Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 160 of 226
Found at i:49604901 original size:107 final size:107
Alignment explanation
Indices: 49604683--49604890 Score: 307
Period size: 107 Copynumber: 2.0 Consensus size: 107
49604673 GCTTGGGCTA
* * *
49604683 TAAAATTACCGAAATACCCTCGAAGGGAAAAATTATCGAAATACCCTCGAAGGGTAAAATTATCA
1 TAAAATTACCGAAATACCCTCGAAGGGAAAAATTATCAAAATACCCTCAAAGGGTAAAATTACCA
* *
49604748 AAATACCCCCACTAGGTAAAATTACAGAAATACCCTCAAAGG
66 AAATACCCCCACAAGGTAAAATTACAGAAATACCCCCAAAGG
*
49604790 TAAAATTACCGAAATACCCTCGAAGGGTAAAATTA-CTAAAATACCCTCAAAGGGTAAAATTACC
1 TAAAATTACCGAAATACCCTCGAAGGGAAAAATTATC-AAAATACCCTCAAAGGGTAAAATTACC
49604854 AAAATA-CCCCA-AAGGTTAAAATTATC-GAAATACCCCC
65 AAAATACCCCCACAAGG-TAAAATTA-CAGAAATACCCCC
49604891 GATGGGTAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
105 3 0.03
106 24 0.26
107 65 0.71
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.20
Consensus pattern (107 bp):
TAAAATTACCGAAATACCCTCGAAGGGAAAAATTATCAAAATACCCTCAAAGGGTAAAATTACCA
AAATACCCCCACAAGGTAAAATTACAGAAATACCCCCAAAGG
Found at i:49604913 original size:80 final size:80
Alignment explanation
Indices: 49604683--49604934 Score: 298
Period size: 80 Copynumber: 3.1 Consensus size: 80
49604673 GCTTGGGCTA
* * *
49604683 TAAAATTACCGAAATACCCTCGAAGGGAAAAATTATCGAAATACCCTCGAAGGGTAAAATTA-TC
1 TAAAATTACCAAAATACCCTC-AAAGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACT-
49604747 AAAATACCCCCACTA-GG
64 AAAATA-CCCCACTAGGG
*
49604764 TAAAATTA-CAGAAATACCCTCAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACTA
1 TAAAATTACCA-AAATACCCTCAAAGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTA
*
49604828 AAATACCCTCA-AAGGG
65 AAATACCC-CACTAGGG
* * ** *
49604844 TAAAATTACCAAAATACCC-CAAAGGTTAAAATTATCGAAATACCCCCGATGGGTAAAACGACTG
1 TAAAATTACCAAAATACCCTCAAAGG-TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTA
* *
49604908 TAATACCCCATTAGGG
65 AAATACCCCACTAGGG
*
49604924 TAAAATAACCA
1 TAAAATTACCA
49604935 TGATGCCCCT
Statistics
Matches: 150, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
79 12 0.08
80 117 0.78
81 21 0.14
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.20
Consensus pattern (80 bp):
TAAAATTACCAAAATACCCTCAAAGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTAA
AATACCCCACTAGGG
Found at i:49610808 original size:24 final size:24
Alignment explanation
Indices: 49610753--49610799 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
49610743 CCCTCAAGGT
* *
49610753 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACTGATTTGTCTATGATG
49610777 TAAATGACTGATTTGTCTATGAT
1 TAAATGACTGATTTGTCTATGAT
49610800 TTGTATGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTATGATG
Found at i:49610813 original size:24 final size:24
Alignment explanation
Indices: 49610753--49610813 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
49610743 CCCTCAAGGT
** *
49610753 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACCGATTTGTCTATGATG
* *
49610777 TAAATGACTGATTTGTCTATGATT
1 TAAATGACCGATTTGTCTATGATG
**
49610801 TGTATGACCGATT
1 TAAATGACCGATT
49610814 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.44
Consensus pattern (24 bp):
TAAATGACCGATTTGTCTATGATG
Found at i:49610958 original size:26 final size:26
Alignment explanation
Indices: 49610929--49610994 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
49610919 TTGGCCACAT
* *
49610929 ATACTATTAATGGCAGCTTTACTGCG
1 ATACTATTGATGGCAGCTTTACTACG
* * *
49610955 ATACTGTTGCTGGCAGCTTTGCTACG
1 ATACTATTGATGGCAGCTTTACTACG
*
49610981 ATGCTATTGATGGC
1 ATACTATTGATGGC
49610995 TTTGTGACGG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (26 bp):
ATACTATTGATGGCAGCTTTACTACG
Found at i:49611043 original size:32 final size:33
Alignment explanation
Indices: 49610988--49611077 Score: 105
Period size: 32 Copynumber: 2.8 Consensus size: 33
49610978 ACGATGCTAT
* ** * *
49610988 TGATGGCTTTGTGACGGTTATATTACCT-TTAC
1 TGATGGCTTTGTGCCAATCATATTACCTACTAC
49611020 TGATGG-TTGTGTGCCAATCATATTA-CTACTAC
1 TGATGGCTT-TGTGCCAATCATATTACCTACTAC
49611052 TGATGGCTTTGTGCCAATCATATTAC
1 TGATGGCTTTGTGCCAATCATATTAC
49611078 TGTACTTATG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
31 4 0.08
32 43 0.88
33 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (33 bp):
TGATGGCTTTGTGCCAATCATATTACCTACTAC
Found at i:49611078 original size:32 final size:32
Alignment explanation
Indices: 49611017--49611078 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
49611007 ATATTACCTT
49611017 TACTGATGGTTGTGTGCCAATCATATTACTAC
1 TACTGATGGTTGTGTGCCAATCATATTACTAC
49611049 TACTGATGGCTT-TGTGCCAATCATATTACT
1 TACTGATGG-TTGTGTGCCAATCATATTACT
49611079 GTACTTATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (32 bp):
TACTGATGGTTGTGTGCCAATCATATTACTAC
Found at i:49624376 original size:6 final size:6
Alignment explanation
Indices: 49624365--49624457 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
49624355 CTTTTCATAG
* * * * *
49624365 TTTTAT TTTTAT TTCTAAT TTTTAT CTTTAT CTTTCAT TTTGA- TTTAAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT
* * * * * *
49624414 TTTAAT TTTAAT CTTTAT TTTTAA TTTTAT TGTTAA TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
49624458 ATTTTATTAA
Statistics
Matches: 68, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
5 4 0.06
6 55 0.81
7 9 0.13
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (6 bp):
TTTTAT
Found at i:49624387 original size:19 final size:18
Alignment explanation
Indices: 49624365--49624441 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 18
49624355 CTTTTCATAG
*
49624365 TTTTATTTTTATTTCTAAT
1 TTTTATCTTTATTT-TAAT
*
49624384 TTTTATCTTTATCTTTCAT
1 TTTTATCTTTAT-TTTAAT
* *
49624403 TTTGAT-TTAATTTTAAT
1 TTTTATCTTTATTTTAAT
*
49624420 TTTAATCTTTATTTTTAAT
1 TTTTATCTTTA-TTTTAAT
49624439 TTT
1 TTT
49624442 ATTGTTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
17 10 0.21
18 7 0.15
19 29 0.60
20 2 0.04
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.70
Consensus pattern (18 bp):
TTTTATCTTTATTTTAAT
Found at i:49624420 original size:36 final size:37
Alignment explanation
Indices: 49624347--49624454 Score: 109
Period size: 36 Copynumber: 3.0 Consensus size: 37
49624337 TTTCTAATTC
* * *
49624347 ATTTTAATCTTT-TC-ATAGTTTTATT-TTTATTTCTA
1 ATTTTAATCTTTATCTTTAATTTTATTGTTAATTT-TA
* *
49624382 ATTTTTATCTTTATCTTTCATTTTGA-T-TTAATTTTA
1 ATTTTAATCTTTATCTTTAATTTT-ATTGTTAATTTTA
*
49624418 ATTTTAATCTTTATTTTTAATTTTATTGTTAATTTTA
1 ATTTTAATCTTTATCTTTAATTTTATTGTTAATTTTA
49624455 TTTATTTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
35 12 0.20
36 26 0.43
37 21 0.35
38 1 0.02
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (37 bp):
ATTTTAATCTTTATCTTTAATTTTATTGTTAATTTTA
Found at i:49624425 original size:12 final size:12
Alignment explanation
Indices: 49624365--49624454 Score: 62
Period size: 13 Copynumber: 7.4 Consensus size: 12
49624355 CTTTTCATAG
*
49624365 TTTT-ATTTTTA
1 TTTTAATTTTAA
*
49624376 TTTCTAATTTTTA
1 TTT-TAATTTTAA
*
49624389 TCTTT-ATCTTTCA
1 T-TTTAAT-TTTAA
*
49624402 TTTTGA-TTTAA
1 TTTTAATTTTAA
49624413 TTTTAATTTTAA
1 TTTTAATTTTAA
*
49624425 TCTTTATTTTTAA
1 T-TTTAATTTTAA
49624438 TTTT-ATTGTTAA
1 TTTTAATT-TTAA
49624450 TTTTA
1 TTTTA
49624455 TTTATTTTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
11 14 0.22
12 23 0.35
13 26 0.40
14 2 0.03
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTAATTTTAA
Found at i:49624452 original size:19 final size:19
Alignment explanation
Indices: 49624375--49624453 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 19
49624365 TTTTATTTTT
* * *
49624375 ATTTCTAATTTTTATCTTT
1 ATTTTTAATTTTAATCTTA
* * *
49624394 ATCTTTCATTTTGAT-TTA
1 ATTTTTAATTTTAATCTTA
*
49624412 A-TTTTAATTTTAATCTTT
1 ATTTTTAATTTTAATCTTA
* *
49624430 ATTTTTAATTTTATTGTTA
1 ATTTTTAATTTTAATCTTA
49624449 ATTTT
1 ATTTT
49624454 ATTTATTTTA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
17 10 0.22
18 6 0.13
19 30 0.65
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTTTTAATTTTAATCTTA
Found at i:49624455 original size:12 final size:11
Alignment explanation
Indices: 49624365--49624465 Score: 73
Period size: 12 Copynumber: 8.6 Consensus size: 11
49624355 CTTTTCATAG
*
49624365 TTTTATTTTTA
1 TTTTATTTTAA
*
49624376 TTTCTAATTTTTA
1 TTT-T-ATTTTAA
*
49624389 TCTTTATCTTTCA
1 T-TTTAT-TTTAA
49624402 TTTTGA-TTTAA
1 TTTT-ATTTTAA
49624413 TTTTAATTTTAA
1 TTTT-ATTTTAA
49624425 TCTTTATTTTTAA
1 T-TTTA-TTTTAA
49624438 TTTTATTGTTAA
1 TTTTATT-TTAA
49624450 TTTTA-TTT-A
1 TTTTATTTTAA
49624459 TTTTATT
1 TTTTATT
49624466 AAAAGGGGTC
Statistics
Matches: 77, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
9 6 0.08
10 3 0.04
11 15 0.19
12 26 0.34
13 25 0.32
14 2 0.03
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:49626456 original size:25 final size:24
Alignment explanation
Indices: 49626416--49626463 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
49626406 TTTCTTTAGT
*
49626416 TTTTATTTCTCTTTAGTTTTTTAA
1 TTTTATTTCTCTTTAGTATTTTAA
49626440 TTTTATTTCT-TAGTTAGTATTTTA
1 TTTTATTTCTCT--TTAGTATTTTA
49626464 CTTTCGCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 10 0.48
25 10 0.48
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (24 bp):
TTTTATTTCTCTTTAGTATTTTAA
Found at i:49641442 original size:42 final size:42
Alignment explanation
Indices: 49641395--49641479 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
49641385 GGGTGTTACA
* **
49641395 TTTAGTGGTATTAGAGCTTGCAGGTTTAGTCGATTCTCAGAC
1 TTTAGTGGTATCAGAGCTTGCAGGTTTAACCGATTCTCAGAC
