Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 102 of 103
Found at i:38488134 original size:23 final size:24
Alignment explanation
Indices: 38488084--38488142 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
38488074 TATATTTATT
* * *
38488084 TTTTGTATTAAAAAGTATTTAACA
1 TTTTATATTAAAAAATATTTAAAA
38488108 -TTTATATTAAAAAAT-TTTAAAA
1 TTTTATATTAAAAAATATTTAAAA
38488130 TTTTA-ATATAAAA
1 TTTTATAT-TAAAA
38488143 TATGTCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (24 bp):
TTTTATATTAAAAAATATTTAAAA
Found at i:38497535 original size:19 final size:18
Alignment explanation
Indices: 38497508--38497549 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38497498 CTTTCCCAAC
38497508 TTTTCTTTCCTCTTTCTTT
1 TTTTCTTTCCTC-TTCTTT
* *
38497527 TTTTGTTTCTTCTTCTTT
1 TTTTCTTTCCTCTTCTTT
38497545 TTTTC
1 TTTTC
38497550 CTTATATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTCTTTCCTCTTCTTT
Found at i:38502017 original size:3 final size:3
Alignment explanation
Indices: 38502009--38502033 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38501999 TCCTTACTCC
38502009 CGA CGA CGA CGA CGA CGA CGA CGA C
1 CGA CGA CGA CGA CGA CGA CGA CGA C
38502034 ATGTCGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CGA
Found at i:38506112 original size:33 final size:33
Alignment explanation
Indices: 38506075--38506139 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
38506065 CCACCTCGTC
*
38506075 TGTGTTATCTTCATCACTTGCGTACACCTTTTG
1 TGTGTTATCTTCATCACTTGCATACACCTTTTG
*
38506108 TGTGTTGTCTTCATCACTTGCATACACCTTTT
1 TGTGTTATCTTCATCACTTGCATACACCTTTT
38506140 TTGGAGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.15, C:0.25, G:0.14, T:0.46
Consensus pattern (33 bp):
TGTGTTATCTTCATCACTTGCATACACCTTTTG
Found at i:38506184 original size:24 final size:24
Alignment explanation
Indices: 38506157--38506203 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38506147 ATAATGATCT
38506157 TGATCCCTACAAGTACCACCCTTC
1 TGATCCCTACAAGTACCACCCTTC
* *
38506181 TGATCTCTACGAGTACCACCCTT
1 TGATCCCTACAAGTACCACCCTT
38506204 TTTACTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (24 bp):
TGATCCCTACAAGTACCACCCTTC
Found at i:38507526 original size:11 final size:10
Alignment explanation
Indices: 38507506--38507554 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 10
38507496 CACTGCAATC
38507506 AAATTTATAA
1 AAATTTATAA
38507516 AAATATTATAA
1 AAAT-TTATAA
38507527 AAATTATATAA
1 AAATT-TATAA
38507538 AAAGTGTTAGTAA
1 AAA-T-TTA-TAA
38507551 AAAT
1 AAAT
38507555 ACTTTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.15
11 18 0.53
12 4 0.12
13 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (10 bp):
AAATTTATAA
Found at i:38510545 original size:2 final size:2
Alignment explanation
Indices: 38510538--38510576 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
38510528 TCACTTGTTA
38510538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38510577 GTTCACCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38510887 original size:22 final size:21
Alignment explanation
Indices: 38510848--38510888 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
38510838 CAATATAATC
* *
38510848 AAATTTATTAAAATTATATAA
1 AAATTTAATAAAAATATATAA
38510869 AAATGTTAATAAAAATATAT
1 AAAT-TTAATAAAAATATAT
38510889 TTTATAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTAATAAAAATATATAA
Found at i:38513104 original size:46 final size:48
Alignment explanation
Indices: 38513021--38513117 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 48
38513011 GAAGTGATGA
*
38513021 TTGTTTTGTTGATTCCTTCCCCTAAAATCGTCCCATTTTGTTTTTCTTGCC
1 TTGTTTTGTTGATTCCTT-CCC--AAATCATCCCATTTTGTTTTTCTTGCC
38513072 TTGTTTTGTTGATTCCTT-CC-AATCATCCCATTTTGTTTTTCTTGCC
1 TTGTTTTGTTGATTCCTTCCCAAATCATCCCATTTTGTTTTTCTTGCC
38513118 ATGAGTCTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
46 25 0.56
49 2 0.04
51 18 0.40
ACGTcount: A:0.11, C:0.25, G:0.11, T:0.53
Consensus pattern (48 bp):
TTGTTTTGTTGATTCCTTCCCAAATCATCCCATTTTGTTTTTCTTGCC
Found at i:38527795 original size:93 final size:94
Alignment explanation
Indices: 38527657--38527842 Score: 302
Period size: 93 Copynumber: 2.0 Consensus size: 94
38527647 GGTGATACAA
** *
38527657 TAGTAAGAAAAAAACATTGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAGGTTTGA
1 TAGTAAGAAAAAAACAAGGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTGA
38527722 TCCACTTACAATTCTACCAAATTTTTTGT
66 TCCACTTACAATTCTACCAAATTTTTTGT
* * *
38527751 TAGTATGAACAAAACAAGGGGTGGTACA-CAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTGA
1 TAGTAAGAAAAAAACAAGGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTGA
*
38527815 TCCACTTATAATTCTACCAAATTTTTTG
66 TCCACTTACAATTCTACCAAATTTTTTG
38527843 GTAACCTGTT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 62 0.73
94 23 0.27
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (94 bp):
TAGTAAGAAAAAAACAAGGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTGA
TCCACTTACAATTCTACCAAATTTTTTGT
Found at i:38530780 original size:50 final size:50
Alignment explanation
Indices: 38530647--38530790 Score: 130
Period size: 50 Copynumber: 2.9 Consensus size: 50
38530637 GAGCCGAAGC
* * * * * *
38530647 CCAAGCTCCCTTTTTGCAGGCAAATTGGCCCAAGATCCTTTACTCCCAGAGT
1 CCAAGATCCC-TTTTGCATGAAAATTAGCCCAAGATCCTTAAC-CCCAAAGT
* * * **
38530699 CTAAAATCCTTTTTTGCAT-AAAGCTAG-CCAAGATCCTTAACCCCAAAGT
1 CCAAGATCC-CTTTTGCATGAAAATTAGCCCAAGATCCTTAACCCCAAAGT
* *
38530748 CCAAGGTCCCTTTTGCATGAAAATTAGCCCAAGATTCTTAACC
1 CCAAGATCCCTTTTGCATGAAAATTAGCCCAAGATCCTTAACC
38530791 ATTTTTTTGG
Statistics
Matches: 71, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
48 8 0.11
49 19 0.27
50 27 0.38
51 4 0.06
52 13 0.18
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (50 bp):
CCAAGATCCCTTTTGCATGAAAATTAGCCCAAGATCCTTAACCCCAAAGT
Found at i:38534013 original size:18 final size:18
Alignment explanation
Indices: 38533990--38534042 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
38533980 CTAGTTTTTT
38533990 TATATATTTATATATATA
1 TATATATTTATATATATA
* *
38534008 TATATATTAATATATCTA
1 TATATATTTATATATATA
*
38534026 -ATAT-TTTTTATATATA
1 TATATATTTATATATATA
38534042 T
1 T
38534043 TAAGAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 9 0.31
17 4 0.14
18 16 0.55
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATATTTATATATATA
Found at i:38534320 original size:20 final size:20
Alignment explanation
Indices: 38534295--38534336 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38534285 ATATTTCGTG
*
38534295 ATATAAAA-TGTTATGAATAT
1 ATATAAAACTG-TATAAATAT
38534315 ATATAAAACTGTATAAATAT
1 ATATAAAACTGTATAAATAT
38534335 AT
1 AT
38534337 TATATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (20 bp):
ATATAAAACTGTATAAATAT
Found at i:38534709 original size:2 final size:2
Alignment explanation
Indices: 38534702--38534752 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
38534692 TAATTTTATC
* *
38534702 TA TA TA TA TA TA -A TA AA GTCA TC TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA
38534744 TA TA TA TA T
1 TA TA TA TA T
38534753 TTAATTTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 1 0.02
4 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38546487 original size:24 final size:23
Alignment explanation
Indices: 38546453--38546514 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
38546443 TTTATTTTTT
* * *
38546453 ATTTTGATATTAAAAAGAATTGA
1 ATTTTAATATTAAAAAAAATTAA
38546476 ATATTTAATATTATAAAAAAATTAA
1 AT-TTTAATATTA-AAAAAAATTAA
38546501 ATTTTAATA-TAAAA
1 ATTTTAATATTAAAA
38546515 TACACCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 3 0.09
23 4 0.12
24 16 0.47
25 11 0.32
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
ATTTTAATATTAAAAAAAATTAA
Found at i:38553812 original size:21 final size:21
