Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008752.1 Hibiscus syriacus cultivar Beakdansim tig00111843_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: 1143363
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:172289 original size:124 final size:123
Alignment explanation
Indices: 172108--172458 Score: 522
Period size: 124 Copynumber: 2.8 Consensus size: 123
172098 GTCGATCTGT
*
172108 TGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCC
1 TGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCC-TTCGTTGTGAAGTTGAGCC
* * * * *
172173 TCGAATTGGATATTCTTTGTTGTGAAGTTGAAATCCAATCTAAGGATGGATGTTACTGG
65 TCAAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGG
* * * *
172232 TGAACACGATATCCTTCGTTGTGAAGTTAAAATCATGGATGGCCCTTTCGTTATGAAGTTGAGCC
1 TGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCC-TTCGTTGTGAAGTTGAGCC
* * **
172297 TCAAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTAAAGATGAATGTTGTTGG
65 TCAAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGG
**
172356 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCC
1 TGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGC-CCTTCGTTGTGAAGTTGAGCC
*
172421 TTAAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA
65 TCAAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA
172459 GGGTTGTTTC
Statistics
Matches: 202, Mismatches: 24, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
124 200 0.99
125 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (123 bp):
TGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCTTCGTTGTGAAGTTGAGCCT
CAAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGG
Found at i:172551 original size:54 final size:56
Alignment explanation
Indices: 172426--172573 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 56
172416 GAGCCTTAAA
*
172426 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGGGTTGTTTCACCAAATTGGTTTTGAG
1 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAA----TGTTTCACCAAATTGGCTTTGAG
* *
172486 TTGGATATCCTTCGTCGTGAAGTTGAAACCCAAT-TTT-ACCAAATTGGCTTTGAG
1 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTTCACCAAATTGGCTTTGAG
* *
172540 TTTGATGTCCTTCGTTGTGAAGTTGAAATCCAAT
1 TTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT
172574 CTCGAGTAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
54 46 0.57
55 3 0.04
56 1 0.01
60 31 0.38
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (56 bp):
TTGGATATCCTTCGTTGTGAAGTTGAAATCCAATGTTTCACCAAATTGGCTTTGAG
Found at i:197610 original size:22 final size:22
Alignment explanation
Indices: 197584--197640 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
197574 TCAAGACTCG
197584 CTGGAGCACCCGAACCGACCCA
1 CTGGAGCACCCGAACCGACCCA
** * *
197606 CTGGAGCACTTGAACCGGCCCG
1 CTGGAGCACCCGAACCGACCCA
197628 CTGGAGCGACCCG
1 CTGGAGC-ACCCG
197641 CTGCACCTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.21, C:0.40, G:0.30, T:0.09
Consensus pattern (22 bp):
CTGGAGCACCCGAACCGACCCA
Found at i:198937 original size:15 final size:13
Alignment explanation
Indices: 198917--198984 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 13
198907 ATTATTCGCA
198917 TTCTTTTAGTATATT
1 TTCTTTTA-TAT-TT
198932 TTCTTTTATATTT
1 TTCTTTTATATTT
* *
198945 TTGTTTTAATTTTGT
1 TTCTTTT-ATATT-T
198960 TTCTTTTATA--T
1 TTCTTTTATATTT
*
198971 TTATTTTATATTT
1 TTCTTTTATATTT
198984 T
1 T
198985 GTTTTGTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 10 0.23
13 10 0.23
14 9 0.20
15 15 0.34
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (13 bp):
TTCTTTTATATTT
Found at i:198959 original size:11 final size:12
Alignment explanation
Indices: 198926--198989 Score: 58
Period size: 13 Copynumber: 5.1 Consensus size: 12
198916 ATTCTTTTAG
*
198926 TATATTTTCTTT
1 TATATTTTGTTT
198938 TATATTTTTGTTT
1 TATA-TTTTGTTT
198951 TA-ATTTTGTTTCT
1 TATATTTTG-TT-T
* *
198964 TTTATATTTATTT
1 TATAT-TTTGTTT
198977 TATATTTTGTTT
1 TATATTTTGTTT
198989 T
1 T
198990 GTTTTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
11 5 0.12
12 14 0.33
13 16 0.38
14 4 0.10
15 3 0.07
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (12 bp):
TATATTTTGTTT
Found at i:198994 original size:28 final size:29
Alignment explanation
Indices: 198930--199003 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
198920 TTTTAGTATA
*
198930 TTTTCTTTTATATTT-TTGTTTTAATTTTG
1 TTTTCTTTTATATTTATT-TTATAATTTTG
198959 -TTTCTTTTATATTTATTTTAT-ATTTTG
1 TTTTCTTTTATATTTATTTTATAATTTTG
*
198986 TTTTGTTTT-TATTTATTT
1 TTTTCTTTTATATTTATTT
199004 ATTTAGTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 15 0.37
28 24 0.59
29 2 0.05
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (29 bp):
TTTTCTTTTATATTTATTTTATAATTTTG
Found at i:198998 original size:27 final size:26
Alignment explanation
Indices: 198931--199003 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
198921 TTTAGTATAT
*
198931 TTTCTTTTATATTTTTGTTTTAATTTTG
1 TTTCTTTTATA--TTTATTTTAATTTTG
198959 TTTCTTTTATATTTATTTTATATTTTG
1 TTTCTTTTATATTTATTTTA-ATTTTG
*
198986 TTT-TGTTTTTATTTATTT
1 TTTCT-TTTATATTTATTT
199004 ATTTAGTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 9 0.22
27 21 0.51
28 11 0.27
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTCTTTTATATTTATTTTAATTTTG
Found at i:200520 original size:20 final size:19
Alignment explanation
Indices: 200481--200522 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
200471 TTTCCTCGAT
200481 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
200500 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
200520 ATT
1 ATT
200523 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:202111 original size:3 final size:3
Alignment explanation
Indices: 202105--202172 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
202095 TTTATTATAT
* * * *
202105 TAA TAA TAA TAA TAA TAA TAA -AA TAT TTA TAA TAA TAT TTA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
202153 TAA -AC TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
202173 AAAAATAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 3 0.06
3 44 0.88
4 3 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:202690 original size:112 final size:112
Alignment explanation
Indices: 202506--203520 Score: 1110
Period size: 112 Copynumber: 8.9 Consensus size: 112
202496 ATAGAGTTAT
* * ** *
202506 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAGCTTCTTCTTTTTCTTCAGATAAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
202571 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* *
202618 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* * *** * * *
202683 TTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTATGATAGAGTCAT
66 TTATGAACTTTCTCTGG-AAA----A-GTTGATCCATC-GAGT-GATG--A-ATTCAA
** *
202741 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTCTTCAGATAAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
202806 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* *
202853 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTT-TCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* * *** * * *
202917 TTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTATGATAGAGTCAT
66 TTATGAACTTTCTCTGG-AAA----A-GTTGATCCATC-GAGT-GATG--A-ATTCAA
*
202975 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
203040 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCTAA
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTC-AA
* ** * *
203089 -CAAAAAGTTGAACAAAATCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* * * * **
203153 TTATGAACTCTAC-CTGGTAATGTTGATCCATCGAGTGATGGATTTGA
66 TTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* * * * *
203200 GTAAAAAGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCGTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
** * * * **
203265 ATTATGAACTCGAC-CTGGTAATGTTGATCCATCGAGTGATGGATTTGA
65 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* * * *
203313 GTAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAAGATTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
** * * * *
203378 ATTATGAACTCGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAA
65 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
*
203426 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTC
* *
203490 ATTATGAACTCTTC-C-GGCAATGTTGATCCAT
65 ATTATGAACT-TTCTCTGGAAAAGTTGATCCAT
203521 TAAATGATGG
Statistics
Matches: 786, Mismatches: 88, Indels: 59
0.84 0.09 0.06
Matches are distributed among these distances:
111 34 0.04
112 263 0.33
113 254 0.32
114 6 0.01
115 3 0.00
116 5 0.01
117 22 0.03
118 22 0.03
119 5 0.01
120 3 0.00
121 1 0.00
122 50 0.06
123 100 0.13
124 18 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
Found at i:202880 original size:235 final size:236
Alignment explanation
Indices: 202430--203387 Score: 1346
Period size: 235 Copynumber: 4.1 Consensus size: 236
202420 ATTTTTCTCT
* * * * * * *
202430 TTCAAATGAGTTCTTCTCATTATGAAC-ACTTCTGGTAATGTTGATGCTGATCTATCTCCTTCTG
1 TTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTA
* * * *
202494 TGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAGCTTCTTCTT-TTTCTTCAGA
66 TGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
202558 TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAA
131 TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAA
*
202623 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
196 AAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
202664 TTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTA
1 TTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTA
*
202729 TGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-TTTCTTCAGA
66 TGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
202793 TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAA
131 TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAA
*
202858 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
196 AAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
202899 TTCAGATGAGTTCTT-TCATTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTA
1 TTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTA
202963 TGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
66 TGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
203028 TGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCTAA-CAA
131 TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTC-AAGCAA
*
203092 AAAGTTGAACAAAATCTTCTCATTATGAATTTCTTCTTCCTC
195 AAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
* * * * *** *
203134 TTCAGATGAGTTCTTCTTATTATGAACTCTAC-CT-G----G-TAATGTTGATCCATC-GAGT-G
1 TTCAGATGAGTTCTTCTCATTATGAACT-TCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCT
* *
203190 ATGGATTTGAGT-A---AAAA-GTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTC
65 AT-GA-TAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* ** * * * **
203250 AGATGAA-TTCGTCTCATTATGAACTCGAC-CTGGTAATGTTGATCCATCGAGTGATGGATTTGA
128 AGAT-AAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* * *
203313 GTAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
191 GCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TC
* *
203360 TTCAGAAGATTTCTTCTCATTATGAACT
1 TTCAGATGAGTTCTTCTCATTATGAACT
203388 CGACCTGGTA
Statistics
Matches: 671, Mismatches: 42, Indels: 30
0.90 0.06 0.04
Matches are distributed among these distances:
224 1 0.00
225 129 0.19
226 33 0.05
228 2 0.00
229 4 0.01
230 18 0.03
231 1 0.00
234 129 0.19
235 337 0.50
236 15 0.02
237 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (236 bp):
TTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTA
TGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAA
AAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC
Found at i:203963 original size:22 final size:22
Alignment explanation
Indices: 203936--203990 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
203926 GATAAAGCTT
*
203936 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* * *
203958 TTATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
203980 TCATCTTTGAA
1 TCATCTTTGAA
203991 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:206817 original size:114 final size:114
Alignment explanation
Indices: 206613--206827 Score: 376
Period size: 114 Copynumber: 1.9 Consensus size: 114
206603 ATGCAGTTCA
* * *
206613 TCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTTAAAGAACAC
1 TCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
* *
206678 TTCCAGAATATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCG
66 TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCG
*
206727 TCTTTCAATTCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
1 TCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
206792 TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACT
66 TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACT
206828 CCGAGAACGT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 95 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (114 bp):
TCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCG
Found at i:214678 original size:20 final size:19
Alignment explanation
Indices: 214639--214680 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
214629 TTTCCTCGAT
214639 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
214658 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
214678 ATT
1 ATT
214681 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:216312 original size:12 final size:12
Alignment explanation
Indices: 216280--216320 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
216270 ATTATATTAC
* *
216280 TAATAATAATAA
1 TAATAATATTTA
216292 TAA-AATATTTA
1 TAATAATATTTA
216303 TAATAATATTTA
1 TAATAATATTTA
216315 TAATAA
1 TAATAA
216321 ATAAACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATATTTA
Found at i:217318 original size:20 final size:19
Alignment explanation
Indices: 217281--217319 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
217271 CTTGATTCTC
*
217281 TTTATTTTGTTTTATATTG
1 TTTATTTTGTTTGATATTG
*
217300 TTTATTTCTGTTTGGTATTG
1 TTTATTT-TGTTTGATATTG
217320 CTTGCTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.13, C:0.03, G:0.15, T:0.69
Consensus pattern (19 bp):
TTTATTTTGTTTGATATTG
Found at i:220022 original size:2 final size:2
Alignment explanation
Indices: 220015--220050 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
220005 GATTGAGATA
220015 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
220051 CTTTAATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220376 original size:24 final size:24
Alignment explanation
Indices: 220344--220403 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
220334 CATTTAATAA
*
220344 ATAAACGAACACGAACGAACGGAC
1 ATAAACGAACACGAACGAACGAAC
220368 ATAAACGAACACGAACGAACGAAC
1 ATAAACGAACACGAACGAACGAAC
220392 ATAAACGAACAC
1 ATAAACGAACAC
220404 AATAAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.53, C:0.25, G:0.17, T:0.05
Consensus pattern (24 bp):
ATAAACGAACACGAACGAACGAAC
Found at i:222339 original size:14 final size:14
Alignment explanation
Indices: 222320--222354 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
222310 CTTGTTTGTA
222320 ATTATAATTTTATT
1 ATTATAATTTTATT
222334 ATTATAATTTTATT
1 ATTATAATTTTATT
*
222348 TTTATAA
1 ATTATAA
222355 AAGATATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATAATTTTATT
Found at i:222584 original size:34 final size:33
Alignment explanation
Indices: 222523--222621 Score: 173
Period size: 34 Copynumber: 3.0 Consensus size: 33
222513 AATAAAGCAA
*
222523 TCGCAATCTTTGAATTATTTTTATTAATTTAAG
1 TCGCAATCTTTGAATTTTTTTTATTAATTTAAG
222556 TCGCAATCTTTGAATTTTGTTTTATTAATTTAAG
1 TCGCAATCTTTGAATTTT-TTTTATTAATTTAAG
222590 TCGCAATCTTTGAA-TTTTTTTATTAATTTAAG
1 TCGCAATCTTTGAATTTTTTTTATTAATTTAAG
222622 AGATTACGTT
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
32 15 0.23
33 20 0.31
34 29 0.45
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (33 bp):
TCGCAATCTTTGAATTTTTTTTATTAATTTAAG
Found at i:223256 original size:17 final size:17
Alignment explanation
Indices: 223229--223277 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
223219 AATATACTTA
*
223229 ATAATATATATTTTAAT
1 ATAATAAATATTTTAAT
*
223246 TTAATAAATA-TTTAAT
1 ATAATAAATATTTTAAT
223262 ATAATTATAATATTTT
1 ATAA-TA-AATATTTT
223278 TACTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 9 0.35
17 10 0.38
18 4 0.15
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAATAAATATTTTAAT
Found at i:223291 original size:27 final size:24
Alignment explanation
Indices: 223261--223325 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 24
223251 AAATATTTAA
*
223261 TATAATTATAATATTTTTACTTAAAAT
1 TATAA-TATAATA-TTTTA-ATAAAAT
223288 TATAGATATAATATTTTAATAAAAT
1 TATA-ATATAATATTTTAATAAAAT
223313 TATTAATATAATA
1 TA-TAATATAATA
223326 ATATTAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 7 0.20
27 11 0.31
28 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TATAATATAATATTTTAATAAAAT
Found at i:223321 original size:25 final size:27
Alignment explanation
Indices: 223267--223342 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 27
223257 TTAATATAAT
*
223267 TATAATATTTTTACTTAAAATTA-TAGA
1 TATAATA-TTTTACATAAAATTATTAGA
223294 TATAATATTTTA-ATAAAATTATTA-A
1 TATAATATTTTACATAAAATTATTAGA
* *
223319 TATAATAATATTAGAT-AAATTATT
1 TATAAT-ATTTTACATAAAATTATT
223343 CTAATATTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 15 0.34
26 20 0.45
27 9 0.20
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (27 bp):
TATAATATTTTACATAAAATTATTAGA
Found at i:223674 original size:20 final size:20
Alignment explanation
Indices: 223633--223728 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
223623 AAATAACTAA
**
223633 CAAATTCGCAACAC-GAACTC
1 CAAATTCGCAACACAG-TTTC
*
223653 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
* *
223673 CAAATTCGCAACTCAGTTTT
1 CAAATTCGCAACACAGTTTC
* **
223693 GAAATTCGCAACACAGAGGT-
1 CAAATTCGCAACACAG-TTTC
223713 CAAATTCGCAACACAG
1 CAAATTCGCAACACAG
223729 AAGTTAAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTC
Found at i:223729 original size:20 final size:20
Alignment explanation
Indices: 223633--223739 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 20
223623 AAATAACTAA
*
223633 CAAATTCGCAACAC-GAACT
1 CAAATTCGCAACACAGAAGT
* **
223652 CCAATTTCGCAACACAG-TTT
1 -CAAATTCGCAACACAGAAGT
* ***
223672 CCAAATTCGCAACTCAGTTTT
1 -CAAATTCGCAACACAGAAGT
* *
223693 GAAATTCGCAACACAGAGGT
1 CAAATTCGCAACACAGAAGT
223713 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
*
223733 TAAATTC
1 CAAATTC
