Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004408.1 Hibiscus syriacus cultivar Beakdansim tig00009663_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: 68112
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1052 original size:22 final size:24
Alignment explanation
Indices: 1024--1078 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 24
1014 GTCTTTAAAA
1024 TTTTAAAT-TA-TAAAA-AATGTT
1 TTTTAAATATATTAAAACAATGTT
1045 TATTTAAATATATTAAAACCAATGTT
1 T-TTTAAATATATTAAAA-CAATGTT
1071 TTTTAAAT
1 TTTTAAAT
1079 GTTACAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.03
22 7 0.24
23 2 0.07
24 5 0.17
25 7 0.24
26 7 0.24
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTTAAATATATTAAAACAATGTT
Found at i:1059 original size:26 final size:25
Alignment explanation
Indices: 1030--1078 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1020 AAAATTTTAA
1030 ATTATAAA-AAATGTTTATTTAAATAT
1 ATTA-AAACAAATGTTT-TTTAAATAT
*
1056 ATTAAAACCAATGTTTTTTAAAT
1 ATTAAAACAAATGTTTTTTAAAT
1079 GTTACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
ATTAAAACAAATGTTTTTTAAATAT
Found at i:1789 original size:15 final size:15
Alignment explanation
Indices: 1771--1800 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1761 TAAAATATTT
1771 TAAATTAGTTAATAA
1 TAAATTAGTTAATAA
*
1786 TAAATTATTTAATAA
1 TAAATTAGTTAATAA
1801 GTTAATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TAAATTAGTTAATAA
Found at i:1807 original size:23 final size:20
Alignment explanation
Indices: 1777--1827 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 20
1767 ATTTTAAATT
1777 AGTTAATAATAAATTATTTAATA
1 AGTTAATAA-AAA-TATTT-ATA
*
1800 AGTTAATAAAAATATTTTTA
1 AGTTAATAAAAATATTTATA
1820 AGTTAATA
1 AGTTAATA
1828 TATATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 5 0.19
22 3 0.11
23 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
AGTTAATAAAAATATTTATA
Found at i:2118 original size:42 final size:42
Alignment explanation
Indices: 2066--2230 Score: 150
Period size: 43 Copynumber: 3.9 Consensus size: 42
2056 TGTGAATAAA
*
2066 AAACGCCGCAACAGGTTAGGACATTTAGCGGCGTTTTTATAC
1 AAACGCCGCAATAGGTTAGGACATTTAGCGGCGTTTTTATAC
* * * * *
2108 AAACGTCGCAATAGGTTAGGACATGTAGTGGTGTTTCTTTTAC
1 AAACGCCGCAATAGGTTAGGACATTTAGCGGCGTTT-TTATAC
* * * * * *
2151 AAACGCCGCAATATGTTAAGCCATTTAGTGGCATTTTTGGTAC
1 AAACGCCGCAATAGGTTAGGACATTTAGCGGCGTTTTT-ATAC
* ** * * *
2194 AAATGATGCAAAATGTTAGGACATATAGCGGCGTTTT
1 AAACGCCGCAATAGGTTAGGACATTTAGCGGCGTTTT
2231 AGAGTAAAAA
Statistics
Matches: 98, Mismatches: 23, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
42 33 0.34
43 65 0.66
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
AAACGCCGCAATAGGTTAGGACATTTAGCGGCGTTTTTATAC
Found at i:2477 original size:28 final size:28
Alignment explanation
Indices: 2423--2494 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
2413 AAATATTCAA
* *
2423 GTAATGTAGCTCAACATTTAAAAGAAAT
1 GTAATGTAGTTCAACATTCAAAAGAAAT
* **
2451 TTAATGTAGTTCAACATTCAAGTGAAAT
1 GTAATGTAGTTCAACATTCAAAAGAAAT
* *
2479 GTAATATAGTTTAACA
1 GTAATGTAGTTCAACA
2495 ATTAGAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (28 bp):
GTAATGTAGTTCAACATTCAAAAGAAAT
Found at i:3284 original size:93 final size:92
Alignment explanation
Indices: 3123--3290 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 92
3113 ATCCACTGAG
*
3123 TTTTTTATCACTGAATTGTACTCTCTTCTATTTTGGTTACTCCATTATTAAATAATTAATGATGT
