Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014289.1 Kokia drynarioides strain JFW-HI SEQ_129323, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 627727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2188 original size:9 final size:9
Alignment explanation
Indices: 2170--2207 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2160 TTTAAAAAAA
2170 TATA-TTTT
1 TATACTTTT
2178 TATACTTTT
1 TATACTTTT
2187 TATACTTTT
1 TATACTTTT
*
2196 AAATACTTTT
1 -TATACTTTT
2206 TA
1 TA
2208 AATTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 4 0.15
9 14 0.54
10 8 0.31
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (9 bp):
TATACTTTT
Found at i:4618 original size:16 final size:16
Alignment explanation
Indices: 4597--4631 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
4587 CCTGTTTTTG
*
4597 TTTAAGTTTCTAGTTT
1 TTTAAGTTTCTAATTT
4613 TTTAAGTTTCTAATTT
1 TTTAAGTTTCTAATTT
4629 TTT
1 TTT
4632 TTTTCTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.06, G:0.09, T:0.66
Consensus pattern (16 bp):
TTTAAGTTTCTAATTT
Found at i:4632 original size:17 final size:16
Alignment explanation
Indices: 4592--4632 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
4582 TTTTTCCTGT
4592 TTTTGTTTAAGTTTCTA
1 TTTT-TTTAAGTTTCTA
*
4609 GTTTTTTAAGTTTCTAA
1 TTTTTTTAAGTTTCT-A
4626 TTTTTTT
1 TTTTTTT
4633 TTTCTCTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (16 bp):
TTTTTTTAAGTTTCTA
Found at i:10373 original size:53 final size:52
Alignment explanation
Indices: 10178--10369 Score: 228
Period size: 52 Copynumber: 3.7 Consensus size: 52
10168 CATTCATTTC
* * ** *
10178 ATTTA-ATACTCATGATGACA-TATAGTCATCGGACC-TTATAATCCACGAGGG
1 ATTTATATACTCACGATGACACT-TAGTCATCAGACCTTTA-AATCCATAAAGG
** * * *
10229 ATTCGTATACTCATGATGACACTTAGTTATCAGACCTTTAAATCCATAAAAG
1 ATTTATATACTCACGATGACACTTAGTCATCAGACCTTTAAATCCATAAAGG
10281 ATTTCATATACTCACGATGACACTTAGTCATCAGACCTTTAAATCCATAAAGG
1 ATTT-ATATACTCACGATGACACTTAGTCATCAGACCTTTAAATCCATAAAGG
* *
10334 ATTTATTTACTCACGATGACACTTAGTCATCGGACC
1 ATTTATATACTCACGATGACACTTAGTCATCAGACC
10370 CTTTTTTCAT
Statistics
Matches: 122, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
51 3 0.02
52 67 0.55
53 52 0.43
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (52 bp):
ATTTATATACTCACGATGACACTTAGTCATCAGACCTTTAAATCCATAAAGG
Found at i:14182 original size:29 final size:28
Alignment explanation
Indices: 14149--14205 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
14139 AATGAAAAAT
14149 CAAAAAAGAAAAAAAA-AGATGAGTTGAGA
1 CAAAAAAGAAAAAAAATA-ATGAG-TGAGA
14178 CAAAAAAGAAAAAAAATAATGAGTGAGA
1 CAAAAAAGAAAAAAAATAATGAGTGAGA
14206 AAGTATATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
29 21 0.78
30 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.11
Consensus pattern (28 bp):
CAAAAAAGAAAAAAAATAATGAGTGAGA
Found at i:16634 original size:25 final size:24
Alignment explanation
Indices: 16601--16651 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
16591 TTCTTTCCCT
16601 TTATGTCTCACTCCATCTCACC-CCC
1 TTATGTCTC-CTCC-TCTCACCACCC
* *
16626 TTATTTCTCCTTCTCTCACCACCC
1 TTATGTCTCCTCCTCTCACCACCC
16650 TT
1 TT
16652 TTTTGTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 8 0.35
25 8 0.35
ACGTcount: A:0.14, C:0.45, G:0.02, T:0.39
Consensus pattern (24 bp):
TTATGTCTCCTCCTCTCACCACCC
Found at i:21076 original size:65 final size:65
Alignment explanation
Indices: 20972--21102 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
20962 CTGGTTAGAT
*
20972 GTGGGCATTATTTACCCAATTTCTGATAGCACGTGGGTAAGCCCAATCCAATGTATTCCTAAAAA
1 GTGGGCATTATTTACCCAATTTCTGATAGCACGTGGGTAAGCCCAATCCAATGTATTCATAAAAA
21037 GTGGGCATTATTTACCCAATTTCTGATAGCACGTGGGTAAGCCCAATCCAATGTATTCATAAAAA
1 GTGGGCATTATTTACCCAATTTCTGATAGCACGTGGGTAAGCCCAATCCAATGTATTCATAAAAA
21102 G
1 G
21103 AGTGGTATCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (65 bp):
GTGGGCATTATTTACCCAATTTCTGATAGCACGTGGGTAAGCCCAATCCAATGTATTCATAAAAA
Found at i:31242 original size:41 final size:41
Alignment explanation
Indices: 31034--31241 Score: 303
Period size: 41 Copynumber: 5.1 Consensus size: 41
31024 TATGCATTAC
*
31034 CGAGTCATAAGTCTTCCTTTAAGTATAAT-TCATGCTCATC-
1 CGAGTCATGAGTCTTCCTTTAA-TATAATCTCATGCTCATCT
* *
31074 CGAGTCATGAGTCTTCCTTTAATATAATCTAATGCTCATTT
1 CGAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCT
* *
31115 TGAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATTT
1 CGAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCT
** *
31156 CGAGTCACAAGTCTTCCTTTAATATAATCTCATGTTCATCT
1 CGAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCT
* *
31197 CGAGACTTGAGTCTTCCTTTAATATAATCTCATGCTCATCT
1 CGAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCT
31238 CGAG
1 CGAG
31242 AAATAATTAG
Statistics
Matches: 151, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 6 0.04
40 30 0.20
41 115 0.76
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.39
Consensus pattern (41 bp):
CGAGTCATGAGTCTTCCTTTAATATAATCTCATGCTCATCT
Found at i:35014 original size:17 final size:17
Alignment explanation
Indices: 34992--35031 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34982 TACTTATTGC
34992 ATTGTCA-TCACATTTTA
1 ATTGTCACT-ACATTTTA
35009 ATTGTCACTACATTTTA
1 ATTGTCACTACATTTTA
*
35026 TTTGTC
1 ATTGTC
35032 GATGCAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (17 bp):
ATTGTCACTACATTTTA
Found at i:36543 original size:28 final size:28
Alignment explanation
Indices: 36503--36557 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
36493 GATATTCGAT
36503 TTACTCACTGTTGACCCAAAGGTCATGC
1 TTACTCACTGTTGACCCAAAGGTCATGC
36531 TTACTC-CTTGTTGACCCAAAGGTCATG
1 TTACTCAC-TGTTGACCCAAAGGTCATG
36558 ATGCTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (28 bp):
TTACTCACTGTTGACCCAAAGGTCATGC
Found at i:39405 original size:60 final size:60
Alignment explanation
Indices: 39312--39431 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
39302 CTACTAATGT
39312 CACCACATTTAGTGTTTAGTTTTGCGTCTAAAGATGTCAATGCAGGAATTTGTCCCAAAA
1 CACCACATTTAGTGTTTAGTTTTGCGTCTAAAGATGTCAATGCAGGAATTTGTCCCAAAA
* *
39372 CACCACATTTAGTGTTTAGTTTTGCTTCTAAAGATGTCAATGCAGGAATTTGTCTCAAAA
1 CACCACATTTAGTGTTTAGTTTTGCGTCTAAAGATGTCAATGCAGGAATTTGTCCCAAAA
39432 GATCAATGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (60 bp):
CACCACATTTAGTGTTTAGTTTTGCGTCTAAAGATGTCAATGCAGGAATTTGTCCCAAAA
Found at i:59164 original size:40 final size:40
Alignment explanation
Indices: 59120--59214 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 40
59110 AGCAATTCTT
*
59120 ACTTGTTTAAAAATCATTTTGA--TGTGTTAAAATGATTTTA
1 ACTTGTTT-AAAATCATTTTGACTTGT-TTAAAATCATTTTA
59160 ACTTGGTTT-AAATCATTTTGACTTGTTTAAAATCATTTTA
1 ACTT-GTTTAAAATCATTTTGACTTGTTTAAAATCATTTTA
59200 ACTTGATTTTAAAAT
1 ACTTG--TTTAAAAT
59215 TGTTTCAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
39 13 0.27
40 21 0.44
41 10 0.21
42 4 0.08
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (40 bp):
ACTTGTTTAAAATCATTTTGACTTGTTTAAAATCATTTTA
Found at i:59189 original size:19 final size:20
Alignment explanation
Indices: 59120--59214 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 20
59110 AGCAATTCTT
*
59120 ACTTGTTTAAAAATCATTTTG
1 ACTTGTTT-AAAATCATTTTA
*
59141 A--TGTGTTAAAATGATTTTA
1 ACTTGT-TTAAAATCATTTTA
*
59160 ACTTGGTTT-AAATCATTTTG
1 ACTT-GTTTAAAATCATTTTA
59180 ACTTGTTTAAAATCATTTTA
1 ACTTGTTTAAAATCATTTTA
59200 ACTTGATTTTAAAAT
1 ACTTG--TTTAAAAT
59215 TGTTTCAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
19 18 0.29
20 30 0.48
21 4 0.06
22 10 0.16
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (20 bp):
ACTTGTTTAAAATCATTTTA
Found at i:59913 original size:37 final size:37
Alignment explanation
Indices: 59862--59954 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 37
59852 GTAATTTTAA
* *
59862 TCCAGAATTGCGCCCAAACA-TGTCACCGCATGAGCACT
1 TCCAG-ATTACGCCCAAA-ATTGTCACCACATGAGCACT
* * *
59900 TCTAGATTACGCCCAAAATTGTCGCTACATGAGCACT
1 TCCAGATTACGCCCAAAATTGTCACCACATGAGCACT
* *
59937 TCCAGATTGCACCCAAAA
1 TCCAGATTACGCCCAAAA
59955 CTATCGTCAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
36 1 0.02
37 41 0.89
38 4 0.09
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (37 bp):
TCCAGATTACGCCCAAAATTGTCACCACATGAGCACT
Found at i:60098 original size:26 final size:26
Alignment explanation
Indices: 60064--60121 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
60054 ATTGCACCCA
60064 AGAA-TGTCACTACATCAACATGTAC
1 AGAATTGTCACTACATCAACATGTAC
* * *
60089 AGAATTGTCACTGCATGAACATGTCC
1 AGAATTGTCACTACATCAACATGTAC
*
60115 ATAATTG
1 AGAATTG
60122 CGCCCAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (26 bp):
AGAATTGTCACTACATCAACATGTAC
Found at i:66518 original size:20 final size:20
Alignment explanation
Indices: 66460--66518 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
66450 TCTCTTTCAA
*
66460 TTTATTTTTCTCCCATTTAT
1 TTTATTTTTCTCTCATTTAT
*
66480 TTT-TTTCTTCTCTCTATTTCT
1 TTTATTT-TTCTCTC-ATTTAT
*
66501 TTTATTTTTCGCTCATTT
1 TTTATTTTTCTCTCATTT
66519 TCTCTCATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 13 0.39
21 14 0.42
22 3 0.09
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTATTTTTCTCTCATTTAT
Found at i:77379 original size:37 final size:37
Alignment explanation
Indices: 77329--77547 Score: 312
Period size: 37 Copynumber: 5.9 Consensus size: 37
77319 AATCACATAG
* * *
77329 CATTATGCTCTAACCAAGACGTAAGCCTTCTATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
*
77366 CATTACGCTCTAACTGAGACGTAAGCCTTCCATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
* ** *
77403 CATTATGCTCTAATTGAGACATAAGCCTTCCATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
* * *
77440 CATTACGCTCTAATCAAGATGTAAGCCTTCCATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
* *
77477 CATTACGCTTTAACCGAGATGTAAGCCTTCCATATAA
1 CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
77514 CATTACGCTCTAACCGAGACGTAAGCCTTTCCAT
1 CATTACGCTCTAACCGAGACGTAAGCC-TTCCAT
77548 TGAAGAAATT
Statistics
Matches: 164, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
37 158 0.96
38 6 0.04
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (37 bp):
CATTACGCTCTAACCGAGACGTAAGCCTTCCATATAA
Found at i:87063 original size:66 final size:66
Alignment explanation
Indices: 86983--87110 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
86973 TAATTAAAAT
*
86983 TGGCATGATTAAATCAATCAAGCCGTTTAAAAAATGCATCCAAAATTTGAATAATTTAAACCCAC
1 TGGCATGATAAAATCAATCAAGCCGTTTAAAAAATGCATCCAAAATTTGAATAATTTAAACCCAC
87048 A
66 A
*** * * *
87049 TGGCATGATAAAATCAATTGCGCCGTTTAAAGAATGCATGCAAAATTTGAATAATTTGAACC
1 TGGCATGATAAAATCAATCAAGCCGTTTAAAAAATGCATCCAAAATTTGAATAATTTAAACC
87111 TGCGTGAGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.28
Consensus pattern (66 bp):
TGGCATGATAAAATCAATCAAGCCGTTTAAAAAATGCATCCAAAATTTGAATAATTTAAACCCAC
A
Found at i:88194 original size:18 final size:18
Alignment explanation
Indices: 88171--88208 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
88161 TAATATAGTT
88171 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
*
88189 TTATTCGAGTTATTTGAA
1 TTATTCGAGTTATTCGAA
88207 TT
1 TT
88209 CGAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:88378 original size:12 final size:12
Alignment explanation
Indices: 88363--88410 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
88353 TTAGGTTGGA
*
88363 TTTAAATTGATT
1 TTTAAATTTATT
*
88375 TTTAAATTTATA
1 TTTAAATTTATT
88387 TTTAAATTTATATT
1 TTTAAA-TT-TATT
88401 TTTAAATTTA
1 TTTAAATTTA
