Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007775.1 Hibiscus syriacus cultivar Beakdansim tig00110056_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: 599510
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:188330 original size:41 final size:39
Alignment explanation
Indices: 188211--188332 Score: 113
Period size: 41 Copynumber: 3.0 Consensus size: 39
188201 TATTTTTAGA
* * * *
188211 TTATATAAATATATTATTTTTATTATCAGTTTTATTAATT
1 TTATATATATATTTTATTTTTATTATTA-TTTTATTTATT
* * *
188251 TATATATATATATATATATATTTACTTTTTA-TTT-TTTATT
1 T-TATATATATAT-TTTATTTTTA-TTATTATTTTATTTATT
188291 TTATATATATATTTTACTCTTTTATTATTATTTTATTTATT
1 TTATATATATATTTTA-T-TTTTATTATTATTTTATTTATT
188332 T
1 T
188333 GTTTTATTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
38 3 0.05
39 17 0.26
40 14 0.22
41 20 0.31
42 7 0.11
43 4 0.06
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (39 bp):
TTATATATATATTTTATTTTTATTATTATTTTATTTATT
Found at i:188338 original size:32 final size:32
Alignment explanation
Indices: 188259--188326 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
188249 TTTATATATA
*
188259 TATATATATATATTTACTTTTTATTTTTTATTT
1 TATATATATAT-TTTACTTTTTATTTATTATTT
188292 TATATATATATTTTACTCTTTTA-TTATTATTT
1 TATATATATATTTTACT-TTTTATTTATTATTT
188324 TAT
1 TAT
188327 TTATTTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (32 bp):
TATATATATATTTTACTTTTTATTTATTATTT
Found at i:188499 original size:15 final size:16
Alignment explanation
Indices: 188481--188511 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
188471 TATTTATTTC
188481 TTACC-TTTTTATCTA
1 TTACCTTTTTTATCTA
188496 TTACCTTTTTTATCTA
1 TTACCTTTTTTATCTA
188512 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
TTACCTTTTTTATCTA
Found at i:194271 original size:25 final size:26
Alignment explanation
Indices: 194242--194301 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
194232 TTGAAATTTT
194242 AAACAAACACAAAC-CAAAAAAAAAC
1 AAACAAACACAAACTCAAAAAAAAAC
* * * *
194267 AAACAAAAACAAGCTTAAAAATAAAC
1 AAACAAACACAAACTCAAAAAAAAAC
194293 AAACAAACA
1 AAACAAACA
194302 TGAACAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.05
Consensus pattern (26 bp):
AAACAAACACAAACTCAAAAAAAAAC
Found at i:198164 original size:14 final size:15
Alignment explanation
Indices: 198145--198177 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
198135 ATGATTTTGA
198145 AAAAATT-AAAAATT
1 AAAAATTAAAAAATT
198159 AAAAATTAAAAAATT
1 AAAAATTAAAAAATT
198174 AAAA
1 AAAA
198178 TATATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTAAAAAATT
Found at i:198178 original size:6 final size:7
Alignment explanation
Indices: 198145--198177 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
198135 ATGATTTTGA
198145 AAAAATT
1 AAAAATT
198152 AAAAATT
1 AAAAATT
198159 AAAAATT
1 AAAAATT
198166 AAAAAATT
1 -AAAAATT
198174 AAAA
1 AAAA
198178 TATATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:198886 original size:49 final size:49
Alignment explanation
Indices: 198828--198938 Score: 195
Period size: 49 Copynumber: 2.3 Consensus size: 49
198818 ATTTAATAAT
198828 ACTCAATTTGAGTCAAATCTCCAATCGAGTTTGAATTTAAATCCAGTAA
1 ACTCAATTTGAGTCAAATCTCCAATCGAGTTTGAATTTAAATCCAGTAA
* * *
198877 ATTCAATTTGAGTCAAATCTCGAATCGAGTTTGAATTTAAATCCAGTAG
1 ACTCAATTTGAGTCAAATCTCCAATCGAGTTTGAATTTAAATCCAGTAA
198926 ACTCAATTTGAGT
1 ACTCAATTTGAGT
198939 GTTGAGTGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (49 bp):
ACTCAATTTGAGTCAAATCTCCAATCGAGTTTGAATTTAAATCCAGTAA
Found at i:198910 original size:23 final size:23
Alignment explanation
Indices: 198834--198910 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
198824 TAATACTCAA
*
198834 TTTGAGTCAAATCTCCAATCGAG
1 TTTGAGTCAAATCTCGAATCGAG
* * *
198857 TTTGAATTTAAATC-CAGTAAATTC-AA
1 TTTG-AGTCAAATCTC-G--AA-TCGAG
198883 TTTGAGTCAAATCTCGAATCGAG
1 TTTGAGTCAAATCTCGAATCGAG
198906 TTTGA
1 TTTGA
198911 ATTTAAATCC
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 2 0.05
23 13 0.32
24 7 0.17
25 8 0.20
26 8 0.20
27 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (23 bp):
TTTGAGTCAAATCTCGAATCGAG
Found at i:198919 original size:24 final size:24
Alignment explanation
Indices: 198842--198919 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
198832 AATTTGAGTC
*
198842 AAATCTCCAATCGAGTTTGAATTT
1 AAATCTCGAATCGAGTTTGAATTT
* * *
198866 AAATC-CAGTAAATTC-AATTTG-AGTC
1 AAATCTC-G--AA-TCGAGTTTGAATTT
198891 AAATCTCGAATCGAGTTTGAATTT
1 AAATCTCGAATCGAGTTTGAATTT
198915 AAATC
1 AAATC
198920 CAGTAGACTC
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 12 0.30
25 8 0.20
26 8 0.20
27 2 0.05
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (24 bp):
AAATCTCGAATCGAGTTTGAATTT
Found at i:200086 original size:21 final size:22
Alignment explanation
Indices: 200042--200083 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
200032 CGAAATCGTG
200042 TAACTTTAAAAAATTTATTAAT
1 TAACTTTAAAAAATTTATTAAT
*
200064 TAAC-TTATAAAATATTATTA
1 TAACTTTAAAAAAT-TTATTA
200084 TTATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TAACTTTAAAAAATTTATTAAT
Found at i:203241 original size:15 final size:15
Alignment explanation
Indices: 203223--203259 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
203213 ATGGGACTGA
203223 ACCCGATGGGTTTCG
1 ACCCGATGGGTTTCG
203238 ACCCGATGGGTTTCG
1 ACCCGATGGGTTTCG
203253 ACCCGAT
1 ACCCGAT
203260 TCGATTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (15 bp):
ACCCGATGGGTTTCG
Found at i:204732 original size:28 final size:28
Alignment explanation
Indices: 204701--204758 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
204691 TCATCACTAA
204701 GGGTTCGTATATAAACCTTCATGGAAGG
1 GGGTTCGTATATAAACCTTCATGGAAGG
204729 GGGTTCGTATATAAACCTTCATGGAAGG
1 GGGTTCGTATATAAACCTTCATGGAAGG
204757 GG
1 GG
204759 TTAAAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (28 bp):
GGGTTCGTATATAAACCTTCATGGAAGG
Found at i:208309 original size:17 final size:18
Alignment explanation
Indices: 208283--208327 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
208273 AACCGAACCG
* *
208283 AAAAACCCGAACCG-TTA
1 AAAAAACCGAACCGATCA
208300 AAAAAACCGAACCGAATCA
1 AAAAAACCGAACCG-ATCA
208319 AAAAAACCG
1 AAAAAACCG
208328 GTTTCGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
19 11 0.46
ACGTcount: A:0.56, C:0.27, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAAAACCGAACCGATCA
Found at i:208321 original size:19 final size:19
Alignment explanation
Indices: 208270--208327 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
208260 ATAAACCGAT
* * *
208270 CCGAACCGAACCGAAAAAC
1 CCGAACCGAATCAAAAAAA
*
208289 CCGAACCG--TTAAAAAAA
1 CCGAACCGAATCAAAAAAA
208306 CCGAACCGAATCAAAAAAA
1 CCGAACCGAATCAAAAAAA
208325 CCG
1 CCG
208328 GTTTCGGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 13 0.41
19 19 0.59
ACGTcount: A:0.50, C:0.31, G:0.14, T:0.05
Consensus pattern (19 bp):
CCGAACCGAATCAAAAAAA
Found at i:208357 original size:10 final size:9
Alignment explanation
Indices: 208329--208358 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
208319 AAAAAACCGG
*
208329 TTTCGGTTT
1 TTTCGATTT
208338 TTTCGATTT
1 TTTCGATTT
208347 TTTCGATTT
1 TTTCGATTT
208356 TTT
1 TTT
208359 AACTATTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.07, C:0.10, G:0.13, T:0.70
Consensus pattern (9 bp):
TTTCGATTT
Found at i:209895 original size:15 final size:15
Alignment explanation
Indices: 209877--209906 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
209867 GGAGTTTTTA
209877 TCTCTTCTTTTTTCT
1 TCTCTTCTTTTTTCT
209892 TCTCTTCTTTTTTCT
1 TCTCTTCTTTTTTCT
209907 CCTCAGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TCTCTTCTTTTTTCT
Found at i:213207 original size:21 final size:21
Alignment explanation
Indices: 213174--213231 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
213164 TTTTTTTTTA
* * *
213174 AATAATAATATAATAATAATG
1 AATAAAAAAATAAAAATAATG
213195 AATAAAAAAATAAAAATAAT-
1 AATAAAAAAATAAAAATAATG
* *
213215 AA-AAAATAATATAAATA
1 AATAAAAAAATAAAAATA
213232 TATAAAGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 13 0.41
20 2 0.06
21 17 0.53
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AATAAAAAAATAAAAATAATG
Found at i:213474 original size:2 final size:2
Alignment explanation
Indices: 213467--213491 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
213457 AAATAATTTA
213467 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
213492 ATAATAACAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213522 original size:17 final size:18
Alignment explanation
Indices: 213489--213524 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
213479 ATATATATAT
*
213489 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
213507 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
213524 A
1 A
213525 AATATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:213536 original size:63 final size:63
Alignment explanation
Indices: 213416--213536 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
213406 TATTAAAGAA
* *
213416 ATATATATATATAATAATAAAATATAGTAAAAAATAAATGAAAATAATTTAATATATATATAT
1 ATATATATATATAATAATAAAATATAATAAAAAATAAATGAAAATAATATAATATATATATAT
*
213479 ATATATATATATAATAATAACATGAATAAT-AAAAATAAATGAATAA-AATATCAATATA
1 ATATATATATATAATAATAAAAT--ATAATAAAAAATAAATGAA-AATAATAT-AATATA
213537 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
63 22 0.43
64 17 0.33
65 12 0.24
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (63 bp):
ATATATATATATAATAATAAAATATAATAAAAAATAAATGAAAATAATATAATATATATATAT
Found at i:213967 original size:37 final size:37
Alignment explanation
Indices: 213885--213986 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
213875 GTGCTTGTGG
* * * * * *
213885 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
213922 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
