Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004239.1 Hibiscus syriacus cultivar Beakdansim tig00009289_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: 69493
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3425 original size:13 final size:13
Alignment explanation
Indices: 3402--3436 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3392 ACCCCAAAAA
3402 ATTGAGATTTAATT
1 ATTG-GATTTAATT
3416 ATTGGATTTAATT
1 ATTGGATTTAATT
*
3429 ATTAGATT
1 ATTGGATT
3437 ATAGTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (13 bp):
ATTGGATTTAATT
Found at i:4303 original size:22 final size:22
Alignment explanation
Indices: 4278--4322 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4268 CCGAGTTGAT
*
4278 TGAGTCAACTCGCTAAGTTAAC
1 TGAGTCAACTCGCCAAGTTAAC
4300 TGAGTCAACTCGCCAAGTTAAC
1 TGAGTCAACTCGCCAAGTTAAC
4322 T
1 T
4323 CAGACCAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (22 bp):
TGAGTCAACTCGCCAAGTTAAC
Found at i:20532 original size:18 final size:18
Alignment explanation
Indices: 20509--20561 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
20499 ACTTAGAATT
*
20509 TGTCCCGAAGGACCACTA
1 TGTCCCGAATGACCACTA
20527 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
20545 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
20562 CCTTAAGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:26718 original size:20 final size:20
Alignment explanation
Indices: 26680--26719 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
26670 GCTCTAAATC
* * *
26680 GTTTTTCAAACTTTCATTTT
1 GTTTTTCAAAATCTAATTTT
26700 GTTTTTCAAAATCTAATTTT
1 GTTTTTCAAAATCTAATTTT
26720 ACTTTCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (20 bp):
GTTTTTCAAAATCTAATTTT
Found at i:27972 original size:21 final size:22
Alignment explanation
Indices: 27946--27986 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
27936 CCAAAATAAG
* *
27946 GAGTATTGATACTT-CTTTAAT
1 GAGTATCGACACTTCCTTTAAT
27967 GAGTATCGACACTTCCTTTA
1 GAGTATCGACACTTCCTTTA
27987 TAATTTTTAA
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:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (22 bp):
GAGTATCGACACTTCCTTTAAT
Found at i:40838 original size:27 final size:27
Alignment explanation
Indices: 40791--40843 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
40781 ATCAATTTTA
40791 TGAAAAATATAAATTTAAGAAGTAAAT
1 TGAAAAATATAAATTTAAGAAGTAAAT
40818 TGAACAAATATGAAA-TT-AGAAGTAAA
1 TGAA-AAATAT-AAATTTAAGAAGTAAA
40844 AATTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 8 0.33
29 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.26
Consensus pattern (27 bp):
TGAAAAATATAAATTTAAGAAGTAAAT
Found at i:41280 original size:2 final size:2
Alignment explanation
Indices: 41254--41923 Score: 203
Period size: 2 Copynumber: 337.0 Consensus size: 2
41244 CTATATAGTT
* * *
41254 TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA AA CTA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * *
41296 AA CTA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
41337 AA CTA TA TA TA TA T- TA TG TA TA AA CTA TA TA CTA TA TA TA AA
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * *
41379 CTA TA TA TA TA TA TA TA T- TA TG TA TA AA CTA TA TA CCA TG TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * *
41421 TA AA CTA TA GA GTT TA TA TA TGA -A T- TA TA TA TA AA CA -A TA
1 TA TA -TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * * * *
41461 TA GTT TA T- TA -A TA TA AA T- TA TA T- TG TT TA TA CA TA TA T-
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
41499 TA TA TA TA AA T- TA TA TA TGA -A T- TA TA TT TA AA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* * * *
41539 TC T- TA TA TT TA TA TA T- TA TG TA TA -A T- TA TA TA TA CTA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
41578 TA TA AA T- TA TA TA GTT TA TA TA GTT TA AA TA TA AA GTA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * * *
41620 -A GTA TA TA TG TA AA CTA TA AA TT TA TA TA TA TA TA TA CA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41663 CA TA TA TA -A TA -A TA TA -A AA TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41702 AA GTA TA -A T- TA TA AA TA -A TA AA GTA TA TA -A GTA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* * *
41741 AA CTA TA AA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
41785 GT- TT TA GTA TA AA CTA TA TA TA CA TA TA -A TA -A TA TA -A TG
1 -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41824 TA TA -A GTA TA T- TA TA TA TA TA AA GTA TA TA AA TA TA TA AA CTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA
* * *
41867 TA TA -A TA -A AA GTA TA TA TA TA TA TA AA TA TA TA -A TA TA AA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41907 GTA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA
41924 AAGTATAATT
Statistics
Matches: 480, Mismatches: 114, Indels: 148
0.65 0.15 0.20
