Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 114 of 190
Found at i:17811637 original size:12 final size:11
Alignment explanation
Indices: 17811608--17811636 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
17811598 ACATAGAAAG
17811608 AAAAAAAGTCA
1 AAAAAAAGTCA
17811619 AAAAAAAGTCA
1 AAAAAAAGTCA
17811630 AAAAAAA
1 AAAAAAA
17811637 AAAGAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAAGTCA
Found at i:17812311 original size:2 final size:2
Alignment explanation
Indices: 17812304--17812333 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17812294 AGCATGTGGT
17812304 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17812334 CGTTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17813047 original size:3 final size:3
Alignment explanation
Indices: 17813041--17813065 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17813031 TTTGACGCCG
17813041 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
17813066 TACTACTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:17814446 original size:31 final size:31
Alignment explanation
Indices: 17814405--17814473 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
17814395 ACTAAAAAAT
*
17814405 TTTAAATTAATTTCATTCGAATCAATTTAAA
1 TTTAAATTAATTTCATTCAAATCAATTTAAA
* * * *
17814436 TTTATATTAATTTGATTCAAATCGATTTGAA
1 TTTAAATTAATTTCATTCAAATCAATTTAAA
17814467 TTTAAAT
1 TTTAAAT
17814474 CATTTGAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (31 bp):
TTTAAATTAATTTCATTCAAATCAATTTAAA
Found at i:17814484 original size:16 final size:16
Alignment explanation
Indices: 17814445--17814481 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
17814435 ATTTATATTA
*
17814445 ATTTG-ATTCAAATCG
1 ATTTGAATTTAAATCG
17814460 ATTTGAATTTAAATC-
1 ATTTGAATTTAAATCG
17814475 ATTTGAA
1 ATTTGAA
17814482 ATTGGATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (16 bp):
ATTTGAATTTAAATCG
Found at i:17816226 original size:17 final size:17
Alignment explanation
Indices: 17816204--17816236 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17816194 TAAAACCCAG
17816204 GGTATCA-AGCTTTCCTA
1 GGTATCATA-CTTTCCTA
17816221 GGTATCATACTTTCCT
1 GGTATCATACTTTCCT
17816237 TTGGAATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (17 bp):
GGTATCATACTTTCCTA
Found at i:17816299 original size:2 final size:2
Alignment explanation
Indices: 17816292--17816317 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17816282 AATAGTTAGC
17816292 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
17816318 AAGAGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17817706 original size:26 final size:26
Alignment explanation
Indices: 17817652--17817721 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
17817642 TTTCACTCTA
*
17817652 TTTCTTTATTTCTTTCTTTCCCTCGT
1 TTTCTTTATTTCTTTCTTACCCTCGT
*
17817678 TTTCTTTATTTTCTTT-TCTACCTTC-T
1 TTTCTTTA-TTTCTTTCT-TACCCTCGT
* *
17817704 TTTCTTTCTTCCTTTCTT
1 TTTCTTTATTTCTTTCTT
17817722 TTTTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.19
26 18 0.49
27 12 0.32
ACGTcount: A:0.04, C:0.26, G:0.01, T:0.69
Consensus pattern (26 bp):
TTTCTTTATTTCTTTCTTACCCTCGT
Found at i:17817708 original size:17 final size:18
Alignment explanation
Indices: 17817681--17817727 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
17817671 CCCTCGTTTT
*
17817681 CTTTATTTTCTTTTCTAC
1 CTTTCTTTTCTTTTCTAC
*
17817699 C-TTCTTTTC-TTTCTTC
1 CTTTCTTTTCTTTTCTAC
17817715 CTTTCTTTT-TTTT
1 CTTTCTTTTCTTTT
17817728 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 7 0.28
17 17 0.68
18 1 0.04
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTCTTTTCTTTTCTAC
Found at i:17818228 original size:18 final size:16
Alignment explanation
Indices: 17818207--17818241 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
17818197 TAAAATATAC
17818207 AAAGAAAGGAAAAATAAA
1 AAAGAAA-G-AAAATAAA
17818225 AAAGAAAGAAAATAAA
1 AAAGAAAGAAAATAAA
17818241 A
1 A
17818242 GTAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (16 bp):
AAAGAAAGAAAATAAA
Found at i:17818241 original size:22 final size:22
Alignment explanation
Indices: 17818207--17818248 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17818197 TAAAATATAC
*
17818207 AAAGAAAGGAAAAATAAAAAAG
1 AAAGAAAAGAAAAATAAAAAAG
* *
17818229 AAAGAAAATAAAAGTAAAAA
1 AAAGAAAAGAAAAATAAAAA
17818249 TTATAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (22 bp):
AAAGAAAAGAAAAATAAAAAAG
Found at i:17821184 original size:3 final size:3
Alignment explanation
Indices: 17821176--17821210 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17821166 TAAAATTGTC
17821176 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17821211 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17822309 original size:18 final size:18
Alignment explanation
Indices: 17822288--17822322 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17822278 TAACATTTAT
17822288 AAAATTAATAAATTATTA
1 AAAATTAATAAATTATTA
*
17822306 AAAATTAATTAATTATT
1 AAAATTAATAAATTATT
17822323 TTATATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTAATAAATTATTA
Found at i:17823077 original size:29 final size:29
Alignment explanation
Indices: 17823021--17823088 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
17823011 CCTTCATTTT
*
17823021 GAAATTATGTAATGATTATCACATTGAAT
1 GAAATTATGTAATGATTATCACATTGAAA
*
17823050 GTAAATTATGTAAT-ATTAT-AGTATTGAAA
1 G-AAATTATGTAATGATTATCA-CATTGAAA
17823079 GAAATTATGT
1 GAAATTATGT
17823089 GAATTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 10 0.29
29 13 0.37
30 12 0.34
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.40
Consensus pattern (29 bp):
GAAATTATGTAATGATTATCACATTGAAA
Found at i:17839000 original size:77 final size:77
Alignment explanation
Indices: 17838904--17839052 Score: 262
Period size: 77 Copynumber: 1.9 Consensus size: 77
17838894 TGAAGTATTT
*
17838904 GATCCCTATCAACTCAACCAATGCCTATTGGTACAATACCATATCTATTAAAGAATGAATAACCA
1 GATCCCTATCAACTCAACCAATGCCTATTGGTACAATACCATACCTATTAAAGAATGAATAACCA
17838969 TGATAATGAATC
66 TGATAATGAATC
* * *
17838981 GATCCTTATCAACTCAACCAATGCCTATTGGTACAGTACCATACCTATTAAATAATGAATAACCA
1 GATCCCTATCAACTCAACCAATGCCTATTGGTACAATACCATACCTATTAAAGAATGAATAACCA
17839046 TGATAAT
66 TGATAAT
17839053 TAATAGATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (77 bp):
GATCCCTATCAACTCAACCAATGCCTATTGGTACAATACCATACCTATTAAAGAATGAATAACCA
TGATAATGAATC
Found at i:17839683 original size:6 final size:6
Alignment explanation
Indices: 17839663--17839750 Score: 81
Period size: 6 Copynumber: 15.0 Consensus size: 6
17839653 AAAGGGCTAA
* * * *
17839663 AATTTT -ATCTT AATTTT AATTTT GATTTT AA-CTT GATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
* * * * *
17839709 GATTTT AGTTTT AATTTT AGTTTT GATTTT GATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
17839751 TCCTAGTTTT
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
5 7 0.11
6 57 0.89
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:17839690 original size:23 final size:23
Alignment explanation
Indices: 17839664--17839750 Score: 111
Period size: 24 Copynumber: 3.7 Consensus size: 23
17839654 AAGGGCTAAA
17839664 ATTTTATCTTAATTTTAATTTTG
1 ATTTTATCTTAATTTTAATTTTG
* *
17839687 ATTTTAACTTGATTTTAATTTTG
1 ATTTTATCTTAATTTTAATTTTG
* *
17839710 ATTTTAGTTTTAATTTTAGTTTTG
1 ATTTTA-TCTTAATTTTAATTTTG
*
17839734 ATTTTGATTTTAATTTT
1 ATTTT-ATCTTAATTTT
17839751 TCCTAGTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 27 0.48
24 28 0.50
25 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.66
Consensus pattern (23 bp):
ATTTTATCTTAATTTTAATTTTG
Found at i:17839692 original size:12 final size:12
Alignment explanation
Indices: 17839675--17839750 Score: 91
Period size: 12 Copynumber: 6.4 Consensus size: 12
17839665 TTTTATCTTA
17839675 ATTTTAATTTTG
1 ATTTTAATTTTG
*
17839687 ATTTTAA-CTTG
1 ATTTTAATTTTG
17839698 ATTTTAATTTTG
1 ATTTTAATTTTG
* *
17839710 ATTTTAGTTTTA
1 ATTTTAATTTTG
*
17839722 ATTTTAGTTTTG
1 ATTTTAATTTTG
* *
17839734 ATTTTGATTTTA
1 ATTTTAATTTTG
17839746 ATTTT
1 ATTTT
17839751 TCCTAGTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
11 10 0.18
12 45 0.82
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (12 bp):
ATTTTAATTTTG
Found at i:17841053 original size:20 final size:20
Alignment explanation
Indices: 17841028--17841109 Score: 78
Period size: 20 Copynumber: 4.1 Consensus size: 20
