Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 45 of 150
Found at i:12674977 original size:19 final size:19
Alignment explanation
Indices: 12674955--12674993 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12674945 TATATAATGT
12674955 ACTACTATTAT-TATATATA
1 ACTACTATTATCTAT-TATA
*
12674974 ACTATTATTATCTATTATA
1 ACTACTATTATCTATTATA
12674993 A
1 A
12674994 TAAAAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (19 bp):
ACTACTATTATCTATTATA
Found at i:12683192 original size:19 final size:19
Alignment explanation
Indices: 12683170--12683209 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12683160 AATAATTTTG
*
12683170 ATCAAGTAAAATAAAATTA
1 ATCAAATAAAATAAAATTA
* *
12683189 ATCAAATCAACTAAAATTA
1 ATCAAATAAAATAAAATTA
12683208 AT
1 AT
12683210 ATGATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.28
Consensus pattern (19 bp):
ATCAAATAAAATAAAATTA
Found at i:12685056 original size:16 final size:16
Alignment explanation
Indices: 12685035--12685068 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12685025 TACCATAGTG
*
12685035 AAATGACTTTATGATT
1 AAATGACTTTATAATT
*
12685051 AAATGAGTTTATAATT
1 AAATGACTTTATAATT
12685067 AA
1 AA
12685069 TAGTCGAAAA
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:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (16 bp):
AAATGACTTTATAATT
Found at i:12685261 original size:14 final size:14
Alignment explanation
Indices: 12685242--12685270 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12685232 AATAATCATG
12685242 GTTTTCTCCAAAAT
1 GTTTTCTCCAAAAT
12685256 GTTTTCTCCAAAAT
1 GTTTTCTCCAAAAT
12685270 G
1 G
12685271 AAAACGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (14 bp):
GTTTTCTCCAAAAT
Found at i:12686780 original size:17 final size:17
Alignment explanation
Indices: 12686758--12686792 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12686748 AAATACATGT
12686758 TTAATTCCATTCGAATG
1 TTAATTCCATTCGAATG
12686775 TTAATTCCATTCGAATG
1 TTAATTCCATTCGAATG
12686792 T
1 T
12686793 CTATGTGTTG
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:0.17, G:0.11, T:0.43
Consensus pattern (17 bp):
TTAATTCCATTCGAATG
Found at i:12688384 original size:29 final size:28
Alignment explanation
Indices: 12688352--12688407 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
12688342 TTTTTTAATT
12688352 AATAAAATT-ATAAATCTATAAAATTATTG
1 AATAAAATTAATAAAT-TA-AAAATTATTG
*
12688381 AATATAATTAGATAAATTAAAAATTAT
1 AATAAAATTA-ATAAATTAAAAATTAT
12688408 AAAAATCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 16 0.67
30 2 0.08
31 6 0.25
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (28 bp):
AATAAAATTAATAAATTAAAAATTATTG
Found at i:12688452 original size:17 final size:17
Alignment explanation
Indices: 12688430--12688474 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
12688420 TTTTAATTAA
12688430 ATAAATATGA-TTTATAT
1 ATAAATATGATTTTAT-T
12688447 ATAAATATGATTTTATT
1 ATAAATATGATTTTATT
*
12688464 TTAAATATGAT
1 ATAAATATGAT
12688475 AATAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
ATAAATATGATTTTATT
Found at i:12688823 original size:16 final size:18
Alignment explanation
Indices: 12688804--12688837 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
12688794 TATGTAAAAT
12688804 AAATAA-TATAA-TATAA
1 AAATAATTATAATTATAA
12688820 AAATAATTATAATTATAA
1 AAATAATTATAATTATAA
12688838 TTATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAATTATAATTATAA
Found at i:12688922 original size:17 final size:17
Alignment explanation
Indices: 12688890--12688923 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12688880 TTACATTCAT
*
12688890 AATAATTTTTAATATAA
1 AATAATTTTGAATATAA
*
12688907 AATAATTTTGATTATAA
1 AATAATTTTGAATATAA
12688924 TCTTGATTTT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AATAATTTTGAATATAA
Found at i:12689486 original size:26 final size:27
Alignment explanation
Indices: 12689443--12689499 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 27
12689433 ATTTAATTAG
12689443 AATATATATTTTAAAAATT-ATAAA-A
1 AATATATATTTTAAAAATTAATAAATA
12689468 AATATAT-TATTTAATAAATTAATAAATA
1 AATATATAT-TTTAA-AAATTAATAAATA
12689496 AATA
1 AATA
12689500 AAATCATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.04
25 12 0.43
26 5 0.18
27 5 0.18
28 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATATATATTTTAAAAATTAATAAATA
Found at i:12697914 original size:26 final size:26
Alignment explanation
Indices: 12697884--12697935 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12697874 AGGTTCTATT
*
12697884 TTTATAGACTAAGAAACTAAAATTAA
1 TTTATAGAATAAGAAACTAAAATTAA
*
12697910 TTTATAGAATAAGAAACTATAATTAA
1 TTTATAGAATAAGAAACTAAAATTAA
12697936 GGCAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.33
Consensus pattern (26 bp):
TTTATAGAATAAGAAACTAAAATTAA
Found at i:12707362 original size:13 final size:13
Alignment explanation
Indices: 12707344--12707396 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
12707334 AATATTATTT
12707344 ATTTAATCAATTA
1 ATTTAATCAATTA
*
12707357 ATTTAATTAATTTA
1 ATTTAATCAA-TTA
* *
12707371 ATTAAATAAATTA
1 ATTTAATCAATTA
12707384 ATTT-ATCAATTA
1 ATTTAATCAATTA
12707396 A
1 A
12707397 ATAATTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 8 0.24
13 15 0.44
14 11 0.32
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAATCAATTA
Found at i:12707366 original size:9 final size:9
Alignment explanation
Indices: 12707352--12707388 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12707342 TTATTTAATC
12707352 AATTAATTT
1 AATTAATTT
12707361 AATTAATTT
1 AATTAATTT
* *
12707370 AATTAAATA
1 AATTAATTT
12707379 AATTAATTT
1 AATTAATTT
12707388 A
1 A
12707389 TCAATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTAATTT
Found at i:12710175 original size:21 final size:21
Alignment explanation
Indices: 12710146--12710191 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12710136 AATATTAATT
*
12710146 TATA-AATTTATTGTGTATCA
1 TATATAATTTATTGTGTAGCA
* *
12710166 TATATAATTTTTTGTTTAGCA
1 TATATAATTTATTGTGTAGCA
12710187 TATAT
1 TATAT
12710192 TATTCAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (21 bp):
TATATAATTTATTGTGTAGCA
Found at i:12712415 original size:13 final size:13
Alignment explanation
Indices: 12712397--12712441 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
12712387 TGGGACAGAC
12712397 TCAAGGAAGAGTT
1 TCAAGGAAGAGTT
* * **
12712410 TCAAGGGACAGAC
1 TCAAGGAAGAGTT
12712423 TCAAGGAAGAGTT
1 TCAAGGAAGAGTT
12712436 TCAAGG
1 TCAAGG
12712442 GTCAGATAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.31, T:0.18
Consensus pattern (13 bp):
TCAAGGAAGAGTT
Found at i:12712417 original size:26 final size:26
Alignment explanation
Indices: 12712388--12712447 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
12712378 AAGCAGGTCT
12712388 GGGACAGACTCAAGGAAGAGTTTCAA
1 GGGACAGACTCAAGGAAGAGTTTCAA
12712414 GGGACAGACTCAAGGAAGAGTTTCAA
1 GGGACAGACTCAAGGAAGAGTTTCAA
*
12712440 GGGTCAGA
1 GGGACAGA
12712448 TAAAACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.33, T:0.15
Consensus pattern (26 bp):
GGGACAGACTCAAGGAAGAGTTTCAA
Found at i:12718221 original size:13 final size:13
Alignment explanation
Indices: 12718203--12718230 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12718193 CGAAAATCAT
12718203 ATGAAGTGTCAAC
1 ATGAAGTGTCAAC
12718216 ATGAAGTGTCAAC
1 ATGAAGTGTCAAC
12718229 AT
1 AT
12718231 TGTACTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (13 bp):
ATGAAGTGTCAAC
Found at i:12722078 original size:221 final size:221
Alignment explanation
Indices: 12721683--12722121 Score: 641
Period size: 221 Copynumber: 2.0 Consensus size: 221
12721673 CTTCCAAGAA
* * * * * *
12721683 GGGTTTCCAATCTCTTTACTCACTCCATTCAGTGAACGTACTTAAAAGCACACATATGGAATTAG
1 GGGTTTCCAATATCTTTACTCACTCCACTCAGTGAACGTACCTAAAAGCAAAAATAAGGAATTAG
12721748 CAAACAGTCAGTACTAAGTACTATTCCAAATTTGGAGCAAAATGCATGCAAATAAGAGATCAAAT
66 CAAACAGTCAGTACTAAGTACTATTCCAAATTTGGAGCAAAATGCATGCAAATAAGAGATCAAAT
* * * * * * *
12721813 ACACAATCCCATACCATAAAAAACCATAACATAAAACAAAAGCAAAGCTTTCAGCTTCATATAAT
131 ACAAAATCCCATACCATAAAAAACCATAACACAAAACAAAAGCAAAGCTTCCAACTCCATACAAC
12721878 TTGCATTTTTTTAAAAGGTTATAAAG
196 TTGCATTTTTTTAAAAGGTTATAAAG
12721904 GGGTTTCCAATATCTTTGA-TCACTCCACTCAGTGAACGTACCTAAAAGCAAAAATAAGGAATTA
1 GGGTTTCCAATATCTTT-ACTCACTCCACTCAGTGAACGTACCTAAAAGCAAAAATAAGGAATTA
* * *
12721968 GCGAACTGTCAGTACTAAGTACT-TCTCCAAATTCT-GAGCAAAATGCATGCAGATAAGAGATCA
65 GCAAACAGTCAGTACTAAGTACTAT-TCCAAATT-TGGAGCAAAATGCATGCAAATAAGAGATCA
* * * *
12722031 AGTACAAAATCCCATAGCATAAAAAACCATAACACAAACCTAAAGCAAAGCTTCCAACTCCATAC
128 AATACAAAATCCCATACCATAAAAAACCATAACACAAAACAAAAGCAAAGCTTCCAACTCCATAC
*
12722096 AACTTGGATTTTTTTAAAAGGTTATA
193 AACTTGCATTTTTTTAAAAGGTTATA
12722122 TATTGTTTCT
Statistics
Matches: 194, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
220 1 0.01
221 191 0.98
222 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (221 bp):
GGGTTTCCAATATCTTTACTCACTCCACTCAGTGAACGTACCTAAAAGCAAAAATAAGGAATTAG
CAAACAGTCAGTACTAAGTACTATTCCAAATTTGGAGCAAAATGCATGCAAATAAGAGATCAAAT
ACAAAATCCCATACCATAAAAAACCATAACACAAAACAAAAGCAAAGCTTCCAACTCCATACAAC
TTGCATTTTTTTAAAAGGTTATAAAG
Found at i:12722915 original size:2 final size:2
Alignment explanation
Indices: 12722908--12722953 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
12722898 GAAATGAGCG
* *
