Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008459.1 Hibiscus syriacus cultivar Beakdansim tig00111272_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 632685
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:182930 original size:71 final size:72
Alignment explanation
Indices: 182846--182980 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 72
182836 TGAGAATTTT
* * * * *
182846 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCT-TTCGAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACA
182910 GCTTTCTA
65 GCTTTCTA
*
182918 AAAACAAA-TTTTGTCTCGTTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
182981 TTTTTCCTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
71 46 0.82
72 10 0.18
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
CTTTCTA
Found at i:183105 original size:102 final size:103
Alignment explanation
Indices: 182947--183140 Score: 275
Period size: 102 Copynumber: 1.9 Consensus size: 103
182937 TTGAGACAAA
* * *
182947 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTG
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA-CTTTCCGTTGAGATACAAATTTCGAATTTG
183012 ATTCAC-TTAAAACAAAATTAATCTCACCTTAGATTGTGT
65 ATTCACATT-AAACAAAATTAATCTCACCTTAGATTGTGT
* * * *
183051 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGAC-CTTTCCGTTGAGATCCAAATTTCGAATTTGT
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACACTTTCCGTTGAGATACAAATTTCGAATTTGA
* *
183115 TTCACATTAAACAAAGTTGATCTCAC
66 TTCACATTAAACAAAATTAATCTCAC
183141 TTGAGATCGT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
102 47 0.59
103 2 0.03
104 31 0.39
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (103 bp):
TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACACTTTCCGTTGAGATACAAATTTCGAATTTGA
TTCACATTAAACAAAATTAATCTCACCTTAGATTGTGT
Found at i:183506 original size:29 final size:29
Alignment explanation
Indices: 183472--183555 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
183462 CTCTTGAGAT
*
183472 AAATCTTTGAGTCTATTCCTTTTGAATA-A
1 AAATCTTTGAGTCTATTTCTTTTGAA-ACA
*
183501 AAATCTTTGAGT-TGTTTCTTTTGAAACA
1 AAATCTTTGAGTCTATTTCTTTTGAAACA
183529 AATATCTTTGAGTCTATTTC-TTTGAAA
1 AA-ATCTTTGAGTCTATTTCTTTTGAAA
183556 AATTTATCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
27 1 0.02
28 14 0.29
29 29 0.59
30 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (29 bp):
AAATCTTTGAGTCTATTTCTTTTGAAACA
Found at i:183563 original size:29 final size:28
Alignment explanation
Indices: 183474--183599 Score: 105
Period size: 29 Copynumber: 4.4 Consensus size: 28
183464 CTTGAGATAA
* *
183474 ATCTTTGAGTCTATTCCTTTTGAATAAAA
1 ATCTTTGAGTCTATTTCTTTTGAA-AAAT
*
183503 ATCTTTGAGT-TGTTTCTTTTGAAACAAAT
1 ATCTTTGAGTCTATTTCTTTTG-AA-AAAT
183532 ATCTTTGAGTCTATTTC-TTTGAAAAATTT
1 ATCTTTGAGTCTATTTCTTTTGAAAAA--T
** * *
183561 ATCTCCTAAAGACAATTTCTTTTGAAAAA-
1 ATCT--TTGAGTCTATTTCTTTTGAAAAAT
183590 ATCTTTGAGT
1 ATCTTTGAGT
183600 TGGTTTCCTT
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
27 6 0.08
28 11 0.14
29 38 0.49
30 5 0.06
31 9 0.12
32 9 0.12
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (28 bp):
ATCTTTGAGTCTATTTCTTTTGAAAAAT
Found at i:183787 original size:15 final size:15
Alignment explanation
Indices: 183764--183807 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
183754 TTTTGAGTCA
*
183764 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
183779 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
183794 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
183808 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:184276 original size:40 final size:40
Alignment explanation
Indices: 184221--184709 Score: 239
Period size: 40 Copynumber: 11.7 Consensus size: 40
184211 CCAGTCGTCC
* * * *
184221 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAGACCAGATCTCT
* * * * *
184261 TCATCACGTATGAACCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * * *
184304 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGA-ATCT
1 TCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
*
184349 TCATCACGTATGAGCCGT-TCATTCCC-CGACCAGATCTC-
1 TCATCACGTATGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * * *
184387 T--TCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * * *
184428 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
*
184474 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* *
184514 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * * *
184556 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
*
184602 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * * *
184642 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-AACTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATCTCT
* *
184684 TCATCACGTATGAGCAGTGTCGTCCC
1 TCATCACGTATGAGCCGTGTCATCCC
184710 CAACAACCAA
Statistics
Matches: 344, Mismatches: 57, Indels: 94
0.69 0.12 0.19
Matches are distributed among these distances:
36 17 0.05
37 4 0.01
38 9 0.03
39 6 0.02
40 93 0.27
41 4 0.01
42 53 0.15
43 57 0.17
44 8 0.02
45 20 0.06
46 67 0.19
47 6 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCTAGACCAGATCTCT
Found at i:184481 original size:46 final size:45
Alignment explanation
Indices: 184251--184703 Score: 213
Period size: 46 Copynumber: 10.7 Consensus size: 45
184241 CATCCCCAGA
* * * * **
184251 CCAGATCTCTTCATCACGTATGAACCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * * *
184294 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC-TTAGATGG
* *
184340 CCAGAA-TCTTCATCACGTATGAGCCGT-TCATTC-CC--CGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTA-TCACCTTAGATGG
* * * **
184378 CCAG-A-TC-TCTTCACGTATGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * * *
184418 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC-TTAGATGG
* *
184464 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC--CGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTA-TCACCTTAGATGG
* * **
184504 CCAGATCTCTTCATCACGTATGAGCCGTG---TCACCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * * *
184546 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC-TTAGATGG
* *
184592 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC--CGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTA-TCACCTTAGATGG
* * * * **
184632 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
*
184675 CCA-AACTCTTCATCACGTATGAGCAGTGT
1 CCAGAACTCTTCATCACGTATGAGCCGTGT
184704 CGTCCCCAAC
Statistics
Matches: 320, Mismatches: 50, Indels: 81
0.71 0.11 0.18
Matches are distributed among these distances:
35 2 0.01
36 19 0.06
37 10 0.03
38 6 0.02
39 2 0.01
40 64 0.20
41 3 0.01
42 49 0.15
43 51 0.16
44 4 0.01
45 31 0.10
46 73 0.23
47 6 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (45 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
Found at i:184693 original size:128 final size:129
Alignment explanation
Indices: 184221--184677 Score: 802
Period size: 128 Copynumber: 3.6 Consensus size: 129
184211 CCAGTCGTCC
* * * *
184221 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAACCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
184285 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAA-TCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
184349 TCATCACGTATGAGCCGT-TCATTCCCCGACCAGATCTC-T--TCACGTATGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
184410 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
184474 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
184538 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
184602 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
184667 ATAGATAACCA
66 ATAGATAACCA
184678 AACTCTTCAT
Statistics
Matches: 315, Mismatches: 7, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
124 81 0.26
125 21 0.07
126 21 0.07
127 15 0.05
128 146 0.46
129 31 0.10
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:184872 original size:14 final size:14
Alignment explanation
Indices: 184851--184903 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
184841 TTTGTCCGGG
184851 TTTT-TTATCGTTA
1 TTTTATTATCGTTA
**
184864 TTTTATTATTATTATA
1 TTTTATTA-TCGT-TA
184880 TTATTATTATCGTTA
1 TT-TTATTATCGTTA
184895 TTTTATTAT
1 TTTTATTAT
184904 TAATATTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 4 0.12
14 10 0.31
15 6 0.19
16 6 0.19
17 6 0.19
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (14 bp):
TTTTATTATCGTTA
Found at i:184874 original size:3 final size:3
Alignment explanation
Indices: 184861--184911 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
184851 TTTTTTATCG
**
184861 TTA TT- TTA TTA TTA TTA -TA TTA TTA TTA TCG TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
184906 ATA TTA
1 TTA TTA
184912 CATTTTTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:184886 original size:17 final size:17
Alignment explanation
Indices: 184862--184911 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
184852 TTTTTATCGT
184862 TATT-TTATTATTATTA
1 TATTATTATTATTATTA
**
184878 TATTATTATTATCGTTA
1 TATTATTATTATTATTA
* *
184895 TTTTATTATTAATATTA
1 TATTATTATTATTATTA
184912 CATTTTTACA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:199940 original size:120 final size:119
Alignment explanation
Indices: 199491--199963 Score: 504
Period size: 120 Copynumber: 3.9 Consensus size: 119
199481 TGATCCCTGA
* * * * * * * *
199491 AAACTACCTCCTGAACTGGTTCAGTAGCAGTTATGCTGATATCTTCAAATTGCATTAAATTCTGA
1 AAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTGA
* *
199556 TCCTCTAGTGC-AGCACTTGTGTCCTCTTTAACTTCAATTTTGTCACTTTCCCAG
66 TCCTCTTGAGCAAG-ACTTGTGTCCTCTTTAACTTCAATTTTGTCACTTTCCCAG
** * * *
199610 AAAACTTGCTCCTGAGCTGGTTCAGCAGCAGTTATGTCGGTATCTTCTAAGTGTATTGAACTGTG
1 -AAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTG
* * * ** *
199675 GT-CTCCTTGAGCAAGAATCGTAACCTCTTTAACTTC-ATCTTTTTCACTTTCCCAG
65 ATCCT-CTTGAGCAAGACTTGTGTCCTCTTTAACTTCAAT-TTTGTCACTTTCCCAG
* * * * * * *
199730 TAAACTACCTCCTGAGCTGGTTCAGCTGCAATTGTGTTGGTATCTTCTAATTGCAGTGAAATCG-
1 -AAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACT-GT
* * * * *
199794 GATCCTCTTCAACAAGACGTGAGTCCTCCTTAACTTCAATTTTGTCACTTTCCCAG
64 GATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTTTCCCAG
199850 ACAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTG
1 A-AACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTG
* * * * * *