17841018 TTTATTATTA
*
17841028 TTGCATGGTAATTAATATAT
1 TTGCATGATAATTAATATAT
* *
17841048 TTGCATGATTATTTATTATAT
1 TTGCATGA-TAATTAATATAT
* *
17841069 TT-CATGATTA-TATATTTAT
1 TTGCATGATAATTA-ATATAT
*
17841088 TTGCATGATTATTAATATAT
1 TTGCATGATAATTAATATAT
17841108 TT
1 TT
17841110 ATTTGCATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.04
19 7 0.14
20 27 0.54
21 14 0.28
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (20 bp):
TTGCATGATAATTAATATAT
Found at i:17841065 original size:24 final size:22
Alignment explanation
Indices: 17841040--17841124 Score: 97
Period size: 24 Copynumber: 4.0 Consensus size: 22
17841030 GCATGGTAAT
17841040 TAATATATTTGCATGATTATT-
1 TAATATATTTGCATGATTATTA
*
17841061 TATTATATTT-CATGATTA-TA
1 TAATATATTTGCATGATTATTA
*
17841081 T-ATTTATTTGCATGATTATTAA
1 TAATATATTTGCATGATTATT-A
*
17841103 TATATTTATTTGCATGATTATT
1 TA-ATATATTTGCATGATTATT
17841125 CATTATTCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
19 7 0.13
20 17 0.31
21 10 0.18
22 2 0.04
24 19 0.35
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (22 bp):
TAATATATTTGCATGATTATTA
Found at i:17841168 original size:24 final size:23
Alignment explanation
Indices: 17841139--17841226 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 23
17841129 ATTCATTATT
17841139 TATTATTGCATGATATGATTTTA
1 TATTATTGCATGATATGATTTTA
17841162 TGATTATTGCATGATATGATTTTA
1 T-ATTATTGCATGATATGATTTTA
* ** * *
17841186 TCTTTATTAAATGGTGTGATTTTA
1 T-ATTATTGCATGATATGATTTTA
17841210 TATTTATTGCATGATAT
1 TA-TTATTGCATGATAT
17841227 TTTTGGCATG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
23 1 0.02
24 51 0.98
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.52
Consensus pattern (23 bp):
TATTATTGCATGATATGATTTTA
Found at i:17841228 original size:14 final size:14
Alignment explanation
Indices: 17841209--17841242 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
17841199 GTGTGATTTT
17841209 ATATTTATT-GCATG
1 ATATTT-TTGGCATG
17841223 ATATTTTTGGCATG
1 ATATTTTTGGCATG
17841237 ATATTT
1 ATATTT
17841243 CTAATTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (14 bp):
ATATTTTTGGCATG
Found at i:17842693 original size:21 final size:23
Alignment explanation
Indices: 17842669--17842712 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17842659 GGGTATTGTG
*
17842669 AATGAAG-A-ATGTGAGCAAGCA
1 AATGAAGCATATGTGAGAAAGCA
*
17842690 AATGAGGCATATGTGAGAAAGCA
1 AATGAAGCATATGTGAGAAAGCA
17842713 TAACCAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.45, C:0.09, G:0.30, T:0.16
Consensus pattern (23 bp):
AATGAAGCATATGTGAGAAAGCA
Found at i:17845645 original size:75 final size:75
Alignment explanation
Indices: 17845515--17845665 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
17845505 CCTATTAGGT
*
17845515 AATGTGTGAAGAATTGGAAGATGATAAAGTTATCTATTATCCTTGAACCTCTGAAAAAGTAATGT
1 AATGAGTGAAGAATTGGAAGATGATAAAGTTATCTATTATCCTTGAACCTCTGAAAAAGTAATGT
17845580 AGTAAGTCAC
66 AGTAAGTCAC
*
17845590 AATGAGTGAAGAATTGGAAGATGATAAAGTTATCTATTATCCTTGAACCTTTGAAAAAGTAATGT
1 AATGAGTGAAGAATTGGAAGATGATAAAGTTATCTATTATCCTTGAACCTCTGAAAAAGTAATGT
*
17845655 AGTGAGTCAC
66 AGTAAGTCAC
17845665 A
1 A
17845666 CCCTAACTAC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (75 bp):
AATGAGTGAAGAATTGGAAGATGATAAAGTTATCTATTATCCTTGAACCTCTGAAAAAGTAATGT
AGTAAGTCAC
Found at i:17846406 original size:17 final size:16
Alignment explanation
Indices: 17846384--17846425 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
17846374 GGAGATTATG
17846384 ATGAAAAAAAAAAAGAA
1 ATGAAAAAAAAAAA-AA
17846401 ATGAAAAGAAAAAAAAA
1 ATGAAAA-AAAAAAAAA
17846418 A-GAAAAAA
1 ATGAAAAAA
17846426 TTGATTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.08
16 5 0.21
17 10 0.42
18 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (16 bp):
ATGAAAAAAAAAAAAA
Found at i:17847973 original size:43 final size:42
Alignment explanation
Indices: 17847873--17847976 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 42
17847863 TCAAATATCT
* *
17847873 CATTTCATTTTTC-AAAGTTTCAAAGCCTAGTTATAGGGGAG
1 CATTTTATTTTTCAAAAGTTTCAAAACCTAGTTATAGGGGAG
* * *
17847914 CATTTTATTTTCCAAAAGTTTCAAAACCTCAGTTGT-GGGGGG
1 CATTTTATTTTTCAAAAGTTTCAAAACCT-AGTTATAGGGGAG
17847956 CTATTTTATTTTTCAAAAGTT
1 C-ATTTTATTTTTCAAAAGTT
17847977 CTAAAGACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
41 11 0.20
42 20 0.37
43 23 0.43
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.40
Consensus pattern (42 bp):
CATTTTATTTTTCAAAAGTTTCAAAACCTAGTTATAGGGGAG
Found at i:17847996 original size:19 final size:19
Alignment explanation
Indices: 17847972--17848010 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
17847962 TATTTTTCAA
*
17847972 AAGTTCTAAAGACTCACTT
1 AAGTTCTAAAAACTCACTT
17847991 AAGTTCTAAAAACTCACTT
1 AAGTTCTAAAAACTCACTT
17848010 A
1 A
17848011 TGAAAGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (19 bp):
AAGTTCTAAAAACTCACTT
Found at i:17848069 original size:43 final size:43
Alignment explanation
Indices: 17848019--17848157 Score: 145
Period size: 43 Copynumber: 3.2 Consensus size: 43
17848009 TATGAAAGAT
* * * * *
17848019 CATTTTATTTTTCAAAATTTTCAAAGCCTTAGTTATGGGGGAG
1 CATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTATGGAGAAG
* *
17848062 CATTTTATTTTCCAAAAGTTTCAAAGCCTCAATTGTGGAGAAG
1 CATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTATGGAGAAG
* * ** * *
17848105 CATTCTATTTTTGAAAAGTTTCAAAATCTCAGTTGTAGGA-AAG
1 CATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTAT-GGAGAAG
17848148 CATTTTATTT
1 CATTTTATTT
17848158 AAAGTTTCAA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 78 0.96
44 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (43 bp):
CATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTATGGAGAAG
Found at i:17848417 original size:6 final size:6
Alignment explanation
Indices: 17848397--17848493 Score: 85
Period size: 6 Copynumber: 16.7 Consensus size: 6
17848387 AATGCCCTAA
* * *
17848397 AATTTT -ATCTT AATTTT AATTTT GATTTT AA-TTT GATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
* * * * *
17848443 GATTTT AGTTTT AGTTTT AATTTT AGTTTT GATTTT GAA-TTT AA-TTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT -AATTTT AATTTT
17848490 AATT
1 AATT
17848494 CTAGTTTTTG
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
5 15 0.21
6 57 0.78
7 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:17848424 original size:23 final size:22
Alignment explanation
Indices: 17848398--17848466 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
17848388 ATGCCCTAAA
17848398 ATTTTATCTTAATTTTAATTTTG
1 ATTTTAT-TTAATTTTAATTTTG
*
17848421 ATTTTAATTTGATTTTAATTTTG
1 ATTTT-ATTTAATTTTAATTTTG
*
17848444 ATTTTAGTTTTAGTTTTAATTTT
1 ATTTTA--TTTAATTTTAATTTT
17848467 AGTTTTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
22 1 0.03
23 24 0.60
24 15 0.38
ACGTcount: A:0.25, C:0.01, G:0.07, T:0.67
Consensus pattern (22 bp):
ATTTTATTTAATTTTAATTTTG
Found at i:17848426 original size:12 final size:12
Alignment explanation
Indices: 17848409--17848489 Score: 96
Period size: 12 Copynumber: 6.8 Consensus size: 12
17848399 TTTTATCTTA
17848409 ATTTTAATTTTG
1 ATTTTAATTTTG
17848421 ATTTTAA-TTTG
1 ATTTTAATTTTG
17848432 ATTTTAATTTTG
1 ATTTTAATTTTG
*
17848444 ATTTTAGTTTT-
1 ATTTTAATTTTG
17848455 AGTTTTAATTTT-
1 A-TTTTAATTTTG
*
17848467 AGTTTTGATTTTG
1 A-TTTTAATTTTG
*
17848480 AATTTAATTT
1 ATTTTAATTT
17848490 AATTCTAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
11 12 0.20
12 48 0.79
13 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (12 bp):
ATTTTAATTTTG
Found at i:17848571 original size:5 final size:5
Alignment explanation
Indices: 17848531--17848559 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
17848521 TTCAAAAGCC
17848531 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
17848560 GGAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:17848757 original size:85 final size:87
Alignment explanation
Indices: 17848600--17848763 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 87
17848590 TTGCTTTTGA
* * * *
17848600 GAGATTTTGTTTCTACTGAAGCCTTGGGATTTGATTTTATCCCTGGATTTAGTATCAGATTATGA
1 GAGATTTTGTTTCTACTGAAGCCTTGGGATTCGATTTCATCCCTGGATCTAGTATCAGATCATGA
17848665 AATTTAATGATGAAGTTTTTAG
66 AATTTAATGATGAAGTTTTTAG
* ** *
17848687 GAGATTTTGTTTTTGTTGAAGCCTT-GGATTCGA-TTCATCCCTGGATCTAGTCTCAGATCATGA
