Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 124 of 182
Found at i:39647323 original size:9 final size:9
Alignment explanation
Indices: 39647311--39647372 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
39647301 TGATATAATG
39647311 TTATAAAAA
1 TTATAAAAA
39647320 TTATAAAGAA
1 TTATAAA-AA
*
39647330 TCATAAAAA
1 TTATAAAAA
* *
39647339 CTTATGAATA
1 -TTATAAAAA
39647349 TTATAAAAA
1 TTATAAAAA
*
39647358 TTCTAATAAA
1 TTATAA-AAA
39647368 TTATA
1 TTATA
39647373 CTTTTTTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 21 0.50
10 21 0.50
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:39648199 original size:20 final size:20
Alignment explanation
Indices: 39648174--39648248 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
39648164 GATCTAATAA
39648174 ATATATTTTTTATAATTTAT
1 ATATATTTTTTATAATTTAT
* *
39648194 ATATATTTATTAT--CTTAT
1 ATATATTTTTTATAATTTAT
39648212 A-AT-TTTATTTA-AA--TAT
1 ATATATTT-TTTATAATTTAT
39648228 ATATATTTTATTATAATTTAT
1 ATATATTTT-TTATAATTTAT
39648249 TAGAACTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 17
0.68 0.05 0.27
Matches are distributed among these distances:
16 7 0.16
17 8 0.19
18 11 0.26
19 2 0.05
20 12 0.28
21 3 0.07
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTTTTTATAATTTAT
Found at i:39648218 original size:16 final size:16
Alignment explanation
Indices: 39648175--39648241 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
39648165 ATCTAATAAA
* *
39648175 TATATTTTTTATAATT
1 TATATATTTTATTATT
39648191 TATATATATTTATTATCT
1 TATATAT-TTTATTAT-T
*
39648209 TATA-ATTTTATTTAAATA
1 TATATATTTTA-TT--ATT
39648227 TATATATTTTATTAT
1 TATATATTTTATTAT
39648242 AATTTATTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 12 0.29
17 11 0.26
18 11 0.26
19 8 0.19
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATATTTTATTATT
Found at i:39648228 original size:30 final size:30
Alignment explanation
Indices: 39648188--39648246 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39648178 ATTTTTTATA
* * *
39648188 ATTTATATATATTTATTATCTTATAATTTT
1 ATTTAAATATATATATTATATTATAATTTT
*
39648218 ATTTAAATATATATATTTTATTATAATTT
1 ATTTAAATATATATATTATATTATAATTT
39648247 ATTAGAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTAAATATATATATTATATTATAATTTT
Found at i:39648249 original size:10 final size:10
Alignment explanation
Indices: 39648208--39648304 Score: 65
Period size: 10 Copynumber: 9.6 Consensus size: 10
39648198 ATTTATTATC
39648208 TTATAATTTTA
1 TTATAA-TTTA
*
39648219 TT-TAA-ATA
1 TTATAATTTA
*
39648227 TATATATTTTA
1 T-TATAATTTA
39648238 TTATAATTTA
1 TTATAATTTA
* *
39648248 TTAGAACTTA
1 TTATAATTTA
* *
39648258 TTATGATTTT
1 TTATAATTTA
*
39648268 TTATAAGTT-
1 TTATAATTTA
39648277 TTATAATCTGTA
1 TTATAAT-T-TA
*
39648289 TGATAATTTA
1 TTATAATTTA
39648299 TTATAA
1 TTATAA
39648305 CATTTTAGAA
Statistics
Matches: 65, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
8 3 0.05
9 7 0.11
10 42 0.65
11 7 0.11
12 6 0.09
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (10 bp):
TTATAATTTA
Found at i:39649020 original size:16 final size:16
Alignment explanation
Indices: 39648980--39649021 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
39648970 TTAAAATTAA
*
39648980 AATATTAAAAATATTT
1 AATATTAAAAATAGTT
*
39648996 AAT-TATAAAAATCGTT
1 AATAT-TAAAAATAGTT
39649012 AATATTAAAA
1 AATATTAAAA
39649022 TAATATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATATTAAAAATAGTT
Found at i:39649710 original size:26 final size:22
Alignment explanation
Indices: 39649666--39649718 Score: 52
Period size: 25 Copynumber: 2.2 Consensus size: 22
39649656 TTGGTTGCAC
*
39649666 AAAAATAAAAAATATTAAATTGA
1 AAAAATAAAAAATATTAAA-AGA
*
39649689 AAAAATGATAAAAATTTGTAAAAGA
1 AAAAAT-A-AAAAATAT-TAAAAGA
39649714 AAAAA
1 AAAAA
39649719 ATATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 6 0.24
24 1 0.04
25 14 0.56
26 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.23
Consensus pattern (22 bp):
AAAAATAAAAAATATTAAAAGA
Found at i:39649753 original size:24 final size:25
Alignment explanation
Indices: 39649713--39649773 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 25
39649703 TTTGTAAAAG
* *
39649713 AAAAAAATATTTATTT-A-TAATTT
1 AAAAAATTAATTATTTAAGTAATTT
39649736 AAAAAATTAATTATTTTAAGTAATTT
1 AAAAAATTAATTA-TTTAAGTAATTT
39649762 AATTAAAATTAA
1 AA--AAAATTAA
39649774 ATTAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 11 0.35
24 3 0.10
25 1 0.03
26 8 0.26
28 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAAAATTAATTATTTAAGTAATTT
Found at i:39649783 original size:29 final size:26
Alignment explanation
Indices: 39649730--39649783 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
39649720 TATTTATTTA
**
39649730 TAATTTAAAAAATTAATTATTTTAAG
1 TAATTTAAAAAATTAATTAAATTAAG
39649756 TAATTTAATTAAAATTAAATTAAATTAA
1 TAATTTAA--AAAATT-AATTAAATTAA
39649784 AAAAATGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
28 6 0.26
29 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTTAAAAAATTAATTAAATTAAG
Found at i:39650748 original size:7 final size:6
Alignment explanation
Indices: 39650725--39650792 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
39650715 CCCAATTTTA
* * *
39650725 AAATTT AAAATTT AAATTTT AAATTATT TAAGTT AAATTT -ATTTT AAATTT
1 AAATTT -AAATTT AAA-TTT AAA-T-TT AAATTT AAATTT AAATTT AAATTT
*
39650776 AAA-TT GAATTT AAATTT
1 AAATTT AAATTT AAATTT
39650793 TAAAAGTCCA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.16
6 23 0.47
7 14 0.29
8 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:39650779 original size:17 final size:16
Alignment explanation
Indices: 39650734--39650792 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
39650724 AAAATTTAAA
39650734 ATTTAAATTTTAAA-TT
1 ATTTAAA-TTTAAATTT
*
39650750 ATTT-AAGTTAAATTT
1 ATTTAAATTTAAATTT
*
39650765 ATTTTAAATTTAAATTGA
1 A-TTTAAATTTAAATT-T
39650783 ATTTAAATTT
1 ATTTAAATTT
39650793 TAAAAGTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.14
15 5 0.14
16 7 0.19
17 18 0.50
18 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:39652632 original size:29 final size:28
Alignment explanation
Indices: 39652576--39652676 Score: 103
Period size: 30 Copynumber: 3.4 Consensus size: 28
39652566 AAGGTCCCTC
*
39652576 AACTGTCCAAAAATCATATATTTGACCCCA
1 AACT-TCCAAAAATCATAT-TTTTACCCCA
* *
39652606 AACTTCTCAAAAATTATATTTTTACCCCCG
1 AACTTC-CAAAAATCATATTTTTA-CCCCA
*
39652636 AACTTCCAAAAATCACATTTTTAACCCCA
1 AACTTCCAAAAATCATATTTTT-ACCCCA
*
39652665 AAATCTCCAAAA
1 AACT-TCCAAAA
39652677 CTTCATCTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 27 0.45
30 33 0.55
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.29
Consensus pattern (28 bp):
AACTTCCAAAAATCATATTTTTACCCCA
Found at i:39659168 original size:15 final size:15
Alignment explanation
Indices: 39659148--39659182 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39659138 TGGTCTTCGG
*
39659148 TTTTCAAACAGAGGA
1 TTTTCAAACAGAGAA
*
39659163 TTTTCACACAGAGAA
1 TTTTCAAACAGAGAA
39659178 TTTTC
1 TTTTC
39659183 CATTTTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTTTCAAACAGAGAA
Found at i:39659580 original size:16 final size:15
Alignment explanation
Indices: 39659551--39659590 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
39659541 AGCATTAATT
39659551 AATTTATAACTTTTA
1 AATTTATAACTTTTA
* *
39659566 TATTTGATAATTTTTA
1 AATTT-ATAACTTTTA
39659582 AATTTATAA
1 AATTTATAA
39659591 ATAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTTATAACTTTTA
Found at i:39660406 original size:17 final size:16
Alignment explanation
Indices: 39660372--39660403 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39660362 AAATAATGTT
39660372 TTGTAAGTTACAAAAA
1 TTGTAAGTTACAAAAA
*
39660388 TTGTGAGTTACAAAAA
1 TTGTAAGTTACAAAAA
39660404 ATTAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (16 bp):
TTGTAAGTTACAAAAA
Found at i:39663645 original size:7 final size:7
Alignment explanation
Indices: 39663633--39663659 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39663623 GGACTTTTGA
39663633 TGGAAGT
1 TGGAAGT
39663640 TGGAAGT
1 TGGAAGT
39663647 TGGAAGT
1 TGGAAGT
39663654 TGGAAG
1 TGGAAG
39663660 CAATCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.44, T:0.26
Consensus pattern (7 bp):
TGGAAGT
Found at i:39667800 original size:28 final size:27
Alignment explanation
Indices: 39667765--39667830 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
39667755 ATCATAAAAA
* *
39667765 ATTA-AAAAATATTAAAATTTATATAAT
1 ATTATAAAAATATAAAAACTTATA-AAT
39667792 GA-TATAAAAATTATAAAAACTTATAAAT
1 -ATTATAAAAA-TATAAAAACTTATAAAT
39667820 ATTATAAAAAT
1 ATTATAAAAAT
39667831 TCTAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 4 0.12
28 17 0.52
29 12 0.36
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
ATTATAAAAATATAAAAACTTATAAAT
Found at i:39667808 original size:9 final size:9
Alignment explanation
Indices: 39667720--39667948 Score: 103
Period size: 9 Copynumber: 24.1 Consensus size: 9
39667710 ATAATTTCTC
39667720 ATTA-AAAA
1 ATTATAAAA
39667728 ATTA-AAAA
1 ATTATAAAA
* *
39667736 ATCATTAAA
1 ATTATAAAA
*
39667745 ATGACTAAAA
1 ATTA-TAAAA
*
39667755 ATCATAAAAA
1 ATTAT-AAAA
39667765 ATTA-AAAA
1 ATTATAAAA
*
39667773 A-TATTAAA
1 ATTATAAAA
*
39667781 ATT-TATATA
1 ATTATA-AAA
39667790 ATGATATAAAA
1 AT--TATAAAA
39667801 ATTATAAAA
1 ATTATAAAA
*
39667810 ACTTATAAAT
1 A-TTATAAAA
39667820 ATTATAAAA
1 ATTATAAAA
*
39667829 ATTCTAATAA
1 ATTATAA-AA
**
39667839 ATTATAATT
1 ATTATAAAA
* *
39667848 TTTTTATAAA
1 ATTATA-AAA
39667858 ATTAATAGAATA
1 ATT-ATA-AA-A
39667870 TATT-TAAAA
1 -ATTATAAAA
*
39667879 TTTTATAATAA
1 -ATTATAA-AA
*
39667890 CTTATAAAA
1 ATTATAAAA
39667899 ATTCATAAATA
1 ATT-ATAAA-A
39667910 ATTATAAATA
1 ATTATAAA-A
39667920 A-TATAAAA
1 ATTATAAAA
*
39667928 ATTAGAAAA
1 ATTATAAAA
39667937 ATATATGAAAA
1 AT-TAT-AAAA
39667948 A
1 A
39667949 ATCATTTAAA
Statistics
Matches: 171, Mismatches: 28, Indels: 41
0.71 0.12 0.17
Matches are distributed among these distances:
7 2 0.01
8 23 0.13
9 59 0.35
10 59 0.35
11 22 0.13
12 3 0.02
13 3 0.02
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
ATTATAAAA
Found at i:39667810 original size:10 final size:10
Alignment explanation
Indices: 39667751--39667845 Score: 51
Period size: 10 Copynumber: 10.1 Consensus size: 10
39667741 TAAAATGACT
*
39667751 AAAAATCATA
1 AAAAATTATA
39667761 AAAAA-T-TA
1 AAAAATTATA
39667769 AAAAA-TAT-
1 AAAAATTATA
*
39667777 TAAAATT-TA
1 AAAAATTATA
* * *
39667786 TATAATGATA
1 AAAAATTATA
39667796 TAAAAATTATA
1 -AAAAATTATA
*
39667807 AAAACTTAT-
1 AAAAATTATA
*
39667816 AAATATTAT-
1 AAAAATTATA
*
39667825 AAAAATTCTA
1 AAAAATTATA
*
39667835 ATAAATTATA
1 AAAAATTATA
39667845 A
1 A
39667846 TTTTTTTATA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
8 13 0.20
9 21 0.32
10 24 0.37
11 7 0.11
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (10 bp):
