Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1533
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: 44648
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:116 original size:16 final size:16
Alignment explanation
Indices: 97--147 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
87 TTTCTAGTAT
97 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
*
113 TTTATTTACTAGCATA
1 TTTATTTACTAGCGTA
*
129 TTCATTTACTAGCGTA
1 TTTATTTACTAGCGTA
145 TTT
1 TTT
148 GCTCTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:2139 original size:12 final size:12
Alignment explanation
Indices: 2122--2148 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2112 GAGGCTAAAG
2122 AAAAAGTGATGA
1 AAAAAGTGATGA
2134 AAAAAGTGATGA
1 AAAAAGTGATGA
2146 AAA
1 AAA
2149 GTTTTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (12 bp):
AAAAAGTGATGA
Found at i:3435 original size:9 final size:9
Alignment explanation
Indices: 3421--3511 Score: 61
Period size: 9 Copynumber: 10.6 Consensus size: 9
3411 ATTAAAAGAA
3421 AATATATAT
1 AATATATAT
3430 AATATATAT
1 AATATATAT
3439 AATATATA-
1 AATATATAT
*
3447 AATAAAT-T
1 AATATATAT
3455 GAATATATA-
1 -AATATATAT
*
3464 AATAAAT-T
1 AATATATAT
*
3472 GAATA-AAAT
1 -AATATATAT
3481 AATATATA-
1 AATATATAT
*
3489 AATAAAT-T
1 AATATATAT
*
3497 GAATATATTT
1 -AATATATAT
3507 AATAT
1 AATAT
3512 TAAATAGAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
8 23 0.35
9 41 0.63
10 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:3504 original size:17 final size:17
Alignment explanation
Indices: 3421--3476 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
3411 ATTAAAAGAA
*
3421 AATATATATAATATATAT-
1 AATATATA-AATAAAT-TG
3439 AATATATAAATAAATTG
1 AATATATAAATAAATTG
3456 AATATATAAATAAATTG
1 AATATATAAATAAATTG
3473 AATA
1 AATA
3477 AAATAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 1 0.03
17 27 0.75
18 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
AATATATAAATAAATTG
Found at i:3530 original size:24 final size:24
Alignment explanation
Indices: 3503--3565 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
3493 AATTGAATAT
3503 ATTTAATATTAAATAGAATTTCGA
1 ATTTAATATTAAATAGAATTTCGA
*
3527 ATTTAATATTTAATAGAATTTCGA
1 ATTTAATATTAAATAGAATTTCGA
*
3551 ATTTAATATAAAATA
1 ATTTAATATTAAATA
3566 TATAAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (24 bp):
ATTTAATATTAAATAGAATTTCGA
Found at i:4037 original size:14 final size:14
Alignment explanation
Indices: 4015--4070 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
4005 TTTTGAATGC
*
4015 CATACTTAATATAA
1 CATATTTAATATAA
4029 CATATTTAATATAA
1 CATATTTAATATAA
*
4043 TA-ATCTTAATATAA
1 CATAT-TTAATATAA
4057 CATATTTAATATAA
1 CATATTTAATATAA
4071 TAATGGTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
CATATTTAATATAA
Found at i:4051 original size:28 final size:28
Alignment explanation
Indices: 4019--4074 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
4009 GAATGCCATA
4019 CTTAATATAACATATTTAATATAATAAT
1 CTTAATATAACATATTTAATATAATAAT
4047 CTTAATATAACATATTTAATATAATAAT
1 CTTAATATAACATATTTAATATAATAAT
4075 GGTAGATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (28 bp):
CTTAATATAACATATTTAATATAATAAT
Found at i:4097 original size:12 final size:12
Alignment explanation
Indices: 4080--4106 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4070 ATAATGGTAG
4080 ATTCAATCTAAT
1 ATTCAATCTAAT
4092 ATTCAATCTAAT
1 ATTCAATCTAAT
4104 ATT
1 ATT
4107 GATAGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTCAATCTAAT
Found at i:4177 original size:9 final size:8
Alignment explanation
Indices: 4165--4203 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 8
4155 AAATTTTAAA
4165 AATTAGTTT
