Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1168
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: 223387
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
File 1 of 2
Found at i:1585 original size:12 final size:12
Alignment explanation
Indices: 1568--1614 Score: 78
Period size: 13 Copynumber: 3.9 Consensus size: 12
1558 AGACCGTATG
1568 CAATTTTTTTTT
1 CAATTTTTTTTT
1580 CAATTTTTTTTTT
1 CAA-TTTTTTTTT
1593 CAA-TTTTTTTT
1 CAATTTTTTTTT
1604 CAATTTTTTTT
1 CAATTTTTTTT
1615 GATTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.33
12 10 0.30
13 12 0.36
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:1619 original size:10 final size:11
Alignment explanation
Indices: 1572--1614 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
1562 CGTATGCAAT
1572 TTTTTTTTCAA
1 TTTTTTTTCAA
1583 TTTTTTTTTTCAA
1 --TTTTTTTTCAA
1596 TTTTTTTTCAA
1 TTTTTTTTCAA
1607 TTTTTTTT
1 TTTTTTTT
1615 GATTTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:4388 original size:30 final size:30
Alignment explanation
Indices: 4354--4450 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
4344 TAAACTAAAA
*
4354 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
4384 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* *
4414 TGAGCTAAGGTTTAGCTCGTAAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
4444 TGAGCTA
1 TGAGCTA
4451 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:15770 original size:19 final size:20
Alignment explanation
Indices: 15733--15783 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
15723 AATGAGCTGA
15733 AACGAGCTAAAATCAAGCTC
1 AACGAGCTAAAATCAAGCTC
*
15753 AACGAGCTGAAA-CAAGCTC
1 AACGAGCTAAAATCAAGCTC
*
15772 AAGTGAGCTAAA
1 AA-CGAGCTAAA
15784 TAGAGCTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.14
Consensus pattern (20 bp):
AACGAGCTAAAATCAAGCTC
Found at i:20078 original size:30 final size:30
Alignment explanation
Indices: 19993--20089 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19983 TAAACTAAAA
* *
19993 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
20023 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
20053 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
20082 ATGAGCTA
1 -TGAGCTA
20090 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:22355 original size:30 final size:30
Alignment explanation
Indices: 22319--22391 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
22309 TTCTTTTGTT
*
22319 TCAAATTCTTTTTCA-TCTTCTTTTTCACTC
1 TCAAATTCTTTTTCATTC-TCTTTTTCAATC
22349 TCAAATT-TCTTTTCATTCTCTTTTTCAATC
1 TCAAATTCT-TTTTCATTCTCTTTTTCAATC
**
22379 TCATTTTCTTTTT
1 TCAAATTCTTTTT
22392 GCTTTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
30 33 0.89
31 3 0.08
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.60
Consensus pattern (30 bp):
TCAAATTCTTTTTCATTCTCTTTTTCAATC
Found at i:22409 original size:12 final size:12
Alignment explanation
Indices: 22394--22424 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
22384 TTCTTTTTGC
22394 TTTTCAAAGGCT
1 TTTTCAAAGGCT
22406 TTTTCAAAGGCT
1 TTTTCAAAGGCT
22418 TTTTCAA
1 TTTTCAA
22425 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:22482 original size:5 final size:5
Alignment explanation
Indices: 22472--22528 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
22462 CTCTTGCCTC
*
22472 TCTTT TCTTT T-TATT TCTTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
22519 TCTTT TCTTT
1 TCTTT TCTTT
22529 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:22492 original size:15 final size:14
Alignment explanation
Indices: 22472--22535 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 14
22462 CTCTTGCCTC
22472 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
22487 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
22502 TCTTTTGCTTTTTCTTT
1 TCTTTT-C-TTTT-TTT
*
22519 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
22533 TCT
1 TCT
22536 CTTTACAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.24
15 9 0.21
16 15 0.36
17 8 0.19
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:22504 original size:25 final size:25
Alignment explanation
Indices: 22476--22524 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
22466 TGCCTCTCTT
22476 TTCTTTT-TATTTCTTTTTCTTTTTC
1 TTCTTTTCTATTTC-TTTTCTTTTTC
*
22501 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTATTTCTTTTCTTTT
22525 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 9 0.43
27 5 0.24
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTATTTCTTTTCTTTTTC
Found at i:22529 original size:21 final size:21
Alignment explanation
Indices: 22472--22539 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
22462 CTCTTGCCTC
*
22472 TCTTTTCTTTT-TATTTCTTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
22493 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
22514 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
22534 CTCTTT
1 -TCTTT
22540 ACAAGAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 7 0.17
21 28 0.70
22 5 0.12
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:23426 original size:11 final size:11
Alignment explanation
Indices: 23400--23440 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
23390 CATTAAACAC
*
23400 TTTTTTTCAGAT
1 TTTTTTTC-GAA
23412 TTTTTTTCGAA
1 TTTTTTTCGAA
*
23423 TTTTTTTTGAA
1 TTTTTTTCGAA
23434 TTTTTTT
1 TTTTTTT
23441 TTACTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:23448 original size:11 final size:11
Alignment explanation
Indices: 23400--23441 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
23390 CATTAAACAC
*
23400 TTTTTTTCAGAT
1 TTTTTTTGA-AT
23412 TTTTTTTCGAAT
1 TTTTTTT-GAAT
23424 TTTTTTTGAAT
1 TTTTTTTGAAT
23435 TTTTTTT
1 TTTTTTT
23442 TACTTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.39
12 16 0.57
13 1 0.04
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:25198 original size:30 final size:30
Alignment explanation
Indices: 25113--25209 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25103 TAAACTAAAA
* *
25113 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
25143 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
25173 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
25202 ATGAGCTA
1 -TGAGCTA
25210 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:31370 original size:19 final size:19
Alignment explanation
Indices: 31346--31385 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31336 AGCTCCCATG
31346 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
* *
31365 TAGCTCGAGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
31384 TA
1 TA
31386 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:32924 original size:29 final size:29
Alignment explanation
Indices: 32891--32950 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
32881 ATAACCAAAC
*
32891 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
32920 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
32949 CT
1 CT
32951 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:32943 original size:15 final size:15
Alignment explanation
Indices: 32897--32944 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
32887 AAACCTACAA
*
32897 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
32912 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
32926 AAACTTCATATCCAT
1 AAACTTCATATCCAT
32941 AAAC
1 AAAC
32945 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:34159 original size:14 final size:12
Alignment explanation
Indices: 34124--34156 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