88411 AATTAATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 18 0.58
13 4 0.13
14 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:90375 original size:30 final size:29
Alignment explanation
Indices: 90283--90656 Score: 311
Period size: 29 Copynumber: 12.8 Consensus size: 29
90273 TTTGATCCTC
*
90283 AAACTTCCAAAAATTCCATTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *** *
90312 AAAATTTTGAAAATTACCA-TTTTACCCCT
1 AAACTTCCAAAAATT-CCATTTTTACCCCA
*
90341 AAACTTCCAAAAATTTCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
90371 AAACTTTCC-AAAATTCTATTTTTACCCCT
1 AAAC-TTCCAAAAATTCCATTTTTACCCCA
*
90400 AAACTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
90430 AAACTTTCC-AAAATTCCATTTTTACCCTC-
1 AAAC-TTCCAAAAATTCCATTTTTACCC-CA
* * * *
90459 AAACTTCCAAAAATTTCATTTTTGATCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
90489 AAACTTTCC-AAAATTCCA-TTTTACCCTC-
1 AAAC-TTCCAAAAATTCCATTTTTACCC-CA
* *
90517 AAACTTCCAAAAATTCCATTTTTGACACTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
90547 AAACTTTCC-CAAATTACATTTTTACCCTC-
1 AAAC-TTCCAAAAATTCCATTTTTACCC-CA
* * *
90576 GAACTTCCAAAAAATCCATTTTTTACCCTA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
* *
90606 AAGCTTTCAAAAATTACCA-TTTTACCCCA
1 AAACTTCCAAAAATT-CCATTTTTACCCCA
* *
90635 GAA-TGTCCAAAATTTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
90657 GATCTCGATT
Statistics
Matches: 275, Mismatches: 45, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.01
28 33 0.12
29 120 0.44
30 99 0.36
31 19 0.07
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:90398 original size:59 final size:59
Alignment explanation
Indices: 90279--90656 Score: 441
Period size: 59 Copynumber: 6.4 Consensus size: 59
90269 ATGTTTTGAT
* **
90279 CCTCAAACTTCCAAAAATTCCA-TTTTGACCCCAAAAATTTTGAAAATTACCATTTTAC
1 CCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTACCATTTTAC
* * *
90337 CC-CTAAACTTCCAAAAATTTCATTTTTAACCCCAAAACTTTCCAAAATT-CTATTTTTAC
1 CCTC-AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTACCA-TTTTAC
*
90396 CC-CTAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCCAAAATT-CCATTTTTAC
1 CCTC-AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTACCA-TTTTAC
* * * *
90455 CCTCAAACTTCCAAAAATTTCATTTTTGATCTCGAAACTTTCCAAAATT-CCATTTTAC
1 CCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTACCATTTTAC
* * *
90513 CCTCAAACTTCCAAAAATTCCATTTTTGACACTAAAACTTTCCCAAATTA-CATTTTTAC
1 CCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTACCA-TTTTAC
* * * * * *
90572 CCTCGAACTTCCAAAAAATCCATTTTTTACCCTAAAGCTTTCAAAAATTACCATTTTAC
1 CCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTACCATTTTAC
*
90631 CC-CAGAA-TGTCCAAAATTTCCATTTT
1 CCTCA-AACT-TCCAAAAATTCCATTTT
90657 GATCTCGATT
Statistics
Matches: 279, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
57 1 0.00
58 73 0.26
59 202 0.72
60 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
CCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTACCATTTTAC
Found at i:90552 original size:176 final size:176
Alignment explanation
Indices: 90279--90738 Score: 512
Period size: 176 Copynumber: 2.6 Consensus size: 176
90269 ATGTTTTGAT
* * * * **
90279 CCTCAAACTTCCAAAAATTCCATTTTGACCCCAAAAATTTTGAAAATTACCATTTTACCCCTAAA
1 CCTCAAACTTCCAAAAATTTCATTTTGATCTCGAAAATTTCAAAAATTACCATTTTACCCCTAAA
* *
90344 CTTCCAAAAATTTCATTTTTAACCCCAAAACTTTCCAAAATT-CTATTTTTACCC-CTAAACTTC
66 CTTCCAAAAATTCCATTTTTAACACCAAAACTTTCCAAAATTAC-ATTTTTACCCTC-AAACTTC
* *
90407 CAAAAATTCCATTTTTGACCCTAAAACTTTCCAAAATT-CCATTTTTAC
129 CAAAAAATCCATTTTTGACCCTAAAACTTTCAAAAATTACCA-TTTTAC
* *
90455 CCTCAAACTTCCAAAAATTTCATTTTTGATCTCGAAACTTTCCAAAATT-CCATTTTA-CCCTCA
1 CCTCAAACTTCCAAAAATTTCA-TTTTGATCTCGAAAATTTCAAAAATTACCATTTTACCCCT-A
* * * *
90518 AACTTCCAAAAATTCCATTTTTGACACTAAAACTTTCCCAAATTACATTTTTACCCTCGAACTTC
64 AACTTCCAAAAATTCCATTTTTAACACCAAAACTTTCCAAAATTACATTTTTACCCTCAAACTTC
* *
90583 CAAAAAATCCATTTTTTACCCTAAAGCTTTCAAAAATTACCATTTTAC
129 CAAAAAATCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTAC
*
90631 CC-CAGAA-TGTCC-AAAATTTCCATTTTGATCTCG--ATTTTCTAAAAATTACCATTTTACCCC
1 CCTCA-AACT-TCCAAAAATTT-CATTTTGATCTCGAAAATTTC-AAAAATTACCATTTTACCCC
** * * *
90691 -CGAGTGT-CTAAAATTCCTTTTTTTAACACCAAAACTTTCCTAAAATTA
62 TAAACT-TCCAAAAATTCC-ATTTTTAACACCAAAACTTTCC-AAAATTA
90739 TAATTTTGCC
Statistics
Matches: 243, Mismatches: 27, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
173 5 0.02
174 17 0.07
175 53 0.22
176 143 0.59
177 25 0.10
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (176 bp):
CCTCAAACTTCCAAAAATTTCATTTTGATCTCGAAAATTTCAAAAATTACCATTTTACCCCTAAA
CTTCCAAAAATTCCATTTTTAACACCAAAACTTTCCAAAATTACATTTTTACCCTCAAACTTCCA
AAAAATCCATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTAC
Found at i:90658 original size:117 final size:115
Alignment explanation
Indices: 90282--90656 Score: 461
Period size: 117 Copynumber: 3.2 Consensus size: 115
90272 TTTTGATCCT
* * **
90282 CAAACTTCCAAAAATTCCA-TTTTGACCCCAAAAATTTTGAAAATTACCA-TTTTACCC-CTAAA
1 CAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCCAAAATTA-CATTTTTACCCTC-AAA
*
90344 CTTCCAAAAATTTCATTTTTAACCCCAAAACTTTCCAAAATTCTATTTTTACCC
64 CTTCCAAAAATTTCATTTTTAACCCC-AAACTTTCCAAAATTCCA-TTTTACCC
*
90398 CTAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCCAAAATTCCATTTTTACCCTCAAAC
1 C-AAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCCAAAATTACATTTTTACCCTCAAAC
* * *
90463 TTCCAAAAATTTCATTTTTGATCTCGAAACTTTCCAAAATTCCATTTTACCC
65 TTCCAAAAATTTCATTTTT-AACCCCAAACTTTCCAAAATTCCATTTTACCC
* * *
90515 TCAAACTTCCAAAAATTCCATTTTTGACACTAAAACTTTCCCAAATTACATTTTTACCCTCGAAC
1 -CAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCCAAAATTACATTTTTACCCTCAAAC
* * * * *
90580 TTCCAAAAAATCCATTTTTTACCCTAAAGCTTTCAAAAATTACCATTTTACCC
65 TTCCAAAAATTTCATTTTTAACCCCAAA-CTTTCCAAAATT-CCATTTTACCC
*
90633 CAGAA-TGTCCAAAATTTCCATTTT
1 CA-AACT-TCCAAAAATTCCATTTT
90657 GATCTCGATT
Statistics
Matches: 228, Mismatches: 21, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
116 6 0.03
117 118 0.52
118 100 0.44
119 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (115 bp):
CAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCCAAAATTACATTTTTACCCTCAAACT
TCCAAAAATTTCATTTTTAACCCCAAACTTTCCAAAATTCCATTTTACCC
Found at i:90700 original size:29 final size:29
Alignment explanation
Indices: 90614--90703 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
90604 TAAAGCTTTC
*
90614 AAAAATTACCATTTTACCCCAGAATGTC-
1 AAAAATTACCATTTTACCCCCGAATGTCT
* * * * * *
90642 CAAAATTTCCATTTTGA-TCTCGATTTTCT
1 AAAAATTACCATTTT-ACCCCCGAATGTCT
*
90671 AAAAATTACCATTTTACCCCCGAGTGTCT
1 AAAAATTACCATTTTACCCCCGAATGTCT
90700 AAAA
1 AAAA
90704 TTCCTTTTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
28 20 0.43
29 26 0.57
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAATGTCT
Found at i:102465 original size:50 final size:48
Alignment explanation
Indices: 102385--102774 Score: 206
Period size: 50 Copynumber: 7.8 Consensus size: 48
102375 GACCCCGACA
* * *
102385 GCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACG
1 GCGGA-CCTGTACCGCAAAGACAC-GAAGGGAAAGGTCTAAGTCACAACG
** * *
102435 GCGGACCGTGTACTTCAGAAGACACGAAGGGAAAGAT-TCAAG-CTGCAACG
1 GCGGACC-TGTACCGCA-AAGACACGAAGGGAAAGGTCT-AAGTC-ACAACG
* * * *
102485 ACGAATCCAGTACCGCAAAGATTCA-AAAGGGAAAGGTCTAAGTCACAACG
1 GCGGA-CCTGTACCGCAAAGA--CACGAAGGGAAAGGTCTAAGTCACAACG
* * * *
102535 GCAGACCGTGTACCTCAAAAGACACGAAGGGAGAGAT-TCAAG-CTACAACG
1 GCGGACC-TGTACCGC-AAAGACACGAAGGGAAAGGTCT-AAGTC-ACAACG
* * * * *
102585 ACGAATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACG
1 GCGGACCT-GTACCGCAAAGACAC-GAAGGGAAAGGTCTAAGTCACAACG
* * * *
102635 GCGGACCATGTACC-CTAGAAG-CATGAAGGG-AAGGATCTAAGACCGCAATG
1 GCGGACC-TGTACCGC-A-AAGACACGAAGGGAAAGG-TCTAAG-TCACAACG
* * * *
102685 GCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACG
1 GCGGA-CCTGTACCGCAAAGACAC-GAAGGGAAAGGTCTAAGTCACAACG
* * *
102735 GCGGAACATGTACCTCAGAAG-CATGAAGGG-AAGGATCTAA
1 GCGG-ACCTGTACCGCA-AAGACACGAAGGGAAAGG-TCTAA
102775 TACCGCAAAG
Statistics
Matches: 256, Mismatches: 53, Indels: 63
0.69 0.14 0.17
Matches are distributed among these distances:
48 8 0.03
49 47 0.18
50 156 0.61
51 41 0.16
52 4 0.02
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (48 bp):
GCGGACCTGTACCGCAAAGACACGAAGGGAAAGGTCTAAGTCACAACG
Found at i:102562 original size:100 final size:99
Alignment explanation
Indices: 102389--102766 Score: 535
Period size: 100 Copynumber: 3.8 Consensus size: 99
102379 CCGACAGCGG
* *
102389 ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCGTGTACTTCAGA
1 ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAGA
102454 AGACACGAAGGGAAAGATTCAAGCTGCAACGACGA
66 AG-CACGAAGGGAAAGATTCAAGCTGCAACGACGA
* * * *
102489 ATCCAGTACCGCAAAGATTCAAAAGGGAAAGGTCTAAGTCACAACGGCAGACCGTGTACCTCAAA
1 ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAGA
* *
102554 AGACACGAAGGGAGAGATTCAAGCTACAACGACGA
66 AG-CACGAAGGGAAAGATTCAAGCTGCAACGACGA
*
102589 ATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACC-CTAG
1 ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTC-AG
* * * * * *
102653 AAGCATGAAGGGAAGGA-TCTAAGACCGCAATGGCGG
65 AAGCACGAAGGGAAAGATTC-AAG-CTGCAACGACGA
* *
102689 ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGA
1 ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAGA
*
102754 AGCATGAAGGGAA
66 AGCACGAAGGGAA
102767 GGATCTAATA
Statistics
Matches: 252, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
98 2 0.01
99 15 0.06
100 234 0.93
101 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (99 bp):
ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAGA
AGCACGAAGGGAAAGATTCAAGCTGCAACGACGA
Found at i:102818 original size:180 final size:180
Alignment explanation
Indices: 102589--102962 Score: 642
Period size: 180 Copynumber: 2.1 Consensus size: 180
102579 ACAACGACGA
*
102589 ATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACC-CTAG
1 ATCTAATACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTC-AG
*
102653 AAGCATGAAGGGAAGGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGGAA
65 AAGCATGAAGGGAAGGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAAGGAA
102718 AGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATGAAGGGAAGG
130 AGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATGAAGGGAAGG
* *
102769 ATCTAATACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGA
1 ATCTAATACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAGA
* *
102834 AGCATGAAGGGAAGGATCTAAGACCGCAATGGCGGATCTAGTACCGCAAAGATACAAAAAGGAGA
66 AGCATGAAGGGAAGGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAAGGAAA
* * *
102899 GGTCTAAGTCGCAACGGTGGACCGTGTACCTCAGAAGCATGAAGGGAAGG
131 GGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATGAAGGGAAGG
*
102949 ATCTAAGACCGCAA
1 ATCTAATACCGCAA
102963 TGGCAAATCC
Statistics
Matches: 183, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
180 182 0.99
181 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.28, T:0.14
Consensus pattern (180 bp):
ATCTAATACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCATGTACCTCAGA
AGCATGAAGGGAAGGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAAGGAAA
GGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATGAAGGGAAGG
Found at i:102827 original size:80 final size:80
Alignment explanation
Indices: 102695--102862 Score: 309
Period size: 80 Copynumber: 2.1 Consensus size: 80
102685 GCGGATCCAG
102695 TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATG
1 TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATG
102760 AAGGGAAGGATCTAA
66 AAGGGAAGGATCTAA
* *
102775 TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCATG
1 TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATG
102840 AAGGGAAGGATCTAA
66 AAGGGAAGGATCTAA
*
102855 GACCGCAA
1 TACCGCAA
102863 TGGCGGATCT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.13
Consensus pattern (80 bp):
TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGAAGCATG
AAGGGAAGGATCTAA
Found at i:102871 original size:100 final size:100
Alignment explanation
Indices: 102767--103015 Score: 385
Period size: 100 Copynumber: 2.5 Consensus size: 100
102757 ATGAAGGGAA
*
102767 GGATCTAATACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
1 GGATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
102832 GAAGCATGAAGGGAAGGATCTAAGACCGCAATGGC
66 GAAGCATGAAGGGAAGGATCTAAGACCGCAATGGC
* * *
102867 GGATCTAGTACCGCAAAGATACAAAAAGGAGAGGTCTAAGTCGCAACGGTGGACCGTGTACCTCA
1 GGATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
102932 GAAGCATGAAGGGAAGGATCTAAGACCGCAATGGC
66 GAAGCATGAAGGGAAGGATCTAAGACCGCAATGGC
** * * * * *
102967 AAATCCAGTACCACAAAG--ACACAAGGGAAAGATCTAAGCCGCAACGGCG
1 GGATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCG
103016 AATCCAGTAC
Statistics
Matches: 135, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
98 25 0.19
100 110 0.81
ACGTcount: A:0.37, C:0.22, G:0.28, T:0.13
Consensus pattern (100 bp):
GGATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCA
GAAGCATGAAGGGAAGGATCTAAGACCGCAATGGC
Found at i:102878 original size:50 final size:48
Alignment explanation
Indices: 102791--103026 Score: 160
Period size: 50 Copynumber: 4.8 Consensus size: 48
102781 AAAGATACAA
* *
102791 AAGGGAAAGG-TCTAAGTCGCAACGGCGGACCGT-GTACCTCAGAAGCATG
1 AAGGG-AAGGATCTAAGCCGCAACGGCGGATC-TAGTACCTCA-AAGCATG
* * *
102840 AAGGGAAGGATCTAAGACCGCAATGGCGGATCTAGTACCGCAAAG-ATACAA
1 AAGGGAAGGATCTAAG-CCGCAACGGCGGATCTAGTACCTCAAAGCAT---G
* * * *
102891 AAAGGAGAGG-TCTAAGTCGCAACGGTGGACCGT-GTACCTCAGAAGCATG
1 AAGGGA-AGGATCTAAGCCGCAACGGCGGATC-TAGTACCTCA-AAGCATG
* ** * * *
102940 AAGGGAAGGATCTAAGACCGCAATGGCAAATCCAGTACCACAAAGACA-C
1 AAGGGAAGGATCTAAG-CCGCAACGGCGGATCTAGTACCTCAAAG-CATG
* * *
102989 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACC
1 AAGGGAAGGATCTAAGCCGCAACGGCGGATCTAGTACC
103027 ACGAAGATTT
Statistics
Matches: 148, Mismatches: 25, Indels: 29
0.73 0.12 0.14
Matches are distributed among these distances:
48 29 0.20
49 44 0.30
50 55 0.37
51 15 0.10
52 5 0.03
ACGTcount: A:0.36, C:0.22, G:0.28, T:0.13
Consensus pattern (48 bp):
AAGGGAAGGATCTAAGCCGCAACGGCGGATCTAGTACCTCAAAGCATG
Found at i:102904 original size:280 final size:278
Alignment explanation
Indices: 102495--103015 Score: 771
Period size: 280 Copynumber: 1.9 Consensus size: 278
102485 ACGAATCCAG
*
102495 TACCGCAAAGATTCAAAAGGGAAAGGTCTAAGTCACAACGGCAGACCGTGTACCTCAAAAGACAC
1 TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCAGACCGTGTACCTCAAAAGACAC
* *
102560 GAAGGGAGAGATTCAAGCTACAACGACGAATCTAGTACCGCAAAGATACAAAAGGGAAAGGTCTA
66 GAAGGGAGAGATTCAAGCCACAACGACGAATCTAGTACCGCAAAGATACAAAAAGGAAAGGTCTA
**
102625 AGTCACAACGGCGGACCATGTACC-CTAGAAGCATGAAGGGAAGGATCTAAGACCGCAATGGCGG
131 AGTCACAACGGCGGACCATGTACCTC-AGAAGCATGAAGGGAAGGATCTAAGACCGCAATGGCAA
* * *
102689 ATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGAACATGTACCTCAGA
195 ATCCAGTACCACAAAG--ACAAAAGGGAAAGATCTAAGCCGCAACGGCGGAACATGTACCTCAGA
102754 AGCATGAAGGGAAGGATCTAA
258 AGCATGAAGGGAAGGATCTAA
* * * *
102775 TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAG-CAT
1 TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCAGACCGTGTACCTCAAAAGACAC
* * * * *
102839 GAAGGGA-AGGA-TCTAAGACCGCAATGGCGGATCTAGTACCGCAAAGATACAAAAAGGAGAGGT
66 GAAGGGAGA-GATTC-AAG-CCACAACGACGAATCTAGTACCGCAAAGATACAAAAAGGAAAGGT
* * *
102902 CTAAGTCGCAACGGTGGACCGTGTACCTCAGAAGCATGAAGGGAAGGATCTAAGACCGCAATGGC
128 CTAAGTCACAACGGCGGACCATGTACCTCAGAAGCATGAAGGGAAGGATCTAAGACCGCAATGGC
*
102967 AAATCCAGTACCACAAAGACACAAGGGAAAGATCTAAGCCGCAACGGCG
193 AAATCCAGTACCACAAAGACAAAAGGGAAAGATCTAAGCCGCAACGGCG
103016 AATCCAGTAC
Statistics
Matches: 216, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
278 31 0.14
279 14 0.06
280 170 0.79
281 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.13
Consensus pattern (278 bp):
TACCGCAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCAGACCGTGTACCTCAAAAGACAC
GAAGGGAGAGATTCAAGCCACAACGACGAATCTAGTACCGCAAAGATACAAAAAGGAAAGGTCTA
AGTCACAACGGCGGACCATGTACCTCAGAAGCATGAAGGGAAGGATCTAAGACCGCAATGGCAAA
TCCAGTACCACAAAGACAAAAGGGAAAGATCTAAGCCGCAACGGCGGAACATGTACCTCAGAAGC
ATGAAGGGAAGGATCTAA
Found at i:102993 original size:49 final size:48
Alignment explanation
Indices: 102940--103033 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
102930 CAGAAGCATG
* *
102940 AAGGGAAGGATCTAAGACCGCAATGGCAAATCCAGTACCACAAAGACAC
1 AAGGGAAAGATCTAAG-CCGCAACGGCAAATCCAGTACCACAAAGACAC
* *
102989 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGA
1 AAGGGAAAGATCTAAGCCGCAACGGCAAATCCAGTACCACAAAGA
103034 TTTGAAGGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 26 0.63
49 15 0.37
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.10
Consensus pattern (48 bp):
AAGGGAAAGATCTAAGCCGCAACGGCAAATCCAGTACCACAAAGACAC
Found at i:103042 original size:49 final size:48
Alignment explanation
Indices: 102938--103075 Score: 150
Period size: 49 Copynumber: 2.8 Consensus size: 48
102928 CTCAGAAGCA
* *
102938 TGAAGGGAAGGATCTAAGACCGCAATGGCAAATCCAGTACCACAAAGAC
1 TGAAGGGAAAGATCTAAG-CCGCAATGGCGAATCCAGTACCACAAAGAC
** * * *
102987 ACAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGATT
1 TGAAGGGAAAGATCTAAGCCGCAATGGCGAATCCAGTACCACAAAGA-C
* * * * *
103036 TGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCCGGTACC
1 TGAAGGGAAAGATCTAAGCCGCAATGGCGAATCCAGTACC
103076 TTAGAAACAT
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 26 0.36
49 47 0.64
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (48 bp):
TGAAGGGAAAGATCTAAGCCGCAATGGCGAATCCAGTACCACAAAGAC
Found at i:103412 original size:7 final size:7
Alignment explanation
Indices: 103400--103425 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
103390 TACACACGAA
103400 AAATTCG
1 AAATTCG
103407 AAATTCG
1 AAATTCG
103414 AAATTCG
1 AAATTCG
103421 AAATT
1 AAATT
103426 TTTTTTGAAT
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:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (7 bp):
AAATTCG
Found at i:104011 original size:17 final size:17
Alignment explanation
Indices: 103989--104021 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
103979 AAAATACTCT
103989 AAAAAATATAAAAATAC
1 AAAAAATATAAAAATAC
*
104006 AAAAAATATAATAATA
1 AAAAAATATAAAAATA
104022 AATATACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAATATAAAAATAC
Found at i:105980 original size:18 final size:18
Alignment explanation
Indices: 105957--105994 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
105947 ATTTGGTATC
105957 TTAATTTGATAAT-TTTTT
1 TTAATTTGAT-ATCTTTTT
105975 TTAATTTGATATCTTTTT
1 TTAATTTGATATCTTTTT
105993 TT
1 TT
105995 CACCTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
TTAATTTGATATCTTTTT
Found at i:115866 original size:20 final size:20
Alignment explanation
Indices: 115843--115882 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
115833 CTACCGGTAG
* *
115843 AACTTCACTTTTATCGATAC
1 AACTTCAATTCTATCGATAC
115863 AACTTCAATTCTATCGATAC
1 AACTTCAATTCTATCGATAC
115883 CTTGAAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (20 bp):
AACTTCAATTCTATCGATAC
Found at i:116105 original size:20 final size:20
Alignment explanation
Indices: 116068--116106 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
116058 CTACCCTGGG
* *
116068 ACTTCTACCGGTAGAACTTC
1 ACTTCTACAGGTACAACTTC
*
116088 ACTTCTACAGTTACAACTT
1 ACTTCTACAGGTACAACTT
116107 TAGTTCTACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (20 bp):
ACTTCTACAGGTACAACTTC
Found at i:128248 original size:22 final size:22
Alignment explanation
Indices: 128220--128277 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
128210 ATAGTTTAAA
128220 TTTAAAATTAAAATTAATAGAG
1 TTTAAAATTAAAATTAATAGAG
*
128242 TTTAAAATTAAAATTAATGGAG
1 TTTAAAATTAAAATTAATAGAG
128264 TTTAAAATTAAAAT
1 TTTAAAATTAAAAT
128278 GGAATTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAATTAAAATTAATAGAG
Found at i:128290 original size:17 final size:18
Alignment explanation
Indices: 128249--128291 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
128239 GAGTTTAAAA
*
128249 TTAAAATT--AATGGAGT
1 TTAAAATTAAAATGGAAT
128265 TTAAAATTAAAATGGAAT
1 TTAAAATTAAAATGGAAT
128283 TT-AAATTAA
1 TTAAAATTAA
128292 TTTATAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (18 bp):
TTAAAATTAAAATGGAAT
Found at i:128323 original size:85 final size:85
Alignment explanation
Indices: 128180--128338 Score: 264
Period size: 85 Copynumber: 1.9 Consensus size: 85
128170 TAAAATGAAA
* * *
128180 TTAAAGTTGAAATAGAATTTAAATTAATTTATAGTTTAAATTTAAAATTAAAATTAATAGAGTTT
1 TTAAAATTAAAATAGAATTTAAATTAATTTATAGTTTAAATTCAAAATTAAAATTAATAGAGTTT
128245 AAAATTAAAATTAATGGAGT
66 AAAATTAAAATTAATGGAGT
* *
128265 TTAAAATTAAAATGGAATTTAAATTAATTTATAGTTTAAATTCGAAATTAAAATTAATAGAGTTT
1 TTAAAATTAAAATAGAATTTAAATTAATTTATAGTTTAAATTCAAAATTAAAATTAATAGAGTTT
*
128330 GAAATTAAA
66 AAAATTAAA
128339 GTTGAAATGA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.40
Consensus pattern (85 bp):
TTAAAATTAAAATAGAATTTAAATTAATTTATAGTTTAAATTCAAAATTAAAATTAATAGAGTTT
AAAATTAAAATTAATGGAGT
Found at i:128351 original size:17 final size:17
Alignment explanation
Indices: 128329--128371 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
128319 TAATAGAGTT
128329 TGAAATTAAAGTTGAAA
1 TGAAATTAAAGTTGAAA
*
128346 TGAAATTAAGGTTGAAA
1 TGAAATTAAAGTTGAAA
128363 TGAAATTAA
1 TGAAATTAA
128372 CATACAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (17 bp):
TGAAATTAAAGTTGAAA
Found at i:128528 original size:19 final size:19
Alignment explanation
Indices: 128490--128560 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
128480 CTAAATTGAA
*
128490 TTTGAAAATAAAA-TACTAG
1 TTTGAAATTAAAATTA-TAG
128509 TTTGAAATTAAAATTATAG
1 TTTGAAATTAAAATTATAG
*
128528 TTT-AAATTTGAAATTA-AG
1 TTTGAAA-TTAAAATTATAG
*
128546 -TTGAAATGAAAATTA
1 TTTGAAATTAAAATTA
128561 AATGAAATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 9 0.20
18 8 0.18
19 26 0.58
20 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTGAAATTAAAATTATAG
Found at i:128551 original size:11 final size:11
Alignment explanation
Indices: 128529--128627 Score: 69
Period size: 12 Copynumber: 8.6 Consensus size: 11
128519 AAATTATAGT
128529 TTAAATTTGAAA
1 TTAAA-TTGAAA
*
128541 TTAAGTTGAAA
1 TTAAATTGAAA
*
128552 TGAAAATT-AAA
1 T-TAAATTGAAA
*
128563 TGAAATTGAAA
1 TTAAATTGAAA
128574 TTAAAGTTGAAA
1 TTAAA-TTGAAA
*
128586 -TAGAATT-AACG
1 TTA-AATTGAA-A
*
128597 TTTAATTGAAAA
1 TTAAATTG-AAA
128609 TTAAATTCGAAA
1 TTAAATT-GAAA
128621 TTAAATT
1 TTAAATT
128628 AATAAAAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
10 7 0.10
11 26 0.38
12 33 0.48
13 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (11 bp):
TTAAATTGAAA
Found at i:128566 original size:16 final size:16
Alignment explanation
Indices: 128535--128578 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
128525 TAGTTTAAAT
*
128535 TTGAAATTAAGTTGAAA
1 TTGAAATTAA-ATGAAA
128552 -TGAAAATTAAATGAAA
1 TTG-AAATTAAATGAAA
128568 TTGAAATTAAA
1 TTGAAATTAAA
128579 GTTGAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.32
