Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002313.1 Hibiscus syriacus cultivar Beakdansim tig00004713_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: 66768
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:8047 original size:25 final size:26
Alignment explanation
Indices: 7990--8047 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
7980 GTCTAATAAT
*
7990 ATATATAAAACATCATTTAACAACTA
1 ATATATAAAACAACATTTAACAACTA
* * *
8016 ATGTATAAAATAACATTT-ATAACTA
1 ATATATAAAACAACATTTAACAACTA
*
8041 TTATATA
1 ATATATA
8048 GTAGTTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (26 bp):
ATATATAAAACAACATTTAACAACTA
Found at i:9426 original size:30 final size:30
Alignment explanation
Indices: 9369--9426 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
9359 ATTTACTCTA
* *
9369 TAACTTTTCAAAATTGTAAAATAGGTCCCC
1 TAACTTTTAAAAATTATAAAATAGGTCCCC
*
9399 TAACTTTTGAAAAATTATAGAAT-GGTCC
1 TAACTTTT-AAAAATTATAAAATAGGTCC
9427 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (30 bp):
TAACTTTTAAAAATTATAAAATAGGTCCCC
Found at i:11541 original size:59 final size:59
Alignment explanation
Indices: 11414--11533 Score: 163
Period size: 59 Copynumber: 2.0 Consensus size: 59
11404 GTAGATCTAA
* * * *
11414 CCCAAATATGACACATGAGGTCGTGCTCACCCTATGCACTAGTTATACTTTAGTACAAT
1 CCCAAATATGACACATAAGGTCATGCTCACCATATGCACTAGGTATACTTTAGTACAAT
*
11473 CCCAAATATGACACATAAGGTCATG-TCCACCATATGCACTAGGTAT-CATTTAGTGCAAT
1 CCCAAATATGACACATAAGGTCATGCT-CACCATATGCACTAGGTATAC-TTTAGTACAAT
11532 CC
1 CC
11534 TGAATATGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 2 0.04
59 52 0.96
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (59 bp):
CCCAAATATGACACATAAGGTCATGCTCACCATATGCACTAGGTATACTTTAGTACAAT
Found at i:17055 original size:27 final size:27
Alignment explanation
Indices: 17025--17090 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
17015 TATATCATTC
* *
17025 AAAATAACTTAAATTAAACATTTGTAT
1 AAAAAAACTTAAATCAAACATTTGTAT
*
17052 AAAAAAACTTAAATCAAATATTTGTAT
1 AAAAAAACTTAAATCAAACATTTGTAT
17079 AAAAAAACTTAA
1 AAAAAAACTTAA
17091 TACTTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAAAAACTTAAATCAAACATTTGTAT
Found at i:18818 original size:21 final size:21
Alignment explanation
Indices: 18773--18815 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
18763 AAAAGAAATC
*
18773 AAATAACATTTTTAAATCATT
1 AAATAACATATTTAAATCATT
18794 AAATAA-ATATTT-AATCATT
1 AAATAACATATTTAAATCATT
18813 AAA
1 AAA
18816 AATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 5 0.24
21 6 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAACATATTTAAATCATT
Found at i:23031 original size:24 final size:26
Alignment explanation
Indices: 22985--23035 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
22975 GCTTAAGTAT
*
22985 AAAGAAGAGGTAAGAAATGAAATGAAA
1 AAAGAAGAGGTAAAAAATGAAAT-AAA
23012 AAAGAA-A-GTAAAAAAT-AAATAAA
1 AAAGAAGAGGTAAAAAATGAAATAAA
23035 A
1 A
23036 GGGTGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 8 0.35
26 1 0.04
27 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (26 bp):
AAAGAAGAGGTAAAAAATGAAATAAA
Found at i:25220 original size:24 final size:24
Alignment explanation
Indices: 25188--25235 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
25178 TGTTTTAGTG
25188 ATCCAATCACACCATAAATAAAAT
1 ATCCAATCACACCATAAATAAAAT
25212 ATCCAATCACACCATAAATAAAAT
1 ATCCAATCACACCATAAATAAAAT
