Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, 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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 89
Found at i:2968440 original size:3 final size:3
Alignment explanation
Indices: 2968426--2968467 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2968416 ATCCCGATAA
* *
2968426 TAT TAA TAT TAT TAT T-T TCTT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
2968468 AATTTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2968565 original size:24 final size:23
Alignment explanation
Indices: 2968522--2968566 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2968512 AATTATAAAT
*
2968522 CAGCAGCCCAACCACCCAAATTA
1 CAGCAGCCCAACCAACCAAATTA
*
2968545 CAGCAGACCCAACCAATCAAAT
1 CAGCAG-CCCAACCAACCAAAT
2968567 CCGGAGCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.42, C:0.40, G:0.09, T:0.09
Consensus pattern (23 bp):
CAGCAGCCCAACCAACCAAATTA
Found at i:2970740 original size:131 final size:131
Alignment explanation
Indices: 2970549--2970861 Score: 409
Period size: 131 Copynumber: 2.4 Consensus size: 131
2970539 ATAAGAAATG
* * * * *
2970549 AGAGGTCATTTATTCTCGATTGGAAATAATAAGATATTACCATTTTCTCTCGAGTTAATATTGAT
1 AGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCGAATCAATATTGAA
* *
2970614 TTTTAAGATG-GATAATGATATCTCATCATTTCGATTGGAGTAATAAATGAATGCTTTGAAGG-T
66 TTTTAAGATGAAATAATGATATCTCATCATTTCAATTGGAGTAATAAATGAATG-TTTGAAGGAT
2970677 GCA
130 G-A
* * *
2970680 AGAGGTCATTTATTCTCGGTTTGAAATCATTAGATATTATCATTTTCAT-TCGAATCAATATTGA
1 AGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTC-TCTCGAATCAATATTGA
* * * * *
2970744 ATTTTAAGATGAAATACTGATATCTCTTCATTTCAATTGGGGTAATAAATGATTGTTTTAAGGCA
65 ATTTTAAGATGAAATAATGATATCTCATCATTTCAATTGGAGTAATAAATGAATGTTTGAAGG-A
2970809 TGA
129 TGA
* *
2970812 A-AGGCCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTC
1 AGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTC
2970862 TTAAAATTAT
Statistics
Matches: 157, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
130 1 0.01
131 114 0.73
132 40 0.25
133 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (131 bp):
AGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCGAATCAATATTGAA
TTTTAAGATGAAATAATGATATCTCATCATTTCAATTGGAGTAATAAATGAATGTTTGAAGGATG
A
Found at i:2973803 original size:16 final size:16
Alignment explanation
Indices: 2973782--2973815 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2973772 TCTCCAATTA
*
2973782 TCTTACTAGCGAATGG
1 TCTTACCAGCGAATGG
2973798 TCTTACCAGCGAATGG
1 TCTTACCAGCGAATGG
2973814 TC
1 TC
2973816 AATGCTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (16 bp):
TCTTACCAGCGAATGG
Found at i:2976849 original size:22 final size:22
Alignment explanation
Indices: 2976824--2976877 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2976814 ACTAAAAGGG
*
2976824 AGTATC-AGTACCATAGTATAGT
1 AGTATCGA-TACCATAGTATAGA
*
2976846 AGTATCGATACTATAGTATAGA
1 AGTATCGATACCATAGTATAGA
2976868 AGTATCGATA
1 AGTATCGATA
2976878 TCATGGTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:2977368 original size:45 final size:45
Alignment explanation
Indices: 2977303--2977670 Score: 610
Period size: 45 Copynumber: 8.2 Consensus size: 45
2977293 ACAATTCCAA
* * *
2977303 AAATAAAATGCATAATGGTGCATTAAAGACATGAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
2977348 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
* * *
2977393 AAATGAAATGCATAACGGTGCATTAAATGCATGAAATGATGGCAT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
2977438 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
* * **
2977483 AAATGAAATGTATAACGGTGCATTAAAGGCATGAAATGACACCAT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
*
2977528 AAATGAAATGCATAACGGTGCATTAAAGGCATAAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
*
2977573 AAATGAAATGCATAACAGTGCATTAAAGGCATGAAAGGATGCCAT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
* *
2977618 AAATGAAATGCATAATGGTGCATTAAAGGCATGAAAGGATGCCTT
1 AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
2977663 AAATGAAA
1 AAATGAAA
2977671 ATAATGAATA
Statistics
Matches: 300, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 300 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.21
Consensus pattern (45 bp):
AAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCAT
Found at i:2977422 original size:19 final size:19
Alignment explanation
Indices: 2977353--2977424 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 19
2977343 GCCATAAATG
2977353 AAATGCATAACGGTGCATT
1 AAATGCATAACGGTGCATT
* *
2977372 AAAGGCATGAAAGGATGCCATAAAT
1 AAATGCAT-AACGG-TG-CAT---T
2977397 GAAATGCATAACGGTGCATT
1 -AAATGCATAACGGTGCATT
2977417 AAATGCAT
1 AAATGCAT
2977425 GAAATGATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
19 15 0.36
20 5 0.12
21 2 0.05
22 3 0.07
23 3 0.07
24 2 0.05
25 5 0.12
26 7 0.17
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (19 bp):
AAATGCATAACGGTGCATT
Found at i:2977620 original size:21 final size:21
Alignment explanation
Indices: 2977596--2977665 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
2977586 AACAGTGCAT
2977596 TAAAGGCATGAAAGGATGCCA
1 TAAAGGCATGAAAGGATGCCA
**
2977617 TAAATGAAATGCATAATGG-TG-CA
1 TAAA-GGCATG-A-AA-GGATGCCA
*
2977640 TTAAAGGCATGAAAGGATGCCT
1 -TAAAGGCATGAAAGGATGCCA
2977662 TAAA
1 TAAA
2977666 TGAAAATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 6 0.16
23 7 0.19
24 8 0.22
25 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.21
Consensus pattern (21 bp):
TAAAGGCATGAAAGGATGCCA
Found at i:2992087 original size:4 final size:4
Alignment explanation
Indices: 2992078--2992140 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
2992068 GCACCTAAGA
* *
2992078 AAAG AAAG AAAT AAAA AAAG AAAAG ATAA- AAAG ATAA- AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG -AAAG A-AAG AAAG A-AAG AAAG AAAG AAAG
*
2992127 TAA- AAAG AAAG AAA
1 AAAG AAAG AAAG AAA
2992141 AAATTAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 6 0.12
4 34 0.71
5 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (4 bp):
AAAG
Found at i:2992096 original size:16 final size:17
Alignment explanation
Indices: 2992077--2992156 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 17
2992067 TGCACCTAAG
2992077 AAAAGAAAGAAA-TAAA
1 AAAAGAAAGAAAGTAAA
**
2992093 AAAAGAAAAGATAAAAAGATA
1 AAAAG-AAAGA-AAGTA-A-A
2992114 AAAAGAAAGAAAGTAAAA
1 AAAAGAAAGAAAGT-AAA
*
2992132 AGAAAGAAA-AAATTAAA
1 A-AAAGAAAGAAAGTAAA
*
2992149 AAATGAAA
1 AAAAGAAA
2992157 AGGGGGTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
16 11 0.21
17 9 0.17
18 8 0.15
19 11 0.21
20 7 0.13
21 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (17 bp):
AAAAGAAAGAAAGTAAA
Found at i:2992106 original size:15 final size:16
Alignment explanation
Indices: 2992077--2992156 Score: 54
Period size: 19 Copynumber: 4.5 Consensus size: 16
2992067 TGCACCTAAG
2992077 AAAAGAAAGAAATAAA
1 AAAAGAAAGAAATAAA
*
2992093 AAAAGAAAAGATAAAAAGATA
1 AAAAG-AAAG--AAATA-A-A
2992114 AAAAGAAAGAAAGTAAAA
1 AAAAGAAAGAAA-T-AAA
2992132 AGAAAGAAA-AAATTAAA
1 A-AAAGAAAGAAA-TAAA
*
2992149 AAATGAAA
1 AAAAGAAA
2992157 AGGGGGTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
16 11 0.21
17 8 0.15
18 9 0.17
19 12 0.23
20 6 0.12
21 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAAAGAAAGAAATAAA
Found at i:2992130 original size:23 final size:24
Alignment explanation
Indices: 2992074--2992143 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 24
2992064 TACTGCACCT
*
2992074 AAGAAAAGA-AAGAA-AT-AAAAA
1 AAGAAAAGATAAAAAGATAAAAAA
2992095 AAGAAAAGATAAAAAGATAAAAAGA
1 AAGAAAAGATAAAAAGATAAAAA-A
2992120 AAG-AAAG-TAAAAAGA-AAGAAAA
1 AAGAAAAGATAAAAAGATAA-AAAA
2992142 AA
1 AA
2992144 TTAAAAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
21 9 0.21
22 9 0.21
23 13 0.30
24 8 0.19
25 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.06
Consensus pattern (24 bp):
AAGAAAAGATAAAAAGATAAAAAA
Found at i:2992609 original size:15 final size:15
Alignment explanation
Indices: 2992589--2992620 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2992579 GCCACATATA
2992589 TACCCAAAAACTCTT
1 TACCCAAAAACTCTT
2992604 TACCCAAAAACTCTT
1 TACCCAAAAACTCTT
2992619 TA
1 TA
2992621 TAGTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (15 bp):
TACCCAAAAACTCTT
Found at i:2993817 original size:134 final size:134
Alignment explanation
Indices: 2993399--2993973 Score: 573
Period size: 134 Copynumber: 4.3 Consensus size: 134
2993389 GCGAATCGAA
* * * ** *
2993399 CTCGATTCAATCTTCCCTAAAGAGCGGTGGAATGAATCAACATTTCCAGATCTGATTTTCCTTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * * * * *
2993464 AGAAACAGTGGAACATATCCCT-TTTTTCTAGATTTGATCTTCCCTGAGAAATAATGAAACAAGT
66 AAAAATAGTGGAACATATCCCTCTTTTTCTATATTTGATCTTCCCTGAGGAACAATGGAACAAGT
2993528 CTAC
131 CTAC
* * * *
2993532 CTCGATTCAATCTTCCATGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTTCCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTC-
* * *
2993597 AAAAAATGGTGGAACATATCCCTCTTTTTCCATATTTGATCTTCCCTGAGGAACAATGGGACAAG
