Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014898.1 Kokia drynarioides strain JFW-HI SEQ_129941, 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: 1273188
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 233 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:2454 original size:19 final size:20
Alignment explanation
Indices: 2420--2469 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2410 AAATTTTCTG
*
2420 TTTAATTTTATAAT-AATTAT
1 TTTAA-TTTATAATAAATAAT
2440 TTATAATTTAT-ATAAATAAT
1 TT-TAATTTATAATAAATAAT
2460 TTTAATTTAT
1 TTTAATTTAT
2470 TCTTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.37
20 14 0.52
21 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTATAATAAATAAT
Found at i:4257 original size:2 final size:2
Alignment explanation
Indices: 4250--4291 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4240 TTCCAAAACA
4250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4292 TACTATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4677 original size:3 final size:3
Alignment explanation
Indices: 4669--4698 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4659 GTACCTACCC
*
4669 CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
4699 GTTCCGCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:10122 original size:45 final size:45
Alignment explanation
Indices: 10054--10147 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
10044 CTAAACTCAG
*
10054 AAAAAATTAATCTTATTTTCTTCAAAAT-AAAAAATAAAACAATT
1 AAAAAATTAATCTTATTTGCTTCAAAATAAAAAAATAAAACAATT
* *
10098 AAAAAATTTAGTCTTATTTGCTTCAAAATAAAAAAAATAAAATAATT
1 AAAAAA-TTAATCTTATTTGCTTCAAAAT-AAAAAAATAAAACAATT
10145 AAA
1 AAA
10148 TTAAATTCGG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 6 0.14
45 20 0.45
47 18 0.41
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (45 bp):
AAAAAATTAATCTTATTTGCTTCAAAATAAAAAAATAAAACAATT
Found at i:10309 original size:15 final size:15
Alignment explanation
Indices: 10289--10318 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10279 TGCACTACTT
10289 GCACAAATCAAAATC
1 GCACAAATCAAAATC
10304 GCACAAATCAAAATC
1 GCACAAATCAAAATC
10319 TTTACCCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.27, G:0.07, T:0.13
Consensus pattern (15 bp):
GCACAAATCAAAATC
Found at i:11672 original size:53 final size:53
Alignment explanation
Indices: 11592--11701 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
11582 ATTACAGCAT
*
11592 CAAAACAATTTGAACAACTCCTCCATCCGGGAATTCTAGTGCATGCATACATA
1 CAAAACAATTTGAACAACTCCTCCATCCAGGAATTCTAGTGCATGCATACATA
11645 CAAAACAATTTGAACAACTCCTCCATCCAGGAATTCTAGTGCATGCATACATA
1 CAAAACAATTTGAACAACTCCTCCATCCAGGAATTCTAGTGCATGCATACATA
11698 CAAA
1 CAAA
11702 TAACAGCAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (53 bp):
CAAAACAATTTGAACAACTCCTCCATCCAGGAATTCTAGTGCATGCATACATA
Found at i:15987 original size:19 final size:20
Alignment explanation
Indices: 15963--16010 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
15953 ATTTATTTAC
15963 TTTTAAAATTTT-ATATATT
1 TTTTAAAATTTTCATATATT
* *
15982 TTTTAAGATTTTCATGTATT
1 TTTTAAAATTTTCATATATT
16002 TTTATAAAA
1 TTT-TAAAA
16011 AAGTTATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
21 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTAAAATTTTCATATATT
Found at i:17735 original size:24 final size:24
Alignment explanation
Indices: 17705--17759 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
17695 CTCGTGTTTC
*
17705 TAGCACTTCCATGCTCCTGATATT
1 TAGCACTTCCATGCTCATGATATT
** *
17729 TAGCACTTTGATGCTCATGGTATT
1 TAGCACTTCCATGCTCATGATATT
17753 T-GCACTT
1 TAGCACTT
17760 ATGTGCCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (24 bp):
TAGCACTTCCATGCTCATGATATT
Found at i:26186 original size:11 final size:11
Alignment explanation
Indices: 26159--26189 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
26149 TCAATCTCGA
26159 ATAATTTTTCT
1 ATAATTTTTCT
26170 AT-ATTTTTCT
1 ATAATTTTTCT
26180 ATAATTTTTC
1 ATAATTTTTC
26190 AAAGTCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (11 bp):
ATAATTTTTCT
Found at i:29136 original size:12 final size:12
Alignment explanation
Indices: 29119--29145 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29109 CCATGAAGAC
29119 TAAAAATACTAG
1 TAAAAATACTAG
29131 TAAAAATACTAG
1 TAAAAATACTAG
29143 TAA
1 TAA
29146 TTATCATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (12 bp):
TAAAAATACTAG
Found at i:33584 original size:135 final size:135
Alignment explanation
Indices: 33338--33603 Score: 361
Period size: 135 Copynumber: 2.0 Consensus size: 135
33328 ACAATTTACT
* * * * * *
33338 TGCAGGGGAAGAGTTTCAACTTTGCTTGGCAGTGATTTCCGAGATACAATGGACCAATTAATGAC
1 TGCAGGGGAAGAGTTTCAACTCTACTTGACAGTGATTTCCGAGAGAAAATGAACCAATTAATGAC
** * *
33403 TTCTCGTGTACAAATGCAAGCGGATGGGGCTGAAAGTCAACAAGAAGCGGATGATAAGGATGGAA
66 TTCTCGTGTACAAATGCAAGCGGATGGAACTGAAAGTCAACAAGAAGCGGAGGATAAGGAAGGAA
33468 TTATA
131 TTATA
* * *
33473 TGCAGGGGAAGAGTTTCAACTCTATTTGACAGTGATTTCCTAGAGAAAATGAACCGATTAATGAC
1 TGCAGGGGAAGAGTTTCAACTCTACTTGACAGTGATTTCCGAGAGAAAATGAACCAATTAATGAC
* * * * **
33538 TTCTCGTGTAGAAATGCAAGCTGATGTAACTGAAAGTCAACGAGAAGTTGAGGATAAGGAAGGAA
66 TTCTCGTGTACAAATGCAAGCGGATGGAACTGAAAGTCAACAAGAAGCGGAGGATAAGGAAGGAA
33603 T
131 T
33604 GGTCGAACCC
Statistics
Matches: 112, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
135 112 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (135 bp):
TGCAGGGGAAGAGTTTCAACTCTACTTGACAGTGATTTCCGAGAGAAAATGAACCAATTAATGAC
TTCTCGTGTACAAATGCAAGCGGATGGAACTGAAAGTCAACAAGAAGCGGAGGATAAGGAAGGAA
TTATA
Found at i:33631 original size:3 final size:3
Alignment explanation
Indices: 33623--33733 Score: 168
Period size: 3 Copynumber: 37.0 Consensus size: 3
33613 CACGTCTTAC
* * *
33623 GAA GAA GAA GAT GAA GAA GAA GAA GAG GAA GAA GAA GAT GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
33671 GAA GAA GAA GAA GAA TAT GAA GAA GAA GAT GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
33719 GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
33734 AGGAGCTTAA
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:35090 original size:18 final size:18
Alignment explanation
Indices: 35050--35084 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35040 TTTTTTATTA
*
35050 TGTCTTGTGGCACGTTTC
1 TGTCTTATGGCACGTTTC
35068 TGTCTTATGGCACGTTT
1 TGTCTTATGGCACGTTT
35085 TCGTCTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.20, G:0.26, T:0.46
Consensus pattern (18 bp):
TGTCTTATGGCACGTTTC
Found at i:37295 original size:30 final size:30
Alignment explanation
Indices: 37231--37297 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
37221 ATTATTCATC
* *
37231 AGTGATTATTTTATTATTTTTTATAATTTT
1 AGTGATTATTTTATTATTTTTTATAAATTG
37261 AGTGATTATTTTATTATTTTTT-TAAAATTG
1 AGTGATTATTTTATTATTTTTTAT-AAATTG
37291 AGTGATT
1 AGTGATT
37298 GAAATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.61
Consensus pattern (30 bp):
AGTGATTATTTTATTATTTTTTATAAATTG
Found at i:39256 original size:6 final size:6
Alignment explanation
Indices: 39231--39269 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
39221 ACAATTCATA
* * *
39231 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
39270 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:39326 original size:22 final size:22
Alignment explanation
Indices: 39291--39344 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
39281 AAATCATTCA
39291 AATTCAAT-TCAAATATACTATT
1 AATTCAATATCAAATATAC-ATT
* *
39313 AATTCAATAT-AAATTTTCATT
1 AATTCAATATCAAATATACATT
39334 AATCTCAATAT
1 AAT-TCAATAT
39345 TAACGCTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 6 0.21
22 21 0.75
23 1 0.04
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTCAATATCAAATATACATT
Found at i:50335 original size:12 final size:12
Alignment explanation
Indices: 50318--50342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50308 TAAAACAATT
50318 ACTTAATTTTTA
1 ACTTAATTTTTA
50330 ACTTAATTTTTA
1 ACTTAATTTTTA
50342 A
1 A
50343 ATTTTTAAAA
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ACTTAATTTTTA
Found at i:59097 original size:18 final size:18
Alignment explanation
Indices: 59076--59110 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
59066 AAATGGGTGT
59076 TAGAAGAAAAATCAAGGC
1 TAGAAGAAAAATCAAGGC
59094 TAGAAGAAAAATCAAGG
1 TAGAAGAAAAATCAAGG
59111 TACTAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.09, G:0.23, T:0.11
Consensus pattern (18 bp):
TAGAAGAAAAATCAAGGC
Found at i:61750 original size:18 final size:18
Alignment explanation
Indices: 61706--61767 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
61696 ATTCTCCCAT
*
61706 TAAAAATCATAAAAATATA
1 TAAAAATCAT-AAAATTTA
*
61725 AAAAAATCATAAAATTTA
1 TAAAAATCATAAAATTTA
* *
61743 TAAGAATC-TAATAAATTA
1 TAAAAATCATAA-AATTTA
61761 TAAAAAT
1 TAAAAAT
61768 ATATATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 3 0.08
18 24 0.67
19 9 0.25
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATCATAAAATTTA
Found at i:63463 original size:16 final size:17
Alignment explanation
Indices: 63433--63466 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
63423 TCAATTTCGC
*
63433 ATTTTATATTTAAAATA
1 ATTTTATATTAAAAATA
63450 ATTTT-TATTAAAAATA
1 ATTTTATATTAAAAATA
63466 A
1 A
63467 CAATTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTATATTAAAAATA
Found at i:64221 original size:12 final size:12
Alignment explanation
Indices: 64184--64244 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
64174 ATGTTCACAA
64184 ATAAGCTCGTTT
1 ATAAGCTCGTTT
* *
64196 AAAAGCTCATTT
1 ATAAGCTCGTTT
