Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 13 of 21
Found at i:1932139 original size:21 final size:20
Alignment explanation
Indices: 1932113--1932186 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 20
1932103 AAGTTAAAAC
1932113 AATTATATATATGATTATTAA
1 AATTATAT-TATGATTATTAA
**
1932134 AATTATATTAAACATTATTAA
1 AATTATATT-ATGATTATTAA
*
1932155 AATTATATT-TGAATTTATCAA
1 AATTATATTATG-A-TTATTAA
1932176 AATTATATTAT
1 AATTATATTAT
1932187 AAGCTTTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.05
21 41 0.93
22 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
AATTATATTATGATTATTAA
Found at i:1932144 original size:11 final size:11
Alignment explanation
Indices: 1932128--1932185 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
1932118 TATATATGAT
1932128 TATTAAAATTA
1 TATTAAAATTA
1932139 TATTAAACA-T-
1 TATTAAA-ATTA
1932149 TATTAAAATTA
1 TATTAAAATTA
**
1932160 TATTTGAATT-
1 TATTAAAATTA
*
1932170 TATCAAAATTA
1 TATTAAAATTA
1932181 TATTA
1 TATTA
1932186 TAAGCTTTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
9 1 0.03
10 15 0.41
11 20 0.54
12 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:1932278 original size:34 final size:34
Alignment explanation
Indices: 1932240--1932361 Score: 162
Period size: 34 Copynumber: 3.7 Consensus size: 34
1932230 TTATGAATAG
* *
1932240 TAATATTTTATATAATTTTGATCATTTATATAAA
1 TAATATTTGATATAATTTTGATAATTTATATAAA
*
1932274 TAATATTTGATATAATTTTGATAATTTATATCAA
1 TAATATTTGATATAATTTTGATAATTTATATAAA
*
1932308 TAATATTTGATATAATTTTGATAACTTT-TA-ATA
1 TAATATTTGATATAATTTTGATAA-TTTATATAAA
*
1932341 TAAT-TTTGATA-AGTTTTGATA
1 TAATATTTGATATAATTTTGATA
1932362 TAAATTTTGA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
31 9 0.11
32 7 0.09
33 5 0.06
34 57 0.70
35 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (34 bp):
TAATATTTGATATAATTTTGATAATTTATATAAA
Found at i:1932336 original size:10 final size:11
Alignment explanation
Indices: 1932273--1932428 Score: 91
Period size: 11 Copynumber: 14.6 Consensus size: 11
1932263 ATTTATATAA
1932273 ATAATATTTGAT
1 ATAAT-TTTGAT
1932285 ATAATTTTG--
1 ATAATTTTGAT
1932294 ATAATTTAT-AT
1 ATAATTT-TGAT
1932305 CAATAATATTTGAT
1 --ATAAT-TTTGAT
1932319 ATAATTTTGAT
1 ATAATTTTGAT
* *
1932330 A-ACTTTTAAT
1 ATAATTTTGAT
1932340 ATAATTTTGAT
1 ATAATTTTGAT
*
1932351 A-AGTTTTGAT
1 ATAATTTTGAT
1932361 ATAAATTTTG--
1 AT-AATTTTGAT
** * *
1932371 ATACCTTTAAC
1 ATAATTTTGAT
*
1932382 ATGATTTT-A-
1 ATAATTTTGAT
*
1932391 AT-ATTTTTAT
1 ATAATTTTGAT
*
1932401 ATGATTTTGAT
1 ATAATTTTGAT
1932412 A-AATTTTGAT
1 ATAATTTTGAT
1932422 ATAATTT
1 ATAATTT
1932429 ACCTTTATTA
Statistics
Matches: 114, Mismatches: 14, Indels: 33
0.71 0.09 0.20
Matches are distributed among these distances:
8 5 0.04
9 14 0.12
10 32 0.28
11 37 0.32
12 16 0.14
13 6 0.05
14 4 0.04
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (11 bp):
ATAATTTTGAT
Found at i:1932341 original size:21 final size:21
Alignment explanation
Indices: 1932317--1932428 Score: 104
Period size: 21 Copynumber: 5.4 Consensus size: 21
1932307 ATAATATTTG
1932317 ATATAATTTTGATAACTTTTA
1 ATATAATTTTGATAACTTTTA
* *
1932338 ATATAATTTTGATAAGTTTTG
1 ATATAATTTTGATAACTTTTA
*
1932359 ATATAAATTTTGAT-ACCTTTA
1 ATAT-AATTTTGATAACTTTTA
* * * *
1932380 ACATGATTTTAAT-A-TTTTT
1 ATATAATTTTGATAACTTTTA
* * *
1932399 ATATGATTTTGATAAATTTTG
1 ATATAATTTTGATAACTTTTA
1932420 ATATAATTT
1 ATATAATTT
1932429 ACCTTTATTA
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.19
20 9 0.12
21 42 0.57
22 9 0.12
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (21 bp):
ATATAATTTTGATAACTTTTA
Found at i:1932369 original size:12 final size:12
Alignment explanation
Indices: 1932313--1932373 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
1932303 ATCAATAATA
1932313 TTTGATAT-AAT
1 TTTGATATAAAT
*
1932324 TTTG--ATAACT
1 TTTGATATAAAT
*
1932334 TTTAATAT-AAT
1 TTTGATATAAAT
*
1932345 TTTG--ATAAGT
1 TTTGATATAAAT
1932355 TTTGATATAAAT
1 TTTGATATAAAT
1932367 TTTGATA
1 TTTGATA
1932374 CCTTTAACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
9 4 0.11
10 11 0.29
11 9 0.24
12 14 0.37
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (12 bp):
TTTGATATAAAT
Found at i:1932515 original size:21 final size:23
Alignment explanation
Indices: 1932491--1932538 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
1932481 TTAAATAGCT
*
1932491 TTTTGATAATCTTTTA-T-ATAA
1 TTTTGATAATATTTTATTCATAA
1932512 TTTTGATAATATTTTATTCATAA
1 TTTTGATAATATTTTATTCATAA
1932535 TTTT
1 TTTT
1932539 TTATAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.62
22 1 0.04
23 8 0.33
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTGATAATATTTTATTCATAA
Found at i:1934960 original size:22 final size:21
Alignment explanation
Indices: 1934942--1934984 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1934932 TTTTTAATAT
1934942 TAAAAAAATTTATACTTAATTA
1 TAAAAAAA-TTATACTTAATTA
* *
1934964 TATAAGAATTATACTTAATTA
1 TAAAAAAATTATACTTAATTA
1934985 ATCATATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAAAAAATTATACTTAATTA
Found at i:1939096 original size:2 final size:2
Alignment explanation
Indices: 1939089--1939124 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1939079 TGCTAAAGAA
1939089 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
1939125 GTATGTATAA
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:1944390 original size:2 final size:2
Alignment explanation
Indices: 1944383--1944407 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1944373 CCTGAGTCAT
1944383 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
1944408 CTTAATACAA
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:1947498 original size:2 final size:2
Alignment explanation
Indices: 1947486--1947516 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1947476 TTGAGAAATC
1947486 AT AT A- 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
1947517 TTGTTAGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1948089 original size:2 final size:2
Alignment explanation
Indices: 1948082--1948118 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1948072 TGGACTTTTA
1948082 AT AT AT AT AT 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 AT AT AT AT AT A
1948119 AAGTTTTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1949390 original size:35 final size:37
Alignment explanation
Indices: 1949351--1949426 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
1949341 TTTAAATCAA
*
1949351 TTTTA-TTCAAATTATAATT-TAATA-ATAAAAATATT
1 TTTTATTTCAAATT-TAATTATAAAATATAAAAATATT
*
1949386 TTTTATTTTAAATTTAATTATAAAATATAAAAATATT
1 TTTTATTTCAAATTTAATTATAAAATATAAAAATATT
1949423 TTTT
1 TTTT
1949427 TAATTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
35 10 0.28
36 11 0.31
37 15 0.42
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (37 bp):
TTTTATTTCAAATTTAATTATAAAATATAAAAATATT
Found at i:1962013 original size:14 final size:14
Alignment explanation
Indices: 1961994--1962021 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1961984 AGAACGTGGG
1961994 GTCTATGTCTATCT
1 GTCTATGTCTATCT
1962008 GTCTATGTCTATCT
1 GTCTATGTCTATCT
1962022 TTTAGGGTGG
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:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTATGTCTATCT
Found at i:1966116 original size:28 final size:28
Alignment explanation
