Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 75 of 345
Found at i:20540408 original size:2 final size:2
Alignment explanation
Indices: 20540356--20540393 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20540346 CATGACGGAC
20540356 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20540394 AGGTTATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20540965 original size:18 final size:18
Alignment explanation
Indices: 20540944--20540982 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20540934 ATATTGAAAA
20540944 ATATATAATTT-TAATATC
1 ATAT-TAATTTATAATATC
*
20540962 ATATTAATTTATAATTTC
1 ATATTAATTTATAATATC
20540980 ATA
1 ATA
20540983 ATTTAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTAATTTATAATATC
Found at i:20542242 original size:31 final size:30
Alignment explanation
Indices: 20542194--20542257 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
20542184 ACTTAACAAG
20542194 CAAATGCCTCTAAAATAATAATAATAAATTAA
1 CAAATGCCTCTAAAATAATAA-AA-AAATTAA
*
20542226 CAAATGCCT-TAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
20542255 CAA
1 CAA
20542258 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 10 0.32
30 1 0.03
31 11 0.35
32 9 0.29
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAAAAAAATTAA
Found at i:20543874 original size:38 final size:38
Alignment explanation
Indices: 20543831--20543903 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
20543821 TTTTTTTTAA
*
20543831 TATTTTATTATACCTTATAGGATACTTGCTATCACCTT
1 TATTTTATTATACCTTATAGGATACTTGCCATCACCTT
20543869 TATTTTATTATACCTTATAGGATACTTGCCATCAC
1 TATTTTATTATACCTTATAGGATACTTGCCATCAC
20543904 TTTCACTCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (38 bp):
TATTTTATTATACCTTATAGGATACTTGCCATCACCTT
Found at i:20545129 original size:54 final size:54
Alignment explanation
Indices: 20545047--20545154 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
20545037 TAAAGAGAAG
20545047 GTCAAATTTGCTTAGAGTGAAGCTTGTACAGTGTCATTCGCTAAGTTTTGATAA
1 GTCAAATTTGCTTAGAGTGAAGCTTGTACAGTGTCATTCGCTAAGTTTTGATAA
20545101 GTCAAATTTGCTTAGAGTGAAGCTTGTACAGTGTCATTCGCTAAGTTTTGATAA
1 GTCAAATTTGCTTAGAGTGAAGCTTGTACAGTGTCATTCGCTAAGTTTTGATAA
20545155 AACCTTTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (54 bp):
GTCAAATTTGCTTAGAGTGAAGCTTGTACAGTGTCATTCGCTAAGTTTTGATAA
Found at i:20551268 original size:17 final size:17
Alignment explanation
Indices: 20551246--20551289 Score: 79
Period size: 17 Copynumber: 2.5 Consensus size: 17
20551236 AAGCTGAGAT
20551246 TAGATATCTAATTATAC
1 TAGATATCTAATTATAC
20551263 TAGATATCTAATTATAC
1 TAGATATCTAATTATAC
20551280 TAGAATATCT
1 TAG-ATATCT
20551290 CTAGTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (17 bp):
TAGATATCTAATTATAC
Found at i:20552098 original size:21 final size:21
Alignment explanation
Indices: 20552060--20552099 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20552050 AGTATTAAAA
*
20552060 TATTTTATTTTAATATTTATG
1 TATTTTATATTAATATTTATG
20552081 TATTTTATGATTAA-ATTTA
1 TATTTTAT-ATTAATATTTA
20552100 AATAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TATTTTATATTAATATTTATG
Found at i:20553433 original size:21 final size:22
Alignment explanation
Indices: 20553400--20553443 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
20553390 ATAAGATAAT
*
20553400 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
20553422 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
20553443 A
1 A
20553444 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:20553661 original size:8 final size:8
Alignment explanation
Indices: 20553648--20553814 Score: 50
Period size: 8 Copynumber: 21.5 Consensus size: 8
20553638 TAAAATGTAA
20553648 AATAATAT
1 AATAATAT
20553656 AATAATAT
1 AATAATAT
*
20553664 AAAAATAT
1 AATAATAT
20553672 -ATAA-AT
1 AATAATAT
* *
20553678 -ATTATGT
1 AATAATAT
* *
20553685 GATAA-AA
1 AATAATAT
20553692 ACATAATAT
1 A-ATAATAT
20553701 AATAA-AT
1 AATAATAT
*
20553708 AATAA-GT
1 AATAATAT
*
20553715 AATGATAT
1 AATAATAT
* ** *
20553723 -GTGTTAA
1 AATAATAT
20553730 AAT-ATAT
1 AATAATAT
*
20553737 ATTAATAT
1 AATAATAT
* *
20553745 GATAATAG
1 AATAATAT
*
20553753 AAAAATAT
1 AATAATAT
20553761 GAAGTAATAT
1 -AA-TAATAT
20553771 AAT-ATAAT
1 AATAAT-AT
20553779 AA-AATAT
1 AATAATAT
20553786 AAGTAA-AT
1 AA-TAATAT
* *
20553794 AATTATAA
1 AATAATAT
20553802 AATATATAT
1 AATA-ATAT
20553811 AATA
1 AATA
20553815 CGTATATTCA
Statistics
Matches: 114, Mismatches: 30, Indels: 29
0.66 0.17 0.17
Matches are distributed among these distances:
6 5 0.04
7 32 0.28
8 57 0.50
9 15 0.13
10 5 0.04
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.34
Consensus pattern (8 bp):
AATAATAT
Found at i:20555973 original size:180 final size:180
Alignment explanation
Indices: 20555661--20556020 Score: 553
Period size: 180 Copynumber: 2.0 Consensus size: 180
20555651 CGCGAAAACC
* *
20555661 AAATCAGCTATGTCTTCGATTTTCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATCTGCT
1 AAATCAGCTATGTCTTCGATTTTCTCCTTGTAAACACAAGGATACCAAACCATCTTGGATCAGCT
* * * ** *
20555726 TGAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCAAATATGGAGACGCCA
66 TCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCCCTCCGTCAAATATGGAGACGCCA
20555791 AACTTCGATTTATTCTCTGACAATACAGAGATGCCAAATCATCTTAGACT
131 AACTTCGATTTATTCTCTGACAATACAGAGATGCCAAATCATCTTAGACT
* * *
20555841 AAATTAGCTATGAT-TTCGATTTGT-TCCTTGTAAACACAAGGATGCCAAATCATCTTGGATCAG
1 AAATCAGCTATG-TCTTCGATTT-TCTCCTTGTAAACACAAGGATACCAAACCATCTTGGATCAG
* * *
20555904 CTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAATATGGAGATGC
64 CTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCCCTCCGTCAAATATGGAGACGC
*
20555969 CAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACT
129 CAAACTTCGATTTATTCTCTGACAATACAGAGATGCCAAATCATCTTAGACT
20556021 TGCTCGTAAG
Statistics
Matches: 163, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
180 161 0.99
181 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (180 bp):
AAATCAGCTATGTCTTCGATTTTCTCCTTGTAAACACAAGGATACCAAACCATCTTGGATCAGCT
TCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCCCTCCGTCAAATATGGAGACGCCA
AACTTCGATTTATTCTCTGACAATACAGAGATGCCAAATCATCTTAGACT
Found at i:20557002 original size:11 final size:10
Alignment explanation
Indices: 20556978--20557028 Score: 56
Period size: 9 Copynumber: 5.5 Consensus size: 10
20556968 GGCCTCTCCA
20556978 TTTTTCTCTT
1 TTTTTCTCTT
20556988 TTTTTCTCTT
1 TTTTTCTCTT
*
20556998 CTTTT-TC-T
1 TTTTTCTCTT
20557006 TTTTTCT-TT
1 TTTTTCTCTT
*
20557015 TTTTT-TGTT
1 TTTTTCTCTT
20557024 TTTTT
1 TTTTT
20557029 TTTATTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 6 0.17
9 16 0.44
10 14 0.39
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:20557002 original size:13 final size:12
Alignment explanation
Indices: 20556978--20557019 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
20556968 GGCCTCTCCA
20556978 TTTTTC-TCTTT
1 TTTTTCTTCTTT
20556989 TTTTCTCTTCTTT
1 TTTT-TCTTCTTT
*
20557002 TTCTTTTTTCTTT
1 TT-TTTCTTCTTT
20557015 TTTTT
1 TTTTT
20557020 TGTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 16 0.59
14 2 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:20557010 original size:18 final size:17
Alignment explanation
Indices: 20556987--20557027 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20556977 ATTTTTCTCT
20556987 TTTTTTCTCTTCTTTTTC
1 TTTTTTCT-TTCTTTTTC
* *
20557005 TTTTTTCTTTTTTTTTG
1 TTTTTTCTTTCTTTTTC
20557022 TTTTTT
1 TTTTTT
20557028 TTTTATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTTCTTTTTC
Found at i:20557028 original size:26 final size:24
Alignment explanation
Indices: 20556978--20557058 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 24
20556968 GGCCTCTCCA
* *
20556978 TTTTTCTCTTTTTTTCTCTTCTTTTT
1 TTTTTTTCTTTTTTT-T-TTTTTTTT
*
20557004 CTTTTTTCTTTTTTTTTGTTTTTTT
1 TTTTTTTCTTTTTTTTT-TTTTTTT
* *
20557029 TTTATTTTCTGTTTGTTTTTTTTTT
1 TTT-TTTTCTTTTTTTTTTTTTTTT
*
20557054 ATTTT
1 TTTTT
20557059 GAAACCTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 3 0.07
25 18 0.39
26 25 0.54
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.84
Consensus pattern (24 bp):
TTTTTTTCTTTTTTTTTTTTTTTT
Found at i:20557030 original size:22 final size:22
Alignment explanation
Indices: 20557000--20557058 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
20556990 TTTCTCTTCT
* *
20557000 TTTTCTTTTTTCTTTT-TTTTTG
1 TTTT-TTTTTTATTTTCTGTTTG
20557022 TTTTTTTTTTATTTTCTGTTTG
1 TTTTTTTTTTATTTTCTGTTTG
20557044 TTTTTTTTTTATTTT
1 TTTTTTTTTTATTTT
20557059 GAAACCTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.86
Consensus pattern (22 bp):
TTTTTTTTTTATTTTCTGTTTG
Found at i:20557030 original size:28 final size:27
Alignment explanation
Indices: 20556978--20557058 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 27
20556968 GGCCTCTCCA
* * * *
20556978 TTTTTCTCTTTTTTTCTCTTCTTTTTCT
1 TTTTTCT-TTTTTTTTTTTTTTTTTTAT
20557006 TTTTTCTTTTTTTTTGTTTTTTTTTTAT
1 TTTTTCTTTTTTTTT-TTTTTTTTTTAT
* * * *
20557034 TTTCTGTTTGTTTTTTTTTTATTTT
1 TTTTTCTTTTTTTTTTTTTTTTTTT
20557059 GAAACCTCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 16 0.36
28 28 0.64
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.84
Consensus pattern (27 bp):
TTTTTCTTTTTTTTTTTTTTTTTTTAT
Found at i:20557048 original size:39 final size:38
Alignment explanation
Indices: 20556986--20557059 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
20556976 CATTTTTCTC
* * *
20556986 TTTTTTTCTCTTCTTTTTCTTTTTTCTTTTTTTTTGTTT
1 TTTTTTTATCTTCTGTTTCTTTTTT-TTTTATTTTGTTT
* *
20557025 TTTTTTTATTTTCTGTTTGTTTTTTTTTTATTTTG
1 TTTTTTTATCTTCTGTTTCTTTTTTTTTTATTTTG
20557060 AAACCTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 9 0.30
39 21 0.70
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (38 bp):
TTTTTTTATCTTCTGTTTCTTTTTTTTTTATTTTGTTT
Found at i:20567773 original size:21 final size:22
