Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 135 of 222
Found at i:43861018 original size:131 final size:130
Alignment explanation
Indices: 43860749--43861023 Score: 322
Period size: 131 Copynumber: 2.1 Consensus size: 130
43860739 CAAAACATCG
* * *
43860749 GGGAGATAGGATTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAAGTT
1 GGGAGATAAGATTCACTGTCCTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGAAAGTT
* * ** * *
43860814 TCAACCTACTCCGCTGCTGCTCAGGGAGATAAGGCTTGTGACTTAAATCTGCTTCCTTACTCCTG
66 TCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTTGTGACTTAAATCAACTTCCCTACTCCTA
* * * *
43860879 GGGAAGATAAGATTCGCTGTCCTCTATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCAATT
1 GGG-AGATAAGATTCACTGTCCTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGAAAGT
* * **
43860944 TTCAACCTACTCCATTACTGCTTAGGGAGATAAGGC-TGAT-ATCTTCGATCAAC-TCCACTACT
65 TTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTTG-TGA-CTTAAATCAACTTCC-CTACT
*
43861006 GCTTA
127 -CCTA
43861011 GGGAGATAAGATT
1 GGGAGATAAGATT
43861024 TGCAATTTTC
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
130 9 0.07
131 108 0.89
132 5 0.04
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (130 bp):
GGGAGATAAGATTCACTGTCCTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGAAAGTT
TCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTTGTGACTTAAATCAACTTCCCTACTCCTA
Found at i:43861399 original size:44 final size:44
Alignment explanation
Indices: 43861351--43862056 Score: 377
Period size: 44 Copynumber: 16.5 Consensus size: 44
43861341 TTTTAATCCA
* * *
43861351 CTCCACTGTAATCTCAAGGAAATAGGATTACTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* **
43861395 CTCCACTGTAATCT-TGGGAGATAAGATTTTTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * ** * *
43861438 CTCCACTGTAA-CTTCAGGGAGATAATATTTGAAAT-TATTCAGTCTA
1 CTCCACTGTAATC-TCAGGGAGATAAGA-TT--ACTGGCTTCAATCTG
* * * * *
43861484 TTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATTCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * * * *** *
43861525 CTCTACTGTAATTTCAGAGAGATAAGA-TCCTTTATTTTAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTAC-TGGCTTCAATCTG
* * * *
43861569 CTGCACTGCAATCTCAGGGA-ATAGGATTACTGGCTTTAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
*
43861612 CTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* ** *
43861656 CTCCACTGTAACCTCAGGGAGATAAGA-T--T--CTTCGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * * * * *
43861695 CTCCATTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * * * *** * *
43861736 TTCTACTGTAATTTCAGAGAGATAAGATT-CTTTATTTTAATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTAC-TGGCTTCAATCTG
* * * * *
43861780 CTCCACTGTAATATCAGGGAAATAGGATTACTGGCTTTAATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* ** * *
43861824 CTTCGTTGTAATCTCAGGAAGATAAGATTTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * * * *
43861868 CTCCACTGTAACCTCAAGAAGATAAGA-T--T--CTTCAGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * * * * * *
43861907 TTCCCCTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * * * * *** *
43861948 CTCTACTGTAATTTTAGAGAGATAAGA-TCCTTTATTTTAAT-TCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTAC-TGGCTTCAATCT-G
* * *
43861992 CTCCATTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
***
43862036 CTCTGTTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAG
43862057 GTAAAATCAG
Statistics
Matches: 506, Mismatches: 128, Indels: 56
0.73 0.19 0.08
Matches are distributed among these distances:
39 62 0.12
40 2 0.00
41 90 0.18
42 6 0.01
43 74 0.15
44 234 0.46
45 6 0.01
46 30 0.06
47 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
Found at i:43861442 original size:87 final size:87
Alignment explanation
Indices: 43861351--43862056 Score: 369
Period size: 87 Copynumber: 8.2 Consensus size: 87
43861341 TTTTAATCCA
* * * *
43861351 CTCCACTGTAATCTCAAGGAAATAGGATTACTGGCTTCAATCTGCTCCACTGTAATCT-TGGGAG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
*
43861415 ATAAGATTTTTGGCTTCAATCTG
66 ATAAGATTTCT-GCTTCAATCTG
* * ** * **
43861438 CTCCACTGTAA-CTTCAGGGAGATAATATTTGAAAT-TATTCAGTCTATTCCACTGTAATCTCAG
1 CTCCACTGTAATC-TCAGGGAGATAAGA-TT--ACTGGCTTCAATCTGCTCCACTGTAATCTCAG
* * * *
43861501 GGAGATAAGA--CCTGATTCGATCTA
62 GGAGATAAGATTTCTGCTTCAATCTG
* * * * *** * * *
43861525 CTCTACTGTAATTTCAGAGAGATAAGA-TCCTTTATTTTAATCTGCTGCACTGCAATCTCAGGGA
1 CTCCACTGTAATCTCAGGGAGATAAGATTAC-TGGCTTCAATCTGCTCCACTGTAATCTCAGGGA
* * *
43861589 -ATAGGATTACTGGCTTTAATCTG
65 GATAAGATTTCT-GCTTCAATCTG
* *
43861612 CTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
** *
43861677 ATAAGA--T-T-CTTCGGTCTA
66 ATAAGATTTCTGCTTCAATCTG
* * * * * ** * * *
43861695 CTCCATTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCTATTCTACTGTAATTTCAGAGAG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
* ** * *
43861757 ATAAGATTCTTTATTTTAATCCG
66 ATAAGATT-TCTGCTTCAATCTG
* * * * * * ** *
43861780 CTCCACTGTAATATCAGGGAAATAGGATTACTGGCTTTAATCCGCTTCGTTGTAATCTCAGGAAG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
43861845 ATAAGATTTCTGGCTTCAATCTG
66 ATAAGATTTCT-GCTTCAATCTG
* * * * ** *
43861868 CTCCACTGTAACCTCAAGAAGATAAGA-T--T--CTTCAGTCTATTCCCCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
* * * * *
43861928 ATAAGA--CCTGATGCGATCTA
66 ATAAGATTTCTGCTTCAATCTG
* * * * * *** * *
43861948 CTCTACTGTAATTTTAGAGAGATAAGA-TCCTTTATTTTAAT-TCGCTCCATTGTAATCTCAGGG
1 CTCCACTGTAATCTCAGGGAGATAAGATTAC-TGGCTTCAATCT-GCTCCACTGTAATCTCAGGG
* * *
43862011 AAATAGGATTACTGGCTTCAATCTG
64 AGATAAGATTTCT-GCTTCAATCTG
***
43862036 CTCTGTTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAG
43862057 GTAAAATCAG
Statistics
Matches: 448, Mismatches: 140, Indels: 61
0.69 0.22 0.09
Matches are distributed among these distances:
80 57 0.13
81 4 0.01
83 62 0.14
84 8 0.02
85 79 0.18
86 3 0.01
87 115 0.26
88 87 0.19
89 20 0.04
90 13 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (87 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
ATAAGATTTCTGCTTCAATCTG
Found at i:43861711 original size:39 final size:42
Alignment explanation
Indices: 43861256--43862056 Score: 363
Period size: 44 Copynumber: 18.7 Consensus size: 42
43861246 ATTTGAAATT
* * * * *
43861256 CTTCGATCTATTCCCCTGTAATCTCAAGGAGATAAGA-CCTG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTCTG
* * * * * * *
43861297 ATGCAATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTA
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGAT--TCTG
* * * * * *
43861341 TTTTAATCCACTCCACTGTAATCTCAAGGAAATAGGATTACTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATT-CT-G
* * *
43861385 CTTCAATCTGCTCCACTGTAATCT-TGGGAGATAAGATTTTTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGA-TTCT-G
* *
43861428 CTTCAATCTGCTCCACTGTAA-CTTCAGGGAGATAATATT-TG
1 CTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATTCTG
* * * *
43861469 AAATTATTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGA-CCTG
1 -----CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTCTG
* * * * * * *
43861515 ATTCGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTA
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGAT--TCTG
* * * * * *
43861559 TTTTAATCTGCTGCACTGCAATCTCAGGGA-ATAGGATTACTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATT-CT-G
* *
43861602 CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGA-TTCT-G
* *
43861646 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA-T-T-
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTCTG
** * *
43861685 CTTCGGTCTACTCCATTGTAATCTCAGGGAGATAAGA-CCTG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTCTG
* * * * * * * *
43861726 ATGCGATCTATTCTACTGTAATTTCAGAGAGATAAGATTCTTTA
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTC--TG
* * ** * * *
43861770 TTTTAATCCGCTCCACTGTAATATCAGGGAAATAGGATTACTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATT-CT-G
* ** * ** *
43861814 CTTTAATCCGCTTCGTTGTAATCTCAGGAAGATAAGATTTCTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGA-TTCT-G
* * * *
43861858 CTTCAATCTGCTCCACTGTAACCTCAAGAAGATAAGA-T-T-
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTCTG
* * * *
43861897 CTTCAGTCTATTCCCCTGTAATCTCAGGGAGATAAGA-CCTG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTCTG
* * * * * * * * *
43861938 ATGCGATCTACTCTACTGTAATTTTAGAGAGATAAGATCCTTTA
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGAT--TCTG
* * * * * *
43861982 TTTTAAT-TCGCTCCATTGTAATCTCAGGGAAATAGGATTACTGG
1 CTTCAATCT-ACTCCACTGTAATCTCAGGGAGATAAGATT-CT-G
* ***
43862026 CTTCAATCTGCTCTGTTGTAATCTCAGGGAG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAG
43862057 GTAAAATCAG
Statistics
Matches: 569, Mismatches: 152, Indels: 75
0.71 0.19 0.09
Matches are distributed among these distances:
39 62 0.11
40 2 0.00
41 119 0.21
42 8 0.01
43 72 0.13
44 267 0.47
45 6 0.01
46 32 0.06
47 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (42 bp):
CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATTCTG
Found at i:43861893 original size:212 final size:212
Alignment explanation
Indices: 43861253--43862056 Score: 1200
Period size: 212 Copynumber: 3.8 Consensus size: 212
43861243 AAGATTTGAA
* * *
43861253 ATTCTTC-GATCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCAATCTACTCTACTGTA
1 ATTCTTCAG-TCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
* *
43861317 ATTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAAGGAAATAGGATTAC
65 ATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
