Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002634.1 Hibiscus syriacus cultivar Beakdansim tig00005368_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: 131683
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10917 original size:20 final size:20
Alignment explanation
Indices: 10892--10949 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
10882 TTTGGTTTAC
*
10892 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
10912 GGAATAAAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
10932 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
10950 GGAATAGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:12333 original size:51 final size:51
Alignment explanation
Indices: 12267--12707 Score: 542
Period size: 51 Copynumber: 8.8 Consensus size: 51
12257 AGATATACAT
* * *
12267 ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * * *
12318 ACTTACACCGTTGTAAGTATGTGTTAAGAGATACAATTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTAC-ACTTTTTTATTTTATTC
*
12370 ACTTACACCGGTGT-AGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * *
12419 ACTTATACCGGTGT-AGTATGTGTTAAGTGATACACTTTTTTGTTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * *
12469 ACTTACATCGGTGTAAATATGTGTTAAGTGCTACACTTGTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * * *
12520 ACCTACACCGGTGTAAGTATGTGTTAAGTGATACACTTGTTTATTTTATTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * *
12571 ACTTACACCAGTGTAA-TATGTATTAAGTGCT--A--TATTT-TTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * * * *
12616 ACTAACATCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * *
12667 ACTTAAACCGATGTAAGTACGTGTTAAGTGCTACA-TTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTT
12708 GTAGTATGAA
Statistics
Matches: 337, Mismatches: 44, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
45 20 0.06
46 18 0.05
48 2 0.01
49 46 0.14
50 48 0.14
51 175 0.52
52 28 0.08
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:12514 original size:202 final size:198
Alignment explanation
Indices: 12267--12701 Score: 584
Period size: 202 Copynumber: 2.2 Consensus size: 198
12257 AGATATACAT
* * * * *
12267 ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTTACTTACACCGTTGT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTCACCTACACCGGTGT
* * * * *
12332 AAGTATGTGTTAAGAGATACAATTTTTTTATTTTATTCACTTACACCGGTGTAGTATGTGTTAAG
66 AAGTATGTGTTAAGAGATAC-ACTTGTTTATTTTATTCACTTACACCAGTGTAATATGTATTAAG
* * * * * * *
12397 TGCTACATTTTTTATTTTATTTACTTATACCGGTGT-AGTATGTGTTAAGTGATACACTTTTTTG
130 TGCT--A-TATTT-TTTTATTCACTAACACCGGTGTAAGTATGTATTAAGTGATACACTTGTTTA
12461 TTTTATTC
191 TTTTATTC
*
12469 ACTTACATCGGTGTAAATATGTGTTAAGTGCTACACTTGTTTATTTTATTCACCTACACCGGTGT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTCACCTACACCGGTGT
* *
12534 AAGTATGTGTTAAGTGATACACTTGTTTATTTTATTTACTTACACCAGTGTAATATGTATTAAGT
66 AAGTATGTGTTAAGAGATACACTTGTTTATTTTATTCACTTACACCAGTGTAATATGTATTAAGT
* *
12599 GCTATATTTTTTTATTCACTAACATCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTATTTTA
131 GCTATATTTTTTTATTCACTAACACCGGTGTAAGTATGTATTAAGTGATACACTTGTTTATTTTA
12664 TTC
196 TTC
* * * *
12667 ACTTAAACCGATGTAAGTACGTGTTAAGTGCTACA
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACA
12702 TTTTTTGTAG
Statistics
Matches: 205, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
197 18 0.09
198 66 0.32
199 1 0.00
201 42 0.20
202 78 0.38
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (198 bp):
ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTCACCTACACCGGTGT
AAGTATGTGTTAAGAGATACACTTGTTTATTTTATTCACTTACACCAGTGTAATATGTATTAAGT
GCTATATTTTTTTATTCACTAACACCGGTGTAAGTATGTATTAAGTGATACACTTGTTTATTTTA
TTC
Found at i:12643 original size:147 final size:149
Alignment explanation
Indices: 12266--12703 Score: 524
Period size: 147 Copynumber: 2.9 Consensus size: 149
12256 GAGATATACA
* * * * * * * * *
12266 TACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTTACTTACACCGTTG
1 TACTTACACCAGTGTAA-TATGTATTAAGTGATA-AC-TATTTGTTTTATTCACTTACATCGGTG
* * *
12331 TAAGTATGTGTTAAGAGATACAATTTTTTTATTTTATTCACTTACACCGGTGT-AGTATGTGTTA
63 TAAGTATGTGTTAAGTGATAC-ACTTGTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTA
*
12395 AGTGCTACATTTTTTATTTTATT
127 AGTGCTACATTGTTTATTTTATT
* * * * *
12418 TACTTATACCGGTGTAGTATGTGTTAAGTGATACACTTTTTTGTTTTATTCACTTACATCGGTGT
1 TACTTACACCAGTGTAATATGTATTAAGTGATA-AC-TATTTGTTTTATTCACTTACATCGGTGT
* * *
12483 AAATATGTGTTAAGTGCTACACTTGTTTATTTTATTCACCTACACCGGTGTAAGTATGTGTTAAG
64 AAGTATGTGTTAAGTGATACACTTGTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAG
*
12548 TGATACACTTGTTTATTTTATT
129 TGCTACA-TTGTTTATTTTATT
* *
12570 TACTTACACCAGTGTAATATGTATTAAGTGCT-A-TATTT-TTTTATTCACTAACATCGGTGTAA
1 TACTTACACCAGTGTAATATGTATTAAGTGATAACTATTTGTTTTATTCACTTACATCGGTGTAA
* * * * *
12632 GTATGTATTAAGTGTTACACTTGTTTATTTTATTCACTTAAACCGATGTAAGTACGTGTTAAGTG
66 GTATGTGTTAAGTGATACACTTGTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTG
12697 CTACATT
131 CTACATT
12704 TTTTGTAGTA
Statistics
Matches: 253, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
146 2 0.01
147 85 0.34
148 4 0.02
150 29 0.11
151 79 0.31
152 54 0.21
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.46
Consensus pattern (149 bp):
TACTTACACCAGTGTAATATGTATTAAGTGATAACTATTTGTTTTATTCACTTACATCGGTGTAA
GTATGTGTTAAGTGATACACTTGTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTG
CTACATTGTTTATTTTATT
Found at i:12658 original size:96 final size:99
Alignment explanation
Indices: 12267--12699 Score: 514
Period size: 101 Copynumber: 4.3 Consensus size: 99
12257 AGATATACAT
* * * * *
