Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 93 of 144
Found at i:28461681 original size:50 final size:50
Alignment explanation
Indices: 28461566--28461814 Score: 302
Period size: 50 Copynumber: 4.8 Consensus size: 50
28461556 GATCATAACA
* ** *
28461566 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
28461617 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACATCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
28461667 TGCCAACT-CCATGTCCCAGGCATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
28461717 TGCCAACGCCACGTCCCAGACATGGTTTTACATGGAACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
*
28461772 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28461815 TCACCCAAAT
Statistics
Matches: 170, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
50 91 0.54
51 35 0.21
53 5 0.03
55 2 0.01
56 37 0.22
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28466049 original size:50 final size:50
Alignment explanation
Indices: 28465881--28466051 Score: 218
Period size: 50 Copynumber: 3.4 Consensus size: 50
28465871 TATCCTAGAT
* * ***
28465881 ATGGTCTTACATGGGAGT-TCTCATATCGGTGCCCATTTCATGTCCCAGAC
1 ATGGTCTTACATGGGA-TCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
** * *
28465931 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
** *
28465981 ATGGTCTTACATAAGATCTCTCATCTCGGTGCCAACGCCATGTCTCAGAC
1 ATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
28466031 ATGGTCTTACATGGGATCTCT
1 ATGGTCTTACATGGGATCTCT
28466052 TTACCCAAAT
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (50 bp):
ATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
Found at i:28471986 original size:50 final size:50
Alignment explanation
Indices: 28471809--28471987 Score: 227
Period size: 50 Copynumber: 3.6 Consensus size: 50
28471799 CAATGTCATA
** ** * *
28471809 TCCTAGATGTGGTCTTACATGGGAGTTCTCATATCGGTGTCC-ATGCCATG
1 TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTG-CCAACGCCATG
* * *
28471859 TCCCAGACATGGTGTTACGA-GGGACCTATCATCTCGGTGCCAACGCCATG
1 TCCTAGACATGGTCTTAC-ATGGGACCTCTCATCTCGGTGCCAACGCCATG
28471909 TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
28471959 TACTAGACATGATCTTACATGGGACCTCT
1 TCCTAGACATGGTCTTACATGGGACCTCT
28471988 TTACCCAAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
49 3 0.03
50 108 0.96
51 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (50 bp):
TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
Found at i:28472788 original size:50 final size:50
Alignment explanation
Indices: 28472729--28472893 Score: 231
Period size: 50 Copynumber: 3.3 Consensus size: 50
28472719 CGGGATGTTA
* * * *
28472729 CAAACATGGTCTAACGGGGGACCTCTCATATCGGTGCCCATGCCATGTCC
1 CAAACATGGTCTTACGGGAGACCTCTCATCTCGGTGCCAATGCCATGTCC
* *
28472779 CAAACATGGTCTTATGGGAGACCTCTCATCTCGGTGCCAACGCCATGTCC
1 CAAACATGGTCTTACGGGAGACCTCTCATCTCGGTGCCAATGCCATGTCC
* ** *
28472829 CAGACATGGTCTTACATGAGACCTCTCGTCTCGGTGCCAATGCCATGTCC
1 CAAACATGGTCTTACGGGAGACCTCTCATCTCGGTGCCAATGCCATGTCC
*
28472879 CAGACATGGTCTTAC
1 CAAACATGGTCTTAC
28472894 ATTGTATCTC
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 103 1.00
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (50 bp):
CAAACATGGTCTTACGGGAGACCTCTCATCTCGGTGCCAATGCCATGTCC
Found at i:28473686 original size:29 final size:29
Alignment explanation
Indices: 28473649--28473779 Score: 86
Period size: 29 Copynumber: 4.5 Consensus size: 29
28473639 AGGATGTTAC
* *
28473649 AACCGTCCCTTTTCACATTCGATGGTCGA
1 AACCATCCCTTTTCACATTCGATAGTCGA
** ** * *
28473678 AACCATCCCTTTTCTTTAACCGATGGTCGT
1 AACCATCCCTTTTC-ACATTCGATAGTCGA
* * *
28473708 CACCATCCGTTTTCATAATT-GATAG-CGA
1 AACCATCCCTTTTCA-CATTCGATAGTCGA
* * *
28473736 AGCTATCCCTTTTCACATTAGATAGTCGA
1 AACCATCCCTTTTCACATTCGATAGTCGA
* *
28473765 AGCTATCCCTTTTCA
1 AACCATCCCTTTTCA
28473780 TTATCTAAGG
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
27 3 0.04
28 18 0.23
29 35 0.44
30 23 0.29
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (29 bp):
AACCATCCCTTTTCACATTCGATAGTCGA
Found at i:28473748 original size:28 final size:30
Alignment explanation
Indices: 28473712--28473780 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
28473702 GGTCGTCACC
*
28473712 ATCCGTTTTCATAATT-GATAG-CGAAGCT
1 ATCCCTTTTCATAATTAGATAGTCGAAGCT
*
28473740 ATCCCTTTTCA-CATTAGATAGTCGAAGCT
1 ATCCCTTTTCATAATTAGATAGTCGAAGCT
28473769 ATCCCTTTTCAT
1 ATCCCTTTTCAT
28473781 TATCTAAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 3 0.08
28 15 0.42
29 18 0.50
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTAGATAGTCGAAGCT
Found at i:28475189 original size:12 final size:12
Alignment explanation
Indices: 28475172--28475198 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28475162 ACGCAAAAAG
28475172 ATTAAATATAAT
1 ATTAAATATAAT
28475184 ATTAAATATAAT
1 ATTAAATATAAT
28475196 ATT
1 ATT
28475199 TACGAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTAAATATAAT
Found at i:28479200 original size:281 final size:281
Alignment explanation
Indices: 28478697--28479258 Score: 1124
Period size: 281 Copynumber: 2.0 Consensus size: 281
28478687 CCAGCGTGTG
28478697 TTATGGATACTCCACAAGTCATGTGAGCATACACGTACAGGATTTGACAGATTACAATTATATGA
1 TTATGGATACTCCACAAGTCATGTGAGCATACACGTACAGGATTTGACAGATTACAATTATATGA
28478762 GTTAGCACACTATGCTTGATCTATCCCGTGTAACATCACTATTTCGAGCCTAGTCAGAACAGTAG
66 GTTAGCACACTATGCTTGATCTATCCCGTGTAACATCACTATTTCGAGCCTAGTCAGAACAGTAG
28478827 TTTTGGGACCACAAATTTTATGAGAAAAAAATTATTTTATTATATTTTTATAGTCTACAATTTCA
131 TTTTGGGACCACAAATTTTATGAGAAAAAAATTATTTTATTATATTTTTATAGTCTACAATTTCA
28478892 CAGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCGACGTTTGGGTACTCAATTTAGTCAAAAG
196 CAGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCGACGTTTGGGTACTCAATTTAGTCAAAAG
28478957 GACTAAATTGTAAAAAGTGAC
261 GACTAAATTGTAAAAAGTGAC
28478978 TTATGGATACTCCACAAGTCATGTGAGCATACACGTACAGGATTTGACAGATTACAATTATATGA
1 TTATGGATACTCCACAAGTCATGTGAGCATACACGTACAGGATTTGACAGATTACAATTATATGA
28479043 GTTAGCACACTATGCTTGATCTATCCCGTGTAACATCACTATTTCGAGCCTAGTCAGAACAGTAG
66 GTTAGCACACTATGCTTGATCTATCCCGTGTAACATCACTATTTCGAGCCTAGTCAGAACAGTAG
28479108 TTTTGGGACCACAAATTTTATGAGAAAAAAATTATTTTATTATATTTTTATAGTCTACAATTTCA
131 TTTTGGGACCACAAATTTTATGAGAAAAAAATTATTTTATTATATTTTTATAGTCTACAATTTCA
28479173 CAGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCGACGTTTGGGTACTCAATTTAGTCAAAAG
196 CAGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCGACGTTTGGGTACTCAATTTAGTCAAAAG
28479238 GACTAAATTGTAAAAAGTGAC
261 GACTAAATTGTAAAAAGTGAC
28479259 AAAGTTGAGT
Statistics
Matches: 281, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
281 281 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (281 bp):
TTATGGATACTCCACAAGTCATGTGAGCATACACGTACAGGATTTGACAGATTACAATTATATGA
GTTAGCACACTATGCTTGATCTATCCCGTGTAACATCACTATTTCGAGCCTAGTCAGAACAGTAG
TTTTGGGACCACAAATTTTATGAGAAAAAAATTATTTTATTATATTTTTATAGTCTACAATTTCA
CAGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCGACGTTTGGGTACTCAATTTAGTCAAAAG
GACTAAATTGTAAAAAGTGAC
Found at i:28480404 original size:50 final size:50
Alignment explanation
Indices: 28480285--28480576 Score: 250
Period size: 50 Copynumber: 5.7 Consensus size: 50
28480275 GGGAATGAGA
* * * *
28480285 TCCCATGTAAGACCATATCTAGGACATGGCAATGGCATCATTGAGATTATGAGAGC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---AGA-TA--AGAGC
* *
28480341 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATAAGAGC
* * * * *
28480391 TCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATAAGAGC
** * * * * * *
28480441 TCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATAAGAGC
* * *
28480491 TCCCATGTAAGACCATATCAGGGATATGGCATTGGCACTACAA-A-AA-A-C
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC--CAAGATAAGAGC
* * *
28480539 ATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28480577 TGTATTATCA
Statistics
Matches: 200, Mismatches: 33, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
48 1 0.00
49 32 0.16
50 124 0.62
51 1 0.00
52 4 0.02
53 3 0.01
56 35 0.17
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATAAGAGC
Found at i:28488780 original size:17 final size:18
Alignment explanation
Indices: 28488754--28488787 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28488744 AGTGCATTGA
28488754 AAGCTCGTTCGG-GTTAG
1 AAGCTCGTTCGGAGTTAG
*
28488771 AAGCTTGTTCGGAGTTA
1 AAGCTCGTTCGGAGTTA
28488788 TATCACACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (18 bp):
AAGCTCGTTCGGAGTTAG
Found at i:28505922 original size:5 final size:5
Alignment explanation
Indices: 28505912--28505940 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28505902 TCTAAACGAT
28505912 AATTC AATTC AATTC AATTC AATTC AATT
1 AATTC AATTC AATTC AATTC AATTC AATT
28505941 TATTAACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTC
Found at i:28507071 original size:26 final size:26
Alignment explanation
Indices: 28507039--28507098 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
28507029 GAATCATTTC
*
28507039 CATTTCCATACTAGGAAACCTACATT
1 CATTTCCATACTAGGAAACCTAAATT
** *
28507065 CATTTCCATTTTTGGAAACCTAAATT
1 CATTTCCATACTAGGAAACCTAAATT
28507091 CATTTCCA
1 CATTTCCA
28507099 AATGATTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (26 bp):
CATTTCCATACTAGGAAACCTAAATT
Found at i:28513173 original size:12 final size:12
Alignment explanation
Indices: 28513146--28513174 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
28513136 ACGAGTCAAT
28513146 TATGGTTTTTAA
1 TATGGTTTTTAA
28513158 -ATGGTTTTTAA
1 TATGGTTTTTAA
28513169 TATGGT
1 TATGGT
28513175 AATTTATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (12 bp):
TATGGTTTTTAA
Found at i:28515987 original size:25 final size:26
Alignment explanation
Indices: 28515931--28515987 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
28515921 AATGGTTGGT
*
28515931 GTTTATATGATTAAATTTATGCATGGT
1 GTTTATATGATTAAATTTAT-CATGGA
28515958 GTTTATATGATT-AATTTGAT-ATGGA
1 GTTTATATGATTAAATTT-ATCATGGA
28515983 GTTTA
1 GTTTA
28515988 GCAAAGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 9 0.32
26 5 0.18
27 14 0.50
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (26 bp):
GTTTATATGATTAAATTTATCATGGA
Found at i:28524985 original size:24 final size:23
Alignment explanation
Indices: 28524936--28524997 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
28524926 TCATTTTTAC
**
28524936 TTTA-TTTTAATTTTAATTTTAA
1 TTTATTTTTAATTTTAAACTTAA
**
28524958 TTTAGTTTTTAATTTTAAACTTCT
1 TTTA-TTTTTAATTTTAAACTTAA
*
28524982 TTTATTTTTATTTTTA
1 TTTATTTTTAATTTTA
28524998 TTTTTCTCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 4 0.12
23 11 0.33
24 18 0.55
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTTTAATTTTAAACTTAA
Found at i:28527349 original size:16 final size:16
Alignment explanation
Indices: 28527328--28527368 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
28527318 AAAGGTATAA
28527328 CATTTACAATATCTAT
1 CATTTACAATATCTAT
* *
28527344 CATTTACAATCTTTAT
1 CATTTACAATATCTAT
*
28527360 CTTTTACAA
1 CATTTACAA
28527369 AGGCTAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (16 bp):
CATTTACAATATCTAT
Found at i:28530098 original size:16 final size:16
Alignment explanation
Indices: 28530079--28530112 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28530069 TGATATTTGG
* *
28530079 TAGTTTTACTATTATT
1 TAGTTTTAATAATATT
28530095 TAGTTTTAATAATATT
1 TAGTTTTAATAATATT
28530111 TA
1 TA
28530113 AATGATTGTG