12722908 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12722950 TA TA
1 TA TA
12722954 GGTGTATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:12730629 original size:13 final size:14
Alignment explanation
Indices: 12730607--12730636 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
12730597 ATAAAAGGCT
12730607 AAAATGATTTTTTA
1 AAAATGATTTTTTA
12730621 AAAAT-ATTTTTTA
1 AAAATGATTTTTTA
12730634 AAA
1 AAA
12730637 TTTTAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AAAATGATTTTTTA
Found at i:12734751 original size:13 final size:13
Alignment explanation
Indices: 12734733--12734757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12734723 TTTTTTTTCT
12734733 AAATGAAAATGAA
1 AAATGAAAATGAA
12734746 AAATGAAAATGA
1 AAATGAAAATGA
12734758 CTTGGAAATG
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
AAATGAAAATGAA
Found at i:12737941 original size:72 final size:72
Alignment explanation
Indices: 12737824--12737971 Score: 278
Period size: 72 Copynumber: 2.1 Consensus size: 72
12737814 CTAGAAGTGT
* *
12737824 TGAAGATAACTTTTATTCTAGAGTTGTCAATGACACATAATCTATAGTGAAAAGATGATGATGAT
1 TGAAGATAACTCTTATTCTAGAGTTGTCAATGACACAAAATCTATAGTGAAAAGATGATGATGAT
12737889 GGAAACG
66 GGAAACG
12737896 TGAAGATAACTCTTATTCTAGAGTTGTCAATGACACAAAATCTATAGTGAAAAGATGATGATGAT
1 TGAAGATAACTCTTATTCTAGAGTTGTCAATGACACAAAATCTATAGTGAAAAGATGATGATGAT
12737961 GGAAACG
66 GGAAACG
12737968 TGAA
1 TGAA
12737972 TCATACTGCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (72 bp):
TGAAGATAACTCTTATTCTAGAGTTGTCAATGACACAAAATCTATAGTGAAAAGATGATGATGAT
GGAAACG
Found at i:12739689 original size:10 final size:10
Alignment explanation
Indices: 12739674--12739707 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12739664 AATTTAGATT
12739674 TTTAGTTTTC
1 TTTAGTTTTC
*
12739684 TTTAGTGTTTT
1 TTTAGT-TTTC
12739695 TTTAGTTTTC
1 TTTAGTTTTC
12739705 TTT
1 TTT
12739708 TATGTTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.09, C:0.06, G:0.12, T:0.74
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:12739700 original size:11 final size:10
Alignment explanation
Indices: 12739672--12739714 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
12739662 TTAATTTAGA
12739672 TTTTTAGTTT
1 TTTTTAGTTT
*
12739682 TCTTTAGTGTT
1 TTTTTAGT-TT
12739693 TTTTTAGTTT
1 TTTTTAGTTT
12739703 TCTTTTATGTTT
1 T-TTTTA-GTTT
12739715 GCTTAATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.36
11 14 0.50
12 4 0.14
ACGTcount: A:0.09, C:0.05, G:0.12, T:0.74
Consensus pattern (10 bp):
TTTTTAGTTT
Found at i:12763604 original size:22 final size:23
Alignment explanation
Indices: 12763559--12763604 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12763549 GTGCATCTCA
* *
12763559 CTTAACCCCTTAAGGTCACAACC
1 CTTAACCCCCTAAGATCACAACC
*
12763582 CTTAACCCCCTAA-ATCACCACC
1 CTTAACCCCCTAAGATCACAACC
12763604 C
1 C
12763605 CGAACACCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.30, C:0.46, G:0.04, T:0.20
Consensus pattern (23 bp):
CTTAACCCCCTAAGATCACAACC
Found at i:12778437 original size:41 final size:41
Alignment explanation
Indices: 12778405--12778486 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
12778395 ATATTTTATT
*
12778405 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGCTTATTAGAATAAGGGAATTATTTTCC
*
12778446 TTATGTTTTAGTAGCTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGCTTATTAGAATAAGGGAATTATTTTCC
12778487 CAATTAGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGCTTATTAGAATAAGGGAATTATTTTCC
Found at i:12781659 original size:24 final size:24
Alignment explanation
Indices: 12781627--12781677 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12781617 TTCTGAGATA
12781627 CTTGAAGAGTTCACCTAGAAAGGG
1 CTTGAAGAGTTCACCTAGAAAGGG
* *
12781651 CTTGAAGAGTTCACCTGGAAATGG
1 CTTGAAGAGTTCACCTAGAAAGGG
12781675 CTT
1 CTT
12781678 ATTCTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (24 bp):
CTTGAAGAGTTCACCTAGAAAGGG
Found at i:12782256 original size:19 final size:19
Alignment explanation
Indices: 12782232--12782269 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12782222 GAGATATGTT
12782232 TTTAGGTAGATAAATCTTA
1 TTTAGGTAGATAAATCTTA
*
12782251 TTTAGGTAGATAAGTCTTA
1 TTTAGGTAGATAAATCTTA
12782270 GAATAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (19 bp):
TTTAGGTAGATAAATCTTA
Found at i:12782363 original size:41 final size:41
Alignment explanation
Indices: 12782307--12782389 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
12782297 ATATTTTATT
**
12782307 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAAAGAATTATTTTCC
* *
12782348 TTATGTTTTATTAGTTTATTAGAATAAAAGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAAAGAATTATTTTCC
12782389 T
1 T
12782390 AATTAGGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAAAGAATTATTTTCC
Found at i:12793862 original size:13 final size:13
Alignment explanation
Indices: 12793844--12793877 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
12793834 TCAAAGAAGA
12793844 TCGAAGAAAACAC
1 TCGAAGAAAACAC
12793857 TCGAAGAAAACAC
1 TCGAAGAAAACAC
12793870 TCGAAGAA
1 TCGAAGAA
12793878 CACTGTCGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.21, G:0.18, T:0.09
Consensus pattern (13 bp):
TCGAAGAAAACAC
Found at i:12793881 original size:11 final size:12
Alignment explanation
Indices: 12793844--12793881 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
12793834 TCAAAGAAGA
12793844 TCGAAGAAAACAC
1 TCGAAG-AAACAC
12793857 TCGAAGAAAACAC
1 TCGAAG-AAACAC
12793870 TCGAAG-AACAC
1 TCGAAGAAACAC
12793881 T
1 T
12793882 GTCGGAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 6 0.24
13 19 0.76
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.11
Consensus pattern (12 bp):
TCGAAGAAACAC
Found at i:12795522 original size:2 final size:2
Alignment explanation
Indices: 12795515--12795553 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12795505 TACATGATTT
12795515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12795554 TAAAAAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12796243 original size:20 final size:19
Alignment explanation
Indices: 12796218--12796256 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
12796208 GTGGAATTAT
12796218 TAAAAAAATAATTAAAACTA
1 TAAAAAAAT-ATTAAAACTA
*
12796238 TAAAAAAATTTTAAAACTA
1 TAAAAAAATATTAAAACTA
12796257 AAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAAATATTAAAACTA
Found at i:12796251 original size:19 final size:19
Alignment explanation
Indices: 12796218--12796271 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
12796208 GTGGAATTAT
*
12796218 TAAAAAAATAATTAAAACTA
1 TAAAAAAAT-TTTAAAACTA
12796238 TAAAAAAATTTTAAAACTA
1 TAAAAAAATTTTAAAACTA
* *
12796257 -AAATAAATTGTAAAA
1 TAAAAAAATTTTAAAA
12796272 AAAGTTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.42
19 9 0.29
20 9 0.29
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAAAAAATTTTAAAACTA
Found at i:12796272 original size:19 final size:19
Alignment explanation
Indices: 12796218--12796272 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
12796208 GTGGAATTAT
12796218 TAAAAAAATAATT-AAAACTA
1 TAAAAAAAT--TTAAAAACTA
*
12796238 TAAAAAAATTTTAAAACTA
1 TAAAAAAATTTAAAAACTA
*
12796257 -AAATAAATTGTAAAAA
1 TAAAAAAATT-TAAAAA
12796273 AAGTTAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 10 0.32
19 12 0.39
20 9 0.29
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAAAATTTAAAAACTA
Found at i:12796296 original size:7 final size:7
Alignment explanation
Indices: 12796284--12796317 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
12796274 AGTTAAACAT
12796284 TATAAAA
1 TATAAAA
12796291 TATAAAAA
1 TAT-AAAA
12796299 TATAAAA
1 TATAAAA
12796306 TATTAAAA
1 TA-TAAAA
12796314 TATA
1 TATA
12796318 TATAGAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TATAAAA
Found at i:12796304 original size:15 final size:15
Alignment explanation
Indices: 12796284--12796317 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12796274 AGTTAAACAT
12796284 TATAAAATATAAAAA
1 TATAAAATATAAAAA
*
12796299 TATAAAATATTAAAA
1 TATAAAATATAAAAA
12796314 TATA
1 TATA
12796318 TATAGAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TATAAAATATAAAAA
Found at i:12796876 original size:43 final size:43
Alignment explanation
Indices: 12796802--12797028 Score: 182
Period size: 43 Copynumber: 5.3 Consensus size: 43
12796792 GCGTCACTAA
* ** * *
12796802 CTTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGACCATGAC
* * *
12796844 CTATAGCGGCGCTTTTCTAACAAACGCCGCTA-AAAACATTGAC
1 CTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGACCA-TGAC
* * * *
12796887 CTTTAGCGGCGCTTTACCAA-AAACGCCGCTATAG-CTCAAGAG
1 CTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGAC-CATGAC
* * * *
12796929 CTTTAGCGGCGCTTTTAC-CACAAACGCCACTATAGATCGTGAC
1 CTTTAGCGGCGCTTTT-CTAACAAACGCCGCTATAGACCATGAC
* *
12796972 CTTTAGCGGCACTTTT-TCCACAAACGCCGCTATAG-CTCGAT-AC
1 CTTTAGCGGCGCTTTTCT-AACAAACGCCGCTATAGAC-C-ATGAC
12797015 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
12797029 CTCACAAAAA
Statistics
Matches: 148, Mismatches: 26, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
42 49 0.33
43 98 0.66
44 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGACCATGAC
Found at i:12796933 original size:42 final size:43
Alignment explanation
Indices: 12796884--12797042 Score: 196
Period size: 43 Copynumber: 3.7 Consensus size: 43