* *
43861382 TGGCTTCAATCTGCTCCACTGTAATCT-TGGGAGATAAGATTTTTGGCTTCAATCTGCTCCACTG
130 TGGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTG
*
43861446 TAACTTCAGGGAGATAATATTTG
195 TAACCTCAGGGAGAT-A-A---G
* *
43861469 AAATTATTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATTCGATCTACTCTACTGT
1 --ATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGT
* * *
43861534 AATTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTGCACTGCAATCTCAGGG-AATAGGATTA
64 AATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTA
*
43861598 CTGGCTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACT
129 CTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACT
43861663 GTAACCTCAGGGAGATAAG
194 GTAACCTCAGGGAGATAAG
* * * *
43861682 ATTCTTCGGTCTACTCCATTGTAATCTCAGGGAGATAAGACCTGATGCGATCTATTCTACTGTAA
1 ATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAA
* *
43861747 TTTCAGAGAGATAAGATTCTTTATTTTAATCCGCTCCACTGTAATATCAGGGAAATAGGATTACT
66 TTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
* * * ** *
43861812 GGCTTTAATCCGCTTCGTTGTAATCTCAGGAAGATAAGATTTCTGGCTTCAATCTGCTCCACTGT
131 GGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGT
* *
43861877 AACCTCAAGAAGATAAG
196 AACCTCAGGGAGATAAG
*
43861894 ATTCTTCAGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAA
1 ATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAA
* * *
43861959 TTTTAGAGAGATAAGATCCTTTATTTTAATTCGCTCCATTGTAATCTCAGGGAAATAGGATTACT
66 TTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
***
43862024 GGCTTCAATCTGCTCTGTTGTAATCTCAGGGAG
131 GGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
43862057 GTAAAATCAG
Statistics
Matches: 536, Mismatches: 47, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
211 106 0.20
212 235 0.44
213 1 0.00
216 1 0.00
217 38 0.07
218 154 0.29
219 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (212 bp):
ATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAA
TTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACT
GGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGT
AACCTCAGGGAGATAAG
Found at i:43879356 original size:19 final size:20
Alignment explanation
Indices: 43879332--43879379 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
43879322 TGCAAACTAA
*
43879332 AGTGAGCTAA-AACGAGCTT
1 AGTGAGCTAAGAACGAGCTC
*
43879351 AGTGAGCTAAGAATGAGCTC
1 AGTGAGCTAAGAACGAGCTC
*
43879371 ATTGAGCTA
1 AGTGAGCTA
43879380 GAGTTGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (20 bp):
AGTGAGCTAAGAACGAGCTC
Found at i:43882388 original size:15 final size:15
Alignment explanation
Indices: 43882368--43882400 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43882358 TCTCTTTTTC
*
43882368 TTCACTCATTTTGTT
1 TTCACTCACTTTGTT
43882383 TTCACTCACTTTGTT
1 TTCACTCACTTTGTT
43882398 TTC
1 TTC
43882401 TCCTCTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.58
Consensus pattern (15 bp):
TTCACTCACTTTGTT
Found at i:43891651 original size:9 final size:9
Alignment explanation
Indices: 43891602--43891764 Score: 55
Period size: 9 Copynumber: 18.6 Consensus size: 9
43891592 TTTTGAAACT
*
43891602 TTTTTATGA
1 TTTTTATAA
43891611 TTTTTATAA
1 TTTTTATAA
*
43891620 TAATTTTACAA
1 T--TTTTATAA
*
43891631 -TTTTATTCA
1 TTTTTA-TAA
43891640 TTTTTATAA
1 TTTTTATAA
43891649 --TTTATAA
1 TTTTTATAA
**
43891656 TAATTAT-A
1 TTTTTATAA
*
43891664 TTGTT-T-A
1 TTTTTATAA
43891671 TTTTTATAA
1 TTTTTATAA
*
43891680 TTTTTTATGA
1 -TTTTTATAA
*
43891690 TTTTTATTAC
1 TTTTTA-TAA
*
43891700 TTTTCTACAAA
1 TTTT-TA-TAA
*
43891711 TTTTTAAAA
1 TTTTTATAA
43891720 GTTTTTA-AA
1 -TTTTTATAA
43891729 --TTT-T-A
1 TTTTTATAA
*
43891734 -TTTTACAA
1 TTTTTATAA
43891742 TTTTTAT-A
1 TTTTTATAA
43891750 TATTTTATAA
1 T-TTTTATAA
43891760 TTTTT
1 TTTTT
43891765 TAAATAATTA
Statistics
Matches: 118, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
5 1 0.01
6 6 0.05
7 13 0.11
8 13 0.11
9 43 0.36
10 28 0.24
11 14 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43891686 original size:10 final size:10
Alignment explanation
Indices: 43891671--43891766 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
43891661 ATATTGTTTA
43891671 TTTTTATAAT
1 TTTTTATAAT
*
43891681 TTTTTATGA-
1 TTTTTATAAT
*
43891690 TTTTTATTACT
1 TTTTTA-TAAT
* * *
43891701 TTTCTACAAA
1 TTTTTATAAT
* *
43891711 TTTTTAAAAG
1 TTTTTATAAT
43891721 TTTTTA-AAT
1 TTTTTATAAT
* *
43891730 TTTATTTTACAA
1 TTT-TTATA-AT
43891742 TTTTTAT-AT
1 TTTTTATAAT
*
43891751 ATTTTATAAT
1 TTTTTATAAT
43891761 TTTTTA
1 TTTTTA
43891767 AATAATTATT
Statistics
Matches: 63, Mismatches: 17, Indels: 12
0.68 0.18 0.13
Matches are distributed among these distances:
9 18 0.29
10 32 0.51
11 9 0.14
12 4 0.06
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:43891754 original size:23 final size:22
Alignment explanation
Indices: 43891712--43891757 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
43891702 TTCTACAAAT
43891712 TTTTAAAAGTTTTTAAATTTTA
1 TTTTAAAAGTTTTTAAATTTTA
*
43891734 TTTTACAA-TTTTTATATATTTTA
1 TTTTAAAAGTTTTTA-A-ATTTTA
43891757 T
1 T
43891758 AATTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 8 0.38
23 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTAAAAGTTTTTAAATTTTA
Found at i:43894552 original size:42 final size:41
Alignment explanation
Indices: 43894503--43894596 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
43894493 GCTGGTGTGA
*
43894503 TATATCAGGCTAAAAGCCTAGCAGGCGTAGTGCCGGTGAATT
1 TATATCAGGCT-AAAGCCTAGCAGGCGTAGAGCCGGTGAATT
* *
43894545 TATATCAGACTAAAGCCTAGCAGGCGTAGAGCTGGTGAATT
1 TATATCAGGCTAAAGCCTAGCAGGCGTAGAGCCGGTGAATT
*
43894586 TTTATCAGGCT
1 TATATCAGGCT
43894597 TATGCCAAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 37 0.79
42 10 0.21
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (41 bp):
TATATCAGGCTAAAGCCTAGCAGGCGTAGAGCCGGTGAATT
Found at i:43898390 original size:46 final size:46
Alignment explanation
Indices: 43898333--43898437 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 46
43898323 CACTAGCAGG
* **
43898333 AAGCCTACTAGGCACAAGGCTCAATACATTACAATACACTGGCATA
1 AAGCCTACTAGGCACAAGGATCAATACATTACAATACACCAGCATA
* ** * *
43898379 AAGCCTTCTAGGCACAAGGATTGATACATTATAGTACACCAGCATA
1 AAGCCTACTAGGCACAAGGATCAATACATTACAATACACCAGCATA
*
43898425 AAGCCTGCTAGGC
1 AAGCCTACTAGGC
43898438 TCAAAGCCCG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (46 bp):
AAGCCTACTAGGCACAAGGATCAATACATTACAATACACCAGCATA
Found at i:43908667 original size:25 final size:25
Alignment explanation
Indices: 43908620--43908686 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
43908610 TACCAATTTT
* **
43908620 AGCTCTTATGAGCTTACTGATACTC
1 AGCTCGTATGAGCTTACCAATACTC
*
43908645 AGCTCGTATGAGCTTACCAATACTT
1 AGCTCGTATGAGCTTACCAATACTC
* * *
43908670 ATCTTGTATGATCTTAC
1 AGCTCGTATGAGCTTAC
43908687 TGCTATTCAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCAATACTC
Found at i:43910661 original size:16 final size:16
Alignment explanation
Indices: 43910626--43910666 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
43910616 CCCGCATAAA
43910626 CAAA-AAATATAAAAC
1 CAAATAAATATAAAAC
43910641 CAAATAAAT-TAAAAC
1 CAAATAAATATAAAAC
43910656 CAAAATAAATA
1 C-AAATAAATA
43910667 AAGTCCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (16 bp):
CAAATAAATATAAAAC
Found at i:43910668 original size:15 final size:14
Alignment explanation
Indices: 43910634--43910668 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
43910624 AACAAAAAAT
43910634 ATAAAACCAAATAA
1 ATAAAACCAAATAA
43910648 ATTAAAACCAAAATAA
1 A-TAAAACC-AAATAA
43910664 ATAAA
1 ATAAA
43910669 GTCCAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 11 0.58
16 7 0.37
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (14 bp):
ATAAAACCAAATAA
Found at i:43911841 original size:23 final size:22
Alignment explanation
Indices: 43911810--43911853 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
43911800 TCATTTTTTA
43911810 ATTTATTTA-AGTATTTATATTTC
1 ATTTATTTATA-TATTTA-ATTTC
*
43911833 ATTTTTTTATATATTTAATTT
1 ATTTATTTATATATTTAATTT
43911854 TTAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTATTTATATATTTAATTTC
Found at i:43911947 original size:24 final size:24
Alignment explanation
Indices: 43911915--43911975 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
43911905 ATTAATATTG
* *
43911915 TTTAAATTTATCGTATATTATTAT
1 TTTAAATTTATCATATATAATTAT
43911939 TTTAAATTTATCATATATAATTAT
1 TTTAAATTTATCATATATAATTAT
*
43911963 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
43911976 GCATTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 4 0.12
24 30 0.88
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (24 bp):
TTTAAATTTATCATATATAATTAT
Found at i:43911984 original size:23 final size:24
Alignment explanation
Indices: 43911915--43911995 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
43911905 ATTAATATTG
* *
43911915 TTTAAATTTATCGTATATTATTAT
1 TTTAAATTTATCATACATTATTAT
* *
43911939 TTTAAATTTATCATATATAATTAT
1 TTTAAATTTATCATACATTATTAT
* *
43911963 TTTAAGTTT-TCATGCATTATTA-
1 TTTAAATTTATCATACATTATTAT
*
43911985 TTCAAATTTAT
1 TTTAAATTTAT
43911996 TATGTATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 7 0.15
23 11 0.23
24 30 0.62
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTAAATTTATCATACATTATTAT
Found at i:43913585 original size:37 final size:37
Alignment explanation
Indices: 43913530--43913639 Score: 211
Period size: 37 Copynumber: 3.0 Consensus size: 37
43913520 AGTGAAATGA
*
43913530 CATAATTCAATATGGTATGACATAGCTAAGTTGAAGG
