Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002144.1 Hibiscus syriacus cultivar Beakdansim tig00004383_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: 293050
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:169716 original size:30 final size:30
Alignment explanation
Indices: 169682--169764 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
169672 AATCAATCTA
*
169682 TATTTTATAATAATTTATTCTAAAATAAAT
1 TATTTTATAATAAATTATTCTAAAATAAAT
*
169712 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTCTAAAATAAAT
* *
169742 AATCTTAT--TAAATTATT-TAAAAT
1 TATTTTATAATAAATTATTCTAAAAT
169765 TATTTTAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 6 0.12
28 9 0.18
30 34 0.69
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
TATTTTATAATAAATTATTCTAAAATAAAT
Found at i:170825 original size:12 final size:12
Alignment explanation
Indices: 170808--170887 Score: 74
Period size: 12 Copynumber: 6.4 Consensus size: 12
170798 TTTATTTAAA
170808 AAAATTAATATT
1 AAAATTAATATT
170820 AAAATTAATATTT
1 AAAATTAATA-TT
*
170833 ATAATATAATATT
1 AAAAT-TAATATT
170846 AAAAAATTAATATT
1 --AAAATTAATATT
* *
170860 -TAATTTAT-TT
1 AAAATTAATATT
170870 AAAAATTAATATT
1 -AAAATTAATATT
170883 AAAAT
1 AAAAT
170888 CAAAATCAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 21 0.38
13 10 0.18
14 12 0.22
15 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:170832 original size:28 final size:27
Alignment explanation
Indices: 170774--170862 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 27
170764 ATCTATAATA
* *
170774 TAATA-TTAAAAAAATAATGTT-TAAT
1 TAATATTTAAAAAAATAATATTAAAAT
170799 T--TATTTAAAAAAATTAATATTAAAAT
1 TAATATTTAAAAAAA-TAATATTAAAAT
* *
170825 TAATATTT-ATAATATAATATTAAAAAAT
1 TAATATTTAAAAAAATAATATT--AAAAT
170853 TAATATTTAA
1 TAATATTTAA
170863 TTTATTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
23 2 0.04
24 9 0.17
25 7 0.13
26 11 0.21
27 4 0.08
28 18 0.35
29 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TAATATTTAAAAAAATAATATTAAAAT
Found at i:170845 original size:65 final size:64
Alignment explanation
Indices: 170753--170904 Score: 222
Period size: 65 Copynumber: 2.4 Consensus size: 64
170743 TTATATGATA
*
170753 TAAAATTAAATATCTATAATATAATATTAAAAAAATAATGTTTAATTTATTTAAAAAAATTAATA
1 TAAAATTAAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTT--AAAAATTAATA
170818 T
64 T
* *
170819 TAAAATT-AATATTTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAATTAATAT
*
170882 TAAAATCAAA-ATC-A-AATATAATA
1 TAAAATTAAATATCTATAATATAATA
170905 CAAAATTAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
61 9 0.11
62 1 0.01
63 20 0.25
64 2 0.03
65 41 0.51
66 7 0.09
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (64 bp):
TAAAATTAAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAATTAATAT
Found at i:170863 original size:26 final size:25
Alignment explanation
Indices: 170810--170883 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 25
170800 TATTTAAAAA
170810 AATTAATATT-AAAATTAATATTTAT
1 AATTAATATTAAAAATTAATA-TTAT
170835 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATT-AAAAATTAATATTAT
*
170861 AATTTAT-TTAAAAATTAATATTA
1 AATTAATATTAAAAATTAATATTA
170884 AAATCAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
23 13 0.30
24 2 0.05
25 6 0.14
26 11 0.25
27 2 0.05
28 10 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTAATATTAAAAATTAATATTAT
Found at i:170880 original size:37 final size:39
Alignment explanation
Indices: 170806--170886 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 39
170796 AATTTATTTA
*
170806 AAAAAATTAATATTAAAATTAATATTTATAATATAATATT
1 AAAAAATTAATATTAAAATT-ATATTTAAAATATAATATT
*
170846 AAAAAATTAATATT-TAATT-TATTTAAAA-ATTAATATT
1 AAAAAATTAATATTAAAATTATATTTAAAATA-TAATATT
170883 AAAA
1 AAAA
170887 TCAAAATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
36 1 0.03
37 19 0.50
39 4 0.11
40 14 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (39 bp):
