Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002701.1 Hibiscus syriacus cultivar Beakdansim tig00005577_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: 54443
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:5044 original size:24 final size:24
Alignment explanation
Indices: 5008--5056 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
4998 GATTGGGTGG
5008 GTCGAGTCAGAACCCGTCGGGATC
1 GTCGAGTCAGAACCCGTCGGGATC
* *
5032 GTCGGGTCGGAACCCGTCGGGATC
1 GTCGAGTCAGAACCCGTCGGGATC
5056 G
1 G
5057 ATGACCATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.39, T:0.16
Consensus pattern (24 bp):
GTCGAGTCAGAACCCGTCGGGATC
Found at i:5265 original size:16 final size:17
Alignment explanation
Indices: 5244--5277 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5234 AATAAATAAA
5244 ACGAACAT-AAACGAAC
1 ACGAACATAAAACGAAC
5260 ACGAACATAAAACGAAC
1 ACGAACATAAAACGAAC
5277 A
1 A
5278 AATATTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.59, C:0.24, G:0.12, T:0.06
Consensus pattern (17 bp):
ACGAACATAAAACGAAC
Found at i:5368 original size:16 final size:16
Alignment explanation
Indices: 5347--5392 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
5337 TAAATAAACA
*
5347 AACATAAACGAATACG
1 AACATAAACGAACACG
*
5363 AACATAAACGGACACG
1 AACATAAACGAACACG
*
5379 AACATAAACAAACA
1 AACATAAACGAACA
5393 TAAATATTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACG
Found at i:6476 original size:14 final size:14
Alignment explanation
Indices: 6459--6499 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
6449 GATTGGGTTA
*
6459 AACATAAATGAACG
1 AACATAAACGAACG
*
6473 AACATAACCGAACG
1 AACATAAACGAACG
6487 AACATAAACGAAC
1 AACATAAACGAAC
6500 ATAACCAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:8560 original size:22 final size:22
Alignment explanation
Indices: 8516--8561 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
8506 TAAACTATTT
* ***
8516 GAAAAAAGAGAAAAGATCGAAA
1 GAAAAAAAAGAAAAGAAAAAAA
8538 GAAAAAAAAGAAAAGAAAAAAA
1 GAAAAAAAAGAAAAGAAAAAAA
8560 GA
1 GA
8562 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (22 bp):
GAAAAAAAAGAAAAGAAAAAAA
Found at i:16471 original size:14 final size:14
Alignment explanation
Indices: 16449--16483 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16439 TTGAGGGACC
*
16449 ATCTTGATTATTCG
1 ATCTCGATTATTCG
16463 ATCTCGATTATTCG
1 ATCTCGATTATTCG
16477 AT-TCGAT
1 ATCTCGAT
16484 AATTGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (14 bp):
ATCTCGATTATTCG
Found at i:16865 original size:29 final size:29
Alignment explanation
Indices: 16807--16865 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
16797 ATTTGTTGAT
* *
16807 AGTTTATAAACAAAGTAAATTTAATCTAA
1 AGTTAATAAACAAAGTAAATTTAAACTAA
* * *
16836 AGTTAATAAATAAAGTAATTTTAAAGTAA
1 AGTTAATAAACAAAGTAAATTTAAACTAA
16865 A
1 A
16866 TAAAGATGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (29 bp):
AGTTAATAAACAAAGTAAATTTAAACTAA
Found at i:18875 original size:2 final size:2
Alignment explanation
Indices: 18868--18893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18858 TTCAAAATTC
18868 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
18894 CACGATTCAG
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):
TA
Found at i:19543 original size:16 final size:17
Alignment explanation
Indices: 19518--19551 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19508 TAATTTTACG
*
19518 TTAAATTTTTTA-AAAT
1 TTAAAATTTTTATAAAT
19534 TTAAAATTTTTATAAAT
1 TTAAAATTTTTATAAAT
19551 T
1 T
19552 AAATTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAATTTTTATAAAT
Found at i:19889 original size:7 final size:7
Alignment explanation
Indices: 19877--19908 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
19867 ATTCTAGTTG
19877 AATTAAA