Indices: 1966084--1966137 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1966074 ATAATTAAAA
*
1966084 AATATTTAAATTT-TATATAATATAAATT
1 AATATTAAAATTTATATA-AATATAAATT
1966112 AATATTAAAATTTATATAAATATAAA
1 AATATTAAAATTTATATAAATATAAA
1966138 ATATGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATATTAAAATTTATATAAATATAAATT
Found at i:1966119 original size:27 final size:29
Alignment explanation
Indices: 1966084--1966137 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
1966074 ATAATTAAAA
*
1966084 AATATTTAAATTTTATAT-AATATAAATT
1 AATATTTAAAATTTATATAAATATAAATT
1966112 AATA-TTAAAATTTATATAAATATAAA
1 AATATTTAAAATTTATATAAATATAAA
1966138 ATATGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AATATTTAAAATTTATATAAATATAAATT
Found at i:1966146 original size:27 final size:25
Alignment explanation
Indices: 1966082--1966176 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 25
1966072 AAATAATTAA
*
1966082 AAAATATTTAAATTTTATATAATAT
1 AAAATATTTAAAATTTATATAATAT
*
1966107 AAATTAATATTAAAATTTATATAAATAT
1 AAAAT-AT-TTAAAATTTATAT-AATAT
*
1966135 AAAATATGTTAAATATAATTATTATATTAT
1 AAAATAT-TTAAA-AT--TTA-TATAATAT
*
1966165 AAAATATATAAA
1 AAAATATTTAAA
1966177 TATGATATAG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
25 4 0.07
26 2 0.04
27 19 0.33
28 11 0.19
29 4 0.07
30 14 0.25
31 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
AAAATATTTAAAATTTATATAATAT
Found at i:1966148 original size:38 final size:38
Alignment explanation
Indices: 1966106--1966180 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
1966096 TTATATAATA
1966106 TAAAT-TAA-TATTAAAATTTATATAAATATA-AAATATGT
1 TAAATATAATTATT-AAA-TTATA-AAATATATAAATATGT
*
1966144 TAAATATAATTATTATATTATAAAATATATAAATATG
1 TAAATATAATTATTAAATTATAAAATATATAAATATG
1966181 ATATAGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 7 0.21
38 17 0.52
39 5 0.15
40 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.43
Consensus pattern (38 bp):
TAAATATAATTATTAAATTATAAAATATATAAATATGT
Found at i:1967041 original size:2 final size:2
Alignment explanation
Indices: 1967034--1967058 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1967024 AGTCTAATTC
1967034 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 A
1967059 AATAGATTCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1967923 original size:1 final size:1
Alignment explanation
Indices: 1967917--1967947 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1967907 ATTGCTGCTT
*
1967917 GGGGGGGGGGGGGGGGGGGGGAGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1967948 TTGCATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:1968712 original size:25 final size:23
Alignment explanation
Indices: 1968662--1968713 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
1968652 TTGACGTAAC
*
1968662 ATTTTTATATATTTTTATGTTAA
1 ATTTTTATATACTTTTATGTTAA
1968685 ATTTTTATATCGACTTTTA-GTTATA
1 ATTTTTATAT--ACTTTTATGTTA-A
1968710 ATTT
1 ATTT
1968714 CATGTAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
25 11 0.44
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (23 bp):
ATTTTTATATACTTTTATGTTAA
Found at i:1969878 original size:19 final size:18
Alignment explanation
Indices: 1969841--1969888 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1969831 TTGAACAGCG
*
1969841 TAAATATTGAATATTAATA
1 TAAATATT-TATATTAATA
*
1969860 TATATATTTATATTGAATA
1 TAAATATTTATATT-AATA
1969879 TAAATATTTA
1 TAAATATTTA
1969889 ACTTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
TAAATATTTATATTAATA
Found at i:1971754 original size:2 final size:2
Alignment explanation
Indices: 1971747--1971779 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1971737 GATCAGCAGC
1971747 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1971780 GAGGAATAAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1975158 original size:2 final size:2
Alignment explanation
Indices: 1975151--1975179 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1975141 CAAAAGCATA
1975151 AT 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 AT A
1975180 ATAGAATAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1990061 original size:21 final size:21
Alignment explanation
Indices: 1990032--1990095 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
1990022 TTTAATTTGA
*
1990032 ATTAATTTAAAATTTTATATT
1 ATTATTTTAAAATTTTATATT
* *
1990053 ATTATTTTATAAATTTAAAATT
1 ATTATTTTA-AAATTTTATATT
* *
1990075 ATTTATATTAAAA-GTTATATT
1 A-TTATTTTAAAATTTTATATT
1990096 TTTAATAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 13 0.38
22 14 0.41
23 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTATTTTAAAATTTTATATT
Found at i:1998899 original size:27 final size:26
Alignment explanation
Indices: 1998841--1998920 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 26
1998831 TTAAGTTAAT
* *
1998841 TAATA-TATTATT-TA-TTATAATAT
1 TAATATTATTATTATATTTAAAATAA
1998864 TAATATTA-TATTATATGTTAAAATTAA
1 TAATATTATTATTATAT-TTAAAA-TAA
* *
1998891 TAATTTTATTTATTATATTTAATATAA
1 TAATATTA-TTATTATATTTAAAATAA
1998918 TAA
1 TAA
1998921 ATATAAATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
23 9 0.20
24 4 0.09
26 5 0.11
27 15 0.33
28 5 0.11
29 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
TAATATTATTATTATATTTAAAATAA
Found at i:1999182 original size:23 final size:22
Alignment explanation
Indices: 1999144--1999186 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1999134 TATAAACATT
1999144 TATTATTTAATAATAAAAATAA
1 TATTATTTAATAATAAAAATAA
1999166 TATTATATTAA-ATATAAAAAT
1 TATTAT-TTAATA-ATAAAAAT
1999187 TAACAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTATTTAATAATAAAAATAA
Found at i:1999331 original size:23 final size:22
Alignment explanation
Indices: 1999295--1999363 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
1999285 TAATAAAATA
1999295 AATAATAA-TAAATAATTATT-T
1 AATAA-AATTAAATAATTATTAT
*
1999316 AATAAAAATTTAAATAA-AATTAT
1 AAT-AAAA-TTAAATAATTATTAT
* *
1999339 AATAAAATAAAATAATTATAAT
1 AATAAAATTAAATAATTATTAT
1999361 AAT
1 AAT
1999364 GATTTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 12 0.31
22 16 0.41
23 11 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAATTAAATAATTATTAT
Found at i:1999348 original size:16 final size:16
Alignment explanation
Indices: 1999327--1999396 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 16
1999317 ATAAAAATTT
1999327 AAATAAAATTATAATA
1 AAATAAAATTATAATA
1999343 AAATAAAATAATTATAATA
1 AAAT--AA-AATTATAATA
* **
1999362 ATGATTTAATT-TAATA
1 A-AATAAAATTATAATA
*
1999378 AAATAAAA-TATTATA
1 AAATAAAATTATAATA
1999393 AAAT
1 AAAT
1999397 TTAATTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
14 1 0.02
15 12 0.29
16 10 0.24
17 4 0.10
18 2 0.05
19 11 0.26
20 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
AAATAAAATTATAATA
Found at i:1999378 original size:30 final size:29
Alignment explanation
Indices: 1999281--1999403 Score: 99
Period size: 30 Copynumber: 4.2 Consensus size: 29
1999271 AAATTTTACG
* *
1999281 AATTTAATAAAATAAATAATAATAAATAATT
1 AATTTAATAAAAT-AATTATAAT-AATATTT
* *
1999312 -ATTTAATAAAA-ATTTA-AATAAAATTAT
1 AATTTAATAAAATAATTATAATAATATT-T
**
1999339 AATAAAATAAAATAATTATAATAATGATTT
1 AATTTAATAAAATAATTATAATAAT-ATTT
* * *
1999369 AATTTAATAAAATAAAATATTATAAAATTT
1 AATTTAATAAAAT-AATTATAATAATATTT
1999399 AATTT
1 AATTT
