Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 100 of 290
Found at i:30824115 original size:56 final size:56
Alignment explanation
Indices: 30824054--30824170 Score: 234
Period size: 56 Copynumber: 2.1 Consensus size: 56
30824044 AACTTATCCA
30824054 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
1 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
30824110 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
1 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
30824166 TAACA
1 TAACA
30824171 ATGTGAAGGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (56 bp):
TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
Found at i:30826340 original size:15 final size:17
Alignment explanation
Indices: 30826309--30826340 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30826299 ATAATATTAT
30826309 ATAATATCATGTAATAG
1 ATAATATCATGTAATAG
30826326 ATAATAT-AT-TAATAG
1 ATAATATCATGTAATAG
30826341 TTTTGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (17 bp):
ATAATATCATGTAATAG
Found at i:30831491 original size:14 final size:15
Alignment explanation
Indices: 30831460--30831493 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
30831450 TTTTACTTAT
*
30831460 TTATTTCTTTATTTG
1 TTATTTCTTTAATTG
30831475 TTATTTC-TTAATTG
1 TTATTTCTTTAATTG
30831489 TTATT
1 TTATT
30831494 CTATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATTTCTTTAATTG
Found at i:30833091 original size:4 final size:5
Alignment explanation
Indices: 30833037--30833093 Score: 53
Period size: 5 Copynumber: 10.6 Consensus size: 5
30833027 TTTGAGTCCA
*
30833037 TTTAT TTTAT TATTAGT ATTATT TTTAAT TTTAAT TTTAT TTTAT TTTA-
1 TTTAT TTTAT T-TTA-T TTTA-T TTT-AT TTT-AT TTTAT TTTAT TTTAT
30833086 TTTAT TTT
1 TTTAT TTT
30833094 TGAAGACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
4 4 0.09
5 20 0.44
6 19 0.42
7 2 0.04
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:30833091 original size:9 final size:10
Alignment explanation
Indices: 30833037--30833093 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 10
30833027 TTTGAGTCCA
30833037 TTTATTTTAT
1 TTTATTTTAT
*
30833047 TATTAGTATTATT
1 T-TTA-TTTTA-T
30833060 TTTAATTTTAAT
1 TTT-ATTTT-AT
30833072 TTTATTTTAT
1 TTTATTTTAT
30833082 TTTA-TTTAT
1 TTTATTTTAT
30833091 TTT
1 TTT
30833094 TGAAGACTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 8 0.20
10 7 0.17
11 8 0.20
12 13 0.32
13 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:30835582 original size:115 final size:115
Alignment explanation
Indices: 30835380--30835609 Score: 442
Period size: 115 Copynumber: 2.0 Consensus size: 115
30835370 CAGATTTTAT
30835380 TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
1 TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
*
30835445 AATATTCTAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
66 AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
*
30835495 TACTATTTGAATCATATGATAAATACTTGTTCTTATTTTCAATTATGAGTTTTAATCATTGCTTT
1 TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
30835560 AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
66 AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
30835610 AAAGTCCTTG
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (115 bp):
TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
Found at i:30836261 original size:14 final size:13
Alignment explanation
Indices: 30836242--30836280 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
30836232 ATAGTAGTGC
30836242 ATTATATATTAATT
1 ATTATATATT-ATT
30836256 ATTATATATTATT
1 ATTATATATTATT
30836269 ATT-TATTATTAT
1 ATTATA-TATTAT
30836281 ACTAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 12 0.50
14 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATATTATT
Found at i:30836905 original size:30 final size:29
Alignment explanation
Indices: 30836827--30836906 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
30836817 TATATTTTTT
*
30836827 TATTATAATCTATATTATTATAATAGTTATA
1 TATTATAATAT-TATT-TTATAATAGTTATA
*
30836858 TATGTATTAACA-T-TTTTAGTAATAGTTATA
1 TAT-TA-TAATATTATTTTA-TAATAGTTATA
30836888 TATTATAATATTATTTTAT
1 TATTATAATATTATTTTAT
30836907 TTATTAGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
28 4 0.10
29 7 0.17
30 21 0.51
31 4 0.10
32 2 0.05
33 3 0.07
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.54
Consensus pattern (29 bp):
TATTATAATATTATTTTATAATAGTTATA
Found at i:30838007 original size:49 final size:49
Alignment explanation
Indices: 30837954--30838048 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
30837944 CTAAATAATT
* *
30837954 ACAAAGTGTAGAATCAAACTATTACAATACAAATAGACTAAAAATTGGA
1 ACAAAGTGTAGAATCAAACAATTACAACACAAATAGACTAAAAATTGGA
* * *
30838003 ACAAAGTGTAGGATTAAACAATTACAACACAAATAGACTAAGAATT
1 ACAAAGTGTAGAATCAAACAATTACAACACAAATAGACTAAAAATT
30838049 AAAATAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.22
Consensus pattern (49 bp):
ACAAAGTGTAGAATCAAACAATTACAACACAAATAGACTAAAAATTGGA
Found at i:30847999 original size:15 final size:15
Alignment explanation
Indices: 30847979--30848028 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
30847969 AGAGCCAGAG
30847979 AAGAAGGAGGAGCCA
1 AAGAAGGAGGAGCCA
* * *
30847994 AAGAAGGAAGAACCC
1 AAGAAGGAGGAGCCA
*
30848009 AAGAAAGAGGAGCCA
1 AAGAAGGAGGAGCCA
30848024 AAGAA
1 AAGAA
30848029 AGAAGAACCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.54, C:0.14, G:0.32, T:0.00
Consensus pattern (15 bp):
AAGAAGGAGGAGCCA
Found at i:30848013 original size:30 final size:30
Alignment explanation
Indices: 30847979--30848112 Score: 146
Period size: 30 Copynumber: 4.4 Consensus size: 30
30847969 AGAGCCAGAG
*
30847979 AAGAAGGAGGAGCCAAAGAAGGAAGAACCC
1 AAGAAGGAGGAGCCAAAGAAAGAAGAACCC
*
30848009 AAGAAAGAGGAGCCAAAGAAAGAAGAACCC
1 AAGAAGGAGGAGCCAAAGAAAGAAGAACCC
* *
30848039 AAGAAGGAAGAAGAG-CAGAAGAAAGAAGAGCCT
1 AAGAAGG-AG--GAGCCA-AAGAAAGAAGAACCC
* *
30848072 AAGAAGGAAGAACCAAA-AAAGGAAGAACCC
1 AAGAAGGAGGAGCCAAAGAAA-GAAGAACCC
*
30848102 AAGAAAGAGGA
1 AAGAAGGAGGA
30848113 AGAGAAGAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
29 3 0.03
30 54 0.62
31 4 0.05
32 3 0.03
33 23 0.26
ACGTcount: A:0.56, C:0.13, G:0.30, T:0.01
Consensus pattern (30 bp):
AAGAAGGAGGAGCCAAAGAAAGAAGAACCC
Found at i:30848042 original size:15 final size:15
Alignment explanation
Indices: 30847994--30848109 Score: 90
Period size: 15 Copynumber: 7.5 Consensus size: 15
30847984 GGAGGAGCCA
*
30847994 AAGAAGGAAGAACCC
1 AAGAAAGAAGAACCC
* * *
30848009 AAGAAAGAGGAGCCA
1 AAGAAAGAAGAACCC
30848024 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
* **
30848039 AAGAAGGAAGAAGAGCAG
1 AAG-A--AAGAAGAACCC
* *
30848057 AAGAAAGAAGAGCCT
1 AAGAAAGAAGAACCC
*
30848072 AAGAAGGAAGAA-CC
1 AAGAAAGAAGAACCC
*
30848086 AAAAAAGGAAGAACCC
1 AAGAAA-GAAGAACCC
30848102 AAGAAAGA
1 AAGAAAGA
30848110 GGAAGAGAAG
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
14 5 0.06
15 53 0.68
16 8 0.10
17 1 0.01
18 11 0.14
ACGTcount: A:0.58, C:0.14, G:0.28, T:0.01
Consensus pattern (15 bp):
AAGAAAGAAGAACCC
Found at i:30848088 original size:63 final size:63
Alignment explanation
Indices: 30847994--30848131 Score: 179
Period size: 63 Copynumber: 2.2 Consensus size: 63
30847984 GGAGGAGCCA
* * * * *
30847994 AAGAAGGAAGAACCCAAGAAAGAGGAGCCAAAGAAA-GAAGAACCCAAGAAGGAAGAAGAGCAG
1 AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAA-AAAGGAAGAACCCAAGAAAGAAGAAGAGAAG
* * * *
30848057 AAGAAAGAAGAGCCTAAGAAGGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAGGAAGAGAAG
1 AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAAGAAGAGAAG
30848120 AAGAAGGAAGAG
1 AAGAAGGAAGAG
30848132 GAGAAAAAGC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 3 0.05
63 61 0.95
ACGTcount: A:0.57, C:0.12, G:0.30, T:0.01
Consensus pattern (63 bp):
AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAAGAAGAGAAG
Found at i:30850115 original size:23 final size:25
Alignment explanation
Indices: 30850089--30850144 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
30850079 AACAATTTAA
30850089 AAATATTAATTTT-AT-TAAATAAT
1 AAATATTAATTTTAATATAAATAAT
* *
30850112 AAATAATATTTTTAAATGATAAATAAT
1 AAATATTAATTTT-AAT-ATAAATAAT
30850139 AAATAT
1 AAATAT
30850145 GTTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
25 2 0.08
27 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATATTAATTTTAATATAAATAAT
Found at i:30851903 original size:27 final size:25
Alignment explanation
Indices: 30851866--30851917 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
30851856 CTTTACTTAC
30851866 ATTTAAAA-TTTAGTTCCTTATATTT
1 ATTTAAAATTTTA-TTCCTTATATTT
*
30851891 ATTTCAAAGATTTTATTCCTTTTATTT
1 ATTT-AAA-ATTTTATTCCTTATATTT
30851918 TTCAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 12 0.52
28 4 0.17
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (25 bp):
ATTTAAAATTTTATTCCTTATATTT
Found at i:30856979 original size:10 final size:10
Alignment explanation
Indices: 30856964--30856990 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30856954 GATATAAGTT
30856964 ATAACATATA
1 ATAACATATA
30856974 ATAACATATA
1 ATAACATATA
30856984 ATAACAT
1 ATAACAT
30856991 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAACATATA
Found at i:30861928 original size:21 final size:21
Alignment explanation
Indices: 30861902--30861957 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
30861892 CAAAAATTCT
30861902 AAATAAATAAAAA-ATCTTAAA
1 AAATAAATAAAAATAT-TTAAA
30861923 AAATAAATAAAAATATTTAAA
1 AAATAAATAAAAATATTTAAA
*
30861944 AAAT-TATAAAAATA
1 AAATAAATAAAAATA
30861958 ATTATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 9 0.27
21 22 0.67
22 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAATAAAAATATTTAAA
Found at i:30863541 original size:14 final size:15
Alignment explanation
Indices: 30863530--30863584 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
30863520 ACTTAAAATT
30863530 TTAAA-TTTAAAAGA
1 TTAAATTTTAAAAGA
30863544 TTAAATTTTAAAA-A
1 TTAAATTTTAAAAGA
* * * *
30863558 ATAACTGTAAAAAGA
1 TTAAATTTTAAAAGA
*
30863573 CTAAATTTTAAA
1 TTAAATTTTAAA
30863585 TATGGAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
14 15 0.48
15 16 0.52