Alignment explanation
Indices: 38553786--38553826 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
38553776 TTTTTTTTCA
38553786 ATTTATAT-TATTATTATTTAT
1 ATTTATATCTATT-TTATTTAT
38553807 ATTTATATCTATTTTATTTA
1 ATTTATATCTATTTTATTTA
38553827 CTCATATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTATATCTATTTTATTTAT
Found at i:38558279 original size:26 final size:26
Alignment explanation
Indices: 38558250--38558302 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
38558240 AATGATGGCC
38558250 CACACCGCAGTCAAATGCATAATCTG
1 CACACCGCAGTCAAATGCATAATCTG
38558276 CACACCGCAGTCAAATGCATAATCTG
1 CACACCGCAGTCAAATGCATAATCTG
38558302 C
1 C
38558303 CGATGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.19
Consensus pattern (26 bp):
CACACCGCAGTCAAATGCATAATCTG
Found at i:38590384 original size:13 final size:13
Alignment explanation
Indices: 38590366--38590394 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38590356 TCTCAAACCC
38590366 CTTTCATTTGTTG
1 CTTTCATTTGTTG
38590379 CTTTCATTTGTTG
1 CTTTCATTTGTTG
38590392 CTT
1 CTT
38590395 ATGTCTTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.14, T:0.62
Consensus pattern (13 bp):
CTTTCATTTGTTG
Found at i:38608118 original size:25 final size:25
Alignment explanation
Indices: 38608087--38608145 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
38608077 CTTGCACACT
38608087 CTTCCTCAATAACCTCTCAAAAACA
1 CTTCCTCAATAACCTCTCAAAAACA
38608112 CTTCCTCAATAACCTCTCAAAAACA
1 CTTCCTCAATAACCTCTCAAAAACA
*
38608137 CTTACTCAA
1 CTTCCTCAA
38608146 ACCACTCTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (25 bp):
CTTCCTCAATAACCTCTCAAAAACA
Found at i:38608146 original size:14 final size:13
Alignment explanation
Indices: 38608101--38608146 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
38608091 CTCAATAACC
38608101 TCTCAAAAACACT
1 TCTCAAAAACACT
*
38608114 TCCTCAATAAC-C-
1 T-CTCAAAAACACT
38608126 TCTCAAAAACACT
1 TCTCAAAAACACT
38608139 TACTCAAA
1 T-CTCAAA
38608147 CCACTCTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 3 0.11
14 14 0.52
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (13 bp):
TCTCAAAAACACT
Found at i:38615333 original size:36 final size:36
Alignment explanation
Indices: 38615286--38615361 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
38615276 CCTCTCAGGT
38615286 AACTGTTGTGCACATGACCTGCACCCCACCATAAAA
1 AACTGTTGTGCACATGACCTGCACCCCACCATAAAA
38615322 AACTGTTGTGCACATGACCTGCACCCCACCATAAAA
1 AACTGTTGTGCACATGACCTGCACCCCACCATAAAA
38615358 AACT
1 AACT
38615362 CATAATTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.34, C:0.33, G:0.13, T:0.20
Consensus pattern (36 bp):
AACTGTTGTGCACATGACCTGCACCCCACCATAAAA
Found at i:38616845 original size:58 final size:56
Alignment explanation
Indices: 38616777--38616890 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 56
38616767 AAATTAAACA
38616777 CAATTAAAATGTTGAGAGACTAAATTGAAGAAAATATTTAAAAAAATATAAATATTT
1 CAATTAAAATGTTGAGAGACTAAATTGAAGAAAATATTT-AAAAAATATAAATATTT
38616834 NCAATTAAAATGTTGAGAGACTAAATTGAAGAAAATATTTAAAAAATATAAATATTT
1 -CAATTAAAATGTTGAGAGACTAAATTGAAGAAAATATTTAAAAAATATAAATATTT
38616891 AAGTAGATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 17 0.30
58 39 0.70
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (56 bp):
CAATTAAAATGTTGAGAGACTAAATTGAAGAAAATATTTAAAAAATATAAATATTT
Found at i:38617555 original size:31 final size:32
Alignment explanation
Indices: 38617508--38617594 Score: 110
Period size: 31 Copynumber: 2.8 Consensus size: 32
38617498 TATTTTTCAA
*
38617508 ATATTTTTTTTCAATTTAGTCTCTCAGTA-TAT
1 ATATTTTTGTTCAATTTAGTCTCT-AGTATTAT
*
38617540 CA-A-TTTTGTTCAATTTAGT-TCTTGTATTAT
1 -ATATTTTTGTTCAATTTAGTCTCTAGTATTAT
38617570 ATATTTTTGTTCAATTTAGTCTCTA
1 ATATTTTTGTTCAATTTAGTCTCTA
38617595 TGATATGACA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
29 4 0.09
30 7 0.15
31 31 0.66
32 4 0.09
33 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.56
Consensus pattern (32 bp):
ATATTTTTGTTCAATTTAGTCTCTAGTATTAT
Found at i:38628855 original size:32 final size:32
Alignment explanation
Indices: 38628819--38628879 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
38628809 ATTGCAAAAA
* *
38628819 AAAAATAGAGTGAAA-ATAAAATAATTATTCGT
1 AAAAATAGAATAAAAGAT-AAATAATTATTCGT
38628851 AAAAATAGAATAAAAGATAAATAATTATT
1 AAAAATAGAATAAAAGATAAATAATTATT
38628880 ATGTAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.28
Consensus pattern (32 bp):
AAAAATAGAATAAAAGATAAATAATTATTCGT
Found at i:38629085 original size:15 final size:14
Alignment explanation
Indices: 38629064--38629130 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
38629054 TTCTTTATTT
*
38629064 TTAAAATATTAAAA
1 TTAAAATTTTAAAA
*
38629078 TATAAAATTTTATAA
1 T-TAAAATTTTAAAA
38629093 TTAAAATTTT--AA
1 TTAAAATTTTAAAA
* * *
38629105 TTTAATTTTTAAAT
1 TTAAAATTTTAAAA
38629119 TTAAAATTTTAA
1 TTAAAATTTTAA
38629131 CTTTCACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
12 10 0.23
14 21 0.49
15 12 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAAATTTTAAAA
Found at i:38635630 original size:15 final size:15
Alignment explanation
Indices: 38635612--38635672 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
38635602 ATTTTTATTT
38635612 TTTAAATATTAATAA
1 TTTAAATATTAATAA
*
38635627 TTT--ATA--ATTAA
1 TTTAAATATTAATAA
*
38635638 TTAAAATATTAATAA
1 TTTAAATATTAATAA
* *
38635653 TTTAAATATCAATAT
1 TTTAAATATTAATAA
38635668 TTTAA
1 TTTAA
38635673 TACAATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 6 0.17
13 6 0.17
15 24 0.67
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:38635682 original size:25 final size:25
Alignment explanation
Indices: 38635651--38635698 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
38635641 AAATATTAAT
38635651 AATTTAAATATCAATATTTTAATAC
1 AATTTAAATATCAATATTTTAATAC
* *
38635676 AATTTAATTATTAATATTTTAAT
1 AATTTAAATATCAATATTTTAAT
38635699 TAATAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTAAATATCAATATTTTAATAC
Found at i:38635697 original size:40 final size:41
Alignment explanation
Indices: 38635611--38635697 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
38635601 TATTTTTATT
* *
38635611 TTTTAAATATTAATAATTTATAATTAATTAAAATATTAATA
1 TTTTAAATATCAATAATTTATAATCAATTAAAATATTAATA
* * *
38635652 ATTTAAATATCAAT-ATTT-TAATACAATTTAATTATTAATA
1 TTTTAAATATCAATAATTTATAAT-CAATTAAAATATTAATA
38635692 TTTTAA
1 TTTTAA
38635698 TTAATAATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
39 4 0.10
40 23 0.59
41 12 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (41 bp):
TTTTAAATATCAATAATTTATAATCAATTAAAATATTAATA
Found at i:38635698 original size:15 final size:16
Alignment explanation
Indices: 38635678--38635711 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
38635668 TTTAATACAA
*
38635678 TTTAATTATTAAT-AT
1 TTTAATTAATAATCAT
38635693 TTTAATTAATAATCAT
1 TTTAATTAATAATCAT
38635709 TTT
1 TTT
38635712 TCATGACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAATTAATAATCAT
Found at i:38635760 original size:23 final size:22
Alignment explanation
Indices: 38635728--38635772 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
38635718 CTAATTTCAA
* *
38635728 TAATAGATAAAATATTAATAATT
1 TAATAAATAAAACATTAA-AATT
38635751 TAATAAATAAAACATTAAAATT
1 TAATAAATAAAACATTAAAATT
38635773 AAAATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATAAATAAAACATTAAAATT
Found at i:38635829 original size:26 final size:24
Alignment explanation
Indices: 38635776--38635850 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 24
38635766 TAAAATTAAA
38635776 ATATTAATATTTAAT-ATTTTAATC
1 ATATTAATA-TTAATAATTTTAATC
*
38635800 ATATTAATATTAATAATGTTTCAATT
1 ATATTAATATTAATAAT-TTT-AATC
*
38635826 ATATATAAAATATTAATATTTTTAA
1 ATAT-T--AATATTAATAATTTTAA