34114 CTTGAAAGAG
*
34124 ATTGAGAAAGTC
1 ATTGAAAAAGTC
34136 ATTGAAAAAGTC
1 ATTGAAAAAGTC
34148 ATTGAAAAA
1 ATTGAAAAA
34157 AAGAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (12 bp):
ATTGAAAAAGTC
Found at i:34292 original size:18 final size:19
Alignment explanation
Indices: 34249--34294 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
34239 CGAGAAAAGC
*
34249 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
34267 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
34285 GAAAAAGAAA
1 GAAAAAGAAA
34295 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:38310 original size:30 final size:30
Alignment explanation
Indices: 38276--38372 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
38266 TAAACTAAAA
38276 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
38306 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
38336 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
38365 ATGAGCTA
1 -TGAGCTA
38373 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:39698 original size:20 final size:20
Alignment explanation
Indices: 39673--39710 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39663 CAAGCCATTA
39673 AACTTGAGCACGAATGAGCT
1 AACTTGAGCACGAATGAGCT
*
39693 AACTTGAGCTCGAATGAG
1 AACTTGAGCACGAATGAG
39711 TTGAACCACA
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:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (20 bp):
AACTTGAGCACGAATGAGCT
Found at i:39914 original size:14 final size:14
Alignment explanation
Indices: 39895--39939 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
39885 AACTCATCTT
*
39895 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
39909 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
39922 AATTTAATTTAATG
1 AGTTTAATTTAATG
39936 AGTT
1 AGTT
39940 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:40952 original size:29 final size:29
Alignment explanation
Indices: 40919--40978 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
40909 ATAACCAAAC
*
40919 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
40948 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
40977 CT
1 CT
40979 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:40971 original size:15 final size:15
Alignment explanation
Indices: 40925--40972 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
40915 AAACCTACAA
*
40925 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
40940 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
40954 AAACTTCATATCCAT
1 AAACTTCATATCCAT
40969 AAAC
1 AAAC
40973 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:42421 original size:26 final size:27
Alignment explanation
Indices: 42391--42466 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
42381 GGTTCGTATC
42391 AATACCCCTGTAGGGT-GAATTATCGA
1 AATACCCCTGTAGGGTAGAATTATCGA
* *
42417 AATA-CCCTCGTAGGGTAGAAATATTGA
1 AATACCCCT-GTAGGGTAGAATTATCGA
42444 AATACCCCTGTAGGGTAGAATTA
1 AATACCCCTGTAGGGTAGAATTA
42467 CCGAGATATC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
25 4 0.09
26 11 0.25
27 25 0.57
28 4 0.09
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAGAATTATCGA
Found at i:42734 original size:28 final size:28
Alignment explanation
Indices: 42692--42753 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
42682 GAGGAAGTGT
42692 TCTGGTGGCTATGCCACAAATATCTATA
1 TCTGGTGGCTATGCCACAAATATCTATA
* *
42720 TTTGGTGGCTATGCCACAAATATCTGTA
1 TCTGGTGGCTATGCCACAAATATCTATA
42748 TCTGGT
1 TCTGGT
42754 ACTCTATCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTATGCCACAAATATCTATA
Found at i:42953 original size:6 final size:6
Alignment explanation
Indices: 42938--43012 Score: 73
Period size: 6 Copynumber: 12.3 Consensus size: 6
42928 TATAGGCTTC
* *
42938 ATTCTG ATTCTA ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
42987 ATTCTA ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
43013 AATGTTTCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
5 2 0.04
6 49 0.88
7 4 0.07
8 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:46621 original size:20 final size:20
Alignment explanation
Indices: 46598--46643 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
46588 CCAGCTCGAA
*
46598 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
46618 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
46638 TTAGCT
1 TTAGCT
46644 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:46625 original size:30 final size:30
Alignment explanation
Indices: 46590--46663 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
46580 AGTTTTTCCC
46590 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
46620 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
46650 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
46664 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:52528 original size:23 final size:22
Alignment explanation
Indices: 52476--52528 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
52466 TCCACGTCTT
*
52476 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
52498 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
52521 TTTCTTTT
1 TTTCTTTT
52529 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:52538 original size:18 final size:18
Alignment explanation
Indices: 52517--52566 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
52507 TCTTCTTTCT
52517 TCAATTTCTTTTTCACTC
1 TCAATTTCTTTTTCACTC
* * *
52535 TCAATCTCTTTTTGATTC
1 TCAATTTCTTTTTCACTC
**
52553 TCTTTTTCTTTTTC
1 TCAATTTCTTTTTC
52567 CTCACTTGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.02, T:0.62
Consensus pattern (18 bp):
TCAATTTCTTTTTCACTC
Found at i:55803 original size:991 final size:991
Alignment explanation
Indices: 54036--56019 Score: 3893
Period size: 991 Copynumber: 2.0 Consensus size: 991
54026 CCAAAATCTG
54036 ATACCAAATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTAC
1 ATACCAAATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTAC
*
54101 GAAAACCCTAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTC
66 GAAAACCCTAAACAATTAGATCTGAAACGAAACAAAAAATTAAAAGATTAGATTTTTGAATTTTC
54166 AGATCTGAAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGT
131 AGATCTGAAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGT
54231 TCTTGAAACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATT
196 TCTTGAAACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATT
54296 TCGACAATCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTG
261 TCGACAATCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTG
54361 ATTCCTTAAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCA
326 ATTCCTTAAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCA
54426 GCACAAGTAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTG
391 GCACAAGTAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTG
54491 AAATCTCGAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATG
456 AAATCTCGAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATG
54556 GCAAGAAGAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAAC
521 GCAAGAAGAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAAC
54621 TCAAGAGAGAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAAT
586 TCAAGAGAGAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAAT
54686 AATAATGATAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTA
651 AATAATGATAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTA
54751 ATCTAATTAGAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGT
716 ATCTAATTAGAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGT
54816 CATTTTATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAAT
781 CATTTTATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAAT
54881 AAATAAAAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACT
846 AAATAAAAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACT
54946 AAGTATGGATGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTAAAGAATTTG
911 AAGTATGGATGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTAAAGAATTTG
55011 GGCTTTTGTGACTCGT
976 GGCTTTTGTGACTCGT
55027 ATACCAAATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTAC
1 ATACCAAATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTAC
55092 GAAAACCCTAAACAATTAGATCTGAAACGAAACAAAAAATTAAAAGATTAGATTTTTGAATTTTC
66 GAAAACCCTAAACAATTAGATCTGAAACGAAACAAAAAATTAAAAGATTAGATTTTTGAATTTTC
55157 AGATCTGAAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGT
131 AGATCTGAAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGT
55222 TCTTGAAACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATT
196 TCTTGAAACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATT
55287 TCGACAATCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTG
261 TCGACAATCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTG
55352 ATTCCTTAAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCA
326 ATTCCTTAAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCA
55417 GCACAAGTAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTG
391 GCACAAGTAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTG
55482 AAATCTCGAAAGATCTCACAACTCCCTTCAAAC-GCTCTAATCTCCCCTCCAAAGAATATCAATG
456 AAATCTCGAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATG
55546 GCAAGAAGAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAAC
521 GCAAGAAGAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAAC
55611 TCAAGAGAGAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAAT
586 TCAAGAGAGAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAAT
55676 AATAATGATAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTA
651 AATAATGATAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTA
55741 ATCTAATTAGAAAACTAAAATAAAAAAAAAACTCCTAATTA-TTTAATATGGAAATT-GGTCAAA
716 ATCTAATTAGAAAACTAAAAT---AAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAA
55804 GGTCATTTTATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATA
778 GGTCATTTTATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATA
*
55869 AATAAATAAAAATAAAAATAGAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCA
843 AATAAATAAAAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCA
*
55934 ACTAAGTATGGATGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAAT
908 ACTAAGTATGGATGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTAAAGAAT
55999 TTGGGCTTTTGTGACTCGT
973 TTGGGCTTTTGTGACTCGT
56018 AT
1 AT
56020 CACTATTGCT
Statistics
Matches: 987, Mismatches: 3, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
990 247 0.25
991 708 0.72
992 15 0.02
993 17 0.02
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (991 bp):
ATACCAAATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTAC
GAAAACCCTAAACAATTAGATCTGAAACGAAACAAAAAATTAAAAGATTAGATTTTTGAATTTTC
AGATCTGAAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGT
TCTTGAAACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATT
TCGACAATCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTG
ATTCCTTAAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCA
GCACAAGTAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTG
AAATCTCGAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATG
GCAAGAAGAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAAC
TCAAGAGAGAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAAT
AATAATGATAAGTGTTTAACAAGGTGGACAGCCATGCCTTTAAATAGGCCTTATAACTAGTCCTA
ATCTAATTAGAAAACTAAAATAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGT
CATTTTATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAAT
AAATAAAAATAAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACT
AAGTATGGATGGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTAAAGAATTTG
GGCTTTTGTGACTCGT
Found at i:56242 original size:47 final size:47
Alignment explanation
Indices: 56179--56693 Score: 772
Period size: 47 Copynumber: 11.1 Consensus size: 47
56169 GAAATGATAG
*
56179 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
56226 TAAGGCCTAATAGCCGATGTGATGAATGCGAAAGTGTATATATGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
56272 -AAAGCCTAATGGCCGATGTGATGAATGTGAAAGT-TATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
56317 TAAGGCCTAATAGCCGATGTGATGAATGCG-AAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
56363 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
56410 TAAGGCCTAATAGCCGATGT-ATGAATGCGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
56456 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
56502 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
56549 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
56596 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
56643 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
56690 TAAG
1 TAAG
56694 TCCCGAAGGG
Statistics
Matches: 422, Mismatches: 40, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
44 8 0.02
45 36 0.09
46 150 0.36
47 228 0.54
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:56450 original size:93 final size:94
Alignment explanation
Indices: 56179--56640 Score: 837
Period size: 93 Copynumber: 5.0 Consensus size: 94
56169 GAAATGATAG
56179 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
56244 GTGATGAATGCGAAAGTGTATATATGTAA
66 GTGATGAATGCGAAAGTGTATATATGTAA
56273 -AA-GCCTAATGGCCGATGTGATGAATGTGAAAGT-TATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
56335 GTGATGAATGCG-AAGTGTATATATGTAA
66 GTGATGAATGCGAAAGTGTATATATGTAA
56363 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
56428 GT-ATGAATGCGAAAGTGTATATATGTAA
66 GTGATGAATGCGAAAGTGTATATATGTAA
*
56456 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
*
56520 GTGATGAATGTGAAAGTGTATATATGTAA
66 GTGATGAATGCGAAAGTGTATATATGTAA
* *
56549 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
*
56614 GTGATGAATGTGAAAGTGTATATATGT
66 GTGATGAATGCGAAAGTGTATATATGT
56641 GACGGGGCCG
Statistics
Matches: 359, Mismatches: 3, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
90 16 0.04
91 43 0.12
92 106 0.30
93 134 0.37
94 60 0.17
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.29
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
GTGATGAATGCGAAAGTGTATATATGTAA
Found at i:56478 original size:139 final size:140
Alignment explanation
Indices: 56179--56642 Score: 767
Period size: 139 Copynumber: 3.3 Consensus size: 140
56169 GAAATGATAG
*
56179 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
* *
56244 GTGATGAATGCGAAAGTGTATATATGTA-AAAGCCTAATGGCCGATGTGATGAATGTGAAAGT-T
66 GTGATGAATGTGAAAGTGTATATATGTATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
56307 ATATGTGTGA
131 ATATATGTGA
* * * *
56317 TAAGGCCTAATAGCCGATGTGATGAATGCG-AAGTGTATATATGTAATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
* * *
56381 GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGT-ATGAATGCGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
56445 TATATATGTAA
130 TATATATGTGA
56456 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
56520 GTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
56585 TATATATGTGA
130 TATATATGTGA
56596 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
56643 CGGGGCCGAG
Statistics
Matches: 300, Mismatches: 21, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
137 56 0.19
