Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 89 of 153
Found at i:28037840 original size:10 final size:8
Alignment explanation
Indices: 28037810--28037858 Score: 55
Period size: 8 Copynumber: 5.8 Consensus size: 8
28037800 AAAATTGTAA
28037810 AAAATTAT
1 AAAATTAT
28037818 AAAATTAT
1 AAAATTAT
28037826 AAAATATAT
1 AAAAT-TAT
28037835 AGAAA-TAT
1 A-AAATTAT
28037843 AAAATTTTAT
1 AAAA--TTAT
28037853 AAAATT
1 AAAATT
28037859 TTATAAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.08
8 19 0.53
9 4 0.11
10 10 0.28
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:28037859 original size:10 final size:10
Alignment explanation
Indices: 28037840--28037865 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28037830 TATATAGAAA
28037840 TATAAAATTT
1 TATAAAATTT
28037850 TATAAAATTT
1 TATAAAATTT
28037860 TATAAA
1 TATAAA
28037866 GTTGTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TATAAAATTT
Found at i:28038081 original size:19 final size:19
Alignment explanation
Indices: 28038045--28038080 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28038035 ATATTTTTAT
28038045 TAAAATTTAATAAATTTTC
1 TAAAATTTAATAAATTTTC
28038064 TAAAATTTAAT-AATTTT
1 TAAAATTTAATAAATTTT
28038081 TTTATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAATTTAATAAATTTTC
Found at i:28038305 original size:3 final size:3
Alignment explanation
Indices: 28038297--28038329 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28038287 ACGAGGGACT
28038297 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28038330 GTTTGAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28039239 original size:3 final size:3
Alignment explanation
Indices: 28039231--28039259 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28039221 GGGTTTTCAT
28039231 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28039260 GTTTATGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28039949 original size:15 final size:15
Alignment explanation
Indices: 28039931--28039964 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28039921 AATTAAATGC
28039931 TGAAAAAATAAGTAT
1 TGAAAAAATAAGTAT
**
28039946 TGAAAATTTAAGTAT
1 TGAAAAAATAAGTAT
28039961 TGAA
1 TGAA
28039965 CTTAAATTAT
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:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (15 bp):
TGAAAAAATAAGTAT
Found at i:28041333 original size:11 final size:11
Alignment explanation
Indices: 28041278--28041355 Score: 68
Period size: 11 Copynumber: 6.9 Consensus size: 11
28041268 TTCCACTTTT
*
28041278 TCAATTCACTC
1 TCAATTCTCTC
28041289 TCAACTCTCTCTC
1 TCAA-T-TCTCTC
28041302 TCAATTCAT-TC
1 TCAATTC-TCTC
*
28041313 TCAATCCTCTC
1 TCAATTCTCTC
*
28041324 TCAGTTCTCTC
1 TCAATTCTCTC
* *
28041335 TTAATTCTCAC
1 TCAATTCTCTC
*
28041346 TTAATTCTCT
1 TCAATTCTCT
28041356 TAGTTCAGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
10 1 0.02
11 42 0.76
12 3 0.05
13 9 0.16
ACGTcount: A:0.21, C:0.35, G:0.01, T:0.44
Consensus pattern (11 bp):
TCAATTCTCTC
Found at i:28042679 original size:23 final size:22
Alignment explanation
Indices: 28042632--28042681 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
28042622 AGTATACATA
* *
28042632 TTTTGAAAATTTATTTTCAATT
1 TTTTAAAAATTTATTTTCAAGT
28042654 TTTTAAAATATTTATTTT-AACGT
1 TTTTAAAA-ATTTATTTTCAA-GT
28042677 TTTTA
1 TTTTA
28042682 GTATTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTTAAAAATTTATTTTCAAGT
Found at i:28042722 original size:11 final size:11
Alignment explanation
Indices: 28042706--28042736 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28042696 TATATATATT
28042706 TAAAAATTATA
1 TAAAAATTATA
*
28042717 TAAAAATAATA
1 TAAAAATTATA
28042728 TAAAAATTA
1 TAAAAATTA
28042737 ATATGGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:28042733 original size:12 final size:11
Alignment explanation
Indices: 28042706--28042740 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28042696 TATATATATT
*
28042706 TAAAAATTATA
1 TAAAAATAATA
28042717 TAAAAATAATA
1 TAAAAATAATA
28042728 TAAAAATTAATA
1 TAAAAA-TAATA
28042740 T
1 T
28042741 GGGTGGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:28049175 original size:16 final size:16
Alignment explanation
Indices: 28049150--28049180 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28049140 TACGTCTTTA
28049150 ATTTTCATAACTCAAC
1 ATTTTCATAACTCAAC
*
28049166 ATTTTTATAACTCAA
1 ATTTTCATAACTCAA
28049181 AAATGCCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTTCATAACTCAAC
Found at i:28058337 original size:50 final size:50
Alignment explanation
Indices: 28058281--28058455 Score: 235
Period size: 50 Copynumber: 3.5 Consensus size: 50
28058271 TGGGCCTTGG
* *
28058281 GCCTTTGTGGCAAGTTATCTGAAAAGCCTATGTGGCGTATTACTTGGGGA
1 GCCTTTGTGGCAAGTTATTTGAAAAGCCTATGTGGCATATTACTTGGGGA
* * *
28058331 ACCTTTGTGGCAAGTTATTTAAAAAGTCTATGTGGCATATTAC-TGGGGTA
1 GCCTTTGTGGCAAGTTATTTGAAAAGCCTATGTGGCATATTACTTGGGG-A
* * *
28058381 GCCTTTGTGGTAAGTTATTTGAAAAGCCTATGTGGCATATTATTTGGCGA
1 GCCTTTGTGGCAAGTTATTTGAAAAGCCTATGTGGCATATTACTTGGGGA
* *
28058431 GCCCTTGTGGCAAGTCATTTAGAAA
1 GCCTTTGTGGCAAGTTATTT-GAAA
28058456 GCATTTATGG
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
49 5 0.05
50 95 0.88
51 8 0.07
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (50 bp):
GCCTTTGTGGCAAGTTATTTGAAAAGCCTATGTGGCATATTACTTGGGGA
Found at i:28058423 original size:25 final size:25
Alignment explanation
Indices: 28058281--28058426 Score: 84
Period size: 25 Copynumber: 5.8 Consensus size: 25
28058271 TGGGCCTTGG
* *
28058281 GCCTTTGTGGCAAGTTATCTGAAAA
1 GCCTATGTGGCAAGTTATTTGAAAA
* * **
28058306 GCCTATGTGGCGTA-TTACTTGGGGAA
1 GCCTATGTGGC-AAGTTA-TTTGAAAA
* *
28058332 -CCTTTGTGGCAAGTTATTTAAAAA
1 GCCTATGTGGCAAGTTATTTGAAAA
* * * ***
28058356 GTCTATGTGGCATA-TTACTGGGGTA
1 GCCTATGTGGCA-AGTTATTTGAAAA
* *
28058381 GCCTTTGTGGTAAGTTATTTGAAAA
1 GCCTATGTGGCAAGTTATTTGAAAA
28058406 GCCTATGTGGCATA-TTATTTG
1 GCCTATGTGGCA-AGTTATTTG
28058427 GCGAGCCCTT
Statistics
Matches: 84, Mismatches: 30, Indels: 14
0.66 0.23 0.11
Matches are distributed among these distances:
24 6 0.07
25 71 0.85
26 7 0.08
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (25 bp):
GCCTATGTGGCAAGTTATTTGAAAA
Found at i:28062519 original size:42 final size:42
Alignment explanation
Indices: 28062473--28062569 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
28062463 TTCCCACCCA
* *
28062473 TGTAACTCACTGAGTAGCCTCACATGCCCGTGTGCTAAGCTG
1 TGTAACTCACTGAGTAGCCACACATGCCCGTGTGCTAAGCCG
* * * * *
28062515 TGTAACTCTCTGAGTTGCCACACATGCCTGTGTGTTAGGCCG
1 TGTAACTCACTGAGTAGCCACACATGCCCGTGTGCTAAGCCG
28062557 TGTAACTCACTGA
1 TGTAACTCACTGA
28062570 CTTAAACACT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTAACTCACTGAGTAGCCACACATGCCCGTGTGCTAAGCCG
Found at i:28071837 original size:22 final size:22
Alignment explanation
Indices: 28071812--28071855 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28071802 CCTTACCGTC
28071812 CAATTATGGTCTAATTGTTATT
1 CAATTATGGTCTAATTGTTATT
28071834 CAATTATGGTCTAATTGTTATT
1 CAATTATGGTCTAATTGTTATT
28071856 TTAGACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (22 bp):
CAATTATGGTCTAATTGTTATT
Found at i:28075593 original size:27 final size:27
Alignment explanation
Indices: 28075281--28075583 Score: 464
Period size: 27 Copynumber: 11.2 Consensus size: 27
28075271 AGCGGTCAAT
* * *
28075281 AAATGACCAAAATATCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
28075308 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
28075335 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
28075362 AAATGATCGAAATACCCTCATAAGGTT
1 AAATGATCGAAATACCCCCATAGGGTA
*
28075389 AAATGATCGAAATACCCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * * * *
28075416 AAATGACCAAAATATCCCTATTGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
28075443 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
28075470 AAATGATCAAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
28075497 AAATGATCAAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
28075524 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
28075551 AAATGA-CTGAAATACCCCCATAGGGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
28075578 AAATGA
1 AAATGA
28075584 CTATTATACC
Statistics
Matches: 254, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
26 1 0.00
27 253 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:28075939 original size:28 final size:27
Alignment explanation
Indices: 28075902--28075979 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 27
28075892 GTATTGTTAT
*
28075902 TGTATTGGGCTAATGCCCACACTATTA
1 TGTATCGGGCTAATGCCCACACTATTA
* * * *
28075929 TGGTATGGGGCTAAAGCTCACACTGTTA
1 T-GTATCGGGCTAATGCCCACACTATTA
*
28075957 CTGTATCGGGCTAGT-CCCACACT
1 -TGTATCGGGCTAATGCCCACACT
28075980 GTACTGATAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 8 0.20
28 32 0.78
29 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.29
Consensus pattern (27 bp):
TGTATCGGGCTAATGCCCACACTATTA
Found at i:28077534 original size:25 final size:25
Alignment explanation
Indices: 28077501--28077548 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
28077491 TTAAAGTGTG
28077501 AAAATTAGTTTAATCTGCTACACTA
1 AAAATTAGTTTAATCTGCTACACTA
28077526 AAAATTAGTTTAATCTGCTACAC