1 AATTA-TTT
4174 AATTATTTT
1 AATTA-TTT
4183 AATTATTT
1 AATTATTT
4191 AAATTATTT
1 -AATTATTT
4200 AATT
1 AATT
4204 CTATTTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
AATTATTT
Found at i:4214 original size:19 final size:18
Alignment explanation
Indices: 4165--4203 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
4155 AAATTTTAAA
4165 AATTAGTTT-AATTATTTT
1 AATTA-TTTAAATTATTTT
4183 AATTATTTAAATTA-TTT
1 AATTATTTAAATTATTTT
4200 AATT
1 AATT
4204 CTATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTATTTAAATTATTTT
Found at i:4687 original size:18 final size:18
Alignment explanation
Indices: 4664--4707 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
4654 CGCATAAAAA
4664 GAAAGAAAATAAATAAAT
1 GAAAGAAAATAAATAAAT
4682 GAAAGAAAATAAATAAAT
1 GAAAGAAAATAAATAAAT
4700 GAAAGAAA
1 GAAAGAAA
4708 GGGGAAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
GAAAGAAAATAAATAAAT
Found at i:4724 original size:18 final size:18
Alignment explanation
Indices: 4703--4738 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4693 AATAAATGAA
4703 AGAAAGGGGAAAGGAAGG
1 AGAAAGGGGAAAGGAAGG
* *
4721 AGAACGGGGGAAGGAAGG
1 AGAAAGGGGAAAGGAAGG
4739 GCATCCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.53, T:0.00
Consensus pattern (18 bp):
AGAAAGGGGAAAGGAAGG
Found at i:8758 original size:13 final size:14
Alignment explanation
Indices: 8740--8769 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
8730 CAAATTCGAA
8740 ATTCTATTTATT-T
1 ATTCTATTTATTCT
8753 ATTCTATTTATTCT
1 ATTCTATTTATTCT
8767 ATT
1 ATT
8770 ATCTATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTCTATTTATTCT
Found at i:8807 original size:13 final size:13
Alignment explanation
Indices: 8789--8817 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8779 ATCAAATTTT
8789 TATTTTATATCTA
1 TATTTTATATCTA
8802 TATTTTATATCTA
1 TATTTTATATCTA
8815 TAT
1 TAT
8818 ATATTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTATATCTA
Found at i:8835 original size:13 final size:13
Alignment explanation
Indices: 8793--8861 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
8783 AATTTTTATT
* *
8793 TTATATCTATATT
1 TTATTTCTATATA
*
8806 TTATATCTATATA
1 TTATTTCTATATA
8819 -TATTTCTATATA
1 TTATTTCTATATA
*
8831 TTATTTAGACTCTATA
1 TTATTT---CTATATA
8847 TTATTTCTATATA
1 TTATTTCTATATA
8860 TT
1 TT
8862 TAATATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
12 11 0.23
13 25 0.52
16 12 0.25
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (13 bp):
TTATTTCTATATA
Found at i:8885 original size:11 final size:11
Alignment explanation
Indices: 8854--8885 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
8844 ATATTATTTC
8854 TATATATTTAA
1 TATATATTTAA
8865 TATATATTTAA
1 TATATATTTAA
8876 TATATATTTA
1 TATATATTTA
8886 TGAGATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATTTAA
Found at i:9532 original size:10 final size:10
Alignment explanation
Indices: 9517--9543 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9507 TAATAAAAAT
9517 GAAAATAATA
1 GAAAATAATA
9527 GAAAATAATA
1 GAAAATAATA
9537 GAAAATA
1 GAAAATA
9544 TAGGGCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (10 bp):
GAAAATAATA
Found at i:13153 original size:14 final size:14
Alignment explanation
Indices: 13134--13166 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
13124 CTTATTATCT
*
13134 TATTATTTAATTTA
1 TATTATCTAATTTA
13148 TATTATCTAATTTA
1 TATTATCTAATTTA
13162 TATTA
1 TATTA
13167 GAATATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATCTAATTTA
Found at i:13209 original size:24 final size:20
Alignment explanation
Indices: 13158--13197 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13148 TATTATCTAA
13158 TTTATATTAGAATATTCATT
