Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005726.1 Hibiscus syriacus cultivar Beakdansim tig00013383_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: 55985
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:1398 original size:57 final size:57
Alignment explanation
Indices: 1331--1559 Score: 359
Period size: 57 Copynumber: 4.0 Consensus size: 57
1321 CATAACCATA
* * *
1331 CAACCCCGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGTAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCCCTCAACACAAAGCCAAGGAACCTGCAAGTATT
* *
1388 CAACCCCGTCAGGAACAGTAAGGCTCTCAACACAAAGCCAAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCCCTCAACACAAAGCCAAGGAACCTGCAAGTATT
* *
1445 CAACCCCGTCAGGAACAGTAAGGCTCTCAACACAAAGCCAAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCCCTCAACACAAAGCCAAGGAACCTGCAAGTATT
* * * *
1502 CAACCCCGTCACGAACAGTAAGGCCCTCAGCACAAAGTCGATGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCCCTCAACACAAAGCCAAGGAACCTGCAAGTATT
1559 C
1 C
1560 TTCCTCCAAC
Statistics
Matches: 161, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 161 1.00
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.14
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCCCTCAACACAAAGCCAAGGAACCTGCAAGTATT
Found at i:1417 original size:27 final size:27
Alignment explanation
Indices: 1387--1475 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1377 CTGTAAGTAT
1387 TCAACCCCGTCAGGAACAGTAAGGCTC
1 TCAACCCCGTCAGGAACAGTAAGGCTC
** * * * **
1414 TCAACACAAAGCCAAGGAACCTGCAAGTAT-
1 TCAAC-C-CCGTC-AGGAA-CAGTAAGGCTC
1444 TCAACCCCGTCAGGAACAGTAAGGCTC
1 TCAACCCCGTCAGGAACAGTAAGGCTC
1471 TCAAC
1 TCAAC
1476 ACAAAGCCAA
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
26 6 0.14
27 15 0.35
28 3 0.07
29 3 0.07
30 10 0.23
31 6 0.14
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (27 bp):
TCAACCCCGTCAGGAACAGTAAGGCTC
Found at i:1432 original size:30 final size:30
Alignment explanation
Indices: 1398--1490 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
1388 CAACCCCGTC
1398 AGGAACAGTAAGGCTCTCAACACAAAGCCA
1 AGGAACAGTAAGGCTCTCAACACAAAGCCA
* * ** ** *
1428 AGGAACCTGCAAGTAT-TCAAC-C-CCGTC-
1 AGGAA-CAGTAAGGCTCTCAACACAAAGCCA
1455 AGGAACAGTAAGGCTCTCAACACAAAGCCA
1 AGGAACAGTAAGGCTCTCAACACAAAGCCA
1485 AGGAAC
1 AGGAAC
1491 CTGCAAGTAT
Statistics
Matches: 44, Mismatches: 14, Indels: 10
0.65 0.21 0.15
Matches are distributed among these distances:
26 6 0.14
27 10 0.23
28 3 0.07
29 3 0.07
30 16 0.36
31 6 0.14
ACGTcount: A:0.40, C:0.28, G:0.20, T:0.12
Consensus pattern (30 bp):
AGGAACAGTAAGGCTCTCAACACAAAGCCA
Found at i:1505 original size:30 final size:30
Alignment explanation
Indices: 1414--1505 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
1404 AGTAAGGCTC
1414 TCAACACAAAGCCAAGGAACCTGCAAGTAT
1 TCAACACAAAGCCAAGGAACCTGCAAGTAT
** * * * **
1444 TCAAC-C-CCGTC-AGGAA-CAGTAAGGCT
1 TCAACACAAAGCCAAGGAACCTGCAAGTAT
1470 CTCAACACAAAGCCAAGGAACCTGCAAGTAT
1 -TCAACACAAAGCCAAGGAACCTGCAAGTAT
1501 TCAAC
1 TCAAC
1506 CCCGTCACGA
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
26 6 0.14
27 10 0.23
28 3 0.07
29 3 0.07
30 15 0.35
31 6 0.14
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.14
Consensus pattern (30 bp):
TCAACACAAAGCCAAGGAACCTGCAAGTAT
Found at i:7855 original size:85 final size:85
Alignment explanation
Indices: 7740--7898 Score: 248
Period size: 85 Copynumber: 1.9 Consensus size: 85
7730 TAAGTCATAC
*
7740 AAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTA-AGTCATACATGCG
1 AAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATG-AGAGTCATAAATGCG
*
7804 TGTCATAAATTTATGATACAT
65 CGTCATAAATTTATGATACAT
* * * *
7825 AAATGTGTGTCATTTTCATTTATGATGGGGGCTTCAATGACGCGCAATGAGCGTCATAAATGCGC
1 AAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGAGAGTCATAAATGCGC
7890 GTCATAAAT
66 GTCATAAAT