1 AATTAAA
19884 AATTAAA
1 AATTAAA
19891 AATTAAA
1 AATTAAA
19898 AATTAAA
1 AATTAAA
19905 AATT
1 AATT
19909 GGAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATTAAA
Found at i:28836 original size:14 final size:14
Alignment explanation
Indices: 28814--28848 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28804 TTGAGGGACC
*
28814 ATCTTGATTATTCG
1 ATCTCGATTATTCG
28828 ATCTCGATTATTCG
1 ATCTCGATTATTCG
28842 AT-TCGAT
1 ATCTCGAT
28849 AATTGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (14 bp):
ATCTCGATTATTCG
Found at i:31212 original size:2 final size:2
Alignment explanation
Indices: 31205--31234 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31195 GCTTCAAAAT
31205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31235 CACGATTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31888 original size:16 final size:17
Alignment explanation
Indices: 31863--31896 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31853 TAATTTTACG
*
31863 TTAAATTTTTTA-AAAT
1 TTAAAATTTTTATAAAT
31879 TTAAAATTTTTATAAAT
1 TTAAAATTTTTATAAAT
31896 T
1 T
31897 AAATTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAATTTTTATAAAT
Found at i:32241 original size:15 final size:15
Alignment explanation
Indices: 32221--32251 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
32211 ATTCTAGTTG
32221 AATTAAAAATTAAAA
1 AATTAAAAATTAAAA
32236 AATTAAAAATTAAAA
1 AATTAAAAATTAAAA
32251 A
1 A
32252 TTGGAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATTAAAAATTAAAA
Found at i:32243 original size:6 final size:7
Alignment explanation
Indices: 32221--32253 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
32211 ATTCTAGTTG
32221 AATTAAA
1 AATTAAA
32228 AATTAAAA
1 AATT-AAA
32236 AATTAAA
1 AATTAAA
32243 AATTAAA
1 AATTAAA
32250 AATT
1 AATT
32254 GGAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATTAAA
Found at i:40950 original size:36 final size:36
Alignment explanation
Indices: 40903--40975 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
40893 ATCGTGCCAT
*
40903 GCACTCGGGGCGACCAAGGATCGGTTCATGCATGGG
1 GCACTCGGGGCGACCAAGGATCAGTTCATGCATGGG
40939 GCACTCGGGGCGACCAAGGATCAGTTCATGCATGGG
1 GCACTCGGGGCGACCAAGGATCAGTTCATGCATGGG
40975 G
1 G
40976 AGATTGGGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.21, C:0.25, G:0.38, T:0.16
Consensus pattern (36 bp):
GCACTCGGGGCGACCAAGGATCAGTTCATGCATGGG
Found at i:41110 original size:17 final size:17
Alignment explanation
Indices: 41088--41121 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41078 GCCCAAACTT
41088 TAACCCTATCCCTCATC
1 TAACCCTATCCCTCATC
41105 TAACCCTATCCCTCATC
1 TAACCCTATCCCTCATC
41122 ATGCATCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (17 bp):
TAACCCTATCCCTCATC
Found at i:41647 original size:21 final size:21
Alignment explanation
Indices: 41622--41665 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
41612 AATCTAGTTA
41622 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
41643 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
41664 AT
1 AT
41666 ATATTATATT
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:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:42109 original size:17 final size:14
Alignment explanation
Indices: 42067--42106 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
42057 GTAATTTATT
42067 ATTTTTTGTTGTCC
1 ATTTTTTGTTGTCC
42081 ATTTTTTGTTGTCC
1 ATTTTTTGTTGTCC
42095 ATTTTTTGTTGT
1 ATTTTTTGTTGT
42107 TGTGTATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.07, C:0.10, G:0.15, T:0.68
Consensus pattern (14 bp):
ATTTTTTGTTGTCC
Found at i:42201 original size:17 final size:17
Alignment explanation
Indices: 42179--42238 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
42169 AGATAATTTT
42179 TGTTTAAAAAAATATTG
