Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2216176 original size:16 final size:17
Alignment explanation
Indices: 2216155--2216194 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2216145 AAAAGTTGAA
2216155 AATTTATAATTTAA-TC
1 AATTTATAATTTAATTC
*
2216171 AATTTA-ACTTTAATTC
1 AATTTATAATTTAATTC
2216187 AATTTATA
1 AATTTATA
2216195 TATTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 14 0.67
17 1 0.05
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTATAATTTAATTC
Found at i:2216249 original size:22 final size:22
Alignment explanation
Indices: 2216202--2216246 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2216192 ATATATTATT
***
2216202 ATTACTATTATAATTTTTTTGA
1 ATTACTATTATAATTTTAAAGA
2216224 ATTACTATTATAAATTTTAAAGA
1 ATTACTATTAT-AATTTTAAAGA
2216247 TTATAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTACTATTATAATTTTAAAGA
Found at i:2220478 original size:31 final size:30
Alignment explanation
Indices: 2220443--2220557 Score: 87
Period size: 29 Copynumber: 3.9 Consensus size: 30
2220433 GGATTACCAT
2220443 TTAAAATAAATATCTAAAGTTATTTTTTTTG
1 TTAAAATAAATATCTAAAG-TATTTTTTTTG
** *
2220474 TTAAAATATGTATTTAAAGTA--TTTTTTG
1 TTAAAATAAATATCTAAAGTATTTTTTTTG
* * *
2220502 ATTAAAATATATACCAAAAGTATTTATTTTT-
1 -TTAAAATAAATATCTAAAGTATTT-TTTTTG
** *
2220533 TT-ATCTAAGTATCT-AAGTATTTTTT
1 TTAAAATAAATATCTAAAGTATTTTTT
2220558 AATTAATGCC
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
27 3 0.04
28 15 0.22
29 23 0.34
30 4 0.06
31 17 0.25
32 5 0.07
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.51
Consensus pattern (30 bp):
TTAAAATAAATATCTAAAGTATTTTTTTTG
Found at i:2220672 original size:3 final size:3
Alignment explanation
Indices: 2220653--2220704 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
2220643 TTTTTCATAC
* * *
2220653 TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT TAT ATAT TATT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT
2220700 TAT TA
1 TAT TA
2220705 CAAAACCCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2221952 original size:20 final size:18
Alignment explanation
Indices: 2221924--2221975 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
2221914 TTTCAAATTA
*
2221924 TTATCTTTATTTTTGATACT
1 TTATATTTATTTTT-ATA-T
*
2221944 TTATATTTAGTTTTATAT
1 TTATATTTATTTTTATAT
*
2221962 TTTTAATTTATTTT
1 TTAT-ATTTATTTT
2221976 ATTTTAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 11 0.41
20 12 0.44
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (18 bp):
TTATATTTATTTTTATAT
Found at i:2222376 original size:114 final size:116
Alignment explanation
Indices: 2222169--2222377 Score: 262
Period size: 114 Copynumber: 1.8 Consensus size: 116
2222159 TATGTTTTAG
** *
2222169 TTATTTATTTATTTAAATATTGAAGGAAAGAGCTGTCTTAAAACAACTAGAAACCCTTTTCTAAT
1 TTATTTATTTATTTAAATATCAAAGGAAAGAACTGTCTTAAAACAACTAGAAACCCTTTTCTAAT
* *
2222234 ATTTTTAAATAAATAAATATCCTATTATATTAAAATAAATTATATAATTAT
66 ATTTCTAAATAAATAAATATACTATTATATTAAAATAAATTATATAATTAT
*** * ** *
2222285 TTATTTATTT-TTT-AATATCAAAGGAAAGAACTGTCTTAAGGTACCTAG-AAGTCTTTTCTGAT
1 TTATTTATTTATTTAAATATCAAAGGAAAGAACTGTCTTAAAACAACTAGAAACCCTTTTCTAAT
* *
2222347 ATTTCTAAATAAGTAAATATATTATTTATAT
66 ATTTCTAAATAAATAAATATACTA-TTATAT
2222378 ATTAATATAT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
113 31 0.40
114 34 0.44
115 3 0.04
116 10 0.13
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.43
Consensus pattern (116 bp):
TTATTTATTTATTTAAATATCAAAGGAAAGAACTGTCTTAAAACAACTAGAAACCCTTTTCTAAT
ATTTCTAAATAAATAAATATACTATTATATTAAAATAAATTATATAATTAT
Found at i:2223464 original size:29 final size:29
Alignment explanation
Indices: 2223418--2223473 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
2223408 TGGCATATTT
* *
2223418 TTTTAATTTAACGGTTAACGTTTATTTCA
1 TTTTAATTTAACAGTTAACATTTATTTCA
* * *
2223447 TTTTAATTTAATATTTAATATTTATTT
1 TTTTAATTTAACAGTTAACATTTATTT
2223474 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (29 bp):
TTTTAATTTAACAGTTAACATTTATTTCA
Found at i:2227254 original size:15 final size:16
Alignment explanation
Indices: 2227220--2227259 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 16
2227210 AATTCAAATG
2227220 CTGAATGATTTAGAGACT
1 CTGAATGATTT--AGACT
2227238 CTGAATGATTT-GACT
1 CTGAATGATTTAGACT
2227253 CTGAATG
1 CTGAATG
2227260 TGACATGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.50
18 11 0.50
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (16 bp):
CTGAATGATTTAGACT
Found at i:2231227 original size:48 final size:46
Alignment explanation
Indices: 2231137--2231227 Score: 103
Period size: 48 Copynumber: 1.9 Consensus size: 46
2231127 CACACTCCAA
* * * * *
2231137 TTTGCCTTTTCATCGACTAGGAGGTTGGTTAGAGCCATTTATCGTG
1 TTTGCCTTTTCATCGACTAGGAGGCTCGATAGAGACACTTATCGTG
2231183 TTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACACTTATC
1 TTTGCCTTTTCA-T-CGACTAGGA-GGCTCGATAGAGACACTTATC
2231228 CATCTATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
46 12 0.32
47 1 0.03
48 17 0.46
49 7 0.19
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (46 bp):
TTTGCCTTTTCATCGACTAGGAGGCTCGATAGAGACACTTATCGTG
Found at i:2231702 original size:11 final size:11
Alignment explanation
Indices: 2231686--2231715 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2231676 TATTTTTTTT
2231686 AAAAAAACAAA
1 AAAAAAACAAA
2231697 AAAAAAACAAA
1 AAAAAAACAAA
2231708 AAACAAAA
1 AAA-AAAA
2231716 AAGGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:2231710 original size:13 final size:13
Alignment explanation
Indices: 2231686--2231742 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
2231676 TATTTTTTTT
2231686 AAAAAAAC--AAA
