Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold246
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: 1425817
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
File 2 of 8
Found at i:113551 original size:5 final size:5
Alignment explanation
Indices: 113534--113563 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
113524 ACACGCTATG
113534 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA
113564 GACAACGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:113729 original size:16 final size:17
Alignment explanation
Indices: 113715--113760 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 17
113705 GAATATATAT
113715 TATAAAATTTATATAAA
1 TATAAAATTTATATAAA
113732 TATAAAATATTTAAATATAAA
1 TAT-AAA-ATTT--ATATAAA
113753 TATAAAAT
1 TATAAAAT
113761 AATAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 6 0.24
20 3 0.12
21 10 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATAAAATTTATATAAA
Found at i:113748 original size:15 final size:15
Alignment explanation
Indices: 113728--113770 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
113718 AAAATTTATA
113728 TAAATATAAAATATT
1 TAAATATAAAATATT
113743 TAAATAT-AAATA-T
1 TAAATATAAAATATT
*
113756 AAAATAATAAAATAT
1 TAAAT-ATAAAATAT
113771 ACTATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 5 0.21
14 7 0.29
15 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATATAAAATATT
Found at i:113751 original size:21 final size:21
Alignment explanation
Indices: 113725--113771 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
113715 TATAAAATTT
* *
113725 ATATAAATATAAAATATTTAA
1 ATATAAATATAAAATAATAAA
113746 ATATAAATATAAAATAATAAA
1 ATATAAATATAAAATAATAAA
113767 ATATA
1 ATATA
113772 CTATTATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATAAATATAAAATAATAAA
Found at i:113765 original size:8 final size:7
Alignment explanation
Indices: 113724--113771 Score: 53
Period size: 8 Copynumber: 6.6 Consensus size: 7
113714 TTATAAAATT
113724 TATATAAA
1 TATA-AAA
113732 TATAAAA
1 TATAAAA
*
113739 TATTTAAA
1 TA-TAAAA
113747 TAT-AAA
1 TATAAAA
113753 TATAAAA
1 TATAAAA
113760 TAATAAAA
1 T-ATAAAA
113768 TATA
1 TATA
113772 CTATTATAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
6 6 0.17
7 13 0.36
8 17 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
TATAAAA
Found at i:113771 original size:15 final size:14
Alignment explanation
Indices: 113724--113771 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
113714 TTATAAAATT
113724 TATATAAATATAAAA
1 TATA-AAATATAAAA
*
113739 TATTTAAATAT-AAA
1 TA-TAAAATATAAAA
113753 TATAAAATAATAAAA
1 TATAAAAT-ATAAAA
113768 TATA
1 TATA
113772 CTATTATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 15 0.54
16 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATAAAATATAAAA
Found at i:113952 original size:26 final size:25
Alignment explanation
Indices: 113906--114022 Score: 77
Period size: 25 Copynumber: 4.7 Consensus size: 25
113896 TCCGGTCAGT
*
113906 TTAAAAATATTTTTTTAAAA-TAATA
1 TTAAAAATATTTTATTAAAATTAA-A
*
113931 TTAAAAATATTTATAATTAAATTTAAA
1 TTAAAAATATTT-T-ATTAAAATTAAA
*
113958 -TAAAAATATTTTTATT-ATA-TAAA
1 TTAAAAATA-TTTTATTAAAATTAAA
* * *
113981 -T-AATA-ATTTTAATAAACTTAAA
1 TTAAAAATATTTTATTAAAATTAAA
114003 TTAAAAAATATTTTACTTAA
1 TT-AAAAATATTTTA-TTAA
114023 GTCTAATTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
20 6 0.08
21 2 0.03
22 7 0.10
23 6 0.08
24 1 0.01
25 18 0.25
26 16 0.23
27 12 0.17
28 3 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAAAAATATTTTATTAAAATTAAA
Found at i:113974 original size:25 final size:26
Alignment explanation
Indices: 113906--113974 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
113896 TCCGGTCAGT
113906 TTAAAAATATTTTT-TTAAAATAATA
1 TTAAAAATATTTTTATTAAAATAATA
* *
113931 TTAAAAATATTTATAATTAAATTTAA-A
1 TTAAAAATATTT-TTATTAAA-ATAATA
113958 -TAAAAATATTTTTATTA
1 TTAAAAATATTTTTATTA
113975 TATAAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 17 0.45
26 12 0.32
27 6 0.16
28 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAAAAATATTTTTATTAAAATAATA
Found at i:114181 original size:14 final size:14
Alignment explanation
Indices: 114162--114234 Score: 60
Period size: 14 Copynumber: 5.0 Consensus size: 14
114152 TATATAAATA
114162 AATTTTAATATATT
1 AATTTTAATATATT
*
114176 AATTTTTATATTATATA
1 AA-TTTTA-A-TATATT
114193 AATTTTAATATATT
1 AATTTTAATATATT
* *
114207 TA-TATAATTATATT
1 AATTTTAA-TATATT
114221 ATATTTTAAT-TATT
1 A-ATTTTAATATATT
114235 TTTGATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
13 4 0.09
14 18 0.38
15 8 0.17
16 10 0.21
17 7 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTTTAATATATT
Found at i:114194 original size:35 final size:35
Alignment explanation
Indices: 114088--114195 Score: 107
Period size: 37 Copynumber: 3.0 Consensus size: 35
114078 AACAACTAAT
*
114088 TAAA-TTTAATA-ATTAATATATTTATATCATATAAA
1 TAAATTTTAATATATTAAT-T-TTTATATTATATAAA
* *
114123 TATATTTT-ATCATAATT-ATTTTAAAATATTATATAAA
1 TAAATTTTAAT-AT-ATTAATTTT--TATATTATATAAA
114160 TAAATTTTAATATATTAATTTTTATATTATATAAA
1 TAAATTTTAATATATTAATTTTTATATTATATAAA
114195 T
1 T
114196 TTTAATATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
35 20 0.33
36 8 0.13
37 27 0.45
38 5 0.08
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (35 bp):
TAAATTTTAATATATTAATTTTTATATTATATAAA
Found at i:114197 original size:31 final size:33
Alignment explanation
Indices: 114150--114224 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 33
114140 ATTTTAAAAT
* *
114150 ATTATA-TAAATAAATTTTAATATA-TTA-ATT
1 ATTATATTATATAAATTTTAATATATTTATATA
*
114180 TTTATATTATATAAATTTTAATATATTTATATA
1 ATTATATTATATAAATTTTAATATATTTATATA
114213 ATTATATTATAT
1 ATTATATTATAT
114225 TTTAATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 5 0.13
31 17 0.45
32 3 0.08
33 13 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATTATATTATATAAATTTTAATATATTTATATA
Found at i:114215 original size:19 final size:19
Alignment explanation
Indices: 114100--114226 Score: 61
Period size: 19 Copynumber: 6.6 Consensus size: 19
114090 AATTTAATAA
* *
114100 TTAATATATTTATATCATA
1 TTAATATATTTATATAATT
*
114119 TAAATATATTTTATCATAATTATT
1 TTAATATA-TTTAT-AT-A--ATT
*
114143 TTAAAATATTATATAAATAAATT
1 TTAATATATT-TAT--AT-AATT
114166 TTAATATA-TTA-AT--TT
1 TTAATATATTTATATAATT
*
114181 TT-ATAT-TATATA-AATT
1 TTAATATATTTATATAATT
114197 TTAATATATTTATATAATT
1 TTAATATATTTATATAATT
* *
114216 ATATTATATTT
1 TTAATATATTT
114227 TAATTATTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
14 6 0.07
15 5 0.06
16 4 0.05
17 4 0.05
18 7 0.08
19 20 0.24
20 5 0.06
21 4 0.05
22 1 0.01
23 12 0.14
24 11 0.13
25 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATATATTTATATAATT
Found at i:114230 original size:16 final size:16
Alignment explanation
Indices: 114163--114233 Score: 64
Period size: 16 Copynumber: 4.7 Consensus size: 16
114153 ATATAAATAA
114163 ATTTTAA-TATATTA-
1 ATTTTAATTATATTAT
*
114177 ATTTTTATATTATA-TAA
1 A-TTTTA-ATTATATTAT
114194 ATTTTAA-TATATT-T
1 ATTTTAATTATATTAT
*
114208 A-TATAATTATATTAT
1 ATTTTAATTATATTAT
114223 ATTTTAATTAT
1 ATTTTAATTAT
114234 TTTTGATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
13 4 0.09
14 12 0.26
15 9 0.20
16 16 0.35
17 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTAATTATATTAT
Found at i:114248 original size:28 final size:26
Alignment explanation
Indices: 114177--114250 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 26
114167 TAATATATTA
*
114177 ATTTTTATATTATATAAATTTTAATAT
1 ATTTATATATTAT-TAAATTTTAATAT
*
114204 ATTTATATAATTATATTATATTTTAATTAT
1 ATTTATAT-A-T-TATTAAATTTTAA-TAT
*
114234 TTTTGATATATTATTAA
1 ATTT-ATATATTATTAA
