Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002034.1 Hibiscus syriacus cultivar Beakdansim tig00004149_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: 97650
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1496 original size:2 final size:2
Alignment explanation
Indices: 1489--1516 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1479 ATTACGTAAA
1489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1517 GATTACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2222 original size:79 final size:77
Alignment explanation
Indices: 2132--2287 Score: 267
Period size: 79 Copynumber: 2.0 Consensus size: 77
2122 AACGTGATAT
2132 TTTTTTATATTATTAAAAATGAAATAATATTATATTATAGTCACAGTCGATAATTTTTTAACCCA
1 TTTTTTATATTATTAAAAATGAAATAATATTATA-TATAGTCACAGTCGAT-ATTTTTTAACCCA
2197 TTGATCAAAATGAA
64 TTGATCAAAATGAA
* * *
2211 TTTTTTATATTATTAAAAATGAAATAATATTATATATAGTGACAGTTGATATTTTTTAACCGATT
1 TTTTTTATATTATTAAAAATGAAATAATATTATATATAGTCACAGTCGATATTTTTTAACCCATT
2276 GATCAAAATGAA
66 GATCAAAATGAA
2288 ATCAAAACTA
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
77 26 0.35
78 14 0.19
79 34 0.46
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (77 bp):
TTTTTTATATTATTAAAAATGAAATAATATTATATATAGTCACAGTCGATATTTTTTAACCCATT
GATCAAAATGAA
Found at i:2311 original size:79 final size:79
Alignment explanation
Indices: 2146--2311 Score: 185
Period size: 77 Copynumber: 2.1 Consensus size: 79
2136 TTATATTATT
2146 AAAAATGAAATAATATTATATTATAGTCACAGTCGATAATTTTTTAACCCATTGATCAAAATGAA
1 AAAAATGAAATAATATTATATTATAGTCACAGTCGATAATTTTTTAACCCATTGATCAAAATGAA
* **** * **
2211 TTTTTTATATTATT
66 ATCAAAATATGAGG
* * *
2225 AAAAATGAAATAATATTATA-TATAGTGACAGTTGAT-ATTTTTTAACCGATTGATCAAAATGAA
1 AAAAATGAAATAATATTATATTATAGTCACAGTCGATAATTTTTTAACCCATTGATCAAAATGAA
2288 ATCAAAACTA-GAGG
66 ATCAAAA-TATGAGG
2302 AGAAGAATGA
1 A-AA-AATGA
2312 TTTAAAAAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
77 30 0.41
78 18 0.25
79 25 0.34
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (79 bp):
AAAAATGAAATAATATTATATTATAGTCACAGTCGATAATTTTTTAACCCATTGATCAAAATGAA
ATCAAAATATGAGG
Found at i:4311 original size:31 final size:31
Alignment explanation
Indices: 4275--4333 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4265 AACTTAAAAG
* *
4275 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
4306 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
4334 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:4418 original size:32 final size:34
Alignment explanation
Indices: 4374--4454 Score: 112
Period size: 32 Copynumber: 2.4 Consensus size: 34
4364 AAATCAATCA
4374 TATTTTAAAATAAATCAATCCATA-CTAATAAAT
1 TATTTTAAAATAAATCAATCCATATCTAATAAAT
* * * *
4407 TA-TTTAAAATAAATCAATTCATATTTTATAATT
1 TATTTTAAAATAAATCAATCCATATCTAATAAAT
4440 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
4455 TATTTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 20 0.48
33 10 0.24
34 12 0.29
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (34 bp):
TATTTTAAAATAAATCAATCCATATCTAATAAAT
Found at i:4457 original size:15 final size:15
Alignment explanation
Indices: 4434--4469 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
4424 TTCATATTTT
*
4434 ATAATTTATTTTAAA
1 ATAAATTATTTTAAA
4449 ATAAATTATTTTAAA
1 ATAAATTATTTTAAA
4464 ATAAAT
1 ATAAAT
4470 AACCTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAAATTATTTTAAA
Found at i:14423 original size:19 final size:19
Alignment explanation
Indices: 14386--14421 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14376 TTTAATGTAT
