Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 12 of 12
Found at i:2930146 original size:20 final size:20
Alignment explanation
Indices: 2930121--2930237 Score: 86
Period size: 20 Copynumber: 6.2 Consensus size: 20
2930111 AAAATCGCAA
2930121 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
2930141 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
** * *
2930161 CGATTTTC-ATTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
*
2930180 CGAT--T---A-TCTCGTTG
1 CGATAGTCAAATTCGCGTTG
2930194 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
2930214 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
2930234 CGAT
1 CGAT
2930238 TTTAAGTTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
14 10 0.13
16 1 0.01
17 1 0.01
19 15 0.19
20 51 0.65
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:2930216 original size:53 final size:54
Alignment explanation
Indices: 2930136--2930238 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 54
2930126 GTCAAATTCG
** * **
2930136 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCA-TTTCGTGTTGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTATCT
2930189 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATT
2930239 TTAAGTTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 29 0.66
54 15 0.34
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTATCT
Found at i:2930259 original size:73 final size:73
Alignment explanation
Indices: 2930121--2930259 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 73
2930111 AAAATCGCAA
* * ***
2930121 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCGTGTTGCGATTA
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTCGAGAAACGATTA
2930186 TCTCGTTG
66 TCTCGTTG
*
2930194 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAAGTTTC-AGAAACTATT
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAA-TTTCGAGAAACGATT
2930258 AT
65 AT
2930260 TATTCTTCTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 55 0.93
74 4 0.07
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.41
Consensus pattern (73 bp):
CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTCGAGAAACGATTA
TCTCGTTG
Found at i:2931591 original size:190 final size:186
Alignment explanation
Indices: 2931235--2931608 Score: 712
Period size: 190 Copynumber: 2.0 Consensus size: 186
2931225 GTAGATTTGG
2931235 ATATTTGAGGCTTTTCCCGACATGCAGACATATCATTAAAACTTCAAATGATATTCCTAGAGCTA
1 ATATTTGAGGCTTTTCCCGACATGCAGACATATCATTAAAACTTCAAATGATATTCCTAGAGCTA
2931300 TTTCCTGGAAGAGAAACGACGGTTGTTGATTTGGGAGTTACTACGGTATACGACAATAAATGATG
66 TTTCCTGGAAGAGAAACGACGGTTGTTGATTTGGGAGTTACTACGGTATACGACAATAAATGATG
2931365 TAAGTTAACACAAATACTACCATATATAAACAAATTATTACTAGTACACGTTTACT
131 TAAGTTAACACAAATACTACCATATATAAACAAATTATTACTAGTACACGTTTACT
2931421 ATATTTGAGGCTTTTCCCGACATGCAGACATATGCATTAAAACTTCAAATGATATTCCTAGAGCT
1 ATATTTGAGGCTTTTCCCGACATGCAGACATAT-CATTAAAACTTCAAATGATATTCCTAGAGCT
2931486 ATTTCCTGGAAGAGAAACGACGGTTGTTGATTTGGGAAGAGTTACTACGGTATACGACAATAAAT
65 ATTTCCTGGAAGAGAAACGACGGTTGTTGATTT-GG--GAGTTACTACGGTATACGACAATAAAT
2931551 GATGTAAGTTAACACAAATACTACCATATATAAACAAATTATTACTAGTACACGTTTA
127 GATGTAAGTTAACACAAATACTACCATATATAAACAAATTATTACTAGTACACGTTTA
2931609 ACTTTGTTTG
Statistics
Matches: 184, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
186 33 0.18
187 64 0.35
188 2 0.01
190 85 0.46
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (186 bp):
ATATTTGAGGCTTTTCCCGACATGCAGACATATCATTAAAACTTCAAATGATATTCCTAGAGCTA
TTTCCTGGAAGAGAAACGACGGTTGTTGATTTGGGAGTTACTACGGTATACGACAATAAATGATG
TAAGTTAACACAAATACTACCATATATAAACAAATTATTACTAGTACACGTTTACT
Found at i:2932203 original size:19 final size:20
Alignment explanation
Indices: 2932173--2932215 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2932163 AATAGTTTCT
2932173 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
* *
2932193 GAAACTT-AAATCGTAACGC
1 GAAACTTAAAATCGCAACAC
2932212 GAAA
1 GAAA
2932216 ATGACTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:2932232 original size:20 final size:20
Alignment explanation
Indices: 2932202--2932270 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
2932192 CGAAACTTAA
*
2932202 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
2932222 ATCACAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
2932242 ATCGCAACGC-AAATTTGACT
1 ATCGCAACGCGAAA-ATGACT
2932262 ATCGCAACG
1 ATCGCAACG
2932271 GAATAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2932301 original size:33 final size:35
Alignment explanation
Indices: 2932262--2932342 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 35
2932252 AAATTTGACT
*
2932262 ATCGCAACG-GAATAATCGCAATGC-GAAATAAAA
1 ATCGCAACGCGAATAATCGCAATGCAAAAATAAAA
* *
2932295 ATCGCAACGTGAA-AATCGCAATGCAAAAATGAAA
1 ATCGCAACGCGAATAATCGCAATGCAAAAATAAAA
2932329 ATCGCAACGCGAAT
1 ATCGCAACGCGAAT
2932343 TTAGTTTCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 20 0.48
34 22 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.15
Consensus pattern (35 bp):
ATCGCAACGCGAATAATCGCAATGCAAAAATAAAA
Found at i:2932379 original size:19 final size:19
Alignment explanation
Indices: 2932346--2932382 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2932336 CGCGAATTTA
2932346 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
2932365 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
2932383 TATTTTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:2932429 original size:20 final size:20
Alignment explanation