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:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
TAGTTTTAATAATATT
Found at i:28536075 original size:28 final size:31
Alignment explanation
Indices: 28536026--28536090 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 31
28536016 GTCCTTATGA
*
28536026 ACATTCCAGTAGTCAAGATAGTGCTTGGCGG
1 ACATTCCAGTAGTCAAGATAGTCCTTGGCGG
28536057 ACATTCCA-TA-T-AAGATAGTCCTTGGCGG
1 ACATTCCAGTAGTCAAGATAGTCCTTGGCGG
28536085 AC-TTCC
1 ACATTCC
28536091 CTTTTCTAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 4 0.12
28 18 0.55
29 1 0.03
30 2 0.06
31 8 0.24
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (31 bp):
ACATTCCAGTAGTCAAGATAGTCCTTGGCGG
Found at i:28538948 original size:4 final size:4
Alignment explanation
Indices: 28538935--28538972 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
28538925 CGGTCATGGG
28538935 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
28538973 GGCCAGATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:28541430 original size:28 final size:29
Alignment explanation
Indices: 28541382--28541481 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 29
28541372 TTTTCTAGAA
*
28541382 TATATATTTTTGAAAAATTAAGT-TTTTTT
1 TATA-ATTTTTGAAAAATTAAATATTTTTT
* *
28541411 TATAATTTTTTAAAAGTTAAATACTTTTTT
1 TATAATTTTTGAAAAATTAAATA-TTTTTT
* *
28541441 TA-AATTTTTATGAAAAATT--TTATTTTTA
1 TATAA-TTTT-TGAAAAATTAAATATTTTTT
28541469 TATAATATTTTGA
1 TATAAT-TTTTGA
28541482 TTTTTTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
28 26 0.45
29 13 0.22
30 12 0.21
31 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (29 bp):
TATAATTTTTGAAAAATTAAATATTTTTT
Found at i:28541478 original size:18 final size:19
Alignment explanation
Indices: 28541444--28541486 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
28541434 CTTTTTTTAA
28541444 ATTTTTATGAAAAATTTT-
1 ATTTTTATGAAAAATTTTG
*
28541462 ATTTTTAT-ATAATATTTTG
1 ATTTTTATGA-AAAATTTTG
28541481 ATTTTT
1 ATTTTT
28541487 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 15 0.68
19 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
ATTTTTATGAAAAATTTTG
Found at i:28541555 original size:21 final size:21
Alignment explanation
Indices: 28541529--28541585 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
28541519 AAAATTTTTT
*
28541529 TAATTATTTATATATTGTATA
1 TAATTATTTATATATTGTAAA
*
28541550 TAATTATTTATAT-TTTTAAA
1 TAATTATTTATATATTGTAAA
28541570 TAATATATTATATATA
1 TAAT-TATT-TATATA
28541586 ATATTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.29
21 17 0.55
22 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATTATTTATATATTGTAAA
Found at i:28541592 original size:24 final size:25
Alignment explanation
Indices: 28541547--28541593 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
28541537 TATATATTGT
* * *
28541547 ATATAATTATTTATATTTTTAAATA
1 ATATAATTATATATAATATTAAATA
28541572 ATAT-ATTATATATAATATTAAA
1 ATATAATTATATATAATATTAAA
28541594 AAACAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATAATTATATATAATATTAAATA
Found at i:28558363 original size:18 final size:16
Alignment explanation
Indices: 28558321--28558363 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
28558311 TTTCGTTCGT
28558321 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
28558338 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
28558357 TTTCAAA
1 TTTCAAA
28558364 ACGTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:28574272 original size:52 final size:52
Alignment explanation
Indices: 28574145--28574429 Score: 308
Period size: 52 Copynumber: 5.4 Consensus size: 52
28574135 ACCCTTCAGG
* * * *
28574145 GGTATTTCTGTAATTCTACCC-TTCAGAGGTATTTCAGTAATTCTACC-CTTCAGA
1 GGTATTTCGGTAATT-TACCCATTAAG-GGTATTTCAGTAATT-TACCTGTTGA-A
* * * ** * *
28574199 GGTATTTCAGTAGTTTTCCCATTAAGGGTATTTTGGCAATTTACCTGTCGACA
1 GGTATTTCGGTAATTTACCCATTAAGGGTATTTCAGTAATTTACCTGTTGA-A
*
28574252 -GTATTTCGGTAATTTACCCATTGAGGGTATTTCAGTAATTTACCTGTTGAA
1 GGTATTTCGGTAATTTACCCATTAAGGGTATTTCAGTAATTTACCTGTTGAA
* * *
28574303 GGCATTTCGATAATTTACCCATTAAGGGTATTTCAGTAATTTACCCGTTGAA
1 GGTATTTCGGTAATTTACCCATTAAGGGTATTTCAGTAATTTACCTGTTGAA
* ** *
28574355 GGCATTTTAGTAATTTACCCATTCAGGGTATTTCAGTAATTTACCTGTTG-A
1 GGTATTTCGGTAATTTACCCATTAAGGGTATTTCAGTAATTTACCTGTTGAA
*
28574406 GTGTATTTTGGTAATTTACCCATT
1 G-GTATTTCGGTAATTTACCCATT
28574430 GAGACTCATA
Statistics
Matches: 197, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
51 3 0.02
52 158 0.80
53 19 0.10
54 17 0.09
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (52 bp):
GGTATTTCGGTAATTTACCCATTAAGGGTATTTCAGTAATTTACCTGTTGAA
Found at i:28574281 original size:26 final size:26
Alignment explanation
Indices: 28574144--28574432 Score: 242
Period size: 26 Copynumber: 11.0 Consensus size: 26
28574134 TACCCTTCAG
* *
28574144 GGGTATTTCTGTAATTCTACCC-TTCA
1 GGGTATTTCAGTAATT-TACCCATTGA
*
28574170 GAGGTATTTCAGTAATTCTACCC-TTCA
1 G-GGTATTTCAGTAATT-TACCCATTGA
* * *
28574197 GAGGTATTTCAGTAGTTTTCCCATTAA
1 G-GGTATTTCAGTAATTTACCCATTGA
** * ** *
28574224 GGGTATTTTGGCAATTTACCTGTCGA
1 GGGTATTTCAGTAATTTACCCATTGA
** *
28574250 CAGTATTTCGGTAATTTACCCATTGA
1 GGGTATTTCAGTAATTTACCCATTGA
**
28574276 GGGTATTTCAGTAATTTACCTGTTGA
1 GGGTATTTCAGTAATTTACCCATTGA
* * *
28574302 AGGCATTTC-GATAATTTACCCATTAA
1 GGGTATTTCAG-TAATTTACCCATTGA
*
28574328 GGGTATTTCAGTAATTTACCCGTTGA
1 GGGTATTTCAGTAATTTACCCATTGA
* * * *
28574354 AGGCATTTTAGTAATTTACCCATTCA
1 GGGTATTTCAGTAATTTACCCATTGA
**
28574380 GGGTATTTCAGTAATTTACCTGTTGA
1 GGGTATTTCAGTAATTTACCCATTGA
* **
28574406 GTGTATTTTGGTAATTTACCCATTGA
1 GGGTATTTCAGTAATTTACCCATTGA
28574432 G
1 G
28574433 ACTCATAACG
Statistics
Matches: 209, Mismatches: 50, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
25 1 0.00
26 163 0.78
27 45 0.22
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (26 bp):
GGGTATTTCAGTAATTTACCCATTGA
Found at i:28581757 original size:26 final size:26
Alignment explanation
Indices: 28581722--28581908 Score: 169
Period size: 26 Copynumber: 7.2 Consensus size: 26
28581712 CGATAGTTTC
*
28581722 CCCATTGAGGGTA-TTCTGGTAATTTA
1 CCCATCGAGGGTATTTC-GGTAATTTA
* * *
28581748 CCCTTCGAGGGTATTTTGATAATTTA
1 CCCATCGAGGGTATTTCGGTAATTTA
* ** *
28581774 ACCATATAGGGTATTTCAGTAATTTA
1 CCCATCGAGGGTATTTCGGTAATTTA
*
28581800 CCCATCGAGGGTATTTCGGTACTTTA
1 CCCATCGAGGGTATTTCGGTAATTTA
* * * **
28581826 CCCGTTGAAGGTATTTCAATAATTTA
1 CCCATCGAGGGTATTTCGGTAATTTA
* * *
28581852 GCTATTGAGGGTATTTCGGTAATTTA
1 CCCATCGAGGGTATTTCGGTAATTTA
* * * *
28581878 CCCGTTGAGTGTATTTCGGTAGTTTA
1 CCCATCGAGGGTATTTCGGTAATTTA
28581904 CCCAT
1 CCCAT
28581909 TAAGACTCAT
Statistics
Matches: 126, Mismatches: 34, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
26 124 0.98
27 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (26 bp):
CCCATCGAGGGTATTTCGGTAATTTA
Found at i:28581828 original size:78 final size:78
Alignment explanation
Indices: 28581722--28581906 Score: 223
Period size: 78 Copynumber: 2.4 Consensus size: 78
28581712 CGATAGTTTC
* **
28581722 CCCATTGAGGGTA-TTCTGGTAATTTACCC-TTCGAGGGTATTTTGATAATTTAACCATAT-AGG
1 CCCATTGAGGGTATTTC-GGTAATTTACCCGTT-GAAGGTATTTCAATAATTTAACCAT-TGAGG
28581784 GTATTTCAGTAATTTA
63 GTATTTCAGTAATTTA
* * * *
28581800 CCCATCGAGGGTATTTCGGTACTTTACCCGTTGAAGGTATTTCAATAATTTAGCTATTGAGGGTA
1 CCCATTGAGGGTATTTCGGTAATTTACCCGTTGAAGGTATTTCAATAATTTAACCATTGAGGGTA
*
28581865 TTTCGGTAATTTA
66 TTTCAGTAATTTA
* * *
28581878 CCCGTTGAGTGTATTTCGGTAGTTTACCC
1 CCCATTGAGGGTATTTCGGTAATTTACCC
28581907 ATTAAGACTC
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
78 86 0.93
79 5 0.05
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (78 bp):
CCCATTGAGGGTATTTCGGTAATTTACCCGTTGAAGGTATTTCAATAATTTAACCATTGAGGGTA
TTTCAGTAATTTA
Found at i:28581839 original size:52 final size:52
Alignment explanation
Indices: 28581740--28581908 Score: 189
Period size: 52 Copynumber: 3.2 Consensus size: 52
28581730 GGGTATTCTG
* * * * * *
28581740 GTAATTTACCCTTCGAGGGTATTTTGATAATTTAACCATAT-AGGGTATTTCA
1 GTAATTTACCCATCGAGGGTATTTCGGTAATTTACCCGT-TGAAGGTATTTCA
*
28581792 GTAATTTACCCATCGAGGGTATTTCGGTACTTTACCCGTTGAAGGTATTTCA
1 GTAATTTACCCATCGAGGGTATTTCGGTAATTTACCCGTTGAAGGTATTTCA
* * * * *
28581844 ATAATTTAGCTATTGAGGGTATTTCGGTAATTTACCCGTTG-AGTGTATTTCG
1 GTAATTTACCCATCGAGGGTATTTCGGTAATTTACCCGTTGAAG-GTATTTCA
*
28581896 GTAGTTTACCCAT
1 GTAATTTACCCAT
28581909 TAAGACTCAT
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
51 3 0.03
52 95 0.97
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (52 bp):
GTAATTTACCCATCGAGGGTATTTCGGTAATTTACCCGTTGAAGGTATTTCA
Found at i:28593670 original size:20 final size:19
Alignment explanation
Indices: 28593645--28593686 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28593635 TTCGAAATTG
*
28593645 AAAATACATGTTTGTTGTGA
1 AAAATA-ATATTTGTTGTGA
*
28593665 AAAATAGTATTTGTTGTGA
1 AAAATAATATTTGTTGTGA
28593684 AAA
1 AAA
28593687 CTTATTTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTGTTGTGA
Found at i:28593694 original size:17 final size:18
Alignment explanation
Indices: 28593655--28593695 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
28593645 AAAATACATG
28593655 TTTGTTGTGAAAAATAGTA
1 TTTGTTGTGAAAAATA-TA
*
28593674 TTTGTTGTGAAAACT-TA
1 TTTGTTGTGAAAAATATA
28593691 TTTGT
1 TTTGT
28593696 GTTCGTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
19 14 0.67
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTGTTGTGAAAAATATA
Found at i:28594479 original size:27 final size:27
Alignment explanation
Indices: 28594448--28594524 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
28594438 TATAACGGTC
* *
28594448 ATTCTATCCTTC-GGGTGTATTTTAGTA
1 ATTCTACCCTTCAGGG-GTATTTCAGTA
*
28594475 GTTCTACCCTTCAGGGGTATTTCAGTA
1 ATTCTACCCTTCAGGGGTATTTCAGTA
28594502 ATTCTACCCTTCAGGGGTATTTC
1 ATTCTACCCTTCAGGGGTATTTC
28594525 GATAGTTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 42 0.93
28 3 0.07
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (27 bp):
ATTCTACCCTTCAGGGGTATTTCAGTA
Found at i:28594567 original size:26 final size:26
Alignment explanation
Indices: 28594489--28594750 Score: 267
Period size: 26 Copynumber: 10.0 Consensus size: 26
28594479 TACCCTTCAG
* *
28594489 GGGTATTTCAGTAATTCTACCC-TTCA
1 GGGTATTTCGGTAATT-TACCCATTGA
* * *
28594515 GGGGTATTTCGATAGTTTTCCCATTGA
1 -GGGTATTTCGGTAATTTACCCATTGA
*
28594542 GGGTATGTT-GGTAATTTACCCTTTGA
1 GGGTAT-TTCGGTAATTTACCCATTGA
* * **
28594568 GGGTATTTCGATAATTTACCTATCAA
1 GGGTATTTCGGTAATTTACCCATTGA
* * *
28594594 GGGTATTTTGATAATTTACCCATCGA
1 GGGTATTTCGGTAATTTACCCATTGA
* *
28594620 GAGTATTTCAGTAATTTACCCATTGA
1 GGGTATTTCGGTAATTTACCCATTGA
*
28594646 GGGTATTTTGGTAATTTACCCATTGA
1 GGGTATTTCGGTAATTTACCCATTGA
* ** *
28594672 GGTTATTTCAATAATTTACCCACTGA
1 GGGTATTTCGGTAATTTACCCATTGA
* * *
28594698 GGATGTTTCTGTAATTTACCCATTGA
1 GGGTATTTCGGTAATTTACCCATTGA
*
28594724 GGGTATTTCTGTAATTTACCCATTGA
1 GGGTATTTCGGTAATTTACCCATTGA
28594750 G
1 G
28594751 ACCCATAATG
Statistics
Matches: 195, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
25 2 0.01
26 175 0.90
27 18 0.09
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (26 bp):
GGGTATTTCGGTAATTTACCCATTGA
Found at i:28599831 original size:138 final size:138
Alignment explanation
Indices: 28599674--28601179 Score: 1942
Period size: 138 Copynumber: 11.0 Consensus size: 138
28599664 AAGAACATAG
* * *
28599674 ATATAATTAATATATGAAATTGATTCATACAAAATATTAAATGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * *
28599739 AATATAAATAGTTACATTAATTAATTTCGTTCAAAATATAAAAGACATGAAAATTAATATTATTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
*
28599804 TGGAAATA
131 TGGAAAGA
* *
28599812 ATATAATTAATATATGAAATTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
** * * * *
28599877 AATATAAACTGTTATATTAACTAATTTCGATCAAAATATAAAATACATGGAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
28599942 TGG-AAGA
131 TGGAAAGA
* * *
28599949 ATATAATTAATATATGAACTTGATTCCTACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* ** * *
28600014 AGTATAAACTGTTATATTAACTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
28600079 TGG-AAGA
131 TGGAAAGA
* * *
28600086 ATATAATTAATATATGAATTTGATTCCTACAAAATATTAATTGTATATATTTTACCAAATTTAAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * * * * *
28600151 AATATAAACAACTATATTAATTAATTGCAGTGAAAATAAAAAAGATATGAAAATTAATATTCCTC
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
*
28600216 TCGAAAGA
131 TGGAAAGA
* * *
28600224 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * * * *
28600289 AATATAAACAACTATATTAATTAATTCCAGTGAGAATA-AAAAGGATATGAAAATTAATATTCCT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA-GACATGAAAATTAATATTCTT
* *
28600353 CTCGAAAGA
130 TTGGAAAGA
* * *
28600362 ATATAATTAATATATGAATTTGATTTATACAAAATATTCATTGTATATA---TACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* *
28600424 AATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTCCTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
*
28600489 TCGAAAGA
131 TGGAAAGA
* * * *
28600497 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATACATTTTACCCATTTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
28600562 AATATAAA-AAGTTATATTAACTAATTTCGGTC-AAATATAAAAGAGATG--GA--AA-ATTC-T
66 AATATAAACAA-TTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
28600619 TTGGAAAGA
130 TTGGAAAGA
* * *
28600628 ATATAATTAATATATGGATTTGATTCATATAAAATATTAATTGTATATGTTTTACCGAA--T-TT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * *
28600690 -AT-TAAACAATTATATTAATTAATTTTGGCCAAAATATAAAAGATATTAAAATTAATATTCTCT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
*
28600753 TGGAAACA
131 TGGAAAGA
* * * *
28600761 ATATAATTAATTTATCAAATTGATTCATACAAAATATTAATTATATATATTTTACCGAA-TTAGT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTA-T
* ** *
28600825 TAATATAAACAATTATATTAATTATTTTCTATCAAAATATAAAAGGCATGAAAATTAATATTCTT
65 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
28600890 TTGGAAAGA
130 TTGGAAAGA
*
28600899 ATATAATTAATAAATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAA-TTACT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTA-T
* * * * * *
28600963 TAATATAAAAAATTATATTAATTAATTTAGATCAAACTATAAAAGACATGGAAATTAAT-TGTCC
65 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATAT-TCT
28601027 TTTGGAAAGA
129 TTTGGAAAGA
* *
28601037 ATATAATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * * * *
28601102 AATATAAATAGTTTTATTAATTACTTTCGATCAAAGTATAAAAGACATG-AAATTAATATTATTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
*
28601166 TGAAAAGA
131 TGGAAAGA
28601174 ATATAA
1 ATATAA
28601180 ATCTTTTTTT
Statistics
Matches: 1227, Mismatches: 118, Indels: 47
0.88 0.08 0.03
Matches are distributed among these distances:
126 22 0.02
127 18 0.01
128 2 0.00
129 2 0.00
131 63 0.05
132 8 0.01
133 62 0.05
134 1 0.00
135 118 0.10
136 6 0.00
137 298 0.24
138 624 0.51
139 3 0.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTT
TGGAAAGA
Found at i:28599912 original size:67 final size:67
Alignment explanation
Indices: 28599841--28600052 Score: 169
Period size: 67 Copynumber: 3.1 Consensus size: 67
28599831 TTGATTCATA
28599841 CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCG
1 CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCG
28599906 AT
66 AT
* * ** ** ** * * * * ** * *
28599908 CAAAATATAAAATACATGGAAATTAAT--ATTCTTTTGGAAGAATATAATTAATATATGAACTTG
1 CAAAATATTAATTGTATATATTTTACTGAATT-TATT--AA-TATA-AACTGTTATATTAAC-TA
* *
28599971 ATTCCTA-
60 ATTTCGAT
*
28599978 CAAAATATTAATTGTATATATTTTACTGAATTTATTAGTATAAACTGTTATATTAACTAATTTCG
1 CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCG
*
28600043 GT
66 AT
28600045 CAAAATAT
1 CAAAATAT
28600053 AAAAGACATG
Statistics
Matches: 98, Mismatches: 38, Indels: 18
0.64 0.25 0.12
Matches are distributed among these distances:
65 3 0.03
66 8 0.08
67 37 0.38
68 5 0.05
69 4 0.04
70 29 0.30
71 9 0.09
72 3 0.03
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (67 bp):
CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCG
AT
Found at i:28599982 original size:70 final size:70
Alignment explanation
Indices: 28599908--28600122 Score: 174
Period size: 70 Copynumber: 3.1 Consensus size: 70
28599898 TAATTTCGAT
28599908 CAAAATATAAAATACATGGAAATTAATATTCTTTTGGAAGAATATAATTAATATATGAACTTGAT
1 CAAAATATAAAATACATGGAAATTAATATTCTTTTGGAAGAATATAATTAATATATGAACTTGAT
28599973 TCCTA
66 TCCTA
* * ** ** ** * * * * ** * *
28599978 CAAAATATTAATTGTATATATTTTACTGAATT-TATT---AGTATA-AACTGTTATATTAAC-TA
1 CAAAATATAAAATACATGGAAATTAAT--ATTCTTTTGGAAGAATATAATTAATATATGAACTTG
*
28600037 ATTTCGGT-
64 A-TTC-CTA
* *
28600045 CAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAGAATATAATTAATATATGAATTTGAT
1 CAAAATATAAAATACATGGAAATTAATATTCTTTTGGAAGAATATAATTAATATATGAACTTGAT
28600110 TCCTA
66 TCCTA
28600115 CAAAATAT
1 CAAAATAT
28600123 TAATTGTATA
Statistics
Matches: 98, Mismatches: 36, Indels: 22
0.63 0.23 0.14
Matches are distributed among these distances:
65 3 0.03
66 5 0.05
67 31 0.32
68 6 0.06
69 6 0.06
70 39 0.40
71 5 0.05
72 3 0.03
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.39
Consensus pattern (70 bp):
CAAAATATAAAATACATGGAAATTAATATTCTTTTGGAAGAATATAATTAATATATGAACTTGAT
TCCTA
Found at i:28601037 original size:675 final size:680
Alignment explanation
Indices: 28599674--28601179 Score: 2029
Period size: 675 Copynumber: 2.2 Consensus size: 680
28599664 AAGAACATAG
* *
28599674 ATATAATTAATATATGAAATTGATTCATACAAAATATTAAATGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATA--TTACTGAATTTATT
* *
28599739 AATATAAATAGTTACATTAATTAATTTCGTTCAAAATATAAAAGACATGAAAATTAATATTATTT
64 AATATAAATAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTA-TT
* * * * **
28599804 TGGAAATAATATAATTAATATATGAAATTGATTCATACAAAATATTAATTGTATATATTTTACTG
128 TCGAAAGAATATAATTAATATATGAAATTGATTCATACAAAATATTAATTATATACATTTTACCC
** *
28599869 AATTTATTAATATAAACTGTTATATTAACTAATTTCGATCAAAATATAAAATACATGGAAATTAA
193 AATTTATTAATATAAAAAGTTATATTAACTAATTTCGATCAAAATATAAAAGACATGG-AA-TAA
*
28599934 TATTCTTTTGGAAGAATATAATTAATATATGAACTTGATTCCTACAAAATATTAATTGTATATAT
256 TATTCTTTTGGAAGAATATAATTAATATATGAACTTGATTCATACAAAATATTAATTGTATATAT
* * *
28599999 TTTACTGAATTTATTAGTATAAACTGTTATATTAACTAATTTCGGTCAAAATATAAAAGACATGG
321 TTTACCGAATTTATTAG-ATAAAC--TTATATTAACTAATTTCGGCCAAAATATAAAAGACATGA
* * * * * *
28600064 AAATTAATATTCTTTTGGAAGAATATAATTAATATATGAATTTGATTCCTACAAAATATTAATTG
383 AAATTAATATTCTCTTGGAACAATATAATTAATATATCAAATTGATTCATACAAAATATTAATTA
*
28600129 TATATATTTTACCAAATTTAATAATATAAACAACTATATTAATTAATTGCAGTGAAAATAAAAAA
448 TATATATTTTACCAAATTTAATAATATAAACAACTATATTAATTAATTGCAGTCAAAATAAAAAA
* *
28600194 GATATGAAAATTAATATTCCTCTCGAAAGAATATAATTAATATATAAATTTGATTCATACAAAAT
513 GACATGAAAATTAATATTCCTCTCGAAAGAATATAATTAATAAATAAATTTGATTCATACAAAAT
* *
28600259 ATTAATTGTATATATTTTACCAAATTTAATAATATAAACAACTATATTAATTAATTCCAGTGAGA
578 ATTAATTGTATATATTTTACCAAATTTAATAATATAAAAAACTATATTAATTAATTCCAGTCAGA
*
28600324 ATAAAAAGGATATGAAAATTAATATTCCTCTCGAAAGA
643 ATAAAAAGGACATGAAAATTAATATTCCTCTCGAAAGA
* * **
28600362 ATATAATTAATATATGAATTTGATTTATACAAAATATTCATTGTATATA-TACCAAATTTATTAA
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTACTGAATTTATTAA
* * * * *
28600426 TATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTCCTTTC
66 TATAAATAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATT-ATTTC
* *
28600491 GAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATACATTTTACCCAT
130 GAAAGAATATAATTAATATATGAAATTGATTCATACAAAATATTAATTATATACATTTTACCCAA
* *
28600556 TTTATTAATATAAAAAGTTATATTAACTAATTTCGGTC-AAATATAAAAGAGATGG-A-AA-ATT
195 TTTATTAATATAAAAAGTTATATTAACTAATTTCGATCAAAATATAAAAGACATGGAATAATATT
* * * *
28600617 C-TTTGGAAAGAATATAATTAATATATGGATTTGATTCATATAAAATATTAATTGTATATGTTTT
260 CTTTTGG-AAGAATATAATTAATATATGAACTTGATTCATACAAAATATTAATTGTATATATTTT
* * * *
28600681 ACCGAATTTATTA-A-ACAA-TTATATTAATTAATTTTGGCCAAAATATAAAAGATATTAAAATT
324 ACCGAATTTATTAGATA-AACTTATATTAACTAATTTCGGCCAAAATATAAAAGACATGAAAATT
*
28600743 AATATTCTCTTGGAAACAATATAATTAATTTATCAAATTGATTCATACAAAATATTAATTATATA
388 AATATTCTCTTGG-AACAATATAATTAATATATCAAATTGATTCATACAAAATATTAATTATATA
* * * * * * *
28600808 TATTTTACCGAA-TTAGTTAATATAAACAATTATATTAATTATTTTCTA-TCAAAATATAAAAGG
452 TATTTTACCAAATTTA-ATAATATAAACAACTATATTAATTAATTGC-AGTCAAAATAAAAAAGA
* * * *
28600871 CATGAAAATTAATATTCTTTTGGAAAGAATATAATTAATAAATGAATTTGATTCATACAAAATAT
515 CATGAAAATTAATATTCCTCTCGAAAGAATATAATTAATAAATAAATTTGATTCATACAAAATAT
* * * *
28600936 TAATTGTATATATTTTACCGAA-TTACTTAATATAAAAAATTATATTAATTAATT-TAGATCA-A
580 TAATTGTATATATTTTACCAAATTTA-ATAATATAAAAAACTATATTAATTAATTCCAG-TCAGA
* * *
28600998 ACTATAAAA-GACATGGAAATTAAT-TGTCCTTTGGAAAGA
643 A-TA-AAAAGGACATGAAAATTAATAT-TCCTCTCGAAAGA
*
28601037 ATATAATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATA--TTACTGAATTTATT
* * *
28601102 AATATAAATAGTTTTATTAATTACTTTCGATCAAAGTATAAAAGACATG-AAATTAATATTATTT
64 AATATAAATAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTATTT
*
28601166 TGAAAAGAATATAA
129 CG-AAAGAATATAA
28601180 ATCTTTTTTT
Statistics
Matches: 721, Mismatches: 82, Indels: 41
0.85 0.10 0.05
Matches are distributed among these distances:
674 61 0.08
675 273 0.38
676 10 0.01
677 25 0.03
678 58 0.08
679 68 0.09
680 2 0.00
682 1 0.00
684 15 0.02
685 163 0.23
688 45 0.06
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (680 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTACTGAATTTATTAA
TATAAATAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTATTTCG
AAAGAATATAATTAATATATGAAATTGATTCATACAAAATATTAATTATATACATTTTACCCAAT
TTATTAATATAAAAAGTTATATTAACTAATTTCGATCAAAATATAAAAGACATGGAATAATATTC
TTTTGGAAGAATATAATTAATATATGAACTTGATTCATACAAAATATTAATTGTATATATTTTAC
CGAATTTATTAGATAAACTTATATTAACTAATTTCGGCCAAAATATAAAAGACATGAAAATTAAT
ATTCTCTTGGAACAATATAATTAATATATCAAATTGATTCATACAAAATATTAATTATATATATT
TTACCAAATTTAATAATATAAACAACTATATTAATTAATTGCAGTCAAAATAAAAAAGACATGAA
AATTAATATTCCTCTCGAAAGAATATAATTAATAAATAAATTTGATTCATACAAAATATTAATTG
TATATATTTTACCAAATTTAATAATATAAAAAACTATATTAATTAATTCCAGTCAGAATAAAAAG
GACATGAAAATTAATATTCCTCTCGAAAGA
Found at i:28610069 original size:13 final size:13
Alignment explanation
Indices: 28610030--28610080 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
28610020 AGTTCTTCAT
28610030 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
28610043 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
28610056 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
28610069 TGCTTTTGAAAA
1 TGCTTTTGAAAA
28610081 ACTTAAGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:28614551 original size:27 final size:27
Alignment explanation
Indices: 28614440--28614556 Score: 94
Period size: 27 Copynumber: 4.4 Consensus size: 27
28614430 TGCCCTTGAC
* * *
28614440 GGGTAAAATGACTGAAATA-CCACTATA
1 GGGTAAAATAACTGAAATACCCCCGA-A
* * * *
28614467 GGATAAAATGACCGAGATACCCCCGAA
1 GGGTAAAATAACTGAAATACCCCCGAA
* * *
28614494 GGGTAGAAT-ACTGAAATACTCTCGAA
1 GGGTAAAATAACTGAAATACCCCCGAA
* * *
28614520 AGGTAAAATAACTGAATTACCCCCGTA