49641437 TTTAGTGGTATCAGAGCTTGCAGGTTTAACCGATTCTCAGAC
1 TTTAGTGGTATCAGAGCTTGCAGGTTTAACCGATTCTCAGAC
49641479 T
1 T
49641480 AAATCGAGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.36
Consensus pattern (42 bp):
TTTAGTGGTATCAGAGCTTGCAGGTTTAACCGATTCTCAGAC
Found at i:49646465 original size:15 final size:16
Alignment explanation
Indices: 49646441--49646484 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
49646431 TAATGTTGTA
*
49646441 TTATATATATAATATT
1 TTATATATATAATATG
49646457 TTA-ATATAT-ATATG
1 TTATATATATAATATG
49646471 TTATATATTATAAT
1 TTATATA-TATAAT
49646485 TAATAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.29
15 9 0.38
16 6 0.25
17 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTATATATATAATATG
Found at i:49657922 original size:13 final size:13
Alignment explanation
Indices: 49657904--49657932 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
49657894 AAATATCCAT
49657904 GTTTTAGAAAATG
1 GTTTTAGAAAATG
49657917 GTTTTAGAAAATG
1 GTTTTAGAAAATG
49657930 GTT
1 GTT
49657933 GCGGCTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (13 bp):
GTTTTAGAAAATG
Found at i:49660021 original size:14 final size:16
Alignment explanation
Indices: 49659992--49660023 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
49659982 TTTTCTATCC
49659992 TATTTTGATAATTATT
1 TATTTTGATAATTATT
49660008 TATTTT-AT-ATTATT
1 TATTTTGATAATTATT
49660022 TA
1 TA
49660024 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TATTTTGATAATTATT
Found at i:49661377 original size:10 final size:10
Alignment explanation
Indices: 49661364--49661432 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
49661354 AAAATTCTCA
49661364 AAAATTTATT
1 AAAATTTATT
49661374 AAAA--TATT
1 AAAATTTATT
49661382 AAAATATTA-T
1 AAAAT-TTATT
*
49661392 AAAATTT-TG
1 AAAATTTATT
*
49661401 AAAA-TTATAG
1 AAAATTTAT-T
*
49661411 AAAATGTA-T
1 AAAATTTATT
49661420 AAAATTTATT
1 AAAATTTATT
49661430 AAA
1 AAA
49661433 TATAATAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
8 10 0.21
9 14 0.30
10 19 0.40
11 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (10 bp):
AAAATTTATT
Found at i:49661409 original size:17 final size:18
Alignment explanation
Indices: 49661364--49661485 Score: 54
Period size: 19 Copynumber: 6.6 Consensus size: 18
49661354 AAAATTCTCA
49661364 AAAAT-TTATTAAAATATT
1 AAAATATTA-TAAAATATT
*
49661382 AAAATATTATAAAATTTT
1 AAAATATTATAAAATATT
* *
49661400 GAAAAT-TATAGAAAATGTAT
1 -AAAATAT-TATAAAATAT-T
*
49661420 AAAAT-TTATTAAATA-T
1 AAAATATTATAAAATATT
* * *
49661436 AATAATGTTTTAAAAAATT
1 AA-AATATTATAAAATATT
* * *
49661455 ATAAAAACTATTAAATATTAT
1 A-AAATATTATAAAATA-T-T
49661476 AAAATATTAT
1 AAAATATTAT
49661486 TCATTTGTTA
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
16 3 0.04
17 3 0.04
18 27 0.35
19 32 0.42
20 10 0.13
21 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATATTATAAAATATT
Found at i:49661415 original size:47 final size:47
Alignment explanation
Indices: 49661354--49661485 Score: 112
Period size: 47 Copynumber: 2.8 Consensus size: 47
49661344 AGGATTATAT
* * *
49661354 AAAATTCTCAAAAATTTATTAAAATATTAAAATATTATAAAATTTT-G
1 AAAATTAT-AAAAATCTATTAAAATATTAAAATATTATAAAATTTTAA
* * **
49661401 AAAATTATAGAAAATGTA-TAAAAT-TTATTAAATATAATAATGTTTTAA
1 AAAATTATA-AAAATCTATTAAAATATTA--AAATATTATAAAATTTTAA
49661449 AAAATTATAAAAA-CTATT-AAATATTATAAAATATTAT
1 AAAATTATAAAAATCTATTAAAATA-T-TAAAATATTAT
49661486 TCATTTGTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
45 3 0.04
46 13 0.19
47 41 0.59
48 10 0.14
49 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.39
Consensus pattern (47 bp):
AAAATTATAAAAATCTATTAAAATATTAAAATATTATAAAATTTTAA
Found at i:49661572 original size:30 final size:30
Alignment explanation
Indices: 49661530--49661598 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
49661520 ATATTATAAA
*
49661530 AATTAGAAATGATAGAAAAT-TATATAAAAAT
1 AATTA-AAATGATAAAAAATCTATA-AAAAAT
*
49661561 AATTAAAATGATAAAAAATCTATAAAAATT
1 AATTAAAATGATAAAAAATCTATAAAAAAT
*
49661591 AATAAAAA
1 AATTAAAA
49661599 AAACTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (30 bp):
AATTAAAATGATAAAAAATCTATAAAAAAT
Found at i:49661928 original size:19 final size:19
Alignment explanation
Indices: 49661904--49661978 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
49661894 GTAGTAATAT
49661904 TTATTAAAAAGTT-TAAAAA
1 TTATTAAAAA-TTATAAAAA
*
49661923 TTATTAGAAATTAGTAAAATA
1 TTATTAAAAATTA-TAAAA-A
* * *
49661944 TTATAAAAAAATTATATAAG
1 TTAT-TAAAAATTATAAAAA
49661964 TTATTAAAAAATTAT
1 TTATT-AAAAATTAT
49661979 TAAATGTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.04
19 9 0.20
20 18 0.40
21 9 0.20
22 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
TTATTAAAAATTATAAAAA
Found at i:49661972 original size:31 final size:32
Alignment explanation
Indices: 49661918--49661978 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
49661908 TAAAAAGTTT
*
49661918 AAAAATTATTAGAAATTAGTAAAATATTATAA
1 AAAAATTATTAGAAATTAGTAAAAAATTATAA
* * *
49661950 AAAAATTA-TATAAGTTATTAAAAAATTAT
1 AAAAATTATTAGAAATTAGTAAAAAATTAT
49661979 TAAATGTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (32 bp):
AAAAATTATTAGAAATTAGTAAAAAATTATAA
Found at i:49661978 original size:11 final size:11
Alignment explanation
Indices: 49661918--49661982 Score: 55
Period size: 11 Copynumber: 6.2 Consensus size: 11
49661908 TAAAAAGTTT
49661918 AAAAATTATT-
1 AAAAATTATTA
* *
49661928 AGAAATTAGTA
1 AAAAATTATTA
* *
49661939 AAATATTATAA
1 AAAAATTATTA
49661950 AAAAATTA-T-
1 AAAAATTATTA
* *
49661959 ATAAGTTATTA
1 AAAAATTATTA
49661970 AAAAATTATTA
1 AAAAATTATTA
49661981 AA
1 AA
49661983 TGTCATAAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
9 6 0.15
10 9 0.22
11 25 0.62
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:49662003 original size:20 final size:21
Alignment explanation
Indices: 49661930--49662003 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 21
49661920 AAATTATTAG
* *
49661930 AAATTAGTAAAATATTATAAAA
1 AAATTA-TAAAATGTCATAAAA
* * *
49661952 AAATTATATAA-GTTATTAAA
1 AAATTATAAAATGTCATAAAA
*
49661972 AAATTATTAAATGTCATAAAA
1 AAATTATAAAATGTCATAAAA
49661993 AAATT-TAAAAT
1 AAATTATAAAAT
49662004 TAATGCTCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 21 0.49
21 16 0.37
22 6 0.14
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATTATAAAATGTCATAAAA
Found at i:49664243 original size:14 final size:14
Alignment explanation
Indices: 49664224--49664253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49664214 TCAGTATTAC
49664224 AAAATTAAATTATA
1 AAAATTAAATTATA
*
49664238 AAAATTAAATTTTA
1 AAAATTAAATTATA
49664252 AA
1 AA
49664254 TTTCGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATTAAATTATA
Found at i:49666969 original size:21 final size:19
Alignment explanation
Indices: 49666932--49667006 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
49666922 AATCATATAT
49666932 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
49666951 TCCAAGATTGCATATATCATA
1 TCCAAGATTGC--ATATCATA
*
49666972 TCTAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
*
49666991 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
49667007 CTTGAAGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 35 0.66
21 18 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:49667428 original size:44 final size:42
Alignment explanation
Indices: 49667353--49667732 Score: 227
Period size: 44 Copynumber: 8.9 Consensus size: 42
49667343 GACTTGTATC
* *
49667353 TTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTACCT
1 TTCGATCTACTTCGCCA--A-TACATGAAGACAAGATCTGCT-CCT
* * **
49667399 TT-GATCTATTTCATGCCGATACATGAAGACAAGATCTGCTTTT
1 TTCGATCTACTTC--GCCAATACATGAAGACAAGATCTGCTCCT
*
49667442 TTCGATCTACTTCGCCAATACATGAAGACAAGA-C--CTAC-
1 TTCGATCTACTTCGCCAATACATGAAGACAAGATCTGCTCCT
* * *** *
49667480 -T---TC-AC--CACCAGTATGGGAAGACAAGATCTGCT-AT
1 TTCGATCTACTTCGCCAATACATGAAGACAAGATCTGCTCCT
* * *
49667514 CTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTATCA
1 -TTCGATCTACTT--CGCCAATACATGAAGACAAGATCTGCT-CCT
*
49667560 TT-GATCTACTTCACGCCAATACATGAAGACAAGATCTGCT-TT
1 TTCGATCTACTT--CGCCAATACATGAAGACAAGATCTGCTCCT
*** *
49667602 CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCT-AT
1 -TTCGATCTACTTCGCCA--A-TACATGAAGACAAGATCTGCTCCT
*
49667647 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCT
1 -TTCGATCTACTT--CGCCAATACATGAAGACAAGATCTGCT-CCT
* *
49667693 TT-GATCCACTTCACGCCAATACATGAAGACAAGATTTGCT
1 TTCGATCTACTT--CGCCAATACATGAAGACAAGATCTGCT
49667733 TTCTTTGATA
Statistics
Matches: 269, Mismatches: 37, Indels: 58
0.74 0.10 0.16
Matches are distributed among these distances:
31 16 0.06
32 1 0.00
33 2 0.01
34 4 0.01
36 1 0.00
37 1 0.00
39 4 0.01
40 2 0.01
41 1 0.00
42 24 0.09
43 5 0.02
44 150 0.56
45 47 0.17
46 3 0.01
47 8 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
TTCGATCTACTTCGCCAATACATGAAGACAAGATCTGCTCCT
Found at i:49667655 original size:89 final size:88
Alignment explanation
Indices: 49667496--49667751 Score: 343
Period size: 89 Copynumber: 2.9 Consensus size: 88
49667486 ACCAGTATGG
* * *
49667496 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTATCAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCAT
49667561 TGATCTACTTCACGCCAATACAT
66 TGATCTACTTCACGCCAATACAT
* * * **
49667584 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATC-
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATACAGGAAGACAAGATCTGCTATCA
49667648 TTCGATCTACTTCACGCCAATACAT
65 TT-GATCTACTTCACGCCAATACAT
* * * * * * *