114251 TCTTCAATCC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
27 7 0.18
28 6 0.16
29 11 0.29
30 10 0.26
31 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
ATTTATATATTATTAAATTTTAATAT
Found at i:114800 original size:30 final size:30
Alignment explanation
Indices: 114738--114802 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
114728 ATAAAGTTTA
* * *
114738 ATTTAATAAATTTATATAATTATTTTTTAT
1 ATTTAATAAATTTAAATAATTAATTTTAAT
*
114768 ATTTAATAAATATTAAAT-TTTAATTTTAAT
1 ATTTAATAAAT-TTAAATAATTAATTTTAAT
114798 ATTTA
1 ATTTA
114803 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTTAATAAATTTAAATAATTAATTTTAAT
Found at i:114950 original size:5 final size:5
Alignment explanation
Indices: 114940--114969 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
114930 TGGAACGAGG
*
114940 GAAAA GAAAA GAAAA GAAAA GAAAG GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
114970 CAACCCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:116131 original size:2 final size:2
Alignment explanation
Indices: 116124--116175 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
116114 TGGGTGTGAA
* *
116124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
116166 AT AT TT AT AT
1 AT AT AT AT AT
116176 TTGATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:116311 original size:2 final size:2
Alignment explanation
Indices: 116304--116334 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
116294 AATATGGCCC
116304 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 T
116335 CTTGCAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117383 original size:14 final size:14
Alignment explanation
Indices: 117364--117396 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
117354 TTTAATAAAT
117364 ATAAAAATAATATA
1 ATAAAAATAATATA
*
117378 ATAAAAATGATATA
1 ATAAAAATAATATA
117392 ATAAA
1 ATAAA
117397 TTTAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
ATAAAAATAATATA
Found at i:123425 original size:16 final size:16
Alignment explanation
Indices: 123404--123434 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
123394 ATCCAACCTG
123404 AATTAACTTGATTCGA
1 AATTAACTTGATTCGA
123420 AATTAACTTGATTCG
1 AATTAACTTGATTCG
123435 TCTAATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
AATTAACTTGATTCGA
Found at i:128102 original size:2 final size:2
Alignment explanation
Indices: 128095--128121 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
128085 GTCAACGAAA
128095 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
128122 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128126 original size:2 final size:2
Alignment explanation
Indices: 128121--128146 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128111 ATATATATAT
128121 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
128147 TACTAAATTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:128424 original size:22 final size:23
Alignment explanation
Indices: 128389--128432 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
128379 AACTATGAAC
*
128389 AAAATTATTTATT-ATTTATAAAT
1 AAAATTATTAATTAATTT-TAAAT
128412 AAAA-TATTAATTAATTTTAAA
1 AAAATTATTAATTAATTTTAAA
128433 AAGTATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATTATTAATTAATTTTAAAT
Found at i:130743 original size:15 final size:15
Alignment explanation
Indices: 130723--130752 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
130713 TGTTTTAGTA
130723 ATCAAATGTTAGCAC
1 ATCAAATGTTAGCAC
130738 ATCAAATGTTAGCAC
1 ATCAAATGTTAGCAC
130753 TTAAACAATA
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:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
ATCAAATGTTAGCAC
Found at i:132596 original size:11 final size:11
Alignment explanation
Indices: 132580--132738 Score: 93
Period size: 11 Copynumber: 15.0 Consensus size: 11
132570 TAATTATGTT
132580 TATTATATTTA
1 TATTATATTTA
132591 TATTATATTTA
1 TATTATATTTA
* *
132602 TATCATAATTA
1 TATTATATTTA
*
132613 TATT-TA-ATA
1 TATTATATTTA
*
132622 AATTAAATATTTA
1 TATT--ATATTTA
*
132635 TA-TAAATTT-
1 TATTATATTTA
** *
132644 TAAAATATTAA
1 TATTATATTTA
132655 TAATT-TATTTA
1 T-ATTATATTTA
*
132666 TA-TAAATTT-
1 TATTATATTTA
*
132675 TAATATATTTA
1 TATTATATTTA
*
132686 TTTTATA-TTA
1 TATTATATTTA
*
132696 TATTTTA-TTA
1 TATTATATTTA
* *
132706 TATTTTATTTT
1 TATTATATTTA
132717 TATTATATTTA
1 TATTATATTTA
*
132728 TATTATGTTTA
1 TATTATATTTA
132739 AAATTAATAA
Statistics
Matches: 113, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
9 10 0.09
10 40 0.35
11 56 0.50
12 4 0.04
13 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (11 bp):
TATTATATTTA
Found at i:132601 original size:20 final size:20
Alignment explanation
Indices: 132572--132728 Score: 70
Period size: 20 Copynumber: 7.5 Consensus size: 20
132562 CAGTCGTGTA
*
132572 ATTATGTTTATTATATTTAT
1 ATTATATTTATTATATTTAT
*
132592 ATTATATTTATATCATAATTAT
1 ATTATATTTAT-T-ATATTTAT
* *
132614 ATTTAATAAATTA-AATATTTAT
1 A-TT-AT-ATTTATTATATTTAT
* ** *
132636 A-TAAATTTTAAAATATTAAT
1 ATTATA-TTTATTATATTTAT
*
132656 AATT-TATTTATATAAATTT-T
1 -ATTATATTTAT-TATATTTAT
* *
132676 AATATATTTATTTTATATTAT
1 ATTATATTTATTATAT-TTAT
* * *
132697 ATTTTATTATATTTTATTTTT
1 ATTATATT-TATTATATTTAT
132718 ATTATATTTAT
1 ATTATATTTAT
132729 ATTATGTTTA
Statistics
Matches: 103, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
18 1 0.01
19 9 0.09
20 36 0.35
21 24 0.23
22 25 0.24
23 2 0.02
24 2 0.02
25 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (20 bp):
ATTATATTTATTATATTTAT
Found at i:132604 original size:17 final size:17
Alignment explanation
Indices: 132582--132731 Score: 61
Period size: 17 Copynumber: 9.1 Consensus size: 17
132572 ATTATGTTTA
132582 TTATATT-TATATTATAT
1 TTATATTATAT-TTATAT
* *
132599 TTATATCATAATTATAT
1 TTATATTATATTTATAT
* *
132616 TTA-A-TAAATTAAATAT
1 TTATATTATATT-TATAT
*
132632 TTATA-TAAATTT-TA-
1 TTATATTATATTTATAT
** *
132646 AAATATTAATAATT-TAT
1 TTATATT-ATATTTATAT
*
132663 TTATA-TAAATTTTAATAT
1 TTATATTATA-TTT-ATAT
*
132681 ATT-TATTTTATATTATAT
1 -TTATATTATAT-TTATAT
132699 TT-TATTATATTT-TAT
1 TTATATTATATTTATAT
*
132714 TTTTATTATATTTATAT
1 TTATATTATATTTATAT
132731 T
1 T
132732 ATGTTTAAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
14 3 0.03
15 13 0.13
16 29 0.29
17 38 0.38
18 12 0.12
19 6 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTATATTTATAT
Found at i:132645 original size:27 final size:31
Alignment explanation
Indices: 132615--132683 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
132605 CATAATTATA
132615 TTTAATAA-ATT-A-AA-TATTTATATAAAT
1 TTTAATAATATTAATAATTATTTATATAAAT
132642 TTTAA-AATATTAATAATTTATTTATATAAAT
1 TTTAATAATATTAATAA-TTATTTATATAAAT
132673 TTTAAT-ATATT
1 TTTAATAATATT
132684 TATTTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
26 2 0.06
27 8 0.22
28 1 0.03
29 2 0.06
31 23 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATAATATTAATAATTATTTATATAAAT
Found at i:132672 original size:23 final size:25
Alignment explanation
Indices: 132646--132716 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
132636 ATAAATTTTA
132646 AAATATTAATA-ATTTA-TTTATAT
1 AAATATTAATATATTTATTTTATAT
*
132669 AAATTTTAATATATTTATTTTATATT
1 AAATATTAATATATTTATTTTATA-T
* * *
132695 ATATTTTATTATATTTTATTTT
1 AAATATTAATATA-TTTATTTT
132717 TATTATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 10 0.24
24 5 0.12
25 6 0.15
26 12 0.29
27 8 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
AAATATTAATATATTTATTTTATAT
Found at i:132699 original size:16 final size:15
Alignment explanation
Indices: 132678--132731 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
132668 TAAATTTTAA
132678 TATATTTATTTTATAT
1 TATATTT-TTTTATAT
*
132694 TATATTTTATTATAT
1 TATATTTTTTTATAT
*
132709 TTTATTTTTATTATATT
