Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold491
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: 232955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:158650 original size:19 final size:18
Alignment explanation
Indices: 158559--158656 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
158549 TTTTCAACGA
158559 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
158578 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
158594 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
158610 TGTTGTTTCGATAC--AA-
1 T-TTGTATCGATACATAAG
158626 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
158642 TTTTGTATCGATACA
1 -TTTGTATCGATACA
158657 ATGTAAGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
19 23 0.36
20 12 0.19
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:158788 original size:52 final size:52
Alignment explanation
Indices: 158732--158912 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
158722 CACTGATCTT
158732 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
158784 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
158836 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
158888 TGTATCGATACATGCAGGCGAATTT
1 TGTATCGATACATGCAGGCAAATTT
158913 TCATATTTTG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:172130 original size:11 final size:10
Alignment explanation
Indices: 172114--172156 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
172104 CGTCCTTCGT
172114 ACAAAAAGAAA
1 ACAAAAA-AAA
172125 ACAAAAAAAA
1 ACAAAAAAAA
172135 TA-AAAAAAAA
1 -ACAAAAAAAA
172145 ACAGAAAAAAA
1 ACA-AAAAAAA
172156 A
1 A
172157 AACAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.03
10 12 0.41
11 16 0.55
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:172139 original size:20 final size:21
Alignment explanation
Indices: 172116--172155 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
172106 TCCTTCGTAC
*
172116 AAAAAGAAAACA-AAAAAAAT
1 AAAAAAAAAACAGAAAAAAAT
172136 AAAAAAAAAACAGAAAAAAA
1 AAAAAAAAAACAGAAAAAAA
172156 AAACAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAACAGAAAAAAAT
Found at i:172143 original size:13 final size:13
Alignment explanation
Indices: 172116--172158 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
172106 TCCTTCGTAC
172116 AAAAAGAAAACAAA
1 AAAAAGAAAA-AAA
*
172130 AAAAATAAAAAAA
1 AAAAAGAAAAAAA
*
172143 AAACAGAAAAAAA
1 AAAAAGAAAAAAA
172156 AAA
1 AAA
172159 CAAACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:172156 original size:17 final size:16
Alignment explanation
Indices: 172114--172169 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 16
172104 CGTCCTTCGT
* *
172114 ACAAAAAGAAAACAAA
1 ACAAAAAAAAAAAAAA
*
172130 A-AAAATAAAAAAAAA
1 ACAAAAAAAAAAAAAA
*
172145 ACAGAAAAAAAAAACAA
1 ACA-AAAAAAAAAAAAA
172162 ACAAAAAA
1 ACAAAAAA
172170 GGGTCCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 12 0.36
16 7 0.21
17 14 0.42
ACGTcount: A:0.86, C:0.09, G:0.04, T:0.02
Consensus pattern (16 bp):
ACAAAAAAAAAAAAAA
Found at i:172159 original size:13 final size:13
Alignment explanation
Indices: 172116--172169 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
172106 TCCTTCGTAC
172116 AAAA-AGAAAACAA
1 AAAACAGAAAA-AA
* *
172129 AAAAAATAAAAAA
1 AAAACAGAAAAAA
172142 AAAACAGAAAAAA
1 AAAACAGAAAAAA
172155 AAAACA-AACAAAA
1 AAAACAGAA-AAAA
172168 AA
1 AA
172170 GGGTCCTAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 2 0.06
13 29 0.81
14 5 0.14
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (13 bp):
AAAACAGAAAAAA
Found at i:173449 original size:28 final size:28
Alignment explanation
Indices: 173417--174007 Score: 629
Period size: 28 Copynumber: 20.6 Consensus size: 28
173407 CGTTTATCTC
* * *
173417 TTCAAAGCCCATAGGTCAGTGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
**
173445 TTCAAAGCCCACAAGTCAGTGGCATTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
173473 TTCAAAGCCCACAGGTCAGTGGCGTCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
173501 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
173529 TTCAAAGCCTACAAGTCAGTGACA-CACT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
173557 TTCAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
173585 TTCAAAGCCCATAAGTTAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
173612 CTTCAAAAGACCACAAGTCAGTGGTATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* * *
173642 TTCAAAGCCCACACAAATTAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
173672 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
173700 TTCAAATCCCACAAGTCAGTGGTA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * * *
173728 TTCAAATCCCACAAGTCAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
173756 TTCAAAGCCCACAAGTCAGTGGCA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
173783 TTCCAAAGCCCACAAGTCAGTGGCATACCCT
1 TT-CAAAGCCCACAAGTCAGTGGCAT--CCT
*
173814 TTCAAAGCCCACAAGTCGGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
173842 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
173870 TTCAAAGCCCACAAGTCGGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
*
173900 TTCAAAGCCCACAAGTCGGTGGCATACCTT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CC-T
* *
173930 TTCAAAGCCCACAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
173958 TTCAAAGCTCACACAAGTTGGTGGCAACTCTT
1 TTCAAAGC-C-CACAAGTCAGTGGC-A-TCCT
173990 TTCAAAGCTCACACAAGT
1 TTCAAAGC-C-CACAAGT
174008 TAATGGCACA
Statistics
Matches: 497, Mismatches: 44, Indels: 40
0.86 0.08 0.07
Matches are distributed among these distances:
27 10 0.02
28 318 0.64
29 32 0.06
30 109 0.22
31 8 0.02
32 20 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:174150 original size:45 final size:45
Alignment explanation
Indices: 174099--174212 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
174089 AAGTTCGATA
*
174099 TCGCTGGCATTGAATCATCATATTAGCACCTTTATTGGCCTAATG
1 TCGCTGGCATTGAATCATCATATTAGCACCTTTATTGGCCCAATG
174144 TCGCTGGCATTGAATCATCATATTAGCACCTTTATTGGCCCAATG
1 TCGCTGGCATTGAATCATCATATTAGCACCTTTATTGGCCCAATG
* * * *
174189 TAGCTGGCCTTAAATCAGCATATT
1 TCGCTGGCATTGAATCATCATATT
174213 GGTCCATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
TCGCTGGCATTGAATCATCATATTAGCACCTTTATTGGCCCAATG
Found at i:175961 original size:10 final size:11
Alignment explanation
Indices: 175946--175974 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
175936 CCACTAGATG
175946 ATTTTTCAAA-
1 ATTTTTCAAAC
175956 ATTTTTCAAAC
1 ATTTTTCAAAC
175967 ATTTTTCA
1 ATTTTTCA
