Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 21
Found at i:1863651 original size:2 final size:2
Alignment explanation
Indices: 1863644--1863674 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1863634 TTTTTAAAAC
1863644 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 A
1863675 CCCCCATCCC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1863866 original size:24 final size:24
Alignment explanation
Indices: 1863839--1863938 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
1863829 GATATCAAAA
*
1863839 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1863863 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
** *
1863887 ATCGGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1863911 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1863935 ATCA
1 ATCA
1863939 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1866438 original size:12 final size:12
Alignment explanation
Indices: 1866421--1866445 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1866411 CTCCGGTCAA
1866421 CGGTCAACGGGT
1 CGGTCAACGGGT
1866433 CGGTCAACGGGT
1 CGGTCAACGGGT
1866445 C
1 C
1866446 AACGGGTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.40, T:0.16
Consensus pattern (12 bp):
CGGTCAACGGGT
Found at i:1866447 original size:20 final size:19
Alignment explanation
Indices: 1866414--1866455 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
1866404 TGGTCAACTC
1866414 CGGTCAACGGTCAACGGGT
1 CGGTCAACGGTCAACGGGT
1866433 CGGTCAACGGGTCAACGGGT
1 CGGTCAAC-GGTCAACGGGT
1866453 CGG
1 CGG
1866456 GTCGGGTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.14
Consensus pattern (19 bp):
CGGTCAACGGTCAACGGGT
Found at i:1866458 original size:13 final size:13
Alignment explanation
Indices: 1866440--1866499 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
1866430 GGTCGGTCAA
1866440 CGGGTCAACGGGT
1 CGGGTCAACGGGT
**
1866453 CGGGTCGGGTCGGGT
1 CGGGTC--AACGGGT
1866468 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
1866481 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
1866494 TGGGTC
1 CGGGTC
1866500 GGGTCAACGG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 27 0.71
15 11 0.29
ACGTcount: A:0.12, C:0.20, G:0.50, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1866485 original size:5 final size:5
Alignment explanation
Indices: 1866448--1866473 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1866438 AACGGGTCAA
1866448 CGGGT CGGGT CGGGT CGGGT CGGGT C
1 CGGGT CGGGT CGGGT CGGGT CGGGT C
1866474 AACGGGTCGG
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:0.00, C:0.23, G:0.58, T:0.19
Consensus pattern (5 bp):
CGGGT
Found at i:1866518 original size:30 final size:31
Alignment explanation
Indices: 1866440--1866545 Score: 159
Period size: 30 Copynumber: 3.6 Consensus size: 31
1866430 GGTCGGTCAA
*
1866440 CGGGTCAACGGGTCGGGT---CGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTTGGGT
1866468 CGGGTCAACGGGTCGGGTAAACGGGTTGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTTGGGT
*
1866499 CGGGTCAACGGG-GGGGTAAACGGGTTGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTTGGGT
1866529 CGGGT-AACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1866546 CGGGTTGTGA
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
28 18 0.25
29 6 0.08
30 26 0.37
31 21 0.30
ACGTcount: A:0.13, C:0.17, G:0.52, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTTGGGT
Found at i:1868680 original size:24 final size:24
Alignment explanation
Indices: 1868653--1868752 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
1868643 GATATCAAAA
*
1868653 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1868677 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
** *
1868701 ATCGGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1868725 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1868749 ATCA
1 ATCA
1868753 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1871203 original size:7 final size:7
Alignment explanation
Indices: 1871191--1871230 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
1871181 TGGTCAACTC
1871191 CGGTCAA
1 CGGTCAA
1871198 CGGTCAA
1 CGGTCAA
1871205 CGGGTCAA
1 C-GGTCAA
1871213 CGGTCAA
1 CGGTCAA
1871220 CGGGTCAA
1 C-GGTCAA
1871228 CGG
1 CGG
1871231 GTCGGGTCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1871212 original size:15 final size:15
Alignment explanation
Indices: 1871192--1871230 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1871182 GGTCAACTCC
1871192 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1871207 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1871222 GGTCAACGG
1 GGTCAACGG
1871231 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1871238 original size:13 final size:13
Alignment explanation
Indices: 1871233--1871288 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 13
1871223 GTCAACGGGT
1871233 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
1871246 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
1871259 CGGGTTGGGTCGGGTCAA
1 C-----GGGTCGGGTCAA
1871277 CGGGTCGGGTCA
1 CGGGTCGGGTCA
1871289 GGTTGTGACC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 24 0.67
18 12 0.33
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1871243 original size:18 final size:18
Alignment explanation
Indices: 1871220--1871287 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 18
1871210 CAACGGTCAA
1871220 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1871238 CGGGTCAA-----CGGGT
1 CGGGTCAACGGGTCGGGT
* *
1871251 CGGGTAAACGGGTTGGGT
1 CGGGTCAACGGGTCGGGT
1871269 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
1871287 C
1 C
1871288 AGGTTGTGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 12 0.29
18 29 0.71
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:1871251 original size:8 final size:8
Alignment explanation
Indices: 1871192--1871233 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
1871182 GGTCAACTCC
1871192 GGTCAAC-
1 GGTCAACG
1871199 GGTCAACG
1 GGTCAACG
1871207 GGTCAAC-
1 GGTCAACG
1871214 GGTCAACG
1 GGTCAACG
1871222 GGTCAACG
1 GGTCAACG
1871230 GGTC
1 GGTC
1871234 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:1871261 original size:31 final size:31
Alignment explanation
Indices: 1871220--1871286 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
1871210 CAACGGTCAA
*
1871220 CGGGTCAACGGGTCGGGTCGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
*
1871251 CGGGTAAACGGGTTGGGTCGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
1871282 CGGGT
1 CGGGT
1871287 CAGGTTGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.18
Consensus pattern (31 bp):
CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
Found at i:1874910 original size:18 final size:18
Alignment explanation
Indices: 1874874--1874912 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1874864 TTTCATCAAA
*
1874874 CATTATTTAAAAATCTTT
1 CATTATTTAAAAATATTT
*
1874892 CATTATTTAAAATTATTT
1 CATTATTTAAAAATATTT
1874910 CAT
1 CAT
1874913 AAAAGCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
CATTATTTAAAAATATTT
Found at i:1876810 original size:28 final size:28
Alignment explanation
Indices: 1876757--1876811 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1876747 TTCAAAGCAA
* * *
1876757 TCTCTCTTGAGATAAAGATCATTTTCAT
1 TCTCTCTTGAAACAAAGATCAATTTCAT
1876785 TCTCTCTTGAAACAAA-ATCAAATTTCA
1 TCTCTCTTGAAACAAAGATC-AATTTCA
1876812 AAGCAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (28 bp):
TCTCTCTTGAAACAAAGATCAATTTCAT
Found at i:1877401 original size:13 final size:13
Alignment explanation
Indices: 1877383--1877409 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1877373 TAGTTCAAAC
1877383 AAAAAAATAAGAG
1 AAAAAAATAAGAG
1877396 AAAAAAATAAGAG
1 AAAAAAATAAGAG
1877409 A
1 A
1877410 TTGTTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAAATAAGAG
Found at i:1877697 original size:10 final size:10
Alignment explanation
Indices: 1877682--1877711 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1877672 CCACCAGAGG
1877682 ACGGTGGCAA
1 ACGGTGGCAA
1877692 ACGGTGGCAA
1 ACGGTGGCAA
*
1877702 ACAGTGGCAA
1 ACGGTGGCAA
1877712 CCACAGAGGT
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:0.33, C:0.20, G:0.37, T:0.10
Consensus pattern (10 bp):
ACGGTGGCAA
Found at i:1879068 original size:33 final size:27
Alignment explanation
Indices: 1878995--1879048 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1878985 TATAGTGTCA
*
1878995 GGTAGCAAGGCATGATTCGAGCAACTT
1 GGTAGCAGGGCATGATTCGAGCAACTT
1879022 GGTAGCAGGGCATGATTCGAGCAACTT
1 GGTAGCAGGGCATGATTCGAGCAACTT
1879049 TATCAGGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (27 bp):
GGTAGCAGGGCATGATTCGAGCAACTT
Found at i:1886372 original size:201 final size:202
Alignment explanation
Indices: 1886027--1886428 Score: 797
Period size: 201 Copynumber: 2.0 Consensus size: 202
1886017 CTTTCCTGTC
1886027 ATCATAACAATACCCCATTCTCCAGGCGATTCTTGTCCCCAAGGATCGAAGTGAGGAAATTGTTG
1 ATCATAACAATACCCCATTCTCCAGGCGATTCTTGTCCCCAAGGATCGAAGTGAGGAAATTGTTG
1886092 TCTCAGTATGGTATAATCCTCCCATGTTGCTTCATTTGATCCCATATTTGTCCATTGAATGAGCA
66 TCTCAGTATGGTATAATCCTCCCATGTTGCTTCATTTGATCCCATATTTGTCCATTGAATGAGCA
