Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005405.1 Hibiscus syriacus cultivar Beakdansim tig00012395_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: 51024
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:348 original size:22 final size:21
Alignment explanation
Indices: 305--348 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
295 TCTATGTTAT
* *
305 AATTATTATATCCCTTTGATA
1 AATTATTAAATCCCTTTCATA
*
326 AATTATTAAACTCGCTTTCATA
1 AATTATTAAA-TCCCTTTCATA
348 A
1 A
349 TTCCTGTGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (21 bp):
AATTATTAAATCCCTTTCATA
Found at i:350 original size:21 final size:20
Alignment explanation
Indices: 303--350 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
293 CATCTATGTT
* *
303 ATAATTATTATATCCCTTTG
1 ATAATTATTAAATCCCTTTC
*
323 ATAAATTATTAAACTCGCTTTC
1 AT-AATTATTAAA-TCCCTTTC
345 ATAATT
1 ATAATT
351 CCTGTGGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (20 bp):
ATAATTATTAAATCCCTTTC
Found at i:9070 original size:85 final size:85
Alignment explanation
Indices: 8839--9477 Score: 724
Period size: 85 Copynumber: 7.5 Consensus size: 85
8829 TCCTAACCTA
* * * * *
8839 TTATAGTATAGCTCAGGGCGAGAAGGGCTATCTGTCAACAAAATACCTTCGAGTTCGATTGCATT
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATT
* * * *
8904 TAGCTCAAATGTACATCAAAT
65 CAGCTCAAAGGCATATCAAAT
* ** * * *
8925 TTACAATATAGCTCAAGGCAAGAAGGGCTATCTATCAACAAAAGACCTTCGAGTTCGATTACATT
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATT
* *
8990 CAGCTCTAAGGCACATCAAAT
65 CAGCTCAAAGGCATATCAAAT
*
9011 TTATAGTATAGCTCAAGGCGA-AAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATT
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATT
*
9075 TAGCTCAAAGGCATATCAAAT
65 CAGCTCAAAGGCATATCAAAT
* * *
9096 TTATAGCATAACTCAAGGCGAGAATGGTTATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTC
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
*
9161 AGGTCAAAGGCATATCAAAT
66 AGCTCAAAGGCATATCAAAT
* * * * *
9181 TTACAGCATAGCTCAAGGCGAGAAGGGTTATTTGTTAACCAAGACCTTTGAGTTCGATTACATTC
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
* *
9246 AGCTTAAAGGCATGTCAAAT
66 AGCTCAAAGGCATATCAAAT
* * * * *
9266 TTATAGCATAACTCAAGGTGAGGAGGGTTATCTGTCAATAAAGACCTTCGAATTCGATTACATTC
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
*
9331 AGCTCAAAGGAATAT-AATAT
66 AGCTCAAAGGCATATCAA-AT
* * ** * * * * *
9351 TTACAACATAGCTCAAGGTTAGAAGGGCTATCTGCCAACAAATACCTTCAAGTTCGATTCCATTC
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
* * * *
9416 AGCTCGAGGGCATGTCATAT
66 AGCTCAAAGGCATATCAAAT
* * * * ** *
9436 TTACAGCATAGCTTAAGTCAAGAAAAGTTATTTGTCAACAAA
1 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAA
9478 AATTGTGGAG
Statistics
Matches: 474, Mismatches: 76, Indels: 7
0.85 0.14 0.01
Matches are distributed among these distances:
84 2 0.00
85 363 0.77
86 109 0.23
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (85 bp):
TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
AGCTCAAAGGCATATCAAAT
Found at i:10253 original size:2 final size:2
Alignment explanation
Indices: 10248--10284 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
10238 ATTTTTTTAT
*
10248 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10285 ATTTACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10311 original size:36 final size:35
Alignment explanation
Indices: 10269--10356 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 35
10259 ATATATATGT
*
10269 ATATATATATATTATAATTTACAAATTATTTTTGAA
1 ATATATATATATTATAATTT-CAAACTATTTTTGAA
* *
10305 ATATATATATAATATATAGTTTTAAACTATTTTTGAA
1 ATATATATAT-AT-TATAATTTCAAACTATTTTTGAA
*
10342 A-ATGTATATATTATA
