Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000792.1 Hibiscus syriacus cultivar Beakdansim tig00001534_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 94138
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:24848 original size:14 final size:14
Alignment explanation
Indices: 24829--24881 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
24819 GCCATCTGTT
24829 CGAACATAAATGAA
1 CGAACATAAATGAA
24843 CGAACATAAAT---
1 CGAACATAAATGAA
24854 -GAACATAAATGAA
1 CGAACATAAATGAA
*
24867 CGAACATAAACGAA
1 CGAACATAAATGAA
24881 C
1 C
24882 ATATAATCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 10 0.29
14 24 0.71
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:24859 original size:24 final size:24
Alignment explanation
Indices: 24829--24894 Score: 105
Period size: 24 Copynumber: 2.7 Consensus size: 24
24819 GCCATCTGTT
24829 CGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
*
24853 TGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
24877 CGAACATATAATCGAACG
1 CGAACATA-AAT-GAACG
24895 TTCACGAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 30 0.79
25 3 0.08
26 5 0.13
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.15
Consensus pattern (24 bp):
CGAACATAAATGAACGAACATAAA
Found at i:25328 original size:15 final size:15
Alignment explanation
Indices: 25265--25315 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
25255 ATAATAATAT
25265 ATAAATTATATTAAAA
1 ATAAATT-TATTAAAA
* *
25281 ATAAAATTATTGAAA
1 ATAAATTTATTAAAA
25296 AT-AATTTATATAAAA
1 ATAAATTTAT-TAAAA
25311 ATAAA
1 ATAAA
25316 AATAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 6 0.21
15 15 0.52
16 8 0.28
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATAAATTTATTAAAA
Found at i:25468 original size:16 final size:16
Alignment explanation
Indices: 25437--25469 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25427 TATATTAAAA
25437 TTTTATATAAATTATT
1 TTTTATATAAATTATT
25453 TTTTGATATAAA-TATT
1 TTTT-ATATAAATTATT
25469 T
1 T
25470 ATTAAACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTATATAAATTATT
Found at i:26717 original size:16 final size:16
Alignment explanation
Indices: 26696--26750 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
26686 CATTTAATAA
26696 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
26712 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
**
26728 ATAAATAAACACGAAC
1 ATAAACGAACACGAAC
26744 ATAAACG
1 ATAAACG
26751 TTGGAAACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:30304 original size:29 final size:29
Alignment explanation
Indices: 30262--30318 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
30252 ACGAACCAGC
30262 ATAGGTCGCCATGCACGCCCGGCATCCTT
1 ATAGGTCGCCATGCACGCCCGGCATCCTT
*
30291 ATAGGTCGCCATGCACGCCCGGCGTCCT
1 ATAGGTCGCCATGCACGCCCGGCATCCT
30319 ATAATCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.39, G:0.26, T:0.19
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCATCCTT
Found at i:30341 original size:32 final size:32
Alignment explanation
Indices: 30300--30363 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
30290 TATAGGTCGC
*
30300 CATGCACGCCCGGCGTCCTATAATCATTATCA
1 CATGCACGCCAGGCGTCCTATAATCATTATCA
30332 CATGCACGCCAGGCGTCCTATAATCATTATCA
1 CATGCACGCCAGGCGTCCTATAATCATTATCA
30364 TTCTCGTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.25
Consensus pattern (32 bp):
CATGCACGCCAGGCGTCCTATAATCATTATCA
Found at i:30926 original size:21 final size:21
Alignment explanation
Indices: 30901--30944 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
30891 AATCTAGTTA
*
30901 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGCTAGTATAAATT
* *
30922 ATTAGTTTGCTAGTTTAAGTT
1 ATTAGTTTGCTAGTATAAATT
30943 AT
1 AT
30945 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (21 bp):
ATTAGTTTGCTAGTATAAATT
Found at i:30954 original size:28 final size:28
Alignment explanation
Indices: 30921--30974 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
30911 TAGTATAAAT
30921 TATTAGTTTGCTAGTTTAAGTTATATTA
1 TATTAGTTTGCTAGTTTAAGTTATATTA
*
30949 TATTAGTTTGTTAGTTTAAGTTATAT
1 TATTAGTTTGCTAGTTTAAGTTATAT
30975 ATTATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.56
Consensus pattern (28 bp):
TATTAGTTTGCTAGTTTAAGTTATATTA
Found at i:31517 original size:22 final size:23
Alignment explanation
Indices: 31474--31517 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31464 ATTATGTTTT
**
31474 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
31497 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
31518 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:34739 original size:49 final size:49
Alignment explanation
Indices: 34669--34856 Score: 340
Period size: 49 Copynumber: 3.8 Consensus size: 49
34659 GGCACCCATC
*
34669 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAAT
34718 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAAT
34767 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAAT
* * *
34816 TATTATTAATATTTAATTATTTGATAGTAATTATAAGTAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
34857 TATTAATAAT
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 135 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (49 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAAAAT
Found at i:34868 original size:17 final size:17
Alignment explanation
Indices: 34843--34885 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
34833 TATTTGATAG
*
34843 TAATTATAAGT-AATTA
1 TAATAATAAGTAAATTA
*
34859 TTAATAATAATTAAATTA
1 -TAATAATAAGTAAATTA
34877 TAATAATAA
1 TAATAATAA
34886 TGATTTACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAATAATAAGTAAATTA
Found at i:35088 original size:12 final size:11
Alignment explanation
Indices: 35067--35109 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
35057 CATAAAAATG
35067 ATTTAATAATA
1 ATTTAATAATA
*
35078 ATTTAAATAATG
1 ATTT-AATAATA
35090 ATTTAATAATGA
1 ATTTAATAAT-A
35102 ATTTAATA
1 ATTTAATA
35110 TTTAATGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:35089 original size:23 final size:23
Alignment explanation
Indices: 35059--35441 Score: 151
Period size: 26 Copynumber: 15.8 Consensus size: 23
35049 CAATTAACCA
35059 TAAA-AATGATTTAATAATAATT
1 TAAATAATGATTTAATAATAATT
35081 TAAATAATGATTTAATAATGAATT
1 TAAATAATGATTTAATAAT-AATT
* *
35105 TAATATTTAATGA-TT--TGATGATT
1 TAA-A--TAATGATTTAATAATAATT
* * *
35128 T-AGTAATGATTTGATAAT-A-G
1 TAAATAATGATTTAATAATAATT
*
35148 T---TAATGATTTGATAATAATCAT
1 TAAATAATGATTTAATAATAAT--T
* *
35170 TATAGTAATGATTTGATAATAATCAT
1 TA-AATAATGATTTAATAATAAT--T
*
35196 TATAATAATGATTTAGTAATAATCAT
1 TA-AATAATGATTTAATAATAAT--T
* *
35222 TATAATAATAATTTAATAATGATT
1 TA-AATAATGATTTAATAATAATT
* * * * * * *
35246 TAAATATTTAATGATTTGATGATT
1 TAAATAATGATTTA-ATAATAATT
* *
35270 T-AGTAATGATTTGATAATAATTAT
1 TAAATAATGATTTAATAATAA-T-T
*
35294 TATAATAATGATTTAGTAATAATCAT
1 TA-AATAATGATTTAATAATAAT--T
35320 TATAATAATGATTTAATAATAA-T
1 TA-AATAATGATTTAATAATAATT
* *
35343 GATAATAATGATTTAATAATAGTAAT
1 TA-AATAATGATTTAATAATA--ATT
* *
35369 GATAATAATGATTTAATAGTAATTAT
1 TA-AATAATGATTTAATAATAA-T-T
* *
35395 TTAGTAATGATTTTATAATAATAATT
1 TAAATAATGA--TT-TAATAATAATT
*
35421 TAATATTAATAATTTAATAAT
1 TAA-A-TAATGATTTAATAAT
35442 TATTACTAAT
Statistics
Matches: 288, Mismatches: 41, Indels: 61
0.74 0.11 0.16
Matches are distributed among these distances:
18 15 0.05
19 7 0.02
20 3 0.01
21 1 0.00
22 13 0.05
23 54 0.19
24 24 0.08
25 17 0.06
26 132 0.46
27 9 0.03
28 13 0.05
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.44
Consensus pattern (23 bp):
TAAATAATGATTTAATAATAATT
Found at i:35128 original size:16 final size:15
Alignment explanation
Indices: 35096--35161 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 15
35086 AATGATTTAA
*
35096 TAATGAATTTAATATT
1 TAATG-ATTTGATATT
35112 TAATGATTTGATGATTT
1 TAATGATTTGAT-A-TT
35129 AGTAATGATTTGATAATAGT
1 --TAATGATTTGAT-AT--T
35149 TAATGATTTGATA
1 TAATGATTTGATA
35162 ATAATCATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
15 6 0.14
16 6 0.14
17 3 0.07
18 13 0.31
19 13 0.31
20 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (15 bp):
TAATGATTTGATATT
Found at i:35138 original size:11 final size:11
Alignment explanation
Indices: 35122--35386 Score: 92
Period size: 12 Copynumber: 22.0 Consensus size: 11
35112 TAATGATTTG
*
35122 ATGATTTAGTA
1 ATGATTTAATA
*
35133 ATGATTTGATA
1 ATGATTTAATA
* *
35144 AT-AGTTAATG
1 ATGATTTAATA
35154 AT--TTGATAATA
1 ATGATT--TAATA
* *
35165 ATCATTATAGTA
1 ATGATT-TAATA
35177 ATGATTTGATAATA
1 ATGATTT---AATA
*
35191 ATCATTATAATA
1 ATGATT-TAATA
35203 ATGATTTAGTAATA
1 ATGA-TT--TAATA
*
35217 ATCATTATAATA
1 ATGATT-TAATA
*
35229 ATAATTTAATA
1 ATGATTTAATA
35240 ATGATTT-A-A
1 ATGATTTAATA
35249 AT-ATTTAATGA
1 ATGATTTAAT-A
*
35260 TTTGATGATTTAGTA
1 ----ATGATTTAATA
35275 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
35289 ATTATTATAATA
1 ATGATT-TAATA
35301 ATGATTTAGTAATA
1 ATGA-TT--TAATA
*
35315 ATCATTATAATA
1 ATGATT-TAATA
35327 ATGATTTAATA
1 ATGATTTAATA
* *
35338 ATAATGATAATA
1 ATGAT-TTAATA
35350 ATGATTTAATA
1 ATGATTTAATA
*
35361 ATAGTAATGATAATA
1 AT-G--AT-TTAATA
35376 ATGATTTAATA
1 ATGATTTAATA
35387 GTAATTATTT
Statistics
Matches: 195, Mismatches: 31, Indels: 56
0.69 0.11 0.20
Matches are distributed among these distances:
8 4 0.02
9 5 0.03
10 8 0.04
11 55 0.28
12 60 0.31
13 12 0.06
14 34 0.17
15 11 0.06
16 6 0.03
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:35154 original size:18 final size:18
Alignment explanation
Indices: 35105--35164 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
35095 ATAATGAATT
*
35105 TAATATTTAATGATTTGA
1 TAATAGTTAATGATTTGA
*
35123 TGATTTAG-TAATGATTTGA
1 T-A-ATAGTTAATGATTTGA
35142 TAATAGTTAATGATTTGA
1 TAATAGTTAATGATTTGA
35160 TAATA
1 TAATA
35165 ATCATTATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.08
18 18 0.50
19 13 0.36
20 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
