Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 83 of 145
Found at i:28132552 original size:41 final size:42
Alignment explanation
Indices: 28132507--28132601 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
28132497 CCAGTATAAA
28132507 ACCTGCTAGGC-ACAAGCCTAATAAAAATTCACCGGCACTAC
1 ACCTGCTAGGCTACAAGCCTAATAAAAATTCACCGGCACTAC
*** * *
28132548 ACCTGCTAGGCTTTTAGCCTGATATAAATTCACCGGCACTAC
1 ACCTGCTAGGCTACAAGCCTAATAAAAATTCACCGGCACTAC
* *
28132590 GCCTACTAGGCT
1 ACCTGCTAGGCT
28132602 TTTAGCCTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 11 0.24
42 35 0.76
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (42 bp):
ACCTGCTAGGCTACAAGCCTAATAAAAATTCACCGGCACTAC
Found at i:28132578 original size:42 final size:42
Alignment explanation
Indices: 28132521--28132615 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
28132511 GCTAGGCACA
* * *
28132521 AGCCTAATAAAAATTCACCGGCACTACACCTGCTAGGCTTTT
1 AGCCTGATATAAATTCACCGGCACTACACCTACTAGGCTTTT
*
28132563 AGCCTGATATAAATTCACCGGCACTACGCCTACTAGGCTTTT
1 AGCCTGATATAAATTCACCGGCACTACACCTACTAGGCTTTT
28132605 AGCCTGATATA
1 AGCCTGATATA
28132616 TCACACCAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (42 bp):
AGCCTGATATAAATTCACCGGCACTACACCTACTAGGCTTTT
Found at i:28142274 original size:9 final size:9
Alignment explanation
Indices: 28142247--28142283 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28142237 TAAGTTTTCG
28142247 AATTCGAAT
1 AATTCGAAT
* *
28142256 AACTCAAAT
1 AATTCGAAT
28142265 AATTCGAAT
1 AATTCGAAT
28142274 AATTCGAAT
1 AATTCGAAT
28142283 A
1 A
28142284 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28143444 original size:13 final size:13
Alignment explanation
Indices: 28143402--28143444 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
28143392 CTACCTAATA
28143402 AATAATTTATTAG
1 AATAATTTATTAG
** * *
28143415 AATTTTTTAATAA
1 AATAATTTATTAG
28143428 AATAATTTATTAG
1 AATAATTTATTAG
28143441 AATA
1 AATA
28143445 TTTGCTTATT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (13 bp):
AATAATTTATTAG
Found at i:28143706 original size:5 final size:5
Alignment explanation
Indices: 28143696--28143756 Score: 122
Period size: 5 Copynumber: 12.2 Consensus size: 5
28143686 TTTTCTACAC
28143696 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
28143746 TTATA TTATA T
1 TTATA TTATA T
28143757 AAGTTATAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:28145433 original size:13 final size:13
Alignment explanation
Indices: 28145415--28145478 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
28145405 AGTTCTTTAT
28145415 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
28145428 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
28145441 TG-TTGTGGAAAAA
1 TGCTT-TTGAAAAG
*
28145454 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
28145467 TGCTTTTGAAAA
1 TGCTTTTGAAAA
28145479 ATTTGAGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 2 0.05
13 39 0.91
14 2 0.05
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:28149126 original size:24 final size:24
Alignment explanation
Indices: 28149094--28149142 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28149084 AAGGCATGTT
28149094 CCTAAAAAAACATTTAAATAAAGG
1 CCTAAAAAAACATTTAAATAAAGG
*
28149118 CCTAAAAAAGCATTTAAATAAAGG
1 CCTAAAAAAACATTTAAATAAAGG
28149142 C
1 C
28149143 AATGTGTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.20
Consensus pattern (24 bp):
CCTAAAAAAACATTTAAATAAAGG
Found at i:28150677 original size:45 final size:46
Alignment explanation
Indices: 28150625--28150758 Score: 175
Period size: 45 Copynumber: 2.9 Consensus size: 46
28150615 TCATACCAAA
28150625 AACGAGTAAGACCATAG-TCGAAAGACGTTATGGCATCATGAATT-T
1 AACGAGTAAGACCATAGCT-GAAAGACGTTATGGCATCATGAATTGT
* * * *
28150670 AATGAGTAAGACCATAACTGAAAGATGTTATGGTATCATG-ATTGT
1 AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGAATTGT
* *
28150715 AACGAGTAAGACCATAGCTAAAAGACTTTAATGGCATCATGAAT
1 AACGAGTAAGACCATAGCTGAAAGACGTT-ATGGCATCATGAAT
28150759 CGGACGAATA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 3 0.04
45 59 0.79
46 11 0.15
47 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (46 bp):
AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGAATTGT
Found at i:28165594 original size:15 final size:16
Alignment explanation
Indices: 28165567--28165596 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28165557 AATAACAATT
28165567 AATATATATTATATAA
1 AATATATATTATATAA
28165583 AATATA-ATTATATA
1 AATATATATTATATA
28165597 TTAGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:28173085 original size:117 final size:118
Alignment explanation
Indices: 28172868--28173102 Score: 454
Period size: 117 Copynumber: 2.0 Consensus size: 118
28172858 TTTTTCTTTG
28172868 ACGGCTACTAGACCCAAAACAAAGAAAAACGAGATTCTTATATATATTTTATTTTAGGGTTTTTA
1 ACGGCTACTAGACCCAAAACAAAGAAAAACGAGATTCTTATATATATTTTATTTTAGGGTTTTTA
*
28172933 GGAATTAAATTAATATAATAATATTTTAAACTGAAAATTATAATTACATTAAT
66 GGAATTAAATTAATATAATAATATTTTAAAATGAAAATTATAATTACATTAAT
28172986 ACGGCTACTA-ACCCAAAACAAAGAAAAACGAGATTCTTATATATATTTTATTTTAGGGTTTTTA
1 ACGGCTACTAGACCCAAAACAAAGAAAAACGAGATTCTTATATATATTTTATTTTAGGGTTTTTA
28173050 GGAATTAAATTAATATAATAATATTTTAAAATGAAAATTATAATTACATTAAT
66 GGAATTAAATTAATATAATAATATTTTAAAATGAAAATTATAATTACATTAAT
28173103 TATAATATAA
Statistics
Matches: 116, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
117 106 0.91
118 10 0.09
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (118 bp):
ACGGCTACTAGACCCAAAACAAAGAAAAACGAGATTCTTATATATATTTTATTTTAGGGTTTTTA
GGAATTAAATTAATATAATAATATTTTAAAATGAAAATTATAATTACATTAAT
Found at i:28179930 original size:17 final size:17
Alignment explanation
Indices: 28179908--28179940 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28179898 TTGATTACCG
28179908 AATTAAGTTAATTCTAT
1 AATTAAGTTAATTCTAT
*
28179925 AATTAATTTAATTCTA
1 AATTAAGTTAATTCTA
28179941 GCGACCCCCA
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:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTAAGTTAATTCTAT
Found at i:28187380 original size:252 final size:252
Alignment explanation
Indices: 28186936--28187426 Score: 752
Period size: 252 Copynumber: 1.9 Consensus size: 252
28186926 ACATTGAACA
* * * *
28186936 TACCATGTCGAATAACATTTGATTCTTTCTCTCTTCCACATCATTCTATTGTGGAGTGCCTAGTG
1 TACCATGTCGAATAACATTCGATTCCTTCTCTCTTCCACACCATTCTATTGTGGAGTGCCCAGTG
* *
28187001 CAGTCAACTGGGATAGAATCTCATTCTCTATGAGGTACCCTAAAAACTAATTAGATCAATATTCC
66 CAGTCAACTGGGATAGAATCACATTCTCTATGAGGTACCCTAAAAACTAATTAGATAAATATTCC
*
28187066 CCACCTCAACCAGACCGAAGTATCTTTATGGGTAAACCTAGTTGTTTCTCCATTTCTGCACAAAA
131 CCACCTCAACCAGACCGAAGTATCTTTATGGGTAAACCTAGTTGTTTCTCAATTTCTGCACAAAA
*
28187131 CTTTTTGAACTAATCAG-AGGTTTCACTATTGCAGTGCATAAGGTTTAACATCAAACG
196 CTTTTAGAACTAAT-AGAAGGTTTCACTATTGCAGTGCATAAGGTTTAACATCAAACG
* **
28187188 TACCATGTCTAATAACATTCGATTCCTTCTCTCTTCCATGCCATTCTATTGTGGAGTGCCCAGTG
1 TACCATGTCGAATAACATTCGATTCCTTCTCTCTTCCACACCATTCTATTGTGGAGTGCCCAGTG
* *
28187253 CAGTCAACTGGGATAGAATCACATTCTCTATGAGGTATCCTAAGAACTAATTAGATAAATATTCC
66 CAGTCAACTGGGATAGAATCACATTCTCTATGAGGTACCCTAAAAACTAATTAGATAAATATTCC
* * * *
28187318 CCACCTCGACCAGACTGAAGTGTCTTTATGGTTAAACCTAGTTGTTTCTCAACTTT-TGCACAAA
131 CCACCTCAACCAGACCGAAGTATCTTTATGGGTAAACCTAGTTGTTTCTCAA-TTTCTGCACAAA
* * * **
28187382 ACTTTTAGAACTTATTGAAGGTTTCACTCTTGTGGTGCATAAGGT
195 ACTTTTAGAACTAATAGAAGGTTTCACTATTGCAGTGCATAAGGT
28187427 ATACATACTT
Statistics
Matches: 215, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
251 1 0.00
252 211 0.98
253 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (252 bp):
TACCATGTCGAATAACATTCGATTCCTTCTCTCTTCCACACCATTCTATTGTGGAGTGCCCAGTG
CAGTCAACTGGGATAGAATCACATTCTCTATGAGGTACCCTAAAAACTAATTAGATAAATATTCC
CCACCTCAACCAGACCGAAGTATCTTTATGGGTAAACCTAGTTGTTTCTCAATTTCTGCACAAAA
CTTTTAGAACTAATAGAAGGTTTCACTATTGCAGTGCATAAGGTTTAACATCAAACG
Found at i:28193791 original size:6 final size:6
Alignment explanation
Indices: 28193780--28193818 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
28193770 AGATTGCAAT
* *
28193780 TTTCCA TTTCCA TTTCCA TTTTCA TTTTCA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
28193819 TTGGAAGCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTCCA
Found at i:28193811 original size:18 final size:19
Alignment explanation
Indices: 28193778--28193819 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
28193768 TAAGATTGCA
28193778 ATTTTCCATTTCCATTTCC
1 ATTTTCCATTTCCATTTCC
*
28193797 ATTTT-CATTTTCATTTCC
1 ATTTTCCATTTCCATTTCC
28193815 ATTTT
1 ATTTT
28193820 TGGAAGCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTCCATTTCCATTTCC
Found at i:28201402 original size:66 final size:66
Alignment explanation
Indices: 28201320--28201455 Score: 200
Period size: 66 Copynumber: 2.1 Consensus size: 66
28201310 TCATCAATTT
* *
28201320 ATCACATTTCCATATTGGTCCCATGGGCTTATATAAAAAATGCTAAATATGTATATGCATCATCC
1 ATCACATTTCCATATTGGCCCCATGGGATTATATAAAAAATGCTAAATATGTATATGCATCATCC
28201385 A
66 A
** *** *
28201386 ATCACATTTCTGTATTGGCCCCATGGGATTATATAATCGATGCTCAATATGTATATGCATCATCC
1 ATCACATTTCCATATTGGCCCCATGGGATTATATAAAAAATGCTAAATATGTATATGCATCATCC
28201451 A
66 A
28201452 ATCA
1 ATCA
28201456 TTGTATCAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (66 bp):
ATCACATTTCCATATTGGCCCCATGGGATTATATAAAAAATGCTAAATATGTATATGCATCATCC
A
Found at i:28209159 original size:27 final size:27
Alignment explanation
Indices: 28209129--28209394 Score: 331
Period size: 27 Copynumber: 9.9 Consensus size: 27
28209119 TCATCTCCTA
** *
28209129 GGGGTATAACAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
28209156 GGGGTATTTCGGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
