Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 98 of 218
Found at i:28257962 original size:20 final size:20
Alignment explanation
Indices: 28257939--28258026 Score: 61
Period size: 18 Copynumber: 4.8 Consensus size: 20
28257929 ATATATTTAG
28257939 AATTTTTTAGAATTTTTATA
1 AATTTTTTAGAATTTTTATA
28257959 AATTTTTTA-AA----TATA
1 AATTTTTTAGAATTTTTATA
* *
28257974 AA-ATTTGA-AATTTTTATA
1 AATTTTTTAGAATTTTTATA
* *
28257992 AATATTTT-GAA-TTTTAAA
1 AATTTTTTAGAATTTTTATA
28258010 AATTATTTT-GAATTTTT
1 AATT-TTTTAGAATTTTT
28258027 GGAAATTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
14 6 0.11
15 6 0.11
18 15 0.27
19 15 0.27
20 13 0.24
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
AATTTTTTAGAATTTTTATA
Found at i:28258032 original size:20 final size:20
Alignment explanation
Indices: 28257977--28258043 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
28257967 AAATATAAAA
*
28257977 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTAAAAATTAT
28257997 TTTGAA-TTTTAAAAATTAT
1 TTTGAATTTTTAAAAATTAT
**
28258016 TTTGAATTTTTGGAAATTAT
1 TTTGAATTTTTAAAAATTAT
28258036 TTTGAATT
1 TTTGAATT
28258044 ATTCTGTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 8 0.19
19 11 0.26
20 23 0.55
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATTAT
Found at i:28265581 original size:17 final size:17
Alignment explanation
Indices: 28265528--28265582 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
28265518 GCCTGAAGTT
*
28265528 AGAAGGAGAGAGGAAGAG
1 AGAA-GAGAGAGAAAGAG
28265546 -GAAG-GAG-GACAAGATG
1 AGAAGAGAGAGA-AAGA-G
28265562 AGAAGAGAGAGAAAGAG
1 AGAAGAGAGAGAAAGAG
28265579 AGAA
1 AGAA
28265583 AAGGGGAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
14 1 0.03
15 7 0.23
16 2 0.06
17 12 0.39
18 7 0.23
19 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.44, T:0.02
Consensus pattern (17 bp):
AGAAGAGAGAGAAAGAG
Found at i:28271874 original size:54 final size:55
Alignment explanation
Indices: 28271812--28271960 Score: 153
Period size: 54 Copynumber: 2.7 Consensus size: 55
28271802 TGTCACATAT
*
28271812 CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGA-CTTCA-CACACGC
1 CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGAGCCT-AGCACACGC
* * * * * * *
28271866 CCGTGTGACTTAAGTTAGAGAGTTACATGCTCTGGCACAC-AGCCTAGCACACGT
1 CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGAGCCTAGCACACGC
* * *
28271920 CTGTGTGACTCAAGCCAAAGAGTTACACAGG-CAGACACACG
1 CCGTGTGACTCAAGTCAGAGAGTTACAC-GGTCAGACACACG
28271961 CCCATGTGAT
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
53 2 0.03
54 71 0.96
55 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (55 bp):
CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGAGCCTAGCACACGC
Found at i:28293927 original size:15 final size:17
Alignment explanation
Indices: 28293902--28293933 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28293892 TAGCTAGGAC
28293902 CTGTATACTGTA-TAAT
1 CTGTATACTGTACTAAT
28293918 CTGT-TACTGTACTAAT
1 CTGTATACTGTACTAAT
28293934 TATTGTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (17 bp):
CTGTATACTGTACTAAT
Found at i:28293942 original size:18 final size:18
Alignment explanation
Indices: 28293919--28293964 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
28293909 CTGTATAATC
28293919 TGTTACTGTACTAATTAT
1 TGTTACTGTACTAATTAT
*
28293937 TGTTACTGTACTGATTAT
1 TGTTACTGTACTAATTAT
28293955 TGTTACTGTA
1 TGTTACTGTA
28293965 ATGCGGCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (18 bp):
TGTTACTGTACTAATTAT
Found at i:28294461 original size:18 final size:18
Alignment explanation
Indices: 28294426--28294463 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28294416 GCAATAAGTG
*
28294426 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
28294444 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
28294462 AC
1 AC
28294464 TTTATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:28297508 original size:31 final size:31
Alignment explanation
Indices: 28297473--28297555 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
28297463 GTATATGTTT
* * *
28297473 TATACATTGTCAAATTTTATTTTTATATAGA
1 TATACATTGCCAAATTTGATTTGTATATAGA
*
28297504 TATACATTGCCAAATTTGATTTGTATATGGA
1 TATACATTGCCAAATTTGATTTGTATATAGA
* *
28297535 TATATATTGCCGAA-TTGATTT
1 TATACATTGCCAAATTTGATTT
28297556 CAGCATTGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 7 0.15
31 39 0.85
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (31 bp):
TATACATTGCCAAATTTGATTTGTATATAGA
Found at i:28301354 original size:45 final size:45
Alignment explanation
Indices: 28301290--28301514 Score: 324
Period size: 45 Copynumber: 5.0 Consensus size: 45
28301280 GCTATACACC
*
28301290 TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGA
* * * *
28301335 TAAAAATAAGTAAGACCATAGTTGAAAGATGTTATGGCATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGA
*
28301380 TAAAAGTGAGTAAGACCATAGCTGAAAAAGATGCTATGACATCATGA
1 TAAAAATGAGTAAGACCATAGCTG--AAAGATGCTATGACATCATGA
*
28301427 TAAAAATGAGTAAGACCATAGCTGAAAGATGATATGACATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGA
* * * * *
28301472 TAGAGATGAGTAAGACTATAGATAAAAGATGCTATGACATCAT
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCAT
28301515 ATGAAAGCGC
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 120 0.74
47 42 0.26
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (45 bp):
TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGA
Found at i:28301445 original size:92 final size:91
Alignment explanation
Indices: 28301290--28301514 Score: 330
Period size: 92 Copynumber: 2.5 Consensus size: 91
28301280 GCTATACACC
* *
28301290 TAAAAATGAGTAAGACCATAGCTG-AAAGATGCTATGGCATCATGATAAAAATAAGTAAGACCAT
1 TAAAAGTGAGTAAGACCATAGCTGAAAAGATGCTATGACATCATGATAAAAATAAGTAAGACCAT
* * *
28301354 AGTTGAAAGATGTTATGGCATCATGA
66 AGCTGAAAGATGATATGACATCATGA
*
28301380 TAAAAGTGAGTAAGACCATAGCTGAAAAAGATGCTATGACATCATGATAAAAATGAGTAAGACCA
1 TAAAAGTGAGTAAGACCATAGCTG-AAAAGATGCTATGACATCATGATAAAAATAAGTAAGACCA
28301445 TAGCTGAAAGATGATATGACATCATGA
65 TAGCTGAAAGATGATATGACATCATGA
* * *
28301472 T-AGAGATGAGTAAGACTATAGAT-AAAAGATGCTATGACATCAT
1 TAAAAG-TGAGTAAGACCATAGCTGAAAAGATGCTATGACATCAT
28301515 ATGAAAGCGC
Statistics
Matches: 123, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
90 43 0.35
91 3 0.02
92 77 0.63
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (91 bp):
TAAAAGTGAGTAAGACCATAGCTGAAAAGATGCTATGACATCATGATAAAAATAAGTAAGACCAT
AGCTGAAAGATGATATGACATCATGA
Found at i:28301478 original size:22 final size:24
Alignment explanation
Indices: 28301359--28301515 Score: 86
Period size: 23 Copynumber: 6.8 Consensus size: 24
28301349 ACCATAGTTG
* *
28301359 AAAGATGTTATGGCATCAT-GATA
1 AAAGATGATATGACATCATAGATA
* *
28301382 AAAG-TGAGTAAGAC--CATAGCTGAA
1 AAAGATGA-TATGACATCATAGAT--A
*
28301406 AAAGATGCTATGACATCAT-GATA
1 AAAGATGATATGACATCATAGATA
* * *
28301429 AAA-ATGAGTAAGAC--CATAGCTG
1 AAAGATGA-TATGACATCATAGATA
28301451 AAAGATGATATGACATCAT-GAT-
1 AAAGATGATATGACATCATAGATA
* *
28301473 AGAGATGAGTAAGAC-T-ATAGATA
1 AAAGATGA-TATGACATCATAGATA
*
28301496 AAAGATGCTATGACATCATA
1 AAAGATGATATGACATCATA
28301516 TGAAAGCGCG
Statistics
Matches: 99, Mismatches: 18, Indels: 33
0.66 0.12 0.22
Matches are distributed among these distances:
21 8 0.08
22 33 0.33
23 35 0.35
24 16 0.16
25 4 0.04
26 3 0.03
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (24 bp):
AAAGATGATATGACATCATAGATA
Found at i:28303989 original size:18 final size:18
Alignment explanation
Indices: 28303959--28304003 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
28303949 ATAATAATAA
28303959 TTAATAAAATATTATTAC
1 TTAATAAAATATTATTAC
* *
28303977 TTATTAAACTATTATTAC
1 TTAATAAAATATTATTAC
28303995 TTAATAAAA
1 TTAATAAAA
28304004 AATCATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATAAAATATTATTAC
Found at i:28305570 original size:25 final size:24
Alignment explanation
Indices: 28305511--28305570 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
28305501 AGTGAACTAC
* **
28305511 AAAAGAAAAATCTACTCTAAAAAG
1 AAAAGAAAAACCTAAACTAAAAAG
* *
28305535 AGAAGAGAAAACCTAAACTAAAACTG
1 AAAAGA-AAAACCTAAACTAAAA-AG
28305561 AAAAGAAAAA
1 AAAAGAAAAA
28305571 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 5 0.18
25 17 0.61
26 6 0.21
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (24 bp):
AAAAGAAAAACCTAAACTAAAAAG
Found at i:28305576 original size:11 final size:11
Alignment explanation
Indices: 28305560--28305594 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28305550 AACTAAAACT
28305560 GAAAAGAAAAA
1 GAAAAGAAAAA
*
28305571 GAAAAGAAAAG
1 GAAAAGAAAAA
*
28305582 GAAAAGAGAAA
1 GAAAAGAAAAA
28305593 GA
1 GA
28305595 GAACCTAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:28308163 original size:20 final size:20
Alignment explanation
Indices: 28308118--28308164 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28308108 TGTGCCCTAG
28308118 CTGTGTGGAGGTCTACACGC
1 CTGTGTGGAGGTCTACACGC
* * *
28308138 CCGTGTGGTGGTCTACATGC
1 CTGTGTGGAGGTCTACACGC
*
28308158 TTGTGTG
1 CTGTGTG
28308165 CAAGATGCAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.21, G:0.36, T:0.32
Consensus pattern (20 bp):
CTGTGTGGAGGTCTACACGC
Found at i:28311323 original size:19 final size:20
Alignment explanation
Indices: 28311299--28311346 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
28311289 GTCACATTGC
*
28311299 AAATATAAATAAA-AATTAT
1 AAATATAAATAAATAATTAA
28311318 AAATAT--ATAAATTAATTAA
1 AAATATAAATAAA-TAATTAA
28311337 AAATATAAAT
1 AAATATAAAT
28311347 TTTCACATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 5 0.21
19 17 0.71
21 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAATAAATAATTAA
Found at i:28311780 original size:25 final size:24
Alignment explanation
Indices: 28311727--28311797 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
28311717 TTTAATTGTA
**
28311727 TATATTTTTATAAATATATATTTTG
1 TATATTTTTA-AAATATATAAATTG
28311752 TATATTTTTAAAATAATAATAAATT-
1 TATATTTTTAAAAT-AT-ATAAATTG
28311777 TATATTTTATAAAA-AT-TAAAT
1 TATATTTT-TAAAATATATAAAT
28311798 ATATAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 5 0.12
24 6 0.15
25 20 0.49
26 10 0.24
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
TATATTTTTAAAATATATAAATTG
Found at i:28311898 original size:20 final size:18
Alignment explanation
Indices: 28311868--28311921 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
28311858 TGTGAAAAAA
*
28311868 TTTACTTTTTAAATTAAT
1 TTTAATTTTTAAATTAAT
*
28311886 TTATATATTTTTAAAGTTTAT
1 TT-TA-ATTTTTAAA-TTAAT
*
28311907 TTTAATTTTTTAATT
1 TTTAATTTTTAAATT