12267 ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTTACTTACACCGTTGT
1 ACTTACACCGGTGTAA-TATGTGTTAAGTGCTA-A-TTATTTATTTTATTCACTTACACCGGTGT
* * *
12332 AAGTATGTGTTAAGAGATACAATTTTTTTATTTTATTC
63 AAGTATGTGTTAAGTGATAC-ACTTGTTTATTTTATTC
* * * *
12370 ACTTACACCGGTGTAGTATGTGTTAAGTGCTACATTTTTTATTTTATTTACTTATACCGGTGT-A
1 ACTTACACCGGTGTAATATGTGTTAAGTGCTA-ATTATTTATTTTATTCACTTACACCGGTGTAA
* *
12434 GTATGTGTTAAGTGATACACTTTTTTGTTTTATTC
65 GTATGTGTTAAGTGATACACTTGTTTATTTTATTC
* * *
12469 ACTTACATCGGTGTAAATATGTGTTAAGTGCTACACTTGTTTATTTTATTCACCTACACCGGTGT
1 ACTTACACCGGTGT-AATATGTGTTAAGTGCTA-A-TTATTTATTTTATTCACTTACACCGGTGT
*
12534 AAGTATGTGTTAAGTGATACACTTGTTTATTTTATTT
63 AAGTATGTGTTAAGTGATACACTTGTTTATTTTATTC
* * * *
12571 ACTTACACCAGTGTAATATGTATTAAGTGCT-A-TATTT-TTTTATTCACTAACATCGGTGTAAG
1 ACTTACACCGGTGTAATATGTGTTAAGTGCTAATTATTTATTTTATTCACTTACACCGGTGTAAG
* *
12633 TATGTATTAAGTGTTACACTTGTTTATTTTATTC
66 TATGTGTTAAGTGATACACTTGTTTATTTTATTC
* * *
12667 ACTTAAACCGATGTAAGTACGTGTTAAGTGCTA
1 ACTTACACCGGTGTAA-TATGTGTTAAGTGCTA
12700 CATTTTTTGT
Statistics
Matches: 293, Mismatches: 32, Indels: 15
0.86 0.09 0.04
Matches are distributed among these distances:
96 66 0.23
97 17 0.06
99 29 0.10
100 37 0.13
101 68 0.23
102 62 0.21
103 14 0.05
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.45
Consensus pattern (99 bp):
ACTTACACCGGTGTAATATGTGTTAAGTGCTAATTATTTATTTTATTCACTTACACCGGTGTAAG
TATGTGTTAAGTGATACACTTGTTTATTTTATTC
Found at i:13302 original size:48 final size:49
Alignment explanation
Indices: 13246--13347 Score: 170
Period size: 48 Copynumber: 2.1 Consensus size: 49
13236 CGTAATATAA
* * *
13246 GGATGTAAGGGATGTGTTTTGTGGGATTCATCTTGTTTCGTATTTAA-T
1 GGATGTAAGGGATGGGTTTTGTGGGACTCATCTTGTTTCATATTTAATT
13294 GGATGTAAGGGATGGGTTTTGTGGGACTCATCTTGTTTCATATTTAATT
1 GGATGTAAGGGATGGGTTTTGTGGGACTCATCTTGTTTCATATTTAATT
13343 GGATG
1 GGATG
13348 GAAATGATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
48 44 0.88
49 6 0.12
ACGTcount: A:0.20, C:0.07, G:0.30, T:0.43
Consensus pattern (49 bp):
GGATGTAAGGGATGGGTTTTGTGGGACTCATCTTGTTTCATATTTAATT
Found at i:16482 original size:2 final size:2
Alignment explanation
Indices: 16475--16522 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
16465 CATAATTTCA
16475 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
16517 AT AT AT
1 AT AT AT
16523 TGAAATTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16546 original size:9 final size:9
Alignment explanation
Indices: 16534--16561 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
16524 GAAATTATTT
16534 TTAAATCCA
1 TTAAATCCA
16543 TTAAATCCA
1 TTAAATCCA
16552 TTAAATCCA
1 TTAAATCCA
16561 T
1 T
16562 ATCCAGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (9 bp):
TTAAATCCA
Found at i:18383 original size:28 final size:28
Alignment explanation
Indices: 18343--18401 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
18333 AAAAATTGAT
18343 TTAATCCTTTTTCTTTGAATAATGGCAA
1 TTAATCCTTTTTCTTTGAATAATGGCAA
18371 TTAATCCTTTTTCTTTGAATAATGGCAA
1 TTAATCCTTTTTCTTTGAATAATGGCAA
18399 TTA
1 TTA
18402 TATTTCACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (28 bp):
TTAATCCTTTTTCTTTGAATAATGGCAA
Found at i:18604 original size:2 final size:2
Alignment explanation
Indices: 18599--18629 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18589 AAAAATTATT
18599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18630 TTAAAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20476 original size:35 final size:35
Alignment explanation
Indices: 20400--20478 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
20390 GCAACACAGT
20400 CTTCAATTTCATTTTAAACCCCAAATTTCAAAATA
1 CTTCAATTTCATTTTAAACCCCAAATTTCAAAATA
** * * *
20435 AATCAATTAT-ATTTTAAACCCTAAATTTTAGAATA
1 CTTCAATT-TCATTTTAAACCCCAAATTTCAAAATA
20470 CTTCAATTT
1 CTTCAATTT
20479 AGGGTTAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
34 1 0.03
35 34 0.94
36 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.41
Consensus pattern (35 bp):
CTTCAATTTCATTTTAAACCCCAAATTTCAAAATA
Found at i:20526 original size:35 final size:34
Alignment explanation
Indices: 20474--20543 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
20464 AGAATACTTC
20474 AATTTAGGGTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTAGAATATAATTAAAGTATTTTGG
* *
20508 AATTTAGGGCTTAGAATATAATTGAAGTGTTTTGG
1 AATTTAGGG-TTAGAATATAATTAAAGTATTTTGG
20543 A
1 A
20544 TTTTTGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 9 0.27
35 24 0.73
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.40
Consensus pattern (34 bp):
AATTTAGGGTTAGAATATAATTAAAGTATTTTGG
Found at i:33849 original size:16 final size:16
Alignment explanation
Indices: 33819--33849 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33809 AACCCAACAT
*
33819 ATTCAAACGAAAAAAC
1 ATTCAAACAAAAAAAC
33835 ATTCAAACAAAAAAA
1 ATTCAAACAAAAAAA
33850 AAACCAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
ATTCAAACAAAAAAAC
Found at i:34734 original size:30 final size:30
Alignment explanation
Indices: 34695--34764 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
34685 TTTACTGTTC
34695 AGTCCTTTAACTGTCTACTTTTGTTATTTT
1 AGTCCTTTAACTGTCTACTTTTGTTATTTT
* * * * * *
34725 AGTCTTTTAAGTTTTTATTTTTTTTATTTT
1 AGTCCTTTAACTGTCTACTTTTGTTATTTT
34755 AGTCCTTTAA
1 AGTCCTTTAA
34765 ATTTATGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (30 bp):
AGTCCTTTAACTGTCTACTTTTGTTATTTT
Found at i:34760 original size:60 final size:60
Alignment explanation
Indices: 34677--34824 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
34667 TGACTTCGGT
* * * * * *
34677 TTTTTATATTTACT-GTTCAGTCCTTTAACTGTCTACTTTTGTTATTTTAGT-CTTTTAAG