12796874 TAAAAACATT
*
12796884 GACCTTTAGCGGCGC-TTTACCAAAAACGCCGCTATAGCTCAA
1 GACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGCTCGA
* * * * *
12796926 GAGCTTTAGCGGCGCTTTTACCACAAACGCCACTATAGATCGT
1 GACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGCTCGA
* * *
12796969 GACCTTTAGCGGCACTTTTTCCACAAACGCCGCTATAGCTCGA
1 GACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGCTCGA
* *
12797012 TACCTTTAGCGGCGCTTCT-CACAAAAACGCC
1 GACCTTTAGCGGCGCTTTTAC-CAAAAACGCC
12797043 ACTAAAAATA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
42 15 0.15
43 84 0.85
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
GACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGCTCGA
Found at i:12797040 original size:86 final size:85
Alignment explanation
Indices: 12796883--12797046 Score: 231
Period size: 86 Copynumber: 1.9 Consensus size: 85
12796873 CTAAAAACAT
* * *
12796883 TGACCTTTAGCGGCGCTTTACCAAAAACGCCGCTATAGCTCAAGAGCTTTAGCGGCGCTTTTACC
1 TGACCTTTAGCGGCACTTTACCAAAAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTCACC
*
12796948 ACAAACGCCACTATAGATCG
66 AAAAACGCCACTATAGATCG
* * * *
12796968 TGACCTTTAGCGGCACTTTTTCCACAAACGCCGCTATAGCTCGATACCTTTAGCGGCGCTTCTCA
1 TGACCTTTAGCGGCAC-TTTACCAAAAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTT-TCA
12797033 -CAAAAACGCCACTA
64 CCAAAAACGCCACTA
12797047 AAAATATAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
85 15 0.22
86 52 0.75
87 2 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (85 bp):
TGACCTTTAGCGGCACTTTACCAAAAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTCACC
AAAAACGCCACTATAGATCG
Found at i:12798737 original size:28 final size:28
Alignment explanation
Indices: 12798697--12798757 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
12798687 AAAACAAGAA
*
12798697 TCAAATTAGTTCAA-CTCCAAGTCCTTAG
1 TCAAATCAGTTCAACCT-CAAGTCCTTAG
* *
12798725 TCAAATCAGTTCAACCTCAAGTTCTTTG
1 TCAAATCAGTTCAACCTCAAGTCCTTAG
12798753 TCAAA
1 TCAAA
12798758 AGAAAAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (28 bp):
TCAAATCAGTTCAACCTCAAGTCCTTAG
Found at i:12801383 original size:19 final size:19
Alignment explanation
Indices: 12801359--12801400 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12801349 AAATTATAAA
*
12801359 TTTTATTTTTTTATTTCAT
1 TTTTATTTTTGTATTTCAT
*
12801378 TTTTATTTTTGTATTTTAT
1 TTTTATTTTTGTATTTCAT
12801397 TTTT
1 TTTT
12801401 TCTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTGTATTTCAT
Found at i:12801810 original size:21 final size:21
Alignment explanation
Indices: 12801737--12801812 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
12801727 CGATCCTTGA
*
12801737 AACCC-TAAATCCCTAAATCTT
1 AACCCTTAAA-CCCTAAATCTC
* *
12801758 AACCCTTAACCCCCTAACTC-C
1 AACCCTTAA-ACCCTAAATCTC
* *
12801779 TAACCCCTAAACCTTAAATCTC
1 -AACCCTTAAACCCTAAATCTC
12801801 AACCCTTAAACC
1 AACCCTTAAACC
12801813 ATAATCCCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
21 23 0.53
22 20 0.47
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCCTTAAACCCTAAATCTC
Found at i:12802120 original size:14 final size:14
Alignment explanation
Indices: 12802103--12802139 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12802093 TTAACCCTTA
* *
12802103 AACCTCTAACCTCT
1 AACCCCTAACCCCT
12802117 AACCCCTAACCCCT
1 AACCCCTAACCCCT
12802131 AACCCCTAA
1 AACCCCTAA
12802140 ACCTTAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.49, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCCCTAACCCCT
Found at i:12802152 original size:21 final size:21
Alignment explanation
Indices: 12802098--12802174 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
12802088 AACTCTTAAC
* *
12802098 CCTTAAACCTCTAACCTCTAAC
1 CCTTAAACC-CTAACCCCTAAA
* *
12802120 CCCTAACCCCTAACCCCTAAA
1 CCTTAAACCCTAACCCCTAAA
* * *
12802141 CCTTAAATCCTAACCCTTACA
1 CCTTAAACCCTAACCCCTAAA
* *
12802162 CCATAATCCCTAA
1 CCTTAAACCCTAA
12802175 TCCATAATCC
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTTAAACCCTAACCCCTAAA
Found at i:12802204 original size:15 final size:15
Alignment explanation
Indices: 12802162--12802204 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12802152 AACCCTTACA
12802162 CCATAATCCCT-AAT
1 CCATAATCCCTAAAT
*
12802176 CCATAATCCATAAAT
1 CCATAATCCCTAAAT
* *
12802191 TCATACTCCCTAAA
1 CCATAATCCCTAAA
12802205 CATTAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.28
Consensus pattern (15 bp):
CCATAATCCCTAAAT
Found at i:12802634 original size:41 final size:41
Alignment explanation
Indices: 12802551--12802867 Score: 390
Period size: 41 Copynumber: 7.8 Consensus size: 41
12802541 TAAAATGTTT
*
12802551 TTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGACCAC-AGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-ACCCCGAGCA
*
12802591 TTAGCGGCGCTTTTT-AAGAAACGCCGCTAAAACCCCGAACA
1 TTAGCGGCGCTTTTTCAA-AAACGCCGCTAAAACCCCGAGCA
* *
12802632 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGAA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** *
12802673 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAATA-CTAGAGAA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-ACCCCGAGCA
* * *
12802714 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAATCCCAGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* *
12802755 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAATCCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
** * * *
12802796 TTAGTAGTGCTTTTTCAAAAACGCCGCTAAATCCCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
** *
12802837 TTAGCGGCGCTTTTTTTAAAACGCCACTAAA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
12802868 GACCATAAAG
Statistics
Matches: 245, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
40 16 0.07
41 226 0.92
42 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
Found at i:12802781 original size:123 final size:122
Alignment explanation
Indices: 12802551--12802867 Score: 431
Period size: 123 Copynumber: 2.6 Consensus size: 122
12802541 TAAAATGTTT
* * * *
12802551 TTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGACCACAGCATTAGCGGCGCTTTTTAAGAAACGC
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAATACTAGAGCATTAGCGGCGCTTTTTAA-AAACGC
* *
12802615 CGCTAAAACCCCGAACATTAGCGGTGCTTTTTCAAAAACGCCGCTAAAACCCCGAGAA
65 CGCTAAAACCCAGAACATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGAA
*
12802673 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAATACTAGAGAATTAGCGGCGCTTTTTGAAAAACGC
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAATACTAGAGCATTAGCGGCGCTTTTT-AAAAACGC
* * * * *
12802738 CGCTAAATCCCAGAGCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAATCCCCGAGCA
65 CGCTAAAACCCAGAACATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGAA
** * *
12802796 TTAGTAGTGCTTTTTCAAAAACGCCGCTAAATCCCT-GAGCATTAGCGGCGCTTTTTTTAAAACG
1 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAT-ACTAGAGCATTAGCGGCGC-TTTTTAAAAACG
*
12802860 CCACTAAA
64 CCGCTAAA
12802868 GACCATAAAG
Statistics
Matches: 173, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
122 9 0.05
123 155 0.90
124 9 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (122 bp):
TTAGCGGTGCTTTTTCAAAAACGCCGCTAAATACTAGAGCATTAGCGGCGCTTTTTAAAAACGCC
GCTAAAACCCAGAACATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGAA
Found at i:12802957 original size:40 final size:40
Alignment explanation
Indices: 12802907--12803042 Score: 161
Period size: 40 Copynumber: 3.4 Consensus size: 40
12802897 GGGCTTTAGT
*
12802907 TTTTTA-CGGCATTTTTGGGAAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCATTTTT-CGAAAAACGCCGCTAATGCTCAA
* *
12802946 TTTTTAGCGGCATTTTTCGAAAAACGCCGCGAATGCTCGA
1 TTTTTAGCGGCATTTTTCGAAAAACGCCGCTAATGCTCAA
* * * *
12802986 TCTTTAGTGGCGA-TTTTCGTAAAGCGCCGCTAATGCTCAA
1 TTTTTAGCGGC-ATTTTTCGAAAAACGCCGCTAATGCTCAA
*
12803026 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCATTTTT
12803043 TATCCAAACG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
39 25 0.30
40 56 0.68
41 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (40 bp):
TTTTTAGCGGCATTTTTCGAAAAACGCCGCTAATGCTCAA
Found at i:12807856 original size:50 final size:50
Alignment explanation
Indices: 12807717--12808247 Score: 409
Period size: 50 Copynumber: 10.6 Consensus size: 50
12807707 TGCCAAAACT
* * * * * *
12807717 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTAC--TGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCT-CGGTGCCAACGCC
* * * * * * * *
12807766 ATATCCTAGATATAGTCTTACATGGGAGT-TCTCATATCGGTGCCCATGCT
1 ATGTCCCAGACATGGTCTTACATGGGA-TCTCTCATCTCGGTGCCAACGCC
** * *
12807816 ATGTCCCAGACATGGTCTTACGGGGGATCGCTCATCTCGGTGCCAACGCT
1 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCC
*
12807866 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCC
** *** ** * * *
12807916 ATGTCCCAGACATGGTCTT-C-T-GTTTGAAT-ATAAC-ATGCCAAAGCT
1 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCC
* * * * * * *
12807961 ATGTCCCAAACATAGTCTTACATGGGATGTTTCTTGTAC--TGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCT-CGGTGCCAACGCC
* * * * *
12808010 ATATCCCAGATATGGTCTTACATGGGAGT-TCTCATATCGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA-TCTCTCATCTCGGTGCCAACGCC
*** * *
12808060 ATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCT
1 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCC
* ** * *
12808110 ATGTCCTAGACATATTCTTACATGGGACCTCTCATCTCGGCGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCC
* * *
12808160 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA--TCTC-TCATCTC---GGTGCCAACGCC
12808216 ATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGTCCCAGACATGGTCTTACATGGGATCTCT
12808248 TTACCCAAAT
Statistics
Matches: 384, Mismatches: 79, Indels: 34
0.77 0.16 0.07
Matches are distributed among these distances:
45 25 0.07
46 4 0.01
47 3 0.01
48 7 0.02
49 68 0.18
50 227 0.59
52 3 0.01
53 7 0.02
54 4 0.01
56 36 0.09
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCC
Found at i:12808114 original size:244 final size:244
Alignment explanation
Indices: 12807685--12808178 Score: 880
Period size: 244 Copynumber: 2.0 Consensus size: 244
12807675 AGGATACTCG
*
12807685 GGTCTTCTGTTTGAATATAACATGCCAAAACTATGTCCCAGACATAGTCTTACATGGGATGTTTC
1 GGTCTTCTGTTTGAATATAACATGCCAAAACTATGTCCCAAACATAGTCTTACATGGGATGTTTC
*
12807750 TTGTACTGCCAATGCCATATCCTAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
66 TTGTACTGCCAATGCCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
* * *
12807815 TATGTCCCAGACATGGTCTTACGGGGGATCGCTCATCTCGGTGCCAACGCTATGTCCCAGACATG
131 CATGTCCCAGACATGGTCTTACGGGGGACCGCTCATCTCGGTGCCAACGCTATGTCCCAGACATA
*
12807880 GTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
196 GTCTTACATGGGACCTCTCATCTCGGCGCCAACGCCATGTCCCAGACAT
*
12807929 GGTCTTCTGTTTGAATATAACATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTC
1 GGTCTTCTGTTTGAATATAACATGCCAAAACTATGTCCCAAACATAGTCTTACATGGGATGTTTC
*
12807994 TTGTACTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
66 TTGTACTGCCAATGCCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
* * *
12808059 CATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCTATGTCCTAGACATA
131 CATGTCCCAGACATGGTCTTACGGGGGACCGCTCATCTCGGTGCCAACGCTATGTCCCAGACATA
*
12808124 TTCTTACATGGGACCTCTCATCTCGGCGCCAACGCCATGTCCCAGACAT
196 GTCTTACATGGGACCTCTCATCTCGGCGCCAACGCCATGTCCCAGACAT
12808173 GGTCTT
1 GGTCTT
12808179 ACATGGGACC
Statistics
Matches: 238, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
244 238 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (244 bp):
GGTCTTCTGTTTGAATATAACATGCCAAAACTATGTCCCAAACATAGTCTTACATGGGATGTTTC
TTGTACTGCCAATGCCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
CATGTCCCAGACATGGTCTTACGGGGGACCGCTCATCTCGGTGCCAACGCTATGTCCCAGACATA
GTCTTACATGGGACCTCTCATCTCGGCGCCAACGCCATGTCCCAGACAT
Found at i:12808620 original size:30 final size:29
Alignment explanation
Indices: 12808586--12808642 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
12808576 CCTCGACTCT
12808586 AACTTTGACAAAATTACAATTTTGACCCTA
1 AACTTTGACAAAATTACAATTTT-ACCCTA
* * *
12808616 AACTTTTACATAATTACACTTTTACCC
1 AACTTTGACAAAATTACAATTTTACCC
12808643 CAAAGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AACTTTGACAAAATTACAATTTTACCCTA
Found at i:12814306 original size:6 final size:6
Alignment explanation
Indices: 12814295--12814351 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
12814285 ATTGAGTTTA
* * *
12814295 TTTATT TTTATT TTTATT TTTA-T CTTATG TTTATT TTTAGTT CTTTTTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT -TTTATT
12814344 TTTATT TT
1 TTTATT TT
12814352 CTCAGACTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 4 0.10
6 31 0.74
7 4 0.10
8 3 0.07
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:12814327 original size:17 final size:16
Alignment explanation
Indices: 12814290--12814350 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 16
12814280 GGACCATTGA
12814290 GTTTATTTATT-TTTAT
1 GTTTATTT-TTATTTAT
*
12814306 TTTTATTTTTATCTTAT
1 GTTTATTTTTAT-TTAT
* *
12814323 GTTTATTTTTAGTTCT
1 GTTTATTTTTATTTAT
12814339 -TTT-TTTTTATTT
1 GTTTATTTTTATTT
12814351 TCTCAGACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.21
15 5 0.13
16 11 0.29
17 14 0.37
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (16 bp):
GTTTATTTTTATTTAT
Found at i:12814327 original size:23 final size:22
Alignment explanation
Indices: 12814291--12814333 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
12814281 GACCATTGAG
*
12814291 TTTATTTATTTTTATTTTTATT
1 TTTATTTATGTTTATTTTTATT
12814313 TTTATCTTATGTTTATTTTTA
1 TTTAT-TTATGTTTATTTTTA
12814334 GTTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTATTTATGTTTATTTTTATT
Found at i:12818819 original size:19 final size:19
Alignment explanation
Indices: 12818792--12818828 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12818782 TATTTCAAGA
*
12818792 TCAAAATCAAATTCGAAAC
1 TCAAAATCAAATTAGAAAC
*
12818811 TCAATATCAAATTAGAAA
1 TCAAAATCAAATTAGAAA
12818829 TAGCATCCCT
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:0.54, C:0.16, G:0.05, T:0.24
Consensus pattern (19 bp):
TCAAAATCAAATTAGAAAC
Found at i:12823593 original size:23 final size:24
Alignment explanation
Indices: 12823563--12823609 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
12823553 AAATTAAATC
12823563 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
12823586 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
12823610 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:12823609 original size:24 final size:23
Alignment explanation
Indices: 12823563--12823628 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 23
12823553 AAATTAAATC
* *
12823563 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGCAATATCATATCT
12823586 TCTAAGATTGCATATATCATA---
1 TCTAAGATTGCA-ATATCATATCT
12823607 TCTAAGATTGC-ATATCATATCT
1 TCTAAGATTGCAATATCATATCT
12823629 AAGATTACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 8 0.22
21 11 0.30
23 11 0.30
24 7 0.19
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
TCTAAGATTGCAATATCATATCT
Found at i:12823612 original size:21 final size:21
Alignment explanation
Indices: 12823586--12823640 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
12823576 AATCATATCT
12823586 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
12823607 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
12823626 TCTAAGATTACATAT
1 TCTAAGATTGCATAT
12823641 CCTCGAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:12830075 original size:14 final size:14
Alignment explanation
Indices: 12830058--12830090 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12830048 AATAATAAAT
*
12830058 GAAAATCAAAGGAA
1 GAAAATAAAAGGAA
12830072 GAAAATAAAAGGAA
1 GAAAATAAAAGGAA
12830086 GAAAA
1 GAAAA
12830091 AGGAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.21, T:0.06
Consensus pattern (14 bp):
GAAAATAAAAGGAA
Found at i:12837225 original size:17 final size:17
Alignment explanation
Indices: 12837203--12837248 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
12837193 TGAGTGAGAT
12837203 AAAGTGAAAAAGGTCA-A
1 AAAGTGAAAAA-GTCAGA
*
12837220 AAAGTGACAAAGTCAGA
1 AAAGTGAAAAAGTCAGA
12837237 AAAGTAGAAAAA
1 AAAGT-GAAAAA
12837249 ATCATTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.16
17 16 0.64
18 5 0.20
ACGTcount: A:0.61, C:0.07, G:0.22, T:0.11
Consensus pattern (17 bp):
AAAGTGAAAAAGTCAGA
Found at i:12843671 original size:20 final size:20
Alignment explanation
Indices: 12843646--12843684 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12843636 TTGCTTCATC
12843646 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
12843666 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
12843685 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:12845051 original size:41 final size:41
Alignment explanation
Indices: 12844993--12845183 Score: 274
Period size: 41 Copynumber: 4.6 Consensus size: 41
12844983 CTTAATTTAA
* *
12844993 CAGATTCACCGGCACTTAGCCTGCTAGGCTTCTAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * *
12845035 CAGATCACCAGCACTTAGCCTGCTAGGCTTCTAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * *
12845076 CAGATCACCAGCACTTAGCCTGCAAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
12845117 TAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
12845158 CAGATCACTGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
12845184 ACGTATTGTC
Statistics
Matches: 139, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
41 135 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:12850753 original size:24 final size:24
Alignment explanation
Indices: 12850697--12850759 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
12850687 AGAAACAAGC
*
12850697 ATGATATGAATTAATAAATGATAA
1 ATGATATGAATTGATAAATGATAA
* *
12850721 ATGACATGAATTGATAAATGATAT
1 ATGATATGAATTGATAAATGATAA
*
12850745 ATGGTATGAATTGAT
1 ATGATATGAATTGAT
12850760 GATGAAATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (24 bp):
ATGATATGAATTGATAAATGATAA
Found at i:12864159 original size:14 final size:14
Alignment explanation
Indices: 12864140--12864192 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
12864130 TAAACATACC
12864140 TATTAAATATAATT
1 TATTAAATATAATT
*
12864154 TATTAAAAATAATTT
1 TATTAAATATAA-TT
*
12864169 TAATTAAAATATTATTT
1 T-ATT-AAATA-TAATT
12864186 TATTAAA
1 TATTAAA
12864193 ATGTTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 11 0.34
15 6 0.19
16 6 0.19
17 7 0.22
18 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTAAATATAATT
Found at i:12864187 original size:17 final size:16
Alignment explanation
Indices: 12864140--12864194 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
12864130 TAAACATACC
12864140 TATT-AAATATAA-TT
1 TATTAAAATATAATTT
12864154 TATTAAAA-ATAATTT