28311922 TATATTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.13
19 10 0.33
20 10 0.33
21 6 0.20
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTAATTTTTAAATTAAT
Found at i:28311927 original size:20 final size:21
Alignment explanation
Indices: 28311873--28311929 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
28311863 AAAAATTTAC
28311873 TTTTTAAATTA-A-TTTATAT
1 TTTTTAAATTATATTTTATAT
28311892 ATTTTTAAAGTT-TATTTTA-AT
1 -TTTTTAAA-TTATATTTTATAT
*
28311913 TTTTTAATTTATATTTT
1 TTTTTAAATTATATTTT
28311930 TCATGTTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 2 0.06
20 21 0.66
21 5 0.16
22 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTAAATTATATTTTATAT
Found at i:28313911 original size:51 final size:51
Alignment explanation
Indices: 28313835--28314025 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 51
28313825 TGCCTATAAA
*
28313835 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATA-GATAATGGT
1 CACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGA-AGGAT-ATGGT
* * * *
28313886 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCTTTGGT
1 CACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAGGATATGGT
* * * * *
28313937 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGGA-CAGGAAAG-TTTGAT
1 CACATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GGAAGGATATGGT
* *
28313987 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCG
28314026 AATGATAATA
Statistics
Matches: 124, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
50 41 0.33
51 79 0.64
52 4 0.03
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (51 bp):
CACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAGGATATGGT
Found at i:28314022 original size:101 final size:102
Alignment explanation
Indices: 28313839--28314022 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 102
28313829 TATAAACACA
* * *
28313839 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACATGTGTAGTACTATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGGATCGAAAGATAATGATCACATGTGTAGTACTATG
* *
28313904 TGCAGGCTACTATGTGTACCGGAAGGCTTTGGTCACG
66 TGAAGGCTACTACGTGTACCGGAAGGCTTTGGTCACG
* * *
28313941 TGTGTAGTACTATGTGCAGGCTACTACGTGGA-CAGGAAAG-T-TTGATCACGTGTGTAGTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGGATC--GAAAGATAATGATCACATGTGTAGTACTA
28314003 TGTGAAGGCTACTACGTGTA
64 TGTGAAGGCTACTACGTGTA
28314023 TCGAATGATA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
101 37 0.51
102 31 0.43
103 4 0.06
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (102 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGGATCGAAAGATAATGATCACATGTGTAGTACTATG
TGAAGGCTACTACGTGTACCGGAAGGCTTTGGTCACG
Found at i:28315386 original size:20 final size:20
Alignment explanation
Indices: 28315363--28315417 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
28315353 AGATTAATTC
28315363 AGCTCAATTTTAGCTCAATA
1 AGCTCAATTTTAGCTCAATA
* *
28315383 AGCTC-GTTCTTAGCTCAATG
1 AGCTCAATT-TTAGCTCAATA
*
28315403 AGCTCATTTTTAGCT
1 AGCTCAATTTTAGCT
28315418 TACTTTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTTAGCTCAATA
Found at i:28316954 original size:13 final size:13
Alignment explanation
Indices: 28316919--28316960 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
28316909 GTGAGTTTGT
*
28316919 AAAAAAATATTCAA
1 AAAAAAAT-TTCGA
28316933 AAAAAAATTTCGA
1 AAAAAAATTTCGA
28316946 AAAAAAATTT-GA
1 AAAAAAATTTCGA
28316958 AAA
1 AAA
28316961 TTCAAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 5 0.19
13 14 0.52
14 8 0.30
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (13 bp):
AAAAAAATTTCGA
Found at i:28318174 original size:12 final size:12
Alignment explanation
Indices: 28318157--28318224 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
28318147 AGTGAAAAGC
28318157 AAAAAGAGATTG
1 AAAAAGAGATTG
*
28318169 AAAAAGAAATTG
1 AAAAAGAGATTG
*
28318181 --AAAGAGA-AG
1 AAAAAGAGATTG
*
28318190 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
28318205 AAAAAGAAATTG
1 AAAAAGAGATTG
28318217 AAAAAGAG
1 AAAAAGAG
28318225 TCTTCAAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
9 1 0.02
10 6 0.14
11 4 0.09
12 20 0.47
13 5 0.12
15 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:28318198 original size:15 final size:15
Alignment explanation
Indices: 28318180--28318213 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28318170 AAAAGAAATT
28318180 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
28318195 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
28318210 GAAA
1 GAAA
28318214 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:28318219 original size:21 final size:20
Alignment explanation
Indices: 28318167--28318219 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
28318157 AAAAAGAGAT
28318167 TGAAAAAGAAATTGAAAGA-
1 TGAAAAAGAAATTGAAAGAG
*
28318186 -GAAGAA-AAA--GAAAGAG
1 TGAAAAAGAAATTGAAAGAG
28318202 TGGAAAAAGAAATTGAAA
1 T-GAAAAAGAAATTGAAA
28318220 AAGAGTCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
15 6 0.23
17 3 0.12
18 10 0.38
19 3 0.12
21 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (20 bp):
TGAAAAAGAAATTGAAAGAG
Found at i:28320033 original size:20 final size:20
Alignment explanation
Indices: 28320000--28320062 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
28319990 AGCTCAATCA
*
28320000 AGTTCAATTCAGCTCAATTTT
1 AGTTCAA-TGAGCTCAATTTT
*
28320021 AGTTCAATGAGCTC-GTTCTT
1 AGTTCAATGAGCTCAATT-TT
* *
28320041 AGCTCAATGAGCTCATTTTT
1 AGTTCAATGAGCTCAATTTT
28320061 AG
1 AG
28320063 CTTACTTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.06
20 25 0.69
21 9 0.25
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (20 bp):
AGTTCAATGAGCTCAATTTT
Found at i:28320063 original size:20 final size:20
Alignment explanation
Indices: 28320010--28320064 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
28320000 AGTTCAATTC
* *
28320010 AGCTCAATTTTAGTTCAATG
1 AGCTCATTTTTAGCTCAATG
* *
28320030 AGCTCGTTCTTAGCTCAATG
1 AGCTCATTTTTAGCTCAATG
28320050 AGCTCATTTTTAGCT
1 AGCTCATTTTTAGCT
28320065 TACTTTAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (20 bp):
AGCTCATTTTTAGCTCAATG
Found at i:28323315 original size:43 final size:43
Alignment explanation
Indices: 28323264--28323350 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
28323254 ACCTTTAAAC
*
28323264 AATTATAGTCTTCTTGATGAGTCCCCAACCAAAACCACCATAG
1 AATTATAGTCCTCTTGATGAGTCCCCAACCAAAACCACCATAG
*
28323307 AATTATAGTCCTCTTGATGAGTCCCCAACCAAAACCACTATAG
1 AATTATAGTCCTCTTGATGAGTCCCCAACCAAAACCACCATAG
28323350 A
1 A
28323351 CTTTACTCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (43 bp):
AATTATAGTCCTCTTGATGAGTCCCCAACCAAAACCACCATAG
Found at i:28325148 original size:22 final size:24
Alignment explanation
Indices: 28325120--28325168 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
28325110 ACAAATTAAT
*
28325120 AAAAAAAT-GAAAGAAATAA-ACA
1 AAAAAAATAGAAAGAAAAAATACA
*
28325142 AAAAAAATATAAAGAAAAAATACA
1 AAAAAAATAGAAAGAAAAAATACA
28325166 AAA
1 AAA
28325169 TATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
24 6 0.26
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.10
Consensus pattern (24 bp):
AAAAAAATAGAAAGAAAAAATACA
Found at i:28325753 original size:21 final size:21
Alignment explanation
Indices: 28325729--28325778 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28325719 ATATATAATA
*
28325729 AAAATAATACTTAATAACAAT
1 AAAATAATACTTAATAAAAAT
*
28325750 AAAATCAA-ATTTAATAAAAAT
1 AAAAT-AATACTTAATAAAAAT
28325771 -AAATAATA
1 AAAATAATA
28325779 AATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.08
20 5 0.20
21 16 0.64
22 2 0.08
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAATACTTAATAAAAAT
Found at i:28327358 original size:130 final size:130
Alignment explanation
Indices: 28327152--28327403 Score: 380
Period size: 130 Copynumber: 1.9 Consensus size: 130
28327142 GATTTGTTTA
* * * **
28327152 TTTAGTCTGCCCCACTGCAATTTCAGGGGGATAAGACTTGCTTTTTTGAGTCTGCTCCACTGCAA
1 TTTAGTCTGCCCCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTGAGTCTGCTCCACTGCAA
* *
28327217 CTTCAGGGAGATAAGACCCGATGTGATCTACTCTAAAGCAACTTCAGAGAGATAAGATTCGCCAC
66 CTTCAGGGAGATAAGACCAGATGCGATCTACTCT-AAGCAACTTCAGAGAGATAAGATTCGCCAC
28327282 C
130 C
*
28327283 TTTAGTCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAA
1 TTTAGTCTGCCCCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTGAGTCTGCTCCACTGCAA
* * **
28327347 CTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGAT
66 CTTCAGGGAGATAAGACCAGATGCGATCTACTCTAAGCAACTTCAGAGAGATAAGAT
28327404 CTGTGATTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
129 21 0.19
130 47 0.43
131 41 0.38
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (130 bp):
TTTAGTCTGCCCCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTGAGTCTGCTCCACTGCAA
CTTCAGGGAGATAAGACCAGATGCGATCTACTCTAAGCAACTTCAGAGAGATAAGATTCGCCACC
Found at i:28327420 original size:84 final size:84
Alignment explanation
Indices: 28327288--28327443 Score: 219
Period size: 84 Copynumber: 1.8 Consensus size: 84
28327278 CCACCTTTAG
* * *
28327288 TCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
1 TCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGATTA-TTAATCTGCTCCACTACAACTTCAG
28327353 GGAGATAAGACTAGATGCGA
65 GGAGATAAGACTAGATGCGA
*
28327373 TCTG-CTCTCTGCAACTTC-AGAGAGATAAGATCTGTGATT-TTAATCTGCTCCACTACAACTTC
1 TCTGCCTCACTGCAACTTCAAGAG-GATAAGA-CT-TGATTATTAATCTGCTCCACTACAACTTC
28327435 AGGGAGATA
63 AGGGAGATA
28327444 GGATTATTGG
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
83 4 0.06
84 50 0.78
85 6 0.09
86 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (84 bp):
TCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGATTATTAATCTGCTCCACTACAACTTCAGG
GAGATAAGACTAGATGCGA
Found at i:28327436 original size:44 final size:43
Alignment explanation
Indices: 28327117--28327491 Score: 196
Period size: 44 Copynumber: 8.7 Consensus size: 43
28327107 TTCTAATCCA
* * * * * *
28327117 CTCCACTACAACTTTAGGGAGATAGGAT-TTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTTG-AT-TTTAATCTG
* * * * * *
28327161 CCCCACTGCAATTTCAGGGGGATAAGA-CTTGCTTTTTTGAGTCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTTG--ATTTT-AATCTG
* ** * * *
28327206 CTCCACTGCAACTTCAGGGAGATAAGA-CCCGA-TGTGATCTA
1 CTCCACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCTG
* ** * * *
28327247 CTCTAAAGCAACTTCAGAGAGATAAGAT-TCGCCACCTTTAGTCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTTG--A-TTTTAATCTG
* *
28327292 C-CTCACTGCAACTTCA-AGAGGATAAGA-CTTGCTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGAGA-GATAAGATCTTGATT--TTAATCTG