Alignment explanation
Indices: 20567740--20567783 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
20567730 ATAAGATAAT
*
20567740 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
20567762 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
20567783 A
1 A
20567784 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:20568002 original size:8 final size:8
Alignment explanation
Indices: 20567989--20568192 Score: 83
Period size: 8 Copynumber: 26.1 Consensus size: 8
20567979 TAAAATGTAA
20567989 AATAATAT
1 AATAATAT
20567997 AATAATAT
1 AATAATAT
20568005 AATAATAT
1 AATAATAT
20568013 AA-AATAT
1 AATAATAT
20568020 -ATAA-AT
1 AATAATAT
* *
20568026 -ATTATGT
1 AATAATAT
* *
20568033 GATAA-AA
1 AATAATAT
20568040 ACATAATAT
1 A-ATAATAT
20568049 AATAA-AT
1 AATAATAT
*
20568056 AATAA-GT
1 AATAATAT
*
20568063 AATGATAT
1 AATAATAT
* ** *
20568071 -GTGTTAA
1 AATAATAT
20568078 AAT-ATAT
1 AATAATAT
*
20568085 ATTAATAT
1 AATAATAT
* *
20568093 GATAATAG
1 AATAATAT
*
20568101 AAAAATAT
1 AATAATAT
20568109 GAAGTAATAT
1 -AA-TAATAT
20568119 AAT-ATAAT
1 AATAAT-AT
20568127 AA-AATAT
1 AATAATAT
20568134 AAGTAA-AT
1 AA-TAATAT
* *
20568142 AATTATAA
1 AATAATAT
20568150 AATATATAT
1 AATA-ATAT
20568159 AATACATAT
1 AATA-ATAT
*
20568168 ATTAATATT
1 AATAATA-T
*
20568177 AA-AATAA
1 AATAATAT
20568184 AATAATAT
1 AATAATAT
20568192 A
1 A
20568193 TGTATAAAGT
Statistics
Matches: 145, Mismatches: 33, Indels: 36
0.68 0.15 0.17
Matches are distributed among these distances:
6 6 0.04
7 38 0.26
8 72 0.50
9 24 0.17
10 5 0.03
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (8 bp):
AATAATAT
Found at i:20572006 original size:26 final size:25
Alignment explanation
Indices: 20571977--20572143 Score: 76
Period size: 24 Copynumber: 6.8 Consensus size: 25
20571967 TTATACAAGA
* * *
20571977 ATATAAACAGGAAGCTCTTTTGATCC
1 ATAT-AACAGGAAGCTCATGTGAGCC
**
20572003 ATATAATGGGAAGCTCATGTGAGCC
1 ATATAACAGGAAGCTCATGTGAGCC
* ** **
20572028 ATGTAACAGGAAGCTCCGGAAAGCC
1 ATATAACAGGAAGCTCATGTGAGCC
* **
20572053 AT-TAACGGGAAGCTCATACGAGCC
1 ATATAACAGGAAGCTCATGTGAGCC
* * *
20572077 A-ATATC-GAGAAGCTCAAGCGAGCC
1 ATATAACAG-GAAGCTCATGTGAGCC
* * *
20572101 A-ATATCGGGAAGCTTCA-GAGAGCC
1 ATATAACAGGAAGC-TCATGTGAGCC
*
20572125 AT-TAATTAGGAAGCTCATG
1 ATATAA-CAGGAAGCTCATG
20572144 AAAGAGCTTT
Statistics
Matches: 109, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
23 1 0.01
24 57 0.52
25 47 0.43
26 4 0.04
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (25 bp):
ATATAACAGGAAGCTCATGTGAGCC
Found at i:20572029 original size:25 final size:25
Alignment explanation
Indices: 20572001--20572144 Score: 79
Period size: 24 Copynumber: 5.9 Consensus size: 25
20571991 CTCTTTTGAT
*
20572001 CCATATAATGGGAAGCTCATGTGAG
1 CCATATAATGGGAAGCTCATGAGAG
* ** ** *
20572026 CCATGTAACAGGAAGCTCCGGAAAG
1 CCATATAATGGGAAGCTCATGAGAG
*
20572051 CCAT-TAACGGGAAGCTCAT-ACGAG
1 CCATATAATGGGAAGCTCATGA-GAG
* * *
20572075 CCA-AT-ATCGAGAAGCTCAAGCGAG
1 CCATATAAT-GGGAAGCTCATGAGAG
20572099 CCA-AT-ATCGGGAAGCTTCA-GAGAG
1 CCATATAAT-GGGAAGC-TCATGAGAG
*
20572123 CCAT-TAATTAGGAAGCTCATGA
1 CCATATAA-TGGGAAGCTCATGA
20572145 AAGAGCTTTA
Statistics
Matches: 92, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
23 2 0.02
24 55 0.60
25 34 0.37
26 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.18
Consensus pattern (25 bp):
CCATATAATGGGAAGCTCATGAGAG
Found at i:20572123 original size:24 final size:23
Alignment explanation
Indices: 20572049--20572125 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 23
20572039 AGCTCCGGAA
* * *
20572049 AGCCATTAACGGGAAGCTCATACG
1 AGCCAATATCGGGAAGCTCAGA-G
* *
20572073 AGCCAATATCGAGAAGCTCAAGCG
1 AGCCAATATCGGGAAGCTC-AGAG
20572097 AGCCAATATCGGGAAGCTTCAGAG
1 AGCCAATATCGGGAAGC-TCAGAG
20572121 AGCCA
1 AGCCA
20572126 TTAATTAGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 41 0.93
25 3 0.07
ACGTcount: A:0.35, C:0.25, G:0.26, T:0.14
Consensus pattern (23 bp):
AGCCAATATCGGGAAGCTCAGAG
Found at i:20572265 original size:25 final size:25
Alignment explanation
Indices: 20572236--20572298 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
20572226 ATCACAACCA
20572236 ATCGGGAAGCTCACAAGAACCATAT
1 ATCGGGAAGCTCACAAGAACCATAT
20572261 ATCGGGAAGCTCACAAGAACCATAT
1 ATCGGGAAGCTCACAAGAACCATAT
*
20572286 AACGGGAAGCTCA
1 ATCGGGAAGCTCA
20572299 TGAGAGCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (25 bp):
ATCGGGAAGCTCACAAGAACCATAT
Found at i:20583147 original size:28 final size:28
Alignment explanation
Indices: 20583115--20583173 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
20583105 AACCACAAAC
20583115 AAATTAATTTATTGATATTGAGATAAAA
1 AAATTAATTTATTGATATTGAGATAAAA
20583143 AAATTAATTTATTGATATTGAGATAAAA
1 AAATTAATTTATTGATATTGAGATAAAA
20583171 AAA
1 AAA
20583174 ATTTAGTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (28 bp):
AAATTAATTTATTGATATTGAGATAAAA
Found at i:20587092 original size:24 final size:24
Alignment explanation
Indices: 20587064--20587313 Score: 111
Period size: 26 Copynumber: 10.0 Consensus size: 24
20587054 ACAAAATATT
* * *
20587064 ATATAAAACAATTTGAAGTCAATA
1 ATATAAAACAATTTAAAATAAATA
*
20587088 ATATAAAACAATTTCAAATAAATA
1 ATATAAAACAATTTAAAATAAATA
*
20587112 ATATGTAAAACAAATTAAAATAAATA
1 ATA--TAAAACAATTTAAAATAAATA
** *
20587138 ATAT---ACAAAGTAATA-AAAT-
1 ATATAAAACAATTTAAAATAAATA
* * *
20587157 ATATAAGACACTTTAAAAT-AA-C
1 ATATAAAACAATTTAAAATAAATA
* *
20587179 ATATAAAAGAGTTTAAAATAAATA
1 ATATAAAACAATTTAAAATAAATA
*
20587203 ATATGTAAAAAGGAAATTTAAAATAAATA
1 ATA--T-AAAA--CAATTTAAAATAAATA
* * *
20587232 ATGTACAAAAACATTTTAAATAAAATA
1 ATATA-AAACA-ATTTAAAAT-AAATA
* **
20587259 TATATATTTAAATAATCCAAAATAAATA
1 -ATATA---AAACAATTTAAAATAAATA
20587287 ATATATATAA-AAGTTTAAAATAAATA
1 ATATA-A-AACAA-TTTAAAATAAATA
20587313 A
1 A
20587314 CATTTAAAAA
Statistics
Matches: 177, Mismatches: 27, Indels: 42
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.02
20 4 0.02
21 9 0.05
22 25 0.14
23 2 0.01
24 28 0.16
25 6 0.03
26 46 0.26
27 18 0.10
28 9 0.05
29 22 0.12
30 4 0.02
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
ATATAAAACAATTTAAAATAAATA
Found at i:20587446 original size:25 final size:23
Alignment explanation
Indices: 20587348--20587440 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 23
20587338 ATAATAGTTT
* *
20587348 AAATACATAATACGTAAAAACTTA
1 AAATAAATAATA-ATAAAAACTTA
*
20587372 ACATAAATAATAATAAAACGACTTAAAAA
1 AAATAAATAATAATAAAA--ACTT----A
* *
20587401 AAATAATATAAGAAAAAAAACTTA
1 AAATAA-ATAATAATAAAAACTTA
20587425 AAATAAATAATAATAA
1 AAATAAATAATAATAA
20587441 CCAAACAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
23 13 0.24
24 17 0.31
25 4 0.07
28 4 0.07
29 6 0.11
30 10 0.19
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (23 bp):
AAATAAATAATAATAAAAACTTA
Found at i:20588255 original size:7 final size:7
Alignment explanation
Indices: 20588245--20588270 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20588235 TAAAGTAGAT
20588245 TAAAAAA
1 TAAAAAA
20588252 TAAAAAA
1 TAAAAAA
20588259 TAAAAAA
1 TAAAAAA
20588266 TAAAA
1 TAAAA
20588271 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:20588263 original size:5 final size:5
Alignment explanation
Indices: 20588248--20588290 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
20588238 AGTAGATTAA
20588248 AAAAT AAAA- AATAA- AAAAT AAAAT AAAAT AAAAT AGAAAT AAA
1 AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAA
20588291 CAAGAAATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.11
5 26 0.74
6 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:20589032 original size:44 final size:44
Alignment explanation
Indices: 20588984--20589104 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 44
20588974 ATCTACAATT
*
20588984 TGCTCCACTGCAACTTAAGGGAGATGAA-ATTTGTAACTTCAACC
1 TGCTCCACTGCAACTTCAGGGAGAT-AAGATTTGTAACTTCAACC
* * * * * *
20589028 TGCTCCATTGCAACTTCAGGGAGATAAGGTTTGTGATTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAACC
* *
20589072 TGCTTCACTACAACTTCAGGGAGATAAGATTTG
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTG
20589105 CTAAGGTAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.03
44 63 0.97
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAACC
Found at i:20597569 original size:20 final size:20
Alignment explanation
Indices: 20597544--20597599 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
20597534 AATGTATATG
20597544 ATGAAATGCAATGCAAATGA
1 ATGAAATGCAATGCAAATGA
20597564 ATGAAATGCAATGCAAATGA
1 ATGAAATGCAATGCAAATGA
20597584 ATGAAATG-AATGCAAA
1 ATGAAATGCAATGCAAA
20597600 AAGAGGCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.22
20 28 0.78
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.20
Consensus pattern (20 bp):
ATGAAATGCAATGCAAATGA
Found at i:20597595 original size:4 final size:5
Alignment explanation
Indices: 20597544--20597593 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
20597534 AATGTATATG
* *
20597544 ATGAA ATGCA ATGCAA ATG-A ATGAA ATGCA ATGCAA ATG-A ATGAA ATGAA
1 ATGAA ATGAA ATG-AA ATGAA ATGAA ATGAA ATG-AA ATGAA ATGAA ATGAA
20597594 TGCAAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 8 0.22
5 21 0.57
6 8 0.22
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (5 bp):
ATGAA
Found at i:20601326 original size:24 final size:24
Alignment explanation
Indices: 20601298--20601544 Score: 116
Period size: 26 Copynumber: 10.0 Consensus size: 24
20601288 ACAAAATATT
* * *
20601298 ATATAAAACAATTTGAAGTCAATA
1 ATATAAAACAATTTAAAATAAATA
*
20601322 ATATAAAACAATTTCAAATAAATA
1 ATATAAAACAATTTAAAATAAATA
*
20601346 ATATGTAAAACAAATTAAAATAAATA
1 ATA--TAAAACAATTTAAAATAAATA
** *
20601372 ATAT---ACAAAGTAATA-AAAT-
1 ATATAAAACAATTTAAAATAAATA
* * *
20601391 ATATAAGACACTTTAAAAT-AA-C
1 ATATAAAACAATTTAAAATAAATA
* *
20601413 ATATAAAAGAGTTTAAAATAAATA
1 ATATAAAACAATTTAAAATAAATA
*
