAA
2296109 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2302296 original size:13 final size:13
Alignment explanation
Indices: 2302278--2302303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2302268 CAATTTTTTG
2302278 TGTATCGATACAT
1 TGTATCGATACAT
2302291 TGTATCGATACAT
1 TGTATCGATACAT
2302304 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2302300 original size:33 final size:33
Alignment explanation
Indices: 2302258--2302322 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2302248 TACAAACCAA
* *
2302258 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
2302291 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
2302323 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:2302427 original size:20 final size:20
Alignment explanation
Indices: 2302375--2302429 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2302365 CATATTTTTG
*
2302375 ATGTATCGATACATTGCAAC
1 ATGTATCGATACTTTGCAAC
*
2302395 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-C
2302415 ATGTATCGATACTTT
1 ATGTATCGATACTTT
2302430 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAC
Found at i:2303216 original size:3 final size:3
Alignment explanation
Indices: 2303208--2303235 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2303198 TGAGTTAACT
2303208 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2303236 TATCTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:2305567 original size:4 final size:4
Alignment explanation
Indices: 2305560--2305605 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
2305550 AAAGTTAGAT
2305560 AAGA AAGA AAGA AAGA AAGA AAG- AAGA TGAAG- AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA --AAGA AAGA AAGA AAGA AA
2305606 AAGAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 6 0.16
4 29 0.76
6 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:2305617 original size:9 final size:9
Alignment explanation
Indices: 2305595--2305625 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2305585 GATGAAGAAG
2305595 AAAGAAAGAA
1 AAAGAAA-AA
2305605 AAAGAAAAA
1 AAAGAAAAA
2305614 AAAGAAAAA
1 AAAGAAAAA
2305623 AAA
1 AAA
2305626 TATGAAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:2305619 original size:15 final size:17
Alignment explanation
Indices: 2305560--2305622 Score: 71
Period size: 16 Copynumber: 3.9 Consensus size: 17
2305550 AAAGTTAGAT
*
2305560 AAGAAAGAAAGAAAGA-
1 AAGAAAGAAAGAAAAAG
**
2305576 AAGAAAG-AAGATGAAG
1 AAGAAAGAAAGAAAAAG
2305592 AAGAAAGAAAGAAAAAG
1 AAGAAAGAAAGAAAAAG
2305609 AA-AAA-AAAGAAAAA
1 AAGAAAGAAAGAAAAA
2305623 AAATATGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 14 0.35
16 17 0.43
17 9 0.22
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAGAAAGAAAGAAAAAG
Found at i:2312072 original size:14 final size:16
Alignment explanation
Indices: 2312041--2312087 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2312031 AAAAAAAGTC
2312041 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
2312057 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
2312071 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
2312087 A
1 A
2312088 TAAAAAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:2312109 original size:37 final size:36
Alignment explanation
Indices: 2312032--2312109 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 36
2312022 CAAAATGACA
* *
2312032 AAAAAAGTCAAAAGCAAAAGCACAAAAAATGAAAAG
1 AAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAAC
*
2312068 AAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGGAACAAC
1 AAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GGAA-AAC
2312105 AAAAA
1 AAAAA
2312110 TAAAAAACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 6 0.17
36 12 0.33
37 18 0.50
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.05
Consensus pattern (36 bp):
AAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAAC
Found at i:2313437 original size:28 final size:28
Alignment explanation
Indices: 2313399--2313730 Score: 496
Period size: 28 Copynumber: 12.0 Consensus size: 28
2313389 CTGTGACCTC
*
2313399 TTTAAAGTCCACAACTCCGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
2313427 TTTAGAGTCCATAACTCCGTGGCATCTCT
1 TTTAAAGTCCACAACTCCGTGGCA-CCCT
*
2313456 TTT-AAGTCCACAACTCTGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
2313483 TTT-AAGTCCACAAGTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
2313510 TTTAAAGTCCACAACTCCGTGGTACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
2313538 TTTAAAGTCCACAACTTCGTGGTACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
2313566 TTTAAAGTCCACAACTTCGTGGCACCCCT
1 TTTAAAGTCCACAACTCCGTGGCA-CCCT
2313595 TTT-AAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
2313622 TTT-AAGTCCACAACTCCGTGGCA-CCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
2313648 TTTAAAGTCCACAACTCCGTGGCACCTT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
2313676 TTTAAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
2313704 TTT-AAGTCCACAAGTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
2313731 CGTAAGTCCA
Statistics
Matches: 281, Mismatches: 18, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
26 6 0.02
27 101 0.36
28 162 0.58
29 12 0.04
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.28
Consensus pattern (28 bp):
TTTAAAGTCCACAACTCCGTGGCACCCT
Found at i:2313518 original size:55 final size:55
Alignment explanation
Indices: 2313399--2313730 Score: 499
Period size: 55 Copynumber: 6.0 Consensus size: 55
2313389 CTGTGACCTC
* * *
2313399 TTTAAAGTCCACAACTCCGTGGCATCCTTTTAGAGTCCATAACTCCGTGGCATCTCT
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTA-AGTCCACAACTCCGTGGCA-CCCT
* *
2313456 TTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAAGTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCT
* * *
2313510 TTTAAAGTCCACAACTCCGTGGTACCCTTTTAAAGTCCACAACTTCGTGGTACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCT
*
2313566 TTTAAAGTCCACAACTTCGTGGCACCCCTTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCT
*
2313622 TTT-AAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCTT
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCT
*
2313676 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAGTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCT
2313731 CGTAAGTCCA
Statistics
Matches: 251, Mismatches: 18, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
53 6 0.02
54 32 0.13
55 103 0.41
56 100 0.40
57 10 0.04
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.28
Consensus pattern (55 bp):
TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:2314780 original size:28 final size:28
Alignment explanation
Indices: 2314699--2314780 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2314689 TTTTGGAGAT
*
2314699 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
2314727 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
2314755 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
2314781 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:2314923 original size:51 final size:51
Alignment explanation
Indices: 2314763--2314933 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2314753 GAAATAACGA
* * *
2314763 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
2314815 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
2314868 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
2314919 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2314934 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:2314979 original size:27 final size:28
Alignment explanation
