Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 110 of 172
Found at i:31707367 original size:24 final size:24
Alignment explanation
Indices: 31707312--31707370 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
31707302 GGTTTAATGC
* *
31707312 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
31707336 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
31707360 AAATGGATATA
1 AAATGGATATA
31707371 AATGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:31707442 original size:17 final size:17
Alignment explanation
Indices: 31707420--31707477 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
31707410 AATTCAAGAC
31707420 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
31707437 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
31707456 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
31707474 TTAT
1 TTAT
31707478 ATAGTGATTC
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 12 0.40
18 5 0.17
19 5 0.17
20 8 0.27
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:31707465 original size:37 final size:37
Alignment explanation
Indices: 31707411--31707523 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
31707401 TTATGTGTTA
31707411 ATTC-AAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
*
31707447 ATTCAAAGACTTATGTAATATTTTTAATTATATAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* * *
31707484 ATTCAAATATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
31707521 ATT
1 ATT
31707524 TAATTCGGGT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
36 4 0.06
37 67 0.94
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:31707542 original size:9 final size:9
Alignment explanation
Indices: 31707524--31707640 Score: 153
Period size: 9 Copynumber: 12.6 Consensus size: 9
31707514 TGTAGTGATT
31707524 TAATTCGGG
1 TAATTCGGG
*
31707533 TAATTTGGG
1 TAATTCGGG
31707542 TAATTTTCGGG
1 TAA--TTCGGG
31707553 TAATTTTCGGG
1 TAA--TTCGGG
31707564 TAATTCGGG
1 TAATTCGGG
31707573 TAATTCGGG
1 TAATTCGGG
*
31707582 TAAGTCGGG
1 TAATTCGGG
31707591 TAATTCGGG
1 TAATTCGGG
*
31707600 TAAGTCGGG
1 TAATTCGGG
31707609 TAATTCGGG
1 TAATTCGGG
*
31707618 TAAGTCGGG
1 TAATTCGGG
*
31707627 TAAGTCGGG
1 TAATTCGGG
31707636 TAATT
1 TAATT
31707641 TTTAACCAAA
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
9 79 0.81
11 19 0.19
ACGTcount: A:0.22, C:0.09, G:0.34, T:0.34
Consensus pattern (9 bp):
TAATTCGGG
Found at i:31707555 original size:11 final size:11
Alignment explanation
Indices: 31707527--31707577 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
31707517 AGTGATTTAA
31707527 TTCGGGTAA-T
1 TTCGGGTAATT
31707537 TT-GGGTAATT
1 TTCGGGTAATT
31707547 TTCGGGTAATT
1 TTCGGGTAATT
31707558 TTCGGGTAA--
1 TTCGGGTAATT
31707567 TTCGGGTAATT
1 TTCGGGTAATT
31707578 CGGGTAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 15 0.41
10 5 0.14
11 17 0.46
ACGTcount: A:0.20, C:0.08, G:0.29, T:0.43
Consensus pattern (11 bp):
TTCGGGTAATT
Found at i:31707763 original size:28 final size:28
Alignment explanation
Indices: 31707703--31707763 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
31707693 TTATTAACTG
* ** *
31707703 AAAAAAATTTTGATTCGGTTAATTTTTT
1 AAAAAAAATTTGATTCGGTTAATGGTTA
* *
31707731 TAAAAAAATTTGGTTCGGTTAATGGTTA
1 AAAAAAAATTTGATTCGGTTAATGGTTA
31707759 AAAAA
1 AAAAA
31707764 TTTGGGAGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (28 bp):
AAAAAAAATTTGATTCGGTTAATGGTTA
Found at i:31710396 original size:19 final size:20
Alignment explanation
Indices: 31710353--31710401 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
31710343 TGAAAATAAA
*
31710353 ATTTT-TTTTCTATTATTATT
1 ATTTTATTTT-TACTATTATT
31710373 A-TTTATTTTTACTATT-TT
1 ATTTTATTTTTACTATTATT
31710391 ATTTTATTTTT
1 ATTTTATTTTT
31710402 GTAGGAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 18 0.69
20 5 0.19
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTATTTTTACTATTATT
Found at i:31714073 original size:13 final size:13
Alignment explanation
Indices: 31714057--31714083 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31714047 CCTACTTGTG
31714057 TCATGGTTCACAT
1 TCATGGTTCACAT
31714070 TCATGGTTCACAT
1 TCATGGTTCACAT
31714083 T
1 T
31714084 TAAGACTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (13 bp):
TCATGGTTCACAT
Found at i:31715131 original size:28 final size:28
Alignment explanation
Indices: 31715086--31715142 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
31715076 AAAAGTGTCC
31715086 ATACTTTAAGCAATGTACAAATACTTTA
1 ATACTTTAAGCAATGTACAAATACTTTA
* *
31715114 ATACTTTAAGTGAA-GTACAGATACTTTA
1 ATACTTTAAG-CAATGTACAAATACTTTA
31715142 A
1 A
31715143 GTAAACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (28 bp):
ATACTTTAAGCAATGTACAAATACTTTA
Found at i:31715232 original size:12 final size:12
Alignment explanation
Indices: 31715211--31715244 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
31715201 CCAAAAATTG
*
31715211 TAGAGATTGATT
1 TAGAGGTTGATT
31715223 TAGAGGTTGATT
1 TAGAGGTTGATT
31715235 TAGAGGTTGA
1 TAGAGGTTGA
31715245 ATTAAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (12 bp):
TAGAGGTTGATT
Found at i:31719346 original size:193 final size:191
Alignment explanation
Indices: 31719011--31719386 Score: 490
Period size: 193 Copynumber: 2.0 Consensus size: 191
31719001 GTAATCTATA
* * **
31719011 ATGGGTTTAAGTCATTGATTTTCATTTGTAGCTTTGTGATTAAAACACAATTATTACTTGAATGG
1 ATGGGTTCAAGTCATTGATTTTCATTTGTAACTTTGTGATTAAAACACAACAATTACTTGAATGG
* * * * * *
31719076 AAATGCATTTGCATTTGTGTATCCTGCAATGCTTTTTAATTGAACTTTGGGGTTGGAATTGTTAT
66 AAATGCACTTGCATTTGTATATCCTGCAAAGCTTTTTAA-TCAACTTTGGAGTTGAAATTGTTAT
* *
31719141 TAGGAAGTAATTGATGTTTTTATGT-TGATGTTAATGAATACAATAGACTAAGTTGAATTTTTT
130 TAGGAAGTAATTGATGTTTTT-T-TATGATGTTAATGAACACAATAGACCAAGTTGAATTTTTT
* * *
31719204 ATGGGTTCGAGTCATTGGTTTTCATTTG-AACTTTGTGATTACAACACAACAATTTACTTGAATG
1 ATGGGTTCAAGTCATTGATTTTCATTTGTAACTTTGTGATTAAAACACAACAA-TTACTTGAATG
**
31719268 GAAATGCACTTGTGTTT-TCATATCCTGCAAAGCTTCTTTAGA-CAACTTTGGAGTTGAAATTGT
65 GAAATGCACTTGCATTTGT-ATATCCTGCAAAGCTT-TTTA-ATCAACTTTGGAGTTGAAATTGT
* *
31719331 TATTAGGATGTAATTGATGTTTTTTTATGATGTTAATGAACATAATAGACCAAGTT
127 TATTAGGAAGTAATTGATGTTTTTTTATGATGTTAATGAACACAATAGACCAAGTT
31719387 TGGGACCTTT
Statistics
Matches: 159, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
191 1 0.01
192 48 0.30
193 105 0.66
194 4 0.03
195 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (191 bp):
ATGGGTTCAAGTCATTGATTTTCATTTGTAACTTTGTGATTAAAACACAACAATTACTTGAATGG
AAATGCACTTGCATTTGTATATCCTGCAAAGCTTTTTAATCAACTTTGGAGTTGAAATTGTTATT
AGGAAGTAATTGATGTTTTTTTATGATGTTAATGAACACAATAGACCAAGTTGAATTTTTT
Found at i:31720421 original size:16 final size:17
Alignment explanation
Indices: 31720382--31720428 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
31720372 CTAAAATCGG
31720382 AATGTTTTTTAAATCCA
1 AATGTTTTTTAAATCCA
* *
31720399 AAT-TTTTTTAATTGC-
1 AATGTTTTTTAAATCCA
*
31720414 AATGTTTTATAAATC
1 AATGTTTTTTAAATC
31720429 GGAATAGTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 3 0.12
16 18 0.75
17 3 0.12
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (17 bp):
AATGTTTTTTAAATCCA
Found at i:31721078 original size:11 final size:12
Alignment explanation
Indices: 31721061--31721089 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
31721051 ATTCTCAAAT
31721061 CATTAAGAACAA
1 CATTAAGAACAA
31721073 -ATTAAGAACAA
1 CATTAAGAACAA
31721084 CATTAA
1 CATTAA
31721090 ATGCGAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (12 bp):
CATTAAGAACAA
Found at i:31724201 original size:28 final size:29
Alignment explanation
Indices: 31724169--31724223 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
31724159 ATATATATCT
*
31724169 CCGGTACAGAGTACCTA-AAATTGTAACA
1 CCGGTACAGAGTACCTAGAAACTGTAACA
*
31724197 CCGGTACATAGTACCTAGAAACTGTAA
1 CCGGTACAGAGTACCTAGAAACTGTAA
31724224 TCATCGACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (29 bp):
CCGGTACAGAGTACCTAGAAACTGTAACA
Found at i:31730850 original size:12 final size:12
Alignment explanation
Indices: 31730833--31730857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31730823 AATGATCATC
31730833 ATAATAATAATG
1 ATAATAATAATG
31730845 ATAATAATAATG
1 ATAATAATAATG
31730857 A
1 A
31730858 AATGTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:31730854 original size:18 final size:18
Alignment explanation
Indices: 31730816--31730855 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31730806 AATTAAACAC
* *
31730816 TAATAAAAATGATCATCA
1 TAATAAAAATGATAATAA
*
31730834 TAATAATAATGATAATAA
1 TAATAAAAATGATAATAA
31730852 TAAT
1 TAAT
31730856 GAAATGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (18 bp):
TAATAAAAATGATAATAA
Found at i:31742242 original size:16 final size:15
Alignment explanation
Indices: 31742208--31742249 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
31742198 AAAAGGGTTG
*
31742208 TAAAAATAAACAAACA
1 TAAAAATAAA-AAAAA
31742224 TAAAAATAAAATAAAA
1 TAAAAATAAAA-AAAA
31742240 T-AAAATAAAA
1 TAAAAATAAAA
31742250 CACAAGAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAATAAAAAAAA
Found at i:31743527 original size:90 final size:90
Alignment explanation
Indices: 31743413--31743594 Score: 319
Period size: 90 Copynumber: 2.0 Consensus size: 90
31743403 TGACCAAATG
* *
31743413 AGCACTTTCAAACTTAATCATGCTTCAACCTTTTTCCCTTTTGCACACAATGAGATATGAGCTCA
1 AGCACTTTCAAACTTAATCATGCTTCAACCTTTTTCCCTCTTGCACACAATGAGAAATGAGCTCA
31743478 TTTAGAGTCTATTTCTCCTTTTGAC
66 TTTAGAGTCTATTTCTCCTTTTGAC
* * *
31743503 AGCACTTTCAGACTTAATCATGCTTCAACCTTTTTTCCTCTTGCACACAATGAGAAATGAGTTCA
1 AGCACTTTCAAACTTAATCATGCTTCAACCTTTTTCCCTCTTGCACACAATGAGAAATGAGCTCA
31743568 TTTAGAGTCTATTTCTCCTTTTGAC
66 TTTAGAGTCTATTTCTCCTTTTGAC
31743593 AG
1 AG
31743595 TTGTAACTTA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (90 bp):
AGCACTTTCAAACTTAATCATGCTTCAACCTTTTTCCCTCTTGCACACAATGAGAAATGAGCTCA
TTTAGAGTCTATTTCTCCTTTTGAC
Found at i:31745885 original size:21 final size:22
Alignment explanation
Indices: 31745861--31745909 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
31745851 GTAAATTAAA
*
31745861 ATTTTAAA-A-TATATTTTGTAT
1 ATTTTAAAGACTATATTATG-AT
*
31745882 ATTTAAAAGACTATATTATGAT
1 ATTTTAAAGACTATATTATGAT
31745904 ATTTTA
1 ATTTTA
31745910 GAACTGTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
23 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (22 bp):
ATTTTAAAGACTATATTATGAT
Found at i:31757275 original size:159 final size:153
Alignment explanation
Indices: 31756986--31757347 Score: 413
Period size: 159 Copynumber: 2.3 Consensus size: 153
31756976 ATGAAATTCG
* * * * * * **
31756986 ATCAGTTCTTGATACATGTATTCAACTCAGCCTCAACACATATATATAATGAAAGTTTATCATCT
1 ATCAGTTCATGATACATGCATTCAGCTCAGCCTCAGCACATATTTGTTGTGAAAGTTTATCATCT
* * * * *
31757051 TTATGCAGACGTTGATGTTGTCAAGCCTTCTTCCATCTTCCATCCGACCATGGTTGATCACGGAT
66 TTATGCAGACATTAATGATGTCAAGCCTACTCCCATCTTCCATCCGACCATGGTTGATCACGGAT