**
28209182 GGGGTATTTTTGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
**
28209209 GGGGTATTTTTGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
28209236 GGGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
28209263 GGGCTATTTCAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
28209290 AGAGTATTTCAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* ** *
28209317 GGAGTATTTTGGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
**
28209344 GGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
28209371 GGGGCATTTC-GATCATTTTACCCT
1 GGGGTATTTCAG-TCATTTTACCCT
28209395 GTTTTAGGGT
Statistics
Matches: 216, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
26 26 0.12
27 189 0.88
28 1 0.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:28211686 original size:20 final size:20
Alignment explanation
Indices: 28211658--28211695 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28211648 AATTAGAATG
*
28211658 TAAAAATTAAATTAAAAACA
1 TAAAAATTAAAATAAAAACA
*
28211678 TAAATATTAAAATAAAAA
1 TAAAAATTAAAATAAAAA
28211696 TAAAAACTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAATTAAAATAAAAACA
Found at i:28217013 original size:13 final size:13
Alignment explanation
Indices: 28216995--28217019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28216985 GTAACTCCTT
28216995 CATGAGTTGTGTC
1 CATGAGTTGTGTC
28217008 CATGAGTTGTGT
1 CATGAGTTGTGT
28217020 AAGCATCAGA
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:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (13 bp):
CATGAGTTGTGTC
Found at i:28234011 original size:12 final size:12
Alignment explanation
Indices: 28233996--28234050 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
28233986 TAAAAAAATC
*
28233996 AAAAAAATTTTG
1 AAAAAAAATTTG
*
28234008 AAAAAAAAATTG
1 AAAAAAAATTTG
28234020 AAAAAAAATTTG
1 AAAAAAAATTTG
* *
28234032 AAAAAAAAATTC
1 AAAAAAAATTTG
28234044 AAAAAAA
1 AAAAAAA
28234051 GAGTTTGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:28234023 original size:24 final size:24
Alignment explanation
Indices: 28233987--28234050 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
28233977 ACGGTATTGT
*
28233987 AAAAAAA-TCAAAAAAATTTTGAA
1 AAAAAAATTCAAAAAAAATTTGAA
*
28234010 AAAAAAATTGAAAAAAAATTTGAA
1 AAAAAAATTCAAAAAAAATTTGAA
28234034 AAAAAAATTCAAAAAAA
1 AAAAAAATTCAAAAAAA
28234051 GAGTTTGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 7 0.19
24 30 0.81
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (24 bp):
AAAAAAATTCAAAAAAAATTTGAA
Found at i:28235154 original size:18 final size:17
Alignment explanation
Indices: 28235121--28235171 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
28235111 AAAAGAAAAC
*
28235121 TGAAAAAGAGATTGAGAA
1 TGAAAAAGA-AATGAGAA
*
28235139 TGAAGAAAGAAATGAGAG
1 TGAA-AAAGAAATGAGAA
*
28235157 TGCAAAAGAAATGAG
1 TGAAAAAGAAATGAG
28235172 TGATATGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 11 0.38
18 13 0.45
19 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (17 bp):
TGAAAAAGAAATGAGAA
Found at i:28242507 original size:6 final size:6
Alignment explanation
Indices: 28242480--28242526 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
28242470 AAATGAATTG
*
28242480 ATTTCTC ATTTTC ACTTT-C ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTC-C ATTTCC A-TTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
28242527 TGGAGAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
5 3 0.08
6 27 0.73
7 7 0.19
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (6 bp):
ATTTCC
Found at i:28242609 original size:56 final size:58
Alignment explanation
Indices: 28242506--28242629 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 58
28242496 TTCATTTCCA
*
28242506 TTTCCATTTCCATTTCCATTTTGGAGAAAACCAAATTCATTTCCAAATGA-TTTC-ATT
1 TTTCCATTTCCATTTCCAATTTGGAGAAAACCAAATTCATTTCCAAAT-ATTTTCTATT
* * **
28242563 TTTCCATTTTCATTTTCAATTTGGAGAAAACCTTA-TCATTTCCAAATATTTTCTATT
1 TTTCCATTTCCATTTCCAATTTGGAGAAAACCAAATTCATTTCCAAATATTTTCTATT
*
28242620 TCTCCATTTC
1 TTTCCATTTC
28242630 TATTCATTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
55 1 0.02
56 16 0.28
57 41 0.71
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (58 bp):
TTTCCATTTCCATTTCCAATTTGGAGAAAACCAAATTCATTTCCAAATATTTTCTATT
Found at i:28248472 original size:20 final size:19
Alignment explanation
Indices: 28248447--28248484 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
28248437 AACATTTTTG
28248447 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
*
28248467 ATTCAGTTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
28248485 GTTATTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:28250066 original size:13 final size:12
Alignment explanation
Indices: 28250042--28250096 Score: 69
Period size: 13 Copynumber: 4.6 Consensus size: 12
28250032 ACGGTATTGT
28250042 AAAAAAA-T-AA
1 AAAAAAATTGAA
28250052 AAAAAAACTTGAA
1 AAAAAAA-TTGAA
28250065 AAAAAAATTCGAA
1 AAAAAAATT-GAA
*
28250078 AAAAAAATTCAA
1 AAAAAAATTGAA
28250090 AAAAAAA
1 AAAAAAA
28250097 GTTTGTATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 7 0.17
12 12 0.30
13 21 0.52
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.13
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:28250167 original size:15 final size:13
Alignment explanation
Indices: 28250137--28250189 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
28250127 ATTTAGTATT
28250137 GAAGAAAAAAAAG
1 GAAGAAAAAAAAG
*
28250150 GAAGAAAAAAATTCG
1 GAAGAAAAAAA--AG
*
28250165 GAATTAAAAAAAA-
1 GAA-GAAAAAAAAG
28250178 GAAGAAAAAAAA
1 GAAGAAAAAAAA
28250190 TCGAAATTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 8 0.24
13 14 0.42
15 4 0.12
16 7 0.21
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.08
Consensus pattern (13 bp):
GAAGAAAAAAAAG
Found at i:28250186 original size:29 final size:29
Alignment explanation
Indices: 28250140--28250211 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
28250130 TAGTATTGAA
* *
28250140 GAAAAAAAAGGAAGAAAAAAATTCGGAATT
1 GAAAAAAAA-GAAGAAAAAAAATCGAAATT
28250170 -AAAAAAAAGAAGAAAAAAAATCGAAATT
1 GAAAAAAAAGAAGAAAAAAAATCGAAATT
*
28250198 GAAAAAAAAAAAGA
1 GAAAAAAAAGAAGA
28250212 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.47
29 20 0.53
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (29 bp):
GAAAAAAAAGAAGAAAAAAAATCGAAATT
Found at i:28257549 original size:30 final size:29
Alignment explanation
Indices: 28257511--28257611 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 29
28257501 AGTAAGCTTT
28257511 TATAAATCTTAGTAAGTTCATCGATTAAA
1 TATAAATCTTAGTAAGTTCATCGATTAAA
* * *
28257540 TAGTAAATCTTACTAAATT-A-CGCATAATAAT
1 TA-TAAATCTTAGTAAGTTCATCG-AT--TAAA
*
28257571 TATAAAGCTTAGTAAGTTCATCGATTAAA
1 TATAAATCTTAGTAAGTTCATCGATTAAA
28257600 TACTAAATCTTA
1 TA-TAAATCTTA
28257612 CTAAATTACG
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
28 2 0.04
29 10 0.18
30 35 0.61
31 8 0.14
32 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (29 bp):
TATAAATCTTAGTAAGTTCATCGATTAAA
Found at i:28257607 original size:60 final size:60
Alignment explanation
Indices: 28257510--28257631 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
28257500 GAGTAAGCTT
* *
28257510 TTATAAATCTTAGTAAGTTCATCGATTAAATAGTAAATCTTACTAAATTACGCATAATAA
1 TTATAAAGCTTAGTAAGTTCATCGATTAAATACTAAATCTTACTAAATTACGCATAATAA
28257570 TTATAAAGCTTAGTAAGTTCATCGATTAAATACTAAATCTTACTAAATTACGCATAATAA
1 TTATAAAGCTTAGTAAGTTCATCGATTAAATACTAAATCTTACTAAATTACGCATAATAA
28257630 TT
1 TT
28257632 CGGTTAATAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (60 bp):
TTATAAAGCTTAGTAAGTTCATCGATTAAATACTAAATCTTACTAAATTACGCATAATAA
Found at i:28257907 original size:35 final size:35
Alignment explanation
Indices: 28257868--28257940 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
28257858 ACATCAAATA
*
28257868 CTCATAAGAGTCAGTACCATCCAGCACACCAGTTG
1 CTCATAAGAGCCAGTACCATCCAGCACACCAGTTG
* *
28257903 CTCATAAGAGCCATTACCATCTAGCACACCAGTTG
1 CTCATAAGAGCCAGTACCATCCAGCACACCAGTTG
28257938 CTC
1 CTC
28257941 GGTTGAAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (35 bp):
CTCATAAGAGCCAGTACCATCCAGCACACCAGTTG
Found at i:28258205 original size:43 final size:42
Alignment explanation
Indices: 28258143--28258375 Score: 217
Period size: 43 Copynumber: 5.5 Consensus size: 42
28258133 TTTGCGGCAT
*
28258143 TTTTTCCTACAAACGCCGCTATAGATTTGGACCTTTAGCGACGC
1 TTTTTCC-ACAAACGCCGCTATAGATAT-GACCTTTAGCGACGC
* * * * *
28258187 TTTTTCCACAAACGCCGCTATAAATCATAAACTTTAGCGGCAC
1 TTTTTCCACAAACGCCGCTATAGAT-ATGACCTTTAGCGACGC
* *
28258230 TTTTT-TACAAACGCCGCTATAGATCAAGACCTTTAGCG--GC
1 TTTTTCCACAAACGCCGCTATAGAT-ATGACCTTTAGCGACGC
* *
28258270 -TTTTCTCACAAACGCCGCTATAGATCATAATCTTTAGCGACGC
1 TTTTTC-CACAAACGCCGCTATAGAT-ATGACCTTTAGCGACGC
* * * *
28258313 TTTTTTCAAAAACGCCGCTATAGCTCAAGACCTTTAGCGACGC
1 TTTTTCCACAAACGCCGCTATAGAT-ATGACCTTTAGCGACGC
28258356 TTTGATT--ACAAACGCCGCTA
1 TTT--TTCCACAAACGCCGCTA
28258376 AAAATACCGT
Statistics
Matches: 158, Mismatches: 23, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
39 4 0.03
40 1 0.01
41 29 0.18
42 28 0.18
43 82 0.52
44 12 0.08
45 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (42 bp):
TTTTTCCACAAACGCCGCTATAGATATGACCTTTAGCGACGC
Found at i:28263781 original size:66 final size:66
Alignment explanation
Indices: 28263699--28263830 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
28263689 TAGGTGTATT
28263699 TACTTGGTGTTGCTGAAAATGGGAAATTTGGGGGCAAATTTTGAGATTAAAAGGGAAAAAGAATT
1 TACTTGGTGTTGCTGAAAATGGGAAATTTGGGGGCAAATTTTGAGATTAAAAGGGAAAAAGAATT
28263764 A
66 A
*
