Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000394.1 Hibiscus syriacus cultivar Beakdansim tig00000724_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 204258
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:11663 original size:39 final size:39
Alignment explanation
Indices: 11608--11934 Score: 406
Period size: 39 Copynumber: 8.4 Consensus size: 39
11598 AATAAGGACT
* *
11608 TGCGGTAAGGACTTACCCTGAGAACAAAGATGAGGAGAC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
* *
11647 TGCGGTAAGGATTTACCCTGAGCACAAAGCCGAGGAGAC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
* *
11686 TGCGGTAAGGA-TTACCCTGAGCACAAAGCCGAGGAGCC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
* *
11724 TGCAGTAAGGACTTACCCTGAGCACAAAGCTGATGAGAC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
* * **
11763 TTCGATAAGGACTTACATTGAGCACAAAGGC-GAGGAGAC
1 TGCGGTAAGGACTTACCCTGAGCACAAA-GCTGAGGAGAC
** * * *
11802 TATGGTAAGGACTTACCTTGAGCACAAAGCTAAGGAGAA
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
** *
11841 TATGGTAAGGACTTACCCTAAGCACAAAGCTGAGGAGAC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
** * *
11880 TGCGGTAAGGACTTACCCTGAGCACAAAGCCAAGAAGCC
1 TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
*
11919 TGCGGTAAAGACTTAC
1 TGCGGTAAGGACTTAC
11935 AAGTCATAGA
Statistics
Matches: 252, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
38 38 0.15
39 212 0.84
40 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (39 bp):
TGCGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGAC
Found at i:13319 original size:30 final size:30
Alignment explanation
Indices: 13276--13332 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
13266 ACTTTCAAAA
*
13276 TTTGGATCCGAATTTA-TTCAAAATTTCAC
1 TTTGGATCCGAATTTAGTTAAAAATTTCAC
*
13305 TTTGGCTCCTGAATTTAGTTAAAAATTT
1 TTTGGATCC-GAATTTAGTTAAAAATTT
13333 AATTTATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 7 0.29
31 9 0.38
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTGGATCCGAATTTAGTTAAAAATTTCAC
Found at i:15046 original size:14 final size:14
Alignment explanation
Indices: 15027--15053 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15017 CCCATTTCGT
15027 TTTCTTTTAATTTG
1 TTTCTTTTAATTTG
15041 TTTCTTTTAATTT
1 TTTCTTTTAATTT
15054 ATTTTCAATT
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:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTCTTTTAATTTG
Found at i:15092 original size:13 final size:13
Alignment explanation
Indices: 15051--15085 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
15041 TTTCTTTTAA
15051 TTTATTTTCAATT
1 TTTATTTTCAATT
15064 TTTAGTTTTCAATT
1 TTTA-TTTTCAATT
15078 TTTATTTT
1 TTTATTTT
15086 TCATTTTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTATTTTCAATT
Found at i:19580 original size:25 final size:25
Alignment explanation
Indices: 19550--19606 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
19540 TCGAATATCT
19550 AATTCAAAGTTGAATAAAATCTTAA
1 AATTCAAAGTTGAATAAAATCTTAA
19575 AATTCAAAGTTGAATAAAATCTTAA
1 AATTCAAAGTTGAATAAAATCTTAA
19600 AATTCAA
1 AATTCAA
19607 TAACACTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.32
Consensus pattern (25 bp):
AATTCAAAGTTGAATAAAATCTTAA
Found at i:19710 original size:13 final size:13
Alignment explanation
Indices: 19692--19725 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
19682 TAAGATTTTC
*
19692 TTTGAAAATCATT
1 TTTGAAAATCAAT
19705 TTTG-AAATCAAT
1 TTTGAAAATCAAT
19717 TTTGAAAAT
1 TTTGAAAAT
19726 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:21056 original size:20 final size:20
Alignment explanation
Indices: 21013--21073 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
21003 TACTGTTCAT
* **
21013 TACTGCTCACACAGTATCGG
1 TACTGTTCACACAGTATCAA
21033 TACTGTTCACACAGTATCAA
1 TACTGTTCACACAGTATCAA
* *
21053 TACTATTCATACAGTA-CAA
1 TACTGTTCACACAGTATCAA
21072 TA
1 TA
21074 TTATTCATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 5 0.14
20 31 0.86
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (20 bp):
TACTGTTCACACAGTATCAA
Found at i:21078 original size:19 final size:20
Alignment explanation
Indices: 21023--21082 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
21013 TACTGCTCAC
** * *
21023 ACAGTATCGGTACTGTTCAC
1 ACAGTATCAATACTATTCAT
21043 ACAGTATCAATACTATTCAT
1 ACAGTATCAATACTATTCAT
*
21063 ACAGTA-CAATATTATTCAT
1 ACAGTATCAATACTATTCAT
21082 A
1 A
21083 AAAACATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (20 bp):
ACAGTATCAATACTATTCAT
Found at i:22630 original size:13 final size:14
Alignment explanation
Indices: 22600--22633 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
22590 CAAATAAATA
22600 TTGAAAACATAGTT
1 TTGAAAACATAGTT
*
22614 TTGAAAACAT-TTT
1 TTGAAAACATAGTT
22627 TTGAAAA
1 TTGAAAA
22634 TATATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (14 bp):
TTGAAAACATAGTT
Found at i:22651 original size:38 final size:38
Alignment explanation
Indices: 22608--22703 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
22598 TATTGAAAAC
* *
22608 ATAGTTTTGAAAACATTTTTTGAAAATATATATAATAT
1 ATAGTTTTGAAAACATTTTTCGAAAACATATATAATAT
* *
22646 ATAGTTTTGAAAATATTTTTCGAAAACATATATATTAT
1 ATAGTTTTGAAAACATTTTTCGAAAACATATATAATAT
*
22684 ATAGTTTTGAAAACCTTTTT
1 ATAGTTTTGAAAACATTTTT
22704 GTAAACCTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (38 bp):
ATAGTTTTGAAAACATTTTTCGAAAACATATATAATAT
Found at i:22714 original size:11 final size:12
Alignment explanation
Indices: 22688--22719 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
22678 TATTATATAG
22688 TTTTGAAAACCT
1 TTTTGAAAACCT
*
22700 TTTTGTAAACCT
1 TTTTGAAAACCT
22712 TTTTGAAA
1 TTTTGAAA
22720 TCATATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (12 bp):
TTTTGAAAACCT
Found at i:22790 original size:36 final size:35
Alignment explanation
Indices: 22706--22803 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 35
22696 ACCTTTTTGT
* *
22706 AAACCTTTTTGAAATCATATATGATATATAGTTTTAA
1 AAACATTTTTGAAAACATATATG-TATATA-TTTTAA
*
22743 AAACATATTTTGAAAACATATATGTATAGT-TTTTTA
1 AAACAT-TTTTGAAAACATATATGTATA-TATTTTAA
*
22779 AAACGGTTTTTGAAAACATAT-TGTA
1 AAAC-ATTTTTGAAAACATATATGTA
22804 GCATCCTCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
35 4 0.07
36 23 0.43
37 10 0.19
38 17 0.31
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (35 bp):
AAACATTTTTGAAAACATATATGTATATATTTTAA
Found at i:24287 original size:18 final size:18
Alignment explanation
Indices: 24261--24295 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24251 AGGGATTATC
24261 AGTGATCCTTCGGGACAT
1 AGTGATCCTTCGGGACAT
*
24279 AGTGGTCCTTCGGGACA
1 AGTGATCCTTCGGGACA
24296 AATATTCAGT
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:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGATCCTTCGGGACAT
Found at i:24982 original size:2 final size:2
Alignment explanation
Indices: 24972--25071 Score: 67
Period size: 2 Copynumber: 54.0 Consensus size: 2
24962 GTTTTTTAAA
*
24972 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