1886157 GTTGAATGACTGCTCAATTCTGTCTTGT-ACCACTCGCTGATCAAAAACTAGGGTTGGATAAATC
131 GTTGAATGACTGCTCAATTCTGTCTTGTAACCACTCGCTGATCAAAAACTAGGGTTGGATAAATC
1886221 TTCAGTG
196 TTCAGTG
1886228 ATCATAACAATACCCCATTCTCCAGGCGATTCTTGTCCCCAAGGATCGAAGTGAGGAAATTGTTG
1 ATCATAACAATACCCCATTCTCCAGGCGATTCTTGTCCCCAAGGATCGAAGTGAGGAAATTGTTG
1886293 TCTCAGTATGGTATAATCCTCCCATGTTGCTTCATTTGATCCCATATTTGTCCATTGAATGAGCA
66 TCTCAGTATGGTATAATCCTCCCATGTTGCTTCATTTGATCCCATATTTGTCCATTGAATGAGCA
1886358 GTTGAATGACTGCTCAATTCTGTCTTGTAACCACTCGCTGATCAAAAACTAGGGTTGGATAAATC
131 GTTGAATGACTGCTCAATTCTGTCTTGTAACCACTCGCTGATCAAAAACTAGGGTTGGATAAATC
1886423 TTCAGT
196 TTCAGT
1886429 TGTCCATCCG
Statistics
Matches: 200, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 158 0.79
202 42 0.21
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (202 bp):
ATCATAACAATACCCCATTCTCCAGGCGATTCTTGTCCCCAAGGATCGAAGTGAGGAAATTGTTG
TCTCAGTATGGTATAATCCTCCCATGTTGCTTCATTTGATCCCATATTTGTCCATTGAATGAGCA
GTTGAATGACTGCTCAATTCTGTCTTGTAACCACTCGCTGATCAAAAACTAGGGTTGGATAAATC
TTCAGTG
Found at i:1888908 original size:29 final size:29
Alignment explanation
Indices: 1888866--1888926 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1888856 GGGCTTTTAC
1888866 TCACCTGAATAATAGAGGAGGACATCATT
1 TCACCTGAATAATAGAGGAGGACATCATT
1888895 TCACCTGAATAATAGAGGAGGACATCATT
1 TCACCTGAATAATAGAGGAGGACATCATT
1888924 TCA
1 TCA
1888927 GTAATTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (29 bp):
TCACCTGAATAATAGAGGAGGACATCATT
Found at i:1895462 original size:2 final size:2
Alignment explanation
Indices: 1895457--1895495 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1895447 TATATATATA
1895457 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1895496 TAATGTGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1898281 original size:23 final size:23
Alignment explanation
Indices: 1898229--1898274 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1898219 TCATATTAAT
*
1898229 ACAATATTAAGTTCTTATTACAA
1 ACAATATTAAGTTATTATTACAA
*
1898252 ACAATATTAATTTATTATTACAA
1 ACAATATTAAGTTATTATTACAA
1898275 CCCATATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (23 bp):
ACAATATTAAGTTATTATTACAA
Found at i:1901311 original size:23 final size:22
Alignment explanation
Indices: 1901262--1901315 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1901252 ATTATCAACT
**
1901262 TATTATTTAGGATTTTATCTTTC
1 TATT-TTTAGGATTTTATCTTAA
1901285 TATTGTTTAGGATTTTAT-TTGAA
1 TATT-TTTAGGATTTTATCTT-AA
1901308 TATTTTTA
1 TATTTTTA
1901316 TTATTATCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.61
Consensus pattern (22 bp):
TATTTTTAGGATTTTATCTTAA
Found at i:1902058 original size:12 final size:12
Alignment explanation
Indices: 1902041--1902065 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1902031 TTTCTTCTTA
1902041 AAATTTACTTTT
1 AAATTTACTTTT
1902053 AAATTTACTTTT
1 AAATTTACTTTT
1902065 A
1 A
1902066 TTATTTTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTTACTTTT
Found at i:1902079 original size:14 final size:13
Alignment explanation
Indices: 1902056--1902095 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1902046 TACTTTTAAA
*
1902056 TTTACTTTTATTAT
1 TTTACCTTTATT-T
1902070 TTTACCTTTATTT
1 TTTACCTTTATTT
1902083 TTTA-CTTTATTT
1 TTTACCTTTATTT
1902095 T
1 T
1902096 CTTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.36
13 5 0.20
14 11 0.44
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTACCTTTATTT
Found at i:1904754 original size:10 final size:10
Alignment explanation
Indices: 1904741--1904765 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1904731 TTTGTCAATT
1904741 TTTTTATTTA
1 TTTTTATTTA
1904751 TTTTTATTTA
1 TTTTTATTTA
1904761 TTTTT
1 TTTTT
1904766 GAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:1912483 original size:16 final size:17
Alignment explanation
Indices: 1912462--1912498 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1912452 TTCGAACAAC
*
1912462 AAAAAAAA-AAGTAAA-
1 AAAAAAAAGAAATAAAT
1912477 AAAAAAAAGAAATAAAT
1 AAAAAAAAGAAATAAAT
1912494 AAAAA
1 AAAAA
1912499 TTGGTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.08
Consensus pattern (17 bp):
AAAAAAAAGAAATAAAT
Found at i:1918252 original size:21 final size:21
Alignment explanation
Indices: 1918226--1918275 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1918216 AACCTGTAAC
*
1918226 TGATTTGACTTGTTAT-TGAAT
1 TGATTTGACTTGTTATAT-AAG
*
1918247 TGATTTTACTTGTTATATAAG
1 TGATTTGACTTGTTATATAAG
1918268 TGATTTGA
1 TGATTTGA
1918276 TATTTACCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.52
Consensus pattern (21 bp):
TGATTTGACTTGTTATATAAG
Found at i:1919066 original size:2 final size:2
Alignment explanation
Indices: 1919055--1919096 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1919045 CTTAAAATTT
1919055 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
1919096 T
1 T
1919097 TAAAAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1923719 original size:36 final size:36
Alignment explanation
Indices: 1923668--1923737 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1923658 GTCATGAAAG
*
1923668 AGTAGGGAACCAAAACTCGATAAACTTAGAAAATAA
1 AGTAGGAAACCAAAACTCGATAAACTTAGAAAATAA
*
1923704 AGTAGGAAACTAAAACTCGATAAACTTAGAAAAT
1 AGTAGGAAACCAAAACTCGATAAACTTAGAAAAT
1923738 GAATTATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.19
Consensus pattern (36 bp):
AGTAGGAAACCAAAACTCGATAAACTTAGAAAATAA
Found at i:1939985 original size:17 final size:18
Alignment explanation
Indices: 1939954--1940000 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
1939944 ATATAGAGTA
1939954 GTATCGGTAACCCC-TTGG
1 GTATCGGT-ACCCCTTTGG
1939972 GTATCGGTACCCCTTTGG
1 GTATCGGTACCCCTTTGG
1939990 GTATCGGTACC
1 GTATCGGTACC
1940001 ATTTTTGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (18 bp):
GTATCGGTACCCCTTTGG
Found at i:1942666 original size:15 final size:15
Alignment explanation
Indices: 1942606--1942666 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
1942596 TATATGTGTG
*
1942606 TGTAT-TATAATGTA
1 TGTATGTATAATTTA
*
1942620 TGTATATATAATTTA
1 TGTATGTATAATTTA
* *
1942635 T-TAATGCATGCATTTA
1 TGT-ATGTAT-AATTTA
1942651 TGTATGTATAATTTA
1 TGTATGTATAATTTA
1942666 T
1 T
1942667 TGATGCATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
14 6 0.16
15 19 0.51
16 11 0.30
17 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (15 bp):
TGTATGTATAATTTA
Found at i:1943238 original size:286 final size:282
Alignment explanation
Indices: 1942700--1943627 Score: 848
Period size: 286 Copynumber: 3.2 Consensus size: 282
1942690 GATATGTATG
* * * *
1942700 TTCAA-TTAGTCCTTACAA-TTATATTTTTATCTAAAATTTGTCC-ATAATTATTTCTACTTTTT
1 TTCAATTTAGTCCTTA-AAGTTATA-TTTTATTTGAAA-TTGGCCTATAATTATTTCTATTTTTT
* * * *
1942762 TAATTTACTCCAAAC-CATATAAATTACATCATAAA---C--TTCAAACTCTATAAATTATATCA
63 TAATTTACACCAAACAC-GATAAATCACATCATAAATTTCATTTCAAAC-CTATAAATTATAGC-
* * * *
1942821 TAAATTCATATTCTCCAAACTCTATAAACTTTTGTTAACCAAC-TTTCAAATGAATGCAGTTTAA
125 ----TT-A-ATT-TCCAAACCCTATAAAC-TTTGTTCACCAACTTTTCAAATGAATGCAATTTAG
* * * ** * * * *
1942885 TCCTTTTTTTATATTAATTTCAAATTTTCATTCCACAATTATTTTAATTTGA-ACATGCATGTTG
182 T-C-TATTTTATATTAATTTCAACTTTACATTTTACAATT-GTTTAATTTGATCCTTGCATATTG
** *
1942949 TTTAATTTATTTAAATTTTAGTTTCTAATTTCATGTTT-
244 TTTAATTTATTTAAATTACAGTTTATAATTTCATGTTTA
* * * * *
1942987 TCCAGTTTGGTCCTTAAAGTTATAGTTTTATTTGAAATTGGCTTATAATTATTTCTATCTTTATT
1 TTCAATTTAGTCCTTAAAGTTATA-TTTTATTTGAAATTGGCCTATAATTATTTCTAT-TTTTTT
* * *
1943052 AATTTACACCAAACACTATAAATCACATTATAAACTTT-ATTTCAAACCATATAAATTAT-GTTA
64 AATTTACACCAAACACGATAAATCACATCATAAA-TTTCATTTCAAACC-TATAAATTATAGCT-
* *
1943115 TAATTTCCAAACCCTATAAACTTTCGTTCGCCAACTTTTCAAATGAATGCAATTTAGTATATTTT
126 TAATTTCCAAACCCTATAAACTTT-GTTCACCAACTTTTCAAATGAATGCAATTTAGTCTATTTT
* * ** * *
1943180 GATATTAATTTCAACTTTACATTTTACAATTGCTCAATTTGATCCTTGTGTTTTGTTTAA-TAAT
190 -ATATTAATTTCAACTTTACATTTTACAATTGTTTAATTTGATCCTTGCATATTGTTTAATTTAT
* *
1943244 TTAAATTACAGTTTGTAATTTTATGTTTA
254 TTAAATTACAGTTTATAATTTCATGTTTA
* * *** * *
1943273 TTCAATTTAGT-CATAAACTTTATATTTTTAACCGAAATTGGCCCATAAATATTTCTATTTTTTT
1 TTCAATTTAGTCCTTAAA-GTTATA-TTTTATTTGAAATTGGCCTATAATTATTTCTATTTTTTT
* * * * *
1943337 AATTTTCTCTAAACCCGATAAATGACATCATAAATTTCATTTCAAACCTATAAATTATAGCTTAA
64 AATTTACACCAAACACGATAAATCACATCATAAATTTCATTTCAAACCTATAAATTATAGCTTAA
* * * * *
1943402 TTTCCAAACCATATAAACTTTTTTCACCAACTTTGT-AAATTAATGCTATTTAGTCCATTTTATA
129 TTTCCAAACCCTATAAACTTTGTTCACCAACTTT-TCAAATGAATGCAATTTAGTCTATTTTATA
* * * * *
1943466 TTAATTTCAACTTTATATTTTACAGTTGTTTTGATTAGATCCTTGCATATTGTTTAATTTAGTTA
193 TTAATTTCAACTTTACATTTTACAATTG-TTTAATTTGATCCTTGCATATTGTTTAATTTATTTA
* * *
1943531 AATTCCAATTTATAATTTCATGTTTG
257 AATTACAGTTTATAATTTCATGTTTA
*
1943557 TTCAATTTAGTCCTTAAAAG-TATATTTGATTTGAAATTGGCCTATAATTATTTCTATTTTTTAT
1 TTCAATTTAGTCCTT-AAAGTTATATTTTATTTGAAATTGGCCTATAATTATTTCTATTTTTT-T
1943621 AATTTAC
64 AATTTAC
1943628 TACAAACCAT
Statistics
Matches: 522, Mismatches: 92, Indels: 57
0.78 0.14 0.08
Matches are distributed among these distances:
282 29 0.06
283 85 0.16
284 85 0.16
285 94 0.18
286 104 0.20
287 32 0.06
288 39 0.07
