Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001201.1 Hibiscus syriacus cultivar Beakdansim tig00002376_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: 69097
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3626 original size:59 final size:59
Alignment explanation
Indices: 3501--3614 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
3491 AACATCGAGC
* * *
3501 GATCATTTTGTAACTTTTAATAGTAAAAGGGTTCAACAAAGCAGTGTCCTACGGTCAGA
1 GATCATTTTATAACTTTTAATAGTAAAAGGATTCAACAAAGCAGTGTCCTACAGTCAGA
* *** * *
3560 TATCATTTTATAACTTTTAATAGTCGGAGGATTC-ACAAAGTAGTGTCCTATAGTC
1 GATCATTTTATAACTTTTAATAGTAAAAGGATTCAACAAAGCAGTGTCCTACAGTC
3615 GGGGGATCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 18 0.39
59 28 0.61
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (59 bp):
GATCATTTTATAACTTTTAATAGTAAAAGGATTCAACAAAGCAGTGTCCTACAGTCAGA
Found at i:4131 original size:22 final size:24
Alignment explanation
Indices: 4099--4147 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
4089 TTTGGAGAAG
4099 TATTAGATAAAAATATAATTT-TT
1 TATTAGATAAAAATATAATTTGTT
*
4122 TATTA-ATAAAAATATGATTTGTT
1 TATTAGATAAAAATATAATTTGTT
4145 TAT
1 TAT
4148 ATATACGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
TATTAGATAAAAATATAATTTGTT
Found at i:5603 original size:16 final size:16
Alignment explanation
Indices: 5584--5617 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5574 TAATATTTTA
*
5584 TTATTATGTATTTAAT
1 TTATTAAGTATTTAAT
*
5600 TTATTAAGTATTTTAT
1 TTATTAAGTATTTAAT
5616 TT
1 TT
5618 TATTTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTATTAAGTATTTAAT
Found at i:5907 original size:107 final size:109
Alignment explanation
Indices: 5689--5912 Score: 346
Period size: 112 Copynumber: 2.1 Consensus size: 109
5679 CTCGGATGGA
* *
5689 AATTATATATCTCTACACTTTGCTAATACGGTAACATTTTAACATTTTAATTTAATTTAAATTAT
1 AATTAAATATCTCGACACTTTGCTAATACGGTAACATTTTAACATTTTAATTTAATTTAAATTAT
*
5754 TAGTAATATTTAGTTGATTTATTTAATGTATGATTATTAGATTAAG
66 TAGTAATA--TAGTTGATTTATTTAATGCATGATTATTAGATTAAG
* * *
5800 AATTAAATATCTCGATACTTTGCTGATACGGTAACATTTTTAACGTTTTAATTTAATTTAAATTA
1 AATTAAATATCTCGACACTTTGCTAATACGGTAACA-TTTTAACATTTTAATTTAATTTAAATTA
5865 TTAGTAATA-A-TT-ATTTATTTAATGCATGATTATTAGATTAAG
65 TTAGTAATATAGTTGATTTATTTAATGCATGATTATTAGATTAAG
5907 AATTAA
1 AATTAA
5913 TTTTTGTAAT
Statistics
Matches: 106, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
107 35 0.33
108 2 0.02
109 1 0.01
111 32 0.30
112 36 0.34
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.46
Consensus pattern (109 bp):
AATTAAATATCTCGACACTTTGCTAATACGGTAACATTTTAACATTTTAATTTAATTTAAATTAT
TAGTAATATAGTTGATTTATTTAATGCATGATTATTAGATTAAG
Found at i:7398 original size:27 final size:27
Alignment explanation
Indices: 7367--7421 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
7357 CTGATCCAGG
*
7367 CGGATTTCTCGGTCATGATCAGAGATC
1 CGGATTTCTCGGTCATGATCAAAGATC
7394 CGGATTTCTCGGTCATGATCAAAGATC
1 CGGATTTCTCGGTCATGATCAAAGATC
7421 C
1 C
7422 CATGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (27 bp):
CGGATTTCTCGGTCATGATCAAAGATC
Found at i:15952 original size:27 final size:27
Alignment explanation
Indices: 15912--15966 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
15902 TTGATCCAGG
15912 CGGATTTCTAGGTCATGAAT-AGAGATC
1 CGGATTTCTAGGTCATG-ATCAGAGATC
*
15939 CGGATTTCTCGGTCATGATCAGAGATC
1 CGGATTTCTAGGTCATGATCAGAGATC
15966 C
1 C
15967 CGTGAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (27 bp):
CGGATTTCTAGGTCATGATCAGAGATC
Found at i:16235 original size:20 final size:20
Alignment explanation
Indices: 16198--16240 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16188 ATTCCACCTC
* *
16198 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
16218 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
16238 ATG
1 ATG