213959 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
213987 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:214833 original size:105 final size:105
Alignment explanation
Indices: 214532--215162 Score: 862
Period size: 105 Copynumber: 6.0 Consensus size: 105
214522 GCATTGTTCC
* * ** *
214532 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
214596 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
214638 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
214698 CAGCGGTTCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
214738 GAGTCCAATATGCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
214803 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
214843 GAGTCCAATATCATTCGTTGCGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
214908 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
214948 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
215013 CAGCGGTCTCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
215053 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGAGAAGTTGTTTGTTGAC-A
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * *
215117 GCCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 G-CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
215159 GAGT
1 GAGT
215163 GTCACGATAT
Statistics
Matches: 472, Mismatches: 45, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
100 81 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 298 0.63
106 80 0.17
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:215422 original size:36 final size:36
Alignment explanation
Indices: 215362--215437 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
215352 TGTTTGGAGA
* * * *
215362 GAAACTGTCTTAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
215398 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
215434 GAAA
1 GAAA
215438 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:215561 original size:106 final size:104
Alignment explanation
Indices: 215337--215656 Score: 470
Period size: 106 Copynumber: 3.1 Consensus size: 104
215327 TTTGTTAAAT
* ** *
215337 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTTAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
215399 AAACTATCTCAAGCGAG-ATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAG-GAGAAAAAAATTCATTTCAAGGGAAA
*
215438 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
215503 AAACCATCTCAAGAGAGAAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAG-GAG-AAAAAAATTCATTTCAAGGGAAA
*
215544 TGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
215609 AAACTATCT-GAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGGAGA-AAAAAATTCATTTCAAGGGAAA
215648 TGTTTTCAA
1 TGTTTTCAA
215657 GAGAAACTGT
Statistics
Matches: 198, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
101 45 0.23
103 4 0.02
104 56 0.28
105 2 0.01
106 91 0.46
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGGAGAAAAAAATTCATTTCAAGGGAAA
Found at i:215835 original size:36 final size:36
Alignment explanation
Indices: 215795--215902 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 36
215785 AGCGAGACAT
215795 ATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAA
1 ATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAA
* ** * **
215831 ATCTTCTTTCGAGAAAAACAGTCTCAAGTGAGACA-AA
1 ATCTTGTTTTAAGAAAAACAATCTTGAGTGA-A-ATAA
* *
215868 AT-ATGTTTTAAGAAAAACAAAT-TTGAGTGAGATAA
1 ATCTTGTTTTAAGAAAAAC-AATCTTGAGTGAAATAA
215903 TCATCTGCAT
Statistics
Matches: 54, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
34 1 0.02
35 2 0.04
36 43 0.80
37 7 0.13
38 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (36 bp):
ATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAA
Found at i:215864 original size:72 final size:75
Alignment explanation
Indices: 215741--215902 Score: 208
Period size: 72 Copynumber: 2.2 Consensus size: 75
215731 AACAAACAGC
* * * *
215741 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGAC-ATATCTTGTTTT
1 CTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAAT-ATGTTTT
215805 AAGAAAAAC-AAT
63 AAGAAAAACAAAT
*
215817 CTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAATATGTTTTAAG
1 CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAATATGTTTTAAG
215880 AAAAACAAAT
66 AAAAACAAAT
*
215890 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
215903 TCATCTGCAT
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
72 45 0.58
73 17 0.22
75 4 0.05
76 12 0.15
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (75 bp):
CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAATATGTTTTAAG
AAAAACAAAT
Found at i:217272 original size:183 final size:183
Alignment explanation
Indices: 216964--217500 Score: 923
Period size: 183 Copynumber: 2.9 Consensus size: 183
216954 ATCAGGTTTA
* *
216964 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGAAAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
* **
217029 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
217093 TTCCTTTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
217147 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
217212 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
217277 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
217330 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
* * * *
217395 GCCAAGTGTCTGAACAGTGTCATAGTTTGAACATAATCTATTCATAAAGACAGGGCTTTTGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
** *
217460 TCCTCTATAACCAATTATCTTAATGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
217501 CGGATTTAAT
Statistics
Matches: 337, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 336 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:223190 original size:27 final size:27
Alignment explanation
Indices: 223160--223227 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
223150 AATGTTTTTT
* *
223160 TAAAAATAATAATATAAT-AATAATGAA
1 TAAAAATAATAAAATAATAAAAAAT-AA
*
223187 TAAAAA-AACAAAAATAATAAAAAATAA
1 TAAAAATAA-TAAAATAATAAAAAATAA
223214 TAAAAATATATAAA
1 TAAAAATA-ATAAA
223228 GTTATAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.06
27 21 0.64
28 9 0.27
29 1 0.03
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.24
Consensus pattern (27 bp):
TAAAAATAATAAAATAATAAAAAATAA
Found at i:223500 original size:18 final size:17
Alignment explanation
Indices: 223479--223521 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
223469 ATATATACAT
223479 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
223497 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
223514 ATAA-AATA
1 ATAATAATA
223522 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:223522 original size:60 final size:63
Alignment explanation
Indices: 223403--223522 Score: 156
Period size: 66 Copynumber: 1.9 Consensus size: 63
223393 TATTAAAGAA
* *
223403 ATATATATATATAATAATAATAAAATGTAGTAAAAAAAATAAATGAAAATAATTTAATATATATA
1 ATATATACATATAATAATAATAAAATGTAATAAAAAAAATAAATG-AAATAA--TAATATATATA
223468 T
63 T
* *
223469 ATATATACATATAATAATAATAACATG-AATAATAAAAATAAATG-AATAA-AATAT
1 ATATATACATATAATAATAATAAAATGTAATAAAAAAAATAAATGAAATAATAATAT
223523 CCATATAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
60 5 0.10
63 5 0.10
65 15 0.30
66 25 0.50
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (63 bp):
ATATATACATATAATAATAATAAAATGTAATAAAAAAAATAAATGAAATAATAATATATATAT
Found at i:223916 original size:37 final size:37
Alignment explanation
Indices: 223866--223970 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
223856 GTGCTTGTGG
* * * *
223866 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
223903 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
223940 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
223971 GACGAAAATG
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:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:225650 original size:17 final size:15
Alignment explanation
Indices: 225615--225649 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
225605 AAGAAAAATG
*
225615 TAATAAATATATATT
1 TAATAAAAATATATT
225630 TAATAAAAATATA-T
1 TAATAAAAATATATT
225644 TAATAA
1 TAATAA
225650 TTTAAGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAAAATATATT
Found at i:226412 original size:18 final size:19
Alignment explanation
Indices: 226374--226412 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
226364 AGATGCCTTA
*
226374 TAGCATAAGTACATTGTTG
1 TAGCATAAGTACATAGTTG
*
226393 TAGCATCAGTACA-AGTTG
1 TAGCATAAGTACATAGTTG
226411 TA
1 TA
226413 TAATCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (19 bp):
TAGCATAAGTACATAGTTG
Found at i:235758 original size:38 final size:39
Alignment explanation
Indices: 235627--235896 Score: 271
Period size: 38 Copynumber: 7.2 Consensus size: 39
235617 TTTTTAAAAT
235627 ATTTTTG-AAAAATATA-A-TATAT-GTTTTTAGAAAA-CG
1 ATTTTTGAAAAAATATATATTATATAG-TTTT-GAAAATCG
* * * *
235663 ATTTTTG--AAAACATATATTATATACTTTTTTAAAAATTG
1 ATTTTTGAAAAAATATATATTATATA--GTTTTGAAAATCG
*
235702 GTTTTTG--AAAATATATATTATATAGTTTTGAAAATCG
1 ATTTTTGAAAAAATATATATTATATAGTTTTGAAAATCG
* *
235739 -GTTTTCAAAAAATATATATTATATAGTTTTGAAAA-CG
1 ATTTTTGAAAAAATATATATTATATAGTTTTGAAAATCG
*
235776 ATTTTTGAAAATATATATATTATATAGTTTTGAAAAT-G
1 ATTTTTGAAAAAATATATATTATATAGTTTTGAAAATCG
* ** *
235814 ATTTTTGAAAATATATATATTATATAGTTTCAAAAAT-A
1 ATTTTTGAAAAAATATATATTATATAGTTTTGAAAATCG
* *
235852 ATTTTTGAAAAAAAAATATATTATATAGTTTTAAAAAT-G
1 ATTTTTG-AAAAAATATATATTATATAGTTTTGAAAATCG
235891 ATTTTT
1 ATTTTT
235897 TGTGGGATTT
Statistics
Matches: 202, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
35 7 0.03
36 12 0.06
37 17 0.08
38 106 0.52
39 60 0.30
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (39 bp):
ATTTTTGAAAAAATATATATTATATAGTTTTGAAAATCG
Found at i:240995 original size:13 final size:13
Alignment explanation
Indices: 240965--241013 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