223740 CCAAAGCACG
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 68 0.94
21 4 0.06
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:223738 original size:40 final size:40
Alignment explanation
Indices: 223633--223739 Score: 94
Period size: 40 Copynumber: 2.7 Consensus size: 40
223623 AAATAACTAA
* * **
223633 CAAATTCGCAACAC-GAACTCCAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAGAACT-TAAATTCGCAACACAGGGTC
* **
223673 CAAATTCGCAACTCAG-TTTTGAAATTCGCAACACAGAGGT-
1 CAAATTCGCAACACAGAACTT-AAATTCGCAACACAG-GGTC
*
223713 CAAATTCGCAACACAGAAGTTAAATTC
1 CAAATTCGCAACACAGAACTTAAATTC
223740 CCAAAGCACG
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
40 49 0.92
41 4 0.08
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.23
Consensus pattern (40 bp):
CAAATTCGCAACACAGAACTTAAATTCGCAACACAGGGTC
Found at i:223934 original size:22 final size:22
Alignment explanation
Indices: 223903--223949 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
223893 TCTCTAAGGT
223903 GACATCCGTCCCCATATCCGGC
1 GACATCCGTCCCCATATCCGGC
*
223925 GACATTCGTCCCCATATCCGGC
1 GACATCCGTCCCCATATCCGGC
223947 GAC
1 GAC
223950 CCCCTCCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.43, G:0.19, T:0.19
Consensus pattern (22 bp):
GACATCCGTCCCCATATCCGGC
Found at i:224366 original size:14 final size:14
Alignment explanation
Indices: 224349--224376 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
224339 TAGTTTTCGC
224349 GTTGCGAATTTCAT
1 GTTGCGAATTTCAT
224363 GTTGCGAATTTCAT
1 GTTGCGAATTTCAT
224377 TTTCGAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
GTTGCGAATTTCAT
Found at i:224380 original size:34 final size:34
Alignment explanation
Indices: 224342--224407 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
224332 GCGATTTTAG
*
224342 TTTTCGCGTTGCGAATTTCATGTTGCGAATTTCA
1 TTTTCGAGTTGCGAATTTCATGTTGCGAATTTCA
**
224376 TTTTCGAGTTGCGCTTTTCATGTTGCGAATTT
1 TTTTCGAGTTGCGAATTTCATGTTGCGAATTT
224408 AAGTTTCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (34 bp):
TTTTCGAGTTGCGAATTTCATGTTGCGAATTTCA
Found at i:225965 original size:42 final size:42
Alignment explanation
Indices: 225906--226016 Score: 150
Period size: 42 Copynumber: 2.6 Consensus size: 42
225896 TGAGCACCCC
* * **
225906 CCACTTCGGCACCGAGATCCATTACCTCATCGAGCCTCTTCT
1 CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
*
225948 CCACTTCGACACCGAGATCCATCACCTGATCGAGCCGATTCT
1 CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
* * *
225990 ACACCTCGACACCGAGAGCCATCACCT
1 CCACTTCGACACCGAGATCCATCACCT
226017 ATTCCATCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.21
Consensus pattern (42 bp):
CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
Found at i:226155 original size:21 final size:21
Alignment explanation
Indices: 226131--226183 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
226121 GTTAGGGGAG
226131 TTACGTGATGAGGTCA-GTGT-T
1 TTACGTGATGAGGT-AGGT-TCT
*
226152 TTACGTTATGAGGTAGGTTCT
1 TTACGTGATGAGGTAGGTTCT
226173 TTACGTGATGA
1 TTACGTGATGA
226184 CAATGGTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.21, C:0.09, G:0.30, T:0.40
Consensus pattern (21 bp):
TTACGTGATGAGGTAGGTTCT
Found at i:226290 original size:63 final size:62
Alignment explanation
Indices: 226131--226293 Score: 168
Period size: 63 Copynumber: 2.6 Consensus size: 62
226121 GTTAGGGGAG
* * *
226131 TTACGTGATGAGGTCAGTGTTTTACGTTATGAGGTAGGTTCTTTACGTGATGACAATGGTGCA
1 TTACGTGATGAGGTAATTGTTTTACGTGATGAGGTA-GTTCTTTACGTGATGACAATGGTGCA
** * * * * *
226194 TGGCATGATGAGGTAGAGTT-TTTT-CTTGGTGAGGTAGTTGTGTTACGTGATGACAATGGTGCT
1 TTACGTGATGAGGTA-A-TTGTTTTACGTGATGAGGTAGTTCT-TTACGTGATGACAATGGTGCA
* *
226257 TTACGTGGTGAGGTATTTGTTTTACGTGATGAGGTAG
1 TTACGTGATGAGGTAATTGTTTTACGTGATGAGGTAG
226294 CTGCTCTGCG
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
61 2 0.03
62 8 0.10
63 62 0.79
64 5 0.06
65 1 0.01
ACGTcount: A:0.20, C:0.09, G:0.33, T:0.38
Consensus pattern (62 bp):
TTACGTGATGAGGTAATTGTTTTACGTGATGAGGTAGTTCTTTACGTGATGACAATGGTGCA
Found at i:226616 original size:21 final size:21
Alignment explanation
Indices: 226590--226722 Score: 124
Period size: 21 Copynumber: 6.3 Consensus size: 21
226580 GAAGAAGCCC
*
226590 GATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATTGTTCAG
226611 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATTGTTCAG
*
226632 GATCCACCCCCCATTGTTCAG
1 GATCCACCTCCCATTGTTCAG
* ** ** *
226653 GATTCACCTGTCATCATTCAA
1 GATCCACCTCCCATTGTTCAG
* ** *
226674 GAGGCC-CCTCCCATCATTCAT
1 GA-TCCACCTCCCATTGTTCAG
**
226695 GATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATTGTTCAG
226716 GATCCAC
1 GATCCAC
226723 ATGGCATACT
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
20 2 0.02
21 89 0.97
22 1 0.01
ACGTcount: A:0.22, C:0.39, G:0.14, T:0.26
Consensus pattern (21 bp):
GATCCACCTCCCATTGTTCAG
Found at i:229474 original size:16 final size:16
Alignment explanation
Indices: 229453--229485 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
229443 CACTTCCCGA
229453 TAAGCTTTTACAACCT
1 TAAGCTTTTACAACCT
*
229469 TAAGCTTTTACAGCCT
1 TAAGCTTTTACAACCT
229485 T
1 T
229486 CTAGTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (16 bp):
TAAGCTTTTACAACCT
Found at i:232107 original size:12 final size:12
Alignment explanation
Indices: 232086--232119 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
232076 GGTTGTGGGT
*
232086 TTTGAGATTGTG
1 TTTGATATTGTG
232098 TTTGATATTGTG
1 TTTGATATTGTG
*
232110 TTTGGTATTG
1 TTTGATATTG
232120 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:233050 original size:24 final size:24
Alignment explanation
Indices: 232992--233044 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
232982 CCGAAACATC
*
232992 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAGTTCGAGTATTGACCAAG
* *
233016 ATCAAAGTTCGGGTATTGATCAAG
1 ATCAAAGTTCGAGTATTGACCAAG
233040 ATCAA
1 ATCAA
233045 GTTTCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (24 bp):
ATCAAAGTTCGAGTATTGACCAAG
Found at i:234010 original size:20 final size:20
Alignment explanation
Indices: 233985--234072 Score: 90
Period size: 20 Copynumber: 4.4 Consensus size: 20
233975 ATAAAAGTTA
*
233985 TTGCGAAATTAAAATTCGTG
1 TTGCGAAATTAAAAATCGTG
*
234005 TTGCG-AATTCAAAAATCGAG
1 TTGCGAAATT-AAAAATCGTG
** *
234025 TTGCGAAAACAAAATTCGTG
1 TTGCGAAATTAAAAATCGTG
*
234045 TTGCG-AATTAGAAAATCTTG
1 TTGCGAAATTA-AAAATCGTG
234065 TTGCGAAA
1 TTGCGAAA
234073 AGGAAACTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.13
20 43 0.80
21 4 0.07
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTGCGAAATTAAAAATCGTG
Found at i:234031 original size:40 final size:39
Alignment explanation
Indices: 233985--234170 Score: 164
Period size: 40 Copynumber: 4.6 Consensus size: 39
233975 ATAAAAGTTA
*
233985 TTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGAG
1 TTGCGAAA-AAAAATTCGTGTTGCGAATTCAAAAATCGAG
**
234025 TTGCGAAAACAAAATTCGTGTTGCGAATT-AGAAAATCTTG
1 TTGCGAAAA-AAAATTCGTGTTGCGAATTCA-AAAATCGAG
* * *
234065 TTGCGAAAAGGAAACTT-GTGTTGCGAATTTAAAAAATTGCA-
1 TTGCGAAAA--AAAATTCGTGTTGCGAA-TTCAAAAATCG-AG
* * *
234106 TTG-GTAAAAAGAAATTCGCGTTGCGAATTCAGAAATCAAG
1 TTGCG-AAAAA-AAATTCGTGTTGCGAATTCAAAAATCGAG
234146 TTGCGAAAAAGAAATTCCGTGTTGC
1 TTGCGAAAAA-AAATT-CGTGTTGC
234171 AAATACCAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 23
0.76 0.10 0.15
Matches are distributed among these distances:
39 3 0.03
40 79 0.66
41 36 0.30
42 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (39 bp):
TTGCGAAAAAAAATTCGTGTTGCGAATTCAAAAATCGAG
Found at i:234078 original size:20 final size:19
Alignment explanation
Indices: 234024--234083 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
234014 CAAAAATCGA
* *
234024 GTTGCGAAAACAAAATTCGT
1 GTTGCGAAAAGAAAA-TCTT
*
234044 GTTGCGAATTAGAAAATCTT
1 GTTGCGAA-AAGAAAATCTT
*
234064 GTTGCGAAAAGGAAA-CTT
1 GTTGCGAAAAGAAAATCTT
234082 GT
1 GT
234084 GTTGCGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 5 0.15
19 5 0.15
20 19 0.56
21 5 0.15
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (19 bp):
GTTGCGAAAAGAAAATCTT
Found at i:234212 original size:20 final size:20
Alignment explanation
Indices: 234187--234313 Score: 89
Period size: 20 Copynumber: 6.3 Consensus size: 20
234177 CAAATTCGCG
234187 TGCGAATTTGGAAAA-TGTGT
1 TGCGAATTT-GAAAACTGTGT
* * **
234207 TGCGAAATTG-GAGTTCGTGT
1 TGCGAATTTGAAAACT-GTGT
* *
234227 TACGAATTTGAAAACCGTGT
1 TGCGAATTTGAAAACTGTGT
*
234247 TGCGAATTTAGAAAA-TCGCGT
1 TGCGAATTT-GAAAACT-GTGT
* * *
234268 TGTGAATTTCAAAACTGAGT
1 TGCGAATTTGAAAACTGTGT
* *
234288 TGCGAATTTCAAAACTGAGT
1 TGCGAATTTGAAAACTGTGT
234308 TGCGAA
1 TGCGAA
234314 ATTGGAGATC
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 64 0.75
21 18 0.21
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (20 bp):
TGCGAATTTGAAAACTGTGT
Found at i:235448 original size:33 final size:33
Alignment explanation
Indices: 235401--235465 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
235391 TATCAATACT
* *
235401 ATTTTAGCATTCTGTTTTGACATTATCGGTACC
1 ATTTCAGCATTCTGTTTTGACAGTATCGGTACC
235434 ATTTCAGCATTCTGTTTTGACAGTATCGGTAC
1 ATTTCAGCATTCTGTTTTGACAGTATCGGTAC
235466 TACCTCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (33 bp):
ATTTCAGCATTCTGTTTTGACAGTATCGGTACC
Found at i:241230 original size:19 final size:19