1 AAAATTAGTTTAATCTGCTACAC
28077549 CGAATTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (25 bp):
AAAATTAGTTTAATCTGCTACACTA
Found at i:28088838 original size:30 final size:30
Alignment explanation
Indices: 28088792--28088915 Score: 230
Period size: 30 Copynumber: 4.1 Consensus size: 30
28088782 TTTTATTATG
*
28088792 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
28088823 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28088853 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28088883 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28088913 CCA
1 CCA
28088916 GGATTATGCA
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
30 85 0.92
31 7 0.08
ACGTcount: A:0.27, C:0.26, G:0.06, T:0.41
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:28088847 original size:15 final size:15
Alignment explanation
Indices: 28088802--28088908 Score: 85
Period size: 15 Copynumber: 7.1 Consensus size: 15
28088792 CCAATATCTC
28088802 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28088817 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28088832 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28088847 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28088862 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28088877 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28088892 GATACCCATATCTTT
1 GATACCCATATCTTT
28088907 GA
1 GA
28088909 CTTTCCAGGA
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
14 12 0.18
15 44 0.65
16 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.42
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:28092142 original size:30 final size:30
Alignment explanation
Indices: 28092096--28092189 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
28092086 TTTTATTATG
*
28092096 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
28092127 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
28092157 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28092187 CCA
1 CCA
28092190 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:28092151 original size:15 final size:15
Alignment explanation
Indices: 28092106--28092183 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
28092096 CCAATATCTC
28092106 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28092121 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28092136 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
28092151 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
28092166 GATACCCATATCTTT
1 GATACCCATATCTTT
28092181 GAT
1 GAT
28092184 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:28106326 original size:13 final size:13
Alignment explanation
Indices: 28106308--28106333 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28106298 TGGAAATAAC
28106308 GAAACAACTTTGG
1 GAAACAACTTTGG
28106321 GAAACAACTTTGG
1 GAAACAACTTTGG
28106334 CTTGCCCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GAAACAACTTTGG
Found at i:28107618 original size:26 final size:26
Alignment explanation
Indices: 28107572--28107621 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
28107562 CTAGTTAACG
*
28107572 TTTCTTCTTCTTTTTTATTTTTTTAA
1 TTTCTTCTTCTTATTTATTTTTTTAA
*
28107598 TTTCTTCTT-TCTATTTCTTTTTTT
1 TTTCTTCTTCT-TATTTATTTTTTT
28107622 CTTTTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTCTTCTTCTTATTTATTTTTTTAA
Found at i:28107628 original size:14 final size:14
Alignment explanation
Indices: 28107605--28107645 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28107595 TAATTTCTTC
*
28107605 TTTCTATTTCTTTT
1 TTTCTTTTTCTTTT
*
28107619 TTTCTTTTTCATTT
1 TTTCTTTTTCTTTT
*
28107633 TTTCTTCTTCTTT
1 TTTCTTTTTCTTT
28107646 ACTTTCAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:28111788 original size:20 final size:20
Alignment explanation
Indices: 28111763--28111804 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
28111753 ACACAATTCG
28111763 CATATCATATTTACACGCGA
1 CATATCATATTTACACGCGA
28111783 CATATCATATTTACACGCGA
1 CATATCATATTTACACGCGA
28111803 CA
1 CA
28111805 AGTTTTTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (20 bp):
CATATCATATTTACACGCGA
Found at i:28111972 original size:15 final size:14
Alignment explanation
Indices: 28111951--28111980 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28111941 CTGCTAACAA
28111951 AGAATATCCTTTTG
1 AGAATATCCTTTTG
28111965 ANGAATATCCTTTTG
1 A-GAATATCCTTTTG
28111980 A
1 A
28111981 CCCAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 1 0.07
15 14 0.93
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.40
Consensus pattern (14 bp):
AGAATATCCTTTTG
Found at i:28115311 original size:41 final size:41
Alignment explanation
Indices: 28115254--28115533 Score: 381
Period size: 41 Copynumber: 6.8 Consensus size: 41
28115244 GAATATAATA
* *
28115254 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
28115295 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
28115336 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
28115377 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
28115418 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
28115459 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
28115500 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
28115534 ATCTGTTTAA
Statistics
Matches: 222, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
39 3 0.01
40 8 0.04
41 209 0.94
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:28116545 original size:19 final size:20
Alignment explanation
Indices: 28116521--28116568 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28116511 AATACTAGCG
28116521 CACAAAGTGCAT-TCTGGCA
1 CACAAAGTGCATATCTGGCA
* *
28116540 CACAAAGCGCATATTTGGCA
1 CACAAAGTGCATATCTGGCA
28116560 CACAAAGTG
1 CACAAAGTG
28116569 TATTGCGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
CACAAAGTGCATATCTGGCA
Found at i:28118845 original size:297 final size:288
Alignment explanation
Indices: 28118058--28118956 Score: 859
Period size: 294 Copynumber: 3.1 Consensus size: 288
28118048 CTGGTTGACT
* * *
28118058 CATGACACCAACTCAGTTAAGGATTTTATTAATAGTATAGATATATACAATTGATG-GAGAAAAT
1 CATGACACCAACTCAGTTAGGGATTTTATTAATAGTATA-ATATATACAACTGATGTGAGATAAT
* * ** *
28118122 AAATTGTGC-TGTTAAATAAAAATGTATAAAATAAATTAAAATGAAGGTTTGATTTAGTGGTAAA
65 AAATTGTGCATATT--A-AAAAATGTATAAAAGAAATTAAAAT-AAATTTTG-TTGAGTGGTAAA
* * * * * *
28118186 TTTAAGGTTTTACCAATGCAATTGGTTTGGGTTTAAATCTTAT-ACAT--ATATTTTTATTGGTT
125 TTTAAGGTTTTA-CTATTCAATTGGTGTGGGTTCAAATCTTATCATATACATATTTTTCTTGGTT
* * * * * *
28118248 TTTCTTAAAATGAAAAGACTAAAGTACTCTCAAATAATATAACTTA-TTTAATTAAGGAATGGT-
189 TTTGTTAAAATGAAAAGACTAAAATACTCTCGAATAATA-GACTTATTTTAATT-ACGAA-AGTA
* * * * * *
28118311 ACTT-CGTAATTTTCCTAAGCAAGTTGGTGCCCAGTTGACT
251 ATTTCCATAATTTT-CTAA-CAAGTTGGTACCGA-TTAACC
* * * * * *
28118351 CATGATACCAACTCAGTCATGGACTTTATTAATGGTAT-AGATATACAACTGAT-TGAGATAATA
1 CATGACACCAACTCAGTTAGGGATTTTATTAATAGTATAATATATACAACTGATGTGAGATAATA
* * *
28118414 AATTGTGCATATTAAAAAATGTATAAAGGAAATTAAAATAAATCTTTGGTTGAATTGTAAATTTA
66 AATTGTGCATATTAAAAAATGTATAAAAGAAATTAAAATAAAT-TTT-GTTGAGTGGTAAATTTA
* * * ** * * *
28118479 A-GATTTACTACTCCAATTGATGCAGGTTCAAGTCTCACCATATACATATTTTTCTTGGTTTTAT
129 AGGTTTTACTA-TTCAATTGGTGTGGGTTCAAATCTTATCATATACATATTTTTCTTGGTTTT-T
* *
28118543 GTTAAAATGAAAAGACTAAAATACTATCGAATAATAGGACTTATTTTTAATTATGAAAGTAAATT
192 GTTAAAATGAAAAGACTAAAATACTCTCGAATAATA-GACTTA-TTTTAATTACGAAAGT-AATT
*
28118608 TCCATAATTTTCTAACTGAGTTGGTATCCGATTAACC
254 TCCATAATTTTCTAAC-AAGTTGGTA-CCGATTAACC
* * * * * * *
28118645 CTTCACACCAACTCAGTTAGGGGTTTTATTAATAGTATAAATATATATAAGTGGTGTGTGATAAT
1 CATGACACCAACTCAGTTAGGGATTTTATTAATAGTAT-AATATATACAACTGATGTGAGATAAT
* *
28118710 AAATTGTGCATATTAAAAAATGTATAAAAGACATTAAAATAAAATTTTAGTTGAGTGGCAAATTT
65 AAATTGTGCATATTAAAAAATGTATAAAAGAAATTAAAAT-AAATTTT-GTTGAGTGGTAAATTT
28118775 AAGGTTTTACTATTCTAATTGGTGTGGGTTCAAATCTTATCATATACATATTTTTCTTGGTTTTT
128 AAGGTTTTACTATTC-AATTGGTGTGGGTTCAAATCTTATCATATACATATTTTTCTTGGTTTTT
* * * * * * *
28118840 GTTAAAATGAAAAAACTAAAATACCCTTGAATAAT-GACTTGTTTTAGTTACGGAAGGACATTTC
192 GTTAAAATGAAAAGACTAAAATACTCTCGAATAATAGACTTATTTTAATTACGAAAGTA-ATTTC
* * *
28118904 TATAATTTTCTAACCAAGTTGATACATGATTAACC
256 CATAATTTTCTAA-CAAGTTGGTAC-CGATTAACC
*
28118939 CGTGACACCAACTCAGTT
1 CATGACACCAACTCAGTT
28118957 TGGGGTTTAT
Statistics
Matches: 495, Mismatches: 86, Indels: 49
0.79 0.14 0.08
Matches are distributed among these distances:
287 2 0.00
288 25 0.05
289 43 0.09
290 2 0.00
291 45 0.09
292 43 0.09
293 40 0.08
294 115 0.23
295 17 0.03
296 11 0.02
297 98 0.20
298 54 0.11
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (288 bp):
CATGACACCAACTCAGTTAGGGATTTTATTAATAGTATAATATATACAACTGATGTGAGATAATA
AATTGTGCATATTAAAAAATGTATAAAAGAAATTAAAATAAATTTTGTTGAGTGGTAAATTTAAG
GTTTTACTATTCAATTGGTGTGGGTTCAAATCTTATCATATACATATTTTTCTTGGTTTTTGTTA
AAATGAAAAGACTAAAATACTCTCGAATAATAGACTTATTTTAATTACGAAAGTAATTTCCATAA
TTTTCTAACAAGTTGGTACCGATTAACC
Found at i:28121699 original size:24 final size:24
Alignment explanation
Indices: 28121642--28121702 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28121632 AAAGAGCCTA
* * *
28121642 TAACAAGTAGCTCCGAAGAGCAAT
1 TAACGAGTAGCTCCAAAAAGCAAT
28121666 TAACGAGTAGCTCCAAAAAGCAAT