28263765 TACTTGGTGTTGCTGAAAATGGGAAATTTTGGGGCAAATTTTGAGATTAAAAGGGAAAAAGAATT
1 TACTTGGTGTTGCTGAAAATGGGAAATTTGGGGGCAAATTTTGAGATTAAAAGGGAAAAAGAATT
28263830 A
66 A
28263831 AGTAGAAACT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (66 bp):
TACTTGGTGTTGCTGAAAATGGGAAATTTGGGGGCAAATTTTGAGATTAAAAGGGAAAAAGAATT
A
Found at i:28264990 original size:7 final size:7
Alignment explanation
Indices: 28264955--28265166 Score: 119
Period size: 7 Copynumber: 30.3 Consensus size: 7
28264945 CTTTTACGAT
28264955 CCTAAACC
1 CCTAAA-C
28264963 CCT-AAC
1 CCTAAAC
* *
28264969 TCTTAAC
1 CCTAAAC
*
28264976 CCTCAACC
1 CCT-AAAC
*
28264984 CCTAACC
1 CCTAAAC
28264991 CCT-AAC
1 CCTAAAC
28264997 TCCTAAAC
1 -CCTAAAC
*
28265005 CTTAAAC
1 CCTAAAC
*
28265012 CC-CAAC
1 CCTAAAC
*
28265018 CCTTAA-
1 CCTAAAC
*
28265024 TCTATAAC
1 CCTA-AAC
*
28265032 CTTAAAC
1 CCTAAAC
*
28265039 CATAAAC
1 CCTAAAC
* *
28265046 CGTAACC
1 CCTAAAC
28265053 CCTAAAC
1 CCTAAAC
28265060 CCTAAAC
1 CCTAAAC
*
28265067 CATAAAC
1 CCTAAAC
*
28265074 CATAAAC
1 CCTAAAC
28265081 CCTAAAC
1 CCTAAAC
28265088 CCTAAAC
1 CCTAAAC
*
28265095 CTTAAAC
1 CCTAAAC
* *
28265102 CATAACC
1 CCTAAAC
28265109 CCTAAAC
1 CCTAAAC
*
28265116 CCATAATC
1 CC-TAAAC
*
28265124 CATAAA-
1 CCTAAAC
*
28265130 CTTAAAC
1 CCTAAAC
*
28265137 CATAAAC
1 CCTAAAC
**
28265144 TGTAAAC
1 CCTAAAC
* *
28265151 CATAACC
1 CCTAAAC
28265158 CCTAAAC
1 CCTAAAC
28265165 CC
1 CC
28265167 ATAATTCATA
Statistics
Matches: 158, Mismatches: 37, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
6 17 0.11
7 123 0.78
8 18 0.11
ACGTcount: A:0.41, C:0.39, G:0.01, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:28265046 original size:14 final size:14
Alignment explanation
Indices: 28265000--28265221 Score: 119
Period size: 14 Copynumber: 15.9 Consensus size: 14
28264990 CCCTAACTCC
*
28265000 TAAACCTTAAACCC
1 TAAACCTTAAACCA
* * * *
28265014 CAACCCTTAATCTA
1 TAAACCTTAAACCA
28265028 T-AACCTTAAACCA
1 TAAACCTTAAACCA
* * *
28265041 TAAACCGTAACCCC
1 TAAACCTTAAACCA
*
28265055 TAAACCCTAAACCA
1 TAAACCTTAAACCA
* *
28265069 TAAACCATAAACCC
1 TAAACCTTAAACCA
* *
28265083 TAAACCCTAAACCT
1 TAAACCTTAAACCA
* * *
28265097 TAAACCATAACCCC
1 TAAACCTTAAACCA
* *
28265111 TAAACCCATAATCCA
1 TAAA-CCTTAAACCA
28265126 TAAA-CTTAAACCA
1 TAAACCTTAAACCA
28265139 TAAA-CTGTAAACCA
1 TAAACCT-TAAACCA
* *
28265153 TAACCCCTAAACCCA
1 TAAACCTTAAA-CCA
** * * *
28265168 TAATTCATAAAACT
1 TAAACCTTAAACCA
*
28265182 TAAA-CTCTATACCA
1 TAAACCT-TAAACCA
* *
28265196 TATACCCTAAACCA
1 TAAACCTTAAACCA
*
28265210 AAAACCTTAAAC
1 TAAACCTTAAAC
28265222 TATAGAGATA
Statistics
Matches: 157, Mismatches: 44, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
13 24 0.15
14 108 0.69
15 25 0.16
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:28265079 original size:35 final size:35
Alignment explanation
Indices: 28265029--28265166 Score: 152
Period size: 35 Copynumber: 3.9 Consensus size: 35
28265019 CTTAATCTAT
* *
28265029 AACCTTAAACCATAAACCGTAACCCCTAAACCCTA
1 AACCATAAACCATAAACCATAACCCCTAAACCCTA
* * *
28265064 AACCATAAACCATAAACCCTAAACCCTAAACCTTA
1 AACCATAAACCATAAACCATAACCCCTAAACCCTA
* * * * *
28265099 AACCATAACCCCTAAACCCATAATCCATAAA-CTTA
1 AACCATAAACCATAAA-CCATAACCCCTAAACCCTA
**
28265134 AACCATAAACTGTAAACCATAACCCCTAAACCC
1 AACCATAAACCATAAACCATAACCCCTAAACCC
28265167 ATAATTCATA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
34 12 0.14
35 63 0.73
36 11 0.13
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.17
Consensus pattern (35 bp):
AACCATAAACCATAAACCATAACCCCTAAACCCTA
Found at i:28265094 original size:49 final size:50
Alignment explanation
Indices: 28265029--28265186 Score: 203
Period size: 49 Copynumber: 3.2 Consensus size: 50
28265019 CTTAATCTAT
* * *
28265029 AACCTTAAACCATAAACCGTAACCCCTAAACCCTAAA-CCATAAACCATA
1 AACCTTAAACCATAAACCGTAAACCATAACCCCTAAACCCATAAACCATA
* * * *
28265078 AACCCTAAACCCTAAACCTTAAACCATAACCCCTAAACCCATAATCCATA
1 AACCTTAAACCATAAACCGTAAACCATAACCCCTAAACCCATAAACCATA
* **
28265128 AA-CTTAAACCATAAACTGTAAACCATAACCCCTAAACCCATAATTCATA
1 AACCTTAAACCATAAACCGTAAACCATAACCCCTAAACCCATAAACCATA
*
28265177 AAACTTAAAC
1 AACCTTAAAC
28265187 TCTATACCAT
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
49 75 0.79
50 20 0.21
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (50 bp):
AACCTTAAACCATAAACCGTAAACCATAACCCCTAAACCCATAAACCATA
Found at i:28265142 original size:28 final size:28
Alignment explanation
Indices: 28265034--28265166 Score: 151
Period size: 28 Copynumber: 4.8 Consensus size: 28
28265024 TCTATAACCT
* *
28265034 TAAACCATAAACCGTAACCCCTAAACCC
1 TAAACCATAAACCATAAACCCTAAACCC
28265062 TAAACCATAAACCATAAACCCTAAACCC
1 TAAACCATAAACCATAAACCCTAAACCC
* *
28265090 TAAACCTTAAACCATAACCCCTAAACCC
1 TAAACCATAAACCATAAACCCTAAACCC
* * * **
28265118 ATAATCCATAAA-CTTAAACCATAAACTG
1 -TAAACCATAAACCATAAACCCTAAACCC
* *
28265146 TAAACCATAACCCCTAAACCC
1 TAAACCATAAACCATAAACCC
28265167 ATAATTCATA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.10
28 70 0.80
29 9 0.10
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (28 bp):
TAAACCATAAACCATAAACCCTAAACCC
Found at i:28265633 original size:41 final size:41
Alignment explanation
Indices: 28265570--28265758 Score: 324
Period size: 41 Copynumber: 4.6 Consensus size: 41
28265560 CTGAGCGCCG
28265570 CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCT
1 CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCT
* *
28265611 CTAAAAACGCCGCTAAATCCCTGAGCATTAGCGGCGCTTCT
1 CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCT
28265652 CCAAAAACGCCGCTAAAGTCCCTGAGCATTAGCGGCGCTTCT
1 CCAAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCT
*
28265694 CCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCT
1 CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCT
* *
28265735 ACAAAAATGCCGCTAAAGCCCTGA
1 CCAAAAACGCCGCTAAAGCCCTGA
28265759 AAGGTAAGAA
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
41 98 0.71
42 41 0.29
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (41 bp):
CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCT
Found at i:28265708 original size:83 final size:82
Alignment explanation
Indices: 28265570--28265758 Score: 324
Period size: 83 Copynumber: 2.3 Consensus size: 82
28265560 CTGAGCGCCG
* * *
28265570 CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCTAAAAACGCCGCTAAATCCCTGA
1 CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTAA
28265635 GCATTAGCGGCGCTTCT
66 GCATTAGCGGCGCTTCT
28265652 CCAAAAACGCCGCTAAAGTCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTA
1 CCAAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTA
28265717 AGCATTAGCGGCGCTTCT
65 AGCATTAGCGGCGCTTCT
* *
28265735 ACAAAAATGCCGCTAAAGCCCTGA
1 CCAAAAACGCCGCTAAAGCCCTGA
28265759 AAGGTAAGAA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
82 24 0.24
83 77 0.76
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (82 bp):
CCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTAA
GCATTAGCGGCGCTTCT
Found at i:28266163 original size:72 final size:72
Alignment explanation
Indices: 28266020--28266185 Score: 183
Period size: 72 Copynumber: 2.3 Consensus size: 72
28266010 AAAGCCATCT
* * * *
28266020 GGATGGAGAGCAAAATGTCCTAGTAGTTGAGTTATATCAAAACGCCATTCGGATGGCGAATATTA
1 GGATGGAGAGCAAACTGTCCTAGTACTTGAGTTATATCAAAACGCCATTCAGATGACGAATATTA
28266085 GTCATTC
66 GTCATTC
* * * * * *
28266092 GGATGGAGAGCAAACTTTCCTAGTACTTGAGTTATA-CTAAAACGTCGTTCAGATGATGGATGTT
1 GGATGGAGAGCAAACTGTCCTAGTACTTGAGTTATATC-AAAACGCCATTCAGATGACGAATATT
28266156 A-TCCATTC
65 AGT-CATTC
* * *
28266164 AGATGGACAGCAAGCTGTCCTA
1 GGATGGAGAGCAAACTGTCCTA
28266186 AAAGTTGAAC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
71 2 0.03
72 76 0.97
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (72 bp):
GGATGGAGAGCAAACTGTCCTAGTACTTGAGTTATATCAAAACGCCATTCAGATGACGAATATTA
GTCATTC
Found at i:28267548 original size:6 final size:6
Alignment explanation
Indices: 28267539--28267568 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28267529 GTATGTGCAT
*
28267539 GTGTGC GTGTGC GTGTGC GTGTGT GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
28267569 CCAGGAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.13, G:0.50, T:0.37
Consensus pattern (6 bp):
GTGTGC
Found at i:28270729 original size:31 final size:29
Alignment explanation
Indices: 28270660--28270730 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
28270650 CCCCAGGTTG
* *
28270660 CATTTTAGTCACTTATGTTTCAAATGTTA
1 CATTTTAGTCACTTAAGTTTCAAATGTAA
* **
28270689 CGTTTTAGTCACTTAAGTTATCATGTTGTAA
1 CATTTTAGTCACTTAAGTT-TCA-AATGTAA
28270720 CATTTTAGTCA
1 CATTTTAGTCA
28270731 TTGAGCCGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.50
30 3 0.09
31 14 0.41
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (29 bp):
CATTTTAGTCACTTAAGTTTCAAATGTAA
Found at i:28271896 original size:20 final size:20
Alignment explanation
Indices: 28271871--28271910 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28271861 AGGTTCTTGT
* *
28271871 AACATTAGTAGTAATACAAG
1 AACATTACTAATAATACAAG
*
28271891 AACATTTCTAATAATACAAG
1 AACATTACTAATAATACAAG
28271911 CAATGAGTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AACATTACTAATAATACAAG
Found at i:28273650 original size:21 final size:21
Alignment explanation
Indices: 28273626--28273695 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
28273616 AAGAGTCAAG
*
28273626 TCAAAACAATAAACAATCGAT
1 TCAAAACAACAAACAATCGAT
* * * *
28273647 TCAAAA-AGCAGAGAATCAAT
1 TCAAAACAACAAACAATCGAT
* *
28273667 TTAAAATAACAAACAATCGAT
1 TCAAAACAACAAACAATCGAT
28273688 TCAAAACA
1 TCAAAACA
28273696 GCAATGAAAC
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.19
