Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_15 ID=scaffold_15-JGI_221_v2.0
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: 253347
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 271 characters in sequence are not A, C, G, or T
Found at i:1928 original size:24 final size:23
Alignment explanation
Indices: 1892--1941 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1882 AATTATTTTA
*
1892 AAATCATTCTATACTATTTACTTT
1 AAATCATTCTATACTAGTTA-TTT
*
1916 AAATCAATT-TATATTAGTTATTT
1 AAATC-ATTCTATACTAGTTATTT
1939 AAA
1 AAA
1942 GCTCATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 14 0.61
25 3 0.13
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATCATTCTATACTAGTTATTT
Found at i:8422 original size:12 final size:12
Alignment explanation
Indices: 8405--8431 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8395 GAAGGGGGAG
8405 CTGTTGGCCTTC
1 CTGTTGGCCTTC
8417 CTGTTGGCCTTC
1 CTGTTGGCCTTC
8429 CTG
1 CTG
8432 GTGCGGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.41
Consensus pattern (12 bp):
CTGTTGGCCTTC
Found at i:10665 original size:12 final size:12
Alignment explanation
Indices: 10648--10672 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10638 TTCCACATCT
10648 GAATGCACCTTC
1 GAATGCACCTTC
10660 GAATGCACCTTC
1 GAATGCACCTTC
10672 G
1 G
10673 TCGATATCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (12 bp):
GAATGCACCTTC
Found at i:13233 original size:13 final size:13
Alignment explanation
Indices: 13215--13239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13205 ATTAAAGAAG
13215 AAAATATTTAATA
1 AAAATATTTAATA
13228 AAAATATTTAAT
1 AAAATATTTAAT
13240 TGATTTTTTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATATTTAATA
Found at i:13479 original size:20 final size:21
Alignment explanation
Indices: 13456--13504 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
13446 ATTTTGTATA
*
13456 TTTTTTTAT-ATTTTTAAATT
1 TTTTTTTATAATTTTAAAATT
*
13476 TTTTTTCATAATTTTAAAATT
1 TTTTTTTATAATTTTAAAATT
13497 TTATTTTT
1 TT-TTTTT
13505 TGTAATTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 12 0.50
22 4 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTTTATAATTTTAAAATT
Found at i:15147 original size:9 final size:9
Alignment explanation
Indices: 15133--15208 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
15123 TTTGCTTAAA
15133 AATTACCCG
1 AATTACCCG
15142 AATTACCCG
1 AATTACCCG
*
15151 AATTAACCG
1 AATTACCCG
**
15160 AATTAATCG
1 AATTACCCG
*
15169 AATTAACCG
1 AATTACCCG
15178 AATTA-CCG
1 AATTACCCG
*
15186 AAAATACCCG
1 -AATTACCCG
15196 AATTACCCG
1 AATTACCCG
15205 AATT
1 AATT
15209 TTTTTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
8 3 0.05
9 54 0.90
10 3 0.05
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:15326 original size:40 final size:38
Alignment explanation
Indices: 15282--15380 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 38
15272 ACTTTAGTAA
**
15282 ATTGGGTTGGTAAATTGGGTAGTCTTTTAGTTTTAATTTT
1 ATTGGGTTGGT-AATTGGGTAAAC-TTTAGTTTTAATTTT
* *
15322 ATTGGATTGAGTAATTGGGTAAACTTTAGTTTTAGTTTT
1 ATTGGGTTG-GTAATTGGGTAAACTTTAGTTTTAATTTT
15361 ATTGGGTTGGGTAATTGGGT
1 ATTGGGTT-GGTAATTGGGT
15381 TTGGGCTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
39 31 0.60
40 19 0.37
41 2 0.04
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.48
Consensus pattern (38 bp):
ATTGGGTTGGTAATTGGGTAAACTTTAGTTTTAATTTT
Found at i:23008 original size:18 final size:17
Alignment explanation
Indices: 22987--23040 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 17
22977 CAATTTTAAT
22987 AATTTTCTATATTTTTTA
1 AATTTT-TATATTTTTTA
* *
23005 AATTTTTTCATAATTTTAA
1 AA-TTTTT-ATATTTTTTA
23024 AATTTTTAT-TTTTTTA
1 AATTTTTATATTTTTTA
23040 A
1 A
23041 TTTACATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 6 0.20
17 2 0.07
18 8 0.27
19 14 0.47
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTTTTATATTTTTTA
Found at i:23011 original size:19 final size:19
Alignment explanation
Indices: 22958--23030 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
22948 TAACTTAATT
* *
22958 ATTTTAAATATTTTATTAACA
1 ATTTTAAA-ATTTT-TTCATA
*
22979 ATTTTAATAATTTTCT-ATA
1 ATTTTAA-AATTTTTTCATA
* *
22998 TTTTTTAAATTTTTTCATA
1 ATTTTAAAATTTTTTCATA
23017 ATTTTAAAATTTTT
1 ATTTTAAAATTTTT
23031 ATTTTTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 7 0.16
19 22 0.51
20 1 0.02
21 12 0.28
22 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTAAAATTTTTTCATA
Found at i:23367 original size:5 final size:5
Alignment explanation
Indices: 23357--23398 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
23347 TTCTTTAGTT
23357 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
23399 CTTATTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:29495 original size:3 final size:3
Alignment explanation
Indices: 29487--29525 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
29477 ACGTATTGCA
29487 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29526 TTGTTCCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31052 original size:6 final size:6
Alignment explanation
Indices: 31039--31170 Score: 111
Period size: 6 Copynumber: 22.0 Consensus size: 6
31029 ACTTGTCGTG
* * * * * * *
31039 ACTCTC ATTCTC ATTCTC GCTCAC ACTCGC ACTCTC ATTCTC ATTCTC
1 ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC
* * * * * * *
31087 GCTCAC ACTCTC ACTCTC ATTCTC GCTCAC ACTCTC AATCTC ACTCAC
1 ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC
* * *
31135 ACTCTC ACTCTC ACCCTC ACTCAC ACTCTC ATTCTC
1 ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC ACTCTC
31171 GTTCTTCATC
Statistics
Matches: 98, Mismatches: 28, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 98 1.00
ACGTcount: A:0.19, C:0.45, G:0.03, T:0.33
Consensus pattern (6 bp):
ACTCTC
Found at i:31075 original size:30 final size:30
Alignment explanation
Indices: 31039--31110 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
31029 ACTTGTCGTG
31039 ACTCTCATTCTCATTCTCGCTCACACTCGC
1 ACTCTCATTCTCATTCTCGCTCACACTCGC
*
31069 ACTCTCATTCTCATTCTCGCTCACACTCTC
1 ACTCTCATTCTCATTCTCGCTCACACTCGC
31099 ACTCTCATTCTC
1 ACTCTCATTCTC
31111 GCTCACACTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.17, C:0.43, G:0.04, T:0.36
Consensus pattern (30 bp):
ACTCTCATTCTCATTCTCGCTCACACTCGC
Found at i:32994 original size:22 final size:22
Alignment explanation
Indices: 32969--33039 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
32959 TAACTTAATT
32969 ATTTTAAATATTTTTATTAACA
1 ATTTTAAATATTTTTATTAACA
** * *
32991 ATTTTATGCTTTTTTTA-TAATA
1 ATTTTA-AATATTTTTATTAACA
* *
33013 GTTTTTAA-A-TTTTATTAACA
1 ATTTTAAATATTTTTATTAACA
33033 ATTTTAA
1 ATTTTAA
33040 TAATTTTCTA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
19 5 0.14
20 9 0.26
22 14 0.40
23 7 0.20
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (22 bp):
ATTTTAAATATTTTTATTAACA
Found at i:33066 original size:20 final size:19
Alignment explanation