Alignment explanation
Indices: 241206--241248 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
241196 CATTGTTACA
241206 AGGACTGAAACTATGTACG
1 AGGACTGAAACTATGTACG
241225 AGGACTGAAACTATGTACG
1 AGGACTGAAACTATGTACG
*
241244 GGGAC
1 AGGAC
241249 AGAGTCAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (19 bp):
AGGACTGAAACTATGTACG
Found at i:242451 original size:2 final size:2
Alignment explanation
Indices: 242437--242490 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
242427 ATGTTATAAT
*
242437 TA TA TA -A TG TA TA TA TA T- TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
242476 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
242491 TATCCTTACA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:242458 original size:18 final size:18
Alignment explanation
Indices: 242431--242493 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
242421 GTCCTTATGT
*
242431 TATA-ATTATATAATGTA
1 TATATATTATATAATATA
242448 TATATATTATATAATATA
1 TATATATTATATAATATA
242466 TATATA-TATATATATATA
1 TATATATTATATA-ATATA
242484 TATATATTAT
1 TATATATTAT
242494 CCTTACATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
17 10 0.24
18 29 0.69
19 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATATTATATAATATA
Found at i:243695 original size:21 final size:20
Alignment explanation
Indices: 243646--243698 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
243636 TAGTATTATT
* *
243646 TTATTTATTATTTTTTTCTCT
1 TTATTTATT-TTGTTTTCTCA
243667 TTCA-TTATTTCTGTTTTCTCA
1 TT-ATTTATTT-TGTTTTCTCA
243688 TTATTTATTTT
1 TTATTTATTTT
243699 TTATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.11
21 23 0.85
22 1 0.04
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (20 bp):
TTATTTATTTTGTTTTCTCA
Found at i:243718 original size:2 final size:2
Alignment explanation
Indices: 243713--243751 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
243703 ATCTAACACC
243713 TA TA 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 TA TA T
243752 TATTTGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:243995 original size:35 final size:34
Alignment explanation
Indices: 243947--244015 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
243937 TTTTCTGTTA
*
243947 TTTTTATCTTTATTTT-ATTATTTTTCCTTTTTCT
1 TTTTTATCTTTATTTTCA-TATTTTTCCATTTTCT
* *
243981 TTTTTATTTATTATTTTCATATTTTTGCATTTTCT
1 TTTTTATCT-TTATTTTCATATTTTTCCATTTTCT
244016 ATCTTAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 8 0.27
35 21 0.70
36 1 0.03
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.74
Consensus pattern (34 bp):
TTTTTATCTTTATTTTCATATTTTTCCATTTTCT
Found at i:243997 original size:20 final size:20
Alignment explanation
Indices: 243944--243997 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
243934 TTATTTTCTG
*
243944 TTATTTTTATCTTTATTTTA
1 TTATTTTTATTTTTATTTTA
* *
243964 TTATTTTTCCTTTTTCTTTT-
1 TTATTTTT-ATTTTTATTTTA
243984 TTATTTATTATTTT
1 TTATTT-TTATTTT
243998 CATATTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (20 bp):
TTATTTTTATTTTTATTTTA
Found at i:246087 original size:2 final size:2
Alignment explanation
Indices: 246015--246073 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
246005 ATTACATAAT
*
246015 TA TA TA TG TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
246056 TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA T
246074 CATTACACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:247104 original size:13 final size:13
Alignment explanation
Indices: 247086--247110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
247076 AATCCTTATT
247086 AAATTTAATTTTC
1 AAATTTAATTTTC
247099 AAATTTAATTTT
1 AAATTTAATTTT
247111 TTTAATTTAG
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
AAATTTAATTTTC
Found at i:247234 original size:9 final size:8
Alignment explanation
Indices: 247222--247261 Score: 53
Period size: 9 Copynumber: 4.6 Consensus size: 8
247212 GTATATATAA
247222 TATTTATTT
1 TATTT-TTT
247231 TATTTTTT
1 TATTTTTT
247239 TATTTTTT
1 TATTTTTT
247247 CTATTTTCTT
1 -TATTTT-TT
247257 TATTT
1 TATTT
247262 CTGTTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.38
9 16 0.55
10 2 0.07
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (8 bp):
TATTTTTT
Found at i:247242 original size:17 final size:18
Alignment explanation
Indices: 247222--247261 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
247212 GTATATATAA
247222 TATTTATTT-TATTTT-TT
1 TATTT-TTTCTATTTTCTT
247239 TATTTTTTCTATTTTCTT
1 TATTTTTTCTATTTTCTT
247257 TATTT
1 TATTT
247262 CTGTTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.14
17 11 0.52
18 7 0.33
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (18 bp):
TATTTTTTCTATTTTCTT
Found at i:247251 original size:22 final size:22
Alignment explanation
Indices: 247226--247285 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
247216 ATATAATATT
*
247226 TATTTTATTTTTTTATTTTTTC
1 TATTTTATTTTTTTATGTTTTC
* * *
247248 TATTTTCTTTATTTCTGTTTTC
1 TATTTTATTTTTTTATGTTTTC
247270 TCATTATTTATTTTTT
1 T-A-T-TTTATTTTTT
247286 ATATCTAACT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 19 0.66
23 1 0.03
24 1 0.03
25 8 0.28
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (22 bp):
TATTTTATTTTTTTATGTTTTC
Found at i:247300 original size:2 final size:2
Alignment explanation
Indices: 247295--247319 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
247285 TATATCTAAC
247295 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 T
247320 TTTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:247533 original size:15 final size:14
Alignment explanation
Indices: 247479--247588 Score: 72
Period size: 15 Copynumber: 7.9 Consensus size: 14
247469 CTTCCATTAT
*
247479 TTTTATTTTTGTTTA
1 TTTTATTTAT-TTTA
* *
247494 GTTTAGTTTAGTTTA
1 TTTTA-TTTATTTTA
*
247509 GTCTTATTTATTTTA
1 -TTTTATTTATTTTA
247524 TTTTATTTTATTTTA
1 TTTTA-TTTATTTTA
*
247539 TCTTATTTATTTTA
1 TTTTATTTATTTTA
247553 --TTATTT-TTCCTT-
1 TTTTATTTATT--TTA
247565 TTTTATTT-TTTTA
1 TTTTATTTATTTTA
247578 -TTTA-TTATTTT
1 TTTTATTTATTTT
247589 CATATTTATA
Statistics
Matches: 78, Mismatches: 8, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
11 4 0.05
12 16 0.21
13 2 0.03
14 21 0.27
15 29 0.37
16 6 0.08
ACGTcount: A:0.17, C:0.04, G:0.05, T:0.75
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:247566 original size:29 final size:30
Alignment explanation
Indices: 247505--247597 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 30
247495 TTTAGTTTAG
*
247505 TTTAGTCTTATTTATTTTATT-TTATTTTA-T
1 TTTA-TCTTATTTATTTTATTATT-TTTCATT
*
247535 TTTATCTTATTTATTTTATTATTTTTCCTTT
1 TTTATCTTATTTATTTTATTATTTTT-CATT
* *
247566 TTTAT-TTTTTTA-TTTATTA-TTTTCATA
1 TTTATCTTATTTATTTTATTATTTTTCATT
247593 TTTAT
1 TTTAT
247598 ACATTTTCTA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
27 7 0.13
28 4 0.07
29 26 0.47
30 12 0.22
31 6 0.11
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.74
Consensus pattern (30 bp):
TTTATCTTATTTATTTTATTATTTTTCATT
Found at i:247573 original size:5 final size:5
Alignment explanation
Indices: 247479--247554 Score: 68
Period size: 5 Copynumber: 15.4 Consensus size: 5
247469 CTTCCATTAT
* * * *
247479 TTTTA TTTT- TGTTTA GTTTA GTTTA GTTTA GTCTTA -TTTA TTTTA TTTTA
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
*
247529 TTTTA TTTTA TCTTA -TTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
247555 ATTTTTCCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
4 7 0.12
5 50 0.83
6 3 0.05
ACGTcount: A:0.18, C:0.03, G:0.07, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:250834 original size:21 final size:20
Alignment explanation
Indices: 250804--250842 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
250794 TGCATTTTAC
250804 TTTCAATGTTTATTTATATTTT
1 TTTCAATG-TT-TTTATATTTT
250826 TTTC-ATGTTTTTATATT
1 TTTCAATGTTTTTATATT
250843 CATATTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 2 0.12
21 3 0.18
22 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTCAATGTTTTTATATTTT
Found at i:256370 original size:31 final size:30
Alignment explanation
Indices: 256299--256370 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
256289 TCTACAAGCC
* * * * *
256299 TTGGAAAAATTTGGGGACCATTTTATAATT
1 TTGGAAAAGTTAGGGGACCAATTCATAACT
*
256329 TTTGAAAAGTTAGGGGACCAATTCAGTAACT
1 TTGGAAAAGTTAGGGGACCAATTCA-TAACT
256360 TTGGAAAAGTT
1 TTGGAAAAGTT
256371 GTAAATGGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (30 bp):
TTGGAAAAGTTAGGGGACCAATTCATAACT
Found at i:256933 original size:24 final size:24
Alignment explanation
Indices: 256906--256977 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
256896 TGCATGACAT
256906 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
*
256930 TGTACATAGATGTTTTGTACATCA
1 TGTACATAGATGTTTTATACATCA
*
256954 TGTATATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
256978 CCAGGAAGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:257317 original size:40 final size:40
Alignment explanation
Indices: 257254--257415 Score: 261
Period size: 40 Copynumber: 4.0 Consensus size: 40
257244 TGCATGTTTA
* *
257254 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATGCACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
257294 TAATGCAGTTCGGTGTATATGGTGGACACGACCTTATATG
