Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 113 of 129
Found at i:20231394 original size:17 final size:17
Alignment explanation
Indices: 20231345--20231394 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
20231335 CTTTTAAGAG
* *
20231345 TTTTTTGTTGTTTTTGT
1 TTTTTTGTTTTTTTTTT
* *
20231362 GTTTATGTTTTTTTTTT
1 TTTTTTGTTTTTTTTTT
20231379 TTTTTTGTTTTTTTTT
1 TTTTTTGTTTTTTTTT
20231395 AATTTAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (17 bp):
TTTTTTGTTTTTTTTTT
Found at i:20231883 original size:46 final size:47
Alignment explanation
Indices: 20231832--20231928 Score: 187
Period size: 46 Copynumber: 2.1 Consensus size: 47
20231822 GGTCTTTGAA
20231832 TGCTCATCGTAATAAAGGTGTTGAAC-TTTAAAAATTTAAAATGCTT
1 TGCTCATCGTAATAAAGGTGTTGAACTTTTAAAAATTTAAAATGCTT
20231878 TGCTCATCGTAATAAAGGTGTTGAACTTTTAAAAATTTAAAATGCTT
1 TGCTCATCGTAATAAAGGTGTTGAACTTTTAAAAATTTAAAATGCTT
20231925 TGCT
1 TGCT
20231929 GGGAGGTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 26 0.52
47 24 0.48
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (47 bp):
TGCTCATCGTAATAAAGGTGTTGAACTTTTAAAAATTTAAAATGCTT
Found at i:20232001 original size:65 final size:65
Alignment explanation
Indices: 20231878--20232003 Score: 150
Period size: 65 Copynumber: 1.9 Consensus size: 65
20231868 TAAAATGCTT
** *
20231878 TGCTCATCGTAATAAAGGTGTTGAACTTTTAAAAATTTAAAATGCTTTGCTGGGAGGTCTTTGAA
1 TGCTCATCGTAATAAAGGCATTGAACTTTTAAAAATTTAAAATGCTTTGCTGGAAGGTCTTTGAA
* * *
20231943 TGCTCTTCGTAATAGAGGCATTGAGAC-TTTAAAAGTTTAAAATAG-TTTGCCT-GAAGGTCTT
1 TGCTCATCGTAATAAAGGCATTGA-ACTTTTAAAAATTTAAAAT-GCTTTG-CTGGAAGGTCTT
20232004 GGAGATTATG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
65 47 0.90
66 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (65 bp):
TGCTCATCGTAATAAAGGCATTGAACTTTTAAAAATTTAAAATGCTTTGCTGGAAGGTCTTTGAA
Found at i:20232411 original size:105 final size:105
Alignment explanation
Indices: 20231935--20232423 Score: 492
Period size: 105 Copynumber: 4.7 Consensus size: 105
20231925 TGCTGGGAGG
* * * *
20231935 TCTTTGAATGCTCTTCGTAAT-AGAGGCATTGAGACTTTAAAAGTTTAAAATAGTTTGCCT--GA
1 TCTTTGAATGCTCTTCCTAATCAAAGGCATTGAAACTTTAAAAATTTAAAATAGTTTG-CTAGGA
* * *
20231997 AGGTCTTGGAGATTATGCTCAAAGGTCATACAAATCTCAACA
65 A-GTCTTGGAGATTATGCTTAGAGGTCTTACAAATCTCAACA
* * * * * *
20232039 -CTTTTGAATGCTCTT-TTCAATCAAAGACATTGAGACTTTAAAATTTTAAAGT-GTTTTACCTA
1 TC-TTTGAATGCTCTTCCT-AATCAAAGGCATTGAAACTTTAAAAATTTAAAATAG-TTT-GCTA
* * * * * ** *
20232101 -GAGGTCTTGGAGATTATACCTGGAGGTCTTACAAACCTTGATA
62 GGAAGTCTTGGAGATTATGCTTAGAGGTCTTACAAATCTCAACA
* * * * * * *
20232144 TCTTCGAGTGCTCCTCCCAATCAAAGGCATTGAAACTTTAAAAATTTAAAATGGTTTGCTTGGAG
1 TCTTTGAATGCTCTTCCTAATCAAAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTAGGAA
* **
20232209 GTCTTGGAGATTATGCCATA-AGGTCTTACAAATCTTGACA
66 GTCTTGGAGATTATG-CTTAGAGGTCTTACAAATCTCAACA
* * *
20232249 TATTTAAATGCT-TCTCCCAATCAAAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTAGGA
1 TCTTTGAATGCTCT-TCCTAATCAAAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTAGGA
* *
20232313 AGTCTTGGAGATTATGCTTAGAGGTTTTACAATTCTCAACA
65 AGTCTTGGAGATTATGCTTAGAGGTCTTACAAATCTCAACA
* * *
20232354 TCTTTGAATGCTCTTCCTAATCAGAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTCGAAA
1 TCTTTGAATGCTCTTCCTAATCAAAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTAGGAA
20232419 GTCTT
66 GTCTT
20232424 AGAAATATAT
Statistics
Matches: 319, Mismatches: 52, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
103 2 0.01
104 22 0.07
105 288 0.90
106 7 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (105 bp):
TCTTTGAATGCTCTTCCTAATCAAAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTAGGAA
GTCTTGGAGATTATGCTTAGAGGTCTTACAAATCTCAACA
Found at i:20232413 original size:210 final size:210
Alignment explanation
Indices: 20231935--20232423 Score: 585
Period size: 210 Copynumber: 2.3 Consensus size: 210
20231925 TGCTGGGAGG
* * * *
20231935 TCTTTGAATGCTCTTCGTAAT-AGAGGCATTGAGACTTTAAAAGTTTAAAATAGTTTGCCTGAAG
1 TCTTTGAATGCTCTTCCTAATCAGAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTTGAAG
* **
20231999 GTCTTGGAGATTATGCTCAAAGGTCATACAAATCTCAACACTTTTGAATGCTCTTTTCAATCAAA
66 GTCTTGGAGATTATGCTCAAAGGTCATACAAATCTCAACACTTTTAAATGCTCTTCCCAATCAAA
* * * * *
20232064 GACATTGAGACTTTAAAATTTTAAAGTGTTTTACCTAGAGGTCTTGGAGATTATACCTGGAGGTC
131 GACATTGAAACTTTAAAAATTTAAAATGTTTTACCTAGAAGTCTTGGAGATTATACCTAGAGGTC
** *
20232129 TTACAAACCTTGATA
196 TTACAAACCTCAACA
* * * * * * *
20232144 TCTTCGAGTGCTCCTCCCAATCAAAGGCATTGAAACTTTAAAAATTTAAAATGGTTTGCTTGGAG
1 TCTTTGAATGCTCTTCCTAATCAGAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTTGAAG
* **
20232209 GTCTTGGAGATTATGC-CATAAGGTCTTACAAATCTTGACA-TATTTAAATGCT-TCTCCCAATC
66 GTCTTGGAGATTATGCTCA-AAGGTCATACAAATCTCAACACT-TTTAAATGCTCT-TCCCAATC
* * * *
20232271 AAAGGCATTGAAACTTTAAAAATTTAAAATAG-TTT-GCTAGGAAGTCTTGGAGATTATGCTTAG
128 AAAGACATTGAAACTTTAAAAATTTAAAAT-GTTTTACCTA-GAAGTCTTGGAGATTATACCTAG
* **
20232334 AGGTTTTACAATTCTCAACA
191 AGGTCTTACAAACCTCAACA
* *
20232354 TCTTTGAATGCTCTTCCTAATCAGAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTCGAAA
1 TCTTTGAATGCTCTTCCTAATCAGAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTTGAAG
20232419 GTCTT
66 GTCTT
20232424 AGAAATATAT
Statistics
Matches: 233, Mismatches: 41, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
209 23 0.10
210 209 0.90
211 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (210 bp):
TCTTTGAATGCTCTTCCTAATCAGAGGCATTGAAACTTTAAAAATTTAAAATAGTTTGCTTGAAG
GTCTTGGAGATTATGCTCAAAGGTCATACAAATCTCAACACTTTTAAATGCTCTTCCCAATCAAA
GACATTGAAACTTTAAAAATTTAAAATGTTTTACCTAGAAGTCTTGGAGATTATACCTAGAGGTC
TTACAAACCTCAACA
Found at i:20234411 original size:15 final size:14
Alignment explanation
Indices: 20234383--20234425 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
20234373 AAGGTATATA
* *
20234383 CCTTTATTTCTTTT
1 CCTTTTTTTTTTTT
20234397 CTCTTTTTCTTTTTTT
1 C-CTTTTT-TTTTTTT
20234413 CCTTTTTTTTTTT
1 CCTTTTTTTTTTT
20234426 GGAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 7 0.28
15 11 0.44
16 7 0.28
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
CCTTTTTTTTTTTT
Found at i:20234794 original size:11 final size:12
Alignment explanation
Indices: 20234778--20234806 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20234768 ACGAGGTGCA
20234778 TTTTTTC-TTTC
1 TTTTTTCTTTTC
20234789 TTTTTTCTTTTC
1 TTTTTTCTTTTC
20234801 TTTTTT
1 TTTTTT
20234807 TGAATATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:20234875 original size:125 final size:126
Alignment explanation
Indices: 20234528--20234902 Score: 352
Period size: 125 Copynumber: 2.9 Consensus size: 126
20234518 CTTTTCCCCC
* * * * * *
20234528 TTTTTTTCTTTTTTTTTTTTTGAAATATTAGACTTCAAT-TTTAGCATTCTACTTTCTGCAATTT
1 TTTTTTTC-TTTTCTTTTTTTG-AATATTTGACTTC-ATCTTTAGCAATCAACTTTTTG-AATTC
* * *** **
20234592 TATTTTCTTGAAGCTTCATTCACTTTTTGT-CCT-AGACTCTCATTTTTAAAATGCATTTTTTTT
62 TATTTTCTTGAAGTTTCATTCACTTTTT-TCCCTGA-ACTCTCATCTACGAGGTGCA-TTTTTTT
20234655 CTT
124 CTT
* * * *
20234658 TTTTTTGCTTTCCCTCTTTTTTTTGGAACATTTGAATTCATCTTTAGCAATCAACTTCTTGAATT
1 TTTTTTTCTTT---TC-TTTTTTT-GAATATTTGACTTCATCTTTAGCAATCAACTTTTTGAATT
*
20234723 CTATTTTCTTGAAGCTTT-ATTTA-TTTTTTCCCTGAACTCTCATCTACGAGGTGCA-TTTTTTC
61 CTATTTTCTTGAAG-TTTCATTCACTTTTTTCCCTGAACTCTCATCTACGAGGTGCATTTTTTTC
20234785 TT
125 TT
*
20234787 TCTTTTTTCTTTTCTTTTTTTGAATATTTGACTTCATCTTCAGCAATCAACTTTTTGAATTCTAT
1 T-TTTTTTCTTTTCTTTTTTTGAATATTTGACTTCATCTTTAGCAATCAACTTTTTGAATTCTAT
* * * *
20234852 TTTC-TAAAGTTTCATTCACTTTTTACCCTTG-ACTTTCATCTCCGAGGTGCA
65 TTTCTTGAAGTTTCATTCACTTTTTTCCC-TGAACTCTCATCTACGAGGTGCA
20234903 AATTAGATGT
Statistics
Matches: 204, Mismatches: 28, Indels: 31
0.78 0.11 0.12
Matches are distributed among these distances:
123 3 0.01
124 8 0.04
125 70 0.34
126 9 0.04
127 2 0.01
129 13 0.06
130 17 0.08
131 22 0.11
132 25 0.12
133 34 0.17
134 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.09, T:0.54
Consensus pattern (126 bp):
TTTTTTTCTTTTCTTTTTTTGAATATTTGACTTCATCTTTAGCAATCAACTTTTTGAATTCTATT
TTCTTGAAGTTTCATTCACTTTTTTCCCTGAACTCTCATCTACGAGGTGCATTTTTTTCTT
Found at i:20238997 original size:3 final size:3
Alignment explanation
Indices: 20238991--20239038 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
20238981 TCAATGACAC
*
20238991 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20239039 ACACTTGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20239853 original size:3 final size:3
Alignment explanation
Indices: 20239845--20239892 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
20239835 TACTAAGGTT
20239845 TTA TTA 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 TTA TTA
20239893 CTATGAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20243492 original size:13 final size:13
Alignment explanation
Indices: 20243474--20243498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20243464 TTAAGCCTAG
20243474 ATAAACAAAATTC
1 ATAAACAAAATTC
20243487 ATAAACAAAATT
1 ATAAACAAAATT
20243499 TATTTCTCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAACAAAATTC
Found at i:20244819 original size:34 final size:31
Alignment explanation
Indices: 20244735--20244834 Score: 114
Period size: 31 Copynumber: 3.1 Consensus size: 31
20244725 TTCAAAATCT
* *
20244735 TTTAGTGGTGAT-TTCTAAAGTCATTTACATC
1 TTTACTGGTGATATTC-AAAGTCATTTGCATC
*
20244766 TTTACTGGTGATATCCAAAGTCATTTGCAT-
1 TTTACTGGTGATATTCAAAGTCATTTGCATC
20244796 TTTACTCGGTGATGATATTCAAAGTCATTTGCATC
1 TTTACT--G-G-TGATATTCAAAGTCATTTGCATC
20244831 TTTA
1 TTTA
20244835 TTCAATAGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.10
31 24 0.41
32 3 0.05
33 1 0.02
34 21 0.36
35 4 0.07
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (31 bp):
TTTACTGGTGATATTCAAAGTCATTTGCATC
Found at i:20244928 original size:57 final size:59
Alignment explanation
Indices: 20244808--20244935 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 59
20244798 TACTCGGTGA
* ** *
20244808 TGATATTCAAAGTCATTTGCATCTTTATTCAATAGTGATATCTAAACTCCCTTCAGTGG
1 TGATATCCAAAGTCATTTGCATCTTTATTCAATAGCAATATCCAAACTCCCTTCAGTGG
* * * * *