1 TAACGAGTAGCTCCAAAAAGCAAT
* *
28121690 TAATGGGTAGCTC
1 TAACGAGTAGCTC
28121703 TGAAGAATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (24 bp):
TAACGAGTAGCTCCAAAAAGCAAT
Found at i:28121797 original size:26 final size:26
Alignment explanation
Indices: 28121762--28121827 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
28121752 AAACGAGCAC
* * * *
28121762 TAACGAGAAGCTCACAAAGAGCC-TT
1 TAACGGGAAGCTCAAAAAAAGCCATA
28121787 TAATCGGGAAGCTCAAAAAAAGCCATA
1 TAA-CGGGAAGCTCAAAAAAAGCCATA
*
28121814 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
28121828 TAAGAGTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.09
26 27 0.79
27 4 0.12
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (26 bp):
TAACGGGAAGCTCAAAAAAAGCCATA
Found at i:28124206 original size:26 final size:26
Alignment explanation
Indices: 28124177--28124279 Score: 91
Period size: 26 Copynumber: 4.0 Consensus size: 26
28124167 ACACCAATAT
* * *
28124177 TGCAGCAAAGTTGCCAGTAATAGTGA
1 TGCAGCAAAGCTGCCAGTAACAGTAA
* *
28124203 TGCAGTAAAGCTGCCAGTAGCAGTAA
1 TGCAGCAAAGCTGCCAGTAACAGTAA
* *
28124229 CGTAGCAAAGCTGCCAGTAACAGTATA
1 TGCAGCAAAGCTGCCAGTAACAGTA-A
** **
28124256 TGTGGCAAAGCCACCAGT-ACAGTA
1 TGCAGCAAAGCTGCCAGTAACAGTA
28124280 CACTTCTCCT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
26 48 0.76
27 15 0.24
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.19
Consensus pattern (26 bp):
TGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:28124448 original size:27 final size:26
Alignment explanation
Indices: 28124426--28124789 Score: 347
Period size: 27 Copynumber: 13.5 Consensus size: 26
28124416 AGGGGTATAA
28124426 CAGTCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCT-TGAGGGTATTT
*
28124453 CAGTCATTTTACCCTTTAGGGGTATTT
1 CAGTCATTTTACCCTTGA-GGGTATTT
* *
28124480 CGGTCATTTTACCCTTCGATGGTATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
*
28124507 C-GATCCTTTTACCCTTCGAGGGTATTT
1 CAG-TCATTTTACCCTT-GAGGGTATTT
* *
28124534 TAGTCATTTTACCCTTCGGGGGTATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
* *
28124561 C-GATGATTTTACCCTTTAGGGGTATTT
1 CAG-TCATTTTACCCTTGA-GGGTATTT
*
28124588 CAATCATTTTACCCTTTGAGGGTATTT
1 CAGTCATTTTACCC-TTGAGGGTATTT
*
28124615 CAGTCATTTTACCCTTTAGGGGTATTT
1 CAGTCATTTTACCCTTGA-GGGTATTT
*
28124642 TAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
* * **
28124669 CGGTTA-TTTACCCTTCGAGCATATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
* * *
28124695 TAATCATTTTACCCTTCGGGGGTATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
* * ** *
28124722 CGGTTATTTTACTGTTTGAGTGTATTT
1 CAGTCATTTTAC-CCTTGAGGGTATTT
* *
28124749 CGGTCATTTTACCCTTCGGGGGTATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
28124776 CAGTCATTTTACCC
1 CAGTCATTTTACCC
28124790 ATGAATTGCA
Statistics
Matches: 278, Mismatches: 46, Indels: 26
0.79 0.13 0.07
Matches are distributed among these distances:
26 29 0.10
27 241 0.87
28 8 0.03
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.44
Consensus pattern (26 bp):
CAGTCATTTTACCCTTGAGGGTATTT
Found at i:28124486 original size:54 final size:55
Alignment explanation
Indices: 28124426--28124789 Score: 406
Period size: 54 Copynumber: 6.7 Consensus size: 55
28124416 AGGGGTATAA
28124426 CAGTCATTTTACCCTAT-GAGGGTATTTCAGTCATTTTACCCTTTAG-GGGTATTT
1 CAGTCATTTTACCCT-TCGAGGGTATTTCAGTCATTTTACCCTTTAGAGGGTATTT
* * * *
28124480 CGGTCATTTTACCCTTCGATGGTATTTC-GATCCTTTTACCC-TTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCAG-TCATTTTACCCTTTAGAGGGTATTT
* * *
28124534 TAGTCATTTTACCCTTCGGGGGTATTTC-GATGATTTTACCCTTTAG-GGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCAG-TCATTTTACCCTTTAGAGGGTATTT
* *
28124588 CAATCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTTAG-GGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTAGAGGGTATTT
* * * * **
28124642 TAGTCATTTTACCCTTCGAGGGTATTTCGGTTA-TTTACCC-TTCGAGCATATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTAGAGGGTATTT
* * * * * ** *
28124695 TAATCATTTTACCCTTCGGGGGTATTTCGGTTATTTTACTGTTT-GAGTGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTAGAGGGTATTT
* *
28124749 CGGTCATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCC
1 CAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCC
28124790 ATGAATTGCA
Statistics
Matches: 265, Mismatches: 37, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
52 3 0.01
53 49 0.18
54 207 0.78
55 6 0.02
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.44
Consensus pattern (55 bp):
CAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTAGAGGGTATTT
Found at i:28124539 original size:81 final size:81
Alignment explanation
Indices: 28124429--28124789 Score: 440
Period size: 81 Copynumber: 4.5 Consensus size: 81
28124419 GGTATAACAG
*
28124429 TCATTTTACCCTAT-GAGGGTATTTCAGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACC
1 TCATTTTACCCT-TCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACC
*
28124493 CTTCGATGGTATTTCGA
65 CTTCGAGGGTATTTCGA
* * * * *
28124510 TCCTTTTACCCTTCGAGGGTATTTTAGTCATTTTACCCTTCGGGGGTATTTCGATGATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCC
* *
28124575 TT-TAGGGGTATTTCAA
66 TTCGA-GGGTATTTCGA
* * **
28124591 TCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTTAGGGGTATTTTAGTCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCC
*
28124656 TTCGAGGGTATTTCGG
66 TTCGAGGGTATTTCGA
* ** * * * * **
28124672 TTA-TTTACCCTTCGAGCATATTTTAATCATTTTACCCTTCGGGGGTATTTCGGTTATTTTACTG
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCC
* * *
28124736 TTTGAGTGTATTTCGG
66 TTCGAGGGTATTTCGA
*
28124752 TCATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCC
28124790 ATGAATTGCA
Statistics
Matches: 234, Mismatches: 42, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
80 67 0.29
81 166 0.71
82 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.44
Consensus pattern (81 bp):
TCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCC
TTCGAGGGTATTTCGA
Found at i:28130503 original size:17 final size:17
Alignment explanation
Indices: 28130481--28130519 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
28130471 CTGAAGCTTG
28130481 AACATTATTATATGAAA
1 AACATTATTATATGAAA
28130498 AACATTATTATATGAAA
1 AACATTATTATATGAAA
28130515 AACAT
1 AACAT
28130520 ATTTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (17 bp):
AACATTATTATATGAAA
Found at i:28132167 original size:24 final size:24
Alignment explanation
Indices: 28132140--28132190 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
28132130 AAAGAGCCTA
*
28132140 TAACGGGTAGCTCTGAAGAGCAAT
1 TAACGGGTAGCTCCGAAGAGCAAT
*
28132164 TAACGGGTAGCTCCGAAGAGCACT
1 TAACGGGTAGCTCCGAAGAGCAAT
28132188 TAA
1 TAA
28132191 TTAGGAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (24 bp):
TAACGGGTAGCTCCGAAGAGCAAT
Found at i:28137292 original size:37 final size:38
Alignment explanation
Indices: 28137241--28137325 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 38
28137231 AATAAACTCT
* *
28137241 TAATCCTAGCCCTAGATTTAAA-CCTAAAGATATCTCA
1 TAATCCTAGCCCTAGATTTAAATCCTAAAGATAACTAA
* *
28137278 TAATCCTAGTCCTAGATTTAAATCCTAAAGGTAACTAA
1 TAATCCTAGCCCTAGATTTAAATCCTAAAGATAACTAA
28137316 TAATCCTAGC
1 TAATCCTAGC
28137326 TATCTATCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 21 0.50
38 21 0.50
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (38 bp):
TAATCCTAGCCCTAGATTTAAATCCTAAAGATAACTAA
Found at i:28140915 original size:25 final size:26
Alignment explanation
Indices: 28140881--28140945 Score: 98
Period size: 25 Copynumber: 2.5 Consensus size: 26
28140871 CTCAATTACC
28140881 AATTGGAAAAAACAGTTTA-GTATCA
1 AATTGGAAAAAACAGTTTAGGTATCA
28140906 AATTGGAAAAAACAGTTTAGGTGTATCA
1 AATTGGAAAAAACAGTTTA-G-GTATCA
28140934 AATT-GAAAAAAC
1 AATTGGAAAAAAC
28140946 GTAAGCATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 19 0.51
27 8 0.22
28 10 0.27
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (26 bp):
AATTGGAAAAAACAGTTTAGGTATCA
Found at i:28141071 original size:18 final size:19
Alignment explanation
Indices: 28141048--28141083 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28141038 TTTAGGAAAC
28141048 TTTATAAAT-ATTTTGAAT
1 TTTATAAATAATTTTGAAT
28141066 TTTATAAATAATTTTGAA
1 TTTATAAATAATTTTGAA
28141084 ATTTGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTATAAATAATTTTGAAT
Found at i:28141093 original size:19 final size:18
Alignment explanation
Indices: 28141051--28141093 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28141041 AGGAAACTTT
*
28141051 ATAAATATTTTGAATTTT
1 ATAAATATTTTGAATTTG
28141069 ATAAATAATTTTGAAATTTG
1 ATAAAT-ATTTTG-AATTTG
28141089 A-AAAT
1 ATAAAT
28141094 TGTCTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (18 bp):
ATAAATATTTTGAATTTG
Found at i:28146246 original size:22 final size:23
Alignment explanation
Indices: 28146212--28146254 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28146202 TTTTTTTTTC
28146212 TTTTTAAGTTTTTATTTATTTAG
1 TTTTTAAGTTTTTATTTATTTAG
28146235 TTTTTAAGTTTTT-TTTATTT
1 TTTTTAAGTTTTTATTTATTT
28146255 GTCCTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (23 bp):
TTTTTAAGTTTTTATTTATTTAG
Found at i:28146379 original size:22 final size:22
Alignment explanation
Indices: 28146363--28146418 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