1 AAAAAAACAAAAA
2231697 AAAAAAACAAAAA
1 AAAAAAACAAAAA
2231710 ACAAAAAAGGCAAAAA
1 A-AAAAAA--CAAAAA
**
2231726 AAAAAGGCAAAAA
1 AAAAAAACAAAAA
2231739 AAAA
1 AAAA
2231743 GAGCCAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 8 0.21
13 14 0.36
14 6 0.15
15 4 0.10
16 7 0.18
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:2231726 original size:18 final size:17
Alignment explanation
Indices: 2231686--2231742 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 17
2231676 TATTTTTTTT
2231686 AAAAAAACAAAAAAAAA
1 AAAAAAACAAAAAAAAA
2231703 ACAAAAAACAAAAAAGGCAAA
1 A-AAAAAACAAAAAA---AAA
2231724 AAAAAAAGGCAAAAAAAAA
1 AAAAAAA--CAAAAAAAAA
2231743 GAGCCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.03
18 13 0.38
19 3 0.09
20 6 0.18
21 4 0.12
22 7 0.21
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAAAA
Found at i:2231738 original size:14 final size:14
Alignment explanation
Indices: 2231694--2231754 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
2231684 TTAAAAAAAC
2231694 AAAAAAAAAA--CAA
1 AAAAAAAAAAGGC-A
2231707 AAAACAAAAAAGGC-
1 AAAA-AAAAAAGGCA
2231721 AAAAAAAAAAGGCA
1 AAAAAAAAAAGGCA
* *
2231735 AAAAAAAAGAGCCA
1 AAAAAAAAAAGGCA
2231749 AAAAAA
1 AAAAAA
2231755 GCCAAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 13 0.31
14 28 0.67
16 1 0.02
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGGCA
Found at i:2231742 original size:27 final size:25
Alignment explanation
Indices: 2231686--2231742 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
2231676 TATTTTTTTT
2231686 AAAAAAA-CAAAAAAAAAACAAAAA
1 AAAAAAAGCAAAAAAAAAACAAAAA
2231710 ACAAAAAAGGCAAAAAAAAAAGGCAAAAA
1 A-AAAAAA-GCAAAAAAAAAA--CAAAAA
2231739 AAAA
1 AAAA
2231743 GAGCCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 1 0.04
25 6 0.21
27 11 0.39
28 3 0.11
29 7 0.25
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (25 bp):
AAAAAAAGCAAAAAAAAAACAAAAA
Found at i:2231743 original size:12 final size:12
Alignment explanation
Indices: 2231712--2231754 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
2231702 AACAAAAAAC
2231712 AAAAAAGGCAAAA
1 AAAAAAGGC-AAA
2231725 AAAAAAGGCAAA
1 AAAAAAGGCAAA
2231737 AAAAAAGAGCCAAA
1 AAAAAAG-G-CAAA
2231751 AAAA
1 AAAA
2231755 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.36
13 10 0.36
14 8 0.29
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGGCAAA
Found at i:2235466 original size:42 final size:44
Alignment explanation
Indices: 2235374--2235473 Score: 107
Period size: 49 Copynumber: 2.2 Consensus size: 44
2235364 AGGATCAGAC
*
2235374 TTATTATTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTA
1 TTATTATTTATTAGGAATTAA-G--GGGTTAAAAC-A-ATGTTTAGTTA
2235423 TTATTATTTATTAGGAATT-A-GGGTTAAAAC-ATGTTTAGTTTA
1 TTATTATTTATTAGGAATTAAGGGGTTAAAACAATGTTTAG-TTA
*
2235465 TTAATATTT
1 TTATTATTT
2235474 TATTCTTTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
41 7 0.15
42 11 0.23
44 10 0.21
48 1 0.02
49 19 0.40
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (44 bp):
TTATTATTTATTAGGAATTAAGGGGTTAAAACAATGTTTAGTTA
Found at i:2239188 original size:59 final size:59
Alignment explanation
Indices: 2239086--2239210 Score: 178
Period size: 59 Copynumber: 2.1 Consensus size: 59
2239076 CAGCAGGCTG
** *
2239086 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATAGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATAGTGGGCACGACCTTATGTGT
* ** * *
2239145 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATAGTGGGCACGACCTTATGTGT
2239204 CATATTC
1 CATATTC
2239211 AGGATATAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATAGTGGGCACGACCTTATGTGT
Found at i:2247258 original size:15 final size:15
Alignment explanation
Indices: 2247238--2247268 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2247228 CAAAAAATAG
2247238 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
2247253 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
2247268 A
1 A
2247269 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:2247442 original size:20 final size:20
Alignment explanation
Indices: 2247406--2247443 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2247396 ATCCTATTCC
**
2247406 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
2247426 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2247444 GTAAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2253802 original size:17 final size:18
Alignment explanation
Indices: 2253769--2253805 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2253759 TTTAAGATTT
2253769 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
2253788 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
2253805 T
1 T
2253806 TCGAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:2271852 original size:2 final size:2
Alignment explanation
Indices: 2271845--2271871 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2271835 TCACATACGA
2271845 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2271872 CCTTGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2277519 original size:6 final size:6
Alignment explanation
Indices: 2277510--2277534 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2277500 TTAATGTTAA
2277510 TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT T
2277535 TTTTAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:2277816 original size:16 final size:16
Alignment explanation
Indices: 2277795--2277831 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2277785 TAACGCCGTC
2277795 AGTGAGGAAACGACTG
1 AGTGAGGAAACGACTG
2277811 AGTGAGGAAACGACTG
1 AGTGAGGAAACGACTG
2277827 AGTGA
1 AGTGA
2277832 CCAAAAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.38, T:0.14
