Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 100 of 214
Found at i:29135862 original size:14 final size:14
Alignment explanation
Indices: 29135843--29135869 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29135833 CACAAGGTAT
29135843 TTTGAAAGGATATG
1 TTTGAAAGGATATG
29135857 TTTGAAAGGATAT
1 TTTGAAAGGATAT
29135870 TGGAAACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (14 bp):
TTTGAAAGGATATG
Found at i:29140619 original size:43 final size:43
Alignment explanation
Indices: 29140558--29140742 Score: 230
Period size: 43 Copynumber: 4.3 Consensus size: 43
29140548 TTATATGAAA
* *
29140558 AAATGCCGCTATAA-AACATGACCTTTAGCGGTGC-TTTACCCAC
1 AAATGCCGCTA-AAGAACATGACCTTTAGCGGAGCTTTTA-TCAC
* *
29140601 AAATGCCGCTAAAGAACATGATCATTAGCGGAGCTTTTATCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGAGCTTTTATCAC
* *
29140644 AAATGCCGCTAAAGAACATGACCTGTAGCGGCGCTTTTATCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGAGCTTTTATCAC
* * * * *
29140687 AAACGCCGCTAAAGAACATGATCTTTACCGGCGTTTTTATCAC
1 AAATGCCGCTAAAGAACATGACCTTTAGCGGAGCTTTTATCAC
*
29140730 AAACGCCGCTAAA
1 AAATGCCGCTAAA
29140743 AGTACCGTTC
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 2 0.02
43 121 0.95
44 4 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
AAATGCCGCTAAAGAACATGACCTTTAGCGGAGCTTTTATCAC
Found at i:29140703 original size:86 final size:85
Alignment explanation
Indices: 29140558--29140743 Score: 257
Period size: 86 Copynumber: 2.2 Consensus size: 85
29140548 TTATATGAAA
* * *
29140558 AAATGCCGCTATAAAACATGACCTTTAGCGGTGCTTTACCCACAAATGCCGCTAAAGAACATGAT
1 AAATGCCGCTA-AAAACATGACCTGTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAT
*
29140623 CATTAGCGGAGCTTTTATCAC
65 CATTACCGGAGCTTTTATCAC
*
29140644 AAATGCCGCTAAAGAACATGACCTGTAGCGGCGCTTTTA-TCACAAACGCCGCTAAAGAACATGA
1 AAATGCCGCTAAA-AACATGACCTGTAGCGGCGC-TTTACCCACAAACGCCGCTAAAGAACATGA
* * *
29140708 TCTTTACCGGCGTTTTTATCAC
64 TCATTACCGGAGCTTTTATCAC
*
29140730 AAACGCCGCTAAAA
1 AAATGCCGCTAAAA
29140744 GTACCGTTCT
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
85 3 0.03
86 82 0.92
87 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (85 bp):
AAATGCCGCTAAAAACATGACCTGTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGATC
ATTACCGGAGCTTTTATCAC
Found at i:29140755 original size:43 final size:43
Alignment explanation
Indices: 29140598--29140765 Score: 176
Period size: 43 Copynumber: 3.9 Consensus size: 43
29140588 GTGCTTTACC
* * * * * *
29140598 CACAAATGCCGCTAAAGAACATGATCATTAGCGGAGCTTTTAT
1 CACAAACGCCGCTAAAGAACACGATCTTTACCGGCGTTTTTAT
* * * * * *
29140641 CACAAATGCCGCTAAAGAACATGACCTGTAGCGGCGCTTTTAT
1 CACAAACGCCGCTAAAGAACACGATCTTTACCGGCGTTTTTAT
*
29140684 CACAAACGCCGCTAAAGAACATGATCTTTACCGGCGTTTTTAT
1 CACAAACGCCGCTAAAGAACACGATCTTTACCGGCGTTTTTAT
* * *
29140727 CACAAACGCCGCTAAAAGTAC-CGTTCTTTAGCGGCGTTT
1 CACAAACGCCGCT-AAAGAACACGATCTTTACCGGCGTTT
29140766 ATAAAAAAAT
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 105 0.95
44 6 0.05
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
CACAAACGCCGCTAAAGAACACGATCTTTACCGGCGTTTTTAT
Found at i:29142478 original size:42 final size:43
Alignment explanation
Indices: 29142421--29142521 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 43
29142411 TGAGATTTAT
* *
29142421 GTGTAAGACCATGTCTAAGACATTGGCGTC-GTATGTGATTAC
1 GTGTAAGACCATGTCTAAGACAATGGCATCAGTATGTGATTAC
* * * *
29142463 GTGTAAGACCCTGTCTGAGACAATGGCATCATTATTTGATTAC
1 GTGTAAGACCATGTCTAAGACAATGGCATCAGTATGTGATTAC
* *
29142506 ATGTAAGACCACGTCT
1 GTGTAAGACCATGTCT
29142522 GGGACGTTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 26 0.53
43 23 0.47
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCATGTCTAAGACAATGGCATCAGTATGTGATTAC
Found at i:29143374 original size:44 final size:44
Alignment explanation
Indices: 29143311--29143490 Score: 272
Period size: 44 Copynumber: 4.1 Consensus size: 44
29143301 TGAAGTAAAT
* * *
29143311 TGTTGATTGGATGCTGTCCAATTGTTGATTAAATGCTATCCAAA
1 TGTTGATTGAATGTTGTCCAATTGTTGATTAAATGCTGTCCAAA
* *
29143355 TGTTGATTGAATGATGTCCAATTGTTGATTAAATGTTGTCCAAA
1 TGTTGATTGAATGTTGTCCAATTGTTGATTAAATGCTGTCCAAA
*
29143399 TGTTGATTGAATGTTGTCCAATTGTTGATTAAATGCTGTTCAAA
1 TGTTGATTGAATGTTGTCCAATTGTTGATTAAATGCTGTCCAAA
* * *
29143443 TGTT-ATTGAATGTTGTCCAATTGTTGATTAAATGTTGTTCGAA
1 TGTTGATTGAATGTTGTCCAATTGTTGATTAAATGCTGTCCAAA
29143486 TGTTG
1 TGTTG
29143491 GTTAATTGCT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
43 41 0.33
44 85 0.67
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (44 bp):
TGTTGATTGAATGTTGTCCAATTGTTGATTAAATGCTGTCCAAA
Found at i:29143477 original size:22 final size:22
Alignment explanation
Indices: 29143308--29143480 Score: 213
Period size: 22 Copynumber: 7.9 Consensus size: 22
29143298 AAGTGAAGTA
** *
29143308 AATTGTTGATTGGATGCTGTCC
1 AATTGTTGATTAAATGTTGTCC
* *
29143330 AATTGTTGATTAAATGCTATCC
1 AATTGTTGATTAAATGTTGTCC
* * *
29143352 AAATGTTGATTGAATGATGTCC
1 AATTGTTGATTAAATGTTGTCC
29143374 AATTGTTGATTAAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCC
* *
29143396 AAATGTTGATTGAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCC
* *
29143418 AATTGTTGATTAAATGCTGTTC
1 AATTGTTGATTAAATGTTGTCC
* *
29143440 AAATGTT-ATTGAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCC
29143461 AATTGTTGATTAAATGTTGT
1 AATTGTTGATTAAATGTTGT
29143481 TCGAATGTTG
Statistics
Matches: 128, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
21 17 0.13
22 111 0.87
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (22 bp):
AATTGTTGATTAAATGTTGTCC
Found at i:29164362 original size:55 final size:54
Alignment explanation
Indices: 29164267--29164416 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
29164257 CTACTTTGTT
* ** * *
29164267 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
29164321 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
29164376 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
29164417 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:29164379 original size:27 final size:27
Alignment explanation
Indices: 29164239--29164416 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
29164229 TAAATTGTAC
29164239 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
29164266 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
29164292 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
29164320 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
29164348 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
29164375 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
29164402 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29164417 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:29164380 original size:82 final size:81
Alignment explanation
Indices: 29164240--29164395 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
29164230 AAATTGTACA
* * * *
29164240 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
29164305 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
29164321 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
29164384 TGTGCGAGTTGA
63 TGTGCGAATTGA
29164396 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:29179392 original size:37 final size:37
Alignment explanation
Indices: 29179320--29179423 Score: 106
Period size: 37 Copynumber: 2.8 Consensus size: 37
29179310 CAATCACTTG
**
29179320 TAAGAGCTAATCCAGCCGATAACACAGCTGATGCTCA
1 TAAGAGCTAATCCAGCCGATAACACAGCCAATGCTCA
*
29179357 TAAGAGCTAATCCA-CACGATAACAC-GCCAATTGCTCC
1 TAAGAGCTAATCCAGC-CGATAACACAGCCAA-TGCTCA
* * * *
29179394 GAAGAGCTAGTCCAACCGAAAACACA-CCAA
1 TAAGAGCTAATCCAGCCGATAACACAGCCAA
29179424 AACAAAGAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
36 4 0.07
37 52 0.91
38 1 0.02
ACGTcount: A:0.38, C:0.30, G:0.16, T:0.15
Consensus pattern (37 bp):
TAAGAGCTAATCCAGCCGATAACACAGCCAATGCTCA
Found at i:29200059 original size:25 final size:25
Alignment explanation
Indices: 29200031--29200079 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29200021 ATATTTTTGA
*
29200031 TAGTATATCCTAAAACTACTATAGG
1 TAGTATATACTAAAACTACTATAGG
* *
29200056 TAGTATATACTGAGACTACTATAG
1 TAGTATATACTAAAACTACTATAG
29200080 ATAGACTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (25 bp):
TAGTATATACTAAAACTACTATAGG
Found at i:29204630 original size:21 final size:22
Alignment explanation
Indices: 29204599--29204639 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29204589 ATAACATATG
29204599 TAAATTATAT-AT-ATTTTTCA
1 TAAATTATATAATAATTTTTCA
29204619 TAAATATATATAATAATTTTT
1 TAAAT-TATATAATAATTTTT
29204640 GCTCCCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 2 0.11
23 6 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAATTATATAATAATTTTTCA
Found at i:29206257 original size:34 final size:35
Alignment explanation
Indices: 29206202--29206268 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
29206192 CAAACACCAG
*
29206202 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
29206237 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
29206269 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:29206997 original size:16 final size:16
Alignment explanation
Indices: 29206976--29207040 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
29206966 TTCGCTGTAT
29206976 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29206992 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
**
29207008 TGGAATAGAGAAGTAA
1 TGGAATAGAGGCGTAA
29207024 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29207040 T
1 T
29207041 AGCAAATCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.40, C:0.05, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:29211111 original size:14 final size:13
Alignment explanation
Indices: 29211092--29211121 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
29211082 TGATAAAGTT
29211092 TATATAAATATAAA
1 TATATAAAT-TAAA
29211106 TATATAAATTAAA
1 TATATAAATTAAA
29211119 TAT
1 TAT
29211122 GAATGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATAAATTAAA
Found at i:29215965 original size:15 final size:15
Alignment explanation
Indices: 29215945--29216003 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
29215935 TTTGACATGT
29215945 ATTAAAATAAAATAA
1 ATTAAAATAAAATAA
*
29215960 ATTAAAATAAATTAA
1 ATTAAAATAAAATAA
* *
29215975 ATTAAATTAAATTAA
1 ATTAAAATAAAATAA
29215990 ATTAAAATAAAATA
1 ATTAAAATAAAATA