Matches are distributed among these distances:
1 39 0.08
2 403 0.84
3 38 0.08
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:41280 original size:9 final size:9
Alignment explanation
Indices: 41268--41395 Score: 55
Period size: 9 Copynumber: 14.7 Consensus size: 9
41258 TTTATATTAT
41268 TATATACTA
1 TATATACTA
*
41277 TATATA-AA
1 TATATACTA
41285 CTATATAC-A
1 -TATATACTA
41294 TA-A-ACTA
1 TATATACTA
41301 TATAGTTTA-TA
1 TATA---TACTA
* *
41312 TTTATATTA
1 TATATACTA
41321 TTATATACTA
1 -TATATACTA
41331 TATATAAACTA
1 TATAT--ACTA
41342 TATATA-TA
1 TATATACTA
*
41350 T-TAT-GTA
1 TATATACTA
41357 TA-A-ACTA
1 TATATACTA
41364 TATACTA-TA
1 TATA-TACTA
*
41373 TATAAACTA
1 TATATACTA
41382 TATATA-TA
1 TATATACTA
41390 TATATA
1 TATATA
41396 TTATGTATAA
Statistics
Matches: 93, Mismatches: 7, Indels: 39
0.67 0.05 0.28
Matches are distributed among these distances:
6 2 0.02
7 15 0.16
8 19 0.20
9 34 0.37
10 8 0.09
11 14 0.15
12 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (9 bp):
TATATACTA
Found at i:41296 original size:13 final size:13
Alignment explanation
Indices: 41275--41304 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41265 TATTATATAC
*
41275 TATATATAAACTA
1 TATACATAAACTA
41288 TATACATAAACTA
1 TATACATAAACTA
41301 TATA
1 TATA
41305 GTTTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
TATACATAAACTA
Found at i:41306 original size:54 final size:54
Alignment explanation
Indices: 41208--41345 Score: 210
Period size: 54 Copynumber: 2.6 Consensus size: 54
41198 ATATATAAAG
* * *
41208 TATATATATTATATA-TA-A-AAAAACTAGATAGAGAAACTATATAGTTTATATT
1 TATAT-TATTATATACTATATATAAACTATATACAGAAACTATATAGTTTATATT
*
41260 TATATTATTATATACTATATATAAACTATATACATAAACTATATAGTTTATATT
1 TATATTATTATATACTATATATAAACTATATACAGAAACTATATAGTTTATATT
41314 TATATTATTATATACTATATATAAACTATATA
1 TATATTATTATATACTATATATAAACTATATA
41346 TATATTATGT
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
51 9 0.11
52 7 0.09
53 1 0.01
54 62 0.78
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (54 bp):
TATATTATTATATACTATATATAAACTATATACAGAAACTATATAGTTTATATT
Found at i:41404 original size:11 final size:11
Alignment explanation
Indices: 41253--41922 Score: 135
Period size: 11 Copynumber: 60.1 Consensus size: 11
41243 ACTATATAGT
*
41253 TTATATTTATA
1 TTATATATATA
41264 TTAT-TATATA
1 TTATATATATA
* *
41274 CTATATATAAA
1 TTATATATATA
* *
41285 CTATATACATA
1 TTATATATATA
*
41296 -AACTATATAGT-
1 TTA-TATATA-TA
*
41307 TTATATTTATA
1 TTATATATATA
41318 TTAT-TATATA
1 TTATATATATA
* *
41328 CTATATATAAA
1 TTATATATATA
*
41339 CTATATATATA
1 TTATATATATA
* *
41350 TTATGTATAAA
1 TTATATATATA
*
41361 CTATATACTATA
1 TTATATA-TATA
*
41373 -TATAAACTATA
1 TTATATA-TATA
41384 TATATATATATA
1 T-TATATATATA
* *
41396 TTATGTATAAA
1 TTATATATATA
* * *
41407 CTATATACCATG
1 TTATATA-TATA
* *
41419 TATAAACTATAGA
1 T-TATA-TATATA
41432 GTT-TATATATGAA
1 -TTATATATAT--A
*
41445 TTATATATAAA
1 TTATATATATA
** *
41456 CAATATAGTTTA
1 TTATATA-TATA
*
41468 TTA-ATATAAA
1 TTATATATATA
*
41478 TTATAT-TGT-
1 TTATATATATA
*
41487 TTATACATATA
1 TTATATATATA
*
41498 TTATATATAAA
1 TTATATATATA
41509 TTATATATGA-A
1 TTATATAT-ATA
*
41520 TTATATTTA-A
1 TTATATATATA
* * *
41530 ATATATACATC
1 TTATATATATA
41541 TTATATTTATATA
1 TTATA--TATATA
*
41554 TTATGTATA-A
1 TTATATATATA
41564 TTATATATACTA
1 TTATATATA-TA
41576 TGTATAAATTATATA
1 T-TAT--A-TATATA
41591 GTT-TATATAGT-
1 -TTATATATA-TA
* *
41602 TTAAATATAAA
1 TTATATATATA
*
41613 GTATATA-AGTA
1 TTATATATA-TA
* *
41624 -TATATGTAAA
1 TTATATATATA
* * *
41634 CTATAAATTTA
1 TTATATATATA
41645 TATATATATATA
1 T-TATATATATA
* *
41657 CATATACATATA
1 -TTATATATATA
*
41669 TAATA-ATATA
1 TTATATATATA
** *
41679 AAATATAAATA
1 TTATATATATA
41690 -TATATATATA
1 TTATATATATA
*
41700 -TAAAGTATA-A
1 TTATA-TATATA
41710 TTATA-A-ATA
1 TTATATATATA
* *
41719 ATAAAGTATATAA
1 TTATA-TATAT-A
* *
41732 GTATATATAAA
1 TTATATATATA
* *
41743 CTATAAAGTATA
1 TTATATA-TATA
41755 -TATATATATA
1 TTATATATATA
41765 -TATATATATA
1 TTATATATATA
*
41775 -TATATATAAA
1 TTATATATATA
* *
41785 GTTTTAGTATAAA
1 -TTATA-TATATA
* *
41798 CTATATATACA
1 TTATATATATA
41809 -TATAATAATATAA
1 TTAT-AT-ATAT-A
41822 TGTATA-AGTATA
1 T-TATATA-TATA
41834 TTATATATATA
1 TTATATATATA
41845 --A-AGTATATA
1 TTATA-TATATA
* *
41854 -AATATATAAA
1 TTATATATATA
*
41864 CTATATA-ATA
1 TTATATATATA
**
41874 AAAGTATATATA
1 TTA-TATATATA
*
41886 TATATAAATATA
1 T-TATATATATA
* *
41898 TAATATAAAGTA
1 TTATATATA-TA
41910 TATATATATATA
1 T-TATATATATA
41922 T
1 T
41923 AAAGTATAAT
Statistics
Matches: 480, Mismatches: 112, Indels: 133
0.66 0.15 0.18
Matches are distributed among these distances:
8 2 0.00
9 17 0.04
10 108 0.22
11 209 0.44
12 78 0.16
13 49 0.10
14 5 0.01
15 7 0.01
16 5 0.01
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (11 bp):
TTATATATATA
Found at i:41466 original size:31 final size:33
Alignment explanation
