Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003283.1 Hibiscus syriacus cultivar Beakdansim tig00006911_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: 75747
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2245 original size:32 final size:32
Alignment explanation
Indices: 2186--2280 Score: 136
Period size: 32 Copynumber: 3.0 Consensus size: 32
2176 ACCCATAGCC
* * *
2186 TACAATAATAAGCTACCCATGGTGGAAGGGCT
1 TACAGTAATAAGCTACCGATAGTGGAAGGGCT
* *
2218 TACAGTAGTAAGCTACCGATAGCGGAAGGGCT
1 TACAGTAATAAGCTACCGATAGTGGAAGGGCT
*
2250 TACGGTAATAAGCTACCGATAGTGGAAGGGC
1 TACAGTAATAAGCTACCGATAGTGGAAGGGC
2281 GAAAAGAGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (32 bp):
TACAGTAATAAGCTACCGATAGTGGAAGGGCT
Found at i:6420 original size:18 final size:17
Alignment explanation
Indices: 6389--6422 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6379 ATAATTCGAG
*
6389 TATTAAAATTAATATTT
1 TATTAAAATCAATATTT
6406 TATTAAAATACAATATT
1 TATTAAAAT-CAATATT
6423 AGATAAGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAAAATCAATATTT
Found at i:7495 original size:21 final size:21
Alignment explanation
Indices: 7466--7518 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
7456 ATTCTGACTA
7466 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
7487 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
7508 TCGCAATGCGA
1 TCGCATTGCGA
7519 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:7533 original size:20 final size:20
Alignment explanation
Indices: 7508--7633 Score: 193
Period size: 20 Copynumber: 6.3 Consensus size: 20
7498 TTTTCCTAAT
7508 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
7528 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
7548 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
7568 TCGCAATGCGAATACGAAAA
1 TCGCAATGCGAATACGTAAA
7588 TCGCAATGC-AATTACGTAAA
1 TCGCAATGCGAA-TACGTAAA
*
7608 TCGCAATACGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
7628 TCGCAA
1 TCGCAA
7634 CGAGATTCTG
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
19 3 0.03
20 93 0.95
21 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:10984 original size:20 final size:20
Alignment explanation
Indices: 10959--11047 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
10949 CAACGCGGAA
10959 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
10979 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
10999 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
11019 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
11039 ATCGCAACG
1 ATCGCAACG
11048 AAAGAATCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:11165 original size:19 final size:19
Alignment explanation
Indices: 11143--11209 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
11133 GCGAAATTAG
*
11143 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
11162 TTTCGCATTGCGA--TTCA
1 TTTCGCATTGCGATTTTCA
*
11179 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
11195 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
11210 CTCTCATTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 7 0.17
19 20 0.50
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:11190 original size:33 final size:33
Alignment explanation
Indices: 11148--11242 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
11138 ATTAGTTTCG
11148 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
11181 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
11214 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
11243 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 46 0.82
34 10 0.18
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:11363 original size:14 final size:14
Alignment explanation
Indices: 11344--11380 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11334 CATCAATTAA
11344 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
11358 ACAAATCATCTTTT
1 ACAAATCAACATTT
11372 ACAAATCAA
1 ACAAATCAA
11381 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:12770 original size:21 final size:21
Alignment explanation
Indices: 12741--12841 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
12731 GGGAAGGACT
* *
12741 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGATGACAGGGGCC
* ** *
12762 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGGGGCC
** *
12783 TCTTGAGGGATGATAGGGGCC
1 TCTTGAACGATGACAGGGGCC
**
12804 TCTTGAACGAT-AGGGGAGGCC
1 TCTTGAACGATGACAGG-GGCC
12825 TCTTGAACGATGACAGG
1 TCTTGAACGATGACAGG
12842 TGAGTCAGGT
Statistics
Matches: 60, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGACAGGGGCC
Found at i:12828 original size:42 final size:42
Alignment explanation
Indices: 12749--12841 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
12739 CTTCTTCAAC
* * *
12749 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
12791 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
12833 GATGACAGG
1 GATGACAGG
12842 TGAGTCAGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:13345 original size:20 final size:20