1 CATACTTCAATATGGTATGACATAGCTAAGTTGAAGG
43913567 CATACTTCAATATGGTATGACATAGCTAAGTTGAAGG
1 CATACTTCAATATGGTATGACATAGCTAAGTTGAAGG
43913604 CATACTTCAATATGGTATGACATAGCTAAGTTGAAG
1 CATACTTCAATATGGTATGACATAGCTAAGTTGAAG
43913640 TATGCATTGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (37 bp):
CATACTTCAATATGGTATGACATAGCTAAGTTGAAGG
Found at i:43914402 original size:19 final size:19
Alignment explanation
Indices: 43914378--43914416 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
43914368 TACATTATCG
43914378 CTATGCATTCCTACAATCA
1 CTATGCATTCCTACAATCA
43914397 CTATGCATTCCTACAATCA
1 CTATGCATTCCTACAATCA
43914416 C
1 C
43914417 CATGTATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (19 bp):
CTATGCATTCCTACAATCA
Found at i:43914449 original size:3 final size:3
Alignment explanation
Indices: 43914441--43914509 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
43914431 ATCATTAGTT
43914441 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
43914489 AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA
43914510 CAACAACACT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43915809 original size:10 final size:10
Alignment explanation
Indices: 43915796--43915821 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
43915786 AATAATAAAA
43915796 AAAGTTCTTT
1 AAAGTTCTTT
43915806 AAAGTTCTTT
1 AAAGTTCTTT
43915816 AAAGTT
1 AAAGTT
43915822 TTTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (10 bp):
AAAGTTCTTT
Found at i:43920526 original size:27 final size:27
Alignment explanation
Indices: 43920458--43920526 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
43920448 TTACGAAGTT
* * * *
43920458 TGCCAAAAAGGCATTCCTTTCATATTT
1 TGCCATAAAGGCGTTCCTTCCATATTG
**
43920485 TGCCATAAATACGTTCCTTCCATATTG
1 TGCCATAAAGGCGTTCCTTCCATATTG
43920512 TGCCATAAAGGCGTT
1 TGCCATAAAGGCGTT
43920527 AATCAGGCCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (27 bp):
TGCCATAAAGGCGTTCCTTCCATATTG
Found at i:43923034 original size:22 final size:21
Alignment explanation
Indices: 43922988--43923043 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
43922978 AAAAATAATA
* *
43922988 TTATTTTAATAGATTTAATAT
1 TTATTTTAATAGATTTAAAAC
43923009 TTATTTTAATTTA-ATTTAAAAC
1 TTATTTTAA--TAGATTTAAAAC
*
43923031 TTATCTT-ATAGAT
1 TTATTTTAATAGAT
43923044 AAATATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 10 0.34
22 13 0.45
23 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
TTATTTTAATAGATTTAAAAC
Found at i:43926314 original size:37 final size:37
Alignment explanation
Indices: 43926264--43926334 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
43926254 CATGACAATA
* *
43926264 GCTCATAAGAGCTAATCCACCCGATAACACGCCAGAT
1 GCTCATAAGAGCTAATCCAACCGAAAACACGCCAGAT
43926301 GCTCATAAGAGCTAATCCAACCGAAAACACGCCA
1 GCTCATAAGAGCTAATCCAACCGAAAACACGCCA
43926335 AAACAAGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.32, G:0.15, T:0.14
Consensus pattern (37 bp):
GCTCATAAGAGCTAATCCAACCGAAAACACGCCAGAT
Found at i:43934379 original size:22 final size:22
Alignment explanation
Indices: 43934351--43934393 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43934341 ATAATAGGAC
43934351 ATTCAATATAAC-ATTTCAATAA
1 ATTCAATATAACTA-TTCAATAA
*
43934373 ATTCAATCTAACTATTCAATA
1 ATTCAATATAACTATTCAATA
43934394 TTCATTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTCAATATAACTATTCAATAA
Found at i:43935590 original size:14 final size:14
Alignment explanation
Indices: 43935552--43935591 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
43935542 TTTGTTTTTC
43935552 TTTT-ACTT-TAACA
1 TTTTAACTTATAA-A
43935565 TTTTAA-TTATAAA
1 TTTTAACTTATAAA
43935578 TTTTAACTTATAAA
1 TTTTAACTTATAAA
43935592 ATCACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAACTTATAAA
Found at i:43941030 original size:16 final size:17
Alignment explanation
Indices: 43941004--43941037 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43940994 AGAAATTTTT
*
43941004 TTATCAAAAATATAAAA
1 TTATCAAAAATAAAAAA
43941021 TTAT-AAAAATAAAAAA
1 TTATCAAAAATAAAAAA
43941037 T
1 T
43941038 ACTTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TTATCAAAAATAAAAAA
Found at i:43941245 original size:16 final size:18
Alignment explanation
Indices: 43941226--43941262 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43941216 TTTGAGAAAA
43941226 AAATT-CTA-TCAATTAT
1 AAATTCCTATTCAATTAT
*
43941242 AAATTCCTATTGAATTAT
1 AAATTCCTATTCAATTAT
43941260 AAA
1 AAA
43941263 ACAATTATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 10 0.56
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATTCCTATTCAATTAT
Found at i:43945112 original size:29 final size:28
Alignment explanation
Indices: 43945079--43945134 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
43945069 TTAAGGGGTC
* *
43945079 AAAATTAAATTATATCTTTTATAATAGTA
1 AAAATAAAATTATATCATTT-TAATAGTA
*
43945108 AAAATAAAATTTTATCATTTTAATAGT
1 AAAATAAAATTATATCATTTTAATAGT
43945135 CTATATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (28 bp):
AAAATAAAATTATATCATTTTAATAGTA
Found at i:43955794 original size:23 final size:20
Alignment explanation
Indices: 43955767--43955820 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
43955757 TTCTAAGTCG
43955767 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT--ACA-CT
43955790 ATATTCATTATTCAATTACACT
1 ATATTCA--ATTCAATTACACT
43955812 -TATTCAATT
1 ATATTCAATT
43955821 TCCCGATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
21 6 0.21
22 2 0.07
23 10 0.34
25 8 0.28
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTCAATTCAATTACACT
Found at i:43955934 original size:44 final size:45
Alignment explanation
Indices: 43955857--43955944 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 45
43955847 CAGATACTCA
* *
43955857 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTTCG
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCG
43955902 GTGGAATCAGCACATA-CAACCACCTTACTAATCAATGATGTTC
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTC
43955945 AGTTCACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 26 0.63
45 15 0.37
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCG
Found at i:43956011 original size:51 final size:50
Alignment explanation
Indices: 43955953--43956135 Score: 188
Period size: 51 Copynumber: 3.6 Consensus size: 50
43955943 TCAGTTCACA
* * * *
43955953 TAGTAGCCTGCACATAGCACTACAAATGTGATCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGATCA-TACCATCCGGTACACG
* * * * ** *
43956004 TAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGATC-ATACCATCCGGTACACG
* * * *
43956055 TAGTAGCCTGCACATAGTACTACACATGCGA-CCTATCATTCCGGTACAGG
1 TAGTAGCCTGCACATAGTACTACACATGTGATCATACCA-TCCGGTACACG
*
43956105 TAGTAGCCTGCACATAGTACTACACACGTGA
1 TAGTAGCCTGCACATAGTACTACACATGTGA
43956136 CCATCACTTT
Statistics
Matches: 106, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 37 0.35
51 66 0.62
52 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGATCATACCATCCGGTACACG
Found at i:43956129 original size:101 final size:102
Alignment explanation
Indices: 43955951--43956135 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
43955941 GTTCAGTTCA
* * *
43955951 CATAGTAGCCTGCACATAGCACTACAAATGTGATCATTACCATCTGATACACGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGCACTACAAATGCGATCACTACCATCCGATACACGTAGTAGCCTACA
43956016 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* * * * * *
43956053 CATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTCCGGTACAGGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGCACTACAAATGCGATCACTACCA-TCCGATACACGTAGTAGCCTAC
43956116 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
43956136 CCATCACTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.53
102 30 0.41
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGCACTACAAATGCGATCACTACCATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:43957743 original size:455 final size:455
Alignment explanation
Indices: 43956885--43957797 Score: 1648
Period size: 455 Copynumber: 2.0 Consensus size: 455
43956875 TAAATTCTTT
*
43956885 TTAATATCTAAATGACCAAAATGCCCTTAATGAAAAACTTTGGAAACATGCCTAACCATACCCAT
1 TTAATAACTAAATGACCAAAATGCCCTTAATGAAAAACTTTGGAAACATGCCTAACCATACCCAT
**
43956950 TTTTCTCCAAAAACTTAACCAATGGTCTAATTACCATATAAAGACCTGGAATTTAAAATTTCATA
66 TTTTCTCCAAAAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAATTTAAAATTTCATA
43957015 ACAATTGGACACCTCTAACATATAGAACTCAACTTTTGAAATTTTTACAATTTAGTCCTTTTGAC
131 ACAATTGGACACCTCTAACATATAGAACTCAACTTTTGAAATTTTTACAATTTAGTCCTTTTGAC
*
43957080 TAAATTGAGTGCCCAAACGTCAAAATTTTCGAACGAAATTTTCACGAAATCATTTTTTGAAATCG
196 TAAATTGAGTGCCCAAACGTCAAAATTTTCGAACGAAATTTTCACGAAATCATTTTGTGAAATCG
*
43957145 TAAACCATAAAAATATAATGAAAATAATTTTTTTTCTCATCAAATTTGTGGTCCAGAAACCACTA
261 TAAACCATAAAAATATAATGAAAATAAATTTTTTTCTCATCAAATTTGTGGTCCAGAAACCACTA
*
43957210 TTCCGACTAGCCCCAAATTCGGGCTATTACAGATTATGGTTCAGACGATGCTCTGGATCCAGAAT
326 TTCCGACTAGCCCCAAATTCGGGCTATTACAGATTATGGTTCAGACGATACTCTGGATCCAGAAT
* *
43957275 CACGATTCAAGGCATATGAACCTCCACCCCACATGCATAACATTGACCTCTTCGCTAAGGGTGGG
391 CACGATTCAAGGCATATGAACCTCCACCCCACATGCATAACATCGACCTCTTCGCTAAGGGTAGG
43957340 TTAATAACTAAATGACCAAAATGCCCTTAATGAAAAACTTTGGAAACATGCCTAACCATACCCAT
1 TTAATAACTAAATGACCAAAATGCCCTTAATGAAAAACTTTGGAAACATGCCTAACCATACCCAT
*
43957405 TTTTCTCCACAAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAATTTAAAATTTCATA
66 TTTTCTCCAAAAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAATTTAAAATTTCATA
* * *
