Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009314.1 Hibiscus syriacus cultivar Beakdansim tig00113068_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: 106728
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4666 original size:11 final size:11
Alignment explanation
Indices: 4650--4674 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4640 ATTAATAAAA
4650 TTATTAAATAT
1 TTATTAAATAT
4661 TTATTAAATAT
1 TTATTAAATAT
4672 TTA
1 TTA
4675 ATAGAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATTAAATAT
Found at i:9908 original size:18 final size:19
Alignment explanation
Indices: 9867--9909 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
9857 ATTAATTACT
9867 AAAATAATAAAAATTTTGA
1 AAAATAATAAAAATTTTGA
*
9886 TAAATAA-AAAAATTTAT-A
1 AAAATAATAAAAATTT-TGA
9904 AAAATA
1 AAAATA
9910 CTTATACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATAATAAAAATTTTGA
Found at i:10333 original size:20 final size:20
Alignment explanation
Indices: 10295--10333 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10285 TACTCAACTG
*
10295 AACTGAAATAGAAGCATAAT
1 AACTGAAATAAAAGCATAAT
* *
10315 AACTTAAATAAAAGTATAA
1 AACTGAAATAAAAGCATAA
10334 CATCTTGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (20 bp):
AACTGAAATAAAAGCATAAT
Found at i:14453 original size:21 final size:20
Alignment explanation
Indices: 14410--14455 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
14400 GAACTGAAAT
*
14410 AGAAGCATAACAACTTAAAC
1 AGAAACATAACAACTTAAAC
*
14430 AGAAACATAACAACTTGTAAC
1 AGAAACATAACAACTT-AAAC
14451 AGAAA
1 AGAAA
14456 ACTCAACTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.15
Consensus pattern (20 bp):
AGAAACATAACAACTTAAAC
Found at i:19803 original size:21 final size:21
Alignment explanation
Indices: 19777--19856 Score: 133
Period size: 21 Copynumber: 3.8 Consensus size: 21
19767 ATTTACCGTG
19777 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
*
19798 ATTGCGGCTGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* *
19819 ATTGCGGCTGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
19840 ATTGCGGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
19857 TAACTCGGAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.06, C:0.30, G:0.42, T:0.21
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:21484 original size:24 final size:23
Alignment explanation
Indices: 21457--21591 Score: 125
Period size: 24 Copynumber: 5.5 Consensus size: 23
21447 AAATTGAACG
21457 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGA-TAAAA
21481 ACCGGTTTTTTTCAAACCGGATAAAA
1 ACCGGTTTTTTT---ACCGGATAAAA
21507 ACCCGG-TTTTTTATCCGGATAAAA
1 A-CCGGTTTTTTTA-CCGGATAAAA
21531 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT---ACCGGAT-AAAA
*
21558 ACTGG-TTTTTTATCC-GA-AAAA
1 ACCGGTTTTTTTA-CCGGATAAAA
21579 ATCCGGTTTTTTT
1 A-CCGGTTTTTTT
21592 GCAAACCGAA
Statistics
Matches: 96, Mismatches: 2, Indels: 27
0.77 0.02 0.22
Matches are distributed among these distances:
21 5 0.05
22 3 0.03
23 14 0.15
24 31 0.32
26 24 0.25
27 19 0.20
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (23 bp):
ACCGGTTTTTTTACCGGATAAAA
Found at i:21534 original size:50 final size:50
Alignment explanation
Indices: 21457--21599 Score: 211
Period size: 50 Copynumber: 2.8 Consensus size: 50
21447 AAATTGAACG
21457 ACCGGTTTTTT-TACCGGATTAAAAACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTAT-CCGGA-TAAAAACCGGTTTTTTTCAAACCGGATAAAAA
*
21508 CCCGGTTTTTTATCCGGATAAAAACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTATCCGGATAAAAACCGGTTTTTTTCAAACCGGATAAAAA
*
21558 ACTGGTTTTTTATCC-GA-AAAAATCCGGTTTTTTTGCAAACCG
1 ACCGGTTTTTTATCCGGATAAAAA-CCGGTTTTTTT-CAAACCG
21600 AAACCGGTTA