Indices: 2932404--2932452 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2932394 GCGATTATCC
2932404 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
2932424 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
2932444 CGTTGCGAT
1 CGTTGCGAT
2932453 TTAAGTTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2932477 original size:20 final size:19
Alignment explanation
Indices: 2932341--2932481 Score: 73
Period size: 19 Copynumber: 7.6 Consensus size: 19
2932331 CGCAACGCGA
2932341 ATTT-AGTTTCGCGTTGCG
1 ATTTAAGTTTCGCGTTGCG
**
2932359 ATTTTGGTTTCGCGTTGCG
1 ATTTAAGTTTCGCGTTGCG
* * *
2932378 ATTTTTA-TTTTGCATTGCG
1 A-TTTAAGTTTCGCGTTGCG
*
2932397 A-TT-A---TCCCGTTGCG
1 ATTTAAGTTTCGCGTTGCG
* *
2932411 ATAGTCAA-ATTCGCGTTGCG
1 AT--TTAAGTTTCGCGTTGCG
* * *
2932431 ATAGTCATTTTCGCGTTGCG
1 AT-TTAAGTTTCGCGTTGCG
*
2932451 ATTTAAGTTTCGTGTTGCG
1 ATTTAAGTTTCGCGTTGCG
2932470 ACTTTAAGTTTC
1 A-TTTAAGTTTC
2932482 AGAAACTATT
Statistics
Matches: 95, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
14 8 0.08
16 1 0.01
17 3 0.03
18 5 0.05
19 40 0.42
20 38 0.40
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.44
Consensus pattern (19 bp):
ATTTAAGTTTCGCGTTGCG
Found at i:2933056 original size:42 final size:42
Alignment explanation
Indices: 2932964--2933086 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2932954 GCCCGACTCA
** * *
2932964 CCTGTCATCGTTCAAGAGGTCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCCCTCAAGAGGTCTCTCCCACCGTTCAAGAGGCC
*
2933006 CCTATCATCCCTCAAGA-GTCTCATCCCACCGTTCAAGAGGCC
1 CCTGTCATCCCTCAAGAGGTCTC-TCCCACCGTTCAAGAGGCC
** ** * * *
2933048 TTTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTGTCATCCCTCAAGAGGTCTCTCCCACCGTTCAAGAG
2933087 CCCGATTCAT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
41 5 0.08
42 57 0.86
43 4 0.06
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (42 bp):
CCTGTCATCCCTCAAGAGGTCTCTCCCACCGTTCAAGAGGCC
Found at i:2934485 original size:27 final size:27
Alignment explanation
Indices: 2934455--2934616 Score: 108
Period size: 27 Copynumber: 5.3 Consensus size: 27
2934445 TATGTTTTGC
2934455 TTGTTTAATTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATTTGTAAAAGTTGAT
* * *
2934482 TTGTTTAATTGATGTGTAAATAATTCTTATTTGT
1 TTGTTTAATTGATTTGT-AA-AAGT-TGA----T
2934516 GCTTGTTTAATTGATTTGTAAAAGTTGAT
1 --TTGTTTAATTGATTTGTAAAAGTTGAT
* * *
2934545 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGT
1 TTGTTTAATTGATTTGT--A-AA-----AGTTG-AT
2934581 TTGTTTAATTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATTTGTAAAAGTTGAT
2934608 TTGTTTAAT
1 TTGTTTAAT
2934617 GTAAATAATT
Statistics
Matches: 105, Mismatches: 12, Indels: 36
0.69 0.08 0.24
Matches are distributed among these distances:
27 42 0.40
28 6 0.06
29 5 0.05
30 4 0.04
33 4 0.04
34 5 0.05
35 6 0.06
36 33 0.31
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (27 bp):
TTGTTTAATTGATTTGTAAAAGTTGAT
Found at i:2934522 original size:36 final size:35
Alignment explanation
Indices: 2934482--2934600 Score: 128
Period size: 36 Copynumber: 3.6 Consensus size: 35
2934472 AAAAGTTGAT
2934482 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
* * *
2934517 CTTGTTTAATTGATTTGT-AA-AAGT-TGA----T-
1 -TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
2934545 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
*
2934580 TTTGTTTAATTGATTTGTAAA
1 -TTGTTTAATTGATGTGTAAA
2934601 AGTTGATTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
27 16 0.24
28 2 0.03
29 4 0.06
30 2 0.03
33 2 0.03
34 4 0.06
35 2 0.03
36 35 0.52
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.54
Consensus pattern (35 bp):
TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
Found at i:2934530 original size:63 final size:63
Alignment explanation
Indices: 2934452--2934673 Score: 348
Period size: 63 Copynumber: 3.6 Consensus size: 63
2934442 TAGTATGTTT
2934452 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
2934515 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
*
2934578 TGTTTGTTTAATTGATTTGTAAAAGTTGATTTGTTT-A---A--TGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
*
2934635 TGCTTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TGCTTGTTTAATTGATT----TGTAAAAGTTGATTTGTT
2934674 GATTTCAATC
Statistics
Matches: 152, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
57 34 0.22
59 1 0.01
61 18 0.12
62 1 0.01
63 98 0.64
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (63 bp):
TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
Found at i:2934591 original size:126 final size:125
Alignment explanation
Indices: 2934383--2934673 Score: 349
Period size: 126 Copynumber: 2.3 Consensus size: 125
2934373 ACTTTTTTGA
** *
2934383 TTGTTTAATTGATTCATAAAAGTCTGATTTGTTTAATTGATGAGGAAAATAAGAATTATTAGTAT
1 TTGTTTAATTGATTTGTAAAAGT-TGATTTGTTTAATTGATGAGGAAAAT-A-AATTACTA-TAT
*
2934448 GTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATT
62 GTTGTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTT-A---A--TGTAAATAATTCTTATT
2934513 TGTGC
121 TGTGC
* *
2934518 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATG-TGTAAAT-AATT-CT-TAT-TTG
1 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAAATAAATTACTATATGTTG
*
2934578 TGTTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATGTAAATAATTCTTATTTGTGC
66 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATGTAAATAATTCTTATTTGTGC
*
2934638 TTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TTGTTTAATTGATT----TGTAAAAGTTGATTTGTT
2934674 GATTTCAATC
Statistics
Matches: 144, Mismatches: 8, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