AAAAAATTAATATTAAAATTATATTTAAAATATAATATT
Found at i:171298 original size:16 final size:16
Alignment explanation
Indices: 171273--171304 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
171263 TTTTTATATA
171273 TATATAATGAATTATT
1 TATATAATGAATTATT
*
171289 TATATTATGAATTATT
1 TATATAATGAATTATT
171305 AGATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TATATAATGAATTATT
Found at i:176429 original size:32 final size:32
Alignment explanation
Indices: 176361--176436 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
176351 GACGGGTCGT
* * *
176361 TTCGGGTCAATATTGCATTTGATTTAAGTTCGG
1 TTCGGGTCAA-ATTGAATCTGATTTAAGTTCAG
** *
176394 TTCGGGTCAAATTGAATCTGATTTGTGTTTAG
1 TTCGGGTCAAATTGAATCTGATTTAAGTTCAG
176426 TTCGGGTCAAA
1 TTCGGGTCAAA
176437 GAAAATTCAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 27 0.73
33 10 0.27
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (32 bp):
TTCGGGTCAAATTGAATCTGATTTAAGTTCAG
Found at i:177432 original size:65 final size:67
Alignment explanation
Indices: 177350--177477 Score: 208
Period size: 65 Copynumber: 1.9 Consensus size: 67
177340 CCAGCTATTA
*
177350 GGACACAATTTTAAATCCA-AATATTATTATT-AACAC-TTTGAGTTAAATATTTAGAAGTTCTT
1 GGACAAAATTTTAAATCCAGAAT-TTATTATTAAACACATTTGAGTTAAATATTTAGAAGTTCTT
177412 TTC
65 TTC
177415 GGACAAAATTTTAAATCCAGAATTTATTATTAAACACATTTTGAGTTAAATATTTAGAAGTTC
1 GGACAAAATTTTAAATCCAGAATTTATTATTAAACACA-TTTGAGTTAAATATTTAGAAGTTC
177478 ATGTGTTATA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
65 26 0.45
66 8 0.14
68 24 0.41
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (67 bp):
GGACAAAATTTTAAATCCAGAATTTATTATTAAACACATTTGAGTTAAATATTTAGAAGTTCTTT
TC
Found at i:186244 original size:21 final size:21
Alignment explanation
Indices: 186220--186270 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
186210 CTTTTGATAT
186220 ATCCGCTATACTCGTAATAGC
1 ATCCGCTATACTCGTAATAGC
186241 ATCCGCTATACTCGTAATAGC
1 ATCCGCTATACTCGTAATAGC
**
186262 GCCCGCTAT
1 ATCCGCTAT
186271 GACCACAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (21 bp):
ATCCGCTATACTCGTAATAGC
Found at i:187838 original size:69 final size:69
Alignment explanation
Indices: 187659--187818 Score: 302
Period size: 69 Copynumber: 2.3 Consensus size: 69
187649 GGCTCAAACT
*
187659 CATCATCACCATGCCTTTTTGATCTACTTCCATCCCTCCTATCTTCTTTTACCCTAGCCTCGTAT
1 CATCATCACCATGCCTTTTTGATCTACTTCCATCCCTCCTATCTTCTTTTACCCTAGCCTCATAT
187724 TCAC
66 TCAC
187728 CATCATCACCATGCCTTTTTGATCTACTTCCATCCCTCCTATCTTCTTTTACCCTAGCCTCATAT
1 CATCATCACCATGCCTTTTTGATCTACTTCCATCCCTCCTATCTTCTTTTACCCTAGCCTCATAT
187793 TCAC
66 TCAC
*
187797 CATCATCACCATGCCTTCTTGA
1 CATCATCACCATGCCTTTTTGA
187819 ACTCTTTTCA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 89 1.00
ACGTcount: A:0.19, C:0.38, G:0.06, T:0.38
Consensus pattern (69 bp):
CATCATCACCATGCCTTTTTGATCTACTTCCATCCCTCCTATCTTCTTTTACCCTAGCCTCATAT
TCAC
Found at i:198248 original size:19 final size:19
Alignment explanation
Indices: 198224--198274 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
198214 ACCAACAAAA
*
198224 TCGCAATGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
198243 TCGCAACGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
198262 TCGCAACGCGATC
1 TCGCAACGCGATC
198275 TCCATTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGATCGCTAAT
Found at i:198373 original size:21 final size:21
Alignment explanation
Indices: 198322--198374 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
198312 ATTATTACTA
198322 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
198343 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
198364 TCGCAATGCGA
1 TCGCAATGCGA
198375 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:198389 original size:20 final size:21
Alignment explanation
Indices: 198364--198415 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
198354 TTTTCCCAAT
*
198364 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