Indices: 33032--33076 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
33022 TTTTATTAAC
33032 AATTTT-AATAATTTTCTAT
1 AATTTTAAATAATTTTC-AT
* *
33051 ATTTTTAAATATTTTTCAT
1 AATTTTAAATAATTTTCAT
33070 AATTTTA
1 AATTTTA
33077 CAATTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTAAATAATTTTCAT
Found at i:33074 original size:38 final size:35
Alignment explanation
Indices: 33014--33100 Score: 86
Period size: 38 Copynumber: 2.4 Consensus size: 35
33004 TTTATAATAG
*
33014 TTTTTAAATTTTATTAACAATTTTAATAATTTTCTAT
1 TTTTTAAATTTTATTAACAATTTT-ACAATTTT-TAT
* *
33051 ATTTTTAAATATTT-TTCATAATTTTACAATTTTTAT
1 -TTTTTAAAT-TTTATTAACAATTTTACAATTTTTAT
*
33087 TTTTTGTAATTTTA
1 TTTTT-AAATTTTA
33101 ATAATGATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
35 8 0.19
36 6 0.14
37 7 0.17
38 18 0.43
39 3 0.07
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (35 bp):
TTTTTAAATTTTATTAACAATTTTACAATTTTTAT
Found at i:33156 original size:16 final size:17
Alignment explanation
Indices: 33122--33185 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
33112 CTTCATACTT
*
33122 TTTGT-TATTTTTATAAA
1 TTTGTATATATTT-TAAA
*
33139 TTTTTA-ATATTTTAAA
1 TTTGTATATATTTTAAA
*
33155 TTTGTATATATTTGTATTA
1 TTTGTATATATTT-TA-AA
33174 TTTGTAT-TATTT
1 TTTGTATATATTT
33186 GTATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.23
17 15 0.38
18 7 0.18
19 8 0.21
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTGTATATATTTTAAA
Found at i:33162 original size:26 final size:28
Alignment explanation
Indices: 33128--33190 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
33118 ACTTTTTGTT
* *
33128 ATTTTTATAAATTTTTAATATTT-TA-A
1 ATTTGTATAAATTTGTAATATTTGTATA
* * *
33154 ATTTGTATATATTTGTATTATTTGTATT
1 ATTTGTATAAATTTGTAATATTTGTATA
33182 ATTTGTATA
1 ATTTGTATA
33191 TATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 19 0.63
27 2 0.07
28 9 0.30
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (28 bp):
ATTTGTATAAATTTGTAATATTTGTATA
Found at i:33177 original size:9 final size:9
Alignment explanation
Indices: 33154--33189 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
33144 AATATTTTAA
33154 ATTTGTATAT
1 ATTTGTAT-T
33164 ATTTGTATT
1 ATTTGTATT
33173 ATTTGTATT
1 ATTTGTATT
33182 ATTTGTAT
1 ATTTGTAT
33190 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (9 bp):
ATTTGTATT
Found at i:33186 original size:18 final size:19
Alignment explanation
Indices: 33154--33203 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
33144 AATATTTTAA
33154 ATTTGTATATATTTGTATT
1 ATTTGTATATATTTGTATT
33173 ATTTGTAT-TATTTGTATAT
1 ATTTGTATATATTTGTAT-T
* *
33192 ATATATATATAT
1 ATTTGTATATAT
33204 ATATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 15 0.56
20 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (19 bp):
ATTTGTATATATTTGTATT
Found at i:33194 original size:2 final size:2
Alignment explanation
Indices: 33187--33222 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
33177 GTATTATTTG
* *
33187 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33223 AAATATCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:33223 original size:12 final size:12
Alignment explanation
Indices: 33188--33233 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
33178 TATTATTTGT
*
33188 ATATATATATAT
1 ATATATATATAA
33200 ATATATATATAA
1 ATATATATATAA
*
33212 ATATAAATATAA
1 ATATATATATAA
33224 A-ATATCATAT
1 ATATAT-ATAT
33234 TCCGTTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 3 0.10
12 27 0.90
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAA
Found at i:46392 original size:20 final size:20
Alignment explanation
Indices: 46356--46394 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
46346 GTGGTTCTAA
*
46356 CCATTTTTAATTATTTATTT
1 CCATTTTTAACTATTTATTT
46376 CCATTCTTTAACT-TTTATT
1 CCATT-TTTAACTATTTATT
46395 CTAACTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
CCATTTTTAACTATTTATTT
Found at i:49674 original size:23 final size:22
Alignment explanation
Indices: 49645--49692 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
49635 AAATGGAATA
* *
49645 AAAAAAACTTTAAGTATCAAACT
1 AAAAAAA-TTCAAATATCAAACT
*
49668 AAAAAAATTCAAATATCAAATT
1 AAAAAAATTCAAATATCAAACT
49690 AAA
1 AAA
49693 CATTAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAAAAATTCAAATATCAAACT
Found at i:49761 original size:54 final size:53
Alignment explanation
Indices: 49659--49761 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
49649 AAACTTTAAG
*
49659 TATCAAACTAAAAAAATTCAAATATCAAATTAAACATTAAAACTAAACTCAAA
1 TATCAAACTAAAAAAATTCAAATATCAAATTAAACATTAAAACGAAACTCAAA
* ** * *
49712 TATCAAATTAAAAAATATTTTAATATCAAATTTAACATTAAAGCGAAACT
1 TATCAAACTAAAAAA-ATTCAAATATCAAATTAAACATTAAAACGAAACT
49762 TAAGTTTAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 14 0.33
54 29 0.67
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (53 bp):
TATCAAACTAAAAAAATTCAAATATCAAATTAAACATTAAAACGAAACTCAAA
Found at i:51956 original size:23 final size:23
Alignment explanation
Indices: 51930--51974 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
51920 AGACATGTAT
*
51930 CAATTTTTATTTTGTGTATTATC
1 CAATTTTTATTTTGTGAATTATC
* *
51953 CAATTTTTTTTTTTTGAATTAT
1 CAATTTTTATTTTGTGAATTAT
51975 GTACTATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (23 bp):
CAATTTTTATTTTGTGAATTATC
Found at i:56731 original size:2 final size:2
Alignment explanation
Indices: 56726--56755 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56716 CTCTCTCTCT
56726 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
56756 TGCACGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:64098 original size:58 final size:61
Alignment explanation
Indices: 64028--64144 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 61
64018 TTAGGATTTA
64028 TAATCTTTGACTTTCC-T-TT-GTATATCTGATTATTAGCATAAATAGGTTGTGTAATGTG
1 TAATCTTTGACTTTCCTTCTTAGTATATCTGATTATTAGCATAAATAGGTTGTGTAATGTG
*
64086 TAATCTTTGACTTTCCTTCTTAGTATATCTGATTATTAGTATAAATAGGTTGTGTAATG
1 TAATCTTTGACTTTCCTTCTTAGTATATCTGATTATTAGCATAAATAGGTTGTGTAATG
64145 GAGTGTATAC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
58 16 0.29
59 1 0.02
60 2 0.04
61 36 0.65
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.47
Consensus pattern (61 bp):
TAATCTTTGACTTTCCTTCTTAGTATATCTGATTATTAGCATAAATAGGTTGTGTAATGTG
Found at i:68663 original size:90 final size:90
Alignment explanation
Indices: 68510--68691 Score: 337
Period size: 90 Copynumber: 2.0 Consensus size: 90
68500 CCCGCGTGGA
68510 TGCATGTTTGGCCATCAGTATGGGATATGATCCTTAAAGGATTCTTCAAATATACAGAAAAACTT
1 TGCATGTTTGGCCATCAGTATGGGATATGATCCTTAAAGGATTCTTCAAATATACAGAAAAACTT
*
68575 AGATAAAACTGAATATTTCCTTATC
66 AGAGAAAACTGAATATTTCCTTATC
* *
68600 TGCATGTTTGGCCATCGGTATGGGATATGCTCCTTAAAGGATTCTTCAAATATACAGAAAAACTT
1 TGCATGTTTGGCCATCAGTATGGGATATGATCCTTAAAGGATTCTTCAAATATACAGAAAAACTT
68665 AGAGAAAACTGAATATTTCCTTATC
66 AGAGAAAACTGAATATTTCCTTATC
68690 TG
1 TG