1 GAGATTTTGTTTCTACTGAAGCCTTGGGATTCGATTTCATCCCTGGATCTAGTATCAGATCATGA
*
17848750 CATTTAATGATGAA
66 AATTTAATGATGAA
17848764 TTAGTTTAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 39 0.57
86 7 0.10
87 22 0.32
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (87 bp):
GAGATTTTGTTTCTACTGAAGCCTTGGGATTCGATTTCATCCCTGGATCTAGTATCAGATCATGA
AATTTAATGATGAAGTTTTTAG
Found at i:17849632 original size:15 final size:15
Alignment explanation
Indices: 17849614--17849664 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
17849604 CTTTTGATTT
17849614 TTTTGATTTGTTTTA
1 TTTTGATTTGTTTTA
* *
17849629 TTTTGCTTTGTTTTG
1 TTTTGATTTGTTTTA
17849644 TTTTG-TTT-TTTTA
1 TTTTGATTTGTTTTA
17849657 TTTT-ATTT
1 TTTTGATTT
17849665 TTATTCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 11 0.34
14 3 0.09
15 18 0.56
ACGTcount: A:0.08, C:0.02, G:0.12, T:0.78
Consensus pattern (15 bp):
TTTTGATTTGTTTTA
Found at i:17849633 original size:10 final size:10
Alignment explanation
Indices: 17849597--17849683 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 10
17849587 TTTTAATTTC
17849597 TATTTTGCTTT
1 TATTTTG-TTT
17849608 TGATTTT-TTT
1 T-ATTTTGTTT
*
17849618 GA-TTTGTTT
1 TATTTTGTTT
*
17849627 TATTTTGCTT
1 TATTTTGTTT
*
17849637 TGTTTTGTTT
1 TATTTTGTTT
*
17849647 T-GTTT-TTT
1 TATTTTGTTT
*
17849655 TATTTTATTT
1 TATTTTGTTT
* *
17849665 T-TATTCTTT
1 TATTTTGTTT
17849674 T-TTTTGTTT
1 TATTTTGTTT
17849683 T
1 T
17849684 TTTATTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
8 7 0.12
9 25 0.42
10 22 0.37
11 1 0.02
12 5 0.08
ACGTcount: A:0.08, C:0.03, G:0.10, T:0.78
Consensus pattern (10 bp):
TATTTTGTTT
Found at i:17849633 original size:30 final size:28
Alignment explanation
Indices: 17849597--17849660 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 28
17849587 TTTTAATTTC
17849597 TATTTTGCTTTTGATTT-TTTTGATTTGTTT
1 TATTTTGC-TTTGATTTGTTTTG-TTT-TTT
*
17849627 TATTTTGCTTTGTTTTGTTTTGTTTTTT
1 TATTTTGCTTTGATTTGTTTTGTTTTTT
17849655 TATTTT
1 TATTTT
17849661 ATTTTTATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 9 0.28
29 10 0.31
30 13 0.41
ACGTcount: A:0.08, C:0.03, G:0.12, T:0.77
Consensus pattern (28 bp):
TATTTTGCTTTGATTTGTTTTGTTTTTT
Found at i:17849791 original size:27 final size:27
Alignment explanation
Indices: 17849740--17849792 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17849730 AGAAAAAAAT
*
17849740 AGTTTGTTTCTGAATGATGTTTTTATG
1 AGTTTGTTTCTGAATGATGTATTTATG
17849767 AGTTTGTTTTCTTGAAT-A-GTATTTAT
1 AGTTTG-TTTC-TGAATGATGTATTTAT
17849793 TATTATTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 13 0.57
28 5 0.22
29 5 0.22
ACGTcount: A:0.21, C:0.04, G:0.19, T:0.57
Consensus pattern (27 bp):
AGTTTGTTTCTGAATGATGTATTTATG
Found at i:17849835 original size:24 final size:21
Alignment explanation
Indices: 17849798--17849978 Score: 153
Period size: 24 Copynumber: 8.5 Consensus size: 21
17849788 TTTATTATTA
* *
17849798 TTGCATGGTAATTA-ATATAT
1 TTGCATGATTATTATATATAT
17849818 TTGCATGATTATT-TAT-TAT
1 TTGCATGATTATTATATATAT
* *
17849837 GTTTCATGATTA-TATATTTAT
1 -TTGCATGATTATTATATATAT
17849858 TTGCATGATTATTAATATATTTAT
1 TTGCATGATTATT-ATATA--TAT
17849882 TTGCATGATTATTAATATATTTAT
1 TTGCATGATTATT-ATATA--TAT
*
17849906 TTGTATGATTATT-TATTATAT
1 TTGCATGATTATTATA-TATAT
17849927 TT-CATGATTA-TATAT-TAT
1 TTGCATGATTATTATATATAT
*
17849945 TTGCATGATTATTAATATGTTTAT
1 TTGCATGATTATT-ATA--TATAT
17849969 TTGCATGATT
1 TTGCATGATT
17849979 GTTCATTTTT
Statistics
Matches: 138, Mismatches: 7, Indels: 28
0.80 0.04 0.16
Matches are distributed among these distances:
18 5 0.04
19 14 0.10
20 46 0.33
21 12 0.09
22 6 0.04
23 3 0.02
24 52 0.38
ACGTcount: A:0.30, C:0.04, G:0.10, T:0.55
Consensus pattern (21 bp):
TTGCATGATTATTATATATAT
Found at i:17849846 original size:20 final size:20
Alignment explanation
Indices: 17849786--17849957 Score: 125
Period size: 20 Copynumber: 8.2 Consensus size: 20
17849776 TCTTGAATAG
* *
17849786 TATTTATTATTATTGCATG-G
1 TATTTATTA-TATTTCATGAT
* *
17849806 TAATTAATATATTTGCATGAT
1 TATTTATTATATTT-CATGAT
*
17849827 TATTTATTATGTTTCATGAT
1 TATTTATTATATTTCATGAT
*
17849847 TATATATT-TATTTGCATGAT
1 TATTTATTATATTT-CATGAT
*
17849867 TATTAATATATTTATTTGCATGAT
1 TATT--TAT-TATATTT-CATGAT
* *
17849891 TATTAATATATTTATTTGTATGAT
1 TATT--TAT-TATATTT-CATGAT
17849915 TATTTATTATATTTCATGAT
1 TATTTATTATATTTCATGAT
* *
17849935 TATATATTAT-TTGCATGAT
1 TATTTATTATATTTCATGAT
17849954 TATT
1 TATT
17849958 AATATGTTTA
Statistics
Matches: 129, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
19 19 0.15
20 47 0.36
21 17 0.13
22 6 0.05
23 1 0.01
24 39 0.30
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (20 bp):
TATTTATTATATTTCATGAT
Found at i:17850025 original size:24 final size:24
Alignment explanation
Indices: 17849998--17850131 Score: 182
Period size: 24 Copynumber: 5.6 Consensus size: 24
17849988 TTATTATTTG
*
17849998 TTATTACATGATATGATTTTATGA
1 TTATTGCATGATATGATTTTATGA
*
17850022 TTATTACATGATATG-TTTTCATGA
1 TTATTGCATGATATGATTTT-ATGA
*
17850046 TTATTGCATGATATAATTTTATGA
1 TTATTGCATGATATGATTTTATGA
**
17850070 TTATTGCATGATATGATTTTATCT
1 TTATTGCATGATATGATTTTATGA
*
17850094 TTATTGCATGGTATGATTTTAT-A
1 TTATTGCATGATATGATTTTATGA
17850117 TTTATTGCATGATAT
1 -TTATTGCATGATAT
17850132 TTCTATTTAT
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
23 4 0.04
24 91 0.92
25 4 0.04
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.51
Consensus pattern (24 bp):
TTATTGCATGATATGATTTTATGA
Found at i:17850742 original size:14 final size:15
Alignment explanation
Indices: 17850725--17850755 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
17850715 TATAATAATA
17850725 ATAATAAT-ATTATT
1 ATAATAATAATTATT
17850739 ATAATAATAATTATT
1 ATAATAATAATTATT
17850754 AT
1 AT
17850756 TAGTATTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATAATAATTATT
Found at i:17850744 original size:20 final size:18
Alignment explanation
Indices: 17850722--17850757 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
17850712 AAATATAATA
17850722 ATAATAATAA-TATTATT
1 ATAATAATAATTATTATT
17850739 ATAATAATAATTATTATT
1 ATAATAATAATTATTATT
17850757 A
1 A
17850758 GTATTAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATAATAATTATTATT
Found at i:17851121 original size:26 final size:28
Alignment explanation
Indices: 17851081--17851133 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
17851071 AATTTAAAAC
*
17851081 AAAAAAATCATAAAAAGTAAAAAAGAAA
1 AAAAAAATCATAAAAAGGAAAAAAGAAA
*
17851109 AAAAAAAT-A-AAAATGGAAAAAAGAA
1 AAAAAAATCATAAAAAGGAAAAAAGAA
17851134 CTCATTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 1 0.04
28 8 0.35
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (28 bp):
AAAAAAATCATAAAAAGGAAAAAAGAAA
Found at i:17853434 original size:18 final size:17
Alignment explanation
Indices: 17853413--17853450 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
17853403 ATCTAATTTG
17853413 AAAAATA-AAAAACTGAA
1 AAAAATAGAAAAACT-AA
17853430 AAAAATAGAAAAACTAA
1 AAAAATAGAAAAACTAA
17853447 AAAA
1 AAAA
17853451 GAAAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAATAGAAAAACTAA
Found at i:17854285 original size:34 final size:34
Alignment explanation
Indices: 17854228--17854345 Score: 105
Period size: 34 Copynumber: 3.5 Consensus size: 34
17854218 TTAAAAATCG
*** * *
17854228 TAACAC-TCTCAAAAATAAATTTTCAATAAGCCA
1 TAACACTTCTCAAAAATGTTTTTTCAAGAAGACA
** *
17854261 TAATTCTTCTCAAAAATGTTTTTTCGAGAAGACA
1 TAACACTTCTCAAAAATGTTTTTTCAAGAAGACA
** *
17854295 TAACACTTCTCAAAAATG-CATTTCAAAGAAGTCA
1 TAACACTTCTCAAAAATGTTTTTTC-AAGAAGACA
*
17854329 TAACACTTCTCGAAAAT
1 TAACACTTCTCAAAAAT
17854346 ATATTTTCGA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
33 8 0.12
34 60 0.88
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (34 bp):
TAACACTTCTCAAAAATGTTTTTTCAAGAAGACA
Found at i:17856788 original size:3 final size:3
Alignment explanation
Indices: 17856780--17856818 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
17856770 GAAATCATGT
*
17856780 TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17856819 AAGCAGACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17858860 original size:31 final size:32
Alignment explanation
Indices: 17858825--17858900 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
17858815 TTTGAATCCC
17858825 TCTTTATTCTCTTC-TTAGTCTCTTCAATTCT