1 TTTTTTATCACTGAATTGTACTCTCTTCTATTTTGGTTACTCCATTATTAAATAATTAATGACGT
3188 AAAAAACGACGTAGTTTGGTACTGAAT
66 AAAAAACGACGTAGTTTGGTACTGAAT
* * * *
3215 TTTTTTATCACTGAACTT-TACTTTCTCTTCTATTTTGGTTATTCTATTGTT-AATAGTTAATGA
1 TTTTTTATCACTGAA-TTGTAC--TCTCTTCTATTTTGGTTACTCCATTATTAAATAATTAATGA
3278 CGTAAAAAACGAC
63 CGTAAAAAACGAC
3291 ATCATTTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
92 18 0.26
93 25 0.37
94 25 0.37
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (92 bp):
TTTTTTATCACTGAATTGTACTCTCTTCTATTTTGGTTACTCCATTATTAAATAATTAATGACGT
AAAAAACGACGTAGTTTGGTACTGAAT
Found at i:6258 original size:31 final size:31
Alignment explanation
Indices: 6222--6282 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
6212 AAACTTAAAA
*
6222 TAGTTTTGCAATACT-AAGATTTAAATAATTT
1 TAGTTTTACAATACTGAA-ATTTAAATAATTT
6253 TAGTTTTACAATACTGAAATTTAAATAATT
1 TAGTTTTACAATACTGAAATTTAAATAATT
6283 CATACAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (31 bp):
TAGTTTTACAATACTGAAATTTAAATAATTT
Found at i:6764 original size:20 final size:20
Alignment explanation
Indices: 6741--6820 Score: 62
Period size: 18 Copynumber: 4.0 Consensus size: 20
6731 AACTGAAATC
6741 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-AAATAATATAT
*
6761 AAAAT--TTTAATAATATAT
1 AAAATAATTAAATAATATAT
*
6779 AAAATAATT-TAT-ATGATAT
1 AAAATAATTAAATAAT-ATAT
*
6798 AAAATTAAATAAATATATATAT
1 AAAA-TAATTAAATA-ATATAT
6820 A
1 A
6821 TATATATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
17 5 0.10
18 13 0.27
19 10 0.21
20 11 0.23
21 2 0.04
22 5 0.10
23 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAATAATTAAATAATATAT
Found at i:6817 original size:2 final size:2
Alignment explanation
Indices: 6810--6841 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
6800 AATTAAATAA
6810 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6842 TAAAAACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6829 original size:37 final size:37
Alignment explanation
Indices: 6757--6838 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
6747 ATTAAAATAA
* *
6757 ATATAAAATTTTAATAATATATAAAATAATTTATATG
1 ATATAAAATTTAAATAATATATAAAATAATATATATG
* *
6794 ATATAAAA-TTAAATAAATATATATATATATATATATATA
1 ATATAAAATTTAAAT-AATATATA-AAATA-ATATATATG
6833 ATATAA
1 ATATAA
6839 TATTAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.13
37 16 0.42
38 4 0.11
39 13 0.34
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (37 bp):
ATATAAAATTTAAATAATATATAAAATAATATATATG
Found at i:6831 original size:39 final size:36
Alignment explanation
Indices: 6756--6845 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 36
6746 AATTAAAATA
* *
6756 AATATAAAATTTTAATAATATATAAAATAATTTATAT
1 AATATAAAA-TTAAATAATATATAAAATAATATATAT
* *
6793 GATATAAAATTAAATAAATATATATATATATATATATAT
1 AATATAAAATTAAAT-AATATATA-AAATA-ATATATAT
*
6832 AATATAATATTAAA
1 AATATAAAATTAAA
6846 AACTTAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
36 5 0.11
37 16 0.36
38 4 0.09
39 19 0.43
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (36 bp):
AATATAAAATTAAATAATATATAAAATAATATATAT
Found at i:6935 original size:12 final size:12
Alignment explanation
Indices: 6918--7023 Score: 94
Period size: 12 Copynumber: 8.7 Consensus size: 12
6908 ATTTATTTAA
6918 AAAATTAATATT
1 AAAATTAATATT
6930 AAAATTAATATCT
1 AAAATTAATAT-T
*
6943 ATAATATAATATT
1 AAAAT-TAATATT
6956 AAAAATTAATATT
1 -AAAATTAATATT
* *
6969 -TAATTTAT-TT
1 AAAATTAATATT
6979 AAAAAATTAATATT
1 --AAAATTAATATT
*