1 TTTTTATTTTTACTATTTTAGTCCTTTAAATGTATACTTTTGCTATTTTAGTAC-TTTAAG
** * ** *
34736 TTTTTATTTTTTTTATTTTAGTCCTTTAAATTTATGTTTTTGCTATTTTAGTACTTTAAT
1 TTTTTATTTTTACTATTTTAGTCCTTTAAATGTATACTTTTGCTATTTTAGTACTTTAAG
* *
34796 TTTTTGTTTTTACTATTTTAGTTCTTTAA
1 TTTTTATTTTTACTATTTTAGTCCTTTAA
34825 GTTTCTGTTT
Statistics
Matches: 71, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 11 0.15
60 59 0.83
61 1 0.01
ACGTcount: A:0.19, C:0.09, G:0.08, T:0.64
Consensus pattern (60 bp):
TTTTTATTTTTACTATTTTAGTCCTTTAAATGTATACTTTTGCTATTTTAGTACTTTAAG
Found at i:34776 original size:30 final size:30
Alignment explanation
Indices: 34719--34855 Score: 150
Period size: 30 Copynumber: 4.6 Consensus size: 30
34709 CTACTTTTGT
* * * **
34719 TATTTTAGTCTTTTAAGTTTTTATTTTTTT
1 TATTTTAGTCCTTTAAATTTTTGTTTTTAC
* *
34749 TATTTTAGTCCTTTAAATTTATGTTTTTGC
1 TATTTTAGTCCTTTAAATTTTTGTTTTTAC
* *
34779 TATTTTAGTACTTTAATTTTTTGTTTTTAC
1 TATTTTAGTCCTTTAAATTTTTGTTTTTAC
* * *
34809 TATTTTAGTTCTTTAAGTTTCTG-TTTTAC
1 TATTTTAGTCCTTTAAATTTTTGTTTTTAC
*
34838 TATTTTGGTCCTTTAAAT
1 TATTTTAGTCCTTTAAAT
34856 CGAATATGAT
Statistics
Matches: 91, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 21 0.23
30 70 0.77
ACGTcount: A:0.19, C:0.08, G:0.09, T:0.64
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAATTTTTGTTTTTAC
Found at i:40797 original size:3 final size:3
Alignment explanation
Indices: 40789--41064 Score: 239
Period size: 3 Copynumber: 89.0 Consensus size: 3
40779 ATCATTATTG
40789 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
40837 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -TGAA
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT--T
* *** ** * ** *
40883 GTT GAG CCA CGTAA AAT CATT ATT GCTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT C-T-T CTT C-TT CTT -CTT CTT CTT CTT CTT CTT CTT CTT
*** * *** ** * ** *
40932 CTT CTT GAA GTT GAG CCA CGTAA AAT CATT ATT GCTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT C-T-T CTT C-TT CTT -CTT CTT CTT CTT CTT
40981 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
41029 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
41065 GAAGTTGAGC
Statistics
Matches: 229, Mismatches: 33, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.00
3 219 0.96
4 6 0.03
5 3 0.01
ACGTcount: A:0.07, C:0.29, G:0.04, T:0.59
Consensus pattern (3 bp):
CTT
Found at i:41101 original size:3 final size:3
Alignment explanation
Indices: 41093--41137 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
41083 ATCATTATTG
41093 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
41138 TGAAGTTGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:41185 original size:3 final size:3
Alignment explanation
Indices: 41179--41249 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
41169 TCTTCTTCTT
41179 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
41227 CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CT
41250 TCTTCTTCTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:44770 original size:12 final size:12
Alignment explanation
Indices: 44753--44778 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44743 TTTTTCATAG
44753 TACTGCAATCGT
1 TACTGCAATCGT
44765 TACTGCAATCGT
1 TACTGCAATCGT
44777 TA
1 TA
44779 ATTGGTATAA
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:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (12 bp):
TACTGCAATCGT
Found at i:47055 original size:16 final size:18
Alignment explanation
Indices: 47013--47058 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
47003 TTCATAGAAT
47013 GTAAGATTACCAGTAGGAA
1 GTAAGATTACCAG-AGGAA
47032 TGTAAGATTACCAG-GGAA
1 -GTAAGATTACCAGAGGAA
47050 -TAAGATTAC
1 GTAAGATTAC
47059 TGAGAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.35
18 4 0.15
20 13 0.50
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
GTAAGATTACCAGAGGAA
Found at i:47275 original size:35 final size:38
Alignment explanation
Indices: 47197--47275 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 38
47187 AAAAAGTTGG
* *
47197 AAAATATTTATATATTTTATTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTATTTAAAAAATTGAAAATCAT
*
47236 -AAAATTTATAT-TTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATATATTTTATTTAAAAAATTGAAAATCAT
47270 AAAAAT
1 AAAAAT
47276 GTTTAATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
34 2 0.06
35 19 0.53
36 4 0.11
37 8 0.22
38 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (38 bp):
AAAAATTTATATATTTTATTTAAAAAATTGAAAATCAT
Found at i:52473 original size:4 final size:4
Alignment explanation
Indices: 52464--52629 Score: 332
Period size: 4 Copynumber: 41.5 Consensus size: 4
52454 GAATCAGATG
52464 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
52512 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
52560 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
52608 TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TA
52630 TATATTGTTA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 162 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:53598 original size:22 final size:20
Alignment explanation
Indices: 53572--53612 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
53562 AATTTAAATT
53572 TTTAAAATTTTAGAGTGATGAA
1 TTTAAAATTTTA-AG-GATGAA
*
53594 TTTAAATTTTTAAGGATGA
1 TTTAAAATTTTAAGGATGA
53613 TAATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
TTTAAAATTTTAAGGATGAA
Found at i:55187 original size:22 final size:22
Alignment explanation
Indices: 55153--55194 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55143 ATAATTATTT
55153 AAAAAATTAAATAA-AAATACA
1 AAAAAATTAAATAACAAATACA
*
55174 AAAAATATTTAATAACAAATA
