Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold226
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: 1170647
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 8
Found at i:134825 original size:2 final size:2
Alignment explanation
Indices: 134820--134853 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
134810 AAGAGCTTAC
134820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
134854 TCTTTCTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:141070 original size:35 final size:35
Alignment explanation
Indices: 141029--141106 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
141019 AATATCTACG
*
141029 GCTAATGTACAATTAATATATCATAATTTTATACA
1 GCTAATGTACAACTAATATATCATAATTTTATACA
* * *
141064 GCTAATGTATAGCTAATATATCATAATTTTATACG
1 GCTAATGTACAACTAATATATCATAATTTTATACA
*
141099 GTTAATGT
1 GCTAATGT
141107 CCAGCCAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (35 bp):
GCTAATGTACAACTAATATATCATAATTTTATACA
Found at i:141886 original size:13 final size:13
Alignment explanation
Indices: 141868--141892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141858 TCTGATTTTT
141868 TTTAATATTTATA
1 TTTAATATTTATA
141881 TTTAATATTTAT
1 TTTAATATTTAT
141893 TTTTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:145772 original size:16 final size:17
Alignment explanation
Indices: 145746--145781 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
145736 TTATTTTATT
145746 ATTTAAAATTAAATTAA
1 ATTTAAAATTAAATTAA
*
145763 ATTT-AAATTAATTTAA
1 ATTTAAAATTAAATTAA
145779 ATT
1 ATT
145782 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAAAATTAAATTAA
Found at i:146645 original size:2 final size:2
Alignment explanation
Indices: 146638--146679 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
146628 AAAGGCTCTT
146638 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
146680 GGAGGGGGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:149386 original size:2 final size:2
Alignment explanation
Indices: 149373--149415 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
149363 AATATCTCCC
*
149373 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149414 AT
1 AT
149416 CTTAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:149603 original size:35 final size:36
Alignment explanation
Indices: 149516--149604 Score: 85
Period size: 35 Copynumber: 2.5 Consensus size: 36
149506 ATTTATTATT
* * * *
149516 TTATTAAAATAATAATTT-TATATTAATATTTATTTA
1 TTATT-AAATAATAATTTAAATATAAAAATTAATTTA
* *
149552 TTTTTATAATTA-AATTTAAATA-AAAAATTAATTTA
1 TTATTA-AATAATAATTTAAATATAAAAATTAATTTA
149587 TTATTAAATAATAATTTA
1 TTATTAAATAATAATTTA
149605 GATTGTGATA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
34 4 0.10
35 27 0.64
36 11 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TTATTAAATAATAATTTAAATATAAAAATTAATTTA
Found at i:155891 original size:14 final size:15
Alignment explanation
Indices: 155873--155907 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
155863 TCAAACGTAA
155873 ATATAATTATAAAAT
1 ATATAATTATAAAAT
*
155888 -TATAATTTTAAAAT
1 ATATAATTATAAAAT
155902 ATATAA
1 ATATAA
155908 AAAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAATTATAAAAT
Found at i:156292 original size:3 final size:3
Alignment explanation
Indices: 156284--156316 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
156274 GCTGTGTTAA
*
156284 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
156317 GTAAAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:158915 original size:23 final size:24
Alignment explanation
Indices: 158889--158960 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
158879 AAATATTAAA
*
158889 TATAAATATA-TTTTTAATAAAAT
1 TATAAATAAATTTTTTAATAAAAT
**
158912 TATATTTAAATTTTTTAATAAAAT
1 TATAAATAAATTTTTTAATAAAAT
** *
158936 TATATTTAAATTTTTTAAAAAAAT
1 TATAAATAAATTTTTTAATAAAAT
158960 T
1 T
158961 TTATGTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 7 0.16
24 37 0.84
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAAATAAATTTTTTAATAAAAT
Found at i:158919 original size:15 final size:15
Alignment explanation
Indices: 158881--158944 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
158871 TTGGACGTAA
*
158881 ATATTAAATATAAATAT
1 ATATTTAATA-AAAT-T
*
158898 ATTTTTAATAAAATT
1 ATATTTAATAAAATT
158913 ATA-TT--T-AAATT
1 ATATTTAATAAAATT
158924 -T-TTTAATAAAATT
1 ATATTTAATAAAATT
158937 ATATTTAA
1 ATATTTAA
158945 ATTTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
10 3 0.08
11 5 0.13
12 2 0.05
13 5 0.13
14 3 0.08
15 8 0.21
16 4 0.11
17 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTAATAAAATT
Found at i:158926 original size:24 final size:24
Alignment explanation
Indices: 158899--158960 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
158889 TATAAATATA
158899 TTTTTAATAAAATTATATTTAAAT
1 TTTTTAATAAAATTATATTTAAAT
158923 TTTTTAATAAAATTATATTTAAAT
1 TTTTTAATAAAATTATATTTAAAT
*
158947 TTTTTAAAAAAATT
1 TTTTTAATAAAATT
158961 TTATGTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTTAATAAAATTATATTTAAAT
Found at i:159767 original size:9 final size:9
Alignment explanation
Indices: 159755--159814 Score: 66
Period size: 9 Copynumber: 6.2 Consensus size: 9
159745 TAATTAAAAA
159755 AATTAATTT
1 AATTAATTT
159764 AATTTAATTT
1 AA-TTAATTT
159774 AATTAATTT
1 AATTAATTT
*
159783 GATTAATTT
1 AATTAATTT
159792 AATTTAAGTTTT
1 AA-TTAA--TTT
*
159804 GATTAATTT
1 AATTAATTT
159813 AA
1 AA
159815 AGTGTTGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 22 0.51
10 13 0.30
11 4 0.09
12 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (9 bp):
AATTAATTT
Found at i:159787 original size:28 final size:29
Alignment explanation
Indices: 159756--159812 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
159746 AATTAAAAAA
159756 ATTAATTTAATTTAA-TTTAATTAATTTG
1 ATTAATTTAATTTAAGTTTAATTAATTTG
*
159784 ATTAATTTAATTTAAGTTTTGATTAATTT
1 ATTAATTTAATTTAAG-TTTAATTAATTT
159813 AAAGTGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 15 0.58
30 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (29 bp):
ATTAATTTAATTTAAGTTTAATTAATTTG
Found at i:159811 original size:16 final size:18
Alignment explanation
Indices: 159788--159829 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
159778 AATTTGATTA
*
159788 ATTTAATTT-AAGTTTTG
1 ATTTAATTTAAAGTGTTG
159805 A-TTAATTTAAAGTGTTG
1 ATTTAATTTAAAGTGTTG
159822 ATTTAATT
1 ATTTAATT
159830 AATCAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
ATTTAATTTAAAGTGTTG
Found at i:159814 original size:5 final size:5
Alignment explanation
Indices: 159757--159798 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
159747 ATTAAAAAAA
*
159757 TTAAT TTAAT TTAAT TTAA- TTAAT TTGA- TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
159799 GTTTTGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 7 0.21
5 26 0.79
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TTAAT
Found at i:159983 original size:19 final size:19
Alignment explanation
Indices: 159959--159996 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
159949 ATTCAAACCC
*
159959 ATTTAAATTTAAAT-TAAAA
