Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000255.1 Hibiscus syriacus cultivar Beakdansim tig00000466_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: 76687
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:4428 original size:9 final size:9
Alignment explanation
Indices: 4414--4501 Score: 58
Period size: 9 Copynumber: 9.4 Consensus size: 9
4404 AAAATTATAT
4414 TATAATAAA
1 TATAATAAA
4423 TATAATAATAA
1 TATAAT-A-AA
*
4434 TAATAATAAT
1 T-ATAATAAA
4444 TAATAATATGAA
1 T-ATAATA--AA
*
4456 T-TATTAAA
1 TATAATAAA
4464 TATAATAAA
1 TATAATAAA
*
4473 TA-ATTAAAA
1 TATAAT-AAA
4482 TATAAT-AA
1 TATAATAAA
4490 TAT-ATAAA
1 TATAATAAA
4498 TATA
1 TATA
4502 GTAATTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
7 2 0.03
8 15 0.24
9 19 0.30
10 16 0.25
11 4 0.06
12 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
TATAATAAA
Found at i:4430 original size:3 final size:3
Alignment explanation
Indices: 4415--4496 Score: 50
Period size: 3 Copynumber: 27.3 Consensus size: 3
4405 AAATTATATT
* *
4415 ATA ATA A-A TATA ATA ATA ATA ATA ATA ATTA ATA AT- ATGA ATT ATT
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA
4461 A-A AT- ATA ATAA ATA ATTA A-A AT- ATA ATA ATA TATA A
1 ATA ATA ATA AT-A ATA A-TA ATA ATA ATA ATA ATA -ATA A
4497 ATATAGTAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 24
0.71 0.02 0.26
Matches are distributed among these distances:
2 10 0.15
3 40 0.62
4 15 0.23
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:4500 original size:16 final size:16
Alignment explanation
Indices: 4418--4506 Score: 68
Period size: 16 Copynumber: 5.9 Consensus size: 16
4408 TTATATTATA
4418 ATAAATATAATAATA-
1 ATAAATATAATAATAT
4433 AT-AATAATAATTAATAAT
1 ATAAAT-ATAA-TAAT-AT
* *
4451 ATGAAT-TATTAA-AT
1 ATAAATATAATAATAT
4465 AT-AATA-AATAAT-T
1 ATAAATATAATAATAT
4478 A-AAATATAATAATAT
1 ATAAATATAATAATAT
*
4493 ATAAATATAGTAAT
1 ATAAATATAATAAT
4507 TAAAATAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
13 13 0.22
14 13 0.22
15 8 0.13
16 18 0.30
17 3 0.05
18 2 0.03
19 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAAATATAATAATAT
Found at i:4508 original size:50 final size:48
Alignment explanation
Indices: 4406--4662 Score: 165
Period size: 50 Copynumber: 5.3 Consensus size: 48
4396 GTAGAAATAA
* *
4406 AATTAT-ATTATAATAAAT-A-TAATAATAATAATAATAATTAATAATA-T
1 AATTATAAATATAATAAATAATTAA-AAT-ATAATAATAATAAAT-ATAGT
4453 GAATTATTAAATATAATAAATAATTAAAATATAATAATATATAAATATAGT
1 -AATTA-TAAATATAATAAATAATTAAAATATAATAATA-ATAAATATAGT
* ** * * * * * *
4504 AATTA-AAATAGAA-ATTTTA-TAAAAGATAATTATAATATATTTTGT
1 AATTATAAATATAATAAATAATTAAAATATAATAATAATAAATATAGT
* * * * * *
4549 AAATTTTGAA-ATAATGAAA-AATTATATTATAATAAATAAATATTATAATATT
1 -AATTATAAATATAAT-AAATAATTAAAATATAAT-AAT-AATA-AAT-ATAGT
4601 AATTATCAAATATAATAAATAATTAAAATATAATAATATATAAATATAGT
1 AATTAT-AAATATAATAAATAATTAAAATATAATAATA-ATAAATATAGT
4651 AATTA-AAATATA
1 AATTATAAATATA
4663 TATTTTATAA
Statistics
Matches: 160, Mismatches: 30, Indels: 38
0.70 0.13 0.17
Matches are distributed among these distances:
45 8 0.05
46 20 0.12
47 6 0.04
48 28 0.17
49 3 0.02
50 41 0.26
51 21 0.13
52 16 0.10
53 17 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (48 bp):
AATTATAAATATAATAAATAATTAAAATATAATAATAATAAATATAGT
Found at i:4597 original size:147 final size:147
Alignment explanation
Indices: 4430--4746 Score: 523
Period size: 147 Copynumber: 2.2 Consensus size: 147
4420 AAATATAATA
*
4430 ATAAT-AAT-AATAATTAATAATATGAATTATTAAATATAATAAATAATTAAAATATAATAATAT
1 ATAATAAATAAATAATT-ATAATATGAATTATCAAATATAATAAATAATTAAAATATAATAATAT
*
4493 ATAAATATAGTAATTAAAATAGAAATTTTATAAAAGATAATTATAATATATTTTGTAAATTTTGA
65 ATAAATATAGTAATTAAAATAGAAATTTTATAAAA-ATAATTATAATATATTTTATAAATTTTGA
4558 AATAATGAAAAATTATATT
129 AATAATGAAAAATTATATT
*
4577 ATAATAAATAAAT-ATTATAATATTAATTATCAAATATAATAAATAATTAAAATATAATAATATA
1 ATAATAAATAAATAATTATAATATGAATTATCAAATATAATAAATAATTAAAATATAATAATATA
* *
4641 TAAATATAGTAATTAAAATATATATTTTATAAAAATAATTATAATATATTTTATAAATTTTGAAA
66 TAAATATAGTAATTAAAATAGAAATTTTATAAAAATAATTATAATATATTTTATAAATTTTGAAA
4706 TAATGAAAAATTATATT
