Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 19 of 25
Found at i:2963663 original size:51 final size:50
Alignment explanation
Indices: 2963582--2963807 Score: 186
Period size: 50 Copynumber: 4.5 Consensus size: 50
2963572 ACCTAAGGTG
* * *
2963582 AAATTCTATAGAGTTAAAGTCCACATAAGCTGGCA-CCGAATATAAAAGATT
1 AAATCCTATAGAGTCAAAGTCCACATAAGCTGGCACCCG-ATA-AAAAGATC
* * * *
2963633 AAGTCCTATAAAGTCAAAGTCCACATAAGCTAGCACCCGATAAAAAGGTC
1 AAATCCTATAGAGTCAAAGTCCACATAAGCTGGCACCCGATAAAAAGATC
* * * ** * * *
2963683 AAATCCTATAGAGTCTAAGT-CACACAAGCTGACACTTGATAGAAAGGTT
1 AAATCCTATAGAGTCAAAGTCCACATAAGCTGGCACCCGATAAAAAGATC
* * * * * * ** *
2963732 AAATCTTATAGAGTCAAAGTCCAAATTAGTTGGTACCTGATAGGACGATC
1 AAATCCTATAGAGTCAAAGTCCACATAAGCTGGCACCCGATAAAAAGATC
* *
2963782 AAATCCTATAAAATCAAAGTCCACAT
1 AAATCCTATAGAGTCAAAGTCCACAT
2963808 TAGTTAGCAT
Statistics
Matches: 139, Mismatches: 34, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
49 40 0.29
50 63 0.45
51 33 0.24
52 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (50 bp):
AAATCCTATAGAGTCAAAGTCCACATAAGCTGGCACCCGATAAAAAGATC
Found at i:2963736 original size:49 final size:49
Alignment explanation
Indices: 2963576--2963752 Score: 160
Period size: 49 Copynumber: 3.6 Consensus size: 49
2963566 GCTAACACCT
* * * * *
2963576 AAGGTGAAATTCTATAGAGTTAAAGTCCACATAAGCTGGCA-CCGAATATAA
1 AAGGTTAAATCCTATAGAGTCAAAGT-CACACAAGCTAGCACCCG-ATA-AA
* * * *
2963627 AAGATTAAGTCCTATAAAGTCAAAGTCCACATAAGCTAGCACCCGATAAA
1 AAGGTTAAATCCTATAGAGTCAAAGT-CACACAAGCTAGCACCCGATAAA
* * ** *
2963677 AAGGTCAAATCCTATAGAGTCTAAGTCACACAAGCT-GACACTTGATAGA
1 AAGGTTAAATCCTATAGAGTCAAAGTCACACAAGCTAG-CACCCGATAAA
*
2963726 AAGGTTAAATCTTATAGAGTCAAAGTC
1 AAGGTTAAATCCTATAGAGTCAAAGTC
2963753 CAAATTAGTT
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 41 0.39
50 23 0.22
51 37 0.35
52 3 0.03
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (49 bp):
AAGGTTAAATCCTATAGAGTCAAAGTCACACAAGCTAGCACCCGATAAA
Found at i:2963836 original size:50 final size:50
Alignment explanation
Indices: 2963576--2963856 Score: 185
Period size: 50 Copynumber: 5.6 Consensus size: 50
2963566 GCTAACACCT
* * * * * * *
2963576 AAGGTGAAATTCTATAGAGTTAAAGTCCACATAAGCTGGCACC-GAATATAA
1 AAGGTTAAATCCTATAAAGTCAAAGTCCACATTAGCTAGCACCTG-ATA-AG
* * * * *
2963627 AAGATTAAGTCCTATAAAGTCAAAGTCCACATAAGCTAGCACCCGATAAA
1 AAGGTTAAATCCTATAAAGTCAAAGTCCACATTAGCTAGCACCTGATAAG
* * * *
2963677 AAGGTCAAATCCTATAGAGTCTAAGTCACACA--AGCT-GACACTTGAT-AG
1 AAGGTTAAATCCTATAAAGTCAAAGTC-CACATTAGCTAG-CACCTGATAAG
* * * * * * *
2963725 AAAGGTTAAATCTTATAGAGTCAAAGTCCAAATTAGTTGGTACCTGATAGG
1 -AAGGTTAAATCCTATAAAGTCAAAGTCCACATTAGCTAGCACCTGATAAG
* * * * * **
2963776 ACGATCAAATCCTATAAAATCAAAGTCCACATTAGTTAGCATTTGATAAG
1 AAGGTTAAATCCTATAAAGTCAAAGTCCACATTAGCTAGCACCTGATAAG
* **
2963826 AAGGTTAAATCCTATGAAGTTTAAGTCCACA
1 AAGGTTAAATCCTATAAAGTCAAAGTCCACA
2963857 CAAACTAGGA
Statistics
Matches: 180, Mismatches: 42, Indels: 17
0.75 0.18 0.07
Matches are distributed among these distances:
48 5 0.03
49 34 0.19
50 95 0.53
51 45 0.25
52 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (50 bp):
AAGGTTAAATCCTATAAAGTCAAAGTCCACATTAGCTAGCACCTGATAAG
Found at i:2964342 original size:16 final size:16
Alignment explanation
Indices: 2964313--2964370 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
2964303 TATTTATTTG
*
2964313 ATATCTAAAAATTT-TA
1 ATAT-TAAATATTTATA
2964329 AGTATTAAATATTTATA
1 A-TATTAAATATTTATA
*
2964346 ATTTTAAATATTTAT-
1 ATATTAAATATTTATA
2964361 ATA-TAAATAT
1 ATATTAAATAT
2964371 ATAAGTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.19
15 2 0.05
16 22 0.59
17 6 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATTAAATATTTATA
Found at i:2964661 original size:20 final size:20
Alignment explanation
Indices: 2964598--2964673 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
2964588 GGGATTTGAG
* *
2964598 TATTTAAAGAATTTTAAT-TA
1 TATTTAAA-TATTTAAATATA
* * *
2964618 TA-TTAAATA-TGAATTATT
1 TATTTAAATATTTAAATATA
2964636 TATTTAAATATTTAAATATA
1 TATTTAAATATTTAAATATA
* *
2964656 TATTTATATATTAAAATA
1 TATTTAAATATTTAAATA
2964674 ATTATATTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 12 0.28
20 24 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTAAATATTTAAATATA
Found at i:2964662 original size:28 final size:28
Alignment explanation
Indices: 2964610--2964677 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
2964600 TTTAAAGAAT
* *
2964610 TTTAATTATATTAAATATGAATTATTTA
1 TTTAAATATATTAAATATGAATTATATA
2964638 TTTAAATAT-TTAAATAT-ATATTTATATA
1 TTTAAATATATTAAATATGA-A-TTATATA
*
2964666 TTAAAATA-ATTA
1 TTTAAATATATTA
2964678 TATTTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.03
27 9 0.26
28 24 0.71
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTAAATATATTAAATATGAATTATATA
Found at i:2964703 original size:44 final size:46
Alignment explanation
Indices: 2964616--2964704 Score: 105
Period size: 44 Copynumber: 2.0 Consensus size: 46
2964606 GAATTTTAAT
** *
2964616 TATATTAAATATGAATTATTTATTTAAATATTTAAATATATATTTA
1 TATATTAAATATGAATTATTTATTTAAATATAAAAATAAATATTTA
2964662 TATATTAAA-AT-AATTATATT-TTT-AATATAAAAATTAAATATTT
1 TATATTAAATATGAATTAT-TTATTTAAATATAAAAA-TAAATATTT
2964705 GAAATTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
43 8 0.21
44 17 0.45
45 4 0.11
46 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (46 bp):
TATATTAAATATGAATTATTTATTTAAATATAAAAATAAATATTTA
Found at i:2965285 original size:29 final size:29
Alignment explanation
Indices: 2965239--2965323 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
2965229 TTTTGAGATA
*
2965239 TTTATATATTTATATTATGTTCGT-ATTATTT
1 TTTA-ATA-TTATATTATATT-GTAATTATTT
* * *
2965270 TTTCATATTATGTTATATTTTAATTATTT
1 TTTAATATTATATTATATTGTAATTATTT
*
2965299 TTTAATATT-TA-TATCTTGTAATTAT
1 TTTAATATTATATTATATTGTAATTAT
2965324 GTCTTATCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 12 0.27
28 2 0.04
29 25 0.56
30 3 0.07
31 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.64
Consensus pattern (29 bp):
TTTAATATTATATTATATTGTAATTATTT
Found at i:2965545 original size:16 final size:16
Alignment explanation
Indices: 2965524--2965608 Score: 52
Period size: 17 Copynumber: 5.2 Consensus size: 16
2965514 TTTATAATCG
2965524 TATTTAATATATTTTA
1 TATTTAATATATTTTA
* *
2965540 TATTTATATAAATTTAA
1 TATTTA-ATATATTTTA
*
2965557 TAAATTAATA-A-TTTA
1 T-ATTTAATATATTTTA
*
2965572 TA-TTATATAGATTTTAA
1 TATTTA-ATATATTTT-A
*
2965589 TATATTTATATA-TTTA
1 TAT-TTAATATATTTTA
2965605 TATT
1 TATT
2965609 ATGTTCATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
13 3 0.05
14 4 0.07
15 6 0.11
16 14 0.25
17 18 0.33
18 8 0.15
19 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
TATTTAATATATTTTA
Found at i:2965573 original size:32 final size:34
Alignment explanation
Indices: 2965527--2965608 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 34
2965517 ATAATCGTAT
2965527 TTAATATATTTTATATTTATATA-AATTTAATAAA
1 TTAATATA-TTTATATTTATATAGAATTTAATAAA
* *
2965561 TTAATA-ATTTATA-TTATATAGATTTTAATATA
1 TTAATATATTTATATTTATATAGAATTTAATAAA
*
2965593 TTTATATATTTATATT
1 TTAATATATTTATATT
2965609 ATGTTCATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 7 0.17
32 20 0.48
33 8 0.19
34 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (34 bp):
TTAATATATTTATATTTATATAGAATTTAATAAA
Found at i:2965601 original size:8 final size:8
Alignment explanation
Indices: 2965524--2965607 Score: 57
Period size: 7 Copynumber: 10.1 Consensus size: 8
2965514 TTTATAATCG
2965524 TATTTAATA
1 TATTT-ATA
2965533 TATTT-TA
1 TATTTATA
2965540 TATTTATA
1 TATTTATA
2965548 TAAATTTAATA
1 T--ATTT-ATA
* *
2965559 AATTAATA
1 TATTTATA
2965567 -ATTTATA
1 TATTTATA
*
2965574 T-TATATA
1 TATTTATA
*
2965581 GATTTTAATA
1 TA-TTT-ATA
2965591 TATTTATA
1 TATTTATA
2965599 TATTTATA
1 TATTTATA
2965607 T
1 T
2965608 TATGTTCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
7 18 0.30
8 18 0.30
9 13 0.22
10 8 0.13
11 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (8 bp):
TATTTATA
Found at i:2966054 original size:39 final size:39
Alignment explanation
Indices: 2965958--2966073 Score: 131
Period size: 36 Copynumber: 3.1 Consensus size: 39
2965948 ATATATAATA
*
2965958 AATAATT-AAAATTTATTAAAATTATA-TTATATTAAAT
1 AATAATTAAAAAATTATTAAAATTATATTTATATTAAAT
*
2965995 AATAA--AATATAAA-TA-T-AAATTATATTTATGTTAAAT
1 AATAATTAA-A-AAATTATTAAAATTATATTTATATTAAAT
*
2966031 AATAATTAAAAAATTATTAAAATTATATTTATACTAAA-
1 AATAATTAAAAAATTATTAAAATTATATTTATATTAAAT
2966069 AATAA
1 AATAA
2966074 ACTTAAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
35 8 0.12
36 20 0.30
37 11 0.17
38 10 0.15
39 17 0.26
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (39 bp):
AATAATTAAAAAATTATTAAAATTATATTTATATTAAAT
Found at i:2966366 original size:21 final size:21
Alignment explanation
Indices: 2966341--2966382 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2966331 TAAAAATTTT
* *
2966341 TATATTTTTTTATTTTAGTAA
1 TATATTTTTTAATATTAGTAA
2966362 TATATTTTTTAATATTAGTAA
1 TATATTTTTTAATATTAGTAA
2966383 CAAATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TATATTTTTTAATATTAGTAA
Found at i:2970097 original size:87 final size:87
Alignment explanation
Indices: 2969955--2970113 Score: 207
Period size: 87 Copynumber: 1.8 Consensus size: 87
2969945 AAATTAGCAG
* * * * *
2969955 CGTTTTTTGAACAAACACCACTAAATATCAAACAATAGCAGCATTTATATAACAAACGCTGCTAA
1 CGTTTCTTGAACAAACACCACTAAATATAAAAAAATAGCAGCATTTATATAACAAACACCGCTAA
2970020 ATAATTGTTACGAAATTAATGA
66 ATAATTGTTACGAAATTAATGA
* *
2970042 CGTTTCTTGAACAAACGCCACTAAATATAAAAAAATAGC-GACGTTTCCA-AT-ACAAACACCGC
1 CGTTTCTTGAACAAACACCACTAAATATAAAAAAATAGCAG-CATTT--ATATAACAAACACCGC
2970104 TAAATAATTG
63 TAAATAATTG
2970114 CCACAAAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
86 1 0.02
87 58 0.94
88 2 0.03
89 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (87 bp):
CGTTTCTTGAACAAACACCACTAAATATAAAAAAATAGCAGCATTTATATAACAAACACCGCTAA
ATAATTGTTACGAAATTAATGA
Found at i:2972213 original size:20 final size:20
Alignment explanation
Indices: 2972188--2972256 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
2972178 CAGATTTATT
* *
2972188 GATACATTTTTTAATGTATC
1 GATACATTTATCAATGTATC
* *
2972208 GATACATGTATGAATGTATC
1 GATACATTTATCAATGTATC
* * *
2972228 AATACATTCATCAATATATC
1 GATACATTTATCAATGTATC
2972248 GATACATTT
1 GATACATTT
2972257 TGTCCTTTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
GATACATTTATCAATGTATC
Found at i:2974146 original size:52 final size:52
Alignment explanation
Indices: 2974011--2974184 Score: 149
Period size: 52 Copynumber: 3.3 Consensus size: 52
2974001 TCGAAAATAA
* * * *
2974011 CAGGGTTGGAGTATCCCCAATTAT-GAAAAATTGATATTTTTGGAAATAAAAT
1 CAGGGTTGGAGTATCCCCGATTATGGAAAAATTG-GAGTTTTGAAAATAAAAT
* * * * *
2974063 C-GGAGTTAGAGTATTCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAAC
1 CAGG-GTTGGAGTATCCCCGATT-ATGGAAAAATTGGAGTTTTGAAAATAAAAT
* * * *
2974115 CAGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAAT
1 CAGGGTTGGAGTATCCCCGATTATGGAAAAATTGGAGTTTTGA-AAATAAAAT
**
2974167 TGGGGTTGGAGTATCCCC
1 CAGGGTTGGAGTATCCCC
2974185 TCGGAAATAA
Statistics
Matches: 97, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