Alignment explanation
Indices: 13322--13410 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
13312 GAAACTTAAA
* *
13322 ATCGCAACGCGAAAATGATT
1 ATCGCAATGCGAAAATGACT
13342 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
13362 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
13382 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
13402 ATCGCAATG
1 ATCGCAATG
13411 AAAGAATCGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:13420 original size:34 final size:38
Alignment explanation
Indices: 13322--13429 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 38
13312 GAAACTTAAA
* *
13322 ATCGCAACGCGAAAATGATTATCGCAATGCGAAAATGACT
1 ATCGCAA-TCGAAAATGA-CATCGCAATGCGAAAATGACT
**
13362 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAAT-CGAAAATGAC-ATCGCAATGCGAAAATGACT
13402 ATCGCAAT-G-AAA-GA-ATCGCAATGCGAAA
1 ATCGCAATCGAAAATGACATCGCAATGCGAAA
13430 TGAAAATCTC
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
34 13 0.21
36 2 0.03
37 3 0.05
38 1 0.02
40 42 0.69
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (38 bp):
ATCGCAATCGAAAATGACATCGCAATGCGAAAATGACT
Found at i:13480 original size:20 final size:20
Alignment explanation
Indices: 13455--13578 Score: 152
Period size: 20 Copynumber: 6.5 Consensus size: 20
13445 TATTCTCTCG
** *
13455 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
13475 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
13495 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
13515 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
13529 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
13549 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
13569 TTGCGATAGT
1 TTGCGATAGT
13579 AAACTATTCT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 6 0.07
20 72 0.79
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:13537 original size:74 final size:74
Alignment explanation
Indices: 13439--13578 Score: 226
Period size: 74 Copynumber: 1.9 Consensus size: 74
13429 ATGAAAATCT
* *
13439 CATTGCTATTCTCTCGTTGCGATAGTCAAATTCGTATTGCGATAGTCATTTTCGCATTGCGATAG
1 CATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
13504 TCATTTTCG
66 TCATTTTCG
** * *
13513 CATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTTGCATTGCGATAG
1 CATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
13578 T
66 T
13579 AAACTATTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (74 bp):
CATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
TCATTTTCG
Found at i:13541 original size:34 final size:34
Alignment explanation
Indices: 13439--13555 Score: 126
Period size: 34 Copynumber: 3.3 Consensus size: 34
13429 ATGAAAATCT
* **
13439 CATTGCTATTCTCTCGTTGCGATAGTCAAATTCG
1 CATTGCGATTCTCTCGTTGCGATAGTCATTTTCG
* *
13473 TATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 CATTGCGAT--TC--TCTCG--TTGCGATAGTCATTTTCG
13513 CATTGCGATTCTCTCGTTGCGATAGTCATTTTCG
1 CATTGCGATTCTCTCGTTGCGATAGTCATTTTCG
*
13547 CGTTGCGAT
1 CATTGCGAT
13556 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
34 33 0.48
36 6 0.09
38 6 0.09
40 24 0.35
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (34 bp):
CATTGCGATTCTCTCGTTGCGATAGTCATTTTCG
Found at i:15509 original size:20 final size:20
Alignment explanation
Indices: 15462--15529 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
15452 AAAACTTTAA
**
15462 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
*
15482 ATTGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
15502 ATCACAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
15522 ATCGCAAC
1 ATCGCAAC
15530 GCAAGAATCG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:15600 original size:20 final size:20
Alignment explanation
Indices: 15575--15621 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
15565 GATTCTCTCG
15575 TTGCGATAATCAAATTCGCA
1 TTGCGATAATCAAATTCGCA
* ** *
15595 TTGCGATAGTCATTTTCGCG
1 TTGCGATAATCAAATTCGCA
15615 TTGCGAT
1 TTGCGAT
15622 TCACTCGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAATCAAATTCGCA
Found at i:16254 original size:21 final size:21
Alignment explanation
Indices: 16212--16263 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
16202 ATAGTCAGAT
*
16212 TCGCATTGCG-ATTTACGTAA
1 TCGCATTGCGAATTTACGAAA
**
16232 TCGCATTGCGAATTTGGGAAA
1 TCGCATTGCGAATTTACGAAA
*
16253 TCGCAATGCGA
1 TCGCATTGCGA
16264 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGAATTTACGAAA
Found at i:17129 original size:28 final size:27
Alignment explanation
Indices: 17098--17154 Score: 62
Period size: 28 Copynumber: 2.0 Consensus size: 27
17088 TCTACTATCA
*
17098 ATAT-TCTTATTATTTATATCTTATAATC
1 ATATCTCTTA-TATCTAT-TCTTATAATC
*
17126 ATATCCTCTTATATCTATTCTTTTAATC
1 ATAT-CTCTTATATCTATTCTTATAATC
17154 A
1 A
17155 ACATATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 14 0.56
29 6 0.24
30 5 0.20
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATCTCTTATATCTATTCTTATAATC
Found at i:17587 original size:31 final size:31
