Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006590.1 Hibiscus syriacus cultivar Beakdansim tig00016160_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: 52118
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:3602 original size:46 final size:45
Alignment explanation
Indices: 3496--3619 Score: 173
Period size: 46 Copynumber: 2.8 Consensus size: 45
3486 GTAAGTATGC
*
3496 AAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
*
3539 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAT-TTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* *
3585 AAATAAGCCTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
3620 AGATTTTATA
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
43 20 0.27
44 14 0.19
46 28 0.38
47 11 0.15
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:6308 original size:17 final size:17
Alignment explanation
Indices: 6286--6389 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
6276 TATATATTAT
6286 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAATAG
6303 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAATAG
6320 AAAACGAAGAAGAAAAAA-ATG
1 --AA-GAAGAA-AAAAAATA-G
6341 AA-AATGAGAAAGAAAATA-
1 AAGAA-GA-AAA-AAAATAG
6359 AA-AAGAGAAAAAAAT-G
1 AAGAAGA-AAAAAAATAG
*
6375 AGAGATGAAAAAAAA
1 A-AGAAGAAAAAAAA
6390 ATATTTCACT
Statistics
Matches: 74, Mismatches: 1, Indels: 24
0.75 0.01 0.24
Matches are distributed among these distances:
16 6 0.08
17 33 0.45
18 11 0.15
19 9 0.12
20 8 0.11
21 7 0.09
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (17 bp):
AAGAAGAAAAAAAATAG
Found at i:6351 original size:40 final size:36
Alignment explanation
Indices: 6286--6392 Score: 89
Period size: 34 Copynumber: 2.9 Consensus size: 36
6276 TATATATTAT
*
6286 AAGAAGAAAAAAAATAGAAGAA-GA-AAAAAAATAGAAAA
1 AAGAAG-AAAAAAAT-GAA-AATGAGAAAAAAA-ATAAAA
*
6324 CGAAGAAGAAAAAAATGAAAATGAGAAAGAAAAT-AAA
1 --AAGAAGAAAAAAATGAAAATGAGAAAAAAAATAAAA
*
6361 AAG-AGAAAAAAATGAGAGATGA-AAAAAAAATA
1 AAGAAGAAAAAAATGA-AAATGAGAAAAAAAATA
6393 TTTCACTTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
34 20 0.34
35 8 0.14
37 5 0.08
38 6 0.10
39 14 0.24
40 6 0.10
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (36 bp):
AAGAAGAAAAAAATGAAAATGAGAAAAAAAATAAAA
Found at i:6356 original size:21 final size:22
Alignment explanation
Indices: 6302--6344 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6292 AAAAAAAATA
6302 GAAGAAGAAAAAAAATAGAAAAC
1 GAAGAAG-AAAAAAATAGAAAAC
6325 GAAGAAGAAAAAAAT-GAAAA
1 GAAGAAGAAAAAAATAGAAAA
6345 TGAGAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (22 bp):
GAAGAAGAAAAAAATAGAAAAC
Found at i:10359 original size:47 final size:45
Alignment explanation
Indices: 10256--10380 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
10246 GTAAGTATGC
**
10256 AAATAAGCTTACGAGCTTAT-GAAT-AATGACAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* *
10299 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* *
10346 AAATAAGCCTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
10381 GGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 11 0.15
46 1 0.01
47 37 0.51
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:14257 original size:29 final size:29
Alignment explanation
Indices: 14224--14311 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
14214 CCCAACACCA
14224 CTACAAGGTCGCCAAGCACTCCCAGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
* *
14253 CTACAAGGTCGTCATGCACTCCCAGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
*** * *
14282 CTTGTAGGTCGCCAAGCAGTCCCGGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
14311 C
1 C
14312 AAGCTTCACG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.39, G:0.24, T:0.15
Consensus pattern (29 bp):
CTACAAGGTCGCCAAGCACTCCCAGCGAC
Found at i:14343 original size:18 final size:19
Alignment explanation
Indices: 14320--14358 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
14310 CCAAGCTTCA
14320 CGTGCTCCCCT-CTGCTCC
1 CGTGCTCCCCTCCTGCTCC
14338 CGTGCTCCCCTCCTGCTCC
1 CGTGCTCCCCTCCTGCTCC
14357 CG
1 CG
14359 CTGCATGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.00, C:0.56, G:0.18, T:0.26
Consensus pattern (19 bp):
CGTGCTCCCCTCCTGCTCC
Found at i:14515 original size:33 final size:33
Alignment explanation
Indices: 14478--14544 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
14468 CAATTGCACA
14478 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
14511 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
14544 A
1 A
14545 CCTAAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (33 bp):
ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
Found at i:14623 original size:26 final size:26
Alignment explanation
Indices: 14590--14647 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
14580 ACATAAAAGA
* *
14590 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTACAGCAG
*
14616 AAGAAAGGGAGAAGAAATTACAGCCG
1 AAGAAAGGGAGAAGAAATTACAGCAG