38635851 ATTTACAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
23 5 0.12
24 11 0.26
25 3 0.07
26 7 0.16
27 3 0.07
28 3 0.07
29 11 0.26
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (24 bp):
ATATTAATATTAATAATTTTAATC
Found at i:38635885 original size:11 final size:10
Alignment explanation
Indices: 38635863--38635905 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
38635853 TTACAAATAA
38635863 TTTATTCTTT
1 TTTATTCTTT
38635873 TTTATTCTATT
1 TTTATTCT-TT
**
38635884 TTTACCCTTT
1 TTTATTCTTT
*
38635894 TTTTTTCTTT
1 TTTATTCTTT
38635904 TT
1 TT
38635906 CATGGCCAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTCTTT
Found at i:38636356 original size:21 final size:20
Alignment explanation
Indices: 38636313--38636358 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
38636303 TCCCGCGACG
*
38636313 AGATCTGGCCTTTGAGTGCC
1 AGATCTGGCCTTTGAGCGCC
38636333 AGATCTGGCCATTATG-GCGCC
1 AGATCTGGCC-TT-TGAGCGCC
38636354 AGATC
1 AGATC
38636359 GACGCTTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 11 0.48
22 2 0.09
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (20 bp):
AGATCTGGCCTTTGAGCGCC
Found at i:38646823 original size:2 final size:2
Alignment explanation
Indices: 38646816--38646840 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38646806 ATAATTGACT
38646816 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38646841 TTGGCCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38648507 original size:30 final size:30
Alignment explanation
Indices: 38648466--38648525 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
38648456 GTGACTGTAA
38648466 CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
1 CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
*
38648496 CCTGTTGCTCCACTCTCTCTTCTTCTTTGT
1 CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
38648526 GTTCATCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.03, C:0.38, G:0.10, T:0.48
Consensus pattern (30 bp):
CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
Found at i:38648537 original size:30 final size:30
Alignment explanation
Indices: 38648473--38648537 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
38648463 TAACCTGCTG
** *
38648473 CTCCACTCTCTCTTCTTCTTTGTCCTGTTG
1 CTCCACTCTCTCTTCTTCTTTGTCCTCATC
**
38648503 CTCCACTCTCTCTTCTTCTTTGTGTTCATC
1 CTCCACTCTCTCTTCTTCTTTGTCCTCATC
38648533 CTCCA
1 CTCCA
38648538 ACATTTCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.06, C:0.38, G:0.08, T:0.48
Consensus pattern (30 bp):
CTCCACTCTCTCTTCTTCTTTGTCCTCATC
Found at i:38648565 original size:45 final size:45
Alignment explanation
Indices: 38648500--38648589 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
38648490 CTTTGTCCTG
* *
38648500 TTGCTCCACTCTCTCTTCTTCTTTGTGTTCATCCTCCAACATTTC
1 TTGCTCCACTCTCTCCTCTTCTTTGTCTTCATCCTCCAACATTTC
* * *
38648545 TTGCTTCACTTTCTCCTCTTCTTTGTCTTCATCCTCCAGCATTTC
1 TTGCTCCACTCTCTCCTCTTCTTTGTCTTCATCCTCCAACATTTC
38648590 CTTGAACATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.10, C:0.36, G:0.07, T:0.48
Consensus pattern (45 bp):
TTGCTCCACTCTCTCCTCTTCTTTGTCTTCATCCTCCAACATTTC
Found at i:38652319 original size:25 final size:26
Alignment explanation
Indices: 38652276--38652329 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
38652266 CGACTTAACT
* *
38652276 AAAATTTCTATTACTTTTATTTTTAA
1 AAAATTTCTATTACGTTTATTTTGAA
*
38652302 AAAATTTTTATTA-GTTTATTTTGAA
1 AAAATTTCTATTACGTTTATTTTGAA
38652327 AAA
1 AAA
38652330 TTATTGGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (26 bp):
AAAATTTCTATTACGTTTATTTTGAA
Found at i:38656730 original size:32 final size:33
Alignment explanation
Indices: 38656677--38656745 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 33
38656667 AATGTCATAT
*
38656677 TTTTTATTATAATATTATATATT-T-TATTTTCA
1 TTTTTAATATAATATTATATATTATATATTTT-A
*
38656709 TTTTTAATATAAT-TTCTTATATTATATATTTTA
1 TTTTTAATATAATATT-ATATATTATATATTTTA
38656742 TTTT
1 TTTT
38656746 ATTTTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 2 0.06
32 18 0.56
33 6 0.19
34 6 0.19
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
TTTTTAATATAATATTATATATTATATATTTTA
Found at i:38661524 original size:14 final size:14
Alignment explanation
Indices: 38661490--38661518 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38661480 CTAAAATTAT
38661490 AACTTATGAAAAAG
1 AACTTATGAAAAAG
38661504 AACTTAT-AAAAAG
1 AACTTATGAAAAAG
38661517 AA
1 AA
38661519 ATTTATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (14 bp):
AACTTATGAAAAAG
Found at i:38669146 original size:12 final size:12
Alignment explanation
Indices: 38669129--38669162 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
38669119 AGCCTGGAGT
38669129 TGCTGCTCCAGC
1 TGCTGCTCCAGC
38669141 TGCTGCTCCAGC
1 TGCTGCTCCAGC
38669153 TGCTGCTCCA
1 TGCTGCTCCA
38669163 ACGGCCGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.09, C:0.41, G:0.24, T:0.26
Consensus pattern (12 bp):
TGCTGCTCCAGC
Found at i:38669356 original size:42 final size:39
Alignment explanation
Indices: 38669259--38669361 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 39
38669249 CAAGCCGACA
* *
38669259 CCCTC-AGAATCTGATCGATGGACTGGTGGCAGCAGGGC
1 CCCTCAAGATTCTGATCGATGGACTAGTGGCAGCAGGGC
* *
38669297 CCCTCAACCGCTATCTGATCGCTGGACTAGTGGCAGCAGGGCCC
1 CCCTCAA--GAT-TCTGATCGATGGACTAGTGGCAGCAGGG--C
38669341 CACCTCAAGATTCTGATCGAT
1 C-CCTCAAGATTCTGATCGAT
38669362 TGGGTGGCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
38 5 0.10
39 1 0.02
41 1 0.02
42 35 0.67
43 2 0.04
44 2 0.04
45 6 0.12
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.20
Consensus pattern (39 bp):
CCCTCAAGATTCTGATCGATGGACTAGTGGCAGCAGGGC
Found at i:38678432 original size:2 final size:2
Alignment explanation
Indices: 38678427--38678453 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38678417 GAGAGCAAGC
38678427 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
38678454 GGTGGGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38688343 original size:22 final size:22
Alignment explanation
Indices: 38688313--38688386 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
38688303 TTTTAAAAGA
*
38688313 TTTC-CTCTCACTTTCTCTCAG
1 TTTCTCTCTCTCTTTCTCTCAG
** **
38688334 TTTCTCTCTCTCTCCCTCTCTC
1 TTTCTCTCTCTCTTTCTCTCAG
* * *
38688356 TTTCTCTCTGTTTTTCTCACAG
1 TTTCTCTCTCTCTTTCTCTCAG
38688378 TTTCTCTCT
1 TTTCTCTCT
38688387 AATATTGAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.05, C:0.38, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTCTCTCTCTCTTTCTCTCAG
Found at i:38697077 original size:2 final size:2
Alignment explanation
Indices: 38697070--38697097 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38697060 TTGTTTTTGC
38697070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38697098 CATGAATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38707997 original size:61 final size:61
Alignment explanation
Indices: 38707922--38708038 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
38707912 GTTGATTGAA
*
38707922 GGGATAATGTTGAAATAATTTCTAAGATTTCTATCATTTTGTAAATATGTATATATCATAT
1 GGGATAATGTTGAAATAATTTCTAAGATTTATATCATTTTGTAAATATGTATATATCATAT
* * * *
38707983 GGGATAATGTTGAAATAATTTGTAATATTTATATTATTTTGTAAATATGTTTATAT
1 GGGATAATGTTGAAATAATTTCTAAGATTTATATCATTTTGTAAATATGTATATAT
38708039 TATGTAATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (61 bp):
GGGATAATGTTGAAATAATTTCTAAGATTTATATCATTTTGTAAATATGTATATATCATAT
Found at i:38708025 original size:19 final size:21
Alignment explanation
Indices: 38708001--38708041 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
38707991 GTTGAAATAA
38708001 TTTGT-AATA-TTTATATTAT
1 TTTGTAAATAGTTTATATTAT
38708020 TTTGTAAATATGTTTATATTAT
1 TTTGTAAATA-GTTTATATTAT