Consensus pattern (16 bp):
TTGAAATTAAATGAAA
Found at i:128575 original size:52 final size:51
Alignment explanation
Indices: 128510--128629 Score: 136
Period size: 52 Copynumber: 2.3 Consensus size: 51
128500 AAATACTAGT
* * *
128510 TTGAAATTAAAATTATAGTTTAAATTTGAAATTAA-GTTGAAATGAAAATTAAA
1 TTGAAATT-AAATTAAAGTTGAAA-TAG-AATTAACGTTGAAATGAAAATTAAA
* *
128563 -TGAAATTGAAATTAAAGTTGAAATAGAATTAACGTTTAATTGAAAATTAAA
1 TTGAAATT-AAATTAAAGTTGAAATAGAATTAACGTTGAAATGAAAATTAAA
128614 TTCGAAATTAAATTAA
1 TT-GAAATTAAATTAA
128630 TAAAAATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
50 6 0.10
51 18 0.31
52 28 0.48
53 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.36
Consensus pattern (51 bp):
TTGAAATTAAATTAAAGTTGAAATAGAATTAACGTTGAAATGAAAATTAAA
Found at i:128862 original size:12 final size:12
Alignment explanation
Indices: 128847--128919 Score: 71
Period size: 11 Copynumber: 6.2 Consensus size: 12
128837 ATTTTAAATG
128847 AAATTGAAATTT
1 AAATTGAAATTT
*
128859 AAATTTAAATTT
1 AAATTGAAATTT
*
128871 AAA-TGAAATTG
1 AAATTGAAATTT
*
128882 AAA-TGAAA-TG
1 AAATTGAAATTT
*
128892 AAATTTAAATTT
1 AAATTGAAATTT
*
128904 AAAATTAAAATTT
1 -AAATTGAAATTT
128917 AAA
1 AAA
128920 ATTGCATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
10 5 0.10
11 18 0.35
12 18 0.35
13 11 0.21
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:128873 original size:29 final size:29
Alignment explanation
Indices: 128831--128919 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
128821 TTATACTTAC
*
128831 AATTTAATTTTAAATGAAATTGAAATTTA
1 AATTTAAATTTAAATGAAATTGAAATTTA
*
128860 AATTTAAATTTAAATGAAATTGAAA-TGA
1 AATTTAAATTTAAATGAAATTGAAATTTA
* * *
128888 AA-TGAAATTTAAATTTAAAATTAAAATTTA
1 AATTTAAATTTAAA--TGAAATTGAAATTTA
128918 AA
1 AA
128920 ATTGCATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.20
28 4 0.08
29 33 0.65
30 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
AATTTAAATTTAAATGAAATTGAAATTTA
Found at i:128892 original size:16 final size:16
Alignment explanation
Indices: 128871--128901 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
128861 ATTTAAATTT
128871 AAATGAAATTGAAATG
1 AAATGAAATTGAAATG
*
128887 AAATGAAATTTAAAT
1 AAATGAAATTGAAAT
128902 TTAAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (16 bp):
AAATGAAATTGAAATG
Found at i:128903 original size:6 final size:6
Alignment explanation
Indices: 128831--128919 Score: 69
Period size: 6 Copynumber: 15.3 Consensus size: 6
128821 TTATACTTAC
* * * *
128831 AATTTA ATTTTA AA-TGA AATTGA AATTTA AATTTA AATTTA AA-TGA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * *
128877 AATTGA AA-TGA AA-TGA AATTTA AATTTAA AATTAA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA AA
128920 ATTGCATAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
5 18 0.25
6 48 0.68
7 5 0.07
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:128914 original size:13 final size:13
Alignment explanation
Indices: 128892--128922 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
128882 AAATGAAATG
*
128892 AAATTTAAATTTA
1 AAATTAAAATTTA
128905 AAATTAAAATTTA
1 AAATTAAAATTTA
128918 AAATT
1 AAATT
128923 GCATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTAAAATTTA
Found at i:129654 original size:20 final size:20
Alignment explanation
Indices: 129622--129660 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
129612 ATTACTTTCA
129622 ATTACCTTTGATCACCTCCG
1 ATTACCTTTGATCACCTCCG
129642 ATTA-CTTTCGATCACCTCC
1 ATTACCTTT-GATCACCTCC
129661 AACTACCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.36, G:0.08, T:0.36
Consensus pattern (20 bp):
ATTACCTTTGATCACCTCCG
Found at i:130724 original size:23 final size:21
Alignment explanation
Indices: 130694--130760 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
130684 TTTCGAATTC
*
130694 TTTTAAATAAATTTTTTTATAT
1 TTTTAAAT-AATATTTTTATAT
130716 TTTTGAAAT-ATATTTTTATATT
1 TTTT-AAATAATATTTTTATA-T
*
130738 TTTTAAAT-ATATATTTATAT
1 TTTTAAATAATATTTTTATAT
130758 TTT
1 TTT
130761 CGAATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.10
21 24 0.59
22 9 0.22
23 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (21 bp):
TTTTAAATAATATTTTTATAT
Found at i:130731 original size:21 final size:21
Alignment explanation
Indices: 130707--130760 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
130697 TAAATAAATT
130707 TTTTTATATTTTTGAAATATA
1 TTTTTATATTTTTGAAATATA
*
130728 TTTTTATATTTTTTAAATATA
1 TTTTTATATTTTTGAAATATA
*
130749 TATTTATATTTT
1 TTTTTATATTTT
130761 CGAATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTATATTTTTGAAATATA
Found at i:130756 original size:29 final size:30
Alignment explanation
Indices: 130735--130791 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
130725 ATATTTTTAT
130735 ATTTTTTAAATATA-TATTTATATTTTCGA
1 ATTTTTTAAATATATTATTTATATTTTCGA
*
130764 ATTTTTTAAATATATTTTTTATATTTTC
1 ATTTTTTAAATATATTATTTATATTTTC
130792 AAAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (30 bp):
ATTTTTTAAATATATTATTTATATTTTCGA
Found at i:130798 original size:72 final size:71
Alignment explanation
Indices: 130679--130890 Score: 248
Period size: 70 Copynumber: 2.9 Consensus size: 71
130669 TATGGTAAGA
* * **
130679 TATATTTTCGAATTCTTTTAAATAAATTTTTTTATATTTTTGAAATATATTTTTATATTTTTTAA
1 TATATTTTCGAATT-TTTTAAATATA-TTTTTTATA-TTTTCAAATATATTTTTATATTTTAAAA
130744 ATATATATT
63 ATATATATT
130753 TATATTTTCGAATTTTTTAAATATATTTTTTATATTTTCAAA-ATATTTTTATATTTTAAAAATA
1 TATATTTTCGAATTTTTTAAATATATTTTTTATATTTTCAAATATATTTTTATATTTTAAAAATA
* *
130817 TTTTTT
66 TATATT
* * * * * *
130823 TACATCTTCGAATTTTTTAAAATATATATTTTTTTAGTTTCAAA-ATATTTTTTACATTTTCAAA
1 TATATTTTCGAATTTTTT-AAATATAT-TTTTTATATTTTCAAATATA-TTTTTATATTTTAAAA
130887 ATAT
63 ATAT
130891 TTTTTGAAAT
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
70 40 0.33
71 15 0.12
72 26 0.21
73 28 0.23
74 14 0.11
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.58
Consensus pattern (71 bp):
TATATTTTCGAATTTTTTAAATATATTTTTTATATTTTCAAATATATTTTTATATTTTAAAAATA
TATATT
Found at i:130803 original size:19 final size:19
Alignment explanation
Indices: 130767--130821 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
130757 TTTTCGAATT
*
130767 TTTTAAATATATTTTTTATA
1 TTTTAAAAATA-TTTTTATA
*
130787 TTTTCAAAATATTTTTATA
1 TTTTAAAAATATTTTTATA
130806 TTTTAAAAATATTTTT
1 TTTTAAAAATATTTTT
130822 TTACATCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAAATATTTTTATA
Found at i:130824 original size:21 final size:21
Alignment explanation
Indices: 130764--130824 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
130754 ATATTTTCGA
*
130764 ATTTTTTAAATATATTTTT-T
1 ATTTTTAAAATATATTTTTAT
*
130784 ATATTTTCAAA-ATATTTTTAT
1 AT-TTTTAAAATATATTTTTAT
* *
130805 ATTTTAAAAATATTTTTTTA
1 ATTTTTAAAATATATTTTTA
130825 CATCTTCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAAAATATATTTTTAT
Found at i:130870 original size:19 final size:20
Alignment explanation
Indices: 130848--130895 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
130838 TTTAAAATAT
*
130848 ATATTTTTT-TAGTTTCAAA
1 ATATTTTTTACAGTTTCAAA
*
130867 ATATTTTTTACATTTTCAAA
1 ATATTTTTTACAGTTTCAAA
130887 ATATTTTTT
1 ATATTTTTT
130896 GAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATTTTTTACAGTTTCAAA
Found at i:132759 original size:59 final size:59
Alignment explanation
Indices: 132687--132801 Score: 187
Period size: 59 Copynumber: 1.9 Consensus size: 59
132677 AGGGAAATTT
*
132687 GGTGTCGGCCATTGGTTGCCAAACACCAAAAAAATT-ATTTTTTAATTCGTATTTTTATG
1 GGTGTCGGCCATTGGTTGCCAAACAACAAAAAAATTAATTTTTT-ATTCGTATTTTTATG
*
132746 GGTGTCGGCCATTGGTTGTCAAACAACAAAAAAATTAAATTTTTTATTCGTATTTT
1 GGTGTCGGCCATTGGTTGCCAAACAACAAAAAAATT-AATTTTTTATTCGTATTTT
132802 GGCTGGATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
59 34 0.65
60 11 0.21
61 7 0.13
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (59 bp):
GGTGTCGGCCATTGGTTGCCAAACAACAAAAAAATTAATTTTTTATTCGTATTTTTATG
Found at i:133070 original size:59 final size:60
Alignment explanation
Indices: 132983--133105 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 60
132973 CAAACACCCG
* ** * * *
132983 AAAAAAAATATTTTTGGGACTCGAAAAAGAGG-GTGTTGACCATGGGTTGGCAGACAC-CA
1 AAAAAAAATATTTTTGGGACTCAAAAAAG-GGAGTGTCAACAATGGCTTGACAGACACTCA
*
133042 AAAAAAAATATTTTTGGTA-TCTAAAAAAGGGAGTGTCAACAATGGCTTGACAGACACTCA
1 AAAAAAAATATTTTTGGGACTC-AAAAAAGGGAGTGTCAACAATGGCTTGACAGACACTCA
133102 AAAA
1 AAAA
133106 GTTAATTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
58 4 0.07
59 44 0.81
60 6 0.11
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (60 bp):
AAAAAAAATATTTTTGGGACTCAAAAAAGGGAGTGTCAACAATGGCTTGACAGACACTCA
Found at i:133913 original size:89 final size:85
Alignment explanation
Indices: 133764--133991 Score: 255
Period size: 89 Copynumber: 2.6 Consensus size: 85
133754 GTGTAAAAAT
* * *
133764 CCCTCAAACATTTTCAAAAAA-AATTAAGCCCCTACTTTTTCTTGCACTCATTTGGATACTTAAA
1 CCCTCAAACTTTTTCAAAAAAGAATTAAACCCCTACTTTTTCTTGCACTCAATTGGATACTTAAA
* *
133828 CTTTCAAAATGTATAAAAAAGG
66 CTTTCAAAATGCAT--AAAAGA
* ** * * *
133850 TCCTCAAACTTTTTCAAAAAAGCAATTAAACCGTTGCTTTTATTTTGCACTCAATTGGATACTTG
1 CCCTCAAACTTTTTCAAAAAAG-AATTAAACCCCTACTTTT-TCTTGCACTCAATTGGATACTTA
133915 AACTTTCAAAATGCATAAAAGA
64 AACTTTCAAAATGCATAAAAGA
* * *
133937 CCCTCAAACTTTTTCAAAAAAAGAAATTAAGCCCCGA-TTTTT-TTGTACTCAATTG
1 CCCTCAAACTTTTTC-AAAAAAG-AATTAAACCCCTACTTTTTCTTGCACTCAATTG
133992 AGTATTTGAA
Statistics
Matches: 119, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
85 12 0.10
86 20 0.17
87 23 0.19
88 29 0.24
89 35 0.29
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (85 bp):
CCCTCAAACTTTTTCAAAAAAGAATTAAACCCCTACTTTTTCTTGCACTCAATTGGATACTTAAA
CTTTCAAAATGCATAAAAGA
Found at i:137211 original size:16 final size:16
Alignment explanation
Indices: 137190--137220 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
137180 ATAATGTGAA
137190 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
137206 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
137221 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:138053 original size:26 final size:26
Alignment explanation
Indices: 138011--138068 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
138001 ATTATGGGCG
*
138011 CAATTCTAGACACGTTCATGTAGCGA
1 CAATTCTAGACACGTTCATGCAGCGA
*
138037 CAATTCT-GTACATGTTCATGCAGCGA
1 CAATTCTAG-ACACGTTCATGCAGCGA
138063 -AATTCT
1 CAATTCT
138069 TGGATGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (26 bp):
CAATTCTAGACACGTTCATGCAGCGA
Found at i:138702 original size:5 final size:5
Alignment explanation
Indices: 138687--138737 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
138677 ATATAAATAT
*
138687 TTTTCC TTTTC TTTTC TTTTC TTTTC TTCTTC TTTTTT TTTTC TTTT-
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TT-TTC -TTTTC TTTTC TTTTC
138734 TTTT
1 TTTT
138738 TTATGTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 26 0.63
6 9 0.22
7 2 0.05
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:138734 original size:11 final size:11
Alignment explanation
Indices: 138693--138739 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
138683 ATATTTTTCC
*
138693 TTTTC-TTTTC
1 TTTTCTTTTTT
*
138703 TTTTCTTTTCT
1 TTTTCTTTTTT
*
138714 TCTTCTTTTTT
1 TTTTCTTTTTT
138725 TTTTCTTTTTT
1 TTTTCTTTTTT
138736 TTTT
1 TTTT
138740 ATGTAATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
10 5 0.16
11 26 0.84
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:141193 original size:16 final size:16
