Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 73
Found at i:176466 original size:21 final size:21
Alignment explanation
Indices: 176436--176483 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
176426 GCAGGGGTAC
* *
176436 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
176457 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
176478 ATGCCA
1 ATGCCA
176484 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:176513 original size:21 final size:21
Alignment explanation
Indices: 176487--176580 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
176477 TATGCCATCT
176487 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
176508 CCGCAGGGTTACATTCCGATC
1 CCGCAGGGTTACATTCCGAGC
*
176529 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
*
176550 CCGCCA-GGTTACATTCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
176571 CCGCAGGGTT
1 CCGCAGGGTT
176581 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.26, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:177149 original size:33 final size:33
Alignment explanation
Indices: 177101--177195 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
177091 AAATGTTTTT
177101 AAAATACAAATATATTATTCGAAATTTAAAATA
1 AAAATACAAATATATTATTCGAAATTTAAAATA
* *
177134 AAAATA-AAATAATATTATTC-AAATTTAAATTT
1 AAAATACAAAT-ATATTATTCGAAATTTAAAATA
* *
177166 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATACAAA-TATATTATTCGAAATTTAA
177196 CATTAAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
32 20 0.36
33 26 0.47
34 9 0.16
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (33 bp):
AAAATACAAATATATTATTCGAAATTTAAAATA
Found at i:178096 original size:128 final size:128
Alignment explanation
Indices: 177591--178844 Score: 2151
Period size: 128 Copynumber: 9.9 Consensus size: 128
177581 TTACCTGATT
*
177591 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
177656 TGAC-AAATAATAGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
177717 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* **
177782 TGATG-AATAATGGAAGGCGCGCCCTTGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
177844 TACTGATATATCTAGTGTCCCCGAGGGACATGA-TGACATAATAGGGCAATGATAACATA-TCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
177907 TGACGAAATAATGGAAGGCGCGCCCCCGGGGACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
177970 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
178035 TGACGAAATAATGGAAGGCGCGCCCCCGGGGACTCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
178098 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
178163 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
178226 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
178291 TGACGAAATAATGAAAGGCGCGCCCCCGGGGACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
178354 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGC-ATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
178418 TGACAAAATAATGAAAGGCGCG-CCCCGGGGACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
178480 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* ****
178545 TGACGAAATAATGGAAGGCGCGCCCCCGTGAACGCGCCTTCATGT--CCCCTGAGAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGA-AATAATAGG
178607 TACTGATATA--TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
178670 TGATGAAAT-ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
178732 TACTG--ATATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
178795 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
178845 ATACTCCGAT
Statistics
Matches: 1075, Mismatches: 39, Indels: 28
0.94 0.03 0.02
Matches are distributed among these distances:
123 3 0.00
124 34 0.03
125 143 0.13
126 330 0.31
127 183 0.17
128 382 0.36
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:186115 original size:36 final size:36
Alignment explanation
Indices: 186075--186148 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
186065 AATCGACCCC
186075 GATCGGTGTGAATTTGTGAACCACTGCAAAAATCAT
1 GATCGGTGTGAATTTGTGAACCACTGCAAAAATCAT
186111 GATCGGTGTGAATTTGTGAACCACTGCAAAAATCAT
1 GATCGGTGTGAATTTGTGAACCACTGCAAAAATCAT
186147 GA
1 GA
186149 GTAGCGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (36 bp):
GATCGGTGTGAATTTGTGAACCACTGCAAAAATCAT
Found at i:192317 original size:15 final size:15
Alignment explanation
Indices: 192297--192331 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
192287 ATCAAAGGTA
192297 GAAACGAAATATGAG
1 GAAACGAAATATGAG
192312 GAAACGAAATATGAG
1 GAAACGAAATATGAG
192327 GAAAC
1 GAAAC
192332 TCATGATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.09, G:0.26, T:0.11
Consensus pattern (15 bp):
GAAACGAAATATGAG
Found at i:194305 original size:21 final size:21
Alignment explanation
Indices: 194281--194339 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
194271 CTGGTGCAGA
*
194281 GGGAATCGATACCCCTTGAAG
1 GGGAACCGATACCCCTTGAAG
*
194302 GGGAACCGATTCCCCATTTGAAG
1 GGGAACCGATACCCC--TTGAAG
*
194325 GGGAACCGATTCCCC
1 GGGAACCGATACCCC
194340 CTATAGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 13 0.38
23 21 0.62
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (21 bp):
GGGAACCGATACCCCTTGAAG
Found at i:194326 original size:23 final size:23
Alignment explanation
Indices: 194296--194339 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
194286 TCGATACCCC
194296 TTGAAGGGGAACCGATTCCCCAT
1 TTGAAGGGGAACCGATTCCCCAT
194319 TTGAAGGGGAACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
194340 CTATAGGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCAT
Found at i:194349 original size:21 final size:22
Alignment explanation
Indices: 194299--194350 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
194289 ATACCCCTTG
*
194299 AAGGGGAACCGATTCCCCATTT
1 AAGGGGAACCGATTCCCCATAT
*
194321 GAAGGGGAACCGATTCCCCCTAT
1 -AAGGGGAACCGATTCCCCATAT
194344 -AGGGGAA
1 AAGGGGAA
194351 TTGATACCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 7 0.26
23 20 0.74
ACGTcount: A:0.29, C:0.25, G:0.29, T:0.17
Consensus pattern (22 bp):
AAGGGGAACCGATTCCCCATAT
Found at i:195971 original size:18 final size:18
Alignment explanation
Indices: 195936--195973 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
195926 AGAACAGCAC
*
195936 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCACCACCA
*
195954 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
195972 GA
1 GA
195974 AGATCAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.26, T:0.03
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:200370 original size:21 final size:21
Alignment explanation
Indices: 200345--200392 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
200335 AAAGTGTAAA
* *
200345 TATAATTTA-AATGTTATATTT
1 TATAATTTACAATATAATA-TT
200366 TATAATTTACAATATAATATT
1 TATAATTTACAATATAATATT
200387 TATAAT
1 TATAAT
200393 GGACTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TATAATTTACAATATAATATT
Found at i:200509 original size:24 final size:25
Alignment explanation
Indices: 200464--200511 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
200454 TGTACTTTTG
* *
200464 TACAGCACTTTTAAAAATTCATTTC
1 TACAACACCTTTAAAAATTCATTTC
200489 TACAACACCTTTAAAAA-TCATTT
1 TACAACACCTTTAAAAATTCATTT
200512 TTCAAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.38
Consensus pattern (25 bp):
TACAACACCTTTAAAAATTCATTTC
Found at i:200514 original size:26 final size:26
Alignment explanation
Indices: 200459--200512 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
200449 TACACTGTAC
* * *
200459 TTTTGTACAGCACTTTTAAAAATTCA
1 TTTTCTACAACACCTTTAAAAATTCA
200485 -TTTCTACAACACCTTTAAAAA-TCA
1 TTTTCTACAACACCTTTAAAAATTCA
200509 TTTT
1 TTTT
200513 TCAAAAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (26 bp):
TTTTCTACAACACCTTTAAAAATTCA
Found at i:201000 original size:15 final size:16
Alignment explanation
Indices: 200961--201004 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
200951 CCCTACTTGA
200961 TTAAATATTTAATAAAT
1 TTAAATATTT-ATAAAT
**
200978 TTTTATATTT-TAAAT
1 TTAAATATTTATAAAT
200993 TTAAATATTTAT
1 TTAAATATTTAT
201005 TTTTACATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATATTTATAAAT
Found at i:201849 original size:20 final size:20
Alignment explanation
Indices: 201824--201868 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
201814 GGAATGAAAA
*
201824 AAAAGAGGCAGAAAGAAGAG
1 AAAAGAGGAAGAAAGAAGAG
*
201844 AAAAGAGGAAGAAATAAGAG
1 AAAAGAGGAAGAAAGAAGAG
201864 AAAAG
1 AAAAG
201869 CGAAAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.02
Consensus pattern (20 bp):
AAAAGAGGAAGAAAGAAGAG
Found at i:201875 original size:20 final size:20
Alignment explanation
Indices: 201833--201891 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
201823 AAAAAGAGGC
* *
201833 AGAAAGAAGAGAAAAGAGGA
1 AGAAATAAGAGAAAAGAGAA
*
201853 AGAAATAAGAGAAAAGCGAA
1 AGAAATAAGAGAAAAGAGAA
201873 AGAAAT--GAGAAGAAGAGAA
1 AGAAATAAGAGAA-AAGAGAA
201892 TATCGGTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.15