65 AAAAAATAGTGGAACATATCCCTCTTTTTCTATATTTGATCTTCCCTGAGGAACAATGGAACAAG
* *
2993662 TGTGC
130 TCTAC
* *
2993667 CTTGATTCAATCTTCCCTAAAGAACAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * ** * * * * *
2993732 ATAAATAATAAAACAAATCCCTCTTTTTCTATATTTGGTCTTCCCTAAGGAACAGTGGAACAATT
66 AAAAATAGTGGAACATATCCCTCTTTTTCTATATTTGATCTTCCCTGAGGAACAATGGAACAAGT
2993797 CTAC
131 CTAC
* * * ** * * *
2993801 CTCGATTCAATCTTCCCTGAAA-AATAATGGAAAT-AATCAACATTTCCATATATGATTTTCCTT
1 CTCGATTCAATCTTCCCT-AAAGAACAGTGG-AATGAATCAACGTCCCCAGATCTGATTTTCCCT
* * * * * * * * * * *
2993864 CAAGAAGTAGTAGAACAAATACCT-TTCTTTCAAGATTTGATATTCCCTGAGTAGCAATGTAACA
64 CAAAAAATAGTGGAACATATCCCTCTT-TTTCTATATTTGATCTTCCCTGAGGAACAATGGAACA
*
2993928 AGTCTGC
128 AGTCTAC
* * * **
2993935 CTCAATTCAATCTTCCCTGAAGAATAGTTAAATGAATCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCA
2993974 TTGTTTCTCG
Statistics
Matches: 363, Mismatches: 72, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
133 61 0.17
134 200 0.55
135 102 0.28
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
AAAAATAGTGGAACATATCCCTCTTTTTCTATATTTGATCTTCCCTGAGGAACAATGGAACAAGT
CTAC
Found at i:2993904 original size:268 final size:268
Alignment explanation
Indices: 2993399--2993973 Score: 638
Period size: 268 Copynumber: 2.1 Consensus size: 268
2993389 GCGAATCGAA
* * * ** *
2993399 CTCGATTCAATCTTCCCTAAAGAGCGGTGGAATGAATCAACATTTCCAGATCTGATTTTCCTTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTAGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
* ** * * *
2993464 AGAAACAGTGGAACATATCCCTTTTTTCTAGATTTGATCTTCCCTGAGAAATAATGAAACAAGTC
66 AGAAACAATAAAACAAATCCCTTTTTTCTAGATTTGATCTTCCCTAAGAAACAATGAAACAAGTC
* * * *
2993529 TACCTCGATTCAATCTTCCATGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTTCC
131 TACCTCGATTCAATCTTCCATGAAAAACAATGGAATGAATCAACATCCCCAAATATGATTTTTCC
* * * * * * * *
2993594 TCAAAAAAATGGTGGAACATATCCCTCTTTTTCCATATTTGATCTTCCCTGAGGAACAATGGGAC
196 TCAAAAAAATAGTAGAACAAATACCTCTTTTTCAAGATTTGATATTCCCTGAGGAACAATGGAAC
*
2993659 AAGTGTGC
261 AAGTCTGC
* *
2993667 CTTGATTCAATCTTCCCTAAAGAACAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTAGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
* * * * * * * *
2993732 ATAAATAATAAAACAAATCCCTCTTTTTCTATATTTGGTCTTCCCTAAGGAACAGTGGAACAATT
66 AGAAACAATAAAACAAATCCCT-TTTTTCTAGATTTGATCTTCCCTAAGAAACAATGAAACAAGT
* * ** *
2993797 CTACCTCGATTCAATCTTCCCTGAAAAATAATGGAAAT-AATCAACATTTCCATATATGA-TTTT
130 CTACCTCGATTCAATCTTCCATGAAAAACAATGG-AATGAATCAACATCCCCAAATATGATTTTT
* * * *
2993860 CCTTC-AAGAAGTAGTAGAACAAATACCT-TTCTTTCAAGATTTGATATTCCCTGAGTAGCAATG
194 CC-TCAAAAAAATAGTAGAACAAATACCTCTT-TTTCAAGATTTGATATTCCCTGAGGAACAATG
*
2993923 TAACAAGTCTGC
257 GAACAAGTCTGC
* * *
2993935 CTCAATTCAATCTTCCCTGAAGAATAGTTA-AATGAATCA
1 CTCGATTCAATCTTCCCTAAAGAACAG-TAGAATGAATCA
2993974 TTGTTTCTCG
Statistics
Matches: 253, Mismatches: 49, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
267 2 0.01
268 164 0.65
269 84 0.33
270 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (268 bp):
CTCGATTCAATCTTCCCTAAAGAACAGTAGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
AGAAACAATAAAACAAATCCCTTTTTTCTAGATTTGATCTTCCCTAAGAAACAATGAAACAAGTC
TACCTCGATTCAATCTTCCATGAAAAACAATGGAATGAATCAACATCCCCAAATATGATTTTTCC
TCAAAAAAATAGTAGAACAAATACCTCTTTTTCAAGATTTGATATTCCCTGAGGAACAATGGAAC
AAGTCTGC
Found at i:2994893 original size:10 final size:10
Alignment explanation
Indices: 2994874--2994907 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2994864 AAGGATCGAT
2994874 GGGTTTTTTA
1 GGGTTTTTTA
*
2994884 GGGTTGTTTA
1 GGGTTTTTTA
2994894 GGGTATTTTTA
1 GGGT-TTTTTA
2994905 GGG
1 GGG
2994908 AGTTTTAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (10 bp):
GGGTTTTTTA
Found at i:2996493 original size:131 final size:131
Alignment explanation
Indices: 2996259--2996502 Score: 371
Period size: 131 Copynumber: 1.9 Consensus size: 131
2996249 TAAATGTATG
* * * *
2996259 TTTTAAGGCGAAATAGTGATTTCTCATCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCAT
1 TTTTAAGACGAAATAGTGATATCTCATCATTTCAATTGGAGTAATAAATGACTGCTTTAAGACAT
* * *
2996324 GAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATCATTTTCATTTGAATCAATATTGA
66 GAAAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTCATTTGAATCAATATTGA
2996389 A
131 A
* * * * *
2996390 TTTTAAGATGAAATAGTGATATCTCTTCATTTCAATTGGGGTAATAAATGATTGTTTTAAGACAT
1 TTTTAAGACGAAATAGTGATATCTCATCATTTCAATTGGAGTAATAAATGACTGCTTTAAGACAT
*
2996455 GAAAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTC
66 GAAAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTC
2996503 TCTCTTAAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 100 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (131 bp):
TTTTAAGACGAAATAGTGATATCTCATCATTTCAATTGGAGTAATAAATGACTGCTTTAAGACAT
GAAAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTCATTTGAATCAATATTGA
A
Found at i:3000513 original size:15 final size:15
Alignment explanation
Indices: 3000459--3000516 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
3000449 CCAGACTAAA
*
3000459 ATAATATAA-ATTGAC
1 ATAA-ATAATATTAAC
*
3000474 ATAAATAATTTTTAA-
1 ATAAATAA-TATTAAC
*
3000489 A-AAATTATATTAAC
1 ATAAATAATATTAAC
3000503 ATAAATAATATTAA
1 ATAAATAATATTAA
3000517 TAAATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
13 5 0.15
14 10 0.29
15 16 0.47
16 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAATAATATTAAC
Found at i:3001380 original size:47 final size:49
Alignment explanation
Indices: 3001291--3001391 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 49
3001281 AGAAAATATA
3001291 GATACTAAAATTACCAAGAATAATAAAATAAAATAGAAAATGTATAAATTAT
1 GATACTAAAATTACC-A-AATAAT-AAATAAAATAGAAAATGTATAAATTAT
3001343 GATACTAAAATTACC-AATAAT-AATAAAATAGAAAATGTATAAATTAT
1 GATACTAAAATTACCAAATAATAAATAAAATAGAAAATGTATAAATTAT
3001390 GA
1 GA
3001392 AAATAATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
47 28 0.57
49 6 0.12
52 15 0.31
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (49 bp):
GATACTAAAATTACCAAATAATAAATAAAATAGAAAATGTATAAATTAT
Found at i:3001413 original size:47 final size:46
Alignment explanation
Indices: 3001312--3001414 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 46
3001302 TACCAAGAAT
* * * ** **
3001312 AATAAAATAAAATAGAAAATGTATAAATTATGATACTAAAATTACC
1 AATATAATAAAATAGAAAATGTATAAATTATGAAAATAAAAAAAAA
3001358 AATAATAATAAAATAGAAAATGTATAAATTATGAAAATAATAAAAAAA
1 AAT-ATAATAAAATAGAAAATGTATAAATTATGAAAATAA-AAAAAAA
3001406 AATATAATA
1 AATATAATA
3001415 TATATAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
46 3 0.06
47 39 0.81
48 6 0.12
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (46 bp):
AATATAATAAAATAGAAAATGTATAAATTATGAAAATAAAAAAAAA
Found at i:3001425 original size:30 final size:31
Alignment explanation
Indices: 3001361--3001426 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 31
3001351 AATTACCAAT
*
3001361 AATAATAAAATAGAAAATGTATAAATTATGAA
1 AATAATAAAATAGAAAA-GTATAAATTATAAA
3001393 AATAATAAAA-A-AAAA-TATAATATATATAAA
1 AATAATAAAATAGAAAAGTATAA-AT-TATAAA
3001423 AATA
1 AATA
3001427 TGAATAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 5 0.16
29 2 0.06
30 13 0.42
31 1 0.03
32 10 0.32
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (31 bp):
AATAATAAAATAGAAAAGTATAAATTATAAA
Found at i:3001544 original size:24 final size:23
Alignment explanation
Indices: 3001517--3001591 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 23
3001507 ATATGTTTAC
3001517 AAATTAATACTATAAAATATAAAT
1 AAATT-ATACTATAAAATATAAAT
* *
3001541 AAA-TATA-TATAATACATAAAT
1 AAATTATACTATAAAATATAAAT
3001562 AAAAATTATATCTAT-AAATATAATAT
1 --AAATTATA-CTATAAAATATAA-AT
3001588 AAAT
1 AAAT
3001592 AGTATAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
21 12 0.29
22 3 0.07
23 4 0.10
24 11 0.27
25 6 0.15
26 5 0.12
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATTATACTATAAAATATAAAT
Found at i:3001597 original size:26 final size:25
Alignment explanation
Indices: 3001526--3001597 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 25
3001516 CAAATTAATA
3001526 CTATAAAATATAA-ATAAATATATAT
1 CTAT-AAATATAATATAAATATATAT
* * *
3001551 -AATACATA-AATAAAAAT-TATAT
1 CTATAAATATAATATAAATATATAT
3001573 CTATAAATATAATATAAATAGTATA
1 CTATAAATATAATATAAATA-TATA
3001598 AAATAACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
22 7 0.19
23 15 0.42
24 10 0.28
26 4 0.11
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (25 bp):
CTATAAATATAATATAAATATATAT
Found at i:3007108 original size:20 final size:20
Alignment explanation
Indices: 3007083--3007129 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3007073 TAAAACGGTT
3007083 CGGTTCGGTTTGATCTTATA
1 CGGTTCGGTTTGATCTTATA
3007103 CGGTTCGGTTTGATCTTATA
1 CGGTTCGGTTTGATCTTATA
3007123 CGGTTCG
1 CGGTTCG
3007130 ATGTTCGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (20 bp):
CGGTTCGGTTTGATCTTATA
Found at i:3007611 original size:13 final size:13
Alignment explanation
Indices: 3007593--3007619 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3007583 AAATTTTCGT