198384 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
198405 TCGCAATGCGA
1 TCGCAATGCGA
198416 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:198437 original size:20 final size:20
Alignment explanation
Indices: 198404--198538 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
198394 AATTTGGAAA
*
198404 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
198424 ATCACAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
198445 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
198465 TTCGCAACGCAATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
198485 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
198505 TTCGTAACGAGA-ATCTGACT
1 ATCGCAACGCGATA-CTGACT
* *
198525 ATCACAACGAGATA
1 ATCGCAACGCGATA
198539 ATACAGAATC
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.02
20 74 0.80
21 15 0.16
22 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:198522 original size:40 final size:40
Alignment explanation
Indices: 198445--198538 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
198435 ATAATACAAA
*
198445 ATCGCAACGCGATACTGACTTTCGCAACGCAATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGCAAATCTGACT
* * *
198485 TTCGCAACGCGATTCTGACTTTCGTAACG-AGAATCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGCA-AATCTGACT
* *
198525 ATCACAACGAGATA
1 ATCGCAACGCGATA
198539 ATACAGAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
39 1 0.02
40 44 0.98
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (40 bp):
ATCGCAACGCGATACTGACTTTCGCAACGCAAATCTGACT
Found at i:199137 original size:20 final size:20
Alignment explanation
Indices: 199080--199137 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
199070 CAACGGGGAA
*
199080 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
199100 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
199120 ATCGCAACGCGAAAATGG
1 ATCGCAACGCGAAAATGG
199138 ATATTGCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:199146 original size:20 final size:20
Alignment explanation
Indices: 199080--199146 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
199070 CAACGGGGAA
199080 ATCGCAACGCGAAAAT-GACT
1 ATCGCAACGCGAAAATGGA-T
*
199100 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGAT
199120 ATCGCAACGCGAAAATGGAT
1 ATCGCAACGCGAAAATGGAT
*
199140 ATTGCAA
1 ATCGCAA
199147 TGAGAAAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 42 0.98
21 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGAT
Found at i:199153 original size:20 final size:20
Alignment explanation
Indices: 199080--199155 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
199070 CAACGGGGAA
*
199080 ATCGCAACGCGAAAAT-GACT
1 ATCGCAACGAGAAAATGGA-T
* *
199100 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGAGAAAATGGAT
*
199120 ATCGCAACGCGAAAATGGAT
1 ATCGCAACGAGAAAATGGAT
* *
199140 ATTGCAATGAGAAAAT
1 ATCGCAACGAGAAAAT
199156 CGCAATGCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 49 0.98
21 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGGAT
Found at i:199154 original size:40 final size:40
Alignment explanation
Indices: 199080--199155 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
199070 CAACGGGGAA
*
199080 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACTATCGCAACGAGAAAATGGCT
* *
199120 ATCGCAACGCGAAAATGGA-TATTGCAATGAGAAAAT
1 ATCGCAACGCGAAAAT-GACTATCGCAACGAGAAAAT
199156 CGCAATGCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (40 bp):
ATCGCAACGCGAAAATGACTATCGCAACGAGAAAATGGCT
Found at i:199198 original size:14 final size:14
Alignment explanation
Indices: 199179--199232 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
199169 GAAAATCGCA
199179 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
199193 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
199210 CATTGCAATTTTCTCG
1 --TTGCGATTTTCTCG
199226 TTGCGAT
1 TTGCGAT
199233 AGTCTGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:199198 original size:33 final size:33
