Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000758.1 Hibiscus syriacus cultivar Beakdansim tig00001465_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: 46200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:325 original size:12 final size:12
Alignment explanation
Indices: 307--347 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
297 ACCATTAAGT
307 TTTATGTTGAAG
1 TTTATGTTGAAG
*
319 ATTATG-TGAA-
1 TTTATGTTGAAG
329 TTTATGTTGAAG
1 TTTATGTTGAAG
341 TTTATGT
1 TTTATGT
348 GAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.20
11 8 0.32
12 12 0.48
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (12 bp):
TTTATGTTGAAG
Found at i:332 original size:22 final size:22
Alignment explanation
Indices: 307--353 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
297 ACCATTAAGT
307 TTTATGTTGAAGATTATGTGAA
1 TTTATGTTGAAGATTATGTGAA
*
329 TTTATGTTGAAGTTTATGTGAA
1 TTTATGTTGAAGATTATGTGAA
351 TTT
1 TTT
354 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (22 bp):
TTTATGTTGAAGATTATGTGAA
Found at i:335 original size:10 final size:10
Alignment explanation
Indices: 320--353 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
310 ATGTTGAAGA
320 TTATGTGAAT
1 TTATGTGAAT
330 TTATGTTGAAGT
1 TTATG-TGAA-T
342 TTATGTGAAT
1 TTATGTGAAT
352 TT
1 TT
354 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.36
11 8 0.36
12 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (10 bp):
TTATGTGAAT
Found at i:339 original size:11 final size:11
Alignment explanation
Indices: 307--355 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
297 ACCATTAAGT
307 TTTATGTTGAAG
1 TTTATG-TGAAG
*
319 ATTATGTGAA-
1 TTTATGTGAAG
329 TTTATGTTGAAG
1 TTTATG-TGAAG
*
341 TTTATGTGAAT
1 TTTATGTGAAG
352 TTTA
1 TTTA
356 AAAAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 5 0.16
11 16 0.50
12 11 0.34
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (11 bp):
TTTATGTGAAG
Found at i:793 original size:9 final size:9
Alignment explanation
Indices: 779--803 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
769 TATTACTTCA
779 AATAAAATG
1 AATAAAATG
788 AATAAAATG
1 AATAAAATG
797 AATAAAA
1 AATAAAA
804 AGTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (9 bp):
AATAAAATG
Found at i:896 original size:18 final size:20
Alignment explanation
Indices: 854--900 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
844 ATAGTGGTTA
854 ATATATTTCCAAACATTCTT
1 ATATATTTCCAAACATTCTT
874 ATATATTTCCAAACATTCTT
1 ATATATTTCCAAACATTCTT
894 ATATATT
1 ATATATT
901 ATTGTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATTTCCAAACATTCTT
Found at i:3211 original size:3 final size:3
Alignment explanation
Indices: 3203--3252 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
3193 TTTTAAAAAA
* * *
3203 TAT TAT TA- TAT TAT TAT TAT TAT TGT TAT TTT TAT TAA TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
3248 TAT TA
1 TAT TA
3253 CATTTGCAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5632 original size:19 final size:19
Alignment explanation
Indices: 5593--5633 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5583 TTCTCTAATT
*
5593 AATTAATTAATTTGAAGTA
1 AATTAATTAATTTCAAGTA
5612 AATTAATTAATATTCAA-TA
1 AATTAATTAAT-TTCAAGTA
5631 AAT
1 AAT
5634 GGATCACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTAATTAATTTCAAGTA
Found at i:6865 original size:20 final size:20
Alignment explanation
Indices: 6840--6877 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6830 TTACTCTGTT
*
6840 GCATTTGTATTTGTATTTTC
1 GCATTTGCATTTGTATTTTC
6860 GCATTTGCATTTGTATTT
1 GCATTTGCATTTGTATTT
6878 GCATCTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (20 bp):
GCATTTGCATTTGTATTTTC
Found at i:6867 original size:26 final size:26
Alignment explanation
Indices: 6838--6895 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
6828 TTTTACTCTG
* * *
6838 TTGCATTTGTATTTGTATTTTCGCAT
1 TTGCATTTGTATTTGCATCTTCACAT
6864 TTGCATTTGTATTTGCATCTTCACAT
1 TTGCATTTGTATTTGCATCTTCACAT
6890 TTGCAT
1 TTGCAT
6896 AATCATCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.17, C:0.16, G:0.14, T:0.53
Consensus pattern (26 bp):
TTGCATTTGTATTTGCATCTTCACAT
Found at i:10411 original size:18 final size:18
Alignment explanation
Indices: 10388--10463 Score: 95
Period size: 18 Copynumber: 4.3 Consensus size: 18
10378 CATCCATCAG
10388 AGAAAAAAGGAAAAAAGA
1 AGAAAAAAGGAAAAAAGA
*
10406 AGAAAAAAGAAAAAAAGAA
1 AGAAAAAAGGAAAAAAG-A
*
10425 AGAAAAAAAAGAAAAAAG-
1 AG-AAAAAAGGAAAAAAGA
10443 AGAAAAAA-GAAAAAA-A
1 AGAAAAAAGGAAAAAAGA
10459 AGAAA
1 AGAAA
10464 TTAAAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
16 12 0.23
17 6 0.12
18 18 0.35
19 3 0.06
20 13 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AGAAAAAAGGAAAAAAGA
Found at i:10415 original size:7 final size:7
Alignment explanation
Indices: 10400--10457 Score: 64
Period size: 8 Copynumber: 7.9 Consensus size: 7
10390 AAAAAAGGAA
10400 AAAAGAAG
1 AAAA-AAG
10408 AAAAAAG
1 AAAAAAG
10415 AAAAAAAG
1 -AAAAAAG
*
10423 AAAGAA-
1 AAAAAAG
10429 AAAAAAG
1 AAAAAAG
10436 AAAAAAGAG
1 -AAAAA-AG
10445 AAAAAAG
1 AAAAAAG
10452 AAAAAA
1 AAAAAA
10458 AAGAAATTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.11
7 16 0.36
8 21 0.48
9 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:10439 original size:38 final size:39
Alignment explanation
Indices: 10390--10477 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 39
10380 TCCATCAGAG
*
10390 AAAAAAGGAAAAAAGAAGAAAAAAG-AAAAAAAGAAA-GA
1 AAAAAAAGAAAAAAG-AGAAAAAAGAAAAAAAAGAAATGA
*
10428 AAAAAAAGAAAAAAGAGAAAAAAGAAAAAAAAGAAATTA
1 AAAAAAAGAAAAAAGAGAAAAAAGAAAAAAAAGAAATGA
10467 AAAAAAAGAAA
1 AAAAAAAGAAA
10478 TTAAATGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 9 0.20
38 25 0.54
39 12 0.26
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (39 bp):
AAAAAAAGAAAAAAGAGAAAAAAGAAAAAAAAGAAATGA