1 TATATTTTT-TTATA-T
132726 TATATT
1 TATATT
132732 ATGTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 14 0.44
16 12 0.38
17 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATATTTTTTTATAT
Found at i:133666 original size:13 final size:16
Alignment explanation
Indices: 133648--133683 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 16
133638 TTTATTTTTA
133648 AATTAAATT-A-A-TT
1 AATTAAATTGATACTT
133661 AATTAAATTGATACTT
1 AATTAAATTGATACTT
133677 AATTAAA
1 AATTAAA
133684 ATATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 1 0.05
15 1 0.05
16 9 0.45
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTAAATTGATACTT
Found at i:136395 original size:11 final size:11
Alignment explanation
Indices: 136376--136416 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
136366 ATAATCATTT
*
136376 ATATATATAAA
1 ATATTTATAAA
136387 ATATTTATAAA
1 ATATTTATAAA
*
136398 ATATTTA-AAT
1 ATATTTATAAA
136408 ATATTTATA
1 ATATTTATA
136417 TCGAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTTATAAA
Found at i:136413 original size:21 final size:20
Alignment explanation
Indices: 136378--136416 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
136368 AATCATTTAT
136378 ATATATAAAATATTTATAAA
1 ATATATAAAATATTTATAAA
*
136398 ATATTTAAATATATTTATA
1 ATATATAAA-ATATTTATA
136417 TCGAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATAAAATATTTATAAA
Found at i:138348 original size:21 final size:20
Alignment explanation
Indices: 138309--138354 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
138299 TTAATTATTT
* *
138309 ATTTAAATAATTAAATTAAC
1 ATTTAAATAATAAAATTAAA
*
138329 ATTTTAATAATAAAATTTAAA
1 ATTTAAATAATAAAA-TTAAA
138350 ATTTA
1 ATTTA
138355 TTACCCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTAAATAATAAAATTAAA
Found at i:138742 original size:5 final size:5
Alignment explanation
Indices: 138732--138767 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
138722 CGAATTATAA
*
138732 AATTT AATTT AATTTT AATTA AATTT AATTT AATTT
1 AATTT AATTT AA-TTT AATTT AATTT AATTT AATTT
138768 TGTATTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:138750 original size:11 final size:11
Alignment explanation
Indices: 138734--138768 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
138724 AATTATAAAA
138734 TTTAATTTAAT
1 TTTAATTTAAT
*
138745 TTTAA-TTAAA
1 TTTAATTTAAT
138755 TTTAATTTAAT
1 TTTAATTTAAT
138766 TTT
1 TTT
138769 GTATTCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:139777 original size:25 final size:27
Alignment explanation
Indices: 139738--139787 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
139728 CCTATTTAAA
*
139738 TTAAATTAGTTAAAATTTAATAAATTT
1 TTAAATTAGTTAAAATTTAAAAAATTT
139765 TTAAA-TA-TTAAAATTTAAAAAAT
1 TTAAATTAGTTAAAATTTAAAAAAT
139788 ACTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 2 0.09
27 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TTAAATTAGTTAAAATTTAAAAAATTT
Found at i:139793 original size:25 final size:27
Alignment explanation
Indices: 139738--139793 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
139728 CCTATTTAAA
* **
139738 TTAAATTAGTTAAAATTTAATAAATTT
1 TTAAATTAGTTAAAATTTAAAAAATAC
139765 TTAAA-TA-TTAAAATTTAAAAAATAC
1 TTAAATTAGTTAAAATTTAAAAAATAC
139790 TTAA
1 TTAA
139794 TTTTTTTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 19 0.73
26 2 0.08
27 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
TTAAATTAGTTAAAATTTAAAAAATAC
Found at i:144519 original size:18 final size:18
Alignment explanation
Indices: 144496--144534 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
144486 TTCATCAATT
144496 TTAAATAAAAATTTT-ATA
1 TTAAAT-AAAATTTTGATA
*
144514 TTAAATATAATTTTGATA
1 TTAAATAAAATTTTGATA
144532 TTA
1 TTA
144535 TTTAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TTAAATAAAATTTTGATA
Found at i:145394 original size:2 final size:2
Alignment explanation
Indices: 145387--145417 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
145377 ATTTTAATGC
145387 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
145418 TTGAATTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:147621 original size:25 final size:22
Alignment explanation
Indices: 147583--147652 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 22
147573 ATTATATAAA
*
147583 TTTTAATATATATAATTTGTATCAAT
1 TTTTTATAT-TATAATTT-TAT--AT
147609 TTTTTATATTAT-ATTTTATAT
1 TTTTTATATTATAATTTTATAT
147630 TTATTTAATATTAT-A-TTTATAT
1 TT-TTT-ATATTATAATTTTATAT
147652 T
1 T
147653 ATATAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 4 0.10
22 11 0.27
23 11 0.27
24 4 0.10
25 3 0.07
26 8 0.20
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (22 bp):
TTTTTATATTATAATTTTATAT
Found at i:147649 original size:29 final size:28
Alignment explanation
Indices: 147612--147671 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
147602 TATCAATTTT
* *
147612 TTATATTATATTTTAT-ATTTATTTAATA
1 TTATATTATATTATATAATTT-TATAATA
147640 TTATATTTATATTATATAATTTTATAATA
1 TTATA-TTATATTATATAATTTTATAATA
147669 TTA
1 TTA
147672 AAATTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.18
29 19 0.68
30 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTATATTATATTATATAATTTTATAATA
Found at i:147656 original size:16 final size:16
Alignment explanation
Indices: 147534--147665 Score: 66
Period size: 16 Copynumber: 8.2 Consensus size: 16
147524 AATATAGATA
147534 TATATTTATATTAT-TT
1 TATA-TTATATTATATT
*
147550 TTTATTATAATTATATT
1 TATATTAT-ATTATATT
*
147567 TAAAATATTATA-TAAATT
1 T---ATATTATATTATATT
*
147585 T-TAATATA-TATAATT
1 TATATTATATTAT-ATT
* *
147600 TGTATCA-ATT-T-TT
1 TATATTATATTATATT
147613 TATATTATATTTTATATT
1 TATATTATA--TTATATT
147631 TAT-TTAATATTATATT
1 TATATT-ATATTATATT
*
147647 TATATTATATAAT-TT
1 TATATTATATTATATT
147662 TATA
1 TATA
147666 ATATTAAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
13 7 0.08
14 9 0.10
15 16 0.18
16 30 0.33
17 8 0.09
18 14 0.15
19 1 0.01
20 6 0.07
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (16 bp):
TATATTATATTATATT
Found at i:147678 original size:29 final size:29
Alignment explanation
Indices: 147616--147678 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
147606 AATTTTTTAT
* * *
147616 ATTATATTTTATATTTATTTAATATTATA
1 ATTATATTATATATTTATATAATATTAAA
*
147645 TTTATATTATATAATTT-TATAATATTAAA
1 ATTATATTATAT-ATTTATATAATATTAAA
147674 ATTAT
1 ATTAT
147679 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTATATTATATATTTATATAATATTAAA
Found at i:147854 original size:26 final size:28
Alignment explanation
Indices: 147790--147855 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
147780 GCAAATCATT
*
147790 ATTTAAATAATAAAAAATATTTAATTATAA
1 ATTTTAAT-ATAAAAAATATTT-ATTATAA
* *
147820 ATATTAATATAAAATATATTT-TTA-AA
1 ATTTTAATATAAAAAATATTTATTATAA
147846 ATTTTAATAT
1 ATTTTAATAT
147856 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 11 0.34
27 3 0.09
29 12 0.38
30 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTTTAATATAAAAAATATTTATTATAA
Found at i:147881 original size:28 final size:29
Alignment explanation
Indices: 147843--147902 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
147833 ATATATTTTT
147843 AAAATTTTAATATT-ATTTAAA-ATAATAA
1 AAAATTTTAAT-TTAATTTAAATATAATAA
*
147871 AAAATTTTAATTTAATTTAAATTTAATAA
1 AAAATTTTAATTTAATTTAAATATAATAA
147900 AAA
1 AAA
147903 TAAAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 2 0.07
28 18 0.62
29 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AAAATTTTAATTTAATTTAAATATAATAA
Found at i:148481 original size:10 final size:10
Alignment explanation
Indices: 148453--148482 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
148443 TTATTTCTCC
*
148453 CTCTCTCTCT
