Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005685.1 Hibiscus syriacus cultivar Beakdansim tig00013296_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: 155328
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3093 original size:13 final size:12
Alignment explanation
Indices: 3076--3161 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
3066 ATATGGGCGT
3076 GATATGGTGATG
1 GATATGGTGATG
3088 GAATATGGTGAT-
1 G-ATATGGTGATG
*
3100 GATATAGGCG-T-
1 GATAT-GGTGATG
3111 GATAATGGTGATG
1 GAT-ATGGTGATG
3124 GACTATGGTGAT-
1 GA-TATGGTGATG
*
3136 GATATAGTCG-T-
1 GATATGGT-GATG
3147 GATAATGGTGATG
1 GAT-ATGGTGATG
3160 GA
1 GA
3162 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:3162 original size:36 final size:36
Alignment explanation
Indices: 3066--3162 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
3056 AGTTGGTGAA
* *
3066 ATATGGGCGTGAT-ATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
3101 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
*
3137 ATATAGTCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
3163 AGATTGTATC
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 12 0.21
36 46 0.79
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
Found at i:8581 original size:15 final size:15
Alignment explanation
Indices: 8563--8592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8553 TAAAAGTAAA
8563 TGAAATGGAAAGAAT
1 TGAAATGGAAAGAAT
*
8578 TGAAATGGATAGAAT
1 TGAAATGGAAAGAAT
8593 AGTAATCAAA
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:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (15 bp):
TGAAATGGAAAGAAT
Found at i:8771 original size:13 final size:12
Alignment explanation
Indices: 8752--8839 Score: 62
Period size: 13 Copynumber: 7.3 Consensus size: 12
8742 ATATGGGCGT
8752 GATATGGTGATG
1 GATATGGTGATG
8764 GAATATGGTGAT-
1 G-ATATGGTGATG
*
8776 GATATAGGCG-T-
1 GATAT-GGTGATG
8787 GATAATGGTGATG
1 GAT-ATGGTGATG
8800 GACTATGGTGAT-
1 GA-TATGGTGATG
*
8812 GATATAGGCG-T-
1 GATAT-GGTGATG
8823 GATAATGGTGATG
1 GAT-ATGGTGATG
8836 GATA
1 GATA
8840 GATTGTATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.34
12 17 0.27
13 23 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:8807 original size:36 final size:36
Alignment explanation
Indices: 8734--8837 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
8724 ATTTATAAGT
* *
8734 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
8769 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
8805 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
8838 TAGATTGTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:22610 original size:19 final size:20
Alignment explanation
Indices: 22580--22617 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
22570 GGGTAATAAT
22580 ATAAGTAATGAAAGGAAAAA
1 ATAAGTAATGAAAGGAAAAA
*
22600 ATAAG-AATGAAATGAAAA
1 ATAAGTAATGAAAGGAAAA
22618 TAAAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (20 bp):
ATAAGTAATGAAAGGAAAAA
Found at i:26864 original size:13 final size:12
Alignment explanation
Indices: 26848--26895 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
26838 CTTTTTGAAC
26848 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
26861 TTCTTTTATTCTT
1 TTCTTTT-TTCTT
*
26874 TTCTGATTTTTCTC
1 TTCT--TTTTTCTT
26888 TTCTTTTT
1 TTCTTTTT