7899 GCGCGTCATA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
84 1 0.01
85 66 0.99
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (85 bp):
AAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGAGAGTCATAAATGCGC
GTCATAAATTTATGATACAT
Found at i:7891 original size:13 final size:13
Alignment explanation
Indices: 7870--7947 Score: 111
Period size: 13 Copynumber: 6.0 Consensus size: 13
7860 AATGACGCGC
*
7870 AATGAGCGTCATA
1 AATGCGCGTCATA
7883 AATGCGCGTCATA
1 AATGCGCGTCATA
7896 AATGCGCGTCATA
1 AATGCGCGTCATA
*
7909 AATGTGCGTCATA
1 AATGCGCGTCATA
**
7922 AATGCATGTCATA
1 AATGCGCGTCATA
*
7935 AATGCGTGTCATA
1 AATGCGCGTCATA
7948 GATTTATGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:11679 original size:19 final size:19
Alignment explanation
Indices: 11656--11727 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
11646 AATTGTTCAA
*
11656 AGTGTATCGATGCACATGA-
1 AGTGCATCGATGCACA-GAT
* * * *
11675 AGTGTACCAATGCATAGAT
1 AGTGCATCGATGCACAGAT
11694 AGTGCATCGATGCACAGAT
1 AGTGCATCGATGCACAGAT
11713 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
11728 CCGTCAAGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 2 0.04
19 43 0.96
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACAGAT
Found at i:12329 original size:18 final size:18
Alignment explanation
Indices: 12306--12340 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12296 AGGGATTATC
12306 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
12324 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
12341 AATATTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:18546 original size:64 final size:64
Alignment explanation
Indices: 18407--18569 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
18397 ATTGTTCAAG
* * * * *
18407 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGACATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCA
* * * ** *
18471 GTGCATTGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGGGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACA-TCA
* *
18536 -TGTACCGATGCA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
18570 GTCAAGGGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 2 0.02
64 78 0.95
65 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCA
Found at i:19156 original size:18 final size:18
Alignment explanation
Indices: 19133--19167 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19123 AGGGATTATC
19133 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
19151 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
19168 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:20572 original size:3 final size:3
Alignment explanation
Indices: 20564--20610 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
20554 ATAATTAAAT
*
20564 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20611 TTTTTGTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:20720 original size:2 final size:2
Alignment explanation
Indices: 20713--20738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20703 GCTATTCCAA
20713 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
20739 CACCCTCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29586 original size:60 final size:59
Alignment explanation
Indices: 29522--29634 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
29512 AACATAATGA
* * *
29522 ATAGTCGGATGACCATTTTGTAACTTTTAATGGTCA-AGGGACTTAACAAAGTAACTCTTT
1 ATAGTCGGA-GACCATTTTGTAACTTTTAATAGTCAGA-AGACTCAACAAAGTAACTCTTT
* *
29582 ATAGTCTGAGATCATTTTGTAACTTTTAATAGTCAGAAGACTCAACAAAGTAA
1 ATAGTCGGAGACCATTTTGTAACTTTTAATAGTCAGAAGACTCAACAAAGTAA
29635 TACCCTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 38 0.81
60 9 0.19
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (59 bp):
ATAGTCGGAGACCATTTTGTAACTTTTAATAGTCAGAAGACTCAACAAAGTAACTCTTT
Found at i:31466 original size:21 final size:21
