Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 47 of 106
Found at i:17637070 original size:16 final size:18
Alignment explanation
Indices: 17637049--17637086 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17637039 AACCCAAGTC
17637049 AAACAAAA-TA-AGAGAA
1 AAACAAAAGTAGAGAGAA
*
17637065 AAACAAAAGTAGAGAGAG
1 AAACAAAAGTAGAGAGAA
17637083 AAAC
1 AAAC
17637087 TAATAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.68, C:0.08, G:0.18, T:0.05
Consensus pattern (18 bp):
AAACAAAAGTAGAGAGAA
Found at i:17648153 original size:39 final size:39
Alignment explanation
Indices: 17648104--17648210 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
17648094 AAAGGAGACA
* * *
17648104 AAAACAAAAAGTTTTTTGCTGCAGCGAGATTTTG-GTCAT
1 AAAA-AAAAAGTTTTTTGCTGCAGCGAGATTGTGACTCAG
* * *
17648143 AAAATAAAAAGTTTCTTGCTGCAGCAAAATTGTGACTCAG
1 AAAA-AAAAAGTTTTTTGCTGCAGCGAGATTGTGACTCAG
*
17648183 AAACAGAAAA-TTTTTTGCTGCAGCGAGA
1 AAA-AAAAAAGTTTTTTGCTGCAGCGAGA
17648211 ATGAATTTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
39 44 0.80
40 10 0.18
41 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (39 bp):
AAAAAAAAAGTTTTTTGCTGCAGCGAGATTGTGACTCAG
Found at i:17654116 original size:14 final size:14
Alignment explanation
Indices: 17654097--17654124 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17654087 AATCTCTTTT
17654097 TGAAAGTTTGTTTA
1 TGAAAGTTTGTTTA
17654111 TGAAAGTTTGTTTA
1 TGAAAGTTTGTTTA
17654125 ATTCTTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TGAAAGTTTGTTTA
Found at i:17656401 original size:20 final size:21
Alignment explanation
Indices: 17656360--17656401 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17656350 CATATATATC
*
17656360 TGAATATATGTTGTGCATTGA
1 TGAATATATGTTGTGCAATGA
*
17656381 TGAATA-ATGTTGTGTAATGA
1 TGAATATATGTTGTGCAATGA
17656401 T
1 T
17656402 ATTGACCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (21 bp):
TGAATATATGTTGTGCAATGA
Found at i:17656531 original size:42 final size:42
Alignment explanation
Indices: 17656404--17656545 Score: 180
Period size: 42 Copynumber: 3.4 Consensus size: 42
17656394 GTAATGATAT
* * *
17656404 TGACCCGGCTATGTGTGAGTAGGAGTGCGCATAAGCCGATGA
1 TGACCTGGCTATGTGCGAGTAGGAGTACGCATAAGCCGATGA
* * *
17656446 T-AACTCGGCTATGTGAGAGT-GAGAGTCCGCATAAGCCGATGA
1 TGACCT-GGCTATGTGCGAGTAG-GAGTACGCATAAGCCGATGA
17656488 TGACCTGGCTATGTGCGAGTAGGAGTACGCATAAGCCGATGA
1 TGACCTGGCTATGTGCGAGTAGGAGTACGCATAAGCCGATGA
* *
17656530 TGACCTAGCCATGTGC
1 TGACCTGGCTATGTGC
17656546 TAGTGGGGAG
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
41 3 0.03
42 80 0.92
43 4 0.05
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.22
Consensus pattern (42 bp):
TGACCTGGCTATGTGCGAGTAGGAGTACGCATAAGCCGATGA
Found at i:17659088 original size:279 final size:279
Alignment explanation
Indices: 17658567--17659126 Score: 915
Period size: 279 Copynumber: 2.0 Consensus size: 279
17658557 TGTCATTGAT
17658567 CTTGGCAGCCACCTTATTTTTTGGAAATCTTCCAAACAACGATCAGTTGCAAGATCATCAATCGA
1 CTTGGCAGCCACCTTATTTTTTGGAAATCTTCCAAACAACGATCAGTTGCAAGATCATCAATCGA
*
17658632 GGCTGAATACAGAGCAATTGCCAATACTACAGCAGTACTTCGATGGATCAAAAATCTTTTTGTTA
66 GGCTGAATACAGAGCAATTGCCAATACTACAGCAGTACTTCGATGGATCAAAAATCTTCTTGTTA
* *
17658697 AGTTGCATTTCTCATCTTCTTAAACTCCAGTTCTGCATTGTGACAATGGTAGAGCAATATATTTG
131 AGTTGCATTTCTCATATTCTTAAACTCCAGTTCTGCATTGTGACAATGGTAGAGCAACATATTTG
* * ** * ** * *
17658762 AGTGCTAATATAGTATTTCATGCAAGAATAAATGACTTAGCACTTGACTATCATTTTATTCATCA
196 AGTGCCAATACAAAATTTCATGCAACAATAAAACACTTAGAACTTGACTATCACTTTATTCATCA
*
17658827 AAATGTTCCATCTTGACAA
261 AAATGTTCCATCTGGACAA
*
17658846 CTTGGCAGCCACCTTATTTTTTGGAAATCTTCCAAACAACGATCAGTTGCAAGATCATCCATCGA
1 CTTGGCAGCCACCTTATTTTTTGGAAATCTTCCAAACAACGATCAGTTGCAAGATCATCAATCGA
*
17658911 GGCTGAATACAGAGCAATTGCCAATACTACAGCAGTACTTCGATGGATCAAAAATCTTCTTGTTG
66 GGCTGAATACAGAGCAATTGCCAATACTACAGCAGTACTTCGATGGATCAAAAATCTTCTTGTTA
* *
17658976 AGTTGCATTTCTCATATT-TTCAAACTCCAGTTCTGCATTGTGACAATGTTAGAGCACCATATTT
131 AGTTGCATTTCTCATATTCTT-AAACTCCAGTTCTGCATTGTGACAATGGTAGAGCAACATATTT
* * * *
17659040 GAGTGCCAATCCAAAATTTCATTCAACAATAAAACACTTAGAACTTGACTATCACTTTGTTCGTC
195 GAGTGCCAATACAAAATTTCATGCAACAATAAAACACTTAGAACTTGACTATCACTTTATTCATC
17659105 AAAATGTTCCATCTGGACAA
260 AAAATGTTCCATCTGGACAA
17659125 CT
1 CT
17659127 CAACATTTTT
Statistics
Matches: 259, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
278 2 0.01
279 257 0.99
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (279 bp):
CTTGGCAGCCACCTTATTTTTTGGAAATCTTCCAAACAACGATCAGTTGCAAGATCATCAATCGA
GGCTGAATACAGAGCAATTGCCAATACTACAGCAGTACTTCGATGGATCAAAAATCTTCTTGTTA
AGTTGCATTTCTCATATTCTTAAACTCCAGTTCTGCATTGTGACAATGGTAGAGCAACATATTTG
AGTGCCAATACAAAATTTCATGCAACAATAAAACACTTAGAACTTGACTATCACTTTATTCATCA
AAATGTTCCATCTGGACAA
Found at i:17662909 original size:20 final size:21
Alignment explanation
Indices: 17662877--17662915 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
17662867 CTACCACCCA
17662877 TTTAACTGATTAA-ACCTTGT
1 TTTAACTGATTAAGACCTTGT
17662897 TTTAACT-AGTTAAGACCTT
1 TTTAACTGA-TTAAGACCTT
17662916 TCTGTCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 11 0.65
21 5 0.29
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTAACTGATTAAGACCTTGT
Found at i:17663373 original size:29 final size:29
Alignment explanation
Indices: 17663337--17663421 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
17663327 ATAAAATATT
17663337 TATAATATCCACAATAGCTAAACAAAATA
1 TATAATATCCACAATAGCTAAACAAAATA
* * * *
17663366 TATAATATCTACAGTAGCTAAGCAAGATA
1 TATAATATCCACAATAGCTAAACAAAATA
* *
17663395 TATTGAATATCCATAATAACTAGAACA
1 TA-T-AATATCCACAATAGCTA-AACA
17663422 TAGTATTCAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 27 0.61
30 1 0.02
31 13 0.30
32 3 0.07
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.27
Consensus pattern (29 bp):
TATAATATCCACAATAGCTAAACAAAATA
Found at i:17667257 original size:40 final size:38
Alignment explanation
Indices: 17667202--17667304 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
17667192 ATCCAGCTCA
* * * *
17667202 TGTGCATCTCTCCACATCGTGCACATAGCCAGAGTCATTG
1 TGTGCATCCCCCCACATCGTGCACA-A-CCAGAGCCATCG
* *
17667242 TGTGCATCCCCCCACATCGTGCACAATCAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAACCAGAGCCATCG
*
17667280 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
17667305 CGGGCACTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 32 0.57
39 1 0.02
40 23 0.41
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.23
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAACCAGAGCCATCG
Found at i:17672176 original size:7 final size:7
Alignment explanation
Indices: 17672164--17672204 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
17672154 ACATGAAAAG
17672164 GGTTTAA
1 GGTTTAA
17672171 GGTTTAA
1 GGTTTAA
*
17672178 GGTTTAT
1 GGTTTAA
17672185 GGTTT-A
1 GGTTTAA
17672191 GGATTT-A
1 GG-TTTAA
17672198 GGTTTAA
1 GGTTTAA
17672205 TGACGCTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (7 bp):
GGTTTAA
Found at i:17672202 original size:20 final size:21
Alignment explanation
Indices: 17672164--17672203 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
17672154 ACATGAAAAG
17672164 GGTTTAAGGTTTAAGGTTTAT
1 GGTTTAAGGTTTAAGGTTTAT
17672185 GGTTT-AGGATTT-AGGTTTA
1 GGTTTAAGG-TTTAAGGTTTA
17672204 ATGACGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
GGTTTAAGGTTTAAGGTTTAT
Found at i:17672448 original size:7 final size:7
Alignment explanation
Indices: 17672436--17672477 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
17672426 CAACATGGAA
17672436 AGGGTTT
1 AGGGTTT
17672443 AGGGTTT
1 AGGGTTT
*
17672450 AAGGTTT
1 AGGGTTT
*
17672457 ATGGTTT
1 AGGGTTT
*
17672464 AGGATTT
1 AGGGTTT
17672471 A-GGTTT
1 AGGGTTT
17672477 A
1 A
17672478 ATTATGCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
AGGGTTT
Found at i:17672464 original size:21 final size:20
Alignment explanation
Indices: 17672438--17672477 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
17672428 ACATGGAAAG
*
17672438 GGTTTAGGGTTTAAGGTTTAT
1 GGTTTAGGATTT-AGGTTTAT
17672459 GGTTTAGGATTTAGGTTTA
1 GGTTTAGGATTTAGGTTTA
17672478 ATTATGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (20 bp):
GGTTTAGGATTTAGGTTTAT
Found at i:17673300 original size:54 final size:56
Alignment explanation
Indices: 17673235--17673360 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 56
17673225 ATAGAGCCTG
* *
17673235 ATGCTTATTATGCCTATCT-A-GCATGGTGCTAGACATGTGTAGTGAGTATGACAC
1 ATGCTTGTTATGCCTATCTAAGGCATGGTGCTAGACATGTGTAGTGAGTAAGACAC
* * * *
17673289 ATGCTTGTTATGCTTATCTAACAAGGCTTGGTGCTAGACATGTGTAGTGAGTAAGGCAT
1 ATGCTTGTTATGCCTATCT---AAGGCATGGTGCTAGACATGTGTAGTGAGTAAGACAC
17673348 ATGCTTGTTATGC
1 ATGCTTGTTATGC
17673361 TTATTACTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
54 17 0.28
58 1 0.02
59 43 0.70
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (56 bp):
ATGCTTGTTATGCCTATCTAAGGCATGGTGCTAGACATGTGTAGTGAGTAAGACAC
Found at i:17675808 original size:19 final size:19
Alignment explanation
Indices: 17675767--17675809 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
17675757 GAGAAGAGAC
* * * *
17675767 AATTTTGAAGCTTGATGCT
1 AATTTTAAAGCTAGATACA
17675786 AATTTTAAAGCTAGATACA
1 AATTTTAAAGCTAGATACA
17675805 AATTT
1 AATTT
17675810 ATCAAACCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (19 bp):
AATTTTAAAGCTAGATACA