25236 TTGGTGGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (24 bp):
ATCCAATCACACCATAAATAAAAT
Found at i:30389 original size:21 final size:21
Alignment explanation
Indices: 30363--30613 Score: 189
Period size: 21 Copynumber: 11.9 Consensus size: 21
30353 CATATAAATT
* *
30363 TGTCCCGAATGACCTCATATA
1 TGTCCCGAAGGACCACATATA
* *
30384 TGTCCCGAAAGACCATATATA
1 TGTCCCGAAGGACCACATATA
*
30405 TGTCCCGAAGGACCATATATAA
1 TGTCCCGAAGGACCACATAT-A
* *
30427 TTGTCCCTAAGGACCACAAATA
1 -TGTCCCGAAGGACCACATATA
** * * *
30449 TGTTACAAAGAACCAAATATA
1 TGTCCCGAAGGACCACATATA
* *
30470 TGTCCCGAATGACCTCATATA
1 TGTCCCGAAGGACCACATATA
* * * *
30491 TATTCCAAAGGATCACATAT-
1 TGTCCCGAAGGACCACATATA
* * * *
30511 TGTCCTGAAGGATCGCAAATA
1 TGTCCCGAAGGACCACATATA
** * *
30532 TGTTACAAAGGACCAAATATA
1 TGTCCCGAAGGACCACATATA
* *
30553 TGTCCCAAAGGACCTCATATA
1 TGTCCCGAAGGACCACATATA
* * * *
30574 TGTTCCAAACGATCACATATA
1 TGTCCCGAAGGACCACATATA
30595 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
30614 GAACCTTAGA
Statistics
Matches: 175, Mismatches: 52, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
20 14 0.08
21 142 0.81
22 2 0.01
23 17 0.10
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:30538 original size:83 final size:83
Alignment explanation
Indices: 30426--30611 Score: 275
Period size: 83 Copynumber: 2.2 Consensus size: 83
30416 ACCATATATA
* *
30426 ATTGTCCCT-AAGGACCACAAATATGTTACAAAGAACCAAATATATGTCCCGAATGACCTCATAT
1 ATTGT-CCTGAAGGACCACAAATATGTTACAAAGAACCAAATATATGTCCCAAAGGACCTCATAT
*
30490 ATATTCCAAAGGATCACAT
65 ATATTCCAAACGATCACAT
* * *
30509 ATTGTCCTGAAGGATCGCAAATATGTTACAAAGGACCAAATATATGTCCCAAAGGACCTCATATA
1 ATTGTCCTGAAGGACCACAAATATGTTACAAAGAACCAAATATATGTCCCAAAGGACCTCATATA
*
30574 TGTTCCAAACGATCACAT
66 TATTCCAAACGATCACAT
*
30592 ATATGTCCCGAAGGACCACA
1 AT-TGTCCTGAAGGACCACA
30612 TAGAACCTTA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
82 3 0.03
83 74 0.81
84 14 0.15
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (83 bp):
ATTGTCCTGAAGGACCACAAATATGTTACAAAGAACCAAATATATGTCCCAAAGGACCTCATATA
TATTCCAAACGATCACAT
Found at i:33349 original size:37 final size:35
Alignment explanation
Indices: 33256--33499 Score: 168
Period size: 37 Copynumber: 7.0 Consensus size: 35
33246 AAAAACACAC
* *
33256 ATATAATATATAGTTTTGAAAATATGTTTGAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTTTTG-AAA-A--T
* *
33295 ATATATTATATAGTTTTTAAAACATTTTTGAAAAT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* *
33330 AAATATAATATATATTTTTTAAAACATTTTTGAAAAT
1 --ATATAATATATAGTTTTGAAAACATTTTTGAAAAT
33367 ATAT-ATATATA-TTTTGAAAACA-TTTTG-----
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAAT
** * **
33394 -TA-AATATATAGTTTAAAAAATATTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAA-AT
* *
33428 ATATATATTATATAATTTTGAAATCA-TTTTGAAAAATT
1 ATATA-A-TATATAGTTTTGAAAACATTTTTG-AAAA-T
* * *
33466 ATATAGTATATAGTTTTAAAAATATTTTTGAAAA
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAA
33500 CATTTTTTAA
Statistics
Matches: 163, Mismatches: 24, Indels: 39
0.72 0.11 0.17
Matches are distributed among these distances:
26 9 0.06
27 8 0.05
28 3 0.02
32 5 0.03
33 10 0.06
34 7 0.04
35 7 0.04
36 19 0.12
37 44 0.27
38 25 0.15
39 26 0.16
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATAATATATAGTTTTGAAAACATTTTTGAAAAT
Found at i:33383 original size:58 final size:59
Alignment explanation
Indices: 33320--33435 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 59