1 ATTT-AATTAAAATATAAAA
159978 ATTTAATTAAAATATAAAA
1 ATTTAATTAAAATATAAAA
159997 TAATAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTAATTAAAATATAAAA
Found at i:160294 original size:5 final size:5
Alignment explanation
Indices: 160281--160313 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
160271 TAAATATTTT
*
160281 TTAAT TTAAA TTAAA TTAAA TTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTA
160314 TTATTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TTAAA
Found at i:160669 original size:19 final size:19
Alignment explanation
Indices: 160640--160709 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
160630 TATATTTTAA
160640 TATATTATTTTAAATTTATT
1 TATATT-TTTTAAATTTATT
* *
160660 TATATTTTTTAAAATTATA
1 TATATTTTTTAAATTTATT
* * *
160679 TATATTTATAATAATTTTTT
1 TATATTTTTTA-AATTTATT
160699 TA-ATTTTTTAA
1 TATATTTTTTAA
160710 TAATAAATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 1 0.03
19 26 0.65
20 13 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTTTTTAAATTTATT
Found at i:160750 original size:25 final size:26
Alignment explanation
Indices: 160717--160765 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
160707 TAATAATAAA
160717 TATTATATA-AATAAATAAATATTTT
1 TATTATATATAATAAATAAATATTTT
* *
160742 TATTATATATATTATATAAATATT
1 TATTATATATAATAAATAAATATT
160766 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTATATATAATAAATAAATATTTT
Found at i:160798 original size:17 final size:18
Alignment explanation
Indices: 160767--160800 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
160757 ATAAATATTA
*
160767 ATTTTAAAATTTTAAATT
1 ATTTTAAAATATTAAATT
160785 ATTTT-AAATATTAAAT
1 ATTTTAAAATATTAAAT
160801 AAATTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAAAATATTAAATT
Found at i:161481 original size:6 final size:6
Alignment explanation
Indices: 161470--161498 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
161460 AAAAATTAAT
161470 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
161499 TCATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:161486 original size:11 final size:11
Alignment explanation
Indices: 161472--161510 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
161462 AAATTAATTA
161472 AAAATAAAAAT
1 AAAATAAAAAT
161483 AAAAATAAAAAT
1 -AAAATAAAAAT
* *
161495 AAAATCATAAT
1 AAAATAAAAAT
161506 AAAAT
1 AAAAT
161511 TTTTGTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:163609 original size:22 final size:22
Alignment explanation
Indices: 163584--163630 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
163574 TTATGTCTTC
*
163584 TATTTACATGTTTAAGGACATT
1 TATTTACATGTTTAAGAACATT
163606 TATTTACATGTTTAAGAACATT
1 TATTTACATGTTTAAGAACATT
163628 TAT
1 TAT
163631 CAAGTACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.47
Consensus pattern (22 bp):
TATTTACATGTTTAAGAACATT
Found at i:163655 original size:24 final size:24
Alignment explanation
Indices: 163623--163684 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
163613 ATGTTTAAGA
163623 ACATTTATCAAGTACCTTCCAAGG
1 ACATTTATCAAGTACCTTCCAAGG
163647 ACATTTATCAAGTACCTTCCAAGG
1 ACATTTATCAAGTACCTTCCAAGG
163671 ACATTTATCAAGTA
1 ACATTTATCAAGTA
163685 ACTATACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (24 bp):
ACATTTATCAAGTACCTTCCAAGG
Found at i:167251 original size:32 final size:33
Alignment explanation
Indices: 167208--167283 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
167198 TAAGATATTT
* *
167208 TTTAT-TTATATAAATTTTAATATATTAATA-A
1 TTTATATTATATAAAATTTAAAATATTAATACA
*
167239 TTTATATTATATAAAATTTAAAATATTTATACA
1 TTTATATTATATAAAATTTAAAATATTAATACA
* *
167272 CTCATATTATAT
1 TTTATATTATAT
167284 TTGTGAATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 5 0.13
32 22 0.58
33 11 0.29
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTATATTATATAAAATTTAAAATATTAATACA
Found at i:168164 original size:18 final size:18
Alignment explanation
Indices: 168143--168189 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
168133 TTTTGAGATT
168143 TATATTTATATTATTTTA
1 TATATTTATATTATTTTA
*
168161 TATA-TTA-AATATTTTA
1 TATATTTATATTATTTTA
168177 TATATATTATATT
1 TATAT-TTATATT
168190 TTTATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 12 0.50
17 3 0.12
18 7 0.29
19 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTATATTATTTTA
Found at i:168166 original size:9 final size:9
Alignment explanation
Indices: 168143--168195 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
168133 TTTTGAGATT
168143 TATA-TTTA
1 TATATTTTA
168151 TATTATTTTA
1 TA-TATTTTA
168161 TATA--TTA
1 TATATTTTA
*
168168 AATATTTTA
1 TATATTTTA
*
168177 TATATATTA
1 TATATTTTA
168186 TAT-TTTTA
1 TATATTTTA
168194 TA
1 TA
168196 ATTATTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 6 0.16
8 8 0.22
9 17 0.46
10 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATATTTTA
Found at i:168188 original size:16 final size:15
Alignment explanation
Indices: 168141--168200 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 15
168131 AATTTTGAGA
168141 TTTATAT-TTATATTAT
1 TTTATATATTATA-T-T
168157 TTTATATATTAAATATT
1 TTTATATATT--ATATT
168174 TTATATATATTATATT
1 TT-TATATATTATATT
168190 TTTATA-ATTAT
1 TTTATATATTAT
168201 TAAATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 5 0.12
15 4 0.10
16 14 0.35
17 5 0.12
18 9 0.22
19 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATATTATATT
Found at i:168190 original size:32 final size:34
Alignment explanation
Indices: 168141--168213 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 34
168131 AATTTTGAGA
*
168141 TTTATATTTATATTA-TTTTAT-A-TATTAAATAT
1 TTTATATATATATTATTTTTATAATTATTAAAT-T
168173 TTTATATATAT-TATATTTTTATAATTATTAAATT
1 TTTATATATATAT-TATTTTTATAATTATTAAATT
*
168207 TTAATAT
1 TTTATAT
168214 GAGTATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 1 0.03
32 12 0.34
33 6 0.17
34 8 0.23
35 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TTTATATATATATTATTTTTATAATTATTAAATT
Found at i:168622 original size:18 final size:18
Alignment explanation
Indices: 168558--168613 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
168548 ATTTATATCA
* *
168558 AAATTTAATTTAAA-ATA
1 AAATTTAATATAAATATG
* * *
168575 AAAATAAATATAAATATT
1 AAATTTAATATAAATATG
168593 AAATTTAATATAAAT-TG
1 AAATTTAATATAAATATG
168610 AAAT
1 AAAT
168614 ATTCATATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATTTAATATAAATATG
Found at i:174324 original size:9 final size:9
Alignment explanation
Indices: 174299--174329 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
174289 TTGATTGAAC
174299 TAAAAAAAT
1 TAAAAAAAT
174308 TAATAAAAAT
1 TAA-AAAAAT
174318 TAAAAAAAT
1 TAAAAAAAT
174327 TAA
1 TAA
174330 TTGATTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:174845 original size:29 final size:29
Alignment explanation
Indices: 174793--174849 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
174783 CATGGATTTT
*
174793 TTTAATTAAAATTTTTAATTTTTATTATA
1 TTTAATTAAAATTTGTAATTTTTATTATA
*
174822 TTTAATTAAAA-TTGTATTTATTTATTAT
1 TTTAATTAAAATTTGTAATT-TTTATTAT