1 TCTTTATTCTCTTCTTTAGTCTCTTCAATTCT
* *
17858856 TCTTTATTATC-TCTTTAGTCTTTTCAATTCT
1 TCTTTATTCTCTTCTTTAGTCTCTTCAATTCT
* *
17858887 CCTCTATTCTCTTC
1 TCTTTATTCTCTTC
17858901 CTATCTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 2 0.05
31 34 0.89
32 2 0.05
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.58
Consensus pattern (32 bp):
TCTTTATTCTCTTCTTTAGTCTCTTCAATTCT
Found at i:17870058 original size:21 final size:21
Alignment explanation
Indices: 17870032--17870071 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17870022 TAATTCATAT
*
17870032 ATAAAATATTAGTAATATTAC
1 ATAAAAGATTAGTAATATTAC
17870053 ATAAAAGATTAGTAATATT
1 ATAAAAGATTAGTAATATT
17870072 TTATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
ATAAAAGATTAGTAATATTAC
Found at i:17870124 original size:19 final size:20
Alignment explanation
Indices: 17870100--17870137 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
17870090 ATATAATTAG
17870100 ATTATTAAA-TTAAAAATAA
1 ATTATTAAACTTAAAAATAA
17870119 ATTATTAAACTTAAAAATA
1 ATTATTAAACTTAAAAATA
17870138 TATGTGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTATTAAACTTAAAAATAA
Found at i:17873534 original size:27 final size:27
Alignment explanation
Indices: 17873465--17873535 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
17873455 ATGTCAATTC
* *
17873465 AAAATAACAAATTTAA-TAAATTTATTTT
1 AAAATAA-AAA-TTAATTAAAATTATATT
** *
17873493 AAAATGTAAAGTAATTAAAATTATATT
1 AAAATAAAAATTAATTAAAATTATATT
17873520 AAAATAAAAATTAATT
1 AAAATAAAAATTAATT
17873536 TGTCCTTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
26 3 0.09
27 26 0.76
28 5 0.15
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (27 bp):
AAAATAAAAATTAATTAAAATTATATT
Found at i:17873912 original size:29 final size:29
Alignment explanation
Indices: 17873860--17873918 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
17873850 GAAAAATATT
*
17873860 AAACCCCAAACTCTCAATCCTAAATCCAA
1 AAACCCCAAACTCTCAAGCCTAAATCCAA
* *
17873889 AAACCCTAAACTCT-AAGCCTTAAATTCAA
1 AAACCCCAAACTCTCAAGCC-TAAATCCAA
17873918 A
1 A
17873919 TTTTGAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (29 bp):
AAACCCCAAACTCTCAAGCCTAAATCCAA
Found at i:17890458 original size:23 final size:23
Alignment explanation
Indices: 17890415--17890457 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
17890405 AAAAAGGAAA
*
17890415 AAAGAGAATGATAAGAAAAAATG
1 AAAGAGAATGAGAAGAAAAAATG
17890438 AAAGAGAAT-AGAAGAAAAAA
1 AAAGAGAATGAGAAGAAAAAA
17890458 AAGAACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (23 bp):
AAAGAGAATGAGAAGAAAAAATG
Found at i:17893341 original size:23 final size:24
Alignment explanation
Indices: 17893294--17893343 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
17893284 TATATTTCTT
17893294 TTTATATTTTGTCTATCTTATTTA
1 TTTATATTTTGTCTATCTTATTTA
*
17893318 TTTATCTTTTAGTCT-T-TTATTTA
1 TTTATATTTT-GTCTATCTTATTTA
17893341 TTT
1 TTT
17893344 GGTTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 10 0.42
25 4 0.17
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATATTTTGTCTATCTTATTTA
Found at i:17896160 original size:8 final size:8
Alignment explanation
Indices: 17896149--17896184 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
17896139 ATTTATTTAC
17896149 ATATATTT
1 ATATATTT
*
17896157 ATATAATT
1 ATATATTT
17896165 ATATATTT
1 ATATATTT
*
17896173 AAATATTT
1 ATATATTT
17896181 ATAT
1 ATAT
17896185 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
ATATATTT
Found at i:17896163 original size:26 final size:24
Alignment explanation
Indices: 17896134--17896184 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
17896124 TAAATTTTTT
*
17896134 TAATTATTTATTTACATATATTTATA
1 TAATTATATATTTA-A-ATATTTATA
17896160 TAATTATATATTTAAATATTTATA
1 TAATTATATATTTAAATATTTATA
17896184 T
1 T
17896185 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATTATATATTTAAATATTTATA
Found at i:17896183 original size:14 final size:16
Alignment explanation
Indices: 17896149--17896201 Score: 67
Period size: 14 Copynumber: 3.5 Consensus size: 16
17896139 ATTTATTTAC
*
17896149 ATATATTTATATAATT
1 ATATATTTAAATAATT
17896165 ATATATTTAAAT-ATT
1 ATATATTTAAATAATT
*
17896180 -TATATTTAAA-AAAT
1 ATATATTTAAATAATT
17896194 ATATATTT
1 ATATATTT
17896202 TATTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 12 0.36
15 10 0.30
16 11 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTAAATAATT
Found at i:17898731 original size:20 final size:21
Alignment explanation
Indices: 17898706--17898745 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17898696 ATACACCTAT
*
17898706 GAAAGA-TCACTTGGATTTAA
1 GAAAGAGTCAATTGGATTTAA
*
17898726 GAAAGAGTGAATTGGATTTA
1 GAAAGAGTCAATTGGATTTA
17898746 TCCATGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (21 bp):
GAAAGAGTCAATTGGATTTAA
Found at i:17899001 original size:16 final size:16
Alignment explanation
Indices: 17898980--17899020 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17898970 TAAAATATGC
17898980 ATTATATATCTCAATA-
1 ATTATATA-CTCAATAT
*
17898996 ATTATATACTTAATAT
1 ATTATATACTCAATAT
17899012 ATTATATAC
1 ATTATATAC
17899021 CTAAATACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATATACTCAATAT
Found at i:17899618 original size:31 final size:30
Alignment explanation
Indices: 17899582--17899646 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
17899572 AAGTCAAAGT
* *
17899582 AAAAAATAAAAAAATAAAGGTTGAAAACCC
1 AAAAAAGAAAAAAAGAAAGGTTGAAAACCC
** *
17899612 GAAAAAAGAAAAATGGAAAGTTTGAAAACCC
1 -AAAAAAGAAAAAAAGAAAGGTTGAAAACCC
17899643 AAAA
1 AAAA
17899647 GAAAAACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.65, C:0.09, G:0.14, T:0.12
Consensus pattern (30 bp):
AAAAAAGAAAAAAAGAAAGGTTGAAAACCC
Found at i:17900559 original size:12 final size:13
Alignment explanation
Indices: 17900544--17900599 Score: 75
Period size: 12 Copynumber: 4.6 Consensus size: 13
17900534 TTAGCTTTCC
*
17900544 TTTTTCTTTCT-A
1 TTTTTGTTTCTAA
17900556 TTTTTGTTTCTAA
1 TTTTTGTTTCTAA
17900569 TTTTT-TTT-TAA
1 TTTTTGTTTCTAA
17900580 TTTTTGTTTCT-A
1 TTTTTGTTTCTAA
17900592 TTTTTGTT
1 TTTTTGTT
17900600 ATTTATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
11 8 0.20
12 25 0.62
13 7 0.17
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTTGTTTCTAA
Found at i:17900712 original size:20 final size:20
Alignment explanation
Indices: 17900687--17900819 Score: 146
Period size: 20 Copynumber: 6.7 Consensus size: 20
17900677 AATTTGGTCT
*
17900687 TTTGCATGTTTATATATTTA
1 TTTGCATGATTATATATTTA
* *
17900707 TTTGCATGACTACT-T-GTTA
1 TTTGCATGATTA-TATATTTA
* *
17900726 TTTGCATGACTATTTA-TTA
1 TTTGCATGATTATATATTTA
17900745 TTTGCATGATTATATATTTA
1 TTTGCATGATTATATATTTA
17900765 TTTGCATGATTATATATTTA
1 TTTGCATGATTATATATTTA
* *
17900785 ATTGCTTGATTTATATATTTA
1 TTTGCATGA-TTATATATTTA
*
17900806 TTTTGGATGATTAT
1 -TTTGCATGATTAT
17900820 TTATACTTGC
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
18 1 0.01
19 33 0.34
20 41 0.42
21 16 0.16
22 6 0.06
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTGCATGATTATATATTTA
Found at i:17900728 original size:19 final size:19
Alignment explanation
Indices: 17900704--17900773 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
17900694 GTTTATATAT
*
17900704 TTATTTGCATGACTACTTG
1 TTATTTGCATGACTACTTA
*
17900723 TTATTTGCATGACTATTTA
1 TTATTTGCATGACTACTTA
*
17900742 TTATTTGCATGATTA-TATA
1 TTATTTGCATGACTACT-TA
17900761 TTTATTTGCATGA
1 -TTATTTGCATGA
17900774 TTATATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 33 0.72
20 12 0.26
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (19 bp):
TTATTTGCATGACTACTTA
Found at i:17905171 original size:21 final size:22
Alignment explanation
Indices: 17905135--17905177 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17905125 AGAAAGATGT
*
17905135 AAAAAGAAAAGAAAAGGGAAAA
1 AAAAAGAAAAGAAAAGAGAAAA
*
17905157 AAAAAGAAAA-CAAAGAGAAAA
1 AAAAAGAAAAGAAAAGAGAAAA
17905178 TTGATGGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAGAGAAAA
Found at i:17906523 original size:18 final size:18
Alignment explanation
Indices: 17906480--17906529 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
17906470 TCTAGATTAC
*
17906480 AAATCTTTGCGAATTTTAG
1 AAATCTTTGC-AAATTTAG
**
17906499 -AGCCTTTGCAAATTTAG
1 AAATCTTTGCAAATTTAG
17906516 AAATCTTTGCAAAT
1 AAATCTTTGCAAAT
17906530 CTGGGAGCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (18 bp):