6993 AAAATTAA-AAT
1 AAAATTAATATT
7004 AAAATATAATA-T
1 AAAAT-TAATATT
7016 AAAATTAA
1 AAAATTAA
7024 ATATAAAACC
Statistics
Matches: 78, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
10 2 0.03
11 16 0.21
12 28 0.36
13 20 0.26
14 12 0.15
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:6935 original size:25 final size:24
Alignment explanation
Indices: 6841--6929 Score: 160
Period size: 24 Copynumber: 3.7 Consensus size: 24
6831 TAATATAATA
*
6841 TTAAAAACTTAATATTTAATTTAT
1 TTAAAAAATTAATATTTAATTTAT
6865 TTAAAAAAATTAATATTTAATTTAT
1 TT-AAAAAATTAATATTTAATTTAT
6890 TTAAAAAATTAATATTTAATTTAT
1 TTAAAAAATTAATATTTAATTTAT
6914 TTAAAAAATTAATATT
1 TTAAAAAATTAATATT
6930 AAAATTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
24 40 0.63
25 23 0.37
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAAAATTAATATTTAATTTAT
Found at i:6936 original size:36 final size:39
Alignment explanation
Indices: 6894--6968 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
6884 ATTTATTTAA
*
6894 AAAATTAATAT-T-TAAT-TTAT-TTAAAAAATTAATATT
1 AAAATTAATATCTATAATATAATATT-AAAAATTAATATT
6930 AAAATTAATATCTATAATATAATATTAAAAATTAATATT
1 AAAATTAATATCTATAATATAATATTAAAAATTAATATT
6969 TAATTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 11 0.32
37 1 0.03
38 4 0.12
39 16 0.47
40 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (39 bp):
AAAATTAATATCTATAATATAATATTAAAAATTAATATT
Found at i:6997 original size:63 final size:62
Alignment explanation
Indices: 6870--7023 Score: 221
Period size: 63 Copynumber: 2.5 Consensus size: 62
6860 TTTATTTAAA
*
6870 AAAATTAATATT-TAAT-TTAT-TTAAAAAATTAATATTTAATTTATTTAAAAAATTAATATT
1 AAAATTAATATTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATATT
6930 AAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATATT
1 AAAATTAATAT-TATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATATT
* *
6993 AAAATTAA-AATAAAATATAATA-T-AAAATTAA
1 AAAATTAATATTATAATATAATATTAAAAATTAA
7024 ATATAAAACC
Statistics
Matches: 87, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
59 8 0.09
60 12 0.14
61 12 0.14
62 5 0.06
63 48 0.55
64 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (62 bp):
AAAATTAATATTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATATT
Found at i:7014 original size:87 final size:84
Alignment explanation
Indices: 6832--7023 Score: 239
Period size: 87 Copynumber: 2.2 Consensus size: 84
6822 ATATATATAT
*
6832 AATATAATATTAAAAACTTAATATTTAATTTATTTAAAAAAATTAATATTTAATTTATTTAAAAA
1 AATATAATATT-AAAA-TTAATATTTAATTAATTT-AAAAAATTAATATTTAATTTATTTAAAAA
* * *
6897 ATTAATATTTAATTTATTTAAAA
63 ATTAATATTAAAATTA-TAAAAA
6920 AAT-TAATATTAAAATTAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAA
1 AATATAATATTAAAATTAATAT-T-TAAT-TAAT-TTAAAAAATTAATATTTAATTTATTTAAAA
6983 AATTAATATTAAAATTA-AAATAA
62 AATTAATATTAAAATTATAAA-AA
7006 AATATAATA-TAAAATTAA
1 AATATAATATTAAAATTAA
7024 ATATAAAACC
Statistics
Matches: 94, Mismatches: 4, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
85 9 0.10
86 19 0.20
87 58 0.62
88 6 0.06
89 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (84 bp):
AATATAATATTAAAATTAATATTTAATTAATTTAAAAAATTAATATTTAATTTATTTAAAAAATT
AATATTAAAATTATAAAAA
Found at i:7026 original size:12 final size:12
Alignment explanation
Indices: 6981--7031 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
6971 ATTTATTTAA
6981 AAAATT-AATATT
1 AAAATTAAATA-T
6993 AAAATTAAA-AT
1 AAAATTAAATAT
7004 AAAA-TATAATAT