14386 AATTAGATTAAATCCTTTA
1 AATTAGATTAAATCCTTTA
*
14405 AATTAG-TTGAATCCTTT
1 AATTAGATTAAATCCTTT
14422 TACTGCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (19 bp):
AATTAGATTAAATCCTTTA
Found at i:14737 original size:18 final size:17
Alignment explanation
Indices: 14710--14748 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
14700 AAAAAATCAA
14710 AATTTCTATTATGAATCT
1 AATTTCTATTAT-AATCT
* *
14728 AATTTTTATTATAATTT
1 AATTTCTATTATAATCT
14745 AATT
1 AATT
14749 AGTTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (17 bp):
AATTTCTATTATAATCT
Found at i:20988 original size:63 final size:63
Alignment explanation
Indices: 20911--21032 Score: 192
Period size: 63 Copynumber: 1.9 Consensus size: 63
20901 AGCCATTTTT
*
20911 CCACAACAAACACCTAAGTGAT-GCAGCAGACAGATTCTCAGTGGTCAATGCCTACAAAGAGTA
1 CCACAACAAACACCTAAGTGATAG-AGCAGACAGATTCTCAGTGGTCAATACCTACAAAGAGTA
* * *
20974 CCACCACAAACACCTAAGTGATAGAGTAGATAGATTCTCAGTGGTCAATACCTACAAAG
1 CCACAACAAACACCTAAGTGATAGAGCAGACAGATTCTCAGTGGTCAATACCTACAAAG
21033 TGTAACTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 53 0.98
64 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (63 bp):
CCACAACAAACACCTAAGTGATAGAGCAGACAGATTCTCAGTGGTCAATACCTACAAAGAGTA
Found at i:22848 original size:436 final size:436
Alignment explanation
Indices: 22163--23039 Score: 1623
Period size: 436 Copynumber: 2.0 Consensus size: 436
22153 ATCATATTAA
*
22163 AATATTCGTATTTATGATTATTTTGGTTGGATATATAATTATTTTACTATTAAAATTGTATGAAT
1 AATATTCGTATTTATGATTATTTTGGTTGGATATATAATTATTTTACTAGTAAAATTGTATGAAT
22228 TTGAAAAATAATTATAAAAAATTGGTGATATTTCAAATAAACAATTTAAAAATGTAACATGAATA
66 TTGAAAAATAATTATAAAAAATTGGTGATATTTCAAATAAACAATTTAAAAATGTAACATGAATA
22293 TTATTATATTTATAAAAAAATATAAAACAATTTAATAACATTGTATTATTATTGTTTTAACTGAA
131 TTATTATATTTATAAAAAAATATAAAACAATTTAATAACATTGTATTATTATTGTTTTAACTGAA
* *
22358 TTAACTTAAAAATTATATTTTTAAGTAATTGCTAATTTTATTAAAAATTTAAAATTACAATTAAA
196 TTAACTTAAAAATTATATTTTTAAGTAATTGCTAATTTTATTAAAAAATTAAAATTAAAATTAAA
* *
22423 GTTTACAACAGTACACGTAAATTAAATACATAATTAGAACATTTTCTATTACTATTGACTCAATA
261 GTTTACAACAGTACACATAAATTAAACACATAATTAGAACATTTTCTATTACTATTGACTCAATA
*
22488 AACTATTCACTCTGAATCATATAATGACCATATAAAAAATTAAAAAACTTGAAAAAAAACTTAAA
326 AACTATTCACTCTGAATCATATAAGGACCATAT-AAAAATTAAAAAACTTGAAAAAAAACTTAAA
22553 TAAAATATATATACAAACAAATCTGACGGTATCGATAGACAAACCAC
390 TAAAATATATATACAAACAAATCTGACGGTATCGATAGACAAACCAC
22600 AATATTCGTATTTATGATTATTTTGGTTGGATATATAATTATTTTACTAGT-AAATTGTATGAAT
1 AATATTCGTATTTATGATTATTTTGGTTGGATATATAATTATTTTACTAGTAAAATTGTATGAAT
22664 TTGAAAAATAATTATAAAAAATTGGTGATATTTCAAATAAACAATTTAAAAATGTAACATGAATA
66 TTGAAAAATAATTATAAAAAATTGGTGATATTTCAAATAAACAATTTAAAAATGTAACATGAATA
*
22729 TTATTATATTTAT-AAAAAATATAAAACAATTTAATAACATTGTATTATTATTGTTTTAATTGAA
131 TTATTATATTTATAAAAAAATATAAAACAATTTAATAACATTGTATTATTATTGTTTTAACTGAA
*
22793 TTAACTTAAAAATTATATTTTTAAGTAATTGCTAGTTTTATTAAAAAAATTAAAATTAAAATTAA
196 TTAACTTAAAAATTATATTTTTAAGTAATTGCTAATTTTATT-AAAAAATTAAAATTAAAATTAA
* * *
22858 AGTTTACAACCGTACACATAAATTAAACACATAATTAGGATATTTTCTATTACTATTGACTCAAT
260 AGTTTACAACAGTACACATAAATTAAACACATAATTAGAACATTTTCTATTACTATTGACTCAAT
22923 AAACTATTCACTCTGAATCATATAAGGACCATATAAAAATTAAAAAACTTGAAAAAAAACTTAAA
325 AAACTATTCACTCTGAATCATATAAGGACCATATAAAAATTAAAAAACTTGAAAAAAAACTTAAA
22988 TAAAATATATATACAAACAAATCTGACGGTATCGATAGACAAACCAC
390 TAAAATATATATACAAACAAATCTGACGGTATCGATAGACAAACCAC
23035 AATAT
1 AATAT
23040 GAGATCAAAT
Statistics
Matches: 428, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