43957470 ACAATTGGACACCTCTAACATATAGAACTCAACTTTTGCACTTTTTACAATTTAGTTCTTTTGAC
131 ACAATTGGACACCTCTAACATATAGAACTCAACTTTTGAAATTTTTACAATTTAGTCCTTTTGAC
*
43957535 TAAATTTAGTGCCCAAACGTCAAAATTTT-GAACGAAATTTTCACGAAATCATTTTGTGAAATCG
196 TAAATTGAGTGCCCAAACGTCAAAATTTTCGAACGAAATTTTCACGAAATCATTTTGTGAAATCG
* * *
43957599 TAAACTATAAAAAATATAATGAAAATAAATTTTTTTCTCATCGAATTTGTGGTCCCGAAACCACT
261 TAAACCAT-AAAAATATAATGAAAATAAATTTTTTTCTCATCAAATTTGTGGTCCAGAAACCACT
* *
43957664 ATTTCGACTAGCCCCAAATTTGGGCTATTACAGATTATGGTTCAGACGATACTCTGGATCCAGAA
325 ATTCCGACTAGCCCCAAATTCGGGCTATTACAGATTATGGTTCAGACGATACTCTGGATCCAGAA
43957729 TCACGATTCAAGGCATATGAACCTCCACCCCACATGCATAACATCGACCTCTTCGCTAAGGGTAG
390 TCACGATTCAAGGCATATGAACCTCCACCCCACATGCATAACATCGACCTCTTCGCTAAGGGTAG
43957794 G
455 G
43957795 TTA
1 TTA
43957798 GTGTTTCCGT
Statistics
Matches: 439, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
454 41 0.09
455 398 0.91
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (455 bp):
TTAATAACTAAATGACCAAAATGCCCTTAATGAAAAACTTTGGAAACATGCCTAACCATACCCAT
TTTTCTCCAAAAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAATTTAAAATTTCATA
ACAATTGGACACCTCTAACATATAGAACTCAACTTTTGAAATTTTTACAATTTAGTCCTTTTGAC
TAAATTGAGTGCCCAAACGTCAAAATTTTCGAACGAAATTTTCACGAAATCATTTTGTGAAATCG
TAAACCATAAAAATATAATGAAAATAAATTTTTTTCTCATCAAATTTGTGGTCCAGAAACCACTA
TTCCGACTAGCCCCAAATTCGGGCTATTACAGATTATGGTTCAGACGATACTCTGGATCCAGAAT
CACGATTCAAGGCATATGAACCTCCACCCCACATGCATAACATCGACCTCTTCGCTAAGGGTAGG
Found at i:43958719 original size:57 final size:57
Alignment explanation
Indices: 43958650--43958764 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
43958640 ATTCTACTGG
43958650 TACTTTACAATAACTCAAGGAGAAAAGGTAGATGATTGGGATTTCTTCCTTAGTTGT
1 TACTTTACAATAACTCAAGGAGAAAAGGTAGATGATTGGGATTTCTTCCTTAGTTGT
43958707 TACTTTACAATAACTCAAGGAGAAAAGGTAGATGATTGGGATTTCTTCCTTAGTTGT
1 TACTTTACAATAACTCAAGGAGAAAAGGTAGATGATTGGGATTTCTTCCTTAGTTGT
43958764 T
1 T
43958765 TGTGTCATCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (57 bp):
TACTTTACAATAACTCAAGGAGAAAAGGTAGATGATTGGGATTTCTTCCTTAGTTGT
Found at i:43960365 original size:22 final size:24
Alignment explanation
Indices: 43960310--43960366 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
43960300 GTCTATATCT
*
43960310 TCTTCATCTTCACCTTGACCCCCCG
1 TCTTCATCTTCA-CTCGACCCCCCG
* *
43960335 TATTCATCTTCA-TCGA-CCCTCG
1 TCTTCATCTTCACTCGACCCCCCG
43960357 TCTTCATCTT
1 TCTTCATCTT
43960367 TATCTCCACC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 14 0.50
23 3 0.11
25 11 0.39
ACGTcount: A:0.14, C:0.40, G:0.07, T:0.39
Consensus pattern (24 bp):
TCTTCATCTTCACTCGACCCCCCG
Found at i:43967728 original size:61 final size:61
Alignment explanation
Indices: 43967633--43967816 Score: 305
Period size: 61 Copynumber: 3.0 Consensus size: 61
43967623 GGAAGTGTAC
* * *
43967633 TGGTTAAGTGATCCTTAACTATCCTTTAAGTCTCTAGTTCGAACCCTTATATGCCTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
*
43967694 TGGTTAAGTGCTCCTTAACAATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
* * *
43967755 TGGTTAAATGCTCTTTAACTATCTTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
43967816 T
1 T
43967817 TTTATTTAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 115 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (61 bp):
TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
Found at i:43978547 original size:45 final size:45
Alignment explanation
Indices: 43978470--43978723 Score: 309
Period size: 45 Copynumber: 5.7 Consensus size: 45
43978460 CATCTTACAG
* * *
43978470 AGCATCTTACAGCTACAG-TCTTACTCATTTTTATCATGACGCCAT
1 AGCATCTTTCAGCTA-TGTTCTTACTCATTTTTATCATGACACCAT
* * * *
43978515 AGCATATTTCAGCTATGTTCTTGCTCACTTTTATCATGACGCCAT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
* *
43978560 AGCATCTTTCAGCTATGGTCTTACTAATTTTTATCATGACACCAT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
* * * * *
43978605 AGCAT-ATTCAACTATGGTT-TTGCTCACTTTTATCATGACACCGT
1 AGCATCTTTCAGCTAT-GTTCTTACTCATTTTTATCATGACACCAT
* *
43978649 AGCATCTTTCAGCTATGGTCTTACTTATTTTTATCATGACACCAT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
*
43978694 AGCATCTTTCAGCTATG-TCTTAATCATTTT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTT
43978724 AGGCTTATAA
Statistics
Matches: 178, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
44 48 0.27
45 130 0.73
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (45 bp):
AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
Found at i:43978662 original size:89 final size:90
Alignment explanation
Indices: 43978470--43978711 Score: 362
Period size: 89 Copynumber: 2.7 Consensus size: 90
43978460 CATCTTACAG
* ** * * *
43978470 AGCATCTTACAGCTACAGTCTTACTCATTTTTATCATGACGCCATAGCATATTTCAGCTATGTTC
1 AGCATCTTTCAGCTATGGTCTTACTAATTTTTATCATGACACCATAGCATATTTCAACTATGTTC
*
43978535 TTGCTCACTTTTATCATGACGCCAT
66 TTGCTCACTTTTATCATGACACCAT
43978560 AGCATCTTTCAGCTATGGTCTTACTAATTTTTATCATGACACCATAGCATA-TTCAACTATGGTT
1 AGCATCTTTCAGCTATGGTCTTACTAATTTTTATCATGACACCATAGCATATTTCAACTAT-GTT
*
43978624 -TTGCTCACTTTTATCATGACACCGT
65 CTTGCTCACTTTTATCATGACACCAT
* * *
43978649 AGCATCTTTCAGCTATGGTCTTACTTATTTTTATCATGACACCATAGCATCTTTCAGCTATGT
1 AGCATCTTTCAGCTATGGTCTTACTAATTTTTATCATGACACCATAGCATATTTCAACTATGT
43978712 CTTAATCATT
Statistics
Matches: 139, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
89 82 0.59
90 57 0.41
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (90 bp):
AGCATCTTTCAGCTATGGTCTTACTAATTTTTATCATGACACCATAGCATATTTCAACTATGTTC
TTGCTCACTTTTATCATGACACCAT
Found at i:43979617 original size:8 final size:8
Alignment explanation
Indices: 43979606--43979652 Score: 76
Period size: 8 Copynumber: 5.9 Consensus size: 8
43979596 TCTCTCTCTC
*
43979606 TATATATA
1 TATATATT
43979614 TATATATT
1 TATATATT
*
43979622 TATTTATT
1 TATATATT
43979630 TATATATT
1 TATATATT
43979638 TATATATT
1 TATATATT
43979646 TATATAT
1 TATATAT
43979653 CTGAGCAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:43982316 original size:17 final size:15
Alignment explanation
Indices: 43982294--43982327 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
43982284 GAGGGCAACG
43982294 GGTGAGGGAGAGAGGGA
1 GGTGAGGGA-A-AGGGA
43982311 GGTGAGGGAAAGGGA
1 GGTGAGGGAAAGGGA
43982326 GG
1 GG
43982328 GGGACTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.65, T:0.06
Consensus pattern (15 bp):
GGTGAGGGAAAGGGA
Found at i:43985678 original size:24 final size:24
Alignment explanation
Indices: 43985651--43985697 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
43985641 TAAGAACATG
43985651 ACAACACCAAAGTACATAATCAAA
1 ACAACACCAAAGTACATAATCAAA
** *
43985675 ACAACACGGAAGTGCATAATCAA
1 ACAACACCAAAGTACATAATCAA
43985698 GATAGCACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
ACAACACCAAAGTACATAATCAAA
Found at i:43990302 original size:37 final size:37
Alignment explanation
Indices: 43990252--43990327 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
43990242 GAATCCGTTT
*
43990252 GTGCATTAATTCACTTGTAACGTTCATGGTATGTTGG
1 GTGCATTAATTCACTTCTAACGTTCATGGTATGTTGG
* *
43990289 GTGCATTAATTCACTTCTGACGTTCATGGTATTTTGG
1 GTGCATTAATTCACTTCTAACGTTCATGGTATGTTGG
43990326 GT
1 GT
43990328 ACCTAAATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (37 bp):
GTGCATTAATTCACTTCTAACGTTCATGGTATGTTGG
Found at i:43992146 original size:40 final size:41
Alignment explanation
Indices: 43992093--43992196 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 41
43992083 AACACACCAG
* * * *
43992093 ATTGGCACCCAGTGCCTCATCGGAT-AATTCAAAGTATTAA
1 ATTGACACCCAGTGCCTCATCGAATAAATCCAAAGTAATAA
* *
43992133 ATTGACACTCAGTGCCTCATCGAATAAATCCGAAGTAATAA
1 ATTGACACCCAGTGCCTCATCGAATAAATCCAAAGTAATAA
* * *
43992174 ATTGAGACCCAATGGCTCATCGA
1 ATTGACACCCAGTGCCTCATCGA
43992197 CTCAAAGTCG
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 22 0.42
41 31 0.58
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (41 bp):
ATTGACACCCAGTGCCTCATCGAATAAATCCAAAGTAATAA
Found at i:43997202 original size:22 final size:22
Alignment explanation
Indices: 43997175--43997220 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
43997165 GAGATCAACA
43997175 AAAATA-TAAACACATACATATC
1 AAAATATTAAACACAT-CATATC
* *
43997197 AAAATATTAATCTCATCATATC
1 AAAATATTAAACACATCATATC
43997219 AA
1 AA
43997221 TCATCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATATTAAACACATCATATC
Found at i:44000187 original size:25 final size:26
Alignment explanation
Indices: 44000142--44000193 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
44000132 TTTAATACAT
*
44000142 ATATTAATAGTATTTTATTAAT-TTA
1 ATATTAATAGTATTATATTAATATTA
*
44000167 ATATTAA-AGTGATTATCTTAATATTA
1 ATATTAATAGT-ATTATATTAATATTA
44000193 A
1 A
44000194 ATTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 16 0.70
26 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (26 bp):
ATATTAATAGTATTATATTAATATTA
Found at i:44001855 original size:33 final size:35
Alignment explanation
Indices: 44001818--44001894 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
44001808 TTTAATATGA
* *
44001818 AATTTAGTTTAATACTTAT-T-ATAGAATTTTATT
1 AATTTAATTTAATAATTATCTGATAGAATTTTATT
*
44001851 AATTTAATTTAATAATTATCGTGATAGTATTTTATT
1 AATTTAATTTAATAATTATC-TGATAGAATTTTATT
44001887 AATTTAAT
1 AATTTAAT
44001895 ATTAGAGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 17 0.45
35 1 0.03
36 20 0.53
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (35 bp):
AATTTAATTTAATAATTATCTGATAGAATTTTATT
Found at i:44001907 original size:20 final size:18
Alignment explanation