Consensus pattern (21 bp):
TCAAAACAACAAACAATCGAT
Found at i:28280800 original size:13 final size:13
Alignment explanation
Indices: 28280784--28280817 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
28280774 TTCTTTTCTT
28280784 TTTTTTTTCACAA
1 TTTTTTTTCACAA
*
28280797 TTTTTTTTCACGA
1 TTTTTTTTCACAA
28280810 TTTTTTTT
1 TTTTTTTT
28280818 TTTGCTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:28280905 original size:12 final size:13
Alignment explanation
Indices: 28280858--28280905 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
28280848 ATGTAAACTA
28280858 AATTTTTTTCTT-G
1 AATTTTTTT-TTCG
28280871 AATTTTTTTTTCG
1 AATTTTTTTTTCG
28280884 AATTTTTTTTTC-
1 AATTTTTTTTTCG
28280896 ATATTTTTTT
1 A-ATTTTTTT
28280906 CAAAGAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.09
13 30 0.91
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (13 bp):
AATTTTTTTTTCG
Found at i:28281939 original size:21 final size:23
Alignment explanation
Indices: 28281894--28281940 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28281884 TCACCTGCAA
* *
28281894 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
28281917 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
28281938 TAA
1 TAA
28281941 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:28283430 original size:24 final size:24
Alignment explanation
Indices: 28283384--28283431 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28283374 AAAAAGTTAA
**
28283384 CAAAAAGATAAAAATTAAATAATT
1 CAAAAAGATAAAAAAAAAATAATT
28283408 CAAAAAG-TAAAAAAAAAATTAATT
1 CAAAAAGATAAAAAAAAAA-TAATT
28283432 TTAAGCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (24 bp):
CAAAAAGATAAAAAAAAAATAATT
Found at i:28292048 original size:19 final size:19
Alignment explanation
Indices: 28292024--28292065 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28292014 CATTTTAAAG
* *
28292024 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGACAAATA
*
28292043 TTATTTGGGTAGACAAATA
1 TTATTTAGGTAGACAAATA
28292062 TTAT
1 TTAT
28292066 AATAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (19 bp):
TTATTTAGGTAGACAAATA
Found at i:28299764 original size:13 final size:13
Alignment explanation
Indices: 28299746--28299775 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
28299736 AGCCCAAACT
28299746 CAATTACCCAACC
1 CAATTACCCAACC
28299759 CAATTACCCAACC
1 CAATTACCCAACC
28299772 CAAT
1 CAAT
28299776 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:28299925 original size:9 final size:9
Alignment explanation
Indices: 28299913--28299980 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
28299903 AAAATAAAAA
28299913 AATTCGGGT
1 AATTCGGGT
28299922 AATTCGGGT
1 AATTCGGGT
* **
28299931 ATTTTTTGGT
1 A-ATTCGGGT
*
28299941 AATTCGGTT
1 AATTCGGGT
28299950 AATTCGGGT
1 AATTCGGGT
28299959 AATTCGGGT
1 AATTCGGGT
28299968 AATTCGGGT
1 AATTCGGGT
28299977 AATT
1 AATT
28299981 TTTAATCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
9 44 0.88
10 6 0.12
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:28300156 original size:12 final size:12
Alignment explanation
Indices: 28300139--28300163 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28300129 AGTAATTTCG
28300139 GGTCGGTTAACC
1 GGTCGGTTAACC
28300151 GGTCGGTTAACC
1 GGTCGGTTAACC
28300163 G
1 G
28300164 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:28302015 original size:24 final size:24
Alignment explanation
Indices: 28301979--28302024 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
28301969 CAACTAATTC
28301979 AAAGCAAATAAATTATTAAAAATCA
1 AAAGCAAATAAA-TATTAAAAATCA
*
28302004 AAAGTAAA-AAATATTAAAAAT
1 AAAGCAAATAAATATTAAAAAT
28302025 TATACAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAGCAAATAAATATTAAAAATCA
Found at i:28303109 original size:2 final size:2
Alignment explanation
Indices: 28303102--28303127 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28303092 CATTGAAATG
28303102 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28303128 AGCTTCGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28303465 original size:105 final size:107
Alignment explanation
Indices: 28303254--28303468 Score: 274
Period size: 105 Copynumber: 2.0 Consensus size: 107
28303244 TCGTAATAAT
* ** * * *
28303254 ATAATTTATCTTAAATATATAAGATTATTTTAGTAATTTTCTTGACTAGGTTAATGTCGAGTTGA
1 ATAATTTATCTTAAATATATAAGATTATTTTAGTAATTTTCTTAACTAAATTAATATCGAATTAA
* * *
28303319 CTCGTGACATCAACTCAATCACACACTTAAATAATAGTATAG
66 CTCGCGACATCAACTCAATCAAACACTTAAATAATAATATAG
* * * *
28303361 ATAATTTATTTTAAATATATAAGGTTATTTTAGT-ATTTT-TTAACTAAATTGATATTGAATTAA
1 ATAATTTATCTTAAATATATAAGATTATTTTAGTAATTTTCTTAACTAAATTAATATCGAATTAA
*
28303424 CTTGCGACA-CTAACTCAATCAAACACTTAAATAATAATATAG
66 CTCGCGACATC-AACTCAATCAAACACTTAAATAATAATATAG
28303466 ATA
1 ATA
28303469 TAATTAAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
104 1 0.01
105 55 0.59
106 5 0.05
107 32 0.34
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (107 bp):
ATAATTTATCTTAAATATATAAGATTATTTTAGTAATTTTCTTAACTAAATTAATATCGAATTAA
CTCGCGACATCAACTCAATCAAACACTTAAATAATAATATAG
Found at i:28303528 original size:25 final size:25
Alignment explanation
Indices: 28303500--28303548 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28303490 CTGTACAGTA
28303500 AAAATTTAATCTATGATTAATAGTG
1 AAAATTTAATCTATGATTAATAGTG
* *
28303525 AAAATTTAATCTATGCTTATTAGT
1 AAAATTTAATCTATGATTAATAGT
28303549 TGTCCATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (25 bp):
AAAATTTAATCTATGATTAATAGTG
Found at i:28303702 original size:15 final size:15
Alignment explanation
Indices: 28303682--28303714 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28303672 AATTTAGTCT
*
28303682 TTTTAATTTTTTTAA
1 TTTTAATTTTTTAAA
28303697 TTTTAATTTTTTAAA
1 TTTTAATTTTTTAAA
28303712 TTT
1 TTT
28303715 CAAAATTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTAATTTTTTAAA
Found at i:28304921 original size:9 final size:8
Alignment explanation
Indices: 28304892--28304921 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
28304882 CCACCATCTA
28304892 TCAAAACT
1 TCAAAACT
28304900 TCAAAACT
1 TCAAAACT
28304908 TCAAAACTT
1 TCAAAAC-T
28304917 TCAAA
1 TCAAA
28304922 CACCAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (8 bp):
TCAAAACT
Found at i:28306957 original size:12 final size:12
Alignment explanation
Indices: 28306924--28306957 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28306914 TGTTTGCAAA
28306924 ACTGTATGGTTG
1 ACTGTATGGTTG
*
28306936 ACTGAATGGTTG
1 ACTGTATGGTTG
*
28306948 ACTGTTTGGT
1 ACTGTATGGT
28306958 ACTAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.32, T:0.41
Consensus pattern (12 bp):
ACTGTATGGTTG
Found at i:28307423 original size:48 final size:48
Alignment explanation
Indices: 28307349--28307447 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 48
28307339 TCTGCATTTA
* * *
28307349 TATATAGTCAGTGCACTGCACTGAGATTAGTGTGTAGACTGGCGGTTC
1 TATATAGTCAGTGCACTGCACCGAGATTACTATGTAGACTGGCGGTTC
*
28307397 TATATAGTCAGTGCACTGCACCGAGATTACTATGTAGACTGGTGGTTC
1 TATATAGTCAGTGCACTGCACCGAGATTACTATGTAGACTGGCGGTTC
28307445 TAT
1 TAT
28307448 CATATTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (48 bp):
TATATAGTCAGTGCACTGCACCGAGATTACTATGTAGACTGGCGGTTC
Found at i:28312074 original size:27 final size:27
Alignment explanation
Indices: 28312039--28312112 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 27
28312029 AATATGCAAT
* * *
28312039 ATAAGATAATGGAAAAGAAATTAACAA
1 ATAAAATAATGGAAAAAAAATAAACAA
* * *
28312066 ATAAAATAAAGTAAAAAAAATAAACTA
1 ATAAAATAATGGAAAAAAAATAAACAA
* *
28312093 ATAAAAGAAT-GAAACAAAAT
1 ATAAAATAATGGAAAAAAAAT
28312113 TTAAAACAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
26 8 0.22
27 29 0.78
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (27 bp):
ATAAAATAATGGAAAAAAAATAAACAA
Found at i:28314696 original size:18 final size:18
Alignment explanation
Indices: 28314673--28314707 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28314663 GACTCACAGT
28314673 CATGTCCCAGCCCGTGTC
1 CATGTCCCAGCCCGTGTC
**
28314691 CATGTCCGTGCCCGTGT
1 CATGTCCCAGCCCGTGT
28314708 AACTCTCTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.40, G:0.26, T:0.26
Consensus pattern (18 bp):
CATGTCCCAGCCCGTGTC
Found at i:28316380 original size:33 final size:33
Alignment explanation
Indices: 28316357--28316427 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
28316347 CCTCCAGCAT
28316357 ACCAATGCTCAGAAGAGCTAATCCAACCAACAC
1 ACCAATGCTCAGAAGAGCTAATCCAACCAACAC
* * *
28316390 ACCAGTGCTCATAAGAGCTAGTCCAACCAACAC
1 ACCAATGCTCAGAAGAGCTAATCCAACCAACAC
28316423 ACCAA
1 ACCAA
28316428 ATAAAGAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.41, C:0.34, G:0.13, T:0.13
Consensus pattern (33 bp):
ACCAATGCTCAGAAGAGCTAATCCAACCAACAC
Found at i:28317616 original size:21 final size:22
Alignment explanation
Indices: 28317592--28317636 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
28317582 ATTAACTATC
*
28317592 GAAACGTTAAAAT-TTCTTAAT
1 GAAACGTTAAAATAATCTTAAT
* *
28317613 GAAACTTTAATATAATCTTAAT
1 GAAACGTTAAAATAATCTTAAT
28317635 GA
1 GA
28317637 CACTCTGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
GAAACGTTAAAATAATCTTAAT
Found at i:28318076 original size:23 final size:23
Alignment explanation
Indices: 28318050--28318093 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
28318040 CTTAAACACA
28318050 AACA-TATACTTATATACTCAACT
1 AACATTATACTTATA-ACTCAACT
28318073 AACATTATACTTATAACTCAA
1 AACATTATACTTATAACTCAA
28318094 TTTACAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (23 bp):
AACATTATACTTATAACTCAACT