1 TGTTTAAAAAAATATTG
* *
42196 TGTTTAAAAATATTTAGTG
1 TGTTTAAAAA-A-ATATTG
*
42215 TTGTTTTAAAAAAATATTT
1 -TG-TTTAAAAAAATATTG
42234 TGTTT
1 TGTTT
42239 TATTTATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 13 0.38
18 3 0.09
19 7 0.21
20 3 0.09
21 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (17 bp):
TGTTTAAAAAAATATTG
Found at i:42503 original size:26 final size:25
Alignment explanation
Indices: 42474--42538 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
42464 AAATCATATT
*
42474 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
42500 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
42526 ATTATT-AATAATA
1 ATTATTAAATAATA
42539 TTAGTAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:45581 original size:17 final size:18
Alignment explanation
Indices: 45555--45589 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
45545 AATGATTAGT
45555 AATTATTAATAATAATGA
1 AATTATTAATAATAATGA
45573 AATTA-TAATAATAATGA
1 AATTATTAATAATAATGA
45590 TTTACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTATTAATAATAATGA
Found at i:45806 original size:12 final size:12
Alignment explanation
Indices: 45791--45822 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
45781 CATTATAATG
45791 ATTTAATAATAA
1 ATTTAATAATAA
*
45803 ATTTAATAATGA
1 ATTTAATAATAA
45815 ATTTAATA
1 ATTTAATA
45823 TTTAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
ATTTAATAATAA
Found at i:45809 original size:20 final size:22
Alignment explanation
Indices: 45764--45822 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 22
45754 TAACCATAAA
*
45764 AATGATTTGATAATAATCATTAT
1 AATGATTTAATAATAA-CATTAT
45787 AATGATTTAATAATAA-ATTTAAT
1 AATGATTTAATAATAACA-TT-AT
45810 AATGAATTTAATA
1 AATG-ATTTAATA
45823 TTTAATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 21 0.66
24 8 0.25
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (22 bp):
AATGATTTAATAATAACATTAT
Found at i:45881 original size:26 final size:26
Alignment explanation
Indices: 45852--46049 Score: 177
Period size: 26 Copynumber: 8.0 Consensus size: 26
45842 AGTAATGATA
45852 TGATAATAATCATTATAATAATAATT
1 TGATAATAATCATTATAATAATAATT
*
45878 TGATAATAATCATTATAATAATGATT
1 TGATAATAATCATTATAATAATAATT
*
45904 T-AGTAATAATCATTATAATAATGATT
1 TGA-TAATAATCATTATAATAATAATT
* * *
45930 TAATAATGAT--TTA-AATATTTAA--
1 TGATAATAATCATTATAATA-ATAATT
* * * *
45952 TGAT-TTGA-CGATT-TAGTAATGATT
1 TGATAATAATC-ATTATAATAATAATT
45976 TGATAATAATCATTATAATAATAATT
1 TGATAATAATCATTATAATAATAATT
* *
46002 TAATAATAATCATTATAATAATCA-T
1 TGATAATAATCATTATAATAATAATT
*
46027 T-ATAATAATGATT-TAATAATAAT
1 TGATAATAATCATTATAATAATAAT
46050 AATTTAATAG
Statistics
Matches: 142, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.02
22 5 0.04
23 17 0.12
24 20 0.14
25 8 0.06
26 88 0.62
27 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (26 bp):
TGATAATAATCATTATAATAATAATT
Found at i:45988 original size:124 final size:122
Alignment explanation
Indices: 45773--46058 Score: 429
Period size: 124 Copynumber: 2.3 Consensus size: 122
45763 AAATGATTTG
45773 ATAATAATCA-T-T-ATAATGATT-TAATAATAAATTTAATAATGAATTTAATATTTAATGATTT
1 ATAATAATCATTATAATAATGATTATAATAAT-AATTTAATAATGAATTTAATATTTAATGATTT
* *
45834 GATGATTTAGTAATGATATGATAATAATCATTATAATAATAATTTGATAATAATCATT
65 GACGATTTAGTAATGATATGATAATAATCATTATAATAATAATTTAATAATAATCATT
* * *
45892 ATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATG-ATTTAAATATTTAATGAT
1 ATAATAATCA-TTA-TAATAATGATTATAATAATAATTTAATAATGAATTT-AATATTTAATGAT
*
45956 TTGACGATTTAGTAATGATTTGATAATAATCATTATAATAATAATTTAATAATAATCATT
63 TTGACGATTTAGTAATGATATGATAATAATCATTATAATAATAATTTAATAATAATCATT
46016 ATAATAATCATTATAATAATGATTTAATAATAATAATTTAATA
1 ATAATAATCATTATAATAATGA-TT-ATAATAATAATTTAATA
46059 GTAATGATTT
Statistics