131 TAATGAAAAATTATATT
* *
4723 ATATTATAATAAATAAATATAATA
1 ATAATA-AATAAATAATTATAATA
4747 ATATTATTAT
Statistics
Matches: 159, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
146 52 0.33
147 90 0.57
148 14 0.09
149 3 0.02
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (147 bp):
ATAATAAATAAATAATTATAATATGAATTATCAAATATAATAAATAATTAAAATATAATAATATA
TAAATATAGTAATTAAAATAGAAATTTTATAAAAATAATTATAATATATTTTATAAATTTTGAAA
TAATGAAAAATTATATT
Found at i:4637 original size:14 final size:14
Alignment explanation
Indices: 4614--4662 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
4604 TATCAAATAT
4614 AATA-AATAATTAA
1 AATATAATAATTAA
4627 AATATAATAATATATA
1 AATATAATAAT-TA-A
*
4643 AATATAGTAATTAA
1 AATATAATAATTAA
4657 AATATA
1 AATATA
4663 TATTTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 4 0.12
14 13 0.41
15 4 0.12
16 11 0.34
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AATATAATAATTAA
Found at i:4644 original size:56 final size:55
Alignment explanation
Indices: 4572--4809 Score: 161
Period size: 56 Copynumber: 4.3 Consensus size: 55
4562 ATGAAAAATT
* * *
4572 ATATTATAATAAATAAATATTA-TAATATTAATTATCAAATATAATAAATAATTAAA
1 ATATAATAATATATAAATATTAGTAATATAAATTAT--AATATAATAAATAATTAAA
* *
4628 ATATAATAATATATAAATA-TAGTAAT-TAAAATATATATTTTATAA-AAATAATTATA
1 ATATAATAATATATAAATATTAGTAATAT-AAAT-TATA--ATATAATAAATAATTAAA
* * * * * * *
4684 ATAT-AT--TTTATAAATTTTGAAATAATGAAAAATTATATTATATTATAATAAAT-AA
1 ATATAATAATATATAAATATT--AGTAAT-ATAAATTATAATATAATA-AATAATTAAA
* * * * *
4739 ATATAATAATATTATTATTATTATTATTATTAATTAT-ATATAATAAATAATTAAA
1 ATATAATAATA-TATAAATATTAGTAATATAAATTATAATATAATAAATAATTAAA
4794 ATATAATAATATATAA
1 ATATAATAATATATAA
4810 GTATAGAAAT
Statistics
Matches: 141, Mismatches: 24, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
53 8 0.06
54 16 0.11
55 31 0.22
56 62 0.44
57 16 0.11
58 1 0.01
59 7 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (55 bp):
ATATAATAATATATAAATATTAGTAATATAAATTATAATATAATAAATAATTAAA
Found at i:6546 original size:28 final size:28
Alignment explanation
Indices: 6514--6573 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
6504 CATTACTTAC
** *
6514 AAATTTTATCATTTTAATTTAATT-GAAT
1 AAATTTTATC-TTACAATTTAATTAGAAA
6542 AAATTTTATCTTACAATTTAATTAGAAA
1 AAATTTTATCTTACAATTTAATTAGAAA
6570 AAAT
1 AAAT
6574 AAATCTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (28 bp):
AAATTTTATCTTACAATTTAATTAGAAA
Found at i:11422 original size:43 final size:43
Alignment explanation
Indices: 11349--11434 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
11339 CCTTTTCTCT
* * * *
11349 TAATTTTACTGATCTAGTATCTTTTTTGACAAGGCGCGGATCC
1 TAATTTTACTGATCTAGCACCCTTTCTGACAAGGCGCGGATCC
* *
11392 TAATTTTACCT-ATCTAGCACCCTTTCTGACAAGGTGTGGATCC
1 TAATTTTA-CTGATCTAGCACCCTTTCTGACAAGGCGCGGATCC
11435 CCATTCGCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (43 bp):
TAATTTTACTGATCTAGCACCCTTTCTGACAAGGCGCGGATCC
Found at i:34021 original size:45 final size:45
Alignment explanation
Indices: 33949--34092 Score: 191
Period size: 46 Copynumber: 3.1 Consensus size: 45
33939 ATTTATTTTC
*
33949 ATTTTTCGAATAAATGCTTGCGAACTAGATATCATGCGGTTAGGTTT
1 ATTTTTCGAA-AAA-GCATGCGAACTAGATATCATGCGGTTAGGTTT
*
33996 ATTTTTCGAACAAGCATGCGAACTAGATATCATGCGGTTAGGTTT
1 ATTTTTCGAAAAAGCATGCGAACTAGATATCATGCGGTTAGGTTT
* * * *
34041 ATTTTTTTGAATAAGCATGCGAATTAGATATCATGTGGTTAGGATTT
1 A-TTTTTCGAAAAAGCATGCGAACTAGATATCATGCGGTTAGG-TTT
34088 -TTTTT
1 ATTTTT
34093 GTGGATAACA
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
45 37 0.42
46 39 0.44
47 13 0.15
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (45 bp):
ATTTTTCGAAAAAGCATGCGAACTAGATATCATGCGGTTAGGTTT
Found at i:34069 original size:46 final size:46
Alignment explanation
Indices: 33967--34092 Score: 193
Period size: 46 Copynumber: 2.8 Consensus size: 46
33957 AATAAATGCT
33967 TGCGAACTAGATATCATGCGGTTAGGTTTA-TTTTTCGAACAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
* *
34012 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTTGAATAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
* * *
34058 TGCGAATTAGATATCATGTGGTTAGGATT-TTTTTT