TAATAGTTAATGATTTGA
Found at i:35155 original size:37 final size:35
Alignment explanation
Indices: 35087--35160 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 35
35077 AATTTAAATA
*
35087 ATGATTTAATAATGAATTTAATATTTAATGATTTG
1 ATGATTTAATAATGAATTTAATAGTTAATGATTTG
* *
35122 ATGATTTAGTAATGATTTGATAATAGTTAATGATTTG
1 ATGATTTAATAATGAATT--TAATAGTTAATGATTTG
35159 AT
1 AT
35161 AATAATCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 16 0.47
37 18 0.53
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (35 bp):
ATGATTTAATAATGAATTTAATAGTTAATGATTTG
Found at i:35185 original size:26 final size:26
Alignment explanation
Indices: 35149--35441 Score: 250
Period size: 26 Copynumber: 11.6 Consensus size: 26
35139 TGATAATAGT
* *
35149 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTAATAATAATCATTATAA
*
35175 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
35201 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
35227 TAAT-AATT--TAATAATGATT-T-A
1 TAATGATTTAATAATAATCATTATAA
* * * *
35248 -AAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTTAAT-A-ATAATCATTATAA
* *
35273 TAATGATTTGATAATAATTATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
35299 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
35325 TAATGATTTAATAAT-A--ATGATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
35348 TAATGATTTAATAATAGTAATGATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
35374 TAATGATTTAATAGTAATTATT-TAG
1 TAATGATTTAATAATAATCATTATAA
* * *
35399 TAATGATTTTATAATAATAATTTAATAT
1 TAATGATTTAATAATAATCA-TT-ATAA
*
35427 TAATAATTTAATAAT
1 TAATGATTTAATAAT
35442 TATTACTAAT
Statistics
Matches: 222, Mismatches: 31, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.03
21 1 0.00
22 2 0.01
23 32 0.14
24 8 0.04
25 29 0.13
26 123 0.55
27 6 0.03
28 15 0.07
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (26 bp):
TAATGATTTAATAATAATCATTATAA
Found at i:35296 original size:98 final size:100
Alignment explanation
Indices: 35149--35441 Score: 337
Period size: 98 Copynumber: 2.9 Consensus size: 100
35139 TGATAATAGT
* * * * *
35149 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
1 TAATGATTTAATAATAGTAATGATAGTAATGATTTGATAATAATTATTATAATAATGATTTAGTA
* *
35214 ATAATCATTATAATAATAATTTAATAATGAT-TTA
66 ATAATCATTATAATAATAATTTAATAATAATATAA
* * *
35248 -AAT-ATTTAATGAT-TTGATGATTTAGTAATGATTTGATAATAATTATTATAATAATGATTTAG
1 TAATGATTTAATAATAGTAATGA--TAGTAATGATTTGATAATAATTATTATAATAATGATTTAG
*
35310 TAATAATCATTATAATAATGATTTAATAATAATGATAA
64 TAATAATCATTATAATAATAATTTAATAATAAT-ATAA
* * * *
35348 TAATGATTTAATAATAGTAATGATAATAATGATTTAATAGTAATTATT-TAGTAATGATTTTA-T
1 TAATGATTTAATAATAGTAATGATAGTAATGATTTGATAATAATTATTATAATAATGA-TTTAGT
* *
35411 AATAATAATTTAATATTAATAATTTAATAAT
65 AATAATCA-TT-ATAATAATAATTTAATAAT
35442 TATTACTAAT
Statistics
Matches: 165, Mismatches: 19, Indels: 17
0.82 0.09 0.08
Matches are distributed among these distances:
96 4 0.02
97 8 0.05
98 73 0.44
100 18 0.11
101 31 0.19
102 26 0.16
103 5 0.03
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (100 bp):
TAATGATTTAATAATAGTAATGATAGTAATGATTTGATAATAATTATTATAATAATGATTTAGTA
ATAATCATTATAATAATAATTTAATAATAATATAA
Found at i:35296 original size:124 final size:120
Alignment explanation
Indices: 35131--35362 Score: 342
Period size: 124 Copynumber: 1.9 Consensus size: 120
35121 GATGATTTAG
*
35131 TAATGATTTGATAATAGTTAATGATTTGATAATAATCATTATAGTAATGATTT-GATAATAATCA
1 TAATGATTTGATAATAGTTAATGATTTGATAATAATCATTATAATAATGATTTAG-TAATAATCA
* *
35195 TTATAATAATGATTTAGTAATAATCATTATAATAATAATTTAATAATGATTTAAATATT
65 TTATAATAATGA-TT--TAATAATAATGATAATAATAATTTAATAATGATTTAAATATT
* *
35254 TAATGATTTGATGATTTAG-TAATGATTTGATAATAATTATTATAATAATGATTTAGTAATAATC
1 TAATGATTTGAT-A-ATAGTTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
*
35318 ATTATAATAATGATTTAATAATAATGATAATAATGATTTAATAAT
64 ATTATAATAATGATTTAATAATAATGATAATAATAATTTAATAAT
35363 AGTAATGATA
Statistics
Matches: 100, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
121 27 0.27
123 14 0.14
124 55 0.55
125 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (120 bp):
TAATGATTTGATAATAGTTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCAT
TATAATAATGATTTAATAATAATGATAATAATAATTTAATAATGATTTAAATATT
Found at i:35337 original size:49 final size:49
Alignment explanation
Indices: 35149--35454 Score: 241
Period size: 49 Copynumber: 6.1 Consensus size: 49
35139 TGATAATAGT
* *
35149 TAATGATTT-GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAA
1 TAATGATTTAG-TAATAATCATTATAATAATGA-TT--TAATAATTATTATAA
* *
35201 TAATGATTTAGTAATAATCATTATAATAATAATTTAATAATGATT-T-A
1 TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATTATTATAA
* * * * *
35248 -AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATTATTATAA
1 TAATGATTTAGT-A-ATAATCATTATAATAATGA-TT--TAATAATTATTATAA
* *
35299 TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATGATAA
1 TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATTATTATAA
* * * * *
35348 TAATGATTTAATAATAGTAATGATAATAATGATTTAATAGTAATTATT-TAG
1 TAATGATTTAGTAATAATCATTATAATAATGATTT-A-A-TAATTATTATAA
* * *
35399 TAATGATTTTA-TAATAATAATTTAATATTAATAATTTAATAATTATTACTAA
1 TAATGA-TTTAGTAATAATCA-TT-ATAATAATGATTTAATAATTATTA-TAA
35451 TAAT
1 TAAT
35455 TATAGAATAA
Statistics
Matches: 206, Mismatches: 29, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
45 6 0.03
46 11 0.05
47 9 0.04
48 1 0.00
49 64 0.31
50 10 0.05
51 29 0.14
52 58 0.28
53 18 0.09
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (49 bp):
TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATTATTATAA
Found at i:35349 original size:9 final size:9
Alignment explanation
Indices: 35335--35380 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
35325 TAATGATTTA
35335 ATAATAATG
1 ATAATAATG
35344 ATAATAATG
1 ATAATAATG
* *
35353 AT-TTAATA
1 ATAATAATG
*
35361 ATAGTAATG
1 ATAATAATG
35370 ATAATAATG
1 ATAATAATG
35379 AT
1 AT
35381 TTAATAGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 6 0.19
9 25 0.81
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (9 bp):
ATAATAATG
Found at i:35606 original size:24 final size:24
Alignment explanation
Indices: 35558--35602 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35548 GATTTGATAC
*
35558 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
35582 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
35603 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:35609 original size:17 final size:17
Alignment explanation
Indices: 35569--35610 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
35559 AATGATTTAC
35569 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
35586 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
35603 TAATTATT
1 TAATTATT
35611 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:37899 original size:16 final size:16
Alignment explanation
Indices: 37866--37912 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
37856 CAAAAAAATT
*
37866 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
*
37881 TAATATATTAAACTAA
1 TAATATAATAAACTAA
37897 TAA-ACTAATAAACTAA
1 TAATA-TAATAAACTAA
37913 ACTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:37988 original size:29 final size:29
Alignment explanation
Indices: 37955--38078 Score: 104
Period size: 29 Copynumber: 4.4 Consensus size: 29
37945 TTCCTTAAAC
37955 AACTAATAAACTATCTTTAATATAACTTT
1 AACTAATAAACTATCTTTAATATAACTTT
*
37984 AAC---T--A-T-TCTTTAATATAACATT
1 AACTAATAAACTATCTTTAATATAACTTT
* *
38006 AACTAATAAACTATTTTTAATATAACTTA
1 AACTAATAAACTATCTTTAATATAACTTT
*
38035 AACTAATAAA-TGATTTTTAATTATAA-TTT
1 AACTAATAAACT-ATCTTTAA-TATAACTTT
*
38064 ATTACTAAAAAACTA
1 A--ACTAATAAACTA
38079 ATTAACTAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
22 18 0.23
23 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 1 0.01
28 2 0.03
29 37 0.48
30 5 0.06
31 9 0.12
32 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (29 bp):
AACTAATAAACTATCTTTAATATAACTTT
Found at i:37993 original size:22 final size:21
Alignment explanation
Indices: 37963--38010 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
37953 ACAACTAATA
*
37963 AACTATCTTTAATATAACTTT
1 AACTATCTTTAATATAACATT
37984 AACTATTCTTTAATATAACATT
1 AACTA-TCTTTAATATAACATT
38006 AACTA
1 AACTA
38011 ATAAACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
AACTATCTTTAATATAACATT
Found at i:38032 original size:15 final size:16
Alignment explanation
Indices: 37983--38032 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
37973 AATATAACTT
*
37983 TAACTATTCTTTAATA
1 TAACTATTATTTAATA
**
37999 TAAC-ATTAACTAATA
1 TAACTATTATTTAATA
38014 -AACTATT-TTTAATA
1 TAACTATTATTTAATA
38028 TAACT
1 TAACT
38033 TAAACTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 8 0.30
15 15 0.56
16 4 0.15
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
TAACTATTATTTAATA
Found at i:38395 original size:34 final size:32
Alignment explanation
Indices: 38358--38436 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 32
38348 GCTAATAATT
38358 TATAACAATAAACTAATTTAAATAATTATTCTTTTA
1 TATAAC-ATAAACTAA-TTAAATAATT-TT-TTTTA
* *
38394 TATAACTTAAACTAATTAACTAATTTTTTTTA
1 TATAACATAAACTAATTAAATAATTTTTTTTA
*
38426 TATAATATAAA
1 TATAACATAAA
38437 TTCAACAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 14 0.36
33 2 0.05
34 9 0.23
35 8 0.21
36 6 0.15
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.46
Consensus pattern (32 bp):
TATAACATAAACTAATTAAATAATTTTTTTTA
Found at i:38614 original size:46 final size:46
Alignment explanation
Indices: 38495--38603 Score: 193
Period size: 46 Copynumber: 2.4 Consensus size: 46
38485 TCTTTTACCT
*
38495 TAAACTAACTAACTAATTAACTAAAATATTGTAAACCCTTAAACCA
1 TAAACTAACTAACTAATTAACTAAAATATTATAAACCCTTAAACCA
38541 TAAACTAACTAACTAATTAACTAAAATATTATAAACCCTTAAACCA
1 TAAACTAACTAACTAATTAACTAAAATATTATAAACCCTTAAACCA
38587 TAAACTAAC-AATCTAAT
1 TAAACTAACTAA-CTAAT