26896 GCACTCTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.23
13 13 0.42
14 8 0.26
15 3 0.10
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:27185 original size:20 final size:21
Alignment explanation
Indices: 27154--27192 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27144 GGGTAATAAT
27154 ATAAGTAATGAAAGGAAAAAA
1 ATAAGTAATGAAAGGAAAAAA
*
27175 ATAAG-AATGAAATGAAAA
1 ATAAGTAATGAAAGGAAAA
27193 TAAAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (21 bp):
ATAAGTAATGAAAGGAAAAAA
Found at i:28836 original size:19 final size:19
Alignment explanation
Indices: 28812--28848 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28802 CGGCCAAGAG
28812 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
28831 CATGTATTTTCATTAAAA
1 CATGTATCTTCATTAAAA
28849 AAATCATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:29426 original size:27 final size:26
Alignment explanation
Indices: 29388--29443 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
29378 CCTACTTTGA
29388 TATCATTCCTTTCCAATTCCATTTCT
1 TATCATTCCTTTCCAATTCCATTTCT
* ***
29414 TATCATTTTCTTTCTTCTTCCATTTCT
1 TATCA-TTCCTTTCCAATTCCATTTCT
29441 TAT
1 TAT
29444 TTCATATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (26 bp):
TATCATTCCTTTCCAATTCCATTTCT
Found at i:31885 original size:25 final size:25
Alignment explanation
Indices: 31853--31909 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
31843 AGAAATCAGA
* *
31853 AAAG-AAATTGAAGCACTCCAAAAG
1 AAAGAAAATTCAAGCACTCAAAAAG
*
31877 AAAGAAAATTCCAGCACTCAAAAAG
1 AAAGAAAATTCAAGCACTCAAAAAG
*
31902 AAAAAAAA
1 AAAGAAAA
31910 AACCAAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.61, C:0.16, G:0.12, T:0.11
Consensus pattern (25 bp):
AAAGAAAATTCAAGCACTCAAAAAG
Found at i:37031 original size:9 final size:9
Alignment explanation
Indices: 37017--37047 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
37007 TATATTCTGA
37017 TTTTTTTCT
1 TTTTTTTCT
37026 TTTTTTTCT
1 TTTTTTTCT
*
37035 TTTCTTTCT
1 TTTTTTTCT
37044 TTTT
1 TTTT
37048 GCACTCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:40829 original size:8 final size:8
Alignment explanation
Indices: 40818--40847 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
40808 TATATTCTGA
40818 TTTTTTTC
1 TTTTTTTC
40826 TTTTTTTC
1 TTTTTTTC
40834 TTTTCTTTC
1 TTTT-TTTC
40843 TTTTT
1 TTTTT
40848 GCACTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:40846 original size:24 final size:23
Alignment explanation
Indices: 40788--40847 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
40778 TCTTTTTGAA
40788 ATTCTTTTTTTTTCTTTTCTTAT
1 ATTCTTTTTTTTTCTTTTCTTAT
* * *
40811 ATTCTGATTTTTTTCTTTTTTTCT
1 ATTCT-TTTTTTTTCTTTTCTTAT
* *
40835 TTTCTTTCTTTTT
1 ATTCTTTTTTTTT
40848 GCACTCTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (23 bp):
ATTCTTTTTTTTTCTTTTCTTAT
Found at i:44467 original size:91 final size:91
Alignment explanation
Indices: 44319--44491 Score: 274
Period size: 91 Copynumber: 1.9 Consensus size: 91
44309 CCGATGTGCC
* * * *
44319 TTGCATATGACCAACCCCCATGTGCCTTGCATGTGGATCATTTAGGCGGCTAGATGAAGAGTTCT
1 TTGCATATGACCAACCCCCATGTGCCTTACATATGGATCATTTAGGCGCCAAGATGAAGAGTTCT
44384 CTCCCTATTCGGCCAAGCCATGTGTT
66 CTCCCTATTCGGCCAAGCCATGTGTT
* * * *
44410 TTGCATGTGATCAGCCCCCATGTGCCTTACATATGGTTCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAACCCCCATGTGCCTTACATATGGATCATTTAGGCGCCAAGATGAAGAGTTCT
