Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007969.1 Hibiscus syriacus cultivar Beakdansim tig00110406_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: 177975
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:147818 original size:20 final size:18
Alignment explanation
Indices: 147744--147813 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
147734 AAGGTTAATA
147744 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* *
147762 TTTACATATAAACTATATAG
1 TTTATATATGAAC--TATAG
147782 TTTATATACT-AACTATAG
1 TTTATATA-TGAACTATAG
*
147800 TTTAGATATGAACT
1 TTTATATATGAACT
147814 GTATATATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.02
18 27 0.61
20 15 0.34
21 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:147928 original size:20 final size:20
Alignment explanation
Indices: 147899--147969 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
147889 ACATATGACC
147899 TATATATATACTATAGT-TTA
1 TATATATATACTATA-TATTA
*
147919 TATTTATATACTATATATTA
1 TATATATATACTATATATTA
* *
147939 TATATATAAACCATATA-TA
1 TATATATATACTATATATTA
147958 CTATATAGTATA
1 -TATATA-TATA
147970 ATTTACATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATATACTATATATTA
Found at i:147936 original size:53 final size:52
Alignment explanation
Indices: 147826--147962 Score: 197
Period size: 51 Copynumber: 2.6 Consensus size: 52
147816 ATATATAAAT
147826 TATATAGTTTACATATGACCTATATATATATACTATAGTTGATATTTATATAC
1 TATATAGTTTACATATGACC-ATATATATATACTATAGTTGATATTTATATAC
*
147879 TATATAGTTTACATATGACC-TATATATATACTATAGTTTATATTTATATAC
1 TATATAGTTTACATATGACCATATATATATACTATAGTTGATATTTATATAC
* *
147930 TATATA-TTATATATATAAACCATATATACTATA
1 TATATAGTT-TACATAT-GACCATATATA-TATA
147963 TAGTATAATT
Statistics
Matches: 77, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
50 2 0.03
51 42 0.55
52 3 0.04
53 26 0.34
54 4 0.05
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (52 bp):
TATATAGTTTACATATGACCATATATATATACTATAGTTGATATTTATATAC
Found at i:148053 original size:18 final size:18
Alignment explanation
Indices: 148030--148175 Score: 119
Period size: 18 Copynumber: 8.1 Consensus size: 18
148020 TATAGTTTAT
148030 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
148048 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
**
148066 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
148081 TAGTATATAT-AACTATA
1 TAGTATATATAAACTATA
*
148098 TAGTATATGATATATAC-AAA
1 TAGTATAT-ATA-A-ACTATA
* *
148118 CTA-TATATTATATAGT-TCA
1 -TAGTATA-TATAAACTAT-A
148137 TTAGTATATATAAACTATA
1 -TAGTATATATAAACTATA
148156 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
148174 TA
1 TA
148176 TTAATTTATT
Statistics
Matches: 103, Mismatches: 11, Indels: 28
0.73 0.08 0.20
Matches are distributed among these distances:
15 4 0.04
16 10 0.10
17 16 0.16
18 43 0.42
19 10 0.10
20 15 0.15
21 5 0.05
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:148065 original size:51 final size:51
Alignment explanation
Indices: 148010--148178 Score: 259
Period size: 51 Copynumber: 3.2 Consensus size: 51
148000 AAACCCTAAT
*
148010 CTATATATTATATAGTTTATTAGTATATATAAACTATATAGTATATATAAA
1 CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAA
148061 CTATATATTATATAGTTCATTAGTATATAT-AACTATATAGTATATGATATATACAAA
1 CTATATATTATATAGTTCATTAGTATATATAAACTATATAG----T-ATATAT--AAA
148118 CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAA
1 CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAA
148169 CTATATATTA
1 CTATATATTA
148179 ATTTATTAAT
Statistics
Matches: 109, Mismatches: 1, Indels: 16
0.87 0.01 0.13
Matches are distributed among these distances:
50 10 0.09
51 42 0.39
53 6 0.06
54 2 0.02
55 6 0.06
57 33 0.30
58 10 0.09
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (51 bp):
CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAA
Found at i:148119 original size:57 final size:55
Alignment explanation
Indices: 148010--148166 Score: 243
Period size: 57 Copynumber: 2.9 Consensus size: 55
148000 AAACCCTAAT
*
148010 CTATATATTATATAGTTTATTAGTATATATAAACTATATAG----TATATATAAA
1 CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATATATAAA
148061 CTATATATTATATAGTTCATTAGTATATAT-AACTATATAGTATATGATATATACAAA
1 CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATAT-ATATAT--AAA
148118 CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATA
1 CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATA
148167 AACTATATAT
Statistics
Matches: 97, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
50 10 0.10
51 29 0.30
54 1 0.01
55 6 0.06
57 36 0.37
58 15 0.15
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (55 bp):
CTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATATATAAA
Found at i:148123 original size:35 final size:33
Alignment explanation
Indices: 148094--148164 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
148084 TATATATAAC
148094 TATATAGTAT-ATGA-TATATACAAACTATATAT
1 TATATAGT-TCATGAGTATATACAAACTATATAT
* * *
148126 TATATAGTTCATTAGTATATATAAACTATATAG
1 TATATAGTTCATGAGTATATACAAACTATATAT
148159 TATATA
1 TATATA
148165 TAAACTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 1 0.03
32 11 0.32
33 22 0.65
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (33 bp):
TATATAGTTCATGAGTATATACAAACTATATAT
Found at i:151048 original size:14 final size:14
Alignment explanation
Indices: 151031--151077 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
151021 TTATTATTTT
151031 TATATAAATTAAAC
1 TATATAAATTAAAC
151045 TATAT-AATT----
1 TATATAAATTAAAC
151054 TATATAAATTAAAC
1 TATATAAATTAAAC
*
151068 TATATTAATT
1 TATATAAATT
151078 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:151055 original size:23 final size:24
Alignment explanation
Indices: 151029--151078 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
151019 TATTATTATT
151029 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
151052 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
151076 TTT
1 TTT
151079 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:151349 original size:16 final size:16
Alignment explanation
Indices: 151328--151378 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
151318 TCATTTACAT
*
151328 GTCAGGTTAAAAACAG
1 GTCAGGTTGAAAACAG
151344 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAG
*
151360 ATCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAG
151376 GTC
1 GTC
151379 GGGTAATACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (16 bp):
GTCAGGTTGAAAACAG
Found at i:157654 original size:64 final size:64
Alignment explanation
Indices: 157584--157771 Score: 190
Period size: 65 Copynumber: 2.9 Consensus size: 64
157574 GGCTGACCAA
* *
157584 GTGCATCAGTGCACAAATATGC-TTCGATGTTTTAA-AATAGC-CGGGGTGCATCGATGCATGGC
1 GTGCATCGGTGCACAAA-AT-CATTCGATGTTTTAATAATA-CACGGAGTGCATCGATGCATGG-
157646 T-T
62 TAT
* *
157648 GTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATGGTAT
1 GTGCATCGGTGCACAAAATC-ATTCGATGTTTTAATAATACACGGAGTGCATCGATGCATGGTAT
* * * * *
157713 GTGCATCGGTACACAAAAGCTATTCGATG-TTCAATTAAAACAAGG-GTGCATCGATGCAT
1 GTGCATCGGTGCACAAAATC-ATTCGATGTTTTAA-TAATACACGGAGTGCATCGATGCAT
157772 TGATTTATGC
Statistics
Matches: 107, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 48 0.45
65 56 0.52
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTGCACAAAATCATTCGATGTTTTAATAATACACGGAGTGCATCGATGCATGGTAT
Found at i:157718 original size:65 final size:64
Alignment explanation
Indices: 157606--157791 Score: 198
Period size: 65 Copynumber: 2.9 Consensus size: 64
157596 ACAAATATGC
