Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold305
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: 704983
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 1 of 5
Found at i:4107 original size:28 final size:28
Alignment explanation
Indices: 4046--4127 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
4036 TTTTGGAGAT
* *
4046 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGAGTTGGAGT-ATCCC-CGATGA
*
4074 AGTAACGGAGTTGGAGTATCCCCGATGA
1 AATAACGGAGTTGGAGTATCCCCGATGA
*
4102 AATAAC-GAGGTTGGAGTATCCTCGAT
1 AATAACGGA-GTTGGAGTATCCCCGAT
4128 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 2 0.04
27 6 0.13
28 38 0.83
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGGAGTTGGAGTATCCCCGATGA
Found at i:4266 original size:51 final size:51
Alignment explanation
Indices: 4110--4277 Score: 219
Period size: 52 Copynumber: 3.3 Consensus size: 51
4100 GAAATAACGA
*
4110 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCTCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCGG
* * * * * *
4162 TGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCTCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCGG
*** *
4214 GGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
4265 GGTTGGAGTATCC
1 GGTTGGAGTATCC
4278 CCTCGGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 36 0.37
52 52 0.53
53 10 0.10
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (51 bp):
GGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
Found at i:4325 original size:27 final size:28
Alignment explanation
Indices: 4262--4337 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
4252 GAAATAAAGT
***
4262 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4290 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4317 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
4338 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.20, C:0.21, G:0.36, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4410 original size:211 final size:211
Alignment explanation
Indices: 4051--4443 Score: 592
Period size: 211 Copynumber: 1.9 Consensus size: 211
4041 GAGATAATAA
* * *
4051 CGGGGTTGGAGTGTTCCCTCGGAAGTAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
* * *
4116 AGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCTCGATT
66 AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
** * * *
4181 AAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCTCGATTATGAAAAATCAAT
131 AAAGGAAAATCAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
4246 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* * *
4262 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
* *
4326 AGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
66 AGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
* *
4391 TTATA-GAAAATCAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
129 TTAAAGGAAAATCAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
4444 GTGGAGAATT
Statistics
Matches: 162, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 28 0.17
211 96 0.59
212 38 0.23
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
AAAGGAAAATCAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:6823 original size:13 final size:13
Alignment explanation
Indices: 6805--6830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6795 ACAAAGATCC
6805 ATGTATCGATACA
1 ATGTATCGATACA
6818 ATGTATCGATACA
1 ATGTATCGATACA
6831 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6826 original size:33 final size:33
Alignment explanation
Indices: 6784--6850 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
6774 AAAATTTCCA
***
6784 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
6817 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
6850 A
1 A
6851 TTTCCTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:6887 original size:19 final size:18
Alignment explanation
Indices: 6863--6930 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
6853 TCCTTGGTAA
6863 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
6882 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
6897 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
6914 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
6931 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:6903 original size:13 final size:13
Alignment explanation
Indices: 6885--6909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6875 ACAATACTTA
6885 TGTATCGATACAT
1 TGTATCGATACAT
6898 TGTATCGATACA
1 TGTATCGATACA
6910 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6907 original size:32 final size:32
Alignment explanation
Indices: 6866--6928 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
6856 TTGGTAATTA
*
6866 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
6898 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
6929 AATTGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:26596 original size:13 final size:12
Alignment explanation
Indices: 26575--26634 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 12
26565 TAAATGTTTT
*
26575 AAAATTATTATTA
1 AAAAATATTA-TA
26588 AAAAATATTATA
1 AAAAATATTATA
*
26600 AAAATTAATATATA
1 AAAAAT-AT-TATA
26614 AAAAATATGTATA
1 AAAAATAT-TATA
26627 AAATAATA
1 AAA-AATA
26635 AAAAACTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
12 7 0.17
13 20 0.50
14 13 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
AAAAATATTATA
Found at i:26603 original size:25 final size:27
Alignment explanation
Indices: 26575--26629 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
26565 TAAATGTTTT
*
26575 AAAATTATTAT-TAAAAAATAT-TATA
1 AAAATTAATATATAAAAAATATGTATA
26600 AAAATTAATATATAAAAAATATGTATA
1 AAAATTAATATATAAAAAATATGTATA
26627 AAA
1 AAA
26630 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 10 0.37
26 10 0.37
27 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
AAAATTAATATATAAAAAATATGTATA
Found at i:28174 original size:39 final size:40
Alignment explanation
Indices: 28127--28202 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
28117 ATACATTATC
* *
28127 ATTTATCTTTTTATTATTTGTCAA-ATAAATATATTATAT
1 ATTTATCTTTTGATTATTTATCAAGATAAATATATTATAT
* *
28166 ATTTATCTTTTGATTATTTATTAAGATTAATATATTA
1 ATTTATCTTTTGATTATTTATCAAGATAAATATATTA
28203 ATTTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 21 0.66
40 11 0.34
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (40 bp):
ATTTATCTTTTGATTATTTATCAAGATAAATATATTATAT
Found at i:28668 original size:14 final size:14
Alignment explanation
Indices: 28649--28681 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28639 AATTAAAAAC
28649 TAATTAAAATTAAA
1 TAATTAAAATTAAA
28663 TAATTAAAATTAAA
1 TAATTAAAATTAAA
*
28677 AAATT
1 TAATT
28682 TTAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATTAAAATTAAA
Found at i:28715 original size:29 final size:30
Alignment explanation
Indices: 28683--28751 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
28673 TAAAAAATTT
* *
28683 TAAATATTATATCAATCGATAT-AAATTAA
1 TAAATATTATATAAATCAATATAAAATTAA
*
28712 TAAA-ATTTATATAAATTAATATAAAATTAA
1 TAAATA-TTATATAAATCAATATAAAATTAA
28742 -AAATA-TATAT
1 TAAATATTATAT
28752 TATTATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 6 0.18
29 20 0.59
30 8 0.24
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
TAAATATTATATAAATCAATATAAAATTAA
Found at i:28733 original size:10 final size:10
Alignment explanation
Indices: 28701--28741 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
28691 ATATCAATCG
28701 ATATAAATTA
1 ATATAAATTA
*
28711 ATA-AAATTT
1 ATATAAATTA
28720 ATATAAATTA
1 ATATAAATTA
28730 ATATAAAATTA
1 ATAT-AAATTA
28741 A
1 A
28742 AAATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 8 0.30
10 12 0.44
11 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATAAATTA
Found at i:29271 original size:29 final size:30
Alignment explanation
Indices: 29238--29304 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
29228 ACCAAACTAG
29238 TATTATTTTAAAAAT-TAATTA-TTAAATAA
1 TATTATTTTAAAAATAT-ATTATTTAAATAA
*