Found at i:17685562 original size:38 final size:40
Alignment explanation
Indices: 17685476--17685578 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
17685466 ACCTAGCTCA
* *
17685476 TGTGTATCCCCCCACATCGTGCACATAGCCAGGGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCCAGGGCCATCG
** *
17685516 TGTGCATCCCCCCACATCGTGCACA-A-TTAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCCAGGGCCATCG
*
17685554 TGTGCATCCCCCCACACCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
17685579 CGCACGGTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 32 0.56
39 1 0.02
40 24 0.42
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.21
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAGCCAGGGCCATCG
Found at i:17687499 original size:3 final size:3
Alignment explanation
Indices: 17687491--17687550 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
17687481 TACGTATACC
* *
17687491 CAT CAT CAT CAT GCA- CAT CAT C-C CAT CAT CAT CAT ACA- CAC CAT
1 CAT CAT CAT CAT -CAT CAT CAT CAT CAT CAT CAT CAT -CAT CAT CAT
17687535 CA- CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CA
17687551 CCAGCTCATG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
2 7 0.15
3 37 0.77
4 4 0.08
ACGTcount: A:0.35, C:0.38, G:0.02, T:0.25
Consensus pattern (3 bp):
CAT
Found at i:17687550 original size:26 final size:23
Alignment explanation
Indices: 17687489--17687548 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
17687479 TATACGTATA
* *
17687489 CCCATCATCATCATGCACATCAT
1 CCCATCATCATCATACACACCAT
17687512 CCCATCATCATCATACACACCAT
1 CCCATCATCATCATACACACCAT
*
17687535 CACATCATCATCAT
1 CCCATCATCATCAT
17687549 CACCAGCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.25
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Found at i:17687646 original size:43 final size:43
Alignment explanation
Indices: 17687562--17687646 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
17687552 CAGCTCATGC
* ** * * *
17687562 GCACTCCCTACTCGCACATGGCTGGGTCATCATCGAGTTATGT
1 GCACTCCCTACGCGCACATAACCGGGTCATCATCAACTTATGT
*
17687605 GCACTCCCTACGCGCACATAACCGGGTCATCCTCAACTTATG
1 GCACTCCCTACGCGCACATAACCGGGTCATCATCAACTTATG
17687647 CTGTCACAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (43 bp):
GCACTCCCTACGCGCACATAACCGGGTCATCATCAACTTATGT
Found at i:17687988 original size:21 final size:20
Alignment explanation
Indices: 17687963--17688022 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
17687953 AGATGTCTAA
*
17687963 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
17687984 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
17688004 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
17688022 A
1 A
17688023 TTCTATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:17688972 original size:13 final size:13
Alignment explanation
Indices: 17688954--17688978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17688944 TCCCAAAACA
17688954 TTTATAAAATCAT
1 TTTATAAAATCAT
17688967 TTTATAAAATCA
1 TTTATAAAATCA
17688979 CAATTTTTCC
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:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17691411 original size:19 final size:19
Alignment explanation
Indices: 17691372--17691411 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17691362 TGAAAAAGAT
*
17691372 GAAGCTGTTGGAGAATGAA
1 GAAGCTGTTGGAGAATAAA
17691391 GAAGCTGTTGGAAGAA-AAA
1 GAAGCTGTTGG-AGAATAAA
17691410 GA
1 GA
17691412 TATTTATAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.42, C:0.05, G:0.35, T:0.17
Consensus pattern (19 bp):
GAAGCTGTTGGAGAATAAA
Found at i:17702240 original size:20 final size:20
Alignment explanation
Indices: 17702217--17702258 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17702207 TGGCAAGGTG
17702217 AAATGGCA-TGGGAGCAATGA
1 AAATGGCATTGGGAGC-ATGA
17702237 AAATGGCATTGGGAGCATGA
1 AAATGGCATTGGGAGCATGA
17702257 AA
1 AA
17702259 GAGAAGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.40, C:0.10, G:0.33, T:0.17
Consensus pattern (20 bp):
AAATGGCATTGGGAGCATGA
Found at i:17703093 original size:17 final size:15
Alignment explanation
Indices: 17703060--17703098 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
17703050 TTTATCTATT
17703060 TAAAAAAAAAATAAA
1 TAAAAAAAAAATAAA
*
17703075 TAAAAAAGACAATATAA
1 TAAAAAA-AAAATA-AA
17703092 TAAAAAA
1 TAAAAAA
17703099 TAGAAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 9 0.43
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (15 bp):
TAAAAAAAAAATAAA
Found at i:17715781 original size:37 final size:37
Alignment explanation
Indices: 17715740--17715928 Score: 306
Period size: 37 Copynumber: 5.1 Consensus size: 37
17715730 CATATGCATT
17715740 CATCATCATGTGTGCACTCCCTACTCGCACACTTTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTTAA
* *
17715777 CATCATCATGTGTGCACTCCCTACTCGTACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTTAA
* *
17715814 CATCATCATGTGTGCACTCCCTACTTGCACACTCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTTAA
* *
17715851 CATCATCATGTGTGCACTTCCTACTCGCACACTCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTTAA
* *
17715888 CATCATCATTTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTTAA
17715925 CATC
1 CATC
17715929 CTCACACAAC
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 140 1.00
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.30
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTTAA
Found at i:17717583 original size:24 final size:24
Alignment explanation
Indices: 17717528--17717574 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
17717518 CAGCACAGCA
17717528 GCCTTACTTCCTCAACGCCACAAC
1 GCCTTACTTCCTCAACGCCACAAC
*
17717552 GCCTTACTTCCTCAGCGCCACAA
1 GCCTTACTTCCTCAACGCCACAA
17717575 TCCTCTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.11, T:0.21
Consensus pattern (24 bp):
GCCTTACTTCCTCAACGCCACAAC
Found at i:17723189 original size:38 final size:39
Alignment explanation
Indices: 17723147--17723246 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 39
17723137 GAGACCAAAG
* * *
17723147 CAGAAAGTTTTTCGTTGCAGCGAAATTGTAACCCAG-AA
1 CAGAAAGTTTCTCGCTGCAGCGAAATTGCAACCCAGAAA
* * *
17723185 CAGAATGTTTCTCGCTGCAACGAAATTGCAACCTAGAAA
1 CAGAAAGTTTCTCGCTGCAGCGAAATTGCAACCCAGAAA
* *
17723224 TAAAAAGTTTCTCGCTGCAGCGA
1 CAGAAAGTTTCTCGCTGCAGCGA
17723247 GAAGCTACAG
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 30 0.59
39 21 0.41
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (39 bp):
CAGAAAGTTTCTCGCTGCAGCGAAATTGCAACCCAGAAA
Found at i:17726171 original size:21 final size:20
Alignment explanation
Indices: 17726147--17726216 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 20
17726137 TCAAAACTGC
17726147 TTGAATGATCTTTGAACTTGT
1 TTGAATGAT-TTTGAACTTGT
* * *
17726168 TTGAATAATTTTTATATTTGT
1 TTGAATGATTTTGA-ACTTGT
17726189 TTGAATGAGTTTTTGAACTTGT
1 TTGAATGA--TTTTGAACTTGT
17726211 TTGAAT
1 TTGAAT
17726217 AGTTTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.10
21 20 0.50
22 11 0.28
23 5 0.12
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (20 bp):
TTGAATGATTTTGAACTTGT
Found at i:17726220 original size:21 final size:21
Alignment explanation
Indices: 17726157--17726223 Score: 91
Period size: 21 Copynumber: 3.1 Consensus size: 21
17726147 TTGAATGATC
*
17726157 TTTGAACTTGTTTGAATAATT
1 TTTGAACTTGTTTGAATAGTT
*
17726178 TTT-ATATTTGTTTGAATGAGTT
1 TTTGA-ACTTGTTTGAAT-AGTT
17726200 TTTGAACTTGTTTGAATAGTT
1 TTTGAACTTGTTTGAATAGTT
17726221 TTT
1 TTT
17726224 AAACATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.03
21 21 0.52
22 17 0.43
23 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (21 bp):
TTTGAACTTGTTTGAATAGTT
Found at i:17726238 original size:21 final size:22
Alignment explanation
Indices: 17726161--17726244 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 22
17726151 ATGATCTTTG
*
17726161 AACTTGTTTGAATAA-TTTTTA
1 AACTTGTTTAAATAAGTTTTTA
* * * * *
17726182 TATTTGTTTGAATGAGTTTTTG
1 AACTTGTTTAAATAAGTTTTTA
*
17726204 AACTTGTTTGAAT-AGTTTTTA
1 AACTTGTTTAAATAAGTTTTTA
17726225 AACATT-TTTAAATAAGTTTT
1 AAC-TTGTTTAAATAAGTTTT
17726245 GAAGTGCCTA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 28 0.54
22 24 0.46
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.54
Consensus pattern (22 bp):
AACTTGTTTAAATAAGTTTTTA
Found at i:17726243 original size:43 final size:43
Alignment explanation
Indices: 17726157--17726244 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
17726147 TTGAATGATC
* * * *
17726157 TTTGAACTTGTTTGAATAATTTTTATATTTGTTTGAATGAGTT
1 TTTGAACTTGTTTGAATAATTTTTAAAATTGTTTAAATAAGTT
*
17726200 TTTGAACTTGTTTGAATAGTTTTTAAACATT-TTTAAATAAGTT
1 TTTGAACTTGTTTGAATAATTTTTAAA-ATTGTTTAAATAAGTT
17726243 TT
1 TT
17726245 GAAGTGCCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 37 0.95
44 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (43 bp):
TTTGAACTTGTTTGAATAATTTTTAAAATTGTTTAAATAAGTT
Found at i:17726552 original size:20 final size:21
Alignment explanation
Indices: 17726506--17726586 Score: 94
Period size: 20 Copynumber: 4.0 Consensus size: 21
17726496 ATGGTTTTGC
* * *
17726506 CCAAAATGTATGGATTCATTT
1 CCAAAATGTATCGATACATTG
17726527 CCAAAATGTATCGATACA-TG
1 CCAAAATGTATCGATACATTG
*
17726547 CCAAAATGTATTGATACATTG
1 CCAAAATGTATCGATACATTG
* *
17726568 -CAACATGTATCAATACATT
1 CCAAAATGTATCGATACATT
17726587 TTGGAATGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 34 0.65