138 42 0.14
139 132 0.44
140 54 0.18
141 16 0.05
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.29
Consensus pattern (140 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
GTGATGAATGTGAAAGTGTATATATGTATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
ATATATGTGA
Found at i:60846 original size:10 final size:10
Alignment explanation
Indices: 60831--60887 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
60821 AACTCCGACC
60831 AGCTCAATTG
1 AGCTCAATTG
* *
60841 AGCTCATTTA
1 AGCTCAATTG
*
60851 AGCTCAATCG
1 AGCTCAATTG
*
60861 AGCTCAATTT
1 AGCTCAATTG
*
60871 AGCTACAATTC
1 AGCT-CAATTG
60882 AGCTCA
1 AGCTCA
60888 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 29 0.76
11 9 0.24
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (10 bp):
AGCTCAATTG
Found at i:60854 original size:20 final size:20
Alignment explanation
Indices: 60831--60891 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
60821 AACTCCGACC
60831 AGCTCAATTGAGCTCATTTA
1 AGCTCAATTGAGCTCATTTA
*
60851 AGCTCAATCGAGCTCAATTT-
1 AGCTCAATTGAGCTC-ATTTA
*
60871 AGCTACAATTCAGCTCATTTA
1 AGCT-CAATTGAGCTCATTTA
60892 TTTTATTGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (20 bp):
AGCTCAATTGAGCTCATTTA
Found at i:65304 original size:20 final size:19
Alignment explanation
Indices: 65281--65345 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
65271 AAGCTCAAAC
65281 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
65301 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
65321 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
65341 GAGCT
1 GAGCT
65346 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:67164 original size:34 final size:33
Alignment explanation
Indices: 67117--67180 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
67107 GATTACTCAC
67117 TTCACTCGTTTCTTTTAC-AGACTCTCTTTCTTT
1 TTCACTCGTTTCTTTTACAAG-CTCTCTTTCTTT
* *
67150 TTCACTTGATTTCTTTTTCAAGCTCTCTTTC
1 TTCACTCG-TTTCTTTTACAAGCTCTCTTTC
67181 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 7 0.26
34 18 0.67
35 2 0.07
ACGTcount: A:0.12, C:0.27, G:0.06, T:0.55
Consensus pattern (33 bp):
TTCACTCGTTTCTTTTACAAGCTCTCTTTCTTT
Found at i:67207 original size:21 final size:21
Alignment explanation
Indices: 67178--67233 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
67168 CAAGCTCTCT
*
67178 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
67199 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
67220 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
67234 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:67213 original size:13 final size:12
Alignment explanation
Indices: 67197--67316 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
67187 TTTTTTCGCT
67197 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
67210 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
67224 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
67235 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
67249 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
67259 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
* *
67272 TTTTCTTCTTCG
1 TTTTCTTTTTCA
*
67284 TTTTCTTTTT-G
1 TTTTCTTTTTCA
67295 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
67305 ATTTCTTTTTCA
1 TTTTCTTTTTCA
67317 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 10 0.12
12 42 0.51
13 12 0.14
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:67226 original size:14 final size:14
Alignment explanation
Indices: 67177--67233 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
67167 TCAAGCTCTC
67177 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
67190 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
67204 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
67218 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
67232 TT
1 TT
67234 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:67261 original size:18 final size:18
Alignment explanation
Indices: 67240--67298 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
67230 TTTTCTCTCA
67240 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
67258 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
67276 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
67294 GTTTT
1 CTTTT
67299 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:67315 original size:6 final size:6
Alignment explanation
Indices: 67195--67302 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
67185 TCTTTTTTCG
* * * **
67195 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
67246 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
67294 -GTTTT CTTT
1 CTTTTT CTTT
67303 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:68392 original size:22 final size:22
Alignment explanation
Indices: 68367--68409 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
68357 TTTTCTTCTT
68367 TTTTTGCTCG-ATTTTTTTTCAC
1 TTTTT-CTCGAATTTTTTTTCAC
*
68389 TTTTTCTTGAATTTTTTTTCA
1 TTTTTCTCGAATTTTTTTTCA
68410 ATCAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTTTCTCGAATTTTTTTTCAC
Found at i:68419 original size:16 final size:14
Alignment explanation
Indices: 68398--68437 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
68388 CTTTTTCTTG
68398 AATTTTTTTTCAATCA
1 AATTTTTTTT--ATCA
*
68414 AATTTTTTTTTTCA
1 AATTTTTTTTATCA
68428 AATTTTTTTT
1 AATTTTTTTT
68438 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (14 bp):
AATTTTTTTTATCA
Found at i:68436 original size:14 final size:14
Alignment explanation
Indices: 68411--68437 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
68401 TTTTTTTCAA
68411 TCAAATTTTTTTTT
1 TCAAATTTTTTTTT
68425 TCAAATTTTTTTT
1 TCAAATTTTTTTT
68438 GATTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TCAAATTTTTTTTT
Found at i:69149 original size:30 final size:30
Alignment explanation
Indices: 69115--69211 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
69105 AGCTCACTCC
69115 TAGCTCATA-TTTAGCTCACGAGCTAAAGCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * **
69145 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
69175 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
69205 TAGCTCA
1 TAGCTCA
69212 TTTTAGTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:70142 original size:22 final size:20
Alignment explanation
Indices: 70110--70158 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
70100 GCCGAATTTA
70110 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
70133 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
70153 TGAACA
1 TGAACA
70159 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:70936 original size:12 final size:11
Alignment explanation
Indices: 70919--70961 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
70909 GAAATTCGAA
70919 AAAAAAAATTTT
1 AAAAAAAA-TTT
**
70931 AAAAAAAATCA
1 AAAAAAAATTT
*
70942 AAAAAAAAATT
1 AAAAAAAATTT
70953 AAAAAAAAT
1 AAAAAAAAT
70962 CGAAGTATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTT
Found at i:70944 original size:22 final size:22
Alignment explanation
Indices: 70917--70962 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
70907 AGGAAATTCG
70917 AAAAAAAAAATTTTAAAAAAAATC
1 AAAAAAAAAA--TTAAAAAAAATC
70941 AAAAAAAAAATTAAAAAAAATC
1 AAAAAAAAAATTAAAAAAAATC
70963 GAAGTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 12 0.55
24 10 0.45
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (22 bp):
AAAAAAAAAATTAAAAAAAATC
Found at i:70945 original size:11 final size:12
Alignment explanation
Indices: 70917--70960 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