1 TATTAAAATATAATTT
*
12864169 TAATTAAAATATTATTT
1 T-ATTAAAATATAATTT
12864186 TATTAAAAT
1 TATTAAAAT
12864195 GTTTAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 8 0.22
15 6 0.17
16 15 0.42
17 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTAAAATATAATTT
Found at i:12865099 original size:22 final size:22
Alignment explanation
Indices: 12865073--12865114 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12865063 ATTTTTTTTA
12865073 TATTCAAATGATATTATAAATT
1 TATTCAAATGATATTATAAATT
*
12865095 TATTCAAATTATATTATAAA
1 TATTCAAATGATATTATAAA
12865115 AGTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTCAAATGATATTATAAATT
Found at i:12872221 original size:5 final size:5
Alignment explanation
Indices: 12872211--12872237 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12872201 TGTGAAGTGT
12872211 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
12872238 ACAAATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:12873007 original size:161 final size:162
Alignment explanation
Indices: 12872741--12873068 Score: 622
Period size: 161 Copynumber: 2.0 Consensus size: 162
12872731 TTTGAGGGAA
12872741 GAATTTGTACTATCCCATATATTTGAGAGATAGCGAATACCGAATTGCAAAGTATTTAGTATGGG
1 GAATTTGTACTATCCCATATATTTGAGAGATAGCGAATACCGAATTGCAAAGTATTTAGTATGGG
* *
12872806 TTCATATCTCATGATTACTTTGTCGGAGTGGTAGCCGGGTTAAGGCT-AAAAGGATTTAGTTAAT
66 TTCATATCTCATGATTACTTTGTCGGAGTGATAACCGGGTTAAGGCTAAAAAGGATTTAGTTAAT
12872870 CATGAAAAGAATCATAATAAATGGTTTAAATG
131 CATGAAAAGAATCATAATAAATGGTTTAAATG
*
12872902 GAATTTGTACTATCCCATATATTTGAGAGATAGCGAATACCGAATTGCAAAGTATTTAGTGTGGG
1 GAATTTGTACTATCCCATATATTTGAGAGATAGCGAATACCGAATTGCAAAGTATTTAGTATGGG
12872967 TTCATATCTCATGATTACTTTGTCGGAGTGATAACCGGGTTAAGGCTAAAAAGGATTTAGTTAAT
66 TTCATATCTCATGATTACTTTGTCGGAGTGATAACCGGGTTAAGGCTAAAAAGGATTTAGTTAAT
12873032 CATGAAAAGAATCATAATAAATGGTTTAAATG
131 CATGAAAAGAATCATAATAAATGGTTTAAATG
12873064 GAATT
1 GAATT
12873069 ATGGAAAGTG
Statistics
Matches: 163, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
161 109 0.67
162 54 0.33
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (162 bp):
GAATTTGTACTATCCCATATATTTGAGAGATAGCGAATACCGAATTGCAAAGTATTTAGTATGGG
TTCATATCTCATGATTACTTTGTCGGAGTGATAACCGGGTTAAGGCTAAAAAGGATTTAGTTAAT
CATGAAAAGAATCATAATAAATGGTTTAAATG
Found at i:12873313 original size:22 final size:23
Alignment explanation
Indices: 12873288--12873338 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
12873278 TAGATTTTTC
12873288 CTAAATATTATCACT-AATAATT
1 CTAAATATTATCACTAAATAATT
*
12873310 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
12873333 CAAAAT
1 CTAAAT
12873339 TTAAAAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:12876380 original size:36 final size:36
Alignment explanation
Indices: 12876333--12876402 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
12876323 ATTAAGTTTC
12876333 GATATGAAACTTAAAAAAGTATAAATTTACCTTTTT
1 GATATGAAACTTAAAAAAGTATAAATTTACCTTTTT
12876369 GATATGAAACTTAAAAAAGTATAAATTTACCTTT
1 GATATGAAACTTAAAAAAGTATAAATTTACCTTT
12876403 ATTTTAGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (36 bp):
GATATGAAACTTAAAAAAGTATAAATTTACCTTTTT
Found at i:12883352 original size:17 final size:18
Alignment explanation
Indices: 12883332--12883368 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
12883322 TAAGGTTTTT
12883332 ATAATAATAAA-AA-TAAA
1 ATAAT-ATAAAGAACTAAA
12883349 ATAATATAAAGAACTAAA
1 ATAATATAAAGAACTAAA
12883367 AT
1 AT
12883369 TAGAGACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (18 bp):
ATAATATAAAGAACTAAA
Found at i:12897536 original size:24 final size:23
Alignment explanation
Indices: 12897498--12897558 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
12897488 GTTAAAACCA
*
12897498 CCAATAACAATATGCAAAAAATTCTG
1 CCAATAA-AA-ATGCAAAAAA-GCTG
*
12897524 CCAATAAAAATGCAAACAAGCTG
1 CCAATAAAAATGCAAAAAAGCTG
*
12897547 CCAGTAAAAATG
1 CCAATAAAAATG
12897559 AGATAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.44
24 9 0.28
25 2 0.06
26 7 0.22
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.18
Consensus pattern (23 bp):
CCAATAAAAATGCAAAAAAGCTG
Found at i:12899565 original size:324 final size:321
Alignment explanation
Indices: 12898920--12899566 Score: 1109
Period size: 324 Copynumber: 2.0 Consensus size: 321
12898910 AAGATTAATC
*
12898920 AAGAAATTGAAGAGAAAAGAGATCTTACCCAAGCTAGTTGAAAGAACTGACAATGACACTTTCTT
1 AAGAAATTAAAGAGAAAAGAGATCTTACCCAAGCTAGTTGAAAGAACTGACAATGACACTTTCTT
** *
12898985 GGCAATGTTTGGGATCGATCTTGGGGTTCAAGATTTCATGTTTGGGGCTGATTTAGATGAGGATA
66 GGCAATGTTCAGGATCGATCTTGGGGTTCAAGATTTCATATTTGGGGCTGATTTAGATGAGGATA
*
12899050 AATGAAAAAAATAGAGTAAAAGAGATGGTGCACAATCTTGATGCAAAAATAAGAAGAAAGATATG
131 AATGAAAAAAATAGACTAAAAGAGATGGTGCACAATCTTGATGCAAAAATAAGAAGAAAGATATG
* *
12899115 TTAAAATGGGAGGTGTAGGCGACAACAACAATAAGAGAAAGAAAGAAAATTGAAGAGAAAAGAGG
196 TTAAAATGAGAGGTGTAGGCAACAACAACAATAAGAGAAAGAAAGAAAATTGAAGAGAAAAGAGG
*
12899180 AGAGGAAGAGGGTGAAACGCTAGGGTAGGTAAAAATTGAATTAGAGGCTAAAAAATACAAT
261 AGAGGAAGAGGGTGAAACACTAGGGTAGGTAAAAATTGAATTAGAGGCTAAAAAATACAAT
12899241 AAGAAATTAAAGAGAAAAGAGATCTTACCCAAGCTAGTTGAAAGAAAC-GACAATGACACTTTCT
1 AAGAAATTAAAGAGAAAAGAGATCTTACCCAAGCTAGTTGAAAG-AACTGACAATGACACTTTCT
*
12899305 TGGCAATGTTCAGGTTCGATCTTGGGGTTCAAGATTTCATATTTGGGGCTGATTTAGATGAGGAT
65 TGGCAATGTTCAGGATCGATCTTGGGGTTCAAGATTTCATATTTGGGGCTGATTTAGATGAGGAT
*
12899370 AACTAGAAAAAAAATAGACTAAAAGAGATGGTGCACAATCTTGATGCAAAAAATAAGAAGAAAGA
130 AAAT-G-AAAAAAATAGACTAAAAGAGATGGTGCACAATCTTGATGC-AAAAATAAGAAGAAAGA
* * *
12899435 TATGTTAAAATGAGAGGTGTAGGCAACGACAATAATAGGAGAAAGAAAGAAAATTGAAGAGAAAA
192 TATGTTAAAATGAGAGGTGTAGGCAACAACAACAATAAGAGAAAGAAAGAAAATTGAAGAGAAAA
*
12899500 GAGGAGAGGAAGAGGGTG-AACAATTAGGGTAGGTAAAAATTGAATTAGAGGCTAAAAAATACAA
257 GAGGAGAGGAAGAGGGTGAAAC-ACTAGGGTAGGTAAAAATTGAATTAGAGGCTAAAAAATACAA
12899564 T
321 T
12899565 AA
1 AA
12899567 AAAGTTGTAT
Statistics
Matches: 307, Mismatches: 14, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
321 123 0.40
322 4 0.01
323 42 0.14
324 138 0.45
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (321 bp):
AAGAAATTAAAGAGAAAAGAGATCTTACCCAAGCTAGTTGAAAGAACTGACAATGACACTTTCTT
GGCAATGTTCAGGATCGATCTTGGGGTTCAAGATTTCATATTTGGGGCTGATTTAGATGAGGATA
AATGAAAAAAATAGACTAAAAGAGATGGTGCACAATCTTGATGCAAAAATAAGAAGAAAGATATG
TTAAAATGAGAGGTGTAGGCAACAACAACAATAAGAGAAAGAAAGAAAATTGAAGAGAAAAGAGG
AGAGGAAGAGGGTGAAACACTAGGGTAGGTAAAAATTGAATTAGAGGCTAAAAAATACAAT
Found at i:12899965 original size:24 final size:25
Alignment explanation
Indices: 12899933--12899979 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
12899923 ACAAACTTGT
*
12899933 ATTATTCATGAATT-GATTAATAAA
1 ATTATTCATGAATTAAATTAATAAA
12899957 ATTATTCATGAATTAAATTAATA
1 ATTATTCATGAATTAAATTAATA
12899980 TATTTTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
ATTATTCATGAATTAAATTAATAAA
Found at i:12902880 original size:24 final size:21
Alignment explanation
Indices: 12902836--12902883 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
12902826 CCTTTTCAGT
12902836 AACTTCTTCTTCTGCAGCAAC
1 AACTTCTTCTTCTGCAGCAAC
** *
12902857 AACTTCTTCTTCTATAGCATC
1 AACTTCTTCTTCTGCAGCAAC
12902878 AACTTC
1 AACTTC
12902884 CTTCACAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (21 bp):
AACTTCTTCTTCTGCAGCAAC
Found at i:12921895 original size:26 final size:26
Alignment explanation
Indices: 12921866--12921951 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
12921856 CAACGACTGT
*
12921866 AGCTTGCCAAGCCCACTGGCGACCCC
1 AGCTTGCCAGGCCCACTGGCGACCCC
* * * *
12921892 AGCTCGCCAGGCCCTCTGGTGAACCCT
1 AGCTTGCCAGGCCCACTGGCG-ACCCC
*
12921919 AGC-TCCCAGGCCCACTGGCGACCCC
1 AGCTTGCCAGGCCCACTGGCGACCCC
12921944 AGCTTGCC
1 AGCTTGCC
12921952 TAACCCCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
25 7 0.15
26 33 0.70
27 7 0.15
ACGTcount: A:0.16, C:0.45, G:0.24, T:0.14
Consensus pattern (26 bp):
AGCTTGCCAGGCCCACTGGCGACCCC
Found at i:12928195 original size:2 final size:2
Alignment explanation
Indices: 12928188--12928214 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12928178 TTTAAATGTT
12928188 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12928215 GCGAATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12932858 original size:57 final size:57
Alignment explanation
Indices: 12932786--12932915 Score: 179
Period size: 57 Copynumber: 2.3 Consensus size: 57
12932776 TTTCTACATT
** **
12932786 TATGTTGTCTTAATGTAATTTATAGTTGCTGTCAAAATGTCTCTTAATGTGCATATA
1 TATGTTGTCAAAATGTAATTTATAGTTGCTGTCAAAATGTCTCTTAATGCACATATA
* * * * *
12932843 TATGTTGTCCAAATGTAATTTATAGTTGTTGTCATAATGTCTCTTGATGCACATATT
1 TATGTTGTCAAAATGTAATTTATAGTTGCTGTCAAAATGTCTCTTAATGCACATATA
12932900 TATGTTGTCAAAATGT
1 TATGTTGTCAAAATGT
12932916 GAATAATGGC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (57 bp):
TATGTTGTCAAAATGTAATTTATAGTTGCTGTCAAAATGTCTCTTAATGCACATATA
Found at i:12932930 original size:57 final size:57
Alignment explanation
Indices: 12932786--12932931 Score: 150
Period size: 57 Copynumber: 2.6 Consensus size: 57
12932776 TTTCTACATT
** * * * **
12932786 TATGTTGTCTTAATGTAATTTATAGTTGCTGTCAAAATGTCTCTTAATGTGCATATA
1 TATGTTGTCAAAATGTAATTAATAGCTGTTGTCAAAATGTCTCTTAATGCACATATA
* * * * * *
12932843 TATGTTGTCCAAATGTAATTTATAGTTGTTGTCATAATGTCTCTTGATGCACATATT
1 TATGTTGTCAAAATGTAATTAATAGCTGTTGTCAAAATGTCTCTTAATGCACATATA
*
12932900 TATGTTGTCAAAATGTGAA-TAATGGCTGTTGT