1 GGGTAAAATAACTGAAATACCCCCGAA
28614547 GGGTAAAATA
1 GGGTAAAATA
28614557 TGGAAATAAC
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
26 20 0.29
27 46 0.66
28 4 0.06
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.20
Consensus pattern (27 bp):
GGGTAAAATAACTGAAATACCCCCGAA
Found at i:28614578 original size:26 final size:27
Alignment explanation
Indices: 28614544--28614770 Score: 129
Period size: 27 Copynumber: 8.5 Consensus size: 27
28614534 AATTACCCCC
*
28614544 GTAGGGTAAAAT-ATGGA-AATAACCTT
1 GTAGGGTAAAATGAT-CATAATAACCTT
**
28614570 GTAGGGTAAAATGATCATAATGCCCTT
1 GTAGGGTAAAATGATCATAATAACCTT
* * ** *
28614597 GTAGGGTAAAATGACCGTAATGCCCCT
1 GTAGGGTAAAATGATCATAATAACCTT
* * * ** *
28614624 GTAAGGTAAAATGACCGTAATGCCCCT
1 GTAGGGTAAAATGATCATAATAACCTT
* * ** *
28614651 GTAGGGTAAAATTATCGTAATGCCCCT
1 GTAGGGTAAAATGATCATAATAACCTT
* * *
28614678 GTAGGGTAAAATGACCGTAA-AACCCCT
1 GTAGGGTAAAATGATCATAATAA-CCTT
* ** *
28614705 GTAGGGTAAAATGATCGTAATGCCCCT
1 GTAGGGTAAAATGATCATAATAACCTT
* * * **
28614732 ATAGGG-AAAATTATCGTAATGCCCTT
1 GTAGGGTAAAATGATCATAATAACCTT
28614758 GTAGGGTAAAATG
1 GTAGGGTAAAATG
28614771 GCTGTAATAC
Statistics
Matches: 174, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
26 36 0.21
27 138 0.79
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (27 bp):
GTAGGGTAAAATGATCATAATAACCTT
Found at i:28614604 original size:27 final size:27
Alignment explanation
Indices: 28614569--28614953 Score: 305
Period size: 27 Copynumber: 14.4 Consensus size: 27
28614559 GAAATAACCT
* *
28614569 TGTAGGGTAAAATGATCATAATGCCCT
1 TGTAGGGTAAAATGATCGTAATGCCCC
*
28614596 TGTAGGGTAAAATGACCGTAATGCCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
* *
28614623 TGTAAGGTAAAATGACCGTAATGCCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
*
28614650 TGTAGGGTAAAATTATCGTAATGCCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
* **
28614677 TGTAGGGTAAAATGACCGTAAAACCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
28614704 TGTAGGGTAAAATGATCGTAATGCCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
* * *
28614731 TATAGGG-AAAATTATCGTAATGCCCT
1 TGTAGGGTAAAATGATCGTAATGCCCC
* * *
28614757 TGTAGGGTAAAATG-GCTGTAATACCAC
1 TGTAGGGTAAAATGATC-GTAATGCCCC
* * *
28614784 TATCA-GGTAAAATGACCGTAATACCCC
1 TGT-AGGGTAAAATGATCGTAATGCCCC
*** * * ** *
28614811 CACATGGTAAAATAATCGTAATATCCT
1 TGTAGGGTAAAATGATCGTAATGCCCC
* * * * * * *
28614838 TGGAAGGT-AAATGACCATTATACCGC
1 TGTAGGGTAAAATGATCGTAATGCCCC
* * *
28614864 -ATAGGGTAAAATGATCATAATACCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
* * * * * *
28614890 TATAGGGTAAAATGAACGGAATACTCT
1 TGTAGGGTAAAATGATCGTAATGCCCC
* *
28614917 TGTATGGTAAAATCA-CTGTAATGCCCC
1 TGTAGGGTAAAATGATC-GTAATGCCCC
28614944 TGTAGGGTAA
1 TGTAGGGTAA
28614954 GTGACCATTT
Statistics
Matches: 288, Mismatches: 62, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
25 4 0.01
26 52 0.18
27 230 0.80
28 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TGTAGGGTAAAATGATCGTAATGCCCC
Found at i:28614645 original size:54 final size:54
Alignment explanation
Indices: 28614519--28614953 Score: 317
Period size: 54 Copynumber: 8.1 Consensus size: 54
28614509 ATACTCTCGA
* * * * * ** *
28614519 AAGGTAAAATAACTG-AATTACCCCCGTAGGGTAAAAT-ATGGAAATAACCTTGT
1 AAGGTAAAATGACCGTAA-TACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGT
* * * * * *
28614572 AGGGTAAAATGATCATAATGCCCTTGTAGGGTAAAATGACCGTAATGCCCCTGT
1 AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGT
* *
28614626 AAGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATTATCGTAATGCCCCTGT
1 AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGT
* * *
28614680 AGGGTAAAATGACCGTAAAACCCCTGTAGGGTAAAATGATCGTAATGCCCCTAT
1 AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGT
* * * * * * * * *
28614734 -AGGGAAAATTATCGTAATGCCCTTGTAGGGTAAAATG-GCTGTAATACCACTAT
1 AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATC-GTAATGCCCCTGT
* *** * * ** * *
28614787 CAGGTAAAATGACCGTAATACCCCCACATGGTAAAATAATCGTAATATCCTTGG
1 AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGT
* * * * * * *
28614841 AAGGT-AAATGACCATTATACCGC-ATAGGGTAAAATGATCATAATACCCCTAT
1 AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGT
* * * * * * *
28614893 AGGGTAAAATGAACGGAATACTCTTGTATGGTAAAATCA-CTGTAATGCCCCTGT
1 AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATC-GTAATGCCCCTGT
*
28614947 AGGGTAA
1 AAGGTAA
28614954 GTGACCATTT
Statistics
Matches: 297, Mismatches: 77, Indels: 15
0.76 0.20 0.04
Matches are distributed among these distances:
52 26 0.09
53 94 0.32
54 176 0.59
55 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (54 bp):
AAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGT
Found at i:28614672 original size:81 final size:81
Alignment explanation
Indices: 28614571--28614953 Score: 396
Period size: 81 Copynumber: 4.8 Consensus size: 81
28614561 AATAACCTTG
* * *
28614571 TAGGGTAAAATGATCATAATGCCCTTGTAGGGTAAAATGACCGTAATGCCCCTGTAAGGTAAAAT
1 TAGGGTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAAT
* *
28614636 GACCGTAATGCCCCTG
66 GACCGTAATACCCCTA
* * *
28614652 TAGGGTAAAATTATCGTAATGCCCCTGTAGGGTAAAATGACCGTAAAACCCCTGTAGGGTAAAAT
1 TAGGGTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAAT
* *
28614717 GATCGTAATGCCCCTA
66 GACCGTAATACCCCTA
* * * * *
28614733 TAGGG-AAAATTATCGTAATGCCCTTGTAGGGTAAAATGGCTGTAATACCACTATCA-GGTAAAA
1 TAGGGTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCCTGT-AGGGTAAAA
*
28614796 TGACCGTAATACCCCCA
65 TGACCGTAATACCCCTA
* * * ** * * * * * *
28614813 CATGGTAAAATAATCGTAATATCCTTGGAAGGT-AAATGACCATTATACCGC-ATAGGGTAAAAT
1 TAGGGTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAAT
* *
28614876 GATCATAATACCCCTA
66 GACCGTAATACCCCTA
* * * * * * * *
28614892 TAGGGTAAAATGAACGGAATACTCTTGTATGGTAAAATCACTGTAATGCCCCTGTAGGGTAA
1 TAGGGTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAA
28614954 GTGACCATTT
Statistics
Matches: 249, Mismatches: 48, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
78 1 0.00
79 47 0.19
80 92 0.37
81 109 0.44
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (81 bp):
TAGGGTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAAT
GACCGTAATACCCCTA
Found at i:28614820 original size:107 final size:108
Alignment explanation
Indices: 28614599--28614904 Score: 289
Period size: 107 Copynumber: 2.9 Consensus size: 108
28614589 ATGCCCTTGT
* * * *
28614599 AGGGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATT
1 AGGGTAAAATGATCGTAATGCCCCTATAAGGGAAAATGACCGTAATGCCCCTGTAGGGTAAAATG
* * * ***
28614664 ATCGTAATGCCCCTGTAGGGTAAAATGACCGTAAAACCCCTGT
66 ATCGTAATACCACTATAGGGTAAAATGACCGTAAAACCCCCAC
* * *
28614707 AGGGTAAAATGATCGTAATGCCCCTAT-AGGGAAAATTATCGTAATGCCCTTGTAGGGTAAAATG
1 AGGGTAAAATGATCGTAATGCCCCTATAAGGGAAAATGACCGTAATGCCCCTGTAGGGTAAAATG
* *
28614771 -GCTGTAATACCACTATCA-GGTAAAATGACCGTAATACCCCCAC
66 ATC-GTAATACCACTAT-AGGGTAAAATGACCGTAAAACCCCCAC
* * ** * ** * * * * * *
28614814 ATGGTAAAATAATCGTAATATCCTTGGAA-GGTAAATGACCATTATACCGC-ATAGGGTAAAATG
1 AGGGTAAAATGATCGTAATGCCCCTATAAGGGAAAATGACCGTAATGCCCCTGTAGGGTAAAATG
* *
28614877 ATCATAATACCCCTATAGGGTAAAATGA
66 ATCGTAATACCACTATAGGGTAAAATGA
28614905 ACGGAATACT
Statistics
Matches: 159, Mismatches: 34, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
105 1 0.01
106 34 0.21
107 97 0.61
108 27 0.17
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (108 bp):
AGGGTAAAATGATCGTAATGCCCCTATAAGGGAAAATGACCGTAATGCCCCTGTAGGGTAAAATG
ATCGTAATACCACTATAGGGTAAAATGACCGTAAAACCCCCAC
Found at i:28614873 original size:25 final size:26
Alignment explanation
Indices: 28614843--28614900 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
28614833 ATCCTTGGAA
* *
28614843 GGTAAATGACCATTATACCGC-ATAG
1 GGTAAATGACCATAATACCCCTATAG
*
28614868 GGTAAAATGATCATAATACCCCTATAG
1 GGT-AAATGACCATAATACCCCTATAG
28614895 GGTAAA
1 GGTAAA
28614901 ATGAACGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 3 0.11
26 18 0.64
27 7 0.25
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (26 bp):
GGTAAATGACCATAATACCCCTATAG
Found at i:28615006 original size:23 final size:23
Alignment explanation
Indices: 28614976--28615085 Score: 85
Period size: 24 Copynumber: 4.7 Consensus size: 23
28614966 CCTCTTGAGA
* *
28614976 TTAAATGATTGATTTTTCTGTGG
1 TTAAATGACTGATTTGTCTGTGG
*
28614999 TTAAATGACTGATTTGTCTGTGT
1 TTAAATGACTGATTTGTCTGTGG
** *
28615022 TTGGTATGACTGATTTGTCTGTGT
1 TT-AAATGACTGATTTGTCTGTGG
** * * *
28615046 TTGGTATGACCGATTTGTATGTGAT
1 TT-AAATGACTGATTTGTCTGTG-G
*
28615071 TTGAATGACTGATTT
1 TTAAATGACTGATTT
28615086 TGAGCACGGC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
23 22 0.29
24 51 0.67
25 3 0.04
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (23 bp):
TTAAATGACTGATTTGTCTGTGG
Found at i:28615035 original size:24 final size:24
Alignment explanation
Indices: 28615003--28615085 Score: 123
Period size: 24 Copynumber: 3.5 Consensus size: 24
28614993 CTGTGGTTAA
28615003 ATGACTGATTTGTCTGTGTTTGGT
1 ATGACTGATTTGTCTGTGTTTGGT
28615027 ATGACTGATTTGTCTGTGTTTGGT
1 ATGACTGATTTGTCTGTGTTTGGT
* * *
28615051 ATGACCGATTTGTATGTGATTT-GA
1 ATGACTGATTTGTCTGTG-TTTGGT
28615075 ATGACTGATTT
1 ATGACTGATTT
28615086 TGAGCACGGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 51 0.94
25 3 0.06
ACGTcount: A:0.18, C:0.08, G:0.27, T:0.47
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGTTTGGT
Found at i:28615265 original size:26 final size:26
Alignment explanation
Indices: 28615212--28615265 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
28615202 CATATTACTA
* *
28615212 GCAGCTTTGCTGCGATACTGCTGCTG
1 GCAGCTTTGCTGCGATACTACTGATG
*
28615238 GCAGCTTTGCTGCGATGCTACTGATG
1 GCAGCTTTGCTGCGATACTACTGATG
28615264 GC
1 GC
28615266 TTTGAGCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.26, G:0.31, T:0.30
Consensus pattern (26 bp):
GCAGCTTTGCTGCGATACTACTGATG
Found at i:28615297 original size:32 final size:32
Alignment explanation
Indices: 28615256--28615458 Score: 248
Period size: 32 Copynumber: 6.4 Consensus size: 32
28615246 GCTGCGATGC
* * *
28615256 TACTGATGGCTTTGAGCTGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
28615288 TACTGATGGCTTTGTGCTGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
28615320 TACTGATGCCTTTGTGCCGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * * *
28615352 TACTGATGCCTTTGTGTCGATTATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * *
28615384 TACTGATGG-TTGTGTACCGATCATATCACTGC
1 TACTGATGGCTT-TGTGCCGATCATATTACTGT
* *
28615416 TACTAATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
28615447 TACTTATGGCTT
1 TACTGATGGCTT
28615459 GTAGCCATTC
Statistics
Matches: 150, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
31 13 0.09
32 135 0.90
33 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:28618520 original size:30 final size:30
Alignment explanation
Indices: 28618479--28618535 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
28618469 TTTAAAGATT
28618479 GATCTTCGTTCTAGCTACTATCAGTTACGA
1 GATCTTCGTTCTAGCTACTATCAGTTACGA
*
28618509 GATCTTTGTTCTAGCTACTATCAGTTA
1 GATCTTCGTTCTAGCTACTATCAGTTA
28618536 TGAGTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (30 bp):
GATCTTCGTTCTAGCTACTATCAGTTACGA
Found at i:28620955 original size:206 final size:206
Alignment explanation
Indices: 28620601--28621010 Score: 775
Period size: 206 Copynumber: 2.0 Consensus size: 206
28620591 AGTATCACCC
* *
28620601 TGGAAGAAAGTTCTTCAGTTCTGTCACAAAGGAAAGTTAAGTCCATGATTTATCGGGCTGTAAGA