20244867 TGATATCCAAAGTCATTTGCAT-TTTCTT-AATGGCAATATCCGAATTCCCTTTAGTGG
1 TGATATCCAAAGTCATTTGCATCTTTATTCAATAGCAATATCCAAACTCCCTTCAGTGG
20244924 TGATATCCAAAG
1 TGATATCCAAAG
20244936 GTTAAGAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
57 34 0.57
58 5 0.08
59 21 0.35
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (59 bp):
TGATATCCAAAGTCATTTGCATCTTTATTCAATAGCAATATCCAAACTCCCTTCAGTGG
Found at i:20245436 original size:18 final size:17
Alignment explanation
Indices: 20245413--20245447 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20245403 AAAAAATAAT
*
20245413 AATAAAAATAACATAAAA
1 AATAAAAA-AACAGAAAA
20245431 AATAAAAAAACAGAAAA
1 AATAAAAAAACAGAAAA
20245448 TAAAGGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (17 bp):
AATAAAAAAACAGAAAA
Found at i:20249014 original size:1 final size:1
Alignment explanation
Indices: 20249010--20249035 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
20249000 TTTTTTTTTT
20249010 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
20249036 CAGTGATGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:20266930 original size:14 final size:14
Alignment explanation
Indices: 20266900--20266929 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20266890 TCTATCATAA
20266900 TTTCCCTTTTTTAT
1 TTTCCCTTTTTTAT
20266914 TTTCCCTTTTTT-T
1 TTTCCCTTTTTTAT
20266927 TTT
1 TTT
20266930 TAGATTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCCCTTTTTTAT
Found at i:20269968 original size:279 final size:280
Alignment explanation
Indices: 20269149--20269986 Score: 1308
Period size: 280 Copynumber: 3.0 Consensus size: 280
20269139 AAAGGTTCTC
* * *
20269149 CATCTAGTC-TTTTTCCTCTAGAGTTAAGTTACTCTCAACTATGGTTCAACCTTGGAATTTTGTT
1 CATCTAGTCTTTTTTCCTCTAAAGTTAAGTTACTCTCAGCTATGGTTCAACCTTGGAATTCTGTT
* * *
20269213 TCTACTCAGGAGTCAAAATCTTTTAGTGATAAAGATTTTGACAATGAGAAAGGTTTTAAAAAAGA
66 TCTACTCAGGAGTCAAAGTCTTTTAGCGATAAAGATTTTAACAATGAGAAAGGTTTTAAAAAAGA
* * * *
20269278 ATAGAAGAAAATGAGTACCTCAACTAAAGAAAGTGACAACAAGGAAGAGAATCTTATAAAGCATA
131 ATAGAAGAAAAGGAGTACCTCAGCTAAAGAAAGTGACAACAAGGAAAAGAATCTTATAGAGCATA
*
20269343 ATGAACTAACTGAGATCCTTTTATATATTTCCTGTGACCTTGGTATGATCCTCAAAGACATGATG
196 ATGAACTAACCGAGATCCTTTTATATATTTCCTGTGACCTTGGTATGATCCTCAAAGACATGATG
20269408 AGTGAATTGAAAGGAACAAT
261 AGTGAATTGAAAGGAACAAT
*
20269428 CATCTAGTCTTTTTTCCTCTAAAGTTAAGTTACTCTCAGCTATGGTTCAACCTTCGAATTCTGTT
1 CATCTAGTCTTTTTTCCTCTAAAGTTAAGTTACTCTCAGCTATGGTTCAACCTTGGAATTCTGTT
* * **
20269493 TCTACTCAGAAGTCAAAGTCTTTTAGCGGTAAAGATTTTAACAATGAGAAAGGTTTTAGGAAAGA
66 TCTACTCAGGAGTCAAAGTCTTTTAGCGATAAAGATTTTAACAATGAGAAAGGTTTTAAAAAAGA
* * * *
20269558 ATAGAAGAAATGGAGTACCTTAGCTAAAAAAAGTGACAATAAGGAAAAGAATCTTATAGAGCATA
131 ATAGAAGAAAAGGAGTACCTCAGCTAAAGAAAGTGACAACAAGGAAAAGAATCTTATAGAGCATA
* * * *
20269623 ATGAACTAACCGAGATCCTTCTATATATTTCTTGTGACCTTGGTATGATCTTCAAAGACGTGATG
196 ATGAACTAACCGAGATCCTTTTATATATTTCCTGTGACCTTGGTATGATCCTCAAAGACATGATG
20269688 AGTGAATTGAAAGGAACAAT
261 AGTGAATTGAAAGGAACAAT
* * *
20269708 CATCTAGTCTTTTTTCCTCTAAAGTTAAGTTACTCCCAGCTATGGTTTAACCTTGGAATTCTATT
1 CATCTAGTCTTTTTTCCTCTAAAGTTAAGTTACTCTCAGCTATGGTTCAACCTTGGAATTCTGTT
*
20269773 TCTACTCAGGAGTCAAAGTCTTTTAGCGATAAAGA-TTTAACAATGAG-AAGGATTTTAATAAAG
66 TCTACTCAGGAGTCAAAGTCTTTTAGCGATAAAGATTTTAACAATGAGAAAGG-TTTTAAAAAAG
* * *
20269836 AATTA-AA-AAAAGAGAGTACCTGAGCTAAAGAAAGTGACAACAAGAAAAAGAATTTTATAGAGC
130 AA-TAGAAGAAAAG-GAGTACCTCAGCTAAAGAAAGTGACAACAAGGAAAAGAATCTTATAGAGC
*
20269899 ATAATGAACTAACCGAGATCTTTTTATATATTTCCTGTGACCTTGGTATGATCCTCAAAGACATG
193 ATAATGAACTAACCGAGATCCTTTTATATATTTCCTGTGACCTTGGTATGATCCTCAAAGACATG
* *
20269964 ATGAGTTAATTGAAAAGAACAAT
258 ATGAGTGAATTGAAAGGAACAAT
20269987 AAATCCTGAA
Statistics
Matches: 510, Mismatches: 45, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
278 8 0.02
279 160 0.31
280 342 0.67
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (280 bp):
CATCTAGTCTTTTTTCCTCTAAAGTTAAGTTACTCTCAGCTATGGTTCAACCTTGGAATTCTGTT
TCTACTCAGGAGTCAAAGTCTTTTAGCGATAAAGATTTTAACAATGAGAAAGGTTTTAAAAAAGA
ATAGAAGAAAAGGAGTACCTCAGCTAAAGAAAGTGACAACAAGGAAAAGAATCTTATAGAGCATA
ATGAACTAACCGAGATCCTTTTATATATTTCCTGTGACCTTGGTATGATCCTCAAAGACATGATG
AGTGAATTGAAAGGAACAAT
Found at i:20280440 original size:30 final size:31
Alignment explanation
Indices: 20280399--20280459 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
20280389 AATAATGTGA
* *
20280399 ATATTTTTTTATCAAAT-TAGTTACGTTCTC
1 ATATTTCTTTATCAAATCCAGTTACGTTCTC
*
20280429 ATATTTCTTTATCAAATCCAGTTACTTTCTC
1 ATATTTCTTTATCAAATCCAGTTACGTTCTC
20280460 TTCTGTTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (31 bp):
ATATTTCTTTATCAAATCCAGTTACGTTCTC
Found at i:20288670 original size:44 final size:44
Alignment explanation
Indices: 20288593--20288852 Score: 241
Period size: 44 Copynumber: 5.9 Consensus size: 44
20288583 TCAGGTGTTA
* * * *
20288593 TCTATATATTTTAAAAGTTGTTGAGCCTTTATTTAGAGGATCAT
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACAT
* * * * * * **
20288637 TCTATATTTTTTAAAAGGTATTGAACCTCTATTTAGAGGAGTAT
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACAT
* * * * * * *
20288681 TCTTTATTTTTTAAAAGTTATTGAGCTTATATTTAGAAGAACTT
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACAT
* * *
20288725 TCTATATCTTTCAAAAGTTGTTGAGTCTCTATTTAGAAGAACCT
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACAT
* ** * *
20288769 TTTATATATTTCAAAAGTTGTTGAATCTCTATTTAGATGAGCAT
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACAT
* * * *
20288813 TCCATATCTTTCAAAAGTTGTTAAGCCTCTGTTTAGAAGA
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGA
20288853 GCTTTTATAT
Statistics
Matches: 178, Mismatches: 38, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 178 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (44 bp):
TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACAT
Found at i:20288755 original size:88 final size:87
Alignment explanation
Indices: 20288595--20288862 Score: 270
Period size: 88 Copynumber: 3.1 Consensus size: 87
20288585 AGGTGTTATC
* * * * * *
20288595 TATATATTTTAAAAGTTGTTGAGCCTTTATTTAGAGGATCATTCTATATTTTTTAAAAGGTATTG
1 TATATATTTTAAAAGTTGTTGAG-CTTTATTTAGAAGAACATTCTATATCTTTCAAAAGTTGTTG
* * **
20288660 AACCTCTATTTAGAGGAGTATTCT
65 AGCCTCTATTTAGAAGAACATT-T
* * *
20288684 T-TATTTTTTAAAAGTTATTGAGCTTATATTTAGAAGAACTTTCTATATCTTTCAAAAGTTGTTG
1 TATATATTTTAAAAGTTGTTGAGCTT-TATTTAGAAGAACATTCTATATCTTTCAAAAGTTGTTG
* *
20288748 AGTCTCTATTTAGAAGAACCTTT
65 AGCCTCTATTTAGAAGAACATTT
* * * * * * *
20288771 TATATATTTCAAAAGTTGTTGAATCTCTATTTAGATGAGCATTCCATATCTTTCAAAAGTTGTTA
1 TATATATTTTAAAAGTTGTTG-AGCTTTATTTAGAAGAACATTCTATATCTTTCAAAAGTTGTTG
* *
20288836 AGCCTCTGTTTAGAAGAGC-TTT
65 AGCCTCTATTTAGAAGAACATTT
20288858 TATAT
1 TATAT
20288863 TATTCAACAA
Statistics
Matches: 148, Mismatches: 28, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
87 13 0.09
88 131 0.89
89 4 0.03
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (87 bp):
TATATATTTTAAAAGTTGTTGAGCTTTATTTAGAAGAACATTCTATATCTTTCAAAAGTTGTTGA
GCCTCTATTTAGAAGAACATTT
Found at i:20288830 original size:132 final size:132
Alignment explanation
Indices: 20288593--20288862 Score: 308
Period size: 132 Copynumber: 2.1 Consensus size: 132
20288583 TCAGGTGTTA
* * * * * *
20288593 TCTATATATTTTAAAAGTTGTTGAGCCTTTATTTAGAGGATCATTCTATATTTTTTAAAAGGTAT
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACATTCTATATATTTCAAAAGGTAT
* ** * * * *
20288658 TGAACCTCTATTTAGAGGAGTATTCTTTATTTTTTAAAAGTTATTGAGCTTATATTTAGAAGAAC
66 TGAACCTCTATTTAGAGGAGCATTCCATATCTTTCAAAAGTTATTAAGCCTATATTTAGAAGAAC
20288723 TT
131 TT
* * * * * *
20288725 TCTATATCTTTCAAAAGTTGTTGAGTCTCTATTTAGAAGAACCTTTTATATATTTCAAAAGTTGT
1 TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACATTCTATATATTTCAAAAGGTAT
* * * * * *
20288790 TGAATCTCTATTTAGATGAGCATTCCATATCTTTCAAAAGTTGTTAAGCCTCTGTTTAGAAGAGC
66 TGAACCTCTATTTAGAGGAGCATTCCATATCTTTCAAAAGTTATTAAGCCTATATTTAGAAGAAC
20288855 TT
131 TT
20288857 T-TATAT
1 TCTATAT
20288863 TATTCAACAA
Statistics
Matches: 113, Mismatches: 25, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
131 5 0.04
132 108 0.96
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (132 bp):
TCTATATATTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAACATTCTATATATTTCAAAAGGTAT
TGAACCTCTATTTAGAGGAGCATTCCATATCTTTCAAAAGTTATTAAGCCTATATTTAGAAGAAC
TT
Found at i:20289291 original size:26 final size:25
Alignment explanation
Indices: 20289224--20289291 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
20289214 ATTAGGCATT
**
20289224 AAAATAATAATAATAATGGTGAAAAA
1 AAAATAATAATAA-AAAAGTGAAAAA
** * *
20289250 AAAATAATTCTTAAAAAGTTAAAAA
1 AAAATAATAATAAAAAAGTGAAAAA
20289275 AATAATAATAATAAAAA
1 AA-AATAATAATAAAAA
20289292 GAAAAGTTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (25 bp):
AAAATAATAATAAAAAAGTGAAAAA
Found at i:20289529 original size:20 final size:21
Alignment explanation
Indices: 20289491--20289529 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20289481 AGAAGAAATT
* *
20289491 AGCATAAAAAAATACAAGATC
1 AGCATAAAAAAAAAAAAGATC
20289512 AGCA-AAAAAAAAAAAAGA
1 AGCATAAAAAAAAAAAAGA
20289530 GAAAGAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.72, C:0.10, G:0.10, T:0.08
Consensus pattern (21 bp):
AGCATAAAAAAAAAAAAGATC
Found at i:20289892 original size:21 final size:21
Alignment explanation
Indices: 20289868--20289912 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
20289858 TGTTTTCTAG
20289868 AGAGAGAACAAAGAAA-A-AAGA
1 AGAG-GAA-AAAGAAAGAGAAGA
20289889 AGAGGAAAAAGAAAGAGAAGA
1 AGAGGAAAAAGAAAGAGAAGA
20289910 AGA
1 AGA
20289913 AATATGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (21 bp):
AGAGGAAAAAGAAAGAGAAGA
Found at i:20290960 original size:54 final size:55
Alignment explanation
Indices: 20290887--20290990 Score: 151
Period size: 54 Copynumber: 1.9 Consensus size: 55
20290877 GAGGTTTTTT
*
20290887 TTTTCTACATTCAACCAAAATGGTGGAAAA-TTTAGAAACAAAACTTGTAAGAAAA
1 TTTTCTACATTCAACCAAAATAGT-GAAAATTTTAGAAACAAAACTTGTAAGAAAA
*
20290942 TTTTCTA-ATT-AGACCAAAATAGTGAAAATTTTAGAAATAAAACTTGTAA
1 TTTTCTACATTCA-ACCAAAATAGTGAAAATTTTAGAAACAAAACTTGTAA