AAAAATTATA
Found at i:39667816 original size:19 final size:18
Alignment explanation
Indices: 39667720--39667948 Score: 103
Period size: 19 Copynumber: 12.1 Consensus size: 18
39667710 ATAATTTCTC
39667720 ATTA-AAAAATTA-AAAA
1 ATTATAAAAATTATAAAA
* * *
39667736 ATCATTAAAATGACTAAAA
1 ATTATAAAAATTA-TAAAA
*
39667755 ATCATAAAAAATTA-AAAA
1 ATTAT-AAAAATTATAAAA
* *
39667773 A-TATTAAAATT-TATATA
1 ATTATAAAAATTATA-AAA
39667790 ATGATATAAAAATTATAAAA
1 AT--TATAAAAATTATAAAA
*
39667810 ACTTATAAATATTATAAAA
1 A-TTATAAAAATTATAAAA
* **
39667829 ATTCTAATAAATTATAATT
1 ATTATAA-AAATTATAAAA
* *
39667848 TTTTTATAAAATTAATAGAATA
1 ATTATA-AAAATT-ATA-AA-A
*
39667870 TATT-TAAAATTTTATAATAA
1 -ATTATAAAA-ATTATAA-AA
*
39667890 CTTATAAAAATTCATAAATA
1 ATTATAAAAATT-ATAAA-A
39667910 ATTATAAATAA-TATAAAA
1 ATTATAAA-AATTATAAAA
*
39667928 ATTAGAAAAATATATGAAAA
1 ATTATAAAAAT-TAT-AAAA
39667948 A
1 A
39667949 ATCATTTAAA
Statistics
Matches: 162, Mismatches: 25, Indels: 48
0.69 0.11 0.20
Matches are distributed among these distances:
16 10 0.06
17 13 0.08
18 18 0.11
19 55 0.34
20 47 0.29
21 13 0.08
22 4 0.02
23 2 0.01
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (18 bp):
ATTATAAAAATTATAAAA
Found at i:39667831 original size:28 final size:27
Alignment explanation
Indices: 39667794--39667948 Score: 60
Period size: 28 Copynumber: 5.3 Consensus size: 27
39667784 TATATAATGA
* *
39667794 TATAAAAATTATAAAAACTTATAAATAT
1 TATAAAAATTATAAATA-TTATAAAAAT
* * ***
39667822 TATAAAAATTCTAATAAATTATAATTTT
1 TATAAAAATTATAA-ATATTATAAAAAT
* * *
39667850 TTTATAAAATTAATAGAATATATTTAAAATTT
1 TATA-AAAATT-ATA-AATAT-TATAAAA-AT
* *
39667882 TATAATAACTTATAAAAATTCATAAATAAT
1 TATAA-AAATTATAAATATT-ATAAA-AAT
* *
39667912 TATAAATAA-TATAAAAATTAGAAAAAT
1 TATAAA-AATTATAAATATTATAAAAAT
39667939 ATATGAAAAA
1 -TAT-AAAAA
39667949 ATCATTTAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
27 3 0.03
28 33 0.33
29 24 0.24
30 20 0.20
31 10 0.10
32 9 0.09
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (27 bp):
TATAAAAATTATAAATATTATAAAAAT
Found at i:39667897 original size:20 final size:20
Alignment explanation
Indices: 39667851--39667938 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
39667841 TATAATTTTT
*
39667851 TTAT-AAAATTAATAGAATATA
1 TTATAAAAATTCATA-AATA-A
* *
39667872 TT-TAAAATTTTAT-AATAA
1 TTATAAAAATTCATAAATAA
39667890 CTTATAAAAATTCATAAATAA
1 -TTATAAAAATTCATAAATAA
39667911 TTATAAATAA-T-ATAAA-AA
1 TTATAAA-AATTCATAAATAA
*
39667929 TTAGAAAAAT
1 TTATAAAAAT
39667939 ATATGAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
17 2 0.04
18 9 0.16
19 11 0.20
20 18 0.32
21 16 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTATAAAAATTCATAAATAA
Found at i:39667906 original size:10 final size:10
Alignment explanation
Indices: 39667881--39667931 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
39667871 ATTTAAAATT
39667881 TTAT-AATAA
1 TTATAAATAA
39667890 CTTATAAA-AA
1 -TTATAAATAA
39667900 TTCATAAATAA
1 TT-ATAAATAA
39667911 TTATAAATAA
1 TTATAAATAA
39667921 -TATAAA-AA
1 TTATAAATAA
39667929 TTA
1 TTA
39667932 GAAAAATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.05
9 10 0.27
10 19 0.51
11 6 0.16
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (10 bp):
TTATAAATAA
Found at i:39668652 original size:9 final size:9
Alignment explanation
Indices: 39668638--39669016 Score: 113
Period size: 9 Copynumber: 39.1 Consensus size: 9
39668628 TCCAATAAAT
39668638 ATTTTTATA
1 ATTTTTATA
39668647 ATTTTTATA
1 ATTTTTATA
*
39668656 TATCTTT-TA
1 -ATTTTTATA
*
39668665 ATATCTTATA
1 AT-TTTTATA
*
39668675 ATTTTATTTA
1 ATTTT-TATA
****
39668685 AAAAATATA
1 ATTTTTATA
*
39668694 TTTTTTATA
1 ATTTTTATA
*
39668703 ATTTATTAGA
1 ATTT-TTATA
*
39668713 ATTTAGTATGA
1 ATTT-TTAT-A
*
39668724 TTTTTTATAA
1 ATTTTTAT-A
39668734 ATTTTT-TA
1 ATTTTTATA
* *
39668742 CTTATTGATA
1 ATT-TTTATA
39668752 ATTTTTATA
1 ATTTTTATA
39668761 ATTTGTATGATA
1 ATTT-T-T-ATA
39668773 ATTTATTATA
1 ATTT-TTATA
*
39668783 ACTTTTTAGA
1 A-TTTTTATA
39668793 ATTTTTATA
1 ATTTTTATA
*
39668802 AGCTTTTATA
1 A-TTTTTATA
*
39668812 ATATTTATA
1 ATTTTTATA
*
39668821 AGTTTTGATGA
1 A-TTTTTAT-A
*
39668832 ATCCTTTATA
1 AT-TTTTATA
39668842 ATTTTTATAA
1 ATTTTTAT-A
* *
39668852 AGTTTATAGAA
1 A-TTTTTA-TA
* *
39668863 AGTTTTAAA
1 ATTTTTATA
39668872 TATTTTTA-A
1 -ATTTTTATA
*
39668881 CATGTTT-TA
1 -ATTTTTATA
* *
39668890 ATTATTATT
1 ATTTTTATA
*
39668899 ATTGTTATAATT
1 ATT-TT-T-ATA
39668911 ATTTTTATA
1 ATTTTTATA
*
39668920 ATTTATTAGA
1 ATTT-TTATA
39668930 A-TTTTATA
1 ATTTTTATA
* *
39668938 ATGTTTAGA
1 ATTTTTATA
*
39668947 AGTTCTTATGATT
1 A-TT-TT-T-ATA
*
39668960 TTTTTTATA
1 ATTTTTATA
39668969 ATTTTTATA
1 ATTTTTATA
*
39668978 AGTTTATATAA
1 A-TTTTTAT-A
39668989 ATTTTTA-A
1 ATTTTTATA
*
39668997 TATTTATATA
1 -ATTTTTATA
*
39669007 TTTTTTATA
1 ATTTTTATA
39669016 A
1 A
39669017 AAAAAAATAT
Statistics
Matches: 269, Mismatches: 66, Indels: 70
0.66 0.16 0.17
Matches are distributed among these distances:
8 15 0.06
9 108 0.40
10 97 0.36
11 31 0.12
12 17 0.06
13 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (9 bp):
ATTTTTATA
Found at i:39668738 original size:10 final size:10
Alignment explanation
Indices: 39668725--39669017 Score: 64
Period size: 10 Copynumber: 30.0 Consensus size: 10
39668715 TTAGTATGAT
39668725 TTTTTATAAA
1 TTTTTATAAA
*
39668735 TTTTT-T-AC
1 TTTTTATAAA
*
39668743 TTATTGAT-AA
1 TT-TTTATAAA
39668753 TTTTTAT-AA
1 TTTTTATAAA
*
39668762 TTTGTATGATAA
1 TTTTTAT-A-AA
*
39668774 TTTATTATAAC
1 TTT-TTATAAA
*
39668785 TTTTTA-GAA
1 TTTTTATAAA
*
39668794 TTTTTATAAG
1 TTTTTATAAA
*
39668804 CTTTTAT-AA
1 TTTTTATAAA
* *
39668813 TATTTATAAG
1 TTTTTATAAA
* *
39668823 TTTTGATGAA
1 TTTTTATAAA
*
39668833 TCCTTTAT-AA
1 T-TTTTATAAA
39668843 TTTTTATAAA
1 TTTTTATAAA
* *
39668853 GTTTATAGAAA
1 -TTTTTATAAA
*
39668864 GTTTTA-AATA
1 TTTTTATAA-A
*
39668874 TTTTTA-ACA
1 TTTTTATAAA
*
39668883 TGTTT-T-AA
1 TTTTTATAAA
* *
39668891 TTATTAT-TA
1 TTTTTATAAA
*
39668900 TTGTTATAATTA
1 TTTTTATAA--A
39668912 TTTTTAT-AA
1 TTTTTATAAA
*
39668921 TTTATTA-GAA
1 TTT-TTATAAA
39668931 -TTTTAT-AA
1 TTTTTATAAA
* * *
39668939 TGTTTAGAAG
1 TTTTTATAAA
* * *
39668949 TTCTTATGAT
1 TTTTTATAAA
*
39668959 TTTTTTTATAA
1 TTTTTATA-AA
*
39668970 TTTTTATAAG
1 TTTTTATAAA
*
39668980 TTTATATAAA
1 TTTTTATAAA
*
39668990 TTTTTA-ATA
1 TTTTTATAAA
* *
39668999 TTTATAT-AT
1 TTTTTATAAA
39669008 TTTTTATAAA
1 TTTTTATAAA
39669018 AAAAAATATA
Statistics
Matches: 198, Mismatches: 60, Indels: 50
0.64 0.19 0.16
Matches are distributed among these distances:
8 12 0.06
9 71 0.36
10 74 0.37
11 25 0.13
12 13 0.07
13 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:39668802 original size:19 final size:19
Alignment explanation
Indices: 39668772--39668848 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
39668762 TTTGTATGAT
39668772 AATTTATTATAACTTTTTAG
1 AATTT-TTATAACTTTTTAG
*
39668792 AATTTTTATAAGC-TTTTAT
1 AATTTTTATAA-CTTTTTAG
* * *
39668811 AATATTTATAAGTTTTGATG
1 AATTTTTATAACTTTTTA-G
*
39668831 AATCCTTTATAA-TTTTTA
1 AAT-TTTTATAACTTTTTA
39668849 TAAAGTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 25 0.54
20 14 0.30
21 7 0.15
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (19 bp):
AATTTTTATAACTTTTTAG
Found at i:39668993 original size:20 final size:18
Alignment explanation
Indices: 39668965--39669016 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
39668955 TGATTTTTTT
39668965 TATAATTTTTATAAGTTTA
1 TATAATTTTTATAA-TTTA
39668984 TATAAATTTTTA-ATATTTA
1 TAT-AATTTTTATA-ATTTA
*
39669003 TATATTTTTTATAA
1 TATAATTTTTATAA
39669017 AAAAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.28
19 12 0.41
20 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATAATTTTTATAATTTA
Found at i:39668994 original size:31 final size:31
Alignment explanation
Indices: 39668931--39668994 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
39668921 TTTATTAGAA
* *
39668931 TTTTATAATGTTTAGAAGTTCTTATGATTTT
1 TTTTATAATGTTTAGAAGTTCTTATAAATTT
* *
39668962 TTTTATAATTTTTATAAGTT-TATATAAATTT
1 TTTTATAATGTTTAGAAGTTCT-TATAAATTT
39668993 TT
1 TT
39668995 AATATTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTATAATGTTTAGAAGTTCTTATAAATTT
Found at i:39674814 original size:46 final size:46
Alignment explanation
Indices: 39674762--39674849 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
39674752 ACTACTAATT
* * * **
39674762 TGTAATATTAGTTACGCACTTGGACGATATTGTAGTTATCATGTGG
1 TGTAATACTAGTTACACACTTGCAAAATATTGTAGTTATCATGTGG
*
39674808 TGTAATACTAGTTATACACTTGCAAAATATTGTAGTTATCAT
1 TGTAATACTAGTTACACACTTGCAAAATATTGTAGTTATCAT
39674850 CAATTCACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (46 bp):
TGTAATACTAGTTACACACTTGCAAAATATTGTAGTTATCATGTGG
Found at i:39675129 original size:19 final size:18
Alignment explanation
Indices: 39675105--39675155 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
39675095 TATCTAAACA
39675105 CCAGAAAATATTAACTTTT
1 CCAGAAAATATTAA-TTTT
*
39675124 CCAGAAAAGTAATTTATTTT
1 CCAGAAAA-T-ATTAATTTT
*
39675144 CCAGAAATTATT
1 CCAGAAAATATT
39675156 TTTCGGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 12 0.43
21 4 0.14
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (18 bp):
CCAGAAAATATTAATTTT
Found at i:39683299 original size:12 final size:12
Alignment explanation
Indices: 39683284--39683315 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39683274 CTCCTTCTCC
39683284 TCCTTATCCTCA
1 TCCTTATCCTCA
*
39683296 TCCTCATCCTCA
1 TCCTTATCCTCA
39683308 TCCTTATC
1 TCCTTATC
39683316 TTTCTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.41
Consensus pattern (12 bp):
TCCTTATCCTCA
Found at i:39683344 original size:18 final size:20
Alignment explanation
Indices: 39683317--39683357 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
39683307 ATCCTTATCT
*
39683317 TTCTTTTTCTC-TCTTT-TC
1 TTCTTCTTCTCTTCTTTCTC
39683335 TTCTTCTTCTCTTCTTTCTC
1 TTCTTCTTCTCTTCTTTCTC
39683355 TTC
1 TTC
39683358 ACCTTCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 5 0.25
20 5 0.25
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTCTTCTCTTCTTTCTC
Found at i:39683391 original size:12 final size:12
Alignment explanation
Indices: 39683374--39683430 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
39683364 TACCCCATCC
39683374 TTCTTCTTTTCT
1 TTCTTCTTTTCT
39683386 TTCTTCTTTTCCT
1 TTCTTCTTTT-CT
* *
39683399 TCGCCTCTTTGTCT
1 T-TCTTCTTT-TCT
39683413 TTCTTCTTTTCT
1 TTCTTCTTTTCT
39683425 TTCTTC
1 TTCTTC
39683431 CCCTTTTCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 19 0.50
13 9 0.24
14 9 0.24
15 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.67
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:39683487 original size:12 final size:12
Alignment explanation
Indices: 39683470--39683521 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
39683460 TTCTACCTCA
39683470 TCCTTCTTCTTT