Found at i:10463 original size:9 final size:9
Alignment explanation
Indices: 10390--10463 Score: 82
Period size: 9 Copynumber: 8.2 Consensus size: 9
10380 TCCATCAGAG
*
10390 AAAAAAGGA
1 AAAAAAAGA
10399 AAAAAGAAGA
1 AAAAA-AAGA
10409 AAAAAGAA-A
1 AAAAA-AAGA
10418 AAAAGAAAGA
1 AAAA-AAAGA
10428 AAAAAAAG-
1 AAAAAAAGA
10436 -AAAAAAGA
1 AAAAAAAGA
*
10444 GAAAAAAGA
1 AAAAAAAGA
10453 AAAAAAAGA
1 AAAAAAAGA
10462 AA
1 AA
10464 TTAAAAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
7 7 0.12
9 34 0.59
10 17 0.29
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:10471 original size:16 final size:16
Alignment explanation
Indices: 10415--10473 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
10405 AAGAAAAAAG
*
10415 AAAAAAAGAAAGAAA-
1 AAAAAAAAAAAGAAAT
*
10430 AAAAAGAAAAAAGAGAAA
1 AAAAA-AAAAAAGA-AAT
10448 AAAGAAAAAAAAGAAATT
1 AAA-AAAAAAAAGAAA-T
10466 AAAAAAAA
1 AAAAAAAA
10474 GAAATTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.14
16 7 0.19
17 9 0.24
18 14 0.38
19 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAT
Found at i:10482 original size:14 final size:13
Alignment explanation
Indices: 10390--10477 Score: 78
Period size: 13 Copynumber: 6.8 Consensus size: 13
10380 TCCATCAGAG
*
10390 AAAAAAGGAAA-A
1 AAAAAAAGAAAGA
10402 AAGAAGAAA-AAAG-
1 AA-AA-AAAGAAAGA
10415 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
10428 AAAAAAAGAAA-A
1 AAAAAAAGAAAGA
*
10440 AAGAGAAA-AAAGA
1 AA-AAAAAGAAAGA
*
10453 AAAAAAAGAAATTA
1 AAAAAAAGAAA-GA
10467 AAAAAAAGAAA
1 AAAAAAAGAAA
10478 TTAAATGAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.05
12 18 0.29
13 28 0.44
14 14 0.22
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:10489 original size:24 final size:23
Alignment explanation
Indices: 10398--10477 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 23
10388 AGAAAAAAGG
10398 AAAAAAGAAGAAAAAAGAAA--AA
1 AAAAAAGAA-AAAAAAGAAATTAA
* **
10420 AAGAAAGAAAAAAAAGAAAAAAGA
1 AAAAAAGAAAAAAAAGAAATTA-A
10444 GAAAAAAGAAAAAAAAGAAATTAA
1 -AAAAAAGAAAAAAAAGAAATTAA
10468 AAAAAAGAAA
1 AAAAAAGAAA
10478 TTAAATGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
21 10 0.20
22 8 0.16
23 11 0.22
24 2 0.04
25 19 0.38
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAGAAATTAA
Found at i:13411 original size:40 final size:40
Alignment explanation
Indices: 13360--13935 Score: 808
Period size: 40 Copynumber: 14.4 Consensus size: 40
13350 CTCATTTAAT
* *
13360 ACAGAAGATTTTATCTCACTCAAGATTGCTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
13400 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
13440 ACA-AAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAA-ATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
13480 ACAGAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
13520 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
13560 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
13600 ACA-AAAGATTTTATTTCATTCAAGATTGTTTTTCCTTGAA
1 ACAGAAA-ATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
13640 ACAGAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * *
13680 ACAGAAGATTTTATTTCATTCAAGATTGTTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
13720 ACA-AAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAA-ATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
13760 ACA-AAAGATTTAATCTCATTCAAGATTGTTTTTCCTTGAA
1 ACAGAAA-ATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
13800 ACA-AAAGATTTTATCTCACTCAAGATTGCTTTTCCTTGAA
1 ACAGAAA-ATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * *
13840 ACAGAAGATTTTATCTCGCTCAAGATTGGTTTTCCTTGAA
1 ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* ** * * *
13880 ACA-AAAGATTTTATCTCGCTTGAGATAG-TTTCCCTCGAA
1 ACAGAAA-ATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
13919 ACA-AAATATTTTATCTC
1 ACAGAAA-ATTTTATCTC
13936 GCTTGAGATA
Statistics
Matches: 496, Mismatches: 33, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
39 34 0.07
40 456 0.92
41 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (40 bp):
ACAGAAAATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
Found at i:13530 original size:20 final size:20
Alignment explanation
Indices: 13468--13531 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
13458 CTCAAGATTG
13468 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
* ** **
13488 TTTTAT-C-TCACTCAAGATTA
1 TTTT-TCCTTGAAAC-AGAAGA
13508 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
13528 TTTT
1 TTTT
13532 ATCTCACTCA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTTTCCTTGAAACAGAAGA
Found at i:13567 original size:23 final size:23
Alignment explanation
Indices: 13541--13649 Score: 64
Period size: 23 Copynumber: 5.3 Consensus size: 23
13531 TATCTCACTC
13541 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * **
13564 AAGA-T-TTTAT-C-T--CACTC
1 AAGATTGTTTTTCCTTGAAACAG
*
13581 AAGATTGTTTTTCCTTGAAACAA
1 AAGATTGTTTTTCCTTGAAACAG
*
13604 AAGATT-TTATTTCATT----C--
1 AAGATTGTT-TTTCCTTGAAACAG
13621 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
13644 AAGATT
1 AAGATT
13650 TTATCTCACT
Statistics
Matches: 62, Mismatches: 10, Indels: 28
0.62 0.10 0.28
Matches are distributed among these distances:
17 18 0.29
18 3 0.05
19 6 0.10
20 2 0.03
21 6 0.10
22 3 0.05
23 24 0.39
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:13573 original size:120 final size:120
Alignment explanation
Indices: 13360--13935 Score: 911
Period size: 120 Copynumber: 4.8 Consensus size: 120
13350 CTCATTTAAT
* *
13360 ACAGAAGATTTTATCTCACTCAAGATTGCTTTTCCTTGAAACAGAAAATTTTATCTCACTCAAGA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
13425 TTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
66 TTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
13480 ACAGAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
*