33310 TTTAAAACAT
* ** * *
33320 TTTTGAAAATA-AATATAATATATATTTTTTAAAACAT-TTTTGAAAATATATATATATA
1 TTTTGAAAACATAATATAA-ATATATAGTTTAAAAAATATTTTGAAAACATATATATATA
** *
33378 TTTTGAAAACATTTTGTAAATATATAGTTTAAAAAATATTTTGAAAACATATATATAT
1 TTTTGAAAACATAATATAAATATATAGTTTAAAAAATATTTTGAAAACATATATATAT
33436 TATATAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 25 0.52
59 23 0.48
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (59 bp):
TTTTGAAAACATAATATAAATATATAGTTTAAAAAATATTTTGAAAACATATATATATA
Found at i:33417 original size:38 final size:37
Alignment explanation
Indices: 33375--33517 Score: 130
Period size: 38 Copynumber: 3.8 Consensus size: 37
33365 ATATATATAT
* *
33375 ATATTTTGAAAACATTTTGTAAATATATAGTTTAAAAA
1 ATATTTTGAAAACATTATATAAATATATAGTTT-AAAA
* * **
33413 ATATTTTGAAAACA-TATATATATTATATAATTTTGAA
1 ATATTTTGAAAACATTATATA-AATATATAGTTTAAAA
*
33450 ATCATTTTGAAAA-ATTATAT-AGTATATAGTTTTAAAA
1 AT-ATTTTGAAAACATTATATAAATATATAG-TTTAAAA
* *
33487 ATATTTTTGAAAACATTTTTTAAAATATATA
1 ATA-TTTTGAAAACATTATAT-AAATATATA
33518 ATATATAATT
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
36 8 0.10
37 25 0.30
38 44 0.52
40 7 0.08
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATTTTGAAAACATTATATAAATATATAGTTTAAAA
Found at i:33493 original size:47 final size:46
Alignment explanation
Indices: 33443--33545 Score: 134
Period size: 46 Copynumber: 2.2 Consensus size: 46
33433 TATTATATAA
* * * *
33443 TTTTGAAATCATTTTGAAAAATTATATAGTATATAGTTTTAAAAATAT
1 TTTTGAAAACATTTTGAAAAA-TATATAATATATA-ATTTAAAAATAC
**
33491 TTTTGAAAACATTTTTTAAAATATATAATATATAATTTAAAAATAC
1 TTTTGAAAACATTTTGAAAAATATATAATATATAATTTAAAAATAC
33537 TTTTGAAAA
1 TTTTGAAAA
33546 TATATATTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 19 0.39
47 12 0.24
48 18 0.37
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (46 bp):
TTTTGAAAACATTTTGAAAAATATATAATATATAATTTAAAAATAC
Found at i:33563 original size:25 final size:27
Alignment explanation
Indices: 33535--33585 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
33525 ATTTAAAAAT
33535 ACTTTT-GAAAATATATAT-TATATAG
1 ACTTTTGGAAAATATATATATATATAG
*
33560 ACTTTTGGAAAGTATATATATATATA
1 ACTTTTGGAAAATATATATATATATA
33586 TATATTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 11 0.48
27 6 0.26
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (27 bp):
ACTTTTGGAAAATATATATATATATAG
Found at i:39116 original size:43 final size:43
Alignment explanation
Indices: 39065--39220 Score: 136
Period size: 43 Copynumber: 3.4 Consensus size: 43
39055 TAGAGCCAAT
39065 TTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACACAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCAGACAACACAAG
** * * * *
39108 TTCAACTTCACGACGAGAGGACCGTTGG-TTGCCAATAAACAATTTCCCAAT
1 TTCAACTTCACGACGA-AGGA-TATTGGACT-CC---AGACAA---CACAAG
* *
39159 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACACAAG
39202 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
39221 GACCGCTGGT
Statistics
Matches: 88, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
43 36 0.41
44 6 0.07
45 6 0.07
46 5 0.06
48 5 0.06
49 6 0.07
50 5 0.06
51 19 0.22
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACACAAG
Found at i:40249 original size:106 final size:105
Alignment explanation
Indices: 39154--40248 Score: 1564
Period size: 106 Copynumber: 10.3 Consensus size: 105
39144 AAACAATTTC
39154 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