68692 ACACAAATTC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (90 bp):
TGCATGTTTGGCCATCAGTATGGGATATGATCCTTAAAGGATTCTTCAAATATACAGAAAAACTT
AGAGAAAACTGAATATTTCCTTATC
Found at i:74937 original size:16 final size:15
Alignment explanation
Indices: 74903--74952 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
74893 ATGTTTTTTA
* *
74903 TTTTGTTATCTGTAA
1 TTTTGTTATTTGTAT
74918 TTTTGTGTATTTGTAT
1 TTTTGT-TATTTGTAT
*
74934 TTTTGTTATATTATAT
1 TTTTGTTAT-TTGTAT
74950 TTT
1 TTT
74953 AATGATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.18, C:0.02, G:0.12, T:0.68
Consensus pattern (15 bp):
TTTTGTTATTTGTAT
Found at i:82777 original size:15 final size:15
Alignment explanation
Indices: 82757--82807 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
82747 TAAAAAATAA
82757 AATAAAAGTAAACAT
1 AATAAAAGTAAACAT
*
82772 AATAAAAATATATA-AT
1 AATAAAAGTA-A-ACAT
82788 ACAATAAAAGTAAACAT
1 --AATAAAAGTAAACAT
82805 AAT
1 AAT
82808 CATTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 12 0.41
16 4 0.14
17 4 0.14
18 9 0.31
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (15 bp):
AATAAAAGTAAACAT
Found at i:82844 original size:2 final size:2
Alignment explanation
Indices: 82833--82861 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
82823 AAATAGGAAA
82833 AT AT -T 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
82862 GAGTTTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:84296 original size:27 final size:28
Alignment explanation
Indices: 84262--84326 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
84252 AAAAAAAATA
84262 ACCAAAATATTATAA-TTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
84289 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
84317 ACCAAAATAT
1 ACCAAAATAT
84327 ACGAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:84997 original size:19 final size:19
Alignment explanation
Indices: 84973--85034 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
84963 TCTAATTAAG
84973 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
84992 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
85010 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
85029 TAATAA
1 TAATAA
85035 GCTAATCTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:85014 original size:37 final size:37
Alignment explanation
Indices: 84973--85050 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
84963 TCTAATTAAG
*
84973 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTAATCTCATT
*
85010 TAATAACTCTATTTTAATTTAATAAGCTAATCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTAATCTCATT
85047 TAAT
1 TAAT
85051 TACCCATCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.47
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTAATCTCATT
Found at i:85049 original size:18 final size:18
Alignment explanation
Indices: 84989--85050 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
84979 CTCTATTTTA
84989 ATTTAATAAACTATTCTC
1 ATTTAATAAACTATTCTC
* * *
85007 ATTTAATAACTCTATTTTA
1 ATTTAATAA-ACTATTCTC
* *
85026 ATTTAATAAGCTAATCTC
1 ATTTAATAAACTATTCTC
85044 ATTTAAT
1 ATTTAAT
85051 TACCCATCGG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 21 0.58
19 15 0.42
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTAATAAACTATTCTC
Found at i:86341 original size:14 final size:15
Alignment explanation
Indices: 86322--86352 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
86312 ATAAAGGAAT
86322 ATTATAATAATG-TA
1 ATTATAATAATGATA
86336 ATTATAATAATGATA
1 ATTATAATAATGATA
86351 AT
1 AT
86353 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
ATTATAATAATGATA
Found at i:86389 original size:35 final size:34
Alignment explanation
Indices: 86285--86389 Score: 88
Period size: 35 Copynumber: 3.1 Consensus size: 34
86275 ATGTGGGTAG
* * * *
86285 AATATTAGAATGATA-AATAATAAAAAAATAAAGG
1 AATATTATAATAATATAATAATAATAAAATAAA-T
* * *
86319 AATATTATAATAATGTAATTATAATAATGAT-AAT
1 AATATTATAATAATATAATAATAATAA-AATAAAT
* *
86353 AATATTAATAATCATATCATAATAATAAAATAAAT
1 AATATT-ATAATAATATAATAATAATAAAATAAAT
86388 AA
1 AA
86390 GGTAACTTAA
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
34 20 0.36
35 33 0.60
36 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (34 bp):
AATATTATAATAATATAATAATAATAAAATAAAT
Found at i:86519 original size:21 final size:21
Alignment explanation
Indices: 86480--86519 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
86470 TAAAAGAAAT
*
86480 AATAAAATAACAAGAACAAAA
1 AATAAAATAACAACAACAAAA
* *
86501 AATAAAATAATAACCACAA
1 AATAAAATAACAACAACAA
86520 TAATAAATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.12
Consensus pattern (21 bp):
AATAAAATAACAACAACAAAA
Found at i:86606 original size:4 final size:4
Alignment explanation
Indices: 86579--86630 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
86569 TCTTAAGCAT
* * *
86579 ATAA AAAA ATAA AGAA GT-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
86626 ATAA A
1 ATAA A
86631 ATAATTTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 2 0.05
4 39 0.95
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:88339 original size:11 final size:11
Alignment explanation
Indices: 88325--88378 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
88315 TAAAATAGTG
88325 AGAAAACAACA
1 AGAAAACAACA
* *
88336 AGAAAATAGCA
1 AGAAAACAACA
*
88347 ACAAAACAACA
1 AGAAAACAACA
88358 AGAAAACAAACA
1 AGAAAAC-AACA
*
88370 AAAAAACAA
1 AGAAAACAA
88379 GATTTTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.74, C:0.17, G:0.07, T:0.02
Consensus pattern (11 bp):
AGAAAACAACA
Found at i:88344 original size:22 final size:22
Alignment explanation
Indices: 88327--88380 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
88317 AAATAGTGAG
88327 AAAACAACAAGAAAATAGCAAC
1 AAAACAACAAGAAAATAGCAAC
*
88349 AAAACAACAAGAAAACA--AAC
1 AAAACAACAAGAAAATAGCAAC
*
88369 AAAAAAACAAGA
1 AAAACAACAAGA
88381 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.47
22 16 0.53
ACGTcount: A:0.74, C:0.17, G:0.07, T:0.02
Consensus pattern (22 bp):
AAAACAACAAGAAAATAGCAAC
Found at i:93745 original size:2 final size:2
Alignment explanation
Indices: 93738--93762 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
93728 TAAGGATTTT
93738 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
93763 AGGAGTTGAT
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:108483 original size:38 final size:38
Alignment explanation
Indices: 108441--108514 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
108431 AACATTTGCT
*
108441 GGTTGTTGGTCCTTTGTGCTTGGTTGTGGTTGTATACC
1 GGTTGTTGGTCCATTGTGCTTGGTTGTGGTTGTATACC
*
108479 GGTTGTTGGTCCATTGTGCTTTGTTGTGGTTGTATA
1 GGTTGTTGGTCCATTGTGCTTGGTTGTGGTTGTATA
108515 AAAGACTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.07, C:0.11, G:0.34, T:0.49
Consensus pattern (38 bp):
GGTTGTTGGTCCATTGTGCTTGGTTGTGGTTGTATACC
Found at i:116155 original size:20 final size:20
Alignment explanation
Indices: 116130--116170 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