16241 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:25274 original size:24 final size:20
Alignment explanation
Indices: 25247--25304 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
25237 GCATGGGTAG
25247 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
25271 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
25291 TGTATCGATGCACT
1 TGCATCGATGCACT
25305 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:27191 original size:19 final size:19
Alignment explanation
Indices: 27167--27203 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27157 AATCAATTCA
*
27167 TATTTTTATTTAAAATAAC
1 TATTTTAATTTAAAATAAC
27186 TATTTTAATTTAAAATAA
1 TATTTTAATTTAAAATAA
27204 AATATTAAAG
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTAATTTAAAATAAC
Found at i:35923 original size:2 final size:2
Alignment explanation
Indices: 35916--35946 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35906 TTGAGAGTTT
35916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35947 GATAATAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39763 original size:29 final size:29
Alignment explanation
Indices: 39702--39763 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
39692 AAAATTGGTT
* *
39702 AATTCGATTCGGTTAATAATTTTTAAATT
1 AATTCGATTCGGTTAATAATTTTCAAATA
* *
39731 AATTCGGTTCGGTTAATAATTTTCCAATA
1 AATTCGATTCGGTTAATAATTTTCAAATA
39760 AATT
1 AATT
39764 TTGGTCCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (29 bp):
AATTCGATTCGGTTAATAATTTTCAAATA
Found at i:39786 original size:139 final size:140
Alignment explanation
Indices: 39589--40018 Score: 571
Period size: 142 Copynumber: 3.0 Consensus size: 140
39579 AAAAATTCGT
* *
39589 TTAATTCGATTCGGTTAATAATTTTCAAAATAAATTTTGGTTCGATTGACCGAACCGAATTAACC
1 TTAATTCGGTTCGGTTAATAATTTTC-AAATAAATTTTGGTTCGATTAACCGAACCGAATTAACC
* *
39654 GATTTGTTTTCTTCGATTAATTT-GATTAATAA-TTTAAAAAAATTGGTTAATTC-GATTCGGTT
65 GAATTGTTTTCTTCGATTAATTTAG-TTAATAATTTTAAAAAAATTAGTTAATTCAG-TTCGGTT
*
39716 AATAATTTTTAAA
128 AATAATTTTCAAA
* * * *
39729 TTAATTCGGTTCGGTTAATAATTTTCCAATAAATTTTGGTCCGATTAACCTAACCGAATTAACTG
1 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCG
* * * *
39794 AATTGTTTGCTTCGATTAATTTAGTTAATAATTTTTTTAAAAAATCAGTTAATTCAGTTTGGTTA
66 AATTGTTTTCTTCGATTAATTTAGTTAATAA--TTTTAAAAAAATTAGTTAATTCAGTTCGGTTA
39859 ATAATTTTCAAA
129 ATAATTTTCAAA
* * *
39871 TTAATTCAGTTTGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCG
1 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCG
* ** *
39936 AATT-TTTTCTTCGATTAATTCAGTTAATAATTTTCAAAAAAATTTCTTTTAATTCAGTTCGATT
66 AATTGTTTTCTTCGATTAATTTAGTTAATAATTTT-AAAAAAA-TT-AGTTAATTCAGTTCGGTT
40000 AATAATTTTCAAA
128 AATAATTTTCAAA
*
40013 TAAATT
1 TTAATT
40019 TTGGTTCAAT
Statistics
Matches: 253, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
139 65 0.26
140 32 0.13
141 25 0.10
142 130 0.51
143 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (140 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCG
AATTGTTTTCTTCGATTAATTTAGTTAATAATTTTAAAAAAATTAGTTAATTCAGTTCGGTTAAT
AATTTTCAAA
Found at i:39875 original size:29 final size:29
Alignment explanation
Indices: 39842--39905 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
39832 AAAAAATCAG
*
39842 TTAATTCAGTTTGGTTAATAATTTTCAAA
1 TTAATTCAGTTTGATTAATAATTTTCAAA
39871 TTAATTCAGTTTGATTAATAATTTTCAAA
1 TTAATTCAGTTTGATTAATAATTTTCAAA
*
39900 TAAATT
1 TTAATT
39906 TTGGTTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (29 bp):
TTAATTCAGTTTGATTAATAATTTTCAAA
Found at i:40129 original size:19 final size:19
Alignment explanation
Indices: 40105--40142 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
40095 ATTAGTCGTG
40105 AATAATTT-ATTTAATTTTT
1 AATAATTTGA-TTAATTTTT
40124 AATAATTTGATTAATTTTT
1 AATAATTTGATTAATTTTT
40143 TATCGTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