199915 ATCCTCTGGAGCATGATTTTTGTCCTCTTTAACTTCCATTTTGTAACTT
65 ATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
199964 GTATAGTTAA
Statistics
Matches: 284, Mismatches: 61, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
119 6 0.02
120 271 0.95
121 7 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (119 bp):
AAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGAACTGTGA
TCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTTTCCCAG
Found at i:206013 original size:14 final size:13
Alignment explanation
Indices: 205991--206029 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
205981 AATAGGAAGT
*
205991 AATCCCTGCAAATA
1 AATCTCTGCAAA-A
206005 AATCTCTGCATAAA
1 AATCTCTGCA-AAA
206019 AATCTCTGCAA
1 AATCTCTGCAA
206030 TATAGACAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (13 bp):
AATCTCTGCAAAA
Found at i:208438 original size:173 final size:169
Alignment explanation
Indices: 208112--208451 Score: 628
Period size: 173 Copynumber: 2.0 Consensus size: 169
208102 AAAACATAAA
208112 CTCACCGCCAAAAGTTCATCGTTAGCTCGGAAAGTAACCTTGAGTTTGTTCTAGTCTTTCGCGGA
1 CTCACCGCCAAAAGTTCATCGTTAGCTCGGAAAGTAACCTTGAGTTTGTTCTAGTCTTTCGCGGA
208177 AGAGATGATGGTGACTGGGTTCCTCTAACATGATCCCACTGCCTTTATTATTTCAACTATTTTTC
66 AGAGATGATGGTGACTGGGTTCCTCTAACATGATCCCACTGCCTTTATTATTTCAACTATTTTTC
208242 GTTCTGCTTGAATCGAGATAAAGCAGCCACAAAGGTGATAC
131 GTTCTGCTTGAATCGAGATAAAGCAG-C-CAAAGGTGATAC
208283 CTCACCCGCCAAAAGTTCATCGTTAGCTCGGAAAGTAACCTTGAGTTTGTTCTAGGTCTTTCGCG
1 CTCA-CCGCCAAAAGTTCATCGTTAGCTCGGAAAGTAACCTTGAGTTTGTTCTA-GTCTTTCGCG
208348 GAAGAGATGAT-GTGACTGGGTTCCTCTAACATGATCCCCACTGCCTTTATTATTTCAACTATTT
64 GAAGAGATGATGGTGACTGGGTTCCTCTAACATGAT-CCCACTGCCTTTATTATTTCAACTATTT
208412 TTCGTTCTGCTTGAATCGAGATAAAGCAGCCAAAGGTGAT
128 TTCGTTCTGCTTGAATCGAGATAAAGCAGCCAAAGGTGAT
208452 GTTCCCATAA
Statistics
Matches: 166, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
171 14 0.08
172 74 0.45
173 78 0.47
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (169 bp):
CTCACCGCCAAAAGTTCATCGTTAGCTCGGAAAGTAACCTTGAGTTTGTTCTAGTCTTTCGCGGA
AGAGATGATGGTGACTGGGTTCCTCTAACATGATCCCACTGCCTTTATTATTTCAACTATTTTTC
GTTCTGCTTGAATCGAGATAAAGCAGCCAAAGGTGATAC
Found at i:210015 original size:35 final size:35
Alignment explanation
Indices: 209976--210111 Score: 175
Period size: 35 Copynumber: 3.9 Consensus size: 35
209966 CGAATAAGAA
209976 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
* * *
210011 GAACGGAAGGAAGCATCGACACTTTCGACTCAAGAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAG-T
* *
210047 GAACGAAATGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
** *
210082 GAACGGGAGGAAGCAT-AAGCACTTTCGATT
1 GAACGAAAGGAAGCATCGA-CACTTTCGATT
210112 TAATTGTTCA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 56 0.65
36 30 0.35
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:210105 original size:71 final size:71
Alignment explanation
Indices: 209971--210109 Score: 226
Period size: 71 Copynumber: 2.0 Consensus size: 71
209961 GAAGGCGAAT
*
209971 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAGCATCGACACTTT
1 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAGCATAGACACTTT
210036 CGACTC
66 CGACTC
* * *
210042 AAGAAGAACGAAATGAAGCATCGGCACTTTCGATTCAAGTGAACGGGAGGAAGCATA-AGCACTT
1 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAGCATAGA-CACTT
210106 TCGA
65 TCGA
210110 TTTAATTGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 1 0.02
71 62 0.98
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAGCATAGACACTTT
CGACTC
Found at i:211500 original size:2 final size:2
Alignment explanation
Indices: 211493--211544 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
211483 AATATTGATT
*
211493 TA TA TA TA T- TA TA TA TA TA TA TA TA TT TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
211533 TA TA TA TA TA TA
1 TA TA TA TA TA TA
211545 ATAATGAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:211514 original size:27 final size:27
Alignment explanation
Indices: 211490--211544 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
211480 TTAAATATTG
*
211490 ATTTATATATATTATATATATATATAT
1 ATTTATATATAATATATATATATATAT
211517 ATTTATATATAATATATATATATATAT
1 ATTTATATATAATATATATATATATAT
211544 A
1 A
211545 ATAATGAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTATATATAATATATATATATATAT
Found at i:211523 original size:25 final size:25
Alignment explanation
Indices: 211490--211543 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
211480 TTAAATATTG
211490 ATTTATATATATTATATATATATATAT
1 ATTTATATATA--ATATATATATATAT
211517 ATTTATATATAATATATATATATAT
1 ATTTATATATAATATATATATATAT
211542 AT
1 AT
211544 AATAATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 16 0.59
27 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTATATATAATATATATATATAT
Found at i:211545 original size:17 final size:17
Alignment explanation
Indices: 211493--211547 Score: 83
Period size: 17 Copynumber: 3.1 Consensus size: 17
211483 AATATTGATT
211493 TATATATATTATATATATA
1 TATATATA-TATATATA-A
*
211512 TATATATTTATATATAA
1 TATATATATATATATAA
211529 TATATATATATATATAA
1 TATATATATATATATAA
211546 TA
1 TA
211548 ATGAATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 19 0.56
18 8 0.24
19 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:213222 original size:20 final size:19
Alignment explanation
Indices: 213209--213269 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 19
213199 TATTTTTAAT
213209 TATATTTTTTTATTTATTA
1 TATATTTTTTTATTTATTA
**
213228 CTATATTCCTTTATTTATT-
1 -TATATTTTTTTATTTATTA
*
213247 TATATTATTTT-TTTATTA
1 TATATTTTTTTATTTATTA
213265 TATAT
1 TATAT
213270 CTTATATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 6 0.17
18 14 0.39
20 16 0.44
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
TATATTTTTTTATTTATTA
Found at i:213256 original size:13 final size:13
Alignment explanation
Indices: 213238--213305 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
213228 CTATATTCCT
213238 TTATTTATTTATA
1 TTATTTATTTATA
213251 TTATTT-TTT-TA
1 TTATTTATTTATA
*
213262 TTATATATCTTATA
1 TTATTTAT-TTATA
*
213276 TCATTATATATATATA
1 TTATT-TAT-T-TATA
* *
213292 TTATCTATATATA
1 TTATTTATTTATA
213305 T
1 T
213306 ATATATATAG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
11 7 0.16
12 4 0.09
13 13 0.30
14 5 0.12
15 7 0.16
16 7 0.16
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTTATTTATA
Found at i:213268 original size:2 final size:2
Alignment explanation
Indices: 213263--213314 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
213253 ATTTTTTTAT
* *
213263 TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA T- TA TC TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
213303 TA TA TA TA TA TA
1 TA TA TA TA TA TA
213315 GATGTATAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.88
3 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:213296 original size:19 final size:20
Alignment explanation
Indices: 213260--213313 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
213250 ATTATTTTTT
*
213260 TATTATATATCT-TA-TATC
1 TATTATATATATATATTATC
213278 -ATTATATATATATATTATC
1 TATTATATATATATATTATC
213297 TATATATATATATATAT
1 TAT-TATATATATATAT
213314 AGATGTATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 10 0.32
18 2 0.06
19 4 0.13
20 2 0.06
21 13 0.42
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATATATATATATTATC
Found at i:213300 original size:17 final size:16
Alignment explanation
Indices: 213259--213309 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
213249 TATTATTTTT
*
213259 TTATTATATATCTTATA
1 TTATTATATAT-ATATA
*
213276 TCATTATATATATATA
1 TTATTATATATATATA
213292 TTATCTATATATATATA
1 TTAT-TATATATATATA
213309 T
1 T
213310 ATATAGATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTATATATATATA
Found at i:213379 original size:18 final size:18
Alignment explanation
Indices: 213356--213421 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
213346 ACTATGTATA
213356 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* *
213374 TATATTTTATACGTTTATAT
1 TATATTTT-TTC-TTAATAT
*
213394 ATATATATTTTCTTAATAT
1 -TATATTTTTTCTTAATAT
*
213413 TCTATTTTT
1 TATATTTTT
213422 GTTTTTATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 15 0.39
19 8 0.21
20 8 0.21
21 7 0.18
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:213463 original size:44 final size:45
Alignment explanation
Indices: 213387--213471 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 45
213377 ATTTTATACG
*
213387 TTTATATATATATATTTTCTTAATATTCTATTTTTGTTTTTATTTA
1 TTTATATATATATATATTCTTAATATTCTATTTTT-TTTTTATTTA
*
213433 TTTATATATAT-TATATT-TTAACT-TTTTATTTTTTTTTTA
1 TTTATATATATATATATTCTTAA-TATTCTATTTTTTTTTTA
213472 ATTTTTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
43 6 0.17
44 13 0.36
45 6 0.17
46 11 0.31
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (45 bp):
TTTATATATATATATATTCTTAATATTCTATTTTTTTTTTATTTA
Found at i:213623 original size:18 final size:18
Alignment explanation
Indices: 213578--213625 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
213568 TATGTACACA
*
213578 TTATTTTTATT-CCTTTT
1 TTATTTTTTTTACCTTTT
* * *
213595 TAAATTCTTTTACCTTTT
1 TTATTTTTTTTACCTTTT
213613 TTATTTTTTTTAC
1 TTATTTTTTTTAC
213626 TCCATTAATA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTTTTACCTTTT
Found at i:214102 original size:13 final size:13
Alignment explanation
Indices: 214084--214115 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
214074 TCAAGTCGAA
214084 GCCCAATTCTGGG
1 GCCCAATTCTGGG
214097 GCCCAATTCTGGG
1 GCCCAATTCTGGG
214110 GCCCAA
1 GCCCAA
214116 CCGAAAGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.34, G:0.28, T:0.19
Consensus pattern (13 bp):
GCCCAATTCTGGG
Found at i:223835 original size:16 final size:16
Alignment explanation
Indices: 223816--223851 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
223806 TTGAAAAAAG
223816 AAAAAAAAAAGAACAA
1 AAAAAAAAAAGAACAA
* *
223832 AAAAGAGAAAGAACAA
1 AAAAAAAAAAGAACAA
223848 AAAA
1 AAAA
223852 TAAAGTGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAACAA
Found at i:225062 original size:110 final size:108
Alignment explanation
Indices: 224855--225114 Score: 343
Period size: 110 Copynumber: 2.4 Consensus size: 108
224845 GACGAAGGGG
* *
224855 TTTCCCAG-T-TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTAGACTCAAGACAACACAA
1 TTTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATGAGACTCAAGACAACACAA
*
224918 GCTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
66 GCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAA
** * *
224961 TTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATCGA-ACTCGAGACAACA
1 TTTCCCAG-TTC-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT-GAGACTCAAGACAACA
* * * *
225025 CAAGCTCAACTTCACAGCGAATGGGCGGCTGGCTGTCAACAAACAA
63 CAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAA
225071 TTTCCCAGTTC--CAGAGCCAATTTCAACTTCAC-GACGAAGGATAT
1 TTTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT
225115 TGGACTTGGA
Statistics
Matches: 134, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
105 1 0.01
106 36 0.27
108 1 0.01
109 3 0.02
110 92 0.69
111 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (108 bp):
TTTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATGAGACTCAAGACAACACAA
GCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAA
Found at i:226439 original size:16 final size:16
Alignment explanation
Indices: 226418--226452 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
226408 TTGTCCCCTA
226418 TATATATATTTTTAAT
1 TATATATATTTTTAAT
*
226434 TATATATATTTTTATT
1 TATATATATTTTTAAT
226450 TAT
1 TAT
226453 TTACTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATATATTTTTAAT
Found at i:226495 original size:13 final size:14
Alignment explanation
Indices: 226470--226508 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
226460 ATTCATTTTT
226470 TTATTTATATTATA
1 TTATTTATATTATA
226484 TTATTT-TATTATA
1 TTATTTATATTATA
226497 TATATCTTATAT
1 T-TAT-TTATAT
226509 CATTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 2 0.09
16 3 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:226500 original size:2 final size:2
Alignment explanation
Indices: 226493--226539 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
226483 ATTATTTTAT
*
226493 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
226534 TA TA TA
1 TA TA TA
226540 GATGTATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:226506 original size:19 final size:19
Alignment explanation
Indices: 226416--226538 Score: 89
Period size: 19 Copynumber: 6.6 Consensus size: 19
226406 TTTTGTCCCC
*
226416 TATATATATATT-TTTAAT
1 TATATATATATTATTTTAT
*
226434 TATATATAT-TTTTATTTAT
1 TATATATATATTAT-TTTAT
*
226453 T-TACTATATTCATTTTTTTAT
1 TATA-TATA-T-ATTATTTTAT
226474 T-TATATTATATTATTTTAT
1 TATATA-TATATTATTTTAT
* * *
226493 TATATATATCTTATATCAT
1 TATATATATATTATTTTAT
*
226512 TATATATATA-TA-TATA-
1 TATATATATATTATTTTAT
226528 TATATATATAT
1 TATATATATAT
226539 AGATGTATTA
Statistics
Matches: 87, Mismatches: 9, Indels: 19
0.76 0.08 0.17
Matches are distributed among these distances:
16 10 0.11
17 3 0.03
18 14 0.16
19 38 0.44
20 8 0.09
21 10 0.11
22 4 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATATATATTATTTTAT
Found at i:226648 original size:37 final size:37
Alignment explanation
Indices: 226571--226702 Score: 132
Period size: 37 Copynumber: 3.6 Consensus size: 37
226561 TTACTATGTA
***
226571 TATATATATTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTTCTTAATATT-TATTTTATTTTTTTT
226609 TATATATATTTTT-TTAATATTCTATTTT-TTTTTTATT
1 TATATATATTTTTCTTAATATT-TATTTTATTTTTT-TT
*
226646 TATATATATTATATT-TTAA-ACTTTATTTTATTTTTTTC
1 TATATATATT-T-TTCTTAATA-TTTATTTTATTTTTTTT
226684 TAT-TAT-TTTTTCTTAATAT
1 TATATATATTTTTCTTAATAT
226703 CATGTATATC
Statistics
Matches: 82, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
34 2 0.02
35 6 0.07
36 6 0.07
37 29 0.35
38 25 0.30
39 14 0.17
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (37 bp):
TATATATATTTTTCTTAATATTTATTTTATTTTTTTT
Found at i:226831 original size:18 final size:17
Alignment explanation
Indices: 226804--226837 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
226794 TTTTTATTCA
226804 TTTTTAATTTCTTTTACC
1 TTTTTAATTT-TTTTACC
*
226822 TTTTTTATTTTTTTAC
1 TTTTTAATTTTTTTAC
226838 TCCATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTAATTTTTTTACC
Found at i:226835 original size:17 final size:17
Alignment explanation
Indices: 226791--226837 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
226781 TATGTACACA
226791 TTATTTTTATT-CATTTT
1 TTATTTTT-TTACATTTT
* *
226808 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACATTTT
226826 TTATTTTTTTAC
1 TTATTTTTTTAC
226838 TCCATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACATTTT
Found at i:226912 original size:19 final size:19
Alignment explanation
Indices: 226890--226967 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 19
226880 ATTTTATTCA
226890 TTTTGTTTATTTTTATTTT
1 TTTTGTTTATTTTTATTTT
** *
226909 TTTT-TATTATTTTTTACGTG
1 TTTTGT-TTA-TTTTTATTTT
226929 TTTTG-TTATTTTCTATTTT
1 TTTTGTTTATTTT-TATTTT
226948 TTCTTGTTTTATTTATTATT
1 TT-TTG-TTTATTT-TTATT
226968 CTCACGTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
18 5 0.11
19 15 0.33
20 14 0.31
22 10 0.22
23 1 0.02
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTGTTTATTTTTATTTT
Found at i:226918 original size:13 final size:13
Alignment explanation
Indices: 226881--226923 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
226871 TTTTTTAACA
226881 TTTTATTCATTTTGT
1 TTTTATT-ATTTT-T
*
226896 TTATTTTTATTTTT
1 TT-TTATTATTTTT
226910 TTTTATTATTTTT
1 TTTTATTATTTTT
226923 T
1 T
226924 ACGTGTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 7 0.28
16 4 0.16
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTATTATTTTT
Found at i:226963 original size:26 final size:27
Alignment explanation
Indices: 226916--226969 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
226906 TTTTTTTTAT
226916 TATTTTTTACGTGTTTTGTTATT-TTC
1 TATTTTTTACGTGTTTTGTTATTATTC
* *
226942 TATTTTTT-CTTGTTTTATTTATTATTC
1 TATTTTTTACGTGTTTT-GTTATTATTC
226969 T
1 T
226970 CACGTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 13 0.54
27 4 0.17
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.72
Consensus pattern (27 bp):
TATTTTTTACGTGTTTTGTTATTATTC
Found at i:230217 original size:16 final size:16
Alignment explanation
Indices: 230196--230239 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
230186 TTTAAAATAA
230196 TAAAAAAAATAAAAAT
1 TAAAAAAAATAAAAAT
230212 TAAAAATAAAT-AAAAT
1 TAAAAA-AAATAAAAAT
*
230228 TCAATAAAAATA
1 T-AAAAAAAATA
230240 TAATATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAAAAATAAAAAT
Found at i:230222 original size:11 final size:10
Alignment explanation
Indices: 230189--230254 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
230179 TTAATTTTTT
230189 AAAAT-AATA
1 AAAATAAATA
230198 AAAA-AAATA
1 AAAATAAATA
230207 AAAAT---TA
1 AAAATAAATA
230214 AAAATAAATA
1 AAAATAAATA
* *
230224 AAATTCAATA
1 AAAATAAATA
230234 AAAATATAATA
1 AAAATA-AATA
230245 TAAAACTAAA
1 -AAAA-TAAA
230255 AAATATCACC
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 7 0.16
9 12 0.27
10 14 0.31
11 4 0.09
12 6 0.13
13 2 0.04
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAATAAATA
Found at i:231420 original size:29 final size:29
Alignment explanation
Indices: 231376--231438 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
231366 TAATTATTAT
231376 TTTTTAACAACAATTAATAATGTT-TATTTA
1 TTTTTAACAACAATTAA-AAT-TTATATTTA
*
231406 TTTTTAATAA-AATTAAAATTTAATATTTA
1 TTTTTAACAACAATTAAAATTT-ATATTTA
231435 TTTT
1 TTTT
231439 ATATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.07
28 3 0.10
29 16 0.53
30 9 0.30
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTTTAACAACAATTAAAATTTATATTTA
Found at i:231532 original size:20 final size:20
Alignment explanation
Indices: 231509--231558 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
231499 TTTACATTAT
231509 ATTTTTATTGAATTTTATT-C
1 ATTTTTATT-AATTTTATTGC
*
231529 ATTTTTAATTCATTTTATTGC
1 ATTTTT-ATTAATTTTATTGC
*
231550 CTTTTTATT
1 ATTTTTATT
231559 TGTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (20 bp):
ATTTTTATTAATTTTATTGC
Found at i:241842 original size:14 final size:16
Alignment explanation
Indices: 241820--241851 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
241810 TAAATTCAAG
241820 TTTAGGAATT-ATCTT
1 TTTAGGAATTCATCTT
241835 TTTA-GAATTCATCTT
1 TTTAGGAATTCATCTT
241850 TT
1 TT
241852 GTATGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.56
Consensus pattern (16 bp):
TTTAGGAATTCATCTT
Found at i:244092 original size:31 final size:32
Alignment explanation
Indices: 244057--244133 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
244047 TAAAAAAACA
*
244057 TAAGATATGATCATTTTC-TTTTTCATTTAAT
1 TAAGATATGATCACTTTCTTTTTTCATTTAAT
*
244088 TAAGATATGATCACTTTCTTTTTTTATTTAAT
1 TAAGATATGATCACTTTCTTTTTTCATTTAAT
*
244120 TAAGATGTGATCAC
1 TAAGATATGATCAC
244134 CTCGAGTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 17 0.40
32 25 0.60
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (32 bp):
TAAGATATGATCACTTTCTTTTTTCATTTAAT
Found at i:244419 original size:27 final size:26
Alignment explanation
Indices: 244375--244444 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
244365 TTTATATATA
* *
244375 TTAACTTAAATT-TTTTA-TGTTAAC
1 TTAATTTAAATTATTTTATTATTAAC
244399 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAT-TATTTTATTATTAAC
244424 TTAATTTTAAATTATTTTATT
1 TTAA-TTTAAATTATTTTATT
244445 TTTATTTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 6 0.15
23 2 0.05
24 7 0.18
25 8 0.21
26 1 0.03
27 9 0.23
28 6 0.15
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (26 bp):
TTAATTTAAATTATTTTATTATTAAC
Found at i:244675 original size:31 final size:31
Alignment explanation
Indices: 244601--244664 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
244591 TAACCTCTGA
* *
244601 TGACCACATCTTAATTAAATAAAAATGAAAG
1 TGACCATATCTTAATTAAATAAAAAAGAAAG
244632 TGACCATATCTTAATTAAATAAAAAAGAAAG
1 TGACCATATCTTAATTAAATAAAAAAGAAAG
244663 TG
1 TG
244665 GACATGTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (31 bp):
TGACCATATCTTAATTAAATAAAAAAGAAAG
Found at i:264528 original size:49 final size:51
Alignment explanation
Indices: 264450--264572 Score: 189
Period size: 49 Copynumber: 2.5 Consensus size: 51
264440 AGCACGTGAG
** *
264450 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCT-A-ATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCATGACATAATTTTA
264499 TATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACTCATGACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACCTTTACTCATGACATAATTTTA
264550 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGCGGGGCAGGTACCGCG
264573 TTTTGTATAA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
49 34 0.50
50 2 0.03
51 32 0.47
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (51 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCATGACATAATTTTA
Found at i:268688 original size:18 final size:18
Alignment explanation
Indices: 268665--268699 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
268655 GCAATGGCGG
*
268665 CATCATATATGGTTGCGA
1 CATCATATATGGCTGCGA
268683 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
268700 GTGGCTGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:270399 original size:110 final size:111
Alignment explanation
Indices: 270205--270425 Score: 363
Period size: 110 Copynumber: 2.0 Consensus size: 111
270195 ATTACAAAAA
* * * * *
270205 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATCTAAATTA
* *
270270 AGTTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
270316 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATCTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATCTAAATTA
270380 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
270426 ATGATTTCCA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 69 0.68
111 33 0.32
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATCTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:270585 original size:11 final size:11
Alignment explanation
Indices: 270556--270591 Score: 58
Period size: 10 Copynumber: 3.5 Consensus size: 11
270546 AAAAGAGAGT
270556 ATTTGAGAGAA
1 ATTTGAGAGAA
270567 ATTT-AGAGAA
1 ATTTGAGAGAA
270577 ATTTGAGAG-A
1 ATTTGAGAGAA
270587 ATTTG
1 ATTTG
270592 GTGTGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:274934 original size:21 final size:23
Alignment explanation
Indices: 274890--274937 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
274880 CATATAATTA
*
274890 TAAATTAGTTGAAAATTTAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
*
274913 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
274934 TAAA
1 TAAA
274938 CTATACCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTGAAAATTAAAAGG
Found at i:281516 original size:24 final size:24
Alignment explanation
Indices: 281489--281537 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
281479 TAAAGAAACT
281489 ATTAAGAACATCGATGGCTAAGAG
1 ATTAAGAACATCGATGGCTAAGAG
281513 ATTAAGAACATCGATGGCTAAGAG
1 ATTAAGAACATCGATGGCTAAGAG
281537 A
1 A
281538 AAACAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (24 bp):
ATTAAGAACATCGATGGCTAAGAG
Found at i:285215 original size:2 final size:2
Alignment explanation
Indices: 285208--285275 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
285198 TTGAGCTGGA
285208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
285250 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
285276 GTGTCAATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:286166 original size:40 final size:41
Alignment explanation
Indices: 286122--286233 Score: 135
Period size: 40 Copynumber: 2.8 Consensus size: 41
286112 AATTTAATTT
* *
286122 TTAAATTCGTAACGTGAATTTGTAAA-TCGCAACACAGAAG
1 TTAAATTCGCAACGTGAATTTCTAAATTCGCAACACAGAAG
* *
286162 TTAAATT-GACAACGTG-ATTTCTAAATTCGCAACACTGAAT
1 TTAAATTCG-CAACGTGAATTTCTAAATTCGCAACACAGAAG
286202 TTCAAATTCGCAAC-TGAATTTC-AAATTCGCAA
1 TT-AAATTCGCAACGTGAATTTCTAAATTCGCAA
286234 TTGAATTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
39 9 0.14
40 39 0.62
41 14 0.22
42 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (41 bp):
TTAAATTCGCAACGTGAATTTCTAAATTCGCAACACAGAAG
Found at i:286219 original size:19 final size:19
Alignment explanation
Indices: 286178--286260 Score: 112
Period size: 19 Copynumber: 4.2 Consensus size: 19
286168 TGACAACGTG
286178 ATTTCTAAATTCGCAACACTGA
1 ATTTC-AAATTCGC-A-ACTGA
286200 ATTTCAAATTCGCAACTGA
1 ATTTCAAATTCGCAACTGA
*
286219 ATTTCAAATTCGCAATTGA
1 ATTTCAAATTCGCAACTGA
* *
286238 ATTTCAAATTTGCAACTCA
1 ATTTCAAATTCGCAACTGA
286257 ATTT
1 ATTT
286261 TTGAATTCGC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
19 43 0.75
20 1 0.02
21 8 0.14
22 5 0.09
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (19 bp):
ATTTCAAATTCGCAACTGA
Found at i:286244 original size:38 final size:38
Alignment explanation
Indices: 286178--286291 Score: 113
Period size: 38 Copynumber: 2.9 Consensus size: 38
286168 TGACAACGTG
* *
286178 ATTTCTAAATTCGCAACACTGAATTTCAAATTCGCAACTGA
1 ATTTC-AAATTCGC-A-ATTGAATTTCAAATTCGCAACTCA
*
286219 ATTTCAAATTCGCAATTGAATTTCAAATTTGCAACTCA
1 ATTTCAAATTCGCAATTGAATTTCAAATTCGCAACTCA
** * *
286257 ATTTTTGAATTCGCAATACGAATTT-AATTTCGCAA
1 A-TTTCAAATTCGCAAT-TGAATTTCAAATTCGCAA
286292 TAGGTTTTAG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
38 22 0.35
39 22 0.35
40 14 0.22
41 5 0.08
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (38 bp):
ATTTCAAATTCGCAATTGAATTTCAAATTCGCAACTCA
Found at i:287267 original size:24 final size:24
Alignment explanation
Indices: 287240--287293 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
287230 GTATTCGAAA
287240 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
287264 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
287288 TTTGAT
1 TTTGAT
287294 GATGTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:287833 original size:18 final size:18
Alignment explanation
Indices: 287810--287845 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
287800 AAGTAAAAGG
287810 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
287828 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
287846 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:288114 original size:20 final size:20
Alignment explanation
Indices: 288089--288154 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
288079 AACGCAAAAA
*
288089 TCGCAATGCAAATTTGACTT
1 TCGCAATGCGAATTTGACTT
288109 TCGCAATGCGAATTTGACTT
1 TCGCAATGCGAATTTGACTT
288129 TCGCAATGCGAATTTGACTT
1 TCGCAATGCGAATTTGACTT
288149 TCGCAA
1 TCGCAA
288155 CAATCGCAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (20 bp):
TCGCAATGCGAATTTGACTT
Found at i:288162 original size:49 final size:49
Alignment explanation
Indices: 288109--288214 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 49
288099 AATTTGACTT
* *
288109 TCGCAATGCGAATTTGACTTTCGCAATGCGAATTTGACT-TTCGCAACAA
1 TCGCAACGCGAATTTGACTTTCGCAATGCGAATTTGACTATT-ACAACAA
* **
288158 TCGCAACGCGAATTTTACTTTCGCGTTGCGAATTTGACTATTACAACAA
1 TCGCAACGCGAATTTGACTTTCGCAATGCGAATTTGACTATTACAACAA
*
288207 TCGAAACG
1 TCGCAACG
288215 AGAAAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 48 0.96
50 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (49 bp):
TCGCAACGCGAATTTGACTTTCGCAATGCGAATTTGACTATTACAACAA
Found at i:288361 original size:25 final size:25
Alignment explanation
Indices: 288325--288372 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
288315 ATCAATTAAG
*
288325 CATTGTTGTGGGTACATTATTTGAA
1 CATTGTTATGGGTACATTATTTGAA
288350 CATTGTTATGGGTACATTATTTG
1 CATTGTTATGGGTACATTATTTG
288373 GAAAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (25 bp):
CATTGTTATGGGTACATTATTTGAA
Found at i:288782 original size:18 final size:18
Alignment explanation
Indices: 288761--288797 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
288751 GTAATTGAAG
288761 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
288779 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
288797 T
1 T
288798 ATATATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:291590 original size:21 final size:21
Alignment explanation
Indices: 291511--291607 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
291501 GTGAATCGGG
*
291511 CTCTTGAACGGTGGGA-GGGAC
1 CTCTTGAACGATGGGATGGG-C
** *
291532 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGATGGGC
*
291553 CTCTTGAACGGTGGGATGGGC
1 CTCTTGAACGATGGGATGGGC
* * *
291574 CTCTTGAACGATAGGATGCGT
1 CTCTTGAACGATGGGATGGGC
*
291595 CTCTTGAATGATG
1 CTCTTGAACGATG
291608 ACAGGTGAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
21 59 0.95
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGATGGGATGGGC
Found at i:291905 original size:21 final size:21
Alignment explanation
Indices: 291881--291930 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
291871 TGAAACAATC
*
291881 TCACGTAGAGCAGCTACCTCA
1 TCACGTAGAGCAGATACCTCA
* *
291902 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
*
291923 CCACGTAG
1 TCACGTAG
291931 TGCACCATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Found at i:293726 original size:20 final size:20
Alignment explanation
Indices: 293703--293765 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
293693 AAACTTAAAT
* *
293703 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATAAAAA
*
293723 TCGCAACGGGAAAATAAAAA
1 TCGCAACGCGAAAATAAAAA
* *
293743 TCACAACGCG-AAATTAAAA
1 TCGCAACGCGAAAATAAAAA
293762 TCGC
1 TCGC
293766 GTTGCGATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 11 0.31
20 25 0.69
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATAAAAA
Found at i:293837 original size:20 final size:20
Alignment explanation
Indices: 293772--293826 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
293762 TCGCGTTGCG
*
293772 ATTTTGGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGATTTTC
293792 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGATTTTC
293812 ATTTTCGTGTTGCGA
1 ATTTTCGTGTTGCGA
293827 ATTTAAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.11, C:0.13, G:0.24, T:0.53
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTC
Found at i:294198 original size:22 final size:22
Alignment explanation
Indices: 294171--294221 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
294161 GATGGAGATA
294171 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
294193 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
294215 GACGGAT
1 GACGGAT
294222 GTTGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:295998 original size:74 final size:74
Alignment explanation
Indices: 295901--296045 Score: 236
Period size: 74 Copynumber: 2.0 Consensus size: 74
295891 ATATATTAGT
* ***
295901 TTACCTATATTATGCATTAACTATTTATTTAGTTCAATTATTTTAATTGGATTTTTTTAACAATT
1 TTACCTATATTATGCATTAACTATTTATCTAGTTCAATTACAGTAATTGGATTTTTTTAACAATT
295966 GTTACATAG
66 GTTACATAG