1 TGGAAGAAAGTTATTCAGTTATGTCACAAAGGAAAGTTAAGTCCATGATTTATCGGGCTGTAAGA
28620666 GATTACTGAAAGAATCGACCTTGTTGCGTATTGGTTAGCTTTACTATCAGAATTCGAAAAGATTC
66 GATTACTGAAAGAATCGACCTTGTTGCGTATTGGTTAGCTTTACTATCAGAATTCGAAAAGATTC
*
28620731 ATAATGTTTTTCATGTGTCTATGTTACGATGTTACCGATCTGACCCTTCACATGTTATCTCCTCG
131 ATAATGTCTTTCATGTGTCTATGTTACGATGTTACCGATCTGACCCTTCACATGTTATCTCCTCG
28620796 ACATGTCGAAA
196 ACATGTCGAAA
28620807 TGGAAGAAAGTTATTCAGTTATGTCACAAAGGAAAGTTAAGTCCATGATTTATCGGGCTGTAAGA
1 TGGAAGAAAGTTATTCAGTTATGTCACAAAGGAAAGTTAAGTCCATGATTTATCGGGCTGTAAGA
*
28620872 GATTACTGAAAGAATCGGCCTTGTTGCGTATTGGTTAGCTTTACTATCAGAATTCGAAAAGATTC
66 GATTACTGAAAGAATCGACCTTGTTGCGTATTGGTTAGCTTTACTATCAGAATTCGAAAAGATTC
*
28620937 ATAATGTCTTTCATGTGTCTATGTTACGATGTTACCGATCTGACCCTTCACATGTTTTCTCCTCG
131 ATAATGTCTTTCATGTGTCTATGTTACGATGTTACCGATCTGACCCTTCACATGTTATCTCCTCG
28621002 ACATGTCGA
196 ACATGTCGA
28621011 GATTTAGCTT
Statistics
Matches: 199, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
206 199 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (206 bp):
TGGAAGAAAGTTATTCAGTTATGTCACAAAGGAAAGTTAAGTCCATGATTTATCGGGCTGTAAGA
GATTACTGAAAGAATCGACCTTGTTGCGTATTGGTTAGCTTTACTATCAGAATTCGAAAAGATTC
ATAATGTCTTTCATGTGTCTATGTTACGATGTTACCGATCTGACCCTTCACATGTTATCTCCTCG
ACATGTCGAAA
Found at i:28621564 original size:20 final size:20
Alignment explanation
Indices: 28621541--28621585 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
28621531 TGTGTAATTT
28621541 TTAAAGTTTTTAAAGGTTAA
1 TTAAAGTTTTTAAAGGTTAA
28621561 TT-AAGTTTTTAAAGGTTAA
1 TTAAAGTTTTTAAAGGTTAA
28621580 TTAAAG
1 TTAAAG
28621586 ATCATACAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (20 bp):
TTAAAGTTTTTAAAGGTTAA
Found at i:28624022 original size:55 final size:55
Alignment explanation
Indices: 28623957--28624067 Score: 152
Period size: 55 Copynumber: 2.0 Consensus size: 55
28623947 GGCACAAGGA
* * * * *
28623957 CGTGTAAGGTTATTTCGAGGGGTACATGACTTGGCACAC-AGGCATGTAGCTTGGC
1 CGTGTAAGGTTATTTCGAAGGCTACACGACCTGGCACACGA-GCATATAGCTTGGC
*
28624012 CGTGTAAGGTTATTTCGAAGGCTACACGACCTGGCACACGAGCATATGGCTTGGC
1 CGTGTAAGGTTATTTCGAAGGCTACACGACCTGGCACACGAGCATATAGCTTGGC
28624067 C
1 C
28624068 ATGTGAGCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
55 48 0.98
56 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.25
Consensus pattern (55 bp):
CGTGTAAGGTTATTTCGAAGGCTACACGACCTGGCACACGAGCATATAGCTTGGC
Found at i:28632218 original size:25 final size:25
Alignment explanation
Indices: 28632153--28632221 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
28632143 CGAATTGTAG
*
28632153 ATCGGTATGCTCTCACGAGCTATAA
1 ATCGGTATGCTCTCATGAGCTATAA
28632178 ATCGGTATGCTCTCATGAGCTATAA
1 ATCGGTATGCTCTCATGAGCTATAA
28632203 ATCGGTATGCTCTCATGAG
1 ATCGGTATGCTCTCATGAG
28632222 TTGTAGATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (25 bp):
ATCGGTATGCTCTCATGAGCTATAA
Found at i:28649523 original size:39 final size:40
Alignment explanation
Indices: 28649478--28649649 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
28649468 GCTCCTCGTT
* * *
28649478 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
28649518 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
28649557 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
28649597 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
28649637 CAAATGCCTTCGG
1 CAAATGCCTTCGG
28649650 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28649578 original size:40 final size:39
Alignment explanation
Indices: 28649480--28649702 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
28649470 TCCTCGTTCA
* * * *
28649480 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
28649519 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28649558 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
28649598 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
28649638 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
28649679 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28649703 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:28649662 original size:80 final size:79
Alignment explanation
Indices: 28649478--28649702 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
28649468 GCTCCTCGTT
* * * * *
28649478 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
28649542 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
28649557 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
28649622 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
28649637 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
28649701 GA
63 GA
28649703 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:28649711 original size:41 final size:41
Alignment explanation
Indices: 28649634--28649711 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28649624 TTTGTATCTC
* * *
28649634 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28649675 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28649712 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28652475 original size:25 final size:25
Alignment explanation
Indices: 28652438--28652501 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
28652428 AAGTACATAA
28652438 ATGCTCATACGAGCCA-AGAATCGGT
1 ATGCTCATACGAGCCATAG-ATCGGT
* *
28652463 ATGCTCACT-CGAGCTATAGATTGGT
1 ATGCTCA-TACGAGCCATAGATCGGT
28652488 ATGCTC-TCACGAGC
1 ATGCTCAT-ACGAGC
28652502 TATAAATCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 1 0.03
25 29 0.88
26 3 0.09
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (25 bp):
ATGCTCATACGAGCCATAGATCGGT
Found at i:28652502 original size:25 final size:25
Alignment explanation
Indices: 28652456--28652542 Score: 102
Period size: 25 Copynumber: 3.5 Consensus size: 25
28652446 ACGAGCCAAG
* *
28652456 AATCGGTATGCTCACTCGAGCTATA
1 AATCGGTATGCTCTCACGAGCTATA
* *
28652481 GATTGGTATGCTCTCACGAGCTATA
1 AATCGGTATGCTCTCACGAGCTATA
* * * *
28652506 AATCAGTTTGCTTTCATGAGCTATA
1 AATCGGTATGCTCTCACGAGCTATA
28652531 AATCGGTATGCT
1 AATCGGTATGCT
28652543 TTTACGAGAT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (25 bp):
AATCGGTATGCTCTCACGAGCTATA
Found at i:28657435 original size:20 final size:19
Alignment explanation
Indices: 28657410--28657463 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
28657400 TAAATTTAAT
*
28657410 TTAATATTAAGATAATCATA
1 TTAATATTAAGATAAT-AAA
*
28657430 TTAATATTAAAATAATAAA
1 TTAATATTAAGATAATAAA
* *
28657449 ATAGTATTAAGATAA
1 TTAATATTAAGATAA
28657464 GTATGAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (19 bp):
TTAATATTAAGATAATAAA
Found at i:28659444 original size:6 final size:6
Alignment explanation
Indices: 28659429--28659487 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
28659419 TTTAATTAGT
* * * * *
28659429 TTATTC TTATTG TTATTA TTACTA TTATTA TTATTA TTATCA TTATCA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
*
28659477 TTATCA TTATT
1 TTATTA TTATT
28659488 CATATGAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (6 bp):
TTATTA
Found at i:28659447 original size:9 final size:9
Alignment explanation
Indices: 28659429--28659487 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
28659419 TTTAATTAGT
*
28659429 TTATTCTTA
1 TTATTATTA
*
28659438 TTGTTATTA
1 TTATTATTA
*
28659447 TTACTATTA
1 TTATTATTA
28659456 TTATTATTA
1 TTATTATTA
*
28659465 TTATCATTA
1 TTATTATTA
* *
28659474 TCATTATCA
1 TTATTATTA
28659483 TTATT
1 TTATT
28659488 CATATGAGGT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (9 bp):
TTATTATTA
Found at i:28672360 original size:6 final size:6
Alignment explanation
Indices: 28672324--28672351 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28672314 TATATTTTCA
28672324 TATATG TATATG TATATG TATATG TATA
1 TATATG TATATG TATATG TATATG TATA
28672352 CATGTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:28674234 original size:15 final size:15
Alignment explanation
Indices: 28674210--28674241 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28674200 TATGCATGCA
*
28674210 AAATATAAAAGACAT
1 AAATACAAAAGACAT
28674225 AAATACAAAAGACAT
1 AAATACAAAAGACAT
28674240 AA
1 AA
28674242 TAGTGAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:28680706 original size:39 final size:40
Alignment explanation
Indices: 28680612--28680778 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 40
28680602 TGTTTGGATA
* *
28680612 AAAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGACACTTTTTG
* *
28680652 AAAAACGTCGCTATAGATC-ACGCATTAGCGGCACTTTTT-
1 AAAAACGCCGCTATAGATCGA-GCATTAGCGACACTTTTTG
* * * *
28680691 AAAAACGCCACTATAGGTCGAGCTTTAGTGGAGC-C-TTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAG-CGA-CACTTTTTG
* * *
28680731 AAAAATGCCGCTATAGGTCGACCATTAGC-ACCACTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGA-CACTTTTTG
28680771 AAAAACGC
1 AAAAACGC
28680779 TGCAAAAAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.02
39 28 0.27
40 72 0.70
41 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCGAGCATTAGCGACACTTTTTG
Found at i:28680743 original size:79 final size:80
Alignment explanation
Indices: 28680612--28680778 Score: 214
Period size: 79 Copynumber: 2.1 Consensus size: 80
28680602 TGTTTGGATA
* * *
28680612 AAAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGAAAAACGTCGCTATAGATC-ACGCA
1 AAAAACGCCACTATAGATCGAGCATTAGTGACGCCTTTTGAAAAACGCCGCTATAGATCGAC-CA
**
28680676 TTAGCGGCACTTTTT-
65 TTAGCACCACTTTTTG
* * * *
28680691 AAAAACGCCACTATAGGTCGAGCTTTAGTGGA-GCCTTTTGAAAAATGCCGCTATAGGTCGACCA
1 AAAAACGCCACTATAGATCGAGCATTAGT-GACGCCTTTTGAAAAACGCCGCTATAGATCGACCA
28680755 TTAGCACCACTTTTTG
65 TTAGCACCACTTTTTG
28680771 AAAAACGC
1 AAAAACGC
28680779 TGCAAAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 64 0.84
80 12 0.16
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (80 bp):
AAAAACGCCACTATAGATCGAGCATTAGTGACGCCTTTTGAAAAACGCCGCTATAGATCGACCAT
TAGCACCACTTTTTG
Found at i:28681003 original size:154 final size:152
Alignment explanation
Indices: 28680685--28681009 Score: 372
Period size: 154 Copynumber: 2.1 Consensus size: 152
28680675 ATTAGCGGCA
* * *
28680685 CTTTTTAAAAACGCCACTATAGGTCGAGCTTTAGTGGAGCCTTTTGAAAAATGCCGCTATAGGTC
1 CTTTTTAAAAACGCCGCTATAGATCGAGCTTTAGCGGAGCCTTTTG-AAAATGCCGCTATAGGTC
* * *
28680750 GACCATTAGCACCACTTTTTGAAAAACGCTGCAAAAAAATTAAGCATAACCCGTCGTTTTATGTT
65 GACCATTAGCACCACTTTTTGAAAAACGCCGCAAAAAAATTAAACACAACCCGTCGTTTTATGTT
28680815 GAGATTTGATGGCATTAGCAGTG
130 GAGATTTGATGGCATTAGCAGTG
* * * *
28680838 -TTTTTCAAAAAACACCGCTATAGATCGAGCTTTAGCGGCGCTTTTTTG-AAATCGCTGCTATAG
1 CTTTTT--AAAAACGCCGCTATAGATCGAGCTTTAGCGGAGC-CTTTTGAAAAT-GCCGCTATAG
* * * * *
28680901 GTCGATCATTAGCGACGA-TTTTTTAAAAACGCCGC-AAAAAATTAAACACAACGCTGTTGTTTT
62 GTCGACCATTAGC-ACCACTTTTTGAAAAACGCCGCAAAAAAATTAAACACAAC-CCGTCGTTTT
* **
28680964 ATGTTGAGCTTT-AGTGGCATTAGTGGTG
125 ATGTTGAGATTTGA-TGGCATTAGCAGTG
28680992 CTTTTTGAAAAACGCCGC
1 CTTTTT-AAAAACGCCGC
28681010 AAAAAATATT
Statistics
Matches: 144, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
152 5 0.03
153 20 0.14
154 106 0.74
155 13 0.09
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (152 bp):
CTTTTTAAAAACGCCGCTATAGATCGAGCTTTAGCGGAGCCTTTTGAAAATGCCGCTATAGGTCG
ACCATTAGCACCACTTTTTGAAAAACGCCGCAAAAAAATTAAACACAACCCGTCGTTTTATGTTG
AGATTTGATGGCATTAGCAGTG
Found at i:28681157 original size:14 final size:14
Alignment explanation
Indices: 28681138--28681185 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
28681128 TAAAAGATAT
28681138 AATATTAATTTTAA