AAATCTTTGCAAATTTAG
Found at i:17906541 original size:18 final size:18
Alignment explanation
Indices: 17906520--17906567 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
17906510 ATTTAGAAAT
*
17906520 CTTTGCAAATCTGGGAGC
1 CTTTACAAATCTGGGAGC
*
17906538 CTTTACGAATCTGGGAGC
1 CTTTACAAATCTGGGAGC
*
17906556 CTTTACGAATCT
1 CTTTACAAATCT
17906568 TGGAATCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (18 bp):
CTTTACAAATCTGGGAGC
Found at i:17906577 original size:18 final size:18
Alignment explanation
Indices: 17906538--17906608 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
17906528 ATCTGGGAGC
* **
17906538 CTTTACGAATCTGGGAGC
1 CTTTACGAATCTTGGAAT
17906556 CTTTACGAATCTTGGAAT
1 CTTTACGAATCTTGGAAT
** **
17906574 CTTTGTGAATCTTAAAAT
1 CTTTACGAATCTTGGAAT
* *
17906592 CATTACAAATCTTGGAA
1 CTTTACGAATCTTGGAA
17906609 ACCTTGTGAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (18 bp):
CTTTACGAATCTTGGAAT
Found at i:17906799 original size:35 final size:36
Alignment explanation
Indices: 17906735--17906879 Score: 111
Period size: 35 Copynumber: 4.1 Consensus size: 36
17906725 ATCTTTGAAC
* * *** *
17906735 CTTTGCGAAACTTGAATCTTTTACAAATTTTT-ATT
1 CTTTGCGAAACCTGAATCCTTTGTGAATTTTTAAAT
** *
17906770 CTTTGCGAGCCCTGAATCTTTTGTGAATTTTTAAAT
1 CTTTGCGAAACCTGAATCCTTTGTGAATTTTTAAAT
* *
17906806 CTTTGCGAAACTTGAATCCTTTGTGAA-TTTTGAAT
1 CTTTGCGAAACCTGAATCCTTTGTGAATTTTTAAAT
* * *
17906841 -TTATGTGAAACTTGAAT-CTTT-TGATAATTTTAAAT
1 CTT-TGCGAAACCTGAATCCTTTGTGA-ATTTTTAAAT
17906876 CTTT
1 CTTT
17906880 TGCAAATTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
33 3 0.03
34 7 0.08
35 54 0.59
36 27 0.30
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (36 bp):
CTTTGCGAAACCTGAATCCTTTGTGAATTTTTAAAT
Found at i:17906810 original size:18 final size:17
Alignment explanation
Indices: 17906782--17906899 Score: 71
Period size: 18 Copynumber: 6.6 Consensus size: 17
17906772 TTGCGAGCCC
17906782 TGAATCTTTTGTGAATTTT
1 TGAATC-TTTGTGAA-TTT
* * **
17906801 TAAATCTTTGCGAAACT
1 TGAATCTTTGTGAATTT
17906818 TGAATCCTTTGTGAATTT
1 TGAAT-CTTTGTGAATTT
**
17906836 TGAAT-TTATGTGAAACT
1 TGAATCTT-TGTGAATTT
17906853 TGAATCTTT-TGATAATTT
1 TGAATCTTTGTG--AATTT
*
17906871 TAAATCTTT-TGCAAATTTT
1 TGAATCTTTGTG--AA-TTT
17906890 TGAATCTTTG
1 TGAATCTTTG
17906900 AATCCTTTTT
Statistics
Matches: 76, Mismatches: 16, Indels: 13
0.72 0.15 0.12
Matches are distributed among these distances:
16 4 0.05
17 18 0.24
18 38 0.50
19 16 0.21
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (17 bp):
TGAATCTTTGTGAATTT
Found at i:17908132 original size:27 final size:24
Alignment explanation
Indices: 17908095--17908162 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
17908085 TTTGGCTTTC
*
17908095 TTTTTTCTTTTTATTTTTGTCTCTAAT
1 TTTTTTATTTTTATTTTT-T-TCT-AT
17908122 TTTTTTATTTTGT-TTTTTTTCTAT
1 TTTTTTATTTT-TATTTTTTTCTAT
*
17908146 TTTGTTATTTATTATTT
1 TTTTTTATTT-TTATTT
17908163 AATTGCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
24 12 0.33
25 7 0.19
26 1 0.03
27 15 0.42
28 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTTTATTTTTATTTTTTTCTAT
Found at i:17908139 original size:15 final size:15
Alignment explanation
Indices: 17908121--17908162 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
17908111 TTGTCTCTAA
17908121 TTTTTTTATTTTGTT
1 TTTTTTTATTTTGTT
17908136 TTTTTTCTATTTTGTT
1 TTTTTT-TATTTTGTT
* *
17908152 ATTTATTATTT
1 TTTTTTTATTT
17908163 AATTGCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTTTTTATTTTGTT
Found at i:17908305 original size:20 final size:20
Alignment explanation
Indices: 17908245--17908415 Score: 136
Period size: 20 Copynumber: 8.7 Consensus size: 20
17908235 AATTTTGTCT
17908245 TTTGCATG-TTATATATTTA
1 TTTGCATGATTATATATTTA
* *
17908264 TTTGCATGACTATTTA-TTA
1 TTTGCATGATTATATATTTA
*
17908283 TTTGCATGATTATACATTTA
1 TTTGCATGATTATATATTTA
*
17908303 TTTACATGATTATATATTTA
1 TTTGCATGATTATATATTTA
* * *
17908323 ATTGCAGGATTATTTA-TTA
1 TTTGCATGATTATATATTTA
* * *
17908342 ATTGCATGAATT-TA-GTTTG
1 TTTGCATG-ATTATATATTTA
* * * *
17908361 CTTACATGAATATATTTTTA
1 TTTGCATGATTATATATTTA
* *
17908381 ATTGCATGATTTATATATCTA
1 TTTGCATGA-TTATATATTTA
17908402 TTTTGCATGATTAT
1 -TTTGCATGATTAT
17908416 TTATACTTGC
Statistics
Matches: 118, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.02
19 45 0.38
20 51 0.43
21 12 0.10
22 8 0.07
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTGCATGATTATATATTTA
Found at i:17908311 original size:39 final size:40
Alignment explanation
Indices: 17908245--17908335 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 40
17908235 AATTTTGTCT
* * *
17908245 TTTGCATG-TTATATATTTATTTGCATGACTATTTA-TTA
1 TTTGCATGATTATACATTTATTTACATGACTATATATTTA
*
17908283 TTTGCATGATTATACATTTATTTACATGATTATATATTTA
1 TTTGCATGATTATACATTTATTTACATGACTATATATTTA
* *
17908323 ATTGCAGGATTAT
1 TTTGCATGATTAT
17908336 TTATTAATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 8 0.18
39 23 0.51
40 14 0.31
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.52
Consensus pattern (40 bp):
TTTGCATGATTATACATTTATTTACATGACTATATATTTA
Found at i:17908316 original size:59 final size:58
Alignment explanation
Indices: 17908249--17908415 Score: 185
Period size: 59 Copynumber: 2.8 Consensus size: 58
17908239 TTGTCTTTTG
* * *
17908249 CATG-TTATATATTTATTTGCATGACTATTTATTATTTGCATGATTATACATTTATTTA
1 CATGATTATATATTTAATTGCATGATTATTTATTATTTGCATGATTATA-ATTTACTTA
* * * *
17908307 CATGATTATATATTTAATTGCAGGATTATTTATTAATTGCATGAATT-TAGTTTGCTTA
1 CATGATTATATATTTAATTGCATGATTATTTATTATTTGCATG-ATTATAATTTACTTA
* * *
17908365 CATGAATATATTTTTAATTGCATGATTTATATATCTATTTTGCATGATTAT
1 CATGATTATATATTTAATTGCATGA-TTATTTAT-TA-TTTGCATGATTAT
17908416 TTATACTTGC
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 32 0.35
59 43 0.47
60 8 0.09
61 8 0.09
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.51
Consensus pattern (58 bp):
CATGATTATATATTTAATTGCATGATTATTTATTATTTGCATGATTATAATTTACTTA
Found at i:17916682 original size:14 final size:13
Alignment explanation
Indices: 17916645--17916720 Score: 72
Period size: 13 Copynumber: 6.0 Consensus size: 13
17916635 CATGTAAAGG
*
17916645 AAAA-AAAGAAAA
1 AAAAGAAAGAAAT
17916657 AAAAGAAAGAAAT
1 AAAAGAAAGAAAT
*
17916670 AAAAGAATTGAAAT
1 AAAAGAA-AGAAAT
17916684 AAAAG---GAAAT
1 AAAAGAAAGAAAT
17916694 GAAAAGAAAGAAA-
1 -AAAAGAAAGAAAT
17916707 AGAAAGAAAGAAAT
1 A-AAAGAAAGAAAT
17916721 TTTTTATTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
10 5 0.09
11 5 0.09
12 5 0.09
13 25 0.46
14 14 0.26
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (13 bp):
AAAAGAAAGAAAT
Found at i:17917176 original size:15 final size:14
Alignment explanation
Indices: 17917158--17917220 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
17917148 GGAAAAAAAA
17917158 AAAAAAAGAGAAATG
1 AAAAAAA-AGAAATG
17917173 AAAAAAAA-AGAATG
1 AAAAAAAAGA-AATG
* *
17917187 -AAAGAAA-AAAGG
1 AAAAAAAAGAAATG
*
17917199 AAAAAAAAGAAAAG
1 AAAAAAAAGAAATG
17917213 AAAAAAAA
1 AAAAAAAA
17917221 TGAATGATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 3 0.07
13 14 0.34
14 17 0.41
15 7 0.17
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAAATG
Found at i:17917176 original size:17 final size:18
Alignment explanation
Indices: 17917156--17917196 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
17917146 GGGGAAAAAA
17917156 AAAAAAAAAG-A-GAAATG
1 AAAAAAAAAGAATGAAA-G
17917173 AAAAAAAAAGAATGAAAG
1 AAAAAAAAAGAATGAAAG
17917191 AAAAAA
1 AAAAAA
17917197 GGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 8 0.36
19 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAGAATGAAAG
Found at i:17917190 original size:25 final size:24
Alignment explanation
Indices: 17917149--17917220 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
17917139 AAAATAAGGG
* *
17917149 GAAAAAAAAA-AAAAAAGAGAAAT
1 GAAAAAAAAAGAAAAAAGAAAAAA
*
17917172 GAAAAAAAAAGAATGAAAGAAAAAA
1 GAAAAAAAAAGAA-AAAAGAAAAAA
*
17917197 GGAAAAAAAAGAAAAGAA-AAAAAA
1 GAAAAAAAAAGAAAA-AAGAAAAAA
17917221 TGAATGATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 10 0.24
24 9 0.22
25 22 0.54
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (24 bp):
GAAAAAAAAAGAAAAAAGAAAAAA
Found at i:17917195 original size:40 final size:39
Alignment explanation
Indices: 17917149--17917227 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 39