175975 TAAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:178727 original size:167 final size:164
Alignment explanation
Indices: 178451--178891 Score: 530
Period size: 167 Copynumber: 2.7 Consensus size: 164
178441 GGTAAAATTT
* * * *
178451 AATATTAATCATTATTCAATCTTTTATATTCCTATGGGGGTCCGTA-GGGTAATAAAAGATTTCA
1 AATATTAATCATTTTTTAATCTTTTATATTCCTATGAGGGTCTGTAGGGGT-ATAAAAGATTTCA
*
178515 AAAACTTTTCGTATCTTTTCGGGCTTCCATTAAGGTACAAAATGGTATTTTTTAAAAATGAATAA
65 AAAACTTTTCGTATCTTTTCGGGCTTCCATTAAGGTACAAAATGGTATTTTTT---AAT-AACAA
* ***
178580 AT-AAATAAAATTAAATTAACACTTTCATAATTGTA-ATA
126 ATAAAATAAAATTAAATCAACACTTTCATAA-CCAAGATA
*
178618 AATATTAATCATTTTTTAATATTTTATATTCCTATGAGGGTCTGTAGGGGTATAAAAGATTTCAA
1 AATATTAATCATTTTTTAATCTTTTATATTCCTATGAGGGTCTGTAGGGGTATAAAAGATTTCAA
* * * * *
178683 AAACTTTTCATATCTTTTTGGGTTTCCATTAAGGTACGAAATGGTATTTTTTGATAACAAATAAA
66 AAACTTTTCGTATCTTTTCGGGCTTCCATTAAGGTACAAAATGGTATTTTTTAATAACAAATAAA
* *
178748 ATTATATTAAATCAACACTTTCATAACCAAGATA
131 ATAAAATTAAATCAACACTTTCATAACCAAGATA
* * *
178782 AATTTTGAATCCTTCTTTTTAAATCTTTTATATTCCTATGAAGGTCTGTAGGGGTATAAAAGATT
1 AATATT-AAT-CAT-TTTTT-AATCTTTTATATTCCTATGAGGGTCTGTAGGGGTATAAAAGATT
* **** *
178847 TCAAAAA-ATTTCGTATCTTTTCAAAATTCCATTAAGGTATAAAAT
62 TCAAAAACTTTTCGTATCTTTTCGGGCTTCCATTAAGGTACAAAAT
178892 AAATTTTTGT
Statistics
Matches: 237, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
163 7 0.03
164 35 0.15
165 3 0.01
166 2 0.01
167 137 0.58
168 53 0.22
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (164 bp):
AATATTAATCATTTTTTAATCTTTTATATTCCTATGAGGGTCTGTAGGGGTATAAAAGATTTCAA
AAACTTTTCGTATCTTTTCGGGCTTCCATTAAGGTACAAAATGGTATTTTTTAATAACAAATAAA
ATAAAATTAAATCAACACTTTCATAACCAAGATA
Found at i:179628 original size:155 final size:154
Alignment explanation
Indices: 179140--179665 Score: 469
Period size: 155 Copynumber: 3.4 Consensus size: 154
179130 CATCCAAATT
* * * * *
179140 TTTTTAAGTCCTTTAGGTATATCGGGTACTTTTACGTCGAAGGTATCCCCTAAGGGTATTTTTGT
1 TTTTTAAGTCCTTTAGGGATATCAGGTACTTTTACGTCGAAGGTATCTCCTAAGGGCA-TTTTGG
* * * * * * * * ** *
179205 AATTTTTTAA-AATTGAGTCTTAGGTTATCACCAGGTCTACTTTCACGTTGAAAGTGGGTATTTA
65 AAATTTTTAAGAACTGAGTCCTAAGTTGTCACCAGGTCTATTTTAATGCCGAAGGTGGGTATTTA
* * * **
179269 GGATAGTTTTATCCTTTCTAT-GGCC
130 GGATAGGTTTGTCC-ATCTATAATCC
* ** * * *
179294 TTTTTAAGTCTTTTAGAGG-TGCCAGGTACTTTTATGTCAAAGGTATCTCCTAAGGGCATTTTTG
1 TTTTTAAGTCCTTTAG-GGATATCAGGTACTTTTACGTCGAAGGTATCTCCTAAGGGCATTTTGG
* ** * *
179358 TAATTGTTT-AGAACCAAGTCCTAAGTTGTCACCAGGTCTACTTTAAATGCC-AATGGAGGGTAT
65 AAATT-TTTAAGAACTGAGTCCTAAGTTGTCACCAGGTCTA-TTTTAATGCCGAA-GGTGGGTAT
* *
179421 TTAGG-TAGGTTCATG-CCATTTTGTAATCC
127 TTAGGATAGGTT--TGTCCA-TCTATAATCC
* * * *
179450 TTCTTAAGTCCTTTAAGGATATCAGGCACTTTTACGTCGAAGATATC-CCTTAAGGGCATTTTGG
1 TTTTTAAGTCCTTTAGGGATATCAGGTACTTTTACGTCGAAGGTATCTCC-TAAGGGCATTTTGG
* * *
179514 AAATTTTTAAGAACTGAGTCCTATGTTGTCACCGGGT-TCATTTTTATGCCGAAGGTGGGTATTT
65 AAATTTTTAAGAACTGAGTCCTAAGTTGTCACCAGGTCT-ATTTTAATGCCGAAGGTGGGTATTT
179578 AGGATAGGTTTGTCTCATCTATAATCC
129 AGGATAGGTTTGTC-CATCTATAATCC
* * * *
179605 TTTTTAAGTCCTTTAGGGGTATCAAGTACTTTTGCGTCGAAGTTATCTCC-AAGGGCATTTT
1 TTTTTAAGTCCTTTAGGGATATCAGGTACTTTTACGTCGAAGGTATCTCCTAAGGGCATTTT
179666 CATAATTTTT
Statistics
Matches: 293, Mismatches: 61, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
153 8 0.03
154 93 0.32
155 100 0.34
156 92 0.31
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (154 bp):
TTTTTAAGTCCTTTAGGGATATCAGGTACTTTTACGTCGAAGGTATCTCCTAAGGGCATTTTGGA
AATTTTTAAGAACTGAGTCCTAAGTTGTCACCAGGTCTATTTTAATGCCGAAGGTGGGTATTTAG
GATAGGTTTGTCCATCTATAATCC
Found at i:179683 original size:155 final size:155
Alignment explanation
Indices: 179140--179675 Score: 439
Period size: 154 Copynumber: 3.5 Consensus size: 155
179130 CATCCAAATT
** * * * * **
179140 TTTTTAAGTCCTTTAGGTATATCGGGTACTTTTACGTCGAAGGTATCCCCTAAGGGTATTTTTGT
1 TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACGTCGAAGATATCTCCTAAGGGCATTTTCAT
* * * * * * ** *
179205 AATTTTTTAAAATTGAGTCTTAGGTTATCACCAGGTCTACTTTCACGTTG--AA-AGTGGGTATT
66 AATTTTTTAGAACTAAGTCCTAAGTTGTCACCAGGTCTACTTT-A-AATGCCAATGGTGGGTATT
* * * **
179267 TAGGATAGTTTTATCCTTTCTAT-GGCC
129 TAGGATAGGTTTGTCC-ATCTATAATCC
* * ** * * * **
179294 TTTTTAAGTCTTTTAGAGGTGCCAGGTACTTTTATGTCAAAGGTATCTCCTAAGGGCATTTTTGT
1 TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACGTCGAAGATATCTCCTAAGGGCATTTTCAT
* * *
179359 AATTGTTTAGAACCAAGTCCTAAGTTGTCACCAGGTCTACTTTAAATGCCAATGGAGGGTATTTA
66 AATTTTTTAGAACTAAGTCCTAAGTTGTCACCAGGTCTACTTTAAATGCCAATGGTGGGTATTTA
* *
179424 GG-TAGGTTCATG-CCATTTTGTAATCC
131 GGATAGGTT--TGTCCA-TCTATAATCC
* * * * *
179450 TTCTTAAGTCCTTTAAGGATATCAGGCACTTTTACGTCGAAGATATC-CCTTAAGGGCATTTTGG
1 TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACGTCGAAGATATCTCC-TAAGGGCATTTT-C
* * * * **
179514 A-AATTTTTAAGAACTGAGTCCTATGTTGTCACCGGGT-T-CATTTTTATGCCGAA-GGTGGGTA
64 ATAATTTTTTAGAACTAAGTCCTAAGTTGTCACCAGGTCTAC-TTTAAATGCC-AATGGTGGGTA
179575 TTTAGGATAGGTTTGTCTCATCTATAATCC
127 TTTAGGATAGGTTTGTC-CATCTATAATCC
* * *
179605 TTTTTAAGTCCTTTAGGGGTATCAAGTACTTTTGCGTCGAAGTTATCTCC-AAGGGCATTTTCAT
1 TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACGTCGAAGATATCTCCTAAGGGCATTTTCAT
179669 AATTTTT
66 AATTTTT
179676 CTTGAACTTA
Statistics
Matches: 304, Mismatches: 62, Indels: 32
0.76 0.16 0.08
Matches are distributed among these distances:
152 2 0.01
153 2 0.01
154 117 0.38
155 90 0.30
156 93 0.31
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (155 bp):
TTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACGTCGAAGATATCTCCTAAGGGCATTTTCAT
AATTTTTTAGAACTAAGTCCTAAGTTGTCACCAGGTCTACTTTAAATGCCAATGGTGGGTATTTA
GGATAGGTTTGTCCATCTATAATCC
Found at i:182056 original size:28 final size:28
Alignment explanation
Indices: 182025--182083 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
182015 TAAGTCTTCA
182025 TCTCTAAACCTGTTTTGTATATAACTTG
1 TCTCTAAACCTGTTTTGTATATAACTTG
*
182053 TCTCTGAACCTGTTTTGTATATAACTTG
1 TCTCTAAACCTGTTTTGTATATAACTTG
182081 TCT
1 TCT
182084 TTTACATGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (28 bp):
TCTCTAAACCTGTTTTGTATATAACTTG
Found at i:193176 original size:52 final size:52
Alignment explanation
Indices: 193098--193248 Score: 248
Period size: 52 Copynumber: 2.9 Consensus size: 52
193088 CGAAATATGA
193098 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
193150 AAATTTGTCTGCATGTATCAATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