21 18 0.35
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (21 bp):
CCAAAATGTATCGATACATTG
Found at i:17726584 original size:40 final size:41
Alignment explanation
Indices: 17726506--17726585 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
17726496 ATGGTTTTGC
* *
17726506 CCAAAATGTATGGATTCATTTCCAAAATGTATCGATACATG
1 CCAAAATGTATGGATACATTTCCAAAATGTATCAATACATG
* * *
17726547 CCAAAATGTATTGATACA-TTGCAACATGTATCAATACAT
1 CCAAAATGTATGGATACATTTCCAAAATGTATCAATACAT
17726586 TTTGGAATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 18 0.53
41 16 0.47
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (41 bp):
CCAAAATGTATGGATACATTTCCAAAATGTATCAATACATG
Found at i:17727056 original size:32 final size:33
Alignment explanation
Indices: 17726993--17727057 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
17726983 GTAAGAGAGA
* * *
17726993 GAAGGTTATGCTTTAGCCTTTAAAAGGCATTGT
1 GAAGGTTATGCTTGAGCCTATAAAAGACATTGT
*
17727026 GAAGGTTATGCTTGATCC-ATAAAAGACATTGT
1 GAAGGTTATGCTTGAGCCTATAAAAGACATTGT
17727058 ATTGAGAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (33 bp):
GAAGGTTATGCTTGAGCCTATAAAAGACATTGT
Found at i:17732887 original size:22 final size:22
Alignment explanation
Indices: 17732847--17732892 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
17732837 TTATCAGCAA
* *
17732847 CAAAATACCATGAACATATTAG
1 CAAAATACCATAAACATATCAG
* *
17732869 CAAAGTACCATAAATATATCAG
1 CAAAATACCATAAACATATCAG
17732891 CA
1 CA
17732893 TCTAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.22
Consensus pattern (22 bp):
CAAAATACCATAAACATATCAG
Found at i:17736868 original size:16 final size:15
Alignment explanation
Indices: 17736840--17736878 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
17736830 GGAAGAGAGG
17736840 AAAA-AAAAGAAAGA
1 AAAAGAAAAGAAAGA
17736854 AAAAGAAAAGAAAAGA
1 AAAAGAAAAG-AAAGA
*
17736870 AATAGAAAA
1 AAAAGAAAA
17736879 TAAATGGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 5 0.23
16 13 0.59
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAGAAAGA
Found at i:17736900 original size:25 final size:25
Alignment explanation
Indices: 17736870--17736928 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
17736860 AAAGAAAAGA
17736870 AATAGAAAATAAATGGGCATGACCC
1 AATAGAAAATAAATGGGCATGACCC
* *
17736895 AATAGAAAATAAGTGGGCATGGCCC
1 AATAGAAAATAAATGGGCATGACCC
17736920 AATAAGAAA
1 AAT-AGAAA
17736929 CAAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 26 0.84
26 5 0.16
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.15
Consensus pattern (25 bp):
AATAGAAAATAAATGGGCATGACCC
Found at i:17745180 original size:15 final size:15
Alignment explanation
Indices: 17745144--17745181 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
17745134 AAAGATGCAA
* *
17745144 GACATGAATATTTAT
1 GACATGAATAATAAT
17745159 G-CATGAATAATAAT
1 GACATGAATAATAAT
17745173 GACATGAAT
1 GACATGAAT
17745182 TATGAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (15 bp):
GACATGAATAATAAT
Found at i:17745799 original size:13 final size:12
Alignment explanation
Indices: 17745753--17745806 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
17745743 TCACTCTTTC
17745753 TTCC-TTTT-TT
1 TTCCTTTTTCTT
*
17745763 TT-CTTTTTATT
1 TTCCTTTTTCTT
*
17745774 TTCCTCTTTCTT
1 TTCCTTTTTCTT
17745786 TTCCTTTCTTCTT
1 TTCCTTT-TTCTT
*
17745799 TTTCTTTT
1 TTCCTTTT
17745807 CACTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 1 0.03
10 6 0.17
11 4 0.11
12 14 0.39
13 11 0.31
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCCTTTTTCTT
Found at i:17747812 original size:18 final size:18
Alignment explanation
Indices: 17747789--17747826 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
17747779 ATATTAGATC
17747789 ATATTTT-ATTTAATTCTA
1 ATATTTTAATTT-ATTCTA
17747807 ATATTTTAATTTATTCTA
1 ATATTTTAATTTATTCTA
17747825 AT
1 AT
17747827 GAGTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTTAATTTATTCTA
Found at i:17760246 original size:2 final size:2
Alignment explanation
Indices: 17760239--17760299 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
17760229 TCTGATATTG
* *
17760239 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT 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
17760281 AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT
17760300 TTAGGGGTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17760264 original size:20 final size:20
Alignment explanation
Indices: 17760239--17760296 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
17760229 TCTGATATTG
17760239 ATATATATATATATATAAAT
1 ATATATATATATATATAAAT
17760259 ATATATATATATATATAAAT
1 ATATATATATATATATAAAT
17760279 ATATATATATATATATAA
1 ATATATATATATATATAA
17760297 TATTTAGGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATATATATATAAAT
Found at i:17762744 original size:19 final size:19
Alignment explanation
Indices: 17762720--17762756 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17762710 GAGAGCAAAC
*
17762720 AACAAAAAAAAATAAAAAA
1 AACAAAAAAAAACAAAAAA
*
17762739 AACAAAAAGAAACAAAAA
1 AACAAAAAAAAACAAAAA
17762757 GGAAAAGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (19 bp):
AACAAAAAAAAACAAAAAA
Found at i:17762757 original size:10 final size:10
Alignment explanation
Indices: 17762720--17762757 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
17762710 GAGAGCAAAC
*
17762720 AACAAAAAAA
1 AACAAAAAGA
*
17762730 AATAAAAA-A
1 AACAAAAAGA
17762739 AACAAAAAGA
1 AACAAAAAGA
17762749 AACAAAAAG
1 AACAAAAAG
17762758 GAAAAGAACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (10 bp):
AACAAAAAGA
Found at i:17763625 original size:31 final size:31
Alignment explanation
Indices: 17763572--17763631 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
17763562 ATTGAAATTT
* *
17763572 ATGAAATGTTTGGAGGACCAAATTGTAAAAG
1 ATGAAAAGTTTGGAGGACCAAATGGTAAAAG
**
17763603 ATGAAAAGTTTGGAGGGTCAAATGGTAAA
1 ATGAAAAGTTTGGAGGACCAAATGGTAAA
17763632 TAAGGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (31 bp):
ATGAAAAGTTTGGAGGACCAAATGGTAAAAG
Found at i:17763640 original size:31 final size:31
Alignment explanation
Indices: 17763574--17763640 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
17763564 TGAAATTTAT
* * *
17763574 GAAATGTTTGGAGGACCAAATTGTAAAAGAT
1 GAAAAGTTTGGAGGACCAAATGGTAAAAGAG
**
17763605 GAAAAGTTTGGAGGGTCAAATGGTAAATA-AG
1 GAAAAGTTTGGAGGACCAAATGGTAAA-AGAG
17763636 GAAAA
1 GAAAA
17763641 AATTTGAGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.22
Consensus pattern (31 bp):
GAAAAGTTTGGAGGACCAAATGGTAAAAGAG
Found at i:17766207 original size:25 final size:25
Alignment explanation
Indices: 17766139--17766218 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 25
17766129 GGGCTATTAG
* *
17766139 ACATGGCTAAGCCACGGTCTATACTTAT
1 ACATGGCTAAGCCACGG-GT-T-GTTAT
* *
17766167 ACGTGGC-AAGGTCACGGGTTGTTAT
1 ACATGGCTAA-GCCACGGGTTGTTAT
* *
17766192 ACATGGCTAAGCCACGAGTTGATAT
1 ACATGGCTAAGCCACGGGTTGTTAT
17766217 AC
1 AC
17766219 GTGGTTACGA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
25 24 0.57
26 3 0.07
27 3 0.07
28 12 0.29
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (25 bp):
ACATGGCTAAGCCACGGGTTGTTAT
Found at i:17770855 original size:17 final size:16
Alignment explanation
Indices: 17770835--17770876 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
17770825 TTACTAAGCC
17770835 TATTAAGTA-TATTATAT
1 TATTAA-TAGTATTA-AT
17770852 TATTAATAGTATTAAT
1 TATTAATAGTATTAAT
17770868 TATTTAATA
1 TA-TTAATA
17770877 ACAATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (16 bp):
TATTAATAGTATTAAT
Found at i:17771173 original size:16 final size:16
Alignment explanation
Indices: 17771152--17771185 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17771142 AGGTAAAATA
*
17771152 AAAGAAAAACAATGAT
1 AAAGAAAAAAAATGAT
17771168 AAAGAAAAAAAATGAT
1 AAAGAAAAAAAATGAT
17771184 AA
1 AA
17771186 TTGCATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAGAAAAAAAATGAT
Found at i:17777273 original size:148 final size:147
Alignment explanation
Indices: 17777005--17777300 Score: 531
Period size: 148 Copynumber: 2.0 Consensus size: 147
17776995 CAAGCAAATA
17777005 AAGGGTTTTCTCACTGTAGCGAAGAAGTAGTGTTGGTTTGCATATGCTTTGGTTTCTCAAGCATA
1 AAGGGTTTTCTCACTGTAGCGAAGAAGTAGTGTTGGTTTGCATATGCTTTGGTTTCTCAAGCATA
* * *
17777070 AATCCCACTACAGAAGTCCAATTGACATGATTTTTAGGTCACTTGCAATCTAAGAGACTGGGCTA
66 AATCCCACTACAGAAGTCCAATTGACATGATTTTTAGGTCACTTGAAATATAAGAGACTGAGCTA
17777135 CAACTTTAATGTTTATC
131 CAACTTTAATGTTTATC
17777152 NAAGGGTTTTCTCACTGTAGCGAAGAAGTAGTGTTGGTTTGCATATGCTTTGGTTTCTCAAGCAT
1 -AAGGGTTTTCTCACTGTAGCGAAGAAGTAGTGTTGGTTTGCATATGCTTTGGTTTCTCAAGCAT
17777217 AAATCCCACTACAGAAGTCCAATTGACATGATTTTTAGGTCA-TTAGAAATATAAGAGACTGAGC
65 AAATCCCACTACAGAAGTCCAATTGACATGATTTTTAGGTCACTT-GAAATATAAGAGACTGAGC
*
17777281 TACAACTTTGATGTTTATC
129 TACAACTTTAATGTTTATC
17777300 A
1 A
17777301 CTTTGCCCAT
Statistics
Matches: 143, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
147 3 0.02
148 140 0.98
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (147 bp):
AAGGGTTTTCTCACTGTAGCGAAGAAGTAGTGTTGGTTTGCATATGCTTTGGTTTCTCAAGCATA
AATCCCACTACAGAAGTCCAATTGACATGATTTTTAGGTCACTTGAAATATAAGAGACTGAGCTA
CAACTTTAATGTTTATC
Found at i:17777724 original size:38 final size:38
Alignment explanation