Indices: 41419--41483 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
41409 ATATACCATG
* *
41419 TATAAACTATAGAGTTTA-T-ATATGAATTATA
1 TATAAACAATAGAGTTTATTAATATAAATTATA
*
41450 TATAAACAATATAGTTTATTAATATAAATTATA
1 TATAAACAATAGAGTTTATTAATATAAATTATA
41483 T
1 T
41484 TGTTTATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 16 0.55
32 1 0.03
33 12 0.41
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (33 bp):
TATAAACAATAGAGTTTATTAATATAAATTATA
Found at i:41506 original size:15 final size:16
Alignment explanation
Indices: 41466--41514 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
41456 CAATATAGTT
41466 TATTA-ATATAAATTA
1 TATTATATATAAATTA
* * *
41481 TATTGTTTATACA-TA
1 TATTATATATAAATTA
41496 TATTATATATAAATTA
1 TATTATATATAAATTA
41512 TAT
1 TAT
41515 ATGAATTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TATTATATATAAATTA
Found at i:41562 original size:17 final size:18
Alignment explanation
Indices: 41542--41581 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
41532 ATATACATCT
*
41542 TATATT-TATATATTATG
1 TATATTATATATACTATG
41559 TATAATTATATATACTATG
1 TAT-ATTATATATACTATG
41578 TATA
1 TATA
41582 AATTATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 4 0.20
19 13 0.65
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (18 bp):
TATATTATATATACTATG
Found at i:41610 original size:29 final size:28
Alignment explanation
Indices: 41578--41656 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
41568 ATATACTATG
*
41578 TATAAATTATATAGTTTATATAGTTTAAA-
1 TATAAATTATATAG-TTATATA-TGTAAAC
*
41607 TATAAAGTATATAAG-TATATATGTAAAC
1 TATAAATTATAT-AGTTATATATGTAAAC
41635 TATAAATTTATATA-TATATATA
1 TATAAA-TTATATAGT-TATATA
41657 CATATACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
27 5 0.12
28 13 0.31
29 22 0.52
30 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44
Consensus pattern (28 bp):
TATAAATTATATAGTTATATATGTAAAC
Found at i:41736 original size:22 final size:21
Alignment explanation
Indices: 41692--42174 Score: 171
Period size: 22 Copynumber: 23.2 Consensus size: 21
41682 TATAAATATA
* *
41692 TATATATATAAAG--TATAAT
1 TATAAATATAAAGTATATAAG
41711 TATAAATAATAAAGTATATAAG
1 TATAAAT-ATAAAGTATATAAG
*
41733 TAT--ATATAAACTATA-AAG
1 TATAAATATAAAGTATATAAG
*
41751 TATATATATATATA-TATATATA-
1 TATA-A-ATATAAAGTATATA-AG
* *
41773 TATATATATAAAGT-T-TTAG
1 TATAAATATAAAGTATATAAG
*
41792 TATAAACTATATATA-CATATAA-
1 TATAAA-TATA-A-AGTATATAAG
*
41814 TAATATAATGTATAAGTATAT---
1 T-ATA-AATATA-AAGTATATAAG
*
41835 TATATATATAAAGTATATAA-
1 TATAAATATAAAGTATATAAG
*
41855 -AT--ATATAAACTATATAA-
1 TATAAATATAAAGTATATAAG
*
41872 TA-AAAGTATATATA-TATATAAA
1 TATAAA-TATA-A-AGTATATAAG
41894 TATATAATATAAAGTATAT-A-
1 TATA-AATATAAAGTATATAAG
* *
41914 TATATATATAAAG--TATAAT
1 TATAAATATAAAGTATATAAG
*
41933 TATAAAGACTAAAGTATATAAG
1 TATAAATA-TAAAGTATATAAG
*
41955 TATATAATATAAAGTATATACACA
1 TATA-AATATAAAGTATATA-A-G
41979 TATAAAGTAT--A-TATATAAG
1 TATAAA-TATAAAGTATATAAG
* *
41998 TTATAAGTATTAAAGTATAT-AT
1 -TATAAATA-TAAAGTATATAAG
* *
42020 TATAAAGTATTACACTATATAA-
1 TATAAA-TA-TAAAGTATATAAG
*
42042 TATAAGTATTAAA-TATA-AAG
1 TATAAATA-TAAAGTATATAAG
*
42062 TATTAAAGTATACCA-TATA-AAG
1 TA-TAAA-TATA-AAGTATATAAG
*
42084 TATTAAAGTATATAA--ATATAAA
1 TA-TAAA-TATA-AAGTATATAAG
42106 TATAAAGTATAAAGTATATAAG
1 TATAAA-TATAAAGTATATAAG
*
42128 TATATAATATAAAGTAT-TAAAC
1 TATA-AATATAAAGTATAT-AAG
42150 TATATAATAT-AAGTAT-TAAAG
1 TATA-AATATAAAGTATAT-AAG
42171 TATA
1 TATA
42175 TAAATAGAAT
Statistics
Matches: 371, Mismatches: 37, Indels: 110
0.72 0.07 0.21
Matches are distributed among these distances:
17 17 0.05
18 17 0.05
19 46 0.12
20 50 0.13
21 66 0.18
22 130 0.35
23 34 0.09
24 11 0.03
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (21 bp):
TATAAATATAAAGTATATAAG
Found at i:42097 original size:115 final size:114
Alignment explanation
Indices: 41840--42174 Score: 362
Period size: 115 Copynumber: 2.9 Consensus size: 114
41830 TATATTATAT
*
41840 ATATAAAGTATATAAATATATAAACTATATAATAAAAGTATATATA-TATATAAA-TATATAATA
1 ATATAAAGTATATAAATATATAAA-TATAT-ATATAAGT-TATA-AGTAT-TAAAGTATATAATA
* * *
41903 TAAAGTATATATATA-TATATAAAGTATAATTA-TAAAGACTAAAGTATATAAGTATATA
61 TAAAGTAT-TA-A-ACTATAT-AA-TATAAGTATTAAATA-TAAAGTATATAAGTATACA
* * *
41961 ATATAAAGTATATACACATATAAAGTATATATATAAGTTATAAGTATTAAAGTATATATTATAAA
1 ATATAAAGTATATAAATATATAAA-TATATATATAAGTTATAAGTATTAAAGTATATAATATAAA
* *
42026 GTATTACACTATATAATATAAGTATTAAATATAAAGTAT-TAAAGTATACC
65 GTATTAAACTATATAATATAAGTATTAAATATAAAGTATAT-AAGTATACA
*
42076 ATATAAAGTAT-TAAAGTATATAAATATAAATATAAAG-TATAAAGTA-TATAAGTATATAATAT
1 ATATAAAGTATATAAA-TATATAAATATATATAT-AAGTTAT-AAGTATTA-AAGTATATAATAT
42138 AAAGTATTAAACTATATAATATAAGTATTAAAGTATA
62 AAAGTATTAAACTATATAATATAAGTATTAAA-TATA
42175 TAAATAGAAT
Statistics
Matches: 189, Mismatches: 15, Indels: 25
0.83 0.07 0.11
Matches are distributed among these distances:
114 17 0.09
115 91 0.48
116 12 0.06