31757116 TTGATTTCCGCACTCAACGGCACATATCC
131 TTGATTTCCG---T-AA--GCACATATCC
* * *
31757145 ATCAGTTCATGAGACATGCATTCAGCTCAGCCTCAGCACATATTTGTTGTGAAATTTTTTCATCT
1 ATCAGTTCATGATACATGCATTCAGCTCAGCCTCAGCACATATTTGTTGTGAAAGTTTATCATCT
* * * **
31757210 TTATGCA-ACCATTAATGATGTCGATCCTACTCCCA-CTTCCAGTCTGACCATGGTTGATTGCGG
66 TTATGCAGA-CATTAATGATGTCAAGCCTACTCCCATCTTCCA-TCCGACCATGGTTGATCACGG
*
31757273 ATTTGATTTCCGTGAGCACATATCC
129 ATTTGATTTCCGTAAGCACATATCC
* **
31757298 ATCATTTCATGATACATGCATTCAGCAAAGCCTCAGCACATATTTGTTGT
1 ATCAGTTCATGATACATGCATTCAGCTCAGCCTCAGCACATATTTGTTGT
31757348 CCATAACCTT
Statistics
Matches: 175, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
153 56 0.32
155 1 0.01
156 1 0.01
158 7 0.04
159 110 0.63
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (153 bp):
ATCAGTTCATGATACATGCATTCAGCTCAGCCTCAGCACATATTTGTTGTGAAAGTTTATCATCT
TTATGCAGACATTAATGATGTCAAGCCTACTCCCATCTTCCATCCGACCATGGTTGATCACGGAT
TTGATTTCCGTAAGCACATATCC
Found at i:31758296 original size:12 final size:12
Alignment explanation
Indices: 31758279--31758303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31758269 CGATTGGACT
31758279 TAAATTTTAAAA
1 TAAATTTTAAAA
31758291 TAAATTTTAAAA
1 TAAATTTTAAAA
31758303 T
1 T
31758304 CCGAAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATTTTAAAA
Found at i:31759891 original size:18 final size:19
Alignment explanation
Indices: 31759870--31759905 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31759860 TGATAACCTA
*
31759870 TAATCTATTTA-TAATATG
1 TAATCTATCTATTAATATG
31759888 TAATCTATCTATTAATAT
1 TAATCTATCTATTAATAT
31759906 ATATATATAT
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:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (19 bp):
TAATCTATCTATTAATATG
Found at i:31776431 original size:110 final size:113
Alignment explanation
Indices: 31776227--31776458 Score: 330
Period size: 116 Copynumber: 2.1 Consensus size: 113
31776217 AAATATAAAA
* * * * *
31776227 TTTTTGGGTCAAAATTAAAATGCTTAAATTAAATTAGTACTTTTTTGAGGGGCCAAATTAAAAAA
1 TTTTGGGGCCAAAATTAAAATGCTTAAATTAAATTACTACTTTTTTGAGGAGACAAATT--AAAA
*
31776292 AAAAATTATTTGACCGAAGTCTAAAAAAGGTTAAATTGAATTTTTTTTAAG
64 AAAAATTATTTGACCAAAGTCTAAAAAAGGTTAAATTGAA-TTTTTTTAAG
*
31776343 TTTTGGGGCCAAAGTTAAAATGCTTAAATTAAATTACTAC-TTTTT-A-GAGAC-AATT-AAAAA
1 TTTTGGGGCCAAAATTAAAATGCTTAAATTAAATTACTACTTTTTTGAGGAGACAAATTAAAAAA
31776403 AAATTCATTTGACCAAAGTCTAAAAAAGGTTAAATTGAATTTTTTTAAG
66 AAATT-ATTTGACCAAAGTCTAAAAAAGGTTAAATTGAATTTTTTTAAG
31776452 TTTTGGG
1 TTTTGGG
31776459 AGGGGCTAGA
Statistics
Matches: 108, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
109 27 0.25
110 32 0.30
112 4 0.04
113 3 0.03
114 1 0.01
115 5 0.05
116 36 0.33
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.37
Consensus pattern (113 bp):
TTTTGGGGCCAAAATTAAAATGCTTAAATTAAATTACTACTTTTTTGAGGAGACAAATTAAAAAA
AAATTATTTGACCAAAGTCTAAAAAAGGTTAAATTGAATTTTTTTAAG
Found at i:31779066 original size:19 final size:19
Alignment explanation
Indices: 31779039--31779089 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
31779029 AAAGCTTTAT
* *
31779039 TTTAATATTTTTCATAAGC
1 TTTACTATTTTTCACAAGC
*
31779058 TTTACTATTATTACACAAGC
1 TTTACTATT-TTTCACAAGC
*
31779078 TTTTCT-TTTTTC
1 TTTACTATTTTTC
31779090 TTTAACTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 3 0.12
19 10 0.38
20 13 0.50
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTACTATTTTTCACAAGC
Found at i:31783670 original size:10 final size:10
Alignment explanation
Indices: 31783655--31783679 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31783645 ATTTTTATTG
31783655 AATTAAATAT
1 AATTAAATAT
31783665 AATTAAATAT
1 AATTAAATAT
31783675 AATTA
1 AATTA
31783680 TTTAACATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTAAATAT
Found at i:31784862 original size:20 final size:17
Alignment explanation
Indices: 31784830--31784880 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
31784820 CCGTTTCTCT
*
31784830 TTTTAAATATTTTTATAA
1 TTTTAAAT-TTTTAATAA
31784848 TGTTTTATAATTTTTAATAA
1 --TTTTA-AATTTTTAATAA
31784868 TTTTAAATTTTTA
1 TTTTAAATTTTTA
31784881 TACCATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.28
18 5 0.17
20 13 0.45
21 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTTTAATAA
Found at i:31785170 original size:13 final size:13
Alignment explanation
Indices: 31785146--31785191 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
31785136 CACTTAAACC
31785146 TATTTA-AATTAA
1 TATTTATAATTAA
31785158 TATTTATAATTAA
1 TATTTATAATTAA
*
31785171 -ATTT-TAAATAAA
1 TATTTAT-AATTAA
31785183 TATTTATAA
1 TATTTATAA
31785192 ATTATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 1 0.03
12 15 0.52
13 12 0.41
14 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTTATAATTAA
Found at i:31795720 original size:30 final size:30
Alignment explanation
Indices: 31795684--31795798 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
31795674 ACTTTTCTCA
*
31795684 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
31795714 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
31795744 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
31795774 ACTAGCCACACATTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
31795799 CTTGTACCTA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.26, C:0.49, G:0.03, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:31796415 original size:25 final size:25
Alignment explanation
Indices: 31796387--31796530 Score: 87
Period size: 25 Copynumber: 5.6 Consensus size: 25
31796377 ATATTACGTA
* *
31796387 TATATATATTTTATACTATTTTATT
1 TATATATATTTAATACTATATTATT
* *
31796412 TATATATCTTTAATATTATATTATT
1 TATATATATTTAATACTATATTATT
* * *
31796437 TATATATATATT-TTTCTACATGTTATCT
1 TATATATAT-TTAATACT--ATATTAT-T
*
31796465 TATGTATATATCTT-A-ACTATATTATG
1 TA--TATATAT-TTAATACTATATTATT
* * *
31796491 TATATATTTTTAACACTATATTATG
1 TATATATATTTAATACTATATTATT
* *
31796516 TACATATTTTTAATA
1 TATATATATTTAATA
31796531 TTATCACGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
23 2 0.02
24 7 0.07
25 55 0.59
26 4 0.04
27 12 0.13
28 3 0.03
29 2 0.02
30 9 0.10
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (25 bp):
TATATATATTTAATACTATATTATT
Found at i:31796697 original size:8 final size:8
Alignment explanation
Indices: 31796679--31796730 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
31796669 TAATTATTAT
*
31796679 TATTCTAA
1 TATTTTAA
*
31796687 TATTTTGA
1 TATTTTAA
31796695 TATTTTAA
1 TATTTTAA
31796703 TA-TTTAA
1 TATTTTAA
31796710 TATTTTATA
1 TATTTTA-A
*
31796719 TATTTTAT
1 TATTTTAA
31796727 TATT
1 TATT
31796731 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:31796721 original size:24 final size:24
Alignment explanation
Indices: 31796679--31796731 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
31796669 TAATTATTAT
31796679 TATTCTAATATTTTGATATTTTAA
1 TATTCTAATATTTTGATATTTTAA
* *
31796703 TATT-TAATATTTTATATATTTTAT
1 TATTCTAATATTTT-GATATTTTAA
31796727 TATTC
1 TATTC
31796732 ACATCATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTCTAATATTTTGATATTTTAA
Found at i:31799909 original size:50 final size:51
Alignment explanation
Indices: 31799809--31799912 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
31799799 ACTGTCGAGG
*
31799809 GAGAAGAAGACATTGTCGTTCTATCTCTGCTGATGCGCCATACCTTGAAGT
1 GAGAAGAAGACATTGTCGATCTATCTCTGCTGATGCGCCATACCTTGAAGT
* *
31799860 GAGAAGAAGACA-TGTCGATCTTATCTCTGCTGATTCGTCA-ACCTTGAAGT
1 GAGAAGAAGACATTGTCGATC-TATCTCTGCTGATGCGCCATACCTTGAAGT
31799910 GAG
1 GAG
31799913 CAAAGACGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 20 0.41
51 29 0.59
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (51 bp):
GAGAAGAAGACATTGTCGATCTATCTCTGCTGATGCGCCATACCTTGAAGT
Found at i:31800095 original size:59 final size:58
Alignment explanation
Indices: 31800004--31800117 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 58
31799994 GCCTAAATTA
*
31800004 TCGAGAAATACTAGAATGGGTGTCAAGTTGACTGTAGGAAGGGGAGCTCGAGTGATTG
1 TCGAGAAATACTAGAATGGGTGTCAAATTGACTGTAGGAAGGGGAGCTCGAGTGATTG
31800062 TCGAGAAAATACTAGAATGGGTGTCAAATTGACTGTAGGAAGGGGAGCTCGAGTGA
1 TCGAG-AAATACTAGAATGGGTGTCAAATTGACTGTAGGAAGGGGAGCTCGAGTGA
31800118 GAAGAGGTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 5 0.09
59 49 0.91
ACGTcount: A:0.32, C:0.11, G:0.35, T:0.23
Consensus pattern (58 bp):
TCGAGAAATACTAGAATGGGTGTCAAATTGACTGTAGGAAGGGGAGCTCGAGTGATTG
Found at i:31801543 original size:159 final size:158
Alignment explanation
Indices: 31801254--31802177 Score: 493
Period size: 162 Copynumber: 5.9 Consensus size: 158
31801244 GAACGGTCAC
* * ** * *
31801254 AAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACACTGAGGTAATTTCAATTTCA
** * * * *
31801319 TTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCTCGGCTCACATGCTGAGGTCTTTTC
66 TCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCTCGACTCACA-GCTGAGGTATTTTC
31801384 AATTTCTCTTCAATTTCTGTTTTAATTCA
130 AATTTCTCTTCAATTTCTGTTTTAATTCA
* * * *
31801413 AAAATCAACTCATATTGTGAGAGGTGAGTTGAACCTCAAGTCACAATTGAGGTATTTTCAATTT-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC-ACTGAGGTAATTTCAATTTC
*
31801477 ATCATCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC-C-C-GTTGAGGTAT
65 ATCATC-AAAAATCAACTCATATTGCGAGAGGTGAGTTG-ACCTC--GACTCACAGCTGAGGTAT
*
31801539 TTTCAA------TT---TTTGTGTTTTAATT--
126 TTTCAATTTCTCTTCAATTTCTGTTTTAATTCA
* * * *
31801561 ----TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGCTGAGGTATTTTTCAATTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACACTGAGGTA-ATTTCAA-TTT
* *
31801621 CGTTTTTTAATTTATGTTTCAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-A-
64 C--------A-TCA----TC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGA-CCTCGAC
** * *
31801684 AGAC-GCTGA-G-----T-AA----T-TTCAATTTTTG-TTT--GTC-
111 TCACAGCTGAGGTATTTTCAATTTCTCTTCAATTTCTGTTTTAATTCA
* * * ** *
31801715 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTGGTTTTAATTT-A
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACACTGAGGTAATTTCAATTTCA
* * * *
31801779 TGTTCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCT-TAGCTCACAAGCTGAGGTA
66 ---TCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA-CCTCGA-CTCAC-AGCTGAGGTA
*
31801843 TTTTCAATTTCTGGTTTTCAATTTCTG-TTT--TTCA
125 TTTTCAATTTC---TCTTCAATTTCTGTTTTAATTCA
* * ** *
31801877 AAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACACTGAGGTAATTTCAATTTC-
* ** * * *
31801942 GTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTT
65 -ATCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA-CCTCGACTCACA-GCTGAGGTATT
* * * *
31802007 TTCAATTTCTGTTCTTTAATTTTTGTTCGTAA--AA
127 TTCAATTTC---TCTTCAATTTCTGTT-TTAATTCA
* * * *
31802041 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACACTGAGGTAATTTCAATTTC-
* ** * * ** * ** *
31802106 GTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACAC-GTTGAGGTATTTT
65 ATCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA-CCTCGACTCACAGCTGAGGTATTTT