3007593 GGGGTAATCAAGG
1 GGGGTAATCAAGG
3007606 GGGGTAATCAAGG
1 GGGGTAATCAAGG
3007619 G
1 G
3007620 AATAACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.48, T:0.15
Consensus pattern (13 bp):
GGGGTAATCAAGG
Found at i:3007813 original size:20 final size:20
Alignment explanation
Indices: 3007775--3007813 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3007765 CATTGCAGGA
3007775 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
3007795 ATTTCATGGCTTCAA-AAAA
1 ATTT-ATGGCCTCAACAAAA
3007814 AACCTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:3012087 original size:18 final size:18
Alignment explanation
Indices: 3012060--3012104 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3012050 ATGTTTTAAG
3012060 TAAT-ATTAATAATTTTA
1 TAATAATTAATAATTTTA
*
3012077 TAATAATTAATATTTTTA
1 TAATAATTAATAATTTTA
* *
3012095 AAAAAATTAA
1 TAATAATTAA
3012105 ATTAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAATTAATAATTTTA
Found at i:3013706 original size:15 final size:17
Alignment explanation
Indices: 3013674--3013706 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3013664 CCAGCCTTGG
3013674 ACACATACCAATGTCCA
1 ACACATACCAATGTCCA
3013691 ACACAT-CCAA-GTCCA
1 ACACATACCAATGTCCA
3013706 A
1 A
3013707 GGAACCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.42, C:0.36, G:0.06, T:0.15
Consensus pattern (17 bp):
ACACATACCAATGTCCA
Found at i:3013823 original size:27 final size:27
Alignment explanation
Indices: 3013782--3013876 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
3013772 TTGTAGGAAT
*
3013782 TATAGAG--ATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
3013807 TATAAAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
3013834 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
3013861 TATAGAGATATGATTT
1 TATAGAGATATGATTT
3013877 TGTAAATAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
25 6 0.09
27 59 0.91
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:3014635 original size:20 final size:21
Alignment explanation
Indices: 3014610--3014649 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3014600 AGGTCATCCT
3014610 AGTTTT-CACTATCTTGCAAA
1 AGTTTTGCACTATCTTGCAAA
3014630 AGTTTTGGCACTATCTTGCA
1 AGTTTT-GCACTATCTTGCA
3014650 TAATGGTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (21 bp):
AGTTTTGCACTATCTTGCAAA
Found at i:3017646 original size:27 final size:27
Alignment explanation
Indices: 3017605--3017699 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
3017595 GTGTAGGAAT
3017605 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
* *
3017630 TATAAAGATATGATTTGTTACCATTCT
1 TATAGAGATATGATTTGTTACCATTCC
3017657 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
3017684 TATAGAGATATGATTT
1 TATAGAGATATGATTT
3017700 TGTAAATAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 6 0.09
27 58 0.91
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:3021334 original size:32 final size:32
Alignment explanation
Indices: 3021286--3021360 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
3021276 CCCTAAACTC
*
3021286 AACCCGAACCCGACCCGAATATCACACTTAAAA
1 AACCCG-ACCCGACCCGAATATCAAACTTAAAA
*
3021319 AACCTGACCCGACCCGAATATCAAACTTAAAA
1 AACCCGACCCGACCCGAATATCAAACTTAAAA
3021351 AACCCGACCC
1 AACCCGACCC
3021361 AAAACCGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.41, C:0.37, G:0.09, T:0.12
Consensus pattern (32 bp):
AACCCGACCCGACCCGAATATCAAACTTAAAA
Found at i:3021422 original size:33 final size:33
Alignment explanation
Indices: 3021347--3021447 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
3021337 TATCAAACTT
*
3021347 AAAAAACCCGACCCAAAAC-CG--AA-TTTTAAA
1 AAAAAACCCGACCC-GAACTCGAAAATTTTTAAA
** * * *
3021377 AAAAAA-ATGACCCGATC-CAGAAATTTTTTGAA
1 AAAAAACCCGACCCGAACTC-GAAAATTTTTAAA
3021409 AAAAAACCCGACCCGAACTCGAAAATTTTTAAA
1 AAAAAACCCGACCCGAACTCGAAAATTTTTAAA
3021442 AAAAAA
1 AAAAAA
3021448 TCCTACCAGA
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
28 3 0.06
29 6 0.11
30 6 0.11
31 1 0.02
32 12 0.22
33 25 0.46
34 1 0.02
ACGTcount: A:0.52, C:0.21, G:0.09, T:0.18
Consensus pattern (33 bp):
AAAAAACCCGACCCGAACTCGAAAATTTTTAAA
Found at i:3040375 original size:24 final size:24
Alignment explanation
Indices: 3040343--3040391 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3040333 TGTCCAAACA
3040343 ACTTCTGTAAATCCTCAAGTTGCT
1 ACTTCTGTAAATCCTCAAGTTGCT
3040367 ACTTCTGTAAATCCTCAAGTTGCT
1 ACTTCTGTAAATCCTCAAGTTGCT
3040391 A
1 A
3040392 TTTAGTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (24 bp):
ACTTCTGTAAATCCTCAAGTTGCT
Found at i:3054851 original size:62 final size:62
Alignment explanation
Indices: 3054749--3054874 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
3054739 GAAAAAATAA
* * *
3054749 CATGGTTACTCAGATTCGAATGTGAGTGTCTAATATGGGTATATGTTCTACATGAGTATGTG
1 CATGGTTACTCAGATTCAAATGTGAGTGTCTAATACGGGTATATGTCCTACATGAGTATGTG
3054811 CATGGTTACTCAGATTCAAATGTGAGTGTCTAATACGGGTATATGTCCTACATGAGTATGTG
1 CATGGTTACTCAGATTCAAATGTGAGTGTCTAATACGGGTATATGTCCTACATGAGTATGTG
3054873 CA
1 CA
3054875 GTTTTTTTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (62 bp):
CATGGTTACTCAGATTCAAATGTGAGTGTCTAATACGGGTATATGTCCTACATGAGTATGTG
Found at i:3064953 original size:21 final size:21
Alignment explanation
Indices: 3064927--3064974 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3064917 AGTTATCTTC
3064927 ATATCTAATCATTTTGTCAGA
1 ATATCTAATCATTTTGTCAGA
3064948 ATATCTAATCATTTTGTCAGA
1 ATATCTAATCATTTTGTCAGA
3064969 ATATCT
1 ATATCT
3064975 TTTAAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (21 bp):
ATATCTAATCATTTTGTCAGA
Found at i:3068154 original size:20 final size:20
Alignment explanation
Indices: 3068129--3068174 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
3068119 ATAAGTCGAG
3068129 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
3068149 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
3068169 AGATGT
1 AGATGT
3068175 TTATAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.22
Consensus pattern (20 bp):
AGATGTAGGGAAATAGAAAT
Found at i:3069146 original size:23 final size:23
Alignment explanation
Indices: 3069113--3069180 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
3069103 ATTATTATAT
3069113 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGTAATTCTACGC
* *
3069136 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGTAATTCTACGC
* * *
3069159 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGTAATTCTACG
3069181 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGTAATTCTACGC
Found at i:3070241 original size:17 final size:17
Alignment explanation
Indices: 3070228--3070261 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3070218 ATTTTTGTTT
3070228 GCGAGCACTTTTTGCTA
1 GCGAGCACTTTTTGCTA
*
3070245 GGGAGCACTTTTTGCTA
1 GCGAGCACTTTTTGCTA
3070262 AGTTCGGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (17 bp):
GCGAGCACTTTTTGCTA
Found at i:3077613 original size:17 final size:16
Alignment explanation
Indices: 3077582--3077615 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3077572 CACGTGAGGA
3077582 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
3077598 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
3077615 T
1 T
3077616 ACTGTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:3089887 original size:32 final size:32
Alignment explanation
Indices: 3089827--3089940 Score: 111
Period size: 32 Copynumber: 3.6 Consensus size: 32
3089817 CCTAAGGCTA
* * **
3089827 TTGTACATTATCTGAATACAACGTTGACATTG
1 TTGTGCATTATCTGAATGCAACACTGACATTG
* * *
3089859 TTGTGCATTATCTGAATGCAGCACTGACACTA
1 TTGTGCATTATCTGAATGCAACACTGACATTG
* * * *
3089891 CTGTGTATTATCTAAATGCAACACTAACATTG
1 TTGTGCATTATCTGAATGCAACACTGACATTG
* *
3089923 TTGTCCATTATTTGAATG
1 TTGTGCATTATCTGAATG
3089941 TAATACAATG
Statistics
Matches: 63, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (32 bp):
TTGTGCATTATCTGAATGCAACACTGACATTG
Found at i:3092735 original size:21 final size:21
Alignment explanation
Indices: 3092709--3092755 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3092699 GGTGTGGATG
*
3092709 CCAATACATCAGGTAT-AGATA
1 CCAATACATCAAGTATGA-ATA
3092730 CCAATACATCAAGTATGAATA
1 CCAATACATCAAGTATGAATA
3092751 CCAAT
1 CCAAT
3092756 GATATCGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (21 bp):
CCAATACATCAAGTATGAATA
Found at i:3102358 original size:18 final size:19
Alignment explanation
Indices: 3102321--3102362 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3102311 CAATAAATAA
3102321 TAGTAAATGAATTTTATTT
1 TAGTAAATGAATTTTATTT
3102340 TAGTAAAT-AATTGTT-TTT
1 TAGTAAATGAATT-TTATTT
3102358 TAGTA
1 TAGTA
3102363 TTTTTGTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (19 bp):
TAGTAAATGAATTTTATTT
Found at i:3103065 original size:2 final size:2
Alignment explanation
Indices: 3103058--3103085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3103048 TTAACGTTGA
3103058 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
3103086 TTGAAATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3106862 original size:21 final size:21