Indices: 44001882--44001934 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
44001872 TGATAGTATT
44001882 TTATTAATTTAATATTAGA
1 TTATTAATTTAATATTA-A
44001901 GTTATT-ATCTTAATATTAA
1 -TTATTAAT-TTAATATTAA
*
44001920 AT-TTAATTTAATATT
1 TTATTAATTTAATATT
44001935 TATCTTATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.33
18 3 0.10
19 3 0.10
20 14 0.47
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TTATTAATTTAATATTAA
Found at i:44011847 original size:14 final size:15
Alignment explanation
Indices: 44011816--44011863 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
44011806 ATTTGAGTAA
44011816 AAATAAAAACATTTATTT
1 AAATAAAAACA---ATTT
44011834 AAATAAAAAC-ATTT
1 AAATAAAAACAATTT
*
44011848 GAATAAAAACAATTT
1 AAATAAAAACAATTT
44011863 A
1 A
44011864 CAAAGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 13 0.48
15 4 0.15
18 10 0.37
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (15 bp):
AAATAAAAACAATTT
Found at i:44015273 original size:17 final size:17
Alignment explanation
Indices: 44015251--44015284 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44015241 TTAATCAAGG
44015251 AATTAAGAGATCAAAGA
1 AATTAAGAGATCAAAGA
44015268 AATTAAGAGATCAAAGA
1 AATTAAGAGATCAAAGA
44015285 TCGAGGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
AATTAAGAGATCAAAGA
Found at i:44017796 original size:6 final size:6
Alignment explanation
Indices: 44017785--44017824 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
44017775 CCAAAAGGAC
* *
44017785 TTTTTA TTTTTA TTTTTA TTTGTAA TTTTTA ATTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTT
44017825 GTAATCAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:44017814 original size:19 final size:19
Alignment explanation
Indices: 44017790--44017829 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
44017780 AGGACTTTTT
*
44017790 ATTTTTATTTTTATTTGTA
1 ATTTTTAATTTTATTTGTA
44017809 ATTTTTAATTTTATTTGTA
1 ATTTTTAATTTTATTTGTA
44017828 AT
1 AT
44017830 CAGAAGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
ATTTTTAATTTTATTTGTA
Found at i:44025592 original size:9 final size:9
Alignment explanation
Indices: 44025581--44025674 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
44025571 TTTGGTTAAA
*
44025581 AATTAACCA
1 AATTAACCG
44025590 AATTAACCG
1 AATTAACCG
*
44025599 AATTAACTG
1 AATTAACCG
*
44025608 AATTACCCG
1 AATTAACCG
44025617 AATTAACCG
1 AATTAACCG
*
44025626 AATTACCCG
1 AATTAACCG
44025635 AATTAACCG
1 AATTAACCG
*
44025644 AATTATCCG
1 AATTAACCG
*
44025653 AATTAACTG
1 AATTAACCG
*
44025662 AATTAACCA
1 AATTAACCG
44025671 AATT
1 AATT
44025675 GAATCACTAC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 73 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:44027019 original size:26 final size:26
Alignment explanation
Indices: 44026989--44027040 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
44026979 GTTAAATGGC
44026989 TATGGAAATGTAAATTAATGGACTTA
1 TATGGAAATGTAAATTAATGGACTTA
44027015 TATGGAAATGTAAATTAATGGACTTA
1 TATGGAAATGTAAATTAATGGACTTA
44027041 AACAGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (26 bp):
TATGGAAATGTAAATTAATGGACTTA
Found at i:44033805 original size:22 final size:22
Alignment explanation
Indices: 44033771--44033813 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
44033761 TTTTCACTCA
44033771 AATTATTAATAT-ATCAAATTTT
1 AATTATTAATATAAT-AAATTTT
**
44033793 AATTATTTTTATAATAAATTT
1 AATTATTAATATAATAAATTT
44033814 ACATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTATTAATATAATAAATTTT
Found at i:44038628 original size:20 final size:20
Alignment explanation
Indices: 44038603--44038646 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
44038593 ACACACGCTT
*
44038603 TCTCCCTCCTTCTCTCTCTC
1 TCTCCCTCCCTCTCTCTCTC
* *
44038623 TCTCCCTCCCTCTTTCTTTC
1 TCTCCCTCCCTCTCTCTCTC
44038643 TCTC
1 TCTC
44038647 TCTTATCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (20 bp):
TCTCCCTCCCTCTCTCTCTC
Found at i:44038631 original size:24 final size:24
Alignment explanation
Indices: 44038604--44038649 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
44038594 CACACGCTTT
44038604 CTCCCTCCTTCTCTCTCTCTCTCC
1 CTCCCTCCTTCTCTCTCTCTCTCC
* *
44038628 CTCCCTCTTTCTTTCTCTCTCT
1 CTCCCTCCTTCTCTCTCTCTCT
44038650 TATCTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (24 bp):
CTCCCTCCTTCTCTCTCTCTCTCC
Found at i:44062007 original size:42 final size:42
Alignment explanation
Indices: 44061961--44062051 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
44061951 GGAAGTTCGT
* * *
44061961 AAGAGCTGAATGGAAACTAATAAGGGTTAAACAGAAGCACAA
1 AAGAGCTGAACGAAAACTAATAAGAGTTAAACAGAAGCACAA
* * * *
44062003 AAGAGCTGAACGAAAACTCATATGAGTTAAACAGAAGCTCGA
1 AAGAGCTGAACGAAAACTAATAAGAGTTAAACAGAAGCACAA
44062045 AAGAGCT
1 AAGAGCT
44062052 AAAAAGAAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.15
Consensus pattern (42 bp):
AAGAGCTGAACGAAAACTAATAAGAGTTAAACAGAAGCACAA
Found at i:44064273 original size:19 final size:19
Alignment explanation
Indices: 44064249--44064287 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
44064239 TTCAAACATA
44064249 TTAATATACATAATTTAGT
1 TTAATATACATAATTTAGT
44064268 TTAATATACATAATTTAGT
1 TTAATATACATAATTTAGT
44064287 T
1 T
44064288 ACACGAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
TTAATATACATAATTTAGT
Found at i:44066622 original size:21 final size:21
Alignment explanation
Indices: 44066596--44066652 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
44066586 GGTGGATCAA
*
44066596 CTCTTATGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
44066617 CTCTTACGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
44066638 CTCTTACGAGCTTCT
1 CTCTTACGAGCTTCT
44066653 ATTTATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTCAG
Found at i:44072768 original size:21 final size:21
Alignment explanation
Indices: 44072724--44072787 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
44072714 ATTGGGTGGA
** * *
44072724 TCAGCTCTTACAAGTTTCTAT
1 TCAGCTCTTATGAGCTTCTGT
*
44072745 TCAGCTCTTATGAGCTTTTGT
1 TCAGCTCTTATGAGCTTCTGT
44072766 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
44072787 T
1 T
44072788 GACGAAGTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:44074419 original size:22 final size:23
Alignment explanation
Indices: 44074378--44074424 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
44074368 ATTGCTAAAA
*
44074378 TATAATATCTCATAATAATATCC
1 TATAATATCCCATAATAATATCC
44074401 TATAATATCCCA-AATAATATCC
1 TATAATATCCCATAATAATATCC
44074423 TA
1 TA
44074425 ACAGGGATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (23 bp):
TATAATATCCCATAATAATATCC
Found at i:44083631 original size:46 final size:44
Alignment explanation
Indices: 44083527--44083634 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
44083517 TGTCTTTGAC
** * * *
44083527 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
44083571 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
44083617 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
44083635 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:44084598 original size:5 final size:5
Alignment explanation
Indices: 44084585--44084657 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
44084575 TTGTTTTATG
44084585 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
44084633 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
44084658 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:44084610 original size:19 final size:19
Alignment explanation
Indices: 44084586--44084628 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
44084576 TGTTTTATGT
44084586 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
44084605 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
44084624 ATATA
1 ATATA
44084629 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:44084638 original size:24 final size:24
Alignment explanation
Indices: 44084592--44084656 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
44084582 ATGTATATAT
* * *
44084592 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
44084616 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
44084640 ATTACTATAATATAATA
1 A-TAATATAATATAATA
44084657 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 19 0.56
25 12 0.35
26 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:44087380 original size:11 final size:11
Alignment explanation
Indices: 44087364--44087392 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
44087354 TATTCGAATT
44087364 TCGAGTTCGAA
1 TCGAGTTCGAA
44087375 TCGAGTTCGAA
1 TCGAGTTCGAA
44087386 TCGAGTT
1 TCGAGTT
44087393 GAGTTTTCGA
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:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (11 bp):
TCGAGTTCGAA
Found at i:44087701 original size:31 final size:30
Alignment explanation
Indices: 44087642--44087701 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
44087632 CAACCTTTTA
*
44087642 TTTTCCCCCAAAATTTTTACTCTCTCCCAC
1 TTTTCCCCCAAAATTTTTACTCACTCCCAC
* * *
44087672 TTTTTCCCTAAAATTTTTATTCACTTCCCA
1 TTTTCCCCCAAAATTTTTACTCAC-TCCCA
44087702 TCCCACCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTTCCCCCAAAATTTTTACTCACTCCCAC
Found at i:44089459 original size:8 final size:8
Alignment explanation
Indices: 44089423--44089457 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
44089413 GATCCTCCAC
44089423 TTTCCCCA
1 TTTCCCCA
44089431 TTTCCCCA
1 TTTCCCCA
44089439 TTTCCCCA
1 TTTCCCCA
*
44089447 TTTTCCCA
1 TTTCCCCA
44089455 TTT
1 TTT