25011 AT AT AT -T AT AT -T GT AC AT AT AT -T AT -T TT AT AGT AT GT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
25051 AT -T AT AT -T AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
25072 TTTATTTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
1 10 0.13
2 64 0.82
3 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (2 bp):
AT
Found at i:24983 original size:24 final size:23
Alignment explanation
Indices: 24928--24986 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
24918 TGTTACATAT
24928 ATATAATATATA-ATTTTAGAAA
1 ATATAATATATATATTTTAGAAA
* **
24950 ACAT-AT-TATATAGTTTTTTAAA
1 ATATAATATATATA-TTTTAGAAA
24972 ATATAATATATATAT
1 ATATAATATATATAT
24987 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.14
21 3 0.10
22 13 0.45
23 3 0.10
24 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (23 bp):
ATATAATATATATATTTTAGAAA
Found at i:26440 original size:9 final size:9
Alignment explanation
Indices: 26407--26479 Score: 82
Period size: 9 Copynumber: 8.4 Consensus size: 9
26397 CAATTTGAAA
26407 ATTT-ATTT
1 ATTTAATTT
26415 ATTT-ATTT
1 ATTTAATTT
26423 -TTT-ATTT
1 ATTTAATTT
26430 ATTTAATTT
1 ATTTAATTT
26439 ATTTAATTT
1 ATTTAATTT
*
26448 ATTTTATTT
1 ATTTAATTT
*
26457 AATTTATTTT
1 -ATTTAATTT
*
26467 ATTTAATTG
1 ATTTAATTT
26476 ATTT
1 ATTT
26480 TTTGTCATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
7 7 0.12
8 11 0.19
9 32 0.56
10 7 0.12
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.71
Consensus pattern (9 bp):
ATTTAATTT
Found at i:26447 original size:5 final size:4
Alignment explanation
Indices: 26407--26471 Score: 78
Period size: 4 Copynumber: 15.2 Consensus size: 4
26397 CAATTTGAAA
26407 ATTT ATTT ATTT ATTT -TTT ATTT ATTT AATTT ATTT AATTT ATTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT -ATTT A-TTT ATTT
26457 AATTT ATTTT ATTT A
1 -ATTT A-TTT ATTT A
26472 ATTGATTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
3 3 0.05
4 32 0.58
5 20 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:26453 original size:14 final size:14
Alignment explanation
Indices: 26406--26480 Score: 97
Period size: 14 Copynumber: 5.7 Consensus size: 14
26396 TCAATTTGAA
26406 AATTTA-TTTATTT
1 AATTTATTTTATTT
26419 -A-TT-TTTTATTT
1 AATTTATTTTATTT
*
26430 -ATTTAATTTATTT
1 AATTTATTTTATTT
26443 AATTTATTTTATTT
1 AATTTATTTTATTT
26457 AATTTATTTTATTT
1 AATTTATTTTATTT
*
26471 AATTGATTTT
1 AATTTATTTT
26481 TTGTCATTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
11 10 0.18
12 3 0.05
13 7 0.13
14 35 0.64
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (14 bp):
AATTTATTTTATTT
Found at i:26673 original size:10 final size:10
Alignment explanation
Indices: 26660--26691 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
26650 ATTTCTCGGC
26660 ATGTATATAT
1 ATGTATATAT
26670 ATGTATATAT
1 ATGTATATAT
*
26680 ATATATATAT
1 ATGTATATAT
26690 AT
1 AT
26692 CTTTTCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATGTATATAT
Found at i:33176 original size:13 final size:13
Alignment explanation
Indices: 33158--33183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33148 TTTCACATTC
33158 TTCCTTCTATCAA
1 TTCCTTCTATCAA
33171 TTCCTTCTATCAA
1 TTCCTTCTATCAA
33184 GCTAACTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCCTTCTATCAA
Found at i:40801 original size:17 final size:18
Alignment explanation
Indices: 40779--40812 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40769 CCCCCCTTAA
40779 ATTTTAAATATT-TATAC
1 ATTTTAAATATTATATAC
*
40796 ATTTTATATATTATATA
1 ATTTTAAATATTATATA
40813 ATTCTTATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAAATATTATATAC
Found at i:41516 original size:13 final size:13
Alignment explanation
Indices: 41496--41526 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
41486 GTTAATTATC
41496 CAAAAAAACAAAAA
1 CAAAAAAA-AAAAA
41510 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
41523 CAAA
1 CAAA
41527 GCCCGCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:52032 original size:27 final size:27
Alignment explanation
Indices: 51981--52035 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
51971 TATAATTTTA
*
51981 AAAAAAATAAAATTTAGGGACCTAAAC
1 AAAAAAATAAAATTTAGAGACCTAAAC
*
52008 AAAAAAATAATAATTTAGATA-CTAAAC
1 AAAAAAATAA-AATTTAGAGACCTAAAC
52035 A
1 A
52036 TGTAGTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (27 bp):
AAAAAAATAAAATTTAGAGACCTAAAC
Found at i:52778 original size:25 final size:23
Alignment explanation
Indices: 52750--52795 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
52740 TATTACATTC
*
52750 AATATTTATTATGTATTGATATTAA
1 AATATATATTAT-TATT-ATATTAA
*
52775 AATATATCTTATTATTATATT
1 AATATATATTATTATTATATT
52796 TAATATCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 4 0.21
25 10 0.53
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
AATATATATTATTATTATATTAA
Found at i:60331 original size:5 final size:5
Alignment explanation
Indices: 60310--60348 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
60300 AGGTAACTCA
60310 TATTAT TATTAT TATTT TATTT TATTT TATTT T-TTT TAT
1 TATT-T TATT-T TATTT TATTT TATTT TATTT TATTT TAT
60349 ACTTTAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.12
5 18 0.56
6 10 0.31
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:60995 original size:21 final size:21
Alignment explanation
Indices: 60961--61009 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
60951 AAGGAAGTGT
60961 AAAAAAAAAGAG-AAAAAACC
1 AAAAAAAAAGAGAAAAAAACC
* *
60981 AAAAAAGAAGAAGAAAAAAATC
1 AAAAAAAAAG-AGAAAAAAACC
61003 AAAAAAA
1 AAAAAAA
61010 TGAGAGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.38
21 2 0.08
22 13 0.54
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGAGAAAAAAACC
Found at i:61020 original size:22 final size:20
Alignment explanation
Indices: 60961--61023 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 20
60951 AAGGAAGTGT
*
60961 AAAAAAAAAGAGAAAAAA-C
1 AAAAAAAGAGAGAAAAAATC
*
60980 CAAAAAAGAAGAAGAAAAAAATC
1 AAAAAAAG-AG-AG-AAAAAATC
61003 AAAAAAATGAGAGTAAAAAAT
1 AAAAAAA-GAGAG-AAAAAAT
61024 AAGCACATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 2 0.06
22 15 0.43
23 9 0.26
24 1 0.03
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.06
Consensus pattern (20 bp):
AAAAAAAGAGAGAAAAAATC
Found at i:61849 original size:17 final size:16
Alignment explanation
Indices: 61826--61866 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
61816 GAAGTTCTAC
61826 TTTTCTTTCATCTTTA
1 TTTTCTTTCATCTTTA
61842 TATTTC-TT--TCTTTA
1 T-TTTCTTTCATCTTTA
61856 TTTTCTTTCAT
1 TTTTCTTTCAT
61867 TATTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
16 4 0.19
17 4 0.19
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCTTTCATCTTTA
Found at i:61860 original size:13 final size:13
Alignment explanation
Indices: 61836--61876 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
61826 TTTTCTTTCA
61836 TCTTTATATTTCTT
1 TCTTTAT-TTTCTT
61850 TCTTTATTTTCTT
1 TCTTTATTTTCTT
*
61863 TCATTATTTTCTT
1 TCTTTATTTTCTT
61876 T
1 T
61877 TCTAAATGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 19 0.73
14 7 0.27