1999404 TTATTAAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
26 4 0.05
27 4 0.05
28 12 0.16
29 4 0.05
30 37 0.51
31 12 0.16
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
AATTTAATAAAATAATTATAATAATATTT
Found at i:1999391 original size:53 final size:53
Alignment explanation
Indices: 1999281--1999396 Score: 134
Period size: 53 Copynumber: 2.3 Consensus size: 53
1999271 AAATTTTACG
* *
1999281 AATT-TAATAAAATAAATAATAATAAATAATTATTTAATAAAAATTTAAATAA
1 AATTATAATAAAATAAATAATAATAAATAATGATTTAATAAAAATTAAAATAA
* **
1999333 AATTATAATAAAATAAAATAATTAT-AATAATGATTTAAT-TTAA-TAAAATAA
1 AATTATAATAAAAT-AAATAATAATAAATAATGATTTAATAAAAATTAAAATAA
*
1999384 AA-TATTATAAAAT
1 AATTATAATAAAAT
1999397 TTAATTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
50 10 0.18
51 9 0.16
52 6 0.11
53 22 0.39
54 9 0.16
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (53 bp):
AATTATAATAAAATAAATAATAATAAATAATGATTTAATAAAAATTAAAATAA
Found at i:1999421 original size:19 final size:19
Alignment explanation
Indices: 1999386--1999424 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1999376 TAAAATAAAA
1999386 TATTATAAAATTTAATTTT
1 TATTATAAAATTTAATTTT
1999405 TATTA-AAAATTTAAATTTT
1 TATTATAAAATTT-AATTTT
1999424 T
1 T
1999425 TAAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTATAAAATTTAATTTT
Found at i:1999427 original size:17 final size:18
Alignment explanation
Indices: 1999386--1999429 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1999376 TAAAATAAAA
*
1999386 TATTATAAAATTTAATTTT
1 TATTA-AAAATTTAAATTT
1999405 TATTAAAAATTTAAATTT
1 TATTAAAAATTTAAATTT
1999423 T-TTAAAA
1 TATTAAAA
1999430 TAATTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTAAAAATTTAAATTT
Found at i:1999434 original size:19 final size:18
Alignment explanation
Indices: 1999392--1999435 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1999382 AAAATATTAT
*
1999392 AAAATTTAATTTTTATTA
1 AAAATTTAATTTTTATAA
1999410 AAAATTTAAATTTTT-TAA
1 AAAATTT-AATTTTTATAA
1999428 AATAATTT
1 AA-AATTT
1999436 TATATTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAAATTTAATTTTTATAA
Found at i:1999492 original size:26 final size:27
Alignment explanation
Indices: 1999448--1999499 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
1999438 TATTTTTCAC
1999448 AATATAAAAATAATCATTTAATAAAAA
1 AATATAAAAATAATCATTTAATAAAAA
* * *
1999475 AATAT-AAATTAATTATTTTATAAAA
1 AATATAAAAATAATCATTTAATAAAA
1999500 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AATATAAAAATAATCATTTAATAAAAA
Found at i:1999515 original size:13 final size:12
Alignment explanation
Indices: 1999485--1999521 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1999475 AATATAAATT
1999485 AATTATTTTATA
1 AATTATTTTATA
1999497 AA--ATTTTAATA
1 AATTATTTT-ATA
1999508 AATTATTTTATA
1 AATTATTTTATA
1999520 AA
1 AA
1999522 ATAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 5 0.23
11 5 0.23
12 7 0.32
13 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATTATTTTATA
Found at i:1999529 original size:16 final size:16
Alignment explanation
Indices: 1999503--1999540 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
1999493 TATAAAATTT
1999503 TAATAAATTATTTTATAA
1 TAAT-AATTA-TTTATAA
1999521 -AATAATTATTTATAA
1 TAATAATTATTTATAA
1999536 TAATA
1 TAATA
1999541 TGCTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.37
16 9 0.47
17 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATAATTATTTATAA
Found at i:2011146 original size:15 final size:15
Alignment explanation
Indices: 2011126--2011160 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2011116 CGTGTTTGGT
2011126 AGGAAGGAAAGGGAA
1 AGGAAGGAAAGGGAA
*
2011141 AGGAAGGAAATGGAA
1 AGGAAGGAAAGGGAA
*
2011156 TGGAA
1 AGGAA
2011161 AGCTACTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.06
Consensus pattern (15 bp):
AGGAAGGAAAGGGAA
Found at i:2015124 original size:20 final size:22
Alignment explanation
Indices: 2015077--2015126 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
2015067 TATTTTATTA
*
2015077 TGATATAATTATATTAAAATAT
1 TGATATATTTATATTAAAATAT
*
2015099 T-TTATATTTATA-TAAAAT-T
1 TGATATATTTATATTAAAATAT
2015118 TGATATATT
1 TGATATATT
2015127 ATCGTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 9 0.38
22 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TGATATATTTATATTAAAATAT
Found at i:2015641 original size:11 final size:11
Alignment explanation
Indices: 2015625--2015649 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2015615 ATTTTATTAT
2015625 TTAAAATAATA
1 TTAAAATAATA
2015636 TTAAAATAATA
1 TTAAAATAATA
2015647 TTA
1 TTA
2015650 TTTATATTAA
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):
TTAAAATAATA
Found at i:2017253 original size:2 final size:2
Alignment explanation
Indices: 2017246--2017299 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
2017236 CAACTTCCTG
2017246 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
2017288 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
2017300 GATCAAGTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2018729 original size:2 final size:2
Alignment explanation
Indices: 2018722--2018756 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2018712 TATAGCGCTG
2018722 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2018757 GATCTGAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2019592 original size:2 final size:2
Alignment explanation
Indices: 2019585--2019614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2019575 GGAATTGCTA
2019585 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
2019615 TTCGCACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2021470 original size:2 final size:2
Alignment explanation
Indices: 2021463--2021491 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2021453 GTCCAAAATA
2021463 AT 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 AT A
2021492 GTATCAAGCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2025615 original size:21 final size:22
Alignment explanation
Indices: 2025589--2025631 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2025579 AATAATAATT
*
2025589 AAAATTTT-TAAATTTAAATAA
1 AAAATTTTAAAAATTTAAATAA
2025610 AAAATTTTAAAAATTTAAATAA
1 AAAATTTTAAAAATTTAAATAA
2025632 TAATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTTTAAAAATTTAAATAA
Found at i:2028330 original size:23 final size:24
Alignment explanation
Indices: 2028289--2028347 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2028279 TTGATAATAT
2028289 ATAATATATTATTAAT-AAATTAA
1 ATAATATATTATTAATAAAATTAA
*
2028312 ATAATATTATT-TTATTAAAATTAAA
1 ATAATA-TATTATTAATAAAATT-AA
*
2028337 ATTATATATTA
1 ATAATATATTA
2028348 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 10 0.33
24 13 0.43
25 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAATATATTATTAATAAAATTAA
Found at i:2028985 original size:28 final size:29
Alignment explanation
Indices: 2028954--2029022 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
2028944 TCATATATCT
* *
2028954 ATATTTTTATATTATA-ATAATATTTAAA
1 ATATTTATATATTATATATAAAATTTAAA
* * *
2028982 ATA-TCATATATTTTATATAAAATTTAAT
1 ATATTTATATATTATATATAAAATTTAAA
2029010 ATATTTATATATT
1 ATATTTATATATT
2029023 TTTATCTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 9 0.27
28 16 0.48
29 8 0.24
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
ATATTTATATATTATATATAAAATTTAAA