38604 AATTTAAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 2 0.03
46 59 0.97
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.28
Consensus pattern (46 bp):
TAAACTAACTAACTAATTAACTAAAATATTATAAACCCTTAAACCA
Found at i:38831 original size:11 final size:11
Alignment explanation
Indices: 38815--38850 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
38805 CTGAAGGATT
38815 GCAATAATGCA
1 GCAATAATGCA
*
38826 GCAATAAGTGCT
1 GCAATAA-TGCA
38838 GCAATAATGCA
1 GCAATAATGCA
38849 GC
1 GC
38851 TGAATTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:41217 original size:2 final size:2
Alignment explanation
Indices: 41210--41248 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41200 ATGTGAGTTG
41210 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
41249 AACGAGAGAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42444 original size:27 final size:26
Alignment explanation
Indices: 42334--42454 Score: 88
Period size: 27 Copynumber: 4.6 Consensus size: 26
42324 AATATTTAAA
**
42334 ATATATT-TATTAATATTTATAATAAT
1 ATATATTATATTTTTATTT-TAATAAT
*
42360 ATAATATTATATTTTTAGTTTAATAAT
1 AT-ATATTATATTTTTATTTTAATAAT
* * *
42387 ATA-ATCA-A-TTATATTATAATAATAT
1 ATATATTATATTTTTATTTTAAT-A-AT
42412 AATATATTATATTTTGTATTTTAATAAT
1 -ATATATTATATTTT-TATTTTAATAAT
* *
42440 ATATAATAAATTTTT
1 ATATATTATATTTTT
42455 TATATATTTA
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
23 9 0.12
24 2 0.03
25 5 0.07
26 7 0.09
27 29 0.39
28 11 0.15
29 3 0.04
30 8 0.11
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTATATTTTTATTTTAATAAT
Found at i:42465 original size:30 final size:29
Alignment explanation
Indices: 42396--42500 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 29
42386 TATAATCAAT
* * *
42396 TATATTATAATAATATAATATATTATATTTTG
1 TATATT-TAATAATAT-ATA-ATAATTTTTTA
42428 TAT-TTTAATAATATATAATAAATTTTTTA
1 TATATTTAATAATATATAAT-AATTTTTTA
*
42457 TATATTTAATAATGA-ATAAT-ATTATTTA
1 TATATTTAATAAT-ATATAATAATTTTTTA
42485 TATATTTAAATAATAT
1 TATATTT-AATAATAT
42501 TTTTTTAGTA
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
28 17 0.27
29 18 0.28
30 23 0.36
31 3 0.05
32 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TATATTTAATAATATATAATAATTTTTTA
Found at i:42493 original size:28 final size:26
Alignment explanation
Indices: 42436--42499 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 26
42426 TGTATTTTAA
*
42436 TAATATATAATAAATTTTTTATATATT
1 TAATA-ATAATAAATTATTTATATATT
42463 TAATAATGAATAATATTATTTATATATT
1 TAATAAT-AATAA-ATTATTTATATATT
42491 TAAATAATA
1 T-AATAATA
42500 TTTTTTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 2 0.06
27 10 0.30
28 15 0.45
29 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAATAATAATAAATTATTTATATATT
Found at i:42675 original size:19 final size:19
Alignment explanation
Indices: 42646--42683 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
42636 TAATAAAATT
42646 ATAAAAAAATA-TTTAATA
1 ATAAAAAAATATTTTAATA
42664 ATAAATAAAATATTTTAATA
1 ATAAA-AAAATATTTTAATA
42684 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAAAAATATTTTAATA
Found at i:42909 original size:20 final size:20
Alignment explanation
Indices: 42830--42900 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
42820 TTTTCCAGAT
42830 ATTTTCCAGAAATGTAATTC
1 ATTTTCCAGAAATGTAATTC
*
42850 ATTTTTCAGAAATGTAATTC
1 ATTTTCCAGAAATGTAATTC
*
42870 ATTTTTCAGAAATGTAATTC
1 ATTTTCCAGAAATGTAATTC
42890 ATTTTCCAGAA
1 ATTTTCCAGAA
42901 TTCAAATTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (20 bp):
ATTTTCCAGAAATGTAATTC
Found at i:42909 original size:40 final size:40
Alignment explanation
Indices: 42830--42909 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
42820 TTTTCCAGAT
* **
42830 ATTTTCCAGAAATGTAATTCATTTTTCAGAAATGTAATTC
1 ATTTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTC
* *
42870 ATTTTTCAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 ATTTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTC
42910 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
ATTTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTC
Found at i:42916 original size:29 final size:30
Alignment explanation
Indices: 42883--42955 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
42873 TTTCAGAAAT
42883 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
42912 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
42942 GTAATTCATTTTCC
1 GTAATTCATTTTCC
42956 GAAAAACCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.37
30 27 0.63
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:42955 original size:15 final size:15
Alignment explanation
Indices: 42883--42955 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
42873 TTTCAGAAAT
42883 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
42898 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
42912 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
42927 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
42942 GTAATTCATTTTCC