* * ***
28327336 CTCCACTGCAACTTCAGGGAGATAAGA-CTAGA-TGCGATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCTG
*
28327377 CT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCT-TGATTTTAATCTG
* * * * *
28327420 CTCCACTACAACTTCAGGGAGATAGGATTATTGGTTTTAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGA-TCTTGATTTTAATCTG
* *
28327464 CTCCACTGCAGCTTCAGGGAGATAAGAT
1 CTCCACTGCAACTTCAGAGAGATAAGAT
28327492 TCACCATCTT
Statistics
Matches: 258, Mismatches: 53, Indels: 41
0.73 0.15 0.12
Matches are distributed among these distances:
40 22 0.09
41 36 0.14
42 5 0.02
43 11 0.04
44 119 0.46
45 65 0.25
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCTG
Found at i:28327486 original size:128 final size:129
Alignment explanation
Indices: 28327152--28327490 Score: 330
Period size: 128 Copynumber: 2.6 Consensus size: 129
28327142 GATTTGTTTA
* * * * * * * * *
28327152 TTTAGTCTGCCCCACTGCAATTTCAGGGGGATAAGACTTGCTTTTTTGAGTCTGCTCCACTGCAA
1 TTTAATCTGCCTCACTACAACTTCAAGAGGATAAGAATTGC-TTATT-AATCTGCTCCACTGCAA
* *
28327217 CTTCAGGGAGATAAGACCCGATGTGATCTACTCTAAAGCAACTTCAGAGAGATAAGATTCGCCAC
64 CTTCAGGGAGATAAGACCAGATGCGATCTACTCTAAAGCAACTTCAGAGAGATAAGATTCGCCAC
28327282 C
129 C
* * * *
28327283 TTTAGTCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAAC
1 TTTAATCTGCCTCACTACAACTTCAAGAGGATAAGAATTGCTTA-TTAATCTGCTCCACTGCAAC
* * ** **
28327348 TTCAGGGAGATAAGACTAGATGCGATCTGCTCT-CTGCAACTTCAGAGAGATAAGA-TCTGTGA-
65 TTCAGGGAGATAAGACCAGATGCGATCTACTCTAAAGCAACTTCAGAGAGATAAGATTC-GCCAC
*
28327410 T
129 C
* * *
28327411 TTTAATCTG-CTCCACTACAACTTC-AGGGAGATAGGATTATTGGTT-TTAATCTGCTCCACTGC
1 TTTAATCTGCCT-CACTACAACTTCAAGAG-GATAAGA--ATTGCTTATTAATCTGCTCCACTGC
*
28327473 AGCTTCAGGGAGATAAGA
62 AACTTCAGGGAGATAAGA
28327491 TTCACCATCT
Statistics
Matches: 180, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
127 5 0.03
128 60 0.33
129 22 0.12
130 54 0.30
131 39 0.22
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (129 bp):
TTTAATCTGCCTCACTACAACTTCAAGAGGATAAGAATTGCTTATTAATCTGCTCCACTGCAACT
TCAGGGAGATAAGACCAGATGCGATCTACTCTAAAGCAACTTCAGAGAGATAAGATTCGCCACC
Found at i:28327979 original size:260 final size:260
Alignment explanation
Indices: 28327518--28328035 Score: 811
Period size: 260 Copynumber: 2.0 Consensus size: 260
28327508 TTTTAATTGT
* * * * *
28327518 AATGTTGGGGAAACAAGATTCGCCGTCGTAGATTCAATTTGTTCCACTACACCGCCAAGGAAGTA
1 AATGTTGAGGAAACAAGATTCACCGTCATAGATTCAATCTATTCCACTACACCGCCAAGGAAGTA
* *
28327583 AGATTCGCCGTTTCGGCTTCAATCTTTTTCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCAC
66 AGATTCACCGTTGCGGCTTCAATCTTTTTCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCAC
** *
28327648 AACTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAGATTCGCTGTTG
131 AACTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAGATTCGCCATCG
* * *
28327713 TGGCTTCAATCTGCTCTGCTACAATGCCAGGGAAGTAAGATTCGCCGTTACGGCTTCAATCTTAC
196 TGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAATAAGATTCGCCGTTACGGCTTCAATCTTAC
* *
28327778 AATGTTGAGGAAACAAGATTCACCGTCATAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
1 AATGTTGAGGAAACAAGATTCACCGTCATAGATTCAATCTATTCCACTACACCGCCAAGGAAGTA
* * *
28327843 AGATTCATCGTTGCGGCTTCAATTTTTTTCACTTTAATGCCAAAGAGATAGGATTCGCTGCCCAC
66 AGATTCACCGTTGCGGCTTCAATCTTTTTCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCAC
* * *
28327908 AGCTTCAATCCGCTCCACTTCAGCTAATCCAAGCCTTAACGCCAGGGAGATAAGATTCGCCATCG
131 AACTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAGATTCGCCATCG
* * **
28327973 TGGCTTCAATCTGCTCCGCTATAACGCTAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTT
196 TGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAATAAGATTCGCCGTTACGGCTTCAATCTT
28328036 TTCCATTGCT
Statistics
Matches: 233, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
260 233 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (260 bp):
AATGTTGAGGAAACAAGATTCACCGTCATAGATTCAATCTATTCCACTACACCGCCAAGGAAGTA
AGATTCACCGTTGCGGCTTCAATCTTTTTCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCAC
AACTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAGATTCGCCATCG
TGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAATAAGATTCGCCGTTACGGCTTCAATCTTAC
Found at i:28328132 original size:45 final size:45
Alignment explanation
Indices: 28328083--28328222 Score: 149
Period size: 45 Copynumber: 3.2 Consensus size: 45
28328073 CGATCTGCTT
* *
28328083 CACTGCTAATACAGGAAGGCAAGATCTGTTATTTTCAACCTACTC
1 CACTGCTAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
** * * * * * * *
28328128 CACTGCTGCT-CAGGGAGACAAG-GCTGGTATCTTCGATCTACTT
1 CACTGCTAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
* *
28328171 CACTGCCAATACAGTAAGACAAGATCTGCTATTTTCAACCTACTC
1 CACTGCTAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
28328216 CACTGCT
1 CACTGCT
28328223 GTTTAGGGAG
Statistics
Matches: 71, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
43 22 0.31
44 20 0.28
45 29 0.41
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (45 bp):
CACTGCTAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
Found at i:28328173 original size:88 final size:88
Alignment explanation
Indices: 28328069--28328238 Score: 277
Period size: 88 Copynumber: 1.9 Consensus size: 88
28328059 AAGACTGATG
* * * *
28328069 TCTTCGATCTGCTTCACTGCTAATACAGGAAGGCAAGATCTGTTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
28328134 TGCTCAGGGAGACAAGGCTGGTA
66 TGCTCAGGGAGACAAGGCTGGTA
*
28328157 TCTTCGATCTACTTCACTGCCAATACAGTAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
28328222 TGTTTAGGGAGACAAGG
66 TGCTCAGGGAGACAAGG
28328239 TTGGAGTTTC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
TGCTCAGGGAGACAAGGCTGGTA
Found at i:28328235 original size:44 final size:44
Alignment explanation
Indices: 28328102--28328237 Score: 130
Period size: 44 Copynumber: 3.1 Consensus size: 44
28328092 TACAGGAAGG
* *
28328102 CAAGATCTGTTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGTTCAGGGAGA
* * * * * * ** * **
28328146 CAAG-GCTGGTATCTTCGATCTACTTCACTGCCAATACAGTAAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTG-CTGTTCAGGGAGA
*
28328190 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGTTTAGGGAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGTTCAGGGAGA
28328234 CAAG
1 CAAG
28328238 GTTGGAGTTT
Statistics
Matches: 66, Mismatches: 24, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
43 20 0.30
44 26 0.39
45 20 0.30
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (44 bp):
CAAGATCTGCTATTTTCAACCTACTCCACTGCTGTTCAGGGAGA
Found at i:28329496 original size:18 final size:17
Alignment explanation
Indices: 28329475--28329539 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 17
28329465 TGGGCCTCTC
*
28329475 CTTTTCCTCTTCTTATTT
1 CTTTTCCTTTTCTT-TTT
*
28329493 CTTTCTCTTTTTCTTTTT
1 CTTT-TCCTTTTCTTTTT
*
28329511 CTTTTTTCTTTTCTTTTT
1 C-TTTTCCTTTTCTTTTT
28329529 CTTTTCCTTTT
1 CTTTTCCTTTT
28329540 TTCCATCATC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.22
18 20 0.50
19 11 0.28
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (17 bp):
CTTTTCCTTTTCTTTTT
Found at i:28329505 original size:25 final size:25
Alignment explanation
Indices: 28329471--28329529 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
28329461 TGCCTGGGCC
*
28329471 TCTCCTTTTCCTCTTCTTATTTCTT
1 TCTCTTTTTCCTCTTCTTATTTCTT
* * *
28329496 TCTCTTTTTCTTTTTCTTTTTTCTT
1 TCTCTTTTTCCTCTTCTTATTTCTT
28329521 T-TCTTTTTC
1 TCTCTTTTTC
28329530 TTTTCCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 8 0.27
25 22 0.73
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (25 bp):
TCTCTTTTTCCTCTTCTTATTTCTT
Found at i:28329507 original size:12 final size:11
Alignment explanation
Indices: 28329484--28329540 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 11
28329474 CCTTTTCCTC
28329484 TTCTTATTTCTT
1 TTCTT-TTTCTT
28329496 TCTCTTTTTCTTT
1 T-TCTTTTTC-TT
28329509 TTCTTTTTTCTT
1 TTC-TTTTTCTT
28329521 TTCTTTTTCTT
1 TTCTTTTTCTT
28329532 TTCCTTTTT
1 TT-CTTTTT
28329541 TCCATCATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.24
12 18 0.44
13 13 0.32
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:28329525 original size:24 final size:25
Alignment explanation
Indices: 28329484--28329542 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
28329474 CCTTTTCCTC
*
28329484 TTCTTATTTCTTTCTCTTTTTCTTT
1 TTCTTTTTTCTTTCTCTTTTTCTTT
28329509 TTCTTTTTTCTTT-TCTTTTTCTTT
1 TTCTTTTTTCTTTCTCTTTTTCTTT
*
28329533 TCCTTTTTTC
1 TTCTTTTTTC
28329543 CATCATCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 20 0.62
25 12 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (25 bp):
TTCTTTTTTCTTTCTCTTTTTCTTT
Found at i:28329568 original size:14 final size:14
Alignment explanation
Indices: 28329535--28329568 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28329525 TTTTCTTTTC
28329535 CTTTTTTCCATCAT
1 CTTTTTTCCATCAT
*
28329549 CATTTTTCCATCAT
1 CTTTTTTCCATCAT
28329563 -TTTTTT
1 CTTTTTT
28329569 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTTTTTCCATCAT
Found at i:28330417 original size:25 final size:25
Alignment explanation
Indices: 28330364--28330429 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
28330354 AAGAAGATCC
* *
28330364 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
28330389 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
28330414 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
28330430 TGTATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:28336602 original size:21 final size:21
Alignment explanation
Indices: 28336557--28336610 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28336547 CAATAATACT
*
28336557 TAATAAAAATAAAATCAAATT
1 TAATAAAAATAAAATCAAATA
28336578 TAATAAAAAT-AAAT--AATA
1 TAATAAAAATAAAATCAAATA
*
28336596 AAATAATAAATAAAA
1 TAATAA-AAATAAAA
28336611 AAAGACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 8 0.28
19 4 0.14
20 7 0.24
21 10 0.34
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
TAATAAAAATAAAATCAAATA
Found at i:28336603 original size:15 final size:15
Alignment explanation
Indices: 28336557--28336612 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
28336547 CAATAATACT
28336557 TAATAAA-AATAAAA
1 TAATAAATAATAAAA
**
28336571 TCAA-ATTTAAT-AAA
1 T-AATAAATAATAAAA
28336585 -AATAAATAATAAAA
1 TAATAAATAATAAAA
28336599 TAATAAATAA-AAAA
1 TAATAAATAATAAAA
28336613 AGACTAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
12 2 0.06
13 5 0.15
14 12 0.36
15 14 0.42
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
TAATAAATAATAAAA
Found at i:28338647 original size:23 final size:22