1 AAAAA-ATTAAATAACAAATA
55195 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAATTAAATAACAAATACA
Found at i:55856 original size:18 final size:17
Alignment explanation
Indices: 55824--55857 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55814 TCAGCCGATC
55824 CGGTTTGAACGGTTCAG
1 CGGTTTGAACGGTTCAG
*
55841 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
55858 CTAGTAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAG
Found at i:56616 original size:3 final size:3
Alignment explanation
Indices: 56608--56633 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56598 AAATTCTGTG
56608 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
56634 ACAAAACGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56781 original size:12 final size:13
Alignment explanation
Indices: 56764--56792 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
56754 GCCAGCTATG
56764 GGACTAGG-ACTA
1 GGACTAGGAACTA
56776 GGACTAGGAACTA
1 GGACTAGGAACTA
56789 GGAC
1 GGAC
56793 AATTAGCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (13 bp):
GGACTAGGAACTA
Found at i:59953 original size:3 final size:3
Alignment explanation
Indices: 59945--59992 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
59935 TTTGTTTTAT
*
59945 TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TT- TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
59987 TTA TTA
1 TTA TTA
59993 AATAATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 7 0.17
3 32 0.80
4 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:61174 original size:29 final size:30
Alignment explanation
Indices: 61141--61199 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
61131 AGGGCTATAA
61141 ATTTTAATATTT-TATATTTTAATC-CTATT
1 ATTTTAAT-TTTATATATTTTAATCACTATT
* *
61170 ATTTTAATTTTATATGTTTTAGTCACTATT
1 ATTTTAATTTTATATATTTTAATCACTATT
61200 TAATTGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (30 bp):
ATTTTAATTTTATATATTTTAATCACTATT
Found at i:62383 original size:20 final size:19
Alignment explanation
Indices: 62349--62391 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
62339 AAATGTTACG
*
62349 TTTATTTTTTTAAAATAATAT
1 TTTA-TTTTTTAAAA-AAAAT
62370 TTTA-TTTTTAAAAAAAAT
1 TTTATTTTTTAAAAAAAAT
62388 TTTA
1 TTTA
62392 AAAATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
21 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATTTTTTAAAAAAAAT
Found at i:62389 original size:18 final size:19
Alignment explanation
Indices: 62355--62391 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
62345 TACGTTTATT
*
62355 TTTTTAAAATAATATTTTA
1 TTTTTAAAATAAAATTTTA
62374 TTTTTAAAA-AAAATTTTA
1 TTTTTAAAATAAAATTTTA
62392 AAAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTAAAATAAAATTTTA
Found at i:64642 original size:27 final size:27
Alignment explanation
Indices: 64604--64657 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
64594 TGCATGTAAG
64604 AAAGAGTTTGGTGATGTAAAAAATATT
1 AAAGAGTTTGGTGATGTAAAAAATATT
*
64631 AAAGAGTTTGGTGATGTATAAAATATT
1 AAAGAGTTTGGTGATGTAAAAAATATT
64658 CTCGTTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (27 bp):
AAAGAGTTTGGTGATGTAAAAAATATT
Found at i:73326 original size:95 final size:95
Alignment explanation
Indices: 73143--73331 Score: 290
Period size: 96 Copynumber: 2.0 Consensus size: 95
73133 AAATTTCAAT
* * * *
73143 TGTTTGGTTCGCTTGAATCCCTTGGAATTAGGGGAATTGGAATCTAATTCTACCACTTTCCCATG
1 TGTTTGCTTCGCTAGAATCCCTTGGAATTAGGGGAATTAGAATCCAATTCTACCACTTTCCCATG
73208 TTTGGTTCAAGTTTTCAAAAGGGGAATTGG
66 TTTGGTTCAAGTTTTCAAAAGGGGAATTGG
* * *
73238 TGTTTGCTTCGCTAGAATCTCTTGGACTTAGGGAGAATTAGAATCCAATTCTACCACTTTCTCAT
1 TGTTTGCTTCGCTAGAATCCCTTGGAATTAGGG-GAATTAGAATCCAATTCTACCACTTTCCCAT
*
73303 GTTTGGTTTAAGTTTTC-AAAGGGGAATTG
65 GTTTGGTTCAAGTTTTCAAAAGGGGAATTG
73332 AAATCCAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
95 41 0.48
96 44 0.52
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (95 bp):
TGTTTGCTTCGCTAGAATCCCTTGGAATTAGGGGAATTAGAATCCAATTCTACCACTTTCCCATG
TTTGGTTCAAGTTTTCAAAAGGGGAATTGG
Found at i:73598 original size:31 final size:31
Alignment explanation
Indices: 73556--73631 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
73546 GTAGTATTTG
73556 GGTCGGGTTTTTTTCAAAACATTTAGGGGT-T
1 GGTCGGGTTTTTTTCAAAA-ATTTAGGGGTCT
* * * * *
73587 GGTCGGATTTTTTTTAAAATTTTCGGGTTCT
1 GGTCGGGTTTTTTTCAAAAATTTAGGGGTCT
73618 GGTCGGGTTTTTTT
1 GGTCGGGTTTTTTT
73632 AAGTTTGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.14, C:0.09, G:0.28, T:0.49
Consensus pattern (31 bp):
GGTCGGGTTTTTTTCAAAAATTTAGGGGTCT
Found at i:73998 original size:18 final size:18
Alignment explanation
Indices: 73975--74010 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
73965 ATTTCAGATT
*
73975 CAGATTTTAATTCCTTCA
1 CAGATTTCAATTCCTTCA
*
73993 CAGATTTCAATTCTTTCA
1 CAGATTTCAATTCCTTCA
74011 AAAATATTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
CAGATTTCAATTCCTTCA
Found at i:77789 original size:10 final size:10
Alignment explanation
Indices: 77774--77803 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
77764 CAAAAATTAT
77774 TTTTATATAA
1 TTTTATATAA
77784 TTTTATAATAA
1 TTTTAT-ATAA
77795 TTTTATATA
1 TTTTATATA
77804 TTTCATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTATATAA
Found at i:77800 original size:21 final size:20
Alignment explanation
Indices: 77774--77812 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
77764 CAAAAATTAT
*
77774 TTTTATATAATTTTATAATAA
1 TTTTATAT-ATTTCATAATAA
77795 TTTTATATATTTCATAAT
1 TTTTATATATTTCATAAT
77813 TTTAGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATATATTTCATAATAA
Found at i:77826 original size:28 final size:29