1 TCCTTCTTCTTT
*
39683482 TCCTTCTTCTTC
1 TCCTTCTTCTTT
*
39683494 TCCTTTGCCTCTTT
1 TCC-TT-CTTCTTT
*
39683508 GTCTTTCTTCTTT
1 -TCCTTCTTCTTT
39683521 T
1 T
39683522 TCCTCTTTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 15 0.47
13 8 0.25
14 7 0.22
15 2 0.06
ACGTcount: A:0.00, C:0.33, G:0.04, T:0.63
Consensus pattern (12 bp):
TCCTTCTTCTTT
Found at i:39683580 original size:3 final size:3
Alignment explanation
Indices: 39683574--39683861 Score: 68
Period size: 3 Copynumber: 95.7 Consensus size: 3
39683564 CCTTATCCTC
* * *
39683574 CTT CTT CTT -TT CTTT CTT CTT CTC CTT -TG CCT CTT -TGT CTTT CTT
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CT-T C-TT CTT
* * *
39683619 CTT -TT CTTT CTT -TC CCT CTT CTAT -TT CTT CAT CTT CTT CTT CTT
1 CTT CTT C-TT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT
* * * * * * *
39683663 CTAC CTT ATC CTT CTT -TC CTTT CTT CTT CTC CTT -TG CCT CTT -TGT
1 CT-T CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CT-T
* * * * * *
39683708 CTTT CTT CTT -TT CTTT CTT -TC CCT CTT CTA ATT CAT CTT CTT CTAC
1 C-TT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T
* * *
39683754 CTT ATC CTT CTT CTT CTT -TT CTTT CTT CTT CTT CTT CTT CTC CTT
1 CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT
* * *
39683799 C-G CCT CTT -TGT CTTT CTT CTT -TT CTTT CTTT CCT CTT CTAT -TT
1 CTT CTT CTT CT-T C-TT CTT CTT CTT C-TT C-TT CTT CTT CT-T CTT
* *
39683842 CTT CAT CTT CAT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CT
39683862 AACTCATGAT
Statistics
Matches: 200, Mismatches: 53, Indels: 64
0.63 0.17 0.20
Matches are distributed among these distances:
2 21 0.10
3 143 0.71
4 33 0.17
5 3 0.01
ACGTcount: A:0.04, C:0.33, G:0.02, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:39683592 original size:12 final size:12
Alignment explanation
Indices: 39683575--39683828 Score: 86
Period size: 12 Copynumber: 19.4 Consensus size: 12
39683565 CTTATCCTCC
39683575 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
39683587 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
*
39683600 TTGCCTCTTTGTCT
1 TT-CTTCTTT-TCT
39683614 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
39683626 TTCTTTCCCTCTTCTAT
1 TTC-TT--CT-TT-TCT
*
39683643 TTCTTCATCTTC-
1 TTCTTC-TTTTCT
*
39683655 TTCTTCTTCTACCT
1 TTCTTCTT-T-TCT
*
39683669 TATCCTTCTTTCCT
1 T-T-CTTCTTTTCT
*
39683683 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
*
39683696 TTGCCTCTTTGTCT
1 TT-CTTCTTT-TCT
39683710 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
39683722 TTCTTTCCCTCTTCT
1 TTC-TT--CTTTTCT
*
39683737 AATTCATCTTCTTCT
1 --TTCTTCTT-TTCT
** * *
39683752 ACCTTATCCTTC-
1 TTCTTCT-TTTCT
39683764 TTCTTCTTTTCT
1 TTCTTCTTTTCT
39683776 TTCTTC--TTC-
1 TTCTTCTTTTCT
*
39683785 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
* *
39683798 TCGCCTCTTTGTCT
1 T-TCTTCTTT-TCT
39683812 TTCTTCTTTTCT
1 TTCTTCTTTTCT
39683824 TTCTT
1 TTCTT
39683829 TCCTCTTCTA
Statistics
Matches: 181, Mismatches: 30, Indels: 62
0.66 0.11 0.23
Matches are distributed among these distances:
9 6 0.03
10 3 0.02
11 4 0.02
12 53 0.29
13 46 0.25
14 35 0.19
15 15 0.08
16 11 0.06
17 8 0.04
ACGTcount: A:0.04, C:0.32, G:0.02, T:0.62
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:39683706 original size:198 final size:197
Alignment explanation
Indices: 39683371--39683868 Score: 704
Period size: 198 Copynumber: 2.5 Consensus size: 197
39683361 TTCTACCCCA
* * *
39683371 TCCTTCTTCTTTTCTTTCTTCTTTTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTCCCCTT
1 TCCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTC
*
39683436 TTCTATTTCTGCATCTTCATCTTCTTCTACCTCATCCTTCTTCTTTTCCTTCTTCTTCTCCTTTG
66 TTCTATTTCTTCATCTTCATCTTCTTCTACCTCATCC-TCTTCTTTTCCTTCTTCTTCTCCTTTG
* * *
39683501 CCTCTTTGTCTTTCTTCTTTT-TCCTCTTTCCCTCTTCTATTTCTGCATCTTCATCT-TCTTCTA
130 CCTCTTTGTCTTTCTTCTTTTCT-CTCTTTCCCTCTTCTA-AT-T-CATCTTCATCTACCTTAT-
39683564 CCTTATCC
190 CCTTATCC
*
39683572 TCCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTC
1 TCCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTC
* *
39683637 TTCTATTTCTTCATCTTCTTCTTCTTCTACCTTAT-C-CTTC-TTTCCTTTCTTCTTCTCCTTTG
66 TTCTATTTCTTCATCTTCATCTTCTTCTACCTCATCCTCTTCTTTTCC-TTCTTCTTCTCCTTTG
* * *
39683699 CCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCATCTTCTTCTACCTTATCCTTC
130 CCTCTTTGTCTTTCTTCTTTTCTCTCTTTCCCTCTTCTAATTCATCTTCATCTACCTTATCCTTA
*
39683764 TTC
195 TCC
*
39683767 TTCTT-TTCTTTCTTCTTCTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTT-
1 TCCTTCTTC-TT-TTC-T-TTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTC
*
39683830 CCTCTTCTATTTCTTCATCTTCATCTTCTTCTAACTCAT
62 CCTCTTCTATTTCTTCATCTTCATCTTCTTCTACCTCAT
39683869 GATCCTTATC
Statistics
Matches: 271, Mismatches: 19, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
194 3 0.01
195 22 0.08
196 8 0.03
197 43 0.16
198 100 0.37
199 1 0.00
200 1 0.00
201 93 0.34
ACGTcount: A:0.05, C:0.33, G:0.02, T:0.59
Consensus pattern (197 bp):
TCCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTC
TTCTATTTCTTCATCTTCATCTTCTTCTACCTCATCCTCTTCTTTTCCTTCTTCTTCTCCTTTGC
CTCTTTGTCTTTCTTCTTTTCTCTCTTTCCCTCTTCTAATTCATCTTCATCTACCTTATCCTTAT
CC
Found at i:39683715 original size:96 final size:98
Alignment explanation
Indices: 39683360--39683862 Score: 631
Period size: 102 Copynumber: 5.1 Consensus size: 98
39683350 TTCTCTTCAC
** * * *
39683360 CTTCTACCCCATCCTTCTTCTTTTCTTTCTTCTTTTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT
1 CTTCTACCTTATCC-TCTTCTTTCCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
* * *
39683425 TTCTTCCCCTTTTCTATTTCTGCATCTTCATCTT
65 TTCTTTCCCTCTTCTATTTCTTCATCTTCATCTT
*
39683459 CTTCTACCTCATCCTTCTTCTTTTCC-TTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTT-
1 CTTCTACCTTATCC-TCTTC-TTTCCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTC
* *
39683522 TCCTCTTTCCCTCTTCTATTTCTGCATCTTCATCTT
64 T-TTCTTTCCCTCTTCTATTTCTTCATCTTCATCTT
*
39683558 CTTCTACCTTATCCTCCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTTA---TCC-TCTTCTTTCCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
39683623 TCTTTCTTTCCCTCTTCTATTTCTTCATCTTCTTCTT
62 TCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCTT
39683660 CTTCTACCTTAT-C-CTTCTTTCCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTT
1 CTTCTACCTTATCCTCTTCTTTCCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTT
* * * *
39683723 TCTTTCCCTCTTCTAATTCATCTTCTTCTACCTT
66 TCTTTCCCTCTTCTATTTCTTCATCTTC-ATCTT
* * * * * * *
39683757 ATCCT-TCTTCTTCTTTTCTTTCTTCTTCTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTTATCCTCTTCTTTC--C-T-TTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
39683821 TCTTTCTTT-CCTCTTCTATTTCTTCATCTTCATCTT
62 TCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCTT
39683857 CTTCTA
1 CTTCTA
39683863 ACTCATGATC
Statistics
Matches: 359, Mismatches: 30, Indels: 28
0.86 0.07 0.07
Matches are distributed among these distances:
96 78 0.22
97 7 0.02
98 9 0.03
99 96 0.27
100 12 0.03
101 24 0.07
102 132 0.37
103 1 0.00
ACGTcount: A:0.05, C:0.34, G:0.02, T:0.59
Consensus pattern (98 bp):
CTTCTACCTTATCCTCTTCTTTCCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTT
TCTTTCCCTCTTCTATTTCTTCATCTTCATCTT
Found at i:39684012 original size:16 final size:17
Alignment explanation
Indices: 39683986--39684027 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
39683976 TCCTTATGCT
* * *
39683986 TCTTTTTCTTTTTTTCT
1 TCTTCTTCTTTTCTTCA
39684003 TC-TCTTCTTTTCTTCA
1 TCTTCTTCTTTTCTTCA
39684019 TCTTCTTCT
1 TCTTCTTCT
39684028 ATCACCTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (17 bp):
TCTTCTTCTTTTCTTCA
Found at i:39684013 original size:13 final size:14
Alignment explanation
Indices: 39683992--39684025 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
39683982 TGCTTCTTTT
*
39683992 TCTTTTTTTCTTC-
1 TCTTCTTTTCTTCA
39684005 TCTTCTTTTCTTCA
1 TCTTCTTTTCTTCA
39684019 TCTTCTT
1 TCTTCTT
39684026 CTATCACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (14 bp):
TCTTCTTTTCTTCA
Found at i:39687878 original size:13 final size:14
Alignment explanation
Indices: 39687862--39687892 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
39687852 AAATTTTTTT
39687862 TATATAAAAA-TAA
1 TATATAAAAATTAA
39687875 TATATAAAAATTAA
1 TATATAAAAATTAA
39687889 TATA
1 TATA
39687893 GGTGGGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATATAAAAATTAA
Found at i:39689277 original size:16 final size:16
Alignment explanation
Indices: 39689244--39689285 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
39689234 TTCTCTTAAG
*
39689244 TTTCTTCTTCATCATC
1 TTTCTTCTTCTTCATC
*
39689260 TTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCATC
39689276 -TTCTT-TTCTT
1 TTTCTTCTTCTT
39689286 TTTCCTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 14 0.58
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTCTTCTTCTTCATC
Found at i:39689280 original size:19 final size:19
Alignment explanation
Indices: 39689245--39689307 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
39689235 TCTCTTAAGT
* *
39689245 TTCTTCTTCATCATCTTTC
1 TTCTTCTTCTTCTTCTTTC
39689264 TTCTTCTTCTTCTTCTTTTC
1 TTCTTCTTCTTCTTC-TTTC
* *
39689284 TTTTTCCTCTT-TGTCTTTC
1 TTCTTCTTCTTCT-TCTTTC
39689303 TTCTT
1 TTCTT
39689308 ACCTTCTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.03, C:0.29, G:0.02, T:0.67
Consensus pattern (19 bp):
TTCTTCTTCTTCTTCTTTC
Found at i:39689337 original size:36 final size:33
Alignment explanation
Indices: 39689248--39689340 Score: 91
Period size: 36 Copynumber: 2.7 Consensus size: 33
39689238 CTTAAGTTTC
*
39689248 TTCTTCATCATCTTTCTTC-TTCTTCTTCTTCTT
1 TTCTTCATCATCCTT-TTCTTTCTTCTTCTTCTT
** *
39689281 TTCTTTTTCCT-CTTTGTCTTTCTTCTTACCTTCTAT
1 TTCTTCATCATCCTTT-TCTTTCTTCTT--CTTCT-T
39689317 TTCTTCATCATCCTTTTCTTTCTT
1 TTCTTCATCATCCTTTTCTTTCTT
39689341 TTCCTTTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 1 0.02
32 4 0.09
33 16 0.34
35 5 0.11
36 17 0.36
37 4 0.09
ACGTcount: A:0.06, C:0.29, G:0.01, T:0.63
Consensus pattern (33 bp):
TTCTTCATCATCCTTTTCTTTCTTCTTCTTCTT
Found at i:39689580 original size:114 final size:114
Alignment explanation
Indices: 39689453--39689688 Score: 402
Period size: 114 Copynumber: 2.1 Consensus size: 114
39689443 TCTTGTCTTC
39689453 ATTTTTCTCTTCCTTGTCTTTCTTCTTCTTTTTCTTCTCATCTTTC-TCTTCATCCTCTTCTCCC
1 ATTTTTCTCTTCCTTGTCTTTCTTCTTCTTTTTCTTCTCATC-TTCATCTTCATCCTCTTCTCCC
*
39689517 TTAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTTT
65 TCAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTTT
* *
39689567 ATTTTTCTCTTCCTTGTCTTTCTTCTTCTTTTTCTTCTCATCTTCATTTTCATCCTTTTCTCCCT
1 ATTTTTCTCTTCCTTGTCTTTCTTCTTCTTTTTCTTCTCATCTTCATCTTCATCCTCTTCTCCCT
* *
39689632 CAACCTCATATTTTCCTTCTTTCTTCTTCTCCGTTTCCTTATCTTTTTT
66 CAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTTT
*
39689681 CTTTTTCT
1 ATTTTTCT