1 AAAATTA-AATAT
7016 AAAATTAAATAT
1 AAAATTAAATAT
7028 AAAA
1 AAAA
7032 CCACTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.06
11 7 0.20
12 22 0.63
13 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:10139 original size:37 final size:37
Alignment explanation
Indices: 10065--10139 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
10055 TATTATAATT
* **
10065 AATTTATATATTTTCTTTAAAAAATTTAAATTCATAA
1 AATTTATATATTTTATTTAAAAAATTTAAAAACATAA
* *
10102 AATTTATATAATTTTATTTACAAAA-TTAAAAAGATAA
1 AATTTATAT-ATTTTATTTAAAAAATTTAAAAACATAA
10139 A
1 A
10140 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.59
38 13 0.41
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
AATTTATATATTTTATTTAAAAAATTTAAAAACATAA
Found at i:10679 original size:2 final size:2
Alignment explanation
Indices: 10672--10723 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
10662 GGGTCTCAAC
10672 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
10714 TA TA TA TA TA
1 TA TA TA TA TA
10724 ATTTGGTCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13719 original size:17 final size:18
Alignment explanation
Indices: 13676--13712 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13666 AACCTACCTA
13676 AAATTTAGTTTTTATTTC
1 AAATTTAGTTTTTATTTC
13694 AAATTTAGTTTTTATTTC
1 AAATTTAGTTTTTATTTC
13712 A
1 A
13713 TTTTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (18 bp):
AAATTTAGTTTTTATTTC
Found at i:18626 original size:102 final size:102
Alignment explanation
Indices: 18450--18841 Score: 624
Period size: 102 Copynumber: 3.8 Consensus size: 102
18440 ACCGACGCCG
*
18450 CAAAATACAGCTCCGCCACCATTCCCTATTGAAGAACATTTACCATCGTTGGCTCCAAGTATTCC
1 CAAAATACAGCTCCGCCACCATTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGTATTCC
*
18515 AGTGGTGTTGCCACCATCTCCTCCATCCGTGCGAACC
66 AGTGGTGTTGCCACCATCTCCTCCATCCGAGCGAACC
* * *
18552 CAAAATACAGCTCCGCCGCCATTCCCTATTGAAGAACATTTACCATCGTTGGCTCCTAGTATTCC
1 CAAAATACAGCTCCGCCACCATTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGTATTCC
* *
18617 AGTGGTGTTGCCACCATCTCCTCCGTCCGCGCGAACC
66 AGTGGTGTTGCCACCATCTCCTCCATCCGAGCGAACC
* *
18654 CAAAATACAGCTCCGCCACCATTCCCTATTGAAGAAAATTTACCATCCTTGGCTCCAAGTTTTCC
1 CAAAATACAGCTCCGCCACCATTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGTATTCC
18719 AGTGGTGTTAG-CACCATCTCCTCCATCCGAGCGAACC
66 AGTGGTGTT-GCCACCATCTCCTCCATCCGAGCGAACC
* * * * * *
18756 CGAAGTACAGCTCCGCCACCATTCCCTATTGAAGAACATTTGCCATCCTTTGCACCAAGTACTCC
1 CAAAATACAGCTCCGCCACCATTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGTATTCC
*
18821 ATTGGTGTTGCCACCATCTCC
66 AGTGGTGTTGCCACCATCTCC
18842 ACCACCTCCG
Statistics
Matches: 268, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
101 1 0.00
102 266 0.99
103 1 0.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (102 bp):
CAAAATACAGCTCCGCCACCATTCCCTATTGAAGAACATTTACCATCCTTGGCTCCAAGTATTCC
AGTGGTGTTGCCACCATCTCCTCCATCCGAGCGAACC
Found at i:19764 original size:239 final size:235
Alignment explanation
Indices: 19371--19867 Score: 841
Period size: 239 Copynumber: 2.1 Consensus size: 235
19361 CCACCGTTGC
*
19371 GGAATTCTCCACAAAATTCCCCAGTCATTAACTCCAGTAGGTCAAGCGCTTTCCCCCCAACTGAC
1 GGAATTCTCCACAAAATTCCCCAGTCATTAACTCCAGTAGGTCAAGAGCTTTCCCCCCAACTGAC
19436 AACGAAGGAAATTCATCTAACAATAAGGCCCCTGTTCTGGAGCCAAGTGCTCCAGGTATATATTC
66 AACGAAGGAAATTCATCTAACAATAAGGCCCCTGTTCTGGAGCCAAGTGCTCCAGGTATATATTC
** *
19501 AGCGGTTTGATCATTGACGAGTCATTTCCTGATAGATTTAAAACCAACTTTGATTCTAACACTGC