44089458 TCTTTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.11, C:0.43, G:0.00, T:0.46
Consensus pattern (8 bp):
TTTCCCCA
Found at i:44091571 original size:31 final size:31
Alignment explanation
Indices: 44091536--44091597 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
44091526 AATTAATTAG
44091536 TATTAAAT-GTTTTAACTTAAATCATTATATA
1 TATTAAATAGTTTTAA-TTAAATCATTATATA
* **
44091567 TATTAAATATTTTTAATTAAATTTTTATATA
1 TATTAAATAGTTTTAATTAAATCATTATATA
44091598 ATTTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (31 bp):
TATTAAATAGTTTTAATTAAATCATTATATA
Found at i:44091609 original size:29 final size:32
Alignment explanation
Indices: 44091536--44091610 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 32
44091526 AATTAATTAG
*
44091536 TATTAAAT-GTTTTAACTTAAATCATTATATA
1 TATTAAATAATTTTAACTTAAATCATTATATA
* **
44091567 TATTAAATATTTTTAA-TTAAATTTTTATATA
1 TATTAAATAATTTTAACTTAAATCATTATATA
*
44091598 -ATT-TATAATTTTA
1 TATTAAATAATTTTA
44091611 GTTTGCATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 8 0.21
30 3 0.08
31 21 0.55
32 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (32 bp):
TATTAAATAATTTTAACTTAAATCATTATATA
Found at i:44091779 original size:18 final size:18
Alignment explanation
Indices: 44091747--44091787 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
44091737 TTTAAAAATT
*
44091747 TAATTTTAAATAATTAAA
1 TAATATTAAATAATTAAA
44091765 -AATATTAATATAATTAAA
1 TAATATTAA-ATAATTAAA
44091783 TAATA
1 TAATA
44091788 CTTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATTAAATAATTAAA
Found at i:44091804 original size:26 final size:27
Alignment explanation
Indices: 44091775--44091825 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
44091765 AATATTAATA
44091775 TAATTAAATAATACTTA-TATTTTTGG
1 TAATTAAATAATACTTATTATTTTTGG
*
44091801 TAATTAAATAATATTTATTATTTTT
1 TAATTAAATAATACTTATTATTTTT
44091826 TATGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (27 bp):
TAATTAAATAATACTTATTATTTTTGG
Found at i:44091971 original size:21 final size:21
Alignment explanation
Indices: 44091947--44091988 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
44091937 TTTTTAAATT
44091947 TAAA-ATAAATATTAAAATTAA
1 TAAATATAAAT-TTAAAATTAA
* *
44091968 TAAATTTAAATTTAGAATTAA
1 TAAATATAAATTTAAAATTAA
44091989 AGAAAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAATATAAATTTAAAATTAA
Found at i:44092078 original size:18 final size:17
Alignment explanation
Indices: 44092025--44092078 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
44092015 TTACGGATTT
*
44092025 TTATTAAAATTAAAATA
1 TTATTAAAATTAAATTA
44092042 TTATTTAAAATTGAAATTA
1 TTA-TTAAAATT-AAATTA
44092061 TTATTAAAATTAATATTA
1 TTATTAAAATTAA-ATTA
44092079 AAATATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 5 0.15
18 20 0.61
19 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TTATTAAAATTAAATTA
Found at i:44094829 original size:22 final size:22
Alignment explanation
Indices: 44094803--44094861 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
44094793 ATAAATTATA
*
44094803 ATGTATATAAAAATATATAAGT
1 ATGTATATAAAAATATATAAAT
*
44094825 ATGTATA-AATATATATATAAAT
1 ATGTATATAA-AAATATATAAAT
*
44094847 AAGT-TATAAAAATAT
1 ATGTATATAAAAATAT
44094862 GTACGTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
ATGTATATAAAAATATATAAAT
Found at i:44094834 original size:18 final size:19
Alignment explanation
Indices: 44094790--44094839 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
44094780 TATCGTTATG
44094790 TATATAAAT-TATAATGTA
1 TATATAAATATATAATGTA
*
44094808 TATAAAAATATATAA-GTA
1 TATATAAATATATAATGTA
*
44094826 TGTATAAATATATA
1 TATATAAATATATA
44094840 TATAAATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TATATAAATATATAATGTA
Found at i:44098159 original size:20 final size:20
Alignment explanation
Indices: 44098123--44098160 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44098113 ATTTGGTTTA
*
44098123 TTTATTTTTATTTATTATTC
1 TTTATTTTTATTGATTATTC
44098143 TTTATTTTT-TGTGATTAT
1 TTTATTTTTAT-TGATTAT
44098161 ATTTTTAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATTGATTATTC
Found at i:44106467 original size:51 final size:51
Alignment explanation
Indices: 44106320--44106515 Score: 188
Period size: 51 Copynumber: 3.9 Consensus size: 51
44106310 AGTGAAAGTG
44106320 ATGGTCA-AGTGTGTAGTACTATGTGCAGGCTACTACGTGT-ACCGGA-A-TA
1 ATGGTCACA-TGTGTAGTACTATGTGCAGGCTACTACGT-TAACCGGATAGTA
* * * *
44106369 ATAGGTCGCATGTGTAGTACTATGTGTAGGCTACTATG-CATACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTTA-ACCGGATAGTA
* * * * * *
44106420 TTCGATCACGTGTGTAGTACTATGTACAGGCTACTACGTTAATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTTAACCGGATAGTA
* * *
44106472 ATGGTCACATGTGTAGCACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTTAACCG
44106516 AACATCATTG
Statistics
Matches: 116, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
49 2 0.02
50 36 0.31
51 75 0.65
52 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTTAACCGGATAGTA
Found at i:44106678 original size:38 final size:37
Alignment explanation
Indices: 44106636--44106708 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
44106626 AGTTGTGGAA
*
44106636 TTGAATTGAATAT-TGACTTAGAAA-TGGAAAAGTGAATT
1 TTGAATTGAAT-TGTGA-TT-GAAAGTGAAAAAGTGAATT
44106674 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
44106709 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAATT
Found at i:44111236 original size:4 final size:4
Alignment explanation
Indices: 44111227--44111276 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
44111217 TGATAGCTTC
44111227 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
44111275 AC
1 AC
44111277 GTTAGATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:44115998 original size:42 final size:42
Alignment explanation
Indices: 44115939--44116099 Score: 209
Period size: 42 Copynumber: 3.8 Consensus size: 42
44115929 TTACAGAAAT
44115939 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCAAAAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCAAAAA
* *
44115981 AAACGCCGCTAAAGGTCATGTTCTTTAACGACGCTTCAAAAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCAAAAA
* * ** *
44116023 AAATC-CCGTTAAAGGTCATGTTCTTTAGCGGCACTTTC-TCAG
1 AAA-CGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTCAAAAA
*
44116065 AAACGCCGCTAAAGGTAATGTTCTTTTAGCGGCGC
1 AAACGCCGCTAAAGGTCATGTTC-TTTAGCGGCGC
44116100 ATTTTCCACA
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 1 0.01
42 88 0.85
43 14 0.14
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCAAAAA
Found at i:44116127 original size:44 final size:42
Alignment explanation
Indices: 44115939--44116180 Score: 145
Period size: 42 Copynumber: 5.7 Consensus size: 42
44115929 TTACAGAAAT
* **** *
44115939 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTCAAAAA
1 AAACGCCGCTAAAGGTAATGTTCTTTAGCGG-GCATTTTCCAC
* * * **** *
44115981 AAACGCCGCTAAAGGTCATGTTCTTTAACGACGC-TTCAAAAA
1 AAACGCCGCTAAAGGTAATGTTCTTTAGCG-GGCATTTTCCAC
* * * *
44116023 AAATC-CCGTTAAAGGTCATGTTCTTTAGC-GGCACTTTCTCAG
1 AAA-CGCCGCTAAAGGTAATGTTCTTTAGCGGGCATTTTC-CAC
44116065 AAACGCCGCTAAAGGTAATGTTCTTTTAGCGGCGCATTTTCCAC
1 AAACGCCGCTAAAGGTAATGTTC-TTTAGCGG-GCATTTTCCAC
* **
44116109 AAACGCCGCTACAA-GTAATGTTCTTTAACGGTGTTTTTTTCCAC
1 AAACGCCGCTA-AAGGTAATGTTCTTTAGCGG-G-CATTTTCCAC
* * *
44116153 AAACGCCGCT-ATGGTCATGCTCTTTAGC
1 AAACGCCGCTAAAGGTAATGTTCTTTAGC
44116181 TTTTAGCGCC
Statistics
Matches: 166, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 85 0.51
43 27 0.16
44 41 0.25
45 9 0.05
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTAATGTTCTTTAGCGGGCATTTTCCAC
Found at i:44116604 original size:21 final size:21
Alignment explanation
Indices: 44116579--44116630 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
44116569 TTTCTTTTGA
*
44116579 ACCTCTGCTTCTCTCGCTG-C
1 ACCTCTGCTTCCCTCGCTGTC
44116599 AGCCTCTGCTTCCCTCGCTGTC
1 A-CCTCTGCTTCCCTCGCTGTC
44116621 ACCTCTGCTT
1 ACCTCTGCTT
44116631 TAAGTTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.06, C:0.44, G:0.15, T:0.35
Consensus pattern (21 bp):
ACCTCTGCTTCCCTCGCTGTC
Found at i:44119461 original size:12 final size:12
Alignment explanation
Indices: 44119444--44119490 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
44119434 ATGTATGTAA
44119444 ATTATGTAAGTT
1 ATTATGTAAGTT
44119456 ATTATGTAAG--
1 ATTATGTAAGTT
44119466 -TTATGTAAGTT
1 ATTATGTAAGTT
* *
44119477 ACTATGTAGGTT
1 ATTATGTAAGTT
44119489 AT
1 AT
44119491 GTTCATTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 9 0.31
12 20 0.69
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (12 bp):
ATTATGTAAGTT
Found at i:44119489 original size:21 final size:21
Alignment explanation
Indices: 44119437--44119492 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
44119427 AATATTTATG
* *
44119437 TATGTAAATTATGTAAGTTAT
1 TATGTAAGTTATGTAAGTTAC
44119458 TATGTAAGTTATGTAAGTTAC
1 TATGTAAGTTATGTAAGTTAC
*
44119479 TATGTAGGTTATGT
1 TATGTAAGTTATGT
44119493 TCATTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (21 bp):
TATGTAAGTTATGTAAGTTAC
Found at i:44119591 original size:91 final size:88
Alignment explanation
Indices: 44119397--44119593 Score: 211
Period size: 91 Copynumber: 2.2 Consensus size: 88
44119387 ATAATTAAGC
*
44119397 TATGTAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAAGTTATTATG
1 TATGTAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAAGTTATAATG
* *
44119462 TAAGTTATGTAAGTTACTATGTAGGT
66 TAAGATATATAAG-T-CTATGTA-GT
* ** * *