Alignment explanation
Indices: 3106836--3106890 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
3106826 GTTGGCCATC
* *
3106836 AGATTTGTTGTTAGCACGTCA
1 AGATTTGTTGATAGCACGTAA
*
3106857 AGATTTATTGATAGCACGTAA
1 AGATTTGTTGATAGCACGTAA
*
3106878 AGATTTGCTGATA
1 AGATTTGTTGATA
3106891 TACATTGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (21 bp):
AGATTTGTTGATAGCACGTAA
Found at i:3107445 original size:23 final size:23
Alignment explanation
Indices: 3107419--3107463 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3107409 CACCACAGCT
*
3107419 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
3107442 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3107464 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:3107628 original size:150 final size:149
Alignment explanation
Indices: 3107431--3107746 Score: 535
Period size: 150 Copynumber: 2.1 Consensus size: 149
3107421 TATAAATGCA
* *
3107431 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
3107495 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTTT-CAAGACTTCACACATGT
* *
3107560 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
**
3107581 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
3107646 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTTTCAAGACTTCACACATGTTC
*
3107711 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
3107730 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
3107747 CCCTCTACCC
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 53 0.34
150 104 0.66
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:3108267 original size:19 final size:20
Alignment explanation
Indices: 3108230--3108267 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3108220 TTTTTATACA
*
3108230 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
3108250 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
3108268 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:3114391 original size:23 final size:23
Alignment explanation
Indices: 3114365--3114409 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3114355 CACCACAGCT
*
3114365 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
3114388 CGTAGAATTGCACTGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3114410 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:3114574 original size:150 final size:149
Alignment explanation
Indices: 3114377--3114692 Score: 535
Period size: 150 Copynumber: 2.1 Consensus size: 149
3114367 TATAAATGCA
*
3114377 CCGAAGTG-CCGCGTAGAATTGCACTGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
3114441 TTCCTTAAGAATCATATACATATATTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* *
3114506 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
**
3114527 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
3114592 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
3114657 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
3114676 CCGAAGGACCGTGTAGA
1 CCGAAGGACCGCGTAGA
3114693 CCCTCTACCC
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 52 0.33
150 105 0.67
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:3117964 original size:18 final size:19
Alignment explanation
Indices: 3117941--3117991 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
3117931 GGTTTTTTTA
*
3117941 TCTCTTCTATCTCTTTC-T
1 TCTCTTCTATCTCTTCCTT
*
3117959 TCTCTTC-ATTTTCTTCCTT
1 TCTCTTCTA-TCTCTTCCTT
3117978 TCTCTTCT-TCTCTT
1 TCTCTTCTATCTCTT
3117992 ATTCTCCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.04
18 18 0.67
19 8 0.30
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.63
Consensus pattern (19 bp):
TCTCTTCTATCTCTTCCTT
Found at i:3119554 original size:21 final size:21
Alignment explanation
Indices: 3119508--3119558 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3119498 GATTCGTTTT
3119508 CAAAAGGATCGATCCATCCGA
1 CAAAAGGATCGATCCATCCGA
* *
3119529 AAAAAGGATCGATCCCT-CGA
1 CAAAAGGATCGATCCATCCGA
3119549 CCAAAAGGAT
1 -CAAAAGGAT
3119559 TAATCCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (21 bp):
CAAAAGGATCGATCCATCCGA
Found at i:3119600 original size:92 final size:92
Alignment explanation
Indices: 3119437--3119614 Score: 218
Period size: 92 Copynumber: 1.9 Consensus size: 92
3119427 TCATTCCCAG
* * * * * * *
3119437 AAAAAGGATTGATCTCTCGATCAAAGGGATCGATCCCAAAGTTTCTATCCAGCAAAGGATCGATT
1 AAAAAGGATCGATCCCTCGACCAAAAGGATCAATCCCAAACTTTATATCCAGCAAAGGATCGATT
*
3119502 CGTTTTCAAAAGGATCGATCCATCCGA
66 CGTTTTCAAAAAGATCGATCCATCCGA
* *
3119529 AAAAAGGATCGATCCCTCGACCAAAAGGATTAATCCCAAACTTTATAT-TATGCATAA-GATCGA
1 AAAAAGGATCGATCCCTCGACCAAAAGGATCAATCCCAAACTTTATATCCA-GCA-AAGGATCGA
3119592 TTTC-TTTTCAAAAAGATCGATCC
64 -TTCGTTTTCAAAAAGATCGATCC
3119615 CTCGAACGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
91 1 0.01
92 67 0.92
93 5 0.07
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (92 bp):
AAAAAGGATCGATCCCTCGACCAAAAGGATCAATCCCAAACTTTATATCCAGCAAAGGATCGATT
CGTTTTCAAAAAGATCGATCCATCCGA
Found at i:3121120 original size:2 final size:2
Alignment explanation
Indices: 3121115--3121156 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3121105 GCACACACAC
3121115 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3121157 GATTTCACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3121619 original size:18 final size:18
Alignment explanation
Indices: 3121598--3121633 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3121588 GTAAAACACA
*
3121598 TATGTCCCGTATGACCAC
1 TATGTCCCGTAGGACCAC
3121616 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
3121634 GTAGAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAC
Found at i:3122031 original size:4 final size:4
Alignment explanation
Indices: 3122022--3122048 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3122012 AACCTATTGT
3122022 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
3122049 TTACATAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:3122154 original size:25 final size:25
Alignment explanation
Indices: 3122126--3122175 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3122116 TTTAGCACCA
3122126 TATCACTACATGTTTATGATTCAGT
1 TATCACTACATGTTTATGATTCAGT
* *
3122151 TATCCCTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGATTCAGT
3122176 ACCCCTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (25 bp):
TATCACTACATGTTTATGATTCAGT
Found at i:3133344 original size:29 final size:30
Alignment explanation
Indices: 3133311--3133367 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
3133301 ATAAAAATAA
* *
3133311 AAAATTGAGTTTAAGATTTTT-ATATTTTT
1 AAAATTAAATTTAAGATTTTTCATATTTTT
*
3133340 AAAATTAAATTTAATATTTTTCATATTT
1 AAAATTAAATTTAAGATTTTTCATATTT
3133368 ATAATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (30 bp):
AAAATTAAATTTAAGATTTTTCATATTTTT
Found at i:3133356 original size:21 final size:23
Alignment explanation
Indices: 3133332--3133378 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3133322 TAAGATTTTT
3133332 ATATTTTT-AAAATTA-AATTTA
1 ATATTTTTCAAAATTATAATTTA
* *
3133353 ATATTTTTCATATTTATAATTTA
1 ATATTTTTCAAAATTATAATTTA
3133376 ATA
1 ATA
3133379 GTTATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 5 0.23
23 9 0.41
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTTTTCAAAATTATAATTTA
Found at i:3139555 original size:29 final size:29
Alignment explanation
Indices: 3139513--3139569 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
3139503 TTAATTTAGA
3139513 GACTGTTTAAAATCGGAAGGACTTATCTT
1 GACTGTTTAAAATCGGAAGGACTTATCTT
3139542 GACTGTTTAAAATCGGAAGGACTTATCT
1 GACTGTTTAAAATCGGAAGGACTTATCT
3139570 CTTCTTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (29 bp):
GACTGTTTAAAATCGGAAGGACTTATCTT
Found at i:3139904 original size:22 final size:22
Alignment explanation
Indices: 3139879--3139923 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3139869 AAACAAGTTA
*
3139879 TATGCAT-ATTTGTTTAGTTTAG
1 TATGCATCATATGTTT-GTTTAG
3139901 TATGCATCATATGTTTGTTTAG
1 TATGCATCATATGTTTGTTTAG
3139923 T
1 T
3139924 TTATTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.22, C:0.07, G:0.18, T:0.53
Consensus pattern (22 bp):
TATGCATCATATGTTTGTTTAG
Found at i:3140955 original size:38 final size:39
Alignment explanation
Indices: 3140913--3140987 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
3140903 TATAAAATCA
* * *
3140913 CTAGATTGTGACA-TGTCACTTAACGGGAAAATTAAGCC
1 CTAGATTCTGACACCGTCACTTAACAGGAAAATTAAGCC
3140951 CTAGATTCTGACACGCGTCACTTAACAGGAAAATTAA
1 CTAGATTCTGACAC-CGTCACTTAACAGGAAAATTAA
3140988 AATCGTAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 12 0.38
40 20 0.62
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (39 bp):
CTAGATTCTGACACCGTCACTTAACAGGAAAATTAAGCC
Found at i:3142112 original size:24 final size:24
Alignment explanation
Indices: 3142085--3142130 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3142075 TGGAGAGGCT
*
3142085 GAGGGTGAGGGTGAAGATGAAGGA
1 GAGGATGAGGGTGAAGATGAAGGA
* *
3142109 GAGGATGATGGTGATGATGAAG