29267 TATTATTTT-AAAATATATTATTTAAATAT
1 TATTATTTTAAAAATATATTATTTAAATAA
29296 TATT-TTTTA
1 TATTATTTTA
29305 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TATTATTTTAAAAATATATTATTTAAATAA
Found at i:29281 original size:13 final size:13
Alignment explanation
Indices: 29238--29301 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 13
29228 ACCAAACTAG
29238 TATTATTTTAAAA
1 TATTATTTTAAAA
29251 -ATTAATTATTAAATAA
1 TATT-ATT-TT-AA-AA
29267 TATTATTTTAAAA
1 TATTATTTTAAAA
*
29280 TA-TATTATTTAAA
1 TATTATT-TTAAAA
29293 TATTATTTT
1 TATTATTTT
29302 TTATTAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
12 7 0.16
13 16 0.37
14 8 0.19
15 4 0.09
16 5 0.12
17 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATTTTAAAA
Found at i:29284 original size:15 final size:15
Alignment explanation
Indices: 29238--29289 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
29228 ACCAAACTAG
29238 TATTATTTTAAAA-A
1 TATTATTTTAAAATA
*
29252 T-TAATTATT-AAATAA
1 TATTATT-TTAAAAT-A
29267 TATTATTTTAAAATA
1 TATTATTTTAAAATA
29282 TATTATTT
1 TATTATTT
29290 AAATATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 7 0.23
14 3 0.10
15 13 0.42
16 8 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTATTTTAAAATA
Found at i:29642 original size:20 final size:20
Alignment explanation
Indices: 29607--29656 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
29597 AAATTTTATC
* * *
29607 TTTTTACTTACTTTTTATGTT
1 TTTTTATTTAATTTTTA-ATT
29628 TTTTTATTTAATTTTTAATT
1 TTTTTATTTAATTTTTAATT
29648 TTTTTATTT
1 TTTTTATTT
29657 TTATTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTATTTAATTTTTAATT
Found at i:30443 original size:18 final size:17
Alignment explanation
Indices: 30420--30467 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
30410 GTATTTTAAA
*
30420 TCATGTTATTTTTTCTT
1 TCATGTTATTTTTTATT
* *
30437 GTCATG-TAGTGTTTATT
1 -TCATGTTATTTTTTATT
30454 TCATGTTATTTTTT
1 TCATGTTATTTTTT
30468 GTGAATTTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.15, C:0.08, G:0.12, T:0.65
Consensus pattern (17 bp):
TCATGTTATTTTTTATT
Found at i:30497 original size:14 final size:13
Alignment explanation
Indices: 30473--30507 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
30463 TTTTTGTGAA
*
30473 TTTACATTATATT
1 TTTATATTATATT
30486 TTATATATTATATT
1 TT-TATATTATATT
30500 TTTATATT
1 TTTATATT
30508 TTTATACCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:30835 original size:29 final size:29
Alignment explanation
Indices: 30793--30864 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
30783 CAAAAATAGT
* *
30793 ATTATTTTGGTAATATATTT-AGATACAAC
1 ATTATTTTGATAATATATTTCA-AAACAAC
* * *
30822 ATTATTTTAATAATATGTTTCAAAACAAT
1 ATTATTTTGATAATATATTTCAAAACAAC
30851 ATTATTTTGATAAT
1 ATTATTTTGATAAT
30865 TAATTTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (29 bp):
ATTATTTTGATAATATATTTCAAAACAAC
Found at i:31058 original size:2 final size:2
Alignment explanation
Indices: 31051--31076 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31041 GACTTATTTA
31051 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
31077 GAGTTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32766 original size:2 final size:2
Alignment explanation
Indices: 32759--32797 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
32749 ATCATAATTT
32759 TA TA TA TA 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 TA TA TA TA T
32798 GAATCCTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33762 original size:15 final size:15
Alignment explanation
Indices: 33728--33771 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
33718 ATAAAATAAA
33728 AATAAATTAATAAATT
1 AATAAATTAA-AAATT
*
33744 -ATAAATTAAATATT
1 AATAAATTAAAAATT
*
33758 AATAAAATAAAAAT
1 AATAAATTAAAAAT
33772 ATTTATATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAATTAAAAATT
Found at i:34268 original size:25 final size:24
Alignment explanation
Indices: 34240--34319 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
34230 TATTTATTGT
*
34240 TAATTAATTCATATTAATTTTATAA
1 TAATAAATT-ATATTAATTTTATAA
*
34265 TAATAAATTATATAATATTTTATAA
1 TAATAAATTATATTA-ATTTTATAA
*
34290 -AATAAAATATATCT-ATTTTATAA
1 TAATAAATTATAT-TAATTTTATAA
*
34313 TAGTAAA
1 TAATAAA
34320 ATTGAATTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 9 0.19
24 21 0.45
25 17 0.36
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (24 bp):
TAATAAATTATATTAATTTTATAA
Found at i:34319 original size:24 final size:25
Alignment explanation
Indices: 34256--34321 Score: 91
Period size: 24 Copynumber: 2.7 Consensus size: 25
34246 ATTCATATTA
*
34256 ATTTTATAATAATAAATTATATAAT
1 ATTTTATAATAATAAAATATATAAT
*
34281 ATTTTATAA-AATAAAATATAT-CT
1 ATTTTATAATAATAAAATATATAAT
*
34304 ATTTTATAATAGTAAAAT
1 ATTTTATAATAATAAAAT
34322 TGAATTTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.27
24 18 0.49
25 9 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTTTATAATAATAAAATATATAAT
Found at i:36310 original size:13 final size:13
Alignment explanation
Indices: 36292--36322 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
36282 CAATTTGTCC
36292 ATGTATCGATACA
1 ATGTATCGATACA
36305 ATGTATCGATACA
1 ATGTATCGATACA
*
36318 TTGTA
1 ATGTA
36323 CCATGTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:36337 original size:33 final size:34
Alignment explanation
Indices: 36271--36338 Score: 104
Period size: 33 Copynumber: 2.0 Consensus size: 34
36261 TGCCAATTTC
*
36271 ATGTATCGATACAATTTGTCCATGTATCGATACA
1 ATGTATCGATACAATTTGTCCATGTATCAATACA
36305 ATGTATCGATAC-A-TTGTACCATGTATCAATACA
1 ATGTATCGATACAATTTGT-CCATGTATCAATACA
36338 A
1 A
36339 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 4 0.12
33 16 0.50
34 12 0.38
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (34 bp):
ATGTATCGATACAATTTGTCCATGTATCAATACA
Found at i:36340 original size:97 final size:97
Alignment explanation
Indices: 36175--36401 Score: 402
Period size: 97 Copynumber: 2.4 Consensus size: 97
36165 GTTACAAGCT
* *
36175 ATGTATCGATAC-ATTTCTTCATGTATCGATACAATGCATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACAATTTGTTCATGTATCGATACAATGCATCGATACATTGTACCATGTATCAATA
36239 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
* *
36271 ATGTATCGATACAATTTGTCCATGTATCGATACAATGTATCGATACATTGTACCATGTATCAATA
1 ATGTATCGATACAATTTGTTCATGTATCGATACAATGCATCGATACATTGTACCATGTATCAATA
36336 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
*
36368 ATGTATTGATACAATTTGTTCATGTATCGATACA
1 ATGTATCGATACAATTTGTTCATGTATCGATACA
36402 TTGAACATGT
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
96 12 0.10
97 112 0.90
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (97 bp):
ATGTATCGATACAATTTGTTCATGTATCGATACAATGCATCGATACATTGTACCATGTATCAATA
CAAATAGTGATAGGGTAGCTACTGCCAATTTC
Found at i:36412 original size:19 final size:19
Alignment explanation
Indices: 36388--36455 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
36378 ACAATTTGTT
36388 CATGTATCGATACATTGAA
1 CATGTATCGATACATTGAA
36407 CATGTATCGAT--A---AA
1 CATGTATCGATACATTGAA
**
36421 -ATGTATCGATACAAGGCAA
1 CATGTATCGATACATTG-AA
36440 CATGTATCGATACATT
1 CATGTATCGATACATT
36456 TGGGTGTGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
13 10 0.25
14 2 0.05
15 1 0.03
17 1 0.03
19 13 0.32
20 13 0.32
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:36447 original size:33 final size:32
Alignment explanation
Indices: 36389--36451 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
36379 CAATTTGTTC
**
36389 ATGTATCGATACATTGAACATGTATCGATAAA
1 ATGTATCGATACAAGGAACATGTATCGATAAA
36421 ATGTATCGATACAAGGCAACATGTATCGATA
1 ATGTATCGATACAAGG-AACATGTATCGATA
36452 CATTTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAGGAACATGTATCGATAAA
Found at i:37008 original size:19 final size:19
Alignment explanation
Indices: 36984--37068 Score: 133
Period size: 19 Copynumber: 4.7 Consensus size: 19
36974 TTAAAAAAAT
36984 TCTCCCCCTTAAACGAATA
1 TCTCCCCCTTAAACGAATA
37003 TCTCCCCCTT-AA--AAT-
1 TCTCCCCCTTAAACGAATA
*
37018 TCTCCCCCTTTAACGAATA
1 TCTCCCCCTTAAACGAATA
37037 TCTCCCCCTTAAACGAATA
