Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009315.1 Hibiscus syriacus cultivar Beakdansim tig00113070_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: 85481
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:55 original size:13 final size:13
Alignment explanation
Indices: 32--163 Score: 87
Period size: 13 Copynumber: 10.1 Consensus size: 13
22 ATAACTACAC
*
32 ATATGTATAAACT
1 ATATATATAAACT
* *
45 ATGTATATAAATT
1 ATATATATAAACT
58 ATATA-AT-AACT
1 ATATATATAAACT
69 ATATAGATATAAACT
1 ATAT--ATATAAACT
84 ATATATAT---CT
1 ATATATATAAACT
*
94 ATATATAT-AGCT
1 ATATATATAAACT
*
106 ACATATGTATAAACT
1 --ATATATATAAACT
* *
121 ATATATGTAATCT
1 ATATATATAAACT
*
134 ATATAGTTTATATACT
1 ATATA---TATAAACT
150 ATATATATAAACT
1 ATATATATAAACT
163 A
1 A
164 ATAAAGTATA
Statistics
Matches: 93, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
10 10 0.11
11 7 0.08
12 4 0.04
13 42 0.45
14 9 0.10
15 11 0.12
16 10 0.11
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:117 original size:37 final size:36
Alignment explanation
Indices: 4--126 Score: 119
Period size: 39 Copynumber: 3.4 Consensus size: 36
1 AAC
*
4 ATAAACTATATA-ATTTATATA-ACTAC-ACATATGT
1 ATAAACTATATATATATATATATA-TACTACATATGT
* * *
38 ATAAACTATGTATATAAAT-TATATAATAACTATATAGAT
1 ATAAACTATATATATATATATATATACT-AC-ATAT-G-T
*
77 ATAAACTATATATATCTATATATATAGCTACATATGT
1 ATAAACTATATATATATATATATATA-CTACATATGT
114 ATAAACTATATAT
1 ATAAACTATATAT
127 GTAATCTATA
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
34 15 0.21
35 5 0.07
36 2 0.03
37 18 0.25
38 2 0.03
39 21 0.29
40 8 0.11
41 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (36 bp):
ATAAACTATATATATATATATATATACTACATATGT
Found at i:125 original size:29 final size:29
Alignment explanation
Indices: 92--159 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
82 CTATATATAT
92 CTATATATAT-AGCTACATA-TGTATAAA
1 CTATATATATAAGCTACATAGTGTATAAA
* * * * *
119 CTATATATGTAATCTATATAGTTTATATA
1 CTATATATATAAGCTACATAGTGTATAAA
148 CTATATATATAA
1 CTATATATATAA
160 ACTAATAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 9 0.27
28 7 0.21
29 17 0.52
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (29 bp):
CTATATATATAAGCTACATAGTGTATAAA
Found at i:245 original size:20 final size:19
Alignment explanation
Indices: 205--269 Score: 71
Period size: 18 Copynumber: 3.3 Consensus size: 19
195 TATTAATATA
*
205 ATATATGTATGTATTAACTAT
1 ATATAT-TAT-TATAAACTAT
226 ATATAGTT-TATATAAACTAT
1 ATATA-TTAT-TATAAACTAT
246 ATA-ATTATTATAAACTAT
1 ATATATTATTATAAACTAT
264 ATATAT
1 ATATAT
270 GTAACCTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 15 0.38
19 4 0.10
20 13 0.33
21 6 0.15
22 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
ATATATTATTATAAACTAT
Found at i:314 original size:56 final size:56
Alignment explanation
Indices: 243--363 Score: 185
Period size: 56 Copynumber: 2.2 Consensus size: 56
233 TTATATAAAC
* * *
243 TATATAA-TTATTATAAACTATATATATGTAACCTATAGTGTATAAAGAATAATTTA
1 TATATAATTTATTATAAACTATATATATATAACCTATAGTCTA-AAACAATAATTTA
299 TATATAATTTA-TATAAACTATATATATATAACCTATAGTCTAAAACAATAATTTA
1 TATATAATTTATTATAAACTATATATATATAACCTATAGTCTAAAACAATAATTTA
354 TATA-AATTTA
1 TATATAATTTA
364 CAACTATATA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
54 6 0.10
55 16 0.26
56 36 0.59
57 3 0.05
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (56 bp):
TATATAATTTATTATAAACTATATATATATAACCTATAGTCTAAAACAATAATTTA
Found at i:759 original size:21 final size:21
Alignment explanation
Indices: 730--769 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
720 TTTATATTAG
*
730 TGTACTATATAGTTTATAACC
1 TGTACTATATAATTTATAACC
*
751 TGTAGTATATAATTTATAA
1 TGTACTATATAATTTATAA
770 ACTATACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (21 bp):
TGTACTATATAATTTATAACC
Found at i:862 original size:36 final size:36
Alignment explanation
Indices: 822--914 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
812 TAATTATCTT
* *
822 AACTATTATTTATATTAATATAATATATAGTTTATA
1 AACTATAATTTATATTAATATAATAGATAGTTTATA
* * *
858 AACTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATATAATAGATAGTTTATA
* * **
894 AAGTATAGTTTGCATTAATAT
1 AACTATAATTTATATTAATAT
915 TGACACATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAATAGATAGTTTATA
Found at i:965 original size:18 final size:17
Alignment explanation
Indices: 926--1177 Score: 72
Period size: 14 Copynumber: 16.4 Consensus size: 17
916 GACACATAAC
926 TATAATTTATATTAATA
1 TATAATTTATATTAATA
943 GTATAATATTAATATTAAT-
1 -TATAAT-TT-ATATTAATA
*
962 TATAGTTTATA--AACTA
1 TATAATTTATATTAA-TA
*
978 TA-AA-CTATATTAATA
1 TATAATTTATATTAATA