Found at i:2029002 original size:21 final size:22
Alignment explanation
Indices: 2028973--2029021 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2028963 TATTATAATA
* *
2028973 ATATTTAAAATATCATATATTT
1 ATATATAAAATATAATATATTT
*
2028995 -TATATAAAATTTAATATATTT
1 ATATATAAAATATAATATATTT
2029016 ATATAT
1 ATATAT
2029022 TTTTATCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATAAAATATAATATATTT
Found at i:2029497 original size:16 final size:16
Alignment explanation
Indices: 2029472--2029531 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
2029462 AGATTTATAT
* *
2029472 TATAAAAAAATTTAAA
1 TATAATAAAATATAAA
2029488 TATAATAAAATATAAA
1 TATAATAAAATATAAA
* *
2029504 AATAATATAATATAAA
1 TATAATAAAATATAAA
2029520 TA-AAT-AAATATA
1 TATAATAAAATATA
2029532 TTAAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 29 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TATAATAAAATATAAA
Found at i:2029498 original size:10 final size:10
Alignment explanation
Indices: 2029485--2029538 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
2029475 AAAAAAATTT
2029485 AAATATAATA
1 AAATATAATA
*
2029495 AAATATAAAA
1 AAATATAATA
2029505 ATAATATAATA
1 A-AATATAATA
2029516 TAAATA-AAT-
1 -AAATATAATA
*
2029525 AAATATATTA
1 AAATATAATA
2029535 AAAT
1 AAAT
2029539 TTATAACATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 5 0.14
9 2 0.05
10 17 0.46
11 12 0.32
12 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATAATA
Found at i:2029515 original size:26 final size:27
Alignment explanation
Indices: 2029472--2029523 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2029462 AGATTTATAT
*
2029472 TATAAAAAAATTTAAATAT-AATAAAA
1 TATAAAAAAATATAAATATAAATAAAA
2029498 TATAAAAATAATAT-AATATAAATAAA
1 TATAAAAA-AATATAAATATAAATAAA
2029524 TAAATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
TATAAAAAAATATAAATATAAATAAAA
Found at i:2029538 original size:18 final size:19
Alignment explanation
Indices: 2029484--2029538 Score: 51
Period size: 22 Copynumber: 2.8 Consensus size: 19
2029474 TAAAAAAATT
*
2029484 TAAATATAATAAAATATAA
1 TAAATATATTAAAATATAA
2029503 -AAATAATATAATATAAATA-AA
1 TAAAT-ATAT--TA-AAATATAA
2029524 TAAATATATTAAAAT
1 TAAATATATTAAAAT
2029539 TTATAACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 11
0.71 0.02 0.26
Matches are distributed among these distances:
18 8 0.27
19 5 0.17
21 8 0.27
22 9 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATATATTAAAATATAA
Found at i:2029576 original size:27 final size:31
Alignment explanation
Indices: 2029484--2029584 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
2029474 TAAAAAAATT
* *
2029484 TAAATATAATAAA-ATATAAAAATAATATAATA
1 TAAATA-AATAAATATATTAAAAT-TTATAATA
*
2029516 TAAATAAATAAATATATTAAAATTTATAACA
1 TAAATAAATAAATATATTAAAATTTATAATA
* *
2029547 TAAATAATTAACT-TATT-AAATTT-T-ATA
1 TAAATAAATAAATATATTAAAATTTATAATA
*
2029574 TAAATATATAA
1 TAAATAAATAA
2029585 TATTTTATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 11 0.18
28 1 0.02
29 6 0.10
30 4 0.07
31 23 0.38
32 15 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAATAAATAAATATATTAAAATTTATAATA
Found at i:2029904 original size:6 final size:6
Alignment explanation
Indices: 2029893--2029951 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
2029883 AAAATTTAAC
*
2029893 ATATTT ATATTT TTATGTT ATATTT AT-TTAT AACTATTT ATA-TT ATATTT
1 ATATTT ATATTT ATAT-TT ATATTT ATATT-T -A-TATTT ATATTT ATATTT
2029943 ATA-TT ATAT
1 ATATTT ATAT
2029952 AATATATTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
5 12 0.27
6 21 0.48
7 7 0.16
8 2 0.05
9 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:2031811 original size:19 final size:18
Alignment explanation
Indices: 2031787--2031824 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2031777 ATATTATATA
*
2031787 TTTTTTATATTTAAATTTT
1 TTTTTTAAATTT-AATTTT
2031806 TTTTTTAAATTTAATTTT
1 TTTTTTAAATTTAATTTT
2031824 T
1 T
2031825 AATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTAAATTTAATTTT
Found at i:2031812 original size:13 final size:15
Alignment explanation
Indices: 2031776--2031817 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
2031766 AAAGTTTACA
*
2031776 TATATTATATATTTTT
1 TATATT-TAAATTTTT
2031792 TATATTTAAATTTTT
1 TATATTTAAATTTTT
2031807 T-T-TTTAAATTT
1 TATATTTAAATTT
2031818 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 1 0.04
15 9 0.36
16 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATATTTAAATTTTT
Found at i:2031823 original size:13 final size:13
Alignment explanation
Indices: 2031796--2031838 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2031786 ATTTTTTATA
**
2031796 TTTAAATTTTTTT
1 TTTAAATTTAATT
2031809 TTTAAATTTAATT
1 TTTAAATTTAATT
2031822 TTTAATAATTTAATT
1 TTT-A-AATTTAATT
2031837 TT
1 TT
2031839 ATATCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 1 0.04
15 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTAAATTTAATT
Found at i:2034652 original size:7 final size:7
Alignment explanation
Indices: 2034630--2034670 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
2034620 TAATTAAATT
2034630 ATAAAAA
1 ATAAAAA
*
2034637 TATATAAA
1 -ATAAAAA
2034645 ATAAAAA
1 ATAAAAA
2034652 ATAAAAA
1 ATAAAAA
2034659 ATAAAAA
1 ATAAAAA
2034666 ATAAA
1 ATAAA
2034671 TATATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
ATAAAAA
Found at i:2034717 original size:18 final size:20
Alignment explanation
Indices: 2034688--2034729 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2034678 TTTAATATAA
*
2034688 AATTTAAATATTTT-TAATT
1 AATTTAAATATTTTAAAATT
2034707 AATTT-AATATTTTAAAATT
1 AATTTAAATATTTTAAAATT
2034726 AATT
1 AATT
2034730 ATGCATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTAAATATTTTAAAATT
Found at i:2034905 original size:8 final size:8
Alignment explanation
Indices: 2034884--2034930 Score: 58
Period size: 8 Copynumber: 5.5 Consensus size: 8
2034874 TTAACGTAAA
2034884 ATATTTTT
1 ATATTTTT
2034892 ATTATTTTT
1 A-TATTTTT
2034901 ATATTTTT
1 ATATTTTT
*
2034909 AAATTTTT
1 ATATTTTT
2034917 ATTATTTTAT
1 A-TATTTT-T
2034927 ATAT
1 ATAT
2034931 ACATTTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 16 0.47
9 16 0.47
10 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
ATATTTTT
Found at i:2036845 original size:17 final size:16
Alignment explanation
Indices: 2036819--2036875 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
2036809 TTATAATTTT
*
2036819 AAATACAATATTAAAAA
1 AAATATAATA-TAAAAA
2036836 AAATATAATATAAAATA
1 AAATATAATATAAAA-A
**
2036853 TGATA-AATATAAAAA
1 AAATATAATATAAAAA
*
2036868 ATATATAA
1 AAATATAA
2036876 ATATTACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 4 0.12
16 16 0.48
17 13 0.39
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATATAATATAAAAA
Found at i:2036876 original size:17 final size:17
Alignment explanation
Indices: 2036825--2036879 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
2036815 TTTTAAATAC
*
2036825 AATATTAAAAAAAATAT-
1 AATA-TAAAAAATATATA
2036842 AATAT--AAAATATGATA
1 AATATAAAAAATAT-ATA
2036858 AATATAAAAAATATATA
1 AATATAAAAAATATATA
2036875 AATAT
1 AATAT
2036880 TACATAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 6 0.18
17 12 0.36
18 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATATAAAAAATATATA
Found at i:2038979 original size:2 final size:2
Alignment explanation