49667673 GAAGACAAGATCTGCTATCTTTGATCCACTTCACGCCAATACATGAAGACAAGATTTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCAT
*
49667738 TGATATACTTCACG
66 TGATCTACTTCACG
49667752 ACAACTTAGG
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
88 68 0.47
89 77 0.53
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (88 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCAT
TGATCTACTTCACGCCAATACAT
Found at i:49667714 original size:133 final size:133
Alignment explanation
Indices: 49667476--49667750 Score: 487
Period size: 133 Copynumber: 2.1 Consensus size: 133
49667466 AAGACAAGAC
49667476 CTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
1 CTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
* *
49667541 AAGATAAGATCTGCTATCATTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
66 AAGACAAGATCTGCTATCATTGATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
49667606 GAT
131 GAT
*
49667609 CTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
1 CTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
* * *
49667674 AAGACAAGATCTGCTATCTTTGATCCACTTCACGCCAATACATGAAGACAAGATTTGCTTTCTTT
66 AAGACAAGATCTGCTATCATTGATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
49667739 GAT
131 GAT
*
49667742 ATACTTCAC
1 CTACTTCAC
49667751 GACAACTTAG
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (133 bp):
CTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
AAGACAAGATCTGCTATCATTGATCCACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
GAT
Found at i:49667738 original size:44 final size:44
Alignment explanation
Indices: 49667496--49667751 Score: 361
Period size: 44 Copynumber: 5.8 Consensus size: 44
49667486 ACCAGTATGG
49667496 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
49667540 GAAGATAAGATCTGCTATCATT-GATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATC-TTCGATCTACTTCACGCCAATACAT
* * * * ***
49667584 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
49667629 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
49667673 GAAGACAAGATCTGCTATCTTTGATCCACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * *
49667717 GAAGACAAGATTTGCTTTCTTTGATATACTTCACG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACG
49667752 ACAACTTAGG
Statistics
Matches: 187, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
43 2 0.01
44 146 0.78
45 39 0.21
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:49667814 original size:88 final size:88
Alignment explanation
Indices: 49667759--49668067 Score: 503
Period size: 88 Copynumber: 3.5 Consensus size: 88
49667749 ACGACAACTT
* * **
49667759 AGGGAGGCAAGGCTAGTATCTTTGATCTATTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATC
49667824 TTCAACCTACTCCACTACAACCC
66 TTCAACCTACTCCACTACAACCC
49667847 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGT-CTAGGAAGGCAAGATCTGCTAT
1 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTAC-AGGAAGGCAAGATCTGCTAT
* *
49667911 CTTCAACCTGCTCCACTACGACCC
65 CTTCAACCTACTCCACTACAACCC
* * *
49667935 AGGGAGGCAAGGTTGGTATCCTCGATCTGCTTCACTGTCGGTACAGGAAGGTAAGATCTGCTATC
1 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATC
*
49668000 TTCAACCTGCTCCACTACAACCC
66 TTCAACCTACTCCACTACAACCC
*
49668023 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCAGTACA
1 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
49668068 AGAACTCCAC
Statistics
Matches: 206, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
87 1 0.00
88 204 0.99
89 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (88 bp):
AGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATC
TTCAACCTACTCCACTACAACCC
Found at i:49667855 original size:44 final size:44
Alignment explanation
Indices: 49667802--49668033 Score: 198
Period size: 44 Copynumber: 5.3 Consensus size: 44
49667792 ACTGTCGGTA
* *
49667802 CAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACC
* * * * * * * **
49667846 CAGGGAGGCAAG-GCTGGTATCTTCGATCTGCTTCACTGTCGGTC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT-ACGACC
*
49667890 TAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACC
* * * * * * * * ***
49667934 CAGGGAGGCAAGGT-TGGTATCCTCGATCTGCTTCACTGTCGGTA
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT-ACGACC
* *
49667978 CAGGAAGGTAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACC
*
49668022 CAGGGAGGCAAG
1 CAGGAAGGCAAG
49668034 GCTGGTATCT
Statistics
Matches: 136, Mismatches: 48, Indels: 8
0.71 0.25 0.04
Matches are distributed among these distances:
43 37 0.27
44 61 0.45
45 38 0.28
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACC
Found at i:49668224 original size:88 final size:88
Alignment explanation
Indices: 49668072--49668715 Score: 939
Period size: 88 Copynumber: 7.3 Consensus size: 88
49668062 AGTACAAGAA
* * *
49668072 CTCCACTACAACCTAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGTAGGAAGG
1 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGG
**
49668137 CAAGATCTATTATCTTCAACCTG
66 CAAGATCTGCTATCTTCAACCTG
* * *
49668160 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTTACTATCGATGCAAGAAGG
1 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGG
* *
49668225 TAAGATCTGCTATCTTCAACCTT
66 CAAGATCTGCTATCTTCAACCTG
* * * * * * *
49668248 CTCCACTAAAACCTAGGGAGGCAAGGTTAGTATCTTCGATCTGCTTCAATGTCGATGTAAGAAGG
1 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGG
49668313 CAAGATCTGCTATCTTCAACCTG
66 CAAGATCTGCTATCTTCAACCTG
*
49668336 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGG
1 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGG
*
49668401 CAAGATCTGCTATCTTCAACCTT
66 CAAGATCTGCTATCTTCAACCTG
*
49668424 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATACAGGAAGG
1 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGG
*
49668489 CAAGATCTGCTATCTTCAACGTG
66 CAAGATCTGCTATCTTCAACCTG
* * * * *
49668512 CTCCACTACAACCAAGGGAGGCAAGGCTAGTATCTTCGATTTGGTTCACTATCGATGCAGGAAGG
1 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGG
49668577 CAAGATCTGCTATCTTCAACCTG
66 CAAGATCTGCTATCTTCAACCTG
* * * * *
49668600 CTCCACTACAACCCATGGAGGCAAGGCTGGTATCTTAGATCTGCTTCGCCGTC-AGTACAGGAAG
1 CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA-TGCAGGAAG
* *
49668664 GCAAGATCTGTTATTTTCAACCTG
65 GCAAGATCTGCTATCTTCAACCTG
* * * *
49668688 CTCCGCTGCAAACCAGGAAGGCAAGGCT
1 CTCCACTACAACCCAGGGAGGCAAGGCT
49668716 TTGTGATTTC
Statistics
Matches: 498, Mismatches: 57, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
87 1 0.00
88 497 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (88 bp):
CTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGG
CAAGATCTGCTATCTTCAACCTG
Found at i:49668705 original size:44 final size:44
Alignment explanation
Indices: 49668308--49668712 Score: 200
Period size: 44 Copynumber: 9.2 Consensus size: 44
49668298 GTCGATGTAA
* * *
49668308 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
* * * * * * * **
49668352 GGAGGCAAG-GCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTG-CAAACCAG
* * * *
49668396 GAAGGCAAGATCTGCTATCTTCAACCTTCTCCACTACAACCCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
* * * * * * * *
49668440 GGAGGCAAG-GCTGGTATCTTCGATCTGCTTCACTGTCGATA-CAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTG-C-AAACCAG
* * *
49668484 GAAGGCAAGATCTGCTATCTTCAACGTGCTCCACTAC-AACCAAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACC-AG
* * * ** * * * * * **
49668528 GGAGGCAAG-GCTAG-TATCTTCGATTTGGTTCACTATCGATGCAG
1 GAAGGCAAGATCT-GCTATCTTCAACCTGCTCCGCT-GCAAACCAG
* * *
49668572 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCATG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCA-G
* * * * * *
49668617 G-AGGCAAG-GCTGGTATCTT-AGATCTGCTTCGCCGTCAGTA-CAG
1 GAAGGCAAGATCTGCTATCTTCA-ACCTGCTCCGCTG-CA-AACCAG
* *
49668660 GAAGGCAAGATCTGTTATTTTCAACCTGCTCCGCTGCAAACCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
49668704 GAAGGCAAG
1 GAAGGCAAG
49668713 GCTTTGTGAT
Statistics
Matches: 262, Mismatches: 79, Indels: 40
0.69 0.21 0.10
Matches are distributed among these distances:
42 2 0.01
43 76 0.29
44 106 0.40
45 77 0.29
46 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (44 bp):
GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
Found at i:49671465 original size:31 final size:31
Alignment explanation
Indices: 49671427--49671488 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
49671417 CATTGAACAA
49671427 GTTTTGATACAGCTCCTTATACGTCATCGGG
1 GTTTTGATACAGCTCCTTATACGTCATCGGG
* *
49671458 GTTTTGATACAGTTTCTTATACGTCATCGGG
1 GTTTTGATACAGCTCCTTATACGTCATCGGG
49671489 ATTGGTGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTTGATACAGCTCCTTATACGTCATCGGG
Found at i:49674459 original size:21 final size:19
Alignment explanation
Indices: 49674422--49674496 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
49674412 AATCATATCT
49674422 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
49674441 TCCAAGATTGCATATATCATA
1 TCCAAGATTGC--ATATCATA
*
49674462 TCTAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
*
49674481 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
49674497 CTTGAAGGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 35 0.66
21 18 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:49675312 original size:37 final size:36
Alignment explanation
Indices: 49675253--49675323 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
49675243 TACATATTTT
* * *
49675253 ATATATATATATTATTTTATTTTCATAATGTATATGG
1 ATATATATATATCATTTCATTTT-ATAATGCATATGG
49675290 ATATATATATA-CATTTACATTTTATAATGCATAT
1 ATATATATATATCATTT-CATTTTATAATGCATAT