Alignment explanation
Indices: 141172--141202 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
141162 ATAATGTGAA
141172 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
141188 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
141203 GGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:142013 original size:26 final size:26
Alignment explanation
Indices: 141971--142024 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
141961 ATTTTGGGCG
141971 CAATTCTGGACACGTTCATGCAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
* *
141997 CAATTCTGTACATGTTCATGCAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
142023 CA
1 CA
142025 TTCCTGGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACACGTTCATGCAGCGA
Found at i:142055 original size:37 final size:38
Alignment explanation
Indices: 142014--142111 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 38
142004 GTACATGTTC
142014 ATGCAGCGACATTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
* * * *
142051 ATGCAGCGATAGTT-CTAGATGCAATTTGAAGAATATTT
1 ATGCAGCGACA-TTCCTGGGTGCAATTTGAAGAATACTT
* *
142089 ATGCAGCGACAATCTTGGGTGCA
1 ATGCAGCGACATTCCTGGGTGCA
142112 TTTCGAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
37 19 0.39
38 30 0.61
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (38 bp):
ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
Found at i:142172 original size:37 final size:37
Alignment explanation
Indices: 142131--142201 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
142121 TATTCCTATA
* *
142131 GCGACAGTTTTGGGTACAATCTGGAAGTGCTCATGTG
1 GCGACAGTTTTGGGCACAATCTAGAAGTGCTCATGTG
*
142168 GCGACAGTTTTGGGCACGATCTAGAAGTGCTCAT
1 GCGACAGTTTTGGGCACAATCTAGAAGTGCTCAT
142202 ACAGCTACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (37 bp):
GCGACAGTTTTGGGCACAATCTAGAAGTGCTCATGTG
Found at i:146345 original size:17 final size:17
Alignment explanation
Indices: 146325--146369 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
146315 CCTTTCTCAT
*
146325 TGCATTTTTATTGTCAC
1 TGCATTTTCATTGTCAC
* * *
146342 TGCATCTACATTGTCAT
1 TGCATTTTCATTGTCAC
146359 TGCATTTTCAT
1 TGCATTTTCAT
146370 ATATCATTGT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (17 bp):
TGCATTTTCATTGTCAC
Found at i:146946 original size:17 final size:17
Alignment explanation
Indices: 146924--146966 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
146914 CCTCAGTCAC
146924 AAAAAAAAGAGAAAAAG
1 AAAAAAAAGAGAAAAAG
* *
146941 AAAAAAAAGGGGAAAAG
1 AAAAAAAAGAGAAAAAG
146958 AAGAAAAAA
1 AA-AAAAAA
146967 AATATATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAAG
Found at i:155640 original size:9 final size:9
Alignment explanation
Indices: 155616--155666 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
155606 GGTTCCTTCA
155616 TTTCATTCTC
1 TTTC-TTCTC
155626 -TTCTTCTC
1 TTTCTTCTC
155634 TTTCTTC-C
1 TTTCTTCTC
155642 TTCTCTTCTTC
1 TT-TCTTC-TC
*
155653 TTCCTTCTC
1 TTTCTTCTC
155662 TTTCT
1 TTTCT
155667 GCTGGTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.23
9 20 0.57
10 4 0.11
11 3 0.09
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTCTTCTC
Found at i:155655 original size:15 final size:14
Alignment explanation
Indices: 155624--155664 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
155614 CATTTCATTC
155624 TCTT-CTTCTC-TT
1 TCTTCCTTCTCTTT
155636 TCTTCCTTCTCTTCT
1 TCTTCCTTCTCTT-T
155651 TCTTCCTTCTCTTT
1 TCTTCCTTCTCTTT
155665 CTGCTGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.15
13 6 0.23
14 2 0.08
15 14 0.54
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TCTTCCTTCTCTTT
Found at i:166164 original size:20 final size:20
Alignment explanation
Indices: 166136--166177 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
166126 ACCTATTCTT
166136 TCACACTAAACACTCCCAAA
1 TCACACTAAACACTCCCAAA
* * *
166156 TCACTCTAAACCCTCTCAAA
1 TCACACTAAACACTCCCAAA
166176 TC
1 TC
166178 CCTTCTCCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.21
Consensus pattern (20 bp):
TCACACTAAACACTCCCAAA
Found at i:170529 original size:12 final size:12
Alignment explanation
Indices: 170512--170561 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
170502 CAGGTTCTGT
170512 TTCTTCTTTCTC
1 TTCTTCTTTCTC
170524 TTCTTCCTTTC-C
1 TTCTT-CTTTCTC
*
170536 TTCTTCTTTTTC
1 TTCTTCTTTCTC
* *
170548 TTCATCCTTCTC
1 TTCTTCTTTCTC
170560 TT
1 TT
170562 GAGCACCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 23 0.72
13 5 0.16
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:171992 original size:24 final size:24
Alignment explanation
Indices: 171965--172022 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
171955 GCGGTGGTCG
171965 GAGTGTTTTTAGAAGAGCGTTTAT
1 GAGTGTTTTTAGAAGAGCGTTTAT
*
171989 GAGTGTTTTTAGAAGAGTGTTTAT
1 GAGTGTTTTTAGAAGAGCGTTTAT
172013 GAGTGTTTTT
1 GAGTGTTTTT
172023 GAAAGCACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (24 bp):
GAGTGTTTTTAGAAGAGCGTTTAT
Found at i:175313 original size:152 final size:152
Alignment explanation
Indices: 175053--175339 Score: 418
Period size: 152 Copynumber: 1.9 Consensus size: 152
175043 TGCCCATCCG
* *
175053 TGAAAACCTTTTCCCCAAACATGTTTAAACTGTGACCTCCAGAGATAAGTAGTCTCTATCGTCTT
1 TGAAAACCTTTTCCCCAAACATGTTTAAACTGTGACATCCAGAGATAAGTAGTCTCTATCCTCTT
* * *
175118 GCTATGCTAGCAAAAGATCGAAAGATCCAATTAGAGTAGTGACTAGTTGATTGGAGGAAAATCCC
66 ACTATGCTAGCAAAAGATCGAAAGATCCAATGAGAGTAGTGACTAATTGATTGGAGGAAAATCCC
175183 CAAAAATGGTATTATCTATCAA
131 CAAAAATGGTATTATCTATCAA
* * * *
175205 TGAAAACCTTTTCCCCAAAC-TAGTTTAAACTTTGACATCTAGCGATAAGTAGTCTTTATCCTCT
1 TGAAAACCTTTTCCCCAAACAT-GTTTAAACTGTGACATCCAGAGATAAGTAGTCTCTATCCTCT
* *
175269 TACTATGTTGGCAAAAGATC-AAGAGATCCAACTGA-AGTAGTGACTAATTGATTGGAGGAAAAT
65 TACTATGCTAGCAAAAGATCGAA-AGATCCAA-TGAGAGTAGTGACTAATTGATTGGAGGAAAAT
*
175332 TCCCAAAA
128 CCCCAAAA
175340 CCCAACAATT
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
151 3 0.03
152 115 0.96
153 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (152 bp):
TGAAAACCTTTTCCCCAAACATGTTTAAACTGTGACATCCAGAGATAAGTAGTCTCTATCCTCTT
ACTATGCTAGCAAAAGATCGAAAGATCCAATGAGAGTAGTGACTAATTGATTGGAGGAAAATCCC
CAAAAATGGTATTATCTATCAA
Found at i:181070 original size:20 final size:21
Alignment explanation
Indices: 181045--181084 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
181035 GGATGTCTTA
*
181045 GGGAGATG-GACGAAGAAAGT
1 GGGAGAAGCGACGAAGAAAGT
*
181065 GGGAGAAGCGACGAGGAAAG
1 GGGAGAAGCGACGAAGAAAG
181085 CCGAGGATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.40, C:0.07, G:0.47, T:0.05
Consensus pattern (21 bp):
GGGAGAAGCGACGAAGAAAGT
Found at i:181798 original size:24 final size:23
Alignment explanation
Indices: 181750--181820 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
181740 ATTCATTAAC
* *
181750 ATTGTTCGTGAACATATTCAATT
1 ATTGTTCGTGAACATGTTCGATT
*
181773 ATATGTTCGTGAACATGTTCGTTT
1 AT-TGTTCGTGAACATGTTCGATT
* *
181797 ATTTTTCGTAAACATGTTCGATT
1 ATTGTTCGTGAACATGTTCGATT
181820 A
1 A
181821 AGTTAAATGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (23 bp):
ATTGTTCGTGAACATGTTCGATT
Found at i:186332 original size:14 final size:12
Alignment explanation
Indices: 186294--186336 Score: 52
Period size: 11 Copynumber: 3.5 Consensus size: 12
186284 TAATTTAGTC
*
186294 ATTTTTATTTTT
1 ATTTTTATTTTA
186306 A-TTTTATTTTA
1 ATTTTTATTTTA
186317 ATTTTTATATTCTA
1 ATTTTTAT-TT-TA
186331 ATTTTT
1 ATTTTT
186337 CGTTTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 10 0.37
12 7 0.26
13 2 0.07
14 8 0.30
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:188634 original size:216 final size:216
Alignment explanation
Indices: 188269--191662 Score: 3999
Period size: 216 Copynumber: 15.7 Consensus size: 216
188259 ATTTTGTTAG
* * * **
188269 TTTGTTAACAACTTTTGATCTTTGAATTAAAATCTTATTTGTGTGAGAATTGTTTCTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * *
188334 TCTTGGCCGAACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT-TAGTTCCTTAAA
66 TCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGA-TTCCTTAAA
* ** ** *
188398 GTATTCAAAACGATCCATTCCTTCGAGCAATTTTTCGAACATTCTGTGCTCGAAAAATCGTATCA
130 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
* *
188463 TTTGGTCTAAATATTTTGTCAG
195 TTTGGTCTAAATAGTTTGTCAT
** * * * *
188485 TTTGTAATA-AACTTTTTTTCTCTAAATTAAACACTTATTTATGTGAGAATAT-TTTCTCTCTTG
1 TTTGTAA-ACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT-TGTTTCTCTCTTG
* * * * *
188548 GTTCTTGGTCGAACTTCTGAAATTGTCAAACTTTTATGTGTTCTTTTATAACTTCGATTCTTTGA
64 GTTCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAA
* * * * *
188613 AGTATTCAAGAC-AGCCCATTCCATAGAGCAATTTTCCGAACATTCCATGCTTGGGAAATCGCAT
129 AGTATTCAAGACGA-TCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCAT
188677 CATTTGGTCTTAAATAGATTT-TCAT
193 CATTTGGTC-TAAATAG-TTTGTCAT
* * * * **
188702 TTTGTAAACAACCTTTGGTTTTTGATTTAAAAACTTATTTACGTGAGAATTGTTTCTTTCTAAGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
** * *
188767 TCTTGGTTGAATTTAC-GAACA-TGTCAAACTTTTACGAGTTCTTTTATAACTTTGGA-TCCTTA
66 TCTTGGCCGAACTT-CTGAA-ATTGTCAAACTTTTACGAGTTCTTTTATAAC-TTCGATTCCTTA
* * * * * *
188829 AAGTATTCAAGACGATCCATTCCTCCGAGCAATTTTCCAAACATTCCATGATAGTGAAATCGCAT
128 AAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCAT
* *
188894 CATTCGGTCTAAATAGTTTATCAT
193 CATTTGGTCTAAATAGTTTGTCAT
* * ** * *
188918 TTTGTAAACAACTATTGGTCTTTGAGTTAAAAACTTATTTGTGTGAGAGTTATTTCTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
***** * * * * *
188983 TCTTAATTTAATTTTTGAACA-TGTCAAACCTTTATGAGTTCTTTTATAACTTCGGTTCCTTAAA
66 TCTTGGCCGAACTTCTGAA-ATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
* * * * **
189047 GAATTGAAGACGATCTATTCCTTCGAGCAATTTTCCGAACATTCCATGCAAGGGAAATCGCATCA
130 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
189112 TTTGGTCTAAATAGTTTGTCAT
195 TTTGGTCTAAATAGTTTGTCAT
* * *
189134 TTTGTAATCTACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
** * * * *
189199 TCTTGGCTAAACTTCCGAACTTGTCAAATTTTTACGAGTTCTTTTATAACTTTATAACTTTGGTT
66 TCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAAC--T-T--C---GATT
* * ** * * * *
189264 CCTTAAAGAATTCAAGGCGATTTATTCCTTTGAGCAATTTTTTGAACATTCCATGCTCAGGAGAT
123 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAAT
189329 CGCATCATTTGGTCTAAATAGTTTGTCAT
188 CGCATCATTTGGTCTAAATAGTTTGTCAT
* * * *
189358 TTTATAAACAACTTTTGGTCTATGAATTAAAAACTAATTTACGGGAGAATTGTTTCTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * * * *
189423 TCTTGGCCGAACTTC-CAAACTTGTCAAACTTTTACAAGTTCTTTTACAACTCCGGTTCCTTAAA
66 TCTTGGCCGAACTTCTGAAA-TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
* * * * * * ** * *
189487 GTATTCAAGATGATCCGTTCCTTCGAGCTATTTTTTGAACATTCTATGTTCAAGAAATTGCAACA
130 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
*
189552 TTTGGTGTAAATAGTTTGTCAT
195 TTTGGTCTAAATAGTTTGTCAT
* *
189574 TTTGTAAACAACTTTTGGTCTTTGATTTAAAAAGTTATTTACGTGAGAATTGTTTCTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * * * *
189639 TCTTGACCGAACTTCCGAACTTGTCAAACTTTTACGAATTCTTTTATAACTTCTG-TTCCTCAAA
66 TCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTC-GATTCCTTAAA
* * * ** * *
189703 GTATTCTAGACGATCCATTCCTTCGAGCAA-ATTTCTGAACATTCGATGCTCGAAAAATAGCATT
130 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCGCATC
*
189767 ATTTGGTCTAAATAGTTTCTCAT
194 ATTTGGTCTAAATAGTTTGTCAT
* * *
189790 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTGTTTACTTGAGAATTGTTTCTCTTTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * * * * * *
189855 TCTTGGCTGAACTT-TCGAACTTTTCAGACTTTTACGATTTCTTTTATAACTTTGGTTCCTTAAA