120 35 0.24
122 1 0.01
124 18 0.12
125 1 0.01
126 37 0.26
127 3 0.02
129 1 0.01
130 4 0.03
133 5 0.03
134 18 0.12
135 21 0.15
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.51
Consensus pattern (125 bp):
TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAAATAAATTACTATATGTTG
TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATGTAAATAATTCTTATTTGTGC
Found at i:2934833 original size:20 final size:20
Alignment explanation
Indices: 2934809--2934953 Score: 146
Period size: 20 Copynumber: 6.8 Consensus size: 20
2934799 TTGCGATTTT
*
2934809 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
2934829 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2934849 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
2934869 CGTTGCGATAATCAAATTTATAG
1 CGTTGCGATAGTCAAA--T-TCG
**
2934892 CAATGCGATAGTCAAATATTCG
1 CGTTGCGATAGTC-AA-ATTCG
2934914 CGATAGTGCGATAGTCAAATTCG
1 CG-T--TGCGATAGTCAAATTCG
*
2934937 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2934954 GAATGTGTAA
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
20 66 0.63
22 5 0.05
23 19 0.18
24 4 0.04
25 11 0.10
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2934906 original size:23 final size:25
Alignment explanation
Indices: 2934872--2934934 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
2934862 AAATTCACGT
*
2934872 TGCGATAATCAAATTTATAGC-A-A-
1 TGCGATAGTCAAATTT-TAGCGATAG
* *
2934895 TGCGATAGTCAAATATTCGCGATAG
1 TGCGATAGTCAAATTTTAGCGATAG
2934920 TGCGATAGTCAAATT
1 TGCGATAGTCAAATT
2934935 CGCGTTGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.09
23 15 0.45
24 1 0.03
25 14 0.42
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (25 bp):
TGCGATAGTCAAATTTTAGCGATAG
Found at i:2935176 original size:140 final size:140
Alignment explanation
Indices: 2934924--2935326 Score: 743
Period size: 140 Copynumber: 2.9 Consensus size: 140
2934914 CGATAGTGCG
2934924 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
* *
2934989 TAGCAATGTTTAAACTCAAGTTACTAATACATGGCTAACTGAAAATGTTAAAAGTTTACAAATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACAAATAA
2935054 AATACACATA
131 AATACACATA
* *
2935064 ATAGTCAAATTCGCGTTGCGATATTCAAGTGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
2935129 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACAAATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACAAATAA
2935194 AATACACATA
131 AATACACATA
* * *
2935204 ATAGTCAAATTCACGTTGTGATATTCAAATGAATGTGTAATAAATGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
2935269 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTA
2935327 GTTTGCATTT
Statistics
Matches: 254, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 254 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACAAATAA
AATACACATA
Found at i:2937445 original size:14 final size:14
Alignment explanation
Indices: 2937426--2937452 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2937416 TCCCGTGGAA
2937426 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
2937440 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
2937453 TTTCTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:2937662 original size:30 final size:30
Alignment explanation
Indices: 2937626--2937686 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2937616 ACACGCATGG
2937626 TCTGTTTCTTCTTATGAAACATCATCAAAA
1 TCTGTTTCTTCTTATGAAACATCATCAAAA
2937656 TCTGTTTCTTCTTATGAAACATCATCAAAA
1 TCTGTTTCTTCTTATGAAACATCATCAAAA
2937686 T
1 T
2937687 TCGAGTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (30 bp):
TCTGTTTCTTCTTATGAAACATCATCAAAA
Found at i:2937746 original size:24 final size:24
Alignment explanation
Indices: 2937679--2937738 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2937669 ATGAAACATC
2937679 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
2937703 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
2937727 ATCAAATTTCGA
1 ATCAAAATTCGA
2937739 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:2938573 original size:20 final size:20
Alignment explanation
Indices: 2938548--2938658 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
2938538 TTGAAATTCA
*
2938548 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
2938568 GCGTTGCGATAGTCAGAATT
1 GCGTTGCGATAGTCAGAATC
**
2938588 GCGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
*
2938609 GTGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* *
2938629 GTGTTGCGATAGTCATAATC
1 GCGTTGCGATAGTCAGAATC
2938649 GCGTTGCGAT
1 GCGTTGCGAT
2938659 TTACATATTC
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:2938665 original size:20 final size:20
Alignment explanation
Indices: 2938642--2938680 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2938632 TTGCGATAGT
*
2938642 CATAATCGCGTTGCGATTTA
1 CATAATCGCATTGCGATTTA
*
2938662 CATATTCGCATTGCGATTT
1 CATAATCGCATTGCGATTT
2938681 TCTAAAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
CATAATCGCATTGCGATTTA
Found at i:2938690 original size:61 final size:61
Alignment explanation
Indices: 2938551--2938678 Score: 143
Period size: 61 Copynumber: 2.1 Consensus size: 61
2938541 AAATTCAGCG
* * * ** **
2938551 TTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATTGCGTTGCGATTATGTATTATCGTG
1 TTGCGATAGTCAAAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTACATATTATCGCA
* * *
2938612 TTGCGATAGTCAGAATCGTGTTGCGATAGTCATAATCGCGTTGCGATTTACATA-T-TCGCA
1 TTGCGATAGTCAAAATCGCGTTGCGATAGTCAGAATCGCGTTGCGA-TTACATATTATCGCA
2938672 TTGCGAT
1 TTGCGAT