**
295975 TTACCTATATTATGCATTAACTATTTATCTAGTTCAATTACAGTAATTGGATTTTTTTAATTATT
1 TTACCTATATTATGCATTAACTATTTATCTAGTTCAATTACAGTAATTGGATTTTTTTAACAATT
296040 GTTACA
66 GTTACA
296046 ACGTAGGCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (74 bp):
TTACCTATATTATGCATTAACTATTTATCTAGTTCAATTACAGTAATTGGATTTTTTTAACAATT
GTTACATAG
Found at i:296653 original size:32 final size:32
Alignment explanation
Indices: 296572--296664 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
296562 TTTTAAACAC
* *
296572 ATATTTTTAACGAAA-ATTTCTTTAAACACTAAA
1 ATATTTTT-TCGAAACA-TTCTTTAGACACTAAA
* * *
296605 ACA-TTTTTCGAGACATTCTTTAGGCACTAAA
1 ATATTTTTTCGAAACATTCTTTAGACACTAAA
296636 ATATTTTTTCGAAACATTCTTTAGACACT
1 ATATTTTTTCGAAACATTCTTTAGACACT
296665 TATTTTTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
31 20 0.40
32 28 0.56
33 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40
Consensus pattern (32 bp):
ATATTTTTTCGAAACATTCTTTAGACACTAAA
Found at i:297013 original size:21 final size:21
Alignment explanation
Indices: 296981--297077 Score: 133
Period size: 21 Copynumber: 4.7 Consensus size: 21
296971 ATTCTGACTA
* *
296981 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAT
* *
297002 TCGCGTTACGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
297023 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
297044 TCGCATTGCGATTTACATAA-
1 TCGCATTGCGATTTTCCTAAT
297064 TCGCATTGCGATTT
1 TCGCATTGCGATTT
297078 AGTAAATCGC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
20 14 0.21
21 54 0.79
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:297085 original size:20 final size:19
Alignment explanation
Indices: 297023--297088 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
297013 TTTTCCTAAT
* *
297023 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTT-ATAAA
*
297044 TCGCATTGCGATTTACATAA
1 TCGCATTGCGATTTATA-AA
297064 TCGCATTGCGATTTAGTAAA
1 TCGCATTGCGATTTA-TAAA
297084 TCGCA
1 TCGCA
297089 ACGAGATTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 26 0.67
21 12 0.31
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (19 bp):
TCGCATTGCGATTTATAAA
Found at i:300021 original size:94 final size:93
Alignment explanation
Indices: 299855--300126 Score: 399
Period size: 94 Copynumber: 2.9 Consensus size: 93
299845 GTAGTTGTAT
*
299855 AAAATGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
1 AAAA-GACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAACAGAATT
299920 GACAGCAACCGAACAAATTTACTTTCAACC
65 GACAGCAACCGAACAAATTTAC-TTCAACC
* *
299950 AAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGTTTAATAGAATTG
1 AAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAACAGAATTG
* *
300015 GCAGCAACCGAATAAATTTACTTCAACC
66 ACAGCAACCGAACAAATTTACTTCAACC
* * *
300043 AAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGCAGTATT
1 AAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAACAGAATT
* *
300104 GACAGCAATCGAATAAATTTACT
65 GACAGCAACCGAACAAATTTACT
300127 AAGCAATCTA
Statistics
Matches: 164, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
90 38 0.23
93 19 0.12
94 103 0.63
95 4 0.02
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (93 bp):
AAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAACAGAATTG
ACAGCAACCGAACAAATTTACTTCAACC
Found at i:301845 original size:20 final size:20
Alignment explanation
Indices: 301820--301920 Score: 127
Period size: 20 Copynumber: 5.2 Consensus size: 20
301810 TTTTGGTTGA
*
301820 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGCGAG
301840 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGCGAG
**
301859 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGCGAG
301879 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
* *
301898 AATTAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGCGAG
301918 AAT
1 AAT
301921 CGCAACGCAA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
19 35 0.49
20 36 0.51
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGAG
Found at i:301882 original size:19 final size:19
Alignment explanation
Indices: 301818--301949 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
301808 TCTTTTGGTT
*
301818 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
301837 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
301857 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
301877 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
301896 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
301913 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
301929 AAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
301948 GA
1 GA
301950 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 47 0.50
20 31 0.33
21 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:301980 original size:14 final size:14
Alignment explanation
Indices: 301961--302017 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
301951 TTTGGTTTCG
301961 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
301975 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
301994 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
302008 CGTTGCGATT
1 CGTTGCGATT
302018 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:301993 original size:33 final size:33
Alignment explanation
Indices: 301945--302025 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
301935 AAAATCGCAA
**
301945 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
301978 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
302011 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
302026 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:302028 original size:21 final size:20
Alignment explanation
Indices: 302009--302080 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
301999 CGATTCTCTC
302009 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
302029 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
302050 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
302070 GTTGCGATTTT
1 GTTGCGATTTT
302081 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:302719 original size:21 final size:21
Alignment explanation
Indices: 302637--302972 Score: 248
Period size: 20 Copynumber: 16.5 Consensus size: 21
302627 AGTCAGATTT
302637 GCATTGCGATTTACGT-ATTC
1 GCATTGCGATTTACGTAATTC
*
302657 GCATTGCGATATACGT-ATTC
1 GCATTGCGATTTACGTAATTC
*
302677 GCATTGCGATATACGT-ATTC
1 GCATTGCGATTTACGTAATTC
* * *
302697 GCATTGCGGTTTTCCTAATTC
1 GCATTGCGATTTACGTAATTC
302718 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACGTAATTC
*
302738 GCGTTGCGATTTACGT-ATTC
1 GCATTGCGATTTACGTAATTC
* * * * *
302758 GCATTGCAAATTAGGAAAATC
1 GCATTGCGATTTACGTAATTC
* ** *
302779 ACAACGCGA-TTACGTAAATC
1 GCATTGCGATTTACGTAATTC
* * *
302799 GCAATGCGAATCTGAC-TAAAATC
1 GCATTGCG-AT-TTACGT-AATTC
* * **
302822 TCAATGC-AAATACGTAA-TC
1 GCATTGCGATTTACGTAATTC
302841 GCATTGCGATTTACGT-ATTC
1 GCATTGCGATTTACGTAATTC
* *
302861 GCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATTC
302882 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACGTAATTC
*
302902 GCGTTGCGATTTACGT-ATTC
1 GCATTGCGATTTACGTAATTC
* * * * *
302922 GCATTTCGAATTAGGAAAATC
1 GCATTGCGATTTACGTAATTC
* * *
302943 GCAATGCGA-ATACGTAAATC
1 GCATTGCGATTTACGTAATTC
*
302963 GCAATGCGAT
1 GCATTGCGAT
302973 AGTCAGAATC
Statistics
Matches: 254, Mismatches: 48, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
19 10 0.04
20 169 0.67
21 60 0.24
22 1 0.00
23 14 0.06
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (21 bp):
GCATTGCGATTTACGTAATTC
Found at i:302909 original size:61 final size:60
Alignment explanation
Indices: 302637--302926 Score: 244
Period size: 61 Copynumber: 4.8 Consensus size: 60
302627 AGTCAGATTT
* * * *
302637 GCATTGCGATTTACGTATTCGCATTGCGATATACGTATTCGCATTGCGATATACGTATTC
1 GCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACCTATTC
* * * * * *
302697 GCATTGCGGTTTTCCTAATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTATTC
1 GCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTATTCGCATTGCGATTTACCTATTC
* * * * * ** * * * *
302758 GCATTGCAAATTAGGAAAATCACAACGCGA-TTACGTAAATCGCAATGCGAATCTGA-CTAAAAT
1 GCATTGCGATTTACG-TAATCGCATTGCGATTTACGT-ATTCGCATTGCG-AT-TTACCT--ATT
302821 C
60 C
* * ** *
302822 TCAATGC-AAATACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACCT-ATTC
*
302882 GCATTGCGATTTACGTAATCGCGTTGCGATTTACGTATTCGCATT
1 GCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATT
302927 TCGAATTAGG
Statistics
Matches: 179, Mismatches: 41, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
60 30 0.17
61 103 0.58
62 25 0.14
63 13 0.07
64 8 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (60 bp):
GCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACCTATTC
Found at i:302938 original size:164 final size:164
Alignment explanation
Indices: 302667--302971 Score: 538
Period size: 164 Copynumber: 1.9 Consensus size: 164
302657 GCATTGCGAT
* *
302667 ATACGTATTCGCATTGCGATATACGTATTCGCATTGCGGTTTTCCTAATTCGCATTGCGATTTAC
1 ATACGTAATCGCATTGCGATATACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTAC
*
302732 GTAATCGCGTTGCGATTTACGTATTCGCATTGCAAATTAGGAAAATCACAACGCGATTACGTAAA
66 GTAATCGCGTTGCGATTTACGTATTCGCATTGCAAATTAGGAAAATCACAACGCGAATACGTAAA
302797 TCGCAATGCGAATCTGACTAAAATCTCAATGCAA
131 TCGCAATGCGAATCTGACTAAAATCTCAATGCAA
*
302831 ATACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTAC
1 ATACGTAATCGCATTGCGATATACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTAC
* * * *
302896 GTAATCGCGTTGCGATTTACGTATTCGCATTTCGAATTAGGAAAATCGCAATGCGAATACGTAAA
66 GTAATCGCGTTGCGATTTACGTATTCGCATTGCAAATTAGGAAAATCACAACGCGAATACGTAAA
302961 TCGCAATGCGA
131 TCGCAATGCGA
302972 TAGTCAGAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
164 133 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (164 bp):
ATACGTAATCGCATTGCGATATACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTAC
GTAATCGCGTTGCGATTTACGTATTCGCATTGCAAATTAGGAAAATCACAACGCGAATACGTAAA
TCGCAATGCGAATCTGACTAAAATCTCAATGCAA
Found at i:302943 original size:41 final size:41
Alignment explanation
Indices: 302612--302951 Score: 196
Period size: 41 Copynumber: 8.3 Consensus size: 41
302602 GGCGCTATGT
* * *
302612 AAATCGCATTGCGATAGT-CAG-ATTTGCATTGCGATTTACG-
1 AAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAATTACGA
* * *
302652 TATTCGCATTGCGATATACGTATTCGCATTGCG-ATATACG-
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAAT-TACGA