Alignment explanation
Indices: 28338604--28338647 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
28338594 CCATTATTCA
* * *
28338604 TTTTCTCCTCTTTTTTTCTATT
1 TTTTCTCATCTTTTGTCCTATT
28338626 TTTTACTCATCTTTTGTCCTAT
1 TTTT-CTCATCTTTTGTCCTAT
28338648 CTCTTTGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTTCTCATCTTTTGTCCTATT
Found at i:28339724 original size:22 final size:22
Alignment explanation
Indices: 28339694--28339764 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
28339684 TCGATTTATT
28339694 TGCAATTTACTGGCAGCTTGTC
1 TGCAATTTACTGGCAGCTTGTC
* * * *
28339716 TACAATTTAATGG-TGACTTATC
1 TGCAATTTACTGGCAG-CTTGTC
28339738 -GCAATTTACTGGCAGCTTGTC
1 TGCAATTTACTGGCAGCTTGTC
28339759 TGCAAT
1 TGCAAT
28339765 CCATTGATAG
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 16 0.42
22 22 0.58
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (22 bp):
TGCAATTTACTGGCAGCTTGTC
Found at i:28341806 original size:13 final size:14
Alignment explanation
Indices: 28341778--28341810 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28341768 TGAGTTGTGC
28341778 GTTTGAGGTCTTGG
1 GTTTGAGGTCTTGG
*
28341792 GTTTG-GGTTTTGG
1 GTTTGAGGTCTTGG
28341805 GTTTGA
1 GTTTGA
28341811 TTCCTTGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.06, C:0.03, G:0.42, T:0.48
Consensus pattern (14 bp):
GTTTGAGGTCTTGG
Found at i:28342872 original size:17 final size:17
Alignment explanation
Indices: 28342845--28342889 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
28342835 CTGGGCTATT
28342845 TGGGCCGTGTGGGCCACA
1 TGGG-CGTGTGGGCCACA
28342863 TGGGCGTGTGGGCCACA
1 TGGGCGTGTGGGCCACA
* *
28342880 CGAGCGTGTG
1 TGGGCGTGTG
28342890 TGAGGCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
TGGGCGTGTGGGCCACA
Found at i:28348342 original size:53 final size:53
Alignment explanation
Indices: 28348261--28348409 Score: 219
Period size: 53 Copynumber: 2.8 Consensus size: 53
28348251 GTATTTTTCA
* * * *
28348261 ATTTGTAAG-ACGCAATGTTATTGTTCTTGAACAAAATCGTTTAATTATGTTTT
1 ATTTGTAAGAAAG-AATGTTGTTGGTCTTGAACAAAATCGTTTAATTATGTATT
28348314 ATTTGTAAGAAAGAATGTTGTTGGTCTTGAACAAAATCGTTTAATTATGTATT
1 ATTTGTAAGAAAGAATGTTGTTGGTCTTGAACAAAATCGTTTAATTATGTATT
* * *
28348367 ATTTGTAAGACACAATTTTGTTGGTCTTGAACAAAATCGTTTA
1 ATTTGTAAGAAAGAATGTTGTTGGTCTTGAACAAAATCGTTTA
28348410 CTTTTTTTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 86 0.98
54 2 0.02
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (53 bp):
ATTTGTAAGAAAGAATGTTGTTGGTCTTGAACAAAATCGTTTAATTATGTATT
Found at i:28348796 original size:16 final size:16
Alignment explanation
Indices: 28348775--28348810 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28348765 GGGGCATTTT
*
28348775 TAAAAGAAATAAAAAA
1 TAAAAGAAACAAAAAA
*
28348791 TAAAAGAACCAAAAAA
1 TAAAAGAAACAAAAAA
28348807 TAAA
1 TAAA
28348811 TATGAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.11
Consensus pattern (16 bp):
TAAAAGAAACAAAAAA
Found at i:28349004 original size:5 final size:5
Alignment explanation
Indices: 28348991--28349022 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
28348981 TTTGAAATAA
*
28348991 AAGAT AAGAG AAGAG AAGAG AAGAG AAGAG AA
1 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AA
28349023 AAACAAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (5 bp):
AAGAG
Found at i:28366251 original size:43 final size:43
Alignment explanation
Indices: 28366201--28366381 Score: 147
Period size: 43 Copynumber: 4.2 Consensus size: 43
28366191 TAATAAAAAT
*
28366201 GCCGCTAAAAGTCAAGACCTTTAGCGACACTTTTCCCACAAAC
1 GCCGCTAAAAGTCAAGACCTTTAGCGACACTTTTACCACAAAC
* * * * * *
28366244 GCCGCTAAAGGCCAGGACCTTTAGCGGCGCTTTTACCACAAAT
1 GCCGCTAAAAGTCAAGACCTTTAGCGACACTTTTACCACAAAC
* * * *
28366287 GCTGCT-AAAGATCATGACCTTTTA-CGACGCTTCTACCACAAAC
1 GCCGCTAAAAG-TCAAGACC-TTTAGCGACACTTTTACCACAAAC
* * * **
28366330 GCCACTATGAAG--AATGACCTTTAGCAACA-TTTTTTCACAAAC
1 GCCGCTA-AAAGTCAA-GACCTTTAGCGACACTTTTACCACAAAC
28366372 GCCGCTAAAA
1 GCCGCTAAAA
28366382 ACATGACTTT
Statistics
Matches: 107, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
41 2 0.02
42 24 0.22
43 74 0.69
44 4 0.04
45 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAAGTCAAGACCTTTAGCGACACTTTTACCACAAAC
Found at i:28366326 original size:86 final size:85
Alignment explanation
Indices: 28366155--28366332 Score: 198
Period size: 86 Copynumber: 2.1 Consensus size: 85
28366145 TTTTAGAAAT
* * * * *
28366155 AAACACCGCTAAAGGTCATGACTTTTAGCAGCGCTTTAATAAAAATGCCGCTAAAAGTCAAGACC
1 AAACGCCGCTAAAGGCCAGGACCTTTAGCAGCGCTTTAACAAAAATGCCGCTAAAAGTCAAGACC
* *
28366220 TTTAGCGACACTTTTCCCAC
66 TTTAGCGACACTTCTACCAC
* * * * *
28366240 AAACGCCGCTAAAGGCCAGGACCTTTAGCGGCGCTTTTACCACAAATGCTGCT-AAAGATCATGA
1 AAACGCCGCTAAAGGCCAGGACCTTTAGCAGCGC-TTTAACAAAAATGCCGCTAAAAG-TCAAGA
*
28366304 CCTTTTA-CGACGCTTCTACCAC
64 CC-TTTAGCGACACTTCTACCAC
28366326 AAACGCC
1 AAACGCC
28366333 ACTATGAAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
85 33 0.43
86 40 0.52
87 4 0.05
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (85 bp):
AAACGCCGCTAAAGGCCAGGACCTTTAGCAGCGCTTTAACAAAAATGCCGCTAAAAGTCAAGACC
TTTAGCGACACTTCTACCAC
Found at i:28369458 original size:6 final size:6
Alignment explanation
Indices: 28369447--28369484 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
28369437 CCCCCCTAAA
*
28369447 AAAAAT AAAAAT AAAACT AAAAAT -AAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
28369485 TCAATCCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:28369462 original size:5 final size:5
Alignment explanation
Indices: 28369443--28369485 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
28369433 AGCACCCCCC
28369443 TAAAA -AAAA TAAAAA TAAAA CTAAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA T-AAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA T
28369486 CAATCCACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.12
5 19 0.56
6 7 0.21
7 4 0.12
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:28370116 original size:65 final size:65
Alignment explanation
Indices: 28370035--28370177 Score: 261
Period size: 65 Copynumber: 2.2 Consensus size: 65
28370025 GGATTTTTTC
28370035 GTTTTTGGGTTTTAGGGGAGAAATTTGGGGAAAAATCAGCGCCAATTTTTTTAAGTAAAATGAAA
1 GTTTTTGGGTTTTAGGGGAGAAATTTGGGGAAAAATCAGCGCCAATTTTTTTAAGTAAAATGAAA
28370100 GTTTTTGGGTTTTAGGGGAGAAATTTGGGGAAAAATCAGCGCCAATTTTTTTAAGTAAAATGAAA
1 GTTTTTGGGTTTTAGGGGAGAAATTTGGGGAAAAATCAGCGCCAATTTTTTTAAGTAAAATGAAA
*
28370165 -TTTGTGGCGTTTT
1 GTTTTTGG-GTTTT
28370178 TATAAAAAAC
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
64 6 0.08
65 70 0.92
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (65 bp):
GTTTTTGGGTTTTAGGGGAGAAATTTGGGGAAAAATCAGCGCCAATTTTTTTAAGTAAAATGAAA
Found at i:28370766 original size:7 final size:7
Alignment explanation
Indices: 28370756--28370829 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
28370746 ACCCCTATAT
28370756 CCTAAAC
1 CCTAAAC
*
28370763 CCTAAAT
1 CCTAAAC
* *
28370770 CATAAAA
1 CCTAAAC
*
28370777 CATAAAC
1 CCTAAAC
*
28370784 ACTAAACC
1 CCTAAA-C
28370792 CCT-AAC
1 CCTAAAC
*
28370798 CCTTAAC
1 CCTAAAC
*
28370805 CCTTAAC
1 CCTAAAC
*
28370812 CTCTAACC
1 C-CTAAAC
28370820 CCTAAAC
1 CCTAAAC
28370827 CCT
1 CCT
28370830 CTTTTACAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 4 0.07
7 42 0.78
8 8 0.15
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:28370817 original size:21 final size:22
Alignment explanation
Indices: 28370779--28370829 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
28370769 TCATAAAACA
* *
28370779 TAAACACTAAACCCCTAAC-CC
1 TAAACCCTTAACCCCTAACCCC
* *
28370800 TTAACCCTTAACCTCTAACCCC
1 TAAACCCTTAACCCCTAACCCC
28370822 TAAACCCT
1 TAAACCCT
28370830 CTTTTACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCCTTAACCCCTAACCCC
Found at i:28371123 original size:14 final size:15
Alignment explanation
Indices: 28371104--28371136 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
28371094 CTTAAACCAG
28371104 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
28371118 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
28371133 AATC
1 AATC
28371137 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:28371634 original size:41 final size:40
Alignment explanation
Indices: 28371541--28371653 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 40
28371531 AAATGTTTTT
*
28371541 GCGGCGCTTTTTCAAAAACGCCGCTAAATCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCGAGCATTA
*
28371581 GCGGCGCTTTTTCAAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTC-AAAAACGCCGCTAAAGC-CCGAGCATTA
*
28371623 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCC
28371654 ACGAAAGGCC
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 14 0.21
41 33 0.49
42 21 0.31
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (40 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCGAGCATTA
Found at i:28371782 original size:39 final size:38
Alignment explanation
Indices: 28371694--28371784 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 38
28371684 TAGGTTTTTT
*
28371694 GCGGCGCTTTTTAAAAAAGCCGCTAATGCTCATTTTTA
1 GCGGCGCTTTTTAAAAAAGCCGCTAATGCTCATCTTTA
* **
28371732 ACGGCG-TTTTTTGAAAAGCGCTGCTAATGCTCGATCTTTA
1 GCGGCGCTTTTTAAAAAAGC-C-GCTAATGCTC-ATCTTTA
*
28371772 GCGGCGTTTTTTA
1 GCGGCGCTTTTTA
28371785 TCCAAACGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
37 11 0.26
38 6 0.14
39 10 0.23
40 11 0.26
41 5 0.12
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (38 bp):
GCGGCGCTTTTTAAAAAAGCCGCTAATGCTCATCTTTA
Found at i:28371799 original size:41 final size:39
Alignment explanation
Indices: 28371695--28371783 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 39
28371685 AGGTTTTTTG
* ** *
28371695 CGGCGCTTTTT-AAAAAAGCCGCTAATGCTCATTTTTAA
1 CGGCGTTTTTTGAAAAGCGCCGCTAATGCTCATCTTTAA
* *
28371733 CGGCGTTTTTTGAAAAGCGCTGCTAATGCTCGATCTTTAG
1 CGGCGTTTTTTGAAAAGCGCCGCTAATGCTC-ATCTTTAA
28371773 CGGCGTTTTTT
1 CGGCGTTTTTT
28371784 ATCCAAACGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 10 0.23
39 16 0.37
40 17 0.40
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (39 bp):
CGGCGTTTTTTGAAAAGCGCCGCTAATGCTCATCTTTAA
Found at i:28372273 original size:21 final size:20
Alignment explanation
Indices: 28372200--28372273 Score: 80
Period size: 19 Copynumber: 3.7 Consensus size: 20
28372190 AAAAAATTAA
* *
28372200 AATTTTTATAAATT-TTTGG
1 AATTTTTAAAAATTATTTTG
*
28372219 AATTTTCAAAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
*
28372238 AATTTTAAAAAAATTATTTTG
1 AATTTT-TAAAAATTATTTTG
28372259 AATTTTTAAATAATT
1 AATTTTTAAA-AATT