Alignment explanation
Indices: 199161--199231 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
199151 AAAATCGCAA
*
199161 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCAATTTTCTCGT
** ** **
199194 TGCGATTTTCATTTCGCATTGCAATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCAATTTTCTCGT
199227 TGCGA
1 TGCGA
199232 TAGTCTGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCAATTTTCTCGT
Found at i:200830 original size:40 final size:42
Alignment explanation
Indices: 200786--200874 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
200776 CCTCTTCAAC
* *
200786 GATGACAATGGCCTCTTGAACG-GT-GTGGGGACTCTTGAGG
1 GATGACAAGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* * *
200826 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAAGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
200868 GATGACA
1 GATGACA
200875 GGTGAGTCGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 19 0.46
41 1 0.02
42 21 0.51
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (42 bp):
GATGACAAGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:200841 original size:21 final size:21
Alignment explanation
Indices: 200812--200872 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
200802 TGAACGGTGT
*
200812 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
200833 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
200854 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
200873 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:200870 original size:42 final size:40
Alignment explanation
Indices: 200795--200872 Score: 120
Period size: 42 Copynumber: 1.9 Consensus size: 40
200785 CGATGACAAT
*
200795 GGCCTCTTGAACGGTGTGGGGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAACGGTGAGGGGACTCTTGAGGGATGATAGG
*
200835 GGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGATGA
1 GGCCTCTTGAACG-GT-GAGGGGACTCTTGAGGGATGA
200873 CAGGTGAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 13 0.38
41 1 0.03
42 20 0.59
ACGTcount: A:0.19, C:0.15, G:0.41, T:0.24
Consensus pattern (40 bp):
GGCCTCTTGAACGGTGAGGGGACTCTTGAGGGATGATAGG
Found at i:201238 original size:20 final size:20
Alignment explanation
Indices: 201213--201284 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
201203 GAAGAATAGT
*
201213 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
201233 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
201253 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
201273 TGACTATCGCAA
1 TTACTTTCGCAA
201285 TGCGGAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:201263 original size:40 final size:40
Alignment explanation
Indices: 201219--201304 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
201209 TAGTTTACTT
* *
201219 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * * *
201259 TCGCAACGCGGAAATGACTATCGCAATGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
201299 TCGCAA
1 TCGCAA
201305 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:201289 original size:20 final size:20
Alignment explanation
Indices: 201239--201314 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
201229 AAACTTACTT
*
201239 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
201259 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
201279 TCGCAATGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
201299 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
201315 AAATCACAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 6 0.12
20 46 0.88
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:201378 original size:19 final size:19
Alignment explanation
Indices: 201356--201486 Score: 66
Period size: 19 Copynumber: 7.3 Consensus size: 19
201346 ACAAATCACA
201356 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
201375 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
* *
201389 TTGCGATTTTCATTTCTCA
1 TTGCGATTTTCATTTCGCG
*