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (15 bp):
TTAAATTTTAAAAGA
Found at i:30865307 original size:31 final size:31
Alignment explanation
Indices: 30865239--30865310 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
30865229 TTTTTGTCCT
* * * * * *
30865239 AATTTGGTACTTGAATTTGGCTTTAGTGTTT
1 AATTTGGTACATAAATTTGACTTAACTGTTC
*
30865270 ACTTTGGTACATAAATTTGACTTAACTGTTC
1 AATTTGGTACATAAATTTGACTTAACTGTTC
30865301 AATTTGGTAC
1 AATTTGGTAC
30865311 CTAAGCTTCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (31 bp):
AATTTGGTACATAAATTTGACTTAACTGTTC
Found at i:30865928 original size:17 final size:20
Alignment explanation
Indices: 30865886--30865925 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
30865876 TTATGTTTAA
30865886 ATGTTTTTTAAAAAACTATG
1 ATGTTTTTTAAAAAACTATG
*
30865906 ATGTTTTTTAAAAAATTATG
1 ATGTTTTTTAAAAAACTATG
30865926 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
ATGTTTTTTAAAAAACTATG
Found at i:30876430 original size:27 final size:27
Alignment explanation
Indices: 30876392--30876446 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
30876382 CTTTTCTTTT
30876392 TGTGTTCTGCCAATTTTCTACTCTCCA
1 TGTGTTCTGCCAATTTTCTACTCTCCA
30876419 TGTGTTCTGCCAATTTTCTACTCTCCA
1 TGTGTTCTGCCAATTTTCTACTCTCCA
30876446 T
1 T
30876447 CTTTTCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.11, T:0.45
Consensus pattern (27 bp):
TGTGTTCTGCCAATTTTCTACTCTCCA
Found at i:30876453 original size:27 final size:27
Alignment explanation
Indices: 30876394--30876453 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
30876384 TTTCTTTTTG
*
30876394 TGTTCTGCCAATTTTCTACTCTCCATG
1 TGTTCTGCCAATTTTCTACTCTCCATC
30876421 TGTTCTGCCAATTTTCTACTCTCCATC
1 TGTTCTGCCAATTTTCTACTCTCCATC
*
30876448 TTTTCT
1 TGTTCT
30876454 TTCTCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.13, C:0.30, G:0.08, T:0.48
Consensus pattern (27 bp):
TGTTCTGCCAATTTTCTACTCTCCATC
Found at i:30886037 original size:28 final size:28
Alignment explanation
Indices: 30886006--30886064 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
30885996 AAATCCATTA
* *
30886006 ATATTATGTAA-AATAAAGACATGCATAT
1 ATATTATATAAGAA-AAAGACATGCACAT
*
30886034 ATATTATATAAGAAAAAGTCATGCACAT
1 ATATTATATAAGAAAAAGACATGCACAT
30886062 ATA
1 ATA
30886065 AATAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (28 bp):
ATATTATATAAGAAAAAGACATGCACAT
Found at i:30888201 original size:40 final size:40
Alignment explanation
Indices: 30888146--30888225 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
30888136 GTCGAGCTTC
30888146 TCAATATTGAACTTTAATGTTGCCATCTCTAAATAAATTG
1 TCAATATTGAACTTTAATGTTGCCATCTCTAAATAAATTG
30888186 TCAATATTGAACTTTAATGTTGCCATCTCTAAATAAATTG
1 TCAATATTGAACTTTAATGTTGCCATCTCTAAATAAATTG
30888226 ACTTCGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (40 bp):
TCAATATTGAACTTTAATGTTGCCATCTCTAAATAAATTG
Found at i:30894717 original size:28 final size:28
Alignment explanation
Indices: 30894669--30894723 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
30894659 AACCGATCCA
*
30894669 AAAACCTCAATTAACATACAAATTAAAG
1 AAAACCTCAATTAACATACAAAATAAAG
* *
30894697 AAAACTTCAATTCA-ATAACAAAATAAA
1 AAAACCTCAATTAACAT-ACAAAATAAA
30894724 AAATGAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (28 bp):
AAAACCTCAATTAACATACAAAATAAAG
Found at i:30895415 original size:90 final size:90
Alignment explanation
Indices: 30895304--30895476 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 90
30895294 TACAAGAAAC
* * *
30895304 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCTAACGAGTAAGACCATAGCT-AAA
1 GAGTAAGACCATAACTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTGAAA
30895368 GAACGTTATGGCATCACAATTCTATT
66 G-ACGTTATGGCATCACAATTCTATT
* *
30895394 GAGTAAGACCATAACTGAAAGACGTCATGGTATCATGATTCTAATGAGTAAAACCATAGCTGAAA
1 GAGTAAGACCATAACTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTGAAA
30895459 GACGTTATGGCATCACAA
66 GACGTTATGGCATCACAA
30895477 ATCAAATGAA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 73 0.95
91 4 0.05
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.24
Consensus pattern (90 bp):
GAGTAAGACCATAACTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTGAAA
GACGTTATGGCATCACAATTCTATT
Found at i:30895485 original size:45 final size:45
Alignment explanation
Indices: 30895304--30895506 Score: 255
Period size: 45 Copynumber: 4.5 Consensus size: 45
30895294 TACAAGAAAC
** *
30895304 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCTAAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
*
30895349 GAGTAAGACCATAGCT-AAAGAACGTTATGGCATCACAATTCTATT
1 GAGTAAGACCATAGCTGAAAG-ACGTTATGGCATCACAATTCTAAT
* * * **
30895394 GAGTAAGACCATAACTGAAAGACGTCATGGTATCATGATTCTAAT
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
* * *
30895439 GAGTAAAACCATAGCTGAAAGACGTTATGGCATCACAAATCAAAT
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
** *
30895484 GAACAAGACCATAGTTGAAAGAC
1 GAGTAAGACCATAGCTGAAAGAC
30895507 ACTATAGCAA
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
44 4 0.03
45 126 0.94
46 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
Found at i:30895492 original size:90 final size:90
Alignment explanation
Indices: 30895308--30895506 Score: 283
Period size: 90 Copynumber: 2.2 Consensus size: 90
30895298 AGAAACGAGT
* *
30895308 AAGACCATAGCTGAAAGACGTTATGGCATCATGATTCTAACGAGTAAGACCATAGCTAAAGAACG
1 AAGACCATAGCTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTAAAGAACG
* * * **
30895373 TTATGGCATCACAATTCTATTGAGT
66 TTATGGCATCACAAATCAAATGAAC
* * *
30895398 AAGACCATAACTGAAAGACGTCATGGTATCATGATTCTAATGAGTAAAACCATAGCTGAAAG-AC
1 AAGACCATAGCTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCT-AAAGAAC
30895462 GTTATGGCATCACAAATCAAATGAAC
65 GTTATGGCATCACAAATCAAATGAAC
*
30895488 AAGACCATAGTTGAAAGAC
1 AAGACCATAGCTGAAAGAC
30895507 ACTATAGCAA
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 92 0.96
91 4 0.04
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (90 bp):
AAGACCATAGCTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTAAAGAACG
TTATGGCATCACAAATCAAATGAAC
Found at i:30895579 original size:45 final size:45
Alignment explanation
Indices: 30895488--30895607 Score: 132
Period size: 45 Copynumber: 2.7 Consensus size: 45
30895478 TCAAATGAAC
* * * *
30895488 AAGACCATAGTTGAAAGACACTATAGCAACACGACAAAAATGAAT
1 AAGACCATAGTTGAAAGACACTATGGCATCAAGACAAAAATAAAT
* * * * *
30895533 AATACCATAGTTGAAAGACTCTATGGCATCAAGTCGAGAATAAAT
1 AAGACCATAGTTGAAAGACACTATGGCATCAAGACAAAAATAAAT
* * *
30895578 AAGACCATGGTTGAAAAACACCATGGCATC
1 AAGACCATAGTTGAAAGACACTATGGCATC
30895608 CTTTAACCAT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.19
Consensus pattern (45 bp):
AAGACCATAGTTGAAAGACACTATGGCATCAAGACAAAAATAAAT
Found at i:30902663 original size:21 final size:18
Alignment explanation
Indices: 30902623--30902673 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 18
30902613 GTTTCAAAAA
30902623 TTTTTATTTTT-AAATAT
1 TTTTTATTTTTAAAATAT
30902640 TTTTTATTTTTAATTAATATT
1 TTTTTATTTTTAA--AATA-T
30902661 TTTTTATTTTTAA
1 TTTTTATTTTTAA
30902674 CTCTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
20 4 0.13
21 14 0.47
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTTAAAATAT
Found at i:30902793 original size:19 final size:20
Alignment explanation
Indices: 30902750--30902805 Score: 87
Period size: 19 Copynumber: 2.8 Consensus size: 20
30902740 CTTATAAAAA
30902750 TAATTAAAAATAAAAATACAT
1 TAATTAAAAATAAAAATA-AT
30902771 TAATTAAAAATAAAAAT-AT
1 TAATTAAAAATAAAAATAAT
*
30902790 TAATTAAAAGTAAAAA
1 TAATTAAAAATAAAAA
30902806 AACTTGAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
TAATTAAAAATAAAAATAAT
Found at i:30903035 original size:141 final size:138
Alignment explanation
Indices: 30902868--30903294 Score: 515
Period size: 141 Copynumber: 3.1 Consensus size: 138
30902858 GGAACATCAT
* *
30902868 ACTCAAGAATGTAATCGCAATTATCTAACCATCTAACGAAAGGAGCTAATATGTTAAAAATATTA
1 ACTCAAG-ATGTAATTGCAATTATCTAACCATCTAACGAAAGGA-CTAATATGTTAAAAAAATTA
* * * *
30902933 ATTAATAATAATT-ATAAGCTTGAAGCAACATAAAATAAAAAATACGAATGTGAGT-AGTAGAGG
64 ATTAA-AATATTTAAAAAGCTTGAAGCAACATAAAATAAAAAATAC-AATATGAGTAAG-AGAGA
30902996 AATCAAACTCGAG
126 AATCAAACTCGAG
* *
30903009 ACTCAACGATGTAATTACAATTATCTAGCCATCTAACGAAAGGACTAATATGTTAAAAGAACATT
1 ACTCAA-GATGTAATTGCAATTATCTAACCATCTAACGAAAGGACTAATATGTTAAAA-AA-ATT
* *
30903074 AATTAAAAT-TTTAAAAAACTTGAAGCAACATGAAATAAAAAAAATACAAATATGAGTAAGAGAG
63 AATTAAAATATTTAAAAAGCTTGAAGCAACAT-AAA-ATAAAAAATAC-AATATGAGTAAGAGAG
*
30903138 AAATCGAACTCGAG
125 AAATCAAACTCGAG
* * * * *
30903152 ACTCAATGATGTAATTGGAACTATCTAATCATCTAACAAAAGAACTAATATGTTAAAAAAATTAA
1 ACTCAA-GATGTAATTGCAATTATCTAACCATCTAACGAAAGGACTAATATGTTAAAAAAATTAA
** * *
30903217 TTAAAA-ATTTAAAAAGCTTGAAGTGACATGAAATAAAAAA-A-AATATGAGTAAGAGAGAAATT
65 TTAAAATATTTAAAAAGCTTGAAGCAACATAAAATAAAAAATACAATATGAGTAAGAGAGAAATC
*
30903279 AAAGTCGAG
130 AAACTCGAG
30903288 ACTCAAG
1 ACTCAAG
30903295 GATAAAAGCA
Statistics
Matches: 250, Mismatches: 28, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
135 1 0.00
136 33 0.13
138 1 0.00
139 7 0.03
140 18 0.07
141 89 0.36
142 15 0.06
143 84 0.34
144 2 0.01
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (138 bp):
ACTCAAGATGTAATTGCAATTATCTAACCATCTAACGAAAGGACTAATATGTTAAAAAAATTAAT
TAAAATATTTAAAAAGCTTGAAGCAACATAAAATAAAAAATACAATATGAGTAAGAGAGAAATCA
AACTCGAG
Found at i:30903177 original size:143 final size:140
Alignment explanation
Indices: 30902889--30903293 Score: 500
Period size: 143 Copynumber: 2.9 Consensus size: 140
30902879 TAATCGCAAT
* * *
30902889 TATCTAACCATCTAACGAAAGGAGCTAATATGTTAAAAATATTAATTAATAATAATT-ATAAGCT
1 TATCTAACCATCTAACGAAAGGA-CTAATATGTTAAAAAAATTAATTAA-AAT-TTTAAAAAGCT
* * * *
30902953 TGAAGCAACATAAAAT-AAAAAATACGAATGTGAGT-AGTAGAGGAATCAAACTCGAGACTCAAC
63 TGAAGCAACATGAAATAAAAAAATACAAATATGAGTAAG-AGAGAAATCAAACTCGAGACTCAAC
*
30903016 GATGTAATTACAAT
127 GATGTAATTACAAC
* *
30903030 TATCTAGCCATCTAACGAAAGGACTAATATGTTAAAAGAACATTAATTAAAATTTTAAAAAACTT
1 TATCTAACCATCTAACGAAAGGACTAATATGTTAAAA-AA-ATTAATTAAAATTTTAAAAAGCTT
* *
30903095 GAAGCAACATGAAATAAAAAAAATACAAATATGAGTAAGAGAGAAATCGAACTCGAGACTCAATG