1 TAATGCACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
257334 TAATACACTTCGGTATATATGGTGGGCACGACCTTATGTG
1 TAATGCACTTCGGTGTATATGGTGGGCACGACCTTATGTG
257374 TAATGCACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATGCACTTCGGTGTATATGGTGGGCACGACCTTATGTG
257414 TA
1 TA
257416 GCACTACGGT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATGCACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:257583 original size:45 final size:45
Alignment explanation
Indices: 257533--257671 Score: 197
Period size: 45 Copynumber: 3.0 Consensus size: 45
257523 GTAACAATGC
* *
257533 AAATAAGCTTACGAGCTTATGGGTTAAATGGTGAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGGTTAAATGATGAGTATATTGGTA
* * *
257578 AAATAAGCTTATGAGCTTATGGGTTAAATGTTTAAGGGTATATTAGTA
1 AAATAAGCTTATGAGCTTATGGGTTAAATG---ATGAGTATATTGGTA
*
257626 AAATAAGCTTATGAGCTTATGGGTTAAATGATAAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGGTTAAATGATGAGTATATTGGTA
257671 A
1 A
257672 GAAATTTTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
45 41 0.50
48 41 0.50
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGGTTAAATGATGAGTATATTGGTA
Found at i:257633 original size:48 final size:45
Alignment explanation
Indices: 257533--257671 Score: 188
Period size: 48 Copynumber: 3.0 Consensus size: 45
257523 GTAACAATGC
* *
257533 AAATAAGCTTACGAGCTTATGGGTTAAATGGTGAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGGTTAAATGGTGAGTATATTAGTA
* *
257578 AAATAAGCTTATGAGCTTATGGGTTAAATGTTTAAGGGTATATTAGTA
1 AAATAAGCTTATGAGCTTATGGGTTAAATG-GT--GAGTATATTAGTA
* * *
257626 AAATAAGCTTATGAGCTTATGGGTTAAATGATAAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGGTTAAATGGTGAGTATATTAGTA
257671 A
1 A
257672 GAAATTTTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
45 40 0.48
46 1 0.01
47 1 0.01
48 41 0.49
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGGTTAAATGGTGAGTATATTAGTA
Found at i:262660 original size:6 final size:6
Alignment explanation
Indices: 262645--262677 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
262635 CTAAATTGAG
262645 AAAAGAA AAAAGA AAAAGA AAAAG- AAAAGA AAA
1 AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAA
262678 TAAGGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:264351 original size:8 final size:8
Alignment explanation
Indices: 264338--264398 Score: 61
Period size: 8 Copynumber: 7.1 Consensus size: 8
264328 GTCCTTATGT
264338 TATAATTA
1 TATAATTA
264346 TATAATTA
1 TATAATTA
264354 TATAATGTA
1 TATAAT-TA
*
264363 TA-CATTA
1 TATAATTA
264370 TATAATATA
1 TATAAT-TA
264379 TATATATATA
1 TATA-AT-TA
264389 TATATATTA
1 TATA-ATTA
264398 T
1 T
264399 CATTACACAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
7 4 0.09
8 18 0.38
9 13 0.28
10 12 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (8 bp):
TATAATTA
Found at i:264412 original size:2 final size:2
Alignment explanation
Indices: 264344--264395 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
264334 ATGTTATAAT
* *
264344 TA TA TA -A T- TA TA TA -A TG TA TA CA T- TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264381 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
264396 TATCATTACA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
1 5 0.12
2 36 0.88
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:265588 original size:23 final size:22
Alignment explanation
Indices: 265544--265602 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
265534 ATAGTATTTA
*
265544 TTTTATTTATTATTTTTTTCTC
1 TTTTATTTATTTTTTTTTTCTC
*
265566 TTTTCTTTATTTTTGTTTTTCTC
1 TTTTATTTATTTTT-TTTTTCTC
*
265589 -ATTATTTATTTTTT
1 TTTTATTTATTTTTT
265603 ATATCTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 23 0.72
23 8 0.25
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTATTTTTTTTTTCTC
Found at i:265626 original size:2 final size:2
Alignment explanation
Indices: 265619--265647 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
265609 AACACCTATT
265619 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 T
265648 TATTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:265884 original size:14 final size:14
Alignment explanation
Indices: 265843--265905 Score: 76
Period size: 14 Copynumber: 4.5 Consensus size: 14
265833 TTATTTTCTC
265843 TTATTTTTATCTTTA
1 TTATTTTT-TCTTTA
*
265858 TT-TTATTTACTTTA
1 TTATT-TTTTCTTTA
*
265872 TTATTTTTCCTTT-
1 TTATTTTTTCTTTA
265885 TTATTTTTTCTTTA
1 TTATTTTTTCTTTA
265899 TTATTTT
1 TTATTTT
265906 CATATTTATG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.29
14 23 0.55
15 7 0.17
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTTTTCTTTA
Found at i:275354 original size:19 final size:19
Alignment explanation
Indices: 275330--275371 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
275320 CCCCCTTTGA
*
275330 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
*
275349 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATACCCCCT
275368 AGGG
1 AGGG
275372 TTCTGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:278169 original size:20 final size:20
Alignment explanation
Indices: 278144--278198 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
278134 TTTACACCTA
278144 GGGAACCGATTCCCCATTAG
1 GGGAACCGATTCCCCATTAG
278164 GGGAACCGATTCCCCATTAG
1 GGGAACCGATTCCCCATTAG
*
278184 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
278199 CCACGCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (20 bp):
GGGAACCGATTCCCCATTAG
Found at i:282144 original size:20 final size:21
Alignment explanation
Indices: 282119--282158 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
282109 TTTACCCCAA
282119 TTCAT-CCAGTATCGATACTT
1 TTCATCCCAGTATCGATACTT
*
282139 TTCATCCCATTATCGATACT
1 TTCATCCCAGTATCGATACT
282159 CAAACCGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.28, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCATCCCAGTATCGATACTT
Found at i:283352 original size:142 final size:142
Alignment explanation
Indices: 283186--283472 Score: 574
Period size: 142 Copynumber: 2.0 Consensus size: 142
283176 GCCTTATATT
283186 TTTACATGATTTTCTAATATAATATCAATATTTATAAATAGATAAAATGATTAAATTTAAAAACT
1 TTTACATGATTTTCTAATATAATATCAATATTTATAAATAGATAAAATGATTAAATTTAAAAACT
283251 ACCAAAAATATATTAATTATCTCCAACATTTTTATCATTGAATGAATTTAAGTTTAAGATTATTA
66 ACCAAAAATATATTAATTATCTCCAACATTTTTATCATTGAATGAATTTAAGTTTAAGATTATTA
283316 AGTATATAAATA
131 AGTATATAAATA
283328 TTTACATGATTTTCTAATATAATATCAATATTTATAAATAGATAAAATGATTAAATTTAAAAACT
1 TTTACATGATTTTCTAATATAATATCAATATTTATAAATAGATAAAATGATTAAATTTAAAAACT
283393 ACCAAAAATATATTAATTATCTCCAACATTTTTATCATTGAATGAATTTAAGTTTAAGATTATTA
66 ACCAAAAATATATTAATTATCTCCAACATTTTTATCATTGAATGAATTTAAGTTTAAGATTATTA
283458 AGTATATAAATA
131 AGTATATAAATA
283470 TTT
1 TTT
283473 TAAATCCAAA
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 145 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (142 bp):
TTTACATGATTTTCTAATATAATATCAATATTTATAAATAGATAAAATGATTAAATTTAAAAACT
ACCAAAAATATATTAATTATCTCCAACATTTTTATCATTGAATGAATTTAAGTTTAAGATTATTA
AGTATATAAATA
Found at i:283941 original size:19 final size:19
Alignment explanation
Indices: 283896--283942 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
283886 ATGCAATTTG
*
283896 ATAAAATATCTAGTATAAT
1 ATAAAATATATAGTATAAT
*
283915 ATATAATATATA-TATATAT
1 ATAAAATATATAGTATA-AT
*
283934 TTAAAATAT
1 ATAAAATAT
283943 TCAATGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAAAATATATAGTATAAT
Found at i:298281 original size:18 final size:18
Alignment explanation
Indices: 298240--298282 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
298230 TATTTCTGAG
*
298240 GCATATATTAATTCCGAA
1 GCATATATTAATTCCAAA
* *
298258 GAATATATTTATTCCAAA
1 GCATATATTAATTCCAAA
*
298276 TCATATA
1 GCATATA
298283 ATATGATTCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (18 bp):
GCATATATTAATTCCAAA
Found at i:307508 original size:177 final size:181
Alignment explanation
Indices: 307285--307618 Score: 568
Period size: 178 Copynumber: 1.9 Consensus size: 181
307275 AAAATCATTA
307285 AAAACCCAATTAATAATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAA
1 AAAACCCAATTAATAATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAA
* *
307350 AA-TTATATAAATTTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTT-AA
66 AATTTATATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTGAA
307413 TTAAAAAATATTAAATATATATATAAAATATGGACTAAGCCCAAACAATTT
131 TTAAAAAATATTAAATATATATATAAAATATGGACTAAGCCCAAACAATTT
307464 AAAACCC-ATTAAT-ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAA
1 AAAACCCAATTAATAATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAA
* * *
307527 AATTTATCTAAAATTTTTATTTTATAATTATTTATTATTTAAATTAATTATAAACTTTTTTTGAA
66 AATTTATATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTGAA
* * *
307592 TTAAAAAATATTTAATTTTTATATAAA
131 TTAAAAAATATTAAATATATATATAAA
307619 TTAGAAAATT
Statistics
Matches: 145, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
177 52 0.36
178 60 0.41
179 33 0.23
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (181 bp):
AAAACCCAATTAATAATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAA
AATTTATATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTGAA
TTAAAAAATATTAAATATATATATAAAATATGGACTAAGCCCAAACAATTT
Found at i:309253 original size:75 final size:75
Alignment explanation