Indices: 2038972--2039006 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2038962 AAACCTGTTA
2038972 AT AT AT AT 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 AT AT AT AT A
2039007 AAGCAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2042593 original size:65 final size:66
Alignment explanation
Indices: 2042471--2042606 Score: 186
Period size: 65 Copynumber: 2.0 Consensus size: 66
2042461 ATACATATAA
* *
2042471 TATACCTCATTCACGTGCTACATTTTTGTTTTTAACTATATTAAGCCTTCAATAATTGAAAAGAA
1 TATACCTCATTCACGTGCTACA---TTGTTTTTAACTATATAAAGCCTACAATAATTGAAAAGAA
2042536 ATAT
63 ATAT
* *
2042540 TATACGTCATTCACGTGCTACA-TGTCTTTT-ACTATATAAAGCCTACAATAATTGAAAATAAAT
1 TATACCTCATTCACGTGCTACATTGT-TTTTAACTATATAAAGCCTACAATAATTGAAAAGAAAT
2042603 AT
65 AT
2042605 TA
1 TA
2042607 AAACTTCATA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
65 37 0.60
66 4 0.06
69 21 0.34
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (66 bp):
TATACCTCATTCACGTGCTACATTGTTTTTAACTATATAAAGCCTACAATAATTGAAAAGAAATA
T
Found at i:2042641 original size:2 final size:2
Alignment explanation
Indices: 2042634--2042666 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2042624 CTTTTAATTA
2042634 AT AT AT 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 AT AT AT A
2042667 CTTTTCCTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2043185 original size:8 final size:8
Alignment explanation
Indices: 2043159--2043208 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
2043149 TATTATGCAC
*
2043159 ATTTATGA
1 ATTTATAA
2043167 ATTATATAA
1 ATT-TATAA
*
2043176 ATTCATAA
1 ATTTATAA
2043184 ATTTA-AA
1 ATTTATAA
2043191 TATTTATAA
1 -ATTTATAA
2043200 A-TTATAA
1 ATTTATAA
2043207 AT
1 AT
2043209 ATAAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
7 9 0.26
8 17 0.49
9 9 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (8 bp):
ATTTATAA
Found at i:2043209 original size:17 final size:17
Alignment explanation
Indices: 2043159--2043210 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2043149 TATTATGCAC
*
2043159 ATTTATGAATTATATAA-
1 ATTTATAAATTATA-AAT
*
2043176 ATTCATAAATT-TAAAT
1 ATTTATAAATTATAAAT
2043192 ATTTATAAATTATAAAT
1 ATTTATAAATTATAAAT
2043209 AT
1 AT
2043211 AAATTAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 12 0.40
17 16 0.53
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATTTATAAATTATAAAT
Found at i:2043239 original size:72 final size:73
Alignment explanation
Indices: 2043103--2043241 Score: 163
Period size: 72 Copynumber: 1.9 Consensus size: 73
2043093 TATTATGAAC
* * * * * *
2043103 ATTCATAAAGTTTGAATATTCATTAACTATAAATATACATAAATATTATTATGCACATTTATGAA
1 ATTCATAAAGTTTAAATATTCATAAACTATAAATATAAATAAATAGTATTAAGCACATTCATGAA
2043168 TTATATAA
66 TTATATAA
* * * * * *
2043176 ATTCATAAA-TTTAAATATTTATAAATTATAAATATAAATTAATGGTATTAAGTATATTCATGAA
1 ATTCATAAAGTTTAAATATTCATAAACTATAAATATAAATAAATAGTATTAAGCACATTCATGAA
2043240 TT
66 TT
2043242 CAAACTTTCA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
72 45 0.83
73 9 0.17
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (73 bp):
ATTCATAAAGTTTAAATATTCATAAACTATAAATATAAATAAATAGTATTAAGCACATTCATGAA
TTATATAA
Found at i:2043918 original size:2 final size:2
Alignment explanation
Indices: 2043911--2043944 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2043901 TCATTGTCAA
2043911 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
2043945 TATTTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2045545 original size:2 final size:2
Alignment explanation
Indices: 2045538--2045566 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2045528 ACCTTTTTAA
2045538 AT 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 AT A
2045567 ATTGATATCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2046723 original size:2 final size:2
Alignment explanation
Indices: 2046716--2046751 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2046706 CATCTTAAGA
2046716 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
2046752 TGAAGTAAAG
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:2048871 original size:3 final size:3
Alignment explanation
Indices: 2048863--2048895 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2048853 GAAGTAGAAC
2048863 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2048896 GATGCCCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2051848 original size:6 final size:6
Alignment explanation
Indices: 2051837--2052016 Score: 86
Period size: 6 Copynumber: 29.3 Consensus size: 6
2051827 TTTTAATTAT
** * **
2051837 TTTAAA TTTAAA TTTAGAA TCAAAA TTTAAA GTTTAAAA TTTGAA TCAAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA -TTT-AAA TTTAAA TTTAAA
*
2051888 TTT-AA TCTTAAA TTTAAA TTT--A TTTAAAA TTTAAA GTTTCAAA TTTATA
1 TTTAAA T-TTAAA TTTAAA TTTAAA TTT-AAA TTTAAA -TTT-AAA TTTAAA
* * * * *
2051937 -TTAAA TTT-AA -TTAAA TTTAACT TTTAAA GTTTGAT TTTGAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA -TTTAAA TTTAAA TTTAAA
** *
2051984 TAAAAA TTAAATTA TTTAAA TTTAAA -TTAAA TT
1 TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TT
2052017 CATTTATCTA
Statistics
Matches: 134, Mismatches: 22, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
4 6 0.04
5 16 0.12
6 69 0.51
7 32 0.24
8 11 0.08
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:2051864 original size:26 final size:25
Alignment explanation
Indices: 2051837--2051903 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 25
2051827 TTTTAATTAT
2051837 TTTAAATTTAAATTTAGAATCAAAA
1 TTTAAATTTAAATTTAGAATCAAAA
2051862 TTTAAAGTTTAAAATTT-GAATCAAAA
1 TTTAAA-TTT-AAATTTAGAATCAAAA
2051888 TTT-AATCTTAAATTTA
1 TTTAAAT-TTAAATTTA
2051904 AATTTATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
24 7 0.18
25 10 0.26
26 15 0.39
27 6 0.16
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (25 bp):
TTTAAATTTAAATTTAGAATCAAAA
Found at i:2051914 original size:10 final size:10
Alignment explanation
Indices: 2051899--2051955 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 10
2051889 TTAATCTTAA
2051899 ATTTAAATTT
1 ATTTAAATTT
2051909 ATTTAAAATTT
1 ATTT-AAATTT
2051920 AAAGTTTCAAATTT
1 --A-TTT-AAATTT
2051934 ATATTAAATTT
1 AT-TTAAATTT
*
2051945 AATTAAATTT
1 ATTTAAATTT
2051955 A
1 A
2051956 ACTTTTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 13 0.32
11 14 0.35
12 3 0.08
13 1 0.03
14 9 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:2051933 original size:25 final size:23
Alignment explanation
Indices: 2051895--2051955 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
2051885 AAATTTAATC
2051895 TTAAATTTAAATTTAT-TTAAAAT
1 TTAAATTTAAATTTATATT-AAAT
2051918 TTAAAGTTTCAAATTTATATTAAAT
1 TTAAA-TTT-AAATTTATATTAAAT
2051943 TT-AA-TTAAATTTA
1 TTAAATTTAAATTTA
2051956 ACTTTTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 7 0.20
22 2 0.06
23 5 0.14
24 5 0.14
25 14 0.40
26 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAAATTTAAATTTATATTAAAT
Found at i:2051955 original size:42 final size:43
Alignment explanation
Indices: 2051885--2051968 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
2051875 ATTTGAATCA
* *
2051885 AAATTTAATCTTAAATTTAAATTTATTTAAAATTTAAAGTTTC
1 AAATTTAATATTAAATTTAAATTAATTTAAAATTTAAAGTTTC
**
2051928 AAATTT-ATATTAAATTT-AATTAAATTTAACTTTTAAAGTTT
1 AAATTTAATATTAAATTTAAATT-AATTTAAAATTTAAAGTTT
2051969 GATTTTGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 4 0.11