51 5 0.05
52 81 0.84
53 10 0.10
54 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (52 bp):
CAGGGTTGGAGTATCCCCGATTATGGAAAAATTGGAGTTTTGAAAATAAAAT
Found at i:2974234 original size:27 final size:28
Alignment explanation
Indices: 2974167--2974242 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
2974157 GCAATAAAAT
***
2974167 TGGGGTTGGAGTATCCCCTCGGAAATAA
1 TGGGGTTGGAGTATCCCCGATGAAATAA
* *
2974195 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 TGGGGTTGGAGTATCCCCGATGAAATAA
2974222 TGGGGTTGGAGTATCCCCGAT
1 TGGGGTTGGAGTATCCCCGAT
2974243 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (28 bp):
TGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2974238 original size:107 final size:107
Alignment explanation
Indices: 2974117--2974639 Score: 364
Period size: 107 Copynumber: 4.9 Consensus size: 107
2974107 AATAAAACCA
*
2974117 GGGTTGGAGTATCCCCGATTGTGGAA-AAATTAGTGTTTTAGCAATAAAATTGGGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGATTGT-GAAGAAATTAGTGTTTTAGCAATAAAATCGGGGTTGGAGTAT
2974181 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAATG
65 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAATG
* * * * *
2974224 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTG--TTTTAGCAATAAAATCGGGGTTGGAGTA
* *** * *** ** *
2974289 T-CCC-C-G-ATTATA-GAAAATT--AGTGT-TTTGAAAATAAAATTG
64 TCCCCTCGGAAATA-ACG-GGGTTGGAGTATCCCCGATGAT-TAA-TG
* * * *
2974329 GAGTTGGAATATCCCCGATTGTGGAG-AATTGAGTGTTTTAGCAATAAAACCGGGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATT-AGTGTTTTAGCAATAAAATCGGGGTTGGAGTAT
* *
2974393 CCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGATTAACG
65 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAATG
* * * * * *
2974436 GGGTTGGAGTATCCCTGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTG--TTTTAGCAATAAAATCGGGGTTGGAGTA
* *** * *** ** *
2974501 T-CCC-C-G-ATTATA-GAAAATT--AGTGT-TTTGAAAATAAAATCG
64 TCCCCTCGGAAATA-ACG-GGGTTGGAGTATCCCCGATGAT-TAAT-G
* * * **
2974541 GAGTTGGAATATCCCCGATTGTGGAG-AATTGAGTGTTTTAGCAATAAAGCCGGGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATT-AGTGTTTTAGCAATAAAATCGGGGTTGGAGTAT
*
2974605 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
65 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
2974640 TGTGAAGAAA
Statistics
Matches: 301, Mismatches: 83, Indels: 62
0.67 0.19 0.14
Matches are distributed among these distances:
103 55 0.18
104 26 0.09
105 63 0.21
106 18 0.06
107 65 0.22
108 20 0.07
109 54 0.18
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (107 bp):
GGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTGTTTTAGCAATAAAATCGGGGTTGGAGTATC
CCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAATG
Found at i:2974365 original size:105 final size:105
Alignment explanation
Indices: 2974226--2974579 Score: 364
Period size: 105 Copynumber: 3.4 Consensus size: 105
2974216 GATTAATGGG
*
2974226 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
1 GTTGGAATATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
*
2974291 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATTGGA
66 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
* * * * * *
2974331 GTTGGAATATCCCCGATTGTGGAG-AATTGAGTG--TTTTAGCAATAAAACCGGGGTTGGAGTAT
1 GTTGGAATATCCCCGATTGTGAAGAAATTG-GTGTTTTTTGGAAATAAAATCGGAGTTAGAGTAT
* ** * *** ** * *
2974393 CCCCTCGGA-AATA-ACAGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
65 -CCC-C-GATTATAGA-A-AATT--AGTGT-TTTGAAAATAAAATCGGA
* *
2974438 GTTGGAGTATCCCTGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
1 GTTGGAATATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
2974503 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
66 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
2974543 GTTGGAATATCCCCGATTGTGGAG-AATTGAGTGTTTT
1 GTTGGAATATCCCCGATTGTGAAGAAATTG-GTGTTTT
2974580 AGCAATAAAG
Statistics
Matches: 191, Mismatches: 41, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
103 28 0.15
104 20 0.10
105 61 0.32
106 8 0.04
107 31 0.16
108 15 0.08
109 28 0.15
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (105 bp):
GTTGGAATATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:2974366 original size:212 final size:212
Alignment explanation
Indices: 2974008--2974639 Score: 1020
Period size: 212 Copynumber: 3.0 Consensus size: 212
2973998 CCCTCGAAAA
* * * * *
2974008 TAACAGGGTTGGAGTATCCCCAATTATGAA-AAATTGAT-ATTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
* * * * * *
2974071 GAGTATTCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGG-GTTGGAGTATCCCCGA
66 GAGTATCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAA-TAGGAGTTGGAATATCCCCGA
* **
2974135 TTGTGGAAAAATT-AGTGTTTTAGCAATAAAATTGGGGTTGGAGTATCCCCTCGGAAATAACGGG
129 TTGTGG-AGAATTGAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGG
2974199 GTTGGAGTATCCCCGATGAT
193 GTTGGAGTATCCCCGATGAT
*
2974219 TAATGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
*
2974284 GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATTGGAGTTGGAATATCCCCGATT
66 GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATAGGAGTTGGAATATCCCCGATT
*
2974349 GTGGAGAATTGAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACAGGGTT
131 GTGGAGAATTGAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTT
2974414 GGAGTATCCCCGATGAT
196 GGAGTATCCCCGATGAT
*
2974431 TAACGGGGTTGGAGTATCCCTGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
*
2974496 GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
66 GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATAGGAGTTGGAATATCCCCGATT
* *
2974561 GTGGAGAATTGAGTGTTTTAGCAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTT
131 GTGGAGAATTGAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTT
2974626 GGAGTATCCCCGAT
196 GGAGTATCCCCGAT
2974640 TGTGAAGAAA
Statistics
Matches: 394, Mismatches: 23, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
211 33 0.08
212 322 0.82
213 39 0.10
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (212 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATAGGAGTTGGAATATCCCCGATT
GTGGAGAATTGAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTT
GGAGTATCCCCGATGAT
Found at i:2974387 original size:52 final size:51
Alignment explanation
Indices: 2974226--2974608 Score: 240
Period size: 51 Copynumber: 7.3 Consensus size: 51
2974216 GATTAATGGG
*
2974226 GTTGGAGTATCCCCGATTGTGAAGAAATTG-GTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAG-AATTGAGTG--TTTT-GAAATAAAATCGGA
* * * * *
2974280 GTTAGAGTATCCCCGATTATAGAAAATT-AGTGTTTTGAAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTGTGGAGAATTGAGTGTTTTG-AAATAAAATCGGA
* * * *
2974331 GTTGGAATATCCCCGATTGTGGAGAATTGAGTGTTTTAGCAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGGAGAATTGAGTGTTTT-GAAATAAAATCGGA
* *** ** * *** * * *
2974383 GTTGGAGTATCCCCTCGGAAAT-AACAGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTAT-CCC-C-G-ATTGTGGAGAATT-GAGTGT-TTTGA-AATAAAATCGGA
* *
2974438 GTTGGAGTATCCCTGATTGTGAAGAAATTG-GTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAG-AATTGAGTG--TTTT-GAAATAAAATCGGA
* * * *
2974492 GTTAGAGTATCCCCGATTATAGAAAATT-AGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAGAATTGAGTGTTTTG-AAATAAAATCGGA
* * ** *
2974543 GTTGGAATATCCCCGATTGTGGAGAATTGAGTGTTTTAGCAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTGTGGAGAATTGAGTGTTTT-GAAATAAAATCGGA
2974595 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2974609 TCGAAAATAA
Statistics
Matches: 248, Mismatches: 59, Indels: 46
0.70 0.17 0.13
Matches are distributed among these distances:
50 2 0.01
51 83 0.33
52 62 0.25
53 26 0.10
54 44 0.18
55 19 0.08
56 10 0.04
57 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGGAGAATTGAGTGTTTTGAAATAAAATCGGA
Found at i:2974442 original size:27 final size:28
Alignment explanation
Indices: 2974379--2974450 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
2974369 GCAATAAAAC
**
2974379 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* * *
2974407 CAGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
2974434 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
2974451 TGATTGTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2974719 original size:51 final size:53
Alignment explanation
Indices: 2974627--2974745 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
2974617 AACGGGGTTG
* * *
2974627 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
2974681 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
2974732 GAATATCCCCGATT
1 GAGTATCCCCGATT
2974746 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:2974743 original size:185 final size:184
Alignment explanation
Indices: 2974409--2974758 Score: 648
Period size: 185 Copynumber: 1.9 Consensus size: 184
2974399 GGAAATAACA
* * *
2974409 GGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCTGATTGTGAAGAAATTGGTGTTT
1 GGGTTGGAGTATCCCCGATAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTT
2974474 TTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAAT
66 TTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAAT
2974539 CGGAGTTGGAATATCCCCGATTGTGGAGAATTGAGTGTTTTAGCAATAAAGCCG
131 CGGAGTTGGAATATCCCCGATTGTGGAGAATTGAGTGTTTTAGCAATAAAGCCG
2974593 GGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGT
1 GGGTTGGAGTAT-CCC-CGATAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGT
2974657 TTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAA
64 TTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAA
2974722 ATCGGAGTTGGAATATCCCCGATTGTGGAGAATTGAG
129 ATCGGAGTTGGAATATCCCCGATTGTGGAGAATTGAG
2974759 AAACTCAACA
Statistics
Matches: 161, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
184 12 0.07
185 146 0.91
186 3 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (184 bp):
GGGTTGGAGTATCCCCGATAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTT
TTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAAT
CGGAGTTGGAATATCCCCGATTGTGGAGAATTGAGTGTTTTAGCAATAAAGCCG
Found at i:2976599 original size:33 final size:33
Alignment explanation
Indices: 2976538--2976604 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2976528 AAAATTTCCA
*** *
2976538 AATGTATCGATACAAAGATCCATTTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2976571 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2976604 A
1 A
2976605 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2976648 original size:19 final size:18
Alignment explanation
Indices: 2976624--2976691 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2976614 CAGTAGCTAA
2976624 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2976643 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2976658 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2976675 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2976692 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2976664 original size:13 final size:13
Alignment explanation
Indices: 2976646--2976670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2976636 ACAATACTTA
2976646 TGTATCGATACAT
1 TGTATCGATACAT
2976659 TGTATCGATACA
1 TGTATCGATACA
2976671 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2976668 original size:32 final size:32
