Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002720.1 Hibiscus syriacus cultivar Beakdansim tig00005612_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: 242320
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:166353 original size:18 final size:17
Alignment explanation
Indices: 166308--166354 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
166298 AGAAGTACAT
166308 TCTGAATCATTCAGAGC
1 TCTGAATCATTCAGAGC
* *
166325 -C-AAACCATTCAGAGCC
1 TCTGAATCATTCAGAG-C
166341 TCTGAATCATTCAG
1 TCTGAATCATTCAG
166355 CACTTAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 1 0.04
18 9 0.39
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (17 bp):
TCTGAATCATTCAGAGC
Found at i:166452 original size:15 final size:15
Alignment explanation
Indices: 166432--166473 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
166422 TTTCTTACCT
166432 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
166447 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
*
166462 CTGACTGATTCA
1 CTGAATGATTCA
166474 ACAAAACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (15 bp):
CTGAATGATTCAGTG
Found at i:166551 original size:27 final size:27
Alignment explanation
Indices: 166486--166551 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
166476 AAAACAATGT
* *
166486 TGAATGATTCAACATCAAAGTATATTT
1 TGAATGATTCAGCATCAAAGTATATTC
*
166513 TGAATGATTCAGCATTAAAGTATATTC
1 TGAATGATTCAGCATCAAAGTATATTC
166540 TGAATGATTCAG
1 TGAATGATTCAG
166552 AACCATTATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (27 bp):
TGAATGATTCAGCATCAAAGTATATTC
Found at i:172530 original size:29 final size:31
Alignment explanation
Indices: 172487--172548 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
172477 TTTATACTAC
172487 TGAATTTTTAA-TTT-TATCAATTATAACAT
1 TGAATTTTTAATTTTGTATCAATTATAACAT
* *
172516 TGAA-TTTTAATTTTTGTTTCAATTATATCAT
1 TGAATTTTTAA-TTTTGTATCAATTATAACAT
172547 TG
1 TG
172549 GGTCGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.21
29 4 0.14
30 3 0.11
31 15 0.54
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (31 bp):
TGAATTTTTAATTTTGTATCAATTATAACAT
Found at i:174855 original size:51 final size:51
Alignment explanation
Indices: 174795--174906 Score: 215
Period size: 51 Copynumber: 2.2 Consensus size: 51
174785 CATGCCAATT
174795 ATATCCAAAATATTATAGAAACAATCAAGGTTTGGGGTTTTAGAATATAAA
1 ATATCCAAAATATTATAGAAACAATCAAGGTTTGGGGTTTTAGAATATAAA
174846 ATATCCAAAATATTATAGAAACAATCAAGGTTTGGGGTTTTAGAATATAAA
1 ATATCCAAAATATTATAGAAACAATCAAGGTTTGGGGTTTTAGAATATAAA
*
174897 ATATCGAAAA
1 ATATCCAAAA
174907 CTTTTACATA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.30
Consensus pattern (51 bp):
ATATCCAAAATATTATAGAAACAATCAAGGTTTGGGGTTTTAGAATATAAA
Found at i:176067 original size:21 final size:21
Alignment explanation
Indices: 176039--176096 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
176029 AGAAACAAAT
* *
176039 GCGTTGCGATTTTGGAGTATC
1 GCGTTGCGAATTTGGACTATC
* * *
176060 GTGTTGCGAATTTCGACTTTC
1 GCGTTGCGAATTTGGACTATC
176081 GCGTTGCGAATTTGGA
1 GCGTTGCGAATTTGGA
176097 ACTTGGGTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.38
Consensus pattern (21 bp):
GCGTTGCGAATTTGGACTATC
Found at i:177237 original size:2 final size:2
Alignment explanation
Indices: 177230--177280 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
177220 TGAAGCACAG
177230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
177272 AT AT AT AT A
1 AT AT AT AT A
177281 ATAATTTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:181999 original size:27 final size:27
Alignment explanation
Indices: 181942--181999 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
181932 TAATATAATC
* * ** *