Alignment explanation
Indices: 77780--77835 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
77770 TTATTTTTAT
77780 ATAATTTTATAATAATTTTATAT-ATTTC
1 ATAATTTTATAATAATTTTATATGATTTC
* *
77808 ATAATTTTAGTAA-ATTTTTTTATGATTT
1 ATAATTTTA-TAATAATTTTATATGATTT
77836 ATGTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (29 bp):
ATAATTTTATAATAATTTTATATGATTTC
Found at i:78294 original size:2 final size:2
Alignment explanation
Indices: 78287--78312 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78277 ATACCAAACT
78287 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
78313 CGCTACCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:82764 original size:2 final size:2
Alignment explanation
Indices: 82757--82802 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
82747 AATTTTAAGA
82757 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
82799 AT AT
1 AT AT
82803 TAAAATATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83265 original size:27 final size:29
Alignment explanation
Indices: 83231--83296 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
83221 AAACAATAAC
*
83231 TAAA-ATAAATGAAA-TTAAAATT-AAAA
1 TAAATATAAATAAAACTTAAAATTAAAAA
* *
83257 TACATATAAA-AAAACTTATAATTAAAAA
1 TAAATATAAATAAAACTTAAAATTAAAAA
83285 TAAATATAAATA
1 TAAATATAAATA
83297 TTGAAATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 6 0.19
27 12 0.38
28 13 0.41
29 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (29 bp):
TAAATATAAATAAAACTTAAAATTAAAAA
Found at i:84545 original size:3 final size:3
Alignment explanation
Indices: 84525--84588 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
84515 TTTGGGCCTG
* * *
84525 TAA T-A TAA TAA -AA TTAA TAA TAAA TAA TAA TAA TAA TAT TAT TAT
1 TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
84570 TAA TTAA TAA TAA TAA TAA
1 TAA -TAA TAA TAA TAA TAA
84589 AATGAATGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 4 0.07
3 42 0.78
4 8 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:84565 original size:25 final size:25
Alignment explanation
Indices: 84525--84587 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
84515 TTTGGGCCTG
*
84525 TAAT-ATAATAAAATTAATAATAAA
1 TAATAATAATAATATTAATAATAAA
* * *
84549 TAATAATAATAATATTATTATTAAT
1 TAATAATAATAATATTAATAATAAA
84574 TAATAATAATAATA
1 TAATAATAATAATA
84588 AAATGAATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATAATAATATTAATAATAAA
Found at i:86000 original size:113 final size:113
Alignment explanation
Indices: 84985--86001 Score: 1505
Period size: 113 Copynumber: 9.0 Consensus size: 113
84975 TAGAGTCATA
* *
84985 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * ** *
85050 TTATGAACT-TTCTCTGAAAAAGTTGATCCATCGAGTGATGAATTCAAA
66 TTATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
* * * *
85098 CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTATTCTC
1 CAAAAGGTT-GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
85163 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTCGAG
65 ATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
* * *
85212 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
85277 TTATGAACTCTACCTGGAAATATTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
*
85325 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
85390 TTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCGAG
66 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
* * * *
85438 CAAAAGGTTGAACAAGATCTTCTTATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
85503 TTATGAACTCTACCTGAAAATGTTGATCCATCAAGTAATGGATTTGAG
66 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
* *
85551 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
85616 TTATGAACTCTACCTAGCAATGCTGATCCATCAAGTGATGAATTCGAG
66 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
* * *
85664 CAAAAGGTTGAACAAGCTCTTCTCCTTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
85729 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTAAG
66 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
** * *
85777 CAAAAGGTTGAACAAGTTCTTCTCATTATTTACTTCCTCTTCCTTCTTCAGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
85842 TTATGAACTCTACCTGGGAATGCTGATCTATCAAGTGATGAATTTGAG
66 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
* * * *
85890 CAAAAGTTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTTTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
85955 TTATGAACTCTACCTAGAAATGCTGATCCATCAAGTGATGGATTTGA
66 TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
86002 ATCTTTGCTA
Statistics
Matches: 813, Mismatches: 89, Indels: 4
0.90 0.10 0.00
Matches are distributed among these distances:
113 712 0.88
114 99 0.12
115 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAG
Found at i:86409 original size:22 final size:22
Alignment explanation
Indices: 86348--86411 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
86338 AAATCCAATA
* * *
86348 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
*
86370 AATCTATCATATTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
86392 AAAT-TATCATCTTTGAAGAG
1 -AATCTATCATCTTTGAAGAG
86412 TGTAGATGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:89778 original size:32 final size:32
Alignment explanation
Indices: 89737--89799 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
89727 TGAAGAAATG
*
89737 ATTGTTATGCTCATCTTGTAGAGATACTTCTC
1 ATTGTTATGCTCATCTCGTAGAGATACTTCTC
89769 ATTGTTATGCTCATCTCGTAGAGATACTTCT
1 ATTGTTATGCTCATCTCGTAGAGATACTTCT
89800 TGTGTCTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (32 bp):
ATTGTTATGCTCATCTCGTAGAGATACTTCTC
Found at i:90263 original size:9 final size:9