49675324 ACATTTCCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.51
Consensus pattern (36 bp):
ATATATATATATCATTTCATTTTATAATGCATATGG
Found at i:49675347 original size:24 final size:23
Alignment explanation
Indices: 49675290--49675351 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
49675280 ATGTATATGG
*
49675290 ATATATATATACATTTACATTTT
1 ATATATATATACATTTACATATT
*
49675313 ATA-ATGCATATACATTTCCTATATT
1 ATATAT--ATATACATTTAC-ATATT
49675338 ATATATATATACAT
1 ATATATATATACAT
49675352 ATATTTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
24 19 0.58
25 7 0.21
26 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATATATACATTTACATATT
Found at i:49675443 original size:48 final size:49
Alignment explanation
Indices: 49675378--49675486 Score: 175
Period size: 50 Copynumber: 2.2 Consensus size: 49
49675368 TATATATTTA
* *
49675378 TATACATACATATTTTTAC-ATATATATACATACTCTATACAAAACTAT
1 TATAAATATATATTTTTACAATATATATACATACTCTATACAAAACTAT
*
49675426 TATAAATATATATTTTTACATATATATATACATACTCTATTCAAAACTAT
1 TATAAATATATATTTTTACA-ATATATATACATACTCTATACAAAACTAT
49675476 TATAAATATAT
1 TATAAATATAT
49675487 TTTCTGCATT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 17 0.30
50 39 0.70
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (49 bp):
TATAAATATATATTTTTACAATATATATACATACTCTATACAAAACTAT
Found at i:49677213 original size:16 final size:16
Alignment explanation
Indices: 49677192--49677226 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49677182 TTGTGTTTTG
49677192 TTTTGAATGCATGACA
1 TTTTGAATGCATGACA
* *
49677208 TTTTGACTGCATGGCA
1 TTTTGAATGCATGACA
49677224 TTT
1 TTT
49677227 CATTATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (16 bp):
TTTTGAATGCATGACA
Found at i:49679687 original size:7 final size:7
Alignment explanation
Indices: 49679675--49679734 Score: 61
Period size: 7 Copynumber: 8.4 Consensus size: 7
49679665 TCAATCCAAA
*
49679675 AAAAAAC
1 AAAAAAG
49679682 AAAAAAG
1 AAAAAAG
49679689 AAAAAAG
1 AAAAAAG
49679696 AAAAGAA-
1 AAAA-AAG
*
49679703 AAGAAAG
1 AAAAAAG
49679710 AGAAAAAG
1 A-AAAAAG
49679718 -AAAAAG
1 AAAAAAG
49679724 AAAAATAG
1 AAAAA-AG
49679732 AAA
1 AAA
49679735 TAAAAAACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
6 8 0.18
7 25 0.56
8 12 0.27
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:49679692 original size:6 final size:6
Alignment explanation
Indices: 49679683--49679728 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
49679673 AAAAAAAACA
*
49679683 AAAAAG AAAAA- AGAAAAG -AAAAG AAAGAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
49679729 TAGAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 6 0.17
6 29 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:49679692 original size:12 final size:11
Alignment explanation
Indices: 49679672--49679728 Score: 62
Period size: 12 Copynumber: 5.1 Consensus size: 11
49679662 GATTCAATCC
*
49679672 AAAAAA-AAAC
1 AAAAAAGAAAA
49679682 AAAAAAGAAAA
1 AAAAAAGAAAA
49679693 AAGAAAAGAAAA
1 AA-AAAAGAAAA
* *
49679705 GAAAGAGAAAA
1 AAAAAAGAAAA
49679716 AGAAAAAGAAAA
1 A-AAAAAGAAAA
49679728 A
1 A
49679729 TAGAAATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 6 0.15
11 13 0.33
12 20 0.51
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:49680263 original size:15 final size:15
Alignment explanation
Indices: 49680238--49680274 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
49680228 AATATGACGA
*
49680238 AAAAAT-GAAAATG-
1 AAAAATGGAAAAAGT
49680251 AAAAATGGAAAAAGT
1 AAAAATGGAAAAAGT
49680266 AAAAATGGA
1 AAAAATGGA
49680275 GAGGCTAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.14
Consensus pattern (15 bp):
AAAAATGGAAAAAGT
Found at i:49681558 original size:44 final size:44
Alignment explanation
Indices: 49681508--49681734 Score: 138
Period size: 44 Copynumber: 5.2 Consensus size: 44
49681498 AAACTTTAGC
49681508 CTTGTCTCCCTGAGTAGTAGTGGAATAGGTTGAAAACAGCAGAT
1 CTTGTCTCCCTGAGTAGTAGTGGAATAGGTTGAAAACAGCAGAT
* * * * * * * *** *
49681552 CTTGTCTTCCTGTATTGGTAG-CGAAGTAGATCGAAGACCTTAG-C
1 CTTGTCTCCCTG-AGTAGTAGTGGAA-TAGGTTGAAAACAGCAGAT
* *
49681596 CTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGAGTAGTAGTGGAATAGGTTGAAAACAGCAGAT
* * * * ** * * *** *
49681640 CTTGTCTTCCTGTATTGGCAG-CAAAGTAGATTGAAGACCTAAG-C
1 CTTGTCTCCCTG-AGTAGTAGTGGAA-TAGGTTGAAAACAGCAGAT
* * *
49681684 CTTGTCTCCCTGGGTAGTAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGAGTAGTAGTGGAATAGGTTGAAAACAGCAGAT
49681728 CTTGTCT
1 CTTGTCT
49681735 TCCTAAATTC
Statistics
Matches: 122, Mismatches: 53, Indels: 16
0.64 0.28 0.08
Matches are distributed among these distances:
43 31 0.25
44 58 0.48
45 33 0.27
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (44 bp):
CTTGTCTCCCTGAGTAGTAGTGGAATAGGTTGAAAACAGCAGAT
Found at i:49681864 original size:44 final size:44
Alignment explanation
Indices: 49681816--49682047 Score: 132
Period size: 44 Copynumber: 5.3 Consensus size: 44
49681806 AATAGTAGAT
* *
49681816 CTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAAACCTCAGC
1 CTTGTCTCCCTGTATTGGCAGCGAAGTAGATCGAAAACCTCAGC
* * * *** *
49681860 CTTGTCTCCCTG-A---GCAGTAGTAGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGTATTGGCAG-CG-A-AGTAGATCGAAAACCTCAG-C
* * * *
49681904 CTTGTCTTCCTGTATTGGCAGCAAAGTAAATCGAATACCTCAGC
1 CTTGTCTCCCTGTATTGGCAGCGAAGTAGATCGAAAACCTCAGC
*** * * * * * *** *
49681948 CTTGTCTCCCTG-AGCAGTAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGTATTGGCAGCGAAGTAGATCGAAAACCTCAG-C
* * *
49681992 CTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGACCTCAGC
1 CTTGTCTCCCTGTATTGGCAGCGAAGTAGATCGAAAACCTCAGC
49682036 CTTGTCTCCCTG
1 CTTGTCTCCCTG
49682048 AGTAGCAGTG
Statistics
Matches: 126, Mismatches: 52, Indels: 20
0.64 0.26 0.10
Matches are distributed among these distances:
40 4 0.03
41 1 0.01
42 1 0.01
43 30 0.24
44 55 0.44
45 30 0.24
46 1 0.01
48 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
CTTGTCTCCCTGTATTGGCAGCGAAGTAGATCGAAAACCTCAGC
Found at i:49682111 original size:88 final size:88
Alignment explanation
Indices: 49681505--49682117 Score: 902
Period size: 88 Copynumber: 7.0 Consensus size: 88
49681495 GTGAAACTTT
* *
49681505 AGCCTTGTCTCCCTGAGTAGTAGTGGAATAGGTTGAAAACAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* *
49681570 TAGCGAAGTAGATCGAAGACCTT
66 CAGCGAAGTAGATCGAAGACCTC
49681593 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* * *
49681658 CAGCAAAGTAGATTGAAGACCTA
66 CAGCGAAGTAGATCGAAGACCTC
* ** *
49681681 AGCCTTGTCTCCCTGGGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTAAATTCG
1 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
*
49681746 CAGCGAAGTAGATCGAAAACCTC
66 CAGCGAAGTAGATCGAAGACCTC
* * * * *
49681769 AGCCTTGTCTCCTTGAGCAATAGTAGAGTAGGTTGAAAATAGTAGATCTTGTCTTCCTGTATTGG
1 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* *
49681834 CAGCGAAGTAGATCAAAAACCTC
66 CAGCGAAGTAGATCGAAGACCTC
* *
49681857 AGCCTTGTCTCCCTGAGCAGTAGTAGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* * *
49681922 CAGCAAAGTAAATCGAATACCTC
66 CAGCGAAGTAGATCGAAGACCTC
*
49681945 AGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
*
49682010 CAGCAAAGTAGATCGAAGACCTC
66 CAGCGAAGTAGATCGAAGACCTC
* * * ** * *
49682033 AGCCTTGTCTCCCTGAGTAGCAGTGCAGTAGGTTGAATATAGCAGATCTTACCTTCCTATACTGG
1 AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* * *
49682098 CAGTGAAGCAGATCAAAGAC
66 CAGCGAAGTAGATCGAAGAC
49682118 ACCAGTTTTA
Statistics
Matches: 479, Mismatches: 46, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 479 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (88 bp):
AGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
CAGCGAAGTAGATCGAAGACCTC
Found at i:49682702 original size:126 final size:125
Alignment explanation
Indices: 49682471--49682763 Score: 310
Period size: 126 Copynumber: 2.3 Consensus size: 125
49682461 AGATGGCGAA
* * *
49682471 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAGTCCTATCTCCCTGAGGTTGCA
1 TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAAGCCAATAGTCCTATCTCCCTAAGGTTGCA
* **
49682536 GTGGAGCTGATTAAAATTAGATATTATCTCCTTACGGTTGCAGAGAGCAGATCACATCAAG
66 GTGGAGCTGATTAAAATCAGATATTATCT-CTTAAAGTTGCAGAGAGCAGATCACATCAAG
*
49682597 TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGACCTAA-A-TCCTATCTCCCTAAGGTTG
1 TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAAG-CC-AATAGTCCTATCTCCCTAAGGTTG
* ** * *
49682660 CAGTGGAG-TGGATTAAAACATCCAGAT-TTATCT-TTAAAGTTGCAATAGAATAAGTTGA-AGT
64 CAGTGGAGCT-GATT-AAA-AT-CAGATATTATCTCTTAAAGTTGC-AGAG-AGCAGATCACA--
49682721 CTCAAG
121 -TCAAG
* *
49682727 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG
1 TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAAG
49682764 ATAGCAAATT
Statistics
Matches: 141, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
125 1 0.01
126 72 0.51
127 10 0.07
128 15 0.11
129 4 0.03
130 39 0.28
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (125 bp):
TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAAGCCAATAGTCCTATCTCCCTAAGGTTGCA
GTGGAGCTGATTAAAATCAGATATTATCTCTTAAAGTTGCAGAGAGCAGATCACATCAAG
Found at i:49683187 original size:21 final size:21
Alignment explanation
Indices: 49683149--49683188 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49683139 CGCAGCAGTC
* *
49683149 CCCCGCACATCTCGCACGTTG
1 CCCCGCACATCGCACACGTTG
*
49683170 CCCCGCACGTCGCACACGT
1 CCCCGCACATCGCACACGT
49683189 CACCCAGCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.50, G:0.20, T:0.15
Consensus pattern (21 bp):
CCCCGCACATCGCACACGTTG