Indices: 309130--309281 Score: 277
Period size: 75 Copynumber: 2.0 Consensus size: 75
309120 TTCATCCAAC
* *
309130 AAATATTATTTTAACCAAAACTTGAAACGTTAGGAATTAAAATACTAACTAATGATCATTTATAC
1 AAATATTATTTTAACCAAAACTTGAAACGTTAGGAATTAAAATACTAACTAATAACCATTTATAC
309195 AAACGTTGAA
66 AAACGTTGAA
*
309205 AAATATTATTTTAACTAAAACTTGAAACGTTAGGAATTAAAATACTAACTAATAACCATTTATAC
1 AAATATTATTTTAACCAAAACTTGAAACGTTAGGAATTAAAATACTAACTAATAACCATTTATAC
309270 AAACGTTGAA
66 AAACGTTGAA
309280 AA
1 AA
309282 GATAATTTTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.32
Consensus pattern (75 bp):
AAATATTATTTTAACCAAAACTTGAAACGTTAGGAATTAAAATACTAACTAATAACCATTTATAC
AAACGTTGAA
Found at i:313907 original size:18 final size:19
Alignment explanation
Indices: 313865--313912 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
313855 AGATGAACAA
*
313865 TATCGATACTGATGCAATTAG
1 TATCGATACTGATG--ATGAG
313886 TATCGATACTGATG-TGAG
1 TATCGATACTGATGATGAG
*
313904 TATCAATAC
1 TATCGATAC
313913 CAAGAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
21 14 0.56
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (19 bp):
TATCGATACTGATGATGAG
Found at i:314406 original size:54 final size:54
Alignment explanation
Indices: 314342--314517 Score: 212
Period size: 54 Copynumber: 3.2 Consensus size: 54
314332 ATTGCAAGTA
314342 TCGTATTGGCACTGTGTGTGAAACCTAAGAAATTCATAATAAGTTTATGAATTT
1 TCGTATTGGCACTGTGTGTGAAACCTAAGAAATTCATAATAAGTTTATGAATTT
*
314396 TCGTATTGGCACTGTGTGT-ACAACTTAAGAAATTCATAATAAGTTTATGAATTT
1 TCGTATTGGCACTGTGTGTGA-AACCTAAGAAATTCATAATAAGTTTATGAATTT
* ** * * * * * *
314450 CCGTATTGGCACTAAGTGTGCAACCCCATGTAATTCATAATGAGTTTGTGAA-TT
1 TCGTATTGGCACTGTGTGTG-AAACCTAAGAAATTCATAATAAGTTTATGAATTT
*
314504 ACTGTATTGGCACT
1 TC-GTATTGGCACT
314518 ACGGGTACAA
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
53 1 0.01
54 70 0.66
55 34 0.32
56 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (54 bp):
TCGTATTGGCACTGTGTGTGAAACCTAAGAAATTCATAATAAGTTTATGAATTT
Found at i:314503 original size:55 final size:54
Alignment explanation
Indices: 314343--314544 Score: 192
Period size: 54 Copynumber: 3.7 Consensus size: 54
314333 TTGCAAGTAT
** * *
314343 CGTATTGGCACTGTGTGTGA-AACCTAAGAAATTCATAATAAGTTTATGAATTTT
1 CGTATTGGCACTAAGTGT-ACAACCCAAGAAATTCATAATAAGTTTATGAATTTC
** **
314397 CGTATTGGCACTGTGTGTACAACTTAAGAAATTCATAATAAGTTTATGAATTTC
1 CGTATTGGCACTAAGTGTACAACCCAAGAAATTCATAATAAGTTTATGAATTTC
* * * * * *
314451 CGTATTGGCACTAAGTGTGCAACCCCATGTAATTCATAATGAGTTTGTGAATTAC
1 CGTATTGGCACTAAGTGTACAA-CCCAAGAAATTCATAATAAGTTTATGAATTTC
* * * * *
314506 TGTATTGGCACTACGGGTACAAACCATAG-AATTTATAAT
1 CGTATTGGCACTAAGTGTACAACCCA-AGAAATTCATAAT
314545 GAATTGAAAT
Statistics
Matches: 126, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 81 0.64
55 44 0.35
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (54 bp):
CGTATTGGCACTAAGTGTACAACCCAAGAAATTCATAATAAGTTTATGAATTTC
Found at i:317314 original size:22 final size:23
Alignment explanation
Indices: 317271--317331 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
317261 AGTTGAAAAG
* *
317271 ATATATTAA-AATAAAATAAATA
1 ATATAATAATAATATAATAAATA
317293 ATATAATAATAATATAAT-AATA
1 ATATAATAATAATATAATAAATA
*
317315 A-ATAGTAATAAATATAA
1 ATATAATAAT-AATATAA
317332 AAGTAGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.21
22 20 0.59
23 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATAATAATAATATAATAAATA
Found at i:317396 original size:19 final size:19
Alignment explanation
Indices: 317358--317420 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
317348 GTTATTTTAA
* *
317358 AAATAAAAG-ATAAGAATT
1 AAATAAAAGAAAAATAATT
317376 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAATAATT
317395 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAATAATT
317414 AAATAAA
1 AAATAAA
317421 CAAATTAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
18 9 0.21
19 33 0.79
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAATAAAAGAAAAATAATT
Found at i:318138 original size:65 final size:65
Alignment explanation
Indices: 317992--318138 Score: 176
Period size: 65 Copynumber: 2.3 Consensus size: 65
317982 CAAATTTTTA
* *
317992 AAAAC-AAGCTAAAATA-TCTTAAATCCTAATTAAAACACTTTAAACTATTTAAACTAAAATACC
1 AAAACAAAGATAAAATATTCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACC
* * * *
318055 AAAAAAAATAATATAATATTC-TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATA
1 AAAACAAA-GATAAAATATTCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATA
*
318118 CTT
64 C-C
318121 AAAACAAAGATAAAATAT
1 AAAACAAAGATAAAATAT
318139 AAAAAAAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
63 4 0.06
64 6 0.09
65 50 0.72
66 9 0.13
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (65 bp):
AAAACAAAGATAAAATATTCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACC
Found at i:319547 original size:20 final size:20
Alignment explanation
Indices: 319522--319567 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
319512 CCAAAAGGAA
319522 TCAAGAGTATAAAGCAAAAT
1 TCAAGAGTATAAAGCAAAAT
*
319542 TCAAGAGTATAAAGCGAAAT
1 TCAAGAGTATAAAGCAAAAT
319562 TCAAGA
1 TCAAGA
319568 TTAGCAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.20
Consensus pattern (20 bp):
TCAAGAGTATAAAGCAAAAT
Found at i:319861 original size:10 final size:10
Alignment explanation
Indices: 319846--319901 Score: 62
Period size: 9 Copynumber: 5.7 Consensus size: 10
319836 TAAGCATCTG
319846 ATAAAATAAA
1 ATAAAATAAA
319856 ATAAAAT-AA
1 ATAAAATAAA
* *
319865 ATGAAATGAA
1 ATAAAATAAA
319875 AT-AAATAAA
1 ATAAAATAAA
319884 ATGAAAATAAA
1 AT-AAAATAAA
*
319895 ACAAAAT
1 ATAAAAT
319902 GTGTTGCCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 16 0.40
10 16 0.40
11 8 0.20
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:319871 original size:14 final size:14
Alignment explanation
Indices: 319849--319894 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
319839 GCATCTGATA
319849 AAATAAAATAAAAT
1 AAATAAAATAAAAT
* *
319863 AAATGAAATGAAAT
1 AAATAAAATAAAAT
319877 AAATAAAATGAAAAT
1 AAATAAAAT-AAAAT
319892 AAA
1 AAA
319895 ACAAAATGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:319876 original size:19 final size:19
Alignment explanation
Indices: 319849--319895 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
319839 GCATCTGATA
319849 AAATAAAATAAA-ATAAATG
1 AAATAAAATAAATA-AAATG
*
319868 AAATGAAATAAATAAAATG
1 AAATAAAATAAATAAAATG
319887 AAAATAAAA
1 -AAATAAAA
319896 CAAAATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (19 bp):
AAATAAAATAAATAAAATG
Found at i:319880 original size:4 final size:5
Alignment explanation
Indices: 319846--319901 Score: 62
Period size: 5 Copynumber: 11.4 Consensus size: 5
319836 TAAGCATCTG
* *
319846 ATAAA ATAAA ATAAA AT-AA ATGAA ATGAA AT-AA ATAAA ATGAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA
*
319895 ACAAA AT
1 ATAAA AT
319902 GTGTTGCCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 8 0.17
5 33 0.72
6 5 0.11
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:321065 original size:20 final size:20
Alignment explanation
Indices: 321036--321074 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
321026 AGAGCTCATT
321036 TAGGACCATATAGATGCATA
1 TAGGACCATATAGATGCATA
* *
321056 TAGGAGCATATAGTTGCAT
1 TAGGACCATATAGATGCAT
321075 GTGGTGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (20 bp):
TAGGACCATATAGATGCATA
Found at i:321449 original size:23 final size:23
Alignment explanation
Indices: 321400--321449 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
321390 ATCTTTATAC
321400 ATAT-AGATACTTATTTCATATG
1 ATATAAGATACTTATTTCATATG
* *
321422 TTATAAGATAGTTATTTTCATAT-
1 ATATAAGATACTTA-TTTCATATG
321445 ATATA
1 ATATA
321450 TATTATACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 3 0.13
23 12 0.52
24 8 0.35
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (23 bp):
ATATAAGATACTTATTTCATATG
Found at i:323124 original size:21 final size:20
Alignment explanation
Indices: 323056--323124 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
323046 ATTGGAGTGC
323056 AAAAA-AAGAAAAAAAAAGA
1 AAAAAGAAGAAAAAAAAAGA
* **
323075 CAAAAGAAGAAAACAAAATCA
1 AAAAAGAAGAAAA-AAAAAGA
* *
323096 TAAAAGAAGAAAAGAAAAGA
1 AAAAAGAAGAAAAAAAAAGA
323116 AAAAGAGAA
1 AAAA-AGAA
323125 AGCAAGCCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 4 0.10
20 14 0.36
21 21 0.54
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAAGAAGAAAAAAAAAGA
Found at i:326028 original size:23 final size:23
Alignment explanation
Indices: 325983--326028 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
325973 TTATACCTAT
*
325983 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
326006 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
326029 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:332813 original size:20 final size:20
Alignment explanation
Indices: 332788--332830 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
332778 TGTAAGAGCT
332788 CATTTAGGA-CAATATAGATG
1 CATTTAGGAGC-ATATAGATG
*
332808 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
332828 CAT
1 CAT
332831 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:333153 original size:18 final size:18
Alignment explanation
Indices: 333130--333166 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