193202 AAATTTGCCTGCATGTATCGATACATTTGAGTAATGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTTCA-TAGTGTATCGATACAT
193249 TTTTTTGCAG
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 76 0.84
53 15 0.16
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:193293 original size:19 final size:19
Alignment explanation
Indices: 193269--193353 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
193259 TAGCTTACAT
193269 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
193288 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
193307 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
193320 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAC-TTA
193340 TGTATCGATACAAA
1 TGTATCGATACAAA
193354 TCGTTGAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.19
14 1 0.02
16 2 0.04
19 30 0.53
20 13 0.23
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:193325 original size:13 final size:13
Alignment explanation
Indices: 193307--193331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193297 ACAACACTTA
193307 TGTATCGATACAT
1 TGTATCGATACAT
193320 TGTATCGATACA
1 TGTATCGATACA
193332 ACACTTTATG
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:193329 original size:32 final size:33
Alignment explanation
Indices: 193288--193351 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
193278 ACAAAACTTA
193288 TGTATCGATACAACAC-TTATGTATCGATACAT
1 TGTATCGATACAACACTTTATGTATCGATACAT
193320 TGTATCGATACAACACTTTATGTATCGATACA
1 TGTATCGATACAACACTTTATGTATCGATACA
193352 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAACACTTTATGTATCGATACAT
Found at i:194419 original size:19 final size:19
Alignment explanation
Indices: 194395--194451 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
194385 TGTATCGATA
194395 CATTGTAT-GCATACATGAT
1 CATTGTATCG-ATACATGAT
194414 CATTGTATCGATACATGCAT
1 CATTGTATCGATACATG-AT
*
194434 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
194452 AACTGGCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:194488 original size:43 final size:43
Alignment explanation
Indices: 194438--194538 Score: 184
Period size: 43 Copynumber: 2.3 Consensus size: 43
194428 ATGCATAATT
194438 GTATCGATACATGAAACTGGCAATAGCTACCCTACCACTGTTC
1 GTATCGATACATGAAACTGGCAATAGCTACCCTACCACTGTTC
* *
194481 GTATCGATACATGAAACTGGCAGTAGCTACCCTACCACTGTTT
1 GTATCGATACATGAAACTGGCAATAGCTACCCTACCACTGTTC
194524 GTATCGATACATGAA
1 GTATCGATACATGAA
194539 GAATTGTATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
GTATCGATACATGAAACTGGCAATAGCTACCCTACCACTGTTC
Found at i:196706 original size:25 final size:24
Alignment explanation
Indices: 196660--196706 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
196650 GGAGCATGAT
*
196660 AAAAAAAAGCAAAAAGAAAAAGTG
1 AAAAAAAAGCAAAAAAAAAAAGTG
* *
196684 AAAAAAATGGAAAAAAAATAAAG
1 AAAAAAAAGCAAAAAAAA-AAAG
196707 CTTTAGAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (24 bp):
AAAAAAAAGCAAAAAAAAAAAGTG
Found at i:198220 original size:21 final size:21
Alignment explanation
Indices: 198194--198250 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
198184 AAATTATCCA
198194 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
198215 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
198236 AATGTATCGATACAT
1 AATGTATCGATACAT
198251 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:198330 original size:19 final size:19
Alignment explanation
Indices: 198306--198373 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
198296 AATTCAACAA
198306 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
198325 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
198340 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
198357 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
198374 TTATCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:198345 original size:13 final size:13
Alignment explanation
Indices: 198327--198351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
198317 ACATAAGTTT
198327 TGTATCGATACAA
1 TGTATCGATACAA
198340 TGTATCGATACA
1 TGTATCGATACA
198352 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:198349 original size:32 final size:32
Alignment explanation
Indices: 198308--198370 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
198298 TTCAACAATT
*
198308 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
198340 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
198371 TAATTATCTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:198431 original size:13 final size:13
Alignment explanation
Indices: 198413--198438 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198403 CATTTTTCTG
198413 TGTATCGATACAT
1 TGTATCGATACAT
198426 TGTATCGATACAT
1 TGTATCGATACAT
198439 GGATCTTTGT
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:198435 original size:33 final size:33
Alignment explanation
Indices: 198393--198459 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
198383 GCCAAGGAAA
***
198393 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
198426 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
198459 T
1 T
198460 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:201064 original size:52 final size:54
Alignment explanation
Indices: 201008--201151 Score: 172
Period size: 52 Copynumber: 2.7 Consensus size: 54
200998 TTTTATCGCT
* * *
201008 AAAACACTAATTTTTCCACAATCGGGGATACTCCAATC-CCGGTTTTATTTTC-
1 AAAACACCAATTTTTCCACAATCGGGGATACTCCAATCTCCGATTTTATTTCCA
* **
201060 AAAACGCCAA-TTTTCCTTTAATCGGGGATACTCCAA-CTCCGATTTTATTTCCA
1 AAAACACCAATTTTTCC-ACAATCGGGGATACTCCAATCTCCGATTTTATTTCCA
* *
201113 AAAATACCAATTTTT-CACAATCGAGGATACTCCAATCTC
1 AAAACACCAATTTTTCCACAATCGGGGATACTCCAATCTC
201152 GTTATTTCAT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
51 7 0.09
52 53 0.70
53 12 0.16
54 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (54 bp):
AAAACACCAATTTTTCCACAATCGGGGATACTCCAATCTCCGATTTTATTTCCA
Found at i:201149 original size:104 final size:103
Alignment explanation
Indices: 200812--201147 Score: 299
Period size: 104 Copynumber: 3.2 Consensus size: 103
200802 CTCAATTCTC
* * * * *
200812 CACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGGGGATACTCCAAC-CCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
200876 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCTAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * **** * * * *
200917 CACAATCGGGGATACTCCAACCCCGTTAATCATTGGGGATACTCCAA---CCCTGTTATTTCCGA
1 CACAATCGGGGATACTCCAACCCGGTT--TTATTTTCAAAACACCAATTTTCCT-TTA-AT-C--
* * *