13545 TTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
66 TTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * *
13600 ACAAAAGATTTTATTTCATTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
* * * *
13665 TTATTTTTCCTTGAAACAGAAGATTTTATTTCATTCAAGATTGTTTTTCCTTGAA
66 TTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * * *
13720 ACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAGATTTAATCTCATTCAAGA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
*
13785 TTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGCTTTTCCTTGAA
66 TTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * * * **
13840 ACAGAAGATTTTATCTCGCTCAAGATTGGTTTTCCTTGAAACAAAAGATTTTATCTCGCTTGAGA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
* * * *
13905 TAG-TTTCCCTCGAAACAAAATATTTTATCTC
66 TTGTTTTTCCTTGAAACAAAAGATTTTATCTC
13936 GCTTGAGATA
Statistics
Matches: 423, Mismatches: 33, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
119 25 0.06
120 398 0.94
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (120 bp):
ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
TTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
Found at i:13690 original size:20 final size:20
Alignment explanation
Indices: 13628--13691 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
13618 TTCAAGATTG
13628 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
* ** **
13648 TTTTAT-C-TCACTCAAGATTA
1 TTTT-TCCTTGAAAC-AGAAGA
13668 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
13688 TTTT
1 TTTT
13692 ATTTCATTCA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTTTCCTTGAAACAGAAGA
Found at i:13727 original size:23 final size:23
Alignment explanation
Indices: 13701--13769 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
13691 TATTTCATTC
13701 AAGATTGTTTTTCCTTGAAACAA
1 AAGATTGTTTTTCCTTGAAACAA
* * **
13724 AAGA-T-TTTAT-C-T--CACTC
1 AAGATTGTTTTTCCTTGAAACAA
13741 AAGATTGTTTTTCCTTGAAACAA
1 AAGATTGTTTTTCCTTGAAACAA
13764 AAGATT
1 AAGATT
13770 TAATCTCATT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 6 0.19
18 1 0.03
19 5 0.16
20 2 0.06
21 5 0.16
22 1 0.03
23 12 0.38
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAA
Found at i:13931 original size:39 final size:39
Alignment explanation
Indices: 13328--14005 Score: 575
Period size: 40 Copynumber: 17.1 Consensus size: 39
13318 TTTCAAACAA
* * * * * *
13328 ATTTTATCTCGCTTGAGACAG-TCTCATTTAATACAGAAG
1 ATTTTATCTCGCTTAAGATAGTTTTCCTTGAA-ACAAAAG
* * *
13367 ATTTTATCTCACTCAAGATTGCTTTTCCTTGAAACAGAAA-
1 ATTTTATCTCGCTTAAGATAG-TTTTCCTTGAAACA-AAAG
* * *
13407 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTAAGATAG-TTTTCCTTGAAACAAAAG
* * * *
13447 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTAAGATAG-TTTTCCTTGAAACAAAAG
* * * *
13487 ATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTAAGA-TAGTTTTCCTTGAAACAAAAG
* * * *
13527 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTAAGATAG-TTTTCCTTGAAACAAAAG
* * *
13567 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTAAGATAG-TTTTCCTTGAAACAAAAG
* * * *
13607 ATTTTATTTC-ATTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTT-AAGATAG-TTTTCCTTGAAACAAAAG
* * * *
13647 ATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTAAGA-TAGTTTTCCTTGAAACAAAAG
* * *
13687 ATTTTATTTC-ATTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTT-AAGATAG-TTTTCCTTGAAACAAAAG
* * *
13727 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTAAGATAG-TTTTCCTTGAAACAAAAG
* * *
13767 ATTTAATCTC-ATTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTT-AAGATAG-TTTTCCTTGAAACAAAAG
* * * *
13807 ATTTTATCTCACTCAAGATTGCTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTAAGATAG-TTTTCCTTGAAACAAAAG
* *
13847 ATTTTATCTCGCTCAAGATTGGTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTAAGA-TAGTTTTCCTTGAAACAAAAG
* * * *
13887 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAT
1 ATTTTATCTCGCTTAAGATAGTTTTCCTTGAAACAAAAG
* *
13926 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC--AA-
1 ATTTTATCTCGCTTAAGATAGTTTTCCTTGAAACAAAAG
* * *
13962 ATTTTGTCTCCCTTGAGATAG-TTTCTCTTGAAACACAAA-
1 ATTTTATCTCGCTTAAGATAGTTTTC-CTTGAAACA-AAAG
14001 ATTTT
1 ATTTT
14006 GAGAACATTT
Statistics
Matches: 565, Mismatches: 55, Indels: 38
0.86 0.08 0.06
Matches are distributed among these distances:
35 3 0.01
36 27 0.05
37 2 0.00
39 81 0.14
40 436 0.77
41 16 0.03
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (39 bp):
ATTTTATCTCGCTTAAGATAGTTTTCCTTGAAACAAAAG
Found at i:14044 original size:66 final size:65
Alignment explanation
Indices: 13938--14107 Score: 216
Period size: 66 Copynumber: 2.6 Consensus size: 65
13928 TTTATCTCGC
* *
13938 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAAAT
1 TTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAA-ACAAAAT
14003 T
65 T
** * * **
14004 TTGAGA-ACATTTCCCTTGAAATGAATTTTGTCTCCCTTGAGATAGTTTCTTTTGGAAACAAGTT
1 TTGAGACA-ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAAACAAAAT
14068 T
65 T
* *
14069 TTGAGACAATTTCTCTTGAAACAAAGTTTTATCTCCCTT
1 TTGAGACAATTTCCCTTGAAACAAA-TTTTGTCTCCCTT
14108 AAAATGGTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 27 0.30
66 63 0.70
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (65 bp):
TTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAAACAAAATT
Found at i:14098 original size:28 final size:29
Alignment explanation
Indices: 14040--14098 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
14030 TTTGTCTCCC
* * *
14040 TTGAGATAGTTTCTTTTGGAAACAAGTTT
1 TTGAGACAATTTCTCTTGGAAACAAGTTT
14069 TTGAGACAATTTCTCTT-GAAACAAAGTTT
1 TTGAGACAATTTCTCTTGGAAAC-AAGTTT
14098 T
1 T
14099 ATCTCCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (29 bp):
TTGAGACAATTTCTCTTGGAAACAAGTTT
Found at i:14154 original size:36 final size:35
Alignment explanation
Indices: 14114--14225 Score: 89
