Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 50 of 62
Found at i:11384884 original size:16 final size:16
Alignment explanation
Indices: 11384832--11384885 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
11384822 CTGTAAAAGA
*
11384832 ATTATATTAGTAAAAT
1 ATTATAATAGTAAAAT
11384848 ATTA-AATAAAGTAAAA-
1 ATTATAAT--AGTAAAAT
11384864 A-TATAATAGTAAAAT
1 ATTATAATAGTAAAAT
11384879 ATTATAA
1 ATTATAA
11384886 AATATATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 7 0.22
15 5 0.16
16 13 0.41
17 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTATAATAGTAAAAT
Found at i:11385155 original size:50 final size:50
Alignment explanation
Indices: 11385052--11385156 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
11385042 AGATATACAT
* * * * **
11385052 GTATAGCGCGCTTCAGGGGCCGCGCTATACTCACGTGGCGCCAGCTCACC
1 GTATAGCGCGCTGCAGGGGCCGCACTATACTCACATGGCACCAAATCACC
* *
11385102 GTATAGCGCGGTGCAGGGG-CGCACTATACATCACATGGCACCAAATCATC
1 GTATAGCGCGCTGCAGGGGCCGCACTATAC-TCACATGGCACCAAATCACC
11385152 GTATA
1 GTATA
11385157 ATTCGATGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 9 0.20
50 37 0.80
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (50 bp):
GTATAGCGCGCTGCAGGGGCCGCACTATACTCACATGGCACCAAATCACC
Found at i:11391704 original size:10 final size:10
Alignment explanation
Indices: 11391689--11391718 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
11391679 TATTTAAATG
11391689 ATAAACGAAC
1 ATAAACGAAC
11391699 ATAAACGAAC
1 ATAAACGAAC
*
11391709 ACAAACGAAC
1 ATAAACGAAC
11391719 GAACATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:11394241 original size:3 final size:3
Alignment explanation
Indices: 11394228--11394266 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
11394218 AAGTTATTCA
11394228 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11394267 TTCCCTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11394290 original size:14 final size:15
Alignment explanation
Indices: 11394273--11394310 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
11394263 TATTTTCCCT
11394273 TTATTTTATCT-TTA
1 TTATTTTATCTCTTA
11394287 TTATTTTA-CTCTTA
1 TTATTTTATCTCTTA
11394301 TTATTCTTAT
1 TTATT-TTAT
11394311 TCAATTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 16 0.76
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTATCTCTTA
Found at i:11402275 original size:17 final size:17
Alignment explanation
Indices: 11402250--11402304 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
11402240 CATTCAAAAT
*
11402250 CAAACATCCAAAACACA
1 CAAATATCCAAAACACA
11402267 CAAATATCC-AAACA-A
1 CAAATATCCAAAACACA
11402282 CCAAATATCCAAAACACA
1 -CAAATATCCAAAACACA
*
11402300 TAAAT
1 CAAAT
11402305 CCATCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 14 0.42
17 17 0.52
18 1 0.03
ACGTcount: A:0.58, C:0.29, G:0.00, T:0.13
Consensus pattern (17 bp):
CAAATATCCAAAACACA
Found at i:11409677 original size:6 final size:6
Alignment explanation
Indices: 11409661--11409719 Score: 77
Period size: 6 Copynumber: 9.7 Consensus size: 6
11409651 TATTACACCT
11409661 AGAAAA A-AAAA AGAAAAA AGAAAA TA-AAAA AGAAAA AGAAAAA AGAAAA
1 AGAAAA AGAAAA AG-AAAA AGAAAA -AGAAAA AGAAAA AG-AAAA AGAAAA
11409710 AGAAAA AGAA
1 AGAAAA AGAA
11409720 GAAAAAATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
5 6 0.12
6 29 0.60
7 13 0.27
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:11409684 original size:13 final size:13
Alignment explanation
Indices: 11409663--11409716 Score: 85
Period size: 13 Copynumber: 4.3 Consensus size: 13
11409653 TTACACCTAG
11409663 AAAAA-AAAAAGA
1 AAAAAGAAAAAGA
*
11409675 AAAAAG-AAAATA
1 AAAAAGAAAAAGA
11409687 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
11409700 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
11409713 AAAA
1 AAAA
11409717 GAAGAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 16 0.42
13 22 0.58
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:11409697 original size:25 final size:25
Alignment explanation
Indices: 11409661--11409719 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
11409651 TATTACACCT
11409661 AGAAAAA-AAAAAGAAAAAAGAAAA
1 AGAAAAAGAAAAAGAAAAAAGAAAA
11409685 TA-AAAAAGAAAAAGAAAAAAGAAAA
1 -AGAAAAAGAAAAAGAAAAAAGAAAA
11409710 AGAAAAAGAA
1 AGAAAAAGAA
11409720 GAAAAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (25 bp):
AGAAAAAGAAAAAGAAAAAAGAAAA
Found at i:11409717 original size:19 final size:18
Alignment explanation
Indices: 11409663--11409726 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 18
11409653 TTACACCTAG
11409663 AAAAAAAAAAGAAAAAAGA
1 AAAAAAAAAAG-AAAAAGA
*
11409682 AAATAAAAAAGAAAAAGA
1 AAAAAAAAAAGAAAAAGA
11409700 AAAAAGAAAAAGAAAAAGA
1 AAAAA-AAAAAGAAAAAGA
11409719 AGAAAAAA
1 A-AAAAAA
11409727 TGAATATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.27
19 26 0.63
20 4 0.10
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAGA
Found at i:11411367 original size:20 final size:20
Alignment explanation
Indices: 11411344--11411381 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11411334 TTAATTTTGC
11411344 ATATTAATTATTATTAATTA
1 ATATTAATTATTATTAATTA
**
11411364 ATATTTCTTATTATTAAT
1 ATATTAATTATTATTAAT
11411382 ATTTCTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTAATTATTATTAATTA
Found at i:11411381 original size:16 final size:16
Alignment explanation
Indices: 11411354--11411395 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
11411344 ATATTAATTA
11411354 TTATTAATTAATATTTC
1 TTATT-ATTAATATTTC
11411371 TTATTATTAATATTTC
1 TTATTATTAATATTTC
11411387 TTATTATTA
1 TTATTATTA
11411396 TTTTATTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTATTAATATTTC
Found at i:11412655 original size:17 final size:17
Alignment explanation
Indices: 11412633--11412672 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
11412623 ATCATGTTTG
* *
11412633 CTCTAATTTTAATCTGA
1 CTCTAATTTGAATATGA
11412650 CTCTAATTTGAATATGA
1 CTCTAATTTGAATATGA
11412667 CTCTAA
1 CTCTAA
11412673 GGTTTACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.42
Consensus pattern (17 bp):
CTCTAATTTGAATATGA
Found at i:11413315 original size:16 final size:16
Alignment explanation
Indices: 11413294--11413357 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
11413284 ATAGTAATAA
11413294 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
** *
11413310 TTTTATAATACTTTAT
1 TTTTATTTTATTTTAT
*
11413326 TTTTAATTTT-TATTAT
1 TTTT-ATTTTATTTTAT
*
11413342 GTTTTATTTAATTTTA
1 -TTTTATTTTATTTTA
11413358 GTATTAACGA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
16 25 0.69
17 11 0.31
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:11413325 original size:21 final size:21
Alignment explanation
Indices: 11413300--11413356 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
11413290 ATAATTTTAT
11413300 TTTATTTTATTTTTATAATAC
1 TTTATTTTATTTTTATAATAC
* **
11413321 TTTATTTTTAATTTTTATTATGT
1 TTTA-TTTT-ATTTTTATAATAC
*
11413344 TTTATTTAATTTT
1 TTTATTTTATTTT
11413357 AGTATTAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 9 0.30
22 7 0.23
23 14 0.47
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTATTTTATTTTTATAATAC
Found at i:11413347 original size:23 final size:22
Alignment explanation
Indices: 11413297--11413350 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
11413287 GTAATAATTT
11413297 TATTTTA-TTTTATTTTTATAA
1 TATTTTATTTTTATTTTTATAA
* *
11413318 TACTTTATTTTTAATTTTTATTA
1 TATTTTATTTTT-ATTTTTATAA
*
11413341 TGTTTTATTT
1 TATTTTATTT
11413351 AATTTTAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.22
22 4 0.15
23 17 0.63
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTATTTTTATTTTTATAA
Found at i:11424262 original size:21 final size:21
Alignment explanation
Indices: 11424223--11424262 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11424213 TGGATAGTAG
*
11424223 ATGATGAAGATGATGTTATGT
1 ATGATGAAAATGATGTTATGT
11424244 ATGATGATAAATGAT-TTAT
1 ATGATGA-AAATGATGTTAT
11424263 AATTATCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (21 bp):
ATGATGAAAATGATGTTATGT
Found at i:11426499 original size:18 final size:19
Alignment explanation
Indices: 11426476--11426519 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
11426466 AAGGATTTTG
11426476 TTATTATTTTCA-GATGAA
1 TTATTATTTTCATGATGAA
* *
11426494 TTATTAATTTCATTATGAA
1 TTATTATTTTCATGATGAA
11426513 TT-TTATT
1 TTATTATT
11426520 CTAGTTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (19 bp):
TTATTATTTTCATGATGAA
Found at i:11429106 original size:18 final size:17
Alignment explanation
Indices: 11429073--11429114 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
11429063 TTGGAACACC
11429073 TAAAATCATTTAATTTTAA
1 TAAAA-CATTTAATTTT-A
*