AATAATTTGATTAATTTTT
Found at i:44515 original size:8 final size:8
Alignment explanation
Indices: 44369--44512 Score: 243
Period size: 8 Copynumber: 18.0 Consensus size: 8
44359 CGCTCTTACA
44369 CATGTATG
1 CATGTATG
*
44377 TATGTATG
1 CATGTATG
*
44385 TATGTATG
1 CATGTATG
*
44393 TATGTATG
1 CATGTATG
44401 CATGTATG
1 CATGTATG
44409 CATGTATG
1 CATGTATG
44417 CATGTATG
1 CATGTATG
44425 CATGTATG
1 CATGTATG
44433 CATGTATG
1 CATGTATG
44441 CATGTATG
1 CATGTATG
44449 CATGTATG
1 CATGTATG
44457 CATGTATG
1 CATGTATG
44465 CATGTATG
1 CATGTATG
44473 CATGTATG
1 CATGTATG
44481 CATGTATG
1 CATGTATG
*
44489 TATGTATG
1 CATGTATG
44497 CATGTATG
1 CATGTATG
*
44505 TATGTATG
1 CATGTATG
44513 TATACATATA
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 131 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (8 bp):
CATGTATG
Found at i:53946 original size:18 final size:18
Alignment explanation
Indices: 53911--53949 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53901 GGATCAGCAC
*
53911 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
53929 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
53947 GAG
1 GAG
53950 TATCAAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:55942 original size:64 final size:64
Alignment explanation
Indices: 55874--56030 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
55864 TTGAAGGCGT
** *
55874 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
55936 GC
63 GC
* *
55938 ATCGATGCGTA-AGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATG
1 ATCGATGC--ACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATG
56001 C
64 C
* *
56002 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
56031 ACCTTCATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 62 0.79
65 11 0.14
66 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:56406 original size:12 final size:12
Alignment explanation
Indices: 56389--56422 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
56379 CAAATACCTG
56389 TGTGATATGATA
1 TGTGATATGATA
56401 TGTGATATGATA
1 TGTGATATGATA
56413 TGTGATATGA
1 TGTGATATGA
56423 GAACATGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (12 bp):
TGTGATATGATA
Found at i:56460 original size:29 final size:29
Alignment explanation
Indices: 56421--56491 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
56411 TATGTGATAT
56421 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
56451 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
56480 GAGAAATGACAT
1 GAGAAATGACAT
56492 ATACAAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 36 0.88
30 5 0.12
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:62858 original size:64 final size:63
Alignment explanation
Indices: 62716--62866 Score: 175
Period size: 64 Copynumber: 2.4 Consensus size: 63
62706 AGGCGTATCA
* * *
62716 ATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAATCGAATGCAATTAGTGCATCG
1 ATGCACAAGTAGTGCATCGATGCATCTCTATTAAAATAAAAATCGAATGCAATTAGTGCACCG
* * *
62778 ATGCATAAGGCA-TGCATCGATGCATC-CTATTAATAATAAAACATCGAATGCATTTTA-TGCAC
1 ATGCACAA-GTAGTGCATCGATGCATCTCTATTAA-AATAAAA-ATCGAATGCA-ATTAGTGCAC
62840 CG
62 CG
*
62842 ATGCACAAGTAGTGCATCAATGCAT
1 ATGCACAAGTAGTGCATCGATGCAT
62867 ACCTTCATTA
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
62 24 0.32
63 12 0.16
64 35 0.47
65 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (63 bp):
ATGCACAAGTAGTGCATCGATGCATCTCTATTAAAATAAAAATCGAATGCAATTAGTGCACCG
Found at i:63291 original size:29 final size:28
Alignment explanation
Indices: 63252--63331 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 28
63242 TATGTGATAT
63252 GAGAACATGACATGACCTACATGATCACAA
1 GAGAA-ATGACATGA-CTACATGATCACAA
63282 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGA-CTACATGATCACAA
*
63311 GA-AAATGACATGAGTACATGA