181942 ATTTTACACTTCAAGGGTATTTTGGTC
1 ATTTTACACTTCAAGGGCAATTTCATA
*
181969 ATTTTACACTTCAGGGGCAATTTCATA
1 ATTTTACACTTCAAGGGCAATTTCATA
181996 ATTT
1 ATTT
182000 CATAATCAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (27 bp):
ATTTTACACTTCAAGGGCAATTTCATA
Found at i:190208 original size:2 final size:2
Alignment explanation
Indices: 190201--190234 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
190191 ATGCATCCAC
190201 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
190235 TGGATACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190359 original size:24 final size:21
Alignment explanation
Indices: 190332--190389 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
190322 ATGTGAAATA
190332 ATGAAAGTGATCACATGTGTGTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
190356 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
190378 ATGAAAAGTGAT
1 ATG-AAAGTGAT
190390 GAGAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:190542 original size:23 final size:21
Alignment explanation
Indices: 190500--190542 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
190490 GTAGTCATTC
*
190500 GGAACATATATGTAATTTTGT
1 GGAACATATATGTAACTTTGT
190521 GGAACATATATGTGATACTTTG
1 GGAACATATATGT-A-ACTTTG
190543 GTACACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 1 0.05
23 5 0.26
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.40
Consensus pattern (21 bp):
GGAACATATATGTAACTTTGT
Found at i:190619 original size:22 final size:20
Alignment explanation
Indices: 190587--190682 Score: 110
Period size: 18 Copynumber: 4.9 Consensus size: 20
190577 GTTCTTAAGG
190587 AGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGACA-AT-C
*
190609 AGTGGTTCTTCGGGAC-AT-
1 AGTGGTCCTTCGGGACAATC
* *
190627 AGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACAATC
190647 AGTGGTCCTTCGGGAC-AT-
1 AGTGGTCCTTCGGGACAATC
*
190665 AGTGGTCCTTTGGGACAA
1 AGTGGTCCTTCGGGACAA
190683 ATATTCAGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
18 30 0.45
19 5 0.08
20 16 0.24
22 15 0.23
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAATC
Found at i:190658 original size:38 final size:40
Alignment explanation
Indices: 190587--190674 Score: 135
Period size: 38 Copynumber: 2.2 Consensus size: 40
190577 GTTCTTAAGG
* *
190587 AGTGGTCCTTCGGGACATATACAGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
*
190627 AGTGGTTCTTCGGAACA-AT-CAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
190665 AGTGGTCCTT
1 AGTGGTCCTT
190675 TGGGACAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 27 0.61
39 2 0.05
40 15 0.34
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (40 bp):
AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
Found at i:196848 original size:19 final size:19
Alignment explanation
Indices: 196799--196850 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
196789 GAATGCAATT
* *
196799 AGTGCATCGATACATGAGG
1 AGTGCATCGATGCAAGAGG
196818 AGTGCATCGATGCAAGAGG
1 AGTGCATCGATGCAAGAGG
196837 AGTGCATCGATGCA
1 AGTGCATCGATGCA
196851 CCTACTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (19 bp):
AGTGCATCGATGCAAGAGG
Found at i:196937 original size:15 final size:15
Alignment explanation
Indices: 196917--196948 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
196907 TCAATGCACC
196917 CGTCAAGGGATGCAT
1 CGTCAAGGGATGCAT
196932 CGTCAAGGGATGCAT
1 CGTCAAGGGATGCAT
196947 CG
1 CG
196949 ATACATGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.34, T:0.19
Consensus pattern (15 bp):
CGTCAAGGGATGCAT
Found at i:197637 original size:22 final size:19
Alignment explanation
Indices: 197605--197700 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 19
197595 GTTCTTAAGG
*