Indices: 17777673--17777748 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
17777663 CACACTCAGC
17777673 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
* ***
17777711 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
17777749 CACGCACTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.26
Consensus pattern (38 bp):
TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
Found at i:17777756 original size:35 final size:37
Alignment explanation
Indices: 17777679--17777759 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
17777669 CAGCTCATGT
*
17777679 GCACTCCCTACACGCACAAGGCAATATCATCATCATGT
1 GCACTCCCTACACGCACAAGGCAATATCATCATCA-GC
* ***
17777717 GCACTCCCTACTCGCACATTTCAATATCATCA-CA-C
1 GCACTCCCTACACGCACAAGGCAATATCATCATCAGC
17777752 GCACTCCC
1 GCACTCCC
17777760 ACCCTCATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
35 8 0.21
37 2 0.05
38 28 0.74
ACGTcount: A:0.28, C:0.40, G:0.10, T:0.22
Consensus pattern (37 bp):
GCACTCCCTACACGCACAAGGCAATATCATCATCAGC
Found at i:17778987 original size:29 final size:29
Alignment explanation
Indices: 17778945--17779007 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
17778935 GCCTTGGGTC
17778945 TACTTAGGCCTTAATATTGTTTGAAAGCA
1 TACTTAGGCCTTAATATTGTTTGAAAGCA
17778974 TACTTAGGCCTTAATATTGTTTGAAAGCA
1 TACTTAGGCCTTAATATTGTTTGAAAGCA
17779003 TACTT
1 TACTT
17779008 CTGGGGCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (29 bp):
TACTTAGGCCTTAATATTGTTTGAAAGCA
Found at i:17785518 original size:38 final size:38
Alignment explanation
Indices: 17785457--17785554 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 38
17785447 CACACTCAGC
17785457 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
* *** *** *
17785495 TCATGTGCACTCTCTATTTGCACATTTCAATATCATTA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
*
17785533 TCATGTGCACT-CCTACTCGCAC
1 TCATGTGCACTCCCTACACGCAC
17785555 TTTTCAATAT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
37 8 0.16
38 41 0.84
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.31
Consensus pattern (38 bp):
TCATGTGCACTCCCTACACGCACAAGGCAATATCATCA
Found at i:17786475 original size:22 final size:21
Alignment explanation
Indices: 17786447--17786490 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
17786437 AGGAAGAAGA
*
17786447 AGAAGAAGTAGCTAGAAAAATG
1 AGAAGAAGCAGCT-GAAAAATG
17786469 AGAAGAAGCAGCTGAAAAATG
1 AGAAGAAGCAGCTGAAAAATG
17786490 A
1 A
17786491 TATTTATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.55, C:0.07, G:0.27, T:0.11
Consensus pattern (21 bp):
AGAAGAAGCAGCTGAAAAATG
Found at i:17789888 original size:2 final size:2
Alignment explanation
Indices: 17789876--17789911 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17789866 ACCATATACC
*
17789876 AT AT AT GT 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
17789912 CAATCATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17790072 original size:42 final size:42
Alignment explanation
Indices: 17789953--17790078 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
17789943 CAACTCATAT
*
17789953 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCCAGGTCA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGGTCA
17789995 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGGTCA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGGTCA
* * * *
17790037 GCATCGACTTATGCACACTCCTACTC-CAACATAGCTGGGTCA
1 GCATCGGCTTATGCGCACTCCCACTCGC-ACATAGCTAGGTCA
17790079 ATATCATTAC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 1 0.01
42 77 0.99
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (42 bp):
GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGGTCA
Found at i:17798231 original size:55 final size:55
Alignment explanation
Indices: 17798159--17798318 Score: 266
Period size: 55 Copynumber: 2.9 Consensus size: 55
17798149 TGCCGGTGAT
*
17798159 GATGAGTGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGTTGATGACCGGTG
1 GATGA-TGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGTTGATGACCGGTG
* * *
17798215 GATGATGATTCAAGCTATGTGCAGTGTGAGAGTGCACATGAGTTGATGACTGGTG
1 GATGATGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGTTGATGACCGGTG
*
17798270 GATGATGATTCCAGCTATGTACAGTGTGGGAGTGCACATGAGTTGATGA
1 GATGATGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGTTGATGA
17798319 GCCAGTGGTT
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 92 0.95
56 5 0.05
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.28
Consensus pattern (55 bp):
GATGATGATTCCAGCTATGTGCAGTGTGGGAGTGCACATGAGTTGATGACCGGTG
Found at i:17806549 original size:43 final size:43
Alignment explanation
Indices: 17806479--17806597 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
17806469 GTAATTATAT
* * * *
17806479 TGACTCGGCTATGTGTGAGTAAGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
* *
17806522 TGACCCGGTTATGTGCGAGTAGGGAGTGCACATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
17806565 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
17806598 GAGCTGGTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:17820868 original size:19 final size:21
Alignment explanation
Indices: 17820830--17820869 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
17820820 TCACTCATGC
*
17820830 CACATTGTACATTAAATCAAG
1 CACATTGTACAATAAATCAAG
17820851 CACATTG-ACAAT-AATCAAG
1 CACATTGTACAATAAATCAAG
17820870 TTTTCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (21 bp):
CACATTGTACAATAAATCAAG
Found at i:17821115 original size:84 final size:83
Alignment explanation
Indices: 17821020--17821268 Score: 385
Period size: 82 Copynumber: 3.0 Consensus size: 83
17821010 ATAGCCAAAG
*
17821020 TCATCATGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATCATGCAC
1 TCATCATGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
17821085 ATGGCATATATCATCATCA
66 ATGGCA-ATATCATCATCA
* * * *
17821104 TCATCATGTGCACCCCCACACCGCGCACAACAAATGCCATCATGTGCTCCCCCCCACATCGTACA
1 TCATCATGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCT-CCCCCCACATCGTGCA
*
17821169 CAGGGC-ATAT-ATCATCA
65 CATGGCAATATCATCATCA
*
17821186 TCATCATGTGCACCCCCACATCACACACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
1 TCATCATGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
*
17821251 ATAGGCAATCTCATCATC
66 AT-GGCAATATCATCATC
17821269 CACACTCCCT
Statistics
Matches: 148, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
81 17 0.11
82 54 0.36
83 7 0.05
84 51 0.34
85 19 0.13
ACGTcount: A:0.28, C:0.39, G:0.12, T:0.21
Consensus pattern (83 bp):
TCATCATGTGCACCCCCACATCACGCACAACTAATGCCATCATGTGCTCCCCCCACATCGTGCAC
ATGGCAATATCATCATCA
Found at i:17821374 original size:2 final size:2
Alignment explanation
Indices: 17821367--17821396 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17821357 AATACACAAC
17821367 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
17821397 CAACATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17828062 original size:22 final size:22
Alignment explanation
Indices: 17828037--17828081 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17828027 GTGTGTTAAA
17828037 TAGTTTGTAATATAAAGAAGTC
1 TAGTTTGTAATATAAAGAAGTC
17828059 TAGTTTGTAATATAAAGAAGTC
1 TAGTTTGTAATATAAAGAAGTC
17828081 T
1 T
17828082 TACTCAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
TAGTTTGTAATATAAAGAAGTC
Found at i:17828116 original size:17 final size:17
Alignment explanation
Indices: 17828091--17828143 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
17828081 TTACTCAAGT
* *
17828091 GTGATTATTCAGATTAA
1 GTGACTATTCAAATTAA
17828108 GTGACTATTCAAATTAAA
1 GTGACTATTCAAATT-AA
*
17828126 GTTACTATTCAAATTAA
1 GTGACTATTCAAATTAA
17828143 G
1 G
17828144 ACATGACTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (17 bp):
GTGACTATTCAAATTAA
Found at i:17828132 original size:18 final size:18
Alignment explanation
Indices: 17828091--17828142 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
17828081 TTACTCAAGT
* *
17828091 GTGATTATTCAGATT-AA
1 GTGACTATTCAAATTAAA
17828108 GTGACTATTCAAATTAAA
1 GTGACTATTCAAATTAAA
*
17828126 GTTACTATTCAAATTAA
1 GTGACTATTCAAATTAA
17828143 GACATGACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
GTGACTATTCAAATTAAA
Found at i:17837319 original size:17 final size:17
Alignment explanation
Indices: 17837289--17837341 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
17837279 TTATTCAGGT
*
17837289 GTGATTATTCAAATTAA
1 GTGACTATTCAAATTAA
17837306 GTGACTACTT-AAATTAAA
1 GTGACTA-TTCAAATT-AA
*
17837324 GTTACTATTCAAATTAA
1 GTGACTATTCAAATTAA
17837341 G
1 G
17837342 ACATGACTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (17 bp):
GTGACTATTCAAATTAA
Found at i:17837330 original size:18 final size:18
Alignment explanation
Indices: 17837289--17837340 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
17837279 TTATTCAGGT
*
17837289 GTGATTATTCAAATT-AA
1 GTGACTATTCAAATTAAA
17837306 GTGACTACTT-AAATTAAA
1 GTGACTA-TTCAAATTAAA
*
17837324 GTTACTATTCAAATTAA
1 GTGACTATTCAAATTAA
17837341 GACATGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (18 bp):
GTGACTATTCAAATTAAA
Found at i:17839467 original size:2 final size:2
Alignment explanation
Indices: 17839460--17839501 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17839450 TTGTAGCAAT
17839460 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
17839502 ATAAAAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17843465 original size:27 final size:27