38708042 GTAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
22 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
TTTGTAAATAGTTTATATTAT
Found at i:38708059 original size:19 final size:19
Alignment explanation
Indices: 38707998--38708062 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
38707988 AATGTTGAAA
*
38707998 TAATT-TGTAATATTTATAT
1 TAATTATGTAATATATA-AT
* **
38708017 T-ATTTTGTAA-ATATGTT
1 TAATTATGTAATATATAAT
38708034 TATATTATGTAATATATAAT
1 TA-ATTATGTAATATATAAT
38708054 TAATTATGT
1 TAATTATGT
38708063 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 2 0.06
18 6 0.17
19 21 0.58
20 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
TAATTATGTAATATATAAT
Found at i:38710993 original size:31 final size:31
Alignment explanation
Indices: 38710955--38711018 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
38710945 TAGGATCTTG
38710955 AAGCTCAATTGTGTTGGACATCAAGCTCCAA
1 AAGCTCAATTGTGTTGGACATCAAGCTCCAA
38710986 AAGCTCAATTGTGTTGGACATCAAGCTCCAA
1 AAGCTCAATTGTGTTGGACATCAAGCTCCAA
38711017 AA
1 AA
38711019 TGTGCCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
AAGCTCAATTGTGTTGGACATCAAGCTCCAA
Found at i:38712617 original size:123 final size:123
Alignment explanation
Indices: 38712398--38712643 Score: 474
Period size: 123 Copynumber: 2.0 Consensus size: 123
38712388 CAACGAAAGC
*
38712398 AATTTTCCATTTCCTTCTTACAACATCCTTTTACAGGTTTACCCCTATGGTTGGAATCCTCCTTC
1 AATTTTCCATTTCCTTCTTACAACATCCTTTTACAGGTTTACCCCTATGGTTGGAATCATCCTTC
38712463 CTCCTCTTATTTCAGAATCTATCAACCCTTCTCACTTGTTTTTGATTATCATGGAGAT
66 CTCCTCTTATTTCAGAATCTATCAACCCTTCTCACTTGTTTTTGATTATCATGGAGAT
38712521 AATTTTCCATTTCCTTCTTACAACATCCTTTTACAGGTTTACCCCTATGGTTGGAATCATCCTTC
1 AATTTTCCATTTCCTTCTTACAACATCCTTTTACAGGTTTACCCCTATGGTTGGAATCATCCTTC
*
38712586 CTCCTTTTATTTCAGAATCTATCAACCCTTCTCACTTGTTTTTGATTATCATGGAGAT
66 CTCCTCTTATTTCAGAATCTATCAACCCTTCTCACTTGTTTTTGATTATCATGGAGAT
38712644 TTGAATGGAA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.43
Consensus pattern (123 bp):
AATTTTCCATTTCCTTCTTACAACATCCTTTTACAGGTTTACCCCTATGGTTGGAATCATCCTTC
CTCCTCTTATTTCAGAATCTATCAACCCTTCTCACTTGTTTTTGATTATCATGGAGAT
Found at i:38716245 original size:23 final size:24
Alignment explanation
Indices: 38716210--38716260 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38716200 AATTCGGTCG
*
38716210 ATTTCATTTATTT-ATTTATAAAA
1 ATTTCATTAATTTAATTTATAAAA
* *
38716233 ATTTGATTAATTTAATTTTTAAAA
1 ATTTCATTAATTTAATTTATAAAA
38716257 ATTT
1 ATTT
38716261 AATAATCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTCATTAATTTAATTTATAAAA
Found at i:38716266 original size:23 final size:23
Alignment explanation
Indices: 38716219--38716266 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
38716209 GATTTCATTT
*
38716219 ATTTATTTATAAAAATTTGATTA
1 ATTTATTTATAAAAATTTGAATA
*
38716242 ATTTAATTTTTAAAAATTT-AATA
1 ATTT-ATTTATAAAAATTTGAATA
38716265 AT
1 AT
38716267 CGAACGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTATTTATAAAAATTTGAATA
Found at i:38717982 original size:21 final size:21
Alignment explanation
Indices: 38717958--38717999 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38717948 CGTTTGTACA
* *
38717958 TATAACGTGTAAAAACTTAAT
1 TATAACATGTAAAAACCTAAT
*
38717979 TATAACATGTAACAACCTAAT
1 TATAACATGTAAAAACCTAAT
38718000 CATGATGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (21 bp):
TATAACATGTAAAAACCTAAT
Found at i:38720877 original size:20 final size:20
Alignment explanation
Indices: 38720852--38720892 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
38720842 ATAACCTTTC
38720852 TTTATAATTTTAATTATTTT
1 TTTATAATTTTAATTATTTT
38720872 TTTATAATTTTAATTATTTT
1 TTTATAATTTTAATTATTTT
38720892 T
1 T
38720893 AATCAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATAATTTTAATTATTTT
Found at i:38721072 original size:24 final size:24
Alignment explanation
Indices: 38721045--38721108 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
38721035 CACCATATAT
38721045 AAAAACATGTGACACGTCATGTAC
1 AAAAACATGTGACACGTCATGTAC
* * *
38721069 AAAAACATATGATACGTCATGTAT
1 AAAAACATGTGACACGTCATGTAC
38721093 AAAAACATGTGACACG
1 AAAAACATGTGACACG
38721109 CTATGATTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (24 bp):
AAAAACATGTGACACGTCATGTAC
Found at i:38721198 original size:28 final size:28
Alignment explanation
Indices: 38721167--38721238 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
38721157 TATATTGAAA
38721167 AAAAATATTATTGTTACACGTCATAT-TC
1 AAAAATATTATTGTTACACGTCA-ATGTC
* * *
38721195 AAAAACATT-TTGTTACACTTTAATGTC
1 AAAAATATTATTGTTACACGTCAATGTC
* *
38721222 TAAAATGTTATTGTTAC
1 AAAAATATTATTGTTAC
38721239 TTACGAACCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 2 0.06
27 19 0.53
28 15 0.42
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (28 bp):
AAAAATATTATTGTTACACGTCAATGTC
Found at i:38735572 original size:2 final size:2
Alignment explanation
Indices: 38735565--38735651 Score: 90
Period size: 2 Copynumber: 44.5 Consensus size: 2
38735555 ATAAAGAACA
* **
38735565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT GN
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
38735606 AT AA AG AT AC A- AT AT AT AT AT AT ACT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
38735647 AT AT A
1 AT AT A
38735652 ATTTGGTGAA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
1 3 0.04
2 67 0.93
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38735636 original size:11 final size:10
Alignment explanation
Indices: 38735617--38735651 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 10
38735607 TAAAGATACA
38735617 ATATATATAT
1 ATATATATAT
38735627 ATACTATATAT
1 ATA-TATATAT
38735638 ATATAT-TAT
1 ATATATATAT
38735647 ATATA
1 ATATA
38735652 ATTTGGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 6 0.25
11 10 0.42
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATATATAT
Found at i:38739261 original size:2 final size:2
Alignment explanation
Indices: 38739254--38739294 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38739244 CCGCGTCTTC
38739254 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
38739295 CGCCTTCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:38745651 original size:17 final size:18
Alignment explanation
Indices: 38745615--38745648 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38745605 AACGGCATTA
38745615 AAAAAATAGAATAAATCC
1 AAAAAATAGAATAAATCC
38745633 AAAAAAT-GAA-AAATCC
1 AAAAAATAGAATAAATCC
38745649 CAAGCTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.68, C:0.12, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAAAATAGAATAAATCC
Found at i:38747301 original size:18 final size:18
Alignment explanation
Indices: 38747267--38747301 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38747257 AATTTTTTAA
*
38747267 TAAAATTATTAAAATATC
1 TAAAATTATGAAAATATC
*
38747285 TAAAATTATGAACATAT
1 TAAAATTATGAAAATAT
38747302 AAATTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (18 bp):
TAAAATTATGAAAATATC
Found at i:38747748 original size:14 final size:14
Alignment explanation
Indices: 38747729--38747771 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
38747719 GAAAATAAAT
38747729 TTATTTTTAAATTA
1 TTATTTTTAAATTA
38747743 TTA-TTTTAAATATA
1 TTATTTTTAAAT-TA
*
38747757 TATATTTTTAGATTA
1 T-TATTTTTAAATTA
38747772 ATAAGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.32
14 6 0.24
15 4 0.16
16 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATTTTTAAATTA
Found at i:38749080 original size:22 final size:22
Alignment explanation
Indices: 38749055--38749096 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38749045 GCCCATTTAT
38749055 TTGGGGCACAAAGCCCGTTTGG
1 TTGGGGCACAAAGCCCGTTTGG
* *
38749077 TTGGGTCATAAAGCCCGTTT
1 TTGGGGCACAAAGCCCGTTT