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTT
34093 GTGGATAACA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
45 36 0.48
46 39 0.52
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (46 bp):
TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTCGAACAAGCA
Found at i:47448 original size:2 final size:2
Alignment explanation
Indices: 47441--47486 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
47431 ATCAAATTAA
47441 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
47483 AT AT
1 AT AT
47487 TAAGGGTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50321 original size:3 final size:3
Alignment explanation
Indices: 50250--50307 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
50240 TTCATTTAAA
* * * *
50250 TAT TAT T-T ATAT TAT TAT TAT AAT AAT AAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
50295 TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TA
50308 AAAAAATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 3 0.06
3 46 0.92
4 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:51802 original size:22 final size:23
Alignment explanation
Indices: 51776--51821 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
51766 TAAATAATAA
*
51776 TTTAT-AT-TTTTTATATATTATT
1 TTTATCATATTTTAATAT-TTATT
51798 TTTATCATATTTTAATATTTATT
1 TTTATCATATTTTAATATTTATT
51821 T
1 T
51822 ATTTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 8 0.38
24 8 0.38
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTATCATATTTTAATATTTATT
Found at i:63171 original size:10 final size:10
Alignment explanation
Indices: 63156--63203 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
63146 ATGCTTGAAG
63156 AAAAAAAGAA
1 AAAAAAAGAA
63166 AAAAAAAGAA
1 AAAAAAAGAA
63176 AAAAAAAGAA
1 AAAAAAAGAA
* *
63186 GAAGAAAGAA
1 AAAAAAAGAA
63196 AAAGAAAA
1 AAA-AAAA
63204 AGAGGGGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 30 0.91
11 3 0.09
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:63177 original size:6 final size:6
Alignment explanation
Indices: 63158--63206 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
63148 GCTTGAAGAA
*
63158 AAAAAG -AAAA- AAAAAG AAAAAA AAAGAAG AAGAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AA-AAAG AAAAAG AAAAAG
63206 A
1 A
63207 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 8 0.22
6 19 0.51
7 9 0.24
8 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:63190 original size:16 final size:16
Alignment explanation
Indices: 63157--63206 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
63147 TGCTTGAAGA
*
63157 AAAAAAGAAAAAAAAAG
1 AAAAAA-AAAGAAAAAG
*
63174 AAAAAAAAAGAAGAAG
1 AAAAAAAAAGAAAAAG
*
63190 AAAGAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
63206 A
1 A
63207 GGGGGTCAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 23 0.79
17 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:63601 original size:19 final size:17
Alignment explanation
Indices: 63559--63607 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
63549 TATTTTCTTT
63559 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
63575 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
63593 AAAATTCAATTTATT
1 -AAATTCAATTTATT
63608 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 1 0.04
19 13 0.46
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:65096 original size:113 final size:114
Alignment explanation
Indices: 64786--65239 Score: 761
Period size: 113 Copynumber: 4.0 Consensus size: 114
64776 AGCAAGTGCC
64786 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
64851 ATCTGATTTGGTATGAACCCGAAAATCAATCATTGGATTTGAAAGATGA
66 ATCTGATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGA
* *
64900 ATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTGTCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
64965 ATCTGATTTGGTATGAACCCCAAAATCAATCATTAGATTTGAAAGATGA
66 ATCTGATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGA
*
65014 ATGTGCTCATAGTA-AAGTAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
65078 ATCTGATTTGATATGAACCCCAAAATCAATCATTGGATTTGAAAGATGA