1 CTCTCTCTTT
148463 CTCTCTCTTT
1 CTCTCTCTTT
148473 CTCTCTCTTT
1 CTCTCTCTTT
148483 GTGTGTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (10 bp):
CTCTCTCTTT
Found at i:150249 original size:27 final size:27
Alignment explanation
Indices: 150218--150270 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
150208 GTATCCTCCA
*
150218 CAGAATCTCCATTGTCTAGTTCCACTG
1 CAGAACCTCCATTGTCTAGTTCCACTG
* *
150245 CAGAACCTGCATTGTCTGGTTCCACT
1 CAGAACCTCCATTGTCTAGTTCCACT
150271 AGCTCTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (27 bp):
CAGAACCTCCATTGTCTAGTTCCACTG
Found at i:153288 original size:2 final size:2
Alignment explanation
Indices: 153281--153312 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
153271 TTCTTCTTCT
153281 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
153313 CCCTGAACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:155610 original size:58 final size:58
Alignment explanation
Indices: 155542--155655 Score: 219
Period size: 58 Copynumber: 2.0 Consensus size: 58
155532 AGTTAAACCC
*
155542 AAACAAAAGCAAACATTCATTTCCAGAAATGAATACTTCGCTCCTAGTAGTTTGGGTT
1 AAACAAAAGCAAACATTCATTTCCAGAAATGAATACTTCACTCCTAGTAGTTTGGGTT
155600 AAACAAAAGCAAACATTCATTTCCAGAAATGAATACTTCACTCCTAGTAGTTTGGG
1 AAACAAAAGCAAACATTCATTTCCAGAAATGAATACTTCACTCCTAGTAGTTTGGG
155656 CTAGGAGTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (58 bp):
AAACAAAAGCAAACATTCATTTCCAGAAATGAATACTTCACTCCTAGTAGTTTGGGTT
Found at i:157032 original size:26 final size:27
Alignment explanation
Indices: 156993--157057 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 27
156983 GCGCACGTAC
156993 TTTTATATAATAATATATAA-AAA-TAA
1 TTTTATATAATAATATA-AATAAATTAA
*
157019 TTTTATATATTAATATAAATTAAATTAA
1 TTTTATATAATAATATAAA-TAAATTAA
157047 TTTTATATAAT
1 TTTTATATAAT
157058 TTTATATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 2 0.06
26 16 0.47
27 3 0.09
28 13 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTATATAATAATATAAATAAATTAA
Found at i:157073 original size:16 final size:16
Alignment explanation
Indices: 157048--157093 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
157038 TTAAATTAAT
*
157048 TTTATATAATTTTATA
1 TTTATTTAATTTTATA
*
157064 TTTATTTAATTATAGTA
1 TTTATTTAATTTTA-TA
157081 -TT-TTTAATTTTAT
1 TTTATTTAATTTTAT
157094 TATATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 9 0.35
16 14 0.54
17 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTATTTAATTTTATA
Found at i:157124 original size:28 final size:28
Alignment explanation
Indices: 157093--157167 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
157083 TTTAATTTTA
*
157093 TTATATAAAT-TAAAAATATTTAAATTAT
1 TTAT-TAAATATAAAAAAATTTAAATTAT
* *
157121 TTATTTAATATAAAAAAATTTTAATTAT
1 TTATTAAATATAAAAAAATTTAAATTAT
* * * *
157149 TAAATATATATGAAAAAAT
1 TTATTAAATATAAAAAAAT
157168 ATTATATTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 4 0.11
28 34 0.89
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
TTATTAAATATAAAAAAATTTAAATTAT
Found at i:158091 original size:16 final size:16
Alignment explanation
Indices: 158072--158105 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
158062 GTTCTGTTGA
*
158072 AAGACAGAGAGCATGG
1 AAGACAGAAAGCATGG
*
158088 AAGAGAGAAAGCATGG
1 AAGACAGAAAGCATGG
158104 AA
1 AA
158106 TAAGCATGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.09, G:0.35, T:0.06
Consensus pattern (16 bp):
AAGACAGAAAGCATGG
Found at i:158251 original size:2 final size:2
Alignment explanation
Indices: 158244--158279 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
158234 ACAAAACAAA
158244 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
158280 TTGTCAGCAT
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:158478 original size:29 final size:30
Alignment explanation
Indices: 158415--158479 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
158405 TTTATATAAA
* *
158415 AAATTTATAAATTTTAATTTTAATTTAATT
1 AAATTTATAAATTATAATTATAATTTAATT
*
158445 -CATTTATATAATTATAATTAT-ATTT-ATT
1 AAATTTATA-AATTATAATTATAATTTAATT
158473 AAATTTA
1 AAATTTA
158480 AATGTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
28 3 0.10
29 16 0.55
30 10 0.34
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
AAATTTATAAATTATAATTATAATTTAATT
Found at i:158801 original size:21 final size:20
Alignment explanation
Indices: 158777--158824 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
158767 TAATAATCAT
*
158777 TTATAAATATATAAACTAAAA
1 TTATAAATATA-AAAATAAAA
*
158798 TTATACATATAAAAATAAAA
1 TTATAAATATAAAAATAAAA
158818 TT-TAAAT
1 TTATAAAT
158825 TTATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 10 0.42
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TTATAAATATAAAAATAAAA
Found at i:162858 original size:14 final size:14
Alignment explanation
Indices: 162835--162888 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
162825 AGAGATAAGA
*
162835 TAAATATTAAATTT
1 TAAATTTTAAATTT
162849 TAAATTTTAAATTT
1 TAAATTTTAAATTT
*
162863 TAAATTTATTAAATAT
1 TAAA-TT-TTAAATTT
162879 T-AATTTTAAA
1 TAAATTTTAAA
162889 AAAATAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
13 5 0.14
14 19 0.53
15 4 0.11
16 8 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATTTTAAATTT
Found at i:168045 original size:19 final size:20
Alignment explanation
Indices: 168010--168050 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
168000 TTTAAAATAT
168010 TTTTATATTAAAATTTAAAA
1 TTTTATATTAAAATTTAAAA
*
168030 TTTTATA-TAAATTTTAAAA
1 TTTTATATTAAAATTTAAAA
168049 TT
1 TT
168051 AATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTATATTAAAATTTAAAA
Found at i:168091 original size:16 final size:16
Alignment explanation
Indices: 168063--168105 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
168053 TTTTTATTTT
*
168063 TATTTTAATTATATTA
1 TATTTTAATTATATAA
168079 T-TTTTATATTATATAA
1 TATTTTA-ATTATATAA
168095 TATTTTAATTA
1 TATTTTAATTA
168106 ATTTTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 14 0.58
17 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTAATTATATAA
Found at i:168109 original size:10 final size:10
Alignment explanation
Indices: 168071--168120 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
168061 TTTATTTTAA
168071 TTATATTATT
1 TTATATTATT
168081 TT-TA-TATT
1 TTATATTATT
* *
168089 ATATAATATT
1 TTATATTATT
168099 TTA-ATTAATT
1 TTATATT-ATT
168109 TTATATTATT
1 TTATATTATT
168119 TT
1 TT
168121 CATCATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.15
9 6 0.18
10 19 0.58
11 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATATTATT
Found at i:169000 original size:7 final size:7
Alignment explanation
Indices: 168990--169038 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
168980 TTTTTTAAGA
168990 TAAAATT
1 TAAAATT
168997 TAAAATT
1 TAAAATT
169004 TAAAATT
1 TAAAATT
*
169011 TATAAATGA
1 TA-AAAT-T
*
169020 AAAAATT
1 TAAAATT
*
169027 TAATATT
1 TAAAATT
169034 TAAAA
1 TAAAA
169039 AATTTTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 25 0.74
8 8 0.24
9 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (7 bp):
TAAAATT
Found at i:172229 original size:89 final size:85
Alignment explanation
Indices: 172012--172243 Score: 267
Period size: 81 Copynumber: 2.7 Consensus size: 85
172002 AGGTTTAATC
* * * *
172012 AAATGACTAGAGTCGTGTCACTAAAGAACATGCAAAATTAGGAGTAATTTACATGAGAATTGGCT
1 AAATGACTA-AGTCATGTCACTGAAGAACATGCAAAATTAGGAGTAATTTACATGAGAATTGACC
* * *
172077 ATGTATAAGTATATATATGTT
65 ATGTACAAGTATAAACATGTT
* *
172098 AAATGACTAATGTCATGTCACTGAAG-A-A---AAAATTAGGCGTAATTTACATGACAATTGACC
1 AAATGACTAA-GTCATGTCACTGAAGAACATGCAAAATTAGGAGTAATTTACATGAGAATTGACC
*
172158 ATGTACCAGTGTATACAACATGTT
65 ATGTA-CA-AGTATA-AACATGTT
* *
