Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003942.1 Hibiscus syriacus cultivar Beakdansim tig00008518_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: 365498
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:307221 original size:3 final size:3
Alignment explanation
Indices: 307215--307287 Score: 93
Period size: 3 Copynumber: 25.7 Consensus size: 3
307205 ATTTTTTTAA
*
307215 TAT TAT TAT TAT TAT TAT TAT T-T TA- TAC TAT T-T TATT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
307257 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
307288 CAAACAGGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
2 10 0.16
3 50 0.79
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:307260 original size:14 final size:16
Alignment explanation
Indices: 307194--307287 Score: 85
Period size: 15 Copynumber: 6.2 Consensus size: 16
307184 CATTTGTTTT
* *
307194 TTATTTTTAATATTT-
1 TTATTATTATTATTTA
*
307209 TT-TTAATATTA-TTA
1 TTATTATTATTATTTA
307223 TTATTATTATTATTT-
1 TTATTATTATTATTTA
*
307238 TATACTATT-TTATTTA
1 T-TATTATTATTATTTA
307254 TT-TTATTATTATTATA
1 TTATTATTATTATT-TA
307270 TTATTATTATTA-TTA
1 TTATTATTATTATTTA
307285 TTA
1 TTA
307288 CAAACAGGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
13 2 0.03
14 12 0.18
15 28 0.43
16 14 0.22
17 9 0.14
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:308665 original size:26 final size:23
Alignment explanation
Indices: 308635--308689 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 23
308625 AGTTTTAATT
308635 TTATTT-ATTTTAGTTACTGTTTAAA
1 TTATTTAATTTTA--TA-TGTTTAAA
308660 TATATTTTAATTTTATATGTTTAAA
1 T-TA-TTTAATTTTATATGTTTAAA
308685 TTATT
1 TTATT
308690 ATTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 10 0.37
26 4 0.15
27 3 0.11
28 6 0.22
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (23 bp):
TTATTTAATTTTATATGTTTAAA
Found at i:308668 original size:27 final size:26
Alignment explanation
Indices: 308626--308702 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 26
308616 TTTATATTTA
*
308626 GTTTTAATT-TTA-TTTATTTTAGTTACT
1 GTTTAAATTATTATTTTATTTTA--TA-T
308653 GTTTAAA-TA-TATTTTAATTTTATAT
1 GTTTAAATTATTATTTT-ATTTTATAT
308678 GTTTAAATTATTATTATTATTTTAT
1 GTTTAAATTATTATT-TTATTTTAT
308703 TTATATATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
25 8 0.19
26 7 0.16
27 20 0.47
28 8 0.19
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (26 bp):
GTTTAAATTATTATTTTATTTTATAT
Found at i:308668 original size:37 final size:37
Alignment explanation
Indices: 308605--308675 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
308595 TAATTACAAG
* * *
308605 TTTTATTACTTTTTATATTTAGTTTTAATTTTATTTA
1 TTTTATTACTGTTTAAATATAGTTTTAATTTTATTTA
308642 TTTTAGTTACTGTTTAAATATA-TTTTAATTTTAT
1 TTTTA-TTACTGTTTAAATATAGTTTTAATTTTAT
308676 ATGTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 17 0.57
38 13 0.43
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (37 bp):
TTTTATTACTGTTTAAATATAGTTTTAATTTTATTTA
Found at i:320358 original size:15 final size:15
Alignment explanation
Indices: 320332--320372 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
320322 GAAATAAAAA
*
320332 AAAAAGAAAAAATGATG
1 AAAATGAAAAAA--ATG
320349 AAAATGAAAAAAATG
1 AAAATGAAAAAAATG
320364 AAAATGAAA
1 AAAATGAAA
320373 TGAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.52
17 11 0.48
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (15 bp):
AAAATGAAAAAAATG
Found at i:320393 original size:20 final size:21
Alignment explanation
Indices: 320346--320398 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
320336 AGAAAAAATG
*
320346 ATGAAAATGAAAAAAATGAAA
1 ATGAAAATGAAAAAAAAGAAA
*
320367 ATG-AAATGAAAAAAAAGAGA
1 ATGAAAATGAAAAAAAAGAAA
320387 A-GAAAAT-AAAAA
1 ATGAAAATGAAAAA
320399 GGAGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.21
20 20 0.69
21 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (21 bp):
ATGAAAATGAAAAAAAAGAAA
Found at i:321474 original size:20 final size:22
Alignment explanation
Indices: 321429--321491 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
321419 ACATCTACAT
321429 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