117 5 0.03
118 7 0.04
119 23 0.12
120 7 0.04
121 27 0.14
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (114 bp):
ATATAAAGTATATAAATATATAAATATATATATAAGTTATAAGTATTAAAGTATATAATATAAAG
TATTAAACTATATAATATAAGTATTAAATATAAAGTATATAAGTATACA
Found at i:42981 original size:17 final size:17
Alignment explanation
Indices: 42959--42992 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42949 AGTATTTAAC
42959 ATGCAATGCAACATGAA
1 ATGCAATGCAACATGAA
*
42976 ATGCAATTCAACATGAA
1 ATGCAATGCAACATGAA
42993 TTAATATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (17 bp):
ATGCAATGCAACATGAA
Found at i:43015 original size:14 final size:14
Alignment explanation
Indices: 42996--43025 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42986 ACATGAATTA
*
42996 ATATGGAATGTCAC
1 ATATGGAATGCCAC
43010 ATATGGAATGCCAC
1 ATATGGAATGCCAC
43024 AT
1 AT
43026 GAATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (14 bp):
ATATGGAATGCCAC
Found at i:43209 original size:14 final size:14
Alignment explanation
Indices: 43192--43232 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
43182 TAATATACAA
*
43192 ACTATACTATATGT
1 ACTATACTATATAT
43206 ACTA-ACTATATAT
1 ACTATACTATATAT
43219 -CGTATACTATATAT
1 AC-TATACTATATAT
43233 TACAAACCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.04
13 10 0.42
14 13 0.54
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (14 bp):
ACTATACTATATAT
Found at i:45302 original size:21 final size:22
Alignment explanation
Indices: 45276--45316 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
45266 CCAAAATAAG
*
45276 GAGTATTGATACTT-CTTTAAT
1 GAGTATCGATACTTCCTTTAAT
45297 GAGTATCGATACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
45317 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:47808 original size:20 final size:20
Alignment explanation
Indices: 47759--47813 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
47749 AATTGAGTCT
*
47759 CCATTAACCTTTAACTGCCA
1 CCATTAACCTTTAATTGCCA
* *
47779 CCATTGACCTTTAATTGCTA
1 CCATTAACCTTTAATTGCCA
* *
47799 TCGTTAACCTTTAAT
1 CCATTAACCTTTAAT
47814 CGTCGTAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.38
Consensus pattern (20 bp):
CCATTAACCTTTAATTGCCA
Found at i:58413 original size:27 final size:27
Alignment explanation
Indices: 58366--58418 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
58356 ATCAATTTTA
58366 TGAAAAATATAAATTTAAGAAGTAAAT
1 TGAAAAATATAAATTTAAGAAGTAAAT
58393 TGAACAAATATGAAA-TT-AGAAGTAAA
1 TGAA-AAATAT-AAATTTAAGAAGTAAA
58419 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 8 0.33
29 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.26
Consensus pattern (27 bp):
TGAAAAATATAAATTTAAGAAGTAAAT
Found at i:58752 original size:2 final size:2
Alignment explanation
Indices: 58747--59522 Score: 226
Period size: 2 Copynumber: 384.5 Consensus size: 2
58737 AAATATTGAA
* * * *
58747 AT AT AT AC AT AT AA ACT AT AT AGT TT AT AT AT AA AGT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T AT AT AT
* * * * * * *
58790 AT AT AT AA AA ACT AC AT AG AG AA ACT AT AT AT AT TT AT AT -T AT
1 AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
58833 AT AT AT ACT AT AT ACT A- ACT AT AC AT AA ACT AT AT AT AT AT TT
1 AT AT AT A-T AT AT A-T AT A-T AT AT AT AT A-T AT AT AT AT AT AT
* * *
58876 AT AT AT AT ACT AT AT AT AA ACT AT AT AT AT -T AT GT AT AA ACT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T
* * *
58918 AT AT ACT AT AT AA ACT AT AT AT AT AT AT -T AT GT AT AA ACT AT
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * * *
58960 AT ACC AT GT AT AA ACT AT AG AGT TT AT AT AT GAT -T AT AT AT AA
1 AT A-T AT AT AT AT A-T AT AT A-T AT AT AT AT -AT AT AT AT AT AT
* * * * *
59003 AC A- AT AGT TT AT -T A- AT AT AA AT -T AT AT AGT TT AT AC AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * *
59043 AT AT AT AT AA AT -T AT AT AT GA- AT -T AT AT TT AA AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
* * * *
59083 AT CT -T AT AT TT AT AT AT -T AT GT AT A- AT -T AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
59121 AT AA AT AT AGT TT AT AT AGT TT AA AT AT AA AGT AT AT A- AGT AT
1 AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT A-T AT AT AT A-T AT
* * *
59164 AT GT A- ACT AT AA AT TT AT AT AT AT AT AT AT ACT AT AT A- AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
59206 AT A- AT A- AT AT AT AT TT AT AT AA AGT AT A- AT -T AT AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
59244 AT AA AGT AT A- AGT AT AT AT A- ACT AT AA AGT AT AT AT AT AT AT
1 AT AT A-T AT AT A-T AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * * *
59286 AA AGT TT AGT AT AA ACT AT AT AT AC AT AT AT A- AT AT AT A- AT
1 AT A-T AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
59327 GT AT A- AT AT AT TT AT AT AT AA AGT AT A- AT -T AT AA AG ACT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT
* * * *