116120 CCAAGTTTTT
116130 TAAATTTATAAAAAAAAATA
1 TAAATTTATAAAAAAAAATA
* * *
116150 TAAATTTTTCAAAAATAATA
1 TAAATTTATAAAAAAAAATA
116170 T
1 T
116171 TTATTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATTTATAAAAAAAAATA
Found at i:116567 original size:31 final size:30
Alignment explanation
Indices: 116510--116569 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
116500 AATAAAAAAA
*
116510 TAAATAATAAAATAAGAGTTATACAATATC
1 TAAATAATAAAATAAAAGTTATACAATATC
116540 TAAATAATAACAATAAAAGATTA-ACAATAT
1 TAAATAATAA-AATAAAAG-TTATACAATAT
116570 AATAGCGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.37
31 14 0.52
32 3 0.11
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (30 bp):
TAAATAATAAAATAAAAGTTATACAATATC
Found at i:117749 original size:22 final size:22
Alignment explanation
Indices: 117707--117749 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
117697 TTTTATTGTT
117707 TTGTTACAATTTCACTATTATA
1 TTGTTACAATTTCACTATTATA
* * *
117729 TTGTTACTATTTTACTGTTAT
1 TTGTTACAATTTCACTATTAT
117750 TATTTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.56
Consensus pattern (22 bp):
TTGTTACAATTTCACTATTATA
Found at i:118891 original size:14 final size:13
Alignment explanation
Indices: 118858--118909 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
118848 CCCAAAATCC
*
118858 TAAATCTTGAACT
1 TAAACCTTGAACT
*
118871 CAAACCTTGAACTT
1 TAAACCTTGAAC-T
118885 TAAACCTTGAAACT
1 TAAACCTTG-AACT
* *
118899 TGAACATTGAA
1 TAAACCTTGAA
118910 GTTTAGGGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 12 0.38
14 17 0.53
15 3 0.09
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (13 bp):
TAAACCTTGAACT
Found at i:118975 original size:20 final size:20
Alignment explanation
Indices: 118952--118991 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
118942 ATGTTCGTGT
*
118952 TTTATGTTCAAGGTTCAAGG
1 TTTAAGTTCAAGGTTCAAGG
*
118972 TTTAAGTTTAAGGTTCAAGG
1 TTTAAGTTCAAGGTTCAAGG
118992 GTCCGGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTAAGTTCAAGGTTCAAGG
Found at i:119036 original size:13 final size:13
Alignment explanation
Indices: 119018--119042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119008 TACAAGCTTG
119018 GAGTTTAAGGTTT
1 GAGTTTAAGGTTT
119031 GAGTTTAAGGTT
1 GAGTTTAAGGTT
119043 ATGGGTTTGA
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:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (13 bp):
GAGTTTAAGGTTT
Found at i:119135 original size:21 final size:22
Alignment explanation
Indices: 119093--119140 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
119083 TTTAAATTTA
**
119093 GGGTTTAGGGTTCATTGCTATG
1 GGGTTTAGGGTTCAAGGCTATG
*
119115 GGGTTT-GGGTTCAAGGTTATG
1 GGGTTTAGGGTTCAAGGCTATG
*
119136 AGGTT
1 GGGTT
119141 GAGTTTAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.15, C:0.06, G:0.40, T:0.40
Consensus pattern (22 bp):
GGGTTTAGGGTTCAAGGCTATG
Found at i:119489 original size:13 final size:14
Alignment explanation
Indices: 119460--119495 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
119450 GGTTTAAGGA
*
119460 TTCAAGGTTATTGG
1 TTCAAGATTATTGG
119474 TTCAAGATTA-TGG
1 TTCAAGATTATTGG
119487 TTCAAGATT
1 TTCAAGATT
119496 TTAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (14 bp):
TTCAAGATTATTGG
Found at i:120189 original size:29 final size:29
Alignment explanation
Indices: 120141--120198 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
120131 TTCCTTCCAC
* * *
120141 CATATTATACTTTCATTATAATTTATTTTA
1 CATATTATAATTTAATTATAAATT-TTTTA
120171 CATATT-TAATTTAATTATAAATTTTTTA
1 CATATTATAATTTAATTATAAATTTTTTA
120199 TAATATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.20
29 14 0.56
30 6 0.24
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (29 bp):
CATATTATAATTTAATTATAAATTTTTTA
Found at i:121632 original size:12 final size:13
Alignment explanation
Indices: 121584--121642 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
121574 TATGAAATAG
*
121584 ATATT-TATTGTT
1 ATATTATATTATT
*
121596 ATAATTAT-TAATT
1 AT-ATTATATTATT
121609 ACTATTACTATTATT
1 A-TATTA-TATTATT
121624 AT-TTATATTATT
1 ATATTATATTATT
121636 ATATTAT
1 ATATTAT
121643 GGAATAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
12 11 0.29
13 18 0.47
14 4 0.11
15 5 0.13
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (13 bp):
ATATTATATTATT
Found at i:128118 original size:5 final size:5
Alignment explanation
Indices: 128108--128132 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
128098 CAATATATAT
128108 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
128133 GAAAAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:136297 original size:17 final size:17
Alignment explanation
Indices: 136261--136309 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
136251 ATTCTTTTTC
136261 TTTTTAATTTATTT-TGA
1 TTTTT-ATTTATTTATGA
*
136278 TTTTTATTTATTTATTA
1 TTTTTATTTATTTATGA
*
136295 TTTATATTT-TTTATG
1 TTTTTATTTATTTATG
136310 CTTTAGGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (17 bp):
TTTTTATTTATTTATGA
Found at i:137329 original size:5 final size:5
Alignment explanation
Indices: 137319--137396 Score: 59
Period size: 6 Copynumber: 14.4 Consensus size: 5
137309 AGTAATAAAT
* * *
137319 AATAA AATAA AATAA AGTAATA AATAA AGT-A AAGAA AATAA AATAAA
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATAA AATAA AAT-AA
137366 AATAAA AATAAA AATAAA AATAAA AATAA AA
1 AAT-AA AAT-AA AAT-AA AAT-AA AATAA AA
137397 ATTGGGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
4 2 0.03
5 27 0.43
6 31 0.49
7 3 0.05
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:137329 original size:12 final size:11
Alignment explanation
Indices: 137312--137396 Score: 82
Period size: 12 Copynumber: 7.2 Consensus size: 11
137302 CCAAATAAGT
137312 AATAAATAATAA
1 AATAAA-AATAA
137324 AAT-AAAATAA
1 AATAAAAATAA
*
137334 AGTAATAAATAA
1 AATAA-AAATAA
*
137346 AGTAAAGAAAATAA
1 A--ATA-AAAATAA
137360 AATAAAAATAAA
1 AATAAAAAT-AA
137372 AATAAAAATAAA
1 AATAAAAAT-AA
137384 AATAAAAATAA
1 AATAAAAATAA
137395 AA
1 AA
137397 ATTGGGTTGC
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
10 7 0.11
11 12 0.19
12 35 0.56
14 8 0.13
15 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:137369 original size:6 final size:6
Alignment explanation
Indices: 137353--137398 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
137343 TAAAGTAAAG
137353 AAAAT- AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
137399 TGGGTTGCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.12
6 35 0.88
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:140099 original size:46 final size:46
Alignment explanation
Indices: 140046--140184 Score: 242
Period size: 46 Copynumber: 3.0 Consensus size: 46
140036 ACATTGCTAT
* * *
140046 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
140092 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
*
140138 AACTCGGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