289 35 0.07
290 1 0.00
293 1 0.00
294 17 0.03
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.46
Consensus pattern (282 bp):
TTCAATTTAGTCCTTAAAGTTATATTTTATTTGAAATTGGCCTATAATTATTTCTATTTTTTTAA
TTTACACCAAACACGATAAATCACATCATAAATTTCATTTCAAACCTATAAATTATAGCTTAATT
TCCAAACCCTATAAACTTTGTTCACCAACTTTTCAAATGAATGCAATTTAGTCTATTTTATATTA
ATTTCAACTTTACATTTTACAATTGTTTAATTTGATCCTTGCATATTGTTTAATTTATTTAAATT
ACAGTTTATAATTTCATGTTTA
Found at i:1948594 original size:38 final size:37
Alignment explanation
Indices: 1948504--1948623 Score: 213
Period size: 37 Copynumber: 3.2 Consensus size: 37
1948494 TTTTGTTCGG
1948504 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1948541 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
*
1948578 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGA
1948616 GTTCGGGT
1 G-TCGGGT
1948624 TTAGGGTGAA
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
37 48 0.60
38 26 0.32
39 6 0.08
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.38
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1948657 original size:301 final size:294
Alignment explanation
Indices: 1948272--1948847 Score: 817
Period size: 301 Copynumber: 1.9 Consensus size: 294
1948262 TTTTGGTCAG
1948272 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAA
1 GTCGGATCGGGTTTTTTTAAGTGTGATATT---GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAA
*
1948337 ACCGGATCGACCCGAAAATATATATAATTCT-GGTCGGGACGGATTAAGTCACTGTTTTTATTAA
63 ACCGGACCGACCCGAAAATATATATAATT-TGGGTCGGGACGGATTAAGTCACTGTTTTTATTAA
* * ** *
1948401 ATAAAAATAATTTTTTATTATTTCGGGTAGGGTCGGGTTTGATTTCTAATTCATATATTCGGGTC
127 ATAAAAAT-ATTTTTTATTATTTC-GATAGAGTCGGGTCGGATTTCTAATT--TATA-T---AT-
1948466 GGGTCGGGTCGGGTCGGATGAAACTTTATTTTGTTC-G-G-GTCGGGTCGGG-TTTTTTAAGTGT
183 ---TCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGCGAGTCGGGTCGGGTTTTTTTAAGTGT
1948527 GATATTCGGGTC-GAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
245 GATATTC-GGTCAG-GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
* *
1948578 GTCGGGTCGGGTTTTTTTAAGTGTGATA-T-TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCC
1 GTCGGATCGGGTTTTTTTAAGTGTGATATTGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACC
* *
1948641 GGACCGACCTGAAAATATATATAATTTGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAA
66 GGACCGACCCGAAAATATATATAATTTGGGTCGGGACGGATTAAGTCACTGTTTTTATTAAATAA
*
1948706 AAATATTTTTTATTATTTCGATCGAGTCGGGTCGGATTTCTAATTTATATATTCGGGTCGGGTCG
131 AAATATTTTTTATTATTTCGATAGAGTCGGGTCGGATTTCTAATTTATATATTCGGGTCGGGTCG
1948771 GATGAAACTTTATTTTGTTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGTCAGG
196 GATGAAACTTTATTTTGTTC-GG-CGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGTCAGG
1948836 TCGGGTCGGGTT
259 TCGGGTCGGGTT
1948848 CGGGTTTAGG
Statistics
Matches: 251, Mismatches: 11, Indels: 28
0.87 0.04 0.10
Matches are distributed among these distances:
289 33 0.13
291 1 0.00
293 2 0.01
294 28 0.11
295 20 0.08
296 1 0.00
297 4 0.02
299 21 0.08
300 16 0.06
301 97 0.39
305 1 0.00
306 27 0.11
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (294 bp):
GTCGGATCGGGTTTTTTTAAGTGTGATATTGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACC
GGACCGACCCGAAAATATATATAATTTGGGTCGGGACGGATTAAGTCACTGTTTTTATTAAATAA
AAATATTTTTTATTATTTCGATAGAGTCGGGTCGGATTTCTAATTTATATATTCGGGTCGGGTCG
GATGAAACTTTATTTTGTTCGGCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGTCAGGTC
GGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1957499 original size:84 final size:82
Alignment explanation
Indices: 1957319--1957499 Score: 191
Period size: 84 Copynumber: 2.2 Consensus size: 82
1957309 TTTTTTTAAC
** * * * * ** *
1957319 AAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGTCGTGATAGTGTTATTTAT
1 AAACGCCGCAATAGAGAAGAAATTTAGCGGCGTTATAAAACAAACGTCGAAATAGTATTATTTAT
* ** *
1957384 AGTGGCATTTTTTTAAC
66 AGTGGCATTTATGCAAA
* *
1957401 AAACGCCGCTATAGAGAAGAAATTTAGCGGCGTCTATAAAACAAACGTCGCAAATAGTATTGTTT
1 AAACGCCGCAATAGAGAAGAAATTTAGCGGCGT-TATAAAACAAACGTCG-AAATAGTATTATTT
*
1957466 ATAGTGGCGTTTATGCAAA
64 ATAGTGGCATTTATGCAAA
*
1957485 AAACACCGCAATAGA
1 AAACGCCGCAATAGA
1957500 TTAATAATAT
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
82 29 0.37
83 13 0.16
84 37 0.47
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (82 bp):
AAACGCCGCAATAGAGAAGAAATTTAGCGGCGTTATAAAACAAACGTCGAAATAGTATTATTTAT
AGTGGCATTTATGCAAA
Found at i:1959046 original size:41 final size:41
Alignment explanation
Indices: 1958968--1959186 Score: 163
Period size: 42 Copynumber: 5.2 Consensus size: 41
1958958 AAGGTAATTA
* * * *
1958968 ACGGCGTTTTTATCAACAAACGCCGCTATAGACCACACTTTT
1 ACGGCGTTTGTATAAAC-AACGGCGCTATAAACCACACTTTT
*
1959010 ACGGCGTTTGTATGAACAACGGCGCTATAAACCACACTTTTTT
1 ACGGCGTTTGTATAAACAACGGCGCTATAAACCACAC--TTTT
* * *
1959053 ACGGCATTTGTATAAAAAAC-GCAGCCATAAACCACACTTTT
1 ACGGCGTTTGTATAAACAACGGC-GCTATAAACCACACTTTT
* ** * * *
1959094 GCGGCGTTTGTATCAAA-AACACCGCCATAAACCCCATTTTTT
1 ACGGCGTTTGTAT-AAACAACGGCGCTATAAACCACA-CTTTT
* * * * * * *
1959136 TCGGCATTTGTATAAAAAAATGCCACCATAAACCACACTTTT
1 ACGGCGTTTGTAT-AAACAACGGCGCTATAAACCACACTTTT
*
1959178 GCGGCGTTT
1 ACGGCGTTT
1959187 ATTTCAAAAA
Statistics
Matches: 147, Mismatches: 23, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
41 48 0.33
42 50 0.34
43 49 0.33
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (41 bp):
ACGGCGTTTGTATAAACAACGGCGCTATAAACCACACTTTT
Found at i:1959083 original size:43 final size:43
Alignment explanation
Indices: 1958985--1959177 Score: 175
Period size: 41 Copynumber: 4.6 Consensus size: 43
1958975 TTTTATCAAC
* * * * *
1958985 AAACGCCGCTATAGACCACAC--TTTTACGGCGTTTGTATGAA
1 AAACGCAGCCATAAACCACACTTTTTTACGGCATTTGTATAAA
* *
1959026 CAACGGC-GCTATAAACCACACTTTTTTACGGCATTTGTATAAA
1 AAAC-GCAGCCATAAACCACACTTTTTTACGGCATTTGTATAAA
* * *
1959069 AAACGCAGCCATAAACCACAC--TTTTGCGGCGTTTGTATCAA
1 AAACGCAGCCATAAACCACACTTTTTTACGGCATTTGTATAAA
* * * *
1959110 AAACACCGCCATAAACCCCA-TTTTTTTCGGCATTTGTATAAAA
1 AAACGCAGCCATAAACCACACTTTTTTACGGCATTTGTAT-AAA
*
1959153 AAATGCCA-CCATAAACCACACTTTT
1 AAACG-CAGCCATAAACCACACTTTT
1959178 GCGGCGTTTA
Statistics
Matches: 124, Mismatches: 19, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
41 50 0.40
42 19 0.15
43 50 0.40
44 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.27
Consensus pattern (43 bp):
AAACGCAGCCATAAACCACACTTTTTTACGGCATTTGTATAAA
Found at i:1959092 original size:84 final size:84
Alignment explanation
Indices: 1958985--1959202 Score: 269
Period size: 84 Copynumber: 2.6 Consensus size: 84
1958975 TTTTATCAAC
* * * * * * ** *
1958985 AAACGCCGCTATAGACCACACTTTTACGGCGTTTGTATGAACAACGGCGCTATAAACCACACTTT
1 AAACGCAGCCATAAACCACACTTTTGCGGCGTTTGTATCAAAAACACCGCCATAAACCACA-TTT
1959050 TTTACGGCATTTGTAT-AAA
65 TTTACGGCATTTGTATAAAA
*
1959069 AAACGCAGCCATAAACCACACTTTTGCGGCGTTTGTATCAAAAACACCGCCATAAACCCCATTTT
1 AAACGCAGCCATAAACCACACTTTTGCGGCGTTTGTATCAAAAACACCGCCATAAACCACATTTT
*
1959134 TTTCGGCATTTGTATAAAA
66 TTACGGCATTTGTATAAAA
* * * *
1959153 AAATGCCA-CCATAAACCACACTTTTGCGGCGTTTATTTCAAAAACGCCGC
1 AAACG-CAGCCATAAACCACACTTTTGCGGCGTTTGTATCAAAAACACCGC
1959203 AATATGTTCA
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
83 18 0.15
84 97 0.83
85 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (84 bp):
AAACGCAGCCATAAACCACACTTTTGCGGCGTTTGTATCAAAAACACCGCCATAAACCACATTTT
TTACGGCATTTGTATAAAA
Found at i:1959196 original size:43 final size:41
Alignment explanation
Indices: 1958999--1959196 Score: 150
Period size: 43 Copynumber: 4.7 Consensus size: 41
1958989 GCCGCTATAG
* * * *** * *
1958999 ACCACACTTTTACGGCGTTTGTATGAACAACGGCGCTATAA
1 ACCACACTTTTGCGGCGTTTGTATCAAAAAAACCACCATAA
* *
1959040 ACCACACTTTTTTACGGCATTTGTAT--AAAAAACGCAGCCATAA
1 ACCACAC--TTTTGCGGCGTTTGTATCAAAAAAAC-CA-CCATAA
* *
1959083 ACCACACTTTTGCGGCGTTTGTATCAAAAACACCGCCATAA
1 ACCACACTTTTGCGGCGTTTGTATCAAAAAAACCACCATAA
* * * *
1959124 ACCCCATTTTTTTCGGCATTTGTAT-AAAAAAATGCCACCATAA
1 ACCACA-CTTTTGCGGCGTTTGTATCAAAAAAA--CCACCATAA
* *
1959167 ACCACACTTTTGCGGCGTTTATTTCAAAAA
1 ACCACACTTTTGCGGCGTTTGTATCAAAAA
1959197 CGCCGCAATA
Statistics
Matches: 124, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
41 42 0.34
42 30 0.24
43 52 0.42
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (41 bp):
ACCACACTTTTGCGGCGTTTGTATCAAAAAAACCACCATAA
Found at i:1963305 original size:42 final size:43
Alignment explanation
Indices: 1963254--1963349 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
1963244 AAAAGTTGCA
1963254 AAATATCAAC-CCTATTACGGCATTTGC-ACTAAAAACACTACG
1 AAATATCAACACCTATTACGGCATTTGCGA-TAAAAACACTACG
* ** * ** *
1963296 AAATCTCAACACCTATTGTGGCGTTTGCGATAAAAACACCGCT
1 AAATATCAACACCTATTACGGCATTTGCGATAAAAACACTACG
1963339 AAATATCAACA
1 AAATATCAACA
1963350 TCTACTGCGA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 9 0.20
43 34 0.77
44 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (43 bp):
AAATATCAACACCTATTACGGCATTTGCGATAAAAACACTACG
Found at i:1963434 original size:129 final size:129
Alignment explanation
Indices: 1963301--1963572 Score: 310
Period size: 129 Copynumber: 2.1 Consensus size: 129
1963291 CTACGAAATC
* * * * * * **