59367 AA AT AT AT A- AGT AT AT A- AT AT AA AGT AT AT AA AT AT AT AA ACT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* * * *
59410 AT AT A- AT AT A- AA AGT AT AT A- AC GT AT AA AGT AT A- AGT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT
* *
59449 AT AT AT AA ACT AT AA AGT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
59492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59523 AGTATAATTA
Statistics
Matches: 559, Mismatches: 130, Indels: 170
0.65 0.15 0.20
Matches are distributed among these distances:
1 39 0.07
2 469 0.84
3 51 0.09
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:58779 original size:13 final size:13
Alignment explanation
Indices: 58763--58945 Score: 55
Period size: 13 Copynumber: 14.2 Consensus size: 13
58753 ACATATAAAC
*
58763 TATATAGTTTATA
1 TATATAGTATATA
*
58776 TATAAAGTATATA
1 TATATAGTATATA
* *
58789 TATATA-TAAAAA
1 TATATAGTATATA
* * *
58801 CTACATAG-AGAAA
1 -TATATAGTATATA
*
58814 CTATATA-TATTTA
1 -TATATAGTATATA
58827 TATTATA-TATATA
1 TA-TATAGTATATA
*
58840 CTATATACTA-ACTA
1 -TATATAGTATA-TA
* *
58854 TACATA-AACTATA
1 TATATAGTA-TATA
*
58867 TATATA-TTTATA
1 TATATAGTATATA
*
58879 TATATACTATATA
1 TATATAGTATATA
*
58892 TA-A-ACTATATA
1 TATATAGTATATA
*
58903 TAT-TATGTATAAA
1 TATATA-GTATATA
*
58916 CTATATACTATATA
1 -TATATAGTATATA
*
58930 AACTATA-TATATA
1 TA-TATAGTATATA
58943 TAT
1 TAT
58946 TATGTATAAA
Statistics
Matches: 130, Mismatches: 24, Indels: 33
0.70 0.13 0.18
Matches are distributed among these distances:
11 10 0.08
12 20 0.15
13 79 0.61
14 19 0.15
15 2 0.02
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (13 bp):
TATATAGTATATA
Found at i:58844 original size:9 final size:9
Alignment explanation
Indices: 58813--58962 Score: 86
Period size: 9 Copynumber: 16.9 Consensus size: 9
58803 ACATAGAGAA
58813 ACTATATAT
1 ACTATATAT
*
58822 A-TTTATATT
1 ACTATATA-T
58831 A-TATATAT
1 ACTATATAT
58839 ACTATATACT
1 ACTATATA-T
*
58849 AACTATACATAA
1 -ACTAT--ATAT
58861 ACTATATAT
1 ACTATATAT
58870 A-TAT-T-T
1 ACTATATAT
58876 A-TATATAT
1 ACTATATAT
58884 ACTATATAT
1 ACTATATAT
58893 AAACTATATAT
1 --ACTATATAT
* *
58904 ATTATGTAT
1 ACTATATAT
*
58913 A-AACTATAT
1 ACTA-TATAT
*
58922 ACTATATAA
1 ACTATATAT
58931 ACTATATAT
1 ACTATATAT
58940 A-TATAT-T
1 ACTATATAT
* *
58947 A-TGTATAA
1 ACTATATAT
58955 ACTATATA
1 ACTATATA
58963 CCATGTATAA
Statistics
Matches: 112, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
6 5 0.04
7 8 0.07
8 19 0.17
9 56 0.50
10 2 0.02
11 19 0.17
13 3 0.03
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (9 bp):
ACTATATAT
Found at i:58858 original size:52 final size:47
Alignment explanation
Indices: 58811--58900 Score: 141
Period size: 45 Copynumber: 1.9 Consensus size: 47
58801 CTACATAGAG
58811 AAACTATATATATTTATATTATATATATACTATATACTAACTATACAT
1 AAACTATATATATTTATATTATATATATACTATATA-TAACTATACAT
58859 AAACTATATATA--TAT-TTATATATATACTATATATAAACTATA
1 AAACTATATATATTTATATTATATATATACTATATAT-AACTATA
58901 TATATTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
44 1 0.02
45 25 0.61
46 3 0.07
48 12 0.29
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (47 bp):
AAACTATATATATTTATATTATATATATACTATATATAACTATACAT
Found at i:59205 original size:22 final size:21
Alignment explanation
Indices: 59180--59579 Score: 174
Period size: 22 Copynumber: 18.3 Consensus size: 21
59170 CTATAAATTT
59180 ATATATATATATATACTATATA
1 ATATATATATATATA-TATATA
59202 ATATATA-ATA-ATATATAT-
1 ATATATATATATATATATATA
* *
59220 TTATATAAAGTATA-AT-TATA
1 ATATATATA-TATATATATATA
*
59240 A-ATAATAAAGTATAAGTATATATA
1 ATAT-ATATA-TAT-A-TATATATA
*
59264 ACTATAAAGTATATATATATATA
1 A-TATATA-TATATATATATATA
* *
59287 A-AGTTTAGTATAAACTATATATA
1 ATA-TATA-TATATA-TATATATA
*
59310 CATATATA-ATATATAATGTATA
1 -ATATATATATATAT-ATATATA
* *
59332 ATATATTTATATATAAAGTATA
1 ATATATATATATATATA-TATA
* * *
59354 AT-TATAAAGACTAAAATATATA
1 ATATATATATA-T-ATATATATA
*
59376 AGTATATA-ATATAAAGTATATA
1 A-TATATATATATATA-TATATA
*
59398 A-ATATATAAACTATATAATATA
1 ATATATATATA-TATAT-ATATA
* *
59420 AAAGTATATA-ACGTATAAAGTATA
1 ATA-TATATATA--TATATA-TATA
59444 AGTATATATATA-A-ACTATA-A
1 A-TATATATATATATA-TATATA
59464 AGTATATATATATA-ATATAT-
1 A-TATATATATATATATATATA
59484 ATATATATATATATATATATA
1 ATATATATATATATATATATA
59505 TATATATATATATATATAAGTATA
1 -ATATATATATATATAT-A-TATA
* * *
59529 AT-TATAAAGACTAAAGTATATA
1 ATATATATATA-TATA-TATATA
59551 AGTATATATATA-AGTATATA-A
1 A-TATATATATATA-TATATATA
59572 AGTATATA
1 A-TATATA
59580 CACATATAAA
Statistics
Matches: 301, Mismatches: 31, Indels: 93
0.71 0.07 0.22
Matches are distributed among these distances:
18 6 0.02
19 23 0.08
20 45 0.15
21 39 0.13
22 94 0.31
23 37 0.12
24 46 0.15
25 8 0.03
26 3 0.01
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (21 bp):
ATATATATATATATATATATA
Found at i:59337 original size:77 final size:75
Alignment explanation
Indices: 59094--59508 Score: 212