28146353 TATTTTTTAA
*
28146363 ATTATTTTTTAAAATTTGAAAT
1 ATTATTTTTTAAAATTTTAAAT
28146385 ATTATTTTTT-AAATTTTAAAT
1 ATTATTTTTTAAAATTTTAAAT
28146406 ATATATTTTTTAA
1 AT-TATTTTTTAA
28146419 TAATATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 12 0.39
22 18 0.58
23 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTATTTTTTAAAATTTTAAAT
Found at i:28146396 original size:34 final size:36
Alignment explanation
Indices: 28146321--28146399 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 36
28146311 ATTTGAAATG
*
28146321 TTTTATAA-TATTTTTTAAAAATTTTAAATATATATT
1 TTTTA-AATTATTTTTTAAAAATTTGAAATATATATT
28146357 TTTTAAATTATTTTTT-AAAATTTGAAATAT-TATT
1 TTTTAAATTATTTTTTAAAAATTTGAAATATATATT
28146391 TTTTAAATT
1 TTTTAAATT
28146400 TTAAATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 13 0.32
35 15 0.37
36 13 0.32
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (36 bp):
TTTTAAATTATTTTTTAAAAATTTGAAATATATATT
Found at i:28146427 original size:23 final size:21
Alignment explanation
Indices: 28146363--28146427 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
28146353 TATTTTTTAA
28146363 ATTATTTTTTAAAATTTGAAAT
1 ATTATTTTTTAAAATTT-AAAT
*
28146385 ATTATTTTTTAAATTTTAAAT
1 ATTATTTTTTAAAATTTAAAT
*
28146406 ATATATTTTTTAATAATATAAA
1 AT-TATTTTTTAA-AATTTAAA
28146428 ACATTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.16
22 26 0.68
23 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTATTTTTTAAAATTTAAAT
Found at i:28146518 original size:31 final size:32
Alignment explanation
Indices: 28146483--28146556 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 32
28146473 TTCTTATAAT
28146483 ATTTTAAATATATATT-TTAA-TTTTAAATCTA
1 ATTTTAAATATATATTATTAATTTTTAAAT-TA
*
28146514 ATTTT---TATAAATTATTAATTTTTTAAATTA
1 ATTTTAAATATATATTATTAA-TTTTTAAATTA
*
28146544 ATTTTAAAGATAT
1 ATTTTAAATATAT
28146557 TCAAACGTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
28 7 0.21
29 4 0.12
30 7 0.21
31 13 0.38
33 3 0.09
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (32 bp):
ATTTTAAATATATATTATTAATTTTTAAATTA
Found at i:28146540 original size:16 final size:17
Alignment explanation
Indices: 28146512--28146543 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28146502 ATTTTAAATC
28146512 TAATTTTTATAAATTAT
1 TAATTTTTATAAATTAT
28146529 TAATTTTT-TAAATTA
1 TAATTTTTATAAATTA
28146544 ATTTTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTTTATAAATTAT
Found at i:28150723 original size:21 final size:21
Alignment explanation
Indices: 28150699--28150753 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
28150689 TGACCAATTA
28150699 TAATATATATTTTTAATTTTC
1 TAATATATATTTTTAATTTTC
* * * *
28150720 TAATTTAAATTTTTACTTTTT
1 TAATATATATTTTTAATTTTC
28150741 TAATATATATTTT
1 TAATATATATTTT
28150754 AAAATAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TAATATATATTTTTAATTTTC
Found at i:28150792 original size:20 final size:20
Alignment explanation
Indices: 28150755--28150816 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
28150745 ATATATTTTA
28150755 AAATAAAGTCATAATTTTTTAAC
1 AAATAAA-TCAT--TTTTTTAAC
28150778 AAATAAATTC-TTTTTTTAAC
1 AAATAAA-TCATTTTTTTAAC
28150798 AAATAAATCATTTTTTTAA
1 AAATAAATCATTTTTTTAA
28150817 AATTCTTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 2 0.05
20 25 0.68
22 1 0.03
23 9 0.24
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATAAATCATTTTTTTAAC
Found at i:28150949 original size:18 final size:18
Alignment explanation
Indices: 28150916--28150979 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 18
28150906 CTTTAAAAAT
28150916 AATTAAAAAATTATATTTAA
1 AATTAAAAAA--ATATTTAA
28150936 AATTAAAAAAATATTTAA
1 AATTAAAAAAATATTTAA
28150954 AATATACATATAAAATATTATAA
1 AAT-TA-A-A-AAAATATT-TAA
28150977 AAT
1 AAT
28150980 AAATAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.28
19 2 0.05
20 11 0.28
21 1 0.03
22 8 0.21
23 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAAAAAATATTTAA
Found at i:28150968 original size:31 final size:32
Alignment explanation
Indices: 28150910--28150969 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
28150900 GAATATCTTT
* *
28150910 AAAAATAATTAAAAAATTATATTTAAAATTAA
1 AAAAATAATTAAAAAATTACATATAAAATTAA
* *
28150942 AAAAATATTTAAAATA-TACATATAAAAT
1 AAAAATAATTAAAAAATTACATATAAAAT
28150970 ATTATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.42
32 14 0.58
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAAATAATTAAAAAATTACATATAAAATTAA
Found at i:28150989 original size:22 final size:22
Alignment explanation
Indices: 28150928--28150980 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 22
28150918 TTAAAAAATT
28150928 ATATTTAAAAT-TA-A-A-AAA
1 ATATTTAAAATATACATATAAA
28150946 ATATTTAAAATATACATATAAA
1 ATATTTAAAATATACATATAAA
28150968 ATATTATAAAATA
1 ATATT-TAAAATA
28150981 AATAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.37
19 2 0.07
20 1 0.03
21 1 0.03
22 8 0.27
23 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTTAAAATATACATATAAA
Found at i:28151065 original size:21 final size:20
Alignment explanation
Indices: 28151039--28151077 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28151029 ATTATTAAAA
28151039 AATATTTAAAATTTAAAAAGT
1 AATATTT-AAATTTAAAAAGT
28151060 AATATTTAAATTTAAAAA
1 AATATTTAAATTTAAAAA
28151078 CAAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATATTTAAATTTAAAAAGT
Found at i:28151087 original size:21 final size:21
Alignment explanation
Indices: 28151038--28151092 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
28151028 TATTATTAAA
*
28151038 AAATATTTAAAATTTAAAAAG
1 AAATATTTAAAATTTAAAAAC
*
28151059 TAATATTT-AAATTTAAAAAC
1 AAATATTTAAAATTTAAAAAC
28151079 AAATAATTTTAAAA
1 AAAT-A-TTTAAAA
28151093 AATATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 14 0.50
21 8 0.29
22 3 0.11
23 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATATTTAAAATTTAAAAAC
Found at i:28151087 original size:35 final size:32
Alignment explanation
Indices: 28151048--28151127 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 32
28151038 AAATATTTAA
*
28151048 AATTTAAAAAGTAATATTTAAATTTAAAAACAAAT
1 AATTTAAAAAGT-ATATTTAAAATT-AAAA-AAAT
*
28151083 AATTTTAAAAAATATATTTAAAATTAAAAAAAT
1 AA-TTTAAAAAGTATATTTAAAATTAAAAAAAT
28151116 -ATTATAAAAAGT
1 AATT-TAAAAAGT
28151128 TTCAAATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 2 0.05
32 8 0.20
33 4 0.10
34 4 0.10
35 13 0.32
36 9 0.22
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (32 bp):
AATTTAAAAAGTATATTTAAAATTAAAAAAAT
Found at i:28151107 original size:21 final size:21
Alignment explanation
Indices: 28151083--28151156 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
28151073 AAAAACAAAT
28151083 AATTTTAAAAAATATATTTAA
1 AATTTTAAAAAATATATTTAA
28151104 AA--TTAAAAAA-ATATTATAAA
1 AATTTTAAAAAATATATT-T-AA
* * * * *
28151124 AAGTTTCAAATATACATTTTA
1 AATTTTAAAAAATATATTTAA
*
28151145 AATTTTATAAAA
1 AATTTTAAAAAA
28151157 CCAATAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 4 0.10
21 11 0.28
22 7 0.17
23 4 0.10
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (21 bp):
AATTTTAAAAAATATATTTAA
Found at i:28151114 original size:20 final size:20
Alignment explanation
Indices: 28151035--28151117 Score: 63
Period size: 21 Copynumber: 4.4 Consensus size: 20
28151025 TTATATTATT
*
28151035 AAAAA-ATATTTAAAATTTA
1 AAAAATATATTTAAAATTAA
* *
28151054 AAAAGTAATATTTAAATTTAA
1 AAAAAT-ATATTTAAAATTAA
*
28151075 AAACAA-ATAATT----TT-A
1 AAA-AATATATTTAAAATTAA
28151090 AAAAATATATTTAAAATTAA
1 AAAAATATATTTAAAATTAA
28151110 AAAAATAT
1 AAAAATAT
28151118 TATAAAAAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
14 2 0.04
15 9 0.18
16 2 0.04
19 6 0.12
20 14 0.29
21 15 0.31
22 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAAATATATTTAAAATTAA
Found at i:28151125 original size:20 final size:19
Alignment explanation
Indices: 28151035--28151124 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
28151025 TTATATTATT
28151035 AAAAA-ATATTTAAAATTTA
1 AAAAATATATTTAAAA-TTA
* *
28151054 AAAAGTAATATTTAAATTTA
1 AAAAAT-ATATTTAAAATTA
**
28151074 AAAACA-A-A--TAATTTTA
1 AAAA-ATATATTTAAAATTA
28151090 AAAAATATATTTAAAATTA
1 AAAAATATATTTAAAATTA
28151109 AAAAA-ATATTATAAAA
1 AAAAATATATT-TAAAA
28151125 AGTTTCAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
15 1 0.02
16 12 0.21
17 1 0.02
18 6 0.11
19 21 0.37
20 7 0.12
21 9 0.16
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAAATATATTTAAAATTA
Found at i:28151234 original size:23 final size:23
Alignment explanation
Indices: 28151190--28151249 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 23
28151180 ATAAATAAGG
28151190 AAAAATAAAAATACTTAAAAAGCAA
1 AAAAATAAAAATA-TTAAAAAG-AA
*
28151215 ATAAATAAAAAT-TTAAAAAGAA
1 AAAAATAAAAATATTAAAAAGAA
28151237 AAAAATGAAAAAT
1 AAAAAT-AAAAAT
28151250 GACAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 7 0.22
23 14 0.44
25 11 0.34
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.18
Consensus pattern (23 bp):
AAAAATAAAAATATTAAAAAGAA
Found at i:28154136 original size:15 final size:15
Alignment explanation
Indices: 28154112--28154144 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28154102 CTGTTTTTAG
28154112 TAAAAAAAATAATAA
1 TAAAAAAAATAATAA