1 ATATATATATATTATA
10357 TAGTTTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 4 0.09
35 2 0.04
36 17 0.37
37 16 0.35
38 7 0.15
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (35 bp):
ATATATATATATTATAATTTCAAACTATTTTTGAA
Found at i:10350 original size:38 final size:37
Alignment explanation
Indices: 10298--10612 Score: 236
Period size: 35 Copynumber: 8.6 Consensus size: 37
10288 TACAAATTAT
*
10298 TTTTGAAATATATATATAATATATAGTTTT-AAACTA
1 TTTTGAAAAATATATATAATATATAGTTTTAAAACTA
* *
10334 TTTTTG-AAAATGTATATATTATATAGTTTTTGAAAAC-A
1 -TTTTGAAAAATATATATAATATATAG-TTTT-AAAACTA
10372 TTTTG---AATATATATAATATATAGTTTTGAAAA-TA
1 TTTTGAAAAATATATATAATATATAGTTTT-AAAACTA
*
10406 TTTT-AAAAACT-TATAT-ATATATAGTTTTGAAA-TCA
1 TTTTGAAAAA-TATATATAATATATAGTTTTAAAACT-A
* *
10441 TTTTGAAAAAACATATATAATATATAAGTTTT-GAAC-A
1 TTTTG-AAAAATATATATAATATAT-AGTTTTAAAACTA
* * * *
10478 TTTTGAAAACT-TGTATAATATATGGTTTTTAAAAACCA
1 TTTTGAAAAATATATATAATATATAG-TTTT-AAAACTA
*
10516 TTTTGAAAACT-TATAT-A-ATATAGTTTTTAAAAC-A
1 TTTTGAAAAATATATATAATATATAG-TTTTAAAACTA
*
10550 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAATA
1 TTTTGAAAA-ATATATATAATATATAG-TTTT-AAAACTA
**
10590 TTTTTTTAAAA-ATATATAATATA
1 -TTTTGAAAAATATATATAATATA
10613 CAATTTTTGA
Statistics
Matches: 233, Mismatches: 19, Indels: 50
0.77 0.06 0.17
Matches are distributed among these distances:
34 29 0.12
35 54 0.23
36 43 0.18
37 36 0.15
38 36 0.15
39 26 0.11
40 2 0.01
41 7 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAAATATATATAATATATAGTTTTAAAACTA
Found at i:10457 original size:73 final size:74
Alignment explanation
Indices: 10298--10612 Score: 298
Period size: 71 Copynumber: 4.3 Consensus size: 74
10288 TACAAATTAT
* * *
10298 TTTTGAAATATATATATAATATATAGTTTT--AAACTATTTTTGAAAA-TGTATATATTATATAG
1 TTTTGAAA-ACATATATAATATATAGTTTTGAAAAC-A-TTTTGAAAACTATATATAATATATAG
10360 TTTTTGAAAACA
63 TTTTTGAAAACA
* * *
10372 TTTTG--AATATATATAATATATAGTTTTGAAAATATTTTAAAAACT-TATAT-ATATATAG-TT
1 TTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAACTATATATAATATATAGTTT
*
10432 TTGAAATCA
66 TTGAAAACA
* *
10441 TTTTGAAAAAACATATATAATATATAAGTTTTG--AACATTTTGAAAACT-TGTATAATATATGG
1 TTTTG--AAAACATATATAATATAT-AGTTTTGAAAACATTTTGAAAACTATATATAATATATAG
*
10503 TTTTTAAAAACCA
63 TTTTTGAAAA-CA
* *
10516 TTTTGAAAACTTATAT-A-ATATAGTTTTTAAAACATTTTGAAAACATATATATAATATATAGTT
1 TTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAAC-TATATATAATATATAGTT
* *
10579 TTTAAAAAATA
65 TTT-GAAAACA
*
10590 TTTTTTTAAAA-ATATATAATATA
1 --TTTTGAAAACATATATAATATA
10613 CAATTTTTGA
Statistics
Matches: 203, Mismatches: 18, Indels: 37
0.79 0.07 0.14
Matches are distributed among these distances:
69 15 0.07
70 13 0.06
71 38 0.19
72 35 0.17
73 36 0.18
74 37 0.18
75 17 0.08
76 9 0.04
77 3 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (74 bp):
TTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAACTATATATAATATATAGTTT
TTGAAAACA
Found at i:10647 original size:41 final size:40
Alignment explanation
Indices: 10555--10646 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
10545 AAACATTTTG
* * *
10555 AAAACATATATATAATATATAGTTTTTAAAAAATATTTTTT
1 AAAA-ATATATATAATATACAATTTTTAAAAAATATTCTTT
* *
10596 TAAAA-ATATATAATATACAATTTTTGAAAAATA-TCTTT
1 AAAAATATATATAATATACAATTTTTAAAAAATATTCTTT
*
10634 AAATATATATATA
1 AAAAATATATATA
10647 TAATTTGAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 7 0.16
39 32 0.74
40 1 0.02
41 3 0.07
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (40 bp):
AAAAATATATATAATATACAATTTTTAAAAAATATTCTTT
Found at i:11152 original size:18 final size:18
Alignment explanation
Indices: 11129--11170 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