28372274 TTTGTCGAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
18 1 0.02
19 20 0.43
20 8 0.17
21 17 0.37
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:28376511 original size:18 final size:18
Alignment explanation
Indices: 28376465--28376515 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
28376455 AGCTCTCAGG
28376465 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
28376483 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
28376501 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
28376516 CTTCATTCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:28379349 original size:20 final size:20
Alignment explanation
Indices: 28379311--28379350 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28379301 AATATTTTCC
* *
28379311 AGTAAATCATTTTATAGAAA
1 AGTAAAACATTTTACAGAAA
*
28379331 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28379351 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28379365 original size:34 final size:35
Alignment explanation
Indices: 28379299--28379365 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28379289 CAAACACCAG
* *
28379299 AAAATATTTTCCAGTAAATCATTTTATAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28379334 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28379366 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28379372 original size:14 final size:14
Alignment explanation
Indices: 28379334--28379373 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28379324 ATAGAAAAGT
*
28379334 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
28379348 AAATCATTTTACGG
1 AAAACATTTTACAG
28379362 AAAACATTTTAC
1 AAAACATTTTAC
28379374 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28380741 original size:15 final size:15
Alignment explanation
Indices: 28380721--28380751 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28380711 CCGAGTTTGT
28380721 AACACCTGAAATCCA
1 AACACCTGAAATCCA
28380736 AACACCTGAAATCCA
1 AACACCTGAAATCCA
28380751 A
1 A
28380752 CCTAAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.32, G:0.06, T:0.13
Consensus pattern (15 bp):
AACACCTGAAATCCA
Found at i:28387374 original size:51 final size:51
Alignment explanation
Indices: 28387319--28387761 Score: 389
Period size: 51 Copynumber: 8.7 Consensus size: 51
28387309 GTGAAAGTGT
* * *
28387319 TGGTCACGTGTGTAGTACTATGTGAAGGCTATTACATGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * * * ** * * * * *
28387370 TGGTCACATATGCAGTACTAAGTGAAGGCTACAATATGTATCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* *
28387421 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * ** * * * *
28387472 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* * ** *
28387523 TGGTTACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * * *
28387574 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAA--TAA
* * *
28387625 TAGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATA-A
* * *
28387675 TGATCACGTGTGTTGTACTATGTGAAGGCTATTACGTGAACCG-TAAA-AA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
*
28387724 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGT
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGT
28387762 CTATCGAATG
Statistics
Matches: 312, Mismatches: 70, Indels: 21
0.77 0.17 0.05
Matches are distributed among these distances:
50 84 0.27
51 225 0.72
52 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
Found at i:28387477 original size:102 final size:102
Alignment explanation
Indices: 28387318--28387761 Score: 581
Period size: 102 Copynumber: 4.4 Consensus size: 102
28387308 AGTGAAAGTG
* * * *
28387318 TTGGTCACGTGTGTAGTACTATGTGAAGGCTATTACATGAATCGATAAATAATGGTCACATATGC
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
*
28387383 AGTACTAAGTGAAGGCTACAATATGTATCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
*
28387420 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
28387485 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* * * *
28387522 TTGGTTACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* * *
28387587 AGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* * * * * *
28387624 TTAGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTG
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTG
* * ** ** * **
28387687 TTGTACTATGTGAAGGCTATTACGTGAACCGTA-AA-AA
65 TAGTACTAAGTGAAGGCTACAATATGTACCG-AGAAGCT
*
28387724 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGT
28387762 CTATCGAATG
Statistics
Matches: 308, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
100 35 0.11
101 42 0.14
102 231 0.75
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
Found at i:28390712 original size:26 final size:27
Alignment explanation
Indices: 28390683--28390737 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
28390673 ACAAATTTCA
28390683 ACTCTTAG-GGGTATAACAGTTATTTT
1 ACTCTTAGAGGGTATAACAGTTATTTT
* ** *
28390709 ACTCTTCGAGGGTATTTCGGTTATTTT
1 ACTCTTAGAGGGTATAACAGTTATTTT
28390736 AC
1 AC
28390738 CCATCTGGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.44
Consensus pattern (27 bp):
ACTCTTAGAGGGTATAACAGTTATTTT
Found at i:28390748 original size:27 final size:27
Alignment explanation
Indices: 28390704--28391004 Score: 342
Period size: 27 Copynumber: 11.1 Consensus size: 27
28390694 TATAACAGTT
* * *
28390704 ATTTTACTCTTCGAGGGTATTTCGGTT
1 ATTTTACCCTTCGAGGGTATTTCGATC
*
28390731 ATTTTACCCATCTG-GGGTATTTCGATC
1 ATTTTACCCTTC-GAGGGTATTTCGATC
* *
28390758 ATTTTACCCATTAGA-GGTATTTCGGTC
1 ATTTTACCC-TTCGAGGGTATTTCGATC
*
28390785 ATTTTACCCATTTG-GGGTATTTCGATC
1 ATTTTACCC-TTCGAGGGTATTTCGATC
* *
28390812 ATTTTACCTTTCG-GAGGTATTTTGATC
1 ATTTTACCCTTCGAG-GGTATTTCGATC
28390839 ATTTTACCCTTCGAGGGTATTTTCG-TC
1 ATTTTACCCTTCGAGGGTA-TTTCGATC
* * *
28390866 ATTTTACCATTTGAGGGTATTTCAATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
*
28390893 ATTTTACCCTTCGAGGGTATTTCAATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
* * *
28390920 ATTCTACTCTTCGAGGGTATTTCGATT
1 ATTTTACCCTTCGAGGGTATTTCGATC
* *
28390947 ATTTTACCCTTCGAGGGTATTTCGGTT
1 ATTTTACCCTTCGAGGGTATTTCGATC
* *
28390974 ATTTTACCATTCGGGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
28391001 ATTT
1 ATTT
28391005 CCCCATGAAT
Statistics
Matches: 236, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
26 8 0.03
27 221 0.94
28 7 0.03
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATC
Found at i:28410283 original size:24 final size:24
Alignment explanation
Indices: 28410251--28410297 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28410241 GTATCTAATT
*
28410251 ATGAAAATACATTTGAATTTGTAC
1 ATGAAAATACATTTGAATCTGTAC
* **
28410275 ATGATAATATGTTTGAATCTGTA
1 ATGAAAATACATTTGAATCTGTA
28410298 TCTATAAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (24 bp):
ATGAAAATACATTTGAATCTGTAC
Found at i:28413667 original size:24 final size:24
Alignment explanation
Indices: 28413640--28413692 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
28413630 TCTGATTATA
28413640 AAAATACATCCGAATTTGTATATG
1 AAAATACATCCGAATTTGTATATG
** ** *
28413664 AAAATATGTTTGAATTTGTATCTG
1 AAAATACATCCGAATTTGTATATG
28413688 AAAAT
1 AAAAT
28413693 GTATATGTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.38
Consensus pattern (24 bp):
AAAATACATCCGAATTTGTATATG
Found at i:28415913 original size:228 final size:228
Alignment explanation
Indices: 28415516--28415938 Score: 846
Period size: 228 Copynumber: 1.9 Consensus size: 228
28415506 GTGTTTGATG
28415516 ATATAGTCATTATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATG
1 ATATAGTCATTATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATG
28415581 TTTTGATGGATGGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTT
66 TTTTGATGGATGGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTT
28415646 GAATGTGATTTTGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAAATGTATGG
131 GAATGTGATTTTGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAAATGTATGG
28415711 TTGATGAATGACTAAAAACATCAAAATCTACTA
196 TTGATGAATGACTAAAAACATCAAAATCTACTA
28415744 ATATAGTCATTATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATG
1 ATATAGTCATTATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATG
28415809 TTTTGATGGATGGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTT
66 TTTTGATGGATGGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTT
28415874 GAATGTGATTTTGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAAATGTATGG
131 GAATGTGATTTTGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAAATGTATGG
28415939 CTTGTAAATG
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
228 195 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.39
Consensus pattern (228 bp):
ATATAGTCATTATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATG
TTTTGATGGATGGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTT
GAATGTGATTTTGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAAATGTATGG
TTGATGAATGACTAAAAACATCAAAATCTACTA
Found at i:28416049 original size:176 final size:176
Alignment explanation
Indices: 28415755--28416110 Score: 712
Period size: 176 Copynumber: 2.0 Consensus size: 176
28415745 TATAGTCATT
28415755 ATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATGTTTTGATGGAT
1 ATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATGTTTTGATGGAT
28415820 GGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTTGAATGTGATTT
66 GGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTTGAATGTGATTT
28415885 TGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAA
131 TGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAA
28415931 ATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATGTTTTGATGGAT
1 ATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATGTTTTGATGGAT
28415996 GGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTTGAATGTGATTT
66 GGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTTGAATGTGATTT
28416061 TGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAA
131 TGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAA
28416107 ATGT
1 ATGT
28416111 GGGCATTGAG
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 180 1.00
ACGTcount: A:0.28, C:0.04, G:0.27, T:0.40
Consensus pattern (176 bp):
ATGTATGGCTTGTAAATGTGGTTTTATGGTTGATGAACTTTTGGCATTTTAATGTTTTGATGGAT
GGTGTTGAAATGGTCAAGTAAAGTTATGTTTTGAATAACAAATTTAGTATGCTTGAATGTGATTT
TGGCATGTGGGCATTGTGGTAAGTTTGGTAAAGAAAAATGTTAGAA
Found at i:28430954 original size:32 final size:31
Alignment explanation
Indices: 28430918--28431019 Score: 134
Period size: 32 Copynumber: 3.2 Consensus size: 31
28430908 TATGGGCCTT
*
28430918 TGTGCTAATCATATTACTGTTACTGATGGCTG