993 T-TAA-TTATATT-A-A
1 TATAATTTATATTAATA
* *
1006 -CT-ATTTATAACTCTACTA
1 TATAATTTAT-A-T-TAATA
1024 TATAATTTATA--AA-A
1 TATAATTTATATTAATA
*
1038 TATAGTTTATATTAATA
1 TATAATTTATATTAATA
1055 T-TAATTTATA--AACTA
1 TATAATTTATATTAA-TA
1070 TAT--TTTATATTAATA
1 TATAATTTATATTAATA
*
1085 T-T-A-TTACA--AAT-
1 TATAATTTATATTAATA
**
1096 TATAAACTATATT-ATAA
1 TATAATTTATATTAAT-A
* *
1113 TATAAGTTA-A-TATTA
1 TATAATTTATATTAATA
1128 T-TAA-TTATATTAATA
1 TATAATTTATATTAATA
*
1143 T-TAA--T-TA-TAATC
1 TATAATTTATATTAATA
1155 TATAATTTATATTAATA
1 TATAATTTATATTAATA
1172 T-TAATT
1 TATAATT
1178 ATAAATGATT
Statistics
Matches: 177, Mismatches: 18, Indels: 80
0.64 0.07 0.29
Matches are distributed among these distances:
11 1 0.01
12 10 0.06
13 15 0.08
14 40 0.23
15 35 0.20
16 30 0.17
17 16 0.09
18 12 0.07
19 4 0.02
20 14 0.08
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
TATAATTTATATTAATA
Found at i:1060 original size:30 final size:28
Alignment explanation
Indices: 983--1198 Score: 127
Period size: 30 Copynumber: 7.3 Consensus size: 28
973 AACTATAAAC
* *
983 TATATTAATATTAATTATATTAA-CTATT
1 TATATTAATATTAATTATA-AAATATATT
*
1011 TATAACTCTACTATATAATTTATAAAATATAGTT
1 TAT-A-T-TAATAT-TAA-TTATAAAATATA-TT
*
1045 TATATTAATATTAATTTATAAACTATATTT
1 TATATTAATATTAA-TTATAAAATATA-TT
* * **
1075 TATATTAATATT-ATTACAAATTATAAAC
1 TATATTAATATTAATTATAAAATAT-ATT
* * *
1103 TATATT-ATAATATAAGTTA-ATATTATTAAT
1 TATATTAAT-AT-TAA-TTATAAAATA-TATT
**
1133 TATATTAATATTAATTATAATCTATAATT
1 TATATTAATATTAATTATAAAATAT-ATT
1162 TATATTAATATTAATTAT-AAATGATTATT
1 TATATTAATATTAATTATAAAAT-A-TATT
1191 TATATTAA
1 TATATTAA
1199 CTCTATTAAG
Statistics
Matches: 152, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.01
28 26 0.17
29 42 0.28
30 47 0.31
31 16 0.11
32 6 0.04
33 8 0.05
34 5 0.03
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (28 bp):
TATATTAATATTAATTATAAAATATATT
Found at i:1170 original size:23 final size:23
Alignment explanation
Indices: 1140--1204 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
1130 AATTATATTA
* *
1140 ATATTAAT-TATAATCTATAATTT
1 ATATTAATAT-TAATCTATAAATG
1163 ATATTAATATTAAT-TATAAATG
1 ATATTAATATTAATCTATAAATG
*
1185 ATTATTTATATTAACTCTAT
1 A-TATTAATATTAA-TCTAT
1205 TAAGTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 7 0.20
23 23 0.66
24 2 0.06
25 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTAATATTAATCTATAAATG
Found at i:1194 original size:58 final size:58
Alignment explanation
Indices: 968--1198 Score: 170
Period size: 58 Copynumber: 3.9 Consensus size: 58
958 TAATTATAGT
* * *
968 TTATAAACTATAAACTATATTAATATTAA-TTAT-ATTAACTATTTATAACTCTACTATATAA
1 TTATAAACTATAAACTATATTAATATTAAGTTATAAAT-ATTATTTAT-A-T-TAATAT-TAA
* *** *
1029 TTTATAAAATATAGTTTATATTAATATTAATTTATAAACTA-TATTTTATATTAATATT-A
1 -TTATAAACTATAAACTATATTAATATTAAGTTATAAA-TATTA-TTTATATTAATATTAA
* * * *
1088 TTACAAATTATAAACTATATT-ATAATATAAGTTA-ATATTATTAATTATATTAATATTAA
1 TTATAAACTATAAACTATATTAAT-AT-TAAGTTATA-AATATTATTTATATTAATATTAA
* **
1147 TTATAATCTATAATTTATATTAATATTAA-TTATAAATGATTATTTATATTAA
1 TTATAAACTATAAACTATATTAATATTAAGTTATAAAT-ATTATTTATATTAA
1199 CTCTATTAAG
Statistics
Matches: 136, Mismatches: 21, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
57 7 0.05
58 51 0.38
59 29 0.21
60 3 0.02
61 5 0.04
62 26 0.19
63 7 0.05
64 7 0.05
65 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (58 bp):
TTATAAACTATAAACTATATTAATATTAAGTTATAAATATTATTTATATTAATATTAA
Found at i:1522 original size:22 final size:21
Alignment explanation
Indices: 1488--1528 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
1478 TAACTCTCCG
1488 ATTCTCTCAAAATT-ATCTAC
1 ATTCTCTCAAAATTCATCTAC
1508 ATTCTCTCTAGAAATTCATCT
1 ATTCTCTC-A-AAATTCATCT
1529 GTGTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 5 0.28
23 4 0.22
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTCTCTCAAAATTCATCTAC
Found at i:2239 original size:19 final size:17
Alignment explanation
Indices: 2215--2257 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
2205 GTTCATTCAT
*
2215 TTTGTTTATTTTAATGTTG
1 TTTGTTTATTATAA--TTG
*
2234 TTTGTTTGTTATAATTG
1 TTTGTTTATTATAATTG
2251 TTTGTTT
1 TTTGTTT
2258 GAATAGCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.45
19 12 0.55
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTGTTTATTATAATTG
Found at i:5545 original size:23 final size:24
Alignment explanation
Indices: 5517--5570 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
5507 ATTATTTTTC
5517 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
*
5540 TTTACAGAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
5564 TTTACAT
1 TTTACAT