64208 ATAAGCTCGTTT
1 ATAAGCTCGTTT
*
64220 ATTAA-CTCATTT
1 A-TAAGCTCGTTT
*
64232 ATGA-CTCGTTT
1 ATAAGCTCGTTT
64243 AT
1 AT
64245 TTATTAATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
11 10 0.24
12 28 0.68
13 3 0.07
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (12 bp):
ATAAGCTCGTTT
Found at i:64243 original size:23 final size:24
Alignment explanation
Indices: 64184--64245 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
64174 ATGTTCACAA
*
64184 ATAAGCTCGTTTA-AAAGCTCATTT
1 ATAAGCTCGTTTATTAA-CTCATTT
64208 ATAAGCTCGTTTATTAACTCATTT
1 ATAAGCTCGTTTATTAACTCATTT
*
64232 ATGA-CTCGTTTATT
1 ATAAGCTCGTTTATT
64246 TATTAATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 10 0.29
24 23 0.66
25 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (24 bp):
ATAAGCTCGTTTATTAACTCATTT
Found at i:64362 original size:23 final size:23
Alignment explanation
Indices: 64336--64404 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
64326 TCATTAACAT
64336 TGTTTGTGAACATGTTCGTTTAA
1 TGTTTGTGAACATGTTCGTTTAA
*
64359 TGTTCGTGAACATGTTCGTTTAA
1 TGTTTGTGAACATGTTCGTTTAA
* *
64382 TGTTTATGAACATGTTCGATTAA
1 TGTTTGTGAACATGTTCGTTTAA
64405 GTTAAATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (23 bp):
TGTTTGTGAACATGTTCGTTTAA
Found at i:64363 original size:11 final size:11
Alignment explanation
Indices: 64347--64385 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
64337 GTTTGTGAAC
64347 ATGTTCGTTTA
1 ATGTTCGTTTA
**
64358 ATGTTCGTGAA
1 ATGTTCGTTTA
64369 CATGTTCGTTTA
1 -ATGTTCGTTTA
64381 ATGTT
1 ATGTT
64386 TATGAACATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (11 bp):
ATGTTCGTTTA
Found at i:64375 original size:12 final size:12
Alignment explanation
Indices: 64331--64399 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
64321 ATTATTCATT
*
64331 AACATTGTTTGTG
1 AACA-TGTTCGTG
*
64344 AACATGTTCGTT
1 AACATGTTCGTG
*
64356 TA-ATGTTCGTG
1 AACATGTTCGTG
*
64367 AACATGTTCGTT
1 AACATGTTCGTG
* **
64379 TA-ATGTTTATG
1 AACATGTTCGTG
64390 AACATGTTCG
1 AACATGTTCG
64400 ATTAAGTTAA
Statistics
Matches: 41, Mismatches: 13, Indels: 5
0.69 0.22 0.08
Matches are distributed among these distances:
11 16 0.39
12 21 0.51
13 4 0.10
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:64413 original size:23 final size:23
Alignment explanation
Indices: 64342--64420 Score: 106
Period size: 23 Copynumber: 3.4 Consensus size: 23
64332 ACATTGTTTG
**
64342 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCGTTTAATGTTAA
*
64365 TGAACATGTTCGTTTAATGTTTA
1 TGAACATGTTCGTTTAATGTTAA
*
64388 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGTTTAATGTT-AA
64411 TGAACATGTT
1 TGAACATGTT
64421 TGTGAACATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 3 0.06
23 48 0.94
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (23 bp):
TGAACATGTTCGTTTAATGTTAA
Found at i:65630 original size:24 final size:23
Alignment explanation
Indices: 65575--65630 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
65565 CTTTTGAAAA
*
65575 AAAAATATAATTTAAAAAAAGTT
1 AAAAATATAAATTAAAAAAAGTT
*
65598 AAAATATATAAATTAGTAAAAA-TAT
1 AAAA-ATATAAATTA-AAAAAAGT-T
65623 AAAAATAT
1 AAAAATAT
65631 TTCTACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 14 0.50
25 10 0.36
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAAATATAAATTAAAAAAAGTT
Found at i:66514 original size:16 final size:16
Alignment explanation
Indices: 66495--66545 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
66485 ATTGAAATTA
66495 AATAAAATTGTAATAG
1 AATAAAATTGTAATAG
*
66511 AATAGAATTGTAATA-
1 AATAAAATTGTAATAG
*
66526 AA-AAAAGATGTAATAG
1 AATAAAA-TTGTAATAG
66542 AATA
1 AATA
66546 GAGTTATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.10
15 9 0.31
16 16 0.55
17 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (16 bp):
AATAAAATTGTAATAG
Found at i:70820 original size:3 final size:3
Alignment explanation
Indices: 70795--70857 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
70785 TTTAGGGTTT
* *
70795 AAG AAG -AG AAA AAA AAG AA- AAG AAG AAG AAG AAG AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
70840 AGG AAG AAG AAT AAG AAG
1 AAG AAG AAG AAG AAG AAG
70858 GAGGAGGAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:70870 original size:23 final size:23
Alignment explanation
Indices: 70809--70870 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
70799 AGAGAAAAAA
* *
70809 AAGAAAAGAAGAAGAAGAAGAAG
1 AAGAGAAGAGGAAGAAGAAGAAG
*
70832 AAGAGAAGAGGAAGAAGAATAAG
1 AAGAGAAGAGGAAGAAGAAGAAG
*
70855 AAG-GAGGAGGAGAGAA
1 AAGAGAAGAGGA-AGAA
70871 AAAATGGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 7 0.21
23 27 0.79
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (23 bp):
AAGAGAAGAGGAAGAAGAAGAAG
Found at i:73973 original size:22 final size:22
Alignment explanation
Indices: 73942--74004 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
73932 AGCGTGCTTA
*
73942 CTGTTTAGCACTGTGTGTGATT
1 CTGTTCAGCACTGTGTGTGATT
*
73964 CTGTTCAGCACTGTGTGTGCTT
1 CTGTTCAGCACTGTGTGTGATT
73986 CTGTTCAGCACTGTGTGTG
1 CTGTTCAGCACTGTGTGTG
74005 GTTACTCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.11, C:0.19, G:0.29, T:0.41
Consensus pattern (22 bp):
CTGTTCAGCACTGTGTGTGATT
Found at i:75952 original size:13 final size:13
Alignment explanation
Indices: 75915--75957 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
75905 CCATTGATCG
*
75915 TTGACCGTTGATT
1 TTGACCGTTGACT
*
75928 GTTGGCCCGTTGACT
1 -TT-GACCGTTGACT
75943 TTGACCGTTGACT
1 TTGACCGTTGACT
75956 TT
1 TT
75958 TTTCGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.48
14 4 0.16
15 9 0.36
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:82415 original size:60 final size:60
Alignment explanation
Indices: 82322--82442 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
82312 GGAATGAAAA
82322 TATAGATAGAGCCATATAGCAGTTTATTCCATCTGCTAAGTCTGTGAGTTTTCTTTTTGT
1 TATAGATAGAGCCATATAGCAGTTTATTCCATCTGCTAAGTCTGTGAGTTTTCTTTTTGT
82382 TATAGATAGAGCCATATAGCAGTTTATTCCATCTGCTAAGTCTGTGAGTTTTCTTTTTGT
1 TATAGATAGAGCCATATAGCAGTTTATTCCATCTGCTAAGTCTGTGAGTTTTCTTTTTGT
82442 T
1 T
82443 CTTCTTTCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (60 bp):
TATAGATAGAGCCATATAGCAGTTTATTCCATCTGCTAAGTCTGTGAGTTTTCTTTTTGT
Found at i:83788 original size:18 final size:17
Alignment explanation
Indices: 83765--83858 Score: 89
Period size: 18 Copynumber: 5.4 Consensus size: 17
83755 TATTTTGGGA
*
83765 TTAAATTTGTTTAAAAAT
1 TTAAATTTATTT-AAAAT
*
83783 TTAAATTTATTTTAAAT
1 TTAAATTTATTTAAAAT
* * *
83800 TTAAATTTAATTCAAGT
1 TTAAATTTATTTAAAAT
*
83817 TTAAATTTATTTTCAAAT
1 TTAAATTTA-TTTAAAAT
*
83835 TTAAAATTATTATAAAAT
1 TTAAATTTATT-TAAAAT
*
83853 TAAAAT
1 TTAAAT
83859 AAATAAAGTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
17 29 0.46
18 34 0.54
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAATTTATTTAAAAT
Found at i:83790 original size:6 final size:6
Alignment explanation
Indices: 83779--83839 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
83769 ATTTGTTTAA
* * *
83779 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTC AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
83825 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
83840 ATTATTATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
5 12 0.28
6 27 0.63
7 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:83798 original size:11 final size:11
Alignment explanation
Indices: 83782--83837 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
83772 TGTTTAAAAA
83782 TTTAAATTTAT
1 TTTAAATTTAT
*
83793 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
83805 TTT-AATTCAAG
1 TTTAAATT-TAT
83816 TTTAAATTTAT
1 TTTAAATTTAT
83827 TTTCAAATTTA
1 TTT-AAATTTA
83838 AAATTATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
11 21 0.58
12 15 0.42
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:83801 original size:17 final size:17
Alignment explanation
Indices: 83747--83856 Score: 96
Period size: 17 Copynumber: 6.4 Consensus size: 17
83737 CCAAACTCAT
**
83747 TTTAAATTTATTTTGGGA
1 TTTAAATTTATTTT-AAA
* *
83765 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
83782 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
83799 TTTAAATTTAATTCAAG
1 TTTAAATTTATTTTAAA
83816 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
83834 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
*
83851 ATTAAA
1 TTTAAA
83857 ATAAATAAAG
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
17 49 0.66
18 25 0.34
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:83804 original size:35 final size:35
Alignment explanation
Indices: 83747--83858 Score: 102
Period size: 35 Copynumber: 3.2 Consensus size: 35
83737 CCAAACTCAT
*** **
83747 TTTAAATTTATTTTGGGA-TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTCAAATTTAAATTTAATT-AAAA
* *
83782 TTTAAATTTATTTT-AAATTTAAATTTAATTCAAG
1 TTTAAATTTATTTTCAAATTTAAATTTAATTAAAA
* *
83816 TTTAAATTTATTTTCAAATTTAAAATTATTATAAAA
1 TTTAAATTTATTTTCAAATTTAAATTTAAT-TAAAA
*
83852 TTAAAAT
1 TTTAAAT
83859 AAATAAAGTT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
34 17 0.27
35 37 0.59
36 9 0.14
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (35 bp):
TTTAAATTTATTTTCAAATTTAAATTTAATTAAAA
Found at i:84615 original size:15 final size:15
Alignment explanation
Indices: 84597--84643 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
84587 ATAAATGTTT
84597 TGATAATAATAATAA
1 TGATAATAATAATAA
*
84612 TGATAATATTAATAA
1 TGATAATAATAATAA
*
84627 TTATTAAATAATAATAA
1 TGA-T-AATAATAATAA