321451 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
321473 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
321492 TATTGGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:321932 original size:122 final size:121
Alignment explanation
Indices: 321778--322109 Score: 506
Period size: 122 Copynumber: 2.7 Consensus size: 121
321768 TCACTCGATG
*
321778 CATCAACTTTTCCATAGAAAGTTCATACTGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
1 CATCAACTTTTCCA-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
* * *
321843 AATGAGAAGAACTTATTCAACCTTTGCATGACTCTATCACTGAAAGAGATAGATCAA
65 AATGAGAAGAACTTGTTCAACCTTTGCATAACTCTATCACAGAAAGAGATAGATCAA
*
321900 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGATGAAGAAGAAGTTCAT
1 CATCAACTTTTCCA-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
* *
321965 AATGAGAAGAACTTGTTCAACCTTTGCATAACTCTATCACAGAAGGAGATAGATCAG
65 AATGAGAAGAACTTGTTCAACCTTTGCATAACTCTATCACAGAAAGAGATAGATCAA
* * * * *
322022 CATCAACATTTCCAA-AACTGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAACAAGTTCA
1 CATCAACTTTTCCAAGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCA
322085 TAATGAGAAGAACTTGTTCAACCTT
64 TAATGAGAAGAACTTGTTCAACCTT
322110 GTCTTAATTC
Statistics
Matches: 194, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
120 2 0.01
121 63 0.32
122 129 0.66
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (121 bp):
CATCAACTTTTCCAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTGCATAACTCTATCACAGAAAGAGATAGATCAA
Found at i:321982 original size:20 final size:20
Alignment explanation
Indices: 321920--321983 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 20
321910 TCCAGAGAAA
321920 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* *
321940 ATCTGA-AGATGAAGAAGAA---
1 GT-TCATA-ATG-AGAAGAACTT
321959 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
321979 GTTCA
1 GTTCA
321984 ACCTTTGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 2 0.06
20 7 0.21
21 5 0.15
22 7 0.21
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:322470 original size:3 final size:3
Alignment explanation
Indices: 322462--322577 Score: 170
Period size: 3 Copynumber: 40.0 Consensus size: 3
322452 ATTCATTTGT
322462 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
322510 TT- TTA TT- CTA TT- TTA TTTA TT- TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
322551 TTA TTA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
322578 CAAACAGGCC
Statistics
Matches: 103, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
2 9 0.09
3 91 0.88
4 3 0.03
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:322523 original size:10 final size:9
Alignment explanation
Indices: 322446--322555 Score: 72
Period size: 9 Copynumber: 12.0 Consensus size: 9
322436 AAGATACTAA
322446 TATTTTATT
1 TATTTTATT
* *
322455 CA-TTTGTT
1 TATTTTATT
322463 TATTATTA-T
1 TATT-TTATT
322472 TATTATTA-T
1 TATT-TTATT
322481 TATTATTA-T
1 TATT-TTATT
322490 TATTATTA-T
1 TATT-TTATT
322499 TATTATTA-T
1 TATT-TTATT
322508 TATTTTATT
1 TATTTTATT
322517 CTATTTTATT
1 -TATTTTATT
322527 TATTTTA-T
1 TATTTTATT
322535 TATTATTATAT
1 TATT-TTAT-T
322546 TATTATTATT
1 TATT-TTATT
322556 ATTAATATTA
Statistics
Matches: 90, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
8 14 0.16
9 54 0.60
10 12 0.13
11 10 0.11
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (9 bp):
TATTTTATT
Found at i:323735 original size:23 final size:23
Alignment explanation
Indices: 323709--323752 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
323699 GTTTTAATTT
*
323709 AATTTAATTTAATTTGATTTTCG
1 AATTTAATATAATTTGATTTTCG
* *
323732 AATTTGATATAATTTTATTTT
1 AATTTAATATAATTTGATTTT
323753 AGTCACTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
AATTTAATATAATTTGATTTTCG
Found at i:323950 original size:26 final size:23
Alignment explanation
Indices: 323920--323974 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 23
323910 AGTTTTAATT
323920 TTATTT-ATTTTAGTTACTGTTTAAA
1 TTATTTAATTTTA--TA-TGTTTAAA
323945 TATATTTTAATTTTATATGTTTAAA
1 T-TA-TTTAATTTTATATGTTTAAA
323970 TTATT
1 TTATT
323975 ATTATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 10 0.37