Period size: 77 Copynumber: 5.6 Consensus size: 75
59084 TCTTATATTT
* * *
59094 ATATATTATGTATAATTATATATAT-GTATAAATATAGT-T-TATAT-AGTTTAAATATAAAGTA
1 ATATATAATGTATAAGTATATATATACTATAAATATA-TATATATATAAGTTT--ATATAAAGTA
*
59155 TATA-AGTATATGTA
63 TATATA--ATATATA
*
59169 ACTATA-AATTTATATA-TATATATATACTATATAATATATA-ATAATATATA-TTTATATAAAG
1 A-TATATAATGTATA-AGTATATATATACTATA-AATATATATAT-ATATA-AGTTTATATAAAG
59230 TATA-AT--TATA-A
61 TATATATAATATATA
* *
59241 ATA-ATAAAGTATAAGTATATATA-ACTATAAAGTATATATATATATAAAGTTTAGTATAAACTA
1 ATATATAATGTATAAGTATATATATACTATAAA-TATATATATATAT-AAGTTTA-TATAAAGTA
59304 TATATACATATATA
63 TATATA-ATATATA
*
59318 ATATATAATGTATAA-TATATTTATA-TATAAAGTATA-AT-TATA-AAG---ACTA-AAA-TAT
1 ATATATAATGTATAAGTATATATATACTATAAA-TATATATATATATAAGTTTA-TATAAAGTAT
*
59373 ATA-AGTATATA
64 ATATAATATATA
* * * * *
59384 ATATA-AA-GTATATA-AATATATAAACTATATAATATA-AAAGTATATAACGTATAAAGTATAA
1 ATATATAATGTATA-AGTATATATATACTATA-AATATATATA-TATATAA-GTTTATA-TA-AA
*
59445 GTATATATATAAACTATA
60 GTATATATA-ATA-TATA
* *
59463 A-AGTATATATATATAA-TATATATATA-TATATATATATATATATATA
1 ATA-TATA-ATGTATAAGTATATATATACTATAAATATATATATATATA
59509 TATATATATA
Statistics
Matches: 271, Mismatches: 23, Indels: 88
0.71 0.06 0.23
Matches are distributed among these distances:
64 5 0.02
65 10 0.04
66 20 0.07
67 3 0.01
68 10 0.04
69 7 0.03
70 23 0.08
71 23 0.08
72 13 0.05
73 9 0.03
74 1 0.00
75 22 0.08
76 23 0.08
77 42 0.15
78 17 0.06
79 21 0.08
80 8 0.03
81 10 0.04
82 4 0.01
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (75 bp):
ATATATAATGTATAAGTATATATATACTATAAATATATATATATATAAGTTTATATAAAGTATAT
ATAATATATA
Found at i:59354 original size:120 final size:110
Alignment explanation
Indices: 59144--59522 Score: 327
Period size: 120 Copynumber: 3.4 Consensus size: 110
59134 ATATAGTTTA
* *
59144 AATATA-AAGTATATAAGTATATGTA-ACTATAAATTTATATATATATATATACTATATAATATA
1 AATATATAA-TATA-AAGTATATATATA-TATAAATTTATATAAATATATATACTATATAATATA
* *
59207 TAATAATATATATTTATATAAAGTATAATTATAAATAATAAAGTATA-
63 TAATAATATATATTTATATAAAGTATAATTATAAAGAATAAAATATAT
59254 AGTATATATAACTATAAAGTATATATATATATAAAGTTTAGTATAAACTATATATACATATATAA
1 A--ATATATAA-TATAAAGTATATATATATATAAA-TTTA-TATAAA-TATATATAC-TATATAA
* *
59319 TATATAATGTATAATATATTTATATATAAAGTATAATTATAAAGACTAAAATATAT
59 TATATAAT-AAT-ATATA-TT-TATATAAAGTATAATTATAAAGAATAAAATATAT
* * * * **
59375 AAGTATATAATATAAAGTATATAAATATATAAA-CTATAT-AATATA-AAAGTATATAACGTATA
1 AA-TATATAATATAAAGTATATATATATATAAATTTATATAAATATATATACTATATAATATATA
* * * * * *
59437 A-AGTATA-A-GTATATATA-TA-AACTATAAAGTAT-ATATATAT
65 ATAATATATATTTATATAAAGTATAATTATAAAGAATAAAATATAT
* * * *
59477 AATATAT-ATATATA-TATATATATATATATATATATATATATATATA
1 AATATATAATATAAAGTATATATATATATAAATTTATATAAATATATA
59523 AGTATAATTA
Statistics
Matches: 226, Mismatches: 26, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
99 14 0.06
100 11 0.05
101 10 0.04
102 10 0.04
103 10 0.04
104 2 0.01
105 7 0.03
108 1 0.00
109 3 0.01
110 2 0.01
112 33 0.15
113 13 0.06
114 9 0.04
115 11 0.05
116 18 0.08
117 4 0.02
118 5 0.02
119 25 0.11
120 37 0.16
121 1 0.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (110 bp):
AATATATAATATAAAGTATATATATATATAAATTTATATAAATATATATACTATATAATATATAA
TAATATATATTTATATAAAGTATAATTATAAAGAATAAAATATAT
Found at i:59528 original size:8 final size:8
Alignment explanation
Indices: 59370--59777 Score: 139
Period size: 8 Copynumber: 54.9 Consensus size: 8
59360 AAGACTAAAA
59370 TATATAAG
1 TATATAAG
59378 TATATAA-
1 TATATAAG
59385 TATA-AAG
1 TATATAAG
*
59392 TATATAAA
1 TATATAAG
*
59400 TATATAAAC
1 TATAT-AAG
59409 TATATAA-
1 TATATAAG
*
59416 TATAAAAG
1 TATATAAG
59424 TATATAACG
1 TATATAA-G
59433 TATA-AAG
1 TATATAAG
59440 --TATAAG
1 TATATAAG
59446 TATAT-A-
1 TATATAAG
*
59452 TATA-AAC
1 TATATAAG
59459 TATA-AAG
1 TATATAAG
59466 TATAT-A-
1 TATATAAG
59472 TATATAA-
1 TATATAAG
59479 TATAT-A-
1 TATATAAG
59485 TATATATA-
1 TATATA-AG
59493 TATATATA-
1 TATATA-AG
59501 TATATATA-
1 TATATA-AG
59509 TATATATA-
1 TATATA-AG
59517 TATATAAG
1 TATATAAG
*
59525 --TATAAT
1 TATATAAG
59531 TATA-AAG
1 TATATAAG
59538 -ACTA-AAG
1 TA-TATAAG
59545 TATATAAG
1 TATATAAG
59553 --TAT-A-
1 TATATAAG
59557 TATATAAG
1 TATATAAG
59565 TATATAAAG
1 TATAT-AAG
59574 TATATACA-
1 TATATA-AG
*
59582 CATATAA-
1 TATATAAG
59589 -AGTAT-A-
1 TA-TATAAG
59595 TATATAAG
1 TATATAAG
59603 T-TATAAG
1 TATATAAG
59610 TAT-TAAAG
1 TATAT-AAG
*
59618 TATAT-AT
1 TATATAAG
59625 TATA-AAG
1 TATATAAG
*
59632 TAT-TACAC
1 TATATA-AG
59640 TATATAA-
1 TATATAAG
*
59647 TAGTATTAAA
1 TA-TA-TAAG
59657 TATA-AAG
1 TATATAAG
59664 TAT-TAAAG
1 TATAT-AAG
59672 TATACCATAAAG
1 TAT---AT-AAG
59684 TAT-TAAAG
1 TATAT-AAG
59692 TATATAA-
1 TATATAAG
*
59699 -ATATAAA
1 TATATAAG
*
59706 TAT-TAAA
1 TATATAAG
59713 TATA-AAG
1 TATATAAG
59720 TATATAAG
1 TATATAAG
59728 TATATAA-
1 TATATAAG
59735 TATA-AAG
1 TATATAAG
*
59742 TAT-TAAAC
1 TATAT-AAG
59750 TATAT-A-