2938679 TTTCTAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 10 0.17
61 43 0.74
62 5 0.09
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (61 bp):
TTGCGATAGTCAAAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTACATATTATCGCA
Found at i:2938748 original size:20 final size:20
Alignment explanation
Indices: 2938725--2938779 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2938715 GCGATAGTCA
2938725 AAATCGCGTTGCGA-ATCTGG
1 AAATCGCGTTGCGATAT-TGG
* **
2938745 AAATTGATTTGCGATATTGG
1 AAATCGCGTTGCGATATTGG
*
2938765 AGATCGCGTTGCGAT
1 AAATCGCGTTGCGAT
2938780 TTAGAGATCG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (20 bp):
AAATCGCGTTGCGATATTGG
Found at i:2938788 original size:19 final size:19
Alignment explanation
Indices: 2938753--2938800 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2938743 GGAAATTGAT
* *
2938753 TTGCGATATTGGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
2938773 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
*
2938792 TTGCTATTT
1 TTGCGATTT
2938801 TGTTGGTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.38
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:2945863 original size:17 final size:14
Alignment explanation
Indices: 2945828--2945856 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2945818 AAGAATTAGA
2945828 AAAAGAAGACTAAG
1 AAAAGAAGACTAAG
2945842 AAAAGAAGACTAAG
1 AAAAGAAGACTAAG
2945856 A
1 A
2945857 GGCAAAGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (14 bp):
AAAAGAAGACTAAG
Found at i:2946928 original size:18 final size:18
Alignment explanation
Indices: 2946888--2946927 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2946878 GAGATAGTCA
*
2946888 CTTTTAGTTTCTGCCTCT
1 CTTTTAGTTCCTGCCTCT
*
2946906 CTTTTAGTTCCTTCCTCT
1 CTTTTAGTTCCTGCCTCT
2946924 -TTTT
1 CTTTT
2946928 TGCATACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.05, C:0.28, G:0.07, T:0.60
Consensus pattern (18 bp):
CTTTTAGTTCCTGCCTCT
Found at i:2955231 original size:16 final size:18
Alignment explanation
Indices: 2955204--2955241 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2955194 TATGAGATTA
2955204 AAAAAATCTAAGAAA-TT
1 AAAAAATCTAAGAAACTT
2955221 AAAAAAT-TAAGAAACTT
1 AAAAAATCTAAGAAACTT
2955238 AAAA
1 AAAA
2955242 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAAATCTAAGAAACTT
Found at i:2963734 original size:21 final size:21
Alignment explanation
Indices: 2963710--2963755 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2963700 GGTAACCAAC
2963710 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
** *
2963731 TTTGGTAAATGTTTTTTAAAG
1 TTTGAAAAATGTTTTTCAAAG
2963752 TTTG
1 TTTG
2963756 GTAAAGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:2963756 original size:21 final size:21
Alignment explanation
Indices: 2963716--2963764 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2963706 CAACTTTGAA
2963716 AAATGTTTTTCAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
*
2963737 AAATGTTTTTTAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
2963758 AAA-GTTT
1 AAATGTTT
2963765 GGTAGATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (21 bp):
AAATGTTTTTCAAAGTTTGGT
Found at i:2963760 original size:10 final size:10
Alignment explanation
Indices: 2963727--2963768 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
2963717 AATGTTTTTC
2963727 AAAGTTTGGT
1 AAAGTTTGGT
**
2963737 AAATGTTTTTT
1 AAA-GTTTGGT
2963748 AAAGTTTGGT
1 AAAGTTTGGT
2963758 AAAGTTTGGT
1 AAAGTTTGGT
2963768 A
1 A
2963769 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (10 bp):
AAAGTTTGGT
Found at i:2964376 original size:23 final size:23
Alignment explanation
Indices: 2964334--2964377 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2964324 AAAAGACGTT
**
2964334 TAAATATTTATTATTTTTTAATA
1 TAAATATTTATTATCCTTTAATA
2964357 TAAATATTTATTATCCTTTAA
1 TAAATATTTATTATCCTTTAA
2964378 GTTGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAATATTTATTATCCTTTAATA
Found at i:2968730 original size:64 final size:64
Alignment explanation
Indices: 2968645--2968793 Score: 264
Period size: 63 Copynumber: 2.3 Consensus size: 64
2968635 AAAAAAACGC
* *
2968645 TCTACTGGTTTCGTTATTATTTTTTTAATATTTTCAATAAAAAATTATCTAAAACATTACTTTT
1 TCTACTGATTTTGTTATTATTTTTTTAATATTTTCAATAAAAAATTATCTAAAACATTACTTTT
2968709 TCTACTGATTTTGTTATTA-TTTTTTAATATTTTCAATAAAAAATTATCTAAAACATTACTTTT
1 TCTACTGATTTTGTTATTATTTTTTTAATATTTTCAATAAAAAATTATCTAAAACATTACTTTT
*
2968772 CCTACTGATTTTGTTATTATTT
1 TCTACTGATTTTGTTATTATTT
2968794 GACGCTTTAC
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
63 62 0.77
64 19 0.23
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (64 bp):
TCTACTGATTTTGTTATTATTTTTTTAATATTTTCAATAAAAAATTATCTAAAACATTACTTTT
Found at i:2973737 original size:215 final size:213
Alignment explanation
Indices: 2973335--2973763 Score: 808
Period size: 215 Copynumber: 2.0 Consensus size: 213
2973325 ATTGATCTTC
2973335 TCTGAGTAATATCGAAGATCATAAAATATGTGTTGAACATTCCTGGACTGAATTTTTTCGACTTC
1 TCTGAGTAATATCGAAGATCATAAAATATGTGTTGAACATTCCTGGACTGAATTTTTTCGACTTC
2973400 CTTTGATCTGTATTGCATTGTGGGGGACTTGTAATAATGAAGTTGTATTTTGTCACTACATTAAA
66 CTTTGATCTGTATTGCATTGTGGGGGACTTGTAATAATGAAGTTGTATTTTGTCACTACATTAAA
2973465 CAATTACAATTGTCAATCATGATCTCTAGAAACATCCCACTCCATGGAAATGATCGCCGCTGCTA
131 CAATTACAATTGTCAATCATGATCTCTAGAAACATCCCACTCCATGGAAATGATCGCCGCTGC--
2973530 ATAATTTGCATGCATCTATCG
194 -TAATTTGCATGCATCTATCG
2973551 TCTGAGTAATATCGAAGATCATAAAATATGTTGTTGAACATTCCTGGACTGAA-TTTTTCGACTT
1 TCTGAGTAATATCGAAGATCATAAAATATG-TGTTGAACATTCCTGGACTGAATTTTTTCGACTT