70907 AGGAAATTCG
*
70917 AAAAAAAAAATT
1 AAAAAAAAAATC
**
70929 TTAAAAAAAATC
1 AAAAAAAAAATC
*
70941 AAAAAAAAAATT
1 AAAAAAAAAATC
70953 AAAAAAAA
1 AAAAAAAA
70961 TCGAAGTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:71051 original size:38 final size:39
Alignment explanation
Indices: 70976--71053 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
70966 GTATAAAAAA
70976 AAAGGAGTGAAAAGTTTTGTGAGTTTTTATTTTGTTTTT
1 AAAGGAGTGAAAAGTTTTGTGAGTTTTTATTTTGTTTTT
71015 AAAGGAGTGAAAAGTTTTGTGAG-TTTTATTTTGTTTTT
1 AAAGGAGTGAAAAGTTTTGTGAGTTTTTATTTTGTTTTT
71053 A
1 A
71054 TTTCTTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 16 0.41
39 23 0.59
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (39 bp):
AAAGGAGTGAAAAGTTTTGTGAGTTTTTATTTTGTTTTT
Found at i:71932 original size:32 final size:30
Alignment explanation
Indices: 71863--71933 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 30
71853 ACATTCTTGT
71863 AAAGAGAAAATAAAGAAAAGAAAAAGAAAA
1 AAAGAGAAAATAAAGAAAAGAAAAAGAAAA
71893 AGCAAGAGAAGAA-AAAGAAAATGAAATAA-AAAGA
1 A--AAGAGAA-AATAAAGAAAA-GAAA-AAGAAA-A
71927 AAAGAGA
1 AAAGAGA
71934 GGCAAGAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
30 1 0.03
32 21 0.60
33 9 0.26
34 4 0.11
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.04
Consensus pattern (30 bp):
AAAGAGAAAATAAAGAAAAGAAAAAGAAAA
Found at i:72011 original size:11 final size:12
Alignment explanation
Indices: 71979--72009 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
71969 TTGAGAGAAC
71979 TTGAAAAAGCCT
1 TTGAAAAAGCCT
71991 TTGAAAAAGCCT
1 TTGAAAAAGCCT
72003 TTGAAAA
1 TTGAAAA
72010 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:72027 original size:11 final size:12
Alignment explanation
Indices: 72012--72043 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
72002 TTTGAAAAGC
72012 AAAAAGAAAATG
1 AAAAAGAAAATG
72024 AAAAAGAAAATG
1 AAAAAGAAAATG
72036 -AAAAGAAA
1 AAAAAGAAA
72044 TTTGAGAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:74200 original size:30 final size:30
Alignment explanation
Indices: 74166--74262 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
74156 AGCTCACTCC
74166 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
74196 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
74226 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
74256 TAGCTCA
1 TAGCTCA
74263 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:75192 original size:22 final size:20
Alignment explanation
Indices: 75160--75208 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
75150 GCCGAATTTA
75160 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
75183 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
75203 TGAACA
1 TGAACA
75209 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:77158 original size:23 final size:22
Alignment explanation
Indices: 77106--77158 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
77096 TCCACGTCTT
*
77106 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
77128 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
77151 TTTCTTTT
1 TTTCTTTT
77159 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:83114 original size:18 final size:20
Alignment explanation
Indices: 83076--83117 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
83066 GTATAACTGA
*
83076 ATTTATTGTGTCTCAATTTG
1 ATTTAATGTGTCTCAATTTG
83096 ATTTAATGTGT-TC-ATTTG
1 ATTTAATGTGTCTCAATTTG
83114 ATTT
1 ATTT
83118 GTGCAGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (20 bp):
ATTTAATGTGTCTCAATTTG
Found at i:83781 original size:14 final size:14
Alignment explanation
Indices: 83734--83781 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
83724 GTACGAATGG
83734 AATGGTAGGAACAA
1 AATGGTAGGAACAA
*
83748 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
83762 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
83776 ATTGGT
1 AATGGT
83782 CGGTTTAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:85201 original size:21 final size:21
Alignment explanation
Indices: 85175--85237 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
85165 TTGATATTTG
85175 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
85196 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
85217 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
85238 ACGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:89760 original size:12 final size:12
Alignment explanation
Indices: 89743--89803 Score: 72
Period size: 12 Copynumber: 5.0 Consensus size: 12
89733 AAACCGTATG
89743 CAATTTTTTTTT
1 CAATTTTTTTTT
89755 CAATTTTTTTTT
1 CAATTTTTTTTT
*
89767 CAAATTTTTTTT
1 CAATTTTTTTTT
89779 --ATTTTTTTTT
1 CAATTTTTTTTT
89789 CGAACTCTTTTTTTT
1 C-AA-T-TTTTTTTT
89804 TTACGTACCT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.21
12 23 0.55
13 1 0.02
14 1 0.02
15 8 0.19
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:89772 original size:25 final size:24
Alignment explanation
Indices: 89744--89803 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
89734 AACCGTATGC
89744 AATTTTTTTTTCAATTTTTTTTTC-A
1 AATTTTTTTTT--ATTTTTTTTTCGA
89769 AA-TTTTTTTTATTTTTTTTTCGA
1 AATTTTTTTTTATTTTTTTTTCGA
*
89792 ACTCTTTTTTTT
1 AAT-TTTTTTTT
89804 TTACGTACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 11 0.35
23 2 0.06
24 8 0.26
25 10 0.32
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (24 bp):
AATTTTTTTTTATTTTTTTTTCGA
Found at i:95931 original size:24 final size:24
Alignment explanation
Indices: 95904--95975 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
95894 AAAAAAAAGA
*
95904 AACCAGCAGCTCATTAAATTCGTC
1 AACCAGCAGCTCATTAAATCCGTC
* *
95928 AACCAGTAGCTCATTAAATCCATC
1 AACCAGCAGCTCATTAAATCCGTC
95952 AACCAGCAGCTCATTAAATCCGTC
1 AACCAGCAGCTCATTAAATCCGTC
95976 CAGGCATGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.35, C:0.31, G:0.11, T:0.24
Consensus pattern (24 bp):
AACCAGCAGCTCATTAAATCCGTC
Found at i:99570 original size:46 final size:46
Alignment explanation
Indices: 99503--99672 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 46
99493 AACCCGCCCC
* *
99503 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
* *
99549 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * ** *
99597 TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
99642 TAAGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
99673 AGATGCTCAA
Statistics
Matches: 102, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 57 0.56
47 27 0.26
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:99616 original size:93 final size:93
Alignment explanation
Indices: 99508--99678 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
99498 GCCCCTAAGT
* ** *
99508 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
99573 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
*
99601 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
99666 CGAGTTCAGATGC
66 CGAGTTCAGATGC
99679 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:104864 original size:56 final size:55
Alignment explanation
Indices: 104748--104865 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
104738 TGCATGCTTT
* * * *
104748 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
104802 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
104858 CATTAAAT
1 CATTAAAT
104866 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:105512 original size:20 final size:20
Alignment explanation
Indices: 105487--105541 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
105477 ACGAGTTAAA
* *
105487 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
