Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000223.1 Hibiscus syriacus cultivar Beakdansim tig00000393_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: 126531
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1935 original size:25 final size:25
Alignment explanation
Indices: 1903--1961 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
1893 TTGCTTAATT
1903 TACTATGTTGTAATTCCTTTAATCG
1 TACTATGTTGTAATTCCTTTAATCG
*
1928 TATTATGTTGTAATTCCTTTAATCG
1 TACTATGTTGTAATTCCTTTAATCG
1953 TACTATGTT
1 TACTATGTT
1962 TTTAATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (25 bp):
TACTATGTTGTAATTCCTTTAATCG
Found at i:2243 original size:17 final size:17
Alignment explanation
Indices: 2214--2260 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
2204 TTGGTTATCG
* *
2214 GAATATAAAATTACTTT
1 GAATATAACATTACTTA
2231 GAGA-ATAACATTA-TTA
1 GA-ATATAACATTACTTA
2247 GAATATAACATTAC
1 GAATATAACATTAC
2261 CATGAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
17 10 0.40
18 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (17 bp):
GAATATAACATTACTTA
Found at i:8283 original size:25 final size:25
Alignment explanation
Indices: 8247--8294 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
8237 TAATGTTTTC
*
8247 TTTTAACCAAAAAATGTTATCATCA
1 TTTTAACCAAAAAATGCTATCATCA
*
8272 TTTTAACTAAAAAATGCTATCAT
1 TTTTAACCAAAAAATGCTATCAT
8295 TGGTAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (25 bp):
TTTTAACCAAAAAATGCTATCATCA
Found at i:13074 original size:88 final size:88
Alignment explanation
Indices: 12924--13086 Score: 238
Period size: 88 Copynumber: 1.9 Consensus size: 88
12914 CACAAGTATA
* *
12924 AAACACACAGACAAGGGTAGACATCATGGTGTGGTCGGAGGGTTTCGCTACATCTCAAAGACACA
1 AAACACACAGACAAGGGTAGACATCATGGTGTGGTCAGAGGGTTTCACTACATCTCAAAGACACA
12989 CACCCCTCTAATATACTTATATC
66 CACCCCTCTAATATACTTATATC
* * * * *
13012 AAACACAC-GAACAAGGGTATATATCATGGTGTGGTCAGAGGGTTTCATTATATCTCAGAGACAC
1 AAACACACAG-ACAAGGGTAGACATCATGGTGTGGTCAGAGGGTTTCACTACATCTCAAAGACAC
*
13076 ATACCCCTCTA
65 ACACCCCTCTA
13087 GCCTACTTAG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
87 1 0.02
88 65 0.98
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (88 bp):
AAACACACAGACAAGGGTAGACATCATGGTGTGGTCAGAGGGTTTCACTACATCTCAAAGACACA
CACCCCTCTAATATACTTATATC
Found at i:14556 original size:20 final size:19
Alignment explanation
Indices: 14531--14578 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
14521 ATGATGAAAG
14531 GATAAAGAAATGAGGATGAA
1 GATAAAGAAATGAGG-TGAA
14551 GAT-AA-AAATGAGGTGAA
1 GATAAAGAAATGAGGTGAA
14568 GATAAATGAAA
1 GATAAA-GAAA
14579 AGAAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.28
18 10 0.40
19 2 0.08
20 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.17
Consensus pattern (19 bp):
GATAAAGAAATGAGGTGAA
Found at i:14569 original size:17 final size:18
Alignment explanation
Indices: 14538--14573 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
14528 AAGGATAAAG
14538 AAATGAGGATGAAGATAA
1 AAATGAGGATGAAGATAA
14556 AAATGAGG-TGAAGATAA
1 AAATGAGGATGAAGATAA
14573 A
1 A
14574 TGAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.17
Consensus pattern (18 bp):
AAATGAGGATGAAGATAA
Found at i:26437 original size:23 final size:21
Alignment explanation
Indices: 26410--26451 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
26400 ACATTATATC
*
26410 AATTTTAGCTTTTTATTTTTTAT
1 AATTTTA--TTTTGATTTTTTAT
26433 AATTTTATTTTGATTTTTT
1 AATTTTATTTTGATTTTTT
26452 TCAGATCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (21 bp):
AATTTTATTTTGATTTTTTAT
Found at i:29112 original size:24 final size:24
Alignment explanation
Indices: 29080--29135 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
29070 TTAGTTTACG
29080 TATCAATTTAGTCTATAAGAAAAA
1 TATCAATTTAGTCTATAAGAAAAA
*
29104 TATCAATTTAGTCTATAAGAAATA
1 TATCAATTTAGTCTATAAGAAAAA
29128 TATCAATT
1 TATCAATT
29136 CTTTCAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (24 bp):
TATCAATTTAGTCTATAAGAAAAA
Found at i:36419 original size:12 final size:13
Alignment explanation
Indices: 36399--36449 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