Consensus pattern (16 bp):
AGTGAGGAAACGACTG
Found at i:2278878 original size:59 final size:60
Alignment explanation
Indices: 2278776--2278901 Score: 166
Period size: 59 Copynumber: 2.1 Consensus size: 60
2278766 TGACATAACA
**** *
2278776 CATTAAAAAAAGTTAATTTTTAATTTAATTCTT-ATTTTTTTTAAATCTCTC-ATCTAAAC
1 CATTAAAAAAAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAAT-TAAAC
*
2278835 CATTAAAAAGAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAATTAAAC
1 CATTAAAAAAAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAATTAAAC
*
2278895 CCTTAAA
1 CATTAAA
2278902 CACCCGACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
59 32 0.55
60 24 0.41
61 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (60 bp):
CATTAAAAAAAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAATTAAAC
Found at i:2291360 original size:50 final size:51
Alignment explanation
Indices: 2291305--2291409 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 51
2291295 TCAAGTTTTT
* * ** * * * *
2291305 TTTTTCAAGATAAGTCGAGTTGAAAGGATT-ATTTTTTAGGTCGAGTAAAA
1 TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAAAA
*
2291355 TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAGAA
1 TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAAAA
2291406 TTTT
1 TTTT
2291410 GCTCAGCTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 25 0.56
51 20 0.44
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (51 bp):
TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAAAA
Found at i:2292482 original size:62 final size:61
Alignment explanation
Indices: 2292376--2292498 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 61
2292366 CCGTGTAAGA
** *
2292376 GAATTAACCAGACAATATTCGAAATCTCCTGGATTTTCTCCCTTATTTACAGGAAAAATTG
1 GAATTAACCAGACAATATTAAAAATCTACTGGATTTTCTCCCTTATTTACAGGAAAAATTG
* * *
2292437 GAATTAACCAGAGAATATTAAAAAATCTACTGGATTGGTT-T-CCTTATTTGCAGGAAAGATTG
1 GAATTAACCAGACAATATT-AAAAATCTACTGGATT--TTCTCCCTTATTTACAGGAAAAATTG
2292499 TTTCCAACTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
61 18 0.34
62 32 0.60
63 1 0.02
64 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (61 bp):
GAATTAACCAGACAATATTAAAAATCTACTGGATTTTCTCCCTTATTTACAGGAAAAATTG
Found at i:2293585 original size:18 final size:18
Alignment explanation
Indices: 2293562--2293596 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2293552 TTTTGGAAAG
* *
2293562 TTGAAATAAAATTAAGAT
1 TTGAAAGAAAATAAAGAT
2293580 TTGAAAGAAAATAAAGA
1 TTGAAAGAAAATAAAGA
2293597 AACTAAATTA
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:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
TTGAAAGAAAATAAAGAT
Found at i:2298073 original size:7 final size:7
Alignment explanation
Indices: 2298061--2298085 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2298051 AATTATGAAG
2298061 TGAATAA
1 TGAATAA
2298068 TGAATAA
1 TGAATAA
2298075 TGAATAA
1 TGAATAA
2298082 TGAA
1 TGAA
2298086 CGGTACATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
TGAATAA
Found at i:2300009 original size:32 final size:31
Alignment explanation
Indices: 2299973--2300041 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2299963 TTGGTTAAAT
* *
2299973 AAATTTCAGTTCGATTAATGGTTATAGAAAAA
1 AAATTT-AGTTCGATTAACGGTTAAAGAAAAA
*
2300005 AAATTTGGTTCGATTAACGGTTAAAGAAAAA
1 AAATTTAGTTCGATTAACGGTTAAAGAAAAA
*
2300036 ATATTT
1 AAATTT
2300042 TATTTGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (31 bp):
AAATTTAGTTCGATTAACGGTTAAAGAAAAA
Found at i:2300017 original size:31 final size:31
Alignment explanation
Indices: 2299981--2300041 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2299971 ATAAATTTCA
* *
2299981 GTTCGATTAATGGTTATAGAAAAAAAATTTG
1 GTTCGATTAACGGTTAAAGAAAAAAAATTTG
*
2300012 GTTCGATTAACGGTTAAAGAAAAAATATTT
1 GTTCGATTAACGGTTAAAGAAAAAAAATTT
2300042 TATTTGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTCGATTAACGGTTAAAGAAAAAAAATTTG
Found at i:2300141 original size:94 final size:94
Alignment explanation
Indices: 2300040--2300251 Score: 388
Period size: 94 Copynumber: 2.3 Consensus size: 94
2300030 GAAAAAATAT
2300040 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAACATTAATCGAACCA
1 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAACATTAATCGAACCA
*
2300105 AAATTATTTGACCGTTAATCGAACCGAAA
66 AAATTATTTGACCGTTAATCAAACCGAAA
*
2300134 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTCTTTACCATTAATCGAACCA
1 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAACATTAATCGAACCA
* *
2300199 AAATTATTTGACTGTTACTCAAACCGAAA
66 AAATTATTTGACCGTTAATCAAACCGAAA
2300228 TTTATTTGAAAATTATTAACCGAA
1 TTTATTTGAAAATTATTAACCGAA
2300252 TTTTTTTCTT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 114 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (94 bp):
TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAACATTAATCGAACCA
AAATTATTTGACCGTTAATCAAACCGAAA
Found at i:2300284 original size:81 final size:80
Alignment explanation
Indices: 2300162--2300333 Score: 281
Period size: 81 Copynumber: 2.1 Consensus size: 80
2300152 ACCGAACCAA
* * * *
2300162 ATTAACCGATTTTTTTTCTTTACCATTAATCGAACCAAAATTATTTGACTGTTACTCAAACCGAA
1 ATTAACCGAATTTTTTTCTTTACCATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAA
2300227 ATTTATTTGAAAATT
66 ATTTATTTGAAAATT
* *
2300242 ATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCCA
1 ATTAACCGAATTTTTTTCTTT-ACCATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCA
2300307 AATTTATTTGAAAATT
65 AATTTATTTGAAAATT
2300323 ATTAACCGAAT
1 ATTAACCGAAT
2300334 AAAATAAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 20 0.24
81 65 0.76