197605 AGTGGTTCTTCGGGACATAT
1 AGTGGTCCTTCGGGACA-AT
197625 ACAGTGGTCCTTCGGGAC-AT
1 --AGTGGTCCTTCGGGACAAT
* *
197645 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGACAAT
*
197664 CAGTGGTCCTTTGGGAC-AT
1 -AGTGGTCCTTCGGGACAAT
197683 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
197701 ATATTCAGTG
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 29 0.45
19 5 0.08
20 15 0.23
22 15 0.23
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:197680 original size:38 final size:39
Alignment explanation
Indices: 197605--197700 Score: 149
Period size: 38 Copynumber: 2.5 Consensus size: 39
197595 GTTCTTAAGG
197605 AGTGGTTCTTCGGGACATATACAGTGGTCCTTCGGGACAT
1 AGTGGTTCTTCGGGACA-ATACAGTGGTCCTTCGGGACAT
* *
197645 AGTGGTTCTTCGGAACAAT-CAGTGGTCCTTTGGGACAT
1 AGTGGTTCTTCGGGACAATACAGTGGTCCTTCGGGACAT
*
197683 AGTGGTCCTTCGGGACAA
1 AGTGGTTCTTCGGGACAA
197701 ATATTCAGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 34 0.65
39 2 0.04
40 16 0.31
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (39 bp):
AGTGGTTCTTCGGGACAATACAGTGGTCCTTCGGGACAT
Found at i:203090 original size:13 final size:13
Alignment explanation
Indices: 203072--203167 Score: 60
Period size: 13 Copynumber: 7.5 Consensus size: 13
203062 ACATGTAATG
203072 TAACATGAATTAA
1 TAACATGAATTAA
*
203085 TAACATGCAA-T-G
1 TAACATG-AATTAA
*
203097 CAACATGAATTAA
1 TAACATGAATTAA
*
203110 TAACATGCAA-TAC
1 TAACATG-AATTAA
*
203123 CAA-ATGAATTAA
1 TAACATGAATTAA
*
203135 TAACATGCA-T-A
1 TAACATGAATTAA
*
203146 TACCACATGAATAAA
1 TA--ACATGAATTAA
203161 TAACATG
1 TAACATG
203168 CAAATATTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 20
0.67 0.12 0.22
Matches are distributed among these distances:
11 7 0.11
12 15 0.24
13 33 0.53
14 4 0.06
15 3 0.05
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (13 bp):
TAACATGAATTAA
Found at i:203096 original size:25 final size:25
Alignment explanation
Indices: 203060--203170 Score: 143
Period size: 25 Copynumber: 4.4 Consensus size: 25
203050 ACTAATTATT
* *
203060 TAACATGTAATGTAACATGAATTAA
1 TAACATGCAATGCAACATGAATTAA
203085 TAACATGCAATGCAACATGAATTAA
1 TAACATGCAATGCAACATGAATTAA
*
203110 TAACATGCAATACCAA-ATGAATTAA
1 TAACATGCAAT-GCAACATGAATTAA
* * *
203135 TAACATGCATATACCACATGAATAAA
1 TAACATGCA-ATGCAACATGAATTAA
203161 TAACATGCAA
1 TAACATGCAA
203171 ATATTATTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
25 55 0.71
26 22 0.29
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (25 bp):
TAACATGCAATGCAACATGAATTAA
Found at i:204354 original size:135 final size:135
Alignment explanation
Indices: 203973--204642 Score: 712
Period size: 135 Copynumber: 5.0 Consensus size: 135
203963 ACATGAAAAA
* * * * * * * * *
203973 TGTTGATGCAACTCCTTCTATGAAGAAACAAAC--AATTTCCAACGCCGATCTACCTCATTCTAT
1 TGTTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGT-CGATGCTGATCTACCTCCTTCTAC
* * * * * * *
204036 AATAGAATCTA-ACAAAATAAGGTTACGTTGATTCAACTCCTTATGTGAAGTATC--G-AATAGA
65 GATAGAATCGAGA-AAAATAAGGTTATGTTGATTCAACTCATTCTGTGAAGAATCGAGCAAAAGA
* * * *
204097 ATAAAAT
129 TTGACAC
* * *
204104 TGTTGATTCAACTCCTTCTGTGAAGATTCAAACAAAATGTCGATGTTGATCTACCTCCTTCT--G
1 TGTTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTCGATGCTGATCTACCTCCTTCTACG
*
204167 ATAGAATCGAGAAAAATAAGGTTATGTTGATTCAACTCATTCTGTGAAGAATCGAGAAAAAGATT
66 ATAGAATCGAGAAAAATAAGGTTATGTTGATTCAACTCATTCTGTGAAGAATCGAGCAAAAGATT
*
204232 GACAT
131 GACAC
* * * * *
204237 TGTTGATCCAACTCTTTCTATGAAGAATCAAACATAATGTTGATGCTGATTTACCTCCTTCTACG
1 TGTTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTCGATGCTGATCTACCTCCTTCTACG
* * * * * * *
204302 ATAAAATCGAGTAAAATAAGGTTACGTTGATTCAACTCATTTTGTGATGAATCAAGCAGAAGATT
66 ATAGAATCGAGAAAAATAAGGTTATGTTGATTCAACTCATTCTGTGAAGAATCGAGCAAAAGATT