66 ATCTGATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGA
*
65127 ATGTGCTCATAGTAGAAATAAG-AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * * * * * *
65191 ATCTGGTTCGGTAGGAACCAC-AAACCAATCATTGGAATTAAAAGATGA
66 ATCTGATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGA
65239 A
1 A
65240 CTGCATGATC
Statistics
Matches: 320, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
112 25 0.08
113 166 0.52
114 129 0.40
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATCTGATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGA
Found at i:65264 original size:227 final size:227
Alignment explanation
Indices: 64786--65239 Score: 723
Period size: 227 Copynumber: 2.0 Consensus size: 227
64776 AGCAAGTGCC
* * *
64786 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGATCATACTA-AAGTAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * *
64851 ATCTGATTTGGTATGAACCCGAAAATCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGA
65 ATCTGATTTGATATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGA
** * *
64916 AATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTGTCTGATCTGATTTGGTATGA
130 AATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATCTGATTCGGTAGGA
* * * *
64981 ACCCCAAAATCAATCATTAGATTTGAAAGATGA
195 ACCACAAAACCAATCATTAGAATTAAAAGATGA
* *
65014 ATGTGCTCATAGTAAAGTAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
1 ATGTGATCATACTAAAGTAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
65079 TCTGATTTGATATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAA
66 TCTGATTTGATATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAA
*
65144 ATAAG-AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATCTGGTTCGGTAGGAA
131 ATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATCTGATTCGGTAGGAA
*
65208 CCAC-AAACCAATCATTGGAATTAAAAGATGA
196 CCACAAAACCAATCATTAGAATTAAAAGATGA
65239 A
1 A
65240 CTGCATGATC
Statistics
Matches: 212, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
225 24 0.11
226 57 0.27
227 117 0.55
228 14 0.07
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (227 bp):
ATGTGATCATACTAAAGTAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
TCTGATTTGATATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAA
ATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATCTGATTCGGTAGGAA
CCACAAAACCAATCATTAGAATTAAAAGATGA
Found at i:66481 original size:113 final size:113
Alignment explanation
Indices: 66160--66906 Score: 947
Period size: 113 Copynumber: 6.6 Consensus size: 113
66150 GATCAGCATT
* * * *
66160 AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAAT
1 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
66225 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTCGGTGGATC
66 GAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATC
* *
66273 AACATTGCCAGGTAGATTTCATAATGAGAAGAACTCATCTGAAGAA-AAAGAAGAAGTTCATAAT
1 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
66337 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATTGATC
66 GAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATC
* * ** *
66385 ATCATTACCATTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
66450 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATC-TCTCGGTGGATC
66 GAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAT-TCGATGGATC
* * *
66498 AACATTGCTAGGTAGATTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAAT
1 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
66563 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATTGATC
66 GAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATC
* * ** * *
66611 AGCATTACCATTTTGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
66676 GAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATC
66 GAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATC
*
66724 AACATTGCCAGGTAGAGTTCATAATGAGAAGAAATCGTCATCTGAAGAA-GAA-TA-AA-TTCAT
1 AACATTGCCAGGTAGAGTTCATAATGAGAAG-AA-C-TCATCTGAAGAAGGAAGAAGAAGTTCAT
**
66785 AATGAGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCACTT-GATGGATC
63 AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCA-TTCGATGGATC
* * * * * * *