200979 GGGGATACTCTAAC-CTCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCTAACTC-CGATTTTATTTC-CAAAAACACCAATTTTT
*
201023 CCACAATCGGGGATACTCCAATCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
* *
201088 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCTAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
201128 CACAATCGAGGATACTCCAA
1 CACAATCGGGGATACTCCAA
201148 TCTCGTTATT
Statistics
Matches: 179, Mismatches: 34, Indels: 37
0.72 0.14 0.15
Matches are distributed among these distances:
104 45 0.25
105 36 0.20
106 27 0.15
107 36 0.20
108 11 0.06
109 24 0.13
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (103 bp):
CACAATCGGGGATACTCCAACCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCTAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:201168 original size:28 final size:28
Alignment explanation
Indices: 201132--201208 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
201122 ATTTTTCACA
* * *
201132 ATCGAGGATACTCCAATCTCGTTATTTC
1 ATCGGGGATACTCCAATCCCGTTACTTC
*
201160 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAATCCCGTTACTTC
***
201188 CGAGGGGATACTCCAATCCCG
1 ATCGGGGATACTCCAATCCCG
201209 ATTTTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAATCCCGTTACTTC
Found at i:201177 original size:212 final size:212
Alignment explanation
Indices: 200810--201200 Score: 599
Period size: 212 Copynumber: 1.8 Consensus size: 212
200800 TTCTCAATTC
* * *
200810 TCCACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
200875 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
200940 CGTTAATCATTGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCTAACCTCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTAACCTCGGTTTTATC
201005 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
201022 TCCACAATCGGGGATACTCCAA-TCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
201086 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAT
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
201149 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTC
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTC
201201 CAATCCCGAT
Statistics
Matches: 161, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
211 28 0.17
212 98 0.61
213 35 0.22
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTAACCTCGGTTTTATC
GCTAAAACACTAATTTT
Found at i:202849 original size:48 final size:48
Alignment explanation
Indices: 202773--203025 Score: 278
Period size: 48 Copynumber: 5.3 Consensus size: 48
202763 TTGATTGTAT
* * *
202773 CTGGTCAAACTCTTTTCAT-TCTCTATTTGACTATATTGGCGTTAGGAC
1 CTGGTCAAACTCTTTTCATCCCTC-ATTTGACTGTATTGGTGTTAGGAC
* * *
202821 CTGGTCAAACTATTTTCATCTCTCATTTGACTGTATTGGTGTTAGGCC
1 CTGGTCAAACTCTTTTCATCCCTCATTTGACTGTATTGGTGTTAGGAC
** * *
202869 CTGGTCAAACTCTTTTCA-CCCTTTGTTTGAATGTATTGGTGTTAGGGC
1 CTGGTCAAACTCTTTTCATCCC-TCATTTGACTGTATTGGTGTTAGGAC
* * * ** * * * *
202917 CTAGTCAAACTTTTTTCATCCTTTGTTTGACTATATTTGTGTTAAGAT
1 CTGGTCAAACTCTTTTCATCCCTCATTTGACTGTATTGGTGTTAGGAC
*
202965 CTAGTCAAACTCTTTTCATCCCTCATTTGACTGTATTGGTGTTAAGG-C
1 CTGGTCAAACTCTTTTCATCCCTCATTTGACTGTATTGGTGTT-AGGAC
203013 CTGGTCAAACTCT
1 CTGGTCAAACTCT
203026 CCTCTTTCTT
Statistics
Matches: 173, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
47 2 0.01
48 163 0.94
49 8 0.05
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (48 bp):
CTGGTCAAACTCTTTTCATCCCTCATTTGACTGTATTGGTGTTAGGAC
Found at i:203091 original size:44 final size:43
Alignment explanation
Indices: 203043--203286 Score: 230
Period size: 44 Copynumber: 5.6 Consensus size: 43
203033 CTTATCTGAT
* *
203043 GTATGGTTACCAACTTAGTCAAATTCTTTTCATTCTGATTTGAC
1 GTATGGTTACCACCCTAGTCAAATTCTTTTC-TTCTGATTTGAC
* *
203087 GTATGGTTACCACCCTAGTCAAATCTACCTTTC-TCTTG-TCTGAC
1 GTATGGTTACCACCCTAGTCAAAT-T-CTTTTCTTC-TGATTTGAC
* *
203131 ATATGGTTACCACCCTAGTCAGATTCTTTTCCTT-TCGATTTGAC
1 GTATGGTTACCACCCTAGTCAAATTCTTTT-CTTCT-GATTTGAC
* ** * *
203175 TTATGGTTACTGCCCTAGTCAAATCTGCCTTTTCTT-TG-TCTGGC
1 GTATGGTTACCACCCTAGTCAAAT-T--CTTTTCTTCTGATTTGAC
*
203219 -TATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGAC
1 GTATGGTTACCACCCTAGTCAAATTCTTTTC-TTCTGATTTGAC
**
203262 GTATGGTTACCACTTTAGTCAAATT
1 GTATGGTTACCACCCTAGTCAAATT
203287 TGCCTCTCTC
Statistics
Matches: 164, Mismatches: 22, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
40 6 0.04
41 2 0.01
42 8 0.05
43 27 0.16
44 102 0.62
45 5 0.03
46 9 0.05
47 5 0.03
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (43 bp):
GTATGGTTACCACCCTAGTCAAATTCTTTTCTTCTGATTTGAC
Found at i:203142 original size:88 final size:88
Alignment explanation
Indices: 203044--203315 Score: 379
Period size: 88 Copynumber: 3.1 Consensus size: 88
203034 TTATCTGATG
* * *
203044 TATGGTTACCAACTTAGTCAAATTCTTTTCATTCTGATTTGACGTATGGTTACCACCCTAGTCAA
1 TATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCACCCTAGTCAA
*
203109 ATCTACCTTTCTCTTGTCTGACA
66 ATCTGCCTTTCTCTTGTCTGACA
* * **
203132 TATGGTTACCACCCTAGTCAGATTCTTTTCCTT-TCGATTTGACTTATGGTTACTGCCCTAGTCA
1 TATGGTTACCACCCTAGTCAGATTCTTTTCATTCT-GATTTGACGTATGGTTACCACCCTAGTCA
*
203196 AATCTGCCTTT-TCTTTGTCTGGC-
65 AATCTGCCTTTCTC-TTGTCTGACA
**
203219 TATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCACTTTAGTCAA
1 TATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCACCCTAGTCAA
* * *
203284 ATTTGCCTCTCTCATGTCTGACA
66 ATCTGCCTTTCTCTTGTCTGACA
203307 TATGGTTAC
1 TATGGTTAC
203316 TGTCGTAACG
Statistics
Matches: 160, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
87 75 0.47
88 85 0.53
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (88 bp):
TATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCACCCTAGTCAA
ATCTGCCTTTCTCTTGTCTGACA
Found at i:206868 original size:21 final size:21
Alignment explanation
Indices: 206842--206897 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
206832 AGAGTGGTTT
*
206842 TGTATCGATACATTTCAGGCA
1 TGTATCGATACATTTCACGCA
**
206863 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACGCA
206883 TGTATCGATACATTT
1 TGTATCGATACATTT
206898 ACTATTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCACGCA
Found at i:206909 original size:21 final size:20
Alignment explanation
Indices: 206842--206915 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
206832 AGAGTGGTTT
***
206842 TGTATCGATACATTTCAGGCA
1 TGTATCGATACA-TTCACTTA
206863 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
* *
206883 TGTATCGATACATTTACTATT
1 TGTATCGATACATTCACT-TA
206904 TGTATCGATACA
1 TGTATCGATACA