1 AATATTAATTTTAA
*
28681152 AATATTAA-ATT-A
1 AATATTAATTTTAA
* *
28681164 AGTACTAATTTTAA
1 AATATTAATTTTAA
28681178 AATATTAA
1 AATATTAA
28681186 ATTAATTATC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
AATATTAATTTTAA
Found at i:28681232 original size:13 final size:14
Alignment explanation
Indices: 28681202--28681247 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
28681192 TATCATTACA
28681202 GTTTAGGGTATATG
1 GTTTAGGGTATATG
28681216 GTTTAGGGTAT-TG
1 GTTTAGGGTATATG
* *
28681229 GTTTAGGGTTTAAG
1 GTTTAGGGTATATG
28681243 GTTTA
1 GTTTA
28681248 AGAGTTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.41
14 17 0.59
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTATATG
Found at i:28681282 original size:15 final size:15
Alignment explanation
Indices: 28681264--28681297 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28681254 ACTATTTTAA
*
28681264 GGTTTATAGATTATG
1 GGTTTAGAGATTATG
*
28681279 GGTTTAGGGATTATG
1 GGTTTAGAGATTATG
28681294 GGTT
1 GGTT
28681298 AAGGGTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (15 bp):
GGTTTAGAGATTATG
Found at i:28681284 original size:22 final size:23
Alignment explanation
Indices: 28681234--28681284 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
28681224 TATTGGTTTA
28681234 GGGTTTAAGGTTTAAGAGTTACT
1 GGGTTTAAGGTTTAAGAGTTACT
**
28681257 -ATTTTAAGGTTTATAGA-TTA-T
1 GGGTTTAAGGTTTA-AGAGTTACT
28681278 GGGTTTA
1 GGGTTTA
28681285 GGGATTATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 5
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.05
22 18 0.82
23 3 0.14
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (23 bp):
GGGTTTAAGGTTTAAGAGTTACT
Found at i:28681302 original size:15 final size:15
Alignment explanation
Indices: 28681272--28681302 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28681262 AAGGTTTATA
*
28681272 GATTATGGGTTTAGG
1 GATTATGGGTTAAGG
28681287 GATTATGGGTTAAGG
1 GATTATGGGTTAAGG
28681302 G
1 G
28681303 TTGGAGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (15 bp):
GATTATGGGTTAAGG
Found at i:28682533 original size:16 final size:17
Alignment explanation
Indices: 28682507--28682564 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 17
28682497 AATTTATATA
28682507 TTAAATAATTTCAAATT
1 TTAAATAATTTCAAATT
* *
28682524 TTAAA-GATTTAAAATT
1 TTAAATAATTTCAAATT
28682540 TTAAATAATTTTCAAGATT
1 TTAAATAA-TTTCAA-ATT
28682559 TTAAAT
1 TTAAAT
28682565 TTTATCTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 14 0.41
17 6 0.18
18 5 0.15
19 9 0.26
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAATAATTTCAAATT
Found at i:28682609 original size:22 final size:22
Alignment explanation
Indices: 28682584--28682629 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
28682574 TTCTTTTAAA
**
28682584 TATTAATTAAAATTTAAAAAAT
1 TATTAATTAAAATGAAAAAAAT
* *
28682606 TATTTATTTAAATGAAAAAAAT
1 TATTAATTAAAATGAAAAAAAT
28682628 TA
1 TA
28682630 AACTATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TATTAATTAAAATGAAAAAAAT
Found at i:28682715 original size:18 final size:17
Alignment explanation
Indices: 28682678--28682712 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
28682668 TATATAACTG
28682678 ATTGTTTTTTAATTTAT
1 ATTGTTTTTTAATTTAT
28682695 ATTG-TTTTTAATTTAT
1 ATTGTTTTTTAATTTAT
28682711 AT
1 AT
28682713 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
ATTGTTTTTTAATTTAT
Found at i:28682851 original size:14 final size:14
Alignment explanation
Indices: 28682832--28682858 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28682822 CGTTCGTAAT
28682832 ATGAAAATCCAACG
1 ATGAAAATCCAACG
28682846 ATGAAAATCCAAC
1 ATGAAAATCCAAC
28682859 ACAAAGCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (14 bp):
ATGAAAATCCAACG
Found at i:28691268 original size:27 final size:27
Alignment explanation
Indices: 28691238--28691293 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
28691228 ATATATAGGG
28691238 TGTTGAATGATGGTGGAAAAGGGCCCA
1 TGTTGAATGATGGTGGAAAAGGGCCCA
28691265 TGTTGAATGATGGTGGAAAAGGGCCCA
1 TGTTGAATGATGGTGGAAAAGGGCCCA
28691292 TG
1 TG
28691294 AAGTCAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.11, G:0.38, T:0.23
Consensus pattern (27 bp):
TGTTGAATGATGGTGGAAAAGGGCCCA
Found at i:28706000 original size:50 final size:50
Alignment explanation
Indices: 28705881--28706120 Score: 311
Period size: 50 Copynumber: 4.8 Consensus size: 50
28705871 AATAATAGCA
* * ** * *
28705881 TGCCAAAGCCATGTCCCAGACATGGTATTACATGGGATGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
28705932 TGCCCATGCTATGTCCCAGACATGGTCTTAC-GGTGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTCGG
*
28705982 TGCCAACGCCATGTCCCAGACATGTTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
28706032 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCACCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
28706082 TGCCAATGTCATGTCCCAAACATGGTCTTACATGGGACC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
28706121 CCTTTACCCA
Statistics
Matches: 166, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
50 135 0.81
51 31 0.19
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28708051 original size:2 final size:2
Alignment explanation
Indices: 28708044--28708073 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28708034 TTGTTGTTGT
28708044 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28708074 CAGATTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28708281 original size:32 final size:34
Alignment explanation
Indices: 28708242--28708313 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 34
28708232 TATATACATA
28708242 CATCTATGGTCCTATTATATA-AC-AGATATATG
1 CATCTATGGTCCTATTATATATACTAGATATATG
* * * *
28708274 CCTCTATGGTTCTGTTATATATACTATATATATG
1 CATCTATGGTCCTATTATATATACTAGATATATG
28708308 CATCTA
1 CATCTA
28708314 GAGATTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 18 0.55
33 2 0.06
34 13 0.39
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (34 bp):
CATCTATGGTCCTATTATATATACTAGATATATG
Found at i:28711855 original size:20 final size:19
Alignment explanation
Indices: 28711832--28711879 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
28711822 AAGTGAGAAT
28711832 AGGGGCACAAACATGCAAAC
1 AGGGGCACAAA-ATGCAAAC
* * *
28711852 AGGGACATCAAAATGTATAC
1 AGGGGCA-CAAAATGCAAAC
28711872 AGGGGCAC
1 AGGGGCAC
28711880 CGAACTACGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.10
Consensus pattern (19 bp):
AGGGGCACAAAATGCAAAC
Found at i:28713129 original size:56 final size:56
Alignment explanation
Indices: 28713025--28713136 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
28713015 GCACATTGCT
* *
28713025 TGGGAACCAAGGGTGCGATGATCATTGATTTGCGGAATAAGAGGTGTTCGGATCGA
1 TGGGAACCAAGAGTGCGATGATCATTGATTTGCAGAATAAGAGGTGTTCGGATCGA
*
28713081 TGGGAACCAAGAGTGTGATAGATCATTGATTTGCAGAATAAGA-GTGTTCGGATCGA
1 TGGGAACCAAGAGTGCGAT-GATCATTGATTTGCAGAATAAGAGGTGTTCGGATCGA
28713137 AAGGAATCTG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
56 30 0.58
57 22 0.42
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (56 bp):
TGGGAACCAAGAGTGCGATGATCATTGATTTGCAGAATAAGAGGTGTTCGGATCGA
Found at i:28713616 original size:27 final size:26
Alignment explanation
Indices: 28713577--28713685 Score: 130
Period size: 26 Copynumber: 4.2 Consensus size: 26
28713567 GAGAGGTCAA
* * *
28713577 TAAATTACTGAAAAACCCCCATAGGG
1 TAAATAACCGAAATACCCCCATAGGG
28713603 TAAAGTAACCGAAATA-CCCCATAGGG
1 TAAA-TAACCGAAATACCCCCATAGGG
* *
28713629 TAAATTATCGAAATACCCCCATAGGG
1 TAAATAACCGAAATACCCCCATAGGG
* *
28713655 TAAAATGACCGAAATACCCCTATAGGG
1 T-AAATAACCGAAATACCCCCATAGGG
28713682 TAAA
1 TAAA
28713686 ATGACTGTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
25 9 0.12
26 32 0.44
27 31 0.43
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (26 bp):
TAAATAACCGAAATACCCCCATAGGG
Found at i:28713655 original size:52 final size:53
Alignment explanation
Indices: 28713577--28713685 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 53
28713567 GAGAGGTCAA
*
28713577 TAAATTACTGAAAAACCCCCATAGGGTAAAGTAACCGAAATACCCC-ATAGGG
1 TAAATTACTGAAAAACCCCCATAGGGTAAAATAACCGAAATACCCCTATAGGG
* *
28713629 TAAATTA-TCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGG
1 TAAATTACT-GAAAAACCCCCATAGGGTAAAATAACCGAAATACCCCTATAGGG
28713682 TAAA
1 TAAA
28713686 ATGACTGTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
51 1 0.02
52 41 0.79
53 10 0.19
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (53 bp):
TAAATTACTGAAAAACCCCCATAGGGTAAAATAACCGAAATACCCCTATAGGG
Found at i:28713699 original size:27 final size:27
Alignment explanation
Indices: 28713586--28713690 Score: 142
Period size: 27 Copynumber: 4.0 Consensus size: 27
28713576 ATAAATTACT
* * *
28713586 GAAAAACCCCCATAGGGTAAAGTAACC
1 GAAATACCCCCATAGGGTAAAATGACC
* *
28713613 GAAATA-CCCCATAGGGT-AAATTATC
1 GAAATACCCCCATAGGGTAAAATGACC
28713638 GAAATACCCCCATAGGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
*
28713665 GAAATACCCCTATAGGGTAAAATGAC
1 GAAATACCCCCATAGGGTAAAATGAC
28713691 TGTTATACCT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
25 11 0.16
26 22 0.32
27 36 0.52
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (27 bp):
GAAATACCCCCATAGGGTAAAATGACC
Found at i:28713911 original size:26 final size:26
Alignment explanation
Indices: 28713882--28713936 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
28713872 TTTGCCACAT
* *
28713882 ATACTGTTACTGGCAGCTTCGCTGTG
1 ATACTATTACTGGCAGCTTCGCTATG
* *
28713908 ATACTATTACTGGTAGCTTTGCTATG
1 ATACTATTACTGGCAGCTTCGCTATG
28713934 ATA
1 ATA
28713937 TTGGTGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTCGCTATG
Found at i:28714398 original size:23 final size:23
Alignment explanation
Indices: 28714367--28714415 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
28714357 AAACTGCTAG
*
28714367 ATAGGAGAAGACGAATTTTTAAA
1 ATAGAAGAAGACGAATTTTTAAA
*
28714390 ATAGAAGAAGATGAATTTTTAAA
1 ATAGAAGAAGACGAATTTTTAAA
28714413 ATA
1 ATA
28714416 ATTACTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.18, T:0.29
Consensus pattern (23 bp):
ATAGAAGAAGACGAATTTTTAAA
Found at i:28725072 original size:26 final size:25
Alignment explanation
Indices: 28725043--28725103 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
28725033 ATCTTACCAT
28725043 GGGTAAAAT-TGTCAAAATTTTAATAG
1 GGGTAAAATCT-TCAAAATTTT-ATAG
*
28725069 GGGTAAAATCTTCAAAATTTTATTG
1 GGGTAAAATCTTCAAAATTTTATAG
28725094 GGAGTAAAAT
1 GG-GTAAAAT
28725104 AGGAATGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 5 0.16
26 26 0.81
27 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (25 bp):
GGGTAAAATCTTCAAAATTTTATAG
Found at i:28732817 original size:79 final size:78
Alignment explanation
Indices: 28732715--28732937 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
28732705 GCTCCTCGTT
* *
28732715 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
28732780 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
28732795 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
28732858 AATTAGTATCTTGCA
64 AATTAGTAACTCGCA
* * * * *
28732873 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
28732936 GA
63 GA
28732938 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 46 0.37
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:28732832 original size:39 final size:40
Alignment explanation
Indices: 28732715--28732937 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
28732705 GCTCCTCGTT
* *