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (80 bp):
ATTAACCGAATTTTTTTCTTTACCATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAA
ATTTATTTGAAAATT
Found at i:2300370 original size:66 final size:66
Alignment explanation
Indices: 2300290--2300533 Score: 278
Period size: 66 Copynumber: 3.7 Consensus size: 66
2300280 AAATTATTTG
2300290 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTT
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTT
2300355 A
66 A
* * ***
2300356 ACCGTTAATTGAACCGAAATTTATTTGAAAATTATTAACCGAA-ACAAATCAACCGATTTTTTTC
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATA-AAAT-AAATTA-TTTTTTC
2300420 TTTA
63 TTTA
* * *** * * * *
2300424 ACCATTAATCGAA-CCAAAATTATTTGACCGTTAATCGAATCGAATAAAATAAATT-CTTTTTCC
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATT-AT-TAACCGAATAAAATAAATTATTTTTTCT
2300487 TTA
64 TTA
* *
2300490 CCCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAT
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAAT
2300534 CGAATTAACC
Statistics
Matches: 143, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
65 8 0.06
66 67 0.47
67 31 0.22
68 26 0.18
69 10 0.07
70 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (66 bp):
ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTT
A
Found at i:2300444 original size:134 final size:137
Alignment explanation
Indices: 2300294--2300585 Score: 387
Period size: 134 Copynumber: 2.2 Consensus size: 137
2300284 TATTTGACCG
* * * *
2300294 TTAATCGAACCCAAATTTATTTGAAAATT-AT-TAACCGAATAAAATAAATTATTTTTTCTTTAA
1 TTAATCGAACCAAAATTTATTTGAAAATTAATCGAACCGAATAAAATAAATT-CTTTTTCCTTAA
*
2300357 CCGTTAATTGAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATCAACCG-A-TTTTTTTC
65 CCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATCAACCGAATTTTTTTTC
**
2300420 TTTAACCA
130 TGGAACCA
*** * *
2300428 TTAATCGAACCAAAA-TTATTTGACCGTTAATCGAATCGAATAAAATAAATTCTTTTTCCTTACC
1 TTAATCGAACCAAAATTTATTTGAAAATTAATCGAACCGAATAAAATAAATTCTTTTTCCTTAAC
* * *
2300492 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAATCGAATTAACCGAATTTTTTTTCT
66 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATCAACCGAATTTTTTTTCT
2300557 GGAACCA
131 GGAACCA
**
2300564 TTAATCGAACTGAAATTTATTT
1 TTAATCGAACCAAAATTTATTT
2300586 AACCAAATAA
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
133 10 0.07
134 75 0.55
135 18 0.13
136 27 0.20
137 6 0.04
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (137 bp):
TTAATCGAACCAAAATTTATTTGAAAATTAATCGAACCGAATAAAATAAATTCTTTTTCCTTAAC
CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATCAACCGAATTTTTTTTCT
GGAACCA
Found at i:2301466 original size:30 final size:30
Alignment explanation
Indices: 2301421--2301512 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
2301411 AAAATTTAAA
*
2301421 AACAG-AAAATAAAAGGGC-TGAAATATAAAT
1 AACAGAAAAAT-AAAGGGCAT-AAATACAAAT
*
2301451 ATA-AGAAAAATAAAGGGCATAAATGCAAAT
1 A-ACAGAAAAATAAAGGGCATAAATACAAAT
* * *
2301481 AACAGAAAAATAAAGTGTATAAATATAAAT
1 AACAGAAAAATAAAGGGCATAAATACAAAT
2301511 AA
1 AA
2301513 ACGAAAGTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 1 0.02
30 44 0.85
31 7 0.13
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.18
Consensus pattern (30 bp):
AACAGAAAAATAAAGGGCATAAATACAAAT
Found at i:2301555 original size:4 final size:4
Alignment explanation
Indices: 2301546--2301592 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
2301536 TTTTCGTCCA
* *
2301546 TATT TATT TATT TATT TATT TATT TATT TGTT T-TT TATT TATA TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
2301593 ATATAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2301725 original size:37 final size:37
Alignment explanation
Indices: 2301585--2301840 Score: 154
Period size: 37 Copynumber: 6.9 Consensus size: 37
2301575 GTTTTTTATT
* *
2301585 TATATATTATATAATTTTGAAAACA-TTTTG--AA-AA
1 TATATAATATATAGTTTT-AAAACATTTTTGAAAAGAA
* * * * * *
2301619 TATATGATATATAATTTTTAAA-ATATTTTAAAAACATT
1 TATATAATATATAGTTTTAAAACAT-TTTTGAAAAGA-A
* * *
2301657 TATATATTATATAGTTTTAAAACGTTTTTGAAAAGGA
1 TATATAATATATAGTTTTAAAACATTTTTGAAAAGAA
*
2301694 -ATATAATATATAGTTTTCAAAACATTTTTGAAAA-TA
1 TATATAATATATAGTTTT-AAAACATTTTTGAAAAGAA
* * * * *
2301730 TACATATTATATAGTTTTTAAA-AGTTTTGAAAATAAA
1 TATATAATATATAGTTTTAAAACATTTTTGAAAA-GAA
* *
2301767 TATATAATATATAATTTTTTGAAAA-ATATTTTG-AAAGCA
1 TATATAATATAT-A-GTTTT-AAAACAT-TTTTGAAAAGAA
* * *
2301806 TATATAATATGTAATTTTTAAAACATTTTTAAAAA
1 TATATAATATAT-AGTTTTAAAACATTTTTGAAAA
2301841 TTATATGGTT
Statistics
Matches: 174, Mismatches: 31, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
32 1 0.01
33 3 0.02
34 20 0.11
35 10 0.06
36 22 0.13
37 50 0.29
38 37 0.21
39 19 0.11
40 7 0.04
41 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAACATTTTTGAAAAGAA
Found at i:2301772 original size:74 final size:75
Alignment explanation
Indices: 2301615--2301784 Score: 204
Period size: 74 Copynumber: 2.3 Consensus size: 75
2301605 AAACATTTTG
* * * * *
2301615 AAAATATATGATATATAATTTTTAAAATATTTTAAAAACATTTATATATTATATAGTTTTAAAAC
1 AAAATATATAATATATAATTTTCAAAACATTTTAAAAACATATACATATTATATAGTTTTAAAAC
2301680 GTTTTTGAAA
66 GTTTTTGAAA
** * **
2301690 AGGA-ATATAATATATAGTTTTCAAAACATTTTTGAAA-ATATACATATTATATAGTTTTTAAAA
1 AAAATATATAATATATAATTTTCAAAACATTTTAAAAACATATACATATTATATAG-TTTTAAAA
2301753 -G-TTTTGAAA
65 CGTTTTTGAAA
2301762 ATAAATATATAATATATAATTTT
1 A-AAATATATAATATATAATTTT
2301785 TTGAAAAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
72 9 0.11
73 17 0.22
74 51 0.65
75 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (75 bp):
AAAATATATAATATATAATTTTCAAAACATTTTAAAAACATATACATATTATATAGTTTTAAAAC
GTTTTTGAAA