1 TATGTTGTCAAAATGT-AATTAATAGCTGTTGT
12932932 TTTGATGTCC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
57 74 0.97
58 2 0.03
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (57 bp):
TATGTTGTCAAAATGTAATTAATAGCTGTTGTCAAAATGTCTCTTAATGCACATATA
Found at i:12934409 original size:13 final size:13
Alignment explanation
Indices: 12934391--12934421 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12934381 GTATATTTTT
*
12934391 TTTCATATAAGCA
1 TTTCATATAACCA
12934404 TTTCATATAACCA
1 TTTCATATAACCA
12934417 TTTCA
1 TTTCA
12934422 CTTAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.42
Consensus pattern (13 bp):
TTTCATATAACCA
Found at i:12934963 original size:20 final size:20
Alignment explanation
Indices: 12934900--12935026 Score: 96
Period size: 20 Copynumber: 6.3 Consensus size: 20
12934890 GTATCATAAA
* *
12934900 TGCATAACAAGAGCACCGAAG
1 TGCA-AACAAGGGCACCAAAG
** *
12934921 TGCGGACAGGGGCA-CAAATG
1 TGCAAACAAGGGCACCAAA-G
*
12934941 TGCAAACAAGGGCACCATAG
1 TGCAAACAAGGGCACCAAAG
*
12934961 TGCGAAC-AGGGACACCAAAG
1 TGCAAACAAGGG-CACCAAAG
* * *
12934981 TGTATACAGGGGCACCAAAG
1 TGCAAACAAGGGCACCAAAG
* * *
12935001 TGCAAACAAAGGCATCGAAG
1 TGCAAACAAGGGCACCAAAG
12935021 TGCAAA
1 TGCAAA
12935027 TCCCGTACAA
Statistics
Matches: 81, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
19 7 0.09
20 65 0.80
21 9 0.11
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.10
Consensus pattern (20 bp):
TGCAAACAAGGGCACCAAAG
Found at i:12945078 original size:20 final size:20
Alignment explanation
Indices: 12945048--12945099 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
12945038 AAACTTAATT
*
12945048 TTATGATGATTTGAAG-CATAG
1 TTAT-ATGATTTG-AGTCATAA
*
12945069 TTATATGATTTGAGTGATAA
1 TTATATGATTTGAGTCATAA
12945089 TTATATGATTT
1 TTATATGATTT
12945100 TTTATCAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 22 0.79
21 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (20 bp):
TTATATGATTTGAGTCATAA
Found at i:12947502 original size:27 final size:28
Alignment explanation
Indices: 12947463--12947516 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
12947453 TTTAAATATA
*
12947463 AAGGGGGTTGCTAAGTGGTGATTCCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCCC
12947491 AAGGGGG-TGCTAAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
12947517 GATTCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.24
Consensus pattern (28 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:12947539 original size:33 final size:34
Alignment explanation
Indices: 12947498--12947629 Score: 115
Period size: 33 Copynumber: 3.7 Consensus size: 34
12947488 CCCAAGGGGG
12947498 TGCTAAGTGCTGATTCC-CCGATTCATTGGTGGT
1 TGCTAAGTGCTGATTCCACCGATTCATTGGTGGT
* * *
12947531 TGCCAAGTGCTGATTCCACCGTATATTTAAATGTGAAGGGGGT
1 TGCTAAGTGCTGATTCCACCG---A-TT-CAT-T---GGTGGT
* *
12947574 TGCTAAGTGCTGATTCC-CCGAATCACTGGTGGT
1 TGCTAAGTGCTGATTCCACCGATTCATTGGTGGT
*
12947607 TGCTAAGTGCTGAATCCACCGAT
1 TGCTAAGTGCTGATTCCACCGAT
12947630 AACGGTTAAC
Statistics
Matches: 78, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
33 37 0.47
34 7 0.09
36 1 0.01
37 2 0.03
38 3 0.04
39 3 0.04
40 1 0.01
42 3 0.04
43 21 0.27
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (34 bp):
TGCTAAGTGCTGATTCCACCGATTCATTGGTGGT
Found at i:12947570 original size:103 final size:103
Alignment explanation
Indices: 12947388--12947592 Score: 338
Period size: 103 Copynumber: 2.0 Consensus size: 103
12947378 ATTGAATATG
* * * *
12947388 AAGGGGTTGCTAAGTGCTGATTCTCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGGTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCCAAGTGCTGATTCCACCGTATA
*
12947453 TTTAAATATAAAGGGGGTTGCTAAGTGGTGATTCCCCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
12947491 AAGGGGGTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCCAAGTGCTGATTCCACCGTATA
1 AAGGGGGTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCCAAGTGCTGATTCCACCGTATA
* *
12947556 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCC
12947593 GAATCACTGG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (103 bp):
AAGGGGGTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCCAAGTGCTGATTCCACCGTATA
TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:12948881 original size:6 final size:6
Alignment explanation
Indices: 12948870--12948900 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12948860 TAATCCGGGA
12948870 CTGATT CTGATT CTGATT CTG-TT CTGATT CT
1 CTGATT CTGATT CTGATT CTGATT CTGATT CT
12948901 AATTGGGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (6 bp):
CTGATT
Found at i:12948896 original size:11 final size:12
Alignment explanation
Indices: 12948870--12948900 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
12948860 TAATCCGGGA
12948870 CTGATTCTGATT
1 CTGATTCTGATT
12948882 CTGATTCTG-TT
1 CTGATTCTGATT
12948893 CTGATTCT
1 CTGATTCT
12948901 AATTGGGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (12 bp):
CTGATTCTGATT
Found at i:12951565 original size:17 final size:17
Alignment explanation
Indices: 12951545--12951617 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 17
12951535 TTGGCAGATA
12951545 AGTATCACCTGGCGGAC
1 AGTATCACCTGGCGGAC
* * *
12951562 AGTATCGCCCGGCAGAC
1 AGTATCACCTGGCGGAC
* * *
12951579 AGCATCACCTGGAGAAC
1 AGTATCACCTGGCGGAC
* * *
12951596 AGTATCGCCTGACGGAT
1 AGTATCACCTGGCGGAC
12951613 AGTAT
1 AGTAT
12951618 TACGTACCAG
Statistics
Matches: 41, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (17 bp):
AGTATCACCTGGCGGAC
Found at i:12956086 original size:13 final size:13
Alignment explanation
Indices: 12956070--12956098 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12956060 AGCCCAGATT
12956070 CCATGTTAGAAAA
1 CCATGTTAGAAAA
12956083 CCATGTTAGAAAA
1 CCATGTTAGAAAA
12956096 CCA
1 CCA
12956099 AATATGGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (13 bp):
CCATGTTAGAAAA
Found at i:12961576 original size:3 final size:3
Alignment explanation
Indices: 12961568--12961620 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
12961558 CATTCTCTAT
12961568 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12961616 TTC TT
1 TTC TT
12961621 TCAGATCAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12968955 original size:19 final size:21
Alignment explanation
Indices: 12968930--12968978 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
12968920 TAATTAAGCA
12968930 TAATTAATTA-TTTTAA-CCT
1 TAATTAATTACTTTTAATCCT
*
12968949 TATTTAATTATCTTTTAATCCT
1 TAATTAATTA-CTTTTAATCCT
12968971 TAATTAAT
1 TAATTAAT
12968979 ACAAATGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
21 6 0.24
22 10 0.40
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATTAATTACTTTTAATCCT
Found at i:12973680 original size:20 final size:21
Alignment explanation
Indices: 12973639--12973680 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
12973629 AATATTTATA
*
12973639 TATTAATATAAGTTTTAAAAT
1 TATTAATATAAGTTTCAAAAT
12973660 TATTAAT-TAAG-TTCAATAAT
1 TATTAATATAAGTTTCAA-AAT
12973680 T
1 T
12973681 GAATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (21 bp):
TATTAATATAAGTTTCAAAAT
Found at i:12976941 original size:22 final size:21
Alignment explanation
Indices: 12976906--12976963 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
12976896 AAAGGGTGTC
* * *
12976906 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAAAT
12976927 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATC-TCTAAAAT
* *
12976950 TTCATATCATATCT
1 TACAAATCATATCT
12976964 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:12976954 original size:17 final size:19
Alignment explanation
Indices: 12976934--12976976 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
12976924 GATTACAAAA
12976934 TCATATC-T-TCTAAAATT
1 TCATATCATATCTAAAATT
*
12976951 TCATATCATATCTAAGATT
1 TCATATCATATCTAAAATT
*
12976970 GCATATC
1 TCATATC
12976977 CTTGAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (19 bp):
TCATATCATATCTAAAATT
Found at i:12977663 original size:44 final size:44
Alignment explanation
Indices: 12977490--12977808 Score: 154
Period size: 44 Copynumber: 7.3 Consensus size: 44
12977480 ACCGTCTTTG
* * *
12977490 ATCTGCTCTACTACTGCTTAGGGAGACAGGATATACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCA
* * * ***** *
12977534 ACCTACTCCACTACTGCTCAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCA
* *
12977577 ATCTGCTTCCTACTA-T-CTT-GGGAAGATAGGATTCGT-C-GTCTTCG
1 ATCTGC-TCC-ACTACTGCTTAGGG-AGATAGGA-TC-TACAATCTTCA
*
12977621 ATCTGCTCCACTACTGCTTAAGGAGATAGGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCA
* * * * ***** *
12977665 ACCTACTCCACTGCTGCTCAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCA
* * ** ** **
12977708 ATCTGTTTCC-CTACTACCTT-GGGAAGATAATAT-TCACCGTCTTTG
1 ATCTG-CTCCACTACT-GCTTAGGG-AGATAGGATCT-ACAATCTTCA
* *
12977753 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCA
* *
12977797 ACCTACTCCACT
1 ATCTGCTCCACT
12977809 GCAAACTCAG
Statistics
Matches: 198, Mismatches: 58, Indels: 38
0.67 0.20 0.13
Matches are distributed among these distances:
42 8 0.04
43 42 0.21
44 122 0.62
45 25 0.13
46 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCA
Found at i:12977809 original size:132 final size:132
Alignment explanation
Indices: 12977419--12977810 Score: 608
Period size: 131 Copynumber: 3.0 Consensus size: 132
12977409 TACTGCAACT