* * * * * *
302692 TATTCGCATTGCGGTTTTCCTAATTCGCATTGCGATTTACG-
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTACGA
* * * *
302733 TAATCGCGTTGCGATTTACGTATTCGCATTGCAAATTAGGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACGA
* ** * * *
302774 AAATCACAACGCGA-TTACGTAAATCGCAATGCGAATCTGACTA
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT-T-ACGA
* * ** * *
302817 AAATCTCAATGC-AAATACGTAATCGCATTGCGATTTACG-
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACGA
* * * * *
302856 TATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACG-
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTACGA
* * * *
302897 TAATCGCGTTGCGATTTACGTATTCGCATTTCGAATTAGGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACGA
*
302938 AAATCGCAATGCGA
1 AAATCGCATTGCGA
302952 ATACGTAAAT
Statistics
Matches: 234, Mismatches: 53, Indels: 25
0.75 0.17 0.08
Matches are distributed among these distances:
39 11 0.05
40 90 0.38
41 100 0.43
42 16 0.07
43 17 0.07
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACGA
Found at i:302945 original size:61 final size:60
Alignment explanation
Indices: 302784--302972 Score: 182
Period size: 61 Copynumber: 3.1 Consensus size: 60
302774 AAATCACAAC
* * * * *
302784 GCGA-TTACGTAAATCGCAATGCGAATCTGACTAAAATCTCAATGCAAATACGTAATCGCATT
1 GCGATTTACGT-ATTCGCATTGCGAAT-T-ACCAAAATCGCAATGCGAATACGTAATCGCATT
* * * * * * *
302846 GCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCGTT
1 GCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAATGCGA-ATACGTAATCGCATT
* ** *
302907 GCGATTTACGTATTCGCATTTCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGCAAT
1 GCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAATGCGAATACGT-AATCGCATT
302968 GCGAT
1 GCGAT
302973 AGTCAGAATC
Statistics
Matches: 101, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
60 16 0.16
61 63 0.62
62 16 0.16
63 6 0.06
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (60 bp):
GCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAATGCGAATACGTAATCGCATT
Found at i:303286 original size:19 final size:17
Alignment explanation
Indices: 303264--303300 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
303254 ATATATATAT
303264 ATATATATATATATTTAAA
1 ATATATA-ATA-ATTTAAA
303283 ATATATAATAATTTAAA
1 ATATATAATAATTTAAA
303300 A
1 A
303301 ATTTTAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATAATTTAAA
Found at i:304851 original size:20 final size:18
Alignment explanation
Indices: 304826--304862 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
304816 GTTTTTTAAG
304826 TTAACATTTTATTTATTTAT
1 TTAACA-TTTATTT-TTTAT
304846 TTAACATTTATTTTTTA
1 TTAACATTTATTTTTTA
304863 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTAACATTTATTTTTTAT
Found at i:304854 original size:15 final size:14
Alignment explanation
Indices: 304836--304882 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 14
304826 TTAACATTTT
304836 ATTTATTTATTTAAC
1 ATTTATTT-TTTAAC
304851 ATTTATTTTTTAA-
1 ATTTATTTTTTAAC
304864 A--TATTTTTTAA-
1 ATTTATTTTTTAAC
304875 ATTT-TTTT
1 ATTTATTTT
304883 GTATCCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.37
12 4 0.13
13 2 0.07
14 5 0.17
15 8 0.27
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTATTTTTTAAC
Found at i:304880 original size:10 final size:11
Alignment explanation
Indices: 304854--304882 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
304844 ATTTAACATT
304854 TATTTTTTAAA
1 TATTTTTTAAA
304865 TATTTTTTAAA
1 TATTTTTTAAA
304876 T-TTTTTT
1 TATTTTTT
304883 GTATCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:304919 original size:18 final size:18
Alignment explanation
Indices: 304894--304928 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
304884 TATCCTATTT
304894 ATTTTTT-CCTTTATTAC
1 ATTTTTTCCCTTTATTAC
304911 ATTTCTTTCCCTTTATTA
1 ATTT-TTTCCCTTTATTA
304929 TTTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 3 0.19
19 9 0.56
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTCCCTTTATTAC
Found at i:305042 original size:45 final size:46
Alignment explanation
Indices: 304922--305045 Score: 117
Period size: 45 Copynumber: 2.7 Consensus size: 46
304912 TTTCTTTCCC
* * *
304922 TTTATTATTTTGTTATTATTTTATTTATTTAATATTTTTCTCTTTTGA
1 TTTATTTTTTTGTT-TTTTTTTA-TTATTTAATATTTTACTCTTTTGA
* * * * *
304970 TTTATATTTATGTTTTTTGTCTGTTATTT-TTATTTTAC-CTTTTGA
1 TTTATTTTTTTGTTTTTT-TTTATTATTTAATATTTTACTCTTTTGA
*
305015 TTTATTTTTTTCTTTTTCTTTTATTATTTAA
1 TTTATTTTTTTGTTTTT-TTTTATTATTTAA
305046 CATTCATTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
45 29 0.49
46 8 0.14
47 9 0.15
48 13 0.22
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.72
Consensus pattern (46 bp):
TTTATTTTTTTGTTTTTTTTTATTATTTAATATTTTACTCTTTTGA
Found at i:305483 original size:3 final size:3
Alignment explanation
Indices: 305477--305537 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
305467 TTACCCATTT
* * * * *
305477 TTA TTA TTA TT- TTT TTA TAA TTA TAA TAA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
305524 TATA TTA TTTA TTA
1 T-TA TTA -TTA TTA
305538 ACATTACAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:305527 original size:26 final size:26
Alignment explanation
Indices: 305479--305537 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
305469 ACCCATTTTT
* *
305479 ATTATTATTTTTTTATAATTATAATA
1 ATTATTATTATTATATAATTATAATA
*
305505 ATTATTATTATTAT-TAATATATATTA
1 ATTATTATTATTATATAAT-TATAATA
*
305531 TTTATTA
1 ATTATTA
305538 ACATTACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTATTATTATTATATAATTATAATA
Found at i:308193 original size:9 final size:9
Alignment explanation
Indices: 308179--308203 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
308169 TTACATGTGA
308179 ATTTAAATT
1 ATTTAAATT
308188 ATTTAAATT
1 ATTTAAATT
308197 ATTTAAA
1 ATTTAAA
308204 AGCATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:310979 original size:15 final size:15
Alignment explanation
Indices: 310959--310990 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
310949 ATCAATACCT
310959 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
310974 TTTTGCATACATTCA
1 TTTTGCATACATGCA
310989 TT
1 TT
310991 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:318330 original size:1 final size:1
Alignment explanation
Indices: 318320--318373 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
318310 GCTTGAAGAG
* * * * **
318320 AAAAATAAAAAAAAAAGAAAAAAAAAAAAAAAAGAAAGAAAAAGGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
318374 GGGGGGTCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (1 bp):
A
Found at i:318340 original size:11 final size:11
Alignment explanation
Indices: 318320--318362 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
318310 GCTTGAAGAG
*
318320 AAAAATAAAAA
1 AAAAAGAAAAA
318331 AAAAAGAAAAA
1 AAAAAGAAAAA
318342 AAAAA-AAAAA
1 AAAAAGAAAAA
*
318352 AGAAAGAAAAA
1 AAAAAGAAAAA
318363 GGAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.91, C:0.00, G:0.07, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:318340 original size:17 final size:17
Alignment explanation
Indices: 318318--318372 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
318308 ATGCTTGAAG
*
318318 AGAAAAATAAAAAAAAA
1 AGAAAAAAAAAAAAAAA
318335 AGAAAAAAAAAAAAAAA
1 AGAAAAAAAAAAAAAAA
318352 AGAAAGAAAAAGGAAAAAAA
1 AGAAA-AAAAA--AAAAAAA
318372 A
1 A
318373 AGGGGGGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 21 0.62
18 5 0.15
20 8 0.24
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAAAAAAAA
Found at i:318344 original size:21 final size:21
Alignment explanation
Indices: 318320--318374 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
318310 GCTTGAAGAG
*
318320 AAAAATAAAAAAA-AAAGAAA
1 AAAAAAAAAAAAAGAAAGAAA
318340 AAAAAAAAAAAAAGAAAGAAA
1 AAAAAAAAAAAAAGAAAGAAA
**
318361 AAGGAAAAAAAAAG
1 AAAAAAAAAAAAAG
318375 GGGGGTCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAAAAGAAAGAAA
Found at i:319993 original size:92 final size:83
Alignment explanation
Indices: 319602--319995 Score: 619
Period size: 83 Copynumber: 4.6 Consensus size: 83
319592 AACAAATGCC
319602 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
*
319667 ATTGAATTTGGAAGAGTA
66 ATTGAATTTGGAAGAGGA
319685 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
**
319750 ATTGAATTTGGAAGAATA
66 ATTGAATTTGGAAGAGGA
319768 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
319833 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
*
319851 ATGTGCTCATTGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCA-C
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA--AA--ATC
*
319915 AGAACCAGTTATTGAATTTGGAAGAGGA
62 ---A--A-TCATTGAATTTGGAAGAGGA
* * *
319943 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
319996 ATATAAAACC
Statistics
Matches: 292, Mismatches: 9, Indels: 11
0.94 0.03 0.04
Matches are distributed among these distances:
83 218 0.75
85 2 0.01
86 1 0.00
87 1 0.00
89 1 0.00
91 1 0.00
92 68 0.23
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.39
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAGGA
Found at i:320010 original size:92 final size:92
Alignment explanation
Indices: 319833--320013 Score: 292
Period size: 92 Copynumber: 2.0 Consensus size: 92
319823 AAAATCAATC
* *
319833 ATTGAATTTGGAAGAGGAATGTGCTCATTGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* *
319898 GGTTTGGTATGAACCACAGAACCAGTT
66 GGTTTGATATAAACCACAGAACCAGTT
* *
319925 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
319990 GGTTTGATATAAAACC-CAGAACCA
66 GGTTTGATAT-AAACCACAGAACCA
320014 ATATTTGGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 78 0.95
93 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (92 bp):
ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGATATAAACCACAGAACCAGTT
Found at i:321039 original size:20 final size:20
Alignment explanation
Indices: 320986--321041 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
320976 CCAGAGAAAG
*
320986 TTCATAATGAGAAGAAAACA
1 TTCATAATGAGAAGAAAAAA
321006 -TC-TGAA-GAAGGAAGAAAAAA
1 TTCAT-AATG-A-GAAGAAAAAA
321026 TTCATAATGAGAAGAA
1 TTCATAATGAGAAGAA
321042 TTTGTTCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
18 2 0.07
19 5 0.17
20 15 0.52
21 5 0.17
22 2 0.07
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (20 bp):
TTCATAATGAGAAGAAAAAA
Found at i:321182 original size:229 final size:229