Period size: 38 Copynumber: 3.1 Consensus size: 35
14104 CCTTAAAATG
14114 GTTTTTCTTAAAATCAACTTCGTCTCGCTTGAGACA
1 GTTTTTCTTAAAA-CAACTTCGTCTCGCTTGAGACA
* * * * **
14150 GTTTTATCTTGAAACAAAGTTTTGTCTCCCTTGAGATG
1 GTTTT-TCTTAAAAC-AA-CTTCGTCTCGCTTGAGACA
* * * *
14188 GTTTTTCTTAAAACCTACTTCTTTTTGCTTGAGACA
1 GTTTTTCTTAAAA-CAACTTCGTCTCGCTTGAGACA
14224 GT
1 GT
14226 CTCCCTTGAG
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
36 19 0.34
37 17 0.30
38 20 0.36
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (35 bp):
GTTTTTCTTAAAACAACTTCGTCTCGCTTGAGACA
Found at i:14167 original size:74 final size:74
Alignment explanation
Indices: 14069--14225 Score: 217
Period size: 74 Copynumber: 2.1 Consensus size: 74
14059 AAACAAGTTT
* * *
14069 TTGAGACA-ATTTCTCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAATCAACT
1 TTGAGACAGTTTTATCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAACCAACT
14133 TCGTCTCGC
66 TCGTCTCGC
* * * *
14142 TTGAGACAGTTTTATCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTTTCTTAAAACCTACT
1 TTGAGACAGTTTTATCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAACCAACT
* * *
14207 TCTTTTTGC
66 TCGTCTCGC
14216 TTGAGACAGT
1 TTGAGACAGT
14226 CTCCCTTGAG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 8 0.11
74 65 0.89
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (74 bp):
TTGAGACAGTTTTATCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAACCAACT
TCGTCTCGC
Found at i:14192 original size:38 final size:37
Alignment explanation
Indices: 14082--14201 Score: 118
Period size: 37 Copynumber: 3.2 Consensus size: 37
14072 AGACAATTTC
* * * *
14082 TCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTT
1 TCTTAAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
* * * **
14119 TCTTAAAATC-AA-CTTCGTCTCGCTTGAGACAGTTTT
1 TCTTAAAA-CAAAGTTTTGTCTCCCTTGAGATGGTTTT
*
14155 ATCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
1 -TCTTAAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
14193 TCTTAAAAC
1 TCTTAAAAC
14202 CTACTTCTTT
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
36 17 0.27
37 26 0.41
38 20 0.32
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (37 bp):
TCTTAAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
Found at i:14235 original size:15 final size:15
Alignment explanation
Indices: 14215--14255 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
14205 CTTCTTTTTG
14215 CTTGAGACAGTCTCC
1 CTTGAGACAGTCTCC
*
14230 CTTGAGACAGTCTCG
1 CTTGAGACAGTCTCC
14245 CTTGAGACAGT
1 CTTGAGACAGT
14256 TTTCATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (15 bp):
CTTGAGACAGTCTCC
Found at i:15269 original size:20 final size:20
Alignment explanation
Indices: 15207--15269 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
15197 CAGTGGAGAG
15207 TTCATAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTCA
* **
15227 TT--TAACGAGGAAGAA-GAA
1 TTCATAATGA-GAAGAACTCA
15245 GTTCATAATGAGAAGAACTCA
1 -TTCATAATGAGAAGAACTCA
15266 TTCA
1 TTCA
15270 ACCTTGCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 12 0.38
21 6 0.19
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTCA
Found at i:15603 original size:40 final size:40
Alignment explanation
Indices: 15549--15653 Score: 156
Period size: 40 Copynumber: 2.6 Consensus size: 40
15539 TAACTAGCCG
* * *
15549 TCCTCATCACGTAGGAACCGTGTCATCACCTGATTTGATC
1 TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
15589 TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
1 TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
* * *
15629 TCCTCTTTATGTAGGAGCAGTGTCA
1 TCCTCATTATGTAGGAACCGTGTCA
15654 ATCCTTGATA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (40 bp):
TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
Found at i:15773 original size:129 final size:130
Alignment explanation
Indices: 15607--15916 Score: 321
Period size: 134 Copynumber: 2.4 Consensus size: 130
15597 ATGTAGGAAC
* *
15607 CGTGTCATCACCTGATCT-GATCTCCTCTTTATGTAGGAGC-AGTGTCAATCCTTGATAACCAAA
1 CGTGTCATCACCTGA-CTAGAT-TTCTCTTTATGTAGGAGCTA-TGTCAA-CCTAGATAACCAAA
* * * * * *
15670 ACTCTTCATCACGTATGAGCTGTGTTATCA-CCTT-T-AGATGACC-AGAACTCTTCATCACGTA
62 ACTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTAAGATGACCAAGAAATCTTCATCACGTA
15731 TGAG
127 TGAG
****
15735 TCGTGTCATCACCTGACTAGATTTGCTCTTTATGTAGGAGCTATGTCAACCTAGATAACCAGTTG
1 -CGTGTCATCACCTGACTAGATTT-CTCTTTATGTAGGAGCTATGTCAACCTAGATAACCAAAAC
*
15800 TCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAAATCTTCATCACGTA
64 TCCTCATCACGTAGGAACCGAGTTATCACCCTT-CT-AAGATGACCAAGAAATCTTCATCACGTA
15865 TGAG
127 TGAG
* *
15869 CAGTGTTATC-CCTTGACTAGATCTTCTCATTATGTAGGAGTCT-TGTCA
1 C-GTGTCATCACC-TGACTAGAT-TTCTCTTTATGTAGGAG-CTATGTCA
15917 CCTTTAGACG
Statistics
Matches: 153, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
128 37 0.24
129 44 0.29
130 1 0.01
131 1 0.01
133 10 0.07
134 56 0.37
135 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (130 bp):
CGTGTCATCACCTGACTAGATTTCTCTTTATGTAGGAGCTATGTCAACCTAGATAACCAAAACTC
CTCATCACGTAGGAACCGAGTTATCACCCTTCTAAGATGACCAAGAAATCTTCATCACGTATGAG
Found at i:16127 original size:3 final size:3
Alignment explanation
Indices: 16119--16173 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
16109 TTTTAAAAAA
* * *
16119 TAT TAT TAT TAT ATAT TAT TAT TAT TAT TGT TAT TTT TAT TAA TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16165 TATT TAT TA
1 TA-T TAT TA
16174 CATTTGCAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16888 original size:2 final size:2
Alignment explanation
Indices: 16881--16917 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
16871 ACAACTATGC
16881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16918 AGGAAGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18566 original size:19 final size:19
Alignment explanation