Indices: 2314916--2314991 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2314906 AAAATAAAGT
*
2314916 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2314944 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2314971 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2314992 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2317471 original size:13 final size:13
Alignment explanation
Indices: 2317453--2317478 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2317443 ACAAAGATCC
2317453 ATGTATCGATACA
1 ATGTATCGATACA
2317466 ATGTATCGATACA
1 ATGTATCGATACA
2317479 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2317474 original size:33 final size:33
Alignment explanation
Indices: 2317432--2317498 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2317422 AAAATTTCCA
***
2317432 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2317465 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2317498 A
1 A
2317499 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2317542 original size:19 final size:18
Alignment explanation
Indices: 2317518--2317585 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2317508 CAGTAGCTAA
2317518 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2317537 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2317552 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2317569 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2317586 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2317558 original size:13 final size:13
Alignment explanation
Indices: 2317540--2317564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2317530 ACAATACTTA
2317540 TGTATCGATACAT
1 TGTATCGATACAT
2317553 TGTATCGATACA
1 TGTATCGATACA
2317565 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2317562 original size:32 final size:32
Alignment explanation
Indices: 2317521--2317583 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2317511 TAGCTAATTA
*
2317521 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2317553 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2317584 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2317647 original size:21 final size:21
Alignment explanation
Indices: 2317621--2317698 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
2317611 GTTGGGACCC
2317621 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
2317642 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
2317662 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
2317683 TGTATCGATACATTTG
1 TGTATCGATACATTTG
2317699 GAAATTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:2317685 original size:41 final size:41
Alignment explanation
Indices: 2317621--2317698 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
2317611 GTTGGGACCC
* *
2317621 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTGTGAA
2317662 TGTATCGATACA-TTCTACAAATGTATCGATACATTTG
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTG
2317699 GAAATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (41 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGTGAA
Found at i:2317902 original size:27 final size:27
Alignment explanation
Indices: 2317872--2317934 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
2317862 CATCCACCAT
2317872 TCCGTGGCACCCTTTTAAGTCCATAAC
1 TCCGTGGCACCCTTTTAAGTCCATAAC
2317899 TCCGTGGCACCCTTTTAAGTCCATAAC
1 TCCGTGGCACCCTTTTAAGTCCATAAC
*
2317926 TCGGTGGCA
1 TCCGTGGCA
2317935 ACACTTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.29
Consensus pattern (27 bp):
TCCGTGGCACCCTTTTAAGTCCATAAC
Found at i:2318086 original size:32 final size:30
Alignment explanation
Indices: 2317902--2318381 Score: 408
Period size: 32 Copynumber: 16.2 Consensus size: 30
2317892 CCATAACTCC
* * *
2317902 GTGGCACCCTTTT--AAGTCCATA-ACTCG
1 GTGGCACCCTTTTCAAAGCCCACACAGTCG
* * *
2317929 GTGGCAACACTTTTCAAAGCCTACA-AGTCA
1 GTGGC-ACCCTTTTCAAAGCCCACACAGTCG
* *
2317959 GTGGCATCCTTTT-AAAGCCCACA-AGTCA
1 GTGGCACCCTTTTCAAAGCCCACACAGTCG
2317987 GTGGCACCC-TTTCAAAGCCCACA-A----
1 GTGGCACCCTTTTCAAAGCCCACACAGTCG
* *
2318011 GTGGCACCC-TTTCAAAGCTCACA-AGTCA
1 GTGGCACCCTTTTCAAAGCCCACACAGTCG
*
2318039 GTGGCACTCTTTTCAAAGCCCACACGAGTCG
1 GTGGCACCCTTTTCAAAGCCCACAC-AGTCG
**
2318070 GTGGCAACCCTTTTCAAAGCCCACA-AGTTA
1 GTGGC-ACCCTTTTCAAAGCCCACACAGTCG
*
2318100 GTGGCATCC-TTTCAAAGCCCACACAAGTCG
1 GTGGCACCCTTTTCAAAGCCCACAC-AGTCG
*
2318130 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGC-ACCCTTTTCAAAGCCCACAC-AGTCG
* *
2318162 ATGGCAACTCTTTTCAAAGCCCACACAAGTCG
1 GTGGC-ACCCTTTTCAAAGCCCACAC-AGTCG
*
2318194 GTGGCAACCCTTTTCAAAGCCCACACAAATCG
1 GTGGC-ACCCTTTTCAAAGCCCACAC-AGTCG
*
2318226 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGC-ACCCTTTTCAAAGCCCACAC-AGTCG
* * * *
2318258 GTGGAAACCTTTTTCAAGGCCCACACAAGTTG
1 GTGG-CACCCTTTTCAAAGCCCACAC-AGTCG
* *
2318290 GTGGCATCC-TTTCAAAGCCCACA-AGTCA
1 GTGGCACCCTTTTCAAAGCCCACACAGTCG
* * *
2318318 GTGGCATCC-TTTCAAAGCCCAC-GAGTCA
1 GTGGCACCCTTTTCAAAGCCCACACAGTCG
* * *
2318346 GTGGCACCTTTTTCAAAGCCCAC-GAGTCA
1 GTGGCACCCTTTTCAAAGCCCACACAGTCG
2318375 GTGGCAC
1 GTGGCAC
2318382 TCACAAGTCG
Statistics
Matches: 392, Mismatches: 42, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
24 23 0.06
27 8 0.02
28 99 0.25
29 48 0.12
30 43 0.11
31 14 0.04
32 157 0.40
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.21
Consensus pattern (30 bp):
GTGGCACCCTTTTCAAAGCCCACACAGTCG
Found at i:2318431 original size:32 final size:32
Alignment explanation
Indices: 2318383--2318489 Score: 178
Period size: 32 Copynumber: 3.3 Consensus size: 32
2318373 CAGTGGCACT
* *
2318383 CACAAGTCGATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTTGCAACCCATTTCAAAGCCCA
*
2318415 CACAAGTTGGTTGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTTGCAACCCATTTCAAAGCCCA
*
2318447 CACAAGTCGGTTGCAACCCATTTCGAAGCCCA
1 CACAAGTCGGTTGCAACCCATTTCAAAGCCCA
2318479 CACAAGTCGGT
1 CACAAGTCGGT
2318490 GCCAATTAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.19
Consensus pattern (32 bp):
CACAAGTCGGTTGCAACCCATTTCAAAGCCCA
Found at i:2318577 original size:44 final size:45
Alignment explanation
Indices: 2318511--2318630 Score: 125
Period size: 49 Copynumber: 2.6 Consensus size: 45
2318501 TCCGATATCG
* *
2318511 CTGGCCTTGAATCAGCATATTGGCACTTT-CTAAGCCCAATGTCA
1 CTGGCCTTGAATTAGCACATTGGCACTTTCCTAAGCCCAATGTCA
* * *
2318555 CTGGCCTTGAGTTAGCACATTGGTCCACTTTTCCCTTAGCCCGATGTCA
1 CTGGCCTTGAATTAGCACATTGG--CAC-TTT-CCTAAGCCCAATGTCA
* * *
2318604 TTGACCTTGAATTGGCACATTGGCACT
1 CTGGCCTTGAATTAGCACATTGGCACT
2318631 CCTTTCATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
44 20 0.32
46 4 0.06
47 6 0.10
49 32 0.52
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.32
Consensus pattern (45 bp):
CTGGCCTTGAATTAGCACATTGGCACTTTCCTAAGCCCAATGTCA
Found at i:2319723 original size:4 final size:4
Alignment explanation
Indices: 2319716--2319761 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
2319706 AAAGTTAGAT
2319716 AAGA AAGA AAGA AAGA AAGA AAG- AAGA TGAAG- AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA --AAGA AAGA AAGA AAGA AA
2319762 AAGAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 6 0.16
4 29 0.76
6 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:2319775 original size:15 final size:17
Alignment explanation
Indices: 2319716--2319778 Score: 71
Period size: 16 Copynumber: 3.9 Consensus size: 17
2319706 AAAGTTAGAT
*
2319716 AAGAAAGAAAGAAAGA-
1 AAGAAAGAAAGAAAAAG
**
2319732 AAGAAAG-AAGATGAAG
1 AAGAAAGAAAGAAAAAG
2319748 AAGAAAGAAAGAAAAAG
1 AAGAAAGAAAGAAAAAG