Statistics
Matches: 86, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
48 5 0.06
49 13 0.15
50 52 0.60
51 15 0.17
52 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (50 bp):
ACCGGTTTTTTATCCGGATAAAAACCGGTTTTTTTCAAACCGGATAAAAA
Found at i:21602 original size:26 final size:25
Alignment explanation
Indices: 21476--21600 Score: 111
Period size: 26 Copynumber: 5.0 Consensus size: 25
21466 TTTACCGGAT
21476 TAAAAACCGGTTTTTTTCAAACCGGA
1 TAAAAACCGGTTTTTTTCAAACC-GA
*
21502 TAAAAACCCGGTTTTTTATC---CGGA
1 TAAAAA-CCGGTTTTTT-TCAAACCGA
21526 TAAAAACCGGTTTTTTTCAAACCGGA
1 TAAAAACCGGTTTTTTTCAAACC-GA
* *
21552 TAAAAAACTGG-TTTTTT--ATCCGA
1 T-AAAAACCGGTTTTTTTCAAACCGA
21575 -AAAAATCCGGTTTTTTTGCAAACCGA
1 TAAAAA-CCGGTTTTTTT-CAAACCGA
21601 AACCGGTTAC
Statistics
Matches: 81, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
21 5 0.06
22 5 0.06
23 18 0.22
24 11 0.14
25 2 0.02
26 20 0.25
27 18 0.22
28 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (25 bp):
TAAAAACCGGTTTTTTTCAAACCGA
Found at i:23274 original size:24 final size:25
Alignment explanation
Indices: 23221--23280 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
23211 TATTGTATTT
* *
23221 CTTTATTTTTATTTTTTTACTTTATT
1 CTTT-TTTTTATTTTTTTACTCTATG
23247 CTTTTTTTTATTTTTTTA-TCTATG
1 CTTTTTTTTATTTTTTTACTCTATG
*
23271 CTTTTATTTA
1 CTTTTTTTTA
23281 ATTCCATTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 13 0.42
25 14 0.45
26 4 0.13
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (25 bp):
CTTTTTTTTATTTTTTTACTCTATG
Found at i:23334 original size:16 final size:17
Alignment explanation
Indices: 23294--23357 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
23284 CCATTACTGT
23294 TTTTGTTT-TATTT-TTG
1 TTTTGTTTGT-TTTATTG
23310 TTTCATGTTTGTTTTATT-
1 TTT--TGTTTGTTTTATTG
23328 TTTTGTTT-TTTTATTG
1 TTTTGTTTGTTTTATTG
23344 TTTTGTTTTGTTTT
1 TTTTG-TTTGTTTT
23358 TTTATCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.17
16 13 0.32
17 3 0.07
18 15 0.37
19 3 0.07
ACGTcount: A:0.06, C:0.02, G:0.12, T:0.80
Consensus pattern (17 bp):
TTTTGTTTGTTTTATTG
Found at i:23358 original size:11 final size:11
Alignment explanation
Indices: 23293--23357 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
23283 TCCATTACTG
23293 TTTTTGTTTTA
1 TTTTTGTTTTA
*
23304 TTTTTGTTTCA
1 TTTTTGTTTTA
*
23315 TGTTTGTTTTA
1 TTTTTGTTTTA
23326 TTTTTTGTTTT-
1 -TTTTTGTTTTA
23337 TTTATTGTTTT-
1 TTT-TTGTTTTA
*
23348 GTTTTGTTTT
1 TTTTTGTTTT
23358 TTTATCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
10 10 0.21
11 28 0.60
12 9 0.19
ACGTcount: A:0.06, C:0.02, G:0.12, T:0.80
Consensus pattern (11 bp):
TTTTTGTTTTA
Found at i:23371 original size:24 final size:22
Alignment explanation
Indices: 23296--23380 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 22
23286 ATTACTGTTT
** *
23296 TTGTTTTATTTTTGTTTCATGT-
1 TTGTTTTA-TTTTGTTTTTTTTA
*
23318 TTGTTTTATTTTTTGTTTTTTTA
1 TTGTTTTATTTTGT-TTTTTTTA
*
23341 TTGTTTTGTTTTGTTTTTTTATCA
1 TTGTTTTATTTTGTTTTTTT-T-A
*
23365 TTTTTTTATTTTGTTT
1 TTGTTTTATTTTGTTT
23381 ATTCTTTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 5 0.10
22 18 0.35
23 13 0.25
24 15 0.29
ACGTcount: A:0.08, C:0.02, G:0.11, T:0.79
Consensus pattern (22 bp):
TTGTTTTATTTTGTTTTTTTTA
Found at i:23388 original size:20 final size:20
Alignment explanation
Indices: 23326--23425 Score: 71
Period size: 20 Copynumber: 4.9 Consensus size: 20
23316 GTTTGTTTTA
* *
23326 TTTTTTGTTTT-TTTATTGT
1 TTTTTTATTTTGTTTATTCT
*
23345 TTTGTTT-TGTTTTTTTA-TCAT
1 TTT-TTTAT-TTTGTTTATTC-T
23366 TTTTTTATTTTGTTTATTCT
1 TTTTTTATTTTGTTTATTCT
* * *
23386 TTTTTTACTTAGTTTATCTTT
1 TTTTTTATTTTGTTTAT-TCT
*
23407 TTTTTTATCTTTTTTTATT
1 TTTTTTAT-TTTGTTTATT