172182 AAATAACTATAGTCATGTCACTGAAGAACATGCAAAATTAGGAGTAATTTAGATGAGAATTG
1 AAATGACTA-AGTCATGTCACTGAAGAACATGCAAAATTAGGAGTAATTTACATGAGAATTG
172244 GGCACGCATA
Statistics
Matches: 122, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
81 33 0.27
82 1 0.01
83 5 0.04
84 30 0.25
85 4 0.03
86 23 0.19
89 26 0.21
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (85 bp):
AAATGACTAAGTCATGTCACTGAAGAACATGCAAAATTAGGAGTAATTTACATGAGAATTGACCA
TGTACAAGTATAAACATGTT
Found at i:172763 original size:21 final size:21
Alignment explanation
Indices: 172713--172765 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
172703 ACATTGTGAC
*
172713 AAAGAAA-AATAATCCAACAA
1 AAAGAAATAATAAGCCAACAA
172733 ATAAGCAAATAATGAAGCCAA-AA
1 A-AAG-AAATAAT-AAGCCAACAA
172756 AAAGAAATAA
1 AAAGAAATAA
172766 ATAAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 9 0.32
22 6 0.21
23 6 0.21
24 6 0.21
ACGTcount: A:0.68, C:0.11, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAGAAATAATAAGCCAACAA
Found at i:179089 original size:15 final size:15
Alignment explanation
Indices: 179069--179102 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
179059 TCAACTCACA
*
179069 TTTTATAATTTTTAT
1 TTTTATAATTTTAAT
*
179084 TTTTATTATTTTAAT
1 TTTTATAATTTTAAT
179099 TTTT
1 TTTT
179103 TTTAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATAATTTTAAT
Found at i:179870 original size:31 final size:31
Alignment explanation
Indices: 179835--179925 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
179825 TTAATATATT
*
179835 AATAATTATATAATTTTATTAATTTTTAA-AA
1 AATAA-TATATAAATTTATTAATTTTTAATAA
*
179866 AATAACTATATATACTTT-TT-A-TTTTAATAA
1 AATAA-TATATA-AATTTATTAATTTTTAATAA
*
179896 TATAATATATAAATTTA-TATATTTTTAATA
1 AATAATATATAAATTTATTA-ATTTTTAATA
179926 CATCAAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
28 5 0.10
29 12 0.24
30 8 0.16
31 21 0.42
32 4 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
AATAATATATAAATTTATTAATTTTTAATAA
Found at i:180146 original size:16 final size:16
Alignment explanation
Indices: 180110--180142 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
180100 TATAATCTAA
*
180110 TATTTGATTTTTATTT
1 TATTTGATTTTAATTT
180126 TATTTGA-TTTAATTT
1 TATTTGATTTTAATTT
180141 TA
1 TA
180143 ATTTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (16 bp):
TATTTGATTTTAATTT
Found at i:180204 original size:5 final size:5
Alignment explanation
Indices: 180196--180221 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
180186 TAAATTAAAA
180196 ATTAT ATTAT ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT A
180222 AATATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:182382 original size:3 final size:3
Alignment explanation
Indices: 182374--182423 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
182364 ATAAAGATTT
*
182374 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
182422 AT
1 AT
182424 GTATATTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:182820 original size:16 final size:16
Alignment explanation
Indices: 182786--182828 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
182776 CAAATTAATT
* *
182786 TTAATATTTATTTTGAA
1 TTAA-ATTTAATTTAAA
182803 TTAAATTTAATTTAAA
1 TTAAATTTAATTTAAA
182819 TTAAAATTTA
1 TT-AAATTTA
182829 GTATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TTAAATTTAATTTAAA
Found at i:184109 original size:23 final size:23
Alignment explanation
Indices: 184066--184117 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
184056 TATGATAGGT
*
184066 TAATA-TTATTAAAATATTAATA
1 TAATATTTAATAAAATATTAATA
184088 TAATATTTAATAAAAT-TATAATA
1 TAATATTTAATAAAATAT-TAATA
*
184111 TATTATT
1 TAATATT
184118 GTATCATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATTTAATAAAATATTAATA
Found at i:201809 original size:98 final size:99
Alignment explanation
Indices: 201627--201825 Score: 289
Period size: 98 Copynumber: 2.0 Consensus size: 99
201617 TTCAAATTAT
* * * **
201627 CATCTTTTGTCTTCATTAAAATTTGTTGTTTTGGTTATTTTAGTTGATTTAACTTTTCAACTTAT
1 CATCTTTTGTCTTCATTAAAATTTGTTGTTTTCGCTATTTCAGTTGATGGAACTTTTCAACTTAT
201692 ATTTATTTTCTCCACTTATATTTCAAATGGTGGA
66 ATTTATTTTCTCCACTTATATTTCAAATGGTGGA
*
201726 CATCTTTTAG-CTTCATTAAAATTTGTTG-TTTCGCTATTTCAGTTAGCA-GGAAC-TTTCATCT
1 CATCTTTT-GTCTTCATTAAAATTTGTTGTTTTCGCTATTTCAGTT-G-ATGGAACTTTTCAACT
201787 TATATTTATTTTCTCCACTTATATTTCAAATGGTGGA
63 TATATTTATTTTCTCCACTTATATTTCAAATGGTGGA
201824 CA
1 CA
201826 ATATCCTGGA
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
98 59 0.65
99 30 0.33
100 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.50
Consensus pattern (99 bp):
CATCTTTTGTCTTCATTAAAATTTGTTGTTTTCGCTATTTCAGTTGATGGAACTTTTCAACTTAT
ATTTATTTTCTCCACTTATATTTCAAATGGTGGA
Found at i:205279 original size:31 final size:30
Alignment explanation
Indices: 205241--205356 Score: 110
Period size: 30 Copynumber: 3.9 Consensus size: 30
205231 TATATTTTAG
205241 TGCATCCAAATAAGCCCTTAAACGTTTAATT
1 TGCATCCAAATAAGCCCTTAAAC-TTTAATT
* ** *
205272 TGCATCCAAGTAAGTTCTTAACCTTTAATT
1 TGCATCCAAATAAGCCCTTAAACTTTAATT
* * *
205302 TACATCCAAATAA-ACCTTAAGCTTTAATT
1 TGCATCCAAATAAGCCCTTAAACTTTAATT
* * *
205331 AGTA-CCTAAATAAACCCTTAAACTTT
1 TGCATCC-AAATAAGCCCTTAAACTTT
205357 CATTATTCCT
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.03
29 20 0.29
30 28 0.41
31 19 0.28
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (30 bp):
TGCATCCAAATAAGCCCTTAAACTTTAATT
Found at i:205341 original size:29 final size:29
Alignment explanation
Indices: 205309--205380 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
205299 ATTTACATCC
*
205309 AAATAAA-CCTTAAGCTTTAATTAGTACCT
1 AAATAAACCCTTAAACTTTAATTA-TACCT
* *
205338 AAATAAACCCTTAAACTTTCATTATTCCT
1 AAATAAACCCTTAAACTTTAATTATACCT
*
205367 AAATAATCCCTTAA
1 AAATAAACCCTTAA
205381 CATAGTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAAACCCTTAAACTTTAATTATACCT
Found at i:211352 original size:2 final size:2
Alignment explanation
Indices: 211347--211372 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
211337 ACACACATTC
211347 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
211373 TATTAACCTT
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:211918 original size:19 final size:19
Alignment explanation
Indices: 211852--211906 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
211842 AGATCGAATC
* *
211852 TTAATTTGAAAATGTTTAA
1 TTAATTTGAAAATTTTTAT
211871 TT--TTT-ATAAA-TTTTAT
1 TTAATTTGA-AAATTTTTAT
211887 TTAATTTGAAAATTTTTAT
1 TTAATTTGAAAATTTTTAT
211906 T
1 T
211907 ATTATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 7 0.24
17 6 0.21
18 6 0.21
19 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTAATTTGAAAATTTTTAT
Found at i:211942 original size:40 final size:41
Alignment explanation
Indices: 211898--211992 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 41
211888 TAATTTGAAA
*
211898 ATTTTTATTATTATTTA-AAAT-AATTTTAA-AAAATAAAATT
1 ATTTTTATTATTATTTATAAATAAATTTAAATAAAAT-AAA-T
* *
211938 ATTTTTATTAATATTTATAATTAAATTTAAATAAAATAAAT
1 ATTTTTATTATTATTTATAAATAAATTTAAATAAAATAAAT
211979 -TTTTTATTACTTAT
1 ATTTTTATTA-TTAT
211993 ATATTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 25 0.53
41 7 0.15
42 10 0.21
43 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (41 bp):
ATTTTTATTATTATTTATAAATAAATTTAAATAAAATAAAT
Found at i:211993 original size:37 final size:38
Alignment explanation
Indices: 211928--212003 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
211918 TAATTTTAAA
* * *
211928 AAATAAAATTATTTTTATTAATATTTATA-ATTAAATTT
1 AAATAAAATAAATTTTATTAATACTTATATATT-AATTT
*
211966 AAATAAAATAAATTTT-TTATTACTTATATATTAATTT
1 AAATAAAATAAATTTTATTAATACTTATATATTAATTT
212003 A
1 A