26 4 0.15
27 3 0.11
28 6 0.22
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (23 bp):
TTATTTAATTTTATATGTTTAAA
Found at i:323953 original size:37 final size:37
Alignment explanation
Indices: 323890--323960 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
323880 TAATTACAAG
* * *
323890 TTTTATTACTTTTTATATTTAGTTTTAATTTTATTTA
1 TTTTATTACTGTTTAAATATAGTTTTAATTTTATTTA
323927 TTTTAGTTACTGTTTAAATATA-TTTTAATTTTAT
1 TTTTA-TTACTGTTTAAATATAGTTTTAATTTTAT
323961 ATGTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 17 0.57
38 13 0.43
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (37 bp):
TTTTATTACTGTTTAAATATAGTTTTAATTTTATTTA
Found at i:323977 original size:3 final size:3
Alignment explanation
Indices: 323969--324005 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
323959 ATATGTTTAA
*
323969 ATT ATT ATT ATT ATT ATT ATT ATT TTT ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
324006 TGATTAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:326370 original size:14 final size:14
Alignment explanation
Indices: 326347--326381 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
326337 GTTTCTTTGA
326347 TTTTTT-TTATTTT
1 TTTTTTATTATTTT
326360 TTTTTTATTATTTT
1 TTTTTTATTATTTT
*
326374 ATTTTTAT
1 TTTTTTAT
326382 GTTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTATTATTTT
Found at i:326379 original size:20 final size:21
Alignment explanation
Indices: 326346--326444 Score: 87
Period size: 20 Copynumber: 4.8 Consensus size: 21
326336 TGTTTCTTTG
*
326346 ATTTTTTTTA-TTTTTTTTTT
1 ATTTATTTTATTTTTTTTTTT
* *
326366 A-TTATTTTATTTTTATGTTT
1 ATTTATTTTATTTTTTTTTTT
* **
326386 ATTTA-TTTATTTATAGTTTT
1 ATTTATTTTATTTTTTTTTTT
* *
326406 ATTTATTTTATTTGTATATTTT
1 ATTTATTTTATTT-TTTTTTTT
326428 ATTTATTATTATTTTTT
1 ATTTATT-TTATTTTTT
326445 ATCTAACATT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.11
20 27 0.43
21 10 0.16
22 13 0.21
23 6 0.10
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (21 bp):
ATTTATTTTATTTTTTTTTTT
Found at i:326379 original size:25 final size:25
Alignment explanation
Indices: 326350--326467 Score: 87
Period size: 29 Copynumber: 4.4 Consensus size: 25
326340 TCTTTGATTT
326350 TTTTTATTTTTTTTTTATTATTTTA
1 TTTTTATTTTTTTTTTATTATTTTA
* *
326375 TTTTTA-TGTTTATTTATTTATTTATA
1 TTTTTATTTTTTTTTTA-TTATTT-TA
* *
326401 GTTTTATTTATTTTATTTGTATATTTTA
1 TTTTTATTT-TTTT-TTTAT-TATTTTA
**
326429 TTTATTATTATTTTTTATCTAACATTTT-
1 TTT-TTATT-TTTTTT-T-TATTATTTTA
326457 TTTTTATTTTT
1 TTTTTATTTTT
326468 GAGAAATTTC
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
24 8 0.11
25 12 0.16
26 10 0.14
27 6 0.08
28 12 0.16
29 23 0.32
30 2 0.03
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTTTTTTTATTATTTTA
Found at i:326392 original size:4 final size:4
Alignment explanation
Indices: 326352--326446 Score: 51
Period size: 4 Copynumber: 24.2 Consensus size: 4
326342 TTTGATTTTT
* *
326352 TTTA TTT- TTTT TTTA -TTA TTTTA TTT- TTATG TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TT-TA TTTA TTTA TTTA TTTA
* * *
326399 TAGT- TTTA TTTA TTTTA TTTG TATA TTTTA TTTA -TTA -TTA TTT- TTTA
1 T-TTA TTTA TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
326446 T
1 T
326447 CTAACATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 22
0.71 0.08 0.22
Matches are distributed among these distances:
3 18 0.25
4 41 0.57
5 13 0.18
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:326444 original size:17 final size:17
Alignment explanation
Indices: 326356--326465 Score: 63
Period size: 17 Copynumber: 6.5 Consensus size: 17
326346 ATTTTTTTTA
326356 TTTTT-TTT-TTATTAT
1 TTTTTATTTATTATTAT
326371 TTTATT-TTTATGT-TTAT
1 TTT-TTATTTAT-TATTAT
326388 TTATTTATTTA-TAGTT-T
1 TT-TTTATTTATTA-TTAT
*
326405 TATTTATTTTATT-TGTAT
1 TTTTTA-TTTATTAT-TAT
*
326423 ATTTTATTTATTATTAT
1 TTTTTATTTATTATTAT
* ** *
326440 TTTTTATCTAACATTTT
1 TTTTTATTTATTATTAT
326457 TTTTTATTT
1 TTTTTATTT
326466 TTGAGAAATT
Statistics
Matches: 74, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
15 3 0.04
16 11 0.15
17 45 0.61
18 15 0.20
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTATTTATTATTAT
Found at i:326525 original size:6 final size:7
Alignment explanation
Indices: 326510--326540 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
326500 TGAATCCGGT
326510 TTTTTAA
1 TTTTTAA
326517 TTTTT-A
1 TTTTTAA
326523 TTTTTAA
1 TTTTTAA
326530 TTTTTAA
1 TTTTTAA
326537 TTTT
1 TTTT
326541 CGCGATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:326528 original size:13 final size:14
Alignment explanation
Indices: 326510--326540 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
326500 TGAATCCGGT
326510 TTTTTAATTTTT-A
1 TTTTTAATTTTTAA
326523 TTTTTAATTTTTAA
1 TTTTTAATTTTTAA
326537 TTTT
1 TTTT
326541 CGCGATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTAATTTTTAA
Found at i:330873 original size:110 final size:110
Alignment explanation
Indices: 330125--330853 Score: 1010
Period size: 110 Copynumber: 6.7 Consensus size: 110
330115 GCTTCCCAGT
*
330125 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * * *
330190 CAACGAAGGGGCGACTGGTTGTCAACAAATAACTTTCCAG--T--
66 CAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
* * *
330231 TTCAGAG-CTGATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATACAAGCTCAACTTC
1 TTCAGAGTC-AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * *
330295 ACAACGAAGGGGCGACTGGTTGTCAACAAACAAC-TTCCAAG--T--
65 ACAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTC-AGTTTCA
* * * * **
330337 TTCAGAATCAATTTCAACTTCACAACGAAGTATATTGGACTCGAGACAATACAATATCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * *
330402 CATCGAAGGGGCGACTGATTGTAAACAAACAAATTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
* ** *
330447 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTACTCGAGATGACACATGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
330512 CAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
* *
330557 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* ** * * *
330622 TATTGAAGGGGCGATTTACTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
* *
330667 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGATAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
*
330732 CAGCGAAGGGCCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
* * * * *
330777 TTCAGAGTCAATTTGAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGTTCAACTTTA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
330842 CAGCGAAGGGGC
66 CAGCGAAGGGGC
330854 AGTTGGATGT
Statistics
Matches: 556, Mismatches: 59, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
105 5 0.01
106 183 0.33
107 4 0.01
108 1 0.00
110 363 0.65
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (110 bp):
TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
Found at i:331417 original size:120 final size:120
Alignment explanation
Indices: 331188--331419 Score: 347
Period size: 120 Copynumber: 1.9 Consensus size: 120
331178 GCAACTTATA
* *
331188 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * *
331253 CCACGGTTTCAACTTCACGACGAAGGGAATTGTGCTCACCAGCAACAATACAAGC
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACAATACAAGC
* * *
331308 TTGGATTTTAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTTACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * * *
331373 CCGCTGTTTCAACTTCATGACGAATGGAATCGTACCCACTAGCAACA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACA
331420 TTCATCTTCA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
120 99 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACAATACAAGC
Found at i:331547 original size:21 final size:21
Alignment explanation
Indices: 331521--331592 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
331511 AACAAAGTTG
331521 TCTCTCTTGAAACAAATTTTT
1 TCTCTCTTGAAACAAATTTTT
* *
331542 TCTCTCTTGAGA-TAA---TT
1 TCTCTCTTGAAACAAATTTTT
*
331559 TC-C-CTTGAAACAAATTTTG
1 TCTCTCTTGAAACAAATTTTT
*
331578 TCTCTCTTGAGACAA
1 TCTCTCTTGAAACAA
331593 TTTCCCTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
15 6 0.15
16 3 0.08
17 4 0.10
19 3 0.08
20 3 0.08
21 20 0.51
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (21 bp):
TCTCTCTTGAAACAAATTTTT
Found at i:331566 original size:36 final size:36
Alignment explanation