1963301 TCAACACCTATTGTGGCGTTTGCGATAAAAACACCGCTAAATATCAACATCTACTGCGACGTTTG
1 TCAACACCTATTGCGGCGTTAGCGAGAAAAACACCGCAAAACATCAACACCTACTGCGACAATTG
** * *
1963366 TGGGAAAAACGCCGCTAAACATCAATACCTACTACGGAGTTTGTGGGAAAAACGCCGCTAAAAA
66 TGAAAAAAACGCCGCTAAACATCAACACCTACTACGGAGTTTGTCGGAAAAACGCCGCTAAAAA
* * * *
1963430 TCAACACCTACTGCGGCGTTAGCGGGAAAAACGCCGCAAAACATCAACACCTACTGCGGCAATTG
1 TCAACACCTATTGCGGCGTTAGCGAGAAAAACACCGCAAAACATCAACACCTACTGCGACAATTG
* * * * * * ** *
1963495 TGAAAAAAATGCCGCTAAACATCAACACTTATTGCGGCGTTTGTCTGCCAAACGCCGCTAAATA
66 TGAAAAAAACGCCGCTAAACATCAACACCTACTACGGAGTTTGTCGGAAAAACGCCGCTAAAAA
*
1963559 TCAACATCTATTGC
1 TCAACACCTATTGC
1963573 AGCATTTTTT
Statistics
Matches: 116, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
129 116 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (129 bp):
TCAACACCTATTGCGGCGTTAGCGAGAAAAACACCGCAAAACATCAACACCTACTGCGACAATTG
TGAAAAAAACGCCGCTAAACATCAACACCTACTACGGAGTTTGTCGGAAAAACGCCGCTAAAAA
Found at i:1963572 original size:43 final size:43
Alignment explanation
Indices: 1963301--1963564 Score: 276
Period size: 43 Copynumber: 6.1 Consensus size: 43
1963291 CTACGAAATC
* * * ** * *
1963301 TCAACACCTATTGTGGCGTTTGCGATAAAAACACCGCTAAATA
1 TCAACACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACA
* *
1963344 TCAACATCTACTGCGACGTTTGTGGGAAAAACGCCGCTAAACA
1 TCAACACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACA
* * * *
1963387 TCAATACCTACTACGGAGTTTGTGGGAAAAACGCCGCTAAAAA
1 TCAACACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACA
* * *
1963430 TCAACACCTACTGCGGCGTTAGCGGGAAAAACGCCGCAAAACA
1 TCAACACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACA
** ** *
1963473 TCAACACCTACTGCGGCAATTGTGAAAAAAATGCCGCTAAACA
1 TCAACACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACA
* * ** ** *
1963516 TCAACACTTATTGCGGCGTTTGTCTGCCAAACGCCGCTAAATA
1 TCAACACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACA
1963559 TCAACA
1 TCAACA
1963565 TCTATTGCAG
Statistics
Matches: 180, Mismatches: 41, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 180 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TCAACACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACA
Found at i:1972419 original size:16 final size:17
Alignment explanation
Indices: 1972394--1972426 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1972384 GCTTGGGTTG
1972394 ATTTGCTTTCC-GGTGA
1 ATTTGCTTTCCAGGTGA
*
1972410 ATTTGGTTTCCAGGTGA
1 ATTTGCTTTCCAGGTGA
1972427 GTGCAGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (17 bp):
ATTTGCTTTCCAGGTGA
Found at i:1982794 original size:72 final size:71
Alignment explanation
Indices: 1982671--1982818 Score: 251
Period size: 72 Copynumber: 2.1 Consensus size: 71
1982661 CTATGTCCAC
* * *
1982671 ATATTTAGCTTATTTAATGCATAGTTATGTTACACATTCCTTGCTTGTGTTATCATATCATTTGC
1 ATATTTAGCTTAATTAATGCATAGTTATGTTACACATTCCTTACTTATGTTATCATATCATTTGC
1982736 ATCATT
66 ATCATT
*
1982742 ATATTTAGCTTAATTCATGCATATGTTATGTTACACATTCCTTACTTATGTTATCATATCATTTG
1 ATATTTAGCTTAATTAATGCATA-GTTATGTTACACATTCCTTACTTATGTTATCATATCATTTG
1982807 CATCATT
65 CATCATT
1982814 ATATT
1 ATATT
1982819 AGGCTTGGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 21 0.29
72 51 0.71
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (71 bp):
ATATTTAGCTTAATTAATGCATAGTTATGTTACACATTCCTTACTTATGTTATCATATCATTTGC
ATCATT
Found at i:1983514 original size:43 final size:43
Alignment explanation
Indices: 1983420--1983515 Score: 149
Period size: 43 Copynumber: 2.2 Consensus size: 43
1983410 TAAGAGAATT
* * *
1983420 CAAGTTCATGAAGGTAGTCGAACCATCATGTTCACATGGGATC
1 CAAGTTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
1983463 CTAA-TTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
1 C-AAGTTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
1983506 CAAGTTCATG
1 CAAGTTCATG
1983516 CAAGGAAGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
42 2 0.04
43 44 0.92
44 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (43 bp):
CAAGTTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
Found at i:1987882 original size:21 final size:22
Alignment explanation
Indices: 1987824--1987900 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 22
1987814 GGCAGTGTGA
1987824 ATCGATGCACATTCAAGGAGTGC
1 ATCGATGCACATTC-AGGAGTGC
* * *
1987847 ATCGGTGCATC-TTCATGA-TGT
1 ATCGATGCA-CATTCAGGAGTGC
1987868 ATCGATGCACATTCAAAGG-GATGC
1 ATCGATGCACATTC--AGGAG-TGC
1987892 ATCGATGCA
1 ATCGATGCA
1987901 TTATTTAGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.02
21 13 0.31
22 3 0.07
23 13 0.31
24 12 0.29
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
ATCGATGCACATTCAGGAGTGC
Found at i:1987913 original size:44 final size:44
Alignment explanation
Indices: 1987824--1987920 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
1987814 GGCAGTGTGA
* *
1987824 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGATGCATATTCATGATGT
*
1987868 ATCGATGCACATTCAAAGG-GATGCATCGATGCATTATTTA-G-TGT
1 ATCGATGCACATTC-AAGGAG-TGCATCGATGCA-TATTCATGATGT
1987912 ATCGATGCA
1 ATCGATGCA
1987921 TTATGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 27 0.57
45 16 0.34
46 4 0.09
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGATGCATATTCATGATGT
Found at i:1996902 original size:13 final size:13
Alignment explanation
Indices: 1996884--1996908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1996874 ACATTCGCGG
1996884 ATATGAAGACTGC
1 ATATGAAGACTGC
1996897 ATATGAAGACTG
1 ATATGAAGACTG
1996909 TTCAACGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:1997994 original size:28 final size:27
Alignment explanation
Indices: 1997954--1998007 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
1997944 TAAAATTATC
*
1997954 AAATTACACAAAATAATTATTAAAAATA
1 AAATTACACAAAAGAA-TATTAAAAATA
* * *
1997982 AAATTATATAAAAGAATGTTAAAAAT
1 AAATTACACAAAAGAATATTAAAAAT
1998008 TCAACTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (27 bp):
AAATTACACAAAAGAATATTAAAAATA
Found at i:2000307 original size:12 final size:12
Alignment explanation
Indices: 2000292--2000337 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2000282 CGGTTTTTTT
*
2000292 ACCGGATAAAAA
1 ACCGGTTAAAAA
2000304 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
2000319 ACCGGTTAAAAA
1 ACCGGTTAAAAA
2000331 ACCGGTT
1 ACCGGTT
2000338 TTTATCTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:2000319 original size:15 final size:13
Alignment explanation
Indices: 2000298--2000338 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
2000288 TTTTACCGGA
2000298 TAAAAAACCGGTT
1 TAAAAAACCGGTT
2000311 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
2000325 TAAAAAACCGGTT
1 TAAAAAACCGGTT
2000338 T
1 T
2000339 TTATCTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:2002651 original size:21 final size:21
Alignment explanation
Indices: 2002627--2002666 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2002617 TTTATTTTAT
2002627 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2002648 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2002667 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2002714 original size:33 final size:33
Alignment explanation
Indices: 2002661--2002759 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
2002651 TTTGTTTCAA
*
2002661 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
2002693 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
** * * *
2002726 TTATTAAACTTGGAAGTATTTAAATATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
2002759 T
1 T
2002760 ATGTTGAGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 11 0.18
33 49 0.82
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
Found at i:2002788 original size:13 final size:13
Alignment explanation
Indices: 2002770--2002799 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2002760 ATGTTGAGTT
2002770 AATTAAGTATTTC
1 AATTAAGTATTTC
*
2002783 AATTAAGTATTTG
1 AATTAAGTATTTC
2002796 AATT
1 AATT
2002800 TATCGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (13 bp):
AATTAAGTATTTC
Found at i:2003045 original size:21 final size:21
Alignment explanation
Indices: 2002995--2003047 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2002985 TCGAGCGTGG
* *
2002995 GGGAATCGATATCCTCTCATA
1 GGGAATCGGTTTCCTCTCATA
2003016 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTTCCTCTCATA
2003037 GGGAATCGGTT
1 GGGAATCGGTT
2003048 CCCTAAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (21 bp):
GGGAATCGGTTTCCTCTCATA
Found at i:2003243 original size:15 final size:15
Alignment explanation
Indices: 2003218--2003274 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
2003208 ATCTAGAATA
*
2003218 TTAAAATCGATTTTT
1 TTAAAACCGATTTTT
*
2003233 TTATAACCGATTTTT
1 TTAAAACCGATTTTT
*
2003248 TAAAAAAACCGATTTTT
1 T--TAAAACCGATTTTT
2003265 TTAAAACCGA
1 TTAAAACCGA
2003275 AACCAGTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 22 0.63
17 13 0.37
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:2003257 original size:17 final size:18
Alignment explanation
Indices: 2003237--2003270 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2003227 ATTTTTTTAT
2003237 AACCGA-TTTTTTAAAAA
1 AACCGATTTTTTTAAAAA