1 GAGGATGAGGGTGAAGATGAAG
3142131 ACGGTGAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (24 bp):
GAGGATGAGGGTGAAGATGAAGGA
Found at i:3152913 original size:2 final size:2
Alignment explanation
Indices: 3152906--3152931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3152896 TCCTTATTCC
3152906 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
3152932 TATTAACAGT
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):
AT
Found at i:3160492 original size:56 final size:57
Alignment explanation
Indices: 3160401--3160516 Score: 171
Period size: 56 Copynumber: 2.1 Consensus size: 57
3160391 GTCCCACAAA
* * * * *
3160401 AGAAAAATAATTTATTCAGAACAGCTTTCCCTAAATATTACATGCTTTCTCAAATAT
1 AGAAAAATAATTTATTCAGAACACCTTTCCATAAATATTACATGCCTGCTCAAAAAT
*
3160458 AGAAAAAT-ATTTATTTAGAACACCTTTCCATAAATATTACATGCCTGCTCAAAAAT
1 AGAAAAATAATTTATTCAGAACACCTTTCCATAAATATTACATGCCTGCTCAAAAAT
3160514 AGA
1 AGA
3160517 GAGAAAAGGA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 45 0.85
57 8 0.15
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (57 bp):
AGAAAAATAATTTATTCAGAACACCTTTCCATAAATATTACATGCCTGCTCAAAAAT
Found at i:3164696 original size:57 final size:58
Alignment explanation
Indices: 3164625--3164769 Score: 151
Period size: 53 Copynumber: 2.6 Consensus size: 58
3164615 TTATGTCATT
* * *
3164625 ATATGAGTATATGTTTTATATGAATAAATGATAAATTGAAT-AATGATATGTGAAATA
1 ATATGAGTAAATGTTTTATGTGAATAAATGATAAATTGAATAAATGATATATGAAATA
* * * * *
3164682 ATATGAGTAAATGTTCTACGTGAATAAATG-----TTGAGTAAATGCTATATGAAATG
1 ATATGAGTAAATGTTTTATGTGAATAAATGATAAATTGAATAAATGATATATGAAATA
*
3164735 CTATGAG-AAATTGTTTTATGTGAATAAATGATAAA
1 ATATGAGTAAA-TGTTTTATGTGAATAAATGATAAA
3164770 GCACAAAGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
52 8 0.11
53 36 0.51
57 26 0.37
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.37
Consensus pattern (58 bp):
ATATGAGTAAATGTTTTATGTGAATAAATGATAAATTGAATAAATGATATATGAAATA
Found at i:3164956 original size:24 final size:24
Alignment explanation
Indices: 3164937--3164983 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3164927 AATCTATGTT
* *
3164937 GCACTTCTATGCATATTCTACGCG
1 GCACTTCGATGCAAATTCTACGCG
3164961 GCACTTCGATGCAAATTCTACGC
1 GCACTTCGATGCAAATTCTACGC
3164984 TGGAGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (24 bp):
GCACTTCGATGCAAATTCTACGCG
Found at i:3168709 original size:17 final size:15
Alignment explanation
Indices: 3168687--3168747 Score: 70
Period size: 15 Copynumber: 3.9 Consensus size: 15
3168677 GTCCCTCCTA
3168687 AATTTAATTTTCATTTT
1 AATTTAATTTT--TTTT
3168704 AATTTAATTGTTTTTT
1 AATTTAATT-TTTTTT
* *
3168720 AATTTTATGTTTTTT
1 AATTTAATTTTTTTT
3168735 AATTT-ATTTTTTT
1 AATTTAATTTTTTT
3168748 CTTTCAATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
14 7 0.17
15 11 0.28
16 11 0.28
17 9 0.22
18 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (15 bp):
AATTTAATTTTTTTT
Found at i:3168763 original size:44 final size:44
Alignment explanation
Indices: 3168709--3168796 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
3168699 ATTTTAATTT
* *
3168709 AATTGTTTTTTAAT-TTTATGTTTTTTAATTTATTTTTTT-CTTTC
1 AATTGCTTTTTAATATTT-TG-TTTTGAATTTATTTTTTTGCTTTC
* *
3168753 AATTGCTTTTTTATATTTTGTTTTGATTTTATTTTTTTGCTTTC
1 AATTGCTTTTTAATATTTTGTTTTGAATTTATTTTTTTGCTTTC
3168797 TTTTTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 16 0.42
44 19 0.50
45 3 0.08
ACGTcount: A:0.16, C:0.06, G:0.07, T:0.72
Consensus pattern (44 bp):
AATTGCTTTTTAATATTTTGTTTTGAATTTATTTTTTTGCTTTC
Found at i:3168908 original size:8 final size:9
Alignment explanation
Indices: 3168872--3168908 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
3168862 TTTTTAGGTT
3168872 TTTTATTTA
1 TTTTATTTA
3168881 TTTTATTTA
1 TTTTATTTA
*
3168890 TTAT-TTTA
1 TTTTATTTA
3168898 TTTT-TTTA
1 TTTTATTTA
3168906 TTT
1 TTT
3168909 AGCCATCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 14 0.54
9 12 0.46
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTATTTA
Found at i:3168909 original size:12 final size:13
Alignment explanation
Indices: 3168873--3168908 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3168863 TTTTAGGTTT
3168873 TTTATTTATTTTA
1 TTTATTTATTTTA
3168886 TTTA-TTATTTTA
1 TTTATTTATTTTA
*
3168898 TTTTTTTATTT
1 TTTATTTATTT
3168909 AGCCATCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:3172015 original size:196 final size:196
Alignment explanation
Indices: 3171660--3172052 Score: 729
Period size: 196 Copynumber: 2.0 Consensus size: 196
3171650 TAAAGGCATG
3171660 AGTGGAATATGCATGTATGTATGTTTGATTATATGGATGATCTGTTCTTTTATGTGTTAGATGAT
1 AGTGGAATATGCATGTATGTATGTTTGATTATATGGATGATCTGTTCTTTTATGTGTTAGATGAT
3171725 AAAGTATAAGTAATTACATAAGAAAGGTTATGAATTATATGAGATATAACTATGTGATATAGTAA
66 AAAGTATAAGTAATTACATAAGAAAGGTTATGAATTATATGAGATATAACTATGTGATATAGTAA
3171790 AATATAATTATTATTATATGATAAGTGAAATAAGCTGGATAATATTGATCTATAGATGAAGTGAG
131 AATATAATTATTATTATATGATAAGTGAAATAAGCTGGATAATATTGATCTATAGATGAAGTGAG
3171855 A
196 A
3171856 AGTGGAATATGCATGTATGTATGTTTGATTATATGGATTGATCTGTTC-TTTATGTGTTAGATGA
1 AGTGGAATATGCATGTATGTATGTTTGATTATATGGA-TGATCTGTTCTTTTATGTGTTAGATGA
3171920 TAAAGTATAAGTAATTACATAAGAAAGGTTATGAATTATATGAGATATAAACTATGTGATCATAG
65 TAAAGTATAAGTAATTACATAAGAAAGGTTATGAATTATATGAGATAT-AACTATGTGAT-ATAG
*
3171985 TAAAATAT-ATTATTATTATATGAT-AGTGAAATAAGCTGGATAATATTGATCTATAGGTGAAGT
128 TAAAATATAATTATTATTATATGATAAGTGAAATAAGCTGGATAATATTGATCTATAGATGAAGT
3172048 GAGA
193 GAGA
3172052 A
1 A
3172053 TAGTACACTA
Statistics
Matches: 193, Mismatches: 1, Indels: 6
0.96 0.00 0.03
Matches are distributed among these distances:
196 144 0.75
197 37 0.19
198 12 0.06
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (196 bp):
AGTGGAATATGCATGTATGTATGTTTGATTATATGGATGATCTGTTCTTTTATGTGTTAGATGAT
AAAGTATAAGTAATTACATAAGAAAGGTTATGAATTATATGAGATATAACTATGTGATATAGTAA
AATATAATTATTATTATATGATAAGTGAAATAAGCTGGATAATATTGATCTATAGATGAAGTGAG
A
Found at i:3173041 original size:144 final size:138
Alignment explanation
Indices: 3172883--3173169 Score: 461
Period size: 144 Copynumber: 2.0 Consensus size: 138
3172873 GTCGAGGGTA
3172883 GCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAG-ACATACTTGA
1 GCGGTTCTTTGGGACATATGTATATTCTTTGGAACA--TGTGAAGTCTTGAAAGAACATAC-TGA
* *
3172947 TCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTA-TATGGCAT
63 TCCATAGTATATG--TATGATTCTTAAGGAATTCTATG-GGTCCTTATGGACATCATTA-GGCAC
3173011 TACGGTGCAATTCTAC
124 TACGGTGC-ATTCTAC
3173027 GCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGAAGTCTTGAAAGACACATACTGATC
1 GCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGAAGTCTTGAAAGA-ACATACTGATC
3173092 CATAGTATATGTATGATTCTTAAGGAATTCTATGGGTCCTTATGGACATCATTAGGCACTACGGT
65 CATAGTATATGTATGATTCTTAAGGAATTCTATGGGTCCTTATGGACATCATTAGGCACTACGGT
3173157 GCATTCTAC
130 GCATTCTAC
3173166 GCGG
1 GCGG
3173170 CACTTCGGTG
Statistics
Matches: 138, Mismatches: 2, Indels: 11
0.91 0.01 0.07
Matches are distributed among these distances:
139 11 0.08
140 28 0.20
141 25 0.18
142 16 0.12
143 16 0.12
144 42 0.30
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (138 bp):
GCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGAAGTCTTGAAAGAACATACTGATCC
ATAGTATATGTATGATTCTTAAGGAATTCTATGGGTCCTTATGGACATCATTAGGCACTACGGTG
CATTCTAC
Found at i:3173188 original size:22 final size:22
Alignment explanation
Indices: 3173146--3173188 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3173136 GACATCATTA
* *
3173146 GGCACTACGGTGCATTCTACGC
1 GGCACTACGGTGCAATATACGC
*
3173168 GGCACTTCGGTGCAATATACG
1 GGCACTACGGTGCAATATACG
3173189 AGCTGTGGTG
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:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (22 bp):
GGCACTACGGTGCAATATACGC
Found at i:3173950 original size:12 final size:12
Alignment explanation
Indices: 3173933--3173958 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3173923 CTGCACAAAA
3173933 TATCAAAATAAG
1 TATCAAAATAAG
3173945 TATCAAAATAAG
1 TATCAAAATAAG
3173957 TA
1 TA
3173959 CACTTATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (12 bp):
TATCAAAATAAG
Found at i:3176338 original size:157 final size:155
Alignment explanation
Indices: 3176104--3176411 Score: 447
Period size: 157 Copynumber: 2.0 Consensus size: 155
3176094 CACATAGCAT
* * *
3176104 GTCAACTAAAACAATATCTGGCTAATTTACTAAATCCCCCAGCCAAAGGAAAACGATATTCTGCT
1 GTCAACTAAAACAATATCTAGATAATTTACTAAATCCCCCAGACAAAGGAAAACGATATTCTGCT
* * * *
3176169 TCACACAACTGATCAATAGATACTTCAGTCATGCAAAAATTGACTTTATCGTACTCAAATGGAC-
66 TCACACAACTGATCAACAGATACTTCAATCAAGCAAAAATTGACTTTAAC--ACTCAAATGGACT
3176233 AGTGAAATTGCTAAACAATATTCTCACC
129 A-TGAAATTGCTAAACAATATTCTCACC
* * * *
3176261 GTCAATTAAAACAATATCTAGATAGTTTAGTAAATCCCCCAGACAAAGGAAAACTATATTCTGCT
1 GTCAACTAAAACAATATCTAGATAATTTACTAAATCCCCCAGACAAAGGAAAACGATATTCTGCT
* * *
3176326 TGACACTACTGATCAACATATACTTCAATCAAGCAAAAATTGACTTTAACACTCAAATGGACTAT
66 TCACACAACTGATCAACAGATACTTCAATCAAGCAAAAATTGACTTTAACACTCAAATGGACTAT
*
3176391 GAAATTGCTAAATAATATTCT
131 GAAATTGCTAAACAATATTCT
3176412 TACCTTCTGC
Statistics