Found at i:2301875 original size:34 final size:33
Alignment explanation
Indices: 2301825--2301892 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
2301815 TGTAATTTTT
* *
2301825 AAAACATTTTTAAAAATTATATGGTTTTTTAAAA
1 AAAACACTTTTAAAAATTATATAG-TTTTTAAAA
*
2301859 AAAACACTTTTGAAAATTATATAGTTTTTAAAA
1 AAAACACTTTTAAAAATTATATAGTTTTTAAAA
2301892 A
1 A
2301893 TGGTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 10 0.32
34 21 0.68
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (33 bp):
AAAACACTTTTAAAAATTATATAGTTTTTAAAA
Found at i:2301979 original size:3 final size:3
Alignment explanation
Indices: 2301971--2302030 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
2301961 GTTTTTATAT
*
2301971 TTA TTA TTA TTA TTA TTA TCA TTA TTTA TTA TTA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
2302015 CTTA TT- TTA TT- TTA TT
1 -TTA TTA TTA TTA TTA TT
2302031 TTTTCACGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 8 0.16
3 36 0.72
4 6 0.12
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2301998 original size:25 final size:24
Alignment explanation
Indices: 2301968--2302034 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
2301958 ATAGTTTTTA
2301968 TATTTATTATTATTATTATTATCA-T
1 TATTTATTATTATT-TT-TTATCACT
*
2301993 TATTTATTATTATTTTTTATTACT
1 TATTTATTATTATTTTTTATCACT
2302017 TATTTTATT-TTATTTTTT
1 TA-TTTATTATTATTTTTT
2302035 CACGTTTCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 5 0.13
24 14 0.36
25 20 0.51
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (24 bp):
TATTTATTATTATTTTTTATCACT
Found at i:2302032 original size:10 final size:11
Alignment explanation
Indices: 2301974--2302030 Score: 59
Period size: 10 Copynumber: 5.5 Consensus size: 11
2301964 TTTATATTTA
2301974 TTATTATTATT
1 TTATTATTATT
*
2301985 ATTATCATTA-T
1 -TTATTATTATT
2301996 TTATTATTATT
1 TTATTATTATT
*
2302007 TT-TTATTA-C
1 TTATTATTATT
2302016 TTATT-TTATT
1 TTATTATTATT
2302026 TTATT
1 TTATT
2302031 TTTTCACGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 5 0.13
10 21 0.55
11 4 0.11
12 8 0.21
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTATTATT
Found at i:2303669 original size:3 final size:3
Alignment explanation
Indices: 2303661--2303692 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2303651 TTACTTACTT
2303661 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2303693 TGATTTATTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2304791 original size:17 final size:17
Alignment explanation
Indices: 2304771--2304803 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2304761 CTCACTAACC
*
2304771 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
2304788 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
2304804 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:2305458 original size:19 final size:19
Alignment explanation
Indices: 2305424--2305468 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2305414 ATTTAGACAT
2305424 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
2305442 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
2305461 TTTGCATT
1 TTTGCATT
2305469 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:2309045 original size:84 final size:82
Alignment explanation
Indices: 2308871--2309665 Score: 779
Period size: 84 Copynumber: 9.7 Consensus size: 82
2308861 TAAACAAACT
* * * * ** * *
2308871 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-T-GCCAAAGTCCCCCGAGTTTGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTAACCAAAGACCTTCGAGTTCGACTACACT
* *
2308934 CAGCTTCGAGGGCACATC
66 CAGC-TCAACGGCACATC
* * * * * * * *
2308952 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAATACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TAACC-AAAGACCTTCGAGTTCGACTACA
*
2309017 CTCAGCTCAACGGCATATC
64 CTCAGCTCAACGGCACATC
** * * ** *
2309036 ATTTGCAGCATAGTTTAAGTCGAGAAGGGCTATC-T-GCCAAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTAACCAAAGACCTTCGAGTTCGACTACACT
* *
2309099 CAGCTTCGAGGGCACATC
66 CAGC-TCAACGGCACATC
* * *
2309117 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT--TAACCAAAGACCTTCGAGTTCGACTACA
2309182 CTCAGCTCTAA-GGCACATC
64 CTCAGCTC-AACGGCACATC
* * * * ** *
2309201 ATTTGCAGCATAGCTTGAGTCGAGAAGGGCTATC-T-GCCAAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTAACCAAAGACCTTCGAGTTCGACTACACT
* *
2309264 CAGCTTCGAGGGCACATC
66 CAGC-TCAACGGCACATC
* * * *
2309282 ATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT--TAACCAAAGACCTTCGAGTTCGACTACA
*
2309347 CTCAGCTCAACGGCACAAC
64 CTCAGCTCAACGGCACATC
* * * ** *
2309366 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATC-T-ACCAAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTAACCAAAGACCTTCGAGTTCGACTACACT
* * *
2309429 CAGCTTCGAGGGTACATC
66 CAGC-TCAACGGCACATC
*
2309447 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT--AACCAAAGACCTTCGAGTTCGACTACA
*
2309512 CTCAGCTCCAA-GGCATATC
64 CTCAGCT-CAACGGCACATC
* * * *
2309531 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTTCCAACAAAAGACCTT-GAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT--AACCAAAGACCTTCGAGTTCGACTACA
*
2309595 CTCAGCTCAACGGTACATC
64 CTCAGCTCAACGGCACATC
* * *
2309614 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC-T-GCTAAAGACCTTCGAGT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTAACCAAAGACCTTCGAGT
2309666 GCAATTATAT
Statistics
Matches: 584, Mismatches: 106, Indels: 49
0.79 0.14 0.07
Matches are distributed among these distances:
79 10 0.02
80 81 0.14
81 151 0.26
82 6 0.01
83 56 0.10
84 176 0.30
85 104 0.18
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (82 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTAACCAAAGACCTTCGAGTTCGACTACACT