2003254 AACCGATTTTTTTAAAA
1 AACCGATTTTTTTAAAA
2003271 CCGAAACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
AACCGATTTTTTTAAAAA
Found at i:2011378 original size:22 final size:21
Alignment explanation
Indices: 2011353--2011394 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2011343 GGATTCTACC
2011353 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
2011375 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
2011395 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:2011752 original size:19 final size:19
Alignment explanation
Indices: 2011728--2011778 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
2011718 GTATATGACC
*
2011728 GTTGAGGCTGTTAATGGTG
1 GTTGAGGTTGTTAATGGTG
2011747 GTTGAGGTTGTTAATGGTG
1 GTTGAGGTTGTTAATGGTG
2011766 GTTGAGGTTGTTA
1 GTTGAGGTTGTTA
2011779 GAGTTGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (19 bp):
GTTGAGGTTGTTAATGGTG
Found at i:2012354 original size:3 final size:3
Alignment explanation
Indices: 2012346--2012414 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
2012336 GAGAAAGTGG
2012346 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2012394 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
2012415 TTGTGGGTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2024742 original size:18 final size:19
Alignment explanation
Indices: 2024705--2024742 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2024695 TTATTTATGA
2024705 GGTATCGATACCTGAAGGGT
1 GGTATCGATACC-GAAGGGT
2024725 GGTATCGATACC-AAGGGT
1 GGTATCGATACCGAAGGGT
2024743 ATCGATACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (19 bp):
GGTATCGATACCGAAGGGT
Found at i:2024768 original size:35 final size:35
Alignment explanation
Indices: 2024705--2024772 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2024695 TTATTTATGA
**
2024705 GGTATCGATACCTGAAGGGTGGTATCGATACCAAG
1 GGTATCGATACCTGAAGGAAGGTATCGATACCAAG
*
2024740 GGTATCGATACCAT-AAGGAAGGTGTCGATACCA
1 GGTATCGATACC-TGAAGGAAGGTATCGATACCA
2024773 TTCTTGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (35 bp):
GGTATCGATACCTGAAGGAAGGTATCGATACCAAG
Found at i:2033500 original size:15 final size:15
Alignment explanation
Indices: 2033480--2033510 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2033470 AAGGAAAACC
2033480 CAAGAGAACAAAGCG
1 CAAGAGAACAAAGCG
2033495 CAAGAGAACAAAGCG
1 CAAGAGAACAAAGCG
2033510 C
1 C
2033511 CAAGCTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.23, G:0.26, T:0.00
Consensus pattern (15 bp):
CAAGAGAACAAAGCG
Found at i:2033603 original size:53 final size:53
Alignment explanation
Indices: 2033527--2033635 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
2033517 TCATCGTCCA
* *
2033527 ACCAAACACATGTTTCATATGATGAAGATGTCAAGTTTGACTTCTATAAAACC
1 ACCAAACACATGTTTCATATGATGAAGATGTCAAGTTCGACTTCCATAAAACC
* *
2033580 ACCAAACACATGTTTCATATGATGAAGATGTCGAGTTCGACTTCCATAAAGCC
1 ACCAAACACATGTTTCATATGATGAAGATGTCAAGTTCGACTTCCATAAAACC
2033633 ACC
1 ACC
2033636 GAACCTTCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (53 bp):
ACCAAACACATGTTTCATATGATGAAGATGTCAAGTTCGACTTCCATAAAACC
Found at i:2036098 original size:22 final size:22
Alignment explanation
Indices: 2036059--2036105 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2036049 AGTTTTTTAA
* * * *
2036059 TTTGAAAATTGTTGAAATTGAT
1 TTTGAAAACTATTCAAATTCAT
2036081 TTTGAAAACTATTCAAATTCAT
1 TTTGAAAACTATTCAAATTCAT
2036103 TTT
1 TTT
2036106 AATTTGCTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTGAAAACTATTCAAATTCAT
Found at i:2040518 original size:2 final size:2
Alignment explanation
Indices: 2040511--2040545 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2040501 TTAAATAATT
2040511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2040546 TAAAGTTATA
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:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2040685 original size:35 final size:34
Alignment explanation
Indices: 2040605--2040685 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 34
2040595 TTTATTTAAT
* *
2040605 TTTTAAAATCAAATTAATTATTTATTTGAAATAA
1 TTTTAAATTTAAATTAATTATTTATTTGAAATAA
* ** *
2040639 TATTATCTTTAAATT-ATCTATTTAATTTTAAATAA
1 TTTTAAATTTAAATTAAT-TATTT-ATTTGAAATAA
2040674 TTTTAAATTTAA
1 TTTTAAATTTAA
2040686 GGTAAATTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
33 2 0.06
34 15 0.42
35 19 0.53
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (34 bp):
TTTTAAATTTAAATTAATTATTTATTTGAAATAA
Found at i:2042085 original size:18 final size:18
Alignment explanation
Indices: 2042062--2042096 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2042052 TTCCATCCGG
*
2042062 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
2042080 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
2042097 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:2043349 original size:13 final size:13
Alignment explanation
Indices: 2043331--2043356 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2043321 GACAGTCAAC
2043331 AGTCAACGGGTCG
1 AGTCAACGGGTCG
2043344 AGTCAACGGGTCG
1 AGTCAACGGGTCG
2043357 GGTCGGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.15
Consensus pattern (13 bp):
AGTCAACGGGTCG
Found at i:2043369 original size:31 final size:31
Alignment explanation
Indices: 2043332--2043390 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2043322 ACAGTCAACA
*
2043332 GTCAACGGGTCGAGTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGAGTAAACGGGTCGGGTCGG
*
2043363 GTCAACGGGTCGGGTAAACGGGTCGGGT
1 GTCAACGGGTCGAGTAAACGGGTCGGGT
2043391 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (31 bp):
GTCAACGGGTCGAGTAAACGGGTCGGGTCGG
Found at i:2043371 original size:13 final size:13
Alignment explanation
Indices: 2043355--2043390 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2043345 GTCAACGGGT
*
2043355 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
2043368 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
2043381 CGGGTCGGGT
1 CGGGTCGGGT
2043391 TGTGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:2043390 original size:18 final size:18
Alignment explanation
Indices: 2043337--2043377 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2043327 CAACAGTCAA
2043337 CGGGTCGAGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
*
2043355 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
2043373 CGGGT
1 CGGGT
2043378 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:2043409 original size:9 final size:9
Alignment explanation
Indices: 2043395--2043421 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2043385 TCGGGTTGTG
2043395 ACCGGTCAA
1 ACCGGTCAA
2043404 ACCGGTCAA
1 ACCGGTCAA
2043413 ACCGGTCAA
1 ACCGGTCAA
2043422 CTATGCACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2045146 original size:35 final size:34
Alignment explanation
Indices: 2045066--2045146 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 34
2045056 TTTTTTTAAT
* *
2045066 TTTTAAAATCAAATTAATTATTTATTTGAAATAA
1 TTTTAAATTTAAATTAATTATTTATTTGAAATAA
* ** *
2045100 TATTATCTTTAAATT-ATCTATTTAATTTTAAATAA
1 TTTTAAATTTAAATTAAT-TATTT-ATTTGAAATAA
2045135 TTTTAAATTTAA
1 TTTTAAATTTAA
2045147 GGTAAATTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
33 2 0.06
34 15 0.42
35 19 0.53
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (34 bp):
TTTTAAATTTAAATTAATTATTTATTTGAAATAA
Found at i:2046465 original size:42 final size:42
Alignment explanation
Indices: 2046323--2046719 Score: 304
Period size: 43 Copynumber: 9.3 Consensus size: 42
2046313 AGAAATGATT
* * * *
2046323 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGTG-TGATGGAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAT-AT-TAAA
* * *
2046366 AAATTATGGACCTCAATTATAAAGGTAAAAA-TGACATTAAAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATT--AAA
* * *
2046409 AAATTAGGGCCCTCAATTTTAAAGATAAAAAGTGATATTAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATTAAA
* * *
2046451 AAATTAGGGGCCTCAATTTTAAAGATAAAAAGTGATATTGAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATTAAA
* * *
2046493 AAATTAGGGGCATTAATTATATAA-GTAAAAAGTGAGATATAAAA
1 AAATTAGGGGCCTCAATTATA-AAGGTAAAAAGT--GATATTAAA
* * *
2046537 AAATTAGGGGCATTAATCATAAAGGTAAAAA-TG-TGATTAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAT-ATTAAA
* * * * *
2046578 AAA-TAAGAGCCTCAATTATAAGGGTAGAAAGTGAGATTGAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATT-AAA
*** * * *
2046620 ATAATTAAAAG-CTCAATTATAAAGGTACAAAGTGAGATTGAA
1 A-AATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATTAAA
* * * * *
2046662 AACTTAGGGTCATCAATTATAAATGTAAAAAAGTGAGATTGAAAA
1 AAATTAGGGGCCTCAATTATAAAGGT-AAAAAGTGATATT--AAA
*
2046707 AAATTAAGGGCCT
1 AAATTAGGGGCCT
2046720 AGATTGAAAA
Statistics
Matches: 289, Mismatches: 47, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
40 21 0.07
41 18 0.06
42 93 0.32
43 101 0.35
44 45 0.16
45 11 0.04
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (42 bp):
AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATTAAA
Found at i:2046723 original size:23 final size:23
Alignment explanation
Indices: 2046697--2046742 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2046687 TAAAAAAGTG