28732715 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
28732755 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28732795 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
28732834 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
28732873 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
28732914 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28732938 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:28736669 original size:50 final size:49
Alignment explanation
Indices: 28736615--28736737 Score: 133
Period size: 49 Copynumber: 2.5 Consensus size: 49
28736605 GAGGTCTCCC
* * * *
28736615 GTAAGACCATGTTTGGGACATGGCATGGGCACCG-ATATGAGAAC-TCCCAT
1 GTAAGACCATGTCTGGGACATGGCAT-GG-ACAGTACAGGA-AACATCCCAT
* * * *
28736665 GTAAGACCATATCTGGGATATGACATTGACAGTACAGGAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATGGACAGTACAGGAAACATCCCAT
28736714 GTAAGACCATGTCTGGGACATGGC
1 GTAAGACCATGTCTGGGACATGGC
28736738 TTTGGTATGT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
48 6 0.10
49 32 0.53
50 22 0.37
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATGGACAGTACAGGAAACATCCCAT
Found at i:28748450 original size:27 final size:27
Alignment explanation
Indices: 28748400--28748779 Score: 358
Period size: 27 Copynumber: 14.1 Consensus size: 27
28748390 GGGTATAACA
* *
28748400 GTCATTTTACCCT-TTGGCGATATTTCG
1 GTCATTTTACCCTATAGG-GGTATTTCG
** * * *
28748427 GTCATACTACTCTTTAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
28748454 GTCGTTTTACCCTAT-GAGGGTATTTCA
1 GTCATTTTACCCTATAG-GGGTATTTCG
* * *
28748481 GTCTTTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
28748508 ATCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTCG
*
28748535 GTCATTTTACCTTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
28748562 GTCATTCTACCTTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * * *
28748589 ATCATTTTACGCTGT-GAGGGTATTTTG
1 GTCATTTTACCCTATAG-GGGTATTTCG
*
28748616 GTTATTTTACCCTA-AGTGGGTATTTCG
1 GTCATTTTACCCTATAG-GGGTATTTCG
* * *
28748643 GTCATTCTATCTTAT-GAGGGTATTTCG
1 GTCATTTTACCCTATAG-GGGTATTTCG
28748670 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* ** *
28748697 GTCATTCTACATTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
28748724 GTCATTTTACCCTATAGAGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
28748751 ATCATTTTACCCTATTA-GGGTATGTCG
1 GTCATTTTACCCTA-TAGGGGTATTTCG
28748778 GT
1 GT
28748780 GCAGATATCG
Statistics
Matches: 289, Mismatches: 56, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.01
27 280 0.97
28 7 0.02
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:28752347 original size:27 final size:27
Alignment explanation
Indices: 28752325--28752645 Score: 270
Period size: 27 Copynumber: 12.0 Consensus size: 27
28752315 ATGGGTATAA
28752325 CAGTCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
* ** * * *
28752352 CGGTCATACTACTCTGTGGGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
*
28752379 CGGTCATTTTACCCTATG-GGAGTATTT
1 CAGTCATTTTACCCTATGAGG-GTATTT
*
28752406 -TGATCATTTTACCCTAT-AGGGGTATTT
1 CAG-TCATTTTACCCTATGA-GGGTATTT
*
28752433 CAGTCATTCTACCCTAT-AGGGATATTT
1 CAGTCATTTTACCCTATGAGGG-TATTT
* *
28752460 C-GATCATTTTACCCTGTGGGGGTATTT
1 CAG-TCATTTTACCCTATGAGGGTATTT
*
28752487 C-GATTATTTTACCCTAT-AGGGGTATTT
1 CAG-TCATTTTACCCTATGA-GGGTATTT
*
28752514 CAGTCATTCTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
**
28752541 TGGTCATTTTACCCTAT-AGAGGTATTT
1 CAGTCATTTTACCCTATGAG-GGTATTT
*
28752568 CAGTCA--CTACCCTATG-GGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
* * * *
28752592 CGGTTATTTTA-CCTGTGGGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
* * * *
28752618 TAGTTATTTTATCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
28752645 C
1 C
28752646 GGTGCAGATA
Statistics
Matches: 242, Mismatches: 35, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.05
25 14 0.06
26 28 0.12
27 181 0.75
28 8 0.03
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGAGGGTATTT
Found at i:28752404 original size:54 final size:54
Alignment explanation
Indices: 28752327--28752648 Score: 309
Period size: 54 Copynumber: 6.0 Consensus size: 54
28752317 GGGTATAACA
* * *
28752327 GTCATTTTACCCTATGAGG-GTATTTCGGTCATACTACTCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATG-GGAGTATTTCGGTCATTCTACCCTATGGGGGTATTTCG
* * * * *
28752381 GTCATTTTACCCTATGGGAGTATTTTGATCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGAGTATTTCGGTCATTCTACCCTATGGGGGTATTTCG
* * * *
28752435 GTCATTCTACCCTATAGGGA-TATTTCGATCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGAGTATTTCGGTCATTCTACCCTATGGGGGTATTTCG
* * * * *
28752489 ATTATTTTACCCTATAGGG-GTATTTCAGTCATTCTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTAT-GGGAGTATTTCGGTCATTCTACCCTATGGGGGTATTTCG
* *
28752543 GTCATTTTACCCTAT-AGAGGTATTTCAGTCA--CTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGA-GTATTTCGGTCATTCTACCCTATGGGGGTATTTCG
* * * ** * * *
28752594 GTTATTTTA-CCTGTGGGGGTATTTTAGTTATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGAGTATTTCGGTCATTCTACCCTATGGGGGTATTTCG
28752647 GT
1 GT
28752649 GCAGATATCG
Statistics
Matches: 224, Mismatches: 35, Indels: 19
0.81 0.13 0.07
Matches are distributed among these distances:
50 14 0.06
51 18 0.08
52 17 0.08
53 15 0.07
54 156 0.70
55 4 0.02
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTATGGGAGTATTTCGGTCATTCTACCCTATGGGGGTATTTCG
Found at i:28752467 original size:81 final size:80
Alignment explanation
Indices: 28752328--28752646 Score: 319
Period size: 81 Copynumber: 4.0 Consensus size: 80
28752318 GGTATAACAG
* * * * *
28752328 TCATTTTACCCTAT-GAGGGTATTTCGGTCATACTACTCTGTGGGGGTATTTCGGTCATTTTACC
1 TCATTTTACCCTATAG-GGGTATTTCAGTCATTCTACCCTAT-AGGGTATTTCGGTCATTTTACC
*
28752392 CTATGGGAGTATTTTGA
64 CTATGGGAGTATTTCGA
*
28752409 TCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTATAGGGATATTTCGATCATTTTACCC
1 TCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTATAGGG-TATTTCGGTCATTTTACCC
* *
28752474 TGTGGGGGTATTTCGA
65 TATGGGAGTATTTCGA
* *
28752490 TTATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTTGGTCATTTTACCC
1 TCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTAT-AGGGTATTTCGGTCATTTTACCC
*
28752555 TAT-AGAGGTATTTC-A
65 TATGGGA-GTATTTCGA
* * * * * * ** * *
28752570 GTCA--CTACCCTAT-GGGGTATTTCGGTTATTTTA-CCTGTGGGGGTATTTTAGTTATTTTATC
1 -TCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTAT-AGGGTATTTCGGTCATTTTACC
*
28752631 CTATGGGGGTATTTCG
64 CTATGGGAGTATTTCG
28752647 GTGCAGATAT
Statistics
Matches: 204, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
77 34 0.17
78 18 0.09
79 8 0.04
80 5 0.02
81 134 0.66
82 5 0.02
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (80 bp):
TCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTATAGGGTATTTCGGTCATTTTACCCT
ATGGGAGTATTTCGA
Found at i:28757698 original size:15 final size:15
Alignment explanation
Indices: 28757678--28757709 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28757668 CATTTCACTA
*
28757678 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
28757693 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
28757708 TT
1 TT
28757710 TACATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:28764282 original size:33 final size:33
Alignment explanation
Indices: 28764235--28764302 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
28764225 ATAGTGTTAG
28764235 AATGCGTAAAGAAATAATAAAAAGTAAAAAACA
1 AATGCGTAAAGAAATAATAAAAAGTAAAAAACA
*
28764268 AATGTGTAAAGAAATAATAAAAAGTAAAAAACA
1 AATGCGTAAAGAAATAATAAAAAGTAAAAAACA
28764301 AA
1 AA
28764303 GGAAAACCTA
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:0.68, C:0.04, G:0.12, T:0.16
Consensus pattern (33 bp):
AATGCGTAAAGAAATAATAAAAAGTAAAAAACA
Found at i:28767409 original size:27 final size:27
Alignment explanation
Indices: 28767379--28767556 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28767369 ATATTGAGTC
* * * *
28767379 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28767406 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28767433 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28767461 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28767488 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28767515 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28767542 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28767557 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28767518 original size:82 final size:81
Alignment explanation
Indices: 28767400--28767555 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28767390 TGCTATATAA
* *
28767400 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28767465 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28767482 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28767546 CACTTAGTGC
65 CACTTAGTGC
28767556 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28770687 original size:33 final size:33
Alignment explanation
Indices: 28770644--28770740 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
28770634 GAGTTGTTCC
28770644 CTTTGCCGAATATTACTTCTCCCCATTCATTGA
1 CTTTGCCGAATATTACTTCTCCCCATTCATTGA
* * *
28770677 CTTTGTCGAATATTACTTCTCTCCATTCATTGT
1 CTTTGCCGAATATTACTTCTCCCCATTCATTGA
* *
28770710 TTTTGCCGAA-ACCT-CTTCTCCCCATTCATTG
1 CTTTGCCGAATA-TTACTTCTCCCCATTCATTG
28770741 TGTTGGCTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
32 17 0.30
33 39 0.70
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (33 bp):
CTTTGCCGAATATTACTTCTCCCCATTCATTGA
Found at i:28771768 original size:27 final size:27
Alignment explanation
Indices: 28771711--28771911 Score: 298
Period size: 27 Copynumber: 7.5 Consensus size: 27
28771701 CCCAAAACTA
28771711 TTATAAAATGACTATTATG-CCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
*
28771737 TTATAAAATGACTATTAGGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
**
28771764 TTATAAAATGACGGTTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
* *
28771791 TTATAAAATGAC-AGTTATGCCCTTTTG
1 TTATAAAATGACTA-TTATGCCCCTATG
** *
28771818 TTATAAAATGACGGTTATGCCCCTAAG
1 TTATAAAATGACTATTATGCCCCTATG
*
28771845 TTATAAAATGACTGTTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
28771872 TTATAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
28771899 TTATAAAATGACT
1 TTATAAAATGACT
28771912 GTGTGCTTAA
Statistics
Matches: 158, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
26 18 0.11
27 140 0.89
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (27 bp):
TTATAAAATGACTATTATGCCCCTATG
Found at i:28775528 original size:41 final size:39
Alignment explanation
Indices: 28775446--28775522 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
28775436 GGGAAAGTGG
**
28775446 AAACACACAAAGCTAGACTTGTAGGGAAAGGGTACACAT
1 AAACACACAAAGCTAGACTTGTAGGGAAAGACTACACAT
*
28775485 AAACACACAAAGCTAGACTTGTAGGTAAAGACTACACA
1 AAACACACAAAGCTAGACTTGTAGGGAAAGACTACACA
28775523 CATAAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (39 bp):
AAACACACAAAGCTAGACTTGTAGGGAAAGACTACACAT
Found at i:28777844 original size:78 final size:78
Alignment explanation
Indices: 28777715--28777870 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
28777705 TATGCCCGAA
* *
28777715 CCAACCTGGCTGTCCAACAATTCCCAAATTTGAATAATCCACCCCAAGAGCCTGTAATGCCATCA
1 CCAACCCGGCTGTCCAACAATTCCCAAATTTGAATAATCCACCCCAAGAGCCTGTAAGGCCATCA
28777780 GTCGCTGATCCTG
66 GTCGCTGATCCTG
28777793 CCAACCCGGCTGTCCAACAATTCCCAAATTTGAATAATCCACCCCAAGAGCCTGTAAGGCCATCA