1 GTAATTCATTTTCC
42956 GAAAAACCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:44584 original size:24 final size:24
Alignment explanation
Indices: 44548--44593 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
44538 GAATACATAC
* * *
44548 AAAGAGTTTCTTGTCAACCAAAGA
1 AAAGAGGTGCTTGCCAACCAAAGA
44572 AAAGAGGTGCTTGCCAACCAAA
1 AAAGAGGTGCTTGCCAACCAAA
44594 CAAGCACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (24 bp):
AAAGAGGTGCTTGCCAACCAAAGA
Found at i:45558 original size:24 final size:24
Alignment explanation
Indices: 45527--45577 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
45517 TATCAGTGCA
45527 ATTTTGCA-TTCCTGAAT-TAGTAC
1 ATTTTGCACTT-CTGAATATAGTAC
*
45550 ATTTGTGCACTTCTGATTATAGTAC
1 ATTT-TGCACTTCTGAATATAGTAC
45575 ATT
1 ATT
45578 CGTGTACTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 9 0.38
25 11 0.46
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (24 bp):
ATTTTGCACTTCTGAATATAGTAC
Found at i:45713 original size:17 final size:17
Alignment explanation
Indices: 45691--45729 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
45681 AAAAATGAAT
*
45691 TAAAAGAAATAGTAAAG
1 TAAAAGAAATAATAAAG
* *
45708 TAAAAGTAATAATATAG
1 TAAAAGAAATAATAAAG
45725 TAAAA
1 TAAAA
45730 AGATACAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (17 bp):
TAAAAGAAATAATAAAG
Found at i:45902 original size:18 final size:17
Alignment explanation
Indices: 45873--45918 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
45863 ACATTGAAAG
*
45873 AAACATTACAAGAAATAA
1 AAACAGTACAAGAAA-AA
* *
45891 AAATAGTACAAGAAAAG
1 AAACAGTACAAGAAAAA
45908 AAACAGTACAA
1 AAACAGTACAA
45919 AAAGAAACGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.13
Consensus pattern (17 bp):
AAACAGTACAAGAAAAA
Found at i:50750 original size:31 final size:31
Alignment explanation
Indices: 50707--50767 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
50697 GATAATATAA
* *
50707 TAATTATTTTATAGT-ATTTAGATAAATTTAT
1 TAATAATTTTATAATCATTTA-ATAAATTTAT
*
50738 TAATAATTTTATAATCTTTTAATAAATTTA
1 TAATAATTTTATAATCATTTAATAAATTTA
50768 ATAAGTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (31 bp):
TAATAATTTTATAATCATTTAATAAATTTAT
Found at i:51461 original size:6 final size:6
Alignment explanation
Indices: 51450--51502 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
51440 GACATGTATT
51450 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
51497 A-CACG A
1 ACCACG A
51503 GACGGACGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
4 1 0.02
5 6 0.13
6 39 0.85
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:52018 original size:6 final size:6
Alignment explanation
Indices: 52007--52045 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
51997 TTTCGTCTCG
52007 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
52046 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:52591 original size:31 final size:30
Alignment explanation
Indices: 52556--52635 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
52546 AGTTTAAAAA
52556 ATTATAAAATACTTATTAAATTTAT-TAAGAG
1 ATTATAAAATA-TTATTAAATTTATCTAA-AG
* *
52587 ATTATAAAATTATTAATAAATTTATCTAAAT
1 ATTATAAAA-TATTATTAAATTTATCTAAAG
*
52618 ACTATAAAATAATTATTA
1 ATTATAAAAT-ATTATTA
52636 TATTATCGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTATAAAATATTATTAAATTTATCTAAAG
Found at i:53458 original size:3 final size:3
Alignment explanation
Indices: 53450--53485 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
53440 ACCACACCAG
*
53450 TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
53486 AACAATGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:61035 original size:18 final size:18
Alignment explanation
Indices: 61012--61062 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
61002 TTGTTCTATA
61012 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
* *
61030 TGGTCCTTCAGAACATAG
1 TGGTCCTTCGGGACATAG
*
61048 TGGTCATTCGGGACA
1 TGGTCCTTCGGGACA
61063 AATTCTATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:69409 original size:28 final size:28
Alignment explanation
Indices: 69366--69419 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
69356 TCAGTTTAGT
*
69366 CCTTAAATTAATTTTTTTGTTAAATTAA
1 CCTTAAATTAATTTTTGTGTTAAATTAA
69394 CCTTAATATTAA-TTTTGTGTTAAATT
1 CCTTAA-ATTAATTTTTGTGTTAAATT
69420 TATTTGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (28 bp):
CCTTAAATTAATTTTTGTGTTAAATTAA
Found at i:70803 original size:25 final size:25
Alignment explanation
Indices: 70754--70806 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
70744 ATTTTCAAAA
*
70754 TGTTGCGTAGATGATTTACAATATT
1 TGTTGCGTAGATGACTTACAATATT
70779 TGTTGCGTAGATGACTTACAATATT
1 TGTTGCGTAGATGACTTACAATATT
70804 TGT
1 TGT
70807 GTAAGAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.43
Consensus pattern (25 bp):
TGTTGCGTAGATGACTTACAATATT
Found at i:72297 original size:186 final size:185
Alignment explanation
Indices: 71929--72319 Score: 615