20290991 AATAAAGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
53 6 0.13
54 32 0.71
55 7 0.16
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.31
Consensus pattern (55 bp):
TTTTCTACATTCAACCAAAATAGTGAAAATTTTAGAAACAAAACTTGTAAGAAAA
Found at i:20298282 original size:30 final size:29
Alignment explanation
Indices: 20298216--20298284 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
20298206 TTTGATATAT
*
20298216 GTTTGCCCATCTTCTATATGTGTAGAAAA
1 GTTTGCCCATCTTCTATATGTATAGAAAA
* *
20298245 GTTTGCCCATGTTCTATATTTATAGAAAA
1 GTTTGCCCATCTTCTATATGTATAGAAAA
20298274 GTTTTGCCCAT
1 G-TTTGCCCAT
20298285 ATACAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (29 bp):
GTTTGCCCATCTTCTATATGTATAGAAAA
Found at i:20301251 original size:21 final size:22
Alignment explanation
Indices: 20301213--20301256 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
20301203 ATTAACTAAA
*
20301213 AAAGTGTACAGAACAAAATTTT
1 AAAGTGTACAGAAAAAAATTTT
20301235 AAAGTGTA-AGAAAAAAATTTT
1 AAAGTGTACAGAAAAAAATTTT
20301256 A
1 A
20301257 TTTATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (22 bp):
AAAGTGTACAGAAAAAAATTTT
Found at i:20301879 original size:6 final size:7
Alignment explanation
Indices: 20301862--20301887 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20301852 GTCTTGGATT
20301862 TTTTTTA
1 TTTTTTA
20301869 TTTTTTA
1 TTTTTTA
20301876 TTTTTTA
1 TTTTTTA
20301883 TTTTT
1 TTTTT
20301888 GGATATAATT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:20306578 original size:23 final size:23
Alignment explanation
Indices: 20306548--20306597 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
20306538 AGCACCATCA
20306548 CAGT-TAACTTTACAAGTACCAG
1 CAGTATAACTTTACAAGTACCAG
20306570 CAGTATAACTTTACAAGTACCAG
1 CAGTATAACTTTACAAGTACCAG
*
20306593 AAGTA
1 CAGTA
20306598 GGTGGGTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (23 bp):
CAGTATAACTTTACAAGTACCAG
Found at i:20307370 original size:17 final size:14
Alignment explanation
Indices: 20307342--20307384 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
20307332 TTATATAATC
20307342 AATTA-AATAATTA
1 AATTATAATAATTA
20307355 ATTATTATATATAATTA
1 A--ATTATA-ATAATTA
20307372 AATTATAATAATT
1 AATTATAATAATT
20307385 GAATAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 6 0.23
15 10 0.38
16 1 0.04
17 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTATAATAATTA
Found at i:20307383 original size:27 final size:27
Alignment explanation
Indices: 20307332--20307384 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
20307322 AATATTATAT
*
20307332 TTATATAATCAATTAAATAATTAATTA
1 TTATATAATCAATTAAATAAATAATTA
20307359 TTATAT-AT-AATTAAATTATAATAATT
1 TTATATAATCAATTAAA-TA-AATAATT
20307385 GAATAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATATAATCAATTAAATAAATAATTA
Found at i:20317394 original size:120 final size:120
Alignment explanation
Indices: 20317178--20317412 Score: 287
Period size: 120 Copynumber: 2.0 Consensus size: 120
20317168 AATTTATTTT
* *
20317178 AATAATAAATACGTATATTTGTTTATTCCAAACGACTGAAGAGGAATCTCAACAACTTATAAGTA
1 AATAATAAATACATATATTTGTTTATTCCAAACGACTAAAGAGGAATCTCAACAACTTATAAGTA
* * *
20317243 TAATTCTTTCGAAGTAAGATTTTCAAAAATATACATGTAGACAAGCATTTGATTC
66 TAATTCTTTAGAAGTAAGATTTTCAAAAATATACATGCAGACAAACATTTGATTC
* * *
20317298 AATAATTAGATACATATATTTGTTTATTCCAAATGA-TAAAGAGGAATCTCAACAATTTATAACT
1 AATAA-TAAATACATATATTTGTTTATTCCAAACGACTAAAGAGGAATCTCAACAACTTATAA--
* * * * * * *
20317362 GTA-AATT-TTTAGCATTATGCTTTTTAATAATATATATGCAGACAAACATTT
63 GTATAATTCTTTAGAAGTAAGATTTTCAAAAATATACATGCAGACAAACATTT
20317413 CTAAATTCTT
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
120 63 0.65
121 31 0.32
122 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (120 bp):
AATAATAAATACATATATTTGTTTATTCCAAACGACTAAAGAGGAATCTCAACAACTTATAAGTA
TAATTCTTTAGAAGTAAGATTTTCAAAAATATACATGCAGACAAACATTTGATTC
Found at i:20319653 original size:26 final size:23
Alignment explanation
Indices: 20319625--20319697 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
20319615 TTAAATATTT
20319625 TTTTATATATTATTAA-ACATAAATA
1 TTTTA-ATATT-TTAATA-ATAAATA
20319650 TTTTAATATTTTAATAATAAATA
1 TTTTAATATTTTAATAATAAATA
* *
20319673 GTATATATTATTTTAATAATAAATA
1 -T-TTTAATATTTTAATAATAAATA
20319698 AGACATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.26
24 7 0.16
25 25 0.58
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
TTTTAATATTTTAATAATAAATA
Found at i:20319705 original size:25 final size:25
Alignment explanation
Indices: 20319656--20319705 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
20319646 AATATTTTAA
*
20319656 TATTTTAATAATAAATAGTATATAT
1 TATTTTAATAATAAATAGTACATAT
20319681 TATTTTAATAATAAATAAG-ACATAT
1 TATTTTAATAATAAAT-AGTACATAT
20319706 ATAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
TATTTTAATAATAAATAGTACATAT
Found at i:20319936 original size:17 final size:16
Alignment explanation
Indices: 20319913--20319955 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
20319903 TTCAATATAA
20319913 ATATAAATATTTTAAT
1 ATATAAATATTTTAAT
20319929 AGTATAAATATTTTAAT
1 A-TATAAATATTTTAAT
20319946 A-ATAAATATT
1 ATATAAATATT
20319956 ACTATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.35
16 1 0.04
17 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATAAATATTTTAAT
Found at i:20320082 original size:14 final size:14
Alignment explanation
Indices: 20320037--20320097 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 14
20320027 TAAAAAATAA
*
20320037 TAAATAGTTTTATTT
1 TAAATA-TTTTATAT
*
20320052 TAAGTACTTTTATAT
1 TAAATA-TTTTATAT
20320067 T-AATATTTTAATAT
1 TAAATATTTT-ATAT
*
20320081 TAAATATTAT-TAT
1 TAAATATTTTATAT
20320094 TAAA
1 TAAA
20320098 ATATAATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 11 0.28
14 8 0.21
15 20 0.51
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (14 bp):
TAAATATTTTATAT
Found at i:20320888 original size:37 final size:36
Alignment explanation
Indices: 20320843--20320913 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
20320833 CTAATTTTTT
* *
20320843 TTTAAAATA-AAAATATTTTCCAAAAATTATAAAAAAA
1 TTTAAAATATAAAATACTTT--AAAAATAATAAAAAAA
*
20320880 TTTAAAATATGAAATACTTTAAAAATAATAAAAA
1 TTTAAAATATAAAATACTTTAAAAATAATAAAAA
20320914 TTAAAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 13 0.43
37 9 0.30
38 8 0.27
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (36 bp):
TTTAAAATATAAAATACTTTAAAAATAATAAAAAAA
Found at i:20320938 original size:9 final size:8
Alignment explanation
Indices: 20320909--20321000 Score: 58
Period size: 9 Copynumber: 10.6 Consensus size: 8
20320899 TAAAAATAAT
20320909 AAAAATTA
1 AAAAATTA
* *
20320917 AAAACTATG
1 AAAAAT-TA
*
20320926 AAAACTTA
1 AAAAATTA
20320934 AAAAATTCA
1 AAAAATT-A
20320943 AAAAATTCA
1 AAAAATT-A
**
20320952 AAATTTTA
1 AAAAATTA
20320960 ATAAAATTTA
1 A-AAAA-TTA
20320970 AAAAATTCA
1 AAAAATT-A
*
20320979 AAAAATTCT
1 AAAAATT-A
*
20320988 TAAAATTA
1 AAAAATTA
20320996 AAAAA
1 AAAAA
20321001 AAATGAAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
8 20 0.30
9 43 0.64
10 4 0.06
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.28
Consensus pattern (8 bp):
AAAAATTA
Found at i:20320938 original size:34 final size:33
Alignment explanation
Indices: 20320871--20320955 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 33
20320861 TCCAAAAATT
* *
20320871 ATAAAAAAATTTAAAATATGAAATACTTTAAAA
1 ATAAAAAAATTAAAAATATGAAATACTTAAAAA
20320904 ATAATAAAAATTAAAAACTATGAAA-ACTTAAAAA
1 ATAA-AAAAATTAAAAA-TATGAAATACTTAAAAA
* *
20320938 ATTCAAAAAATTCAAAAT
1 A-TAAAAAAATTAAAAAT
20320956 TTTAATAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 5 0.11
34 31 0.69
35 9 0.20
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (33 bp):
ATAAAAAAATTAAAAATATGAAATACTTAAAAA
Found at i:20320965 original size:27 final size:26
Alignment explanation
Indices: 20320931--20320981 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
20320921 CTATGAAAAC
20320931 TTAAAAAATTCAAAAAATTCAAAATT
1 TTAAAAAATTCAAAAAATTCAAAATT
*
20320957 TTAATAAAATTTAAAAAATTCAAAA
1 TTAA-AAAATTCAAAAAATTCAAAA
20320982 AATTCTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (26 bp):
TTAAAAAATTCAAAAAATTCAAAATT
Found at i:20320991 original size:27 final size:27
Alignment explanation
Indices: 20320926--20321001 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 27
20320916 AAAAACTATG
* *
20320926 AAAACTTAA-AAAATTCAAAAAATTCA
1 AAAAATTAATAAAATTAAAAAAATTCA
** *
20320952 AAATTTTAATAAAATTTAAAAAATTCA
1 AAAAATTAATAAAATTAAAAAAATTCA
**
20320979 AAAAATTCTTAAAATTAAAAAAA
1 AAAAATTAATAAAATTAAAAAAA
20321002 AATGAAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAAATTAATAAAATTAAAAAAATTCA
Found at i:20321001 original size:9 final size:9
Alignment explanation
Indices: 20320933--20321000 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
20320923 ATGAAAACTT
20320933 AAAAAATTC
1 AAAAAATTC
20320942 AAAAAATTC
1 AAAAAATTC
* *
20320951 -AAAATTTT
1 AAAAAATTC
*
20320959 AATAAAATTT
1 AA-AAAATTC
20320969 AAAAAATTC
1 AAAAAATTC
20320978 AAAAAATTC
1 AAAAAATTC
**
20320987 TTAAAATT-
1 AAAAAATTC
20320995 AAAAAA
1 AAAAAA
20321001 AAATGAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
8 10 0.20
9 31 0.63
10 8 0.16
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAAATTC
Found at i:20321009 original size:17 final size:18
Alignment explanation
Indices: 20320989--20321026 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
20320979 AAAAATTCTT
20320989 AAAATTAAAAAAAAAT-G
1 AAAATTAAAAAAAAATAG
* *
20321006 AAAATTACATAAAAATAG
1 AAAATTAAAAAAAAATAG
20321024 AAA
1 AAA
20321027 TTTCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAATTAAAAAAAAATAG
Found at i:20321102 original size:21 final size:21
Alignment explanation
Indices: 20321076--20321137 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
20321066 ATTGAAAATA
*
20321076 AAAAAATCTAAAACTTTTTTT
1 AAAAAATCTAAAAATTTTTTT
20321097 AAAAAATCTAAAAATTTTTTT
1 AAAAAATCTAAAAATTTTTTT
20321118 AAAAAATTCTTAAAAATTTT
1 AAAAAA-TC-TAAAAATTTT
20321138 AAAAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 26 0.68
22 2 0.05
23 10 0.26