*
2046697 AGATTGAAAAAAATTAAGGGCCT
1 AGATTGAAAAAAATGAAGGGCCT
2046720 AGATTGAAAAAAATGAAGGGCCT
1 AGATTGAAAAAAATGAAGGGCCT
2046743 CAATTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.24, T:0.20
Consensus pattern (23 bp):
AGATTGAAAAAAATGAAGGGCCT
Found at i:2046788 original size:43 final size:44
Alignment explanation
Indices: 2046741--2046848 Score: 125
Period size: 44 Copynumber: 2.5 Consensus size: 44
2046731 AATGAAGGGC
* *
2046741 CTCAATTATAAATATAAAAGGT-GAAATT-AAAAAAATTA-A-AA
1 CTCAATTATAAATATAAAA-ATAAAAATTAAAAAAAATTAGAGAA
*
2046782 GTCTCAATTATAAAAATAAAAATAAAAATTAAAAAAAATTAGAGAA
1 --CTCAATTATAAATATAAAAATAAAAATTAAAAAAAATTAGAGAA
2046828 CTCAATTATAAATATATAAAA
1 CTCAATTATAAATATA-AAAA
2046849 ATATAATAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
42 1 0.02
43 23 0.41
44 25 0.45
45 5 0.09
46 2 0.04
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.27
Consensus pattern (44 bp):
CTCAATTATAAATATAAAAATAAAAATTAAAAAAAATTAGAGAA
Found at i:2046801 original size:21 final size:22
Alignment explanation
Indices: 2046741--2046802 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
2046731 AATGAAGGGC
*
2046741 CTCAATTATAAATATAAAAGGT
1 CTCAATTATAAAAATAAAAGGT
** *
2046763 -GAAATTAAAAAAATTAAAA-GT
1 CTCAATTATAAAAA-TAAAAGGT
2046784 CTCAATTATAAAAATAAAA
1 CTCAATTATAAAAATAAAA
2046803 ATAAAAATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (22 bp):
CTCAATTATAAAAATAAAAGGT
Found at i:2046818 original size:44 final size:43
Alignment explanation
Indices: 2046741--2046851 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 43
2046731 AATGAAGGGC
* * *
2046741 CTCAATTATAAATATAAAAGGT-GAAATTAAAAAAATTA-A-AA
1 CTCAATTATAAAAATAAAA-ATAAAAATTAAAAAAATTAGAGAA
2046782 GTCTCAATTATAAAAATAAAAATAAAAATTAAAAAAAATTAGAGAA
1 --CTCAATTATAAAAATAAAAATAAAAATT-AAAAAAATTAGAGAA
2046828 CTCAATTATAAATATATAAAAATA
1 CTCAATTATAAA-A-ATAAAAATA
2046852 TAATAAAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
42 1 0.02
43 23 0.39
44 22 0.37
45 2 0.03
46 11 0.19
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (43 bp):
CTCAATTATAAAAATAAAAATAAAAATTAAAAAAATTAGAGAA
Found at i:2046859 original size:11 final size:11
Alignment explanation
Indices: 2046837--2046865 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2046827 ACTCAATTAT
2046837 AAATAT-ATAA
1 AAATATAATAA
2046847 AAATATAATAA
1 AAATATAATAA
2046858 AAATATAA
1 AAATATAA
2046866 AAATCCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATATAATAA
Found at i:2046876 original size:19 final size:18
Alignment explanation
Indices: 2046834--2046884 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2046824 AGAACTCAAT
*
2046834 TATAAATATATAAAAATA
1 TATAAAAATATAAAAATA
*
2046852 TAATAAAAATATAAAAATCC
1 T-ATAAAAATATAAAAAT-A
2046872 TAT-AAAATATAAA
1 TATAAAAATATAAA
2046885 GCCCTAAGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 11 0.38
19 17 0.59
20 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
TATAAAAATATAAAAATA
Found at i:2047623 original size:37 final size:37
Alignment explanation
Indices: 2047571--2047675 Score: 174
Period size: 37 Copynumber: 2.8 Consensus size: 37
2047561 ATAATGCTAG
* *
2047571 AGTTTTACTATGATTCAAACTCTTAAAAATATGATAT
1 AGTTTTACTATGATTCAAACTCCTAAAAATATGATAA
*
2047608 AGTTTTACTAGGATTCAAACTCCTAAAAATATGATAA
1 AGTTTTACTATGATTCAAACTCCTAAAAATATGATAA
*
2047645 AGTTCTACTATGATTCAAACTCCTAAAAATA
1 AGTTTTACTATGATTCAAACTCCTAAAAATA
2047676 ATCCACAAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (37 bp):
AGTTTTACTATGATTCAAACTCCTAAAAATATGATAA
Found at i:2048316 original size:40 final size:39
Alignment explanation
Indices: 2048206--2048350 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 39
2048196 CTTTAGTATA
* * *
2048206 TATTTTTATTTTTTTAGATTA-CATATATATGTATATGTTAC
1 TATTTTTA-TTTTTTA-TTTATTATATATATATATAT-TTAC
* *
2048247 TTTTTATTATATGTTTTATTAATTA-ATATATATATATTTAC
1 TATTT-TTAT-T-TTTTATTTATTATATATATATATATTTAC
* *
2048288 TATTTTTATGTTTTTATTTATTATATATATATATATATAT
1 TATTTTTAT-TTTTTATTTATTATATATATATATATTTAC
*
2048328 TACTTTTACTTTTTTA-TTATTAT
1 TATTTTTA-TTTTTTATTTATTAT
2048351 TTTATTTATT
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
39 18 0.21
40 32 0.37
41 14 0.16
42 17 0.20
43 6 0.07
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (39 bp):
TATTTTTATTTTTTATTTATTATATATATATATATTTAC
Found at i:2048360 original size:15 final size:15
Alignment explanation
Indices: 2048340--2048432 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 15
2048330 CTTTTACTTT
2048340 TTTATTATTATTT-TA
1 TTTATT-TTATTTATA
2048355 TTTATTTTATTTATA
1 TTTATTTTATTTATA
* * * *
2048370 TTTTTCTTCTTCTTTTTC
1 --TTTATT-TTATTTATA
*
2048388 TTTA-TTTCTTTATA
1 TTTATTTTATTTATA
2048402 TTTA-TTTA-TT-TA
1 TTTATTTTATTTATA
*
2048414 TTTATTTTACTTACTA
1 TTTATTTTATTTA-TA
2048430 TTT
1 TTT
2048433 TATCTTTGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
12 6 0.10
13 6 0.10
14 22 0.35
15 9 0.15
16 8 0.13
17 5 0.08
18 6 0.10
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTATTTATA
Found at i:2048361 original size:9 final size:9
Alignment explanation
Indices: 2048347--2048420 Score: 55
Period size: 9 Copynumber: 8.2 Consensus size: 9
2048337 TTTTTTATTA
2048347 TTATTTTAT
1 TTATTTTAT
2048356 TTATTTTAT
1 TTATTTTAT
*
2048365 TTATATT-T
1 TTATTTTAT
* *
2048373 TTCTTCTTCT
1 TTATT-TTAT
*
2048383 TTTTCTTTAT
1 TTAT-TTTAT
*
2048393 TTCTTTATAT
1 TTATTT-TAT
2048403 TTA-TTTAT
1 TTATTTTAT
2048411 TTA-TTTAT
1 TTATTTTAT
2048419 TT
1 TT
2048421 TACTTACTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
8 17 0.31
9 21 0.39
10 15 0.28
11 1 0.02
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTTTAT
Found at i:2048362 original size:20 final size:20
Alignment explanation
Indices: 2048325--2048365 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2048315 TATATATATA
2048325 TATTACTTTTACTTTTTTAT
1 TATTACTTTTACTTTTTTAT
*
2048345 TATTA-TTTTATTTATTTTAT
1 TATTACTTTTACTT-TTTTAT
2048365 T
1 T
2048366 TATATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTACTTTTACTTTTTTAT
Found at i:2048411 original size:18 final size:17
Alignment explanation
Indices: 2048291--2048422 Score: 63
Period size: 17 Copynumber: 7.3 Consensus size: 17
2048281 TATTTACTAT
2048291 TTTTATGTT-TTTATTTA
1 TTTTAT-TTATTTATTTA
* * * *
2048308 TTATATATATATATATA
1 TTTTATTTATTTATTTA
*
2048325 TATTACTTTTACTTT-TTTA
1 TTTTA--TTTA-TTTATTTA
2048344 TTATTATTTTATTTATTTTA
1 TT-TTA-TTTATTTA-TTTA
* *
2048364 TTTATATTTTTCTTCTTCT-
1 TTT-TATTTAT-TTATT-TA
* *
2048383 TTTTCTTTATTTCTTTA
1 TTTTATTTATTTATTTA
2048400 TATTTATTTATTTATTTA
1 T-TTTATTTATTTATTTA
2048418 TTTTA
1 TTTTA
2048423 CTTACTATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 24
0.69 0.13 0.19
Matches are distributed among these distances:
16 2 0.02
17 24 0.28
18 23 0.26
19 22 0.25
20 16 0.18
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (17 bp):
TTTTATTTATTTATTTA
Found at i:2048514 original size:27 final size:27
Alignment explanation
Indices: 2048443--2048514 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
2048433 TATCTTTGCA
*
2048443 TTATTTA--TCTTATCTTTTATTTAAT
1 TTATTTATTTCTTATCTTTTAATTAAT
* *
2048468 TTGTTT-TTT-TTCTTCATTTTAATTAAT
1 TTATTTATTTCTT-ATC-TTTTAATTAAT
2048495 TTATTTATTTCTTATCTTTT
1 TTATTTATTTCTTATCTTTT
2048515 TATCTAACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
25 7 0.19
26 3 0.08
27 19 0.53
28 5 0.14
29 2 0.06
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.71
Consensus pattern (27 bp):
TTATTTATTTCTTATCTTTTAATTAAT
Found at i:2052698 original size:103 final size:103
Alignment explanation
Indices: 2052519--2052731 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 103
2052509 AGGTCTACGC
* *
2052519 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATACTTGAT
1 GGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
2052584 CCTTGGCATATGTATATGATTCTTAAGGAATGACATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGACATGT
*
2052622 GGTCCTTCGAGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
2052687 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGACATGT
2052725 GGTCCTT
1 GGTCCTT
2052732 ATGGACATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGACATGT
Found at i:2052807 original size:23 final size:23
Alignment explanation
Indices: 2052751--2052807 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
2052741 ATTATATGGC
*
2052751 ACTTCGGTGCAATTCTATGCGAA
1 ACTTCGGTGCAATTCTACGCGAA
* * * **
2052774 ACTACGATGCAATTCTACGTGGT
1 ACTTCGGTGCAATTCTACGCGAA
2052797 ACTTCGGTGCA
1 ACTTCGGTGCA
2052808 TTTATATGAG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGAA
Found at i:2056088 original size:23 final size:22
Alignment explanation
Indices: 2056040--2056088 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2056030 ACAGAATGTC
2056040 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
2056061 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
2056084 AAGGA
1 AAGGA
2056089 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2057738 original size:103 final size:103
Alignment explanation
Indices: 2057559--2057769 Score: 377
Period size: 103 Copynumber: 2.0 Consensus size: 103