1 GAGAAATGACATGACTACATGA
63332 ACATATAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
27 7 0.15
28 11 0.23
29 25 0.52
30 5 0.10
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (28 bp):
GAGAAATGACATGACTACATGATCACAA
Found at i:64907 original size:11 final size:11
Alignment explanation
Indices: 64872--64909 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
64862 TCACTTTTTA
64872 AAAAATA-AAT
1 AAAAATACAAT
64882 AAAAATACAAT
1 AAAAATACAAT
*
64893 -AAAATTCAAT
1 AAAAATACAAT
64903 AAAAATA
1 AAAAATA
64910 TAATGTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATACAAT
Found at i:66086 original size:25 final size:25
Alignment explanation
Indices: 66053--66106 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
66043 TAATAAAATT
* ** *
66053 AAAATTTAATATTATTTTATATTTA
1 AAAAATTAATATTAAATAATATTTA
66078 AAAAATTAATATTAAATAATATTTA
1 AAAAATTAATATTAAATAATATTTA
66103 AAAA
1 AAAA
66107 GAGGTGATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAAATTAATATTAAATAATATTTA
Found at i:66394 original size:21 final size:21
Alignment explanation
Indices: 66368--66550 Score: 106
Period size: 21 Copynumber: 9.1 Consensus size: 21
66358 GTTTCCAGAT
*
66368 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
66389 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
66410 TCGCAATGCG-A-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
66429 TCGCAATGCGAA-AT-GTA-AA
1 TCGCAATGCGAACTTCG-ACTA
* *
66448 TCGCAATGCGATA-GTCGGCTA
1 TCGCAATGCGA-ACTTCGACTA
* *
66469 TCGCAATGCGAA--TAGTA-AA
1 TCGCAATGCGAACTTCG-ACTA
**
66488 TCGCAATGCG-A-TAGGACTA
1 TCGCAATGCGAACTTCGACTA
*
66507 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
66528 TCGCAAAGCGAACTTCG-CTA
1 TCGCAATGCGAACTTCGACTA
66548 TCG
1 TCG
66551 TCGACTTCGC
Statistics
Matches: 135, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.01
19 55 0.41
20 14 0.10
21 64 0.47
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:66433 original size:40 final size:38
Alignment explanation
Indices: 66387--66538 Score: 144
Period size: 40 Copynumber: 3.8 Consensus size: 38
66377 GAACTTCGAC
* *
66387 TATCGCAATGCGAACTTGGACTATCGCAATGCGATATGTA
1 TATCGCAATGCGAA-TTGGA-AATCGCAATGCGATATGGA
* * * *
66427 AATCGCAATGCGAAATGTAAATCGCAATGCGATAGTCGGC
1 TATCGCAATGCGAATTGGAAATCGCAATGCGATA-T-GGA
* *
66467 TATCGCAATGCGAATAGTAAATCGCAATGCGATA-GGA
1 TATCGCAATGCGAATTGGAAATCGCAATGCGATATGGA
* *
66504 CTATCGCAATGCGAACTTGGACTATCGCAAAGCGA
1 -TATCGCAATGCGAA-TTGGA-AATCGCAATGCGA
66539 ACTTCGCTAT
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
37 2 0.02
38 28 0.30
39 7 0.08
40 56 0.60
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (38 bp):
TATCGCAATGCGAATTGGAAATCGCAATGCGATATGGA
Found at i:66457 original size:59 final size:59
Alignment explanation
Indices: 66388--66539 Score: 202
Period size: 59 Copynumber: 2.6 Consensus size: 59
66378 AACTTCGACT
*
66388 ATCGCAATGCGAACTTGGACTATCGCAATGCG-ATATGTAAATCGCAATGCGAAATGTA-A
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATA-GTAAATCGCAATGCGAAA-GGACA
* * * *
66447 ATCGCAATGCGATAGTCGG-CTATCGCAATGCGAATAGTAAATCGCAATGCGATAGGACT
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATAGTAAATCGCAATGCGAAAGGACA
*
66506 ATCGCAATGCGAACTTGGACTATCGCAAAGCGAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA
66540 CTTCGCTATC
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
58 6 0.07
59 68 0.84
60 7 0.09
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (59 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATAGTAAATCGCAATGCGAAAGGACA
Found at i:66509 original size:19 final size:19
Alignment explanation
Indices: 66384--66538 Score: 109
Period size: 19 Copynumber: 7.8 Consensus size: 19
66374 CGCGAACTTC
*
66384 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCG-A-TAG
66405 GACTATCGCAATGCGATATG