19 6 0.18
20 23 0.68
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.03
Consensus pattern (20 bp):
AGAAATAAGAGAAAAGAGAA
Found at i:205492 original size:14 final size:14
Alignment explanation
Indices: 205473--205515 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
205463 AATAATATAA
*
205473 TAAATAAATGAAGT
1 TAAATAAATGAAAT
*
205487 TAAATAAATTAAAT
1 TAAATAAATGAAAT
*
205501 TAAATTAAATTAAAT
1 TAAA-TAAATGAAAT
205516 AGTATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (14 bp):
TAAATAAATGAAAT
Found at i:205501 original size:5 final size:5
Alignment explanation
Indices: 205473--205515 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
205463 AATAATATAA
* *
205473 TAAA- TAAAT GAAGT TAAA- TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
205516 AGTATAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
4 8 0.24
5 25 0.76
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (5 bp):
TAAAT
Found at i:206541 original size:21 final size:20
Alignment explanation
Indices: 206495--206534 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
206485 TTAATTATAA
*
206495 AATAAACATTTATAATATTT
1 AATAAACAATTATAATATTT
206515 AATAAACAATTATAATATTT
1 AATAAACAATTATAATATTT
206535 TATTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAAACAATTATAATATTT
Found at i:206798 original size:20 final size:20
Alignment explanation
Indices: 206773--206820 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
206763 TCTTCTTCTC
*
206773 ATTTCTTTCTATTTTCT-CTT
1 ATTTCTTCCTATTTTCTAC-T
206793 ATTTCTTCCTATTTTCTACT
1 ATTTCTTCCTATTTTCTACT
206813 ATTTCTTC
1 ATTTCTTC
206821 TCCTCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTCTTCCTATTTTCTACT
Found at i:210433 original size:37 final size:37
Alignment explanation
Indices: 210392--210465 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
210382 AATCTGTGTA
210392 GTTTCCATTTGACACGATGACTTCAAGCTCTAGGGGG
1 GTTTCCATTTGACACGATGACTTCAAGCTCTAGGGGG
210429 GTTTCCATTTGACACGATGACTTCAAGCTCTAGGGGG
1 GTTTCCATTTGACACGATGACTTCAAGCTCTAGGGGG
210466 AGGCATTCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (37 bp):
GTTTCCATTTGACACGATGACTTCAAGCTCTAGGGGG
Found at i:216989 original size:20 final size:21
Alignment explanation
Indices: 216964--217027 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 21
216954 ATTTTGGTGC
*
216964 TGAGGGAATCGA-TCCCCCCA
1 TGAGGGAACCGATTCCCCCCA
**
216984 TGAGGGAACCGATTCCCCCTT
1 TGAGGGAACCGATTCCCCCCA
217005 TGAAGGGGAACCGATTCCCCCCA
1 TG-A-GGGAACCGATTCCCCCCA
217028 CAGGGGAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.31
21 8 0.22
22 1 0.03
23 16 0.44
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.17
Consensus pattern (21 bp):
TGAGGGAACCGATTCCCCCCA
Found at i:218676 original size:12 final size:13
Alignment explanation
Indices: 218655--218686 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
218645 AGATGAGCCT
218655 GAGC-AGCCCGAG
1 GAGCAAGCCCGAG
218667 GAG-AAGCCCGAG
1 GAGCAAGCCCGAG
218679 GAGCAAGC
1 GAGCAAGC
218687 ACAACAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.31, C:0.28, G:0.41, T:0.00
Consensus pattern (13 bp):
GAGCAAGCCCGAG
Found at i:219310 original size:17 final size:17
Alignment explanation
Indices: 219288--219328 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
219278 GGGAGAAGTG
*
219288 TTAAATTTGTTTTAAAT
1 TTAAATGTGTTTTAAAT
219305 TTAAATGTGTTTTAAAT
1 TTAAATGTGTTTTAAAT
219322 TTAAATG
1 TTAAATG
219329 ATAAATGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (17 bp):
TTAAATGTGTTTTAAAT
Found at i:222337 original size:23 final size:23
Alignment explanation
Indices: 222311--222443 Score: 146
Period size: 23 Copynumber: 5.7 Consensus size: 23
222301 CTTGTACTTT
* *
222311 AATTATTAATTGGTATTGAACAC
1 AATTATTAATTGTTATCGAACAC
* *
222334 AATTATTAATT-TTATCAAACTAAT
1 AATTATTAATTGTTATCGAAC--AC
*
222358 AATTATTAATTGGTATCGAACAC
1 AATTATTAATTGTTATCGAACAC
* *
222381 AATTATTAATT-TTATCAAACTAAT
1 AATTATTAATTGTTATCGAAC--AC
222405 AATTATTAATTGTTATCGAACAC
1 AATTATTAATTGTTATCGAACAC
222428 AATTATTAATT-TTATC
1 AATTATTAATTGTTATC
222444 AAACTAATAA
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
22 18 0.20
23 35 0.38
24 24 0.26
25 15 0.16
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (23 bp):
AATTATTAATTGTTATCGAACAC
Found at i:222366 original size:24 final size:24
Alignment explanation
Indices: 222334--222454 Score: 151
Period size: 24 Copynumber: 5.1 Consensus size: 24
222324 TATTGAACAC
222334 AATTATTAATTTTATCAAACTAAT
1 AATTATTAATTTTATCAAACTAAT
* * *
222358 AATTATTAATTGGTATCGAAC--AC
1 AATTATTAATT-TTATCAAACTAAT
222381 AATTATTAATTTTATCAAACTAAT
1 AATTATTAATTTTATCAAACTAAT
* *
222405 AATTATTAATTGTTATCGAAC--AC
1 AATTATTAATT-TTATCAAACTAAT
222428 AATTATTAATTTTATCAAACTAAT
1 AATTATTAATTTTATCAAACTAAT
222452 AAT
1 AAT
222455 AATTTGGTAT
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
22 15 0.19
23 24 0.30
24 27 0.33
25 15 0.19
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (24 bp):
AATTATTAATTTTATCAAACTAAT
Found at i:222379 original size:47 final size:47
Alignment explanation
Indices: 222310--222454 Score: 272
Period size: 47 Copynumber: 3.1 Consensus size: 47
222300 TCTTGTACTT
*
222310 TAATTATTAATTGGTATTGAACACAATTATTAATTTTATCAAACTAA
1 TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAA
222357 TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAA
1 TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAA
*
222404 TAATTATTAATTGTTATCGAACACAATTATTAATTTTATCAAACTAA
1 TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAA
222451 TAAT
1 TAAT
222455 AATTTGGTAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (47 bp):
TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAA
Found at i:222459 original size:20 final size:20
Alignment explanation
Indices: 222387--222459 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 20
222377 ACACAATTAT
222387 TAATTTTATCAAACTAATAATTA
1 TAATTTTATCAAACTAAT-A--A
*
222410 TTAATTGTTATCGAACAC-AATTAT
1 -TAATT-TTATC-AA-ACTAA-TAA
222434 TAATTTTATCAAACTAATAA
1 TAATTTTATCAAACTAATAA
222454 TAATTT
1 TAATTT
222460 GGTATTTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
20 10 0.24
21 4 0.10
22 5 0.12
23 5 0.12
24 5 0.12
25 5 0.12
26 5 0.12
27 3 0.07
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (20 bp):
TAATTTTATCAAACTAATAA
Found at i:222500 original size:94 final size:93
Alignment explanation
Indices: 222310--222513 Score: 234
Period size: 94 Copynumber: 2.2 Consensus size: 93
222300 TCTTGTACTT
*
222310 TAATTATTAATTGGTATTGAACACAATTATTAATTTTATCAAACTAATAATTATTAATTGGTATC
1 TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAATAATTA-TAATTGGTATC
* * ** *
222375 GAACACAATTATTAATTTTATCAAACTAA
65 GAACACAATTACTAAATACAACAAACTAA
* * *
222404 TAATTATTAATTGTTATCGAACACAATTATTAATTTTATCAAACTAATAA-TA-ATTTGGTATTT
1 TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAATAATTATAATTGGTA-TC
* *
222467 GAATATAATT-CTAAATACAACAAACTTAAAA
65 GAACACAATTACTAAATACAACAAAC-T--AA
*
222498 TAAGTATTAATTGGTA
1 TAATTATTAATTGGTA
222514 AATAATAATC
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
91 17 0.18
92 10 0.11
93 2 0.02
94 64 0.69
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.41
Consensus pattern (93 bp):
TAATTATTAATTGGTATCGAACACAATTATTAATTTTATCAAACTAATAATTATAATTGGTATCG
AACACAATTACTAAATACAACAAACTAA
Found at i:222595 original size:34 final size:34
Alignment explanation
Indices: 222555--222647 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
222545 AATGGTAATA
* *
222555 AACAAAATTATCAAAATAAATTAAGAAAAAGTCC
1 AACAAAATTAACAAAATAAATTAAGAAAAAATCC
* * **
222589 AACAAAATAAACAAAAAAAAATTAA-AAAAAATTT
1 AACAAAATTAAC-AAAATAAATTAAGAAAAAATCC
* *
222623 AACCAAATTAACAAAATAAAATAAG
1 AACAAAATTAACAAAATAAATTAAG
222648 TATTTAATGA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
33 10 0.21
34 26 0.55
35 11 0.23
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTAAGAAAAAATCC
Found at i:225528 original size:6 final size:6
Alignment explanation
Indices: 225517--225541 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
225507 AATTAGTGGG
225517 ATTCTC ATTCTC ATTCTC ATTCTC A
1 ATTCTC ATTCTC ATTCTC ATTCTC A
225542 ACCCACCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTCTC
Found at i:228311 original size:18 final size:20
Alignment explanation
Indices: 228287--228329 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
228277 CCCCGTAATC
228287 ATATTTCT-T-GGTAATCTT
1 ATATTTCTATCGGTAATCTT
*
228305 TTATTTCTATCGGTAATCTT
1 ATATTTCTATCGGTAATCTT
228325 ATATT
1 ATATT
228330 CTGTGAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 13 0.62
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (20 bp):
ATATTTCTATCGGTAATCTT
Found at i:233105 original size:28 final size:24
Alignment explanation
Indices: 233068--233129 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
233058 ACATATATTC
233068 TTTC-AAGTTGACACTTAAGAATTTTT
1 TTTCAAAGTTGACAC---AGAATTTTT