42 26 0.72
43 6 0.17
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (43 bp):
AAATTTAATATTAAATTTAAATTAATTTAAAATTTAAAGTTTC
Found at i:2052003 original size:20 final size:21
Alignment explanation
Indices: 2051978--2052041 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 21
2051968 TGATTTTGAT
2051978 TTTAAATAAAAATTAAATT-A
1 TTTAAATAAAAATTAAATTCA
**
2051998 TTTAAATTTAAATTAAATTCA
1 TTTAAATAAAAATTAAATTCA
2052019 TTTATCTAATAAAAAATTAAATT
1 TTTA---AAT-AAAAATTAAATT
2052042 TAATTTTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 17 0.49
21 5 0.14
24 3 0.09
25 10 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAAATAAAAATTAAATTCA
Found at i:2052148 original size:21 final size:23
Alignment explanation
Indices: 2052092--2052148 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
2052082 TAAAAATCGA
2052092 ATTTAAATTAAAC-TTATAAACT
1 ATTTAAATTAAACGTTATAAACT
*
2052114 ATTTAAATCAAACGTTA-AAA-T
1 ATTTAAATTAAACGTTATAAACT
*
2052135 ATTTAAATTTAACG
1 ATTTAAATTAAACG
2052149 CATTTAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.42
22 15 0.48
23 3 0.10
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (23 bp):
ATTTAAATTAAACGTTATAAACT
Found at i:2052469 original size:2 final size:2
Alignment explanation
Indices: 2052464--2052488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2052454 ATGATATAGT
2052464 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
2052489 TCACACACAA
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:2056158 original size:87 final size:87
Alignment explanation
Indices: 2056012--2056188 Score: 309
Period size: 87 Copynumber: 2.0 Consensus size: 87
2056002 AGTTGACTGC
***
2056012 ATCAATCCTCAGAGTTCTTTGTGTTCCTTCCAAGGAATGCTTATATAACCAGATCAAGTTAATAA
1 ATCAATCCTCAGAGTTCTCCATGTTCCTTCCAAGGAATGCTTATATAACCAGATCAAGTTAATAA
2056077 AACTGAATGCTCCAAAAAATTA
66 AACTGAATGCTCCAAAAAATTA
2056099 ATCAATCCTCAGAGTTCTCCATGTTCCTTCCAAGGAATGCTTATATAACCAGATCAAGTTAATAA
1 ATCAATCCTCAGAGTTCTCCATGTTCCTTCCAAGGAATGCTTATATAACCAGATCAAGTTAATAA
* *
2056164 AATTGGATGCTCCAAAAAATTA
66 AACTGAATGCTCCAAAAAATTA
2056186 ATC
1 ATC
2056189 TTCAAAATGC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (87 bp):
ATCAATCCTCAGAGTTCTCCATGTTCCTTCCAAGGAATGCTTATATAACCAGATCAAGTTAATAA
AACTGAATGCTCCAAAAAATTA
Found at i:2063246 original size:15 final size:15
Alignment explanation
Indices: 2063226--2063255 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2063216 AAAAGTTGGC
*
2063226 GGTGGTGGAGGTGGA
1 GGTGGTGGAAGTGGA
2063241 GGTGGTGGAAGTGGA
1 GGTGGTGGAAGTGGA
2063256 AGTAGCGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.63, T:0.20
Consensus pattern (15 bp):
GGTGGTGGAAGTGGA
Found at i:2064038 original size:20 final size:20
Alignment explanation
Indices: 2063969--2064041 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
2063959 TTATATTATT
*
2063969 TTTATATTATA-ATT-ATAT
1 TTTATATTATATATTAATAA
*
2063987 TTAATATATTAAATATTTATATAA
1 TT--TATATTATATA-TTA-ATAA
*
2064011 ATT-T-TTATATATTAATAA
1 TTTATATTATATATTAATAA
2064029 TTTATATTATATA
1 TTTATATTATATA
2064042 AATTTTTACA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
18 8 0.19
19 4 0.10
20 21 0.50
21 2 0.05
22 3 0.07
24 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATATTATATATTAATAA
Found at i:2064041 original size:32 final size:35
Alignment explanation
Indices: 2063981--2064055 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 35
2063971 TATATTATAA
2063981 TTATAT-TTAATATATTAAATATTTATATAAATTT
1 TTATATATTAATATATTAAATATTTATATAAATTT
*
2064015 TTATATATTAATA-ATT-TATA-TTATATAAATTT
1 TTATATATTAATATATTAAATATTTATATAAATTT
*
2064047 TTACATATT
1 TTATATATT
2064056 TTTATCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 20 0.53
33 3 0.08
34 9 0.24
35 6 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (35 bp):
TTATATATTAATATATTAAATATTTATATAAATTT
Found at i:2064044 original size:44 final size:44
Alignment explanation
Indices: 2063958--2064060 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
2063948 TTATATTGTG
*
2063958 TTTATATTATTTTTATATTATAATTATATTTAATATATTAAATA
1 TTTATATAATTTTTATATTATAATTATATTTAATATATTAAATA
*
2064002 TTTATATAAATTTTTATA-TATTAA-TA-ATTT-ATATTATATAAATT
1 TTTATAT-AATTTTTATATTA-TAATTATATTTAATA-TAT-TAAATA
*
2064046 TTTACAT-ATTTTTAT
1 TTTATATAATTTTTAT
2064061 CTATATTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
42 11 0.21
43 7 0.13
44 22 0.42
45 12 0.23
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (44 bp):
TTTATATAATTTTTATATTATAATTATATTTAATATATTAAATA
Found at i:2064333 original size:93 final size:94
Alignment explanation
Indices: 2064229--2064416 Score: 297
Period size: 93 Copynumber: 2.0 Consensus size: 94
2064219 ATCTATTATT
* *
2064229 TACTATATAACTAATTTGAACTACATAAGATGTTAAGGGATTGATACTTGTTAA-TTTTTTTTAT
1 TACTATATAACTAATTTGAACTACATAAGATGTTAAGGGATTGACACCTGTTAATTTTTTTTTAT
*
2064293 TCAGCTGAAAAATGAAAGAAAGAAAAATA
66 TCAACTGAAAAATGAAAGAAAGAAAAATA
* * *
2064322 TACTATGTAACTAATTTGAATTACATAAGATGTTAAGGGATTGACACCTGTTAATTTTTTTTTTG
1 TACTATATAACTAATTTGAACTACATAAGATGTTAAGGGATTGACACCTGTTAA-TTTTTTTTTA
*
2064387 TTCAACTGAAAATTGAAAGAAAGAAAAATA
65 TTCAACTGAAAAATGAAAGAAAGAAAAATA
2064417 AAAAAAGAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
93 50 0.58
95 36 0.42
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (94 bp):
TACTATATAACTAATTTGAACTACATAAGATGTTAAGGGATTGACACCTGTTAATTTTTTTTTAT
TCAACTGAAAAATGAAAGAAAGAAAAATA
Found at i:2064533 original size:23 final size:23
Alignment explanation
Indices: 2064457--2064597 Score: 93
Period size: 23 Copynumber: 6.1 Consensus size: 23
2064447 TTTATTATTT
*
2064457 TTTATATTTA--AAATATATATA
1 TTTATATTTATTATATATATATA
2064478 TTTATATATT-TTATATAT-TAATAA
1 TTTATAT-TTATTATATATAT-AT-A
*
2064502 TTCAT-TTTATTATATATATATA
1 TTTATATTTATTATATATATATA
2064524 TTTATATTTATTAT-TAT-TATTA
1 TTTATATTTATTATATATATA-TA
* *
2064546 TTGT-TCTTTATTATCTATTTATCTATA
1 TT-TATATTTATTA--TA--TATATATA
2064573 TTTATATTTATTAT-TATTATATA
1 TTTATATTTATTATATA-TATATA
2064596 TT
1 TT
2064598 ATCTATCTAT
Statistics
Matches: 96, Mismatches: 6, Indels: 34
0.71 0.04 0.25
Matches are distributed among these distances:
21 9 0.09
22 27 0.28
23 34 0.35
24 7 0.07
25 1 0.01
26 1 0.01
27 15 0.16
28 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (23 bp):
TTTATATTTATTATATATATATA
Found at i:2064598 original size:40 final size:40
Alignment explanation
Indices: 2064540--2064617 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
2064530 TTTATTATTA
* * * * *
2064540 TTATTATTGTTCTTTATTATCTATTTATCTATATTTATAT
1 TTATTATTATTATATATTATCTATCTATCTATACTTATAT
2064580 TTATTATTATTATATATTATCTATCTATCTATACTTAT
1 TTATTATTATTATATATTATCTATCTATCTATACTTAT
2064618 CGTGTATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (40 bp):
TTATTATTATTATATATTATCTATCTATCTATACTTATAT
Found at i:2064599 original size:16 final size:16
Alignment explanation
Indices: 2064479--2064599 Score: 73
Period size: 16 Copynumber: 7.7 Consensus size: 16
2064469 ATATATATAT
2064479 TTATATATT-TTATATA
1 TTATATATTATTAT-TA
2064495 TTA-ATAATTCATT-TTA
1 TTATAT-ATT-ATTATTA
2064511 TTATATA-TA-TA-TA
1 TTATATATTATTATTA
2064524 TT-TATATTTATTATTA
1 TTATATA-TTATTATTA
* *
2064540 TTAT-TATTGTTCTTTA
1 TTATATATTATT-ATTA
*
2064556 TTATCTATTTATCTA-TA
1 TTATATA-TTAT-TATTA
2064573 TT-TATATTTATTATTA
1 TTATATA-TTATTATTA