435 174 0.41
436 204 0.48
437 50 0.12
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (436 bp):
AATATTCGTATTTATGATTATTTTGGTTGGATATATAATTATTTTACTAGTAAAATTGTATGAAT
TTGAAAAATAATTATAAAAAATTGGTGATATTTCAAATAAACAATTTAAAAATGTAACATGAATA
TTATTATATTTATAAAAAAATATAAAACAATTTAATAACATTGTATTATTATTGTTTTAACTGAA
TTAACTTAAAAATTATATTTTTAAGTAATTGCTAATTTTATTAAAAAATTAAAATTAAAATTAAA
GTTTACAACAGTACACATAAATTAAACACATAATTAGAACATTTTCTATTACTATTGACTCAATA
AACTATTCACTCTGAATCATATAAGGACCATATAAAAATTAAAAAACTTGAAAAAAAACTTAAAT
AAAATATATATACAAACAAATCTGACGGTATCGATAGACAAACCAC
Found at i:23480 original size:3 final size:3
Alignment explanation
Indices: 23468--23520 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
23458 TCCTTAAAAC
23468 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23515 ATT ATT
1 ATT ATT
23521 GGGTTCGTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:27233 original size:18 final size:18
Alignment explanation
Indices: 27207--27241 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27197 TCAAAAGGAC
*
27207 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
27225 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
27242 CCGAATGGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:28365 original size:24 final size:23
Alignment explanation
Indices: 28338--28424 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
28328 ATCTCCGAAT
*
28338 TGAATTCTGTTCTGATACGTTACC
1 TGAATTCTGTTCTGATAC-TGACC
* *
28362 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTGACC
* **
28385 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATA-CTGACC
* *
28409 TGAATTATGTTTTGAT
1 TGAATTCTGTTCTGAT
28425 TTCTAATATC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGACC
Found at i:28405 original size:12 final size:11
Alignment explanation
Indices: 28341--28405 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
28331 TCCGAATTGA
28341 ATTCTGTTCTG
1 ATTCTGTTCTG
*
28352 ATAC-GTTACCTG
1 ATTCTGTT--CTG
28364 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
28376 ATTCTGATCTGG
1 ATTCTGTTCT-G
28388 ATTCTGTTCTG
1 ATTCTGTTCTG
28399 ATATCTG
1 AT-TCTG
28406 ATATGAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 15 0.34
12 20 0.45
13 3 0.07
14 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:32624 original size:17 final size:18
Alignment explanation
Indices: 32602--32636 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32592 TAGGGTTCAA
*
32602 TTATAAT-ATTTTAAAAT
1 TTATAATCAATTTAAAAT
32619 TTATAATCAATTTAAAAT
1 TTATAATCAATTTAAAAT
32637 CTAAATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATAATCAATTTAAAAT
Found at i:34191 original size:21 final size:20
Alignment explanation
Indices: 34160--34295 Score: 123
Period size: 21 Copynumber: 6.5 Consensus size: 20
34150 GTTTCCAGAT
*
34160 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAA-TTCGACTA
* *
34181 TCGCATTGCGAACTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
*
34202 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
*
34223 TCGCAATGCGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
*
34243 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTCGACTA
*
34264 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
*
34285 TCGCATTGCGA
1 TCGCAATGCGA
34296 TTTACATATT
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.17
21 82 0.83
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATTCGACTA
Found at i:34263 original size:41 final size:42
Alignment explanation
Indices: 34160--34295 Score: 152
Period size: 42 Copynumber: 3.3 Consensus size: 42