11119 AAAAACACAA
*
11129 GATCGAACCCACATCAAC
1 GATCGAAACCACATCAAC
*
11147 GATCGAAACCACATCAAT
1 GATCGAAACCACATCAAC
11165 GATCGA
1 GATCGA
11171 GAAAACAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.31, G:0.14, T:0.14
Consensus pattern (18 bp):
GATCGAAACCACATCAAC
Found at i:12013 original size:14 final size:14
Alignment explanation
Indices: 11968--12018 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
11958 TTTATTTATC
*
11968 TTTTTTCATTACTA
1 TTTTTTCATTAATA
*
11982 TTATTAT-ATTAATA
1 TT-TTTTCATTAATA
*
11996 -TTTTTCATTATTA
1 TTTTTTCATTAATA
12009 TTTTTTCATT
1 TTTTTTCATT
12019 TTTACAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 17 0.57
15 3 0.10
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTCATTAATA
Found at i:14258 original size:15 final size:16
Alignment explanation
Indices: 14238--14274 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
14228 TATGAGTTTT
14238 TTTTAAAGTATA-TAA
1 TTTTAAAGTATATTAA
*
14253 TTTT-AAGTTTATTAA
1 TTTTAAAGTATATTAA
14268 TTTTAAA
1 TTTTAAA
14275 TAAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 11 0.58
16 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TTTTAAAGTATATTAA
Found at i:15282 original size:15 final size:12
Alignment explanation
Indices: 15251--15275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15241 TTCGGTAAAA
15251 AAATAATATTTT
1 AAATAATATTTT
15263 AAATAATATTTT
1 AAATAATATTTT
15275 A
1 A
15276 CCGAATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:15372 original size:42 final size:42
Alignment explanation
Indices: 15326--15421 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
15316 TATTCTCAGT
15326 AAAAATAATAATATTTTAAATAATATTTTACTAAAAATATTA
1 AAAAATAATAATATTTTAAATAATATTTTACTAAAAATATTA
*
15368 AAAAATAATAATATTTTATATAATATTTTACTAAAAATATTA
1 AAAAATAATAATATTTTAAATAATATTTTACTAAAAATATTA
15410 AAAAATAATAAT
1 AAAAATAATAAT
15422 TTCAATAACA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (42 bp):
AAAAATAATAATATTTTAAATAATATTTTACTAAAAATATTA
Found at i:16089 original size:11 final size:11
Alignment explanation
Indices: 16070--16132 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
16060 TAAATTACAT
16070 TATTAAAAATA
1 TATTAAAAATA
*
16081 TATTTAAAATA
1 TATTAAAAATA
* ***
16092 TACTATTGATA
1 TATTAAAAATA
16103 -ATTATAAAAT-
1 TATTA-AAAATA
16113 T-TTAAAAATA
1 TATTAAAAATA
16123 TATTAAAAAT
1 TATTAAAAAT
16133 TCTATAATAC
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 26 0.68
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:16671 original size:7 final size:7
Alignment explanation
Indices: 16659--16784 Score: 51
Period size: 7 Copynumber: 18.0 Consensus size: 7
16649 TTTAAAACCA
16659 AAACCCT
1 AAACCCT
16666 AAACCCT
1 AAACCCT
* *
16673 TAACCAT
1 AAACCCT
*
16680 -AATCCT
1 AAACCCT
* *
16686 TAACCTAT
1 AAACC-CT
*
16694 AAATCCT
1 AAACCCT
16701 AAACCCT
1 AAACCCT
**
16708 AAA-TAT
1 AAACCCT
*
16714 CAATCCCT
1 -AAACCCT
* *
16722 AATCCTT
1 AAACCCT
*
16729 AATC-CT
1 AAACCCT
*
16735 AAACACT
1 AAACCCT
16742 AAACCCCT
1 AAA-CCCT
*
16750 AAACCAT
1 AAACCCT
**
16757 AAACATT
1 AAACCCT
16764 AAACCCT
1 AAACCCT
16771 AAACCCT
1 AAACCCT
*
16778 AATCCCT
1 AAACCCT
16785 TAATTCAATT
Statistics
Matches: 88, Mismatches: 25, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
6 9 0.10
7 68 0.77
8 11 0.12
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (7 bp):
AAACCCT
Found at i:16686 original size:13 final size:15
Alignment explanation
Indices: 16665--16705 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
16655 ACCAAAACCC
*
16665 TAAACCCTTAACC-A
1 TAAATCCTTAACCTA
16679 T-AATCCTTAACCTA
1 TAAATCCTTAACCTA