105507 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
105527 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
105542 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:107061 original size:17 final size:15
Alignment explanation
Indices: 107024--107062 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
107014 TATCTCCCAC
107024 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
107040 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
107057 TCATTT
1 TCATTT
107063 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:107973 original size:13 final size:13
Alignment explanation
Indices: 107957--107981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107947 TAATTCCAAA
107957 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
107970 TTTTTTTTCTTC
1 TTTTTTTTCTTC
107982 AATACTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:108875 original size:20 final size:20
Alignment explanation
Indices: 108850--108904 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
108840 ACGAGTTAAA
* *
108850 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
108870 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
108890 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
108905 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:112832 original size:23 final size:23
Alignment explanation
Indices: 112806--112849 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
112796 TTTCTTTTGT
112806 TTCTTT-TTCTAATTCATTTTCTC
1 TTCTTTCTTC-AATTCATTTTCTC
*
112829 TTCTTTCTTCAATTCTTTTTC
1 TTCTTTCTTCAATTCATTTTC
112850 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (23 bp):
TTCTTTCTTCAATTCATTTTCTC
Found at i:115688 original size:10 final size:10
Alignment explanation
Indices: 115673--115718 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
115663 TATACAAGTT
115673 AAAAAAATAA
1 AAAAAAATAA
*
115683 AAAAAAATCA
1 AAAAAAATAA
115693 AAAAAAAT-A
1 AAAAAAATAA
115702 AAAAAAATAA
1 AAAAAAATAA
115712 AAAAAAA
1 AAAAAAA
115719 GTGATTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
9 9 0.26
10 25 0.74
ACGTcount: A:0.89, C:0.02, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:117746 original size:30 final size:30
Alignment explanation
Indices: 117712--117808 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
117702 TAAACTAAAA
117712 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
117742 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
117772 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
117801 ATGAGCTA
1 -TGAGCTA
117809 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:120000 original size:12 final size:12
Alignment explanation
Indices: 119985--120015 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
119975 TTCTTTTTGC
119985 TTTTCAAAGGCT
1 TTTTCAAAGGCT
119997 TTTTCAAAGGCT
1 TTTTCAAAGGCT
120009 TTTTCAA
1 TTTTCAA
120016 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:120092 original size:6 final size:6
Alignment explanation
Indices: 120076--120125 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
120066 TTTCTTTTTA
*
120076 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
120125 T
1 T
120126 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:120108 original size:37 final size:37
Alignment explanation
Indices: 120065--120135 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
120055 CTTGCCTCTC
120065 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
120102 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
120136 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:120136 original size:16 final size:16
Alignment explanation
Indices: 120061--120121 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
120051 GCCTCTTGCC
*
120061 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
120077 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
120093 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
120109 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
120122 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:121075 original size:24 final size:24
Alignment explanation
Indices: 121043--121093 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
121033 TTTTATATAC
*
121043 TTCGA-TTTTTTTT-AATTTTTTT
1 TTCGATTTTTTTTTAAAATTTTTT
121065 TTCGATTTTTTTTTAAAATTTTTT
1 TTCGATTTTTTTTTAAAATTTTTT
121089 TTCGA
1 TTCGA
121094 ATTTCCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 5 0.19
23 8 0.31
24 13 0.50
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (24 bp):
TTCGATTTTTTTTTAAAATTTTTT
Found at i:121096 original size:12 final size:12
Alignment explanation
Indices: 121043--121097 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
121033 TTTTATATAC
121043 TTCG-ATTTTTT
1 TTCGAATTTTTT
121054 TT--AATTTTTTT
1 TTCGAA-TTTTTT
*
121065 TTCGATTTTTTT
1 TTCGAATTTTTT
**
121077 TTAAAATTTTTT
1 TTCGAATTTTTT
121089 TTCGAATTT
1 TTCGAATTT
121098 CCTCTTCTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
10 1 0.03
11 10 0.29
12 22 0.65
13 1 0.03
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (12 bp):
TTCGAATTTTTT
Found at i:122809 original size:30 final size:30
Alignment explanation
Indices: 122775--122862 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
122765 TAAACTAAAA
122775 TGAGCTAAGCTTTAGCCCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCCCGTGAGCTAAAGT
* * * * *
122805 TGAGCTGAGGC-TAAACTCC-TAAGCTGAAGT
1 TGAGCT-AAGCTTTAGC-CCGTGAGCTAAAGT
* *
122835 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
1 TGAGCTAAGCTTTAGCCCGTGAGCTAAA
122863 AATATGAGCT
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
29 3 0.07
30 34 0.81
31 5 0.12
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCCCGTGAGCTAAAGT
Found at i:126770 original size:15 final size:15
Alignment explanation
Indices: 126750--126797 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
126740 TCAAAGATGG
126750 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
126765 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
126779 GTTTATGGATATAAA
1 GTTTATGGATATGAA
126794 GTTT
1 GTTT
126798 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:126784 original size:14 final size:14
Alignment explanation
Indices: 126744--126787 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
126734 AAGGATTCAA
126744 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
126758 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
126773 AGATGGGTTTATGG
1 AGATGGGTTTATGG
126787 A
1 A
126788 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:126813 original size:29 final size:29
Alignment explanation
Indices: 126744--126803 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
126734 AAGGATTCAA
*
126744 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
126773 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
126802 AG
1 AG
126804 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:128701 original size:21 final size:21
Alignment explanation
Indices: 128652--128718 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
128642 CCTCTTTGAA
* * *
128652 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
128675 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
128696 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
128717 CC
1 CC
128719 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:129561 original size:14 final size:14
Alignment explanation
Indices: 129519--129563 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
129509 TTAAAGAAGC
129519 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