212004 GATTAGATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (38 bp):
AAATAAAATAAATTTTATTAATACTTATATATTAATTT
Found at i:213468 original size:85 final size:85
Alignment explanation
Indices: 213325--213495 Score: 297
Period size: 85 Copynumber: 2.0 Consensus size: 85
213315 CGTCAAGAAG
* *
213325 TTGCTCTTAGGTATGCATTTTCCTTCTCTTAAGTGCTGTTACATTAGCTGGAGGGGCTTGTAAAA
1 TTGCTCTTAGGTATGCATTTTCCTTCTCTTAAATGCAGTTACATTAGCTGGAGGGGCTTGTAAAA
*
213390 TTTTGAACTAGGAAAGTCAA
66 TTTTGAACTAGGAAAGGCAA
* *
213410 TTGCTCTTAGGTATGCATTTTCCTTGTCTTAAATGCAGTTATATTAGCTGGAGGGGCTTGTAAAA
1 TTGCTCTTAGGTATGCATTTTCCTTCTCTTAAATGCAGTTACATTAGCTGGAGGGGCTTGTAAAA
213475 TTTTGAACTAGGAAAGGCAA
66 TTTTGAACTAGGAAAGGCAA
213495 T
1 T
213496 ATGTTGTTCC
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (85 bp):
TTGCTCTTAGGTATGCATTTTCCTTCTCTTAAATGCAGTTACATTAGCTGGAGGGGCTTGTAAAA
TTTTGAACTAGGAAAGGCAA
Found at i:215729 original size:28 final size:28
Alignment explanation
Indices: 215696--215752 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
215686 CGGGAGTGGT
215696 GTAAACAGTATCACTGATTCATGGATGG
1 GTAAACAGTATCACTGATTCATGGATGG
* *
215724 GTAAACAGTGTCATTGATTCATGGATGG
1 GTAAACAGTATCACTGATTCATGGATGG
215752 G
1 G
215753 GTTTGGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (28 bp):
GTAAACAGTATCACTGATTCATGGATGG
Found at i:217083 original size:32 final size:33
Alignment explanation
Indices: 217022--217083 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
217012 TTTTTAAAAT
217022 ATTATATATATTTATATAAAATTTAATACAATA
1 ATTATATATATTTATATAAAATTTAATACAATA
* * *
217055 ATTATTTATA-TTATATAAATTTTGATACA
1 ATTATATATATTTATATAAAATTTAATACA
217084 TTAGTGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (33 bp):
ATTATATATATTTATATAAAATTTAATACAATA
Found at i:217526 original size:23 final size:20
Alignment explanation
Indices: 217499--217564 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 20
217489 TTATATGTAT
217499 TATTTATATGATAAAAATTACA
1 TATTTATAT-ATAAAAATTA-A
217521 TAATTTATA-ATATAAAATTAA
1 T-ATTTATATATA-AAAATTAA
217542 TATTTATTATAATTAAAAATTAA
1 TATTTA-TAT-A-TAAAAATTAA
217565 GTTAATCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
20 5 0.13
21 7 0.18
22 8 0.21
23 16 0.42
24 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TATTTATATATAAAAATTAA
Found at i:218203 original size:19 final size:17
Alignment explanation
Indices: 218171--218218 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
218161 AAATATACAA
* *
218171 ATATAATATATAAATAT
1 ATATTATATTTAAATAT
*
218188 ATGATTTATATTTAAATTT
1 AT-A-TTATATTTAAATAT
218207 ATATTATATTTA
1 ATATTATATTTA
218219 TGTTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.42
18 2 0.08
19 13 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATATTATATTTAAATAT
Found at i:218210 original size:23 final size:22
Alignment explanation
Indices: 218184--218239 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
218174 TAATATATAA
*
218184 ATATATGATTTATATTTAAATTT
1 ATATAT-ATTTATATTTAAAATT
*
218207 ATATTATATTTATGTTTAAAATT
1 ATA-TATATTTATATTTAAAATT
218230 A-ATATATTTA
1 ATATATATTTA
218240 ATAATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.27
22 1 0.03
23 18 0.60
24 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
ATATATATTTATATTTAAAATT
Found at i:218489 original size:15 final size:16
Alignment explanation
Indices: 218463--218495 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
218453 AAATTAGAAT
218463 AAAATCACAATAAAAA
1 AAAATCACAATAAAAA
218479 AAAATCA-AATAAAAA
1 AAAATCACAATAAAAA
218494 AA
1 AA
218496 GCATCAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATCACAATAAAAA
Found at i:218698 original size:2 final size:2
Alignment explanation
Indices: 218687--218727 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
218677 ATTTTCTTTT
218687 TA TA -A TA TA TA 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
218728 ATTTGAGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:224075 original size:2 final size:2
Alignment explanation
Indices: 224068--224118 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
224058 TTAGTTTTGG
224068 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
224110 TC TC TC TC T
1 TC TC TC TC T
224119 ATGATGAGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:226410 original size:29 final size:29
Alignment explanation
Indices: 226378--226441 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
226368 TTTATATTTG
226378 TTATTTAA-ATATATTAAAATTTAAA-AAAA
1 TTATTTAATATA-ATT-AAATTTAAATAAAA
**
226407 TTATATTTTTATAATTAAATTTAAATAAAA
1 TTAT-TTAATATAATTAAATTTAAATAAAA
226437 TTATT
1 TTATT
226442 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
29 14 0.47
30 13 0.43
31 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATTTAATATAATTAAATTTAAATAAAA
Found at i:227047 original size:12 final size:11
Alignment explanation
Indices: 227018--227043 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
227008 AATCGATAAT
227018 TAAATTTTTTA
1 TAAATTTTTTA
227029 TAAATTTTTTA
1 TAAATTTTTTA
227040 TAAA
1 TAAA
227044 ATTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TAAATTTTTTA
Found at i:227635 original size:15 final size:15
Alignment explanation
Indices: 227611--227658 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
227601 GGAAATCATA
227611 TTATTATTGAGTGTT
1 TTATTATTGAGTGTT
*
227626 TTATTTTTGAGTGTTT
1 TTATTATTGAGTG-TT
*
227642 TTATTATTGGGTGTT
1 TTATTATTGAGTGTT
227657 TT
1 TT
227659 TAATTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (15 bp):
TTATTATTGAGTGTT
Found at i:227645 original size:16 final size:16
Alignment explanation
Indices: 227611--227665 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
227601 GGAAATCATA
227611 TTATTATTGAGTG-TT
1 TTATTATTGAGTGTTT
*
227626 TTATTTTTGAGTGTTT
1 TTATTATTGAGTGTTT
*
227642 TTATTATTGGGTGTTT
1 TTATTATTGAGTGTTT
227658 TTAATTAT
1 TT-ATTAT
227666 AAATTGGATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
15 12 0.34
16 18 0.51
17 5 0.14
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (16 bp):
TTATTATTGAGTGTTT
Found at i:227738 original size:9 final size:9
Alignment explanation
Indices: 227719--227762 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
227709 TTGCAAAATT
227719 TAAAATTAA
1 TAAAATTAA
*
227728 -AAAATTTA
1 TAAAATTAA
227736 -AAAATTAA
1 TAAAATTAA
227744 TAAAATTAA
1 TAAAATTAA
227753 TAAAATTAA
1 TAAAATTAA
227762 T
1 T
227763 TTGTAGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 14 0.44
9 18 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAATTAA
Found at i:227741 original size:16 final size:17
Alignment explanation
Indices: 227713--227762 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 17
227703 AATTTATTGC
227713 AAAATTT-AAAATTAA-
1 AAAATTTAAAAATTAAT
227728 AAAATTTAAAAATTAAT
1 AAAATTTAAAAATTAAT
*
227745 AAAATTAATAAAATTAAT
1 AAAATTTA-AAAATTAAT
227763 TTGTAGGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 7 0.23
16 8 0.26
17 7 0.23
18 9 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTTAAAAATTAAT
Found at i:228172 original size:17 final size:19
Alignment explanation
Indices: 228145--228184 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
228135 TTTAAAATTA
228145 AAAAAACTATACATTTT-T
1 AAAAAACTATACATTTTAT
*
228163 AAAAAA-TATATATTTTAT
1 AAAAAACTATACATTTTAT
228181 AAAA
1 AAAA
228185 CTACCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAACTATACATTTTAT
Found at i:229565 original size:3 final size:3
Alignment explanation
Indices: 229557--229594 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
229547 CAGTTGACAA
229557 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
229595 AAGTGTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:234396 original size:20 final size:22