39689689 TCTCATTATT
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
113 3 0.03
114 112 0.97
ACGTcount: A:0.08, C:0.31, G:0.02, T:0.59
Consensus pattern (114 bp):
ATTTTTCTCTTCCTTGTCTTTCTTCTTCTTTTTCTTCTCATCTTCATCTTCATCCTCTTCTCCCT
CAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTTT
Found at i:39689725 original size:114 final size:114
Alignment explanation
Indices: 39689501--39689725 Score: 265
Period size: 114 Copynumber: 2.0 Consensus size: 114
39689491 CATCTTTCTC
*
39689501 TTCATCCTCTTCTCCCTTAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTT
1 TTCATCCTCTTCTCCCTCAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTT
* * ** ** ** ** *
39689566 TATTTTTCTCTTCCTTGTCTTTCTTCTTCTTTTTCTTCTCATCTTCATT
66 TATTTTTCTCTTCATTATCTCACACCAGCTTCATCTCCTCATCTTCATT
* * *
39689615 TTCATCCTTTTCTCCCTCAACCTCATATTTTCCTTCTTTCTTCTTCTCCGTTTCCTTATCTTTTT
1 TTCATCCTCTTCTCCCTCAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTT
* *
39689680 TCTTTTTCT-TCTCATTAT-TCACACCAGCTTCATCATCCTCGTCTTC
66 TATTTTTCTCT-TCATTATCTCACACCAGCTTCATC-TCCTCATCTTC
39689726 TTCTCTTATA
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
113 9 0.10
114 83 0.90
ACGTcount: A:0.10, C:0.33, G:0.02, T:0.55
Consensus pattern (114 bp):
TTCATCCTCTTCTCCCTCAACCTCATATTTTCCCTCTTTCTTCATCTCCGTTTCCTTATCTTTTT
TATTTTTCTCTTCATTATCTCACACCAGCTTCATCTCCTCATCTTCATT
Found at i:39690507 original size:23 final size:23
Alignment explanation
Indices: 39690473--39690516 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
39690463 AAAAAAAATT
39690473 TAATTCTAA-TTTTATCAATTTAA
1 TAATTCTAATTTTTAT-AATTTAA
39690496 TAATT-TATATTTTTATAATTT
1 TAATTCTA-ATTTTTATAATTT
39690517 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.11
23 11 0.58
24 6 0.32
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATTCTAATTTTTATAATTTAA
Found at i:39691823 original size:22 final size:22
Alignment explanation
Indices: 39691794--39691835 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
39691784 TATGCCATCG
*
39691794 AAAAATTAATAAAA-TAAAACC
1 AAAAATTAAGAAAATTAAAACC
39691815 AAAAGATTAAGAAAATTAAAA
1 AAAA-ATTAAGAAAATTAAAA
39691836 AAAACTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAATTAAGAAAATTAAAACC
Found at i:39702690 original size:8 final size:8
Alignment explanation
Indices: 39702677--39702702 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39702667 GGAAAGGAAC
39702677 AGAAGAGA
1 AGAAGAGA
39702685 AGAAGAGA
1 AGAAGAGA
39702693 AGAAGAGA
1 AGAAGAGA
39702701 AG
1 AG
39702703 TGATTCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
AGAAGAGA
Found at i:39704209 original size:26 final size:26
Alignment explanation
Indices: 39704179--39704229 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39704169 TTTATCGTGG
39704179 TTATTAATTTATTGATAAATGAATAT
1 TTATTAATTTATTGATAAATGAATAT
*
39704205 TTATTAATTTATTGATAAATTAATA
1 TTATTAATTTATTGATAAATGAATA
39704230 AATTTAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (26 bp):
TTATTAATTTATTGATAAATGAATAT
Found at i:39706283 original size:14 final size:15
Alignment explanation
Indices: 39706233--39706283 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
39706223 ATAAAAAAAT
39706233 ATATT-ATTTAATCGA
1 ATATTAATTT-ATCGA
39706248 GATTATTAATTTATCGA
1 -A-TATTAATTTATCGA
*
39706265 ATATTCATTTATC-A
1 ATATTAATTTATCGA
39706279 ATATT
1 ATATT
39706284 TTATTGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.19
15 11 0.34
16 2 0.06
17 9 0.28
18 4 0.12
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (15 bp):
ATATTAATTTATCGA
Found at i:39710989 original size:20 final size:20
Alignment explanation
Indices: 39710936--39710991 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
39710926 CTACCTTGGG
*
39710936 ACTTCTATC-GATAAAACTTC
1 ACTTCTA-CGGATACAACTTC
**
39710956 ACTTCTACTAATACAACTTC
1 ACTTCTACGGATACAACTTC
*
39710976 AGTTCTACGGATACAA
1 ACTTCTACGGATACAA
39710992 GTATGCTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (20 bp):
ACTTCTACGGATACAACTTC
Found at i:39713450 original size:16 final size:16
Alignment explanation
Indices: 39713429--39713461 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39713419 GCTTGAATTG
39713429 AAAATGACTTTCATTA
1 AAAATGACTTTCATTA
39713445 AAAATGACTTTCATTA
1 AAAATGACTTTCATTA
39713461 A
1 A
39713462 GGGGAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (16 bp):
AAAATGACTTTCATTA
Found at i:39713652 original size:20 final size:20
Alignment explanation
Indices: 39713615--39713668 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
39713605 CGACTGTAAG
* *
39713615 ACTTCTACTGGTAGAACTTC
1 ACTTCTACTGATACAACTTC
*
39713635 ACTTCTACTGATACAACTTT
1 ACTTCTACTGATACAACTTC
* *
39713655 AGTTCTACCGATAC
1 ACTTCTACTGATAC
39713669 CTTAAAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (20 bp):
ACTTCTACTGATACAACTTC
Found at i:39713868 original size:20 final size:20
Alignment explanation
Indices: 39713831--39713869 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39713821 TCTACCCTGG
*
39713831 ACTTCTACCTGTAGAACTTT
1 ACTTCTACCTGTACAACTTT
39713851 ACTTCTACC-GATACAACTT
1 ACTTCTACCTG-TACAACTT
39713870 CAGTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (20 bp):
ACTTCTACCTGTACAACTTT
Found at i:39720295 original size:349 final size:349
Alignment explanation
Indices: 39719656--39720356 Score: 1251
Period size: 349 Copynumber: 2.0 Consensus size: 349
39719646 TCCTCGTTTC
39719656 GAGTAAGATATTTTACTTATCTGCAAAAATTTAAGGCTAGATCGGATCTATCATAATCACACTAT
1 GAGTAAGATATTTTACTTATCTGCAAAAATTTAAGGCTAGATCGGATCTATCATAATCACACTAT
*
39719721 CACAGTTTATATGACATGTATTCTCTAAACTCTTTAATTCATAAATTCAGTCTAAGAACCGACTA
66 CACAGTTTATATGACATGTATTCTCTAAACTCTTTAATTCATAAATTCAGTCCAAGAACCGACTA
* ** **
39719786 ACTCGTAAGCTTTGATACCATTAAATATAACACTCAAAATTCGTTACCGTCGTCGACTAGGGCAC
131 ACTCGTAAGCTTTGATACCACTAAATATAACACTCAAAACCCGTTACCGTCACCGACTAGGGCAC
* *
39719851 CGAGGTCCCTTTATTCATCAATCCTAGATTAACATTTAATATTACTTCCTTTAATCATACTTTAA
196 CGAGGTCCCTTCATTCATCAATCCTAGATTAACATTTAATATTACTGCCTTTAATCATACTTTAA
39719916 TAAAACATTTCATTATACACGTCATAAATCATGAAAGAAAAGTCAATACAATTAAAATAGGGATA
261 TAAAACATTTCATTATACACGTCATAAATCATGAAAGAAAAGTCAATACAATTAAAATAGGGATA
*
39719981 AAAAGGTCATTTCTATAATTTTGG
326 AAAAGGTCATTTCTACAATTTTGG
39720005 GAGTAAGATATTTTACTTATCTGCAAAAATTTAAGGCTAGATCGGATCTATCATAATCACACTAT
1 GAGTAAGATATTTTACTTATCTGCAAAAATTTAAGGCTAGATCGGATCTATCATAATCACACTAT
39720070 CACAGTTTATATGACATGTATTCTCTAAACTCTTTAATTCATAAATTCAGTCCAAGAACCGACTA
66 CACAGTTTATATGACATGTATTCTCTAAACTCTTTAATTCATAAATTCAGTCCAAGAACCGACT-
*
39720135 AAC-CGTAAGCTTTGATACCACTAAATATAACACTCAAAACCCGTTACCGTCACCGACTAGGGCG
130 AACTCGTAAGCTTTGATACCACTAAATATAACACTCAAAACCCGTTACCGTCACCGACTAGGGCA
* *
39720199 TCGGGGTCCCTTCATTCATCAATCCTAGATTAACATTTAATATTACTGCCTTTAATCATACTTTA
195 CCGAGGTCCCTTCATTCATCAATCCTAGATTAACATTTAATATTACTGCCTTTAATCATACTTTA
* *
39720264 ATAAAGCATTTCATTATACACGTCATAAATCATGAAAGAAAATTCAATACAATTAAAATAGGGAT
260 ATAAAACATTTCATTATACACGTCATAAATCATGAAAGAAAAGTCAATACAATTAAAATAGGGAT
*
39720329 AAAAATGTCATTTCTACAATTTTGG
325 AAAAAGGTCATTTCTACAATTTTGG
39720354 GAG
1 GAG
39720357 ACTTCTACCG
Statistics
Matches: 336, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
349 333 0.99
350 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (349 bp):
GAGTAAGATATTTTACTTATCTGCAAAAATTTAAGGCTAGATCGGATCTATCATAATCACACTAT
CACAGTTTATATGACATGTATTCTCTAAACTCTTTAATTCATAAATTCAGTCCAAGAACCGACTA
ACTCGTAAGCTTTGATACCACTAAATATAACACTCAAAACCCGTTACCGTCACCGACTAGGGCAC
CGAGGTCCCTTCATTCATCAATCCTAGATTAACATTTAATATTACTGCCTTTAATCATACTTTAA
TAAAACATTTCATTATACACGTCATAAATCATGAAAGAAAAGTCAATACAATTAAAATAGGGATA
AAAAGGTCATTTCTACAATTTTGG
Found at i:39721008 original size:18 final size:18
Alignment explanation
Indices: 39720975--39721026 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
39720965 CTTCGGGGAT
*
39720975 CCAGTAATGCTTTTACGAG
1 CCAGT-ATGCTCTTACGAG
39720994 CCAGTATGCTCTTACGAG
1 CCAGTATGCTCTTACGAG
39721012 CCAGTATGCTCTTAC
1 CCAGTATGCTCTTAC
39721027 AAGCTAGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 27 0.84
19 5 0.16
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (18 bp):
CCAGTATGCTCTTACGAG
Found at i:39727018 original size:23 final size:21
Alignment explanation
Indices: 39726992--39727038 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
39726982 AAATTTTAAA
*
39726992 TTAATATATAATAAAATTATATT
1 TTAAT-TATAATAAAAATAT-TT
*
39727015 TTAATTATCATAAAAATATTT
1 TTAATTATAATAAAAATATTT
39727036 TTA
1 TTA
39727039 CCCCCTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 12 0.55
23 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTATAATAAAAATATTT
Found at i:39730972 original size:19 final size:18
Alignment explanation
Indices: 39730924--39730992 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
39730914 AACTTATTTA
39730924 AAAATTATAAATAATTATT
1 AAAATTATAAA-AATTATT
39730943 AAAATTATAAAAA-TATT
1 AAAATTATAAAAATTATT
* **
39730960 AATAATTATTAAAAGAATCT
1 AA-AATTATAAAAATTAT-T
*
39730980 AAAATCATAAAAA
1 AAAATTATAAAAA
39730993 AATATGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
17 6 0.14
18 12 0.28
19 22 0.51
20 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (18 bp):
AAAATTATAAAAATTATT
Found at i:39734875 original size:2 final size:2
Alignment explanation
Indices: 39734868--39734893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39734858 AATTTTTAAT
39734868 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
39734894 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39735004 original size:15 final size:16
Alignment explanation
Indices: 39734975--39735004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39734965 TTGAAGACGT
39734975 TGAAAATTATTTAATA
1 TGAAAATTATTTAATA
39734991 TGAAAATT-TTTAAT
1 TGAAAATTATTTAAT
39735005 TATTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (16 bp):
TGAAAATTATTTAATA
Found at i:39735760 original size:2 final size:2
Alignment explanation
Indices: 39735755--39735779 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39735745 TTTTAATAGT
39735755 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39735780 GCAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39736685 original size:22 final size:22
Alignment explanation
Indices: 39736658--39736709 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
39736648 GTGTGTCTCG
39736658 TATTATTCTCTCAATTAAATTT
1 TATTATTCTCTCAATTAAATTT
* * *
39736680 TATTATTTTTTTAATTAAATTT
1 TATTATTCTCTCAATTAAATTT
39736702 TGATTATT
1 T-ATTATT
39736710 TTAGGGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTATTCTCTCAATTAAATTT
Found at i:39743090 original size:38 final size:34
Alignment explanation
Indices: 39743018--39743087 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
39743008 TATAAATAAT
39743018 CCTCCTCCCTCGAAACCACTTGCTCATTTCCCAC
1 CCTCCTCCCTCGAAACCACTTGCTCATTTCCCAC
*
39743052 CCTCCTTCCTCGAAACCTAC-TGCTCATTTCCCAC
1 CCTCCTCCCTCGAAACC-ACTTGCTCATTTCCCAC