CAGCTCAACGGCACATC
Found at i:2309145 original size:165 final size:164
Alignment explanation
Indices: 2308871--2309650 Score: 1161
Period size: 165 Copynumber: 4.7 Consensus size: 164
2308861 TAAACAAACT
* *
2308871 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGTCCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * ** *
2308936 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAATAC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGAC
*
2309000 CTTTGAGTTCGACTACGCTCAGCTCAACGGCATATC
130 CTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATC
*
2309036 ATTTGCAGCATAGTTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
2309101 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
2309166 TTTGAGTTCGACTACGCTCAGCTCTAAGGCACATC
131 TTTGAGTTCGACTACGCTCAGCTC-AAGGCACATC
*
2309201 ATTTGCAGCATAGCTTGAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
2309266 GCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
*
2309331 TTTGAGTTCGACTACGCTCAGCTCAACGGCACAAC
131 TTTGAGTTCGACTACGCTCAGCTCAA-GGCACATC
* *
2309366 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* *
2309431 GCTTCGAGGGTACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
* *
2309496 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
131 TTTGAGTTCGACTACGCTCAGCT-CAAGGCACATC
* * * * * * ** *
2309531 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTTCCAACAAAAGA-CCTTGAGTTCGACTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-TGC--C-AAAGACCCCCGAGTTCGATTACA
* * * *
2309595 CTCAGC-TCAACGGTACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGC
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
2309651 TAAAGACCTT
Statistics
Matches: 569, Mismatches: 38, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
164 2 0.00
165 485 0.85
166 10 0.02
167 46 0.08
168 21 0.04
169 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (164 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTTGAGTTCGACTACGCTCAGCTCAAGGCACATC
Found at i:2310269 original size:4 final size:4
Alignment explanation
Indices: 2310260--2310297 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
2310250 TTTTCGTCCA
2310260 TATT TATT TATT TATT TATT T-TT TATT ATATAT TATT T
1 TATT TATT TATT TATT TATT TATT TATT -TAT-T TATT T
2310298 TGAAAACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 3 0.10
4 21 0.68
5 6 0.19
6 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2310398 original size:36 final size:36
Alignment explanation
Indices: 2310351--2310472 Score: 140
Period size: 36 Copynumber: 3.4 Consensus size: 36
2310341 TAAAAACATT
2310351 TATATATTATATAGTTTTAAAACGTTTTTGAAAAGGA
1 TATATATTATATAGTTTTAAAACGTTTTTGAAAA-GA
* * *
2310388 -ATATAATATATAGTTTTCAAAACATTTTTGAAAATA
1 TATATATTATATAGTTTT-AAAACGTTTTTGAAAAGA
* *
2310424 TACATATTATATAGTTTTTAAAACG-TTTTGAAAATA
1 TATATATTATATAG-TTTTAAAACGTTTTTGAAAAGA
* *
2310460 AATATATAATATA
1 TATATATTATATA
2310473 TAATTTTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
36 38 0.52
37 31 0.42
38 4 0.05
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TATATATTATATAGTTTTAAAACGTTTTTGAAAAGA
Found at i:2310410 original size:74 final size:73
Alignment explanation
Indices: 2310313--2310472 Score: 198
Period size: 74 Copynumber: 2.2 Consensus size: 73
2310303 ACATTTTGAA
* * *
2310313 AATATATGATATAATTTTTAAAACATTTTAAAAACATTTATATATTATATAG-TTTTAAAACGTT
1 AATATATGATATAATTTTCAAAACATTTTAAAAA-ATATACATATTATATAGTTTTTAAAACG-T
2310377 TTTGAAAAGG
64 TTTGAAAAGG
* **
2310387 AATATAAT-ATATAGTTTTCAAAACATTTTTGAAAATATACATATTATATAGTTTTTAAAACGTT
1 AATAT-ATGATATAATTTTCAAAACATTTTAAAAAATATACATATTATATAGTTTTTAAAACGTT
**
2310451 TTGAAAATA
65 TTGAAAAGG
*
2310460 AATATATAATATA
1 AATATATGATATA
2310473 TAATTTTTTG
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
72 2 0.03
73 34 0.45
74 37 0.49
75 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (73 bp):
AATATATGATATAATTTTCAAAACATTTTAAAAAATATACATATTATATAGTTTTTAAAACGTTT
TGAAAAGG
Found at i:2310419 original size:37 final size:38
Alignment explanation
Indices: 2310313--2310535 Score: 176
Period size: 37 Copynumber: 6.0 Consensus size: 38
2310303 ACATTTTGAA
* * *
2310313 AATATATGATATA-A-TTTTTAAAACA-TTTTAAAAAC
1 AATATATAATATATAGTTTTTAAAACATTTTTGAAAAG
* * *
2310348 ATTTATATATTATATAG-TTTTAAAACGTTTTTGAAAAG
1 A-ATATATAATATATAGTTTTTAAAACATTTTTGAAAAG
* *
2310386 GA-ATATAATATATAGTTTTCAAAACATTTTTGAAAA-
1 AATATATAATATATAGTTTTTAAAACATTTTTGAAAAG
* * * * *
2310422 TATACATATTATATAGTTTTTAAAAC-GTTTTGAAAATA
1 AATATATAATATATAGTTTTTAAAACATTTTTGAAAA-G
*
2310460 AATATATAATATATAATTTTTTGAAAAACA-TTTTG-AAAG
1 AATATATAATATAT-AGTTTTT--AAAACATTTTTGAAAAG
* * * *
2310499 CATATATAATATGTAATTTTTAAAACATTTTTAAAAA
1 AATATATAATATATAGTTTTTAAAACATTTTTGAAAA
2310536 TTATATGGTT
Statistics
Matches: 149, Mismatches: 25, Indels: 25
0.75 0.13 0.13
Matches are distributed among these distances:
35 1 0.01
36 37 0.25
37 52 0.35
38 28 0.19
39 18 0.12
40 3 0.02
41 10 0.07
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (38 bp):
AATATATAATATATAGTTTTTAAAACATTTTTGAAAAG
Found at i:2310503 original size:73 final size:72
Alignment explanation
Indices: 2310354--2310497 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 72
2310344 AAACATTTAT
** *
2310354 ATATTATATAGTTTTAAAACGTTTTTGAAAAGGAATATAATATATAGTTTTCAAAACATTTTTGA
1 ATATTATATAGTTTTAAAACGTTTTTGAAAAAAAATATAATATATAGTTTTAAAAACATTTTTG-
2310419 AAATATAC
65 AAATATAC
*
2310427 ATATTATATAGTTTTTAAAACG-TTTTGAAAATAAATATATAATATATAATTTTTTGAAAAACA-
1 ATATTATATAG-TTTTAAAACGTTTTTGAAAA-AAA-ATATAATATAT-A-GTTTT-AAAAACAT
2310490 TTTTGAAA
60 TTTTGAAA