66 TCTTGGCCGAACTTCT-GAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
* * **
189919 GTATTCAAGACGATCCATTCATTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGTGTCA
130 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCA
*
189984 TTTGGTCTAAATAGTTTGTTAT
195 TTTGGTCTAAATAGTTTGTCAT
* * *
190006 TTTGTAAACAACTTTTGGTCTATGAATTAAAATCTTATTTACGTGAGAATTG-TT-TATCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * *
190069 TCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAG
66 TCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAG
* * *
190134 TATTCAAGA-AATCCATTCTTTTGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCAT
131 TATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCAT
190198 TTGGTCTAAATAGTTTGTCAT
196 TTGGTCTAAATAGTTTGTCAT
* *
190219 TTTGTAAACAACTTTTGGTCTTTGAACTAAAAACTTATTTACGTGAGAAATT-TTTCCCTCTTGG
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAG-AATTGTTTCTCTCTTGG
* * * *
190283 TTCTTGGTCGAACTT-TCAAACTTGTCAAACTTTTACGAGTTCTTTTATAAGTTCGGTTCCTTAA
65 TTCTTGGCCGAACTTCTGAAA-TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAA
* * *
190347 AGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAATATTCCATGCTCGAGAAATCGCATC
129 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATC
*
190412 ATTTGGTCTAAATAGATTGTCAT
194 ATTTGGTCTAAATAGTTTGTCAT
190435 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * *
190500 T-TATGGTCC-AACTTC-CAAAGTTCTCAAACTTTTACGAGTTCTTTTATAACTT-TAGTTCCTT
66 TCT-TGG-CCGAACTTCTGAAA-TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGA-TTCCTT
* * * *
190561 AAAGTATTCAAGACAATCCATTCCTTCGAGTAATTTTTCGAACATGT-GATGCTTGGGAAATCGC
127 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACAT-TCCATGCTCGGGAAATCGC
* *
190625 ATCATTTGTTCTAAATAGTTTGTTAT
191 ATCATTTGGTCTAAATAGTTTGTCAT
* * * * * * * *
190651 TTTGAAAACAACTTTTTGACATTAAATAAAAAACTTATTTACTTGAGAATTGTTTCTATCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * * * * *
190716 TCTTGGCCAAACTTCTGAACTTTTCAGACTTTTACGATTTCTTTTTTAACTTCGATTCCTTAAAG
66 TCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAG
* * * * *
190781 TATTCAGGACGATCTATTCCTTCAAGCAATTTTCCAAACATTCCATGCTCGGGAAATCGC-TACA
131 TATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCAT-CA
* * *
190845 TTTGGCCTAAATAATTTGTTAT
195 TTTGGTCTAAATAGTTTGTCAT
*
190867 TTTGTAAA-ATAC-TTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGG
1 TTTGTAAACA-ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGG
*
190930 TTCTTGGTCGAACTTCT-AAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAA
65 TTCTTGGCCGAACTTCTGAAA-TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAA
* * *
190994 ATTATTCAAGACGATCCATTCC-TCTGAGCAATTTTTCGAACATTCCATGCTTGGGAAATTGCAT
129 AGTATTCAAGACGATCCATTCCTTC-GAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCAT
* *
191058 CATTAGGTTTAAATAGTTTGTCAT
193 CATTTGGTCTAAATAGTTTGTCAT
* * * * * * * *
191082 TCTGTAATCAACTTTTAGTCTTTGAATTATAAACTTAGTTACTTGAGAATTTTTTCCCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
** * * * * * * *
191147 TCTTGGCTAAACTTCTGAACTTGTAAAATTTTTATGAGCTCTTTTATAACTTTGGTTCCTTAAAG
66 TCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAG
* * * ** * **
191212 TATTCAGGACGATCCATTCTTTCAAATAATTTTTCGAACATTCCAAGCTCGGGAAATCGGTTCAT
131 TATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCAT
*
191277 TTGGTCTAAATAGTTTGTAAT
196 TTGGTCTAAATAGTTTGTCAT
* * * *
191298 TTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATATCTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * * * *
191363 TCTTGACCGAACTT-TCGAACTTATCAAACTTTTACTAGTTATTTTATAACTTCGATTCCTTAAA
66 TCTTGGCCGAACTTCT-GAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAA
* * * * *
191427 GTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTCCAATCACTCCATGCTTGGGAAATTGCATG
130 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAA-CATTCCATGCTCGGGAAATCGCATC
* * *
191491 ATTTCGTTTAAATATTTTGTCAT
194 ATTTGGTCTAAATAGTTTGTCAT
* * * *
191514 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAGCTTTTTTACATGAGAATTGTTTTTCTCTTGGT
1 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
* * * *
191579 TCTTGGCCGAAGTT-TCAAACTTGTCAAACTTTTATGTGTTCTTTTATAACTTC-AGTTCCTTAA
66 TCTTGGCCGAACTTCTGAAA-TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGA-TTCCTTAA
*
191642 AGTATTCAAGATGATCCATTC
129 AGTATTCAAGACGATCCATTC
191663 TTACGAGAAC
Statistics
Matches: 2721, Mismatches: 396, Indels: 122
0.84 0.12 0.04
Matches are distributed among these distances:
213 113 0.04
214 88 0.03
215 282 0.10
216 1849 0.68
217 186 0.07
218 11 0.00
219 2 0.00
221 1 0.00
222 1 0.00
223 2 0.00
224 186 0.07
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (216 bp):
TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGT
TCTTGGCCGAACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAG
TATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCAT
TTGGTCTAAATAGTTTGTCAT
Found at i:190534 original size:861 final size:861
Alignment explanation
Indices: 188256--191662 Score: 4201
Period size: 861 Copynumber: 3.9 Consensus size: 861
188246 AGGATGTACT
* * * * * **
188256 AATATTTTGTTAGTTTGTTAACAACTTTTGATCTTTGAATTAAAATCTTATTTGTGTGAGAATTG
1 AATAGTTTGTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
*
188321 TTTCTCTCTTGGTTCTTGGCCGAACTTTTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
66 TTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
* * **
188386 TAGTTCCTTAAAGTATTCAA-AACGATCCATTCCTTCGAGCAATTTTTCGAACATTCTGTGCTCG
131 TGGTTCCTTAAAGTATTCAAGAA--ATCCATTCCTTTGAGCAATTTTTCGAACATTCCATGCTCG
** * * * ** * *
188450 AAAAATCGTATCATTTGGTCTAAATATTTTGTCAGTTTGTAATA-AACTTTTTTTCTCTAAATTA
194 GGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA-ACAACTTTTGGTCTTTGAATTA
* * * *
188514 AACACTTATTTATGTGAGAATATTTTCTCTCTTGGTTCTTGGTCGAACTTCTGAAA-TTGTCAAA
258 AAAACTTATTTACGTGAGAAT-TTTTCCCTCTTGGTTCTTGGTCGAACTT-TCAAACTTGTCAAA
* * * * * * *
188578 CTTTTATGTGTTCTTTTATAACTTCGATTCTTTGAAGTATTCAAGAC-AGCCCATTCCAT-AGAG
321 CTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA-TCCATTCCTTCA-AG
* * * *
188641 CAATTTTCCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTTAAATAGATTTTCATTTTG
384 CAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTC-TAAATAGATTGTCATTTTG
* * * * **
188706 TAAACAACCTTTGGTTTTTGATTTAAAAACTTATTTACGTGAGAATTGTTTCTTTCTAAGTTCTT
448 TAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTT
*** * * * * *
188771 GGTTGAATTTACGAACATGTCAAACTTTTACGAGTTCTTTTATAACTTTGGATCCTTAAAGTATT
513 GACCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTAGTTCCTTAAAGTATT
* * ** * * * *
188836 CAAGACGATCCATTCCTCCGAGCAATTTTCCAAACATTCCATGATAGTGAAATCGCATCATTCGG
578 CAAGACGATCCATTCCTTCGAGCAAATTTCTGAACATTCCATGCTTGGGAAATCGCATCATTTGG
* * * *
188901 TCTAAATAGTTTATCATTTTGTAAACAACTATTGGTCTTTGAGTTAAAAACTTATTT-GTGTGAG
643 TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACT-TGAG
* * ***** * * * * * *
188965 AGTTATTTCTCTCTTGGTTCTTAATTTAATTTTTGAACATGTCAAACCTTTATGAGTTCTTTTAT
707 AATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGATTTCTTTTAT
* * *
189030 AACTTCGGTTCCTTAAAGAATTGAAGACGATCTATTCCTTCGAGCAATTTTCCGAACATTCCATG
772 AACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATG
** *
189095 CAAGGGAAATCGCATCATTTGGTCTA
837 CTCGGGAAATCG-TTCATTTGGTCTA
* * *
189121 AATAGTTTGTCATTTTGTAATCTACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
1 AATAGTTTGTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* ** * *
189186 TTTCTCTTTTGGTTCTTGGCTAAACTTCCGAACTTGTCAAATTTTTACGAGTTCTTTTATAACTT
66 TTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTC-----T---TT
* ** ** *
189251 TATAACTTTGGTTCCTTAAAGAATTCAAGGCGATTTATTCCTTTGAGCAATTTTTTGAACATTCC
123 TATAACTTTGGTTCCTTAAAGTATTCAA-GAAATCCATTCCTTTGAGCAATTTTTCGAACATTCC
* * * *
189316 ATGCTCAGGAGATCGCATCATTTGGTCTAAATAGTTTGTCATTTTATAAACAACTTTTGGTCTAT
187 ATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTT
* * * * *
189381 GAATTAAAAACTAATTTACGGGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCAAACTTG
252 GAATTAAAAACTTATTTACGTGAGAATT-TTTCCCTCTTGGTTCTTGGTCGAACTTTCAAACTTG
* * * * *
189446 TCAAACTTTTACAAGTTCTTTTACAACTCCGGTTCCTTAAAGTATTCAAGATGATCCGTTCCTTC
316 TCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTC
* * * * * * * * * *
189511 GAGCTATTTTTTGAACATTCTATGTTCAAGAAATTGCAACATTTGGTGTAAATAGTTTGTCATTT
381 AAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGATTGTCATTT
* *
189576 TGTAAACAACTTTTGGTCTTTGATTTAAAAAGTTATTTACGTGAGAATTGTTTCTCTCTTGGTTC
446 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTC
* *
189641 TTGACCGAACTTCCGAACTTGTCAAACTTTTACGAATTCTTTTATAACTTCT-GTTCCTCAAAGT
511 TTGACCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT-TAGTTCCTTAAAGT
* * * ** * *
189705 ATTCTAGACGATCCATTCCTTCGAGCAAATTTCTGAACATTCGATGCTCGAAAAATAGCATTATT
575 ATTCAAGACGATCCATTCCTTCGAGCAAATTTCTGAACATTCCATGCTTGGGAAATCGCATCATT
* *
189770 TGGTCTAAATAGTTTCTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTGTTTACTTG
640 TGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACTTG
* * * *
189835 AGAATTGTTTCTCTTTTGGTTCTTGGCTGAACTTTCGAACTTTTCAGACTTTTACGATTTCTTTT
705 AGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGATTTCTTTT
* * **
189900 ATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCATTCGAGCAATTTTTTGAACATTCCA
770 ATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCA
189965 TGCTCGGGAAATCGTGTCATTTGGTCTA
835 TGCTCGGGAAATCGT-TCATTTGGTCTA
* *
189993 AATAGTTTGTTATTTTGTAAACAACTTTTGGTCTATGAATTAAAATCTTATTTACGTGAGAATTG
1 AATAGTTTGTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
*
190058 -TT-TATCTTGGTTCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
66 TTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
*
190121 TGGTTCCTTAAAGTATTCAAGAAATCCATTCTTTTGAGCAATTTTTCGAACATTCCATGCTCGGG
131 TGGTTCCTTAAAGTATTCAAGAAATCCATTCCTTTGAGCAATTTTTCGAACATTCCATGCTCGGG
*
190186 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAACTAAAA
196 AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
190251 ACTTATTTACGTGAGAAATTTTTCCCTCTTGGTTCTTGGTCGAACTTTCAAACTTGTCAAACTTT
261 ACTTATTTACGTGAG-AATTTTTCCCTCTTGGTTCTTGGTCGAACTTTCAAACTTGTCAAACTTT
*
190316 TACGAGTTCTTTTATAAGTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTT
325 TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTT
*
190381 TTCGAATATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGATTGTCATTTTGTAAACAA
390 TTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGATTGTCATTTTGTAAACAA
*
190446 CTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTT-TATGGTCC-
455 CTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCT-T-GACCG
* * *
190509 AACTTCCAAAGTTCTCAAACTTTTACGAGTTCTTTTATAACTTTAGTTCCTTAAAGTATTCAAGA
518 AACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTAGTTCCTTAAAGTATTCAAGA
* * * * *
190574 CAATCCATTCCTTCGAG-TAATTTTTCGAACATGT-GATGCTTGGGAAATCGCATCATTTGTTCT
583 CGATCCATTCCTTCGAGCAAATTTCT-GAACAT-TCCATGCTTGGGAAATCGCATCATTTGGTCT
* * * * * * *
190637 AAATAGTTTGTTATTTTGAAAACAACTTTTTGACATTAAATAAAAAACTTATTTACTTGAGAATT
646 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACTTGAGAATT
* * * * *
190702 GTTTCTATCTTGGTTCTTGGCCAAAC-TTCTGAACTTTTCAGACTTTTACGATTTCTTTTTTAAC
711 GTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACTTGTCAAACTTTTACGATTTCTTTTATAAC
* * * * *
190766 TTCGATTCCTTAAAGTATTCAGGACGATCTATTCCTTCAAGCAATTTTCCAAACATTCCATGCTC
775 TTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTC
* *
190831 GGGAAATCGCTACATTTGGCCTA