36389 TCGTGTTTGA
*
36399 ATTTTTT-TCTTT
1 ATTTTTTCTCTCT
36411 ATGTTTTTCTCTCT
1 AT-TTTTTCTCTCT
* *
36425 ATTTTTTCTGTTT
1 ATTTTTTCTCTCT
36438 GATTTTTTCTCT
1 -ATTTTTTCTCT
36450 ATTTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 14 0.44
14 16 0.50
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.73
Consensus pattern (13 bp):
ATTTTTTCTCTCT
Found at i:36429 original size:25 final size:24
Alignment explanation
Indices: 36401--36460 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
36391 GTGTTTGAAT
36401 TTTTTTCTTTATG-TTTTTCTCTCTA
1 TTTTTTCTTT-TGATTTTT-TCTCTA
36426 TTTTTTCTGTTTGATTTTTTCTCTA
1 TTTTTTCT-TTTGATTTTTTCTCTA
36451 -TTTTTCTTTT
1 TTTTTTCTTTT
36461 CGAATGGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.09
24 7 0.21
25 16 0.48
26 7 0.21
ACGTcount: A:0.07, C:0.13, G:0.05, T:0.75
Consensus pattern (24 bp):
TTTTTTCTTTTGATTTTTTCTCTA
Found at i:39043 original size:2 final size:2
Alignment explanation
Indices: 39038--39070 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39028 TATTTACAAA
39038 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39071 ATCTATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39079 original size:2 final size:2
Alignment explanation
Indices: 39074--39098 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39064 TCTCTCTATC
39074 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39099 TAGGGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40365 original size:4 final size:4
Alignment explanation
Indices: 40356--40386 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
40346 CAATGCATGT
40356 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
40387 CATAGTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:45781 original size:12 final size:12
Alignment explanation
Indices: 45764--45807 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
45754 AGGTAACGCC
45764 TTTTTCTTTCTT
1 TTTTTCTTTCTT
45776 TTTTTCTTTCTT
1 TTTTTCTTTCTT
* * *
45788 CTATTCTTTTTGT
1 TTTTTCTTTCT-T
45801 TTTTTCT
1 TTTTTCT
45808 CCTTTTCCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:58268 original size:20 final size:20
Alignment explanation
Indices: 58224--58274 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
58214 CCAATAGGGG
* * *
58224 GTATCGATACCAATGGTTCA
1 GTATCGATACTAAGGGTCCA
*
58244 ATATCGATACTAAGGGTCCA
1 GTATCGATACTAAGGGTCCA
*
58264 GTATCGGTACT
1 GTATCGATACT
58275 GACGGACAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
GTATCGATACTAAGGGTCCA
Found at i:65171 original size:25 final size:25
Alignment explanation
Indices: 65138--65191 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
65128 ATCATCTTCA
*
65138 ATCTCTTACATAACACACTCCTTTC
1 ATCTCTTACACAACACACTCCTTTC
* *
65163 ATCTGTTACACAACACACTCCTTTT
1 ATCTCTTACACAACACACTCCTTTC
65188 ATCT
1 ATCT
65192 TCATTCTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (25 bp):
ATCTCTTACACAACACACTCCTTTC
Found at i:71520 original size:62 final size:62
Alignment explanation
Indices: 71454--71580 Score: 218
Period size: 62 Copynumber: 2.0 Consensus size: 62
71444 ATTGTTACAA
* *
71454 AATGGCCACTCTGTCGTTATAATAATTTGTAACATTTCGATAAAATTTAATGATTGTTTTGT
1 AATGGCCACTCTGTCGTTATAACAATCTGTAACATTTCGATAAAATTTAATGATTGTTTTGT
* *
71516 AATGGTCACTTTGTCGTTATAACAATCTGTAACATTTCGATAAAATTTAATGATTGTTTTGT
1 AATGGCCACTCTGTCGTTATAACAATCTGTAACATTTCGATAAAATTTAATGATTGTTTTGT
71578 AAT
1 AAT
71581 AGTTCAAGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (62 bp):
AATGGCCACTCTGTCGTTATAACAATCTGTAACATTTCGATAAAATTTAATGATTGTTTTGT
Found at i:71593 original size:31 final size:30
Alignment explanation
Indices: 71557--71642 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 30
71547 ACATTTCGAT
*
71557 AAAATTTAATGATTGTTTTGTAA-TAGTTCA
1 AAAATTTAATGATTGTTTTGTAACTA-TCCA
*
71587 AGAAATTTAATGATTATTTTGTAACTATCCA
1 A-AAATTTAATGATTGTTTTGTAACTATCCA
* *
71618 AAAATTTAATGATAGCTTTGTAACT
1 AAAATTTAATGATTGTTTTGTAACT
71643 TTTGAAAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 22 0.45
31 25 0.51
32 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (30 bp):