11429092 TAAAACATTTTATTTTA
1 TAAAACATTTAATTTTA
11429109 TAAAAC
1 TAAAAC
11429115 CAAATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 10 0.45
19 5 0.23
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAACATTTAATTTTA
Found at i:11431026 original size:90 final size:88
Alignment explanation
Indices: 11430881--11431044 Score: 265
Period size: 90 Copynumber: 1.8 Consensus size: 88
11430871 CTATTTATAG
* *
11430881 CCAAGTTACCCTAATCATATTAGGCTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
1 CCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAAACTATATTTAATTAAT
*
11430946 TAGAATTTAATAATCCTTTTATGT
66 T-GAAATTAATAATCCTTTTATGT
* *
11430970 CCAAGTTACCCTATTCATATTAGGGATTTTATTATTTTAAATTAATTAAAACTATATTTAATTAA
1 CCAAGTTACCCTAATCATATTA-GGATTTTATTATTTCAAATTAATTAAAACTATATTTAATTAA
11431035 TTGAAATTAA
65 TTGAAATTAA
11431045 ATATTCGGGA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
89 28 0.41
90 41 0.59
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
CCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAAACTATATTTAATTAAT
TGAAATTAATAATCCTTTTATGT
Found at i:11433182 original size:167 final size:166
Alignment explanation
Indices: 11432906--11433243 Score: 635
Period size: 167 Copynumber: 2.0 Consensus size: 166
11432896 ACCTAGAAGT
11432906 CTTATTGATCTATCTCTATAGATCTTAACTCCTAAGATATACGCTACCTCACCCAAGTCTTAACA
1 CTTATTGATCTATCTCTATAGATCTTAACTCCTAAGATATACGCTACCTCACCCAAGTCTTAACA
11432971 GACTGTAAAGTAGGTAAATCATTTCCTATAATGAGTATGTCGTCTACATACAAGATTAGGATAGA
66 GACTGTAAAGTAGGTAAATCATTTCCTATAATGAGTATGTCGTCTACATACAAGATTAGGATAGA
11433036 AAAAATGCTCCCACTAGCAGCCTTTTAAT-AA-ACAAGG
131 AAAAATGCTCCCACT---AGCCTTTTAATAAACACAAGG
11433073 CTTATTGATCTATCTCTATAGATCTTAACTCCTAAGATATACGCTACCTCACCCAAGTCTTAACA
1 CTTATTGATCTATCTCTATAGATCTTAACTCCTAAGATATACGCTACCTCACCCAAGTCTTAACA
11433138 GACTGTAAAGTAGGTAAATCATTTCCTATAATGAGTATGTCGTCTACATACAAGATTAGGATAGA
66 GACTGTAAAGTAGGTAAATCATTTCCTATAATGAGTATGTCGTCTACATACAAGATTAGGATAGA
11433203 AAAAATGCTCCCACTAGCCTTTTAATAAACACAAGG
131 AAAAATGCTCCCACTAGCCTTTTAATAAACACAAGG
11433239 CTTAT
1 CTTAT
11433244 CTTCATTTCT
Statistics
Matches: 169, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
164 11 0.07
165 2 0.01
166 11 0.07
167 145 0.86
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (166 bp):
CTTATTGATCTATCTCTATAGATCTTAACTCCTAAGATATACGCTACCTCACCCAAGTCTTAACA
GACTGTAAAGTAGGTAAATCATTTCCTATAATGAGTATGTCGTCTACATACAAGATTAGGATAGA
AAAAATGCTCCCACTAGCCTTTTAATAAACACAAGG
Found at i:11434042 original size:25 final size:25
Alignment explanation
Indices: 11434011--11434059 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11434001 CTCTTTCGAG
* *
11434011 AAAAACTTCTGTTCGAGCAACAAAA
1 AAAAACTCCTGTTAGAGCAACAAAA
11434036 AAAAACTCCTGTTAGAGCAACAAA
1 AAAAACTCCTGTTAGAGCAACAAA
11434060 CACTTTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.18
Consensus pattern (25 bp):
AAAAACTCCTGTTAGAGCAACAAAA
Found at i:11437110 original size:2 final size:2
Alignment explanation
Indices: 11437098--11437215 Score: 227
Period size: 2 Copynumber: 58.5 Consensus size: 2
11437088 CAAAACAAAC
11437098 AT AT CAT 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
11437141 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
11437183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11437216 CGCGTTCTTA
Statistics
Matches: 115, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 113 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11446760 original size:20 final size:20
Alignment explanation
Indices: 11446730--11446809 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
11446720 TAAATGAAAT
*
11446730 GCATAAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
11446750 GGATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
11446776 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
11446796 GCATGAAAGGATGC
1 GCATGAAAGGATGC
11446810 CATAAAAGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 27 0.55
21 3 0.06
22 1 0.02
24 1 0.02
25 3 0.06
26 14 0.29
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.19
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:11446770 original size:46 final size:46
Alignment explanation
Indices: 11446717--11446821 Score: 183
Period size: 46 Copynumber: 2.3 Consensus size: 46
11446707 TAAAACGAAT
*
11446717 CCATAAATGAAATGCATAAAAGGATGCATTAAGGGATGAAAGGATG
1 CCATAAATGAAATGCATAAAAGGATGCATTAAGGCATGAAAGGATG
*
11446763 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAAAAGGATGCATTAAGGCATGAAAGGATG
*
11446809 CCATAAAAGAAAT
1 CCATAAATGAAAT
11446822 TAACGAATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.47, C:0.10, G:0.24, T:0.19
Consensus pattern (46 bp):
CCATAAATGAAATGCATAAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:11447298 original size:81 final size:81
Alignment explanation
Indices: 11447212--11447372 Score: 234
Period size: 81 Copynumber: 2.0 Consensus size: 81
11447202 TAAATCATCC
* *
11447212 TAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAGTAAAAGCCTAATTGTGCT-TTTGGCAT
1 TAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAATAAAAGCCTAATTGTG-TATTTGGCAG
* *
11447276 AAAGGTGTCAATAATGT
65 AAAGATGCCAATAATGT
* * **
11447293 TAGTTAGATGAAAGGTTAAATACCTTTGGGTAAAAGAATAAATGTGTAATTGTGTATTTGGCAGA
1 TAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAATAAAAGCCTAATTGTGTATTTGGCAGA
11447358 AAGATGCCAATAATG
66 AAGATGCCAATAATG
11447373 CAAGTTGGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 1 0.01
81 70 0.99
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (81 bp):
TAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAATAAAAGCCTAATTGTGTATTTGGCAGA
AAGATGCCAATAATGT
Found at i:11448835 original size:2 final size:2
Alignment explanation
Indices: 11448828--11448858 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11448818 AAATGATGTC
11448828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11448859 ATTTCACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11452315 original size:26 final size:26
Alignment explanation
Indices: 11452249--11452321 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
11452239 TAAAATGAAT
*
11452249 CCATAAATGAAATGCATAAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
* *
11452275 -CAT---T--AAGGGATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
11452295 CCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
11452321 C
1 C
11452322 ATTATGGCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
20 13 0.36
21 3 0.08
22 1 0.03
24 1 0.03
25 3 0.08
26 15 0.42
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.19
Consensus pattern (26 bp):
CCATAAATGAAATGCATGAAAGGATG
Found at i:11452333 original size:20 final size:20
Alignment explanation
Indices: 11452262--11452339 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
11452252 TAAATGAAAT
* *
11452262 GCATAAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTATG
* *
11452282 GGATGAAAGGATGCCATAAATG
1 GCATGAAAGGATG-CAT-TATG
11452304 AAATGCATGAAAGGATGCATTATG
1 ----GCATGAAAGGATGCATTATG
11452328 GCATGAAAGGAT
1 GCATGAAAGGAT
11452340 TCCATAAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
20 23 0.50
21 3 0.07
22 2 0.04
24 3 0.07
25 3 0.07
26 12 0.26
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTATG
Found at i:11452360 original size:46 final size:46
Alignment explanation
Indices: 11452248--11452353 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
11452238 CTAAAATGAA
* *
11452248 TCCATAAATGAAATGCATAAAAGGATGCATTAAGGGATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
11452294 GCCATAAATGAAATGCATGAAAGGATGCATTATGGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
11452340 TCCATAAACGAAAT
1 TCCATAAATGAAAT
11452354 TAATGAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (46 bp):
TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
Found at i:11452877 original size:81 final size:80
Alignment explanation
Indices: 11452715--11452919 Score: 250
Period size: 81 Copynumber: 2.5 Consensus size: 80
11452705 ATGGCCTAGC
* * *
11452715 TGTGTATTTGACATAAATGTGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
1 TGTGTATTTGGCAGAAA-GTGTCAATCATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
*
11452780 AGAGTAAAAGCCTAAT
65 AGAATAAAAGCCTAAT
* * *
11452796 TGTGCT-TTTGGTAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGGGTAA
1 TGTG-TATTTGGCAG-AAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
* **
11452860 AAGAATAAATGTGTAAT
64 AAGAATAAAAGCCTAAT
* * *
11452877 TGTGTATTTGGCAGAAAGATGCCAATAATGCAAGTTGGATGAA
1 TGTGTATTTGGCAGAAAG-TGTCAATCATGCAAGTTAGATGAA
11452920 GGACTGATTG
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
80 5 0.05
81 97 0.92
82 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (80 bp):
TGTGTATTTGGCAGAAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
GAATAAAAGCCTAAT
Found at i:11453538 original size:76 final size:78
Alignment explanation
Indices: 11453448--11453606 Score: 304
Period size: 77 Copynumber: 2.1 Consensus size: 78
11453438 TCAACAACTG
11453448 TTTTATGGTGGTACTAAAATGTTTTAGTTTAAATTTC-AAAAAAAAAACTTTTACGAGTTTTACA
1 TTTTATGGTGGTACTAAAATGTTTTAGTTTAAATTTCAAAAAAAAAAACTTTTACGAGTTTTACA
11453512 AATGGGTGAAT-T
66 AATGGGTGAATGT
11453524 TTTTATGGTGGTACTAAAATGTTTTAGTTTAAATTTCAAAAAAAAAAACTTTTACGAGTTTTACA
1 TTTTATGGTGGTACTAAAATGTTTTAGTTTAAATTTCAAAAAAAAAAACTTTTACGAGTTTTACA
11453589 AATGGGTGAATGT
66 AATGGGTGAATGT
11453602 TTTTA
1 TTTTA
11453607 AAAGTCATGT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
76 37 0.46
77 38 0.47
78 6 0.07
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (78 bp):
TTTTATGGTGGTACTAAAATGTTTTAGTTTAAATTTCAAAAAAAAAAACTTTTACGAGTTTTACA
AATGGGTGAATGT
Found at i:11457908 original size:46 final size:45
Alignment explanation
Indices: 11457850--11458130 Score: 360
Period size: 46 Copynumber: 6.3 Consensus size: 45
11457840 GAAATGAATC
* * *
11457850 CATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGAATG
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
11457895 TCATAAATGAAATGCATGAAAGGATGCATTATGGCATGAAAGCACG
1 -CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
11457941 CTATAAATGAAATGTATGAAAGGATGCATTAAGGCATAAAAGGATG
1 C-ATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
11457987 CCATAAATGAAATGCATG-AAGGATGCATTAAGGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
11458032 -AGT---T-AAGT-CATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CA-TAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
11458072 CCATAAATGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATTC
1 -CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA-TG
11458119 CATAAATGAAAT
1 CATAAATGAAAT
11458131 TAACGAATAA
Statistics
Matches: 208, Mismatches: 15, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
39 4 0.02
40 30 0.14
41 2 0.01
42 1 0.00
43 1 0.00
44 2 0.01
45 30 0.14
46 136 0.65
47 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:11457933 original size:20 final size:20
Alignment explanation
Indices: 11457862--11458116 Score: 154
Period size: 20 Copynumber: 11.6 Consensus size: 20
11457852 TAAATAAAAT
*
11457862 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
11457882 GCATGAAAGAATGTCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
11457908 GCATGAAAGGATGCATTATG
1 GCATGAAAGGATGCATTAAG
* * *
11457928 GCATGAAAGCACGCTATAAATGAAAT
1 GCATGAAAGGATGC-AT---T--AAG
*
11457954 GTATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
11457974 GCATAAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
11458000 GCATG-AAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
11458019 GCATGAAAGGATG-AGTTAAG
1 GCATGAAAGGATGCA-TTAAG
*
11458039 TCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
11458059 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
11458085 ACATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
11458105 GCATGAAAGGAT
1 GCATGAAAGGAT
11458117 TCCATAAATG
Statistics
Matches: 183, Mismatches: 25, Indels: 54
0.70 0.10 0.21
Matches are distributed among these distances:
19 8 0.04
20 91 0.50
21 13 0.07
22 3 0.02
24 7 0.04
25 15 0.08
26 46 0.25
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:11458654 original size:81 final size:81
Alignment explanation
Indices: 11458498--11458672 Score: 260
Period size: 81 Copynumber: 2.2 Consensus size: 81
11458488 CTAGTTGTGT
* *
11458498 ATTTGACAGAAAGGTGTCAACCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACT
1 ATTTGGCAGAAAGGTGTCAACCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAACACT
*
11458563 AAAAGCCTAATTGTGC
66 AAAAGCCTAATGGTGC
* * *
11458579 CTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGGGTAAAACACT
1 ATTTGGCAGAAAGGTGTCAACCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAACACT
* * **
11458644 AAATGTCTAATGGTTT
66 AAAAGCCTAATGGTGC
11458660 ATTTGGCAGAAAG
1 ATTTGGCAGAAAG
11458673 ATGACAATAA
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (81 bp):
ATTTGGCAGAAAGGTGTCAACCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAACACT
AAAAGCCTAATGGTGC
Found at i:11458696 original size:81 final size:81
Alignment explanation
Indices: 11458520--11458697 Score: 221
Period size: 81 Copynumber: 2.2 Consensus size: 81
11458510 GGTGTCAACC
* * * *
11458520 ATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAAAAGCCTAATTGTGCCTTTGG
1 ATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAACACTAAAAGCCTAATGGTGCATTTGG
* * *
11458585 CAGAAAGGTGTCAATC
66 CAGAAAGATGACAATA
* * * * **
11458601 ATGCCAGTTAGATGAAAGGTTAAATACCTTTGGGTAAAACACTAAATGTCTAATGGTTTATTTGG
1 ATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAACACTAAAAGCCTAATGGTGCATTTGG
11458666 CAGAAAGATGACAATA
66 CAGAAAGATGACAATA
* *
11458682 ATGTAAGTTGGATGAA
1 ATGCAAGTTAGATGAA
11458698 GGACTAATTG
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
ATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAACACTAAAAGCCTAATGGTGCATTTGG
CAGAAAGATGACAATA
Found at i:11465600 original size:38 final size:38
Alignment explanation
Indices: 11465522--11465692 Score: 236
Period size: 38 Copynumber: 4.5 Consensus size: 38
11465512 CGAGTCAAAT
* *
11465522 ATATGCACCGTAGTGCTTACACATAATGG-CGTTCCCACC
1 ATATGCACCGAAGTGC-TACACATAA-GGTCGTGCCCACC
* *
11465561 ATATGCACCGAAGTGCTACACATAAGGTCATGCCTACC
1 ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
** * *
11465599 ATATGCAATGAAGTGCTACACATAAGGTTGTGCCCACA
1 ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
11465637 ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
*
11465675 ATATGCATCGAAGTGCTA
1 ATATGCACCGAAGTGCTA
11465693 AATTTTTATG
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
37 2 0.02
38 99 0.85
39 15 0.13
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (38 bp):
ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
Found at i:11476042 original size:24 final size:24
Alignment explanation
Indices: 11476009--11476054 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
11475999 TCTTCCAGAT
*
11476009 GATGTCTAAAGCATCAATGTACAC
1 GATGTCTAAAACATCAATGTACAC
* *
11476033 GATGTGTAAAACATCTATGTAC
1 GATGTCTAAAACATCAATGTAC
11476055 CATATCATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (24 bp):
GATGTCTAAAACATCAATGTACAC
Found at i:11484404 original size:30 final size:30
Alignment explanation
Indices: 11484370--11484436 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
11484360 AAAATTACAT
11484370 TTTGGTCCTTAAACTTTTCAAAGTTTATAC
1 TTTGGTCCTTAAACTTTTCAAAGTTTATAC
11484400 TTTGGTCCTTAAACTTTTCAAAGTTTATAC
1 TTTGGTCCTTAAACTTTTCAAAGTTTATAC
11484430 TTTGGTC
1 TTTGGTC
11484437 ACCAAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (30 bp):
TTTGGTCCTTAAACTTTTCAAAGTTTATAC
Found at i:11484444 original size:30 final size:31
Alignment explanation
Indices: 11484370--11484468 Score: 118
Period size: 30 Copynumber: 3.3 Consensus size: 31
11484360 AAAATTACAT
*
11484370 TTTGGTC-CTTAAACTTTTCAAAGTTTATAC
1 TTTGGTCACTCAAACTTTTCAAAGTTTATAC
*
11484400 TTTGGTC-CTTAAACTTTTCAAAGTTTATAC
1 TTTGGTCACTCAAACTTTTCAAAGTTTATAC
* *
11484430 TTTGGTCAC-CAAACTTTACCAAA--TTATAA
1 TTTGGTCACTCAAACTTT-TCAAAGTTTATAC
11484459 TTTGGTCACT
1 TTTGGTCACT
11484469 AAATAAATCC
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
29 14 0.22
30 44 0.70
31 5 0.08
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.43
Consensus pattern (31 bp):
TTTGGTCACTCAAACTTTTCAAAGTTTATAC
Found at i:11486473 original size:46 final size:46
Alignment explanation
Indices: 11486393--11486621 Score: 309
Period size: 46 Copynumber: 5.0 Consensus size: 46
11486383 ATACCATAGC
* * *
11486393 GGCA-CCTTTTATACCGATAATGCACCGTTGTGCATTTTCATTTGT
1 GGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTGT
* * *
11486438 GGTATCTTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTGT
1 GGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTGT
* *
11486484 GGAATCCTTTCATGCTGATAATGCACCGTTATGCATTTTCATTTGT
1 GGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTGT
* * * * *
11486530 GACATCCTTTCATGTCAATAATGCACC-TTAATGTATTTTCATTTAT
1 GGCATCCTTTCATGCCGATAATGCACCGTT-ATGCATTTTCATTTGT
*
11486576 GGCATCATTTCATGCCGATAATGCACCGTTATGCATTTTCATTTGT
1 GGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTGT
11486622 TCATTCATTT
Statistics
Matches: 158, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
45 5 0.03
46 151 0.96
47 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (46 bp):
GGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTGT
Found at i:11487057 original size:19 final size:19
Alignment explanation