Alignment explanation
Indices: 90249--90277 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
90239 CTCATCTCGG
90249 TTCAATTTT
1 TTCAATTTT
90258 TTCAATTTT
1 TTCAATTTT
90267 TTC-ATTTT
1 TTCAATTTT
90275 TTC
1 TTC
90278 CTTTTTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (9 bp):
TTCAATTTT
Found at i:90273 original size:8 final size:8
Alignment explanation
Indices: 90253--90293 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
90243 TCTCGGTTCA
90253 ATTTTTTC
1 ATTTTTTC
90261 AATTTTTTC
1 -ATTTTTTC
90270 ATTTTTTC
1 ATTTTTTC
*
90278 CTTTTTTC
1 ATTTTTTC
*
90286 CTTTTTTC
1 ATTTTTTC
90294 CCAAGTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 23 0.74
9 8 0.26
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTTC
Found at i:93115 original size:23 final size:23
Alignment explanation
Indices: 93088--93133 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
93078 TGAACTTTGG
93088 TGGGAGAACTAGGTTGGGGACCA
1 TGGGAGAACTAGGTTGGGGACCA
93111 TGGGAGAACTAGGTTGGGGACCA
1 TGGGAGAACTAGGTTGGGGACCA
93134 AACTTAGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.43, T:0.17
Consensus pattern (23 bp):
TGGGAGAACTAGGTTGGGGACCA
Found at i:95560 original size:26 final size:28
Alignment explanation
Indices: 95517--95583 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
95507 AATAAAATAA
*
95517 AAATATTA-AAAAATAAT-A-TACATAT
1 AAATATTATGAAAATAATAAGTACATAT
*
95542 AAATATTATGAAAATAATAAGTATATAT
1 AAATATTATGAAAATAATAAGTACATAT
* *
95570 AAAAATTTTGAAAA
1 AAATATTATGAAAA
95584 GAAAGAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.23
26 8 0.23
27 1 0.03
28 18 0.51
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
AAATATTATGAAAATAATAAGTACATAT
Found at i:96059 original size:2 final size:2
Alignment explanation
Indices: 96052--96079 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96042 AATTTTAAGA
96052 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
96080 TATTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96102 original size:17 final size:18
Alignment explanation
Indices: 96080--96117 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
96070 ATATATATAT
*
96080 TATTTATTTATTTA-AAA
1 TATTTATTTACTTAGAAA
96097 TATTTATTTACTTAGAAA
1 TATTTATTTACTTAGAAA
96115 TAT
1 TAT
96118 CAGAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
TATTTATTTACTTAGAAA
Found at i:97839 original size:3 final size:3
Alignment explanation
Indices: 97819--97888 Score: 81
Period size: 3 Copynumber: 23.0 Consensus size: 3
97809 TTTGGGACTG
97819 TAA T-A TAA TAA -AA TTAA TAA TAA TAA TAA GTAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* *
97864 TAA TAT TAA TTAT TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA
97889 AACGAATGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
2 4 0.07
3 47 0.81
4 7 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:97856 original size:28 final size:28
Alignment explanation
Indices: 97823--97888 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
97813 GGACTGTAAT
97823 ATAATAA-AATTAATAATAATAATAAGTA
1 ATAATAATAA-TAATAATAATAATAAGTA
* * *
97851 ATAATAATAATAATAATATTAATTATTA
1 ATAATAATAATAATAATAATAATAAGTA
97879 ATAATAATAA
1 ATAATAATAA
97889 AACGAATGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 32 0.94
29 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
ATAATAATAATAATAATAATAATAAGTA
Found at i:97857 original size:19 final size:18
Alignment explanation
Indices: 97819--97888 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 18
97809 TTTGGGACTG
97819 TAAT-ATAATAA-AATTAA
1 TAATAATAATAATAA-TAA
97836 TAATAATAATAAGTAATAA
1 TAATAATAATAA-TAATAA
*
97855 TAATAATAATAATATTAA
1 TAATAATAATAATAATAA
*
97873 TTATTAATAATAATAA
1 -TAATAATAATAATAA
97889 AACGAATGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.09
18 12 0.26
19 28 0.61
20 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (18 bp):
TAATAATAATAATAATAA
Found at i:97861 original size:22 final size:22
Alignment explanation
Indices: 97830--97888 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
97820 AATATAATAA
97830 AATTAATAATAATAAT-A-AGT
1 AATTAATAATAATAATAATAGT
*
97850 AA-TAATAATAATAATAATATT
1 AATTAATAATAATAATAATAGT
*
97871 AATTATTAATAATAATAA
1 AATTAATAATAATAATAA
97889 AACGAATGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.38
20 3 0.09
21 4 0.12
22 14 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTAATAATAATAATAATAGT
Found at i:97861 original size:25 final size:25
Alignment explanation
Indices: 97824--97888 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
97814 GACTGTAATA
97824 TAATAA-AATTAATAATAATAATAAG
1 TAATAATAA-TAATAATAATAATAAG
* *
97849 TAATAATAATAATAATAATATTAAT
1 TAATAATAATAATAATAATAATAAG
*
97874 TATTAATAATAATAA
1 TAATAATAATAATAA
97889 AACGAATGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 34 0.94
26 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
TAATAATAATAATAATAATAATAAG
Found at i:98252 original size:29 final size:30
Alignment explanation
Indices: 98204--98265 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
98194 TGTATATGAC
* *
98204 AATGTTACGTCATCATTTTAGACACATAAT
1 AATGTTACGTCATCACTTTAAACACATAAT
* *
98234 AATGTTA-TTCATCACTTTAAACACGTAAT
1 AATGTTACGTCATCACTTTAAACACATAAT
98263 AAT
1 AAT
98266 ATCAAGTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (30 bp):
AATGTTACGTCATCACTTTAAACACATAAT
Found at i:101816 original size:21 final size:21
Alignment explanation
Indices: 101792--101838 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
101782 TTTGAATGTT
101792 GAGTTTATAAAATTACGAGTC
1 GAGTTTATAAAATTACGAGTC
*
101813 GAGTTTATAAAATTACGAGTT