44119488 TATGTTCA-TTATGTAAGTTGTGATATGATTAATATTTATGTATGTAAATTATGATATGATTGAT
1 TATG-TAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATG-TAAG-TT-AT
*
44119552 AAATTTAAGATATATAAG-CTATGTA-T
62 -AATGTAAGATATATAAGTCTATGTAGT
44119578 TATGTAAGTTTATGTA
1 TATGTAAG-TTATGTA
44119594 TGTAGGAATA
Statistics
Matches: 89, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
89 2 0.02
90 5 0.06
91 53 0.60
92 12 0.13
93 2 0.02
94 2 0.02
95 13 0.15
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.46
Consensus pattern (88 bp):
TATGTAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAAGTTATAATG
TAAGATATATAAGTCTATGTAGT
Found at i:44119624 original size:9 final size:9
Alignment explanation
Indices: 44119610--44119646 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44119600 AATAAGTATA
*
44119610 ATGTAAGCT
1 ATGTAAGTT
44119619 ATGTAAGTT
1 ATGTAAGTT
44119628 ATGTAAGTT
1 ATGTAAGTT
44119637 ATGTAAGTT
1 ATGTAAGTT
44119646 A
1 A
44119647 AGATATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.41
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:44119691 original size:39 final size:40
Alignment explanation
Indices: 44119638--44119713 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 40
44119628 ATGTAAGTTA
*
44119638 TGTAAGTTAAGATATAATATATATCCCGGTAAGTTATAAG
1 TGTAAGTTAAGATATAATATACATCCCGGTAAGTTATAAG
44119678 TGTAA-TTAAGATATAATATACATCCCGGTAAGTTAT
1 TGTAAGTTAAGATATAATATACATCCCGGTAAGTTAT
44119714 GTAGGTTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 30 0.86
40 5 0.14
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (40 bp):
TGTAAGTTAAGATATAATATACATCCCGGTAAGTTATAAG
Found at i:44119709 original size:22 final size:21
Alignment explanation
Indices: 44119645--44119709 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
44119635 TTATGTAAGT
44119645 TAAGATATAATATATATCCCGG
1 TAAGATATAATATA-ATCCCGG
* *
44119667 TAAGTTATAAGTGTAAT-----
1 TAAGATATAA-TATAATCCCGG
44119684 TAAGATATAATATACATCCCGG
1 TAAGATATAATATA-ATCCCGG
44119706 TAAG
1 TAAG
44119710 TTATGTAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
22 15 0.47
23 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (21 bp):
TAAGATATAATATAATCCCGG
Found at i:44119723 original size:9 final size:9
Alignment explanation
Indices: 44119709--44119823 Score: 76
Period size: 9 Copynumber: 12.6 Consensus size: 9
44119699 ATCCCGGTAA
44119709 GTTATGTAG
1 GTTATGTAG
44119718 GTTATGTA-
1 GTTATGTAG
* *
44119726 TTATATGTAA
1 GT-TATGTAG
44119736 GTTATGTAG
1 GTTATGTAG
* *
44119745 GTTATTAATAA
1 GTTA-T-GTAG
44119756 GTTATGTA-
1 GTTATGTAG
*
44119764 TTATATGTA-
1 GT-TATGTAG
* *
44119773 TTATATGTAA
1 GT-TATGTAG
44119783 GTTATGTAG
1 GTTATGTAG
44119792 GTTATGTA-
1 GTTATGTAG
*
44119800 TTATATGTAG
1 GT-TATGTAG
44119810 GTTATGTAG
1 GTTATGTAG
44119819 GTTAT
1 GTTAT
44119824 TATATTTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.03
9 73 0.84
10 5 0.06
11 6 0.07
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (9 bp):
GTTATGTAG
Found at i:44119734 original size:18 final size:18
Alignment explanation
Indices: 44119711--44119817 Score: 103
Period size: 18 Copynumber: 5.8 Consensus size: 18
44119701 CCCGGTAAGT
44119711 TATGTAGGTTATGTATTA
1 TATGTAGGTTATGTATTA
*
44119729 TATGTAAGTTATGTAGGTTA
1 TATGTAGGTTATGTA--TTA
* *
44119749 T-TAATAAGTTATGTATTA
1 TAT-GTAGGTTATGTATTA
* *
44119767 TATGTA-TTATATGTAAGT-
1 TATGTAGGT-TATGT-ATTA
44119785 TATGTAGGTTATGTATTA
1 TATGTAGGTTATGTATTA
44119803 TATGTAGGTTATGTA
1 TATGTAGGTTATGTA
44119818 GGTTATTATA
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
17 3 0.04
18 51 0.69
19 5 0.07
20 15 0.20
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (18 bp):
TATGTAGGTTATGTATTA
Found at i:44119743 original size:27 final size:27
Alignment explanation
Indices: 44119705--44119823 Score: 153
Period size: 27 Copynumber: 4.7 Consensus size: 27
44119695 ATACATCCCG
44119705 GTAAGTTATGTAGGTTATGTATTATAT
1 GTAAGTTATGTAGGTTATGTATTATAT
44119732 GTAAGTTATGTAGG---T-TATTA-A-
1 GTAAGTTATGTAGGTTATGTATTATAT
***
44119753 -TAAGTTATGTATTATATGTATTATAT
1 GTAAGTTATGTAGGTTATGTATTATAT
44119779 GTAAGTTATGTAGGTTATGTATTATAT
1 GTAAGTTATGTAGGTTATGTATTATAT
*
44119806 GTAGGTTATGTAGGTTAT
1 GTAAGTTATGTAGGTTAT
44119824 TATATTTTTA
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
20 11 0.14
22 1 0.01
23 6 0.08
24 6 0.08
25 1 0.01
27 54 0.68
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (27 bp):
GTAAGTTATGTAGGTTATGTATTATAT
Found at i:44122768 original size:7 final size:7
Alignment explanation
Indices: 44122753--44122800 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
44122743 AACTATAAAC
*
44122753 CCCTAAA
1 CCCTTAA
44122760 CCCTTAA
1 CCCTTAA
*
44122767 CCTTTAA
1 CCCTTAA
*
44122774 CCC-CAA
1 CCCTTAA
44122780 CCCTTAA
1 CCCTTAA
*
44122787 CCCTTCA
1 CCCTTAA
44122794 CCCTTAA
1 CCCTTAA
44122801 ACCCAAAACA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.25
Consensus pattern (7 bp):
CCCTTAA
Found at i:44122788 original size:27 final size:27
Alignment explanation
Indices: 44122753--44122806 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
44122743 AACTATAAAC
* *
44122753 CCCTAAACCCTTAACCTTTAACCCCAA
1 CCCTAAACCCTTAACCCTTAAACCCAA
* *
44122780 CCCTTAACCCTTCACCCTTAAACCCAA
1 CCCTAAACCCTTAACCCTTAAACCCAA
44122807 AACACCAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.22
Consensus pattern (27 bp):
CCCTAAACCCTTAACCCTTAAACCCAA
Found at i:44122796 original size:20 final size:20
Alignment explanation
Indices: 44122758--44122796 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44122748 TAAACCCCTA
*
44122758 AACCCTTAACCTTTAACCCC
1 AACCCTTAACCCTTAACCCC
*
44122778 AACCCTTAACCCTTCACCC
1 AACCCTTAACCCTTAACCC
44122797 TTAAACCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (20 bp):
AACCCTTAACCCTTAACCCC
Found at i:44124585 original size:39 final size:40
Alignment explanation
Indices: 44124484--44124668 Score: 182
Period size: 40 Copynumber: 4.7 Consensus size: 40
44124474 TTGAATGATG
* * * *
44124484 TCCGGGCTAAGTCCTGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * * *
44124523 ATCTGGACTAAGAT-CCGAAGGCATTTTTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
44124564 TCCGGGCTAAG-CTCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
44124603 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
44124642 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
44124669 AACGAGGAGC
Statistics
Matches: 119, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 34 0.29
40 76 0.64
41 9 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:44124682 original size:40 final size:40
Alignment explanation
Indices: 44124565--44124687 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
44124555 GATACTAATT
* ** *
44124565 CCGGGCTAAG-CTCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATAA
* ** *
44124603 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATAA
* *
44124644 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTATAA
44124684 CCGG
1 CCGG
44124688 TTAAATTTCG
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 10 0.14
40 61 0.84
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTATAA
Found at i:44124690 original size:79 final size:79
Alignment explanation
Indices: 44124537--44124691 Score: 181
Period size: 79 Copynumber: 2.0 Consensus size: 79
44124527 GGACTAAGAT
* * * ** *
44124537 CCGAAGGCATTTTTGCGAGATACTAATTCCGGGCTAAGCTCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
44124602 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
44124616 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-C
*
44124679 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
44124692 ATTTCGAAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
78 2 0.03
79 38 0.59
80 24 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:44132082 original size:79 final size:81
Alignment explanation
Indices: 44131946--44132130 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
44131936 TTGAATGATG
*
44131946 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
44132010 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
44132025 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
44132087 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
44132105 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
44132131 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:44132144 original size:40 final size:40
Alignment explanation
Indices: 44131947--44132130 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
44131937 TGAATGATGT
* * * *
44131947 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
44131987 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
44132027 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
44132065 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
44132106 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
44132131 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:44132152 original size:79 final size:79
Alignment explanation
Indices: 44131947--44132163 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
44131937 TGAATGATGT
** * * * **
44131947 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
44132010 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
44132027 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
44132092 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
44132106 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
44132164 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:44133653 original size:7 final size:7