64 GAAGCAACATGAAAT-AAAAAAATACAAATATGAGTAAGAGAGAAATCAAACTCGAGACTCAACG
**
30903160 ATGTAATTGGAAC
128 ATGTAATTACAAC
* * * *
30903173 TATCTAATCATCTAACAAAAGAACTAATATGTTAAAAAAATTAATTAAAAATTTAAAAAGCTTGA
1 TATCTAACCATCTAACGAAAGGACTAATATGTTAAAAAAATTAATTAAAATTTTAAAAAGCTTGA
** * *
30903238 AGTGACATGAAAT--AAAAA-A-AAATATGAGTAAGAGAGAAATTAAAGTCGAGACTCAA
66 AGCAACATGAAATAAAAAAATACAAATATGAGTAAGAGAGAAATCAAACTCGAGACTCAA
30903294 GGATAAAAGC
Statistics
Matches: 233, Mismatches: 25, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
136 34 0.15
137 1 0.00
138 5 0.02
140 16 0.07
141 81 0.35
142 11 0.05
143 83 0.36
144 2 0.01
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (140 bp):
TATCTAACCATCTAACGAAAGGACTAATATGTTAAAAAAATTAATTAAAATTTTAAAAAGCTTGA
AGCAACATGAAATAAAAAAATACAAATATGAGTAAGAGAGAAATCAAACTCGAGACTCAACGATG
TAATTACAAC
Found at i:30908228 original size:3 final size:3
Alignment explanation
Indices: 30908220--30908254 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30908210 TTTGTCAAGC
30908220 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30908255 TTCAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30913049 original size:47 final size:48
Alignment explanation
Indices: 30912996--30913347 Score: 231
Period size: 47 Copynumber: 7.5 Consensus size: 48
30912986 TAGTGAACAA
30912996 CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGAC
*
30913043 CATGTCTGGGACATGGCATCGG---CATTGGGATGAGAGCTAGTGTAAGA-
1 CATGTCTGGGACATGGCATCGGCCACATT---ATGAGAGCCAGTGTAAGAC
* * *
30913090 CATGTCTGGGACAT-GCATCGGCCCCATGACGTA-AGCCAGTGTAAGA-
1 CATGTCTGGGACATGGCATCGGCCACATTATG-AGAGCCAGTGTAAGAC
* * * *
30913136 CATGTCTGGGACAT-GCATCGGCTAC--GA-GATTAGTCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCACATTATGA-GAGCCAGTGTAAGAC
* * * * * * *
30913181 CCTGTCT-GAACATGGAATC-GACACGAATATGTGAGAACTAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCAC--AT-TATGAGAGCCAGTGTAAGAC
* * * * * *
30913230 CATGTCTGGGACATGGCGTTGGTCTCGATT-TCGATAGTCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCAC-ATTAT-GAGAGCCAGTGTAAGAC
*
30913279 CATGTCTGGGATC-TGGCATC-G--AC-TTGATGAATGAGCCAATGTAAGAC
1 CATGTCTGGGA-CATGGCATCGGCCACATT-ATG-A-GAGCCAGTGTAAGAC
*
30913326 CATGTCTAGGACATGGCATCGG
1 CATGTCTGGGACATGGCATCGG
30913348 TATTATACCC
Statistics
Matches: 240, Mismatches: 37, Indels: 55
0.72 0.11 0.17
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 24 0.10
45 15 0.06
46 48 0.20
47 58 0.24
48 27 0.11
49 50 0.21
50 13 0.05
51 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
CATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGAC
Found at i:30913131 original size:46 final size:46
Alignment explanation
Indices: 30912995--30913157 Score: 215
Period size: 46 Copynumber: 3.5 Consensus size: 46
30912985 CTAGTGAACA
*
30912995 ACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAG
1 ACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAG
* *
30913041 ACCATGTCTGGGACATGGCATCGG-CA-TTGGGATGAGAGCTAGTGTAAG
1 A-CATGTCTGGGACAT-GCATCGGCCACAT--GATGAGAGCCAGTGTAAG
* *
30913089 ACATGTCTGGGACATGCATCGGCCCCATGACGTA-AGCCAGTGTAAG
1 ACATGTCTGGGACATGCATCGGCCACATGATG-AGAGCCAGTGTAAG
30913135 ACATGTCTGGGACATGCATCGGC
1 ACATGTCTGGGACATGCATCGGC
30913158 TACGAGATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
46 46 0.45
47 32 0.31
48 25 0.24
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (46 bp):
ACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAG
Found at i:30921914 original size:40 final size:40
Alignment explanation
Indices: 30921870--30921949 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
30921860 AATTATTGAC
*
30921870 ACAAGATTCCCGAACCGAATCCAAGAAACAAACGAAGGTT
1 ACAAGATTCCCAAACCGAATCCAAGAAACAAACGAAGGTT
* *
30921910 ACAAGATTCCCAAACCGAATCCAAGGAACGAACGAAGGTT
1 ACAAGATTCCCAAACCGAATCCAAGAAACAAACGAAGGTT
30921950 TACCAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (40 bp):
ACAAGATTCCCAAACCGAATCCAAGAAACAAACGAAGGTT
Found at i:30922044 original size:5 final size:5
Alignment explanation
Indices: 30922036--30922077 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
30922026 GAAAAGAAAC
* *
30922036 TAAAA TAAAA TAAAAA TAAAA -AGAA TAAAG TAAAA TAAAA TA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
30922078 TTTCAAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 3 0.10
5 23 0.74
6 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:30934769 original size:14 final size:14
Alignment explanation
Indices: 30934750--30934782 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
30934740 ACGCCTAACT
30934750 TGGCCTAGCCCGTA
1 TGGCCTAGCCCGTA
30934764 TGGCCTAGCCCGTA
1 TGGCCTAGCCCGTA
30934778 TGGCC
1 TGGCC
30934783 CACACAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (14 bp):
TGGCCTAGCCCGTA
Found at i:30935364 original size:5 final size:5
Alignment explanation
Indices: 30935354--30935405 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
30935344 GAGAAAATTT
* * *
30935354 TAAAA TAAAA TAAAA TTAAA TAAAA TTAAAA -CAAA TAAAG TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA
30935404 TA
1 TA
30935406 TTTCAACTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 3 0.08
5 31 0.79
6 5 0.13
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:30942147 original size:19 final size:19
Alignment explanation
Indices: 30942119--30942155 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30942109 GTCGATTCCA
*
30942119 AGCTGCTACGAAATGTTTC
1 AGCTGCTACGAAAAGTTTC
*
30942138 AGCTGTTACGAAAAGTTT
1 AGCTGCTACGAAAAGTTT
30942156 TAGCCTCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (19 bp):
AGCTGCTACGAAAAGTTTC
Found at i:30942414 original size:39 final size:38
Alignment explanation
Indices: 30942365--30942464 Score: 114
Period size: 39 Copynumber: 2.6 Consensus size: 38
30942355 CAAATATAAT
* *
30942365 AATTATAATTACCATAATTATAATAATGTTTGA-CCGAAA
1 AATTATAATTACCATAATTATAATAATATGTGATCC--AA
* *
30942404 AATTACAATTA-CAGTAATTATAATAATATGTGATCCTA
1 AATTATAATTACCA-TAATTATAATAATATGTGATCCAA
*
30942442 AATTATAATTACAATAATTATAA
1 AATTATAATTACCATAATTATAA
30942465 CAAAGGTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
38 22 0.42
39 28 0.54
40 2 0.04
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (38 bp):
AATTATAATTACCATAATTATAATAATATGTGATCCAA
Found at i:30943062 original size:23 final size:23
Alignment explanation
Indices: 30943036--30943081 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
30943026 CCCATTACGT
30943036 AAGAGGGACAAAATTTATATTAA
1 AAGAGGGACAAAATTTATATTAA
*
30943059 AAGAGGGACAAATTTTATATTAA
1 AAGAGGGACAAAATTTATATTAA
30943082 TAAACCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (23 bp):
AAGAGGGACAAAATTTATATTAA
Found at i:30945786 original size:43 final size:42
Alignment explanation
Indices: 30945734--30945844 Score: 136
Period size: 42 Copynumber: 2.6 Consensus size: 42
30945724 ACATATCGAT
* *
30945734 GCCACTGTCCTAGACATGGTCTTACACGA-AATCA-AATAACGAC
1 GCCAATGTCC-AGACATGGTCTTACAC-ATAATCACAAT-ACAAC
* *
30945777 GCCAATGTCCAAACATGGTCTTACACATAATCACAATACAAT
1 GCCAATGTCCAGACATGGTCTTACACATAATCACAATACAAC
30945819 GCCAATGTCCCAGACATGGTCTTACA
1 GCCAATGT-CCAGACATGGTCTTACA
30945845 TGTAATCGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
41 1 0.02
42 31 0.52
43 28 0.47
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (42 bp):
GCCAATGTCCAGACATGGTCTTACACATAATCACAATACAAC
Found at i:30945851 original size:43 final size:43
Alignment explanation
Indices: 30945709--30945851 Score: 157
Period size: 43 Copynumber: 3.3 Consensus size: 43
30945699 CCCAAATATT
* * * *
30945709 GTCTTACATGTTATCAC-ATATCGATGCCACTGTCCTAGACATG
1 GTCTTACACGTAATCACAATA-CGATGCCAATGTCCCAGACATG
* * *
30945752 GTCTTACACGAAATCA-AATAACGACGCCAATGT-CCAAACATG
1 GTCTTACACGTAATCACAAT-ACGATGCCAATGTCCCAGACATG
* *
30945794 GTCTTACACATAATCACAATACAATGCCAATGTCCCAGACATG
1 GTCTTACACGTAATCACAATACGATGCCAATGTCCCAGACATG
*
30945837 GTCTTACATGTAATC
1 GTCTTACACGTAATC
30945852 GCATCTCAGT
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
42 32 0.39
43 49 0.60
44 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
GTCTTACACGTAATCACAATACGATGCCAATGTCCCAGACATG
Found at i:30947713 original size:33 final size:33
Alignment explanation
Indices: 30947671--30947738 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
30947661 TCACTAAGTT
*
30947671 CAGTCCAGTACAATGGTGTTTGACACTTCTGAC
1 CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
30947704 CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
1 CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
30947737 CA
1 CA
30947739 TATAAAGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (33 bp):
CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
Found at i:30953921 original size:43 final size:44
Alignment explanation
Indices: 30953872--30954041 Score: 159
Period size: 43 Copynumber: 4.0 Consensus size: 44
30953862 GGTTACTGAG
*
30953872 ATGTGATTACATGTAAGACAATGTCTGGGACATTGGCATTG-TA
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTA
* * * * *
30953915 TTGTGATTACCTATAAGACCATGTCTAGGACATTAGCATTGTTA
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTA
* * * * *
30953959 AT-TGATTACGTGTAAGACCTTGTCTGGGACAGTGGCATCGAT-
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTA
* * * * * *
30954001 ATGTTATAATATGTAAGACCATATTTGGGATA-TGGCATTGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGT
30954042 ACGAGTTTAT
Statistics
Matches: 100, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
42 9 0.09
43 88 0.88
44 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTA
Found at i:30966597 original size:43 final size:43
Alignment explanation
Indices: 30966436--30966602 Score: 162
Period size: 43 Copynumber: 3.9 Consensus size: 43
30966426 CATAAAGATC
* * * *
30966436 ATACAATG-CTATATCCCAGATATGGTCTTACATGTTATCAC-
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
* * * * * ***
30966477 ATATCGATGCCACTGTCCCAAACAGGGTTTTACACAAAATCA-A
1 ATA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
*
30966520 ATA-ATGATGCCAATGACCCAGACATGGTCTTACATGTAATCACA
1 ATACA--ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
30966564 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAAT
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAAT
30966603 TACATCTCAG
Statistics
Matches: 97, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
41 3 0.03
42 4 0.04
43 85 0.88
44 4 0.04
45 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (43 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
Found at i:30972626 original size:129 final size:132
Alignment explanation
Indices: 30972213--30972703 Score: 498
Period size: 131 Copynumber: 3.8 Consensus size: 132
30972203 AGGGATCTTT
* ** ** * * * *
30972213 GATTGTTTTGAGCAAATGAAAAAGCGCAACCCAGCACGATAGGGC-TCGATT-CTCAAATTGCCA
1 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAT-GATTCCGCGAATTGCCA
* * * ** * *
30972276 AACATCGAA-CGTCGCCTTCGTTTTGAAAA-ATTTTTAATAA-ACATGAGTGAAAACCTAAAGGA
65 AACATCAAATC-TCGTCTTCGTTTT-AAAAGATTTTTAA-AAGACATGAGTGGAAATTTGAAGTA
30972338 ATATTC
127 ATATTC
* * ** * * * *
30972344 GATTGTTTTGAGCAAATGAGAAATCACAACCCAGCACGATAAGGCATGATTCC-CGAATTACCAA
1 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
* * * * * * * *
30972408 ACACCGAGTATCGCCTTTGTTTTAAAAGATTTTTAGAAGACATGAGTGGAATTTTGAAGTAATAT
66 ACATCAAATCTCGTCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGGAAATTTGAAGTAATAT
30972473 TC
131 TC
30972475 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
1 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
** * *
30972540 ACATCAAATCTCGTCTTCG-TTTAAGGGA-TTTTAAAAGATATGAGT-GAAATTTGAAGTGATAT
66 ACATCAAATCTCGTCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGGAAATTTGAAGTAATAT
30972602 TC
131 TC
* *
30972604 GATTATTTCGAGC-AATCGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCA
1 GATTATTTTGAGCAAAT-GCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCA
* *
30972668 AACATCAAATCTCGTCTTCATTTTAAAGAGTTTTTT
65 AACATCAAATCTCGTCTTCGTTTTAAA-AGATTTTT
30972704 TTTAAATGTG
Statistics
Matches: 307, Mismatches: 43, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
128 3 0.01
129 94 0.31
130 26 0.08
131 155 0.50
132 29 0.09
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (132 bp):
GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
ACATCAAATCTCGTCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGGAAATTTGAAGTAATAT
TC
Found at i:30974855 original size:18 final size:17
Alignment explanation
Indices: 30974834--30974867 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30974824 ATCGATGGAA
30974834 AAAAAATAAAAATGACTG
1 AAAAAATAAAAA-GACTG
*
30974852 AAAAATTAAAAAGACT
1 AAAAAATAAAAAGACT
30974868 AAGAAAGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAAAATAAAAAGACTG
Found at i:30978107 original size:44 final size:44
Alignment explanation
Indices: 30978044--30978131 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
30978034 AAATACAACA
* *
30978044 GATAACTTTTAAAATGCATTCGAACTTAGGGTACATATGATGTT
1 GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
30978088 GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
1 GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
30978132 TACCTTGGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (44 bp):
GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
Found at i:30981170 original size:33 final size:33
Alignment explanation
Indices: 30981133--30981289 Score: 113
Period size: 33 Copynumber: 4.8 Consensus size: 33
30981123 ACTTACCCTC
* *
30981133 TGTTTACTATCCCAGCGGACTATCTTTATTTTG
1 TGTTTACTATCCCAGCAGACTATCTTTATTCTG
* *
30981166 TGTTTACTATTCCAGCAGATTATCTTTATTCTG
1 TGTTTACTATCCCAGCAGACTATCTTTATTCTG
* ** * * * * *
30981199 TGTTTACT-GCCTTGGCAAATTATCTATGTTTTG
1 TGTTTACTATCC-CAGCAGACTATCTTTATTCTG
*
30981232 TGTTTACTGTCCCAGC-GAACTAT-TATTATTCTG
1 TGTTTACTATCCCAGCAG-ACTATCT-TTATTCTG
* * * *
30981265 TGTTTATTGTCCTAGCAAACTATCT
1 TGTTTACTATCCCAGCAGACTATCT
30981290 CTATGGATGC
Statistics
Matches: 95, Mismatches: 23, Indels: 11
0.74 0.18 0.09
Matches are distributed among these distances:
32 2 0.02
33 90 0.95
34 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (33 bp):
TGTTTACTATCCCAGCAGACTATCTTTATTCTG
Found at i:30981283 original size:66 final size:66
Alignment explanation
Indices: 30981151--30981289 Score: 158
Period size: 66 Copynumber: 2.1 Consensus size: 66
30981141 ATCCCAGCGG
* * * * *
30981151 ACTATCTTTATTTTGTGTTTACTATTCCAGCAGATTATCTTTATTCTGTGTTTACTGCCTTGGCA
1 ACTATCTATGTTTTGTGTTTACTATCCCAGCAGACTATCTTTATTCTGTGTTTACTGCCTTAGCA
30981216 A
66 A
* * *
30981217 ATTATCTATGTTTTGTGTTTACTGTCCCAGC-GAACTAT-TATTATTCTGTGTTTATTGTCC-TA
1 ACTATCTATGTTTTGTGTTTACTATCCCAGCAG-ACTATCT-TTATTCTGTGTTTACTG-CCTTA
30981279 GCAA
63 GCAA
30981283 ACTATCT
1 ACTATCT
30981290 CTATGGATGC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
65 2 0.03
66 57 0.93
67 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (66 bp):
ACTATCTATGTTTTGTGTTTACTATCCCAGCAGACTATCTTTATTCTGTGTTTACTGCCTTAGCA
A
Found at i:30983886 original size:10 final size:10
Alignment explanation
Indices: 30983871--30983909 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
30983861 AATTTTAGCT
30983871 TTTATCTTTA
1 TTTATCTTTA
*
30983881 TTTATCCTTA
1 TTTATCTTTA
30983891 TTTATCTTTA
1 TTTATCTTTA
30983901 TTTATCTTT
1 TTTATCTTT
30983910 TAGAATTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:30987541 original size:14 final size:14
Alignment explanation
Indices: 30987490--30987541 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
30987480 TAGAATTGAG
30987490 TTAATAAAATT-AT
1 TTAATAAAATTAAT
30987503 TTAATGGAAAAATTAA-
1 TTAAT---AAAATTAAT
30987519 TTAATTAAAATTAAT
1 TTAA-TAAAATTAAT
30987534 TTAATAAA
1 TTAATAAA
30987542 TAATGTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.15
14 12 0.36
15 4 0.12
16 10 0.30
17 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (14 bp):
TTAATAAAATTAAT
Found at i:30993926 original size:33 final size:33
Alignment explanation
Indices: 30993855--30993934 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
30993845 CTTGAGCTGG
* *
30993855 GAGGAGTAGAATACGACGGTGGATACAGGCCGA
1 GAGGAGTAGAGTACGACGGTGGATACAGACCGA
*
30993888 GAGGAGTAGAGTGCGACGGTGGATAC-GACTCTGA
1 GAGGAGTAGAGTACGACGGTGGATACAGAC-C-GA
*
30993922 -AGGAGTTGAGTAC
1 GAGGAGTAGAGTAC
30993935 ATGGGTGGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.05
33 36 0.90
34 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.40, T:0.16
Consensus pattern (33 bp):
GAGGAGTAGAGTACGACGGTGGATACAGACCGA
Found at i:30996011 original size:15 final size:16
Alignment explanation
Indices: 30995991--30996022 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30995981 ATAAATAATA
30995991 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
30996006 ATATAAAAATTACATT
1 ATATAAAAATTACATT
30996022 A
1 A
30996023 AAAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:30996402 original size:113 final size:114
Alignment explanation
Indices: 30996134--30996496 Score: 588
Period size: 114 Copynumber: 3.2 Consensus size: 114
30996124 TAAAAAATCA
*
30996134 TAATACACTAAACCACTAAACACTACCAATTTATATAACCTAATCTTAAATTACTAATAAAATAG
1 TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAG
*
30996199 CTATAAAAATA-TTTTTTAAAATTATATTACTAAAAAAATCACAATACAC
66 CTATAAAATTATTTTTTTAAAA-TATATTACTAAAAAAATCACAATACAC
30996248 TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAG
1 TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAG
30996313 CTATAAAATTATTTTTTTAAAATATATTACT-AAAAAATCACAATACAC
66 CTATAAAATTATTTTTTTAAAATATATTACTAAAAAAATCACAATACAC
* * * *
30996361 TAATACACTAAACTACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAACAGAATAA
1 TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAG
*
30996426 CTATAAAATTATTTTTTTTAAAATATATTATTACTAAAAAAATCACAATAAAC
66 CTATAAAATTA-TTTTTTT-AAA-ATA-TATTACTAAAAAAATCACAATACAC
*
30996479 TAATACATTAAA-CACTAA
1 TAATACACTAAACCACTAA
30996497 CAATTTGTAA
Statistics
Matches: 234, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
113 89 0.38
114 90 0.38
115 13 0.06
116 3 0.01
117 12 0.05
118 27 0.12
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.33
Consensus pattern (114 bp):
TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAG
CTATAAAATTATTTTTTTAAAATATATTACTAAAAAAATCACAATACAC
Found at i:30996544 original size:114 final size:111
Alignment explanation
Indices: 30996108--30996545 Score: 436
Period size: 114 Copynumber: 3.9 Consensus size: 111
30996098 TTTAAATAAA
* * * *
30996108 AAAATACATTACTAAATAAA-A-AAT-CA-TAATACACTAAACCACTAAACACTACCAATTTATA
1 AAAATATATTACTAAA-AAACACAATACACTAATAAACTAAACTACTAAACACTAACAATTTATA
* * *
30996169 TAACCTAATCTTAAATTACTAATA-AAATAGCTATAAAAATA-TTTTTT
65 TAACCTAATCTAAAATTAC-AA-ACAAATAACTATAAAATTATTTTTTT
* *
30996216 AAAATTATATTACTAAAAAAATCACAATACACTAATACACTAAACCACTAAACACTAACAATTTA
1 AAAA-TATATTACT-AAAAAA-CACAATACACTAATAAACTAAACTACTAAACACTAACAATTTA
* *
30996281 TATAACCTAATCTTAAATTACTAATA-AAATAGCTATAAAATTATTTTTTT
63 TATAACCTAATCTAAAATTAC-AA-ACAAATAACTATAAAATTATTTTTTT
*
30996331 AAAATATATTACTAAAAAATCACAATACACTAATACACTAAACTACTAAACACTAACAATTTATA
1 AAAATATATTACTAAAAAA-CACAATACACTAATAAACTAAACTACTAAACACTAACAATTTATA
* *
30996396 TAACCTAATCTTAAATTACTAACAGAATAACTATAAAATTATTTTTTTT
65 TAACCTAATCTAAAATTACAAACA-AATAACTATAAAATTA-TTTTTTT
* * *
30996445 AAAATATATTATTACTAAAA-A-AAT-CAC-AATAAACTAATAC-ATTAAACACTAACAA-TT-T
1 AAAATATATTACTA-AAAAACACAATACACTAATAAACTAA-ACTACTAAACACTAACAATTTAT
*
30996503 GTAACCTAATCCCATAAATTATTAGCAAAACAAATAACTATAA
64 ATAACCTAAT--C-TAAA--ATTA-C-AAACAAATAACTATAA
30996546 CAAAATACAA
Statistics
Matches: 297, Mismatches: 13, Indels: 34
0.86 0.04 0.10
Matches are distributed among these distances:
108 14 0.05
109 13 0.04
110 27 0.09
111 10 0.03
112 8 0.03
113 92 0.31
114 115 0.39
115 18 0.06
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (111 bp):
AAAATATATTACTAAAAAACACAATACACTAATAAACTAAACTACTAAACACTAACAATTTATAT
AACCTAATCTAAAATTACAAACAAATAACTATAAAATTATTTTTTT
Found at i:30996701 original size:3 final size:3
Alignment explanation
Indices: 30996695--30996732 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
30996685 ACCCTTTTTT
*
30996695 TTC TTC TTC TTC TTC TTC TTCC TTC TTC TTC TCC TTC T
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC T