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAAATCTAAAAATTTTTTT
Found at i:20321139 original size:9 final size:9
Alignment explanation
Indices: 20321114--20321170 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
20321104 CTAAAAATTT
20321114 TTTTAAAAAA
1 TTTT-AAAAA
20321124 TTCTTAAAAA
1 TT-TTAAAAA
20321134 TTTTAAAAA
1 TTTTAAAAA
20321143 TTTTAAGAAA
1 TTTTAA-AAA
**
20321153 -ACTAAAAA
1 TTTTAAAAA
*
20321161 TTTTCAAAA
1 TTTTAAAAA
20321170 T
1 T
20321171 CTGAAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.08
9 22 0.56
10 12 0.31
11 2 0.05
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:20321211 original size:20 final size:20
Alignment explanation
Indices: 20321182--20321219 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20321172 TGAAATATTC
*
20321182 TAAAACAATTATGAAAAAAT
1 TAAAAAAATTATGAAAAAAT
*
20321202 TAAAAAAATTTTGAAAAA
1 TAAAAAAATTATGAAAAA
20321220 TAAAAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAAAAAATTATGAAAAAAT
Found at i:20321220 original size:19 final size:19
Alignment explanation
Indices: 20321182--20321226 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
20321172 TGAAATATTC
*
20321182 TAAAACAATTATGAAAAAA
1 TAAAAAAATTATGAAAAAA
*
20321201 TTAAAAAAATTTTG-AAAAA
1 -TAAAAAAATTATGAAAAAA
20321220 TAAAAAA
1 TAAAAAA
20321227 TTGAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 5 0.22
20 11 0.48
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (19 bp):
TAAAAAAATTATGAAAAAA
Found at i:20323187 original size:15 final size:14
Alignment explanation
Indices: 20323164--20323197 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
20323154 TGATGATTTT
*
20323164 AAAATGAAAAAGATA
1 AAAAAGAAAAAGA-A
20323179 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
20323193 AAAAA
1 AAAAA
20323198 CGAAGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:20323823 original size:9 final size:9
Alignment explanation
Indices: 20323811--20323835 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20323801 ATTACTATTA
20323811 TTTTTTTAT
1 TTTTTTTAT
20323820 TTTTTTTAT
1 TTTTTTTAT
20323829 TTTTTTT
1 TTTTTTT
20323836 CTCTTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:20324685 original size:18 final size:17
Alignment explanation
Indices: 20324664--20324731 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 17
20324654 GTCATTTTAT
20324664 TTTTTATTTATTTT-GA
1 TTTTTATTTATTTTAGA
*
20324680 GCTTTTATTTTATTTTTA-A
1 -TTTTTA-TTTA-TTTTAGA
*
20324699 TTTTTATTTAATTTTACTGG
1 TTTTTATTT-ATTTTA--GA
20324719 TTTTTATTTATTT
1 TTTTTATTTATTT
20324732 AATTGTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
17 13 0.32
18 10 0.24
19 9 0.22
20 9 0.22
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTTATTTATTTTAGA
Found at i:20324714 original size:17 final size:17
Alignment explanation
Indices: 20324657--20324714 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
20324647 TTCCATTGTC
*
20324657 ATTTTATTTTTTATTT-
1 ATTTTAATTTTTATTTA
**
20324673 ATTTTGAGCTTTTATTTTA
1 ATTTT-AATTTTTA-TTTA
*
20324692 TTTTTAATTTTTATTTA
1 ATTTTAATTTTTATTTA
20324709 ATTTTA
1 ATTTTA
20324715 CTGGTTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 5 0.15
17 15 0.45
18 9 0.27
19 4 0.12
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (17 bp):
ATTTTAATTTTTATTTA
Found at i:20326677 original size:20 final size:20
Alignment explanation
Indices: 20326462--20326668 Score: 238
Period size: 20 Copynumber: 10.3 Consensus size: 20
20326452 TGAAATTGAT
20326462 ATCATGCAAATAT-TTAATAA
1 ATCATGCAAATATATTAAT-A
*
20326482 ATCATGCAAATA-AATAATAA
1 ATCATGCAAATATATTAAT-A
** *
20326502 ATCATATAAATAAATTAATA
1 ATCATGCAAATATATTAATA
* *
20326522 ACCATGTAAATATATTAATA
1 ATCATGCAAATATATTAATA
* *
20326542 GTTATGCAAATATATTAATA
1 ATCATGCAAATATATTAATA
*
20326562 ATCATACAAATATATTAATAA
1 ATCATGCAAATATATTAAT-A
* * * *
20326583 ATTATACAAATAAATTAAAA
1 ATCATGCAAATATATTAATA
20326603 ATCATGCAAATATATTAATA
1 ATCATGCAAATATATTAATA
* *
20326623 ATCATGCAAACATATTGATA
1 ATCATGCAAATATATTAATA
20326643 ATCATGCAAATATATTAATA
1 ATCATGCAAATATATTAATA
20326663 ATCATG
1 ATCATG
20326669 TAAGTATATA
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
20 137 0.86
21 22 0.14
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (20 bp):
ATCATGCAAATATATTAATA
Found at i:20326677 original size:101 final size:101
Alignment explanation
Indices: 20326462--20326677 Score: 283
Period size: 101 Copynumber: 2.1 Consensus size: 101
20326452 TGAAATTGAT
* *
20326462 ATCATGCAAATAT-TTAATAAATCATGCAAATAAATAATAAATCATATAAATAAATTAATAACCA
1 ATCATGCAAATATATTAATAAATCATACAAATAAATAATAAATCATACAAATAAATTAATAACCA
* * * *
20326526 TGTAAATATATTAATAGTTATGCAAATATATTAATA
66 TGCAAACATATTAATAATCATGCAAATATATTAATA
* * * * *
20326562 ATCATACAAATATATTAATAAATTATACAAATAAATTAA-AAATCATGCAAATATATTAATAATC
1 ATCATGCAAATATATTAATAAATCATACAAATAAA-TAATAAATCATACAAATAAATTAATAACC
*
20326626 ATGCAAACATATTGATAATCATGCAAATATATTAATA
65 ATGCAAACATATTAATAATCATGCAAATATATTAATA
* *
20326663 ATCATGTAAGTATAT
1 ATCATGCAAATATAT
20326678 ATAAAAAAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
100 12 0.12
101 84 0.85
102 3 0.03
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (101 bp):
ATCATGCAAATATATTAATAAATCATACAAATAAATAATAAATCATACAAATAAATTAATAACCA
TGCAAACATATTAATAATCATGCAAATATATTAATA
Found at i:20326684 original size:81 final size:81
Alignment explanation
Indices: 20326462--20326667 Score: 283
Period size: 81 Copynumber: 2.6 Consensus size: 81
20326452 TGAAATTGAT
* *
20326462 ATCATGCAAATAT-TTAATAAATCATGCAAATA-AATAATAAATCATATAAATAAATTAATAACC
1 ATCATGCAAATATATTAAT-AATCATGCAAATATATTAATAAATCATATAAATAAATTAAAAACC
*
20326525 ATGTAAATATATTAATA
65 ATGCAAATATATTAATA
* * * * * *
20326542 GTTATGCAAATATATTAATAATCATACAAATATATTAATAAATTATACAAATAAATTAAAAATCA
1 ATCATGCAAATATATTAATAATCATGCAAATATATTAATAAATCATATAAATAAATTAAAAACCA
20326607 TGCAAATATATTAATA
66 TGCAAATATATTAATA
* *
20326623 ATCATGCAAACATATTGATAATCATGCAAATATATTAAT-AATCAT
1 ATCATGCAAATATATTAATAATCATGCAAATATATTAATAAATCAT
20326668 GTAAGTATAT
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
80 28 0.26
81 81 0.74
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (81 bp):
ATCATGCAAATATATTAATAATCATGCAAATATATTAATAAATCATATAAATAAATTAAAAACCA
TGCAAATATATTAATA
Found at i:20326832 original size:14 final size:15
Alignment explanation
Indices: 20326807--20326863 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 15
20326797 AATCAACAAT
*
20326807 AAATATATAATAAAA
1 AAATAGATAATAAAA
20326822 AAATA-ATAAT-AAA
1 AAATAGATAATAAAA
*
20326835 AAATA-A-AATAGCAA
1 AAATAGATAATA-AAA
*
20326849 AAATAGAAAATAAAA
1 AAATAGATAATAAAA
20326864 TCAAAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 3 0.08
13 9 0.25
14 12 0.33
15 8 0.22
16 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (15 bp):
AAATAGATAATAAAA
Found at i:20327554 original size:28 final size:28
Alignment explanation
Indices: 20327522--20327578 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
20327512 AGTTTATTGG
20327522 GAAAATAAATCTCTAATTTGTTAATATT
1 GAAAATAAATCTCTAATTTGTTAATATT
20327550 GAAAATAAATCTCTAATTTGTTAATATT
1 GAAAATAAATCTCTAATTTGTTAATATT
20327578 G
1 G
20327579 GCTTTGTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (28 bp):
GAAAATAAATCTCTAATTTGTTAATATT
Found at i:20333249 original size:17 final size:17
Alignment explanation
Indices: 20333227--20333264 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
20333217 CTTTTATAGT
20333227 ATTGTAATTTATTTGGA
1 ATTGTAATTTATTTGGA
20333244 ATTGTAATTTATTTGGA
1 ATTGTAATTTATTTGGA
20333261 ATTG
1 ATTG
20333265 ACCATACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (17 bp):
ATTGTAATTTATTTGGA
Found at i:20336940 original size:14 final size:15
Alignment explanation
Indices: 20336910--20336942 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
20336900 CCAAAAATAT
*
20336910 AATAAATCATTCAAA
1 AATAAATCATGCAAA
20336925 AATAAA-CATGCAAA
1 AATAAATCATGCAAA
20336939 AATA
1 AATA
20336943 TTATGCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAAATCATGCAAA
Found at i:20336994 original size:20 final size:20
Alignment explanation
Indices: 20336977--20337273 Score: 373
Period size: 20 Copynumber: 14.8 Consensus size: 20
20336967 ACAAATAACA
*
20336977 AATCATGCAAATA-AATAAT
1 AATCATGCAAATATATTAAT
** *
20336996 AAATCATATAAATAAATTAAT
1 -AATCATGCAAATATATTAAT
*
20337017 AATTATGCAAATATATTAAT
1 AATCATGCAAATATATTAAT
*
20337037 AATCATGTAAATATATTAAT
1 AATCATGCAAATATATTAAT
*
20337057 AAACATGCAAATATATTAAT
1 AATCATGCAAATATATTAAT
20337077 AATCATGCAAATATATTAAT
1 AATCATGCAAATATATTAAT
* *
20337097 AAATTATGCAAATAAATTAAT
1 -AATCATGCAAATATATTAAT
20337118 AATCATGCAAATATATTAAT
1 AATCATGCAAATATATTAAT
* *
20337138 AATCATGCAAAAATATTGAT
1 AATCATGCAAATATATTAAT
*
20337158 AATCATGCAAATATATCAAT
1 AATCATGCAAATATATTAAT
**
20337178 AATCATATAAATATATTAAT
1 AATCATGCAAATATATTAAT
20337198 AATCATGCAAATATATTAAT
1 AATCATGCAAATATATTAAT
* *
20337218 AATCATACAAAAATA-TAGAT
1 AATCATGCAAATATATTA-AT
** *
20337238 AATCATATAAATACATTAAT
1 AATCATGCAAATATATTAAT
*
20337258 AATCATGTAAATATAT
1 AATCATGCAAATATAT
20337274 CAAAACAAAA
Statistics
Matches: 240, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
19 2 0.01
20 213 0.89
21 25 0.10
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (20 bp):
AATCATGCAAATATATTAAT
Found at i:20337006 original size:16 final size:16
Alignment explanation
Indices: 20336956--20337010 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
20336946 TGCAAATGTT
*
20336956 TAATAAATCATACAAA
1 TAATAAATCATATAAA
*
20336972 TAACAAATCATGCAAATAAA
1 TAATAAATCAT----ATAAA
20336992 TAATAAATCATATAAA
1 TAATAAATCATATAAA
20337008 TAA
1 TAA
20337011 ATTAATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 18 0.56
20 14 0.44
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25
Consensus pattern (16 bp):
TAATAAATCATATAAA
Found at i:20337801 original size:35 final size:35
Alignment explanation
Indices: 20337760--20337832 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
20337750 AAAATTCAAA
* *
20337760 CCAAACCCAGAACAATTCTCAAATCTAGAAAATGG