23426 ATTTATGTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.06
20 33 0.51
21 21 0.32
22 7 0.11
ACGTcount: A:0.10, C:0.05, G:0.06, T:0.79
Consensus pattern (20 bp):
TTTTTTATTTTGTTTATTCT
Found at i:23391 original size:21 final size:20
Alignment explanation
Indices: 23326--23421 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 20
23316 GTTTGTTTTA
* *
23326 TTTTTTGTTTTTTTATTGTT
1 TTTTTTATTTTTTTATTCTT
* *
23346 TTGTTTTGTTTTTTTA-TCAT
1 TT-TTTTATTTTTTTATTCTT
23366 TTTTTTATTTTGTTTATTC-T
1 TTTTTTATTTT-TTTATTCTT
**
23386 TTTTTTACTTAGTTTA-TCTTT
1 TTTTTTA-TTTTTTTATTC-TT
23407 TTTTTTATCTTTTTT
1 TTTTTTAT-TTTTTT
23422 TATTATTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
19 10 0.16
20 23 0.37
21 29 0.47
ACGTcount: A:0.09, C:0.05, G:0.06, T:0.79
Consensus pattern (20 bp):
TTTTTTATTTTTTTATTCTT
Found at i:23401 original size:29 final size:29
Alignment explanation
Indices: 23369--23431 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
23359 TTATCATTTT
23369 TTTAT-TTTGTTTAT-TCTTTTTTTACTTA
1 TTTATCTTTGTTTATATCTTTTTTTA-TTA
* *
23397 GTTTATCTTTTTTTTTATCTTTTTTTATTA
1 -TTTATCTTTGTTTATATCTTTTTTTATTA
23427 TTTAT
1 TTTAT
23432 GTTTTAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.33
30 10 0.33
31 10 0.33
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.76
Consensus pattern (29 bp):
TTTATCTTTGTTTATATCTTTTTTTATTA
Found at i:23418 original size:31 final size:30
Alignment explanation
Indices: 23354--23436 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
23344 TTTTGTTTTG
* * *
23354 TTTTTTTATCATTTTTTTATTTTGTTTATTC
1 TTTTTTTATTATTTATCT-TTTTGTTTATTC
*
23385 TTTTTTTACTTAGTTTATCTTTTTTTTTA-TC
1 TTTTTTTA-TTA-TTTATCTTTTTGTTTATTC
*
23416 TTTTTTTATTATTTATGTTTT
1 TTTTTTTATTATTTATCTTTT
23437 AATTCGACTC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 9 0.20
30 3 0.07
31 18 0.40
32 10 0.22
33 5 0.11
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (30 bp):
TTTTTTTATTATTTATCTTTTTGTTTATTC
Found at i:23422 original size:13 final size:12
Alignment explanation
Indices: 23398--23427 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
23388 TTTTACTTAG
23398 TTTATCTTTTTT
1 TTTATCTTTTTT
23410 TTTATCTTTTTT
1 TTTATCTTTTTT
23422 TATTAT
1 T-TTAT
23428 TTATGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTATCTTTTTT
Found at i:24033 original size:13 final size:13
Alignment explanation
Indices: 23997--24033 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
23987 TTCATCTAAG
* *
23997 GCTCTAAACCCGA
1 GCTCCAAACCTGA
24010 GCTCCAAACCTGA
1 GCTCCAAACCTGA
24023 GCTCCAAACCT
1 GCTCCAAACCT
24034 ATTTTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.41, G:0.14, T:0.16
Consensus pattern (13 bp):
GCTCCAAACCTGA
Found at i:31501 original size:3 final size:3
Alignment explanation
Indices: 31493--31567 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
31483 AATTTATTTT
31493 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31541 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
31568 TGATAGTCTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31986 original size:137 final size:137
Alignment explanation
Indices: 31731--32585 Score: 1234
Period size: 137 Copynumber: 6.2 Consensus size: 137
31721 CAACTATTGT
* * *
31731 ATGACATTGTTCTTTCGTGATGAGGACGTCTGACCATCTTTGAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * * * * * *
31796 CCTTCATGATGAGGACGTCTGGTTATCTGAGGATGA-CTCGACTCATACATGATGAGGAATTCTG
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTG-TTCATTCGTGATGAGGAGTTCTG
*
31860 GTC-AGTGG
130 ATCGA-TGG
* * *
31868 ATGACATTGTTCCTTTGTGATGAGGACGTCTAGCCATCTTTATAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * *
31933 CCTTCGTGATGAGGACGTATGGTTATCTAAGGATGATGTTGTTCTTTCGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTGTTCATTCGTGATGAGGAGTTCTGA
*
31998 TCGGTGG
131 TCGATGG
* *
32005 ATGACATTGTTCCTTCGTGATGAGAACGTCTGGACATCTTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * *
32070 CCTTCGTAACGAGGACATCTGGCTATCTAAGGATGATGTTGCTTC-TTCGTGATGAGGAGTTCTG
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTG-TTCATTCGTGATGAGGAGTTCTG
32134 ATCGATGG
130 ATCGATGG
* * * *
32142 ATGACATTGTTCCTTCATGATGAGAACGTATGGCCATATTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * *
32207 CCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATGTTGCTCCTTCGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTGTTCATTCGTGATGAGGAGTTCTGA
32272 TCGATGG
131 TCGATGG
*
32279 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACATGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * *
32344 CATTCGTGATGAGGACGTCTGATTATCTAAGGATGATGTTGTTCATTCGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTGTTCATTCGTGATGAGGAGTTCTGA
*
32409 TCGATAG
131 TCGATGG
* ** *
32416 ATGACATTGTTTCTTCACGATGAGGACGTCTGGCCATCTTTAAAGATATTTAAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
*
32481 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTGTTTC-TTCGTGATGAGGAGTTCTT
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTG-TTCATTCGTGATGAGGAGTTCTG
32545 ATC-AGTGG
130 ATCGA-TGG
* *
32553 ATGACATTGTTCCTTCGTGATGAGAACATCTGG
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGG
32586 TTATCTAAGG
Statistics
Matches: 649, Mismatches: 63, Indels: 12
0.90 0.09 0.02
Matches are distributed among these distances:
136 3 0.00
137 638 0.98
138 8 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTT
CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTTGTTCATTCGTGATGAGGAGTTCTGA
TCGATGG
Found at i:32293 original size:40 final size:42
Alignment explanation
Indices: 32204--32312 Score: 123
Period size: 40 Copynumber: 2.6 Consensus size: 42
32194 AGATAACACG
* **
32204 GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATGTT
1 GTTCCTTCGTGATGAGGACATCTGGC-ATCGAAGGATGACATT
* ** *
32247 GCTCCTTCGTGATGAGGAGTTCT-G-ATCGATGGATGACATT
1 GTTCCTTCGTGATGAGGACATCTGGCATCGAAGGATGACATT
*
32287 GTTCCTTCGTGATGAGGACGTCTGGC
1 GTTCCTTCGTGATGAGGACATCTGGC
32313 CATCTTTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
40 32 0.59
41 1 0.02
42 1 0.02
43 20 0.37
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (42 bp):
GTTCCTTCGTGATGAGGACATCTGGCATCGAAGGATGACATT
Found at i:32530 original size:43 final size:43
Alignment explanation
Indices: 32478--32603 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 43
32468 AGATAACACG
32478 GTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTT
1 GTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTT
* * * * **
32521 GTTTCTTCGTGATGAGGA-GT-T-CTTATC-AGTGGATGACATT
1 GTTCCTTCGTGATGAGGACATCTGGTTATCTA-AGGATGATGTT
*
32561 GTTCCTTCGTGATGAGAACATCTGGTTATCTAAGGATGATGTT
1 GTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTT
32604 TCCTAAAATA
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.02
40 29 0.45
41 2 0.03
42 2 0.03
43 30 0.46
44 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (43 bp):
GTTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGTT
Found at i:40592 original size:22 final size:22
Alignment explanation
Indices: 40558--40613 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
40548 ATGAATGCAA
40558 AAAATGCTAAATA-AA-AAAATAT
1 AAAATGC-AAATATAACAAAA-AT
*
40580 AATAATGCAAATATAACACAAAT
1 AA-AATGCAAATATAACAAAAAT
40603 AAAATGCAAAT
1 AAAATGCAAAT
40614 GCATGTATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 16 0.53
23 11 0.37
24 3 0.10