66836 AGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAAAG-A-AAGTTCATAA
1 AACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
66898 TGAGAAGAA
65 TGAGAAGAA
66907 CTCATCCGAA
Statistics
Matches: 549, Mismatches: 74, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
109 10 0.02
110 6 0.01
111 18 0.03
112 173 0.32
113 322 0.59
114 4 0.01
115 4 0.01
116 12 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATC
Found at i:66803 original size:20 final size:20
Alignment explanation
Indices: 66739--66803 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
66729 TGCCAGGTAG
*
66739 AGTTCATAATGAGAAGAAAT
1 AGTTCATAATGAGAAGAATT
* * *
66759 CG-TCAT-CTGAAGAAGAATA
1 AGTTCATAATG-AGAAGAATT
*
66778 AATTCATAATGAGAAGAATT
1 AGTTCATAATGAGAAGAATT
*
66798 TGTTCA
1 AGTTCA
66804 ACCTTTTGCT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 17 0.53
21 2 0.06
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAATT
Found at i:66890 original size:38 final size:38
Alignment explanation
Indices: 66847--66926 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
66837 GCTTTTCCAG
66847 AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
1 AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
*
66885 AGAAAGTTCATAATGAGAAGAACTCATCCGAAAAAGAA
1 AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
66923 AGAA
1 AGAA
66927 GAAACTCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.55, C:0.11, G:0.19, T:0.15
Consensus pattern (38 bp):
AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
Found at i:67193 original size:3 final size:3
Alignment explanation
Indices: 67187--67229 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
67177 TTCATTTAAA
67187 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
67230 AATGCCCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.08
3 33 0.89
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:68732 original size:23 final size:20
Alignment explanation
Indices: 68590--68746 Score: 54
Period size: 22 Copynumber: 7.6 Consensus size: 20
68580 GTTCTAATTG
* *
68590 TATTTTTATTATTGTTTATT-
1 TATTTTTAATATTATTT-TTA
*
68610 TATGTTTTAATTTTACTTGTTTA
1 TAT-TTTTAATATTA-TT-TTTA
*
68633 TATATTTAAATATTATTTTT-
1 TAT-TTTTAATATTATTTTTA
* ***
68653 TATTATTATATAGTATATAAATA
1 TATTTTTA-ATA-T-TATTTTTA
* * * *
68676 TATATATAATAATA-ATTTA
1 TATTTTTAATATTATTTTTA
*
68695 TATTTTTTATATTATTTTTA
1 TATTTTTAATATTATTTTTA
*
68715 TCATATTTTAATATT-TATTTA
1 T-AT-TTTTAATATTATTTTTA
*
68736 T-TTTTCAATAT
1 TATTTTTAATAT
68747 CGAAGAAAGT
Statistics
Matches: 101, Mismatches: 25, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
18 8 0.08
19 17 0.17
20 16 0.16
21 20 0.20
22 22 0.22
23 18 0.18
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (20 bp):
TATTTTTAATATTATTTTTA
Found at i:69052 original size:19 final size:19
Alignment explanation
Indices: 69024--69066 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
69014 TGAATTTTTA
*
69024 AATTTCTAATAATAAAG-AC
1 AATTTATAATAA-AAAGTAC
*
69043 AATTTATAATTAAAAGTAC
1 AATTTATAATAAAAAGTAC
69062 AATTT
1 AATTT
69067 TGGGCGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (19 bp):
AATTTATAATAAAAAGTAC
Found at i:71549 original size:13 final size:13
Alignment explanation
Indices: 71501--71549 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
71491 TGACCGGTCA
*
71501 CGACCCGTTTACC
1 CGACCCGTTGACC
71514 CGACCCGTTGACC
1 CGACCCGTTGACC
*
71527 CTACCC---GACC
1 CGACCCGTTGACC
71537 CGACCCGTTGACC
1 CGACCCGTTGACC
71550 GGTGCTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.30
13 21 0.70
ACGTcount: A:0.16, C:0.49, G:0.18, T:0.16
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:71611 original size:29 final size:29
Alignment explanation
Indices: 71550--71625 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
71540 CCCGTTGACC
** *
71550 GGTGCTATTCTGGGAATTAATTCAGTTTT
1 GGTGCTATTCTGGGAATTAATTCAGAATG
71579 GGTGCTATTCTGGGAATTAATTC-GAAATG
1 GGTGCTATTCTGGGAATTAATTCAG-AATG
* *
71608 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
71626 TTTTTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAGAATG
Done.