129533 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
129546 AACTCATTTAATTA
1 AACTCATTAAATTA
129560 AACT
1 AACT
129564 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:132042 original size:18 final size:18
Alignment explanation
Indices: 132021--132070 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
132011 AAACTCTTTT
132021 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
132039 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
132057 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
132071 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:132076 original size:24 final size:24
Alignment explanation
Indices: 131996--132073 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
131986 CTTGTTCACA
*
131996 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
132020 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
132044 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
132068 TTCTTT
1 TTCTTT
132074 TTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:132198 original size:12 final size:12
Alignment explanation
Indices: 132181--132214 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
132171 TGTTCTTTTT
*
132181 CTTTTTCAATGG
1 CTTTTTCAATGA
132193 CTTTTTCAATGA
1 CTTTTTCAATGA
*
132205 CTTTCTCAAT
1 CTTTTTCAAT
132215 CTCTTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.50
Consensus pattern (12 bp):
CTTTTTCAATGA
Found at i:133394 original size:15 final size:15
Alignment explanation
Indices: 133374--133421 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
133364 TCAAAGATGG
133374 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
133389 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
133403 GTTTATGGATATAAA
1 GTTTATGGATATGAA
133418 GTTT
1 GTTT
133422 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:133408 original size:14 final size:14
Alignment explanation
Indices: 133368--133411 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
133358 AAGGATTCAA
133368 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
133382 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
133397 AGATGGGTTTATGG
1 AGATGGGTTTATGG
133411 A
1 A
133412 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:133437 original size:29 final size:29
Alignment explanation
Indices: 133368--133427 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
133358 AAGGATTCAA
*
133368 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
133397 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
133426 AG
1 AG
133428 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:134434 original size:14 final size:14
Alignment explanation
Indices: 134392--134436 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
134382 TTAAAGAAGC
134392 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
134406 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
134419 AACTCATTTAATTA
1 AACTCATTAAATTA
134433 AACT
1 AACT
134437 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:137292 original size:14 final size:14
Alignment explanation
Indices: 137270--137317 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
137260 ACCTAAACCG
* *
137270 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
137284 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
137298 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
137312 ACCATT
1 ACCATT
137318 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:139152 original size:17 final size:18
Alignment explanation
Indices: 139132--139170 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
139122 TGCACACACA
139132 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
139149 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
139167 AATT
1 AATT
139171 TTCAATTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:140348 original size:16 final size:16
Alignment explanation
Indices: 140327--140358 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
140317 TAATGTGTTT
*
140327 TGCTGCTGTTGTTTAA
1 TGCTGCTATTGTTTAA
140343 TGCTGCTATTGTTTAA
1 TGCTGCTATTGTTTAA
140359 ATGCAGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.22, T:0.50
Consensus pattern (16 bp):
TGCTGCTATTGTTTAA
Found at i:140653 original size:73 final size:72
Alignment explanation
Indices: 140545--140715 Score: 177
Period size: 72 Copynumber: 2.4 Consensus size: 72
140535 GCAGGTACAT
* * * * *
140545 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACAGCATTTAAAGAAAAGGTGGCTGCTGCA-TTTTCCAAACCAGCCAAATTTAGTGAGTGCAT
140610 GGGACTTG
65 GGGACTTG
* * * * * *
140618 GGACAGCATTTAAAGCGAAA-GTTGCTGTTGTATTTTCCCAACCAGCCAAATTTAGTGTGTGCAT
1 GGACAGCATTTAAAG-AAAAGGTGGCTGCTGCATTTTCCAAACCAGCCAAATTTAGTGAGTGCAT
140682 GGGACTTG
65 GGGACTTG
* * *
140690 GGATAGCA-TTAAA-AAGAGGAGGCTGC
1 GGACAGCATTTAAAGAAAAGGTGGCTGC
140716 CGTTGCAATT
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
69 2 0.03
70 5 0.06
71 5 0.06
72 41 0.52
73 23 0.29
74 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (72 bp):
GGACAGCATTTAAAGAAAAGGTGGCTGCTGCATTTTCCAAACCAGCCAAATTTAGTGAGTGCATG
GGACTTG
Found at i:144320 original size:12 final size:12
Alignment explanation
Indices: 144302--144335 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
144292 TCCCTCGTTT
144302 CTTTTCACTCAC
1 CTTTTCACTCAC
* *
144314 TTTTTCACACAC
1 CTTTTCACTCAC
144326 CTTTTCACTC
1 CTTTTCACTC
144336 TTTTCTTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTTTCACTCAC
Found at i:145286 original size:14 final size:14
Alignment explanation
Indices: 145269--145308 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
145259 CGAATGGAAT
*
145269 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
*
145283 GGTAGGAACAAAAT
1 GGTAGGAACAAAAG
*
145297 GGTATGAACAAA
1 GGTAGGAACAAA
145309 TTGATCGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.07, G:0.33, T:0.12
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:149702 original size:30 final size:30
Alignment explanation
Indices: 149668--149764 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
149658 AAAACTAAAA
149668 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
149698 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
149728 TGAGCTAAGCTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
149757 ATGAGCTA
1 -TGAGCTA
149765 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:152034 original size:6 final size:6
Alignment explanation
Indices: 152018--152067 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
152008 TTTCTTTTTA
*
152018 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
152067 T
1 T
152068 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:152050 original size:37 final size:37
Alignment explanation
Indices: 152007--152077 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
151997 CTTGCCTCTC
152007 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
152044 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
152078 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:152078 original size:16 final size:16
Alignment explanation
Indices: 152003--152063 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
151993 GCCTCTTGCC
*
152003 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
152019 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
152035 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
152051 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
152064 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:152993 original size:11 final size:11
Alignment explanation