206916 AATTATGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 22 0.47
21 25 0.53
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:207357 original size:44 final size:44
Alignment explanation
Indices: 207217--208100 Score: 257
Period size: 44 Copynumber: 20.3 Consensus size: 44
207207 GTGTCTATAA
*
207217 TTACCACCTTGGTCAGATTCTTTTCATTTTGATTTGATGTATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* * * * * ** * *
207261 TTACCACTTTGGTCAAAATCTGCCTCCCTCCTG-TCTGACGTATGG
1 TTACCACCTTGGTCAAATTCT--TTTCATTTTGATTTGATGTATGG
*
207306 TTACCACCTTGGTCAAATTCTTTTCTTTTTGATTTGATGTATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* ** * *
207350 -TACCCACCCTGGTCAAA-TCTGCCTCATTCTTG-TCTGCT-TATGG
1 TTA-CCACCTTGGTCAAATTCT-TTTCATT-TTGATTTGATGTATGG
* ** * * * *
207393 TTACCACCCTATTCAGATTCTTTTCATTTCGATTTAACGTATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* * * * * * *
207437 TTACCATCC-TAGTCAAATCTACCTCTC-TCTT-ATCTAACGTATGG
1 TTACCA-CCTTGGTCAAAT-T-CTTTTCATTTTGATTTGATGTATGG
* ***
207481 TTACCA-C-----C-----CTTTTCATTTCGATTTGACACATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* ** * ***
207514 TTACCACCCTAATCAAATT-TGTCTTC-TTCTTG-TATGGCATATGG
1 TTACCACCTTGGTCAAATTCT-T-TTCATT-TTGATTTGATGTATGG
* *** **
207558 TTACCACCTTGG-CTAGATTCTTTTCATTCCAATTTGACATATGG
1 TTACCACCTTGGTC-AAATTCTTTTCATTTTGATTTGATGTATGG
* * * ** * *
207602 TTACCACCGTAGTC-AAGTCTACATCCTTCTT-ATTTGACGTATGG
1 TTACCACCTTGGTCAAATTCT-TTTCATT-TTGATTTGATGTATGG
* * **
207646 TTACCA-CTCTGGTTAGATTCTTTTCATTTCAATTTGATGTATGG
1 TTACCACCT-TGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* * * **
207690 TTACCACCTTGGTCAGATTTTTTTCATTTCGATTTGACATATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* * * * * **
207734 TTACCACCTTGGTTAAA-TCTGCCTTC-TTCTT-CTCTAACATATGG
1 TTACCACCTTGGTCAAATTCT--TTTCATT-TTGATTTGATGTATGG
* *
207778 TTACCACCTTGGTCAGATTCTTTTCATTCTGATTTG-TAGTATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGAT-GTATGG
** * * *
207822 TTACCACCTTTTTGAAATATGC-CTTC-TTCTTG-TCT-A-GCATATGG
1 TTACCACCTTGGTCAAAT-T-CTTTTCATT-TTGATTTGATG--TATGG
* * * *
207866 TTACCACCCTAGTCAGATTCTTTTCATTTTGATTTGACGTATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* * * ** * * * *
207910 TTACCACCCTGATCAAGTT-TGCATCCTTTCT-ATCTGACGTGTGG
1 TTACCACCTTGGTCAAATTCT-TTTCATTT-TGATTTGATGTATGG
* * * * *
207954 TTACCACCCTAGTCAAATTCGTTTCATTTCGATTTGACGTATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
* * * * * *
207998 TTACCACCCTAGTCAAATCTGCCTATTTC---TTG-TCTAACGTAGGG
1 TTACCACCTTGGTCAAAT-T--CT-TTTCATTTTGATTTGATGTATGG
* * * * *
208042 TTACCACCTTGGTTAGATTCTTTTAATTCTAATTTGATGTATGG
1 TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
208086 TTACCACCTTGGTCA
1 TTACCACCTTGGTCA
208101 TATGATTTGC
Statistics
Matches: 615, Mismatches: 155, Indels: 140
0.68 0.17 0.15
Matches are distributed among these distances:
31 4 0.01
32 2 0.00
33 15 0.02
34 1 0.00
38 1 0.00
39 1 0.00
40 3 0.00
41 2 0.00
42 5 0.01
43 60 0.10
44 437 0.71
45 68 0.11
46 11 0.02
47 1 0.00
48 4 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (44 bp):
TTACCACCTTGGTCAAATTCTTTTCATTTTGATTTGATGTATGG
Found at i:207363 original size:89 final size:88
Alignment explanation
Indices: 207217--207704 Score: 371
Period size: 88 Copynumber: 5.7 Consensus size: 88
207207 GTGTCTATAA
**
207217 TTACCACCTTGGTCAGATTCTTTTCATTTTGATTTGATGTATGGTTACCACTTTGGTCAAAATCT
1 TTACCACCTTGGTCAGATTCTTTTCATTTTGATTTGATGTATGGTTACCACCCTGGTC-AAATCT
* *
207282 GCCTCCCTCCTGTCTGACGTATGG
65 GCCTCACTCTTGTCTGACGTATGG
* *
207306 TTACCACCTTGGTCAAATTCTTTTCTTTTTGATTTGATGTATGG-TACCCACCCTGGTCAAATCT
1 TTACCACCTTGGTCAGATTCTTTTCATTTTGATTTGATGTATGGTTA-CCACCCTGGTCAAATCT
* *
207370 GCCTCATTCTTGTCTG-CTTATGG
65 GCCTCACTCTTGTCTGACGTATGG
* ** * * * * * *
207393 TTACCACCCTATTCAGATTCTTTTCATTTCGATTTAACGTATGGTTACCATCCTAGTCAAATCTA
1 TTACCACCTTGGTCAGATTCTTTTCATTTTGATTTGATGTATGGTTACCACCCTGGTCAAATCTG
* * *
207458 CCTCTCTCTTATCTAACGTATGG
66 CCTCACTCTTGTCTGACGTATGG
* *** ** *
207481 TTACCA-C-----C-----CTTTTCATTTCGATTTGACACATGGTTACCACCCTAATCAAATTTG
1 TTACCACCTTGGTCAGATTCTTTTCATTTTGATTTGATGTATGGTTACCACCCTGGTCAAATCTG
* * * * *
207535 TCTTC-TTCTTGTATGGCATATGG
66 -CCTCACTCTTGTCTGACGTATGG
*** ** * * *
207558 TTACCACCTTGG-CTAGATTCTTTTCATTCCAATTTGACATATGGTTACCACCGTAGTCAAGTCT
1 TTACCACCTTGGTC-AGATTCTTTTCATTTTGATTTGATGTATGGTTACCACCCTGGTCAAATCT
* * * *
207622 ACATC-CTTCTTATTTGACGTATGG
65 GCCTCAC-TCTTGTCTGACGTATGG
* ** *
207646 TTACCA-CTCTGGTTAGATTCTTTTCATTTCAATTTGATGTATGGTTACCACCTTGGTCA
1 TTACCACCT-TGGTCAGATTCTTTTCATTTTGATTTGATGTATGGTTACCACCCTGGTCA
207705 GATTTTTTTC
Statistics
Matches: 323, Mismatches: 58, Indels: 37
0.77 0.14 0.09
Matches are distributed among these distances:
77 57 0.18
78 4 0.01
82 2 0.01
87 74 0.23
88 135 0.42
89 51 0.16
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (88 bp):
TTACCACCTTGGTCAGATTCTTTTCATTTTGATTTGATGTATGGTTACCACCCTGGTCAAATCTG
CCTCACTCTTGTCTGACGTATGG
Found at i:207725 original size:88 final size:85
Alignment explanation
Indices: 207553--208005 Score: 307
Period size: 88 Copynumber: 5.2 Consensus size: 85
207543 TTGTATGGCA
* * * *
207553 TATGGTTACCACCTTGGCTAGATTCTTTTCATTCCAATTTGACATATGGTTACCACCGTAGTCA-
1 TATGGTTACCACC-TGGTTAAATTCTTTTC-TTTC-ATTTGACATATGGTTACCACCCTAGTCAG
* * *
207617 AGTC--TACATCCTTCTTATTTGACG
63 ATTCTTTTCAT--TTC-GATTTGACG
* ** * *
207641 TATGGTTACCACTCTGGTTAGATTCTTTTCATTTCAATTTGATGTATGGTTACCACCTTGGTCAG
1 TATGGTTACCAC-CTGGTTAAATTCTTTTC-TTTC-ATTTGACATATGGTTACCACCCTAGTCAG
* *
207706 ATTTTTTTCATTTCGATTTGACA
63 ATTCTTTTCATTTCGATTTGACG
* * * *
207729 TATGGTTACCACCTTGGTTAAATCTGCCTTCTTC-TTC-TCTAACATATGGTTACCACCTTGGTC
1 TATGGTTACCACC-TGGTTAAAT-T--CTT-TTCTTTCATTTGACATATGGTTACCACCCTAGTC
207792 AGATTCTTTTCA-TTCTGATTTGTA-G
61 AGATTCTTTTCATTTC-GATTTG-ACG
** *
207817 TATGGTTACCACCTTTTTGAAATATGCCTTCTTCTTGTC--TAG-CATATGGTTACCACCCTAGT
1 TATGGTTACCACCTGGTT-AAAT-T--CTT-TTCTT-TCATTTGACATATGGTTACCACCCTAGT
*
207879 CAGATTCTTTTCATTTTGATTTGACG
60 CAGATTCTTTTCATTTCGATTTGACG
* * * * * * * *
207905 TATGGTTACCACCCTGATCAAGTT-TGCATCCTTTCTATCTGACGTGTGGTTACCACCCTAGTCA
1 TATGGTTACCA-CCTGGTTAAATTCT--TTTCTTTC-ATTTGACATATGGTTACCACCCTAGTCA
* *
207969 AATTCGTTTCATTTCGATTTGACG
62 GATTCTTTTCATTTCGATTTGACG
207993 TATGGTTACCACC
1 TATGGTTACCACC
208006 CTAGTCAAAT
Statistics
Matches: 302, Mismatches: 40, Indels: 47
0.78 0.10 0.12
Matches are distributed among these distances:
84 3 0.01
85 4 0.01
87 12 0.04
88 253 0.84
89 15 0.05
90 5 0.02
91 7 0.02
92 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (85 bp):