14642 -AGAAAG
1 AAGAAAG
14648 AAAGAAAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.50, C:0.09, G:0.34, T:0.07
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAAATTACAGCAG
Found at i:15168 original size:16 final size:16
Alignment explanation
Indices: 15136--15182 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
15126 TTTAAAAAGT
*
15136 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
15152 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
15168 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
15183 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:15177 original size:15 final size:14
Alignment explanation
Indices: 15157--15187 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
15147 GTTTATTAGT
15157 TTATTATATTATAAG
1 TTATTATATTA-AAG
15172 TTATTATATTAAAG
1 TTATTATATTAAAG
15186 TT
1 TT
15188 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:17419 original size:14 final size:14
Alignment explanation
Indices: 17402--17443 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
17392 TGGAAAATAG
17402 TTACTATCAAATCA
1 TTACTATCAAATCA
17416 TTAC--T-AAATCA
1 TTACTATCAAATCA
*
17427 TTAATATCAAATCA
1 TTACTATCAAATCA
17441 TTA
1 TTA
17444 AATATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (14 bp):
TTACTATCAAATCA
Found at i:17459 original size:21 final size:22
Alignment explanation
Indices: 17406--17453 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
17396 AAATAGTTAC
17406 TATCAAATCATTACTAAATCATTAA
1 TATCAAATCA-T--TAAATCATTAA
17431 TATCAAATCATTAAAT-ATTAA
1 TATCAAATCATTAAATCATTAA
17452 TA
1 TA
17454 ATAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
22 5 0.22
24 1 0.04
25 10 0.43
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TATCAAATCATTAAATCATTAA
Found at i:17464 original size:21 final size:22
Alignment explanation
Indices: 17415--17501 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 22
17405 CTATCAAATC
*
17415 ATTACTAAATCATTAATATCAA
1 ATTATTAAATCATTAATATCAA
* *
17437 ATCATTAAAT-ATTAATAATAAA
1 ATTATTAAATCATTAAT-ATCAA
*
17459 TTATTATTACTAATCATTACTATCAA
1 --ATTATTA--AATCATTAATATCAA
* *
17485 ATAATTAAA-AATTAATA
1 ATTATTAAATCATTAATA
17502 ATAATTTCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
21 12 0.24
22 14 0.28
24 12 0.24
26 7 0.14
27 5 0.10
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTATTAAATCATTAATATCAA
Found at i:17477 original size:48 final size:49
Alignment explanation
Indices: 17415--17526 Score: 172
Period size: 48 Copynumber: 2.3 Consensus size: 49
17405 CTATCAAATC
* *
17415 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATAATTAAAAATTAATAATAAATTCATT
* *
17464 ATTACTAATCATTACTATCAAATAATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATAATTAAAAATTAATAATAAATTCATT
17513 ATTACTAATCATTA
1 ATTACTAATCATTA
17527 CTAAATCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 35 0.60
49 23 0.40
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATAATTAAAAATTAATAATAAATTCATT
Found at i:17708 original size:10 final size:10
Alignment explanation
Indices: 17693--17719 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17683 TAATTTCATT
17693 ATTACTAATC
1 ATTACTAATC
17703 ATTACTAATC
1 ATTACTAATC
17713 ATTACTA
1 ATTACTA
17720 TCAAATCATT
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:17741 original size:239 final size:238
Alignment explanation
Indices: 17411--18075 Score: 1172
Period size: 239 Copynumber: 2.8 Consensus size: 238
17401 GTTACTATCA
17411 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-A----A--ATTA-T--T-A
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
17465 TTACTAATCATTACTATCAAATAATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
66 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT-ATTACTA
* *
17530 AATCATTACTATCAAATCATTAAATATAAATAATAATTTCATTATTACTAATCATTACTAAATCA
130 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
17595 TTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
195 TTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
17639 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
17704 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATAATTACTA
66 TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT-ATTACTA
17769 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
130 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
17834 TTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
195 TTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
*
17878 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* *
17943 TTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATATTACTA
66 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATATTACTA
18008 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
130 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
18073 TTA
195 TTA
18076 TTATAAGTTC
Statistics
Matches: 418, Mismatches: 7, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