1 TCTCCCCCTTAAACGAATA
37056 TCTCCCCCTTAAA
1 TCTCCCCCTTAAA
37069 TAGTTATCTT
Statistics
Matches: 61, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
15 10 0.16
16 5 0.08
18 5 0.08
19 41 0.67
ACGTcount: A:0.28, C:0.39, G:0.04, T:0.29
Consensus pattern (19 bp):
TCTCCCCCTTAAACGAATA
Found at i:37020 original size:34 final size:35
Alignment explanation
Indices: 36978--37068 Score: 139
Period size: 34 Copynumber: 2.5 Consensus size: 35
36968 TTTTCCTTAA
36978 AAAAATTCTCCCCCTTAAACGAATATCTCCCCCTT
1 AAAAATTCTCCCCCTTAAACGAATATCTCCCCCTT
*
37013 -AAAATTCTCCCCCTTTAACGAATATCTCCCCCTT
1 AAAAATTCTCCCCCTTAAACGAATATCTCCCCCTT
37047 AAACGAATATCTCCCCCTTAAA
1 AAA--AAT-TCTCCCCCTTAAA
37069 TAGTTATCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
34 33 0.66
35 2 0.04
37 3 0.06
38 12 0.24
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (35 bp):
AAAAATTCTCCCCCTTAAACGAATATCTCCCCCTT
Found at i:37077 original size:19 final size:19
Alignment explanation
Indices: 36972--37068 Score: 114
Period size: 19 Copynumber: 5.4 Consensus size: 19
36962 TTTCATTTTT
*
36972 CCTTAAAAAAAT-TCTCCC
1 CCTTAAAAGAATATCTCCC
*
36990 CCTTAAACGAATATCTCCC
1 CCTTAAAAGAATATCTCCC
37009 CCTT--AA-AAT-TCTCCC
1 CCTTAAAAGAATATCTCCC
* *
37024 CCTTTAACGAATATCTCCC
1 CCTTAAAAGAATATCTCCC
*
37043 CCTTAAACGAATATCTCCC
1 CCTTAAAAGAATATCTCCC
37062 CCTTAAA
1 CCTTAAA
37069 TAGTTATCTT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
15 10 0.14
16 3 0.04
17 2 0.03
18 13 0.19
19 41 0.59
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (19 bp):
CCTTAAAAGAATATCTCCC
Found at i:38915 original size:13 final size:13
Alignment explanation
Indices: 38897--38924 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38887 AATAGTACCT
38897 AATGTATCGATAC
1 AATGTATCGATAC
38910 AATGTATCGATAC
1 AATGTATCGATAC
38923 AA
1 AA
38925 GGAATGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:44308 original size:24 final size:24
Alignment explanation
Indices: 44259--44318 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
44249 ACAAGCGATT
*
44259 AATAAAAA-CAAAATTATTAATATA
1 AATAAAAATC-AAATTATCAATATA
44283 AATAAAAATCAAATTATCAAGT-TA
1 AATAAAAATCAAATTATCAA-TATA
*
44307 AATGAAAATCAA
1 AATAAAAATCAA
44319 TCTTACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (24 bp):
AATAAAAATCAAATTATCAATATA
Found at i:55106 original size:20 final size:20
Alignment explanation
Indices: 55081--55137 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 20
55071 GTTACAAGCT
55081 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
55101 ATGTATCGATACATACATTTCTTC
1 ATGTATCG----ATACATTTCTTC
55125 ATGTATCGATACA
1 ATGTATCGATACA
55138 ATGTATCGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 13 0.39
24 20 0.61
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTCTTC
Found at i:55121 original size:24 final size:24
Alignment explanation
Indices: 55089--55137 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
55079 CTATGTATCG
55089 ATACATTTCTTCATGTATCGATAC
1 ATACATTTCTTCATGTATCGATAC
55113 ATACATTTCTTCATGTATCGATAC
1 ATACATTTCTTCATGTATCGATAC
55137 A
1 A
55138 ATGTATCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (24 bp):
ATACATTTCTTCATGTATCGATAC
Found at i:55155 original size:20 final size:20
Alignment explanation
Indices: 55132--55190 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
55122 TTCATGTATC
55132 GATACAATGTATCGATACAT
1 GATACAATGTATCGATACAT
55152 GATACAATGTATCGATACAT
1 GATACAATGTATCGATACAT
*
55172 GATACAATGTATTGATACA
1 GATACAATGTATCGATACA
55191 AATAGTGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (20 bp):
GATACAATGTATCGATACAT
Found at i:55170 original size:13 final size:13
Alignment explanation
Indices: 55125--55150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55115 ACATTTCTTC
55125 ATGTATCGATACA
1 ATGTATCGATACA
55138 ATGTATCGATACA
1 ATGTATCGATACA
55151 TGATACAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:55251 original size:84 final size:84
Alignment explanation
Indices: 55156--55369 Score: 270
Period size: 95 Copynumber: 2.4 Consensus size: 84
55146 ATACATGATA
*
55156 CAATGTATCGATACATGATACAATGTATTGATACAAATAGTGATAGGGTAGCTACTGCCAATTTC
1 CAATGTATCGATACATGATACAATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTC
55221 ATGTATCGATACAATTCGT
66 ATGTATCGATACAATTCGT
*
55240 CAATGTATCGATAATGTATCGATACATTGTACCATGTATCGATACAAATAGTGATAGGGTAGCTA
1 CAATGTATCGAT-A--CAT-GATAC-----A--ATGTATCGATACAAATAGTGATAGGGTAGCTA
*
55305 CTGCCAATTTCATGTATCGATACAATTTGT
55 CTGCCAATTTCATGTATCGATACAATTCGT
*
55335 CCATGTATCGATACATTGA-AC-ATGTATCGATACAA
1 CAATGTATCGATACA-TGATACAATGTATCGATACAA
55370 TGTATCGACA
Statistics
Matches: 113, Mismatches: 5, Indels: 25
0.79 0.03 0.17
Matches are distributed among these distances:
83 14 0.12
84 12 0.11
85 1 0.01
87 2 0.02
88 5 0.04
91 2 0.02
92 3 0.03
93 2 0.02
94 1 0.01
95 71 0.63
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (84 bp):
CAATGTATCGATACATGATACAATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTC
ATGTATCGATACAATTCGT
Found at i:55277 original size:95 final size:95
Alignment explanation
Indices: 55157--55347 Score: 330
Period size: 95 Copynumber: 2.0 Consensus size: 95
55147 TACATGATAC
*
55157 AATGTATCGATACATGATACAATGTATTGATACAAATAGTGATAGGGTAGCTACTGCCAATTTCA
1 AATGTATCGATACATGATACAATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTCA
55222 TGTATCGATACAATTCGTCAATGTATCGAT
66 TGTATCGATACAATTCGTCAATGTATCGAT
*
55252 AATGTATCGATACATTG-TACCATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTC
1 AATGTATCGATACA-TGATACAATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTC
* *
55316 ATGTATCGATACAATTTGTCCATGTATCGAT
65 ATGTATCGATACAATTCGTCAATGTATCGAT
55347 A
1 A
55348 CATTGAACAT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 89 0.98
96 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (95 bp):
AATGTATCGATACATGATACAATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTCA
TGTATCGATACAATTCGTCAATGTATCGAT
Found at i:55280 original size:31 final size:32
Alignment explanation
Indices: 55221--55283 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
55211 TGCCAATTTC
55221 ATGTATCGATACAATTCGTCAATGTATCGATA
1 ATGTATCGATACAATTCGTCAATGTATCGATA
*
55253 ATGTATCGATAC-ATT-GTACCATGTATCGATA
1 ATGTATCGATACAATTCGT-CAATGTATCGATA
55284 CAAATAGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 2 0.07
31 15 0.52
32 12 0.41
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
ATGTATCGATACAATTCGTCAATGTATCGATA
Found at i:55341 original size:21 final size:21
Alignment explanation
Indices: 55315--55370 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
55305 CTGCCAATTT
**
55315 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
55336 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
55355 CATGTATCGATACAAT
1 CATGTATCGATACAAT
55371 GTATCGACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:56249 original size:16 final size:16
Alignment explanation
Indices: 56220--56273 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
56210 CTTGAATTTC
*
56220 ACTTAAATTG-CTTAA
1 ACTTAAAATGACTTAA
56235 ACTTAAAATGACTTAAA
1 ACTTAAAATGACTT-AA
*
56252 AC-T-AAATGACATAA
1 ACTTAAAATGACTTAA
*
56266 ACTCAAAA
1 ACTTAAAA
56274 ATAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.12
15 17 0.53
16 7 0.22
17 4 0.12
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.28
Consensus pattern (16 bp):
ACTTAAAATGACTTAA
Found at i:56292 original size:17 final size:17
Alignment explanation
Indices: 56272--56305 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56262 ATAAACTCAA
56272 AAATAATTTAAAAAATT
1 AAATAATTTAAAAAATT
* *
56289 AAATATTTTAAATAATT
1 AAATAATTTAAAAAATT
56306 CAACTCGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAATTTAAAAAATT
Found at i:57727 original size:2 final size:2
Alignment explanation
Indices: 57714--57745 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
57704 TGAAACTCTT
*
57714 TA TA TT 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
57746 ATTGAGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:59113 original size:17 final size:17