Indices: 18527--18567 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18517 TTCTCTAATT
*
18527 AATTAATTAATTTGAAGTA
1 AATTAATTAATTTCAAGTA
18546 AATTAATTAATATTCAA-TA
1 AATTAATTAAT-TTCAAGTA
18565 AAT
1 AAT
18568 GGATCACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTAATTAATTTCAAGTA
Found at i:19801 original size:20 final size:20
Alignment explanation
Indices: 19776--19813 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19766 TTACTCTGTT
*
19776 GCATTTGTATTTGTATTTTC
1 GCATTTGCATTTGTATTTTC
19796 GCATTTGCATTTGTATTT
1 GCATTTGCATTTGTATTT
19814 GCATCTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (20 bp):
GCATTTGCATTTGTATTTTC
Found at i:19803 original size:26 final size:26
Alignment explanation
Indices: 19774--19831 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
19764 TTTTACTCTG
* * *
19774 TTGCATTTGTATTTGTATTTTCGCAT
1 TTGCATTTGTATTTGCATCTTCACAT
19800 TTGCATTTGTATTTGCATCTTCACAT
1 TTGCATTTGTATTTGCATCTTCACAT
19826 TTGCAT
1 TTGCAT
19832 AATCATCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.17, C:0.16, G:0.14, T:0.53
Consensus pattern (26 bp):
TTGCATTTGTATTTGCATCTTCACAT
Found at i:23342 original size:8 final size:8
Alignment explanation
Indices: 23329--23407 Score: 61
Period size: 8 Copynumber: 9.5 Consensus size: 8
23319 ATCCATCAGA
23329 GAAAAAAG
1 GAAAAAAG
23337 GAAAAAAG
1 GAAAAAAG
*
23345 AAGAAAAAAA
1 --GAAAAAAG
*
23355 GAAAAAAA
1 GAAAAAAG
*
23363 G-AGAAAG
1 GAAAAAAG
*
23370 AAAAAAAG
1 GAAAAAAG
23378 AGAAAAAAG
1 -GAAAAAAG
23387 AGAAAAAAG
1 -GAAAAAAG
* *
23396 AAAAAAAA
1 GAAAAAAG
23404 GAAA
1 GAAA
23408 TAAAAAAAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
7 4 0.07
8 31 0.53
9 16 0.28
10 7 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
GAAAAAAG
Found at i:23351 original size:9 final size:9
Alignment explanation
Indices: 23339--23420 Score: 66
Period size: 8 Copynumber: 9.3 Consensus size: 9
23329 GAAAAAAGGA
23339 AAAAAGAAG
1 AAAAAGAAG
23348 AAAAA-AAG
1 AAAAAGAAG
23356 AAAAA-AAG
1 AAAAAGAAG
*
23364 AGAAAGAA-
1 AAAAAGAAG
23372 AAAAAG-AG
1 AAAAAGAAG
23380 AAAAA-AGAG
1 AAAAAGA-AG
*
23389 AAAAAAGAAA
1 -AAAAAGAAG
*
23399 AAAAAGAAAT
1 AAAAAG-AAG
*
23409 AAAAAAAAG
1 AAAAAGAAG
23418 AAA
1 AAA
23421 TTAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
7 1 0.02
8 25 0.42
9 20 0.33
10 13 0.22
11 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:23371 original size:14 final size:13
Alignment explanation
Indices: 23330--23420 Score: 80
Period size: 14 Copynumber: 6.8 Consensus size: 13
23320 TCCATCAGAG
*
23330 AAAAAAGGAAA-A
1 AAAAAAAGAAAGA
*
23342 AAGAAGAAAAAAAGA
1 AA-AA-AAAGAAAGA
23357 AAAAAAGAGAAAGA
1 AAAAAA-AGAAAGA
23371 AAAAAAGAGAAA-A
1 AAAAAA-AGAAAGA
*
23384 AAGAGAAA-AAAGA
1 AA-AAAAAGAAAGA
*
23397 AAAAAAAGAAATA
1 AAAAAAAGAAAGA
23410 AAAAAAAGAAA
1 AAAAAAAGAAA
23421 TTAAATGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
12 9 0.14
13 26 0.39
14 28 0.42
15 3 0.05
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:23405 original size:18 final size:18
Alignment explanation
Indices: 23326--23405 Score: 90
Period size: 18 Copynumber: 4.2 Consensus size: 18
23316 CTCATCCATC
23326 AGAGAAAAAAGGAAAAAAGA
1 AGAGAAAAAA-GAAAAAA-A
23346 AGA-AAAAAAGAAAAAAA
1 AGAGAAAAAAGAAAAAAA
*
23363 GAGAAAGAAAAAAAGAGAAAAA
1 -AG--AG-AAAAAAGAAAAAAA
23385 AGAGAAAAAAGAAAAAAA
1 AGAGAAAAAAGAAAAAAA
23403 AGA
1 AGA
23406 AATAAAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.02
18 25 0.47
19 8 0.15
20 4 0.08
21 2 0.04
22 13 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AGAGAAAAAAGAAAAAAA
Found at i:23412 original size:18 final size:17
Alignment explanation
Indices: 23330--23416 Score: 83
Period size: 18 Copynumber: 5.1 Consensus size: 17
23320 TCCATCAGAG
*
23330 AAAAAAGGAAAAAAGAAGA
1 AAAAAAGAAAAAAAG-A-A
23349 AAAAAAGAAAAAAAG--
1 AAAAAAGAAAAAAAGAA
* *
23364 -AGAAAGAAAAAAAGAG
1 AAAAAAGAAAAAAAGAA
23380 AAAAAAGAGAAAAAAGAA
1 AAAAAAGA-AAAAAAGAA
23398 AAAAAAGAAATAAAA-AA
1 AAAAAAGAAA-AAAAGAA
23415 AA
1 AA
23417 GAAATTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
14 13 0.22
17 12 0.20
18 20 0.34
19 14 0.24
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAAAAAAGAA
Found at i:23425 original size:14 final size:13
Alignment explanation
Indices: 23356--23421 Score: 64
Period size: 13 Copynumber: 5.0 Consensus size: 13
23346 AGAAAAAAAG
*
23356 AAAAAAAGAGAAAG
1 AAAAAAA-AGAAAT
23370 AAAAAAAGAGAAA-
1 AAAAAAA-AGAAAT
* *
23383 AAAGAGAAA-AAAG
1 AAA-AAAAAGAAAT
23396 AAAAAAAAGAAAT
1 AAAAAAAAGAAAT
23409 AAAAAAAAGAAAT
1 AAAAAAAAGAAAT
23422 TAAATGAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
12 7 0.15
13 23 0.50
14 16 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAAAT
Found at i:26352 original size:40 final size:40
Alignment explanation
Indices: 26303--26877 Score: 929
Period size: 40 Copynumber: 14.4 Consensus size: 40
26293 CTCATTTAAT
*
26303 ACAGAAGATTTTATCTCACTCAAGATTGCTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
26343 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
26383 ACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
26423 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
26463 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
26503 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * *
26543 ACAAAAGATTTTATTTCATTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
26583 ACAGAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
26623 ACAGAAGATTTTATTTCATTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
26663 ACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
26703 ACAAAAGA-TTTATCTCATTCAAGATTGTTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
26742 ACAAAAGATTTTATCTCACTCAAGATTGCTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* *
26782 ACAGAAGATTTTATCTCGCTCAAGATTGGTTTTCCTTGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
* * ** * * *