44475 CTCCCTATTCGGCCAAG
66 CTCCCTATTCGGCCAAG
44492 AATCAACTAC
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
TTGCATATGACCAACCCCCATGTGCCTTACATATGGATCATTTAGGCGCCAAGATGAAGAGTTCT
CTCCCTATTCGGCCAAGCCATGTGTT
Found at i:49914 original size:11 final size:13
Alignment explanation
Indices: 49882--49911 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
49872 TGGCCAAAGA
49882 TGAAAAGGTATGT
1 TGAAAAGGTATGT
49895 TGAAAAGGTATG-
1 TGAAAAGGTATGT
49907 TGAAA
1 TGAAA
49912 GGTGTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:59127 original size:298 final size:291
Alignment explanation
Indices: 58570--59152 Score: 951
Period size: 287 Copynumber: 2.0 Consensus size: 291
58560 CTTTCTTGTT
58570 TGATACAGTTCAACCTAGCCTCACTTAAATAGATGGTGAAGTCAAGGTTGTACCTTTGACTGTTT
1 TGATACAGTTCAACCTAGCCTCACTTAAATAGATGGTGAAGTCAAGGTTGTACCTTTGACTGTTT
*
58635 CGATCTAGGAAAGCAACAAGGATCATGCACAAACATGAAAGCAAAAAAATAGTTAAATGGAAGTA
66 CGATCTAGGAAAGCAACAAGGATCATGCACAAACAAGAAAGCAAAAAAATAGTTAAATGGAAGTA
* * *
58700 ATGAATTGAAAGATAAATATGGTAGCGGAATATATATAAGTTGGTGATATGTTTAAAGGAAATGA
131 ATGAAATG--AG--AAATATGATA---GAATATATATAAGTCGGTGATATGTTTAAAGGAAATGA
*
58765 TGAAGTATGGTAATGGAAGTAGAATCAAGGTGATGGAGATGAATATGAAAAGTAGTATCTCAAAG
189 TGAAGTATGGTAATGGAAGTAGAATCAAGGTGATGGAGATGAATATGAAAAGTAATATCTCAAAG
58830 AAGACTCAAAGAAGAAGCAATTTTAAAGAACAAAGATA
254 AAGACTCAAAGAAGAAGCAATTTTAAAGAACAAAGATA
* *
58868 TGATACAGTTCAACCTAGCCTCACTTAAATGGATGGTGAAGTCAAGGTTGTACCTTTGATTGTTT
1 TGATACAGTTCAACCTAGCCTCACTTAAATAGATGGTGAAGTCAAGGTTGTACCTTTGACTGTTT
* *
58933 CGATCTAGGAAAGTAACAAGGATCATGCACAAATAAGAAAGCTAAAAAAATAGTTAAATGGAAGT
66 CGATCTAGGAAAGCAACAAGGATCATGCACAAACAAGAAAGC-AAAAAAATAGTTAAATGGAAGT
58998 AATGAAATG-G-AA-A-GATA-AATATATATAAGTCGGTGATATGTTTAAAGGAAATGATGAAGT
130 AATGAAATGAGAAATATGATAGAATATATATAAGTCGGTGATATGTTTAAAGGAAATGATGAAGT
*
59058 ATGGTAATGGAAGTAGAATGAAGGTGATGGAGATGAATATGAAAAGTAATATCTCAAAGAAGACT
195 ATGGTAATGGAAGTAGAATCAAGGTGATGGAGATGAATATGAAAAGTAATATCTCAAAGAAGACT
* *
59123 CAAAGAAGAACCAATGTTAAAGAACAAAGA
260 CAAAGAAGAAGCAATTTTAAAGAACAAAGA
59153 CCCAGACTTT
Statistics
Matches: 272, Mismatches: 12, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
287 133 0.49
291 3 0.01
292 1 0.00
293 2 0.01
296 1 0.00
298 102 0.38
299 30 0.11
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (291 bp):
TGATACAGTTCAACCTAGCCTCACTTAAATAGATGGTGAAGTCAAGGTTGTACCTTTGACTGTTT
CGATCTAGGAAAGCAACAAGGATCATGCACAAACAAGAAAGCAAAAAAATAGTTAAATGGAAGTA
ATGAAATGAGAAATATGATAGAATATATATAAGTCGGTGATATGTTTAAAGGAAATGATGAAGTA
TGGTAATGGAAGTAGAATCAAGGTGATGGAGATGAATATGAAAAGTAATATCTCAAAGAAGACTC
AAAGAAGAAGCAATTTTAAAGAACAAAGATA
Found at i:64868 original size:25 final size:25
Alignment explanation
Indices: 64808--64861 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
64798 GGTAGCTAAC
64808 CAAGTGAGTTATAGCTTGATAAAAT
1 CAAGTGAGTTATAGCTTGATAAAAT
64833 CAAGTGAGTTATAGCTTGATAAAAT
1 CAAGTGAGTTATAGCTTGATAAAAT
64858 CAAG
1 CAAG
64862 CTAGTTAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (25 bp):
CAAGTGAGTTATAGCTTGATAAAAT
Found at i:69410 original size:20 final size:20
Alignment explanation
Indices: 69373--69409 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
69363 TGCTTCACCT
*
69373 TTTTTTTCTTTTGCTTTTAA