174850 TATACGTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTAATTAAAATTTGTAATTTTTATTATA
Found at i:174936 original size:9 final size:9
Alignment explanation
Indices: 174922--174985 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
174912 TTATAATTTA
174922 ATTTAATAT
1 ATTTAATAT
174931 ATTTAATA-
1 ATTTAATAT
174939 ATTT-ATAT
1 ATTTAATAT
174947 ATTATATATTAT
1 ATT-TA-A-TAT
*
174959 ATTTTATAT
1 ATTTAATAT
* *
174968 TTTTTATAT
1 ATTTAATAT
174977 ATTT-ATAT
1 ATTTAATAT
174985 A
1 A
174986 AATAAATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
7 3 0.06
8 12 0.26
9 23 0.49
10 1 0.02
11 2 0.04
12 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTTAATAT
Found at i:175002 original size:12 final size:11
Alignment explanation
Indices: 174981--175023 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 11
174971 TTATATATTT
174981 ATATAAATA-A
1 ATATAAATATA
174991 ATATAAATATA
1 ATATAAATATA
175002 ATATAAATTATTA
1 ATATAAA-TA-TA
175015 A-ATAAATAT
1 ATATAAATAT
175024 TACTTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.33
11 10 0.33
12 7 0.23
13 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:175024 original size:11 final size:12
Alignment explanation
Indices: 174975--175025 Score: 56
Period size: 11 Copynumber: 4.5 Consensus size: 12
174965 TATTTTTTAT
*
174975 ATATTTATATAA
1 ATATTAATATAA
174987 ATA--AATATAA
1 ATATTAATATAA
174997 ATA-TAATATAA
1 ATATTAATATAA
175008 ATTATTAA-ATAA
1 A-TATTAATATAA
175020 ATATTA
1 ATATTA
175026 CTTTCAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
10 9 0.26
11 13 0.37
12 10 0.29
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTAATATAA
Found at i:180083 original size:3 final size:3
Alignment explanation
Indices: 180075--180116 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
180065 AGTAGCCATG
180075 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
180117 AATGCTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:182472 original size:11 final size:10
Alignment explanation
Indices: 182451--182493 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
182441 TGTAACCAAA
182451 TATATTTAAT
1 TATATTTAAT
182461 TATATCTTAAT
1 TATAT-TTAAT
182472 TATATTTTAAT
1 TATA-TTTAAT
182483 T-TAATTTAAT
1 TAT-ATTTAAT
182493 T
1 T
182494 TTTATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 13 0.43
11 16 0.53
12 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTTAAT
Found at i:182627 original size:18 final size:18
Alignment explanation
Indices: 182604--182657 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
182594 CATCACCACC
* *
182604 AATAATACTAATACTAAA
1 AATAATAATAATAATAAA
182622 AATAATAATAATAATAAA
1 AATAATAATAATAATAAA
182640 AATAAATAAATAA-AATAA
1 AAT-AAT-AATAATAATAA
182658 GAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 19 0.59
19 8 0.25
20 5 0.16
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAATAATAATAATAAA
Found at i:182656 original size:22 final size:22
Alignment explanation
Indices: 182621--182663 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
182611 CTAATACTAA
*
182621 AAATAATAATAATAATAAAAAT
1 AAATAATAATAATAAGAAAAAT
182643 AAATAAATAA-AATAAGAAAAA
1 AAAT-AATAATAATAAGAAAAA
182664 AAAAAGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (22 bp):
AAATAATAATAATAAGAAAAAT
Found at i:183548 original size:22 final size:22
Alignment explanation
Indices: 183523--183564 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
183513 TGATTTTTTT
183523 ATTTTTAAAATTTTAAAAATTG
1 ATTTTTAAAATTTTAAAAATTG
* **
183545 ATTTTTTATTTTTTAAAAAT
1 ATTTTTAAAATTTTAAAAAT
183565 AATTATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTTTAAAATTTTAAAAATTG
Found at i:185332 original size:2 final size:2
Alignment explanation
Indices: 185325--185353 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
185315 CTAGTATGTG
185325 TA TA 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 TA TA T
185354 TCAGTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:185784 original size:34 final size:34
Alignment explanation
Indices: 185738--185955 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
185728 GTAAAAACCA
*
185738 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
185772 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
185806 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
185840 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
185873 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
185907 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
185940 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
185956 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:185852 original size:68 final size:67
Alignment explanation
Indices: 185736--185955 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
185726 TGGTAAAAAC
* * *
185736 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
185801 AT
66 AT
* * *
185803 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
185868 AAT
65 AAT
* * * * * *
185871 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
185936 AT
66 AT
185938 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
185956 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:190048 original size:19 final size:19
Alignment explanation
Indices: 190021--190083 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
190011 TCACGTGTAC
* *
190021 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
190040 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
190059 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
190078 AGTACC
1 AGTACC
190084 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:190435 original size:34 final size:34
Alignment explanation
Indices: 190389--190605 Score: 280
Period size: 34 Copynumber: 6.4 Consensus size: 34
190379 GTAAAAACCA
*
190389 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
190423 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
190457 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
190491 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
190524 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
190558 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
190591 CCATTTAATCAACAA
1 CCATTTAATCAACAA
190606 GGAAAAGGAT
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 44 0.27
34 115 0.71
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:190503 original size:68 final size:67
Alignment explanation
Indices: 190387--190605 Score: 321
Period size: 67 Copynumber: 3.3 Consensus size: 67
190377 TGGTAAAAAC
* * *
190387 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
190452 AT
66 AT
* * *
190454 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
190519 AAT
65 AAT
* * * * * *
190522 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
190587 AT
66 AT
190589 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
190606 GGAAAAGGAT
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:195282 original size:16 final size:16
Alignment explanation
Indices: 195246--195283 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
195236 TTTAAACTCG
*
195246 AAATAATTTAAATTTA