140184 A
1 A
140185 TTTTTCCATG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 89 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
Found at i:141435 original size:17 final size:16
Alignment explanation
Indices: 141411--141452 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
141401 ATTTAAATCG
141411 CAAAAATTCACTAAAT
1 CAAAAATTCACTAAAT
* *
141427 CACAAAATTCACTCATT
1 CA-AAAATTCACTAAAT
141444 CAAAAATTC
1 CAAAAATTC
141453 TTCTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (16 bp):
CAAAAATTCACTAAAT
Found at i:144200 original size:29 final size:29
Alignment explanation
Indices: 144160--144218 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
144150 ATAAAATAAA
* *
144160 ATCTTAAAATTAGATAATCCTTA-ATAATT
1 ATCTTAAAATTAAAT-ATCCTAATATAATT
*
144189 ATCTTAATATTAAATATCCTAATATAATT
1 ATCTTAAAATTAAATATCCTAATATAATT
144218 A
1 A
144219 AAATAGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (29 bp):
ATCTTAAAATTAAATATCCTAATATAATT
Found at i:146819 original size:20 final size:22
Alignment explanation
Indices: 146767--146821 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
146757 GGTGGATCAA
146767 CTCTTACGAGCTT-CTGTTCAG
1 CTCTTACGAGCTTCCTGTTCAG
146788 CTCTTACGAGCTTCCTGTTCAG
1 CTCTTACGAGCTTCCTGTTCAG
146810 CT-TT-CGAGCTTC
1 CTCTTACGAGCTTC
146822 TATTGCCGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.24
21 15 0.45
22 10 0.30
ACGTcount: A:0.13, C:0.31, G:0.18, T:0.38
Consensus pattern (22 bp):
CTCTTACGAGCTTCCTGTTCAG
Found at i:147363 original size:2 final size:2
Alignment explanation
Indices: 147356--147408 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
147346 GTATGAGTGA
147356 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
147398 TG TG TG TG TG T
1 TG TG TG TG TG T
147409 TCCTAATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:158403 original size:12 final size:12
Alignment explanation
Indices: 158386--158410 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
158376 TCCCTGAAGT
158386 ATCAAGAGGCTC
1 ATCAAGAGGCTC
158398 ATCAAGAGGCTC
1 ATCAAGAGGCTC
158410 A
1 A
158411 CCAGAATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (12 bp):
ATCAAGAGGCTC
Found at i:160718 original size:7 final size:6
Alignment explanation
Indices: 160697--160726 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
160687 TACATATTAC
160697 TCAAAA TCAAAA TCAGAAA TCAAAA TCAAA
1 TCAAAA TCAAAA TCA-AAA TCAAAA TCAAA
160727 TGCATTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.63, C:0.17, G:0.03, T:0.17
Consensus pattern (6 bp):
TCAAAA
Found at i:160718 original size:13 final size:13
Alignment explanation
Indices: 160700--160724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160690 ATATTACTCA
160700 AAATCAAAATCAG
1 AAATCAAAATCAG
160713 AAATCAAAATCA
1 AAATCAAAATCA
160725 AATGCATTTT
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:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAATCAAAATCAG
Found at i:163009 original size:6 final size:6
Alignment explanation
Indices: 162998--163030 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
162988 AAAACCTAAA
162998 TATAAT TATAAT TATAAT TATAAT TATAAT TAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT TAT
163031 TAGTTAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:166873 original size:15 final size:16
Alignment explanation
Indices: 166853--166889 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
166843 ACAAAATCAA
166853 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
166868 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
166884 ATAAAA
1 ATAAAA
166890 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:167081 original size:60 final size:60
Alignment explanation
Indices: 167007--167128 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
166997 ATACTAAACT
* * * * *
167007 AAACACAACAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
167067 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
167127 AA
1 AA
167129 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:167150 original size:23 final size:23
Alignment explanation
Indices: 167122--167255 Score: 177
Period size: 23 Copynumber: 5.8 Consensus size: 23
167112 TTATAAAATA
167122 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
167145 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
*
167168 ATTACAATATCCATAC--A-AA-
1 ATTACAATATTCATACAAACAAT
*
167187 ATTACAATATTCATACAAAAAAT
1 ATTACAATATTCATACAAACAAT
*
167210 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--ACAAT
167237 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
167256 ATACTAATCC
Statistics
Matches: 99, Mismatches: 4, Indels: 16
0.83 0.03 0.13
Matches are distributed among these distances:
19 15 0.15
20 2 0.02
21 2 0.02
22 2 0.02
23 55 0.56
25 4 0.04
27 19 0.19
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTACAATATTCATACAAACAAT
Found at i:167197 original size:65 final size:67
Alignment explanation
Indices: 167121--167257 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 67
167111 ATTATAAAAT
* *
167121 AATTACAATATTCATACAAACAATATTACAATATTCATAC-AA-ACAATATTACAATATCCATAC
1 AATTACAATATTCATACAAAAAATATTACAATATTCATACAAATACAAAATTACAATATCCATAC
167184 AA
66 AA
*
167186 AATTACAATATTCATACAAAAAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAAAAATATTACAATATTCATAC-AAA-TACAAAATTACAATATCCAT
167251 ACAA
64 ACAA
167255 AAT
1 AAT
167258 ACTAATCCAA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
65 39 0.60
67 2 0.03
69 24 0.37
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (67 bp):
AATTACAATATTCATACAAAAAATATTACAATATTCATACAAATACAAAATTACAATATCCATAC
AA
Found at i:167204 original size:42 final size:42
Alignment explanation
Indices: 167116--167235 Score: 168
Period size: 42 Copynumber: 2.7 Consensus size: 42
167106 AATTAATTAT
*
167116 AAAATAATTACAATATTCATACAAACAATATTACAATATTCATACAA
1 AAAAT-ATTACAATATCCATAC--A-AA-ATTACAATATTCATACAA
*
167163 ACAATATTACAATATCCATACAAAATTACAATATTCATACAA
1 AAAATATTACAATATCCATACAAAATTACAATATTCATACAA
*
167205 AAAATATTACAATATTCATACAAAATTACAA
1 AAAATATTACAATATCCATACAAAATTACAA
167236 AATTACAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
42 47 0.68
43 2 0.03
44 1 0.01
46 15 0.22
47 4 0.06
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (42 bp):
AAAATATTACAATATCCATACAAAATTACAATATTCATACAA
Found at i:167245 original size:27 final size:27
Alignment explanation
Indices: 167181--167257 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
167171 ACAATATCCA
167181 TACAAAATTACAATATTCATAC-AAA-
1 TACAAAATTACAATATTCATACAAAAT
*
167206 -A-AATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
167231 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
167258 ACTAATCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 18 0.39
24 4 0.09
26 1 0.02
27 23 0.50
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:167256 original size:19 final size:19
Alignment explanation