* * * *
12977419 TCAGGGAGATAAGG-CTGGTGGTTTAAATCTGTTTCCCTACTACCTCGAGAAGATAAGACTCACC
1 TCAGGGAGAT-AGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAAGATAAGATTCACC
* * *
12977483 GTCTTTGATCTGCTCTACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTAC
65 GTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGC
12977548 TGC
130 TGC
* * * **
12977551 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTT-CCTACTATCTTGGGAAGATAGGATTCGTCG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAAGATAAGATTCACCG
* * *
12977615 TCTTCGATCTGCTCCACTACTGCTTAAGGAGATAGGATCTACAATCTTCAACCTACTCCACTGCT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCT
12977680 GC
131 GC
*
12977682 TCAGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAAGATAATATTCACCG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAAGATAAGATTCACCG
*
12977747 TCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGC
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGC
12977811 AAACTCAGAG
Statistics
Matches: 233, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
131 120 0.52
132 113 0.48
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
TCAGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAAGATAAGATTCACCG
TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCT
GC
Found at i:12978069 original size:45 final size:44
Alignment explanation
Indices: 12977941--12978076 Score: 116
Period size: 45 Copynumber: 3.0 Consensus size: 44
12977931 TCTGCTTTGT
* *
12977941 TGCCAATACAAGAAGACAAGATTTGCTATCTTCAGTCTGCTTCGC
1 TGCCAATAC-AGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
* * * * * *
12977986 TGCAAACT-CAGAGAGGCAAG-GCTGGTGTCTTC-GATCTACTTGGC
1 TGCCAA-TACAGA-AGACAAGATCTGCTATCTTCAG-TCTACTTCGC
* *
12978030 TGCCAATACAGGAAGACAAGATCTGTTATCTTCAGTCTACTCCGC
1 TGCCAATACA-GAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
12978075 TG
1 TG
12978077 TAAATTCAGA
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
43 2 0.03
44 32 0.46
45 33 0.48
46 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (44 bp):
TGCCAATACAGAAGACAAGATCTGCTATCTTCAGTCTACTTCGC
Found at i:12978096 original size:89 final size:89
Alignment explanation
Indices: 12977776--12978114 Score: 347
Period size: 89 Copynumber: 3.8 Consensus size: 89
12977766 CTACTTAGGG
* * * ** * *
12977776 AGACAGGATCTACAATCTTCAACCTACTCCACTGCAAACTCAGAGAGGTC-AGGCTGGTGTTTTC
1 AGACAAGATCTGCTATCTTCAGTCTACTCCGCTGCAAACTCAGAGAGG-CAAGGCTGGTGTCTTC
* * *
12977840 AATCTGCTTCACTGCCAGTATAGGA
65 AATCTGCTTCGCTGCCAATACAGGA
* * * * * * **
12977865 AGACAAGATCTACTGTTTTCAGTCTACTCTGCTGCAACCTCAGGGAGGCAAGGCTGGTGTCTTTG
1 AGACAAGATCTGCTATCTTCAGTCTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCA
* * * *
12977930 CTCTGCTTTGTTGCCAATACAAGA
66 ATCTGCTTCGCTGCCAATACAGGA
* * * *
12977954 AGACAAGATTTGCTATCTTCAGTCTGCTTCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCG
1 AGACAAGATCTGCTATCTTCAGTCTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCA
* *
12978019 ATCTACTTGGCTGCCAATACAGGA
66 ATCTGCTTCGCTGCCAATACAGGA
* * * *** *
12978043 AGACAAGATCTGTTATCTTCAGTCTACTCCGCTGTAAATTCAGAGATATAAGGCTGGTGGCTTCA
1 AGACAAGATCTGCTATCTTCAGTCTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCA
12978108 ATCTGCT
66 ATCTGCT
12978115 CTATTATAAC
Statistics
Matches: 202, Mismatches: 47, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
88 1 0.00
89 201 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (89 bp):
AGACAAGATCTGCTATCTTCAGTCTACTCCGCTGCAAACTCAGAGAGGCAAGGCTGGTGTCTTCA
ATCTGCTTCGCTGCCAATACAGGA
Found at i:12978278 original size:143 final size:143
Alignment explanation
Indices: 12978056--12978380 Score: 393
Period size: 143 Copynumber: 2.3 Consensus size: 143
12978046 CAAGATCTGT
* * * * * * *
12978056 TATCTTCAGTCTACTCCGCTGTAAATTCAGAGATATAAGGCTGGTGGCTTCAATCTGCTCTATTA
1 TATCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCAACTA
* * * * * ** **
12978121 TAACTTCAGAAAGATAAGATCTGTCATAATTTGTAGCTTTAATCTACTCCACTGTAA-TTCTAGG
66 CAACTTAAGAAAGATAAAATCTGCCATAATTTGTAGCTTTAATATACTCCACTACAACAGC-AGG
12978185 GAAATAAGATTCGA
130 GAAATAAGATTCGA
* * *
12978199 TGTCTTCAGTCTGCTCCGCTGTAACTTTAGGGAGATAAGTCTAGTGGCTTCAATCTGCTCAACTA
1 TATCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCAACTA
**
12978264 CAACTTTAAG-AAGATAAAATCTGCCATAATTTGTAGCTTTAATATGTTCCACTACAACAGCAGG
66 CAAC-TTAAGAAAGATAAAATCTGCCATAATTTGTAGCTTTAATATACTCCACTACAACAGCAGG
*
12978328 GAAATAAGATTCGC
130 GAAATAAGATTCGA
* **
12978342 TATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAG
1 TATCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAG
12978381 ACTTGTAACT
Statistics
Matches: 153, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
143 148 0.97
144 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (143 bp):
TATCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCAACTA
CAACTTAAGAAAGATAAAATCTGCCATAATTTGTAGCTTTAATATACTCCACTACAACAGCAGGG
AAATAAGATTCGA
Found at i:12978419 original size:44 final size:44
Alignment explanation
Indices: 12978351--12978647 Score: 213
Period size: 44 Copynumber: 6.7 Consensus size: 44
12978341 CTATCTTCAG
*
12978351 TCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA
* * * * * **
12978395 TCCGCTCCACTGCAACCTCGGGGAGATAGGA-TTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTTAA
* * * * * * * *
12978439 TCTTCTTCACTGTAACTTCAGGGAGATAAGATTTGCCATCTTCAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAA
* ** * * ** * *
12978484 TCTGC-CGCACTGCAATTTTGGGGGGTTAAGACTTGATTTCTTCAG
1 TCTGCTC-CACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAA
*
12978529 TCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA
* ** * * **
12978573 TCTGCTCCACTGCAACTTTAAAGAGATAGGA-TTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTTAA
* *
12978617 TCTGCTCCACTGTAACTTTAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
12978648 TTTGCCATCT
Statistics
Matches: 191, Mismatches: 56, Indels: 12
0.74 0.22 0.05
Matches are distributed among these distances:
43 4 0.02
44 122 0.64
45 64 0.34
46 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA
Found at i:12978422 original size:143 final size:143
Alignment explanation
Indices: 12978131--12978413 Score: 325
Period size: 143 Copynumber: 2.0 Consensus size: 143
12978121 TAACTTCAGA
* * * ** **
12978131 AAGATAAGATCTGTCATAATTTGTAGCTTTAATCTACTCCACTGTAATTCTAGGGAAATAAGATT
1 AAGATAAAATCTGCCATAATTTGTAGCTTTAATATACTCCACTACAAAGCTAGGGAAATAAGATT
* * ** * * ** *
12978196 CGATGTCTTCAGTCTGCTCCGCTGTAACTTTAGGGAGATAAGTCTAGTGGCTTCAATCTGCTCAA
66 CGATATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGTAACTTCAATCCGCTCAA
* *
12978261 CTACAACTTTAAG
131 CTACAACCTCAAG
**
12978274 AAGATAAAATCTGCCATAATTTGTAGCTTTAATATGTTCCACTACAACAGC-AGGGAAATAAGAT
1 AAGATAAAATCTGCCATAATTTGTAGCTTTAATATACTCCACTACAA-AGCTAGGGAAATAAGAT
* * * *
12978338 TCGCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATCCGCTCC
65 TCGATATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGTAACTTCAATCCGCTCA
*
12978403 ACTGCAACCTC
130 ACTACAACCTC
12978414 GGGGAGATAG
Statistics
Matches: 114, Mismatches: 25, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
143 113 0.99
144 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (143 bp):
AAGATAAAATCTGCCATAATTTGTAGCTTTAATATACTCCACTACAAAGCTAGGGAAATAAGATT
CGATATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGTAACTTCAATCCGCTCAA
CTACAACCTCAAG
Found at i:12979009 original size:24 final size:24
Alignment explanation
Indices: 12978977--12979032 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
12978967 CAGATTGCCC
12978977 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
12979001 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
12979025 CCACTGTA
1 CCACTGTA
12979033 CTTTTGGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTCAAT
Found at i:12985898 original size:15 final size:16
Alignment explanation
Indices: 12985880--12985912 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12985870 AAATGTAAAC
12985880 AAATTTAAAAAT-AAT
1 AAATTTAAAAATGAAT
*
12985895 AAATTTGAAAATGAAT
1 AAATTTAAAAATGAAT
12985911 AA
1 AA
12985913 TAAGGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AAATTTAAAAATGAAT
Found at i:12986772 original size:22 final size:21
Alignment explanation
Indices: 12986737--12986794 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
12986727 AAAGGGTATC
* * *
12986737 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
12986758 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
12986781 TGCATATCATATCT
1 TACAAATCATATCT
12986795 AAGATTGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:12986812 original size:14 final size:14
Alignment explanation
Indices: 12986788--12986822 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12986778 GATTGCATAT
*
12986788 CATATCTAAGATTG
1 CATATCCAAGATTG
*
12986802 CTTATCCAAGATTG
1 CATATCCAAGATTG
12986816 CATATCC
1 CATATCC
12986823 TTGAAGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (14 bp):
CATATCCAAGATTG
Found at i:12994509 original size:41 final size:41
Alignment explanation
Indices: 12994395--12994513 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 41
12994385 AGTGATATTC
* * * *** *
12994395 AGGCTTTGTGCCTAGCAGACCTT-ATGCCGGTGAATTTTATC
1 AGGCTTTATGCCTAGCA-AGCTTCATGCCGGTGTATCAGATT
** * *
12994436 AGGCTTTATGCCTAGCTGGCTTTATGCTGGTGTATCAGATT
1 AGGCTTTATGCCTAGCAAGCTTCATGCCGGTGTATCAGATT