5571 TTAATCATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:5644 original size:13 final size:13
Alignment explanation
Indices: 5590--5652 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
5580 GTTCAATGCC
5590 AATAATTTTATT-
1 AATAATTTTATTA
* *
5602 AATCATGTT-TTA
1 AATAATTTTATTA
* *
5614 TATAATTTACATTTA
1 AATAATTT-TA-TTA
5629 AATAATTTTATTA
1 AATAATTTTATTA
5642 AATAATTTTAT
1 AATAATTTTAT
5653 ATAATAAGTC
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
11 2 0.05
12 12 0.31
13 14 0.36
14 1 0.03
15 10 0.26
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (13 bp):
AATAATTTTATTA
Found at i:5822 original size:16 final size:15
Alignment explanation
Indices: 5790--5829 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
5780 ATTCATCCAT
5790 GGTAATATATAAGTCA
1 GGTAA-ATATAAGTCA
*
5806 GGTAAATATCAGATCA
1 GGTAAATATAAG-TCA
5822 GGTAAATA
1 GGTAAATA
5830 ACACGTAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (15 bp):
GGTAAATATAAGTCA
Found at i:5867 original size:16 final size:16
Alignment explanation
Indices: 5846--5884 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5836 AGGATCATTT
5846 ACAGGTCAAGTTAAAA
1 ACAGGTCAAGTTAAAA
* *
5862 ACAGGTCAGGTTGAAA
1 ACAGGTCAAGTTAAAA
5878 ACAGGTC
1 ACAGGTC
5885 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (16 bp):
ACAGGTCAAGTTAAAA
Found at i:6765 original size:20 final size:21
Alignment explanation
Indices: 6746--6784 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6736 TATGCTGGAT
6746 TTAAGAC-AA-AAAACAAGGA
1 TTAAGACAAAGAAAACAAGGA
*
6765 TTAGGACAAAGAAAACAAGG
1 TTAAGACAAAGAAAACAAGG
6785 GTAATGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.59, C:0.10, G:0.21, T:0.10
Consensus pattern (21 bp):
TTAAGACAAAGAAAACAAGGA
Found at i:8424 original size:20 final size:22
Alignment explanation
Indices: 8381--8426 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
8371 GATAGCTGTT
8381 CAAATATTTTCAATTTTCTTTG
1 CAAATATTTTCAATTTTCTTTG
8403 CAAATATTTTC-ATTTT-TTTG
1 CAAATATTTTCAATTTTCTTTG
8423 CAAA
1 CAAA
8427 AGCTTCCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.33
21 5 0.21
22 11 0.46
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.52
Consensus pattern (22 bp):
CAAATATTTTCAATTTTCTTTG
Found at i:9746 original size:21 final size:21
Alignment explanation
Indices: 9721--9760 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9711 AAGACTTTAT
9721 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
9742 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
9761 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:14156 original size:17 final size:16
Alignment explanation
Indices: 14128--14164 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
14118 TTGTTTTAAC
14128 ATTT-TGGATGTTTGA
1 ATTTGTGGATGTTTGA
14143 ATTTGTGGATTGTTTGA
1 ATTTGTGGA-TGTTTGA
14160 ATTTG
1 ATTTG
14165 GATGCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 12 0.60
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (16 bp):
ATTTGTGGATGTTTGA
Found at i:16734 original size:9 final size:9
Alignment explanation
Indices: 16710--16767 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 9
16700 GGTCCTTGTA
16710 TTTATGTTTAT
1 TTTAT-TTT-T
16721 TTTATTTTT
1 TTTATTTTT
16730 TTTATTTTGTT
1 TTTA-TTT-TT
16741 TTTACTATTTT
1 TTTA-T-TTTT
16752 TTTATTTTT
1 TTTATTTTT
*
16761 ATTATTT
1 TTTATTT
16768 AGGTTTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 15 0.36
10 7 0.17
11 18 0.43
12 2 0.05
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTATTTTT
Found at i:16735 original size:14 final size:13
Alignment explanation
Indices: 16716--16763 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
16706 TGTATTTATG
16716 TTTATTTTATTTTT
1 TTTATTTT-TTTTT
16730 TTTATTTTGTTTTT
1 TTTATTTT-TTTTT
**
16744 ACTATTTTTTTATT
1 TTTATTTTTTT-TT
16758 TTTATT
1 TTTATT
16764 ATTTAGGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 3 0.11
14 25 0.89
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTATTTTTTTTT
Found at i:16759 original size:17 final size:17
Alignment explanation
Indices: 16734--16767 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16724 ATTTTTTTTA
*
16734 TTTTGTTTTTACTATTT
1 TTTTATTTTTACTATTT
*
16751 TTTTATTTTTATTATTT
1 TTTTATTTTTACTATTT
16768 AGGTTTATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTACTATTT
Found at i:18717 original size:5 final size:5
Alignment explanation
Indices: 18704--18742 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
18694 CGACCACGAC
* *
18704 CCCGA CCCGG CCCGG CCCGG CCCGG CCCGG CCCGA CCCG
1 CCCGG CCCGG CCCGG CCCGG CCCGG CCCGG CCCGG CCCG