Matches: 149, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
119 9 0.06
121 1 0.01
122 8 0.05
123 10 0.07
124 114 0.77
125 7 0.05
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (122 bp):
ATAATAATCATTATAATAATGATTATAATAATAATTTAATAATGAATTTAATATTTAATGATTTG
ACGATTTAGTAATGATATGATAATAATCATTATAATAATAATTTAATAATAATCATT
Found at i:45996 original size:3 final size:3
Alignment explanation
Indices: 45978--46052 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
45968 TAATGATTTG
* * * * * *
45978 ATA ATA ATC ATT ATA ATA ATA AT- TTA ATA ATA ATC ATT ATA ATA ATC
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
46025 ATT ATA ATA ATG AT- TTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
46053 TTAATAGTAA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:46063 original size:11 final size:11
Alignment explanation
Indices: 45979--46049 Score: 61
Period size: 12 Copynumber: 5.9 Consensus size: 11
45969 AATGATTTGA
*
45979 TAATAATCATT
1 TAATAATAATT
45990 ATAATAATAATT
1 -TAATAATAATT
46002 TAATAATAATCATT
1 TAATAAT-A--ATT
*
46016 ATAATAATCATT
1 -TAATAATAATT
*
46028 ATAATAATGATT
1 -TAATAATAATT
46040 TAATAATAAT
1 TAATAATAAT
46050 AATTTAATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
11 16 0.31
12 25 0.49
14 3 0.06
15 7 0.14
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:46081 original size:21 final size:20
Alignment explanation
Indices: 46057--46145 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
46047 AATAATTTAA
46057 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
46078 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
46096 TATTAATATTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
*
46117 TATTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
46138 TAGTAATA
1 TAGTAATA
46146 ATGAAATTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
18 13 0.26
19 2 0.04
20 5 0.10
21 22 0.44
22 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:46126 original size:60 final size:58
Alignment explanation
Indices: 46046--46450 Score: 492
Period size: 60 Copynumber: 7.4 Consensus size: 58
46036 GATTTAATAA
* *
46046 TAATAATTTAATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAAT-AAATTATTATTAATATT
* *
46106 TAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAAT-AAATTATTATTAATATT
46166 TAATGATTTGATAGTAATGATTAG---T-A--A-TAATAAT---TTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAAATTATTATTAATATT
*
46214 TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAAATTATTATTAATATT
46272 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAAT-AAATTATTATTAATATT
46332 TAATGA-TT--T-G--AT-A-T--TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAAT-AAATTATTATTAATATT
46381 TAATGATTTGATAGTAATGATTAG---T-A--A-TAATAAT---TTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAAATTATTATTAATATT
46429 TAATGATTTGATAGTAATGATT
1 TAATGATTTGATAGTAATGATT
46451 TACGACTTGA
Statistics
Matches: 315, Mismatches: 8, Indels: 56
0.83 0.02 0.15
Matches are distributed among these distances:
48 73 0.23
49 40 0.13
50 2 0.01
51 2 0.01
52 16 0.05
53 4 0.01
54 3 0.01
55 11 0.03
56 4 0.01
57 2 0.01
58 34 0.11
59 27 0.09
60 97 0.31
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (58 bp):
TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAAATTATTATTAATATT
Found at i:46186 original size:49 final size:48
Alignment explanation
Indices: 46128--46450 Score: 394
Period size: 49 Copynumber: 6.2 Consensus size: 48
46118 ATTAATGATT
*
46128 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAAT-AAATTATTATTAATATTTAATGATTTGA
*
46177 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGA
46225 TAGTAATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAAT
1 TAGTAATGATTAG---T-A--A-TAAT-A-AA-TTATTATTAATATTT-A--A--TGAT--T--T