Alignment explanation
Indices: 59061--59117 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
59051 CAAATTTGAA
*
59061 TATTTAAATTTGATA-TT
1 TATTT-AATTTTATATTT
*
59078 TATTTATTATTTA-ACTTT
1 TATTTAAT-TTTATA-TTT
59096 TATTTAATTTTATATTT
1 TATTTAATTTTATATTT
59113 TATTT
1 TATTT
59118 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.09
17 20 0.61
18 10 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTAATTTTATATTT
Found at i:59117 original size:12 final size:12
Alignment explanation
Indices: 59060--59118 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 12
59050 GCAAATTTGA
*
59060 ATATTTAAATTTG
1 ATATTT-AATTTT
59073 ATATTT-A-TTT
1 ATATTTAATTTT
*
59083 ATTATTTAACTTT
1 A-TATTTAATTTT
59096 -TATTTAATTTT
1 ATATTTAATTTT
*
59107 ATATTTTATTTT
1 ATATTTAATTTT
59119 TTAAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 3 0.08
11 16 0.41
12 11 0.28
13 9 0.23
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:59150 original size:17 final size:17
Alignment explanation
Indices: 59128--59164 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
59118 TTTAAAAATT
*
59128 TATTTAATAAATTTAAA
1 TATTTAAAAAATTTAAA
*
59145 TATTTAAAAAATTTCAA
1 TATTTAAAAAATTTAAA
59162 TAT
1 TAT
59165 ATGATGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTAAAAAATTTAAA
Found at i:59255 original size:26 final size:24
Alignment explanation
Indices: 59212--59260 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
59202 AGATAATACG
59212 TGGATAATAAATAAATTTAAATTT
1 TGGATAATAAATAAATTTAAATTT
*
59236 TGGATAAATTAAATAGATTTAAATT
1 TGGAT-AA-TAAATAAATTTAAATT
59261 CAAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
26 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (24 bp):
TGGATAATAAATAAATTTAAATTT
Found at i:61586 original size:23 final size:24
Alignment explanation
Indices: 61552--61605 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
61542 TTAAAAAAAA
61552 TTTT-ATTAAAATTTTTTAT-TA-AG
1 TTTTAATTAAAA--TTTTATGTAGAG
61575 TTTTAATT-AAATTTTATGTAGAG
1 TTTTAATTAAAATTTTATGTAGAG
61598 TTTTAATT
1 TTTTAATT
61606 TTGAATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.21
22 2 0.07
23 17 0.61
24 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTTAATTAAAATTTTATGTAGAG
Found at i:62923 original size:37 final size:37
Alignment explanation
Indices: 62889--62976 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
62879 TGGATTGGTG
*
62889 CTGCCACCCAAATTCTAACAATCATAGTAGATTGGCA
1 CTGCCACCCAAATACTAACAATCATAGTAGATTGGCA
* *
62926 CTGCCACCCAAATACTAATAATCATAGTGGATTGGCTA
1 CTGCCACCCAAATACTAACAATCATAGTAGATTGGC-A
*
62964 -AGCCACCCAAATA
1 CTGCCACCCAAATA
62977 TTACTTGTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 45 0.98
38 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (37 bp):
CTGCCACCCAAATACTAACAATCATAGTAGATTGGCA
Found at i:68390 original size:20 final size:21
Alignment explanation
Indices: 68365--68406 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
68355 ATTTGCCTGC
68365 ATGTATCGATACAT-TGAATA
1 ATGTATCGATACATCTGAATA
68385 ATGTATCGATACATCTGAATA
1 ATGTATCGATACATCTGAATA
68406 A
1 A
68407 AATTTCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATCTGAATA
Found at i:68455 original size:13 final size:13
Alignment explanation
Indices: 68416--68458 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
68406 AAATTTCCCA
68416 AATGTATCGATAC
1 AATGTATCGATAC
*
68429 AAAGATCAATCGATAC
1 AATG-T--ATCGATAC
68445 AATGTATCGATAC
1 AATGTATCGATAC
68458 A
1 A
68459 TTGAGTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 12 0.48
14 1 0.04
15 1 0.04
16 11 0.44
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:68534 original size:19 final size:21
Alignment explanation
Indices: 68510--68562 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
68500 AGCGATACAT
68510 TGTATCGATACAA-CACT-TA
1 TGTATCGATACAATCACTATA
* *
68529 TGTATCGATACAATTACTATT
1 TGTATCGATACAATCACTATA
68550 TGTATCGATACAA
1 TGTATCGATACAA
68563 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTATCGATACAATCACTATA
Found at i:71093 original size:37 final size:37
Alignment explanation
Indices: 71041--71139 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
71031 TTTATTTTTC
** * *
71041 GTGGATTGGCGCTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGAACTGCCACCAAAATACTAACAATCATA
71078 GTGGATTGGAACTGCCACCAAAATACTAACAATCATA
1 GTGGATTGGAACTGCCACCAAAATACTAACAATCATA
71115 GTGGATTGGCCAA--GCCACCAAAATA
1 GTGGATTGG--AACTGCCACCAAAATA
71140 TCACTTGTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
37 54 0.96
39 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (37 bp):
GTGGATTGGAACTGCCACCAAAATACTAACAATCATA
Found at i:76508 original size:35 final size:33
Alignment explanation
Indices: 76451--76516 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 33
76441 ATTTAACATG
76451 AATAATAAAAAAAATAAAAATAAAAAAGTAAGA
1 AATAATAAAAAAAATAAAAATAAAAAAGTAAGA
* *
76484 AATAATAATAAAAATATAATAATAAAATAGTAA
1 AATAATAA-AAAAA-ATAAAAATAAAAAAGTAA
76517 TAGTTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 8 0.28
34 5 0.17
35 16 0.55
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (33 bp):
AATAATAAAAAAAATAAAAATAAAAAAGTAAGA
Found at i:76518 original size:14 final size:14
Alignment explanation
Indices: 76463--76510 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
76453 TAATAAAAAA
*
76463 AATAAAAATA-AAA
1 AATAAAAATATAAT
*
76476 AAGTAAGAA-ATAAT
1 AA-TAAAAATATAAT
76490 AATAAAAATATAAT
1 AATAAAAATATAAT
76504 AATAAAA
1 AATAAAA
76511 TAGTAATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (14 bp):
AATAAAAATATAAT
Found at i:77202 original size:22 final size:22
Alignment explanation
Indices: 77153--77202 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
77143 GAAACCGATG
* * *
77153 CAGCAATGAAGATATCAATGGG
1 CAGCAATGAAGACATCAACGGA
*
77175 CTGCAATGAAGACATCAACGGA
1 CAGCAATGAAGACATCAACGGA
77197 CAGCAA
1 CAGCAA
77203 AGAATGCAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (22 bp):
CAGCAATGAAGACATCAACGGA
Found at i:78818 original size:162 final size:161
Alignment explanation
Indices: 78592--79368 Score: 953
Period size: 163 Copynumber: 4.8 Consensus size: 161
78582 TTTTTATATT
* * * *
78592 AAAATGGTC-TTTTATGCTCACTCGAGTCATATTTTTATATTCCTATGATTTTTTATTA-GGGTA
1 AAAATGGTCGTTTT-TGC-CACTCGAGTCATGTTCTCATATTCCTATGATTTTTCA-TAGGGGTA
* * * *
78655 TAAAAATTTTTAAAACCTTTCATATCTCTTAA-TTTTCTATCGGGTACGAAACGTAATTTTCAAA
63 TAAAAATTTTTAAAACCTTTCGTATCCCCTAATTTTTC-GTCGGGTACGAAACGTAATTTTCAAA
* *
78719 ATTTAGAAGTGTTTGTCCCATTTACATTGATATAAA
127 ATTTAAAAGTGTTTG-CCCTTTTACATTGATATAAA
* *
78755 AAAATGGTCGTTTTTGCCACTCAAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATAC
1 AAAATGGTCGTTTTTGCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATAA
* * *
78820 AAATTTTTAAAACCTTTCGTATCCCCTAGTTTTTCGTCGGGTACGAAATGTAATTTTTAAAATTT
66 AAATTTTTAAAACCTTTCGTATCCCCTAATTTTTCGTCGGGTACGAAACGTAATTTTCAAAATTT
78885 AAAAGTGTTTGGCCCCTTTTACATTGATATAAA
131 AAAAGTGTTT-G-CCCTTTTACATTGATATAAA
* **
78918 AAAAT-GACGTTTTTGCCCACTTAAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
1 AAAATGGTCGTTTTTG-CCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
* * * *
78982 AAAATGTTTAAAACCTTTTGTATCCCCTGATTTTTCGTCGGGTACGAAACGTAATTTTTAAAATT
65 AAAATTTTTAAAACCTTTCGTATCCCCTAATTTTTCGTCGGGTACGAAACGTAATTTTCAAAATT
* *
79047 TAAAAGTATTTGACCTTTTTACATTGATATAAA
130 TAAAAGTGTTTG-CCCTTTTACATTGATATAAA
* * * *
79080 AAAAGGGTCGTTTTTGCTTACTCGAGTCATGTTCTTATATTCCTATGATTTTTCATAGAGGTATA
1 AAAATGGTCGTTTTTGC-CACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
* * *
79145 AAAATTTTTAAAACCTTTCGTATCCCCTGATTTTTCGTCAGATACGAAACGTAATTTTCAAAATT
65 AAAATTTTTAAAACCTTTCGTATCCCCTAATTTTTCGTCGGGTACGAAACGTAATTTTCAAAATT
* *
79210 TAGAAGTGTTCTGCCCCTTTACATTGATATAAA
130 TAAAAGTGTT-TGCCCTTTTACATTGATATAAA
* * * * ** *
79243 AGAAAAGATCGTTTTTGCC-CGTTCGAGTCATGTTTTCATATTCCTATGGTTTTTTGTAGGAGTA
1 A-AAATGGTCGTTTTTGCCAC--TCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTA
* * * *
79307 TAAAAATTTTTAAAA-CATT--TATCCCCTGATATTTT-GTCGGGTATGAAACATAATTTT-AAA