204367 GACAC
131 GACAC
* * * * *
204372 TGTTGATCCAACTCCTTCTGTGAA-AGATCAAACAAAATGTCGATGTTTATCTACCTCTTTTTAT
1 TGTTGATCCAACTCCTTCTGTGAAGA-ATCAAACAAAATGTCGATGCTGATCTACCTCCTTCTAC
* * * * *
204436 GGTAGAATCGAGCAAAATAAGGTTATGATGATTCAACTTC-TTCTGTGAAAAATTGAGCAAAAGA
65 GATAGAATCGAGAAAAATAAGGTTATGTTGATTCAAC-TCATTCTGTGAAGAATCGAGCAAAAGA
204500 TTGACAC
129 TTGACAC
* * * * * * *
204507 TGTTGATCCAACTCCTTTTGTGAAGAATCAAACAGAATATCGATGCTAATCTACTTCCTTATGCG
1 TGTTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTCGATGCTGATCTACCTCCTTCTACG
** *
204572 ATAGAATCGAGAAAAATAAGGTTATACTGATTCAACTCCTTCTGTGAAGAATCGAGCAAAAGATT
66 ATAGAATCGAGAAAAATAAGGTTATGTTGATTCAACTCATTCTGTGAAGAATCGAGCAAAAGATT
*
204637 GGCAC
131 GACAC
204642 T
1 T
204643 AATCCATCTC
Statistics
Matches: 452, Mismatches: 75, Indels: 20
0.83 0.14 0.04
Matches are distributed among these distances:
130 46 0.10
131 30 0.07
132 18 0.04
133 67 0.15
134 3 0.01
135 285 0.63
136 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (135 bp):
TGTTGATCCAACTCCTTCTGTGAAGAATCAAACAAAATGTCGATGCTGATCTACCTCCTTCTACG
ATAGAATCGAGAAAAATAAGGTTATGTTGATTCAACTCATTCTGTGAAGAATCGAGCAAAAGATT
GACAC
Found at i:205200 original size:14 final size:13
Alignment explanation
Indices: 205181--205251 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
205171 TTTTATTCTA
205181 TTTTTCTTTCTCTT
1 TTTTTCTTTCT-TT
205195 TTTTTCTTTCCTATT
1 TTTTTCTTT-CT-TT
* *
205210 TTTTATTTTTATTT
1 TTTT-TCTTTCTTT
*
205224 TTCTTCTTTCTTT
1 TTTTTCTTTCTTT
*
205237 TTCTTCTTTCTTT
1 TTTTTCTTTCTTT
205250 TT
1 TT
205252 CCTTGGTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
13 22 0.45
14 14 0.29
15 9 0.18
16 4 0.08
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:205239 original size:6 final size:6
Alignment explanation
Indices: 205209--205252 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
205199 TCTTTCCTAT
* *
205209 TTTTTA TTTTTA TTTTTC TTCTTTC TTTTTC TTCTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TT-TTTC TTTTTC
205253 CTTGGTAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
6 23 0.66
7 12 0.34
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:205964 original size:10 final size:10
Alignment explanation
Indices: 205949--206007 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
205939 TGAACCCTCT
*
205949 TTTTATTTTA
1 TTTTATTTTC
205959 TTTTATTTTC
1 TTTTATTTTC
*
205969 TTTCT-TTTTA
1 TTT-TATTTTC
* *
205979 TCTT-TTCTC
1 TTTTATTTTC
205988 TTTTATTTTC
1 TTTTATTTTC
205998 TTTTCATTTT
1 TTTT-ATTTT
206008 TCTCTTTTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 7 0.18
10 26 0.67
11 6 0.15
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTATTTTC
Found at i:205996 original size:12 final size:13
Alignment explanation
Indices: 205959--206015 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 13
205949 TTTTATTTTA
*
205959 TTTTATTTTCTTTC
1 TTTTATTTT-TCTC
205973 TTTTTATCTTTTCTC
1 -TTTTAT-TTTTCTC
205988 TTTTA-TTTTCT-
1 TTTTATTTTTCTC
*
205999 TTTCATTTTTCTC
1 TTTTATTTTTCTC
206012 TTTT
1 TTTT
206016 TCATTTCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 4 0.11
12 12 0.33
13 3 0.08
14 5 0.14
15 9 0.25
16 3 0.08
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTTCTC
Found at i:205997 original size:25 final size:24
Alignment explanation
Indices: 205969--206015 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
205959 TTTTATTTTC
*
205969 TTTCTTTTTATCTTTTCTCTTTTAT
1 TTTCTTTTCAT-TTTTCTCTTTTAT
205994 TTTCTTTTCATTTTTCTCTTTT
1 TTTCTTTTCATTTTTCTCTTTT
206016 TCATTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTCTTTTCATTTTTCTCTTTTAT
Found at i:206016 original size:25 final size:25
Alignment explanation