Indices: 331526--331608 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
331516 AGTTGTCTCT
* *
331526 CTTGAAACAAATTTTTTCTCTCTTGAGATAATTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
331562 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
331598 CTTGAAACAAA
1 CTTGAAACAAA
331609 ATCTTTGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
Found at i:331749 original size:73 final size:73
Alignment explanation
Indices: 331629--331781 Score: 207
Period size: 73 Copynumber: 2.1 Consensus size: 73
331619 ATGTTTTACA
* * ** * *
331629 TTAAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 TTAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
331694 ATTTCTCT
66 ATTTCTCT
* * *
331702 TTAAATAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 TTAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
*
331767 GTTTCTCT
66 ATTTCTCT
*
331775 TGAAACA
1 TTAAACA
331782 CACAAAAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (73 bp):
TTAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
ATTTCTCT
Found at i:331779 original size:37 final size:36
Alignment explanation
Indices: 331631--331781 Score: 185
Period size: 37 Copynumber: 4.1 Consensus size: 36
331621 GTTTTACATT
* * * * *
331631 AAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
* * *
331667 GAACTAAGTTTTGTCTCTCTTGAGACAATTTCTCTTT
1 AAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTG
* *
331704 AAATAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
*
331740 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAATTTCTCTTG
331777 AAACA
1 AAACA
331782 CACAAAAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
36 38 0.39
37 59 0.61
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
Found at i:331976 original size:84 final size:84
Alignment explanation
Indices: 331823--332005 Score: 258
Period size: 84 Copynumber: 2.2 Consensus size: 84
331813 GAAACACCAA
* * *
331823 ACCTTCGAGTTCGAGTACACTCAACTTCAAGGCACATCATTTGCAACATAGCCCAAGGCAAGAAG
1 ACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTGCAACATAGCCCAAGGCAAGAAA
*
331888 GGCTATTTGCCAACCAAAG
66 GGCTATCTGCCAACCAAAG
* * ** * *
331907 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAA
1 ACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTGCAACATAGCCCAAGGCAAGAAA
331972 GGCTATCTGCCAACCAAAG
66 GGCTATCTGCCAACCAAAG
*
331991 ACCTGACGAGTTCGA
1 ACCT-TCGAGTTCGA
332006 TTTCATTCAG
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 78 0.90
85 9 0.10
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (84 bp):
ACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTGCAACATAGCCCAAGGCAAGAAA
GGCTATCTGCCAACCAAAG
Found at i:338203 original size:21 final size:21
Alignment explanation
Indices: 338177--338224 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
338167 GCAAAAGGAA
*
338177 AAGGCATCCAAACTGACGACG
1 AAGGCATCCAAACTAACGACG
338198 AAGGCATCCAAACTAACGACG
1 AAGGCATCCAAACTAACGACG
338219 AAGGCA
1 AAGGCA
338225 AAGAAGAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.27, G:0.23, T:0.08
Consensus pattern (21 bp):
AAGGCATCCAAACTAACGACG
Found at i:339088 original size:8 final size:8
Alignment explanation
Indices: 339077--339164 Score: 52
Period size: 9 Copynumber: 10.2 Consensus size: 8
339067 TTTCTTTGAT
339077 TTTTTTTA
1 TTTTTTTA
339085 TTTTTTTTA
1 -TTTTTTTA
339094 TTATTATTT-
1 TT-TT-TTTA
*
339103 TATTTTTA
1 TTTTTTTA
339111 TGTTTATTTA
1 T-TTT-TTTA
*
339121 TTTATTTA
1 TTTTTTTA
**
339129 TAGTTTTA
1 TTTTTTTA
339137 TTTATTTTA
1 TTT-TTTTA
* *
339146 TTTGTATA
1 TTTTTTTA
339154 TTTTATTTA
1 TTTT-TTTA
339163 TT
1 TT
339165 ATTATTTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
7 3 0.05
8 21 0.35
9 28 0.47
10 8 0.13
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.76
Consensus pattern (8 bp):
TTTTTTTA
Found at i:339100 original size:6 final size:5
Alignment explanation
Indices: 339075--339172 Score: 73
Period size: 6 Copynumber: 19.0 Consensus size: 5
339065 TGTTTCTTTG
339075 ATTTT -TTTT ATTTT -TTTT ATTATT ATTTT ATTTTT ATGTTT A-TTT
1 ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT A-TTTT AT-TTT ATTTT
339120 A-TTT ATTTAT AGTTTT A-TTT ATTTT ATTTGT ATATTT -TATTT ATTATT