Indices: 11487033--11487074 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
11487023 TAGTATCGGT
11487033 TAATATCACTTAACCCAAC
1 TAATATCACTTAACCCAAC
11487052 TAATATCACTTAACCCAAC
1 TAATATCACTTAACCCAAC
11487071 TAAT
1 TAAT
11487075 TTTCCTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
TAATATCACTTAACCCAAC
Found at i:11493088 original size:46 final size:46
Alignment explanation
Indices: 11493030--11493241 Score: 343
Period size: 46 Copynumber: 4.6 Consensus size: 46
11493020 TTTATGCCGT
11493030 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCTGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCTGA
* * *
11493076 TAATACACCGTTATGAATTTTCATTTGTGGCATCCTTTCATGATGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCTGA
* * * **
11493122 TAATGCACTGTTATGTATTTTCATTCGTGGCATCCTTTCATGCCCA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCTGA
*
11493168 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGTTGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCTGA
11493214 TAATGCACCGTTATGCATTTTCATTTGT
1 TAATGCACCGTTATGCATTTTCATTTGT
11493242 TCATTCATTT
Statistics
Matches: 150, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 150 1.00
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.42
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCTGA
Found at i:11493805 original size:21 final size:21
Alignment explanation
Indices: 11493775--11493830 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
11493765 TCGTTACCCA
* *
11493775 CATCAGTATCGATACTAATTG
1 CATCAATATCGATACAAATTG
11493796 CATCAATATCGATACAAATTG
1 CATCAATATCGATACAAATTG
11493817 CATCAATATCGATA
1 CATCAATATCGATA
11493831 TTGTTAATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (21 bp):
CATCAATATCGATACAAATTG
Found at i:11497565 original size:20 final size:21
Alignment explanation
Indices: 11497542--11497580 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
11497532 GAAAAGAGGA
11497542 TGAAAAGAT-GAA-TAAGATGG
1 TGAAAA-ATGGAATTAAGATGG
11497562 TGAAAAATGGAATTAAGAT
1 TGAAAAATGGAATTAAGAT
11497581 CGGATGCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (21 bp):
TGAAAAATGGAATTAAGATGG
Found at i:11512997 original size:37 final size:39
Alignment explanation
Indices: 11512946--11513026 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
11512936 CACGATACAA
* * *
11512946 AACACTATGATGTA-TA-AGGTGGGCAAGGCTCGACCTG
1 AACACTAAGATGTATTATAGGTGAGCAAGGCTCGACCTC
*
11512983 AACACTAAGGTGTATTATTAGGTGAGCAAGGCTCGACCTC
1 AACACTAAGATGTATTA-TAGGTGAGCAAGGCTCGACCTC
11513023 AACA
1 AACA
11513027 ATACGGTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 12 0.32
38 2 0.05
40 23 0.62
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (39 bp):
AACACTAAGATGTATTATAGGTGAGCAAGGCTCGACCTC
Found at i:11513014 original size:40 final size:40
Alignment explanation
Indices: 11512962--11513041 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
11512952 ATGATGTATA
* * * *
11512962 AGGTGGGCAAGGCTCGACCTGAACACTAAGGTGTATTATT
1 AGGTGAGCAAGGCTCGACCTCAACAATAAGGTGCATTATT
*
11513002 AGGTGAGCAAGGCTCGACCTCAACAATACGGTGCATTATT
1 AGGTGAGCAAGGCTCGACCTCAACAATAAGGTGCATTATT
11513042 TGACTCCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (40 bp):
AGGTGAGCAAGGCTCGACCTCAACAATAAGGTGCATTATT
Found at i:11516174 original size:17 final size:17
Alignment explanation
Indices: 11516152--11516207 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
11516142 AATAATCTAA
11516152 TTTAATTAATGTACTAG
1 TTTAATTAATGTACTAG
*
11516169 TTTAATGAAT-TAACTAG
1 TTTAATTAATGT-ACTAG
* *
11516186 TTTAATTAGTGAACTAG
1 TTTAATTAATGTACTAG
11516203 CTTTA
1 -TTTA
11516208 TTGAATGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 27 0.84
18 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTAATTAATGTACTAG
Found at i:11519144 original size:58 final size:58
Alignment explanation
Indices: 11519046--11519171 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
11519036 AAGCAATGCA
* * * *
11519046 ACCATTTGGCCAAGCCTTCCTAACCACAGATTTGGTCACCA-AGATGAAAGGTTACAAC
1 ACCATTCGGCCAAGCCTTCCTAACCACACATTTGGGCACCATA-ATGAAAGGTCACAAC
* *
11519104 ATCATTCGGCCAAGCCTTCCTAACCACACATTTGGGCACCATAATGAAATGTCACAAC
1 ACCATTCGGCCAAGCCTTCCTAACCACACATTTGGGCACCATAATGAAAGGTCACAAC
11519162 ACCATTCGGC
1 ACCATTCGGC
11519172 TAAGAACTCC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 59 0.98
59 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (58 bp):
ACCATTCGGCCAAGCCTTCCTAACCACACATTTGGGCACCATAATGAAAGGTCACAAC
Found at i:11522381 original size:14 final size:15
Alignment explanation
Indices: 11522352--11522382 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11522342 CATGCTTTCC
11522352 GTGAATCCACATTGT
1 GTGAATCCACATTGT
11522367 GTGAATCCA-ATTGT
1 GTGAATCCACATTGT
11522381 GT
1 GT
11522383 CTTCTGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (15 bp):
GTGAATCCACATTGT
Found at i:11530003 original size:28 final size:28
Alignment explanation
Indices: 11529969--11530025 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11529959 ATCAAGTCAG
*
11529969 TTTTTATACATTTATGTATTTTATACGA
1 TTTTTATACATTTATATATTTTATACGA
11529997 TTTTTATACATTTATATATTTTATACGA
1 TTTTTATACATTTATATATTTTATACGA
11530025 T
1 T
11530026 AAAATGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTTTATACATTTATATATTTTATACGA
Found at i:11537817 original size:45 final size:45
Alignment explanation
Indices: 11537717--11538265 Score: 760
Period size: 45 Copynumber: 12.2 Consensus size: 45
11537707 ATACTTTTCT
*
11537717 TTTCATTTATGGCATCCTTTCATGCCGATACTGCA-CGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
11537761 TTTCATTTATGGCATCCTTTAATGCCGATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
11537806 TTTCATTTATGGCATCCTTTCATGCCGATAATTCATCGTTCTGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
11537851 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * *
11537896 TTTTATTTATGGTACCCTTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* ** * *
11537941 TTTCAATTATGGCATCCTTAAATGCCGATAATGCATCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* ** *
11537986 TTTCACTTATGGCATCCTTTCATGTTGATAATGCATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
*
11538031 TTTCATTTATGGCATCCTTTCAAGCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * * * *
11538076 TTTTATTTATGGCATCCTGTCATGTCGATAATACACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
11538121 TTTCATTTATGGCATTCTTTCATGTCGATAATGCACCGTTATGGA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
11538166 TTTCATTTATAGCATCCATTT-ATGCCGATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCC-TTTCATGCCGATAATGCACCGTTATGCA
* * *
11538211 TTTTATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATTCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
11538256 TTTCATTTAT
1 TTTCATTTAT
11538266 TATCCCAAAG
Statistics
Matches: 440, Mismatches: 62, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
44 36 0.08
45 401 0.91
46 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:11540890 original size:18 final size:18
Alignment explanation
Indices: 11540867--11540907 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11540857 TTGATTAATG
11540867 AACTAAAATTATTCAATC
1 AACTAAAATTATTCAATC
** *
11540885 AACTAACTTTATTCAATG
1 AACTAAAATTATTCAATC
11540903 AACTA
1 AACTA
11540908 GATGCATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.34
Consensus pattern (18 bp):
AACTAAAATTATTCAATC
Found at i:11543134 original size:90 final size:89
Alignment explanation
Indices: 11542981--11543155 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 89
11542971 TAACACACCT
* *
11542981 TTTTATAGCTAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
*
11543046 TTAATTAATTAGAATTTAATAATCC
66 TTAATTAATTA-AATTAAATAATCC
* *
11543071 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAACTCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
11543136 TTAATTAATTAAATTAAATA
66 TTAATTAATTAAATTAAATA
11543156 TTCGGGATTA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 8 0.10
90 72 0.90
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTAAATTAAATAATCC
Found at i:11555340 original size:20 final size:20
Alignment explanation
Indices: 11555317--11555372 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
11555307 TTAGCTGGAT
*
11555317 GAGCTAACATGTAGCTTAAG
1 GAGCTAACATGTAGCTGAAG
* *
11555337 GAGCTTCAAC-T-TAGCTGGAT
1 GAGC-T-AACATGTAGCTGAAG
11555357 GAGCTAACATGTAGCT
1 GAGCTAACATGTAGCT
11555373 AAACTTAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
18 3 0.10
19 2 0.07
20 19 0.66
21 2 0.07
22 3 0.10
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (20 bp):
GAGCTAACATGTAGCTGAAG
Found at i:11555805 original size:19 final size:20
Alignment explanation
Indices: 11555781--11555831 Score: 95