2310498 GCATATATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
73 20 0.33
74 11 0.18
75 11 0.18
76 4 0.07
77 9 0.15
78 6 0.10
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (72 bp):
ATATTATATAGTTTTAAAACGTTTTTGAAAAAAAATATAATATATAGTTTTAAAAACATTTTTGA
AATATAC
Found at i:2310541 original size:36 final size:36
Alignment explanation
Indices: 2310287--2310541 Score: 171
Period size: 37 Copynumber: 7.0 Consensus size: 36
2310277 ATTTTTTATT
* * *
2310287 ATATATTATTTTGAAAACA-TTTTGAAAA-TATAT-
1 ATATATAATTTTTAAAACATTTTTAAAAATTATATA
* *
2310320 -GATATAATTTTTAAAACATTTTAAAAACATTTATATA
1 ATATATAATTTTTAAAACATTTTTAAAA-A-TTATATA
* * * ***
2310357 TTATAT-AGTTTTAAAACGTTTTTGAAAAGGAATATA
1 ATATATAATTTTTAAAACATTTTT-AAAAATTATATA
* * * *
2310393 ATATATAGTTTTCAAAACATTTTTGAAAATATACATA
1 ATATATAATTTTTAAAACATTTTTAAAAAT-TATATA
* * * * *
2310430 TTATATAGTTTTTAAAACGTTTTGAAAATAAATATATA
1 ATATATAATTTTTAAAACATTTT-TAAA-AATTATATA
* *
2310468 ATATATAATTTTTTGAAAAACATTTTGAAAGCA-TATATA
1 ATATATAA-TTTTT--AAAACATTTTTAAA-AATTATATA
*
2310507 ATATGTAATTTTTAAAACATTTTTAAAAATTATAT
1 ATATATAATTTTTAAAACATTTTTAAAAATTATAT
2310542 GGTTTTTTAA
Statistics
Matches: 169, Mismatches: 38, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
32 15 0.09
33 6 0.04
34 1 0.01
35 1 0.01
36 36 0.21
37 51 0.30
38 26 0.15
39 20 0.12
40 4 0.02
41 9 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATATATAATTTTTAAAACATTTTTAAAAATTATATA
Found at i:2310570 original size:34 final size:34
Alignment explanation
Indices: 2310520--2310587 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2310510 TGTAATTTTT
* *
2310520 AAAACATTTTTAAAAATTATATGGTTTTTTAAAA
1 AAAACACTTTTAAAAATTATATAGTTTTTTAAAA
*
2310554 AAAACACTTTTGAAAATTATATAGTTTTTTAAAA
1 AAAACACTTTTAAAAATTATATAGTTTTTTAAAA
2310588 TGGTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (34 bp):
AAAACACTTTTAAAAATTATATAGTTTTTTAAAA
Found at i:2310674 original size:3 final size:3
Alignment explanation
Indices: 2310666--2310715 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
2310656 GTTTTTATAT
*
2310666 TTA TTA TTA TTA TTA TTA TCA TTA TT- TT- TTA TTA CTTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
2310709 TT- TTA TT
1 TTA TTA TT
2310716 TTTTCCCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.20
3 30 0.73
4 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2312031 original size:12 final size:12
Alignment explanation
Indices: 2311999--2312033 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2311989 TTACTTACTT
*
2311999 TTATTATTATTA
1 TTATTATTTTTA
2312011 TTATTATTTTTA
1 TTATTATTTTTA
*
2312023 TTTTTATTTTT
1 TTATTATTTTT
2312034 TGATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:2312745 original size:2 final size:2
Alignment explanation
Indices: 2312733--2312809 Score: 111
Period size: 2 Copynumber: 38.0 Consensus size: 2
2312723 TATTACTCCC
* *
2312733 AT AT AT GAT AT AT A- AC AT AT GAA 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
2312776 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
2312810 GATTATAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.01
2 65 0.94
3 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2313241 original size:18 final size:18
Alignment explanation
Indices: 2313218--2313256 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2313208 TTTTCAATGA
2313218 AAAATACATAAAAATTTT
1 AAAATACATAAAAATTTT
* * *
2313236 AAAATATATGACAATTTT
1 AAAATACATAAAAATTTT
2313254 AAA
1 AAA
2313257 TTTCAAGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAATACATAAAAATTTT
Found at i:2313573 original size:20 final size:20
Alignment explanation
Indices: 2313537--2313587 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2313527 AAATCTCAAT
2313537 TGAGTCTTAGG--TATGCTC
1 TGAGTCTTAGGTATATGCTC
2313555 TGAGTCTTAGGTATATGCTC
1 TGAGTCTTAGGTATATGCTC
*
2313575 TGAGTTTTAGGTA
1 TGAGTCTTAGGTA
2313588 GGGATGGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 11 0.37
20 19 0.63
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (20 bp):
TGAGTCTTAGGTATATGCTC
Found at i:2317548 original size:23 final size:23
Alignment explanation
Indices: 2317512--2317574 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2317502 CTGAATGATT
* *
2317512 CAGTGCTGACTGATTCAACAAAA
1 CAGTGTTGAATGATTCAACAAAA
* *
2317535 TAGTGTTGAATGATTCATCAAAA
1 CAGTGTTGAATGATTCAACAAAA
2317558 CAGTGTTGAATGATTCA
1 CAGTGTTGAATGATTCA
2317575 GCACAGAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (23 bp):
CAGTGTTGAATGATTCAACAAAA
Found at i:2320575 original size:2 final size:2
Alignment explanation
Indices: 2320568--2320605 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2320558 ATCGATGATT
*
2320568 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2320606 CTTTTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2321371 original size:18 final size:18
Alignment explanation
Indices: 2321348--2321383 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2321338 TGGTTTGATC
*
2321348 CGTCTCGAGTCTAAGGGA
1 CGTCTCAAGTCTAAGGGA
2321366 CGTCTCAAGTCTAAGGGA
1 CGTCTCAAGTCTAAGGGA
2321384 ATCGACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (18 bp):
CGTCTCAAGTCTAAGGGA
Found at i:2323314 original size:13 final size:12
Alignment explanation
Indices: 2323296--2323346 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
2323286 TTTTTAATAA
2323296 AAAAAGTATATTT
1 AAAAAGTAT-TTT
*
2323309 AAAAAGTGATGTT
1 AAAAAGT-ATTTT
2323322 AAAAAGTATTTT
1 AAAAAGTATTTT
*
2323334 TAAAAGTGATTTT
1 AAAAAGT-ATTTT
2323347 GAAAGTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 10 0.30
13 21 0.64
14 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (12 bp):