** * * *
157606 TTCGATGTTTTAA-AATAGCCGGGGTGCATCGATGCATGGCTTGTGCATCGGTGCATAAAATCAA
1 TTCGATGTTTTAATAATA-CAAGGGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAAGCAA
* *
157670 TTCGATGTTTTAATAATACATGGAGTGCATCGATGCATGG-TATGTGCATCGGTACACAAAAGCT
1 TTCGATGTTTTAATAATACAAGG-GTGCATCGATGCATGGCT-TGTGCATCGGTACACAAAAGCA
157734 A
64 A
* * ** *
157735 TTCGATG-TTCAATTAAAACAAGGGTGCATCGATGCATTGATTTATGCATCGGTACAC
1 TTCGATGTTTTAA-TAATACAAGGGTGCATCGATGCA-TGGCTTGTGCATCGGTACAC
157792 TTACCTAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
64 34 0.32
65 70 0.67
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (64 bp):
TTCGATGTTTTAATAATACAAGGGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAAGCAA
Found at i:159507 original size:45 final size:45
Alignment explanation
Indices: 159338--159604 Score: 386
Period size: 43 Copynumber: 6.0 Consensus size: 45
159328 TCCAACTTTC
* * * *
159338 TTACCAATACACATATCATTTA-TCCTATAAGCTCGTAAGATTATT
1 TTACCAATATACTTACCATTTATTCC-ATAAGCTCGTAAGCTTATT
*
159383 TTATCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTT-ATTCCATAAGCTCGTAAGCTTATT
159429 TTACCAATAT--TTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* *
159472 TTACCAATATACTTATCATTTATTCCATAAGCTCGTAAGCATATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
159517 TTACCAATAT--TTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
*
159560 TTACCAATATACTTGCCA-TTATTTCC-TAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTA-TTCCATAAGCTCGTAAGCTTATT
159604 T
1 T
159605 GCATGCTTAC
Statistics
Matches: 204, Mismatches: 11, Indels: 15
0.89 0.05 0.07
Matches are distributed among these distances:
43 75 0.37
44 31 0.15
45 67 0.33
46 28 0.14
47 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:159538 original size:88 final size:88
Alignment explanation
Indices: 159354--159604 Score: 409
Period size: 88 Copynumber: 2.9 Consensus size: 88
159344 ATACACATAT
* *
159354 CATTTA-TCCTATAAGCTCGTAAGATTATTTTATCAATATACTTACCATTTAATTCCATAAGCTC
1 CATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTT-ATTCCATAAGCTC
159418 GTAAGCTTATTTTACCAATATTTAC
64 GTAAGCTTATTTTACCAATATTTAC
*
159443 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTATCATTTATTCCATAAGCTCGT
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGT
*
159508 AAGCATATTTTACCAATATTTAC
66 AAGCTTATTTTACCAATATTTAC
*
159531 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA-TTATTTCC-TAAGCTCG
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA-TTCCATAAGCTCG
159594 TAAGCTTATTT
65 TAAGCTTATTT
159605 GCATGCTTAC
Statistics
Matches: 153, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
87 21 0.14
88 86 0.56
89 43 0.28
90 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (88 bp):
CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGT
AAGCTTATTTTACCAATATTTAC
Found at i:159754 original size:40 final size:40
Alignment explanation
Indices: 159709--159910 Score: 314
Period size: 40 Copynumber: 5.0 Consensus size: 40
159699 ACCATGGTGC
* *
159709 TACACATAAGGTCGTGTCCACCATATGCACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
159749 TACACATAAGGCCGTGCCTACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
159789 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
159829 TACACATAAGATCATGCCCACCATACACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
159869 TACACATAAGGTTGTTCCCACCATATACACCGAAGTATAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
159909 TA
1 TA
159911 TAAACTTGCA
Statistics
Matches: 147, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 147 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:160715 original size:11 final size:11
Alignment explanation
Indices: 160701--160731 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
160691 AGTACATCAA