63 TAAAAATTTTTAAAACCTTTCGTATCCCCTAAT-TTTTCGTCGGGTACGAAACGTAATTTTCAAA
79367 AT
127 AT
79369 AAAATAAATT
Statistics
Matches: 544, Mismatches: 58, Indels: 27
0.86 0.09 0.04
Matches are distributed among these distances:
160 5 0.01
161 31 0.06
162 139 0.26
163 299 0.55
164 70 0.13
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (161 bp):
AAAATGGTCGTTTTTGCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATAA
AAATTTTTAAAACCTTTCGTATCCCCTAATTTTTCGTCGGGTACGAAACGTAATTTTCAAAATTT
AAAAGTGTTTGCCCTTTTACATTGATATAAA
Found at i:79233 original size:325 final size:326
Alignment explanation
Indices: 78628--79368 Score: 1011
Period size: 325 Copynumber: 2.3 Consensus size: 326
78618 TCATATTTTT
* * * *
78628 ATATTCCTATGATTTTTTATTA-GGGTATAAAAATTTTTAAAACCTTTCATAT-CTCTTAATTTT
1 ATATTCCTATGATTTTTTA-TAGGGGTATAAAAATTTTTAAAACCTTT-TTATCCCCTGATTTTT
* * * * *
78691 CTATCGGGTACGAAACGTAATTTTCAAAATTTAGAAGTGTTTGTCCCATTTACATTGATATAAAA
64 C-GTCGGGTACGAAACGTAATTTTTAAAATTTAAAAGTATTTGACCCATTTACATTGATATAAAA
* * *
78756 AAATGGTCGTTTTTGCCACTCAAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATACA
128 AAAGGGTCGTTTTTGCCACTCAAGTCATGTTCTCATATTCCTATGATTTTTCATAGAGGTATAAA
* * * *
78821 AATTTTTAAAACCTTTCGTATCCCCTAGTTTTTCGTCGGGTACGAAATGTAATTTTTAAAATTTA
193 AATTTTTAAAACCTTTCGTATCCCCTAGTTTTTCGTCAGATACGAAACGTAATTTTCAAAATTTA
*
78886 AAAGTGTTTGGCCCCTTTTACATTGATATAAAA-AAATGA-CGTTTTTGCCCACTT-AAGTCATG
258 AAAGTGTTTGGCCCCTTTTACATTGATATAAAAGAAAAGATCGTTTTTGCCC-CTTCAAGTCATG
78948 TTCTC
322 TTCTC
* *
78953 ATATTCCTATGATTTTTCATAGGGGTATAAAAATGTTTAAAACCTTTTGTATCCCCTGATTTTTC
1 ATATTCCTATGATTTTTTATAGGGGTATAAAAATTTTTAAAACCTTTT-TATCCCCTGATTTTTC
**
79018 GTCGGGTACGAAACGTAATTTTTAAAATTTAAAAGTATTTGACCTTTTTACATTGATATAAAAAA
65 GTCGGGTACGAAACGTAATTTTTAAAATTTAAAAGTATTTGACCCATTTACATTGATATAAAAAA
* * *
79083 AGGGTCGTTTTTGCTTACTCGAGTCATGTTCTTATATTCCTATGATTTTTCATAGAGGTATAAAA
130 AGGGTCGTTTTTGC-CACTCAAGTCATGTTCTCATATTCCTATGATTTTTCATAGAGGTATAAAA
79148 ATTTTTAAAACCTTTCGTATCCCCT-GATTTTTCGTCAGATACGAAACGTAATTTTCAAAATTTA
194 ATTTTTAAAACCTTTCGTATCCCCTAG-TTTTTCGTCAGATACGAAACGTAATTTTCAAAATTTA
* * *
79212 GAAGTGTTCT-GCCCC-TTTACATTGATATAAAAGAAAAGATCGTTTTTGCCCGTTCGAGTCATG
258 AAAGTGTT-TGGCCCCTTTTACATTGATATAAAAGAAAAGATCGTTTTTGCCCCTTCAAGTCATG
*
79275 TTTTC
322 TTCTC
* * * *
79280 ATATTCCTATGGTTTTTTGTAGGAGTATAAAAATTTTTAAAA-C-ATTTATCCCCTGATATTTT-
1 ATATTCCTATGATTTTTTATAGGGGTATAAAAATTTTTAAAACCTTTTTATCCCCTGAT-TTTTC
* *
79342 GTCGGGTATGAAACATAA-TTTTAAAAT
65 GTCGGGTACGAAACGTAATTTTTAAAAT
79369 AAAATAAATT
Statistics
Matches: 370, Mismatches: 36, Indels: 22
0.86 0.08 0.05
Matches are distributed among these distances:
323 9 0.02
324 29 0.08
325 140 0.38
326 132 0.36
327 60 0.16
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (326 bp):
ATATTCCTATGATTTTTTATAGGGGTATAAAAATTTTTAAAACCTTTTTATCCCCTGATTTTTCG
TCGGGTACGAAACGTAATTTTTAAAATTTAAAAGTATTTGACCCATTTACATTGATATAAAAAAA
GGGTCGTTTTTGCCACTCAAGTCATGTTCTCATATTCCTATGATTTTTCATAGAGGTATAAAAAT
TTTTAAAACCTTTCGTATCCCCTAGTTTTTCGTCAGATACGAAACGTAATTTTCAAAATTTAAAA
GTGTTTGGCCCCTTTTACATTGATATAAAAGAAAAGATCGTTTTTGCCCCTTCAAGTCATGTTCT
C
Found at i:81750 original size:166 final size:167
Alignment explanation
Indices: 81554--81874 Score: 468
Period size: 167 Copynumber: 1.9 Consensus size: 167
81544 CTAAAAGTTG
*
81554 AGGCTATCCACGAGTCAACTATT-TTTTTTTTCATTTTTCCTTTGATTG-TCGTGTAGTCATTTC
1 AGGCTATCCACGAGTCAACTATTATTTTTTTTCATTTTTCCGTTGATTGCT-GTGTAGTCATTTC
*
81617 TATTACTTTTTCTCCATTCTTTGTACTTAACCTATTTGT-TCAAGTTAAAAAACTGATGAGTTTA
65 TATTACTTTTTCTCCATTCTTTGTACTCAACCTATTTGTCT-AAGTTAAAAAACTGATGAGTTTA
* *
81681 GAAAAGATTTTACAGAGACATTAAAAGATTTAATAGCTA
129 AAAAAGATTTTACAAAGACATTAAAAGATTTAATAGCTA
* * *
81720 AGGCTATCCATGTGTCAACTATTATTTTTTTTCATTTTTCCGTTGGTTGCTGTGTAGTCATTTCT
1 AGGCTATCCACGAGTCAACTATTATTTTTTTTCATTTTTCCGTTGATTGCTGTGTAGTCATTTCT
* * * * ** *
81785 ATTGCTTTTTCTTCATTCTTTGTACTCAGCCTTTTTGTCTAAGTTAAAAAGTTTATGAGTTTAAA
66 ATTACTTTTTCTCCATTCTTTGTACTCAACCTATTTGTCTAAGTTAAAAAACTGATGAGTTTAAA
*
81850 AAAGATTTTACAAAGATATTAAAAG
131 AAAGATTTTACAAAGACATTAAAAG
81875 CTTTTATGTA
Statistics
Matches: 137, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
166 21 0.15
167 114 0.83
168 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (167 bp):
AGGCTATCCACGAGTCAACTATTATTTTTTTTCATTTTTCCGTTGATTGCTGTGTAGTCATTTCT
ATTACTTTTTCTCCATTCTTTGTACTCAACCTATTTGTCTAAGTTAAAAAACTGATGAGTTTAAA
AAAGATTTTACAAAGACATTAAAAGATTTAATAGCTA
Found at i:82628 original size:13 final size:12
Alignment explanation
Indices: 82606--82640 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
82596 TTCTTAATAC
82606 TTTTTTTTTATT
1 TTTTTTTTTATT
82618 TTTTGTTTTTATT
1 TTTT-TTTTTATT
82631 TTTATTTTTT
1 TTT-TTTTTT
82641 TTACTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 16 0.76
14 1 0.05
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:84024 original size:20 final size:22
Alignment explanation
Indices: 83999--84055 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 22
83989 CATTATTTAA
83999 TATTGGCATG-G-CTATTATTC
1 TATTGGCATGTGACTATTATTC
84019 TATTGGCATGTGTAATCTATTATTC
1 TATTGGCATGTG--A-CTATTATTC
84044 TATTGGCATGTG
1 TATTGGCATGTG
84056 TAATTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.31
21 1 0.03
25 21 0.66
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (22 bp):
TATTGGCATGTGACTATTATTC
Found at i:84039 original size:25 final size:25
Alignment explanation
Indices: 84010--84059 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
84000 ATTGGCATGG
84010 CTATTATTCTATTGGCATGTGTAAT
1 CTATTATTCTATTGGCATGTGTAAT
84035 CTATTATTCTATTGGCATGTGTAAT
1 CTATTATTCTATTGGCATGTGTAAT
84060 TTTTGTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (25 bp):
CTATTATTCTATTGGCATGTGTAAT
Found at i:86484 original size:19 final size:19
Alignment explanation
Indices: 86452--86506 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
86442 TTATATTATT
86452 TATATAATTA-TAAATATAA
1 TATA-AATTATTAAATATAA
* *
86471 TATAAATTATTAAATTTAT
1 TATAAATTATTAAATATAA
*
86490 TA-AAATT-TTAAAAATAA
1 TATAAATTATTAAATATAA
86507 ATGTTATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.23
18 10 0.33
19 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAAATTATTAAATATAA
Found at i:86558 original size:17 final size:17
Alignment explanation
Indices: 86538--86589 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
86528 ATAATATTTA
86538 TTATAATATTTTTATAT
1 TTATAATATTTTTATAT
* * *
86555 TTATAAAAATTTAATAT
1 TTATAATATTTTTATAT
*
86572 TTATATTATATTTTATAT
1 TTATAATAT-TTTTATAT
86590 AGTATATAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATAATATTTTTATAT
Found at i:86570 original size:37 final size:38
Alignment explanation
Indices: 86529--86600 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
86519 GATAATTATA
*
86529 TAATATTTATTATAATATTTT-TATA-TTTATAAAAATT
1 TAATATTTA-TATAATATTTTATATAGTATATAAAAATT
*
86566 TAATATTTATATTATATTTTATATAGTATATAAAA
1 TAATATTTATATAATATTTTATATAGTATATAAAA
86601 TTATGCAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 10 0.32
37 13 0.42
38 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (38 bp):
TAATATTTATATAATATTTTATATAGTATATAAAAATT
Found at i:87930 original size:24 final size:26
Alignment explanation
Indices: 87903--87953 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
87893 ATGATATGTA
87903 TTAAATATATCATATTA-ATT-GTGT
1 TTAAATATATCATATTATATTGGTGT
* *
87927 TTAAATATGTTATATTATATTGGTGT
1 TTAAATATATCATATTATATTGGTGT
87953 T
1 T
87954 GATTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (26 bp):
TTAAATATATCATATTATATTGGTGT
Found at i:90329 original size:2 final size:2
Alignment explanation
Indices: 90324--90350 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
90314 GTTTTTTGGT
90324 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 T
90351 GCATATGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93804 original size:26 final size:27
Alignment explanation
Indices: 93775--93825 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
93765 TTTCTTGATT
*
93775 GAAA-AACGGGGTTGGAGTATCCCCTC