1 AAATGATTTAAATTTA
*
195262 AAATGATTTAGATTTA
1 AAATGATTTAAATTTA
195278 AAATGA
1 AAATGA
195284 CTTGAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (16 bp):
AAATGATTTAAATTTA
Found at i:195664 original size:16 final size:17
Alignment explanation
Indices: 195618--195664 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
195608 TTTTAAAATT
195618 TTCAAGTCATTTTTAAG
1 TTCAAGTCATTTTTAAG
195635 TTCAAGTCATTTTTAAG
1 TTCAAGTCATTTTTAAG
*
195652 TTCAGGTCATTTT
1 TTCAAGTCATTTT
195665 GGGTTCAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (17 bp):
TTCAAGTCATTTTTAAG
Found at i:195686 original size:16 final size:15
Alignment explanation
Indices: 195667--195714 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
195657 GTCATTTTGG
195667 GTTCAGATCATTTCGA
1 GTTC-GATCATTTCGA
* *
195683 GTTCGAATTATTTTGA
1 GTTCG-ATCATTTCGA
195699 GTTCGAGTCATTTCGA
1 GTTCGA-TCATTTCGA
195715 ATTTGAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.42
Consensus pattern (15 bp):
GTTCGATCATTTCGA
Found at i:197544 original size:15 final size:14
Alignment explanation
Indices: 197507--197549 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
197497 TTATTTTTTG
*
197507 TATTAATCATGTAAA
1 TATTAAT-ATATAAA
197522 TA-TAATATATAAA
1 TATTAATATATAAA
197535 TTATTAATATATAAA
1 -TATTAATATATAAA
197550 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 13 0.52
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
TATTAATATATAAA
Found at i:197552 original size:17 final size:17
Alignment explanation
Indices: 197526--197560 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
197516 TGTAAATATA
*
197526 ATATATAAATTATTAAT
1 ATATAAAAATTATTAAT
*
197543 ATATAAAAATTTTTAAT
1 ATATAAAAATTATTAAT
197560 A
1 A
197561 CGATGTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAAAAATTATTAAT
Found at i:197626 original size:24 final size:23
Alignment explanation
Indices: 197599--197669 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 23
197589 ATTGTGTTTG
*
197599 AATATATTATATTATATTAATTAA
1 AATATATTATATTATATTAAAT-A
*
197623 AATATTTTTATATT-TATTAAATA
1 AATA-TATTATATTATATTAAATA
*
197646 AATAATATTTATGTTATATCTAAA
1 AAT-ATA-TTATATTATAT-TAAA
197670 ATTATCGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 5 0.13
24 18 0.47
25 11 0.29
26 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATATTATATTATATTAAATA
Found at i:197787 original size:2 final size:2
Alignment explanation
Indices: 197780--197840 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
197770 CCTAAACATA
197780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
197822 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
197841 GGTCCATAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:198190 original size:11 final size:12
Alignment explanation
Indices: 198100--198195 Score: 52
Period size: 13 Copynumber: 7.4 Consensus size: 12
198090 TAAATTATTA
198100 ATATATTAAAAT
1 ATATATTAAAAT
*
198112 TTATA-TAAATAT
1 ATATATTAAA-AT
* *
198124 AAAATATCTTAAAT
1 -ATATAT-TAAAAT
*
198138 ATGATAATAAAAT
1 AT-ATATTAAAAT
198151 ATATTATTAATACATT
1 ATA-TATTAA-A-A-T
198167 AATATATTAAAAT
1 -ATATATTAAAAT
*
198180 TTATA-TAAAAT
1 ATATATTAAAAT
198191 ATATA
1 ATATA
198196 CATATAATAG
Statistics
Matches: 64, Mismatches: 10, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
11 14 0.22
12 11 0.17
13 17 0.27
14 7 0.11
15 5 0.08
16 7 0.11
17 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (12 bp):
ATATATTAAAAT
Found at i:202876 original size:216 final size:216
Alignment explanation
Indices: 202478--202914 Score: 687
Period size: 216 Copynumber: 2.0 Consensus size: 216
202468 TAATTTGTCA
* **
202478 TTTAATGTGGCAAATTATGCATGCATGTATGACGGGCACAAATTGACCCAAATTCAATGACTCAA
1 TTTAATGTGGCAAATTATGCATGCATGTATGACGGGCACAAATTAACCCAAACCCAATGACTCAA
** * * *
202543 ATTACATGAAGTAATTTGATTCATTAAAATAATTTTTTTTTTGAAAAATTTTAAAAAATTCATTT
66 ATTACATGAAGTAATTTGATTCATTAAAATAATTTAATTTTTAAAAAATTTTAAAAAACTCAATT
* * *
202608 TACTTAAAATTTTTAAAAACTTAGAGAGTCAGTAAATTACAACTAGTTCAGCTTAATTAAAATTT
131 TACTTAAAATTTTTAAAAACTTAAAGAGTCAGTAAACTACAACTAATTCAGCTTAATTAAAATTT
202673 TATAATGACAGAGTGATAGAG
196 TATAATGACAGAGTGATAGAG
*
202694 TTTAATGTTGCAAATTATGCATGCATGTATGACGGGCACAAATTAACCCAAACCCAATGACTCAA
1 TTTAATGTGGCAAATTATGCATGCATGTATGACGGGCACAAATTAACCCAAACCCAATGACTCAA
202759 ATTACATGAAGTAATTTGATTCATTAAAATAAGTTTAATTTTTAAAAAATTTT-AAAAACTCAAT
66 ATTACATGAAGTAATTTGATTCATTAAAATAA-TTTAATTTTTAAAAAATTTTAAAAAACTCAAT
* * * * * *
202823 TTACTTAAAGTTTTTAGAAGCTTAAAGAGTTAGTAAACTACAATTAATTCAGCTTAATTAGAATT
130 TTACTTAAAATTTTTAAAAACTTAAAGAGTCAGTAAACTACAACTAATTCAGCTTAATTAAAATT
*
202888 TTATAATGATAGAGTGATAGAG
195 TTATAATGACAGAGTGATAGAG
202910 TTTAA
1 TTTAA
202915 AATTACCTAA
Statistics
Matches: 201, Mismatches: 19, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
216 184 0.92
217 17 0.08
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (216 bp):
TTTAATGTGGCAAATTATGCATGCATGTATGACGGGCACAAATTAACCCAAACCCAATGACTCAA
ATTACATGAAGTAATTTGATTCATTAAAATAATTTAATTTTTAAAAAATTTTAAAAAACTCAATT
TACTTAAAATTTTTAAAAACTTAAAGAGTCAGTAAACTACAACTAATTCAGCTTAATTAAAATTT
TATAATGACAGAGTGATAGAG
Found at i:206364 original size:15 final size:17
Alignment explanation
Indices: 206344--206385 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
206334 AAAAATAAAA
206344 TAAAATTATAAA-AT-T
1 TAAAATTATAAATATAT
206359 TAAAATT-TAAATATAT
1 TAAAATTATAAATATAT
206375 TAAATATTATA
1 TAAA-ATTATA
206386 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 5 0.22
17 3 0.13
18 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTATAAATATAT
Found at i:209652 original size:2 final size:2
Alignment explanation
Indices: 209645--209688 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
209635 GCAACATAGA
209645 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
209687 CT
1 CT
209689 ATAGGGTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:211775 original size:6 final size:6
Alignment explanation
Indices: 211764--211806 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
211754 CCGAGGTGGT
*
211764 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGGAGA G
1 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA G
211807 TGAGAATTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GGAAGA
Found at i:213456 original size:18 final size:18
Alignment explanation
Indices: 213433--213471 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
213423 CGGTCTATCC
213433 AAAGAAGTATTTGGATCT
1 AAAGAAGTATTTGGATCT
213451 AAAGAAGTATTTGGATCT
1 AAAGAAGTATTTGGATCT
213469 AAA
1 AAA
213472 TACAGCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (18 bp):
AAAGAAGTATTTGGATCT
Found at i:214262 original size:2 final size:2
Alignment explanation
Indices: 214257--214295 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
214247 ATCGTGTGTG
214257 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
214296 TTCTACAGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:217825 original size:19 final size:19
Alignment explanation
Indices: 217778--217825 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