160701 TTATACAACAC
1 TTATACAACAC
160712 TTATACAACAC
1 TTATACAACAC
160723 TTATACAAC
1 TTATACAAC
160732 CCCCTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (11 bp):
TTATACAACAC
Found at i:161632 original size:30 final size:30
Alignment explanation
Indices: 161596--161654 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
161586 TTTGGTCCCT
* *
161596 AAACTTT-TCAAATTTTATACTTTGATCACC
1 AAACTTTACCAAA-TTTATAATTTGATCACC
*
161626 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTGATCAC
161655 TAAATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGATCACC
Found at i:163462 original size:24 final size:23
Alignment explanation
Indices: 163428--163513 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 23
163418 ATATTAATCA
*
163428 TTTCTCATTTTTTTCTCTTTTTCT
1 TTTCTC-TTTTTTTTTCTTTTTCT
*
163452 TTTCTCTTTTTATTTGTTTTTTTTCAT
1 TTTCTC-TTTT-TTT-TTCTTTTTC-T
*
163479 TTTCT-TTTTATTCTTTCTTTTTGT
1 TTTCTCTTTT-TT-TTTCTTTTTCT
163503 TTTCTTCTTTT
1 TTTC-TCTTTT
163514 CTGTTTTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
24 15 0.29
25 18 0.35
26 12 0.24
27 6 0.12
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTCTCTTTTTTTTTCTTTTTCT
Found at i:163484 original size:25 final size:25
Alignment explanation
Indices: 163445--163527 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
163435 TTTTTTTCTC
*
163445 TTTTTCTTTTCTCTTTTTATTTGTTT
1 TTTTTCATTT-TCTTTTTATTTGTTT
*
163471 TTTTTCATTTTCTTTTTATTCT-TTC
1 TTTTTCATTTTCTTTTTATT-TGTTT
* *
163496 TTTTT-GTTTTCTTCTTT-TCTGTTT
1 TTTTTCATTTTCTT-TTTATTTGTTT
163520 TTTTTCAT
1 TTTTTCAT
163528 ATATATATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
23 1 0.02
24 15 0.32
25 21 0.45
26 10 0.21
ACGTcount: A:0.05, C:0.13, G:0.04, T:0.78
Consensus pattern (25 bp):
TTTTTCATTTTCTTTTTATTTGTTT
Found at i:163494 original size:34 final size:33
Alignment explanation
Indices: 163435--163510 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 33
163425 TCATTTCTCA
*
163435 TTTTTTTCTCTTTTTCTTTTCTCTTT-TTATTTG
1 TTTTTTTCTCATTTTCTTTTCTCTTTCTT-TTTG
*
163468 TTTTTTT-TCATTTTCTTTTTATTCTTTCTTTTTG
1 TTTTTTTCTCATTTTC-TTTT-CTCTTTCTTTTTG
*
163502 TTTTCTTCT
1 TTTTTTTCT
163511 TTTCTGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
32 7 0.19
33 11 0.31
34 15 0.42
35 3 0.08
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (33 bp):
TTTTTTTCTCATTTTCTTTTCTCTTTCTTTTTG
Found at i:163510 original size:14 final size:13
Alignment explanation
Indices: 163437--163522 Score: 59
Period size: 13 Copynumber: 6.5 Consensus size: 13
163427 ATTTCTCATT
*
163437 TTTTTCTCTTTTTC
1 TTTTT-TCTTTTTG
* *
163451 TTTTCTCTTTTTA
1 TTTTTTCTTTTTG
163464 TTTGTTT-TTTTT-
1 TTT-TTTCTTTTTG
** *
163476 CATTTTCTTTTTA
1 TTTTTTCTTTTTG
*
163489 TTCTTTCTTTTTG
1 TTTTTTCTTTTTG
163502 TTTTCTTCTTTTCTG
1 TTTT-TTCTTTT-TG
163517 TTTTTT
1 TTTTTT
163523 TTCATATATA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
11 3 0.05
12 6 0.11
13 27 0.47
14 15 0.26
15 6 0.11
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTTCTTTTTG
Found at i:163514 original size:19 final size:18
Alignment explanation
Indices: 163445--163525 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 18
163435 TTTTTTTCTC
*
163445 TTTTTCTT-TTCTCTTTT
1 TTTTTCTTCTTTTCTTTT
*
163462 TATTTGT-TTTTTTTCATTTT
1 T-TTT-TCTTCTTTTC-TTTT
*
163482 CTTTTTATTC-TTTCTTTT
1 -TTTTTCTTCTTTTCTTTT
163500 TGTTTTCTTCTTTTCTGTTT
1 T-TTTTCTTCTTTTCT-TTT
163520 TTTTTC
1 TTTTTC
163526 ATATATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
17 2 0.04
18 16 0.31
19 20 0.38
20 13 0.25
21 1 0.02
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTTCTTCTTTTCTTTT
Found at i:166336 original size:45 final size:45
Alignment explanation
Indices: 166182--166432 Score: 361