*
233094 GTTTCAAAGTTGACACATAATTTTT
1 -TTTCAAAGTTGACACAGAATTTTT
233119 TTTCAAAGTTG
1 TTTCAAAGTTG
233130 GTATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 11 0.33
25 8 0.24
27 4 0.12
28 10 0.30
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (24 bp):
TTTCAAAGTTGACACAGAATTTTT
Found at i:233947 original size:16 final size:15
Alignment explanation
Indices: 233917--233957 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
233907 AAGAAAGATT
*
233917 TTTAAAAATAAAATA
1 TTTAAAAAAAAAATA
233932 TTTAAAATAAAAAATA
1 TTTAAAA-AAAAAATA
233948 TATTAAAAAA
1 T-TTAAAAAA
233958 TTAATCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTTAAAAAAAAAATA
Found at i:235184 original size:42 final size:36
Alignment explanation
Indices: 235099--235169 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
235089 GAATTAAATG
**
235099 GGGACGGGAAAAAATCGTTTATGCTAAACGGGGACA
1 GGGACGGGAAAAAATAATTTATGCTAAACGGGGACA
*
235135 GGGACGGGGAAAAATAATTTATGCTAAACGGGGAC
1 GGGACGGGAAAAAATAATTTATGCTAAACGGGGAC
235170 GGAGATAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.34, T:0.17
Consensus pattern (36 bp):
GGGACGGGAAAAAATAATTTATGCTAAACGGGGACA
Found at i:235256 original size:4 final size:4
Alignment explanation
Indices: 235247--235360 Score: 91
Period size: 4 Copynumber: 30.5 Consensus size: 4
235237 TAAAAATAAT
* * * *
235247 TATA TATA TATA TATA TATA CATA -ATA T-TA -ATA AATT TA-A TTTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
235291 AAT- TA-A TATA TATA TATA TATA TATA TATA TATA TATA -ATA TTTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
235336 TATA TTTA -ATT TAAA TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TA
235361 CCCGACCCGA
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
3 15 0.17
4 71 0.83
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:235258 original size:6 final size:6
Alignment explanation
Indices: 235247--235360 Score: 91
Period size: 6 Copynumber: 20.3 Consensus size: 6
235237 TAAAAATAAT
* * * *
235247 TATATA TATATA TATATA TACATA -ATAT- TA-ATA AATTTA -ATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
235291 AAT-TA -ATATA TATATA TATATA TATATA TATATA TATA-A TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
235336 TATATT TA-ATT TAAATA TATATA TA
1 TATATA TATATA TATATA TATATA TA
235361 CCCGACCCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
4 4 0.04
5 23 0.25
6 64 0.70
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:235333 original size:58 final size:56
Alignment explanation
Indices: 235247--235360 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 56
235237 TAAAAATAAT
235247 TATATATATATATATATATACATAATATTAATAAATTTAATTTAAATTAATATATATA
1 TATATATATATATATATATACATAATATTAATAAATTTAATTTAAA-T-ATATATATA
* * *
235305 TATATATATATATATATATATATAATATTTATATATTTAATTTAAATATATATATA
1 TATATATATATATATATATACATAATATTAATAAATTTAATTTAAATATATATATA
235361 CCCGACCCGA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
56 9 0.17
57 1 0.02
58 43 0.81
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (56 bp):
TATATATATATATATATATACATAATATTAATAAATTTAATTTAAATATATATATA
Found at i:237792 original size:64 final size:64
Alignment explanation
Indices: 237691--237816 Score: 234
Period size: 64 Copynumber: 2.0 Consensus size: 64
237681 CCGTCATGGC
* *
237691 TCGTCCATGTCATGTCATCGTGCCGTTAACGGATTAACGGCGGGGTGACTTAATTGGAGTAAGG
1 TCGTCCATGCCATGTCATCGTGCCGTTAACGGATTAACGGCAGGGTGACTTAATTGGAGTAAGG
237755 TCGTCCATGCCATGTCATCGTGCCGTTAACGGATTAACGGCAGGGTGACTTAATTGGAGTAA
1 TCGTCCATGCCATGTCATCGTGCCGTTAACGGATTAACGGCAGGGTGACTTAATTGGAGTAA
237817 AACATAAACG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (64 bp):
TCGTCCATGCCATGTCATCGTGCCGTTAACGGATTAACGGCAGGGTGACTTAATTGGAGTAAGG
Found at i:238204 original size:24 final size:24
Alignment explanation
Indices: 238162--238224 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
238152 ACTTACATAA
*
238162 TATATTAACTTTAAGAAATATTTTT
1 TATATTAA-TTTAAGAAATATATTT
**
238187 TATATTAATTTATTAAATATATTT
1 TATATTAATTTAAGAAATATATTT
*
238211 GATTATTAATTTAA
1 TA-TATTAATTTAA
238225 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 14 0.44
25 18 0.56
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
TATATTAATTTAAGAAATATATTT
Found at i:243396 original size:20 final size:20
Alignment explanation
Indices: 243373--243422 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
243363 GGAAAACTAT
243373 ATGAGTTAATTGAATATATG
1 ATGAGTTAATTGAATATATG
*
243393 ATGAGTTAATTGATTATATG
1 ATGAGTTAATTGAATATATG
243413 ATGAGTTAAT
1 ATGAGTTAAT
243423 CGAGTTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (20 bp):
ATGAGTTAATTGAATATATG
Found at i:243432 original size:20 final size:19
Alignment explanation
Indices: 243373--243434 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
243363 GGAAAACTAT
*
243373 ATGAGTTAATTGAATATATG
1 ATGAGTTAATTG-ATTTATG
243393 ATGAGTTAATTGATTATATG
1 ATGAGTTAATTGATT-TATG
*
243413 ATGAGTTAATCGAGTTTATG
1 ATGAGTTAATTGA-TTTATG
243433 AT
1 AT
243435 TTTTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.05
20 34 0.89
21 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (19 bp):
ATGAGTTAATTGATTTATG
Found at i:245593 original size:24 final size:24
Alignment explanation
Indices: 245566--245764 Score: 94
Period size: 21 Copynumber: 8.1 Consensus size: 24
245556 TTGATATAAT
245566 ATACATATTATATAGTTTTTGAAA
1 ATACATATTATATAGTTTTTGAAA
*
245590 ATACATA-TATGT--TTTTTAGAAA
1 ATACATATTATATAGTTTTT-GAAA
* *
245612 AT--ATATAATATAATTTTTGAATATA
1 ATACATATTATATAGTTTTTG-A-A-A
*
245637 TATATATATATATATAGTTTTT-AAA
1 -ATACATAT-TATATAGTTTTTGAAA
* * *
245662 TAAAAATATTATATATAGTATGATTTTAAA
1 -ATACATA-T-TATATAGT-T--TTTGAAA
245692 A-ACATATTATATATAGTTTTTGAAA
1 ATACATA-T-TATATAGTTTTTGAAA
* * * *
245717 ACATATATAACATAGTTTTTGAAA
1 ATACATATTATATAGTTTTTGAAA
*
245741 AT--AT-GTATATAGTTTTTGAAA
1 ATACATATTATATAGTTTTTGAAA
245762 ATA
1 ATA
245765 TTTTTGAAAA
Statistics
Matches: 141, Mismatches: 16, Indels: 38
0.72 0.08 0.19
Matches are distributed among these distances:
20 3 0.02
21 24 0.17
22 9 0.06
23 10 0.07
24 23 0.16
25 16 0.11
26 17 0.12
27 3 0.02
28 19 0.13
29 14 0.10
30 3 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (24 bp):
ATACATATTATATAGTTTTTGAAA
Found at i:245599 original size:26 final size:26
Alignment explanation
Indices: 245570--245743 Score: 88
Period size: 24 Copynumber: 6.9 Consensus size: 26
245560 TATAATATAC
245570 ATATTATATAGTTTTTGAAAATACAT
1 ATATTATATAGTTTTTGAAAATACAT
* *
245596 ATA-TGT-T--TTTTAGAAAAT--AT
1 ATATTATATAGTTTTTGAAAATACAT
* *
245616 ATA--ATATAATTTTTGAATATATATAT
1 ATATTATATAGTTTTTGAA-A-ATACAT
* *
245642 ATATATATATAGTTTTT--AAATAAAA
1 ATAT-TATATAGTTTTTGAAAATACAT
*
245667 ATATTATATATAGTATGATTTTAAAA-ACAT
1 ATA-T-TATATAGT-T--TTTGAAAATACAT
245697 AT-TATATATAGTTTTTG-AAA-ACAT
1 ATAT-TATATAGTTTTTGAAAATACAT
* *
245721 ATATAACATAGTTTTTGAAAATA
1 ATATTATATAGTTTTTGAAAATA
245744 TGTATATAGT
Statistics
Matches: 117, Mismatches: 12, Indels: 38
0.70 0.07 0.23
Matches are distributed among these distances:
19 1 0.01
20 6 0.05
22 17 0.15
23 1 0.01
24 23 0.20
25 16 0.14
26 20 0.17
27 3 0.03
28 10 0.09
29 13 0.11
30 4 0.03
31 3 0.03
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (26 bp):
ATATTATATAGTTTTTGAAAATACAT
Found at i:245628 original size:22 final size:23
Alignment explanation
Indices: 245570--245646 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 23
245560 TATAATATAC
* *
245570 ATAT-TATATAGTTTTTGAAAAT
1 ATATATATATAATTTTAGAAAAT
* * *
245592 ACATATATGT-TTTTTAGAAAAT
1 ATATATATATAATTTTAGAAAAT
* *
245614 ATATA-ATATAATTTTTGAATAT
1 ATATATATATAATTTTAGAAAAT
245636 ATATATATATA
1 ATATATATATA
245647 TATATAGTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.07
22 31 0.72
23 9 0.21
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (23 bp):
ATATATATATAATTTTAGAAAAT
Found at i:245648 original size:30 final size:31
Alignment explanation
Indices: 245612--245706 Score: 92
Period size: 29 Copynumber: 3.2 Consensus size: 31
245602 TTTTTAGAAA
* * *
245612 ATATATAATATAATTTTTGAATATATATA-T
1 ATATATAATATAATTTTTAAATAAAAATATT
*
245642 ATATAT-ATATAGTTTTTAAATAAAAATATT
1 ATATATAATATAATTTTTAAATAAAAATATT
* * *
245672 ATATATAGTATGA-TTTT-AA-AAACATATT
1 ATATATAATATAATTTTTAAATAAAAATATT
245700 ATATATA
1 ATATATA
245707 GTTTTTGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
28 15 0.27
29 20 0.36
30 17 0.31
31 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (31 bp):
ATATATAATATAATTTTTAAATAAAAATATT
Found at i:245657 original size:28 final size:27
Alignment explanation
Indices: 245610--245680 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
245600 GTTTTTTAGA
*
245610 AAATATATA-ATATA-ATTTTTGAATAT
1 AAATATATATATATATAGTTTTGAA-AT
* *
245636 ATATATATATATATATAGTTTTTAAAT
1 AAATATATATATATATAGTTTTGAAAT
*
245663 AAAAATAT-TATATATAGT
1 AAATATATATATATATAGT
245681 ATGATTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 18 0.47
27 13 0.34