1 GAAAGAACGGGGTTAGAGTATCCCCTC
*
93801 GAAAGAATGGGGTTAGAGTATCCCC
1 GAAAGAACGGGGTTAGAGTATCCCC
93826 GATGATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (27 bp):
GAAAGAACGGGGTTAGAGTATCCCCTC
Found at i:96154 original size:20 final size:19
Alignment explanation
Indices: 96125--96196 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
96115 AAAAAGACAT
96125 AATGTATCGATATATTGTA
1 AATGTATCGATATATTGTA
* * *
96144 GAATATATCGATACATTCATA
1 -AATGTATCGATATATT-GTA
* *
96165 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTG-TA
96185 AATGTATCGATA
1 AATGTATCGATA
96197 CATCAAGGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
AATGTATCGATATATTGTA
Found at i:96181 original size:40 final size:39
Alignment explanation
Indices: 96122--96199 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
96112 GGTAAAAAGA
* *
96122 CATAATGTATCGATATATTGTAGAATATATCGATACATT
1 CATAATGTATCGATATATTGAAAAATATATCGATACATT
*
96161 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATATATTGAAAAATATATCGATACAT
96200 CAAGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATATATTGAAAAATATATCGATACATT
Found at i:97084 original size:16 final size:16
Alignment explanation
Indices: 97023--97103 Score: 74
Period size: 16 Copynumber: 5.1 Consensus size: 16
97013 CAGGTTCAGA
* *
97023 TTATTTTGGGTTCAGG
1 TTATTTTGAGTTCGGG
** *
97039 TCCTTTCGAGTTCGGG
1 TTATTTTGAGTTCGGG
* *
97055 TCATTTCG-GATTCGGG
1 TTATTTTGAG-TTCGGG
*
97071 TTGTTTTGAGTTCGGG
1 TTATTTTGAGTTCGGG
97087 TTATTTTGAGTTCGGG
1 TTATTTTGAGTTCGGG
97103 T
1 T
97104 CAATCGGGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
15 1 0.02
16 51 0.96
17 1 0.02
ACGTcount: A:0.10, C:0.12, G:0.32, T:0.46
Consensus pattern (16 bp):
TTATTTTGAGTTCGGG
Found at i:97101 original size:32 final size:31
Alignment explanation
Indices: 97023--97104 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
97013 CAGGTTCAGA
*
97023 TTATTTTGGGTTCAGGTCCTTTCGAGTTCGGG
1 TTATTTT-GGTTCGGGTCCTTTCGAGTTCGGG
* * ** *
97055 TCATTTCGGATTCGGGTTGTTTTGAGTTCGGG
1 TTATTTTGG-TTCGGGTCCTTTCGAGTTCGGG
97087 TTATTTTGAGTTCGGGTC
1 TTATTTTG-GTTCGGGTC
97105 AATCGGGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
31 2 0.05
32 36 0.92
33 1 0.03
ACGTcount: A:0.10, C:0.13, G:0.32, T:0.45
Consensus pattern (31 bp):
TTATTTTGGTTCGGGTCCTTTCGAGTTCGGG
Found at i:97157 original size:44 final size:45
Alignment explanation
Indices: 97107--97191 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
97097 TTCGGGTCAA
* **
97107 TCGGGTTTAACACTCAGGTT-AATTGGGTTCGGGTCATTTTGGAT
1 TCGGGTTTAACACTCAGGTTAAATTAGGTTCAAGTCATTTTGGAT
* *
97151 TCGGGTTTAACATTCGGGTTAAATTAGGTTCAAGTCATTTT
1 TCGGGTTTAACACTCAGGTTAAATTAGGTTCAAGTCATTTT
97192 AAATTTAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 18 0.51
45 17 0.49
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (45 bp):
TCGGGTTTAACACTCAGGTTAAATTAGGTTCAAGTCATTTTGGAT
Found at i:98556 original size:15 final size:15
Alignment explanation
Indices: 98538--98588 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
98528 ATCTTCTTCT
98538 TTCTTCTTCTCTTGC
1 TTCTTCTTCTCTTGC
*
98553 TTCTTCATATTTTCTT-C
1 TTCTTC---TTCTCTTGC
98570 TTTCTTCTTCTCTTGC
1 -TTCTTCTTCTCTTGC
98586 TTC
1 TTC
98589 CTCCAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 15 0.52
16 1 0.03
17 1 0.03
18 12 0.41
ACGTcount: A:0.04, C:0.29, G:0.04, T:0.63
Consensus pattern (15 bp):
TTCTTCTTCTCTTGC
Found at i:98561 original size:33 final size:33
Alignment explanation
Indices: 98524--98588 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
98514 TTGGAGTTGC
98524 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
1 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
*
98557 TCATATTTTCTTCTTTCTTCTTCTCTTGCTTC
1 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTC
98589 CTCCAACCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.06, C:0.29, G:0.03, T:0.62
Consensus pattern (33 bp):
TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
Found at i:98574 original size:18 final size:18
Alignment explanation
Indices: 98524--98576 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
98514 TTGGAGTTGC
*
98524 TCATATCTTCTTCTTTCT
1 TCATATTTTCTTCTTTCT
*
98542 TC---TTCTCTTGC-TTCT
1 TCATATTTTCTT-CTTTCT
98557 TCATATTTTCTTCTTTCT
1 TCATATTTTCTTCTTTCT
98575 TC
1 TC
98577 TTCTCTTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
15 11 0.41
16 1 0.04
17 1 0.04
18 14 0.52
ACGTcount: A:0.08, C:0.28, G:0.02, T:0.62
Consensus pattern (18 bp):
TCATATTTTCTTCTTTCT
Found at i:100328 original size:117 final size:114
Alignment explanation
Indices: 100111--100339 Score: 370
Period size: 117 Copynumber: 2.0 Consensus size: 114
100101 TCCAAGGCCA
** *
100111 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTCGTAAAAAGAAACATTTC
1 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTCAAAAAAAAAAACATTTC
* *
100176 TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTTGTCTATCCACTC
66 TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTTATCCATCCACTC
100225 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTTGCAAAAAAAAAAAAACA
1 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAA-TTTT-C--AAAAAAAAAAACA
100290 TTT-TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTTATCCATCCAC
62 TTTCTTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTTATCCATCCAC
100340 CTAAGTATTT
Statistics
Matches: 106, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
114 43 0.41
115 4 0.04
116 1 0.01
117 45 0.42
118 13 0.12
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (114 bp):
AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTCAAAAAAAAAAACATTTC
TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTTATCCATCCACTC
Found at i:101309 original size:2 final size:2
Alignment explanation
Indices: 101302--101371 Score: 81
Period size: 2 Copynumber: 35.5 Consensus size: 2
101292 ATCTAACAAG
* *
101302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
101344 A- AT GT A- AT ACC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A
101372 ATTTTACTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
1 2 0.03
2 55 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:102588 original size:41 final size:40
Alignment explanation
Indices: 102524--102630 Score: 97
Period size: 42 Copynumber: 2.6 Consensus size: 40
102514 TAGTGGAGAT
* * * * * * *
102524 ATTTAGCAACGTTTTTTAGCAAAATGTTGCTGTATTGACAG
1 ATTTAGC-ACGTTTGTCACCAAAACGCTGCTATATGGACAG
* *
102565 CTTTAGCGACGTTTGTCACCAAAAACGCTGCTATATGGATAG
1 ATTTAGC-ACGTTTGTCACC-AAAACGCTGCTATATGGACAG
102607 ATTTAGCAGCGTTTGTCACCAAAA
1 ATTTAGCA-CGTTTGTCACCAAAA
102631 ATGCCATTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 20 0.38
42 33 0.62
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (40 bp):
ATTTAGCACGTTTGTCACCAAAACGCTGCTATATGGACAG
Found at i:104408 original size:33 final size:33
Alignment explanation
Indices: 104361--104428 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
104351 TTTTGTCATA
* * * *
104361 AATTTAGTAGTATTAGAGATAAATATTGTTTTT
1 AATTTAATAATATTAGAGACAAATATTATTTTT
104394 AATTTAATAATATTAGAGACAAATATTATTTTT
1 AATTTAATAATATTAGAGACAAATATTATTTTT
104427 AA
1 AA
104429 AACTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (33 bp):
AATTTAATAATATTAGAGACAAATATTATTTTT
Found at i:106279 original size:2 final size:2
Alignment explanation
Indices: 106272--106316 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
106262 CAAACAATAA
106272 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
106314 TC T
1 TC T
106317 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:106321 original size:2 final size:2
Alignment explanation
Indices: 106316--106347 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
106306 TCTCTCTCTC
106316 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
106348 ACTGAGCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107619 original size:27 final size:28
Alignment explanation
Indices: 107558--107643 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 28
107548 TTTTAAGGTA
*
107558 AAAAATAATAAAAATTTT-ATTTTTATCTT