30996733 CCTTTCCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:30996721 original size:19 final size:18
Alignment explanation
Indices: 30996697--30996736 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
30996687 CCTTTTTTTT
*
30996697 CTTCTTCTTCTTCTTCTTC
1 CTTCTTCTTCTCCTTC-TC
30996716 CTTCTTCTTCTCCTTCTC
1 CTTCTTCTTCTCCTTCTC
30996734 CTT
1 CTT
30996737 TCCCTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (18 bp):
CTTCTTCTTCTCCTTCTC
Found at i:31004004 original size:6 final size:6
Alignment explanation
Indices: 31003993--31004021 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31003983 TTTTTGTTCT
31003993 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
31004022 TAACAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:31004185 original size:20 final size:20
Alignment explanation
Indices: 31004152--31004243 Score: 68
Period size: 20 Copynumber: 4.6 Consensus size: 20
31004142 TGAAAAATAA
*
31004152 TAAAATAAATAAATAATACAT
1 TAAATTAAA-AAATAATACAT
*
31004173 TAAATTAAAAAATAATTC-T
1 TAAATTAAAAAATAATACAT
31004192 TAAATTAAAGAAAATAA-ACA-
1 TAAATT-AA-AAAATAATACAT
*
31004212 TAATTATTTAAAAATAATA-AT
1 TAA--ATTAAAAAATAATACAT
*
31004233 TTAA-TAAAAAA
1 TAAATTAAAAAA
31004244 AATTATCAGT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
18 6 0.10
19 8 0.14
20 22 0.38
21 19 0.33
22 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (20 bp):
TAAATTAAAAAATAATACAT
Found at i:31004196 original size:19 final size:21
Alignment explanation
Indices: 31004152--31004200 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
31004142 TGAAAAATAA
*
31004152 TAAAATAAATAAATAATACAT
1 TAAATTAAATAAATAATACAT
*
31004173 TAAATTAAA-AAATAATTC-T
1 TAAATTAAATAAATAATACAT
31004192 TAAATTAAA
1 TAAATTAAA
31004201 GAAAATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
20 8 0.31
21 8 0.31
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATTAAATAAATAATACAT
Found at i:31007803 original size:16 final size:16
Alignment explanation
Indices: 31007782--31007816 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31007772 GAAATTATTA
31007782 AAATATTATAAAATTG
1 AAATATTATAAAATTG
31007798 AAATATTATAAAATTG
1 AAATATTATAAAATTG
31007814 AAA
1 AAA
31007817 GAATTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAATATTATAAAATTG
Found at i:31009180 original size:24 final size:24
Alignment explanation
Indices: 31009153--31009199 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
31009143 TTATTATTTT
*
31009153 AATTATTTTCTAATAATTCTTATA
1 AATTATTTTCTAAAAATTCTTATA
* *
31009177 AATTATTTTTTAAAAATTTTTAT
1 AATTATTTTCTAAAAATTCTTAT
31009200 GATTTTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTATTTTCTAAAAATTCTTATA
Found at i:31011208 original size:35 final size:35
Alignment explanation
Indices: 31011168--31011252 Score: 161
Period size: 35 Copynumber: 2.4 Consensus size: 35
31011158 CTATAAAGTG
*
31011168 CATCTATGACAACCTAGAGAAATATAAAAGGAAAT
1 CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
31011203 CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
1 CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
31011238 CATCTATGATAACCT
1 CATCTATGATAACCT
31011253 GCATATTAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (35 bp):
CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
Found at i:31014770 original size:23 final size:25
Alignment explanation
Indices: 31014725--31014772 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
31014715 TATTTTAGTT
**
31014725 TTTATTACTTTTTTAACTTTAATCA
1 TTTATTACTTTTTTAACCCTAATCA
31014750 TTTATT-CTTTTTT-ACCCTAATCA
1 TTTATTACTTTTTTAACCCTAATCA
31014773 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 7 0.33
25 6 0.29
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTATTACTTTTTTAACCCTAATCA
Found at i:31015989 original size:14 final size:15
Alignment explanation
Indices: 31015970--31016000 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31015960 TTTATATATT
31015970 TTTAT-AATTTTAAA
1 TTTATAAATTTTAAA
31015984 TTTATAAATTTTAAA
1 TTTATAAATTTTAAA
31015999 TT
1 TT
31016001 CTTTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATAAATTTTAAA
Found at i:31016055 original size:49 final size:49
Alignment explanation
Indices: 31015968--31016061 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
31015958 CTTTTATATA
* *
31015968 TTTTTATAATTTTAAATTTATAAATTTTAAATTCTTTATAAATTTTGTT
1 TTTTTATAAATTTAAATGTATAAATTTTAAATTCTTTATAAATTTTGTT
* * * *
31016017 TTTTTATAAATTTATATGT-TACATTTTATAATTTTTTATACATTT
1 TTTTTATAAATTTAAATGTATAAATTTTA-AATTCTTTATAAATTT
31016062 CCGAAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 8 0.21
49 30 0.79
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (49 bp):
TTTTTATAAATTTAAATGTATAAATTTTAAATTCTTTATAAATTTTGTT
Found at i:31016846 original size:17 final size:17
Alignment explanation
Indices: 31016824--31016858 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
31016814 ACTAAACCGA
31016824 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
31016841 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
31016858 C
1 C
31016859 TACTTGCCAC
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:0.29, C:0.54, G:0.00, T:0.17
Consensus pattern (17 bp):
CCACTAACTCCATCACC
Found at i:31016894 original size:13 final size:13
Alignment explanation
Indices: 31016876--31016901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31016866 CACTAATTCC
31016876 ATCACCCCACTAA
1 ATCACCCCACTAA
31016889 ATCACCCCACTAA
1 ATCACCCCACTAA
31016902 TCCCATTACC
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:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCCCACTAA
Found at i:31017478 original size:21 final size:22
Alignment explanation
Indices: 31017433--31017475 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31017423 TTTTATGAAC
31017433 ATTTTTTAAATATTATATTATT
1 ATTTTTTAAATATTATATTATT
*
31017455 ATTTTTATATATATTAT-TTAT
1 ATTTTT-TAAATATTATATTAT
31017476 ATTAAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTTTAAATATTATATTATT
Found at i:31023161 original size:25 final size:25
Alignment explanation
Indices: 31023133--31023187 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
31023123 AAAAGAAAAA
31023133 GAAAAAAAAAAGGAAAGGCCAAGGC
1 GAAAAAAAAAAGGAAAGGCCAAGGC
31023158 GAAAAAAAAAAGGAAAGGCCAAGGC
1 GAAAAAAAAAAGGAAAGGCCAAGGC
31023183 GAAAA
1 GAAAA
31023188 CCCGCAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.62, C:0.11, G:0.27, T:0.00
Consensus pattern (25 bp):
GAAAAAAAAAAGGAAAGGCCAAGGC
Found at i:31024359 original size:64 final size:64
Alignment explanation
Indices: 31024258--31024384 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
31024248 CATTCATAGT
* * * *
31024258 ACATCTAGTTAGGATCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGGCATAAGCATC
1 ACATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAACTATTTGGCATAAGCATC
* *
31024322 ACATCTAGCTAGGAGCATTTGATTTATTTCGATCATAGCATCCTAACTGTTTGGCATAAGCAT
1 ACATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAACTATTTGGCATAAGCAT
31024385 ATATACATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (64 bp):
ACATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAACTATTTGGCATAAGCATC
Found at i:31024997 original size:178 final size:177
Alignment explanation
Indices: 31024587--31025072 Score: 722
Period size: 178 Copynumber: 2.7 Consensus size: 177
31024577 TTAGCTGCAG
* *
31024587 GTCTTATCCTCCTGAAGTTGCAGGAAATAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
1 GTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
* *
31024652 TATGGAGCAGATCGAAAATGGCGAGTCTTATCTCTATGTATCGGCTATGGAGCAGA-TTTAGCCA
66 TATGGAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
* * **
31024716 CCACCCTTATCTCTCTGAGGTAGCAAGAGAGTTGGTTGAAGATAAAA
131 CCACCCTCATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATAAAA
*
31024763 GTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTAAAAATTTACAGATCTTATCTCCATGTATCGG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTGAAAA-TTACAGATCTTATCTCCATGTATCGG
* * * *
31024828 CTATGGAGCAGATAAAAAATGGCGAATTTTATCTCCATGTATCGGCTATGGAGCATATTTTAGCC
65 CTATGGAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
* * * *
31024893 ATCAGCCTCATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATACAT
130 ACCACCCTCATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATAAAA
* * * * * *
31024941 GTCTTATCTTCCTGAAGTTGTAAGAAGCAAATTGAAAAGTTATAGATCTTATCTCCATGTATCGG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTGAAAA-TTACAGATCTTATCTCCATGTATCGG
* *
31025006 CTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAACC
65 CTATGGAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
31025071 AC
130 AC
31025073 TAATCTTATC
Statistics
Matches: 276, Mismatches: 32, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
176 35 0.13
177 77 0.28
178 164 0.59
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (177 bp):
GTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTGAAAATTACAGATCTTATCTCCATGTATCGGC
TATGGAGCAGATCAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
CCACCCTCATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATAAAA
Found at i:31025036 original size:45 final size:45
Alignment explanation
Indices: 31024987--31025189 Score: 157
Period size: 45 Copynumber: 4.5 Consensus size: 45
31024977 AAGTTATAGA
*
31024987 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGACGAG
*** ** * *
31025032 TCTTATCTCCATGTATCGGCTATGGAGCAGAT-TTTAACCACTAA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGACGAG
* * * * * *
31025076 TCTTATCTTCTTGAAGT-TGC-A-GGAAGCAGA-CTGAAAAGTTAC-AG
1 TCTTATCTCCATGTA-TCGGCTATGG-AGCAGATCAG-AAA-TGACGAG
* * *
31025120 ATCTTATCTCCATGTATCGACTATGGAGTAGATCAGAAATGGCGAG
1 -TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGACGAG
*
31025166 TCTTATCTCCATGTATCAGCTATG
1 TCTTATCTCCATGTATCGGCTATG
31025190 CTGCATATTT
Statistics
Matches: 119, Mismatches: 28, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
42 2 0.02
43 8 0.07
44 22 0.18
45 72 0.61
46 11 0.09
47 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (45 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGACGAG
Found at i:31025351 original size:134 final size:134