131 AGAAGTTTGATAATTGACGAGTCATTTCCTGATAGATTTAAAACCAACTTTGATTCTAACACTGC
19566 TTCTTTTACTCTCTATCTTGTAGCTCCGGTTGCGCCACAATTGA
196 TTCTTTTA----CTATCTTGTAGCTCCGGTTGCGCCACAATTGA
* *
19610 GGAATTCTCCACAAAATTCCCCAGTCATTAATTCCAGTAGGTCAAGAGCTTTCCCCCCAACTGTC
1 GGAATTCTCCACAAAATTCCCCAGTCATTAACTCCAGTAGGTCAAGAGCTTTCCCCCCAACTGAC
*
19675 AATGAAGGAAATTCATCTAACAATAAGGCCCCTGTTCTGGAGCCAAGTGCTCCAGGTATATATTC
66 AACGAAGGAAATTCATCTAACAATAAGGCCCCTGTTCTGGAGCCAAGTGCTCCAGGTATATATTC
* *
19740 AGAAGTTTGATAATTGATGAGTCATTTCCTGATAGATTTAAAACCGACTTTGATTCTAACACTGC
131 AGAAGTTTGATAATTGACGAGTCATTTCCTGATAGATTTAAAACCAACTTTGATTCTAACACTGC
**
19805 TTCTTTTACTATCTTGTAGCTCCGGTTGCGCCACGCTTGA
196 TTCTTTTACTATCTTGTAGCTCCGGTTGCGCCACAATTGA
* *
19845 GGAATTCACCACAAAGTTCCCCA
1 GGAATTCTCCACAAAATTCCCCA
19868 CCCTTGCAAC
Statistics
Matches: 245, Mismatches: 13, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
235 51 0.21
239 194 0.79
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (235 bp):
GGAATTCTCCACAAAATTCCCCAGTCATTAACTCCAGTAGGTCAAGAGCTTTCCCCCCAACTGAC
AACGAAGGAAATTCATCTAACAATAAGGCCCCTGTTCTGGAGCCAAGTGCTCCAGGTATATATTC
AGAAGTTTGATAATTGACGAGTCATTTCCTGATAGATTTAAAACCAACTTTGATTCTAACACTGC
TTCTTTTACTATCTTGTAGCTCCGGTTGCGCCACAATTGA
Found at i:25475 original size:3 final size:3
Alignment explanation
Indices: 25467--25499 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
25457 CCACAGGGTA
25467 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
25500 GACAAGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:35709 original size:14 final size:14
Alignment explanation
Indices: 35679--35740 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 14
35669 ATATATATAT
35679 ATATATAATTAATA
1 ATATATAATTAATA
*
35693 ATAT-TAATTATTA
1 ATATATAATTAATA
*
35706 A-ATATAATAAATA
1 ATATATAATTAATA
*
35719 A-ATAAAATATAATA
1 ATATATAAT-TAATA
*
35733 ATAAATAA
1 ATATATAA
35741 ATATAGTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.05
13 23 0.61
14 9 0.24
15 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATATAATTAATA
Found at i:35713 original size:13 final size:12
Alignment explanation
Indices: 35681--35772 Score: 57
Period size: 13 Copynumber: 7.5 Consensus size: 12
35671 ATATATATAT
35681 ATATAATTAATA
1 ATATAATTAATA
*
35693 ATATTAATTATTAA
1 ATA-TAATTAAT-A
*
35707 ATATAATAAATAA
1 ATATAATTAAT-A
*
35720 ATAAAATATAATA
1 ATATAAT-TAATA
*
35733 ATA-AATAAAT-
1 ATATAATTAATA
35743 ATAGTAATT-A-A
1 ATA-TAATTAATA
*
35754 ATATAAATAATA
1 ATATAATTAATA
35766 ATTATAA
1 A-TATAA
35773 CATATTTTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
10 7 0.11
11 8 0.13
12 11 0.17
13 30 0.48
14 7 0.11
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (12 bp):
ATATAATTAATA
Found at i:35767 original size:17 final size:17
Alignment explanation
Indices: 35677--35769 Score: 83
Period size: 17 Copynumber: 5.7 Consensus size: 17
35667 AAATATATAT
35677 ATATATATAATT-AAT-A
1 ATATA-ATAATTAAATAA
*
35693 ATAT--TAATT-ATTAA
1 ATATAATAATTAAATAA
*
35707 ATATAATAAATAAATAAA
1 ATATAATAATTAAAT-AA
35725 ATATAATAA-TAAATAA
1 ATATAATAATTAAATAA
*
35741 ATATAGTAATTAAATATA
1 ATATAATAATTAAATA-A
35759 A-ATAATAATTA
1 ATATAATAATTA
35770 TAACATATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
13 7 0.11
14 5 0.08
16 18 0.28
17 22 0.34
18 13 0.20
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (17 bp):
ATATAATAATTAAATAA
Found at i:38283 original size:21 final size:21
Alignment explanation