1 GAGTTTATAAAATTACGAGTC
101834 GAGTT
1 GAGTT
101839 GAATCAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (21 bp):
GAGTTTATAAAATTACGAGTC
Found at i:102914 original size:21 final size:21
Alignment explanation
Indices: 102890--102933 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
102880 GTTTGTCATT
102890 TATCATTTTAGGTGATATTTG
1 TATCATTTTAGGTGATATTTG
102911 TATCATTTTAGGTGATATTTG
1 TATCATTTTAGGTGATATTTG
102932 TA
1 TA
102934 GCCTTGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (21 bp):
TATCATTTTAGGTGATATTTG
Found at i:102943 original size:21 final size:21
Alignment explanation
Indices: 102893--102944 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
102883 TGTCATTTAT
* *
102893 CATTTTAGGTGATATTTGTAT
1 CATTGTAGGTGATATTTGTAG
*
102914 CATTTTAGGTGATATTTGTAG
1 CATTGTAGGTGATATTTGTAG
*
102935 CCTTGTAGGT
1 CATTGTAGGT
102945 TTTGGTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.48
Consensus pattern (21 bp):
CATTGTAGGTGATATTTGTAG
Found at i:106000 original size:23 final size:23
Alignment explanation
Indices: 105982--106041 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
105972 CTCGTATAAA
105982 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
106005 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
106028 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
106042 ATATAATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:106727 original size:23 final size:23
Alignment explanation
Indices: 106666--106728 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
106656 AATGAAGGTA
106666 TGCATCGATGCACTA--TA-CAG
1 TGCATCGATGCACTACCTATCAG
* * * *
106686 TGTATCGATGCATTCCCTATCGG
1 TGCATCGATGCACTACCTATCAG
106709 TGCATCGATGCACTACCTAT
1 TGCATCGATGCACTACCTAT
106729 GCATCGGTGC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 12 0.36
22 2 0.06
23 19 0.58
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (23 bp):
TGCATCGATGCACTACCTATCAG
Found at i:108205 original size:20 final size:20
Alignment explanation
Indices: 108180--108228 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
108170 CAACGAGTGA
108180 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
108200 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
108220 ATCGCAACG
1 ATCGCAACG
108229 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:108325 original size:20 final size:20
Alignment explanation
Indices: 108302--108341 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
108292 ATTGTGATAG
108302 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
108322 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
108342 AAAGTTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.55
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:108349 original size:20 final size:20
Alignment explanation
Indices: 108306--108349 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
108296 TGATAGTCAT
** *
108306 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
108326 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
108346 TTTC
1 TTTC
108350 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:110245 original size:20 final size:20
Alignment explanation
Indices: 110220--110323 Score: 130
Period size: 20 Copynumber: 5.5 Consensus size: 20
110210 AGAATAGTTT
110220 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
110240 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
110260 ACTATCGCAA--C-AAGA-G
1 ACTATCGCAATGCGAAAATG
110276 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
110294 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
110314 ACTATCGCAA
1 ACTATCGCAA
110324 CGAAAGAATC
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
14 7 0.10
16 3 0.04
17 6 0.08
18 3 0.04
20 54 0.74
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:110309 original size:54 final size:54
Alignment explanation
Indices: 110223--110344 Score: 201
Period size: 54 Copynumber: 2.3 Consensus size: 54
110213 ATAGTTTACT
110223 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAAC-AAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAA-AGA
* **
110277 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGA
110331 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
110345 TGAAAATCGC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
54 62 0.97
55 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.17
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGA
Found at i:110485 original size:20 final size:20
Alignment explanation
Indices: 110460--110543 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
110450 TCTCTCGTTA
**
110460 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
110480 CGATAGTCATTTTCGCATTA
1 CGATAGTCATTTTCGCATTG
*
110500 CGACAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
* *
110520 CGATAGTCATTTTCACGTTG
1 CGATAGTCATTTTCGCATTG
110540 CGAT
1 CGAT
110544 TTTAAGTTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:110515 original size:40 final size:40
Alignment explanation
Indices: 110457--110533 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
110447 GATTCTCTCG
*
110457 TTACGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
1 TTACGACAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
**
110497 TTACGACAGTCATTTTCGCATTGCGATAGTCATTTTC
1 TTACGACAGTCAAATTCGCATTGCGATAGTCATTTTC
110534 ACGTTGCGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (40 bp):
TTACGACAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
Found at i:111118 original size:21 final size:21
Alignment explanation
Indices: 111023--111130 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