Alignment explanation
Indices: 17549--17643 Score: 129
Period size: 31 Copynumber: 3.0 Consensus size: 31
17539 GTATAATAAT
*
17549 CTGTCCATATATCCCGAAGAACATAGGTAAA
1 CTGTCCATATGTCCCGAAGAACATAGGTAAA
* *
17580 CTGTCCATATGTCCCGAAGAATATAGGTAATC
1 CTGTCCATATGTCCCGAAGAACATAGGTAA-A
*
17612 CTGTCCATATGTCCCGAA-AGACATATGTAAA
1 CTGTCCATATGTCCCGAAGA-ACATAGGTAAA
17643 C
1 C
17644 CCTCGACTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
31 30 0.54
32 26 0.46
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (31 bp):
CTGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:17621 original size:32 final size:31
Alignment explanation
Indices: 17545--17629 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
17535 TCTCGTATAA
*
17545 TAATCTGTCCATATATCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* *
17576 TAAACTGTCCATATGTCCCGAAGAATATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
17607 TAATCCTGTCCATATGTCCCGAA
1 TAAT-CTGTCCATATGTCCCGAA
17630 AGACATATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 31 0.63
32 18 0.37
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCCGAAGAACATAGG
Found at i:22123 original size:12 final size:12
Alignment explanation
Indices: 22108--22142 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
22098 ATATACGTAC
*
22108 ACAGATACAGAT
1 ACAGATACAAAT
22120 ACAGATACAAAT
1 ACAGATACAAAT
*
22132 ACATATACAAA
1 ACAGATACAAA
22143 AGAGTGTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (12 bp):
ACAGATACAAAT
Found at i:28072 original size:30 final size:30
Alignment explanation
Indices: 28036--28166 Score: 244
Period size: 30 Copynumber: 4.4 Consensus size: 30
28026 CGAAGGACCA
28036 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28066 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28096 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
28126 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
* *
28156 GTCCATAGGTC
1 ATCCAGAGGTC
28167 CCGAAGAACC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 99 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (30 bp):
ATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:28183 original size:60 final size:60
Alignment explanation
Indices: 28036--28191 Score: 231
Period size: 60 Copynumber: 2.6 Consensus size: 60
28026 CGAAGGACCA
*
28036 ATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
*
28096 ATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
* * * * * *
28156 GTCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 ATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
28192 TATGTTCCTT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
60 79 0.90
61 9 0.10
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (60 bp):
ATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:28272 original size:32 final size:32
Alignment explanation
Indices: 28153--28276 Score: 121
Period size: 31 Copynumber: 3.9 Consensus size: 32
28143 ATCCTCGGTA
* * * *
28153 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
28184 ACTATCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
28215 ACTTTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
28247 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAGAACATAGGTA
28277 TACCCTCAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
30 5 0.07
31 43 0.57
32 23 0.31
33 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:38336 original size:30 final size:30
Alignment explanation
Indices: 38300--38400 Score: 175
Period size: 30 Copynumber: 3.4 Consensus size: 30
38290 CGAAGGACCA
38300 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
38330 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
38360 ATCCAGAGGTCATAAAGATCCTCAGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
* *
38390 GTCCATAGGTC
1 ATCCAGAGGTC
38401 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
ATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:38417 original size:60 final size:61
Alignment explanation
Indices: 38300--38425 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 61
38290 CGAAGGACCA
* * * *
38300 ATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AACT
1 ATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAACT
* * * *
38360 ATCCAGAGGTCATAAAGATCCTCAGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACT
1 ATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAACT
38421 ATCCA
1 ATCCA
38426 TATGTTCCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 48 0.84
61 9 0.16
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (61 bp):
ATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAACT
Found at i:38506 original size:32 final size:32
Alignment explanation
Indices: 38387--38510 Score: 121
Period size: 31 Copynumber: 3.9 Consensus size: 32
38377 ATCCTCAGTA
* * * *
38387 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
38418 ACTATCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
38449 ACTTTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