Period size: 186 Copynumber: 2.1 Consensus size: 185
71919 TTTTCTAATT
* * *
71929 TATATAA-AAATTAAATATTTTATAATTAAAAAAATAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTATAATTAAAAAAACAGTTTATAATTAATTTAAATAATATATAA
71993 TTATAAAATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* *
72058 TGGATCTTAAATTATTAATTGGGTTTTAAATTGTTTGGGCTGAGCCCATATGTTA
131 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* *
72113 TATATAATATATTTAATATTTTTTAATTCAGAAAAACAGTTT-TCAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATT-AAAAAAACAGTTTAT-AATTAATTTAAATAATATAT
* ** *
72177 AATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAATTT
64 AATTATAAAATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
* **
72242 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCTTATATGTTA
129 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
72299 TATAAAATATATTTAATATTT
1 TATATAATATATTTAATATTT
72320 AAAATTTTAT
Statistics
Matches: 189, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
184 7 0.04
185 18 0.10
186 164 0.87
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTATAATTAAAAAAACAGTTTATAATTAATTTAAATAATATATAA
TTATAAAATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:72709 original size:26 final size:26
Alignment explanation
Indices: 72660--72710 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
72650 TCTATAGAAA
*
72660 CAGTTAATCAAATCAATTTCTCAAAT
1 CAGTTAATCAAATCAATTGCTCAAAT
* *
72686 CAGTTAATCAAATCAGTTGGTCAAA
1 CAGTTAATCAAATCAATTGCTCAAA
72711 CTTGCTACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (26 bp):
CAGTTAATCAAATCAATTGCTCAAAT
Found at i:72710 original size:13 final size:13
Alignment explanation
Indices: 72660--72703 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
72650 TCTATAGAAA
72660 CAGTTAATCAAAT
1 CAGTTAATCAAAT
* **
72673 CAATTTCTCAAAT
1 CAGTTAATCAAAT
72686 CAGTTAATCAAAT
1 CAGTTAATCAAAT
72699 CAGTT
1 CAGTT
72704 GGTCAAACTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (13 bp):
CAGTTAATCAAAT
Found at i:74045 original size:44 final size:44
Alignment explanation
Indices: 73929--74045 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
73919 AAGTCCTTTA
* * * * *
73929 GCGGCGTTTATATCCGACAAACAC-TC-CTATTTACGAGACCTTTT
1 GCGGCGTTTGTATCCGA-AAA-ACGTCGCTATATACCACACCTATT
* * * *
73973 ACGGCGTTTGTATCCAAAAAATGCCGCTATATACCACACCTATT
1 GCGGCGTTTGTATCCGAAAAACGTCGCTATATACCACACCTATT
74017 GCGGCGTTTGTATCCGAAAAACGTCGCTA
1 GCGGCGTTTGTATCCGAAAAACGTCGCTA
74046 AATATCTTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
42 1 0.02
43 4 0.07
44 53 0.91
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
GCGGCGTTTGTATCCGAAAAACGTCGCTATATACCACACCTATT
Found at i:86257 original size:12 final size:12
Alignment explanation
Indices: 86240--86272 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
86230 TTTTCAGAAC
86240 CGGACCGGTTAG
1 CGGACCGGTTAG
86252 CGGACCGGTTAG
1 CGGACCGGTTAG
*
86264 CGAACCGGT
1 CGGACCGGT
86273 CATGCTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.39, T:0.15
Consensus pattern (12 bp):
CGGACCGGTTAG
Found at i:86384 original size:22 final size:21
Alignment explanation
Indices: 86350--86390 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
86340 ATAATTATTT
86350 AAAAAATTAAATAAAAATACA
1 AAAAAATTAAATAAAAATACA
*
86371 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
86391 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACA
Found at i:86867 original size:16 final size:16
Alignment explanation
Indices: 86842--86872 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86832 GCTTCTAATT
*
86842 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
86858 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
86873 TTTCAATATT
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:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:88418 original size:20 final size:20
Alignment explanation
Indices: 88395--88545 Score: 128
Period size: 20 Copynumber: 7.5 Consensus size: 20
88385 GTTTCCAGAT
*
88395 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
88415 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
88435 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
*
88455 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
88476 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
* *
88496 TCGCAACGTGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
* * *
88517 TCGTAACGCGATTCTGACTG
1 TCGCAACGCGATTATGACTA
88537 TCGCAACGC
1 TCGCAACGC
88546 TGAATTTCAA
Statistics
Matches: 102, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.05
20 64 0.63
21 29 0.28
22 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:88487 original size:41 final size:41
Alignment explanation
Indices: 88395--88545 Score: 216
Period size: 41 Copynumber: 3.7 Consensus size: 41
88385 GTTTCCAGAT
* * **
88395 TCGCAACGCGATTTTGACTATCGCAATGCG--AATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT-AA
88435 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