17917139 AAAATAAGGG
*
17917149 GAAAAAAAAAAAAAAAGAGAAATGAAAAAAAAAGAATGAAA
1 GAAAAAAGAAAAAAAAGA-AAA-GAAAAAAAAAGAATGAAA
*
17917190 GAAAAAAGGAAAAAAAAGAAAAGAAAAAAAATGAATGA
1 GAAAAAA-GAAAAAAAAGAAAAGAAAAAAAAAGAATGA
17917228 TTAAGTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 15 0.43
41 10 0.29
42 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (39 bp):
GAAAAAAGAAAAAAAAGAAAAGAAAAAAAAAGAATGAAA
Found at i:17917204 original size:50 final size:50
Alignment explanation
Indices: 17917129--17917224 Score: 119
Period size: 50 Copynumber: 1.9 Consensus size: 50
17917119 ATAAAAGGTG
*
17917129 AAAGAATGAGAAAATAAGGGGAAAAAAAA-AAAA-AAAGAGAAATGAAAAAA
1 AAAGAATGAGAAAATAA-GGGAAAAAAAAGAAAAGAAA-AAAAATGAAAAAA
17917179 AAAGAATGAAAGAAAA-AA-GGAAAAAAAAGAAAAGAAAAAAAATGAA
1 AAAGAATG--AGAAAATAAGGGAAAAAAAAGAAAAGAAAAAAAATGAA
17917225 TGATTAAGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
49 10 0.24
50 20 0.49
51 5 0.12
52 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (50 bp):
AAAGAATGAGAAAATAAGGGAAAAAAAAGAAAAGAAAAAAAATGAAAAAA
Found at i:17917593 original size:17 final size:18
Alignment explanation
Indices: 17917573--17917607 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
17917563 AAAAAGGAAA
17917573 AAGAGAAGAAA-AAAAAT
1 AAGAGAAGAAAGAAAAAT
17917590 AAGAGAAGAAAGAAAAAT
1 AAGAGAAGAAAGAAAAAT
17917608 GAATGTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (18 bp):
AAGAGAAGAAAGAAAAAT
Found at i:17917653 original size:38 final size:38
Alignment explanation
Indices: 17917611--17917685 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
17917601 GAAAAATGAA
* * *
17917611 TGTGGTTCTAGGGTAAAAACCTTATGAAAAGGTTAGTT
1 TGTGGCTCTAGGGTAAAAACCCTATGAAAAGGGTAGTT
17917649 TGTGGCTCTAGGGTAAAAACCCTATGAAAAGGGTAGT
1 TGTGGCTCTAGGGTAAAAACCCTATGAAAAGGGTAGT
17917686 CTATGGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (38 bp):
TGTGGCTCTAGGGTAAAAACCCTATGAAAAGGGTAGTT
Found at i:17919361 original size:40 final size:40
Alignment explanation
Indices: 17919243--17919363 Score: 95
Period size: 40 Copynumber: 3.0 Consensus size: 40
17919233 AAATGAGTAT
* * * *
17919243 AAGAATTTCAAGAACT-TCG-GGCAGAATTTTTAATTTTTGA
1 AAGAATTTCAAG-ACTCT-GAGGCAAAATCTTAAAATTTTGA
* * * * * **
17919283 AAGAATTTCAAGACTTTTAGGTATAATTTTAATTTTTTGA
1 AAGAATTTCAAGACTCTGAGGCAAAATCTTAAAATTTTGA
17919323 AAGAATTTCAAGACCTCTGA-GCAAAATCTTAAAATTTTGA
1 AAGAATTTCAAGA-CTCTGAGGCAAAATCTTAAAATTTTGA
17919363 A
1 A
17919364 TGATTTATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
39 3 0.05
40 59 0.89
41 4 0.06
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (40 bp):
AAGAATTTCAAGACTCTGAGGCAAAATCTTAAAATTTTGA
Found at i:17919491 original size:39 final size:39
Alignment explanation
Indices: 17919317--17919557 Score: 171
Period size: 40 Copynumber: 6.1 Consensus size: 39
17919307 AATTTTAATT
* * *
17919317 TTTTGAAAGAATTT-CAAGACCTCTGAGCAAAATCTTAAAA
1 TTTTGAATG-ATTTCCAAAACCTCTAAGCAAAATCTT-AAA
** * * ** *
17919357 TTTTGAATGATTTATAAGACCTTTAAGTGAAATCCTAAA
1 TTTTGAATGATTTCCAAAACCTCTAAGCAAAATCTTAAA
* * * * * *
17919396 TTTTTGAATAACTTCCAAAACCTGTAGGCCAAACCTTAAA
1 -TTTTGAATGATTTCCAAAACCTCTAAGCAAAATCTTAAA
*
17919436 TTTTTGAATGATTTCCAAAACCTCCAAGCAAAATCTTAAA
1 -TTTTGAATGATTTCCAAAACCTCTAAGCAAAATCTTAAA
* ** *
17919476 TTTTGAATGATTTCCAAGATATCAAAGCAAAAT-TGTAAA
1 TTTTGAATGATTTCCAAAACCTCTAAGCAAAATCT-TAAA
** * * ** *
17919515 TTTTGAACAATTTCTAACATGTCTAGGCAAAATCTTAAA
1 TTTTGAATGATTTCCAAAACCTCTAAGCAAAATCTTAAA
17919554 TTTT
1 TTTT
17919558 TTAAGACTCT
Statistics
Matches: 161, Mismatches: 36, Indels: 9
0.78 0.17 0.04
Matches are distributed among these distances:
38 1 0.01
39 74 0.46
40 86 0.53
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (39 bp):
TTTTGAATGATTTCCAAAACCTCTAAGCAAAATCTTAAA
Found at i:17919994 original size:18 final size:19
Alignment explanation
Indices: 17919971--17920016 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
17919961 ACAAAACATA
17919971 AAAAAAGATA-ATAAAA-AC
1 AAAAAAGATAGA-AAAACAC
*
17919989 AAAAAAAATAGAAAAAGCAC
1 AAAAAAGATAGAAAAA-CAC
17920009 AAAAAAGA
1 AAAAAAGA
17920017 GGGGGCACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 13 0.57
19 1 0.04
20 9 0.39
ACGTcount: A:0.78, C:0.07, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAAGATAGAAAAACAC
Found at i:17921926 original size:7 final size:7
Alignment explanation
Indices: 17921896--17922090 Score: 150
Period size: 7 Copynumber: 30.0 Consensus size: 7
17921886 AAATCCAAAT
17921896 CCTAAA-
1 CCTAAAC
17921902 CCTAAA-
1 CCTAAAC
17921908 CCTAAA-
1 CCTAAAC
17921914 CCTAAAC
1 CCTAAAC
*
17921921 CCTAAAT
1 CCTAAAC
17921928 CCTAAAC
1 CCTAAAC
*
17921935 ACT--AC
1 CCTAAAC
17921940 CC-AAAC
1 CCTAAAC
17921946 CCTAAA-
1 CCTAAAC
*
17921952 -CTAAAA
1 CCTAAAC
*
17921958 CCTAAAA
1 CCTAAAC
17921965 CC-AAAC
1 CCTAAAC
*
17921971 CC-AAAA
1 CCTAAAC
*
17921977 CATAAAC
1 CCTAAAC
*
17921984 CCCAAAC
1 CCTAAAC
17921991 CCTAAA-
1 CCTAAAC
*
17921997 CCTAAAT
1 CCTAAAC
*
17922004 CGTAAAC
1 CCTAAAC
17922011 CCTAAAC
1 CCTAAAC
17922018 CC-AAAC
1 CCTAAAC
17922024 CCTAAAC
1 CCTAAAC
17922031 CCTAAAC
1 CCTAAAC
*
17922038 CTTAAAC
1 CCTAAAC
*
17922045 CTTAAA-
1 CCTAAAC
* *
17922051 CCAAAAT
1 CCTAAAC
*
17922058 CCT-AAT
1 CCTAAAC
17922064 CCTAAAC
1 CCTAAAC
17922071 CCT-AAC
1 CCTAAAC
*
17922077 CCTAAAT
1 CCTAAAC
17922084 CCTAAAC
1 CCTAAAC
17922091 TAATTCCCAA
Statistics
Matches: 156, Mismatches: 21, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
5 8 0.05
6 59 0.38
7 89 0.57
ACGTcount: A:0.47, C:0.36, G:0.01, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:17921926 original size:13 final size:13
Alignment explanation
Indices: 17921896--17922090 Score: 147
Period size: 13 Copynumber: 15.0 Consensus size: 13
17921886 AAATCCAAAT
17921896 CCTAAACCTAAA-
1 CCTAAACCTAAAC
17921908 CCTAAACCTAAAC
1 CCTAAACCTAAAC
17921921 CCTAAATCCTAAAC
1 CCTAAA-CCTAAAC
* *
17921935 ACT--ACCCAAAC
1 CCTAAACCTAAAC
*
17921946 CCTAAA-CTAAAA
1 CCTAAACCTAAAC
17921958 CCTAAAACC-AAAC
1 CCT-AAACCTAAAC
* *
17921971 CCAAAACATAAAC
1 CCTAAACCTAAAC
*
17921984 CCCAAACCCTAAA-
1 CCTAAA-CCTAAAC
*
17921997 CCTAAATCGTAAAC
1 CCTAAA-CCTAAAC
*
17922011 CCTAAACCCAAAC
1 CCTAAACCTAAAC
17922024 CCTAAACCCTAAAC
1 CCTAAA-CCTAAAC
*
17922038 CTTAAACCTTAAA-
1 CCTAAACC-TAAAC
* *
17922051 CCAAAATCCT-AAT
1 CCTAAA-CCTAAAC
17922064 CCTAAACCCT-AAC
1 CCTAAA-CCTAAAC
17922077 CCTAAATCCTAAAC
1 CCTAAA-CCTAAAC
17922091 TAATTCCCAA
Statistics
Matches: 146, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
11 8 0.05
12 26 0.18
13 71 0.49
14 41 0.28
ACGTcount: A:0.47, C:0.36, G:0.01, T:0.16
Consensus pattern (13 bp):
CCTAAACCTAAAC
Found at i:17923464 original size:17 final size:16
Alignment explanation
Indices: 17923429--17923474 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
17923419 AATGAGAGAT
*
17923429 AAATGAAAAAAATGAA
1 AAATGAAAAAAAGGAA
*
17923445 AAATGAAAAGGAAGGAA
1 AAATGAAAA-AAAGGAA
17923462 AAATGAGAAAAAA
1 AAATGA-AAAAAA
17923475 ACTAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 9 0.36
17 13 0.52
18 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.09
Consensus pattern (16 bp):
AAATGAAAAAAAGGAA
Found at i:17923643 original size:14 final size:15
Alignment explanation
Indices: 17923617--17923646 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17923607 AAAATACAAG
17923617 AAATGAGAAAAAAAT
1 AAATGAGAAAAAAAT
17923632 AAATGA-AAAAAAAT
1 AAATGAGAAAAAAAT
17923646 A
1 A
17923647 GAAGAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAATGAGAAAAAAAT
Found at i:17924045 original size:48 final size:47
Alignment explanation
Indices: 17923975--17924085 Score: 186
Period size: 48 Copynumber: 2.3 Consensus size: 47
17923965 TCACTTTATA
*
17923975 ATGAGATTTTAAAGTTGTTGAGCCTCTGTTTAAAGGAGTTTTTCAAT
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGTTTAAAGGAGTTTTTCAAC
*
17924022 ATGAGATTTTTAAAGTTGTTGAGCCTTTGTTTAAAGGAGTTTTTCAAC
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGTTTAAAGGAGTTTTTCAAC
*
17924070 ATAAGATTTTAAAGTT
1 ATGAGATTTTAAAGTT
17924086 ATCGAGCTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 16 0.27
48 44 0.73
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (47 bp):
ATGAGATTTTAAAGTTGTTGAGCCTCTGTTTAAAGGAGTTTTTCAAC
Found at i:17924102 original size:47 final size:47
Alignment explanation
Indices: 17923978--17924103 Score: 180