Indices: 205969--206044 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
205959 TTTTATTTTC
*
205969 TTTCTTTTTATCTTTTCTC-TTTTAT
1 TTTCTTTTCAT-TTTTCTCTTTTTAT
205994 TTTCTTTTCATTTTTCTCTTTTTCA-
1 TTTCTTTTCATTTTTCTCTTTTT-AT
* *
206019 TTTCATTTCTTTTTTCT-TTTCTTAT
1 TTTCTTTTCATTTTTCTCTTT-TTAT
206044 T
1 T
206045 CAAACATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
24 11 0.25
25 32 0.73
26 1 0.02
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTCTTTTCATTTTTCTCTTTTTAT
Found at i:214027 original size:17 final size:18
Alignment explanation
Indices: 213993--214027 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
213983 ATTAGTATTG
*
213993 TCATAATGATAATTAAAT
1 TCATAATGATAATAAAAT
214011 TCATAAT-ATAATAAAAT
1 TCATAATGATAATAAAAT
214028 CTAGCCCGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (18 bp):
TCATAATGATAATAAAAT
Found at i:214167 original size:37 final size:37
Alignment explanation
Indices: 214114--214218 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
214104 CCTTTTCGCC
*
214114 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * * *
214151 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * *
214188 CTATTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
214219 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
Found at i:214767 original size:22 final size:21
Alignment explanation
Indices: 214679--214771 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 21
214669 TTCAATTGAT
*
214679 TTTTTTACACTATATATTATTA
1 TTTTTTATACTATAT-TTATTA
* * *
214701 TTATCTATACATATATTTTTTA
1 TTTTTTATAC-TATATTTATTA
*
214723 TTTATTTATA-T-TCATTTGGTTA
1 TTT-TTTATACTAT-ATTT-ATTA
214745 TTTTTTAATACTATATTTATTA
1 TTTTTT-ATACTATATTTATTA
214767 TTTTT
1 TTTTT
214772 ATGTATATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
20 1 0.02
21 8 0.14
22 31 0.55
23 15 0.27
24 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTTATACTATATTTATTA
Found at i:215013 original size:18 final size:19
Alignment explanation
Indices: 214987--215022 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
214977 TTTTTGGTTT
*
214987 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
215005 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
215023 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:215066 original size:2 final size:2
Alignment explanation
Indices: 215059--215107 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
215049 TTTACTCATT
215059 TA TA TA TA TA TA TA TA 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
215101 TA TA TA T
1 TA TA TA T
215108 TTCATTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:220636 original size:22 final size:22
Alignment explanation
Indices: 220562--220638 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
220552 GCTACCCCAT
*
220562 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
220584 CAAACCTATGAGCATTAAATGC
1 CAAACCTTTGAGCATCAAATGC
220606 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
220628 CAAACCTTTGA
1 CAAACCTTTGA
220639 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:221676 original size:106 final size:106
Alignment explanation
Indices: 221462--222942 Score: 2050
Period size: 106 Copynumber: 14.0 Consensus size: 106
221452 ATATCGTGCC
* * * ** * *
221462 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAAAGCTGGTTGTCAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
221526 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
221567 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
221632 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
221673 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
221738 AATTTCAGAGCCAATTTCAACTTCAGAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