Matches: 135, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
155 33 0.24
156 1 0.01
157 101 0.75
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (155 bp):
GTCAACTAAAACAATATCTAGATAATTTACTAAATCCCCCAGACAAAGGAAAACGATATTCTGCT
TCACACAACTGATCAACAGATACTTCAATCAAGCAAAAATTGACTTTAACACTCAAATGGACTAT
GAAATTGCTAAACAATATTCTCACC
Found at i:3179782 original size:31 final size:32
Alignment explanation
Indices: 3179746--3179828 Score: 123
Period size: 31 Copynumber: 2.6 Consensus size: 32
3179736 CATACCTAAT
*
3179746 GTTTACTTTTTGTTTCATTTTATTA-CCCGGC
1 GTTTACTTTTTGTTTCATTTTATTACCCCAGC
**
3179777 GTTTACTTTTTGTTTCATTTTATTACCCCATT
1 GTTTACTTTTTGTTTCATTTTATTACCCCAGC
*
3179809 GTTAACTTTTTGTTTCATTT
1 GTTTACTTTTTGTTTCATTT
3179829 AGTACCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.59
Consensus pattern (32 bp):
GTTTACTTTTTGTTTCATTTTATTACCCCAGC
Found at i:3180246 original size:13 final size:13
Alignment explanation
Indices: 3180230--3180277 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
3180220 CCCCATGCGA
*
3180230 GGTGGCCATACGG
1 GGTGGACATACGG
3180243 GGT-GACATAC-G
1 GGTGGACATACGG
*
3180254 GGTTGACATACGG
1 GGTGGACATACGG
3180267 GGT-GACATACG
1 GGTGGACATACG
3180278 AGCCATACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 4 0.12
12 21 0.66
13 7 0.22
ACGTcount: A:0.23, C:0.19, G:0.40, T:0.19
Consensus pattern (13 bp):
GGTGGACATACGG
Found at i:3180253 original size:12 final size:12
Alignment explanation
Indices: 3180236--3180277 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
3180226 GCGAGGTGGC
3180236 CATACGGGGTGA
1 CATACGGGGTGA
*
3180248 CATACGGGTTGA
1 CATACGGGGTGA
3180260 CATACGGGGTGA
1 CATACGGGGTGA
3180272 CATACG
1 CATACG
3180278 AGCCATACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (12 bp):
CATACGGGGTGA
Found at i:3180312 original size:35 final size:35
Alignment explanation
Indices: 3180272--3180359 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
3180262 TACGGGGTGA
3180272 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
3180307 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
*
3180342 CATAGGAGCCATACGAGC
1 CATACGAGCCATACGAGC
3180360 GTTCTCCCCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (35 bp):
CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
Found at i:3180376 original size:26 final size:26
Alignment explanation
Indices: 3180347--3180401 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
3180337 CCATGCATAG
3180347 GAGCCATACGAGCGTTCTCCCCATGC
1 GAGCCATACGAGCGTTCTCCCCATGC
3180373 GAGCCATACGAGCGTTCTCCCCATGC
1 GAGCCATACGAGCGTTCTCCCCATGC
3180399 GAG
1 GAG
3180402 GTGGCCATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.18
Consensus pattern (26 bp):
GAGCCATACGAGCGTTCTCCCCATGC
Found at i:3180474 original size:29 final size:29
Alignment explanation
Indices: 3180442--3180561 Score: 231
Period size: 29 Copynumber: 4.1 Consensus size: 29
3180432 ATGCAGCCTA
3180442 GGCGACCTTGTAGGTCGCCATGTGGTCCC
1 GGCGACCTTGTAGGTCGCCATGTGGTCCC
3180471 GGCGACCTTGTAGGTCGCCATGTGGTCCC
1 GGCGACCTTGTAGGTCGCCATGTGGTCCC
3180500 GGCGACCTTGTAGGTCGCCATGTGGTCCC
1 GGCGACCTTGTAGGTCGCCATGTGGTCCC
*
3180529 GGCGACCTTGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTGGTCCC
3180558 GGCG
1 GGCG
3180562 CCATTCCCAT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.11, C:0.31, G:0.35, T:0.23
Consensus pattern (29 bp):
GGCGACCTTGTAGGTCGCCATGTGGTCCC
Found at i:3180504 original size:58 final size:58
Alignment explanation
Indices: 3180424--3180561 Score: 233
Period size: 58 Copynumber: 2.4 Consensus size: 58
3180414 TGGAATAGAG
* *
3180424 AGGTCGCCATGCAG-CCTAGGCGACCTTGTAGGTCGCCATGTGGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGTAGGTCGCCATGTGGTCCCGGCGACCTTGT
*
3180482 AGGTCGCCATGTGGTCCCGGCGACCTTGTAGGTCGCCATGTGGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGTAGGTCGCCATGTGGTCCCGGCGACCTTGT
3180540 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
3180562 CCATTCCCAT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
58 73 0.97
59 2 0.03
ACGTcount: A:0.12, C:0.31, G:0.34, T:0.22
Consensus pattern (58 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGTAGGTCGCCATGTGGTCCCGGCGACCTTGT
Found at i:3180580 original size:13 final size:13
Alignment explanation
Indices: 3180562--3180593 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3180552 AGTCCCGGCG
3180562 CCATTCCCATCAT
1 CCATTCCCATCAT
3180575 CCATTCCCATCAT
1 CCATTCCCATCAT
3180588 CCATTC
1 CCATTC
3180594 ATGCAGCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.47, G:0.00, T:0.31
Consensus pattern (13 bp):
CCATTCCCATCAT
Found at i:3180787 original size:25 final size:25
Alignment explanation
Indices: 3180758--3180809 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3180748 TGTACAATTA
3180758 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
3180783 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
3180808 TT
1 TT
3180810 ATAAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:3180849 original size:23 final size:23
Alignment explanation
Indices: 3180821--3180866 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3180811 TAAAGAAAGA
3180821 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
3180844 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
3180867 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:3180879 original size:4 final size:4
Alignment explanation
Indices: 3180870--3180952 Score: 62
Period size: 4 Copynumber: 20.5 Consensus size: 4
3180860 ATTGCAGCCG
** **
3180870 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGGG AGAA AGGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA AGAA
** *
3180920 AGAA AGGG AGAA AGGAA AGTA AG-A AG-A AGAA AG
1 AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG
3180953 GGAGATAAGG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
3 6 0.10
4 44 0.71
5 12 0.19
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:3180881 original size:25 final size:23
Alignment explanation
Indices: 3180821--3180881 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
3180811 TAAAGAAAGA
**
3180821 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
3180844 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
3180867 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
3180882 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:3180895 original size:21 final size:21
Alignment explanation
Indices: 3180871--3180944 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
3180861 TTGCAGCCGA
3180871 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
3180892 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
3180913 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
3180934 GAAAGTAAGAA
1 GAAAGAAAGAA
3180945 GAAGAAAGGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.01
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:3180937 original size:13 final size:13
Alignment explanation
Indices: 3180873--3180944 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 13
3180863 GCAGCCGAGA
3180873 AAGAAA-GAAAGG
1 AAGAAAGGAAAGG
* *
3180885 GAGAAAGGAAAGA
1 AAGAAAGGAAAGG
3180898 AAGAAAGGGAGAAAGG
1 AAGAAA--G-GAAAGG
3180914 AAAGAAA-GAAAGG
1 -AAGAAAGGAAAGG
* *
3180927 GAGAAAGGAAAGT
1 AAGAAAGGAAAGG
3180940 AAGAA
1 AAGAA
3180945 GAAGAAAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 10 0.21
13 25 0.53
15 1 0.02
16 5 0.11
17 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.01
Consensus pattern (13 bp):
AAGAAAGGAAAGG
Found at i:3181207 original size:45 final size:45
Alignment explanation
Indices: 3181104--3181235 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
3181094 TACATAAATT
*
3181104 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
3181146 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
3181190 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
3181236 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:3183601 original size:17 final size:17
Alignment explanation
Indices: 3183579--3183611 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3183569 ACAATGATTT
*
3183579 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
3183596 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
3183612 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:3183628 original size:24 final size:22
Alignment explanation
Indices: 3183596--3183664 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
3183586 AAATCATTAC
3183596 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
3183618 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
3183643 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
3183665 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:3183869 original size:19 final size:20
Alignment explanation
Indices: 3183828--3183875 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3183818 AATTATTATA
* *
3183828 AAATCATTATTATAATTATC
1 AAATCATTACTATAATCATC
3183848 AAATCATTACTA-AATCATC
1 AAATCATTACTATAATCATC
3183867 AAATCATTA
1 AAATCATTA