39743086 CC
1 CC
39743088 ACCTTCTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.17, C:0.50, G:0.06, T:0.27
Consensus pattern (34 bp):
CCTCCTCCCTCGAAACCACTTGCTCATTTCCCAC
Found at i:39748811 original size:27 final size:26
Alignment explanation
Indices: 39748773--39748828 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
39748763 TTCCTTTTCA
39748773 TGTGAATATATTGTTCAATTCTAAGTT
1 TGTGAATATATTGTTCAATTCTAA-TT
*
39748800 TGTGTATATATTGTTCAATTCTAATT
1 TGTGAATATATTGTTCAATTCTAATT
39748826 TGT
1 TGT
39748829 TTTCTTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (26 bp):
TGTGAATATATTGTTCAATTCTAATT
Found at i:39749517 original size:21 final size:21
Alignment explanation
Indices: 39749491--39749536 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
39749481 GAGCTAAGAC
39749491 TTAATCAATTAAAGTAAAGTG
1 TTAATCAATTAAAGTAAAGTG
39749512 TTAATCAATTAAAGTAAAGTG
1 TTAATCAATTAAAGTAAAGTG
39749533 TTAA
1 TTAA
39749537 ACGATTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (21 bp):
TTAATCAATTAAAGTAAAGTG
Found at i:39750396 original size:21 final size:21
Alignment explanation
Indices: 39750372--39750417 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39750362 GAAATAACCG
*
39750372 AATTAATCATATTAA-TCGATT
1 AATTAATCA-ATTAATTCAATT
*
39750393 AATTAATTAATTAATTCAATT
1 AATTAATCAATTAATTCAATT
39750414 AATT
1 AATT
39750418 GATTAAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTAATCAATTAATTCAATT
Found at i:39750399 original size:4 final size:4
Alignment explanation
Indices: 39750390--39750423 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
39750380 ATATTAATCG
*
39750390 ATTA ATTA ATTA ATTA ATTCA ATTA ATTG ATTA A
1 ATTA ATTA ATTA ATTA ATT-A ATTA ATTA ATTA A
39750424 ATCGATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:39751801 original size:16 final size:16
Alignment explanation
Indices: 39751780--39751811 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39751770 TATTTTTTAA
39751780 ATTTAATTTATTATTT
1 ATTTAATTTATTATTT
39751796 ATTTAATTTATTATTT
1 ATTTAATTTATTATTT
39751812 TCTACATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTAATTTATTATTT
Found at i:39753579 original size:92 final size:90
Alignment explanation
Indices: 39753376--39753611 Score: 314
Period size: 92 Copynumber: 2.6 Consensus size: 90
39753366 CTGTACTTCG
* * * *
39753376 AAAATGTCCAATGTGGTACTTTTAATTTGAAAATGTCCAATGTGGTACTTAAACTATTAATGTGC
1 AAAATGTCCAATGTAGTACTTGTAATTTGAAAATGTCCAATGTGGTACCTAAACCATTAATGTGC
*
39753441 TTTTATATGGTACATGTACTTTCGT
66 TTTTATATGGTACATGTACTTTCAT
* * * * *
39753466 AAAATGTCTAATGTAGCACTTGTAATTTGGAAATGTCGAATGTGATACCTAAACCATTAATACGT
1 AAAATGTCCAATGTAGTACTTGTAATTTGAAAATGTCCAATGTGGTACCTAAACCATTAAT--GT
*
39753531 G-TTTTATTATGGTACATGTATTTTCAT
64 GCTTTTA-TATGGTACATGTACTTTCAT
*
39753558 AAAATATCCAATGTAGTACTTGTAATTTGAAAATGTCCAACT-TGGTACCTAAAC
1 AAAATGTCCAATGTAGTACTTGTAATTTGAAAATGTCCAA-TGTGGTACCTAAAC
39753612 AATTGATATA
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
90 52 0.42
91 5 0.04
92 67 0.54
93 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (90 bp):
AAAATGTCCAATGTAGTACTTGTAATTTGAAAATGTCCAATGTGGTACCTAAACCATTAATGTGC
TTTTATATGGTACATGTACTTTCAT
Found at i:39754442 original size:9 final size:9
Alignment explanation
Indices: 39754430--39754458 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39754420 ATTTTTTAAA
39754430 TTATAATTT
1 TTATAATTT
39754439 TTATAATTT
1 TTATAATTT
39754448 TTA-AATTT
1 TTATAATTT
39754456 TTA
1 TTA
39754459 AAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTATAATTT
Found at i:39764725 original size:28 final size:28
Alignment explanation
Indices: 39764685--39764740 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
39764675 ACCTTTTGAT
39764685 GAGGATTTCACAAATAAGGAATGACCTG
1 GAGGATTTCACAAATAAGGAATGACCTG
39764713 GAGGATTTCACAAATAAGGAATGACCTG
1 GAGGATTTCACAAATAAGGAATGACCTG
39764741 CCTGGTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (28 bp):
GAGGATTTCACAAATAAGGAATGACCTG
Found at i:39768356 original size:3 final size:3
Alignment explanation
Indices: 39768348--39768377 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
39768338 TAGGAAGTGC
*
39768348 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39768378 CAAGGGACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39770978 original size:27 final size:27
Alignment explanation
Indices: 39770945--39771025 Score: 162
Period size: 27 Copynumber: 3.0 Consensus size: 27
39770935 CGAAAGGATG
39770945 TTTTCTTCTTGATGAATCACTTATGAC
1 TTTTCTTCTTGATGAATCACTTATGAC
39770972 TTTTCTTCTTGATGAATCACTTATGAC
1 TTTTCTTCTTGATGAATCACTTATGAC
39770999 TTTTCTTCTTGATGAATCACTTATGAC
1 TTTTCTTCTTGATGAATCACTTATGAC
39771026 AGTTGAATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (27 bp):
TTTTCTTCTTGATGAATCACTTATGAC
Found at i:39778815 original size:14 final size:15
Alignment explanation
Indices: 39778786--39778818 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39778776 TTTTCCTGTT
39778786 TTTTCACTACTTTCA
1 TTTTCACTACTTTCA
*
39778801 TTTTCTCTA-TTTCA
1 TTTTCACTACTTTCA
39778815 TTTT
1 TTTT
39778819 ACAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTCACTACTTTCA
Found at i:39800853 original size:31 final size:29
Alignment explanation
Indices: 39800753--39800854 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 29
39800743 TACGACAACT
* *
39800753 ATATAAACAATTTTCAATAAATAAAAAAT-
1 ATATAAA-AATTTTTAAAAAATAAAAAATA
* * *
39800782 ATAT-AAAATTATTAAATATTAAAAAATTTA
1 ATATAAAAATTTTTAAAAAATAAAAAA--TA
39800812 ATATAAAAATTTTTAAAAAATAAAAAATA
1 ATATAAAAATTTTTAAAAAATAAAAAATA
39800841 ATATAGACAAATTT
1 ATATA-A-AAATTT
39800855 AGGTAAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
27 15 0.25
28 2 0.03
29 12 0.20
30 5 0.08
31 25 0.42
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (29 bp):
ATATAAAAATTTTTAAAAAATAAAAAATA
Found at i:39805276 original size:12 final size:12
Alignment explanation
Indices: 39805259--39805289 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39805249 TAGATCCGTT
39805259 TAGATCTATGCC
1 TAGATCTATGCC
39805271 TAGATCTATGCC
1 TAGATCTATGCC
39805283 TAGATCT
1 TAGATCT
39805290 GTTTTGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TAGATCTATGCC
Found at i:39806048 original size:30 final size:29
Alignment explanation
Indices: 39805979--39806333 Score: 337
Period size: 30 Copynumber: 12.0 Consensus size: 29
39805969 CCCATTTGAC
* * *
39805979 CCCTAAACTTCTCTAAAATT--ATATTGA
1 CCCTAAACTTCTCCAAAATTACATTTTAA
* *
39806006 CCCTTTAAACTTCTCAAAAATTATATTTTAA
1 CCC--TAAACTTCTCCAAAATTACATTTTAA
** *
39806037 CCCTCAAACTTCTCCAAAATCCCAATTTAA
1 CCCT-AAACTTCTCCAAAATTACATTTTAA
* *
39806067 CCCCTAAACTTTTCCAAAATTACATTTTGA
1 -CCCTAAACTTCTCCAAAATTACATTTTAA
* *
39806097 CCCATAAACTT-TTC-AAATTATATTTTAA
1 CCC-TAAACTTCTCCAAAATTACATTTTAA
*
39806125 CCCTTAAACTT-TCCTAAAATTATATTTTAA
1 CCC-TAAACTTCTCC-AAAATTACATTTTAA
* * *
39806155 CCCTAAAACTTTTTCAAAATTATATTTTAA
1 CCCT-AAACTTCTCCAAAATTACATTTTAA
* *
39806185 CCCTTAAACTTCTCTAAAATCACATTTTAA
1 CCC-TAAACTTCTCCAAAATTACATTTTAA
39806215 CCCTAAACCTTC-CCAAAATTACATTTTAA
1 CCCTAAA-CTTCTCCAAAATTACATTTTAA
* * *
39806244 CCTTAAACTTATCCAAAATCACATTTTAA
1 CCCTAAACTTCTCCAAAATTACATTTTAA
*
39806273 CCCTAAACTT-TCCCAAAATTACATTTTTTAC
1 CCCTAAACTTCT-CCAAAATTACA--TTTTAA
*
39806304 CCCTAAACTTTTCCAAAATTACATTTTAA
1 CCCTAAACTTCTCCAAAATTACATTTTAA
39806333 C
1 C
39806334 TTCGAATTCT
Statistics
Matches: 277, Mismatches: 33, Indels: 34
0.81 0.10 0.10
Matches are distributed among these distances:
27 3 0.01
28 28 0.10
29 89 0.32
30 115 0.42
31 41 0.15
32 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTCTCCAAAATTACATTTTAA
Found at i:39806331 original size:118 final size:117
Alignment explanation
Indices: 39806005--39806333 Score: 387
Period size: 118 Copynumber: 2.8 Consensus size: 117
39805995 AATTATATTG
* * ** *
39806005 ACCCTTTAAACTTCTCAAAAATTATATTTTAACCCTCAAAC-TTCTCCAAAATCCCAATTTAACC
1 ACCC-TTAAACTT-TCCAAAATTATATTTTAACCCTAAAACTTTC-CCAAAATTACATTTTAACC
* ** *
39806069 CCTAAACTTTTCCAAAATTACATTTTGACCCATAAACTTTTCAAATTATATTTTA
63 CCTAAACTTTTCCAAAATTACATTTTAACCCATAAACTTCCCAAATTACATTTTA
** * *
39806124 ACCCTTAAACTTTCCTAAAATTATATTTTAACCCTAAAACTTTTTCAAAATTATATTTTAACCCT
1 ACCCTTAAACTTTCC-AAAATTATATTTTAACCCTAAAACTTTCCCAAAATTACATTTTAACCCC
* * *
39806189 TAAACTTCTCTAAAATCACATTTTAACCC-TAAACCTTCCCAAAATTACATTTTA
65 TAAACTTTTCCAAAATTACATTTTAACCCATAAA-CTTCCC-AAATTACATTTTA
* * *
39806243 A-CCTTAAACTTATCCAAAATCACATTTTAACCCT-AAACTTTCCCAAAATTACATTTTTTACCC
1 ACCCTTAAACTT-TCCAAAATTATATTTTAACCCTAAAACTTTCCCAAAATTACA-TTTTAACCC
39806306 CTAAACTTTTCCAAAATTACATTTTAAC
64 CTAAACTTTTCCAAAATTACATTTTAAC
39806334 TTCGAATTCT
Statistics
Matches: 178, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
117 22 0.12
118 134 0.75
119 22 0.12
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.37
Consensus pattern (117 bp):
ACCCTTAAACTTTCCAAAATTATATTTTAACCCTAAAACTTTCCCAAAATTACATTTTAACCCCT
AAACTTTTCCAAAATTACATTTTAACCCATAAACTTCCCAAATTACATTTTA
Found at i:39817140 original size:39 final size:39
Alignment explanation
Indices: 39817077--39817323 Score: 221
Period size: 39 Copynumber: 6.3 Consensus size: 39
39817067 GAAGATCCCG
* * *
39817077 ATCTTTTACCCTGAGCTTGGGGCAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* *
39817116 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCATCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * *
39817155 ATCTCTTACTCCGACCTTGGGGCAGATTGCAGCCAT---TCA
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCA
* * * * *
39817194 ATCTTTTACCCCGATCATGGGGTAGATCACCGTCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * ** * * * *
39817233 ATCTCTTACCCCGAACCTAGGGCAGATTGCAACCATCCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * *
39817272 ATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
39817311 ATCTCTTACCCCG
1 ATCTCTTACCCCG
39817324 GACCTAGGGT
Statistics
Matches: 162, Mismatches: 40, Indels: 12
0.76 0.19 0.06
Matches are distributed among these distances:
36 3 0.02
37 2 0.01
38 1 0.01
39 149 0.92
40 1 0.01
41 2 0.01
42 4 0.02
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
Found at i:39817221 original size:78 final size:77
Alignment explanation
Indices: 39817115--39817365 Score: 315
Period size: 78 Copynumber: 3.2 Consensus size: 77
39817105 ACCATCAGCT
* * * * * *
39817115 AATCTCTTACCCCGAGCTTGAGGCAGATCACCATCATCCAATCTCTTACTCCGACCTTGGGGCAG
1 AATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAGCCAATCTCTTACCCCGACC-TAGGGCAG
39817180 ATTGCAGCCATTC
65 ATTGCAGCCATTC
* * *
39817193 AATCTTTTACCCCGATCATGGGGTAGATCACCGTCAGCCAATCTCTTACCCCGAACCTAGGGCAG
1 AATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAGCCAATCTCTTACCCCG-ACCTAGGGCAG
* *
39817258 ATTGCAACCATCC
65 ATTGCAGCCATTC
* * *
39817271 GATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCAATCTCTTACCCCGGACCTAGGGTAG