46290 GA
47 GA
46292 TTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
1 --TAGTAATGATTAGTAATAAT-AAATTATTATTAATATTTAATGATTTGA
*
46343 TATTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAAT-AAATTATTATTAATATTTAATGATTTGA
*
46392 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGA
46440 TAGTAATGATT
1 TAGTAATGATT
46451 TACGACTTGA
Statistics
Matches: 246, Mismatches: 7, Indels: 43
0.83 0.02 0.15
Matches are distributed among these distances:
48 77 0.31
49 86 0.35
51 4 0.02
52 1 0.00
53 1 0.00
54 1 0.00
55 8 0.03
56 1 0.00
57 2 0.01
58 15 0.06
59 2 0.01
60 15 0.06
61 3 0.01
62 6 0.02
63 5 0.02
65 2 0.01
66 1 0.00
67 3 0.01
69 13 0.05
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (48 bp):
TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGA
Found at i:46240 original size:10 final size:10
Alignment explanation
Indices: 46225--46251 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
46215 AATGATTTGA
46225 TAGTAATGAT
1 TAGTAATGAT
46235 TAGTAATGAT
1 TAGTAATGAT
46245 TAGTAAT
1 TAGTAAT
46252 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:46281 original size:166 final size:166
Alignment explanation
Indices: 46046--46452 Score: 645
Period size: 166 Copynumber: 2.5 Consensus size: 166
46036 GATTTAATAA
* *
46046 TAATAATTTAATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAAT-ATTTGATAGTAATGA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATG
* * *
46111 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
63 ATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTG
*
46176 ATAGTAATGATTAGTAATAAT-AATTTATTATTAATATT
128 ATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
46214 TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGAT
1 TAAT-ATTTGATAGTAATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGAT
46279 TTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGAT
65 TTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGAT
*
46344 ATTAATGATTAGTAATAATGAAATTATTATTAATATT
130 AGTAATGATTAGTAATAATGAAATTATTATTAATATT
46381 T-A-A--TGAT--T--TGA-TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATT
1 TAATATTTGATAGTAATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATT
46437 TGATAGTAATGATTTA
66 TGATAGTAATGATTTA
46453 CGACTTGAAC
Statistics
Matches: 230, Mismatches: 8, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
157 61 0.27
158 3 0.01
160 1 0.00
162 4 0.02
164 1 0.00
166 104 0.45
167 38 0.17
168 18 0.08
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (166 bp):
TAATATTTGATAGTAATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATT
TGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATA
GTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:46371 original size:215 final size:219
Alignment explanation
Indices: 46046--46627 Score: 703
Period size: 215 Copynumber: 2.6 Consensus size: 219
46036 GATTTAATAA
*
46046 TAATAATTTAATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAATAATTTAATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
*
46111 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
66 ATTTG-----AATGA-TTA-TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG
46176 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
124 ATAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
46241 TGATTAGTAATAATAATTTATTATTAATATT
189 TGATTAGTAATAATAATTTATTATTAATATT
* *
46272 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
1 TAATAATTTAATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
46337 ATTTG-AT-A-T-TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAA
66 ATTTGAATGATTATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAA
*
46398 TGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGATT--T-ACGACTTG