3183876 AATATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATCATTACTATAATCATC
Found at i:3183922 original size:26 final size:25
Alignment explanation
Indices: 3183888--3184351 Score: 369
Period size: 26 Copynumber: 18.6 Consensus size: 25
3183878 TATTTAAATC
*
3183888 ATTATTAAATCATTTTTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
3183914 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
3183940 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
3183966 ATTATCAAATCATTACTA-AATCATCAA
1 ATTAT-AAATCATTATTATAATGAT--T
* *
3183993 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
3184015 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
3184038 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
3184064 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
3184090 ATTATCAAATCATTACTA-AATCATCAA
1 ATTAT-AAATCATTATTATAATGAT--T
* * *
3184117 ATCATTAAA--AAT-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
3184139 A-T-TAAATCATT-TTATAATGATT
1 ATTATAAATCATTATTATAATGATT
3184161 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
3184187 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
3184213 ATTATCAAATCATTACTA-AATCATCAA
1 ATTAT-AAATCATTATTATAATGAT--T
* *
3184240 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
3184262 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
3184285 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
3184311 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
3184337 ATTATCAAATCATTA
1 ATTAT-AAATCATTA
3184352 CTAAATCATC
Statistics
Matches: 373, Mismatches: 31, Indels: 68
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.04
20 2 0.01
21 7 0.02
22 16 0.04
23 15 0.04
24 26 0.07
25 32 0.09
26 238 0.64
27 20 0.05
28 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (25 bp):
ATTATAAATCATTATTATAATGATT
Found at i:3183988 original size:124 final size:124
Alignment explanation
Indices: 3183842--3184409 Score: 1111
Period size: 124 Copynumber: 4.6 Consensus size: 124
3183832 CATTATTATA
3183842 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3183907 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
66 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
3183966 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3184031 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
66 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
*
3184090 ATTATCAAATCATTACTAAATCATCAAATCATTAAAAATTTAAATCATTATTAAATCA-TTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3184154 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
66 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
3184213 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3184278 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
66 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
*
3184337 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAATAAATCATTTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3184402 AATGATTA
66 AATGATTA
3184410 ATAAATACAT
Statistics
Matches: 440, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
123 122 0.28
124 318 0.72
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (124 bp):
ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
Found at i:3184064 original size:23 final size:23
Alignment explanation
Indices: 3183888--3184415 Score: 192
Period size: 26 Copynumber: 21.4 Consensus size: 23
3183878 TATTTAAATC
* *
3183888 ATTATTAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
3183911 ATTATTACTAAATCATTATTATAATG
1 ATTA--A-TAAATCATTATTATAATG
*
3183937 ATTATTATCAAATCATTACTATAATG
1 ATTA--AT-AAATCATTATTATAATG
* *
3183963 ATTATTATCAAATCATTACTA-AATC
1 ATTA--AT-AAATCATTATTATAATG
* * * * * *
3183988 ATCAAATCATTAAATATT-TAAATC
1 AT-TAATAAATCATTATTAT-AATG
* *
3184012 ATTATTAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
3184035 ATTATTACTAAATCATTATTATAATG
1 ATTA--A-TAAATCATTATTATAATG
*
3184061 ATTATTATCAAATCATTACTATAATG
1 ATTA--AT-AAATCATTATTATAATG
* *
3184087 ATTATTATCAAATCATTACTA-AATC
1 ATTA--AT-AAATCATTATTATAATG
* * * * ** *
3184112 ATCAAATCATTAAAAATT-TAAATC
1 AT-TAATAAATCATTATTAT-AATG
*
3184136 ATTATTAAATCATT-TTATAATG
1 ATTAATAAATCATTATTATAATG
3184158 ATTATTACTAAATCATTATTATAATG
1 ATTA--A-TAAATCATTATTATAATG
*
3184184 ATTATTATCAAATCATTACTATAATG
1 ATTA--AT-AAATCATTATTATAATG
* *
3184210 ATTATTATCAAATCATTACTA-AATC
1 ATTA--AT-AAATCATTATTATAATG
* * * * * *
3184235 ATCAAATCATTAAATATT-TAAATC
1 AT-TAATAAATCATTATTAT-AATG
* *
3184259 ATTATTAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
3184282 ATTATTACTAAATCATTATTATAATG
1 ATTA--A-TAAATCATTATTATAATG
*
3184308 ATTATTATCAAATCATTACTATAATG
1 ATTA--AT-AAATCATTATTATAATG
* *
3184334 ATTATTATCAAATCATTACTA-AATC
1 ATTA--AT-AAATCATTATTATAATG
* * * * * *
3184359 ATCAAATCATTAAATATT-TAAATC
1 AT-TAATAAATCATTATTAT-AATG
*
3184383 ATTAATAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
3184406 ATTAATAAAT
1 ATTAATAAAT
3184416 ACATAGAAAT
Statistics
Matches: 401, Mismatches: 71, Indels: 66
0.75 0.13 0.12
Matches are distributed among these distances:
22 9 0.02
23 85 0.21
24 35 0.09
25 33 0.08
26 239 0.60
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTAATAAATCATTATTATAATG
Found at i:3184117 original size:19 final size:18
Alignment explanation
Indices: 3184093--3184148 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
3184083 AATGATTATT
3184093 ATCAAATCATTACTAAATC
1 ATCAAATCATTA-TAAATC
*
3184112 ATCAAATCATTAAAAAT-
1 ATCAAATCATTATAAATC
*
3184129 -TTAAATCATTATTAAATC
1 ATCAAATCATTA-TAAATC
3184147 AT
1 AT
3184149 TTTATAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
18 4 0.13
19 13 0.42
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (18 bp):
ATCAAATCATTATAAATC
Found at i:3184201 original size:247 final size:248
Alignment explanation
Indices: 3183842--3184409 Score: 1111
Period size: 247 Copynumber: 2.3 Consensus size: 248
3183832 CATTATTATA
3183842 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3183907 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATC
66 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATC
3183972 AAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGAT
131 AAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGAT
3184037 TATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
196 TATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
*
3184090 ATTATCAAATCATTACTAAATCATCAAATCATTAAAAATTTAAATCATTATTAAATCA-TTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3184154 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATC
66 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATC
3184219 AAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGAT
131 AAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGAT
3184284 TATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
196 TATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
*
3184337 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAATAAATCATTTTTAT
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
3184402 AATGATTA
66 AATGATTA
3184410 ATAAATACAT
Statistics
Matches: 316, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
247 245 0.78
248 71 0.22
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (248 bp):
ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTAT
AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATC
AAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGAT
TATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATT
Found at i:3188142 original size:28 final size:29
Alignment explanation
Indices: 3188095--3188156 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
3188085 ATTTTTTATA
*
3188095 TAATATAATAATAACTTAAACTAATAAAC
1 TAATATAATAATAACTTAAACTAACAAAC
3188124 TAATATAAT-ATAACTTAAACTAACAAAC
1 TAATATAATAATAACTTAAACTAACAAAC
3188152 TAATA
1 TAATA
3188157 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 23 0.72
29 9 0.28
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (29 bp):
TAATATAATAATAACTTAAACTAACAAAC
Found at i:3188166 original size:21 final size:21
Alignment explanation
Indices: 3188133--3188181 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3188123 CTAATATAAT
3188133 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
3188154 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
3188175 ATTAACT
1 A-TAACT
3188182 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:3188757 original size:15 final size:15
Alignment explanation
Indices: 3188737--3188800 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
3188727 CCATCCCCTC
3188737 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
3188752 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
3188767 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
3188785 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
3188800 C
1 C
3188801 GTCCCATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
15 17 0.40
16 12 0.29
17 12 0.29
18 1 0.02
ACGTcount: A:0.17, C:0.55, G:0.08, T:0.20
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:3188775 original size:17 final size:16