18743 AGACGAGACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.05, C:0.62, G:0.33, T:0.00
Consensus pattern (5 bp):
CCCGG
Found at i:18727 original size:15 final size:15
Alignment explanation
Indices: 18704--18742 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
18694 CGACCACGAC
18704 CCCGACCCGGCCCGG
1 CCCGACCCGGCCCGG
*
18719 CCCGGCCCGGCCCGG
1 CCCGACCCGGCCCGG
18734 CCCGACCCG
1 CCCGACCCG
18743 AGACGAGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.62, G:0.33, T:0.00
Consensus pattern (15 bp):
CCCGACCCGGCCCGG
Found at i:19409 original size:21 final size:21
Alignment explanation
Indices: 19393--19500 Score: 116
Period size: 21 Copynumber: 5.2 Consensus size: 21
19383 AAATCGTAAC
19393 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
19414 GCGAA-TAT-GTA-AATCGCAAT
1 GCGAACT-TCG-ACTATCGCAAT
* *
19434 GCGATA-GTCGACTATCGCAAC
1 GCGA-ACTTCGACTATCGCAAT
*
19455 GCGAACTTCAACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
19476 GCGAACTTCGACTATCGCATT
1 GCGAACTTCGACTATCGCAAT
19497 GCGA
1 GCGA
19501 TTTACATATT
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
20 17 0.24
21 55 0.76
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:19487 original size:42 final size:41
Alignment explanation
Indices: 19383--19494 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 41
19373 AATTTGGAAT
* * * *
19383 AAATCGTAACGCGAACTTCGACTATCGCAATGCGAATATGT
1 AAATCGCAATGCGAACTTCGACTATCGCAACGCGAATATGC
*
19424 AAATCGCAATGCGATA-GTCGACTATCGCAACGCGAACT-T-C
1 AAATCGCAATGCGA-ACTTCGACTATCGCAACGCGAA-TATGC
19464 AACTATCGCAATGCGAACTTCGACTATCGCA
1 AA--ATCGCAATGCGAACTTCGACTATCGCA
19495 TTGCGATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
40 2 0.03
41 32 0.53
42 26 0.43
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (41 bp):
AAATCGCAATGCGAACTTCGACTATCGCAACGCGAATATGC
Found at i:19535 original size:21 final size:21
Alignment explanation
Indices: 19509--19625 Score: 198
Period size: 21 Copynumber: 5.6 Consensus size: 21
19499 GATTTACATA
*
19509 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
19530 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
19551 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
19572 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
19593 TTCGCAATGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
19614 TTCGCGTTGCGA
1 TTCGCATTGCGA
19626 ATCTGGAAAC
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 91 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:19556 original size:83 final size:83
Alignment explanation
Indices: 19393--19626 Score: 219
Period size: 83 Copynumber: 2.8 Consensus size: 83
19383 AAATCGTAAC
* * **
19393 GCGAACTTCGACTATCGCAATGCGAATATGTA-AA-TCGCAATGCGATAGTCG-ACTATCGCAAC
1 GCGAACTTCGACTATCGCATTGCG-ATAT-TACAATTCGCAATGCGATAGTCGAAGT-TCGCATT
*
19455 GCGAACTTCAACTATCGCAAT
63 GCGAACTCCAACTATCGCAAT
*
19476 GCGAACTTCGACTATCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCGAAGTTCGCATTGC
1 GCGAACTTCGACTATCGCATTGCGATATTACA-ATTCGCAATGCGATAGTCGAAGTTCGCATTGC
* * *
19540 GATAGTCCAAGT-TCGCATT
65 GA-ACTCCAACTATCGCAAT
* * * * * * *
19559 GCGATAGTCCAAGT-TCGCATTGCGATAGTCCAAGTTCGCAATGCGATAGTCGAAGTTCGCGTTG
1 GCGA-ACTTCGACTATCGCATTGCGATATTACAA-TTCGCAATGCGATAGTCGAAGTTCGCATTG
19623 CGAA
64 CGAA
19627 TCTGGAAACT
Statistics
Matches: 126, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 3 0.02
83 72 0.57
84 47 0.37
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (83 bp):
GCGAACTTCGACTATCGCATTGCGATATTACAATTCGCAATGCGATAGTCGAAGTTCGCATTGCG
AACTCCAACTATCGCAAT
Found at i:28652 original size:18 final size:18
Alignment explanation
Indices: 28625--28661 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28615 CTGGAATGTT
*
28625 TATGAGGGAATTGAAATC
1 TATGAAGGAATTGAAATC
28643 TATGAAGGAATTGAAATC
1 TATGAAGGAATTGAAATC
28661 T
1 T
28662 GTCAAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (18 bp):
TATGAAGGAATTGAAATC
Found at i:28672 original size:17 final size:18
Alignment explanation
Indices: 28631--28677 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
28621 TGTTTATGAG
*
28631 GGAATTGAAATCTATGAA
1 GGAATTGAAATCTATCAA
*
28649 GGAATTGAAATCTGTCAA
1 GGAATTGAAATCTATCAA
*
28667 -GAATTGGAATC
1 GGAATTGAAATC
28678 CAATTTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTATCAA
Found at i:29295 original size:37 final size:37
Alignment explanation
Indices: 29239--29326 Score: 158
Period size: 37 Copynumber: 2.4 Consensus size: 37
29229 TTTTCACCCT
29239 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAA
*
29277 AAACCCGACCCGATCCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
29314 AAACCCGACCCGA