84644 AAACGAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 16 0.59
16 1 0.04
17 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (15 bp):
TGATAATAATAATAA
Found at i:84792 original size:18 final size:18
Alignment explanation
Indices: 84771--84820 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
84761 ACAAAAGTAT
84771 AAAAAAGATTT-AAAAAA
1 AAAAAAGATTTAAAAAAA
* *
84788 AAAAACGGTTTCAAAAAAA
1 AAAAAAGATTT-AAAAAAA
*
84807 AGAAAA-ATTTAAAA
1 AAAAAAGATTTAAAA
84821 CCAAAAAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 13 0.50
18 3 0.12
19 10 0.38
ACGTcount: A:0.70, C:0.04, G:0.08, T:0.18
Consensus pattern (18 bp):
AAAAAAGATTTAAAAAAA
Found at i:90429 original size:42 final size:42
Alignment explanation
Indices: 90369--91050 Score: 825
Period size: 42 Copynumber: 16.3 Consensus size: 42
90359 AAGGAAAGCA
* * *
90369 TTCATTGCATTTAAAGGCCCAGGTGTGGAGGTCTATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
90411 TTCATCGCATTTAGAGGCCAAGGTATGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
90453 TTCATCGCATTTAGAGGCCCAGGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
* * * *
90495 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGCCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
90537 TTTATTGCATTTAGAGG-CTAGGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
* * * *
90578 TTCATTGCATTTAGAGGCCCATGTATGAAGGTCCTTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
90620 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
90662 TTCATTACATTTAGAGGTCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
90704 TTCATTGCACTTAGAGACCCAAGTGTAGAGGTCCATTTTCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
90746 TTCATTGCATTTAGAGGCTTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * *
90788 TTCATTGCATTTAGAGGTCTAAGTGTGAAGGCCCATTTTCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
90830 TTCACTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
90872 TTAATTGCATGTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* ** * * *
90914 TTCTTTGCATTTAGAGGCCCAAATATGGAGGCCCAATTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * **
90956 TTTATTGCACTTAGAAACCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
90998 TTCATTGCATTTAGAGGCCTAGGTGTAGAGG-CTGATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
91040 TTCATTGCATT
1 TTCATTGCATT
91051 CAAAGGCCTA
Statistics
Matches: 552, Mismatches: 82, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
40 1 0.00
41 38 0.07
42 511 0.93
43 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:92113 original size:19 final size:19
Alignment explanation
Indices: 92089--92126 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
92079 TTTTAAAGAA
92089 AAAGTTTAAATTTTTTAAC
1 AAAGTTTAAATTTTTTAAC
**
92108 AAAGTTTTGATTTTTTAAC
1 AAAGTTTAAATTTTTTAAC
92127 TATTTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
AAAGTTTAAATTTTTTAAC
Found at i:92651 original size:151 final size:150
Alignment explanation
Indices: 91970--92623 Score: 794
Period size: 151 Copynumber: 4.4 Consensus size: 150
91960 AGTTTTGGGT
*
91970 TTTTTTTAAACAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTT-AAAA
1 TTTTTTT-AACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAA
* * * * * *
92034 AAGAGAAATTTTATATTTTT-AAAAAT-AAAATATATTTTTTAGTTATTTTAAAGAAAAAGTTTA
65 AAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAGTTTA
* *
92097 AATTTTTTAACAAAGTTTTGA
130 AATTTTTAAACAAAATTTTGA
* * * *
92118 -TTTTTTAACTATTTCAAAATAAAA-TTTTATATTTTTAAGTAAATTAGTGATTTTGTTTAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTT-GATTTTTAAGTAAAATAGTGATTTTCTTT--AAA
* * * *
92181 AAAAAGAGAAAATTTAGA-TTTTAAAAAATAAAAATCAGTGTTTTAGTTATTTTAAAGAAAAA--
63 AAAAA-AGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAGT
* *
92243 -TAAATTTTTATACAAAGTTTTGA
127 TTAAATTTTTAAACAAAATTTTGA
* * *
92266 TTTTTTTTAAACCATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTCTTTAACA
1 -TTTTTTT-AACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAAAA
* * * *
92331 AAAAAGAAAGTTTAAATTCTT-AAAAATAAAAATCTGTTTTTTTAATGATTTTAAAGAAAAAATT
64 AAAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTG-TTTTTTAGTGATTTTAAAGAAAAAGTT
*
92395 TAAATTTTTAAA-AAAAGTTTTTA
128 TAAATTTTTAAACAAAA-TTTTGA
* * * *
92418 TTTTTTTAACTATTTCAAAATAAAAG-TCTGAATTTTTTAGTAAAATAGTGATTTTCATTAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAATAGTGATTTTCTTTAAAAA
* *
92482 AGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATTTGTTTTTTAGTGATTTTAAAGAAATAGTTT
65 A-AAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAGTTT
92547 AAATTTTTAAACAAAATTTTGA
129 AAATTTTTAAACAAAATTTTGA
* *
92569 -TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTAAAAGTAAAGTAGTGATTTT
1 TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTT-TAAGTAAAATAGTGATTTT
92624 GTTTTAATCA
Statistics
Matches: 433, Mismatches: 50, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
145 4 0.01
146 42 0.10
147 6 0.01
148 45 0.10
149 43 0.10
150 99 0.23
151 157 0.36
152 37 0.09
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (150 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAA
AAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAGTTTAA
ATTTTTAAACAAAATTTTGA
Found at i:94095 original size:238 final size:237
Alignment explanation
Indices: 93672--94142 Score: 775
Period size: 238 Copynumber: 2.0 Consensus size: 237
93662 TAATAATAAA
* *
93672 GATAAAAGATCAAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTTTTAG
1 GATAAAAAATCAAATAAGTTGGAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTTTTAG
* *
93737 GTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTTACTAAAGTTATTTA
66 GTTTTTTTAAGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAAAGTTATTTA
*
93802 GGTATCCTTTAGGGTTCTCGTTAGAAGTAAAAATCTATAATTCAAGTTTTAAATTAGATAAGTTT
131 GGTATCCTTTAGGGTTCTCGTTAGAAGTAAAAATCTATAATTCAAGTTGTAAATTAGATAAGTTT
93867 GGTGAACATGTCTTAGTCAAGTTACAAGTAAATCGGAGTAAT
196 GGTGAACATGTCTTAGTCAAGTTACAAGTAAATCGGAGTAAT
* *
93909 GATAAAAAATCGAATAAGTTGGAGATGAATTTTAATATTTCTCTTAATTTATTAGTAATTTATTA
1 GATAAAAAATCAAATAAGTTGGAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTT-TTA
93974 GGTTTTTTTAAGATAT-TAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAA-TTAT
65 GGTTTTTTTAAGAT-TCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTA-AAGTTAT
* * * *
94037 TTAGGTATCCTTTAGGGTTCTTGTTAGATGTAAAAATCTCTAATTTAAGTTGTAAATTAGATAAG
128 TTAGGTATCCTTTAGGGTTCTCGTTAGAAGTAAAAATCTATAATTCAAGTTGTAAATTAGATAAG
* * *
94102 TTTGGTGAATATGTCTTAGTTAAGTTACAAGTAAATTGGAG
193 TTTGGTGAACATGTCTTAGTCAAGTTACAAGTAAATCGGAG
94143 GCATTTTTTA
Statistics
Matches: 217, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
237 57 0.26
238 157 0.72
239 3 0.01
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.42
Consensus pattern (237 bp):
GATAAAAAATCAAATAAGTTGGAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTTTTAG
GTTTTTTTAAGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAAAGTTATTTA
GGTATCCTTTAGGGTTCTCGTTAGAAGTAAAAATCTATAATTCAAGTTGTAAATTAGATAAGTTT
GGTGAACATGTCTTAGTCAAGTTACAAGTAAATCGGAGTAAT
Found at i:101624 original size:21 final size:21
Alignment explanation
Indices: 101598--101653 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
101588 GTGTATGCTG
*
101598 CTACCGATACAAGTGACAGTT
1 CTACCGATACAAGTGACACTT
* *
101619 CTACCGATATAAGTGACTCTT
1 CTACCGATACAAGTGACACTT
*
101640 CTACCGAAACAAGT
1 CTACCGATACAAGT
101654 CTTACTTCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGTGACACTT
Found at i:104114 original size:93 final size:94
Alignment explanation
Indices: 103931--104118 Score: 342
Period size: 93 Copynumber: 2.0 Consensus size: 94
103921 TTGTAAAGAC
103931 TAGGACGCGTGTCAAACATCCATAGGGACAAAGAAAAATATCTAGGTAACCCAGGTAAGAAATAA
1 TAGGACGCGTGTCAAACATCCATAGGGACAAAGAAAAATATCTAGGTAACCCAGGTAAGAAATAA
*
103996 GAACTATTCTCTTACTTCTTCAGAAGTAG
66 AAACTATTCTCTTACTTCTTCAGAAGTAG
*
104025 TAGGACGCGTGTCAAACATCCATAGGGACAAAGGAAAATATCTA-GTAACCCAGGTAAGAAATAA
1 TAGGACGCGTGTCAAACATCCATAGGGACAAAGAAAAATATCTAGGTAACCCAGGTAAGAAATAA
*
104089 AAACTATTCTTTTACTTCTTCAGAAGTAG
66 AAACTATTCTCTTACTTCTTCAGAAGTAG
104118 T
1 T
104119 TTTTGTTTAT
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 48 0.53
94 43 0.47
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (94 bp):
TAGGACGCGTGTCAAACATCCATAGGGACAAAGAAAAATATCTAGGTAACCCAGGTAAGAAATAA
AAACTATTCTCTTACTTCTTCAGAAGTAG
Found at i:105883 original size:12 final size:12
Alignment explanation
Indices: 105874--105899 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
105864 TTGTTTTGTA
105874 GATCGTTTTGCT
1 GATCGTTTTGCT
105886 GATCGTTTTGCT
1 GATCGTTTTGCT
105898 GA
1 GA
105900 CTGAAGATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46
Consensus pattern (12 bp):
GATCGTTTTGCT
Found at i:112806 original size:30 final size:30
Alignment explanation
Indices: 112772--112833 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
112762 TTAACCATTG
112772 ATATTGAACTAAAGATGTTGAAATCTTACT
1 ATATTGAACTAAAGATGTTGAAATCTTACT
112802 ATATTGAACTAAAGATGTTGAAATCTTACT
1 ATATTGAACTAAAGATGTTGAAATCTTACT
112832 AT
1 AT
112834 TATGATGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (30 bp):
ATATTGAACTAAAGATGTTGAAATCTTACT
Found at i:117364 original size:13 final size:13
Alignment explanation
Indices: 117346--117393 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
117336 TCTATCAAGT
117346 ATGAGTTTGCATG
1 ATGAGTTTGCATG
** *
117359 ATGAGTTTGTGTC
1 ATGAGTTTGCATG
*
117372 TTGAGTTTGCATG
1 ATGAGTTTGCATG
117385 ATGAGTTTG
1 ATGAGTTTG
117394 TGTCTTTCTC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (13 bp):