31802170 CAATTTCT
129 CAATTTCT
31802178 GTTTTCAAAA
Statistics
Matches: 618, Mismatches: 78, Indels: 139
0.74 0.09 0.17
Matches are distributed among these distances:
142 41 0.07
143 8 0.01
144 39 0.06
146 7 0.01
147 1 0.00
148 1 0.00
150 16 0.03
152 3 0.00
153 9 0.01
154 2 0.00
155 3 0.00
156 5 0.01
157 3 0.00
158 48 0.08
159 69 0.11
160 49 0.08
161 75 0.12
162 133 0.22
163 43 0.07
164 63 0.10
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (158 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACACTGAGGTAATTTCAATTTCA
TCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCTCGACTCACAGCTGAGGTATTTTCA
ATTTCTCTTCAATTTCTGTTTTAATTCA
Found at i:31801546 original size:71 final size:72
Alignment explanation
Indices: 31801412--31801619 Score: 249
Period size: 72 Copynumber: 2.9 Consensus size: 72
31801402 GTTTTAATTC
* * **
31801412 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAACCTCAAGTCACAATTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC-CCGTTGAGGTATTTTCAATTT
31801477 AT-CATCA
65 ATGCATCA
*
31801484 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGGTATTTTCAATTTA
** **
31801549 TGTGTTT
66 TGCATCA
* ** * * *
31801556 TAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA-CCGCTGAGGTATTTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGGTA-TTTTCAATTT
31801620 TCGTTTTTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
71 30 0.25
72 89 0.75
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGGTATTTTCAATTTA
TGCATCA
Found at i:31801743 original size:69 final size:72
Alignment explanation
Indices: 31801645--31801852 Score: 233
Period size: 69 Copynumber: 2.9 Consensus size: 72
31801635 TGTTTCAAAA
* * *
31801645 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCA-AGACGCTGA-GTAATTTCAATTTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTAATTTCAATTTAT
**
31801708 GTTTGTC
66 GTTCATC
** *
31801715 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTGGTTTTAATTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGCTGAGGTAATTTCAATTTA
31801779 TGTTCATC
65 TGTTCATC
* * * * * *
31801787 AAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTAGCTCACAAGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG---ACACGCTGAGGTAATTTCAATT
31801852 T
63 T
31801853 CTGGTTTTCA
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
69 37 0.32
71 8 0.07
72 17 0.15
73 34 0.30
75 19 0.17
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTAATTTCAATTTAT
GTTCATC
Found at i:31801777 original size:158 final size:160
Alignment explanation
Indices: 31801483--31801777 Score: 454
Period size: 158 Copynumber: 1.9 Consensus size: 160
31801473 ATTTATCATC
* * *
31801483 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCAAGA-CCGCTGAGGTAATTTCAATTT
* ** *
31801548 TTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGCTGAGGTATTTT
65 TTGTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGCTGAGGTAGTTT
31801613 TCAATTTTCGTTTTTTAATTTATGTTTCAAA
130 TCAATTTTCGTTTTTTAATTTATGTTTCAAA
*
31801644 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGA-CGCTGA-GTAATTTCAATTTT
1 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCAAGACCGCTGAGGTAATTTCAATTTT
*
31801707 TGT-TTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTGGTT
66 TGTGTT-TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGCTGAGGTAGTT
31801771 TT-AATTT
129 TTCAATTT
31801778 ATGTTCATCA
Statistics
Matches: 123, Mismatches: 9, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
157 2 0.02
158 62 0.50
159 18 0.15
161 41 0.33
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (160 bp):
AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCAAGACCGCTGAGGTAATTTCAATTTT
TGTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGCTGAGGTAGTTTT
CAATTTTCGTTTTTTAATTTATGTTTCAAA
Found at i:31801805 original size:73 final size:70
Alignment explanation
Indices: 31801625--31801823 Score: 229
Period size: 69 Copynumber: 2.8 Consensus size: 70
31801615 AATTTTCGTT
** * *
31801625 TTTTAATTTATGTTTCAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACGC
1 TTTTAATTTATG-TTC-ATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACGC
31801690 TGAGTAA
64 TGAGTAA
* * **
31801697 TTTCAATTTTTGTTTGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA--ACACGC
**
31801761 TGAGGTGG
64 TGA-GTAA
* * *
31801769 TTTTAATTTATGTTCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCT
1 TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
31801824 TAGCTCACAA
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
69 37 0.35
71 10 0.09
72 26 0.25
73 33 0.31
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (70 bp):
TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACGCTG
AGTAA
Found at i:31801862 original size:14 final size:14
Alignment explanation
Indices: 31801843--31801877 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
31801833 AGCTGAGGTA
31801843 TTTTCAATTTCTGG
1 TTTTCAATTTCTGG
*
31801857 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
31801871 TTTTCAA
1 TTTTCAA
31801878 AAATCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:31801977 original size:73 final size:74
Alignment explanation
Indices: 31801858--31802019 Score: 245
Period size: 73 Copynumber: 2.2 Consensus size: 74
31801848 AATTTCTGGT
* * *
31801858 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GACACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACG
31801922 CTGAGGTAA
66 CTGAGGTAA
* *
31801931 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-CACAC
**
31801996 GCTGAGGTCT
65 GCTGAGGTAA
31802006 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
31802020 CTTTAATTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
73 55 0.69
75 25 0.31
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (74 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACG
CTGAGGTAA
Found at i:31801994 original size:162 final size:160
Alignment explanation
Indices: 31801697--31802306 Score: 690
Period size: 162 Copynumber: 3.8 Consensus size: 160
31801687 CGCTGAGTAA
***
31801697 TTTCAATTTTTGTTT-GTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTTTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
** * * * * * *
31801761 TGAGGTGGTTTTAATTTATGTTCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTA
66 TGAGGTAATTTCAATTTCTGTT-TTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
31801826 GCTCACAAGCTGAGGTATTTTCAATTTCTGGT
130 GCTCACAAGCTGAGGTATTTTCAATTTCT-GT
* *** * *
31801858 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
1 TTTCAATTTTTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
31801923 TGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
66 TGAGGTAATTTCAATTTCTGTTT-TCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* *
31801988 GCTCACATGCTGAGGTCTTTTCAATTTCTGT
130 GCTCACAAGCTGAGGTATTTTCAATTTCTGT
* *
31802019 TCTTTAATTTTTGTTCGTAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACA
1 T-TTCAATTTTTGTT--TAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* **
31802084 CGCTGAGGTAATTTCAATTTCTGTTTTC-AAAATTCAACTTATATTGCGAGAAATGAGTTGAGCC
63 CGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATT-AACTCATATTGCGAGAGGTGAGTTGAGCC
* *
31802148 TCAAG---ACACGTTGAGGTATTTTCAATTTCTGT
127 TC-AGCTCACAAGCTGAGGTATTTTCAATTTCTGT
* *
31802180 TTTCAA--------AAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACA
1 TTTCAATTTTTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
* * * *
31802236 TGCTGAGGTATTTTCAATTTCTGTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
63 CGCTGAGGTAATTTCAATTTCTGTTTT---CAAAAATTAACTCATATTGCGAGAGGTGAGTTGAG
*
31802301 CTTCAG
125 CCTCAG
31802307 ATTACACACT
Statistics
Matches: 391, Mismatches: 44, Indels: 35
0.83 0.09 0.07
Matches are distributed among these distances:
149 2 0.01
150 39 0.10
152 28 0.07
154 2 0.01
155 27 0.07
156 5 0.01
160 4 0.01
161 42 0.11
162 143 0.37
163 30 0.08
164 69 0.18
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (160 bp):
TTTCAATTTTTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTCTGTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
CTCACAAGCTGAGGTATTTTCAATTTCTGT
Found at i:31802222 original size:78 final size:75
Alignment explanation
Indices: 31802037--31802306 Score: 341
Period size: 72 Copynumber: 3.6 Consensus size: 75
31802027 TTTTGTTCGT
* * * *
31802037 AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
1 AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTACACGCTGAGGTATTTTCAAT
31802102 TTCTGTTTT-
66 TTCTGTTTTA
* * ** *
31802111 --CAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGTTGAGGTATTTTCAA
1 AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-AGTACACGCTGAGGTATTTTCAA
31802173 TTTCTGTTTTCAAA
65 TTTCTGTTTT---A
* *
31802187 AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCA
1 AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAG-T-ACACGCTGAGGTATTTTCA
31802252 ATTTCTGTTTTA
64 ATTTCTGTTTTA
* *
31802264 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAG
31802307 ATTACACACT
Statistics
Matches: 168, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
72 61 0.36
73 2 0.01
77 42 0.25
78 35 0.21
80 28 0.17
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (75 bp):
AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTACACGCTGAGGTATTTTCAAT
TTCTGTTTTA
Found at i:31802541 original size:72 final size:73
Alignment explanation
Indices: 31802460--31802601 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 73
31802450 TCAAAATCAG
* * *
31802460 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTG-TGTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
31802524 AATTTCAA
66 AATTTCAA
* *
31802532 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
31802597 AATTT
66 AATTT
31802602 ATGTTTTAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 54 0.84
73 10 0.16
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (73 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
AATTTCAA
Found at i:31802714 original size:71 final size:72
Alignment explanation
Indices: 31802612--31802821 Score: 251
Period size: 73 Copynumber: 2.9 Consensus size: 72
31802602 ATGTTTTAAA
* * *
31802612 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCA-AGACGCTGAGGTAATTTCAATTTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTAATTTCAATTTAT
**
31802676 GTTTGTC
66 GTTCATC
** *
31802683 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTGGTTTTAATTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGCTGAGGTAATTTCAATTTA
31802748 TGTTCATC
65 TGTTCATC
* * * ** *
31802756 AAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-T--CAGACACGCTGAGGTAATTTCAATT
31802821 T
63 T
31802822 CTGGTTTTCA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
71 38 0.32
73 58 0.49
74 1 0.01
75 20 0.17
76 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTAATTTCAATTTAT
GTTCATC
Found at i:31802758 original size:73 final size:71