228 45 0.11
229 1 0.00
233 1 0.00
235 4 0.01
236 1 0.00
238 1 0.00
239 315 0.75
240 50 0.12
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.41
Consensus pattern (238 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATATTACTAA
ATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCAT
TACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
Found at i:17838 original size:299 final size:299
Alignment explanation
Indices: 17464--18075 Score: 1102
Period size: 299 Copynumber: 2.1 Consensus size: 299
17454 ATAAATTATT
*
17464 ATTACT-AATCATTACTATCAAATAATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATAATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
17528 TAAATCATTACTATCAAATCATTAAATATAAATAATAATTTCATTATTACTAATCATTACTAAAT
66 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
17593 CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTA
131 CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTA
* *
17658 ATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT-AATCATTACTATC
196 ATATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT-ATTACTAAATCATTAATATC
17722 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATA
260 AAATCATTAAAAATTAATAATAATTTCATTATTACTAATA
* *
17762 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATAATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
17827 TAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAAT
66 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
*
17892 CATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
131 CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTA
*
17957 CTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATATTACTAAATCATTAATATCA
196 ATATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATATTACTAAATCATTAATATCA
* *
18022 AATCATTAAATATTAATAATAATTTCATTATTACTAATC
261 AATCATTAAAAATTAATAATAATTTCATTATTACTAATA
18061 ATTACTAAATCATTA
1 ATTACTAAATCATTA
18076 TTATAAGTTC
Statistics
Matches: 301, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
298 12 0.04
299 289 0.96
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (299 bp):
ATTACTAAATCATTAATATCAAATAATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTA
ATATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATATTACTAAATCATTAATATCA
AATCATTAAAAATTAATAATAATTTCATTATTACTAATA
Found at i:17977 original size:21 final size:20
Alignment explanation
Indices: 17528--17977 Score: 92
Period size: 21 Copynumber: 22.4 Consensus size: 20
17518 TAATCATTAC
17528 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
* *
17550 TAAATA-TA-AAT-AATAATT
1 TAAATATTACTATCAATCA-T
* * * *
17568 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
17588 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
* *
17610 TAAATATTAATAACAAT--T
1 TAAATATTACTATCAATCAT
* * * *
17628 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
*
17648 TAAATCATTAATATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
*
17670 TAAATATTA--AT-AATAATT
1 TAAATATTACTATCAATCA-T
* *
17688 TCATTATTAC--T-AATCAT
1 TAAATATTACTATCAATCAT
17705 TACTAATCATTACTATCAAATCAT
1 TA--AAT-ATTACTATC-AATCAT
* *
17729 TAAAAATTA--AT-AATAATT
1 TAAATATTACTATCAATCA-T
* * * *
17747 TCATTATTACTAAT-AATTAC
1 TAAATATTACT-ATCAATCAT
*
17767 TAAATCATTAATATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
*
17789 TAAATATTA--AT-AATAATT
1 TAAATATTACTATCAATCA-T
* * * *
17807 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
17827 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
* *
17849 TAAATATTAATAACAAT--T
1 TAAATATTACTATCAATCAT
* * * *
17867 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
17887 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
*
17909 TAAATATTA--AT-AATAATT
1 TAAATATTACTATCAATCA-T
* * * *
17927 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
17947 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
17969 TAAATATTA
1 TAAATATTA
17978 ATAACAATTT
Statistics
Matches: 306, Mismatches: 70, Indels: 105
0.64 0.15 0.22
Matches are distributed among these distances:
17 22 0.07
18 63 0.21
19 18 0.06
20 48 0.16
21 90 0.29
22 57 0.19
24 8 0.03
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATTACTATCAATCAT
Found at i:18038 original size:21 final size:21
Alignment explanation
Indices: 17947--18039 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 21
17937 TAATCATTAC
*
17947 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTAATATCAAATCAT
* *
17969 TAAATATTAATAACAATTTCAT
1 TAAATATTAATATCAA-ATCAT
* * *
17991 T-ATTACTAATAT----T-AC
1 TAAATATTAATATCAAATCAT
18006 TAAATCATTAATATCAAATCAT
1 TAAAT-ATTAATATCAAATCAT
18028 TAAATATTAATA
1 TAAATATTAATA
18040 ATAATTTCAT
Statistics
Matches: 53, Mismatches: 10, Indels: 17
0.66 0.12 0.21
Matches are distributed among these distances:
15 2 0.04
16 3 0.06
17 7 0.13
21 25 0.47
22 16 0.30
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATCAAATCAT
Found at i:18089 original size:60 final size:60
Alignment explanation
Indices: 17464--18075 Score: 1104
Period size: 60 Copynumber: 10.2 Consensus size: 60
17454 ATAAATTATT
* *
17464 ATTACT-AATCATTACTATCAAATAATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
17523 ATTACTAAATCATTACTATCAAATCATTAAATATAAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
17583 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
17643 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
17703 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATA
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
17762 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
17822 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
17882 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
17942 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT-
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
18001 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
18061 ATTACTAAATCATTA
1 ATTACTAAATCATTA
18076 TTATAAGTTC
Statistics
Matches: 531, Mismatches: 19, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
59 119 0.22
60 412 0.78
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:18168 original size:14 final size:14
Alignment explanation
Indices: 18149--18196 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
18139 TTCAAGTCGT
18149 AAATCATTACTATC
1 AAATCATTACTATC
18163 AAATCATTAC--T-
1 AAATCATTACTATC
*
18174 AAATCATTAATATC
1 AAATCATTACTATC
18188 AAATCATTA
1 AAATCATTA
18197 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:18176 original size:25 final size:25
Alignment explanation
Indices: 18148--18196 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
18138 GTTCAAGTCG
*
18148 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
18173 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
18197 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:18212 original size:21 final size:22
Alignment explanation
Indices: 18148--18206 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
18138 GTTCAAGTCG
*
18148 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
18171 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
18195 TAAAT-ATTAATA
1 TAAATCATTAATA
18207 ATAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
24 1 0.03
25 20 0.61
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:18217 original size:21 final size:22
Alignment explanation
Indices: 18148--18217 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
18138 GTTCAAGTCG
* *
18148 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATC-AA--ATTAT
*
18173 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATTAT
18195 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
18216 TA
1 TA
18218 TTACTAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
24 2 0.05
25 14 0.35
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:18229 original size:59 final size:59
Alignment explanation
Indices: 18164--18342 Score: 218
Period size: 49 Copynumber: 3.2 Consensus size: 59
18154 ATTACTATCA
*
18164 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACT-AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
*
18223 AATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT--A---A-T-TT-C-
1 AATCATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
* * * *
18273 -ATTATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATCATTACT
1 AATCATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
18331 AATCATTACTAA
1 AATCATTACTAA
18343 ATCTTATAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 20
0.78 0.06 0.15
Matches are distributed among these distances:
49 40 0.39
51 1 0.01
52 2 0.02
53 1 0.01
54 2 0.02
56 3 0.03
57 1 0.01
58 32 0.31
59 20 0.20
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (59 bp):
AATCATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
Found at i:18232 original size:10 final size:10
Alignment explanation
Indices: 18217--18243 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18207 ATAAATTATT
18217 ATTACTAATC
1 ATTACTAATC
18227 ATTACTAATC
1 ATTACTAATC
18237 ATTACTA
1 ATTACTA
18244 TCAAATCATT
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:21889 original size:28 final size:30
Alignment explanation
Indices: 21841--21902 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
21831 ATTTTTTATA
21841 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
21871 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
21899 TAAT
1 TAAT
21903 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:22396 original size:45 final size:45
Alignment explanation
Indices: 22329--22418 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
22319 AATCTCCCAG
* * *
22329 CTATGGATGGAATCCATGCACGAGGGAGAAGGGTTAAGTTTGGTC
1 CTATGGATGCAACCCATACACGAGGGAGAAGGGTTAAGTTTGGTC
*
22374 CTATGGATGCAACCCATACACGAGGGAGCAGGGTTAAGTTTGGTC
1 CTATGGATGCAACCCATACACGAGGGAGAAGGGTTAAGTTTGGTC