Found at i:49683337 original size:18 final size:18
Alignment explanation
Indices: 49683305--49683344 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
49683295 TATTGTATTT
*
49683305 AAAAGAATAATGAAATAAA
1 AAAAGAATAAGGAAA-AAA
49683324 AAAAGAA-AAGGAAAAAA
1 AAAAGAATAAGGAAAAAA
49683341 AAAA
1 AAAA
49683345 CAAATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 6 0.30
19 7 0.35
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAGAATAAGGAAAAAA
Found at i:49684037 original size:3 final size:3
Alignment explanation
Indices: 49684020--49684077 Score: 64
Period size: 3 Copynumber: 18.3 Consensus size: 3
49684010 ATTTCAATAG
*
49684020 TAT TA- TAT TATT TAT TATT TAT TATT TAT TATT TAT TAT TAT TGT TAT
1 TAT TAT TAT TA-T TAT TA-T TAT TA-T TAT TA-T TAT TAT TAT TAT TAT
49684068 TAT TAT TAT T
1 TAT TAT TAT T
49684078 TCTATATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 2 0.04
3 34 0.71
4 12 0.25
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:49684037 original size:7 final size:7
Alignment explanation
Indices: 49684020--49684078 Score: 79
Period size: 7 Copynumber: 8.7 Consensus size: 7
49684010 ATTTCAATAG
49684020 TATTATAT
1 TATT-TAT
49684028 TATTTAT
1 TATTTAT
49684035 TATTTAT
1 TATTTAT
49684042 TATTTAT
1 TATTTAT
49684049 TATTTAT
1 TATTTAT
49684056 TA-TTAT
1 TATTTAT
*
49684062 T-GTTAT
1 TATTTAT
49684068 TA-TTAT
1 TATTTAT
49684074 TATTT
1 TATTT
49684079 CTATATTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
6 16 0.33
7 28 0.58
8 4 0.08
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:49689556 original size:3 final size:3
Alignment explanation
Indices: 49689548--49689577 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
49689538 TGCGCTGTGA
49689548 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49689578 TCTCTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:49690073 original size:9 final size:9
Alignment explanation
Indices: 49690059--49690118 Score: 75
Period size: 9 Copynumber: 6.2 Consensus size: 9
49690049 GACTAAAATT
49690059 TTCGGGTAA
1 TTCGGGTAA
49690068 TTCGGGTAA
1 TTCGGGTAA
*
49690077 TTCGAGTAA
1 TTCGGGTAA
49690086 TTAAGTCGGGTAA
1 -T---TCGGGTAA
49690099 TTCGGGTAA
1 TTCGGGTAA
49690108 TTCGGGTAA
1 TTCGGGTAA
49690117 TT
1 TT
49690119 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
9 36 0.80
10 1 0.02
12 1 0.02
13 7 0.16
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:49690095 original size:31 final size:31
Alignment explanation
Indices: 49690060--49690118 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
49690050 ACTAAAATTT
49690060 TCGGGTAATTCGGGTAATTCGAGTAATTAAG
1 TCGGGTAATTCGGGTAATTCGAGTAATTAAG
*
49690091 TCGGGTAATTCGGGTAATTCGGGTAATT
1 TCGGGTAATTCGGGTAATTCGAGTAATT
49690119 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.31, T:0.34
Consensus pattern (31 bp):
TCGGGTAATTCGGGTAATTCGAGTAATTAAG
Found at i:49690239 original size:28 final size:28
Alignment explanation
Indices: 49690181--49690239 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
49690171 TTATTAACCG
* * *** *
49690181 AAAAAATTTCGGTTCGGTTAATTTTTTA
1 AAAAAAATTAGGTTCGGTTAACGGTTAA
49690209 AAAAAAATTAGGTTCGGTTAACGGTTAA
1 AAAAAAATTAGGTTCGGTTAACGGTTAA
49690237 AAA
1 AAA
49690240 TTTTGAGAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (28 bp):
AAAAAAATTAGGTTCGGTTAACGGTTAA
Found at i:49693378 original size:28 final size:28
Alignment explanation
Indices: 49693314--49693399 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
49693304 TTGGAGCGTT
* * *
49693314 TTTCTTCAAAATTATTTCTTCAGAACCTA
1 TTTCGTCAAAATTATTT-TTTAGAACCCA
49693343 TCTT-GTCAAAATTATTTTTTAGAACCCA
1 T-TTCGTCAAAATTATTTTTTAGAACCCA
49693371 TTTCGTCAAAATTATTTTTTTCAGAACCC
1 TTTCGTCAAAATTA-TTTTTT-AGAACCC
49693400 CTAAACCCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 2 0.04
28 20 0.40
29 19 0.38
30 9 0.18
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (28 bp):
TTTCGTCAAAATTATTTTTTAGAACCCA
Found at i:49693514 original size:22 final size:20
Alignment explanation
Indices: 49693489--49693555 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 20
49693479 AACTTACAAA
49693489 TTAAGAAACCTTAAACCCTAAT
1 TTAA-AAACC-TAAACCCTAAT
* *
49693511 TTAAAATTCCCACAACCCTAAT
1 TTAAAA-ACCTA-AACCCTAAT
*
49693533 TTAATAAACCCTAAGCCCTAAT
1 TTAA-AAA-CCTAAACCCTAAT
49693555 T
1 T
49693556 AGCAATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 3 0.08
22 28 0.78
23 5 0.14
ACGTcount: A:0.42, C:0.27, G:0.03, T:0.28
Consensus pattern (20 bp):
TTAAAAACCTAAACCCTAAT
Found at i:49694293 original size:9 final size:9
Alignment explanation
Indices: 49694279--49694309 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49694269 CCGCTTTAGC
49694279 TTTTCTTTT
1 TTTTCTTTT
49694288 TTTTCTTTT
1 TTTTCTTTT
*
49694297 GTTTCTTTT
1 TTTTCTTTT
49694306 TTTT
1 TTTT
49694310 TCCTTTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:49694308 original size:19 final size:19
Alignment explanation
Indices: 49694280--49694316 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
49694270 CGCTTTAGCT
49694280 TTTCTTTTTTTT-CTTTTG
1 TTTCTTTTTTTTCCTTTTG
49694298 TTTCTTTTTTTTTCCTTTT
1 TTTC-TTTTTTTTCCTTTT
49694317 TGGATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (19 bp):
TTTCTTTTTTTTCCTTTTG
Found at i:49699562 original size:19 final size:18
Alignment explanation
Indices: 49699538--49699585 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
49699528 TTTGATATTG
*
49699538 TTAAATTTCTATAATTAGT
1 TTAAATTT-GATAATTAGT
**
49699557 TTAAATTTGATCTTTAGT
1 TTAAATTTGATAATTAGT
49699575 TTAAATTTGAT
1 TTAAATTTGAT
49699586 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.54
Consensus pattern (18 bp):
TTAAATTTGATAATTAGT
Found at i:49699575 original size:18 final size:18
Alignment explanation
Indices: 49699552--49699590 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
49699542 ATTTCTATAA
49699552 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
*
49699570 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTGATCT
49699588 TTA
1 TTA
49699591 AATTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:49701079 original size:19 final size:18
Alignment explanation
Indices: 49701055--49701102 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
49701045 TCGTGACTGC
49701055 AAAATAAATTAAGCGAAAT
1 AAAATAAATTAAG-GAAAT
*
49701074 AAAATAAATT-AGTAAAT
1 AAAATAAATTAAGGAAAT
*
49701091 AAAATATATTAA
1 AAAATAAATTAA
49701103 AGCTTAGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 3 0.12
19 10 0.38
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAATAAATTAAGGAAAT
Found at i:49703658 original size:50 final size:50
Alignment explanation
Indices: 49703568--49703746 Score: 168
Period size: 50 Copynumber: 3.6 Consensus size: 50
49703558 GGTAAAGATG
* * **
49703568 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
49703618 TCCTC-TGTAAGACCATGTCTGGGACATGGTATGGGTACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* ** * * * *
49703668 TCCCATGTAAGACCATATCTTAGATATGGCATTGGCA--GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCG-AGATGAGAAC
*
49703716 ATCCCATGTAAGACCATGTATGGGACATGGC
1 -TCCCATGTAAGACCATGTCTGGGACATGGC
49703747 TTTGGCATGT
Statistics
Matches: 104, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
48 4 0.04
49 30 0.29
50 69 0.66
51 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:49706392 original size:15 final size:16
Alignment explanation
Indices: 49706372--49706401 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49706362 TTTAATCTGG
49706372 AAAAGG-TTTTATATA
1 AAAAGGATTTTATATA
49706387 AAAAGGATTTTATAT
1 AAAAGGATTTTATAT
49706402 GACAATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (16 bp):
AAAAGGATTTTATATA
Found at i:49706627 original size:28 final size:28
Alignment explanation
Indices: 49706569--49706630 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
49706559 AAAAAGCCCT
49706569 TTTTTTTAAATTTACCGAAATGGGCCAA
1 TTTTTTTAAATTTACCGAAATGGGCCAA
* * *
49706597 TTTTTTTATTATTTACCGGAATGGTCC-A
1 TTTTTTTA-AATTTACCGAAATGGGCCAA
49706625 TTTTTT
1 TTTTTT
49706631 GAGAAATCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (28 bp):
TTTTTTTAAATTTACCGAAATGGGCCAA
Found at i:49707066 original size:123 final size:125
Alignment explanation
Indices: 49706847--49707124 Score: 508
Period size: 123 Copynumber: 2.2 Consensus size: 125
49706837 TTATTTCGAG
49706847 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
49706911 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAT-A-TTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTT
*
49706970 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
49707035 AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTT
*
49707095 TTGATGTTTCTGAGCAAATAGTATAAAATC
1 TTGACGTTTCTGAGCAAATAGTATAAAATC
49707125 ACACCCTCGT
Statistics
Matches: 150, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
123 113 0.75
124 2 0.01
125 35 0.23
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTT
Found at i:49707384 original size:16 final size:16
Alignment explanation
Indices: 49707363--49707399 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
49707353 TCATTTAACT
49707363 AGAACATAGATTTGAC
1 AGAACATAGATTTGAC
49707379 AGAACATAGATTTGAC
1 AGAACATAGATTTGAC
49707395 AGAAC
1 AGAAC
49707400 TTCGTAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.22
Consensus pattern (16 bp):
AGAACATAGATTTGAC
Found at i:49710342 original size:29 final size:29
Alignment explanation
Indices: 49710277--49710447 Score: 308
Period size: 29 Copynumber: 5.9 Consensus size: 29