26822 ACAAAAGATTTTATCTCGCTTGAGATAG-TTTCCCTCGAA
1 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
*
26861 ACAGAATATTTTATCTC
1 ACAGAAGATTTTATCTC
26878 GCTTGAGATA
Statistics
Matches: 504, Mismatches: 30, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
39 62 0.12
40 442 0.88
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (40 bp):
ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAA
Found at i:26633 original size:20 final size:20
Alignment explanation
Indices: 26571--26634 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
26561 TTCAAGATTG
26571 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
* ** **
26591 TTTTAT-C-TCACTCAAGATTA
1 TTTT-TCCTTGAAAC-AGAAGA
26611 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
26631 TTTT
1 TTTT
26635 ATTTCATTCA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTTTCCTTGAAACAGAAGA
Found at i:26919 original size:36 final size:38
Alignment explanation
Indices: 26271--26947 Score: 351
Period size: 40 Copynumber: 17.1 Consensus size: 38
26261 TTTCAAACAA
* * * *
26271 ATTTTATCTCGCTTGAGACAGTCT-CATTTAATACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAA-ACA-AAG
* ** * *
26310 ATTTTATCTCACTCAAGATTGCTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAACA-AAG
* ** * *
26350 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAAC-AAAG
* ** * *
26390 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAACA-AAG
* ** * *
26430 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAACA-AAG
* ** * *
26470 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAACA-AAG
* ** * *
26510 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAAC-AAAG
* * * * *
26550 ATTTTATTTC-ATTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTT-GAGATAG-TTTCCCTTGAAACA-AAG
* ** * *
26590 ATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGA-TAGTTTCCCTTGAAACA-AAG
* * * * *
26630 ATTTTATTTC-ATTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTT-GAGATAG-TTTCCCTTGAAAC-AAAG
* ** * *
26670 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAAC-AAAG
* * * *
26710 A-TTTATCTC-ATTCAAGATTGTTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTT-GAGATAG-TTTCCCTTGAAAC-AAAG
* ** * *
26749 ATTTTATCTCACTCAAGATTGCTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAG-TTTCCCTTGAAACA-AAG
** * *
26789 ATTTTATCTCGCTCAAGATTGGTTTTCCTTGAAACAAAAG
1 ATTTTATCTCGCTTGAGA-TAGTTTCCCTTGAAAC-AAAG
* *
26829 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA-AAG
26868 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-AA-
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAG
* * * *
26904 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA-AAG
26943 ATTTT
1 ATTTT
26948 GAGAACATTT
Statistics
Matches: 573, Mismatches: 42, Indels: 46
0.87 0.06 0.07
Matches are distributed among these distances:
36 31 0.05
37 2 0.00
38 4 0.01
39 110 0.19
40 411 0.72
41 15 0.03
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (38 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAG
Found at i:26937 original size:75 final size:77
Alignment explanation
Indices: 26271--26947 Score: 453
Period size: 80 Copynumber: 8.6 Consensus size: 77
26261 TTTCAAACAA
* * * * * * *
26271 ATTTTATCTCGCTTGAGACAGTCTCATTTAATACAGAAGATTTTATCTCACTCAAGATT-GCTTT
1 ATTTTATCTCCCTTGAGATAGTTTCCTTGAA-ACAGAAAATTTTATCTCGCTCAAGATTAG-TTT
*
26335 TCCTTGAAACAGAAG
64 CCCTTGAAACA-AAG
* ** * *
26350 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA-AAAGATTTTATCTCACTCAAGATT-GTT
1 ATTTTATCTCCCTTGAGATAG--TTTCCTTGAAACAGAAA-ATTTTATCTCGCTCAAGATTAG-T
*
26413 TTTCCTTGAAACAGAAG
62 TTCCCTTGAAACA-AAG
* ** * * *
26430 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATT-GTTT
1 ATTTTATCTCCCTTGAGATAG--TTTCCTTGAAACAGAAAATTTTATCTCGCTCAAGATTAG-TT
*
26494 TTCCTTGAAACAGAAG
63 TCCCTTGAAACA-AAG
* ** * * **
26510 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA-AAAGATTTTATTTCATTCAAGATT-GTT
1 ATTTTATCTCCCTTGAGATAG--TTTCCTTGAAACAGAAA-ATTTTATCTCGCTCAAGATTAG-T
*
26573 TTTCCTTGAAACAGAAG
62 TTCCCTTGAAACA-AAG
* ** * * * **
26590 ATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATTTCATTCAAGATT-GTTT
1 ATTTTATCTCCCTTGAGA-TA-GTTTCCTTGAAACAGAAAATTTTATCTCGCTCAAGATTAG-TT
*
26654 TTCCTTGAAACAAAAG
63 TCCCTTGAAAC-AAAG
* ** * **
26670 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA-AAAGA-TTTATCTCATTCAAGATT-GTT
1 ATTTTATCTCCCTTGAGATAG--TTTCCTTGAAACAGAAA-ATTTTATCTCGCTCAAGATTAG-T
*
26732 TTTCCTTGAAACAAAAG
62 TTCCCTTGAAAC-AAAG
* ** * * *
26749 ATTTTATCTCACTCAAGATTGCTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGGTTT
1 ATTTTATCTCCCTTGAGATAG--TTTCCTTGAAACAGAAAATTTTATCTCGCTCAAGATTAGTTT
*
26814 TCCTTGAAACAAAAG
64 CCCTTGAAAC-AAAG
* * * **
26829 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAATATTTTATCTCGCTTGAGA-TAGTTTC
1 ATTTTATCTCCCTTGAGATAGTTT-CCTTGAAACAGAAAATTTTATCTCGCTCAAGATTAGTTTC
26893 CCTTGAAAC-AA-
65 CCTTGAAACAAAG
* *
26904 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAAATTTT
1 ATTTTATCTCCCTTGAGATAGTTTC-CTTGAAACAGAAAATTTT
26948 GAGAACATTT
Statistics
Matches: 541, Mismatches: 40, Indels: 38
0.87 0.06 0.06
Matches are distributed among these distances:
74 1 0.00
75 37 0.07
76 2 0.00
78 17 0.03
79 124 0.23
80 346 0.64
81 14 0.03
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (77 bp):
ATTTTATCTCCCTTGAGATAGTTTCCTTGAAACAGAAAATTTTATCTCGCTCAAGATTAGTTTCC
CTTGAAACAAAG
Found at i:26986 original size:66 final size:65
Alignment explanation
Indices: 26880--27049 Score: 216
Period size: 66 Copynumber: 2.6 Consensus size: 65
26870 TTTATCTCGC
* *
26880 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAAAT
1 TTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAA-ACAAAAT
26945 T
65 T
** * * **
26946 TTGAGA-ACATTTCCCTTGAAATGAATTTTGTCTCCCTTGAGATAGTTTCTTTTGGAAACAAGTT
1 TTGAGACA-ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAAACAAAAT
27010 T
65 T
* *
27011 TTGAGACAATTTCTCTTGAAACAAAGTTTTATCTCCCTT
1 TTGAGACAATTTCCCTTGAAACAAA-TTTTGTCTCCCTT
27050 AAAATGGTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 27 0.30
66 63 0.70
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (65 bp):
TTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAAACAAAATT
Found at i:27040 original size:28 final size:29
Alignment explanation
Indices: 26982--27040 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
26972 TTTGTCTCCC
* * *
26982 TTGAGATAGTTTCTTTTGGAAACAAGTTT
1 TTGAGACAATTTCTCTTGGAAACAAGTTT
27011 TTGAGACAATTTCTCTT-GAAACAAAGTTT
1 TTGAGACAATTTCTCTTGGAAAC-AAGTTT
27040 T
1 T
27041 ATCTCCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (29 bp):
TTGAGACAATTTCTCTTGGAAACAAGTTT
Found at i:27096 original size:36 final size:35
Alignment explanation
Indices: 27056--27167 Score: 89
Period size: 38 Copynumber: 3.1 Consensus size: 35
27046 CCTTAAAATG
27056 GTTTTTCTTAAAATCAACTTCGTCTCGCTTGAGACA
1 GTTTTTCTTAAAA-CAACTTCGTCTCGCTTGAGACA
* * * * **
27092 GTTTTATCTTGAAACAAAGTTTTGTCTCCCTTGAGATG
1 GTTTT-TCTTAAAAC-AA-CTTCGTCTCGCTTGAGACA
* * * *
27130 GTTTTTCTTAAAACCTACTTCTTTTTGCTTGAGACA
1 GTTTTTCTTAAAA-CAACTTCGTCTCGCTTGAGACA
27166 GT
1 GT
27168 CTCGCTTGAG
Statistics
Matches: 56, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
36 19 0.34
37 17 0.30
38 20 0.36
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (35 bp):
GTTTTTCTTAAAACAACTTCGTCTCGCTTGAGACA
Found at i:27109 original size:74 final size:74
Alignment explanation
Indices: 27011--27167 Score: 217
Period size: 74 Copynumber: 2.1 Consensus size: 74
27001 AAACAAGTTT
* * *
27011 TTGAGACA-ATTTCTCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAATCAACT
1 TTGAGACAGTTTTATCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAACCAACT
27075 TCGTCTCGC
66 TCGTCTCGC
* * * *
27084 TTGAGACAGTTTTATCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTTTCTTAAAACCTACT
1 TTGAGACAGTTTTATCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAACCAACT
* * *
27149 TCTTTTTGC
66 TCGTCTCGC
27158 TTGAGACAGT
1 TTGAGACAGT
27168 CTCGCTTGAG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 8 0.11
74 65 0.89
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (74 bp):
TTGAGACAGTTTTATCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTTTCTTAAAACCAACT
TCGTCTCGC
Found at i:27134 original size:38 final size:37
Alignment explanation
Indices: 27024--27143 Score: 118
Period size: 37 Copynumber: 3.2 Consensus size: 37
27014 AGACAATTTC
* * * *
27024 TCTTGAAACAAAGTTTTATCTCCCTTAAAATGGTTTT
1 TCTTAAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
* * * **
27061 TCTTAAAATC-AA-CTTCGTCTCGCTTGAGACAGTTTT
1 TCTTAAAA-CAAAGTTTTGTCTCCCTTGAGATGGTTTT
*
27097 ATCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
1 -TCTTAAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
27135 TCTTAAAAC
1 TCTTAAAAC
27144 CTACTTCTTT
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
36 17 0.27
37 26 0.41
38 20 0.32
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (37 bp):
TCTTAAAACAAAGTTTTGTCTCCCTTGAGATGGTTTT
Found at i:27930 original size:136 final size:135
Alignment explanation
Indices: 27766--28099 Score: 455
Period size: 136 Copynumber: 2.5 Consensus size: 135
27756 CACATCAGTG
*
27766 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAAT-GAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * * * *
27831 AAGAGCTTGTTTGACCTATCACTTGATTCACGATATTTCGAATTAGTGACACCTCACTTGAGGGA
65 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCACTGACACCTCACTTGAGGGA
*
27896 TTGACA
130 TTAACA
* *
27902 TTTCCAATTGAGAGTTCATAATAAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAA-TGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * * *
27967 AAGAGCTTGTTCGACTTATCACTCGATTCACGACATTTTGAATCACTGACGCCTCGCTTGAGGGA
65 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCACTGACACCTCACTTGAGGGA
*
28032 TTAATA
130 TTAACA
* * *
28038 TTTCCAA-AAGAGTTCATAATGAGAAGAACTCGTCCTAC--A-GGAG-A-AAGTTCATAATGAGA
1 TTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGA
28097 AGA
66 AGA
28100 ATTTGTTCCT
Statistics
Matches: 178, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
129 18 0.10
130 1 0.01
131 4 0.02
132 1 0.01
134 26 0.15
136 127 0.71
137 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (135 bp):
TTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGA
AGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCACTGACACCTCACTTGAGGGAT
TAACA
Found at i:28334 original size:20 final size:20
Alignment explanation
Indices: 28272--28334 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
28262 CAGTGGAGAG
28272 TTCATAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTCA
* **
28292 TT--TAACGAGGAAGAA-GAA
1 TTCATAATGA-GAAGAACTCA
28310 GTTCATAATGAGAAGAACTCA
1 -TTCATAATGAGAAGAACTCA
28331 TTCA
1 TTCA
28335 ACCTTGCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 12 0.38
21 6 0.19
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTCA
Found at i:28668 original size:40 final size:40
Alignment explanation
Indices: 28614--28718 Score: 174
Period size: 40 Copynumber: 2.6 Consensus size: 40
28604 TAACTAGCCG
* *
28614 TCCTCATCACGTAGGAACCGTGTCATCACCTGATCTGATC
1 TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
28654 TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
1 TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
* *
28694 TCCTCATTATGTAGGAGCAGTGTCA
1 TCCTCATTATGTAGGAACCGTGTCA
28719 ATCCTTGATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (40 bp):
TCCTCATTATGTAGGAACCGTGTCATCACCTGATCTGATC
Found at i:28967 original size:134 final size:129
Alignment explanation
Indices: 28672--28981 Score: 328
Period size: 134 Copynumber: 2.4 Consensus size: 129
28662 ATGTAGGAAC
* *
28672 CGTGTCATCACCTGATCT-GATCTCCTCATTATGTAGGAGC-AGTGTCAATCCTTGATAACCAAA