39219 GGGACCGCTGGTTGTCAATAAACAATTTTCCAA-TTCTATAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC-AGAG
* * * * *
39260 TCAATTTCAACTTCACAGCAAATGATAGTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
39325 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
* *
39366 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGGA
1 CCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
39431 GGGACCGCTAGTTGTCAATAAACAATTTTCCAA-TTCTAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC-AGAG
* * *
39472 TCAATTTCAACTTCACAGCGAAGGATAGTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
39537 GGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
* * *
39578 CCAATTTCAACTTCACAAGGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTTACGACGAA
1 CCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
39643 GGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAAAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
* *
39684 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
39749 GGGACCACTGGTTCTCAACAAACAACTTCTCAATTTCAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
39790 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
39855 GGGACCGCTGGTTGTCAATAAATAACTTCTCAATTTCAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
* *
39896 CCAATTTCAACTTCACAACGAAAGATATTGAACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
39961 GGGACCGCTGGTTGTAAATAAACAATTTCCCAATTTCAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
*
40002 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
** *
40067 GGGACCGCTGGTTGTCAGCAAACAATTTCCCAATTTCAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
* * * *
40108 CCAATTTCAACCTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * * * ** *
40173 GGTACGGTTGGTTGTCAACAAACAATTTCCCGGTTCCAGAG
65 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
* *
40214 CCACTTTCAACTTCACGACGGAGGATATTGGACTC
1 CCAATTTCAACTTCAC-ACGAAGGATATTGGACTC
40249 GGAACAATGC
Statistics
Matches: 892, Mismatches: 86, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
105 7 0.01
106 875 0.98
107 10 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CCAATTTCAACTTCACACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
Found at i:40258 original size:212 final size:212
Alignment explanation
Indices: 39045--40248 Score: 1758
Period size: 212 Copynumber: 5.7 Consensus size: 212
39035 ACGAAGGGGC
39045 TTCCCAA-TTCTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGT
1 TTCCCAATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGT
*
39109 TCAACTTCACGACG-AGAGGACCGTTGGTTG-C--CAATA-AA-----CAATTTC----CCAATT
65 TCAACTTCACGACGAAG-GGACCGCTGGTTGTCAACAA-ACAACTTCTCAATTTCAGAGCCAATT
*
39160 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
128 TCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACC
39225 GCTGGTTGTCAATAAACAAT
193 GCTGGTTGTCAATAAACAAT
* * * * * *
39245 TTTCCAA-TTCTATAGTCAATTTCAACTTCACAGCAAATGATAGTGGACTCCAGACAACACAAGT
1 TTCCCAATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGT
*
39309 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTC
65 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTC
*
39374 AACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGGAGGGACCGC
130 AACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGC
*
39439 TAGTTGTCAATAAACAAT
195 TGGTTGTCAATAAACAAT
* * *
39457 TTTCCAA-TTCTAGAGTCAATTTCAACTTCACAGCGAAGGATAGTGGACTCCAGACAACACAAGT