*
16693 TAAATCCTAAACC
1 TAAATCCTTAACC
16706 CTAAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 10 0.43
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATCCTTAACCTA
Found at i:16732 original size:49 final size:49
Alignment explanation
Indices: 16666--16787 Score: 120
Period size: 49 Copynumber: 2.5 Consensus size: 49
16656 CCAAAACCCT
* * * * *
16666 AAACCCTTAACCATAATCCTTAAC-CTATAAATCCTAAACCCTAAATATC
1 AAACCCTAAACCCTAATCCTTAACACTA-AAACCCTAAACCATAAACATC
* * * * * *
16715 AATCCCTAATCCTTAATCCTAAACACTAAACCCCTAAACCATAAACATT
1 AAACCCTAAACCCTAATCCTTAACACTAAAACCCTAAACCATAAACATC
16764 AAACCCTAAACCCTAATCCCTTAA
1 AAACCCTAAACCCTAAT-CCTTAA
16788 TTCAATTATA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
49 49 0.86
50 8 0.14
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.25
Consensus pattern (49 bp):
AAACCCTAAACCCTAATCCTTAACACTAAAACCCTAAACCATAAACATC
Found at i:16759 original size:22 final size:21
Alignment explanation
Indices: 16734--16775 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
16724 TCCTTAATCC
16734 TAAACACTAAACCCCTAAACCA
1 TAAACACTAAA-CCCTAAACCA
*
16756 TAAACATTAAACCCTAAACC
1 TAAACACTAAACCCTAAACC
16776 CTAATCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACACTAAACCCTAAACCA
Found at i:18926 original size:11 final size:12
Alignment explanation
Indices: 18902--18930 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
18892 TTGAATTTTT
18902 GTTTGAGTTCGA
1 GTTTGAGTTCGA
18914 GTTTGAG-TCGA
1 GTTTGAGTTCGA
18925 GTTTGA
1 GTTTGA
18931 ATATTATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.17, C:0.07, G:0.34, T:0.41
Consensus pattern (12 bp):
GTTTGAGTTCGA
Found at i:20483 original size:27 final size:28
Alignment explanation
Indices: 20445--20501 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
20435 AGGGATTAGA
*
20445 TTTAAGATTTTC-AAAATT-TGAGGTTTT
1 TTTAAGACTTTCGAAAATTATGA-GTTTT
20472 TTTAAGACTTTCGAAAATTATGAGTTTT
1 TTTAAGACTTTCGAAAATTATGAGTTTT
20500 TT
1 TT
20502 CTAAAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.41
28 13 0.48
29 3 0.11
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (28 bp):
TTTAAGACTTTCGAAAATTATGAGTTTT
Found at i:22309 original size:20 final size:21
Alignment explanation
Indices: 22280--22320 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
22270 TTTCAACTCA
22280 TAAAATTATTTTTTAAAAAAT
1 TAAAATTATTTTTTAAAAAAT
*
22301 TAAAA-TATTTTTTTAAAAAT
1 TAAAATTATTTTTTAAAAAAT
22321 AATTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAATTATTTTTTAAAAAAT
Found at i:22321 original size:14 final size:14
Alignment explanation
Indices: 22302--22339 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
22292 TTAAAAAATT
*
22302 AAAATATTTTTTTA
1 AAAATATTTTTTAA
22316 AAAATAATTTTTTAA
1 AAAAT-ATTTTTTAA
22331 AAAATATTT
1 AAAATATTT
22340 GAGTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAATATTTTTTAA
Found at i:24258 original size:24 final size:24
Alignment explanation
Indices: 24231--24303 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
24221 CGTTCATTTA
24231 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
24255 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
24279 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
24303 C
1 C
24304 TTTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:24260 original size:14 final size:14
Alignment explanation
Indices: 24241--24296 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
24231 CGTTCGTGAA
24241 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
24255 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
24269 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