1 TTTATATTAGAATATTCATT
13178 TTTATATTAGAATATTCATT
1 TTTATATTAGAATATTCATT
13198 CTATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTATATTAGAATATTCATT
Found at i:13234 original size:25 final size:25
Alignment explanation
Indices: 13226--13319 Score: 58
Period size: 23 Copynumber: 3.9 Consensus size: 25
13216 TTCTATTCTA
*
13226 TATTCTATTATAT-TAATA-TATTC
1 TATTCTATTATATATTATATTATTC
*
13249 TATTCTATTA-AT-TCTAT-TAATTC
1 TATTCTATTATATAT-TATATTATTC
* *
13272 TATTATATTAATATATTCTATTCTATT-
1 TATTCTATT-ATATATTATA-T-TATTC
*
13299 AATTCTATTATATA-TATATTA
1 TATTCTATTATATATTATATTA
13320 ATATATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
22 3 0.05
23 26 0.47
24 2 0.04
25 7 0.13
26 6 0.11
27 8 0.15
28 3 0.05
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTCTATTATATATTATATTATTC
Found at i:13236 original size:32 final size:32
Alignment explanation
Indices: 13190--13318 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 32
13180 TATATTAGAA
* **
13190 TATTCATTCTATTATATATTCTATTATTCTATTC
1 TATTAATTCTATTATAT-TAATA-TATTCTATTC
13224 TA-T-ATTCTATTATATTAATATATTCTATTCTATTAATTC
1 TATTAATTCTATTATATT-A-ATA---TATTCTA-T---TC
13263 TATTAATTCTATTATATTAATATATTCTATTC
1 TATTAATTCTATTATATTAATATATTCTATTC
13295 TATTAATTCTATTATA-T-ATATATT
1 TATTAATTCTATTATATTAATATATT
13319 AATATATATA
Statistics
Matches: 82, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
30 7 0.09
31 2 0.02
32 30 0.37
33 3 0.04
34 2 0.02
35 8 0.10
36 8 0.10
39 7 0.09
40 2 0.02
41 13 0.16
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTAATTCTATTATATTAATATATTCTATTC
Found at i:13256 original size:23 final size:23
Alignment explanation
Indices: 13226--13299 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
13216 TTCTATTCTA
13226 TATTCTATTATATTAATATATTC
1 TATTCTATTATATTAATATATTC
*
13249 TATTCTATTA-A-T--TCTATT-
1 TATTCTATTATATTAATATATTC
*
13267 AATTCTATTATATTAATATATTC
1 TATTCTATTATATTAATATATTC
13290 TATTCTATTA
1 TATTCTATTA
13300 ATTCTATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
20 1 0.02
21 1 0.02
22 6 0.14
23 19 0.45
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTCTATTATATTAATATATTC
Found at i:13264 original size:9 final size:9
Alignment explanation
Indices: 13250--13308 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
13240 AATATATTCT
13250 ATTCTATTA
1 ATTCTATTA
13259 ATTCTATTA
1 ATTCTATTA
13268 ATTCTATT-
1 ATTCTATTA
13276 A---TATTA
1 ATTCTATTA
* *
13282 A-TATATTCT
1 ATTCTATT-A
13291 ATTCTATTA
1 ATTCTATTA
13300 ATTCTATTA
1 ATTCTATTA
13309 TATATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
8 5 0.12
9 27 0.64
10 5 0.12
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTCTATTA
Found at i:13279 original size:41 final size:41
Alignment explanation
Indices: 13206--13335 Score: 178
Period size: 41 Copynumber: 3.2 Consensus size: 41
13196 TTCTATTATA
13206 TATTCTATT-ATTCTATTCTATATTCTATTATATTAATATATTC
1 TATTCTATTAATTCTA-T-TA-ATTCTATTATATTAATATATTC
13249 TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
1 TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
* *
13290 TATTCTATTAATTCTATT-A-TATA-TATATTAATATATATA
1 TATTCTATTAATTCTATTAATTCTATTATATTAATATAT-TC
13329 TATTCTA
1 TATTCTA
13336 ATTTAACTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
38 13 0.16
39 11 0.13
40 1 0.01
41 40 0.48
42 2 0.02
43 10 0.12
44 6 0.07
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (41 bp):
TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
Found at i:17936 original size:14 final size:14
Alignment explanation
Indices: 17900--17949 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
17890 ACTCGCTTAG
17900 ATATACTTAGTATTTA
1 ATATACTTAGTA--TA
17916 TATATACTTAGTATA