22419 GCCAGCAGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (45 bp):
CTATGGATGCAACCCATACACGAGGGAGAAGGGTTAAGTTTGGTC
Found at i:22428 original size:22 final size:22
Alignment explanation
Indices: 22400--22441 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
22390 TACACGAGGG
*
22400 AGCAGGGTTAAGTTTGGTCGCC
1 AGCAGGGATAAGTTTGGTCGCC
22422 AGCAGGGATAAGTTTGGTCG
1 AGCAGGGATAAGTTTGGTCG
22442 AGGCTTGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
AGCAGGGATAAGTTTGGTCGCC
Found at i:22508 original size:29 final size:29
Alignment explanation
Indices: 22476--22559 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
22466 GCGACCTACA
22476 AGGTCGCTGGGAGTGCATGGCGACCTTGT
1 AGGTCGCTGGGAGTGCATGGCGACCTTGT
*
22505 AGGTCGCTGGGAGTGCATGGCGACCTTTT
1 AGGTCGCTGGGAGTGCATGGCGACCTTGT
* *
22534 AGGTCGCTGGGACTACATGGCGACCT
1 AGGTCGCTGGGAGTGCATGGCGACCT
22560 GTGTTGGGTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.24
Consensus pattern (29 bp):
AGGTCGCTGGGAGTGCATGGCGACCTTGT
Found at i:22590 original size:16 final size:16
Alignment explanation
Indices: 22569--22602 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
22559 TGTGTTGGGT
22569 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
22585 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
22601 GT
1 GT
22603 GCATGGCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.56, T:0.26
Consensus pattern (16 bp):
GTTGGGTGCTGGGGAC
Found at i:26833 original size:90 final size:92
Alignment explanation
Indices: 26727--26898 Score: 285
Period size: 91 Copynumber: 1.9 Consensus size: 92
26717 AATTTCAATT
*
26727 AATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGATTAGGGTAACTTGGA
1 AATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTGGA
*
26791 TATAAAAG-GTTTGTTAAATTCTAATC
66 TATAAAAGAGTGTGTTAAATTCTAATC
* * *
26817 AATTAAATATATATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTTGC
1 AATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTGGA
26882 TATAAAAGAGTGTGTTA
66 TATAAAAGAGTGTGTTA
26899 GGTCTAGCAG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
90 32 0.43
91 36 0.48
92 7 0.09
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.37
Consensus pattern (92 bp):
AATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTGGA
TATAAAAGAGTGTGTTAAATTCTAATC
Found at i:27393 original size:20 final size:21
Alignment explanation
Indices: 27363--27402 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
27353 AGCCGTTGCG
27363 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
27384 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
27403 CTATTCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:34788 original size:47 final size:45
Alignment explanation
Indices: 34695--34826 Score: 169
Period size: 47 Copynumber: 2.9 Consensus size: 45
34685 GTAAGTATGC
* *
34695 AAATAAGCTTACGAGCTTAT-GAAT-AATGGAAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGATA
* *
34738 AAATAAGCTTACGAGCTTGTGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGATA
* *
34785 AAATAAGCCTACGAGCTTATGGGATAAATGGTAAGATATTTT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG-TATTTT
34827 ATATTATTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
43 19 0.25
44 3 0.04
45 11 0.14
46 7 0.09
47 37 0.48
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGATA
Found at i:37509 original size:17 final size:17
Alignment explanation
Indices: 37487--37592 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
37477 TATATATTAT
37487 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAATAG
37504 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAATAG
37521 AAAACGAAGAAGAAAAAA-ATG
1 --AA-GAAGAA-AAAAAATA-G
37542 AA-AATGAGAAAGAAAATA-
1 AAGAA-GA-AAA-AAAATAG
37560 AA-AAGAGAAAAAAAT-G
1 AAGAAGA-AAAAAAATAG
*
37576 AGAGATGAAAAAAAATA
1 A-AGAAGAAAAAAAATA
37593 TTTCACTTGT
Statistics
Matches: 75, Mismatches: 1, Indels: 25
0.74 0.01 0.25
Matches are distributed among these distances:
16 6 0.08
17 34 0.45
18 11 0.15
19 9 0.12
20 8 0.11
21 7 0.09
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.08
Consensus pattern (17 bp):
AAGAAGAAAAAAAATAG
Found at i:37552 original size:40 final size:39
Alignment explanation
Indices: 37487--37563 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
37477 TATATATTAT
*
37487 AAGAAGAAAAAAAATAGAAGAAGAAAAAAAATAGAAAACG
1 AAGAAGAAAAAAAATAAAAGAAGAAAAAAAATA-AAAACG
*
37527 AAGAAG-AAAAAAATGAAAATG-AGAAAGAAAATAAAAA
1 AAGAAGAAAAAAAAT-AAAA-GAAGAAAAAAAATAAAAA
37564 GAGAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 12 0.36
40 20 0.61
41 1 0.03
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.06
Consensus pattern (39 bp):
AAGAAGAAAAAAAATAAAAGAAGAAAAAAAATAAAAACG
Found at i:37557 original size:21 final size:22
Alignment explanation
Indices: 37503--37545 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
37493 AAAAAAAATA
37503 GAAGAAGAAAAAAAATAGAAAAC