24279 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
24293 CGTT
1 CGTT
24297 TATGTTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:24313 original size:24 final size:23
Alignment explanation
Indices: 24242--24316 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
24232 GTTCGTGAAC
* *
24242 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
24266 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
24290 GTTCGTTTATGTTCTTTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
24314 GTT
1 GTT
24317 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:25314 original size:10 final size:10
Alignment explanation
Indices: 25296--25370 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
25286 GGGTCTCCAA
*
25296 CGTTGATGTT
1 CGTTTATGTT
25306 CGTTTATGTT
1 CGTTTATGTT
25316 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
25327 ATGTTCATGTT
1 -CGTTTATGTT
25338 CGTTTATGTT
1 CGTTTATGTT
25348 CG----TGTT
1 CGTTTATGTT
25354 CGTTTATGTT
1 CGTTTATGTT
25364 CGTTTAT
1 CGTTTAT
25371 TTATTAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
10 35 0.67
11 7 0.13
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:25327 original size:16 final size:16
Alignment explanation
Indices: 25302--25366 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
25292 CCAACGTTGA
25302 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
25318 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
25334 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
25350 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
25366 T
1 T
25367 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:27656 original size:27 final size:27
Alignment explanation
Indices: 27617--27688 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 27
27607 ACTAAATATT
27617 TTATGAAATTATAAAATTAGGGACCCTAA
1 TTAT-AAA-TATAAAATTAGGGACCCTAA
* **
27646 TTATAAATATAAAAAATTGGGGGTCCTAA
1 TTATAAATAT--AAAATTAGGGACCCTAA
*
27675 TGATAAATATAAAA
1 TTATAAATATAAAA
27689 AATTAGGGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 7 0.19
28 3 0.08
29 27 0.73
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31
Consensus pattern (27 bp):
TTATAAATATAAAATTAGGGACCCTAA
Found at i:27697 original size:29 final size:29
Alignment explanation
Indices: 27629--27699 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
27619 ATGAAATTAT
* *
27629 AAAATTAGGGACCCTAATTATAAATATAA
1 AAAATTAGGGGCCCTAATGATAAATATAA
* *
27658 AAAATTGGGGGTCCTAATGATAAATATAA
1 AAAATTAGGGGCCCTAATGATAAATATAA
27687 AAAATTAGGGGCC
1 AAAATTAGGGGCC
27700 TGAGCAGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (29 bp):
AAAATTAGGGGCCCTAATGATAAATATAA
Found at i:28742 original size:64 final size:64
Alignment explanation
Indices: 28671--28793 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
28661 AATGCATTTT
* * *
28671 ATGCATCGATGCACTCAGG-TT-TTATGAAAACATCGAATGCATTTTATGCATCGATGCACAGAC
1 ATGCATCGATGCACTCAGGCTTGTT-TG-AAACAGCGAATGCACTTCATGCATCGATGCACAGAC
28734 C
64 C
28735 ATGCATCGATGCACTCAGGCTTGTTTGAAACAGCGAATGCACTTCATGCATCGATGCAC
1 ATGCATCGATGCACTCAGGCTTGTTTGAAACAGCGAATGCACTTCATGCATCGATGCAC
28794 TCTTGACGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
64 48 0.89
65 4 0.07
66 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGGCTTGTTTGAAACAGCGAATGCACTTCATGCATCGATGCACAGACC
Found at i:29004 original size:36 final size:36
Alignment explanation
Indices: 28962--29037 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
28952 TTATAGCTAA
*
28962 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
28998 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
29034 AAAA
1 AAAA