49710267 TTTTGTTAAT
49710277 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49710306 GATTTAGGGTTTTTAATTAAATTAGGTTAG
1 G-GTTAGGGTTTTTAATTAAATTAGGTTAG
49710336 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
49710365 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
49710395 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
49710424 GGTTA-GGTTTTTAATTAAATTAGG
1 GGTTAGGGTTTTTAATTAAATTAGG
49710448 ATTTTTATTA
Statistics
Matches: 138, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
28 19 0.14
29 62 0.45
30 57 0.41
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:49710371 original size:59 final size:59
Alignment explanation
Indices: 49710277--49710447 Score: 319
Period size: 59 Copynumber: 2.9 Consensus size: 59
49710267 TTTTGTTAAT
*
49710277 GGTTAGGGTTTTTAATTAAATTAGGTTAGGATTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
49710336 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
49710395 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTA-GGTTTTTAATTAAATTAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGG
49710448 ATTTTTATTA
Statistics
Matches: 111, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
57 19 0.17
58 3 0.03
59 89 0.80
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (59 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:49712801 original size:20 final size:20
Alignment explanation
Indices: 49712761--49712804 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
49712751 ATGAAAATAT
49712761 AAAAAATTAAAATTATTTTTA
1 AAAAAATTAAAATTA-TTTTA
49712782 AAAAAATATAAAATTA-TTTA
1 AAAAAAT-TAAAATTATTTTA
49712802 AAA
1 AAA
49712805 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATTAAAATTATTTTA
Found at i:49712808 original size:32 final size:30
Alignment explanation
Indices: 49712754--49712818 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 30
49712744 ACCATTGATG
49712754 AAAATATAAAAAATTAAAATTATTTTTAAA
1 AAAATATAAAAAATTAAAATTATTTTTAAA
*
49712784 AAAATATAAAATTATTTAAAATTATTTTTAAA
1 AAAATATAAAA--AATTAAAATTATTTTTAAA
49712816 AAA
1 AAA
49712819 TGAAATTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 11 0.34
32 21 0.66
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAATATAAAAAATTAAAATTATTTTTAAA
Found at i:49712878 original size:22 final size:22
Alignment explanation
Indices: 49712853--49712924 Score: 128
Period size: 22 Copynumber: 3.3 Consensus size: 22
49712843 TAATATGGAT
49712853 TTGAGA-GATTTTTGGAAGGAAA
1 TTGAGAGGA-TTTTGGAAGGAAA
49712875 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTGGAAGGAAA
49712897 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTGGAAGGAAA
49712919 TTGAGA
1 TTGAGA
49712925 TAGGATTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 47 0.96
23 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.35, T:0.29
Consensus pattern (22 bp):
TTGAGAGGATTTTGGAAGGAAA
Found at i:49716741 original size:25 final size:24
Alignment explanation
Indices: 49716713--49716780 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 24
49716703 TTTTAAAACT
*
49716713 TATATGTAAAATATATTTATATGAA
1 TATAT-TAAAATATATTTACATGAA
* * *
49716738 TATAATTTAGATATATTTACATGTA
1 TAT-ATTAAAATATATTTACATGAA
*
49716763 TATA-TAATATATAATTTA
1 TATATTAAAATAT-ATTTA
49716781 TTTTTACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 6 0.17
24 6 0.17
25 21 0.60
26 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (24 bp):
TATATTAAAATATATTTACATGAA
Found at i:49719534 original size:64 final size:64
Alignment explanation
Indices: 49719413--49719535 Score: 140
Period size: 64 Copynumber: 1.9 Consensus size: 64
49719403 TCCCGATCAG
* * ** * * ****
49719413 TATTGATCGTGCATGTGTTGCGGACATACCGCAGCTCTTTGTGAATGTCTTGTTATATGATTGA
1 TATTGATCCTGCATATGTTGCAAACATACCGCAGCTCTTTATGAACGTCCCAATATATGATTGA
49719477 TATTGATCCTGCATATGTTGCAAACATACCGCAGCTCTTTAT-AAGCGTCCCAATATATG
1 TATTGATCCTGCATATGTTGCAAACATACCGCAGCTCTTTATGAA-CGTCCCAATATATG
49719536 GCTCTTCATG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
63 2 0.04
64 46 0.96
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (64 bp):
TATTGATCCTGCATATGTTGCAAACATACCGCAGCTCTTTATGAACGTCCCAATATATGATTGA
Found at i:49721287 original size:23 final size:23
Alignment explanation
Indices: 49721258--49721301 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49721248 TTGGTAAACT
*
49721258 TTAGTTACAAATATGCATATAAG
1 TTAGTTACAAATATGAATATAAG
* *
49721281 TTAGTTATACATATGAATATA
1 TTAGTTACAAATATGAATATA
49721302 TTAAAAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (23 bp):
TTAGTTACAAATATGAATATAAG
Found at i:49725339 original size:28 final size:28
Alignment explanation
Indices: 49725296--49725352 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
49725286 CCTTTCTCTG
* *
49725296 GTTAGCACTTACTGATCTGTTAGTATTT
1 GTTAACACTTAATGATCTGTTAGTATTT
49725324 GTTAACACTTAATGATCTGTTAGTATTT
1 GTTAACACTTAATGATCTGTTAGTATTT
49725352 G
1 G
49725353 ATGCTAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (28 bp):
GTTAACACTTAATGATCTGTTAGTATTT
Found at i:49726142 original size:13 final size:13
Alignment explanation
Indices: 49726124--49726149 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49726114 TTTAAATGAA
49726124 TTCCATTCAAATT
1 TTCCATTCAAATT
49726137 TTCCATTCAAATT
1 TTCCATTCAAATT
49726150 CTTGATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCCATTCAAATT
Found at i:49727916 original size:35 final size:36
Alignment explanation
Indices: 49727872--49727940 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
49727862 ATTTGTTAGA
49727872 TATTGATTATGTTTTAACCTTGTTGGAGATTGAATT
1 TATTGATTATGTTTTAACCTTGTTGGAGATTGAATT
* *
49727908 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAACCTTGTTGGAGATTGAA
49727941 ATGATTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (36 bp):
TATTGATTATGTTTTAACCTTGTTGGAGATTGAATT
Found at i:49729315 original size:34 final size:35
Alignment explanation
Indices: 49729257--49729323 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49729247 CAAACACCAG
49729257 AAAATACTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATACTTTCCAGTAAATCATTTTACAGAAAAGT
* *
49729292 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATACTTTCCAGTAAATCATTTTACAGAAAA
49729324 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAATACTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:49730650 original size:3 final size:3
Alignment explanation
Indices: 49730642--49730682 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
49730632 TAGTATTGTT
*
49730642 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49730683 GGCAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:49739071 original size:47 final size:47
Alignment explanation
Indices: 49738959--49739425 Score: 830
Period size: 47 Copynumber: 9.9 Consensus size: 47
49738949 TAGTATGGCG
49738959 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT-AGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
49739007 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
49739054 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
49739101 TAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
49739147 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
49739194 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
49739241 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
49739288 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* *
49739335 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * * * *
49739382 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
49739426 TCCCGAAGGG
Statistics
Matches: 407, Mismatches: 10, Indels: 5
0.96 0.02 0.01
Matches are distributed among these distances:
46 58 0.14
47 320 0.79
48 29 0.07
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
Found at i:49739599 original size:36 final size:37
Alignment explanation
Indices: 49739544--49739621 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
49739534 CCGAGCTCTA
* *
49739544 AAGACCCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
49739580 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
49739617 AAGAC
1 AAGAC
49739622 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:49741560 original size:29 final size:29
Alignment explanation
Indices: 49741525--49741598 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
49741515 GTTGTGAGAT
* *
49741525 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
49741554 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
49741583 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
49741599 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:49741966 original size:40 final size:40
Alignment explanation
Indices: 49741910--49742130 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 40
49741900 TCGAATGATG
*
49741910 TCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAAGTGATGTA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCT-AGTGATGTA
49741950 TCC-GACTAAGTTCCGAAGAGCATT-GTGCTAGTGATGTA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
49741988 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
49742028 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*** * * *
49742068 TCCGTG-CTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCG-GACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
* * *
49742108 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGACTAAGTTCCGAAGAGCA
49742131 ATCATGCTGG
Statistics
Matches: 166, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
38 12 0.07
39 33 0.20
40 120 0.72