29216004 TTATTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTAAAATAAAATAA
Found at i:29216003 original size:5 final size:5
Alignment explanation
Indices: 29215945--29216000 Score: 76
Period size: 5 Copynumber: 11.2 Consensus size: 5
29215935 TTTGACATGT
* * *
29215945 ATTAA AATAA AATAA ATTAA AATAA ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
*
29215995 AATAA A
1 ATTAA A
29216001 ATATTATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (5 bp):
ATTAA
Found at i:29222152 original size:14 final size:14
Alignment explanation
Indices: 29222133--29222166 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
29222123 TCATGATGAA
29222133 TGTATCAAATGTGT
1 TGTATCAAATGTGT
29222147 TGTATCAAATGTGT
1 TGTATCAAATGTGT
29222161 TGTATC
1 TGTATC
29222167 TTTGTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (14 bp):
TGTATCAAATGTGT
Found at i:29228119 original size:10 final size:10
Alignment explanation
Indices: 29228076--29228110 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29228066 ATGCATTAAC
*
29228076 CACATATAGT
1 CACATATAAT
*
29228086 CACAAATAAT
1 CACATATAAT
29228096 CACATATAAT
1 CACATATAAT
29228106 CACAT
1 CACAT
29228111 TTAGTCACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (10 bp):
CACATATAAT
Found at i:29230699 original size:27 final size:27
Alignment explanation
Indices: 29230669--29230743 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
29230659 AAAATTATTG
* *
29230669 AAATACCCTCGAAGGGTAAAATAATCA
1 AAATACCCTCGATGGGTAAAATAACCA
* *
29230696 AAATACCCTCGATGGGT-AAATGACCG
1 AAATACCCTCGATGGGTAAAATAACCA
*
29230722 AAATACCTTCGATGGGTAAAAT
1 AAATACCCTCGATGGGTAAAAT
29230744 GACCGTAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 22 0.52
27 20 0.48
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATACCCTCGATGGGTAAAATAACCA
Found at i:29230725 original size:26 final size:27
Alignment explanation
Indices: 29230668--29230800 Score: 112
Period size: 27 Copynumber: 5.0 Consensus size: 27
29230658 TAAAATTATT
* * *
29230668 GAAATACCCTCGAAGGGTAAAATAATC
1 GAAATACCCTCGATGGGTAAAATGACC
*
29230695 AAAATACCCTCGATGGGT-AAATGACC
1 GAAATACCCTCGATGGGTAAAATGACC
*
29230721 GAAATACCTTCGATGGGTAAAATGACC
1 GAAATACCCTCGATGGGTAAAATGACC
* ** *
29230748 GTAATGGCCT-TATAGGGTAAAATGACC
1 GAAATACCCTCGAT-GGGTAAAATGACC
* *
29230775 -ATAATGCCC-CTATAGGGTAAAATGAC
1 GA-AATACCCTCGAT-GGGTAAAATGAC
29230801 TGTAACACCC
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
26 24 0.27
27 65 0.73
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (27 bp):
GAAATACCCTCGATGGGTAAAATGACC
Found at i:29230765 original size:27 final size:27
Alignment explanation
Indices: 29230735--29230935 Score: 240
Period size: 27 Copynumber: 7.4 Consensus size: 27
29230725 TACCTTCGAT
* *
29230735 GGGTAAAATGACCGTAATGGCCTTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
*
29230762 GGGTAAAATGACCATAATGCCCCTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
* ** *
29230789 GGGTAAAATGACTGTAACACCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTATA
* *
29230816 GGGTAAAATGACCATAATGCACCTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
*
29230843 GGGTAAAATAACCGTAATGCCCCTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
* *
29230870 GGGTAAAATAACCGTAATGCCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTATA
*** * *
29230897 GGGTAAAATGATTATAATGCCCTTGTA
1 GGGTAAAATGACCGTAATGCCCCTATA
*
29230924 GGATAAAATGAC
1 GGGTAAAATGAC
29230936 TATTTTGCCC
Statistics
Matches: 149, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 149 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (27 bp):
GGGTAAAATGACCGTAATGCCCCTATA
Found at i:29230947 original size:81 final size:81
Alignment explanation
Indices: 29230735--29230935 Score: 278
Period size: 81 Copynumber: 2.5 Consensus size: 81
29230725 TACCTTCGAT
* * *
29230735 GGGTAAAATGACCGTAATGGCCTTATAGGGTAAAATGACCATAATGCCCCTATAGGGTAAAATGA
1 GGGTAAAATGACCATAATGCCCTTATAGGGTAAAATGACCATAATGCCCCTATAGGGTAAAATAA
*
29230800 CTGTAACACCCCTGTA
66 CCGTAACACCCCTGTA
* *
29230816 GGGTAAAATGACCATAATGCACC-TATAGGGTAAAATAACCGTAATGCCCCTATAGGGTAAAATA
1 GGGTAAAATGACCATAATGC-CCTTATAGGGTAAAATGACCATAATGCCCCTATAGGGTAAAATA
**
29230880 ACCGTAATGCCCCTGTA
65 ACCGTAACACCCCTGTA
** * *
29230897 GGGTAAAATGATTATAATGCCCTTGTAGGATAAAATGAC
1 GGGTAAAATGACCATAATGCCCTTATAGGGTAAAATGAC
29230936 TATTTTGCCC
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
80 2 0.02
81 101 0.96
82 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (81 bp):
GGGTAAAATGACCATAATGCCCTTATAGGGTAAAATGACCATAATGCCCCTATAGGGTAAAATAA
CCGTAACACCCCTGTA
Found at i:29230988 original size:24 final size:24
Alignment explanation
Indices: 29230952--29231086 Score: 162
Period size: 24 Copynumber: 5.6 Consensus size: 24
29230942 GCCCCTCAGG
*
29230952 GTAAATGATTGATTTGTCTGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
* * * *
29230976 GTAAATAAATGATTTGTCCGAGAT
1 GTAAATGACTGATTTGTCTGTGAT
*
29231000 GTAAATGACTGATTTGTTTGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
* *
29231024 TTAAATGACTGATTTGTTTGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
*
29231048 TTAAATGACTGATTTGTCTGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
* **
29231072 TTGTATGACTGATTT
1 GTAAATGACTGATTT
29231087 TGTGGATGGC
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 98 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (24 bp):
GTAAATGACTGATTTGTCTGTGAT
Found at i:29231197 original size:27 final size:27
Alignment explanation
Indices: 29231154--29231213 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
29231144 AGAAGTACTG
29231154 TACTGGTGGCTCTGCCACA-ATCACTAT
1 TACTGGTGGCTCTGCCACATAT-ACTAT
*
29231181 TACTGGTGGCT-TGGCCACATATATTAT
1 TACTGGTGGCTCT-GCCACATATACTAT
29231208 TACTGG
1 TACTGG
29231214 CAGCTTTGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 1 0.03
27 27 0.90
28 2 0.07
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACATATACTAT
Found at i:29231285 original size:32 final size:32
Alignment explanation
Indices: 29231249--29231419 Score: 209
Period size: 32 Copynumber: 5.4 Consensus size: 32
29231239 GCTTTCTACA
* * *
29231249 GATCATATTACCATTACTGGTGGCTATGTGCC
1 GATCATATTACTATTACTGATGGCTGTGTGCC
* *
29231281 GATCATATTACCATTACTGATGGTTGTGTGCC
1 GATCATATTACTATTACTGATGGCTGTGTGCC
* * *
29231313 GATTATATTACTACTA-TGATGGCTTTGTGCC
1 GATCATATTACTATTACTGATGGCTGTGTGCC
* *
29231344 GATCATACTACTATTACTGATGGTTGTGTGCC
1 GATCATATTACTATTACTGATGGCTGTGTGCC
* * *
29231376 GATCATATTACTACTACTGATGACTTTGTGCC
1 GATCATATTACTATTACTGATGGCTGTGTGCC
*
29231408 AATCATATTACT
1 GATCATATTACT
29231420 GTACTTATGG
Statistics
Matches: 119, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
31 26 0.22
32 93 0.78
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (32 bp):
GATCATATTACTATTACTGATGGCTGTGTGCC
Found at i:29231345 original size:63 final size:64
Alignment explanation
Indices: 29231249--29231418 Score: 252
Period size: 63 Copynumber: 2.7 Consensus size: 64
29231239 GCTTTCTACA
* * * *
29231249 GATCATATTACCATTACTGGTGGCTATGTGCCGATCATATTACCATTACTGATGGTTGTGTGCC
1 GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGTTGTGTGCC
* * *
29231313 GATTATATTACTACTA-TGATGGCTTTGTGCCGATCATACTACTATTACTGATGGTTGTGTGCC
1 GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGTTGTGTGCC
* *
29231376 GATCATATTACTACTACTGATGACTTTGTGCCAATCATATTAC
1 GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTAC
29231419 TGTACTTATG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
63 58 0.62
64 36 0.38
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (64 bp):
GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGTTGTGTGCC
Found at i:29231432 original size:95 final size:95
Alignment explanation
Indices: 29231234--29231419 Score: 239
Period size: 95 Copynumber: 2.0 Consensus size: 95
29231224 GCGATGCTAT
* * * * * *
29231234 TGATGGCTTTCTACAGATCATATTACCATTACTGGTGGCTATGTGCCGATCATATTACCATTACT
1 TGATGGCTTTGTGCCGATCATACTACCATTACTGATGGCTATGTGCCGATCATATTACCACTACT
* * *
29231299 GATGGTTGTGTGCCGATTATATTACTACTA
66 GATGCTTGTGTGCCAATCATATTACTACTA
* * * *
29231329 TGATGGCTTTGTGCCGATCATACTACTATTACTGATGGTTGTGTGCCGATCATATTACTACTACT
1 TGATGGCTTTGTGCCGATCATACTACCATTACTGATGGCTATGTGCCGATCATATTACCACTACT
29231394 GATGACTT-TGTGCCAATCATATTACT
66 GATG-CTTGTGTGCCAATCATATTACT
29231420 GTACTTATGG
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 75 0.97
96 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (95 bp):
TGATGGCTTTGTGCCGATCATACTACCATTACTGATGGCTATGTGCCGATCATATTACCACTACT
GATGCTTGTGTGCCAATCATATTACTACTA
Found at i:29232553 original size:20 final size:20
Alignment explanation
Indices: 29232528--29232566 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29232518 TACTTTCTTC
29232528 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
29232548 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
29232567 AAATAAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:29232954 original size:50 final size:50
Alignment explanation
Indices: 29232775--29233009 Score: 190
Period size: 50 Copynumber: 4.6 Consensus size: 50
29232765 ACACTCTAAA
* * *
29232775 GCCATGTCCCAGACATGGTCTTACATGGGA-TGTTTCCTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATCT-CGGTGCCAAT
* * * * *
29232824 GCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATAC-CGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-CTCGGTGCCAAT
* * * ** *
29232874 GCCATGTCCTAGACATAGTGTTACGGGGGACTTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTGCCAAT
* * * **
29232924 GCCATGTCCCCGATATGGTCTTACATGGGACATCTCATAACCTCAATAATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT---CTC---GGTGCCAAT
29232980 GCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
29233010 TCTCATTCCC
Statistics
Matches: 144, Mismatches: 31, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
48 1 0.01
49 32 0.22
50 74 0.51
53 3 0.02
56 34 0.24
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTGCCAAT
Found at i:29240146 original size:10 final size:10
Alignment explanation
Indices: 29240128--29240162 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29240118 ATGCATTAAC
29240128 CACATATAAT
1 CACATATAAT
* *
29240138 CACAAATAAC
1 CACATATAAT
29240148 CACATATAAT
1 CACATATAAT
29240158 CACAT
1 CACAT
29240163 CTAGTCACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (10 bp):
CACATATAAT