1 CGTGTCATCACCTGA-CTAGATCTTCTCATTATGTAGGAGCTA-TGTCAATCCTAGATAACCAAA
* * * * * *
28735 ACTCTTCATCACGTATGAGCTGTGTTATCACCTTTAGATGACCAGAACTCTTCATCACGTATGAG
64 ACTCCTCATCACGTAGGAACCGAGTTATCACCTTTAGATGACCAGAAATCTTCATCACGTATGAG
28800 T
129 T
* ***
28801 CGTGTCATCACCTGACTAGAT-TTGCTCTTTATGTAGGAGCTATGTCAA-CCTAGATAACCAGTT
1 CGTGTCATCACCTGACTAGATCTT-CTCATTATGTAGGAGCTATGTCAATCCTAGATAACCAAAA
* *
28864 GTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAAATCTTCATCACGT
65 CTCCTCATCACGTAGGAACCGAGTTATCA-CCTT--T--AGATGACC-AGAAATCTTCATCACGT
28929 ATGAG-
124 ATGAGT
*
28934 CAGTGTTATC-CCTTGACTAGATCTTCTCATTATGTAGGAGTCT-TGTCA
1 C-GTGTCATCACC-TGACTAGATCTTCTCATTATGTAGGAG-CTATGTCA
28982 CCTTTAGACG
Statistics
Matches: 152, Mismatches: 16, Indels: 21
0.80 0.08 0.11
Matches are distributed among these distances:
128 37 0.24
129 43 0.28
130 1 0.01
131 1 0.01
133 10 0.07
134 56 0.37
135 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (129 bp):
CGTGTCATCACCTGACTAGATCTTCTCATTATGTAGGAGCTATGTCAATCCTAGATAACCAAAAC
TCCTCATCACGTAGGAACCGAGTTATCACCTTTAGATGACCAGAAATCTTCATCACGTATGAGT
Found at i:29191 original size:3 final size:3
Alignment explanation
Indices: 29183--29232 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
29173 TTTTAAAAAA
* * *
29183 TAT TAT TAT TA- TAT TAT TAT TGT TAT TTT TAT TAT TAA TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
29228 TAT TA
1 TAT TA
29233 CATTTGCAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31611 original size:19 final size:19
Alignment explanation
Indices: 31572--31612 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31562 TTCTCTAATT
*
31572 AATTAATTAATTTGAAGTA
1 AATTAATTAATTTCAAGTA
31591 AATTAATTAATATTCAA-TA
1 AATTAATTAAT-TTCAAGTA
31610 AAT
1 AAT
31613 GGATCACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTAATTAATTTCAAGTA
Found at i:33109 original size:13 final size:13
Alignment explanation
Indices: 33077--33114 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
33067 AAAAAATTGC
*
33077 AAAATAATAA-TA
1 AAAATTATAATTA
*
33089 ATAATTATAATTA
1 AAAATTATAATTA
33102 AAAATTATAATTA
1 AAAATTATAATTA
33115 TAATTAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATTATAATTA
Found at i:33124 original size:13 final size:13
Alignment explanation
Indices: 33083--33125 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
33073 TTGCAAAATA
33083 ATAA-TAATAATT
1 ATAATTAATAATT
*
33095 ATAATTAAAAATT
1 ATAATTAATAATT
33108 ATAATT-ATAATT
1 ATAATTAATAATT
33120 AATAAT
1 -ATAAT
33126 ATTTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATTAATAATT
Found at i:34888 original size:25 final size:25
Alignment explanation
Indices: 34841--34915 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
34831 GTCTTGAACC
*
34841 CTTTTTATTTATTTATTAT-TTTTTT
1 CTTTTT-TTTATTTATTTTCTTTTTT
*
34866 CTTTTTTTTTTTTATTTTC-TTTTT
1 CTTTTTTTTATTTATTTTCTTTTTT
* * *
34890 CTCTATTTTTCTTCATTTTCTTTTTT
1 CT-TTTTTTTATTTATTTTCTTTTTT
34916 TCCCATTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
24 17 0.40
25 20 0.48
26 5 0.12
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (25 bp):
CTTTTTTTTATTTATTTTCTTTTTT
Found at i:34944 original size:20 final size:19
Alignment explanation
Indices: 34862--34963 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 19
34852 TTTATTATTT
* *
34862 TTTTC-TTTTTTTTTTTTA
1 TTTTCATTTTCTTTTTTTC
*
34880 TTTTCTTTTTCTCTATTTTTC
1 TTTTCATTTTCT-T-TTTTTC
34901 --TTCATTTTCTTTTTTTCC
1 TTTTCATTTTCTTTTTTT-C
**
34919 CATTCATTTTCATTTTTTTC
1 TTTTCATTTTC-TTTTTTTC
34939 TTTTCATTCTTCTTTCTTTTTC
1 TTTTCATT-TTC-TT-TTTTTC
34961 TTT
1 TTT
34964 CTTCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
17 5 0.07
18 7 0.10
19 14 0.20
20 17 0.25
21 17 0.25
22 9 0.13
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCATTTTCTTTTTTTC
Found at i:34963 original size:10 final size:10
Alignment explanation
Indices: 34859--34966 Score: 59
Period size: 10 Copynumber: 11.1 Consensus size: 10
34849 TTATTTATTA
34859 TTTT-TTTCT
1 TTTTCTTTCT
34868 TTTT-TTT-T
1 TTTTCTTTCT
34876 TTTAT-TTTCT
1 TTT-TCTTTCT
* *
34886 TTTTCTCTAT
1 TTTTCTTTCT
*
34896 TTTTC-TTCA
1 TTTTCTTTCT
34905 TTTTCTTT-T
1 TTTTCTTTCT
* * *
34914 TTTCCCATTCA
1 TTT-TCTTTCT
*
34925 TTTTCATT-T
1 TTTTCTTTCT
34934 TTTTCTTTTCAT
1 TTTTC-TTTC-T
*
34946 TCTTCTTTCT
1 TTTTCTTTCT
34956 TTTTCTTTCT
1 TTTTCTTTCT
34966 T
1 T
34967 CTGGTGAAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
8 4 0.05
9 26 0.34
10 34 0.45
11 7 0.09
12 5 0.07
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:34965 original size:17 final size:16
Alignment explanation
Indices: 34925--34968 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
34915 TTCCCATTCA
34925 TTTTCATT-TT-TTTC
1 TTTTCATTCTTCTTTC
34939 TTTTCATTCTTCTTTC
1 TTTTCATTCTTCTTTC
*
34955 TTTTTCTTTCTTCT
1 -TTTTCATTCTTCT
34969 GGTGAAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
15 2 0.08
16 4 0.15
17 12 0.46
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCATTCTTCTTTC
Found at i:38512 original size:2 final size:2
Alignment explanation
Indices: 38505--38529 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38495 TAATGAAATA
38505 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 A
38530 CATAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41844 original size:30 final size:30
Alignment explanation
Indices: 41810--41890 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
41800 TAATTCACTT
**
41810 ATCACATTTCTCATGTCATATTCTCATATG
1 ATCACATAACTCATGTCATATTCTCATATG
*
41840 ATCACATAACTCATGTCACT-TTCTCATGTG
1 ATCACATAACTCATGTCA-TATTCTCATATG
* *
41870 GTCACATAGCTCATGTCATAT
1 ATCACATAACTCATGTCATAT
41891 AATCTCTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 1 0.02
30 42 0.95
31 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (30 bp):
ATCACATAACTCATGTCATATTCTCATATG
Done.