AAAATTTAATGATTGTTTTGTAACTATCCA
Found at i:75971 original size:16 final size:16
Alignment explanation
Indices: 75950--75983 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
75940 TTACTATTCA
*
75950 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
75966 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
75982 CG
1 CG
75984 ATCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:96852 original size:10 final size:10
Alignment explanation
Indices: 96837--96861 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
96827 AAATAAGTAA
96837 TATAAGCATG
1 TATAAGCATG
96847 TATAAGCATG
1 TATAAGCATG
96857 TATAA
1 TATAA
96862 CATAGAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (10 bp):
TATAAGCATG
Found at i:104399 original size:20 final size:20
Alignment explanation
Indices: 104376--104417 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
104366 CATGCCACAG
104376 CAACATGTTGGATGCCTCAT
1 CAACATGTTGGATGCCTCAT
104396 CAACATGTTGGATGCCTCAT
1 CAACATGTTGGATGCCTCAT
104416 CA
1 CA
104418 TATTATACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (20 bp):
CAACATGTTGGATGCCTCAT
Found at i:106079 original size:60 final size:59
Alignment explanation
Indices: 105976--106138 Score: 174
Period size: 58 Copynumber: 2.8 Consensus size: 59
105966 TTTGGATGAA
* * * * *
105976 TTTGAGGATGAAATTAGAA-GATCTAAAAGTTTATGTACCAATTTAG-AATGAGATTCATAG
1 TTTGAGGATGAAATTGGAATGTTC-AAAAGTTTAAGGACTAATTTAGAAATGAG--TCATAG
*
106036 TTTGAGGATGAAATTGGAATGTTCAAAAGATTAAGGACTAATTT-GAAATGAGTCATAG
1 TTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAAATGAGTCATAG
* *
106094 TTT-AGGGATGAAATTGAAATGTTTAAAAGTTTAAGGA-TCAATTTA
1 TTTGA-GGATGAAATTGGAATGTTCAAAAGTTTAAGGACT-AATTTA
106139 AAACGAGGCT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
57 2 0.02
58 43 0.48
59 1 0.01
60 40 0.45
61 3 0.03
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (59 bp):
TTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAAATGAGTCATAG
Found at i:106124 original size:29 final size:29
Alignment explanation
Indices: 106034--106131 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
106024 TGAGATTCAT
* * *
106034 AGTTTGAGGATGAAATTGGAATGTTCAAA
1 AGTTTAAGGATGAAATTGAAATGTTTAAA
* * ** * *
106063 AGATTAAGGACT-AATTTGAAATGAGTCAT
1 AGTTTAAGGA-TGAAATTGAAATGTTTAAA
*
106092 AGTTTAGGGATGAAATTGAAATGTTTAAA
1 AGTTTAAGGATGAAATTGAAATGTTTAAA
106121 AGTTTAAGGAT
1 AGTTTAAGGAT
106132 CAATTTAAAA
Statistics
Matches: 50, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
28 1 0.02
29 48 0.96
30 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTGAAATGTTTAAA
Found at i:108179 original size:20 final size:20
Alignment explanation
Indices: 108154--108194 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
108144 ATCAGATTGT
108154 CCAGGGAGTACAGATTCCCC
1 CCAGGGAGTACAGATTCCCC
* *
108174 CCAGGGGGTACCGATTCCCC
1 CCAGGGAGTACAGATTCCCC
108194 C
1 C
108195 TGTCTAACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.15
Consensus pattern (20 bp):
CCAGGGAGTACAGATTCCCC
Found at i:110968 original size:21 final size:20
Alignment explanation
Indices: 110926--111005 Score: 99
Period size: 19 Copynumber: 3.9 Consensus size: 20
110916 GATTGTCCAG
110926 GGGGTACAGATTCCCCCC-A
1 GGGGTACAGATTCCCCCCAA
*
110945 GGGGTATAGATTCCCCCCTAA
1 GGGGTACAGATTCCCCCC-AA
*
110966 GGGGAACAGATTCCCCCCCCCAA
1 GGGGTACAGATT---CCCCCCAA
110989 GGGGTACAGATTCCCCC
1 GGGGTACAGATTCCCCC
111006 TGTCTAACGG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
19 17 0.33
20 5 0.10
21 11 0.21
23 13 0.25
24 6 0.12
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCCAA
Found at i:110990 original size:23 final size:23
Alignment explanation
Indices: 110957--111005 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
110947 GGTATAGATT
*
110957 CCCCCCTAAGGGGAACAGATTCC
1 CCCCCCCAAGGGGAACAGATTCC
*
110980 CCCCCCCAAGGGGTACAGATTCC
1 CCCCCCCAAGGGGAACAGATTCC
111003 CCC
1 CCC
111006 TGTCTAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.45, G:0.20, T:0.12
Consensus pattern (23 bp):
CCCCCCCAAGGGGAACAGATTCC
Found at i:112037 original size:20 final size:20