Found at i:29240171 original size:20 final size:20
Alignment explanation
Indices: 29240124--29240161 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29240114 TGACATGCAT
29240124 TAACCACATATAATCACAAA
1 TAACCACATATAATCACAAA
29240144 TAACCACATATAATCACA
1 TAACCACATATAATCACA
29240162 TCTAGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (20 bp):
TAACCACATATAATCACAAA
Found at i:29249383 original size:50 final size:50
Alignment explanation
Indices: 29249310--29249409 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
29249300 ATTGAAATGG
29249310 ATAATACATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTAATTA
1 ATAATACATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTAATTA
*
29249360 ATAATACATGTATATGAGATATAATTATATGTTGTGTTCATTCTTAATTA
1 ATAATACATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTAATTA
29249410 CATAGCCTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (50 bp):
ATAATACATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTAATTA
Found at i:29250468 original size:11 final size:11
Alignment explanation
Indices: 29250447--29250515 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
29250437 AGCCCAGCCC
29250447 ATTTAAATATAT
1 ATTT-AATATAT
29250459 ATTTAATATAT
1 ATTTAATATAT
*
29250470 ATAATATATATAT
1 AT-TTA-ATATAT
* *
29250483 ATTTGAT-TAA
1 ATTTAATATAT
**
29250493 AAATAATATAT
1 ATTTAATATAT
29250504 ATTTAATATAT
1 ATTTAATATAT
29250515 A
1 A
29250516 ATTCGGGCCG
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
10 6 0.14
11 23 0.52
12 7 0.16
13 8 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (11 bp):
ATTTAATATAT
Found at i:29267215 original size:41 final size:41
Alignment explanation
Indices: 29267158--29267361 Score: 241
Period size: 41 Copynumber: 5.0 Consensus size: 41
29267148 AAGTATATCC
*
29267158 AAGGGTACCGAAGTACAAACAGGGGCATGTATGTGCAATTT
1 AAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTT
* * ** * *
29267199 AAGGGTACTGAAGTAC-AACTAGGGGCAAGGGTGTGGAA-CT
1 AAGGGTACCGAAGTACAAAC-AGGGGCACGTATGTGCAATTT
* *
29267239 CAGGCGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTC
1 AAGG-GTACCGAAGTACAAACAGGGGCACGTATGTGCAATTT
* * *
29267281 AAGGGTACCGAATTACAAACAAGGGCACGTATATGCAATTT
1 AAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTT
* * *
29267322 AAGGGTACTGAAGTACAAACAGGGTCACGTATGTCCAATT
1 AAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATT
29267362 CATCATTATA
Statistics
Matches: 134, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
40 7 0.05
41 121 0.90
42 6 0.04
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.20
Consensus pattern (41 bp):
AAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTT
Found at i:29270439 original size:25 final size:25
Alignment explanation
Indices: 29270411--29270463 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
29270401 GCTCATACAT
* *
29270411 GCTGAATATCGATAAGCTCTCTCGA
1 GCTGAATATCGATAAACTCTCTCAA
* *
29270436 GCTGAATATTGGTAAACTCTCTCAA
1 GCTGAATATCGATAAACTCTCTCAA
29270461 GCT
1 GCT
29270464 AAGAATCGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (25 bp):
GCTGAATATCGATAAACTCTCTCAA
Found at i:29273758 original size:138 final size:136
Alignment explanation
Indices: 29273493--29273761 Score: 333
Period size: 137 Copynumber: 2.0 Consensus size: 136
29273483 CGAGCCATAA
* * * **
29273493 ATGGGTCTGCTAACACAAGCTGATGGTCAAAATATAGCTACATGATGTCACTTACACAAGCTGGC
1 ATGGGTCTGCTAACACAAGCTGATAGTCAAAATATAGCTACACGATGTCACTCACACAAGCTAAC
* * * * **
29273558 GATTATCCGCAAAAAATGTCGATCTCAGCCATCGGTAGGACATTCAAGTCAAGCACCTGAAACAT
66 GAGTATCCGCAAAAAATGTAGAACTCAGCCATCAGTAGGACATTCAAAACAAGCACCTGAAACAT
29273623 GGTAAC
131 GGTAAC
* * **
29273629 ATGGGTCTGCTCACACAAGCTGATAGTCAAAATTTAAGCTACACGATGTTGCTCACACAAGCTAA
1 ATGGGTCTGCTAACACAAGCTGATAGTCAAAATAT-AGCTACACGATGTCACTCACACAAGCTAA
* * * *
29273694 TGAGTATTCGCAATAAATGCTAGAACTCAGCCATCAGTAGGACATTCAAAACCAGCA-CTCGAAA
65 CGAGTATCCGCAAAAAATG-TAGAACTCAGCCATCAGTAGGACATTCAAAACAAGCACCT-GAAA
29273758 CATG
128 CATG
29273762 AAAACCCTAA
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
136 32 0.29
137 40 0.36
138 39 0.35
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (136 bp):
ATGGGTCTGCTAACACAAGCTGATAGTCAAAATATAGCTACACGATGTCACTCACACAAGCTAAC
GAGTATCCGCAAAAAATGTAGAACTCAGCCATCAGTAGGACATTCAAAACAAGCACCTGAAACAT
GGTAAC
Found at i:29275475 original size:26 final size:26
Alignment explanation
Indices: 29275439--29275505 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
29275429 TACATCATTA
* *
29275439 CTCACACGAGCTGTGAAATGGGCTTG
1 CTCACACGAGCTGTGAAATAGGCCTG
* *
29275465 CTCACATGAGCTATGAAATAGGCCTG
1 CTCACACGAGCTGTGAAATAGGCCTG
*
29275491 CTCACACGAGTTGTG
1 CTCACACGAGCTGTG
29275506 GGGAGTCCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (26 bp):
CTCACACGAGCTGTGAAATAGGCCTG
Found at i:29276396 original size:257 final size:259
Alignment explanation
Indices: 29275937--29276458 Score: 942
Period size: 257 Copynumber: 2.0 Consensus size: 259
29275927 AGGACAATAG
*
29275937 TTTTAGGACCACAAATCTGACGAGCAAATTATTATTATTTATTATTTTAATGTTTATGAGATGTT
1 TTTTAGGACCACAAATCTGACGAGCAAA-TATTATTATTTATTAGTTTAATGTTTATGAGATGTT
*
29276002 AGTGAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAA
65 AGTAAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAA
*
29276067 AAGTAGAGTTTTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
130 AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
29276132 GGTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
195 GGTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
* *
29276197 TTTTAGGACCACAAATCTGACGAG-TAA-ATTATTATTTATTAGTTTAATGTTTATGGGATGTTA
1 TTTTAGGACCACAAATCTGACGAGCAAATATTATTATTTATTAGTTTAATGTTTATGAGATGTTA
* *
29276260 GTAAGGTCGTATTGATGTTTGCATGATTAATTAAGTAAAAAGGAA-TAAATTGTAAAAGGTTCAA
66 GTAAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAA-GAACTAAATCGTAAAAGGTTCAA
29276324 AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
130 AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
29276389 GGTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
195 GGTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
29276454 TTTTA
1 TTTTA
29276459 AAGGTTAAAA
Statistics
Matches: 254, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
257 225 0.89
258 3 0.01
259 2 0.01
260 24 0.09
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (259 bp):
TTTTAGGACCACAAATCTGACGAGCAAATATTATTATTTATTAGTTTAATGTTTATGAGATGTTA
GTAAGGTCGTATTAATGTTTGCATGATTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAAA
AGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATATG
GTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
Found at i:29278512 original size:196 final size:196
Alignment explanation
Indices: 29278178--29278570 Score: 741
Period size: 196 Copynumber: 2.0 Consensus size: 196
29278168 GTATTGAGCT
*
29278178 TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTTTGGATGAATGCATTAG
1 TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTGTGGATGAATGCATTAG
*
29278243 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTGAATTTGTCATTAAATGTAAGT
66 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTAAATTTGTCATTAAATGTAAGT
29278308 TTTGGTCATGTTTTGATGTCTTGATTATGTGTACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
131 TTTGGTCATGTTTTGATGTCTTGATTATGTGTACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
29278373 G
196 G
*
29278374 TGATGTTAATGATTGAAATGTGGTAACATATGCATGTTTAGGTAAGTTGTGGATGAATGCATTAG
1 TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTGTGGATGAATGCATTAG
*
29278439 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTAAATTTGTCATTACATGTAAGT
66 AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTAAATTTGTCATTAAATGTAAGT
*
29278504 TTTGGTCATGTTTTGATGTCTTGATTATGTGTACAAAAGGCCTTTAGGTGTGTGCATGGTTTGGT
131 TTTGGTCATGTTTTGATGTCTTGATTATGTGTACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
29278569 G
196 G
29278570 T
1 T
29278571 TTGAAATGGC
Statistics
Matches: 192, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
196 192 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.42
Consensus pattern (196 bp):
TGATGTTAATGATTGAAATGTGGTAACATATGAATGTTTAGGTAAGTTGTGGATGAATGCATTAG
AGATGCCTTGTATGGAATATTGGTTGATTGATTTTAGACTATTAAATTTGTCATTAAATGTAAGT
TTTGGTCATGTTTTGATGTCTTGATTATGTGTACAAAAAGCCTTTAGGTGTGTGCATGGTTTGGT
G
Found at i:29279499 original size:15 final size:15
Alignment explanation
Indices: 29279479--29279507 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29279469 GTGTTGTTGC
29279479 TTGATAACACGGTGA
1 TTGATAACACGGTGA
29279494 TTGATAACACGGTG
1 TTGATAACACGGTG
29279508 TGTGAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:29282258 original size:21 final size:21
Alignment explanation
Indices: 29282218--29282258 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29282208 TCACACTTCA
*
29282218 ATCACATACTCATATTTGTTT
1 ATCACATACTCATATCTGTTT
29282239 ATCA-ATACTCATATCCTGTT
1 ATCACATACTCATAT-CTGTT
29282259 GAACACATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
ATCACATACTCATATCTGTTT
Found at i:29282401 original size:50 final size:51
Alignment explanation
Indices: 29282336--29282460 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 51
29282326 TTCGATACAT
* * * * * *
29282336 GTAGTAGCCTTCACATAGTACTACACACGTGATCAAA-CTTTCCGGTTCAC
1 GTAGTAACCTACACATAGTACTACACACGTGACCAAAGCCTTCCAGTGCAC
* *
29282386 GTAGTATCCTACACATAGTACTACACACGTGACCAAAGCCTTCTAGTGCAC
1 GTAGTAACCTACACATAGTACTACACACGTGACCAAAGCCTTCCAGTGCAC
* *
29282437 ATAGTAACCTGCACATAGTACTAC
1 GTAGTAACCTACACATAGTACTAC
29282461 GCATGCGACC
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
50 34 0.53
51 30 0.47
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (51 bp):
GTAGTAACCTACACATAGTACTACACACGTGACCAAAGCCTTCCAGTGCAC
Found at i:29290113 original size:51 final size:51
Alignment explanation
Indices: 29289988--29290171 Score: 194
Period size: 51 Copynumber: 3.6 Consensus size: 51
29289978 TATCATTCGA
* * * *
29289988 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAACTTTTCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACTTTCCGG
* *
29290038 TTCACATAGCAGCCTGCACATAGTACTACACACGTGACCAAAGAC-TTCCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAA-ACTTTCCGG
* * * * * *
29290089 TACACATAGTAGCCTGGACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCA-AAACTTTCCGG
* * *