Found at i:28326782 original size:104 final size:104
Alignment explanation
Indices: 28326599--28326818 Score: 324
Period size: 104 Copynumber: 2.1 Consensus size: 104
28326589 ATTTTGTCAA
* * *
28326599 ATTA-TATATATTTTATTTAAGAATGTATTGGCTCTTTTGACATGAAGTGGAATGACAACCCAAG
1 ATTATTAT-TATTTTATTTAAGAATGTATTGACCCTTTTGACACGAAGTGGAATGACAACCCAAG
28326663 CACCCCACCCTGGTTACTCAGCCCAACACACT-CTGAATTT
65 CACCCCACCCTGGTTACTCAGCCCAACACACTCCT-AATTT
* *
28326703 ATTATTATTATTTTGTTTAAGAATGTATTGACCCTTTTGACGCGAAGTGGAATGACAACCCAAGC
1 ATTATTATTATTTTATTTAAGAATGTATTGACCCTTTTGACACGAAGTGGAATGACAACCCAAGC
*
28326768 ACCCCATCCC-GGTTACTCAGCCCAATACACTCCTAATTT
66 ACCCCA-CCCTGGTTACTCAGCCCAACACACTCCTAATTT
28326807 ATT-TT-TTATTTT
1 ATTATTATTATTTT
28326819 TATCCATAAT
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
102 7 0.07
103 2 0.02
104 90 0.84
105 8 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (104 bp):
ATTATTATTATTTTATTTAAGAATGTATTGACCCTTTTGACACGAAGTGGAATGACAACCCAAGC
ACCCCACCCTGGTTACTCAGCCCAACACACTCCTAATTT
Found at i:28330393 original size:21 final size:21
Alignment explanation
Indices: 28330352--28330393 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28330342 ATAGAATTAA
*
28330352 AAATATGATTGAGTTGAAATT
1 AAATATGATTGAATTGAAATT
*
28330373 AAATA-GATTGAAATTGTAATT
1 AAATATGATTG-AATTGAAATT
28330394 GTGATAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (21 bp):
AAATATGATTGAATTGAAATT
Found at i:28333176 original size:17 final size:17
Alignment explanation
Indices: 28333150--28333183 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28333140 GTTCTTATAA
*
28333150 ATTATTTACTTTAAATT
1 ATTATCTACTTTAAATT
28333167 ATTATCTACTTTAAATT
1 ATTATCTACTTTAAATT
28333184 GTTTTGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATCTACTTTAAATT
Found at i:28337241 original size:35 final size:35
Alignment explanation
Indices: 28337057--28337223 Score: 226
Period size: 35 Copynumber: 4.7 Consensus size: 35
28337047 AATCCAGCCA
* * * * *
28337057 AAACACACCAAATGCTTACAAGAGCCAATCCATTCA
1 AAACACACC-AATGCTCATAAGAGCTAATCCCTTCG
* *
28337093 AAACACACCAATGCTCAAAAGAGTTAATCCCTTCG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTTCG
*
28337128 AAACACACCAATGCTCATAAGAGTTAATCCCTTCG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTTCG
**
28337163 AAACACACCAATGCTCATAAGAGCTAATCCCCCCG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTTCG
*
28337198 AAACACACCGATGCTCATAAGAGCTA
1 AAACACACCAATGCTCATAAGAGCTA
28337224 GTCCAACTGA
Statistics
Matches: 120, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 111 0.93
36 9 0.08
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.18
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCCTTCG
Found at i:28339578 original size:27 final size:27
Alignment explanation
Indices: 28339545--28339811 Score: 263
Period size: 27 Copynumber: 9.9 Consensus size: 27
28339535 ACATGTTAGG
28339545 AAAGGAAGCCTTTGTGGCT-ACATCTGA
1 AAAGGAAGCCTTTGTGGCTAAC-TCTGA
*
28339572 AAGGGAAGCCTTTGTGGCTAACTCT-A
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* *
28339598 AAAGGGATGCTTTTGTGGCTAACAT-TGA
1 AAA-GGAAGCCTTTGTGGCTAAC-TCTGA
** * *
28339626 AAATTAAGCCTTTATGACTAACTCTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
*
28339653 AAAGGAAGCCTTTGTGGCAAACTCTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* *
28339680 AATGGAAGCCTTTGTGGCTAACTCTAA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* *
28339707 AAAGGAAGCATTTTTGGCTAACTCT-A
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* * * **
28339733 AACATGAAGCCTTTATAGCTATTTCTGA
1 AA-AGGAAGCCTTTGTGGCTAACTCTGA
* * *
28339761 AAAGGAAGCCTTTGTAGCGAACACTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* * *
28339788 AAAGGGAGCCATTGTGGCGAACTC
1 AAAGGAAGCCTTTGTGGCTAACTC
28339812 CAAAGGAATA
Statistics
Matches: 196, Mismatches: 37, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
26 7 0.04
27 179 0.91
28 10 0.05
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGGCTAACTCTGA
Found at i:28339743 original size:108 final size:107
Alignment explanation
Indices: 28339545--28339811 Score: 326
Period size: 108 Copynumber: 2.5 Consensus size: 107
28339535 ACATGTTAGG
* * * *
28339545 AAAGGAAGCCTTTGTGGCTACATCTGAAAGGGAAGCCTTTGTGGCTAACTCTAAAAGGGATGCTT
1 AAAGGAAGCCTTTGTGGCAAC-TCTGAAAAGGAAGCCTTTGTGGCTAACTCTAAAAAGGAAGCTT
*
28339610 TTGTGGCTAACATTGAAAATTAAGCCTTTAT-GACTAACTCTGA
65 TTGTGGCTAACATTGAAAATGAAGCCTTTATAG-CTAACTCTGA
*
28339653 AAAGGAAGCCTTTGTGGCAAACTCTGAAATGGAAGCCTTTGTGGCTAACTCTAAAAAGGAAGCAT
1 AAAGGAAGCCTTTGTGGC-AACTCTGAAAAGGAAGCCTTTGTGGCTAACTCTAAAAAGGAAGC-T
**
28339718 TTT-TGGCTAAC-TCT-AAACATGAAGCCTTTATAGCTATTTCTGA
64 TTTGTGGCTAACAT-TGAAA-ATGAAGCCTTTATAGCTAACTCTGA
* * * * *
28339761 AAAGGAAGCCTTTGTAGCGAACACTGAAAAGGGAGCCATTGTGGCGAACTC
1 AAAGGAAGCCTTTGTGGC-AACTCTGAAAAGGAAGCCTTTGTGGCTAACTC
28339812 CAAAGGAATA
Statistics
Matches: 140, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
107 4 0.03
108 129 0.92
109 7 0.05
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (107 bp):
AAAGGAAGCCTTTGTGGCAACTCTGAAAAGGAAGCCTTTGTGGCTAACTCTAAAAAGGAAGCTTT
TGTGGCTAACATTGAAAATGAAGCCTTTATAGCTAACTCTGA
Found at i:28339879 original size:27 final size:27
Alignment explanation
Indices: 28339849--28339928 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
28339839 TGATATGATA
*
28339849 GCCTTTATGGTGCAATATGAAAGGAAC
1 GCCTTTATGGCGCAATATGAAAGGAAC
* *
28339876 GCCTTTGTGGCGCAATATGAAAGAAAC
1 GCCTTTATGGCGCAATATGAAAGGAAC
* *
28339903 GACTTTATGGCGCAAAATGAAAGGAA
1 GCCTTTATGGCGCAATATGAAAGGAA
28339929 TGCTTGAGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (27 bp):
GCCTTTATGGCGCAATATGAAAGGAAC
Found at i:28343706 original size:50 final size:50
Alignment explanation
Indices: 28343649--28343892 Score: 258
Period size: 50 Copynumber: 4.9 Consensus size: 50
28343639 CATTGAGATT
*
28343649 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * * *
28343699 ATGAGAGGTTCTATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * *
28343749 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * * * *
28343799 ATGAGAACTCCCATGTAAGACCATATTTGAGATATGGCATTGGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AG
* * ** * *
28343848 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28343893 TGTTATTATC
Statistics
Matches: 160, Mismatches: 33, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
49 36 0.22
50 124 0.77
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:28347960 original size:434 final size:435
Alignment explanation
Indices: 28347151--28348453 Score: 2396
Period size: 434 Copynumber: 3.0 Consensus size: 435
28347141 GCACATTGTC
28347151 TCAGGTGATGGTATTAAAGTTGATCCGAGTAAAATTTCAGCAATTGTTGAGTGGAAACCACCTAG
1 TCAGGTGATGGTATTAAAGTTGATCCGAGTAAAATTTCAGCAATTGTTGAGTGGAAACCACCTAG
28347216 GAATGTATCAGAGGTTAGAAGTTTTCTTGGATTAGCTGGTTATTACAGACGGTTTGTAAAGGGAT
66 GAATGTATCAGAGGTTAGAAGTTTTCTTGGATTAGCTGGTTATTACAGACGGTTTGTAAAGGGAT
28347281 TTTCCATGATAGTTACCCCATTGACAAGATTGTTCCAGAAAGATATCAAGTTTTAATGGACTGAG
131 TTTCCATGATAGTTACCCCATTGACAAGATTGTTCCAGAAAGATATCAAGTTTTAATGGACTGAG
28347346 AAGTGTCAGCAAAGTTTTGACAAGTTAAAGGCATTGTTCACTCAAGCTCCTGTTTTAGTACAGCT
196 AAGTGTCAGCAAAGTTTTGACAAGTTAAAGGCATTGTTCACTCAAGCTCCTGTTTTAGTACAGCT
*
28347411 AGAACCGGGTAAAGAATTTGTGATTTACAGTAATGTATCCTTGAATGGATTGGGTTGTGTACTTA
261 AGAACCGGGTAAAGAATTTGTGATTTACAGTAATGCATCCTTGAATGGATTGGGTTGTGTACTTA
* * *
28347476 TGTAGGAAGGTAAAGTACTAGCATGTCCTTCCATACAGTTAAAGCTACATGAGAAAAACTACCCG
326 TGTAGGAAGGTAAAGTAATAGCATATGCTTCCATACAGTTAAAGCTACATGAGAAAAACTACCCG
28347541 ACGCATGATTTAGAGCTAGCTGCCATTGTATTTGCGTTGAAGATT
391 ACGCATGATTTAGAGCTAGCTGCCATTGTATTTGCGTTGAAGATT
28347586 TCAGGTGATGGTATTAAAGTTGATCCGAGTAAAATTTCAGCAATTGTTGAGTGGAAACCACCTAG
1 TCAGGTGATGGTATTAAAGTTGATCCGAGTAAAATTTCAGCAATTGTTGAGTGGAAACCACCTAG
28347651 GAATGTATCAGAGGTTAGAAGTTTTCTTGGATTAGCTGGTTATTACAGACGG-TTGTAAAGGGAT
66 GAATGTATCAGAGGTTAGAAGTTTTCTTGGATTAGCTGGTTATTACAGACGGTTTGTAAAGGGAT
28347715 TTTCCATGATAGTTACCCCATTGACAAGATTGTTCCAGAAAGATATCAAGTTTTAATGGACTGAG
131 TTTCCATGATAGTTACCCCATTGACAAGATTGTTCCAGAAAGATATCAAGTTTTAATGGACTGAG
* * *
28347780 AAGTGTCAGCAGAGTTTTGACAAGTTAAAGGAATTGTTCACTCGAGCTCCTGTTTTAGTACAGCT
196 AAGTGTCAGCAAAGTTTTGACAAGTTAAAGGCATTGTTCACTCAAGCTCCTGTTTTAGTACAGCT
*
28347845 AGAACCAGGTAAAGAATTTGTGATTTACAGTAATGCATCCTTGAATGGATTGGGTTGTGTACTTA
261 AGAACCGGGTAAAGAATTTGTGATTTACAGTAATGCATCCTTGAATGGATTGGGTTGTGTACTTA
* *
28347910 TGTAGGAAGGTAAAGTAAGAGCATATGCTTCCGTACAGTTAAAGCTACATGAGAAAAACTACCCG
326 TGTAGGAAGGTAAAGTAATAGCATATGCTTCCATACAGTTAAAGCTACATGAGAAAAACTACCCG
*
28347975 ACGCATGATTTAGAGCTAGCTGCCATTGTATTTGTGTTGAAGATT
391 ACGCATGATTTAGAGCTAGCTGCCATTGTATTTGCGTTGAAGATT
*
28348020 TCAGGTGATGGTATTAAAGTTGATCCGAGTAAAATTTTAGCAATTGTTGAGTGGAAACCACCTAG
1 TCAGGTGATGGTATTAAAGTTGATCCGAGTAAAATTTCAGCAATTGTTGAGTGGAAACCACCTAG
* * * *
28348085 GAATGTATCAAAGGTTATAAGTTTTCTTGGACTAGCTGGTTATTACAGATGGTTTGTAAAGGGAT
66 GAATGTATCAGAGGTTAGAAGTTTTCTTGGATTAGCTGGTTATTACAGACGGTTTGTAAAGGGAT
*
28348150 TTTCCATGATAGTTACCCCATTGACAAGATTTTTCCAGAAAGATATCAAGTTTTAATGGACTGAG
131 TTTCCATGATAGTTACCCCATTGACAAGATTGTTCCAGAAAGATATCAAGTTTTAATGGACTGAG
*
28348215 AAGTGTCAGCAAAGTTTTGACAAGTTAAAGGCATTGTTCACTCAAGCTCCTATTTTAGTACAGCT
196 AAGTGTCAGCAAAGTTTTGACAAGTTAAAGGCATTGTTCACTCAAGCTCCTGTTTTAGTACAGCT
28348280 AGAACCGGGTAAAGAATTTGTGATTTACAGTAATGCATCCTTGAATGGATTGGG-T-TGTACTTA
261 AGAACCGGGTAAAGAATTTGTGATTTACAGTAATGCATCCTTGAATGGATTGGGTTGTGTACTTA
* * *
28348343 TGTAGGAAGGTAAAGTAATAGTATATGCTTCCCTATAGTTAAAGCTACATGAGAAAAACTACCCG
326 TGTAGGAAGGTAAAGTAATAGCATATGCTTCCATACAGTTAAAGCTACATGAGAAAAACTACCCG
28348408 ACGCATGATTTAGAGCTAGCTGCCATTGTATTTGCGTTGAAGATT