1 -ATATACTTAGTATA
* *
17931 ATATACTAATTATA
1 ATATACTTAGTATA
17945 ATATA
1 ATATA
17950 ATCATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 17 0.55
15 2 0.06
17 12 0.39
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (14 bp):
ATATACTTAGTATA
Found at i:22550 original size:11 final size:11
Alignment explanation
Indices: 22536--22572 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
22526 AGGATAATAT
22536 AATAAGTATAA
1 AATAAGTATAA
22547 AATAAGTAT-A
1 AATAAGTATAA
22557 AATAAGTATAA
1 AATAAGTATAA
*
22568 TATAA
1 AATAA
22573 TAAGGAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (11 bp):
AATAAGTATAA
Found at i:22560 original size:21 final size:19
Alignment explanation
Indices: 22508--22574 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
22498 AGATTTACTT
* *
22508 ATAATAGAATAAGTAATAAGG
1 ATAATATAATAAGT-ATAA-A
22529 ATAATATAATAAGTATAAA
1 ATAATATAATAAGTATAAA
*
22548 ATAAGTATAAATAAGTATAAT
1 ATAA-TAT-AATAAGTATAAA
22569 ATAATA
1 ATAATA
22575 AGGAATGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.10
20 9 0.22
21 28 0.68
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (19 bp):
ATAATATAATAAGTATAAA
Found at i:27122 original size:21 final size:21
Alignment explanation
Indices: 27082--27120 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27072 AAATCATGGA
27082 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
27103 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
27121 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:27486 original size:9 final size:8
Alignment explanation
Indices: 27471--27513 Score: 54
Period size: 7 Copynumber: 5.4 Consensus size: 8
27461 GTGTCGTAAG
27471 AAAGAAAT
1 AAAGAAAT
27479 ATAAGAAA-
1 A-AAGAAAT
27487 AAAGAAAT
1 AAAGAAAT
27495 ATAAGAAA-
1 A-AAGAAAT
27503 AAAGAAAT
1 AAAGAAAT
27511 AAA
1 AAA
27514 TAAAAGAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 12 0.39
8 7 0.23
9 12 0.39
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAGAAAT
Found at i:27492 original size:16 final size:16
Alignment explanation
Indices: 27471--27511 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
27461 GTGTCGTAAG
27471 AAAGAAATATAAGAAA
1 AAAGAAATATAAGAAA
27487 AAAGAAATATAAGAAA
1 AAAGAAATATAAGAAA
27503 AAAGAAATA
1 AAAGAAATA
27512 AATAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAGAAATATAAGAAA
Found at i:27493 original size:20 final size:19
Alignment explanation
Indices: 27468--27521 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 19
27458 GTCGTGTCGT
27468 AAGAAAGAAATATAAG--A
1 AAGAAAGAAATATAAGAAA
27485 AA-AAAGAAATATAAGAAAA
1 AAGAAAGAAATATAAG-AAA
* *
27504 AAGAAATAAATAAAAGAA
1 AAGAAAGAAATATAAGAA
27522 TCGAATACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
19 5 0.16
20 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (19 bp):
AAGAAAGAAATATAAGAAA
Found at i:30914 original size:22 final size:22
Alignment explanation
Indices: 30883--30927 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
30873 TCTTATTTAT
*
30883 ATTTATAATTTTTAAATAAAAA
1 ATTTAGAATTTTTAAATAAAAA
30905 ATTTAGAATTTTTAAATAAAAA
1 ATTTAGAATTTTTAAATAAAAA
30927 A
1 A
30928 AAAATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTTAGAATTTTTAAATAAAAA
Found at i:41760 original size:14 final size:14
Alignment explanation
Indices: 41741--41793 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
41731 ATATTTATAT
41741 TAAATATTATTAAA
1 TAAATATTATTAAA
41755 TAAATATTATTAAA
1 TAAATATTATTAAA
* *
41769 TTATTATTATTAAAA
1 TAAATATTATT-AAA
41784 TGAAATATTA
1 T-AAATATTA
41794 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 23 0.70
15 4 0.12
16 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATTATTAAA
Done.