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAATGCAAATATAACAAAAAT
Found at i:41636 original size:16 final size:15
Alignment explanation
Indices: 41610--41641 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
41600 ATATAAGGCT
41610 ATAAAAAATAAAATA
1 ATAAAAAATAAAATA
41625 ATAAATAAATAAAATA
1 ATAAA-AAATAAAATA
41641 A
1 A
41642 ATTGAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
ATAAAAAATAAAATA
Found at i:43136 original size:23 final size:23
Alignment explanation
Indices: 43105--43152 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
43095 CCGGAGGAGC
43105 TCCGACCACCA-GTCGGTCACTAT
1 TCCGACCA-CAGGTCGGTCACTAT
* *
43128 TCCGGCCACAGGTCGGTTACTAT
1 TCCGACCACAGGTCGGTCACTAT
43151 TC
1 TC
43153 ACCATCACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.19, C:0.35, G:0.21, T:0.25
Consensus pattern (23 bp):
TCCGACCACAGGTCGGTCACTAT
Found at i:43692 original size:3 final size:3
Alignment explanation
Indices: 43684--43757 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
43674 ATTTATTTTG
43684 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43732 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
43758 TGATAGTCTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:49009 original size:121 final size:119
Alignment explanation
Indices: 48844--49249 Score: 478
Period size: 121 Copynumber: 3.3 Consensus size: 119
48834 AATTTGCTCG
* * * *
48844 AGATTGGATTTTAACTTAACGACGAAGGATCTCTC-ATTCTAGGCTCAACTTCACAACGAAGGGG
1 AGATTGGATTTCAACTTCACGACGAAGGATATC-CAATTCAAGGCTCAACTTCACAACGAAGGGG
* *
48908 CCATCCACAATTTCAACTTCATGAAGAAGGATATCATGCCCACAACCAACTTACTCA
65 CCATCCACGATTTCAACTTCA-GAAGAAGGATATCATGCCCACAAGCAAC-TACTCA
* * * *
48965 AGATTGGATTTCAACTTCACGATGAAGGATATCTAATTCAAGGCTCAAATTCACAACGAATGGGC
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGC
* * * * *
49030 CATCCACGATTTTAACTTC-GCAACGAAGGATATCGTGTCCACCAGCAAC-ACACA
66 CATCCACGATTTCAACTTCAG-AA-GAAGGATATCATGCCCACAAGCAACTACTCA
* **
49084 ATACTTGGATTTCAACTTTGCGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGG
1 AGA-TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGG
* * * *
49149 CCATCCACGATTTCAACTTCACGATGAAAGATAT-AGTGCCCACAAGCAGCATCAATCTCT
65 CCATCCACGATTTCAACTTCA-GAAGAAGGATATCA-TGCCCACAAGCA--A-CTA-CTCA
49209 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAA
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAA
49250 AGAAGGAGTG
Statistics
Matches: 240, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
119 7 0.03
120 94 0.39
121 95 0.40
122 2 0.01
123 1 0.00
124 37 0.15
125 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (119 bp):
AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGC
CATCCACGATTTCAACTTCAGAAGAAGGATATCATGCCCACAAGCAACTACTCA
Found at i:49138 original size:120 final size:118
Alignment explanation
Indices: 48846--49249 Score: 452
Period size: 120 Copynumber: 3.3 Consensus size: 118
48836 TTTGCTCGAG
* * * *
48846 ATTGGATTTTAACTTAACGACGAAGGATCTCTC-ATTCTAGGCTCAACTTCACAACGAAGGGGCC
1 ATTGGATTTCAACTTCACGACGAAGGATATC-CAATTCAAGGCTCAACTTCACAACGAAGGGGCC
* * * * *
48910 ATCCACAATTTCAACTTCATG-AAGAAGGATATCATGCCCACAACCAACTTACTCAAG
65 ATCCACGATTTCAACTTC--GCAAGAAGGATATCGTGCCCACAAGCAAC--ACACAAT
* * * *
48967 ATTGGATTTCAACTTCACGATGAAGGATATCTAATTCAAGGCTCAAATTCACAACGAATGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* * *
49032 TCCACGATTTTAACTTCGCAACGAAGGATATCGTGTCCACCAGCAACACACAAT
66 TCCACGATTTCAACTTCGCAA-GAAGGATATCGTGCCCACAAGCAACACACAAT
**
49086 ACTTGGATTTCAACTTTGCGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCC
1 A-TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCC
* * * * * * *
49151 ATCCACGATTTCAACTTCACGATGAAAGATATAGTGCCCACAAGCAGCATCAATCTCTAG