TATGGTTACCACCTGGTTAAATTCTTTTCTTTCATTTGACATATGGTTACCACCCTAGTCAGATT
CTTTTCATTTCGATTTGACG
Found at i:207867 original size:176 final size:176
Alignment explanation
Indices: 207685--208100 Score: 464
Period size: 176 Copynumber: 2.4 Consensus size: 176
207675 CAATTTGATG
* * *
207685 TATGGTTACCACCTTGGTCAGATTTTTTTCATTTCGATTTGACATATGGTTACCACCTTGGTTAA
1 TATGGTTACCACCTTGGTCAGATTCTTTTCATTTCGATTTGACGTATGGTTACCACCTTGGTCAA
* * * * * * *
207750 ATCTGCCTTC-TTCTTCTCTAACATATGGTTACCACCTTGGTCAGATTCTTTTCA-TTCTGATTT
66 ATCTGCATCCTTTC-TATCTAACATATGGTTACCACCCTAGTCAAATTCGTTTCATTTC-GATTT
* ** * *
207813 GTA-GTATGGTTACCACCTTTTTGAAATATGCCT-TCTTCTTGTCTAGCA
129 G-ACGTATGGTTACCACCCTAGTCAAATATGCCTAT-TTCTTGTCTAACA
* * * * *
207861 TATGGTTACCACCCTAGTCAGATTCTTTTCATTTTGATTTGACGTATGGTTACCACCCTGATCAA
1 TATGGTTACCACCTTGGTCAGATTCTTTTCATTTCGATTTGACGTATGGTTACCACCTTGGTCAA
* * * * *
207926 GTTTGCATCCTTTCTATCTGACGTGTGGTTACCACCCTAGTCAAATTCGTTTCATTTCGATTTGA
66 ATCTGCATCCTTTCTATCTAACATATGGTTACCACCCTAGTCAAATTCGTTTCATTTCGATTTGA
* *
207991 CGTATGGTTACCACCCTAGTCAAATCTGCCTATTTCTTGTCTAACG
131 CGTATGGTTACCACCCTAGTCAAATATGCCTATTTCTTGTCTAACA
* * * * *
208037 TAGGGTTACCACCTTGGTTAGATTCTTTT-AATTCTAATTTGATGTATGGTTACCACCTTGGTCA
1 TATGGTTACCACCTTGGTCAGATTCTTTTCATTTC-GATTTGACGTATGGTTACCACCTTGGTCA
208101 TATGATTTGC
Statistics
Matches: 198, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
175 4 0.02
176 187 0.94
177 7 0.04
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (176 bp):
TATGGTTACCACCTTGGTCAGATTCTTTTCATTTCGATTTGACGTATGGTTACCACCTTGGTCAA
ATCTGCATCCTTTCTATCTAACATATGGTTACCACCCTAGTCAAATTCGTTTCATTTCGATTTGA
CGTATGGTTACCACCCTAGTCAAATATGCCTATTTCTTGTCTAACA
Found at i:208044 original size:88 final size:87
Alignment explanation
Indices: 207688--208093 Score: 401
Period size: 88 Copynumber: 4.6 Consensus size: 87
207678 TTTGATGTAT
* * * *
207688 GGTTACCACCTTGGTCAGATTTTTTTCATTTCGATTTGACATATGGTTACCACCTTGGTTAAATC
1 GGTTACCACCTTGGTCAGATTCTTTTCATTTCGATTTGACGTATGGTTACCACCCT-GTCAAATC
* *
207753 TGCCTTCTTCTTCTCTAACATAT
65 TGCCTTCTTCTTGTCTAACATAG
* * *
207776 GGTTACCACCTTGGTCAGATTCTTTTCA-TTCTGATTTGTA-GTATGGTTACCACCTTTTTGAAA
1 GGTTACCACCTTGGTCAGATTCTTTTCATTTC-GATTTG-ACGTATGGTTACCACC-CTGTCAAA
* * *
207839 TATGCCTTCTTCTTGTCTAGCATAT
63 TCTGCCTTCTTCTTGTCTAACATAG
* * * * *
207864 GGTTACCACCCTAGTCAGATTCTTTTCATTTTGATTTGACGTATGGTTACCACCCTGATCAAGTT
1 GGTTACCACCTTGGTCAGATTCTTTTCATTTCGATTTGACGTATGGTTACCACCCTG-TCAAATC
* * * * *
207929 TGCATCCTT-TCTATCTGACGT-G
65 TGCCTTCTTCT-TGTCTAACATAG
* * * *
207951 TGGTTACCACCCTAGTCAAATTCGTTTCATTTCGATTTGACGTATGGTTACCACCCTAGTCAAAT
1 -GGTTACCACCTTGGTCAGATTCTTTTCATTTCGATTTGACGTATGGTTACCACCCT-GTCAAAT
*
208016 CTGCCTAT-TTCTTGTCTAACGTAG
64 CTGCCT-TCTTCTTGTCTAACATAG
* * * *
208040 GGTTACCACCTTGGTTAGATTCTTTT-AATTCTAATTTGATGTATGGTTACCACC
1 GGTTACCACCTTGGTCAGATTCTTTTCATTTC-GATTTGACGTATGGTTACCACC
208094 TTGGTCATAT
Statistics
Matches: 266, Mismatches: 39, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
87 10 0.04
88 248 0.93
89 8 0.03
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (87 bp):
GGTTACCACCTTGGTCAGATTCTTTTCATTTCGATTTGACGTATGGTTACCACCCTGTCAAATCT
GCCTTCTTCTTGTCTAACATAG
Found at i:209239 original size:83 final size:83
Alignment explanation
Indices: 209085--209325 Score: 267
Period size: 83 Copynumber: 2.9 Consensus size: 83
209075 GAGGGGTAAC
* * * *
209085 GTAAACAAGGGATGAAAGGTTGACCAAGGCTGAA-CTTATAAGTCAACAAAAGGT-AAGGAAGTT
1 GTAAATAAGAGATGAAAAGTTGACCAAGGCTGAATC-AATAAGTCAAC-AAAGGTAAAGG-AGTT
209148 TACCAGGGATTAAGCCGACAA-
63 TACCAGGGATTAAGCC-ACAAG
* * * *
209169 GTAAAT-AGAGATGAAAAGTTGACCAAGGCTAAATCGATAAGTCAACAAAGGATAAAAGAGTTCA
1 GTAAATAAGAGATGAAAAGTTGACCAAGGCTGAATCAATAAGTCAACAAAGG-TAAAGGAGTTTA
* * *
209233 CTAGGGACTGAGCCACAAG
65 CCAGGGATTAAGCCACAAG
* *
209252 GTAAATAAGGGAT-AAAAGGTTGACCAGGGCTGAATCAATAAGTCAACAAAGGGTAAAGGAGTTT
1 GTAAATAAGAGATGAAAA-GTTGACCAAGGCTGAATCAATAAGTCAACAAA-GGTAAAGGAGTTT
209316 ACCAGGGATT
64 ACCAGGGATT
209326 GAGTTGACAA
Statistics
Matches: 132, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
82 9 0.07
83 61 0.46
84 60 0.45
85 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.18
Consensus pattern (83 bp):
GTAAATAAGAGATGAAAAGTTGACCAAGGCTGAATCAATAAGTCAACAAAGGTAAAGGAGTTTAC
CAGGGATTAAGCCACAAG
Found at i:209300 original size:84 final size:83
Alignment explanation
Indices: 209085--209355 Score: 282
Period size: 84 Copynumber: 3.2 Consensus size: 83
209075 GAGGGGTAAC
* * *
209085 GTAAACAAGGGATGAAAGGTTGACCAAGGCTGAA-CTTATAAGTCAACAAAAGGT-AAGGAAGTT
1 GTAAATAAGGGATAAAAGGTTGACCAAGGCTGAATC-AATAAGTCAAC-AAAGGTAAAGG-AGTT
*
209148 TACCAGGGATTAAGCCGACAA
63 TACCAGGGATTGAGCCGACAA
* * * * *
209169 GTAAAT-AGAGATGAAAA-GTTGACCAAGGCTAAATCGATAAGTCAACAAAGGATAAAAGAGTTC
1 GTAAATAAGGGAT-AAAAGGTTGACCAAGGCTGAATCAATAAGTCAACAAAGG-TAAAGGAGTTT
* *
209232 ACTAGGGACTGAGCC-ACAA
64 ACCAGGGATTGAGCCGACAA
*
209251 GGTAAATAAGGGATAAAAGGTTGACCAGGGCTGAATCAATAAGTCAACAAAGGGTAAAGGAGTTT
1 -GTAAATAAGGGATAAAAGGTTGACCAAGGCTGAATCAATAAGTCAACAAA-GGTAAAGGAGTTT
**
209316 ACCAGGGATTGAGTTGACAA
64 ACCAGGGATTGAGCCGACAA
* * * *
209336 GCAAACAATGAATAAAAGGT
1 GTAAATAAGGGATAAAAGGT
209356 ATCAGATAAG
Statistics
Matches: 154, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
82 9 0.06
83 57 0.37
84 82 0.53
85 6 0.04
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.18
Consensus pattern (83 bp):
GTAAATAAGGGATAAAAGGTTGACCAAGGCTGAATCAATAAGTCAACAAAGGTAAAGGAGTTTAC
CAGGGATTGAGCCGACAA
Found at i:209449 original size:44 final size:43
Alignment explanation
Indices: 209396--209494 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
209386 CTAAGGCTAG
** *
209396 ACCATTACGTCAA-ATAAGAATGCAAACCATTTGACTAGGGTGGTA
1 ACCA-TACGTCAATATAAGAA-G-AAAAAATTTGACTAGGGTAGTA
* *
209441 ACCATACGTCAATCTAGGAAGAAAAAATTTGACTAGGGTAGTA
1 ACCATACGTCAATATAAGAAGAAAAAATTTGACTAGGGTAGTA
209484 ACCATACGTCA
1 ACCATACGTCA
209495 TATCTACATA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 30 0.62
44 9 0.19
45 9 0.19
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (43 bp):
ACCATACGTCAATATAAGAAGAAAAAATTTGACTAGGGTAGTA
Found at i:209637 original size:44 final size:44
Alignment explanation
Indices: 209520--209862 Score: 203
Period size: 44 Copynumber: 7.8 Consensus size: 44
209510 CATCTAATTG
** * *
209520 GGGTGGTAACCATACACCAAACT-GAAATGAGAAA-TGTTTGACAA
1 GGGTGGTAACCATACGTCAAA-TAGAAATGA-AAAGAGTTTGACCA
* * * * * *
209564 GAGTGGTAATCACACATCAAA-CGAAAATGAAAAGAGCTTGACCA
1 GGGTGGTAACCATACGTCAAATAG-AAATGAAAAGAGTTTGACCA