1 ATTTT ATTT-T A-TTTT ATTTT ATTTT ATTT-T AT-TTT AT-TTT ATT-TT
339168 ATTTT
1 ATTTT
339173 TTATCTAACA
Statistics
Matches: 80, Mismatches: 0, Indels: 26
0.75 0.00 0.25
Matches are distributed among these distances:
4 20 0.25
5 27 0.34
6 28 0.35
7 5 0.06
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:339105 original size:20 final size:22
Alignment explanation
Indices: 339080--339172 Score: 81
Period size: 22 Copynumber: 4.2 Consensus size: 22
339070 CTTTGATTTT
339080 TTTTA-TTTTT-TTTATTATTA
1 TTTTAGTTTTTATTTATTATTA
339100 TTTTA-TTTTTATGTTTATTTATTTA
1 TTTTAGTTTTTA--TTTA-TTA-TTA
339125 TTTATAG-TTTTATTTATT-TTA
1 TTT-TAGTTTTTATTTATTATTA
339146 TTTGTA-TATTTTATTTATTATTA
1 TTT-TAGT-TTTTATTTATTATTA
339169 TTTT
1 TTTT
339173 TTATCTAACA
Statistics
Matches: 62, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
20 10 0.16
21 8 0.13
22 12 0.19
23 12 0.19
24 7 0.11
25 6 0.10
26 7 0.11
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTTAGTTTTTATTTATTATTA
Found at i:339110 original size:17 final size:17
Alignment explanation
Indices: 339088--339176 Score: 59
Period size: 17 Copynumber: 5.4 Consensus size: 17
339078 TTTTTTATTT
339088 TTTTTATTATTATTTTA
1 TTTTTATTATTATTTTA
339105 TTTTTATGT-TTA-TTTA
1 TTTTTAT-TATTATTTTA
*
339121 TTTAT-TTA-TAGTTTTA
1 TTTTTATTATTA-TTTTA
339137 --TTTATT-TTATTTGTA
1 TTTTTATTATTATTT-TA
*
339152 TATTTTATTTATTATTAT-
1 T-TTTTA-TTATTATTTTA
339170 TTTTTAT
1 TTTTTAT
339177 CTAACATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 25
0.67 0.04 0.29
Matches are distributed among these distances:
14 8 0.14
15 7 0.12
16 13 0.23
17 15 0.26
18 6 0.11
19 3 0.05
20 5 0.09
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTATTATTATTTTA
Found at i:339248 original size:6 final size:7
Alignment explanation
Indices: 339233--339263 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
339223 TGAATCCGGT
339233 TTTTTAA
1 TTTTTAA
339240 TTTTT-A
1 TTTTTAA
339246 TTTTTAA
1 TTTTTAA
339253 TTTTTAA
1 TTTTTAA
339260 TTTT
1 TTTT
339264 CGCGATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:339251 original size:13 final size:14
Alignment explanation
Indices: 339233--339263 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
339223 TGAATCCGGT
339233 TTTTTAATTTTT-A
1 TTTTTAATTTTTAA
339246 TTTTTAATTTTTAA
1 TTTTTAATTTTTAA
339260 TTTT
1 TTTT
339264 CGCGATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTAATTTTTAA
Found at i:340339 original size:43 final size:42
Alignment explanation
Indices: 340287--340453 Score: 183
Period size: 43 Copynumber: 3.9 Consensus size: 42
340277 TTTGTATTTT
* *
340287 CAAACGCCGCAATAGCTATGTTATTTAGCGGCGTTTTTAGGCA
1 CAAACGCCGCAATAG-TTTGTTATTTAGCGGCATTTTTAGGCA
* * * ** *
340330 CAAATGCCGCAAAAAGTTTGTTATTTAGCAGTGTTTTTAAGCA
1 CAAACGCCGC-AATAGTTTGTTATTTAGCGGCATTTTTAGGCA
* *
340373 CAAACGCCACAATAGGTTTTTTATTTAGCGGCATTTTTAGGCA
1 CAAACGCCGCAATA-GTTTGTTATTTAGCGGCATTTTTAGGCA
*
340416 CAAATGCCGCAACATA-TTTGTTATTTAGCGGCATTTTT
1 CAAACGCCGC-A-ATAGTTTGTTATTTAGCGGCATTTTT
340454 CCTGAAAGCG
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
42 3 0.03
43 92 0.89
44 5 0.05
45 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (42 bp):
CAAACGCCGCAATAGTTTGTTATTTAGCGGCATTTTTAGGCA
Found at i:340386 original size:86 final size:86
Alignment explanation
Indices: 340287--340444 Score: 246
Period size: 86 Copynumber: 1.8 Consensus size: 86
340277 TTTGTATTTT
* *
340287 CAAACGCCGCAATAGCTATGTTATTTAGCGGCGTTTTTAGGCACAAATGCCGCAA-AAAGTTTGT
1 CAAACGCCACAATAGCTATGTTATTTAGCGGCATTTTTAGGCACAAATGCCGCAACAAA-TTTGT
340351 TATTTAGCAGTGTTTTTAAGCA
65 TATTTAGCAGTGTTTTTAAGCA
* * * *
340373 CAAACGCCACAATAGGTTTTTTATTTAGCGGCATTTTTAGGCACAAATGCCGCAACATATTTGTT
1 CAAACGCCACAATAGCTATGTTATTTAGCGGCATTTTTAGGCACAAATGCCGCAACAAATTTGTT
340438 ATTTAGC
66 ATTTAGC
340445 GGCATTTTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
86 63 0.97
87 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (86 bp):
CAAACGCCACAATAGCTATGTTATTTAGCGGCATTTTTAGGCACAAATGCCGCAACAAATTTGTT
ATTTAGCAGTGTTTTTAAGCA
Found at i:340641 original size:41 final size:41
Alignment explanation
Indices: 340596--340676 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