Alignment explanation
Indices: 320759--321394 Score: 934
Period size: 229 Copynumber: 2.8 Consensus size: 229
320749 TGTCAGTTAG
* * *
320759 AGTTCATAATGAGAAGAACTCATCTGAAG-AGAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCATAATGAGAAGAAATCATCTGAAGAAG-GAAGAAAAAGTTCATAATGAGAAGAACTTGTT
* *
320823 CAA-CTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATAAGAAG
65 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAG
* *
320887 AACTCA-T-C-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
130 AACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
*
320949 AATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
195 AATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
* * *
320984 AGTTCATAATGAGAAGAAAACATCTGAAGAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* *
321049 AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAG-GTAGAGTTCATAATAAGAAG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATAAGAAG
321113 AACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
130 AACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
* ** *
321178 AATCCATCACTTGATGGATCAGCTTTTCCAGTTAG
195 AATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
* *
321213 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * *
321278 AACCTTTTGTTCAAATTCATCACTTGATGGATCA-CATTTCCAGAGAAAGTTCATAATAAGAAGA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGA
* * * **
321342 A--C-TTATTTGAA-GAGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTT
131 ACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
321395 TTGAATGACT
Statistics
Matches: 372, Mismatches: 32, Indels: 15
0.89 0.08 0.04
Matches are distributed among these distances:
224 38 0.10
225 67 0.18
226 64 0.17
227 1 0.00
228 28 0.08
229 174 0.47
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (229 bp):
AGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGA
ACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCAA
ATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
Found at i:321183 original size:116 final size:113
Alignment explanation
Indices: 320759--321397 Score: 894
Period size: 113 Copynumber: 5.7 Consensus size: 113
320749 TGTCAGTTAG
* * *
320759 AGTTCATAATGAGAAGAACTCATCTGAAG-AGAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAG-GAAGAAGAAATTCATAATGAGAAGAACTTGTT
* *
320823 CAA-CTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
65 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
*
320871 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* *
320936 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
* ** * *
320984 AGTTCATAATGAGAAGAAAACATCTGAAGAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* *
321049 AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAG-GTAG
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AA
* *
321097 AGTTCATAATAAGAAGAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTG
1 AGTTCATAATAAGAAGAACTCA-T-C-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTG
* ** *
321162 TTCAACCTTATGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTAG
63 TTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
* *
321213 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAA-AAAGTTCATAATGAGAAGAACTTGTT
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATGAGAAGAACTTGTT
* * * *
321277 TAACCTTTTGTTCAAATTCATCACTTGATGGATCA-CATTTCCAGAGAA
65 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
* * * * *
321325 AGTTCATAATAAGAAGAACTTATTTGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
321389 AACCTTTTG
66 AACCTTTTG
321398 AATGACTCTA
Statistics
Matches: 478, Mismatches: 40, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
111 37 0.08
112 100 0.21
113 234 0.49
114 2 0.00
115 2 0.00
116 103 0.22
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
Found at i:328001 original size:18 final size:18
Alignment explanation
Indices: 327978--328050 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
327968 ACTGAATATT
*
327978 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
327996 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
328015 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
328034 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
328051 GATTATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:334875 original size:18 final size:17
Alignment explanation
Indices: 334852--334910 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
334842 ACTGAATATT
334852 TGTCCCGAATGACCACTA
1 TGTCCCGAA-GACCACTA
334870 TGTCCCGAAAGACCACTGA
1 TGTCCCG-AAGACCACT-A
*
334889 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAG-ACCACTA
334908 TGT
1 TGT
334911 ACTGAAGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 17 0.47
19 7 0.19
20 12 0.33
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (17 bp):
TGTCCCGAAGACCACTA
Found at i:334922 original size:18 final size:18
Alignment explanation
Indices: 334856--334922 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
334846 AATATTTGTC
* *
334856 CCGAATGACCACTATGTC
1 CCGAAGGACCACTATGTA
* *
334874 CCGAAAGACCACTGATTGTT
1 CCGAAGGACCACT-A-TGTA
*
334894 CCGAAGAACCACTATGTA
1 CCGAAGGACCACTATGTA
*
334912 CTGAAGGACCA
1 CCGAAGGACCA
334923 TTGATTATCC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 24 0.60
19 2 0.05
20 14 0.35
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (18 bp):
CCGAAGGACCACTATGTA
Found at i:337194 original size:84 final size:83
Alignment explanation
Indices: 337053--337535 Score: 447
Period size: 84 Copynumber: 5.8 Consensus size: 83
337043 TAAAGAAACT
* * * * * *
337053 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCAACTACA
*
337118 CTCAGCTCAAAGGCACAAC
65 CTCAGCTCCAAGGCACAAC
* * * **
337137 ATTTGTAGCATAACTTAAATCGAGAAGGGCTATCTGCCATACAAAGATATTCGAGTTCAACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA-ACAAAGACCTTCGAGTTCAACTACA
*
337202 CTCAGCTCCAAGGCACATC
65 CTCAGCTCCAAGGCACAAC
* * * * * *
337221 ATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTG-C--CAAAGACCCTCAAGTTCGATTTCAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACAC
* * * *
337283 TCAGCTTCGAGTGTATAAC
66 TCAGCTCCAAG-GCACAAC
* * *
337302 ATTTACAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTAACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCAACTACA
* *
337367 CTGAGCTCCAAGGCACATC
65 CTCAGCTCCAAGGCACAAC
* * ** * * *
337386 ATTTGCAGCATAGCTTAAGTCGAGAATGCCTATCTGCC-A-AAA-ACCCTCGAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACAC
* * * *
337448 TCAGCTTCGAGGGAACATC
66 TCAGC-TCCAAGGCACAAC
* * * * * * * *
337467 ATTTACATCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCAACTACA
337532 CTCA
65 CTCA
337536 TCTCAAAGTG
Statistics
Matches: 317, Mismatches: 71, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
80 47 0.15
81 78 0.25
82 2 0.01
83 2 0.01
84 139 0.44
85 49 0.15
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (83 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACAC
TCAGCTCCAAGGCACAAC
Found at i:337338 original size:165 final size:164
Alignment explanation
Indices: 337145--337535 Score: 541
Period size: 165 Copynumber: 2.4 Consensus size: 164
337135 ACATTTGTAG
* * **
337145 CATAACTTAAATCGAGAAGGGCTATCTGCCATACAAAGATATTCGAGTTCAACTACACTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCA-ACAAAGACCTTCGAGTTCAACTACACTCAGCTC
** *
337210 CAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTGCCAAAGACCCTCAAGTTC
65 CAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAATGCCTATCTGCCAAAAACCCTCAAGTTC
* * * *
337275 GATTTCACTCAGCTTCGAGTGTATAACATTTACAGT
130 GATTACACTCAGCTTCGAGGGAACAACATTTACA-T
* *
337311 -ATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTAACTACACTGAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCAACTACACTCAGCTC
* *
337375 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAATGCCTATCTGCCAAAAACCCTCGAGTTC
65 CAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAATGCCTATCTGCCAAAAACCCTCAAGTTC
*
337440 GATTACACTCAGCTTCGAGGGAACATCATTTACAT
130 GATTACACTCAGCTTCGAGGGAACAACATTTACAT
* * * * * *
337475 CATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCAACTACACTCA
337536 TCTCAAAGTG
Statistics
Matches: 198, Mismatches: 24, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
164 3 0.02
165 195 0.98
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (164 bp):
CATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACACTCAGCTCC
AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAATGCCTATCTGCCAAAAACCCTCAAGTTCG
ATTACACTCAGCTTCGAGGGAACAACATTTACAT
Found at i:339065 original size:18 final size:18
Alignment explanation
Indices: 339042--339110 Score: 102
Period size: 18 Copynumber: 3.7 Consensus size: 18
339032 AGGGATAACC
339042 AGTGGTCCTTCGGAACAT
1 AGTGGTCCTTCGGAACAT
339060 AGTGGTCCTTCGGAACAT
1 AGTGGTCCTTCGGAACAT
*
339078 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGAAC-AT
*
339097 CAGTGGTCATTCGG
1 -AGTGGTCCTTCGG
339111 GACAAATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 33 0.72
19 2 0.04
20 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:345716 original size:30 final size:30
Alignment explanation
Indices: 345680--345742 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
345670 TAAAACTTGC
345680 GATAAGTCTATCTCTTATCATTGAATTTAT
1 GATAAGTCTATCTCTTATCATTGAATTTAT
345710 GATAAGTCTATCTCTTATCATTGAATTTAT
1 GATAAGTCTATCTCTTATCATTGAATTTAT
345740 GAT
1 GAT
345743 TCTATATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (30 bp):
GATAAGTCTATCTCTTATCATTGAATTTAT
Found at i:346047 original size:18 final size:18
Alignment explanation
Indices: 346024--346092 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
346014 AGGGATAATC
*
346024 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACAT
* *
346042 AGTGGTTCTTCAGAACAAT
1 AGTGGTCCTTCGGAAC-AT
* *
346061 CAGTGGTCTTTCTGAACAT
1 -AGTGGTCCTTCGGAACAT
346080 AGTGGTCCTTCGG
1 AGTGGTCCTTCGG
346093 GACAAATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 24 0.59
19 4 0.10
20 13 0.32
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:349040 original size:21 final size:22
Alignment explanation
Indices: 349011--349063 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
349001 CGTGGGGGGT
*
349011 ATCGATTCCC-TC-AAGAAGGGA
1 ATCGGTTCCCATCAAAG-AGGGA
*
349032 ATCGGTTCCCATTCAAAGGGGGA
1 ATCGGTTCCCA-TCAAAGAGGGA