65 ATCCACGATTTCAACTTCGC-AAGAAGGATATCGTGCCCACAAGCA--A-C-A-CACAAT
49211 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAA
49250 AGAAGGAGTG
Statistics
Matches: 239, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
119 7 0.03
120 96 0.40
121 93 0.39
122 1 0.00
123 1 0.00
124 37 0.15
125 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (118 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
TCCACGATTTCAACTTCGCAAGAAGGATATCGTGCCCACAAGCAACACACAAT
Found at i:51334 original size:23 final size:21
Alignment explanation
Indices: 51306--51378 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 21
51296 TGTTTCATGT
51306 TTGTTTTATTTTGTATTTTTGTA
1 TTGTTTTATTTTGT-TTTTT-TA
* *
51329 TTGTTTTGTATTGTTTTTTTA
1 TTGTTTTATTTTGTTTTTTTA
* *
51350 TCGTTTTATTTATTTTGTTTATTA
1 TTGTTTTATTT-TGTT-TTT-TTA
51374 TTGTT
1 TTGTT
51379 ACATTTTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
21 10 0.25
22 8 0.20
23 15 0.38
24 7 0.17
ACGTcount: A:0.12, C:0.01, G:0.12, T:0.74
Consensus pattern (21 bp):
TTGTTTTATTTTGTTTTTTTA
Found at i:51335 original size:10 final size:10
Alignment explanation
Indices: 51314--51345 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
51304 GTTTGTTTTA
51314 TTTTGTA-T-
1 TTTTGTATTG
51322 TTTTGTATTG
1 TTTTGTATTG
51332 TTTTGTATTG
1 TTTTGTATTG
51342 TTTT
1 TTTT
51346 TTTATCGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.32
9 1 0.05
10 14 0.64
ACGTcount: A:0.09, C:0.00, G:0.16, T:0.75
Consensus pattern (10 bp):
TTTTGTATTG
Found at i:57999 original size:63 final size:63
Alignment explanation
Indices: 57900--58032 Score: 257
Period size: 63 Copynumber: 2.1 Consensus size: 63
57890 ATATATATAT
57900 ATATTCATTCACTCATAAGATCAGCCCCTAATTCATACCCTGATCAGGAACAGTAACAAGCTC
1 ATATTCATTCACTCATAAGATCAGCCCCTAATTCATACCCTGATCAGGAACAGTAACAAGCTC
*
57963 ATATTCATTTACTCATAAGATCAGCCCCTAATTCATACCCTGATCAGGAACAGTAACAAGCTC
1 ATATTCATTCACTCATAAGATCAGCCCCTAATTCATACCCTGATCAGGAACAGTAACAAGCTC
58026 ATATTCA
1 ATATTCA
58033 ACTAAAGAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (63 bp):
ATATTCATTCACTCATAAGATCAGCCCCTAATTCATACCCTGATCAGGAACAGTAACAAGCTC
Found at i:66296 original size:24 final size:23
Alignment explanation
Indices: 66246--66297 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
66236 AATTGCAATA
* *
66246 TAGAATTGCACCGAAGTCCCGCG
1 TAGAATTGCACAGAAGTCCCACG
* *
66269 TAGAATATGCACAGAAGTGCCACT
1 TAGAAT-TGCACAGAAGTCCCACG
66293 TAGAA
1 TAGAA
66298 ATTGTTCCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (23 bp):
TAGAATTGCACAGAAGTCCCACG
Found at i:70456 original size:49 final size:49
Alignment explanation
Indices: 70345--70745 Score: 367
Period size: 49 Copynumber: 8.0 Consensus size: 49
70335 AATGCACTGT
* *
70345 TTTGT-ATTTAACTTGCATTAGTGACACCTTTCTACAAAAAAATGCACCG
1 TTTGTCATCTAACTTGCATTAGTGACACCTTTCTAC-AAAAAATGCACCA
* * * *
70394 TTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACAAAAAATGCACCA
1 TTTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCACCA
* * *
70443 TTTGTCATCTAACTTGCATTAGTGGCACATTTCTACCAAAAATGCACCGTTAGACA
1 TTTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCA-C------CA
* * * * *
70499 TTTAACTTTTCATCTAACTTGCATTAGTGACACCTTTCTGC-CATAATGCACCG
1 --T---TTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCACCA
* * * * * * *
70552 TTAGACATTTAACTTGCATTAGTGGCTCATTTCTGCAAAAAATGCACCA
1 TTTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCACCA
* * * * *
70601 TTTGTCATCTAACTTGCATTAGTGACACCTTTATGC-TAGAATGCACCG
1 TTTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCACCA
* * * * * *
70649 TTAGACATTTAACTTGCATTAGTGACACATTTCTGCCAAAAATGCACCA
1 TTTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCACCA
*
70698 TTTGTCATCTAACTTGCATTAGTGGCACCTTTCTACAAAAAATGCACC