Period size: 43 Copynumber: 5.7 Consensus size: 45
166172 GCCATAAAAT
* *
166182 CATTTA-TCCAATAAGCTCGTAAGCTTATTTAATCAATATACTTAC
1 CATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
*
166227 CATTTAATTCCATAAGCTCGTCAGCTTATTTTACCAATAT--TTAC
1 CATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
* *
166271 CATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTAT
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
*
166316 CATTTATTCCATAAGTTCGTAAGCTTATTTTACCAATAT--TTAC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
* *
166359 CGTTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
*
166404 CA-TTATTTCATAAGCTCGTAAGCTTATTT
1 CATTTATTCCATAAGCTCGTAAGCTTATTT
166433 GCATGCTTAC
Statistics
Matches: 186, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
43 72 0.39
44 35 0.19
45 49 0.26
46 27 0.15
47 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (45 bp):
CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
Found at i:166366 original size:88 final size:88
Alignment explanation
Indices: 166182--166432 Score: 398
Period size: 88 Copynumber: 2.9 Consensus size: 88
166172 GCCATAAAAT
*
166182 CATTTA-TCCAATAAGCTCGTAAGCTTATTTAATCAATATACTTACCATTTAATTCCATAAGCTC
1 CATTTATTCC-ATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTT-ATTCCATAAGCTC
*
166246 GTCAGCTTATTTTACCAATATTTAC
64 GTAAGCTTATTTTACCAATATTTAC
* *
166271 CATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTATCATTTATTCCATAAGTTCGT
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTATTCCATAAGCTCGT
166336 AAGCTTATTTTACCAATATTTAC
66 AAGCTTATTTTACCAATATTTAC
* * * *
166359 CGTTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA-TTATTTCATAAGCTCGT
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTATTCCATAAGCTCGT
166423 AAGCTTATTT
66 AAGCTTATTT
166433 GCATGCTTAC
Statistics
Matches: 151, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
87 25 0.17
88 79 0.52
89 44 0.29
90 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (88 bp):
CATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTATTCCATAAGCTCGT
AAGCTTATTTTACCAATATTTAC
Found at i:166581 original size:40 final size:40
Alignment explanation
Indices: 166537--166698 Score: 252
Period size: 40 Copynumber: 4.0 Consensus size: 40
166527 ACCGTAGTGC
*
166537 TACACATAAGGTCGTGCCCACCATATACACCGGAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * * *
166577 TACACATAAGGTCGTACCCACCATATACACTGAAATATAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
166617 TACACATAAGGTCGTGCCCACCATACACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
166657 TACATATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
166697 TA
1 TA
166699 TAAACATCCA
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:168383 original size:30 final size:29
Alignment explanation
Indices: 168329--168419 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 29
168319 ACCCATATGT
* * *
168329 AACTTTTTAAAATTACATTTTGGTCCCTA
1 AACTTTTTAAATTTATAATTTGGTCCCTA
*
168358 AACTTTTTAAAGTTTATACTTTGGTCACC-A
1 AACTTTTTAAA-TTTATAATTTGGTC-CCTA
** *
168388 AACTTTACCAAATTTATAATTTGGTCACTA
1 AACTTT-TTAAATTTATAATTTGGTCCCTA
168418 AA
1 AA
168420 TAAATCCATT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 12 0.24
30 34 0.67
31 5 0.10
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (29 bp):
AACTTTTTAAATTTATAATTTGGTCCCTA
Found at i:176847 original size:16 final size:16
Alignment explanation
Indices: 176823--176856 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
176813 TATCGCCGAC
*
176823 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
176839 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
176855 CG
1 CG
176857 TGAATAGTAA
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:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Done.