1 GAAGAAG-AAAAAAATAGAAAAC
37526 GAAGAAGAAAAAAAT-GAAAA
1 GAAGAAGAAAAAAATAGAAAA
37546 TGAGAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (22 bp):
GAAGAAGAAAAAAATAGAAAAC
Found at i:41551 original size:47 final size:45
Alignment explanation
Indices: 41448--41572 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
41438 GTAAGTATGC
**
41448 AAATAAGCTTACGAGCTTAT-GAAT-AATGACAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* *
41491 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* *
41538 AAATAAGCCTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
41573 GGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 11 0.15
46 1 0.01
47 37 0.51
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:45486 original size:28 final size:29
Alignment explanation
Indices: 45402--45488 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
45392 CCCCACACCA
45402 CTACAAGGTCGCCAAGCACTCCCAGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
* *
45431 CTACAAGGTCGTCATGCACTCCCAGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
*** * *
45460 CTTGTA-GTCGCCAAGCAGTCCCGGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
45488 C
1 C
45489 AAGCTTCACG
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 19 0.39
29 30 0.61
ACGTcount: A:0.23, C:0.39, G:0.23, T:0.15
Consensus pattern (29 bp):
CTACAAGGTCGCCAAGCACTCCCAGCGAC
Found at i:45520 original size:18 final size:19
Alignment explanation
Indices: 45497--45535 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
45487 CCAAGCTTCA
45497 CGTGCTCCCCT-CTGCTCC
1 CGTGCTCCCCTCCTGCTCC
45515 CGTGCTCCCCTCCTGCTCC
1 CGTGCTCCCCTCCTGCTCC
45534 CG
1 CG
45536 CTGCATGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.00, C:0.56, G:0.18, T:0.26
Consensus pattern (19 bp):
CGTGCTCCCCTCCTGCTCC
Found at i:45692 original size:33 final size:32
Alignment explanation
Indices: 45655--45720 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
45645 CAATTGCACA
45655 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCC-GTGAC
45688 ATTATTGGTGAAATAATTGAGGCAGCCGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGTGAC
45720 A
1 A
45721 CCTAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.18
33 27 0.82
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (32 bp):
ATTATTGGTGAAATAATTGAGGCAGCCGTGAC
Found at i:45799 original size:26 final size:26
Alignment explanation
Indices: 45766--45815 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
45756 ACATAAAAGA
* *
45766 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTACAGCAG
45792 AAGAAAGGGAGAAGAAATTACAGC
1 AAGAAAGGGAGAAGAAATTACAGC
45816 CGAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.34, T:0.08
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAAATTACAGCAG
Found at i:46064 original size:39 final size:38
Alignment explanation
Indices: 46020--46143 Score: 99
Period size: 39 Copynumber: 3.1 Consensus size: 38
46010 ATTACATAAA
46020 TAAAAATTATTTAATTAGTATGTTTGATAGTTATATAGT
1 TAAAAATTATTTAATTAGT-TGTTTGATAGTTATATAGT
* * *
46059 TAAAAAATAATTAATTAGTTTGTTTTGTTAATCGTTAGTTATA-T
1 TAAAAATTATTTAATTAG-TTG-TTTG---ATAGTTA--TATAGT
* * *
46103 AAAAGAATTATTTAATTAGTT-TTTGGTAGTTAAATAGT
1 TAAA-AATTATTTAATTAGTTGTTTGATAGTTATATAGT
46141 TAA
1 TAA
46144 GTTATATTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
37 3 0.05
38 3 0.05
39 23 0.35
40 5 0.08
42 4 0.06
43 6 0.09
44 6 0.09
45 16 0.24
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (38 bp):
TAAAAATTATTTAATTAGTTGTTTGATAGTTATATAGT
Found at i:46339 original size:15 final size:15
Alignment explanation
Indices: 46316--46348 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
46306 GTTTGTTAGT
*
46316 TTATTAGTTATTATA
1 TTATAAGTTATTATA
46331 TTATAAGTTATTATA
1 TTATAAGTTATTATA
46346 TTA
1 TTA
46349 AGTTTAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TTATAAGTTATTATA
Found at i:48577 original size:14 final size:14
Alignment explanation
Indices: 48560--48601 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
48550 TGGAAAATAG
48560 TTACTATCAAATCA
1 TTACTATCAAATCA
48574 TTAC--T-AAATCA
1 TTACTATCAAATCA
*
48585 TTAATATCAAATCA
1 TTACTATCAAATCA
48599 TTA
1 TTA
48602 AATATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (14 bp):
TTACTATCAAATCA
Found at i:48617 original size:21 final size:22
Alignment explanation
Indices: 48564--48611 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
48554 AAATAGTTAC
48564 TATCAAATCATTACTAAATCATTAA
1 TATCAAATCA-T--TAAATCATTAA
48589 TATCAAATCATTAAAT-ATTAA
1 TATCAAATCATTAAATCATTAA
48610 TA
1 TA
48612 ATAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
22 5 0.22
24 1 0.04
25 10 0.43
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TATCAAATCATTAAATCATTAA
Found at i:48622 original size:21 final size:22
Alignment explanation
Indices: 48573--48659 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 22
48563 CTATCAAATC
*
48573 ATTACTAAATCATTAATATCAA