ATGAGTTTGCATG
Found at i:117379 original size:26 final size:26
Alignment explanation
Indices: 117347--117399 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
117337 CTATCAAGTA
117347 TGAGTTTGCATGATGAGTTTGTGTCT
1 TGAGTTTGCATGATGAGTTTGTGTCT
117373 TGAGTTTGCATGATGAGTTTGTGTCT
1 TGAGTTTGCATGATGAGTTTGTGTCT
117399 T
1 T
117400 TCTCCGGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.08, G:0.30, T:0.47
Consensus pattern (26 bp):
TGAGTTTGCATGATGAGTTTGTGTCT
Found at i:121127 original size:24 final size:24
Alignment explanation
Indices: 121083--121128 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
121073 GGTCAACTAA
* **
121083 ATTATCCTAATAAATGTTAAATTT
1 ATTATACTAATAAATACTAAATTT
121107 ATTATACTAATAAATACTAAAT
1 ATTATACTAATAAATACTAAAT
121129 CTTCTAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATTT
Found at i:123417 original size:21 final size:21
Alignment explanation
Indices: 123370--123429 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
123360 AATAGTGCAG
* *
123370 ACTTCTACCGATACAAATGAT
1 ACTTCTACCAATACAAGTGAT
*
123391 AGTTCTACCAATACAAGTGACT
1 ACTTCTACCAATACAAGTGA-T
123413 -CTTCTACCGAA-ACAAGT
1 ACTTCTACC-AATACAAGT
123430 CTTCCTTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (21 bp):
ACTTCTACCAATACAAGTGAT
Found at i:123538 original size:45 final size:42
Alignment explanation
Indices: 123487--123583 Score: 104
Period size: 42 Copynumber: 2.2 Consensus size: 42
123477 CTTGCAACTT
*
123487 CTACCGATACAAGTATCCCAACTATCGATACCTTAGTAAGTAGAA
1 CTACCGATACAACTATCCCAAC--T-GATACCTTAGTAAGTAGAA
** ** *
123532 CTACCGATACTTCTATTGCTACTGATACCTTAGTAAGTAGAA
1 CTACCGATACAACTATCCCAACTGATACCTTAGTAAGTAGAA
*
123574 CTATCGATAC
1 CTACCGATAC
123584 TTCTATTGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 28 0.62
43 1 0.02
45 16 0.36
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (42 bp):
CTACCGATACAACTATCCCAACTGATACCTTAGTAAGTAGAA
Found at i:123539 original size:24 final size:24
Alignment explanation
Indices: 123506--123583 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
123496 CAAGTATCCC
*
123506 AACTATCGATACCTTAGTAAGTAG
1 AACTACCGATACCTTAGTAAGTAG
* *
123530 AACTACCGATA-CTT-CT-A-TTG
1 AACTACCGATACCTTAGTAAGTAG
*
123550 --CTACTGATACCTTAGTAAGTAG
1 AACTACCGATACCTTAGTAAGTAG
*
123572 AACTATCGATAC
1 AACTACCGATAC
123584 TTCTATTGCT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 8 0.20
19 3 0.08
20 3 0.08
21 2 0.05
22 3 0.08
23 3 0.08
24 18 0.45
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (24 bp):
AACTACCGATACCTTAGTAAGTAG
Found at i:123564 original size:42 final size:42
Alignment explanation
Indices: 123513--123596 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
123503 CCCAACTATC
123513 GATACCTTAGTAAGTAGAACTACCGATACTTCTATTGCTACT
1 GATACCTTAGTAAGTAGAACTACCGATACTTCTATTGCTACT
*
123555 GATACCTTAGTAAGTAGAACTATCGATACTTCTATTGCTACT
1 GATACCTTAGTAAGTAGAACTACCGATACTTCTATTGCTACT
123597 ACCGATACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (42 bp):
GATACCTTAGTAAGTAGAACTACCGATACTTCTATTGCTACT
Found at i:126653 original size:20 final size:20
Alignment explanation
Indices: 126617--126666 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
126607 TCATTAAGCT
*
126617 TTAATTAATCACTTTTA-ATC
1 TTAATTAAACACTTTTACA-C
126637 TTAATTAAAC-CTATTTACAC
1 TTAATTAAACACT-TTTACAC
126657 TTAATATAAA
1 TTAAT-TAAA
126667 TCATGCTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTACAC
Found at i:127098 original size:20 final size:20
Alignment explanation
Indices: 127072--127155 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
127062 TTAAAATTAA
*
127072 ACAAGGGCATCGAAGTGCAT
1 ACAAGGGCACCGAAGTGCAT
* *
127092 TCAAGGGCACCGAAGTGTAT
1 ACAAGGGCACCGAAGTGCAT
* *
127112 AGAGGGGCACCGAAGTGCAT
1 ACAAGGGCACCGAAGTGCAT
*
127132 ACGCA-GGCACCGAAGTGCAT
1 AC-AAGGGCACCGAAGTGCAT
127152 ACAA
1 ACAA
127156 AAATTTATTA
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
19 1 0.02
20 51 0.98
ACGTcount: A:0.33, C:0.23, G:0.31, T:0.13
Consensus pattern (20 bp):
ACAAGGGCACCGAAGTGCAT
Found at i:132194 original size:80 final size:78
Alignment explanation
Indices: 131961--132245 Score: 347
Period size: 79 Copynumber: 3.6 Consensus size: 78
131951 CGATTCTGGA
* *
131961 ACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCTCAACTCTAGTTGGATTAACCAACAACATC
1 ACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAACTCTAGTTGGATTAACCAACAAAATC
132026 CGTCAAATCCTGAC
66 CGTCAAATCCTG-C
* * * * *
132040 ACCCAGTGCCTAGTGGACAAACCGCAAATGTGAGCCTAGCTCTAGTTGGATTAACCAACAAAATC
1 ACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAACTCTAGTTGGATTAACCAACAAAATC
132105 CGTCAAATCCTAGC
66 CGTCAAATCCT-GC
* * * * *
132119 ACCCAGTGCCTAGCGGATAAACCGCAAAAAATAAGCCCAACTCTAGCTGGATTAACTAACAATAT
1 ACCCAGTGCCTAGCGGATAAACCGC-AAAAGTGAGCCCAACTCTAGTTGGATTAACCAACAAAAT
*
132184 TCGTCAAATCCTGGC
65 CCGTCAAATCCT-GC
* * ** * *
132199 ACCTAGTGTCTAGCAAATAAACCGCAAATA-TGAGTCCAGCTCTAGTT
1 ACCCAGTGCCTAGCGGATAAACCGCAAA-AGTGAGCCCAACTCTAGTT
132246 AGTTAAACTG
Statistics
Matches: 176, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
79 109 0.62
80 67 0.38
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (78 bp):
ACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAACTCTAGTTGGATTAACCAACAAAATC
CGTCAAATCCTGC
Found at i:132262 original size:159 final size:158
Alignment explanation
Indices: 131961--132251 Score: 406
Period size: 159 Copynumber: 1.8 Consensus size: 158
131951 CGATTCTGGA
* * * *
131961 ACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCTCAACTCTAGTTGGATTAACCAACAACATC
1 ACCCAGTGCCTAGCGGATAAACCGCAAAAATAAGCCCAACTCTAGCTGGATTAACCAACAACATC
*** * *
132026 CGTCAAATCCTGACACCCAGTGCCTAGTGGACAAACCGCAAATGTGAGCCTAGCTCTAGTTGGAT
66 CGTCAAATCCTGACACCCAGTGCCTAGCAAACAAACCGCAAATATGAGCCTAGCTCTAGTTAGAT
132091 TAACCAACAAAATCCGTCAAATCCTAGC
131 TAACCAACAAAATCCGTCAAATCCTAGC
* *
132119 ACCCAGTGCCTAGCGGATAAACCGCAAAAAATAAGCCCAACTCTAGCTGGATTAACTAACAATAT
1 ACCCAGTGCCTAGCGGATAAACCGC-AAAAATAAGCCCAACTCTAGCTGGATTAACCAACAACAT
* * * * *
132184 TCGTCAAATCCTGGCACCTAGTGTCTAGCAAATAAACCGCAAATATGAGTCC-AGCTCTAGTTAG
65 CCGTCAAATCCTGACACCCAGTGCCTAGCAAACAAACCGCAAATATGAG-CCTAGCTCTAGTTAG
132248 -TTAA
129 ATTAA
132252 ACTGACAAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
158 29 0.25
159 84 0.73
160 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (158 bp):
ACCCAGTGCCTAGCGGATAAACCGCAAAAATAAGCCCAACTCTAGCTGGATTAACCAACAACATC
CGTCAAATCCTGACACCCAGTGCCTAGCAAACAAACCGCAAATATGAGCCTAGCTCTAGTTAGAT
TAACCAACAAAATCCGTCAAATCCTAGC
Found at i:138016 original size:20 final size:20
Alignment explanation
Indices: 137993--138068 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
137983 CTGCATATAA
*
137993 GGGCATCGAAGTGCATTCAG
1 GGGCACCGAAGTGCATTCAG
*
138013 GGGCACCAAAGTGCATTCAG
1 GGGCACCGAAGTGCATTCAG
*
138033 GGGCACTGAAGTGCATAT-AG
1 GGGCACCGAAGTGCAT-TCAG
138053 GGGCACCGAAGTGCAT
1 GGGCACCGAAGTGCAT
138069 ACATAAGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 49 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.34, T:0.17
Consensus pattern (20 bp):
GGGCACCGAAGTGCATTCAG
Found at i:138048 original size:60 final size:60
Alignment explanation
Indices: 137950--138068 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
137940 TAAAATTAAA
* * * *
137950 CAGGGGTACCGAAGTGCATACAAGGCCATTGAACTGCATATAAGGGCATCGAAGTGCATT
1 CAGGGGCACCAAAGTGCATACAAGGCCACTGAACTGCATATAAGGGCACCGAAGTGCATT
* * * * *
138010 CAGGGGCACCAAAGTGCATTCAGGGGCACTGAAGTGCATATAGGGGCACCGAAGTGCAT
1 CAGGGGCACCAAAGTGCATACAAGGCCACTGAACTGCATATAAGGGCACCGAAGTGCAT
138069 ACATAAGTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.30, C:0.21, G:0.31, T:0.18
Consensus pattern (60 bp):
CAGGGGCACCAAAGTGCATACAAGGCCACTGAACTGCATATAAGGGCACCGAAGTGCATT
Found at i:138069 original size:20 final size:20
Alignment explanation
Indices: 137951--138069 Score: 107
Period size: 20 Copynumber: 6.0 Consensus size: 20
137941 AAAATTAAAC
* *
137951 AGGGGTACCGAAGTGCATAC
1 AGGGGCACCGAAGTGCATAT
* * ** *
137971 AAGGCCATTGAACTGCATAT
1 AGGGGCACCGAAGTGCATAT
* *
137991 AAGGGCATCGAAGTGCAT-T
1 AGGGGCACCGAAGTGCATAT
*
138010 CAGGGGCACCAAAGTGCAT-T
1 -AGGGGCACCGAAGTGCATAT
*
138030 CAGGGGCACTGAAGTGCATAT
1 -AGGGGCACCGAAGTGCATAT
138051 AGGGGCACCGAAGTGCATA
1 AGGGGCACCGAAGTGCATA
138070 CATAAGTTTA
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.01
20 79 0.98
21 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (20 bp):
AGGGGCACCGAAGTGCATAT
Found at i:139494 original size:66 final size:66
Alignment explanation
Indices: 139393--139524 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
139383 TTTAGATAAG
139393 AAAGAACCAAGAGAAATACCTCTCATCCTTTAAGCTGAGGCTAGGATGTAGATCTAACCTCTTAG
1 AAAGAACCAAGAGAAATACCTCTCATCCTTTAAGCTGAGGCTAGGATGTAGATCTAACCTCTTAG
139458 A
66 A
*
139459 AAAGAACCAAGAGAAATACCTCTCATCCTTTAAGCTGAGGCTAGGATGTGGATCTAACCTCTTAG
1 AAAGAACCAAGAGAAATACCTCTCATCCTTTAAGCTGAGGCTAGGATGTAGATCTAACCTCTTAG
139524 A
66 A
139525 TGCCTTTTTC
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:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (66 bp):
AAAGAACCAAGAGAAATACCTCTCATCCTTTAAGCTGAGGCTAGGATGTAGATCTAACCTCTTAG
A
Found at i:140645 original size:28 final size:28
Alignment explanation
Indices: 140614--140668 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
140604 GAAACCTTTG
*
140614 TGGTGAATTCTATTAAAGGAAGTCTTCA
1 TGGTGAATTCTATTAAAAGAAGTCTTCA
* *
140642 TGGTTAATTCTGTTAAAAGAAGTCTTC
1 TGGTGAATTCTATTAAAAGAAGTCTTC
140669 GTGGCTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (28 bp):
TGGTGAATTCTATTAAAAGAAGTCTTCA