1 AATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAGCCAATCTCTTACCCC-GACCTAGGGCAG
39817336 ATTGCAGCCA-TC
65 ATTGCAGCCATTC
* *
39817348 TGATCTTTTACCTCGAGC
1 -AATCTTTTACCCCGAGC
39817366 CTGAGGCAGA
Statistics
Matches: 150, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
77 1 0.01
78 145 0.97
79 4 0.03
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (77 bp):
AATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAGCCAATCTCTTACCCCGACCTAGGGCAGA
TTGCAGCCATTC
Found at i:39817291 original size:117 final size:117
Alignment explanation
Indices: 39817077--39817298 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 117
39817067 GAAGATCCCG
* * * * *
39817077 ATCTTTTACCCTGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCCCGAGCTTGAGGCAGA
1 ATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGACCTAGAGGCAGA
* * *
39817142 TCACCATCATCCAATCTCTTACTCCGACCTTGGGGCAGATTGCAGCCATTCA
66 TCACAACCATCCAATCTCTTACCCCGACCTTGGGGCAGATTGCAGCCATTCA
* * *
39817194 ATCTTTTACCCCGATCATGGGGTAGATCACCGTCAGCCAATCTCTTACCCCGAACCTAG-GGCAG
1 ATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCG-ACCTAGAGGCAG
** * * * *
39817258 ATTGCAACCATCCGATCTTTTACCCCGAGCTTGGGGTAGAT
65 ATCACAACCATCCAATCTCTTACCCCGACCTTGGGGCAGAT
39817299 CACTATCAGC
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
117 83 0.95
118 4 0.05
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (117 bp):
ATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGACCTAGAGGCAGA
TCACAACCATCCAATCTCTTACCCCGACCTTGGGGCAGATTGCAGCCATTCA
Found at i:39817313 original size:117 final size:117
Alignment explanation
Indices: 39817077--39817323 Score: 255
Period size: 117 Copynumber: 2.1 Consensus size: 117
39817067 GAAGATCCCG
* * * * *
39817077 ATCTTTTACCCTGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCCCGAGCTTGAGGCAGA
1 ATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGACCTAGAGGCAGA
* * * ** **
39817142 TCACCATCATCCAATCTCTTACTCCGACCTTGGGGCAGATTGCAGCCATTCA
66 TCACAACCATCCAATCTCTTACCCCGACCTTGGGGCAGATCACAGCCAGCCA
* * *
39817194 ATCTTTTACCCCGATCATGGGGTAGATCACCGTCAGCCAATCTCTTACCCCGAACCTAG-GGCAG
1 ATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCG-ACCTAGAGGCAG
** * * * * *
39817258 ATTGCAACCATCCGATCTTTTACCCCGAGCTTGGGGTAGATCACTA-TCAGCCA
65 ATCACAACCATCCAATCTCTTACCCCGACCTTGGGGCAGATCAC-AGCCAGCCA
*
39817311 ATCTCTTACCCCG
1 ATCTTTTACCCCG
39817324 GACCTAGGGT
Statistics
Matches: 105, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
117 100 0.95
118 5 0.05
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (117 bp):
ATCTTTTACCCCGAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGACCTAGAGGCAGA
TCACAACCATCCAATCTCTTACCCCGACCTTGGGGCAGATCACAGCCAGCCA
Found at i:39817359 original size:39 final size:38
Alignment explanation
Indices: 39817233--39817359 Score: 98
Period size: 39 Copynumber: 3.3 Consensus size: 38
39817223 CCGTCAGCCA
* * *
39817233 ATCTCTTACCCCGAACCTAGGGCAGATTGCAACCATCCG
1 ATCTCTTACCCCGGACCTAGGGTAGATTGC-ACCATCAG
* * * *
39817272 ATCTTTTACCCC-GAGCTTGGGGTAGA-T-CACTATCAG
1 ATCTCTTACCCCGGA-CCTAGGGTAGATTGCACCATCAG
*
39817308 CCAATCTCTTACCCCGGACCTAGGGTAGATTGCAGCCATCTG
1 ---ATCTCTTACCCCGGACCTAGGGTAGATTGCA-CCATCAG
*
39817350 ATCTTTTACC
1 ATCTCTTACC
39817360 TCGAGCCTGA
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
36 6 0.09
37 1 0.01
38 2 0.03
39 48 0.72
40 3 0.04
41 2 0.03
42 5 0.07
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (38 bp):
ATCTCTTACCCCGGACCTAGGGTAGATTGCACCATCAG
Found at i:39817390 original size:78 final size:78
Alignment explanation
Indices: 39817116--39817393 Score: 281
Period size: 78 Copynumber: 3.6 Consensus size: 78
39817106 CCATCAGCTA
* * * * * *
39817116 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCATCCAATCTCTTACTCC-GACCTTGGGGCAG
1 ATCTTTTACCCCGAGCTTGAGGCAGATCACAACCAGCCAATCTCTTACCCCGGACC-TAGGGCAG
*
39817180 ATTGCAGCCAT-TCA
65 ATTGCAGCCATCT-G
* * * * *** *
39817194 ATCTTTTACCCCGATCATGGGGTAGATCACCGTCAGCCAATCTCTTACCCCGAACCTAGGGCAGA
1 ATCTTTTACCCCGAGCTTGAGGCAGATCACAACCAGCCAATCTCTTACCCCGGACCTAGGGCAGA
* *
39817259 TTGCAACCATCCG
66 TTGCAGCCATCTG
* * * * *
39817272 ATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCAATCTCTTACCCCGGACCTAGGGTAGA
1 ATCTTTTACCCCGAGCTTGAGGCAGATCACAACCAGCCAATCTCTTACCCCGGACCTAGGGCAGA
39817337 TTGCAGCCATCTG
66 TTGCAGCCATCTG
* * ** *
39817350 ATCTTTTACCTCGAGCCTGAGGCAGATTGCAACCATCCAATCTC
1 ATCTTTTACCCCGAGCTTGAGGCAGATCACAACCAGCCAATCTC
39817394 AAAAAAAAAA
Statistics
Matches: 168, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
78 165 0.98
79 3 0.02
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCTTTTACCCCGAGCTTGAGGCAGATCACAACCAGCCAATCTCTTACCCCGGACCTAGGGCAGA
TTGCAGCCATCTG
Found at i:39817959 original size:42 final size:40
Alignment explanation
Indices: 39817909--39817986 Score: 129
Period size: 42 Copynumber: 1.9 Consensus size: 40
39817899 ATAAAGACAA
*
39817909 ATTTTAAATTTAAATTTACTTTAAATATTAAATGTCCAATAC
1 ATTTTAAATTTAAATTTA-TTTAAAT-TTAAAAGTCCAATAC
39817951 ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCA
1 ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCA
39817987 TTTACAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 10 0.29
41 7 0.20
42 18 0.51
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (40 bp):
ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCAATAC
Found at i:39819534 original size:30 final size:30
Alignment explanation
Indices: 39819431--39819780 Score: 231
Period size: 30 Copynumber: 11.9 Consensus size: 30
39819421 TTTGACCCCC
* * * *
39819431 AAACTTCTCCTAAATTACATTTTAACCC-G
1 AAACTTTTCCAAAATCACATTTTAACCCTT
* * * * *
39819460 AAACTTTTCAAAAATTATATTTTTACCCTC
1 AAACTTTTCCAAAATCACATTTTAACCCTT
* *
39819490 AAA-TATCTCCAAAATCCCATTTTAACCCTT
1 AAACT-TTTCCAAAATCACATTTTAACCCTT
* * ** *
39819520 AAACTTTTCTAAAATTATGTTTTGATCCC-T
1 AAACTTTTCCAAAATCACATTTT-AACCCTT
* ***
39819550 AAACTTTTTCAAAATTGTATTTTAACCCTT
1 AAACTTTTCCAAAATCACATTTTAACCCTT
* *
39819580 AAAC-TTTCTTAAAATCACATTTTAACCCTA
1 AAACTTTTC-CAAAATCACATTTTAACCCTT
* *
39819610 AAACTTTTCCAAAATTACATTTTGACCCTT
1 AAACTTTTCCAAAATCACATTTTAACCCTT
* *
39819640 AAACTTCTCCAAAATCACATTTT---TCTT
1 AAACTTTTCCAAAATCACATTTTAACCCTT
* * *
39819667 AAAC-CTTCATAAAATCACATTTTGACCC-T
1 AAACTTTTC-CAAAATCACATTTTAACCCTT
* *
39819696 AAACTTCTCCAAAATCAC-TTTTAACCC-C
1 AAACTTTTCCAAAATCACATTTTAACCCTT
* * *
39819724 AAA-ATTTCCTAAAATTACATTTTTATCCC-T
1 AAACTTTTCC-AAAATCACA-TTTTAACCCTT
* *
39819754 AAACTTTTCCAAAATTATATTTTAACC
1 AAACTTTTCCAAAATCACATTTTAACC
39819781 TCAAATTATC
Statistics
Matches: 250, Mismatches: 55, Indels: 32
0.74 0.16 0.09
Matches are distributed among these distances:
26 2 0.01
27 24 0.10
28 18 0.07
29 51 0.20
30 141 0.56
31 14 0.06
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
AAACTTTTCCAAAATCACATTTTAACCCTT
Found at i:39821406 original size:9 final size:9
Alignment explanation
Indices: 39821392--39821449 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
39821382 GTTAAAATTA
39821392 TTTAATAAT
1 TTTAATAAT
39821401 TTTAATAAT
1 TTTAATAAT
39821410 TTT-AT-AT
1 TTTAATAAT
* *
39821417 TTAAAAAAT
1 TTTAATAAT
*
39821426 AATATAATAAT
1 --TTTAATAAT
39821437 TTTAATAAT
1 TTTAATAAT
39821446 TTTA
1 TTTA
39821450 TATTTAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 4 0.10
8 3 0.08
9 26 0.67
11 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAATAAT
Found at i:39821434 original size:36 final size:37
Alignment explanation
Indices: 39821385--39821465 Score: 137
Period size: 36 Copynumber: 2.2 Consensus size: 37
39821375 CGATGAGGTT
* *
39821385 AAAATTATTTAATAATTTTAATAATTTTATATTT-AA
1 AAAATAATATAATAATTTTAATAATTTTATATTTAAA
39821421 AAAATAATATAATAATTTTAATAATTTTATATTTAAA
1 AAAATAATATAATAATTTTAATAATTTTATATTTAAA
39821458 AAAATAAT
1 AAAATAAT
39821466 TTTAAATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 32 0.76
37 10 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
AAAATAATATAATAATTTTAATAATTTTATATTTAAA
Found at i:39821463 original size:20 final size:19
Alignment explanation
Indices: 39821404--39821469 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
39821394 TAATAATTTT
39821404 AATAATTTTATATTTAAAA
1 AATAATTTTATATTTAAAA
* * *
39821423 AATAATATAATAATTT---T
1 AATAATTTTAT-ATTTAAAA
39821440 AATAATTTTATATTTAAAAA
1 AATAATTTTATATTT-AAAA
39821460 AATAATTTTA
1 AATAATTTTA
39821470 AATTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
16 4 0.11
17 9 0.25
19 9 0.25
20 14 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAATTTTATATTTAAAA
Found at i:39823920 original size:21 final size:21
Alignment explanation
Indices: 39823896--39823935 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39823886 TACTCATGGC
39823896 TACTTAATTTAGCGAAGTGGA
1 TACTTAATTTAGCGAAGTGGA
*
39823917 TACTTAATTTAGCGGAGTG
1 TACTTAATTTAGCGAAGTG
39823936 TTTGCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (21 bp):
TACTTAATTTAGCGAAGTGGA
Found at i:39844484 original size:15 final size:15
Alignment explanation
Indices: 39844464--39844493 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39844454 GCTCTAAGCG
39844464 ATAGCTCTTTTATGC
1 ATAGCTCTTTTATGC
39844479 ATAGCTCTTTTATGC
1 ATAGCTCTTTTATGC
39844494 TCCTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (15 bp):
ATAGCTCTTTTATGC
Found at i:39848852 original size:28 final size:28
Alignment explanation
Indices: 39848811--39848871 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
39848801 ACAAAAAGAG
39848811 ATAAAAAAAACAAGAATTTAAACTAAGC
1 ATAAAAAAAACAAGAATTTAAACTAAGC
* *
39848839 ATAAACAAAGCAAGAATTTAAACTAAGC
1 ATAAAAAAAACAAGAATTTAAACTAAGC
39848867 ATAAA
1 ATAAA
39848872 TGAGTTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.62, C:0.11, G:0.08, T:0.18
Consensus pattern (28 bp):
ATAAAAAAAACAAGAATTTAAACTAAGC
Found at i:39863735 original size:18 final size:17
Alignment explanation
Indices: 39863711--39863753 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
39863701 CGACCTATGG
39863711 CACCTCCGATAAGGCCTC
1 CACCTCCG-TAAGGCCTC
*
39863729 TACCTCCCGTAAGGCCTC
1 CACCT-CCGTAAGGCCTC
39863747 CACCTCC
1 CACCTCC
39863754 TCCTGTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 17 0.77
19 3 0.14
ACGTcount: A:0.19, C:0.49, G:0.14, T:0.19
Consensus pattern (17 bp):
CACCTCCGTAAGGCCTC
Found at i:39866878 original size:24 final size:24
Alignment explanation
Indices: 39866846--39866935 Score: 128
Period size: 24 Copynumber: 3.8 Consensus size: 24
39866836 GTATACTGGT
* *
39866846 TAACTATTCTTGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
*
39866870 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
*
39866894 TAACCATTCTGGGCTCGTAAAAGC
1 TAACCATTCTGGGCTCGTAAGAGC
39866918 TAACCA-TCTTGGGCTCGT
1 TAACCATTC-TGGGCTCGT
39866936 GAAACCTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 2 0.03
24 58 0.97
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:39870182 original size:26 final size:25