28 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (27 bp):
AAATATATATATATATAGTTTTGAAAT
Found at i:245698 original size:28 final size:31
Alignment explanation
Indices: 245636--245708 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 31
245626 TTTTGAATAT
*
245636 ATATATATATATA-TATAGTTTTTAAATAAAA
1 ATAT-TATATATAGTATAGATTTTAAATAAAA
*
245667 ATATTATATATAGTAT-GATTTT-AA-AAAC
1 ATATTATATATAGTATAGATTTTAAATAAAA
245695 ATATTATATATAGT
1 ATATTATATATAGT
245709 TTTTGAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 17 0.44
29 2 0.05
30 13 0.33
31 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (31 bp):
ATATTATATATAGTATAGATTTTAAATAAAA
Found at i:245749 original size:26 final size:24
Alignment explanation
Indices: 245685--245762 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
245675 TATAGTATGA
* *
245685 TTTTAAAAACATAT-TATATATAGT
1 TTTTGAAAACATATATA-ACATAGT
245709 TTTTGAAAACATATATAACATAGT
1 TTTTGAAAACATATATAACATAGT
* *
245733 TTTTG-AAA-ATATGT-ATATAGT
1 TTTTGAAAACATATATAACATAGT
245754 TTTTGAAAA
1 TTTTGAAAA
245763 TATTTTTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.23
22 8 0.17
23 3 0.06
24 24 0.50
25 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (24 bp):
TTTTGAAAACATATATAACATAGT
Found at i:245796 original size:22 final size:25
Alignment explanation
Indices: 245765--245826 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 25
245755 TTTGAAAATA
* *
245765 TTTTTGAAAACATGTTACA-TA-AG
1 TTTTTAAAAACATATTACATTATAG
*
245788 -TTTTAAAAATATATTACATTATAG
1 TTTTTAAAAACATATTACATTATAG
*
245812 TTTTTAAAAATATAT
1 TTTTTAAAAACATAT
245827 ATAATATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 15 0.45
23 2 0.06
24 2 0.06
25 14 0.42
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTTAAAAACATATTACATTATAG
Found at i:248873 original size:23 final size:23
Alignment explanation
Indices: 248847--248924 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
248837 CACCACAGCT
248847 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
248870 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
248893 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
248916 TATAATAAT
1 CAT-ATAAT
248925 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:249102 original size:103 final size:103
Alignment explanation
Indices: 248931--249148 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
248921 TAATGTCCAT
* * *
248931 AAGGATCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
248996 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
249034 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
*
249099 GACTTCACTCATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
249137 AAGGACCACATA
1 AAGGACCACATA
249149 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:255117 original size:23 final size:22
Alignment explanation
Indices: 255073--255138 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
255063 TTTCAATAAG
* * *
255073 TATGCTTGTATGACACGATTTCA
1 TATGCTT-TATGGCATGTTTTCA
*
255096 TATGCCTTTATGGCATGTTTTCT
1 TATG-CTTTATGGCATGTTTTCA
*
255119 TATGCTTTTTGGCATGTTTT
1 TATGCTTTATGGCATGTTTT
255139 TTTATTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.41
23 19 0.51
24 3 0.08
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (22 bp):
TATGCTTTATGGCATGTTTTCA
Found at i:255139 original size:23 final size:23
Alignment explanation
Indices: 255091--255143 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
255081 TATGACACGA
*
255091 TTTCATATGCCTTTATGGCATGT
1 TTTCTTATGCCTTTATGGCATGT
*
255114 TTTCTTATG-CTTTTTGGCATGT
1 TTTCTTATGCCTTTATGGCATGT
*
255136 TTTTTTAT
1 TTTCTTAT
255144 TGTTTGGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.58
Consensus pattern (23 bp):
TTTCTTATGCCTTTATGGCATGT
Found at i:256204 original size:14 final size:14
Alignment explanation
Indices: 256187--256219 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
256177 ATTTCTATGT
*
256187 AGGGAATTATTTGC
1 AGGGAATTATTTAC
256201 AGGGAATTATTTAC
1 AGGGAATTATTTAC
256215 AGGGA
1 AGGGA
256220 TTACTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:257313 original size:22 final size:22
Alignment explanation
Indices: 257288--257332 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
257278 TTTAATTTGA
*
257288 AACAAAACTACATTGGATTAAC
1 AACAAAACTACATTGGACTAAC
* **
257310 AACAGAACTGTATTGGACTAAC
1 AACAAAACTACATTGGACTAAC
257332 A
1 A
257333 GATATTCATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (22 bp):
AACAAAACTACATTGGACTAAC
Found at i:258289 original size:20 final size:19
Alignment explanation
Indices: 258253--258291 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
258243 TGTCTATTAT
258253 ATTTTTTTTATTTTCTTTA
1 ATTTTTTTTATTTTCTTTA
258272 ATTTTATTTT-TTTATCTTTA
1 ATTTT-TTTTATTT-TCTTTA
258292 TAATCGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTTTTTATTTTCTTTA
Found at i:260008 original size:17 final size:17
Alignment explanation
Indices: 259986--260021 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
259976 CAACGTTTTG
259986 ACTTAATAATATTTCAT
1 ACTTAATAATATTTCAT
260003 ACTTAATAATATTTCAT
1 ACTTAATAATATTTCAT
260020 AC
1 AC
260022 GTTGTACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (17 bp):
ACTTAATAATATTTCAT
Found at i:261089 original size:20 final size:20
Alignment explanation
Indices: 261060--261107 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
261050 TAATATTGTG
*
261060 ATTTTGAATGGACAA-ATATT
1 ATTTTTAATGGACAAGATA-T
* *
261080 ATTTTTAATGTATAAGATAT
1 ATTTTTAATGGACAAGATAT
261100 ATTTTTAA
1 ATTTTTAA
261108 AAACTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (20 bp):
ATTTTTAATGGACAAGATAT
Found at i:261820 original size:31 final size:31
Alignment explanation
Indices: 261785--261862 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
261775 TTTAACATCC
261785 AAGTGACCAAAACTTAATAAAACGATAACAT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
* *
261816 AAGTGACCAAAACTTAATAAAACTATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
261847 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
261863 TTTTTTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAACAT
Found at i:265136 original size:19 final size:18
Alignment explanation
Indices: 265112--265147 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
265102 ATCTTCCCTG
*
265112 ATTTGGATTCTCGATTTGA
1 ATTTGGATACT-GATTTGA
265131 ATTTGGATACTGATTTG
1 ATTTGGATACTGATTTG
265148 CGTTCGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (18 bp):
ATTTGGATACTGATTTGA
Found at i:266832 original size:65 final size:64
Alignment explanation
Indices: 266730--266850 Score: 217
Period size: 65 Copynumber: 1.9 Consensus size: 64
266720 AGGAAAAGAG
266730 TGGACCTTGGCGGAATAGCAACATTGAATGAGAATATCATACCGGGCAA-GCCTAATTAGCCTA
1 TGGACCTTGGCGGAATAGCAACATTGAATGAGAATATCATACCGGGCAATGCCTAATTAGCCTA
266793 TGGACCTTGGCGGAATATAGCAACATTGAATGAGAATATCATACCGGGCAATGCCTAA
1 TGGACCTTGGCGG-A-ATAGCAACATTGAATGAGAATATCATACCGGGCAATGCCTAA
266851 AAGAGCACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
63 13 0.24
64 1 0.02
65 35 0.64
66 6 0.11
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (64 bp):
TGGACCTTGGCGGAATAGCAACATTGAATGAGAATATCATACCGGGCAATGCCTAATTAGCCTA
Found at i:277758 original size:22 final size:23
Alignment explanation
Indices: 277728--277801 Score: 100
Period size: 22 Copynumber: 3.3 Consensus size: 23
277718 CACCACAGCT
*
277728 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
277751 CGTA-AAATTGCACCGAAGTG-CC
1 CGTAGAAA-TGCACCGAAGTGCCC
*
277773 CGTAGAATTGCACCGAAGTG-CC
1 CGTAGAAATGCACCGAAGTGCCC
277795 CGTAGAA
1 CGTAGAA
277802 TTATGTCCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
22 30 0.62
23 18 0.38
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:277802 original size:22 final size:22
Alignment explanation
Indices: 277736--277803 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
277726 CTCGTATAAA
*
277736 TGCACCGAAGTGCCCCGTAAAAT
1 TGCACCGAAGTG-CCCGTAGAAT
277759 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
277781 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
277803 T
1 T
277804 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 32 0.73
23 12 0.27
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:278059 original size:30 final size:30
Alignment explanation
Indices: 278014--278072 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
278004 ATCGCGTAGT
* *
278014 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
278044 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
278073 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:278473 original size:18 final size:19
Alignment explanation
Indices: 278436--278472 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
278426 CTTTTTCTCA
*
278436 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
278455 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
278473 TCAAGCAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:278598 original size:67 final size:66