131 TGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGA-TT-
** * *
46460 AACAATGAACAATGTTTGGTTCAATTCACCATATTTTCCT
194 AGTAAT-AATAA--TTT-ATT--ATT-A--ATA---T--T
** * * * *
46500 TACGAAATT-ATAATAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAATAATTTAATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
46564 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
66 ATTTG-----AATGA-TTA-TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
46628 AGTAATGATT
Statistics
Matches: 313, Mismatches: 16, Indels: 42
0.84 0.04 0.11
Matches are distributed among these distances:
212 3 0.01
213 3 0.01
214 4 0.01
215 108 0.35
217 4 0.01
218 2 0.01
219 1 0.00
220 5 0.02
221 1 0.00
223 3 0.01
226 68 0.22
227 57 0.18
228 6 0.02
233 2 0.01
234 1 0.00
236 1 0.00
238 44 0.14
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (219 bp):
TAATAATTTAATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
ATTTGAATGATTATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAA
TGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGATTAG
TAATAATAATTTATTATTAATATT
Found at i:46446 original size:21 final size:22
Alignment explanation
Indices: 46374--46452 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 22
46364 AAATTATTAT
46374 TAAT-ATTTAATGATTTGATAG
1 TAATGATTTAATGATTTGATAG
* * *
46395 TAATGATTAGTAATAATAATTTATTAT
1 TAATGATT--TAATGAT--TTGA-TAG
46422 TAAT-ATTTAATGATTTGATAG
1 TAATGATTTAATGATTTGATAG
46443 TAATGATTTA
1 TAATGATTTA
46453 CGACTTGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
21 10 0.22
22 11 0.24
24 12 0.27
26 6 0.13
27 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TAATGATTTAATGATTTGATAG
Found at i:46537 original size:21 final size:20
Alignment explanation
Indices: 46513--46598 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 20
46503 GAAATTATAA
46513 TAATGATTTAATAATGATTAG
1 TAAT-ATTTAATAATGATTAG
* * * *
46534 TAATA-ATGA-AATTATTAT
1 TAATATTTAATAATGATTAG
* *
46552 TAATATTTAATGATTTGA-TAT
1 TAATATTTAAT-A-ATGATTAG
*
46573 TAATGATTTAGTAATGATTAG
1 TAAT-ATTTAATAATGATTAG
46594 TAATA
1 TAATA
46599 ATGAAATTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
18 12 0.25
19 4 0.08
20 5 0.10
21 19 0.40
22 8 0.17
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (20 bp):
TAATATTTAATAATGATTAG
Found at i:46539 original size:13 final size:12
Alignment explanation
Indices: 46506--46602 Score: 62
Period size: 11 Copynumber: 8.1 Consensus size: 12
46496 TCCTTACGAA
46506 ATTATAATAATG
1 ATTATAATAATG
46518 ATT-TAATAATG
1 ATTATAATAATG
46529 ATTAGTAATAATG
1 ATTA-TAATAATG
*
46542 AAATTATTATTAAT-
1 --ATTA-TAATAATG
*
46556 ATT-TAATGAT-
1 ATTATAATAATG
*
46566 -TTGATATTAATG
1 ATT-ATAATAATG
*
46578 ATT-TAGTAATG
1 ATTATAATAATG
46589 ATTAGTAATAATG
1 ATTA-TAATAATG
46602 A
1 A
46603 AATTATTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
9 2 0.03
10 5 0.07
11 26 0.39
12 6 0.09
13 18 0.27
15 10 0.15
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:46580 original size:60 final size:60
Alignment explanation
Indices: 46513--46627 Score: 221
Period size: 60 Copynumber: 1.9 Consensus size: 60
46503 GAAATTATAA
46513 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
*
46573 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
46628 AGTAATGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (60 bp):
TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:47542 original size:23 final size:23
Alignment explanation
Indices: 47516--47560 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47506 AAAATTACAA
*
47516 AAATAATAAAATTTATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
47539 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
47561 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:48869 original size:22 final size:22