Period size: 48 Copynumber: 2.7 Consensus size: 47
17923968 CTTTATAATG
* * *
17923978 AGATTTTAAAGTTGTTGAGCCTCTGTTTAAAGGAGTTTTTCAATATG
1 AGATTTTAAAGTTGTTGAGCCTTTGTTTAAAGGAGTTTTTCAACATA
17924025 AGATTTTTAAAGTTGTTGAGCCTTTGTTTAAAGGAGTTTTTCAACATA
1 AGA-TTTTAAAGTTGTTGAGCCTTTGTTTAAAGGAGTTTTTCAACATA
* * * *
17924073 AGATTTTAAAGTTATCGAGCTTTTTTTTAAA
1 AGATTTTAAAGTTGTTGAGCCTTTGTTTAAA
17924104 AAAAAATTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
47 27 0.38
48 44 0.62
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.44
Consensus pattern (47 bp):
AGATTTTAAAGTTGTTGAGCCTTTGTTTAAAGGAGTTTTTCAACATA
Found at i:17924252 original size:34 final size:35
Alignment explanation
Indices: 17924197--17924268 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
17924187 TATCGAGTCT
* * *
17924197 TTGCTTAAAAAAGCTTTTAAATTTA-TTTTCAAAG
1 TTGCTCAAAAAAGCTTTTAAATATATTTTTAAAAG
*
17924231 TTGCTCAAAAGAG-TTTATAAATATATTTTTAAAAG
1 TTGCTCAAAAAAGCTTT-TAAATATATTTTTAAAAG
17924266 TTG
1 TTG
17924269 TTAAACTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 3 0.09
34 18 0.56
35 11 0.34
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (35 bp):
TTGCTCAAAAAAGCTTTTAAATATATTTTTAAAAG
Found at i:17924378 original size:19 final size:19
Alignment explanation
Indices: 17924354--17924397 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17924344 AAAGAGAAAA
* *
17924354 AAAAAAAACAAAACACATT
1 AAAAAAAACAAAAAAAATT
**
17924373 AAAAAATCCAAAAAAAATT
1 AAAAAAAACAAAAAAAATT
17924392 AAAAAA
1 AAAAAA
17924398 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAATT
Found at i:17925635 original size:28 final size:25
Alignment explanation
Indices: 17925593--17925662 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 25
17925583 TTCAACTAAA
* *
17925593 AAAAGAGGGAGAAAAGATAAAGAAGAAG
1 AAAAGAAGGA-AAAA-AAAAAG-AGAAG
*
17925621 AAAAGAAGGAAAAAAAAAAGGGAAG
1 AAAAGAAGGAAAAAAAAAAGAGAAG
*
17925646 GAAA-AAGGAAAAAAAAA
1 AAAAGAAGGAAAAAAAAA
17925663 GGAGTGGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.34
25 7 0.18
26 5 0.13
27 4 0.11
28 9 0.24
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.01
Consensus pattern (25 bp):
AAAAGAAGGAAAAAAAAAAGAGAAG
Found at i:17925806 original size:32 final size:33
Alignment explanation
Indices: 17925770--17925848 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
17925760 TTTGGGACAT
* *
17925770 GAAAAAGAAGAGGGAAAAATGTAAAA-AAAGAA
1 GAAAAAGAAGAAGGAAAAATGGAAAACAAAGAA
*
17925802 GAAAAAGGAGAAGGAAAAATGGAAAAGCAAAGAA
1 GAAAAAGAAGAAGGAAAAATGGAAAA-CAAAGAA
*
17925836 GAAAGAGAGAGAA
1 GAAAAAGA-AGAA
17925849 AAAAAGTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 23 0.59
34 12 0.31
35 4 0.10
ACGTcount: A:0.66, C:0.01, G:0.29, T:0.04
Consensus pattern (33 bp):
GAAAAAGAAGAAGGAAAAATGGAAAACAAAGAA
Found at i:17934175 original size:31 final size:27
Alignment explanation
Indices: 17934121--17934183 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
17934111 AAGAACTCTA
17934121 TTTTCTTTCTGTTTCACGATAGGTAGG
1 TTTTCTTTCTGTTTCACGATAGGTAGG
17934148 TTTTCTTTCTGTTTCACGATAGGTAGG
1 TTTTCTTTCTGTTTCACGATAGGTAGG
17934175 TTTTCTTTC
1 TTTTCTTTC
17934184 ATCTAATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (27 bp):
TTTTCTTTCTGTTTCACGATAGGTAGG
Found at i:17936023 original size:37 final size:39
Alignment explanation
Indices: 17935973--17936047 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 39
17935963 CTACTCTCCA
17935973 TCTCTTCTTAGCTCATGC-TACTGGGTT-ATTTTTTGTT
1 TCTCTTCTTAGCTCATGCTTACTGGGTTCATTTTTTGTT
* **
17936010 TCTCTTCTTAGCTCTTGCTTTGTGGGTTCATTTTTTGT
1 TCTCTTCTTAGCTCATGCTTACTGGGTTCATTTTTTGT
17936048 CTATCTAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 17 0.52
38 7 0.21
39 9 0.27
ACGTcount: A:0.08, C:0.19, G:0.17, T:0.56
Consensus pattern (39 bp):
TCTCTTCTTAGCTCATGCTTACTGGGTTCATTTTTTGTT
Found at i:17936637 original size:16 final size:17
Alignment explanation
Indices: 17936615--17936650 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17936605 GAACTTTAGT
*
17936615 TTTTTTAAATATTTATA
1 TTTTTAAAATATTTATA
*
17936632 TTTTTAAAATATTTTTA
1 TTTTTAAAATATTTATA
17936649 TT
1 TT
17936651 GACCCTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAAAATATTTATA
Found at i:17936796 original size:24 final size:24
Alignment explanation
Indices: 17936752--17936806 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
17936742 AACTATGGAG
* *
17936752 GAGACCACTACCCCTAACATCGAC
1 GAGACCACCACCCCTAACATCAAC
*
17936776 GAGACCACCA-CCCTCAGCATCAAC
1 GAGACCACCACCCCT-AACATCAAC
*
17936800 AAGACCA
1 GAGACCA
17936807 TAGCCTGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.36, C:0.42, G:0.13, T:0.09
Consensus pattern (24 bp):
GAGACCACCACCCCTAACATCAAC
Found at i:17937364 original size:14 final size:14
Alignment explanation
Indices: 17937331--17937374 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
17937321 ACAAAATGGT
*
17937331 TTGGGGTTTAGA-T
1 TTGGGGTTTAGAGG
*
17937344 TTAGGGGTTTAGGGG
1 TT-GGGGTTTAGAGG
17937359 TTGGGGTTTAGAGG
1 TTGGGGTTTAGAGG
17937373 TT
1 TT
17937375 AGGTTAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (14 bp):
TTGGGGTTTAGAGG
Found at i:17939300 original size:23 final size:23
Alignment explanation
Indices: 17939285--17939327 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
17939275 ATTTATTTAA
17939285 TAAAAATATAATAA-TTATAAATG
1 TAAAAATATAATAATTTATAAA-G
17939308 TAAAAATATAATAA-TTATAA
1 TAAAAATATAATAATTTATAA
17939328 TCATTAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAATATAATAATTTATAAAG
Found at i:17939855 original size:24 final size:25
Alignment explanation
Indices: 17939826--17939880 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
17939816 CATAAAATAT
17939826 TAAATAAACAATTT-ACATGTTAAA
1 TAAATAAACAATTTAACATGTTAAA
* *
17939850 TCAATAAATAATTTAACATGTTAAA
1 TAAATAAACAATTTAACATGTTAAA
17939875 TAAATA
1 TAAATA
17939881 GGTTAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAATAAACAATTTAACATGTTAAA
Found at i:17940104 original size:29 final size:28
Alignment explanation
Indices: 17940067--17940130 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
17940057 AATTAATAAA
*
17940067 TTTATAATTCAAATATTAAAATAAATATT
1 TTTAAAATTCAAATATTAAAATAAA-ATT
* * * *
17940096 TTTAAAATTTAAGTATTACATTAAAATT
1 TTTAAAATTCAAATATTAAAATAAAATT
17940124 TATTAAA
1 T-TTAAA
17940131 TATTTCACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTAAAATTCAAATATTAAAATAAAATT
Found at i:17940334 original size:22 final size:22
Alignment explanation
Indices: 17940304--17940346 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17940294 GTAAGGATTA
* *
17940304 TTCATTTCCGAAATCTATCAAG
1 TTCAGTTCCAAAATCTATCAAG
*
17940326 TTCAGTTCCAAAATCTGTCAA
1 TTCAGTTCCAAAATCTATCAA
17940347 ATAAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (22 bp):
TTCAGTTCCAAAATCTATCAAG
Found at i:17941140 original size:2 final size:2
Alignment explanation
Indices: 17941133--17941162 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17941123 TGAATAATTA
17941133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17941163 GAAAACCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17942375 original size:3 final size:3
Alignment explanation
Indices: 17942367--17942409 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
17942357 CTCTTCAAAT
*
17942367 TAA TAA TAA TAAA TAC TAA TAA TAA TAA TTAA TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA
17942410 TATTTGACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17942388 original size:16 final size:16
Alignment explanation
Indices: 17942367--17942409 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
17942357 CTCTTCAAAT
*
17942367 TAATAATAATAAATAC
1 TAATAATAATAAATAA
*
17942383 TAATAATAATAATTAA
1 TAATAATAATAAATAA
17942399 TAATAATAATA
1 TAATAATAATA
17942410 TATTTGACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:17942405 original size:13 final size:13
Alignment explanation
Indices: 17942364--17942408 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 13
17942354 CTGCTCTTCA
17942364 AATTAATAATAAT
1 AATTAATAATAAT
17942377 AAATACTAATAATAAT
1 -AAT--TAATAATAAT
17942393 AATTAATAATAAT
1 AATTAATAATAAT
17942406 AAT
1 AAT
17942409 ATATTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.45
14 3 0.10
15 3 0.10
16 10 0.34
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:17944247 original size:42 final size:42