Alignment explanation
Indices: 2976627--2976689 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2976617 TAGCTAATTA
*
2976627 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2976659 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2976690 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2976753 original size:21 final size:22
Alignment explanation
Indices: 2976727--2976784 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
2976717 GTTGGGACCC
*
2976727 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGTACAAA
*
2976748 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
2976769 TGTATCGATACATTTG
1 TGTATCGATACATTTG
2976785 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.81
22 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:2977446 original size:119 final size:116
Alignment explanation
Indices: 2977237--2977449 Score: 254
Period size: 119 Copynumber: 1.8 Consensus size: 116
2977227 AGGGTGTCCA
* * * * *
2977237 CTTTTCAAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAAGACCAATGAAGAGAAG
1 CTTTTCAAGGACAAAGAAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAG
2977302 AAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTATGCCCC
66 AAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTATGCCCC
* *
2977353 CTTTTCCAAGGACAAATGAAAAAGGGAAATGAAATACGTCCTGCT-CTCTGAGGACAAAAGAA-A
1 CTTTT-CAAGGACAAA-GAAAAAGAG-AATGAAATACGTCCTGCTCCT-TGAAGACAAAAGAAGA
* *
2977416 GAGGAAAA-TAAAGTGTATCCTGC-TCTTTGAGGAC
62 GAAGAAAAGGAAAGTG--TCCTGCTTC-TTGAGGAC
2977450 TAAAAAGTGC
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
116 5 0.06
117 16 0.20
118 19 0.23
119 41 0.51
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (116 bp):
CTTTTCAAGGACAAAGAAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAG
AAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTATGCCCC
Found at i:2977620 original size:26 final size:26
Alignment explanation
Indices: 2977591--2977678 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
2977581 GTGGGCTTTA
*
2977591 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTACTCTTTGGGGACTG
*
2977617 AAAGGTG-CC-ACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTA-C-TCTT-TG-GGGAC--TG
*
2977646 AAAGGGGTCCTACTCTTTGGGGACTG
1 AAAGGTGTCCTACTCTTTGGGGACTG
2977672 AAAGGTG
1 AAAGGTG
2977679 CCACCAACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 6 0.12
28 6 0.12
29 11 0.23
30 3 0.06
31 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTACTCTTTGGGGACTG
Found at i:2977793 original size:59 final size:59
Alignment explanation
Indices: 2977433--2978373 Score: 995
Period size: 55 Copynumber: 16.3 Consensus size: 59
2977423 ATAAAGTGTA
* * *
2977433 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
2977488 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * *
2977543 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
2977598 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
2977653 TCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
*
2977714 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * * *
2977773 TCCCACCCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAATAAAATGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
2977832 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
2977891 TCCCGCTCTTTGAAGACTGAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* *
2977951 TCCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGA-AGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* * *
2978012 TCCTACTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGC-TT--CA-AAATGG-G
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
2978067 TCCTGCTCTTTGGGGA-TGGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AGAGGTG
1 TCCTGCTCTTTGAGGACT-G-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
2978122 TCTTGCTCTTTGAGGATTGAAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
2978182 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
* * *
2978243 TCCTTCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGG
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * * *
2978298 TCCTGTTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
2978359 TCCTGCTCTTTGAGG
1 TCCTGCTCTTTGAGG
2978374 GCTAAAAAAC
Statistics
Matches: 769, Mismatches: 75, Indels: 78
0.83 0.08 0.08
Matches are distributed among these distances:
53 3 0.00
54 9 0.01
55 307 0.40
56 11 0.01
57 1 0.00
58 1 0.00
59 162 0.21
60 114 0.15
61 154 0.20
62 5 0.01
63 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:2978092 original size:469 final size:461
Alignment explanation
Indices: 2977482--2978371 Score: 1256
Period size: 469 Copynumber: 1.9 Consensus size: 461
2977472 TGGGCTTTGA
*
2977482 AAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCT
1 AAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGCGTCCT
* *
2977547 GCTCTTTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGG
66 ACTCTTTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTCAAAAGGTGTCCTGCTCTTTGGG
*
2977612 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTACTCTTTGGGGACTGAAAGG
131 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTACTCTTTGAGGACTGAAAGG
* **
2977677 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACT-GAAGGTGCC
196 TGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGCATCCCGCTCTTTGAGGACTGGAAAATGCC
2977741 ACCAACTTGGGTGGGCTTTAAAA-GAAAAGGCGTCCCACCCTTTGAGGACT-GAAGGTGCCACCA
260 ACCAACTTGGGTGGGCTTTAAAAGGAAAAGGCGTCCCACCCTTTGAGGACTGGAA-GTGCCACCA
* *
2977804 ACTTGTGTGGGCTTTAAAATAAAATGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTG
324 ACTTGTGTGGGC-TT----CAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGGTGCCACCAACTTG
* *
2977868 GGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAAGACTGAAGGTGCCACCAACTTATGTGG
384 GGTGGGCTTTGAAAAGAAAAAGCATCCCGCTCTTTGAAGACTGAAGGTGCCACCAACTTATGTGG
2977932 GCTTTAAAAAGAG
449 GCTTTAAAAAGAG
2977945 AAGGCGTCCTGCTCTTTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 AAGGCGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT---A--AG-AG
* * *
2978009 GCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCAAAATGG-GTCCTGC
59 GCGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTCAAAA-GGTGTCCTGC
* * * *
2978073 TCTTTGGGGA-TGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCTTGCTCTTTGAGG
123 TCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTACTCTTTGAGG
* * * *
2978137 ATTGAAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGG
187 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCCGCTCTTTGAGGACTGG
* * ** *
2978202 AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTTCTCTTTGAGGACTGGGAAG
252 AAAATGCCACCAACTTGGGTGGGCTTTAAAAGGAAAAGGCGTCCCACCCTTTGAGGACT-GGAAG
* * * * *
2978267 TGCCACCAACTTGTGTGGGCTTCGAAAGGGGTCCTGTTCTTTGGGGACTGAAAGGTGCCACCAAC
316 TGCCACCAACTTGTGTGGGCTTCAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGGTGCCACCAAC
* * *
2978332 TTGTGTGGGCTTTGAAAGGAAAAAGCATCCTGCTCTTTGA
381 TTGGGTGGGCTTTGAAAAGAAAAAGCATCCCGCTCTTTGA
2978372 GGGCTAAAAA
Statistics
Matches: 377, Mismatches: 35, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
463 50 0.13
464 2 0.01
466 22 0.06
467 26 0.07
468 53 0.14
469 173 0.46
470 27 0.07
471 21 0.06
472 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (461 bp):
AAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGCGTCCT
ACTCTTTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTCAAAAGGTGTCCTGCTCTTTGGG
GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCCTACTCTTTGAGGACTGAAAGG
TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCCGCTCTTTGAGGACTGGAAAATGCCA
CCAACTTGGGTGGGCTTTAAAAGGAAAAGGCGTCCCACCCTTTGAGGACTGGAAGTGCCACCAAC
TTGTGTGGGCTTCAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGGGTGGGC
TTTGAAAAGAAAAAGCATCCCGCTCTTTGAAGACTGAAGGTGCCACCAACTTATGTGGGCTTTAA
AAAGAG
Found at i:2978195 original size:231 final size:230
Alignment explanation
Indices: 2977433--2978350 Score: 1188
Period size: 231 Copynumber: 4.0 Consensus size: 230
2977423 ATAAAGTGTA
* * *
2977433 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT-----G-AAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCT
* *
2977492 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---A-AG-AGGTGTCCTGCTCT
66 GCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTACTCT
* * * *
2977552 TTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTTAAAA-GGTGTCCTGCTCTTTGGGGACT
130 TTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCAAAATGG-GTCCTGCTCTTTGGGGACT
*
2977616 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGG
194 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * * *
2977653 TCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCT
* * * * *
2977718 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCACCCTT
66 GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTACTCTT
* * * *
2977783 TGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAATAAAATGCGTCCCGCTCTTTGAG
131 TGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGC-TT----CAAAATGGGTCCTGCTCTTTGGG
*
2977846 GACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
190 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * * *
2977891 TCCCGCTCTTTGAAGACTG-AAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAGAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCT
2977955 GCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTACTC
66 GCTCTTTGAGGACTGA-AAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAGGCGTCCTACTC
2978020 TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCAAAATGGGTCCTGCTCTTTGGGGA-T
129 TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCAAAATGGGTCCTGCTCTTTGGGGACT
* *
2978084 GGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
194 -GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
2978122 TCTTGCTCTTTGAGGATTGAAAGGTGCCACTAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCC
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCT
* *
2978186 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTTCTC
66 GCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAGGCGTCCTACTC
* * *
2978251 TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCGAAAGGGGTCCTGTTCTTTGGGGACT
129 TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCAAAATGGGTCCTGCTCTTTGGGGACT
2978316 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
194 GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
2978351 AAAAAGCATC
Statistics
Matches: 609, Mismatches: 57, Indels: 53
0.85 0.08 0.07
Matches are distributed among these distances:
220 42 0.07
225 24 0.04
226 26 0.04
228 3 0.00
229 20 0.03
230 21 0.03
231 189 0.31
232 29 0.05
233 26 0.04
234 24 0.04
235 23 0.04
236 26 0.04
237 57 0.09
238 49 0.08
239 26 0.04
240 21 0.03
241 3 0.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (230 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCCT
GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCGTCCTACTCTT
TGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCAAAATGGGTCCTGCTCTTTGGGGACTGA
AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:2979385 original size:13 final size:13