221779 ACTCCAAACAACGCAAGTTCAACTTCATGACGAAGGGATCACTGGTTTTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
221844 AATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
221885 ACTCCAGACAACGCAGGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
221950 AATTTCAGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
221991 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
222056 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
222097 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* **
222162 AATTTCAGAGCCAATTTCAACTTCACAACGAAATATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
222203 ACTCCAGATAACGCAACTTCAACTTCACGACGAAGGGACCGCTGATTGTCAGCAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
222268 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
222309 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAAAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
222374 AATTCCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
*
222415 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
222480 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
222521 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
222586 AATTTCAGAGCCAATTTCAACTTCACAGC-ATAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGG
* *
222627 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT-ACATAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA-ACAAACAACTTCC
* * *
222691 CAATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGA
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
222733 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
222793 C-A-TTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * * * * *
222833 ACTAGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * *
222898 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
222939 ACTC
1 ACTC
222943 AGAACAATGC
Statistics
Matches: 1225, Mismatches: 135, Indels: 31
0.88 0.10 0.02
Matches are distributed among these distances:
100 77 0.06
101 3 0.00
102 3 0.00
103 4 0.00
104 2 0.00
105 54 0.04
106 1080 0.88
107 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:223726 original size:37 final size:37
Alignment explanation
Indices: 223673--223777 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
223663 CCTTTTCATC
*
223673 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
223710 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
223747 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
223778 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:224576 original size:17 final size:16
Alignment explanation
Indices: 224545--224579 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
224535 TTTTTGGTTT
*
224545 TTTTTATATTATATTA
1 TTTTCATATTATATTA
224561 TTTTCATATTACTATTA
1 TTTTCATATTA-TATTA
224578 TT
1 TT
224580 ATTGTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCATATTATATTA
Found at i:224622 original size:2 final size:2
Alignment explanation
Indices: 224615--224655 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
224605 TTTACTCATT
* * *
224615 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
224656 TTCATTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:224664 original size:15 final size:14
Alignment explanation
Indices: 224612--224678 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
224602 TATTTTACTC
* *
224612 ATTTATATATATAT
1 ATTTATTTATTTAT
* * *
224626 ATATATATATATAT
1 ATTTATTTATTTAT
224640 ATTTATTTATTTAT
1 ATTTATTTATTTAT
224654 ATTTCATTTA-TT-T
1 ATTT-ATTTATTTAT
224667 ATTTATTTATTT
1 ATTTATTTATTT
224679 TTCCTTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
12 5 0.11
13 7 0.15
14 30 0.64