Alignment explanation
Indices: 17944199--17944286 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
17944189 TTAATTCAAC
17944199 CAAAAGACAGTAGACATGGATAGTATTGAAAATGTA-ACATAA
1 CAAAAGACAGTAGACATGGATAGTATTGAAAATGTAGA-ATAA
17944241 CAAAAGACAGTAGACATGGATAGTATTGAAAATGTAGAATAA
1 CAAAAGACAGTAGACATGGATAGTATTGAAAATGTAGAATAA
17944283 CAAA
1 CAAA
17944287 TGGAATTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.20
Consensus pattern (42 bp):
CAAAAGACAGTAGACATGGATAGTATTGAAAATGTAGAATAA
Found at i:17953892 original size:25 final size:25
Alignment explanation
Indices: 17953842--17953893 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
17953832 TAATAAAATC
* *
17953842 TTAAACCTTACATTTTGAATCCTAT
1 TTAAACCTTACATTTTCAAACCTAT
*
17953867 TTAAACC-TCCATTTTCAAACCTTAT
1 TTAAACCTTACATTTTCAAACC-TAT
17953892 TT
1 TT
17953894 CTAAACCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.31, C:0.23, G:0.02, T:0.44
Consensus pattern (25 bp):
TTAAACCTTACATTTTCAAACCTAT
Found at i:17954044 original size:10 final size:9
Alignment explanation
Indices: 17954029--17954054 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
17954019 TTTAAGGAAT
17954029 AAAAAAATA
1 AAAAAAATA
17954038 AAAAAAATA
1 AAAAAAATA
17954047 AAAAAAAT
1 AAAAAAAT
17954055 GATTGTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:17955986 original size:16 final size:16
Alignment explanation
Indices: 17955942--17955989 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
17955932 TCTATTATAG
17955942 TAATTTAATATGTAAT
1 TAATTTAATATGTAAT
17955958 TAAGTTT--TATGTAAT
1 TAA-TTTAATATGTAAT
17955973 TAATTTAATATGTAAT
1 TAATTTAATATGTAAT
17955989 T
1 T
17955990 TAATAGAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.10
15 11 0.38
16 12 0.41
17 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (16 bp):
TAATTTAATATGTAAT
Found at i:17956304 original size:128 final size:129
Alignment explanation
Indices: 17955974--17956306 Score: 406
Period size: 128 Copynumber: 2.6 Consensus size: 129
17955964 TTATGTAATT
* * * *
17955974 AATTTAATATGTAATTTAATAGAGGTATTGTAGTAATTTT--CATAAAATGCCACATGTCAAATT
1 AATTTAATATGTAATTTAATAGAGGTATTATAGTAATTTTAAAACAAAATGTCACATGTCAAA-T
* * * * * *
17956037 TCC-ATAAAGCAATGGCAAGGGTACTTTAGTAATTTAATAGGTAGTTAATTTTATATTATGTTAA
65 TCCTATAAAGTAATGGCAAAGGTACTTTAGTAATTTAATAGATAGTAAATGTTATATTATATTAA
** * * *
17956101 AATTTAATATGTAATTTAATAGAAATATTTTAGTAAATTTAAAACATAATGTCACATGTCAAATT
1 AATTTAATATGTAATTTAATAGAGGTATTATAGTAATTTTAAAACAAAATGTCACATGTCAAATT
** * * *
17956166 TTTATGAAGTAATGGCAAAGGTA-TTTAGTAATTTAGTATATAGTAAATGTTATATTATATTAA
66 CCTATAAAGTAATGGCAAAGGTACTTTAGTAATTTAATAGATAGTAAATGTTATATTATATTAA
* * *
17956229 AATTTAATACGCAATTTAATATG-GGTATTATAGTAATTTTAAAACAAAATGTCACATGTCAACT
1 AATTTAATATGTAATTTAATA-GAGGTATTATAGTAATTTTAAAACAAAATGTCACATGTCAAAT
17956293 TCCTATAAAGTAAT
65 TCCTATAAAGTAAT
17956307 CACTAAAGTA
Statistics
Matches: 172, Mismatches: 30, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
127 36 0.21
128 101 0.59
129 35 0.20
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (129 bp):
AATTTAATATGTAATTTAATAGAGGTATTATAGTAATTTTAAAACAAAATGTCACATGTCAAATT
CCTATAAAGTAATGGCAAAGGTACTTTAGTAATTTAATAGATAGTAAATGTTATATTATATTAA
Found at i:17956414 original size:25 final size:25
Alignment explanation
Indices: 17956386--17956448 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
17956376 CATATTCACG
*
17956386 ATTATGGTAGAA-TGGCATTTTTG-TA
1 ATTATGGTAGAAGT-G-ATATTTGATA
*
17956411 ATTATGATAGAAGTGATATTTGCATA
1 ATTATGGTAGAAGTGATATTTG-ATA
17956437 ATTATGGTAGAA
1 ATTATGGTAGAA
17956449 AGGGAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 6 0.19
25 12 0.38
26 14 0.44
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (25 bp):
ATTATGGTAGAAGTGATATTTGATA
Found at i:17956656 original size:21 final size:21
Alignment explanation
Indices: 17956632--17956676 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
17956622 GATTTCTTTC
17956632 AATATATTATTTAATATTTTA
1 AATATATTATTTAATATTTTA
17956653 AATATATTATTTAATATTTTA
1 AATATATTATTTAATATTTTA
17956674 AAT
1 AAT
17956677 TTTAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATATTATTTAATATTTTA
Found at i:17957891 original size:133 final size:134
Alignment explanation
Indices: 17957728--17957975 Score: 385
Period size: 133 Copynumber: 1.9 Consensus size: 134
17957718 TAATTTAGCC
* * *
17957728 TTCTCGAGCTTGAATTTTTATGAAACTTTTTAGATCTTAATTTTATAATATTTTTATGATTTTTG
1 TTCTCGAGCTTGAATTTTTATGAAACTTTTTACATCTTAATTTCATAATA-TTTCATGATTTTTG
* * *
17957793 GTGCATTTGAAATCATAGCAGTACCCC-AAAAATGTGAAATTACTAAAATATAAGGGTAGTTTTT
65 GTGCATTTAAAATCATAGCAGTACCCCTAAAAATATGAAATTACCAAAATATAAGGGTAGTTTTT
17957857 GGCCT
130 GGCCT
17957862 TTCT-GAGCTCTG-ATTTTTATGAAACTTTTTACATCTTAATTTCATAATATTTCATGATTTTTG
1 TTCTCGAGCT-TGAATTTTTATGAAACTTTTTACATCTTAATTTCATAATATTTCATGATTTTTG
* *
17957925 GTGCATTTAAAATTATAGCAGTACCCCTAAAAGTATGAAATTACCAAAATA
65 GTGCATTTAAAATCATAGCAGTACCCCTAAAAATATGAAATTACCAAAATA
17957976 CCCTATAAGG
Statistics
Matches: 104, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
132 38 0.37
133 60 0.58
134 6 0.06
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (134 bp):
TTCTCGAGCTTGAATTTTTATGAAACTTTTTACATCTTAATTTCATAATATTTCATGATTTTTGG
TGCATTTAAAATCATAGCAGTACCCCTAAAAATATGAAATTACCAAAATATAAGGGTAGTTTTTG
GCCT
Found at i:17960145 original size:3 final size:3
Alignment explanation
Indices: 17960137--17960171 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
17960127 GAAAGGATAT
* *
17960137 TAA TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17960172 TTGATGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:17960154 original size:12 final size:12
Alignment explanation
Indices: 17960133--17960173 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
17960123 AAAAGAAAGG
17960133 ATATTAATAATA
1 ATATTAATAATA
17960145 ATGA-TAATAATA
1 AT-ATTAATAATA
17960157 ATATTAATAATA
1 ATATTAATAATA
17960169 ATATT
1 ATATT
17960174 GATGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
ATATTAATAATA
Found at i:17962993 original size:30 final size:30
Alignment explanation
Indices: 17962950--17963019 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
17962940 ATACATGCAT
* * *
17962950 TGCATTCCTTCCAC-ATCAATGGATAGTACA
1 TGCATCCCATCCACAAT-AATGAATAGTACA
17962980 TGCATCCCATCCACAATAATGAATAGTACA
1 TGCATCCCATCCACAATAATGAATAGTACA
17963010 TGCATCCCAT
1 TGCATCCCAT
17963020 TTTATGCACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.27
Consensus pattern (30 bp):
TGCATCCCATCCACAATAATGAATAGTACA
Found at i:17968375 original size:133 final size:132
Alignment explanation
Indices: 17968060--17968389 Score: 396
Period size: 134 Copynumber: 2.5 Consensus size: 132
17968050 TGGAATCCCA
* * *
17968060 AGAATTCAAGAAAGTAGATTGTTAAAGATGAAATCAAATATCTAATAAAAAAATAAG-AAAATAA
1 AGAATTCAAGAAAGTTGATTGTTAAAGATGAAATCAAATAT-TCA-AAAAAAA-AAGAAAAAAAA
* * * * * * * *
17968124 GCAAAGAAAGAAATAATACACCTTGGAGATGAGAGTCTGAGGTAAAAAGTGAATGAAGCTTTAGG
63 GCAAAGAAAGAAAGAATACACCTCGAAGATGAAAGTCTGAGGCAAAAAGTGAATAAAGCTTCAAG
17968189 AAAAT
128 AAAAT
* * * *
17968194 AGAATTCAAGAAAGTTGATTGCTAAAGATGAAGTCAAATGTTCAAAAAAAAAAGAAAAAAAGAGT
1 AGAATTCAAGAAAGTTGATTGTTAAAGATGAAATCAAATATTCAAAAAAAAAAGAAAAAAA-AGC
** * * *
17968259 AAAGAAAGAAAGACATATGCCTCGAAGATGAAAGTTTGGGGCAAAAAGTGAATAAAGCTTCAATA
65 AAAGAAAGAAAGA-ATACACCTCGAAGATGAAAGTCTGAGGCAAAAAGTGAATAAAGCTTCAAGA
17968324 AAAT
129 AAAT
17968328 A-AATTTCAAG-AAGTTGATTGTTAAAGATGAAATCAAATATTCCAAAAAAAAAAGAAAAAAAA
1 AGAA-TTCAAGAAAGTTGATTGTTAAAGATGAAATCAAATATT-CAAAAAAAAAAGAAAAAAAA
17968390 AGGGAAAATA
Statistics
Matches: 168, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
131 3 0.02
132 12 0.07
133 47 0.28
134 106 0.63
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (132 bp):
AGAATTCAAGAAAGTTGATTGTTAAAGATGAAATCAAATATTCAAAAAAAAAAGAAAAAAAAGCA
AAGAAAGAAAGAATACACCTCGAAGATGAAAGTCTGAGGCAAAAAGTGAATAAAGCTTCAAGAAA
AT
Found at i:17968415 original size:18 final size:18
Alignment explanation
Indices: 17968382--17968416 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17968372 AAAAAAAAAG
**
17968382 AAAAAAAAAGGGAAAATA
1 AAAAAAAAAGAAAAAATA
17968400 AAAAAAAAAGAAAAAAT
1 AAAAAAAAAGAAAAAAT
17968417 GTATTTCAAA
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:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAATA
Done.