Alignment explanation
Indices: 2979362--2979401 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
2979352 TTTTCTCTTC
2979362 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
2979376 TTTTTTTGTTTTG
1 TTTTTTTGTTTTG
*
2979389 TTTTTTTTTTTTG
1 TTTTTTTGTTTTG
2979402 AAGAGAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:2979390 original size:18 final size:18
Alignment explanation
Indices: 2979367--2979401 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2979357 TCTTCTTTTC
2979367 TTTGTTTTGTTTTTTTGT
1 TTTGTTTTGTTTTTTTGT
*
2979385 TTTGTTTTTTTTTTTTG
1 TTTGTTTTGTTTTTTTG
2979402 AAGAGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (18 bp):
TTTGTTTTGTTTTTTTGT
Found at i:2992051 original size:52 final size:52
Alignment explanation
Indices: 2991918--2992089 Score: 161
Period size: 52 Copynumber: 3.3 Consensus size: 52
2991908 GAAAATTACT
* * * * *
2991918 GGGTTGGAGTATCCCCAATTGT-GAAAAATTGATATTTTTGGAAATAAAATCA
1 GGGTTGGAGTATCCCCGATTGTGGAAAAATTG-GAGTTTTGAAAATAAAACCA
* ** ** *
2991970 GAGTTAAAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCA
1 GGGTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACCA
* * * *
2992022 GGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCG
1 GGGTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCA
2992074 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
2992090 TCAAAAATAA
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
51 3 0.03
52 85 0.89
53 7 0.07
54 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (52 bp):
GGGTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCA
Found at i:2992135 original size:27 final size:27
Alignment explanation
Indices: 2992072--2992147 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
2992062 GCAATAAAAC
* *
2992072 CGGGGTTGGAGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCC-GATAAATAA
* * *
2992100 CAGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
2992127 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2992148 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:2992148 original size:107 final size:107
Alignment explanation
Indices: 2992022--2992379 Score: 349
Period size: 107 Copynumber: 3.4 Consensus size: 107
2992012 AATAAAACCA
2992022 GGGTTGGAGTATCCCCGATTGTGGAA-AAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGATTGT-GAAGAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTAT
2992086 CCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGATTAACG
65 CCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGATTAACG
* * * * * *
2992129 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTG--TTTTAGCAATAAAACCGGGGTTGGAGTA
* * * * *** ** *
2992194 TCCCCGATTATAGA-AA-A---TT--AGTGT-TTTGAAAATAAAATCG
64 TCCCC--TCAAAAATAACAGGGTTGGAGTATCCCCGATGAT-TAA-CG
* * * * *
2992234 GAGTTGCAATATCCCCGATTGTGGAG-AATTGAGTGTTTTAGCAATAAAACCGAGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATT-AGTGTTTTAGCAATAAAACCGGGGTTGGAGTAT
* * *
2992298 CTCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATTAACG
65 CCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGATTAACG
*
2992341 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTT
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTGTTTT
2992380 TTGGAAATAA
Statistics
Matches: 189, Mismatches: 45, Indels: 34
0.71 0.17 0.13
Matches are distributed among these distances:
101 3 0.02
102 2 0.01
103 30 0.16
104 10 0.05
105 27 0.14
106 7 0.04
107 61 0.32
108 10 0.05
109 33 0.17
110 2 0.01
111 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (107 bp):
GGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATC
CCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGATTAACG
Found at i:2992229 original size:212 final size:213
Alignment explanation
Indices: 2991918--2992478 Score: 900
Period size: 212 Copynumber: 2.7 Consensus size: 213
2991908 GAAAATTACT
* * * * *
2991918 GGGTTGGAGTATCCCCAATTGTGAA-AAATTGAT-ATTTTTGGAAATAAAATCAGAGTTAAAGTA
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * * *
2991981 TCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGG-GTTGGAGTATCCCCGATTGTG
66 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATC-GGAGTTGGAATATCCCCGATTGTG
*
2992045 GAAAAATT-AGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGG
129 GAAAAATTGAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGG
2992109 AGTATCCCCGATGATTAACG
194 AGTATCCCCGATGATTAACG
2992129 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
*
2992194 TCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGCAATATCCCCGATTGTGG-
66 TCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
* * * *
2992258 AGAATTGAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAG
131 AAAATTGAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAG
2992323 TATCCCCGATGATTAACG
196 TATCCCCGATGATTAACG
2992341 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
1 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
*
2992406 ACCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGG-
66 TCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
*
2992470 AGAATTGAG
131 AAAATTGAG
2992479 AAACTCAACA
Statistics
Matches: 328, Mismatches: 18, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
211 31 0.09
212 259 0.79
213 38 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (213 bp):
GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
TCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
AAAATTGAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAG
TATCCCCGATGATTAACG
Found at i:2992231 original size:51 final size:52
Alignment explanation
Indices: 2992131--2992465 Score: 204
Period size: 51 Copynumber: 6.3 Consensus size: 52
2992121 GATTAACGGG
* * *
2992131 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAG-AGAAATTAGTG--TTTTGAAAATAAAATCGGA
*
2992185 GTTAGAGTATCCCCGATTATAGA-AAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAGAAATTAGTGTTTTGAAAATAAAATCGGA
* * * * * *
2992236 GTTGCAATATCCCCGATTGTGGAG-AATTGAGTGTTTT-AGCAATAAAA-CCGA
1 GTTGGAGTATCCCCGATTATAGAGAAATT-AGTGTTTTGA-AAATAAAATCGGA
** *** * *** ** * *
2992287 GGTTGGAGTATCTCCTCGAAAATA-ACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 -GTTGGAGTATC-CC-CGATTATAGA-GAAATT--AGTGT-TTTGAAAATAAAATCGGA
* * *
2992343 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAG-AGAAATTAGTG--TTTTGAAAATAAAATCGGA
* *
2992397 GTTAGAGTAACCCCGATTATAGA-AAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAGAAATTAGTGTTTTGAAAATAAAATCGGA
*
2992448 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
2992466 GTGGAGAATT
Statistics
Matches: 210, Mismatches: 52, Indels: 41
0.69 0.17 0.14
Matches are distributed among these distances:
51 79 0.38
52 27 0.13
53 29 0.14
54 48 0.23
55 15 0.07
56 9 0.04
57 2 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATAGAGAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:2992270 original size:105 final size:105
Alignment explanation
Indices: 2991920--2992473 Score: 350
Period size: 105 Copynumber: 5.2 Consensus size: 105
2991910 AAATTACTGG
* * * * * *
2991920 GTTGGAGTATCCCCAATTGTGAA-AAATTGAT-ATTTTTGGAAATAAAATCAGAGTTAAAGTATC
1 GTTGGAATATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * * *
2991983 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGG-
66 CCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATC-GGA
* * * * * * *
2992024 GTTGGAGTATCCCCGATTGTGGAA-AAATTAGTG--TTTTAGCAATAAAACCGGGGTTGGAGTAT
1 GTTGGAATATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTAT
* * * * *** ** * *
2992086 CCCC--TCAAAAATAACAGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
65 CCCCGATTATAGA-AA-A---TT--AGTGT-TTTGAAAATAAAATCGGA
*
2992131 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
1 GTTGGAATATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
2992196 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
66 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
* * * * * *
2992236 GTTGCAATATCCCCGATTGTGGAG-AATTGAGTG--TTTTAGCAATAAAA-CCGAGGTTGGAGTA
1 GTTGGAATATCCCCGATTGTGAAGAAATTG-GTGTTTTTTGGAAATAAAATCGGA-GTTAGAGTA
** *** * *** ** * *
2992297 TCTCCTCGAAAATA-ACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
64 TC-CC-CGATTATAGA--AAATT--AGTGT-TTTGAAAATAAAATCGGA
* *
2992343 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTAAC
1 GTTGGAATATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
2992408 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
66 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
2992448 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAATATCCCCGATTGTGAAGAA
2992474 TTGAGAAACT
Statistics
Matches: 335, Mismatches: 81, Indels: 67
0.69 0.17 0.14
Matches are distributed among these distances:
101 1 0.00
102 9 0.03
103 31 0.09
104 65 0.19
105 69 0.21
106 13 0.04
107 62 0.19
108 18 0.05
109 58 0.17
110 5 0.01
111 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (105 bp):
GTTGGAATATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:2992347 original size:27 final size:27
Alignment explanation
Indices: 2992287--2992359 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
2992277 ATAAAACCGA
2992287 GGTTGGAGTATCTCCTCGA-AAATAACGG
1 GGTTGGAGTATC-CC-CGATAAATAACGG
* *
2992315 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGATAAATAACGG
2992342 GGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCGAT
2992360 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
26 3 0.07
27 27 0.64
28 12 0.29
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGATAAATAACGG
Found at i:2994839 original size:13 final size:13
Alignment explanation
Indices: 2994821--2994846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2994811 ACAAAGATCC
2994821 ATGTATCGATACA
1 ATGTATCGATACA
2994834 ATGTATCGATACA
1 ATGTATCGATACA
2994847 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2994842 original size:33 final size:33
Alignment explanation
Indices: 2994800--2994866 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2994790 AAAATTTCCA
***
2994800 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2994833 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2994866 A
1 A
2994867 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2994910 original size:19 final size:18
Alignment explanation
Indices: 2994886--2994953 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2994876 CAGTAGATAA
2994886 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2994905 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2994920 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2994937 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2994954 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2994926 original size:13 final size:13
Alignment explanation
Indices: 2994908--2994932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2994898 ACAATACTTA
2994908 TGTATCGATACAT
1 TGTATCGATACAT
2994921 TGTATCGATACA
1 TGTATCGATACA
2994933 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2994930 original size:32 final size:32
Alignment explanation
Indices: 2994889--2994951 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2994879 TAGATAATTA
*