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (13 bp):
TCTTTATTTTCTT
Found at i:63930 original size:14 final size:14
Alignment explanation
Indices: 63912--63944 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
63902 CATACAGTGT
63912 ATAAAAATA-TACA
1 ATAAAAATATTACA
*
63925 ATTAAAATATTACA
1 ATAAAAATATTACA
63939 ATAAAA
1 ATAAAA
63945 TTTTTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAAATATTACA
Found at i:65151 original size:24 final size:25
Alignment explanation
Indices: 65116--65166 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
65106 ACTAATATGT
*
65116 CATTTTTCAAAAATTACGAAAATAG
1 CATTTTTCAAAAATTACAAAAATAG
*
65141 CATTTTT-AAAATTTACAAAAATAG
1 CATTTTTCAAAAATTACAAAAATAG
65165 CA
1 CA
65167 CCTTTTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (25 bp):
CATTTTTCAAAAATTACAAAAATAG
Found at i:65245 original size:14 final size:14
Alignment explanation
Indices: 65226--65255 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
65216 AAATATCACT
65226 CGATCAACGGTTAA
1 CGATCAACGGTTAA
65240 CGATCAACGGTTAA
1 CGATCAACGGTTAA
65254 CG
1 CG
65256 GGTCAGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (14 bp):
CGATCAACGGTTAA
Found at i:67722 original size:16 final size:16
Alignment explanation
Indices: 67679--67712 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
67669 AGGAAAATGG
67679 TAAAAAATAGTAAATAAA
1 TAAAAAATA--AAATAAA
67697 TAAAAAATAAAATAAA
1 TAAAAAATAAAATAAA
67713 AAGAAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
TAAAAAATAAAATAAA
Found at i:69063 original size:14 final size:14
Alignment explanation
Indices: 69044--69074 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
69034 TGATTGTCCT
69044 CAAGCAATGGATAA
1 CAAGCAATGGATAA
69058 CAAGCAATGGATAA
1 CAAGCAATGGATAA
69072 CAA
1 CAA
69075 TTAACACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (14 bp):
CAAGCAATGGATAA
Found at i:70568 original size:15 final size:15
Alignment explanation
Indices: 70535--70577 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
70525 AAAATAATAT
* *
70535 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
70550 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
70564 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
70578 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:73777 original size:23 final size:23
Alignment explanation
Indices: 73733--73781 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
73723 ATAAAGAACC
*
73733 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
73756 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
73779 AAA
1 AAA
73782 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:78416 original size:14 final size:14
Alignment explanation
Indices: 78398--78430 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
78388 CATACAGTGT
78398 ATAAAAATA-TACA
1 ATAAAAATATTACA
*
78411 ATTAAAATATTACA
1 ATAAAAATATTACA
78425 ATAAAA
1 ATAAAA
78431 TTTTGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAAATATTACA
Found at i:79626 original size:27 final size:30
Alignment explanation
Indices: 79594--79666 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 30
79584 TTTTCAATAT
*
79594 ATTTACTAAAAT-GTCATTTTT-TTC-AAAA
1 ATTTACAAAAATAG-CATTTTTCTTCTAAAA
*
79622 A-TTACGAAAATAGCATTTTTCTTCTAAAA
1 ATTTACAAAAATAGCATTTTTCTTCTAAAA
79651 ATTTACAAAAATAGCA
1 ATTTACAAAAATAGCA
79667 CCCTTTTCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 16 0.41
28 5 0.13
29 5 0.13
30 13 0.33
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.38
Consensus pattern (30 bp):
ATTTACAAAAATAGCATTTTTCTTCTAAAA
Found at i:79664 original size:30 final size:28
Alignment explanation
Indices: 79584--79666 Score: 89
Period size: 27 Copynumber: 2.9 Consensus size: 28
79574 TATAGCACCA
* *
79584 TTTTCAATATATTTACTAAAAT-GTCATTT
1 TTTTCAA-AAATTTACAAAAATAG-CATTT
*
79613 TTTTCAAAAA-TTACGAAAATAGCATTT
1 TTTTCAAAAATTTACAAAAATAGCATTT
79640 TTCTTCTAAAAATTTACAAAAATAGCA
1 TT-TTC-AAAAATTTACAAAAATAGCA
79667 CCCTTTTCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
27 16 0.34
28 6 0.13
29 12 0.26
30 13 0.28
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (28 bp):
TTTTCAAAAATTTACAAAAATAGCATTT
Found at i:79768 original size:23 final size:23
Alignment explanation
Indices: 79742--79785 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
79732 AACGGTTAAC
79742 GGTCAACG-GGTAGGGTCGGGTTG
1 GGTCAACGAGGTA-GGTCGGGTTG
*
79765 GGTCAACGAGTTAGGTCGGGT
1 GGTCAACGAGGTAGGTCGGGT
79786 CAATGGGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.16, C:0.14, G:0.48, T:0.23
Consensus pattern (23 bp):
GGTCAACGAGGTAGGTCGGGTTG
Found at i:79799 original size:18 final size:18
Alignment explanation
Indices: 79754--79801 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
79744 TCAACGGGTA
*
79754 GGGTCGGGTTGGGTCAAC
1 GGGTCGGGTCGGGTCAAC
* ** *
79772 GAGTTAGGTCGGGTCAAT
1 GGGTCGGGTCGGGTCAAC
79790 GGGTCGGGTCGG
1 GGGTCGGGTCGG
79802 AACCGGTCAA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.15, G:0.50, T:0.23
Consensus pattern (18 bp):
GGGTCGGGTCGGGTCAAC
Found at i:82630 original size:23 final size:22
Alignment explanation
Indices: 82600--82643 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
82590 AAATGATCAC
* *
82600 AATTAATATCAATTTAAAATTAA
1 AATTAATACCAA-TAAAAATTAA
82623 AATTAATACCAATAAAAATTA
1 AATTAATACCAATAAAAATTA
82644 GGTGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
AATTAATACCAATAAAAATTAA
Found at i:84598 original size:42 final size:42
Alignment explanation
Indices: 84547--84854 Score: 508
Period size: 42 Copynumber: 7.3 Consensus size: 42
84537 CATATTCGCA
*
84547 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* *
84589 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
84631 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
84673 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
84715 TTGCGATAGTCCAAGTTCGTGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* *
84757 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
84799 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* *
84841 TTACGATAATCCAA
1 TTGCGATAGTCCAA
84855 AATCGTAACG
Statistics
Matches: 246, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 246 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:84641 original size:84 final size:84
Alignment explanation
Indices: 84547--84848 Score: 559
Period size: 84 Copynumber: 3.6 Consensus size: 84
84537 CATATTCGCA
*
84547 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTTGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
84612 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATTCG
*
84631 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTTGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
84696 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATTCG
*
84715 TTGCGATAGTCCAAGTTCGTGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
84780 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATTCG
* *
84799 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAGTTCGTTACGATA
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATA
84849 ATCCAAAATC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 211 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATTCG
Found at i:84930 original size:6 final size:6
Alignment explanation
Indices: 84919--84956 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
84909 TATTCGCACG
84919 GACCAC GACCAC GACCAC GACCAC GACCAC GA-CAC GAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GAC
84957 TCGAGACGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.34, C:0.47, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:85643 original size:21 final size:21
Alignment explanation
Indices: 85591--85756 Score: 185
Period size: 21 Copynumber: 7.9 Consensus size: 21
85581 CGTTGCGATT
*
85591 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
* *
85610 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
**
85633 TTGGACTATCGCAATTAGATA-
1 TTGGACTATCGCAATGCGA-AC
* *
85654 GTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
85675 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
85696 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
85717 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
* *
85738 TTCGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
85757 TTTACATATT
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 6 0.05
20 1 0.01
21 105 0.85
22 1 0.01
23 10 0.08
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:85791 original size:21 final size:21
Alignment explanation
Indices: 85765--85953 Score: 201
Period size: 21 Copynumber: 9.1 Consensus size: 21
85755 GATTTACATA
* *
85765 TTCGCATTACGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
85786 TTCGCATTGCGATAGCCCAAG
1 TTCGCATTGCGATAGTCCAAG
85807 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
85828 TTCGCAATGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
85848 TATCGCATTGCGAT-TTAC-A-
1 T-TCGCATTGCGATAGTCCAAG
* * *
85867 TATCGCATTTCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
85888 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
85909 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
85930 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
85951 TTC
1 TTC
85954 ACGTTACGAA
Statistics
Matches: 147, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.12
20 17 0.12
21 113 0.77
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:85894 original size:20 final size:19
Alignment explanation
Indices: 85848--85900 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
85838 GATAGTCGAC
85848 TATCGCATTGCGATTTACA
1 TATCGCATTGCGATTTACA
*
85867 TATCGCATTTCGATTTACA
1 TATCGCATTGCGATTTACA
85886 TATTCGCATTGCGAT
1 TA-TCGCATTGCGAT
85901 AGTCGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (19 bp):
TATCGCATTGCGATTTACA
Found at i:94209 original size:8 final size:8
Alignment explanation
Indices: 94196--94229 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
94186 TTTCTTTTCG
94196 TTTATTTT
1 TTTATTTT
94204 TTTATTTT
1 TTTATTTT
94212 TTTATTTT
1 TTTATTTT
94220 TTTATTTT
1 TTTATTTT
94228 TT
1 TT
94230 CCTTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:94260 original size:14 final size:14
Alignment explanation
Indices: 94237--94266 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
94227 TTTCCTTTAA
*
94237 TTTATTTAATATTT
1 TTTATCTAATATTT
94251 TTTATCTAATATTT
1 TTTATCTAATATTT
94265 TT
1 TT
94267 GACTTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATCTAATATTT
Found at i:94336 original size:13 final size:13
Alignment explanation
Indices: 94318--94347 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
94308 TGAATCGGGT
94318 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
94331 TTTTAATTTTTAA
1 TTTTAAATTTTAA
94344 TTTT
1 TTTT
94348 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:97347 original size:35 final size:34
Alignment explanation
Indices: 97262--97347 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 34
97252 CCAATCATAA
*
97262 CAAAAAGAGGAAAAAAAGAAAAACAAAGAAAAAG
1 CAAAAAGAGAAAAAAAAGAAAAACAAAGAAAAAG
* * *
97296 CAAAGAGAAAATAAAAAAGAGAAACAAA-AACAAAG
1 CAAAAAGAGAA-AAAAAAGAAAAACAAAGAA-AAAG
* *
97331 GAAAAAGAGAAGAAAAA
1 CAAAAAGAGAAAAAAAA
97348 TGATAAGATG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 15 0.36
35 27 0.64
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (34 bp):
CAAAAAGAGAAAAAAAAGAAAAACAAAGAAAAAG
Found at i:97868 original size:37 final size:36
Alignment explanation
Indices: 97793--97868 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
97783 TTTTTATATT
*
97793 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
97829 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
97866 TTT
1 TTT
97869 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:100395 original size:40 final size:40
Alignment explanation
Indices: 100322--100401 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
100312 GTAGGAGTCA
* * *
100322 AATATTGCACAGTAGTGCTGAGGTTGAGCCTTGCTCACCT
1 AATAATGCACAGTAGTGCTGAGGTCGAGCCTTGCCCACCT
* * *
100362 AATAATGCACTGTAGTGCTGAGGTCGGGTCTTGCCCACCT
1 AATAATGCACAGTAGTGCTGAGGTCGAGCCTTGCCCACCT
100402 GGTAGAGGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (40 bp):
AATAATGCACAGTAGTGCTGAGGTCGAGCCTTGCCCACCT
Found at i:107447 original size:31 final size:33
Alignment explanation
Indices: 107400--107478 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
107390 TTTAAAAAGT
*
107400 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAATAATATTTATATAAA
*
107432 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
107466 TATTATTTATTTA
1 TATTATTTTTTTA
107479 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:109228 original size:21 final size:21
Alignment explanation
Indices: 109198--109245 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
109188 GCAGGGGTAC
* *
109198 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
109219 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
109240 ATGCCA
1 ATGCCA
109246 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:109292 original size:63 final size:63
Alignment explanation
Indices: 109219--109355 Score: 154
Period size: 63 Copynumber: 2.2 Consensus size: 63
109209 TCCACTTCAT
* * * * *
109219 ATGCCAAGCCCACCAGTTTATATGCC-ATCTCCG-CAGGGTTACATTCCGAGCCCG-CAGGGTTA
1 ATGCCTAGCCCACCAGGTTACATGCCTAGC-CCGCCA-GGTTACATGCCGAGCCCGCCA-GGTTA
109281 C
63 C
* * *
109282 ATTCCTAGCCCGCCAGGTTACATGCCTAGCCCGCCAGGTTACATGCCTAGCCCGCCAGGTTAC
1 ATGCCTAGCCCACCAGGTTACATGCCTAGCCCGCCAGGTTACATGCCGAGCCCGCCAGGTTAC
109345 ATGCCTAGCCC
1 ATGCCTAGCCC
109356 GCAGGGTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
63 56 0.90
64 6 0.10
ACGTcount: A:0.20, C:0.36, G:0.22, T:0.21
Consensus pattern (63 bp):
ATGCCTAGCCCACCAGGTTACATGCCTAGCCCGCCAGGTTACATGCCGAGCCCGCCAGGTTAC
Found at i:109363 original size:21 final size:21
Alignment explanation
Indices: 109255--109357 Score: 163
Period size: 21 Copynumber: 4.9 Consensus size: 21
109245 ATCTCCGCAG
* *
109255 GGTTACATTCCGAGCCCG-CA
1 GGTTACATGCCTAGCCCGCCA
*
109275 GGGTTACATTCCTAGCCCGCCA
1 -GGTTACATGCCTAGCCCGCCA