1 AAACCCGACCCGA
29327 ATATATGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 42 0.86
38 7 0.14
ACGTcount: A:0.39, C:0.40, G:0.11, T:0.10
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:29412 original size:2 final size:2
Alignment explanation
Indices: 29405--29433 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29395 ACTTAATTGA
29405 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 A
29434 GGGATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30688 original size:246 final size:253
Alignment explanation
Indices: 30218--30821 Score: 884
Period size: 246 Copynumber: 2.4 Consensus size: 253
30208 CATCCGAGAT
30218 CCGAACCGACCAAAATAAAGTTTCACCCGACCGACCCGAATATATGAATTAGAAACCCGACCGAC
1 CCGAACCGA-CAAAATAAAGTTTCA--C--CCGACCCGAATATATGAATTAGAAACCCGACCGAC
30283 CCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATATATATA
61 CCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATATATATA
30348 TATAGAGAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATATATTTTCGGG
125 TATA-AGAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATATATTTTCGGG
*
30413 TCGGGTATTTTTCACACTAAACCCGAACTCAACCCAACCCGAATATCGCACTTAAAAAAACCAAC
189 TCGGGTATTTTTCACACTAAACCCGAACTCAACCCAACCCGAATATCACACTTAAAAAAACCAAC
*
30478 CC-AACC-A-AAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACTGACCCGAA
1 CCGAACCGACAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCGACCCGAA
*
30540 ATAATAAAAAAATATTTTTATTCAATAAAAGA-AGTGACTTAATTG-AAAAA-AT-TATATAT-A
66 ATAATAAAAAAATATTTTTATTCAATAAAA-ACAATGACTTAATTGAAAAAATATATATATATAA
* * *
30600 GAGTGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTTGGGT
130 GAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGT
* * * * **
30665 ATTTTTCACCCTAAACCCGAACTCGACCCGACTCGAATATCACACTTAAAAAAACGGAC
195 ATTTTTCACACTAAACCCGAACTCAACCCAACCCGAATATCACACTTAAAAAAACCAAC
* *
30724 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCTACCCG
1 CCGAACCGA-CAAAATAAAGTTT----C-ACCCGACCCGAATATATGAATTAGAAACCCGA-CCG
30789 ACCCGAAATAAT-AAAAAATATTTTTATTCAATA
59 ACCCGAAATAATAAAAAAATATTTTTATTCAATA
30822 TATAAATAAG
Statistics
Matches: 318, Mismatches: 15, Indels: 27
0.88 0.04 0.08
Matches are distributed among these distances:
246 117 0.37
247 3 0.01
248 8 0.03
249 2 0.01
250 17 0.05
251 30 0.09
252 52 0.16
254 2 0.01
255 52 0.16
256 28 0.09
258 1 0.00
259 4 0.01
260 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (253 bp):
CCGAACCGACAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCGACCCGAA
ATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATATATATATATAAG
AGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTA
TTTTTCACACTAAACCCGAACTCAACCCAACCCGAATATCACACTTAAAAAAACCAAC
Found at i:31141 original size:108 final size:108
Alignment explanation
Indices: 30952--31162 Score: 318
Period size: 108 Copynumber: 2.0 Consensus size: 108
30942 GTTGAAGCCA
* *
30952 TGAGGGATTCAAATTCTCTTGGAAAACTTGAACCAAACATGGGAAAGTGGTGGAATTGGATTCCA
1 TGAGGGATTCAAATTCCCTTGGAAAACTTGAACCAAACATGGGAAAGTGATGGAATTGGATTCCA
*
31017 ATTCCCCCTAATTCCAAGAGATT-CATGCGAACCAAACGCCGTC
66 ATTCCCCCTAATTCCAAGAGATTCCAT-CCAACCAAACGCCGTC
* * * * *
31060 TGAGGGATTCCAATTCCCTTGGAAAACTTGAATCAAACATGGTAAATTGATGGAATTGGATTTCA
1 TGAGGGATTCAAATTCCCTTGGAAAACTTGAACCAAACATGGGAAAGTGATGGAATTGGATTCCA
31125 ATT-CCCCTAAATTCCAAGAGATTCCATCCAACCAAACG
66 ATTCCCCCT-AATTCCAAGAGATTCCATCCAACCAAACG
31163 TCACCTTAAG
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
107 5 0.05
108 85 0.91
109 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (108 bp):
TGAGGGATTCAAATTCCCTTGGAAAACTTGAACCAAACATGGGAAAGTGATGGAATTGGATTCCA
ATTCCCCCTAATTCCAAGAGATTCCATCCAACCAAACGCCGTC
Found at i:33268 original size:41 final size:41
Alignment explanation
Indices: 33155--33364 Score: 257
Period size: 41 Copynumber: 5.2 Consensus size: 41
33145 GCTTAGGAAT
* **
33155 GTATGTTTGCATGCATGTGTCTCATGGATAAGCTGAGCCTGA
1 GTATGTATGCATGCATGTGTCTCATGGATAAGCTGAG-CAAA
* * * * * **
33197 GCAAAGTACGCATTCATGTGTCTCTTGGATAAGCTGAGCCTA
1 G-TATGTATGCATGCATGTGTCTCATGGATAAGCTGAGCAAA
* *
33239 GTATGTATGCAAGCATGTGTCTCATGGATATGCTGAGCAAA
1 GTATGTATGCATGCATGTGTCTCATGGATAAGCTGAGCAAA
33280 GTATGTATGCATGCATGTGTCTCATGGATAAGCTGAGCAAA
1 GTATGTATGCATGCATGTGTCTCATGGATAAGCTGAGCAAA
*
33321 GTATG--T-C-TGCATGCGTCTCATGGATAAGCTGAGCAAA
1 GTATGTATGCATGCATGTGTCTCATGGATAAGCTGAGCAAA
33358 GTATGTA
1 GTATGTA
33365 GCAAATATAA
Statistics
Matches: 145, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
37 34 0.23
38 1 0.01
39 1 0.01
41 75 0.52
42 4 0.03
43 30 0.21
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (41 bp):
GTATGTATGCATGCATGTGTCTCATGGATAAGCTGAGCAAA