201408 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
* *
201422 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCG
***
201441 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
201461 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
201481 TTGCGA
1 TTGCGA
201487 AAGTAACTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
14 15 0.17
15 6 0.07
16 4 0.05
17 4 0.05
18 6 0.07
19 26 0.30
20 22 0.26
21 3 0.03
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:201392 original size:14 final size:14
Alignment explanation
Indices: 201373--201431 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
201363 TTTCATTTCG
201373 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
201387 CGTTGCGATTTTCATTTCT
1 CGTTGCGA---T--TTTGT
*
201406 CATTGCGATTTTGT
1 CGTTGCGATTTTGT
201420 CGTTGCGATTTT
1 CGTTGCGATTTT
201432 CATTTCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 23 0.64
16 1 0.03
17 1 0.03
19 11 0.31
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:201398 original size:33 final size:33
Alignment explanation
Indices: 201356--201447 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
201346 ACAAATCACA
* *
201356 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
*
201389 TTGCGATTTTCATTTCTCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
201422 TTGCGATTTTCATTTCACATTGCGAT
1 TTGCGATTTTCATTTCACATTGCGAT
201448 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACATTGCGATTTTGTCG
Found at i:201466 original size:20 final size:20
Alignment explanation
Indices: 201441--201486 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
201431 TCATTTCACA
201441 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
201461 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
201481 TTGCGA
1 TTGCGA
201487 AAGTAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:202073 original size:18 final size:18
Alignment explanation
Indices: 202026--202073 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
202016 CGGGTCGATC
*
202026 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
* *
202044 AGGTAATAGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
202062 AGGTGATGGCTC
1 AGGTGATGGCTC
202074 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.42, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:203433 original size:20 final size:20
Alignment explanation
Indices: 203400--203449 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
203390 TGAAATTGAA
* *
203400 AATCGCAGCACGAAAATGAC
1 AATCGCAACGCGAAAATGAC
**
203420 AATCGCAACGCGAATTTGAC
1 AATCGCAACGCGAAAATGAC
*
203440 TATCGCAACG
1 AATCGCAACG
203450 AGAGAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGAAAATGAC
Found at i:203742 original size:22 final size:22
Alignment explanation
Indices: 203712--203755 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
203702 GATGGAGATA
203712 GACGAATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
* *
203734 GACGTATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
203756 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:203970 original size:20 final size:20
Alignment explanation
Indices: 203942--204055 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
203932 GATTATGTAT
*
203942 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
203962 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
203982 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
204002 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
204023 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
204043 TATCGCATTGCGA
1 TATCGCGTTGCGA
204056 TTTTCCAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:204059 original size:41 final size:41
Alignment explanation
Indices: 203922--204057 Score: 186
Period size: 41 Copynumber: 3.3 Consensus size: 41
203912 CGCTTTGAAA
*
203922 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
203963 ATCGCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * *
204003 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
204044 ATCGCATTGCGATT
1 ATCGCATTGCGATT
204058 TTCCAAATTC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
39 3 0.04
40 33 0.40
41 45 0.54
42 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:204071 original size:21 final size:20
Alignment explanation
Indices: 204045--204096 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
204035 ATAGTCAGTA
*
204045 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
204066 TCGCATTTCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
204086 TCGCATTGCGA
1 TCGCATTGCGA
204097 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:210143 original size:17 final size:18
Alignment explanation
Indices: 210113--210148 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
210103 TTAATGATTA
210113 ATTTTAAATAATTTATAT
1 ATTTTAAATAATTTATAT
*
210131 ATTTTTAAT-ATTTATAT
1 ATTTTAAATAATTTATAT
210148 A
1 A
210149 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTAAATAATTTATAT
Found at i:210508 original size:2 final size:2
Alignment explanation
Indices: 210501--210531 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
210491 TCATATTTAA
210501 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
210532 TTTATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218304 original size:12 final size:12
Alignment explanation
Indices: 218289--218354 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
218279 CTTTTTTGGC
218289 TTTTTTTG-TTT
1 TTTTTTTGTTTT
**
218300 TTTTTTTGGCTT
1 TTTTTTTGTTTT
*
218312 TTTTTTTGCCTTT
1 TTTTTTTG-TTTT
***
218325 TTTTTTT-TACC
1 TTTTTTTGTTTT
218336 TTTTTTTGTTTT
1 TTTTTTTGTTTT
218348 TTTTTTT
1 TTTTTTT
218355 TGAAAAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
11 15 0.36
12 18 0.43
13 9 0.21
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.83
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:218314 original size:14 final size:14
Alignment explanation
Indices: 218297--218347 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
218287 GCTTTTTTTG
*
218297 TTTTTTTTTTGGC-
1 TTTTTTTTTTGCCT
218310 -TTTTTTTTTGCCT
1 TTTTTTTTTTGCCT
*
218323 TTTTTTTTTTACCT
1 TTTTTTTTTTGCCT
218337 TTTTTTGTTTT
1 TTTTTT-TTTT
218348 TTTTTTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 11 0.33
14 18 0.55
15 4 0.12
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTGCCT
Found at i:218317 original size:24 final size:23
Alignment explanation
Indices: 218289--218356 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 23
218279 CTTTTTTGGC
*
218289 TTTTTTTGTTTTTTTTTTGGCTT
1 TTTTTTTGTTTTTTTTTTGCCTT
*
218312 TTTTTTTGCCTTTTTTTTTTTACCTT
1 TTTTTTTG---TTTTTTTTTTGCCTT
218338 TTTTTGTT-TTTTTTTTTTG
1 TTTTT-TTGTTTTTTTTTTG
218357 AAAAAAATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 18 0.47
26 18 0.47
27 2 0.05
ACGTcount: A:0.01, C:0.07, G:0.09, T:0.82
Consensus pattern (23 bp):
TTTTTTTGTTTTTTTTTTGCCTT
Found at i:221246 original size:42 final size:42
Alignment explanation
Indices: 221187--221271 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
221177 AATCGTATCC
221187 GGAACTCTTATTAAAGTTCCCGTAGCATAAATTTCTGCACCA
1 GGAACTCTTATTAAAGTTCCCGTAGCATAAATTTCTGCACCA
*
221229 GGAACTCTTATTCAAGTTCCCGTAGCATAAATTTCTGCACCA
1 GGAACTCTTATTAAAGTTCCCGTAGCATAAATTTCTGCACCA
221271 G
1 G
221272 TTAGTTCTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (42 bp):
GGAACTCTTATTAAAGTTCCCGTAGCATAAATTTCTGCACCA
Found at i:225039 original size:27 final size:28
Alignment explanation
Indices: 225009--225065 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
224999 ATAAATATTT
225009 AATATTCATTTAATAGTT-TTTTATAAA
1 AATATTCATTTAATAGTTATTTTATAAA
* *
225036 AATATTCATTTGATAGTTATTTTTTAAA
1 AATATTCATTTAATAGTTATTTTATAAA
225064 AA
1 AA
225066 AAATAGCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (28 bp):
AATATTCATTTAATAGTTATTTTATAAA
Found at i:226619 original size:30 final size:32
Alignment explanation