34150 GTTTCCAGAT
* * * *
34160 TCGCAACGCGAACTTCGACTATCGCATTGCGAACTTGGACTA
1 TCGCAATGCGAACGTCGACTATCGCAATGCGAACTTGGACAA
* * *
34202 TCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACGTCGACTATCGCAATGCGAACT-TGGACAA
*
34243 TCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTA
1 TCGCAATGCGA-ACGTCGACTATCGCAATGCGAACTTGGACAA
*
34285 TCGCATTGCGA
1 TCGCAATGCGA
34296 TTTACATATT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
41 34 0.43
42 46 0.57
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (42 bp):
TCGCAATGCGAACGTCGACTATCGCAATGCGAACTTGGACAA
Found at i:34309 original size:62 final size:62
Alignment explanation
Indices: 34197--34336 Score: 196
Period size: 62 Copynumber: 2.3 Consensus size: 62
34187 TGCGAACTTG
*
34197 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATACGATAGTC
* *
34259 GACTATCGCAATGCGAACTTGGACTATCGCATTGCG-AT-T-TACATATTCGCATTACGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A-TCGCAATACGATAGTC
*
34321 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
34337 TAGTCAAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
59 2 0.03
60 2 0.03
61 3 0.04
62 64 0.90
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (62 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATACGATAGTC
Found at i:34349 original size:21 final size:21
Alignment explanation
Indices: 34305--34351 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
34295 ATTTACATAT
* **
34305 TCGCATTACGATAGTCGACTA
1 TCGCATTACGATAGTCAAAAA
*
34326 TCGCATTGCGATAGTCAAAAA
1 TCGCATTACGATAGTCAAAAA
34347 TCGCA
1 TCGCA
34352 ACGACTGGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
TCGCATTACGATAGTCAAAAA
Found at i:36002 original size:23 final size:23
Alignment explanation
Indices: 35970--36013 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35960 CTTTGTTATT
35970 TTATTATTAATTAAATATTTACA
1 TTATTATTAATTAAATATTTACA
* *
35993 TTATTTTTAATTTAATATTTA
1 TTATTATTAATTAAATATTTA
36014 ATAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATTATTAATTAAATATTTACA
Found at i:43679 original size:19 final size:20
Alignment explanation
Indices: 43650--43690 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
43640 GGAAATATTA
*
43650 AAAAAATTAATGTTTTAGGT
1 AAAAAATTAATATTTTAGGT
43670 AAAAAA-TAATATTTTAGGT
1 AAAAAATTAATATTTTAGGT
43689 AA
1 AA
43691 TTTTTTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (20 bp):
AAAAAATTAATATTTTAGGT
Found at i:49967 original size:40 final size:40
Alignment explanation
Indices: 49892--49967 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
49882 ACAATGTCAG
*
49892 TAATTAATTATTTCACAATATTTCAATACAAAATATCCCT
1 TAATTAATTATTTCACAATATTTCAATAAAAAATATCCCT
* *
49932 TAATTAATTATTTTACAATCTTTC-ATAAAATAATAT
1 TAATTAATTATTTCACAATATTTCAATAAAA-AATAT
49968 ACACTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 5 0.16
40 27 0.84
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (40 bp):
TAATTAATTATTTCACAATATTTCAATAAAAAATATCCCT
Found at i:51032 original size:2 final size:2
Alignment explanation
Indices: 51021--51053 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
51011 TTTTATTAAT
*
51021 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51054 CACGACTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:54970 original size:31 final size:30
Alignment explanation
Indices: 54903--54971 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
54893 AGTTTCTGAA
* * *
54903 ATTACAAAATGGTTATTAAACTTCCCAAAT
1 ATTACAAAATGATCATTAAACTTCCAAAAT
* *
54933 AGTTACAAAATGATCATTAAATTTGTCAAAAT