Alignment explanation
Indices: 31441--31484 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
31431 GAAAATATTA
* *
31441 AAAAATATTAATATTTTAGAT
1 AAAAATAATAATATTTTAAAT
31462 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
31483 AA
1 AA
31485 TTTTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:38987 original size:19 final size:18
Alignment explanation
Indices: 38960--38995 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38950 AACGCTGTAT
38960 TTATATTAAATTATATTTA
1 TTATATTAAATTA-ATTTA
*
38979 TTATTTTAAATTAATTT
1 TTATATTAAATTAATTT
38996 CTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTAAATTAATTTA
Found at i:43224 original size:19 final size:18
Alignment explanation
Indices: 43201--43245 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43191 ATGTAAGAAA
* *
43201 TAAATAAATAAATAAAAT
1 TAAATAAAGAAAAAAAAT
*
43219 TAAAATGAAGAAAAAAAAT
1 T-AAATAAAGAAAAAAAAT
43238 TAAATAAA
1 TAAATAAA
43246 AGATAAGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
TAAATAAAGAAAAAAAAT
Found at i:43314 original size:29 final size:27
Alignment explanation
Indices: 43194--43342 Score: 94
Period size: 27 Copynumber: 5.4 Consensus size: 27
43184 GATAAAAATG
*
43194 TAAGAAATAAATA-AATAAATAAAATTAAAA
1 TAAGAAAAAAATATAA-AAATAAAA-T--AA
* *
43224 TGAAGAAAAAAA-AT-TAAATAAAA-GA
1 T-AAGAAAAAAATATAAAAATAAAATAA
* * *
43249 TAAGATAAAGAAA-GTAAAGATAAAATAG
1 TAAGA-AAA-AAATATAAAAATAAAATAA
43277 TAAGTAAAAAAATA-AAAAATAAAGAATAA
1 TAAG-AAAAAAATATAAAAAT-AA-AATAA
*
43306 TAAGAAAAAAATATATAAATAAAATAA
1 TAAGAAAAAAATATAAAAATAAAATAA
*
43333 TAATAAAAAA
1 TAAGAAAAAA
43343 GTAAAAATAA
Statistics
Matches: 95, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
24 4 0.04
25 5 0.05
26 4 0.04
27 29 0.31
28 20 0.21
29 22 0.23
30 2 0.02
31 9 0.09
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (27 bp):
TAAGAAAAAAATATAAAAATAAAATAA
Found at i:43335 original size:44 final size:44
Alignment explanation
Indices: 43281--43388 Score: 112
Period size: 47 Copynumber: 2.4 Consensus size: 44
43271 AAATAGTAAG
*
43281 TAAAAAAATAAAAAATAAAGAATAATA-AGAAAAAAATATATAAA
1 TAAAATAATAAAAAATAAA-AATAATATAGAAAAAAATATATAAA
* * * *
43325 TAAAATAATAATAAAAAAGTAAAAATAATATATATATATATATATAAA
1 T--AA-AATAATAAAAAA-TAAAAATAATATAGAAAAAAATATATAAA
43373 T-AAATAATAAAAAATA
1 TAAAATAATAAAAAATA
43389 GTATATATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
43 2 0.04
44 13 0.24
45 1 0.02
46 2 0.04
47 18 0.33
48 18 0.33
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (44 bp):
TAAAATAATAAAAAATAAAAATAATATAGAAAAAAATATATAAA
Found at i:43472 original size:27 final size:25
Alignment explanation
Indices: 43416--43473 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
43406 AAACTGATAA
* * *
43416 TAAAAAAATATATATATATATAATC
1 TAAAAAAATAAAAATATATATAAAC
*
43441 TAAAAAAATAAAAATATATACTAAAG
1 TAAAAAAATAAAAATATATA-TAAAC
43467 TAAAAAA
1 TAAAAAA
43474 GAAATGTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAAAAAATAAAAATATATATAAAC
Found at i:44643 original size:39 final size:36
Alignment explanation
Indices: 44589--44679 Score: 119
Period size: 39 Copynumber: 2.4 Consensus size: 36
44579 CGAGGGTTTG
*
44589 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT-T-T-T
* * *
44628 GTGTTTGAAGAGAAACAATTTCGAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
44664 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
44680 TGTCTCAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
36 16 0.34
37 1 0.02
38 1 0.02
39 29 0.62
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
Found at i:44705 original size:36 final size:36
Alignment explanation
Indices: 44665--44899 Score: 236
Period size: 36 Copynumber: 6.6 Consensus size: 36
44655 TTTTTTTTTG
*
44665 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
44701 TGTTTCAAAAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