Alignment explanation
Indices: 31802593--31802792 Score: 256
Period size: 73 Copynumber: 2.8 Consensus size: 71
31802583 ATTTTCGTTT
** * *
31802593 TTTTAATTTATGTTTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACGCT
1 TTTTAATTTATG-TTTATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACGCT
31802658 GAGGTAA
65 GAGGTAA
* * *
31802665 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTTAATTTATGTTTATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA--ACACGC
**
31802730 TGAGGTGG
64 TGAGGTAA
* * * *
31802738 TTTTAATTTATGTTCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCT
1 TTTTAATTTATGTTTATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
31802793 TGGCTCACAC
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
71 41 0.37
72 10 0.09
73 59 0.54
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (71 bp):
TTTTAATTTATGTTTATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACGCTG
AGGTAA
Found at i:31802831 original size:14 final size:14
Alignment explanation
Indices: 31802812--31802846 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
31802802 CGCTGAGGTA
31802812 TTTTCAATTTCTGG
1 TTTTCAATTTCTGG
*
31802826 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
31802840 TTTTCAA
1 TTTTCAA
31802847 AAATCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:31802883 original size:162 final size:163
Alignment explanation
Indices: 31802665--31802995 Score: 454
Period size: 162 Copynumber: 2.0 Consensus size: 163
31802655 GCTGAGGTAA
*
31802665 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
** * ** * *
31802730 TGAGGTGGTTTTAATTTATG-T-TCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCT
66 TGAGGTAATTTCAATTTATGTTGTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
* *
31802793 -TGGCTCACACGCTGAGGTA-TTTTCAATTTCTGGT
131 CAGG---ACACGCTGAGGTATTTTTAAATTTCTGGT
* * *
31802827 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* * *
31802892 TGAGGTAATTTCAATTTTTGTTGTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
66 TGAGGTAATTTCAATTTATGTTGTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
*
31802957 CAGGACACGCTGAGGTATTTTTAAATTTCTGTT
131 CAGGACACGCTGAGGTATTTTTAAATTTCTGGT
31802990 TTTCAA
1 TTTCAA
31802996 AAATCAACTC
Statistics
Matches: 148, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
162 90 0.61
163 20 0.14
164 36 0.24
165 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (163 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTATGTTGTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
CAGGACACGCTGAGGTATTTTTAAATTTCTGGT
Found at i:31802948 original size:75 final size:74
Alignment explanation
Indices: 31802831--31803030 Score: 285
Period size: 75 Copynumber: 2.7 Consensus size: 74
31802821 TCTGGTTTTC
** * *
31802831 AATTTCTGTTTTTCAAAAATCGACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
31802896 GTA-ATTTC
66 GTATATTTA
*
31802904 AATTTTTGTTGTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
1 AATTTCTGTT-TT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
31802969 AGGTATTTTTA
64 AGGTATATTTA
** *
31802980 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCT
1 AATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
31803031 TGGGTTCACA
Statistics
Matches: 113, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
73 9 0.08
74 38 0.34
75 54 0.48
76 12 0.11
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (74 bp):
AATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTATATTTA
Found at i:31803778 original size:30 final size:30
Alignment explanation
Indices: 31803742--31803856 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
31803732 ACATTTCTCA
*
31803742 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
31803772 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
31803802 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
31803832 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
31803857 CTTGTACCTA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.25, C:0.50, G:0.03, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:31803975 original size:27 final size:25
Alignment explanation
Indices: 31803937--31803987 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
31803927 TTTTGTATAT
31803937 GGGGGGATTTTTTTGGAGAGTTTTA
1 GGGGGGATTTTTTTGGAGAGTTTTA
31803962 GGGGGGATTTTTTTTTGGAGAGTTTT
1 GGGGGGA--TTTTTTTGGAGAGTTTT
31803988 TGGGAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 7 0.29
27 17 0.71
ACGTcount: A:0.14, C:0.00, G:0.39, T:0.47
Consensus pattern (25 bp):
GGGGGGATTTTTTTGGAGAGTTTTA
Found at i:31804468 original size:14 final size:13
Alignment explanation
Indices: 31804449--31804505 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 13
31804439 CGTATATATA
31804449 TATTTATACTATTT
1 TATTTATA-TATTT
31804463 TATTTATATATCTT
1 TATTTATATAT-TT
31804477 TAATATTATAT-TATT
1 T-AT-TTATATAT-TT
*
31804492 TATATATATATTT
1 TATTTATATATTT
31804505 T
1 T
31804506 TCTACATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 11 0.30
14 14 0.38
15 6 0.16
16 6 0.16
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTATATATTT
Found at i:31804562 original size:24 final size:22
Alignment explanation
Indices: 31804519--31804579 Score: 86
Period size: 24 Copynumber: 2.7 Consensus size: 22
31804509 ACATGTTATC
*
31804519 TTATGTATATATCTTAACTATA
1 TTATGTATATATTTTAACTATA
31804541 TTATGTATATATTTTAACACTATA
1 TTATGTATATATTTT-A-ACTATA
*
31804565 TTATGTACATATTTT
1 TTATGTATATATTTT
31804580 TAATATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.40
23 1 0.03
24 20 0.57
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (22 bp):
TTATGTATATATTTTAACTATA
Found at i:31804751 original size:8 final size:8
Alignment explanation
Indices: 31804740--31804778 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
31804730 TATTATTCTA
31804740 ATATTTTT
1 ATATTTTT
*
31804748 ATATTTTA
1 ATATTTTT
31804756 ATA-TTTT
1 ATATTTTT
31804763 ATATTTTAT
1 ATATTTT-T
31804772 ATATTTT
1 ATATTTT
31804779 ATTATTCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 6 0.22
8 13 0.48
9 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
ATATTTTT
Found at i:31804757 original size:16 final size:16
Alignment explanation
Indices: 31804733--31804778 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
31804723 TAATTATTAT
*
31804733 TATTCTAATATTTTTA
1 TATTTTAATATTTTTA
31804749 TATTTTAATA-TTTTA
1 TATTTTAATATTTTTA
31804764 TATTTTATATATTTT
1 TATTTTA-ATATTTT
31804779 ATTATTCACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 12 0.44
16 12 0.44
17 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTAATATTTTTA
Found at i:31804766 original size:7 final size:7
Alignment explanation
Indices: 31804744--31804773 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
31804734 ATTCTAATAT
31804744 TTTTATA
1 TTTTATA
31804751 TTTTAATA
1 TTTT-ATA
31804759 TTTTATA
1 TTTTATA
31804766 TTTTATA
1 TTTTATA
31804773 T
1 T
31804774 ATTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTATA
Found at i:31804779 original size:16 final size:16
Alignment explanation
Indices: 31804740--31804780 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
31804730 TATTATTCTA
31804740 ATAT-TTTTATATTTT
1 ATATATTTTATATTTT
31804755 A-ATATTTTATATTTT
1 ATATATTTTATATTTT
31804770 ATATATTTTAT
1 ATATATTTTAT
31804781 TATTCACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.08
15 13 0.54
16 9 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATATTTTATATTTT
Found at i:31807496 original size:12 final size:12
Alignment explanation
Indices: 31807472--31807550 Score: 55
Period size: 11 Copynumber: 7.0 Consensus size: 12
31807462 TGATTAATAA
*
31807472 AAAATAT-TTTT
1 AAAATATATATT
*
31807483 AAAATATATGTT
1 AAAATATATATT
31807495 -AAATA-ATAATT
1 AAAATATAT-ATT
31807506 -AAA-ATATATT
1 AAAATATATATT
31807516 -AAATATATATT
1 AAAATATATATT
* *
31807527 AAGTATATATATC
1 AA-AATATATATT
31807540 AAAAT-TATATT
1 AAAATATATATT
31807551 TATCTTAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
10 9 0.16
11 31 0.55
12 6 0.11
13 10 0.18
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (12 bp):
AAAATATATATT
Found at i:31807517 original size:21 final size:22
Alignment explanation
Indices: 31807473--31807528 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
31807463 GATTAATAAA
*
31807473 AAATAT-TTTTAAAATATATGTT
1 AAATATATATTAAAATATA-GTT
31807495 AAATA-ATAATTAAAATATA-TT
1 AAATATAT-ATTAAAATATAGTT
31807516 AAATATATATTAA
1 AAATATATATTAA
31807529 GTATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 12 0.40
22 8 0.27
23 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATATATATTAAAATATAGTT
Found at i:31807538 original size:13 final size:11
Alignment explanation
Indices: 31807484--31807536 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
31807474 AATATTTTTA
*
31807484 AAATATATGTT
1 AAATATATATT
31807495 AAATA-ATAATT
1 AAATATAT-ATT
31807506 AAA-ATATATT
1 AAATATATATT
31807516 AAATATATATT
1 AAATATATATT
*
31807527 AAGTATATAT
1 AAATATATAT
31807537 ATCAAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 9 0.24
11 28 0.76
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (11 bp):
AAATATATATT
Found at i:31809453 original size:32 final size:32
Alignment explanation
Indices: 31809407--31809477 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
31809397 TTAAATCTTT
* * * *
31809407 AATTTTTTTTTAAATTTCAATTAGACTTCTCA
1 AATTTTTTTATAAATTTCAATTAAACCTCTAA
*
31809439 AATTTTTTTATAAATTTTAATTAAACCTCTAA
1 AATTTTTTTATAAATTTCAATTAAACCTCTAA
31809471 AATTTTT
1 AATTTTT
31809478 GAAAGTCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.54
Consensus pattern (32 bp):
AATTTTTTTATAAATTTCAATTAAACCTCTAA
Found at i:31809477 original size:31 final size:31
Alignment explanation
Indices: 31809411--31809547 Score: 109
Period size: 31 Copynumber: 4.4 Consensus size: 31
31809401 ATCTTTAATT
* * * * *
31809411 TTTTTTTAAATTTCAATTAGACTTCTCAAAT
1 TTTTTTAAAATTTTAATTAAACCTCTCAAAA
31809442 TTTTTTATAAATTTTAATTAAACCTCT-AAAA
1 TTTTTTA-AAATTTTAATTAAACCTCTCAAAA
* * * *
31809473 TTTTTGAAAGTCTTAATTAAAACTGC-CAAAA
1 TTTTTTAAAATTTTAATTAAACCT-CTCAAAA
* * *
31809504 TTATTTAAAATTCTCATTAAAACC-CTCAAAA
1 TTTTTTAAAATTTTAATT-AAACCTCTCAAAA
*
31809535 TTTTTAAAAATTT
1 TTTTTTAAAATTT
31809548 AGTTAGCTAT
Statistics
Matches: 82, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
30 15 0.18
31 47 0.57
32 20 0.24
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (31 bp):
TTTTTTAAAATTTTAATTAAACCTCTCAAAA
Found at i:31820608 original size:20 final size:21
Alignment explanation
Indices: 31820578--31820627 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
31820568 TAAATTAGTG
31820578 ATTTAAATAATTTTTTAAATA
1 ATTTAAATAATTTTTTAAATA
31820599 ATTT-AATAATTTTTT-AA-A
1 ATTTAAATAATTTTTTAAATA
31820617 A-TTAAATAATT
1 ATTTAAATAATT
31820628 AAAACGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.07