Alignment explanation
Indices: 31024941--31025340 Score: 613
Period size: 134 Copynumber: 3.0 Consensus size: 134
31024931 GAAGATACAT
* * * * * * *
31024941 GTCTTATCTTCCTGAAGTTGTAAGAAGCAAATTGAAAAGTTATAGATCTTATCTCCATGTATCGG
1 GTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGATCTTATCTCCATGTATCGA
*
31025006 CTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAACC
66 CTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
31025071 ACTA
131 ACTA
*
31025075 ATCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGATCTTATCTCCATGTATCGA
1 GTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGATCTTATCTCCATGTATCGA
* * ** *
31025140 CTATGGAGTAGATCAGAAATGGCGAGTCTTATCTCCATGTATCAGCTATGCTGCATATTTTAGCC
66 CTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
31025205 ACTA
131 ACTA
31025209 GTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAGAA-TTACAGATCTTATCTCCATGTATCG
1 GTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAA-AAGTTACAGATCTTATCTCCATGTATCG
* * * * *
31025273 ACTATGGAGCAGATAAAAAATGGTGAGTTTTATCTCCATATATCGGCTATGGAGCAGATTTTAGC
65 ACTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
31025338 CAC
130 CAC
31025341 CGGCCTTATC
Statistics
Matches: 240, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
134 238 0.99
135 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (134 bp):
GTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAAGTTACAGATCTTATCTCCATGTATCGA
CTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
ACTA
Found at i:31025554 original size:177 final size:178
Alignment explanation
Indices: 31025205--31025585 Score: 500
Period size: 177 Copynumber: 2.1 Consensus size: 178
31025195 TATTTTAGCC
* * *
31025205 ACTAGTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAGAATTACAGATCTTATCTCCATGTA
1 ACTAGTCTTATCTTCTTGAAGTTGCAAGAAGCAGACTGAAAAATTACAGATCTTATCTCCATATA
*** *
31025270 TCGACTATGGAGCAGATAAAAAATGGTGAGTTTTATCTCCATATATCGGCTATGGAGCAGATTTT
66 TCGACTATGGAGCAGATAAAAAATGACAAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTT
* * * * *
31025335 AGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGA-T
131 AGCCACCGACCTCATCTCCCTGAAGTAGCAAGAGAACAGGTTGAA-ATT
* *
31025383 ACTAGTCTTATCTTCTTGAAGTTGTAAGAAGGAGACT-AAAAATTACAGATCTTATCTCCATATA
1 ACTAGTCTTATCTTCTTGAAGTTGCAAGAAGCAGACTGAAAAATTACAGATCTTATCTCCATATA
* * *
31025447 TCGGCTATGGAGCAGATCAGAAATGACAAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTT
66 TCGACTATGGAGCAGATAAAAAATGACAAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTT
** * *
31025512 AGCCATTGACCTCATCTCCCTGAAGTTGC-AGTGGAACAGGTTGAAATT
131 AGCCACCGACCTCATCTCCCTGAAGTAGCAAG-AGAACAGGTTGAAATT
**
31025560 AC-AAACGTTATCTTCTTGAAGTTGCA
1 ACTAGTC-TTATCTTCTTGAAGTTGCA
31025586 GTAGGACTAC
Statistics
Matches: 176, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
176 5 0.03
177 137 0.78
178 34 0.19
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (178 bp):
ACTAGTCTTATCTTCTTGAAGTTGCAAGAAGCAGACTGAAAAATTACAGATCTTATCTCCATATA
TCGACTATGGAGCAGATAAAAAATGACAAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTT
AGCCACCGACCTCATCTCCCTGAAGTAGCAAGAGAACAGGTTGAAATT
Found at i:31026414 original size:15 final size:14
Alignment explanation
Indices: 31026389--31026420 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
31026379 TTTTAAATAT
31026389 TATATTATTATTTA
1 TATATTATTATTTA
31026403 TATATATATTATTTA
1 TATAT-TATTATTTA
31026418 TAT
1 TAT
31026421 TAAGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATTATTATTTA
Found at i:31026418 original size:19 final size:20
Alignment explanation
Indices: 31026376--31026423 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
31026366 TTTTATGAAC
31026376 ATTT-TTTAAATATTATATT
1 ATTTATTTAAATATTATATT
*
31026395 A-TTATTTATATA-TATATT
1 ATTTATTTAAATATTATATT
31026413 ATTTATATTAA
1 ATTTAT-TTAA
31026424 GCTATTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 9 0.38
19 12 0.50
20 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATTTAAATATTATATT
Found at i:31027282 original size:129 final size:127
Alignment explanation
Indices: 31027140--31027560 Score: 473
Period size: 129 Copynumber: 3.3 Consensus size: 127
31027130 GTGTTTGGAG
* *
31027140 GTCTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTCCGTTCAACTAAAATACGAAAT
1 GTCTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGA-TTTTTTCCATTCGACTAAAATACGAAAT
* *
31027205 ATCCTTTGGAAATTTTGTCCATGCTTTT-TAAAACTAAAACGAGGCAATATTTCATGTTTAAAGA
65 ATCCTTTTGAAATTTTATCCATG-TTTTCTAAAACTAAAACGAGGCAATATTTCATGTTTAAA-A
* *
31027269 GTCTGAGAGATCGTGCCCAATCGTGCTGGGTTTC-AATTTTT-CATTCGACTAAAATACGAAATA
1 GTCTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTCCATTCGACTAAAATACGAAATA
** * * **
31027332 GCTTTTTTTTGAAATTTTATTCATGTTTTCTTAAACTAAAACGAGGCAATATTT-AGTGTTTGGA
66 ---TCCTTTTGAAATTTTATCCATGTTTTCTAAAACTAAAACGAGGCAATATTTCA-TGTTTAAA
31027396 A
127 A
* * *
31027397 GTTTGAGAGATCGTGCCCAATTGTGCTGGGTTTCGA--TTTTCCATTCGACTAAAATAC-AGAAT
1 GTCTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTCCATTCGACTAAAATACGA-AAT
* * * * * **
31027459 ATCCTTTTGAAATTTCATCCATGTTTTCTCAAATTAAAATGAGGCAATGTTTCACATTTGAAAA
65 ATCCTTTTGAAATTTTATCCATGTTTTCTAAAACTAAAACGAGGCAATATTTCATGTTT-AAAA
* *
31027523 CTC-G-GTAAATCGTGCCCAATCGTGCTGGGTTTCAATTT
1 GTCTGAG-AAATCGTGCCCAATCGTGCTGGGTTTCGATTT
31027561 ACCGTTTGGG
Statistics
Matches: 248, Mismatches: 31, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
124 1 0.00
125 73 0.29
126 24 0.10
127 11 0.04
128 59 0.24
129 80 0.32
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (127 bp):
GTCTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTCCATTCGACTAAAATACGAAATA
TCCTTTTGAAATTTTATCCATGTTTTCTAAAACTAAAACGAGGCAATATTTCATGTTTAAAA
Found at i:31027548 original size:125 final size:125
Alignment explanation
Indices: 31027144--31027560 Score: 457
Period size: 125 Copynumber: 3.3 Consensus size: 125
31027134 TTGGAGGTCT
* * *
31027144 GAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTTCCGTTCAACTAAAATACGAAATATCC
1 GAGAAATCGTGCCCAATCGTGCTGGGTTTC-A--ATTTTCCATTCGACTAAAATACGAAATATCC
* * *
31027209 TTTGGAAATTTTGTCCATGCTTTT-TAAAACTAAAACGAGGCAATATTTCATGTTT-AAAGAGTC
63 TTTTGAAATTTTATCCATG-TTTTCTAAAACTAAAACGAGGCAATATTTCATGTTTGAAA-ACTC
* * *
31027272 TGAGAGATCGTGCCCAATCGTGCTGGGTTTCAATTTTTCATTCGACTAAAATACGAAATAGCTTT
1 -GAGAAATCGTGCCCAATCGTGCTGGGTTTCAATTTTCCATTCGACTAAAATACGAAATA---TC
* * * * ** *
31027337 TTTTTGAAATTTTATTCATGTTTTCTTAAACTAAAACGAGGCAATATTT-AGTGTTTGGAAGTTT
62 CTTTTGAAATTTTATCCATGTTTTCTAAAACTAAAACGAGGCAATATTTCA-TGTTTGAAAACTC
* * *
31027401 GAGAGATCGTGCCCAATTGTGCTGGGTTTCGATTTTCCATTCGACTAAAATAC-AGAATATCCTT
1 GAGAAATCGTGCCCAATCGTGCTGGGTTTCAATTTTCCATTCGACTAAAATACGA-AATATCCTT
* * * * * **
31027465 TTGAAATTTCATCCATGTTTTCTCAAATTAAAATGAGGCAATGTTTCACATTTGAAAACTC
65 TTGAAATTTTATCCATGTTTTCTAAAACTAAAACGAGGCAATATTTCATGTTTGAAAACTC
31027526 G-GTAAATCGTGCCCAATCGTGCTGGGTTTCAATTT
1 GAG-AAATCGTGCCCAATCGTGCTGGGTTTCAATTT
31027561 ACCGTTTGGG
Statistics
Matches: 244, Mismatches: 35, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
124 1 0.00
125 80 0.33
126 25 0.10
127 1 0.00
128 60 0.25
129 75 0.31
130 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (125 bp):
GAGAAATCGTGCCCAATCGTGCTGGGTTTCAATTTTCCATTCGACTAAAATACGAAATATCCTTT
TGAAATTTTATCCATGTTTTCTAAAACTAAAACGAGGCAATATTTCATGTTTGAAAACTC
Found at i:31028858 original size:15 final size:12
Alignment explanation
Indices: 31028827--31028851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31028817 TTATTATAAA
31028827 AATAATATACTT
1 AATAATATACTT
31028839 AATAATATACTT
1 AATAATATACTT
31028851 A
1 A
31028852 CTCATAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAATATACTT
Found at i:31028958 original size:21 final size:20
Alignment explanation
Indices: 31028920--31028959 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31028910 ATAAAAAATA
*
31028920 TTATGAAATTTTTGAATAAT
1 TTATAAAATTTTTGAATAAT
*
31028940 TTATAAAACTTTTTTAATAA
1 TTATAAAA-TTTTTGAATAA
31028960 AGGTGATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATAAAATTTTTGAATAAT
Found at i:31035176 original size:20 final size:20
Alignment explanation
Indices: 31035151--31035197 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
31035141 TACAACATTC
** *
31035151 AAAAATCCTTAAAATTATAA
1 AAAAATCCCAAAAAATATAA
31035171 AAAAATCCCAAAAAATATAA
1 AAAAATCCCAAAAAATATAA
31035191 AATAAAT
1 AA-AAAT
31035198 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATCCCAAAAAATATAA
Found at i:31044193 original size:16 final size:16
Alignment explanation
Indices: 31044160--31044193 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31044150 GGTAAGTGTT
* *
31044160 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
31044176 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
31044192 AA
1 AA
31044194 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:31047019 original size:21 final size:21
Alignment explanation
Indices: 31046993--31047033 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31046983 AGACGAGCAA
* *
31046993 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
31047014 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
31047034 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:31048971 original size:16 final size:16
Alignment explanation
Indices: 31048938--31048971 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31048928 GGAGATTGTT
* *
31048938 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
31048954 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
31048970 AA
1 AA
31048972 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:31051880 original size:14 final size:14
Alignment explanation
Indices: 31051852--31051884 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31051842 CGATACTATG
31051852 TTTAA-ATTTAAAT
1 TTTAATATTTAAAT
*
31051865 TTTAATATTTATAT
1 TTTAATATTTAAAT
31051879 TTTAAT
1 TTTAAT
31051885 TTGACATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATATTTAAAT
Found at i:31052905 original size:20 final size:20
Alignment explanation
Indices: 31052880--31052919 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31052870 GAAAGTTTAA
31052880 TTTGAAAATCGTAGATGAGG