240955 TTTTAAATTT
*
240965 TTATTATATATTA
1 TTATTATTTATTA
* *
240978 ATATTATTTATTT
1 TTATTATTTATTA
240991 TTATTATTTTATTA
1 TTATTA-TTTATTA
*
241005 TTAATATTT
1 TTATTATTT
241014 TTTCTTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:242354 original size:36 final size:36
Alignment explanation
Indices: 242309--242378 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
242299 TCCTATTATT
*
242309 CTTTCTTTAACCTTGATTTTATTTATT-TATTTTAAA
1 CTTTCTTTAACATTGA-TTTATTTATTCTATTTTAAA
* * *
242345 CTTTTTTTAATATTTATTTATTTATTCTATTTTA
1 CTTTCTTTAACATTGATTTATTTATTCTATTTTA
242379 CAATCTAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 10 0.34
36 19 0.66
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.66
Consensus pattern (36 bp):
CTTTCTTTAACATTGATTTATTTATTCTATTTTAAA
Found at i:248627 original size:200 final size:199
Alignment explanation
Indices: 247852--248768 Score: 870
Period size: 201 Copynumber: 4.6 Consensus size: 199
247842 TAGAGGAACC
** * ** * *
247852 ATTTACAGAATAGCTCAAGGCGAGAAGGGTTATCTATCAATGAAAACTTTTGAGTTCAATTCCAT
1 ATTTACATCATAGCTCAAGGCGAGAAGGGCTATCT-TCAACAAAAACTTTCGAGTTCGATTCCAT
* * * ** * *
247917 TCAG-TCTAGTTTG--TATCAACTGCATGGTAGCAACGATGAACTACTTTTCGGTTG-AGTTTCA
65 TCAGCTC-A-ATGGCATATCAACCGCATGGTAGCAGTGA-GAACTACTTTCCGGTTGAAGCTT-A
* * * * *
247978 AACTAAAGTCTTTAAGTCAAGAATAAGACCTATGTTGGCTACGATTTAGCAATAATGAACTATAT
126 AACTAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATAT
*
248043 CCCAGCCTA
191 CCCAGACTA
* * * * * * * ** *
248052 ATTTACAGCTTAACACAAGGCAAGAAGGGTTATCTATCCACGGAAACTTTCGAGTTTGATTCCAT
1 ATTTACATCATAGCTCAAGGCGAGAAGGGCTATCT-TCAACAAAAACTTTCGAGTTCGATTCCAT
* * * * *
248117 TCAGCT-AGA-GG-ATGTATCAACCGCATGGTAGTAGTAAGGAACTACTTTCTGGTTAAAGTTTA
65 TCAGCTCA-ATGGCA--TATCAACCGCATGGTAGCAGTGA-GAACTACTTTCCGGTTGAAGCTTA
* * * * * * *
248179 AACTGAGGTCTTTACA-TCAAGAAGAATACCTAGTTTGGCTACAATTTAGCAACAATGATCTATC
126 AACTAAGGTCTTTA-AGTCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATA
* *
248243 TCTC-GACCCA
190 TCCCAGA-CTA
* * * * *
248253 ATTAACAACATAGCTCAAGGCGAGAAGGGTTATCTTCTAACAAAATCTTTCGAGTTCGATTCTAT
1 ATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTTC-AACAAAAACTTTCGAGTTCGATTCCAT
** ** * * *
248318 TCAGCTCGGTAACATATCAACCGCATAGTAGCAGCGAAGAACTACTTTCCGATTGAAGCTTAAAC
65 TCAGCTCAATGGCATATCAACCGCATGGTAGCAGTG-AGAACTACTTTCCGGTTGAAGCTTAAAC
* * *
248383 TAAGGTCTTTAAGTTAAGAAGAAGACCTATGTTGGCTGCGATTTAGCAACAAGGAACTATATCCC
129 TAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATATCCC
248448 AG-CTGA
194 AGACT-A
* * * *
248454 ATTTACATTATAGCTCAAGGCGAGAAGGGCTATATGTTAACAAAAACCTTCGAGTTCGATTCCAT
1 ATTTACATCATAGCTCAAGGCGAGAAGGGCTATCT-TCAACAAAAACTTTCGAGTTCGATTCCAT
* *
248519 TCAGCTCAATGGCATATCGACCG-TTGGTAGCAGTGAGTAACTACTTTCCGGTTGAAGCTTAAAC
65 TCAGCTCAATGGCATATCAACCGCATGGTAGCAGTGAG-AACTACTTTCCGGTTGAAGCTTAAAC
* *
248583 TAAGGTCTTTAAGTCAAGAAAAAGACCTGGGTTGGCTACGATTTAGCAACAAGGAACTATATCCC
129 TAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATATCCC
*
248648 A-ATCAA
194 AGA-CTA
* * * * *
248654 ATTTACAGCATAGCTCAAGACGAAAAGGGCTATCCTCAACAAAAACTTTCGAGTTCGATTCTATT
1 ATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTTCAACAAAAACTTTCGAGTTCGATTCCATT
* * * *
248719 CAGCTCGAGGGCATATTAACCACATGGTAGCA-TCGAGAAACTACTTTCCG
66 CAGCTCAATGGCATATCAACCGCATGGTAGCAGT-GAG-AACTACTTTCCG
248769 ATCAATTTTT
Statistics
Matches: 585, Mismatches: 111, Indels: 42
0.79 0.15 0.06
Matches are distributed among these distances:
198 1 0.00
199 49 0.08
200 211 0.36
201 314 0.54
202 9 0.02
203 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (199 bp):
ATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTTCAACAAAAACTTTCGAGTTCGATTCCATT
CAGCTCAATGGCATATCAACCGCATGGTAGCAGTGAGAACTACTTTCCGGTTGAAGCTTAAACTA
AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATATCCCAG
ACTA
Found at i:248834 original size:400 final size:401
Alignment explanation
Indices: 247985--248835 Score: 927
Period size: 401 Copynumber: 2.1 Consensus size: 401
247975 TCAAACTAAA
* * * * * *
247985 GTCTTTAAGTCAAGAATAAGACCTATGTTGGCTACGATTTAGCAATAATGAACTATATCCCAGCC
1 GTCTTTAAGACAAGAAGAAGACCAATGTTGACTACGATTTAGCAACAAGGAACTATATCCCAG-C
* * * * * ** ** * *
248050 T-AATTTACAGCTTA-A-CACAAGGCAAGAAGGGTTATCTATCCACGGAAACTTTCGAGTTTGAT
65 TGAATTTACA--TTATAGCTCAAGGCGAGAAGGGCTATATGTTAACAAAAACCTTCGAGTTCGAT
* * *
248112 TCCATTCAGCTAGAGGATGTATCAACCGCATGGTAGTAGTAAGGAACTACTTTCTGGTTAAAGTT
128 TCCATTCAGCTAGAGGA-GTATCAACCGCATGGTAGCAGTAAGGAACTACTTTCCGGTTAAAGCT
* * * * * *
248177 TAAACTGAGGTCTTTACATCAAGAAGAATACCTAGTTTGGCTACAATTTAGCAACAATGATCTAT
192 TAAACTAAGGTCTTTACATCAAGAAAAAGACCTAGGTTGGCTACAATTTAGCAACAAGGAACTAT
* * * * * * * * *
248242 CTCTCGACCCAATTAACAACATAGCTCAAGGCGAGAAGGGTTATCTTCTAACAAAATCTTTCGAG
257 ATCCCAACCAAATTAACAACATAGCTCAAGACGAAAAGGGCTATCCTCTAACAAAAACTTTCGAG
*
248307 TTCGATTCTATTCAGCTCGGTAACATATCAACCGCATAGTAGCAGCGAAGAACTACTTTCCGATT
322 TTCGATTCTATTCAGCTCGGTAACATATCAACCACATAGTAGCAGCGAAGAACTACTTTCCGATT
* *
248372 GAAGCTTAAACTAAG
387 CAAGCTTAAACCAAG
** * * *
248387 GTCTTTAAGTTAAGAAGAAGACCTATGTTGGCTGCGATTTAGCAACAAGGAACTATATCCCAGCT
1 GTCTTTAAGACAAGAAGAAGACCAATGTTGACTACGATTTAGCAACAAGGAACTATATCCCAGCT
248452 GAATTTACATTATAGCTCAAGGCGAGAAGGGCTATATGTTAACAAAAACCTTCGAGTTCGATTCC
66 GAATTTACATTATAGCTCAAGGCGAGAAGGGCTATATGTTAACAAAAACCTTCGAGTTCGATTCC
* * * * *
248517 ATTCAGCTCA-ATGGCA-TATCGACCG-TTGGTAGCAGTGAGTAACTACTTTCCGGTTGAAGCTT
131 ATTCAGCT-AGA-GG-AGTATCAACCGCATGGTAGCAGTAAGGAACTACTTTCCGGTTAAAGCTT
* *
248579 AAACTAAGGTCTTTA-AGTCAAGAAAAAGACCTGGGTTGGCTACGATTTAGCAACAAGGAACTAT
193 AAACTAAGGTCTTTACA-TCAAGAAAAAGACCTAGGTTGGCTACAATTTAGCAACAAGGAACTAT
* * *
248643 ATCCCAATCAAATTTACAGCATAGCTCAAGACGAAAAGGGCTATCCTC-AACAAAAACTTTCGAG
257 ATCCCAACCAAATTAACAACATAGCTCAAGACGAAAAGGGCTATCCTCTAACAAAAACTTTCGAG
** * * *
248707 TTCGATTCTATTCAGCTCGAG-GGCATATTAACCACATGGTAGCATCG-AGAAACTACTTTCCGA
322 TTCGATTCTATTCAGCTCG-GTAACATATCAACCACATAGTAGCAGCGAAG-AACTACTTTCCGA
** *
248770 -TCAATTTTTAAACCGAG
385 TTCAA-GCTTAAACCAAG
* *
248787 GTCTTTAA-ACAGAGAAGAAGACCAA-GTTTGACTACGCTTTGGCAACAAG
1 GTCTTTAAGACA-AGAAGAAGACCAATG-TTGACTACGATTTAGCAACAAG
248836 AAGTCACATT
Statistics
Matches: 375, Mismatches: 62, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
399 7 0.02
400 117 0.31
401 125 0.33
402 122 0.33
403 3 0.01
404 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (401 bp):
GTCTTTAAGACAAGAAGAAGACCAATGTTGACTACGATTTAGCAACAAGGAACTATATCCCAGCT
GAATTTACATTATAGCTCAAGGCGAGAAGGGCTATATGTTAACAAAAACCTTCGAGTTCGATTCC
ATTCAGCTAGAGGAGTATCAACCGCATGGTAGCAGTAAGGAACTACTTTCCGGTTAAAGCTTAAA
CTAAGGTCTTTACATCAAGAAAAAGACCTAGGTTGGCTACAATTTAGCAACAAGGAACTATATCC
CAACCAAATTAACAACATAGCTCAAGACGAAAAGGGCTATCCTCTAACAAAAACTTTCGAGTTCG
ATTCTATTCAGCTCGGTAACATATCAACCACATAGTAGCAGCGAAGAACTACTTTCCGATTCAAG
CTTAAACCAAG
Found at i:249194 original size:36 final size:36
Alignment explanation
Indices: 249144--249418 Score: 256
Period size: 36 Copynumber: 7.5 Consensus size: 36
249134 ATATGATAAT
*
249144 TTTTGAAAAT-ATTTTTGAAAA-ATATAATAT-TTG
1 TTTTGAAAATGATTTTTGAAAATATATAATATATAG
* *
249177 TTTTCAAAAAATGATTTTTTGAAAACATATAATATAT--
1 TTTT--GAAAATGA-TTTTTGAAAATATATAATATATAG
* * *
249214 TTTTAAAAAAAATCAGTTTTTGAAAAAATATATATTATATAG
1 TTTT---GAAAATGA-TTTTTG--AAAATATATAATATATAG
*
249256 TTTTGAAAATCGATTTTTGAAAATATATATTATATAG
1 TTTTGAAAAT-GATTTTTGAAAATATATAATATATAG
*
249293 TTTTGAAAATGATTTTTGAAAATATATATTATATAG
1 TTTTGAAAATGATTTTTGAAAATATATAATATATAG
* *
249329 TTTTGAAAACGATTTTTGAAAATATATATTATATAG
1 TTTTGAAAATGATTTTTGAAAATATATAATATATAG
* * * * *
249365 TTTCGAAAATAATTTTTAAAAATATATATATTATGTTG
1 TTTTGAAAATGATTTTTGAAAATATATA-A-TATATAG
*
249403 TTTTAAAAAT-ATTTTT
1 TTTTGAAAATGATTTTT
249419 TGTGAAAACA
Statistics
Matches: 210, Mismatches: 18, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
33 4 0.02
35 5 0.02
36 86 0.41
37 48 0.23
38 36 0.17
39 12 0.06
40 15 0.07
42 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTGAAAATGATTTTTGAAAATATATAATATATAG
Found at i:249224 original size:38 final size:37
Alignment explanation
Indices: 249155--249249 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 37
249145 TTTGAAAATA
** * *
249155 TTTTTGAAAAATATAATATTTGTTTTCAAAAAATGAT
1 TTTTTGAAAAATATAATATTTGTTTAAAAAAAATCAG
249192 TTTTTGAAAACATATAATATATT-TTTAAAAAAAATCAG
1 TTTTTGAAAA-ATATAATAT-TTGTTTAAAAAAAATCAG
249230 TTTTTGAAAAA-ATATATATT
1 TTTTTGAAAAATATA-ATATT
249250 ATATAGTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
36 4 0.08
37 15 0.29
38 30 0.59
39 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAAATATAATATTTGTTTAAAAAAAATCAG
Found at i:249450 original size:3 final size:3
Alignment explanation
Indices: 249429--249498 Score: 52
Period size: 3 Copynumber: 22.3 Consensus size: 3
249419 TGTGAAAACA
* * * *
249429 TAT TAT TTT TAAT TTT TAT TAT ATAT TAA TAT TATT TAT TTT TATT TAT
1 TAT TAT TAT T-AT TAT TAT TAT -TAT TAT TAT TA-T TAT TAT TA-T TAT
*
249478 TAT T-T TAT TAT TAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
249499 TTTTTATTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
2 2 0.04
3 39 0.75
4 11 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:249504 original size:28 final size:27
Alignment explanation
Indices: 249429--249506 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 27
249419 TGTGAAAACA
* *
249429 TATTATTTTTAATTTTTATTA-TATAT
1 TATTATTATTAATTTTTTTTATTATAT
* * *
249455 TAATATTATTTATTTTTATTTATTATTT
1 TATTATTATTAATTTTT-TTTATTATAT
249483 TATTATTATTAATATTTTTTTATT
1 TATTATTATTAAT-TTTTTTTATT
249507 TTTCTCGATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 14 0.33
27 3 0.07
28 21 0.50
29 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TATTATTATTAATTTTTTTTATTATAT
Found at i:249506 original size:17 final size:17
Alignment explanation
Indices: 249429--249506 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
249419 TGTGAAAACA
*
249429 TATTATTTTTAAT-TTT