Alignment explanation
Indices: 112012--112071 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
112002 CCGTTAGACA
*
112012 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
* *
112032 GGGGGAATCTATTCCCCCTG
1 GGGGGAATCTGTACCCCCTG
112052 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
112072 AGCAATCTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:113558 original size:19 final size:20
Alignment explanation
Indices: 113515--113562 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
113505 TCTAAATCCT
*
113515 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
113535 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
113554 TTTTCAAAA
1 TTTTCAAAA
113563 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:114875 original size:19 final size:19
Alignment explanation
Indices: 114853--114918 Score: 114
Period size: 19 Copynumber: 3.4 Consensus size: 19
114843 GAATGAATAC
*
114853 CCCCTGGGGGGAATCTGTT
1 CCCCTGGGGGGAATCTGTA
114872 CCCCTGGGGGGAATCTGTA
1 CCCCTGGGGGGAATCTGTA
114891 CCCCTGGGGGGAATCTGTA
1 CCCCTGGGGGGAATCTGTA
114910 CCCCCTGGG
1 -CCCCTGGG
114919 CAATCTGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 37 0.82
20 8 0.18
ACGTcount: A:0.12, C:0.30, G:0.36, T:0.21
Consensus pattern (19 bp):
CCCCTGGGGGGAATCTGTA
Found at i:115384 original size:2 final size:2
Alignment explanation
Indices: 115373--115410 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
115363 GGGAATCAAT
115373 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
115411 TAGTTAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:115451 original size:14 final size:14
Alignment explanation
Indices: 115432--115469 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
115422 AAAAAAAATA
115432 AAAACTTACAAGTG
1 AAAACTTACAAGTG
115446 AAAACTTACAAGTG
1 AAAACTTACAAGTG
*
115460 AGAACTTACA
1 AAAACTTACA
115470 TCTAGGCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (14 bp):
AAAACTTACAAGTG
Found at i:115648 original size:25 final size:26
Alignment explanation
Indices: 115620--115678 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
115610 TAGTTAAAGA
*
115620 ATAATTTAATATTT-AAATT-ATAATC
1 ATAATTTAAAATTTAAAATTCAT-ATC
*
115645 ATAA-ATAAAATTTAAAATTCATATC
1 ATAATTTAAAATTTAAAATTCATATC
115670 ATAAATTTA
1 AT-AATTTA
115679 TCTTTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
24 7 0.26
25 14 0.52
26 4 0.15
27 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAATTTAAAATTTAAAATTCATATC
Found at i:117783 original size:30 final size:31
Alignment explanation
Indices: 117727--117784 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
117717 TTGCATAGTT
**
117727 AAATATTTTTATATTTAAACTTAAAATTTTA
1 AAATATTTTTATATTTAAACAAAAAATTTTA
117758 AAATAATTTTTAT-TTTAAA-AAAAAATT
1 AAAT-ATTTTTATATTTAAACAAAAAATT
117785 AAATAAGCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.25
31 10 0.42
32 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATATTTTTATATTTAAACAAAAAATTTTA
Found at i:119903 original size:38 final size:38
Alignment explanation
Indices: 119852--119943 Score: 143
Period size: 37 Copynumber: 2.4 Consensus size: 38
119842 GTTCTTTTAT
**
119852 GAAAAAGGGTAAGTTTTTTTACTAAAAAGGGTAA-AAAA
1 GAAAAAGGGTAAGTTTTTTTACTAAAAA-GAAAAGAAAA
119890 GAAAAAGGGTAAG-TTTTTTACTAAAAAGAAAAGAAAA
1 GAAAAAGGGTAAGTTTTTTTACTAAAAAGAAAAGAAAA
119927 GAAAAAGGGTAAGTTTT
1 GAAAAAGGGTAAGTTTT
119944 AGTTTTACAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 31 0.62
38 16 0.32
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.25
Consensus pattern (38 bp):
GAAAAAGGGTAAGTTTTTTTACTAAAAAGAAAAGAAAA
Found at i:126056 original size:17 final size:17
Alignment explanation
Indices: 126010--126057 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
126000 TAGTGCTATT
* *
126010 AAGAAGAAAAATAGATG
1 AAGAAGAGATATAGATG
126027 AAGAAGAGAAGATATAGATG
1 AAG-A-AG-AGATATAGATG
126047 AAGAAGAGATA
1 AAGAAGAGATA
126058 ATAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 3 0.12
20 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.12
Consensus pattern (17 bp):
AAGAAGAGATATAGATG
Done.