29290140 TACACGTAGTAGCCTACACTTAGTACTACACA
1 TACACATAGTAGCCTGCACATAGTACTACACA
29290172 AGTGTTTATA
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
50 34 0.30
51 74 0.66
52 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACTTTCCGG
Found at i:29302705 original size:16 final size:16
Alignment explanation
Indices: 29302684--29302720 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
29302674 TTTGGAGAGA
29302684 TTCTTTCCACCATTAT
1 TTCTTTCCACCATTAT
* *
29302700 TTCTTTCCACCTTTCT
1 TTCTTTCCACCATTAT
29302716 TTCTT
1 TTCTT
29302721 CTTCCCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.57
Consensus pattern (16 bp):
TTCTTTCCACCATTAT
Found at i:29311965 original size:27 final size:26
Alignment explanation
Indices: 29311886--29311967 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 26
29311876 CACGATATAT
*
29311886 AAAGAAAGCTTTTGTGACATAAT-AT-A
1 AAAGAAAGC-TTTGTGGCA-AATCATGA
*
29311912 AAAGAAAGCCTTTGTGGTAAA-CAATGA
1 AAAGAAAG-CTTTGTGGCAAATC-ATGA
29311939 AAAGAAAGCTTATGTGGCAAATCATGA
1 AAAGAAAGCTT-TGTGGCAAATCATGA
29311966 AA
1 AA
29311968 TAAAAGCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
25 2 0.04
26 20 0.43
27 24 0.51
28 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (26 bp):
AAAGAAAGCTTTGTGGCAAATCATGA
Found at i:29324918 original size:17 final size:17
Alignment explanation
Indices: 29324896--29324928 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29324886 GTTAGTGCAC
*
29324896 ATTGTCATTGCATTTTT
1 ATTGTCATCGCATTTTT
29324913 ATTGTCATCGCATTTT
1 ATTGTCATCGCATTTT
29324929 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (17 bp):
ATTGTCATCGCATTTTT
Found at i:29330549 original size:13 final size:13
Alignment explanation
Indices: 29330528--29330560 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
29330518 CGTGTTGTAG
29330528 TTGTATTTACTTA
1 TTGTATTTACTTA
*
29330541 TTGTGTTTACTTA
1 TTGTATTTACTTA
29330554 TT-TATTT
1 TTGTATTT
29330561 TAGTTTGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (13 bp):
TTGTATTTACTTA
Found at i:29330992 original size:25 final size:25
Alignment explanation
Indices: 29330958--29331006 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
29330948 GGATTGATGG
29330958 ATGTATGAAGGCCTTGTAAAAGGCT
1 ATGTATGAAGGCCTTGTAAAAGGCT
*
29330983 ATGTATGAAGGCCTTGTAATAGGC
1 ATGTATGAAGGCCTTGTAAAAGGC
29331007 CTATTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (25 bp):
ATGTATGAAGGCCTTGTAAAAGGCT
Found at i:29331000 original size:13 final size:13
Alignment explanation
Indices: 29330959--29331000 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
29330949 GATTGATGGA
29330959 TGTATGAAGGCCT
1 TGTATGAAGGCCT
*
29330972 TGTA-AAAGG-CT
1 TGTATGAAGGCCT
29330983 ATGTATGAAGGCCT
1 -TGTATGAAGGCCT
29330997 TGTA
1 TGTA
29331001 ATAGGCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 12 0.50
14 2 0.08
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (13 bp):
TGTATGAAGGCCT
Found at i:29358120 original size:16 final size:14
Alignment explanation
Indices: 29358082--29358120 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
29358072 CTTAAAGATA
29358082 TCTTCCTTTTTTGT
1 TCTTCCTTTTTTGT
*
29358096 TCATCCTTTTTGTGTT
1 TCTTCCTTTTT-TG-T
29358112 TCTTCCTTT
1 TCTTCCTTT
29358121 CTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.48
15 2 0.10
16 9 0.43
ACGTcount: A:0.03, C:0.23, G:0.08, T:0.67
Consensus pattern (14 bp):
TCTTCCTTTTTTGT
Found at i:29368038 original size:15 final size:15
Alignment explanation
Indices: 29368020--29368049 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29368010 TAGGTAGAAA
29368020 TTAAATTAAACAAAT
1 TTAAATTAAACAAAT
*
29368035 TTAAATTAAGCAAAT
1 TTAAATTAAACAAAT
29368050 GGAATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
TTAAATTAAACAAAT
Found at i:29377625 original size:19 final size:19
Alignment explanation
Indices: 29377601--29377646 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
29377591 TGTCAACTAT
*
29377601 ACTTGCATCGACAGTGTAC
1 ACTTGCACCGACAGTGTAC
*
29377620 ACTTGCACCGATAGTGTAC
1 ACTTGCACCGACAGTGTAC
29377639 ACTTGCAC
1 ACTTGCAC
29377647 ATTATTGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (19 bp):
ACTTGCACCGACAGTGTAC
Found at i:29387598 original size:41 final size:41
Alignment explanation
Indices: 29387536--29387683 Score: 215
Period size: 41 Copynumber: 3.6 Consensus size: 41
29387526 GTTAATTATT
29387536 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * *
29387577 CCCTGAATTGTACATACGTGCCCCTATTTATACTTCGATAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* **
29387618 CCTTAAATTGCACATACGTGCCCCTATTTGTACTTTAGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* *
29387659 CCATGAATTGCACATACGTGCCCCT
1 CCCTAAATTGCACATACGTGCCCCT
29387684 GTTTACACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
Found at i:29387600 original size:21 final size:20
Alignment explanation
Indices: 29387536--29387683 Score: 77
Period size: 21 Copynumber: 7.2 Consensus size: 20
29387526 GTTAATTATT
*
29387536 CCCTAAATTGCACATACGTGC
1 CCCT-AATTGTACATACGTGC
* * *
29387557 CCCTATTTGTAC-TTCGGTAC
1 CCCTAATTGTACATAC-GTGC
29387577 CCCTGAATTGTACATACGTGC
1 CCCT-AATTGTACATACGTGC
* * * *
29387598 CCCTATTTATAC-TTCGATAC
1 CCCTAATTGTACATACG-TGC
* *
29387618 CCTTAAATTGCACATACGTGC
1 CCCT-AATTGTACATACGTGC
* * *
29387639 CCCTATTTGTACTTTA-GTAC
1 CCCTAATTGTAC-ATACGTGC
* *
29387659 CCATGAATTGCACATACGTGC
1 CCCT-AATTGTACATACGTGC
29387680 CCCT
1 CCCT
29387684 GTTTACACTC
Statistics
Matches: 90, Mismatches: 28, Indels: 18
0.66 0.21 0.13
Matches are distributed among these distances:
19 5 0.06
20 38 0.42
21 42 0.47
22 5 0.06
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (20 bp):
CCCTAATTGTACATACGTGC
Found at i:29387676 original size:82 final size:82
Alignment explanation
Indices: 29387539--29387698 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 82
29387529 AATTATTCCC
* * *
29387539 TAAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGAATTGTACATACGTGCCCCTAT
1 TAAATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCATGAATTGCACATACGTGCCCCTAT
* *
29387604 TTATACTTCGATACCCT
66 TTACACTCCGATACCCT
* *
29387621 TAAATTGCACATACGTGCCCCTATTTGTACTTTAGTACCCATGAATTGCACATACGTGCCCCTGT
1 TAAATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCATGAATTGCACATACGTGCCCCTAT
29387686 TTACACTCCGATA
66 TTACACTCCGATA
29387699 ACTTTGACTC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (82 bp):
TAAATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCATGAATTGCACATACGTGCCCCTAT
TTACACTCCGATACCCT
Found at i:29391446 original size:4 final size:4
Alignment explanation
Indices: 29391437--29391548 Score: 189
Period size: 4 Copynumber: 29.2 Consensus size: 4
29391427 AGATAGCCAT
29391437 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29391485 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA- ATA- ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29391531 A-A- ATA- ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG A
29391549 AAAAAAAAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
2 1 0.01
3 11 0.10
4 93 0.89
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:29391554 original size:1 final size:1
Alignment explanation
Indices: 29391548--29391637 Score: 180
Period size: 1 Copynumber: 90.0 Consensus size: 1
29391538 AGATAGATAG
29391548 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29391613 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
29391638 TAGATAGATA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 89 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29391644 original size:4 final size:4
Alignment explanation
Indices: 29391637--29392957 Score: 2042
Period size: 4 Copynumber: 333.0 Consensus size: 4
29391627 AAAAAAAAAA
29391637 ATAG ATAG ATAG ATAG ATAG ATAG ATA- ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29391684 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29391732 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* *
29391780 AAAA ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* *
29391828 ATAG ATAG ATA- ATAG ATAG ATA- AAAA ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* *
29391874 ATAG ATAG ATAG AAAA ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29391922 ATAG ATAAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG AT-AG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29391971 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392019 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392067 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392115 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA- ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392162 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392210 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA- ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392257 ATAG AATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG -ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * * * * * * * * * * * * * *
29392306 ATAG ATA- A-AA AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * * * * * * * * * * * * * * *
29392352 AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* *
29392400 ATAG ATAG ATA- A-AG AAAA ATAG ATAG ATAG ATAG ATAG ATAG A-A-
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392444 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392492 ATAG ATA- ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392539 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392587 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG -ATAG ATAG
29392636 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392684 ATAG ATAG ATA- ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392731 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA- A-AG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * *
29392777 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAA AAAA ATAAA ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT-AG ATAG
29392826 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392874 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392922 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
29392958 CCACAAATGT
Statistics
Matches: 1278, Mismatches: 20, Indels: 38
0.96 0.01 0.03
Matches are distributed among these distances:
2 4 0.00
3 28 0.02