Alignment explanation
Indices: 17843434--17843563 Score: 138
Period size: 27 Copynumber: 4.9 Consensus size: 27
17843424 GTGCTTCTAC
*
17843434 GCTTGGAACGCCCCTAAGCACTTTTGT
1 GCTTGGAACGCCCCTAGGCACTTTTGT
* *
17843461 GCTTGGAACACCCCTAGGCACTTCTGT
1 GCTTGGAACGCCCCTAGGCACTTTTGT
*
17843488 GCTTGGAACGCCCCTAGGC-GTTTATGT
1 GCTTGGAACGCCCCTAGGCACTTT-TGT
** * * *
17843515 GCTTGGAATTCCCAT-GGCACTTCTCT
1 GCTTGGAACGCCCCTAGGCACTTTTGT
* *
17843541 GCTTGGAATGCTCCTAGGCACTT
1 GCTTGGAACGCCCCTAGGCACTT
17843564 CCACGCTTGG
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
26 19 0.22
27 66 0.78
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (27 bp):
GCTTGGAACGCCCCTAGGCACTTTTGT
Found at i:17843557 original size:53 final size:54
Alignment explanation
Indices: 17843434--17843559 Score: 157
Period size: 54 Copynumber: 2.4 Consensus size: 54
17843424 GTGCTTCTAC
* * * *
17843434 GCTTGGAACGCCCCTAAGCACTTT-TGTGCTTGGAACACCCCTAGGCACTTCTGT
1 GCTTGGAACGCCCCTAGGC-GTTTATGTGCTTGGAACACCCATAGGCACTTCTCT
**
17843488 GCTTGGAACGCCCCTAGGCGTTTATGTGCTTGGAATTCCCAT-GGCACTTCTCT
1 GCTTGGAACGCCCCTAGGCGTTTATGTGCTTGGAACACCCATAGGCACTTCTCT
* *
17843541 GCTTGGAATGCTCCTAGGC
1 GCTTGGAACGCCCCTAGGC
17843560 ACTTCCACGC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
53 30 0.48
54 33 0.52
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29
Consensus pattern (54 bp):
GCTTGGAACGCCCCTAGGCGTTTATGTGCTTGGAACACCCATAGGCACTTCTCT
Found at i:17843591 original size:53 final size:53
Alignment explanation
Indices: 17843534--17843634 Score: 121
Period size: 53 Copynumber: 1.9 Consensus size: 53
17843524 TCCCATGGCA
* ** *
17843534 CTTCTCTGCTTGGAATGCTCCTAGGCACTTCCACGCTTGGAACACCCTGGGAG
1 CTTCTCTGCTTAGAACACCCCTAGGCACTTCCACGCTTGGAACACCCTGGGAG
* * ** *
17843587 CTTCTGTGCTTAGAACACCCCTGGGTGCTTCTACGCTTGGAACACCCT
1 CTTCTCTGCTTAGAACACCCCTAGGCACTTCCACGCTTGGAACACCCT
17843635 AGGTGTTTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 39 1.00
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.28
Consensus pattern (53 bp):
CTTCTCTGCTTAGAACACCCCTAGGCACTTCCACGCTTGGAACACCCTGGGAG
Found at i:17843616 original size:27 final size:26
Alignment explanation
Indices: 17843567--17843670 Score: 118
Period size: 27 Copynumber: 3.9 Consensus size: 26
17843557 GGCACTTCCA
*
17843567 CGCTTGGAACACCCTGGGAGCTTCTG
1 CGCTTGGAACACCCTGGGTGCTTCTG
* * *
17843593 TGCTTAGAACACCCCTGGGTGCTTCTA
1 CGCTTGGAACA-CCCTGGGTGCTTCTG
* *
17843620 CGCTTGGAACACCCTAGGTGTTTCTG
1 CGCTTGGAACACCCTGGGTGCTTCTG
* *
17843646 CGCTTGAAACACCCCTGAGTGCTTC
1 CGCTTGGAACA-CCCTGGGTGCTTC
17843671 CATGCTTGGA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
26 31 0.49
27 32 0.51
ACGTcount: A:0.17, C:0.31, G:0.25, T:0.27
Consensus pattern (26 bp):
CGCTTGGAACACCCTGGGTGCTTCTG
Found at i:17843645 original size:53 final size:53
Alignment explanation
Indices: 17843561--17843688 Score: 168
Period size: 53 Copynumber: 2.4 Consensus size: 53
17843551 CTCCTAGGCA
* * *
17843561 CTTCCACGCTTGGAACACCCTGGGAGCTTCTGTGCTT-AGAACACCCCTGGGTG
1 CTTCCACGCTTGGAACACCCTAGGAGCTTCTGCGCTTGA-AACACCCCTGAGTG
* * *
17843614 CTTCTACGCTTGGAACACCCTAGGTGTTTCTGCGCTTGAAACACCCCTGAGTG
1 CTTCCACGCTTGGAACACCCTAGGAGCTTCTGCGCTTGAAACACCCCTGAGTG
* *
17843667 CTTCCATGCTTGGAGCACCCTA
1 CTTCCACGCTTGGAACACCCTA
17843689 AATGCTTCCA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
53 64 0.98
54 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.23, T:0.27
Consensus pattern (53 bp):
CTTCCACGCTTGGAACACCCTAGGAGCTTCTGCGCTTGAAACACCCCTGAGTG
Found at i:17843751 original size:26 final size:26
Alignment explanation
Indices: 17843561--17843752 Score: 136
Period size: 26 Copynumber: 7.3 Consensus size: 26
17843551 CTCCTAGGCA
* * *
17843561 CTTCCACGCTTGGAACACCCTGGGAG
1 CTTCCATGCTTGGAACACCCTAGGTG
** * *
17843587 CTTCTGTGCTTAGAACACCCCTGGGTG
1 CTTCCATGCTTGGAACA-CCCTAGGTG
* *
17843614 CTTCTACGCTTGGAACACCCTAGGTG
1 CTTCCATGCTTGGAACACCCTAGGTG
* *** *
17843640 TTTCTGCGCTTGAAACACCCCT-GAGTG
1 CTTCCATGCTTGGAACA-CCCTAG-GTG
* **
17843667 CTTCCATGCTTGGAGCACCCTAAATG
1 CTTCCATGCTTGGAACACCCTAGGTG
* * *
17843693 CTTCCA-ACTTGGAACACCCTTGGGCG
1 CTTCCATGCTTGGAACACCC-TAGGTG
* *
17843719 CTACCATGCTTGGAACACCTTAGGTG
1 CTTCCATGCTTGGAACACCCTAGGTG
17843745 CTTCCATG
1 CTTCCATG
17843753 GAACACCCCT
Statistics
Matches: 128, Mismatches: 32, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
25 11 0.09
26 66 0.52
27 51 0.40
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (26 bp):
CTTCCATGCTTGGAACACCCTAGGTG
Found at i:17844580 original size:25 final size:25
Alignment explanation
Indices: 17844533--17844581 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
17844523 CTTAATTATG
**
17844533 AAATAAGTAGAGATATATGAGGAAA
1 AAATAAGTAGAGATATACAAGGAAA
17844558 AAATAAGTAGAGATATACAAGGAA
1 AAATAAGTAGAGATATACAAGGAA
17844582 GAGCAATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.18
Consensus pattern (25 bp):
AAATAAGTAGAGATATACAAGGAAA
Found at i:17863420 original size:21 final size:21
Alignment explanation
Indices: 17863396--17863438 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17863386 TCCCCGTTGG
*
17863396 CTTCTTCTTTCT-TTCTTTCTC
1 CTTC-TCTTTCTGTCCTTTCTC
17863417 CTTCTCTTTCTGTCCTTTCTC
1 CTTCTCTTTCTGTCCTTTCTC
17863438 C
1 C
17863439 CTACGGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.60
Consensus pattern (21 bp):
CTTCTCTTTCTGTCCTTTCTC
Found at i:17863613 original size:17 final size:17
Alignment explanation
Indices: 17863581--17863615 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17863571 CTCTCTCTTC
17863581 TTTTTCTTCCTCTTTTT
1 TTTTTCTTCCTCTTTTT
*
17863598 TTTTTCTTGCT-TTTTT
1 TTTTTCTTCCTCTTTTT
17863614 TT
1 TT
17863616 GGGGTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTCTTCCTCTTTTT
Found at i:17863881 original size:18 final size:21
Alignment explanation
Indices: 17863860--17863900 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
17863850 AATTATTTTC
17863860 TTTA-TTTATTTT-TTAT-AT
1 TTTATTTTATTTTATTATCAT
17863878 TTTATTTTATTTTATTATCAT
1 TTTATTTTATTTTATTATCAT
17863899 TT
1 TT
17863901 AAATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 4 0.20
21 4 0.20
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTTTATTTTATTATCAT
Found at i:17863895 original size:27 final size:28
Alignment explanation
Indices: 17863852--17863918 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
17863842 TTTTTTTAAA
* ** *
17863852 TTATTTT-CTTTATTTATTTTTTATATT
1 TTATTTTATTTTATTTATCATTTAAATT
17863879 TTATTTTATTTTA-TTATCATTTAAATT
1 TTATTTTATTTTATTTATCATTTAAATT
*
17863906 TTTTATTTATTTT
1 TTAT-TTTATTTT
17863919 TTAGGTGTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (28 bp):
TTATTTTATTTTATTTATCATTTAAATT
Found at i:17876835 original size:39 final size:39
Alignment explanation
Indices: 17876792--17876908 Score: 115
Period size: 39 Copynumber: 3.2 Consensus size: 39
17876782 ACGGGAGTTA
17876792 ATGATGGTGATGTGGATGCTGCTACTAGAGTTGGTGGTG
1 ATGATGGTGATGTGGATGCTGCTACTAGAGTTGGTGGTG
* *
17876831 ATGAT-GTGGATATGGATGCTGCTAC-AGGAG-T--T--AG
1 ATGATGGT-GATGTGGATGCTGCTACTA-GAGTTGGTGGTG
* * *
17876865 A-AATGATGATGTGGATGCTGCTACTGGAGTTGGTGGTG
1 ATGATGGTGATGTGGATGCTGCTACTAGAGTTGGTGGTG
17876903 ATGATG
1 ATGATG
17876909 TGAATGCCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
33 21 0.35
34 4 0.07
36 2 0.03
38 6 0.10
39 27 0.45
ACGTcount: A:0.22, C:0.08, G:0.38, T:0.32
Consensus pattern (39 bp):
ATGATGGTGATGTGGATGCTGCTACTAGAGTTGGTGGTG
Found at i:17876836 original size:33 final size:33
Alignment explanation
Indices: 17876799--17876915 Score: 110
Period size: 33 Copynumber: 3.4 Consensus size: 33
17876789 TTAATGATGG
17876799 TGATGTGGATGCTGCTACTAGAGTTGGTGGTGA
1 TGATGTGGATGCTGCTACTAGAGTTGGTGGTGA
* ***
17876832 TGATGTGGATATGGATGCTGCTAC-AGGAGTTAGAAATGA
1 TGA--T-G---TGGATGCTGCTACTA-GAGTTGGTGGTGA
*
17876871 TGATGTGGATGCTGCTACTGGAGTTGGTGGTGA
1 TGATGTGGATGCTGCTACTAGAGTTGGTGGTGA
*
17876904 TGATGTGAATGC
1 TGATGTGGATGC
17876916 CATTAACCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
33 36 0.55
35 1 0.02
36 2 0.03
37 1 0.02
38 1 0.02
39 25 0.38
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.32
Consensus pattern (33 bp):
TGATGTGGATGCTGCTACTAGAGTTGGTGGTGA
Found at i:17877177 original size:39 final size:39
Alignment explanation
Indices: 17877069--17877192 Score: 113
Period size: 39 Copynumber: 3.2 Consensus size: 39
17877059 TCGCAATATC
* * * * *
17877069 TCTTCTTTCGAGGGTGTTCTGAATGTTAGTCGCGATGCT
1 TCTTCTTTTGAGGGTGTTCTGAATATTACTTGCAATGCT
* * * *
17877108 TCTTCTCTTAAGGGTGTTCTGAATACTACTTGCAATGGT
1 TCTTCTTTTGAGGGTGTTCTGAATATTACTTGCAATGCT
* * * * *
17877147 TCTTCTTTTGGGGGTGTTCCGAATTTTACTTACAATTCT
1 TCTTCTTTTGAGGGTGTTCTGAATATTACTTGCAATGCT
*
17877186 TCCTCTT
1 TCTTCTT
17877193 CTCTTAGAGG
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.44
Consensus pattern (39 bp):
TCTTCTTTTGAGGGTGTTCTGAATATTACTTGCAATGCT
Found at i:17878207 original size:15 final size:15
Alignment explanation
Indices: 17878187--17878217 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17878177 TGCGGTTAAA
17878187 AATGAATTTACTTTG
1 AATGAATTTACTTTG
*
17878202 AATGAATTTATTTTG
1 AATGAATTTACTTTG
17878217 A
1 A
17878218 CATATCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (15 bp):
AATGAATTTACTTTG
Found at i:17884005 original size:43 final size:43
Alignment explanation