2994889 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2994921 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2994952 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2995017 original size:21 final size:21
Alignment explanation
Indices: 2994991--2995065 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
2994981 TGGGACCCTA
* *
2994991 TATCGATACATTTGTA-GAATG
1 TATCGATACA-TTCTACAAATG
*
2995012 TATCGATACATTCCACAAATG
1 TATCGATACATTCTACAAATG
2995033 TATCGATACATTCTACAAATG
1 TATCGATACATTCTACAAATG
2995054 TATCGATACATT
1 TATCGATACATT
2995066 TGAATTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (21 bp):
TATCGATACATTCTACAAATG
Found at i:3007515 original size:12 final size:12
Alignment explanation
Indices: 3007498--3007537 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
3007488 AAAAACAAGC
*
3007498 AAAACAAACAAA
1 AAAACAAATAAA
3007510 AAAACAAATAAA
1 AAAACAAATAAA
*
3007522 CAAACAAATAAA
1 AAAACAAATAAA
3007534 AAAA
1 AAAA
3007538 GAGGTTCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.05
Consensus pattern (12 bp):
AAAACAAATAAA
Found at i:3008967 original size:28 final size:28
Alignment explanation
Indices: 3008748--3009052 Score: 342
Period size: 29 Copynumber: 10.8 Consensus size: 28
3008738 CTAGAACGTT
* * * * *
3008748 CATCTCTTCAAAACCCACAGGTTAGCGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* ** * *
3008776 CATCTCTTCAAAAAACCACAAGTCAATAG
1 CATCTTTTC-AAAGCCCACAAGTCAGTGG
** *
3008805 CATCTTTTCAAAAAACCATAAGTCAGTGG
1 CATCTTTTC-AAAGCCCACAAGTCAGTGG
*
3008834 CATCCTTCTCAAAGCCCACAAGTCAGTGG
1 CAT-CTTTTCAAAGCCCACAAGTCAGTGG
* *
3008863 CATCCTTCTCAAAACCCACAAGTCAGTGG
1 CAT-CTTTTCAAAGCCCACAAGTCAGTGG
* *
3008892 CATCCTTCTCAAAGCCCACAAGTTAGTGG
1 CAT-CTTTTCAAAGCCCACAAGTCAGTGG
3008921 CATC-TTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
3008948 CATCTTTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
3008976 CACCCTTTCAAAGCCCATAAGGCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
3009004 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
3009032 CATCCTTTCAAAGCCCACAAG
1 CATCTTTTCAAAGCCCACAAG
3009053 CTAGTAGTAA
Statistics
Matches: 248, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
27 25 0.10
28 103 0.42
29 115 0.46
30 5 0.02
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (28 bp):
CATCTTTTCAAAGCCCACAAGTCAGTGG
Found at i:3008984 original size:56 final size:57
Alignment explanation
Indices: 3008791--3009052 Score: 377
Period size: 56 Copynumber: 4.6 Consensus size: 57
3008781 CTTCAAAAAA
* * * ** *
3008791 CCACAAGTCAATAGCATCTTTTCAAAAAACCATAAGTCAGTGGCATCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGC
*
3008849 CCACAAGTCAGTGGCATCCTTCTCAAAACCCACAAGTCAGTGGCATCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGC
* *
3008907 CCACAAGTTAGTGGCAT-CTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGC
* * *
3008962 CCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGGCAGTGGCATCCTT-TCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGC
3009018 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
3009053 CTAGTAGTAA
Statistics
Matches: 187, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
55 25 0.13
56 88 0.47
57 6 0.03
58 66 0.35
59 2 0.01
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (57 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGC
Found at i:3009107 original size:44 final size:44
Alignment explanation
Indices: 3009039--3009122 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
3009029 TGGCATCCTT
3009039 TCAAAGCCCACAAGCTAGTAGTAACTCTTTTCAAAACCCATAAG
1 TCAAAGCCCACAAGCTAGTAGTAACTCTTTTCAAAACCCATAAG
* *
3009083 TCAAAGCCCACAAG-TCAGTGGTAACTCTTTTCAAAGCCCA
1 TCAAAGCCCACAAGCT-AGTAGTAACTCTTTTCAAAACCCA
3009123 CACAAGTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 1 0.03
44 36 0.97
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.23
Consensus pattern (44 bp):
TCAAAGCCCACAAGCTAGTAGTAACTCTTTTCAAAACCCATAAG
Found at i:3010123 original size:24 final size:20
Alignment explanation
Indices: 3010105--3010201 Score: 117
Period size: 20 Copynumber: 4.9 Consensus size: 20
3010095 CTTTTATCCA
3010105 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
3010125 AATGTATCGATACATGTGTG
1 AATGTATCGATACATTTTTC
* *
3010145 AATGTATTGATACATTTTTT
1 AATGTATCGATACATTTTTC
3010165 AATGTATCGATACATTCTTT-
1 AATGTATCGATACATT-TTTC
*
3010185 AA-GTATCGATATATTTT
1 AATGTATCGATACATTTT
3010202 GTCTTTTTAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 2 0.03
19 12 0.18
20 50 0.75
21 3 0.04
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:3011147 original size:20 final size:22
Alignment explanation
Indices: 3011107--3011147 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3011097 TAGCCTTTAA
*
3011107 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
3011129 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
3011148 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:3016344 original size:2 final size:2
Alignment explanation
Indices: 3016337--3016363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3016327 AAATGATTTA
3016337 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3016364 CACTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3016743 original size:18 final size:19
Alignment explanation
Indices: 3016717--3016768 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
3016707 CATTTTTAAA
*
3016717 TTATCATTATAAATATT-T
1 TTATTATTATAAATATTAT
*
3016735 TTATTATTAATAAAAATTAT
1 TTATTATT-ATAAATATTAT
*
3016755 TTAAT-TTATAAATA
1 TTATTATTATAAATA
3016769 AGAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 13 0.46
19 10 0.36
20 5 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTATTATAAATATTAT
Found at i:3017287 original size:17 final size:17
Alignment explanation
Indices: 3017246--3017279 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3017236 TGATAAAAAC
*
3017246 ATTAAAAATAATAATTT
1 ATTAAATATAATAATTT
*
3017263 ATTTAATATAATAATTT
1 ATTAAATATAATAATTT
3017280 TATAAATACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAAATATAATAATTT
Found at i:3018112 original size:75 final size:75
Alignment explanation
Indices: 3017972--3018210 Score: 279
Period size: 75 Copynumber: 3.2 Consensus size: 75
3017962 TCCACGGCGC
* * * * *
3017972 CAATCAGAC-GGTCCCTGATGCTGCAGCAGAAAACAGCACCCATGATCATGAACAACAAGTTTCT
1 CAATCAG-CTGGTCCCTGATGCT---GCAGAAAACAGCACCGATGATCATGCACAAGAGGTCTCT
*
3018036 AGACTAGAGGAGAA
62 AGAGTAGAGGAGAA
* * *
3018050 CAATCAGCTGGTCCCTTATGCTGCAGAAAACAACATCGATGATCATGCACAAGAGGTCTCTAGAG
1 CAATCAGCTGGTCCCTGATGCTGCAGAAAACAGCACCGATGATCATGCACAAGAGGTCTCTAGAG
*
3018115 TGGAGGAGAA
66 TAGAGGAGAA
* * *
3018125 CAATCAGAC-GGTCCCTGATGCTGCAGAAAACAGCACCGATTATCATGCACAAGAGGTCACTACA
1 CAATCAG-CTGGTCCCTGATGCTGCAGAAAACAGCACCGATGATCATGCACAAGAGGTCTCTAGA
3018189 GTAG-GG-GAA
65 GTAGAGGAGAA
*
3018198 CAAGCAGCTGGTC
1 CAATCAGCTGGTC
3018211 ATCATCATCA
Statistics
Matches: 140, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
72 1 0.01
73 13 0.09
74 2 0.01
75 103 0.74
76 1 0.01
77 1 0.01
78 19 0.14
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (75 bp):
CAATCAGCTGGTCCCTGATGCTGCAGAAAACAGCACCGATGATCATGCACAAGAGGTCTCTAGAG
TAGAGGAGAA
Found at i:3020101 original size:16 final size:16
Alignment explanation
Indices: 3020082--3020112 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3020072 TTTGTTTATT
3020082 AATAAATAAAGAAAAA
1 AATAAATAAAGAAAAA
*
3020098 AATAAATGAAGAAAA
1 AATAAATAAAGAAAA
3020113 GCTTTAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (16 bp):
AATAAATAAAGAAAAA
Found at i:3020787 original size:17 final size:17
Alignment explanation
Indices: 3020748--3020792 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3020738 AATAAATAAT
* *
3020748 AAAAAAAGATATATTTG
1 AAAAAAAGAAATATTTA
*
3020765 ATAAAAAGAAATATTTA
1 AAAAAAAGAAATATTTA
*
3020782 AAAAAATGAAA
1 AAAAAAAGAAA
3020793 ATACCAACCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAAAAGAAATATTTA
Found at i:3022213 original size:2 final size:2
Alignment explanation
Indices: 3022206--3022235 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3022196 CTTCTGCCAA
3022206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3022236 CGGAGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3022433 original size:2 final size:2
Alignment explanation
Indices: 3022421--3022457 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3022411 TGCTACACCT
3022421 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3022458 CAAACATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3031923 original size:22 final size:21
Alignment explanation
Indices: 3031890--3031931 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3031880 AGAAAATTAT
*
3031890 GTCAAAAACAAAAATAAAAAA
1 GTCAAAAACAAAAAGAAAAAA
*
3031911 GTCATAAATCAAAAAGAAAAA
1 GTCA-AAAACAAAAAGAAAAA
3031932 GATTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.71, C:0.10, G:0.07, T:0.12
Consensus pattern (21 bp):
GTCAAAAACAAAAAGAAAAAA
Found at i:3036376 original size:28 final size:28
Alignment explanation
Indices: 3036337--3036411 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
3036327 TGGAGATAAC
*
3036337 AACGGGGCTGGAGTATCTCCTCA-GAAAT
1 AACGGGGTTGGAGTATC-CCTCACGAAAT
3036365 AACGGGGTTGGAGTATCCCTCACGAAAT
1 AACGGGGTTGGAGTATCCCTCACGAAAT
3036393 AACGGGGTTGGAGTATCCC
1 AACGGGGTTGGAGTATCCC
3036412 CGATTGTGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (28 bp):
AACGGGGTTGGAGTATCCCTCACGAAAT
Found at i:3036462 original size:51 final size:51
Alignment explanation
Indices: 3036403--3036514 Score: 188
Period size: 51 Copynumber: 2.2 Consensus size: 51
3036393 AACGGGGTTG
*
3036403 GAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGAAGTTA
1 GAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGAAGTTA
** *
3036454 GAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTG
1 GAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGAAGTTA
3036505 GAGTATCCCC
1 GAGTATCCCC
3036515 TTAGAAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGAAGTTA
Found at i:3036591 original size:51 final size:50
Alignment explanation
Indices: 3036515--3036643 Score: 154
Period size: 51 Copynumber: 2.6 Consensus size: 50
3036505 GAGTATCCCC
* * * *
3036515 TTAGAAAT--AACAGGGTTAGAGTATCCCTGATGGTGGAAAATCGATGTT
1 TTAGAAATAAAACCGGGTTGGAGTATCCCTGATGATGAAAAATCGATGTT
* * * *
3036563 TTGGAAATAAAACCGAGGTTGGAGTATCCTTGATTATGAAAAATTGATGTT
1 TTAGAAATAAAACCG-GGTTGGAGTATCCCTGATGATGAAAAATCGATGTT
3036614 TTAGAAATAAAACCGGGATTGGAGTATCCC
1 TTAGAAATAAAACCGGG-TTGGAGTATCCC
3036644 CTTGAAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 7 0.10
50 6 0.09
51 54 0.81
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (50 bp):
TTAGAAATAAAACCGGGTTGGAGTATCCCTGATGATGAAAAATCGATGTT
Found at i:3036603 original size:130 final size:129
Alignment explanation
Indices: 3036367--3036722 Score: 466
Period size: 130 Copynumber: 2.7 Consensus size: 129
3036357 TCAGAAATAA
* * *
3036367 CGGGGTTGGAGTAT-CCCTCACGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTTA-GAAATAACAGGGTTGGAGTATCCCTGATTGTGAAAAA-TGATG
* * *
3036431 TTTTGGAAATAAAATCGAAGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAA
64 TTTTGGAAATAAAATCGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAA
*
3036496 T
129 C
* * *
3036497 CGGGGTTGGAGTATCCCCTTAGAAATAACAGGGTTAGAGTATCCCTGATGGTGGAAAATCGATGT
1 CGGGGTTGGAGTATCCCCTTAGAAATAACAGGGTTGGAGTATCCCTGATTGTGAAAAAT-GATGT
* **
3036562 TTTGGAAATAAAACCGAGGTTGGAGTATCCTTGATTATGAAAAATTGATGTTTTAGAAATAAAAC
65 TTTGGAAATAAAATCGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAAC
* * * *
3036627 CGGGATTGGAGTATCCCCTT-GAAA-AAAATGGGGTTGGAGTATCCCTGATTATGAAAAATTAGT
1 CGGGGTTGGAGTATCCCCTTAGAAATAACA--GGGTTGGAGTATCCCTGATTGTGAAAAATGA-T
* *
3036690 GTTTTGAAAATAAAATCGAGATTGGAGTATCCC
63 GTTTTGGAAATAAAATCGAGGTTGGAGTATCCC
3036723 TTCGAAAATA
Statistics
Matches: 197, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
128 3 0.02
129 6 0.03
130 183 0.93
131 5 0.03
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (129 bp):
CGGGGTTGGAGTATCCCCTTAGAAATAACAGGGTTGGAGTATCCCTGATTGTGAAAAATGATGTT
TTGGAAATAAAATCGAGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAAC
Found at i:3036667 original size:79 final size:78
Alignment explanation
Indices: 3036566--3036783 Score: 251
Period size: 79 Copynumber: 2.7 Consensus size: 78
3036556 CGATGTTTTG
*
3036566 GAAATAAAACCGAGGTTGGAGTATCCTTGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGG
1 GAAA-AAAA-CGAGGTTGGAGTATCCTTGATTATGAAAAATTGATGTTTT-GAAATAAAACCGAG
3036631 ATTGGAGTATCCCCTT-
63 ATTGGAGTAT-CCCTTC
* * * *
3036647 GAAAAAAATGGGGTTGGAGTATCCCTGATTATGAAAAATT-AGTGTTTTGAAAATAAAATCGAGA
1 GAAAAAAACGAGGTTGGAGTATCCTTGATTATGAAAAATTGA-TGTTTTG-AAATAAAACCGAGA
3036711 TTGGAGTATCCCTTC
64 TTGGAGTATCCCTTC
* * * * * * *
3036726 GAAAATAACGAGATTGGAGTATCGTCGATTGTAAAAAATTGGTGTTTTGGAAATAAAA
1 GAAAAAAACGAGGTTGGAGTATCCTTGATTATGAAAAATTGATGTTTT-GAAATAAAA
3036784 ACATGAATGA
Statistics
Matches: 117, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
78 7 0.06
79 101 0.86
80 5 0.04
81 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (78 bp):
GAAAAAAACGAGGTTGGAGTATCCTTGATTATGAAAAATTGATGTTTTGAAATAAAACCGAGATT
GGAGTATCCCTTC
Found at i:3039201 original size:20 final size:20
Alignment explanation
Indices: 3039170--3039224 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
3039160 GTAAACCCTG
3039170 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
* *
3039190 AATGTGTTGATACAATGAAC
1 AATGTATCGATACAATGAAC
3039210 AATGTATCGATACAA
1 AATGTATCGATACAA
3039225 ATTGTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:3040003 original size:42 final size:43
Alignment explanation
Indices: 3039924--3040092 Score: 157
Period size: 42 Copynumber: 3.8 Consensus size: 43
3039914 AAAAAGAGTA
* *
3039924 CGTCCTACT-TTTCGAGGACAAAGGAAAAAAAAGGAAAATGAAATG
1 CGTCCTGCTCTTT-GAGGATAAAGG--AAAAAAGGAAAATGAAATG
* *
3039969 CGTCTTGCTCTTTGAGGATAAAAG-AAAAAGGAAAAT-AAAGTG
1 CGTCCTGCTCTTTGAGGATAAAGGAAAAAAGGAAAATGAAA-TG
* * * *
3040011 CATCCTGCTCTTTGAGAACTAGAAGGGAAAAGAAGG-AAATGAATTA
1 CGTCCTGCTCTTTGAGGA-TA-AA-GGAAAA-AAGGAAAATGAAATG
*
3040057 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAAA
1 CGTCCTGCTCTTTGAGGATAAAGGAAAAAAGGAAAA
3040093 AGTGTCATGC
Statistics
Matches: 102, Mismatches: 13, Indels: 20
0.76 0.10 0.15
Matches are distributed among these distances:
41 3 0.03
42 33 0.32
43 11 0.11
44 4 0.04
45 18 0.18
46 27 0.26
47 6 0.06
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (43 bp):
CGTCCTGCTCTTTGAGGATAAAGGAAAAAAGGAAAATGAAATG
Found at i:3040302 original size:61 final size:61
Alignment explanation
Indices: 3040120--3040662 Score: 582
Period size: 61 Copynumber: 9.1 Consensus size: 61
3040110 GGCAAAGGAG
* *
3040120 AAAAGGAAAAGGCGTCCTGCTCTTTGAAGATTGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
3040181 -AAAGGAGAAGGCGTCTTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * **
3040240 AAAAGGAAAAGGTGTCATGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGCATGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* ** *
3040301 ------AAAAGGTGTCCCACTCTTTGAGGACTGGGAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * * *
3040356 AAAAAGAAAAGGCATCCTGCTCTTCGAGTACT-AGAAGGTGCCACCGACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
3040417 AAATGGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACTAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
3040479 ------AAAAGGCGTCCTACTCTTTGAGGACTGGGAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
3040534 AAAAGGAAAAAGCATCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGCGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
* * * * * *
3040595 AAAAGGAAAAGGTGTCCAGCTCTTTAAGGACTAGAAAAGTGCCACCAGCTTGTATGGGTTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
*
3040657 GAAAGG
1 AAAAGG
3040663 CATCCTACTC
Statistics
Matches: 400, Mismatches: 59, Indels: 45
0.79 0.12 0.09
Matches are distributed among these distances:
55 65 0.16
56 32 0.08
59 26 0.06
60 61 0.15
61 164 0.41
62 50 0.12
63 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:3040509 original size:178 final size:178
Alignment explanation
Indices: 3040126--3040682 Score: 825
Period size: 178 Copynumber: 3.1 Consensus size: 178
3040116 GGAGAAAAGG
* * * * *
3040126 AAAAGGCGTCCTGCTCTTTGAAGA-TTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGAGA
1 AAAAGGCGTCCTACTCTTTGAGGACTGGGAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* *
3040189 AGGCGTCTTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGT
65 AGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGT
* * *
3040253 GTCATGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGCATGGGCTTT
130 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTATGGGCTTT
* * *
3040301 AAAAGGTGTCCCACTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
1 AAAAGGCGTCCTACTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* * * * * *
3040366 GGCATCCTGCTCTTCGAGTACTAGAAGGTGCCACCGACTTGTGTGGGCTTTAAATGGAAAAAGCG
66 GGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTG
* *
3040431 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACTAGCTTGTGTGGGCTTT
131 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTATGGGCTTT
3040479 AAAAGGCGTCCTACTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
1 AAAAGGCGTCCTACTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* *
3040544 AGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGCGTGGGCTTTAAAAGGAAAAGGTG
66 GGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTG
* * *
3040609 TCCAGCTCTTTAAGGACTAGAAAAGTGCCACCAGCTTGTATGGGTTTT
131 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTATGGGCTTT
* *
3040657 GAAAGGCATCCTACTCTTTGAGGACT
1 AAAAGGCGTCCTACTCTTTGAGGACT
3040683 AAAGGGTAAA
Statistics
Matches: 339, Mismatches: 39, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
175 43 0.13
176 30 0.09
177 55 0.16
178 211 0.62
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (178 bp):
AAAAGGCGTCCTACTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
GGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTG
TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAGCTTGTATGGGCTTT
Found at i:3041776 original size:1 final size:1
Alignment explanation
Indices: 3041770--3041821 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
3041760 TTCTTTTCTC
* * * * *
3041770 TTTTTTTTTGTTTTTTTTTATTTTTTTGTTTTTTTTGTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3041822 GAAAAAAGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.00, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:3041783 original size:9 final size:9
Alignment explanation
Indices: 3041771--3041821 Score: 70
Period size: 9 Copynumber: 5.7 Consensus size: 9
3041761 TCTTTTCTCT
3041771 TTTTTTTTG
1 TTTTTTTTG
3041780 TTTTTTTT-
1 TTTTTTTTG
3041788 TATTTTTTTG
1 T-TTTTTTTG
3041798 TTTTTTTTG
1 TTTTTTTTG
3041807 TTTTTGTTT-
1 TTTTT-TTTG
3041816 TTTTTT
1 TTTTTT
3041822 GAAAAAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.05
9 33 0.85
10 4 0.10
ACGTcount: A:0.02, C:0.00, G:0.08, T:0.90
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3041793 original size:18 final size:17
Alignment explanation
Indices: 3041770--3041821 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
3041760 TTCTTTTCTC
3041770 TTTTTTTTTGTTTTTTT
1 TTTTTTTTTGTTTTTTT
3041787 TTATTTTTTTG--TTTTT
1 TT-TTTTTTTGTTTTTTT
*
3041803 TTTGTTTTTGTTTTTTT
1 TTTTTTTTTGTTTTTTT
3041820 TT
1 TT
3041822 GAAAAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 7 0.23
16 7 0.23
17 9 0.29
18 8 0.26
ACGTcount: A:0.02, C:0.00, G:0.08, T:0.90
Consensus pattern (17 bp):
TTTTTTTTTGTTTTTTT
Found at i:3041793 original size:27 final size:28
Alignment explanation
Indices: 3041758--3041821 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
3041748 AAGTAGTTTC
*
3041758 TTTTCTTTTCTCT-TTTTTTTTGTTTTT-
1 TTTTATTTT-TCTGTTTTTTTTGTTTTTG
*
3041785 TTTTATTTTTTTGTTTTTTTTGTTTTTG
1 TTTTATTTTTCTGTTTTTTTTGTTTTTG
3041813 TTTT-TTTTT
1 TTTTATTTTT
3041822 GAAAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.06
27 27 0.82
28 4 0.12
ACGTcount: A:0.02, C:0.05, G:0.06, T:0.88
Consensus pattern (28 bp):
TTTTATTTTTCTGTTTTTTTTGTTTTTG
Found at i:3050390 original size:17 final size:17
Alignment explanation
Indices: 3050368--3050402 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3050358 GTTTGGTGGG
3050368 AATCTAGTGCATATGAA
1 AATCTAGTGCATATGAA
3050385 AATCTAGTGCATATGAA
1 AATCTAGTGCATATGAA
3050402 A
1 A
3050403 GTACACGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (17 bp):
AATCTAGTGCATATGAA
Found at i:3051667 original size:28 final size:28
Alignment explanation
Indices: 3051628--3051706 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
3051618 TGGAGATAAC
*
3051628 AACGGGGCTGGAGTATCCCC-TTAGAAAT
1 AACGGGGCTGGAGTATCCCCAAT-GAAAT
*
3051656 AACGGGGTTGGAGTATCCCCAATGAAAT
1 AACGGGGCTGGAGTATCCCCAATGAAAT
*
3051684 AACGGGGCTGGAGTATCTCCAAT
1 AACGGGGCTGGAGTATCCCCAAT
3051707 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 45 0.98
29 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (28 bp):
AACGGGGCTGGAGTATCCCCAATGAAAT
Found at i:3051760 original size:51 final size:51
Alignment explanation
Indices: 3051694--3051804 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 51
3051684 AACGGGGCTG
* *
3051694 GAGTATCTCCAATTGTGAAAAATTGATGTTTTGGAAATAAAATC-GGAGTTA
1 GAGTATCCCCAATTGTGAAAAATTGATGTTTTAGAAATAAAA-CAGGAGTTA
* * *
3051745 GAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACAGGGGTTG
1 GAGTATCCCCAATTGTGAAAAATTGATGTTTTAGAAATAAAACAGGAGTTA
3051796 GAGTATCCC
1 GAGTATCCC
3051805 TTTGGAAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 53 0.98
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (51 bp):
GAGTATCCCCAATTGTGAAAAATTGATGTTTTAGAAATAAAACAGGAGTTA
Found at i:3051887 original size:51 final size:51
Alignment explanation
Indices: 3051825--3051935 Score: 168
Period size: 51 Copynumber: 2.2 Consensus size: 51
3051815 ACGGGATTAG
* *
3051825 AGTATCTCCGATGGTGGAAAATCGATGTTTTGAAAATAAAATCGGGGTTGA
1 AGTATCCCCGATGGTAGAAAATCGATGTTTTGAAAATAAAATCGGGGTTGA
* * * *
3051876 AGTATCCCCGATTGTAGAAAATTGATGTTTTGGAAATAAAATCGGGGTTGG
1 AGTATCCCCGATGGTAGAAAATCGATGTTTTGAAAATAAAATCGGGGTTGA
3051927 AGTATCCCC
1 AGTATCCCC
3051936 TTAGAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