349055 ATCGGTTCC
1 ATCGGTTCC
349064 TCTTCAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.33
23 15 0.56
24 3 0.11
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (22 bp):
ATCGGTTCCCATCAAAGAGGGA
Found at i:349054 original size:23 final size:23
Alignment explanation
Indices: 349028--349090 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
349018 CCCTCAAGAA
349028 GGGAATCGGTTCC-CATTCAAAGG
1 GGGAATCGGTTCCTC-TTCAAAGG
*
349051 GGGAATCGGTTCCTCTTCAAGGG
1 GGGAATCGGTTCCTCTTCAAAGG
* *
349074 GGGTATCGATTCTCTCT
1 GGGAATCGGTTC-CTCT
349091 GCACTAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 30 0.86
24 5 0.14
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (23 bp):
GGGAATCGGTTCCTCTTCAAAGG
Found at i:353152 original size:117 final size:117
Alignment explanation
Indices: 352932--353152 Score: 295
Period size: 117 Copynumber: 1.9 Consensus size: 117
352922 CTTTCAAATC
* *
352932 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
352997 CATTTTGATTTTCAAAATCTATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCTATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * *
353049 GAAAATTTCTTTTTCAA-AGTTTTCAAATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * * *
353112 TTTATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCTATTTTAG-TTTCTAAAAGAA
353153 TATCATTTTC
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
116 2 0.02
117 84 0.93
118 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCTATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:355516 original size:84 final size:84
Alignment explanation
Indices: 355223--356038 Score: 813
Period size: 84 Copynumber: 9.8 Consensus size: 84
355213 GTGTTACACA
* * * * *
355223 AAGGCACAACATTTGCAGCACAGCTTAAATCGAGAAGGGTTATCTTCCATA-CAAAGACCTTCGA
1 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA-ACCAAAGACCTTCGA
* *
355287 GTTCGACTACACTCAGCTCC
65 GTTCGACTACGCTCAGCTTC
* *
355307 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* * * *
355368 TTCGATTTCACTCAGCTTTG
66 TTCGACTACGCTCAGC-TTC
* * * *
355388 ATGGCATATCATTTACAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
355453 TTCGACTACGCTCAGCTTC
66 TTCGACTACGCTCAGCTTC
* * * *
355472 AAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG----CCAAAG-CCCTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* *
355532 TTCGATTACACTCAGCTTC
66 TTCGACTACGCTCAGCTTC
* * * * * * * * * *
355551 GAGGGCATATCATTTACAGTATAACTCAAGGCTAGAAGGATTATCTGCCAACAAAAGACCTTTGA
1 -AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGA
355616 GTTCGACTACGCTCAGC-TC
65 GTTCGACTACGCTCAGCTTC
* * * * * **
355635 AAAGGCATAACATTTGCAGCATAGCTTAAATCGAGAAGGGATATCTGATATA-CAAAGACCTTCG
1 -AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA-ACCAAAGACCTTCG
* *
355699 AGTTCAACTACGCTCAGCTCC
64 AGTTCGACTACGCTCAGCTTC
* *
355720 AAGGAATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
** *
355785 TTCGACTACGCTTGGCTCC
66 TTCGACTACGCTCAGCTTC
* * * * * *
355804 AAGTCACATCTTTTGCAGCATAACTAAAATCGAGAAGGGCTATCTG----CCAAAGACCCTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* * *
355865 TTCGATTACACTCAACTTC
66 TTCGACTACGCTCAGCTTC
* ** * * * * * *
355884 GAGGGCACATCATTTAAAGCATAACTCAAGGCTATAAGGGTTATTTGTC-ACCAAAGACCTTCGA
1 -AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGA
355948 GTTCGACTACGCTCAGC-TC
65 GTTCGACTACGCTCAGCTTC
* * * *
355967 TAAGGCACATCATTTGCAGTATAGCTTAAGTCAAGAAGGGTTATCTGTCAACCAAAGACCTTTCG
1 -AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC-TTCG
356032 AGTTCGA
64 AGTTCGA
356039 TTTCATTCAT
Statistics
Matches: 596, Mismatches: 115, Indels: 41
0.79 0.15 0.05
Matches are distributed among these distances:
79 24 0.04
80 96 0.16
81 76 0.13
83 41 0.07
84 299 0.50
85 60 0.10
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
TTCGACTACGCTCAGCTTC
Found at i:355625 original size:164 final size:165
Alignment explanation
Indices: 355253--356040 Score: 976
Period size: 164 Copynumber: 4.7 Consensus size: 165
355243 CAGCTTAAAT
* * *
355253 CGAGAAGGGTTATCTTCCATA-CAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
1 CGAGAAGGGTTATCTGCCA-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATC
* *
355317 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTTCACTCA
65 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* * * * *
355382 GCTTTGATGGCATATCATTTACAGTATAACTTAAGT
130 GCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
355418 CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCA
1 CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCA
*
355483 TTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAG-CCCTCGAGTTCGATTACACTCAG
66 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
*
355547 CTTCGAGGGCATATCATTTACAGTATAACTCAAGG
131 CTTCGAGGGCATATCATTTACAGCATAACTCAAGG
* * * * * *
355582 CTAGAAGGATTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAAAGGCATAAC
1 CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATC
* * * * * * *
355646 ATTTGCAGCATAGCTTAAATCGAGAAGGGATATCTGATATACAAAGACCTTCGAGTTCAACTACG
65 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACA
* * * * * *
355711 CTCAGC-TCCAAGGAATATCATTTGCAGCATAACTTAAGT
126 CTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
** * * *
355750 CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTTGGCTCCAAGTCACATCT
1 CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCA
* * * *
355815 TTTGCAGCATAACTAAAATCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAA
66 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
* *
355880 CTTCGAGGGCACATCATTTAAAGCATAACTCAAGG
131 CTTCGAGGGCATATCATTTACAGCATAACTCAAGG
* * * *
355915 CTATAAGGGTTATTTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACATC
1 CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATC
* * * *
355978 ATTTGCAGTATAGCTTAAGTCAAGAAGGGTTATCTGTCAACCAAAGACCTTTCGAGTTCGATT
65 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACC-CTCGAGTTCGATT
356041 TCATTCATCT
Statistics
Matches: 533, Mismatches: 75, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
163 3 0.01
164 235 0.44
165 138 0.26
168 124 0.23
169 33 0.06
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (165 bp):
CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCA
TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
CTTCGAGGGCATATCATTTACAGCATAACTCAAGG
Found at i:355858 original size:248 final size:247
Alignment explanation
Indices: 355223--356038 Score: 944
Period size: 248 Copynumber: 3.3 Consensus size: 247
355213 GTGTTACACA
* * * * *
355223 AAGGCACAACATTTGCAGCACAGCTTAAATCGAGAAGGGTTATCTTCCATA-CAAAGACCTTCGA
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCA-ACCAAAGACCTTCGA
*
355287 GTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCT
65 GTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTAAAGTCGAGAAGGGCTATCT
* * * *
355352 GCCAAAGACCCTCGAGTTCGATTTCACTCAGCTTTGATGGCATATCATTTACAGTATAACTTAAG
130 GCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCATATCATTTACAGCATAACTTAAG
* *
355417 TCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC
195 TCGAGAAGGGTTATCTG-TAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
* *
355472 AAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG----CCAAAG-CCCTCGAG
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* * * * * * * * * **
355532 TTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGTATAACTCAAGGCTAGAAGGATTATCT
66 TTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTAAAGTCGAGAAGGGCTATCT
* * * * * * * *
355597 GCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAAAGGCATAACATTTGCAGCATAGCT
130 G-C--C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCATATCATTTACAGCATAACT
* * *
355661 TAAATCGAGAAGGGATATCTGATATACAAAGACCTTCGAGTTCAACTACGCTCAGCTCC
191 TAAGTCGAGAAGGGTTATCTG-TA-ACAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
* * * *
355720 AAGGAATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* ** * * *
355785 TTCGACTACGCTTGGCTCCAAGTCACATCTTTTGCAGCATAACTAAAATCGAGAAGGGCTATCTG
66 TTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTAAAGTCGAGAAGGGCTATCTG
* * * * * *
355850 CCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTAAAGCATAACTCAAGG
131 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCATATCATTTACAGCATAACTTAAGT
* * * * *
355915 CTATAAGGGTTATTTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCT
196 CGAGAAGGGTTATCTGT-AACAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
* *
355968 AAGGCACATCATTTGCAGTATAGCTTAAGTCAAGAAGGGTTATCTGTCAACCAAAGACCTTTCGA
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACC-TTCGA
356033 GTTCGA
65 GTTCGA
356039 TTTCATTCAT
Statistics
Matches: 465, Mismatches: 87, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
244 22 0.05
245 44 0.09
246 1 0.00
248 223 0.48
249 113 0.24
251 1 0.00
252 42 0.09
253 19 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (247 bp):
AAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
TTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTAAAGTCGAGAAGGGCTATCTG
CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCATATCATTTACAGCATAACTTAAGT
CGAGAAGGGTTATCTGTAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
Found at i:357645 original size:15 final size:15
Alignment explanation
Indices: 357627--357692 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
357617 GTTAAGATTT
357627 TTTATTTATTTAAC-A
1 TTTATTT-TTTAACTA
357642 TTTATTTTTTAACTA
1 TTTATTTTTTAACTA
357657 -TT-TTTTTTAA--A
1 TTTATTTTTTAACTA
* *
357668 TTT-TTTTGTATCATA
1 TTTATTTTTTAAC-TA
357683 TTTATTTTTT
1 TTTATTTTTT
357693 TCCTTTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
11 1 0.02
12 8 0.19
13 8 0.19
14 8 0.19
15 12 0.29
16 5 0.12
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTATTTTTTAACTA
Found at i:357750 original size:27 final size:28
Alignment explanation
Indices: 357715--357795 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 28
357705 TTTCTCTCCC
*
357715 TTTATTATTTTGT-TATTATTTTATTTA
1 TTTAATATTTTGTCTATTATTTTATTTA
* *
357742 TTTAATATTTT-TCT-CT-TTTGATTTA
1 TTTAATATTTTGTCTATTATTTTATTTA
*
357767 TATTTATATTTTGTCTATTATTTTTATTT
1 T-TTAATATTTTGTCTATTA-TTTTATTT
357796 TACATTTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
25 9 0.21
26 11 0.26
27 14 0.33
28 1 0.02
30 7 0.17
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (28 bp):
TTTAATATTTTGTCTATTATTTTATTTA
Done.