2064589 TTATATATTAT
1 TTATATATTAT
2064600 CTATCTATCT
Statistics
Matches: 84, Mismatches: 5, Indels: 32
0.69 0.04 0.26
Matches are distributed among these distances:
12 4 0.05
13 5 0.06
14 3 0.04
15 11 0.13
16 41 0.49
17 14 0.17
18 5 0.06
19 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (16 bp):
TTATATATTATTATTA
Found at i:2064815 original size:25 final size:25
Alignment explanation
Indices: 2064775--2064832 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2064765 CACACGAAAA
2064775 AAAATTATTAATAAATAA-TATTTT
1 AAAATTATTAATAAATAATTATTTT
2064799 AAAATT-TTAATTAAAATAATTA-TTT
1 AAAATTATTAA-T-AAATAATTATTTT
*
2064824 ATAATTATT
1 AAAATTATT
2064833 TATTATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 4 0.14
24 7 0.24
25 14 0.48
26 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAATTATTAATAAATAATTATTTT
Found at i:2064837 original size:26 final size:25
Alignment explanation
Indices: 2064775--2064823 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
2064765 CACACGAAAA
2064775 AAAATTATTAA-T-AAATAATATTTT
1 AAAATT-TTAATTAAAATAATATTTT
2064799 AAAATTTTAATTAAAATAATTATTT
1 AAAATTTTAATTAAAATAA-TATTT
2064824 ATAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 7 0.32
25 6 0.27
26 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAAATTTTAATTAAAATAATATTTT
Found at i:2065037 original size:2 final size:2
Alignment explanation
Indices: 2065030--2065060 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2065020 CGTATAAATT
2065030 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
2065061 GCAAAAGGAG
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:2065819 original size:23 final size:22
Alignment explanation
Indices: 2065789--2065847 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
2065779 AAAAATTTTA
2065789 TATTTTTATGTTTATGTTATATT
1 TATTTTTATGTTTATGTTA-ATT
* *
2065812 TATTTTTATATTTTATTTTAATT
1 TATTTTTAT-GTTTATGTTAATT
*
2065835 AATTTTTAATGTT
1 TATTTTT-ATGTT
2065848 ATAAGCGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TATTTTTATGTTTATGTTAATT
Found at i:2065827 original size:19 final size:20
Alignment explanation
Indices: 2065783--2065831 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
2065773 TTTATAAAAA
2065783 ATTTTATATTT-TTATGTTT
1 ATTTTATATTTATTATGTTT
*
2065802 ATGTTATATTTATT-T-TTAT
1 ATTTTATATTTATTATGTT-T
2065821 ATTTTAT-TTTA
1 ATTTTATATTTA
2065832 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 6 0.23
19 18 0.69
20 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
ATTTTATATTTATTATGTTT
Found at i:2066791 original size:26 final size:27
Alignment explanation
Indices: 2066734--2066793 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
2066724 ATAATTATTT
*
2066734 AATA-TAATTTAATTTAAATTTATATG
1 AATATTAATTTAATTTAAATTTATATA
*
2066760 ATTATTAATTTAA-TTAAATGTT-TATA
1 AATATTAATTTAATTTAAAT-TTATATA
2066786 AATATTAA
1 AATATTAA
2066794 AAATCTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (27 bp):
AATATTAATTTAATTTAAATTTATATA
Found at i:2066952 original size:14 final size:13
Alignment explanation
Indices: 2066927--2066980 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
2066917 AAAAACTTCA
2066927 TATTTTTT-ATTT
1 TATTTTTTAATTT
2066939 GTATTTTTTAATTTT
1 -TATTTTTTAA-TTT
*
2066954 TAATTTTTAATTT
1 TATTTTTTAATTT
2066967 TA-TTTTTAATTT
1 TATTTTTTAATTT
2066979 TA
1 TA
2066981 AATTATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
12 12 0.32
13 13 0.34
14 10 0.26
15 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TATTTTTTAATTT
Found at i:2066954 original size:8 final size:7
Alignment explanation
Indices: 2066928--2066984 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
2066918 AAAACTTCAT
*
2066928 ATTTTTT
1 ATTTTTA
*
2066935 ATTTGTA
1 ATTTTTA
*
2066942 TTTTTTA
1 ATTTTTA
2066949 ATTTTTA
1 ATTTTTA
2066956 ATTTTTA
1 ATTTTTA
2066963 A-TTTT-
1 ATTTTTA
2066968 ATTTTTA
1 ATTTTTA
*
2066975 ATTTTAA
1 ATTTTTA
2066982 ATT
1 ATT
2066985 ATATATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
5 1 0.02
6 8 0.19
7 33 0.79
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:2066971 original size:19 final size:19
Alignment explanation
Indices: 2066944--2067001 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2066934 TATTTGTATT
*
2066944 TTTTAATTTTTAATTTTTAA
1 TTTT-ATTTTTAATTTTAAA
2066964 TTTTATTTTTAATTTTAAA
1 TTTTATTTTTAATTTTAAA
* *
2066983 TTATATATTTTAATGTTAA
1 TTTTAT-TTTTAATTTTAA
2067002 TTTGCATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATTTTTAATTTTAAA
Found at i:2066992 original size:26 final size:25
Alignment explanation
Indices: 2066934--2067004 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
2066924 TCATATTTTT
* *
2066934 TATTTGTATTTTTTAATTTTTAATTTT
1 TATTT-TA-TTTTTAATTTTAAATTTA
2066961 TAATTTTATTTTTAATTTTAAATTATA
1 T-ATTTTATTTTTAATTTTAAATT-TA
* *
2066988 TATTTTAATGTTAATTT
1 TATTTTATTTTTAATTT
2067005 GCATTGTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 29 0.76
27 5 0.13
28 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (25 bp):
TATTTTATTTTTAATTTTAAATTTA
Found at i:2067109 original size:6 final size:6
Alignment explanation
Indices: 2067074--2067124 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
2067064 TTTTTCTGTC
*
2067074 TTTTATA TTTTAA ATTTAGA TTTTAA TTTTAA TTTTTTAA TTTT-A TTTTAA
1 TTTTA-A TTTTAA TTTTA-A TTTTAA TTTTAA --TTTTAA TTTTAA TTTTAA
2067125 AATAATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 5 0.13
6 17 0.45
7 10 0.26
8 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:2067113 original size:14 final size:13
Alignment explanation
Indices: 2067074--2067122 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2067064 TTTTTCTGTC
*
2067074 TTTTATATTTTAA
1 TTTTATTTTTTAA
* **
2067087 ATTTAGATTTTAA
1 TTTTATTTTTTAA
2067100 TTTTAATTTTTTAA
1 TTTT-ATTTTTTAA
2067114 TTTTATTTT
1 TTTTATTTT
2067123 AAAATAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTTAA
Found at i:2067367 original size:18 final size:18
Alignment explanation
Indices: 2067339--2067374 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2067329 ATTTTAAATT
2067339 TTTTATATTTAAGTTTTTA
1 TTTTATATTTAA-TTTTTA
2067358 TTTT-TATTTAATTTTTA
1 TTTTATATTTAATTTTTA
2067375 AATGGTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTATATTTAATTTTTA
Found at i:2077691 original size:27 final size:28
Alignment explanation
Indices: 2077657--2077724 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
2077647 AATTTTTAAA
*
2077657 ATTTTAAAATTGATTAAATTAAGTAA-T
1 ATTTTAAAATTAATTAAATTAAGTAATT
* *
2077684 ATTTTAAAATTAATTAATTTAATTAATT
1 ATTTTAAAATTAATTAAATTAAGTAATT
*
2077712 TTTTTAAAATTAA
1 ATTTTAAAATTAA
2077725 ATTTAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
ATTTTAAAATTAATTAAATTAAGTAATT
Found at i:2077872 original size:27 final size:28
Alignment explanation
Indices: 2077841--2077894 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
2077831 ATTATTTACA
2077841 TATTTAAATTATTA-AT-AAATATAATTT
1 TATTTAAATTA-TACATAAAATATAATTT
*
2077868 TATTTATATTATACATAAAATATAATT
1 TATTTAAATTATACATAAAATATAATT
2077895 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 12 0.50
28 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTTAAATTATACATAAAATATAATTT
Found at i:2077980 original size:18 final size:17
Alignment explanation
Indices: 2077959--2077997 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2077949 TAAATTTGTC