217768 TAATATTTAT
*
217778 ATTTAATAATTATTAATAA
1 ATTTAATTATTATTAATAA
* *
217797 ATATATTTATTATTTAA-AA
1 ATTTAATTATTA-TTAATAA
217816 ATTTAATTAT
1 ATTTAATTAT
217826 ATATATACAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTAATTATTATTAATAA
Found at i:217829 original size:29 final size:29
Alignment explanation
Indices: 217770--217831 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
217760 CAAACATTTA
*
217770 ATATTTATATTTAATAATTATTAATAAAT
1 ATATTTATATTTAATAAATATTAATAAAT
*
217799 ATATTTATTATTTAA-AAAT-TTAATTATAT
1 ATATTTA-TATTTAATAAATATTAA-TAAAT
217828 ATAT
1 ATAT
217832 ACACACGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.14
29 18 0.62
30 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATTTATATTTAATAAATATTAATAAAT
Found at i:220794 original size:2 final size:2
Alignment explanation
Indices: 220787--220812 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
220777 TGTATAATGC
220787 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
220813 GAAAGAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:223962 original size:16 final size:16
Alignment explanation
Indices: 223941--223976 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
223931 TTCAAAAAAT
* *
223941 TATTTTTATTTTTATA
1 TATTTTTATTATTAAA
223957 TATTTTTATTATTAAA
1 TATTTTTATTATTAAA
223973 TATT
1 TATT
223977 AATTCAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTATTATTAAA
Found at i:224265 original size:22 final size:21
Alignment explanation
Indices: 224237--224278 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
224227 CTTTTTAAAA
224237 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
224257 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
224278 A
1 A
224279 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:224997 original size:106 final size:109
Alignment explanation
Indices: 224811--225035 Score: 300
Period size: 106 Copynumber: 2.1 Consensus size: 109
224801 CAAATATTTT
* * *
224811 TTAATACAAAG-AGTTCA-TCGTAACATTGATCAATAGAGCTTTCAGTCTTGAAAATACTCGGGA
1 TTAATACAAAGCA-TTCACT-GCAACATTGATCAATAGAGCTTTCAGTCTTGAAAATACTCAGAA
*
224874 AAACTTTCATAACACAAT-C-TATTCGAGTTTCACAATTATTTTCC
64 AAACTTTCATAACACAATACTTATTCGAGCTTCACAATTATTTTCC
*
224918 -TAATACAAAGCATTCACTGCAACATTGATTAATA-ATGCTTTCAGTCTTGAAAATACTCAGAAA
1 TTAATACAAAGCATTCACTGCAACATTGATCAATAGA-GCTTTCAGTCTTGAAAATACTCAGAAA
224981 AACTTTCATAACACAATACCAACTTATTCGAGCTTCACAATTATTTTCC
65 AACTTTCATAACACAAT----ACTTATTCGAGCTTCACAATTATTTTCC
225030 TTAATA
1 TTAATA
225036 ATCTTGTCGA
Statistics
Matches: 103, Mismatches: 5, Indels: 14
0.84 0.04 0.11
Matches are distributed among these distances:
105 1 0.01
106 70 0.68
107 2 0.02
111 1 0.01
112 24 0.23
113 5 0.05
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (109 bp):
TTAATACAAAGCATTCACTGCAACATTGATCAATAGAGCTTTCAGTCTTGAAAATACTCAGAAAA
ACTTTCATAACACAATACTTATTCGAGCTTCACAATTATTTTCC
Found at i:227230 original size:2 final size:2
Alignment explanation
Indices: 227214--227256 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
227204 AATGTCAAGC
* *
227214 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
227256 T
1 T
227257 TCCTAACTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:228255 original size:17 final size:17
Alignment explanation
Indices: 228235--228279 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
228225 TTCATTTGTT
228235 TTTTTTAAAAAAAAAAA
1 TTTTTTAAAAAAAAAAA
*
228252 --TTTT-AAAAAATAAA
1 TTTTTTAAAAAAAAAAA
228266 TTTATTTAAAAAAA
1 TTT-TTTAAAAAAA
228280 TAATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 9 0.39
15 4 0.17
16 1 0.04
17 3 0.13
18 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTTTTAAAAAAAAAAA
Found at i:228280 original size:18 final size:19
Alignment explanation
Indices: 228251--228290 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
228241 AAAAAAAAAA
*
228251 ATTTTAAAAAATAA-ATTT
1 ATTTAAAAAAATAATATTT
228269 ATTTAAAAAAATAATATTT
1 ATTTAAAAAAATAATATTT
228288 ATT
1 ATT
228291 AAGTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAAAAAATAATATTT
Found at i:228286 original size:15 final size:15
Alignment explanation
Indices: 228238--228288 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 15
228228 ATTTGTTTTT
*
228238 TTTAAAAAAA-AAAA
1 TTTAAAAAAATAATA
*
228252 TTTTAAAAAATAAATTTA
1 TTTAAAAAAAT-AA--TA
228270 TTTAAAAAAATAATA
1 TTTAAAAAAATAATA
228285 TTTA
1 TTTA
228289 TTAAGTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.30
15 6 0.20
16 2 0.07
17 2 0.07
18 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAAAAATAATA
Found at i:228347 original size:18 final size:19
Alignment explanation
Indices: 228314--228349 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
228304 TATATATTTT
*
228314 AAATATAATTATAATATAA
1 AAATATAATTAAAATATAA
228333 AAATAT-ATTAAAATATA
1 AAATATAATTAAAATATA
228350 TGAATTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATAATTAAAATATAA
Found at i:228576 original size:23 final size:22
Alignment explanation
Indices: 228540--228596 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
228530 AATTAAGGTA
**
228540 TATTTTTATGATTTAAAATTAAT
1 TATTTTTAAAATTTAAAATT-AT
*
228563 T-TTATTTAAAATTTATAATTAT
1 TATT-TTTAAAATTTAAAATTAT
228585 TATTTTTAAAAT
1 TATTTTTAAAAT
228597 ATAATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTTTTAAAATTTAAAATTAT
Found at i:228599 original size:20 final size:18
Alignment explanation
Indices: 228545--228631 Score: 71
Period size: 16 Copynumber: 4.9 Consensus size: 18
228535 AGGTATATTT
*
228545 TTATGATTTAAAAT-TAA
1 TTATTATTTAAAATATAA
228562 TT-TTATTTAAAATTTATAA
1 TTATTATTTAAAA--TATAA
228581 TTATTATTTTTAAAATAT-A
1 TTATTA--TTTAAAATATAA
228600 --ATTATTT-AAATATAA
1 TTATTATTTAAAATATAA
228615 TTATT-TTTATAAATATA
1 TTATTATTTA-AAATATA
228632 TCTTTATCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 21
0.73 0.01 0.26
Matches are distributed among these distances:
14 6 0.10
15 4 0.07
16 12 0.21
17 9 0.16
18 8 0.14
19 6 0.10
20 6 0.10
22 7 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
TTATTATTTAAAATATAA
Found at i:228612 original size:14 final size:14
Alignment explanation
Indices: 228593--228620 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
228583 ATTATTTTTA
228593 AAATATAATTATTT
1 AAATATAATTATTT
228607 AAATATAATTATTT
1 AAATATAATTATTT
228621 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATAATTATTT
Found at i:228632 original size:20 final size:19
Alignment explanation
Indices: 228576--228631 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 19
228566 ATTTAAAATT
*
228576 TATAATTATTATTTTTAAAA
1 TATAATTATT-TTTATAAAA
228596 TATAATTA---TT-T-AAA
1 TATAATTATTTTTATAAAA
228610 TATAATTATTTTTAT-AAA
1 TATAATTATTTTTATAAAA
228628 TATA
1 TATA
228632 TCTTTATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.34
15 1 0.03
16 2 0.06
17 2 0.06
18 8 0.25
20 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATTATTTTTATAAAA
Found at i:228930 original size:18 final size:17
Alignment explanation
Indices: 228890--228929 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
228880 TTTATATAAA