1 ATTATTAAATCATTAATATCAA
* *
48595 ATCATTAAAT-ATTAATAATAAA
1 ATTATTAAATCATTAAT-ATCAA
*
48617 TTATTATTACTAATCATTACTATCAA
1 --ATTATTA--AATCATTAATATCAA
* *
48643 ATAATTAAA-AATTAATA
1 ATTATTAAATCATTAATA
48660 ATTTCATTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
21 12 0.24
22 14 0.28
24 12 0.24
26 7 0.14
27 5 0.10
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTATTAAATCATTAATATCAA
Found at i:48747 original size:11 final size:11
Alignment explanation
Indices: 48725--48805 Score: 55
Period size: 11 Copynumber: 7.4 Consensus size: 11
48715 TAATTTCATT
48725 ATTACT-AATC
1 ATTACTAAATC
48735 ATTACTAAATC
1 ATTACTAAATC
48746 ATTACTATCAAATC
1 ATTAC--T-AAATC
*
48760 ATTA--AATATA
1 ATTACTAA-ATC
* *
48770 ATAAC-AATTTC
1 ATTACTAA-ATC
48781 ATTACT-AATC
1 ATTACTAAATC
48791 ATTACTAAATC
1 ATTACTAAATC
48802 ATTA
1 ATTA
48806 ATATCAATCA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
9 2 0.04
10 19 0.33
11 26 0.46
13 1 0.02
14 9 0.16
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:48794 original size:10 final size:10
Alignment explanation
Indices: 48779--48863 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
48769 AATAACAATT
48779 TCATTACTAA
1 TCATTACTAA
48789 TCATTACTAAA
1 TCATTACT-AA
*
48800 TCATTAATATCAA
1 TCATT-A-CT-AA
48813 TCATTA--AA
1 TCATTACTAA
*
48821 T-ATTAATAA
1 TCATTACTAA
48830 TTTCATTATTACTAA
1 --TCA-T-T-ACTAA
48845 TCATTACTAA
1 TCATTACTAA
48855 TCATTACTA
1 TCATTACTA
48864 TCAAATCATT
Statistics
Matches: 61, Mismatches: 3, Indels: 22
0.71 0.03 0.26
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
9 2 0.03
10 22 0.36
11 9 0.15
12 4 0.07
13 12 0.20
14 1 0.02
15 4 0.07
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (10 bp):
TCATTACTAA
Found at i:48985 original size:291 final size:287
Alignment explanation
Indices: 48622--49217 Score: 943
Period size: 291 Copynumber: 2.1 Consensus size: 287
48612 ATAAATTATT
* *
48622 ATTACT-AATCATTACTATCAAATAATTAAAAATTAATAATTTCATTATTAATCATTACTAAATC
1 ATTACTAAATCATTAATATCAAATAATTAAAAAATAATAATTTCATTATTAATCATTACTAAATC
*
48686 ATTACTATCAAATCATTAAATATAAATAATAATTTCATTATTACTAATCATTACTAAATCATTAC
66 ATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAATCATTAC
48751 TATCAAATCATTAA-ATATAATAACAATTTC-ATTACTAATCATTACTAAATCATTAATATC-AA
131 TATCAAATCATTAATAT-TAATAACAATTTCTATTACTAATCATTACTAAATCATTAATATCAAA
*
48813 TCATTAAATATTAAT-AATTTCATTATTACTAATCATTACT-AATCATTACTATCAAATCATTAA
195 TCATTAAATATTAATAAATTTCATTATTACTAAT-ATTACTAAATCATTAATATCAAATCATT-A
48876 AAATTAATAATAATTTCATTATTACTAATA
258 AAATTAATAATAATTTCATTATTACTAATA
*
48906 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATAATTAAA-A--AATAATAATTTCATTA-T--TAATCATTAC
*
48971 TAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAAT
60 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
* *
49036 CATTACTATCAAATCATTAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAC
125 CATTACTATCAAATCATTAATATTAATAACAATTTC--TATTACTAATCATTACTAAATCATTAA
49101 TATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATATTACTAAATCATTAATATCAA
188 TATCAAATCATTAAATATTAAT-A-AATTTCATTATTACTAATATTACTAAATCATTAATATCAA
* *
49166 ATCATTAATATTAATAATAATTTCATTATTACTAATC
251 ATCATTAAAATTAATAATAATTTCATTATTACTAATA
49203 ATTACTAAATCATTA
1 ATTACTAAATCATTA
49218 TTATAAGTTC
Statistics
Matches: 286, Mismatches: 10, Indels: 19
0.91 0.03 0.06
Matches are distributed among these distances:
284 6 0.02
285 22 0.08
286 1 0.00
288 15 0.05
289 1 0.00
291 105 0.37
292 2 0.01
294 29 0.10
295 17 0.06
297 50 0.17
298 38 0.13
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (287 bp):
ATTACTAAATCATTAATATCAAATAATTAAAAAATAATAATTTCATTATTAATCATTACTAAATC
ATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAATCATTAC
TATCAAATCATTAATATTAATAACAATTTCTATTACTAATCATTACTAAATCATTAATATCAAAT
CATTAAATATTAATAAATTTCATTATTACTAATATTACTAAATCATTAATATCAAATCATTAAAA
TTAATAATAATTTCATTATTACTAATA
Found at i:49038 original size:11 final size:11
Alignment explanation
Indices: 49016--49102 Score: 52
Period size: 11 Copynumber: 7.6 Consensus size: 11
49006 CAATTTCATT
49016 ATTACT-AATC
1 ATTACTAAATC
49026 ATTACTAAATC
1 ATTACTAAATC
49037 ATTACTATCAAATC
1 ATTAC--T-AAATC
* *
49051 ATTAATATTAATA
1 ATTACTA--AATC
* * ** *
49064 ATAATTTCATT
1 ATTACTAAATC
49075 ATTACT-AATC
1 ATTACTAAATC
49085 ATTACTAAATC
1 ATTACTAAATC
49096 ATTACTA
1 ATTACTA
49103 TCAAATCATT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
10 14 0.24
11 27 0.46
12 1 0.02
13 8 0.14
14 9 0.15
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:49120 original size:21 final size:20
Alignment explanation
Indices: 48796--49120 Score: 68
Period size: 21 Copynumber: 16.4 Consensus size: 20
48786 TAATCATTAC
*
48796 TAAATCATTAATATCAATCAT
1 TAAAT-ATTACTATCAATCAT
48817 TAAATATTA--AT-AAT--T
1 TAAATATTACTATCAATCAT
* *
48832 TCATTATTAC--T-AATCAT
1 TAAATATTACTATCAATCAT
48849 TACTAATCATTACTATCAAATCAT
1 TA--AAT-ATTACTATC-AATCAT