1 A-TTACAAAATGATCATTAAACTT-CCAAAAT
54965 ATTACAA
1 ATTACAA
54972 TATAGTCGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 25 0.78
32 6 0.19
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (30 bp):
ATTACAAAATGATCATTAAACTTCCAAAAT
Found at i:55200 original size:3 final size:3
Alignment explanation
Indices: 55192--55231 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
55182 GAAATTTGAT
55192 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55232 ATGCCTTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56535 original size:53 final size:53
Alignment explanation
Indices: 56433--56535 Score: 120
Period size: 53 Copynumber: 1.9 Consensus size: 53
56423 TCATTGGATG
** * ***
56433 ACTCTAAATAGATGGTTGAGATTAAAATCTTGTGCATTAGTTTTATATATATA
1 ACTCTAAATAGATGACTGAGATTAAAATCTTGTACATTAGACATATATATATA
56486 ACTCTAAATAGATGACTGAGATTTAAAAATCTTGTACATTA-ACAT-TATAT
1 ACTCTAAATAGATGACTGAGA-TT-AAAATCTTGTACATTAGACATATATAT
56536 TTCTCTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
53 24 0.57
54 3 0.07
55 15 0.36
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (53 bp):
ACTCTAAATAGATGACTGAGATTAAAATCTTGTACATTAGACATATATATATA
Found at i:56676 original size:2 final size:2
Alignment explanation
Indices: 56669--56693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56659 ATCCTACTCC
56669 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
56694 TCTCATAAGC
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:64218 original size:20 final size:20
Alignment explanation
Indices: 64182--64219 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
64172 ATCCTATTCC
**
64182 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
64202 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
64220 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:67238 original size:21 final size:21
Alignment explanation
Indices: 67205--67244 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
67195 AGTCTAAATG
* *
67205 TACCAAGTGTTTTACTAAACA
1 TACCAAGTCTTTTAATAAACA
*
67226 TACCAATTCTTTTAATAAA
1 TACCAAGTCTTTTAATAAA
67245 ATAATAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (21 bp):
TACCAAGTCTTTTAATAAACA
Found at i:67753 original size:277 final size:277
Alignment explanation
Indices: 67259--67813 Score: 1101
Period size: 277 Copynumber: 2.0 Consensus size: 277
67249 TAAAATAGGA
67259 ATGCTTTGTCAGCATTTGGACAGCAACTCACCTTTTTCTATGTTTCACGTGCGCTGAACTCAACG
1 ATGCTTTGTCAGCATTTGGACAGCAACTCACCTTTTTCTATGTTTCACGTGCGCTGAACTCAACG
67324 TACCCAACCGCCTCCCATTCATTCCAACCGGATCTTACACAATATATATTTTCATAAATTAAATA
66 TACCCAACCGCCTCCCATTCATTCCAACCGGATCTTACACAATATATATTTTCATAAATTAAATA
67389 TTATAAAACATTATTACAGATAATTTTTAGCTCTATTTTTTATTCATTATATCGGATTTCAATCT
131 TTATAAAACATTATTACAGATAATTTTTAGCTCTATTTTTTATTCATTATATCGGATTTCAATCT
67454 TTAATTCCAATTAAAGAAATCAATATTATTTATAACATTGATAATTTAAATTAGGATAAGTCTAC
196 TTAATTCCAATTAAAGAAATCAATATTATTTATAACATTGATAATTTAAATTAGGATAAGTCTAC
67519 AACGTATGTTGTATACC
261 AACGTATGTTGTATACC
67536 ATGCTTTGTCAGCATTTGGACAGCAACTCACCTTTTTCTATGTTTCACGTGCGCTGAACTCAACG
1 ATGCTTTGTCAGCATTTGGACAGCAACTCACCTTTTTCTATGTTTCACGTGCGCTGAACTCAACG
*
67601 TACCCAACCGCCTCCCATTCATTCCAACCGGATCTTGCACAATATATATTTTCATAAATTAAATA
66 TACCCAACCGCCTCCCATTCATTCCAACCGGATCTTACACAATATATATTTTCATAAATTAAATA
67666 TTATAAAACATTATTACAGATAATTTTTAGCTCTATTTTTTATTCATTATATCGGATTTCAATCT
131 TTATAAAACATTATTACAGATAATTTTTAGCTCTATTTTTTATTCATTATATCGGATTTCAATCT
67731 TTAATTCCAATTAAAGAAATCAATATTATTTATAACATTGATAATTTAAATTAGGATAAGTCTAC
196 TTAATTCCAATTAAAGAAATCAATATTATTTATAACATTGATAATTTAAATTAGGATAAGTCTAC