Indices: 38257--38325 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
38247 GGACCTATCA
38257 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
38278 TCCCGAAGGA---CA--TGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
38295 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
38316 TCCCGTAGGA
1 TCCCGAAGGA
38326 CCTATCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 3 0.08
17 10 0.26
18 2 0.05
20 1 0.03
21 19 0.50
22 3 0.08
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:38296 original size:38 final size:38
Alignment explanation
Indices: 38238--38333 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
38228 CTCATATAAA
* *
38238 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACATATCATCCCGAAGGATGTAATCTG
*
38276 TGTCCCGAAGGACATGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACATATCATCCCGAAGGATGTAATCTG
* *
38314 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACATATCAT
38334 ATATCTTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACATATCATCCCGAAGGATGTAATCTG
Found at i:44469 original size:17 final size:17
Alignment explanation
Indices: 44447--44511 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
44437 CGTATAAATG
44447 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
** *
44464 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGACCT-ATC---A
*
44485 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
44502 TCCCGAAGGA
1 TCCCGAAGGA
44512 TGTAATCTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 21 0.57
18 3 0.08
20 2 0.05
21 11 0.30
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:44490 original size:21 final size:21
Alignment explanation
Indices: 44464--44532 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
44454 GGACCTATCA
44464 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
44485 TCCCGAAGGA---C--CTGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
44502 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
44523 TCCCGTAGGA
1 TCCCGAAGGA
44533 CCTATCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:44496 original size:38 final size:38
Alignment explanation
Indices: 44445--44540 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
44435 CTCGTATAAA
*
44445 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
44483 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
44521 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
44541 ATGTCTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:45417 original size:21 final size:21
Alignment explanation
Indices: 45388--45439 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
45378 AAGAGGGGGA
*
45388 ATCGATTCCCATTCATAGGAT
1 ATCGGTTCCCATTCATAGGAT
45409 ATCGGTTCCCATTCATAGGAT
1 ATCGGTTCCCATTCATAGGAT
45430 ATCGGTTCCC
1 ATCGGTTCCC
45440 TCTACCCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (21 bp):
ATCGGTTCCCATTCATAGGAT
Found at i:67133 original size:27 final size:28
Alignment explanation
Indices: 67050--67135 Score: 156
Period size: 28 Copynumber: 3.1 Consensus size: 28
67040 TAACCTCTAA
67050 TATAAAATCATACATCTATCCCTGAATT
1 TATAAAATCATACATCTATCCCTGAATT
67078 TATAAAATCATACATCTATCCCTGAATT
1 TATAAAATCATACATCTATCCCTGAATT
*
67106 TATAAAATCATACATC-ATCCCTAAATT
1 TATAAAATCATACATCTATCCCTGAATT
67133 TAT
1 TAT
67136 TCAGCTTAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 13 0.23
28 44 0.77
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (28 bp):
TATAAAATCATACATCTATCCCTGAATT
Done.