Alignment explanation
Indices: 234357--234403 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
234347 AAATGGATTA
234357 TTCATTATTGAATAATGTTGAGT
1 TTCATTATT-AATAATGTTGAGT
*
234380 TTCATTATT-AT-ATGTTGGGT
1 TTCATTATTAATAATGTTGAGT
234400 TTCA
1 TTCA
234404 ACTTCAAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
23 9 0.39
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (22 bp):
TTCATTATTAATAATGTTGAGT
Found at i:235474 original size:2 final size:2
Alignment explanation
Indices: 235469--235504 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
235459 AGATATACTC
235469 TA TA TA 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
235505 CACACATTTA
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):
TA
Found at i:236325 original size:21 final size:22
Alignment explanation
Indices: 236301--236356 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
236291 TTGTGTTTAT
236301 ATTTTTTTATATTAT-ATCATA-
1 ATTTTTTTATATTATAAT-ATAG
** *
236322 ATTTGATTATATTTTAATATAG
1 ATTTTTTTATATTATAATATAG
236344 A-TTTTTTATATTA
1 ATTTTTTTATATTA
236357 ATTTTATATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
ATTTTTTTATATTATAATATAG
Found at i:241176 original size:2 final size:2
Alignment explanation
Indices: 241169--241206 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
241159 GGGGAACACT
241169 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
241207 ATTACGTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:243799 original size:28 final size:30
Alignment explanation
Indices: 243746--243820 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 30
243736 GCGATTGAGA
243746 TTAACATTTAATTAATAAAAATATTTTTAT
1 TTAACATTTAATTAATAAAAATATTTTTAT
*
243776 TTAA-ATTTAATT-AT-AAAATAATTTT-T
1 TTAACATTTAATTAATAAAAATATTTTTAT
* *
243802 TTAATATTTTAAATAATAA
1 TTAACA-TTTAATTAATAA
243821 TTTAAACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 5 0.13
27 11 0.28
28 8 0.21
29 10 0.26
30 5 0.13
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAACATTTAATTAATAAAAATATTTTTAT
Found at i:245790 original size:16 final size:17
Alignment explanation
Indices: 245757--245817 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 17
245747 TTTTTTACTA
245757 ATTAAAATATTAATATT
1 ATTAAAATATTAATATT
*
245774 ATTAAAA-ATTGATATT
1 ATTAAAATATTAATATT
245790 A--AAAATATT-ATATT
1 ATTAAAATATTAATATT
245804 A--AAAATATTAATAT
1 ATTAAAATATTAATAT
245818 AATATCTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
14 18 0.44
15 7 0.17
16 9 0.22
17 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTAAAATATTAATATT
Found at i:246275 original size:498 final size:500
Alignment explanation
Indices: 245313--246280 Score: 1854
Period size: 498 Copynumber: 1.9 Consensus size: 500
245303 TATTGGTTTA
245313 AATATAATATCTAATTTATTAATCAATTACCTTACTAGTGGGTAGACCTTATCTTTGAATTTATA
1 AATATAATATCTAATTTATTAATCAATTACCTTACTAGTGGGTAGACCTTATCTTTGAATTTATA
245378 TAATATTTTATATCAAATAAGTTTGAGACAAAATTGATTAGTAAGTAGCATTACTTATAATATTA
66 TAATATTTTATATCAAATAAGTTTGAGACAAAATTGATTAGTAAGTAGCATTACTTATAATATTA
*
245443 AATATATATTTTTAAATATTATCAATGCTCATTATAAAATTTAAAAAAATTAAGAATATTAAATT
131 AATATATATTTTTAAATATTATCAATGCTCATTATAAAATTTAAAAAAATTAAGAAGATTAAATT
245508 ATTATCTTGAAAAGATAAAAAATAATTTTTTAAAAAATTAAAAAAAAAATCATTTTTAATACTCA
196 ATTATCTTGAAAAGATAAAAAATAATTTTTTAAAAAATTAAAAAAAAAATCATTTTTAATACTCA
245573 TCTTTTAAAATTATATTTTTTAAAAAATTTTAAAATAACATTCATTTCAAATATTATTAAATTAA
261 TCTTTTAAAATTATATTTTTTAAAAAATTTTAAAATAACATTCATTTCAAATATTATTAAATTAA
*
245638 AAATAATATTCATCCTTAATATAACAAAAATCAATATAAAAAATTAATTTTTTAATTATTTTTAA
326 AAATAATATTCATCCTTAATATAACAAAAATCAATATAAAAAAGTAATTTTTTAATTATTTTTAA
245703 TTTATCTCTAAAAATATTTTATTTTATAATATCTTTTATTAATATTTTTTACTAATTAAAATATT
391 TTTATCTCTAAAAATATTTTATTTTATAATATCTTTTATTAATATTTTTTACTAATTAAAATATT
245768 AATATTATTAAAAATTGATATTAAAAATATTATATTAAAAATATT
456 AATATTATTAAAAATTGATATTAAAAATATTATATTAAAAATATT
245813 AATATAATATCTAATTTATTAATCAATTACCTTACTAGTGGGTAGACCTTATCTTTGAATTTATA
1 AATATAATATCTAATTTATTAATCAATTACCTTACTAGTGGGTAGACCTTATCTTTGAATTTATA
245878 TAATATTTTATATCAAAT-AGTTTTGAGAC-AAATTGATTAGTAAGTAGCATTACGTTATAATAT
66 TAATATTTTATATCAAATAAG-TTTGAGACAAAATTGATTAGTAAGTAGCATTAC-TTATAATAT
*
245941 TAAATATATATTTTTAAATATTATCAATGCTCATTATAAAATTTTAAAAAATTAAGAAGATTAAA
129 TAAATATATATTTTTAAATATTATCAATGCTCATTATAAAATTTAAAAAAATTAAGAAGATTAAA
246006 TTATTATCTTG-AAAGATAAAAAATAATTTTTTAAAAAATTAAAAAAAAAATCATTTTTAATACT
194 TTATTATCTTGAAAAGATAAAAAATAATTTTTTAAAAAATTAAAAAAAAAATCATTTTTAATACT
246070 CATCTTTTAAAATTATATTTTTT-AAAAATTTTAAAATAACATTCATTTCAAATATTATTAAATT
259 CATCTTTTAAAATTATATTTTTTAAAAAATTTTAAAATAACATTCATTTCAAATATTATTAAATT
*
246134 AAAAATAATATTCATCCTTAATATAATAAAAATCAATATAAAAAAGTAATTTTTTAATTATTTTT
324 AAAAATAATATTCATCCTTAATATAACAAAAATCAATATAAAAAAGTAATTTTTTAATTATTTTT
246199 AATTTATCTCTAAAAATATTTTATTTTATAATATCTTTTATTAATATTTTTTACTAATTAAAATA
389 AATTTATCTCTAAAAATATTTTATTTTATAATATCTTTTATTAATATTTTTTACTAATTAAAATA
246264 TTAATATTATTAAAAAT
454 TTAATATTATTAAAAAT
246281 AACTAATTAA
Statistics
Matches: 462, Mismatches: 4, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
498 186 0.40
499 102 0.22
500 174 0.38
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (500 bp):
AATATAATATCTAATTTATTAATCAATTACCTTACTAGTGGGTAGACCTTATCTTTGAATTTATA
TAATATTTTATATCAAATAAGTTTGAGACAAAATTGATTAGTAAGTAGCATTACTTATAATATTA
AATATATATTTTTAAATATTATCAATGCTCATTATAAAATTTAAAAAAATTAAGAAGATTAAATT
ATTATCTTGAAAAGATAAAAAATAATTTTTTAAAAAATTAAAAAAAAAATCATTTTTAATACTCA
TCTTTTAAAATTATATTTTTTAAAAAATTTTAAAATAACATTCATTTCAAATATTATTAAATTAA
AAATAATATTCATCCTTAATATAACAAAAATCAATATAAAAAAGTAATTTTTTAATTATTTTTAA
TTTATCTCTAAAAATATTTTATTTTATAATATCTTTTATTAATATTTTTTACTAATTAAAATATT
AATATTATTAAAAATTGATATTAAAAATATTATATTAAAAATATT
Found at i:246675 original size:15 final size:15
Alignment explanation
Indices: 246657--246705 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
246647 TATACAATAT
* *
246657 TATTATTATTTTTTA
1 TATTATTATATTTAA
246672 TATTATTATATTTAA
1 TATTATTATATTTAA
* *
246687 AATTATTAAATTT-A
1 TATTATTATATTTAA
246701 TATTA
1 TATTA
246706 AAAGAGGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTATATTTAA
Found at i:247312 original size:29 final size:33
Alignment explanation
Indices: 247243--247363 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 33
247233 ATAAATTTTT
* *
247243 TATTTAAATTTAATTATAAAATATATAAATATAA
1 TATTTAAAATTAATTAT-AAATATATAAACATAA
247277 TATTTTAAAATT-ATTATAAATA-AT-AACATAA
1 TA-TTTAAAATTAATTATAAATATATAAACATAA
* *
247308 -ATTTAAAATTAATT-TAAAT-T-TAAATAAAAA
1 TATTTAAAATTAATTATAAATATATAAA-CATAA
*
247338 TTTTTAAAATTTAATTTATAAATATA
1 TATTTAAAA-TTAA-TTATAAATATA
247364 ATTTATTATG
Statistics
Matches: 71, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
28 1 0.01
29 16 0.23
30 7 0.10
31 13 0.18
32 6 0.08
33 7 0.10
34 12 0.17
35 9 0.13
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
TATTTAAAATTAATTATAAATATATAAACATAA
Found at i:247323 original size:11 final size:11
Alignment explanation
Indices: 247307--247368 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
247297 TAATAACATA
247307 AATTTAAAATT
1 AATTTAAAATT
*
247318 AATTTAAATTT
1 AATTTAAAATT
* *
247329 AAATAAAAATT
1 AATTTAAAATT
247340 --TTTAAAATTT
1 AATTTAAAA-TT
247350 AATTTATAAATAT
1 AATTTA-AAAT-T
247363 AATTTA
1 AATTTA
247369 TTATGTTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 5 0.12
10 2 0.05
11 18 0.45
12 5 0.12
13 10 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:247730 original size:14 final size:12
Alignment explanation
Indices: 247696--247739 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 12
247686 CATTCGATAT
247696 TTTAAA-AAAAA
1 TTTAAATAAAAA
247707 TTTAAATAAAAA
1 TTTAAATAAAAA