1 TTCCCAATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGT
*
39521 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTC
65 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTC
* * *
39586 AACTTCACAAGGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTTACGACGAAGGGACCGT
130 AACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGC
*
39651 TGGTTGTCAATAAACAAC
195 TGGTTGTCAATAAACAAT
* ** *
39669 TTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
* *
39734 CAACTTCACGACGAAGGGACCACTGGTTCTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCA
*
39799 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
131 ACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCT
* *
39864 GGTTGTCAATAAATAAC
196 GGTTGTCAATAAACAAT
* * * * *
39881 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGAACTCCAGACAACGCAAGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
* * * *
39946 CAACTTCACGACGAAGGGACCGCTGGTTGTAAATAAACAATTTCCCAATTTCAGAGCCAATTTCA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCA
*
40011 ACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCT
131 ACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCT
**
40076 GGTTGTCAGCAAACAAT
196 GGTTGTCAATAAACAAT
* *
40093 TTCCCAATTTCAGAGCCAATTTCAACCTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
* * * * * * ** * *
40158 CAACTTCACAACGAAGGTACGGTTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCACTTTCA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCA
* *
40223 ACTTCACGACGGAGGATATTGGACTC
131 ACTTCACAACGAAGGATATTGGACTC
40249 GGAACAATGC
Statistics
Matches: 913, Mismatches: 76, Indels: 18
0.91 0.08 0.02
Matches are distributed among these distances:
200 84 0.09
201 3 0.00
202 1 0.00
203 4 0.00
208 7 0.01
212 811 0.89
213 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (212 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTT
CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCA
ACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCT
GGTTGTCAATAAACAAT
Found at i:40971 original size:37 final size:37
Alignment explanation
Indices: 40855--41104 Score: 200
Period size: 36 Copynumber: 6.9 Consensus size: 37
40845 AAAAACACAC
* * * *
40855 ATATAATATATAGTTTTGAAAATATGTTTGAAAACATTT
1 ATATAATATATAGTTTTTAAAACATTTTTG-AAA-ATAT
* *
40894 ATATATTATATAGTTTTTAAAACA-TTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATAT
*
40930 ATATAATATATATTTTTTAAAACATTTTTGAAAATAT
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATAT
*
40967 ATATATTATATA-TTTTTAAAAC-TTTTTG----TA-
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATAT
* * *
40997 A-AT-ATATATTGTTTTAAAAAAATATTTTGAAAACATAT
1 ATATAATATATAGTTTTTAAAACAT-TTTTG-AAA-ATAT
* * * *
41035 ATATATTATATAATTTTGAAATCA-TTTTGAAAA-ATT
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATA-T
* * *
41071 ATATAGTATATAGTTTTAAAAATATTTTTGAAAA
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAA
41105 CATTTTTTAA
Statistics
Matches: 171, Mismatches: 25, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
28 5 0.03
29 10 0.06
30 2 0.01
31 7 0.04
35 7 0.04
36 55 0.32
37 39 0.23
38 10 0.06
39 23 0.13
40 13 0.08
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (37 bp):
ATATAATATATAGTTTTTAAAACATTTTTGAAAATAT
Found at i:41098 original size:47 final size:46
Alignment explanation
Indices: 41048--41140 Score: 123
Period size: 48 Copynumber: 2.0 Consensus size: 46