391 ACGCATGATTTAGAGCTAGCTGCCATTGTATTTGCGTTGAAGATT
28348453 T
1 T
28348454 GGAGACATCA
Statistics
Matches: 840, Mismatches: 27, Indels: 4
0.96 0.03 0.00
Matches are distributed among these distances:
433 114 0.14
434 419 0.50
435 307 0.37
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (435 bp):
TCAGGTGATGGTATTAAAGTTGATCCGAGTAAAATTTCAGCAATTGTTGAGTGGAAACCACCTAG
GAATGTATCAGAGGTTAGAAGTTTTCTTGGATTAGCTGGTTATTACAGACGGTTTGTAAAGGGAT
TTTCCATGATAGTTACCCCATTGACAAGATTGTTCCAGAAAGATATCAAGTTTTAATGGACTGAG
AAGTGTCAGCAAAGTTTTGACAAGTTAAAGGCATTGTTCACTCAAGCTCCTGTTTTAGTACAGCT
AGAACCGGGTAAAGAATTTGTGATTTACAGTAATGCATCCTTGAATGGATTGGGTTGTGTACTTA
TGTAGGAAGGTAAAGTAATAGCATATGCTTCCATACAGTTAAAGCTACATGAGAAAAACTACCCG
ACGCATGATTTAGAGCTAGCTGCCATTGTATTTGCGTTGAAGATT
Found at i:28353954 original size:50 final size:51
Alignment explanation
Indices: 28353878--28354006 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 51
28353868 GTTAAAAAGT
* *
28353878 CCCATTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATCC
1 CCCATTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGATCC
* * *
28353929 CCCA-TAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGA-A-CT
1 CCCATTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGATCC
* * *
28353977 CCCATGCAAGACCATAT-TGGGATATGGCAT
1 CCCAT-TAAGACCATGTCTGGGACATGGCAT
28354007 TGGTAGTACA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 5 0.07
49 13 0.19
50 46 0.68
51 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (51 bp):
CCCATTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGATCC
Found at i:28354053 original size:49 final size:48
Alignment explanation
Indices: 28353877--28354060 Score: 144
Period size: 50 Copynumber: 3.8 Consensus size: 48
28353867 TGTTAAAAAG
* * *
28353877 TCCCAT-TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATC
1 TCCCATGTAAGACCATGT-TGGGACATGGCATTGGCA-CGACA--AGAGAAC
* * * *
28353928 CCCCA--TAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATG-TTGGGACATGGCATTGGCA-CGACAAGAGAAC
* * * *
28353976 TCCCATGCAAGACCATATTGGGATATGGCATTGGTA-GTACAAGA-AAC
1 TCCCATGTAAGACCATGTTGGGACATGGCATTGGCACG-ACAAGAGAAC
*
28354023 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGT-TGGGACATGGCATTGGCA
28354061 TGTTATTATC
Statistics
Matches: 108, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
47 4 0.04
48 29 0.27
49 31 0.29
50 39 0.36
51 5 0.05
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (48 bp):
TCCCATGTAAGACCATGTTGGGACATGGCATTGGCACGACAAGAGAAC
Found at i:28360527 original size:12 final size:12
Alignment explanation
Indices: 28360510--28360539 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28360500 GAGCCGTGGG
*
28360510 CACGACTTTTGC
1 CACGACTTTTGA
28360522 CACGACTTTTGA
1 CACGACTTTTGA
28360534 CACGAC
1 CACGAC
28360540 AAAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (12 bp):
CACGACTTTTGA
Found at i:28373206 original size:27 final size:27
Alignment explanation
Indices: 28373152--28373606 Score: 400
Period size: 27 Copynumber: 16.9 Consensus size: 27
28373142 ACACATCAGG
* * * *
28373152 AAAGGAATCCTTTATTGCTAACACTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
** * *
28373179 AAATAAAGCTTTTGTGGCTAACTTTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
*
28373206 AAAGGAAGCCTTTGTGGCTAACACTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
*
28373233 AAAGGAAGCCTTTATGGCTAACTCTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* * * * *
28373260 GAAGGAAGACTTTGCGGCGAACTTTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
*
28373287 AAAAGAAGCCTTTGTGG-TGAACAT-TGA
1 AAAGGAAGCCTTTGTGGCT-AAC-TCTGA
* * * *
28373314 AAAGAAAACCTTTGTGG-TGAACACTGG
1 AAAGGAAGCCTTTGTGGCT-AACTCTGA
* * *
28373341 AAATGAAGTCTTTGTGGCTAACTATGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
*
28373368 AAAGGAAGCCTTTGTAG-TGAACAT-TGA
1 AAAGGAAGCCTTTGTGGCT-AAC-TCTGA
* *
28373395 AAAAGAAGCCTTTATGGCTAACTCTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* * * *
28373422 AAATGAAGCATTTGTGGCTAACTTTAA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* * *
28373449 AAAGTAAGCCTTTGTGG-TGAACACTAA
1 AAAGGAAGCCTTTGTGGCT-AACTCTGA
* * * * *
28373476 AAAAGAAGTCTTTATGGCGAACACTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* *
28373503 AAAGAAAGCATTTGTGGCTAACTCTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
*
28373530 AAAGGAAGCCTTTGTGGCTAACTCTAA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* *
28373557 AAAGGAAGCCTTTGTGGCGAACACTGA
1 AAAGGAAGCCTTTGTGGCTAACTCTGA
* * *
28373584 AAAGGGATCCTTTGTGGCAAACT
1 AAAGGAAGCCTTTGTGGCTAACT
28373607 TCGAAGGAAT
Statistics
Matches: 341, Mismatches: 77, Indels: 20
0.78 0.18 0.05
Matches are distributed among these distances:
26 3 0.01
27 334 0.98
28 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGGCTAACTCTGA
Found at i:28373287 original size:81 final size:81
Alignment explanation
Indices: 28373152--28373607 Score: 490
Period size: 81 Copynumber: 5.6 Consensus size: 81
28373142 ACACATCAGG
* * ** *
28373152 AAAGGAATCCTTTATTGCTAACACTGAAAATAAAGCTTTTGTGGCTAACTTTGAAAAGGAAGCCT
1 AAAGGAAGCCTTTATGGCTAACACTGAAAAGGAAGCATTTGTGGCTAACTTTGAAAAGGAAGCCT
28373217 TTGTGGCT-AACACTGA
66 TTGTGG-TGAACACTGA
* * * * *
28373233 AAAGGAAGCCTTTATGGCTAACTCTGAGAAGGAAG-ACTTTGCGGCGAACTTTGAAAAAGAAGCC
1 AAAGGAAGCCTTTATGGCTAACACTGAAAAGGAAGCA-TTTGTGGCTAACTTTGAAAAGGAAGCC
*
28373297 TTTGTGGTGAACATTGA
65 TTTGTGGTGAACACTGA
* * * * * *
28373314 AAAGAAAACCTTTGTGG-TGAACACTGGAAATGAAGTC-TTTGTGGCTAACTATGAAAAGGAAGC
1 AAAGGAAGCCTTTATGGCT-AACACTGAAAAGGAAG-CATTTGTGGCTAACTTTGAAAAGGAAGC
* *
28373377 CTTTGTAGTGAACATTGA
64 CTTTGTGGTGAACACTGA
* * * * *
28373395 AAAAGAAGCCTTTATGGCTAACTCTGAAAATGAAGCATTTGTGGCTAACTTTAAAAAGTAAGCCT
1 AAAGGAAGCCTTTATGGCTAACACTGAAAAGGAAGCATTTGTGGCTAACTTTGAAAAGGAAGCCT
*
28373460 TTGTGGTGAACACTAA
66 TTGTGGTGAACACTGA
* * * * *
28373476 AAAAGAAGTCTTTATGGCGAACACTGAAAAGAAAGCATTTGTGGCTAACTCTGAAAAGGAAGCCT
1 AAAGGAAGCCTTTATGGCTAACACTGAAAAGGAAGCATTTGTGGCTAACTTTGAAAAGGAAGCCT
* *
28373541 TTGTGGCT-AACTCTAA
66 TTGTGG-TGAACACTGA
* * * * * *
28373557 AAAGGAAGCCTTTGTGGCGAACACTGAAAAGGGATCCTTTGTGGCAAACTT
1 AAAGGAAGCCTTTATGGCTAACACTGAAAAGGAAGCATTTGTGGCTAACTT
28373608 CGAAGGAATA
Statistics
Matches: 314, Mismatches: 53, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
80 3 0.01
81 309 0.98
82 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (81 bp):
AAAGGAAGCCTTTATGGCTAACACTGAAAAGGAAGCATTTGTGGCTAACTTTGAAAAGGAAGCCT
TTGTGGTGAACACTGA
Found at i:28382010 original size:31 final size:29
Alignment explanation
Indices: 28381972--28382092 Score: 125
Period size: 31 Copynumber: 4.0 Consensus size: 29
28381962 GGCCCATTTT
*
28381972 TATTTTAAAAATTTTAAAAAATTAAAAAAA
1 TATTTT-AAAATTTAAAAAAATTAAAAAAA
* **
28382002 GTATTTTAAAATTAAAAAAAGTATTTTAAAAA
1 -TATTTTAAAATTTAAAAAA--ATTAAAAAAA
* **
28382034 TATTTTAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAA--ATTAAAAAAA
28382065 TATTTTAAAATTTAAAAAAATTAAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAA
28382093 GTATGTAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
29 7 0.09
30 11 0.14
31 55 0.68
32 8 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAA
Found at i:28382033 original size:21 final size:21
Alignment explanation
Indices: 28381982--28382034 Score: 90
Period size: 20 Copynumber: 2.5 Consensus size: 21
28381972 TATTTTAAAA
28381982 ATTTTAAAAAATTAAAAAAAGT
1 ATTTT-AAAAATTAAAAAAAGT
28382004 ATTTT-AAAATTAAAAAAAGT
1 ATTTTAAAAATTAAAAAAAGT
28382024 ATTTTAAAAAT
1 ATTTTAAAAAT
28382035 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.67
21 5 0.17
22 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
ATTTTAAAAATTAAAAAAAGT
Found at i:28382104 original size:40 final size:40
Alignment explanation
Indices: 28382040--28382124 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
28382030 AAAATATTTT
* *
28382040 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAA
1 AAAATTAAAAAAAGTATGTAAAAAATATTTTAAAA-TTAAA
28382081 AAAATT-AAAAAAGTATGTAAAAAATATTTTAAAATTAAA
1 AAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
28382120 AAAAT
1 AAAAT
28382125 AAATATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 10 0.24
40 26 0.62
41 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (40 bp):
AAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
Found at i:28384627 original size:9 final size:9
Alignment explanation
Indices: 28384613--28384643 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28384603 GTTAAACGAA
28384613 TCGAGTTAT
1 TCGAGTTAT
*
28384622 TCGAGTTAA
1 TCGAGTTAT
28384631 TCGAGTTAT
1 TCGAGTTAT
28384640 TCGA
1 TCGA
28384644 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28385532 original size:5 final size:5
Alignment explanation
Indices: 28385522--28385549 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28385512 GAAAATTTTT
28385522 GATTC GATTC GATTC GATTC GATTC GAT
1 GATTC GATTC GATTC GATTC GATTC GAT
28385550 CGAATGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
GATTC
Found at i:28387763 original size:35 final size:36
Alignment explanation
Indices: 28387702--28387776 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 36
28387692 AGACGTTAGC
28387702 TTTTTCCTTTTCTCTTTTTTTTATTAATTTTTTTGG
1 TTTTTCCTTTTCTCTTTTTTTTATTAATTTTTTTGG
*
28387738 TTTTTTCTTTTCTC-TTTTTTTATTAATTTTTTTGG
1 TTTTTCCTTTTCTCTTTTTTTTATTAATTTTTTTGG
28387773 TTTT
1 TTTT
28387777 CTTGTCAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 25 0.66
36 13 0.34
ACGTcount: A:0.08, C:0.09, G:0.05, T:0.77
Consensus pattern (36 bp):
TTTTTCCTTTTCTCTTTTTTTTATTAATTTTTTTGG
Found at i:28397642 original size:38 final size:39
Alignment explanation