1 CCAAACCCAAAACAATTCTCAAACCTAGAAAATGG
* *
20337795 CCAAACCCAAAACAGTTTTCAAACCTAGAAAATGG
1 CCAAACCCAAAACAATTCTCAAACCTAGAAAATGG
20337830 CCA
1 CCA
20337833 TCCCTTCCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.16
Consensus pattern (35 bp):
CCAAACCCAAAACAATTCTCAAACCTAGAAAATGG
Found at i:20338441 original size:18 final size:18
Alignment explanation
Indices: 20338418--20338489 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 18
20338408 CTAACTAAAC
20338418 TTAAAAATAAAA-CAAAAA
1 TTAAAAATAAAATC-AAAA
*
20338436 TTAAAATTAAAATCAAAA
1 TTAAAAATAAAATCAAAA
*
20338454 TT-AAAATCAACATCAAAA
1 TTAAAAAT-AAAATCAAAA
* * *
20338472 TCAAAATTAAAATTAAAA
1 TTAAAAATAAAATCAAAA
20338490 ATGAAAATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 4 0.09
18 35 0.80
19 5 0.11
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (18 bp):
TTAAAAATAAAATCAAAA
Found at i:20338447 original size:12 final size:12
Alignment explanation
Indices: 20338413--20338510 Score: 79
Period size: 12 Copynumber: 8.1 Consensus size: 12
20338403 TGACTCTAAC
* *
20338413 TAAACTTAAAAA
1 TAAAATTAAAAT
**
20338425 TAAAACAAAAAT
1 TAAAATTAAAAT
20338437 TAAAATTAAAAT
1 TAAAATTAAAAT
*
20338449 CAAAATTAAAAT
1 TAAAATTAAAAT
* * *
20338461 CAACATCAAAAT
1 TAAAATTAAAAT
*
20338473 CAAAATTAAAAT
1 TAAAATTAAAAT
*
20338485 TAAAAATGAAAAT
1 T-AAAATTAAAAT
* *
20338498 TGAAATTGAAAT
1 TAAAATTAAAAT
20338510 T
1 T
20338511 TTTAGGCTTT
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
12 58 0.84
13 11 0.16
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (12 bp):
TAAAATTAAAAT
Found at i:20340517 original size:13 final size:13
Alignment explanation
Indices: 20340482--20340508 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20340472 AAAAAAATTC
20340482 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
20340495 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
20340508 A
1 A
20340509 GATAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:20340761 original size:31 final size:31
Alignment explanation
Indices: 20340715--20341095 Score: 125
Period size: 31 Copynumber: 12.4 Consensus size: 31
20340705 AGAGGAGAAT
* * *
20340715 TTTAAGCTCAGTTTAGCTGGCACTGATGAAA
1 TTTAAGCCCAATTTAGCTGGCACTGATGATA
* **
20340746 TTTAAGCCCAATTTAGCTTGCACCAATGATA
1 TTTAAGCCCAATTTAGCTGGCACTGATGATA
* * *** * *
20340777 TTTAAGCTCAGTTT-GACCAACAAC-AATGAGA
1 TTTAAGCCCAATTTAG-CTGGC-ACTGATGATA
* ** * * ** *
20340808 TTGAAGCTTAGTTTAACTGGCACCAATGAGA
1 TTTAAGCCCAATTTAGCTGGCACTGATGATA
* * * *
20340839 CTTAAGCCTAATTTAGTTGGCACCT-A-GATT
1 TTTAAGCCCAATTTAGCTGGCA-CTGATGATA
* ** * *
20340869 TTTAAGCTCAATTTATTTGGCACCGATGAGA
1 TTTAAGCCCAATTTAGCTGGCACTGATGATA
* * * *
20340900 TTTAGGCCCAATTTAGTTGGTA-TCGA-GATT
1 TTTAAGCCCAATTTAGCTGGCACT-GATGATA
* * * * *
20340930 TTTAAGCTCAATTTAGCTAGCATTGATAAGA
1 TTTAAGCCCAATTTAGCTGGCACTGATGATA
* * * * *
20340961 TATAAGCCTAGTTTAGCCT-GCACT-AAGATT
1 TTTAAGCCCAATTTAG-CTGGCACTGATGATA
* * * *
20340991 TTTAAGCCCAATTTAACTAGCATTGATGAGA
1 TTTAAGCCCAATTTAGCTGGCACTGATGATA
* * * * *
20341022 TTTAAGTCCAATTTAGCTCGTAC-GTATAAGA
1 TTTAAGCCCAATTTAGCTGGCACTG-ATGATA
* * * *
20341053 TTTAAGCCCAATTTAACTAGCACT-AAGATT
1 TTTAAGCCCAATTTAGCTGGCACTGATGATA
20341083 TTTAAGCCCAATT
1 TTTAAGCCCAATT
20341096 AAGTTAGCAT
Statistics
Matches: 255, Mismatches: 80, Indels: 31
0.70 0.22 0.08
Matches are distributed among these distances:
29 3 0.01
30 79 0.31
31 168 0.66
32 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (31 bp):
TTTAAGCCCAATTTAGCTGGCACTGATGATA
Found at i:20340882 original size:30 final size:30
Alignment explanation
Indices: 20340840--20340945 Score: 115
Period size: 30 Copynumber: 3.5 Consensus size: 30
20340830 CCAATGAGAC
*
20340840 TTAAGC-CTAATTTAGTTGGCACCTAGATTT
1 TTAAGCTC-AATTTAGTTGGCACCGAGATTT
* **
20340870 TTAAGCTCAATTTATTTGGCACCGATGAGAT
1 TTAAGCTCAATTTAGTTGGCACCGA-GATTT
* * * *
20340901 TTAGGCCCAATTTAGTTGGTATCGAGATTT
1 TTAAGCTCAATTTAGTTGGCACCGAGATTT
20340931 TTAAGCTCAATTTAG
1 TTAAGCTCAATTTAG
20340946 CTAGCATTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
30 37 0.61
31 24 0.39
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (30 bp):
TTAAGCTCAATTTAGTTGGCACCGAGATTT
Found at i:20340976 original size:61 final size:60
Alignment explanation
Indices: 20340833--20341037 Score: 198
Period size: 61 Copynumber: 3.4 Consensus size: 60
20340823 ACTGGCACCA
* * ** * **
20340833 ATGAGACTTAAGCCTAATTTAGTTGGCACCTAGATTTTTAAGCTCAATTTATTTGGCACCG
1 ATGAGATTTAAGCCTAATTTAGTTGGCA-CAAGATTTTTAAGCTCAATTTAACTAGCATTG
* * * * *
20340894 ATGAGATTTAGGCCCAATTTAGTTGGTATCGAGATTTTTAAGCTCAATTTAGCTAGCATTG
1 ATGAGATTTAAGCCTAATTTAGTTGGCA-CAAGATTTTTAAGCTCAATTTAACTAGCATTG
* * * * *
20340955 ATAAGATATAAGCCTAGTTTAGCCT-GCACTAAGATTTTTAAGCCCAATTTAACTAGCATTG
1 ATGAGATTTAAGCCTAATTTAG-TTGGCAC-AAGATTTTTAAGCTCAATTTAACTAGCATTG
20341016 ATGAGATTTAAGTCC-AATTTAG
1 ATGAGATTTAAG-CCTAATTTAG
20341038 CTCGTACGTA
Statistics
Matches: 117, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
60 1 0.01
61 113 0.97
62 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (60 bp):
ATGAGATTTAAGCCTAATTTAGTTGGCACAAGATTTTTAAGCTCAATTTAACTAGCATTG
Found at i:20341038 original size:61 final size:62
Alignment explanation
Indices: 20340925--20341074 Score: 175
Period size: 61 Copynumber: 2.4 Consensus size: 62
20340915 GTTGGTATCG
* * *
20340925 AGATTTTTAAGCTCAATTTAGCTAGCATTGATAAGATATAAGCCTAGTTTAGC-CTGCAC-TA
1 AGATTTTTAAGCCCAATTTAACTAGCATTGATAAGATATAAGCCTAATTTAGCTC-GCACATA
* * *
20340986 AGATTTTTAAGCCCAATTTAACTAGCATTGATGAGATTTAAGTCC-AATTTAGCTCGTACGTATA
1 AGATTTTTAAGCCCAATTTAACTAGCATTGATAAGATATAAG-CCTAATTTAGCTCGCAC--ATA
20341050 AGA--TTTAAGCCCAATTTAACTAGCA
1 AGATTTTTAAGCCCAATTTAACTAGCA
20341075 CTAAGATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
61 48 0.62
62 25 0.32
64 5 0.06
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (62 bp):
AGATTTTTAAGCCCAATTTAACTAGCATTGATAAGATATAAGCCTAATTTAGCTCGCACATA
Found at i:20341104 original size:30 final size:30
Alignment explanation
Indices: 20341053--20341147 Score: 86
Period size: 35 Copynumber: 3.0 Consensus size: 30
20341043 ACGTATAAGA
*
20341053 TTTAAGCCCAATTTAA-CTAGCACTAAGATT
1 TTTAAGCCCAA-TTAAGTTAGCACTAAGATT
* *
20341083 TTTAAGCCCAATTAAGTTAGCATTGGATAAGGTTT
1 TTTAAGCCCAATTAAGTTAGCA----CTAA-GATT
20341118 TTTAAGCCCAATCT-AGTTAGCACTAAGATT
1 TTTAAGCCCAAT-TAAGTTAGCACTAAGATT
20341148 AGATTATTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
29 4 0.08
30 19 0.36
31 3 0.06
34 3 0.06
35 23 0.43
36 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (30 bp):
TTTAAGCCCAATTAAGTTAGCACTAAGATT
Found at i:20341835 original size:162 final size:162
Alignment explanation
Indices: 20341623--20341937 Score: 384
Period size: 162 Copynumber: 1.9 Consensus size: 162
20341613 CTATCAATAG
* * * * *
20341623 TGATATCCGAGTTCTCTTTAGTAGTGATATCCAAAGTTATTTGTATTCACTCAGTAGTGGTATCT
1 TGATATCCGAGTTCTCTTCAATAGTGATATCCAAAGTCATTTGCATTCACTCAGTAGTGATATCT
* * * * **
20341688 -AAGTTCTCCTCAATGGTGATATTTAAGTTCTTTTTAATGATGATATTCGAGTCCTCTTT-G-AT
66 GAA-TTCTCCTCAATGGTGATATTCAAGTTCTCTTCAAGGATGATATTAAAGTCCTCTTTAGTA-
*
20341750 GATGATATCCAAAGTTGTCTGCATTTTTTCAGTGA
129 G-CGATATCCAAAGTTGTCTGCATTTTTTCAGTGA
* * ** *
20341785 TGATATTCGAGTTCTCTTCAATGGTGATATCTGAAGTCATTTGCATTCACTCGGTAGTGATATCT
1 TGATATCCGAGTTCTCTTCAATAGTGATATCCAAAGTCATTTGCATTCACTCAGTAGTGATATCT
** * *
20341850 GAATTCTCCTTGATGGTGATATTCAAGTTCTCTTCAAGGGTGATATTAAAGTCTTCTTTAGTAGC
66 GAATTCTCCTCAATGGTGATATTCAAGTTCTCTTCAAGGATGATATTAAAGTCCTCTTTAGTAGC
*
20341915 GATATCCAAAGTTGTTTGCATTT
131 GATATCCAAAGTTGTCTGCATTT
20341938 CCTTAATGGT
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
162 123 0.96
163 4 0.03
164 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (162 bp):
TGATATCCGAGTTCTCTTCAATAGTGATATCCAAAGTCATTTGCATTCACTCAGTAGTGATATCT
GAATTCTCCTCAATGGTGATATTCAAGTTCTCTTCAAGGATGATATTAAAGTCCTCTTTAGTAGC
GATATCCAAAGTTGTCTGCATTTTTTCAGTGA
Found at i:20342691 original size:17 final size:17
Alignment explanation
Indices: 20342642--20342707 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
20342632 AAAAGAGTTT
* *
20342642 TTCATAAATTTAAAAAA
1 TTCATAAAATAAAAAAA
**
20342659 TTC-TAAAATTCTAAAAA
1 TTCATAAAA-TAAAAAAA
20342676 TTCATAAAATAAAAAAA
1 TTCATAAAATAAAAAAA
* *
20342693 TCCAAAAAATAAAAA
1 TTCATAAAATAAAAA
20342708 TTTAAAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 4 0.10
17 31 0.77
18 5 0.12
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
TTCATAAAATAAAAAAA
Found at i:20342733 original size:26 final size:25
Alignment explanation
Indices: 20342685--20342732 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20342675 ATTCATAAAA
*
20342685 TAAAAAAATCCAAAAAATAAAAATT
1 TAAAAAAATCCAAAAAAAAAAAATT
*
20342710 TAAAAGAATCCAAAAAAAAAAAA
1 TAAAAAAATCCAAAAAAAAAAAA
20342733 ACCTAGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (25 bp):
TAAAAAAATCCAAAAAAAAAAAATT
Found at i:20345402 original size:17 final size:17
Alignment explanation
Indices: 20345365--20345402 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
20345355 AAAATATTTT
*
20345365 TTAATTTTTAAAATTGA
1 TTAATTTTTAAAAATGA
20345382 TTAATTTTTTAAAAATG-
1 TTAA-TTTTTAAAAATGA
20345399 TTAA
1 TTAA
20345403 ACTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TTAATTTTTAAAAATGA
Found at i:20346607 original size:14 final size:14
Alignment explanation
Indices: 20346590--20346617 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20346580 TTTCAGTGAT
20346590 TGATTTTTATTTAA
1 TGATTTTTATTTAA
20346604 TGATTTTTATTTAA
1 TGATTTTTATTTAA
20346618 AAGGTAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TGATTTTTATTTAA
Found at i:20349733 original size:20 final size:21
Alignment explanation
Indices: 20349694--20349733 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20349684 TAAATTTTTA
* *
20349694 AAATTTAAATTTTATTTATTG
1 AAATTAAAATTTTATATATTG
20349715 AAATTAAAATTTTA-ATATT
1 AAATTAAAATTTTATATATT
20349734 TTATTATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
AAATTAAAATTTTATATATTG
Found at i:20352731 original size:18 final size:18
Alignment explanation