247719 TATTAAATTAAAAAA
1 T-TTAAA-T-AAAAA
247734 TTTAAA
1 TTTAAA
247740 AAATTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 6 0.21
13 5 0.17
14 6 0.21
15 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTTAAATAAAAA
Found at i:248091 original size:41 final size:41
Alignment explanation
Indices: 248001--248091 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
247991 AAAAGACAAT
* * ** * *
248001 AATATGAGATAATTTAAATGAGTTTTAATTATTTATTTAAA
1 AATATGAGTTAATTTAAATAAGCATGAATTATTCATTTAAA
*
248042 AATATGAGTTAATTTAAATAAGCATGAATTATTCATTTATA
1 AATATGAGTTAATTTAAATAAGCATGAATTATTCATTTAAA
248083 AATATGAGT
1 AATATGAGT
248092 AGATTCCGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (41 bp):
AATATGAGTTAATTTAAATAAGCATGAATTATTCATTTAAA
Found at i:249212 original size:2 final size:2
Alignment explanation
Indices: 249207--249231 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
249197 ATGTATTATT
249207 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
249232 TTCATATTCA
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:251062 original size:19 final size:19
Alignment explanation
Indices: 251038--251074 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
251028 GCTATTACCA
*
251038 ATGTATCGATACATATTTT
1 ATGTATCGATACAAATTTT
251057 ATGTATCGATACAAATTT
1 ATGTATCGATACAAATTT
251075 GGCTACTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACAAATTTT
Found at i:251119 original size:53 final size:53
Alignment explanation
Indices: 251039--251175 Score: 195
Period size: 53 Copynumber: 2.6 Consensus size: 53
251029 CTATTACCAA
* *
251039 TGTATCGATACATATTTTATGTATCGATACAAATTTGGCTACTG-CTAATGACC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGTC-AATGACC
* *
251092 TGTATCGATACATATTGTGTGTATCGATATAAATTTGGCTACTGTCAATGTCC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGTCAATGACC
* *
251145 TATATTGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATA-TTGTGTGTATCGATAC
251176 TATGCAATCT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
53 59 0.79
54 16 0.21
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (53 bp):
TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGTCAATGACC
Found at i:251208 original size:20 final size:20
Alignment explanation
Indices: 251163--251216 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
251153 TACATATTTG
*
251163 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
251183 TCTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
251203 TGTGTATCGATACT
1 TGTGTATCGATACT
251217 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Found at i:251281 original size:21 final size:21
Alignment explanation
Indices: 251255--251295 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
251245 GTCAACCTTG
251255 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATATGTATA
*
251276 TGTATTGATACAATATGTAT
1 TGTATTAATACAATATGTAT
251296 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (21 bp):
TGTATTAATACAATATGTATA
Found at i:252468 original size:16 final size:15
Alignment explanation
Indices: 252447--252480 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
252437 AATTAGAATA
252447 TAATTTAATAATAAAT
1 TAATTTAATAAT-AAT
252463 TAATTTAATAATAAT
1 TAATTTAATAATAAT
252478 TAA
1 TAA
252481 AAATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTTAATAATAAT
Found at i:252658 original size:29 final size:28
Alignment explanation
Indices: 252623--252701 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
252613 AACTTAAGAG
252623 ATAAATATTTTTTTATCAAATTTTAAAAA
1 ATAAATATTTTTTTAT-AAATTTTAAAAA
* *
252652 ATAAATAAATATTTTT-TAAATATTAAAAAA
1 ATAAAT--ATTTTTTTATAAAT-TTTAAAAA
*
252682 ATAAATATATCTTTTATAAA
1 ATAAATAT-TTTTTTATAAA
252702 ATGTTAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.05
29 14 0.34
30 18 0.44
31 7 0.17
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
ATAAATATTTTTTTATAAATTTTAAAAA
Found at i:252678 original size:22 final size:22
Alignment explanation
Indices: 252643--252684 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
252633 TTTTATCAAA
*
252643 TTTTAAAAAATAAATAAATATT
1 TTTTAAAAAATAAAAAAATATT
* *
252665 TTTTAAATATTAAAAAAATA
1 TTTTAAAAAATAAAAAAATA
252685 AATATATCTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAAAATAAAAAAATATT
Found at i:252930 original size:5 final size:5
Alignment explanation
Indices: 252920--253085 Score: 50
Period size: 5 Copynumber: 34.2 Consensus size: 5
252910 AGGTACGTGT
* * *
252920 TTATA TTATA TT-T- TTAAA TT-TAA TTATA TTATAA TAATA TATAAA
1 TTATA TTATA TTATA TTATA TTAT-A TTATA TTAT-A TTATA T-TATA
* * * * *
252965 ATATT TTATA TT-TA TATAAA TTATTA ATATA TTA-A TAAT- TTATA TTATA
1 TTATA TTATA TTATA T-TATA TTA-TA TTATA TTATA TTATA TTATA TTATA
* * ** *
253014 TAAAA TT-TA AAATA TT-TA TTTATA TTATA TTATA -TATTA TT-T- TTAAA
1 TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTA-TA TTATA TTATA
* *
253061 TTATA TTTTA TT-TT TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA T
253086 AATCATATTA
Statistics
Matches: 113, Mismatches: 29, Indels: 38
0.63 0.16 0.21
Matches are distributed among these distances:
3 4 0.04
4 19 0.17
5 75 0.66
6 15 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:253020 original size:34 final size:33
Alignment explanation
Indices: 252954--253043 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 33
252944 TATATTATAA
* *
252954 TAATATATAAAATATTTTATATT-TATATAAATTAT
1 TAATATAT-TAATAATTTATATTATATATAAA-T-T
252989 TAATATATTAATAATTTATATTATATA-AAATT
1 TAATATATTAATAATTTATATTATATATAAATT
*
253021 TAAAATATT--T-ATTTATATTATAT
1 TAATATATTAATAATTTATATTATAT
253044 TATATATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
29 13 0.25
30 1 0.02
32 9 0.18
33 1 0.02
34 15 0.29
35 12 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TAATATATTAATAATTTATATTATATATAAATT
Found at i:253044 original size:34 final size:33
Alignment explanation
Indices: 252964--253052 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 33
252954 TAATATATAA
* * *
252964 AATATTTTATATTTATATAAATTATTAATATATT
1 AATAATTTATA-TTATATAAAATATTAAAATATT
252998 AATAATTTATATTATATAAAAT-TTAAAATATT
1 AATAATTTATATTATATAAAATATTAAAATATT
* *
253030 --T-ATTTATATTATATTATATATTA
1 AATAATTTATATTATATAAAATATTA
253053 TTTTTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.33
30 4 0.08
32 9 0.18
33 10 0.20
34 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATAATTTATATTATATAAAATATTAAAATATT
Found at i:253054 original size:25 final size:24
Alignment explanation
Indices: 253026--253108 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 24
253016 AAATTTAAAA
253026 TATTTATTTATATTATATTATATAT
1 TATTT-TTTATATTATATTATATAT
*
253051 TA--TTTT-TA--A-ATTATATTT
1 TATTTTTTATATTATATTATATAT
*
253069 TATTTTTTATATTATATAATCATAT
1 TATTTTTTATATTATATTAT-ATAT
*
253094 TATTTTTAATATTAT
1 TATTTTTTATATTAT
253109 TAAATTTAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
18 10 0.21
19 1 0.02
20 4 0.09
21 4 0.09
22 3 0.06
23 2 0.04
24 4 0.09
25 19 0.40
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTTTTATATTATATTATATAT
Found at i:253062 original size:42 final size:43
Alignment explanation
Indices: 253016--253113 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
253006 ATATTATATA
*
253016 AAATT-TAAAATATTTATTTATATTATATTAT-ATATTATTTTT
1 AAATTATAAAATATTT-TTTATATTATATAATCATATTATTTTT
***
253058 AAATTATATTTTATTTTTTATATTATATAATCATATTATTTTT
1 AAATTATAAAATATTTTTTATATTATATAATCATATTATTTTT
*
253101 AATATTATTAAAT
1 AA-ATTATAAAAT
253114 TTAGTGATGG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
42 19 0.42
43 20 0.44
44 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (43 bp):
AAATTATAAAATATTTTTTATATTATATAATCATATTATTTTT
Done.