109297 GGTTACATGCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
109318 GGTTACATGCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
109339 GGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
109358 AGGGTTTTAT
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
21 77 0.97
22 2 0.03
ACGTcount: A:0.18, C:0.37, G:0.24, T:0.20
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:109950 original size:27 final size:28
Alignment explanation
Indices: 109883--109976 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
109873 GATAAATGTT
* *
109883 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
109911 TTTAAAATAAAAATAATATTATTC-AAA
1 TTTAAAATAAAAATAATATTATTCGAAA
*
109938 TTTAAATTTAAAATATAAATTATAGTATTCGAAA
1 TTTAAA-ATAAAA-AT-AA-TAT--TATTCGAAA
109972 TTTAA
1 TTTAA
109977 CATTAAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
27 9 0.16
28 27 0.48
29 2 0.04
30 2 0.04
31 3 0.05
33 5 0.09
34 8 0.14
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCGAAA
Found at i:110589 original size:126 final size:126
Alignment explanation
Indices: 110364--111220 Score: 1651
Period size: 126 Copynumber: 6.8 Consensus size: 126
110354 TTTAAGTTAT
* *
110364 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGACAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
110429 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
110490 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATAGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
110555 GCGCCCTCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
110616 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
110681 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
* *
110742 TCCCCGAGGGACATGAGTGACATGATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
110807 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
110868 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
110933 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
110994 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
111059 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
111120 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
111185 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
111221 CCGATTATAG
Statistics
Matches: 719, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 719 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:111301 original size:8 final size:8
Alignment explanation
Indices: 111288--111328 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
111278 TCACAATCTT
111288 TCAAATTC
1 TCAAATTC
111296 TCAAATTC
1 TCAAATTC
* *
111304 CCAAACTC
1 TCAAATTC
111312 T-AAATTC
1 TCAAATTC
111319 TCAAATTC
1 TCAAATTC
111327 TC
1 TC
111329 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:114343 original size:13 final size:13
Alignment explanation
Indices: 114324--114360 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
114314 ATACATAAAT
*
114324 ATATTTAATATAT
1 ATATTTAATATAA
*
114337 TTATTTAATATAA
1 ATATTTAATATAA
114350 ATATTTAATAT
1 ATATTTAATAT
114361 TATTAGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTTAATATAA
Found at i:116459 original size:42 final size:42
Alignment explanation
Indices: 116409--116566 Score: 164
Period size: 41 Copynumber: 3.8 Consensus size: 42
116399 AAAATGATAC
*
116409 TTTAGCGGCGTTTTTTAAACAAACACCATAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTAAACAAACACCGTAATAGAGTGGTAA
* ** *
116451 TTTAGCGGCG-TTTATAGCTCAAACGA-CGTAATAGAGTTGT--
1 TTTAGCGGCGTTTTTTA-AACAAAC-ACCGTAATAGAGTGGTAA
* * *
116491 TTATAGTGGCGTTTTTTCAACAAACACCGTAATAGAGTGATAA
1 TT-TAGCGGCGTTTTTTAAACAAACACCGTAATAGAGTGGTAA
* *
116534 TTTAGCGGC-TTTTTTATACAAACACCGTGATAG
1 TTTAGCGGCGTTTTTTAAACAAACACCGTAATAG
116567 TGTTGTTTAT
Statistics
Matches: 93, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
40 3 0.03
41 50 0.54
42 37 0.40
43 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTAAACAAACACCGTAATAGAGTGGTAA
Found at i:116951 original size:40 final size:41
Alignment explanation
Indices: 116905--116989 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 41
116895 CAAACGCCAC
* * *
116905 AATATCCATG-TACTTTAGCGGCGTTTGT-AAAAAACGTCGT
1 AATATCCATGAT-CTTTAGCGCCGTATATAAAAAAACGTCGT
*
116945 AATATCCATGATCTTTAGTGCCGTATATAAAAAAACGTCGT
1 AATATCCATGATCTTTAGCGCCGTATATAAAAAAACGTCGT
116986 AATA
1 AATA
116990 GTTTTGTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
40 22 0.56
41 17 0.44
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
AATATCCATGATCTTTAGCGCCGTATATAAAAAAACGTCGT
Found at i:117062 original size:43 final size:43
Alignment explanation
Indices: 116983--117064 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
116973 AAAAAAACGT
* **
116983 CGTAATAGTTTTGTCATTTAGTGGTGTTTCTTTAATAAAAAGG
1 CGTAATAGTTTTGTCATTTAGGGGCATTTCTTTAATAAAAAGG
* *
117026 CGTAGTAGTTTTGTCCTTTAGGGGCATTT-TTGTAATAAA
1 CGTAATAGTTTTGTCATTTAGGGGCATTTCTT-TAATAAA
117065 CGCCACAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 31 0.94
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.44
Consensus pattern (43 bp):
CGTAATAGTTTTGTCATTTAGGGGCATTTCTTTAATAAAAAGG
Found at i:119972 original size:21 final size:21
Alignment explanation
Indices: 119890--119972 Score: 53
Period size: 21 Copynumber: 4.0 Consensus size: 21
119880 GCTAACTTGA
119890 AAGCAGA-AAATGAAGCAAG-GG
1 AAGCAGAGAAA-GAAGC-AGCGG
* * **
119911 AAGCAGAGAGAGAAACAGTAG
1 AAGCAGAGAAAGAAGCAGCGG
** * * *
119932 AAGCAGCTAGAGCAGTAGCGG
1 AAGCAGAGAAAGAAGCAGCGG
119953 AAGCAGAGAAAGAAGCAGCG
1 AAGCAGAGAAAGAAGCAGCG
119973 ACAACACATA
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.47, C:0.13, G:0.35, T:0.05
Consensus pattern (21 bp):
AAGCAGAGAAAGAAGCAGCGG
Found at i:120014 original size:21 final size:21
Alignment explanation
Indices: 119954--120027 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
119944 CAGTAGCGGA
* *
119954 AGCAGAGAAAGAAGCAGCGAC
1 AGCACAGAGAGAAGCAGCGAC
* * * *
119975 AACACATAGAGATGTAGCGAC
1 AGCACAGAGAGAAGCAGCGAC
*
119996 AGCACAGAGAGAAGCAGCGTC
1 AGCACAGAGAGAAGCAGCGAC
120017 AGCACAGAGAG
1 AGCACAGAGAG
120028 GCAACATATC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.43, C:0.20, G:0.31, T:0.05
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGCGAC
Found at i:120513 original size:43 final size:43
Alignment explanation
Indices: 120444--120653 Score: 201
Period size: 43 Copynumber: 4.9 Consensus size: 43
120434 TATTTTTAGC
* * *
120444 AAAAACACCGCAAAACATTAATACCTACTGCGGCGTTTGTCAG
1 AAAAACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGTCAG
* *
120487 AAAAACGCCGCAAAACATCAAAACCTACTGCGACGTTTGT-GG
1 AAAAACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGTCAG
* * * *
120529 AAAAAATGCCG-ATAAACATCAACACCTACTACGGCGTTT-TAGAG
1 -AAAAACGCCGCA-AAACATCAAAACCTACTGCGGCGTTTGT-CAG
* * * * * *
120573 AAAAACGCCGCTAAACATCATAACCTATTACGGCATTTGTCAT
1 AAAAACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGTCAG
* * * *
120616 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
1 AAAAACGCCGCAAAACATCAAAACCTACTGCGGCGTTT
120654 TGCTAAATAT
Statistics