840 GGGAAATCG-TTCATTTGGTCTA
* *
190854 AATAATTTGTTATTTTGTAAA-ATAC-TTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATT
1 AATAGTTTGTTATTTTGTAAACA-ACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* *
190917 GTTTCTCTCTTGGTTCTTGGTCGAACTTCTAAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
65 GTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACT
* * * * * *
190982 TCGATTCCTTAAATTATTCAAGACGATCCATTCCTCTGAGCAATTTTTCGAACATTCCATGCTTG
130 TTGGTTCCTTAAAGTATTCAAGA-AATCCATTCCTTTGAGCAATTTTTCGAACATTCCATGCTCG
* * * * * * *
191047 GGAAATTGCATCATTAGGTTTAAATAGTTTGTCATTCTGTAATCAACTTTTAGTCTTTGAATTAT
194 GGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * * * *
191112 AAACTTAGTTACTTGAGAATTTTTTCCCTCTTGGTTCTTGG-CTAAAC-TTCTGAACTTGTAAAA
259 AAACTTATTTACGTGAGAA-TTTTTCCCTCTTGGTTCTTGGTC-GAACTTTC-AAACTTGTCAAA
* * * * * * **
191175 TTTTTATGAGCTCTTTTATAACTTTGGTTCCTTAAAGTATTCAGGACGATCCATTCTTTCAAATA
321 CTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCA
* * ** * *
191240 ATTTTTCGAACATTCCAAGCTCGGGAAATCGGTTCATTTGGTCTAAATAGTTTGTAATTTTGTAA
386 ATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGATTGTCATTTTGTAA
* * * *
191305 ACAACTTTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATATCTCTCTTGGTTCTTGAC
451 ACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGAC
* * * * *
191370 CGAACTTTCGAACTTATCAAACTTTTACTAGTTATTTTATAAC-TTCGATTCCTTAAAGTATTCA
516 CGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTAG-TTCCTTAAAGTATTCA
* * * * * *
191434 AGACGATCCATTCCTTCGAGCAATTTTC-CAATCACTCCATGCTTGGGAAATTGCATGATTTCGT
580 AGACGATCCATTCCTTCGAGCAAATTTCTGAA-CATTCCATGCTTGGGAAATCGCATCATTTGGT
* * * * *
191498 TTAAATATTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAGCTTTTTTACATGAGAA
644 CTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACTTGAGAA
* * * *
191563 TTGTTTTTCTCTTGGTTCTTGGCCGAAGTTTCAAACTTGTCAAACTTTTATG-TGTTCTTTTATA
709 TTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGAT-TTCTTTTATA
* *
191627 ACTTCAGTTCCTTAAAGTATTCAAGATGATCCATTC
773 ACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTC
191663 TTACGAGAAC
Statistics
Matches: 2192, Mismatches: 309, Indels: 84
0.85 0.12 0.03
Matches are distributed among these distances:
860 48 0.02
861 633 0.29
862 131 0.06
863 540 0.25
864 8 0.00
865 104 0.05
870 45 0.02
871 2 0.00
872 434 0.20
873 246 0.11
874 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (861 bp):
AATAGTTTGTTATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
TTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
TGGTTCCTTAAAGTATTCAAGAAATCCATTCCTTTGAGCAATTTTTCGAACATTCCATGCTCGGG
AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAA
ACTTATTTACGTGAGAATTTTTCCCTCTTGGTTCTTGGTCGAACTTTCAAACTTGTCAAACTTTT
ACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTT
TCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGATTGTCATTTTGTAAACAAC
TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGACCGAAC
TTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTAGTTCCTTAAAGTATTCAAGACGA
TCCATTCCTTCGAGCAAATTTCTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATA
GTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACTTGAGAATTGTTTC
TCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGATTTCTTTTATAACTTCGGT
TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGGGAAA
TCGTTCATTTGGTCTA
Found at i:193885 original size:13 final size:13
Alignment explanation
Indices: 193867--193891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193857 ATTAATTTAG
193867 TTTAGATTAATAC
1 TTTAGATTAATAC
193880 TTTAGATTAATA
1 TTTAGATTAATA
193892 TCCTTCACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:197686 original size:13 final size:11
Alignment explanation
Indices: 197648--197679 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
197638 TTTAAAAATA
197648 TAAAATTA--T
1 TAAAATTATTT
197657 TAAAATTATTT
1 TAAAATTATTT
197668 TAAAATTATTT
1 TAAAATTATTT
197679 T
1 T
197680 TTAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 8 0.38
11 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:197691 original size:20 final size:22
Alignment explanation
Indices: 197615--197697 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 22
197605 TAGCAAATGA
*
197615 TTTTAAAATTATTCAAATTATT
1 TTTTAAAATTATTAAAATTATT
*
197637 TTTTAAAAATA-TAAAATTA--
1 TTTTAAAATTATTAAAATTATT
197656 --TTAAAATTATTTTAAAATTATT
1 TTTTAAAATTA--TTAAAATTATT
197678 TTTTAAAA-TA-TAAAATTATT
1 TTTTAAAATTATTAAAATTATT
197698 AAAATCATCA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
17 8 0.16
20 18 0.35
21 7 0.14
22 10 0.20
23 2 0.04
24 6 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTATT
Found at i:197691 original size:40 final size:39
Alignment explanation
Indices: 197617--197702 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 39
197607 GCAAATGATT
*
197617 TTAAAATTATTCAAATTATTTTTTAAAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTAAAAATATAAAATTA
197656 TTAAAATTATTTTAAAATTATTTTTT-AAAATATAAAATTA
1 TTAAAATTA--TTAAAATTATTTTTTAAAAATATAAAATTA
197696 TTAAAAT
1 TTAAAAT
197703 CATCATCATC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 9 0.20
40 21 0.48
41 14 0.32
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (39 bp):
TTAAAATTATTAAAATTATTTTTTAAAAATATAAAATTA
Found at i:198656 original size:33 final size:33
Alignment explanation
Indices: 198619--198703 Score: 161
Period size: 33 Copynumber: 2.6 Consensus size: 33
198609 ATTAAAATTA
198619 TTTAATAATTTTATTTTTTTCAAAAAAAATAAT
1 TTTAATAATTTTATTTTTTTCAAAAAAAATAAT
198652 TTTAATAATTTTATTTTTTTCAAAAAAAATAAT
1 TTTAATAATTTTATTTTTTTCAAAAAAAATAAT
*
198685 TTTAATAATTTTATATTTT
1 TTTAATAATTTTATTTTTT
198704 AAAAAATAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTAATAATTTTATTTTTTTCAAAAAAAATAAT
Found at i:198725 original size:29 final size:32
Alignment explanation
Indices: 198675--198739 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 32
198665 TTTTTTTCAA
*
198675 AAAAAATAATTTTAA-TAATTTT-AT-ATTTT
1 AAAAAATAATTTAAATTAATTTTAATAATTTT
**
198704 AAAAAATAATTTAAATTTTTTTTAATAATTTT
1 AAAAAATAATTTAAATTAATTTTAATAATTTT
198736 AAAA
1 AAAA
198740 TAATTTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 14 0.47
30 5 0.17
31 2 0.07
32 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
AAAAAATAATTTAAATTAATTTTAATAATTTT
Found at i:198736 original size:20 final size:20
Alignment explanation
Indices: 198684--198738 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
198674 AAAAAAATAA
*
198684 TTTTAATAATTTTATATTTT
1 TTTTAATAATTTTAAATTTT
****
198704 AAAAAATAA-TTTAAATTTT
1 TTTTAATAATTTTAAATTTT
198723 TTTTAATAATTTTAAA
1 TTTTAATAATTTTAAA
198739 ATAATTTGTT
Statistics
Matches: 25, Mismatches: 9, Indels: 2
0.69 0.25 0.06
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTAATAATTTTAAATTTT
Found at i:201571 original size:19 final size:20
Alignment explanation
Indices: 201524--201571 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
201514 TTGATAATTC
201524 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
201542 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
201561 TTAATTATTAT
1 TTAATTATTAT
201572 CAAAGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:203158 original size:15 final size:15
Alignment explanation
Indices: 203140--203180 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
203130 TGAAGAAGAA
203140 GAAGAAGAAGATCCT
1 GAAGAAGAAGATCCT
* *
203155 GAAGAAAAAGATCTT
1 GAAGAAGAAGATCCT
203170 GAAGAAGAAGA
1 GAAGAAGAAGA
203181 AGATCCTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.54, C:0.07, G:0.27, T:0.12
Consensus pattern (15 bp):
GAAGAAGAAGATCCT
Found at i:203160 original size:18 final size:18
Alignment explanation
Indices: 203137--203195 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
203127 AGCTGAAGAA
203137 GAAGAAGAAGAAGATCCT
1 GAAGAAGAAGAAGATCCT
*
203155 GAAG-A-AA-AAGATCTT
1 GAAGAAGAAGAAGATCCT
203170 GAAGAAGAAGAAGATCCT
1 GAAGAAGAAGAAGATCCT
*
203188 GAGGAAGA
1 GAAGAAGA
203196 TCCTATAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.31
16 3 0.09
17 3 0.09
18 18 0.51
ACGTcount: A:0.51, C:0.08, G:0.29, T:0.12
Consensus pattern (18 bp):
GAAGAAGAAGAAGATCCT
Found at i:203194 original size:15 final size:15
Alignment explanation
Indices: 203143--203195 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
203133 AGAAGAAGAA
*
203143 GAAGAAGATCCTGAA
1 GAAGAAGATCCTGAG
* *
203158 GAAAAAGATCTTGAAG
1 GAAGAAGATCCTG-AG
203174 AAGAAGAAGATCCTGAG
1 --GAAGAAGATCCTGAG
203191 GAAGA
1 GAAGA
203196 TCCTATAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 16 0.53
16 1 0.03
17 2 0.07
18 11 0.37
ACGTcount: A:0.49, C:0.09, G:0.28, T:0.13
Consensus pattern (15 bp):
GAAGAAGATCCTGAG
Found at i:206747 original size:27 final size:28
Alignment explanation
Indices: 206697--206756 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
206687 GCATTGGAAT
* *
206697 TTAATTTAGTTTTAGCTTTAAC-TTAGA
1 TTAATTTAGTTTTAGATTAAACTTTAGA
206724 TTAATTTAG-TTTAGATTAACACTTTAGA
1 TTAATTTAGTTTTAGATTAA-ACTTTAGA
206752 TTAAT
1 TTAAT
206757 ATCCTCCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 11 0.38
28 10 0.34
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (28 bp):
TTAATTTAGTTTTAGATTAAACTTTAGA
Found at i:213632 original size:18 final size:19
Alignment explanation
Indices: 213609--213644 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
213599 AATATTTTTT
213609 TATTTTT-TATTTTTCTCA
1 TATTTTTCTATTTTTCTCA
*
213627 TATTTTTCTTTTTTTCTC
1 TATTTTTCTATTTTTCTC
213645 GACTTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (19 bp):
TATTTTTCTATTTTTCTCA
Found at i:215765 original size:45 final size:44
Alignment explanation
Indices: 215669--215787 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 44
215659 TGCCATATTG
* *
215669 TCTTTCATCTATGGTCTTACTCATCTTCTATCATGATGCCATAACA
1 TCTTTCA-CTATGGTCTTACTCAT-TTTTATCATGATACCATAACA
* * * *
215715 TCTTTCAGCTATGGTCTTACTCATTTTTATTATGATATCGTAGCA
1 TCTTTCA-CTATGGTCTTACTCATTTTTATCATGATACCATAACA
*
215760 TCTTTCTACTATGGTTTTACTCATTTTT
1 TCTTTC-ACTATGGTCTTACTCATTTTT
215788 GGCATATAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 40 0.62
46 24 0.38
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (44 bp):
TCTTTCACTATGGTCTTACTCATTTTTATCATGATACCATAACA
Found at i:225780 original size:45 final size:44
Alignment explanation
Indices: 225684--225802 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 44
225674 TGCCATATTG
* *
225684 TCTTTCATCTATGGTCTTACTCATCTTCTATCATGATGCCATAACA
1 TCTTTCA-CTATGGTCTTACTCAT-TTTTATCATGATACCATAACA
* * * *
225730 TCTTTCAGCTATGGTCTTACTCATTTTTATTATGATATCGTAGCA
1 TCTTTCA-CTATGGTCTTACTCATTTTTATCATGATACCATAACA
*
225775 TCTTTCTACTATGGTTTTACTCATTTTT
1 TCTTTC-ACTATGGTCTTACTCATTTTT
225803 GGCATATAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 40 0.62
46 24 0.38
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (44 bp):
TCTTTCACTATGGTCTTACTCATTTTTATCATGATACCATAACA
Found at i:235007 original size:22 final size:22
Alignment explanation
Indices: 234945--235007 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
234935 TGATACCCGA
*
234945 TAAAACGTATCGATACTTTTTG
1 TAAAAGGTATCGATACTTTTTG
*
234967 -AAAAGGTATCGACACTTTTTG
1 TAAAAGGTATCGATACTTTTTG
* *
234988 TAAAAGGTATAGATAATTTT
1 TAAAAGGTATCGATACTTTT
235008 CCCAAATCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
TAAAAGGTATCGATACTTTTTG
Found at i:235109 original size:19 final size:19
Alignment explanation