1 AAAAAT-AT-AAAATTTTAATTTTGATCTT
* *
107587 AAAAAT-TTATATTTTAATTTTGATCTT
1 AAAAATATAAAATTTTAATTTTGATCTT
**
107614 TTAAATATAAAATTTTTAA-TTTGATCTT
1 AAAAATATAAAA-TTTTAATTTTGATCTT
107642 AA
1 AA
107644 TTACAAATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
26 6 0.13
27 15 0.33
28 12 0.27
29 12 0.27
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.51
Consensus pattern (28 bp):
AAAAATATAAAATTTTAATTTTGATCTT
Found at i:107910 original size:3 final size:3
Alignment explanation
Indices: 107902--107927 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
107892 AAACAACTTC
107902 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
107928 GTATAGATTC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:108363 original size:5 final size:5
Alignment explanation
Indices: 108353--108392 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
108343 GGCAAACATC
* *
108353 TATAT TATAT TATTT TATAT TACAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
108393 AAATTGCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:109629 original size:2 final size:2
Alignment explanation
Indices: 109622--109655 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
109612 AGCAATATGA
109622 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
109656 CATCTCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110145 original size:19 final size:19
Alignment explanation
Indices: 110123--110170 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
110113 ATATAATTTT
110123 TATTATATAAATTTTAATA
1 TATTATATAAATTTTAATA
* ** **
110142 TATTTTATTTATTTTTTTA
1 TATTATATAAATTTTAATA
110161 TATTATATAA
1 TATTATATAA
110171 TATATATATA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATATAAATTTTAATA
Found at i:111304 original size:2 final size:2
Alignment explanation
Indices: 111297--111321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111287 CTAACTGATA
111297 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
111322 ATGGGCAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113029 original size:16 final size:18
Alignment explanation
Indices: 112999--113032 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
112989 GCATGTTATA
112999 ATTTTATATATAATTAAT
1 ATTTTATATATAATTAAT
113017 ATTTTA-ATA-AATTAAT
1 ATTTTATATATAATTAAT
113033 TATTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATATATAATTAAT
Found at i:113684 original size:2 final size:2
Alignment explanation
Indices: 113677--113709 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
113667 ATTAATTAAT
113677 TA 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 TA T
113710 GATTACAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:113773 original size:22 final size:22
Alignment explanation
Indices: 113732--113773 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
113722 GTTTCATTTT
* *
113732 TTTATTATTACCTTTTAATACA
1 TTTATTATTACCATTAAATACA
*
113754 TTTATTATTATCATTAAATA
1 TTTATTATTACCATTAAATA
113774 AAATTCTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATTATTACCATTAAATACA
Found at i:114132 original size:2 final size:2
Alignment explanation
Indices: 114125--114159 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
114115 TGCTTAATGC
114125 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
114160 TCATAGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:116662 original size:26 final size:25
Alignment explanation
Indices: 116625--116674 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
116615 CATAAGTCAT
*
116625 TTTTTTTAATTATTCTTTATTTAAA
1 TTTTTTTAATTATTCTTTAATTAAA
*
116650 TTTTTTTATATTATTTTTTAATTAA
1 TTTTTTTA-ATTATTCTTTAATTAA
116675 TTTACTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTTAATTATTCTTTAATTAAA
Found at i:135496 original size:63 final size:61
Alignment explanation
Indices: 135397--135552 Score: 163
Period size: 63 Copynumber: 2.5 Consensus size: 61
135387 AAAAATACGT
* * * * * * *
135397 CAAGCAAGTAACTAAGTTACTATGCATAAATGCTACAAAGACACCGATTTCCCATACAA-CATA
1 CAAGCGAGTAACCAAGTTACCACGCAAAAATGCTACAAAGACACCAAATT-CC-TA-AAGCATA
**
135460 CAAGCGAGTAACC-AGATTACCACGCAAAAATGCTACAAAGTTACCAAATTCCTAAAGGCATA
1 CAAGCGAGTAACCAAG-TTACCACGCAAAAATGCTACAAAGACACCAAATTCCTAAA-GCATA
*
135522 CAAGCGAGTAACCAAGTTACCACGCATAAAT
1 CAAGCGAGTAACCAAGTTACCACGCAAAAAT
135553 ACTATAAAAC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
60 2 0.03
61 2 0.03
62 35 0.44
63 40 0.51
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.19
Consensus pattern (61 bp):
CAAGCGAGTAACCAAGTTACCACGCAAAAATGCTACAAAGACACCAAATTCCTAAAGCATA
Found at i:138480 original size:21 final size:21
Alignment explanation
Indices: 138454--138527 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
138444 CTTCCCCTAC
138454 CCTAGTCGACATAAATCTGTT
1 CCTAGTCGACATAAATCTGTT
* *
138475 CCTAGTC-A-ATAATAGCCAGTT
1 CCTAGTCGACATAA-A-TCTGTT
* * *
138496 CTTGGTCGACATAAATCTATT
1 CCTAGTCGACATAAATCTGTT
138517 CCTAGTCGACA
1 CCTAGTCGACA
138528 ACAACCTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 28 0.70
22 2 0.05
23 4 0.10
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (21 bp):
CCTAGTCGACATAAATCTGTT
Found at i:138539 original size:42 final size:42
Alignment explanation
Indices: 138458--138551 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
138448 CCCTACCCTA
* * * * *
138458 GTCGACATAAATCTGTTCCTAGTCAATAATAGCCAGTTCTTG
1 GTCGACATAAATCTATTCCTAGTCAACAACAACCAGTTCTCG
* *
138500 GTCGACATAAATCTATTCCTAGTCGACAACAACCTGTTCTCG
1 GTCGACATAAATCTATTCCTAGTCAACAACAACCAGTTCTCG
*
138542 GTTGACATAA
1 GTCGACATAA
138552 GACAAACACT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (42 bp):
GTCGACATAAATCTATTCCTAGTCAACAACAACCAGTTCTCG
Found at i:139691 original size:41 final size:41
Alignment explanation
Indices: 139639--139721 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
139629 CCCCATGGCC
139639 TTACTTCAAACAATTTCCTCTTAACCCTTTCGATTGAGTAT
1 TTACTTCAAACAATTTCCTCTTAACCCTTTCGATTGAGTAT
139680 TTACTTCAAACAATTTCCTCTTAACCCTTTCGATTGAGTAT
1 TTACTTCAAACAATTTCCTCTTAACCCTTTCGATTGAGTAT
139721 T
1 T
139722 AGGGTTGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (41 bp):
TTACTTCAAACAATTTCCTCTTAACCCTTTCGATTGAGTAT
Found at i:140118 original size:3 final size:3
Alignment explanation
Indices: 140110--140150 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
140100 AAAAGGGTTT
*
140110 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
140151 TACATAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:145531 original size:2 final size:2
Alignment explanation
Indices: 145526--145550 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
145516 AAAATTATAA
145526 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
145551 ACAGTAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:145629 original size:16 final size:16
Alignment explanation
Indices: 145610--145640 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
145600 CTAGAATGGC
*
145610 CCAAACTCGAAATGAA
1 CCAAACCCGAAATGAA
145626 CCAAACCCGAAATGA
1 CCAAACCCGAAATGA
145641 TCGAACAATT
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:0.48, C:0.29, G:0.13, T:0.10
Consensus pattern (16 bp):
CCAAACCCGAAATGAA
Found at i:145869 original size:16 final size:16
Alignment explanation
Indices: 145847--145904 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
145837 CCCAAACCTG
145847 AAATGACCCGAAACTA
1 AAATGACCCGAAACTA
* * *
145863 AAGTGACTCGAAACCA
1 AAATGACCCGAAACTA
* *
145879 AAATAACCTGAAACTAA
1 AAATGACCCGAAACT-A
145896 AAATGACCC
1 AAATGACCC
145905 AACCCGACTC
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
16 23 0.74
17 8 0.26
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.14
Consensus pattern (16 bp):
AAATGACCCGAAACTA
Found at i:155028 original size:10 final size:10
Alignment explanation
Indices: 155007--155041 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
154997 CTAATTATAA
155007 AAATATTAATT
1 AAATA-TAATT
155018 AAATATAATT
1 AAATATAATT
155028 AAATA-AATT
1 AAATATAATT
155037 AAATA
1 AAATA
155042 ATATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 10 0.42