18 9 0.32
19 2 0.07
20 11 0.39
21 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAAATAATTTTTTAAATA
Found at i:31820771 original size:2 final size:2
Alignment explanation
Indices: 31820766--31820800 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31820756 ATATTTCTGT
31820766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31820801 TCCTGTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31821538 original size:6 final size:7
Alignment explanation
Indices: 31821520--31821545 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31821510 TCATGATTCA
31821520 ATTTTTT
1 ATTTTTT
31821527 ATTTTTT
1 ATTTTTT
31821534 ATTTTTT
1 ATTTTTT
31821541 ATTTT
1 ATTTT
31821546 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:31822384 original size:17 final size:17
Alignment explanation
Indices: 31822351--31822383 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31822341 AAAAAGTATT
*
31822351 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
31822368 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
31822384 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:31822389 original size:40 final size:41
Alignment explanation
Indices: 31822332--31822466 Score: 231
Period size: 40 Copynumber: 3.3 Consensus size: 41
31822322 AATTTATTTT
31822332 AAAAA-TTAAAAAAAGTATTTTAAAAATATTTTAAAATT-A
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
31822371 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAA-TTAA
31822413 AAAAATTTAAAAAAAGTATTTTAAAAATA-TTTAAAATTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
*
31822453 AAAAATTTTAAAAA
1 AAAAATTTAAAAAA
31822467 TAAATATATT
Statistics
Matches: 92, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
39 5 0.05
40 48 0.52
41 9 0.10
42 30 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (41 bp):
AAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:31822396 original size:12 final size:11
Alignment explanation
Indices: 31822368--31822448 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
31822358 TATTTTAAAA
31822368 TTAAAAA-ATT
1 TTAAAAATATT
*
31822378 TAAAAAAAGTATT
1 T-TAAAAA-TATT
31822391 TTAAAAATATT
1 TTAAAAATATT
31822402 TT--AAA-A-T
1 TTAAAAATATT
*
31822409 TTAAAAAAATT
1 TTAAAAATATT
*
31822420 TAAAAAAAGTATT
1 T-TAAAAA-TATT
31822433 TTAAAAATA-T
1 TTAAAAATATT
31822443 TTAAAA
1 TTAAAA
31822449 TTAAAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
7 3 0.05
8 1 0.02
9 6 0.11
10 9 0.16
11 15 0.26
12 15 0.26
13 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:31822454 original size:16 final size:16
Alignment explanation
Indices: 31822433--31822478 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
31822423 AAAAAGTATT
31822433 TTAAAAATATTTAAAA
1 TTAAAAATATTTAAAA
*
31822449 TTAAAAAAATTTTAAAA
1 TTAAAAATA-TTTAAAA
* *
31822466 ATAAATATATTTA
1 TTAAAAATATTTA
31822479 TTATATTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAAATATTTAAAA
Found at i:31825428 original size:3 final size:3
Alignment explanation
Indices: 31825420--31825454 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31825410 GTGAAATGGA
31825420 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
31825455 AAAAATATAT
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:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:31826117 original size:27 final size:27
Alignment explanation
Indices: 31826087--31826160 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
31826077 ATGAAATGCT
* *
31826087 CCGAAGAGCCACTATCATTAAGTTGCA
1 CCGAAGTGCCACTATCACTAAGTTGCA
* * *
31826114 CCGAAGTGCCTCTATCACTGATTTGCA
1 CCGAAGTGCCACTATCACTAAGTTGCA
* *
31826141 CCAAAGTGCCACAATCACTA
1 CCGAAGTGCCACTATCACTA
31826161 TATGCATTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (27 bp):
CCGAAGTGCCACTATCACTAAGTTGCA
Found at i:31829066 original size:18 final size:17
Alignment explanation
Indices: 31829034--31829073 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
31829024 AAATAATTAA
*
31829034 ATAAACAATTTAAAATT
1 ATAAAAAATTTAAAATT
31829051 ATAAAAAATATTAAAATT
1 ATAAAAAAT-TTAAAATT
31829069 ATAAA
1 ATAAA
31829074 TTAATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAAATTTAAAATT
Found at i:31829534 original size:21 final size:21
Alignment explanation
Indices: 31829508--31829594 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
31829498 TTTGCTCTTT
* *
31829508 GCTGGTTTCCTTTGCTGCTAC
1 GCTGGTTCCCTCTGCTGCTAC
31829529 GCTGGTTCCCTCTGCTGCTAC
1 GCTGGTTCCCTCTGCTGCTAC
* * * **
31829550 ACTGCTCTCTGCTCTTTGCT-CTTT
1 GCTGGT-TC--C-CTCTGCTGCTAC
31829574 GCTGGTTCCCTCTGCTGCTAC
1 GCTGGTTCCCTCTGCTGCTAC
31829595 ACTGCTCTCT
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
20 6 0.12
21 26 0.53
22 2 0.04
23 2 0.04
24 7 0.14
25 6 0.12
ACGTcount: A:0.05, C:0.34, G:0.21, T:0.40
Consensus pattern (21 bp):
GCTGGTTCCCTCTGCTGCTAC
Found at i:31831576 original size:13 final size:13
Alignment explanation
Indices: 31831558--31831584 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31831548 ATTTTTGTTC
31831558 ATGTATATAGTTA
1 ATGTATATAGTTA
31831571 ATGTATATAGTTA
1 ATGTATATAGTTA
31831584 A
1 A
31831585 ATATTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
ATGTATATAGTTA
Found at i:31831598 original size:24 final size:24
Alignment explanation
Indices: 31831571--31831641 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
31831561 TATATAGTTA
31831571 ATGTATATAGTTAAATATTTTT-TC
1 ATGTATATAGTTAAAT-TTTTTATC
*
31831595 ATGTATATAGTTTAATTTTTTATC
1 ATGTATATAGTTAAATTTTTTATC
31831619 ATGTATATAGTTAAATTTTTTAT
1 ATGTATATAGTTAAATTTTTTAT
31831642 ACTGTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.11
24 39 0.89
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (24 bp):
ATGTATATAGTTAAATTTTTTATC
Found at i:31833653 original size:27 final size:26
Alignment explanation
Indices: 31833606--31833658 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
31833596 GGTAAATTAC
*
31833606 CTTTTCTTTCTTTCGTACTTTTTTTT
1 CTTTTCTTTCTTTCCTACTTTTTTTT
* *
31833632 CTTTTCATTTTTTTCCTTCTTTTTTTT
1 CTTTTC-TTTCTTTCCTACTTTTTTTT
31833659 TTCTGTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (26 bp):
CTTTTCTTTCTTTCCTACTTTTTTTT
Found at i:31834569 original size:104 final size:104
Alignment explanation
Indices: 31834350--31834578 Score: 271
Period size: 104 Copynumber: 2.2 Consensus size: 104
31834340 AATCTTTGCC
* * * *
31834350 CTAGATACGAAAATTCAGGATCCTAGAGACAAATGTTTTAGGGAAAACAAAGAGAGTGTGTAATA
1 CTAGATACGAAAA-TCAGGGTCCTAGAGACAAATATTTTAGGGAAAACAAAGAGAGTGTATAACA
31834415 TAGGTTACAAACATTTGAACATTGATCGATGGTCAAGATT
65 TAGGTTACAAACATTTGAACATTGATCGATGGTCAAGATT
* * * * * * * **
31834455 CAAAAAACGAAAATCAGGGTCCTGGTGATAAATATTTTAGGGAAAACTAAGAGTTTGTATAACAT
1 CTAGATACGAAAATCAGGGTCCTAGAGACAAATATTTTAGGGAAAACAAAGAGAGTGTATAACAT
* ** * *
31834520 AGGTTACAATCATTTGAATGTTGATCGATGTTCAAAGCTT
66 AGGTTACAAACATTTGAACATTGATCGATGGTC-AAGATT
31834560 -TAGATACGAAAATCAGGGT
1 CTAGATACGAAAATCAGGGT
31834579 TTGAGCAATA
Statistics
Matches: 102, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
104 87 0.85
105 15 0.15
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.28
Consensus pattern (104 bp):
CTAGATACGAAAATCAGGGTCCTAGAGACAAATATTTTAGGGAAAACAAAGAGAGTGTATAACAT
AGGTTACAAACATTTGAACATTGATCGATGGTCAAGATT
Found at i:31850259 original size:108 final size:106
Alignment explanation
Indices: 31850081--31850280 Score: 301
Period size: 108 Copynumber: 1.9 Consensus size: 106
31850071 TGAATTGAGA
* * * *
31850081 TTTAAGAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACATTAGGGGACATTT
1 TTTAAAAGGATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACACTAGGGCACATTT
*
31850146 CCTCGAGTTTCCAAACGCAAAATATTGTCTTACTTCGAAAT
66 CCTCGAATTTCCAAACGCAAAATATTGTCTTACTTCGAAAT
* *
31850187 TTTAAAAGGATATTTGGCTATTTAGTCGAACGAGAAAAATCGAAACCCAGCACACTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTAGTCAAACGAG--AAATCGAAACCCAGCACACTAGGGCACAT
* *
31850252 TTTCTCGAATTTCCAAACGTAAAATATTG
64 TTCCTCGAATTTCCAAACGCAAAATATTG
31850281 CCTTTATTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 31 0.37
108 52 0.63
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.28
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACACTAGGGCACATTT
CCTCGAATTTCCAAACGCAAAATATTGTCTTACTTCGAAAT
Found at i:31850934 original size:12 final size:12
Alignment explanation
Indices: 31850906--31850939 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
31850896 AATTAAAAAA
31850906 ATGTATATAGAT
1 ATGTATATAGAT
31850918 A--TATATAGAT
1 ATGTATATAGAT
31850928 ATGTATATAGAT
1 ATGTATATAGAT
31850940 TATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (12 bp):
ATGTATATAGAT
Found at i:31851051 original size:3 final size:3
Alignment explanation
Indices: 31851043--31851107 Score: 59
Period size: 3 Copynumber: 22.3 Consensus size: 3
31851033 GAATTAAAAG
*
31851043 ATA ATA ATA ATA ATA ATA ATA ATA ATA AGGTA GAAA ATA A-A ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA -ATA ATA ATA ATA ATA
31851089 ATA A-A ATA A-A ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
31851108 AACAATGATA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
2 10 0.19
3 38 0.73
4 1 0.02
5 2 0.04
6 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:31851054 original size:6 final size:5
Alignment explanation
Indices: 31851043--31851109 Score: 62
Period size: 5 Copynumber: 12.2 Consensus size: 5
31851033 GAATTAAAAG
* *
31851043 ATAATA ATAATA ATAATA ATAATA ATAAG GTAGAA AATAAA ATAAA ATAAA
1 ATAA-A ATAA-A ATAA-A ATAA-A ATAAA ATA-AA A-TAAA ATAAA ATAAA
31851094 ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA A
31851110 CAATGATACA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
5 27 0.49
6 26 0.47
7 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (5 bp):
ATAAA
Found at i:31851086 original size:5 final size:5
Alignment explanation
Indices: 31851076--31851109 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
31851066 AATAAGGTAG
31851076 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
31851110 CAATGATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:31855314 original size:13 final size:13
Alignment explanation
Indices: 31855296--31855349 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
31855286 AGTTCTTCAT
31855296 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
31855309 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
** * *
31855322 TGCAGTGGAAAAA
1 TGCTTTTGAAAAG
31855335 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
31855348 TG
1 TG
31855350 GTTTAAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:31860593 original size:16 final size:15
Alignment explanation
Indices: 31860556--31860606 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
31860546 TATTATGCCT
*
31860556 AAAAAAACA-AAAAAC
1 AAAAAAA-AGAAAAAG
*
31860571 AAAAAAAATAAAAAG
1 AAAAAAAAGAAAAAG
31860586 AAACAAAAAGAAAAAG
1 AAA-AAAAAGAAAAAG
31860602 AAAAA
1 AAAAA