1 TTTTCTTCTTTTGCTTTTAA
69393 TTTTCTTCTTTT-CTTTT
1 TTTTCTTCTTTTGCTTTT
69410 TCTTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTCTTCTTTTGCTTTTAA
Found at i:69454 original size:6 final size:6
Alignment explanation
Indices: 69443--69491 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
69433 GATGTAGGAG
*
69443 TCTTTT TC-TTT TCTTTT TCTTTT TCTTTT TCTTCTT TCTTTC TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT
69491 T
1 T
69492 GTTGCTTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 5 0.13
6 28 0.72
7 6 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:78194 original size:25 final size:25
Alignment explanation
Indices: 78160--78211 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
78150 AACCATATGT
*
78160 AAGGAACATGGGGCTGATCACATGC
1 AAGGAACATGGGACTGATCACATGC
78185 AAGGAACATGGGACTGATCACATGC
1 AAGGAACATGGGACTGATCACATGC
78210 AA
1 AA
78212 AACACATGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (25 bp):
AAGGAACATGGGACTGATCACATGC
Found at i:78218 original size:25 final size:25
Alignment explanation
Indices: 78164--78220 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
78154 ATATGTAAGG
* *
78164 AACATGGGGCTGATCACATGCAAGG
1 AACATGGGACTGATCACATGCAAGA
78189 AACATGGGACTGATCACATGCAA-A
1 AACATGGGACTGATCACATGCAAGA
78213 ACACATGG
1 A-ACATGG
78221 CTTGGCCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (25 bp):
AACATGGGACTGATCACATGCAAGA
Found at i:80058 original size:25 final size:24
Alignment explanation
Indices: 80029--80076 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
80019 CCACCAATGC
*
80029 TCTGATTACTGCTTGATGTAAGGCT
1 TCTGATGACT-CTTGATGTAAGGCT
*
80054 TCTGATGCCTCTTGATGTAAGGC
1 TCTGATGACTCTTGATGTAAGGC
80077 ACTTGTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (24 bp):
TCTGATGACTCTTGATGTAAGGCT
Found at i:92704 original size:9 final size:9
Alignment explanation
Indices: 92689--92725 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
92679 GAAAGCACTC
92689 AAAAAAGAA
1 AAAAAAGAA
*
92698 GAAAAAGAA
1 AAAAAAGAA
92707 AAAAAAGAA
1 AAAAAAGAA
92716 AAAGAAAGAA
1 AAA-AAAGAA
92726 TGTTGAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 19 0.76
10 6 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:92707 original size:25 final size:23
Alignment explanation
Indices: 92648--92707 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
92638 AAATCCAGCA
*
92648 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
92671 AAGAAATTGAAAGCACTCAAAAAAG
1 AAGAAAATGAAAGCACTC--AAAAG
*
92696 AAGAAAAAGAAA
1 AAGAAAATGAAA
92708 AAAAAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 16 0.52
25 15 0.48
ACGTcount: A:0.65, C:0.12, G:0.15, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:92714 original size:15 final size:16
Alignment explanation
Indices: 92689--92722 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
92679 GAAAGCACTC
92689 AAAAAAGAAGAAAAAG
1 AAAAAAGAAGAAAAAG
92705 AAAAAA-AAGAAAAAG
1 AAAAAAGAAGAAAAAG
92720 AAA
1 AAA
92723 GAATGTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAGAAAAAG
Found at i:96546 original size:2 final size:2
Alignment explanation
Indices: 96539--96580 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
96529 CATATCACCG
96539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96581 TCCGCTTCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97776 original size:23 final size:23