*
28154127 TAAAAGAAATAATAA
1 TAAAAAAAATAATAA
28154142 TAA
1 TAA
28154145 TATCCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
TAAAAAAAATAATAA
Found at i:28164667 original size:53 final size:54
Alignment explanation
Indices: 28164610--28164722 Score: 131
Period size: 53 Copynumber: 2.1 Consensus size: 54
28164600 CCCTAAAACA
* * * **
28164610 TTTTTCTTTTACTTTTCC-CCAAAACTTTTACTTCCTCCAAACCTTTAAAAC-TT
1 TTTTTCCTTTAC-CTTCCTCCAAAACTTTTACTTCCCCCAAACCTCAAAAACATT
* * *
28164663 TTTTTCCTTTGCCTTCCTCCAAAACTTTTATTTCCCCCAAATCTCAAAAACATT
1 TTTTTCCTTTACCTTCCTCCAAAACTTTTACTTCCCCCAAACCTCAAAAACATT
28164717 TTTTTC
1 TTTTTC
28164723 GAATTTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
52 4 0.08
53 38 0.76
54 8 0.16
ACGTcount: A:0.24, C:0.29, G:0.01, T:0.46
Consensus pattern (54 bp):
TTTTTCCTTTACCTTCCTCCAAAACTTTTACTTCCCCCAAACCTCAAAAACATT
Found at i:28165921 original size:12 final size:12
Alignment explanation
Indices: 28165896--28165929 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28165886 TCATTAATCG
*
28165896 ATAAACGAGTCA
1 ATAAACGAGCCA
*
28165908 ATAAATGAGCCA
1 ATAAACGAGCCA
28165920 ATAAACGAGC
1 ATAAACGAGC
28165930 TTTTAAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.15
Consensus pattern (12 bp):
ATAAACGAGCCA
Found at i:28170603 original size:73 final size:71
Alignment explanation
Indices: 28170457--28170627 Score: 243
Period size: 73 Copynumber: 2.4 Consensus size: 71
28170447 AAAATAAGCA
* ** * *
28170457 TTAGTGGCGTTTTCCAGAAAGCGCCGCAAAAACTTAAGCCCAACGACGTCGTTTTCTGAGCTTTC
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTTC
28170522 GGGAAT
66 GGGAAT
*
28170528 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAGACATAAGCCCAATGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAA-ACATAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
28170593 TTGGGGAT
64 TCGGGAAT
*
28170601 TTAGCGGCGTTTTTGAGAAAGCACCGC
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC
28170628 TAATGCTCAG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
71 24 0.27
72 4 0.04
73 61 0.69
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (71 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTTC
GGGAAT
Found at i:28170834 original size:229 final size:227
Alignment explanation
Indices: 28170527--28170950 Score: 668
Period size: 229 Copynumber: 1.9 Consensus size: 227
28170517 CTTTCGGGAA
* * * *
28170527 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAGACATAAGCCCAATGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGCT
* *
28170592 TTTGGGGATTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTTGGGGATTTAGCGGCGTTTCTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
*
28170657 AGAAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
131 AGAAAGCGCCGC-AAAAAACATAAGCACAACAACCCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
28170722 CGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
195 CGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
* * *
28170755 TTTAGCGGTGTTTTTGAGAAAGCGCCGTAAAAAAAACCTAAGCACAACGACGCTGTTTTCTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCG-AAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGC
* *
28170820 TTTTGGGGATTTAGCGGCGTTTCTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTT
65 TTTTGGGGATTTAGCGGCGTTTCTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
* * * * * *
28170885 GAGAAAGCGCCGCAAAAAACCTAAGCAGAACGACGCCGTTTTTTGAGCTTTTGGGGATTTAGCGG
130 GAGAAAGCGCCGCAAAAAACATAAGCACAACAACCCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
28170950 C
195 C
28170951 AAAAAATTTG
Statistics
Matches: 177, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
228 72 0.41
229 105 0.59
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (227 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGCT
TTTGGGGATTTAGCGGCGTTTCTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
AGAAAGCGCCGCAAAAAACATAAGCACAACAACCCCGTTTTGTGAGCTTTCGGGGATTTAGCGGC
GTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
Found at i:28170851 original size:115 final size:114
Alignment explanation
Indices: 28170527--28170950 Score: 652
Period size: 114 Copynumber: 3.7 Consensus size: 114
28170517 CTTTCGGGAA
* * *
28170527 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAGACATAAGCCCAATGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGCT
* *
28170592 TTTGGGGATTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTCAGGGC
66 TTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
28170641 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGCT
* *
28170706 TTCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
66 TTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
28170755 TTTAGCGGTGTTTTTGAGAAAGCGCCGTAAAAAAAACCTAAGCACAACGACGCTGTTTTCTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCG-CAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGC
*
28170820 TTTTGGGGATTTAGCGGCGTTTCTAAGAAAGCGCCGCTAATGCTCAGGGC
65 TTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
28170870 TTTAGCGGTGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCAGAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGCT
28170934 TTTGGGGATTTAGCGGC
66 TTTGGGGATTTAGCGGC
28170951 AAAAAATTTG
Statistics
Matches: 285, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
113 50 0.18
114 131 0.46
115 104 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCACAACGACGCCGTTTTCTGAGCT
TTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:28171004 original size:41 final size:41
Alignment explanation
Indices: 28170959--28171037 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
28170949 GCAAAAAATT
* * *
28170959 TGGGGGCTTTGGCGGTGTTTTTGATAAAGCGCCGCTAATGC
1 TGGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
28171000 TGGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
1 TGGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
28171038 AAATACTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (41 bp):
TGGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:28171305 original size:15 final size:15
Alignment explanation
Indices: 28171285--28171329 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
28171275 CATATTTTAA
*
28171285 GGTTTAGGGAGTATG
1 GGTTTAGGGATTATG
28171300 GGTTTAGGGATTAT-
1 GGTTTAGGGATTATG
*
28171314 GGATTAGGGATTATG
1 GGTTTAGGGATTATG
28171329 G
1 G
28171330 ATTAAGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:28171322 original size:14 final size:14
Alignment explanation
Indices: 28171288--28171333 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
28171278 ATTTTAAGGT
* *
28171288 TTAGGGAGTATGGGT
1 TTAGGGATTAT-GGA
28171303 TTAGGGATTATGGA
1 TTAGGGATTATGGA
28171317 TTAGGGATTATGGA
1 TTAGGGATTATGGA
28171331 TTA
1 TTA
28171334 AGGGTTGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:28171604 original size:15 final size:15
Alignment explanation
Indices: 28171584--28171615 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28171574 TATTTTAAGG
28171584 TTTAGGGAGTATAGA
1 TTTAGGGAGTATAGA
*
28171599 TTTAGGGATTATAGA
1 TTTAGGGAGTATAGA
28171614 TT
1 TT
28171616 AAGGATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATAGA
Found at i:28171695 original size:22 final size:22
Alignment explanation
Indices: 28171654--28171729 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
28171644 TGAGATTTAA
* *
28171654 GGTTTAGGGGTTAGGGGTTAGG
1 GGTTTAGAGGTTAGAGGTTAGG
* *
28171676 GGTTTAGAGGTTAGATGTTAGT
1 GGTTTAGAGGTTAGAGGTTAGG
* *
28171698 GGTTAAGA-GTTAGAGATTTA-G
1 GGTTTAGAGGTTAGAG-GTTAGG
28171719 GGTTTAG-GGTT
1 GGTTTAGAGGTT
28171730 TCAAAGGTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
21 15 0.35
22 28 0.65
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (22 bp):
GGTTTAGAGGTTAGAGGTTAGG
Found at i:28171728 original size:297 final size:293
Alignment explanation
Indices: 28171185--28171730 Score: 787
Period size: 297 Copynumber: 1.8 Consensus size: 293
28171175 ATTATTTAAA
* * *
28171185 ATAATTGTAAAAGGGATAATAATAAATTTGTTCAGGGTTTTTGGTTTAGGGTATATGATTTATTT
1 ATAATTGTAAAAGAGATAATAATAAATTTGTTCAGGGTTTTTAGTTTAGGGTATATGATTAATTT
* * * *
28171250 AAGATTTAAGGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGGTTTAGGGATTATG
66 AAGATTTAAAGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATA
* *
28171315 GATTAGGGATTATGGATTAAGGGTTGGGATTTAAAGTTTAGGGGTTAAAGGGTTAGAGGTTGAGG
131 GATTAAGGATTATGGATTAAGGGTTGGGATTTAAAGTTTAGGGGTTAAAGGGTTAGAGGTTGAGA
*
28171380 GGTTAGATGTGCTATGGGTTAAAAGTTAGGGATTCAGGGGTCGAGTTAGGGTTTTGGGTTTAGAT
196 GGTTAGATGT-CTATGGGTTAAAAGTTAGAGATTCAGGGGT---GTTAGGGTTTTGGGTTTAGAT
28171445 TAATTATTTTTAATTTATATTTTAAATATGTTCTTAT
257 TAATTATTTTTAATTTATATTTTAAATATGTTCTTAT
*
28171482 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
1 ATAATTGTAAAAGAGATAATAATAAATTTGTTCAGGGTTTTTAGTTTAGGGTATATGATTAATTT
28171547 AAGATTTAAAGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATA
66 AAGATTTAAAGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATA
* * *
28171612 GATTAAGGATTATGGTTTAATTAAGGGTTGGCTGAGATTTAAGGTTTAGGGGTT-AGGGGTTAGG
131 GATTAAGGATTATGG----ATTAAGGGTT-G--G-GATTTAAAGTTTAGGGGTTAAAGGGTTAGA
* * *
28171676 GGTTTAGAGGTTAGATGT-TA-GTGGTTAAGAGTTAGAGATTTA-GGGT-TTAGGGTTT
188 GGTTGAGAGGTTAGATGTCTATG-GGTTAAAAGTTAGAGATTCAGGGGTGTTAGGGTTT