Found at i:38026 original size:31 final size:31
Alignment explanation
Indices: 37953--38030 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
37943 CAGTTATGTC
*
37953 AGGGACTATATTGAAAAAGGACTAAATGTTG
1 AGGGACTATATTGCAAAAGGACTAAATGTTG
* *
37984 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACTATATTGCAAAAGGACTAAATGTTG
* *
38015 GGGGATTATATTGCAA
1 AGGGACTATATTGCAA
38031 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (31 bp):
AGGGACTATATTGCAAAAGGACTAAATGTTG
Found at i:39791 original size:31 final size:31
Alignment explanation
Indices: 39756--39823 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
39746 TTAAAACTTA
*
39756 CAATATAATCACC-CAATATTTAGCCCGTTTG
1 CAATATAATC-CCTCAACATTTAGCCCGTTTG
** *
39787 CAATATGGTCCCTCAACATTTAGTCCGTTTG
1 CAATATAATCCCTCAACATTTAGCCCGTTTG
39818 CAATAT
1 CAATAT
39824 GGTCCCTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (31 bp):
CAATATAATCCCTCAACATTTAGCCCGTTTG
Found at i:40116 original size:22 final size:23
Alignment explanation
Indices: 40074--40116 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40064 AATATTTAAA
* *
40074 TTTTAAAATAATGAATGTATAAT
1 TTTTAAAAAAATAAATGTATAAT
40097 TTTTAAAAAAATAAAT-TATA
1 TTTTAAAAAAATAAATGTATA
40117 CTACTGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
TTTTAAAAAAATAAATGTATAAT
Found at i:42266 original size:2 final size:2
Alignment explanation
Indices: 42259--42353 Score: 51
Period size: 2 Copynumber: 51.0 Consensus size: 2
42249 TAAAAATAAT
* * * *
42259 TA TA TA TA TA TA TA TA TA TA TA TA AA TT TA -A TA AA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
42299 TT TA -A TT TA AA T- TA -A TA TA TA TA TA -A TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
42337 TA -A TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
42354 CCCGGCCCGA
Statistics
Matches: 66, Mismatches: 20, Indels: 14
0.66 0.20 0.14
Matches are distributed among these distances:
1 7 0.11
2 59 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:50806 original size:16 final size:16
Alignment explanation
Indices: 50770--50810 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
50760 AATTTCATCC
50770 TTATA-TTATATAATA
1 TTATATTTATATAATA
50785 TATATATTTATTATAA-A
1 T-TATATTTA-TATAATA
50802 TTATATTTA
1 TTATATTTA
50811 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 5 0.22
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATATAATA
Found at i:51834 original size:20 final size:19
Alignment explanation
Indices: 51799--51839 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
51789 TAATTATCTT
51799 TTTATATTACATTATAATA
1 TTTATATTACATTATAATA
* *
51818 TTTATATATATATTATATTA
1 TTTATAT-TACATTATAATA
51838 TT
1 TT
51840 ATTAGTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTACATTATAATA
Found at i:51921 original size:18 final size:17
Alignment explanation
Indices: 51900--51943 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
51890 CTTATACGTT
51900 TTATTATATATATATATA
1 TTATTAT-TATATATATA
*
51918 TTATTATTGT-TAT-TA
1 TTATTATTATATATATA
51933 TTATTATTATA
1 TTATTATTATA
51944 CGTATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 2 0.09
18 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATTATTATATATATA
Found at i:51922 original size:3 final size:3
Alignment explanation
Indices: 51900--51942 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
51890 CTTATACGTT
*
51900 TTA TTA TATA TATA TATA TTA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
51943 ACGTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:51943 original size:48 final size:51
Alignment explanation
Indices: 51858--51968 Score: 124
Period size: 46 Copynumber: 2.2 Consensus size: 51
51848 TTTACACTCG
*
51858 TATATATGTATTATTAGTATAGTATTATGTCACTTATACGTTTTATTATATATA
1 TATATAT-TATTATTAGTATAGTATTATGTCACTTATACG-TATA-TATATATA
* *
51912 TATATATTATTATT-GT-TATTATTAT-T-A-TTATACGTATATATATGTA
1 TATATATTATTATTAGTATAGTATTATGTCACTTATACGTATATATATATA
*
51958 TATATTTTATT
1 TATATATTATT
51969 TCTTTTTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 17 0.32
47 3 0.06
48 7 0.13
49 1 0.02
50 1 0.02
51 8 0.15
52 2 0.04
53 7 0.13
54 7 0.13
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (51 bp):
TATATATTATTATTAGTATAGTATTATGTCACTTATACGTATATATATATA
Found at i:52023 original size:18 final size:18
Alignment explanation
Indices: 52000--52059 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
51990 TTTTTATTTT
52000 TATTATTATTATTCTTTA
1 TATTATTATTATTCTTTA
** * *
52018 TATTATCCTTATTATTTC
1 TATTATTATTATTCTTTA
*
52036 TATTATTACTATTCTTTA
1 TATTATTATTATTCTTTA
52054 T-TTATT
1 TATTATT