Found at i:140687 original size:28 final size:28
Alignment explanation
Indices: 140619--140676 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
140609 CTTTGTGGTG
* * *
140619 AATTCTATTAAAGGAAGTCTTCATGGTT
1 AATTCTGTTAAAAGAAGTCTTCATGGCT
*
140647 AATTCTGTTAAAAGAAGTCTTCGTGGCT
1 AATTCTGTTAAAAGAAGTCTTCATGGCT
140675 AA
1 AA
140677 CTTTTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (28 bp):
AATTCTGTTAAAAGAAGTCTTCATGGCT
Found at i:156609 original size:10 final size:10
Alignment explanation
Indices: 156586--156611 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
156576 TCTTTTCTCT
156586 TTTCTTCTTC
1 TTTCTTCTTC
156596 TTTCTTCTTC
1 TTTCTTCTTC
156606 TTTCTT
1 TTTCTT
156612 TTTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTCTTC
Found at i:159217 original size:20 final size:20
Alignment explanation
Indices: 159194--159232 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
159184 AGCTTAGTAA
159194 AAAGAATAA-AAGAAACTTGC
1 AAAGAA-AAGAAGAAACTTGC
*
159214 AAAGAAAAGAATAAACTTG
1 AAAGAAAAGAAGAAACTTG
159233 TGAGAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAGAAAAGAAGAAACTTGC
Found at i:169120 original size:11 final size:11
Alignment explanation
Indices: 169104--169152 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
169094 TTTCACCCAA
169104 AAAGAAACAAG
1 AAAGAAACAAG
*
169115 AAAGAAAAAAG
1 AAAGAAACAAG
169126 AAAG-AA-AA-
1 AAAGAAACAAG
*
169134 AAAGAAAACAAA
1 AAAG-AAACAAG
169146 AAAGAAA
1 AAAGAAA
169153 AAATGAGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 4 0.12
9 2 0.06
10 4 0.12
11 19 0.58
12 4 0.12
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAGAAACAAG
Found at i:169153 original size:12 final size:11
Alignment explanation
Indices: 169102--169155 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 11
169092 AATTTCACCC
169102 AAAAAGAAACAAG
1 AAAAA-AAA-AAG
*
169115 AAAGAAAAAAG
1 AAAAAAAAAAG
169126 AAAGAAAAAAAG
1 AAA-AAAAAAAG
169138 AAAACAAAAAAG
1 AAAA-AAAAAAG
169150 AAAAAA
1 AAAAAA
169156 TGAGAGGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
11 9 0.24
12 24 0.65
13 4 0.11
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:170078 original size:49 final size:49
Alignment explanation
Indices: 170024--170306 Score: 266
Period size: 49 Copynumber: 5.8 Consensus size: 49
170014 AAAGACGTAA
* * *** *
170024 AGGGAAAGATTGAAGTCATAACGACAAATCTTATACCTTAGAGATATAG
1 AGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCCTAGAGATATAG
* * *
170073 AGGGAATGATTGAAGCCGCAATGGTGAATCTTATACCCTAGAGATATAG
1 AGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCCTAGAGATATAG
** * ** *
170122 -GGGAAAGATTGAAATCGTAACGGTGAATCTTATACCCCAGAGACGTGG
1 AGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCCTAGAGATATAG
* * * *
170170 AGGGAAAGGA-TGAAGCCGCAACGGTAAACCTTATACCCTAGAGATATGG
1 AGGGAAA-GATTGAAGCCGTAACGGTGAATCTTATACCCTAGAGATATAG
* * * * *
170219 AGGGAAAGGTTGAAGCCGTAACGGCGAACCTTATACCCTTGAGATGT-G
1 AGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCCTAGAGATATAG
* ** * *
170267 AAGGGAAAGATTGAGGCCACAAAGGCGAATCTTATACCCT
1 -AGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCCT
170307 GAAGATAAGG
Statistics
Matches: 192, Mismatches: 38, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
48 41 0.21
49 149 0.78
50 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (49 bp):
AGGGAAAGATTGAAGCCGTAACGGTGAATCTTATACCCTAGAGATATAG
Found at i:170173 original size:97 final size:98
Alignment explanation
Indices: 170024--170306 Score: 327
Period size: 97 Copynumber: 2.9 Consensus size: 98
170014 AAAGACGTAA
* * * * * * *
170024 AGGGAAAGATTGAAGTCATAACGACAAATCTTATACCTTAGAGATATAGAGGGAATGATTGAAGC
1 AGGGAAAGATTGAAGTCGTAACGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAGATTGAAGC
*
170089 CGCAATGGTGAATCTTATACCCTAGAGATATAG
66 CGCAAAGGTGAATCTTATACCCTAGAGATATAG
* * * *
170122 -GGGAAAGATTGAAATCGTAACGGTGAATCTTATACCCCAGAGACGTGGAGGGAAAGGA-TGAAG
1 AGGGAAAGATTGAAGTCGTAACGGCGAATCTTATACCCTAGAGATGTGGAGGGAAA-GATTGAAG
* * * *
170185 CCGCAACGGTAAACCTTATACCCTAGAGATATGG
65 CCGCAAAGGTGAATCTTATACCCTAGAGATATAG
* * * * * *
170219 AGGGAAAGGTTGAAGCCGTAACGGCGAACCTTATACCCTTGAGATGTGAAGGGAAAGATTGAGGC
1 AGGGAAAGATTGAAGTCGTAACGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAGATTGAAGC
* *
170284 CACAAAGGCGAATCTTATACCCT
66 CGCAAAGGTGAATCTTATACCCT
170307 GAAGATAAGG
Statistics
Matches: 152, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
97 81 0.53
98 71 0.47
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (98 bp):
AGGGAAAGATTGAAGTCGTAACGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAGATTGAAGC
CGCAAAGGTGAATCTTATACCCTAGAGATATAG
Found at i:170478 original size:42 final size:42
Alignment explanation
Indices: 170431--171123 Score: 539
Period size: 42 Copynumber: 17.1 Consensus size: 42
170421 AAGCAAAGCA
170431 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
** * * * * *
170473 AAGACATCATTTAATCTCTTACCTCGACCATGGTGCAAATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * * *
170515 AAG---TCATTCAATCTCTTACCCCGATCATGAGGCAAATTA
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * *
170554 AAGACCTCATCCAATCTCTTACCCCGACCATGAGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* ***
170596 AAGACATCATCTAATCTCTTACCCCAATCATAAAGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
*
170638 AAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * * *
170680 AAGACA-CA-CTAATTTCTTACCCCGATCATGGGGTAGATTA
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* **
170720 AAG-CATC-T--AATCTTTTACCTTAATCA-GAGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATG-GGGCAGATTG
* *
170758 AAGACATCATCCAATCTCTTACCCAAATCATGGGGTAGATT-
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * ** * *
170799 ---ACAGCATCCAATCTTTTACCCTAATCAAAGAGTAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* *
170838 AAGACAT--TTCAATCTCTTACCCCGATCATGGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* * ** *
170878 AAG-CA-C--CTAATAT-TTTTCCCAATCATGGGACAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* *
170915 AAGACATCAACCAATCTCTTACCCCAATCATGGGGCAAATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* * **
170957 AAG----CATCCAATCTTTTACCCTAATCAAAAGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATC-ATGGGGCAGATTG
* * *
170996 AAGACA-CA-CTAATCTCTTACCTCGATCATGGGGCA-AGTTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGA-TTG
** * **
171036 -A-A-ATCATCCAATCTCTTACCCTGATCATGAGATAGATTG
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * *
171075 AAGGCATCATGCAATCTTTTACCCCTAAATCAAAAGGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCC--AATC--ATGGGGCAGATTG
171121 AAG
1 AAG
171124 CTACCATCTC
Statistics
Matches: 514, Mismatches: 101, Indels: 68
0.75 0.15 0.10
Matches are distributed among these distances:
37 25 0.05
38 84 0.16
39 81 0.16
40 70 0.14
41 21 0.04
42 217 0.42
43 1 0.00
44 3 0.01
46 12 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (42 bp):
AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTG
Found at i:170756 original size:38 final size:38
Alignment explanation
Indices: 170603--171064 Score: 214
Period size: 38 Copynumber: 11.7 Consensus size: 38
170593 TTGAAGACAT
* * *** *
170603 CATCTAATCTCTTACCCCAATCATAAAGCAGATTGAAG
1 CATCTAATCTTTTACCCTAATCATGGGGCAGATTAAAG
* * *
170641 ACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTGAAG
1 -CATC--T-AATCTTTTACCCTAATCATGGGGCAGATTAAAG
* ** *
170683 ACACACTAAT-TTCTTACCCCGATCATGGGGTAGATTAAAG
1 -CA-TCTAATCTT-TTACCCTAATCATGGGGCAGATTAAAG
* *
170723 CATCTAATCTTTTACCTTAATCA-GAGGGCAGATTGAAG
1 CATCTAATCTTTTACCCTAATCATG-GGGCAGATTAAAG
* * * *
170761 ACATCATCCAATCTCTTACCCAAATCATGGGGTAGATTACAG
1 -CATC-T--AATCTTTTACCCTAATCATGGGGCAGATTAAAG
* ** * * *
170803 CATCCAATCTTTTACCCTAATCAAAGAGTAGATTGAAG
1 CATCTAATCTTTTACCCTAATCATGGGGCAGATTAAAG
* * ** *
170841 ACATTTCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
1 -CATCT-AATCTTTTACCCTAATCATGGGGCAGATTAAAG
* * * * *
170881 CACCTAATATTTTTCCC-AATCATGGGACAGATTGAAG
1 CATCTAATCTTTTACCCTAATCATGGGGCAGATTAAAG
* * * * *
170918 ACATCAACCAATCTCTTACCCCAATCATGGGGCAAATTGAAG
1 -CAT---CTAATCTTTTACCCTAATCATGGGGCAGATTAAAG
* ** *
170960 CATCCAATCTTTTACCCTAATCAAAAGGGCAGATTGAAG
1 CATCTAATCTTTTACCCTAATC-ATGGGGCAGATTAAAG
* * * *
170999 ACACACTAATCTCTTA-CCTCGATCATGGGGCA-AGTTGAAAT
1 -CA-TCTAATCTTTTACCCT-AATCATGGGGCAGA-TT-AAAG
* * *
171040 CATCCAATCTCTTACCCTGATCATG
1 CATCTAATCTTTTACCCTAATCATG
171065 AGATAGATTG
Statistics
Matches: 331, Mismatches: 66, Indels: 52
0.74 0.15 0.12
Matches are distributed among these distances:
37 19 0.06
38 79 0.24
39 50 0.15
40 72 0.22
41 33 0.10
42 76 0.23
43 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (38 bp):
CATCTAATCTTTTACCCTAATCATGGGGCAGATTAAAG
Found at i:170759 original size:120 final size:121
Alignment explanation
Indices: 170431--171056 Score: 475
Period size: 120 Copynumber: 5.2 Consensus size: 121
170421 AAGCAAAGCA
*
170431 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATTTAATCTCTTACC
1 AAGACATCA-CCAATCTCTTACCCCAATCATGGGGCAGATTAAAG-CATC---TAATCTCTTACC
* * * * * * * * *
170496 TCGACCATG-GTGCAAATTGAAG---TCATTCAATCTCTTACCCCGATCATGAGGCAAATTA
61 CCAATCA-GAGGGCAGATTGAAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * * *
170554 AAGACCTCATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAGACATCATCTAATCTCTTACC
1 AAGACATCA-CCAATCTCTTACCCCAATCATGGGGCAGATT--A-A-AGCATCTAATCTCTTACC
* **
170619 CCAATCATAAAGCAGATTGAAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTG
61 CCAATCAGAGGGCAGATTGAAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * * * **
170680 AAGACA-CACTAATTTCTTACCCCGATCATGGGGTAGATTAAAGCATCTAATCTTTTACCTTAAT
1 AAGACATCACCAATCTCTTACCCCAATCATGGGGCAGATTAAAGCATCTAATCTCTTACCCCAAT
* * *
170744 CAGAGGGCAGATTGAAGACATCATCCAATCTCTTACCCAAATCATGGGGTAGATT-
66 CAGAGGGCAGATTGAAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTG
* * ** * * * *
170799 ACAG-CAT--CCAATCTTTTACCCTAATCAAAGAGTAGATTGAAGACATTTCAATCTCTTACCCC
1 A-AGACATCACCAATCTCTTACCCCAATCATGGGGCAGATTAAAG-CATCT-AATCTCTTACCCC
* * * ** *
170861 GATCATG-GGGCAGATTGAAG-CA-C-CT-AATAT-TTTTCCCAATCATGGGACAGATTG
63 AATCA-GAGGGCAGATTGAAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTG
* * * * *
170915 AAGACATCAACCAATCTCTTACCCCAATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCTAA
1 AAGACATC-ACCAATCTCTTACCCCAATCATGGGGCAGATTAAAGCATCTAATCTCTTACCCCAA
* * * *
170980 TCAAAAGGGCAGATTGAAGACA-CACT-AATCTCTTACCTCGATCATGGGGCA-AGTTG
65 TC-AGAGGGCAGATTGAAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGA-TTG
171036 -A-A-ATCATCCAATCTCTTACCC
1 AAGACATCA-CCAATCTCTTACCC
171057 TGATCATGAG
Statistics
Matches: 404, Mismatches: 74, Indels: 55
0.76 0.14 0.10
Matches are distributed among these distances:
115 20 0.05
116 8 0.02
117 15 0.04
118 61 0.15
119 41 0.10
120 105 0.26
121 19 0.05
122 1 0.00
123 63 0.16
124 26 0.06
125 2 0.00
126 42 0.10
127 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.27
Consensus pattern (121 bp):
AAGACATCACCAATCTCTTACCCCAATCATGGGGCAGATTAAAGCATCTAATCTCTTACCCCAAT
CAGAGGGCAGATTGAAGACATCATTCAATCTCTTACCCCAATCATGGGGCAGATTG
Found at i:170856 original size:158 final size:158
Alignment explanation
Indices: 170431--171124 Score: 641
Period size: 158 Copynumber: 4.3 Consensus size: 158
170421 AAGCAAAGCA
* *
170431 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATTTAATCTCTTA-C
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAG-CATC---CAATCTTTTACC
* * * * * ** * *
170495 CTCGA-CCATGGTGCAAATTGAAGTCATTC-AATCTCTTACCCCGATCATGAGGCAAATTAAAGA
62 CT-AATCAAAGG-GCAGATTGAAGACACACTAATCTCTTACCCCGATCATGGGGCAGATTAAAG-
* * *
170558 CCTCATCCAATCTCTTACCCCGACCATGAGGCAGATTG
124 ---CATCCAATCTCTTACCCCAATCATGAGACAGATTG
* *** *
170596 AAGACATCATCTAATCTCTTACCCCAATCATAAAGCAGATTGAAGACATCATTCAATCTCTTACC
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAG-CATC---CAATCTTTTACC
* ** * *
170661 CCAATCATGGGGCAGATTGAAGACACACTAATTTCTTACCCCGATCATGGGGTAGATTAAAGCAT
62 CTAATCAAAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATCATGGGGCAGATTAAAGCAT
* * ** *
170726 CTAATCTTTTACCTTAATCA-GAGGGCAGATTG
127 CCAATCTCTTACCCCAATCATGA-GACAGATTG
* *
170758 AAGACATCATCCAATCTCTTACCCAAATCATGGGGTAGATT-ACAGCATCCAATCTTTTACCCTA
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGA-AGCATCCAATCTTTTACCCTA
* * ** *
170822 ATCAAAGAGTAGATTGAAGACA-TTTCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCA-CC
65 ATCAAAGGGCAGATTGAAGACACACT-AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCC
* ** *
170885 TAATAT-TTTTCCCAATCATGGGACAGATTG
129 -AATCTCTTACCCCAATCATGAGACAGATTG
* *
170915 AAGACATCAACCAATCTCTTACCCCAATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCTAA
1 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAA
* *
170980 TCAAAAGGGCAGATTGAAGACACACTAATCTCTTACCTCGATCATGGGGCA-AGTTGAAATCATC
66 TC-AAAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATCATGGGGCAGA-TT-AAAGCATC
** *
171044 CAATCTCTTACCCTGATCATGAGATAGATTG
128 CAATCTCTTACCCCAATCATGAGACAGATTG
* * * *
171075 AAGGCATCATGCAATCTTTTACCCCTAAATCAAAAGGGGCAGATTGAAGC
1 AAGACATCATCCAATCTCTTACCCC--AATC--ATGGGGCAGATTGAAGC
171125 TACCATCTCA
Statistics
Matches: 437, Mismatches: 73, Indels: 39
0.80 0.13 0.07
Matches are distributed among these distances:
157 80 0.18
158 112 0.26
159 9 0.02
160 41 0.09
161 7 0.02
162 67 0.15
164 15 0.03
165 72 0.16
166 34 0.08
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (158 bp):
AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAA
TCAAAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAA
TCTCTTACCCCAATCATGAGACAGATTG
Found at i:173098 original size:17 final size:18
Alignment explanation
Indices: 173076--173119 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
173066 AATCAATTCG
173076 TATATTTTTTA-TTATTT
1 TATATTTTTTATTTATTT
* *
173093 TATATTGTGTATTTATTT
1 TATATTTTTTATTTATTT
*
173111 AATATTTTT
1 TATATTTTT
173120 GCTACTTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (18 bp):
TATATTTTTTATTTATTT
Found at i:176331 original size:59 final size:57
Alignment explanation
Indices: 176184--176330 Score: 149
Period size: 57 Copynumber: 2.6 Consensus size: 57
176174 TCCGAATTTG
* * *
176184 ATTTTTTTT-ATTTGGTATCTAAAGTTTTTTTTATCCAATTTAGTATTTAAATTTGAT
1 ATTTTTTTTAATTTGGTATCTAAA-TTTTTTTTATCCAATTTAGTACTTAAATTTAAC
* * * * *
176241 ATTTTTTCCTAGTTTGATA-CTTAAATTTTTTTGGATCCAATTT-GATACTTGAA-TTAAC
1 ATTTTTT-TTAATTTGGTATC-TAAATTTTTTT-TATCCAATTTAG-TACTTAAATTTAAC
176299 ATTTTTTTTAATTTGGTATCTAAATTTTTTTT
1 ATTTTTTTTAATTTGGTATCTAAATTTTTTTT
176331 TTTAAGATTC
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
57 26 0.36
58 21 0.29
59 25 0.35
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (57 bp):
ATTTTTTTTAATTTGGTATCTAAATTTTTTTTATCCAATTTAGTACTTAAATTTAAC
Found at i:176555 original size:30 final size:29
Alignment explanation
Indices: 176519--176629 Score: 138
Period size: 30 Copynumber: 3.8 Consensus size: 29
176509 GAATCTCAAA
*
176519 AAATTTAAATATCAACTTAAAAAAAATGTC
1 AAATTTAAATATCAAATTAAAAAAAAT-TC
*
176549 AAATTTAGATATCAAATTAAAAAAAATATC
1 AAATTTAAATATCAAATTAAAAAAAAT-TC
* *
176579 AAATTTAAATATTAAATTAAACTAAAA---
1 AAATTTAAATATCAAATTAAA-AAAAATTC
176606 AAATTTAAATATCAAATTAAAAAA
1 AAATTTAAATATCAAATTAAAAAA
176630 TATTAATTCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.03
27 20 0.28
30 46 0.64
31 4 0.06
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (29 bp):
AAATTTAAATATCAAATTAAAAAAAATTC
Found at i:176590 original size:13 final size:13
Alignment explanation
Indices: 176572--176623 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
176562 AAATTAAAAA
176572 AAATATCAAATTT
1 AAATATCAAATTT
*
176585 AAATATTAAA-TT
1 AAATATCAAATTT
**
176597 AAACTAAAAAAATTT
1 AAA-T-ATCAAATTT
176612 AAATATCAAATT
1 AAATATCAAATT
176624 AAAAAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 5 0.16
13 16 0.52
14 5 0.16
15 5 0.16
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATATCAAATTT
Found at i:176613 original size:20 final size:23
Alignment explanation
Indices: 176585--176635 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
176575 TATCAAATTT
176585 AAATATTAAAT-T-AAACTAAAA
1 AAATATTAAATATCAAACTAAAA
*
176606 AAAT-TTAAATATCAAA-TTAAA
1 AAATATTAAATATCAAACTAAAA
176627 AAATATTAA
1 AAATATTAA
176636 TTCAGATACC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 13 0.50
22 7 0.27
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATATTAAATATCAAACTAAAA
Found at i:181052 original size:25 final size:25
Alignment explanation
Indices: 181023--181115 Score: 123
Period size: 25 Copynumber: 3.7 Consensus size: 25
181013 ATAGAATTTA
181023 CGCTCTTACGAGCCAGACAGAATAT
1 CGCTCTTACGAGCCAGACAGAATAT
**
181048 CGCTCTTACGAGCCAGATGGAATAT
1 CGCTCTTACGAGCCAGACAGAATAT
* * *
181073 CGCTCTTACGAGCCAAATAAAATAT
1 CGCTCTTACGAGCCAGACAGAATAT
* *
181098 CGCTCTTATGAGCAAGAC
1 CGCTCTTACGAGCCAGAC
181116 TTTAGAAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (25 bp):
CGCTCTTACGAGCCAGACAGAATAT
Found at i:186589 original size:22 final size:21
Alignment explanation
Indices: 186544--186589 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
186534 TAGAGGTAAG
*
186544 ACTTGTATCGGTAGAACTTTC
1 ACTTGTATCGGTAAAACTTTC
*
186565 ACTTGTATCGGTACAAATTTTC
1 ACTTGTATCGGTA-AAACTTTC
186587 ACT
1 ACT
186590 ATTCTTGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (21 bp):
ACTTGTATCGGTAAAACTTTC
Found at i:190325 original size:25 final size:25
Alignment explanation
Indices: 190294--190381 Score: 131
Period size: 25 Copynumber: 3.5 Consensus size: 25
190284 ATAGAATTTA
*
190294 CGCTCTTACGAGCCGGACAGAATAT
1 CGCTCTTACGAGCCAGACAGAATAT
*
190319 CGCTCTTACGAGCCAGACGGAATAT
1 CGCTCTTACGAGCCAGACAGAATAT
* *
190344 CGCTCTTACGAGCCAAATAGAATAT
1 CGCTCTTACGAGCCAGACAGAATAT
*
190369 CACTCTTACGAGC
1 CGCTCTTACGAGC
190382 TAAACTTTAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (25 bp):
CGCTCTTACGAGCCAGACAGAATAT
Found at i:193329 original size:209 final size:209
Alignment explanation
Indices: 192969--193383 Score: 740
Period size: 209 Copynumber: 2.0 Consensus size: 209
192959 TGATTGAGTC
*
192969 ATCATTCTGAAGATTAGAACACTTCCATGCATGTCCCTGATAACTATTCCCATTCCTGCTTTACA
1 ATCATTCTGAAGACTAGAACACTTCCATGCATGTCCCTGATAACTATTCCCATTCCTGCTTTACA
* *
193034 ACTACCAAAGTCAAAGCTGGCATCAAAGTTGATTTTTACGACATTCCTTGGAGGAGGATCCCAAC
66 ACTACCAAAGTAAAAGCTGGCATCAAAGTTGATTTTTACGACATTCCTTGGAAGAGGATCCCAAC
*
193099 GGGCGTTCCTTTTTGACAAGATAAGTCGCTTTTCTTTAGTAGATTCAATCTTCTTTACATAGCTT
131 GGGCGTTCCTTTTTGACAAGATAAGTCGCTTTTCTTTAGTAGATTCAATCTCCTTTACATAGCTT
*
193164 CTAATGAAACATGT
196 CTAACGAAACATGT
* * *
193178 ATCATTCTGGAGACTAGAACACTTTCATGCATGTCCCTGATAACTATTCCCATTCTTGCTTTACA
1 ATCATTCTGAAGACTAGAACACTTCCATGCATGTCCCTGATAACTATTCCCATTCCTGCTTTACA
*
193243 ACTACTAAAGTAAAAGCTGGCATCAAAGTTGATTTTTACGACATTCCTTGGAAGAGGATCCCAAC
66 ACTACCAAAGTAAAAGCTGGCATCAAAGTTGATTTTTACGACATTCCTTGGAAGAGGATCCCAAC
*
193308 GGGCGTTCCTTTTTTACAAGATAAGTCGCTTTTCTTTAGTAGATTCAATCTCCTTTACATAGCTT
131 GGGCGTTCCTTTTTGACAAGATAAGTCGCTTTTCTTTAGTAGATTCAATCTCCTTTACATAGCTT
193373 CTAACGAAACA
196 CTAACGAAACA
193384 GGCAATATCA
Statistics