2973615 CCTTTGATCTGTATTGCATTGTGGGGGACTTGTAATAATG-AGTTGTATTTTGTCACTACATTAA
65 CCTTTGATCTGTATTGCATTGTGGGGGACTTGTAATAATGAAGTTGTATTTTGTCACTACATTAA
2973679 ACAATTACAATTGTCAATCATGATCTCTAGAAACATCCCACTCCATGGAAATGATCGCCGCTGCT
130 ACAATTACAATTGTCAATCATGATCTCTAGAAACATCCCACTCCATGGAAATGATCGCCGCTGCT
2973744 AATTTGCATGCATCTATCG
195 AATTTGCATGCATCTATCG
2973763 T
1 T
2973764 AAGGATGTGA
Statistics
Matches: 212, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
212 21 0.10
215 88 0.42
216 81 0.38
217 22 0.10
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (213 bp):
TCTGAGTAATATCGAAGATCATAAAATATGTGTTGAACATTCCTGGACTGAATTTTTTCGACTTC
CTTTGATCTGTATTGCATTGTGGGGGACTTGTAATAATGAAGTTGTATTTTGTCACTACATTAAA
CAATTACAATTGTCAATCATGATCTCTAGAAACATCCCACTCCATGGAAATGATCGCCGCTGCTA
ATTTGCATGCATCTATCG
Found at i:2974766 original size:18 final size:19
Alignment explanation
Indices: 2974740--2974784 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2974730 CCCTTAAAAA
2974740 TTTTAAA-TTAATATATAT
1 TTTTAAATTTAATATATAT
* **
2974758 TTTTTAATTTTTTATATAT
1 TTTTAAATTTAATATATAT
2974777 TTTTAAAT
1 TTTTAAAT
2974785 GATAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAAATTTAATATATAT
Found at i:2974819 original size:28 final size:25
Alignment explanation
Indices: 2974763--2974819 Score: 60
Period size: 28 Copynumber: 2.2 Consensus size: 25
2974753 TATATTTTTT
** *
2974763 AATTTTTTATATATTTTTAAATGAT
1 AATTTTTTATATATTTTTAAAAAAA
2974788 AATTTATTTATATATTTTTTTAAAAAAA
1 AATTT-TTTATATA--TTTTTAAAAAAA
2974816 AATT
1 AATT
2974820 AAAAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 8 0.31
28 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTTTTTATATATTTTTAAAAAAA
Found at i:2975201 original size:21 final size:21
Alignment explanation
Indices: 2975177--2975224 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2975167 ACTATCGCAA
*
2975177 TGCGATAGTCCAAATTCG-CGT
1 TGCGATAGCCCAAATT-GACGT
*
2975198 TGCGATAGCCCGAATTGACGT
1 TGCGATAGCCCAAATTGACGT
2975219 TGCGAT
1 TGCGAT
2975225 TGACTGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
TGCGATAGCCCAAATTGACGT
Found at i:2975242 original size:20 final size:20
Alignment explanation
Indices: 2975217--2975283 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
2975207 CCGAATTGAC
*
2975217 GTTGCGATTGACTGTTCACT
1 GTTGCGATAGACTGTTCACT
*
2975237 GTTGCGATAACACTGTTCAC-
1 GTTGCGAT-AGACTGTTCACT
*
2975257 ATTGCGATAGCACTGTTCACT
1 GTTGCGATAG-ACTGTTCACT
2975278 -TTGCGA
1 GTTGCGA
2975284 ATTTGCGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 30 0.75
21 9 0.22
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGACTGTTCACT
Found at i:2975549 original size:22 final size:22
Alignment explanation
Indices: 2975511--2975570 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
2975501 ACACTGAAAG
*
2975511 TAAAAAATT-TACAAAAACAAGA
1 TAAAAATTTGTAC-AAAACAAGA
*
2975533 TAAAAATTTGTACAAAATAAGA
1 TAAAAATTTGTACAAAACAAGA
*
2975555 TAAAAATTTGAACAAA
1 TAAAAATTTGTACAAA
2975571 TTTTGTAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 31 0.91
23 3 0.09
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (22 bp):
TAAAAATTTGTACAAAACAAGA
Found at i:2975859 original size:16 final size:17
Alignment explanation
Indices: 2975830--2975881 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
2975820 ATCATAAATA
*
2975830 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
2975847 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
2975862 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
2975880 AT
1 AT
2975882 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:2976177 original size:20 final size:19
Alignment explanation
Indices: 2976154--2976199 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2976144 GAAAACTTAT
* *
2976154 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
2976174 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
2976193 TTGCGAT
1 TTGCGAT
2976200 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:2976189 original size:19 final size:19
Alignment explanation
Indices: 2976165--2976201 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2976155 TGCGATACTG
*
2976165 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2976184 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2976202 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2990129 original size:2 final size:2
Alignment explanation
Indices: 2990122--2990158 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2990112 TGACTCGATC
*
2990122 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2990159 TATTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2993394 original size:71 final size:71
Alignment explanation
Indices: 2993303--2993442 Score: 271
Period size: 71 Copynumber: 2.0 Consensus size: 71
2993293 CATATCTTCC
2993303 TTTGACGTGAGCCTTGTGATGCATATATCATTGTTATATTCATATAAATTGTAAATTGTATACTC
1 TTTGACGTGAGCCTTGTGATGCATATATCATTGTTATATTCATATAAATTGTAAATTGTATACTC
2993368 TATAAT
66 TATAAT
*
2993374 TTTGACGTGAGCCTTGTGATGCATATATCATTGTTATATTCATATAAATTGTAAATTGTATACTT
1 TTTGACGTGAGCCTTGTGATGCATATATCATTGTTATATTCATATAAATTGTAAATTGTATACTC
2993439 TATA
66 TATA
2993443 TTCATGTGAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (71 bp):
TTTGACGTGAGCCTTGTGATGCATATATCATTGTTATATTCATATAAATTGTAAATTGTATACTC
TATAAT
Found at i:2994087 original size:47 final size:48
Alignment explanation
Indices: 2994031--2994123 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 48
2994021 AGTTTTATGA
* *
2994031 TAAAAGGTGACAATGTTCGAATTTTTATGTTTAT-TAGAGGTATATAT