28171731 CAAAGGTCGA
Statistics
Matches: 223, Mismatches: 17, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
297 145 0.65
301 15 0.07
302 20 0.09
304 25 0.11
305 18 0.08
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.40
Consensus pattern (293 bp):
ATAATTGTAAAAGAGATAATAATAAATTTGTTCAGGGTTTTTAGTTTAGGGTATATGATTAATTT
AAGATTTAAAGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATA
GATTAAGGATTATGGATTAAGGGTTGGGATTTAAAGTTTAGGGGTTAAAGGGTTAGAGGTTGAGA
GGTTAGATGTCTATGGGTTAAAAGTTAGAGATTCAGGGGTGTTAGGGTTTTGGGTTTAGATTAAT
TATTTTTAATTTATATTTTAAATATGTTCTTAT
Found at i:28172238 original size:18 final size:18
Alignment explanation
Indices: 28172217--28172253 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28172207 TAACAAATGG
*
28172217 AATTAAATTAAAATAAAA
1 AATTAAAATAAAATAAAA
*
28172235 AATTAAAATGAAATAAAA
1 AATTAAAATAAAATAAAA
28172253 A
1 A
28172254 CACTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTAAAATAAAATAAAA
Found at i:28172260 original size:19 final size:18
Alignment explanation
Indices: 28172227--28172262 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28172217 AATTAAATTA
*
28172227 AAATAAAAAATTAAAATG
1 AAATAAAAAACTAAAATG
28172245 AAATAAAAACACTAAAAT
1 AAATAAAAA-ACTAAAAT
28172263 TTATAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATAAAAAACTAAAATG
Found at i:28174842 original size:22 final size:22
Alignment explanation
Indices: 28174811--28174853 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28174801 ATTTGATCAA
28174811 TTGTTGTAGCCAAGGCAAATTG
1 TTGTTGTAGCCAAGGCAAATTG
* *
28174833 TTGTTTTAGCCAATGCAAATT
1 TTGTTGTAGCCAAGGCAAATT
28174854 TTATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (22 bp):
TTGTTGTAGCCAAGGCAAATTG
Found at i:28175438 original size:19 final size:20
Alignment explanation
Indices: 28175406--28175443 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28175396 ACATTACTTA
* *
28175406 TTAATATTTTTATA-ATTTT
1 TTAATATATATATATATTTT
28175425 TTAATATATATATATATTT
1 TTAATATATATATATATTT
28175444 AAAATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAATATATATATATATTTT
Found at i:28175466 original size:19 final size:18
Alignment explanation
Indices: 28175414--28175472 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
28175404 TATTAATATT
*
28175414 TTTATA-ATTTTTTAATA
1 TTTATATATTTTTTAAAA
* *
28175431 TATATATA-TATTTAAAA
1 TTTATATATTTTTTAAAA
28175448 TTTATATATTTTTTCAAAA
1 TTTATATATTTTTT-AAAA
*
28175467 CTTATA
1 TTTATA
28175473 AATCATATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 19 0.58
18 5 0.15
19 9 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATATATTTTTTAAAA
Found at i:28175621 original size:12 final size:12
Alignment explanation
Indices: 28175606--28175639 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28175596 TAACCTACAT
28175606 AACTTACATAGA
1 AACTTACATAGA
*
28175618 AACTTATATAGA
1 AACTTACATAGA
*
28175630 AACTTGCATA
1 AACTTACATA
28175640 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:28175648 original size:9 final size:9
Alignment explanation
Indices: 28175630--28175836 Score: 82
Period size: 9 Copynumber: 23.7 Consensus size: 9
28175620 CTTATATAGA
*
28175630 AACTTGCAT
1 AACTTACAT
28175639 AACTTACAT
1 AACTTACAT
*
28175648 AA-TAACAT
1 AACTTACAT
*
28175656 AAAAACTTAGAT
1 ---AACTTACAT
28175668 AA--TACAT
1 AACTTACAT
* *
28175675 AGCCTACAT
1 AACTTACAT
28175684 AACTTACAT
1 AACTTACAT
28175693 AACTTACAT
1 AACTTACAT
*
28175702 AA--TACAC
1 AACTTACAT
*
28175709 CACTTACAT
1 AACTTACAT
*
28175718 AAATAACTAGCAT
1 AACT---TA-CAT
*
28175731 AA--TACGT
1 AACTTACAT
* *
28175738 AGCCTACAT
1 AACTTACAT
*
28175747 AACTTACTT
1 AACTTACAT
28175756 AACTTACAT
1 AACTTACAT
*
28175765 AA--TACAC
1 AACTTACAT
*
28175772 CACTTACAT
1 AACTTACAT
*
28175781 AACTTAAAT
1 AACTTACAT
28175790 AACTTACAT
1 AACTTACAT
*
28175799 AA--TACTT
1 AACTTACAT
*
28175806 AAATTTA-AT
1 -AACTTACAT
*
28175815 AA--TACAC
1 AACTTACAT
28175822 AACTTACAT
1 AACTTACAT
28175831 AACTTA
1 AACTTA
28175837 ATTACATTAT
Statistics
Matches: 146, Mismatches: 30, Indels: 44
0.66 0.14 0.20
Matches are distributed among these distances:
6 2 0.01
7 25 0.17
8 11 0.08
9 93 0.64
10 2 0.01
11 2 0.01
12 6 0.04
13 5 0.03
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:28175697 original size:63 final size:63
Alignment explanation
Indices: 28175648--28175782 Score: 193
Period size: 63 Copynumber: 2.2 Consensus size: 63
28175638 TAACTTACAT
28175648 AATAACATAAA-AACTTAG-ATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
1 AATAACATAAATAAC-TAGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
* * * *
28175710 ACTTACATAAATAACTAGCATAATACGTAGCCTACATAACTTACTTAACTTACATAATACACC
1 AATAACATAAATAACTAGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
* *
28175773 ACTTACATAA
1 AATAACATAA
28175783 CTTAAATAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
62 12 0.18
63 55 0.82
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (63 bp):
AATAACATAAATAACTAGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
Found at i:28175704 original size:34 final size:33
Alignment explanation
Indices: 28175649--28175803 Score: 142
Period size: 34 Copynumber: 4.8 Consensus size: 33
28175639 AACTTACATA
* *
28175649 ATAACATAAA-AACTTAGATAATACATAGCCTAC
1 ATAACTTAAATAACTTACATAATACATA-CCTAC
*
28175682 ATAACTTACATAACTTACATAATAC--ACC-AC
1 ATAACTTAAATAACTTACATAATACATACCTAC
* * *
28175712 -TTACATAAATAAC-TAGCATAATACGTAGCCTAC
1 ATAACTTAAATAACTTA-CATAATACATA-CCTAC
** * *
28175745 ATAACTTACTTAACTTACATAATACACCACTTAC
1 ATAACTTAAATAACTTACATAATACA-TACCTAC
28175779 ATAACTTAAATAACTTACATAATAC
1 ATAACTTAAATAACTTACATAATAC
28175804 TTAAATTTAA
Statistics
Matches: 98, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
28 2 0.02
29 18 0.18
30 2 0.02
31 3 0.03
32 3 0.03
33 10 0.10
34 57 0.58
35 3 0.03
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.28
Consensus pattern (33 bp):
ATAACTTAAATAACTTACATAATACATACCTAC
Found at i:28175849 original size:29 final size:31
Alignment explanation
Indices: 28175790--28175862 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
28175780 TAACTTAAAT
28175790 AACTTACATAATACTTAAATTTAATAATACAC
1 AACTTACAT-ATACTTAAATTTAATAATACAC
*
28175822 AACTTACATA-ACTT-AA-TTACATTATACAC
1 AACTTACATATACTTAAATTTA-ATAATACAC
*
28175851 AACATACATATA
1 AACTTACATATA
28175863 TCATAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 3 0.08
29 19 0.51
30 5 0.14
31 1 0.03
32 9 0.24
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (31 bp):
AACTTACATATACTTAAATTTAATAATACAC
Found at i:28177695 original size:43 final size:43
Alignment explanation
Indices: 28177641--28177868 Score: 341
Period size: 43 Copynumber: 5.3 Consensus size: 43
28177631 CGTTTTAAAA
* *
28177641 AAAAGCGCCGCTAAAGGTAATGGTTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* * *
28177684 AAAAGCTCCGCTAAAGTTCATGGTCTTTAGCGGCG-TTGTTGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* * *
28177726 AAAAGTGCCGCTAGAGGTTATGGTCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTTGTGGG
* *
28177770 AAAAGCGCCGCTAAAGGTCTTGGCCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
*
28177813 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
28177856 AAAAGCGCCGCTA
1 AAAAGCGCCGCTA
28177869 GAAGCCTGTT
Statistics
Matches: 164, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
42 26 0.16
43 112 0.68
44 26 0.16
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
Found at i:28180161 original size:19 final size:21
Alignment explanation
Indices: 28180109--28180163 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
28180099 AAAACTTTAT
* *
28180109 TTATATTAATTTAATCATTTT
1 TTATTTTAATTTAATCATTTC
*
28180130 TTATTTTATTTTAAT-A-TTC
1 TTATTTTAATTTAATCATTTC
*
28180149 TTGTTTTAATTTAAT
1 TTATTTTAATTTAAT
28180164 TTTTACATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 1 0.03
21 13 0.45
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATTTTAATTTAATCATTTC
Found at i:28180173 original size:25 final size:25
Alignment explanation
Indices: 28180127--28180174 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28180117 ATTTAATCAT
* * *
28180127 TTTTTATTTTATTTTAATATTCTTG
1 TTTTAATTTAATTTTAACATTCTTG
*
28180152 TTTTAATTTAATTTTTACATTCT
1 TTTTAATTTAATTTTAACATTCT
28180175 AATTTTTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTAATTTAATTTTAACATTCTTG
Found at i:28187909 original size:8 final size:8
Alignment explanation
Indices: 28187892--28187932 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
28187882 AAATAGTGAT
28187892 AAAAAATA
1 AAAAAATA
*
28187900 AAATAATA
1 AAAAAATA
28187908 AAAAAATA
1 AAAAAATA
28187916 AAAAAAGTA
1 AAAAAA-TA
28187925 AAAAAATA
1 AAAAAATA
28187933 GTAGGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (8 bp):
AAAAAATA
Found at i:28187910 original size:15 final size:15
Alignment explanation
Indices: 28187892--28187932 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 15
28187882 AAATAGTGAT
28187892 AAAAAATAAAATAATA
1 AAAAAATAAAA-AATA
28187908 AAAAAATAAAAAAAGTA
1 AAAAAAT-AAAAAA-TA
28187925 AAAAAATA
1 AAAAAATA
28187933 GTAGGTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:28189595 original size:15 final size:16
Alignment explanation