1 TATTATTATTAATATTT
249445 TATTATATATTAATATTATT
1 TATTAT-TATTAATA-T-TT
* *
249465 TATTTTTATTTATTATTT
1 TATTATTA-TTAATATTT
249483 TATTATTATTAATATTT
1 TATTATTATTAATATTT
*
249500 TTTTATT
1 TATTATT
249507 TTTCTCGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
16 6 0.12
17 20 0.39
18 9 0.18
19 4 0.08
20 12 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTATTAATATTT
Found at i:250623 original size:28 final size:29
Alignment explanation
Indices: 250592--250649 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
250582 AATTTAGCCC
* *
250592 TTTAAGTTTCTTATGTTTTTTTC-TACTT
1 TTTAAGTTTATTATGTTTTTTACTTACTT
**
250620 TTTATTTTTATTATGTTTTTTACTTACTT
1 TTTAAGTTTATTATGTTTTTTACTTACTT
250649 T
1 T
250650 CAAAATTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.71
Consensus pattern (29 bp):
TTTAAGTTTATTATGTTTTTTACTTACTT
Found at i:252116 original size:31 final size:32
Alignment explanation
Indices: 252058--252119 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
252048 TCTTAACATT
** *
252058 AAAAATATATTTTAGTTTTTATCTTAACTTAA
1 AAAAATATATTTTAGTTCCTATATTAACTTAA
252090 AAAAATATATTTTA-TTCCTATATTAACTTA
1 AAAAATATATTTTAGTTCCTATATTAACTTA
252120 TTAAATAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (32 bp):
AAAAATATATTTTAGTTCCTATATTAACTTAA
Found at i:252151 original size:29 final size:28
Alignment explanation
Indices: 252112--252183 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
252102 TATTCCTATA
*
252112 TTAACTTATTAAATAAGTTATATTCTAAC
1 TTAAATTATTAAATAA-TTATATTCTAAC
* * *
252141 TTAAATTATTAAATTTATTGTATTCTTAC
1 TTAAATTATTAAA-TAATTATATTCTAAC
252170 TT-AATTATTAAATA
1 TTAAATTATTAAATA
252184 TAATTCATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 10 0.27
29 24 0.65
30 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (28 bp):
TTAAATTATTAAATAATTATATTCTAAC
Found at i:252193 original size:28 final size:29
Alignment explanation
Indices: 252133--252196 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
252123 AATAAGTTAT
* * *
252133 ATTCTAACTTAAATTATTAAATTTATTGT
1 ATTCTTACTTAAATTATTAAATTAATTGC
252162 ATTCTTACTT-AATTATTAAATATAATT-C
1 ATTCTTACTTAAATTATTAAAT-TAATTGC
252190 ATTCTTA
1 ATTCTTA
252197 TTTGAACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.52
Consensus pattern (29 bp):
ATTCTTACTTAAATTATTAAATTAATTGC
Found at i:252222 original size:24 final size:23
Alignment explanation
Indices: 252194--252274 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 23
252184 TAATTCATTC
252194 TTATTTGAACTTAAAACATATATT
1 TTATTTGAACTTAAAA-ATATATT
*
252218 TTATTCTTG-TCTTAACTAAAATATATTT
1 TTA-T-TTGAACTT-A--AAAATATA-TT
*
252246 TTATTTTAAC-TACAAAATATATT
1 TTATTTGAACTTA-AAAATATATT
252269 TTATTT
1 TTATTT
252275 TTATCCTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
23 8 0.17
24 11 0.24
25 5 0.11
26 7 0.15
27 7 0.15
28 8 0.17
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTTGAACTTAAAAATATATT
Found at i:252224 original size:30 final size:29
Alignment explanation
Indices: 252156--252314 Score: 77
Period size: 30 Copynumber: 5.7 Consensus size: 29
252146 TTATTAAATT
* * *
252156 TATTGTATTCTTA-CTTAATTATTAA-ATA
1 TATTTTATTCTTATCTTAACTA-AAACATA
* *
252184 TAATTCATTCTTAT-TTGAACTTAAAACATA
1 TATTTTATTCTTATCTT-AAC-TAAAACATA
* *
252214 TATTTTATTCTTGTCTTAACTAAAATATA
1 TATTTTATTCTTATCTTAACTAAAACATA
*
252243 T-TTTTATT-TTAAC-T-AC--AAA-ATA
1 TATTTTATTCTTATCTTAACTAAAACATA
* * *
252265 TATTTTATTTTTATCCTAACTACTAAATATA
1 TATTTTATTCTTATCTTAACTA--AAACATA
* * *
252296 TATTATATTTTTATATTAA
1 TATTTTATTCTTATCTTAA
252315 ATTTAAAATA
Statistics
Matches: 102, Mismatches: 15, Indels: 25
0.72 0.11 0.18
Matches are distributed among these distances:
22 4 0.04
23 10 0.10
24 4 0.04
25 3 0.03
26 3 0.03
27 3 0.03
28 19 0.19
29 13 0.13
30 22 0.22
31 21 0.21
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (29 bp):
TATTTTATTCTTATCTTAACTAAAACATA
Found at i:252271 original size:51 final size:54
Alignment explanation
Indices: 252194--252306 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 54
252184 TAATTCATTC
* * *
252194 TTATTTGAACTTAAAACATATATTTTATTCTTGTCTTAACTA-AAATATAT-TT
1 TTATTTTAACTTAAAACATATATTTTATTCTTATCCTAACTACAAATATATATT
*
252246 TTATTTTAAC-TACAAA-ATATATTTTATTTTTATCCTAACTACTAAATATATATT
1 TTATTTTAACTTA-AAACATATATTTTATTCTTATCCTAACTAC-AAATATATATT
*
252300 ATATTTT
1 TTATTTT
252307 TATATTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
51 24 0.46
52 12 0.23
53 8 0.15
54 8 0.15
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (54 bp):
TTATTTTAACTTAAAACATATATTTTATTCTTATCCTAACTACAAATATATATT
Found at i:252278 original size:29 final size:31
Alignment explanation
Indices: 252239--252314 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
252229 TTAACTAAAA
*
252239 TATATTTTTATTTTAACTAC-AAA-ATATAT
1 TATATTTTTATATTAACTACTAAATATATAT
* **
252268 TTTATTTTTATCCTAACTACTAAATATATAT
1 TATATTTTTATATTAACTACTAAATATATAT
252299 TATATTTTTATATTAA
1 TATATTTTTATATTAA
252315 ATTTAAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 17 0.44
30 3 0.08
31 19 0.49
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (31 bp):
TATATTTTTATATTAACTACTAAATATATAT
Found at i:252305 original size:31 final size:29
Alignment explanation
Indices: 252239--252309 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
252229 TTAACTAAAA
**
252239 TATATTTTTATTTTAACTACAAAATATAT
1 TATATTTTTATCCTAACTACAAAATATAT
*
252268 TTTATTTTTATCCTAACTACTAAATATATAT
1 TATATTTTTATCCTAACTAC-AAA-ATATAT
252299 TATATTTTTAT
1 TATATTTTTAT
252310 ATTAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 17 0.47
30 3 0.08
31 16 0.44
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (29 bp):
TATATTTTTATCCTAACTACAAAATATAT
Found at i:252401 original size:11 final size:11
Alignment explanation
Indices: 252382--252421 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
252372 ATTTTTTAAT
*
252382 TTAAGATAAGA
1 TTAAAATAAGA
252393 TTAAAATAA-A
1 TTAAAATAAGA
252403 TTAAAATAAGA
1 TTAAAATAAGA
*
252414 ATAAAATA
1 TTAAAATA
252422 CATTTTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (11 bp):
TTAAAATAAGA
Found at i:252411 original size:21 final size:21
Alignment explanation
Indices: 252382--252421 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
252372 ATTTTTTAAT
* *
252382 TTAAGATAAGATTAAAATAAA
1 TTAAAATAAGAATAAAATAAA
252403 TTAAAATAAGAATAAAATA
1 TTAAAATAAGAATAAAATA
252422 CATTTTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (21 bp):
TTAAAATAAGAATAAAATAAA
Found at i:252467 original size:25 final size:26
Alignment explanation
Indices: 252439--252510 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 26
252429 AGGTTATAGA
252439 AAGAATAAAATATATTTAATAA-GTT
1 AAGAATAAAATATATTTAATAATGTT
* **
252464 AAG-ATAAAAAATATTTTTTAATGTT
1 AAGAATAAAATATATTTAATAATGTT
*
252489 AAGATGTAAAAT-TAATTTAATA
1 AAGA-ATAAAATAT-ATTTAATA
252511 TGAGAATTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
24 15 0.42
25 9 0.25
26 1 0.03
27 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (26 bp):
AAGAATAAAATATATTTAATAATGTT
Found at i:256733 original size:29 final size:26
Alignment explanation
Indices: 256677--256742 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
256667 ATTCTTTTTA
*
256677 CTCTTATCTTCTTTTTCTTTGAAGAT
1 CTCTTATCTTCTTTTTCTTTGAAAAT
* *
256703 CTCTTATTTTCTCTTTTTTTTAGAAAAAT
1 CTCTTATCTTCT-TTTTCTTT-G-AAAAT
*
256732 CT-TTTTCTTCT
1 CTCTTATCTTCT
256743 CTCTCAATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 11 0.34
27 7 0.22
28 8 0.25
29 6 0.19
ACGTcount: A:0.17, C:0.18, G:0.05, T:0.61
Consensus pattern (26 bp):
CTCTTATCTTCTTTTTCTTTGAAAAT
Found at i:259149 original size:17 final size:17
Alignment explanation
Indices: 259127--259173 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
259117 ATAAAGTAAC
259127 ATGC-TTAATTGAACTAT
1 ATGCTTTAA-TGAACTAT
*
259144 ATGCTTTAATGAACTAC
1 ATGCTTTAATGAACTAT
*
259161 ATGATTTAATGAA
1 ATGCTTTAATGAA
259174 GTACATGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (17 bp):
ATGCTTTAATGAACTAT
Found at i:259178 original size:17 final size:16
Alignment explanation
Indices: 259120--259197 Score: 59
Period size: 17 Copynumber: 4.6 Consensus size: 16
259110 TACTTAAATA
*
259120 AAGTAACATGCTTAATTG
1 AAGT-ACATGTTTAA-TG
* *
259138 AACTATATGCTTTAATG
1 AAGTACATG-TTTAATG
*
259155 AACTACATGATTTAATG
1 AAGTACATG-TTTAATG
259172 AAGTACATG-TTAGATG
1 AAGTACATGTTTA-ATG
259188 AAGTAGCATG
1 AAGTA-CATG
259198 CTTATTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
15 3 0.06
16 8 0.16
17 33 0.65
18 7 0.14
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (16 bp):
AAGTACATGTTTAATG
Found at i:259769 original size:2 final size:2
Alignment explanation
Indices: 259751--259783 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
259741 ATAATGATTG
*
259751 AT AT A- AT AT AT AA 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
259784 TCCCAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:265646 original size:5 final size:5
Alignment explanation
Indices: 265617--265646 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
265607 ATATAATATA
*
265617 ATACA ATACG ATACG ATACG ATACG ATACG
1 ATACG ATACG ATACG ATACG ATACG ATACG
265647 TATATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (5 bp):
ATACG
Found at i:265664 original size:2 final size:2
Alignment explanation
Indices: 265659--265763 Score: 87
Period size: 2 Copynumber: 53.0 Consensus size: 2
265649 TATATAAAAC
* * * *
265659 AT AT AT AT AA AT ACT A- AA AT AT AT AT AT AA AT AT AA AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265701 ACT AT AT ACT A- AT A- AT AT A- AT AT AT AT AT AT AT -T AT A- AT
1 A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265740 AT AT AT ACT AT AT AT AT ACT AT AT
1 AT AT AT A-T AT AT AT AT A-T AT AT
265764 TAATATTTTA
Statistics
Matches: 85, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