Alignment explanation
Indices: 39870124--39870204 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 25
39870114 CCTTTTTCAA
*
39870124 TATTTTTATTTATTATTTCTTTTATT
1 TATTTTTATTTATTATTT-TATTATT
*
39870150 TAATTTTATTTATTATTTTATTATCT
1 TATTTTTATTTATTATTTTATTAT-T
39870176 GT-TTTTTAGGTTTTATTATTATTATTATT
1 -TATTTTTA---TTTATTATT-TTATTATT
39870205 CGTGTCGAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 5 0.11
26 23 0.50
27 1 0.02
29 10 0.22
30 7 0.15
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (25 bp):
TATTTTTATTTATTATTTTATTATT
Found at i:39872519 original size:13 final size:13
Alignment explanation
Indices: 39872501--39872526 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39872491 TGTTTTATTC
39872501 ATTAACCCATAAT
1 ATTAACCCATAAT
39872514 ATTAACCCATAAT
1 ATTAACCCATAAT
39872527 CCATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTAACCCATAAT
Found at i:39877972 original size:21 final size:22
Alignment explanation
Indices: 39877948--39877992 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
39877938 CCATTTGAAA
39877948 TTCTTTACTTTTACTTT-TAAT
1 TTCTTTACTTTTACTTTCTAAT
*
39877969 TTCTTTACTTTTAGTTTCTAAT
1 TTCTTTACTTTTACTTTCTAAT
39877991 TT
1 TT
39877993 TAGTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCTTTACTTTTACTTTCTAAT
Found at i:39877977 original size:15 final size:15
Alignment explanation
Indices: 39877957--39877987 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39877947 ATTCTTTACT
39877957 TTTACTTTTAATTTC
1 TTTACTTTTAATTTC
*
39877972 TTTACTTTTAGTTTC
1 TTTACTTTTAATTTC
39877987 T
1 T
39877988 AATTTTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTACTTTTAATTTC
Found at i:39879417 original size:23 final size:23
Alignment explanation
Indices: 39879373--39879418 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39879363 AAAAAAAATT
**
39879373 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
39879396 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
39879419 ATTCGAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:39885581 original size:10 final size:10
Alignment explanation
Indices: 39885563--39885596 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
39885553 CATAAATAAA
39885563 AAAGAGAAAG
1 AAAGAGAAAG
*
39885573 AACGAGAAAG
1 AAAGAGAAAG
*
39885583 AAAGAAAAAG
1 AAAGAGAAAG
39885593 AAAG
1 AAAG
39885597 TAAGGTATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAGAGAAAG
Found at i:39889120 original size:57 final size:57
Alignment explanation
Indices: 39889049--39889310 Score: 271
Period size: 58 Copynumber: 4.6 Consensus size: 57
39889039 AAACGGGCAT
* * * **
39889049 TTTTGGATAC-TCGGGGGTAAAATGGTAATTTTGATGAAATTAAGGTCGAAATGGAA
1 TTTTGGAAACTTCGGGGGTAAAATGGTAATTTTGGTGAAATTAGGGTAAAAATGGAA
* * * *
39889105 TTTTGGAAAGTTCGGGGGCAAAATGGTAATTTTTGGTAAAATT-GGGTTAAAATGGAA
1 TTTTGGAAACTTCGGGGGTAAAATGGTAA-TTTTGGTGAAATTAGGGTAAAAATGGAA
* ** * * * *
39889162 TTTTGGAAAATTCAAGGGTGAAATGGCAATTTTGGTAAAATCAGGGTTAAAAATGGAA
1 TTTTGGAAACTTCGGGGGTAAAATGGTAATTTTGGTGAAATTAGGG-TAAAAATGGAA
** *
39889220 TTTTAAAAACTTCGAGGGTAAAATGGTAATTTTGGTGAAATTAGGGGTAAAAATGGAA
1 TTTTGGAAACTTCGGGGGTAAAATGGTAATTTTGGTGAAATTA-GGGTAAAAATGGAA
*
39889278 TTTTGAAAAACTT-GGGGGTCAAAAT-GTAATTTT
1 TTTTG-GAAACTTCGGGGGT-AAAATGGTAATTTT
39889311 TAGAAAGTTT
Statistics
Matches: 173, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
56 20 0.12
57 54 0.31
58 84 0.49
59 15 0.09
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (57 bp):
TTTTGGAAACTTCGGGGGTAAAATGGTAATTTTGGTGAAATTAGGGTAAAAATGGAA
Found at i:39889332 original size:59 final size:58
Alignment explanation
Indices: 39889097--39889466 Score: 221
Period size: 59 Copynumber: 6.3 Consensus size: 58
39889087 ATTAAGGTCG
* *
39889097 AAATGGAATTTTGG--AAAGTTCGGGGG-CAAAATGGTAATTTTTGGTAAA-ATT-GGGTTA
1 AAATGGAATTTTGGAAAAACTT-GGGGGTCAAAAT-GTAATTTTT-G-AAAGTTTAGGGTTA
** * * * * *
39889154 AAATGGAATTTTGG-AAAA-TTCAAGGGT-GAAATGGCAATTTTGGTAAA-ATCAGGGTTAA
1 AAATGGAATTTTGGAAAAACTT-GGGGGTCAAAAT-GTAATTTTTG-AAAGTTTAGGGTT-A
* *
39889212 AAATGGAATTTT--AAAAACTTCGAGGGT-AAAATGGTAATTTTGGTGAAA--TTAGGGGTAA
1 AAATGGAATTTTGGAAAAACTT-GGGGGTCAAAAT-GTAATTTT--TGAAAGTTTA-GGGTTA
*
39889270 AAATGGAATTTT-GAAAAACTTGGGGGTCAAAATGTAATTTTTAGAAAGTTTTAAGGTTA
1 AAATGGAATTTTGGAAAAACTTGGGGGTCAAAATGTAATTTTT-GAAAG-TTTAGGGTTA
** * ** * * * *
39889329 AAATATAATTTTGGAGAAGTTTGGTGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTCA
1 AAATGGAATTTTGGAAAAACTTGGGGGTCAAAATGTAATTTTTG-AAAGTTTAGGGTTA
* * * * * *
39889388 CAATGTAATTTTGGAAAAGCTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTCA
1 AAATGGAATTTTGGAAAAACTTGGGGGTCAAAATGTAATTTTTG-AAAGTTTA-GGGTTA
*
39889448 AAATGTAATTTTGGAAAAA
1 AAATGGAATTTTGGAAAAA
39889467 TTTTAGGGAC
Statistics
Matches: 261, Mismatches: 34, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
56 8 0.03
57 45 0.17
58 64 0.25
59 89 0.34
60 55 0.21
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (58 bp):
AAATGGAATTTTGGAAAAACTTGGGGGTCAAAATGTAATTTTTGAAAGTTTAGGGTTA
Found at i:39889349 original size:30 final size:29
Alignment explanation
Indices: 39889092--39889474 Score: 225
Period size: 30 Copynumber: 13.1 Consensus size: 29
39889082 ATGAAATTAA
* * **
39889092 GGTCGAAATGGAATTTTGG-AAAGTTCGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAG
*
39889120 GGGCAAAATGGTAATTTTTGGTAAAA--TT-G
1 GGTCAAAAT-GTAA-TTTTGG-AAAAGTTTAG
* * *
39889149 GGTTAAAATGGAATTTTGGAAAA-TTCAAG
1 GGTCAAAATGTAATTTTGGAAAAGTT-TAG
* * *
39889178 GGT-GAAATGGCAATTTTGGTAAAA--TCAG
1 GGTCAAAAT-GTAATTTTGG-AAAAGTTTAG
* * * * *
39889206 GGTTAAAAATGGAATTTT-AAAAACTTCGAG
1 GG-TCAAAATGTAATTTTGGAAAAGTT-TAG
*
39889236 GGT-AAAATGGTAATTTTGGTGAAA--TTAGG
1 GGTCAAAAT-GTAATTTTGG-AAAAGTTTA-G
* * * * **
39889265 GGTAAAAATGGAATTTTGAAAAACTTGGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAG
* *
39889294 GGTCAAAATGTAATTTT-TAGAAAGTTTTAA
1 GGTCAAAATGTAATTTTGGA-AAAG-TTTAG
* * * *
39889324 GGTTAAAATATAATTTTGGAGAAGTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAG
*
39889353 TGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 -GGTCAAAATGTAATTTTGGAAAAGTTTAG
* *
39889383 GGTCACAATGTAATTTTGGAAAAGCTTAGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTA-G
39889413 GGTCAAAATGTAATTTTGGAAAAGTTTAGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTA-G
*
39889443 GGTCAAAATGTAATTTTGGAAAAATTTTAG
1 GGTCAAAATGTAATTTTGG-AAAAGTTTAG
39889473 GG
1 GG
39889475 ACCTCCAAAG
Statistics
Matches: 282, Mismatches: 46, Indels: 52
0.74 0.12 0.14
Matches are distributed among these distances:
26 4 0.01
27 11 0.04
28 28 0.10
29 102 0.36
30 122 0.43
31 12 0.04
32 3 0.01
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTAG
Found at i:39889369 original size:89 final size:88
Alignment explanation
Indices: 39889211--39889466 Score: 234
Period size: 89 Copynumber: 2.9 Consensus size: 88
39889201 ATCAGGGTTA
* * * * * *
39889211 AAAATGGAATTTTA-AAAA-CTTCGAGGGT-AAAATGGTAATTTTGGTGAAATTAGGGGTAAAAA
1 AAAATGTAATTTTAGAAAAGCTTAGA-GGTCAAAAT-ATAATTTTGGAGAAGTTTGGGGTAAAAA
* *
39889273 TGGAATTTTGAAAAACTTGGGGGTC
64 TGTAATTTTGAAAAACTTGAGGGTC
* * *
39889298 AAAATGTAATTTTTAG-AAAGTTTTA-AGGTTAAAATATAATTTTGGAGAAGTTTGGTGGTTAAA
1 AAAATGTAA-TTTTAGAAAAG-CTTAGAGGTCAAAATATAATTTTGGAGAAGTTTGG-GGTAAAA
* * *
39889361 ATGTAATTTTGGAAAAGTTTAGGGTC
63 ATGTAATTTTGAAAAACTTGAGGGTC
* * * * * *
39889387 ACAATGTAATTTTGGAAAAGCTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAAT
1 AAAATGTAATTTTAGAAAAGCTTAGAGGTCAAAATATAATTTTGGAGAAGTTT-GGGGTAAAAAT
39889452 GTAATTTTGGAAAAA
65 GTAATTTT-GAAAAA
39889467 TTTTAGGGAC
Statistics
Matches: 137, Mismatches: 22, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
87 8 0.06
88 35 0.26
89 85 0.62
90 9 0.07
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (88 bp):
AAAATGTAATTTTAGAAAAGCTTAGAGGTCAAAATATAATTTTGGAGAAGTTTGGGGTAAAAATG
TAATTTTGAAAAACTTGAGGGTC
Found at i:39891122 original size:17 final size:17
Alignment explanation
Indices: 39891078--39891132 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
39891068 TTAAACTTTT
39891078 TTTTAAATTT-AAAT--
1 TTTTAAATTTAAAATAA
*
39891092 TTTT-AATTCGAAAATAA
1 TTTTAAATT-TAAAATAA
39891109 TTTTAAATTTAAAATAA
1 TTTTAAATTTAAAATAA
*
39891126 ATTTAAA
1 TTTTAAA
39891133 CTCCAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 4 0.12
17 17 0.52
18 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTTAAATTTAAAATAA
Found at i:39891128 original size:18 final size:19
Alignment explanation
Indices: 39891087--39891129 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
39891077 TTTTTAAATT
*
39891087 TAAATTTTTAATTCGAAAA
1 TAAATTTTAAATTCGAAAA
*
39891106 T-AATTTTAAATT-TAAAA
1 TAAATTTTAAATTCGAAAA
39891123 TAAATTT
1 TAAATTT
39891130 AAACTCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 15 0.71
19 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATTTTAAATTCGAAAA
Found at i:39891860 original size:86 final size:86
Alignment explanation
Indices: 39891751--39891955 Score: 313
Period size: 86 Copynumber: 2.4 Consensus size: 86
39891741 CTTGGGTTTG
** *
39891751 ATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACTGCATCACTTGTTTTAATTCGCTTCTC
1 ATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTC
39891816 TGGATC-TCCTCAACAAGACGA
66 TGGATCTTCC-CAACAAGACGA
* *
39891837 ATTTGGTCCACTTCTCAGTGTCTCATGAAGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTC
1 ATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTC
*
39891902 TGGATCTTCCCAAGAAGACGA
66 TGGATCTTCCCAACAAGACGA
* * *
39891923 ATTTGGTCCACTTCTCAGTATCTTATTAGGAAG
1 ATTTGGTCCACTTCTCAGTGTCTCATCAGGAAG
39891956 CTAACCGTTT
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 105 0.97
87 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (86 bp):
ATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTC
TGGATCTTCCCAACAAGACGA
Found at i:39892224 original size:205 final size:205
Alignment explanation
Indices: 39891853--39892238 Score: 580
Period size: 205 Copynumber: 1.9 Consensus size: 205
39891843 TCCACTTCTC
39891853 AGTGTCTCATGAAGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTTCCCAAGAA
1 AGTGTCTCATGAAGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTTCCCAAGAA
* * *
39891918 GACGAATTTGGTCCACTTCTCAGTATCTTATTAGGAAGCTAACCGTTTTATTGCTTCGACCTGCT
66 GACAAATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCT
* ** * * * * *
39891983 TCTCAGTGTCTCATCAGGAAGTTGGGGTTTGAAGATTTGCTCGCATTGAGCCTGAGTTTGATTTG
131 TCTCAATGTCTCATCAAAAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCCTGAGTTTGATTTG
39892048 GTCTTCTCTG
196 GTCTTCTCTG
* *
39892058 AGTGTCTCATTAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATC-TCCTCAAGA
1 AGTGTCTCATGAAGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTTCC-CAAGA
* * *
39892122 AGACAAATTTGGTCCTCTTCTCCA-TAT-TTCATCGGGAAGCTAACCATTTTATTGCTTTGACCT
65 AGACAAATTTGGTCCACTTCT-CAGTATCTT-ATCAGGAAGCTAACCATTTTATTGCTTCGACCT