Alignment explanation
Indices: 3188738--3188808 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 16
3188728 CATCCCCTCC
3188738 CCCATGCATTCCCAC-
1 CCCATGCATTCCCACT
3188753 CCCATGCATTCCCACGT
1 CCCATGCATTCCCAC-T
* * *
3188770 CCCATGCATCCCCTCC
1 CCCATGCATTCCCACT
3188786 CCCATGCATTCCCACGT
1 CCCATGCATTCCCAC-T
3188803 CCCATG
1 CCCATG
3188809 TTGATTGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.32
16 13 0.28
17 19 0.40
ACGTcount: A:0.17, C:0.52, G:0.10, T:0.21
Consensus pattern (16 bp):
CCCATGCATTCCCACT
Found at i:3188789 original size:16 final size:16
Alignment explanation
Indices: 3188728--3188794 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
3188718 TCCAATGCAC
3188728 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
* *
3188744 CATTCCC-ACCCCATG
1 CATCCCCTCCCCCATG
* * *
3188759 CATTCCCACGTCCCATG
1 CATCCCCTC-CCCCATG
3188776 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
3188792 CAT
1 CAT
3188795 TCCCACGTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
15 14 0.33
16 15 0.36
17 13 0.31
ACGTcount: A:0.16, C:0.55, G:0.07, T:0.21
Consensus pattern (16 bp):
CATCCCCTCCCCCATG
Found at i:3188793 original size:33 final size:32
Alignment explanation
Indices: 3188738--3188808 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 32
3188728 CATCCCCTCC
*
3188738 CCCATGCATTCCCACCCCATGCATTCCCACGT
1 CCCATGCATCCCCACCCCATGCATTCCCACGT
*
3188770 CCCATGCATCCCCTCCCCCATGCATTCCCACGT
1 CCCATGCATCCCC-ACCCCATGCATTCCCACGT
3188803 CCCATG
1 CCCATG
3188809 TTGATTGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.17, C:0.52, G:0.10, T:0.21
Consensus pattern (32 bp):
CCCATGCATCCCCACCCCATGCATTCCCACGT
Found at i:3188890 original size:29 final size:29
Alignment explanation
Indices: 3188848--3188936 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
3188838 AAATACACAC
3188848 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
3188877 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
3188906 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
3188935 AG
1 AG
3188937 ACCACTGTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:3193788 original size:24 final size:23
Alignment explanation
Indices: 3193714--3193794 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
3193704 CATGCCCCTG
*
3193714 TGCATCGATGCACATTC-AAGGCG
1 TGCATCGATGCACATTCAAAGG-A
* *
3193737 TGCATCGGTGCATCA--CCAA-GA
1 TGCATCGATGCA-CATTCAAAGGA
*
3193758 TGAATCGATGCACATTCAAAGTGA
1 TGCATCGATGCACATTCAAAG-GA
3193782 TGCATCGATGCAC
1 TGCATCGATGCAC
3193795 TGTTAAGTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.04
21 10 0.22
22 5 0.11
23 13 0.28
24 16 0.35
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAAGGA
Found at i:3197653 original size:22 final size:21
Alignment explanation
Indices: 3197611--3197650 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3197601 GAGTTTATTT
*
3197611 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3197632 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3197651 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3209588 original size:57 final size:57
Alignment explanation
Indices: 3209507--3209638 Score: 237
Period size: 57 Copynumber: 2.3 Consensus size: 57
3209497 ATTTCTTAGA
*
3209507 TTTTGCACATAAAGTGCCCGTACGGAAATTCATAAACTAATTATGAATTTCTGAACT
1 TTTTGCACATAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTGAACT
*
3209564 TTTTGCACATAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAACT
1 TTTTGCACATAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTGAACT
*
3209621 TTTTGCACACAAAGTGCC
1 TTTTGCACATAAAGTGCC
3209639 ATTTGGTAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 72 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (57 bp):
TTTTGCACATAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTGAACT
Found at i:3210004 original size:22 final size:21
Alignment explanation
Indices: 3209978--3210018 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3209968 TACCCCTACC
*
3209978 ATGGTATCGATACTACTATTTT
1 ATGGTACCGATACT-CTATTTT
3210000 ATGGTACCGATACTCTATT
1 ATGGTACCGATACTCTATT
3210019 ACAGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (21 bp):
ATGGTACCGATACTCTATTTT
Found at i:3220404 original size:24 final size:29
Alignment explanation
Indices: 3220376--3220435 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 29
3220366 GTTCCTTTTT
3220376 ATAAAACAT-TTT-AATTTA-ATA-AT-A
1 ATAAAACATCTTTAAATTTACATACATAA
3220400 ATAAAACATGCTTTAAATTTACATACATAA
1 ATAAAACAT-CTTTAAATTTACATACATAA
3220430 ATAAAA
1 ATAAAA
3220436 GTGATTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 9 0.30
26 3 0.10
27 6 0.20
28 3 0.10
29 2 0.07
30 7 0.23
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (29 bp):
ATAAAACATCTTTAAATTTACATACATAA
Found at i:3220919 original size:57 final size:57
Alignment explanation
Indices: 3220822--3221078 Score: 462
Period size: 57 Copynumber: 4.5 Consensus size: 57
3220812 AAATTCATAT
* * * *
3220822 AATTTCTT-AGTTTTTGCACATAAAGTGCCCATATGAAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
*
3220878 AATTTCTTAACTTTTTGCACACAAAGTGCTCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
3220935 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
3220992 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
3221049 AATTTCTTAACTTTTTGCACACAAAGTGCC
1 AATTTCTTAACTTTTTGCACACAAAGTGCC
3221079 ATTTGGTAAT
Statistics
Matches: 194, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
56 8 0.04
57 186 0.96
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (57 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
Found at i:3221445 original size:22 final size:19
Alignment explanation
Indices: 3221418--3221471 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
3221408 TACCCCTACC
*
3221418 ATGGTATCAATACTACTATTCT
1 ATGGTATCGATACT-CTA-T-T
*
3221440 ATGGTACCGATACTCTATT
1 ATGGTATCGATACTCTATT
3221459 ATGGTATCGATAC
1 ATGGTATCGATAC
3221472 CATTTTTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 13 0.45
20 1 0.03
21 3 0.10
22 12 0.41
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (19 bp):
ATGGTATCGATACTCTATT
Found at i:3233058 original size:2 final size:2
Alignment explanation
Indices: 3233051--3233103 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
3233041 TTCTTGTTTA
* *
3233051 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3233093 AT AT AT AT AT A
1 AT AT AT AT AT A
3233104 ACTTTTAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3234591 original size:25 final size:25
Alignment explanation
Indices: 3234563--3234612 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3234553 AACATGTGGA
3234563 CAAATTTACTCATATATATATATAT
1 CAAATTTACTCATATATATATATAT
3234588 CAAATTTACTCATATATATATATAT
1 CAAATTTACTCATATATATATATAT
3234613 ATAATAGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (25 bp):
CAAATTTACTCATATATATATATAT
Found at i:3235831 original size:20 final size:20
Alignment explanation
Indices: 3235806--3235857 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3235796 TGTCCAAGAC
3235806 ATCGATCCTTTATC-AAGGGG
1 ATCGATCCTTTATCTAA-GGG
*
3235826 ATCGATCCTTTTTCTAAGGG
1 ATCGATCCTTTATCTAAGGG
3235846 ATCGATCCTTTA
1 ATCGATCCTTTA
3235858 AGCCAGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
ATCGATCCTTTATCTAAGGG
Found at i:3239489 original size:27 final size:29
Alignment explanation
Indices: 3239447--3239515 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
3239437 ATATGAGAAA
* *
3239447 ATATGAGAATAAGAAATAAG-TC-ATGTG-
1 ATATGTGAATATGAAA-AAGATCTATGTGT
*
3239474 ATATGTGAATATGAAAATGATCTATGTGT
1 ATATGTGAATATGAAAAAGATCTATGTGT
3239503 ATATGTGATATAT
1 ATATGTGA-ATAT
3239516 ATATGATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 16 0.46
28 5 0.14
29 8 0.23
30 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (29 bp):
ATATGTGAATATGAAAAAGATCTATGTGT
Found at i:3240188 original size:2 final size:2
Alignment explanation
Indices: 3240119--3240172 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
3240109 TATGAAACAT
*
3240119 TA TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3240160 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3240173 GTTATTCTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3247447 original size:2 final size:2
Alignment explanation
Indices: 3247442--3247517 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
3247432 TATCTTATTC
3247442 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3247484 AT AT 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 AT AT
3247518 CCGCAAATAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3247718 original size:20 final size:20
Alignment explanation
Indices: 3247693--3247738 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
3247683 AATCATGCAT
3247693 ACATACATTTCATATTAATC
1 ACATACATTTCATATTAATC
3247713 ACATACATTTCATATTAATC
1 ACATACATTTCATATTAATC
3247733 ACATAC
1 ACATAC
3247739 TTCATGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (20 bp):
ACATACATTTCATATTAATC
Done.