1 6 0.07
2 69 0.81
3 10 0.12
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:265725 original size:18 final size:16
Alignment explanation
Indices: 265647--265746 Score: 65
Period size: 18 Copynumber: 5.5 Consensus size: 16
265637 ATACGATACG
265647 TATATATAAAACATATATA
1 TATATAT-AAA-ATATA-A
*
265666 TAAATACTAAAATATATA
1 TATATA-TAAAATATA-A
*
265684 TATAAATATAAATATATAC
1 TAT--ATATAAA-ATATAA
265703 TATATACTAATAATATAA
1 TATATA-TAA-AATATAA
*
265721 TATATATATATATTATAA
1 TATATATA-A-AATATAA
265739 TATATATA
1 TATATATA
265747 CTATATATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
17 5 0.07
18 39 0.57
19 16 0.23
20 9 0.13
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAAAATATAA
Found at i:265737 original size:29 final size:29
Alignment explanation
Indices: 265659--265769 Score: 97
Period size: 31 Copynumber: 3.8 Consensus size: 29
265649 TATATAAAAC
* *
265659 ATATATATAAATACTA-AAATATATATATAA
1 ATATATATATATACTATATA-ATATATAT-A
* *
265689 ATATAAATATATACTATATACTAATAATATA
1 ATATATATATATACTATATAAT-AT-ATATA
265720 ATATATATATATA-T-TATAATATATAT-
1 ATATATATATATACTATATAATATATATA
*
265746 A-CTATATATATACTATATTAATAT
1 ATATATATATATACTATA-TAATAT
265770 TTTATATTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
25 10 0.15
26 2 0.03
27 6 0.09
28 8 0.12
29 5 0.07
30 16 0.24
31 17 0.25
32 4 0.06
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATATATATATACTATATAATATATATA
Found at i:265755 original size:18 final size:18
Alignment explanation
Indices: 265659--265769 Score: 99
Period size: 18 Copynumber: 6.2 Consensus size: 18
265649 TATATAAAAC
*
265659 ATATATATAA-ATACTAAA
1 ATATATATAATATA-TATA
*
265677 ATATATAT-ATAAATATA
1 ATATATATAATATATATA
*
265694 A-ATATATACTATATACTA
1 ATATATATAATATATA-TA
265712 ATA-ATATAATATATAT-
1 ATATATATAATATATATA
265728 ATATATTATAATATATATA
1 ATATA-TATAATATATATA
*
265747 CTATATAT-ATACTATATTA
1 ATATATATAATA-TATA-TA
265766 ATAT
1 ATAT
265770 TTTATATTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
16 9 0.12
17 15 0.19
18 43 0.56
19 10 0.13
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATATATAATATATATA
Found at i:265757 original size:20 final size:19
Alignment explanation
Indices: 265647--265763 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 19
265637 ATACGATACG
* *
265647 TATATATAAAACATATATA
1 TATATATATAATATATATA
* *
265666 TAAATACTAAAATATATATA
1 TATATA-TATAATATATATA
* *
265686 TAAATATAAATATATACTATA
1 TATATATATA-ATATA-TATA
265707 TACTAATAATATAATATATATA
1 TA-T-AT-ATATAATATATATA
265729 TATAT-TATAATATATATA
1 TATATATATAATATATATA
*
265747 CTATATATATACTATAT
1 -TATATATATAATATAT
265764 TAATATTTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.15
19 14 0.16
20 34 0.40
21 7 0.08
22 6 0.07
23 7 0.08
24 4 0.05
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TATATATATAATATATATA
Found at i:265775 original size:38 final size:38
Alignment explanation
Indices: 265663--265780 Score: 111
Period size: 38 Copynumber: 3.1 Consensus size: 38
265653 TAAAACATAT
* * *
265663 ATATAAATACTAA-AATAT-ATATATAAATATA-AATA
1 ATATATATACTAATAATATAATATATATATATATTATA
265698 TATACTATATACTAATAATATAATATATATATATATTATA
1 -ATA-TATATACTAATAATATAATATATATATATATTATA
* *
265738 ATATATATACT-ATATATATACTATAT-TAATATTTTATA
1 ATATATATACTAATA-ATATAATATATAT-ATATATTATA
*
265776 TTATA
1 ATATA
265781 ATAAAACATT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
36 3 0.04
37 13 0.19
38 36 0.51
39 15 0.21
40 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (38 bp):
ATATATATACTAATAATATAATATATATATATATTATA
Found at i:267220 original size:23 final size:23
Alignment explanation
Indices: 267192--267240 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
267182 TTGGCCTAAC
267192 ACTGACGCAGTCATTATAAATTA
1 ACTGACGCAGTCATTATAAATTA
267215 ACTGACGCAGTCATTATAAATTA
1 ACTGACGCAGTCATTATAAATTA
267238 ACT
1 ACT
267241 AACATTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
ACTGACGCAGTCATTATAAATTA
Found at i:269182 original size:19 final size:19
Alignment explanation
Indices: 269160--269208 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
269150 TGAAAAGATT
* *
269160 TAATAAAATAAATAGATAA
1 TAATAAAATAAAGAGAAAA
269179 TAAT-AAATAAAAGAGAAAA
1 TAATAAAAT-AAAGAGAAAA
*
269198 TAATAATATAA
1 TAATAAAATAA
269209 TAAAAATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (19 bp):
TAATAAAATAAAGAGAAAA
Found at i:281701 original size:19 final size:19
Alignment explanation
Indices: 281684--281742 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
281674 TGAAAAGATT
281684 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
* *
281704 TAATAAATAAAAGAGAAAA
1 TAATAAATAAAATAGATAA
* *
281723 TAATAAA-ATAATAAATAA
1 TAATAAATAAAATAGATAA
281741 TA
1 TA
281743 TTAGTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 9 0.27
19 20 0.61
20 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:281709 original size:20 final size:20
Alignment explanation
Indices: 281684--281733 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
281674 TGAAAAGATT
* *
281684 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAGAGAAAA
281704 TAAT-AAATAAAAGAGAAAA
1 TAATAAAATAAAAGAGAAAA
281723 TAATAAAATAA
1 TAATAAAATAA
281734 TAAATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAAGAGAAAA
Found at i:292256 original size:20 final size:20
Alignment explanation
Indices: 292231--292268 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
292221 TGATTCAATC
*
292231 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCAAAGGGGG
292251 AGTATCGATACCAAAGGG
1 AGTATCGATACCAAAGGG
292269 AAGGTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (20 bp):
AGTATCGATACCAAAGGGGG
Found at i:292906 original size:57 final size:57
Alignment explanation
Indices: 292821--293250 Score: 639
Period size: 57 Copynumber: 7.5 Consensus size: 57
292811 AAGTGTGCAA
* *
292821 AAATATTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
*
292878 AAATGTTAAGAAATTCATACTAACTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
* *
292935 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
* *
292992 AAATGTTAAAAAATTCATACTATGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
* * *
293049 AAAAT-TTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGTACTTCGTGTGC
1 -AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
* * *
293106 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
* * * * *
293163 AAAAGTTAAGAAATTCATACTAACTGTATGAATTTCCATATAT-GGCACTTTGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT-TGGGCACTTCGTGTGC
* *
293220 AAATGGTTAGGAGATTCATACTAAGTGTATG
1 AAAT-GTTAAGAAATTCATACTAAGTGTATG
293251 GATCTCCATA
Statistics
Matches: 343, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
56 3 0.01
57 312 0.91
58 28 0.08
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (57 bp):
AAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGC
Found at i:293441 original size:57 final size:57
Alignment explanation
Indices: 293375--293735 Score: 560
Period size: 57 Copynumber: 6.3 Consensus size: 57
293365 GATATATAAA
* *
293375 CATACTAAGTGTATGAATTTCCGTATTGGACACTTCGTGTGCAAATGTTAGGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAATGTTAAGAAATT
* * *
293432 CGTACTAAGTGTATGAATTTCCGTATTGGGCACGTCGTGTGCAAAAGTTAAGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAATGTTAAGAAATT
* * * *
293489 CATACTAAGTGTATGAATTTTCATATTAGGCACTTTGTGTGCAAATGTTAAGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAATGTTAAGAAATT
* *
293546 TATACTAAGTGTATGAATTTTCGTATTGGGCACTTCGTGTGCAAATGTTAAGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAATGTTAAGAAATT
** *
293603 CATACTAAGTGTATGAATTTTTGTATTGGGCACTTCGTGTGCAAAAGTTAAGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAATGTTAAGAAATT
* *
293660 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAATGATTAAGAGATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAATG-TTAAGAAATT
*
293718 CATACTATGTGTATGAAT
1 CATACTAAGTGTATGAAT
293736 CTCCATATGG
Statistics
Matches: 278, Mismatches: 25, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
57 252 0.91
58 26 0.09
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (57 bp):
CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAATGTTAAGAAATT
Found at i:299899 original size:20 final size:20
Alignment explanation
Indices: 299874--299968 Score: 154
Period size: 20 Copynumber: 4.8 Consensus size: 20
299864 ATTCAATCAA
299874 TATCGATGCCGAAGGGGGAG
1 TATCGATGCCGAAGGGGGAG
*
299894 TATCGATGCCGAAGGAGGAG
1 TATCGATGCCGAAGGGGGAG
*
299914 TATCGATGTCGAAGGGGGAG
1 TATCGATGCCGAAGGGGGAG
*
299934 TATCGATACCGAAGGGGGAG
1 TATCGATGCCGAAGGGGGAG
*
299954 TATCGATACCGAAGG
1 TATCGATGCCGAAGG
299969 AAAGGTATCG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.28, C:0.15, G:0.40, T:0.17
Consensus pattern (20 bp):
TATCGATGCCGAAGGGGGAG
Found at i:299976 original size:20 final size:20
Alignment explanation
Indices: 299874--299981 Score: 101
Period size: 20 Copynumber: 5.4 Consensus size: 20
299864 ATTCAATCAA
* **
299874 TATCGATGCCGAAGGGGGAG
1 TATCGATACCGAAGGAAGAG
* *
299894 TATCGATGCCGAAGGAGGAG
1 TATCGATACCGAAGGAAGAG
** **
299914 TATCGATGTCGAAGGGGGAG
1 TATCGATACCGAAGGAAGAG
**
299934 TATCGATACCGAAGGGGGAG
1 TATCGATACCGAAGGAAGAG
299954 TATCGATACCGAAGGAA-AGG
1 TATCGATACCGAAGGAAGA-G
299974 TATCGATA
1 TATCGATA
299982 TCATTTTGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
19 1 0.01
20 79 0.99
ACGTcount: A:0.31, C:0.14, G:0.38, T:0.18
Consensus pattern (20 bp):
TATCGATACCGAAGGAAGAG
Found at i:299977 original size:40 final size:40
Alignment explanation
Indices: 299874--299981 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
299864 ATTCAATCAA
* ** *
299874 TATCGATGCCGAAGGGGGAGTATCGATGCCGAAGGAGGAG
1 TATCGATACCGAAGGAAGAGTATCGATACCGAAGGAGGAG
** ** *
299914 TATCGATGTCGAAGGGGGAGTATCGATACCGAAGGGGGAG
1 TATCGATACCGAAGGAAGAGTATCGATACCGAAGGAGGAG