Alignment explanation
Indices: 97746--97793 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
97736 CGAAGCATAT
97746 TTGGGTGATGAAGTCTCTTAACA
1 TTGGGTGATGAAGTCTCTTAACA
97769 TTGGGTGATGAAGTCTCTTAACA
1 TTGGGTGATGAAGTCTCTTAACA
97792 TT
1 TT
97794 TAATCCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (23 bp):
TTGGGTGATGAAGTCTCTTAACA
Found at i:98855 original size:17 final size:16
Alignment explanation
Indices: 98828--98865 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
98818 GAAAATAAAT
98828 AATAAGAATGAAATGA
1 AATAAGAATGAAATGA
98844 AATAATGAATGAAATGA
1 AATAA-GAATGAAATGA
98861 AATAA
1 AATAA
98866 AGAAGGATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.21
Consensus pattern (16 bp):
AATAAGAATGAAATGA
Found at i:101858 original size:29 final size:29
Alignment explanation
Indices: 101793--101858 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
101783 CAACTTCTTT
**
101793 CTTTTTTTTTCTTCTTTTTGAGTGCTGGA
1 CTTTTTTTTTCTTCTTTTTGAGTGCTCCA
101822 -TTTTTTTTTCTT-TCTTTTGAGTGCTCCA
1 CTTTTTTTTTCTTCT-TTTTGAGTGCTCCA
*
101850 CTTTGTTTT
1 CTTTTTTTT
101859 CTAATTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.06, C:0.15, G:0.14, T:0.65
Consensus pattern (29 bp):
CTTTTTTTTTCTTCTTTTTGAGTGCTCCA
Found at i:106072 original size:29 final size:29
Alignment explanation
Indices: 106012--106072 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
106002 CTTTATTTTC
** * *
106012 TTTTCTTCTTTTTGAGTGCTGGATTTTTT
1 TTTTCTTCTTTTTGAGTGCTCCACTTTGT
106041 TTTTCTT-TCTTTTGAGTGCTCCACTTTGT
1 TTTTCTTCT-TTTTGAGTGCTCCACTTTGT
106070 TTT
1 TTT
106073 CTGATTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.64
Consensus pattern (29 bp):
TTTTCTTCTTTTTGAGTGCTCCACTTTGT
Found at i:115072 original size:11 final size:11
Alignment explanation
Indices: 115048--115081 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
115038 TTGGTGCTGG
115048 AAACAAGATAA
1 AAACAAGATAA
* *
115059 AAATAAGATGA
1 AAACAAGATAA
115070 AAACAAGATAA
1 AAACAAGATAA
115081 A
1 A
115082 GAAATGATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.12
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:119759 original size:11 final size:11
Alignment explanation
Indices: 119735--119779 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
119725 TTGGTGCTGG
119735 AAACAAGATAA
1 AAACAAGATAA
* *
119746 AAATAAGATTA
1 AAACAAGATAA
119757 AAACAAGATAA
1 AAACAAGATAA
119768 AGAA-AAGATAA
1 A-AACAAGATAA
119779 A
1 A
119780 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:119763 original size:22 final size:22
Alignment explanation
Indices: 119735--119776 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
119725 TTGGTGCTGG
119735 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
119757 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
119777 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:125787 original size:91 final size:90
Alignment explanation
Indices: 125608--125789 Score: 242
Period size: 91 Copynumber: 2.0 Consensus size: 90
125598 GATAGTTGAT
*
125608 GCTTGGCCGAATAGGAGAAAACTCTTCATCTTGGCGCCTAAATGAACCATATGCAAGGCACATGG
1 GCTTGGCCGAATAGGAGAAAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATGG
* *
125673 GTGCTGATCGCATGGAAAACACATG