4 1230 0.96
5 16 0.01
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.23
Consensus pattern (4 bp):
ATAG
Found at i:29392318 original size:1 final size:1
Alignment explanation
Indices: 29392312--29392392 Score: 162
Period size: 1 Copynumber: 81.0 Consensus size: 1
29392302 ATAGATAGAT
29392312 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29392377 AAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAA
29392393 TAGATAGATA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29393551 original size:16 final size:15
Alignment explanation
Indices: 29393511--29393561 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
29393501 CATGCAACCT
*
29393511 ATGCACAGACTCATC
1 ATGCAAAGACTCATC
*
29393526 ATGCAGAGACTCATTC
1 ATGCAAAGACTCA-TC
*
29393542 ATGTAAAGACTCCATC
1 ATGCAAAGACT-CATC
29393558 ATGC
1 ATGC
29393562 TTTCAAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.40
16 16 0.53
17 2 0.07
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (15 bp):
ATGCAAAGACTCATC
Found at i:29398238 original size:21 final size:21
Alignment explanation
Indices: 29398214--29398254 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29398204 TCATAAGCCA
29398214 ATTTCATCATCAAAT-GCATAT
1 ATTTCAT-ATCAAATGGCATAT
*
29398235 ATTTCATATCATATGGCATA
1 ATTTCATATCAAATGGCATA
29398255 CCGCATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTTCATATCAAATGGCATAT
Found at i:29403754 original size:39 final size:40
Alignment explanation
Indices: 29403659--29403881 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
29403649 TTGAATGATG
*
29403659 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
29403697 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
29403738 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
29403777 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
29403816 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
29403855 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
29403882 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 58 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:29403853 original size:79 final size:81
Alignment explanation
Indices: 29403659--29403881 Score: 266
Period size: 79 Copynumber: 2.8 Consensus size: 81
29403649 TTGAATGATG
* * *
29403659 TCCGGGCTAAGTCCCGAAGGC--TTGTGCT-AAGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTG-TGAA-TTACTAATATCCGGGCTAAGACCCGAAGGCA
*
29403720 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
*
29403738 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGA-ATTACTAATATCCGGGCTAAGACCCGAAGGCAT
*
29403799 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * *
29403816 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAATTACTAATATCCGGGCTAAGACCCGAAGGCATT
29403880 TG
66 TG
29403882 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
78 47 0.38
79 54 0.43
80 23 0.18
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAATTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:29403903 original size:79 final size:79
Alignment explanation
Indices: 29403659--29403914 Score: 208
Period size: 79 Copynumber: 3.3 Consensus size: 79
29403649 TTGAATGATG
* * * *
29403659 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
29403720 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
29403738 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
29403802 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
29403816 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
29403879 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
29403896 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29403915 TACGTGATTT
Statistics
Matches: 152, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 68 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:29411580 original size:40 final size:40
Alignment explanation
Indices: 29411397--29411580 Score: 175
Period size: 40 Copynumber: 4.7 Consensus size: 40
29411387 TTGAATGATG
* * *
29411397 TCCGGGCTAAGTCCAGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAA-A
* * *
29411436 TCCGGACTAAGAT-CCGAAGGCATTTATGCGAGA-TACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTAAA
*
29411476 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
* * *
29411515 TTCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AA
*
29411556 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29411581 AACGAGGAGC
Statistics
Matches: 119, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
39 49 0.41
40 59 0.50
41 10 0.08
42 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:29413820 original size:15 final size:15
Alignment explanation
Indices: 29413779--29413820 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
29413769 ATTTCAACTC
29413779 TTTGAGTTATTTCTCT
1 TTTGA-TTATTTCTCT
*
29413795 TTATGA-GATTTCTCT
1 TT-TGATTATTTCTCT
29413810 TTTGATTATTT
1 TTTGATTATTT
29413821 TAGAGGTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 3 0.14
15 14 0.64
16 2 0.09
17 3 0.14
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.62
Consensus pattern (15 bp):
TTTGATTATTTCTCT
Found at i:29428510 original size:13 final size:13
Alignment explanation
Indices: 29428492--29428516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29428482 CATGAGTATT
29428492 AAGAAAAAATTAA
1 AAGAAAAAATTAA
29428505 AAGAAAAAATTA
1 AAGAAAAAATTA
29428517 TTTTGTAATT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAGAAAAAATTAA
Found at i:29432410 original size:30 final size:30
Alignment explanation
Indices: 29432376--29432435 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
29432366 CATTACATAG
*
29432376 CTATTATCAAATTGATGTCAAACGGTGTAT
1 CTATTATCAAATTGATGTCAAACAGTGTAT
29432406 CTATTATCAAATTGATGTCAAACAGTGTAT
1 CTATTATCAAATTGATGTCAAACAGTGTAT
29432436 GAGCATGGGA
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:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (30 bp):
CTATTATCAAATTGATGTCAAACAGTGTAT
Found at i:29434823 original size:17 final size:20
Alignment explanation
Indices: 29434806--29434854 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
29434796 TGGAGTAGGA
*
29434806 ATATTGATACCTTAGGAAAT
1 ATATCGATACCTTAGGAAAT
*
29434826 ATATCGATACCTTAAGAAA-
1 ATATCGATACCTTAGGAAAT
29434845 AGTATCGATA
1 A-TATCGATA
29434855 GTAGATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (20 bp):
ATATCGATACCTTAGGAAAT
Found at i:29441775 original size:3 final size:3
Alignment explanation
Indices: 29441767--29441795 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29441757 GATCCCAAAA
29441767 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29441796 AGTGAGGATC
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29441926 original size:3 final size:3
Alignment explanation
Indices: 29441918--29441991 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
29441908 TTGTTTGCTT
29441918 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29441966 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
29441992 AGTGAGGATC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29450919 original size:37 final size:37
Alignment explanation
Indices: 29450869--29450947 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29450859 TTATTACGAA
* * *
29450869 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
29450906 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
29450943 GTCTT
1 GTCTT
29450948 TAGAGCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:29451143 original size:47 final size:47
Alignment explanation
Indices: 29451065--29451747 Score: 1114
Period size: 47 Copynumber: 14.4 Consensus size: 47
29451055 CCCTTCGGGA
* * * * * * *
29451065 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29451112 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29451159 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29451206 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29451253 CTTATCACATATATACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29451300 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29451349 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29451396 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29451443 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29451490 CTTATCACATATATATACACTTTCACATTGATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29451539 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29451586 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29451633 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29451680 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29451729 CTTATCACATATATACACT
1 CTTATCACATATATACACT
29451748 GTCTTGGCTG
Statistics
Matches: 603, Mismatches: 27, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
47 467 0.77
49 136 0.23
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29451373 original size:143 final size:141
Alignment explanation
Indices: 29451065--29451747 Score: 1123
Period size: 143 Copynumber: 4.8 Consensus size: 141
29451055 CCCTTCGGGA
* * * * * * * * * *
29451065 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
29451130 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
29451195 GGCCATTAGGC
131 GGCCATTAGGC
*
29451206 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
29451271 TTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
29451336 TCGGCCATTAGGC
129 TCGGCCATTAGGC
*
29451349 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
* *
29451414 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
29451479 GGCCATTAGGC
131 GGCCATTAGGC
*
29451490 CTTATCACATATATATACACTTTCACATTGATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
* *
29451555 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
29451620 TCGGCTATTAGGC
129 TCGGCCATTAGGC
* *
29451633 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC--ATATATAC
29451698 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
29451748 GTCTTGGCTG
Statistics
Matches: 511, Mismatches: 25, Indels: 10
0.94 0.05 0.02
Matches are distributed among these distances:
141 180 0.35
143 331 0.65
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:29451386 original size:190 final size:190
Alignment explanation
Indices: 29451065--29451747 Score: 1199
Period size: 190 Copynumber: 3.6 Consensus size: 190
29451055 CCCTTCGGGA
** * * * * * * * *
29451065 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