Matches: 196, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 196 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (209 bp):
ATCATTCTGAAGACTAGAACACTTCCATGCATGTCCCTGATAACTATTCCCATTCCTGCTTTACA
ACTACCAAAGTAAAAGCTGGCATCAAAGTTGATTTTTACGACATTCCTTGGAAGAGGATCCCAAC
GGGCGTTCCTTTTTGACAAGATAAGTCGCTTTTCTTTAGTAGATTCAATCTCCTTTACATAGCTT
CTAACGAAACATGT
Found at i:198172 original size:21 final size:21
Alignment explanation
Indices: 198146--198209 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
198136 CAAACAATGA
* *
198146 CAAAAATTATCGACACCTTTT
1 CAAAAAATATCGATACCTTTT
*
198167 CAAAAAAATATCGTTACCTTTT
1 C-AAAAAATATCGATACCTTTT
* * *
198189 CAAGAAGTACCGATACCTTTT
1 CAAAAAATATCGATACCTTTT
198210 ATCAAGTATC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.33
Consensus pattern (21 bp):
CAAAAAATATCGATACCTTTT
Found at i:234873 original size:68 final size:69
Alignment explanation
Indices: 234799--234932 Score: 225
Period size: 68 Copynumber: 2.0 Consensus size: 69
234789 TTAAAAAATA
* *
234799 TAATATTAAATTTAATCCAATACTTATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTGATT
1 TAATATTAAATTTAATCCAATACTTATCTTAATAAGTATTATATTAATTTAATATTAAAATGATT
234863 ATCT
66 ATCT
* *
234867 TAATATTAAATTTAATCTAATATTTATCTTAATAAGTATTATATTAATTTAATATTAAAATGATT
1 TAATATTAAATTTAATCCAATACTTATCTTAATAAGTATTATATTAATTTAATATTAAAATGATT
234932 A
66 A
234933 AGTTTAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
68 31 0.51
69 30 0.49
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.49
Consensus pattern (69 bp):
TAATATTAAATTTAATCCAATACTTATCTTAATAAGTATTATATTAATTTAATATTAAAATGATT
ATCT
Found at i:239856 original size:91 final size:91
Alignment explanation
Indices: 239696--239869 Score: 276
Period size: 91 Copynumber: 1.9 Consensus size: 91
239686 CGTGATAGAA
* *
239696 AATGTTTAGCCTACAAGCTTTGGATTATGTGCATCTGGCGTGTTATCGGTTGGAAAACTCTTATG
1 AATGTTTAGCCTACAAGCTTTGCATTATGTGCATCTGGCGTGTTATCGGTTGGAAAACTCTTATA
*
239761 AGCAAATTGGAGTGTTATCGGGGGAT
66 AGCAAACTGGAGTGTTATCGGGGGAT
** * *
239787 AATGTTTAGCCTACGGGCTTTGCATTATTTGCATCTGGCGTGTTATCGGTTGGAAAGCTCTTATA
1 AATGTTTAGCCTACAAGCTTTGCATTATGTGCATCTGGCGTGTTATCGGTTGGAAAACTCTTATA
*
239852 AGCAAACTGGTGTGTTAT
66 AGCAAACTGGAGTGTTAT
239870 TGGATGGTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (91 bp):
AATGTTTAGCCTACAAGCTTTGCATTATGTGCATCTGGCGTGTTATCGGTTGGAAAACTCTTATA
AGCAAACTGGAGTGTTATCGGGGGAT
Found at i:250227 original size:11 final size:11
Alignment explanation
Indices: 250213--250248 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
250203 ATATAAAAAA
250213 AATTTAAATTT
1 AATTTAAATTT
250224 AATTTAAATTT
1 AATTTAAATTT
*
250235 AATAATAAATTT
1 AAT-TTAAATTT
250247 AA
1 AA
250249 AAACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:254022 original size:30 final size:31
Alignment explanation
Indices: 253966--254033 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
253956 GTCCTCTGAA
* * *
253966 ATGTAAAAGCCTTTGTGGTTGATCTCTA-AT
1 ATGTGAAAGCCATTGTGGCTGATCTCTATAT
253996 ATGTGAAAGCCATTGTGGCT-ACTCTCTATTAT
1 ATGTGAAAGCCATTGTGGCTGA-TCTCTA-TAT
254028 ATGTGA
1 ATGTGA
254034 GCCCTAGTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 23 0.72
32 8 0.25
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (31 bp):
ATGTGAAAGCCATTGTGGCTGATCTCTATAT
Found at i:254280 original size:30 final size:30
Alignment explanation
Indices: 254188--254288 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
254178 CATTGACGCA
* * * *
254188 TTTGTGGCTACCTAATGTTATCTGGACACC
1 TTTGTGGCTATCTAATGATATATAGACACC
** *
254218 -TTGCTATCTATCTAATGATATCTAGACACC
1 TTTG-TGGCTATCTAATGATATATAGACACC
* * *
254248 TTTGTGGCTATCTAATGATGTATGGACGCC
1 TTTGTGGCTATCTAATGATATATAGACACC
254278 TTTGTGGCTAT
1 TTTGTGGCTAT
254289 TTGTTGATCA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
29 3 0.05
30 52 0.90
31 3 0.05
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (30 bp):
TTTGTGGCTATCTAATGATATATAGACACC
Found at i:256408 original size:66 final size:66
Alignment explanation
Indices: 256334--256466 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
256324 AACTATGAGA
256334 TTGAGACTAAGACTAAACTGAGATAATTATGTGATCATACCATTGCGTGTTCATGGGGTGGGTTT
1 TTGAGACTAAGACTAAACTGAGATAATTATGTGATCATACCATTGCGTGTTCATGGGGTGGGTTT
256399 G
66 G
256400 TTGAGACTAAGACTAAACTGAGATAATTATGTGATCATACCATTGCGTGTTCATGGGGTGGGTTT
1 TTGAGACTAAGACTAAACTGAGATAATTATGTGATCATACCATTGCGTGTTCATGGGGTGGGTTT
256465 G
66 G
256466 T
1 T
256467 ACGGTGGAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (66 bp):
TTGAGACTAAGACTAAACTGAGATAATTATGTGATCATACCATTGCGTGTTCATGGGGTGGGTTT
G
Found at i:256956 original size:6 final size:6
Alignment explanation
Indices: 256934--256967 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
256924 AATTATAGAC
*
256934 TTTATA -TTATA TATATA TTTATA TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTAT
256968 GAATGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTATA
Found at i:264650 original size:44 final size:44
Alignment explanation
Indices: 264600--264690 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
264590 GTGGATAGTG
264600 AGACCGTAGAGTTGGATAGTGCAATGGTTAGTCGAGAATTATTA
1 AGACCGTAGAGTTGGATAGTGCAATGGTTAGTCGAGAATTATTA
264644 AGACCGTAGAGTTGGATAGTGCAATGGTTAGTCGAGAATTATTA
1 AGACCGTAGAGTTGGATAGTGCAATGGTTAGTCGAGAATTATTA
264688 AGA
1 AGA
264691 TTACTCCATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (44 bp):
AGACCGTAGAGTTGGATAGTGCAATGGTTAGTCGAGAATTATTA
Found at i:271169 original size:23 final size:23
Alignment explanation
Indices: 271139--271237 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 23
271129 TGGGTAATAA
271139 AGGGCACAAAAAGTGCTAATCAG
1 AGGGCACAAAAAGTGCTAATCAG
**
271162 AGGGCACATGAAGTGCTAATAACAG
1 AGGGCACAAAAAGTGCTAAT--CAG
* * * *
271187 AGGACACACACAGTGTTGAA-CAG
1 AGGGCACAAAAAGTGCT-AATCAG
* * *
271210 AGGGCACGAAACGTGCTAAACAG
1 AGGGCACAAAAAGTGCTAATCAG
271233 AGGGC
1 AGGGC
271238 GCGCTAGTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
22 2 0.03
23 40 0.68
25 15 0.25
26 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.12
Consensus pattern (23 bp):
AGGGCACAAAAAGTGCTAATCAG
Found at i:274285 original size:31 final size:30
Alignment explanation
Indices: 274249--274308 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
274239 TCTACAGAGA
* *
274249 TAGTCCGCTAGGATAGTAAACACAAGATAGG
1 TAGTCCACTAGGACAGTAAACACAA-ATAGG
*
274280 TAGTCCACTGGGACAGTAAACACAAATAG
1 TAGTCCACTAGGACAGTAAACACAAATAG
274309 AGTCCATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (30 bp):
TAGTCCACTAGGACAGTAAACACAAATAGG
Found at i:278251 original size:19 final size:19
Alignment explanation
Indices: 278227--278266 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
278217 ATAAAAGGAA
278227 ATCTTGCACGTGCATTGAT
1 ATCTTGCACGTGCATTGAT
278246 ATCTTGCACGTGCATTGAT
1 ATCTTGCACGTGCATTGAT
278265 AT
1 AT
278267 GAATACTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (19 bp):
ATCTTGCACGTGCATTGAT
Found at i:279993 original size:21 final size:21
Alignment explanation
Indices: 279950--280021 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
279940 TGCAGATTTG
**
279950 TACCGATACAAGTGATAGTTC
1 TACCGATACAAGTGATACCTC
279971 TACCGATACAAGTGACT-CCTC
1 TACCGATACAAGTGA-TACCTC
* **
279992 TACCAATACAAGTCTTACCTC
1 TACCGATACAAGTGATACCTC
*
280013 TACTGATAC
1 TACCGATAC
280022 TAAAAACTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
TACCGATACAAGTGATACCTC
Found at i:280106 original size:21 final size:21
Alignment explanation
Indices: 280082--280133 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
280072 AGTATGCAAA
280082 CTACTGATACTTATTATTCAT
1 CTACTGATACTTATTATTCAT
280103 CTACTGATACTTATTATTCAT
1 CTACTGATACTTATTATTCAT
280124 CTACTGATAC
1 CTACTGATAC
280134 AACCCAAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (21 bp):
CTACTGATACTTATTATTCAT
Found at i:283719 original size:20 final size:20
Alignment explanation
Indices: 283683--283727 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
283673 TCATTAAGCT
*
283683 TTAATTAATCTCTTTTAATC
1 TTAATTAAGCTCTTTTAATC
*
283703 TTAATTAAGC-CTATTTACTC
1 TTAATTAAGCTCT-TTTAATC
283723 TTAAT
1 TTAAT
283728 AGAAATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAATTAAGCTCTTTTAATC
Found at i:290195 original size:61 final size:61
Alignment explanation
Indices: 290090--290207 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 61
290080 TTAAACTGTC
* **
290090 ACGCTTTATTCTTGAATACAATAACCAGATTAAGTGTAAGGTATTACGTAATAAATACATGTG
1 ACGCTTTATTCTTGAATACAAT-A-CAAATTAAGTGTAAGGTATTACACAATAAATACATGTG
*
290153 ACGCTTTATTTTTGAATAACAAT-CAAATTAAGTGTAAGGTATTACACAATAAATA
1 ACGCTTTATTCTTGAAT-ACAATACAAATTAAGTGTAAGGTATTACACAATAAATA
290208 AAAAGACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 29 0.58
63 16 0.32
64 5 0.10
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (61 bp):
ACGCTTTATTCTTGAATACAATACAAATTAAGTGTAAGGTATTACACAATAAATACATGTG
Found at i:298499 original size:22 final size:23
Alignment explanation
Indices: 298439--298501 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
298429 TTTGTATTAT
*
298439 AAATTAAATTATAATTTTTATGA
1 AAATTAAATTATAATTTTTATAA
* * *
298462 TAATAAAAATATAATTTTTA-AA
1 AAATTAAATTATAATTTTTATAA
*
298484 AAATTAAATTAAAATTTT
1 AAATTAAATTATAATTTT
298502 ATTATTTTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATTAAATTATAATTTTTATAA
Found at i:305195 original size:21 final size:21
Alignment explanation
Indices: 305169--305245 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
305159 AATAGTGCAA
305169 ACTTCTACCGATACAAGTGTC
1 ACTTCTACCGATACAAGTGTC
* *
305190 AATTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGTC
* * * *
305211 TCTTTTACCGATACAAGTCTT
1 ACTTCTACCGATACAAGTGTC
305232 ACTTCTACCGATAC
1 ACTTCTACCGATAC
305246 TAAAAATTCC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGTC
Found at i:306204 original size:19 final size:19
Alignment explanation
Indices: 306180--306237 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 19
306170 CCGTTGACCA
*
306180 TTGACCATTGATCATTGAC
1 TTGACCGTTGATCATTGAC
*
306199 TTGACCGTTGGTCATTGAC
1 TTGACCGTTGATCATTGAC
* *
306218 TTGACCGTTAACCATTGAC
1 TTGACCGTTGATCATTGAC
306237 T
1 T
306238 GTTGAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGACCGTTGATCATTGAC
Found at i:314543 original size:21 final size:21
Alignment explanation
Indices: 314469--314543 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
314459 AATAGTGCAG
* *
314469 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTTAT
* * *
314490 AGTTCTAGCGATACAAG-TCT
1 ACTTCTACCGATACAAGTTAT
* * *
314510 -CTTTTATCGATACAAGTTTT
1 ACTTCTACCGATACAAGTTAT
314530 ACTTCTACCGATAC
1 ACTTCTACCGATAC
314544 TAAAAACTCC
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 26 0.63
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTTAT
Found at i:319002 original size:24 final size:24
Alignment explanation
Indices: 318974--319036 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
318964 AGAAATAATC
*
318974 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
318998 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
319022 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
319037 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:320980 original size:24 final size:24
Alignment explanation
Indices: 320953--321033 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
320943 AATCTTTTAG
*
320953 TTAAACTCTGTTTAATTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
320977 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
* * *
321001 TTAAACTCTATTTATTTGTTTGAG
1 TTAAACTCTGTTTATTTGTTTCAA
321025 TTAAACTCT
1 TTAAACTCT
321034 TATTAGTCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:322915 original size:30 final size:30
Alignment explanation
Indices: 322840--322903 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
322830 TTTGTTTTAG
*
322840 AGTGGATTTATTAATTTGAGAGTTAATTTT
1 AGTGAATTTATTAATTTGAGAGTTAATTTT
*
322870 AGTGAATTTATTAATTTGGGAGTTAATTTT
1 AGTGAATTTATTAATTTGAGAGTTAATTTT
322900 AGTG
1 AGTG
322904 TTTTAGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (30 bp):
AGTGAATTTATTAATTTGAGAGTTAATTTT
Found at i:325429 original size:6 final size:6
Alignment explanation
Indices: 325418--325448 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
325408 CGCAATGAAT
325418 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
325449 AACATTTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:325641 original size:14 final size:14
Alignment explanation
Indices: 325622--325648 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
325612 AGAAAATATT
325622 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
325636 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
325649 AACTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:325871 original size:21 final size:21
Alignment explanation
Indices: 325847--325910 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
325837 CACTTCAAAC
325847 AAATTTACTATAAAGCCCCAA
1 AAATTTACTATAAAGCCCCAA
* *
325868 AAATTTA-TATAAA----TAC
1 AAATTTACTATAAAGCCCCAA
*
325884 AAATTTACTATAACGCCCCAA
1 AAATTTACTATAAAGCCCCAA
325905 AAATTT
1 AAATTT
325911 TGATATGACA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 8 0.24
17 5 0.15
20 6 0.18
21 14 0.42
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (21 bp):
AAATTTACTATAAAGCCCCAA
Found at i:327117 original size:30 final size:30
Alignment explanation
Indices: 327083--327139 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
327073 AGGAAAACGA
*
327083 GGCCAAATCCAAATTTTTGGAAAGTTTGGG
1 GGCCAAATCCAAATTTTTGAAAAGTTTGGG
*
327113 GGCCAAATCTAAATTTTTGAAAAGTTT
1 GGCCAAATCCAAATTTTTGAAAAGTTT
327140 AAGGGTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (30 bp):
GGCCAAATCCAAATTTTTGAAAAGTTTGGG
Found at i:327158 original size:30 final size:29
Alignment explanation
Indices: 327124--327248 Score: 160
Period size: 30 Copynumber: 4.2 Consensus size: 29
327114 GCCAAATCTA
*
327124 AATTTTTGAAAAGTTTAAGGGTCAAAATAT
1 AATTTTTGAAAA-TTTAAGGGTCAAAACAT
327154 AATTTTTGGAAAATTTAAGGGTCAAAACAT
1 AATTTTT-GAAAATTTAAGGGTCAAAACAT
* * *
327184 AATTTTTAGAAAGTTTAGGGGTCAAAATAT
1 AATTTTT-GAAAATTTAAGGGTCAAAACAT
* **
327214 AATTTTTTAAAAACTAAGGGTCAAAACAT
1 AATTTTTGAAAATTTAAGGGTCAAAACAT
327243 AATTTT
1 AATTTT
327249 AGACAGCTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.27
30 56 0.67
31 5 0.06
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (29 bp):
AATTTTTGAAAATTTAAGGGTCAAAACAT
Found at i:327160 original size:60 final size:60
Alignment explanation
Indices: 327094--327268 Score: 187
Period size: 60 Copynumber: 3.0 Consensus size: 60
327084 GCCAAATCCA
* ** *
327094 AATTTTTGGAAAGTTTGGGGGCCAAATC-TAAATTTTT-GAAAAGTTTAAGGGTCAAAATAT
1 AATTTTTGGAAAATTTAAGGGCCAAAACAT-AATTTTTAG-AAAGTTTAAGGGTCAAAATAT
* *
327154 AATTTTTGGAAAATTTAAGGGTCAAAACATAATTTTTAGAAAGTTTAGGGGTCAAAATAT
1 AATTTTTGGAAAATTTAAGGGCCAAAACATAATTTTTAGAAAGTTTAAGGGTCAAAATAT
* ** * * * *
327214 AATTTTT-TAAAAACTAAGGGTCAAAACATAA-TTTTAGACAGCTTAAGGATCAAAA
1 AATTTTTGGAAAATTTAAGGGCCAAAACATAATTTTTAGAAAGTTTAAGGGTCAAAA
327269 CACCATTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 20 0.20
59 21 0.21
60 57 0.57
61 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (60 bp):
AATTTTTGGAAAATTTAAGGGCCAAAACATAATTTTTAGAAAGTTTAAGGGTCAAAATAT
Found at i:327260 original size:29 final size:30
Alignment explanation
Indices: 327124--327279 Score: 149
Period size: 30 Copynumber: 5.3 Consensus size: 30
327114 GCCAAATCTA
* *
327124 AATTTTT-GAAAAGTTTAAGGGTCAAAATAT
1 AATTTTTAGAAAA-CTTAAGGGTCAAAACAT
* *
327154 AATTTTTGGAAAATTTAAGGGTCAAAACAT
1 AATTTTTAGAAAACTTAAGGGTCAAAACAT
** * *
327184 AATTTTTAGAAAGTTTAGGGGTCAAAATAT
1 AATTTTTAGAAAACTTAAGGGTCAAAACAT
327214 AATTTTTTA-AAAAC-TAAGGGTCAAAACAT
1 AA-TTTTTAGAAAACTTAAGGGTCAAAACAT
* * * *
327243 AA-TTTTAGACAGCTTAAGGATCAAAACAC
1 AATTTTTAGAAAACTTAAGGGTCAAAACAT
*
327272 CATTTTTA
1 AATTTTTA
327280 ATTAAAACAG
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
27 5 0.05
28 3 0.03
29 29 0.27
30 59 0.55
31 11 0.10
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (30 bp):
AATTTTTAGAAAACTTAAGGGTCAAAACAT
Found at i:334512 original size:26 final size:26
Alignment explanation
Indices: 334463--334512 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
334453 TCTAGATGAC
*
334463 TTGCCACAAAGGCTTCCCAGATAACT
1 TTGCCACAAAGGCTTCCCAAATAACT
* * *
334489 TTGCCACTAAGTCTTCTCAAATAA
1 TTGCCACAAAGGCTTCCCAAATAA
334513 TACTCCACAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (26 bp):
TTGCCACAAAGGCTTCCCAAATAACT
Found at i:336448 original size:91 final size:91
Alignment explanation
Indices: 336293--336476 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 91
336283 TAAAAGGTGT
336293 AAAAATGAGTCTTTTATTGATTTTAGGGCCGATTGAGGCCTAAAGGTTGGCTAATATACTTTGTG
1 AAAAATGAGTCTTTTATTGATTTTAGGGCCGATTGAGGCCTAAAGGTTGGCTAATATACTTTGTG
*
336358 AGTGTGTAGGAAATCATTAGAAGAAG
66 AGTGTGCAGGAAATCATTAGAAGAAG
336384 AAAAATGAGTCTTTTATTGATTTTAGGGCCGATTGAGGCCTAAAGGTTGGCTAATATACTTTGTG
1 AAAAATGAGTCTTTTATTGATTTTAGGGCCGATTGAGGCCTAAAGGTTGGCTAATATACTTTGTG
336449 AGTGTGCAGGAAATCATTAGAAGAAG
66 AGTGTGCAGGAAATCATTAGAAGAAG
336475 AA
1 AA
336477 TCATATCAAG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (91 bp):
AAAAATGAGTCTTTTATTGATTTTAGGGCCGATTGAGGCCTAAAGGTTGGCTAATATACTTTGTG
AGTGTGCAGGAAATCATTAGAAGAAG
Found at i:336599 original size:33 final size:33
Alignment explanation
Indices: 336557--336624 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
336547 GAATCCTGAA
336557 GTTGTCTTCTATGTCGCGACACAACATAAGGGT
1 GTTGTCTTCTATGTCGCGACACAACATAAGGGT
* *
336590 GTTGTCTTCTATGTTGTGACACAACATAAGGGT
1 GTTGTCTTCTATGTCGCGACACAACATAAGGGT
336623 GT
1 GT
336625 GGCAACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (33 bp):
GTTGTCTTCTATGTCGCGACACAACATAAGGGT
Found at i:336913 original size:22 final size:22
Alignment explanation
Indices: 336887--336930 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
336877 TCTTTGTAAT
* *
336887 TTAGGTTTAGTCATTTTTTTTC
1 TTAGGCTTAGTCATTTTATTTC
*
336909 TTAGGCTTAGTTATTTTATTTC
1 TTAGGCTTAGTCATTTTATTTC
336931 GTTCTTGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (22 bp):
TTAGGCTTAGTCATTTTATTTC
Found at i:345483 original size:25 final size:23
Alignment explanation
Indices: 345455--345500 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
345445 GTTGGATCCA
345455 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
345480 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
345501 TCCTAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:346133 original size:22 final size:22
Alignment explanation
Indices: 346106--346203 Score: 97
Period size: 22 Copynumber: 4.1 Consensus size: 22
346096 ATTGATTTAA
346106 ATTGAATAAATTATTCTGATTG
1 ATTGAATAAATTATTCTGATTG
* *
346128 GTTGAATAAATTATTTTGATTG
1 ATTGAATAAATTATTCTGATTG
*
346150 ATTTTAAATTGAATAAATTATTTTGATTG
1 -------ATTGAATAAATTATTCTGATTG
*
346179 ATTGAATAAATTATTCTAATTG
1 ATTGAATAAATTATTCTGATTG
346201 ATT
1 ATT
346204 TTAAATTGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
22 43 0.67
29 21 0.33
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTGAATAAATTATTCTGATTG
Done.