66 GTGCTGATCACATGCAAAACACATG
* *
125698 GCTTGGCTGAATAGG-GAAAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACAT
1 GCTTGGCCGAATAGGAG-AA-AACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACAT
* * **
125762 AGGG-GCTGGTCATATGCAAGGCACATG
64 -GGGTGCTGATCACATGCAAAACACATG
125789 G
1 G
125790 GTATTCTAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
89 1 0.01
90 16 0.20
91 60 0.75
92 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (90 bp):
GCTTGGCCGAATAGGAGAAAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATGG
GTGCTGATCACATGCAAAACACATG
Found at i:130167 original size:24 final size:21
Alignment explanation
Indices: 130132--130174 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
130122 GGCACATTCT
*
130132 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
130155 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
130175 GTCTTGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:131415 original size:5 final size:5
Alignment explanation
Indices: 131400--131436 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
131390 AGTGCTTCAA
*
131400 TTTTC -TTTC TTTTC TTTTC TTTGC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
131437 GATTGTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:131428 original size:15 final size:15
Alignment explanation
Indices: 131400--131437 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
131390 AGTGCTTCAA
131400 TTTTCTTT-CTTTTC
1 TTTTCTTTGCTTTTC
131414 TTTTCTTTGCTTTTC
1 TTTTCTTTGCTTTTC
*
131429 TTTTTTTTG
1 TTTTCTTTG
131438 ATTGTTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTTCTTTGCTTTTC
Found at i:138288 original size:10 final size:11
Alignment explanation
Indices: 138254--138288 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
138244 TTTTTTTTTC
*
138254 AAAAAAA-CAA
1 AAAAAAAGCCA
138264 AAAAAAAGCCA
1 AAAAAAAGCCA
138275 AAAAAAAGCCA
1 AAAAAAAGCCA
138286 AAA
1 AAA
138289 TTTCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCCA
Found at i:147916 original size:25 final size:23
Alignment explanation
Indices: 147861--147916 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
147851 TCCAGCAAAG
* *
147861 AAAACAAATCACTCAAAAGAAGA
1 AAAAGAAAGCACTCAAAAGAAGA
**
147884 AATTGAAAGCACTCAAAAAGGAAGA
1 AAAAGAAAGCACTC-AAAA-GAAGA
147909 AAAAGAAA
1 AAAAGAAA
147917 AGAAAAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
25 11 0.44
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.09
Consensus pattern (23 bp):
AAAAGAAAGCACTCAAAAGAAGA
Found at i:154777 original size:88 final size:89
Alignment explanation
Indices: 154674--154837 Score: 260
Period size: 88 Copynumber: 1.9 Consensus size: 89
154664 ATTTAATTTA
** * *
154674 AATTAATTAAATATAGATTTAATTAATTTG-AATAATAAAATTCCTGATATGATTAGGGTAAC-T
1 AATTAATTAAATATAGATTTAATTAA-TTGAAATAATAAAAACCCTAATATGACTAGGGTAACTT
154737 GGATATAAAAGGATTATTAAATTCT
65 GGATATAAAAGGATTATTAAATTCT
154762 AATTAATTAAATATAGATTTAATTAATTGAAATAATAAAAACCCTAATATGACTAGGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTGAAATAATAAAAACCCTAATATGACTAGGGTAACTTG
*
154827 GCTATAAAAGG
66 GATATAAAAGG
154838 GTGTGTTAGA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
87 3 0.04
88 54 0.78
89 12 0.17
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTGAAATAATAAAAACCCTAATATGACTAGGGTAACTTG
GATATAAAAGGATTATTAAATTCT
Done.