299954 TATCGATACCGAAGGAA-AGGTATCGATA
1 TATCGATACCGAAGGAAGA-GTATCGATA
299982 TCATTTTGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 59 0.98
ACGTcount: A:0.31, C:0.14, G:0.38, T:0.18
Consensus pattern (40 bp):
TATCGATACCGAAGGAAGAGTATCGATACCGAAGGAGGAG
Found at i:300685 original size:57 final size:57
Alignment explanation
Indices: 300618--301050 Score: 731
Period size: 57 Copynumber: 7.6 Consensus size: 57
300608 AAGTGTGCAT
* * * *
300618 AAATGTTAAGAAATTTATACTAAGTGTATGAATTTCAGCATTAGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
300675 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * *
300732 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATTAGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
300789 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
300846 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * *
300903 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCATTTCGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * *
300960 AAAAGTTAAGAAATTCATACTAAGTATATGAATTTCCGTATTGGGCACTTTGTGTGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
*
301017 AAATGGTTAAGAGATTCATACTAAGTGTATGAAT
1 AAAT-GTTAAGAAATTCATACTAAGTGTATGAAT
301051 CTCCATATAG
Statistics
Matches: 355, Mismatches: 20, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
57 328 0.92
58 27 0.08
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (57 bp):
AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
Found at i:302369 original size:46 final size:46
Alignment explanation
Indices: 302264--302369 Score: 108
Period size: 46 Copynumber: 2.3 Consensus size: 46
302254 TATATGTCAT
* * * * *
302264 TAATATACCGATATGTATTTTCATTTGTAGTATCCTTTCATGCTTA
1 TAATACACCGTTATGAATTTTCATTTATAGTATCCTTTCATGCTGA
*
302310 TTATACACCGTTATGAATTTTCATTTATA-TCATCCTTTCATG-TCGA
1 TAATACACCGTTATGAATTTTCATTTATAGT-ATCCTTTCATGCT-GA
* *
302356 TAATTCACTGTTAT
1 TAATACACCGTTAT
302370 ACATTTAGTC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
45 2 0.04
46 47 0.96
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (46 bp):
TAATACACCGTTATGAATTTTCATTTATAGTATCCTTTCATGCTGA
Found at i:302513 original size:81 final size:81
Alignment explanation
Indices: 302378--302708 Score: 545
Period size: 81 Copynumber: 4.1 Consensus size: 81
302368 ATACATTTAG
* *
302378 TCTTTTACTCAAAAGTATTTAACATTTCATCTAACTGGTATGATTGACACCTTTCTGTAAAATGC
1 TCTTTTACTCAAAAGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
302443 ACAACTAGGCAATTAA
66 ACAACTAGGCAATTAA
* *
302459 TCTTTTACTCAAAAGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGC
1 TCTTTTACTCAAAAGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
302524 ACAGCTAGGCAATTAA
66 ACAACTAGGCAATTAA
* * *
302540 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAAGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
302605 ACAACTAGGCAATTAA
66 ACAACTAGGCAATTAA
* * *
302621 TCTTTTACTCAAAGGTATTTAACATTTCATCTAAATGGCATGATTGACACCTTTATGTCAAATGC
1 TCTTTTACTCAAAAGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
* *
302686 ACAGCTATGCAATTAA
66 ACAACTAGGCAATTAA
302702 TCTTTTA
1 TCTTTTA
302709 TTTTAAAATA
Statistics
Matches: 235, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 235 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAAGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
ACAACTAGGCAATTAA
Found at i:304416 original size:282 final size:282
Alignment explanation
Indices: 303897--304471 Score: 1044
Period size: 282 Copynumber: 2.0 Consensus size: 282
303887 CCAAAATACC
* *
303897 CTTTCATTCTTCCACTCTTACTAATTGGTCTTAAATCACAATTTCTAAATAATTTTTTGTACTTT
1 CTTTTATT-TTCCACTCTTACTAATCGGTCTTAAATCACAATTTCTAAATAATTTTTTGTACTTT
*
303962 ACCATTTATTCAATTTAATCCTCAAATTTTTTAAATTTGTTCAATATAGTTACTGACTTGATATT
65 ACCATTTATTCAATTTAATCCTCAAATTTTTTAAATCTGTTCAATATAGTTACTGACTTGATATT
304027 TGGGGTATTACAACCTTCTAGAAGCTTCATCCTAGCCGTCTATCTCATCCAACAAGCTAAGATTT
130 TGGGGTATTACAACCTTCTAGAAGCTTCATCCTAGCCGTCTATCTCATCCAACAAGCTAAGATTT
304092 CAAATTCCTAGTTTTCATCATTATCATTGAATCAAACACTACATCAATAGCTCACATTGTGTCGC
195 CAAATTCCTAGTTTTCATCATTATCATTGAATCAAACACTACATCAATAGCTCACATTGTGTCGC
304157 CCATCCCATTTAGAGTAGGATAG
260 CCATCCCATTTAGAGTAGGATAG
* *
304180 CTTTTATTTTCCATTCTTACTAATCGGTCTTAAATCACAATTTCTAAATCATTTTTTGTACTTTA
1 CTTTTATTTTCCACTCTTACTAATCGGTCTTAAATCACAATTTCTAAATAATTTTTTGTACTTTA
304245 CCATTTATTCAATTTAATCCTCGAAA-TTTTTAAATCTGTTCAATATAGTTACTGACTTGATATT
66 CCATTTATTCAATTTAATCCTC-AAATTTTTTAAATCTGTTCAATATAGTTACTGACTTGATATT
*
304309 TGGGGTATTACAACCTTCTAGAAGCTTCATCCTAGCCGTCTATCTCATCCTACAAGCTAAGATTT
130 TGGGGTATTACAACCTTCTAGAAGCTTCATCCTAGCCGTCTATCTCATCCAACAAGCTAAGATTT
* *
304374 CAAATTCCTTGTTTTCATCATTATCATTGAATCAAACACTACATCAATGGCTCACATTGTGTCGC
195 CAAATTCCTAGTTTTCATCATTATCATTGAATCAAACACTACATCAATAGCTCACATTGTGTCGC
*
304439 CCATCCTATTTAGAGTAGGATAG
260 CCATCCCATTTAGAGTAGGATAG
304462 CTTTTATTTT
1 CTTTTATTTT
304472 TTATTTTTAT
Statistics
Matches: 282, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
282 272 0.96
283 10 0.04
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (282 bp):
CTTTTATTTTCCACTCTTACTAATCGGTCTTAAATCACAATTTCTAAATAATTTTTTGTACTTTA
CCATTTATTCAATTTAATCCTCAAATTTTTTAAATCTGTTCAATATAGTTACTGACTTGATATTT
GGGGTATTACAACCTTCTAGAAGCTTCATCCTAGCCGTCTATCTCATCCAACAAGCTAAGATTTC
AAATTCCTAGTTTTCATCATTATCATTGAATCAAACACTACATCAATAGCTCACATTGTGTCGCC
CATCCCATTTAGAGTAGGATAG
Found at i:305859 original size:3 final size:3
Alignment explanation
Indices: 305851--305887 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
305841 CACATTTATA
305851 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
305888 CTACAGGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:306098 original size:3 final size:3
Alignment explanation
Indices: 306090--306124 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
306080 CACATTTATA
306090 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
306125 CTACAGGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:311014 original size:21 final size:21
Alignment explanation
Indices: 310989--311034 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
310979 AATATTCTAG
310989 AGATGTGTGGAAACTTATGGA
1 AGATGTGTGGAAACTTATGGA
*
311010 AGATGTGTGGAACCTTATGGA
1 AGATGTGTGGAAACTTATGGA
311031 AGAT
1 AGAT
311035 TATGGAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (21 bp):
AGATGTGTGGAAACTTATGGA
Found at i:311037 original size:10 final size:10
Alignment explanation
Indices: 311003--311052 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
310993 GTGTGGAAAC
311003 TTATGGAAGA
1 TTATGGAAGA
* **
311013 TGTGTGGAACC
1 T-TATGGAAGA
311024 TTATGGAAGA
1 TTATGGAAGA
311034 TTATGGAAGA
1 TTATGGAAGA
*
311044 ATATGGAAG
1 TTATGGAAG
311053 GGAGTGGAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.36, C:0.04, G:0.32, T:0.28
Consensus pattern (10 bp):
TTATGGAAGA
Found at i:315048 original size:22 final size:22
Alignment explanation
Indices: 315023--315075 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
315013 AAATTTTTCT
**
315023 CGAAGGACCTA-TGTATTTGTCC
1 CGAAGGACC-ACTGTATACGTCC
*
315045 CGAATGACCACTGTATACGTCC
1 CGAAGGACCACTGTATACGTCC
315067 CGAAGGACC
1 CGAAGGACC
315076 GCATAGACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (22 bp):
CGAAGGACCACTGTATACGTCC
Found at i:315577 original size:2 final size:2
Alignment explanation
Indices: 315539--315564 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
315529 ACATATAAGA
315539 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
315565 CCATTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321310 original size:21 final size:22
Alignment explanation
Indices: 321260--321314 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
321250 ATATGAAATT
* *
321260 TCCCAAAGGACCTATGTATTTG
1 TCCCGAAGGACCTATGTATATG
321282 TCCCGAAGGACC-ACTGTATATG
1 TCCCGAAGGACCTA-TGTATATG
321304 T-CCGAAGGACC
1 TCCCGAAGGACC
321315 GCGTAGACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (22 bp):
TCCCGAAGGACCTATGTATATG
Found at i:321823 original size:2 final size:2
Alignment explanation
Indices: 321773--321810 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
321763 ACATATAAGA
321773 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
321811 CCATTTCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324655 original size:5 final size:5
Alignment explanation
Indices: 324624--324677 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
324614 GATTGGCATT
* *
324624 AAAAG AAAAA ATAAAG AAATTG AAAAG AAAAG -AAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG A-AAAG AAA-AG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
324675 AAA
1 AAA
324678 GCTTTATTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 30 0.71
6 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (5 bp):
AAAAG
Found at i:324661 original size:9 final size:9
Alignment explanation
Indices: 324647--324678 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
324637 AAGAAATTGA
324647 AAAGAAAAG
1 AAAGAAAAG
324656 AAAGAAAAG
1 AAAGAAAAG
324665 AAAAGAAAAG
1 -AAAGAAAAG
324675 AAAG
1 AAAG
324679 CTTTATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:324669 original size:19 final size:20
Alignment explanation
Indices: 324631--324678 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
324621 ATTAAAAGAA
* *
324631 AAAATAAAGAAATTGAAAAG
1 AAAAGAAAGAAATAGAAAAG
324651 AAAAGAAAGAAA-AGAAAAG
1 AAAAGAAAGAAATAGAAAAG
324670 AAAAGAAAG
1 AAAAGAAAG
324679 CTTTATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (20 bp):
AAAAGAAAGAAATAGAAAAG
Found at i:325424 original size:17 final size:17
Alignment explanation
Indices: 325382--325414 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
325372 CTACCAATAA
325382 AAAATAAATTAAAAAAC
1 AAAATAAATTAAAAAAC
325399 AAAATAAATTAAAAAA
1 AAAATAAATTAAAAAA
325415 TAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAAATTAAAAAAC
Found at i:327837 original size:16 final size:17
Alignment explanation
Indices: 327818--327852 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
327808 TTATGATAAC
327818 TTAATTTT-CTTTCCTT
1 TTAATTTTACTTTCCTT
*
327834 TTAATTTTATTTTCCTT
1 TTAATTTTACTTTCCTT
327851 TT
1 TT
327853 TACTAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (17 bp):
TTAATTTTACTTTCCTT
Found at i:335692 original size:22 final size:18
Alignment explanation
Indices: 335650--335719 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
335640 TTAAGGAGTA
*
335650 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
335668 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
**
335690 GTCCTTTGGGACATAGTG
1 GTCCTACGGGACATAGTG
335708 GTCCTACGGGAC
1 GTCCTACGGGAC
335720 GAATACTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 25 0.58
20 4 0.09
22 14 0.33
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:347398 original size:20 final size:21
Alignment explanation
Indices: 347362--347407 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
347352 CAAATACACG
347362 ATAATTAAAAGTTACAAGTCC
1 ATAATTAAAAGTTACAAGTCC
347383 ATAATTAAAA-TTACAAGTCC
1 ATAATTAAAAGTTACAAGTCC
347403 ATAAT
1 ATAAT
347408 ATAGTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (21 bp):
ATAATTAAAAGTTACAAGTCC
Found at i:351204 original size:19 final size:19
Alignment explanation
Indices: 351188--351238 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
351178 AGAAATAAGG
351188 AAAAATAT-TAAAAATAAA
1 AAAAATATATAAAAATAAA
351206 AAAAATATATAAATATATAAA
1 AAAAATATATAAA-A-ATAAA
* *
351227 ATAAATAAATAA
1 AAAAATATATAA
351239 CTAAAAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.29
19 4 0.14
20 1 0.04
21 15 0.54
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAATATATAAAAATAAA
Found at i:351219 original size:17 final size:17
Alignment explanation
Indices: 351188--351238 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
351178 AGAAATAAGG
*
351188 AAAAATATTAAAAATAAA
1 AAAAATA-TATAAATAAA
*
351206 AAAAATATATAAATATA
1 AAAAATATATAAATAAA
* *
351223 TAAAATAAATAAATAA
1 AAAAATATATAAATAA
351239 CTAAAAACTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATATATAAATAAA
Found at i:352763 original size:31 final size:32
Alignment explanation
Indices: 352704--352763 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
352694 TGAAAAAAAC
*
352704 ATTAGTAAATAATATAATAATATGATATATGT
1 ATTAGTAAATAATATAATAATATCATATATGT
*
352736 ATTA-TAAATAATATAGT-ATACTCATATA
1 ATTAGTAAATAATATAATAATA-TCATATA
352764 AATTTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.12
31 18 0.72
32 4 0.16
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (32 bp):
ATTAGTAAATAATATAATAATATCATATATGT
Found at i:353319 original size:86 final size:86
Alignment explanation
Indices: 353221--353630 Score: 423
Period size: 86 Copynumber: 4.8 Consensus size: 86
353211 CATTCCCTTG
* * * * *
353221 AGCTGTATGTAATCGCACTCGAAGGTCTTTTTTTGACGGATATCCCTTCTCGCCTTGAGCTATGC
1 AGCTGAATGTAATCGAACTCGAAGGTCTTTTTTTAACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
353286 TATAAA-TCGAATATGCCTTTA
66 TGTAAATTTG-ATGTGCCTTTA
* * * *
353307 AGCTGAATGTAATCGAACTAGAAGGTCTTTTTTTAACATATAGCCATTCTCGTCTTGAGCTATGC
1 AGCTGAATGTAATCGAACTCGAAGGTCTTTTTTTAACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
353372 TGTAAATTTGATTTGCATTTG
66 TGTAAATTTGATGTGCCTTTA
* * ** ** * * *
353393 AGCTGAATGTAATTGAACTCGAAGGTCTTTTGTGGACAGATAATCCTTCTCACCTTAAGTTATGC
1 AGCTGAATGTAATCGAACTCGAAGGTCTTTTTTTAACAGATAGCCCTTCTCGCCTTGAGCTATGC
353458 TGTAAATTTGATGTGCC-TTA
66 TGTAAATTTGATGTGCCTTTA
* * * * * **
353478 GAGCTGAATGTAATCGAACTCGAATGTCATTTGTTAATAGATAGCTCTTCTCATCTTGAGCTATG
1 -AGCTGAATGTAATCGAACTCGAAGGTCTTTTTTTAACAGATAGCCCTTCTCGCCTTGAGCTATG
*
353543 CTGTAAATTTGATGTGCCTTTG
65 CTGTAAATTTGATGTGCCTTTA
* * * * * *
353565 AGCTGAGTGTAATCGAACTTGAAGGT-TTTGGTTT-ACAGTTAACCCTTCTCGCCTTGAGTTATG
1 AGCTGAATGTAATCGAACTCGAAGGTCTTT-TTTTAACAGATAGCCCTTCTCGCCTTGAGCTATG
353628 CTG
65 CTG
353631 CACTGGGCTG
Statistics
Matches: 264, Mismatches: 56, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
85 29 0.11
86 231 0.88
87 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (86 bp):
AGCTGAATGTAATCGAACTCGAAGGTCTTTTTTTAACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATGTGCCTTTA
Found at i:353485 original size:172 final size:172
Alignment explanation
Indices: 353218--353630 Score: 512
Period size: 172 Copynumber: 2.4 Consensus size: 172
353208 TGACATTCCC
* * * * *
353218 TTGAGCTGTATGTAATCGCACTCGAAGGTCTTTTTTTGACGGAT-ATCCCTTCTCGCCTTGAGCT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAAT-CCTTCTCGCCTTGAGTT
* * * *
353282 ATGCTATAAATCGAATATGCCTTTAAGCTGAATGTAATCGAACTAGAAGGTCTTTTTTTAACATA
65 ATGCTGTAAATCGAATATGCCTTTAAGCTGAATGTAATCGAACTAGAAGGTCATTTGTTAACAGA
* *
353347 TAGC-CATTCTCGTCTTGAGCTATGCTGTAAATTTGATTTGCAT
130 TAGCTC-TTCTCATCTTGAGCTATGCTGTAAATTTGATGTGCAT
* * * *
353390 TTGAGCTGAATGTAATTGAACTCGAAGGTCTTTTGTGGACAGATAATCCTTCTCACCTTAAGTTA
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAATCCTTCTCGCCTTGAGTTA
* * * * *
353455 TGCTGTAAATTTG-ATGTGCC-TTAGAGCTGAATGTAATCGAACTCGAATGTCATTTGTTAATAG
66 TGCTGTAAA-TCGAATATGCCTTTA-AGCTGAATGTAATCGAACTAGAAGGTCATTTGTTAACAG
*
353518 ATAGCTCTTCTCATCTTGAGCTATGCTGTAAATTTGATGTGCCT
129 ATAGCTCTTCTCATCTTGAGCTATGCTGTAAATTTGATGTGCAT
* * * * * *
353562 TTGAGCTGAGTGTAATCGAACTTGAAGGT-TTTGGTTTACAGTTAACCCTTCTCGCCTTGAGTTA
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAATCCTTCTCGCCTTGAGTTA
353626 TGCTG
66 TGCTG
353631 CACTGGGCTG
Statistics
Matches: 206, Mismatches: 31, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
171 36 0.17
172 165 0.80
173 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (172 bp):
TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAATCCTTCTCGCCTTGAGTTA
TGCTGTAAATCGAATATGCCTTTAAGCTGAATGTAATCGAACTAGAAGGTCATTTGTTAACAGAT
AGCTCTTCTCATCTTGAGCTATGCTGTAAATTTGATGTGCAT
Found at i:354268 original size:309 final size:309
Alignment explanation
Indices: 353705--354335 Score: 974
Period size: 309 Copynumber: 2.0 Consensus size: 309
353695 ATCCTTCATC
* *
353705 GTGAAGTTGAAATCGTGGATAGCTCATTCGTCATGAAGTTGAGCTTTGAATTGGATATCATTCGT
1 GTGAAGTTGAAATCATGGATAGCTCATTCGTCATGAAGTTGAGCTTTAAATTGGATATCATTCGT
* *
353770 TGTGAAGTTGAAATCCAATCTAGAGATGGATGCTCCTTGTGGGAAAGATATCATTCTTCGTGAAG
66 TGTAAAGTTGAAATCCAATCTAGAGATGGATGCTCCTTGTGGGAAAGATATCATTCGTCGTGAAG
* * * *
353835 TTGAAATCATTGATGGCTCTTTTGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAA
131 TTGAAATCATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTAGATATCCTTCGTTGTGAA
* * * *
353900 GTTGAAATACAAGGGTTGTTTCACCAAATTGGTTTTGATTTGGATATCCTTCGTCGTGAAGTTGA
196 ATTGAAATACAAGGGTTGTTTCACCAAATTGGTTTTGAGTTGGATATCCTTCATCGTGAAGTTAA
* * *
353965 AATCCAATCTTATATAAGTTGCATTGTTTCGAGTCCAGTATCATTCGAT
261 AATCCAATCTTATATAAGTTGCATTGTTTCAAGTCCAATATCACTCGAT
* ** *
354014 GTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTAAATTGGATATCCTTCGT
1 GTGAAGTTGAAATCATGGATAGCTCATTCGTCATGAAGTTGAGCTTTAAATTGGATATCATTCGT
* * * *
354079 TGTAAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGGGTATGATATCCTTCGTCGTGAAG
66 TGTAAAGTTGAAATCCAATCTAGAGATGGATGCTCCTTGTGGGAAAGATATCATTCGTCGTGAAG
*
354144 TTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTAGATATCCTTCGTTGTGAA
131 TTGAAATCATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTAGATATCCTTCGTTGTGAA
* * * *
354209 ATTGAAATCCAAGGGTTGTTTCACCAAATTGGTTTTGAGTTGGTTATCCTTTATCGTGAATTTAA
196 ATTGAAATACAAGGGTTGTTTCACCAAATTGGTTTTGAGTTGGATATCCTTCATCGTGAAGTTAA
* * * *
354274 AATCCAATCTTGTGTAAGTTGCATTGTTTCAAGTCCAATATCCCTCGTT
261 AATCCAATCTTATATAAGTTGCATTGTTTCAAGTCCAATATCACTCGAT
354323 GTGAAGTTGAAAT
1 GTGAAGTTGAAAT
354336 TTACTCTGAA
Statistics
Matches: 290, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
309 290 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (309 bp):
GTGAAGTTGAAATCATGGATAGCTCATTCGTCATGAAGTTGAGCTTTAAATTGGATATCATTCGT
TGTAAAGTTGAAATCCAATCTAGAGATGGATGCTCCTTGTGGGAAAGATATCATTCGTCGTGAAG
TTGAAATCATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTAGATATCCTTCGTTGTGAA
ATTGAAATACAAGGGTTGTTTCACCAAATTGGTTTTGAGTTGGATATCCTTCATCGTGAAGTTAA
AATCCAATCTTATATAAGTTGCATTGTTTCAAGTCCAATATCACTCGAT
Found at i:354379 original size:64 final size:64
Alignment explanation
Indices: 354305--354727 Score: 630
Period size: 64 Copynumber: 6.6 Consensus size: 64
354295 CATTGTTTCA
* *
354305 AGTCCAATATCCCTCGTTGTGAAGTTGAAATTTACTCTGAATGAAACTGGAAAGTTGTTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
** * *
354369 AGTCCAATATCCTTCACTGTGAAGTTGAAATTAACTCTGAATGAAACTGGAAAGTTATTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* * * *
354433 AGTCCAATATCCTCCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* * * * *
354497 AGTCCAATATCCTTCGATGTGAAGTTAAAATTAACTCTGAATAAAACTGAAAAGTTGTTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* *
354561 AGTCCAATATCCTTCGTTGTGAAGTTGATATTGACTCTGAATGAAACTAGAAAGTTGTTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* * * *
354625 AGTCCAATATCATTCGTTGTGAAGTTGAAATGGACTCTGAATGAAACTGGAACATTTTTTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAA-AGTTGTTTGTTG
**
354690 AGTCCAATATCCTTCAATGTGAAGTTGAAATTGACTCT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
354728 AAAATATGCA
Statistics
Matches: 326, Mismatches: 32, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
64 282 0.87
65 44 0.13
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (64 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
Found at i:354650 original size:34 final size:34
Alignment explanation
Indices: 354548--354651 Score: 81
Period size: 34 Copynumber: 3.2 Consensus size: 34
354538 TAAAACTGAA
*
354548 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTG
1 AAGTTGTTTGTTGAGTCCAATATCATTCGTTGTG
* * * ** * ** * *
354582 AAGTTG-ATATTGACTCTGA-ATGAAAC-TAG-A