Matches: 138, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
42 3 0.02
43 133 0.96
44 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (43 bp):
AAAAACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGTCAG
Found at i:120612 original size:86 final size:85
Alignment explanation
Indices: 120456--120654 Score: 229
Period size: 86 Copynumber: 2.3 Consensus size: 85
120446 AAACACCGCA
* * *
120456 AAACATTAATACCTACTGCGGCGTTTGTCAGAAAAACGCCGCAAAACATCAAAACCTACTGCGAC
1 AAACATCAACACCTACTGCGGCGTTT-TCAGAAAAACGCCGCAAAACATCAAAACCTACTACGAC
* * *
120521 GTTTGTGGA-AAAAATGCCGAT
65 ATTTGT-CATAAAAACGCCGAT
* * * * * *
120542 AAACATCAACACCTACTACGGCGTTTTAGAGAAAAACGCCGCTAAACATCATAACCTATTACGGC
1 AAACATCAACACCTACTGCGGCGTTTT-CAGAAAAACGCCGCAAAACATCAAAACCTACTACGAC
*
120607 ATTTGTCATAAAAACGCCGCT
65 ATTTGTCATAAAAACGCCGAT
* *
120628 AAATATCAACACCTATTGCGGCGTTTT
1 AAACATCAACACCTACTGCGGCGTTTT
120655 GCTAAATATC
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
85 2 0.02
86 93 0.98
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (85 bp):
AAACATCAACACCTACTGCGGCGTTTTCAGAAAAACGCCGCAAAACATCAAAACCTACTACGACA
TTTGTCATAAAAACGCCGAT
Found at i:120661 original size:30 final size:30
Alignment explanation
Indices: 120625--120683 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
120615 TAAAAACGCC
120625 GCTAAATATCAACACCTATTGCGGCGTTTT
1 GCTAAATATCAACACCTATTGCGGCGTTTT
120655 GCTAAATATCAACACCTATTGCGGCGTTT
1 GCTAAATATCAACACCTATTGCGGCGTTT
120684 GTGTGACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (30 bp):
GCTAAATATCAACACCTATTGCGGCGTTTT
Found at i:120716 original size:43 final size:43
Alignment explanation
Indices: 120655--120765 Score: 168
Period size: 43 Copynumber: 2.6 Consensus size: 43
120645 GCGGCGTTTT
* ***
120655 GCTAAATATCAACACCTATTGCGGCGTTTGTGTGACAAACGCC
1 GCTAAATATCAACACCTATTGCGGCGATTGTCACACAAACGCC
120698 GCTAAATATCAACACCTATTGCGGCGATTGTCACACAAACGCC
1 GCTAAATATCAACACCTATTGCGGCGATTGTCACACAAACGCC
**
120741 GCTAAATATCATTACCTATTGCGGC
1 GCTAAATATCAACACCTATTGCGGC
120766 ATATTTTGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
GCTAAATATCAACACCTATTGCGGCGATTGTCACACAAACGCC
Found at i:120750 original size:116 final size:116
Alignment explanation
Indices: 120541--120765 Score: 303
Period size: 116 Copynumber: 1.9 Consensus size: 116
120531 AAAATGCCGA
120541 TAAACATCAACACCTACTACGGCGTTTTAGAGAAAAACGCCGCTAAACATCATAACCTATTACGG
1 TAAACATCAACACCTACTACGGCGTTTTAGAGAAAAACGCCGCTAAACATCATAACCTATTACGG
*
120606 CATTTGTCATAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTGC
66 CATTTGTCACAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTGC
* * * * * * *
120657 TAAATATCAACACCTATTGCGGCGTTTGT-GTGACAAACGCCGCTAAATATCA-ACACCTATTGC
1 TAAACATCAACACCTACTACGGCGTTT-TAGAGAAAAACGCCGCTAAACATCATA-ACCTATTAC
* **
120720 GGCGA-TTGTCACACAAACGCCGCTAAATATCATTACCTATTGCGGC
64 GGC-ATTTGTCACAAAAACGCCGCTAAATATCAACACCTATTGCGGC
120766 ATATTTTGTT
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
115 1 0.01
116 92 0.97
117 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (116 bp):
TAAACATCAACACCTACTACGGCGTTTTAGAGAAAAACGCCGCTAAACATCATAACCTATTACGG
CATTTGTCACAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTGC
Found at i:120951 original size:14 final size:14
Alignment explanation
Indices: 120934--120967 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
120924 ATGACTAATA
*
120934 ATTAGTTTTGAAGC
1 ATTAGTTTTGAAAC
120948 ATTAGTTTTGAAAC
1 ATTAGTTTTGAAAC
120962 ATTAGT
1 ATTAGT
120968 AGAAACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (14 bp):
ATTAGTTTTGAAAC
Found at i:129549 original size:20 final size:20
Alignment explanation
Indices: 129520--129558 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
129510 TTTCCACCAC
*
129520 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
129540 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
129559 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:139822 original size:23 final size:27
Alignment explanation
Indices: 139792--139875 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 27
139782 CAGTGATGAC
139792 TGATTCAGCA-A-AA-CA-ATGCTGAA
1 TGATTCAGCATAGAAGCACATGCTGAA
* *
139815 TGATTCAGCATAGAAGTACATTCTGAA
1 TGATTCAGCATAGAAGCACATGCTGAA
* * *
139842 TGATTCAGCACAGAAGTACATTCTGAA
1 TGATTCAGCATAGAAGCACATGCTGAA
139869 TGATTCA
1 TGATTCA
139876 AAGCCATTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
23 10 0.19
24 1 0.02
25 2 0.04
26 1 0.02
27 40 0.74
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (27 bp):
TGATTCAGCATAGAAGCACATGCTGAA
Found at i:139840 original size:27 final size:27
Alignment explanation
Indices: 139810--139875 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
139800 CAAAACAATG
*
139810 CTGAATGATTCAGCATAGAAGTACATT
1 CTGAATGATTCAGCACAGAAGTACATT
139837 CTGAATGATTCAGCACAGAAGTACATT
1 CTGAATGATTCAGCACAGAAGTACATT
139864 CTGAATGATTCA
1 CTGAATGATTCA
139876 AAGCCATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (27 bp):
CTGAATGATTCAGCACAGAAGTACATT
Found at i:139966 original size:15 final size:16
Alignment explanation
Indices: 139928--139968 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
139918 ACAGAGCCTC
*
139928 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
139944 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
139960 T-AATCATTC
1 TGAATCATTC
139969 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:142319 original size:26 final size:26
Alignment explanation
Indices: 142281--142330 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
142271 AAGGAAAAAG
142281 TCAATGATAAATGAAATAA-TCAACGA
1 TCAATGATAAATGAAA-AAGTCAACGA
142307 TCAATGACT-AATGAAAAAGTCAAC
1 TCAATGA-TAAATGAAAAAGTCAAC
142331 AAGTTGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.09
26 19 0.86
27 1 0.05
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (26 bp):
TCAATGATAAATGAAAAAGTCAACGA
Found at i:145151 original size:30 final size:30
Alignment explanation
Indices: 145115--145217 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
145105 TCCGAAGGAC
145115 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
145145 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
145175 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
145205 CTGTCCATAGGTC
1 CTATCCAGAGGTC
145218 CCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:145234 original size:30 final size:30
Alignment explanation
Indices: 145191--145284 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
145181 AGAGGTCATA
* * *
145191 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
145221 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
145252 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
145283 AA
1 AA
145285 AGACATAGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:145234 original size:60 final size:61
Alignment explanation
Indices: 145115--145242 Score: 186
Period size: 60 Copynumber: 2.1 Consensus size: 61
145105 TCCGAAGGAC
* * *
145115 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * * *
145175 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