29038 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:33525 original size:15 final size:15
Alignment explanation
Indices: 33507--33536 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33497 CCACGGTGCT
33507 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
33522 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
33537 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:34000 original size:35 final size:35
Alignment explanation
Indices: 33959--34034 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
33949 TATAGCTAAA
*
33959 AAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
33994 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
34029 AAAATC
1 AAAATC
34035 CCGAAAATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (35 bp):
AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:38520 original size:15 final size:15
Alignment explanation
Indices: 38502--38531 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38492 CCACGGTGCT
38502 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
38517 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
38532 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:38995 original size:36 final size:36
Alignment explanation
Indices: 38953--39028 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
38943 TTATAGCTAA
*
38953 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
38989 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
39025 AAAA
1 AAAA
39029 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:42996 original size:65 final size:63
Alignment explanation
Indices: 42870--43060 Score: 237
Period size: 65 Copynumber: 3.0 Consensus size: 63
42860 GTGCACTAAG
*
42870 AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGC
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGGC
*
42933 TAGTGCATCGATGCATCAAATGCATTCGTTAT-TTTCATAAA-ACCCTGAGTGCATCGATGCATG
1 -AGTGCATCGATGCATAAAATGCATTCG--ATGTTTCA-AAATACCCTGAGTGCATCGATGCATG
42996 GC
62 GC
* * * *
42998 ATGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGG
1 A-GTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACCCTGAGTGCATCGATGCATGG
43061 ATTGGTGCAT
Statistics
Matches: 113, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 44 0.39
65 57 0.50
66 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATGGC
Found at i:43445 original size:24 final size:24
Alignment explanation
Indices: 43413--43472 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
43403 CCTTACTCTA
*
43413 ACACTTCTCCCTTTTAACACTTTT
1 ACACTTCTCCCCTTTAACACTTTT
43437 ACACTTCTCCCCTTTAACACTTTT
1 ACACTTCTCCCCTTTAACACTTTT
43461 ACACTTCTCCCC
1 ACACTTCTCCCC
43473 CTTTTTGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (24 bp):
ACACTTCTCCCCTTTAACACTTTT
Found at i:45790 original size:21 final size:22
Alignment explanation
Indices: 45732--45815 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 22
45722 CAAACCCGAT
*
45732 GGATACATCGATGCACATTCAA
1 GGATGCATCGATGCACATTCAA
* * *
45754 GGCATGCATCGGTGCACCTTCAT
1 GG-ATGCATCGATGCACATTCAA
*
45777 GG-TGTATCGATGCACATTCAA
1 GGATGCATCGATGCACATTCAA
45798 GGGGATGCATCGATGCAC
1 --GGATGCATCGATGCAC
45816 TGTTAGGTGT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 20 0.41
24 12 0.24
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (22 bp):
GGATGCATCGATGCACATTCAA
Found at i:49654 original size:22 final size:21
Alignment explanation
Indices: 49612--49651 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49602 GAGTTTATTT
*
49612 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
49633 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
49652 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Done.