Indices: 28397546--28397658 Score: 167
Period size: 39 Copynumber: 2.9 Consensus size: 39
28397536 AAATTCGGTT
* *
28397546 AATTACCCAATCCAATAAAATTAAAACTAAAGTCTACCA
1 AATTACCCAACCCAATAAAAATAAAACTAAAGTCTACCA
* *
28397585 AATTATCCAACCCAATAAAACTAAAACTAAAGTCTACTC-
1 AATTACCCAACCCAATAAAAATAAAACTAAAGTCTAC-CA
28397624 AATTA-CCAACCCAATAAAAATAAAACTAAAGTCTA
1 AATTACCCAACCCAATAAAAATAAAACTAAAGTCTA
28397659 ACTCTTAAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
38 29 0.42
39 39 0.57
40 1 0.01
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.22
Consensus pattern (39 bp):
AATTACCCAACCCAATAAAAATAAAACTAAAGTCTACCA
Found at i:28397870 original size:9 final size:9
Alignment explanation
Indices: 28397856--28397914 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
28397846 GTAGTGATTC
28397856 AATTCGGGT
1 AATTCGGGT
28397865 AATTCGGGT
1 AATTCGGGT
*
28397874 AACTCGGGT
1 AATTCGGGT
28397883 AATTCGGGT
1 AATTCGGGT
*
28397892 AATTCGGTT
1 AATTCGGGT
*
28397901 AATTCGGTT
1 AATTCGGGT
28397910 AATTC
1 AATTC
28397915 AGTTAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.36
Consensus pattern (9 bp):
AATTCGGGT
Found at i:28397919 original size:9 final size:9
Alignment explanation
Indices: 28397856--28397922 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
28397846 GTAGTGATTC
*
28397856 AATTCGGGT
1 AATTCGGTT
*
28397865 AATTCGGGT
1 AATTCGGTT
* *
28397874 AACTCGGGT
1 AATTCGGTT
*
28397883 AATTCGGGT
1 AATTCGGTT
28397892 AATTCGGTT
1 AATTCGGTT
28397901 AATTCGGTT
1 AATTCGGTT
*
28397910 AATTCAGTT
1 AATTCGGTT
28397919 AATT
1 AATT
28397923 TTTAACCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28398475 original size:21 final size:20
Alignment explanation
Indices: 28398435--28398475 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28398425 TTCTTTAGCT
*
28398435 TAGAAACAATTCTTTTAAAA
1 TAGAAACAATTCTATTAAAA
*
28398455 TAGAAGCAATTCCTATTAAAA
1 TAGAAACAATT-CTATTAAAA
28398476 ATTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (20 bp):
TAGAAACAATTCTATTAAAA
Found at i:28402629 original size:25 final size:24
Alignment explanation
Indices: 28402574--28402630 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
28402564 GAATAGTTTA
* *
28402574 TTAAATAAAAATAAAATATTTTTT
1 TTAAATTAAAACAAAATATTTTTT
28402598 TTGAAATTAAAACAAAATATTTTTT
1 TT-AAATTAAAACAAAATATTTTTT
28402623 TGTAAATT
1 T-TAAATT
28402631 TCTTGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 26 0.90
26 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TTAAATTAAAACAAAATATTTTTT
Found at i:28402689 original size:21 final size:20
Alignment explanation
Indices: 28402656--28402695 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28402646 ACTTAACACT
28402656 TAATCACTATTTTGAAATTTC
1 TAATCACTATTTT-AAATTTC
* *
28402677 TAATTACTCTTTTAAATTT
1 TAATCACTATTTTAAATTT
28402696 TATATTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.53
Consensus pattern (20 bp):
TAATCACTATTTTAAATTTC
Found at i:28406770 original size:66 final size:66
Alignment explanation
Indices: 28406653--28406785 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 66
28406643 TGATGAGCTT
* * **
28406653 AAAATGAGATGAAGTATATTCTTGCTTTACAATTCAATTAAAACAGGTAATTACAAGACCAAGGG
1 AAAATAAGATGAAGTATATTCTTGCTTGACAATTCAATTAAAACACATAATTACAAGACCAAGGG
28406718 A
66 A
* * * *
28406719 AAAATAAGATGAGGTATATTCTTGCCTTGA-AATTCAATTCAAACCCATAATTACAAGACTAAGG
1 AAAATAAGATGAAGTATATTCTTG-CTTGACAATTCAATTAAAACACATAATTACAAGACCAAGG
28406783 GA
65 GA
28406785 A
1 A
28406786 CCATTATCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 54 0.93
67 4 0.07
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.27
Consensus pattern (66 bp):
AAAATAAGATGAAGTATATTCTTGCTTGACAATTCAATTAAAACACATAATTACAAGACCAAGGG
A
Found at i:28416093 original size:1 final size:1
Alignment explanation
Indices: 28416087--28416124 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
28416077 CACCAAAGAC
28416087 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28416125 TGAAATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28423243 original size:32 final size:32
Alignment explanation
Indices: 28423202--28423265 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28423192 ATGTTAGCTC
28423202 ACTAGTTGTTTAATGTTTAACTAATATTAAGT
1 ACTAGTTGTTTAATGTTTAACTAATATTAAGT
28423234 ACTAGTTGTTTAATGTTTAACTAATATTAAGT
1 ACTAGTTGTTTAATGTTTAACTAATATTAAGT
28423266 GGTATTACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (32 bp):
ACTAGTTGTTTAATGTTTAACTAATATTAAGT
Found at i:28425261 original size:10 final size:10
Alignment explanation
Indices: 28425245--28425283 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
28425235 ATCAAATTTC
28425245 ATTAATTATT
1 ATTAATTATT
*
28425255 TTTAATTATT
1 ATTAATTATT
28425265 ATTAATCTGATT
1 ATTAAT-T-ATT
28425277 ATTAATT
1 ATTAATT
28425284 TAGTGTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 14 0.56
11 2 0.08
12 9 0.36
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (10 bp):
ATTAATTATT
Found at i:28430309 original size:21 final size:21
Alignment explanation
Indices: 28430285--28430325 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28430275 CTCAATTCTA
28430285 AATTCTCTCAATAATTTCGTC
1 AATTCTCTCAATAATTTCGTC
*
28430306 AATTCTCTCGATAATTTCGT
1 AATTCTCTCAATAATTTCGT
28430326 TTCAAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTCTCTCAATAATTTCGTC
Found at i:28432370 original size:26 final size:23
Alignment explanation
Indices: 28432338--28432398 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 23
28432328 CGAAATTCTC
28432338 TTATTTATGTTTACTCTTAATATAA-T
1 TTATTTATGTTTA--C-TAAT-TAATT
*
28432364 TTATTTA-ATTTACTAATTAATT
1 TTATTTATGTTTACTAATTAATT
28432386 TTATTTATGTTTA
1 TTATTTATGTTTA
28432399 GGTTAACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 3 0.10
22 12 0.39
23 5 0.16
25 4 0.13
26 7 0.23
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (23 bp):
TTATTTATGTTTACTAATTAATT
Found at i:28437749 original size:26 final size:25
Alignment explanation
Indices: 28437701--28437754 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
28437691 TAATTAGTAT
* *
28437701 AAAATATTAATAATTCAATAAATTG
1 AAAATATTAATAATTAAATAAATGG
28437726 AAAA-ATTAAATAATTAAATAAAATGG
1 AAAATATT-AATAATTAAAT-AAATGG
28437752 AAA
1 AAA
28437755 TTCAGGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.56
26 8 0.32
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (25 bp):
AAAATATTAATAATTAAATAAATGG
Found at i:28438744 original size:30 final size:30
Alignment explanation
Indices: 28438687--28438744 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
28438677 TGCCTTTGAA
* *
28438687 AATATTTACAAAAAGAGACATCTAATTTCT
1 AATATTTACAAAAAGAGACACCAAATTTCT
*
28438717 AATATTTACAAAAAG-GGCAACCAAATTT
1 AATATTTACAAAAAGAGAC-ACCAAATTT
28438745 TGAAAATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTCT
Found at i:28438796 original size:106 final size:106
Alignment explanation
Indices: 28438665--28438868 Score: 354
Period size: 106 Copynumber: 1.9 Consensus size: 106
28438655 AATTAAAAAC
28438665 ATTTATTCTAGATGCCTTTGAAAATATTTACAAAAAGAGACATCTAATTTCTAATATTTACAAAA
1 ATTTATTCTAGATGCCTTTGAAAATATTTACAAAAAGAGACATCTAATTTCTAATATTTACAAAA
* *
28438730 AGGGCAACCAAATTTTGAAAATAGTTCAATTAAATACCTAT
66 AGAGCAACCAAATTTTGAAAATAATTCAATTAAATACCTAT
* * *
28438771 ATTTATTCTTGATGCCTTTGAAAATATTTGCAAAAAGAGACATCTAATTTTTAATATTTACAAAA
1 ATTTATTCTAGATGCCTTTGAAAATATTTACAAAAAGAGACATCTAATTTCTAATATTTACAAAA
*
28438836 AGAGCAACTAAATTTTGAAAATAATTCAATTAA
66 AGAGCAACCAAATTTTGAAAATAATTCAATTAA
28438869 GTACTTAGAC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (106 bp):
ATTTATTCTAGATGCCTTTGAAAATATTTACAAAAAGAGACATCTAATTTCTAATATTTACAAAA
AGAGCAACCAAATTTTGAAAATAATTCAATTAAATACCTAT
Found at i:28438851 original size:29 final size:30
Alignment explanation
Indices: 28438793--28438851 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28438783 TGCCTTTGAA
* * *
28438793 AATATTTGCAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAACTAAATTTT
28438823 AATATTTACAAAAAGAG-CAACTAAATTTT
1 AATATTTACAAAAAGAGACAACTAAATTTT
28438852 GAAAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACTAAATTTT
Found at i:28442939 original size:28 final size:27
Alignment explanation
Indices: 28442880--28442940 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
28442870 AATGCATGCA
28442880 TTTAATATGTCTTAGTTAGTACATATC
1 TTTAATATGTCTTAGTTAGTACATATC
* * *
28442907 ATTAATTTGTCTTAGTATATTACATCAT-
1 TTTAATATGTCTTAGT-TAGTACAT-ATC
28442935 TTTAAT
1 TTTAAT
28442941 GTGTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 14 0.50
28 12 0.43
29 2 0.07
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (27 bp):
TTTAATATGTCTTAGTTAGTACATATC
Found at i:28444041 original size:27 final size:27
Alignment explanation
Indices: 28444008--28444060 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
28443998 AAGTGACTTA
28444008 TAAGTTTCGGGTCAATACTCTCTATAC
1 TAAGTTTCGGGTCAATACTCTCTATAC
28444035 TAAGTTTCGGGTCAATACTCTCTATA
1 TAAGTTTCGGGTCAATACTCTCTATA
28444061 GTATTGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (27 bp):
TAAGTTTCGGGTCAATACTCTCTATAC
Found at i:28445077 original size:32 final size:32
Alignment explanation
Indices: 28445022--28445131 Score: 141
Period size: 32 Copynumber: 3.5 Consensus size: 32
28445012 GAATGCCTAC
* * *
28445022 AAGCCATAAGTA-TAGTAATATGATTGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
*
28445053 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
* * *
28445085 CAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
*
28445117 AAGCCATTAGTAGCA
1 AAGCCATCAGTAGCA