2057549 GTCTACGCGA
* *
2057559 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
1 TCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCC
* *
2057624 TTGGCATATGTATATGATTCTTAAGGAATGATATGTGG
66 CTAGCATATGTATATGATTCTTAAGGAATGATATGTGG
2057662 TCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCC
1 TCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCC
*
2057727 CTAGTATATGTATATGATTCTTAAGGAATGATATGTGG
66 CTAGCATATGTATATGATTCTTAAGGAATGATATGTGG
2057765 TCCTT
1 TCCTT
2057770 ATGGACATAA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (103 bp):
TCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCC
CTAGCATATGTATATGATTCTTAAGGAATGATATGTGG
Found at i:2057853 original size:23 final size:23
Alignment explanation
Indices: 2057785--2057845 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2057775 CATAATTATA
2057785 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
2057808 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
2057831 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
2057846 TTTATATGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:2059933 original size:18 final size:18
Alignment explanation
Indices: 2059907--2059972 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
2059897 AGATCCAATC
*
2059907 AGAACAAAAAGAAAAAAG
1 AGAAAAAAAAGAAAAAAG
*
2059925 AGAAAAAAAGGAAAAAAG
1 AGAAAAAAAAGAAAAAAG
*
2059943 CA-AATAAAAAATAAAAAAG
1 -AGAA-AAAAAAGAAAAAAG
2059962 AGAAACAAAAA
1 AGAAA-AAAAA
2059973 CAAAGAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 20 0.50
19 20 0.50
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAAGAAAAAAG
Found at i:2059982 original size:30 final size:30
Alignment explanation
Indices: 2059914--2059998 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
2059904 ATCAGAACAA
* *
2059914 AAAGAAAAAAGAGAAAAAAAGGAAAAAAGC
1 AAAGAAAAAAGAGAAAAAAAGAAAAAAAAC
* * *
2059944 AAATAAAAAATA-AAAAAGAGAAACAAAAAC
1 AAAGAAAAAAGAGAAAAAAAGAAA-AAAAAC
* *
2059974 AAAGAAAAAAGTGAAGAAAAGAAAA
1 AAAGAAAAAAGAGAAAAAAAGAAAA
2059999 GACAAGACGT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 9 0.21
30 25 0.58
31 9 0.21
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.04
Consensus pattern (30 bp):
AAAGAAAAAAGAGAAAAAAAGAAAAAAAAC
Found at i:2061588 original size:36 final size:36
Alignment explanation
Indices: 2061515--2061845 Score: 286
Period size: 36 Copynumber: 9.1 Consensus size: 36
2061505 AATTTACTCA
* *
2061515 AAACAAAGTTTTGTCTCTCCTGATACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
2061552 AAACAAATTTTATCTCTCTTGAGACAGCTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
2061588 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
2061624 AATCAAA------ATCT-TTGA-ATATGTTT-TACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-C-TTG
* * * *
2061653 AAACAAATTTTGTCTCCCTTGAGAAAGTTCCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * * *
2061689 GAACTAAGTTTTGTCTCTCTTAAGACAATTTCTTTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
2061726 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2061763 AAACAAATTTTGCCTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA---T---TTTGTCTCTCTTGAGACAGTTTCTCTTG
*
2061805 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2061841 AAACA
1 AAACA
2061846 CCAATCTTTG
Statistics
Matches: 244, Mismatches: 30, Indels: 41
0.77 0.10 0.13
Matches are distributed among these distances:
28 3 0.01
29 15 0.06
30 5 0.02
35 4 0.02
36 107 0.44
37 73 0.30
39 2 0.01
42 35 0.14
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2061782 original size:42 final size:36
Alignment explanation
Indices: 2061653--2061845 Score: 206
Period size: 37 Copynumber: 5.1 Consensus size: 36
2061643 GTTTTACATT
* * * *
2061653 AAACAAATTTTGTCTCCCTTGAGAAAGTTCCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * * *
2061689 GAACTAAGTTTTGTCTCTCTTAAGACAATTTCTTTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
2061726 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2061763 AAACAAATTTTGCCTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA---T---TTTGTCTCTCTTGAGACAGTTTCTCTTG
*
2061805 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2061841 AAACA
1 AAACA
2061846 CCAATCTTTG
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
36 37 0.27
37 63 0.46
39 2 0.01
42 35 0.26
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2061836 original size:78 final size:79
Alignment explanation
Indices: 2061698--2061845 Score: 235
Period size: 78 Copynumber: 1.9 Consensus size: 79
2061688 GGAACTAAGT
* * * *
2061698 TTTGTCTCTCTTAAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTAAGACAATTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
2061763 AAACAAATTTTGCC
66 AAACAAATTTTGCC
* *
2061777 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTG
1 TTTGTCTCTCTTAAGACAATTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
2061841 AAACA
66 AAACA
2061846 CCAATCTTTG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 35 0.56
79 28 0.44
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.43
Consensus pattern (79 bp):
TTTGTCTCTCTTAAGACAATTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
AAACAAATTTTGCC
Found at i:2061961 original size:35 final size:36
Alignment explanation
Indices: 2061898--2061982 Score: 145
Period size: 35 Copynumber: 2.4 Consensus size: 36
2061888 CCTTGGGACA
* *
2061898 GTTTATCTTGAAACACAAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
2061934 GTTTCTCTTGAAACAC-AAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
2061969 GTTTCTCTTGAAAC
1 GTTTCTCTTGAAAC
2061983 CCAAGACCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 32 0.68
36 15 0.32
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
Found at i:2062664 original size:37 final size:37
Alignment explanation
Indices: 2062573--2062683 Score: 163
Period size: 37 Copynumber: 3.0 Consensus size: 37
2062563 AACATAATGT
2062573 TAGAGTTTTACTATGATTCAAACTCCT-AAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
* * *
2062609 TATAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
2062646 TAGAGTTCTT-TTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTT-TTACTATGATTCAAACTCCTAAAAATAGGA
2062683 T
1 T
2062684 CCACAAGTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 25 0.38
37 39 0.59
38 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:2063199 original size:22 final size:21
Alignment explanation
Indices: 2063169--2063229 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
2063159 TATTTTATTT
2063169 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
2063191 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
2063214 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
2063230 ATTTTTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
22 7 0.22
23 12 0.38
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:2063226 original size:24 final size:23
Alignment explanation
Indices: 2063183--2063228 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2063173 CATGTAATAT
*
2063183 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
2063206 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
2063229 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:2063274 original size:42 final size:38
Alignment explanation
Indices: 2063228--2063364 Score: 123
Period size: 42 Copynumber: 3.3 Consensus size: 38
2063218 GTATATATTT
*
2063228 TTATTTTTTTAGATTACATATATATGTATATGTTACTTTTTA
1 TTATTTTTTT--ATTA-ATATATATATATAT-TTACTTTTTA
*
2063270 TTATTTGTTTTATTAAT-TAATATATATATTTACTATTTTT
1 TTATTT-TTTTATTAATAT-ATATATATATTTACT-TTTTA
* *
2063310 TTGTTTTTATTTATTATATATATATATATTTTTACTTTTTTA
1 TT-ATTTT-TTTATTA-ATATATATATATATTTAC-TTTTTA
*
2063352 TTATTATTTTATT
1 TTATTTTTTTATT
2063365 TATTTTATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
39 6 0.08
40 24 0.30
41 17 0.21
42 27 0.34
43 6 0.08
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.66
Consensus pattern (38 bp):
TTATTTTTTTATTAATATATATATATATTTACTTTTTA
Found at i:2063333 original size:40 final size:39
Alignment explanation
Indices: 2063245--2063376 Score: 124
Period size: 40 Copynumber: 3.2 Consensus size: 39
2063235 TTTAGATTAC
* * *
2063245 ATATATATGTATATGTTACTTTTTATTATTTGT-TTTATT
1 ATATATATATATAT-TTACTTTTTTTTATTTTTATTTATT
*
2063284 A-ATTAATATATATATTTACTATTTTTTTGTTTTTATTTATT
1 ATA-T-ATATATATATTTACT-TTTTTTTATTTTTATTTATT
2063325 ATATATATATATATTTTTACTTTTTTATTATTATTTTATTTATT
1 ATATATATATATA--TTTACTTTTTT-TTA-T-TTTTATTTATT
*
2063369 TTATATAT
1 ATATATAT
2063377 TTTTTTCTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
38 1 0.01
39 7 0.09
40 28 0.36
41 13 0.17
42 9 0.12
43 1 0.01
44 18 0.23
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (39 bp):
ATATATATATATATTTACTTTTTTTTATTTTTATTTATT
Found at i:2063342 original size:32 final size:34
Alignment explanation
Indices: 2063268--2063358 Score: 84
Period size: 36 Copynumber: 2.7 Consensus size: 34
2063258 TGTTACTTTT
* *
2063268 TATTATTTG-TTTTATTAATTAATATATATATTTAC
1 TATTTTTTGTTTTTATTTATT-ATATATATA-TTAC
2063303 TATTTTTTTGTTTTTATTTATTATATATATA-TA-
1 TA-TTTTTTGTTTTTATTTATTATATATATATTAC
2063336 TATTTTTACT-TTTTTA-TTATTAT
1 TATTTTT--TGTTTTTATTTATTAT