1 TTTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCACC
70746 GTTAGACATT
Statistics
Matches: 286, Mismatches: 51, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
48 68 0.24
49 144 0.50
50 30 0.10
51 1 0.00
53 1 0.00
56 2 0.01
58 1 0.00
59 1 0.00
60 7 0.02
61 31 0.11
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (49 bp):
TTTGTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGCACCA
Found at i:70517 original size:61 final size:60
Alignment explanation
Indices: 70447--70566 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 60
70437 GCACCATTTG
*
70447 TCATCTAACTTGCATTAGTGGCACATTTCTACCAAAAATGCACCGTTAGACATTTAACTTT
1 TCATCTAACTTGCATTAGTGACACATTTCTACC-AAAATGCACCGTTAGACATTTAACTTT
* * *
70508 TCATCTAACTTGCATTAGTGACACCTTTCTGCCATAATGCACCGTTAGACATTTAACTT
1 TCATCTAACTTGCATTAGTGACACATTTCTACCAAAATGCACCGTTAGACATTTAACTT
70567 GCATTAGTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
60 25 0.45
61 30 0.55
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (60 bp):
TCATCTAACTTGCATTAGTGACACATTTCTACCAAAATGCACCGTTAGACATTTAACTTT
Found at i:70680 original size:97 final size:97
Alignment explanation
Indices: 70508--70761 Score: 409
Period size: 97 Copynumber: 2.6 Consensus size: 97
70498 ATTTAACTTT
* *
70508 TCATCTAACTTGCATTAGTGACACCTTTCTGCCATAATGCACCGTTAGACATTTAACTTGCATTA
1 TCATCTAACTTGCATTAGTGACACCTTTCTGCAAAAATGCACCGTTAGACATTTAACTTGCATTA
* *
70573 GTGGCTCATTTCTGCAAAAAATGCACCATTTG
66 GTGACACATTTCTGCAAAAAATGCACCATTTG
* * *
70605 TCATCTAACTTGCATTAGTGACACCTTTATGCTAGAATGCACCGTTAGACATTTAACTTGCATTA
1 TCATCTAACTTGCATTAGTGACACCTTTCTGCAAAAATGCACCGTTAGACATTTAACTTGCATTA
*
70670 GTGACACATTTCTGCCAAAAATGCACCATTTG
66 GTGACACATTTCTGCAAAAAATGCACCATTTG
* *
70702 TCATCTAACTTGCATTAGTGGCACCTTTCTACAAAAAATGCACCGTTAGACATTTAACTT
1 TCATCTAACTTGCATTAGTGACACCTTTCTGC-AAAAATGCACCGTTAGACATTTAACTT
70762 TTCATCTAAC
Statistics
Matches: 145, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
97 120 0.83
98 25 0.17
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (97 bp):
TCATCTAACTTGCATTAGTGACACCTTTCTGCAAAAATGCACCGTTAGACATTTAACTTGCATTA
GTGACACATTTCTGCAAAAAATGCACCATTTG
Found at i:71906 original size:36 final size:37
Alignment explanation
Indices: 71858--71945 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 37
71848 AAAGGAAAAC
71858 ATAA-ATATAGTTTTTTAAAA-CATTTTTGAAAACAT
1 ATAATATATAGTTTTTTAAAATCATTTTTGAAAACAT
* *
71893 ATAGTATATAG-TTTTTAAAATGATTTTTGAAAACAT
1 ATAATATATAGTTTTTTAAAATCATTTTTGAAAACAT
71929 ATAATATATAGTTTTTT
1 ATAATATATAGTTTTTT
71946 TTCTAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
35 12 0.26
36 30 0.64
37 5 0.11
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (37 bp):
ATAATATATAGTTTTTTAAAATCATTTTTGAAAACAT
Found at i:72031 original size:13 final size:13
Alignment explanation
Indices: 72013--72060 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
72003 ATTATTAGTA
*
72013 TTTTATTTTTCAT
1 TTTTATTTTCCAT
72026 TTTTATTTTCCAT
1 TTTTATTTTCCAT
* *
72039 TATTATTATCCAT
1 TTTTATTTTCCAT
72052 TTTTATTTT
1 TTTTATTTT
72061 ATTTTTCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTTTCCAT
Found at i:75334 original size:21 final size:22
Alignment explanation
Indices: 75294--75334 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
75284 CCCTGGAAAT
*
75294 GAAGCATTTCCCATGCCAACCA
1 GAAGCATTTCCCATGACAACCA
*
75316 GAAGC-TTTCCCATTACAAC
1 GAAGCATTTCCCATGACAAC
75335 TAATCATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (22 bp):
GAAGCATTTCCCATGACAACCA
Found at i:81149 original size:3 final size:3
Alignment explanation
Indices: 81143--81172 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
81133 TTTTATTGAC