Indices: 20352708--20352742 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20352698 TTGGGTCTTT
20352708 TTTCCTTGCCTTTTTGTC
1 TTTCCTTGCCTTTTTGTC
**
20352726 TTTCCTTTTCTTTTTGT
1 TTTCCTTGCCTTTTTGT
20352743 TGGGTCAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTCCTTGCCTTTTTGTC
Found at i:20357431 original size:14 final size:14
Alignment explanation
Indices: 20357412--20357448 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
20357402 ATTATAAAAT
*
20357412 CTAATATTTTTATA
1 CTAATATTTATATA
20357426 CTAATATTTATATA
1 CTAATATTTATATA
20357440 --AATATTTAT
1 CTAATATTTAT
20357449 TTTAATCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.41
14 13 0.59
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (14 bp):
CTAATATTTATATA
Found at i:20358719 original size:25 final size:23
Alignment explanation
Indices: 20358690--20358751 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
20358680 ATAAAATTAC
**
20358690 AAAGAAGATTATCATTCTCTTAAT
1 AAAGAAGATTATCA-TCTCAAAAT
*
20358714 ATAAGATGATTCAATCATCTCAAAAT
1 A-AAGAAGATT--ATCATCTCAAAAT
20358740 AAAGAAGATTAT
1 AAAGAAGATTAT
20358752 TCTTAATCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
23 2 0.06
24 1 0.03
25 16 0.52
26 8 0.26
27 4 0.13
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (23 bp):
AAAGAAGATTATCATCTCAAAAT
Found at i:20364319 original size:35 final size:35
Alignment explanation
Indices: 20364273--20364347 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
20364263 TAAATAAGCC
20364273 AGTAAAAGAAAAGTATAAACCAGTAAACGAGGAGT
1 AGTAAAAGAAAAGTATAAACCAGTAAACGAGGAGT
*
20364308 AGTAAAAGAAAAGTATAAACCAGTAAATGAGGAGT
1 AGTAAAAGAAAAGTATAAACCAGTAAACGAGGAGT
20364343 AGTAA
1 AGTAA
20364348 GGCTATAACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.55, C:0.07, G:0.23, T:0.16
Consensus pattern (35 bp):
AGTAAAAGAAAAGTATAAACCAGTAAACGAGGAGT
Found at i:20366034 original size:23 final size:22
Alignment explanation
Indices: 20365982--20366034 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
20365972 ATAGAGTCAA
*
20365982 ATAG-GACAATAAGAAAGCAGC
1 ATAGAGACAATAAGAAAGCAAC
* *
20366003 ATAAAAGACAATAATAAAGCGAAC
1 AT-AGAGACAATAAGAAAGC-AAC
20366027 ATAGAGAC
1 ATAGAGAC
20366035 CACTCCTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 1 0.04
23 18 0.72
24 4 0.16
ACGTcount: A:0.57, C:0.13, G:0.19, T:0.11
Consensus pattern (22 bp):
ATAGAGACAATAAGAAAGCAAC
Found at i:20369379 original size:14 final size:14
Alignment explanation
Indices: 20369352--20369393 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
20369342 AAAATATTGT
20369352 ATATAATAAA-TTTA
1 ATAT-ATAAATTTTA
*
20369366 ATATTTAAATTTTA
1 ATATATAAATTTTA
20369380 ATATATATAATTTT
1 ATATATA-AATTTT
20369394 TTAGATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATAAATTTTA
Found at i:20370361 original size:19 final size:21
Alignment explanation
Indices: 20370334--20370381 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
20370324 TTGTTCTTTT
20370334 AAATAAAATATGAA-AA-AAA
1 AAATAAAATATGAATAATAAA
*
20370353 AAATCAAATATGAATAATAAA
1 AAATAAAATATGAATAATAAA
20370374 AAATAAAA
1 AAATAAAA
20370382 AGTAGGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 2 0.08
21 10 0.40
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (21 bp):
AAATAAAATATGAATAATAAA
Found at i:20373032 original size:26 final size:26
Alignment explanation
Indices: 20372997--20373073 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 26
20372987 TATAAAAATT
20372997 AATTTT-AAATATATTTATTTTTAAA
1 AATTTTAAAATATATTTATTTTTAAA
*
20373022 AATTTTAAAAT-TAATT-TTTTTATAA
1 AATTTTAAAATATATTTATTTTTA-AA
* ** *
20373047 AATATTATTATATGATTTATTTATAAA
1 AATTTTAAAATAT-ATTTATTTTTAAA
20373074 TTTATATCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
24 6 0.15
25 20 0.49
26 5 0.12
27 5 0.12
28 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
AATTTTAAAATATATTTATTTTTAAA
Found at i:20383790 original size:14 final size:14
Alignment explanation
Indices: 20383757--20383799 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
20383747 TTTTTTTGTA
*
20383757 TTATTTTATATA-T
1 TTATTTTATTTATT
*
20383770 GTATTTTATTTATT
1 TTATTTTATTTATT
20383784 TTATTTTATTTATT
1 TTATTTTATTTATT
20383798 TT
1 TT
20383800 TGATAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:20387220 original size:19 final size:18
Alignment explanation
Indices: 20387179--20387235 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
20387169 ATAATATATG
* *
20387179 TAATAATAAATTTTACATG
1 TAATAATAAATTTTA-TTA
20387198 TAATAATAAATTTTTATTA
1 TAATAATAAA-TTTTATTA
20387217 TAAT-ATAAAATTTT-TTA
1 TAATAAT-AAATTTTATTA
20387234 TA
1 TA
20387236 TTTTCAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 5 0.15
18 6 0.18
19 18 0.53
20 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATAATAAATTTTATTA
Found at i:20388458 original size:28 final size:28
Alignment explanation
Indices: 20388383--20388458 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 28
20388373 AACATTTATA
**
20388383 TTTTTTATTCCTTCCACTTTCCTTTTTTTT
1 TTTTTTATTATTTCCA--TTCCTTTTTTTT
*
20388413 TTTTTTATTATTTGCATTCCTTTCTTCTTT
1 TTTTTTATTATTTCCATTCCTTT-TT-TTT
20388443 TTTTTT-TT-TTTCCATT
1 TTTTTTATTATTTCCATT
20388459 GTATAAAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 14 0.35
29 4 0.10
30 22 0.55
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.72
Consensus pattern (28 bp):
TTTTTTATTATTTCCATTCCTTTTTTTT
Found at i:20391206 original size:16 final size:18
Alignment explanation
Indices: 20391180--20391213 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20391170 AAATCTTGCA
20391180 TTTTTTGTTCA-AGTTTC
1 TTTTTTGTTCATAGTTTC
20391197 TTTTTT-TTCATAGTTTC
1 TTTTTTGTTCATAGTTTC
20391214 ATAATCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.68
Consensus pattern (18 bp):
TTTTTTGTTCATAGTTTC
Found at i:20393952 original size:21 final size:22
Alignment explanation
Indices: 20393928--20393971 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20393918 AATTTTATCT
*
20393928 AATTTATAT-TTATAAATAATG
1 AATTTATATATAATAAATAATG
* *
20393949 AATTTTTATATAATAATTAATG
1 AATTTATATATAATAAATAATG
20393971 A
1 A
20393972 GTCATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTTATATATAATAAATAATG
Found at i:20394017 original size:21 final size:21
Alignment explanation
Indices: 20393975--20394017 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20393965 TTAATGAGTC
**
20393975 ATAATTTAAGTATTATGTTAA
1 ATAATTTAAGTATTATAATAA
20393996 ATAA-TTATAGTATTATAATAA
1 ATAATTTA-AGTATTATAATAA
20394017 A
1 A
20394018 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
ATAATTTAAGTATTATAATAA
Found at i:20394196 original size:21 final size:22
Alignment explanation
Indices: 20394172--20394215 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20394162 AATTTTATCT
*
20394172 AATTTATAT-TTATAAATAATG
1 AATTTATATATAATAAATAATG
* *
20394193 AATTTTTATATAATAATTAATG
1 AATTTATATATAATAAATAATG
20394215 A
1 A
20394216 GTCATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTTATATATAATAAATAATG
Found at i:20394227 original size:244 final size:244
Alignment explanation
Indices: 20393798--20394287 Score: 962
Period size: 244 Copynumber: 2.0 Consensus size: 244
20393788 TTCATTGAAA
20393798 TCACAGAATTGTCACGTAGATAACGTCATTTTAAACAGAACACATTTAAAAAAACATTTCGCTTA
1 TCACAGAATTGTCACGTAGATAACGTCATTTTAAACAGAACACATTTAAAAAAACATTTCGCTTA
20393863 TCATTACTGTTAAATAATTAATCAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCT
66 TCATTACTGTTAAATAATTAATCAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCT
*
20393928 AATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAGTATTATGT
131 AATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAGCATTATGT
20393993 TAAATAATTATAGTATTATAATAAAAAAAATTAAAGATAATATGTTTCT
196 TAAATAATTATAGTATTATAATAAAAAAAATTAAAGATAATATGTTTCT
20394042 TCACAGAATTGTCACGTAGATAACGTCATTTTAAACAGAACACATTTAAAAAAACATTTCGCTTA
1 TCACAGAATTGTCACGTAGATAACGTCATTTTAAACAGAACACATTTAAAAAAACATTTCGCTTA
20394107 TCATTACTGTTAAATAATTAATCAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCT
66 TCATTACTGTTAAATAATTAATCAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCT
20394172 AATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAGCATTATGT
131 AATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAGCATTATGT
*
20394237 TAAATAATTATAGTATTATAATAAAAAAAATTATAGATAATATGTTTCT
196 TAAATAATTATAGTATTATAATAAAAAAAATTAAAGATAATATGTTTCT
20394286 TC
1 TC
20394288 GTTTGAATAG
Statistics
Matches: 244, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
244 244 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.40
Consensus pattern (244 bp):
TCACAGAATTGTCACGTAGATAACGTCATTTTAAACAGAACACATTTAAAAAAACATTTCGCTTA
TCATTACTGTTAAATAATTAATCAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCT
AATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAGCATTATGT
TAAATAATTATAGTATTATAATAAAAAAAATTAAAGATAATATGTTTCT
Found at i:20394257 original size:120 final size:120
Alignment explanation
Indices: 20393864--20394246 Score: 322
Period size: 120 Copynumber: 3.2 Consensus size: 120
20393854 TTTCGCTTAT
20393864 CATTACTGTTAAATAATTAATCAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCTA
1 CATTACTGTTAAATAATTAAT-AATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCTA
20393929 ATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAG
65 ATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAG
* * * * * * *
20393985 TATTA-TGTTAAATAATT-ATAGTATTATAA--TAAAA-AAAATTAAA-GA-TAATATGTT-TCT
1 CATTACTGTTAAATAATTAATA--ATTATAACTTAAAATTATATGAAATCATTAAAATTTTATC-
* *** * * * * * * * ** **
20394042 TCACAGA-ATTGTCACGTAGATAACGTCATTTTAAACAGAACACATTTAAAAAAACAT--TTCGC
63 TAATTTATATT-T-A--TAAATAATG-AATTTT-TATATAATA-A-TTAATGAGTCATAATT---
* *
20394104 TTAT
117 TAAG
20394108 CATTACTGTTAAATAATTAATCAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCTA
1 CATTACTGTTAAATAATTAAT-AATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCTA
20394173 ATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAG
65 ATTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAG
20394229 CATTA-TGTTAAATAATTA
1 CATTACTGTTAAATAATTA
20394247 TAGTATTATA