38749097 CTTCTCCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (22 bp):
TTGGGGCACAAAGCCCGTTTGG
Found at i:38750847 original size:209 final size:206
Alignment explanation
Indices: 38750459--38750878 Score: 506
Period size: 209 Copynumber: 2.0 Consensus size: 206
38750449 TTTGATGATT
* * *
38750459 AAGATTTGGTTTCAACATTAAGAAGTAAAAGTGAATGAATAGGGGACTTAATATGCTGCCTTTAG
1 AAGATTTGGTTTCAACATTAAGAAGCAAAAGTGAATGAAAAGGGGACATAATATGCTGCCTTTAG
** * * * *
38750524 CTTCTCTTAAGTAAAGAAAATAATCATCTTCTTTGTGGATGGATTTAACTTAATGATTGTGCCAT
66 CTTCTCTTAAGTAAAGAAAATAATCATCTTCTTTGTCAATGCACTTAACCTAATGATTGTGCCAG
* *
38750589 GAGATTTTAAAAGGCTTAATAAAGTGCAAGGAGCTTGATAACAATGGAGTTAAACTTACTGTTTC
131 GAGATTTTAAAAGGCTTAATAAAATGCAAGGAGCTTGATAACAATGGAGTTAAACTTACTGTTCC
38750654 TTTAGATGACA
196 TTTAGATGACA
* *
38750665 AAGATTTGGTTTCAACATTAAGAAAGCACAAGTGAATGATTAAAGGGCTGA-ATAATATGCTGGC
1 AAGATTTGGTTTCAACATTAAG-AAGCAAAAGTGAATGA--AAAGGG--GACATAATATGCTGCC
* * * * * * *
38750729 TTTAGTTTCTCTTACA-TATAGAAACTGATCATCTTGTTTGTCAATGCACTT-GCCTAATGGTTG
61 TTTAGCTTCTCTTA-AGTAAAGAAAATAATCATCTTCTTTGTCAATGCACTTAACCTAATGATTG
* * ** * * *
38750792 TTCCAGGTGATTTTTGAAGGCTTAGA-AAAATGTAAGGAGCTTGATAACGATGGAGTTAAACTTG
125 TGCCAGGAGATTTTAAAAGGCTTA-ATAAAATGCAAGGAGCTTGATAACAATGGAGTTAAACTTA
38750856 CTGTTCCTTTAGATGACA
189 CTGTTCCTTTAGATGACA
38750874 AAGAT
1 AAGAT
38750879 CTAGAATATA
Statistics
Matches: 180, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
206 22 0.12
207 14 0.08
209 89 0.49
210 52 0.29
211 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (206 bp):
AAGATTTGGTTTCAACATTAAGAAGCAAAAGTGAATGAAAAGGGGACATAATATGCTGCCTTTAG
CTTCTCTTAAGTAAAGAAAATAATCATCTTCTTTGTCAATGCACTTAACCTAATGATTGTGCCAG
GAGATTTTAAAAGGCTTAATAAAATGCAAGGAGCTTGATAACAATGGAGTTAAACTTACTGTTCC
TTTAGATGACA
Found at i:38760922 original size:2 final size:2
Alignment explanation
Indices: 38760915--38760940 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38760905 GGTGGCCTCC
38760915 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
38760941 TTTCTTCTTT
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):
CT
Found at i:38765716 original size:210 final size:210
Alignment explanation
Indices: 38765354--38765740 Score: 618
Period size: 210 Copynumber: 1.8 Consensus size: 210
38765344 GGGGTACAGT
* * *
38765354 GGGGAGTTATGTAAGAACTTATTTCTTATGCTGGAAGTCTTCTTTTCCAGGATGAATGCCGGAGG
1 GGGGAGTTATGTAAGAACTTATTACTTATGCTGAAAGTCTTCTTTTCCAGGACGAATGCCGGAGG
38765419 CAAATGCTACTTGAACACTTTGGAGAGTCTTTCGACAGAAAAGACTGTAAACATGGTTCAAATCC
66 CAAATGCTACTTGAACACTTTGGAGAGTCTTTCGACAGAAAAGACTGTAAACATGGTTCAAATCC
*
38765484 TTGTGATAATTGTCTCAGGACTTCCTAATCAGCATA-GACATGTTTGTACACTTTGCAACTAAGC
131 TTGTGATAATTGTCTCAGGACTTCATAATCAGCATATG-CATGTTTGTACACTTTGCAACTAAGC
38765548 TTGGGGGTAGGGGGTG
195 TTGGGGGTAGGGGGTG
*
38765564 GGGGAGTTATGTAAGAACTTATTACTTATGCTGAAAGTCTTCTTTTCCAGGACGAATGCCGG-GT
1 GGGGAGTTATGTAAGAACTTATTACTTATGCTGAAAGTCTTCTTTTCCAGGACGAATGCCGGAGG
* * * *
38765628 CAAAT-CTTACTTGAACACTTTGGAGAGTCTTTTGACAGAAAAGGCCTGTAAATATTGTTCAAAT
66 CAAATGC-TACTTGAACACTTTGGAGAGTCTTTCGACAGAAAA-GACTGTAAACATGGTTCAAAT
* * *
38765692 CCTTGTGATAATTGTCTGAGGACTTCATAGTGAGCATATGCATGTTTGT
129 CCTTGTGATAATTGTCTCAGGACTTCATAATCAGCATATGCATGTTTGT
38765741 GTACATTGCA
Statistics
Matches: 162, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
208 1 0.01
209 40 0.25
210 120 0.74
211 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (210 bp):
GGGGAGTTATGTAAGAACTTATTACTTATGCTGAAAGTCTTCTTTTCCAGGACGAATGCCGGAGG
CAAATGCTACTTGAACACTTTGGAGAGTCTTTCGACAGAAAAGACTGTAAACATGGTTCAAATCC
TTGTGATAATTGTCTCAGGACTTCATAATCAGCATATGCATGTTTGTACACTTTGCAACTAAGCT
TGGGGGTAGGGGGTG
Found at i:38766464 original size:28 final size:28
Alignment explanation
Indices: 38766423--38766487 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
38766413 ATATTTAAAT
* *
38766423 TATAAAAAAAATTAAATTTAAATTTTAA
1 TATAAAATAAATTAAATTAAAATTTTAA
*
38766451 TATAAAATACATTAAATTAAAATTTTAA
1 TATAAAATAAATTAAATTAAAATTTTAA
38766479 TATAAAATA
1 TATAAAATA
38766488 TATAATTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TATAAAATAAATTAAATTAAAATTTTAA
Found at i:38789533 original size:18 final size:20
Alignment explanation
Indices: 38789498--38789540 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
38789488 CTAAAATATT
*
38789498 AAAAAAATTACCCTAAAAGA
1 AAAAAAATTACCCTAAAACA
38789518 AAAAAAATT-CCC-AAAACA
1 AAAAAAATTACCCTAAAACA
38789536 AAAAA
1 AAAAA
38789541 TTGAATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 3 0.14
20 9 0.41
ACGTcount: A:0.70, C:0.16, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAAAAATTACCCTAAAACA
Found at i:38821605 original size:2 final size:2
Alignment explanation
Indices: 38821598--38821643 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
38821588 ATGAACAAAC
38821598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38821640 AT AT
1 AT AT
38821644 TTAGATTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38825491 original size:3 final size:3
Alignment explanation
Indices: 38825485--38825514 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38825475 CGTTCTTCTA
38825485 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38825515 ATAGTGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38829058 original size:15 final size:15
Alignment explanation
Indices: 38829038--38829080 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
38829028 TGTTTTTCAT
*
38829038 TTTATATTCATTCTC
1 TTTATATTCATTATC
*
38829053 TTTATATTCTATTTATT
1 TTTATATTC-A-TTATC
38829070 TTTATATTCAT
1 TTTATATTCAT
38829081 ATATTGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATATTCATTATC
Found at i:38829497 original size:188 final size:186
Alignment explanation
Indices: 38829024--38829633 Score: 723
Period size: 190 Copynumber: 3.2 Consensus size: 186
38829014 TTTTTAGTCT
38829024 GGTATGTTTTTCATTTTATATTCATTCTCTTTATATTCTATTTATTTTTATATTCATATATTGAA
1 GGTATGTTTTTCATTTTATATTCATTCTCTTTATA---T-TTTATTTTTATATTCATATATTGAA
* * * * * *
38829089 TTTAATCTAAGAGAAGAAAGAGAAATAATTGCAAGGAAGCTTCTATTTACAAATTCAAATTAAGT
62 TTAAATCTAAGTGAAGAAAGAAAAATAATTG-AAAGAAGCTTCTATTTGCATATTC-AATTAA-T
* * * * *
38829154 CTTAGAGGATTT-AAGG-TGTTTTTAATTGCAAATT---CTATCGAAGAAAATCTCATTAATTC
124 TTTAGAGGATTTGGAGGCT-TTTCTAATTGCATATTCAACTATCGAAGAAAATCTCGTTAATTC
* * *
38829213 AGTGTGTTTTTCATTTTATATTCATTCTCTTTTTTATTCTTTTTATTTTTATATTCATATATTGA
1 GGTATGTTTTTCATTTTATATTCATTCTC---TTTA-T-ATTTTATTTTTATATTCATATATTGA
* * *
38829278 ATTAAATCTAAGTGAAGAAAGAAAAATAATTGTAAGAAGGCTTCCATCTGCATATTCAAGTTAAC
61 ATTAAATCTAAGTGAAGAAAGAAAAATAATTGAAAGAA-GCTTCTATTTGCATATTCAA-TTAA-
38829343 TTTTAGAGGATTTGGAGGCTTTTCTAATTGCATATTCAACTATCGAAGAAAATCTCGTTAA-TC
123 TTTTAGAGGATTTGGAGGCTTTTCTAATTGCATATTCAACTATCGAAGAAAATCTCGTTAATTC
38829406 TGGTATGTTTTTCATTTTATATTCATTCTCTTTATATTTT-TTTTTATATTCATATATTGAATTA
1 -GGTATGTTTTTCATTTTATATTCATTCTCTTTATATTTTATTTTTATATTCATATATTGAATTA
* *
38829470 AATCTAAGTGAAGAAAGAAAAATAATTGCAAAGAAGCTTCTATTTGCATTTTCATATGAATTCTT
65 AATCTAAGTGAAGAAAGAAAAATAATTG-AAAGAAGCTTCTATTTGCATATTCA-ATTAATT-TT
* * * * * *
38829535 AAAGGATTTGGAGGCGTTTCTAATTGCATATTCTACTATATCAAAGAATAA-CTTGTTGATTC
127 AGAGGATTTGGAGGCTTTTCTAATTGCATATTCAAC--TATCGAAGAA-AATCTCGTTAATTC
*
38829597 GGTATGTTTTTCATTTTATATTCATCCTCTTTATATT
1 GGTATGTTTTTCATTTTATATTCATTCTCTTTATATT
38829634 CTAATATTGA
Statistics
Matches: 368, Mismatches: 33, Indels: 39
0.84 0.08 0.09
Matches are distributed among these distances:
187 2 0.01
188 106 0.29
189 43 0.12
190 135 0.37
191 26 0.07
192 5 0.01
193 3 0.01
194 48 0.13
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (186 bp):
GGTATGTTTTTCATTTTATATTCATTCTCTTTATATTTTATTTTTATATTCATATATTGAATTAA
ATCTAAGTGAAGAAAGAAAAATAATTGAAAGAAGCTTCTATTTGCATATTCAATTAATTTTAGAG
GATTTGGAGGCTTTTCTAATTGCATATTCAACTATCGAAGAAAATCTCGTTAATTC