Indices: 226554--226621 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
226544 ATAAATTGAG
* * *
226554 GAAAAATTCTTATAATATATATATATATATAT
1 GAAAATTTCTTATAATATATATATAAAAATAT
226586 GAAAATTTCTTATAATATAT-T-TAAAAACT-T
1 GAAAATTTCTTATAATATATATATAAAAA-TAT
226616 GAAAAT
1 GAAAAT
226622 ATCTGTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 11 0.34
31 2 0.06
32 19 0.59
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (32 bp):
GAAAATTTCTTATAATATATATATAAAAATAT
Found at i:234206 original size:26 final size:25
Alignment explanation
Indices: 234186--234270 Score: 125
Period size: 26 Copynumber: 3.3 Consensus size: 25
234176 TATTTCATTT
234186 TTAAGCTTATTCGGTTGATTTTTGGA
1 TTAAGCTTATTCGGTTGATTTTT-GA
*
234212 TTAAACTTATTCGGTTGATTTTTGGA
1 TTAAGCTTATTCGGTTGATTTTT-GA
*
234238 TTAAGCTTATTCAGTTGATTTTTGGA
1 TTAAGCTTATTCGGTTGATTTTT-GA
234264 TTAAGCT
1 TTAAGCT
234271 ATTAGATAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.49
Consensus pattern (25 bp):
TTAAGCTTATTCGGTTGATTTTTGA
Found at i:236753 original size:2 final size:2
Alignment explanation
Indices: 236746--236784 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
236736 TTTTAAAATA
236746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
236785 TATGAATGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:236788 original size:8 final size:9
Alignment explanation
Indices: 236748--236789 Score: 56
Period size: 8 Copynumber: 5.1 Consensus size: 9
236738 TTAAAATAAT
236748 ATATATAT-
1 ATATATATG
236756 ATATATAT-
1 ATATATATG
236764 ATATATAT-
1 ATATATATG
236772 ATATATATG
1 ATATATATG
236781 ATAT-TATG
1 ATATATATG
236789 A
1 A
236790 ATGATAATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 29 0.88
9 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (9 bp):
ATATATATG
Found at i:238732 original size:21 final size:20
Alignment explanation
Indices: 238703--238741 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
238693 GAAGAAGTTT
238703 CAGAAAATGGAA-GTGAAACG
1 CAGAAAAT-GAACGTGAAACG
238723 CAGACAAATGAACGTGAAA
1 CAGA-AAATGAACGTGAAA
238742 GTAGTAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.51, C:0.13, G:0.26, T:0.10
Consensus pattern (20 bp):
CAGAAAATGAACGTGAAACG
Found at i:262615 original size:23 final size:24
Alignment explanation
Indices: 262588--262632 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
262578 TTTAAGGTAT
262588 ATTTT-ATTATATTTAA-TATTTTA
1 ATTTTAATT-TATTTAAGTATTTTA
262611 ATTTTAATTTATTTAAGTATTT
1 ATTTTAATTTATTTAAGTATTT
262633 AAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
ATTTTAATTTATTTAAGTATTTTA
Found at i:262654 original size:33 final size:31
Alignment explanation
Indices: 262597--262659 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
262587 TATTTTATTA
* *
262597 TATTTAATATTTTAATTTTAATTTATTTAAG
1 TATTTAAAATTTTAATTTTAATTTAATTAAG
*
262628 TATTTAAAATTTTTAATATTTTATTTAATTAA
1 TATTTAAAA-TTTTAAT-TTTAATTTAATTAA
262660 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 8 0.30
32 7 0.26
33 12 0.44
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (31 bp):
TATTTAAAATTTTAATTTTAATTTAATTAAG
Found at i:264988 original size:34 final size:33
Alignment explanation
Indices: 264914--264988 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
264904 CTTTATTTCA
* *
264914 TTAATTTGGTTGGATTTATTTTTATTTATTTTG
1 TTAATTTGGTTGGATTTATTTTAATGTATTTTG
264947 TTAAATTT-GTTGGACTTT-TTGTTAATGTATTTTGG
1 TT-AATTTGGTTGGA-TTTATT-TTAATGTATTTT-G
264982 TTAATTT
1 TTAATTT
264989 ATTTATTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
33 10 0.28
34 23 0.64
35 3 0.08
ACGTcount: A:0.20, C:0.01, G:0.16, T:0.63
Consensus pattern (33 bp):
TTAATTTGGTTGGATTTATTTTAATGTATTTTG
Found at i:265037 original size:38 final size:36
Alignment explanation
Indices: 264986--265068 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 36
264976 TTTTGGTTAA
264986 TTTATTTATTACCATTTAATATCAGTTATTGTAA-TTTG
1 TTTATTTATTACCATTTAATA-C--TTATTGTAAGTTTG