31860607 GAAAAATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 1 0.03
15 17 0.53
16 14 0.44
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.02
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:31860618 original size:22 final size:21
Alignment explanation
Indices: 31860565--31860618 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
31860555 TAAAAAAACA
* *
31860565 AAAAACAAAAAAAATAAAAAG
1 AAAAACAAGAAAAAGAAAAAG
*
31860586 AAACAAAAAGAAAAAGAAAAAG
1 AAA-AACAAGAAAAAGAAAAAG
31860608 AAAAATCAAGA
1 AAAAA-CAAGA
31860619 TGAAAACCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.04
Consensus pattern (21 bp):
AAAAACAAGAAAAAGAAAAAG
Found at i:31861680 original size:79 final size:75
Alignment explanation
Indices: 31861487--31862112 Score: 588
Period size: 79 Copynumber: 8.1 Consensus size: 75
31861477 TTTGTCTCTT
* *
31861487 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
*
31861550 TCTGTTTTTC
66 TCTATTTTTC
*
31861560 AAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTC
1 -----AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTA----
*
31861625 TTTTAAATTTCTATTTTTC
57 TTTTCAATTTCTATTTTTC
* * * *
31861644 AAAAATCAAATCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
*
31861707 TCTGTTTTTC
66 TCTATTTTTC
31861717 AAAAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTT
1 ------AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTA---
*
31861782 CTTTTAAATTTCTATTTTTC
57 -TTTTCAATTTCTATTTTTC
* * * * * *
31861802 AAAAATCAAATCATAATGCGAGAGGTGAGTTGAGCCCCAGGCCGCACACCGAGGTATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
*
31861867 TCTATTTTTTT
66 TCTA-TTTTTC
* * * * * *
31861878 TAAAATCAACTCATAATGCGAGATGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
31861943 TCCGT-TATTTTC
66 T-C-TAT-TTTTC
* * * * *
31861955 AAAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCATC-GG-GACACGCTAAGGTATTTT
1 -----AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTA-TTT
* *
31862018 CTCAATTTATGTTTTTC
60 -TCAATTTCTATTTTTC
* * * *
31862035 AAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTC--G-AATCATGCTGAGGCATTTTCAAT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCA-CACGCTGAGGTATTTTCAAT
31862097 TTCTATTTTTC
65 TTCTATTTTTC
31862108 AAAAA
1 AAAAA
31862113 AACAATAATA
Statistics
Matches: 468, Mismatches: 49, Indels: 67
0.80 0.08 0.11
Matches are distributed among these distances:
73 36 0.08
74 5 0.01
75 55 0.12
76 66 0.14
77 16 0.03
78 42 0.09
79 129 0.28
80 28 0.06
81 17 0.04
82 40 0.09
84 17 0.04
85 17 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
TCTATTTTTC
Found at i:31861799 original size:158 final size:154
Alignment explanation
Indices: 31861487--31862072 Score: 713
Period size: 158 Copynumber: 3.7 Consensus size: 154
31861477 TTTGTCTCTT
*
31861487 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAAATCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTC
*
31861552 TGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGA
66 TGTTTTTC---AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGA
31861617 GGTATTTCTTTTAAATTTCTATTTTTC
128 GGTATTTCTTTTAAATTTCTATTTTTC
*
31861644 AAAAATCAAATCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCATGCTGAGGTATTTTCAATTTC
1 AAAAATCAAATCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTC
31861709 TGTTTTTCAAAAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTG
66 TGTTTTTC----AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTG
31861774 AGGTATTTCTTTTAAATTTCTATTTTTC
127 AGGTATTTCTTTTAAATTTCTATTTTTC
* * * *
31861802 AAAAATCAAATCATAATGCGAGAGGTGAGTTGAGCCCCAGGCCG-CACACCGAGGTATTTTCAAT
1 AAAAATCAAATCATATTGCGAGAGGTGAGTTGAGCCTC-GG--GTCACGCTGAGGTATTTTCAAT
* *** * * * * *
31861866 TTCTATTTTT-TTTAAAATCAACTCATAATGCGAGATGTGAGTTGAGCCTCGGGCCGCACGCCGA
63 TTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGA
*
31861930 GGTA----TTTTCAATTTCCGT-TATTTTC
128 GGTATTTCTTTTAAATTT-C-TAT-TTTTC
* * * * *
31861955 AAAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCATCGGGACACGCTAAGGTATTTTCT
1 -----AAAAATCAAATCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTT-T
* *
31862020 CAATTTATGTTTTTC--AAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTC
59 CAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
31862073 GAATCATGCT
Statistics
Matches: 382, Mismatches: 31, Indels: 32
0.86 0.07 0.07
Matches are distributed among these distances:
151 9 0.02
152 2 0.01
153 6 0.02
155 51 0.13
156 9 0.02
157 111 0.29
158 165 0.43
159 2 0.01
160 26 0.07
161 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (154 bp):
AAAAATCAAATCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTC
TGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGT
ATTTCTTTTAAATTTCTATTTTTC
Found at i:31862252 original size:5 final size:5
Alignment explanation
Indices: 31862242--31862303 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
31862232 GTAGTTCATG
* * **
31862242 TTTTA TTTTA TTTTA TCTTA TTTTA TTTTA -TATA TATGAA TTTTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA -TTTTA -TTTTA
31862294 TTTTA TTTTA
1 TTTTA TTTTA
31862304 AATTATGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 3 0.06
5 33 0.70
6 10 0.21
7 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:31862287 original size:31 final size:30
Alignment explanation
Indices: 31862252--31862316 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 30
31862242 TTTTATTTTA
*
31862252 TTTTA-TCTTATTTTATTTTATATATATGAAT
1 TTTTATTCTTATTTTATTTTAAAT-TATG-AT
*
31862283 TTTTATTTTTATTTTATTTTAAATTATGAT
1 TTTTATTCTTATTTTATTTTAAATTATGAT
31862313 TTTT
1 TTTT
31862317 CTGGGCCGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 6 0.19
31 9 0.29
32 16 0.52
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (30 bp):
TTTTATTCTTATTTTATTTTAAATTATGAT
Found at i:31862525 original size:30 final size:29
Alignment explanation
Indices: 31862487--31862624 Score: 93
Period size: 30 Copynumber: 4.7 Consensus size: 29
31862477 ACAAAAAATA
31862487 TAAATTACATTTTGGCCCTTAAACTTTTC
1 TAAATTACATTTTGGCCCTTAAACTTTTC
* * * * *
31862516 TAAATTTACATTGTGACCCCTAACCTTTTTT
1 TAAA-TTACATTTTGGCCCTTAAAC-TTTTC
* * * * * *
31862547 TGAATTTGCATCTTGACCCCTAATA-TTTTT
1 T-AAATTACATTTTGGCCCTTAA-ACTTTTC
*
31862577 TAAATTACA-TTTGGGCCTTAAAC-TTTC
1 TAAATTACATTTTGGCCCTTAAACTTTTC
31862604 TAGAAATTACATTTTGGCCCT
1 T--AAATTACATTTTGGCCCT
31862625 ATGTTTTCTT
Statistics
Matches: 83, Mismatches: 18, Indels: 15
0.72 0.16 0.13
Matches are distributed among these distances:
27 5 0.06
28 8 0.10
29 18 0.22
30 30 0.36
31 20 0.24
32 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.43
Consensus pattern (29 bp):
TAAATTACATTTTGGCCCTTAAACTTTTC
Found at i:31863178 original size:28 final size:26
Alignment explanation
Indices: 31863133--31863194 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
31863123 GTTCGGCCCG
31863133 AAGAGAAAGAAGAAAAAGAGAGAAGAAA
1 AAGAGAAAGAAGAAAAAGA-AGAA-AAA
31863161 AAGAGAAAGAA-AAGAAAGAAGAAAAA
1 AAGAGAAAGAAGAA-AAAGAAGAAAAA
*
31863187 AAAAGAAA
1 AAGAGAAA
31863195 AAATATATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 10 0.31
27 6 0.19
28 16 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (26 bp):
AAGAGAAAGAAGAAAAAGAAGAAAAA
Found at i:31863191 original size:13 final size:13
Alignment explanation
Indices: 31863136--31863197 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
31863126 CGGCCCGAAG
31863136 AGAAAGAAGAAAA
1 AGAAAGAAGAAAA
*
31863149 AGAGAGAAGAAAA
1 AGAAAGAAGAAAA
*
31863162 AGAGA-AAG-AAA
1 AGAAAGAAGAAAA
31863173 AGAAAGAAGAAAA
1 AGAAAGAAGAAAA
*
31863186 AAAAAGAA-AAAA
1 AGAAAGAAGAAAA
31863198 TATATCACAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
11 7 0.16
12 10 0.23
13 27 0.61
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAGAAGAAAA
Found at i:31863197 original size:24 final size:25
Alignment explanation
Indices: 31863142--31863196 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
31863132 GAAGAGAAAG
*
31863142 AAGAAAAAGAGAGAAGAAAAAGAGA
1 AAGAAAAAGAAAGAAGAAAAAGAGA
31863167 AAG-AAAAGAAAGAAGAAAAA-A-A
1 AAGAAAAAGAAAGAAGAAAAAGAGA
31863189 AAGAAAAA
1 AAGAAAAA
31863197 ATATATCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 5 0.18
24 16 0.57
25 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (25 bp):
AAGAAAAAGAAAGAAGAAAAAGAGA
Found at i:31864064 original size:17 final size:17
Alignment explanation
Indices: 31864008--31864195 Score: 105
Period size: 17 Copynumber: 10.3 Consensus size: 17
31863998 AAAAAAAAAG
*
31864008 AAAAAAATTCGTGTTT-
1 AAAAAATTTCGTGTTTC
* * *
31864024 TAAAATTTTCCATGTTTC
1 AAAAAATTT-CGTGTTTC
31864042 AAAAAAAATTCTCGTGTTT-
1 --AAAAAATT-TCGTGTTTC
* *
31864061 AAAAATTTTCGCGTTTTC
1 AAAAAATTTCGTG-TTTC
31864079 AAAAAAATTTCGTGTTTC
1 -AAAAAATTTCGTGTTTC
*
31864097 AAAAAATTTTCACGT-TTTAAA
1 AAAAAA-TTT--CGTGTTT--C
*
31864118 AAAAAATTTCGTGCTTC
1 AAAAAATTTCGTGTTTC
*
31864135 AAAAAATCTCGTGTTTTC
1 AAAAAATTTCGTG-TTTC
31864153 AAAAAAATATTCTTGTGTTTC
1 -AAAAAAT-TTC--GTGTTTC
*
31864174 -AAAAATTTTGTGTTTTC
1 AAAAAATTTCGTG-TTTC
31864191 AAAAA
1 AAAAA
31864196 TTATTATGTT
Statistics
Matches: 133, Mismatches: 18, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
16 13 0.10
17 38 0.29
18 19 0.14
19 29 0.22
20 20 0.15
21 11 0.08
22 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:31864064 original size:18 final size:19
Alignment explanation
Indices: 31864036--31864178 Score: 111
Period size: 18 Copynumber: 7.6 Consensus size: 19
31864026 AAATTTTCCA
31864036 TGTTTCAAAAAAAATTCTCG
1 TGTTTC-AAAAAAATTCTCG
** *
31864056 TGTTT-AAAAATTTTCGCG
1 TGTTTCAAAAAAATTCTCG
31864074 T-TTTCAAAAAAATT-TCG
1 TGTTTCAAAAAAATTCTCG
* *
31864091 TGTTTCAAAAAATTTTCACG
1 TGTTTCAAAAAA-ATTCTCG
*
31864111 T-TTTAAAAAAAAATT-TCG
1 TGTTT-CAAAAAAATTCTCG
*
31864129 TGCTTC-AAAAAA-TCTCG
1 TGTTTCAAAAAAATTCTCG
*
31864146 TGTTTTCAAAAAAATATTCTTG
1 TG-TTTC-AAAAAA-ATTCTCG
31864168 TGTTTCAAAAA
1 TGTTTCAAAAA
31864179 TTTTGTGTTT
Statistics
Matches: 96, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
16 1 0.01
17 17 0.18
18 34 0.35
19 9 0.09
20 24 0.25
21 5 0.05
22 6 0.06
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (19 bp):
TGTTTCAAAAAAATTCTCG
Found at i:31864195 original size:37 final size:38
Alignment explanation
Indices: 31864008--31864195 Score: 189
Period size: 37 Copynumber: 5.1 Consensus size: 38
31863998 AAAAAAAAAG
* *
31864008 AAAAAAA-TTCGTGTTT--TAAAATTTTC-CATGTTTCA
1 AAAAAAATTTCGTGTTTCAAAAAATTTTCGCGT-TTTCA
31864043 AAAAAAATTCTCGTGTTT--AAAAATTTTCGCGTTTTC-
1 AAAAAAATT-TCGTGTTTCAAAAAATTTTCGCGTTTTCA
* *
31864079 AAAAAAATTTCGTGTTTCAAAAAATTTTCACGTTTTAA
1 AAAAAAATTTCGTGTTTCAAAAAATTTTCGCGTTTTCA
* * *
31864117 AAAAAAATTTCGTGCTTCAAAAAA-TCTCGTGTTTTCA
1 AAAAAAATTTCGTGTTTCAAAAAATTTTCGCGTTTTCA
* *
31864154 AAAAAATATTCTTGTGTTTC-AAAAATTTT-GTGTTTTCA
1 AAAAAA-ATT-TCGTGTTTCAAAAAATTTTCGCGTTTTCA
31864192 AAAA
1 AAAA
31864196 TTATTATGTT
Statistics