11 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATATAATT
Found at i:155038 original size:9 final size:9
Alignment explanation
Indices: 155014--155072 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
155004 TAAAAATATT
155014 AATTAAATA
1 AATTAAATA
155023 TAATTAAATA
1 -AATTAAATA
155033 AATTAAATA
1 AATTAAATA
** *
155042 ATATTATTTT
1 A-ATTAAATA
155052 AATTAAA-A
1 AATTAAATA
*
155060 AATTTAATA
1 AATTAAATA
155069 AATT
1 AATT
155073 CATGATATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
8 6 0.15
9 19 0.47
10 15 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATA
Found at i:155123 original size:14 final size:15
Alignment explanation
Indices: 155104--155133 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
155094 TATATGATTA
155104 TATTATAA-ATTTTT
1 TATTATAATATTTTT
155118 TATTATAATATTTTT
1 TATTATAATATTTTT
155133 T
1 T
155134 TGAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATAATATTTTT
Found at i:155418 original size:62 final size:63
Alignment explanation
Indices: 155347--155555 Score: 230
Period size: 62 Copynumber: 3.2 Consensus size: 63
155337 ATTAAAATTT
* *
155347 ATTAAAATTATATTTTTATCAAATAATAAAATATAAATT-AATTATATTATTGTTAAATAATA
1 ATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAATTATATTATTGTTAAATAATA
*
155409 ATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAAATTATGTT-TATGTTAAATAATT
1 ATTAAAATTATATTTATATAAAATAATAAAATATAAATT-AAATTATATTAT-TGTTAAAT-A--
155473 ATGAA
61 AT--A
* * *
155478 TTATTAAAATTATATTTATATTAAATAATAAAATATATATTAAAATTATATTTACTG-T--ATAA
1 --ATTAAAATTATATTTATATAAAATAATAAAATATAAATT-AAATTATA-TTATTGTTAAATAA
155540 TA
62 TA
155542 ATTAAAATTATATT
1 ATTAAAATTATATT
155556 AAAAATAATA
Statistics
Matches: 128, Mismatches: 7, Indels: 24
0.81 0.04 0.15
Matches are distributed among these distances:
62 51 0.40
63 1 0.01
64 17 0.13
65 1 0.01
66 2 0.02
67 2 0.02
68 1 0.01
69 3 0.02
71 46 0.36
72 4 0.03
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (63 bp):
ATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAATTATATTATTGTTAAATAATA
Found at i:155448 original size:36 final size:36
Alignment explanation
Indices: 155408--155559 Score: 159
Period size: 36 Copynumber: 4.2 Consensus size: 36
155398 GTTAAATAAT
155408 AATTAAAATTATATTTATATAAAATAA-TAAAATATA
1 AATTAAAATTATATTTATATAAAATAATTAAAAT-TA
* * * *
155444 AATTAAAATTATGTTTATGTTAAATAATTATGAATT-
1 AATTAAAATTATATTTATATAAAATAATTA-AAATTA
*
155480 -ATTAAAATTATATTTATATTAAATAA-TAAAATATA
1 AATTAAAATTATATTTATATAAAATAATTAAAAT-TA
* * *
155515 TATTAAAATTATATTTACTGTATAATAATTAAAATTA
1 AATTAAAATTATATTTA-TATAAAATAATTAAAATTA
*
155552 TATTAAAA
1 AATTAAAA
155560 ATAATAAATA
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
33 3 0.03
34 3 0.03
35 24 0.24
36 40 0.40
37 20 0.20
38 9 0.09
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (36 bp):
AATTAAAATTATATTTATATAAAATAATTAAAATTA
Found at i:155495 original size:71 final size:72
Alignment explanation
Indices: 155409--155545 Score: 224
Period size: 71 Copynumber: 1.9 Consensus size: 72
155399 TTAAATAATA
*
155409 ATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAAATTATGTTTA-TGT-TAAATAAT
1 ATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAAATTATATTTACTGTAT-AATAAT
155472 TATGAATT
65 TATGAATT
* *
155480 ATTAAAATTATATTTATATTAAATAATAAAATATATATTAAAATTATATTTACTGTATAATAATT
1 ATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAAATTATATTTACTGTATAATAATT
155545 A
66 A
155546 AAATTATATT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
71 49 0.80
72 11 0.18
73 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (72 bp):
ATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAAATTATATTTACTGTATAATAATT
ATGAATT
Found at i:155570 original size:133 final size:132
Alignment explanation
Indices: 155331--155572 Score: 332
Period size: 133 Copynumber: 1.8 Consensus size: 132
155321 ATATATATAA
*
155331 TAAATAATTAAAATTTATTAAAATTATATTTTTATCAAATAATAAAATATAAATTAATTATATTA
1 TAAATAATTAAAATTTATTAAAATTATATTTATATCAAATAATAAAATATAAATTAATTATATTA
* *
155396 TTGTTAAATAATAATTAAAATTATATTTATATAAAATAATAAAATATAAATTAAAATTATGTTTA
66 CTGTT-AATAATAATTAAAATTATATTTATAAAAAATAATAAAATATAAATTAAAATTATGTTTA
155461 TGT
130 TGT
* * *
155464 TAAATAATTATGAA-TTATTAAAATTATATTTATATTAAATAATAAAATATATATTAAAATTATA
1 TAAATAATTA-AAATTTATTAAAATTATATTTATATCAAATAATAAAATATAAATT--AATTATA
155528 TTTACTG-T-ATAATAATTAAAATTATA-TTA-AAAATAATAAATAAAA
63 -TTACTGTTAATAATAATTAAAATTATATTTATAAAA-AAT-AATAAAA
155573 AAATAGAGGT
Statistics
Matches: 97, Mismatches: 6, Indels: 12
0.84 0.05 0.10
Matches are distributed among these distances:
131 3 0.03
132 6 0.06
133 73 0.75
134 2 0.02
135 8 0.08
136 5 0.05
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (132 bp):
TAAATAATTAAAATTTATTAAAATTATATTTATATCAAATAATAAAATATAAATTAATTATATTA
CTGTTAATAATAATTAAAATTATATTTATAAAAAATAATAAAATATAAATTAAAATTATGTTTAT
GT
Found at i:156105 original size:28 final size:28
Alignment explanation
Indices: 156072--156130 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
156062 TAATTTTCAC
156072 TCTTTCATATATTTTTTAACAAATTTTT
1 TCTTTCATATATTTTTTAACAAATTTTT
*
156100 TCTTTCATATATTTTTTAACAATTTTTT
1 TCTTTCATATATTTTTTAACAAATTTTT
156128 TCT
1 TCT
156131 ATTCCATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (28 bp):
TCTTTCATATATTTTTTAACAAATTTTT
Found at i:157237 original size:34 final size:34
Alignment explanation
Indices: 157173--157355 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
157163 GTCTTAGAAA
* *
157173 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
157206 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
157240 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
157274 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
157308 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
157342 TGTTGATTAAATGG
1 TGTTGATTAAATGG
157356 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:157718 original size:19 final size:19
Alignment explanation
Indices: 157662--157724 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
157652 TGGTTGTCGA
**
157662 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
157681 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
157700 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
157719 GTTACT
1 GGTACT
157725 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:161811 original size:34 final size:34
Alignment explanation
Indices: 161745--161929 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
161735 AAGTGGGAGA
* *
161745 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
161778 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
161812 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
161846 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
161880 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
161914 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
161930 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:162761 original size:15 final size:16
Alignment explanation
Indices: 162738--162770 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
162728 AATTTTTAAA
162738 AATATATATATAATATT
1 AATATATATA-AATATT
162755 AATATATATAAATATT
1 AATATATATAAATATT
162771 TTTATCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATATATAAATATT
Found at i:162994 original size:22 final size:22
Alignment explanation
Indices: 162969--163024 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
162959 CTTTTTAAAA
162969 AAAAAAACTATCCACCAATCAT
1 AAAAAAACTATCCACCAATCAT
* * *
162991 --AAAAACTATCCACTAGTCTT
1 AAAAAAACTATCCACCAATCAT
*
163011 AAAAAATCTATCCA
1 AAAAAAACTATCCA
163025 TGTATAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAAAACTATCCACCAATCAT
Found at i:167406 original size:2 final size:2
Alignment explanation
Indices: 167399--167445 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
167389 TTAAGTCTTT
167399 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
167441 TA TA T
1 TA TA T
167446 GTGTATGGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.