1 GACTATCGCAATGCGATA-G
* * *
66425 TA-AATCGCAATGCGAAATG
1 GACTATCGCAATGCGATA-G
* *
66444 TA-AATCGCAATGCGATAG
1 GACTATCGCAATGCGATAG
*
66462 TCGGCTATCGCAATGCGAATAG
1 --GACTATCGCAATGCG-ATAG
* *
66484 TA-AATCGCAATGCGATAG
1 GACTATCGCAATGCGATAG
*
66502 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCG-A-TAG
*
66523 GACTATCGCAAAGCGA
1 GACTATCGCAATGCGA
66539 ACTTCGCTAT
Statistics
Matches: 111, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.05
19 54 0.49
20 5 0.05
21 42 0.38
22 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (19 bp):
GACTATCGCAATGCGATAG
Found at i:67304 original size:21 final size:21
Alignment explanation
Indices: 67278--67444 Score: 173
Period size: 21 Copynumber: 7.8 Consensus size: 21
67268 ATTTCGGACT
67278 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
67299 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
67320 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
67341 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
67364 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
67385 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AACTTGGAATAA
67406 ATCGCAACGAACTTGGAAT-A
1 ATCGCAACGAACTTGGAATAA
67426 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
67445 CTATCGCAAT
Statistics
Matches: 123, Mismatches: 12, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
19 17 0.14
20 7 0.06
21 52 0.42
22 10 0.08
23 37 0.30
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:67336 original size:42 final size:42
Alignment explanation
Indices: 67274--67453 Score: 281
Period size: 42 Copynumber: 4.3 Consensus size: 42
67264 TGCGATTTCG
67274 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
67316 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
67358 GAATAAATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTC
1 GACT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
67402 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
67443 GACTATCGCAA
1 GACTATCGCAA
67454 TGCGAATATG
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
41 27 0.21
42 61 0.48
44 39 0.31
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:67423 original size:86 final size:85
Alignment explanation
Indices: 67278--67444 Score: 298
Period size: 86 Copynumber: 2.0 Consensus size: 85
67268 ATTTCGGACT
* *
67278 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACGAACTTGGAAT-AAT
67343 CGCAACGCGAACTTGGAATAA
65 CGCAACGCGAACTTGGAATAA
*
67364 ATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACGAACTTGGAATAATC
1 ATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACGAACTTGGAATAATC
67429 GCAACGCGAACTTGGA
66 GCAACGCGAACTTGGA
67445 CTATCGCAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 20 0.26
86 58 0.74
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (85 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACGAACTTGGAATAATC
GCAACGCGAACTTGGAATAA
Found at i:67548 original size:19 final size:19
Alignment explanation
Indices: 67526--67588 Score: 126
Period size: 19 Copynumber: 3.3 Consensus size: 19
67516 GCGATACGGA
67526 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
67545 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
67564 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
67583 GATCGC
1 GATCGC
67589 ATTGATTTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:68639 original size:23 final size:24
Alignment explanation
Indices: 68612--68664 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
68602 TCTACAAGGT
*
68612 TGTTGTCGTTGTTATTGTTTTGAC
1 TGTTGGCGTTGTTATTGTTTTGAC
*
68636 -GTTGGGGTTGTTATTGTTTTGAC
1 TGTTGGCGTTGTTATTGTTTTGAC
68659 TGTTGG
1 TGTTGG
68665 GGGTTGTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.08, C:0.06, G:0.32, T:0.55
Consensus pattern (24 bp):
TGTTGGCGTTGTTATTGTTTTGAC
Done.