39892185 GCTTCTCAATGTCTCATCAAAAAGCTAGGGTTCGAAGATTTGCTCACATCGAGC
128 GCTTCTCAATGTCTCATCAAAAAGCTAGGGTTCGAAGATTTGCTCACATCGAGC
39892239 GTCGAGTTGG
Statistics
Matches: 162, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
204 5 0.03
205 155 0.96
206 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (205 bp):
AGTGTCTCATGAAGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTTCCCAAGAA
GACAAATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCT
TCTCAATGTCTCATCAAAAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCCTGAGTTTGATTTG
GTCTTCTCTG
Found at i:39892466 original size:78 final size:78
Alignment explanation
Indices: 39892344--39892489 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 78
39892334 TGGAGTCTGG
* * *
39892344 TGATATGCCCCAAGCTCGGGATAAAGGATCAAATGGTTGCAATCTGCCTCAAGCTCGAGGTAAGA
1 TGATATGCCCCAAGCTCGGGATAAAAGATCAAATGCTTGCAATCTGCCCCAAGCTCGAGGTAAGA
39892409 GATTGGTCGATAA
66 GATTGGTCGATAA
* * * * ** *
39892422 TGATTTGCCCTAAGCTCGGGGTAAAAGATCAAATGACTT-TAATCTGCCCCTGGCTCGGGGTAAG
1 TGATATGCCCCAAGCTCGGGATAAAAGATCAAATG-CTTGCAATCTGCCCCAAGCTCGAGGTAAG
39892486 AGAT
65 AGAT
39892490 CAACATCTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
78 55 0.96
79 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (78 bp):
TGATATGCCCCAAGCTCGGGATAAAAGATCAAATGCTTGCAATCTGCCCCAAGCTCGAGGTAAGA
GATTGGTCGATAA
Found at i:39892810 original size:49 final size:49
Alignment explanation
Indices: 39892751--39892938 Score: 245
Period size: 49 Copynumber: 3.8 Consensus size: 49
39892741 TCCCTTCAAA
* * *
39892751 TCTTCGTGGTA-TGGGATCCGTCATCGCGGCTTAGATCTTTCTCTTTATT
1 TCTTCGTGGTACT-GGATCCGCCATCGCGGCTTAGATCTTTCTCTTCATG
* *
39892800 TCTTCGTGGTACTGGATCCACCATCGCGGCTTAGATCTTTCCCTTCATG
1 TCTTCGTGGTACTGGATCCGCCATCGCGGCTTAGATCTTTCTCTTCATG
*
39892849 TCTTCG-GGATACTGGATCCGCCGTCGCGGCTTAGATCTTTCTCTTCATG
1 TCTTCGTGG-TACTGGATCCGCCATCGCGGCTTAGATCTTTCTCTTCATG
* * * * *
39892898 TCTTCGTGGTACTGAATCCGCCGTCCCAGCTTAGATATTTC
1 TCTTCGTGGTACTGGATCCGCCATCGCGGCTTAGATCTTTC
39892939 CCTTTTGTCT
Statistics
Matches: 124, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
48 2 0.02
49 119 0.96
50 3 0.02
ACGTcount: A:0.14, C:0.28, G:0.22, T:0.37
Consensus pattern (49 bp):
TCTTCGTGGTACTGGATCCGCCATCGCGGCTTAGATCTTTCTCTTCATG
Found at i:39892866 original size:98 final size:98
Alignment explanation
Indices: 39892738--39892942 Score: 270
Period size: 98 Copynumber: 2.1 Consensus size: 98
39892728 CAACTTAAAC
* * *
39892738 CTTTCCCTTCAAATCTTCGTGGTATGGGATCCGTCATCGCGGCTTAGATCTTTCTCTTTATTTCT
1 CTTTCCCTTCAAATCTTCGTGGTATGGGATCCGCCATCGCGGCTTAGATCTTTCTCTTCATGTCT
* * *
39892803 TCGTGGTACTGGATCCACCATCGCGGCTTAGAT
66 TCGTGGTACTGAATCCACCATCCCAGCTTAGAT
** *
39892836 CTTTCCCTTCATGTCTTCG-GGATACT-GGATCCGCCGTCGCGGCTTAGATCTTTCTCTTCATGT
1 CTTTCCCTTCAAATCTTCGTGG-TA-TGGGATCCGCCATCGCGGCTTAGATCTTTCTCTTCATGT
* *
39892899 CTTCGTGGTACTGAATCCGCCGTCCCAGCTTAGAT
64 CTTCGTGGTACTGAATCCACCATCCCAGCTTAGAT
*
39892934 ATTTCCCTT
1 CTTTCCCTT
39892943 TTGTCTTTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
97 2 0.02
98 90 0.97
99 1 0.01
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (98 bp):
CTTTCCCTTCAAATCTTCGTGGTATGGGATCCGCCATCGCGGCTTAGATCTTTCTCTTCATGTCT
TCGTGGTACTGAATCCACCATCCCAGCTTAGAT
Found at i:39892990 original size:51 final size:51
Alignment explanation
Indices: 39892927--39893294 Score: 207
Period size: 51 Copynumber: 7.3 Consensus size: 51
39892917 GCCGTCCCAG
* *
39892927 CTTAGATATTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGTCGTTACGGT
1 CTTAGATCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGTCGTTGCGGT
* ** * ** * * * *
39892978 TTTAGATCTTTCCCGTCGTGTC-TTCTAAGGTACACGG-TCTATCGTTG-TGA
1 CTTAGATCTTTCCC-TTTTGTCTTTTTGCGGTAC-TGGATCTGTCGTTGCGGT
* * * *
39893028 CTTAGACCTTTCCCTTTTGTCTTTTTACGGTACTGGATTTGCCGTTGCGGT
1 CTTAGATCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGTCGTTGCGGT
* * * * * *
39893079 CTTAGATCTTTTTCGTTGTGTC-TTTTGAGGTAAAC-GG-TCTGCCGTTGC-GA
1 CTTAGATC-TTTCCCTTTTGTCTTTTTGCGGT--ACTGGATCTGTCGTTGCGGT
* * * * *
39893129 CTTAGACCTTTCCCTTTTATCTTTTTGCGATATTGGATCTGTCGTTGCGAT
1 CTTAGATCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGTCGTTGCGGT
* * * * * * * ** * *
39893180 CTTAGATCTTTCTC-GTCGTATCTTCTGAGGTGCACGATCTGCCGTTGC-GA
1 CTTAGATCTTTCCCTTTTGTCT-TTTTGCGGTACTGGATCTGTCGTTGCGGT
* * ** **
39893230 CTTAGACCTTTCCCTTTTGTCTTTTTGCGGTATTGGAT-TCACCGTCACGGT
1 CTTAGATCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCT-GTCGTTGCGGT
39893281 CTTAGATCTTTCCC
1 CTTAGATCTTTCCC
39893295 ATCGTGTCTT
Statistics
Matches: 226, Mismatches: 75, Indels: 32
0.68 0.23 0.10
Matches are distributed among these distances:
48 1 0.00
49 19 0.08
50 84 0.37
51 101 0.45
52 19 0.08
53 2 0.01
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (51 bp):
CTTAGATCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGTCGTTGCGGT
Found at i:39893042 original size:101 final size:101
Alignment explanation
Indices: 39892935--39893307 Score: 478
Period size: 101 Copynumber: 3.7 Consensus size: 101
39892925 AGCTTAGATA
* *
39892935 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGTCGTTACGGTTTTAGATCTTTCCCGTCGTGTC
1 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTACGGTCTTAGATCTTTCCCGTCGTGTC
* ** *
39893000 TTCTAAGGTACACGGTCTATCGTTGTGACTTAGACC
66 TTCTGAGGTACACGGTCTGCCGTTGCGACTTAGACC
* * * ** *
39893036 TTTCCCTTTTGTCTTTTTACGGTACTGGATTTGCCGTTGCGGTCTTAGATCTTTTTCGTTGTGTC
1 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTACGGTCTTAGATCTTTCCCGTCGTGTC
* *
39893101 TTTTGAGGTAAACGGTCTGCCGTTGCGACTTAGACC
66 TTCTGAGGTACACGGTCTGCCGTTGCGACTTAGACC
* * * * * * * *
39893137 TTTCCCTTTTATCTTTTTGCGATATTGGATCTGTCGTTGCGATCTTAGATCTTTCTCGTCGTATC
1 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTACGGTCTTAGATCTTTCCCGTCGTGTC
* *
39893202 TTCTGAGGTGCACGATCTGCCGTTGCGACTTAGACC
66 TTCTGAGGTACACGGTCTGCCGTTGCGACTTAGACC
* * * *
39893238 TTTCCCTTTTGTCTTTTTGCGGTATTGGAT-TCACCGTCACGGTCTTAGATCTTTCCCATCGTGT
1 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCT-GCCGTTACGGTCTTAGATCTTTCCCGTCGTGT
39893302 CTTCTG
65 CTTCTG
39893308 GTGTTGAGAC
Statistics
Matches: 233, Mismatches: 38, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
100 1 0.00
101 232 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (101 bp):
TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTACGGTCTTAGATCTTTCCCGTCGTGTC
TTCTGAGGTACACGGTCTGCCGTTGCGACTTAGACC
Found at i:39894203 original size:6 final size:6
Alignment explanation
Indices: 39894194--39894265 Score: 65
Period size: 6 Copynumber: 11.5 Consensus size: 6
39894184 CGACCTCTCC
* * *
39894194 TTTTCT TTTTCTT TTTTCTTT TTTTCT TTTTAT TTTTGT TTTTGT TTTTCT
1 TTTTCT TTTTC-T TTTTC--T TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
*
39894245 TCTTCT TTTT-T CTTTTCT TTT
1 TTTTCT TTTTCT -TTTTCT TTT
39894266 ATTCATTGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
5 1 0.02
6 42 0.74
7 7 0.12
8 7 0.12
ACGTcount: A:0.01, C:0.12, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:39894211 original size:7 final size:7
Alignment explanation
Indices: 39894194--39894260 Score: 57
Period size: 7 Copynumber: 9.3 Consensus size: 7
39894184 CGACCTCTCC
39894194 TTTTC-T
1 TTTTCTT
39894200 TTTTCTT
1 TTTTCTT
39894207 TTTTCTTT
1 TTTTC-TT
39894215 TTTTCTT
1 TTTTCTT
*
39894222 TTTATTTT
1 TTT-TCTT
*
39894230 TGTTTTTGT
1 T-TTTCT-T
39894239 TTTTC-T
1 TTTTCTT
*
39894245 TCTTCTT
1 TTTTCTT
39894252 TTTTCTT
1 TTTTCTT
39894259 TT
1 TT
39894261 CTTTTATTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
6 10 0.20
7 20 0.39
8 17 0.33
9 4 0.08
ACGTcount: A:0.01, C:0.12, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:39895092 original size:15 final size:15
Alignment explanation
Indices: 39895074--39895103 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39895064 TTCATCTTGA
39895074 CTTTTTCTTTCTTTT
1 CTTTTTCTTTCTTTT
*
39895089 CTTTTTTTTTCTTTT
1 CTTTTTCTTTCTTTT
39895104 GATAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTCTTTCTTTT
Found at i:39899285 original size:29 final size:27
Alignment explanation
Indices: 39899248--39899409 Score: 100
Period size: 28 Copynumber: 5.7 Consensus size: 27
39899238 TGGATACTCG
39899248 GGGGTAAAATGGTAATTTTGATGAAATT
1 GGGGTAAAATGGTAATTTTG-TGAAATT
39899276 GGGGTAAAAATGG-AATTTTG-GAAAGTT
1 GGGGT-AAAATGGTAATTTTGTGAAA-TT
* *
39899303 CGAGGGTAAAATAGTAATTTTTGGTAAAATT
1 -G-GGGTAAAATGGTAA-TTTT-GTGAAATT
*
39899334 GGGGTTAAAAT-GAAATTTTG-GAAAATT
1 GGGG-TAAAATGGTAATTTTGTG-AAATT
* * * * *
39899361 CGAGAGTGAAATGGCAATTTTGGTAAAATC
1 -G-GGGTAAAATGGTAATTTT-GTGAAATT
39899391 GGGGTTAAAATGG-AATTTT
1 GGGG-TAAAATGGTAATTTT
39899410 AAAAAGTTCG
Statistics
Matches: 107, Mismatches: 11, Indels: 32
0.71 0.07 0.21
Matches are distributed among these distances:
26 4 0.04
27 8 0.07
28 37 0.35
29 36 0.34
30 16 0.15
31 3 0.03
32 3 0.03
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (27 bp):
GGGGTAAAATGGTAATTTTGTGAAATT
Found at i:39899344 original size:58 final size:57
Alignment explanation
Indices: 39899251--39899440 Score: 254
Period size: 57 Copynumber: 3.3 Consensus size: 57
39899241 ATACTCGGGG
* * * *
39899251 GTAAAATGGTAATTTTGATGAAATTGGGGTAAAAATGGAATTTTGGAAAGTTCGAGG
1 GTAAAATGGTAATTTTGGTAAAATTGGGGTTAAAATGGAATTTTGGAAAGTTCGAGA
* * *
39899308 GTAAAATAGTAATTTTTGGTAAAATTGGGGTTAAAATGAAATTTTGGAAAATTCGAGA
1 GTAAAATGGTAA-TTTTGGTAAAATTGGGGTTAAAATGGAATTTTGGAAAGTTCGAGA
* * * **
39899366 GTGAAATGGCAATTTTGGTAAAATCGGGGTTAAAATGGAATTTTAAAAAGTTCGAGA
1 GTAAAATGGTAATTTTGGTAAAATTGGGGTTAAAATGGAATTTTGGAAAGTTCGAGA
*
39899423 GTAAAATGATAATTTTGG
1 GTAAAATGGTAATTTTGG
39899441 AGAAATCAGG
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
57 66 0.58
58 48 0.42
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.33
Consensus pattern (57 bp):
GTAAAATGGTAATTTTGGTAAAATTGGGGTTAAAATGGAATTTTGGAAAGTTCGAGA
Found at i:39899440 original size:57 final size:57
Alignment explanation
Indices: 39899251--39899473 Score: 227
Period size: 57 Copynumber: 3.9 Consensus size: 57
39899241 ATACTCGGGG
* * * * * *
39899251 GTAAAATGGTAATTTTGATGAAATTGGGGTAAAAATGGAATTTTGGAAAGTTCGAGG
1 GTAAAATGATAATTTTGGTAAAATCGGGGTAAAAATGGAATTTTGAAAAGTTCGAGA
* * *
39899308 GTAAAAT-AGTAATTTTTGGTAAAATTGGGGTTAAAATGAAATTTTGGAAAA-TTCGAGA
1 GTAAAATGA-TAA-TTTTGGTAAAATCGGGGTAAAAATGGAATTTT-GAAAAGTTCGAGA
* ** * *
39899366 GTGAAATGGCAATTTTGGTAAAATCGGGGTTAAAATGGAATTTTAAAAAGTTCGAGA
1 GTAAAATGATAATTTTGGTAAAATCGGGGTAAAAATGGAATTTTGAAAAGTTCGAGA
* *
39899423 GTAAAATGATAATTTTGG-AGAAATCAGGGGCAAAAATAGAATTTTGTAAAA
1 GTAAAATGATAATTTTGGTA-AAATC-GGGGTAAAAATGGAATTTTG-AAAA
39899474 CTTAAGGGTC
Statistics
Matches: 138, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
56 5 0.04
57 67 0.49
58 58 0.42
59 8 0.06
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (57 bp):
GTAAAATGATAATTTTGGTAAAATCGGGGTAAAAATGGAATTTTGAAAAGTTCGAGA
Done.