228890 AATTTTAATATATTATT
1 AATTTTAATATATTATT
228907 AATTTTAA-ATATGTATT
1 AATTTTAATATAT-TATT
*
228924 TATTTT
1 AATTTT
228930 TTTCGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
AATTTTAATATATTATT
Found at i:229181 original size:16 final size:16
Alignment explanation
Indices: 229160--229234 Score: 87
Period size: 16 Copynumber: 4.7 Consensus size: 16
229150 GAATCGATTT
229160 ATTTTAAATTATTTTA
1 ATTTTAAATTATTTTA
*
229176 ATTTTAAATTATGTTA
1 ATTTTAAATTATTTTA
* * *
229192 AGTTTATAGTATTTTA
1 ATTTTAAATTATTTTA
**
229208 ATTTTATGTTATTTTA
1 ATTTTAAATTATTTTA
*
229224 AATTTAAATTA
1 ATTTTAAATTA
229235 ATTAAATTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTTTAAATTATTTTA
Found at i:229237 original size:10 final size:10
Alignment explanation
Indices: 229224--229357 Score: 55
Period size: 10 Copynumber: 13.0 Consensus size: 10
229214 TGTTATTTTA
229224 AATTTAAATT
1 AATTTAAATT
229234 AA-TTAAATTT
1 AATTTAAA-TT
*
229244 GATTTAAATT
1 AATTTAAATT
*
229254 ATTTTAAATT
1 AATTTAAATT
*
229264 AAGATT-AATT
1 AA-TTTAAATT
*
229274 AATTTTGAGTTATT
1 AA-TTT-A--AATT
* **
229288 ATTTTTTTATTT
1 A-ATTTAAAT-T
229300 AAT-TAAATT
1 AATTTAAATT
*
229309 AAATTAAATT
1 AATTTAAATT
229319 AA-TTAAATT
1 AATTTAAATT
229328 AAATTTAAATTT
1 -AATTTAAA-TT
*
229340 AA-ATAAATT
1 AATTTAAATT
229349 AA-TTAAATT
1 AATTTAAATT
229358 TTTTTATTCA
Statistics
Matches: 95, Mismatches: 16, Indels: 27
0.69 0.12 0.20
Matches are distributed among these distances:
9 25 0.26
10 41 0.43
11 18 0.19
12 4 0.04
14 7 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (10 bp):
AATTTAAATT
Found at i:229243 original size:32 final size:32
Alignment explanation
Indices: 229162--229243 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
229152 ATCGATTTAT
*
229162 TTTAAATTATTTTAATTTTAAATTATGTTAAG
1 TTTAAATTATTTTAATTTTAAATTATGTTAAA
* * ** *
229194 TTTATAGTATTTTAATTTTATGTTATTTTAAA
1 TTTAAATTATTTTAATTTTAAATTATGTTAAA
* *
229226 TTTAAATTAATTAAATTT
1 TTTAAATTATTTTAATTT
229244 GATTTAAATT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (32 bp):
TTTAAATTATTTTAATTTTAAATTATGTTAAA
Found at i:229310 original size:5 final size:5
Alignment explanation
Indices: 229300--229357 Score: 77
Period size: 5 Copynumber: 11.8 Consensus size: 5
229290 TTTTTTATTT
229300 AATTA AATTA AATTA AATT- AATTA AATTA AATTTA AATTTA AA-TA AATT-
1 AATTA AATTA AATTA AATTA AATTA AATTA AA-TTA AA-TTA AATTA AATTA
229349 AATTA AATT
1 AATTA AATT
229358 TTTTTATTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
4 12 0.24
5 26 0.53
6 11 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:229358 original size:19 final size:20
Alignment explanation
Indices: 229296--229358 Score: 94
Period size: 19 Copynumber: 3.2 Consensus size: 20
229286 TTATTTTTTT
229296 ATTTAATTAAATTAAATTAA
1 ATTTAATTAAATTAAATTAA
229316 A-TTAATTAAATTAAATTTAA
1 ATTTAATTAAATTAAA-TTAA
*
229336 ATTTAAATAAATT-AATTAA
1 ATTTAATTAAATTAAATTAA
229355 ATTT
1 ATTT
229359 TTTTATTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 22 0.55
20 8 0.20
21 10 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTAATTAAATTAAATTAA
Found at i:229587 original size:17 final size:19
Alignment explanation
Indices: 229552--229596 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
229542 AAAAAATAAA
229552 ATATATTAATATATATATTT
1 ATAT-TTAATATATATATTT
229572 ATATTTAATAT-T-TATTT
1 ATATTTAATATATATATTT
*
229589 AAATTTAA
1 ATATTTAA
229597 AAATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 12 0.50
18 1 0.04
19 7 0.29
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTAATATATATATTT
Found at i:231916 original size:25 final size:26
Alignment explanation
Indices: 231841--231919 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 26
231831 ACCCATTGAT
* *
231841 TTATTTTATTATTAAAAAAATTAAAATA
1 TTATTTT-TTATTAAATAAA-TAAAAAA
231869 TTATTTTTATAATTAAATTTAAATAAAAAA
1 TTATTTTT-T-ATTAAA--TAAATAAAAAA
231899 TTA-TTTTTATTAAATAAATAA
1 TTATTTTTTATTAAATAAATAA
231920 TAATTTAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
25 7 0.16
27 7 0.16
28 9 0.20
29 10 0.22
30 9 0.20
31 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATTTTTTATTAAATAAATAAAAAA
Found at i:232008 original size:16 final size:16
Alignment explanation
Indices: 231977--232020 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
231967 TAATATAAAT
*
231977 TAAA-TTATTCATGAA
1 TAAATTTATTTATGAA
231992 T-AATTTAATTTATGAA
1 TAAATTT-ATTTATGAA
232008 TAAATTTATTTAT
1 TAAATTTATTTAT
232021 ATCTAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 15 0.60
17 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (16 bp):
TAAATTTATTTATGAA
Found at i:232549 original size:22 final size:22
Alignment explanation
Indices: 232515--232564 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
232505 AGAGAAAATT
*
232515 TTATATTGGTTTATTTTATA-A
1 TTATATTGGTTTATATTATATA
**
232536 CTTATATTTTTTTATATTATATA
1 -TTATATTGGTTTATATTATATA
232559 TTATAT
1 TTATAT
232565 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (22 bp):
TTATATTGGTTTATATTATATA
Found at i:232749 original size:20 final size:21
Alignment explanation
Indices: 232726--232775 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
232716 TATGTATCAA
**
232726 ATATAAATTTTAAA-TTTAAT
1 ATATAAATAATAAATTTTAAT
*
232746 ATATTAATAATAAATTTTAAT
1 ATATAAATAATAAATTTTAAT
*
232767 ATATTAATA
1 ATATAAATA
232776 TATTTATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATAAATAATAAATTTTAAT
Found at i:232766 original size:21 final size:20
Alignment explanation
Indices: 232736--232775 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
232726 ATATAAATTT
232736 TAAATTTAATATATTAATAA
1 TAAATTTAATATATTAATAA
232756 TAAATTTTAATATATTAATA
1 TAAA-TTTAATATATTAATA
232776 TATTTATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTTAATATATTAATAA
Found at i:232803 original size:46 final size:46
Alignment explanation
Indices: 232752--232844 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
232742 TAATATATTA
*
232752 ATAATAAATTTTAA-TATATTAATATATTTATATCATATTAAAAATT
1 ATAATAAATTATAATTATATTAATAT-TTTATATCATATTAAAAATT
* * * * *
232798 ATAATATATTATAATTATTTTATTATTTTTTATCATATTCAAAATT
1 ATAATAAATTATAATTATATTAATATTTTATATCATATTAAAAATT
232844 A
1 A
232845 ATGGAGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 31 0.77
47 9 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (46 bp):
ATAATAAATTATAATTATATTAATATTTTATATCATATTAAAAATT
Found at i:232810 original size:10 final size:10
Alignment explanation
Indices: 232742--232816 Score: 56
Period size: 10 Copynumber: 7.9 Consensus size: 10
232732 ATTTTAAATT
232742 TAATATATTAA
1 TAATATATT-A
* *
232753 TAATAAATTT
1 TAATATATTA
232763 TAATATA-T-
1 TAATATATTA
232771 TAATATATT-
1 TAATATATTA
232780 TATATCATATTA
1 TA-AT-ATATTA
232792 -AA-A-ATTA
1 TAATATATTA
232799 TAATATATTA
1 TAATATATTA
232809 TAAT-TATT
1 TAATATATT
232817 TTATTATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
7 4 0.07
8 10 0.19
9 9 0.17
10 17 0.31
11 14 0.26
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (10 bp):
TAATATATTA
Found at i:233677 original size:17 final size:17