Indices: 167231--167337 Score: 58
Period size: 19 Copynumber: 5.4 Consensus size: 19
167221 CATACAAAAT
167231 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
167250 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
* * *
167268 AACTATAAA-TACAAAATTAA
1 TAC-A-AAATTACAATATTCA
*
167288 TTATAAAATAATTACAATATTCA
1 -TACAAAAT--T-ACAATATTCA
* *
167311 TACAACATTATAATATTCA
1 TACAAAATTACAATATTCA
167330 TACAAAAT
1 TACAAAAT
167338 ACTAATCAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
17 3 0.05
18 7 0.11
19 27 0.42
20 10 0.15
21 3 0.05
22 7 0.11
23 8 0.12
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:167281 original size:88 final size:88
Alignment explanation
Indices: 167105--167491 Score: 489
Period size: 88 Copynumber: 4.5 Consensus size: 88
167095 AATTACTAAC
*
167105 AAATTAATTATAAAATAATTACAATATTCATAC--AA--ACAATATTACAATATTCATACAAACA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAA-A
* ** *
167166 -A-TATTACAATATCCATACAAAATTACA
65 TACTAAT-CAA-AAAC-TA-TAAA-TACA
* * * *
167193 ATATTCA-TACAAAAAATATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAA
1 AAATTAATTATAAAATA-ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAA
*
167257 TACTAATCCAAAACTATAAATACA
65 TACTAATCAAAAACTATAAATACA
*
167281 AAATTAATTATAAAATAATTACAATATTCATAC---A--AC---ATTATAATATTCATACAAAAT
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
167338 ACTAATCAAAAACTATAAATACA
66 ACTAATCAAAAACTATAAATACA
167361 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
*
167426 ACTAATAAAAAACTATAAATACA
66 ACTAATCAAAAACTATAAATACA
*
167449 AAATTAATTATAAAATAATTACAATATTCATAAAAAATTACAA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAA
167492 TATTCATACA
Statistics
Matches: 264, Mismatches: 19, Indels: 32
0.84 0.06 0.10
Matches are distributed among these distances:
80 75 0.28
83 3 0.01
85 3 0.01
87 7 0.03
88 130 0.49
89 10 0.04
90 4 0.02
91 3 0.01
92 26 0.10
93 3 0.01
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (88 bp):
AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAT
ACTAATCAAAAACTATAAATACA
Found at i:167326 original size:80 final size:80
Alignment explanation
Indices: 167231--167504 Score: 431
Period size: 80 Copynumber: 3.3 Consensus size: 80
167221 CATACAAAAT
*
167231 TACAAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
167296 TAATTACAATATTCA
66 TAATTACAATATTCA
* *
167311 TACAACATTATAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
167376 TAATTACAATATTCATACAAAA
66 TAATTACAATA-T--T-C---A
*
167398 TTACAAAATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAATTAATTATAAA
1 -TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAA
167463 ATAATTACAATATTCA
65 ATAATTACAATATTCA
*
167479 TAAAAAATTACAATATTCATACAAAA
1 TACAAAATTACAATATTCATACAAAA
167505 AATTACACTA
Statistics
Matches: 179, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
80 98 0.55
81 2 0.01
83 1 0.01
84 2 0.01
85 1 0.01
87 2 0.01
88 73 0.41
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (80 bp):
TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
TAATTACAATATTCA
Found at i:167343 original size:19 final size:19
Alignment explanation
Indices: 167303--167343 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
167293 AAATAATTAC
*
167303 AATATTCATACAACATTAT
1 AATATTCATACAACAATAT
167322 AATATTCATACAA-AATACT
1 AATATTCATACAACAATA-T
167341 AAT
1 AAT
167344 CAAAAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATTCATACAACAATAT
Found at i:167401 original size:19 final size:19
Alignment explanation
Indices: 167399--167630 Score: 111
Period size: 19 Copynumber: 11.6 Consensus size: 19
167389 CATACAAAAT
167399 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
**
167418 TACAAAA-TACTAATA-AAA
1 TACAAAATTAC-AATATTCA
* * *
167436 AACTATAAA-TACAAAATTAA
1 TAC-A-AAATTACAATATTCA
*
167456 TTATAAAATAATTACAATATTCA
1 -TACAAAAT--T-ACAATATTCA
*
167479 TAAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
167498 TACAAAAAATTACACTATTCA
1 TAC--AAAATTACAATATTCA
**
167519 TACAAAATACTAATCCAAAATTATAAA
1 TACAAAAT--T-A--C--AA-TATTCA
167546 TACAAAATT---A-ATT-A
1 TACAAAATTACAATATTCA
*
167560 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
*
167580 TACAAAATTATAATATTCA
1 TACAAAATTACAATATTCA
*
167599 TACAAAAAGTTACAATATACA
1 TAC-AAAA-TTACAATATTCA
167620 TACAAAATTAC
1 TACAAAATTAC
167631 CCATTGGCGC
Statistics
Matches: 165, Mismatches: 21, Indels: 54
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.03
15 6 0.04
17 1 0.01
18 7 0.04
19 58 0.35
20 23 0.14
21 33 0.20
22 9 0.05
23 8 0.05
24 1 0.01
25 1 0.01
26 1 0.01
27 12 0.07
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:167504 original size:21 final size:21
Alignment explanation
Indices: 167460--167626 Score: 122
Period size: 21 Copynumber: 8.2 Consensus size: 21
167450 AATTAATTAT
167460 AAAATAATTACAATATTCAT--
1 AAAA-AATTACAATATTCATAC
167480 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
167501 AAAAAATTACACTATTCATAC
1 AAAAAATTACAATATTCATAC
* * * *
167522 AAAATACTAATCCAAAATT-ATAA
1 AAAA-A--ATTACAATATTCATAC
167545 ATACAAAATT---A-ATT-ATA-
1 A-A-AAAATTACAATATTCATAC
*
167562 AAATAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
167583 --AAAATTATAATATTCATAC
1 AAAAAATTACAATATTCATAC
* *
167602 AAAAAGTTACAATATACATAC
1 AAAAAATTACAATATTCATAC
167623 AAAA
1 AAAA
167627 TTACCCATTG
Statistics
Matches: 119, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
15 5 0.04
16 1 0.01
17 1 0.01
18 7 0.06
19 36 0.30
20 7 0.06
21 44 0.37
22 3 0.03
23 4 0.03
24 9 0.08
25 2 0.02
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.30
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:167544 original size:101 final size:101
Alignment explanation
Indices: 167370--167627 Score: 381
Period size: 101 Copynumber: 2.5 Consensus size: 101
167360 AAAATTAATT
167370 ATAAAATAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATACTAATAAA
1 ATAAAA-AATTACAATATTCATAC---A--A-AAAATTACAATATTCATACAAAATACTAATAAA
167435 AAACTATAAATACAAAATTAATTATAAAATAATTACAATATTC
59 AAACTATAAATACAAAATTAATTATAAAATAATTACAATATTC
* ** *
167478 ATAAAAAATTACAATATTCATACAAAAAATTACACTATTCATACAAAATACTAATCCAAAATTAT
1 ATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATAAAAAACTAT
167543 AAATACAAAATTAATTATAAAATAATTACAATATTC
66 AAATACAAAATTAATTATAAAATAATTACAATATTC
* * * *
167579 ATACAAAATTATAATATTCATACAAAAAGTTACAATATACATACAAAAT
1 ATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAAT
167628 TACCCATTGG
Statistics
Matches: 141, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
101 116 0.82
102 1 0.01
104 1 0.01
107 17 0.12
108 6 0.04
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (101 bp):
ATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATAAAAAACTAT
AAATACAAAATTAATTATAAAATAATTACAATATTC
Found at i:169642 original size:30 final size:30
Alignment explanation
Indices: 169603--169671 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
169593 TTAAATTAGT
* *