1 TAAAAGGTGACAATGTTCGAATTATTATATTTATCTAGAGGTATATAT
*
2994078 TAAAAGGTGACAATGTTCGAATTATTATATTTTTCTAGAGGTATAT
1 TAAAAGGTGACAATGTTCGAATTATTATATTTATCTAGAGGTATAT
2994124 GTGAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 31 0.74
48 11 0.26
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (48 bp):
TAAAAGGTGACAATGTTCGAATTATTATATTTATCTAGAGGTATATAT
Found at i:3006626 original size:25 final size:25
Alignment explanation
Indices: 3006594--3006643 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3006584 CTATAAATGC
3006594 CCTTGTTCTAATACCTATTTTGAGA
1 CCTTGTTCTAATACCTATTTTGAGA
3006619 CCTTGTTCTAATACCTATTTTGAGA
1 CCTTGTTCTAATACCTATTTTGAGA
3006644 GAAGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (25 bp):
CCTTGTTCTAATACCTATTTTGAGA
Found at i:3010953 original size:79 final size:80
Alignment explanation
Indices: 3010821--3010986 Score: 217
Period size: 79 Copynumber: 2.1 Consensus size: 80
3010811 ATACAGCTAA
* * * **
3010821 ATTCATGTATTATACAACCTAGATTAATGCTTTAACTCCTGCCATTAATGTGGCTCATGTATTCA
1 ATTCATGCATTATACAACCTAGACTAATGCCTTAACTCCAACCATTAATGTGGCTCATGTATTCA
*
3010886 CACTTTACTGCATGG
66 CACTTCACTGCATGG
** * * *
3010901 -TTCATGCATTATACAGTCTAGACTAATGCCTTAATTCCAACCATTACTGTGGCTCATGTGTTCA
1 ATTCATGCATTATACAACCTAGACTAATGCCTTAACTCCAACCATTAATGTGGCTCATGTATTCA
*
3010965 CACTTCATTGCATGG
66 CACTTCACTGCATGG
3010980 ATTCATG
1 ATTCATG
3010987 GATTGTACGG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 67 0.92
80 6 0.08
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (80 bp):
ATTCATGCATTATACAACCTAGACTAATGCCTTAACTCCAACCATTAATGTGGCTCATGTATTCA
CACTTCACTGCATGG
Found at i:3011970 original size:31 final size:33
Alignment explanation
Indices: 3011914--3011988 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 33
3011904 CATGTGTCAT
* * *
3011914 AATAACAAAATATATTTTTAAAAATTTAGAT-AAG
1 AATAA-AATATATATTTTT-AAAATTAAAATCAAG
3011948 AATAAAATATATATTTTT-AAATTAAAATCAAG
1 AATAAAATATATATTTTTAAAATTAAAATCAAG
3011980 -ATAAAATAT
1 AATAAAATAT
3011989 TTTTAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 17 0.46
32 3 0.08
33 12 0.32
34 5 0.14
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (33 bp):
AATAAAATATATATTTTTAAAATTAAAATCAAG
Found at i:3012010 original size:27 final size:26
Alignment explanation
Indices: 3011958--3012083 Score: 100
Period size: 27 Copynumber: 4.8 Consensus size: 26
3011948 AATAAAATAT
* * *
3011958 ATATTTTTAAATTAAAATCAAGATAAA
1 ATATTTTTAAATT-AAGTTAATATAAA
3011985 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAGTTAAT-ATAAA
3012012 AT-TTATTT-AA-TAAGTTAATATAAAA
1 ATATT-TTTAAATTAAGTTAATAT-AAA
3012037 ATATTTTTAAAAGTTAA--TATATATAAA
1 ATATTTTT-AAA-TTAAGTTA-ATATAAA
* * *
3012064 ATATTATGAAGTTAAGTTAA
1 ATATTTTTAAATTAAGTTAA
3012084 ATATTTATAT
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
24 2 0.02
25 21 0.26
26 14 0.17
27 38 0.46
28 4 0.05
29 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.42
Consensus pattern (26 bp):
ATATTTTTAAATTAAGTTAATATAAA
Found at i:3012050 original size:24 final size:26
Alignment explanation
Indices: 3011980--3012068 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 26
3011970 TAAAATCAAG
3011980 ATAAAATATTTTTAAATTAAGTTAATA-
1 ATAAAATATTTTT-AA-TAAGTTAATAT
3012007 ATAAAAT-TTATTTAATAAGTTAATAT
1 ATAAAATATT-TTTAATAAGTTAATAT
3012033 A-AAAATATTTTTAA-AAGTTAATATAT
1 ATAAAATATTTTTAATAAGTT-A-ATAT
3012059 ATAAAATATT
1 ATAAAATATT
3012069 ATGAAGTTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
24 5 0.09
25 21 0.38
26 12 0.21
27 18 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (26 bp):
ATAAAATATTTTTAATAAGTTAATAT
Found at i:3016873 original size:64 final size:64
Alignment explanation
Indices: 3016755--3016877 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 64
3016745 GCACAGGTAG
** * *
3016755 TGCATCGATGCACTCTTTTAAAATAAAAACATCGAATGCAATTAGTGCATCGATGCATAAGGCA
1 TGCATCGATGCACTCCATTAAAATAAAAACATCGAATACAATTAGTGCACCGATGCATAAGGCA
*
3016819 TGCATCGATGCA-TCCCATTAATAAT-AAAACATCGAATACATTTTA-TGCACCGATGCATA
1 TGCATCGATGCACT-CCATTAA-AATAAAAACATCGAATACA-ATTAGTGCACCGATGCATA
3016878 CTTTCATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
63 1 0.02
64 44 0.86
65 6 0.12
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCACTCCATTAAAATAAAAACATCGAATACAATTAGTGCACCGATGCATAAGGCA
Found at i:3029332 original size:22 final size:22
Alignment explanation
Indices: 3029282--3029341 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
3029272 ATGGAGAAAA
3029282 ATAT-AAAT-TATAAAAATATT
1 ATATCAAATATATAAAAATATT
*
3029302 ATATCAAATATTTAAAAATATT
1 ATATCAAATATATAAAAATATT
* *
3029324 -TAATGAAATCTATAAAAA
1 AT-ATCAAATATATAAAAA
3029342 ACCATATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 24 0.73
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATCAAATATATAAAAATATT
Found at i:3029663 original size:16 final size:16
Alignment explanation
Indices: 3029642--3029681 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3029632 TTACTAATAA
3029642 AGTATCATTTGTTATC
1 AGTATCATTTGTTATC
3029658 AGTATCATTTGTTATC
1 AGTATCATTTGTTATC
*
3029674 AGTGTCAT
1 AGTATCAT
3029682 GCCCTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (16 bp):
AGTATCATTTGTTATC
Found at i:3036135 original size:26 final size:28
Alignment explanation
Indices: 3036104--3036160 Score: 100
Period size: 26 Copynumber: 2.1 Consensus size: 28
3036094 AAAATCGAAG
3036104 AAACCTGTAAAGAA-TGATAC-TAAGAT
1 AAACCTGTAAAGAAGTGATACATAAGAT
3036130 AAACCTGTAAAGAAGTGATACATAAGAT