Matches: 132, Mismatches: 12, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
35 15 0.11
36 10 0.08
37 52 0.39
38 46 0.35
39 9 0.07
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (38 bp):
AAAAAAATTTCGTGTTTCAAAAAATTTTCGCGTTTTCA
Found at i:31864196 original size:17 final size:17
Alignment explanation
Indices: 31864165--31864222 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
31864155 AAAAATATTC
31864165 TTGTGTTTCAAAAATT-
1 TTGTGTTTCAAAAATTA
31864181 TTGTGTTTTCAAAAATTA
1 TTGTG-TTTCAAAAATTA
* * *
31864199 TTATGTTAC-AAAATTC
1 TTGTGTTTCAAAAATTA
31864215 TTGTGTTT
1 TTGTGTTT
31864223 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 17 0.49
17 14 0.40
18 4 0.11
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (17 bp):
TTGTGTTTCAAAAATTA
Found at i:31864205 original size:18 final size:18
Alignment explanation
Indices: 31864146--31864205 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 18
31864136 AAAAATCTCG
* *
31864146 TGTTTTCAAAAAAATATTCT
1 TGTTTTC-AAAAATTATT-A
*
31864166 TGTGTTTCAAAAATT-TTG
1 TGT-TTTCAAAAATTATTA
31864184 TGTTTTCAAAAATTATTA
1 TGTTTTCAAAAATTATTA
31864202 TGTT
1 TGTT
31864206 ACAAAATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 11 0.31
18 9 0.26
19 2 0.06
20 9 0.26
21 4 0.11
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (18 bp):
TGTTTTCAAAAATTATTA
Found at i:31870063 original size:13 final size:13
Alignment explanation
Indices: 31870045--31870076 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31870035 TAATTATTTC
*
31870045 TAAAATGTAAAAT
1 TAAAATCTAAAAT
31870058 TAAAATCTAAAAT
1 TAAAATCTAAAAT
31870071 TAAAAT
1 TAAAAT
31870077 TTCAATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (13 bp):
TAAAATCTAAAAT
Found at i:31879113 original size:2 final size:2
Alignment explanation
Indices: 31879106--31879134 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31879096 TCGTAAAGTG
31879106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31879135 GTTTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31881435 original size:17 final size:17
Alignment explanation
Indices: 31881413--31881448 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31881403 TTGAAAACCG
31881413 TGCTAGATAAATACACA
1 TGCTAGATAAATACACA
*
31881430 TGCTAGATAAATACCCA
1 TGCTAGATAAATACACA
31881447 TG
1 TG
31881449 TTCAAGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (17 bp):
TGCTAGATAAATACACA
Found at i:31882777 original size:30 final size:30
Alignment explanation
Indices: 31882741--31882797 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
31882731 CTTTAGTCTC
*
31882741 CTTTAAAAATGATAAAAATTTAATTTAATT
1 CTTTAAAAATGATAAAAATATAATTTAATT
* *
31882771 CTTTAAAAATTATAAATATATAATTTA
1 CTTTAAAAATGATAAAAATATAATTTA
31882798 TTAAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (30 bp):
CTTTAAAAATGATAAAAATATAATTTAATT
Found at i:31883633 original size:114 final size:114
Alignment explanation
Indices: 31883392--31884137 Score: 841
Period size: 114 Copynumber: 6.6 Consensus size: 114
31883382 TATTTGTAAG
* * * * ** * * * *
31883392 CGCCGCAAAAAATGTTAGCCAAAACGCATCGTTTGTTCCCGAGCTATATTAGACTTGGTGGCGTT
1 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGGT
* * * * * * * * *
31883457 TA-TGATAAACGCCGCTATAGTATATTATTAGTGGCG-TTTTTTAGTAAA
66 TACGGAAAAACGCCGCTAAAGCACAGTATTAGAGGCGCTTTGTAAG-AAA
*
31883505 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCGGT
1 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGGT
* *
31883570 TACGGAAAAACGCCGCTAAAGGAGAGTATTAGAGGCGCTTTGTAAGAAA
66 TACGGAAAAACGCCGCTAAAGCACAGTATTAGAGGCGCTTTGTAAGAAA
* * * * * * * *
31883619 CGCCGCTAATTATCTTAACCAAAACGTAGCGTTTTGTCTTAATGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGGT
** * * * * *
31883684 TGTGGAAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATACGAAA
66 TACGGAAAAACGCCGCTAAAGCACAGTATTAGAGGCGCTTTGTAAGAAA
* * * * *
31883733 CGCCACAAAATATCTTAACCAAAACCCATCGTTTTGTCTTGAGGTATATAAGATTTAGTGGCGGT
1 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGGT
* * *
31883798 TACGGAAAAACGCCGCTAAAGGATAGTATTAGAGGTGCTTTGTAAGAAA
66 TACGGAAAAACGCCGCTAAAGCACAGTATTAGAGGCGCTTTGTAAGAAA
* * * * * *
31883847 CGCCGCAAATTATCTTAACCAAAACACAGCGTTTGGTCTTAATGTATATTAGAATTAGTGGCGAT
1 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGGT
** * * * * *
31883912 TGTGGGAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATACA-AAA
66 TACGGAAAAACGCCGCTAAAGCACAGTATTAGAGGCGCTTTGTA-AGAAA
* * *
31883961 CGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGTCTTGAGGTATATAAGAATTAGTGGCGGT
1 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGGT
* * ** *
31884026 TACGGAAAAAGGCCGCTAAAGCAGAGTATTAGAGATGCTTTGTAAGAAT
66 TACGGAAAAACGCCGCTAAAGCACAGTATTAGAGGCGCTTTGTAAGAAA
* *
31884075 CGCCGCAAAATATCTTAACCAAAACGCAACGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
1 CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCG
31884138 CTCATGTAAA
Statistics
Matches: 524, Mismatches: 105, Indels: 7
0.82 0.17 0.01
Matches are distributed among these distances:
113 57 0.11
114 460 0.88
115 7 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGGT
TACGGAAAAACGCCGCTAAAGCACAGTATTAGAGGCGCTTTGTAAGAAA
Found at i:31883736 original size:228 final size:228
Alignment explanation
Indices: 31883436--31884139 Score: 1106
Period size: 228 Copynumber: 3.1 Consensus size: 228
31883426 GTTCCCGAGC
* * * * * * * * * *
31883436 TATATTAGACTTGGTGGCGTTTAT-GATAAACGCCGCTATAGTATATTATTAGTGGCGTTTTTTA
1 TATATTAGAATTAGTGGCGCTTGTGGAAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATA
*
31883500 -GTAAACGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATAAGAATTAGT
66 CG-AAACGCCGCAAAATATCTTAACCAAAACGCATCGTTTTGTCTTGAGGTATATAAGAATTAGT
* *
31883564 GGCGGTTACGGAAAAACGCCGCTAAAGGAGAGTATTAGAGGCGCTTTGTAAGAAACGCCGCTAAT
130 GGCGGTTACGGAAAAACGCCGCTAAAGGAGAGTATTAGAGGTGCTTTGTAAGAAACGCCGCAAAT
* *
31883629 TATCTTAACCAAAACGTAGCGTTTTGTCTTAATG
195 TATCTTAACCAAAACGCAGCGTTTGGTCTTAATG
31883663 TATATTAGAATTAGTGGCGCTTGTGGAAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATA
1 TATATTAGAATTAGTGGCGCTTGTGGAAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATA
* * *
31883728 CGAAACGCCACAAAATATCTTAACCAAAACCCATCGTTTTGTCTTGAGGTATATAAGATTTAGTG
66 CGAAACGCCGCAAAATATCTTAACCAAAACGCATCGTTTTGTCTTGAGGTATATAAGAATTAGTG
*
31883793 GCGGTTACGGAAAAACGCCGCTAAAGGATAGTATTAGAGGTGCTTTGTAAGAAACGCCGCAAATT
131 GCGGTTACGGAAAAACGCCGCTAAAGGAGAGTATTAGAGGTGCTTTGTAAGAAACGCCGCAAATT
*
31883858 ATCTTAACCAAAACACAGCGTTTGGTCTTAATG
196 ATCTTAACCAAAACGCAGCGTTTGGTCTTAATG
* *
31883891 TATATTAGAATTAGTGGCGATTGTGGGAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATA
1 TATATTAGAATTAGTGGCGCTTGTGGAAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATA
* *
31883956 CAAAACGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGTCTTGAGGTATATAAGAATTAGTG
66 CGAAACGCCGCAAAATATCTTAACCAAAACGCATCGTTTTGTCTTGAGGTATATAAGAATTAGTG
* * * * *
31884021 GCGGTTACGGAAAAAGGCCGCTAAAGCAGAGTATTAGAGATGCTTTGTAAGAATCGCCGCAAAAT
131 GCGGTTACGGAAAAACGCCGCTAAAGGAGAGTATTAGAGGTGCTTTGTAAGAAACGCCGCAAATT
* *
31884086 ATCTTAACCAAAACGCAACGTTTGGTCTTGATG
196 ATCTTAACCAAAACGCAGCGTTTGGTCTTAATG
31884119 TATATTAGAATTAGTGGCGCT
1 TATATTAGAATTAGTGGCGCT
31884140 CATGTAAAAA
Statistics
Matches: 438, Mismatches: 37, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
227 20 0.05
228 417 0.95
229 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (228 bp):
TATATTAGAATTAGTGGCGCTTGTGGAAAAACGCCGCTATAGCACAGTATTAGCGGCGTTTTATA
CGAAACGCCGCAAAATATCTTAACCAAAACGCATCGTTTTGTCTTGAGGTATATAAGAATTAGTG
GCGGTTACGGAAAAACGCCGCTAAAGGAGAGTATTAGAGGTGCTTTGTAAGAAACGCCGCAAATT
ATCTTAACCAAAACGCAGCGTTTGGTCTTAATG
Found at i:31884419 original size:7 final size:7
Alignment explanation
Indices: 31884409--31884498 Score: 60
Period size: 7 Copynumber: 13.0 Consensus size: 7
31884399 GGAGTTTTGA
31884409 GTTTAGG
1 GTTTAGG
*
31884416 GTTTATG
1 GTTTAGG
* *
31884423 ATGTA-G
1 GTTTAGG
31884429 GTTTAGTG
1 GTTTAG-G
*
31884437 TTTTA-G
1 GTTTAGG
31884443 GTTTAGG
1 GTTTAGG
* *
31884450 GGTTGGG
1 GTTTAGG
*
31884457 AGTTTGGG
1 -GTTTAGG
*
31884465 GTTTAAG
1 GTTTAGG
31884472 GTTTAGG
1 GTTTAGG
31884479 GTTT-GG
1 GTTTAGG
*
31884485 GTTTGGG
1 GTTTAGG
31884492 GTTTAGG
1 GTTTAGG
31884499 TTGCTTTAGT
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
6 15 0.23
7 38 0.59
8 11 0.17
ACGTcount: A:0.13, C:0.00, G:0.42, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:31884488 original size:20 final size:21
Alignment explanation
Indices: 31884458--31884498 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
31884448 GGGGTTGGGA
31884458 GTTTGGGGTTTAAGGTTTAGG
1 GTTTGGGGTTTAAGGTTTAGG
**
31884479 GTTT-GGGTTTGGGGTTTAGG
1 GTTTGGGGTTTAAGGTTTAGG
31884499 TTGCTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (21 bp):
GTTTGGGGTTTAAGGTTTAGG
Found at i:31886432 original size:14 final size:15
Alignment explanation
Indices: 31886413--31886441 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31886403 GGCACATTAC
31886413 TTGGTATTCT-TTTT
1 TTGGTATTCTGTTTT
31886427 TTGGTATTCTGTTTT
1 TTGGTATTCTGTTTT
31886442 GGCACAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (15 bp):
TTGGTATTCTGTTTT
Found at i:31886440 original size:39 final size:38
Alignment explanation
Indices: 31886369--31886447 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 38
31886359 GACTTTGTAG
31886369 ATTACTTGGTATTCTGTTTTGGTAGGATTGTTTTGGCAC
1 ATTACTTGGTATTCTGTTTTGGTA-GATTGTTTTGGCAC
* *
31886408 ATTACTTGGTATTCTTTTTTTGGTA-TTCTGTTTTGGCAC
1 ATTACTTGGTATTC-TGTTTTGGTAGAT-TGTTTTGGCAC
31886447 A
1 A
31886448 GTTTCTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 1 0.03
39 26 0.72
40 9 0.25
ACGTcount: A:0.15, C:0.11, G:0.22, T:0.52
Consensus pattern (38 bp):
ATTACTTGGTATTCTGTTTTGGTAGATTGTTTTGGCAC
Found at i:31887763 original size:25 final size:24
Alignment explanation
Indices: 31887679--31887763 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 24
31887669 ACTTTTTTAT
31887679 ATTTTCATAGTACATAACTTACATA
1 ATTTTCA-AGTACATAACTTACATA
* * * * *
31887704 ATATTGAACTTACTTAACTTTAATAATA
1 ATTTTCAA-GTACATAAC-TT-A-CATA
31887732 ATTTTCACAGTACATAACTTACATA
1 ATTTTCA-AGTACATAACTTACATA
31887757 ATTTTCA
1 ATTTTCA
31887764 TAACCTACAT
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
24 1 0.02
25 22 0.49
26 3 0.07
27 3 0.07
28 15 0.33
29 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTTTCAAGTACATAACTTACATA
Found at i:31887897 original size:126 final size:126
Alignment explanation
Indices: 31887747--31888018 Score: 429
Period size: 126 Copynumber: 2.2 Consensus size: 126
31887737 CACAGTACAT
* * *
31887747 AACTTACATAATTTTCATAACCTACATAACTTATTCAATACACAACTTACATAATTGTTTATAAT
1 AACTTACATAATTTTCATAACCTACATAACTTATACAATACACAACTTACATAAAT-TTCATAAT
* *
31887812 ACACAGCTTACATAATATT-TAACTTACATAATTTTCATAGTACATAACTTACATAATATTG
65 ACACAGCTTACATAATATTGGAACTTACATAATTTTCATAATACATAACTTACATAATATTG
* *
31887873 AACTTACATAATTTTCATAACCTACATAACTTATACAATACACAGCTTACTTAAATTTCATAATA