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:49743123 original size:24 final size:25
Alignment explanation
Indices: 49743087--49743136 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
49743077 ATTGATGCTC
49743087 ATTATATGTACATGTGCATGTGTGA
1 ATTATATGTACATGTGCATGTGTGA
*
49743112 ATTATA-GTACATGTGCATGTTTGA
1 ATTATATGTACATGTGCATGTGTGA
49743136 A
1 A
49743137 AATTTCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (25 bp):
ATTATATGTACATGTGCATGTGTGA
Found at i:49745977 original size:48 final size:47
Alignment explanation
Indices: 49745862--49746241 Score: 546
Period size: 48 Copynumber: 7.9 Consensus size: 47
49745852 TAGTATGGCG
* *
49745862 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
*
49745911 TAATGGCCGATAGTGATGAATGTGAAAGTGTATATATTATGATAAGGCC
1 TAATGGCCGAT-GTGATGAATGTGAAAGTGTATATA-TGTGATAAGGCC
*
49745960 TAATGGCCGATGTGATGAATGTGAAAGTGTATAATATGTAATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTAT-ATATGTGATAAGGCC
* *
49746008 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
49746057 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
*
49746104 TAATAGCCGATGTTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATG-TGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* *
49746152 TAATGGCCGATGTGATGAATGTGAAA-TGTATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * * * *
49746198 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
49746242 TCCCGAAGGG
Statistics
Matches: 302, Mismatches: 22, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
46 39 0.13
47 56 0.19
48 111 0.37
49 75 0.25
50 21 0.07
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
Found at i:49746062 original size:97 final size:96
Alignment explanation
Indices: 49745862--49746241 Score: 547
Period size: 97 Copynumber: 4.0 Consensus size: 96
49745852 TAGTATGGCG
* * *
49745862 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATAGTGA
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGAT-GTGA
*
49745927 TGAATGTGAAAGTGTATATAT-TATGATAAGGCC
63 TGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
49745960 TAATGGCCGATGTGATGAATGTGAAAGTGTATAATATGTAATAAGGCCTAATAGCCGATGTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTAT-ATATGTGATAAGGCCTAATAGCCGATGTGATG
*
49746025 AATGTGAAAGTGTATATATATGTGATAGGGCC
65 AATGTGAAAGTGTATATATATGTGATAAGGCC
49746057 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATG-TGATG
49746122 AATGTGAAAGTG--TATATATGTGATAAGGCC
65 AATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * * * * *
49746152 TAATGGCCGATGTGATGAATGTGAAA-TGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
49746216 ATGTGAAAGTGTATA-A-ATGTGATAAG
66 ATGTGAAAGTGTATATATATGTGATAAG
49746242 TCCCGAAGGG
Statistics
Matches: 261, Mismatches: 16, Indels: 15
0.89 0.05 0.05
Matches are distributed among these distances:
93 26 0.10
94 26 0.10
95 45 0.17
96 54 0.21
97 82 0.31
98 28 0.11
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (96 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
ATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:49746417 original size:37 final size:37
Alignment explanation
Indices: 49746361--49746439 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
49746351 CCGAGCTCTA
* *
49746361 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
49746398 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
49746435 AAGAC
1 AAGAC
49746440 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:49747887 original size:13 final size:14
Alignment explanation
Indices: 49747869--49747907 Score: 71
Period size: 13 Copynumber: 2.9 Consensus size: 14
49747859 TAGCTTCTTC
49747869 TTTTTTTCACAATT
1 TTTTTTTCACAATT
49747883 TTTTTTTCACAA-T
1 TTTTTTTCACAATT
49747896 TTTTTTTCACAA
1 TTTTTTTCACAA
49747908 CTTGATATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:49747965 original size:13 final size:12
Alignment explanation
Indices: 49747946--49747989 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
49747936 GGAAACTAAT
49747946 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
49747958 TTTCTTTTTCAAA
1 TTT-TTTTTCGAA
* *
49747971 TGTTTTTTCGAG
1 TTTTTTTTCGAA
49747983 TTTTTTT
1 TTTTTTT
49747990 CGAGAAACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:49748198 original size:16 final size:16
Alignment explanation
Indices: 49748174--49748207 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49748164 AATGGCTTCA
*
49748174 AAAAAAGATAATAAAC
1 AAAAAAGATAAGAAAC
*
49748190 AAAATAGATAAGAAAC
1 AAAAAAGATAAGAAAC
49748206 AA
1 AA
49748208 TAACAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAAAGATAAGAAAC
Found at i:49754112 original size:34 final size:35
Alignment explanation
Indices: 49754068--49754134 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
49754058 CAGTAAAATA
*
49754068 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
49754102 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
49754135 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:49756697 original size:22 final size:24
Alignment explanation
Indices: 49756650--49756698 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
49756640 TAAAATAATT
49756650 GGTCACACTGTATGAAAATTAATAG
1 GGTCACACTGTATG-AAATTAATAG
49756675 GGTCACACTGTATG-AA-TAATAG
1 GGTCACACTGTATGAAATTAATAG
49756697 GG
1 GG
49756699 AGAATTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 2 0.08
25 14 0.58
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (24 bp):
GGTCACACTGTATGAAATTAATAG
Found at i:49757377 original size:30 final size:30
Alignment explanation
Indices: 49757341--49757402 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
49757331 ACTTATTTTA
49757341 TTGTTAATTTTGCTATTATTTTAAAGACAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
* * *
49757371 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
49757401 TT
1 TT
49757403 ACTTATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGCTATTATTTTAAAGACAT
Found at i:49768032 original size:20 final size:20
Alignment explanation
Indices: 49768007--49768055 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
49767997 TGAGTTTAGA
*
49768007 AAAAAATCTAGATAATT-ATT
1 AAAAAATATAGA-AATTAATT
*
49768027 AAAAAATATTGAAATTAATT
1 AAAAAATATAGAAATTAATT
49768047 AAAAAATAT
1 AAAAAATAT
49768056 TAAAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAAAATATAGAAATTAATT
Found at i:49769342 original size:63 final size:62
Alignment explanation
Indices: 49769275--49769443 Score: 196
Period size: 63 Copynumber: 2.7 Consensus size: 62
49769265 ACACACCCAA
* *
49769275 GTCTCTGGCCTGTGTGACTCTAATTCCAAAACAGTGAGTTACACGACTTGGACACACTCTTGT
1 GTCTCTGGCCTGTGTGACTCTAATT-CAAAACAGTGAGTTACACGACCTGGACACACACTTGT
* * * * *
49769338 GTCTCTGGCCCGTGTGACCCTAATTTACAAATAGTGAGTTACACGGCCTGGACACACACTTGT
1 GTCTCTGGCCTGTGTGACTCTAATTCA-AAACAGTGAGTTACACGACCTGGACACACACTTGT
* * * *
49769401 GCCTCTAGCCTATGTGACTCT-ATCTGCAAAACAATGAGTTACA
1 GTCTCTGGCCTGTGTGACTCTAAT-T-CAAAACAGTGAGTTACA
49769444 TGGTCTACCA
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
62 3 0.03
63 84 0.95
64 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (62 bp):
GTCTCTGGCCTGTGTGACTCTAATTCAAAACAGTGAGTTACACGACCTGGACACACACTTGT
Found at i:49770450 original size:10 final size:9
Alignment explanation
Indices: 49770432--49770489 Score: 71
Period size: 10 Copynumber: 6.1 Consensus size: 9
49770422 GAAAGTTGTT
49770432 TAAAAATTA
1 TAAAAATTA
49770441 TAATAAATTA
1 TAA-AAATTA
49770451 TAAATAATTA
1 TAAA-AATTA
* *
49770461 TTAAAATTT
1 TAAAAATTA
49770470 TAAAAATTAA
1 TAAAAATT-A
49770480 TAAAAATTA
1 TAAAAATTA
49770489 T
1 T
49770490 TATAAAAGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 17 0.40
10 25 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAAATTA
Found at i:49770477 original size:18 final size:18
Alignment explanation
Indices: 49770430--49770484 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
49770420 TAGAAAGTTG
*
49770430 TTTAAAAATTATAATAAAT
1 TTTAAAAATTATTA-AAAT
*
49770449 TATAAATAATTATTAAAAT
1 TTTAAA-AATTATTAAAAT
*
49770468 TTTAAAAATTAATAAAA
1 TTTAAAAATTATTAAAA
49770485 ATTATTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 10 0.32
19 14 0.45
20 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAAATTATTAAAAT
Found at i:49770487 original size:28 final size:29
Alignment explanation
Indices: 49770434--49770491 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
49770424 AAGTTGTTTA
49770434 AAAATTATAATAAATTATAAATAATTATT
1 AAAATTATAATAAATTATAAATAATTATT
*
49770463 AAAATTTTAA-AAATTAATAAA-AATTATT
1 AAAATTATAATAAATT-ATAAATAATTATT
49770491 A
1 A
49770492 TAAAAGGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AAAATTATAATAAATTATAAATAATTATT
Found at i:49772236 original size:21 final size:20
Alignment explanation
Indices: 49772212--49772250 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49772202 AATAAATAAA
49772212 TAATAATATAATTTAAAATCT
1 TAAT-ATATAATTTAAAATCT
**
49772233 TAATATATGGTTTAAAAT
1 TAATATATAATTTAAAAT
49772251 TTGTTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TAATATATAATTTAAAATCT
Found at i:49776214 original size:13 final size:13
Alignment explanation
Indices: 49776196--49776221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49776186 CGTGTTTCTA
49776196 AAAACCATTTGTT
1 AAAACCATTTGTT
49776209 AAAACCATTTGTT
1 AAAACCATTTGTT
49776222 TACGTAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:49784875 original size:13 final size:13
Alignment explanation
Indices: 49784857--49784882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49784847 CGTGTTTTCA