Statistics
Matches: 188, Mismatches: 48, Indels: 53
0.65 0.17 0.18
Matches are distributed among these distances:
114 5 0.03
115 11 0.06
116 2 0.01
117 6 0.03
118 13 0.07
119 7 0.04
120 39 0.21
121 12 0.06
122 16 0.09
123 7 0.04
124 26 0.14
125 7 0.04
126 13 0.07
127 6 0.03
128 2 0.01
129 11 0.06
130 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (120 bp):
CATTACTGTTAAATAATTAATAATTATAACTTAAAATTATATGAAATCATTAAAATTTTATCTAA
TTTATATTTATAAATAATGAATTTTTATATAATAATTAATGAGTCATAATTTAAG
Found at i:20394693 original size:12 final size:13
Alignment explanation
Indices: 20394671--20394702 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20394661 TGGCCAACTC
20394671 GAAAGAAAAAAAT
1 GAAAGAAAAAAAT
20394684 GAAA-AAAAAAAT
1 GAAAGAAAAAAAT
20394696 -AAAGAAA
1 GAAAGAAA
20394703 CTGCTACGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 11 0.61
13 4 0.22
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (13 bp):
GAAAGAAAAAAAT
Found at i:20397081 original size:27 final size:28
Alignment explanation
Indices: 20397037--20397090 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
20397027 AGATTAAGTT
*
20397037 GTTAGAGACCCAAAAAAGACATAACTGA
1 GTTAGAGAACCAAAAAAGACATAACTGA
*
20397065 GTTAGA-AACCAAGAAAGACATAACTG
1 GTTAGAGAACCAAAAAAGACATAACTG
20397091 TCTGAGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.15
Consensus pattern (28 bp):
GTTAGAGAACCAAAAAAGACATAACTGA
Found at i:20397098 original size:27 final size:27
Alignment explanation
Indices: 20397046--20397098 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
20397036 TGTTAGAGAC
* *
20397046 CCAAAAAAGACATAACTGAGTTAGAAA
1 CCAAAAAAGACATAACTGACTGAGAAA
* *
20397073 CCAAGAAAGACATAACTGTCTGAGAA
1 CCAAAAAAGACATAACTGACTGAGAA
20397099 GACAATGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (27 bp):
CCAAAAAAGACATAACTGACTGAGAAA
Found at i:20399734 original size:20 final size:20
Alignment explanation
Indices: 20399709--20399776 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 20
20399699 TTATTATTAA
20399709 AATTATTAATATTTAAAAAT
1 AATTATTAATATTTAAAAAT
*
20399729 AATTA-T-AT-TTTAATAAT
1 AATTATTAATATTTAAAAAT
20399746 AA-TATTTAATA-TT-AAAAT
1 AATTA-TTAATATTTAAAAAT
*
20399764 ATTATATTAATAT
1 AAT-TATTAATAT
20399777 AAAAAATACT
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
16 2 0.05
17 10 0.26
18 8 0.21
19 11 0.29
20 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTATTAATATTTAAAAAT
Found at i:20399736 original size:16 final size:18
Alignment explanation
Indices: 20399707--20399748 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
20399697 ATTTATTATT
*
20399707 AAAATTATTAATA-TTTA
1 AAAATAATTAATATTTTA
20399724 AAAATAATT-ATATTTTA
1 AAAATAATTAATATTTTA
*
20399741 ATAATAAT
1 AAAATAAT
20399749 ATTTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATAATTAATATTTTA
Found at i:20399881 original size:15 final size:16
Alignment explanation
Indices: 20399830--20399910 Score: 67
Period size: 15 Copynumber: 4.8 Consensus size: 16
20399820 AATATATTAC
20399830 AATATTATTTATTAAT
1 AATATTATTTATTAAT
20399846 AATATTTATTAATAGATTAAT
1 AATA-TTATT--T--ATTAAT
20399867 -ATATTATTTATTAAT
1 AATATTATTTATTAAT
* *
20399882 CA-ATTATTTGTTAATAT
1 AATATTATTTATT-A-AT
20399899 AATATTATTTAT
1 AATATTATTTAT
20399911 AAGTAAAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
15 15 0.28
16 6 0.11
17 9 0.17
18 8 0.15
19 6 0.11
20 3 0.06
21 6 0.11
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (16 bp):
AATATTATTTATTAAT
Found at i:20399887 original size:23 final size:21
Alignment explanation
Indices: 20399840--20399881 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
20399830 AATATTATTT
20399840 ATTAATAATATTTATTAATAG
1 ATTAATAATATTTATTAATAG
20399861 ATTAATATATTATTTATTAAT
1 ATTAATA-A-TATTTATTAAT
20399882 CAATTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTAATAATATTTATTAATAG
Found at i:20399909 original size:33 final size:34
Alignment explanation
Indices: 20399795--20399910 Score: 103
Period size: 36 Copynumber: 3.3 Consensus size: 34
20399785 CTTAAAATAA
* * *
20399795 ATTATTTATTATTCTATATTATTTTAATATATTACAAT
1 ATTATTTATTAAT-AATATT-TATTAATA-ATTA-AAT
20399833 ATTATTTATTAATAATATTTATTAATAGATTAATAT
1 ATTATTTATTAATAATATTTATTAATA-ATTAA-AT
*
20399869 ATTATTTATTAATCAATTATTTGTTAAT-A-T-AAT
1 ATTATTTATTAAT-AA-TATTTATTAATAATTAAAT
20399902 ATTATTTAT
1 ATTATTTAT
20399911 AAGTAAAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
33 11 0.16
34 1 0.01
35 2 0.03
36 27 0.39
37 7 0.10
38 22 0.31
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (34 bp):
ATTATTTATTAATAATATTTATTAATAATTAAAT
Found at i:20401774 original size:300 final size:303
Alignment explanation
Indices: 20401198--20401801 Score: 1045
Period size: 300 Copynumber: 2.0 Consensus size: 303
20401188 AAAATTTAGA
*
20401198 ATATTCTTTACATATAACATGATAAAAAAAATTTGTTAATAGATATTTTGAATGCATGATTCATT
1 ATATTCTTTACATATAACATGATAAAAAAAATTTGTTAATAGATATTTTGAATGCATGATCCATT
* * *
20401263 CAGTTTTATTTACAAGTGAAATTATATAGTAATTCATGGTAGTAATTTGTATGTAATTCTTTACC
66 CAATTTTATTCACAAGTGAAATTATATAGTAATTCATGGTAGCAATTTGTATGTAATTCTTTACC
* *
20401328 AAGGTAGGACTTATTCCAACATTTGTGTTAGTCATCAGGCATTGACACACAAAATTATCAAAGTT
131 AAGATAGGACTTATTCCAACATTTGTGTTAGTCATCAGGCATTGAAACACAAAATTATCAAAGTT
*
20401393 AGCATCATTTTTATTTTCTGCATGATAATCAAAATTAAAAGTTGTTAAACTTTTTTATTTTTCTT
196 AGCATCATTTTTAGTTTCTGCATGATAATCAAAATTAAAAGTTGTTAAACTTTTTTATTTTTCTT
20401458 TAATTAAAACAGTAG-AAAAAATAATAAGTATAATTTAAGTGC
261 TAATTAAAACAGTAGAAAAAAATAATAAGTATAATTTAAGTGC
*
20401500 ATATTCTTTACATATAACATGAT-AAAAAAA-TTGTTAATAGATATTTT-AATTGCATGGTCCAT
1 ATATTCTTTACATATAACATGATAAAAAAAATTTGTTAATAGATATTTTGAA-TGCATGATCCAT
20401562 TCAATTTTATTCACAAGTGAAATTATATAGTAATTCATGGTAGCAATTTGTATGTAATTCTTTAC
65 TCAATTTTATTCACAAGTGAAATTATATAGTAATTCATGGTAGCAATTTGTATGTAATTCTTTAC
* * * *
20401627 CAAGATAGGACTTATTCTAACATTTGTGTTAGTCATTAGGCATTGAAACACAAGATTATCAGAGT
130 CAAGATAGGACTTATTCCAACATTTGTGTTAGTCATCAGGCATTGAAACACAAAATTATCAAAGT
*
20401692 TAGCATCATTTTTAGTTTCTGCATGATAATCAGAATTAAAAGTTGTTAAACTTTTTTATTTTTCT
195 TAGCATCATTTTTAGTTTCTGCATGATAATCAAAATTAAAAGTTGTTAAACTTTTTTATTTTTCT
*
20401757 TTAATTAAAATAGTAGAAAAAAATAATAAGTATAATTTAAGTGC
260 TTAATTAAAACAGTAGAAAAAAATAATAAGTATAATTTAAGTGC
20401801 A
1 A
20401802 AAAGAAATAA
Statistics
Matches: 286, Mismatches: 14, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
299 2 0.01
300 226 0.79
301 35 0.12
302 23 0.08
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (303 bp):
ATATTCTTTACATATAACATGATAAAAAAAATTTGTTAATAGATATTTTGAATGCATGATCCATT
CAATTTTATTCACAAGTGAAATTATATAGTAATTCATGGTAGCAATTTGTATGTAATTCTTTACC
AAGATAGGACTTATTCCAACATTTGTGTTAGTCATCAGGCATTGAAACACAAAATTATCAAAGTT
AGCATCATTTTTAGTTTCTGCATGATAATCAAAATTAAAAGTTGTTAAACTTTTTTATTTTTCTT
TAATTAAAACAGTAGAAAAAAATAATAAGTATAATTTAAGTGC
Found at i:20403463 original size:23 final size:23
Alignment explanation
Indices: 20403432--20403492 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
20403422 TGAGTTGATT
* *
20403432 AAGGCTGGGTATATGGGGTATAG
1 AAGGTTGGGTATATGGGATATAG
*
20403455 AAGGTTGGGTATATAGGATATAG
1 AAGGTTGGGTATATGGGATATAG
*
20403478 AAGGTTGAGTATATG
1 AAGGTTGGGTATATG
20403493 AGTTTGTGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.02, G:0.38, T:0.30
Consensus pattern (23 bp):
AAGGTTGGGTATATGGGATATAG
Found at i:20404142 original size:28 final size:28
Alignment explanation
Indices: 20404099--20404195 Score: 106
Period size: 28 Copynumber: 3.5 Consensus size: 28
20404089 TAGAGTCTTT
** *
20404099 TTTAACAAAAACAGAACATCAACAGCTA
1 TTTAACAAAATGAGAACATCAAAAGCTA
* *
20404127 TTTAACAAAATGAGAACATCAATAG-TT
1 TTTAACAAAATGAGAACATCAAAAGCTA
* *
20404154 TTTCAACAAAATGATAACATCAAAAGCTG
1 TTT-AACAAAATGAGAACATCAAAAGCTA
*
20404183 TTCAACAAAATGA
1 TTTAACAAAATGA
20404196 TCACATTAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.07
28 52 0.88
29 3 0.05
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.24
Consensus pattern (28 bp):
TTTAACAAAATGAGAACATCAAAAGCTA
Found at i:20405265 original size:20 final size:21
Alignment explanation
Indices: 20405240--20405278 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20405230 GATCAGTAAT
*
20405240 TATCATCAAAATAG-CATTTA
1 TATCATAAAAATAGACATTTA
20405260 TATCATAAAAATAGACATT
1 TATCATAAAAATAGACATT
20405279 GAATGTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (21 bp):
TATCATAAAAATAGACATTTA
Found at i:20405989 original size:165 final size:167
Alignment explanation
Indices: 20405717--20406055 Score: 436
Period size: 165 Copynumber: 2.0 Consensus size: 167
20405707 TGAACATTAG
* * * *
20405717 TAAATTACCTGTTTAGCTTTCATTATGATAAAATAAATATATAAAGCAAATATGTGGTTAATACA
1 TAAATTACCTGTTTAGCTTTCACTATGATAAAATAAATATAGAAAACAAATATGTGATTAATACA
** * *
20405782 ATAAATACACAAAGGTAAATACTTTTTTAATTTTGTTTACAT-ATGTAAACTACTTGAAA-TTAA
66 ATAAATACACAAAGACAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATTTAA
* *
20405845 TTTGAATATAACATGCAAAGCAAATACAATACATAAC
131 TTAGAATACAACATGCAAAGCAAATACAATACATAAC
* * *
20405882 TAAATTATCTGTTTAGCTTTC-CTACT-ACTAAAATAAATATAGAAAATAAATATGCT-ATTGAT
1 TAAATTACCTGTTTAGCTTTCACTA-TGA-TAAAATAAATATAGAAAACAAATATG-TGATTAAT
* *
20405944 ACAATAAATATACAGAGACAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATT
63 ACAATAAATACACAAAGACAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATT
* * ** *
20406009 TGATTAGAATACAACATGTAAAGTGAATACAATACATAAG
128 TAATTAGAATACAACATGCAAAGCAAATACAATACATAAC
20406049 TAAATTA
1 TAAATTA
20406056 AACAAACAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
164 3 0.02
165 87 0.58
166 18 0.12
167 41 0.28
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (167 bp):
TAAATTACCTGTTTAGCTTTCACTATGATAAAATAAATATAGAAAACAAATATGTGATTAATACA
ATAAATACACAAAGACAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATTTAA
TTAGAATACAACATGCAAAGCAAATACAATACATAAC
Found at i:20407500 original size:15 final size:15
Alignment explanation
Indices: 20407480--20407524 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
20407470 NNNNNNNATA
20407480 TATTAATATATTATT
1 TATTAATATATTATT
20407495 TATTAATCA-ATTATT
1 TATTAAT-ATATTATT
* *
20407510 TGTTAATATAATATT