1 TATATAAG
59756 -ATATAAG
1 TATATAAG
59763 TAT-TAAAG
1 TATAT-AAG
59771 TATATAA
1 TATATAA
59778 ATAGAATTAT
Statistics
Matches: 326, Mismatches: 14, Indels: 120
0.71 0.03 0.26
Matches are distributed among these distances:
5 7 0.02
6 47 0.14
7 97 0.30
8 133 0.41
9 32 0.10
10 2 0.01
12 8 0.02
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (8 bp):
TATATAAG
Found at i:59635 original size:22 final size:22
Alignment explanation
Indices: 59375--59777 Score: 181
Period size: 22 Copynumber: 18.5 Consensus size: 22
59365 TAAAATATAT
59375 AAGTATATAATATAAAGTATATA
1 AAGTATATAATATAAAGTAT-TA
*
59398 AA-TATATAAACTATATAA-TATAA
1 AAGTATAT-AA-TATA-AAGTATTA
59421 AAGTATATAACGTATAAAGTA-T-
1 AAGTATATAA--TATAAAGTATTA
*
59443 AAGTATAT-ATATAAACTA-TA
1 AAGTATATAATATAAAGTATTA
59463 AAGTATAT-ATATATAA-TATATA
1 AAGTATATAATATA-AAGTAT-TA
* *
59485 TA-TATATATATATATA-TATATA
1 AAGTATATA-ATATAAAGTAT-TA
*
59507 TA-TATATATATATATAAGTA-T-
1 AAGTATATA-ATATA-AAGTATTA
* *
59528 AATTATA-AAGACTAAAGTA-TA
1 AAGTATATAATA-TAAAGTATTA
59549 TAAGTATAT-ATAT-AAGTATATA
1 -AAGTATATAATATAAAGTAT-TA
59571 AAGTATATACACATATAAAGTA-T-
1 AAGTATAT--A-ATATAAAGTATTA
59594 -A-TATATAAGT-TATAAGTATTA
1 AAGTATATAA-TATA-AAGTATTA
*
59615 AAGTATATATTATAAAGTATTA
1 AAGTATATAATATAAAGTATTA
* *
59637 CACTATAT-A-AT--AGTATTA
1 AAGTATATAATATAAAGTATTA
59655 AA-TATA-AAGTATTAAAGTATACCATA
1 AAGTATATAA-TA-TAAAGTAT----TA
*
59681 AAGTAT-TAAAGTATATAAATA-TA
1 AAGTATAT-AA-TATA-AAGTATTA
59704 AA-TAT-TAAATATAAAGTA-TA
1 AAGTATAT-AATATAAAGTATTA
59724 TAAGTATATAATATAAAGTATTA
1 -AAGTATATAATATAAAGTATTA
*
59747 AACTATATAATAT-AAGTATTA
1 AAGTATATAATATAAAGTATTA
59768 AAGTATATAA
1 AAGTATATAA
59778 ATAGAATTAT
Statistics
Matches: 309, Mismatches: 20, Indels: 104
0.71 0.05 0.24
Matches are distributed among these distances:
17 5 0.02
18 11 0.04
19 17 0.06
20 38 0.12
21 49 0.16
22 107 0.35
23 32 0.10
24 21 0.07
25 6 0.02
26 9 0.03
27 5 0.02
28 9 0.03
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (22 bp):
AAGTATATAATATAAAGTATTA
Found at i:59645 original size:58 final size:56
Alignment explanation
Indices: 59566--59756 Score: 182
Period size: 58 Copynumber: 3.4 Consensus size: 56
59556 ATATATAAGT
*
59566 ATATAAAGTATATACAC-ATATAAAGTATATATATAAGTTATAAGTATTAAAGTATATA
1 ATATAAAGTAT-TAAACTATATAAAGTATATATATAA--TATAAGTATTAAAGTATATA
* * *
59624 TTATAAAGTATTACACTATATAATAGTAT-TAAAT-ATA-AAGTATTAAAG--TATA
1 ATATAAAGTATTAAACTATATAA-AGTATATATATAATATAAGTATTAAAGTATATA
** * *
59676 CCATAAAGTATTAAAGTATATAAA-TATAAATATTAAATATAAAGTA-TATAAGTATATA
1 ATATAAAGTATTAAACTATATAAAGTATATATA-T-AATAT-AAGTATTA-AAGTATATA
59734 ATATAAAGTATTAAACTATATAA
1 ATATAAAGTATTAAACTATATAA
59757 TATAAGTATT
Statistics
Matches: 111, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
50 3 0.03
51 3 0.03
52 24 0.22
54 14 0.13
55 4 0.04
56 8 0.07
57 6 0.05
58 44 0.40
59 5 0.05
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (56 bp):
ATATAAAGTATTAAACTATATAAAGTATATATATAATATAAGTATTAAAGTATATA
Found at i:59703 original size:43 final size:40
Alignment explanation
Indices: 59648--59780 Score: 145
Period size: 43 Copynumber: 3.3 Consensus size: 40
59638 ACTATATAAT
59648 AGTAT-TAAATATAAAGTATTAAAGTATACCATAAAGTATTAA
1 AGTATATAAATATAAAGTATTAAA-TATA--ATAAAGTATTAA
59690 AGTATATAAATATAAA-TATT-AA-AT-ATAAAGTA-TATA
1 AGTATATAAATATAAAGTATTAAATATAATAAAGTATTA-A
59726 AGTATAT-AATATAAAGTATTAAACTATATAATATAAGTATTAA
1 AGTATATAAATATAAAGTATT-AA--ATATAATA-AAGTATTAA
59769 AGTATATAAATA
1 AGTATATAAATA
59781 GAATTATATA
Statistics
Matches: 79, Mismatches: 0, Indels: 22
0.78 0.00 0.22
Matches are distributed among these distances:
35 10 0.13
36 20 0.25
38 1 0.01
39 2 0.03
40 1 0.01
41 4 0.05
42 12 0.15
43 23 0.29
44 6 0.08
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (40 bp):
AGTATATAAATATAAAGTATTAAATATAATAAAGTATTAA
Found at i:60610 original size:14 final size:14
Alignment explanation
Indices: 60591--60620 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
60581 ACATGAATTA
*
60591 ATATGGAATGTCAC
1 ATATGGAATGCCAC
60605 ATATGGAATGCCAC
1 ATATGGAATGCCAC
60619 AT
1 AT
60621 GAATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (14 bp):
ATATGGAATGCCAC
Found at i:62008 original size:15 final size:16
Alignment explanation
Indices: 61988--62018 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61978 TTGCACTCTG
61988 GATGC-AAAAATTAAA
1 GATGCAAAAAATTAAA
62003 GATGCAAAAAATTAAA
1 GATGCAAAAAATTAAA
62019 CAAAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (16 bp):
GATGCAAAAAATTAAA
Found at i:64703 original size:14 final size:14
Alignment explanation
Indices: 64661--64711 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
64651 TCAGATGGAC
*
64661 AAGAAGGAAA-AGA
1 AAGAAGTAAAGAGA
* *
64674 AAAAAG-AAAGATA
1 AAGAAGTAAAGAGA
64687 AAGAAGTAAAGAGA
1 AAGAAGTAAAGAGA
64701 AAGAAGTAAAG
1 AAGAAGTAAAG
64712 CTAAGGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 3 0.09