1 AACTTACATAATTTTCATAACCTACATAACTTATACAATACACAACTTACATAAATTTCATAATA
* *
31887938 CATAGCTTACATAATATTGGAACTTACATAATTTTCGTAATACATAACTTACATAATATTG
66 CACAGCTTACATAATATTGGAACTTACATAATTTTCATAATACATAACTTACATAATATTG
* *
31887999 AACTTACATAACTTACATAA
1 AACTTACATAATTTTCATAA
31888019 TATTGAACTT
Statistics
Matches: 134, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
125 25 0.19
126 109 0.81
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (126 bp):
AACTTACATAATTTTCATAACCTACATAACTTATACAATACACAACTTACATAAATTTCATAATA
CACAGCTTACATAATATTGGAACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:31887947 original size:84 final size:83
Alignment explanation
Indices: 31887681--31887988 Score: 256
Period size: 84 Copynumber: 3.7 Consensus size: 83
31887671 TTTTTTATAT
* * * *
31887681 TTTCATAGTACATAACTTACATAATATT-GAACTTACTTAA-CTT--TAATA-ATAA-TTTTCAC
1 TTTCATAATACATAACTTACATAATATTGGAACTTACATAATTTTCATAATACATAACTTAT-AC
* * * *
31887740 AGTACATAACTTACATAAT
65 AATACACAGCTTACATAAA
* *** * * *
31887759 TTTCATAACCTACATAACTTA-TTCAATA-CACAACTTACATAATTGTTTATAATACACAGCTTA
1 TTTCATAA--TACATAACTTACAT-AATATTGGAACTTACATAATT-TTCATAATACATAACTTA
* * *** * *
31887822 CATAATATTTAACTTACATAAT
62 TACAATACACAGCTTACATAAA
*
31887844 TTTCATAGTACATAACTTACATAATATT-GAACTTACATAATTTTCATAACCTACATAACTTATA
1 TTTCATAATACATAACTTACATAATATTGGAACTTACATAATTTTCATAA--TACATAACTTATA
*
31887908 CAATACACAGCTTACTTAAA
64 CAATACACAGCTTACATAAA
* *
31887928 TTTCATAATACATAGCTTACATAATATTGGAACTTACATAATTTTCGTAATACATAACTTA
1 TTTCATAATACATAACTTACATAATATTGGAACTTACATAATTTTCATAATACATAACTTA
31887989 CATAATATTG
Statistics
Matches: 183, Mismatches: 32, Indels: 25
0.76 0.13 0.10
Matches are distributed among these distances:
78 7 0.04
79 1 0.01
80 25 0.14
82 8 0.04
83 39 0.21
84 55 0.30
85 46 0.25
86 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (83 bp):
TTTCATAATACATAACTTACATAATATTGGAACTTACATAATTTTCATAATACATAACTTATACA
ATACACAGCTTACATAAA
Found at i:31887947 original size:151 final size:150
Alignment explanation
Indices: 31887810--31888262 Score: 514
Period size: 151 Copynumber: 3.0 Consensus size: 150
31887800 ATTGTTTATA
* ** *
31887810 ATACACAGCTTACATAATATTTAACTTACATAATTTTCATA-GTACATAACTTACATAATATTGA
1 ATACACAACTTACATAATACATAACTTACATAATATTCA-ACGTACATAACTTACATAATATTGA
31887874 ACTTACATAATTTTCATAACCTACATAACTTATACAATACACAGCTTACTTAAATTTCATAATAC
65 ACTTACATAATTTTCATAACCTACATAACTTATACAATACACAGCTTACTTAAATTTCATAATAC
31887939 ATAGCTTACATAATATTGGAAC
130 ATAGCTTACATAAT-TTGGAAC
* * * * * * *
31887961 TTACATAATTTTCGTAATACATAACTTACATAATATTGAACTTACATAACTTACATAATATTGAA
1 ATACACAACTTACATAATACATAACTTACATAATATTCAACGTACATAACTTACATAATATTGAA
31888026 CTTACATAATTTTCATAACCTACATAACTTATACAATACACAGCTTACTTAAATTTCATAATACA
66 CTTACATAATTTTCATAACCTACATAACTTATACAATACACAGCTTACTTAAATTTCATAATACA
*
31888091 TAGCTTACATAATTTTTGAAC
131 TAGCTTACATAA-TTTGGAAC
* * * * * * * * * * *
31888112 TTGCATAATTTTCGTAATACATAACTTACATAATATTGAACTTACATAATTTTCATAATACAT-A
1 ATACACAACTTACATAATACATAACTTACATAATATTCAACGTACATAACTTACATAATA-TTGA
** * * * *
31888176 ACTTATTTAATTTTCATAATATAAAACTTACATAACTTATACAGTACACAGCTTACATAATTTTC
65 ACTTACATAATTTTC-----AT--AACCTACATAACTTATACAATACACAGCTTACTTAAATTTC
* *
31888241 ATAATACATAACTAACATAATT
123 ATAATACATAGCTTACATAATT
31888263 CTTCATAATA
Statistics
Matches: 268, Mismatches: 24, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
150 1 0.00
151 206 0.77
152 2 0.01
156 2 0.01
157 2 0.01
158 55 0.21
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (150 bp):
ATACACAACTTACATAATACATAACTTACATAATATTCAACGTACATAACTTACATAATATTGAA
CTTACATAATTTTCATAACCTACATAACTTATACAATACACAGCTTACTTAAATTTCATAATACA
TAGCTTACATAATTTGGAAC
Found at i:31887992 original size:25 final size:24
Alignment explanation
Indices: 31887958--31888043 Score: 102
Period size: 25 Copynumber: 3.5 Consensus size: 24
31887948 ATAATATTGG
*
31887958 AACTTACATAATTTTCGTAA-TACAT
1 AACTTACATAATATT-G-AACTACAT
31887983 AACTTACATAATATTGAACTTACAT
1 AACTTACATAATATTGAAC-TACAT
31888008 AACTTACATAATATTGAACTTACAT
1 AACTTACATAATATTGAAC-TACAT
* *
31888033 AATTTTCATAA
1 AACTTACATAA
31888044 CCTACATAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 2 0.04
24 1 0.02
25 53 0.95
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.38
Consensus pattern (24 bp):
AACTTACATAATATTGAACTACAT
Found at i:31888027 original size:16 final size:16
Alignment explanation
Indices: 31887983--31888035 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
31887973 CGTAATACAT
31887983 AACTTACATAATATTG
1 AACTTACATAATATTG
31887999 AACTTAC-----A-T-
1 AACTTACATAATATTG
31888008 AACTTACATAATATTG
1 AACTTACATAATATTG
31888024 AACTTACATAAT
1 AACTTACATAAT
31888036 TTTCATAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
9 7 0.23
10 1 0.03
11 1 0.03
14 1 0.03
15 1 0.03
16 19 0.63
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (16 bp):
AACTTACATAATATTG
Found at i:31888122 original size:41 final size:42
Alignment explanation
Indices: 31888003--31888189 Score: 191
Period size: 41 Copynumber: 4.5 Consensus size: 42
31887993 ATATTGAACT
*
31888003 TACATAACTTACATAA-TATTGAACTTACATAATTTTCATAA
1 TACATAACTTACATAATTTTTGAACTTACATAATTTTCATAA
* * **** * * *
31888044 CCTACATAACTTATACAA-TACACAGCTTACTTAAATTTCATAA
1 --TACATAACTTACATAATTTTTGAACTTACATAATTTTCATAA
* * *
31888087 TACATAGCTTACATAATTTTTGAACTTGCATAATTTTCGTAA
1 TACATAACTTACATAATTTTTGAACTTACATAATTTTCATAA
*
31888129 TACATAACTTACATAA-TATTGAACTTACATAATTTTCATAA
1 TACATAACTTACATAATTTTTGAACTTACATAATTTTCATAA
**
31888170 TACATAACTTATTTAATTTT
1 TACATAACTTACATAATTTT
31888190 CATAATATAA
Statistics
Matches: 115, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
41 49 0.43
42 33 0.29
43 33 0.29
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (42 bp):
TACATAACTTACATAATTTTTGAACTTACATAATTTTCATAA
Found at i:31888157 original size:25 final size:24
Alignment explanation
Indices: 31888129--31888214 Score: 73
Period size: 25 Copynumber: 3.5 Consensus size: 24
31888119 ATTTTCGTAA
31888129 TACATAACTTACATAATATTGAACT
1 TACATAACTTACATAATATT-AACT
* * *
31888154 TACATAATTTTCATAATACATAACT
1 TACATAACTTACATAATA-TTAACT
** * * *
31888179 TATTTAATTTTCATAATATAAAACT
1 TACATAACTTACATAATAT-TAACT
31888204 TACATAACTTA
1 TACATAACTTA
31888215 TACAGTACAC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (24 bp):
TACATAACTTACATAATATTAACT
Found at i:31888204 original size:50 final size:50
Alignment explanation
Indices: 31888129--31888288 Score: 146
Period size: 50 Copynumber: 3.2 Consensus size: 50
31888119 ATTTTCGTAA
* * ** *
31888129 TACATAACTTACATAATATTGAACTTACATAATTTTCATAATACATAACT
1 TACATAATTTTCATAATATAAAACTTACATAATTTTCATAATACACAACT
** * *
31888179 TATTTAATTTTCATAATATAAAACTTACATAA-CTT-ATACAGTACACAGCT
1 TACATAATTTTCATAATATAAAACTTACATAATTTTCATA-A-TACACAACT
* * * *
31888229 TACATAATTTTCATAATACATAACTAACATAATTCTTCATAATACAGC-AGT
1 TACATAATTTTCATAATATAAAACTTACATAATT-TTCATAATACA-CAACT
31888280 TACATAATT
1 TACATAATT
31888289 CTTAAAGAAT
Statistics
Matches: 87, Mismatches: 17, Indels: 11
0.76 0.15 0.10
Matches are distributed among these distances:
48 3 0.03
49 3 0.03
50 60 0.69
51 14 0.16
52 4 0.05
53 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (50 bp):
TACATAATTTTCATAATATAAAACTTACATAATTTTCATAATACACAACT
Found at i:31888248 original size:25 final size:25
Alignment explanation
Indices: 31888150--31888288 Score: 131
Period size: 25 Copynumber: 5.5 Consensus size: 25
31888140 CATAATATTG
*
31888150 AACTTACATAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAC
** * *
31888175 AACTTATTTAATTTTCATAATATAA
1 AACTTACATAATTTTCATAATACAC
*
31888200 AACTTACATAA-CTT-ATACAGTACAC
1 AACTTACATAATTTTCATA-A-TACAC
* *
31888225 AGCTTACATAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAC
*
31888250 AACTAACATAATTCTTCATAATACAGC
1 AACTTACATAATT-TTCATAATACA-C
*
31888277 -AGTTACATAATT
1 AACTTACATAATT
31888289 CTTAAAGAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
23 3 0.03
24 3 0.03
25 58 0.64
26 24 0.26
27 3 0.03
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (25 bp):
AACTTACATAATTTTCATAATACAC
Found at i:31893738 original size:21 final size:21
Alignment explanation
Indices: 31893709--31893758 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
31893699 CTACAACTTA
*
31893709 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
31893730 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
*
31893751 AAGTAGAG
1 AAGCAGAG
31893759 CAGAGCAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.48, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:31894141 original size:42 final size:42
Alignment explanation
Indices: 31894078--31894336 Score: 362
Period size: 42 Copynumber: 6.2 Consensus size: 42
31894068 CGTTTTTGTA
* * *
31894078 AAAAAACACTGCTAAAG-ACATGTTCTTTAGCGGCGCTTAAG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG
31894119 AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTT-AG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG
* * *
31894160 AAAAAAACGCCGTTAAAGACCATATTCTTTAGAGGCGCTT-AG
1 -AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG
* * *
31894202 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAA
1 -AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG
* * *
31894245 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGTGCTTAAA
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG
*
31894287 AAAAAACGCCGCTAAAGAACATGTTCTTTTGAGGCGCTTAAG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG
31894329 AAAAAACG
1 AAAAAACG
31894337 ACGTTTTTTT
Statistics
Matches: 199, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
41 17 0.09
42 181 0.91
43 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG
Found at i:31894259 original size:126 final size:126
Alignment explanation
Indices: 31894077--31894334 Score: 410
Period size: 126 Copynumber: 2.0 Consensus size: 126
31894067 GCGTTTTTGT
* *
31894077 AAAAAAACACTGCTAAAGACATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGAACATG
1 AAAAAAACACCGCTAAAGACATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGAACATG
* * *
31894142 TTCTTTAGAGGCGCTTAGAAAAAAACGCCGTTAAAGACCATATTCTTTAGAGGCGCTT-AG
66 TTCTTTAGAGGCGCTTAAAAAAAAACGCCGCTAAAGAACATATTCTTTAGAGGCGCTTAAG
*
31894202 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGAACAT
1 AAAAAAACACCGCTAAAGA-CATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGAACAT
* * * *
31894267 GTTCTTTAGCGGTGCTTAAAAAAAAACGCCGCTAAAGAACATGTTCTTTTGAGGCGCTTAAG
65 GTTCTTTAGAGGCGCTTAAAAAAAAACGCCGCTAAAGAACATATTCTTTAGAGGCGCTTAAG
31894329 AAAAAA
1 AAAAAA
31894335 CGACGTTTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
125 17 0.14
126 96 0.79
127 8 0.07
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (126 bp):
AAAAAAACACCGCTAAAGACATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGAACATG
TTCTTTAGAGGCGCTTAAAAAAAAACGCCGCTAAAGAACATATTCTTTAGAGGCGCTTAAG
Done.