*
88476 TCGCAACGCGATTCTGACTATCGCAACGTGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
* *
88517 TCGTAACGCGATTCTGACTGTCGCAACGC
1 TCGCAACGCGATTCTGACTATCGCAACGC
88546 TGAATTTCAA
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
40 28 0.28
41 68 0.67
42 5 0.05
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
Found at i:91976 original size:140 final size:139
Alignment explanation
Indices: 91724--92005 Score: 519
Period size: 140 Copynumber: 2.0 Consensus size: 139
91714 GCAAACGTTG
91724 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
*
91789 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTCATTACACATTCA-TTGAATATCGCAACG
91854 CGAATTTGAC
130 CGAATTTGAC
*
91864 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
* *
91929 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTCATTACACATTCATTGAATATCGCAGCGC
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTCATTACACATTCATTGAATATCGCAACGC
91994 GAATTTGAC
131 GAATTTGAC
92003 TAT
1 TAT
92006 CGCAACTCAA
Statistics
Matches: 138, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
139 27 0.20
140 111 0.80
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (139 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTCATTACACATTCATTGAATATCGCAACGC
GAATTTGAC
Found at i:92060 original size:20 final size:20
Alignment explanation
Indices: 92022--92086 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
92012 TCAAAAATTA
92022 CAACGCGAATTTGGACTATCG
1 CAACGCGAATTT-GACTATCG
92043 CAACGCGAATTTGACTATCG
1 CAACGCGAATTTGACTATCG
* *
92063 CAACTCAAATTTG-CTATCG
1 CAACGCGAATTTGACTATCG
92082 CAACG
1 CAACG
92087 AGAAAATCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.24
20 19 0.46
21 12 0.29
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
CAACGCGAATTTGACTATCG
Found at i:92135 original size:19 final size:20
Alignment explanation
Indices: 92092--92135 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
92082 CAACGAGAAA
*
92092 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
92112 ATCGCAATGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
92131 TTCGC
1 ATCGC
92136 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:92141 original size:19 final size:19
Alignment explanation
Indices: 92119--92183 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
92109 ACTATCGCAA
* * *
92119 TGCGAATTGACTTTCGCGT
1 TGCGATTTGACTTTCACAT
*
92138 TGCGATTTTGGCTTT-ACAT
1 TGCGA-TTTGACTTTCACAT
92157 TGCGATTTGACTTTCACAT
1 TGCGATTTGACTTTCACAT
92176 TGCGATTT
1 TGCGATTT
92184 TGAGTTTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 8 0.21
19 24 0.62
20 7 0.18
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (19 bp):
TGCGATTTGACTTTCACAT
Found at i:92345 original size:13 final size:14
Alignment explanation
Indices: 92318--92348 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
92308 CATCAATTAA
92318 ACAAATCAACTTTT
1 ACAAATCAACTTTT
92332 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
92345 ACAA
1 ACAA
92349 CAATTAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:92367 original size:74 final size:77
Alignment explanation
Indices: 92272--92439 Score: 272
Period size: 75 Copynumber: 2.2 Consensus size: 77
92262 TTTACATTTC
*
92272 AATCAATTAAATAAGCACAAATAAGAATTATTTACACATC-A-ATTAAACAAATCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTA-TTACACATCAATATTAAACAAATCAACTTTTACA
92335 AATCAACTTTAC-
65 AATCAACTTTACA
92347 AA-CAATTAAACAAGCACAAATAAGAATTATTACACATCAATATTAAACAAATCAACTTTTACAA
1 AATCAATTAAACAAGCACAAATAAGAATTATTACACATCAATATTAAACAAATCAACTTTTACAA
**
92411 ATCATTTTTACA
66 ATCAACTTTACA
92423 AATCAATTAAACAAGCA
1 AATCAATTAAACAAGCA
92440 AAAAATGCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
73 9 0.10
74 27 0.31
75 34 0.40
76 2 0.02
77 14 0.16
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (77 bp):
AATCAATTAAACAAGCACAAATAAGAATTATTACACATCAATATTAAACAAATCAACTTTTACAA
ATCAACTTTACA
Found at i:92412 original size:14 final size:14
Alignment explanation
Indices: 92393--92428 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
92383 TCAATATTAA
92393 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
92407 ACAAATC-ATTTTT
1 ACAAATCAACTTTT
92420 ACAAATCAA
1 ACAAATCAA
92429 TTAAACAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:93851 original size:42 final size:42
Alignment explanation
Indices: 93792--93912 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
93782 ATGAATCGGG
* *
93792 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAAGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGC
* ** * *
93834 CTCTTAAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAAGGGC
* *
93876 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACA
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACA
93913 GGTGAGTCGG
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
41 1 0.02
42 58 0.92
43 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGC
Done.