2319765 AA-AAA-AAAGAAAAA
1 AAGAAAGAAAGAAAAA
2319779 TATGAAATCG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 14 0.35
16 17 0.43
17 9 0.22
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAGAAAGAAAGAAAAAG
Found at i:2321823 original size:34 final size:35
Alignment explanation
Indices: 2321785--2321851 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2321775 CCTTACAACA
2321785 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2321819 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2321852 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2322340 original size:13 final size:13
Alignment explanation
Indices: 2322321--2322359 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2322311 ACTATTTATG
2322321 ATGTATCGATACA
1 ATGTATCGATACA
*
2322334 CTGTATCGATACA
1 ATGTATCGATACA
2322347 ATGTATCGATACA
1 ATGTATCGATACA
2322360 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2322421 original size:47 final size:48
Alignment explanation
Indices: 2322354--2322451 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 48
2322344 ACAATGTATC
* ** * *
2322354 GATACATGAATAGTGATGAACAATGATTTTTAACGATACATGAATAGT
1 GATACATGAACAGTGATGAACAATGACATGTAACGATACATGAACAGT
* * *
2322402 GATACGTGAACAGTG-TGAACAGTGACATGTATCGATACATGAACAGT
1 GATACATGAACAGTGATGAACAATGACATGTAACGATACATGAACAGT
2322449 GAT
1 GAT
2322452 GAATAGTGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 29 0.69
48 13 0.31
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (48 bp):
GATACATGAACAGTGATGAACAATGACATGTAACGATACATGAACAGT
Found at i:2322459 original size:10 final size:10
Alignment explanation
Indices: 2322440--2322471 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2322430 GTATCGATAC
2322440 ATGAACAGTG
1 ATGAACAGTG
*
2322450 ATGAATAGTG
1 ATGAACAGTG
2322460 ATGAACAGTG
1 ATGAACAGTG
2322470 AT
1 AT
2322472 AATGAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.25
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:2322558 original size:53 final size:53
Alignment explanation
Indices: 2322494--2322630 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
2322484 CTACTACCGA
*
2322494 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAGTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
2322547 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
2322600 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
2322631 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:2322663 original size:20 final size:20
Alignment explanation
Indices: 2322600--2322670 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
2322590 GCCAATGTCC
**
2322600 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
2322620 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
2322640 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
2322660 TGTATCGATAC
1 TGTATCGATAC
2322671 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:2326095 original size:21 final size:21
Alignment explanation
Indices: 2326071--2326129 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2326061 TAATATTCTT
* *
2326071 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
2326092 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
2326113 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
2326130 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:2330765 original size:20 final size:20
Alignment explanation
Indices: 2330740--2330791 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2330730 TACAATGAAC
2330740 ATGTATCGATACA-A-AGCATT
1 ATGTATCGATACATATAG-A-T
**
2330760 ATGTATTAATACATATAGAT
1 ATGTATCGATACATATAGAT
2330780 ATGTATCGATAC
1 ATGTATCGATAC
2330792 TTTCAAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 22 0.85
21 2 0.08
22 2 0.08
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATATAGAT
Found at i:2333763 original size:13 final size:13
Alignment explanation
Indices: 2333747--2333800 Score: 65
Period size: 12 Copynumber: 4.0 Consensus size: 13
2333737 AAAATAATAA
2333747 TATTTTAATAAAT
1 TATTTTAATAAAT
2333760 TATTTTAAAATAATAT
1 TATTTT--AATAA-AT
*
2333776 TATTTTAATAATT
1 TATTTTAATAAAT
2333789 TA-TTTAATAAAT
1 TATTTTAATAAAT
2333801 AAAAATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
12 9 0.25
13 9 0.25
14 5 0.14
15 5 0.14
16 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTTTAATAAAT
Found at i:2333770 original size:29 final size:29
Alignment explanation
Indices: 2333736--2333809 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
2333726 CATTTAAATA
2333736 AAAAATAATAATATTTTAATAAATTATTT
1 AAAAATAATAATATTTTAATAAATTATTT
* * *
2333765 TAAAATAATATTATTTTAATAATTTATTT
1 AAAAATAATAATATTTTAATAAATTATTT
*
2333794 AATAAATAAAAATATT
1 AA-AAATAATAATATT
2333810 AATTTTTTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
29 27 0.71
30 11 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AAAAATAATAATATTTTAATAAATTATTT
Found at i:2336321 original size:232 final size:231
Alignment explanation
Indices: 2335886--2336343 Score: 747
Period size: 232 Copynumber: 2.0 Consensus size: 231
2335876 AAAATGCTAG
* *
2335886 AAGAAGGCTCGATTGAGATGTACCCATAATAGTTGTCAGTTATCTAGAAAGAAACCACTTAACAA
1 AAGAAGGCTCAATTGAGATGTACCCATAATAGTTGTCAATTATCTAGAAAGAAACCACTTAACAA
* * *
2335951 CTTGAAGATACACTTGATAAGAAGATTAACGCAAGAAAGCCAAGGTTTGGTTTGAAAATCCAAGG
66 CTTCAAGATACACTTGATAAGAAGATTAACGCAAGAAAACCAAGGTTTGGTTTAAAAATCCAAGG
* **
2336016 AAAACTAGGAAAGAAAAAATTTTGATTTTTTGGTTAAATTTTTGAAAATGGGTTTTTCAAAACCC
131 AAAACTAGGAAAGAAAAAATTTTGATTTTTTGGTTAAATTTTTGAAAATGGGGTTTGAAAAACCC
* *
2336081 AAAAGGATAAAAATGGTAATTTTTGA-AAAACCTAT
196 AAAAGGATAAAAACGGTAATATTTGAGAAAACCTAT
* *
2336116 AAGAAGGCTCAATTGAGATGTATCTCATAGTAGTTGTCAATTATCTAGAAAGAAACCACTTAACA
1 AAGAAGGCTCAATTGAGATGTA-CCCATAATAGTTGTCAATTATCTAGAAAGAAACCACTTAACA
* * *
2336181 ACTTCAAGATACACTTGGATAGGAAGATTAACGCAAGAAAACCAAGTTTTGGTTTAAAAATTCAA
65 ACTTCAAGATACACTT-GATAAGAAGATTAACGCAAGAAAACCAAGGTTTGGTTTAAAAATCCAA
2336246 GGAAAACTAGGAAAGAAAAAATTTTGATTTTTTGGTTAAATTTTTGAAAATGGGGTTTGAAAAAC
129 GGAAAACTAGGAAAGAAAAAATTTTGATTTTTTGGTTAAATTTTTGAAAATGGGGTTTGAAAAAC
*
2336311 CCATAAGGATAAAAACGGTAATATTTGAGAAAA
194 CCAAAAGGATAAAAACGGTAATATTTGAGAAAA
2336344 TGAAAACATG
Statistics
Matches: 209, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
230 21 0.10
231 54 0.26
232 130 0.62
233 4 0.02
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.28
Consensus pattern (231 bp):
AAGAAGGCTCAATTGAGATGTACCCATAATAGTTGTCAATTATCTAGAAAGAAACCACTTAACAA
CTTCAAGATACACTTGATAAGAAGATTAACGCAAGAAAACCAAGGTTTGGTTTAAAAATCCAAGG
AAAACTAGGAAAGAAAAAATTTTGATTTTTTGGTTAAATTTTTGAAAATGGGGTTTGAAAAACCC
AAAAGGATAAAAACGGTAATATTTGAGAAAACCTAT
Found at i:2339381 original size:19 final size:21
Alignment explanation
Indices: 2339336--2339386 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2339326 TTTCAACAAT
2339336 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
2339357 TTGTATCGATACATA-AGT-G
1 TTGTATCGATACAAACAGTAA
2339376 TTGTATCGATA
1 TTGTATCGATA
2339387 TAATGCATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.39
20 3 0.11
21 14 0.50
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:2339506 original size:21 final size:20
Alignment explanation
Indices: 2339482--2339523 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2339472 TCTGAAAATT
*
2339482 TTATCCAATTGTATCGATACA
1 TTATCCAA-TGTATCAATACA
*
2339503 TTATTCAATGTATCAATACA
1 TTATCCAATGTATCAATACA
2339523 T
1 T
2339524 GCAGGCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (20 bp):
TTATCCAATGTATCAATACA
Found at i:2342743 original size:17 final size:17
Alignment explanation