340586 ATCACCTTAA
*
340596 ATTTAATTACGATTCGAATTAAGTAATAATAAATAAAAACT
1 ATTTAATTACGATTCGAATTAAGTAACAATAAATAAAAACT
*
340637 ATTTAATTACGATTCGAATTAAGTAACAATACATAAAAAC
1 ATTTAATTACGATTCGAATTAAGTAACAATAAATAAAAAC
340677 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (41 bp):
ATTTAATTACGATTCGAATTAAGTAACAATAAATAAAAACT
Found at i:340853 original size:19 final size:19
Alignment explanation
Indices: 340829--340876 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
340819 AAGTAGACAT
340829 TCTTCTGCCAAGAACACAC
1 TCTTCTGCCAAGAACACAC
340848 TCTTCTGCCAAGAACACAC
1 TCTTCTGCCAAGAACACAC
*
340867 TCTTCAGCCA
1 TCTTCTGCCA
340877 GCATAGAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.23
Consensus pattern (19 bp):
TCTTCTGCCAAGAACACAC
Found at i:343920 original size:41 final size:41
Alignment explanation
Indices: 343854--343950 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 41
343844 TTTTAAACAC
* *** * *
343854 AAACACCACTAAAGTACAAGTCTATAGTGGCATTTGTATAA
1 AAACGCCACTAAAGTGTGAGTCTATAGAGGCATTTATATAA
* * **
343895 AACCGCCATTAAAGTGTGAGTCTATAGAGGTGTTTATATAA
1 AAACGCCACTAAAGTGTGAGTCTATAGAGGCATTTATATAA
343936 AAACGCCACTAAAGT
1 AAACGCCACTAAAGT
343951 ACTATTCTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTGTGAGTCTATAGAGGCATTTATATAA
Found at i:357613 original size:22 final size:20
Alignment explanation
Indices: 357586--357702 Score: 79
Period size: 20 Copynumber: 6.1 Consensus size: 20
357576 TCAGAAAAAA
357586 ATATATTTATAATATATGCTAT
1 ATATATTTATAATATAT--TAT
* * * *
357608 ATATATTTTTAAAACATAAT
1 ATATATTTATAATATATTAT
*
357628 ATATA-CTATAATATA-TAT
1 ATATATTTATAATATATTAT
357646 ATATA--TAT-ATATA-TAT
1 ATATATTTATAATATATTAT
* *
357662 ATATATTCA-AATATAATAT
1 ATATATTTATAATATATTAT
*
357681 ATAT-TTATATAATATAATAT
1 ATATATT-TATAATATATTAT
357701 AT
1 AT
357703 TTTAAAACCT
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
16 13 0.17
17 3 0.04
18 15 0.19
19 14 0.18
20 19 0.24
22 14 0.18
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (20 bp):
ATATATTTATAATATATTAT
Found at i:357616 original size:40 final size:40
Alignment explanation
Indices: 357553--357653 Score: 99
Period size: 40 Copynumber: 2.6 Consensus size: 40
357543 ATATTATGAC
357553 ATATACTATAATA-A-ATA-A-A-ATTTTCAGAAA-AAAAT
1 ATATACTATAATATATATATATATATTTTCA-AAACAAAAT
* * * *
357588 ATAT-TTATAATATATGCTATATATATTTTTAAAACATAAT
1 ATATACTATAATATAT-ATATATATATTTTCAAAACAAAAT
357628 ATATACTATAATATATATATATATAT
1 ATATACTATAATATATATATATATAT
357654 ATATATATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
34 7 0.13
35 5 0.10
37 2 0.04
38 1 0.02
39 4 0.08
40 23 0.44
41 10 0.19
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (40 bp):
ATATACTATAATATATATATATATATTTTCAAAACAAAAT
Found at i:357703 original size:18 final size:18
Alignment explanation
Indices: 357585--357704 Score: 70
Period size: 18 Copynumber: 6.5 Consensus size: 18
357575 TTCAGAAAAA
*
357585 AATATATTTATAATATATGCT
1 AATATATTTAT-ATA-AT-AT
* * *
357606 ATATATATTTTTAAAACAT
1 A-ATATATTTATATAATAT
357625 AATATA--TACTATAATAT
1 AATATATTTA-TATAATAT
*
357642 -ATATATATATATATATAT
1 AATATATTTATATA-ATAT
* *
357660 ATATATATTCAAAT-ATA-
1 A-ATATATTTATATAATAT
357677 ATATATATTTATATAATAT
1 A-ATATATTTATATAATAT
357696 AATATATTT
1 AATATATTT
357705 TAAAACCTAC
Statistics
Matches: 78, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
16 6 0.08
17 22 0.28
18 25 0.32
19 3 0.04
20 10 0.13
21 3 0.04
22 9 0.12
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (18 bp):
AATATATTTATATAATAT
Found at i:357722 original size:2 final size:2
Alignment explanation
Indices: 357626--357702 Score: 83
Period size: 2 Copynumber: 40.0 Consensus size: 2
357616 TTAAAACATA
357626 AT AT AT ACT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
357668 -T CAA AT AT A- AT AT AT AT TT AT AT A- AT AT A- AT AT AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
357703 TTTAAAACCT
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
1 5 0.08
2 57 0.89
3 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:358512 original size:36 final size:34
Alignment explanation
Indices: 358471--358555 Score: 111