Indices: 235087--235143 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
235077 AAGGATTTTC
235087 CCAAATCCACTAGATTTGT
1 CCAAATCCACTAGATTTGT
235106 CCAAATCCACTAGATTTGT
1 CCAAATCCACTAGATTTGT
235125 CCAAATCCACTAGATTTGT
1 CCAAATCCACTAGATTTGT
235144 ATAAACTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
CCAAATCCACTAGATTTGT
Found at i:237055 original size:41 final size:41
Alignment explanation
Indices: 236998--237232 Score: 163
Period size: 40 Copynumber: 5.8 Consensus size: 41
236988 TAAGTTATAT
*
236998 TGATAGAAATTCAAGCTATGACTTAGCAGGCTATGTGCCGG
1 TGATAGAAATTCAAGCTATGACTTAGCAGGCTACGTGCCGG
** *
237039 TGATAGAAATTCAAGCTACAACTTAGTAGGCTACGTGCCGG
1 TGATAGAAATTCAAGCTATGACTTAGCAGGCTACGTGCCGG
* * * * ** **
237080 TGATAGAAATTGAAGTTATGGCTTAGCAAGCTACAAGCTAG
1 TGATAGAAATTCAAGCTATGACTTAGCAGGCTACGTGCCGG
* * * * ** **
237121 TGATA-AAATACAAGCTACGGCTTAGCAAGCTACCAGCTAG
1 TGATAGAAATTCAAGCTATGACTTAGCAGGCTACGTGCCGG
* * * * * *
237161 TGTTA-AAATACAAGCTA-CAGTTTAGCAAGCTACGAGCCGG
1 TGATAGAAATTCAAGCTATGA-CTTAGCAGGCTACGTGCCGG
* * * *
237201 TGTTA-AAATACAAGCTACGGCTTAGCAGGCTA
1 TGATAGAAATTCAAGCTATGACTTAGCAGGCTA
237233 TGAGTCGATG
Statistics
Matches: 161, Mismatches: 31, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
40 89 0.55
41 72 0.45
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (41 bp):
TGATAGAAATTCAAGCTATGACTTAGCAGGCTACGTGCCGG
Found at i:237149 original size:40 final size:40
Alignment explanation
Indices: 237099--237232 Score: 196
Period size: 40 Copynumber: 3.4 Consensus size: 40
237089 TTGAAGTTAT
*
237099 GGCTTAGCAAGCTACAAGCTAGTGATAAAATACAAGCTAC
1 GGCTTAGCAAGCTACAAGCTAGTGTTAAAATACAAGCTAC
*
237139 GGCTTAGCAAGCTACCAGCTAGTGTTAAAATACAAGCTAC
1 GGCTTAGCAAGCTACAAGCTAGTGTTAAAATACAAGCTAC
* * * **
237179 AGTTTAGCAAGCTACGAGCCGGTGTTAAAATACAAGCTAC
1 GGCTTAGCAAGCTACAAGCTAGTGTTAAAATACAAGCTAC
*
237219 GGCTTAGCAGGCTA
1 GGCTTAGCAAGCTA
237233 TGAGTCGATG
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (40 bp):
GGCTTAGCAAGCTACAAGCTAGTGTTAAAATACAAGCTAC
Found at i:237796 original size:26 final size:25
Alignment explanation
Indices: 237760--237808 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
237750 ATGGAATCAA
237760 ATGATGGTTATAT-TTTGGGTGATGTT
1 ATGATGGTTAT-TGTTT-GGTGATGTT
*
237786 ATGATGTTTATTGTTTGGTGATG
1 ATGATGGTTATTGTTTGGTGATG
237809 GAAGATACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (25 bp):
ATGATGGTTATTGTTTGGTGATGTT
Found at i:241395 original size:21 final size:21
Alignment explanation
Indices: 241369--241425 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
241359 AATACCTGAT
241369 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
* *
241390 AAAAGGAATCAATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
241411 AAAAGGTATCGATAC
1 AAAAGGTATCGATAC
241426 GTTATGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:241855 original size:14 final size:15
Alignment explanation
Indices: 241836--241875 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
241826 CAGCAAATGA
241836 TTTAAAATTAAT-TT
1 TTTAAAATTAATATT
241850 TTTAAAATATAATATT
1 TTTAAAAT-TAATATT
*
241866 ATTAAAATTA
1 TTTAAAATTA
241876 TTATATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAATTAATATT
Found at i:241883 original size:17 final size:16
Alignment explanation
Indices: 241837--241885 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
241827 AGCAAATGAT
*
241837 TTAAAAT-TAAT-TTT
1 TTAAAATATAATATTA
241851 TTAAAATATAATATTA
1 TTAAAATATAATATTA
*
241867 TTAAAATTATTATATTA
1 TTAAAA-TATAATATTA
241884 TT
1 TT
241886 TTTGTGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 8 0.27
17 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAATATAATATTA
Found at i:241897 original size:38 final size:37
Alignment explanation
Indices: 241844--241925 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 37
241834 GATTTAAAAT
* *
241844 TAATTTTTTAAAATATAATATTATTAAAATTATTATA
1 TAATTTTTTAAAATATAAAATTATTAAAATTATTAAA
* *
241881 TTATTTTTGTGAAATATAAAATTATTAAAATTATTAAA
1 TAATTTTT-TAAAATATAAAATTATTAAAATTATTAAA
241919 TAATTTT
1 TAATTTT
241926 AATCTCATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 7 0.18
38 32 0.82
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (37 bp):
TAATTTTTTAAAATATAAAATTATTAAAATTATTAAA
Found at i:242924 original size:9 final size:9
Alignment explanation
Indices: 242910--242976 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
242900 ATTAAAATTA
242910 TTTAATAAT
1 TTTAATAAT
242919 TTTAATAAT
1 TTTAATAAT
242928 TTT-AT-AT
1 TTTAATAAT
* *
242935 TTCAAAAAAT
1 TT-TAATAAT
*
242945 AATATAATAAT
1 --TTTAATAAT
242956 TTTAATAAT
1 TTTAATAAT
242965 TTT-AT-AT
1 TTTAATAAT
242972 TTTAA
1 TTTAA
242977 AAAATTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
7 9 0.20
8 5 0.11
9 24 0.52
10 2 0.04
11 5 0.11
12 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAATAAT
Found at i:242945 original size:20 final size:19
Alignment explanation
Indices: 242922--242989 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 19
242912 TAATAATTTT
242922 AATAATTTTATATTTCAAAA
1 AATAATTTTATATTT-AAAA
* * *
242942 AATAATATAATAATTT---T
1 AATAATTTTAT-ATTTAAAA
242959 AATAATTTTATATTTTAAAA
1 AATAATTTTATA-TTTAAAA
242979 AATTAATTTTA
1 AA-TAATTTTA
242990 AATTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
16 1 0.03
17 12 0.33
20 11 0.31
21 12 0.33
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (19 bp):
AATAATTTTATATTTAAAA
Found at i:242953 original size:37 final size:37
Alignment explanation
Indices: 242903--242981 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
242893 CGATAAGATT
* *
242903 AAAATTATTTAATAATTTTAATAATTTTATATTTCAA
1 AAAATAATATAATAATTTTAATAATTTTATATTTCAA
*
242940 AAAATAATATAATAATTTTAATAATTTTATATTTTAA
1 AAAATAATATAATAATTTTAATAATTTTATATTTCAA
242977 AAAAT
1 AAAAT
242982 TAATTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (37 bp):
AAAATAATATAATAATTTTAATAATTTTATATTTCAA
Found at i:242994 original size:11 final size:11
Alignment explanation
Indices: 242978--243003 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
242968 ATATTTTAAA
242978 AAATTAATTTT
1 AAATTAATTTT
242989 AAATTAATTTT
1 AAATTAATTTT
243000 AAAT
1 AAAT
243004 CATTTGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATTAATTTT
Found at i:243343 original size:67 final size:67
Alignment explanation
Indices: 243235--243365 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 67
243225 CCTTACTTTC
* * *
243235 ATTCAAAAACACTTTAATTTGTTATATCGAAATATATTATCCAATAGGGCTTAGTTTAACAATCG
1 ATTCAAAAACACTTTAATTTGTTATATCGAAACATATTATCCAATAAGGCTTAATTTAACAATCG
243300 TT
66 TT
* *
243302 ATTCAAAAACACTTTAATTTGTTATATCTAAACATATTATCCAATAAGTCTTAATTTAACAATC
1 ATTCAAAAACACTTTAATTTGTTATATCGAAACATATTATCCAATAAGGCTTAATTTAACAATC
243366 TCCCATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.39
Consensus pattern (67 bp):
ATTCAAAAACACTTTAATTTGTTATATCGAAACATATTATCCAATAAGGCTTAATTTAACAATCG
TT
Found at i:251276 original size:26 final size:26
Alignment explanation
Indices: 251247--251327 Score: 137
Period size: 26 Copynumber: 3.1 Consensus size: 26
251237 AATTCTAGGC
251247 ACAATTCTGGACACGTTCATTCAGCG
1 ACAATTCTGGACACGTTCATTCAGCG
251273 ACAATTCTGGACACGTTCATTCAGCG
1 ACAATTCTGGACACGTTCATTCAGCG
*
251299 ACAATTCTGGACATGTTCATGT-AGCG
1 ACAATTCTGGACACGTTCAT-TCAGCG
251325 ACA
1 ACA
251328 TTCATGGGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
26 52 0.98
27 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (26 bp):
ACAATTCTGGACACGTTCATTCAGCG
Found at i:251429 original size:38 final size:37
Alignment explanation
Indices: 251336--251442 Score: 133
Period size: 37 Copynumber: 2.9 Consensus size: 37
251326 CATTCATGGG
* *
251336 TGCAATTGAAGAATACTTATGCAGCGATAGTCCTGGA
1 TGCAATTGAAGAATATTTATGCAACGATAGTCCTGGA
* * *
251373 TACAATTGAAGTATATTTATGCAACGATAGTTCTGGA
1 TGCAATTGAAGAATATTTATGCAACGATAGTCCTGGA
* * *
251410 TGCAATTTGAAAAATATTTATGCATCGACAGTC
1 TGCAA-TTGAAGAATATTTATGCAACGATAGTC
251443 TTAGGTGCAT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
37 36 0.62
38 22 0.38
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (37 bp):
TGCAATTGAAGAATATTTATGCAACGATAGTCCTGGA
Found at i:251508 original size:37 final size:37
Alignment explanation
Indices: 251467--251543 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
251457 AAAATATTCC
* * * *
251467 TGCGATGATAGTTTTGGGTGCAATCTGGAAATGCTCA
1 TGCGACGATAGTTTTGAGCGCAATCTAGAAATGCTCA
*
251504 TGCGACGATAGTTTTGAGCGCAATCTAGAAGTGCTCA
1 TGCGACGATAGTTTTGAGCGCAATCTAGAAATGCTCA
251541 TGC
1 TGC
251544 AGCGACATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (37 bp):
TGCGACGATAGTTTTGAGCGCAATCTAGAAATGCTCA
Found at i:258255 original size:95 final size:95
Alignment explanation
Indices: 258141--258348 Score: 382
Period size: 95 Copynumber: 2.2 Consensus size: 95
258131 CTACATCTTT
258141 TAAAT-ATGACATGCATTATGTGATCTGCATTTAATAAAGTCGTGCATTATGTAATCACATCCAT
1 TAAATAATGACATGCATTATGTGATCTGCATTTAATAAAGTCGTGCATTATGTAATCACATCCAT
* *
258205 TAACTCTCATGATAAGTTAAGTTTGTATCA
66 TAACTCTCATGATAAGTTAAGTTTGCATAA
258235 TAAATAATGACATGCATTATGTGATCTGCATTTAATAAAGTCGTGCATTATGTAATCACATCCAT
1 TAAATAATGACATGCATTATGTGATCTGCATTTAATAAAGTCGTGCATTATGTAATCACATCCAT
258300 TAACTCTCATGATAAGTTAAGTTTGCATAA
66 TAACTCTCATGATAAGTTAAGTTTGCATAA
*
258330 AAAATAATGACATGCATTA
1 TAAATAATGACATGCATTA
258349 AGTAACTTAC
Statistics
Matches: 110, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
94 5 0.05
95 105 0.95
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (95 bp):
TAAATAATGACATGCATTATGTGATCTGCATTTAATAAAGTCGTGCATTATGTAATCACATCCAT
TAACTCTCATGATAAGTTAAGTTTGCATAA
Found at i:258348 original size:47 final size:46
Alignment explanation
Indices: 258192--258349 Score: 117
Period size: 47 Copynumber: 3.3 Consensus size: 46
258182 GTGCATTATG
*
258192 TAATCACATCCATTAACTCTCATGATAAGTTAAGTTTGTATCATAAA
1 TAATCACATCCATTAACTCTCATGATAAGTTAAGTTTGCAT-ATAAA
* * * * * **
258239 TAATGACATGCATTATGTGA-TCTGCAT-TTAA-TAAAGTCGTGCAT-TATG
1 TAATCACATCCATTA----ACTCT-CATGATAAGTTAAGT-TTGCATATAAA
*
258287 TAATCACATCCATTAACTCTCATGATAAGTTAAGTTTGCATAAAAAA
1 TAATCACATCCATTAACTCTCATGATAAGTTAAGTTTGCAT-ATAAA
* *
258334 TAATGACATGCATTAA
1 TAATCACATCCATTAA
258350 GTAACTTACA
Statistics
Matches: 82, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
44 4 0.05
45 11 0.13
46 5 0.06
47 28 0.34
48 15 0.18
49 5 0.06
50 10 0.12
51 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (46 bp):
TAATCACATCCATTAACTCTCATGATAAGTTAAGTTTGCATATAAA
Found at i:258369 original size:50 final size:50
Alignment explanation
Indices: 258300--258421 Score: 120
Period size: 50 Copynumber: 2.4 Consensus size: 50
258290 TCACATCCAT
* * * *
258300 TAACTCTCATGATAAGTTAAGTTTGCATAAAAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATAAAAAATAAT-ATCATGCATTAAG
* * * ** *
258351 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATAAAAAATAATATCATGCATTAAG
*
258401 TAACTCCCATGTTAGTTAAAT
1 TAACTCACATGTTAGTTAAAT
258422 GCATCATTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
49 1 0.02
50 48 0.83
51 9 0.16
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATAAAAAATAATATCATGCATTAAG
Found at i:259703 original size:16 final size:16
Alignment explanation
Indices: 259682--259725 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
259672 TCAAACTTTC
*
259682 TTCAAAGTTTGTGGCG
1 TTCAAAATTTGTGGCG
259698 TTCAAAATTTGTGGCG
1 TTCAAAATTTGTGGCG
259714 TTCAAAATTTGT
1 TTCAAAATTTGT
259726 CTTATCACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (16 bp):
TTCAAAATTTGTGGCG
Done.