15 5 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTATTTATTTAT
Found at i:224666 original size:4 final size:4
Alignment explanation
Indices: 224639--224678 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
224629 TATATATATA
224639 TATT TATT TATT TA-- TATT TCATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT T-ATT TATT TATT TATT TATT T
224679 TTCCTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
4 27 0.82
5 4 0.12
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:224666 original size:23 final size:24
Alignment explanation
Indices: 224639--224699 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
224629 TATATATATA
224639 TATTTATTTATTTATATTT-CATT
1 TATTTATTTATTTATATTTCCATT
* *
224662 TATTTATTTATTTATTTTTCCTTT
1 TATTTATTTATTTATATTTCCATT
* *
224686 TATTTGTTTTTTTA
1 TATTTATTTATTTA
224700 CTTATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (24 bp):
TATTTATTTATTTATATTTCCATT
Found at i:227785 original size:25 final size:25
Alignment explanation
Indices: 227752--227829 Score: 111
Period size: 25 Copynumber: 3.1 Consensus size: 25
227742 TTTAACACAT
*
227752 AATGTAACATGAATTAATAGCATGC
1 AATGCAACATGAATTAATAGCATGC
*
227777 AATGCAACATGAATTAATAGCGTGC
1 AATGCAACATGAATTAATAGCATGC
* * *
227802 AATACCACATGAATTAATAACATGC
1 AATGCAACATGAATTAATAGCATGC
227827 AAT
1 AAT
227830 TATTATTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (25 bp):
AATGCAACATGAATTAATAGCATGC
Found at i:227947 original size:2 final size:2
Alignment explanation
Indices: 227934--227967 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
227924 AATACCTAAA
227934 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
227968 CTATGCCCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:229008 original size:16 final size:16
Alignment explanation
Indices: 228971--229002 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
228961 ATATTTACTT
*
228971 TATTATTTTTAATATA
1 TATTATTTTTAATAAA
228987 TATTATTTTTAATAAA
1 TATTATTTTTAATAAA
229003 ATTTATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTTTAATAAA
Found at i:229010 original size:25 final size:25
Alignment explanation
Indices: 228982--229032 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
228972 ATTATTTTTA
228982 ATATAT-ATTATTTTTAATAAAATTT
1 ATATATAATT-TTTTTAATAAAATTT
*
229007 ATATATAATTTTTTTTATAAAATTT
1 ATATATAATTTTTTTAATAAAATTT
229032 A
1 A
229033 AAAGATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATATAATTTTTTTAATAAAATTT
Found at i:229040 original size:26 final size:25
Alignment explanation
Indices: 228992--229040 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
228982 ATATATATTA
* *
228992 TTTTTAATAAAATTTATATATAATT
1 TTTTTAATAAAATTTAAAGATAATT
*
229017 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
229041 ATGGATAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTTAATAAAATTTAAAGATAATT
Found at i:239680 original size:24 final size:24
Alignment explanation
Indices: 239648--239718 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
239638 ACATTACCTA
* *
239648 AATTTTGTTCTGATTTCTAATATG
1 AATTCTGTTCTGATTTCTGATATG
* * *
239672 GATTCTGTTCTGATATCTGATCTG
1 AATTCTGTTCTGATTTCTGATATG
*
239696 AATTCTGTTTTGATTTCTGATAT
1 AATTCTGTTCTGATTTCTGATAT
239719 CACCGTTTAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.52
Consensus pattern (24 bp):
AATTCTGTTCTGATTTCTGATATG
Found at i:239885 original size:2 final size:2
Alignment explanation
Indices: 239878--239937 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
239868 CGGATAGGGG
239878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
*
239919 TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA T
239938 CTTTTTACTG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.