333120 TTTCCAGATG
333130 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
333148 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
333166 C
1 C
333167 TAATCCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:334545 original size:142 final size:143
Alignment explanation
Indices: 334289--334573 Score: 563
Period size: 142 Copynumber: 2.0 Consensus size: 143
334279 CCCTATGGAG
334289 AATGATACTCACTCATCACTGTATTACTTGTTCGATTGTGTATACTTGCACATATTTCCACACCA
1 AATGATACTCACTCATCACTGTATTACTTGTTCGATTGTGTATACTTGCACATATTTCCACACCA
334354 TTTATAGTACTCACAAAGAGCGGACAAAGAGGTATATTGACTTGAACTTTTTGGAACA-CTCTAA
66 TTTATAGTACTCACAAAGAGCGGACAAAGAGGTATATTGACTTGAACTTTTTGGAACACCTCTAA
334418 GATTTTATTTTCT
131 GATTTTATTTTCT
334431 AATGATACTCACTCATCACTGTATTACTTGTTCGATTGTGTATACTTGCACATATTTCCACACCA
1 AATGATACTCACTCATCACTGTATTACTTGTTCGATTGTGTATACTTGCACATATTTCCACACCA
334496 TTTATAGTACTCACAAAGAGCGGACAAAGAGGTATATTGACTTGAACTTTTTGGAACACCTCTAA
66 TTTATAGTACTCACAAAGAGCGGACAAAGAGGTATATTGACTTGAACTTTTTGGAACACCTCTAA
334561 GATTTTATTTTCT
131 GATTTTATTTTCT
334574 TCAGCTCTTT
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 123 0.87
143 19 0.13
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (143 bp):
AATGATACTCACTCATCACTGTATTACTTGTTCGATTGTGTATACTTGCACATATTTCCACACCA
TTTATAGTACTCACAAAGAGCGGACAAAGAGGTATATTGACTTGAACTTTTTGGAACACCTCTAA
GATTTTATTTTCT
Found at i:337796 original size:29 final size:31
Alignment explanation
Indices: 337739--337863 Score: 131
Period size: 29 Copynumber: 4.3 Consensus size: 31
337729 TTTTATAGAT
* *
337739 ATAGCACCC-TTTTTAAAATAATTAC-AAAA
1 ATAGCACCCATTTTCAAATTAATTACTAAAA
*
337768 ATAGCA-CC-TTTTCGAATTAATTACTAAAA
1 ATAGCACCCATTTTCAAATTAATTACTAAAA
* *
337797 ATAGCA-CCAATTTCAAATTAATTACT-GAA
1 ATAGCACCCATTTTCAAATTAATTACTAAAA
*
337826 ATAGCACCCATTTT-GAATTAATTACT-AAA
1 ATAGCACCCATTTTCAAATTAATTACTAAAA
*
337855 ATAGTACCC
1 ATAGCACCC
337864 CAGTCAACGG
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
28 15 0.18
29 47 0.57
30 21 0.25
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.32
Consensus pattern (31 bp):
ATAGCACCCATTTTCAAATTAATTACTAAAA
Found at i:337829 original size:58 final size:59
Alignment explanation
Indices: 337739--337855 Score: 157
Period size: 58 Copynumber: 2.0 Consensus size: 59
337729 TTTTATAGAT
** *
337739 ATAGCACCCTTTTTAAAATAATTACAAAAATAGCA-CC-TTTTCGAATTAATTACTAAAA
1 ATAGCACCAATTTCAAAATAATTACAAAAATAGCACCCATTTT-GAATTAATTACTAAAA
* **
337797 ATAGCACCAATTTCAAATTAATTACTGAAATAGCACCCATTTTGAATTAATTACTAAAA
1 ATAGCACCAATTTCAAAATAATTACAAAAATAGCACCCATTTTGAATTAATTACTAAAA
337856 TAGTACCCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 29 0.57
59 18 0.35
60 4 0.08
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (59 bp):
ATAGCACCAATTTCAAAATAATTACAAAAATAGCACCCATTTTGAATTAATTACTAAAA
Found at i:337900 original size:13 final size:13
Alignment explanation
Indices: 337882--337907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
337872 GGTCAACGAT
337882 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
337895 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
337908 AACCGATCAA
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:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:345032 original size:30 final size:29
Alignment explanation
Indices: 344952--345077 Score: 130
Period size: 29 Copynumber: 4.4 Consensus size: 29
344942 CATTTTACAG
* * * *
344952 AAATAACACCCTTTTTAAAATAATTAC-A
1 AAATAGCACCCATTTCAAATTAATTACTA
* * *
344980 AAATAGTA-CCTTTTCGAATTAATTACTAA
1 AAATAGCACCCATTTCAAATTAATTACT-A
*
345009 AAATAGCACCCATTTCAAATTAATTACTG
1 AAATAGCACCCATTTCAAATTAATTACTA
* *
345038 AAATAGCACCTATTTCGAATTAATTACTA
1 AAATAGCACCCATTTCAAATTAATTACTA
*
345067 AAATAACACCC
1 AAATAGCACCC
345078 GGTCAACGGT
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
27 15 0.19
28 6 0.07
29 43 0.53
30 17 0.21
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAATTAATTACTA
Found at i:345066 original size:59 final size:56
Alignment explanation
Indices: 344952--345077 Score: 171
Period size: 57 Copynumber: 2.2 Consensus size: 56
344942 CATTTTACAG
* * *
344952 AAATAACACCCTTTTTAAAATAATTACAAAATAGTACCTTTTCGAATTAATTACTAA
1 AAATAACACCCATTTCAAAATAATTACAAAATAGCACCTTTTCGAATTAATTACT-A
* * *
345009 AAATAGCACCCATTTCAAATTAATTACTGAAATAGCACCTATTTCGAATTAATTACTA
1 AAATAACACCCATTTCAAAATAATTAC-AAAATAGCACCT-TTTCGAATTAATTACTA
345067 AAATAACACCC
1 AAATAACACCC
345078 GGTCAACGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 23 0.38
58 21 0.35
59 16 0.27
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (56 bp):
AAATAACACCCATTTCAAAATAATTACAAAATAGCACCTTTTCGAATTAATTACTA
Found at i:346218 original size:65 final size:65
Alignment explanation
Indices: 346091--346218 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 65
346081 TAAAACATCT
* * * * *
346091 TAAATCCTAATTAAAACACTTGAAACTATTTAAACTGAAATACCTAAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACATAAAAAAACAATAAAATATTC
* * *
346156 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACATAAAACAACGATAAAATAT
1 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACATAAAAAAACAATAAAATAT
346219 AAAAATAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 4 0.07
65 50 0.93
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (65 bp):
TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACATAAAAAAACAATAAAATATTC
Found at i:353428 original size:43 final size:41
Alignment explanation
Indices: 353153--353599 Score: 418
Period size: 41 Copynumber: 10.9 Consensus size: 41
353143 TGTTTTGAAC
* * * *
353153 AAACGCCGCAAAAGA-TCTTACTTTAGTGGCGTTTGTATAA
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAA
* * * * * * *
353193 AAACGCTGCTAAAGATTAGTA-TTGTAGTGACGTTTTTACAC
1 AAACGCCGCTATAGACTCGTACTT-TAGTGGCGTTTTTATAA
* * * * *
353234 AAACGCCGGTATAGAATCGTTCTTTAGGGGCGTTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAA
*
353275 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAA
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAA
* * * * *
353316 AAGCGCTGCTATA-ACTCATACTTTACTGGCATTTTTATAA
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAA
* * * *
353356 AAATGCTGCTATA-ACTCATACTTTAGTGGCGTTTTTGTTTAA
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCG-TTTT-TATAA
*
353398 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATTTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTA--TAA
* * * * *
353441 AAACGTCGCTATAGACTTGTACTTTAGTGGCATTTTTGTTTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGC-GTTTT-TATAA
* *
353484 AAACGTCGCTATAGACTTGTACTTTAGTGGCGTTTTTATAA
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAA
* * ** * *
353525 AAACGCCGCAAAAGACTCGTACGCTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAA
* *
353566 AAACGCCGCAAAAGACTCGTAC-TTAGTGGCGTTT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
353600 GTACCGCAAA
Statistics
Matches: 341, Mismatches: 56, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
40 76 0.22
41 153 0.45
42 25 0.07
43 82 0.24
44 4 0.01
45 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAA
Found at i:356277 original size:43 final size:43
Alignment explanation
Indices: 356208--356529 Score: 231
Period size: 43 Copynumber: 7.2 Consensus size: 43
356198 ATGGTAATTA
* *
356208 GCGGCGTTTGTATCCAAAAGCGCCGCTATATATCTGATC-TTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA-CATTTT
* * *
356251 GTGGCGTTTGTATCCAAAAACCCCGCTATAGGTCTGACATTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
* * * *
356294 GCGGCGTTTGTGTCCAAAAACGCCACTATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
356337 ACGACGTTTGTTCTAACGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
1 --G-CG---G------CGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
* * * * * * *
356392 GCGGCATTT-TTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACATTTT
* * * *
356435 GCGGCGTTTAT-TCCAAAAACGCCACTATAGATATCGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACATTTT
* * * * *
356478 ACGGCGTTTGT-TCAAAAAACGCCG-TAATAGATATTGACCTATT
1 GCGGCGTTTGTATCCAAAAACGCCGCT-ATAGAT-CTGACATTTT
356521 GCGGCGTTT
1 GCGGCGTTT
356530 TTTGTTCTCA
Statistics
Matches: 225, Mismatches: 36, Indels: 36
0.76 0.12 0.12
Matches are distributed among these distances:
42 23 0.10
43 157 0.70
44 2 0.01
45 1 0.00
46 2 0.01
49 2 0.01
52 2 0.01
53 1 0.00
55 35 0.16
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTT
Found at i:356406 original size:55 final size:55
Alignment explanation
Indices: 356298--356406 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
356288 CATTTTGCGG
* * * *
356298 CGTTTGTGTCCAAAAACGCCACTATAGGTCTGACCTTTTACGACGTTTGTTCTAA
1 CGTTTGTATCCAAAAACGCCACTATAGATCTGACATTTTACGACATTTGTTCTAA
* * * *
356353 CGTTTGTATCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCATTTTTTCTA
1 CGTTTGTATCCAAAAACGCCACTATAGATCTGACATTTTACGACATTTGTTCTA
356407 GAAACGCCGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (55 bp):
CGTTTGTATCCAAAAACGCCACTATAGATCTGACATTTTACGACATTTGTTCTAA
Found at i:356474 original size:141 final size:141
Alignment explanation
Indices: 356212--356490 Score: 366
Period size: 141 Copynumber: 2.0 Consensus size: 141
356202 TAATTAGCGG
* * * *
356212 CGTTTGTATCCAAAAGCGCCGCTATATATCTGATCTTTTGTGGCGTTTGTATCCAAAAACCCCGC