Indices: 17883946--17884162 Score: 233
Period size: 43 Copynumber: 5.0 Consensus size: 43
17883936 TTGTGTGATA
* *
17883946 ATGATGACCCAACTATGTACGGTGTGGGAGTGCAAATGAGCTG
1 ATGATGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
17883989 ATGATGACCCAACTATGTGCGGTGTGGGAGTGCGCATGAGTTG
1 ATGATGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTG
*** *
17884032 ATGATGACCTGGCTATGTGCGAGT-AGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCG-GTGTGGGAGTGCACATGAGCTG
* * *
17884075 AGTG-TGGCGGCAACTATGTGCGGTGTGGGAGTGCACATGAGTTG
1 A-TGATGAC-CCAACTATGTGCGGTGTGGGAGTGCACATGAGCTG
* *** *
17884119 ATGTTGACCTGGCTATGTGCGAGT-AGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCG-GTGTGGGAGTGCACATGAGCTG
17884162 A
1 A
17884163 GTGTGACGAG
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
43 108 0.75
44 36 0.25
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (43 bp):
ATGATGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGCTG
Found at i:17884118 original size:87 final size:86
Alignment explanation
Indices: 17883971--17884169 Score: 328
Period size: 87 Copynumber: 2.3 Consensus size: 86
17883961 TGTACGGTGT
* *
17883971 GGGAGTGCAAATGAGCTGA-TGATGACCCAACTATGTGCGGTGTGGGAGTGCGCATGAGTTGATG
1 GGGAGTGCACATGAGCTGAGTG-TGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGTTGATG
17884035 ATGACCTGGCTATGTGCGAGTA
65 ATGACCTGGCTATGTGCGAGTA
* *
17884057 GGGAGTGCACATGAGCTGAGTGTGGCGGCAACTATGTGCGGTGTGGGAGTGCACATGAGTTGATG
1 GGGAGTGCACATGAGCTGAGTGTGAC-CCAACTATGTGCGGTGTGGGAGTGCACATGAGTTGATG
*
17884122 TTGACCTGGCTATGTGCGAGTA
65 ATGACCTGGCTATGTGCGAGTA
17884144 GGGAGTGCACATGAGCTGAGTGTGAC
1 GGGAGTGCACATGAGCTGAGTGTGAC
17884170 GAGATGTTAT
Statistics
Matches: 105, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
86 21 0.20
87 84 0.80
ACGTcount: A:0.22, C:0.15, G:0.39, T:0.24
Consensus pattern (86 bp):
GGGAGTGCACATGAGCTGAGTGTGACCCAACTATGTGCGGTGTGGGAGTGCACATGAGTTGATGA
TGACCTGGCTATGTGCGAGTA
Found at i:17884437 original size:22 final size:22
Alignment explanation
Indices: 17884412--17884454 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17884402 TTGCAGCGTG
17884412 AATGGATTCTCGCTACAGCGAA
1 AATGGATTCTCGCTACAGCGAA
17884434 AATGGATTCTCGCTACAGCGA
1 AATGGATTCTCGCTACAGCGA
17884455 GAAACTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (22 bp):
AATGGATTCTCGCTACAGCGAA
Found at i:17885303 original size:53 final size:53
Alignment explanation
Indices: 17885240--17885345 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
17885230 ATTCACCATT
17885240 GAGAATTACAACACATGGTTTTAAAGATGATGGATGGAATGAGGAACAGGATC
1 GAGAATTACAACACATGGTTTTAAAGATGATGGATGGAATGAGGAACAGGATC
*
17885293 GAGAATTACAACACATGGTTTTAAAGATGATGGATGGAATGAGGAATAGGATC
1 GAGAATTACAACACATGGTTTTAAAGATGATGGATGGAATGAGGAACAGGATC
17885346 TCATAAAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (53 bp):
GAGAATTACAACACATGGTTTTAAAGATGATGGATGGAATGAGGAACAGGATC
Found at i:17886900 original size:27 final size:27
Alignment explanation
Indices: 17886870--17887020 Score: 92
Period size: 27 Copynumber: 5.6 Consensus size: 27
17886860 CTCTTTGGGT
* *
17886870 GCTTGTACGCTTAGAACGCCCCTAGGC
1 GCTTCTACGCTTGGAACGCCCCTAGGC
** * *
17886897 GCTTCTGTGCTTGGAATGCCCCTAGGT
1 GCTTCTACGCTTGGAACGCCCCTAGGC
* *
17886924 GCTTCTACTCTTGGAACACCCCT-GG-
1 GCTTCTACGCTTGGAACGCCCCTAGGC
* * * *
17886949 GCTTTTATGTGCTTGGAATGCCCCTAGGT
1 GCTTCTA--CGCTTGGAACGCCCCTAGGC
* * * *
17886978 GCTTCCACACTTGGAACACCTC-AGGC
1 GCTTCTACGCTTGGAACGCCCCTAGGC
* * *
17887004 ACTTTTACACTTGGAAC
1 GCTTCTACGCTTGGAAC
17887021 ATCCTTGGGT
Statistics
Matches: 93, Mismatches: 27, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
25 6 0.06
26 19 0.20
27 61 0.66
28 2 0.02
29 5 0.05
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.29
Consensus pattern (27 bp):
GCTTCTACGCTTGGAACGCCCCTAGGC
Found at i:17887062 original size:27 final size:27
Alignment explanation
Indices: 17887028--17887131 Score: 113
Period size: 27 Copynumber: 3.9 Consensus size: 27
17887018 AACATCCTTG
17887028 GGTG-TTTCTGTGCTTAGAACACCCCTA
1 GGTGCTTT-TGTGCTTAGAACACCCCTA
* * * * * *
17887055 GG-CCTTTCTGCGCTTTGAGCACCTCTG
1 GGTGCTTT-TGTGCTTAGAACACCCCTA
*
17887082 GGTGCTTTTGTGCTTGGAACACCCCTA
1 GGTGCTTTTGTGCTTAGAACACCCCTA
17887109 GGTGCTTTTGTGCTTAGAACACC
1 GGTGCTTTTGTGCTTAGAACACC
17887132 TCAAACACTT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
27 58 0.94
28 4 0.06
ACGTcount: A:0.14, C:0.27, G:0.25, T:0.34
Consensus pattern (27 bp):
GGTGCTTTTGTGCTTAGAACACCCCTA
Found at i:17887132 original size:54 final size:54
Alignment explanation
Indices: 17887017--17887133 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
17887007 TTTACACTTG
*
17887017 GAACATCCT-TGGGTGTTTCTGTGCTTAGAACACCCCTAGGCCTTTCTGCGCTTT
1 GAACA-CCTCTGGGTGTTTCTGTGCTTAGAACACCCCTAGGCCTTTCTGCGCTTA
* * * *
17887071 GAGCACCTCTGGGTGCTTT-TGTGCTTGGAACACCCCTAGGTGCTTT-TGTGCTTA
1 GAACACCTCTGGGTG-TTTCTGTGCTTAGAACACCCCTAGG-CCTTTCTGCGCTTA
17887125 GAACACCTC
1 GAACACCTC
17887134 AAACACTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
53 3 0.06
54 44 0.81
55 7 0.13
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.33
Consensus pattern (54 bp):
GAACACCTCTGGGTGTTTCTGTGCTTAGAACACCCCTAGGCCTTTCTGCGCTTA
Found at i:17887215 original size:26 final size:26
Alignment explanation
Indices: 17887196--17887256 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
17887186 AGGCGGTTTC
17887196 AGCTTGGAATACCCCTAGGCTCTTCT
1 AGCTTGGAATACCCCTAGGCTCTTCT
17887222 AGCTTGGAATACCCCTAGGCTCTTCT
1 AGCTTGGAATACCCCTAGGCTCTTCT
17887248 AGCTTGGAA
1 AGCTTGGAA
17887257 CATCCTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (26 bp):
AGCTTGGAATACCCCTAGGCTCTTCT
Found at i:17888421 original size:22 final size:22
Alignment explanation
Indices: 17888372--17888421 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
17888362 CTCGCGGAAT
*
17888372 AGAATAAAATAGGTCTTTTATG
1 AGAATAAAATAGGTATTTTATG
* *
17888394 -GAAATAGAATAGGTATTTTGTG
1 AG-AATAAAATAGGTATTTTATG
17888416 AGAATA
1 AGAATA
17888422 TATAGAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.04
22 21 0.91
23 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (22 bp):
AGAATAAAATAGGTATTTTATG
Found at i:17890323 original size:2 final size:2
Alignment explanation
Indices: 17890316--17890345 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17890306 ACAGAATGGA
17890316 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
17890346 CTCAATGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17890814 original size:107 final size:107
Alignment explanation
Indices: 17890646--17890855 Score: 375
Period size: 107 Copynumber: 2.0 Consensus size: 107
17890636 AAAGCAATGA
* *
17890646 AAAAAAGACAAAGAGTTATCGGATAGCTGCATTAAAATAATATGGCACCTACCCCAGAAAAGAAA
1 AAAAAAGACAAAGAGTCATCGGATAGCGGCATTAAAATAATATGGCACCTACCCCAGAAAAGAAA
*
17890711 AAGAATTGTTGCAGAGAAAGACTCATCGCTCGTCAATGTAAT
66 AAGAATTGTTGCAGAGAAAGACTCATCACTCGTCAATGTAAT
*
17890753 AAAAAAGACAAAGAGTCATCGGATAGCGGCATTAAAATAATATGGCACGTACCCCAGAAAAGAAA
1 AAAAAAGACAAAGAGTCATCGGATAGCGGCATTAAAATAATATGGCACCTACCCCAGAAAAGAAA
*
17890818 AAGAATTGTTGTAGAGAAAGACTCATCACTCGTCAATG
66 AAGAATTGTTGCAGAGAAAGACTCATCACTCGTCAATG
17890856 CAAAAAGATT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 98 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (107 bp):
AAAAAAGACAAAGAGTCATCGGATAGCGGCATTAAAATAATATGGCACCTACCCCAGAAAAGAAA
AAGAATTGTTGCAGAGAAAGACTCATCACTCGTCAATGTAAT
Found at i:17895740 original size:4 final size:4
Alignment explanation
Indices: 17895731--17895858 Score: 148
Period size: 4 Copynumber: 32.0 Consensus size: 4
17895721 TATTTTATCC
* * * *
17895731 ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT ATAT ATAT ATAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
17895779 GTAT GTAT ATAT ATAT ATAT ATGT ATGT ATAT ATAT ATAT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
17895827 ATGT ATAT ATAT ATAT ATAT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
17895859 GTAAAACCAT
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 114 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:17895764 original size:28 final size:28
Alignment explanation
Indices: 17895733--17895856 Score: 170
Period size: 28 Copynumber: 4.6 Consensus size: 28
17895723 TTTTATCCAT
* *
17895733 ATATATATATATATATATGTATGTATGT
1 ATATATATATATATGTATGTATGTATAT
17895761 ATATATATATATATGTATGTATG--TAT
1 ATATATATATATATGTATGTATGTATAT
17895787 ATATATATATATATGTATGTA--TA--T
1 ATATATATATATATGTATGTATGTATAT
*
17895811 ATATATATATATATGTATGTATATATAT
1 ATATATATATATATGTATGTATGTATAT
*
17895839 ATATATATATGTATGTAT
1 ATATATATATATATGTAT
17895857 ATGTAAAACC
Statistics
Matches: 87, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
24 22 0.25
26 25 0.29
28 40 0.46
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (28 bp):
ATATATATATATATGTATGTATGTATAT
Found at i:17895768 original size:24 final size:24
Alignment explanation
Indices: 17895732--17895858 Score: 227
Period size: 24 Copynumber: 5.2 Consensus size: 24
17895722 ATTTTATCCA
17895732 TATATATATATATATATATGTATG
1 TATATATATATATATATATGTATG
*
17895756 TATGTATATATATATATATGTATG
1 TATATATATATATATATATGTATG
17895780 TATGTATATATATATATATATGTATG
1 TA--TATATATATATATATATGTATG
17895806 TATATATATATATATATATGTATG
1 TATATATATATATATATATGTATG
17895830 TATATATATATATATATATGTATG
1 TATATATATATATATATATGTATG
17895854 TATAT
1 TATAT