1 TGTGCCAATCATATTACTG-TACTGATGGCTG
* *
28430950 TGTGCCAATCATATCACTGCTACTGATGGCTT
1 TGTGCCAATCATATTACTG-TACTGATGGCTG
*
28430982 TGTGCCAATCATATTACTGTACTTATGGCT-
1 TGTGCCAATCATATTACTGTACTGATGGCTG
28431012 TGTAGCCA
1 TGT-GCCA
28431020 TTGAGTTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
30 3 0.05
31 14 0.22
32 46 0.73
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (31 bp):
TGTGCCAATCATATTACTGTACTGATGGCTG
Found at i:28438019 original size:22 final size:21
Alignment explanation
Indices: 28437994--28438037 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
28437984 TGATAAACTT
28437994 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
28438016 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
28438037 T
1 T
28438038 TAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:28447307 original size:30 final size:30
Alignment explanation
Indices: 28447245--28447309 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
28447235 TCTACATGTT
*
28447245 TGTGGCTCACAAGGGTGTGTGGCCTGCTCG
1 TGTGGCTCACAAGGGTGTGTGGCCGGCTCG
*
28447275 TGTGGCTCACACGGGTGTGTGGCCAGGC-CG
1 TGTGGCTCACAAGGGTGTGTGGCC-GGCTCG
28447305 TGTGG
1 TGTGG
28447310 AAATGCCCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.09, C:0.23, G:0.43, T:0.25
Consensus pattern (30 bp):
TGTGGCTCACAAGGGTGTGTGGCCGGCTCG
Found at i:28452528 original size:19 final size:19
Alignment explanation
Indices: 28452490--28452603 Score: 138
Period size: 19 Copynumber: 5.8 Consensus size: 19
28452480 AAATTAAATC
*
28452490 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
28452510 TCTAAGATTATATATCATA
1 TCTAAGATTACATATCATA
*
28452529 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
28452548 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
* *
28452569 TCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
28452588 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
28452604 CTCAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
19 56 0.68
20 10 0.12
21 16 0.20
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28452578 original size:40 final size:40
Alignment explanation
Indices: 28452490--28452602 Score: 176
Period size: 40 Copynumber: 2.9 Consensus size: 40
28452480 AAATTAAATC
* *
28452490 TCTAAGATTACAAAATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGC-ATATCATATCTAAGATTGCATATATCATA
28452529 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
28452569 TCTAGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
28452603 CCTCAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
38 16 0.23
39 10 0.14
40 43 0.62
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:28452586 original size:59 final size:58
Alignment explanation
Indices: 28452490--28452603 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 58
28452480 AAATTAAATC
*
28452490 TCTAAGATTACAAAATCATATCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
* * * *
28452548 TCTAAGATTGCATATATCATATCTAGGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACA-AAATCATATCTAAGATTACATATCATATCTAAGATTGCATATC
28452604 CTCAAAAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 11 0.22
59 39 0.78
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (58 bp):
TCTAAGATTACAAAATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:28453184 original size:44 final size:44
Alignment explanation
Indices: 28453123--28453406 Score: 231
Period size: 44 Copynumber: 6.5 Consensus size: 44
28453113 CTGTCGGTGC
* * * * *
28453123 AGGAAGGCAAGACCTGCTATTTTCGTTCTACTTCACGCCAATAA
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCACACCAATAT
* * * *
28453167 ATGAAGACAAGATCTGCT-TTCTTCAATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATT-TTCGATCTACTTC-ACACCAATAT
* *
28453212 GGGAAGACAAGATCTG-TATCTTT-GATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTTCGATCTACTTCAC-ACCAATAT
* * ** *
28453255 AGGAAGACAGGACCTGCTATTTTCGATCTACTTCAGGCCAATAC
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCACACCAATAT
* * *
28453299 ATGAAGACAAGATCTGCT-TTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATT-TTCGATCTACTTC-ACACCAATAT
* * *
28453344 AGGAAGATAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCAC-ACCAATAT
* * *
28453387 AGAAAGATAAGACCTGCTAT
1 AGGAAGACAAGATCTGCTAT
28453407 CACGCCAATA
Statistics
Matches: 191, Mismatches: 36, Indels: 26
0.75 0.14 0.10
Matches are distributed among these distances:
42 2 0.01
43 49 0.26
44 95 0.50
45 44 0.23
46 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATTTTCGATCTACTTCACACCAATAT
Found at i:28453261 original size:88 final size:88
Alignment explanation
Indices: 28453122--28453661 Score: 216
Period size: 88 Copynumber: 6.3 Consensus size: 88
28453112 ACTGTCGGTG
* * * * * * * * *
28453122 CAGGAAGGCAAGACCTGCTATTTTCGTTCTACTTC-ACGCCAATAAATGAAGACAAGATCTGCT-
1 CAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGCTA
28453185 TTCTTCAATCTACTTC-GCCACCAGTA
66 TT-TTCAATCTACTTCAGCCA--A-TA
** * * * *
28453211 TGGGAAGACAAGATCTG-TATCTTTGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTA
1 CAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGCTA
*
28453274 TTTTCGATCTACTTCAGGCCAATA
66 TTTTCAATCTACTTCA-GCCAATA
* * * * *
28453298 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGATAAGATCTGC-A
1 CAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGCTA
* * *
28453362 TCTTCGATCCACTTCCTA-CCAATA
66 TTTTCAATCTACTT-C-AGCCAATA
* * * * * * * * * * *
28453386 TAGAAAGATAAGACCTGCTATC-ACG--CCA-AT----A-C-ATGA-AGACAATATC-TGCT-TT
1 CAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCCACCAAT-ATAG-GAAGA-CAAGATCTG
** * * * *
28453438 CT-TCGATCTA-CTTCTCCA-CCAGTA
63 CTAT-TTTCAATCTACTTCAGCCAATA
** * * * *
28453462 TGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGACCTGCTA
1 CAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGCTA
* *
28453525 TCTTCGATCTACTTCACGCCAATA
66 TTTTCAATCTACTTCA-GCCAATA
* * * * * * *
28453549 AATGAAAACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGC-A
1 CAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGCTA
* *
28453613 TCTTCAATCCACTTCCTA-CCAATA
66 TTTTCAATCTACTT-C-AGCCAATA
* * *
28453637 TAGGAAGACAGGACCTGCTATCTTC
1 CAGGAAGACAAGATCTGCTATCTTC
28453662 ACTGATCTGC
Statistics
Matches: 328, Mismatches: 91, Indels: 65
0.68 0.19 0.13
Matches are distributed among these distances:
75 3 0.01
76 22 0.07
77 1 0.00
78 12 0.04
79 11 0.03
80 1 0.00
82 1 0.00
83 6 0.02
84 11 0.03
85 9 0.03
87 37 0.11
88 147 0.45
89 61 0.19
90 6 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (88 bp):
CAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGCTA
TTTTCAATCTACTTCAGCCAATA
Found at i:28453365 original size:132 final size:132
Alignment explanation
Indices: 28453123--28453657 Score: 781
Period size: 132 Copynumber: 4.2 Consensus size: 132
28453113 CTGTCGGTGC
* * *
28453123 AGGAAGGCAAGACCTGCTATTTTCGTTCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTC
1 AGGAAGACAGGACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTC
* * *
28453188 TTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTTGATCCACTTCCTACCAAT
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
28453253 AT
131 AT
* *
28453255 AGGAAGACAGGACCTGCTATTTTCGATCTACTTCAGGCCAATACATGAAGACAAGATCTGCTTTC
1 AGGAAGACAGGACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTC
* *
28453320 TTCGATCTACTTCGCCACCAGTATAGGAAGATAAGATCTGCATCTTCGATCCACTTCCTACCAAT
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
28453385 AT
131 AT
* * * * *
28453387 AGAAAGATAAGA-C--C-----T-G--CTA--TCACGCCAATACATGAAGACAATATCTGCTTTC
1 AGGAAGACAGGACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTC
*
28453439 TTCGATCTACTTCTCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
28453504 AT
131 AT
* * *
28453506 AGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATAAATGAAAACAAGATCTGCTTTC
1 AGGAAGACAGGACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTC
* * *
28453571 TTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTTCAATCCACTTCCTACCAAT
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
28453636 AT
131 AT
28453638 AGGAAGACAGGACCTGCTAT
1 AGGAAGACAGGACCTGCTAT
28453658 CTTCACTGAT
Statistics
Matches: 362, Mismatches: 28, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
119 105 0.29
120 1 0.00
121 3 0.01
122 1 0.00
123 1 0.00
124 1 0.00
127 1 0.00
128 1 0.00
129 1 0.00
130 3 0.01
131 1 0.00
132 243 0.67
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (132 bp):
AGGAAGACAGGACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTC
TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
AT
Found at i:28453495 original size:44 final size:44
Alignment explanation
Indices: 28453411--28453661 Score: 254
Period size: 44 Copynumber: 5.7 Consensus size: 44
28453401 TGCTATCACG
* * * *
28453411 CCAATACATGAAGACAATATCTGCTTTCTTCGATCTACTTCTCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CCA
* * * *
28453456 CCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCCA
* * * * *
28453499 CCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCCA
* * * * *
28453543 CCAATAAATGAAAACAAGATCTGCTTTCTTCGATCTACTCCGCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CCA
* * * *
28453588 CCAATATGGGAAGACAAGATCTGC-ATCTTCAATCCACTTCCTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCCA
* *
28453631 CCAATATAGGAAGACAGGACCTGCTATCTTC
1 CCAATATAGGAAGACAAGATCTGCTATCTTC
28453662 ACTGATCTGC
Statistics
Matches: 164, Mismatches: 39, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
43 44 0.27
44 80 0.49
45 40 0.24
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (44 bp):
CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCCCA
Found at i:28453502 original size:119 final size:119
Alignment explanation
Indices: 28453291--28453658 Score: 502
Period size: 119 Copynumber: 3.0 Consensus size: 119
28453281 TCTACTTCAG
* *
28453291 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGATAAGA
1 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
*
28453356 TCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAAGACCTGCTATCAC
66 TCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGACCTGCTATCAC
* *
28453410 GCCAATACATGAAGACAATATCTGCTTTCTTCGATCTACTTCTCCACCAGTATGGGAAGACAAGA
1 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
*
28453475 TCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTC
66 TCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATA--A---G--A-CCT-G--CTA--TC
28453540 AC
118 AC
* * * *
28453542 GCCAATAAATGAAAACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGA
1 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
* * *