1 CGTTTGTATCCAAAAACGCCGCTATAGATCTGATCTTTTGCGGCATTTGTATCCAAAAACCCCGC
* * * * *
356277 TATAGGTCTGACATTTTGCGGCGTTTGTGTCCAAAAACGCCACTATAGGTCTGACCTTTTACGAC
66 TATAGATCTAACATTTTGCGGCGTTTATGTCCAAAAACGCCACTATAGATATGACCTTTTACGAC
356342 GTTTGTTCTAA
131 GTTTGTTCTAA
* * * *
356353 CGTTTGTATCCAAAAACGCCGCTATAGATCTGA-CATTTTGCGGCATTT-TTTCTAGAAACGCCG
1 CGTTTGTATCCAAAAACGCCGCTATAGATCTGATC-TTTTGCGGCATTTGTATCCAAAAACCCCG
* *
356416 CTATATATCATAACTTTTTGCGGCGTTTAT-TCCAAAAACGCCACTATAGATATCGACCTTTTAC
65 CTATAGATC-TAACATTTTGCGGCGTTTATGTCCAAAAACGCCACTATAGATAT-GACCTTTTAC
*
356480 GGCGTTTGTTC
128 GACGTTTGTTC
356491 AAAAAACGCC
Statistics
Matches: 119, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
140 40 0.34
141 79 0.66
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (141 bp):
CGTTTGTATCCAAAAACGCCGCTATAGATCTGATCTTTTGCGGCATTTGTATCCAAAAACCCCGC
TATAGATCTAACATTTTGCGGCGTTTATGTCCAAAAACGCCACTATAGATATGACCTTTTACGAC
GTTTGTTCTAA
Found at i:362350 original size:2 final size:2
Alignment explanation
Indices: 362343--362382 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
362333 ACATGCATAA
*
362343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
362383 TATGTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367892 original size:55 final size:56
Alignment explanation
Indices: 367825--367952 Score: 177
Period size: 56 Copynumber: 2.3 Consensus size: 56
367815 ATTACCAAAT
* * *
367825 GGCACTATGTGTGCAAAA-CTATGAAATTCATAATAAGGTTATGAATTTCCGTATA
1 GGCACTATGTGTGCAAAAGCTAAGAAATTCATAACAAGGTTATGAATTACCGTATA
* * *
367880 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAACAAGTTTATGAATTACCGTATT
1 GGCACTATGTGTGCAAAAGCTAAGAAATTCATAACAAGGTTATGAATTACCGTATA
* *
367936 GGCACTACGCGTGCAAA
1 GGCACTATGTGTGCAAA
367953 CTATAGAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
55 17 0.27
56 46 0.73
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (56 bp):
GGCACTATGTGTGCAAAAGCTAAGAAATTCATAACAAGGTTATGAATTACCGTATA
Found at i:368224 original size:46 final size:45
Alignment explanation
Indices: 368172--368258 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 45
368162 TTAGATGAAG
*
368172 AACAATGCATAATTGACATGAAAGGATGCCATAAATGAAAATGTAT
1 AACAATGCATAATTGACATGAAAGG-TGCCACAAATGAAAATGTAT
*
368218 AACAATGCATAATTGGCATGAAAGGTGCCACAAATGAAAAT
1 AACAATGCATAATTGACATGAAAGGTGCCACAAATGAAAAT
368259 ATGTAGAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 15 0.38
46 24 0.62
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (45 bp):
AACAATGCATAATTGACATGAAAGGTGCCACAAATGAAAATGTAT
Found at i:372364 original size:56 final size:55
Alignment explanation
Indices: 372208--372452 Score: 336
Period size: 56 Copynumber: 4.5 Consensus size: 55
372198 AATTGCACTA
*
372208 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGAGCACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTG
*
372263 TGTGC-AAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCATTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTG
* **
372317 TGTGCAAAAGCTAATAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTG
1 TGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTG
* * **
372373 TGTGCAAAAGCTAAGAAATACATAATAAGTTTATGAATTATC-GTATTGGCACTACG
1 TGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATT-TCTGTATGGGCACTTTG
*
372429 TGTGC-AAACTATAGAAGTT-ATAAT
1 TGTGCAAAACTA-AGAAATTCATAAT
372453 GAATTGAAAG
Statistics
Matches: 172, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
54 60 0.35
55 16 0.09
56 94 0.55
57 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTG
Found at i:372452 original size:110 final size:109
Alignment explanation
Indices: 372208--372452 Score: 320
Period size: 110 Copynumber: 2.2 Consensus size: 109
372198 AATTGCACTA
**
372208 TGTGCAAAACTA-AGAAATTCATAATAAGTTTATGAATTTCTGTATGAGCACTTTGTGTGCAAAC
1 TGTGCAAAACTATAG-AATTCATAATAAGTTTATGAATTTCCATATGAGCACTTTGTGTGCAAAC
* * **
372272 TAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCATTTTG
65 TAAGAAATACATAATAAGTTTATGAATTTCTGTATGGGCACTACG
*
372317 TGTGCAAAAGCTAATA-AATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTGTGTGCAAA
1 TGTGCAAAA-CT-ATAGAATTCATAATAAGTTTATGAATTTCCATATGAGCACTTTGTGTGC-AA
*
372381 AGCTAAGAAATACATAATAAGTTTATGAATTATC-GTATTGGCACTACG
63 A-CTAAGAAATACATAATAAGTTTATGAATT-TCTGTATGGGCACTACG
372429 TGTGC-AAACTATAGAAGTT-ATAAT
1 TGTGCAAAACTATAGAA-TTCATAAT
372453 GAATTGAAAG
Statistics
Matches: 120, Mismatches: 8, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
109 12 0.10
110 53 0.44
111 9 0.08
112 44 0.37
113 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (109 bp):
TGTGCAAAACTATAGAATTCATAATAAGTTTATGAATTTCCATATGAGCACTTTGTGTGCAAACT
AAGAAATACATAATAAGTTTATGAATTTCTGTATGGGCACTACG
Found at i:374646 original size:18 final size:19
Alignment explanation
Indices: 374612--374649 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
374602 TTTAGGTTAA
374612 TTTAGGATCTTTGTATTAT
1 TTTAGGATCTTTGTATTAT
*
374631 TTTAGGAT-TTTTTATTAT
1 TTTAGGATCTTTGTATTAT
374649 T
1 T
374650 GTATCTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.63
Consensus pattern (19 bp):
TTTAGGATCTTTGTATTAT
Found at i:375068 original size:2 final size:2
Alignment explanation
Indices: 375063--375099 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
375053 ACATTGTGTG
375063 TA 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 TA T
375100 CAGTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:378250 original size:10 final size:10
Alignment explanation
Indices: 378235--378300 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
378225 AGAATATACA
*
378235 TATTTTTACT
1 TATTTTTATT
378245 TA-TTTTATT
1 TATTTTTATT
* *
378254 TATCTCTATT
1 TATTTTTATT
378264 TACTTTTTATT
1 TA-TTTTTATT
*
378275 TATTCTTATT
1 TATTTTTATT
378285 TATTTTT-TT
1 TATTTTTATT
378294 ATATTTT
1 -TATTTT
378301 CTCTTTACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
9 10 0.22
10 28 0.61
11 8 0.17
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTTTTATT
Found at i:378273 original size:21 final size:21
Alignment explanation
Indices: 378247--378322 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
378237 TTTTTACTTA
378247 TTTTATTTA-TCTCTATTTACT
1 TTTTATTTATTCT-TATTTACT
378268 TTTTATTTATTCTTATTTA-T
1 TTTTATTTATTCTTATTTACT
* *
378288 TTTT-TTATATTTTCTCTTTACT
1 TTTTATT-TATTCT-TATTTACT
*
378310 TTCTA-TTATTCTT
1 TTTTATTTATTCTT
378323 GTCATATGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.04
20 11 0.24
21 25 0.54
22 8 0.17
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATTTATTCTTATTTACT
Found at i:378302 original size:22 final size:22
Alignment explanation
Indices: 378239--378311 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
378229 TATACATATT
378239 TTTACTTATTT-TATTTATCTCTA
1 TTTACTT-TTTATATTT-TCTCTA
378262 TTTACTTTTTAT-TTATTCT-TA
1 TTTACTTTTTATATT-TTCTCTA
*
378283 TTTATTTTTTTATATTTTCTC--
1 TTTA-CTTTTTATATTTTCTCTA
378304 TTTACTTT
1 TTTACTTT
378312 CTATTATTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
20 3 0.07
21 10 0.23
22 19 0.44
23 11 0.26
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTACTTTTTATATTTTCTCTA
Found at i:383572 original size:35 final size:35
Alignment explanation
Indices: 383526--383597 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
383516 TTGTCATCCC
383526 TTAGAATTTTATAAATTCG-TCTTTATAATATAAAA
1 TTAGAATTTTATAAATTCGAT-TTTATAATATAAAA
383561 TTAGAATTTTATAAATTCGATTTTATAATATAAAA
1 TTAGAATTTTATAAATTCGATTTTATAATATAAAA
383596 TT
1 TT
383598 TTACGTCCGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (35 bp):
TTAGAATTTTATAAATTCGATTTTATAATATAAAA
Found at i:385455 original size:20 final size:19
Alignment explanation
Indices: 385430--385471 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
385420 TTTATTTCTT
385430 AATATTTATTTACTAAAATA
1 AATATTTATTTA-TAAAATA
*
385450 AATATTTATTTATTAAATA
1 AATATTTATTTATAAAATA
385469 AAT
1 AAT
385472 TTAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATTTATTTATAAAATA
Found at i:385470 original size:24 final size:25
Alignment explanation
Indices: 385432--385480 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
385422 TATTTCTTAA
* *
385432 TATTTATTTACTAAA-ATAAATATT
1 TATTTATTAAATAAATATAAATATT
*
385456 TATTTATTAAATAAATTTAAATATT
1 TATTTATTAAATAAATATAAATATT
385481 AAATAGTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTTATTAAATAAATATAAATATT
Found at i:387010 original size:46 final size:45
Alignment explanation
Indices: 386939--387029 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 45
386929 TTTATGAGCA
* *
386939 TAAAGTTATTATGACCACTAGTAGATTGATATGATAAATAGATATG
1 TAAAGTTATTATGACCACTAATAGATTGACATGA-AAATAGATATG
*
386985 TAAAGTTATTATGACTACTAATAGATTGACATGAAAATAGATATG
1 TAAAGTTATTATGACCACTAATAGATTGACATGAAAATAGATATG
387030 ATCACATGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (45 bp):
TAAAGTTATTATGACCACTAATAGATTGACATGAAAATAGATATG
Found at i:396807 original size:30 final size:30
Alignment explanation
Indices: 396771--396827 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
396761 ACAGTCAGAA
*
396771 GAACATTTATAAATGAAATTTGCTCTAAGG
1 GAACATTAATAAATGAAATTTGCTCTAAGG
*
396801 GAACATTAATAAATGAAGTTTGCTCTA
1 GAACATTAATAAATGAAATTTGCTCTA
396828 TGGGCACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (30 bp):
GAACATTAATAAATGAAATTTGCTCTAAGG
Done.