44738 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* **
44774 TGTTTCAAG-GAAA-------AAGATATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-A-TT
*
44804 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
44840 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
44877 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
44900 AACTCGTTTT
Statistics
Matches: 167, Mismatches: 18, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.04
29 1 0.01
30 11 0.07
31 4 0.02
35 4 0.02
36 73 0.44
37 58 0.35
38 9 0.05
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:44828 original size:103 final size:103
Alignment explanation
Indices: 44699--44886 Score: 265
Period size: 103 Copynumber: 1.8 Consensus size: 103
44689 TGAGACAAAA
* *
44699 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGATAAAACTTAG-TTCTAAAAGAAACTGTCTCAAGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTTC-AAAAGAAACTGTCTCAAGA
44763 GAGACGAA-A-TTTGTTTCAAGGAAAAAGATATTCAAAGAT
64 GAGAC-AAGATTTTGTTTCAAGGAAAAAGATATTCAAAGAT
** * **
44802 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAAGAAACTGTCTCAAGAGA
44867 GACAAGATTTTGTTTCAAGG
66 GACAAGATTTTGTTTCAAGG
44887 GAAACTGTCT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
101 2 0.03
102 25 0.33
103 48 0.64
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (103 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAAGAAACTGTCTCAAGAGA
GACAAGATTTTGTTTCAAGGAAAAAGATATTCAAAGAT
Found at i:45015 original size:37 final size:37
Alignment explanation
Indices: 44964--45036 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
44954 TCAAGGTTTA
*
44964 TGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCACAAGAGAGACAAAATTT
* *
45001 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCACAAGAGAGACAAAATT
45037 AATTTCAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCACAAGAGAGACAAAATTT
Found at i:45050 original size:36 final size:37
Alignment explanation
Indices: 44966--45050 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
44956 AAGGTTTATG
* **
44966 TTTC-AAGAGAAACTATCACAAGGGAGACAAAATTTTG
1 TTTCAAAG-GAAACTATCACAAGAGAGACAAAATTTAA
* *
45003 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTAA
1 TTTCAAAGGAAACTATCACAAGAGAGACAAAATTTAA
45039 TTTCAAAGGAAA
1 TTTCAAAGGAAA
45051 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 13 0.32
37 26 0.63
38 2 0.05
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.24
Consensus pattern (37 bp):
TTTCAAAGGAAACTATCACAAGAGAGACAAAATTTAA
Found at i:45058 original size:102 final size:103
Alignment explanation
Indices: 44937--45177 Score: 367
Period size: 102 Copynumber: 2.3 Consensus size: 103
44927 ATATTTTGTG
* *
44937 TTTCAAGGGAAAAGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
* * * *
45002 GTTTCAAGGGAAACTATCTCAAG-AGAGACAAAATTAA
66 ATTTCAAGGGAAACTACCCCAAGCAAAGACAAAATTAA
* * * *
45039 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
* *
45104 ATTTCAAGGGAAACTACCCCAAGCAAAGATAAAATTTA
66 ATTTCAAGGGAAACTACCCCAAGCAAAGACAAAATTAA
45142 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
45178 GGAGACAAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
102 79 0.64
103 45 0.36
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (103 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
ATTTCAAGGGAAACTACCCCAAGCAAAGACAAAATTAA
Found at i:45611 original size:106 final size:106
Alignment explanation
Indices: 45423--45741 Score: 417
Period size: 106 Copynumber: 3.0 Consensus size: 106
45413 TTGTTCCGAA
* * * ** *
45423 TCCAATATCC-TCTGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACAGCC
1 TCCAATATCCTTC-GCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACC
* * * * * *
45487 AGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAG
65 AGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
* * *
45529 TCCAATATCCTTCACCGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACCA
1 TCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
*
45594 GCTGTCCATTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
66 GCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
* * * *
45635 TCTAATATCCTTCGCTGTGAATTTGAAATTGGCTATGAAATTGGGAAATTGTTTGTTGACAACCA
1 TCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
*
45700 G-TCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTATCTCGAG
66 GCT-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
45741 T
1 T
45742 GGCACGATAT
Statistics
Matches: 186, Mismatches: 25, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
105 1 0.01
106 183 0.98
107 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (106 bp):
TCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
GCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
Found at i:46375 original size:31 final size:32
Alignment explanation
Indices: 46339--46424 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
46329 CCCAAAGATG
* * *
46339 CCCCAATATTCAATG-TGAATCTCAAAAAATG
1 CCCCAATATTCAATGTTAAATCTAAAAAAATA
* * **
46370 TCCCAACATTTGATGTTAAATCTAAAAAAATA
1 CCCCAATATTCAATGTTAAATCTAAAAAAATA
**
46402 CCCCAATATTTGATGTTAAATCT
1 CCCCAATATTCAATGTTAAATCT
46425 TCAAAGATGC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 11 0.24
32 34 0.76
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (32 bp):
CCCCAATATTCAATGTTAAATCTAAAAAAATA
Found at i:46392 original size:32 final size:32
Alignment explanation
Indices: 46356--46429 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
46346 ATTCAATGTG
**
46356 AATCTCAAAAAATGTCCCAACATTTGATGTTA
1 AATCTCAAAAAATACCCCAACATTTGATGTTA
* *
46388 AATCTAAAAAAATACCCCAATATTTGATGTTA
1 AATCTCAAAAAATACCCCAACATTTGATGTTA
46420 AATCTTCAAA
1 AATC-TCAAA
46430 GATGCCCTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.31
Consensus pattern (32 bp):
AATCTCAAAAAATACCCCAACATTTGATGTTA
Found at i:47470 original size:69 final size:69
Alignment explanation
Indices: 47366--47496 Score: 226
Period size: 69 Copynumber: 1.9 Consensus size: 69
47356 CTCTTGATTT
* *
47366 TCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCATTTG
1 TCTATGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCATTTG
47431 ATGC
66 ATGC
* *
47435 TCTATGATCTTCGAGTGAAGGGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
1 TCTATGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCAT
47497 AGTTTGAATC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (69 bp):
TCTATGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCATTTG
ATGC
Found at i:47612 original size:15 final size:13
Alignment explanation
Indices: 47569--47620 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
47559 TTTTCTTCAA
*
47569 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
47581 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
47594 TTTTCTCTTTACTTT
1 TTTTCTCTTT--TTT
*
47609 TTTTTTCTTTTT
1 TTTTCTCTTTTT
47621 GTTCTGATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 5 0.15
13 17 0.52
15 11 0.33
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:51900 original size:4 final size:4
Alignment explanation
Indices: 51891--52142 Score: 80
Period size: 4 Copynumber: 62.5 Consensus size: 4
51881 AAATGGTAAG
* * * *
51891 AATA AATA AATA AATA AATTA AATG AAGA AAAA AACA AATTA AATAA AGATA
1 AATA AATA AATA AATA AA-TA AATA AATA AATA AATA AA-TA AAT-A A-ATA
* * * *
51943 AGATA AAGAA AATAA AGATA AAT- AGTA AGTAA AAAA AATA AA-A AATA
1 A-ATA AA-TA AAT-A A-ATA AATA AATA AAT-A AATA AATA AATA AATA
*
51990 AAGA AA-A AGA-A GAA-A AATA ATATA AATA AA-A CAATA AATA AAT-
1 AATA AATA A-ATA -AATA AATA A-ATA AATA AATA -AATA AATA AATA
* * * *
52033 AAT- AATA AA-A AAGTA AA-A AAT- AATA TATA TATA TATA TATA TAATA
1 AATA AATA AATA AA-TA AATA AATA AATA AATA AATA AATA AATA -AATA