* * * *
209608 GGGTGGTAACCATACGTCAAGTAGGAATGAGAAGAGTCTGACCA
1 GGGTGGTAACCATACGTCAAATAGAAATGAAAAGAGTTTGACCA
* * * ** *
209652 AGGTGGTATCCATATGTC-AATCCAACATAAAAAGAGTTTGACCA
1 GGGTGGTAACCATACGTCAAATAGAA-ATGAAAAGAGTTTGACCA
* * * **
209696 GGGTAGTAACCATACATTAAATAGAAATGAGGCAGA-TTTGACCA
1 GGGTGGTAACCATACGTCAAATAGAAATGA-AAAGAGTTTGACCA
* ** * * * *
209740 AGGTGGTAACCATGTGTTAAATCAG-AATGAAAAGAATCTGACTA
1 GGGTGGTAACCATACGTCAAAT-AGAAATGAAAAGAGTTTGACCA
* * ** * *
209784 GGGTGGTAACCATACGTTAGACCGAAATGAGAAGAGTTTGACTA
1 GGGTGGTAACCATACGTCAAATAGAAATGAAAAGAGTTTGACCA
* ** * *
209828 GAGTGGTAACCATATATCAAACATAAATGAAAAGA
1 GGGTGGTAACCATACGTCAAATAGAAATGAAAAGA
209863 AATTTGGTTA
Statistics
Matches: 225, Mismatches: 64, Indels: 20
0.73 0.21 0.06
Matches are distributed among these distances:
43 11 0.05
44 203 0.90
45 11 0.05
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (44 bp):
GGGTGGTAACCATACGTCAAATAGAAATGAAAAGAGTTTGACCA
Found at i:209857 original size:88 final size:86
Alignment explanation
Indices: 209520--209863 Score: 268
Period size: 88 Copynumber: 3.9 Consensus size: 86
209510 CATCTAATTG
** * * *
209520 GGGTGGTAACCATACACCAAACTGAAATGAGAA-ATGTTTGA-CAAGAGTGGTAATCACACATCA
1 GGGTGGTAACCATACATTAAAC-GAAATGAGAAGA-GTTTGACCAAG-GTGGTAACCATATATCA
*
209583 AACGAAAATGAAAAG-AGCTTGACCA
63 AAC-AAAATGAAAAGAATC-TGACCA
* * * * * *
209608 GGGTGGTAACCATACGTCAAGTA-GGAATGAGAAGAGTCTGACCAAGGTGGTATCCATATGTCAA
1 GGGTGGTAACCATACATTAA--ACGAAATGAGAAGAGTTTGACCAAGGTGGTAACCATATATCAA
* * * * *
209672 TCCAACATAAAAAGAGTTTGACCA
64 -ACAAAATGAAAAGAATCTGACCA
* * * * * *
209696 GGGTAGTAACCATACATTAAATAGAAATGAGGCAGA-TTTGACCAAGGTGGTAACCATGTGTTAA
1 GGGTGGTAACCATACATTAAA-CGAAATGA-GAAGAGTTTGACCAAGGTGGTAACCATATATCAA
* *
209760 ATCAGAATGAAAAGAATCTGACTA
64 A-CAAAATGAAAAGAATCTGACCA
* * *
209784 GGGTGGTAACCATACGTTAGACCGAAATGAGAAGAGTTTGA-CTAGAGTGGTAACCATATATCAA
1 GGGTGGTAACCATACATTA-AACGAAATGAGAAGAGTTTGACCAAG-GTGGTAACCATATATCAA
209848 ACATAAATGAAAAGAA
64 ACA-AAATGAAAAGAA
209864 ATTTGGTTAG
Statistics
Matches: 201, Mismatches: 41, Indels: 28
0.74 0.15 0.10
Matches are distributed among these distances:
86 1 0.00
87 9 0.04
88 179 0.89
89 11 0.05
90 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (86 bp):
GGGTGGTAACCATACATTAAACGAAATGAGAAGAGTTTGACCAAGGTGGTAACCATATATCAAAC
AAAATGAAAAGAATCTGACCA
Found at i:211711 original size:9 final size:9
Alignment explanation
Indices: 211697--211736 Score: 53
Period size: 9 Copynumber: 4.1 Consensus size: 9
211687 CCCTTTTGTG
211697 TTATTTTTT
1 TTATTTTTT
211706 TTATTTTTTCTT
1 TTA--TTTT-TT
211718 TTATTTTTT
1 TTATTTTTT
211727 TTATTTTTT
1 TTATTTTTT
211736 T
1 T
211737 AGTTCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 15 0.54
10 4 0.14
11 4 0.14
12 5 0.18
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (9 bp):
TTATTTTTT
Found at i:211714 original size:21 final size:21
Alignment explanation
Indices: 211690--211735 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
211680 ACTTTTCCCC
*
211690 TTTTGTGTTATTTTTTTTATT
1 TTTTCTGTTATTTTTTTTATT
*
211711 TTTTCTTTTATTTTTTTTATT
1 TTTTCTGTTATTTTTTTTATT
211732 TTTT
1 TTTT
211736 TAGTTCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.85
Consensus pattern (21 bp):
TTTTCTGTTATTTTTTTTATT
Found at i:211719 original size:12 final size:11
Alignment explanation
Indices: 211700--211736 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
211690 TTTTGTGTTA
211700 TTTTTTTTATT
1 TTTTTTTTATT
211711 TTTTCTTTTA--
1 TTTT-TTTTATT
211721 TTTTTTTTATT
1 TTTTTTTTATT
211732 TTTTT
1 TTTTT
211737 AGTTCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.22
10 4 0.17
11 9 0.39
12 5 0.22
ACGTcount: A:0.08, C:0.03, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:212407 original size:19 final size:19
Alignment explanation
Indices: 212385--212421 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
212375 CAACTGAATT
*
212385 TTCTTTTTTCTTTTTTTTC
1 TTCTTTTTGCTTTTTTTTC
212404 TTCTTTTTGCTTTTTTTT
1 TTCTTTTTGCTTTTTTTT
212422 TTTTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (19 bp):
TTCTTTTTGCTTTTTTTTC
Found at i:212410 original size:10 final size:9
Alignment explanation
Indices: 212388--212425 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
212378 CTGAATTTTC
212388 TTTTTTCTT
1 TTTTTTCTT
212397 TTTTTTCTT
1 TTTTTTCTT
*
212406 CTTTTTGCTT
1 -TTTTTTCTT
212416 TTTTTT-TT
1 TTTTTTCTT
212424 TT
1 TT
212426 GAAAATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 4 0.15
9 14 0.54
10 8 0.31
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:216798 original size:14 final size:13
Alignment explanation
Indices: 216754--216808 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
216744 TAATATCTGT
216754 AAAATTACAATATAA
1 AAAATTA-AATAT-A
216769 AAAATT-AATA-A
1 AAAATTAAATATA
216780 AAAATTAAATTATA
1 AAAATTAAA-TATA
216794 AAAATTAAAT-TA
1 AAAATTAAATATA
216806 AAA
1 AAA
216809 TTTTATATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 7 0.19
12 7 0.19
13 7 0.19
14 10 0.27
15 6 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTAAATATA
Found at i:216808 original size:25 final size:26
Alignment explanation
Indices: 216753--216810 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
216743 ATAATATCTG
216753 TAAAATTACAATATAAAAAATTAATA
1 TAAAATTACAATATAAAAAATTAATA
*
216779 AAAAATTA-AAT-TATAAAAATTAA-A
1 TAAAATTACAATATA-AAAAATTAATA
216803 TTAAAATT
1 -TAAAATT
216811 TTATATGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 18 0.64
26 7 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAAATTACAATATAAAAAATTAATA
Found at i:220958 original size:156 final size:157
Alignment explanation
Indices: 220673--220967 Score: 416
Period size: 156 Copynumber: 1.9 Consensus size: 157
220663 GGTTAAATAT
* * *
220673 AAAATTACCAAAATACCCTTAGAATCTACCTTCAATGTGAAAGTATTCCGATAACCCTAAAGGAC
1 AAAATTACAAAAATACCCTTAGAATATACCTTCAATATGAAAGTATTCCGATAACCCTAAAGGAC
* * *
220738 TTGAAAATGGTCATAAATAGGATGAACCTATCCTAAATACCCACATTTAGCATAAAAGCATCCCG
66 TTAAAAATGATCATAAATAGGATGAACCTATCCTAAATACACACATTTAGCATAAAAGCATCCCG
*
220803 GTGACAACCTAAGACTCGATTTTGAAA
131 ATGACAACCTAAGACTCGATTTTGAAA
* *
220830 AAAATTACAAAAATACCCTTA-AGGTATACTTTCAATATGAAAGTA-TCTCG-TAACCCTAAAGG
1 AAAATTACAAAAATACCCTTAGA-ATATACCTTCAATATGAAAGTATTC-CGATAACCCTAAAGG
* * * * * *
220892 ACTTAAAAATGATCATCAATGGGATGAACTTATCCTAAATGCACACCTTTGGCATAAAAGCATCC
64 ACTTAAAAATGATCATAAATAGGATGAACCTATCCTAAATACACACATTTAGCATAAAAGCATCC
220957 CGATGACAACC
129 CGATGACAACC
220968 AATTCTAGGA