17895859 GTAAAACCAT
Statistics
Matches: 99, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
24 76 0.77
26 23 0.23
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.50
Consensus pattern (24 bp):
TATATATATATATATATATGTATG
Found at i:17909394 original size:20 final size:20
Alignment explanation
Indices: 17909369--17909406 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17909359 CGCTTTAATC
*
17909369 TTGTTAATCATATCAATCAT
1 TTGTTAAGCATATCAATCAT
17909389 TTGTTAAGCATATCAATC
1 TTGTTAAGCATATCAATC
17909407 GTGTTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (20 bp):
TTGTTAAGCATATCAATCAT
Found at i:17910461 original size:18 final size:18
Alignment explanation
Indices: 17910438--17910484 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 18
17910428 TCTCATTTTC
17910438 ACGATTAACACGATTGAT
1 ACGATTAACACGATTGAT
17910456 ACGATTAACACACGATTGAT
1 ACGATT-A-ACACGATTGAT
17910476 ACGATTAAC
1 ACGATTAAC
17910485 TTGATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.30
19 2 0.07
20 17 0.63
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (18 bp):
ACGATTAACACGATTGAT
Found at i:17910470 original size:20 final size:20
Alignment explanation
Indices: 17910445--17910484 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17910435 TTCACGATTA
17910445 ACACGATTGATACGATTAAC
1 ACACGATTGATACGATTAAC
17910465 ACACGATTGATACGATTAAC
1 ACACGATTGATACGATTAAC
17910485 TTGATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (20 bp):
ACACGATTGATACGATTAAC
Found at i:17917331 original size:17 final size:17
Alignment explanation
Indices: 17917309--17917346 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
17917299 TTATTTTACT
*
17917309 AAATTAAAATGAATTTA
1 AAATTAAAATAAATTTA
17917326 AAATTAAAATAAATTTA
1 AAATTAAAATAAATTTA
17917343 AAAT
1 AAAT
17917347 ACAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATTAAAATAAATTTA
Found at i:17920773 original size:55 final size:55
Alignment explanation
Indices: 17920656--17920866 Score: 332
Period size: 55 Copynumber: 3.8 Consensus size: 55
17920646 ACAACCGTCG
* * * * *
17920656 GTCATCAGCTCAAGTGCACTCTCACACCGCACGATAGCTGGAATCATCATCCTCCG
1 GTCATCAGCTCATGTGCACTCCCACACCGCAC-ATAGCTGGAATCATCACCCACCA
*
17920712 GTCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCACCCACCA
1 GTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCACCA
* *
17920767 GTCATCAGCTCATGTGCACTCCCACACCGCACGTAGCTGGAATCATCACCCACTA
1 GTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCACCA
*
17920822 GTCATTAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
1 GTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
17920867 CCCGTCATCA
Statistics
Matches: 144, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 115 0.80
56 29 0.20
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (55 bp):
GTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCACCA
Found at i:17920887 original size:49 final size:53
Alignment explanation
Indices: 17920669--17920896 Score: 225
Period size: 55 Copynumber: 4.2 Consensus size: 53
17920659 ATCAGCTCAA
* * * *
17920669 GTGCACTCTCACACCGCACGATAGCTGGAATCATCATCCTC-CGGTCATCAGCTCAT
1 GTGCACTCCCACACCGCAC-ATAGCTGGAA-CATCA-CC-CACAGTCATCACCGCAT
* * *
17920725 GTGCACTCCCACACTGCACATAGCTGGAATCATCACCCACCAGTCATCAGCTCAT
1 GTGCACTCCCACACCGCACATAGCTGGAA-CATCACCCA-CAGTCATCACCGCAT
* * * *
17920780 GTGCACTCCCACACCGCACGTAGCTGGAATCATCACCCACTAGTCATTAGCTCAT
1 GTGCACTCCCACACCGCACATAGCTGGAA-CATCACCCAC-AGTCATCACCGCAT
17920835 GTGCACTCCCACACCGCACATAGCTGG-A-ATCA-CC-C-GTCATCACCGGCAT
1 GTGCACTCCCACACCGCACATAGCTGGAACATCACCCACAGTCATCACC-GCAT
*
17920884 GTGCACTCTCACA
1 GTGCACTCCCACA
17920897 TCACACATGC
Statistics
Matches: 157, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
48 7 0.04
49 15 0.10
50 1 0.01
51 2 0.01
52 4 0.03
53 1 0.01
54 4 0.03
55 106 0.68
56 17 0.11
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.21
Consensus pattern (53 bp):
GTGCACTCCCACACCGCACATAGCTGGAACATCACCCACAGTCATCACCGCAT
Found at i:17921830 original size:14 final size:15
Alignment explanation
Indices: 17921796--17921839 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
17921786 GAAGAAGTAA
17921796 GAAAAGAAAAGAAAG
1 GAAAAGAAAAGAAAG
*
17921811 GAAAAGAAAA-CAAG
1 GAAAAGAAAAGAAAG
*
17921825 GGAAAGAAAATGAAA
1 GAAAAGAAAA-GAAA
17921840 AATCTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 12 0.50
15 10 0.42
16 2 0.08
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.02
Consensus pattern (15 bp):
GAAAAGAAAAGAAAG
Found at i:17927488 original size:25 final size:25
Alignment explanation
Indices: 17927442--17927491 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17927432 GATATTCAAT
* * * *
17927442 TATCAACATTCGAATAATATAAACA
1 TATCAACATCCCAACAACATAAACA
17927467 TATCAACATCCCAACAACATAAACA
1 TATCAACATCCCAACAACATAAACA
17927492 ACAAAGTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.22
Consensus pattern (25 bp):
TATCAACATCCCAACAACATAAACA
Found at i:17937732 original size:30 final size:29
Alignment explanation
Indices: 17937681--17937815 Score: 132
Period size: 30 Copynumber: 4.6 Consensus size: 29
17937671 TTAAGACAAC
*
17937681 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
*
17937711 ATCTTGTCTAAATTGAGAC--AAATATGTTT
1 -TCTTGTCTAAATTAAGACAAAAATAT-TTT
* * * *
17937740 TCTTGCCCAGATTAAAACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAAAATATTTT
*
17937770 TCTTGTCTTAAATTAAGACAAACATATTTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
*
17937800 T-TTGTCTTAATTAAGA
1 TCTTGTCTAAATTAAGA
17937816 TAAACATGTT
Statistics
Matches: 86, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
28 28 0.33
29 8 0.09
30 29 0.34
31 21 0.24
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAAATATTTT
Found at i:17937813 original size:59 final size:58
Alignment explanation
Indices: 17937681--17937813 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 58
17937671 TTAAGACAAC
* * * *
17937681 TCTTGTCTTTAATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTC-TTAATTAAAACAAAAATATTTTATCTTGTCTAAATTAAGACAAACATATTT
**
17937740 TCTTG-CCCAGATTAAAACAAAAAATATTTT-TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTCTTA-ATTAAAAC-AAAAATATTTTATCTTGTC-TAAATTAAGACAAACATATTT
*
17937799 TTTTGTCTTAATTAA
1 TCTTGTCTTAATTAA
17937814 GATAAACATG
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
57 1 0.02
58 15 0.25
59 43 0.70
60 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (58 bp):
TCTTGTCTTAATTAAAACAAAAATATTTTATCTTGTCTAAATTAAGACAAACATATTT
Found at i:17937820 original size:28 final size:30
Alignment explanation
Indices: 17937681--17937822 Score: 134
Period size: 28 Copynumber: 4.8 Consensus size: 30
17937671 TTAAGACAAC
* *
17937681 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTCTTAAATTAAGACAAACATATTTT
*
17937711 ATCTTGTC-TAAATTGAGAC-AA-ATATGTTT
1 -TCTTGTCTTAAATTAAGACAAACATAT-TTT
** * * *
17937740 TCTTG-CCCAGATTAAAACAAAAAATATTTT
1 TCTTGTCTTAAATTAAGAC-AAACATATTTT
17937770 TCTTGTCTTAAATTAAGACAAACATATTTT
1 TCTTGTCTTAAATTAAGACAAACATATTTT
*
17937800 T-TTGTCTT-AATTAAGATAAACAT
1 TCTTGTCTTAAATTAAGACAAACAT
17937823 GTTAAAGTTG
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.01
28 30 0.32
29 12 0.13
30 30 0.32
31 20 0.22
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (30 bp):
TCTTGTCTTAAATTAAGACAAACATATTTT
Found at i:17952924 original size:21 final size:21
Alignment explanation
Indices: 17952900--17952940 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17952890 TCATCAGCTG
*
17952900 AATTTTGCTGCAGCGAGAAAA
1 AATTTCGCTGCAGCGAGAAAA
17952921 AATTTCGCTGCAGCGAGAAA
1 AATTTCGCTGCAGCGAGAAA
17952941 CCTTCTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (21 bp):
AATTTCGCTGCAGCGAGAAAA
Found at i:17952950 original size:60 final size:60
Alignment explanation
Indices: 17952842--17953006 Score: 169
Period size: 60 Copynumber: 2.8 Consensus size: 60
17952832 TAGAACTGGT
** *
17952842 TTTCGCTGCAGC-A-AAAAGGAATCTCGCTGTGGCGAAAAACTCTT-TGTTTCATCA-GCT-GAA
1 TTTCGCTGCAGCGAGAAAA--AATCTCGCTGCAGCGAAAAAC-CTTCTGTTTC-T-AGGCTACAA
* * * *
17952902 TTTTGCTGCAGCGAGAAAAAATTTCGCTGCAGCGAGAAACCTTCTGTTTCTAGGTTACAA
1 TTTCGCTGCAGCGAGAAAAAATCTCGCTGCAGCGAAAAACCTTCTGTTTCTAGGCTACAA
* *
17952962 TTTCGCTGCAGCGAGAAAGAATCTCGCTGCAACGAAAAACCTTCT
1 TTTCGCTGCAGCGAGAAAAAATCTCGCTGCAGCGAAAAACCTTCT
17953007 ATTTTGGTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
58 1 0.01
59 6 0.07
60 76 0.86
61 1 0.01
62 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (60 bp):
TTTCGCTGCAGCGAGAAAAAATCTCGCTGCAGCGAAAAACCTTCTGTTTCTAGGCTACAA
Found at i:17954408 original size:63 final size:63
Alignment explanation
Indices: 17954298--17954479 Score: 193
Period size: 63 Copynumber: 2.9 Consensus size: 63
17954288 GCCCAAAGTG
* * * * *
17954298 CAAAAAGAATAAACTTATTAAAAATGCACTAATCGATTTTTTTAAAACAGAATGCTCTAGAGA
1 CAAAAAGAATAAACTTCTTAAAAATGCACTGATCGATTCTTTCAAAACAAAATGCTCTAGAGA
* ** * * * * *
17954361 CAAAAAGAATCAACTTCTTAGGAATGCATTGATTGATTCTTTCAAAACAAAATTCTTTAGCGA
1 CAAAAAGAATAAACTTCTTAAAAATGCACTGATCGATTCTTTCAAAACAAAATGCTCTAGAGA
* ** * * *
17954424 TAAAAAGAATTGACTTCTCAAAAAAGCACTGATCGATTCTTTCAAGACAAAATGCT
1 CAAAAAGAATAAACTTCTTAAAAATGCACTGATCGATTCTTTCAAAACAAAATGCT
17954480 TCAGATTAAA
Statistics
Matches: 95, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 95 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (63 bp):