13 12 0.38
14 17 0.53
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (14 bp):
AAGAAGTAAAGAGA
Found at i:69112 original size:20 final size:21
Alignment explanation
Indices: 69063--69116 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 21
69053 TCATGGCATG
*
69063 TCAATTTTTTTAATTTCCACA
1 TCAATATTTTTAATTTCCACA
*
69084 TC-ATCTTTTT-ATTTCTC-CA
1 TCAATATTTTTAATTTC-CACA
69103 TCAATA-TTTTAATT
1 TCAATATTTTTAATT
69117 AATTTTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 13 0.46
20 13 0.46
21 2 0.07
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (21 bp):
TCAATATTTTTAATTTCCACA
Found at i:69190 original size:466 final size:467
Alignment explanation
Indices: 67906--69274 Score: 2075
Period size: 467 Copynumber: 3.0 Consensus size: 467
67896 CTTACGGGAT
67906 ATAAATGATCAATATTTTTTT-ATTAAATAAATGATCAATATT-AAATATTATTTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
67969 TAAAAATATC---TT-ATGGCAT--G--TACAGTGCA---CACACACGCAACACACCGAAATATA
66 TAAAAATATCTTATTAATGG-ATGAGTTTACAGTGCATGTCACA-ACGCAACACACCGAAA-ATA
*
68023 CTGTTAATTAAATATTAGAAAGGTAAATTATACATTTAGTACTTATACTATTATTTTTATTTTGT
128 CTGTTAATTAAATATTAGAAAGGT-AATTATACATTTAGTAATTATACTATTATTTTTATTTTGT
*
68088 TTTACTACCTAAA-TTCTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACACGTCAA
192 TTTACTACCTAAACTT-TATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAA
* * *
68152 TTTTTTTAATTTTCCACATCATATTTTTATTT-TTCATCAGTATTTTAATTAATTTTATTCAACC
256 TTTTTTTAA-TTTCCACATCATCTTTTTATTTCTCCATCAATATTTTAATTAATTTTATTCAACC
* *
68216 AATTAAATGAT-ACATGTGTCA-CAACTAT-GGGTTAAAATAAAAG-AAATATTTTTTTAGCATG
320 AATTAAATGATGACATGTGTCACCAACTATGGGGAT-AAATAAAAGAAAATATTTTCTTAGCATG
* * *
68277 AACCGTACATAAATCTCTTACATGAAATGCAAGGCACTCAACCATTGAGTTAA-ATAATCATTTG
384 AACCGTACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGATAGTCATTTG
68341 TTAATTTCATCATATTAAA
449 TTAATTTCATCATATTAAA
*
68360 AT-AATGATCAATATTTTTTTGATTAAAT-AATGATTAATA-TAAAATATTATTTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
* *
68422 TAAAAATATCTTA-CAATGGATGAGTTTACGGTGCATGT-------C-ACACACCGAAAATACTG
66 TAAAAATATCTTATTAATGGATGAGTTTACAGTGCATGTCACAACGCAACACACCGAAAATACTG
*
68478 TTAATTAAATATTAGTAAGGTAATTATACATTTAGT-ATTATACTATTA-TTTTATTTTGTTTTA
131 TTAATTAAATATTAGAAAGGTAATTATACATTTAGTAATTATACTATTATTTTTATTTTGTTTTA
* *
68541 CTATCTAAACTTTA-TTTTAACGCCATTAACGACAATGATGATGTTTTATGACATGTCAATTTTT
196 CTACCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAA--TTT
*
68605 TTTTAATTTTCACATCATCTTTTTATTTCTCCATCAATA-TTTAATTAATTTTATTCAACCAATT
259 TTTTAATTTCCACATCATCTTTTTATTTCTCCATCAATATTTTAATTAATTTTATTCAACCAATT
* *
68669 AAATGATGACATGTGCCACCAACTATGGGGATAAA-ATAAATAAAATATTTTCTTAGCATGAA-C
324 AAATGATGACATGTGTCACCAACTATGGGGATAAATA-AAAGAAAATATTTTCTTAGCATGAACC
* *
68732 -TACATAAATCTCTTACATCAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAA
388 GTACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGATAGTCATTTGTTAA
68796 TTTCATCATATTAAA
453 TTTCATCATATTAAA
* *
68811 ATAAATTATGAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
68876 T-AAAATATCTTATTAATGGATGAGTTTACAGTGCATGTCACAAACCGCAACACACCGAAACATA
66 TAAAAATATCTTATTAATGGATGAGTTTACAGTGCATGTCAC-AA-CGCAACACACCGAAA-ATA
* * *
68940 CTGTTAATTAAATATTAAAAAGATAATTATACATTTAGTAATTATACTATCATTTTTATTTTGTT
128 CTGTTAATTAAATATTAGAAAGGTAATTATACATTTAGTAATTATACTATTATTTTTATTTTGTT
*
69005 TTACTACCTAAACTTTATTTTTAACGCCATTAACG-CAATGATGATGTTTCATGGCATGTCAATT
193 TTACTACCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATT
69069 TTTTTAATTTCCACATCATCTTTTTATTTCTCCATCAATATTTTAATTAATTTTATTCAACCAAT
258 TTTTTAATTTCCACATCATCTTTTTATTTCTCCATCAATATTTTAATTAATTTTATTCAACCAAT
69134 TAAATGATGACATGTGTCACCAACTATGGGGATAAATAAAAGAAAATATTTTCTTAGCATGAACC
323 TAAATGATGACATGTGTCACCAACTATGGGGATAAATAAAAGAAAATATTTTCTTAGCATGAACC
*
69199 GTACAT-AATCTCTTACATGAAATGCAAGGCACTCGATCATTGAATTAAGATAGTCATTTGTTAA
388 GTACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGATAGTCATTTGTTAA
69263 TTTCATCATATT
453 TTTCATCATATT
69275 TTTTATTTAA
Statistics
Matches: 831, Mismatches: 39, Indels: 77
0.88 0.04 0.08
Matches are distributed among these distances:
448 43 0.05
449 77 0.09
450 85 0.10
451 59 0.07
452 74 0.09
453 91 0.11
454 57 0.07
455 2 0.00
456 4 0.00
457 1 0.00
459 8 0.01
463 1 0.00
464 11 0.01
465 80 0.10
466 94 0.11
467 122 0.15
468 22 0.03
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (467 bp):
ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
TAAAAATATCTTATTAATGGATGAGTTTACAGTGCATGTCACAACGCAACACACCGAAAATACTG
TTAATTAAATATTAGAAAGGTAATTATACATTTAGTAATTATACTATTATTTTTATTTTGTTTTA
CTACCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATTTTT
TTAATTTCCACATCATCTTTTTATTTCTCCATCAATATTTTAATTAATTTTATTCAACCAATTAA
ATGATGACATGTGTCACCAACTATGGGGATAAATAAAAGAAAATATTTTCTTAGCATGAACCGTA
CATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGATAGTCATTTGTTAATTT
CATCATATTAAA
Done.