Period size: 32 Copynumber: 2.5 Consensus size: 34
358461 AAGAGAAAAG
*
358471 ATCTCAAGTGAGATGAACTTTTTTTCGAGACAAATT
1 ATCTCAAGTGAGATGAA--TTGTTTCGAGACAAATT
*
358507 GTCTCAAGTGAGATG--TTGTTTCGAGACAAATT
1 ATCTCAAGTGAGATGAATTGTTTCGAGACAAATT
*
358539 ATCTCGAGTGAGATGAA
1 ATCTCAAGTGAGATGAA
358556 AAATTCCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
32 29 0.67
36 14 0.33
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (34 bp):
ATCTCAAGTGAGATGAATTGTTTCGAGACAAATT
Found at i:358787 original size:33 final size:33
Alignment explanation
Indices: 358682--358791 Score: 103
Period size: 34 Copynumber: 3.3 Consensus size: 33
358672 AACTGTTTCG
* * *
358682 AGTGAGATTAAAATTTTCAAGGGAAATATCTCA
1 AGTGAGATGAAAATTTTCAAGGAAAACATCTCA
* ** ** * *
358715 AGTGAAATGTAATTTTTTTTAGTAAAACTATCTCG
1 AGTGAGATG-AAAATTTTCAAGGAAAAC-ATCTCA
*
358750 AGTGAGACGAAAATTTTCAAGGAAAACATCTCA
1 AGTGAGATGAAAATTTTCAAGGAAAACATCTCA
358783 AGTGAGATG
1 AGTGAGATG
358792 CAATTTTGTT
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
33 20 0.36
34 24 0.43
35 12 0.21
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (33 bp):
AGTGAGATGAAAATTTTCAAGGAAAACATCTCA
Found at i:358923 original size:19 final size:21
Alignment explanation
Indices: 358899--358945 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
358889 GTTTGGTTCA
*
358899 GTAAAAGCC-TT-TGGTCAAT
1 GTAAAAGCCATTATGGTCAAC
358918 GTAAAA-CCAATTATGGTCAAC
1 GTAAAAGCC-ATTATGGTCAAC
358939 GTAAAAG
1 GTAAAAG
358946 AAGCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
20 2 0.09
21 13 0.57
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (21 bp):
GTAAAAGCCATTATGGTCAAC
Found at i:360945 original size:20 final size:18
Alignment explanation
Indices: 360916--360975 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 18
360906 CCAAACAATG
*
360916 TAATTGGTTTTCTAGAAAT
1 TAATTAGTTTTCTA-AAAT
360935 ATAATTAGTTTTCTAAAAT
1 -TAATTAGTTTTCTAAAAT
360954 TAA-T--TTTTCTGAAAAT
1 TAATTAGTTTTCT-AAAAT
360970 TAATTA
1 TAATTA
360976 CAGCCAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.17
16 8 0.22
17 2 0.06
18 3 0.08
19 4 0.11
20 13 0.36
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.48
Consensus pattern (18 bp):
TAATTAGTTTTCTAAAAT
Found at i:360960 original size:14 final size:15
Alignment explanation
Indices: 360937--360974 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
360927 CTAGAAATAT
*
360937 AATTAGTTTTCT-AA
1 AATTAATTTTCTGAA
360951 AATTAATTTTTCTGAA
1 AATTAA-TTTTCTGAA
360967 AATTAATT
1 AATTAATT
360975 ACAGCCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (15 bp):
AATTAATTTTCTGAA
Found at i:360963 original size:15 final size:16
Alignment explanation
Indices: 360943--360974 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
360933 ATATAATTAG
360943 TTTTCT-AAAATTAAT
1 TTTTCTGAAAATTAAT
360958 TTTTCTGAAAATTAAT
1 TTTTCTGAAAATTAAT
360974 T
1 T
360975 ACAGCCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTCTGAAAATTAAT
Found at i:361545 original size:21 final size:21
Alignment explanation
Indices: 361521--361567 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
361511 TAATCAAATT
361521 AAATAAAACATAAAATTATAA
1 AAATAAAACATAAAATTATAA
** * *
361542 AAATAAAATTTAAAGTTATAT
1 AAATAAAACATAAAATTATAA
361563 AAATA
1 AAATA
361568 TTCTAAAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATAAAACATAAAATTATAA
Found at i:361549 original size:14 final size:15
Alignment explanation
Indices: 361523--361555 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
361513 ATCAAATTAA
361523 ATAAAACATAAAATT
1 ATAAAACATAAAATT
361538 ATAAAA-ATAAAATT
1 ATAAAACATAAAATT
361552 -TAAA
1 ATAAA
361556 GTTATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 8 0.44
15 6 0.33
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAACATAAAATT
Found at i:362397 original size:22 final size:21
Alignment explanation
Indices: 362371--362414 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
362361 TTAAAAATAT
*
362371 TAAAAAAATTTAAT-TTTTAAA
1 TAAAAAAA-ATAATATTTTAAA
*
362392 TAAAAATAATAATATTTTAAA
1 TAAAAAAAATAATATTTTAAA
362413 TA
1 TA
362415 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAAAAATAATATTTTAAA
Done.