29451128 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
* * *
29451193 TCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
29451253 CTTATCACATATATACACTTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
29451318 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
29451383 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
29451443 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
29451508 ACTTTCACATTGATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
29451573 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
29451633 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
29451698 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
29451748 GTCTTGGCTG
Statistics
Matches: 474, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
188 45 0.09
190 429 0.91
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (190 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:29456269 original size:18 final size:18
Alignment explanation
Indices: 29456243--29456278 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29456233 GGTCTCAGTT
*
29456243 TTTCTAAAGGTATCGATA
1 TTTCCAAAGGTATCGATA
*
29456261 TTTCCAAAGTTATCGATA
1 TTTCCAAAGGTATCGATA
29456279 CCTGGCCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
TTTCCAAAGGTATCGATA
Found at i:29456366 original size:20 final size:20
Alignment explanation
Indices: 29456341--29456392 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
29456331 GACAATCATT
*
29456341 TTAAAATGATTTTGACTTGG
1 TTAAAATGATTTTGACATGG
29456361 TTAAAATGATTTTGACATGG
1 TTAAAATGATTTTGACATGG
*
29456381 TTAAAATCATTT
1 TTAAAATGATTT
29456393 GCACTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (20 bp):
TTAAAATGATTTTGACATGG
Found at i:29456640 original size:30 final size:29
Alignment explanation
Indices: 29456604--29456674 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
29456594 TCCACTTGAC
* *
29456604 TTAGATAGCCACAGAGGTG-TCTACACATCA
1 TTAGATAGCCACA-AGG-GATCCAAACATCA
*
29456634 TTAGATAGCCATAAGGGCATCCAAACATCA
1 TTAGATAGCCACAAGGG-ATCCAAACATCA
29456664 TTAGATAGCCA
1 TTAGATAGCCA
29456675 TAAAGGCATC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 32 0.89
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (29 bp):
TTAGATAGCCACAAGGGATCCAAACATCA
Found at i:29456675 original size:30 final size:30
Alignment explanation
Indices: 29456628--29456686 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
29456618 AGGTGTCTAC
*
29456628 ACATCATTAGATAGCCATAAGGGCATCCAA
1 ACATCATTAGATAGCCATAAAGGCATCCAA
29456658 ACATCATTAGATAGCCATAAAGGCATCCA
1 ACATCATTAGATAGCCATAAAGGCATCCA
29456687 TACACATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (30 bp):
ACATCATTAGATAGCCATAAAGGCATCCAA
Found at i:29458136 original size:20 final size:20
Alignment explanation
Indices: 29458111--29458149 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29458101 TACTTTCTTC
29458111 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
29458131 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
29458150 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:29459783 original size:50 final size:50
Alignment explanation
Indices: 29459718--29459947 Score: 354
Period size: 50 Copynumber: 4.6 Consensus size: 50
29459708 GAGCCAATGT
* * * * *
29459718 CATGTCCCAGACATGGTCTTACACTGACTCTTCTCTGT-TCGTGCCGATGG
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCT-GTGCCGATGC
* *
29459768 CATATCCCAAACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
*
29459818 CATGTCCTAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
* *
29459868 CATGTCCTAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGTCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
29459918 CATGTCCCAGACATGGTCTTACACTGGCAC
1 CATGTCCCAGACATGGTCTTACACTGGCAC
29459948 ACTTACTGCC
Statistics
Matches: 167, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 166 0.99
51 1 0.01
ACGTcount: A:0.18, C:0.32, G:0.22, T:0.28
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
Found at i:29460032 original size:44 final size:44
Alignment explanation
Indices: 29459975--29460062 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
29459965 AACCATGGTA
* * *
29459975 TTTTTCGTTAATTCTTTCTTAATTGCCATGTTATAAACATGGAC
1 TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
29460019 TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
1 TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
29460063 CTTGAGATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (44 bp):
TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
Found at i:29461643 original size:50 final size:50
Alignment explanation
Indices: 29461572--29461755 Score: 163
Period size: 50 Copynumber: 3.6 Consensus size: 50
29461562 CTGTACTGCA
* * * ** * *
29461572 AATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCAGTACC
* * * * *
29461622 CATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCAGTACC
1 AATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCAGTACC
* * *
29461672 AACGCCATGTCCCAGACATGGTCTTAC-GTGGGACCTCTCATAACCTCAATAATGCC
1 AATGCCATGTCCCAGACATGGTCTTACAG-GAGACCTCTCAT-A--TCAGT-A--CC
29461728 AATGCCATGTCCCAGACATGGTCTTACA
1 AATGCCATGTCCCAGACATGGTCTTACA
29461756 TGATGTCTCA
Statistics
Matches: 108, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 74 0.69
53 4 0.04
54 1 0.01
56 28 0.26
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCAGTACC
Found at i:29461744 original size:56 final size:52
Alignment explanation
Indices: 29461618--29461754 Score: 179
Period size: 50 Copynumber: 2.6 Consensus size: 52
29461608 CTCATATCGG
* * *
29461618 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCAGTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAATA
* *
29461670 --CCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT---CTCAAT-A
29461724 TGCCAATGCCATGTCCCAGACATGGTCTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC
29461755 ATGATGTCTC
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
50 39 0.53
53 5 0.07
54 1 0.01
56 28 0.38
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAATA
Found at i:29462849 original size:50 final size:50
Alignment explanation
Indices: 29462795--29462961 Score: 120
Period size: 50 Copynumber: 3.2 Consensus size: 50
29462785 TATCCCAAAT
* ** * * * *
29462795 ATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACAGGAGACCTCTCATATCAGTACCAATGACATGTCCCAGAC
** * *
29462845 ATGGTCTTATGGGGGACCTCTCATCTCAGTACCAATGACATGTCCCAGAC
1 ATGGTCTTACAGGAGACCTCTCATATCAGTACCAATGACATGTCCCAGAC
* * * * *
29462895 ATGGTCTTA-TGTGGGACCTCTCATAACCTCAATAATGTCAATGTCATGTCCCAGAC
1 ATGGTCTTACAG-GAGACCTCTCAT-A--TCAGT-A--CCAATGACATGTCCCAGAC
29462951 ATGGTCTTACA
1 ATGGTCTTACA
29462962 TAGGGTCTCA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
49 1 0.01
50 60 0.65
53 4 0.04
54 1 0.01
56 26 0.28
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (50 bp):
ATGGTCTTACAGGAGACCTCTCATATCAGTACCAATGACATGTCCCAGAC
Found at i:29462950 original size:56 final size:50
Alignment explanation
Indices: 29462833--29462959 Score: 164
Period size: 50 Copynumber: 2.4 Consensus size: 50
29462823 GTGCCCATGC
*
29462833 CATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCAGTACCAATGA
1 CATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCAATACCAATGA
* * *
29462883 CATGTCCCAGACATGGTCTTATGTGGGACCTCTCATAACCTCAATAATGTCAATGT
1 CATGTCCCAGACATGGTCTTATGGGGGACCTCTCAT---CTCAAT-A--CCAATGA
29462939 CATGTCCCAGACATGGTCTTA
1 CATGTCCCAGACATGGTCTTA
29462960 CATAGGGTCT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
50 35 0.52
53 5 0.07
54 1 0.01
56 26 0.39
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCAATACCAATGA
Found at i:29466147 original size:48 final size:49
Alignment explanation
Indices: 29466087--29466183 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 49
29466077 CTAATCCAAG
*
29466087 AAAACTTCTAACCTCTGACACATTTCTGGGT-GTTTCCACTCAACAATT
1 AAAACTTCTAACCTCTCACACATTTCTGGGTGGTTTCCACTCAACAATT
* *
29466135 AAAACTTTTAACCTCTCACACATTTTTGGGTGGTTTCCACTCAACAATT
1 AAAACTTCTAACCTCTCACACATTTCTGGGTGGTTTCCACTCAACAATT
29466184 GCTGAAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 28 0.62
49 17 0.38
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (49 bp):
AAAACTTCTAACCTCTCACACATTTCTGGGTGGTTTCCACTCAACAATT
Found at i:29474507 original size:20 final size:18
Alignment explanation
Indices: 29474482--29474518 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
29474472 CTACCTAATA
29474482 AAAGAAGGAGAGAGAAGAAG
1 AAAGAA-GA-AGAGAAGAAG
29474502 AAAGAAGAAGAGAAGAA
1 AAAGAAGAAGAGAAGAA
29474519 TTTGTGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AAAGAAGAAGAGAAGAAG
Found at i:29482545 original size:26 final size:27
Alignment explanation
Indices: 29482516--29482571 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
29482506 GAGGGTGGTT
*
29482516 CTTA-AGAGTGTGCCACGAAGGCATTC
1 CTTACAGAGTGTGCCACAAAGGCATTC
* *
29482542 CTTACAGAGTTTGCGACAAAGGCATTC
1 CTTACAGAGTGTGCCACAAAGGCATTC
29482569 CTT
1 CTT
29482572 CCATATTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (27 bp):
CTTACAGAGTGTGCCACAAAGGCATTC
Found at i:29482650 original size:25 final size:26
Alignment explanation
Indices: 29482557--29482650 Score: 100
Period size: 26 Copynumber: 3.6 Consensus size: 26
29482547 AGAGTTTGCG
* * *
29482557 ACAAAGGCATTCCTTCCATATTCCACC
1 ACAAAGGC-TTTCTTTCATATTACACC
** *
29482584 GTAAAGGCTTTCTTTCATATTACGCC
1 ACAAAGGCTTTCTTTCATATTACACC
29482610 ACAAAGGCTTTCTTTCATATTACACC
1 ACAAAGGCTTTCTTTCATATTACACC
* *
29482636 A-AAAGGATTTATTTC
1 ACAAAGGCTTTCTTTC
29482651 TGGATGTGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 12 0.21
26 38 0.68
27 6 0.11
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.34
Consensus pattern (26 bp):
ACAAAGGCTTTCTTTCATATTACACC
Found at i:29487638 original size:7 final size:7
Alignment explanation
Indices: 29487626--29487657 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
29487616 TTCCATGTCA
29487626 TTTTCAT
1 TTTTCAT
29487633 TTTTCAT
1 TTTTCAT
29487640 TTTTCAT
1 TTTTCAT
29487647 TTTTCAT
1 TTTTCAT
29487654 TTTT
1 TTTT
29487658 GAGAAAACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCAT
Found at i:29487704 original size:41 final size:43
Alignment explanation
Indices: 29487627--29487719 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 43