1 CCAACCCGGCTGTCCAACAATTCCCAAATTTGAATAATCCACCCCAAGAGCCTGTAAGGCCATCA
28777858 GTCGCTGATCCTG
66 GTCGCTGATCCTG
28777871 TGAGGCTGAG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (78 bp):
CCAACCCGGCTGTCCAACAATTCCCAAATTTGAATAATCCACCCCAAGAGCCTGTAAGGCCATCA
GTCGCTGATCCTG
Found at i:28788227 original size:31 final size:31
Alignment explanation
Indices: 28788189--28788250 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
28788179 TTTATCATCT
**
28788189 TTCCCTATTCTATTTTTCCGAATATACCTGA
1 TTCCCTATTCTATTTGGCCGAATATACCTGA
* *
28788220 TTCCCTATTGTGTTTGGCCGAATATACCTGA
1 TTCCCTATTCTATTTGGCCGAATATACCTGA
28788251 ACTATTCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (31 bp):
TTCCCTATTCTATTTGGCCGAATATACCTGA
Found at i:28790256 original size:29 final size:27
Alignment explanation
Indices: 28790238--28790307 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
28790228 ATATTAAGTC
28790238 CACACACTCAGTGCTATATAATCAACT
1 CACACACTCAGTGCTATATAATCAACT
* *
28790265 CGCACACTTAGTGCTATATAATCAAACT
1 CACACACTCAGTGCTATATAATC-AACT
* *
28790293 CGCACACTTAGTGCT
1 CACACACTCAGTGCT
28790308 GTACAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.27
Consensus pattern (27 bp):
CACACACTCAGTGCTATATAATCAACT
Found at i:28790301 original size:28 final size:28
Alignment explanation
Indices: 28790240--28790335 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
28790230 ATTAAGTCCA
*
28790240 CACACTCAGTGCTATATAATC-AACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
28790267 CACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
* * * *
28790295 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCTATATAA-TCAAACTCG
28790324 CACACTTAGTGC
1 CACACTTAGTGC
28790336 CAATCTCATG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.32
28 23 0.37
29 19 0.31
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CACACTTAGTGCTATATAATCAAACTCG
Found at i:28823311 original size:28 final size:28
Alignment explanation
Indices: 28823254--28823461 Score: 332
Period size: 28 Copynumber: 7.5 Consensus size: 28
28823244 TAAATTGTGC
* *
28823254 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
28823281 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
28823309 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28823337 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28823365 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28823392 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28823420 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28823447 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28823462 GACTTAATAA
Statistics
Matches: 171, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
27 65 0.38
28 106 0.62
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:28823318 original size:55 final size:55
Alignment explanation
Indices: 28823254--28823461 Score: 344
Period size: 55 Copynumber: 3.8 Consensus size: 55
28823244 TAAATTGTGC
*
28823254 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
* *
28823309 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
*
28823365 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
* * *
28823420 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
28823462 GACTTAATAA
Statistics
Matches: 143, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
55 90 0.63
56 53 0.37
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:28825718 original size:29 final size:29
Alignment explanation
Indices: 28825693--28825897 Score: 211
Period size: 29 Copynumber: 7.1 Consensus size: 29
28825683 AAGAAAATGA
28825693 ATAGCTTCGGCTATCAATTATGAAAAGGG
1 ATAGCTTCGGCTATCAATTATGAAAAGGG
28825722 ATAGCTTCGGCTATCAATTATGAAAAGGG
1 ATAGCTTCGGCTATCAATTATGAAAAGGG
* * * * **
28825751 AT-GGTGACGACCATCAAACATGAAAAGGG
1 ATAGCT-TCGGCTATCAATTATGAAAAGGG
* *
28825780 ATAGCTTCAGCTATCAAATATG-AAAGGAG
1 ATAGCTTCGGCTATCAATTATGAAAAGG-G
*
28825809 ATAGCTTCGACTATCGAA-TATGAAAAGGG
1 ATAGCTTCGGCTATC-AATTATGAAAAGGG
* *
28825838 ATAGCTCCAGCTATCGAA-TATGAAAAGGG
1 ATAGCTTCGGCTATC-AATTATGAAAAGGG
** * *
28825867 ATAGCTTTTGCTATCGATTATGAAAAAGG
1 ATAGCTTCGGCTATCAATTATGAAAAGGG
28825896 AT
1 AT
28825898 GGTGACGACC
Statistics
Matches: 148, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
28 8 0.05
29 131 0.89
30 9 0.06
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (29 bp):
ATAGCTTCGGCTATCAATTATGAAAAGGG
Found at i:28825795 original size:87 final size:86
Alignment explanation
Indices: 28825693--28825939 Score: 259
Period size: 87 Copynumber: 2.8 Consensus size: 86
28825683 AAGAAAATGA
* *
28825693 ATAGCTTCGGCTATCAATTATGAAAAGGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGTGA
1 ATAGCTTCAGCTATCAATTATGAAAAGGGATAGCTTCGACTATCAA-TATGAAAAGGGATGGTGA
28825758 CGACCATCAAACATGAAAAGGG
65 CGACCATCAAACATGAAAAGGG
* *
28825780 ATAGCTTCAGCTATCAAATATG-AAAGGAGATAGCTTCGACTATCGAATATGAAAAGGGATAGCT
1 ATAGCTTCAGCTATCAATTATGAAAAGG-GATAGCTTCGACTATC-AATATGAAAAGGGAT-GGT
* * * *
28825844 --CCAGCTATCGAATATGAAAAGGG
63 GACGA-CCATCAAACATGAAAAGGG
** * * * * *
28825867 ATAGCTTTTGCTATCGATTATGAAAAAGGAT-GGTGACGACCATCAACTATGAAAAGGGATGGTG
1 ATAGCTTCAGCTATCAATTATGAAAAGGGATAGCT-TCGACTATCAA-TATGAAAAGGGATGGTG
*
28825931 ATGACCATC
64 ACGACCATC
28825940 GTTATTCCAT
Statistics
Matches: 131, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
86 13 0.10
87 109 0.83
88 9 0.07
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (86 bp):
ATAGCTTCAGCTATCAATTATGAAAAGGGATAGCTTCGACTATCAATATGAAAAGGGATGGTGAC
GACCATCAAACATGAAAAGGG
Found at i:28833203 original size:29 final size:28
Alignment explanation
Indices: 28833164--28833345 Score: 199
Period size: 29 Copynumber: 6.3 Consensus size: 28
28833154 CCATCGACTA
*
28833164 ATGAAAAGGGATAGCTTCTGCTATCGATT
1 ATGAAAAGGGATAGCTTC-GCTATCGAAT
* * * * *
28833193 AT-AAATAGGGAT-GGTAACGACCATCAAAC
1 ATGAAA-AGGGATAGCT-TCG-CTATCGAAT
28833222 ATGAAAAGGGATAGCTTCAGCTATCGAAT
1 ATGAAAAGGGATAGCTTC-GCTATCGAAT
28833251 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTC-GCTATCGAAT
28833280 ATGAAAAGGGATAGCTTCGACTATCG-AT
1 ATGAAAAGGGATAGCTTCG-CTATCGAAT
*
28833308 AATGAAAAGGGATAGCTTCGGCTATCGATT
1 -ATGAAAAGGGATAGCTTC-GCTATCGAAT
28833338 ATGAAAAG
1 ATGAAAAG
28833346 TGATGGTGAC
Statistics
Matches: 130, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.07
29 113 0.87
30 8 0.06
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (28 bp):
ATGAAAAGGGATAGCTTCGCTATCGAAT
Found at i:28833264 original size:87 final size:87
Alignment explanation
Indices: 28833164--28833345 Score: 244
Period size: 87 Copynumber: 2.1 Consensus size: 87
28833154 CCATCGACTA
* * *
28833164 ATGAAAAGGGATAGCTTCTGCTATCGATTAT-AAATAGGGAT-GGTAACGACCATC-AAACATGA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAA-AGGGATAGCT-ACGACCATCGAAA-ATGA
28833226 AAAGGGATAGCTTCAGCTATCGAAT
63 AAAGGGATAGCTTCAGCTATCGAAT
* * *
28833251 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGACTATCGATAATGAAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTACGACCATCGAAAATGAAAA
* *
28833316 GGGATAGCTTCGGCTATCGATT
66 GGGATAGCTTCAGCTATCGAAT
28833338 ATGAAAAG
1 ATGAAAAG
28833346 TGATGGTGAC
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
87 77 0.92
88 7 0.08
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTACGACCATCGAAAATGAAAA
GGGATAGCTTCAGCTATCGAAT
Found at i:28833371 original size:58 final size:57
Alignment explanation
Indices: 28833222--28833378 Score: 183
Period size: 58 Copynumber: 2.7 Consensus size: 57
28833212 ACCATCAAAC
* *
28833222 ATGAAAAGGGATAGCTTC-AGCTATCGAATATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTACGA-CCATC-AATATGAAAAGGGATAGCTTCGGCTATCGAAT
* * * *
28833280 ATGAAAAGGGATAGCTTCGACTATCGATAATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTACGACCATCAAT-ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
28833338 ATGAAAAGTGAT-GGTGACGACCATCAACTATGAAAAGGGAT
1 ATGAAAAGGGATAGCT-ACGACCATCAA-TATGAAAAGGGAT
28833379 GGTGATGACC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
57 4 0.05
58 82 0.93
59 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (57 bp):
ATGAAAAGGGATAGCTACGACCATCAATATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:28835611 original size:16 final size:16
Alignment explanation
Indices: 28835581--28835622 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
28835571 TTATTTATTA
28835581 AATTAA-TTT-TAATT
1 AATTAATTTTCTAATT
28835595 AATTAATTTTCTAATT
1 AATTAATTTTCTAATT
*
28835611 AAATAATTTTCT
1 AATTAATTTTCT
28835623 CAACCCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 3 0.12
16 16 0.64
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTAATTTTCTAATT
Found at i:28846243 original size:11 final size:10
Alignment explanation
Indices: 28846227--28846282 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
28846217 CATAATTGTG
28846227 AAATAGTAACA
1 AAATAGTAA-A
*
28846238 AAATAGTGAA
1 AAATAGTAAA
*
28846248 AAATAGCAACA
1 AAATAGTAA-A
*
28846259 AAATAATAAA
1 AAATAGTAAA
*
28846269 AAATAGAAAA
1 AAATAGTAAA
28846279 AAAT
1 AAAT
28846283 TGTAGTTCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (10 bp):
AAATAGTAAA
Found at i:28846252 original size:10 final size:11
Alignment explanation
Indices: 28846227--28846274 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
28846217 CATAATTGTG
28846227 AAATAGTAACA
1 AAATAGTAACA
*
28846238 AAATAGTGA-A
1 AAATAGTAACA
*
28846248 AAATAGCAACA
1 AAATAGTAACA
*
28846259 AAATAATAA-A
1 AAATAGTAACA
28846269 AAATAG
1 AAATAG
28846275 AAAAAAATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
10 14 0.47
11 16 0.53
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.17
Consensus pattern (11 bp):
AAATAGTAACA
Found at i:28846253 original size:21 final size:20
Alignment explanation
Indices: 28846227--28846282 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
28846217 CATAATTGTG
* *
28846227 AAATAGTAACAAAATAGTGAA
1 AAATAG-AACAAAATAATAAA
28846248 AAATAGCAACAAAATAATAAA
1 AAATAG-AACAAAATAATAAA
*
28846269 AAATAGAAAAAAAT
1 AAATAGAACAAAAT
28846283 TGTAGTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 7 0.23
21 24 0.77
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (20 bp):
AAATAGAACAAAATAATAAA
Found at i:28849466 original size:27 final size:27
Alignment explanation
Indices: 28849435--28849612 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
28849425 TAAATTGTAC
28849435 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * ** *
28849462 TGCACTAAGTGTGCAAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28849488 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28849516 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28849544 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28849571 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28849598 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28849613 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28849576 original size:82 final size:81
Alignment explanation
Indices: 28849436--28849591 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28849426 AAATTGTACA
* *
28849436 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCAAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGATGCACTAAGTGT
28849501 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
28849517 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGAT-GCACTAAGT
*
28849581 GTGCGAGTTGA
64 GTGCGAATTGA
28849592 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Done.