1 AAACCTGTAAAGAAGTGATACATAAGAT
3036158 AAA
1 AAA
3036161 TATATGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 14 0.48
27 6 0.21
28 9 0.31
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.21
Consensus pattern (28 bp):
AAACCTGTAAAGAAGTGATACATAAGAT
Found at i:3051737 original size:19 final size:18
Alignment explanation
Indices: 3051713--3051839 Score: 74
Period size: 18 Copynumber: 7.1 Consensus size: 18
3051703 ATTTTGCTTG
3051713 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAA-AAAAGAGAA
*
3051732 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAAAGAGAA
* *
3051750 AA-AATAAAAAATGATGGAA
1 AAGAAGAAAAAAAGA--GAA
3051769 AA-AACGAAAAGAAA-A-AA
1 AAGAA-GAAAA-AAAGAGAA
3051786 AAGAAGAGAAAAAATG-GAA
1 AAGAAGA-AAAAAA-GAGAA
3051805 AATG--GAAGAAAAAGAGAA
1 AA-GAAGAA-AAAAAGAGAA
*
3051823 AA-ATG-AAAAAAGAGAA
1 AAGAAGAAAAAAAGAGAA
3051839 A
1 A
3051840 TAAAAGGAGG
Statistics
Matches: 90, Mismatches: 4, Indels: 31
0.72 0.03 0.25
Matches are distributed among these distances:
16 11 0.12
17 23 0.26
18 28 0.31
19 20 0.22
20 6 0.07
21 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.06
Consensus pattern (18 bp):
AAGAAGAAAAAAAGAGAA
Found at i:3051758 original size:17 final size:18
Alignment explanation
Indices: 3051713--3051839 Score: 74
Period size: 19 Copynumber: 7.1 Consensus size: 18
3051703 ATTTTGCTTG
*
3051713 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAA-AAATGAGAA
3051732 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAATGAGAA
*
3051750 AA-AATAAAAAATGATGGAA
1 AAGAAGAAAAAATGA--GAA
*
3051769 AA-AACGAAAAGAA--AAAA
1 AAGAA-GAAAA-AATGAGAA
3051786 AAGAAGAGAAAAAATG-GAA
1 AAG-A-AGAAAAAATGAGAA
3051805 AATGGAAG-AAAAA-GAGAA
1 AA--GAAGAAAAAATGAGAA
*
3051823 AA-ATGAAAAAA-GAGAA
1 AAGAAGAAAAAATGAGAA
3051839 A
1 A
3051840 TAAAAGGAGG
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
15 2 0.02
16 11 0.12
17 16 0.18
18 22 0.25
19 29 0.33
20 6 0.07
21 3 0.03
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.06
Consensus pattern (18 bp):
AAGAAGAAAAAATGAGAA
Found at i:3051760 original size:27 final size:27
Alignment explanation
Indices: 3051730--3051806 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
3051720 AATAAAAGAG
3051730 AAAAGA-AGAAAAAATGAGAAAAAATAA
1 AAAAGAGAGAAAAAATGAGAAAAAA-AA
* *
3051757 AAAATGATG-GAAAAAACGA-AAAGAAAA
1 AAAA-GA-GAGAAAAAATGAGAAAAAAAA
3051784 AAAAGAAGAGAAAAAATG-GAAAA
1 AAAAG-AGAGAAAAAATGAGAAAA
3051807 TGGAAGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
26 2 0.05
27 22 0.55
28 7 0.17
29 9 0.22
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.06
Consensus pattern (27 bp):
AAAAGAGAGAAAAAATGAGAAAAAAAA
Found at i:3051824 original size:46 final size:46
Alignment explanation
Indices: 3051723--3051838 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 46
3051713 AAGAAGAAAT
* * *
3051723 AAAAGAGAAAAGAAGAAAAA-ATGAGAAAAAATAAAAAATGATGGA
1 AAAAGAGAAAAGAAAAAAAAGAAGAGAAAAAATAAAAAATGATAGA
**
3051768 AAAA-ACGAAAAGAAAAAAAAGAAGAGAAAAAATGGAAAATGGA-AGA
1 AAAAGA-GAAAAGAAAAAAAAGAAGAGAAAAAATAAAAAAT-GATAGA
*
3051814 AAAAGAGAAAAATGAAAAAAGAGAA
1 AAAAGAG-AAAA-GAAAAAAAAGAA
3051839 ATAAAAGGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
44 1 0.02
45 17 0.29
46 23 0.39
47 7 0.12
48 11 0.19
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (46 bp):
AAAAGAGAAAAGAAAAAAAAGAAGAGAAAAAATAAAAAATGATAGA
Found at i:3053039 original size:51 final size:51
Alignment explanation
Indices: 3052974--3053438 Score: 599
Period size: 51 Copynumber: 9.0 Consensus size: 51
3052964 AAGCAAATTC
* *
3052974 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGTCAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
3053025 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
3053076 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* *
3053127 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* *
3053178 GTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * **
3053229 GTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCC
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * * *
3053280 GTTTTGTTGAAGATTTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACAC
1 G-TTCGTTGAAGA--TT-GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACAA
* * * * **
3053335 GTTTGTTAAAGACTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCT
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
** * *
3053386 GTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
3053439 CCGTTTTATT
Statistics
Matches: 371, Mismatches: 33, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.00
51 283 0.76
52 10 0.03
54 13 0.04
55 62 0.17
56 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (51 bp):
GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
Found at i:3053418 original size:55 final size:51
Alignment explanation
Indices: 3052978--3053545 Score: 557
Period size: 51 Copynumber: 10.8 Consensus size: 51
3052968 AAATTCGTTC
* * * * *
3052978 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGTCAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAGTTT
* *
3053029 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAGTTT
* *
3053080 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAGTTT
* * *
3053131 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAGTTT
* * *
3053182 GTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAGTTT
* * * *
3053233 ATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAG-TTT
* * * * *
3053285 GTTGAAGATTTTCGAGTTCTATACTCCCTGAACGGATAGGGAGC-GAACACGTTT