2063359 TTTATTTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
32 12 0.24
33 8 0.16
34 3 0.06
35 2 0.04
36 15 0.30
37 10 0.20
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (34 bp):
TATTTTTTGTTTTTATTTATTATATATATATTAC
Found at i:2063367 original size:9 final size:9
Alignment explanation
Indices: 2063355--2063422 Score: 56
Period size: 9 Copynumber: 7.9 Consensus size: 9
2063345 TTTTTTATTA
2063355 TTATTTTAT
1 TTATTTTAT
2063364 TTATTTTAT
1 TTATTTTAT
*
2063373 ATATTTT-T
1 TTATTTTAT
*
2063381 TTCTTCTT-T
1 TTATT-TTAT
*
2063390 TT-CTTTAT
1 TTATTTTAT
2063398 TT-TTTTAT
1 TTATTTTAT
2063406 ATT-TTTTAT
1 -TTATTTTAT
2063415 TTATTTTA
1 TTATTTTA
2063423 CTTACTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
7 2 0.04
8 15 0.30
9 33 0.66
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTAT
Found at i:2063374 original size:42 final size:40
Alignment explanation
Indices: 2063246--2063425 Score: 117
Period size: 42 Copynumber: 4.5 Consensus size: 40
2063236 TTAGATTACA
* * * *
2063246 TATATATGTATATGTTACTTTTTATTATTTGTTT-TATTA-AT
1 TATATATATAT-TTTTACTTTTTTTTATTT-TTTAT-TTATTT
* *
2063287 TA-ATATATATATTTACTATTTTTTT-GTTTTTATTTATTAT
1 TATATATATATTTTTACT-TTTTTTTATTTTTTATTTATT-T
2063327 ATATATATATATTTTTACTTTTTTATTATTATTTTATTTATTT
1 -TATATATATATTTTTACTTTTTT-TTATT-TTTTATTTATTT
* * *
2063370 TATATAT-TTTTTTCTTCTTTTTCTTTATTTTTT-TATATTT
1 TATATATATATTTT-TACTTTTT-TTTATTTTTTATTTATTT
*
2063410 T-T-TATTTA-TTTTACTT
1 TATATATATATTTTTACTT
2063426 ACTATTTTAT
Statistics
Matches: 114, Mismatches: 13, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
37 4 0.04
38 12 0.11
39 10 0.09
40 21 0.18
41 18 0.16
42 35 0.31
43 3 0.03
44 11 0.10
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (40 bp):
TATATATATATTTTTACTTTTTTTTATTTTTTATTTATTT
Found at i:2063377 original size:21 final size:21
Alignment explanation
Indices: 2063314--2063437 Score: 73
Period size: 20 Copynumber: 5.8 Consensus size: 21
2063304 ATTTTTTTGT
2063314 TTTTATTTATTATATATATATATA
1 TTTTATTTATT-T-TATATAT-TA
*
2063338 TTTTTACTT-TTTTAT-TATTA
1 -TTTTATTTATTTTATATATTA
2063358 TTTTATTTATTTTATATATT-
1 TTTTATTTATTTTATATATTA
* *
2063378 TTTT-TCTTCTTTT-TCT-TTA
1 TTTTAT-TTATTTTATATATTA
* *
2063397 TTTTTTTATATTTTTTAT-TTA
1 TTTTATT-TATTTTATATATTA
2063418 TTTTACTTACTATTTTATAT
1 TTTTA-TT--TATTTTATAT
2063438 TTGCATTCTT
Statistics
Matches: 81, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
18 2 0.02
19 15 0.19
20 24 0.30
21 16 0.20
22 5 0.06
23 10 0.12
24 2 0.02
25 7 0.09
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTATTTATTTTATATATTA
Found at i:2063382 original size:40 final size:38
Alignment explanation
Indices: 2063260--2063425 Score: 117
Period size: 39 Copynumber: 4.2 Consensus size: 38
2063250 TATGTATATG
* * * * *
2063260 TTACTTTTTATTATTTGTTTTA-TTAATTAATATATATAT
1 TTACTTTTT-TT-TTTATTTTATTTATTTTATATATTTTT
*
2063299 TTACTATTTTTTTGT-TTTTATTTATTATATATATATATATTT
1 TTACT-TTTTTTTTTATTTTATTTATT-T-TATATAT-T-TTT
2063341 TTACTTTTTTATTATTATTTTATTTATTTTATATATTTTT
1 TTACTTTTTT-TT-TTATTTTATTTATTTTATATATTTTT
*
2063381 TT-CTTCTTTTTCTTTATTTT-TTTATATTT-TTTATTTATT
1 TTACTT-TTTTT-TTTATTTTATTTAT-TTTATATATTT-TT
2063420 TTACTT
1 TTACTT
2063426 ACTATTTTAT
Statistics
Matches: 106, Mismatches: 7, Indels: 27
0.76 0.05 0.19
Matches are distributed among these distances:
37 5 0.05
38 17 0.16
39 26 0.25
40 23 0.22
41 6 0.06
42 16 0.15
43 2 0.02
44 11 0.10
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (38 bp):
TTACTTTTTTTTTTATTTTATTTATTTTATATATTTTT
Found at i:2063405 original size:38 final size:40
Alignment explanation
Indices: 2063260--2063425 Score: 112
Period size: 40 Copynumber: 4.2 Consensus size: 40
2063250 TATGTATATG
* * *
2063260 TTAC-TTTTTATTATTTGTTTTATTAATTAATATATATATTT
1 TTACTTTTTTATTA-TTATTTTATTTATT-TTATATATATTT
* * * * *
2063301 ACTATTTTTTTGTTTTTA-TTTA-TTATATATATATATATTT
1 -TTACTTTTTTATTATTATTTTATTTAT-TTTATATATATTT
2063341 TTACTTTTTTATTATTATTTTATTTATTTTATATAT-TTT
1 TTACTTTTTTATTATTATTTTATTTATTTTATATATATTT
* * * *
2063380 TTTCTTCTTTT-TCT-TTATTTTTTTATATTTTTTATTTA-TT
1 TTACTT-TTTTAT-TATTATTTTATT-TATTTTATATATATTT
2063420 TTACTT
1 TTACTT
2063426 ACTATTTTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
39 31 0.31
40 49 0.49
41 9 0.09
42 4 0.04
43 7 0.07
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (40 bp):
TTACTTTTTTATTATTATTTTATTTATTTTATATATATTT
Found at i:2063405 original size:82 final size:82
Alignment explanation
Indices: 2063225--2063405 Score: 183
Period size: 82 Copynumber: 2.2 Consensus size: 82
2063215 TTAGTATATA
* *
2063225 TTTTTATTTTTTTAGATTACATATATATGTATATGTTACTTTTTATTATTTGTTTTATTAATTAA
1 TTTTTATTTTTTT--ATTACATATATATATATATGTTACTTTTTATTATTTATTTTATTAATTAA
2063290 TATATATATTTACTATTTT
64 TATATATATTTACTATTTT
* * * * *
2063309 TTTGTT-TTTATTTATTATATATATATATAT-TTTTACTTTTTTATTA-TTATTTTATTTATT-T
1 TTT-TTATTTTTTTATTACATATATATATATATGTTAC-TTTTTATTATTTATTTTATTAATTAA
* *
2063370 TATATATTTTTTTCT-TCTTT
64 TATATA-TATTTACTAT-TTT
2063390 TTCTTTATTTTTTTAT
1 TT-TTTATTTTTTTAT
2063406 ATTTTTTATT
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
80 7 0.09
81 30 0.37
82 33 0.41
84 9 0.11
85 2 0.02
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (82 bp):
TTTTTATTTTTTTATTACATATATATATATATGTTACTTTTTATTATTTATTTTATTAATTAATA
TATATATTTACTATTTT
Found at i:2063896 original size:25 final size:25
Alignment explanation
Indices: 2063858--2063905 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2063848 TCCGACAGTG
* *
2063858 AGGCATAAATATGTTTTATTGATCT
1 AGGCATAAACATGTTCTATTGATCT
*
2063883 AGGCATATACATGTTCTATTGAT
1 AGGCATAAACATGTTCTATTGAT
2063906 GAAATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (25 bp):
AGGCATAAACATGTTCTATTGATCT
Found at i:2065367 original size:27 final size:26
Alignment explanation
Indices: 2065316--2065368 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
2065306 AATTACTCAA
* *
2065316 GCTATTAGGGAATTTTTAGTCATTTT
1 GCTATTAGGGAAATTTTAGTAATTTT
*
2065342 GCTATTAGGAGAAATTTTGGTAATTTT
1 GCTATTAGG-GAAATTTTAGTAATTTT
2065369 TCTAATGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (26 bp):
GCTATTAGGGAAATTTTAGTAATTTT
Found at i:2071752 original size:19 final size:19
Alignment explanation
Indices: 2071728--2071764 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2071718 GCTCAGCTCA
* *
2071728 GGCGGTTTAGACCGATTTG
1 GGCGGTCTAGACCAATTTG
2071747 GGCGGTCTAGACCAATTT
1 GGCGGTCTAGACCAATTT
2071765 CTAGAACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (19 bp):
GGCGGTCTAGACCAATTTG
Found at i:2076137 original size:34 final size:35
Alignment explanation
Indices: 2076073--2076138 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2076063 AAGGAGGATA
2076073 TATTTGTTTAATATTTTAAATTTAAAAGATATTAT
1 TATTTGTTTAATATTTTAAATTTAAAAGATATTAT
*
2076108 TATTTGTTTAA-A-TTTAGATATTAAAAGATAT
1 TATTTGTTTAATATTTTAAAT-TTAAAAGATAT
2076139 CTAGTTGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 6 0.21
34 12 0.41
35 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.52
Consensus pattern (35 bp):
TATTTGTTTAATATTTTAAATTTAAAAGATATTAT
Found at i:2078735 original size:149 final size:151
Alignment explanation
Indices: 2078529--2078829 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 151
2078519 GGCTATACCG
2078529 AACATAGAAATGCATACTGATTTCTTGTGTAATAACAAAGAATCCTGAGATACACAAGAACACGA
1 AACATAGAAATGCATACTGATTTCTTGTGTAATAACAAAGAATCCTGAGATACACAAGAACACGA
2078594 TAATAGAATCAAATAATGCATCATTCTTTTAAAATATTTT-TCTTATAAATCTAAGAGG-TGTTC
66 TAATAGAATCAAATAATGCATCATTCTTTTAAAATATTTTCTCTTATAAATCTAAGAGGTTGTTC
2078657 AAAGTTTAATAAAAAG-ACTTT
131 AAAG-TTAATAAAAAGAACTTT
*
2078678 AACATAGAAATGCATATTGATTTCTTGTGTAATAACAAAGAATCCTGAGATACACAAGAACACGA
1 AACATAGAAATGCATACTGATTTCTTGTGTAATAACAAAGAATCCTGAGATACACAAGAACACGA
2078743 TAATAGAATCAAATAATGCATCATTCTTTTAAAATATTTTCTCTTATAAATCTAAGAGGTTGTTC
66 TAATAGAATCAAATAATGCATCATTCTTTTAAAATATTTTCTCTTATAAATCTAAGAGGTTGTTC
*
2078808 AAAGTTAATAAAATGAACTTT
131 AAAGTTAATAAAAAGAACTTT
2078829 A
1 A
2078830 GAGATTAATA
Statistics
Matches: 147, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
149 104 0.71
150 28 0.19
151 15 0.10
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (151 bp):
AACATAGAAATGCATACTGATTTCTTGTGTAATAACAAAGAATCCTGAGATACACAAGAACACGA
TAATAGAATCAAATAATGCATCATTCTTTTAAAATATTTTCTCTTATAAATCTAAGAGGTTGTTC
AAAGTTAATAAAAAGAACTTT
Found at i:2085058 original size:17 final size:18
Alignment explanation
Indices: 2085032--2085069 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2085022 ATATGTTTGA
* *
2085032 ATTATTTTAAA-ATTCTG
1 ATTATATTAAATATTATG
2085049 ATTATATTAAATATTATG
1 ATTATATTAAATATTATG
2085067 ATT
1 ATT
2085070 GCATGATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTATATTAAATATTATG
Found at i:2102573 original size:25 final size:26
Alignment explanation
Indices: 2102524--2102573 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2102514 ATTTTATGTT
* *
2102524 AGAAGATCAATTTATAACATTTTAAA
1 AGAAGATCAACTTACAACATTTTAAA
*
2102550 AGAAGATGAACTTACAA-ATTTTAA
1 AGAAGATCAACTTACAACATTTTAA
2102574 GAAACAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (26 bp):
AGAAGATCAACTTACAACATTTTAAA
Done.