* * * * * * *
52079 AATA AAAA AATA AA-A AAT- AGTA AATA TATA TATA TATA TATA TATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* *
52125 TATA AATA AATT AATA AA
1 AATA AATA AATA AATA AA
52143 ACTGATAAAA
Statistics
Matches: 201, Mismatches: 23, Indels: 48
0.74 0.08 0.18
Matches are distributed among these distances:
3 30 0.15
4 130 0.65
5 37 0.18
6 4 0.02
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:51963 original size:26 final size:27
Alignment explanation
Indices: 51952--52019 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 27
51942 AAGATAAAGA
* *
51952 AAAT-AAAGATAAATAGTAAGTAAAAA
1 AAATAAAAAATAAAGAGTAAGTAAAAA
** *
51978 AAATAAAAAATAAAGAAAAAG-AAGAA
1 AAATAAAAAATAAAGAGTAAGTAAAAA
52004 AAATAATATAAATAAA
1 AAATAA-A-AAATAAA
52020 ACAATAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 14 0.41
27 13 0.38
28 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (27 bp):
AAATAAAAAATAAAGAGTAAGTAAAAA
Found at i:52060 original size:2 final size:2
Alignment explanation
Indices: 52055--52179 Score: 66
Period size: 2 Copynumber: 64.5 Consensus size: 2
52045 GTAAAAAATA
* * * * * *
52055 AT AT AT AT AT AT AT AT AT AT A- AT AA AT AA AA AA AT A- AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
52095 AT AGT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT -T
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
52137 A- AT A- AA ACT GAT A- AA AA AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52177 AT A
1 AT A
52180 ATCTAAAAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
1 7 0.07
2 89 0.89
3 3 0.03
4 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.37
Consensus pattern (2 bp):
AT
Found at i:52096 original size:43 final size:42
Alignment explanation
Indices: 52031--52169 Score: 143
Period size: 43 Copynumber: 3.1 Consensus size: 42
52021 CAATAAATAA
* *
52031 ATAATAATAAAAAAGTAAAAAATAATATATATATATATATAT
1 ATAATAATAAAAAAATAAAAAATAATAAATATATATATATAT
*
52073 ATAATAAATAAAAAAATAAAAAATAGTAAATATATATATATAT
1 ATAAT-AATAAAAAAATAAAAAATAATAAATATATATATATAT
* *
52116 ATATATATATATAAATAAATTAATAAAACTGATAAAAAATAATATATATAT
1 ATA-ATA-ATA-AAA-AAA-TAA-AAAA-TAAT-AAATAT-ATATATATAT
52167 ATA
1 ATA
52170 TATATATATA
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
42 5 0.06
43 38 0.47
44 5 0.06
45 3 0.04
46 3 0.04
47 3 0.04
48 4 0.05
49 2 0.02
50 5 0.06
51 13 0.16
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (42 bp):
ATAATAATAAAAAAATAAAAAATAATAAATATATATATATAT
Found at i:52101 original size:53 final size:51
Alignment explanation
Indices: 52023--52197 Score: 214
Period size: 51 Copynumber: 3.4 Consensus size: 51
52013 AAATAAAACA
52023 ATAAATAAATAATAATAAAAA-AGTAAAAAATAATATATATATATATATATAT
1 ATAAATAAA-AA-AATAAAAATAGTAAAAAATAATATATATATATATATATAT
*
52075 AATAAATAAAAAAATAAAAAATAGT-AAATAT-ATATATATATATATATATAT
1 -ATAAATAAAAAAAT-AAAAATAGTAAAAAATAATATATATATATATATATAT
** *
52126 ATAAATAAATTAATAAAACT-GATAAAAAATAATATATATATATATATATAT
1 ATAAATAAAAAAATAAAAATAG-TAAAAAATAATATATATATATATATATAT
*
52177 ATAATCTAAAAAAAATAAAAA
1 ATAA-AT-AAAAAAATAAAAA
52198 ATATACTAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
48 1 0.01
49 6 0.06
50 17 0.16
51 47 0.44
52 13 0.12
53 22 0.21
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (51 bp):
ATAAATAAAAAAATAAAAATAGTAAAAAATAATATATATATATATATATAT
Found at i:54187 original size:25 final size:26
Alignment explanation
Indices: 54159--54214 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 26
54149 GTATGTATAT
*
54159 TTTTTTAAATTTTCTAG-TA-ATTTAA
1 TTTTTT-AATTTTATAGTTATATTTAA
*
54184 -TTTTTATTTTTATAGTTATATTTAA
1 TTTTTTAATTTTATAGTTATATTTAA
54209 TTTTTT
1 TTTTTT
54215 GTTTGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.31
24 7 0.27
25 6 0.23
26 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTTTAATTTTATAGTTATATTTAA
Done.