Indices: 28189566--28189597 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
28189556 ATATTGAAAG
28189566 TTTATCTGCAAAAAAT
1 TTTATCTGCAAAAAAT
28189582 TTTATCTG-AAAAAAT
1 TTTATCTGCAAAAAAT
28189597 T
1 T
28189598 GGTTGTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
TTTATCTGCAAAAAAT
Found at i:28192223 original size:13 final size:14
Alignment explanation
Indices: 28192192--28192223 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28192182 GATTAAATGT
28192192 TAAAATAAGTAAAA
1 TAAAATAAGTAAAA
28192206 T-AAATAA-TAAAA
1 TAAAATAAGTAAAA
28192218 TAAAAT
1 TAAAAT
28192224 GTTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 10 0.59
14 1 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAAATAAGTAAAA
Found at i:28192518 original size:18 final size:18
Alignment explanation
Indices: 28192481--28192518 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
28192471 TAAATGATGA
28192481 ATTTAAAATATTAATTGTT
1 ATTTAAAATATT-ATTGTT
28192500 ATTTAAAAATATT-TTGTT
1 ATTT-AAAATATTATTGTT
28192518 A
1 A
28192519 AGCGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTTAAAATATTATTGTT
Found at i:28193158 original size:20 final size:20
Alignment explanation
Indices: 28193135--28193363 Score: 127
Period size: 20 Copynumber: 11.4 Consensus size: 20
28193125 GAAGTGTCAT
*
28193135 TGTTTGCACATCAGTGCCCC
1 TGTTTGTACATCAGTGCCCC
* * *
28193155 TGTTTGTACTTCAATACCCC
1 TGTTTGTACATCAGTGCCCC
* *
28193175 TATTTGTACATCAGTGCCCT
1 TGTTTGTACATCAGTGCCCC
* * * *
28193195 TGATTGTACTTC-GATACCAC
1 TGTTTGTACATCAG-TGCCCC
* *
28193215 TATTTGCACATCAGTGCCCC
1 TGTTTGTACATCAGTGCCCC
* * ** *
28193235 TGATTGTACTTTGGTACCCC
1 TGTTTGTACATCAGTGCCCC
* * * *
28193255 TATTTGCACATAAATGCCCC
1 TGTTTGTACATCAGTGCCCC
** * ** *
28193275 TAATTGTACTTTGGTACCCC
1 TGTTTGTACATCAGTGCCCC
*
28193295 TGTTTGCACATCAGTGCCCC
1 TGTTTGTACATCAGTGCCCC
* * *
28193315 TGTTTGTACTTCGGTACCCC
1 TGTTTGTACATCAGTGCCCC
* * *
28193335 TATTTGCACATCAGTGCTCC
1 TGTTTGTACATCAGTGCCCC
*
28193355 TGATTGTAC
1 TGTTTGTAC
28193364 TTCGATTCCC
Statistics
Matches: 144, Mismatches: 63, Indels: 4
0.68 0.30 0.02
Matches are distributed among these distances:
19 1 0.01
20 142 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (20 bp):
TGTTTGTACATCAGTGCCCC
Found at i:28193202 original size:40 final size:40
Alignment explanation
Indices: 28193137--28193395 Score: 338
Period size: 40 Copynumber: 6.5 Consensus size: 40
28193127 AGTGTCATTG
* *
28193137 TTTGCACATCAGTGCCCCTGTTTGTACTTCAATACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* * *
28193177 TTTGTACATCAGTGCCCTTGATTGTACTTCGATACCACTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* *
28193217 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* * * * * *
28193257 TTTGCACATAAATGCCCCTAATTGTACTTTGGTACCCCTG
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* *
28193297 TTTGCACATCAGTGCCCCTGTTTGTACTTCGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
* *
28193337 TTTGCACATCAGTGCTCCTGATTGTACTTCGATTCCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
** *
28193377 AATGCACATCTGTGCCCCT
1 TTTGCACATCAGTGCCCCT
28193396 ATTTGCACTT
Statistics
Matches: 191, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 191 1.00
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.35
Consensus pattern (40 bp):
TTTGCACATCAGTGCCCCTGATTGTACTTCGATACCCCTA
Found at i:28193402 original size:20 final size:20
Alignment explanation
Indices: 28193137--28193403 Score: 121
Period size: 20 Copynumber: 13.3 Consensus size: 20
28193127 AGTGTCATTG
*
28193137 TTTGCACATCAGTGCCCCTG
1 TTTGCACATCAGTGCCCCTA
* * * *
28193157 TTTGTACTTCAATACCCCTA
1 TTTGCACATCAGTGCCCCTA
* *
28193177 TTTGTACATCAGTGCCCTTGA
1 TTTGCACATCAGTGCCCCT-A
* * * *
28193198 -TTGTACTTC-GATACCACTA
1 TTTGCACATCAG-TGCCCCTA
28193217 TTTGCACATCAGTGCCCCTGA
1 TTTGCACATCAGTGCCCCT-A
* * ** *
28193238 -TTGTACTTTGGTACCCCTA
1 TTTGCACATCAGTGCCCCTA
* *
28193257 TTTGCACATAAATGCCCCTA
1 TTTGCACATCAGTGCCCCTA
* * * ** * *
28193277 ATTGTACTTTGGTACCCCTG
1 TTTGCACATCAGTGCCCCTA
*
28193297 TTTGCACATCAGTGCCCCTG
1 TTTGCACATCAGTGCCCCTA
* * * *
28193317 TTTGTACTTCGGTACCCCTA
1 TTTGCACATCAGTGCCCCTA
*
28193337 TTTGCACATCAGTGCTCCTGA
1 TTTGCACATCAGTGCCCCT-A
* * *
28193358 -TTGTACTTC-GATTCCCCTA
1 TTTGCACATCAG-TGCCCCTA
** *
28193377 AATGCACATCTGTGCCCCTA
1 TTTGCACATCAGTGCCCCTA
28193397 TTTGCAC
1 TTTGCAC
28193404 TTTGGTGCCC
Statistics
Matches: 175, Mismatches: 62, Indels: 20
0.68 0.24 0.08
Matches are distributed among these distances:
19 5 0.03
20 165 0.94
21 5 0.03
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.35
Consensus pattern (20 bp):
TTTGCACATCAGTGCCCCTA
Found at i:28193411 original size:20 final size:20
Alignment explanation
Indices: 28193214--28193469 Score: 81
Period size: 20 Copynumber: 12.8 Consensus size: 20
28193204 TTCGATACCA
* **
28193214 CTATTTGCACATCAGTGCCC
1 CTATTTGCACTTTGGTGCCC
* *
28193234 CTGA-TTGTACTTTGGTACCC
1 CT-ATTTGCACTTTGGTGCCC
* ***
28193254 CTATTTGCACATAAATGCCC
1 CTATTTGCACTTTGGTGCCC
* * *
28193274 CTAATTGTACTTTGGTACCC
1 CTATTTGCACTTTGGTGCCC
* * **
28193294 CTGTTTGCACATCAGTGCCC
1 CTATTTGCACTTTGGTGCCC
* * * *
28193314 CTGTTTGTACTTCGGTACCC
1 CTATTTGCACTTTGGTGCCC
* ** *
28193334 CTATTTGCACATCAGTGCTC
1 CTATTTGCACTTTGGTGCCC
* * * *
28193354 CTGA-TTGTACTTCGATTCCC
1 CT-ATTTGCACTTTGGTGCCC
** *
28193374 CTAAATGCACATCT-GTGCCC
1 CTATTTGCAC-TTTGGTGCCC
28193394 CTATTTGCACTTTGGTGCCC
1 CTATTTGCACTTTGGTGCCC
** * * *
28193414 CTGA-TCACACATTCGTGCTC
1 CT-ATTTGCACTTTGGTGCCC
*
28193434 CTGA-TTGCACTTTGGTGCTC
1 CT-ATTTGCACTTTGGTGCCC
* *
28193454 CTAATTGCATTTTGGT
1 CTATTTGCACTTTGGT
28193470 TCCCTGTTAT
Statistics
Matches: 168, Mismatches: 60, Indels: 16
0.69 0.25 0.07
Matches are distributed among these distances:
19 5 0.03
20 159 0.95
21 4 0.02
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (20 bp):
CTATTTGCACTTTGGTGCCC
Found at i:28193415 original size:40 final size:40
Alignment explanation
Indices: 28193137--28193449 Score: 326
Period size: 40 Copynumber: 7.8 Consensus size: 40
28193127 AGTGTCATTG
* ***
28193137 TTTGCACATCAGTGCCCCTGTTTGTACTTCAATACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* * * * *
28193177 TTTGTACATCAGTGCCCTTGATTGTACTTCGATACCACTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
28193217 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* * * *
28193257 TTTGCACATAAATGCCCCTAATTGTACTTTGGTACCCCTG
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* *
28193297 TTTGCACATCAGTGCCCCTGTTTGTACTTCGGTACCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
* * * *
28193337 TTTGCACATCAGTGCTCCTGATTGTACTTCGATTCCCCTA
1 TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
** * * *
28193377 AATGCACATCTGTGCCCCT-ATTTGCACTTTGGTGCCCCTGA
1 TTTGCACATCAGTGCCCCTGA-TTGTACTTTGGTACCCCT-A
** * *
28193418 -TCACACATTC-GTGCTCCTGATTGCACTTTGGT
1 TTTGCACA-TCAGTGCCCCTGATTGTACTTTGGT
28193450 GCTCCTAATT
Statistics
Matches: 233, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.00
40 228 0.98
41 4 0.02
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (40 bp):
TTTGCACATCAGTGCCCCTGATTGTACTTTGGTACCCCTA
Found at i:28199088 original size:18 final size:17
Alignment explanation
Indices: 28199068--28199118 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 17
28199058 TAAGATTAAT
28199068 AAAATAAAATAAACGAATA
1 AAAATAAAATAAA--AATA
28199087 AAAATAAAAATAAAAATA
1 AAAAT-AAAATAAAAATA
*
28199105 AAAACAAAATAAAA
1 AAAATAAAATAAAA
28199119 TTTAAAACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 9 0.30
18 8 0.27
19 5 0.17
20 8 0.27
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:28199094 original size:6 final size:6
Alignment explanation
Indices: 28199068--28199118 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
28199058 TAAGATTAAT
*
28199068 AAAAT- AAAATA AACGAATA AAAATA AAAATA AAAATA AAAA-C AAAATA
1 AAAATA AAAATA AA--AATA AAAATA AAAATA AAAATA AAAATA AAAATA
28199116 AAA
1 AAA
28199119 TTTAAAACAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 9 0.22
6 25 0.62
8 6 0.15
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:28205486 original size:26 final size:25
Alignment explanation
Indices: 28205442--28205492 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
28205432 GTTTTTTCTC
28205442 TTCTTTTTATTATTATTTTTTCTTTT
1 TTCTTTTTATTA-TATTTTTTCTTTT
* * *
28205468 TTCTTTTTCTTCTTTTTTTTCTTTT
1 TTCTTTTTATTATATTTTTTCTTTT
28205493 ATAACATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (25 bp):
TTCTTTTTATTATATTTTTTCTTTT
Found at i:28214024 original size:18 final size:17
Alignment explanation
Indices: 28213978--28214031 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
28213968 TTTCCAATTC
28213978 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
28213995 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
28214013 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
28214031 T
1 T
28214032 TTCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:28214114 original size:32 final size:32
Alignment explanation
Indices: 28214074--28214138 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28214064 TAGAACACAT
28214074 ATATACATAATATCTATCACCAAATAAAATTC
1 ATATACATAATATCTATCACCAAATAAAATTC
28214106 ATATACATAATATCTATCACCAAATAAAATTC
1 ATATACATAATATCTATCACCAAATAAAATTC