169603 AATGGTAAAATTGTACTTT-ATCCCCCTAAA
1 AATGATAAAATTGTAATTTAAT-CCCCTAAA
* *
169633 AATGATAAAATTTTAATTTAATCCTCTAAA
1 AATGATAAAATTGTAATTTAATCCCCTAAA
*
169663 AATTATAAA
1 AATGATAAA
169672 TATAGAGGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (30 bp):
AATGATAAAATTGTAATTTAATCCCCTAAA
Found at i:174585 original size:29 final size:29
Alignment explanation
Indices: 174529--174589 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
174519 TTTAATAAAT
*
174529 TTAATATTAAATTTAATTTAATCCTTATC
1 TTAATATTAAATTTAATTTAATACTTATC
* *
174558 TTAATATTAAATTTAATTTTATATTTATC
1 TTAATATTAAATTTAATTTAATACTTATC
174587 TTA
1 TTA
174590 TAGATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAATATTAAATTTAATTTAATACTTATC
Found at i:174597 original size:29 final size:29
Alignment explanation
Indices: 174529--174598 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
174519 TTTAATAAAT
* *
174529 TTAATATTAAATTTAATTTAATCCTTATC
1 TTAATAATAAATTTAATTTAATACTTATC
* * *
174558 TTAATATTAAATTTAATTTTATATTTATC
1 TTAATAATAAATTTAATTTAATACTTATC
174587 TT-ATAGATAAAT
1 TTAATA-ATAAAT
174599 ATTCTATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAATAATAAATTTAATTTAATACTTATC
Found at i:186285 original size:45 final size:41
Alignment explanation
Indices: 186212--186301 Score: 94
Period size: 45 Copynumber: 2.1 Consensus size: 41
186202 AAAGAAATGG
*
186212 GAAACATTTAGAAATGATTATGGTTTTCTCTGAAATGGAGAAAT
1 GAAACATTTAGAAATGATTATGGTTTTCTC-AAAAT-G-GAAAT
*
186256 GAAATCATTTGGAAATGAATGTA-GG-TTTCTCAAAATGGAAAT
1 GAAA-CATTTAGAAATG-AT-TATGGTTTTCTCAAAATGGAAAT
186298 GAAA
1 GAAA
186302 ATGGAAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
42 9 0.22
43 1 0.02
44 8 0.20
45 17 0.41
46 4 0.10
47 2 0.05
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (41 bp):
GAAACATTTAGAAATGATTATGGTTTTCTCAAAATGGAAAT
Found at i:186304 original size:12 final size:12
Alignment explanation
Indices: 186287--186317 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
186277 TAGGTTTCTC
186287 AAAATGGAAATG
1 AAAATGGAAATG
186299 AAAATGGAAATG
1 AAAATGGAAATG
186311 AGAAATG
1 A-AAATG
186318 ATTCATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:196743 original size:16 final size:16
Alignment explanation
Indices: 196722--196752 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
196712 AAAAATCAAG
196722 ATATTTATAAAAATTT
1 ATATTTATAAAAATTT
*
196738 ATATTTTTAAAAATT
1 ATATTTATAAAAATT
196753 ATAAAAATTA
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:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTATAAAAATTT
Found at i:200788 original size:39 final size:39
Alignment explanation
Indices: 200731--200809 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
200721 CACATCTAAC
200731 TTTCAATAGTACCAAAAAATATTACTACCAGATCATAAG
1 TTTCAATAGTACCAAAAAATATTACTACCAGATCATAAG
*
200770 TTTCAATAGGTACCAAAAAATATTACTACTAGATCATAAG
1 TTTCAATA-GTACCAAAAAATATTACTACCAGATCATAAG
200810 CCCCGTTCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (39 bp):
TTTCAATAGTACCAAAAAATATTACTACCAGATCATAAG
Found at i:218047 original size:5 final size:5
Alignment explanation
Indices: 218037--218062 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
218027 CCTCCATTAT
218037 TCTTC TCTTC TCTTC TCTTC TCTTC T
1 TCTTC TCTTC TCTTC TCTTC TCTTC T
218063 GCTCACTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCTTC
Found at i:219371 original size:19 final size:17
Alignment explanation
Indices: 219333--219366 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
219323 AACTAGAAAT
219333 AAATATATAAAAATTTA
1 AAATATATAAAAATTTA
219350 AAATATATAAAAATTTA
1 AAATATATAAAAATTTA
219367 GAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATATAAAAATTTA
Found at i:219376 original size:19 final size:17
Alignment explanation
Indices: 219337--219389 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
219327 AGAAATAAAT
*
219337 ATATAAAAATTTAAAAT
1 ATATAAAAATTTAAAAA
219354 ATATAAAAATTTAGAAAA
1 ATATAAAAATTTA-AAAA
*
219372 A-ATATAAATTATAAAAA
1 ATATAAAAATT-TAAAAA
219389 A
1 A
219390 GTAAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 26 0.81
18 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
ATATAAAAATTTAAAAA
Found at i:219729 original size:46 final size:46
Alignment explanation
Indices: 219662--219751 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
219652 ATGAATGATG
* * * *
219662 TTATGTATTTAATATATTGTTGAAAAATGGAGTGTTGTTAAATTTA
1 TTATGTATTTAACATATTGTTGAAAAATGAAATATTGTTAAATTTA
*
219708 TTATGTATTTAGCATATTGTTGAAAAATGAAATATTGTTAAATT
1 TTATGTATTTAACATATTGTTGAAAAATGAAATATTGTTAAATT
219752 ATGAATTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.47
Consensus pattern (46 bp):
TTATGTATTTAACATATTGTTGAAAAATGAAATATTGTTAAATTTA
Found at i:219977 original size:21 final size:21
Alignment explanation
Indices: 219953--220003 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
219943 CCTAATGGGT
219953 TTCCATTCAGCTCCTATGAGC
1 TTCCATTCAGCTCCTATGAGC
* *
219974 TTCCGTTCAGCTCTTATGAGC
1 TTCCATTCAGCTCCTATGAGC
*
219995 TTCCTTTCA
1 TTCCATTCA
220004 ACCCTTACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.31, G:0.14, T:0.39
Consensus pattern (21 bp):
TTCCATTCAGCTCCTATGAGC
Found at i:220010 original size:21 final size:21
Alignment explanation
Indices: 219932--220010 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
219922 ACTCATAAGT
* * *
219932 TTCCATTCAACCCTAATGGGT
1 TTCCATTCAACCCTTATGAGC
*
219953 TTCCATTCAGCTCC-TATGAGC
1 TTCCATTCAAC-CCTTATGAGC
* * *
219974 TTCCGTTCAGCTCTTATGAGC
1 TTCCATTCAACCCTTATGAGC
*
219995 TTCCTTTCAACCCTTA
1 TTCCATTCAACCCTTA
220011 CGGGTTTCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.37
Consensus pattern (21 bp):
TTCCATTCAACCCTTATGAGC
Found at i:227224 original size:30 final size:30
Alignment explanation
Indices: 227168--227225 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
227158 AGCTTAGGGA
*
227168 CAAAAGTGTAAATATGTAAAAGTTTGGGGG
1 CAAAAGTGTAAATATGTAAAAATTTGGGGG
* *
227198 CAAAATTGTAAAT-TTTCAAAAATTTGGG
1 CAAAAGTGTAAATATGT-AAAAATTTGGG
227226 TGGAGGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.31
Consensus pattern (30 bp):
CAAAAGTGTAAATATGTAAAAATTTGGGGG
Found at i:227636 original size:43 final size:43
Alignment explanation
Indices: 227588--227726 Score: 181
Period size: 43 Copynumber: 3.5 Consensus size: 43
227578 ATTCATTGGT
227588 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATATGAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATATGAAAGGG
* * *
227631 GGTTGCTAAGTGCTGGTTCC-CCG-A--TT-CAT-T----GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATATGAAAGGG
227664 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATATGAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATATGAAAGGG
227707 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
227727 CCCGAGGGGT
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
33 21 0.26
34 3 0.04
35 1 0.01
37 3 0.04
38 4 0.05
39 3 0.04
41 1 0.01
42 3 0.04