CAAAAAGAATAAACTTCTTAAAAATGCACTGATCGATTCTTTCAAAACAAAATGCTCTAGAGA
Found at i:17957137 original size:86 final size:86
Alignment explanation
Indices: 17956986--17957585 Score: 904
Period size: 86 Copynumber: 7.0 Consensus size: 86
17956976 TGCTCAAGTG
17956986 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
*
17957051 ATAAATTAATTTTACATTTGT
66 ATAAATTAATTTTACATTTAT
* * * * *
17957072 TAGTTTACAAGTTCAACTTATATAAAAGTTTAATATATTTAAATTTTCATCATAGTT--A-TAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
* * *
17957134 A-ATA-TAAATTTACATTTTT
66 ATAAATTAATTTTACATTTAT
* * *
17957153 TAGTTTGCAAGTTCAACTAATATAAAAATTTTATATATTTAACTTTGTATCATAGTTCAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
17957218 ATAAATTAATTTTACATTTAT
66 ATAAATTAATTTTACATTTAT
* * *
17957239 TAGTTTACAAGCTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCGTAGTTCAAGCAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
*
17957304 ATAAATTAATTTTACATTTGT
66 ATAAATTAATTTTACATTTAT
* * *
17957325 TAGTTTGCAAGTTCAACTAATATAAACATTTTATATATTTAAGTTTGCATCATAGTTCCAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTT-CA--AGT
17957390 ATATATAAATTAATTTTACATTTAT
63 A-ATATAAATTAATTTTACATTTAT
* * * *
17957415 TAATTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGTACCATAATTCAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
17957480 ATAAATTAATTTTACATTTAT
66 ATAAATTAATTTTACATTTAT
*
17957501 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTTAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
*
17957566 ATCAATTAATTTTACATTTA
66 ATAAATTAATTTTACATTTA
17957586 ATAATTCACA
Statistics
Matches: 460, Mismatches: 45, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
81 63 0.14
82 2 0.00
83 6 0.01
84 6 0.01
85 2 0.00
86 299 0.65
87 5 0.01
89 4 0.01
90 73 0.16
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (86 bp):
TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
ATAAATTAATTTTACATTTAT
Found at i:17957483 original size:176 final size:172
Alignment explanation
Indices: 17956986--17957591 Score: 873
Period size: 176 Copynumber: 3.5 Consensus size: 172
17956976 TGCTCAAGTG
*
17956986 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAATAAT
* * * * * *
17957051 ATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTTATATAAAAGTTTAATATATTTAAAT
66 ATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGT
* * *
17957116 TT-TCATCATAGTT--A-TAATA-ATA-TAAATTTACATTTTT
131 TTGT-ATCATAGTTCAAGTAATATAAATTAATTTTACATTTAT
* * * *
17957153 TAGTTTGCAAGTTCAACTAATATAAAAATTTTATATATTTAACTTTGTATCATAGTTCAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAATAAT
* *
17957218 ATAAATTAATTTTACATTTATTAGTTTACAAGCTCAACTAATATAAAAATTTTATATATTTAAGT
66 ATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGT
* * * *
17957283 TTGCATCGTAGTTCAAGCAATATAAATTAATTTTACATTTGT
131 TTGTATCATAGTTCAAGTAATATAAATTAATTTTACATTTAT
* *
17957325 TAGTTTGCAAGTTCAACTAATATAAACATTTTATATATTTAAGTTTGCATCATAGTTCCAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTT-CA--AAT
17957390 ATATATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAAATTTTATATATTT
63 A-ATATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAAATTTTATATATTT
* *
17957455 AAGTTTGTACCATAATTCAAGTAATATAAATTAATTTTACATTTAT
127 AAGTTTGTATCATAGTTCAAGTAATATAAATTAATTTTACATTTAT
* *
17957501 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTTAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAATAAT
* *
17957566 ATCAATTAATTTTACATTTAATAATT
66 ATAAATTAATTTTACATTTATTAATT
17957592 CACATAAAAA
Statistics
Matches: 396, Mismatches: 33, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
167 131 0.33
169 1 0.00
170 4 0.01
171 2 0.01
172 93 0.23
173 5 0.01
175 4 0.01
176 156 0.39
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (172 bp):
TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAATAAT
ATAAATTAATTTTACATTTATTAATTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGT
TTGTATCATAGTTCAAGTAATATAAATTAATTTTACATTTAT
Found at i:17957542 original size:262 final size:253
Alignment explanation
Indices: 17956986--17957584 Score: 957
Period size: 262 Copynumber: 2.3 Consensus size: 253
17956976 TGCTCAAGTG
17956986 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
*
17957051 ATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTTATATAAAAGTTTAATATATTTAAAT
66 ATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAGTTTAATATATTTAAAT
* * * *
17957116 TTTCATCATAGTTATAATAATATAAATTTACATTTTTTAGTTTGCAAGTTCAACTAATATAAAAA
131 TTGCATCATAGTTATAATAATATAAATTTACATTTATTAATTTACAAGTTCAACTAATATAAAAA
* *
17957181 TTTTATATATTTAACTTTGTATCATAGTTCAAGTAATATAAATTAATTTTACATTTAT
196 TTTTATATATTTAACTTTGTACCATAATTCAAGTAATATAAATTAATTTTACATTTAT
* * *
17957239 TAGTTTACAAGCTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCGTAGTTCAAGCAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
* * *
17957304 ATAAATTAATTTTACATTTGTTAGTTTGCAAGTTCAACTAATATAAACA-TTTTATATATTTAAG
66 ATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAA-AGTTTAATATATTTAAA
17957368 TTTGCATCATAGTTCCAGTAATATATATAAATTAATTTTACATTTATTAATTTACAAGTTCAACT
130 TTTGCATCATAGTT--A-TAATA-ATAT--A--AA-TTTACATTTATTAATTTACAAGTTCAACT
*
17957433 AATATAAAAATTTTATATATTTAAGTTTGTACCATAATTCAAGTAATATAAATTAATTTTACATT
186 AATATAAAAATTTTATATATTTAACTTTGTACCATAATTCAAGTAATATAAATTAATTTTACATT
17957498 TAT
251 TAT
*
17957501 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTTAAGTAAT
1 TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
*
17957566 ATCAATTAATTTTACATTT
66 ATAAATTAATTTTACATTT
17957585 AATAATTCAC
Statistics
Matches: 317, Mismatches: 19, Indels: 11
0.91 0.05 0.03
Matches are distributed among these distances:
253 133 0.42
254 1 0.00
255 1 0.00
256 5 0.02
257 4 0.01
259 1 0.00
261 2 0.01
262 170 0.54
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (253 bp):
TAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAAT
ATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAGTTTAATATATTTAAAT
TTGCATCATAGTTATAATAATATAAATTTACATTTATTAATTTACAAGTTCAACTAATATAAAAA
TTTTATATATTTAACTTTGTACCATAATTCAAGTAATATAAATTAATTTTACATTTAT
Found at i:17967417 original size:16 final size:15
Alignment explanation
Indices: 17967385--17967413 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17967375 TAAAAAATTC
17967385 AAAAAAATATTTTGG
1 AAAAAAATATTTTGG
17967400 AAAAAAA-ATTTTGG
1 AAAAAAATATTTTGG
17967414 GGAAGGGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (15 bp):
AAAAAAATATTTTGG
Found at i:17967985 original size:33 final size:33
Alignment explanation
Indices: 17967955--17968022 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
17967945 ATATTTTTAT
17967955 TTATTTATTTATTT-TTTCTCTTCTCTTTTTTC
1 TTATTTATTTATTTCTTTCTCTTCTCTTTTTTC
* * * *
17967987 TTCTTTATTTTTTTCTTTTTTTTCTCTTTTCTTC
1 TTATTTATTTATTTCTTTCTCTTCTCTTTT-TTC
17968021 TT
1 TT
17968023 CTATTTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 12 0.40
33 13 0.43
34 5 0.17
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (33 bp):
TTATTTATTTATTTCTTTCTCTTCTCTTTTTTC
Found at i:17967991 original size:15 final size:15
Alignment explanation
Indices: 17967966--17968024 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
17967956 TATTTATTTA
17967966 TTTTTTC-TCTTCTC
1 TTTTTTCTTCTTCTC
*
17967980 TTTTTTCTTCTT-TAT
1 TTTTTTCTTCTTCT-C
* *
17967995 TTTTTTCTTTTTTTTC
1 TTTTTTC-TTCTTCTC
*
17968011 TCTTTTCTTCTTCT
1 TTTTTTCTTCTTCT
17968025 ATTTGTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
14 8 0.23
15 16 0.46
16 10 0.29
17 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTCTTCTTCTC
Found at i:17970830 original size:3 final size:3
Alignment explanation
Indices: 17970822--17970850 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17970812 ACTTTATCTC
17970822 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
17970851 ACTATATTTA
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:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:17972021 original size:54 final size:55
Alignment explanation
Indices: 17971948--17972110 Score: 262
Period size: 54 Copynumber: 3.0 Consensus size: 55
17971938 CATACAGCAC
* *
17971948 CATCTCGCCCAGCTCATGTGCATCCCCTCACATCGTGCACATAGCCGGACA-TC-T
1 CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGA-AGTCAT
*
17972002 CGTCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCC-GAAGTCAT
1 CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGAAGTCAT
17972056 CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCC-GAAGTCAT
1 CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGAAGTCAT
17972110 C
1 C
17972111 GTGTGCATCC
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
52 1 0.01
53 4 0.04
54 98 0.95
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.21
Consensus pattern (55 bp):
CATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGAAGTCAT
Found at i:17974464 original size:4 final size:4
Alignment explanation
Indices: 17974444--17974501 Score: 52
Period size: 4 Copynumber: 15.2 Consensus size: 4
17974434 CTATGCCCAC
* * *
17974444 TCTT TCTT T-TT TGTT TCTT TCTT TCTT CCTT TC-- TCGTT TCTT CCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT
17974490 TCTT TC-T TCTT T
1 TCTT TCTT TCTT T
17974502 TCCTCTCTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
2 2 0.05
3 6 0.14
4 34 0.77
5 2 0.05
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (4 bp):
TCTT
Done.