Indices: 2342717--2342769 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
2342707 TTATCTAATT
*
2342717 TTATAATTATTAGATAA
1 TTATATTTATTAGATAA
*
2342734 TTATATTTATTAAATGAA
1 TTATATTTATTAGAT-AA
2342752 -TATTATTTATTAAGATAA
1 TTA-TATTTATT-AGATAA
2342770 ATACAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 15 0.50
18 12 0.40
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATATTTATTAGATAA
Found at i:2344577 original size:20 final size:20
Alignment explanation
Indices: 2344524--2344580 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2344514 ATTGAGCATA
* *
2344524 ATGTATCGATACAATTCTTC
1 ATGTATCGATACATTTCTCC
2344544 ATGTATCGATACATTATC-CC
1 ATGTATCGATACATT-TCTCC
2344564 ATGTATCGATACATTTC
1 ATGTATCGATACATTTC
2344581 ACTTAGGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTCTCC
Found at i:2344650 original size:19 final size:20
Alignment explanation
Indices: 2344605--2344659 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2344595 CTATCACTTT
2344605 CATGTATCGATACAATTAAG
1 CATGTATCGATACAATTAAG
*
2344625 TATGTATCGATACAATTAA-
1 CATGTATCGATACAATTAAG
2344644 CATGTATCGATACAAT
1 CATGTATCGATACAAT
2344660 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTAAG
Found at i:2344663 original size:13 final size:13
Alignment explanation
Indices: 2344645--2344671 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2344635 TACAATTAAC
2344645 ATGTATCGATACA
1 ATGTATCGATACA
2344658 ATGTATCGATACA
1 ATGTATCGATACA
2344671 A
1 A
2344672 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2351689 original size:13 final size:13
Alignment explanation
Indices: 2351671--2351697 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2351661 ACAATTGAGT
2351671 ATGTATCGATACA
1 ATGTATCGATACA
2351684 ATGTATCGATACA
1 ATGTATCGATACA
2351697 A
1 A
2351698 ATCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2351693 original size:33 final size:33
Alignment explanation
Indices: 2351651--2351716 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2351641 TGCCATTTTC
* *
2351651 ATGTATCGATACAATTGAGT-ATGTATCGATACA
1 ATGTATCGATACAAATCA-TAATGTATCGATACA
2351684 ATGTATCGATACAAATCATAATGTATCGATACA
1 ATGTATCGATACAAATCATAATGTATCGATACA
2351717 TCTGGATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAATCATAATGTATCGATACA
Found at i:2352358 original size:179 final size:179
Alignment explanation
Indices: 2352052--2352409 Score: 662
Period size: 179 Copynumber: 2.0 Consensus size: 179
2352042 TTGTGACATA
*
2352052 TTGTAAAAACCAAATGAAAGGAGTAGTGAAGATAGATCATAAAAATGGCAATCTTACAGATATTG
1 TTGTAAAAACCAAATGAAAGGAGTAGTGAAAATAGATCATAAAAATGGCAATCTTACAGATATTG
*
2352117 ACCAAAGCTTGCCTTTTTAATATTTTTGAAACATTATAATTTATTTTGGCAAATCATAGAATTTA
66 ACCAAAGCTTGCCTTTTTAATATTTTTGAAACATTATAATTTATTTTGGCAAACCATAGAATTTA
*
2352182 TTCTATGTGATGGTCTTGTTATTCTCAAACATCTACTTGCAATAGCATT
131 TTCTATGTCATGGTCTTGTTATTCTCAAACATCTACTTGCAATAGCATT
* *
2352231 TTGTAAAAACCAAATGAAAGGAGTAGTGAAAATAGATCATGAAAATGGCAATCTTATAGATATTG
1 TTGTAAAAACCAAATGAAAGGAGTAGTGAAAATAGATCATAAAAATGGCAATCTTACAGATATTG
*
2352296 ACCAAAGCTTGCCTTTTTAATATTTTTGAAACATTATAATTTATTTTGGCAAACCGTAGAATTTA
66 ACCAAAGCTTGCCTTTTTAATATTTTTGAAACATTATAATTTATTTTGGCAAACCATAGAATTTA
2352361 TTCTATGTCATGGTCTTGTTATTCTCAAACATCTACTTGCAATAGCATT
131 TTCTATGTCATGGTCTTGTTATTCTCAAACATCTACTTGCAATAGCATT
2352410 GAGAAACAAT
Statistics
Matches: 173, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
179 173 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (179 bp):
TTGTAAAAACCAAATGAAAGGAGTAGTGAAAATAGATCATAAAAATGGCAATCTTACAGATATTG
ACCAAAGCTTGCCTTTTTAATATTTTTGAAACATTATAATTTATTTTGGCAAACCATAGAATTTA
TTCTATGTCATGGTCTTGTTATTCTCAAACATCTACTTGCAATAGCATT
Found at i:2353095 original size:17 final size:18
Alignment explanation
Indices: 2353075--2353124 Score: 84
Period size: 17 Copynumber: 2.8 Consensus size: 18
2353065 GATAATAGAG
2353075 TTTATTAGATAAATG-TA
1 TTTATTAGATAAATGTTA
2353092 TTTATTAGATAAATGTTA
1 TTTATTAGATAAATGTTA
2353110 TTTATTAAGATAAAT
1 TTTATT-AGATAAAT
2353125 ATAGGGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 15 0.48
18 8 0.26
19 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (18 bp):
TTTATTAGATAAATGTTA
Found at i:2354005 original size:2 final size:2
Alignment explanation
Indices: 2353998--2354022 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2353988 AAATCTGATG
2353998 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2354023 GTATGTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2354702 original size:15 final size:14
Alignment explanation
Indices: 2354682--2354723 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2354672 TCTCGACCAC
2354682 TTCTTTTTCTTTTTT
1 TTCTTTTT-TTTTTT
2354697 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
*
2354711 TGCATTTTTTTTT
1 TTC-TTTTTTTTT
2354724 AGTTTTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:2358442 original size:62 final size:62
Alignment explanation
Indices: 2358345--2358468 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
2358335 TCAAGCAATC
2358345 TTGACATGTTTTAATACTTTTTATGCATTTTTAACCATTTAAGGATTAAATTAAATCAGAAA
1 TTGACATGTTTTAATACTTTTTATGCATTTTTAACCATTTAAGGATTAAATTAAATCAGAAA
*
2358407 TTGACATGTTTTAATACTTTTTATGCATTTTTAACCATTTAAGGATTAAATTGAATCAGAAA
1 TTGACATGTTTTAATACTTTTTATGCATTTTTAACCATTTAAGGATTAAATTAAATCAGAAA
2358469 AATTTTAAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (62 bp):
TTGACATGTTTTAATACTTTTTATGCATTTTTAACCATTTAAGGATTAAATTAAATCAGAAA
Found at i:2366378 original size:21 final size:22
Alignment explanation
Indices: 2366340--2366385 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2366330 ATCTGTTGAA
* **
2366340 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2366361 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2366383 ACT
1 ACT
2366386 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2372200 original size:20 final size:20
Alignment explanation
Indices: 2372164--2372206 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2372154 GAATATTAGG
* *
2372164 AAAAATTATTTATTTTTC-A
1 AAAAATTATTCACTTTTCTA
2372183 AAAAATTTATTCACTTTTCTA
1 AAAAA-TTATTCACTTTTCTA
2372204 AAA
1 AAA
2372207 TAACTATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAAATTATTCACTTTTCTA
Found at i:2375403 original size:42 final size:42
Alignment explanation
Indices: 2375356--2375444 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
2375346 TTATTTAAAA
2375356 TTTTATAAAAATAGAGTTAATAGAGTTTAAATTTATCTAGAG
1 TTTTATAAAAATAGAGTTAATAGAGTTTAAATTTATCTAGAG
2375398 TTTTATAAAAATAGAGTTAATAGAGTTTAAATTTATCTAGAG
1 TTTTATAAAAATAGAGTTAATAGAGTTTAAATTTATCTAGAG
2375440 TTTTA
1 TTTTA
2375445 AATTTTGTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (42 bp):
TTTTATAAAAATAGAGTTAATAGAGTTTAAATTTATCTAGAG
Found at i:2377743 original size:81 final size:80
Alignment explanation
Indices: 2377448--2377810 Score: 385
Period size: 80 Copynumber: 4.5 Consensus size: 80
2377438 AAGAACCAGA
* * * *
2377448 GTTGGAGTATCCCTTC-AAAGATAGTGGGGTTGGAGTATCCCCATAAATGAAAATTTTGATATTT
1 GTTGGAGTATCCC-TCGGAA-ATGGTGGGGTTGGAGTATCCCCGTAAATGAAAAATTTGATATTT
* * *
2377512 TTGGAAGTAAAAATAAG
64 TTAGAAGTAAAAACAGG
* * * * *
2377529 GTTGGAATATCTCCT-GGAAATGGTGGGGTTAGAGTATCCTCGTAGATGAAAAATTCGATATTTT
1 GTTGGAGTATC-CCTCGGAAATGGTGGGGTTGGAGTATCCCCGTAAATGAAAAATTTGATATTTT
*
2377593 TAGAAGTAAAAACGGG
65 TAGAAGTAAAAACAGG
** * * *
2377609 GTT-GAGTATCCCCTTAGAAATTGTGGGGTTGGAGTATCCTCG-AAGATGAAAAATTTGATGTTT
1 GTTGGAGTAT-CCCTCGGAAATGGTGGGGTTGGAGTATCCCCGTAA-ATGAAAAATTTGATATTT
* *
2377672 TTAGAGGTAAAGACAGG
64 TTAGAAGTAAAAACAGG
*