38481 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAGAACATAGGTA
38511 TACCCTCAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
30 5 0.07
31 43 0.57
32 23 0.31
33 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:43261 original size:30 final size:30
Alignment explanation
Indices: 43225--43355 Score: 244
Period size: 30 Copynumber: 4.4 Consensus size: 30
43215 CGAAGGACCA
43225 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
43255 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
43285 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
43315 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
* *
43345 GTCCATAGGTC
1 ATCCAGAGGTC
43356 CCGAAGAACC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 99 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (30 bp):
ATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:43372 original size:60 final size:60
Alignment explanation
Indices: 43225--43380 Score: 231
Period size: 60 Copynumber: 2.6 Consensus size: 60
43215 CGAAGGACCA
*
43225 ATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
*
43285 ATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
* * * * * *
43345 GTCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 ATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
43381 TATGTTCCTT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
60 79 0.90
61 9 0.10
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (60 bp):
ATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:43457 original size:63 final size:62
Alignment explanation
Indices: 43338--43468 Score: 176
Period size: 63 Copynumber: 2.1 Consensus size: 62
43328 AAAGATCCTC
* *
43338 GGTA-ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTATCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATA
* * * *
43399 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGTATACTGTCCATAGGTCCCGAAGA-ACATAGGTAA-ACTATCCATATGTTCCGTAGAACATA
43462 GGTATAC
1 GGTATAC
43469 CCTCAACTCT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 5 0.08
62 26 0.43
63 30 0.49
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (62 bp):
GGTATACTGTCCATAGGTCCCGAAGAACATAGGTAAACTATCCATATGTTCCGTAGAACATA
Found at i:43461 original size:32 final size:32
Alignment explanation
Indices: 43342--43465 Score: 130
Period size: 31 Copynumber: 3.9 Consensus size: 32
43332 ATCCTCGGTA
* * * *
43342 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
43373 ACTATCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
43404 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
43436 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAGAACATAGGTA
43466 TACCCTCAAC
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 5 0.07
31 43 0.57
32 24 0.32
33 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:54111 original size:2 final size:2
Alignment explanation
Indices: 54104--54135 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54094 CTTTACATAC
54104 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
54136 GCCAAGTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57187 original size:76 final size:77
Alignment explanation
Indices: 57049--57197 Score: 228
Period size: 76 Copynumber: 1.9 Consensus size: 77
57039 TTTTAGTAAT
* * *
57049 TAATAATAGAAGAATGTGTGAAAACGTTGAGATGTTGTGTGATTTTCGTCGTACACCCGGATCTT
1 TAATAATAGAAGAATGTGTGAAAAAGTTGAGATGTTATGTGATTTTCGTCGCACACCCGGATCTT
57114 ATATAGATTAAC
66 ATATAGATTAAC
* * *
57126 TAATAATGGAA-AATGTGTGAAAAAGTTGAGATGTTATGTGCTTTTCGTTGCACACCCGGATCTT
1 TAATAATAGAAGAATGTGTGAAAAAGTTGAGATGTTATGTGATTTTCGTCGCACACCCGGATCTT
*
57190 CTATAGAT
66 ATATAGAT
57198 GAATTATGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 55 0.85
77 10 0.15
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (77 bp):
TAATAATAGAAGAATGTGTGAAAAAGTTGAGATGTTATGTGATTTTCGTCGCACACCCGGATCTT
ATATAGATTAAC
Found at i:67568 original size:63 final size:62
Alignment explanation
Indices: 67465--67597 Score: 221
Period size: 63 Copynumber: 2.1 Consensus size: 62
67455 AGACAAGGAC
67465 TCAGGCTGCTGGGGGTATGAGAGTCAGCATTATCAATATTGTTTTTCGACCTTGGTAAAGGT
1 TCAGGCTGCTGGGGGTATGAGAGTCAGCATTATCAATATTGTTTTTCGACCTTGGTAAAGGT
* * * *
67527 TCAGGCTGTTGGGGAGTATGAGATTCAGCGTTATCAGTATTGTTTTTCGACCTTGGTAAAGGT
1 TCAGGCTGCTGGGG-GTATGAGAGTCAGCATTATCAATATTGTTTTTCGACCTTGGTAAAGGT
67590 TCAGGCTG
1 TCAGGCTG
67598 GTGATACGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
62 13 0.20
63 53 0.80
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (62 bp):
TCAGGCTGCTGGGGGTATGAGAGTCAGCATTATCAATATTGTTTTTCGACCTTGGTAAAGGT
Found at i:71162 original size:21 final size:23
Alignment explanation
Indices: 71136--71183 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
71126 GTTCTATCTT
71136 ATTATTTTAATCAA-TTAA-ATA
1 ATTATTTTAATCAATTTAAGATA
* *
71157 ATTATTTTTATTAATTTAAGATA
1 ATTATTTTAATCAATTTAAGATA
71180 ATTA
1 ATTA
71184 CAAGATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTATTTTAATCAATTTAAGATA
Done.