20601437 ATATGTAAAAAGGAAATTTAAAATAAATA
1 ATA--T-AAAA--CAATTTAAAATAAATA
* * *
20601466 ATGTCCAAAAACAGTTT-AAATAAAAA
1 ATAT---AAAACAATTTAAAATAAATA
* **
20601492 TATATATAAATAATCCAAAATAAATA
1 -ATATA-AAACAATTTAAAATAAATA
20601518 ATATATATAA-AAGTTTAAAATAAATA
1 ATATA-A-AACAA-TTTAAAATAAATA
20601544 A
1 A
20601545 CATTTAAAAA
Statistics
Matches: 173, Mismatches: 29, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.02
20 4 0.02
21 9 0.05
22 25 0.14
23 2 0.01
24 29 0.17
25 14 0.08
26 53 0.31
27 12 0.07
29 21 0.12
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.28
Consensus pattern (24 bp):
ATATAAAACAATTTAAAATAAATA
Found at i:20601617 original size:27 final size:25
Alignment explanation
Indices: 20601578--20601669 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 25
20601568 GATAATAGTT
*
20601578 TAAATACATAATACGTAAAAACTTAACA
1 TAAATA-ATAATA-G-AAAAACTTAAAA
* *
20601606 TAAATAATAATA-AAACGATTTAAAA
1 TAAATAATAATAGAAA-AACTTAAAA
20601631 TAAATAAT-ATAAGAAAAAAACTTAAAA
1 TAAATAATAAT-AG--AAAAACTTAAAA
20601658 TAAATAATAATA
1 TAAATAATAATA
20601670 ACCAAACAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
24 5 0.09
25 15 0.28
27 22 0.42
28 11 0.21
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (25 bp):
TAAATAATAATAGAAAAACTTAAAA
Found at i:20604854 original size:22 final size:22
Alignment explanation
Indices: 20604828--20604902 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
20604818 GAACAAAATT
20604828 TTATTAACAATCTTAGATAGAG
1 TTATTAACAATCTTAGATAGAG
* * * *
20604850 TTATTATATATTTGGTATTACATAGAG
1 TTATTA-ACA----ATCTTAGATAGAG
20604877 TTATTAACAATCTTAGATAGAG
1 TTATTAACAATCTTAGATAGAG
20604899 TTAT
1 TTAT
20604903 GATATATTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 20 0.50
23 2 0.05
26 2 0.05
27 16 0.40
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (22 bp):
TTATTAACAATCTTAGATAGAG
Found at i:20616172 original size:3 final size:3
Alignment explanation
Indices: 20616164--20616200 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20616154 TAAAAGATAT
20616164 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20616201 GTCATACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20617426 original size:37 final size:38
Alignment explanation
Indices: 20617379--20617473 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 38
20617369 GATAGATTCG
*
20617379 ATGAGGCGTTGGTCGCCAC-TTTACTTCG-GCTTAGCCA
1 ATGAGGCGTTGGTCGCCACTTTTACTTCGAAC-TAGCCA
* * *
20617416 ATGAGACGTTGGTCGTCACTTATTTACTTCGAACTATCCA
1 ATGAGGCGTTGGTCGCCAC-T-TTTACTTCGAACTAGCCA
20617456 ATGAGGCGTTGGTCGCCA
1 ATGAGGCGTTGGTCGCCA
20617474 TTCGGGTGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
37 17 0.35
40 30 0.62
41 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (38 bp):
ATGAGGCGTTGGTCGCCACTTTTACTTCGAACTAGCCA
Found at i:20629253 original size:19 final size:19
Alignment explanation
Indices: 20629216--20629253 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20629206 TATTTTAATA
*
20629216 ATAAATATATATTACAATT
1 ATAAATATATAATACAATT
20629235 ATAAATATAATAATA-AATT
1 ATAAATAT-ATAATACAATT
20629254 GTTAGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAATATATAATACAATT
Found at i:20636379 original size:102 final size:101
Alignment explanation
Indices: 20636250--20636454 Score: 374
Period size: 102 Copynumber: 2.0 Consensus size: 101
20636240 AGCTTTTTTC
* *
20636250 AATTATTTTGATTTTAAAGCTGATTGTTTGGCATTGCTTATGCTGTCAAAAAGTGCTTTTCCACC
1 AATTAATTTGATTTAAAAGCTGATTGTTTGGCATTGCTTATGCTGTCAAAAAGTGCTTTTCCACC
*
20636315 TCTATGAGCAATGGTAAACAAAACCTTAGTGGTGAA
66 TCTATGAGCAATGCTAAACAAAACCTTAGTGGTGAA
20636351 AATTAATTTGATGTTAAAAGCTGATTGTTTGGCATTGCTTATGCTGTCAAAAAGTGCTTTTCCAC
1 AATTAATTTGAT-TTAAAAGCTGATTGTTTGGCATTGCTTATGCTGTCAAAAAGTGCTTTTCCAC
20636416 CTCTATGAGCAATGCTAAACAAAACCTTAGTGGTGAA
65 CTCTATGAGCAATGCTAAACAAAACCTTAGTGGTGAA
20636453 AA
1 AA
20636455 GTTAGAAGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
101 11 0.11
102 89 0.89
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (101 bp):
AATTAATTTGATTTAAAAGCTGATTGTTTGGCATTGCTTATGCTGTCAAAAAGTGCTTTTCCACC
TCTATGAGCAATGCTAAACAAAACCTTAGTGGTGAA
Found at i:20636694 original size:26 final size:26
Alignment explanation
Indices: 20636653--20636708 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
20636643 CTTATATAGT
*
20636653 AAAAATAACTTT-AAAATACTATATA
1 AAAAATAACTTTAAAAATACAATATA
20636678 AAAAACTAA-TTTGAAAAAATACAATATA
1 AAAAA-TAACTTT--AAAAATACAATATA
20636706 AAA
1 AAA
20636709 GTTATAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 8 0.31
26 3 0.12
28 15 0.58
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (26 bp):
AAAAATAACTTTAAAAATACAATATA
Found at i:20640162 original size:4 final size:4
Alignment explanation
Indices: 20640153--20640422 Score: 429
Period size: 4 Copynumber: 68.2 Consensus size: 4
20640143 CAACTTTCAC
20640153 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
20640201 ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT AC-T ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
20640247 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * *
20640295 AC-T ACAT ACAT ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAG
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
20640342 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
20640390 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
20640423 TTCCGATTGA
Statistics
Matches: 258, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
3 9 0.03
4 249 0.97
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:20640313 original size:2 final size:2
Alignment explanation
Indices: 20640306--20640340 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20640296 CTACATACAT
20640306 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20640341 GACATACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20649664 original size:42 final size:42
Alignment explanation
Indices: 20649617--20649727 Score: 179
Period size: 42 Copynumber: 2.6 Consensus size: 42
20649607 ACGTGTTAAT
*
20649617 TAAACTAAAATTTAATTCACATTGAGAAACAACCGTACTAAC
1 TAAACTAAAATTTAATCCACATTGAGAAACAACCGTACTAAC
* *
20649659 TAAACTAAAATTTAATCCACATTAAGAAACAACCGTGCTAAC
1 TAAACTAAAATTTAATCCACATTGAGAAACAACCGTACTAAC
20649701 TAAACTAAATATTT-ATCCACATTGAGA
1 TAAACTAAA-ATTTAATCCACATTGAGA
20649728 GTATACATTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.27
Consensus pattern (42 bp):
TAAACTAAAATTTAATCCACATTGAGAAACAACCGTACTAAC
Found at i:20650310 original size:3 final size:3
Alignment explanation
Indices: 20650302--20650343 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
20650292 ATGCATTATC
20650302 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20650344 GAGAGCTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20659902 original size:41 final size:41
Alignment explanation
Indices: 20659855--20659937 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
20659845 CATTCTTCAC
*
20659855 ATAACAGTTAATACATAGTTCTATACTAATATTCAAATACA
1 ATAACAGTTAATACAGAGTTCTATACTAATATTCAAATACA
20659896 ATAACAGTTAATACAGAGTTCTATACTAATATTCAAATACA
1 ATAACAGTTAATACAGAGTTCTATACTAATATTCAAATACA
20659937 A
1 A
20659938 CTCATACTCG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (41 bp):
ATAACAGTTAATACAGAGTTCTATACTAATATTCAAATACA
Found at i:20660925 original size:36 final size:35
Alignment explanation
Indices: 20660882--20660953 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
20660872 ACGTAATCAA
* *
20660882 AAAGAAAAGTA-AAAGGAAAAAGGAGAAAGGAGAAAG
1 AAAGAAAAGAAGAAAAGAAAAAGGA-AAAGG-GAAAG
*
20660918 AAAGAAAAGAAGAAAAGAAAATGGAAAAGGGAAAG
1 AAAGAAAAGAAGAAAAGAAAAAGGAAAAGGGAAAG
20660953 A
1 A
20660954 GATAAAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 6 0.19
36 15 0.47
37 11 0.34
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (35 bp):
AAAGAAAAGAAGAAAAGAAAAAGGAAAAGGGAAAG
Found at i:20664281 original size:40 final size:40
Alignment explanation
Indices: 20664207--20664466 Score: 413
Period size: 40 Copynumber: 6.6 Consensus size: 40
20664197 AACCCAAGTA
* *
20664207 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
20664246 CCTTC-GGATCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATG
*
20664286 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
20664326 CCTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
20664365 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
20664405 CCTTCGGGACTTAGCCC-GATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
20664444 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
20664467 CATCCGAATA
Statistics
Matches: 206, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
38 3 0.01
39 83 0.40
40 116 0.56
41 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:20664352 original size:79 final size:79
Alignment explanation
Indices: 20664207--20664466 Score: 427
Period size: 79 Copynumber: 3.3 Consensus size: 79
20664197 AACCCAAGTA
* * *
20664207 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCACAAATGCCTTC-GGATCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCATAAATGCCTTCGGGA-CTTAG-CCGGATAT
*
20664269 AGTCACTAGCACAAATG
63 AGTCACTAGCACAAAGG
20664286 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCGGATATAGT
20664351 CACTAGCACAAAGG
66 CACTAGCACAAAGG
*
20664365 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCGGATATAGT
20664430 CACTAGCACAAAGG
66 CACTAGCACAAAGG
20664444 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
20664467 CATCCGAATA
Statistics
Matches: 173, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
79 138 0.80
80 31 0.18
81 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCGGATATAGT
CACTAGCACAAAGG
Found at i:20664418 original size:119 final size:118
Alignment explanation
Indices: 20664207--20664466 Score: 416
Period size: 119 Copynumber: 2.2 Consensus size: 118
20664197 AACCCAAGTA