Indices: 152977--153019 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
152967 ATATACTTCG
152977 ATTTTTTTTTA
1 ATTTTTTTTTA
**
152988 ATTTTTTTTCG
1 ATTTTTTTTTA
**
152999 ATTTTTTTAAA
1 ATTTTTTTTTA
153010 ATTTTTTTTT
1 ATTTTTTTTT
153020 TCGAATTTCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTTA
Found at i:152998 original size:22 final size:22
Alignment explanation
Indices: 152973--153018 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
152963 TTTTATATAC
**
152973 TTCGATTTTTTTTTAATTTTTT
1 TTCGATTTTTTTAAAATTTTTT
152995 TTCGATTTTTTTAAAATTTTTT
1 TTCGATTTTTTTAAAATTTTTT
153017 TT
1 TT
153019 TTCGAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (22 bp):
TTCGATTTTTTTAAAATTTTTT
Found at i:162391 original size:30 final size:30
Alignment explanation
Indices: 162357--162453 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
162347 AAAACTAAAA
162357 TGAGCTAAGCTTTAGATCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGATCGTGAGCTAAAGT
* * * * *
162387 TGAGCTGAGGC--TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGA-TCGTGAGCTAAAGT
*
162417 TGAGCTAAGCTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGATCGTGAGCTAAAGT
162446 ATGAGCTA
1 -TGAGCTA
162454 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
29 7 0.14
30 39 0.76
31 5 0.10
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGATCGTGAGCTAAAGT
Found at i:164155 original size:11 final size:10
Alignment explanation
Indices: 164130--164190 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
164120 ACCAATAAAA
164130 TAAA-TGAGC
1 TAAATTGAGC
*
164139 TGAATTGTAGC
1 TAAATTG-AGC
164150 TAAATTGAGC
1 TAAATTGAGC
**
164160 TCGATTGAGC
1 TAAATTGAGC
164170 TGAAA-TGAGC
1 T-AAATTGAGC
*
164180 TCAATTGAGC
1 TAAATTGAGC
164190 T
1 T
164191 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:164191 original size:20 final size:20
Alignment explanation
Indices: 164131--164191 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
164121 CCAATAAAAT
*
164131 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
164151 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
164172 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
164192 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:166282 original size:18 final size:18
Alignment explanation
Indices: 166261--166295 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
166251 TTTTTCTTTT
166261 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
166279 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
166296 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:167208 original size:16 final size:15
Alignment explanation
Indices: 167189--167281 Score: 62
Period size: 16 Copynumber: 6.6 Consensus size: 15
167179 TTTAACTTGA
*
167189 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCA-AT
167205 TTTTTTTTGCTCAA-
1 TTTTTTTTGCTCAAT
*
167219 -TTTTTTT--TCACT
1 TTTTTTTTGCTCAAT
167231 TTTTTTTTG---AAT
1 TTTTTTTTGCTCAAT
167243 TTTTTTTT-CAATCAAT
1 TTTTTTTTGC--TCAAT
167259 TTTTTTTT--TCGAAT
1 TTTTTTTTGCTC-AAT
167273 TTTTTTTTG
1 TTTTTTTTG
167282 ATTTTTTTGT
Statistics
Matches: 64, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
11 3 0.05
12 10 0.16
13 16 0.25
14 11 0.17
16 24 0.38
ACGTcount: A:0.13, C:0.12, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTTTTTTGCTCAAT
Found at i:167222 original size:14 final size:13
Alignment explanation
Indices: 167205--167279 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 13
167195 TTGCTCACCT
167205 TTTTTTTTGCTCAA
1 TTTTTTTT-CTCAA
*
167219 -TTTTTTT-TCAC
1 TTTTTTTTCTCAA
*
167230 TTTTTTTT-TGAA
1 TTTTTTTTCTCAA
167242 TTTTTTTTTCAATCAA
1 -TTTTTTTTC--TCAA
*
167258 TTTTTTTTTTCGAA
1 TTTTTTTTCTC-AA
167272 TTTTTTTT
1 TTTTTTTT
167280 TGATTTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
11 3 0.06
12 9 0.18
13 17 0.34
14 10 0.20
15 8 0.16
16 3 0.06
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCTCAA
Found at i:167234 original size:12 final size:12
Alignment explanation
Indices: 167205--167254 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
167195 TTGCTCACCT
167205 TTTTTTTTGCTCAA
1 TTTTTTTT--TCAA
*
167219 -TTTTTTTTCAC
1 TTTTTTTTTCAA
*
167230 TTTTTTTTTGAA
1 TTTTTTTTTCAA
167242 TTTTTTTTTCAA
1 TTTTTTTTTCAA
167254 T
1 T
167255 CAATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 3 0.10
12 21 0.68
13 7 0.23
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:167285 original size:11 final size:13
Alignment explanation
Indices: 167219--167289 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 13
167209 TTTTGCTCAA
*
167219 TTTTTTTTC-ACT
1 TTTTTTTTCGAAT
167231 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
*
167243 TTTTTTTTCAATCAATT
1 TTTTTTTTC---GAA-T
167260 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
167273 TTTTTTTT-G-AT
1 TTTTTTTTCGAAT
167284 TTTTTT
1 TTTTTT
167290 GTTACTCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
11 8 0.16
12 19 0.38
13 9 0.18
14 2 0.04
16 2 0.04
17 10 0.20
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:168092 original size:4 final size:4
Alignment explanation
Indices: 168083--168116 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
168073 AAGTTTTATT
168083 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
168117 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:168124 original size:22 final size:22
Alignment explanation
Indices: 168066--168125 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
168056 AAGTGGCCCA
*
168066 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
168090 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
168111 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
168126 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:168725 original size:20 final size:20
Alignment explanation
Indices: 168669--168725 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
168659 AGCTCCGTTT
* *
168669 AGCTCATTTCCAGCTCACTCG
1 AGCTCAATT-CAGCTCACTCA
* * *
168690 AGCTCAAGTCAACTCATTCA
1 AGCTCAATTCAGCTCACTCA
168710 AGCTCAATTCAGCTCA
1 AGCTCAATTCAGCTCA
168726 ATCTTAACCC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.26
Consensus pattern (20 bp):
AGCTCAATTCAGCTCACTCA
Found at i:181522 original size:11 final size:11
Alignment explanation
Indices: 181491--181535 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
181481 CATAAATCAC
*
181491 TTTTTTTTTCAA
1 TTTTTTTTT-GA
181503 TTTTTTTTTGA
1 TTTTTTTTTGA
181514 TTTTTTTTTGAA
1 TTTTTTTTTG-A
181526 TTTTGTTTTT
1 TTTT-TTTTT
181536 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.37
12 14 0.47
13 5 0.17
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:181543 original size:23 final size:22
Alignment explanation
Indices: 181491--181546 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
181481 CATAAATCAC
181491 TTTTTTTTTCAATTTTTTTTTGA
1 TTTTTTTTTCAATTTTTTTTT-A
* *
181514 TTTTTTTTTGAATTTTGTTTTTT
1 TTTTTTTTTCAATTTT-TTTTTA
181537 TTATTTTTTT
1 TT-TTTTTTT
181547 AACTCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (22 bp):
TTTTTTTTTCAATTTTTTTTTA
Found at i:181545 original size:11 final size:11
Alignment explanation
Indices: 181491--181548 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
181481 CATAAATCAC
181491 TTTTTTTTTCAA
1 TTTTTTTTT-AA
*
181503 TTTTTTTTTGA
1 TTTTTTTTTAA
181514 TTTTTTTTTGAA
1 TTTTTTTTT-AA
*
181526 TTTTGTTTTT-T
1 TTTT-TTTTTAA
181537 TTATTTTTTTAA
1 TT-TTTTTTTAA
181549 CTCTTATAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 17 0.45
12 16 0.42
13 5 0.13
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTAA
Done.