Found at i:38834874 original size:30 final size:30
Alignment explanation
Indices: 38834821--38834896 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
38834811 TTGTAGGTAC
* * * *
38834821 AAAATTATAAATTTTTTTTAAAAA-TAAAGAT
1 AAAATTATAAA-ATTTTTAAAAAAGCAAAG-G
38834852 AAAATTATAAAATTTTTAAAAAAGCAAAGG
1 AAAATTATAAAATTTTTAAAAAAGCAAAGG
38834882 AAAATTATAAAATTT
1 AAAATTATAAAATTT
38834897 AAAAACTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.62
31 15 0.38
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATTATAAAATTTTTAAAAAAGCAAAGG
Found at i:38837066 original size:2 final size:2
Alignment explanation
Indices: 38837059--38837122 Score: 96
Period size: 2 Copynumber: 32.5 Consensus size: 2
38837049 CTCGTTTGAA
*
38837059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38837099 NAT AT AT AT AT AT AT AT AT AT AT A
1 -AT AT AT AT AT AT AT AT AT AT AT A
38837123 ATTAAAAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.03
2 54 0.93
3 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38856773 original size:40 final size:40
Alignment explanation
Indices: 38856728--38856868 Score: 185
Period size: 40 Copynumber: 3.5 Consensus size: 40
38856718 TATTTTAAAC
*
38856728 ATAAACTTAAATAACTAAAAATAAATATCCATACAACAAT
1 ATAAACTTAAATAACTAAAAATAAATATCCAAACAACAAT
* * * *
38856768 ATAAACTTAAATAACTATACATAAATACCCAAATAACAAT
1 ATAAACTTAAATAACTAAAAATAAATATCCAAACAACAAT
* * * *
38856808 ATAAACTTAAATAACTAAACACAAATATCCAAACAAATAAC
1 ATAAACTTAAATAACTAAAAATAAATATCCAAAC-AACAAT
38856849 ATAAACTTAAATAAC-AAAAA
1 ATAAACTTAAATAACTAAAAA
38856869 NAGTAACTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 69 0.78
41 19 0.22
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (40 bp):
ATAAACTTAAATAACTAAAAATAAATATCCAAACAACAAT
Found at i:38856821 original size:18 final size:18
Alignment explanation
Indices: 38856762--38856822 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
38856752 ATATCCATAC
38856762 AACAATATAAACTTAAAT
1 AACAATATAAACTTAAAT
* **
38856780 AACTATACATAAATACCCAAAT
1 AAC-A-ATAT-AA-ACTTAAAT
38856802 AACAATATAAACTTAAAT
1 AACAATATAAACTTAAAT
38856820 AAC
1 AAC
38856823 TAAACACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
20 6 0.18
21 3 0.09
22 9 0.27
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (18 bp):
AACAATATAAACTTAAAT
Found at i:38856826 original size:14 final size:14
Alignment explanation
Indices: 38856769--38856863 Score: 56
Period size: 14 Copynumber: 7.0 Consensus size: 14
38856759 TACAACAATA
38856769 TAAACTTAAATAAC
1 TAAACTTAAATAAC
* * *
38856783 TATACATAAATACC
1 TAAACTTAAATAAC
* *
38856797 CAAA-TAACAAT-A-
1 TAAACTTA-AATAAC
38856809 TAAACTTAAATAAC
1 TAAACTTAAATAAC
** *
38856823 TAAACACAAATATC
1 TAAACTTAAATAAC
*
38856837 CAAAC--AAATAAC
1 TAAACTTAAATAAC
38856849 ATAAACTTAAATAAC
1 -TAAACTTAAATAAC
38856864 AAAAANAGTA
Statistics
Matches: 58, Mismatches: 16, Indels: 13
0.67 0.18 0.15
Matches are distributed among these distances:
12 12 0.21
13 8 0.14
14 31 0.53
15 7 0.12
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACTTAAATAAC
Found at i:38857013 original size:15 final size:15
Alignment explanation
Indices: 38856993--38857030 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
38856983 GGTATATATA
38856993 TTATAATTAATAATT-
1 TTATAATT-ATAATTG
38857008 TTATAAGTTATAATTG
1 TTATAA-TTATAATTG
38857024 TTATAAT
1 TTATAAT
38857031 GTTAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TTATAATTATAATTG
Found at i:38858042 original size:2 final size:2
Alignment explanation
Indices: 38858035--38858059 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38858025 TTTGATACAA
38858035 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38858060 AATTACAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38861280 original size:2 final size:2
Alignment explanation
Indices: 38861273--38861298 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38861263 AAATAAATAA
38861273 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38861299 GTGTGTGTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38862260 original size:2 final size:2
Alignment explanation
Indices: 38862253--38862277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38862243 ACATCCTACC
38862253 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
38862278 CACCATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:38865966 original size:11 final size:11
Alignment explanation
Indices: 38865950--38865974 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38865940 ATTTAATGCC
38865950 AAAAAAAGAAA
1 AAAAAAAGAAA
38865961 AAAAAAAGAAA
1 AAAAAAAGAAA
38865972 AAA
1 AAA
38865975 CAACATTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:38867289 original size:6 final size:6
Alignment explanation
Indices: 38867281--38867317 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
38867271 ATTAGAGAAA
*
38867281 CCAAAA CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG C
1 CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG C
38867318 AAACCCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.51, C:0.35, G:0.14, T:0.00
Consensus pattern (6 bp):
CCAAAG
Found at i:38867495 original size:2 final size:2
Alignment explanation
Indices: 38867478--38867515 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
38867468 ATAGAAAGAA
*
38867478 AG AG AA AG AG AG -G 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 AG AG A
38867516 ATGTTGGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38870578 original size:2 final size:2
Alignment explanation
Indices: 38870571--38870710 Score: 133
Period size: 2 Copynumber: 69.0 Consensus size: 2
38870561 TTGTCATGTG
38870571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
38870613 TA TA TNA TGG TT TA CT- TT TC TT TA TGA AA GTA CA TA -A TA T- TT
1 TA TA T-A T-A TA TA -TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA
*
38870655 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38870697 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
38870711 AATGAATAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
1 3 0.03
2 108 0.92
3 6 0.05
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38879143 original size:1 final size:1
Alignment explanation
Indices: 38879137--38879170 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
38879127 NNNNNACCAT
*
38879137 CCCCCCCCCCCCCCCCCCCGCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
38879171 AAAAAAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:38882269 original size:116 final size:116
Alignment explanation
Indices: 38882036--38882257 Score: 302
Period size: 116 Copynumber: 1.9 Consensus size: 116
38882026 TTACATCGAA
* * * * *
38882036 AAGAAACTCCCAACGAGAAGTAAGGGACAACGAGGAGTAAAAGAGGATGTCATGATCTTAGAGAG
1 AAGAAACTCCCAACGAAAAGTAAGGGACAACAAGAAGTAAAAGAGGATATCATGATCTTAAAGAG
* * *
38882101 AGGAGTCACGAATCCTACATCGGCTATGTAGTAGAGTGATACTGAAAATAT
66 AGGAATCACGAATCCTACATCGACTATGTACTAGAGTGATACTGAAAATAT
* * * *
38882152 AAGAAACTCCCAACGAAAAGTAAGGGACAGCAAGAAGTAAGAGATGATATCATGATTTTAAAGAG
1 AAGAAACTCCCAACGAAAAGTAAGGGACAACAAGAAGTAAAAGAGGATATCATGATCTTAAAGAG
* *
38882217 AGGAATCATGAAT-CTCACATCGATTATGTACTAGAGTGATA
66 AGGAATCACGAATCCT-ACATCGACTATGTACTAGAGTGATA
38882258 TTAGAAATAT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
115 2 0.02
116 89 0.98
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (116 bp):
AAGAAACTCCCAACGAAAAGTAAGGGACAACAAGAAGTAAAAGAGGATATCATGATCTTAAAGAG
AGGAATCACGAATCCTACATCGACTATGTACTAGAGTGATACTGAAAATAT
Found at i:38888659 original size:23 final size:23
Alignment explanation
Indices: 38888626--38888673 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
38888616 AATATGTTAA
*
38888626 TTCATATATCGTTATCATTTATT
1 TTCATACATCGTTATCATTTATT
38888649 TTCATACATCGTTATCATTTATT