111013 GACCGACTCA
111023 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
** *
111044 TCCCCT-ATCATTCAAGAGGCC
1 -CCTGTCATCGTTCAAGAGGCC
* ** *
111065 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
*
111086 CCT-TCCACCGTTCAAGAGGCC
1 CCTGT-CATCGTTCAAGAGGCC
* * *
111107 ACTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
111128 CCT
1 CCT
111131 CCCAACATTC
Statistics
Matches: 66, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
20 4 0.06
21 58 0.88
22 4 0.06
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:112506 original size:14 final size:14
Alignment explanation
Indices: 112487--112522 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
112477 ATTGTTTAAT
112487 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
112501 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
112515 TGATTTGT
1 TGATTTGT
112523 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:112712 original size:34 final size:34
Alignment explanation
Indices: 112624--112719 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
112614 AAAACAGACT
* ** *
112624 ATCGCAACGCGAAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
112658 ATCACAATGCG-AAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
112691 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
112720 CGATGCGATT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:112812 original size:20 final size:20
Alignment explanation
Indices: 112787--112875 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
112777 TTGATTCTCT
112787 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
112807 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
** *
112827 TATTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
112847 TGTTGCGATAGTCATATT-TG
1 CGTTGCGATAGTCAT-TTCCG
112867 CGTTGCGAT
1 CGTTGCGAT
112876 TTCTGTGTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 57 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:115349 original size:24 final size:24
Alignment explanation
Indices: 115322--115368 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
115312 CAATATCCGA
115322 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
115346 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
115369 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:115377 original size:24 final size:24
Alignment explanation
Indices: 115326--115377 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
115316 ATCCGAGTAT
** *
115326 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
115350 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
115374 TGAC
1 TGAC
115378 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:116297 original size:20 final size:20
Alignment explanation
Indices: 116223--116314 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
116213 GTCAGAATCT
*
116223 CGTTGCGATTTACAG-ATTCA
1 CGTTGCGATTTAC-GTATTCG
*
116243 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* * *
116263 CATTGGGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
116283 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
116303 CGTTGCAATTTA
1 CGTTGCGATTTA
116315 GGAAAATCGC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.02
20 62 0.98
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:116331 original size:21 final size:21
Alignment explanation
Indices: 116307--116347 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
116297 TATTCGCGTT
*
116307 GCAATTTAGGAAAATCGCAAC
1 GCAAATTAGGAAAATCGCAAC
* *
116328 GCAAATTCGGGAAATCGCAA
1 GCAAATTAGGAAAATCGCAA
116348 TGCGATAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (21 bp):
GCAAATTAGGAAAATCGCAAC
Found at i:123914 original size:23 final size:23
Alignment explanation
Indices: 123856--123924 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
123846 CATTATTATA
*
123856 TGGCACTTCGGTGAATTTCTACG
1 TGGCACTTAGGTGAATTTCTACG
*
123879 CGGCAC-TACGGTGTAA-TTCTACG
1 TGGCACTTA-GGTG-AATTTCTACG
* *
123902 TGGCACTTAGGTGCATTTATACG
1 TGGCACTTAGGTGAATTTCTACG
123925 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
22 2 0.05
23 31 0.84
24 4 0.11
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTAGGTGAATTTCTACG
Found at i:125015 original size:21 final size:22
Alignment explanation
Indices: 124991--125041 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
124981 CACCACAACT
124991 CGTATAAA-TGCACCGAAGTGC
1 CGTATAAATTGCACCGAAGTGC
*
125012 CGTATAGAATTGCACCGTAGTGC
1 CGTATA-AATTGCACCGAAGTGC
*
125035 CATATAA
1 CGTATAA
125042 TAATATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 17 0.65
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
CGTATAAATTGCACCGAAGTGC
Found at i:126771 original size:23 final size:23
Alignment explanation
Indices: 126745--126819 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
126735 TCCTTATGGA
* *
126745 CATTTCTACGTGCCACTTCAGTG
1 CATTTCTACGTGGCACTTCGGTG
*
126768 CATTTCTACGCGGCACTTCGGTTG
1 CATTTCTACGTGGCACTTCGG-TG
*
126792 CA-ATCTTACGTGGCACTTCGGTG
1 CATTTC-TACGTGGCACTTCGGTG
126815 CATTT
1 CATTT
126820 ATACAAGCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 24 0.56
24 19 0.44
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.35
Consensus pattern (23 bp):
CATTTCTACGTGGCACTTCGGTG
Found at i:127678 original size:24 final size:24
Alignment explanation
Indices: 127646--127694 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
127636 TATGAGCTGA
127646 AACAAGACTTATGAGCAATGTTTC
1 AACAAGACTTATGAGCAATGTTTC
*
127670 AACATGACTTATGAGCAATGTTTC
1 AACAAGACTTATGAGCAATGTTTC
127694 A
1 A
127695 GCGTCATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (24 bp):
AACAAGACTTATGAGCAATGTTTC
Done.