67796 AACGTATGTTGTATACC
261 AACGTATGTTGTATACC
67813 A
1 A
67814 CTATATATTA
Statistics
Matches: 277, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
277 277 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (277 bp):
ATGCTTTGTCAGCATTTGGACAGCAACTCACCTTTTTCTATGTTTCACGTGCGCTGAACTCAACG
TACCCAACCGCCTCCCATTCATTCCAACCGGATCTTACACAATATATATTTTCATAAATTAAATA
TTATAAAACATTATTACAGATAATTTTTAGCTCTATTTTTTATTCATTATATCGGATTTCAATCT
TTAATTCCAATTAAAGAAATCAATATTATTTATAACATTGATAATTTAAATTAGGATAAGTCTAC
AACGTATGTTGTATACC
Found at i:76315 original size:6 final size:6
Alignment explanation
Indices: 76306--76331 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
76296 ATATATATAT
76306 ATATTG ATATTG ATATTG ATATTG AT
1 ATATTG ATATTG ATATTG ATATTG AT
76332 GCTCATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATATTG
Found at i:76576 original size:17 final size:17
Alignment explanation
Indices: 76556--76588 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
76546 AACATGCTTT
*
76556 TGTTAAAGACATTATGG
1 TGTTAAAGAAATTATGG
76573 TGTTAAAGAAATTATG
1 TGTTAAAGAAATTATG
76589 CAAATATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.36
Consensus pattern (17 bp):
TGTTAAAGAAATTATGG
Found at i:78382 original size:99 final size:99
Alignment explanation
Indices: 78211--78403 Score: 332
Period size: 99 Copynumber: 1.9 Consensus size: 99
78201 TCTCCTCCAA
* *
78211 CTTCTTCAGCTGTTGTTCCTTCAAATACTTCCTTCTAGCCCCGTACCTTTAAATGACATGAGCAT
1 CTTCTTCAGCTGTTGTTCCTTCAAATACTTCCTTCTAGCCCCATACCTTTAAATGACACGAGCAT
**
78276 ATGTAGATGCATCATAACCGTTCCATCTATCGCT
66 ATGTAGATGCATCATAACCACTCCATCTATCGCT
* *
78310 CTTCTTCAGCTGTTGTTCCTTCAAATACTTCCTTCTAGCCTCATACCTTTGAATGACACGAGCAT
1 CTTCTTCAGCTGTTGTTCCTTCAAATACTTCCTTCTAGCCCCATACCTTTAAATGACACGAGCAT
78375 ATGTAGATGCATCATAACCACTCCATCTA
66 ATGTAGATGCATCATAACCACTCCATCTA
78404 CCCCTCTTGC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.35
Consensus pattern (99 bp):
CTTCTTCAGCTGTTGTTCCTTCAAATACTTCCTTCTAGCCCCATACCTTTAAATGACACGAGCAT
ATGTAGATGCATCATAACCACTCCATCTATCGCT
Found at i:81025 original size:2 final size:2
Alignment explanation
Indices: 81018--81071 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
81008 AGGATACACA
81018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81060 AT AT AT AT AT AT
1 AT AT AT AT AT AT
81072 TAATAAACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82540 original size:2 final size:2
Alignment explanation
Indices: 82533--82570 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
82523 ATGAAAAGTT
82533 TA TA TA TA 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 TA TA TA TA
82571 CACCCTCCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83439 original size:16 final size:16
Alignment explanation
Indices: 83415--83455 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
83405 ATAATTTTAT
* *
83415 TTTTA-AAATTTATTA
1 TTTTATAAATTCAATA
83430 TTTTATAAATTCAATA
1 TTTTATAAATTCAATA
83446 -TTTATAAATT
1 TTTTATAAATT
83456 AAATCTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTATAAATTCAATA
Found at i:84519 original size:23 final size:24
Alignment explanation
Indices: 84493--84539 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
84483 ATACTGTAAA
*
84493 TTTTTTGA-ACCGTAAATGATATG
1 TTTTTTAATACCGTAAATGATATG
84516 TTTTTTAATCTACCGTAAATGATA
1 TTTTTTAA--TACCGTAAATGATA
84540 ATTTGATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
26 13 0.65
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (24 bp):
TTTTTTAATACCGTAAATGATATG
Done.