1 TTCATACATCGTTATCATTTATT
38888672 TT
1 TT
38888674 ATCATAACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (23 bp):
TTCATACATCGTTATCATTTATT
Found at i:38896967 original size:2 final size:2
Alignment explanation
Indices: 38896960--38897021 Score: 108
Period size: 2 Copynumber: 31.0 Consensus size: 2
38896950 TCGAGTTCGG
38896960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T ANT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
38897002 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
38897022 TTTTTTAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38897417 original size:2 final size:2
Alignment explanation
Indices: 38897410--38897434 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38897400 AAGCAGGGTT
38897410 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38897435 GTTTTCTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38902887 original size:5 final size:5
Alignment explanation
Indices: 38902874--38902919 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
38902864 AGTACCTTTT
* * * *
38902874 TTTCT TTTCC TTTCC TTTCG TTTCC TTTCT TTTCC TTTCA TTTCC T
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC T
38902920 CCCCCCTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.65
Consensus pattern (5 bp):
TTTCC
Found at i:38902902 original size:20 final size:20
Alignment explanation
Indices: 38902874--38902919 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
38902864 AGTACCTTTT
* *
38902874 TTTCTTTTCCTTTCCTTTCG
1 TTTCCTTTCCTTTCCTTTCA
*
38902894 TTTCCTTTCTTTTCCTTTCA
1 TTTCCTTTCCTTTCCTTTCA
38902914 TTTCCT
1 TTTCCT
38902920 CCCCCCTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTCCTTTCCTTTCCTTTCA
Found at i:38909278 original size:17 final size:17
Alignment explanation
Indices: 38909253--38909292 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
38909243 CATTTTTCTG
38909253 TTTTTAAATTCT-TTTT
1 TTTTTAAATTCTCTTTT
38909269 TTTTTCAAATTCTCTTTT
1 TTTTT-AAATTCTCTTTT
38909287 TATTTT
1 T-TTTT
38909293 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 5 0.24
19 4 0.19
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTAAATTCTCTTTT
Found at i:38912104 original size:2 final size:2
Alignment explanation
Indices: 38912097--38912123 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38912087 ATCTTTTATT
38912097 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38912124 GCGGCGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38924541 original size:34 final size:34
Alignment explanation
Indices: 38924498--38924568 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
38924488 GATGTGTGTT
38924498 CTTATCAGAGTACATAACATCTTTATCATATGAC
1 CTTATCAGAGTACATAACATCTTTATCATATGAC
*
38924532 CTTATCAGAGTACATAACATCTTTATTATATGAC
1 CTTATCAGAGTACATAACATCTTTATCATATGAC
38924566 CTT
1 CTT
38924569 TATTATCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (34 bp):
CTTATCAGAGTACATAACATCTTTATCATATGAC
Found at i:38930827 original size:12 final size:12
Alignment explanation
Indices: 38930810--38930852 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
38930800 AAGTCGTCCA
38930810 CCTCTCCTCTCT
1 CCTCTCCTCTCT
38930822 CCTCTCCT-TCCT
1 CCTCTCCTCT-CT
*
38930834 CCTCTCACTCTCA
1 CCTCTC-CTCTCT
38930847 CCTCTC
1 CCTCTC
38930853 ACCTCCGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 1 0.04
12 16 0.59
13 9 0.33
14 1 0.04
ACGTcount: A:0.05, C:0.58, G:0.00, T:0.37
Consensus pattern (12 bp):
CCTCTCCTCTCT
Found at i:38934407 original size:13 final size:14
Alignment explanation
Indices: 38934382--38934410 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38934372 TTTTTTAATT
38934382 TTTAAAAATTAAAA
1 TTTAAAAATTAAAA
38934396 TTTAAAAA-TAAAA
1 TTTAAAAATTAAAA
38934409 TT
1 TT
38934411 CACATAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTAAAAATTAAAA
Found at i:38942881 original size:25 final size:25
Alignment explanation
Indices: 38942853--38942906 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
38942843 AGCCTAAAGG
38942853 AGAAAAACCCAAAAAACTAACAACT
1 AGAAAAACCCAAAAAACTAACAACT
38942878 AGAAAAACCCAAAAAACTAACAACT
1 AGAAAAACCCAAAAAACTAACAACT
38942903 AGAA
1 AGAA
38942907 CGCAAACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.65, C:0.22, G:0.06, T:0.07
Consensus pattern (25 bp):
AGAAAAACCCAAAAAACTAACAACT
Found at i:38955960 original size:15 final size:15
Alignment explanation
Indices: 38955896--38955960 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
38955886 GTAAAGTTTT
*
38955896 TATTTA-ATTTTTTC
1 TATTTATATTTATTC
*
38955910 TATTTATA-TTATTAT
1 TATTTATATTTATT-C
*
38955925 TATTTATATTTATTT
1 TATTTATATTTATTC
*
38955940 TTTTTA-ATTATATTC
1 TATTTATATT-TATTC
38955955 TATTTA
1 TATTTA
38955961 CTCATATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
14 13 0.31
15 24 0.57
16 5 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTATATTTATTC
Found at i:38968043 original size:38 final size:38
Alignment explanation
Indices: 38967992--38968068 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
38967982 TTGCATTTCT
38967992 ACATTGTGAGTGGGTATGGATTGCAATTAACACTGACA
1 ACATTGTGAGTGGGTATGGATTGCAATTAACACTGACA
38968030 ACATTGTGAGTGGGTATGGATTGCAATTAACACTGACA
1 ACATTGTGAGTGGGTATGGATTGCAATTAACACTGACA
38968068 A
1 A
38968069 TTTTGCATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (38 bp):
ACATTGTGAGTGGGTATGGATTGCAATTAACACTGACA
Found at i:38970077 original size:2 final size:2
Alignment explanation
Indices: 38970024--38970062 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
38970014 TCATCCATTT
38970024 AG AG 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 AG AG A
38970063 AGTACAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38989820 original size:2 final size:2
Alignment explanation
Indices: 38989815--38989840 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38989805 ATATATATAA
38989815 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
38989841 TCTATCANAT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38989876 original size:2 final size:2
Alignment explanation
Indices: 38989871--38989898 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38989861 ATATATATAA
38989871 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38989899 TCTTCATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38992654 original size:7 final size:7
Alignment explanation
Indices: 38992623--38992653 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
38992613 AAAGCACGAA
38992623 TTCCTTC
1 TTCCTTC
38992630 TTCCTTC
1 TTCCTTC
38992637 TTCCTTC
1 TTCCTTC
*
38992644 TTCTTTC
1 TTCCTTC
38992651 TTC
1 TTC
38992654 TATGAAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (7 bp):
TTCCTTC
Found at i:38994229 original size:18 final size:19
Alignment explanation
Indices: 38994186--38994229 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
38994176 TCGATAAATC
* *
38994186 CAATCAGTTATTTTGGTTT
1 CAATAAGTTATTTTGGATT
*
38994205 CAATAAGTTATTTTTGATT
1 CAATAAGTTATTTTGGATT
38994224 -AATAAG
1 CAATAAG
38994230 ATTTATATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (19 bp):
CAATAAGTTATTTTGGATT
Found at i:39007061 original size:17 final size:18
Alignment explanation
Indices: 39007039--39007072 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39007029 GGCCGGCTAG
*
39007039 TCCT-AAAGTGAACATTA
1 TCCTAAAAGTAAACATTA
39007056 TCCTAAAAGTAAACATT
1 TCCTAAAAGTAAACATT
39007073 TTGCATTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (18 bp):
TCCTAAAAGTAAACATTA
Found at i:39015723 original size:20 final size:21
Alignment explanation
Indices: 39015678--39015723 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
39015668 ATAAGTTGAA
39015678 TAAATTTATAATTTTTAATAT
1 TAAATTTATAATTTTTAATAT
* * *
39015699 AAAATTTA-ATTTTTTAATTT