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
156 81 0.67
157 40 0.33
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (157 bp):
AAAATTACAAAAATACCCTTAGAATATACCTTCAATATGAAAGTATTCCGATAACCCTAAAGGAC
TTAAAAATGATCATAAATAGGATGAACCTATCCTAAATACACACATTTAGCATAAAAGCATCCCG
ATGACAACCTAAGACTCGATTTTGAAA
Found at i:222323 original size:22 final size:22
Alignment explanation
Indices: 222281--222323 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
222271 AAGCTTAAAA
* *
222281 AACATGAAATCACTAATATATC
1 AACATGAAATCACAAAAATATC
222303 AACATG-AATCAACAAAAATAT
1 AACATGAAATC-ACAAAAATAT
222324 GACATGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (22 bp):
AACATGAAATCACAAAAATATC
Found at i:223281 original size:154 final size:153
Alignment explanation
Indices: 223117--223672 Score: 488
Period size: 153 Copynumber: 3.6 Consensus size: 153
223107 GGCAAAAATG
* *
223117 TAAAATTCATAAAAATAAATTAAATTTTCACAAATTGATTTAATATGAATTTAATAAAAATATTT
1 TAAAATTCATAAAAATAAATTAAATTTTCA-AAATTGATTTAATATGAATTAAATAATAATATTT
* * *
223182 GATGCATTTTAAAAATTTTAAA-TTGAGAAAAATAAAA-CTGGAGAAATTTA-TGGAATAGAAAA
65 GAAGAATTTT-AAAATTATAAACTT-AGAAAAATAAAATC-GGAGAAATTTACT-GAATAGAAAA
* * *
223244 CTCCATATCTTGGTGT-CAA-AAAAATTT
126 CTCCATATCTCGGT-TAAAAGAAAAATTC
* * * ** *
223271 TAAAACTCATAAAACA-AACTGAAATTTTCAAAATTGAATTT-ATATGGGTTAAACAATAATATT
1 TAAAATTCATAAAA-ATAAATTAAATTTTCAAAATTG-ATTTAATATGAATTAAATAATAATATT
* * * ***
223334 TGAAGAACTTTGAAAATTAAAAACTTAGGAAAATTCTATCGGAGAAATTTACTGAATAGAAAACT
64 TGAAGAA-TTTTAAAATTATAAACTTAGAAAAATAAAATCGGAGAAATTTACTGAATAGAAAACT
**
223399 CTGTATCTCGGTTAAAAGAAAAATTC
128 CCATATCTCGGTTAAAAGAAAAATTC
* * * *
223425 TAAAATTCAT-AAAATAAATTGAATTTT-TAAACTGATTTAATATGAATTAAATAATAAGATTTG
1 TAAAATTCATAAAAATAAATTAAATTTTCAAAATTGATTTAATATGAATTAAATAATAATATTTG
* *** * * * *
223488 AAGAATTTTGAAATTATAAACTTAGAAAAATCTTACCGAAAAAATTTAC-GAAGTAAAAAACTCC
66 AAGAATTTTAAAATTATAAACTTAGAAAAATAAAATCGGAGAAATTTACTGAA-TAGAAAACTCC
* ***
223552 GTATCTC-AACAACAAGAAAAATTC
130 ATATCTCGGTTAA-AAGAAAAATTC
* * * * * *
223576 TAAAACTCAT-AAAATAAATTGATTTTGTCTAAACTAATTTAATATGAATTAAATAATAATATTT
1 TAAAATTCATAAAAATAAATTAAATTT-TCAAAATTGATTTAATATGAATTAAATAATAATATTT
* * *
223640 AAAAAATTTTAAAAGCTATAAACTTAGAAAAAT
65 GAAGAATTTTAAAA-TTATAAACTTAGAAAAAT
223673 CTTACAAGAG
Statistics
Matches: 333, Mismatches: 54, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
150 5 0.02
151 90 0.27
152 33 0.10
153 135 0.41
154 69 0.21
155 1 0.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.33
Consensus pattern (153 bp):
TAAAATTCATAAAAATAAATTAAATTTTCAAAATTGATTTAATATGAATTAAATAATAATATTTG
AAGAATTTTAAAATTATAAACTTAGAAAAATAAAATCGGAGAAATTTACTGAATAGAAAACTCCA
TATCTCGGTTAAAAGAAAAATTC
Found at i:223727 original size:154 final size:151
Alignment explanation
Indices: 223263--223709 Score: 447
Period size: 151 Copynumber: 2.9 Consensus size: 151
223253 TTGGTGTCAA
* * * * * ** *
223263 AAAAATTTTAAAACTCATAAAACAAACTGAAATTTTCAAAATTGAATTT-ATATGGGTTAAACAA
1 AAAAATTCTAAAACTCATAAAATAAATTG-AATTTT-TAAACT-AATTTAATATGAATTAAATAA
* * * * * * * * * *
223327 TAATATTTGAAGAACTTTGAAAATTAAAAACTTAGGAAAAT-TCTATCGGAGAAATTTACTGAA-
63 TAAGATTT-AAAAAATTTTAAAACTATAAACTTAGAAAAATCT-TACCGAAAAAATTTAC-GAAG
* * ***
223390 TAGAAAACTCTGTATCTCGGTTAA-AAG
125 TAAAAAACTCCGTATCTC-AACAACAAG
* *
223417 AAAAATTCTAAAATTCATAAAATAAATTGAATTTTTAAACTGATTTAATATGAATTAAATAATAA
1 AAAAATTCTAAAACTCATAAAATAAATTGAATTTTTAAACTAATTTAATATGAATTAAATAATAA
* * * *
223482 GATTTGAAGAATTTTGAAATTATAAACTTAGAAAAATCTTACCGAAAAAATTTACGAAGTAAAAA
66 GATTTAAAAAATTTTAAAACTATAAACTTAGAAAAATCTTACCGAAAAAATTTACGAAGTAAAAA
223547 ACTCCGTATCTCAACAACAAG
131 ACTCCGTATCTCAACAACAAG
*
223568 AAAAATTCTAAAACTCATAAAATAAATTGATTTTGTCTAAACTAATTTAATATGAATTAAATAAT
1 AAAAATTCTAAAACTCATAAAATAAATTGAATTT-T-TAAACTAATTTAATATGAATTAAATAAT
* *
223633 AATATTTAAAAAATTTTAAAAGCTATAAACTTAGAAAAATCTTA-C-AAGAGAAATTTACGGAGT
64 AAGATTTAAAAAATTTTAAAA-CTATAAACTTAGAAAAATCTTACCGAA-A-AAATTTACGAAGT
*
223696 AAAAAACTCTGTAT
126 AAAAAACTCCGTAT
223710 TTTGAAAATA
Statistics
Matches: 247, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
150 5 0.02
151 92 0.37
152 27 0.11
153 52 0.21
154 71 0.29
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (151 bp):
AAAAATTCTAAAACTCATAAAATAAATTGAATTTTTAAACTAATTTAATATGAATTAAATAATAA
GATTTAAAAAATTTTAAAACTATAAACTTAGAAAAATCTTACCGAAAAAATTTACGAAGTAAAAA
ACTCCGTATCTCAACAACAAG
Found at i:231380 original size:43 final size:43
Alignment explanation
Indices: 231296--231383 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
231286 TTAAAGATGA
* * * * *
231296 TAAAGGTGTCAATATGCTAATTCAAGGCTAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACACTGGACT
* *
231339 TAAAGGTGCCAGTATGCTGATTCAAGGCCAGCAACACTGGACT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACACTGGACT
231382 TA
1 TA
231384 GAAAGAGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACACTGGACT
Found at i:231831 original size:32 final size:32
Alignment explanation
Indices: 231395--231840 Score: 423
Period size: 32 Copynumber: 13.9 Consensus size: 32
231385 AAAGAGATAG
* * *
231395 CACCAACTTGTGTGGGTTTTAGAA-AAAGTTGC
1 CACCAGCTTGTGTGGGCTTT-GAAGAAGGTTGC
* *
231427 CACCAGCTTGTGTGGGCTTTAAAGAAAGTTGC
1 CACCAGCTTGTGTGGGCTTTGAAGAAGGTTGC
*
231459 CACCAGCTTGTGTGGGCTTT-AAAAAGGGTTGC
1 CACCAGCTTGTGTGGGCTTTGAAGAA-GGTTGC
* *
231491 CATC-GACTTGTGTGGGCTTTGACA-AATGTTGC
1 CACCAG-CTTGTGTGGGCTTTGA-AGAAGGTTGC
* * * *
231523 CACTAGCTTGTGTGGACTTTGGAA-ATGGTCGC
1 CACCAGCTTGTGTGGGCTTT-GAAGAAGGTTGC
* * * *
231555 CACCAACTTATGTGGGCTTTAGAA-AGGGTCGC
1 CACCAGCTTGTGTGGGCTTT-GAAGAAGGTTGC
* * *
231587 CACCAACTTGTGTGGGCTTTAGAA-AGGGTCGC
1 CACCAGCTTGTGTGGGCTTT-GAAGAAGGTTGC
* *
231619 CACCAACTTGTGTGGGCTATGAAGAAGGTTGC
1 CACCAGCTTGTGTGGGCTTTGAAGAAGGTTGC
231651 CACCTA-CTTGTGTGGGCTTTG--GTAATGGTTGC
1 CACC-AGCTTGTGTGGGCTTTGAAG-AA-GGTTGC
**
231683 CACC-GACTTGTGTGGGCTTTAGAA-AAGGTCAC
1 CACCAG-CTTGTGTGGGCTTT-GAAGAAGGTTGC
* *
231715 CACCAACTTGTGT-GGCTTTGAAGAAAGTTGC
1 CACCAGCTTGTGTGGGCTTTGAAGAAGGTTGC
231746 CACCAGCTTGTGTGGGCTTTGAAGAAAGGTTGC
1 CACCAGCTTGTGTGGGCTTTGAAG-AAGGTTGC
* * * *
231779 TACCAACTTGTGTAGACTTTGAAGAAGGTTGC
1 CACCAGCTTGTGTGGGCTTTGAAGAAGGTTGC
231811 CACCAGCTTGTGTGGGCTTTGAAGAAGGTT
1 CACCAGCTTGTGTGGGCTTTGAAGAAGGTT
231841 TCTCCACTGG
Statistics
Matches: 354, Mismatches: 40, Indels: 40
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.01
31 35 0.10
32 277 0.78
33 37 0.10
34 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (32 bp):
CACCAGCTTGTGTGGGCTTTGAAGAAGGTTGC
Done.