1 TTTGAAAATCGTAGATGAGG
31052900 TTTGAAAATCGTAGATGAGG
1 TTTGAAAATCGTAGATGAGG
31052920 AGGAAGATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (20 bp):
TTTGAAAATCGTAGATGAGG
Found at i:31069596 original size:20 final size:21
Alignment explanation
Indices: 31069557--31069596 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31069547 GTCGAGTTGG
31069557 TCACACGGGCGTGTTGCCCTT
1 TCACACGGGCGTGTTGCCCTT
*
31069578 TCACACTGGCGTG-TGCCCT
1 TCACACGGGCGTGTTGCCCT
31069597 GTTTTAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.35, G:0.28, T:0.28
Consensus pattern (21 bp):
TCACACGGGCGTGTTGCCCTT
Found at i:31074480 original size:50 final size:49
Alignment explanation
Indices: 31074356--31074544 Score: 234
Period size: 50 Copynumber: 3.8 Consensus size: 49
31074346 TGAGGTCGCA
* * * *
31074356 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCACG
* * **
31074407 TGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
* * *
31074457 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* *
31074506 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
31074545 GCTTTGGCTA
Statistics
Matches: 119, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
49 41 0.34
50 45 0.38
51 33 0.28
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:31076841 original size:18 final size:18
Alignment explanation
Indices: 31076818--31076852 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31076808 TTTAAGAAGG
*
31076818 GTTTTCAATGAAAACACA
1 GTTTTCAATAAAAACACA
*
31076836 GTTTTCACTAAAAACAC
1 GTTTTCAATAAAAACAC
31076853 TTCAATGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
GTTTTCAATAAAAACACA
Found at i:31079820 original size:28 final size:29
Alignment explanation
Indices: 31079789--31079849 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
31079779 GTGAGCATGA
*
31079789 ATAT-AAGGTGATTTGGGCCTAGCGGGCC
1 ATATAAAGGTGATTTGGGCCTAACGGGCC
*
31079817 ATATAAAGGTGATTTGGGCCTAATGGGCC
1 ATATAAAGGTGATTTGGGCCTAACGGGCC
31079846 ATAT
1 ATAT
31079850 GAATATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (29 bp):
ATATAAAGGTGATTTGGGCCTAACGGGCC
Found at i:31079862 original size:29 final size:29
Alignment explanation
Indices: 31079801--31079935 Score: 100
Period size: 28 Copynumber: 4.7 Consensus size: 29
31079791 ATAAGGTGAT
** * ** *
31079801 TTGGGCCTAGCGGGCCATATAAAGGTGAT
1 TTGGGCCTAATGGGCCATATGAATATGAA
31079830 TTGGGCCTAATGGGCCATATGAATATGAA
1 TTGGGCCTAATGGGCCATATGAATATGAA
* * *
31079859 TTGGG-CTGATGGGTCGA-ATGAATGTGAA
1 TTGGGCCTAATGGG-CCATATGAATATGAA
* *
31079887 TTGGGCATAATGGGCTATATG-A-ATGAGA
1 TTGGGCCTAATGGGCCATATGAATATGA-A
*
31079915 TTGGGCC-AAGTGGGCTATATG
1 TTGGGCCTAA-TGGGCCATATG
31079936 CATGTATGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.06
28 43 0.49
29 39 0.45
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.27
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATGAATATGAA
Found at i:31081024 original size:17 final size:18
Alignment explanation
Indices: 31080991--31081025 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31080981 TTTTAAGAAG
31080991 GGTTTTCAATGAAAACAC
1 GGTTTTCAATGAAAACAC
*
31081009 GGTTTTCACT-AAAACAC
1 GGTTTTCAATGAAAACAC
31081026 TTCAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAC
Found at i:31084627 original size:47 final size:46
Alignment explanation
Indices: 31084507--31084674 Score: 155
Period size: 47 Copynumber: 3.6 Consensus size: 46
31084497 TATGAGAGCT
* * * * *
31084507 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGACGCGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATTGGCCTCGAGATG-TAGCC
* *
31084555 AGTGTAAGA-CATGTCTAGGATATGCATTGGTCCTCGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATTGG-CCTCGAGATGT-AGCC
* * * *
31084602 AGTGTAAGA-CATGTCTGGGACATGCATCGG-CTACAAAATGT-GTC
1 AGTGTAAGACCATGTCTGGGACATGCATTGGCCT-CGAGATGTAGCC
31084646 AGTGTAAGACCATGTCTGGGACATTGCAT
1 AGTGTAAGACCATGTCTGGGACA-TGCAT
31084675 CAGGATGGTT
Statistics
Matches: 102, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
44 11 0.11
45 15 0.15
46 18 0.18
47 49 0.48
48 9 0.09
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATTGGCCTCGAGATGTAGCC
Found at i:31085576 original size:13 final size:13
Alignment explanation
Indices: 31085558--31085588 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
31085548 GCCCCATGGG
31085558 CGTGTTTTCCAGT
1 CGTGTTTTCCAGT
31085571 CGTGTTTTCCAGT
1 CGTGTTTTCCAGT
31085584 CGTGT
1 CGTGT
31085589 GTCCCCTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.26, T:0.45
Consensus pattern (13 bp):
CGTGTTTTCCAGT
Found at i:31091787 original size:93 final size:93
Alignment explanation
Indices: 31091680--31091942 Score: 438
Period size: 93 Copynumber: 2.8 Consensus size: 93
31091670 CCCATAAGTG
* * *
31091680 AACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
*
31091745 TAGCTCGGATGCCTAGTTACATCTTACA
66 TAGCTCGGATGCCTAGTTACATCTCACA
*
31091773 AACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA-
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
*
31091837 TGAGCTCGGATGCCTAGTTACATCTCACG
66 T-AGCTCGGATGCCTAGTTACATCTCACA
31091866 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
* *
31091931 AAGTTCGGATGC
66 TAGCTCGGATGC
31091943 TTAACCATCC
Statistics
Matches: 159, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
92 1 0.01
93 158 0.99
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.23
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
TAGCTCGGATGCCTAGTTACATCTCACA
Found at i:31091790 original size:47 final size:47
Alignment explanation
Indices: 31091726--31091893 Score: 170
Period size: 47 Copynumber: 3.6 Consensus size: 47
31091716 TCCATAAGTG
31091726 AACTCGGACTCAACTCAACT-AGCTCGGATGCCTAGTTACATCTTACA
1 AACTCGGACTCAACTCAA-TGAGCTCGGATGCCTAGTTACATCTTACA
* * *
31091773 AACTCGGACTCAACTCAATGAGTTCGGA---C-A-TTCGCATCCATA-A
1 AACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT-CTTACA
* *
31091816 GTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTACATCTCACG
1 ---AACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTACATCTTACA
* *
31091866 AACTCGGACTCAACTCAACGAGTTCGGA
1 AACTCGGACTCAACTCAATGAGCTCGGA
31091894 CATTCGCATC
Statistics
Matches: 99, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 4 0.04
46 28 0.28
47 51 0.52
49 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (47 bp):
AACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTACATCTTACA
Found at i:31091939 original size:46 final size:46
Alignment explanation
Indices: 31091671--31091939 Score: 259
Period size: 46 Copynumber: 5.8 Consensus size: 46
31091661 TGTAACCCGC
* *
31091671 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
31091717 CCATAAGTGAACTCGGACTCAACTCAACTAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* * *
31091767 -CTTACA---AACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATA-AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
31091810 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* * *
31091860 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
31091903 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
31091940 TGCTTAACCA
Statistics
Matches: 183, Mismatches: 20, Indels: 40
0.75 0.08 0.16
Matches are distributed among these distances:
42 4 0.02
43 9 0.05
44 6 0.03
45 2 0.01
46 89 0.49
47 52 0.28
48 2 0.01
49 6 0.03
50 9 0.05
51 4 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:31103248 original size:22 final size:22
Alignment explanation
Indices: 31103223--31103273 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
31103213 AATTCTATGC
31103223 TAAATTGATAA-AGAT-TAATATA
1 TAAATT-ATAATAGATATAAT-TA
31103245 TAAATTATAATAGATATAATTA
1 TAAATTATAATAGATATAATTA
31103267 TAAATTA
1 TAAATTA
31103274 AAGATTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.15
22 19 0.70
23 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (22 bp):
TAAATTATAATAGATATAATTA
Found at i:31103480 original size:29 final size:30
Alignment explanation
Indices: 31103423--31103480 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
31103413 CTTTTGAAAA
* * **
31103423 TATTTACAAAAAGAGACATCTAGTTTTTAT
1 TATTTACAAAAAGAGACAACCAAATTTTAT
31103453 TATTTACAAAAAGAG-CAACCAAATTTTA
1 TATTTACAAAAAGAGACAACCAAATTTTA
31103481 AAAATGATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (30 bp):
TATTTACAAAAAGAGACAACCAAATTTTAT
Found at i:31115176 original size:16 final size:17
Alignment explanation
Indices: 31115149--31115183 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
31115139 TAAAATCGGG
*
31115149 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
31115166 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
31115182 TT
1 TT
31115184 TACATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:31122032 original size:9 final size:9
Alignment explanation
Indices: 31122018--31122042 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31122008 CTTTGACAAG
31122018 AAGGGTGCC
1 AAGGGTGCC
31122027 AAGGGTGCC
1 AAGGGTGCC
31122036 AAGGGTG
1 AAGGGTG
31122043 GCCGGAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.48, T:0.12
Consensus pattern (9 bp):
AAGGGTGCC
Found at i:31129757 original size:40 final size:39
Alignment explanation
Indices: 31129700--31129964 Score: 228
Period size: 40 Copynumber: 6.6 Consensus size: 39
31129690 AATTATTGTA
* ** *
31129700 TGAATACACATACGTGCCCCTGATTGTACTTCAATACTAC
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTAC-CC
* * *
31129740 TGAATGCACATATGTGCCCCTGTTTGTACTTCGATACCCC
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTA-CCC
*** * *
31129780 TGAATGCACACGTGTGCCCCTGTTTGTACTTTGGTACCC
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCC
* * *
31129819 TTAAATGTACATACGTGCCCCT-ATTTGTACTTCAGTACCC
1 -TGAATGCACATACGTGCCCCTGA-TTGTACTTCGGTACCC
* *
31129859 TTAGATGCACATACATGCCCCT-ATTTGTACTTCGGTACCCC
1 TGA-ATGCACATACGTGCCCCTGA-TTGTACTTCGGTA-CCC
* * *
31129900 TAAATGCACATACGTGCCCTTGATTGTACTTCGGTACTTC
1 TGAATGCACATACGTGCCCCTGATTGTACTTCGGTAC-CC
* * * *
31129940 TGAAAGCATATACATGCTCCTGATT
1 TGAATGCACATACGTGCCCCTGATT
31129965 TTATTCTGGT
Statistics
Matches: 187, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