1 TAAATTTATAATTTTTAATAT
39015719 TAAAT
1 TAAAT
39015724 AATTAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAATTTATAATTTTTAATAT
Found at i:39016075 original size:100 final size:107
Alignment explanation
Indices: 39015896--39016103 Score: 279
Period size: 100 Copynumber: 2.0 Consensus size: 107
39015886 TAAGTTATAA
*
39015896 TTTTGGTTAAAATTATCGTAAAAAGTATTTCTTTATTTGAGAGGGTAATATTGTAATTATATTTA
1 TTTTGGTTAAAATTATCGT-AAAAGTAGTTCTTTATTTGAGAGGGTAATATTGTAATTATATTTA
39015961 AAACAAATGAGGATATTTTTAAAACAAAAAAAAAAAATATCTT
65 AAACAAATGAGGATATTTTTAAAACAAAAAAAAAAAATATCTT
39016004 NTTTTGGTTAAAATTATCGT-AAA-T-GTT-TTT-TTT-AGAGGGTAATATTGTAATTAT-TTT-
1 -TTTTGGTTAAAATTATCGTAAAAGTAGTTCTTTATTTGAGAGGGTAATATTGTAATTATATTTA
* ** * * *
39016061 TAGTAAATGAGGATATTTTTGAAACAAAAATAAAAATTATCTT
65 AAACAAATGAGGATATTTTTAAAACAAAAAAAAAAAATATCTT
39016104 GTATTTTTTA
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
100 37 0.40
101 3 0.03
102 21 0.23
103 3 0.03
104 3 0.03
105 2 0.02
106 1 0.01
107 3 0.03
109 19 0.21
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (107 bp):
TTTTGGTTAAAATTATCGTAAAAGTAGTTCTTTATTTGAGAGGGTAATATTGTAATTATATTTAA
AACAAATGAGGATATTTTTAAAACAAAAAAAAAAAATATCTT
Found at i:39016621 original size:20 final size:21
Alignment explanation
Indices: 39016576--39016642 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 21
39016566 CTTAAATATT
*
39016576 TTATTTTTAATAAATTAGTTAA
1 TTATTTTAAATAAATTA-TTAA
39016598 --ATTTTAAATAAATT-TTAA
1 TTATTTTAAATAAATTATTAA
*
39016616 TTATTTTATAAAAATATTAGTTAA
1 TTATTTTA-AATAA-ATTA-TTAA
39016640 TTA
1 TTA
39016643 GCCATCACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.11
20 19 0.51
21 4 0.11
22 3 0.08
24 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TTATTTTAAATAAATTATTAA
Found at i:39019279 original size:281 final size:282
Alignment explanation
Indices: 39018776--39019336 Score: 973
Period size: 281 Copynumber: 2.0 Consensus size: 282
39018766 ATGGATACAA
* * *
39018776 ACAAATACATGTATGCCACAAAGCAGATAGCCTTTCTCCAATAGCCAGAGGAAAAACTTGTAAGA
1 ACAAATACATGTATGCCACAAAGCAGATAGCCTTCCTCCAATAGCCAAAGGAAAAACTTGAAAGA
* *
39018841 CAAGGTAGCACTGGTAAATATAGCTTATGATTATGTTATGTGCTAAGGGAGAACATCTAGTTAGC
66 CAAGGCAGCACTGGTAAATATAGCTTATGATTATGTTATGTGCTAACGGAGAACATCTAGTTAGC
39018906 ACAAGACCGTCAATAAGCACTCAAATTCATCACCAGCAACTATAATGCACTGAGTAAACCTAAAA
131 ACAAGACCGTCAATAAGCACTCAAATTCATCACCAGCAACTATAATGCACTGAGTAAACCTAAAA
* *
39018971 CCATTAATATCTGAATAAAGATAGGACTTAAGC-TAACAGTGAGCCTACCACATACATTGATTAA
196 CCATTAATATCTGAATAAAGATAGGACTTAAGCAAAACAGTGAACCTACCACATACATTGATTAA
39019035 AAAGAAAAA-CCCTAGAATCAAT
261 AAAGAAAAAGCCC-AGAATCAAT
* * *
39019057 ACAAATACATGTATGCCACAATGCAGATAGCCTTCCTCCAGTAGCCAAAGGAAGAACTTGAAAGA
1 ACAAATACATGTATGCCACAAAGCAGATAGCCTTCCTCCAATAGCCAAAGGAAAAACTTGAAAGA
39019122 CAAGGCAGCACTGGTAAATATAGCTTATGATTATGTTATGTGCTAACGGAGAACATCTAGTTAGC
66 CAAGGCAGCACTGGTAAATATAGCTTATGATTATGTTATGTGCTAACGGAGAACATCTAGTTAGC
*
39019187 ACAAGACCGTCAATAAGCACTCAAATTCATCACCAGCAACTATAATGCACTGGGTAAACCTAAAA
131 ACAAGACCGTCAATAAGCACTCAAATTCATCACCAGCAACTATAATGCACTGAGTAAACCTAAAA
* *
39019252 CCATTAATATTTGAATAAAGATAGGACTTAAGCAAAACAGTTAACCTACCACATACATTGATTAA
196 CCATTAATATCTGAATAAAGATAGGACTTAAGCAAAACAGTGAACCTACCACATACATTGATTAA
*
39019317 AAGGAAAAAGCCCAGAATCA
261 AAAGAAAAAGCCCAGAATCA
39019337 CATGTAACAT
Statistics
Matches: 264, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
281 218 0.83
282 43 0.16
283 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (282 bp):
ACAAATACATGTATGCCACAAAGCAGATAGCCTTCCTCCAATAGCCAAAGGAAAAACTTGAAAGA
CAAGGCAGCACTGGTAAATATAGCTTATGATTATGTTATGTGCTAACGGAGAACATCTAGTTAGC
ACAAGACCGTCAATAAGCACTCAAATTCATCACCAGCAACTATAATGCACTGAGTAAACCTAAAA
CCATTAATATCTGAATAAAGATAGGACTTAAGCAAAACAGTGAACCTACCACATACATTGATTAA
AAAGAAAAAGCCCAGAATCAAT
Found at i:39021551 original size:23 final size:23
Alignment explanation
Indices: 39021524--39021567 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39021514 TAGTAAAATC
39021524 ATAAAATTAT-AAAATTTTGAAAA
1 ATAAAATT-TGAAAATTTTGAAAA
*
39021547 ATAAAATTTGTAAATTTTGAA
1 ATAAAATTTGAAAATTTTGAA
39021568 TTCAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
ATAAAATTTGAAAATTTTGAAAA
Found at i:39034834 original size:3 final size:3
Alignment explanation
Indices: 39034822--39034862 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
39034812 ACTTCTCCAC
* *
39034822 CTT C-T CTT CTT CTT CTT CTT CAT CAT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
39034863 GATTCCCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:39041001 original size:2 final size:2
Alignment explanation
Indices: 39040994--39041021 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39040984 GATAAATTAC
39040994 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39041022 TAGTCTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39046071 original size:2 final size:2
Alignment explanation
Indices: 39046064--39046099 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39046054 TGTTTGTAGG
39046064 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39046100 ATGATGGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39061009 original size:12 final size:12
Alignment explanation
Indices: 39060991--39061022 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39060981 AGATGATGAG
39060991 GAAGAAGACTCA
1 GAAGAAGACTCA
*
39061003 GATGAAGACTCA
1 GAAGAAGACTCA
39061015 GAAGAAGA
1 GAAGAAGA
39061023 TGAAGGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.28, T:0.09
Consensus pattern (12 bp):
GAAGAAGACTCA
Found at i:39079718 original size:30 final size:29
Alignment explanation
Indices: 39079650--39079746 Score: 131
Period size: 30 Copynumber: 3.3 Consensus size: 29
39079640 ATATTTAATT
* *
39079650 TTTTTATATTTTTATTTTAAATTTAATAA
1 TTTTTATATTTTTATTTTGAATTAAATAA
* *
39079679 TTATTATATTTTTATTTTGAGTTAAATAA
1 TTTTTATATTTTTATTTTGAATTAAATAA
*
39079708 GTTTTTATATTTTTATTTTGAATCAAATAAA
1 -TTTTTATATTTTTATTTTGAATTAAAT-AA
39079739 TTTTTATA
1 TTTTTATA
39079747 ATTAATGATT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.42
30 32 0.54
31 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (29 bp):
TTTTTATATTTTTATTTTGAATTAAATAA
Found at i:39080005 original size:23 final size:24
Alignment explanation
Indices: 39079979--39080024 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
39079969 ATAAAATTTT
39079979 ATTTAACTT-AAAATAA-AAAAAAG
1 ATTTAA-TTGAAAATAATAAAAAAG
*
39080002 ATTTAATTGAATATAATAAAAAA
1 ATTTAATTGAAAATAATAAAAAA
39080025 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 12 0.60
24 6 0.30
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
ATTTAATTGAAAATAATAAAAAAG
Found at i:39095691 original size:3 final size:3
Alignment explanation
Indices: 39095683--39095714 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
39095673 CTACTGGAAA
*
39095683 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
39095715 AAAGTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39106987 original size:2 final size:2
Alignment explanation
Indices: 39106980--39107019 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39106970 ACAACTGTGT
39106980 TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC
39107020 GTGCTTCGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39129623 original size:42 final size:42
Alignment explanation
Indices: 39129564--39129648 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
39129554 GGCCCAAGAT
39129564 AGCCTCGTAGCCATCCAAGTTGAAGGAAACATATTAGTGCTA
1 AGCCTCGTAGCCATCCAAGTTGAAGGAAACATATTAGTGCTA
*
39129606 AGCCTCGTAGCCATCCAAGTTGAAGGAATCATATTAGTGCTA
1 AGCCTCGTAGCCATCCAAGTTGAAGGAAACATATTAGTGCTA
39129648 A
1 A
39129649 TACCCTTCAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (42 bp):
AGCCTCGTAGCCATCCAAGTTGAAGGAAACATATTAGTGCTA
Done.