265024 TTTA-TTATTTACCATTTAATACTTATTGTAAGTTTG
1 TTTATTTA-TTACCATTTAATACTTATTGTAAGTTTG
265060 TTGTATTTA
1 TT-TATTTA
265069 AAATTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
35 9 0.22
36 6 0.15
37 6 0.15
38 20 0.49
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (36 bp):
TTTATTTATTACCATTTAATACTTATTGTAAGTTTG
Found at i:268494 original size:16 final size:16
Alignment explanation
Indices: 268452--268500 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
268442 TATTTTTTTC
268452 AAATAATCATAAT-AAA
1 AAATAAT-ATAATAAAA
*
268468 CAATAAGTATAATAAAA
1 AAATAA-TATAATAAAA
*
268485 AAATAATATAACAAAA
1 AAATAATATAATAAAA
268501 TTACCTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAATATAATAAAA
Found at i:271328 original size:23 final size:24
Alignment explanation
Indices: 271302--271353 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
271292 AGAGATTATT
* * *
271302 AATAATTTAATATATT-ATATTTA
1 AATAATTTAAAAAATTAATATCTA
271325 AAT-ATTTAAAAAATTAATATCTA
1 AATAATTTAAAAAATTAATATCTA
271348 AATAAT
1 AATAAT
271354 GTAAGATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 10 0.42
23 12 0.50
24 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATAATTTAAAAAATTAATATCTA
Found at i:273333 original size:105 final size:109
Alignment explanation
Indices: 273204--273420 Score: 388
Period size: 106 Copynumber: 2.0 Consensus size: 109
273194 TCCACGCCGT
273204 ACGCCTTCCGTTCTTGGACTCATATCGCAA-TTAATTAATAAAGTCACAGTCCGTTAATTTTATC
1 ACGCCTTCCGTTCTTGGACTCATATCGCAATTTAATTAATAAAGTCACAGTCCGTTAATTTTATC
273268 AGAAACCACTTG-GAGTCGACTTT-ATA-CCTTGCTGACGATGG
66 AGAAACCACTTGCGAGTCGACTTTAATACCCTTGCTGACGATGG
273309 ACGCCTTCCGTTCTTGGACTCATATCGCAATTTAATTAATAAAGTCACAGTCCGTTAATTTTATC
1 ACGCCTTCCGTTCTTGGACTCATATCGCAATTTAATTAATAAAGTCACAGTCCGTTAATTTTATC
273374 AGAAACCACTTGCGAGTCGACTTTAAAATACCCTTGCTGACGATGG
66 AGAAACCACTTGCGAGTCGACTTT--AATACCCTTGCTGACGATGG
273420 A
1 A
273421 AACCACTTGC
Statistics
Matches: 106, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
105 30 0.28
106 46 0.43
107 11 0.10
110 3 0.03
111 16 0.15
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (109 bp):
ACGCCTTCCGTTCTTGGACTCATATCGCAATTTAATTAATAAAGTCACAGTCCGTTAATTTTATC
AGAAACCACTTGCGAGTCGACTTTAATACCCTTGCTGACGATGG
Found at i:273409 original size:24 final size:24
Alignment explanation
Indices: 273382--273454 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
273372 TCAGAAACCA
273382 CTTGCGAGTCGACTTTAAAATACC
1 CTTGCGAGTCGACTTTAAAATACC
**
273406 CTTGCTGA--CGA---TGGAA-ACC
1 CTTGC-GAGTCGACTTTAAAATACC
273425 ACTTGCGAGTCGACTTTAAAATACC
1 -CTTGCGAGTCGACTTTAAAATACC
273450 CTTGC
1 CTTGC
273455 TGACGATGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
19 5 0.14
20 8 0.22
21 3 0.08
23 3 0.08
24 13 0.35
25 5 0.14
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (24 bp):
CTTGCGAGTCGACTTTAAAATACC
Found at i:273438 original size:44 final size:44
Alignment explanation
Indices: 273375--273464 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
273365 AATTTTATCA
273375 GAAACCACTTGCGAGTCGACTTTAAAATACCCTTGCTGACGATG
1 GAAACCACTTGCGAGTCGACTTTAAAATACCCTTGCTGACGATG
273419 GAAACCACTTGCGAGTCGACTTTAAAATACCCTTGCTGACGATG
1 GAAACCACTTGCGAGTCGACTTTAAAATACCCTTGCTGACGATG
273463 GA
1 GA
273465 GGTACGTCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (44 bp):
GAAACCACTTGCGAGTCGACTTTAAAATACCCTTGCTGACGATG
Found at i:291030 original size:32 final size:31
Alignment explanation
Indices: 290962--291050 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 31
290952 ATGACCACTA
* * *
290962 TCCATATGTTCCAAAGAACATAGGT-AGCTG
1 TCCATATGTCCCGAAGGACATAGGTAAGCTG
*
290992 TCCATATGTCCCGAAGGACATAGGTAATCATG
1 TCCATATGTCCCGAAGGACATAGGTAAGC-TG
291024 TCCATATGTCCCGAAGGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
291051 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.42
31 2 0.04
32 29 0.55
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAAGCTG
Done.