Alignment explanation
Indices: 278437--278608 Score: 220
Period size: 68 Copynumber: 2.6 Consensus size: 66
278427 TTTTTCTCAT
* * *
278437 GGGGGAATCGGTTCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATG
1 GGGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
278502 A
66 A
* * * *
278503 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTT--CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
278567 TGA
64 TGA
* *
278570 GGGGGTATCGGTTCCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCTG--GGGGTACCGATTCCCCT
278609 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
65 6 0.06
66 12 0.13
67 35 0.38
68 40 0.43
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
A
Found at i:284575 original size:21 final size:22
Alignment explanation
Indices: 284536--284601 Score: 109
Period size: 21 Copynumber: 3.0 Consensus size: 22
284526 CAGCTATAAA
284536 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
284559 TGCA-CGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
284580 TGCACCGAAGTGCCCG-AGAAT
1 TGCACCGAAGTGCCCGTAGAAT
284601 T
1 T
284602 ATGTCCATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.48
22 18 0.43
23 4 0.10
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:285355 original size:65 final size:66
Alignment explanation
Indices: 285234--285379 Score: 192
Period size: 65 Copynumber: 2.3 Consensus size: 66
285224 TTTTTCTCAT
* * *
285234 GGGGGAATCGGTT-CCCCCCTGGGGGTATCGATTCCCTCAAGCAATCTGGAATTTCA-TACGATG
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCTCAAGCAATCTGGAAATTCATTACGATG
285297 A
66 A
* * * *
285298 GGGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATT-CCCTCAAGCAATCTGGAAATTCATTACGAT
285362 GA
65 GA
285364 GGGGGTATC-GTTCCCC
1 GGGGGTATCGGTTCCCC
285380 TTGAATGGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 23 0.32
65 34 0.47
66 15 0.21
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:285396 original size:66 final size:64
Alignment explanation
Indices: 285234--285401 Score: 189
Period size: 66 Copynumber: 2.6 Consensus size: 64
285224 TTTTTCTCAT
* * *
285234 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATT-CCCTCAAGCAATCTGGAATTTCATACGATGA
1 GGGGGTATCGGTTCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATACGATGA
* * * *
285298 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTTG
1 GGGGGTATCGGTT-CCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCA-TACGATG
285363 A
64 A
*
285364 GGGGGTATC-GTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG---GGGTACCGATTCCCCT
285402 AACCCAGAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
63 6 0.07
64 23 0.26
65 30 0.33
66 31 0.34
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (64 bp):
GGGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATACGATGA
Found at i:292319 original size:18 final size:16
Alignment explanation
Indices: 292296--292330 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
292286 AATTCCAAGA
292296 AAATATATTAATTTTTAT
1 AAATATA-T-ATTTTTAT
292314 AAATATATATTTTTAT
1 AAATATATATTTTTAT
292330 A
1 A
292331 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATATATTTTTAT
Found at i:292452 original size:33 final size:33
Alignment explanation
Indices: 292415--292493 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
292405 CTTAATATAA
292415 AAAAATAAATAAATATTAATAAAATATTTCTCT
1 AAAAATAAATAAATATTAATAAAATATTTCTCT
292448 AAAAATAAATAAATATTAATAAAATATTTCTCT
1 AAAAATAAATAAATATTAATAAAATATTTCTCT
*
292481 AAAAATAATTAAA
1 AAAAATAAATAAA
292494 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (33 bp):
AAAAATAAATAAATATTAATAAAATATTTCTCT
Found at i:292454 original size:19 final size:19
Alignment explanation
Indices: 292432--292488 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
292422 AATAAATATT
292432 AATAAAATATTTCTCTAAA
1 AATAAAATATTTCTCTAAA
** *
292451 AAT-AAATAAATAT-T---
1 AATAAAATATTTCTCTAAA
292465 AATAAAATATTTCTCTAAA
1 AATAAAATATTTCTCTAAA
292484 AATAA
1 AATAA
292489 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 10
0.63 0.14 0.23
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 1 0.04
17 1 0.04
18 7 0.26
19 8 0.30
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATAAAATATTTCTCTAAA
Found at i:292690 original size:16 final size:17
Alignment explanation
Indices: 292659--292693 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
292649 AATTTTTATT
292659 TAATAGAAAAAAATAAA
1 TAATAGAAAAAAATAAA
*
292676 TAATA-AAATAAATAAA
1 TAATAGAAAAAAATAAA
292692 TA
1 TA
292694 TTATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
TAATAGAAAAAAATAAA
Found at i:293009 original size:13 final size:13
Alignment explanation
Indices: 292991--293015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
292981 AAATATAAAT
292991 AAAACAAAATTAC
1 AAAACAAAATTAC
293004 AAAACAAAATTA
1 AAAACAAAATTA
293016 AAATGCACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAACAAAATTAC
Found at i:294017 original size:3 final size:3
Alignment explanation
Indices: 294011--294065 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
294001 ATTTATTATT
* * * *
294011 TAA TAA TAA TAA TAT TAA TAA TAA TAA T-A TAA TTA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
294058 TAA TAA TA
1 TAA TAA TA
294066 TTTATAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:294031 original size:12 final size:12
Alignment explanation
Indices: 294011--294074 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
294001 ATTTATTATT
*
294011 TAATAATAATAA
1 TAATAATATTAA
* *
294023 TATTAATAATAA
1 TAATAATATTAA
294035 TAAT-ATAATT-A
1 TAATAAT-ATTAA
*
294046 TAATAATATTTA
1 TAATAATATTAA
*
294058 TAATAATATTTA
1 TAATAATATTAA
294070 TAATA
1 TAATA
294075 TAAATAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.22
12 36 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:294565 original size:122 final size:121
Alignment explanation
Indices: 294411--294740 Score: 545
Period size: 122 Copynumber: 2.7 Consensus size: 121
294401 GAATTAAGGC
*
294411 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC-TTCTTCAGATGAGTTCTTCTCATTAT
* *
294476 GAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
65 GAACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAA
* *
294533 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCTTCTTCAGATGAGTTCTTCTCATTAT
*
294598 GAACTCTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAA
65 GAACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAA
294655 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-TTCTTTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTC--TTCAGATGAGTTCTTCTCATTA
*
294719 TGAACTTCCTCTGGAAATGTTG
64 TGAAC-TCTTCTGGAAATGTTG
294741 GTCCATCGAG
Statistics
Matches: 195, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
120 2 0.01
121 1 0.01
122 175 0.90
123 17 0.09
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (121 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTCTTCAGATGAGTTCTTCTCATTATG
AACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAA
Found at i:294840 original size:73 final size:71
Alignment explanation
Indices: 294761--294978 Score: 305
Period size: 73 Copynumber: 3.0 Consensus size: 71
294751 TGGTGGAAAT
*
294761 TTTTGTTTCTAGTGAAACTGTCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAATCTCAAGTG
1 TTTTGTTTCGAGTGAAACTGTCTCAAGCGAGACGAAT-TTGTTTTAAGAAAAACAATCTCAAGTG
294826 AGATAAA
65 AGATAAA
* * *
294833 TTGTTGTTTCGAGTGAAACTGTCTCAAGCGAGCCAAATTTTGTTTTAAGAAAAACAATCTCATGT
1 TT-TTGTTTCGAGTGAAACTGTCTCAAGCGAGACGAA-TTTGTTTTAAGAAAAACAATCTCAAGT
294898 GAGATAAA
64 GAGATAAA
* * * *
294906 TTTCTATTTCGAGTAAAACTGTCTCAA--GAGACGCAGTTTGTTTTAAGAAAAACAATCTCAATT
1 TTT-TGTTTCGAGTGAAACTGTCTCAAGCGAGACG-AATTTGTTTTAAGAAAAACAATCTCAAGT
294969 GAGATAAA
64 GAGATAAA
294977 TT
1 TT
294979 ACTATTTGAA
Statistics
Matches: 131, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
71 39 0.30
72 4 0.03
73 87 0.66
74 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (71 bp):
TTTTGTTTCGAGTGAAACTGTCTCAAGCGAGACGAATTTGTTTTAAGAAAAACAATCTCAAGTGA
GATAAA
Found at i:294858 original size:37 final size:36
Alignment explanation
Indices: 294761--294933 Score: 130
Period size: 36 Copynumber: 4.8 Consensus size: 36
294751 TGGTGGAAAT
* * *
294761 TTTTGTTTCTAGTGAAACTGTCTCAAGCGAGACGAA
1 TTTTGTTTCAAGTAAAACTGTCTCAAGCGAGACAAA
* * * ** * *
294797 TCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 TTTTGTTTCAAGTAAAACTGTCTCAAGCGAGACAAA
* * *
294833 TTGTTGTTTCGAGTGAAACTGTCTCAAGCGAGCCAAA
1 TT-TTGTTTCAAGTAAAACTGTCTCAAGCGAGACAAA
* * ** * * *
294870 TTTTGTTTTAAGAAAAACAATCTCATGTGAGATAAA
1 TTTTGTTTCAAGTAAAACTGTCTCAAGCGAGACAAA
* *
294906 TTTCTATTTCGAGTAAAACTGTCTCAAG
1 TTT-TGTTTCAAGTAAAACTGTCTCAAG
294934 AGACGCAGTT
Statistics
Matches: 98, Mismatches: 37, Indels: 3
0.71 0.27 0.02
Matches are distributed among these distances:
36 54 0.55
37 44 0.45
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (36 bp):