1 AAGTTGTTTGTTGAGTCCAATATCATTCGTTGTG
354612 AAGTTGTTTGTTGAGTCCAATATCATTCGTTGTG
1 AAGTTGTTTGTTGAGTCCAATATCATTCGTTGTG
354646 AAGTTG
1 AAGTTG
354652 AAATGGACTC
Statistics
Matches: 45, Mismatches: 21, Indels: 8
0.61 0.28 0.11
Matches are distributed among these distances:
30 6 0.13
31 10 0.22
32 7 0.16
33 10 0.22
34 12 0.27
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (34 bp):
AAGTTGTTTGTTGAGTCCAATATCATTCGTTGTG
Found at i:358581 original size:4 final size:4
Alignment explanation
Indices: 358572--358622 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
358562 ATTAAAATTA
* * *
358572 AAAT AAAT AAAT AAAT -AAT ATAT ATAT ATAT ATAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
358620 AAA
1 AAA
358623 AATGTAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 3 0.07
4 37 0.86
5 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:364632 original size:23 final size:23
Alignment explanation
Indices: 364577--364665 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
364567 ACCGATGTAT
*
364577 CCTTGAATGTGCATCGAT--ACA
1 CCTTGAATGTGCATCGATGCACG
* * *
364598 CCATGAAGGTGCACCGATGCACG
1 CCTTGAATGTGCATCGATGCACG
*
364621 CCTTGAATGTGCATCGATGCATG
1 CCTTGAATGTGCATCGATGCACG
364644 CCTTGAATGTGCATCGATGCAC
1 CCTTGAATGTGCATCGATGCAC
364666 AAGGCCATGC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 15 0.26
23 42 0.74
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (23 bp):
CCTTGAATGTGCATCGATGCACG
Found at i:364634 original size:44 final size:43
Alignment explanation
Indices: 364544--364665 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
364534 TTGTGCTTAA
* *
364544 TGCATCGATACACCT-AACAGTGCACCGATGTA-TCCTTGAATG
1 TGCATCGATACACCTGAA-AGTGCACCGATGCACGCCTTGAATG
*
364586 TGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACC-TGAAAGTGCACCGATGCACGCCTTGAATG
* * *
364630 TGCATCGATGCATGCCTTGAATGTGCATCGATGCAC
1 TGCATCGATACA--CC-TGAAAGTGCACCGATGCAC
364666 AAGGCCATGC
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
42 14 0.21
43 13 0.19
44 22 0.32
46 19 0.28
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (43 bp):
TGCATCGATACACCTGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:367140 original size:26 final size:26
Alignment explanation
Indices: 367104--367175 Score: 135
Period size: 26 Copynumber: 2.8 Consensus size: 26
367094 ACATCGAATA
*
367104 CATTTTATGCATCGATGCACTCAGTG
1 CATTTGATGCATCGATGCACTCAGTG
367130 CATTTGATGCATCGATGCACTCAGTG
1 CATTTGATGCATCGATGCACTCAGTG
367156 CATTTGATGCATCGATGCAC
1 CATTTGATGCATCGATGCAC
367176 AAACCATGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (26 bp):
CATTTGATGCATCGATGCACTCAGTG
Found at i:367322 original size:21 final size:21
Alignment explanation
Indices: 367296--367352 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
367286 ATTTTGCACT
367296 GATGCACCGATGCACCATGGG
1 GATGCACCGATGCACCATGGG
367317 GATGCACCGATGCACCATGGG
1 GATGCACCGATGCACCATGGG
* *
367338 TATGCATCGATGCAC
1 GATGCACCGATGCAC
367353 TGACGCTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.18
Consensus pattern (21 bp):
GATGCACCGATGCACCATGGG
Found at i:369045 original size:19 final size:20
Alignment explanation
Indices: 369010--369050 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
369000 GGCGAGGAGT
369010 CTTCGGATGAGGGGGGAAGG
1 CTTCGGATGAGGGGGGAAGG
369030 CTTCGGATGA-GGGGGAAGG
1 CTTCGGATGAGGGGGGAAGG
369049 CT
1 CT
369051 ATGCGGTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (20 bp):
CTTCGGATGAGGGGGGAAGG
Found at i:370145 original size:2 final size:2
Alignment explanation
Indices: 370138--370162 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
370128 CTCATTAATA
370138 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
370163 GACACACAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:373997 original size:2 final size:2
Alignment explanation
Indices: 373992--374089 Score: 153
Period size: 2 Copynumber: 49.5 Consensus size: 2
373982 ACACACACAC
*
373992 AT AT AT AT AT AT AT AT AT AT AT AT AA 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
* * *
374034 AT AT AT AT AT AA AA AT AT AT AT AT AT AT AT AT A- AA 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
374075 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
374090 ATAATAAAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
1 1 0.01
2 89 0.99
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:374613 original size:37 final size:37
Alignment explanation
Indices: 374563--374711 Score: 262
Period size: 37 Copynumber: 4.0 Consensus size: 37
374553 ACGCTTGTGG
*
374563 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
374600 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
374637 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
374674 ATCATATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
374711 A
1 A
374712 ATGTTATGTT
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 107 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:376007 original size:110 final size:110
Alignment explanation
Indices: 375828--376111 Score: 469
Period size: 110 Copynumber: 2.6 Consensus size: 110
375818 GCTTCAAGTT
* * * *
375828 CAATATCCTTCACTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTATTTGTTGACAGT
1 CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGATAGC
375893 CAGTCGCCCTTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTC
66 CAGTCGCCCTTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTC
* * *
375938 CTATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATAAAACTGAAAAGTTATTTGTTGATAGC
1 CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGATAGC
* * *
376003 CAGTCGCCCTTTTGCTGTGCAGTTGAGCTTGTGTTGTCTCGAGTC
66 CAGTCGCCCTTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTC
*
376048 CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGATAG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGATAG
376112 TCAGCTTTTC
Statistics
Matches: 160, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 160 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (110 bp):
CAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGATAGC
CAGTCGCCCTTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTC
Found at i:376701 original size:32 final size:32
Alignment explanation
Indices: 376651--376738 Score: 140
Period size: 32 Copynumber: 2.8 Consensus size: 32
376641 ATCCCCGAAG
* * * *
376651 ATGCCCCAATATTCGATGTTGCATTTCTAAAA
1 ATGCCCCAACATTTGATGTTGAATTTCCAAAA
376683 ATGCCCCAACATTTGATGTTGAATTTCCAAAA
1 ATGCCCCAACATTTGATGTTGAATTTCCAAAA
376715 ATGCCCCAACATTTGATGTTGAAT
1 ATGCCCCAACATTTGATGTTGAAT
376739 CTTCAAAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATTTCCAAAA
Found at i:380850 original size:36 final size:38
Alignment explanation
Indices: 380809--380894 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 38
380799 ATAAAATAGT
*
380809 AAGTAAAATAAAAATATATATAT-AAA-AAATAAAGAA
1 AAGTAAAATAAAAATATATAAATAAAACAAATAAAGAA
* * *
380845 AAGT--AAGAAAAATTTATAAATAAAACAAATAAATAA
1 AAGTAAAATAAAAATATATAAATAAAACAAATAAAGAA
380881 AA-TAATAATAAAAA
1 AAGTAA-AATAAAAA
380895 AGTAAATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
34 14 0.35
35 4 0.10
36 15 0.38
38 7 0.17
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (38 bp):
AAGTAAAATAAAAATATATAAATAAAACAAATAAAGAA
Found at i:380876 original size:13 final size:12
Alignment explanation
Indices: 380860--380902 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 12
380850 AGAAAAATTT
380860 ATAAATAAAACAA
1 ATAAATAAAA-AA
*
380873 ATAAATAAAATA
1 ATAAATAAAAAA
380885 AT-AATAAAAAA
1 ATAAATAAAAAA
*
380896 GTAAATA
1 ATAAATA
380903 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.35
12 7 0.27
13 10 0.38
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (12 bp):
ATAAATAAAAAA
Found at i:380905 original size:2 final size:2
Alignment explanation
Indices: 380900--380974 Score: 55
Period size: 2 Copynumber: 38.5 Consensus size: 2
380890 AAAAAAGTAA
* * * *
380900 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A- AT AA AT AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
380941 AC AT AA AA AA AT AG A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
380975 AATTAATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
1 2 0.03
2 59 0.97
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (2 bp):
AT
Found at i:381040 original size:24 final size:23
Alignment explanation
Indices: 381013--381080 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
381003 ACATATATAT
381013 ATATATATAATCTAAAAAATAAAA
1 ATATATATAATCTAAAAAA-AAAA
** *
381037 ATATATACTAAAGTAAAAAAGAAA
1 ATATATA-TAATCTAAAAAAAAAA
** *
381061 ATGCATAAAATCTAAAAAAA
1 ATATATATAATCTAAAAAAA
381081 CATTACATGA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
23 9 0.26
24 15 0.44
25 10 0.29
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (23 bp):
ATATATATAATCTAAAAAAAAAA
Found at i:381526 original size:37 final size:37
Alignment explanation
Indices: 381476--381587 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
381466 ACGCTTGTGG
*
381476 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
381513 ATCCTATTTTTAGGAGTTTAAATCATAGTAAAAATCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
381550 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
381587 A
1 A
381588 ACGTTATGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:382015 original size:22 final size:23
Alignment explanation
Indices: 381978--382035 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
381968 AATTTTAATT
*
381978 TTTTTAATAAA-T-TTAATATCA-
1 TTTTTAA-AAATTATTAAGATCAC
381999 TTTTTAAAAATTATTAAGATCAC
1 TTTTTAAAAATTATTAAGATCAC
382022 TTTTTAAAATATTA
1 TTTTTAAAA-ATTA
382036 ACATTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 8 0.25
22 8 0.25
23 9 0.28
24 4 0.12
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTTAAAAATTATTAAGATCAC
Done.