2377689 GTTGGAGTATCCCATCGGAAATGGTGGGATTGGAGTATCCCCGTAAAT-AGAAAATTTGATATTT
1 GTTGGAGTATCCC-TCGGAAATGGTGGGGTTGGAGTATCCCCGTAAATGA-AAAATTTGATATTT
* *
2377753 TTAGAAGTATAAATAGG
64 TTAGAAGTAAAAACAGG
* * *
2377770 GTTGGAGTATCTCCTCGAAAATGGTGGGGCTAGAGTATCCC
1 GTTGGAGTATC-CCTCGGAAATGGTGGGGTTGGAGTATCCC
2377811 TAAAGATAAA
Statistics
Matches: 235, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
79 9 0.04
80 115 0.49
81 105 0.45
82 6 0.03
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (80 bp):
GTTGGAGTATCCCTCGGAAATGGTGGGGTTGGAGTATCCCCGTAAATGAAAAATTTGATATTTTT
AGAAGTAAAAACAGG
Found at i:2377758 original size:161 final size:161
Alignment explanation
Indices: 2377448--2377780 Score: 399
Period size: 161 Copynumber: 2.1 Consensus size: 161
2377438 AAGAACCAGA
* *
2377448 GTTGGAGTAT-CCCTTCA-AAGATAGTGGGGTTGGAGTATCCCCATAAATGAAAATTTTGATATT
1 GTTGGAGTATCCCCTT-AGAA-ATTGTGGGGTTGGAGTATCCCCATAAATGAAAAATTTGATATT
* * * * *
2377511 TTTGGAAGTAAAAATAAGGTTGGAATATCTCCTGGAAATGGTGGGGTTAGAGTATCCTCGTAGAT
64 TTTAGAAGTAAAAACAAGGTTGGAATATCTCCTGGAAATGGTGGGATTAGAGTATCCCCGTAAAT
*
2377576 GAAAAATTCGATATTTTTAGAAGTAAAAACGGG
129 GAAAAATTCGATATTTTTAGAAGTAAAAACAGG
* * *
2377609 GTT-GAGTATCCCCTTAGAAATTGTGGGGTTGGAGTATCCTCGA-AGATGAAAAATTTGATGTTT
1 GTTGGAGTATCCCCTTAGAAATTGTGGGGTTGGAGTATCC-CCATAAATGAAAAATTTGATATTT
* * * * *
2377672 TTAGAGGTAAAGACAGGGTTGGAGTATC-CCATCGGAAATGGTGGGATTGGAGTATCCCCGTAAA
65 TTAGAAGTAAAAACAAGGTTGGAATATCTCC-T-GGAAATGGTGGGATTAGAGTATCCCCGTAAA
* * *
2377736 T-AGAAAATTTGATATTTTTAGAAGTATAAATAGG
128 TGA-AAAATTCGATATTTTTAGAAGTAAAAACAGG
2377770 GTTGGAGTATC
1 GTTGGAGTATC
2377781 TCCTCGAAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
159 2 0.01
160 67 0.46
161 70 0.48
162 7 0.05
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (161 bp):
GTTGGAGTATCCCCTTAGAAATTGTGGGGTTGGAGTATCCCCATAAATGAAAAATTTGATATTTT
TAGAAGTAAAAACAAGGTTGGAATATCTCCTGGAAATGGTGGGATTAGAGTATCCCCGTAAATGA
AAAATTCGATATTTTTAGAAGTAAAAACAGG
Found at i:2380316 original size:52 final size:52
Alignment explanation
Indices: 2380256--2380368 Score: 147
Period size: 52 Copynumber: 2.2 Consensus size: 52
2380246 TCGATACATT
* * *
2380256 GATACATTTGGGTAAAAAACCTAGAATGTATCGATAAAATGA-ATAATGTATC
1 GATACATTTAGGTAAAAAACCCAGAATGTATCGATAAAATGAGA-AATATATC
* * * *
2380308 GATACATTTAGGTCAAGAACCCAGAATGTATCTATACAATGAGAAATATATC
1 GATACATTTAGGTAAAAAACCCAGAATGTATCGATAAAATGAGAAATATATC
2380360 GATACATTT
1 GATACATTT
2380369 TCTTTTGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
52 52 0.98
53 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.29
Consensus pattern (52 bp):
GATACATTTAGGTAAAAAACCCAGAATGTATCGATAAAATGAGAAATATATC
Found at i:2380476 original size:21 final size:20
Alignment explanation
Indices: 2380425--2380478 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2380415 CATTTTAGAC
*
2380425 ATGTATTGATACATTCACTT
1 ATGTATAGATACATTCACTT
*
2380445 ATGTAAAGATACATTCACTT
1 ATGTATAGATACATTCACTT
*
2380465 ATTGTATCGATACA
1 A-TGTATAGATACA
2380479 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATAGATACATTCACTT
Found at i:2382182 original size:13 final size:13
Alignment explanation
Indices: 2382164--2382193 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2382154 ACAAACAGTA
2382164 AATGTATCAATAC
1 AATGTATCAATAC
*
2382177 AATGTATCGATAC
1 AATGTATCAATAC
2382190 AATG
1 AATG
2382194 AAAAATGTAT
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:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:2384363 original size:157 final size:157
Alignment explanation
Indices: 2384066--2384461 Score: 473
Period size: 157 Copynumber: 2.5 Consensus size: 157
2384056 TCATTGATGT
* * *
2384066 TTTTATTTCTAAAATAC-CGATTTTCCACCATTGGGGGTACTCCAACC-CGTTATTT-TCGAGAG
1 TTTTATTT-TAAAA-ACACGATTTTTCACCATTGGGGATACTCTAACCTCGTTATTTCT-GAGAG
* ** * *
2384128 GATACTCGAACCTCCGTTTTATTTCTAAAACATTTATTTTCCACCATCGGGGCTATTCCAACCCC
63 GATACTCCAACCTCCGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCC
2384193 GTAACATTCGAGGGGATACTCTAA-CCCAG
128 GTAACATTCGAGGGGATACTCTAACCCCAG
* *
2384222 TTTTATTTTAAAAACATCGATTTTTCACCATTAGGGATATTCTAACCTCGTTATTTCTGA-AGGG
1 TTTTATTTTAAAAACA-CGATTTTTCACCATTGGGGATACTCTAACCTCGTTATTTCTGAGA-GG
* * * * *
2384286 ATACTCCAGCCTCGGTTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCTG
64 ATACTCCAACCTCCGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCCG
* ** * *
2384351 TTATTTTTGAGGGGATATTCTAACCCCAG
129 TAACATTCGAGGGGATACTCTAACCCCAG
* * *
2384380 TTTTATTTTTAAAATAC-CAATTTTTCACCATCGGGGATACTCTAACCTTGTTATTTCTGAGAGG
1 TTTTA-TTTTAAAA-ACACGATTTTTCACCATTGGGGATACTCTAACCTCGTTATTTCTGAGAGG
2384444 ATACTCCAACC-CCGTTTT
64 ATACTCCAACCTCCGTTTT
2384462 TATCTACAAA
Statistics
Matches: 204, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
154 2 0.01
155 5 0.02
156 34 0.17
157 91 0.45
158 61 0.30
159 9 0.04
160 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (157 bp):
TTTTATTTTAAAAACACGATTTTTCACCATTGGGGATACTCTAACCTCGTTATTTCTGAGAGGAT
ACTCCAACCTCCGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCCGTA
ACATTCGAGGGGATACTCTAACCCCAG
Found at i:2384464 original size:79 final size:78
Alignment explanation
Indices: 2384066--2384461 Score: 379
Period size: 79 Copynumber: 5.1 Consensus size: 78
2384056 TCATTGATGT
* * * * * *
2384066 TTTTATTTCTAAAATACCGATTTTCCACCATTGGGGGTACTCCAA-CCCGTTATTT-TCGAGAGG
1 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCGTTATTTCT-GAGAGG
*
2384129 ATACTCGAACCTCCG
65 ATACTCCAACC-CCG
** * * * * * * *
2384144 TTTTATTTCTAAAACATTTATTTTCCACCATCGGGGCTATTCCAACCCCGTAACATTC-GAGGGG
1 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCGTTA-TTTCTGAGAGG
* *
2384208 ATACTCTAACCCAG
65 ATACTCCAACCCCG
** * *
2384222 TTTTATTT-TAAAAACATCGATTTTTCACCATTAGGGATATTCTAACCTCGTTATTTCTGA-AGG
1 TTTTATTTCT-AAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCGTTATTTCTGAGA-G
* *
2384285 GATACTCCAGCCTCGG
64 GATACTCCAACC-CCG
* * *
2384301 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTTGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCGTTATTTCTGAGAGGA
* *
2384366 TATTCTAACCCCAG
66 TACTCCAACCCC-G
* * * * **
2384380 TTTTATTTTTAAAATACCAATTTTTCACCATCGGGGATACTCTAACCTTGTTATTTCTGAGAGGA
1 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCGTTATTTCTGAGAGGA
2384445 TACTCCAACCCCG
66 TACTCCAACCCCG
2384458 TTTT
1 TTTT
2384462 TATCTACAAA
Statistics
Matches: 262, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
77 4 0.02
78 101 0.39
79 154 0.59
80 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (78 bp):
TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCGTTATTTCTGAGAGGA
TACTCCAACCCCG
Found at i:2386274 original size:22 final size:22
Alignment explanation
Indices: 2386246--2386290 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2386236 GAATGCCATC
2386246 ACCATAATGCCCTATGTCCTCA
1 ACCATAATGCCCTATGTCCTCA
2386268 ACCATAATGCCCTATGTCCTCA
1 ACCATAATGCCCTATGTCCTCA
2386290 A
1 A
2386291 TAAACTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.36, G:0.09, T:0.27
Consensus pattern (22 bp):
ACCATAATGCCCTATGTCCTCA
Found at i:2389422 original size:24 final size:24
Alignment explanation
Indices: 2389395--2389444 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2389385 CAAGAGAAAC
2389395 AAAAACAAA-AAAATCAAA-AAATAA
1 AAAAACAAACAAAA--AAAGAAATAA
*
2389419 AAAAAGAAACAAAAAAAGAAATAA
1 AAAAACAAACAAAAAAAGAAATAA
2389443 AA
1 AA
2389445 GGGGAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.13
24 16 0.70
25 4 0.17
ACGTcount: A:0.84, C:0.06, G:0.04, T:0.06
Consensus pattern (24 bp):
AAAAACAAACAAAAAAAGAAATAA
Found at i:2390006 original size:32 final size:30