Period size: 19 Copynumber: 2.6 Consensus size: 20
11555771 CGGCCACGAG
11555781 CATGTATTTTCATTAC-AAT
1 CATGTATTTTCATTACAAAT
11555800 CATGTATTTTCATTACAAAT
1 CATGTATTTTCATTACAAAT
11555820 CATGTATTTTCA
1 CATGTATTTTCA
11555832 AAGGGATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTACAAAT
Found at i:11558829 original size:20 final size:21
Alignment explanation
Indices: 11558801--11558839 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11558791 CATTAATTAA
*
11558801 TTAGCTCATGTTAT-TTTATT
1 TTAGATCATGTTATGTTTATT
11558821 TTAGATCATGTTATGTTTA
1 TTAGATCATGTTATGTTTA
11558840 CATTAGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.56
Consensus pattern (21 bp):
TTAGATCATGTTATGTTTATT
Found at i:11560887 original size:57 final size:56
Alignment explanation
Indices: 11560669--11560905 Score: 237
Period size: 57 Copynumber: 4.2 Consensus size: 56
11560659 TTGGCACTAA
* * * * *
11560669 GTGTGTAAAAA-CTAAGAAATTCATAATAAGTTTATTAA-TTTCTGTATAGGCACTTT
1 GTGTGCAAAAAGCT-AGAAATTCATAATTAGTTTATGAATTTTC-ATATGGGCACTTT
* * * *
11560725 GTGTGAAAAAAAACAAAGAAATTCATAATTAGTTTATGAATTATCATATGGGCACTTT
1 GTGTG-CAAAAAGC-TAGAAATTCATAATTAGTTTATGAATTTTCATATGGGCACTTT
* * * * *
11560783 GTGTGCAAAAAGCTA-AAATTCATAGTTAGTTTGTGAATTTCCTTATGGGAACTTT
1 GTGTGCAAAAAGCTAGAAATTCATAATTAGTTTATGAATTTTCATATGGGCACTTT
* * * *
11560838 GTGTGCAAAAAGTTATGAAATTTATAATTAGTTTATGGATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGCTA-GAAATTCATAATTAGTTTATGAATTTTCATATGGGCACTTT
*
11560895 ATGTGCAAAAA
1 GTGTGCAAAAA
11560906 AACTAAGAAA
Statistics
Matches: 150, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
55 48 0.32
56 6 0.04
57 54 0.36
58 39 0.26
59 3 0.02
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (56 bp):
GTGTGCAAAAAGCTAGAAATTCATAATTAGTTTATGAATTTTCATATGGGCACTTT
Found at i:11560920 original size:57 final size:57
Alignment explanation
Indices: 11560675--11560917 Score: 267
Period size: 58 Copynumber: 4.3 Consensus size: 57
11560665 CTAAGTGTGT
* * * *
11560675 AAAAACTAAGAAATTCATAATAAGTTTATTAA-TTTCTGTATAGGCACTTTGTGTGAAA
1 AAAAACTAAGAAATTCATAATTAGTTTATGAATTTTC-GTATGGGCACTTTGTGTG-CA
* * *
11560733 AAAAACAAAGAAATTCATAATTAGTTTATGAATTATCATATGGGCACTTTGTGTGCA
1 AAAAACTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
* * * * * *
11560790 AAAAGCT-A-AAATTCATAGTTAGTTTGTGAATTTCCTTATGGGAACTTTGTGTGCA
1 AAAAACTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
** * * * *
11560845 AAAAGTTATGAAATTTATAATTAGTTTATGGATTTTCGTATGGGCACTTTATGTGCAA
1 AAAAACTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTTGTGTGC-A
11560903 AAAAACTAAGAAATT
1 AAAAACTAAGAAATT
11560918 ATATTAATTT
Statistics
Matches: 153, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
55 47 0.31
56 1 0.01
57 44 0.29
58 58 0.38
59 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (57 bp):
AAAAACTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
Found at i:11561735 original size:20 final size:19
Alignment explanation
Indices: 11561686--11561736 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
11561676 TCGCCAAGAG
*
11561686 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAAT
*
11561705 CATGGATTTTCATTATAAAT
1 CATGTATTTTCATTA-AAAT
*
11561725 CTTGTATTTTCA
1 CATGTATTTTCA
11561737 AAGGGATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:11563289 original size:16 final size:17
Alignment explanation
Indices: 11563258--11563290 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11563248 ATACAAACAA
11563258 ATTTTGTCTTTTAAAATG
1 ATTTTGTC-TTTAAAATG
11563276 ATTTTGTC-TTAAAAT
1 ATTTTGTCTTTAAAAT
11563291 TCAGTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (17 bp):
ATTTTGTCTTTAAAATG
Found at i:11572065 original size:24 final size:24
Alignment explanation
Indices: 11572033--11572081 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11572023 TGCATGGCAT
11572033 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
11572057 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
11572081 T
1 T
11572082 CTGGAAGACT
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:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:11573096 original size:20 final size:21
Alignment explanation
Indices: 11573048--11573097 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
11573038 ATTTTGAGTT
11573048 TATGTATTT-AATATACATATA
1 TATGT-TTTGAATATACATATA
11573069 TATGTTTTGAATAT-CATATGA
1 TATGTTTTGAATATACATAT-A
*
11573090 TATTTTTT
1 TATGTTTT
11573098 ATTTGAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (21 bp):
TATGTTTTGAATATACATATA
Found at i:11583652 original size:5 final size:5
Alignment explanation
Indices: 11583621--11583672 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
11583611 AGAAATGATT
* *
11583621 AAATGG AAAAG AAAT- AAATG -AAGG AAATG AAATG AAATG AAAATG AAATG
1 AAAT-G AAATG AAATG AAATG AAATG AAATG AAATG AAATG -AAATG AAATG
11583671 AA
1 AA
11583673 GGATTAGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
4 7 0.18
5 24 0.62
6 8 0.21
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.15
Consensus pattern (5 bp):
AAATG
Found at i:11583666 original size:11 final size:11
Alignment explanation
Indices: 11583644--11583672 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
11583634 ATAAATGAAG
11583644 GAAATG-AAAT
1 GAAATGAAAAT
11583654 GAAATGAAAAT
1 GAAATGAAAAT
11583665 GAAATGAA
1 GAAATGAA
11583673 GGATTAGAGA
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:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (11 bp):
GAAATGAAAAT
Found at i:11590189 original size:47 final size:45
Alignment explanation
Indices: 11590121--11590292 Score: 229
Period size: 47 Copynumber: 3.8 Consensus size: 45
11590111 ATAAAATCTA
* *
11590121 TTACCATTTATCCCATAAGCTCGTAAGTTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
11590166 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
11590213 TTACCATTTAAATTCCATAAGCTCGAAAGCTTATTTTTCCAATATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
11590260 TTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
11590293 GCATGGTTAC
Statistics
Matches: 116, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
44 22 0.19
45 9 0.08
46 2 0.02
47 83 0.72
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:11597557 original size:47 final size:47
Alignment explanation
Indices: 11597505--11597664 Score: 218
Period size: 47 Copynumber: 3.5 Consensus size: 47
11597495 ACCATTTATC
*
11597505 CCATAAGCTCGTAAGTTTATTTTACCAAAATACTTAACATTTAAATT
1 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAAATT
*
11597552 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATT
1 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAAATT
* * * **
11597599 CCATAAGATCGTAAGCTTATTTTTCCAATATACTTGCCA-TT--ATT
1 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAAATT
* *
11597643 CCGTAAGCTCATAAGCTTATTT
1 CCATAAGCTCGTAAGCTTATTT
11597665 GTATGGTTAC
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
44 22 0.21
46 2 0.02
47 80 0.77
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (47 bp):
CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAAATT
Found at i:11597611 original size:94 final size:90
Alignment explanation
Indices: 11597485--11597664 Score: 227
Period size: 94 Copynumber: 2.0 Consensus size: 90
11597475 AAAATAATAT
* *
11597485 AAAATATCTTACCATTTATCCCATAAGCTCGTAAGTTTATTTTACCAAAATACTTAACATTTAAA
1 AAAATATCTTACCATTTATCCCATAAGATCGTAAGCTTATTTTACCAAAATACTTAACA-TT--A
*
11597550 TTCCATAAGCTCGTAAGCTTATTTTACC
63 TTCCATAAGCTCATAAGCTTATTTTACC
* * * **
11597578 AAAATA-CTTACCATTTAAATTCCATAAGATCGTAAGCTTATTTTTCCAATATACTTGCCATTAT
1 AAAATATCTTACCATTT--ATCCCATAAGATCGTAAGCTTATTTTACCAAAATACTTAACATTAT
*
11597642 TCCGTAAGCTCATAAGCTTATTT
64 TCCATAAGCTCATAAGCTTATTT
11597665 GTATGGTTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
91 23 0.30
92 10 0.13
93 8 0.11
94 35 0.46
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.38
Consensus pattern (90 bp):
AAAATATCTTACCATTTATCCCATAAGATCGTAAGCTTATTTTACCAAAATACTTAACATTATTC
CATAAGCTCATAAGCTTATTTTACC
Found at i:11601228 original size:14 final size:15
Alignment explanation
Indices: 11601189--11601234 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
11601179 AATGTAAGCC
*
11601189 ATGAGCTAAGTATATG
1 ATGAGCTAA-TATATA
11601205 ATGATG-TAATAT-TA
1 ATGA-GCTAATATATA
11601219 ATGAGCTAATATATA
1 ATGAGCTAATATATA
11601234 A
1 A
11601235 GCCTTAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
15 6 0.23
16 7 0.27
17 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (15 bp):
ATGAGCTAATATATA
Found at i:11601414 original size:35 final size:35
Alignment explanation
Indices: 11601368--11601444 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
11601358 AGTAAACAAA
* *