43 41 0.51
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATATGAAAGGG
Found at i:227637 original size:76 final size:76
Alignment explanation
Indices: 227546--227728 Score: 325
Period size: 76 Copynumber: 2.4 Consensus size: 76
227536 AGCATATTGC
**
227546 ATAT-AAA-GGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 ATATGAAAGGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA
227609 CCGTATTTTAA
66 CCGTATTTTAA
*
227620 ATATGAAAGGGGGTTGCTAAGTGCTGGTTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 ATATGAAAGGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA
227685 CCGTATTTTAA
66 CCGTATTTTAA
227696 ATATGAAAGGGGGTTGCTAAGTGCTGATTCCCC
1 ATATGAAAGGGGGTTGCTAAGTGCTGATTCCCC
227729 CGAGGGGTTG
Statistics
Matches: 103, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
74 4 0.04
75 3 0.03
76 96 0.93
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.34
Consensus pattern (76 bp):
ATATGAAAGGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA
CCGTATTTTAA
Found at i:227754 original size:103 final size:103
Alignment explanation
Indices: 227629--227893 Score: 388
Period size: 103 Copynumber: 2.6 Consensus size: 103
227619 AATATGAAAG
* * * *
227629 GGGGTTGCTAAGTGCTGGTTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCTG
*
227694 AAATATGAAAGGGGGTTGCTAAGTGCTGATT-CCCCCGA
66 AAATATG-AAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
* * *
227732 GGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCACATCTG
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCTG
*
227797 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
66 AAATATGAAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
** * * *
227835 GGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGTTTGCTAAGTGCGGAATCCACCG
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
227894 ATAATGGTTA
Statistics
Matches: 144, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
102 23 0.16
103 121 0.84
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.32
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCTG
AAATATGAAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
Found at i:232166 original size:19 final size:19
Alignment explanation
Indices: 232139--232176 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
232129 AAAATATTAA
*
232139 TTATTTTTTACAATTTTTT
1 TTATATTTTACAATTTTTT
232158 TTATATTTTACAATTTTTT
1 TTATATTTTACAATTTTTT
232177 ACATTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATATTTTACAATTTTTT
Found at i:232311 original size:18 final size:18
Alignment explanation
Indices: 232274--232312 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
232264 TAGATTATAA
*
232274 TATGTTTTTCTAAATTTT
1 TATGTTTTTCTAAATGTT
232292 TATGTATTTTCT-AATGTT
1 TATGT-TTTTCTAAATGTT
232310 TAT
1 TAT
232313 ATACATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (18 bp):
TATGTTTTTCTAAATGTT
Found at i:242188 original size:16 final size:16
Alignment explanation
Indices: 242169--242205 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
242159 CAAACAAATT
242169 TTAAA-CAAAACAGCAC
1 TTAAATCAAAACA-CAC
242185 TTAAATCAAAACACAC
1 TTAAATCAAAACACAC
242201 TTAAA
1 TTAAA
242206 ACTTGAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.57, C:0.22, G:0.03, T:0.19
Consensus pattern (16 bp):
TTAAATCAAAACACAC
Found at i:250908 original size:6 final size:6
Alignment explanation
Indices: 250897--251059 Score: 89
Period size: 6 Copynumber: 26.8 Consensus size: 6
250887 TTGTCGTGAC
** * * * *
250897 TCTCAT TCTCAT TCTCAT TCTCGC TCACAC TCTCAT TCTCGCT T-TCAC
1 TCTCAT TCTCAT TCTCAT TCTCAT TCTCAT TCTCAT TCTC-AT TCTCAT
* * * * * *
250945 TCTCTT TCTCACAC TCTCAT TCTCACT T-TCAC TCTCAC TCACAC TCTCAT
1 TCTCAT TCT--CAT TCTCAT TCTCA-T TCTCAT TCTCAT TCTCAT TCTCAT
* * * * * * *
250995 TCTCAA TCTCAT TCTCAC TCTCGT TCTTAT TCTCAC TCACACT T-TCAC
1 TCTCAT TCTCAT TCTCAT TCTCAT TCTCAT TCTCAT TCTCA-T TCTCAT
251043 TCTCAT TCTCAT TCTCA
1 TCTCAT TCTCAT TCTCA
251060 CTCACACTTG
Statistics
Matches: 117, Mismatches: 32, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
5 3 0.03
6 105 0.90
7 5 0.04
8 4 0.03
ACGTcount: A:0.17, C:0.39, G:0.02, T:0.42
Consensus pattern (6 bp):
TCTCAT
Found at i:251011 original size:30 final size:30
Alignment explanation
Indices: 250895--251062 Score: 158
Period size: 30 Copynumber: 5.5 Consensus size: 30
250885 ACTTGTCGTG
* *
250895 ACTCTCATTCTCATTCTCATTCTCGCTCAC
1 ACTCTCATTCTCACTCTCATTCTCACTCAC
* * **
250925 ACTCTCATTCTCGCTTTCACTCTCTTTCTCAC
1 ACTCTCATTCTCACTCTCA-T-TCTCACTCAC
* *
250957 ACTCTCATTCTCACTTTCACTCTCACTCAC
1 ACTCTCATTCTCACTCTCATTCTCACTCAC
* *
250987 ACTCTCATTCTCAATCTCATTCTCACTCTC
1 ACTCTCATTCTCACTCTCATTCTCACTCAC
** * * *
251017 GTTCTTATTCTCACTCACACTT-TCACTCTC
1 ACTCTCATTCTCACTCTCA-TTCTCACTCAC
*
251047 ATTCTCATTCTCACTC
1 ACTCTCATTCTCACTC
251063 ACACTTGCAC
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
30 86 0.75
31 3 0.03
32 26 0.23
ACGTcount: A:0.17, C:0.40, G:0.02, T:0.41
Consensus pattern (30 bp):
ACTCTCATTCTCACTCTCATTCTCACTCAC
Found at i:251062 original size:18 final size:18
Alignment explanation
Indices: 250897--251082 Score: 117
Period size: 18 Copynumber: 10.2 Consensus size: 18
250887 TTGTCGTGAC
*
250897 TCTCATTCTCATTCTCAT
1 TCTCACTCTCATTCTCAT
* * *
250915 TCTCGCTCACACTCTCAT
1 TCTCACTCTCATTCTCAT
* * * *
250933 TCTCGCTTTCACTCTCTT
1 TCTCACTCTCATTCTCAT
250951 TCTCACACTCTCATTCTCACT
1 TCT--CACTCTCATTCTCA-T
* * *
250972 T-TCACTCTCACTCACAC
1 TCTCACTCTCATTCTCAT
* *
250989 TCTCATTCTCAATCTCAT
1 TCTCACTCTCATTCTCAT
* *
251007 TCTCACTCTCGTTCTTAT
1 TCTCACTCTCATTCTCAT
* *
251025 TCTCACTCACACTT-TCAC
1 TCTCACTCTCA-TTCTCAT
* *
251043 TCTCATTCTCATTCTCAC
1 TCTCACTCTCATTCTCAT
* *
251061 TCACACT-TGCACTCTCAT
1 TCTCACTCT-CATTCTCAT
251079 TCTC
1 TCTC
251083 GTTCTTCATC
Statistics
Matches: 128, Mismatches: 33, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
17 4 0.03
18 109 0.85
19 2 0.02
20 11 0.09
21 2 0.02
ACGTcount: A:0.17, C:0.40, G:0.02, T:0.41
Consensus pattern (18 bp):
TCTCACTCTCATTCTCAT
Found at i:251074 original size:30 final size:30
Alignment explanation
Indices: 251028--251087 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
251018 TTCTTATTCT
*
251028 CACTCACACTTTCACTCTCATTCTCATTCT
1 CACTCACACTTGCACTCTCATTCTCATTCT
*
251058 CACTCACACTTGCACTCTCATTCTCGTTCT
1 CACTCACACTTGCACTCTCATTCTCATTCT
251088 TCATCTCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.40, G:0.03, T:0.38
Consensus pattern (30 bp):
CACTCACACTTGCACTCTCATTCTCATTCT
Found at i:251587 original size:32 final size:32
Alignment explanation
Indices: 251551--251614 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
251541 GCACGTCTAG
* *
251551 AATGAACTTA-AACAAATTGTTGTCTAGATTCA
1 AATGAA-TTAGAACAAATAGATGTCTAGATTCA
*
251583 AATGAATTAGAAGAAATAGATGTCTAGATTCA
1 AATGAATTAGAACAAATAGATGTCTAGATTCA
251615 TTTTGAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (32 bp):
AATGAATTAGAACAAATAGATGTCTAGATTCA
Done.