* *
48873 TAAAAATTA--AT-AATAATT
1 TAAATATTACTATCAATCA-T
* * * *
48891 TCATTATTACTAAT-AATTAC
1 TAAATATTACT-ATCAATCAT
*
48911 TAAATCATTAATATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
*
48933 TAAATATTA--AT-AATAATT
1 TAAATATTACTATCAATCA-T
* * * *
48951 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
48971 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
* *
48993 TAAATATTAATAACAAT--T
1 TAAATATTACTATCAATCAT
* * * *
49011 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
49031 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
*
49053 T-AATATTA--AT-AATAATT
1 TAAATATTACTATCAATCA-T
* * * *
49070 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
49090 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
49112 TAAATATTA
1 TAAATATTA
49121 ATAACAATTT
Statistics
Matches: 220, Mismatches: 44, Indels: 80
0.64 0.13 0.23
Matches are distributed among these distances:
15 12 0.05
16 4 0.02
17 15 0.07
18 36 0.16
19 8 0.04
20 39 0.18
21 66 0.30
22 32 0.15
24 8 0.04
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATTACTATCAATCAT
Found at i:49162 original size:17 final size:16
Alignment explanation
Indices: 49140--49178 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
49130 TCATTATTAC
49140 TAATATTACTAAATCAT
1 TAATATTAC-AAATCAT
49157 TAATA-T-CAAATCAT
1 TAATATTACAAATCAT
49171 TAATATTA
1 TAATATTA
49179 ATAATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.60
15 2 0.10
16 1 0.05
17 5 0.25
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATATTACAAATCAT
Found at i:49193 original size:21 final size:21
Alignment explanation
Indices: 49049--49193 Score: 55
Period size: 21 Copynumber: 7.3 Consensus size: 21
49039 TACTATCAAA
49049 TCATTAATATTAATAATAATT
1 TCATTAATATTAATAATAATT
* *
49070 TCA-T--TATTACTAATCATT
1 TCATTAATATTAATAATAATT
* * * *
49088 AC-TAAATCATTACT-ATCAA-A
1 TCATTAAT-ATTAATAAT-AATT
*
49108 TCATTAAATATTAATAACAATT
1 TCATT-AATATTAATAATAATT
*
49130 TCA-T--TATTACTAAT-ATT
1 TCATTAATATTAATAATAATT
* * *
49147 AC-TAAATCATTAAT-ATCAA-A
1 TCATTAAT-ATTAATAAT-AATT
49167 TCATTAATATTAATAATAATT
1 TCATTAATATTAATAATAATT
49188 TCATTA
1 TCATTA
49194 TTACTAATCA
Statistics
Matches: 86, Mismatches: 20, Indels: 36
0.61 0.14 0.25
Matches are distributed among these distances:
17 4 0.05
18 21 0.24
19 3 0.03
20 19 0.22
21 32 0.37
22 7 0.08
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.43
Consensus pattern (21 bp):
TCATTAATATTAATAATAATT
Found at i:49231 original size:59 final size:60
Alignment explanation
Indices: 48622--49217 Score: 960
Period size: 60 Copynumber: 10.2 Consensus size: 60
48612 ATAAATTATT
* *
48622 ATTACT-AATCATTACTATCAAATAATTAAA-A--ATTAATAATTTCATTA-T--TAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
48675 ATTACTAAATCATTACTATCAAATCATTAAATATAAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
48735 ATTACTAAATCATTACTATCAAATCATTAAATA-TAATAACAATTTC---ATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
48791 ATTACTAAATCATTAATATC-AATCATTAAATA-T--TAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
48847 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATA
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
48906 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
48966 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
49026 ATTACTAAATCATTACTATCAAATCATT-AATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
49085 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT-
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
49144 ATTACTAAATCATTAATATCAAATCATT-AATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
49203 ATTACTAAATCATTA
1 ATTACTAAATCATTA
49218 TTATAAGTTC
Statistics
Matches: 508, Mismatches: 18, Indels: 28
0.92 0.03 0.05
Matches are distributed among these distances:
53 15 0.03
54 23 0.05
55 26 0.05
56 56 0.11
57 16 0.03
58 30 0.06
59 139 0.27
60 203 0.40
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:49310 original size:14 final size:14
Alignment explanation
Indices: 49291--49338 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
49281 TTCAAGTCGT
49291 AAATCATTACTATC
1 AAATCATTACTATC
49305 AAATCATTAC--T-
1 AAATCATTACTATC
*
49316 AAATCATTAATATC
1 AAATCATTACTATC
49330 AAATCATTA
1 AAATCATTA
49339 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:49372 original size:48 final size:49
Alignment explanation
Indices: 49310--49469 Score: 261
Period size: 49 Copynumber: 3.3 Consensus size: 49
49300 CTATCAAATC
*
49310 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
* *
49359 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
*
49408 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATC
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
49457 ATTACT-ATCATTA
1 ATTACTAATCATTA
49470 CTAAATCTTA
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
48 43 0.41
49 61 0.59
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
Done.