TTTTGTTTCAAGTAAAACTGTCTCAAGCGAGACAAA
Found at i:295709 original size:22 final size:22
Alignment explanation
Indices: 295684--295734 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
295674 AAGTTTTTAA
295684 CTTTGAAAAGAGAATCTATCAT
1 CTTTGAAAAGAGAATCTATCAT
295706 CTTTGAAAAGAGAATCTATCAT
1 CTTTGAAAAGAGAATCTATCAT
295728 CTTTGAA
1 CTTTGAA
295735 GAATGTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
CTTTGAAAAGAGAATCTATCAT
Found at i:297465 original size:77 final size:77
Alignment explanation
Indices: 297315--297466 Score: 198
Period size: 77 Copynumber: 2.0 Consensus size: 77
297305 TATTTCCTGA
* * *
297315 TGATATGAGCTTTCAAAAAGCCCCACATAGATCATTTCTGTCTGGAATGGGCCTTCAAAATTCCC
1 TGATATGAGCCTTCAAAAAGCCCCACATAGATCATTTCTGTCTGGAATGGGACTTCAAAATACCC
*
297380 AAATATTCAAAC
66 AAACATTCAAAC
* * * *
297392 TGATGTGAGCCTTCAAAATGCCCCACATGGATCATTTCTGTCT-GAATTGGTACTTCAAAATACC
1 TGATATGAGCCTTCAAAAAGCCCCACATAGATCATTTCTGTCTGGAA-TGGGACTTCAAAATACC
**
297456 TTAACATTCAA
65 CAAACATTCAA
297467 TTTTTGGTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
76 3 0.05
77 61 0.95
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (77 bp):
TGATATGAGCCTTCAAAAAGCCCCACATAGATCATTTCTGTCTGGAATGGGACTTCAAAATACCC
AAACATTCAAAC
Found at i:301661 original size:34 final size:36
Alignment explanation
Indices: 301619--301712 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 36
301609 GAAAAGATGC
*
301619 AAATGCAAAAATGAAAATGTAAATAC-AA-ACGTAA
1 AAATGCAAAAATGAAAATGCAAATACAAATACGTAA
* * * *
301653 AAATGCAAAGATGCAAATGCAAATACAAATATGTAG
1 AAATGCAAAAATGAAAATGCAAATACAAATACGTAA
301689 AAATGCAAAAAT-AAGAATGCAAAT
1 AAATGCAAAAATGAA-AATGCAAAT
301713 TGTGTAATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 23 0.46
35 3 0.06
36 24 0.48
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.18
Consensus pattern (36 bp):
AAATGCAAAAATGAAAATGCAAATACAAATACGTAA
Found at i:305087 original size:15 final size:16
Alignment explanation
Indices: 305061--305101 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
305051 TTTAATATCT
305061 AAAA-ATAA-AATAAA
1 AAAATATAATAATAAA
*
305075 AACAT-TAATAATAAA
1 AAAATATAATAATAAA
305090 AAAATATAATAA
1 AAAATATAATAA
305102 ATATTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.27
15 10 0.45
16 6 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATATAATAATAAA
Found at i:305786 original size:44 final size:41
Alignment explanation
Indices: 305709--305790 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
305699 GCAACGCGAT
* *
305709 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
305750 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
305791 TTGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 2 0.06
44 25 0.69
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:305796 original size:19 final size:20
Alignment explanation
Indices: 305704--305801 Score: 85
Period size: 19 Copynumber: 4.8 Consensus size: 20
305694 GATTCGCAAC
*
305704 GCGATTTTGAAAAATGTGTT
1 GCGATTGTGAAAAATGTGTT
* *
305724 GCGATAGT-TAAAATGTGTT
1 GCGATTGTGAAAAATGTGTT
305743 GCGAGAGTT-TGAAAAACGTGTTGTT
1 GC--GA-TTGTGAAAAA--TG-TGTT
*
305768 GCGATAGTGAAAAA-GTGTT
1 GCGATTGTGAAAAATGTGTT
305787 GCGATTGTGAAAAAT
1 GCGATTGTGAAAAAT
305802 CGAAAATAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
19 29 0.47
20 7 0.11
21 3 0.05
22 6 0.10
23 9 0.15
24 2 0.03
25 6 0.10
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.33
Consensus pattern (20 bp):
GCGATTGTGAAAAATGTGTT
Found at i:306241 original size:21 final size:21
Alignment explanation
Indices: 306214--306321 Score: 80
Period size: 21 Copynumber: 5.3 Consensus size: 21
306204 ATTTTGGAAA
306214 ATCGCAACACGAACTTGGATT
1 ATCGCAACACGAACTTGGATT
* * **
306235 ATTGC-A-ACGAATTTGGAAA
1 ATCGCAACACGAACTTGGATT
* *
306254 ATCGCAACGCGAACTTCGATT
1 ATCGCAACACGAACTTGGATT
* **
306275 ATCGC-A-ACGAATTTGGAAA
1 ATCGCAACACGAACTTGGATT
* * *
306294 ATCGCAACGCGAACTTCGACT
1 ATCGCAACACGAACTTGGATT
306315 ATCGCAA
1 ATCGCAA
306322 AGAATTTGGA
Statistics
Matches: 63, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
19 27 0.43
20 4 0.06
21 32 0.51
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACACGAACTTGGATT
Found at i:306250 original size:19 final size:19
Alignment explanation
Indices: 306222--306331 Score: 76
Period size: 19 Copynumber: 5.6 Consensus size: 19
306212 AAATCGCAAC
*
306222 ACGAACTTGGATTATTGCA
1 ACGAACTTGGATTATCGCA
* **
306241 ACGAATTTGGAAAATCGCA
1 ACGAACTTGGATTATCGCA
*
306260 ACGCGAACTTCGATTATCGCA
1 A--CGAACTTGGATTATCGCA
* **
306281 ACGAATTTGGAAAATCGCA
1 ACGAACTTGGATTATCGCA
* *
306300 ACGCGAACTTCGACTATCGCA
1 A--CGAACTTGGATTATCGCA
* *
306321 AAGAATTTGGA
1 ACGAACTTGGA
306332 CTAACGTAAA
Statistics
Matches: 68, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
19 38 0.56
21 30 0.44
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (19 bp):
ACGAACTTGGATTATCGCA
Found at i:306261 original size:40 final size:40
Alignment explanation
Indices: 306206--306331 Score: 207
Period size: 40 Copynumber: 3.1 Consensus size: 40
306196 TCGTTGCGAT
* * *
306206 TTTGGAAAATCGCAACACGAACTTGGATTATTGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGATTATCGCAACGAA
306246 TTTGGAAAATCGCAACGCGAACTTCGATTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGATTATCGCAACGAA
* *
306286 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAAGAA
1 TTTGGAAAATCGCAACGCGAACTTCGATTATCGCAACGAA
306326 TTTGGA
1 TTTGGA
306332 CTAACGTAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGCGAACTTCGATTATCGCAACGAA
Found at i:306366 original size:21 final size:21
Alignment explanation
Indices: 306349--306519 Score: 154
Period size: 21 Copynumber: 8.3 Consensus size: 21
306339 AAATTTGGAA
306349 AATCGCGTTGCGATTTTGTAT
1 AATCGCGTTGCGATTTTGTAT
* * *
306370 TATCGCGTTGCGA--TAGTCAG
1 AATCGCGTTGCGATTTTGT-AT
306390 AATCGCGTTGCGATTTTGTAT
1 AATCGCGTTGCGATTTTGTAT
* * * *
306411 TATCGAGTTGCGA--TAGTCAG
1 AATCGCGTTGCGATTTTGT-AT
306431 AATCGCGTTGCGATTTTGTAT
1 AATCGCGTTGCGATTTTGTAT
* *
306452 TATCGCGTTGCGCTTTTGTAT
1 AATCGCGTTGCGATTTTGTAT
* *
306473 TATCGCGTTGCGA-TTTATAT
1 AATCGCGTTGCGATTTTGTAT
* * * *
306493 ATTCGCATTGCGATTTTCTAA
1 AATCGCGTTGCGATTTTGTAT
306514 AATCGC
1 AATCGC
306520 AACGCGAATT
Statistics
Matches: 119, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.05
20 41 0.34
21 66 0.55
22 6 0.05
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (21 bp):
AATCGCGTTGCGATTTTGTAT
Found at i:306396 original size:20 final size:20
Alignment explanation
Indices: 306371--306444 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
306361 ATTTTGTATT
306371 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
306391 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
*
306412 ATCGAGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
306432 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
306445 TTTGTATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 25 0.58
21 12 0.28
22 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:306406 original size:41 final size:41
Alignment explanation
Indices: 306349--306463 Score: 221
Period size: 41 Copynumber: 2.8 Consensus size: 41
306339 AAATTTGGAA
306349 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
*
306390 AATCGCGTTGCGATTTTGTATTATCGAGTTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
306431 AATCGCGTTGCGATTTTGTATTATCGCGTTGCG
1 AATCGCGTTGCGATTTTGTATTATCGCGTTGCG
306464 CTTTTGTATT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
Found at i:306519 original size:41 final size:41
Alignment explanation
Indices: 306474--306564 Score: 51
Period size: 41 Copynumber: 2.2 Consensus size: 41
306464 CTTTTGTATT
* **
306474 ATCGCGTTGCGA-TTTATA-TATTCGCATTGCGATTTTCTAAA
1 ATCGCGTTGCGATTTTGTATTA-TCGCATTGCGATAGTC-AAA
*** * * ** *
306515 ATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAA
1 ATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAAA
306556 ATCGCGTTG
1 ATCGCGTTG
306565 TGAATCTGGA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
41 18 0.50
42 17 0.47
43 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAAA
Found at i:306519 original size:62 final size:62
Alignment explanation
Indices: 306350--306519 Score: 168
Period size: 62 Copynumber: 2.7 Consensus size: 62
306340 AATTTGGAAA
* ** *
306350 ATCGCGTTGCGATTT-TGTATTATCGCGTTGCGATAGTC-AGAATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTATATA-T-TCGCGTTGCGATTTTCTAAAATCGCGTTGCGATTTTGTATT
* * * * ** *
306412 ATCGAGTTGCGA--TAGTCAGAATCGCGTTGCGATTTTGTATTATCGCGTTGCGCTTTTGTATT
1 ATCGCGTTGCGATTTA-T-ATATTCGCGTTGCGATTTTCTAAAATCGCGTTGCGATTTTGTATT
*
306474 ATCGCGTTGCGATTTATATATTCGCATTGCGATTTTCTAAAATCGC
1 ATCGCGTTGCGATTTATATATTCGCGTTGCGATTTTCTAAAATCGC
306520 AACGCGAATT
Statistics
Matches: 85, Mismatches: 17, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
60 1 0.01
61 13 0.15
62 67 0.79
63 2 0.02
64 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (62 bp):