49784857 AAAACCATTTGTT
1 AAAACCATTTGTT
49784870 AAAACCATTTGTT
1 AAAACCATTTGTT
49784883 TGCGTAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:49786645 original size:16 final size:16
Alignment explanation
Indices: 49786624--49786661 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
49786614 CCTTTTTTCT
**
49786624 TTTCCATTTTCCACCA
1 TTTCCATTTTAAACCA
49786640 TTTCCA-TTTAAACCA
1 TTTCCATTTTAAACCA
49786655 TTTCCAT
1 TTTCCAT
49786662 ACACCAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTCCATTTTAAACCA
Found at i:49788079 original size:16 final size:16
Alignment explanation
Indices: 49788060--49788090 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49788050 ATAAAAAATA
*
49788060 AAAAAAATTATAATTC
1 AAAAAAATTAAAATTC
49788076 AAAAAAATTAAAATT
1 AAAAAAATTAAAATT
49788091 ATTTCAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAAATTAAAATTC
Found at i:49789414 original size:18 final size:18
Alignment explanation
Indices: 49789393--49789427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49789383 TAGAAAATTA
*
49789393 TTAAAATTTAATAAAAAT
1 TTAAAAATTAATAAAAAT
*
49789411 TTAAAAATTATTAAAAA
1 TTAAAAATTAATAAAAA
49789428 GTATATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAAATTAATAAAAAT
Found at i:49789424 original size:10 final size:10
Alignment explanation
Indices: 49789377--49789427 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
49789367 AATAAATAAT
49789377 AAATT-TTAGA
1 AAATTATTA-A
49789387 AAATTATTAA
1 AAATTATTAA
* *
49789397 AATTTAATAA
1 AAATTATTAA
49789407 AAA-T-TTAA
1 AAATTATTAA
49789415 AAATTATTAA
1 AAATTATTAA
49789425 AAA
1 AAA
49789428 GTATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 23 0.68
11 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (10 bp):
AAATTATTAA
Found at i:49789732 original size:9 final size:9
Alignment explanation
Indices: 49789694--49789755 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
49789684 ACTTGATAAA
49789694 ATTTTATAAT
1 ATTTTAT-AT
* *
49789704 TTTTTTTAT
1 ATTTTATAT
49789713 ATTTCTATAT
1 ATTT-TATAT
49789723 ATTTTATAT
1 ATTTTATAT
*
49789732 ATTTT-TACG
1 ATTTTATA-T
49789741 ATTTTTATAT
1 A-TTTTATAT
49789751 ATTTT
1 ATTTT
49789756 TCTAATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
8 2 0.05
9 20 0.48
10 18 0.43
11 2 0.05
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTATAT
Found at i:49789763 original size:9 final size:10
Alignment explanation
Indices: 49789695--49789783 Score: 71
Period size: 10 Copynumber: 9.2 Consensus size: 10
49789685 CTTGATAAAA
49789695 TTTTATA-ATT
1 TTTTATATA-T
*
49789705 TTTTTTATAT
1 TTTTATATAT
*
49789715 TTCTATATA-
1 TTTTATATAT
49789724 TTTTATATAT
1 TTTTATATAT
**
49789734 TTTTA-CGAT
1 TTTTATATAT
49789743 TTTTATATAT
1 TTTTATATAT
*
49789753 TTTTCTA-AT
1 TTTTATATAT
*
49789762 TTTTAATAAAT
1 TTTT-ATATAT
49789773 TTTTA-ATAT
1 TTTTATATAT
49789782 TT
1 TT
49789784 GAATTTTTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
9 26 0.41
10 30 0.48
11 7 0.11
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTTATATAT
Found at i:49789763 original size:19 final size:19
Alignment explanation
Indices: 49789695--49789776 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
49789685 CTTGATAAAA
* *
49789695 TTTTATAATTTTT-TTTAT
1 TTTTCTAATTTTTATATAT
*
49789713 ATTTCTATATATTTTATATAT
1 TTTTCTA-AT-TTTTATATAT
*
49789734 TTTTAC-GATTTTTATATAT
1 TTTT-CTAATTTTTATATAT
*
49789753 TTTTCTAATTTTTAATAAAT
1 TTTTCTAATTTTT-ATATAT
49789773 TTTT
1 TTTT
49789777 AATATTTGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
18 6 0.12
19 22 0.43
20 15 0.29
21 7 0.14
22 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTCTAATTTTTATATAT
Found at i:49789949 original size:89 final size:89
Alignment explanation
Indices: 49789851--49790058 Score: 237
Period size: 93 Copynumber: 2.3 Consensus size: 89
49789841 AATTTTTAAT
* * *
49789851 AAAAGTAGGGGCTTAATGGCTTTTTTTTAAAAAATTTTGAGGG-TCTTTTTGATGCATTTTGAAA
1 AAAAGTAGGGGCTTAATTGCTTTTTTTTAAAAAAGTTTGAGGGCTCTTTTTGATACATTTTGAAA
* *
49789915 GTTCAAGTACCCAATTCAGTGCAAA
66 GTTCAAGTACCCAACTCAGTAC-AA
** * **
49789940 AAAAGTAGGGGCTTAATTG-TTTTTTAAGAAAAAAAAGTTTGAGGGCTTTTTTTTTTTACATTTT
1 AAAAGTAGGGGCTTAATTGCTTTTTT---TTAAAAAAGTTTGAGGGC-TCTTTTTGATACATTTT
*
49790004 GAAAGTTCAAGTACCCAACTGAGTACAA
62 GAAAGTTCAAGTACCCAACTCAGTACAA
49790032 AAAA--A-GGGCTTAATTGCTTTTTTTTAA
1 AAAAGTAGGGGCTTAATTGCTTTTTTTTAA
49790059 GAGATTGAGG
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
87 2 0.02
88 6 0.06
89 29 0.29
90 7 0.07
91 14 0.14
92 6 0.06
93 36 0.36
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (89 bp):
AAAAGTAGGGGCTTAATTGCTTTTTTTTAAAAAAGTTTGAGGGCTCTTTTTGATACATTTTGAAA
GTTCAAGTACCCAACTCAGTACAA
Found at i:49790167 original size:10 final size:10
Alignment explanation
Indices: 49790147--49790207 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 10
49790137 ATTGCTTTAA
*
49790147 TTTCGTATAT
1 TTTCATATAT
*
49790157 TTTCATTTAT
1 TTTCATATAT
*
49790167 TTCCATATAT
1 TTTCATATAT
49790177 TTGT--TATAT
1 TT-TCATATAT
*
49790186 TTTCATTTAT
1 TTTCATATAT
*
49790196 TTCCATATAT
1 TTTCATATAT
49790206 TT
1 TT
49790208 GTTTTTCTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
8 1 0.03
9 7 0.17
10 32 0.80
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTCATATAT
Found at i:49790186 original size:29 final size:29
Alignment explanation
Indices: 49790152--49790210 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
49790142 TTTAATTTCG
49790152 TATATTTTCATTTATTTCCATATATTTGT
1 TATATTTTCATTTATTTCCATATATTTGT
49790181 TATATTTTCATTTATTTCCATATATTTGT
1 TATATTTTCATTTATTTCCATATATTTGT
49790210 T
1 T
49790211 TTTCTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.03, T:0.63
Consensus pattern (29 bp):
TATATTTTCATTTATTTCCATATATTTGT
Found at i:49798694 original size:44 final size:41
Alignment explanation
Indices: 49798583--49798695 Score: 95
Period size: 44 Copynumber: 2.7 Consensus size: 41
49798573 AATTCTTCGG
* * *
49798583 TCCATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGA
1 TCCACTCCGCTGTAATCTCAAGGAGATAAGACCTGATGCAA
* * * **
49798624 TCTACTCTGCTGTAA-CTTC-AGAGAGATAAGATCCTTTATTTTAA
1 TCCACTCCGCTGTAATC-TCAAG-GAGATAAGA-CC-TGA-TGCAA
49798668 TCCACTCCGCTGTAATCTCAAGGAGATA
1 TCCACTCCGCTGTAATCTCAAGGAGATA
49798696 GGATTACTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
40 3 0.05
41 22 0.40
42 2 0.04
43 2 0.04
44 23 0.42
45 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (41 bp):
TCCACTCCGCTGTAATCTCAAGGAGATAAGACCTGATGCAA
Found at i:49798725 original size:44 final size:44
Alignment explanation
Indices: 49798672--49798930 Score: 218
Period size: 44 Copynumber: 5.7 Consensus size: 44
49798662 TTTTAATCCA
* * *
49798672 CTCCGCTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
* * *
49798716 CTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATTTGATG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAA--T-CTG
* * * * * * *
49798763 CGATCTACTCTGCTATAACTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCG
1 C--TC--CACTG-TA-ATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCTG
* *
49798814 CTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
** *
49798858 CTCTGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
49798902 CTCCACTGTAA-CATCAGGGAGATAAGATT
1 CTCCACTGTAATC-TCAGGGAGATAAGATT
49798931 CACCATTTTT
Statistics
Matches: 169, Mismatches: 31, Indels: 30
0.73 0.13 0.13
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 119 0.70
45 2 0.01
46 3 0.02
47 6 0.04
49 4 0.02
51 6 0.04
52 3 0.02
53 2 0.01
54 18 0.11
55 1 0.01
56 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
Found at i:49798872 original size:142 final size:142
Alignment explanation
Indices: 49798616--49798898 Score: 494
Period size: 142 Copynumber: 2.0 Consensus size: 142
49798606 AGATAAGACC
* * *
49798616 TGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCGCTGT
1 TGATGCGATCTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTAT
49798681 AATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT
*
49798746 CTGGCTTCAATT
131 CTAGCTTCAATT
*
49798758 TGATGCGATCTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTAT
1 TGATGCGATCTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTAT
* **
49798823 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT
49798888 CTAGCTTCAAT
131 CTAGCTTCAAT
49798899 CTGCTCCACT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 133 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
TGATGCGATCTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTAT
AATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT
CTAGCTTCAATT
Found at i:49817219 original size:7 final size:7
Alignment explanation
Indices: 49817207--49817236 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
49817197 GGTCTTTTTT
49817207 TTATTTA
1 TTATTTA
49817214 TTATTTA
1 TTATTTA
49817221 TTATTTA
1 TTATTTA
49817228 TT-TTTA
1 TTATTTA
49817234 TTA
1 TTA
49817237 AATTTGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:49817296 original size:30 final size:31
Alignment explanation
Indices: 49817261--49817319 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
49817251 GTTATTAAGT
49817261 TATTATTATTAC-T-ATATATATACATACGCA
1 TATTATT-TTACATAATATATATACATACGCA
49817291 TATTATTTTACAATAATATATATACATAC
1 TATTATTTTAC-ATAATATATATACATAC
49817320 ATTTGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 7 0.27
31 1 0.04
32 14 0.54
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (31 bp):
TATTATTTTACATAATATATATACATACGCA
Done.