29487617 TCCATGTCAT
* *
29487627 TTTCATTT-TTCATTTTTCATTTTTCATTTTTGAGAAAACGACA
1 TTTCATTTCTCCA-TTTTCATTTTTCATTTTTGAGAAAACCACA
29487670 -TTCATTTCTCCATTTTCA-TTTTCA-TTTTGCAGAAAACCACA
1 TTTCATTTCTCCATTTTCATTTTTCATTTTTG-AGAAAACCACA
29487711 TTTCATTTC
1 TTTCATTTC
29487720 CAAATGTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
40 5 0.11
41 16 0.36
42 21 0.47
43 3 0.07
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.51
Consensus pattern (43 bp):
TTTCATTTCTCCATTTTCATTTTTCATTTTTGAGAAAACCACA
Found at i:29492069 original size:42 final size:42
Alignment explanation
Indices: 29491988--29492114 Score: 139
Period size: 43 Copynumber: 3.0 Consensus size: 42
29491978 TTCCAATATT
* * * ** *
29491988 GATTTGAGATCCCGTATAATACCATATATGGGATA-TGGCATC
1 GATTTGAGAT-TCGTGTAAGACCATAGCTGGGCTATTGGCATC
*
29492030 GATTTGAGATTCGTGTAAGACCATAGCTGGGCTATTGGCATT
1 GATTTGAGATTCGTGTAAGACCATAGCTGGGCTATTGGCATC
* * *
29492072 GATTTAAGATTTTGTGTAAGACTATAGCTGGGCTATTGGCATC
1 GATTTGAGA-TTCGTGTAAGACCATAGCTGGGCTATTGGCATC
29492115 AATACGAGAT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 18 0.25
42 24 0.33
43 30 0.42
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (42 bp):
GATTTGAGATTCGTGTAAGACCATAGCTGGGCTATTGGCATC
Found at i:29492125 original size:43 final size:43
Alignment explanation
Indices: 29492042--29492140 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
29492032 TTTGAGATTC
** **
29492042 GTGTAAGACCATAGCTGGGCTATTGGCATTGATTTAAGATTTT
1 GTGTAAGACCATAGCTGGGCTATTGGCATCAATACAAGATTTT
* * *
29492085 GTGTAAGACTATAGCTGGGCTATTGGCATCAATACGAGATTTCC
1 GTGTAAGACCATAGCTGGGCTATTGGCATCAATACAAGATTT-T
*
29492129 ATGTAAGACCAT
1 GTGTAAGACCAT
29492141 GTTTGGGACA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 36 0.78
44 10 0.22
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATTGGCATCAATACAAGATTTT
Found at i:29497340 original size:10 final size:10
Alignment explanation
Indices: 29497325--29497366 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
29497315 AACTTCAATT
29497325 ATTTCTATTC
1 ATTTCTATTC
29497335 ATTTCTA-TC
1 ATTTCTATTC
29497344 ATTTGC-ATTC
1 ATTT-CTATTC
29497354 ATTTCTATTC
1 ATTTCTATTC
29497364 ATT
1 ATT
29497367 GGTTCTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.57
Consensus pattern (10 bp):
ATTTCTATTC
Found at i:29507986 original size:42 final size:41
Alignment explanation
Indices: 29507890--29507986 Score: 151
Period size: 42 Copynumber: 2.4 Consensus size: 41
29507880 TACTTAGTGA
*
29507890 GTTACACAGC-TGGGACACACCGTGTGTCCCTTGTTTGAAT
1 GTTACACAGCTTGGGACACACCGTGTGTCCCTTGTTCGAAT
* *
29507930 GTTACACGGGTTGGGACACAACCGTGTGTCCCTTGTTCGAAT
1 GTTACACAGCTTGGGACAC-ACCGTGTGTCCCTTGTTCGAAT
29507972 GTTACACAGCTTGGG
1 GTTACACAGCTTGGG
29507987 GAGATATTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 8 0.16
41 8 0.16
42 34 0.68
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.29
Consensus pattern (41 bp):
GTTACACAGCTTGGGACACACCGTGTGTCCCTTGTTCGAAT
Found at i:29508083 original size:21 final size:21
Alignment explanation
Indices: 29508057--29508096 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29508047 TTTTCTTAAA
*
29508057 AGTTCTCATTTGCTTCAAATT
1 AGTTCTCAATTGCTTCAAATT
*
29508078 AGTTCTGAATTGCTTCAAA
1 AGTTCTCAATTGCTTCAAA
29508097 GTTATTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
AGTTCTCAATTGCTTCAAATT
Found at i:29526547 original size:33 final size:32
Alignment explanation
Indices: 29526505--29526570 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
29526495 CTTACCTCGA
29526505 TAAACAAAGCATAAAAACATAATCGATCAATC
1 TAAACAAAGCATAAAAACATAATCGATCAATC
29526537 TAAACGAAAGCATAAAAACATAATCGATCAATC
1 TAAAC-AAAGCATAAAAACATAATCGATCAATC
29526570 T
1 T
29526571 GAAGCTTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.55, C:0.18, G:0.08, T:0.20
Consensus pattern (32 bp):
TAAACAAAGCATAAAAACATAATCGATCAATC
Found at i:29529614 original size:558 final size:558
Alignment explanation
Indices: 29528184--29529860 Score: 3180
Period size: 558 Copynumber: 3.0 Consensus size: 558
29528174 CCCAAAAAAT
29528184 AGAGACATAGATGTGACTGACTAGACTAGCAATACGTTGGACTGGACCTAAAAAGAATAGATCTT
1 AGAGACATAGATGTGACTGACTAGACTAGCAATACGTTGGACTGGACCTAAAAAGAATAGATCTT
**
29528249 GAATCCATTTATGTATAAATTCACTTGTGATGTTCATAGTGTGGTATACCTAAATCCTGAGTGGA
66 GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGTATACCTAAATCCTGAGTGGA
*
29528314 TGACGGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
131 TGACAGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
29528379 AGAAACCGAAAGCTGGTGTGTTGGATGTACGACTTCTACAATATGTAGCTTAATTTACAATAATG
196 AGAAACCGAAAGCTGGTGTGTTGGATGTACGACTTCTACAATATGTAGCTTAATTTACAATAATG
*
29528444 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATAAAAAG
261 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
29528509 TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTGA
326 TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTGA
29528574 CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAAAT
391 CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAAAT
29528639 ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
456 ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
29528704 GCATTGGT-GAGTTGATTTCGTAATGGCATGCCATTGG
521 GCATTGGTAGAGTTGATTTCGTAATGGCATGCCATTGG
29528741 AGAGACATAGATGTGACTGACTAGACTAGCAATACGTTGGACTGGACCTAAAAAGAATAGATCTT
1 AGAGACATAGATGTGACTGACTAGACTAGCAATACGTTGGACTGGACCTAAAAAGAATAGATCTT
*
29528806 GAATCCATTTATGTATTTA-TCACTTGTGATGTTCATAGTGTGGTATACCTAAATCCTGAGTGCA
66 GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGTATACCTAAATCCTGAGTGGA
29528870 TGACAGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
131 TGACAGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
*
29528935 AGAAACCGAAAGCTGGTGTGCTGGATGTACGACTTCTACAATATGTAGCTTAATTTACAATAATG
196 AGAAACCGAAAGCTGGTGTGTTGGATGTACGACTTCTACAATATGTAGCTTAATTTACAATAATG
29529000 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
261 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
*
29529065 TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTTA
326 TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTGA
29529130 CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAAAT
391 CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAAAT
29529195 ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
456 ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
29529260 GCATTGGTAGAGTTGATTTCGTAATGGCATGCCATTGG
521 GCATTGGTAGAGTTGATTTCGTAATGGCATGCCATTGG
* *
29529298 AGAGACATAGATGTGACTGACTAGACTAGCAATACGTTGGACTGGACCTAAGAAGAATAGATCCT
1 AGAGACATAGATGTGACTGACTAGACTAGCAATACGTTGGACTGGACCTAAAAAGAATAGATCTT
*
29529363 GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGCATACCTAAATCCTGAGTGGA
66 GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGTATACCTAAATCCTGAGTGGA
*
29529428 TGACAGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTGAGTTTGAATAGATA
131 TGACAGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
29529493 AGAAACCGAAAGCTGGTGTGTTGGATGTACGACTTCTACAATATGTAGCTTAATTTACAATAATG
196 AGAAACCGAAAGCTGGTGTGTTGGATGTACGACTTCTACAATATGTAGCTTAATTTACAATAATG
29529558 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
261 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
*
29529623 TAAATGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTGA
326 TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTGA
29529688 CTT-TTCATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAAA
391 CTTCTT-ATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAAA
* *
29529752 TATTATCCCAAAGAGATTAAGGATATCCTATTAGGGTAACACACATAAGACAAGGTCATTGGACG
455 TATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACG
* *
29529817 AGCATTGGTAGAGTTGATTTCATAATGGTATGCCATTGG
520 AGCATTGGTAGAGTTGATTTCGTAATGGCATGCCATTGG
29529856 AGAGA
1 AGAGA
29529861 GCTCAGTCTG
Statistics
Matches: 1098, Mismatches: 19, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
556 438 0.40
557 195 0.18
558 465 0.42
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (558 bp):
AGAGACATAGATGTGACTGACTAGACTAGCAATACGTTGGACTGGACCTAAAAAGAATAGATCTT
GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGTATACCTAAATCCTGAGTGGA
TGACAGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
AGAAACCGAAAGCTGGTGTGTTGGATGTACGACTTCTACAATATGTAGCTTAATTTACAATAATG
GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTGA
CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAAAT
ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
GCATTGGTAGAGTTGATTTCGTAATGGCATGCCATTGG
Found at i:29532243 original size:13 final size:13
Alignment explanation
Indices: 29532225--29532249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29532215 TAATGGTATA
29532225 TTGAATCCATGAC
1 TTGAATCCATGAC
29532238 TTGAATCCATGA
1 TTGAATCCATGA
29532250 AAATTTAGTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:29532827 original size:27 final size:27
Alignment explanation
Indices: 29532796--29532973 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29532786 TAAATTGTAC
29532796 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29532823 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29532849 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29532877 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29532905 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29532932 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29532959 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29532974 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29532910 original size:82 final size:81
Alignment explanation
Indices: 29532797--29532952 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29532787 AAATTGTACA
* *
29532797 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29532861 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29532878 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29532943 TGCGAGTTGA
65 TGCGAATTGA
29532953 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29532964 original size:82 final size:81
Alignment explanation
Indices: 29532793--29532973 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29532783 GATTAAATTG
* *