ATCGCGTTGCGATTTATATATTCGCGTTGCGATTTTCTAAAATCGCGTTGCGATTTTGTATT
Found at i:306526 original size:21 final size:21
Alignment explanation
Indices: 306502--306548 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
306492 TATTCGCATT
*
306502 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
306523 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
306544 GCGAT
1 GCGAT
306549 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:306855 original size:17 final size:18
Alignment explanation
Indices: 306822--306857 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
306812 AATTCCAAGA
306822 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
306840 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
306857 A
1 A
306858 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:307173 original size:4 final size:4
Alignment explanation
Indices: 307166--307198 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
307156 AATAGAAAAG
307166 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
307199 TTATAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:308594 original size:3 final size:3
Alignment explanation
Indices: 308588--308644 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
308578 ATTTATTATT
* * * *
308588 TAA TAA TAA TAA T-A TAA TAT TAA TAA -AA TAA TTA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
308634 TAA TAA AAA TA
1 TAA TAA TAA TA
308645 TAAATAAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:308606 original size:11 final size:11
Alignment explanation
Indices: 308590--308647 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
308580 TTATTATTTA
308590 ATAATAATAAT
1 ATAATAATAAT
*
308601 ATAATATTAAT
1 ATAATAATAAT
*
308612 AAAATAAT--T
1 ATAATAATAAT
*
308621 ATAATAATATTT
1 ATAATAATA-AT
*
308633 ATAATAAAAAT
1 ATAATAATAAT
308644 ATAA
1 ATAA
308648 ATAAAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 8 0.21
11 21 0.55
12 9 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:308611 original size:14 final size:14
Alignment explanation
Indices: 308588--308630 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
308578 ATTTATTATT
*
308588 TAATAATAATAATA
1 TAATATTAATAATA
*
308602 TAATATTAATAAAA
1 TAATATTAATAATA
308616 TAAT-TATAATAATA
1 TAATAT-TAATAATA
308630 T
1 T
308631 TTATAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 1 0.04
14 24 0.96
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATATTAATAATA
Found at i:310751 original size:42 final size:41
Alignment explanation
Indices: 310692--310842 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 41
310682 GTGAATCGGG
* *
310692 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * * *
310734 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGA
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
310776 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
310818 CTCTTGAACGGTGGGAGGGGACTCT
1 CTCTTGAACGGTGGGA-GGGACTCT
310843 CGCATTGCGA
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
41 5 0.06
42 73 0.85
43 8 0.09
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:310758 original size:21 final size:21
Alignment explanation
Indices: 310692--310842 Score: 67
Period size: 21 Copynumber: 7.2 Consensus size: 21
310682 GTGAATCGGG
*
310692 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
310712 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
310734 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* **
310755 CTCTCG-A-GGAATGATAGGGGA
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
310776 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
310797 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
310818 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
310839 CTCT
1 CTCT
310843 CGCATTGCGA
Statistics
Matches: 88, Mismatches: 35, Indels: 14
0.64 0.26 0.10
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 76 0.86
22 6 0.07
23 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:310867 original size:20 final size:20
Alignment explanation
Indices: 310842--310893 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
310832 GAGGGGACTC
310842 TCGCATTGCGATAGTAAGTA
1 TCGCATTGCGATAGTAAGTA
*
310862 TCGCATTGCGATAGTCAGTA
1 TCGCATTGCGATAGTAAGTA
310882 TCGCATTGCGAT
1 TCGCATTGCGAT
310894 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTAAGTA
Found at i:313357 original size:37 final size:37
Alignment explanation
Indices: 313307--313436 Score: 199
Period size: 37 Copynumber: 3.5 Consensus size: 37
313297 AATTTACAGA
313307 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
313344 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
* * **
313381 AAATATAAATATATTATTTATAAATTTATATTAAATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
313418 AAAATACG-AATATATTATT
1 -AAATA-GAAATATATTATT
313437 ACGAATTTAT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
37 70 0.81
38 16 0.19
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATAGAAATATATTATTTATAAATCTATATTTGATT
Found at i:313368 original size:15 final size:15
Alignment explanation
Indices: 313313--313405 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
313303 CAGAAAATAG
313313 AAATATATTATTTAT
1 AAATATATTATTTAT
*
313328 AAATCTATATTTGATTAAATAG
1 AAA--TATA-TT-ATT---TAT
313350 AAATATATTATTTAT
1 AAATATATTATTTAT
313365 AAATCTATATTTGATTAAATAT
1 AAA--TATA-TT-ATT---TAT
313387 AAATATATTATTTAT
1 AAATATATTATTTAT
313402 AAAT
1 AAAT
313406 TTATATTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 28
0.67 0.02 0.30
Matches are distributed among these distances:
15 15 0.24
17 8 0.13
18 10 0.16
19 10 0.16
20 8 0.13
22 11 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATATATTATTTAT
Found at i:313453 original size:74 final size:75
Alignment explanation
Indices: 313307--313460 Score: 197
Period size: 74 Copynumber: 2.1 Consensus size: 75
313297 AATTTACAGA
** *
313307 AAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAATCTA
1 AAATAGAAATATATTATTTATAAATCTATATTAAATTAAATAGAAATATATTATTTACAAATCTA
*
313372 TATTTGATT-
66 TAATTGATTG
* * * *
313381 AAATATAAATATATTATTTATAAATTTATATTAAATTAAAATACG-AATATATTA-TTACGAATT
1 AAATAGAAATATATTATTTATAAATCTATATTAAATT-AAATA-GAAATATATTATTTACAAATC
313444 TATAATTGATTG
64 TATAATTGATTG
313456 AAATA
1 AAATA
313461 CAATATTTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
74 49 0.71
75 19 0.28
76 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (75 bp):
AAATAGAAATATATTATTTATAAATCTATATTAAATTAAATAGAAATATATTATTTACAAATCTA
TAATTGATTG
Found at i:313460 original size:37 final size:37
Alignment explanation
Indices: 313314--313466 Score: 161
Period size: 37 Copynumber: 4.1 Consensus size: 37
313304 AGAAAATAGA
*
313314 AATATATTATTTATAAATCTATATTTGATTAAATA-G
1 AATATATTATTTATAAATCTATAATTGATTAAATACG
* **
313350 AAATATATTATTTATAAATCTATATTTGATTAAATATA
1 -AATATATTATTTATAAATCTATAATTGATTAAATACG
* *
313388 AATATATTATTTATAAATTTAT-ATTAAATTAAAATACG
1 AATATATTATTTATAAATCTATAATT-GATT-AAATACG
** *
313426 AATATATTA-TTACGAATTTATAATTGATTGAAATAC-
1 AATATATTATTTATAAATCTATAATTGATT-AAATACG
313462 AATAT
1 AATAT
313467 TTCTAGAAGG
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
36 7 0.07
37 78 0.76
38 17 0.17
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
AATATATTATTTATAAATCTATAATTGATTAAATACG
Found at i:313824 original size:17 final size:17
Alignment explanation
Indices: 313802--313861 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
313792 AAAATAGAAA
313802 TATATTATTTATAAATC
1 TATATTATTTATAAATC
* *
313819 TATATTTGATTAAATAGAA-A
1 TATA-TT-ATT-TATA-AATC
313839 TATATTATTTATAAATC
1 TATATTATTTATAAATC
313856 TATATT
1 TATATT
313862 TGATTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 5 0.15
20 7 0.21
21 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TATATTATTTATAAATC
Found at i:313843 original size:37 final size:37
Alignment explanation
Indices: 313793--313922 Score: 190
Period size: 37 Copynumber: 3.5 Consensus size: 37
313783 AATTTACCGA
313793 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
313830 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
* * * **
313867 AAATATAAATACATTATTTATAAATTTATATTCAATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
313904 AAAATACG-AATATATTATT
1 -AAATA-GAAATATATTATT
313923 ACGAATTTAT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
37 69 0.82
38 15 0.18
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATAGAAATATATTATTTATAAATCTATATTTGATT
Found at i:314333 original size:37 final size:37
Alignment explanation
Indices: 314283--314412 Score: 199
Period size: 37 Copynumber: 3.5 Consensus size: 37
314273 AATTTACCGA
314283 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
314320 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
* * **
314357 AAATATAAATATATTATTTATAAATTTATATTCAATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
314394 AAAATACG-AATATATTATT
1 -AAATA-GAAATATATTATT
314413 ACGAATTTAT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