* * *
20664207 CCTTCGGGAATTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAAGGCCTTCGGATCTTAGCCCGGATATAGT
* *
20664272 CACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
66 CACTAGCACAAATGCCTTCGGGACTTAGCCC-GATATAGTCACTAGCACAAAGG
20664326 CCTTCGGGACTTAGCCGGATATAGTC-ACTAGCACAAAGGCCTTCGGGA-CTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCGGATATAG-CAACTAGCACAAAGGCCTTC-GGATCTTAGCCCGGATATA
*
20664389 GTCACTAGCATAAATGCCTTCGGGACTTAGCCCGATATAGTCACTAGCACAAAGG
64 GTCACTAGCACAAATGCCTTCGGGACTTAGCCCGATATAGTCACTAGCACAAAGG
20664444 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAG-CCGGATAT
20664467 CATCCGAATA
Statistics
Matches: 132, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
118 34 0.26
119 94 0.71
120 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (118 bp):
CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAAGGCCTTCGGATCTTAGCCCGGATATAGT
CACTAGCACAAATGCCTTCGGGACTTAGCCCGATATAGTCACTAGCACAAAGG
Found at i:20672245 original size:40 final size:40
Alignment explanation
Indices: 20672171--20672432 Score: 429
Period size: 40 Copynumber: 6.6 Consensus size: 40
20672161 AACCCAAGTA
* *
20672171 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
20672210 CCTTCGGGTCTTAGCCCTGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
20672250 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
20672290 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
20672330 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
20672370 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
20672410 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
20672433 CATCCGAATA
Statistics
Matches: 208, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
39 12 0.06
40 195 0.94
41 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:20676571 original size:46 final size:44
Alignment explanation
Indices: 20676512--20676626 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
20676502 ACAGAACAGA
* *
20676512 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
20676558 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
20676602 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
20676627 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:20676607 original size:44 final size:45
Alignment explanation
Indices: 20676512--20676645 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
20676502 ACAGAACAGA
* *
20676512 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
20676558 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
20676602 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20676646 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:20678134 original size:16 final size:15
Alignment explanation
Indices: 20678094--20678151 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
20678084 AGTATAAGAT
20678094 ATTTAATATATAATA
1 ATTTAATATATAATA
*
20678109 AATT-AT-TATAATA
1 ATTTAATATATAATA
20678122 ATTTAATAATATAATA
1 ATTTAAT-ATATAATA
* *
20678138 GTTAAAATATATAA
1 ATT-TAATATATAA
20678152 AGAAACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 10 0.29
14 4 0.11
15 3 0.09
16 15 0.43
17 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTTAATATATAATA
Found at i:20678885 original size:44 final size:45
Alignment explanation
Indices: 20678829--20678924 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 45
20678819 GCATGGCTAT
20678829 TGAA-ATTAAGGTAAGTATTGATATTGTGGTATTGTGTTGACTTA
1 TGAATATTAAGGTAAGTATTGATATTGTGGTATTGTGTTGACTTA
20678873 TGAATATT-AGGTAAGTATTGATATTGTGGTATTGTGTTGACTTA
1 TGAATATTAAGGTAAGTATTGATATTGTGGTATTGTGTTGACTTA
20678917 TGAATATT
1 TGAATATT
20678925 TTAATTAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 48 0.94
45 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.45
Consensus pattern (45 bp):
TGAATATTAAGGTAAGTATTGATATTGTGGTATTGTGTTGACTTA
Found at i:20682766 original size:13 final size:13
Alignment explanation
Indices: 20682748--20682775 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20682738 TAAACTGGAT
20682748 TTTTCAACCGTAC
1 TTTTCAACCGTAC
20682761 TTTTCAACCGTAC
1 TTTTCAACCGTAC
20682774 TT
1 TT
20682776 GGATCAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (13 bp):
TTTTCAACCGTAC
Found at i:20685480 original size:8 final size:8
Alignment explanation
Indices: 20685455--20685504 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
20685445 TATTTAACAT
20685455 ATAATATA
1 ATAATATA
* *
20685463 TTATTATA
1 ATAATATA
*
20685471 ATAATTTA
1 ATAATATA
20685479 ATAATATA
1 ATAATATA
*
20685487 ATAA-AGA
1 ATAATATA
20685494 ATAATATA
1 ATAATATA
20685502 ATA
1 ATA
20685505 GTTAAAATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
ATAATATA
Found at i:20685528 original size:17 final size:17
Alignment explanation
Indices: 20685508--20685540 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20685498 TATAATAGTT
20685508 AAAATA-AATAAAGAAAC
1 AAAATAGAA-AAAGAAAC
20685525 AAAATAGAAAAAGAAA
1 AAAATAGAAAAAGAAA
20685541 GAACAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAAGAAAC
Found at i:20690018 original size:3 final size:3
Alignment explanation
Indices: 20690010--20690059 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
20690000 TATTCCAATT
20690010 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
20690055 TTA TT
1 TTA TT
20690060 TCTTTTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:20690806 original size:6 final size:6
Alignment explanation
Indices: 20690795--20690837 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
20690785 TCGAAGCCGG
20690795 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
20690838 CGGTACACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:20690883 original size:6 final size:6
Alignment explanation
Indices: 20690872--20690902 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20690862 ACAAATCCGA
*
20690872 AACAGT AACAGT AACAGT AACGGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
20690903 TTCGACACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:20690942 original size:12 final size:12
Alignment explanation
Indices: 20690925--20690949 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20690915 AGTGTCGAAT
20690925 CGGTAACAGTAA
1 CGGTAACAGTAA
20690937 CGGTAACAGTAA
1 CGGTAACAGTAA
20690949 C
1 C
20690950 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:20691594 original size:5 final size:5
Alignment explanation
Indices: 20691584--20691623 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
20691574 TTTCTTTTAT
20691584 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
20691624 CTTAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:20692418 original size:27 final size:27
Alignment explanation
Indices: 20692380--20692432 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
20692370 TAAAATATGG
*
20692380 GTGGAGGGTACCCCATAGGCGGCACCA
1 GTGGAGGGTACCCCACAGGCGGCACCA
20692407 GTGGAGGGTACCCCACAGGCGGCACC
1 GTGGAGGGTACCCCACAGGCGGCACC
20692433 GCTGACTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.38, T:0.09
Consensus pattern (27 bp):
GTGGAGGGTACCCCACAGGCGGCACCA
Found at i:20692582 original size:6 final size:6
Alignment explanation
Indices: 20692573--20692673 Score: 163
Period size: 6 Copynumber: 17.2 Consensus size: 6
20692563 AAGAAAGGGG
*
20692573 GAAGGA GAAG-A GAAAGA- GAAG-A GAAGAA GAAGAA GAAGAA GAAGAA
1 GAAGAA GAAGAA G-AAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA
20692619 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA
1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA
20692667 GAAGAA G
1 GAAGAA G
20692674 GAGGAGGAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
5 9 0.10
6 82 0.90
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GAAGAA
Found at i:20692602 original size:3 final size:3
Alignment explanation
Indices: 20692589--20692673 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
20692579 GAAGAGAAAG
20692589 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
20692636 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
20692674 GAGGAGGAGG
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20692717 original size:6 final size:6
Alignment explanation
Indices: 20692706--20692736 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20692696 TGAGGGAAGA
*
20692706 AAAAAG AAAAAG AAAAAG AGAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
20692737 GAAGGAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:20692731 original size:18 final size:18
Alignment explanation
Indices: 20692708--20692754 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
20692698 AGGGAAGAAA
20692708 AAAGAAAAAGAAAAAGAG
1 AAAGAAAAAGAAAAAGAG
* *
20692726 AAAGAAAAAGAGAAGGAG
1 AAAGAAAAAGAAAAAGAG
*
20692744 -AAGAAGAAGAA
1 AAAGAAAAAGAA
20692755 GAGGGAGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAAAAAGAG
Found at i:20692737 original size:12 final size:12
Alignment explanation
Indices: 20692706--20692739 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
20692696 TGAGGGAAGA
*
20692706 AAAAAGAAAAAG
1 AAAAAGAGAAAG
20692718 AAAAAGAGAAAG
1 AAAAAGAGAAAG
20692730 AAAAAGAGAA
1 AAAAAGAGAA
20692740 GGAGAAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:20693213 original size:14 final size:14
Alignment explanation
Indices: 20693194--20693222 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20693184 AGCTTAATAG
20693194 TATATTTTAAAAAA
1 TATATTTTAAAAAA
20693208 TATATTTTAAAAAA
1 TATATTTTAAAAAA
20693222 T
1 T
20693223 CTGAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATTTTAAAAAA
Found at i:20693366 original size:14 final size:14
Alignment explanation
Indices: 20693324--20693376 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
20693314 AAAATAATAA
*
20693324 AAAAATAAAATATG
1 AAAAATAAAATTTG
* *
20693338 AAATAATATATTTTG
1 AAA-AATAAAATTTG
20693353 AAAAATAAAATTTG
1 AAAAATAAAATTTG