52060 CATGTAATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTATTCTTTA
Found at i:52577 original size:14 final size:14
Alignment explanation
Indices: 52558--52584 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52548 TATATATTTT
52558 ATTATTATTTCATC
1 ATTATTATTTCATC
52572 ATTATTATTTCAT
1 ATTATTATTTCAT
52585 TACTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTATTTCATC
Found at i:63224 original size:1 final size:1
Alignment explanation
Indices: 63218--63244 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
63208 TCCTAAGTTG
63218 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
63245 GGTGAAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:64840 original size:419 final size:420
Alignment explanation
Indices: 64038--64960 Score: 1769
Period size: 419 Copynumber: 2.2 Consensus size: 420
64028 GGTTTTACCC
64038 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64103 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
64168 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
131 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
64233 ACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
196 ACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
64298 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATT
261 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATT
64363 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
326 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
*
64428 GCTGGTTGTCACTAAACATTTCTCAAATTT
391 GCTGGTTGTCACCAAACATTTCTCAAATTT
* *
64458 AGAGTCAATTTCAACTTCACAGC-AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
64522 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAGCGA
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
64587 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
131 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
*
64652 ACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
196 ACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
64717 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATT
261 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATT
64782 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
326 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
64847 GCTGGTTGTCACCAAACATTTCTCAAATTT
391 GCTGGTTGTCACCAAACATTTCTCAAATTT
* *
64877 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAGGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64942 CGAA-GGACCGCTGGTTGTC
66 CGAAGGGACCGCTGGTTGTC
64961 GATAAACAAT
Statistics
Matches: 493, Mismatches: 9, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
419 429 0.87
420 64 0.13
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (420 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGA
AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
ACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATT
TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
GCTGGTTGTCACCAAACATTTCTCAAATTT
Found at i:64973 original size:105 final size:105
Alignment explanation
Indices: 64038--64960 Score: 1760
Period size: 105 Copynumber: 8.8 Consensus size: 105
64028 GGTTTTACCC
*
64038 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64103 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
64143 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64208 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
64248 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64313 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
64353 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
64418 CGAAGGGACCGCTGGTTGTCACTAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
64458 AGAGTCAATTTCAACTTCACAGC-AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64522 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
64562 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64627 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
64667 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64732 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
64772 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64837 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
* * *
64877 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAGGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
64942 CGAA-GGACCGCTGGTTGTC
66 CGAAGGGACCGCTGGTTGTC
64961 GATAAACAAT
Statistics
Matches: 809, Mismatches: 8, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
104 117 0.14
105 692 0.86
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
Found at i:65066 original size:20 final size:20
Alignment explanation