Alignment explanation
Indices: 233655--233690 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
233645 TTGATTTTAT
233655 AATTT-AAAAATTAAATA
1 AATTTAAAAAATT-AATA
233672 AATTTAAAAAATTAATA
1 AATTTAAAAAATTAATA
233689 AA
1 AA
233691 AATATAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAAAAATTAATA
Found at i:234353 original size:12 final size:13
Alignment explanation
Indices: 234326--234359 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
234316 TACTCACTTG
*
234326 ATTTAATATTTTA
1 ATTTAATATATTA
234339 ATTTAAT-TATTA
1 ATTTAATATATTA
234351 ATTTAATAT
1 ATTTAATAT
234360 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTAATATATTA
Found at i:234487 original size:18 final size:18
Alignment explanation
Indices: 234446--234487 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
234436 ATTTAAATTT
234446 TAATAAAATAATTAATAA
1 TAATAAAATAATTAATAA
234464 TCAATAAAA-AATTAATACA
1 T-AATAAAATAATTAATA-A
234483 TAATA
1 TAATA
234488 TAAGTGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
TAATAAAATAATTAATAA
Found at i:234713 original size:3 final size:3
Alignment explanation
Indices: 234705--234734 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
234695 TATTTAACCC
*
234705 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
234735 TTATTATATT
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:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:234739 original size:3 final size:3
Alignment explanation
Indices: 234733--234765 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
234723 ACAATAATAA
*
234733 TAT TAT TA- TAT TAT TAT TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
234766 GCTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:235195 original size:11 final size:11
Alignment explanation
Indices: 235179--235203 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
235169 CATGTGTCCG
235179 AAATAATTTAT
1 AAATAATTTAT
235190 AAATAATTTAT
1 AAATAATTTAT
235201 AAA
1 AAA
235204 ATTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATAATTTAT
Found at i:235953 original size:2 final size:2
Alignment explanation
Indices: 235946--235979 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
235936 ATGGCACTAT
235946 TC TC TC TC T- TGC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC
235980 ATTCGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 28 0.93
3 1 0.03
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:238237 original size:11 final size:11
Alignment explanation
Indices: 238217--238263 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
238207 TTAATTCAAA
*
238217 TTATTAAAATT
1 TTATTTAAATT
238228 TTATTTAAATT
1 TTATTTAAATT
*
238239 TAATTT-AATT
1 TTATTTAAATT
* *
238249 TAAATTAAATT
1 TTATTTAAATT
238260 TTAT
1 TTAT
238264 CTATACATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATTTAAATT
Found at i:238249 original size:16 final size:16
Alignment explanation
Indices: 238223--238260 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
238213 CAAATTATTA
*
238223 AAATTTTATTTAAATT
1 AAATTTAATTTAAATT
*
238239 TAATTTAATTTAAATT
1 AAATTTAATTTAAATT
238255 AAATTT
1 AAATTT
238261 TATCTATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATTTAATTTAAATT
Found at i:238438 original size:8 final size:8
Alignment explanation
Indices: 238427--238528 Score: 59
Period size: 8 Copynumber: 12.6 Consensus size: 8
238417 ATATATGTTT
238427 ATATATAA
1 ATATATAA
238435 ATATA-AA
1 ATATATAA
238442 AT-TATAA
1 ATATATAA
*
238449 ATAT-TTA
1 ATATATAA
*
238456 ATATTTAAA
1 ATATAT-AA
* *
238465 ATTTTTAA
1 ATATATAA
*
238473 ATGT-TAA
1 ATATATAA
*
238480 ATAAATAA
1 ATATATAA
*
238488 ATAAATAA
1 ATATATAA
*
238496 ATATAAAA
1 ATATATAA
238504 ATATAATAA
1 ATAT-ATAA
238513 ATTATTATTAA
1 A-TA-TA-TAA
238524 ATATA
1 ATATA
238529 ATGATCTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
6 2 0.03
7 19 0.25
8 33 0.43
9 12 0.16
10 5 0.07
11 5 0.07
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (8 bp):
ATATATAA
Found at i:238486 original size:4 final size:4
Alignment explanation
Indices: 238477--238514 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
238467 TTTTAAATGT
238477 TAAA TAAA TAAA TAAA TAAA TATAA -AAA TATAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TA-AA TAAA T
238515 TATTATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.06
4 23 0.74
5 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:240150 original size:13 final size:13
Alignment explanation
Indices: 240132--240170 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
240122 TATTTTTTTA
240132 AATATTTATATTT
1 AATATTTATATTT
240145 AATATTTATATTT
1 AATATTTATATTT
*
240158 GATA--TATATTT
1 AATATTTATATTT
240169 AA
1 AA
240171 ATATGAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 8 0.33
13 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:242014 original size:22 final size:21
Alignment explanation
Indices: 241989--242029 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
241979 ATATTAATAT
*
241989 AATAATATTTTAATATTTTTTG
1 AATAATAGTTTAAT-TTTTTTG
242011 AATAATAGTTTAATTTTTT
1 AATAATAGTTTAATTTTTT
242030 CAAATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
AATAATAGTTTAATTTTTTTG
Found at i:242318 original size:9 final size:9
Alignment explanation
Indices: 242288--242399 Score: 53
Period size: 8 Copynumber: 12.6 Consensus size: 9
242278 GTAACTCGTG
242288 TATA-AATT
1 TATATAATT
242296 TA-ATAATT
1 TATATAATT
242304 TA-ATAATT
1 TATATAATT
242312 TATATAATATT
1 TATAT-A-ATT
*
242323 TATATATTT
1 TATATAATT
*
242332 TATTATATTAT
1 TA-TATAAT-T
242343 TAT-TATATT
1 TATATA-ATT
*
242352 TATTATATTT
1 TA-TATAATT
*
242362 TATAT-TTT
1 TATATAATT
242370 TATA-AATT
1 TATATAATT
242378 T-TGAT-ATAT
1 TAT-ATAAT-T
242387 TA-ATAATT
1 TATATAATT
242395 TATAT
1 TATAT
242400 TATATAAATT
Statistics
Matches: 84, Mismatches: 4, Indels: 31
0.71 0.03 0.26
Matches are distributed among these distances:
7 2 0.02
8 34 0.40
9 20 0.24
10 15 0.18
11 13 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (9 bp):
TATATAATT
Found at i:242329 original size:8 final size:8
Alignment explanation
Indices: 242318--242430 Score: 59
Period size: 8 Copynumber: 13.0 Consensus size: 8
242308 AATTTATATA
242318 ATATTTAT
1 ATATTTAT
242326 ATATTTTATT
1 ATA-TTTA-T
242336 ATATTATTATT
1 ATA-T-TTA-T
242347 ATATTTATT
1 ATATTTA-T
242356 ATATTTTAT
1 ATA-TTTAT
*
242365 ATTTTTAT
1 ATATTTAT
*
242373 AAATTTTGAT
1 ATA-TTT-AT
*
242383 ATATTAAT
1 ATATTTAT
242391 A-ATTTAT
1 ATATTTAT
*
242398 AT-TATAT
1 ATATTTAT
* *
242405 AAATTTAAAA
1 ATATTT--AT
242415 ATATTTAT
1 ATATTTAT
242423 ATATTTAT
1 ATATTTAT
242431 TTTATTCGTA
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
7 11 0.13
8 23 0.28
9 20 0.24
10 21 0.25
11 8 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
ATATTTAT
Found at i:242333 original size:20 final size:20
Alignment explanation
Indices: 242296--242428 Score: 72
Period size: 20 Copynumber: 6.8 Consensus size: 20
242286 TGTATAAATT
*
242296 TAATAATTTA-ATAATTTATA
1 TAAT-ATTTATATATTTTATA
242316 TAATATTTATATATTTTATTA
1 TAATATTTATATATTTTA-TA
*