145236 CTATCCA
1 CTATCCA
145243 TATGTTCCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
60 51 0.85
61 9 0.15
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:145291 original size:31 final size:30
Alignment explanation
Indices: 145200--145295 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
145190 AAAGATCCTC
* * *
145200 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
145230 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
145261 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
145292 GGTA
1 GGTA
145296 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:146423 original size:21 final size:21
Alignment explanation
Indices: 146399--146441 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
146389 TCATATTCGT
* *
146399 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
146420 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
146441 T
1 T
146442 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:149810 original size:30 final size:30
Alignment explanation
Indices: 149774--149871 Score: 196
Period size: 30 Copynumber: 3.3 Consensus size: 30
149764 TCCGAAGGAC
149774 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
149804 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
149834 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
149864 CTATCCAG
1 CTATCCAG
149872 TCCCGAAGAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:151020 original size:19 final size:20
Alignment explanation
Indices: 150983--151020 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
150973 TTTTTCATTA
*
150983 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
151003 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
151021 TCTAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:154457 original size:30 final size:30
Alignment explanation
Indices: 154421--154545 Score: 250
Period size: 30 Copynumber: 4.2 Consensus size: 30
154411 TCCGAAGGAC
154421 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
154451 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
154481 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
154511 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
154541 CTATC
1 CTATC
154546 TAGTCCCGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 95 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:155701 original size:19 final size:20
Alignment explanation
Indices: 155664--155701 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
155654 TTTTTCATTA
*
155664 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
155684 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
155702 TCTAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:155753 original size:21 final size:21
Alignment explanation
Indices: 155729--155771 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
155719 TCATATTCGA
* *
155729 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
155750 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
155771 T
1 T
155772 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:157628 original size:29 final size:29
Alignment explanation
Indices: 157545--157621 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
157535 TAGAACGAAT
* * *
157545 ATATAATCTTATGCAGAATCAGAACATGG
1 ATATAATCTCATGCAGAATCAGGACATGA
157574 ATATAATC-CAATGCAGAATCAGGACATGA
1 ATATAATCTC-ATGCAGAATCAGGACATGA
157603 ATATAATCTCATGCAGAAT
1 ATATAATCTCATGCAGAAT
157622 GGGGACAAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 42 0.98
30 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (29 bp):
ATATAATCTCATGCAGAATCAGGACATGA
Found at i:158689 original size:14 final size:14
Alignment explanation
Indices: 158670--158705 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
158660 ATCATTAACT
158670 TTGACTTATGACT-A
1 TTGACTT-TGACTCA
158684 TTGACTTTGACTCA
1 TTGACTTTGACTCA
158698 TTGACTTT
1 TTGACTTT
158706 TTTGAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (14 bp):
TTGACTTTGACTCA
Found at i:159237 original size:10 final size:10
Alignment explanation
Indices: 159222--159266 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
159212 TGTCGAAGCA
159222 TTTTTTTTA-
1 TTTTTTTTAT
159231 TTTTTTTTAT
1 TTTTTTTTAT
*
159241 ATTTTTTTAT
1 TTTTTTTTAT
* *
159251 ATTTTTATAT
1 TTTTTTTTAT
159261 TTTTTT
1 TTTTTT
159267 CAGTGTGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 9 0.28
10 23 0.72
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:159247 original size:18 final size:19
Alignment explanation
Indices: 159221--159266 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
159211 ATGTCGAAGC
*
159221 ATTTTTTTTAT-TTTTTTT
1 ATTTTTTTTATATTTTTAT
159239 ATATTTTTTTATATTTTTAT
1 AT-TTTTTTTATATTTTTAT
159259 ATTTTTTT
1 ATTTTTTT
159267 CAGTGTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
20 8 0.32
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (19 bp):
ATTTTTTTTATATTTTTAT
Found at i:164711 original size:11 final size:12
Alignment explanation
Indices: 164692--164716 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
164682 TGGAGGAAAA
164692 AGAAAAAAAGGT
1 AGAAAAAAAGGT
164704 AGAAAAAAAGGT
1 AGAAAAAAAGGT
164716 A
1 A
164717 TTTAAAATAC
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:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (12 bp):
AGAAAAAAAGGT
Found at i:168030 original size:2 final size:2
Alignment explanation
Indices: 168025--168064 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
168015 ATCATAACCC
168025 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
168065 GCAGGTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168172 original size:16 final size:16
Alignment explanation
Indices: 168151--168181 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
168141 ATAAATAAAT
168151 GAACATAAACGAACAC
1 GAACATAAACGAACAC
168167 GAACATAAACGAACA
1 GAACATAAACGAACA
168182 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:168276 original size:16 final size:16
Alignment explanation
Indices: 168251--168315 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
168241 TAATAAATAA
*
168251 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
*
168267 ACGGACATAAACAAAC
1 ACGAACATAAACAAAC
**
168283 ACGAACATAAATGAAC
1 ACGAACATAAACAAAC
168299 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
168315 A
1 A
168316 TAAACGTTGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:168287 original size:32 final size:32
Alignment explanation
Indices: 168251--168315 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
168241 TAATAAATAA
*
168251 ACGAACATAAACGAACACGGACATAAACAAAC
1 ACGAACATAAACGAACACGAACATAAACAAAC
*
168283 ACGAACATAAATGAACACGAACATAAACAAAC
1 ACGAACATAAACGAACACGAACATAAACAAAC
168315 A
1 A
168316 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (32 bp):
ACGAACATAAACGAACACGAACATAAACAAAC
Found at i:168537 original size:12 final size:11
Alignment explanation
Indices: 168514--168561 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 11
168504 TTAAGATCTT
*
168514 GATTCAAGCTC
1 GATTCGAGCTC