81143 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
81173 TACTTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:87414 original size:14 final size:14
Alignment explanation
Indices: 87392--87448 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
87382 TCGATTATTT
87392 ATTCGTTTATGTTC
1 ATTCGTTTATGTTC
*
87406 ATTCATTTATGTTC
1 ATTCGTTTATGTTC
* *
87420 GTTCGTTTATGTTT
1 ATTCGTTTATGTTC
* *
87434 GTTCGTTTATATTC
1 ATTCGTTTATGTTC
87448 A
1 A
87449 ACTCAATCTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (14 bp):
ATTCGTTTATGTTC
Found at i:89414 original size:27 final size:26
Alignment explanation
Indices: 89363--89453 Score: 75
Period size: 27 Copynumber: 3.6 Consensus size: 26
89353 AATAAATTAT
* ** *
89363 ATATTTTTAAATGAAAATAAAAATACA
1 ATATTTTTAAATTAAGTTAATAATA-A
89390 ATATTTTTAAATTAAGTTAATAATAA
1 ATATTTTTAAATTAAGTTAATAATAA
*
89416 ATA--TAT-AA-TAAGTTAAT-ATAAA
1 ATATTTTTAAATTAAGTTAATAAT-AA
89438 AGTATTTTTAAATTAA
1 A-TATTTTTAAATTAA
89454 TATATGTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.04
22 12 0.23
23 4 0.08
24 2 0.04
25 2 0.04
26 6 0.12
27 24 0.46
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATTTTTAAATTAAGTTAATAATAA
Found at i:89793 original size:146 final size:146
Alignment explanation
Indices: 89593--89889 Score: 522
Period size: 146 Copynumber: 2.0 Consensus size: 146
89583 TGTAATATAT
89593 ATAATCCACACATAAATTTTAAAAATTCAAAATACATATTGAAAATAAAATTTATTAAAAATTAA
1 ATAATCCACACATAAATTTTAAAAATTCAAAATACATATTGAAAATAAAATTTATTAAAAATTAA
89658 AATAAAGGAATACAATTAAATTTCAAATGTTTTGAAGTTAAAATAAATATTTTAAAAAATAATTT
66 AATAAAGGAATACAATTAAATTTCAAATGTTTTGAAGTTAAAATAAATATTTTAAAAAATAATTT
**
89723 AGAATGTTAATGTGAA
131 AGAACATTAATGTGAA
* * *
89739 ATAATCCACACATAAATTTTAAAAATTCAAATTATATATTGAAAATAAATTTTATTAAAAATTAA
1 ATAATCCACACATAAATTTTAAAAATTCAAAATACATATTGAAAATAAAATTTATTAAAAATTAA
* * *
89804 AATAAAGTAATACAATTAATTTTTAAATGTTTTGAAGTTAAAATAAATATTTTAAAAAATAATTT
66 AATAAAGGAATACAATTAAATTTCAAATGTTTTGAAGTTAAAATAAATATTTTAAAAAATAATTT
89869 AGAACATTAATGTGAA
131 AGAACATTAATGTGAA
89885 ATAAT
1 ATAAT
89890 TTAAGAAATT
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
146 143 1.00
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (146 bp):
ATAATCCACACATAAATTTTAAAAATTCAAAATACATATTGAAAATAAAATTTATTAAAAATTAA
AATAAAGGAATACAATTAAATTTCAAATGTTTTGAAGTTAAAATAAATATTTTAAAAAATAATTT
AGAACATTAATGTGAA
Found at i:89806 original size:18 final size:19
Alignment explanation
Indices: 89757--89804 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 19
89747 CACATAAATT
89757 TTAAAAATTCAAATTATATA
1 TTAAAAATT-AAATTATATA
*
89777 TTGAAAA-TAAATT-T-TA
1 TTAAAAATTAAATTATATA
89793 TTAAAAATTAAA
1 TTAAAAATTAAA
89805 ATAAAGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.32
17 5 0.20
18 5 0.20
19 1 0.04
20 6 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAAAAATTAAATTATATA
Found at i:90558 original size:25 final size:26
Alignment explanation
Indices: 90525--90575 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
90515 CAAGTTTGAA
90525 ATTAAATTATAAATTTT-GAAA-AATT
1 ATTAAATTAT-AATTTTAGAAATAATT
*
90550 ATTATATTATAATTTTAGAAATAATT
1 ATTAAATTATAATTTTAGAAATAATT
90576 TTTCAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 13 0.57
26 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
ATTAAATTATAATTTTAGAAATAATT
Found at i:91047 original size:21 final size:21
Alignment explanation
Indices: 91022--91061 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
91012 AGTTACAAAA
91022 TAATTACTAGAGTCACAAATG
1 TAATTACTAGAGTCACAAATG
* *
91043 TAATTACTTGAGTTACAAA
1 TAATTACTAGAGTCACAAA
91062 CGGATGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
TAATTACTAGAGTCACAAATG
Done.