11601368 TTATATATCATTATGCAACATATAATATGACTATG
1 TTATATATCATTATGCAACATATAACATGACTAAG
* *
11601403 TTATATATCATTATGTAGCATATAACATGACTAAG
1 TTATATATCATTATGCAACATATAACATGACTAAG
*
11601438 TAATATA
1 TTATATA
11601445 GTTTTCATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (35 bp):
TTATATATCATTATGCAACATATAACATGACTAAG
Found at i:11601967 original size:166 final size:169
Alignment explanation
Indices: 11601742--11602083 Score: 663
Period size: 166 Copynumber: 2.0 Consensus size: 169
11601732 TTGGGATGTG
11601742 ATGAAGAACAACCAAGTTTAAGGGAGGATTTCATCTTTTACTTGTGCATGAATTTGAATGAGTGT
1 ATGAAGAACAACCAAGTTTAAGGGAGGATTTCATCTTTTACTTGTGCATGAATTTGAATGAGTGT
11601807 TAACAAATTTACATAACGTTAAGTTGCATAAATAAATAAACATTCTACTTCATTTAATCATGTA-
66 TAACAAATTTACATAACGTTAAGTTGCATAAATAAATAAACATTCTACTTCATTTAATCATGTAT
11601871 TTT-TTAGAGCAAGAGTTCATTAAAGCATGTAGTTTTTT
131 TTTATTAGAGCAAGAGTTCATTAAAGCATGTAGTTTTTT
11601909 ATGAAGAACAACCAAG-TTAAGGGAGGATTTCATCTTTTACTTGTGCATGAATTTGAATGAGTGT
1 ATGAAGAACAACCAAGTTTAAGGGAGGATTTCATCTTTTACTTGTGCATGAATTTGAATGAGTGT
11601973 TAACAAATTTACATAACGTTAAGTTGCATAAATAAATAAACATTCTACTTCATTTAATCATGTAT
66 TAACAAATTTACATAACGTTAAGTTGCATAAATAAATAAACATTCTACTTCATTTAATCATGTAT
11602038 TTTATTAGAGCAAGAGTTCATTAAAGCATGTAGTTTTTT
131 TTTATTAGAGCAAGAGTTCATTAAAGCATGTAGTTTTTT
11602077 ATGAAGA
1 ATGAAGA
11602084 TACTTCATTG
Statistics
Matches: 173, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
166 112 0.65
167 19 0.11
168 42 0.24
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (169 bp):
ATGAAGAACAACCAAGTTTAAGGGAGGATTTCATCTTTTACTTGTGCATGAATTTGAATGAGTGT
TAACAAATTTACATAACGTTAAGTTGCATAAATAAATAAACATTCTACTTCATTTAATCATGTAT
TTTATTAGAGCAAGAGTTCATTAAAGCATGTAGTTTTTT
Found at i:11602145 original size:35 final size:35
Alignment explanation
Indices: 11602100--11602174 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
11602090 ATTGAAGTTT
* *
11602100 ACTATTTCATTCAATGAAGCTCGTTCACTAATTAA
1 ACTAGTTCATTCAATGAAACTCGTTCACTAATTAA
* * * *
11602135 ACTAGTTCATTCATTTAAACTCGTTTATTAATTAA
1 ACTAGTTCATTCAATGAAACTCGTTCACTAATTAA
11602170 ACTAG
1 ACTAG
11602175 CTATTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (35 bp):
ACTAGTTCATTCAATGAAACTCGTTCACTAATTAA
Found at i:11602154 original size:18 final size:17
Alignment explanation
Indices: 11602122--11602174 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
11602112 AATGAAGCTC
*
11602122 GTTCACTAATTAAACTA
1 GTTCATTAATTAAACTA
* *
11602139 GTTCATTCATTTAAACTC
1 GTTCATT-AATTAAACTA
*
11602157 GTTTATTAATTAAACTA
1 GTTCATTAATTAAACTA
11602174 G
1 G
11602175 CTATTTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (17 bp):
GTTCATTAATTAAACTA
Found at i:11606259 original size:143 final size:143
Alignment explanation
Indices: 11605992--11606270 Score: 393
Period size: 143 Copynumber: 2.0 Consensus size: 143
11605982 AGTTTAGTTT
* * * *
11605992 TCATTTTGTAATGAAAGCAATTGACTTTGTTTAATTAAATATTTATGAGAGTTTCTCTCTTTAGT
1 TCATTTTGTAATGAAAGCAATTGACTTTGTTTAATCAAATATTTATAAGAGTTTCTATATTTAGT
* * *
11606057 TATTAAGCGAACTTTATCGACTTATCAAACTTATGCTTCTGGCGTCACCCCTATCTATTTCAC-C
66 TATTAAGCGAACTTTATCAACTTATCAAACTTATGCTTATGGCGTCACCCCTATATATTTCACTC
11606121 TTGATACCCCTAGC
131 -TGATACCCCTAGC
*
11606135 TCATATTT-TAATGAAAGCAATTGACTTTGTTTAATCAAATATTTGTAAGAGTTTCTATATTTAG
1 TCAT-TTTGTAATGAAAGCAATTGACTTTGTTTAATCAAATATTTATAAGAGTTTCTATATTTAG
* * * * *
11606199 TTCTTAA-CTGAACTTTATCAACTTATTAAGCTTATTCTTATGGCGTCACCCTTATATATTTCAC
65 TTATTAAGC-GAACTTTATCAACTTATCAAACTTATGCTTATGGCGTCACCCCTATATATTTCAC
11606263 TCTGATAC
129 TCTGATAC
11606271 TTTTGGTTCC
Statistics
Matches: 120, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
142 1 0.01
143 115 0.96
144 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.42
Consensus pattern (143 bp):
TCATTTTGTAATGAAAGCAATTGACTTTGTTTAATCAAATATTTATAAGAGTTTCTATATTTAGT
TATTAAGCGAACTTTATCAACTTATCAAACTTATGCTTATGGCGTCACCCCTATATATTTCACTC
TGATACCCCTAGC
Found at i:11619243 original size:24 final size:24
Alignment explanation
Indices: 11619215--11619261 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11619205 TCATTTTTAA
*
11619215 TTACTTATCTATTTCA-TTATATTC
1 TTACTAATC-ATTTCACTTATATTC
*
11619239 TTACTAATCATTTTACTTATATT
1 TTACTAATCATTTCACTTATATT
11619262 TATTTGTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (24 bp):
TTACTAATCATTTCACTTATATTC
Found at i:11621800 original size:47 final size:45
Alignment explanation
Indices: 11621706--11621831 Score: 177
Period size: 47 Copynumber: 2.8 Consensus size: 45
11621696 GGTAAGTATG
*
11621706 AAAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGAT
*
11621749 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAGT-TTGGT
1 AAAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTA-TATTGAT
*
11621796 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
11621832 AGATTTTATA
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
43 21 0.28
44 3 0.04
45 11 0.15
46 1 0.01
47 38 0.51
48 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGAT
Found at i:11624648 original size:14 final size:14
Alignment explanation
Indices: 11624627--11624664 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
11624617 ATATATTATA
11624627 AGAAGAAAAAAAAC
1 AGAAGAAAAAAAAC
11624641 TA-AAGAAAAAAAAC
1 -AGAAGAAAAAAAAC
11624655 AGAAGAAAAA
1 AGAAGAAAAA
11624665 CAAATAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (14 bp):
AGAAGAAAAAAAAC
Found at i:11626236 original size:20 final size:19
Alignment explanation
Indices: 11626211--11626261 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
11626201 TCGAATATGT
11626211 ATGTTACAAAAATTTGAAGA
1 ATGTTACAAAAA-TTGAAGA
*
11626231 ATGTTACAAACAATTGAAGG
1 ATGTTACAAA-AATTGAAGA
*
11626251 ATGTTATAAAA
1 ATGTTACAAAA
11626262 TGTTTGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.89
21 2 0.07
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (19 bp):
ATGTTACAAAAATTGAAGA
Found at i:11628341 original size:47 final size:45
Alignment explanation
Indices: 11628248--11628372 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
11628238 GTAAGTATGC
* *
11628248 AAATAAGCTTATGAGCTTAT-GAAT-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
*
11628291 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAGT-TTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTA-TATTGATA
*
11628338 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
11628373 AGATTTTATA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 19 0.26
44 3 0.04
45 11 0.15
46 1 0.01
47 38 0.52
48 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:11631530 original size:43 final size:46
Alignment explanation
Indices: 11631482--11631606 Score: 136
Period size: 47 Copynumber: 2.8 Consensus size: 46
11631472 GTAAGTATGC
*
11631482 AAATAAGCTTACAAGCTTATG-AA-T-AAT-GTCAAGTA-TATTGATA
1 AAATAAGCTTACGAGCTTATGAAATTAAATGGT-AAGTAGT-TTGATA
* *
11631525 AAATAAGCTTATGAGCTTATGAAATTTAAATGGTAAGTAGTTTGGTA
1 AAATAAGCTTACGAGCTTATGAAA-TTAAATGGTAAGTAGTTTGATA
**
11631572 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGAAATTAAATGGTAAG
11631607 AGATTTTATA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
43 19 0.27
44 2 0.03
45 11 0.16
46 1 0.01
47 34 0.49
48 3 0.04
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGAAATTAAATGGTAAGTAGTTTGATA
Found at i:11631940 original size:12 final size:12
Alignment explanation
Indices: 11631923--11631947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11631913 TATTTTCGGA
11631923 AGTTACTGTAGT
1 AGTTACTGTAGT
11631935 AGTTACTGTAGT
1 AGTTACTGTAGT
11631947 A
1 A
11631948 TGCACAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
AGTTACTGTAGT
Found at i:11633043 original size:19 final size:19
Alignment explanation
Indices: 11633019--11633062 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
11633009 TGCATAAATG
*
11633019 GTATCGATATTGAAAGGGA
1 GTATCGATACTGAAAGGGA
11633038 GTATCGATACTGAAAGGGA
1 GTATCGATACTGAAAGGGA
11633057 GTATCG
1 GTATCG
11633063 GTACCATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.32, T:0.25
Consensus pattern (19 bp):
GTATCGATACTGAAAGGGA
Found at i:11633632 original size:45 final size:45
Alignment explanation
Indices: 11633581--11633817 Score: 296
Period size: 45 Copynumber: 5.2 Consensus size: 45
11633571 TATGAATCTA
* *
11633581 CATAAAAGGTGTCATAAATAAAAATGCATAACGGTGCATTATCGG
1 CATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATCGG
* * * *
11633626 CATAAAAGGTTCCATAAATGAAAACGCATAACGGGGCATTATTGG
1 CATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATCGG
* ** *
11633671 TATAAAAATATGCCATAAATGAAAATGCATAACAGTGCATTATCGG
1 CAT-AAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATCGG
* * *
11633717 CATGAAATGTGCCATAAATGAAAATACATAACGGTGCATTATCGG
1 CATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATCGG
* * * *
11633762 CGTAAAAGGTGCCACT-AATAAAAATGCATAATGGTGCATTATTGG
1 CATAAAAGGTGCCA-TAAATGAAAATGCATAACGGTGCATTATCGG
11633807 CATAAAAGGTG
1 CATAAAAGGTG
11633818 TCACTCAAGG
Statistics
Matches: 163, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
45 125 0.77
46 38 0.23
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (45 bp):
CATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATCGG
Found at i:11633748 original size:91 final size:91
Alignment explanation
Indices: 11633593--11633817 Score: 283
Period size: 91 Copynumber: 2.5 Consensus size: 91
11633583 TAAAAGGTGT
* * *
11633593 CATAAATAAAAATGCATAACGGTGCATTATCGGCATAAAAGGTTCCATAAATGAAAACGCATAAC
1 CATAAATAAAAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCATAAATGAAAACACATAAC
11633658 GGGGCATTATTGGTATAAAAATATGC
66 GGGGCATTATTGGTATAAAAATATGC
* * * *
11633684 CATAAATGAAAATGCATAACAGTGCATTATCGGCATGAAATGTGCCATAAATGAAAATACATAAC
1 CATAAATAAAAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCATAAATGAAAACACATAAC
* * ** **
11633749 GGTGCATTATCGGCGT-AAAAGGTGC
66 GGGGCATTATTGGTATAAAAATATGC
** *
11633774 CACT-AATAAAAATGCATAATGGTGCATTATTGGCATAAAAGGTG
1 CA-TAAATAAAAATGCATAACAGTGCATTATCGGCATAAAAGGTG
11633818 TCACTCAAGG
Statistics
Matches: 114, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
90 43 0.38
91 71 0.62
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (91 bp):
CATAAATAAAAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCATAAATGAAAACACATAAC
GGGGCATTATTGGTATAAAAATATGC
Found at i:11637757 original size:24 final size:24
Alignment explanation
Indices: 11637730--11637783 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
11637720 ATGGACATGA
11637730 CTTTTGAAGAACCAAACAATATGT
1 CTTTTGAAGAACCAAACAATATGT
**
11637754 CTTTTGGGGAACCAAACAATATGT
1 CTTTTGAAGAACCAAACAATATGT
11637778 CTTTTG
1 CTTTTG
11637784 GGGTACCAAG
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:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (24 bp):
CTTTTGAAGAACCAAACAATATGT
Found at i:11637800 original size:24 final size:24
Alignment explanation
Indices: 11637738--11637792 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
11637728 GACTTTTGAA
11637738 GAACCAAACAATATGTCTTTTGGG
1 GAACCAAACAATATGTCTTTTGGG
11637762 GAACCAAACAATATGTCTTTTGGG
1 GAACCAAACAATATGTCTTTTGGG
*
11637786 GTACCAA
1 GAACCAA
11637793 GAGATATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (24 bp):
GAACCAAACAATATGTCTTTTGGG
Found at i:11641778 original size:19 final size:20
Alignment explanation
Indices: 11641751--11641801 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
11641741 AAGCCAAGAG
* *
11641751 CATGCATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
*
11641770 CATGTATTTACATTAAAAAT
1 CATGTATTTTCATTAAAAAT
11641790 CATGTATTTTCA
1 CATGTATTTTCA
11641802 AAGCTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:11643415 original size:18 final size:18
Alignment explanation
Indices: 11643392--11643427 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11643382 TTCATGTATC
11643392 TAGTTCATTTAATAAAGT
1 TAGTTCATTTAATAAAGT
*
11643410 TAGTTCATTTATTAAAGT
1 TAGTTCATTTAATAAAGT
11643428 AACTCTTAAT
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:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (18 bp):
TAGTTCATTTAATAAAGT
Found at i:11649354 original size:20 final size:20
Alignment explanation
Indices: 11649315--11649354 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11649305 GCCTCCGAAG
* **
11649315 GAAAAGAAAAATCATGAAAA
1 GAAAAAAAAAATCACAAAAA
11649335 GAAAAAAAAAATCACAAAAA
1 GAAAAAAAAAATCACAAAAA
11649355 AGATTCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.07
Consensus pattern (20 bp):
GAAAAAAAAAATCACAAAAA
Found at i:11651943 original size:15 final size:16
Alignment explanation
Indices: 11651909--11651950 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
11651899 GAGTTGTAAG
*
11651909 TTATCTTCATTTTCTCT
1 TTAT-TTCATTTCCTCT
11651926 TTATTTCATTTCCT-T
1 TTATTTCATTTCCTCT
11651941 TTATTTCATT
1 TTATTTCATT
11651951 CTTTCTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTCATTTCCTCT
Found at i:11657747 original size:20 final size:20
Alignment explanation
Indices: 11657724--11657768 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
11657714 GTGTAGATTC
11657724 CTCTTATATCATGATGTGCA
1 CTCTTATATCATGATGTGCA
*
11657744 CTCTTATTTCATGATGTGCA
1 CTCTTATATCATGATGTGCA
11657764 CTCTT
1 CTCTT
11657769 TGATAGGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (20 bp):
CTCTTATATCATGATGTGCA
Found at i:11662503 original size:23 final size:23
Alignment explanation
Indices: 11662458--11662503 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11662448 TTATACCTAT
*
11662458 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
11662481 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
11662504 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:11667083 original size:23 final size:23
Alignment explanation
Indices: 11667038--11667083 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11667028 TTATACCTAT
*
11667038 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
11667061 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
11667084 TATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:11676300 original size:19 final size:20
Alignment explanation
Indices: 11676276--11676325 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
11676266 GACCAAGAGC
*
11676276 ATGTATCTTCATT-AAAATA
1 ATGTATTTTCATTAAAAATA
*
11676295 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATTAAAAATA
11676315 ATGTATTTTCA
1 ATGTATTTTCA
11676326 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATA
Found at i:11691744 original size:22 final size:23
Alignment explanation
Indices: 11691719--11691765 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
11691709 TATGAATATG
*
11691719 GATGAACATTA-CCGTGAACAGT
1 GATGAACAATACCCGTGAACAGT
* *
11691741 GATGGATAATACCCGTGAACAGT
1 GATGAACAATACCCGTGAACAGT
11691764 GA
1 GA
11691766 ACAGTGCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (23 bp):
GATGAACAATACCCGTGAACAGT
Found at i:11698648 original size:18 final size:18
Alignment explanation
Indices: 11698606--11698648 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
11698596 ACTTGTGAGG
*
11698606 TTTCTTGCTTTCTTAAAT
1 TTTCTTTCTTTCTTAAAT
* *
11698624 TTTCTTTCTTTGTTGAAT
1 TTTCTTTCTTTCTTAAAT
11698642 TTTCTTT
1 TTTCTTT
11698649 GTTTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTCTTTCTTTCTTAAAT
Found at i:11701959 original size:10 final size:10
Alignment explanation
Indices: 11701946--11701978 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
11701936 TTTATTTTCA
*
11701946 ATTTCTTTAT
1 ATTTTTTTAT
11701956 ATTTTTTTAT
1 ATTTTTTTAT
11701966 ATTTTTTTAT
1 ATTTTTTTAT
11701976 ATT
1 ATT
11701979 GTTTAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:11706838 original size:17 final size:16
Alignment explanation
Indices: 11706798--11706840 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
11706788 TAAGTATATT
* *
11706798 ATTCATTAAAGCATGC
1 ATTCATTTAAGCATGA
11706814 ATTACATTTAAGCATGTA
1 ATT-CATTTAAGCATG-A
11706832 ATTCATTTA
1 ATTCATTTA
11706841 GGGAAGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (16 bp):
ATTCATTTAAGCATGA
Found at i:11706919 original size:18 final size:18
Alignment explanation
Indices: 11706896--11706941 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
11706886 ATTCACGCAT
11706896 TTAGTTCATTGAATGAA-G
1 TTAGTTCATTGAAT-AATG
11706914 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAATG
*
11706932 TTATTTCATT
1 TTAGTTCATT
11706942 AATCAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAATG
Found at i:11708628 original size:45 final size:44
Alignment explanation
Indices: 11708558--11708760 Score: 282
Period size: 45 Copynumber: 4.6 Consensus size: 44
11708548 CATTTCTTAT
* *
11708558 CAATCTACTTACCATTTATCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTAC
*
11708602 CAATATACTTACCTTTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTT-TTCCATAAGCTCGTAAGCTTATTTTAC
11708647 CAATATACTTACCATTATTT-CATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTAC
* * *
11708691 CAATATACGTACCATTTGTTCCATAAGCTCTTAAGCTTATTTTAA
1 CAATATACTTACCATTT-TTCCATAAGCTCGTAAGCTTATTTTAC
* * * *
11708736 AAATACACTTGCCATTATTCCATAA
1 CAATATACTTACCATTTTTCCATAA
11708761 CCATATACAA
Statistics
Matches: 143, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.01
44 64 0.45
45 77 0.54
46 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (44 bp):
CAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:11708671 original size:89 final size:89
Alignment explanation
Indices: 11708558--11708760 Score: 309