1 TATTAATATATTATT
20407525 ATTTATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TATTAATATATTATT
Found at i:20409360 original size:301 final size:301
Alignment explanation
Indices: 20408818--20409422 Score: 1066
Period size: 301 Copynumber: 2.0 Consensus size: 301
20408808 AAAAACTAGA
* *
20408818 ATATTCTTTACATATAATATGATCAAAAAATTGTTAATACATATTTTGAATGCATGGTTCATTCA
1 ATATTCTTTACATATAACATGATAAAAAAATTGTTAATACATATTTTGAATGCATGGTTCATTCA
* *
20408883 GTTTTATTCACAAGTGAAATTATATAGTAATTCTTGATAGTAATTTGTATGTAATTCTTTACCGA
66 GTTTTATTCACAAGTGAAATTATATAGTAATTCATGATAGTAATTTGTATGTAATTCTTTACCAA
20408948 GGTAGGACTTATTCCAACATTTGTGTTAGTCATCAAGCATTGAAACACAAAATTATCAGAGTTAG
131 GGTAGGACTTATTCCAACATTTGTGTTAGTCATCAAGCATTGAAACACAAAATTATCAGAGTTAG
*
20409013 CATCATTTTTATTTTATGCATGATAATCAAAATTAAAAGTTGTTAAACTTTTTTTATTTTTCTTT
196 CATCATTTTTATTTTATGCATGATAATCAAAATTAAAAGTTGTTAAAATTTTTTTATTTTTCTTT
*
20409078 AATTAAAGCAGTAGAAAAAATAATAAGTATAATTTAAGTGC
261 AATTAAAACAGTAGAAAAAATAATAAGTATAATTTAAGTGC
* * *
20409119 ATATTCTTTACATATAACATGATAAAAAAATTGTTAATAGATATTTTTAATGCATGGTTCATTCT
1 ATATTCTTTACATATAACATGATAAAAAAATTGTTAATACATATTTTGAATGCATGGTTCATTCA
* *
20409184 GTTTTATTCACAAGTGAAATTATATAGTAATTCATGGTAGTAATTTGTATGTAATTTTTTACCAA
66 GTTTTATTCACAAGTGAAATTATATAGTAATTCATGATAGTAATTTGTATGTAATTCTTTACCAA
* * *
20409249 GGTAGGACTTATTCCTACATTTGTGTTAGTCATCAGGCATTGAAACACAAGATTATCAGAGTTAG
131 GGTAGGACTTATTCCAACATTTGTGTTAGTCATCAAGCATTGAAACACAAAATTATCAGAGTTAG
* *
20409314 CATCATTTTTATTTTCTGCATGATAATCAGAATTAAAAGTTGTTAAAATTTTTTTATTTTTCTTT
196 CATCATTTTTATTTTATGCATGATAATCAAAATTAAAAGTTGTTAAAATTTTTTTATTTTTCTTT
20409379 AATTAAAACAGTAGAAAAAATAATAAGTATAATTTAAGTGC
261 AATTAAAACAGTAGAAAAAATAATAAGTATAATTTAAGTGC
20409420 ATA
1 ATA
20409423 AGAAATAAAT
Statistics
Matches: 288, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
301 288 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (301 bp):
ATATTCTTTACATATAACATGATAAAAAAATTGTTAATACATATTTTGAATGCATGGTTCATTCA
GTTTTATTCACAAGTGAAATTATATAGTAATTCATGATAGTAATTTGTATGTAATTCTTTACCAA
GGTAGGACTTATTCCAACATTTGTGTTAGTCATCAAGCATTGAAACACAAAATTATCAGAGTTAG
CATCATTTTTATTTTATGCATGATAATCAAAATTAAAAGTTGTTAAAATTTTTTTATTTTTCTTT
AATTAAAACAGTAGAAAAAATAATAAGTATAATTTAAGTGC
Found at i:20411725 original size:28 final size:28
Alignment explanation
Indices: 20411685--20411778 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 28
20411675 AGTCCTTTTT
** * * * *
20411685 AACAAAAACAGAACATCAACAGCTATTT
1 AACAAAATGAGAACATCAAAAGTTGTTC
*
20411713 AACAAAATGAGAACATCAATAGTTGTTC
1 AACAAAATGAGAACATCAAAAGTTGTTC
* *
20411741 AACAAAATGATAATATCAAAAGTTGTTC
1 AACAAAATGAGAACATCAAAAGTTGTTC
20411769 AACAAAATGA
1 AACAAAATGA
20411779 TCACATTAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (28 bp):
AACAAAATGAGAACATCAAAAGTTGTTC
Found at i:20411779 original size:28 final size:28
Alignment explanation
Indices: 20411713--20411784 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
20411703 ACAGCTATTT
* *
20411713 AACAAAATGAGAACATCAATAGTTGTTC
1 AACAAAATGATAACATCAAAAGTTGTTC
*
20411741 AACAAAATGATAATATCAAAAGTTGTTC
1 AACAAAATGATAACATCAAAAGTTGTTC
*
20411769 AACAAAATGATCACAT
1 AACAAAATGATAACAT
20411785 TAGAATAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (28 bp):
AACAAAATGATAACATCAAAAGTTGTTC
Found at i:20412845 original size:20 final size:21
Alignment explanation
Indices: 20412820--20412858 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20412810 GATCAGTAAT
*
20412820 TATCATTAAAATAG-CATTTA
1 TATCATAAAAATAGACATTTA
20412840 TATCATAAAAATAGACATT
1 TATCATAAAAATAGACATT
20412859 GAATGTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
TATCATAAAAATAGACATTTA
Found at i:20413479 original size:165 final size:167
Alignment explanation
Indices: 20413298--20413636 Score: 447
Period size: 165 Copynumber: 2.0 Consensus size: 167
20413288 TGAACATTAA
* *
20413298 TAAATTACCTGTTTAGCTTTCATTA-TGA-TAAAATAAATATACAAAGCAAATATG-TGGTTGAT
1 TAAATTACCTGTTTAGCTTTC-CTACT-ACTAAAATAAATATACAAAACAAATATGCT-GTTGAT
* * * *
20413360 ACAATAACTACACAAAGGTAAATACTTTTTTAATTTTGTTTACAT-ATGTAAACTACTTGAAA-T
63 ACAATAAATACACAAAGATAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATT
* *
20413423 TAATTTGAATATAACATG-CAAAGCAAATACAATACATAAC
128 TAATTAGAATACAACATGTC-AAGCAAATACAATACATAAC
* * *
20413463 TAAATTATCTGTTTAGCTTTCCTACTACTAAAATAAATATAGAAAATAAATATGCTGTTGATACA
1 TAAATTACCTGTTTAGCTTTCCTACTACTAAAATAAATATACAAAACAAATATGCTGTTGATACA
* * *
20413528 ATAAATATACAGAGATAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATTTGA
66 ATAAATACACAAAGATAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATTTAA
* * *
20413593 TTAGAATACAACATGTCAAGCGAATACAATACGTAAG
131 TTAGAATACAACATGTCAAGCAAATACAATACATAAC
20413630 TAAATTA
1 TAAATTA
20413637 AATAAACAAA
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
164 3 0.02
165 89 0.59
166 18 0.12
167 40 0.26
168 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (167 bp):
TAAATTACCTGTTTAGCTTTCCTACTACTAAAATAAATATACAAAACAAATATGCTGTTGATACA
ATAAATACACAAAGATAAATACTTGTTTAATTTTATTTACATAATGTAAACTACTTGAAATTTAA
TTAGAATACAACATGTCAAGCAAATACAATACATAAC
Found at i:20415166 original size:5 final size:5
Alignment explanation
Indices: 20415156--20415206 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
20415146 TAGTTGTTTG
*
20415156 TTATT TTATT TTATT TTATTT TTGATT TT-TT TGATTAT TTATT TTATT
1 TTATT TTATT TTATT TTA-TT TT-ATT TTATT TTA-T-T TTATT TTATT
20415204 TTA
1 TTA
20415207 AGATAATGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 3 0.08
5 22 0.56
6 10 0.26
7 4 0.10
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:20416450 original size:21 final size:22
Alignment explanation
Indices: 20416426--20416467 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
20416416 ATCGACAATG
*
20416426 GATGAAAGATGAGAA-AAAAAT
1 GATGAAAGATGAAAAGAAAAAT
20416447 GATGAAAGATGAAAAGAAAAA
1 GATGAAAGATGAAAAGAAAAA
20416468 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (22 bp):
GATGAAAGATGAAAAGAAAAAT
Found at i:20416504 original size:9 final size:9
Alignment explanation
Indices: 20416492--20416554 Score: 58
Period size: 9 Copynumber: 7.2 Consensus size: 9
20416482 GGAAATGGAT
20416492 GAAAAAAAA
1 GAAAAAAAA
20416501 GAAAAAAAA
1 GAAAAAAAA
**
20416510 GTGAAAAAA
1 GAAAAAAAA
*
20416519 GAAAAAATA
1 GAAAAAAAA
* *
20416528 -AAAAATAT
1 GAAAAAAAA
*
20416536 GAAAAGAAA
1 GAAAAAAAA
20416545 -AAAAAAAA
1 GAAAAAAAA
20416553 GA
1 GA
20416555 CTCAAATTGA
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
8 12 0.30
9 28 0.70
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:20416518 original size:22 final size:22
Alignment explanation
Indices: 20416493--20416552 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
20416483 GAAATGGATG
* *
20416493 AAAAAAAAGAAAAAAAA-GTGA
1 AAAAAAAAAAAAAAAAATATGA
20416514 AAAAAGAAAAAATAAAAAATATGA
1 AAAAA-AAAAAA-AAAAAATATGA
*
20416538 AAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAA
20416553 GACTCAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 5 0.15
22 9 0.27
23 12 0.36
24 7 0.21
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAATATGA
Found at i:20416525 original size:20 final size:21
Alignment explanation
Indices: 20416491--20416530 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20416481 GGGAAATGGA
20416491 TGAAAAAAAAGAAAA-AAAAG
1 TGAAAAAAAAGAAAATAAAAG
20416511 TGAAAAAAGAA-AAAATAAAA
1 TGAAAAAA-AAGAAAATAAAA
20416531 AATATGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (21 bp):
TGAAAAAAAAGAAAATAAAAG
Found at i:20418760 original size:5 final size:5
Alignment explanation
Indices: 20418750--20418799 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
20418740 GCCTAGTTTA
*
20418750 TTATT TTATT TTATT TTATTT TTGATT TTTTT ATTA-T TTATT TTATT
1 TTATT TTATT TTATT TTA-TT TT-ATT TTATT -TTATT TTATT TTATT
20418797 TTA
1 TTA
20418800 GGATAATGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 3 0.08
5 25 0.64
6 10 0.26
7 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:20420750 original size:59 final size:59
Alignment explanation
Indices: 20420665--20420890 Score: 273
Period size: 58 Copynumber: 3.9 Consensus size: 59
20420655 AAAATAAAAA
* * * *
20420665 TTTTCAAAAAGAAATATTTTTAAGAAAAA-ATGAAAAATATTAATTTTCCTTGAAAATAAG
1 TTTTCTAAAA-AAATATTTTTAAGAAAAAGTTG-AAAGTATCAATTTTCCTTGAAAATAAG
*
20420725 TTTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG
1 TTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG
* * * * * *
20420784 TTTTCT-AAAAAAGATTTTCAAGAAAAATTTGAAAGCATCAATTTTCTTTGAAATTAAAG
1 TTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAG
* *
20420843 -TTTC-AAAAAAATA-TTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 TTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTG
20420891 TACAAAAGCA
Statistics
Matches: 144, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
57 29 0.20
58 53 0.37
59 51 0.35
60 11 0.08
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (59 bp):
TTTTCTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG
Found at i:20430966 original size:24 final size:24
Alignment explanation
Indices: 20430933--20430985 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
20430923 AAAAAATATT
20430933 AAAAAATAAAAT-AAAATCAAAAA
1 AAAAAATAAAATCAAAATCAAAAA
*
20430956 ATAAAAATAAAATCAAAATGAAAAA
1 A-AAAAATAAAATCAAAATCAAAAA
20430981 AAAAA
1 AAAAA
20430986 CCTGTGATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 15 0.56
25 11 0.41
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (24 bp):
AAAAAATAAAATCAAAATCAAAAA
Found at i:20430981 original size:19 final size:19
Alignment explanation
Indices: 20430899--20430973 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
20430889 TTCTCTCTTT
* *
20430899 TAAAAAAAAAACCAAAAAA
1 TAAAAATAAAATCAAAAAA
* *
20430918 TAATAAAAAAATATTAAAAAA
1 TAA-AAATAAA-ATCAAAAAA
20430939 T-AAAATAAAATCAAAAAA
1 TAAAAATAAAATCAAAAAA
20430957 TAAAAATAAAATCAAAA
1 TAAAAATAAAATCAAAA
20430974 TGAAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.18
19 24 0.49
20 8 0.16
21 8 0.16
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (19 bp):
TAAAAATAAAATCAAAAAA
Done.