Alignment explanation
Indices: 2389875--2390087 Score: 239
Period size: 32 Copynumber: 6.8 Consensus size: 30
2389865 ACCTTCTTAC
* *
2389875 AGTCCACGACTCAATGGCAATCTCTTCTCAA
1 AGTCCACGACTCAGTGGC-ATCTTTTCTCAA
* *
2389906 AGCCCACGACTTAGTGGCAT-TTTGTCTCAA
1 AGTCCACGACTCAGTGGCATCTTT-TCTCAA
*
2389936 AGTCCACGACTCAGTGGCAATCTCTTCTCAA
1 AGTCCACGACTCAGTGGC-ATCTTTTCTCAA
*
2389967 AGCCCACGACTCAGTGGCATCCTTTTCTTCAA
1 AGTCCACGACTCAGTGGCAT-CTTTTC-TCAA
2389999 AGTCCACGACTCAGTGGCATCCTTTTCTTCAA
1 AGTCCACGACTCAGTGGCAT-CTTTTC-TCAA
* *
2390031 AGTCCACGACTTAGTGGCATCATTTTCTTCTA
1 AGTCCACGACTCAGTGGCATC-TTTTC-TCAA
* *
2390063 AGTCCACAACTCCGTGGCACTCTTT
1 AGTCCACGACTCAGTGGCA-TCTTT
2390088 CACCCTTTTA
Statistics
Matches: 160, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
29 2 0.01
30 26 0.16
31 46 0.29
32 84 0.52
33 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (30 bp):
AGTCCACGACTCAGTGGCATCTTTTCTCAA
Found at i:2390051 original size:64 final size:62
Alignment explanation
Indices: 2389875--2390081 Score: 285
Period size: 61 Copynumber: 3.3 Consensus size: 62
2389865 ACCTTCTTAC
*
2389875 AGTCCACGACTCAATGGCAATCTCTTCTCAAAGCCCACGACTTAGTGGCAT-TTTGTC-TCAA
1 AGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACGACTTAGTGGCATCTTT-TCTTCAA
*
2389936 AGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATCCTTTTCTTCAA
1 AGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACGACTTAGTGGCAT-CTTTTCTTCAA
* * *
2389999 AGTCCACGACTCAGTGGC-ATCCTTTTCTTCAAAGTCCACGACTTAGTGGCATCATTTTCTTCTA
1 AGTCCACGACTCAGTGGCAAT-CTCTTC-TCAAAGCCCACGACTTAGTGGCATC-TTTTCTTCAA
* *
2390063 AGTCCACAACTCCGTGGCA
1 AGTCCACGACTCAGTGGCA
2390082 CTCTTTCACC
Statistics
Matches: 131, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
61 49 0.37
62 4 0.03
63 31 0.24
64 47 0.36
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (62 bp):
AGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACGACTTAGTGGCATCTTTTCTTCAA
Found at i:2390123 original size:27 final size:27
Alignment explanation
Indices: 2390092--2390306 Score: 160
Period size: 27 Copynumber: 7.2 Consensus size: 27
2390082 CTCTTTCACC
*
2390092 CTTTTAAGCCCACAACTCTGTGGCACT
1 CTTTTAAGCCCACAACTCCGTGGCACT
*
2390119 CTTTTTCCTTCTAAGCCCACAACTCCGTGGCACC
1 C----T--TT-TAAGCCCACAACTCCGTGGCACT
2390153 CTTTTAAGCCCACAACTCCGTGGCACTATTTTT
1 CTTTTAAGCCCACAACTCCGTGGCAC------T
* * *
2390186 CCTTCTAAGCCCATAACTCCGTGGCACC
1 -CTTTTAAGCCCACAACTCCGTGGCACT
*
2390214 CTTTTAAACCCACAACTCCGTGGCACT
1 CTTTTAAGCCCACAACTCCGTGGCACT
* * *
2390241 CTTTTTCCTTCTAAGTCCATAACTCCGTGGCACC
1 C----T--TT-TAAGCCCACAACTCCGTGGCACT
2390275 CTTTTAAGCCCACAACTCCGTGGCACT
1 CTTTTAAGCCCACAACTCCGTGGCACT
2390302 CTTTT
1 CTTTT
2390307 TCCTTCTAAG
Statistics
Matches: 150, Mismatches: 17, Indels: 42
0.72 0.08 0.20
Matches are distributed among these distances:
27 72 0.48
28 4 0.03
30 2 0.01
31 2 0.01
33 4 0.03
34 66 0.44
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.31
Consensus pattern (27 bp):
CTTTTAAGCCCACAACTCCGTGGCACT
Found at i:2390139 original size:34 final size:33
Alignment explanation
Indices: 2389966--2390332 Score: 281
Period size: 34 Copynumber: 11.6 Consensus size: 33
2389956 TCTCTTCTCA
* * * *
2389966 AAGCCCACGACTCAGTGGCATCCTTTT-CTTCA
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
* * * * *
2389998 AAGTCCACGACTCAGTGGCATCCTTTT-CTTCA
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
* * ** *
2390030 AAGTCCACGACTTAGTGGCATCATTTT-CTTCT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
* ** *
2390062 AAGTCCACAACTCCGTGGCACTCTTTCACCCTTTT
1 AAGCCCACAACTCCGTGGCA-TCTTT-TTCCTTCT
*
2390097 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCA-TCTTTTTCCTTCT
*
2390131 AAGCCCACAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
*
2390158 AAGCCCACAACTCCGTGGCACTATTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCA-TCTTTTTCCTTCT
* *
2390192 AAGCCCATAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
*
2390219 AAACCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCA-TCTTTTTCCTTCT
* * *
2390253 AAGTCCATAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
2390280 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCA-TCTTTTTCCTTCT
*
2390314 AAGTCCACAACTCCGTGGC
1 AAGCCCACAACTCCGTGGC
2390333 GCATTTTTCT
Statistics
Matches: 277, Mismatches: 34, Indels: 46
0.78 0.10 0.13
Matches are distributed among these distances:
27 71 0.26
29 2 0.01
32 79 0.29
33 4 0.01
34 93 0.34
35 28 0.10
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
Found at i:2390185 original size:61 final size:61
Alignment explanation
Indices: 2390088--2390332 Score: 427
Period size: 61 Copynumber: 4.0 Consensus size: 61
2390078 GGCACTCTTT
*
2390088 CACCCTTTTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGG
1 CACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGG
* *
2390149 CACCCTTTTAAGCCCACAACTCCGTGGCACTATTTTTCCTTCTAAGCCCATAACTCCGTGG
1 CACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGG
* * *
2390210 CACCCTTTTAAACCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCATAACTCCGTGG
1 CACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGG
*
2390271 CACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGG
1 CACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGG
2390332 C
1 C
2390333 GCATTTTTCT
Statistics
Matches: 176, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 176 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (61 bp):
CACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGG
Found at i:2390356 original size:34 final size:34
Alignment explanation
Indices: 2390280--2390356 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
2390270 GCACCCTTTT
* *
2390280 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTATTTTTCCTTCA
* * *
2390314 AAGTCCACAACTCCGTGGCGC-ATTTTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACTATTTTTC-CTTCA
2390348 AAGCCCACA
1 AAGCCCACA
2390357 CAAGTCGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 6 0.17
34 30 0.83
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACTATTTTTCCTTCA
Found at i:2390393 original size:33 final size:32
Alignment explanation
Indices: 2390341--2390506 Score: 190
Period size: 32 Copynumber: 5.1 Consensus size: 32
2390331 GCGCATTTTT
*
2390341 CTTTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTCCAAAGCCCACACAAGTCGGTGGCAACC
* * * *
2390373 TTTTTCTAAAACCCACACAAGTTGGTGGCAATCC
1 -CTTTCCAAAGCCCACACAAGTCGGTGGCAA-CC
*
2390407 C-CTCCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTCCAAAGCCCACACAAGTCGGTGGCAACC
* *
2390438 CTTTCCAAAGCCCACACAAGTCAAGTGCCAACC
1 CTTTCCAAAGCCCACACAAGTC-GGTGGCAACC
* * *
2390471 ACTCTCTAAAGCCCACACAAGTCGGTGGTAACC
1 -CTTTCCAAAGCCCACACAAGTCGGTGGCAACC
2390504 CTT
1 CTT
2390507 CTAAGCCCAA
Statistics
Matches: 110, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
31 3 0.03
32 45 0.41
33 40 0.36
34 22 0.20
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (32 bp):
CTTTCCAAAGCCCACACAAGTCGGTGGCAACC
Found at i:2390428 original size:65 final size:66
Alignment explanation
Indices: 2390346--2390506 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 66
2390336 TTTTTCTTTT
* * ** *
2390346 CAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAACCCACACAAGT-TGGTGGCAATCC-C-
1 CAAAGCCCACACAAGTCGGTGGCAACC-CTTTCCAAAACCCACACAAGTCAAGTGCCAA-CCACT
2390408 CTC
64 CTC
*
2390411 CAAAGCCCACACAAGTCGGTGGCAACCCTTTCCAAAGCCCACACAAGTCAAGTGCCAACCACTCT
1 CAAAGCCCACACAAGTCGGTGGCAACCCTTTCCAAAACCCACACAAGTCAAGTGCCAACCACTCT
2390476 C
66 C
* *