20693367 -AAAATAAAAT
1 AAAAATAAAAT
20693377 AAAAAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
13 10 0.30
14 12 0.36
15 11 0.33
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (14 bp):
AAAAATAAAATTTG
Found at i:20693447 original size:145 final size:147
Alignment explanation
Indices: 20693226--20694399 Score: 1563
Period size: 147 Copynumber: 8.1 Consensus size: 147
20693216 AAAAAATCTG
* * * *
20693226 AAAATAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAATATACTAAAATA
1 AAAATAAAA-AAAAACGGCCAAAATCAGAGATTTTTTACTAAATTAATATAAAAAAACTAAAATA
* * * * *
20693291 ATACATATGAAACGTTATGTACTAAAATAATA-AAAAAATAAAATATG-AAATAATATATTTTGA
65 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAAAATAGTATATTTTAA
**
20693354 AAAATAAAATTTGAAAAT
130 AAAATAAAATCCGAAAAT
20693372 AAAATAAAAAACAAACGGCCAAAATCAGA-ATTTTTTACTAAATTAATATAAAAAAACTAAAATA
1 AAAATAAAAAA-AAACGGCCAAAATCAGAGATTTTTTACTAAATTAATATAAAAAAACTAAAATA
*
20693436 ATACATTTGAAACATTATGTACAAAAATAATATAAAAAATAAAATACA-AAAATAGTATATTTTA
65 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA-AGAAAATAGTATATTTTA
*
20693500 AAATAA-AAAATCCGAAAAC
129 AAA-AATAAAATCCGAAAAT
* * *
20693519 AAAAT-AAATAAAA-GGCCAAAACCACAGA-TTTTTACTAAATTAATATAAAAAAACTAAAATAA
1 AAAATAAAAAAAAACGGCCAAAATCAGAGATTTTTTACTAAATTAATATAAAAAAACTAAAATAA
* * * *
20693581 TACA--TGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATAATATATCTTAAA
66 TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAAAATAGTATATTTTAAA
**
20693644 AAATAAAATTTGAAAAT
131 AAATAAAATCCGAAAAT
* * *
20693661 -AAA-AATAAAAAA-GACCAAAATCAGAG-TTTTTTTCTAAATTAATATAAAAAAAACTAAAATA
1 AAAATAAAAAAAAACGGCCAAAATCAGAGATTTTTTACTAAATTAATAT-AAAAAAACTAAAATA
* *
20693722 ATACATTTCAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTA
65 ATACATTTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATAAGAAAATAGTATATTTTA
*
20693787 AAAAATAAAATCCGAAAAA
129 AAAAATAAAATCCGAAAAT
* *
20693806 AAAAT-AAATAAAACGGCCAAAATCACAGA-TTTTTACTAAATTAATATAAAAAAAACTAAAATA
1 AAAATAAAAAAAAACGGCCAAAATCAGAGATTTTTTACTAAATTAATAT-AAAAAAACTAAAATA
* *
20693869 ATACA--TGAAACATTATGTACAAAAATAATATAAAAAATAAAATAAGAAAATAGTATATTTTGA
65 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAAAATAGTATATTTTAA
20693932 AAAATAAAATCCGAAAAT
130 AAAATAAAATCCGAAAAT
* * * *
20693950 -AAA-AAATAAAAA-GTGCCAAAATCAGAGTTTTTTTTCTATATTAATATAAAAAAACTAAAATA
1 AAAATAAAAAAAAACG-GCCAAAATCAGAGATTTTTTACTAAATTAATATAAAAAAACTAAAATA
* **
20694012 ATACATTTTAAACATTATGTACTAAAATAATATAAAAAACATAAAATTCGAAAATAGTATATTTT
65 ATACATTTGAAACATTATGTACTAAAATAATAT-AAAAA-ATAAAATAAGAAAATAGTATATTTT
20694077 AAAAAAATAAAATCCGAAAAT
128 -AAAAAATAAAATCCGAAAAT
*
20694098 AAAATAAAAAATAAACGGCCAAAATCAGAG-TTTTTTATTAAATTAATAT-AAAAAACTAAAATA
1 AAAATAAAAAA-AAACGGCCAAAATCAGAGATTTTTTACTAAATTAATATAAAAAAACTAAAATA
* * * *
20694161 ATACATTTGGAACATTATATACTAAAATAATATAAAAAATAAAATATGAAAATAGTTTATTTTAA
65 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAAAATAGTATATTTTAA
* *
20694226 AAAGTAAAATCCGAGAAT
130 AAAATAAAATCCGAAAAT
* * *
20694244 AAAATAAAAAAACAAACGGTCAAAATCAGAG-TTTTTTATTAAATTAATATAAAAGAAACAAAAA
1 AAAAT-AAAAAA-AAACGGCCAAAATCAGAGATTTTTTACTAAATTAATATAAAA-AAACTAAAA
* *
20694308 TAGTACATTTGAAACATTATGTACTAAAATAATAT-AAAAATAAAATACA-AAAATAATATATTT
63 TAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA-AGAAAATAGTATATTT
20694371 TAAAAAATAAAATCCGAAAAT
127 TAAAAAATAAAATCCGAAAAT
20694392 AAAATAAA
1 AAAATAAA
20694400 TACTAAAATA
Statistics
Matches: 913, Mismatches: 81, Indels: 67
0.86 0.08 0.06
Matches are distributed among these distances:
141 39 0.04
142 85 0.09
143 41 0.04
144 137 0.15
145 159 0.17
146 79 0.09
147 171 0.19
148 77 0.08
149 87 0.10
150 21 0.02
151 16 0.02
152 1 0.00
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (147 bp):
AAAATAAAAAAAAACGGCCAAAATCAGAGATTTTTTACTAAATTAATATAAAAAAACTAAAATAA
TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAAAATAGTATATTTTAAA
AAATAAAATCCGAAAAT
Found at i:20693475 original size:12 final size:13
Alignment explanation
Indices: 20693455--20693494 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
20693445 AAACATTATG
20693455 TACAAAAATAATA
1 TACAAAAATAATA
*
20693468 TA-AAAAATAAAA
1 TACAAAAATAATA
*
20693480 TACAAAAATAGTA
1 TACAAAAATAATA
20693493 TA
1 TA
20693495 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (13 bp):
TACAAAAATAATA
Found at i:20693486 original size:13 final size:13
Alignment explanation
Indices: 20693455--20693489 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
20693445 AAACATTATG
*
20693455 TACAAAAATAATA
1 TACAAAAATAAAA
20693468 TA-AAAAATAAAA
1 TACAAAAATAAAA
20693480 TACAAAAATA
1 TACAAAAATA
20693490 GTATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (13 bp):
TACAAAAATAAAA
Found at i:20693577 original size:289 final size:286
Alignment explanation
Indices: 20693218--20694401 Score: 1632
Period size: 289 Copynumber: 4.1 Consensus size: 286
20693208 TATATTTTAA
* * * *
20693218 AAAATCTGAAAATAAAAT-AA-AAAAGGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAATA
1 AAAATCCGAAAATAAAATAAATAAAAGGCCAAAATCACAG-ATTTTTACTAAATTAATATAAAAA
* *
20693281 TACTAAAATAATACATATGAAACGTTATGTACTAAAATAATA-AAAAAATAAAATATG-AAATAA
65 AACTAAAATAATAC--ATGAAACATTATGTACTAAAATAATATAAAAAATAAAATATGAAAATAA
** *
20693344 TATATTTTGAAAAATAAAATTTGAAAATAAAATAAAAAACAAACGGCCAAAATCAGAATTTTTTA
128 TATATTTTGAAAAATAAAATCCGAAAAT-AAA-AAAAAA-AAA-GGCCAAAATCAGAGTTTTTTA
*
20693409 CTAAATTAATATAAAAAAACTAAAATAATACATTTGAAACATTATGTACAAAAATAATAT-AAAA
189 CTAAATTAATATAAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAA
20693473 AATAAAATACAAAAATAGTATATTTTAAAATAA-
254 AATAAAATACAAAAATAGTATATTTTAAAA-AAT
* *
20693506 AAAATCCGAAAACAAAATAAATAAAAGGCCAAAACCACAGATTTTTACTAAATTAATATAAAAAA
1 AAAATCCGAAAATAAAATAAATAAAAGGCCAAAATCACAGATTTTTACTAAATTAATATAAAAAA
* *
20693571 ACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATAATAT
66 ACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAATAAAATATGAAAATAATAT
* * ** * * *
20693636 ATCTTAAAAAATAAAATTTGAAAATAAAAATAAAAAAGACCAAAATCAGAGTTTTTTTCTAAATT
131 ATTTTGAAAAATAAAATCCGAAAATAAAAAAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATT
*
20693701 AATATAAAAAAAACTAAAATAATACATTTCAAACATTATGTACTAAAATAATATAAAAAAATAAA
196 AATAT-AAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAA
*
20693766 ATACGAAAATAGTATATTTTAAAAAAT
260 ATACAAAAATAGTATATTTTAAAAAAT
*
20693793 AAAATCCGAAAAAAAAATAAATAAAACGGCCAAAATCACAGATTTTTACTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAATAAATAAAA-GGCCAAAATCACAGATTTTTACTAAATTAATAT-AAAA
* * *
20693858 AAACTAAAATAATACATGAAACATTATGTACAAAAATAATATAAAAAATAAAATAAGAAAATAGT
64 AAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAATAAAATATGAAAATAAT
* *
20693923 ATATTTTGAAAAATAAAATCCGAAAATAAAAAATAAAAAGTGCCAAAATCAGAGTTTTTTTTCTA
129 ATATTTTGAAAAATAAAATCCGAAAATAAAAAAAAAAAAG-GCCAAAATCAGAG-TTTTTTACTA
* *
20693988 TATTAATATAAAAAAACTAAAATAATACATTTTAAACATTATGTACTAAAATAATATAAAAAACA
192 AATTAATATAAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAA-A
* *
20694053 TAAAATTCGAAAATAGTATATTTTAAAAAAAT
256 TAAAATACAAAAATAGTATATTTT-AAAAAAT
* * * *
20694085 AAAATCCGAAAATAAAATAAAAAATAAACGGCCAAAATCAGAGTTTTTTATTAAATTAATAT-AA
1 AAAATCCGAAAATAAAAT---AAATAAAAGGCCAAAATCACAGATTTTTACTAAATTAATATAAA
* *
20694149 AAAACTAAAATAATACATTTGGAACATTATATACTAAAATAATATAAAAAATAAAATATGAAAAT
63 AAAACTAAAATAATACA--TGAAACATTATGTACTAAAATAATATAAAAAATAAAATATGAAAAT
* * * *
20694214 AGTTTATTTT-AAAAAGTAAAATCCGAGAATAAAATAAAAAAACAAACGGTCAAAATCAGAGTTT
126 AATATATTTTGAAAAA-TAAAATCCGA-AA-ATAA-AAAAAAA-AAA-GGCCAAAATCAGAGTTT
* * *
20694278 TTTATTAAATTAATATAAAAGAAACAAAAATAGTACATTTGAAACATTATGTACTAAAATAATAT
185 TTTACTAAATTAATATAAAA-AAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT
*
20694343 --AAAAATAAAATACAAAAATAATATATTTTAAAAAAT
249 AAAAAAATAAAATACAAAAATAGTATATTTTAAAAAAT
20694379 AAAATCCGAAAATAAAATAAATA
1 AAAATCCGAAAATAAAATAAATA
20694402 CTAAAATATA
Statistics
Matches: 814, Mismatches: 57, Indels: 47
0.89 0.06 0.05
Matches are distributed among these distances:
285 30 0.04
286 51 0.06
287 88 0.11
288 64 0.08
289 168 0.21
290 81 0.10
291 47 0.06
292 43 0.05
293 5 0.01
294 116 0.14
295 31 0.04
296 7 0.01
297 26 0.03
298 56 0.07
299 1 0.00
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (286 bp):
AAAATCCGAAAATAAAATAAATAAAAGGCCAAAATCACAGATTTTTACTAAATTAATATAAAAAA
ACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAATAAAATATGAAAATAATAT
ATTTTGAAAAATAAAATCCGAAAATAAAAAAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATT
AATATAAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAA
TACAAAAATAGTATATTTTAAAAAAT
Found at i:20694280 original size:147 final size:147
Alignment explanation
Indices: 20693226--20694399 Score: 1593
Period size: 145 Copynumber: 8.1 Consensus size: 147
20693216 AAAAAATCTG
* *
20693226 AAAATAAAATAAAAAA-GGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAATATACTAAAAT
1 AAAATAAAA-AAAAAACGGCCAAAATCAGAG-TTTTTTACTAAATTAATATAAAAAAACTAAAAT
* * * * *
20693290 AATACATATGAAACGTTATGTACTAAAATAATA-AAAAAATAAAATATG-AAATAATATATTTTG
64 AATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTA
**
20693353 AAAAATAAAATTTGAAAAT
129 AAAAATAAAATCCGAAAAT
* *
20693372 AAAATAAAAAACAAACGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAAACTAAAATAA
1 AAAATAAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAAACTAAAATAA
* *
20693437 TACATTTGAAACATTATGTACAAAAATAATATAAAAAATAAAATACAAAAATAGTATATTTTAAA
66 TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
*
20693502 ATAA-AAAATCCGAAAAC
131 A-AATAAAATCCGAAAAT
* * * *
20693519 AAAAT--AAATAAAA-GGCCAAAACCACAGATTTTTACTAAATTAATATAAAAAAACTAAAATAA
1 AAAATAAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAAACTAAAATAA
* * *
20693581 TACA--TGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATAATATATCTTAAA
66 TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