28214138 A
1 A
28214139 CTTTAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (32 bp):
ATATACATAATATCTATCACCAAATAAAATTC
Found at i:28215946 original size:30 final size:30
Alignment explanation
Indices: 28215903--28215977 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
28215893 CTTATATACT
*
28215903 AAATATAATAAAATAATA-ATATCTCATTA
1 AAATATAATAAAATAATATATATCTAATTA
* *
28215932 AAATATTATTAAAATAATATTTATCTAATTA
1 AAATA-TAATAAAATAATATATATCTAATTA
* *
28215963 AAAAATCATAAAATA
1 AAATATAATAAAATA
28215978 TTATTAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 5 0.13
30 20 0.53
31 13 0.34
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATATAATAAAATAATATATATCTAATTA
Found at i:28216991 original size:17 final size:17
Alignment explanation
Indices: 28216961--28216998 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28216951 ACATGAAATT
28216961 TAATCATTTTATTGAAA
1 TAATCATTTTATTGAAA
*
28216978 TAAT-ATTTTAATTGAGA
1 TAATCATTTT-ATTGAAA
28216995 TAAT
1 TAAT
28216999 TTTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (17 bp):
TAATCATTTTATTGAAA
Found at i:28217331 original size:31 final size:29
Alignment explanation
Indices: 28217295--28217366 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
28217285 GATTAAATCA
*
28217295 AAATTAAAGTTTTA-TGTATACATTTGAACC
1 AAATTAAAGTTTCACTGTATA-A-TTGAACC
* *
28217325 ACAATTAGAGTTTCACGTGTATAATTGCACC
1 A-AATTAAAGTTTCAC-TGTATAATTGAACC
28217356 AAATTAAAGTT
1 AAATTAAAGTT
28217367 CTTCTATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.29
31 18 0.51
32 1 0.03
33 6 0.17
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (29 bp):
AAATTAAAGTTTCACTGTATAATTGAACC
Found at i:28217569 original size:16 final size:17
Alignment explanation
Indices: 28217532--28217575 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
28217522 TTTTAAAACC
28217532 TGGTTGTTATAGCGAAA
1 TGGTTGTTATAGCGAAA
**
28217549 T-GTTGTTATAGC-ATG
1 TGGTTGTTATAGCGAAA
28217564 TGGTTGTTATAG
1 TGGTTGTTATAG
28217576 AGAGGATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 21 0.88
17 1 0.04
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.43
Consensus pattern (17 bp):
TGGTTGTTATAGCGAAA
Found at i:28217797 original size:13 final size:13
Alignment explanation
Indices: 28217779--28217803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28217769 TTAATATATA
28217779 CAATATTATAGAT
1 CAATATTATAGAT
28217792 CAATATTATAGA
1 CAATATTATAGA
28217804 GATATCAAAT
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
CAATATTATAGAT
Found at i:28220659 original size:20 final size:20
Alignment explanation
Indices: 28220634--28220676 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
28220624 AAATATCATT
28220634 AAACCGTTTACTGATAACGG
1 AAACCGTTTACTGATAACGG
*
28220654 AAACCGTTTACTGGTAACGG
1 AAACCGTTTACTGATAACGG
28220674 AAA
1 AAA
28220677 AATGATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (20 bp):
AAACCGTTTACTGATAACGG
Found at i:28221754 original size:24 final size:21
Alignment explanation
Indices: 28221730--28221773 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28221720 AAGAAGAAAG
*
28221730 GGAAAAGAGAGAAAATAAAATAA
1 GGAAAA-AAAGAAAA-AAAATAA
28221753 GGAAAAAAAGAAAAAAAATAA
1 GGAAAAAAAGAAAAAAAATAA
28221774 AAATTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (21 bp):
GGAAAAAAAGAAAAAAAATAA
Found at i:28227719 original size:3 final size:3
Alignment explanation
Indices: 28227711--28227743 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28227701 ATTAAGGGGA
28227711 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28227744 TTGAGTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28251604 original size:23 final size:24
Alignment explanation
Indices: 28251567--28251626 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
28251557 AGCTTCTCGT
* *
28251567 TAATGGCTCTCCGGAGCTTCCCGA
1 TAATGGCTCTTCGGAGCTACCCGA
* *
28251591 T-ATGGCTATTCGGAGCTACCCGT
1 TAATGGCTCTTCGGAGCTACCCGA
28251614 TAATGGCTCTTCG
1 TAATGGCTCTTCG
28251627 AAGTTGCCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (24 bp):
TAATGGCTCTTCGGAGCTACCCGA
Found at i:28251626 original size:24 final size:24
Alignment explanation
Indices: 28251546--28251646 Score: 98
Period size: 24 Copynumber: 4.2 Consensus size: 24
28251536 CTTGATCATA
* *
28251546 GGCTCTTCTTGAGCTTCTCGTTAAT
1 GGCTCTTC-GGAGCTTCCCGTTAAT
* *
28251571 GGCTCTCCGGAGCTTCCCGAT-AT
1 GGCTCTTCGGAGCTTCCCGTTAAT
* *
28251594 GGCTATTCGGAGCTACCCGTTAAT
1 GGCTCTTCGGAGCTTCCCGTTAAT
* *
28251618 GGCTCTTCGAAG-TTGCCCGTTATT
1 GGCTCTTCGGAGCTT-CCCGTTAAT
28251642 GGCTC
1 GGCTC
28251647 GCATGAGCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
23 20 0.32
24 35 0.56
25 7 0.11
ACGTcount: A:0.14, C:0.28, G:0.25, T:0.34
Consensus pattern (24 bp):
GGCTCTTCGGAGCTTCCCGTTAAT
Found at i:28253743 original size:10 final size:10
Alignment explanation
Indices: 28253728--28253782 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
28253718 CATTCAAATA
28253728 TTTTTATAAT
1 TTTTTATAAT
* *
28253738 TTTTTAAAAC
1 TTTTTATAAT
*
28253748 TTTATATAAT
1 TTTTTATAAT
*
28253758 TTTTT-TTAT
1 TTTTTATAAT
28253767 ATTTTTA-AAT
1 -TTTTTATAAT
28253777 TTTTTA
1 TTTTTA
28253783 AGTGATTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
9 9 0.26
10 26 0.74
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:28255198 original size:36 final size:36
Alignment explanation
Indices: 28255153--28255229 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
28255143 TACACATCAA
*
28255153 CAAG-CCATGACAATGCATTCAACACAGGCTAAAAT
1 CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
28255188 CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
1 CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
28255224 CAAGTC
1 CAAGTC
28255230 TTAAACATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.18
Consensus pattern (36 bp):
CAAGTCCATGACAATGCATTCAACACAAGCTAAAAT
Found at i:28255376 original size:4 final size:4
Alignment explanation
Indices: 28255367--28255392 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28255357 TATATTTCAA
28255367 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
28255393 CACTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:28257902 original size:37 final size:37
Alignment explanation
Indices: 28257852--28257937 Score: 172
Period size: 37 Copynumber: 2.3 Consensus size: 37
28257842 GGATTTTTTG
28257852 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
1 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
28257889 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
1 TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
28257926 TATTGGGTTATC
1 TATTGGGTTATC
28257938 AAGTTAGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (37 bp):
TATTGGGTTATCGCAAAAGGTATTGTACTATCAGTTT
Found at i:28258301 original size:28 final size:28
Alignment explanation
Indices: 28258261--28258319 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
28258251 GATTTATGAC
28258261 TCTTCCTATTATATTGTCAAATAGTAAG
1 TCTTCCTATTATATTGTCAAATAGTAAG
28258289 TCTTCCTATTATATTGTCAAATAGTAAG
1 TCTTCCTATTATATTGTCAAATAGTAAG
28258317 TCT
1 TCT
28258320 GTTGGATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (28 bp):
TCTTCCTATTATATTGTCAAATAGTAAG
Found at i:28261230 original size:18 final size:17
Alignment explanation
Indices: 28261203--28261237 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28261193 GCAACTATAT
28261203 GAATGAATGTTATAGATA
1 GAATGAATGTTAT-GATA
*
28261221 GAATGCATGTTATGATA
1 GAATGAATGTTATGATA
28261238 TGGAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (17 bp):
GAATGAATGTTATGATA
Found at i:28261618 original size:26 final size:26
Alignment explanation
Indices: 28261589--28261649 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
28261579 TTAGGAAGGA
* *
28261589 AAAGCCTTTGTGGCATAATATGAAAG
1 AAAGCCTTTATGGCACAATATGAAAG
* *
28261615 AAAGCCTTTATGGCGCAATATGAAAT
1 AAAGCCTTTATGGCACAATATGAAAG
28261641 AAATGCCTT
1 AAA-GCCTT
28261650 CAGGCCGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (26 bp):
AAAGCCTTTATGGCACAATATGAAAG
Found at i:28267952 original size:2 final size:2
Alignment explanation
Indices: 28267945--28267970 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28267935 TCAATGGATA
28267945 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
28267971 ACACTACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:28283718 original size:16 final size:17
Alignment explanation
Indices: 28283688--28283720 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28283678 TTGTTTATTA
*
28283688 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
28283705 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
28283721 AATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:28283874 original size:11 final size:11
Alignment explanation
Indices: 28283847--28283890 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
28283837 TTTCACAATA
28283847 TAATAAT-ATT
1 TAATAATAATT
28283857 T-ATAATAATT
1 TAATAATAATT
28283867 TAATAATAATT
1 TAATAATAATT
28283878 TAATAATATATT
1 TAATAATA-ATT
28283890 T
1 T
28283891 TACACATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.16
10 5 0.16
11 17 0.55
12 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATAATAATT
Done.