29532793 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29532858 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29532874 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29532938 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29532956 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29532974 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29532984 original size:27 final size:27
Alignment explanation
Indices: 29532878--29532984 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
29532868 TGACCATGCG
* * * *
29532878 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
29532906 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
29532933 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
29532960 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
29532985 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:29540146 original size:13 final size:13
Alignment explanation
Indices: 29540128--29540152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29540118 TAATGGTATA
29540128 TTGAATCCATGAC
1 TTGAATCCATGAC
29540141 TTGAATCCATGA
1 TTGAATCCATGA
29540153 AAATTTAGTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:29540730 original size:27 final size:27
Alignment explanation
Indices: 29540699--29540876 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29540689 TAAATTGTAC
29540699 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29540726 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29540752 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29540780 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29540808 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29540835 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29540862 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29540877 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29540813 original size:82 final size:81
Alignment explanation
Indices: 29540700--29540855 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29540690 AAATTGTACA
* *
29540700 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29540764 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29540781 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29540846 TGCGAGTTGA
65 TGCGAATTGA
29540856 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29540867 original size:82 final size:81
Alignment explanation
Indices: 29540696--29540876 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29540686 GATTAAATTG
* *
29540696 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29540761 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29540777 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29540841 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29540859 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29540877 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29540887 original size:27 final size:27
Alignment explanation
Indices: 29540781--29540887 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
29540771 TGACCATGCG
* * * *
29540781 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
29540809 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
29540836 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
29540863 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
29540888 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:29554367 original size:21 final size:23
Alignment explanation
Indices: 29554333--29554374 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
29554323 TTATACAAAC
29554333 AAAATACATAATACA-ATAAAGA
1 AAAATACATAATACATATAAAGA
*
29554355 AAAATATAT-ATACATATAAA
1 AAAATACATAATACATATAAA
29554375 TTATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAATACATAATACATATAAAGA
Found at i:29554587 original size:30 final size:31
Alignment explanation
Indices: 29554514--29554596 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 31
29554504 ACATATATAA
* ** *
29554514 AAATAATAATTATCTACATATATATAGATTAT
1 AAATAATAATAAT-TACATATATATAGAAAAC
29554546 AAA-AA-AGATAATTACATATATATA-AAAAC
1 AAATAATA-ATAATTACATATATATAGAAAAC
*
29554575 AAATAATAATAATTAAATATAT
1 AAATAATAATAATTACATATAT
29554597 TGAAATTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 5 0.12
30 28 0.65
31 7 0.16
32 3 0.07
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (31 bp):
AAATAATAATAATTACATATATATAGAAAAC
Found at i:29554755 original size:17 final size:17
Alignment explanation
Indices: 29554733--29554776 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
29554723 TAGGAAATAA
29554733 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
29554750 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
29554767 -ATATGTATAT
1 AAAATGTATAT
29554777 AAAAGTCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:29555137 original size:88 final size:88
Alignment explanation
Indices: 29554965--29555554 Score: 664
Period size: 88 Copynumber: 6.7 Consensus size: 88
29554955 AATAAATAAA
* * * *
29554965 AAGACTGATGTCTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTACTATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* ** *
29555030 ACTCCACTGC-TGCTCAGGGAGAC
66 GCTCCACTGCAACCT-AGGGAGGC
* * * * * **
29555053 AAGGCCGGAT-TTTTCGATCTGCTTCGCTACCGGTACAGGAAGGCAAGATCTGCTATCTTCAGTC
1 AAGACTGG-TGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACC
*
29555117 TGCTCCACTACAACCTAGGGAGGC
65 TGCTCCACTGCAACCTAGGGAGGC
* * * * * * * * *
29555141 AAGACTGGCGTCTTCAATTTGCTTCGCTGTCAGTATAGGAAGCCAAGATCTACAATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* * *
29555206 GCTCCGCTACAATCC-AAGGAGGC
66 GCTCCACTGCAA-CCTAGGGAGGC
* * * * **
29555229 AAGGCTGGTGTCTTCGATCTGCTTCGTTGCCGGTACAGGAAGGCAAGATCTGCTGTCTTCAGTCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* * * * *
29555294 GCTCCATTGTAACCTAAGGACGT
66 GCTCCACTGCAACCTAGGGAGGC
* **
29555317 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
29555382 GCTCCACTGCAACCTAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* * * * *
29555405 AAGACTGGTGTCTTCGATCTACTTCACTGTCAGTACAGGAAGGCAATATCTGCTATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* *
29555470 GCTCCGCTGCAACCCAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* * *
29555493 AAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTATCTTCAA
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAA
29555555 TGATCTGTTC
Statistics
Matches: 416, Mismatches: 81, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
87 2 0.00
88 409 0.98
89 5 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (88 bp):
AAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
GCTCCACTGCAACCTAGGGAGGC
Found at i:29555465 original size:264 final size:264
Alignment explanation
Indices: 29555065--29555553 Score: 798
Period size: 264 Copynumber: 1.9 Consensus size: 264
29555055 GGCCGGATTT
*
29555065 TTCGATCTGCTTCGCTACCGGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTACAA
1 TTCGATCTGCTTCGCTACCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTACAA
* * * *
29555130 CCTAGGGAGGCAAGACTGGCGTCTTCAATTTGCTTCGCTGTCAGTATAGGAAGCCAAGATCTACA
66 CCTAGGGAGGCAAGACTGGCGTCTTCAATCTACTTCACTGTCAGTACAGGAAGCCAAGATCTACA
* *
29555195 ATTTTCAACCTGCTCCGCTACAATCCAAGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGCC
131 ATTTTCAACCTGCTCCGCTACAACCCAAGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCC
*
29555260 GGTACAGGAAGGCAAGATCTGCTGTCTTCAGTCTGCTCCATTGTAACCTAAGGACGTAAGACTGG
196 GGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCATTGTAACCTAAGGACGTAAGACTGG
29555325 TGTC
261 TGTC
** *
29555329 TTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAA
1 TTCGATCTGCTTCGCTACCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTACAA
* * * * * *
29555394 CCTAGGGAGGCAAGACTGGTGTCTTCGATCTACTTCACTGTCAGTACAGGAAGGCAATATCTGCT
66 CCTAGGGAGGCAAGACTGGCGTCTTCAATCTACTTCACTGTCAGTACAGGAAGCCAAGATCTACA
* * *
29555459 ATTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCC
131 ATTTTCAACCTGCTCCGCTACAACCCAAGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCC
29555524 GGTACAGGAAGGCAAGATCTGCTATCTTCA
196 GGTACAGGAAGGCAAGATCTGCTATCTTCA
29555554 ATGATCTGTT
Statistics
Matches: 205, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
264 205 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (264 bp):
TTCGATCTGCTTCGCTACCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTACAA
CCTAGGGAGGCAAGACTGGCGTCTTCAATCTACTTCACTGTCAGTACAGGAAGCCAAGATCTACA
ATTTTCAACCTGCTCCGCTACAACCCAAGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCC
GGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCATTGTAACCTAAGGACGTAAGACTGG
TGTC
Found at i:29557796 original size:25 final size:26
Alignment explanation
Indices: 29557745--29557805 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
29557735 AAGAAAATCC
* **
29557745 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
29557771 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
29557796 AAAATGAATG
1 AAAA-GAATG
29557806 TAAAGATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:29561485 original size:21 final size:23
Alignment explanation
Indices: 29561451--29561492 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
29561441 TTATACAAAC
29561451 AAAATACATAATACA-ATAAAGA
1 AAAATACATAATACATATAAAGA
*
29561473 AAAATATAT-ATACATATAAA
1 AAAATACATAATACATATAAA
29561493 TTATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAATACATAATACATATAAAGA
Found at i:29561706 original size:30 final size:31
Alignment explanation
Indices: 29561633--29561715 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
29561623 ACATATATAA
* ** *
29561633 AAATAATAATTATCTACATATATATAGATTAT
1 AAATAATAATAAT-TACATATATATAGAAAAC
29561665 AAA-AA-AGATAATTACATATATATA-AAAAC
1 AAATAATA-ATAATTACATATATATAGAAAAC
29561694 AAATAATAATAATTACATATAT
1 AAATAATAATAATTACATATAT
29561716 TGAAGTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 5 0.11
30 29 0.66
31 7 0.16
32 3 0.07
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (31 bp):
AAATAATAATAATTACATATATATAGAAAAC
Found at i:29562415 original size:21 final size:20
Alignment explanation
Indices: 29562378--29562429 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
29562368 AATCACATCT
29562378 TCTAAGATTGC-ATATCATA
1 TCTAAGATTGCAATATCATA
29562397 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
29562418 TCTAAGATTGCA
1 TCTAAGATTGCA
29562430 CATCCTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 11 0.35
21 20 0.65
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Done.