**
20693644 AAATAAAATTTGAAAAT
131 AAATAAAATCCGAAAAT
* * *
20693661 --AA-AAATAAAAAA-GACCAAAATCAGAGTTTTTTTCTAAATTAATATAAAAAAAACTAAAATA
1 AAAATAAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AAAAAAACTAAAATA
*
20693722 ATACATTTCAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTA
65 ATACATTTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTA
20693787 AAAAATAAAATCCGAAAA-
129 AAAAATAAAATCCGAAAAT
* * * *
20693805 AAAA-ATAAATAAAACGGCCAAAATCACAGATTTTTACTAAATTAATATAAAAAAAACTAAAATA
1 AAAATAAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AAAAAAACTAAAATA
* * *
20693869 ATACA--TGAAACATTATGTACAAAAATAATATAAAAAATAAAATAAGAAAATAGTATATTTTGA
65 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAA
20693932 AAAATAAAATCCGAAAAT
130 AAAATAAAATCCGAAAAT
* * *
20693950 --AA-AAAATAAAAA-GTGCCAAAATCAGAGTTTTTTTTCTATATTAATATAAAAAAACTAAAAT
1 AAAATAAAAAAAAAACG-GCCAAAATCAGAG-TTTTTTACTAAATTAATATAAAAAAACTAAAAT
* *
20694011 AATACATTTTAAACATTATGTACTAAAATAATATAAAAAACATAAAATTCGAAAATAGTATATTT
64 AATACATTTGAAACATTATGTACTAAAATAATAT-AAAAA-ATAAAATACGAAAATAGTATATTT
20694076 TAAAAAAATAAAATCCGAAAAT
127 T-AAAAAATAAAATCCGAAAAT
* *
20694098 AAAATAAAAAATAAACGGCCAAAATCAGAGTTTTTTATTAAATTAATAT-AAAAAACTAAAATAA
1 AAAATAAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAAACTAAAATAA
* * * *
20694162 TACATTTGGAACATTATATACTAAAATAATATAAAAAATAAAATATGAAAATAGTTTATTTTAAA
66 TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
* *
20694227 AAGTAAAATCCGAGAAT
131 AAATAAAATCCGAAAAT
* * *
20694244 AAAATAAAAAAACAAACGGTCAAAATCAGAGTTTTTTATTAAATTAATATAAAAGAAACAAAAAT
1 AAAATAAAAAAA-AAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAA-AAACTAAAAT
* * *
20694309 AGTACATTTGAAACATTATGTACTAAAATAATAT-AAAAATAAAATACAAAAATAATATATTTTA
64 AATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTA
20694373 AAAAATAAAATCCGAAAAT
129 AAAAATAAAATCCGAAAAT
20694392 AAAATAAA
1 AAAATAAA
20694400 TACTAAAATA
Statistics
Matches: 910, Mismatches: 89, Indels: 56
0.86 0.08 0.05
Matches are distributed among these distances:
140 2 0.00
141 36 0.04
142 86 0.09
143 41 0.05
144 137 0.15
145 164 0.18
146 78 0.09
147 162 0.18
148 80 0.09
149 84 0.09
150 18 0.02
151 21 0.02
152 1 0.00
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (147 bp):
AAAATAAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAAACTAAAATAA
TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
AAATAAAATCCGAAAAT
Found at i:20698549 original size:17 final size:17
Alignment explanation
Indices: 20698527--20698560 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20698517 ACAAAATTAC
*
20698527 CTTCTCTTTTCTTTCTT
1 CTTCTCCTTTCTTTCTT
20698544 CTTCTCCTTTCTTTCTT
1 CTTCTCCTTTCTTTCTT
20698561 TCTATCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTCTCCTTTCTTTCTT
Found at i:20698678 original size:27 final size:27
Alignment explanation
Indices: 20698648--20698730 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
20698638 GGGGTCAAGG
**
20698648 CTGTGAGAAAGGCACCACTGGTGCCGC
1 CTGTGAGAAACCCACCACTGGTGCCGC
* ** *
20698675 CTGTGGGGTACCCTCCACTGGTGCCGC
1 CTGTGAGAAACCCACCACTGGTGCCGC
* ** *
20698702 CTGTGGGGTACCCTCCACTGGTGCCGC
1 CTGTGAGAAACCCACCACTGGTGCCGC
20698729 CT
1 CT
20698731 TTGGGGTACC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.12, C:0.35, G:0.33, T:0.20
Consensus pattern (27 bp):
CTGTGAGAAACCCACCACTGGTGCCGC
Found at i:20698735 original size:27 final size:27
Alignment explanation
Indices: 20698662--20698743 Score: 155
Period size: 27 Copynumber: 3.0 Consensus size: 27
20698652 GAGAAAGGCA
20698662 CCACTGGTGCCGCCTGTGGGGTACCCT
1 CCACTGGTGCCGCCTGTGGGGTACCCT
20698689 CCACTGGTGCCGCCTGTGGGGTACCCT
1 CCACTGGTGCCGCCTGTGGGGTACCCT
*
20698716 CCACTGGTGCCGCCTTTGGGGTACCCT
1 CCACTGGTGCCGCCTGTGGGGTACCCT
20698743 C
1 C
20698744 TACCCTTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.07, C:0.38, G:0.32, T:0.23
Consensus pattern (27 bp):
CCACTGGTGCCGCCTGTGGGGTACCCT
Found at i:20700368 original size:2 final size:2
Alignment explanation
Indices: 20700361--20700391 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20700351 ACAGCAGGTG
20700361 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
20700392 GATGTCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20703615 original size:7 final size:7
Alignment explanation
Indices: 20703598--20703632 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
20703588 AATAATAGTT
20703598 GTAGA-A
1 GTAGAGA
20703604 GTAGAGA
1 GTAGAGA
20703611 GTAGAGA
1 GTAGAGA
20703618 GTAGAGA
1 GTAGAGA
20703625 GTAGAGA
1 GTAGAGA
20703632 G
1 G
20703633 AGGACAGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (7 bp):
GTAGAGA
Found at i:20712539 original size:31 final size:30
Alignment explanation
Indices: 20712466--20712539 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
20712456 TTTAAAAAGC
* *
20712466 TATACAATTGAATCAAAATCAAAGTTTATG
1 TATACAATTGAACCAAAATCAAAATTTATG
* * *
20712496 TGTTCAATTGAACCAAAATCAAAATTTCATT
1 TATACAATTGAACCAAAATCAAAATTT-ATG
*
20712527 TATAGAATTGAAC
1 TATACAATTGAAC
20712540 AAAGTTTTGC
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 23 0.66
31 12 0.34
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (30 bp):
TATACAATTGAACCAAAATCAAAATTTATG
Found at i:20717161 original size:15 final size:15
Alignment explanation
Indices: 20717141--20717171 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20717131 CTGTCGGGGA
20717141 AATAACATGCAATGG
1 AATAACATGCAATGG
20717156 AATAACATGCAATGG
1 AATAACATGCAATGG
20717171 A
1 A
20717172 TCGGATCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (15 bp):
AATAACATGCAATGG
Found at i:20717280 original size:24 final size:25
Alignment explanation
Indices: 20717247--20717300 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 25
20717237 AATACTAGCT
20717247 GATAAGCCACTAATCTGACTCGCTC
1 GATAAGCCACTAATCTGACTCGCTC
*
20717272 -ATAAGCCACTAGTCTGACTCGCTC
1 GATAAGCCACTAATCTGACTCGCTC
20717296 GATAA
1 GATAA
20717301 TCTCATAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (25 bp):
GATAAGCCACTAATCTGACTCGCTC
Found at i:20743305 original size:22 final size:23
Alignment explanation
Indices: 20743275--20743325 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
20743265 AGATTAAATG
*
20743275 TTACATTAT-ATTTTATAATTTTT
1 TTACATTATAAGTTTA-AATTTTT
20743298 TTAC-TTATAGAGTTTAAATTTTT
1 TTACATTATA-AGTTTAAATTTTT
20743321 TTACA
1 TTACA
20743326 AAAAGTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (23 bp):
TTACATTATAAGTTTAAATTTTT
Found at i:20747055 original size:48 final size:45
Alignment explanation
Indices: 20746987--20747075 Score: 106
Period size: 48 Copynumber: 1.9 Consensus size: 45
20746977 TCCCTATTTT
*
20746987 TTTGATTTTCTTGTTCTAAAAATAAATTTAGAAATATTTTTTAGA
1 TTTGATTTTCTTGTTCTAAAAAGAAATTTAGAAATATTTTTTAGA
* ** *
20747032 TTTGACTTTTCTTGTGTTTTAAAAAGAGTTTTGGAAATATTTTT
1 TTTGA-TTTTC-T-TGTTCTAAAAAGAAATTTAGAAATATTTTT
20747076 AGGTTTGGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 5 0.14
46 5 0.14
47 1 0.03
48 25 0.69
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.53
Consensus pattern (45 bp):
TTTGATTTTCTTGTTCTAAAAAGAAATTTAGAAATATTTTTTAGA
Found at i:20747118 original size:11 final size:11
Alignment explanation
Indices: 20747102--20747126 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20747092 GGATCCAAAT
20747102 AAAAAAAAAGA
1 AAAAAAAAAGA
20747113 AAAAAAAAAGA
1 AAAAAAAAAGA
20747124 AAA
1 AAA
20747127 GCAAAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:20749325 original size:4 final size:4
Alignment explanation
Indices: 20749316--20749340 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20749306 CCTAGCAAAT
20749316 ATTC ATTC ATTC ATTC ATTC ATTC A
1 ATTC ATTC ATTC ATTC ATTC ATTC A
20749341 ATACCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTC
Found at i:20756422 original size:20 final size:20
Alignment explanation
Indices: 20756397--20756445 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
20756387 GGTACACGCT
**
20756397 CGTGTGGCCTGGGGCATGGC
1 CGTGTGGCCTGGAACATGGC
20756417 CGTGTGGCCTGGAACATGGC
1 CGTGTGGCCTGGAACATGGC
*
20756437 CGTGGGGCC
1 CGTGTGGCC
20756446 AGGCCATGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.08, C:0.27, G:0.47, T:0.18
Consensus pattern (20 bp):
CGTGTGGCCTGGAACATGGC
Found at i:20761580 original size:2 final size:2
Alignment explanation
Indices: 20761546--20761570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20761536 TCTCTCTCTC
20761546 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20761571 GTTCATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20768873 original size:17 final size:18
Alignment explanation
Indices: 20768839--20768874 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20768829 TGAATTTCTG
20768839 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
20768857 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
20768874 T
1 T
20768875 AACTCATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:20769338 original size:20 final size:21
Alignment explanation
Indices: 20769305--20769348 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
20769295 TTCTTTTTTT
*
20769305 TTTCTATTTCTTTTACTTT-G
1 TTTCTATTTATTTTACTTTCG
*
20769325 TTTCTTTTTATTTTACTTTCG
1 TTTCTATTTATTTTACTTTCG
20769346 TTT
1 TTT
20769349 ATTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTCTATTTATTTTACTTTCG
Found at i:20769680 original size:12 final size:12
Alignment explanation
Indices: 20769663--20769695 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20769653 CCTGCAAAAC
20769663 CAAAACAACAAG
1 CAAAACAACAAG
20769675 CAAAACAA-AAG
1 CAAAACAACAAG
20769686 CAAAGACAAC
1 CAAA-ACAAC
20769696 GGCAACAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.67, C:0.24, G:0.09, T:0.00
Consensus pattern (12 bp):
CAAAACAACAAG
Found at i:20777782 original size:64 final size:64