AGTATCCCCGATGGTAGAAAATCGATGTTTTGAAAATAAAATCGGGGTTGA
Found at i:3051897 original size:130 final size:127
Alignment explanation
Indices: 3051648--3052010 Score: 403
Period size: 130 Copynumber: 2.8 Consensus size: 127
3051638 GAGTATCCCC
* * *
3051648 TTAGAAAT--AACGGGGTTGGAGTATCCCCAATGAAATAACGGGGCTGGAGTATCTCCAATTGTG
1 TTAGAAATAAAACGGGGTTGGAGTAT-CCCATTGAAATAAC-GGGTTGGAGTATCTCCAATGGTG
* *
3051711 AAAAATTGATGTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTGTGAAAAATTGATGTT
64 AAAAATCGATGTTTTGAAAATAAAATCGGAGTTAGAGTATCCCCGATTGTGAAAAATTGATGTT
* * *
3051775 TTAGAAATAAAACAGGGGTTGGAGTATCCCTTTGGAAATAACGGGATTAGAGTATCTCCGATGGT
1 TTAGAAATAAAAC-GGGGTTGGAGTATCCCATT-GAAATAACGGG-TTGGAGTATCTCCAATGGT
* *
3051840 GGAAAATCGATGTTTTGAAAATAAAATCGGGGTT-GAAGTATCCCCGATTGT-AGAAAATTGATG
63 GAAAAATCGATGTTTTGAAAATAAAATCGGAGTTAG-AGTATCCCCGATTGTGA-AAAATTGATG
3051903 TT
126 TT
* * * **
3051905 TTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAGAAATAACGAGGTTGGAGTATC-CACGATTA
1 TTAGAAATAAAA-CGGGGTTGGAGTATCCCATT-GAAATAACG-GGTTGGAGTATCTC-CAATGG
* * * * * *
3051969 TGAAAAATTGGTATTTTAAAAATAAAACCGGAGTTGGAGTAT
62 TGAAAAATCGATGTTTTGAAAATAAAATCGGAGTTAGAGTAT
3052011 TCCCTCGGAA
Statistics
Matches: 202, Mismatches: 23, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
127 8 0.04
129 13 0.06
130 177 0.88
131 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (127 bp):
TTAGAAATAAAACGGGGTTGGAGTATCCCATTGAAATAACGGGTTGGAGTATCTCCAATGGTGAA
AAATCGATGTTTTGAAAATAAAATCGGAGTTAGAGTATCCCCGATTGTGAAAAATTGATGTT
Found at i:3052005 original size:79 final size:79
Alignment explanation
Indices: 3051871--3052074 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
3051861 TAAAATCGGG
* * * * * ** * *
3051871 GTTGAAGTATCCCCGATTGTAGAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGAAGTATCCACGATTATAAAAAATTGGTATTTTAAAAATAAAACCGGAGTTGGAGTATCCCC
*
3051936 TTAGAAATAAC-GA
66 TCAGAAATAACGGA
* * *
3051949 GGTTGGAGTATCCACGATTATGAAAAATTGGTATTTTAAAAATAAAACCGGAGTTGGAGTATTCC
1 -GTTGAAGTATCCACGATTATAAAAAATTGGTATTTTAAAAATAAAACCGGAGTTGGAGTATCCC
*
3052014 CTCGGAAATAACGGA
65 CTCAGAAATAACGGA
* * * **
3052029 GTTGAAGTATCCTCGATTGTAAAAAATTGGTGTTTTGGAAATAAAA
1 GTTGAAGTATCCACGATTATAAAAAATTGGTATTTTAAAAATAAAA
3052075 ACATGAATGA
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
79 101 0.98
80 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (79 bp):
GTTGAAGTATCCACGATTATAAAAAATTGGTATTTTAAAAATAAAACCGGAGTTGGAGTATCCCC
TCAGAAATAACGGA
Found at i:3055852 original size:1 final size:1
Alignment explanation
Indices: 3055848--3055905 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
3055838 CTTTTCTCTC
* * * * * *
3055848 TTTTTTTCTTTTTTTGTTTTCTTTTGTTTTTTTTTTTTGTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3055906 AAAAAGAATG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:3055852 original size:10 final size:8
Alignment explanation
Indices: 3055832--3055905 Score: 64
Period size: 8 Copynumber: 9.4 Consensus size: 8
3055822 TTAAGCATGC
3055832 TTTTTTCT
1 TTTTTTCT
*
3055840 TTTCTCTCT
1 TTT-TTTCT
3055849 TTTTTTCT
1 TTTTTTCT
*
3055857 TTTTTTGT
1 TTTTTTCT
3055865 TTTCTTT-T
1 TTT-TTTCT
*
3055873 GTTTTT-T
1 TTTTTTCT
*
3055880 TTTTTTGT
1 TTTTTTCT
*
3055888 TTTTTTGT
1 TTTTTTCT
3055896 TTTTTT-T
1 TTTTTTCT
3055903 TTT
1 TTT
3055906 AAAAAGAATG
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
7 13 0.22
8 35 0.60
9 10 0.17
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.86
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3055872 original size:18 final size:16
Alignment explanation
Indices: 3055832--3055905 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 16
3055822 TTAAGCATGC
* *
3055832 TTTTTTCTTTTCTCTCT
1 TTTTTTCTTTT-TTTTT
3055849 TTTTTTCTTTTTTTGTT
1 TTTTTTCTTTTTTT-TT
*
3055866 TTCTTTTGTTTTTTTTT
1 TT-TTTTCTTTTTTTTT
3055883 TTTGTTT-TTTTGTTTTT
1 TTT-TTTCTTTT-TTTTT
3055900 TTTTTT
1 TTTTTT
3055906 AAAAAGAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
16 10 0.20
17 29 0.58
18 11 0.22
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.86
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTT
Found at i:3055872 original size:21 final size:21
Alignment explanation
Indices: 3055846--3055905 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
3055836 TTCTTTTCTC
3055846 TCTTT-TTTTCTTTTTTTGTTT
1 TCTTTGTTTT-TTTTTTTGTTT
3055867 TCTTTTGTTTTTTTTTTTTGTTT
1 TC-TTTG-TTTTTTTTTTTGTTT
3055890 T-TTTGTTTTTTTTTTT
1 TCTTTGTTTTTTTTTTT
3055906 AAAAAGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.31
21 6 0.17
22 3 0.08
23 12 0.33
24 4 0.11
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (21 bp):
TCTTTGTTTTTTTTTTTGTTT
Found at i:3066619 original size:52 final size:51
Alignment explanation
Indices: 3066541--3066659 Score: 159
Period size: 52 Copynumber: 2.3 Consensus size: 51
3066531 AATAGTCTAC
* ** **
3066541 ATGTATCGATACATTTGGGTCAAAAACCTAGAATGTATGGATACAAT-GAATA
1 ATGTATCGATACATTTGGGTAAAAAACCTAGAACATATCAATACAATAG-A-A
3066593 ATGTATCGATACATTTGGGTAAAAAACCTAGAACATATCAATACAATAGAA
1 ATGTATCGATACATTTGGGTAAAAAACCTAGAACATATCAATACAATAGAA
*
3066644 ATATATCGATACATTT
1 ATGTATCGATACATTT
3066660 TCTTTCTAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 16 0.27
52 43 0.72
53 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACATTTGGGTAAAAAACCTAGAACATATCAATACAATAGAA
Found at i:3069151 original size:51 final size:49
Alignment explanation
Indices: 3069074--3069615 Score: 256
Period size: 50 Copynumber: 10.9 Consensus size: 49
3069064 CCTAGTGATA
*
3069074 AGAGTCTAAA-TCCACATTAGCTAGCACCTGATATAAAGGTCAAGTCCTAT
1 AGAGT-TAAAGTCCACATTAGCTAGCACCTAATA-AAAGGTCAAGTCCTAT
* * * *
3069124 AGAGTTAAAAGTCCACATTAGCAAGCACCCAATAAAAAGGTTAAGTCTTAT
1 AGAGTT-AAAGTCCACATTAGCTAGCACCTAAT-AAAAGGTCAAGTCCTAT
* * * * * *
3069175 AGAGTCAAAGTCCACATGAACT-GTCATCTGATAAAAGAGTTAAGTCCTAT
1 AGAGTTAAAGTCCACATTAGCTAG-CACCTAATAAAAG-GTCAAGTCCTAT
* * * * *
3069225 AGACTTAAAGTCCACACTAGCTAGTATCTAATAAGAAGGTCAAGTTCTAT
1 AGAGTTAAAGTCCACATTAGCTAGCACCTAATAA-AAGGTCAAGTCCTAT
* * ** * * * * * *
3069275 AGAGTCAAAGTCTAC-CGAGTTGGCACCCAATAGGAGGGTCAAGTCTTAT
1 AGAGTTAAAGTCCACATTAGCTAGCACCTAATA-AAAGGTCAAGTCCTAT
* * * * * * * ** *
3069324 AAAGTCAAAATCCACACTAGTTAGCACTTGATAAGAAGGAAAAGTCCTTT
1 AGAGTTAAAGTCCACATTAGCTAGCACCTAATAA-AAGGTCAAGTCCTAT
* * * * * * **
3069374 AGAGTCAAAGTCGATATGAGCTAACACCTGATAGGAAA-GTCAAGTTTTAT
1 AGAGTTAAAGTCCACATTAGCTAGCACCTAATA--AAAGGTCAAGTCCTAT
* * * * * *
3069424 AGACTCAAAGTCCATATTATCTAGCATCTAATAAAAAGAT-AAGTCCTAT
1 AGAGTTAAAGTCCACATTAGCTAGCACCTAAT-AAAAGGTCAAGTCCTAT
* * * * ** * *
3069473 AAAGTCAAAGTTCGCACA-T--CTTGAACCTAATAGGGAGGTCAAATCCTAA
1 AGAGTTAAAG-TC-CACATTAGCTAGCACCTAATA-AAAGGTCAAGTCCTAT
* * *
3069522 AGAGTCTAAA-TCCACATTAACTAGCACTTAATAAGAAGGTAAAGTCCTAT
1 AGAGT-TAAAGTCCACATTAGCTAGCACCTAATAA-AAGGTCAAGTCCTAT
* * * * * *
3069572 AGAATCAAAGTCTACACTAGCTAGCACCTGATAGAGAGGTCAAG
1 AGAGTTAAAGTCCACATTAGCTAGCACCTAATA-AAAGGTCAAG
3069616 CCCTGCAAAT
Statistics
Matches: 364, Mismatches: 103, Indels: 50
0.70 0.20 0.10
Matches are distributed among these distances:
47 5 0.01
48 15 0.04
49 74 0.20
50 219 0.60
51 49 0.13
52 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.25
Consensus pattern (49 bp):
AGAGTTAAAGTCCACATTAGCTAGCACCTAATAAAAGGTCAAGTCCTAT
Found at i:3073933 original size:26 final size:26
Alignment explanation
Indices: 3073893--3073945 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3073883 ATAATGAACT
* * *
3073893 TATTCTAAGATTCAGTTTTAGAAAAA
1 TATTCTAAGACTCAGTTCTAAAAAAA
3073919 TATTCTAAGACTCAGTTCTAAAAAAA
1 TATTCTAAGACTCAGTTCTAAAAAAA
3073945 T
1 T
3073946 TACCAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (26 bp):
TATTCTAAGACTCAGTTCTAAAAAAA
Found at i:3074218 original size:156 final size:154
Alignment explanation
Indices: 3074047--3074333 Score: 371
Period size: 154 Copynumber: 1.9 Consensus size: 154
3074037 CCTGAACAAC
* * *
3074047 ACCTTTGGCATAAAAGTGACTC-GACAACTACCTAAGATTCGGTTATAAGAAAAAAATTATCAAA
1 ACCTTTGGCATAAAAGAGACTCAG-CAACCACCTAAGATTCGATTAT-A-AAAAAAATTATCAAA
* * * * *
3074111 ATGCCCCTAAAATATACCTTTAACGTAAAAGTACCTAGTAATCTTAAAGGACATGAAAAT-ATTA
63 ATGCCCCTAAAATATACCTTCAACATAAAAGTACCTAGTAACCATAAAAGACATGAAAATGA-TA
3074175 TAAAATGATGAACATGTCCTAAATGTAA
127 TAAAATGATGAACATGTCCTAAATGTAA
** * * *
3074203 ACCTTTGGCATAAAAGAGACTCAGTGACCATCTAGGATTCGATTCTAAAAAAAATTATCAAAATG
1 ACCTTTGGCATAAAAGAGACTCAGCAACCACCTAAGATTCGATTATAAAAAAAATTATCAAAATG
* * * *
3074268 TCCCTAAGATATATCTTCAACATGAAAGTACCTAGTAACCATAAAAGACATGAAAATGATATAAA
66 CCCCTAAAATATACCTTCAACATAAAAGTACCTAGTAACCATAAAAGACATGAAAATGATATAAA
3074333 A
131 A
3074334 GAATAAGTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
154 73 0.65
155 2 0.02
156 36 0.32
157 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (154 bp):
ACCTTTGGCATAAAAGAGACTCAGCAACCACCTAAGATTCGATTATAAAAAAAATTATCAAAATG
CCCCTAAAATATACCTTCAACATAAAAGTACCTAGTAACCATAAAAGACATGAAAATGATATAAA
ATGATGAACATGTCCTAAATGTAA
Found at i:3076416 original size:14 final size:14
Alignment explanation
Indices: 3076390--3076416 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3076380 AAATTTTAAA
3076390 CAAAAAAATTTATC
1 CAAAAAAATTTATC
3076404 CAAAAAAATTTAT
1 CAAAAAAATTTAT
3076417 GAAATACAAA
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:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
CAAAAAAATTTATC
Found at i:3077271 original size:22 final size:20
Alignment explanation
Indices: 3077237--3077290 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
3077227 TCTGGTGACC
3077237 TTTAGCTGCTGCCAGCGGCTAG
1 TTTAG-TGCTGCCAGCGGCT-G
*
3077259 TTTCAGTGCTGCCAGCTGCTG
1 TTT-AGTGCTGCCAGCGGCTG
*
3077280 TTTTGTGCTGC
1 TTTAGTGCTGC
3077291 TGCCAGCAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 7 0.24
21 4 0.14
22 16 0.55
23 2 0.07
ACGTcount: A:0.09, C:0.26, G:0.30, T:0.35
Consensus pattern (20 bp):
TTTAGTGCTGCCAGCGGCTG
Found at i:3077984 original size:21 final size:21
Alignment explanation
Indices: 3077942--3077985 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3077932 CAATTAGTTC
**
3077942 TTAAATAATTTAATATAAAAA
1 TTAAATAATAAAATATAAAAA
3077963 TTAAATAATAAAAT-TAATAAA
1 TTAAATAATAAAATATAA-AAA
3077984 TT
1 TT
3077986 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAATAATAAAATATAAAAA
Found at i:3082063 original size:2 final size:2
Alignment explanation
Indices: 3082046--3082084 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3082036 AGTCTACTGC
* *
3082046 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3082085 GATCTTATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3083914 original size:13 final size:13
Alignment explanation
Indices: 3083896--3083921 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3083886 CAATTTTTTG
3083896 TGTATCGATACAT
1 TGTATCGATACAT
3083909 TGTATCGATACAT
1 TGTATCGATACAT
3083922 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3086469 original size:13 final size:13
Alignment explanation
Indices: 3086451--3086489 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3086441 ATAATCACCC
*
3086451 TGTATCGATACAG
1 TGTATCGATACAA
3086464 TGTATCGATACAA
1 TGTATCGATACAA
3086477 TGTATCGATACAA
1 TGTATCGATACAA