1 GTTGAAGA--TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCA-GTTT
* * * *
3053339 GTTAAAGACTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAGTTT
* * * * *
3053390 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAG-TTT
* * * * * *
3053446 ATTGAAGATTGTTCGAGTTCTATACTC-CTTGAACGGATAGGGAGCGAACCTGTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTC-TGAATGAATAGGGAGCGGACCAGTTT
* * *
3053501 GTCGAAGATTATTCGAGTCTTATACTC-CTTGAACGAATAGGGAGC
1 GTTGAAG---ATT-GAGTCCTATACTCTC-TGAATGAATAGGGAGC
3053546 AGACACGTTT
Statistics
Matches: 455, Mismatches: 47, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
51 277 0.61
52 13 0.03
54 16 0.04
55 101 0.22
56 47 0.10
58 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCAGTTT
Found at i:3053571 original size:55 final size:55
Alignment explanation
Indices: 3053243--3053609 Score: 217
Period size: 55 Copynumber: 6.7 Consensus size: 55
3053233 ATTGAAGATT
* * * * * **
3053243 GAGTCCTATACT-CTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATT-TTC
1 GAGTCTTATACTCCT-TGAACGAATAGGGAGCAGACACG-TTTGTCCAAGATTGTTC
* * ** *
3053298 GAGT-TCTATACTCCCTGAACGGATAGGGAGC-GAACACGTTTGTTAAAGA---CT-
1 GAGTCT-TATACTCCTTGAACGAATAGGGAGCAG-ACACGTTTGTCCAAGATTGTTC
* * * * ** *
3053349 GAGTCCTATACT-CTCTGAAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCCT-TGAACGAATAGGGAGCAGACAC-GTTTGTCCAAGATTGTTC
* * * * * **
3053404 GAGT-TCTATACT-CTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTCT-TATACTCCT-TGAACGAATAGGGAGCAGACACG-TTTGTCCAAGATTGTTC
* * *
3053460 GAGT-TCTATACTCCTTGAACGGATAGGGAGC-GA-ACCTGTTTGTCGAAGATTATTC
1 GAGTCT-TATACTCCTTGAACGAATAGGGAGCAGACA-C-GTTTGTCCAAGATTGTTC
3053515 GAGTCTTATACTCCTTGAACGAATAGGGAGCAGACACGTTTG-CCAAGGATTGTTC
1 GAGTCTTATACTCCTTGAACGAATAGGGAGCAGACACGTTTGTCCAA-GATTGTTC
* * *
3053570 GAGTCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCGTT
1 GAGTCTTATACTCCTTGAACGAATAGGGAGCAGACACGTT
3053610 ATTTGAAGAT
Statistics
Matches: 259, Mismatches: 32, Indels: 42
0.78 0.10 0.13
Matches are distributed among these distances:
50 2 0.01
51 36 0.14
52 2 0.01
54 15 0.06
55 153 0.59
56 48 0.19
57 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (55 bp):
GAGTCTTATACTCCTTGAACGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
Found at i:3056555 original size:3 final size:3
Alignment explanation
Indices: 3056547--3056576 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3056537 TTAAAACATA
*
3056547 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3056577 GAAGAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3066915 original size:24 final size:23
Alignment explanation
Indices: 3066879--3066951 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
3066869 ATTCATTTGT
*
3066879 ATTCATTTATTGTGTTCGTTTAC
1 ATTCGTTTATTGTGTTCGTTTAC
* *
3066902 ATTCGTTCTTTTGTGTTCCTTTA-
1 ATTCGTT-TATTGTGTTCGTTTAC
*
3066925 AGTTTGTTTATTGTGTTCGTTTAC
1 A-TTCGTTTATTGTGTTCGTTTAC
3066949 ATT
1 ATT
3066952 AATTCGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.14, C:0.12, G:0.15, T:0.59
Consensus pattern (23 bp):
ATTCGTTTATTGTGTTCGTTTAC
Found at i:3068230 original size:4 final size:4
Alignment explanation
Indices: 3068221--3068245 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3068211 ATTAGTAATA
3068221 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
3068246 ATGCATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:3069888 original size:33 final size:33
Alignment explanation
Indices: 3069824--3069888 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
3069814 AATGTCGCCA
** ** *
3069824 CCGCCGCCACCGTCACCTAGTTTTATAACCCCG
1 CCGCCGCCACAATCACAAAGTTATATAACCCCG
*
3069857 CCGCCGCCACAATCACAAAGTTATATGACCCC
1 CCGCCGCCACAATCACAAAGTTATATAACCCC
3069889 TCGTGGAGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.43, G:0.14, T:0.18
Consensus pattern (33 bp):
CCGCCGCCACAATCACAAAGTTATATAACCCCG
Found at i:3073582 original size:46 final size:45
Alignment explanation
Indices: 3073489--3073614 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 45
3073479 GATAAACTGG
* *
3073489 AAAATAAGCTTACGAGCTTATGGAAT-AATGGAAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
* *
3073533 AAAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATATTGGT
3073579 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
3073615 AGATTTTATC
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.31
45 12 0.16
46 40 0.53
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
Found at i:3093177 original size:33 final size:33
Alignment explanation
Indices: 3093132--3093231 Score: 138
Period size: 31 Copynumber: 3.2 Consensus size: 33
3093122 ATAAAGTTTA
*
3093132 CGAT-AATT-AAATACTTAAATACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
* *
3093163 TGATAAATTCAAATACTTAAAAACTTCCAAG-T
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
3093195 CGATAAA-TCAAATACTTAAAAAC-TTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
3093226 CGATAA
1 CGATAA
3093232 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
30 5 0.08
31 26 0.43
32 11 0.18
33 19 0.31
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTTCAAGTT
Found at i:3093249 original size:20 final size:20
Alignment explanation
Indices: 3093224--3093265 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3093214 AAACTTCAAG
*
3093224 TTCGATAATTGAAACAAAGT
1 TTCGATAATTGAAAAAAAGT
3093244 TTCGATAATTGAAAAAAAGT
1 TTCGATAATTGAAAAAAAGT
3093264 TT
1 TT
3093266 AAAATAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (20 bp):
TTCGATAATTGAAAAAAAGT
Done.