39 6 0.03
40 174 0.93
41 7 0.04
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (39 bp):
TGAATGCACATACGTGCCCCTGATTGTACTTCGGTACCC
Found at i:31129847 original size:20 final size:20
Alignment explanation
Indices: 31129824--31129888 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
31129814 TACCCTTAAA
31129824 TGTACATACGTGCCCCTATT
1 TGTACATACGTGCCCCTATT
* * * **
31129844 TGTAC-TTCAGTACCCTTAGA
1 TGTACATAC-GTGCCCCTATT
* *
31129864 TGCACATACATGCCCCTATT
1 TGTACATACGTGCCCCTATT
31129884 TGTAC
1 TGTAC
31129889 TTCGGTACCC
Statistics
Matches: 30, Mismatches: 13, Indels: 4
0.64 0.28 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (20 bp):
TGTACATACGTGCCCCTATT
Found at i:31129867 original size:120 final size:120
Alignment explanation
Indices: 31129707--31129936 Score: 302
Period size: 120 Copynumber: 1.9 Consensus size: 120
31129697 GTATGAATAC
** *
31129707 ACATACGTGCCCCTGATTGTACTTCAATACTACTGAATGCACATATGTGCCCCTGTTTGTACTTC
1 ACATACGTGCCCCTGATTGTACTTCAATACTACTGAATGCACATACATGCCCCTATTTGTACTTC
* ** * *
31129772 GATACCCCTGAATGCACACGTGTGCCCCTGTTTGTACTTTGGTACCCTTAAATGT
66 GATACCCCTAAATGCACACACGTGCCCCTGATTGTACTTCGGTACCCTTAAATGT
* * *
31129827 ACATACGTGCCCCT-ATTTGTACTTCAGTAC-CCTTAGATGCACATACATGCCCCTATTTGTACT
1 ACATACGTGCCCCTGA-TTGTACTTCAATACTACTGA-ATGCACATACATGCCCCTATTTGTACT
* * *
31129890 TCGGTACCCCTAAATGCACATACGTGCCCTTGATTGTACTTCGGTAC
64 TCGATACCCCTAAATGCACACACGTGCCCCTGATTGTACTTCGGTAC
31129937 TTCTGAAAGC
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
119 4 0.04
120 90 0.96
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.33
Consensus pattern (120 bp):
ACATACGTGCCCCTGATTGTACTTCAATACTACTGAATGCACATACATGCCCCTATTTGTACTTC
GATACCCCTAAATGCACACACGTGCCCCTGATTGTACTTCGGTACCCTTAAATGT
Found at i:31132300 original size:15 final size:16
Alignment explanation
Indices: 31132282--31132315 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31132272 AAATTAAATT
*
31132282 AATTAA-CTAGATGCA
1 AATTAACCTAAATGCA
31132297 AATTAACCTAAATGCA
1 AATTAACCTAAATGCA
31132313 AAT
1 AAT
31132316 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGCA
Found at i:31134807 original size:17 final size:17
Alignment explanation
Indices: 31134769--31134808 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
31134759 GCTAAACAGA
*
31134769 AGAGTCCACCAAACCCT
1 AGAGTTCACCAAACCCT
*
31134786 AGAGTTCACCAAATCCT
1 AGAGTTCACCAAACCCT
*
31134803 GGAGTT
1 AGAGTT
31134809 TGCCAAATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (17 bp):
AGAGTTCACCAAACCCT
Found at i:31141636 original size:36 final size:36
Alignment explanation
Indices: 31141596--31141670 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
31141586 AATATACCAT
31141596 TTTGATAAATAATGATATTAACGTACTATTTTAATA
1 TTTGATAAATAATGATATTAACGTACTATTTTAATA
31141632 TTTGATAAATAATGATATTAACGTACTATTTTAATA
1 TTTGATAAATAATGATATTAACGTACTATTTTAATA
31141668 TTT
1 TTT
31141671 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (36 bp):
TTTGATAAATAATGATATTAACGTACTATTTTAATA
Found at i:31147706 original size:17 final size:18
Alignment explanation
Indices: 31147686--31147719 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31147676 ATAATAAATC
31147686 AATTA-AAAAAATAAAAG
1 AATTACAAAAAATAAAAG
*
31147703 AATTACAAAGAATAAAA
1 AATTACAAAAAATAAAA
31147720 ACGTAAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (18 bp):
AATTACAAAAAATAAAAG
Found at i:31149392 original size:133 final size:133
Alignment explanation
Indices: 31149229--31149498 Score: 380
Period size: 133 Copynumber: 2.0 Consensus size: 133
31149219 CTACCTTAGA
* * * *
31149229 GAGATAAGGCTAGTGGCTAAAATCTACTCCATTGTCGATACATGGAGATAAGA-TCTGCCGTCTT
1 GAGACAAGGCTAGTGGCTAAAATCTACTCCATTATCGATACATAGAGATAAGATTC-ACCGTCTT
* * * * *
31149293 CGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAGTTTGCTTCACTGCAACTT
65 CGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGCAATTTTCAGTCTGCTCCACTGCAACCT
31149358 CAGG
130 CAGG
* * * * * *
31149362 GAGACAAGGCTGGTGGCTTAAATTTGCTCCATTATCGATACATAGAGATAAGATTCACCGTTTTT
1 GAGACAAGGCTAGTGGCTAAAATCTACTCCATTATCGATACATAGAGATAAGATTCACCGTCTTC
*
31149427 GATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGTCTGCTCCACTGCAACCTC
66 GATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGCAATTTTCAGTCTGCTCCACTGCAACCTC
31149492 AGG
131 AGG
31149495 GAGA
1 GAGA
31149499 TAGGACTTGT
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
133 118 0.98
134 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (133 bp):
GAGACAAGGCTAGTGGCTAAAATCTACTCCATTATCGATACATAGAGATAAGATTCACCGTCTTC
GATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGCAATTTTCAGTCTGCTCCACTGCAACCTC
AGG
Found at i:31149477 original size:44 final size:43
Alignment explanation
Indices: 31149429--31149660 Score: 139
Period size: 44 Copynumber: 5.3 Consensus size: 43
31149419 CCGTTTTTGA
31149429 TCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAG
1 TCTGCTCCACTACTGCTTAAGGAGATAAGATCTGT-ATTTTCAG
* ** * * * * *
31149473 TCTGCTCCACTGCAACCTCAGGGAGATAGGA-CTTGTATATTGAG
1 TCTGCTCCACTAC-TGCTTAAGGAGATAAGATC-TGTATTTTCAG
** * *
31149517 TCTGCTCCACTACTGCTTCAAGGAGATAAGA-CTAGTGGTTTAAA
1 TCTGCTCCACTACTGCTT-AAGGAGATAAGATCT-GTATTTTCAG
* * * * * * *
31149561 TCTGCTCCATTGCCG-ATACATGGAGATAAGATCCGTCGTCTTC-G
1 TCTGCTCCACTACTGCTTA-A-GGAGATAAGATCTGT-ATTTTCAG
* * * *
31149605 ATCTGTTCCACTACTACTTAGGGAGATAAGATCTGTAATTTTTAG
1 -TCTGCTCCACTACTGCTTAAGGAGATAAGATCTGT-ATTTTCAG
31149650 TCTGCTCCACT
1 TCTGCTCCACT
31149661 GCAATCTCAG
Statistics
Matches: 136, Mismatches: 41, Indels: 22
0.68 0.21 0.11
Matches are distributed among these distances:
42 1 0.01
43 5 0.04
44 98 0.72
45 30 0.22
46 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
TCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTATTTTCAG
Found at i:31149581 original size:177 final size:177
Alignment explanation
Indices: 31149347--31150170 Score: 1010
Period size: 177 Copynumber: 4.7 Consensus size: 177
31149337 CAGTTTGCTT
* * * * * ** *
31149347 CACTGCAACTTCAGGGAGACAAGGCTGGTGGCTTAAATTTGCTCCATTATCGATACATAGAGATA
1 CACTACAACTTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATA
* * *
31149412 AGATTCACCGTTTTTGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGTCTG
66 AGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGTCTG
* * *
31149477 CTCCACTGCAACCTCAGGGAGATAGGACTTGTATATTGAGTCTGCTC
131 CTCCACTGCAACCTCAGGGAGATAAGACTTGTATATTGAGCCTACTC
** * *
31149524 CACTACTGCTTCAAGGAGATAAGACTAGTGGTTTAAATCTGCTCCATTGCCGATACATGGAGATA
1 CACTACAACTTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATA
* * * * * *
31149589 AGATCCGTCGTCTTCGATCTGTTCCACTACTACTTAGGGAGATAAGATCTGTAATTTTTAGTCTG
66 AGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGTCTG
*
31149654 CTCCACTGCAATCTCAGGGAGATAAGACTTGTATATTGAGCCTACTC
131 CTCCACTGCAACCTCAGGGAGATAAGACTTGTATATTGAGCCTACTC
* *
31149701 CAC-AGCAACTTCAAGGAGATAGGGCTAGTGACTTAAATCTGCTCCATTGCCGATACATGGAGAT
1 CACTA-CAACTTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGAT
** * * * *
31149765 AAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAATATCTGTAATTTTTAGTCT
65 AAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGTCT
* *
31149830 GCTCCACTGCAACCTTAGGGAGATAAGACTTATATATTGAGCCTACTC
130 GCTCCACTGCAACCTCAGGGAGATAAGACTTGTATATTGAGCCTACTC
*
31149878 CACTGCAACTTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATA
1 CACTACAACTTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATA
* *
31149943 AGATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGCAATTTTCAGTCTG
66 AGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGTCTG
* * * * * * * * *
31150008 CTTCC-TTACTACCTCAGGAAGATAAGACTTGTATCTTCAACTTGCTC
131 C-TCCACTGCAACCTCAGGGAGATAAGACTTGTATATTGAGCCTACTC
* * * * * * * * * *
31150055 TC-TTGCTACCTC-AGAGAGATAAGACTAGTTGCTAAAATCTACTTCATTGTCGATACATGGAGA
1 -CACTACAACTTCAAG-GAGATAAGGCTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGA
*** * *
31150118 TAAGATTTTTCGTCTTCAATCTGCTCCACTACTGCTT-AGAAAGATAAGATCTG
64 TAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAAG-GAGATAAGATCTG
31150171 CGAATTCACC
Statistics
Matches: 562, Mismatches: 79, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
176 5 0.01
177 553 0.98
178 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (177 bp):
CACTACAACTTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATA
AGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGTCTG
CTCCACTGCAACCTCAGGGAGATAAGACTTGTATATTGAGCCTACTC
Found at i:31150298 original size:24 final size:23
Alignment explanation
Indices: 31150250--31150298 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
31150240 GTTTATGCCC
*
31150250 AAATGATTAGGATGCTATAATCA
1 AAATGATTAGGATGCTATAACCA
*
31150273 AAATGAATTA-GATGCTCCTAACCA
1 AAATG-ATTAGGATGCT-ATAACCA
31150297 AA
1 AA
31150299 TGCGCTATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (23 bp):
AAATGATTAGGATGCTATAACCA
Found at i:31157397 original size:17 final size:18
Alignment explanation
Indices: 31157377--31157410 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31157367 ATAATAAATC
31157377 AATTA-AAAAAATAAAAG
1 AATTACAAAAAATAAAAG
*
31157394 AATTACAAAGAATAAAA
1 AATTACAAAAAATAAAA
31157411 ACGTAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (18 bp):
AATTACAAAAAATAAAAG
Found at i:31160272 original size:31 final size:31
Alignment explanation
Indices: 31160226--31160288 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
31160216 TATACTTTAG
*
31160226 ACTTTTATTTGGATGTACTTAGCAAACTTAT
1 ACTTTTATTTAGATGTACTTAGCAAACTTAT
* *
31160257 ACTTTTTTTTAGATGTACTTAGCTAACTTAT
1 ACTTTTATTTAGATGTACTTAGCAAACTTAT
31160288 A
1 A
31160289 TAAAGGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.48
Consensus pattern (31 bp):
ACTTTTATTTAGATGTACTTAGCAAACTTAT
Found at i:31160639 original size:23 final size:22
Alignment explanation
Indices: 31160605--31160652 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
31160595 CTATTTATTA
*
31160605 TTTTGAATATTTATTTTTTGTT
1 TTTTGAATATTTATTCTTTGTT
*
31160627 TTTTTAATAATTTATTCTTTGTT
1 TTTTGAAT-ATTTATTCTTTGTT
31160650 TTT
1 TTT
31160653 AAATTTCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTTGAATATTTATTCTTTGTT
Done.