Alignment explanation
Indices: 48844--48892 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
48834 ACAACTAATA
*
48844 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACGTT
*
48866 AACTGTTCTTTAATATAACGTT
1 AACTATTCTTTAATATAACGTT
48888 AACTA
1 AACTA
48893 ATAAACTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (22 bp):
AACTATTCTTTAATATAACGTT
Found at i:49178 original size:29 final size:29
Alignment explanation
Indices: 49145--49238 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 29
49135 TGTTTTACCC
49145 TAATTTATAATAATAAACTAATTAACTAA
1 TAATTTATAATAATAAACTAATTAACTAA
* *
49174 TAATTTATAACAATAAACTAATTTAAATAA
1 TAATTTATAATAATAAACTAA-TTAACTAA
* *
49204 TTATTCTTTTATATAACTTAAACTAATTAACTAA
1 -TAAT-TTATA-ATAA--TAAACTAATTAACTAA
49238 T
1 T
49239 TTTTTATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 20 0.38
30 7 0.13
31 3 0.06
32 4 0.08
33 4 0.08
34 7 0.13
35 8 0.15
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATTTATAATAATAAACTAATTAACTAA
Found at i:49197 original size:18 final size:18
Alignment explanation
Indices: 49144--49198 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
49134 TTGTTTTACC
*
49144 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
49162 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
49174 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
49191 CTAATTTA
1 CTAATTTA
49199 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:49246 original size:30 final size:31
Alignment explanation
Indices: 49150--49248 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 31
49140 TACCCTAATT
* **
49150 TATAATAATAAACTAATTAACTAA-TAATT-
1 TATAACAATAAACTAATTAACTAATTTTTTA
*
49179 TATAACAATAAACTAATTTAAATAATTATTCTTTTA
1 TATAACAATAAACTAA-TTAACT-A--ATT-TTTTA
*
49215 TATAAC-TTAAACTAATTAACTAATTTTTTA
1 TATAACAATAAACTAATTAACTAATTTTTTA
49245 TATA
1 TATA
49249 TATAAATTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
29 15 0.26
30 14 0.25
31 4 0.07
33 2 0.04
34 6 0.11
35 10 0.18
36 6 0.11
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (31 bp):
TATAACAATAAACTAATTAACTAATTTTTTA
Found at i:49808 original size:28 final size:28
Alignment explanation
Indices: 49768--49825 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
49758 CATGCATAGC
*
49768 ACCAAAGCAGAGCATCAGCAGGCAAAGA
1 ACCAAAGCAGAGCAGCAGCAGGCAAAGA
*
49796 ACCAAAGCAGAGCAGCAGCGGGCAAAGA
1 ACCAAAGCAGAGCAGCAGCAGGCAAAGA
49824 AC
1 AC
49826 GTTGGACGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.26, G:0.28, T:0.02
Consensus pattern (28 bp):
ACCAAAGCAGAGCAGCAGCAGGCAAAGA
Found at i:50000 original size:29 final size:29
Alignment explanation
Indices: 49829--49998 Score: 254
Period size: 29 Copynumber: 5.9 Consensus size: 29
49819 AAAGAACGTT
49829 GGACGCCGGGCGTGCATGGCGACCTTATA
1 GGACGCCGGGCGTGCATGGCGACCTTATA
*
49858 GGACGCCGGGCGTGCATGGCAACCTTATA
1 GGACGCCGGGCGTGCATGGCGACCTTATA
*
49887 GGACGCCGGGCGTGCATGGCAACCTTATA
1 GGACGCCGGGCGTGCATGGCGACCTTATA
** *
49916 GGACGCTAGGCATGCATGGCGACC-TATAA
1 GGACGCCGGGCGTGCATGGCGACCTTAT-A
49945 GGACGCCGGGCGTGCATGGCGACC-TATAA
1 GGACGCCGGGCGTGCATGGCGACCTTAT-A
*
49974 GGACGCCGGGCGTGCATAGCGACCT
1 GGACGCCGGGCGTGCATGGCGACCT
49999 ATGCTGGTTG
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
28 3 0.02
29 127 0.98
ACGTcount: A:0.21, C:0.28, G:0.36, T:0.16
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTTATA
Found at i:52625 original size:23 final size:23
Alignment explanation
Indices: 52595--52640 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
52585 GTGACATGGT
*
52595 GCCCAGTCAGCAACTTCTAGAAG
1 GCCCAGTCAACAACTTCTAGAAG
*
52618 GCCCAGTCAACAGCTTCTAGAAG
1 GCCCAGTCAACAACTTCTAGAAG
52641 ATCTAATCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (23 bp):
GCCCAGTCAACAACTTCTAGAAG
Done.