Alignment explanation
Indices: 20777703--20777829 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
20777693 CATATAATAA
*
20777703 CACATCTAGTTAGGAGCAGTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCAGTTGATTCATTTCAATCATAACATCCTAATTATTTGACATAAGCAT
* * *
20777767 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGGCATAAGCA
1 CACATCTAGTTAGGAGCAGTTGATTCATTTCAATCATAACATCCTAATTATTTGACATAAGCA
20777830 CTGATACATG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCAGTTGATTCATTTCAATCATAACATCCTAATTATTTGACATAAGCAT
Found at i:20778113 original size:133 final size:132
Alignment explanation
Indices: 20777903--20778196 Score: 480
Period size: 133 Copynumber: 2.2 Consensus size: 132
20777893 ACTCACAAGC
* * *
20777903 CCTATCTCCCTAAGTTGTAGTGGAGTACGCTACAGATTGTAGATCTTGTCTCCCTGAAGTTGCAG
1 CCTATCTCCCTAAGTTGTAGTGGAGTAGGCTAAAGATTGTAGATCTTGTCTCCCTGAAGTTGCAA
* *
20777968 TGGAGCAGATCGAAGACGGCGAATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATTTAAGCCACC
66 TGGAGCAAATCGAAGACGGCGAATCTTGTCTCCCTGAAGTTGCAGTAGAGCAAATTTAAGCCACC
20778033 AT
131 AT
*
20778035 CCTATCTCCCTAAGTTGTAGTGGAGTAGGTTAAAAGATTGTAGATCTTGTCTCCCTGAAGTTGCA
1 CCTATCTCCCTAAGTTGTAGTGGAGTAGGCT-AAAGATTGTAGATCTTGTCTCCCTGAAGTTGCA
* *
20778100 ATGGAGCAAATCGAAGACGGTGAATCTTGTCTCCCTGAAGTTGCAGTAGAGCAGATTTAAGCCAC
65 ATGGAGCAAATCGAAGACGGCGAATCTTGTCTCCCTGAAGTTGCAGTAGAGCAAATTTAAGCCAC
20778165 CAT
130 CAT
* *
20778168 CTTATCTCTCTGAAGTTGTAGTGGAGTAG
1 CCTATCTCCCT-AAGTTGTAGTGGAGTAG
20778197 ATTGAAGCCA
Statistics
Matches: 150, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 29 0.19
133 104 0.69
134 17 0.11
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (132 bp):
CCTATCTCCCTAAGTTGTAGTGGAGTAGGCTAAAGATTGTAGATCTTGTCTCCCTGAAGTTGCAA
TGGAGCAAATCGAAGACGGCGAATCTTGTCTCCCTGAAGTTGCAGTAGAGCAAATTTAAGCCACC
AT
Found at i:20778228 original size:44 final size:44
Alignment explanation
Indices: 20777945--20778571 Score: 296
Period size: 45 Copynumber: 14.0 Consensus size: 44
20777935 CAGATTGTAG
* * * ** *
20777945 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGACGGCGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG-CTACAA
* * * * * *
20777990 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATTTAAGCCAC-C
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
* * * * * ** *
20778033 ATCCTATCTCCCT-AAGTTGTAGTGGAGTAGGTTAAAAGATTGTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT-GAAG-CTACAA
* * * * * ****
20778078 ATCTTGTCTCCCTGAAGTTGCAATGGAGCAAATCGAAGACGGTGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG-CTACAA
* * * * * *
20778123 ATCTTGTCTCCCTGAAGTTGCAGTAGAGCAGATTTAAGCCAC-C
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
* * *
20778166 ATCTTATCTCTCTGAAGTTGTAGTGGAGTAGATTGAAGCCACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
* * * * * **
20778210 ATCTTATCCCCCTGAAGTTACAGTAGG-GCAGGTCGAAATTACAA
1 ATCTTATCTCCCTGAAGTTGCAGT-GGAGTAGATTGAAGCTACAA
* * ** *
20778254 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGCCTGAAGATAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA-CAA
* * *
20778299 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAAGCTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
* * * ** * *
20778343 ATCCTATACGT--CTGAAGTTGCAGTAG-GTCGGATCAAATCTACCATGTTGG
1 ATCTTAT-C-TCCCTGAAGTTGCAGTGGAGT-AGATTGAAGCTA-CA-----A
* *
20778393 ATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
* * * * * * * * **
20778437 ACCTTACCCCCCTGAAGTTGCATTGGGGCAGGTCGAAATTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
* * * ** ** ** *
20778481 GTCTTATCTCTCTGAAGTTACAGTAAAGCGGCCTGAAGATATCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA-CAA
* * *
20778526 ATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
20778570 AT
1 AT
20778572 TATAGATCTT
Statistics
Matches: 435, Mismatches: 126, Indels: 43
0.72 0.21 0.07
Matches are distributed among these distances:
42 16 0.04
43 54 0.12
44 158 0.36
45 160 0.37
46 15 0.03
48 1 0.00
49 3 0.01
50 26 0.06
51 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
Found at i:20780339 original size:2 final size:2
Alignment explanation
Indices: 20780332--20780370 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
20780322 AATCCTCATT
*
20780332 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20780371 TTGTTGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20783435 original size:26 final size:26
Alignment explanation
Indices: 20783379--20783436 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
20783369 CATGAAATTC
*
20783379 TTATAATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
20783405 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
20783431 TTATCA
1 TTATCA
20783437 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:20784863 original size:8 final size:8
Alignment explanation
Indices: 20784852--20784879 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
20784842 TACATTTGTC
20784852 AATTTATT
1 AATTTATT
20784860 AATTTATT
1 AATTTATT
20784868 AATTTATT
1 AATTTATT
20784876 AATT
1 AATT
20784880 AATGTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTTATT
Found at i:20785460 original size:3 final size:3
Alignment explanation
Indices: 20785452--20785483 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20785442 AACTTATTTC
20785452 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20785484 TATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20785488 original size:3 final size:3
Alignment explanation
Indices: 20785482--20785521 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
20785472 AATAATAATA
20785482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
20785522 AACCTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20786476 original size:105 final size:105
Alignment explanation
Indices: 20786293--20786482 Score: 308
Period size: 105 Copynumber: 1.8 Consensus size: 105
20786283 TATGTTAATG
* * *
20786293 AGCTATAGAGGCATTAGTGGCGTTTTACTTAAAATGCCGCAATATATCAGAATTAGCGGCACTTC
1 AGCTATAGAGGCATTAGTGGCGTTTTACTAAAAATGCCGCAATATATAACAATTAGCGGCACTTC
* *
20786358 TTTAGAAACGCCGCAAAAGTCTTGAGAGAAACTACGACGT
66 TATAAAAACGCCGCAAAAGTCTTGAGAGAAACTACGACGT
* *
20786398 AGCTATAGAGGCATTAGTGGCTTTTTACTAAAAATGCCGCAATATATAACAATTAGCGGCGCTTC
1 AGCTATAGAGGCATTAGTGGCGTTTTACTAAAAATGCCGCAATATATAACAATTAGCGGCACTTC
*
20786463 TATAAAAATGCCGCAAAAGT
66 TATAAAAACGCCGCAAAAGT
20786483 GGCTATAGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 77 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (105 bp):
AGCTATAGAGGCATTAGTGGCGTTTTACTAAAAATGCCGCAATATATAACAATTAGCGGCACTTC
TATAAAAACGCCGCAAAAGTCTTGAGAGAAACTACGACGT
Found at i:20786803 original size:15 final size:14
Alignment explanation
Indices: 20786747--20786804 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
20786737 TTTGGGGTAT
*
20786747 GGGTTTATGTTTTA
1 GGGTTTAAGTTTTA
* *
20786761 GAGTTTGAGTTTTA
1 GGGTTTAAGTTTTA
20786775 GGGTTTATTA-TTTTA
1 GGGTTTA--AGTTTTA
20786790 GGGTTTAAGGTTTTA
1 GGGTTTAA-GTTTTA
20786805 ATATTAATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 1 0.03
14 16 0.46
15 17 0.49
16 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (14 bp):
GGGTTTAAGTTTTA
Found at i:20787287 original size:21 final size:21
Alignment explanation
Indices: 20787254--20787308 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20787244 TATGATTTTG
**
20787254 GGGTTTAAAGTTTGGGGTTTA
1 GGGTTTAGTGTTTGGGGTTTA
* *
20787275 GGGTTTGGTGTTTGGTGTTTA
1 GGGTTTAGTGTTTGGGGTTTA
*
20787296 TGGTTTAGTGTTT
1 GGGTTTAGTGTTT
20787309 ATGATTTTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.11, C:0.00, G:0.38, T:0.51
Consensus pattern (21 bp):
GGGTTTAGTGTTTGGGGTTTA
Found at i:20788184 original size:24 final size:25
Alignment explanation
Indices: 20788148--20788198 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
20788138 GTTTGCCCCG
* *
20788148 ATTCTGAAATCCC-AATTTCCCTAA
1 ATTCAGAAATCCCTAATTTCCCCAA
*
20788172 ATTCAGAAGTCCCTAATTTCCCCAA
1 ATTCAGAAATCCCTAATTTCCCCAA
20788197 AT
1 AT
20788199 CGGTAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.31
Consensus pattern (25 bp):
ATTCAGAAATCCCTAATTTCCCCAA
Found at i:20788331 original size:37 final size:37
Alignment explanation
Indices: 20788225--20788342 Score: 155
Period size: 37 Copynumber: 3.2 Consensus size: 37
20788215 AAATCTCCCT
* * *
20788225 GTGCATTGCAACCCATCTCCTCCGTCGCCTTCTCCCC
1 GTGCATCGCAACCCATCTCCTCCATCGCCTTCGCCCC
* * **
20788262 GTGCATCGCAAACCATCCCCTCCATCGCCTTCGCCTT
1 GTGCATCGCAACCCATCTCCTCCATCGCCTTCGCCCC
*
20788299 GTGTATCGCAACCCATCTCCTCCATCGCCTTCGCCCC
1 GTGCATCGCAACCCATCTCCTCCATCGCCTTCGCCCC
*
20788336 GTACATC
1 GTGCATC
20788343 TGCTGCATAG
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.14, C:0.47, G:0.14, T:0.25
Consensus pattern (37 bp):
GTGCATCGCAACCCATCTCCTCCATCGCCTTCGCCCC
Found at i:20790447 original size:14 final size:15
Alignment explanation
Indices: 20790421--20790457 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
20790411 TTACTATAAT
*
20790421 AATTATTTGAAGTAA
1 AATTATATGAAGTAA
20790436 AA-TATATGAAGTAA
1 AATTATATGAAGTAA
20790450 AATTATAT
1 AATTATAT
20790458 TGTCTACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (15 bp):
AATTATATGAAGTAA
Found at i:20792014 original size:62 final size:62
Alignment explanation
Indices: 20791936--20792075 Score: 226
Period size: 62 Copynumber: 2.3 Consensus size: 62
20791926 CCAGCAACTC
* * *
20791936 ACATAATTTACATAATACATAACTTATATAATTTAAAGTTCAAATTTCATAACTTACATAAT
1 ACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAAT
* * *
20791998 GCATAACTTACATAATACATGACTTACATAATTTAAAGATCAAATTTCATAACTTACATGAT
1 ACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAAT
20792060 ACATAACTTACATAAT
1 ACATAACTTACATAAT
20792076 TTAAAGACCA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.36
Consensus pattern (62 bp):
ACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAAT
Found at i:20792049 original size:46 final size:46
Alignment explanation
Indices: 20791999--20792322 Score: 232
Period size: 46 Copynumber: 6.8 Consensus size: 46
20791989 TTACATAATG
*
20791999 CATAACTTACATAATACATGACTTACATAATTTAAAGATCAAATTT
1 CATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTT
* *
20792045 CATAACTTACATGATACATAACTTACATAATTTAAAGACCAAATTT
1 CATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTT
* * *
20792091 CATAAGTTACATAATTTACATAACTTGCATAATAATTTAAAGTTCAAATTT
1 CATAACTTACATAA--TACATAACTT--A-CATAATTTAAAGATCAAATTT
* * * *
20792142 CATAACTTACATAAT--TTAA--TCCATCAAATTTCATAAGTTACTTAATTT
1 CATAACTTACATAATACATAACTTACAT--AATTT-A-AAGAT-C-AAATTT
* ** ** *
20792190 ACATAACTTATATAATA-ATTTAA-AGATCA-AATTTCATAACTTACATAA-TA
1 -CATAACTTACATAATACA--TAACTTA-CATAATTT-A-AAGAT-CA-AATTT
* *
20792240 CATAACTTACATAATACGTAACTTACATAATTTAAAGATCAAAATT
1 CATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTT
*
20792286 CATAACTTACATAATTTACATAACTTACATAACTTAA
1 CATAACTTACATAA--TACATAACTTACATAATTTAA
20792323 TTATACTTAT
Statistics
Matches: 225, Mismatches: 29, Indels: 46
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.01
44 5 0.02
45 4 0.02
46 77 0.34
47 7 0.03
48 40 0.18
49 36 0.16
50 2 0.01
51 47 0.21
52 3 0.01
54 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (46 bp):
CATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTT
Found at i:20792121 original size:18 final size:17
Alignment explanation
Indices: 20791937--20792317 Score: 187
Period size: 16 Copynumber: 23.8 Consensus size: 17
20791927 CAGCAACTCA
* *
20791937 CATAATTTACATAA-TA
1 CATAACTTACATAATTT
*
20791953 CATAACTTATATAATTT
1 CATAACTTACATAATTT
*
20791970 -A-AAGTT-CA-AATTT
1 CATAACTTACATAATTT
*
20791983 CATAACTTACATAA-TG
1 CATAACTTACATAATTT
*
20791999 CATAACTTACATAA-TA
1 CATAACTTACATAATTT
*
20792015 CATGACTTACATAATTT
1 CATAACTTACATAATTT
**
20792032 -A-AAGAT-CA-AATTT
1 CATAACTTACATAATTT
* *
20792045 CATAACTTACATGA-TA
1 CATAACTTACATAATTT
20792061 CATAACTTACATAATTT
1 CATAACTTACATAATTT
*
20792078 -A-AA--GACCA-AATTT
1 CATAACTTA-CATAATTT
*
20792091 CATAAGTTACATAATTT
1 CATAACTTACATAATTT
*
20792108 ACATAACTTGCATAATAATT
1 -CATAACTTACATAAT--TT
* *
20792128 TA-AAGTT-CA-AATTT
1 CATAACTTACATAATTT
20792142 CATAACTTACATAATTT
1 CATAACTTACATAATTT
* * *
20792159 AAT-CCAT-CA-AATTT
1 CATAACTTACATAATTT
* *
20792173 CATAAGTTACTTAATTT
1 CATAACTTACATAATTT
*
20792190 ACATAACTTATATAATAATT
1 -CATAACTTACATAAT--TT
* **
20792210 TA-AAGAT-CA-AATTT
1 CATAACTTACATAATTT
*
20792224 CATAACTTACATAA-TA
1 CATAACTTACATAATTT
*
20792240 CATAACTTACATAA-TA
1 CATAACTTACATAATTT
*
20792256 CGTAACTTACATAATTT
1 CATAACTTACATAATTT
** *
20792273 -A-AAGAT-CA-AAATT
1 CATAACTTACATAATTT
20792286 CATAACTTACATAATTT
1 CATAACTTACATAATTT
20792303 ACATAACTTACATAA
1 -CATAACTTACATAA
20792318 CTTAATTATA
Statistics
Matches: 272, Mismatches: 55, Indels: 74
0.68 0.14 0.18
Matches are distributed among these distances:
13 20 0.07
14 24 0.09
15 33 0.12
16 109 0.40
17 34 0.12
18 46 0.17
19 2 0.01
20 4 0.01
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (17 bp):
CATAACTTACATAATTT
Found at i:20792188 original size:82 final size:81
Alignment explanation
Indices: 20792061--20792238 Score: 284
Period size: 82 Copynumber: 2.2 Consensus size: 81
20792051 TTACATGATA
* *
20792061 CATAACTTACATAATTTAAAGACCAAATTTCATAAGTTACATAATTTACATAACTTGCATAATAA
1 CATAACTTACATAATTTAAACACCAAATTTCATAAGTTACATAATTTACATAACTTACATAATAA
*
20792126 TTTAAAGTTCAAATTT
66 TTTAAAGATCAAATTT
* * * *
20792142 CATAACTTACATAATTTAATCCATCAAATTTCATAAGTTACTTAATTTACATAACTTATATAATA
1 CATAACTTACATAATTTAA-ACACCAAATTTCATAAGTTACATAATTTACATAACTTACATAATA
20792207 ATTTAAAGATCAAATTT
65 ATTTAAAGATCAAATTT
20792224 CATAACTTACATAAT
1 CATAACTTACATAAT
20792239 ACATAACTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 19 0.21
82 70 0.79
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.38
Consensus pattern (81 bp):
CATAACTTACATAATTTAAACACCAAATTTCATAAGTTACATAATTTACATAACTTACATAATAA
TTTAAAGATCAAATTT
Found at i:20792205 original size:49 final size:48
Alignment explanation
Indices: 20792137--20792254 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 48
20792127 TTAAAGTTCA
* * *
20792137 AATTT-CATAACTTACATAATTTAATCCATCAAATTTCATAAGTTACTT
1 AATTTACATAACTTACATAATTTAA-ACATCAAATTTCATAACTTACAT
* *
20792185 AATTTACATAACTTATATAATAATTTAAAGATCAAATTTCATAACTTACAT
1 AATTTACATAAC-T-TA-CATAATTTAAACATCAAATTTCATAACTTACAT
20792236 AA--TACATAACTTACATAAT
1 AATTTACATAACTTACATAAT
20792255 ACGTAACTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
46 5 0.08
47 2 0.03
48 6 0.10
49 14 0.23
50 1 0.02
51 23 0.38
52 9 0.15
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (48 bp):
AATTTACATAACTTACATAATTTAAACATCAAATTTCATAACTTACAT
Found at i:20792318 original size:9 final size:9
Alignment explanation
Indices: 20792224--20792321 Score: 80
Period size: 9 Copynumber: 11.0 Consensus size: 9
20792214 GATCAAATTT
20792224 CATAACTTA
1 CATAACTTA
20792233 CATAA--TA
1 CATAACTTA
20792240 CATAACTTA
1 CATAACTTA
20792249 CATAA--TA
1 CATAACTTA
*
20792256 CGTAACTTA
1 CATAACTTA
*
20792265 CATAATTTAAA
1 CATAACTT--A
* *
20792276 GATCAAAATT-
1 CAT--AACTTA
20792286 CATAACTTA
1 CATAACTTA
*
20792295 CATAATTTA
1 CATAACTTA
20792304 CATAACTTA
1 CATAACTTA
20792313 CATAACTTA
1 CATAACTTA
20792322 ATTATACTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
7 13 0.18
8 4 0.06
9 45 0.63
10 2 0.03
11 3 0.04
13 4 0.06
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:20797378 original size:13 final size:14
Alignment explanation
Indices: 20797362--20797390 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20797352 TTACAAATAT
20797362 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
20797375 TTATAATGGTTTAA
1 TTATAATGGTTTAA
20797389 TT
1 TT
20797391 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:20798119 original size:31 final size:31
Alignment explanation
Indices: 20798077--20798142 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
20798067 TGTATTTTTT
*
20798077 ATGCTACATTTGCTGTTTTTGGTTGGATTTC
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
*
20798108 ATGCTATATTTGCTGTTTTTGGTTGGATTTA
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
20798139 ATGC
1 ATGC
20798143 AGGAAGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.15, C:0.11, G:0.23, T:0.52
Consensus pattern (31 bp):
ATGCTACATTTGCTGTTTTTGGTTGGATTTA
Found at i:20798729 original size:14 final size:15
Alignment explanation
Indices: 20798696--20798729 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
20798686 AACTTGAAAA
20798696 TTTTTCATTGCTACG
1 TTTTTCATTGCTACG
20798711 TTTTTCATTGCTACG
1 TTTTTCATTGCTACG
20798726 TTTT
1 TTTT
20798730 AGGGACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTTTCATTGCTACG
Found at i:20799710 original size:18 final size:19
Alignment explanation
Indices: 20799689--20799727 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20799679 TTTTAAAAAA
20799689 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
20799707 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
20799726 TA
1 TA
20799728 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:20801267 original size:20 final size:21
Alignment explanation
Indices: 20801237--20801275 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
20801227 ACCCAGCAAA
20801237 CCCAGACTTAAACTAGACCAG
1 CCCAGACTTAAACTAGACCAG
20801258 CCCA-ACTTAAACTAGACC
1 CCCAGACTTAAACTAGACC
20801276 CAAACAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.15
Consensus pattern (21 bp):
CCCAGACTTAAACTAGACCAG
Found at i:20802527 original size:21 final size:22
Alignment explanation
Indices: 20802501--20802560 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
20802491 TATCATATAT
*
20802501 TATTTTCCTATAT-ATTTATTA
1 TATTTTACTATATAATTTATTA
*
20802522 TATTTTATTATATAACATTTATTA
1 TATTTTACTATAT-A-ATTTATTA
*
20802546 TATTTTTATTATATA
1 TA-TTTTACTATATA
20802561 TTACTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 11 0.33
24 11 0.33
25 11 0.33
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTACTATATAATTTATTA
Found at i:20802553 original size:11 final size:11
Alignment explanation
Indices: 20802509--20802581 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
20802499 ATTATTTTCC
*
20802509 TATATATTTAT
1 TATATTTTTAT
20802520 TATA-TTTTAT
1 TATATTTTTAT
*
20802530 TATATAACATTTAT
1 TATAT---TTTTAT
20802544 TATATTTTTAT
1 TATATTTTTAT
*
20802555 TATA-TATTACT
1 TATATTTTTA-T
*
20802566 TATTTTTTTAT
1 TATATTTTTAT
20802577 TATAT
1 TATAT
20802582 GTTATGTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
10 13 0.27
11 22 0.45
12 4 0.08
14 10 0.20
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:20802558 original size:25 final size:24
Alignment explanation
Indices: 20802514--20802581 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 24
20802504 TTTCCTATAT
20802514 ATTTATTATATTTTATTATATAAC
1 ATTTATTATATTTTATTATATAAC
**
20802538 ATTTATTATATTTTTATTATATATT
1 ATTTATTATA-TTTTATTATATAAC
*
20802563 ACTTATT-T-TTTTATTATAT
1 ATTTATTATATTTTATTATAT
20802582 GTTATGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.28
24 11 0.28
25 18 0.45
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTATTATATTTTATTATATAAC
Found at i:20802568 original size:22 final size:22
Alignment explanation
Indices: 20802509--20802581 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 22
20802499 ATTATTTTCC
20802509 TATATATTTATTATA-TTTTAT
1 TATATATTTATTATATTTTTAT
20802530 TATATAACATTTATTATATTTTTAT
1 TATAT---ATTTATTATATTTTTAT
*
20802555 TATATA-TTACTTATTTTTTTAT
1 TATATATTTA-TTATATTTTTAT
20802577 TATAT
1 TATAT
20802582 GTTATGTATA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
21 8 0.17
22 17 0.37
24 10 0.22
25 11 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATATTTATTATATTTTTAT
Done.