2390477 TAAAGCCCACACAAGTCGGTGGTAACCCTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCTT
2390507 CTAAGCCCAA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 20 0.24
65 34 0.40
66 31 0.36
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.17
Consensus pattern (66 bp):
CAAAGCCCACACAAGTCGGTGGCAACCCTTTCCAAAACCCACACAAGTCAAGTGCCAACCACTCT
C
Found at i:2390585 original size:49 final size:48
Alignment explanation
Indices: 2390521--2391280 Score: 880
Period size: 49 Copynumber: 16.0 Consensus size: 48
2390511 GCCCAATATC
*
2390521 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTT-TCTTTAAGTCCAATGTA
*
2390570 GCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
*
2390619 GCTGGCCTTCAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
* *
2390668 GCTGGCCTTGAATCAGCACATTGGCA-C----CTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTTCTTTAAGTCCAATGTA
*
2390711 GCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
*
2390760 GCTGGCCTTGAATCATCACATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
* *
2390809 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
*
2390858 GCTGGCCTTGAATCAGCACATTGGCA-C----CTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTTCTTTAAGTCCAATGTA
* *
2390901 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
* * *
2390950 GCTGGCCTTGAATCAACACATTGGCA-C----ATTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTTCTTTAAGTCCAATGTA
* * *
2390993 GCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
* * *
2391042 GCTGGCCTTGAATCAACACATTGGCA-C---T-TTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTTCTTTAAGTCCAATGTA
* * * * *
2391085 GTTGGCCTTGAATCACCAGATTAGCACCTTCTTCTTTAAGTCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
* * * *
2391134 GCTGGCCTTGATTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATGTA
* ** *
2391183 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAAACCCAATGTT
1 GCTGGCCTTGAATCAGCACATTGGCACCTT--T--TCTTT-AAGTCCAATGTA
* * * *
2391236 GTTGGCCTTGAATCAGCGCATCGGCA--TTCTTCTTTAAGTCTAATG
1 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCTTTAAGTCCAATG
2391281 ACGCTGACCG
Statistics
Matches: 625, Mismatches: 57, Indels: 60
0.84 0.08 0.08
Matches are distributed among these distances:
43 152 0.24
44 5 0.01
47 7 0.01
48 10 0.02
49 412 0.66
50 2 0.00
51 2 0.00
52 5 0.01
53 30 0.05
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (48 bp):
GCTGGCCTTGAATCAGCACATTGGCACCTTTTCTTTAAGTCCAATGTA
Found at i:2390746 original size:92 final size:92
Alignment explanation
Indices: 2390603--2391261 Score: 922
Period size: 92 Copynumber: 7.0 Consensus size: 92
2390593 GCACCTTCTT
* * *
2390603 CTTTAAGTCCAATGTAGCTGGCCTTCAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
2390668 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
2390695 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
*
2390760 GCTGGCCTTGAATCATCACATTGGCACCTTC
66 GCTGGCCTTGAATCAGCACATTGGCA----C
* *
2390791 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
2390856 TAGCTGGCCTTGAATCAGCACATTGGCAC
64 TAGCTGGCCTTGAATCAGCACATTGGCAC
*
2390885 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
*
2390950 GCTGGCCTTGAATCAACACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
2390977 ATTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
*
2391042 GCTGGCCTTGAATCAACACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * * * *
2391069 TTTTAAGTCCAATATCGTTGGCCTTGAATCACCAGATTAGCACCTTCTTCTTTAAGTCCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
*
2391134 GCTGGCCTTGATTCAGCACATTGGCACCTTC
66 GCTGGCCTTGAATCAGCACATTGGCA----C
* **
2391165 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAAACCC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC-T--TCTTT-AAGTCC
* * * *
2391230 AATGTTGTTGGCCTTGAATCAGCGCATCGGCA
60 AATGTAGCTGGCCTTGAATCAGCACATTGGCA
2391262 TTCTTCTTTA
Statistics
Matches: 515, Mismatches: 36, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
92 346 0.67
94 1 0.00
96 2 0.00
98 129 0.25
99 1 0.00
101 5 0.01
102 31 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2390774 original size:141 final size:143
Alignment explanation
Indices: 2390521--2391280 Score: 913
Period size: 141 Copynumber: 5.3 Consensus size: 143
2390511 GCCCAATATC
*
2390521 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
* *
2390586 CATATTGGCACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTCAATCAGCACATTGGCACCTTCT
62 CATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCT
2390651 TCTTTAAGTCCAATGTA
127 TCTTTAAGTCCAATGTA
* *
2390668 GCTGGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
1 GCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATA
* *
2390731 TTGGCACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCATCACATTGGCACCTTCTTCTT
66 TTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCTTCTT
2390796 TAAGTCCAATGTA
131 TAAGTCCAATGTA
*
2390809 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCACATTGGCA-C--C-TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
* * * *
2390874 CACATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
62 CATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCT
2390933 TCTTTAAGTCCAATGTA
127 TCTTTAAGTCCAATGTA
* * *
2390950 GCTGGCCTTGAATCAACACATTGGCA-C-ATTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
1 GCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATA
* *
2391013 TTGGCAACTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA----C-T-TT
66 TTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCTTCTT
* *
2391072 TAAGTCCAATATC
131 TAAGTCCAATGTA
* * * * * *
2391085 GTTGGCCTTGAATCACCAGATTAGCACCTTCTTCTTTAAGTCCAATGTCGCTGGCCTTGATTCAG
1 GCTGGCCTTGAATCAGCACATTGGCA-C--C-TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
* * * *
2391150 CACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCG
62 CATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTC-
** *
2391215 TCATCTTTAAAACCCAATGTT
126 T--TCTTT-AAGTCCAATGTA
* * * * *
2391236 GTTGGCCTTGAATCAGCGCATCGGCATTCTTCTTTAAGTCTAATG
1 GCTGGCCTTGAATCAGCACATTGGCA--CCTCTTTAAGTCCAATG
2391281 ACGCTGACCG
Statistics
Matches: 535, Mismatches: 49, Indels: 56
0.84 0.08 0.09
Matches are distributed among these distances:
135 74 0.14
136 1 0.00
137 2 0.00
139 2 0.00
141 340 0.64
143 1 0.00
145 2 0.00
146 1 0.00
147 64 0.12
149 15 0.03
150 3 0.01
151 29 0.05
152 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (143 bp):
GCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATA
TTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCTTCTT
TAAGTCCAATGTA
Found at i:2392091 original size:13 final size:13
Alignment explanation
Indices: 2392073--2392100 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2392063 ATTACTCAAA
2392073 TGTATCGATACAT
1 TGTATCGATACAT
2392086 TGTATCGATACAT
1 TGTATCGATACAT
2392099 TG
1 TG
2392101 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2395487 original size:62 final size:62
Alignment explanation
Indices: 2395416--2396774 Score: 978
Period size: 61 Copynumber: 22.4 Consensus size: 62
2395406 TTTTTTATCT
* * * * *
2395416 TTTTAGTCCTCAAAAAGCAGGATGCTTTTTTCTTTTCAAAGCCCACAAGAGTTGATGGCACA
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * * * *
2395478 TTTTAGTCCTCAAAAAGCAAGACGCATTTTTCTTTTCAAAGCCCATAAGAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * * * * * *
2395540 TTTTAGTTCTCAAAAAACAGGACGCCTTTTTCTGTTCAAAGCCTACACAA-A-CTGATGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCC--CACAAGAGTTGGTGGCACC
* * * * * *
2395602 TTTTTAATCCTCAAAAAGCATG--GCACTTTTCCTTTTTAAAGCCCACACGAGTTGGTGGTACC
1 -TTTTAGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * * *
2395664 TTTTAGCCCTCAAAGAGTAGGATGTTTGCCTTTTTCTTTTTAAAGCCTACACA-AGTTAGTGGTA
1 TTTTAGTCCTCAAAGAGCAGGA----TGCCTTTTTCTTTTTAAAGCCCACA-AGAGTTGGTGGCA
2395728 CC
61 CC
* * *
2395730 TTTTAGTCCTCAAAGAGCAAGACACTTGCCTTTTTCTTTTTAAAGCCCACACGAGTTTGTGGCAC
1 TTTTAGTCCTCAAAGAGC-AG-GA--TGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCAC
2395795 C
62 C
* ** * *
2395796 TTTTTAGTCCTCAAAGAG-A-AATGTGTTCTTCCTTTTTAAAGCCCATATA-A-------G--CC
1 -TTTTAGTCCTCAAAGAGCAGGATGCCTT-TTTCTTTTTAAAGCCCACA-AGAGTTGGTGGCACC
* *
2395849 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCTGCAC-A-TGTTGGTTGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCC--CACAAGAGTTGGTGGCACC
* * * * *
2395910 TTTTAGTCTTCAAAGAGCA--AGGCACTTTTCCTTTTTAAATCCCACACA-AGTTGGTGGCACA
1 TTTTAGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTTAAAGCCCACA-AGAGTTGGTGGCACC
* * **
2395971 TTTTAGTCCTCAAAGAGCAGGACGCCATTTTC-TTTTAAAGCCCACACA-AGTTGGTGGTGCC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACA-AGAGTTGGTGGCACC
** * *
2396032 TTTTAGTCCTTGAAGAGTAGGATGCCTTTTTC-TTTTAAAGCCCACACA-AGTTAGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACA-AGAGTTGGTGGCACC
* * * *
2396093 TTCTAGTCCTCAAAGAGCAAGATG-CTTTTTCTTTTTAAAACCCACACGAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * ** * * ** *
2396154 TTTTAGTCTTTAAAGAGCAAAATG-C-----CTTTTTAATGCCCACACGAGTTACTTGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * *
2396210 TGTTAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * * **
2396272 TTTTAGTCTTCAAAGAGCAAGACGCATTCTTTCTTTTTAAAGCCCACACCAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTT-TTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * * * * * * **
2396335 TTTTCGTCCTCAAAAAACAGGACG-CTTGCTTTTTTTTTAAAGCTCACACGAGTTAGTGGCATTT
1 TTTTAGTCCTCAAAGAGCAGGATGCCTT--TTTCTTTTTAAAGCCCACAAGAGTTGGTGGCA-CC
* * * * *
2396399 TTTTAATCCTCAAAGAGCAGGGT-ACTTTTCCTTTTTAAAGCCCAC---A------CGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * * *
2396451 TTTTAGTCCTCAAA-AGTAGGA--CATCTTT-TTTTTAAAGCCCACACGAGTTGGTGGCACT
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
** ** * *
2396509 TTTTAGTCCTCAAAGAATAGGACACC---TTATTTTTAAAGCCCACACGAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * *
2396568 TTTTAGTCCTCAAAGAGCAAGATGCC-TTTT-TTTTTAAAACCCACACGAGTTGGTGGCATC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
** * ** * * *
2396628 TTCAAGTCCTCAAAAAGCAGGACACC-TTTTC-TTTTAAAGCCCACATGTGTTCGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
* * * *
2396688 TTTTAGTCCTCAAAGAGCAAGACGCTTCTTTTTTCCTTTTAAAGCCTACACA-AGTTGGTGGCAC
1 TTTTAGTCCTCAAAGAGCAGGATGC--C-TTTTTCTTTTTAAAGCCCACA-AGAGTTGGTGGCAC
2396752 C
62 C
* *
2396753 TTTTAGTCTTCAAAGAGTAGGA
1 TTTTAGTCCTCAAAGAGCAGGA
2396775 CTCATTTCCT
Statistics
Matches: 1046, Mismatches: 179, Indels: 141
0.77 0.13 0.10
Matches are distributed among these distances:
49 14 0.01
50 3 0.00
51 5 0.00
52 42 0.04
53 9 0.01
54 7 0.01
55 1 0.00
56 44 0.04
57 1 0.00
58 20 0.02
59 64 0.06
60 113 0.11
61 227 0.22
62 215 0.21
63 102 0.10
64 29 0.03
65 44 0.04
66 84 0.08
67 21 0.02
68 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (62 bp):
TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACAAGAGTTGGTGGCACC
Found at i:2396612 original size:60 final size:60
Alignment explanation
Indices: 2396446--2396775 Score: 378
Period size: 60 Copynumber: 5.5 Consensus size: 60
2396436 AAGCCCACAC
* *
2396446 GCACCTTTTAGTCCTCAAA-AGTAGGACATC-TTTTTTTTAAAGCCCACACGAGTTGGTG
1 GCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTTTAAAGCCCACACGAGTTGGTG
* ** *
2396504 GCACTTTTTAGTCCTCAAAGAATAGGACACC-TTATTTTTAAAGCCCACACGAGTTGGTG
1 GCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTTTAAAGCCCACACGAGTTGGTG
* ** *
2396563 GCACCTTTTAGTCCTCAAAGAGCAAGATGCCTTTTTTTTTAAAACCCACACGAGTTGGTG
1 GCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTTTAAAGCCCACACGAGTTGGTG
* ** * * * * *
2396623 GCATCTTCAAGTCCTCAAAAAGCAGGACACCTTTTCTTTTAAAGCCCACATGTGTTCGTG
1 GCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTTTAAAGCCCACACGAGTTGGTG
* * * *
2396683 GCACCTTTTAGTCCTCAAAGAGCAAGACGCTTCTTTTTTCCTTTTAAAGCCTACACAAGTTGGTG
1 GCACCTTTTAGTCCTCAAAGAGCAGGACAC--C-TTTTT--TTTTAAAGCCCACACGAGTTGGTG
* *
2396748 GCACCTTTTAGTCTTCAAAGAGTAGGAC
1 GCACCTTTTAGTCCTCAAAGAGCAGGAC
2396776 TCATTTCCTT
Statistics
Matches: 226, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
58 18 0.08
59 61 0.27
60 98 0.43
62 1 0.00
63 4 0.02
65 44 0.19
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (60 bp):
GCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTTTTTAAAGCCCACACGAGTTGGTG
Found at i:2396863 original size:43 final size:43
Alignment explanation
Indices: 2396776--2396901 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
2396766 AGAGTAGGAC
* * *
2396776 TCATTTCCTTCTTTTCCCTTCGTTCTCAAAGAGCAGGACACACT
1 TCATTTCCTTCTTTT-CCTTTGTCCTCAAAGAGCAGGACGCACT
*
2396820 TCATTTCCTTCATTTCCTTTGTCCTCAAAGAGCAGGACGCACT
1 TCATTTCCTTCTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
* * * * * *
2396863 TCATTTCTTTTTTTTTCTTTATCCCCGAAGAGCAGGACG
1 TCATTTCCTTCTTTTCCTTTGTCCTCAAAGAGCAGGACG
2396902 TACATTTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 57 0.80
44 14 0.20
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (43 bp):
TCATTTCCTTCTTTTCCTTTGTCCTCAAAGAGCAGGACGCACT
Found at i:2397717 original size:20 final size:21
Alignment explanation
Indices: 2397672--2397726 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
2397662 CATAAGTAAA
**
2397672 TGTATTGATACATTTACTGTT
1 TGTATTGATACATTTACTCAT
*
2397693 TGTATTGATACATTT-TTCAT
1 TGTATTGATACATTTACTCAT
*
2397713 TGTATCGATACATT
1 TGTATTGATACATT
2397727 CTAGGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (21 bp):
TGTATTGATACATTTACTCAT
Found at i:2400884 original size:52 final size:52
Alignment explanation
Indices: 2400795--2400923 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2400785 CGAAATATGA
* *
2400795 AAATTTGCCTGCATGTATCGATATATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
2400847 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
2400899 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2400924 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:2400936 original size:52 final size:51
Alignment explanation
Indices: 2400795--2400943 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
2400785 CGAAATATGA
*
2400795 AAATTTGCCTGCATGTATCGATATATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
2400847 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
2400899 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2400944 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:2400950 original size:13 final size:13
Alignment explanation
Indices: 2400932--2400990 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
2400922 CAAAGATCAG
2400932 TGTATCGATACAA
1 TGTATCGATACAA
2400945 TGTATCGATAC-A
1 TGTATCGATACAA
2400957 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
2400966 TGTATCGATACAA
1 TGTATCGATACAA
2400979 TGTATCGATACA
1 TGTATCGATACA
2400991 TTTGAGCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 4 0.10
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2400975 original size:34 final size:34
Alignment explanation
Indices: 2400932--2400996 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
2400922 CAAAGATCAG
2400932 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
2400966 TGTATCGATACAATGTATCGATACATTTGAG
1 TGTATCGATACAATGTATCGATACATTTGAG
2400997 CATTTTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAGTAA
Done.