37 70 0.81
38 16 0.19
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATAGAAATATATTATTTATAAATCTATATTTGATT
Found at i:314344 original size:15 final size:15
Alignment explanation
Indices: 314289--314381 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
314279 CCGAAAATAG
314289 AAATATATTATTTAT
1 AAATATATTATTTAT
*
314304 AAATCTATATTTGATTAAATAG
1 AAA--TATA-TT-ATT---TAT
314326 AAATATATTATTTAT
1 AAATATATTATTTAT
314341 AAATCTATATTTGATTAAATAT
1 AAA--TATA-TT-ATT---TAT
314363 AAATATATTATTTAT
1 AAATATATTATTTAT
314378 AAAT
1 AAAT
314382 TTATATTCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 28
0.67 0.02 0.30
Matches are distributed among these distances:
15 15 0.24
17 8 0.13
18 10 0.16
19 10 0.16
20 8 0.13
22 11 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATATATTATTTAT
Found at i:314420 original size:37 final size:37
Alignment explanation
Indices: 314290--314442 Score: 123
Period size: 37 Copynumber: 4.1 Consensus size: 37
314280 CGAAAATAGA
* * * ** *
314290 AATATATTATTTATAAATCTATATTTGATT-AAATAGA
1 AATATATTATTTACAAATTTATAATCAATTAAAATA-C
* * * **
314327 AATATATTATTTATAAATCTATATTTGATTAAATATA-
1 AATATATTATTTACAAATTTATAATCAATTAAA-ATAC
* *
314364 AATATATTATTTATAAATTTATATTCAATTAAAATAC
1 AATATATTATTTACAAATTTATAATCAATTAAAATAC
* *
314401 GAATATATTA-TTACGAATTTATAATCGATTAAAATAC
1 -AATATATTATTTACAAATTTATAATCAATTAAAATAC
314438 AATAT
1 AATAT
314443 TACAGTTCTA
Statistics
Matches: 105, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
36 8 0.08
37 83 0.79
38 11 0.10
39 3 0.03
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (37 bp):
AATATATTATTTACAAATTTATAATCAATTAAAATAC
Found at i:314431 original size:74 final size:74
Alignment explanation
Indices: 314283--314442 Score: 191
Period size: 74 Copynumber: 2.2 Consensus size: 74
314273 AATTTACCGA
* ** *
314283 AAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAATCTA
1 AAATATAAATATATTATTTATAAATCTATATTCAATTAAATAGAAATATATTATTTACAAATCTA
* *
314348 TATTTGATT
66 TAATCGATT
* * *
314357 AAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACG-AATATATTA-TTACGAATT
1 AAATATAAATATATTATTTATAAATCTATATTCAATT-AAATA-GAAATATATTATTTACAAATC
314420 TATAATCGATT
64 TATAATCGATT
314431 AAA-ATACAATAT
1 AAATATA-AATAT
314443 TACAGTTCTA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
73 3 0.04
74 56 0.76
75 14 0.19
76 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (74 bp):
AAATATAAATATATTATTTATAAATCTATATTCAATTAAATAGAAATATATTATTTACAAATCTA
TAATCGATT
Found at i:314483 original size:491 final size:491
Alignment explanation
Indices: 313238--314710 Score: 2706
Period size: 491 Copynumber: 3.0 Consensus size: 491
313228 CAAAATAGAA
*
313238 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAGGTACGGTGTAATTTA
1 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAGGAACGGTGTAATTTA
*
313303 CAGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
66 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
*
313368 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTAAATTAAAATACGAATATAT
131 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
*
313433 TATTACGAATTTATAATTGATTGAAATACAATA-T----TTCTAGAAGGATTGTTTTACTTTGAG
196 TATTACGAATTTATAATCGATTGAAATACAATATTACAGTTCTAGAAGGATTGTTTTACTTTGAG
* *
313493 AACCCCTATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCACAAGTTTTCATATTTCGG
261 AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
* *
313558 ATTTCAAGAGTTTAAAAGAAAAATCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAATGA
326 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
* **
313623 CAATGTAACCTCGTACTTTATAATTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
391 CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
*
313688 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAT
456 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
313724 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAGGAACGGTGTAATTTA
1 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAGGAACGGTGTAATTTA
313789 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
66 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
*
313854 TCTATATTTGATTAAATATAAATACATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
131 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
313919 TATTACGAATTTATAATCGATTGAAATACAATATTACAGTTCTAGAAGGATTGTTTTACTTTGAG
196 TATTACGAATTTATAATCGATTGAAATACAATATTACAGTTCTAGAAGGATTGTTTTACTTTGAG
*
313984 AACCCCCATAAATATTGTGCTAACCTTATAAGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
261 AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
314049 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
326 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
*
314114 CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTGCATATTATTATCATT-ATTTT
391 CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
314178 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
456 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
* *
314214 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAAGAACGGTATAATTTA
1 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAGGAACGGTGTAATTTA
314279 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
66 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
314344 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
131 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
*
314409 TATTACGAATTTATAATCGATTAAAATACAATATTACAGTTCTAGAAGGATTGTTTTACTTTGAG
196 TATTACGAATTTATAATCGATTGAAATACAATATTACAGTTCTAGAAGGATTGTTTTACTTTGAG
314474 AACCCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCG
261 AA-CCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCG
*
314539 GATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTTCACTAGTTTTTCGGTGAACTGTGCAGTG
325 GATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTG
314604 ACAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTT
390 ACAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTT
**
314669 TTTTATCGGATTAACAAAATTTTAACAATCTTAAGAC
455 TTTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
314706 AAATT
1 AAATT
314711 TATTCTTAAT
Statistics
Matches: 956, Mismatches: 24, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
486 223 0.23
487 1 0.00
490 298 0.31
491 390 0.41
492 44 0.05
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (491 bp):
AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAGGAACGGTGTAATTTA
CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
TATTACGAATTTATAATCGATTGAAATACAATATTACAGTTCTAGAAGGATTGTTTTACTTTGAG
AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
Found at i:315830 original size:19 final size:19
Alignment explanation
Indices: 315806--315852 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
315796 CTGTTTGGAT
315806 AAAGGAATGTGGGATTCCC
1 AAAGGAATGTGGGATTCCC
315825 AAAGGAATGTGGGATTCCC
1 AAAGGAATGTGGGATTCCC
*
315844 ATAGGAATG
1 AAAGGAATG
315853 GAATCCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (19 bp):
AAAGGAATGTGGGATTCCC
Found at i:315887 original size:30 final size:30
Alignment explanation
Indices: 315851--315925 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
315841 CCCATAGGAA
315851 TGGAATCCACATTCCCATGTTTGGTTGGCC
1 TGGAATCCACATTCCCATGTTTGGTTGGCC
*
315881 TGGAATCCACATCCCCATGTTTGGTTGGCC
1 TGGAATCCACATTCCCATGTTTGGTTGGCC
* *
315911 GGGAAT-CTCATTCCC
1 TGGAATCCACATTCCC
315926 GATAATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 7 0.17
30 34 0.83
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (30 bp):
TGGAATCCACATTCCCATGTTTGGTTGGCC
Found at i:316239 original size:2 final size:2
Alignment explanation
Indices: 316232--316258 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
316222 GTTAATTTTG
316232 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 T
316259 TTTATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:339130 original size:21 final size:21
Alignment explanation
Indices: 339105--339145 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
339095 GGAAACTACT
*
339105 CAACCACAATAGTCTACGCCC
1 CAACCACAATAATCTACGCCC
339126 CAACCACAATAATCTACGCC
1 CAACCACAATAATCTACGCC
339146 TGGCAAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (21 bp):
CAACCACAATAATCTACGCCC
Found at i:347073 original size:3 final size:3
Alignment explanation
Indices: 347065--347094 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
347055 GAAGACTTCC
347065 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
347095 CTACTCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:348652 original size:21 final size:20
Alignment explanation
Indices: 348609--348653 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
348599 TACATAATTC
**
348609 TTTTAAAAAAATTATTATTT
1 TTTTAAAAAAATTATTACAT
*
348629 TTTTATAAAAGATTATTACAT
1 TTTTA-AAAAAATTATTACAT
348650 TTTT
1 TTTT
348654 GAAATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTAAAAAAATTATTACAT
Done.