168525 GATTCTGAGCTC
1 GATTC-GAGCTC
*
168537 GATTCAAGCTC
1 GATTCGAGCTC
168548 GATTCCGAGCTC
1 GATT-CGAGCTC
168560 GA
1 GA
168562 CATTGCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 14 0.44
12 18 0.56
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (11 bp):
GATTCGAGCTC
Found at i:168540 original size:23 final size:23
Alignment explanation
Indices: 168514--168561 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
168504 TTAAGATCTT
*
168514 GATTCAAGCTCGATTCTGAGCTC
1 GATTCAAGCTCGATTCCGAGCTC
168537 GATTCAAGCTCGATTCCGAGCTC
1 GATTCAAGCTCGATTCCGAGCTC
168560 GA
1 GA
168562 CATTGCTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
GATTCAAGCTCGATTCCGAGCTC
Found at i:168546 original size:11 final size:11
Alignment explanation
Indices: 168514--168552 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
168504 TTAAGATCTT
168514 GATTCAAGCTC
1 GATTCAAGCTC
*
168525 GATTCTGAGCTC
1 GATTC-AAGCTC
168537 GATTCAAGCTC
1 GATTCAAGCTC
168548 GATTC
1 GATTC
168553 CGAGCTCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (11 bp):
GATTCAAGCTC
Found at i:169451 original size:14 final size:14
Alignment explanation
Indices: 169434--169476 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
169424 GAACATAAAT
169434 GAACATAACCGAAC
1 GAACATAACCGAAC
169448 GAACATAACCGAAC
1 GAACATAACCGAAC
169462 GAACATAACCGAAC
1 GAACATAACCGAAC
169476 G
1 G
169477 TTCACAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.49, C:0.28, G:0.16, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:175319 original size:5 final size:5
Alignment explanation
Indices: 175309--175337 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
175299 AGAAGAATAT
175309 GAAGA GAAGA GAAGA GAAGA GAAGA GAAG
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAG
175338 GGGTGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:175627 original size:2 final size:2
Alignment explanation
Indices: 175620--175674 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
175610 CCATTCGGAT
175620 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
175662 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
175675 TCTTTTATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:186568 original size:3 final size:3
Alignment explanation
Indices: 186553--186612 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
186543 ATTTCAATAT
*
186553 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
186601 TTC TATA TTA TT
1 TTA T-TA TTA TT
186613 CTTGAATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 50 0.96
4 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:187656 original size:46 final size:46
Alignment explanation
Indices: 187606--187907 Score: 453
Period size: 46 Copynumber: 6.6 Consensus size: 46
187596 TTTATACCGT
* * *
187606 TAATGCACTGTTATACATTTTCATTTGTGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * **
187652 TAATGCACCGTTATGCATTTTCATTTGTGGCATCATTTCATATCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
187698 TAAAT-CACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
1 T-AATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
187744 TAATACACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
187790 TAATGCACCGTTATGAATTTTCATTTATGGCATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
187836 TAATGCACCGTTATACATTTTCATTTATGGCATTCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
187882 TAATGCACCGTTATGCATTTTAATTT
1 TAATGCACCGTTATGCATTTTCATTT
187908 GTTCATTCAT
Statistics
Matches: 233, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 3 0.01
46 227 0.97
47 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.41
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
Found at i:194544 original size:46 final size:46
Alignment explanation
Indices: 194494--194749 Score: 413
Period size: 46 Copynumber: 5.6 Consensus size: 46
194484 TTTATGTTGT
* *
194494 TAATGCACAGTTACGCATTTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * *
194540 TAATGCACCATTATGCATTTTCATTTGTGGGATCATTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
194586 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTACATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
194632 TAATGAACCGTTATACATTTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
194678 TAATGCACTGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
194724 TAATGCACCGTTATGCATTTTCATTT
1 TAATGCACCGTTATGCATTTTCATTT
194750 GTTCATTCAT
Statistics
Matches: 191, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 191 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.39
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
Found at i:195652 original size:46 final size:46
Alignment explanation
Indices: 195590--195866 Score: 405
Period size: 46 Copynumber: 6.0 Consensus size: 46
195580 AATACCGTGA
* * * *
195590 GTGGCA-CCTTTTATGCCGTTAATGCACAGTTATACATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
195635 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
* * *
195681 GTGGGATCATTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
* * *
195727 ATGGCATCCTTACATGCCGATAATG-ATCCGTTATTCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCA-CCGTTATGCATTTTCATTT
* * *
195773 ATGGCATCCTTTCATGCCGATAATGCACCGTTGTACATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
*
195819 ATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
195865 GT
1 GT
195867 TCATTCATTT
Statistics
Matches: 210, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
45 7 0.03
46 202 0.96
47 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (46 bp):
GTGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
Found at i:195786 original size:23 final size:23
Alignment explanation
Indices: 195760--195833 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
195750 TGATCCGTTA
195760 TTCATTTTCATTTATGGCATCCT
1 TTCATTTTCATTTATGGCATCCT
** *
195783 TTCA-TGCCGA-TAAT-GCA-CCGT
1 TTCATTTTC-ATTTATGGCATCC-T
195804 TGTACATTTTCATTTATGGCATCCT
1 T-T-CATTTTCATTTATGGCATCCT
195829 TTCAT
1 TTCAT
195834 GCCGATAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 2 0.05
21 5 0.14
22 6 0.16
23 11 0.30
24 6 0.16
25 5 0.14
26 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (23 bp):
TTCATTTTCATTTATGGCATCCT
Found at i:198215 original size:24 final size:24
Alignment explanation
Indices: 198156--198215 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
198146 TTCACACGGT
* * *
198156 AGTCCACCATCGTACGGCGGTGGA
1 AGTCCACCAACTTACGGAGGTGGA
* * *
198180 AGTCCGCCAACTTATGGAGGTGGC
1 AGTCCACCAACTTACGGAGGTGGA
198204 AGTCCACCAACT
1 AGTCCACCAACT
198216 CCCACTATTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.18
Consensus pattern (24 bp):
AGTCCACCAACTTACGGAGGTGGA
Found at i:203886 original size:15 final size:14
Alignment explanation
Indices: 203862--203891 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
203852 ACAGTACGAC
203862 AAGCGAAGCTAACA
1 AAGCGAAGCTAACA
203876 AAGCAGAAGCTAACA
1 AAGC-GAAGCTAACA
203891 A
1 A
203892 GGCTTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (14 bp):
AAGCGAAGCTAACA
Done.