28453607 TCTGCATCTTCAATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATC
66 TCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGACCTGCTATC
28453659 TTCACTGATC
Statistics
Matches: 220, Mismatches: 16, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
119 102 0.46
121 4 0.02
123 1 0.00
124 3 0.01
125 1 0.00
126 1 0.00
127 3 0.01
128 1 0.00
130 3 0.01
132 101 0.46
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (119 bp):
GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
TCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGACCTGCTATCAC
Found at i:28453609 original size:251 final size:251
Alignment explanation
Indices: 28453155--28453658 Score: 837
Period size: 251 Copynumber: 2.0 Consensus size: 251
28453145 TCGTTCTACT
28453155 TCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGAC
1 TCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGAC
* * *
28453220 AAGATCTGTATCTTTGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATTTTCGATCTA
66 AAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTA
* * * * *
28453285 CTTCAGGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAG
131 CTTCACGCCAATAAATGAAAACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATAGGAAG
* * *
28453350 ATAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAAGACCTGCTA
196 ACAAGATCTGCATCTTCAATCCACTTCCTACCAATATAGAAAGACAAGACCTGCTA
* * * *
28453406 TCACGCCAATACATGAAGACAATATCTGCTTTCTTCGATCTACTTCTCCACCAGTATGGGAAGAC
1 TCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGAC
*
28453471 AAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTA
66 AAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTA
*
28453536 CTTCACGCCAATAAATGAAAACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAG
131 CTTCACGCCAATAAATGAAAACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATAGGAAG
* *
28453601 ACAAGATCTGCATCTTCAATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTA
196 ACAAGATCTGCATCTTCAATCCACTTCCTACCAATATAGAAAGACAAGACCTGCTA
28453657 TC
1 TC
28453659 TTCACTGATC
Statistics
Matches: 234, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
251 234 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (251 bp):
TCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGAC
AAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTA
CTTCACGCCAATAAATGAAAACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATAGGAAG
ACAAGATCTGCATCTTCAATCCACTTCCTACCAATATAGAAAGACAAGACCTGCTA
Found at i:28458279 original size:13 final size:14
Alignment explanation
Indices: 28458248--28458276 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28458238 AATAGCATAG
28458248 AAATG-ATATAAAT
1 AAATGAATATAAAT
28458261 AAATGAATATAAAT
1 AAATGAATATAAAT
28458275 AA
1 AA
28458277 TGACGTGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAATGAATATAAAT
Found at i:28459077 original size:39 final size:38
Alignment explanation
Indices: 28459033--28459164 Score: 176
Period size: 39 Copynumber: 3.4 Consensus size: 38
28459023 AAATTAAATC
* *
28459033 TCTAAGATTACAAAATCATATCTAAGATTATATATCATA
1 TCTAAGATTGC-ATATCATATCTAAGATTATATATCATA
28459072 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
* **
28459112 TCTAAGA-TGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
28459149 TCTAAGACTGCATATC
1 TCTAAGATTGCATATC
28459165 CTCAAAAATT
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
37 15 0.18
38 24 0.28
39 29 0.34
40 17 0.20
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.36
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:28459126 original size:58 final size:59
Alignment explanation
Indices: 28459033--28459163 Score: 194
Period size: 58 Copynumber: 2.3 Consensus size: 59
28459023 AAATTAAATC
* * *
28459033 TCTAAGATTACA-AAATCATATCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
28459091 TCTAAGATTGCATATATCATATCTAAGA-TGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
28459149 TCTAAGACTGCATAT
1 TCTAAGATTGCATAT
28459164 CCTCAAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 52 0.79
59 14 0.21
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (59 bp):
TCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:28459160 original size:19 final size:19
Alignment explanation
Indices: 28459033--28459164 Score: 176
Period size: 19 Copynumber: 6.8 Consensus size: 19
28459023 AAATTAAATC
* *
28459033 TCTAAGATTACAAAATCATA
1 TCTAAGATTGC-ATATCATA
**
28459053 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
28459072 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28459091 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
28459112 TCTAAGA-TGCATATCATA
1 TCTAAGATTGCATATCATA
*
28459130 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28459149 TCTAAGACTGCATATC
1 TCTAAGATTGCATATC
28459165 CTCAAAAATT
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.14
19 60 0.59
20 13 0.13
21 15 0.15
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28470400 original size:26 final size:26
Alignment explanation
Indices: 28470360--28470425 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
28470350 CATTCTGATC
* *
28470360 CACAACTCGTATGAGCAGGCCCATTT
1 CACAACTCGTGTGAGCAGACCCATTT
* * *
28470386 CACAACTCATGTGAGCATACCTATTT
1 CACAACTCGTGTGAGCAGACCCATTT
28470412 CACAACTCGTGTGA
1 CACAACTCGTGTGA
28470426 ACAACTATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (26 bp):
CACAACTCGTGTGAGCAGACCCATTT
Found at i:28480701 original size:19 final size:19
Alignment explanation
Indices: 28480663--28480701 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28480653 TGTAAACATG
* * *
28480663 AGTGTTTAAATTGGTTTTT
1 AGTGGTTAAATTGATATTT
28480682 AGTGGTTAAATTGATATTT
1 AGTGGTTAAATTGATATTT
28480701 A
1 A
28480702 AGCTTGTTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (19 bp):
AGTGGTTAAATTGATATTT
Found at i:28492598 original size:20 final size:20
Alignment explanation
Indices: 28492549--28492650 Score: 107
Period size: 20 Copynumber: 5.1 Consensus size: 20
28492539 TAACAGAGGT
* *
28492549 ACCAAAGTGGAATCAGGAGC
1 ACCAAAGTGCAATCAGGGGC
** * *
28492569 AGGAATGTGCGATCAGGGGC
1 ACCAAAGTGCAATCAGGGGC
*
28492589 ACCGAAGTGCAATCAGGGGC
1 ACCAAAGTGCAATCAGGGGC
*
28492609 A-CAAATGTGCATTCAGGGGC
1 ACCAAA-GTGCAATCAGGGGC
*
28492629 ACCAAAGTGCAAACAGGGGC
1 ACCAAAGTGCAATCAGGGGC
28492649 AC
1 AC
28492651 ATATTTGCAT
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 3 0.05
20 58 0.89
21 4 0.06
ACGTcount: A:0.33, C:0.22, G:0.33, T:0.12
Consensus pattern (20 bp):
ACCAAAGTGCAATCAGGGGC
Found at i:28492616 original size:40 final size:40
Alignment explanation
Indices: 28492572--28492730 Score: 185
Period size: 40 Copynumber: 4.0 Consensus size: 40
28492562 CAGGAGCAGG
*
28492572 AATGTGCGA-TCAGGGGCACCGAAGTGCAATCAGGGGCACA
1 AATGTGC-ATTCAGGGGCACCGAAGTGCAAACAGGGGCACA
*
28492612 AATGTGCATTCAGGGGCACCAAAGTGCAAACAGGGGCACA
1 AATGTGCATTCAGGGGCACCGAAGTGCAAACAGGGGCACA
* * * * * *
28492652 TATTTGCATTCAAGGGTACTGAAGTACAAACAGGGGCACA
1 AATGTGCATTCAGGGGCACCGAAGTGCAAACAGGGGCACA
* * * * *
28492692 AATGTGCATTCAAGGGTATCGAAGTACAAACAGGTGCAC
1 AATGTGCATTCAGGGGCACCGAAGTGCAAACAGGGGCAC
28492731 TTTTTCATTT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
39 1 0.01
40 103 0.99
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (40 bp):
AATGTGCATTCAGGGGCACCGAAGTGCAAACAGGGGCACA
Found at i:28497937 original size:370 final size:371
Alignment explanation
Indices: 28497426--28498140 Score: 1005
Period size: 370 Copynumber: 1.9 Consensus size: 371
28497416 TACCATTGAG
* * ** * *
28497426 AGTATGATGATGCTGTCAATAGCATCTAAAATGACTTGGGTTTTGCTTCTCTCCTGGTTTTATTT
1 AGTATGAAGATGCTGTCAATAGCATCTAAAATGACTCGAATTTTGCTTATCTACTGGTTTTATTT
* * * *
28497491 TATGACGCATGAAATATCGCAATGTCTGCATCAAATTTATATAGAAAATAATACATGAAGAAAAT
66 TATGACGCATGAAATATCGCAATGTCTGCATCAAAGTTATATAAAAAAGAATACATGAACAAAAT
*
28497556 CAAACTGTTCTAAGTTTTAAGAATTCAACTCTTAGTGTTACTA-CCAATTACAGTAATAACAAGT
131 CAAACTGTTCTAAGTTTTAAGAATTCAACTCTTAGTCTTAC-AGCCAATTACAGTAATAACAA--
*
28497620 TGTTGAATGAAAATTGAACACCT-AAATTAAATCAACTTCA-AATTGAAAAAGGTTATCTAGTTT
193 -GTTGAATGAAAATTGAACACCTAAAATTAAA-CAACTTCATAA-TGAAAAAGGTTATCTACTTT
* * * *
28497683 AGGATTTTCCATGTGCACTAA-CTTGATGAGGAATCTTGTAAGAGGAGAGA-A-AGCATATTCCA
255 AGGATTTTCCATATGCA-AAAGCTTGAAGAGGAATCATGTAAGAGGAGAGAGAGAGCATATTCCA
* *
28497745 CTTTGATATATTCTTGTCTTTATGTTGATGTGGAATCTTGTACTATTGTTAAA
319 CTATGATATATTCTTATCTTTATGTTGATGTGGAATCTTGTACTATTGTTAAA
* * *
28497798 AGTATGAAGATGTTGTCAATAGCATCTGAAATGACTCGAATTTTGCTTATCTATTGG-TTT-TTT
1 AGTATGAAGATGCTGTCAATAGCATCTAAAATGACTCGAATTTTGCTTATCTACTGGTTTTATTT
* *
28497861 TATGATGCATGAAATATCGCAATGTCTGCATCAAAGTTATATAAAAAAGAATAGATGAACAAAAT
66 TATGACGCATGAAATATCGCAATGTCTGCATCAAAGTTATATAAAAAAGAATACATGAACAAAAT
* ** *
28497926 CAAATTGTTCTAAGTTTTAAGAATTCAACTCTTAGTCTTACAGTGAATTGCAGTAATAACAAGTT
131 CAAACTGTTCTAAGTTTTAAGAATTCAACTCTTAGTCTTACAGCCAATTACAGTAATAACAAGTT
* * * *
28497991 GAATGAAAATTGAGCACCTAAAATTAAACAACTTCATAATGAATAAGTTTATTTACTTTAGGATT
196 GAATGAAAATTGAACACCTAAAATTAAACAACTTCATAATGAAAAAGGTTATCTACTTTAGGATT
* *
28498056 TTCCATATGTAAAAGCTTGAAGTGGAATCATGTAAGAGGAGAGAGAGAGCATATTCCACTATGAT
261 TTCCATATGCAAAAGCTTGAAGAGGAATCATGTAAGAGGAGAGAGAGAGCATATTCCACTATGAT
*
28498121 ATATTTTTATCTTTATGTTG
326 ATATTCTTATCTTTATGTTG
28498141 CATGAAAACT
Statistics
Matches: 303, Mismatches: 34, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
366 2 0.01
367 86 0.28
368 11 0.04
369 36 0.12
370 117 0.39
371 3 0.01
372 48 0.16
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (371 bp):
AGTATGAAGATGCTGTCAATAGCATCTAAAATGACTCGAATTTTGCTTATCTACTGGTTTTATTT
TATGACGCATGAAATATCGCAATGTCTGCATCAAAGTTATATAAAAAAGAATACATGAACAAAAT
CAAACTGTTCTAAGTTTTAAGAATTCAACTCTTAGTCTTACAGCCAATTACAGTAATAACAAGTT
GAATGAAAATTGAACACCTAAAATTAAACAACTTCATAATGAAAAAGGTTATCTACTTTAGGATT
TTCCATATGCAAAAGCTTGAAGAGGAATCATGTAAGAGGAGAGAGAGAGCATATTCCACTATGAT
ATATTCTTATCTTTATGTTGATGTGGAATCTTGTACTATTGTTAAA
Found at i:28499442 original size:15 final size:14
Alignment explanation
Indices: 28499424--28499458 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
28499414 TTTGCTTGTT
28499424 TCTTTTATCTTTTGA
1 TCTTTTATCTTTT-A
28499439 TCTTTTATCTTTTA
1 TCTTTTATCTTTTA
28499453 TCTTTT
1 TCTTTT
28499459 TGTAACGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.71
Consensus pattern (14 bp):
TCTTTTATCTTTTA
Found at i:28499459 original size:8 final size:7
Alignment explanation
Indices: 28499424--28499458 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
28499414 TTTGCTTGTT
28499424 TCTTTTA
1 TCTTTTA
28499431 TCTTTTGA
1 TCTTTT-A
28499439 TCTTTTA
1 TCTTTTA
28499446 TCTTTTA
1 TCTTTTA
28499453 TCTTTT