Alignment explanation
Indices: 44133641--44133722 Score: 51
Period size: 7 Copynumber: 11.7 Consensus size: 7
44133631 ATTAACTATA
44133641 AACCCCT
1 AACCCCT
44133648 AACCCC-
1 AACCCCT
* *
44133654 AGCCCTT
1 AACCCCT
*
44133661 AACCCTT
1 AACCCCT
44133668 AACCCCT
1 AACCCCT
*
44133675 AAACCCTT
1 -AACCCCT
44133683 AACCCC-
1 AACCCCT
*
44133689 AACCCTT
1 AACCCCT
* *
44133696 AAACCAT
1 AACCCCT
* *
44133703 AATCCAT
1 AACCCCT
44133710 AAACCCCT
1 -AACCCCT
44133718 AACCC
1 AACCC
44133723 ATATCCCTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
6 9 0.15
7 39 0.66
8 11 0.19
ACGTcount: A:0.34, C:0.48, G:0.01, T:0.17
Consensus pattern (7 bp):
AACCCCT
Found at i:44133679 original size:15 final size:15
Alignment explanation
Indices: 44133656--44133738 Score: 64
Period size: 15 Copynumber: 5.7 Consensus size: 15
44133646 CTAACCCCAG
*
44133656 CCCTTAACCCTTAAC
1 CCCTAAACCCTTAAC
44133671 CCCTAAACCCTTAAC
1 CCCTAAACCCTTAAC
*
44133686 CCC--AACCCTTAAA
1 CCCTAAACCCTTAAC
* * * *
44133699 CCATAATCCATAAAC
1 CCCTAAACCCTTAAC
* *
44133714 CCCT-AACCCATATC
1 CCCTAAACCCTTAAC
*
44133728 CCTTAAACCCT
1 CCCTAAACCCT
44133739 AAATCATAGA
Statistics
Matches: 50, Mismatches: 15, Indels: 6
0.70 0.21 0.08
Matches are distributed among these distances:
13 11 0.22
14 8 0.16
15 31 0.62
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.22
Consensus pattern (15 bp):
CCCTAAACCCTTAAC
Found at i:44133680 original size:35 final size:35
Alignment explanation
Indices: 44133638--44133736 Score: 119
Period size: 35 Copynumber: 2.8 Consensus size: 35
44133628 AACATTAACT
* * *
44133638 ATAAACCCCTAACCCCAGCCCTTAACCCTTAACCC
1 ATAAACCCCTAACCCCAACCCTTAAACCATAACCC
* * *
44133673 CTAAACCCTTAACCCCAACCCTTAAACCATAATCC
1 ATAAACCCCTAACCCCAACCCTTAAACCATAACCC
44133708 ATAAACCCCTAA-CCCATATCCCTTAAACC
1 ATAAACCCCTAACCCCA-A-CCCTTAAACC
44133737 CTAAATCATA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 4 0.07
35 40 0.74
36 10 0.19
ACGTcount: A:0.35, C:0.44, G:0.01, T:0.19
Consensus pattern (35 bp):
ATAAACCCCTAACCCCAACCCTTAAACCATAACCC
Found at i:44133684 original size:22 final size:22
Alignment explanation
Indices: 44133660--44133741 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 22
44133650 CCCCAGCCCT
*
44133660 TAACCCTTAACCCCTAAACCCT
1 TAACCCTTAACCCCTAAACCCA
* *
44133682 TAACCC-CAACCCTTAAA-CCA
1 TAACCCTTAACCCCTAAACCCA
* *
44133702 TAATCCATAAACCCCT-AACCCA
1 TAA-CCCTTAACCCCTAAACCCA
* *
44133724 TATCCCTTAAACCCTAAA
1 TAACCCTTAACCCCTAAA
44133742 TCATAGAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 5 0.11
21 22 0.48
22 19 0.41
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (22 bp):
TAACCCTTAACCCCTAAACCCA
Found at i:44133785 original size:39 final size:41
Alignment explanation
Indices: 44133731--44133817 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
44133721 CCATATCCCT
44133731 TAAACCCTAAATCATAG-A-ACATATATAAACTATAAACTC
1 TAAACCCTAAATCATAGCATACATATATAAACTATAAACTC
* * * * *
44133770 TAAACCCTGATTCATAGCATATATATATAAACTATAAAGTG
1 TAAACCCTAAATCATAGCATACATATATAAACTATAAACTC
44133811 TAAACCC
1 TAAACCC
44133818 CATCCATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
39 15 0.37
40 1 0.02
41 25 0.61
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.28
Consensus pattern (41 bp):
TAAACCCTAAATCATAGCATACATATATAAACTATAAACTC
Found at i:44134613 original size:114 final size:115
Alignment explanation
Indices: 44134390--44134726 Score: 340
Period size: 114 Copynumber: 2.9 Consensus size: 115
44134380 GTTTCTAAGA
* * ** * *
44134390 AAGCGCCACTAACGTCTCTAAAACCTAAATTAAAAACGACTACGTTTTCTTAACAGTTTTGCGGC
1 AAGCGCCACTAACGTCCCTAAAACATAAACCAAAAACGGCAACGTTTTCTTAACAGTTTTGCGGC
* * * * * * *
44134455 GCTT-TGTCTAAAGCGCCGCTAAATCTTGGCTATTACGACATTTTTTGA-T
66 GCTTATG-ATAAAGCGCCGCTAATTCTTGACTATTGCGGCGTTTTTTCAGT
** * * * * *
44134504 AATTGCCACTATCGT-CTTGAAAAGATAAACGAAAAACGGCAATGTTTTCTTAACAGTTTTGCGG
1 AAGCGCCACTAACGTCCCT-AAAACATAAACCAAAAACGGCAACGTTTTCTTAACAGTTTTGCGG
* * *
44134568 CGCTTATGATAAAGCGCCGCTAATTCTTAACTGTTGTGGCG-TTTTTCAGT
65 CGCTTATGATAAAGCGCCGCTAATTCTTGACTATTGCGGCGTTTTTTCAGT
* * * * *
44134618 AAGCGCCACTAACGTCCCTAAAACCTAAACCTAAAATGGCACCGTTTTCTTAACAGTTTTTGCTG
1 AAGCGCCACTAACGTCCCTAAAACATAAACCAAAAACGGCAACGTTTTCTTAACAG-TTTTGCGG
* * *
44134683 CGTTTATGATAAAACGCCGGTAATTCTTGACTATTGCGGCGTTT
65 CGCTTATGATAAAGCGCCGCTAATTCTTGACTATTGCGGCGTTT
44134727 CTAAAGAAAG
Statistics
Matches: 177, Mismatches: 40, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
113 7 0.04
114 122 0.69
115 46 0.26
116 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (115 bp):
AAGCGCCACTAACGTCCCTAAAACATAAACCAAAAACGGCAACGTTTTCTTAACAGTTTTGCGGC
GCTTATGATAAAGCGCCGCTAATTCTTGACTATTGCGGCGTTTTTTCAGT
Found at i:44138410 original size:12 final size:12
Alignment explanation
Indices: 44138393--44138417 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44138383 ATTTAATCAC
44138393 TTTAATATTAAA
1 TTTAATATTAAA
44138405 TTTAATATTAAA
1 TTTAATATTAAA
44138417 T
1 T
44138418 CTTATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:44138550 original size:37 final size:39
Alignment explanation
Indices: 44138456--44138553 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 39
44138446 GTAGATAAAC
44138456 ATTAAATTTAAT-TT-AA-TATTAAGATAATCATTTTAAT
1 ATTAAATTTAATATTAAACTATTAAGATAATCA-TTTAAT
*
44138493 ATTAAA-TTAATA-AAATACTATTAAGATAAGT-A-TTAA-
1 ATTAAATTTAATATTAA-ACTATTAAGATAA-TCATTTAAT
44138529 ATTAAATTTAATATTAAACTATTAA
1 ATTAAATTTAATATTAAACTATTAA
44138554 AATGATATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
36 11 0.21
37 25 0.48
38 3 0.06
39 12 0.23
40 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (39 bp):
ATTAAATTTAATATTAAACTATTAAGATAATCATTTAAT
Found at i:44145049 original size:26 final size:26
Alignment explanation
Indices: 44145020--44145074 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
44145010 TCAAGTTACA
*
44145020 AGACTAATTTGTAATGTAAACTAACT
1 AGACTAATTTGTAATGTAAACGAACT
44145046 AGACTAATTTGTAATGTAAACGAACT
1 AGACTAATTTGTAATGTAAACGAACT
44145072 AGA
1 AGA
44145075 GAATCAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (26 bp):
AGACTAATTTGTAATGTAAACGAACT
Found at i:44145818 original size:10 final size:10
Alignment explanation
Indices: 44145803--44145830 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
44145793 TCAATGTCAT
44145803 ATGCTCAATC
1 ATGCTCAATC
44145813 ATGCTCAATC
1 ATGCTCAATC
44145823 ATGCTCAA
1 ATGCTCAA
44145831 ACAAGTGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (10 bp):
ATGCTCAATC
Found at i:44147583 original size:5 final size:5
Alignment explanation
Indices: 44147573--44147608 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
44147563 CTTATTTTAC
44147573 AATTA AATTA AATTA AATTA AATTA ATATTTA AATT
1 AATTA AATTA AATTA AATTA AATTA A-A-TTA AATT
44147609 TAACTCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
AATTA
Found at i:44147593 original size:15 final size:17
Alignment explanation
Indices: 44147568--44147608 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
44147558 TTTCCCTTAT
44147568 TTTACAATTAAATTAA-A
1 TTTA-AATTAAATTAATA
44147585 -TTAAATTAAATTAATA
1 TTTAAATTAAATTAATA
44147601 TTTAAATT
1 TTTAAATT
44147609 TAACTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATTAAATTAATA
Found at i:44153664 original size:51 final size:52
Alignment explanation
Indices: 44153578--44153706 Score: 174
Period size: 52 Copynumber: 2.5 Consensus size: 52
44153568 CGGATACCCG
* *
44153578 GTGG-CTTGCACATAGCACCACCCTTGTAGCCAAAGCTA-CCTTCTTCACAAA
1 GTGGCCTT-CACATAGTACCACACTTGTAGCCAAAGCTATCCTTCTTCACAAA
* * *
44153629 TTGGCCTTCACATAGTACCACACTTGT-GACTAAAGCTATCTTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTAG-CCAAAGCTATCCTTCTTCACAAA
44153681 GTGGCCTTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
44153707 AGTCATTAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
50 1 0.01
51 28 0.41
52 40 0.58
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTAGCCAAAGCTATCCTTCTTCACAAA
Found at i:44159288 original size:5 final size:5
Alignment explanation
Indices: 44159272--44159310 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
44159262 AAATTTATTA
*
44159272 AAAAT GAAAAT AAAAT -AAAT AAAAT AAAAT AAGAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
44159311 GTGAATAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
6 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:44159297 original size:14 final size:14
Alignment explanation
Indices: 44159273--44159310 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
44159263 AATTTATTAA
44159273 AAATGAAAATAAAAT
1 AAAT-AAAATAAAAT
44159288 AAATAAAATAAAAT
1 AAATAAAATAAAAT
44159302 AAGATAAAA
1 AA-ATAAAA
44159311 GTGAATAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:44160827 original size:14 final size:15
Alignment explanation
Indices: 44160805--44160833 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44160795 TTTTGAGCTG
44160805 GTAATTTGGGTTATT
1 GTAATTTGGGTTATT
44160820 GTAA-TTGGGTTATT
1 GTAATTTGGGTTATT
44160834 TTTGGACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
GTAATTTGGGTTATT
Found at i:44170199 original size:16 final size:17
Alignment explanation
Indices: 44170178--44170209 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
44170168 ACCATTACAG
44170178 TTGTTGTTTAA-AATAA
1 TTGTTGTTTAAGAATAA
44170194 TTGTTGTTTAAGAATA
1 TTGTTGTTTAAGAATA
44170210 GCTATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (17 bp):
TTGTTGTTTAAGAATAA
Done.