41038 TATTATATAA
* * *
41048 TTTTGAAATCATTTTGAAAAATTATATAGTATATAGTTTTAAAAATAT
1 TTTTGAAAACATTTTGAAAAA-TATATAATATATA-ATTTAAAAATAT
**
41096 TTTTGAAAACATTTTTTAAAATATATAATATATAATTTAAAAATA
1 TTTTGAAAACATTTTGAAAAATATATAATATATAATTTAAAAATA
41141 CCCATCGACT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 10 0.25
47 12 0.30
48 18 0.45
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (46 bp):
TTTTGAAAACATTTTGAAAAATATATAATATATAATTTAAAAATAT
Found at i:46406 original size:2 final size:2
Alignment explanation
Indices: 46399--46453 Score: 101
Period size: 2 Copynumber: 27.0 Consensus size: 2
46389 CGTAACAATG
46399 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
46441 AT AT AT AT GAT AT
1 AT AT AT AT -AT AT
46454 GTTTGTTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53207 original size:24 final size:24
Alignment explanation
Indices: 53180--53237 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
53170 TAGAACTCTG
*
53180 ATCAATCAATACCAAAACACATTT
1 ATCATTCAATACCAAAACACATTT
*
53204 ATCATTCAATACCAAAACATATTT
1 ATCATTCAATACCAAAACACATTT
53228 ATCATTCAAT
1 ATCATTCAAT
53238 TGGAAAGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (24 bp):
ATCATTCAATACCAAAACACATTT
Found at i:55182 original size:23 final size:22
Alignment explanation
Indices: 55139--55212 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 22
55129 AAATGCAATC
55139 ATAACCATCATATAACGATTCATCT
1 ATAA-CAT-ATATAAC-ATTCATCT
55164 ATAACATATATGAACATTCAT-T
1 ATAACATATAT-AACATTCATCT
55186 ATCAA-ATA-ATAACATGTCATCTT
1 AT-AACATATATAACAT-TCATC-T
55209 ATAA
1 ATAA
55213 GTAAGTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.11
21 6 0.14
22 8 0.18
23 15 0.34
24 6 0.14
25 4 0.09
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (22 bp):
ATAACATATATAACATTCATCT
Found at i:55381 original size:21 final size:20
Alignment explanation
Indices: 55357--55514 Score: 109
Period size: 21 Copynumber: 7.5 Consensus size: 20
55347 TGTCCCGAAT
*
55357 GACCTCATATATGTCTAGAAG
1 GACCACATATATGTCTA-AAG
*
55378 GACCACATATATGTCCCAAAG
1 GACCACATATATGT-CTAAAG
*
55399 GACCACATATAATTGTCCTTAAG
1 GACCACATAT-A-TGT-CTAAAG
* * *
55422 GACCACGTATATGTTCCAAAA
1 GACCACATATATG-TCTAAAG
* **
55443 GACCAAATATATGTTCGGAAG
1 GACCACATATATG-TCTAAAG
* *
55464 GACCTCATATATGTTTCAAAG
1 GACCACATATATGTCT-AAAG
* *
55485 GATCACATATATGTCCTGAAG
1 GACCACATATATGT-CTAAAG
*
55506 GACAACATA
1 GACCACATA
55515 GAACCCTCGA
Statistics
Matches: 107, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.01
21 83 0.78
22 6 0.06
23 17 0.16
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (20 bp):
GACCACATATATGTCTAAAG
Found at i:55433 original size:44 final size:42
Alignment explanation
Indices: 55357--55514 Score: 174
Period size: 42 Copynumber: 3.7 Consensus size: 42
55347 TGTCCCGAAT
* *
55357 GACCTCATATATGT-CTAGAAGGACCACATATATGTCCCAAAG
1 GACCACATATATGTCCT-GAAGGACCACATATATGTTCCAAAG
* * *
55399 GACCACATATAATTGTCCTTAAGGACCACGTATATGTTCCAAAA
1 GACCACATAT-A-TGTCCTGAAGGACCACATATATGTTCCAAAG
* * * * *
55443 GACCAAATATATGTTCGGAAGGACCTCATATATGTTTCAAAG
1 GACCACATATATGTCCTGAAGGACCACATATATGTTCCAAAG
* *
55485 GATCACATATATGTCCTGAAGGACAACATA
1 GACCACATATATGTCCTGAAGGACCACATA
55515 GAACCCTCGA
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 57 0.61
43 2 0.02
44 33 0.35
45 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (42 bp):
GACCACATATATGTCCTGAAGGACCACATATATGTTCCAAAG
Done.