Indices: 65041--65082 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
65031 CCAGAACTCT
65041 GAGTTCGACTTCAACTTCAC
1 GAGTTCGACTTCAACTTCAC
* *
65061 GAGTTCGATTTCAATTTCAC
1 GAGTTCGACTTCAACTTCAC
65081 GA
1 GA
65083 CGAAGGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
GAGTTCGACTTCAACTTCAC
Found at i:65327 original size:16 final size:18
Alignment explanation
Indices: 65296--65331 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
65286 TTCATCCTTA
65296 TATTATATAATATATATT
1 TATTATATAATATATATT
65314 TATTATA-AAT-TATATT
1 TATTATATAATATATATT
65330 TA
1 TA
65332 CATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 3 0.17
18 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATATAATATATATT
Found at i:66350 original size:18 final size:19
Alignment explanation
Indices: 66319--66357 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
66309 TAATTATCTT
66319 TTTATATTACATTATAATA
1 TTTATATTACATTATAATA
* *
66338 TTTATA-TATATTATATTA
1 TTTATATTACATTATAATA
66356 TT
1 TT
66358 ATTAGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTACATTATAATA
Found at i:66458 original size:46 final size:54
Alignment explanation
Indices: 66375--66475 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 54
66365 TTTACACTCG
*
66375 TATATATGTATTATTAGTATAGTATTATGTCACTTATACGT-TTTAT-TATATA
1 TATATATGTATTATTAGTATAGTATTATGTCACTTATACGTATATATGTATATA
*
66427 TATATAT-TATTATT-GT-TATTATTAT-T-A-TTATACGTATATATGTATATA
1 TATATATGTATTATTAGTATAGTATTATGTCACTTATACGTATATATGTATATA
66475 T
1 T
66476 TTTATTTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
46 8 0.18
47 5 0.11
48 8 0.18
49 8 0.18
50 2 0.04
51 7 0.16
52 7 0.16
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (54 bp):
TATATATGTATTATTAGTATAGTATTATGTCACTTATACGTATATATGTATATA
Found at i:66540 original size:18 final size:18
Alignment explanation
Indices: 66519--66569 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
66509 TTTTTTATTA
*
66519 TTATTCTTTATATTATCC
1 TTATTCTTTATATTATAC
* *
66537 TTATTATTTCTATTATTAC
1 TTATTCTTTATATTA-TAC
66556 -TATTCTTTAT-TTAT
1 TTATTCTTTATATTAT
66570 TCATGTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 1 0.04
17 3 0.11
18 21 0.78
19 2 0.07
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTCTTTATATTATAC
Found at i:68971 original size:2 final size:2
Alignment explanation
Indices: 68964--69008 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
68954 TATTCATTAC
68964 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69006 TA T
1 TA T
69009 GTAAAACTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77298 original size:43 final size:44
Alignment explanation
Indices: 77250--77337 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
77240 CTTCCTGATG
77250 ATGTATAAAACATCCATGTATAATGTCATGCATGTA-TGCACTT
1 ATGTATAAAACATCCATGTATAATGTCATGCATGTATTGCACTT
77293 ATGTATAAAACATCCATGTATAATGTCATGCATGTATTGCACTT
1 ATGTATAAAACATCCATGTATAATGTCATGCATGTATTGCACTT
77337 A
1 A
77338 CCTTGACACT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 36 0.82
44 8 0.18
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (44 bp):
ATGTATAAAACATCCATGTATAATGTCATGCATGTATTGCACTT
Found at i:81641 original size:12 final size:12
Alignment explanation
Indices: 81624--81662 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
81614 ATAGGTAGGT
81624 TAGGTAGCTAGC
1 TAGGTAGCTAGC
81636 TAGGTAG-TA--
1 TAGGTAGCTAGC
81645 TAGGTAGCTAGC
1 TAGGTAGCTAGC
81657 TAGGTA
1 TAGGTA
81663 CTTAGTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 7 0.29
10 2 0.08
11 2 0.08
12 13 0.54
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.28
Consensus pattern (12 bp):
TAGGTAGCTAGC
Found at i:81668 original size:25 final size:21
Alignment explanation
Indices: 81615--81662 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
81605 GGTGGATGCA
81615 TAGGTAGGT-TAGGTAGCTAGC
1 TAGGTA-GTATAGGTAGCTAGC
81636 TAGGTAGTATAGGTAGCTAGC
1 TAGGTAGTATAGGTAGCTAGC
81657 TAGGTA
1 TAGGTA
81663 CTTAGTGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.27, C:0.08, G:0.35, T:0.29
Consensus pattern (21 bp):
TAGGTAGTATAGGTAGCTAGC
Found at i:83000 original size:17 final size:16
Alignment explanation
Indices: 82958--83021 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 16
82948 TTTATGCATC
*
82958 TAGTTCATTGAATAAATT
1 TAGTTCATTG-ATTAA-T
82976 TAAGTTCATTGATTACAT
1 T-AGTTCATTGATTA-AT
* *
82994 TAGTTCATTCATTTAAC
1 TAGTTCATTGA-TTAAT
83011 TAGTTCATTGA
1 TAGTTCATTGA
83022 ATAAATTAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 20 0.51
18 9 0.23
19 10 0.26
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (16 bp):
TAGTTCATTGATTAAT
Done.