*
12994477 AGGCTTTATGCCTAGCAAGCTTCGTGCCGGTGTATCA
1 AGGCTTTATGCCTAGCAAGCTTCATGCCGGTGTATCA
12994514 TATCTAAATT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 3 0.05
41 59 0.95
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (41 bp):
AGGCTTTATGCCTAGCAAGCTTCATGCCGGTGTATCAGATT
Found at i:13002422 original size:41 final size:41
Alignment explanation
Indices: 13002365--13002468 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
13002355 TCAGGGATAT
* * ***
13002365 TCAGGCTCTGTGCCTAGCAGGCCTTATGCCGGTGAATTTTA
1 TCAGGCTTTATGCCTAGCAGGCCTTATGCCGGTGAATCAGA
* * * *
13002406 TCAGGCTTTATGCCTAGCAAGCTTTATGCTGGTGTATCAGA
1 TCAGGCTTTATGCCTAGCAGGCCTTATGCCGGTGAATCAGA
* *
13002447 TCTGACTTTATGCCTAGCAGGC
1 TCAGGCTTTATGCCTAGCAGGC
13002469 TTCGTGCTGG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCCTTATGCCGGTGAATCAGA
Found at i:13002491 original size:41 final size:42
Alignment explanation
Indices: 13002411--13002499 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 42
13002401 TTTTATCAGG
* *
13002411 CTTTATGCCTAGCAAGCTTTATGCTGGTGTATCAGATCT-GA
1 CTTTATGCCTAGCAAGCTTCATGCTGGTGTATAAGATCTGGA
* * *
13002452 CTTTATGCCTAGCAGGCTTCGTGCTGGTGTATAATATCTGGA
1 CTTTATGCCTAGCAAGCTTCATGCTGGTGTATAAGATCTGGA
13002494 -TTTATG
1 CTTTATG
13002500 ATTAGTAGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 40 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (42 bp):
CTTTATGCCTAGCAAGCTTCATGCTGGTGTATAAGATCTGGA
Found at i:13002510 original size:41 final size:41
Alignment explanation
Indices: 13002411--13002511 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 41
13002401 TTTTATCAGG
* * ** *
13002411 CTTTATGCCTAGCAAGCTTTATGCTGGTGTATCAGATCTGA
1 CTTTATGACTAGCAGGCTTCGTGCTGGTGTATAAGATCTGA
* *
13002452 CTTTATGCCTAGCAGGCTTCGTGCTGGTGTATAATATCTGGA
1 CTTTATGACTAGCAGGCTTCGTGCTGGTGTATAAGATCT-GA
* *
13002494 -TTTATGATTAGTAGGCTT
1 CTTTATGACTAGCAGGCTT
13002512 TATGCCGATG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 49 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
CTTTATGACTAGCAGGCTTCGTGCTGGTGTATAAGATCTGA
Found at i:13010374 original size:24 final size:24
Alignment explanation
Indices: 13010342--13010396 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
13010332 TCGGTCACAG
*
13010342 TGAACATGTTAAGTTGTGAGATAT
1 TGAACATGTTAAGTTGTGAAATAT
*
13010366 TGAACATGTTGAGTTGTGAAATAT
1 TGAACATGTTAAGTTGTGAAATAT
*
13010390 TAAACAT
1 TGAACAT
13010397 ATTTTCTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (24 bp):
TGAACATGTTAAGTTGTGAAATAT
Found at i:13018165 original size:14 final size:14
Alignment explanation
Indices: 13018148--13018278 Score: 95
Period size: 14 Copynumber: 9.2 Consensus size: 14
13018138 CCCTATCCTC
*
13018148 TAAACCCTAAATCA
1 TAAACCCTAAACCA
* *
13018162 TAAAACATAAACCA
1 TAAACCCTAAACCA
*
13018176 TAATCCCTAAACCCA
1 TAAACCCTAAA-CCA
* * *
13018191 TAATCCATAATCCA
1 TAAACCCTAAACCA
* *
13018205 TAAA-CCTTAA-GA
1 TAAACCCTAAACCA
*
13018217 TAGTAACTCCTAAACCT
1 TA--AAC-CCTAAACCA
*
13018234 TAAACCCTATACCA
1 TAAACCCTAAACCA
*
13018248 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
13018262 TAAACCCTAAACTA
1 TAAACCCTAAACCA
13018276 TAA
1 TAA
13018279 TAATAATTAA
Statistics
Matches: 89, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
12 3 0.03
13 3 0.03
14 61 0.69
15 15 0.17
16 5 0.06
17 2 0.02
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:13018198 original size:22 final size:22
Alignment explanation
Indices: 13018167--13018210 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13018157 AATCATAAAA
*
13018167 CATAAACCATAATCCCTAAACC
1 CATAAACCATAATCCATAAACC
*
13018189 CATAATCCATAATCCATAAACC
1 CATAAACCATAATCCATAAACC
13018211 TTAAGATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.20
Consensus pattern (22 bp):
CATAAACCATAATCCATAAACC
Found at i:13018239 original size:7 final size:7
Alignment explanation
Indices: 13018225--13018273 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
13018215 GATAGTAACT
13018225 CCTAAAC
1 CCTAAAC
*
13018232 CTTAAAC
1 CCTAAAC
*
13018239 CCTATAC
1 CCTAAAC
* *
13018246 CATATAC
1 CCTAAAC
13018253 CCTAAAC
1 CCTAAAC
*
13018260 CATAAAC
1 CCTAAAC
13018267 CCTAAAC
1 CCTAAAC
13018274 TATAATAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:13018335 original size:7 final size:7
Alignment explanation
Indices: 13018323--13018410 Score: 54
Period size: 7 Copynumber: 12.1 Consensus size: 7
13018313 ACTAGTTAAT
13018323 CTAAACC
1 CTAAACC
13018330 CTAAACC
1 CTAAACC
*
13018337 ATAAA-C
1 CTAAACC
*
13018343 CTAAATC
1 CTAAACC
*
13018350 TTAAAACC
1 CT-AAACC
*
13018358 CTAAAATC
1 CT-AAACC
13018366 CTAAAACC
1 CT-AAACC
13018374 CTAAACC
1 CTAAACC
* *
13018381 CTTAACA
1 CTAAACC
13018388 C-ATAACC
1 CTA-AACC
13018395 TCTAAACC
1 -CTAAACC
*
13018403 TTAAACC
1 CTAAACC
13018410 C
1 C
13018411 CAGCCTTTAA
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
6 5 0.08
7 33 0.52
8 24 0.38
9 1 0.02
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:13018370 original size:16 final size:16
Alignment explanation
Indices: 13018345--13018378 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13018335 CCATAAACCT
*
13018345 AAATCTTAAAACCCTA
1 AAATCCTAAAACCCTA
13018361 AAATCCTAAAACCCTA
1 AAATCCTAAAACCCTA
13018377 AA
1 AA
13018379 CCCTTAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATCCTAAAACCCTA
Found at i:13018860 original size:40 final size:41
Alignment explanation
Indices: 13018816--13019086 Score: 266
Period size: 41 Copynumber: 6.6 Consensus size: 41
13018806 TTTTGTCGCA
* * **
13018816 CTTTTTCAAAAGCGTCGCTAAA-AATAGAGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTAGCGGCG
* * *
13018856 CTTTTTCAAAAACGCCGCTAAAGCCCCAAATCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAG-CCTAGAGCATTAGCGGCG
* * ** * **
13018898 GTTATTGGAAAACGACGCTAAA-AATAGAGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTAGCGGCG
* * *
13018938 CTATTTGAAAAACGCCACTAAAGCCCT-GAGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAG-CCTAGAGCATTAGCGGCG
*
13018979 C-TTTTCTAAAAACGCCACTAAAGCCTAGAGCATTAGCGGCG
1 CTTTTTC-AAAAACGCCGCTAAAGCCTAGAGCATTAGCGGCG
* * *
13019020 CTTTTTGAGAAACGCCGCTAAAGCCCCA-AGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAG-CCTAGAGCATTAGCGGCG
13019061 CCTTTTT-AAAAACGCCGCTAAAGCCT
1 -CTTTTTCAAAAACGCCGCTAAAGCCT
13019087 CGAAAGCTCA
Statistics
Matches: 189, Mismatches: 33, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
40 57 0.30
41 88 0.47
42 44 0.23
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (41 bp):
CTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTAGCGGCG
Found at i:13019008 original size:82 final size:81
Alignment explanation
Indices: 13018840--13019086 Score: 316
Period size: 82 Copynumber: 3.0 Consensus size: 81
13018830 TCGCTAAAAA
* * * *
13018840 TAGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAATCATTAGCGGCGGTTATTG
1 TAGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAAG-CCCAAAGCATTAGCGGCGCTT-TTT
* * **
13018905 GAAAACGACGCTAAA-AA
64 AAAAACGCCGCTAAAGCC
* * **
13018922 TAGAGCATTAGCGGCGCTATTTGAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCGCTTTTCTA
1 TAGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCAAAGCATTAGCGGCGCTTTT-TA
*
13018987 AAAACGCCACTAAAGCC
65 AAAACGCCGCTAAAGCC
* *
13019004 TAGAGCATTAGCGGCGCTTTTTGAGAAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCCTTTTTA
1 TAGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCAAAGCATTAGCGGCG-CTTTTTA
13019069 AAAACGCCGCTAAAGCC
65 AAAACGCCGCTAAAGCC
13019086 T
1 T
13019087 CGAAAGCTCA
Statistics
Matches: 143, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.01
81 29 0.20
82 107 0.75
83 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (81 bp):
TAGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCAAAGCATTAGCGGCGCTTTTTAA
AAACGCCGCTAAAGCC
Found at i:13019052 original size:123 final size:123
Alignment explanation
Indices: 13018842--13019085 Score: 300
Period size: 123 Copynumber: 2.0 Consensus size: 123
13018832 GCTAAAAATA
* * *
13018842 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAATCATTAGCGGCGGTTATTGGA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAAAGCATTAGCGGCGCTTATTGGA
*
13018907 AAACGACGCTAAAAATAGAGCATTAGCGGCG-CTATTTGAAAAACGCCACTAAAGCCCT
66 AAACGACGCTAAAAACAGAGCATTAGCGGCGCCT-TTTGAAAAACGCCACTAAAGCCCT
* * *
13018965 GAGCATTAGCGGCGC-TTTTCTAAAAACGCCACTAAAG-CCTAGAGCATTAGCGGCGCTT-TTTG
1 GAGCATTAGCGGCGCTTTTTC-AAAAACGCCACTAAAGCCCCAAAGCATTAGCGGCGCTTATTGG
* ** * *
13019027 AGAAACGCCGCTAAAGCCCCA-AGCATTAGCGGCGCCTTTTTAAAAACGCCGCTAAAGCC
65 A-AAACGACGCTAAA--AACAGAGCATTAGCGGCGCCTTTTGAAAAACGCCACTAAAGCC
13019086 TCGAAAGCTC
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
121 4 0.04
122 34 0.33
123 63 0.61
124 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (123 bp):
GAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAAAGCATTAGCGGCGCTTATTGGA
AAACGACGCTAAAAACAGAGCATTAGCGGCGCCTTTTGAAAAACGCCACTAAAGCCCT
Found at i:13019499 original size:25 final size:25
Alignment explanation
Indices: 13019471--13019520 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
13019461 TTCAACGTAC
*
13019471 TTAAAAATTCATGTGAAATGCCTTA
1 TTAAAAATTCATGCGAAATGCCTTA
*
13019496 TTAAAAATTCATGCGAAATGTCTTA
1 TTAAAAATTCATGCGAAATGCCTTA
13019521 CCCCCTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (25 bp):
TTAAAAATTCATGCGAAATGCCTTA
Done.