3086490 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3086500 original size:20 final size:20
Alignment explanation
Indices: 3086475--3086553 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
3086465 GTATCGATAC
3086475 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3086495 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
3086520 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
3086540 CATGTATCGATACA
1 AATGTATCGATACA
3086554 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3090426 original size:21 final size:21
Alignment explanation
Indices: 3090397--3090441 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3090387 AAGTTTTCAT
*
3090397 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3090417 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3090439 TTT
1 TTT
3090442 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3092670 original size:13 final size:13
Alignment explanation
Indices: 3092652--3092677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3092642 CAATTTTTTG
3092652 TGTATCGATACAT
1 TGTATCGATACAT
3092665 TGTATCGATACAT
1 TGTATCGATACAT
3092678 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3107033 original size:28 final size:28
Alignment explanation
Indices: 3106974--3107033 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3106964 CCAAATCCAT
* *** **
3106974 TTTTCTTGCTCCACCATCATCTTTTCTT
1 TTTTCTCGCTCCACCATCATCAACTCCC
3107002 TTTTCTCGCTCCACCATCATCAACTCCC
1 TTTTCTCGCTCCACCATCATCAACTCCC
3107030 TTTT
1 TTTT
3107034 TCTTTCATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.13, C:0.37, G:0.03, T:0.47
Consensus pattern (28 bp):
TTTTCTCGCTCCACCATCATCAACTCCC
Found at i:3108034 original size:25 final size:25
Alignment explanation
Indices: 3107993--3108045 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
3107983 TGAATTTTTA
*
3107993 AAAAAATATTAAATAAA-TAAACTC
1 AAAAAATAATAAATAAACTAAACTC
*
3108017 AAAAAATAATAATTTAAATCTAAACTC
1 AAAAAATAATAA-ATAAA-CTAAACTC
3108044 AA
1 AA
3108046 GCCAAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 4 0.17
27 9 0.38
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAAAATAATAAATAAACTAAACTC
Found at i:3108299 original size:13 final size:14
Alignment explanation
Indices: 3108263--3108317 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
3108253 ATCACTTTTT
3108263 TTATTTATTATAACTA
1 TTATTTA-TATAA-TA
*
3108279 TTAATTATATAATA
1 TTATTTATATAATA
*
3108293 -TATTTATACAATA
1 TTATTTATATAATA
3108306 TGTATTTATATA
1 T-TATTTATATA
3108318 TGACAACTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 11 0.33
14 2 0.06
15 14 0.42
16 6 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (14 bp):
TTATTTATATAATA
Found at i:3111781 original size:21 final size:21
Alignment explanation
Indices: 3111755--3111807 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3111745 TTAAACAATT
*
3111755 TGTATCGATACAAT-AGGGTAA
1 TGTATCGATACAATAAGTG-AA
*
3111776 TGTATCGATA-TATAAGTGAA
1 TGTATCGATACAATAAGTGAA
3111796 TGTATCGATACA
1 TGTATCGATACA
3111808 TGTTAGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:3111959 original size:51 final size:52
Alignment explanation
Indices: 3111864--3111986 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 52
3111854 TTTGGAAAGA
* * *
3111864 AAATGTATCGATACATTTTTCATTGTATCGATAAATTCTAGG-TTTTGACCC
1 AAATGTATCGATACATTCTTCATTGTATCAATAAATTCTAGGTTTTTGAACC
* * * *
3111915 AAATGTATCGATACATTCTTCATTGTATCAATACATTTTGGGTTTTTGAATC
1 AAATGTATCGATACATTCTTCATTGTATCAATAAATTCTAGGTTTTTGAACC
* *
3111967 AAATATATCGATGCATTCTT
1 AAATGTATCGATACATTCTT
3111987 TAATATATCG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 37 0.60
52 25 0.40
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCAATAAATTCTAGGTTTTTGAACC
Found at i:3115044 original size:13 final size:13
Alignment explanation
Indices: 3115026--3115051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3115016 CAATTTTTGG
3115026 TGTATCGATACAT
1 TGTATCGATACAT
3115039 TGTATCGATACAT
1 TGTATCGATACAT
3115052 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3115063 original size:32 final size:33
Alignment explanation
Indices: 3115006--3115069 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3114996 TACAAGCCAA
**
3115006 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
3115039 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
3115070 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:3115076 original size:19 final size:18
Alignment explanation
Indices: 3115006--3115076 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
3114996 TACAAGCCAA
3115006 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
3115026 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
3115039 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
3115058 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
3115077 CTATTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:3117614 original size:13 final size:13
Alignment explanation
Indices: 3117596--3117634 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3117586 ATAATCACCC
3117596 TGTATCGATACAA
1 TGTATCGATACAA
*
3117609 TGTATCGATACAG
1 TGTATCGATACAA
*
3117622 TGTATCAATACAA
1 TGTATCGATACAA
3117635 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3121543 original size:21 final size:21
Alignment explanation
Indices: 3121514--3121558 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3121504 AAGTTTTTAT
*
3121514 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3121534 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3121556 TTT
1 TTT
3121559 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3127184 original size:20 final size:20
Alignment explanation
Indices: 3127159--3127196 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3127149 GGGTAAAAAG
3127159 AGAATGTATCAATACATTAA
1 AGAATGTATCAATACATTAA
*
3127179 AGAATGTATCGATACATT
1 AGAATGTATCAATACATT
3127197 GATACATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
AGAATGTATCAATACATTAA
Found at i:3130803 original size:23 final size:23
Alignment explanation
Indices: 3130770--3130820 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
3130760 TGTTTCTAAT
*
3130770 AAAAATGAAAAA-AAAAAGAGAAA
1 AAAAAT-AAAAAGAAAAAAAGAAA
*
3130793 GAAAATAAAAAGAAAAAAAGAAA
1 AAAAATAAAAAGAAAAAAAGAAA
3130816 AAAAA
1 AAAAA
3130821 AGCTTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (23 bp):
AAAAATAAAAAGAAAAAAAGAAA
Found at i:3130819 original size:11 final size:11
Alignment explanation
Indices: 3130770--3130821 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
3130760 TGTTTCTAAT
*
3130770 AAAAATGAAAA
1 AAAAAAGAAAA
3130781 AAAAAAGAGAAA
1 AAAAAAGA-AAA
3130793 GAAAATAA-AAAGA
1 -AAAA-AAGAAA-A
3130806 AAAAAAGAAAA
1 AAAAAAGAAAA
3130817 AAAAA
1 AAAAA
3130822 GCTTTTTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 15 0.43
12 12 0.34
13 6 0.17
14 2 0.06
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.04
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:3130822 original size:29 final size:29
Alignment explanation
Indices: 3130767--3130822 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3130757 TTTTGTTTCT
* *
3130767 AATAAAAATGAAAAAAAAAAGAGAAAGAA
1 AATAAAAATGAAAAAAAAAAAAAAAAGAA
3130796 AATAAAAA-GAAAAAAAGAAAAAAAAAG
1 AATAAAAATGAAAAAAA-AAAAAAAAAG
3130823 CTTTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (29 bp):
AATAAAAATGAAAAAAAAAAAAAAAAGAA
Found at i:3131590 original size:58 final size:58
Alignment explanation
Indices: 3131528--3131834 Score: 212
Period size: 58 Copynumber: 5.3 Consensus size: 58
3131518 AATTTAGTAG
* *
3131528 TTTTCATCAATTTAGAGCCATTTAGATTATTTAAAATGATCTAGAGTCATTTTAGCAA
1 TTTTCATCAATTTAGAGCCATTTAGATTATTTAACATAATCTAGAGTCATTTTAGCAA
* * * * * **
3131586 TTTTCATCATTTTAGGGCCATTGAGATTATTTAACATAAGCTAGGGTCATTTTATTAA
1 TTTTCATCAATTTAGAGCCATTTAGATTATTTAACATAATCTAGAGTCATTTTAGCAA
* * * * * * *
3131644 TTTTCATCATTTTAG-GACTATTTAGGTTTTTTTAACATAACCTAAGAAT-ATTTTAACAA
1 TTTTCATCAATTTAGAG-CCATTTA-GATTATTTAACATAATCT-AGAGTCATTTTAGCAA
* * * * * * * * *
3131703 TTTTCATC-ATTTTGAGGTCATGTAGGTTGTTTGACATGATTTAGAGTCATTTTAGCAG
1 TTTTCATCAATTTAGA-GCCATTTAGATTATTTAACATAATCTAGAGTCATTTTAGCAA
* * * * * * *
3131761 TTTTCATCAGTTAAG-GTCATTTAGGTTGTTTAACACAA-CTTAG-GATCATTTTAACAA
1 TTTTCATCAATTTAGAGCCATTTAGATTATTTAACATAATC-TAGAG-TCATTTTAGCAA
* *
3131818 TTTTCGTCATTTTAGAG
1 TTTTCATCAATTTAGAG
3131835 TCACTAAAGT
Statistics
Matches: 194, Mismatches: 45, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
56 1 0.01
57 49 0.25
58 102 0.53
59 38 0.20
60 4 0.02
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (58 bp):
TTTTCATCAATTTAGAGCCATTTAGATTATTTAACATAATCTAGAGTCATTTTAGCAA
Found at i:3131997 original size:79 final size:80
Alignment explanation
Indices: 3131901--3132085 Score: 193
Period size: 79 Copynumber: 2.4 Consensus size: 80
3131891 ATTATAAGTT
* * * *
3131901 TGAGTCCTCAA-GATCATGTTAGCATTTTCATACCAATACATGGT-CATTATGGTCATTTTAATC
1 TGAGTCCTTAAGGATCATGTTAGCATTTTCATACCAATACATAGTCCA-TAAGGTCATTTCAATC
3131964 ATTTTCATGATAAATA
65 ATTTTCATGATAAATA
* * * ** *
3131980 TGAGTTCTT-AGGATCATGTT-GATATTTTCATATCAATACATAGTCCATAAGGTTGTTTCAATG
1 TGAGTCCTTAAGGATCATGTTAG-CATTTTCATACCAATACATAGTCCATAAGGTCATTTCAATC
* *
3132043 ATTTTCATGGTAAATT
65 ATTTTCATGATAAATA
3132059 TGAGTCCTTAAGG-TCATG-TAGGCATTT
1 TGAGTCCTTAAGGATCATGTTA-GCATTT
3132086 CCACATTAAT
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
78 3 0.03
79 77 0.90
80 6 0.07
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (80 bp):
TGAGTCCTTAAGGATCATGTTAGCATTTTCATACCAATACATAGTCCATAAGGTCATTTCAATCA
TTTTCATGATAAATA
Found at i:3132967 original size:17 final size:16
Alignment explanation
Indices: 3132947--3132988 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3132937 ATTCAATGAA
3132947 CATATTTATTTCAATAT
1 CATATTTATTTCAA-AT
3132964 CATA-TTATTTTCAAAT
1 CATATTTA-TTTCAAAT
*
3132980 CACATTTAT
1 CATATTTAT
3132989 CAAATAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (16 bp):
CATATTTATTTCAAAT
Found at i:3145608 original size:13 final size:13
Alignment explanation
Indices: 3145590--3145626 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
3145580 AGTTTGATAA
3145590 ATAATTTATGAAT
1 ATAATTTATGAAT
*
3145603 ATAATTT-TAAAT
1 ATAATTTATGAAT
3145615 ATAATTTATGAA
1 ATAATTTATGAA
3145627 ATTAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (13 bp):
ATAATTTATGAAT
Found at i:3146695 original size:16 final size:15
Alignment explanation
Indices: 3146669--3146700 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3146659 ATTTTTAATT
3146669 ATAATAAGAAATATA
1 ATAATAAGAAATATA
3146684 ATAATAAAGAAATATA
1 ATAAT-AAGAAATATA
3146700 A
1 A
3146701 AATTGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (15 bp):
ATAATAAGAAATATA
Found at i:3148412 original size:20 final size:20
Alignment explanation
Indices: 3148375--3148429 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
3148365 TTCTATGATT
*
3148375 TGTATCGATACAATAAGTGAA
1 TGTATCAATAC-ATAAGTGAA
3148396 TGTATCAATACATAAGTGAA
1 TGTATCAATACATAAGTGAA
*
3148416 TATATCAATACATA
1 TGTATCAATACATA
3148430 CTTGAAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (20 bp):
TGTATCAATACATAAGTGAA
Done.