242337 TATTA-TTAT-TATATTTAT-
1 TAATATTTATATAT-TTTATA
242355 T-ATATTT-TATATTTT-TA
1 TAATATTTATATATTTTATA
*
242372 TAA-ATTT-TGATATATTA-A
1 TAATATTTAT-ATATTTTATA
*
242390 TAATTTATATTATATAAATTTA-A
1 TAA--TAT-TTATAT-ATTTTATA
*
242413 AAATATTTATATATTT
1 TAATATTTATATATTT
242429 ATTTTATTCG
Statistics
Matches: 90, Mismatches: 8, Indels: 31
0.70 0.06 0.24
Matches are distributed among these distances:
16 1 0.01
17 12 0.13
18 17 0.19
19 12 0.13
20 25 0.28
21 11 0.12
22 4 0.04
23 8 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TAATATTTATATATTTTATA
Found at i:242403 original size:18 final size:17
Alignment explanation
Indices: 242306--242404 Score: 77
Period size: 16 Copynumber: 5.9 Consensus size: 17
242296 TAATAATTTA
*
242306 ATAATTTATATAATATTT
1 ATAATTTATATTATA-TT
242324 ATATATTT-TATTATATT
1 ATA-ATTTATATTATATT
*
242341 ATTA-TTATATT-TATT
1 ATAATTTATATTATATT
*
242356 ATATTTTATATT-T-TT
1 ATAATTTATATTATATT
242371 ATAAATTT-TGA-TATATT
1 AT-AATTTAT-ATTATATT
242388 AATAATTTATATTATAT
1 -ATAATTTATATTATAT
242405 AAATTTAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
15 14 0.21
16 19 0.29
17 12 0.18
18 17 0.26
19 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (17 bp):
ATAATTTATATTATATT
Found at i:242419 original size:32 final size:31
Alignment explanation
Indices: 242352--242435 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 31
242342 TTATTATATT
* * ** *
242352 TATTATATTTTATATTTTTATAAATTTTGATA
1 TATTATAATTTATA-TTATATAAATTTAAAAA
242384 TATTAATAATTTATATTATATAAATTTAAAAA
1 TATT-ATAATTTATATTATATAAATTTAAAAA
*
242416 TATTTATATATTTATTTTAT
1 TA-TTATA-ATTTATATTAT
242436 TCGTATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
32 22 0.51
33 21 0.49
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
TATTATAATTTATATTATATAAATTTAAAAA
Found at i:242435 original size:38 final size:37
Alignment explanation
Indices: 242346--242436 Score: 89
Period size: 40 Copynumber: 2.4 Consensus size: 37
242336 ATATTATTAT
* ** *
242346 TATATTTA-TTATATTTTATATTTTTATAAATTTTGA
1 TATATTTATTTATATTATATAAATTTAAAAATTTTGA
242382 TATATTAATAATTTATATTATATAAATTTAAAAATATTT-A
1 TATATT--T-ATTTATATTATATAAATTTAAAAAT-TTTGA
242422 TATATTTATTT-TATT
1 TATATTTATTTATATT
242437 CGTATTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
36 10 0.22
37 4 0.09
38 2 0.04
39 1 0.02
40 26 0.57
41 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (37 bp):
TATATTTATTTATATTATATAAATTTAAAAATTTTGA
Found at i:242782 original size:2 final size:2
Alignment explanation
Indices: 242775--242810 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
242765 TGAACATCAA
242775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
242811 GTTTCTAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244500 original size:18 final size:18
Alignment explanation
Indices: 244466--244500 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
244456 ATTAATTAAG
244466 AAATGGAGAAAAGAAAAA
1 AAATGGAGAAAAGAAAAA
244484 AAAT-GAGAAAAGAAAAA
1 AAATGGAGAAAAGAAAAA
244501 TTATTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (18 bp):
AAATGGAGAAAAGAAAAA
Found at i:245225 original size:21 final size:22
Alignment explanation
Indices: 245201--245246 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
245191 TCTTTTAAAA
245201 ATATTAAAAAGTAT-TATTTTT
1 ATATTAAAAAGTATATATTTTT
* **
245222 ATATTAATATTTATATATTTTT
1 ATATTAAAAAGTATATATTTTT
245244 ATA
1 ATA
245247 ATTTAGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATTAAAAAGTATATATTTTT
Found at i:245476 original size:6 final size:7
Alignment explanation
Indices: 245429--245502 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
245419 ATTTTAAATT
245429 TTATATA
1 TTATATA
*
245436 TTCATATC
1 TT-ATATA
*
245444 TTATTTA
1 TTATATA
* *
245451 TATATTTT
1 T-TATATA
245459 TTATATA
1 TTATATA
245466 TTATA-A
1 TTATATA
245472 TTATAT-
1 TTATATA
*
245478 TTAAAATA
1 TT-ATATA
245486 TTATATA
1 TTATATA
*
245493 TTATAAA
1 TTATATA
245500 TTA
1 TTA
245503 CAAATTTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
6 8 0.15
7 31 0.58
8 14 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:247137 original size:22 final size:21
Alignment explanation
Indices: 247107--247148 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
247097 AATTTTATTT
247107 AAAATTTAAT-TATAAAATATA
1 AAAATTTAATGTA-AAAATATA
247128 AAAATATTAATGTAAAAATAT
1 AAAAT-TTAATGTAAAAATAT
247149 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATTTAATGTAAAAATATA
Found at i:247513 original size:2 final size:2
Alignment explanation
Indices: 247506--247538 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
247496 AACTAACTTT
247506 TA TA TA TA 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 TA TA TA TA T
247539 CCAATAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:252673 original size:37 final size:37
Alignment explanation
Indices: 252564--252695 Score: 135
Period size: 37 Copynumber: 3.6 Consensus size: 37
252554 CACTATTCTT
* * *
252564 AATTATTATTCTTACCGGTGGCAT-AGGTTGGAACAAA
1 AATTACTATTCTTATCGGTGGCATGA-GTTAGAACAAA
* * * *
252601 AATCACTATTATTA-CTAGTGGCATG-GTTTGAAACAAA
1 AATTACTATTCTTATC-GGTGGCATGAGTTAG-AACAAA
*
252638 AATTACTATTCTTATCGGTGGGATGAGTTAGAACAAA
1 AATTACTATTCTTATCGGTGGCATGAGTTAGAACAAA
*
252675 AACTACTATTCTTATCGGTGG
1 AATTACTATTCTTATCGGTGG
252696 TACGGATCTA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
36 5 0.06
37 69 0.87
38 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (37 bp):
AATTACTATTCTTATCGGTGGCATGAGTTAGAACAAA
Found at i:252711 original size:37 final size:37
Alignment explanation
Indices: 252632--252725 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 37
252622 CATGGTTTGA
* *
252632 AACAAAAATTACTATTCTTATCGGTGGGATGAGTTAG
1 AACAAAAACTACTATTCTTATCGGTGGGAGGAGTTAG
*
252669 AACAAAAACTACTATTCTTATCGGTGGTACGGA-TCTAG
1 AACAAAAACTACTATTCTTATCGGTGGGA-GGAGT-TAG
*
252707 -ACAAAAACTATTATTCTTA
1 AACAAAAACTACTATTCTTA
252726 ACTGGTAGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
37 46 0.90
38 5 0.10
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (37 bp):
AACAAAAACTACTATTCTTATCGGTGGGAGGAGTTAG
Found at i:253863 original size:10 final size:11
Alignment explanation
Indices: 253837--253865 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
253827 TTAATATATT
253837 TAAAAAATAAA
1 TAAAAAATAAA
253848 TAAAAAATAAA
1 TAAAAAATAAA
253859 TAAAAAA
1 TAAAAAA
253866 CTTGTCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:254087 original size:2 final size:2
Alignment explanation
Indices: 254080--254108 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
254070 AGTTAATTTT
254080 TA TA 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 TA TA T
254109 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:256172 original size:15 final size:15
Alignment explanation
Indices: 256144--256176 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
256134 ATGATATATT
256144 TAATAAATATAAAAA
1 TAATAAATATAAAAA
256159 TAATATAATA-AAAAA
1 TAATA-AATATAAAAA
256174 TAA
1 TAA
256177 CATGATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATAAATATAAAAA
Done.