Period size: 89 Copynumber: 2.3 Consensus size: 89
11708548 CATTTCTTAT
* * *
11708558 CAATCTACTTACCATT-TATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCTTTTGTT
1 CAATATACTTACCATTAT-TCCATAAGCTCGTAAGCTTATTTTACCAATATACGTACCATTTGTT
*
11708622 CCATAAGCTCGTAAGCTTATTTTAC
65 CCATAAGCTCGTAAGCTTATTTTAA
*
11708647 CAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACGTACCATTTGTTC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACGTACCATTTGTTC
*
11708712 CATAAGCTCTTAAGCTTATTTTAA
66 CATAAGCTCGTAAGCTTATTTTAA
* * *
11708736 AAATACACTTGCCATTATTCCATAA
1 CAATATACTTACCATTATTCCATAA
11708761 CCATATACAA
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
89 102 0.99
90 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (89 bp):
CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACGTACCATTTGTTC
CATAAGCTCGTAAGCTTATTTTAA
Found at i:11708968 original size:59 final size:59
Alignment explanation
Indices: 11708848--11708969 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 59
11708838 CAATCCTGAG
* * * ** **
11708848 TATGATACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCTGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCCAA
* * * *
11708907 TATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCCCAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCCAA
11708966 TATG
1 TATG
11708970 CAGTCTACTA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCCAA
Found at i:11714372 original size:25 final size:26
Alignment explanation
Indices: 11714309--11714372 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 26
11714299 CATGATATTG
*
11714309 TTTCATAGCTCATAAGTAATCATTCA
1 TTTCATAGCTCATAAGTAATCAATCA
** * *
11714335 -CACATGGCATCAT-ATTAATCAATCA
1 TTTCATAGC-TCATAAGTAATCAATCA
11714360 TTTCATAGCTCAT
1 TTTCATAGCTCAT
11714373 TATACTTTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (26 bp):
TTTCATAGCTCATAAGTAATCAATCA
Found at i:11714456 original size:29 final size:31
Alignment explanation
Indices: 11714399--11714456 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
11714389 TCACAAGTCA
11714399 TATATGTTAGCTCACTAATATCATACCATCT
1 TATATGTTAGCTCACTAATATCATACCATCT
* *
11714430 TATAT-TTAGCTCA-TGATATCATCCCAT
1 TATATGTTAGCTCACTAATATCATACCAT
11714457 AGCTCACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.48
30 8 0.32
31 5 0.20
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (31 bp):
TATATGTTAGCTCACTAATATCATACCATCT
Found at i:11736690 original size:21 final size:21
Alignment explanation
Indices: 11736651--11736690 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11736641 AAGGAATATT
*
11736651 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
11736672 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
11736691 ATGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:11740678 original size:21 final size:21
Alignment explanation
Indices: 11740639--11740678 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11740629 AAGGAAGATT
*
11740639 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
11740660 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
11740679 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:11740727 original size:22 final size:21
Alignment explanation
Indices: 11740701--11740741 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
11740691 GTTGTAGAAT
11740701 TGATGGTGTTGATGGATGAAGA
1 TGATGGTGTTGAT-GATGAAGA
11740723 TGATGGTGTTGATGATGAA
1 TGATGGTGTTGATGATGAA
11740742 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.39, T:0.34
Consensus pattern (21 bp):
TGATGGTGTTGATGATGAAGA
Found at i:11744376 original size:20 final size:21
Alignment explanation
Indices: 11744352--11744401 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
11744342 TCATTCATTA
11744352 ATTAGCTCATGTCATGTTT-T
1 ATTAGCTCATGTCATGTTTAT
* *
11744372 TTTAGCTCATGTTATGTTTAT
1 ATTAGCTCATGTCATGTTTAT
11744393 ATTAGCTCA
1 ATTAGCTCA
11744402 CTAGCTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (21 bp):
ATTAGCTCATGTCATGTTTAT
Found at i:11772677 original size:23 final size:23
Alignment explanation
Indices: 11772651--11772702 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
11772641 TCGTTGTAAG
11772651 AATTTCTTTGTAGTAAATTTACT
1 AATTTCTTTGTAGTAAATTTACT
* *
11772674 AATTTTTTTTGTAGTAAGTTTACT
1 AA-TTTCTTTGTAGTAAATTTACT
11772698 AATTT
1 AATTT
11772703 TTTTCATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (23 bp):
AATTTCTTTGTAGTAAATTTACT
Found at i:11772685 original size:24 final size:24
Alignment explanation
Indices: 11772657--11772706 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
11772647 TAAGAATTTC
11772657 TTTGTAGTAAATTTACTAATTTTT
1 TTTGTAGTAAATTTACTAATTTTT
*
11772681 TTTGTAGTAAGTTTACTAATTTTT
1 TTTGTAGTAAATTTACTAATTTTT
11772705 TT
1 TT
11772707 CATCAATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (24 bp):
TTTGTAGTAAATTTACTAATTTTT
Found at i:11793600 original size:17 final size:17
Alignment explanation
Indices: 11793578--11793618 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
11793568 CGAAGATTCA
11793578 AAGCATATCTATTCGGT
1 AAGCATATCTATTCGGT
11793595 AAGCATATCTATTCGGT
1 AAGCATATCTATTCGGT
11793612 AAGCATA
1 AAGCATA
11793619 ATGTGAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (17 bp):
AAGCATATCTATTCGGT
Found at i:11808215 original size:16 final size:16
Alignment explanation
Indices: 11808194--11808225 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11808184 AATGGAAATG
*
11808194 ATAGGATGAAATATGT
1 ATAGGATGAAAGATGT
11808210 ATAGGATGAAAGATGT
1 ATAGGATGAAAGATGT
11808226 GTGGAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (16 bp):
ATAGGATGAAAGATGT
Found at i:11809581 original size:17 final size:17
Alignment explanation
Indices: 11809561--11809603 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
11809551 TAGTATGACG
* *
11809561 AATGAAGTAGTTTAATT
1 AATGAACTAGTTTAATC
11809578 AATGAACTAGTTTAATC
1 AATGAACTAGTTTAATC
11809595 AATGAACTA
1 AATGAACTA
11809604 CTTAGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTAATC
Found at i:11818576 original size:18 final size:19
Alignment explanation
Indices: 11818543--11818581 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
11818533 CATGGAGTAC
*
11818543 ATTATTCATTTATTTA-TT
1 ATTATTCATTCATTTACTT
*
11818561 ATTATTCATTCCTTTACTT
1 ATTATTCATTCATTTACTT
11818580 AT
1 AT
11818582 GAGAGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTCATTCATTTACTT
Found at i:11821872 original size:2 final size:2
Alignment explanation
Indices: 11821865--11821899 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11821855 ATCACCAACT
11821865 TA TA TA TA 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 T
11821900 CCGCTACCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11823524 original size:19 final size:20
Alignment explanation
Indices: 11823477--11823527 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11823467 GAAACCCCTT
**
11823477 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11823497 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11823516 TGAAGATACATG
1 TGAAAATACATG
11823528 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:11828049 original size:13 final size:13
Alignment explanation
Indices: 11828031--11828056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11828021 GCTCTTGAAA
11828031 AGTCATATCCTTT
1 AGTCATATCCTTT
11828044 AGTCATATCCTTT
1 AGTCATATCCTTT
11828057 GGCGTGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
AGTCATATCCTTT
Found at i:11828490 original size:14 final size:11
Alignment explanation
Indices: 11828458--11828513 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
11828448 ATTGGAGTAC
11828458 AAAAAGAAGAA
1 AAAAAGAAGAA
11828469 AAAAAGAAGAA
1 AAAAAGAAGAA
* **
11828480 AATAATCAGAA
1 AAAAAGAAGAA
11828491 AAGAAA-AA-AA
1 AA-AAAGAAGAA
11828501 GAAAAAGAAGAA
1 -AAAAAGAAGAA
11828513 A
1 A
11828514 TTCAAAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 5 0.14
11 27 0.75
12 4 0.11
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:11832996 original size:16 final size:16
Alignment explanation
Indices: 11832975--11833006 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11832965 TGTGACCTTT
11832975 CATGAATGATTCTGCC
1 CATGAATGATTCTGCC
11832991 CATGAATGATTCTGCC
1 CATGAATGATTCTGCC
11833007 ATGCATATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
CATGAATGATTCTGCC
Found at i:11833851 original size:7 final size:8
Alignment explanation
Indices: 11833835--11833860 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11833825 AAATAATCAG
11833835 AAAAGAAA
1 AAAAGAAA
11833843 AAAAGAAA
1 AAAAGAAA
11833851 AAAAGAAA
1 AAAAGAAA
11833859 AA
1 AA
11833861 GAATAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Done.