1 TCTTTT
28499459 TGTAACGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.71
Consensus pattern (7 bp):
TCTTTTA
Found at i:28500802 original size:73 final size:73
Alignment explanation
Indices: 28500684--28500830 Score: 240
Period size: 73 Copynumber: 2.0 Consensus size: 73
28500674 TACTTTAGGA
* * * * *
28500684 TTTTCCATGTGTAGAACATGATGTGGAATCTTGTGAGAAGAGAGAAAGCATATTCCATTGTGATA
1 TTTTCCATGTGCAAAACATGATATGGAATCTTGTAAGAAGAGAGAAAGCATATTCCACTGTGATA
*
28500749 TATTCTTG
66 TATTATTG
28500757 TTTTCCATGTGCAAAACATGATATGGAATCTTGTAAGAAGAGAGAAAGCATATTCCACTGTGATA
1 TTTTCCATGTGCAAAACATGATATGGAATCTTGTAAGAAGAGAGAAAGCATATTCCACTGTGATA
28500822 TATTATTG
66 TATTATTG
28500830 T
1 T
28500831 CTTTATGTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (73 bp):
TTTTCCATGTGCAAAACATGATATGGAATCTTGTAAGAAGAGAGAAAGCATATTCCACTGTGATA
TATTATTG
Found at i:28502792 original size:25 final size:24
Alignment explanation
Indices: 28502764--28502810 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
28502754 GTAAGTTATG
*
28502764 TAATT-AAATCATGTTTATATGTTTT
1 TAATTGAAAT-ATGTATA-ATGTTTT
28502789 TAATTGAAATATGTATAATGTT
1 TAATTGAAATATGTATAATGTT
28502811 ATGAAATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 11 0.55
26 4 0.20
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (24 bp):
TAATTGAAATATGTATAATGTTTT
Found at i:28503012 original size:25 final size:25
Alignment explanation
Indices: 28502973--28503106 Score: 99
Period size: 25 Copynumber: 5.4 Consensus size: 25
28502963 ACAACCTGTG
** *
28502973 AGAGCATACTGATTTATAGCTCATA
1 AGAGCATACCAATTTATAGCTCGTA
* * *
28502998 AGAGTATACCAATTTGTAGCTTGTA
1 AGAGCATACCAATTTATAGCTCGTA
* * * *
28503023 AAAGCATACCGATTTATAGTTCGTG
1 AGAGCATACCAATTTATAGCTCGTA
* *
28503048 AGAGCATACCAATCTACAGCTCG-A
1 AGAGCATACCAATTTATAGCTCGTA
* * * *
28503072 GTGAGCATACCGATTCATAGCACGTA
1 -AGAGCATACCAATTTATAGCTCGTA
*
28503098 TGAGCATAC
1 AGAGCATAC
28503107 ATGAGCATGA
Statistics
Matches: 82, Mismatches: 25, Indels: 4
0.74 0.23 0.04
Matches are distributed among these distances:
25 81 0.99
26 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (25 bp):
AGAGCATACCAATTTATAGCTCGTA
Found at i:28504264 original size:14 final size:14
Alignment explanation
Indices: 28504245--28504271 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28504235 TACATTGGGC
28504245 AGATTCATGCATGT
1 AGATTCATGCATGT
28504259 AGATTCATGCATG
1 AGATTCATGCATG
28504272 GGACGATGCA
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:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
AGATTCATGCATGT
Found at i:28506201 original size:25 final size:26
Alignment explanation
Indices: 28506173--28506242 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
28506163 AGCTCGTGAA
*
28506173 AGCATACTAATTTATAGCTCA-AAAG
1 AGCATACTGATTTATAGCTCAGAAAG
*
28506198 AGCATA-TCGATTTATAGCT-AGTAAG
1 AGCATACT-GATTTATAGCTCAGAAAG
*
28506223 AGCATGCTGATTTATAGCTC
1 AGCATACTGATTTATAGCTC
28506243 GTATGAGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.05
25 35 0.92
26 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (26 bp):
AGCATACTGATTTATAGCTCAGAAAG
Found at i:28507531 original size:13 final size:13
Alignment explanation
Indices: 28507513--28507537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28507503 CCATTTCGAA
28507513 TGGCCACACGGCT
1 TGGCCACACGGCT
28507526 TGGCCACACGGC
1 TGGCCACACGGC
28507538 CTTGTGATCC
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:0.16, C:0.40, G:0.32, T:0.12
Consensus pattern (13 bp):
TGGCCACACGGCT
Found at i:28510704 original size:22 final size:21
Alignment explanation
Indices: 28510679--28510719 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28510669 CTTGCATGGT
*
28510679 ATGAATTTTAGCTTCATTTTCA
1 ATGAATTTTAG-GTCATTTTCA
*
28510701 ATGATTTTTAGGTCATTTT
1 ATGAATTTTAGGTCATTTT
28510720 ACCTTAGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (21 bp):
ATGAATTTTAGGTCATTTTCA
Found at i:28528814 original size:2 final size:2
Alignment explanation
Indices: 28528807--28528841 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28528797 TCATGTTAGA
28528807 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28528842 TCATATTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28541699 original size:87 final size:87
Alignment explanation
Indices: 28541540--28541700 Score: 236
Period size: 87 Copynumber: 1.9 Consensus size: 87
28541530 CCTACCTATT
* ** *
28541540 TTTTTCACATGGAAAATCATAAACTAGATAACTTTATTCTGTGTGAAGTTGTTTAACTTTAGGTG
1 TTTTACACATGGAAAATCATAAACTAGATAACTTTATTCAATGTGAAGTTGTTTAACTTTAGCTG
*
28541605 TTTAATTTTTTGCACATCAAGG
66 TTCAATTTTTTGCACATCAAGG
*
28541627 TTTTACACATGGAAAATCCAT-AACTAGATAAAC-TTATTCAATGTGAAGTTGTTTAATTTTAGC
1 TTTTACACATGGAAAAT-CATAAACTAGAT-AACTTTATTCAATGTGAAGTTGTTTAACTTTAGC
28541690 TGTTCAATTTT
64 TGTTCAATTTT
28541701 CACCCAACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 60 0.91
88 6 0.09
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (87 bp):
TTTTACACATGGAAAATCATAAACTAGATAACTTTATTCAATGTGAAGTTGTTTAACTTTAGCTG
TTCAATTTTTTGCACATCAAGG
Found at i:28558285 original size:87 final size:87
Alignment explanation
Indices: 28558139--28558299 Score: 259
Period size: 87 Copynumber: 1.9 Consensus size: 87
28558129 GCTAACTAAT
* ** * *
28558139 TTTTGCACATGGAAAATCCTAAACTAGATAACCTTATTCTCTGTGAACTTGTTTGATTTTAGGTG
1 TTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAACTTGTTTAATTTTAGCTG
*
28558204 TTCAATTTTTTGCACATCAAGG
66 TTAAATTTTTTGCACATCAAGG
*
28558226 TTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAAGTTGTTTAATTTTAGCTG
1 TTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAACTTGTTTAATTTTAGCTG
28558291 TTAAATTTT
66 TTAAATTTT
28558300 CACCCAACAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (87 bp):
TTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAACTTGTTTAATTTTAGCTG
TTAAATTTTTTGCACATCAAGG
Found at i:28560063 original size:87 final size:87
Alignment explanation
Indices: 28559917--28560077 Score: 277
Period size: 87 Copynumber: 1.9 Consensus size: 87
28559907 TTGTTGGGTG
* *
28559917 AAAATTGAACAACTAAAATTAAACAACTTCACATTGAATAAGTTTATCTAGTTTAGGATTTTCCA
1 AAAATTGAACAACTAAAATTAAACAACTTCACATAGAATAAGGTTATCTAGTTTAGGATTTTCCA
28559982 TGTCCAAAACCTTGATGTGCAA
66 TGTCCAAAACCTTGATGTGCAA
* *
28560004 AAAATTGAACACCTAAAATTAAACAAGTTCACATAGAATAAGGTTATCTAGTTTAGGATTTTCCA
1 AAAATTGAACAACTAAAATTAAACAACTTCACATAGAATAAGGTTATCTAGTTTAGGATTTTCCA
*
28560069 TGTGCAAAA
66 TGTCCAAAA
28560078 ATTAGGGAGT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (87 bp):
AAAATTGAACAACTAAAATTAAACAACTTCACATAGAATAAGGTTATCTAGTTTAGGATTTTCCA
TGTCCAAAACCTTGATGTGCAA
Found at i:28566204 original size:19 final size:20
Alignment explanation
Indices: 28566154--28566206 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
28566144 TGATGTTTGT
28566154 GATATTTTTAATTAATTAATTA
1 GATA-TTTT-ATTAATTAATTA
* *
28566176 GATA-TATATTATTTAATTA
1 GATATTTTATTAATTAATTA
28566195 -ATATTTTATTAA
1 GATATTTTATTAA
28566207 GATTTTTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 3 0.12
19 17 0.65
20 2 0.08
22 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
GATATTTTATTAATTAATTA
Found at i:28572703 original size:52 final size:52
Alignment explanation
Indices: 28572646--28572749 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
28572636 AGCAGAAAGT
*
28572646 AAGGGAACAAACTTGACTATAGAGACATCATTGATGCACAAAATAAAACATA
1 AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
28572698 AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
1 AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
28572750 TCGAGAAGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.18
Consensus pattern (52 bp):
AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
Found at i:28573191 original size:15 final size:15
Alignment explanation
Indices: 28573170--28573204 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28573160 AAGGCCGAGG
28573170 AAGAAAATACTAAGA
1 AAGAAAATACTAAGA
* *
28573185 TAGAAAATGCTAAGA
1 AAGAAAATACTAAGA
28573200 AAGAA
1 AAGAA
28573205 TCTGTTGACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.17, T:0.14
Consensus pattern (15 bp):
AAGAAAATACTAAGA
Found at i:28573461 original size:72 final size:72
Alignment explanation
Indices: 28573376--28573522 Score: 231
Period size: 72 Copynumber: 2.0 Consensus size: 72
28573366 ACCTAACTAA
* * ****
28573376 TTTTTGTACATGGAAAATCCTAAACTAGATAACCTTATTGTGTGTGAAGTTGTTTAATTTTAGGT
1 TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAAAGTGAAGTTGTTTAATTTTAGGT
28573441 GTTCAAT
66 GTTCAAT
*
28573448 TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAAAGTGAAGTTGTTTAGTTTTAGGT
1 TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAAAGTGAAGTTGTTTAATTTTAGGT
28573513 GTTCAAT
66 GTTCAAT
28573520 TTT
1 TTT
28573523 CACCCAACAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (72 bp):
TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAAAGTGAAGTTGTTTAATTTTAGGT
GTTCAAT
Found at i:28578361 original size:87 final size:87
Alignment explanation
Indices: 28578213--28578371 Score: 237
Period size: 87 Copynumber: 1.8 Consensus size: 87
28578203 TACCTAATTG
* ** * * *
28578213 TTGCACATGGAAAATCCTAAACTAGATACCCTTATTCTGTCTGAGGTTGTTTAATTTTAGGTTTT
1 TTGCACATGGAAAATCCTAAACTAGATAACCTTATTCAATCTGAAGTTGTTTAATTCTAGGTGTT
28578278 CAATTTTTTGCACATCAAGGTT
66 CAATTTTTTGCACATCAAGGTT
* * *
28578300 TTGCACATGGAAAATCTTAAACTAGATAAGCTTATTCAATGTGAAGTTGTTTAATTCTAGGTGTT
1 TTGCACATGGAAAATCCTAAACTAGATAACCTTATTCAATCTGAAGTTGTTTAATTCTAGGTGTT
28578365 CAATTTT
66 CAATTTT
28578372 CACCCAACAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 63 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (87 bp):
TTGCACATGGAAAATCCTAAACTAGATAACCTTATTCAATCTGAAGTTGTTTAATTCTAGGTGTT
CAATTTTTTGCACATCAAGGTT
Found at i:28580689 original size:7 final size:7
Alignment explanation
Indices: 28580677--28580704 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28580667 GTCAATAAAA
28580677 GGAAGTG
1 GGAAGTG
28580684 GGAAGTG
1 GGAAGTG
28580691 GGAAGTG
1 GGAAGTG
28580698 GGAAGTG
1 GGAAGTG
28580705 ATCCTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
GGAAGTG
Found at i:28594872 original size:24 final size:23
Alignment explanation
Indices: 28594845--28594890 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
28594835 TTTGGAGTAT
28594845 TTTGTGTTTAGGTTTTGAGGGTTC
1 TTTGTGTTTAGGTTTTG-GGGTTC
*
28594869 TTTGTTTTTAGGTTTTGGGGTT
1 TTTGTGTTTAGGTTTTGGGGTT
28594891 TAGTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.07, C:0.02, G:0.33, T:0.59
Consensus pattern (23 bp):
TTTGTGTTTAGGTTTTGGGGTTC
Done.