28445132 ACGCACCAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
31 11 0.17
32 55 0.83
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAGCAGTAATATGATCGGCACA
Found at i:28445316 original size:24 final size:24
Alignment explanation
Indices: 28445276--28445322 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28445266 TGCTCAAAAT
* *
28445276 CAGTCATTCAAATCACAGACAAAC
1 CAGTCATCCAAATCACAAACAAAC
28445300 CAGTCATACCAAA-CACAAACAAA
1 CAGTCAT-CCAAATCACAAACAAA
28445323 TAAGTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.51, C:0.30, G:0.06, T:0.13
Consensus pattern (24 bp):
CAGTCATCCAAATCACAAACAAAC
Found at i:28445625 original size:27 final size:27
Alignment explanation
Indices: 28445364--28445624 Score: 308
Period size: 27 Copynumber: 9.7 Consensus size: 27
28445354 TTGACCTCGA
* *
28445364 GGGTATTACGATCATTTTACCTTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* *
28445391 GGGCATTACGGTCATTTTACCCTA-AA
1 GGGTATTACGGTCATTTTACCCTACAG
* *
28445417 GGGTATTACGGTCATTTTACCCTAAAA
1 GGGTATTACGGTCATTTTACCCTACAG
* *
28445444 GGGCATTACGATCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
28445471 GGGTGTTACAGTCATTTTACCCTATAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * * *
28445498 AGGTATAACAGTCATTTTACCTTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* *
28445525 GGGCATTACGATCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
28445552 GGGTATTACAGTCATTTTAACCTACAA
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
28445579 GGGCATTATGGTCATTTTATCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
28445606 GGGTATTACGGTCATTTTA
1 GGGTATTACGGTCATTTTA
28445625 TAACATTTTC
Statistics
Matches: 196, Mismatches: 37, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 24 0.12
27 172 0.88
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (27 bp):
GGGTATTACGGTCATTTTACCCTACAG
Found at i:28467160 original size:35 final size:35
Alignment explanation
Indices: 28467120--28467190 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
28467110 GGAGAAAAAG
28467120 AAAAACCTTTTTCAGAACCCTTCTGACTCATATGT
1 AAAAACCTTTTTCAGAACCCTTCTGACTCATATGT
28467155 AAAAACCTTTTTCAGAACCCTTCTGACTCATATGT
1 AAAAACCTTTTTCAGAACCCTTCTGACTCATATGT
28467190 A
1 A
28467191 TAACCCAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.34
Consensus pattern (35 bp):
AAAAACCTTTTTCAGAACCCTTCTGACTCATATGT
Found at i:28477149 original size:20 final size:20
Alignment explanation
Indices: 28477116--28477159 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28477106 TAAAGAAAGT
* *
28477116 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAATAATA
28477136 AAATGCAAAT-GAAAATAATA
1 AAATGC-AATGGAAAATAATA
28477156 AAAT
1 AAAT
28477160 TTGAAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (20 bp):
AAATGCAATGGAAAATAATA
Found at i:28481234 original size:20 final size:20
Alignment explanation
Indices: 28481197--28481237 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28481187 GTTTCCATTG
* *
28481197 ATGTTAATTGAAGTTTTTGA
1 ATGTTAATGGAAGATTTTGA
*
28481217 ATGTTAATGGTAGATTTTGA
1 ATGTTAATGGAAGATTTTGA
28481237 A
1 A
28481238 GCTTAGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (20 bp):
ATGTTAATGGAAGATTTTGA
Found at i:28498597 original size:24 final size:23
Alignment explanation
Indices: 28498557--28498610 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
28498547 CCAGATCATT
*
28498557 CAGAATTAGCCACAAAGGCCAAA
1 CAGAAGTAGCCACAAAGGCCAAA
*
28498580 CAGAAGTATGCCATAAAGGCCAAA
1 CAGAAGTA-GCCACAAAGGCCAAA
*
28498604 CAAAAGT
1 CAGAAGT
28498611 GCACCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (23 bp):
CAGAAGTAGCCACAAAGGCCAAA
Found at i:28498621 original size:24 final size:24
Alignment explanation
Indices: 28498570--28498627 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
28498560 AATTAGCCAC
* ** *
28498570 AAAGGCCAAACAGAAGTATGCCAT
1 AAAGGCCAAACAAAAGTACACCAA
*
28498594 AAAGGCCAAACAAAAGTGCACCAA
1 AAAGGCCAAACAAAAGTACACCAA
*
28498618 AAAGGACAAA
1 AAAGGCCAAA
28498628 TAGAATGTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.21, G:0.19, T:0.07
Consensus pattern (24 bp):
AAAGGCCAAACAAAAGTACACCAA
Found at i:28500134 original size:22 final size:21
Alignment explanation
Indices: 28500109--28500155 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28500099 AAGCCGTCAC
*
28500109 ATAAATGCCGATAAATGACCAT
1 ATAAATGCCGAT-AATAACCAT
* *
28500131 ATAATTGTCGATAATAACCAT
1 ATAAATGCCGATAATAACCAT
28500152 ATAA
1 ATAA
28500156 TCGTAGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (21 bp):
ATAAATGCCGATAATAACCAT
Found at i:28500152 original size:21 final size:21
Alignment explanation
Indices: 28500117--28500165 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28500107 ACATAAATGC
* *
28500117 CGATAAATGACCATATAATTGT
1 CGAT-AATAACCATATAATCGT
28500139 CGATAATAACCATATAATCGT
1 CGATAATAACCATATAATCGT
*
28500160 AGATAA
1 CGATAA
28500166 ACCACCACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (21 bp):
CGATAATAACCATATAATCGT
Found at i:28500335 original size:7 final size:7
Alignment explanation
Indices: 28500323--28500351 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28500313 GTAAACATGC
28500323 TCACATA
1 TCACATA
28500330 TCACATA
1 TCACATA
28500337 TCACATA
1 TCACATA
28500344 TCACATA
1 TCACATA
28500351 T
1 T
28500352 TATTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (7 bp):
TCACATA
Found at i:28510386 original size:98 final size:98
Alignment explanation
Indices: 28510217--28510857 Score: 1257
Period size: 98 Copynumber: 6.5 Consensus size: 98
28510207 ATACAATAAA
*
28510217 ACTTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTAT
1 ACTTTAAAAGAA-AGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTAT
28510281 TCCTTTAGAATCCCAAACTCGGAATATTTCCTTT
65 TCCTTTAGAATCCCAAACTCGGAATATTTCCTTT
28510315 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
28510380 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
28510413 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
28510478 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
28510511 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
28510576 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
28510609 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
28510674 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
28510707 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
28510772 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
28510805 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGT
1 ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGT
28510858 NNNNNNNNNN
Statistics
Matches: 541, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
97 1 0.00
98 540 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAAAGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:28511913 original size:20 final size:19
Alignment explanation
Indices: 28511888--28511952 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
28511878 CTTGTTTACA
28511888 TTGATTTTATTCTCAATCTT
1 TTGATTTTATTCTCAATC-T
* *
28511908 TTGATTTCT-TTC-CATTACA
1 TTGATTT-TATTCTCAAT-CT
*
28511927 TTGATTTGATTCTCAATCCT
1 TTGATTTTATTCTCAAT-CT
28511947 TTGATT
1 TTGATT
28511953 CCTTTCCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 13 0.37
20 21 0.60
21 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.55
Consensus pattern (19 bp):
TTGATTTTATTCTCAATCT
Found at i:28511939 original size:39 final size:39
Alignment explanation
Indices: 28511883--28511963 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
28511873 AAAATCTTGT
* * *
28511883 TTACATTGATTTTATTCTCAATCTTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTCCTTTCCA
28511922 TTACATTGATTTGATTCTCAATCCTTTGATTCCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTCCTTTCCA
28511961 TTA
1 TTA
28511964 TTGTTTTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (39 bp):
TTACATTGATTTGATTCTCAATCCTTTGATTCCTTTCCA
Found at i:28525915 original size:24 final size:24
Alignment explanation
Indices: 28525865--28525916 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
28525855 AATCACAGTC
** *
28525865 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
28525889 AAATATATTATACTCATAAATATT
1 AAATATATTATACTAATAAATACT
28525913 AAAT
1 AAAT
28525917 CTTCTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:28529478 original size:16 final size:15
Alignment explanation
Indices: 28529459--28529488 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28529449 AGTATCAATT
28529459 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
28529475 TTTGATTGGGATGA
1 TTTGATTGGGATGA
28529489 TGGTTTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:28536396 original size:50 final size:50
Alignment explanation
Indices: 28536338--28536580 Score: 315
Period size: 50 Copynumber: 4.9 Consensus size: 50
28536328 CATTTGGGTA
28536338 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGAGAT
* * * *
28536388 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTACTGAGAT
1 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGAGAT
*
28536438 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACTGAGAT
1 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGAGAT
* *** * * *
28536488 GAGAGGTCCCCCATAAGACCATGTTTGGGACATGGCATGGGCACCGATAT
1 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGAGAT
* ** * * * *
28536538 GAGAACTCCCATGTAAGACCATATCTGAGATATGGCATTGGCA
1 AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCA
28536581 GTACAGGAAA
Statistics
Matches: 168, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 168 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGAGAT
Done.