2077959 AAATAAATTAATTTTTAA
1 AAATAAATTAA-TTTTAA
* *
2077977 AAATTAATTTATTTTAA
1 AAATAAATTAATTTTAA
2077994 AAAT
1 AAAT
2077998 GGAGTAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATAAATTAATTTTAA
Found at i:2082041 original size:3 final size:3
Alignment explanation
Indices: 2082033--2082064 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2082023 AAATTGCACA
2082033 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2082065 AAGAACAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2082918 original size:3 final size:3
Alignment explanation
Indices: 2082906--2082951 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
2082896 ATAATATATT
*
2082906 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2082952 CATGTGCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2083053 original size:21 final size:21
Alignment explanation
Indices: 2083008--2083052 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2082998 CTCACGACCC
**
2083008 AAAACAAGACATCTTTCATTA
1 AAAACAAGACATCTCCCATTA
2083029 AAAACAAGACATC-CCCATTA
1 AAAACAAGACATCTCCCATTA
2083049 AAAA
1 AAAA
2083053 AGAAATCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.53, C:0.22, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAACAAGACATCTCCCATTA
Found at i:2084012 original size:16 final size:16
Alignment explanation
Indices: 2083982--2084058 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
2083972 ATCACTTTTG
**
2083982 ATTTAAATTGCTTTAA
1 ATTTAAATTATTTTAA
*
2083998 ATTTAAATTATTTTAGTTTTG
1 ATTTAAATTATTTTA-----A
2084019 ATTTAAATTATTTTAA
1 ATTTAAATTATTTTAA
*
2084035 ATTTAAATTAATTT-A
1 ATTTAAATTATTTTAA
*
2084050 TTTTAAATT
1 ATTTAAATT
2084059 TAAATCAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 9 0.18
16 26 0.52
21 15 0.30
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:2084027 original size:37 final size:36
Alignment explanation
Indices: 2083977--2084063 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
2083967 TTTAAATCAC
* *
2083977 TTTTGATTTAAATTGCTTTAAATTTAAATTATTTTA
1 TTTTGATTTAAATTACTTTAAATTTAAATTAATTTA
*
2084013 GTTTTGATTTAAATTATTTTAAATTTAAATTAATTTA
1 -TTTTGATTTAAATTACTTTAAATTTAAATTAATTTA
*
2084050 TTTTAAATTTAAAT
1 TTTT-GATTTAAAT
2084064 CAATTAAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 4 0.09
37 41 0.91
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (36 bp):
TTTTGATTTAAATTACTTTAAATTTAAATTAATTTA
Found at i:2084045 original size:21 final size:21
Alignment explanation
Indices: 2083993--2084063 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
2083983 TTTAAATTGC
**
2083993 TTTAAATTTAAATTATTTTAGT
1 TTTAAA-TTAAATTATTTTAAA
* *
2084015 TTTGATTTAAATTATTTTAAA
1 TTTAAATTAAATTATTTTAAA
*
2084036 TTTAAATTAATTTATTTTAAA
1 TTTAAATTAAATTATTTTAAA
2084057 TTTAAAT
1 TTTAAAT
2084064 CAATTAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 38 0.90
22 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTAAATTAAATTATTTTAAA
Found at i:2084068 original size:21 final size:21
Alignment explanation
Indices: 2084026--2084068 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2084016 TTGATTTAAA
*
2084026 TTATTTTAAATTTAAATTAAT
1 TTATTTTAAATTTAAATCAAT
2084047 TTATTTTAAATTTAAATCAAT
1 TTATTTTAAATTTAAATCAAT
2084068 T
1 T
2084069 AAGTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTTTAAATTTAAATCAAT
Found at i:2084075 original size:21 final size:21
Alignment explanation
Indices: 2084030--2084107 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
2084020 TTTAAATTAT
* * *
2084030 TTTAAATTTAAATTAATTTAT
1 TTTAAATTTAAATCAATTAAA
*
2084051 TTTAAATTTAAATCAATTAAG
1 TTTAAATTTAAATCAATTAAA
* *
2084072 TTT-AATATAAAGATCAAATAAA
1 TTTAAAT-TTAA-ATCAATTAAA
2084094 TTTAATATTTAAAT
1 TTTAA-ATTTAAAT
2084108 TTATCAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
20 3 0.07
21 24 0.52
22 13 0.28
23 4 0.09
24 2 0.04
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTAAATTTAAATCAATTAAA
Found at i:2084209 original size:28 final size:29
Alignment explanation
Indices: 2084174--2084230 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
2084164 TTGATAAAAG
2084174 TTTAAATTTAAA-T-AAATTAATCAAATTT
1 TTTAAATTTAAATTAAAATTAAT-AAATTT
2084202 TTTAAATTTAAATTAAAATTAATAAATTT
1 TTTAAATTTAAATTAAAATTAATAAATTT
2084231 ACTTTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 12 0.44
29 7 0.26
30 8 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAAATTTAAATTAAAATTAATAAATTT
Found at i:2084245 original size:29 final size:29
Alignment explanation
Indices: 2084174--2084250 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
2084164 TTGATAAAAG
*
2084174 TTTAAATTTAAAT-AAATTAATCAAATTT
1 TTTAAATTTAATTAAAATTAATCAAATTT
2084202 TTTAAATTTAAATTAAAATTAAT-AAATTT
1 TTTAAATTT-AATTAAAATTAATCAAATTT
*
2084231 ACTTTCAATTT-ATTAAAATT
1 --TTTAAATTTAATTAAAATT
2084251 TATTTTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 9 0.21
29 18 0.42
30 8 0.19
31 8 0.19
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTAAATTTAATTAAAATTAATCAAATTT
Found at i:2093888 original size:19 final size:18
Alignment explanation
Indices: 2093840--2093890 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
2093830 TATACATTAT
2093840 TTTTTAAA-ATATAAATA
1 TTTTTAAATATATAAATA
* * *
2093857 TATTAAAATTATATAATTTA
1 TTTTTAAA-TATATAA-ATA
2093877 TTTTTAAATATATA
1 TTTTTAAATATATA
2093891 TGATATACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTAAATATATAAATA
Found at i:2103805 original size:17 final size:17
Alignment explanation
Indices: 2103780--2103815 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2103770 AAAAATAAAT
* *
2103780 TTATTTTATTTATTATA
1 TTATATTATATATTATA
2103797 TTATATTATATATTATA
1 TTATATTATATATTATA
2103814 TT
1 TT
2103816 TTAATCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTATATATTATA
Found at i:2103841 original size:25 final size:25
Alignment explanation
Indices: 2103802--2103874 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 25
2103792 TTATATTATA
2103802 TTATA-TATTATATTTTAATCAA-ATT
1 TTATATTATTA-ATTTTAAT-AATATT
2103827 TTATATTATTAATTTT-ATAATATT
1 TTATATTATTAATTTTAATAATATT
* * *
2103851 TAAAATTATTAAATTTAATAATAT
1 TTATATTATTAATTTTAATAATAT
2103875 ATATTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.05
24 18 0.43
25 17 0.40
26 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
TTATATTATTAATTTTAATAATATT
Found at i:2106462 original size:28 final size:28
Alignment explanation
Indices: 2106417--2106486 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
2106407 TCTCACAATT
*
2106417 TATTTGTATAAA-TATAAATAAAAATTAA
1 TATTT-TATAAATTTTAAATAAAAATTAA
** *
2106445 TATTTTATAAATTTTAAATTTAAATTAT
1 TATTTTATAAATTTTAAATAAAAATTAA
*
2106473 TA-TTTATAATTTTT
1 TATTTTATAAATTTT
2106487 TATTATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TATTTTATAAATTTTAAATAAAAATTAA
Found at i:2106742 original size:28 final size:26
Alignment explanation
Indices: 2106709--2106760 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
2106699 TATATATATT
2106709 TAAATTTTATAAAAATAATTAATTAACA
1 TAAATTTTATAAAAA-AATT-ATTAACA
* *
2106737 TAAATTTTTTTAAAAAATTATTAA
1 TAAATTTTATAAAAAAATTATTAA
2106761 ATATTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 4 0.18
28 13 0.59
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAATTTTATAAAAAAATTATTAACA
Done.