AAAAAGTATTTT
Found at i:2323460 original size:10 final size:10
Alignment explanation
Indices: 2323445--2323470 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2323435 AAATTAAAAA
2323445 TAAATTATTT
1 TAAATTATTT
2323455 TAAATTATTT
1 TAAATTATTT
2323465 TAAATT
1 TAAATT
2323471 TATTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TAAATTATTT
Found at i:2324113 original size:2 final size:2
Alignment explanation
Indices: 2324106--2324136 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2324096 CTCACAACTT
2324106 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2324137 GAAAGTCGCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2324530 original size:33 final size:33
Alignment explanation
Indices: 2324488--2324555 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
2324478 TCTTCTTGAT
2324488 CAATCGTGACGATGTCATGAATAGAACATATGC
1 CAATCGTGACGATGTCATGAATAGAACATATGC
2324521 CAATCGTGACGATGTCATGAATAGAACATATGC
1 CAATCGTGACGATGTCATGAATAGAACATATGC
2324554 CA
1 CA
2324556 TGGGGGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (33 bp):
CAATCGTGACGATGTCATGAATAGAACATATGC
Found at i:2324619 original size:2 final size:2
Alignment explanation
Indices: 2324612--2324665 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
2324602 TAATAATCTC
* *
2324612 AT AT AT AT AT AT AT AC AT AT TT 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
* *
2324654 AC AC AT AT AT AT
1 AT AT AT AT AT AT
2324666 CAATTTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2331122 original size:2 final size:2
Alignment explanation
Indices: 2331115--2331142 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2331105 TCCAGTCCCA
2331115 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2331143 GTGCTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2337465 original size:21 final size:21
Alignment explanation
Indices: 2337416--2337465 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2337406 TCCTTTCTCT
* *
2337416 CCCAAATCCAACCCATTTGAA
1 CCCAAATTCAACCCACTTGAA
*
2337437 CCCGAATTCAACCCACTT-AA
1 CCCAAATTCAACCCACTTGAA
2337457 CCCCAAATT
1 -CCCAAATT
2337466 GGCCTCTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.36, C:0.40, G:0.04, T:0.20
Consensus pattern (21 bp):
CCCAAATTCAACCCACTTGAA
Found at i:2340407 original size:21 final size:22
Alignment explanation
Indices: 2340373--2340413 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2340363 ACTTTTAATG
2340373 TAATTTTTAAATTA-AAAAATT
1 TAATTTTTAAATTACAAAAATT
**
2340394 TAATTTTTTTATTACAAAAA
1 TAATTTTTAAATTACAAAAA
2340414 AAATTGATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATTTTTAAATTACAAAAATT
Found at i:2341836 original size:21 final size:22
Alignment explanation
Indices: 2341805--2341845 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2341795 TTCTTTCACC
*
2341805 AAATCTGAAATTTTAAATTTAA
1 AAATCTGAAATCTTAAATTTAA
*
2341827 AAAT-TGAAATCTTGAATTT
1 AAATCTGAAATCTTAAATTT
2341846 CGAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (22 bp):
AAATCTGAAATCTTAAATTTAA
Found at i:2342567 original size:12 final size:13
Alignment explanation
Indices: 2342554--2342588 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
2342544 TAAAAATGAT
2342554 AATCAAATAAATA
1 AATCAAATAAATA
2342567 AAT-AAAT-AATA
1 AATCAAATAAATA
2342578 AATCAAATAAA
1 AATCAAATAAA
2342589 AATATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.35
12 8 0.40
13 5 0.25
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (13 bp):
AATCAAATAAATA
Found at i:2342577 original size:15 final size:15
Alignment explanation
Indices: 2342558--2342592 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2342548 AATGATAATC
2342558 AAATAAAT-AAATAA
1 AAATAAATCAAATAA
2342572 ATAATAAATCAAATAA
1 A-AATAAATCAAATAA
2342588 AAATA
1 AAATA
2342593 TAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 11 0.58
16 7 0.37
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAATCAAATAA
Found at i:2342605 original size:20 final size:20
Alignment explanation
Indices: 2342544--2342605 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
2342534 TAAATTAATT
*
2342544 TAAAAATGATAATCAAATAAA
1 TAAAAAT-ATAATTAAATAAA
2342565 TAAATAA-ATAA-TAAATCAAA
1 TAAA-AATATAATTAAAT-AAA
*
2342585 TAAAAATATAATTTAATAAA
1 TAAAAATATAATTAAATAAA
2342605 T
1 T
2342606 TTATTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 6 0.17
20 19 0.54
21 8 0.23
22 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAAAATATAATTAAATAAA
Found at i:2346113 original size:23 final size:24
Alignment explanation
Indices: 2346079--2346149 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
2346069 CAATCTTATA
*
2346079 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
2346102 TGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
2346126 TAGCACTTCAGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
2346150 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 13 0.32
24 28 0.68
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:2348398 original size:59 final size:60
Alignment explanation
Indices: 2348268--2348385 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
2348258 TTAGTGCAAG
* * * * *
2348268 ATATTTTAATTTCATCCTCAAATTATGACTTTTATTATAAATTAGTCATTAAACTTTTGA
1 ATATTATAATTTCATCCTCAAACTATGACTCTCATTATAAATTAGTCATCAAACTTTTGA
* *
2348328 ATATTATAATTTCATCCTCAAACTATGACTCTCA-TCTAAATTGGTTC-TCAAACTTTTG
1 ATATTATAATTTCATCCTCAAACTATGACTCTCATTATAAATTAG-TCATCAAACTTTTG
2348386 CATCTTTCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 18 0.36
60 32 0.64
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (60 bp):
ATATTATAATTTCATCCTCAAACTATGACTCTCATTATAAATTAGTCATCAAACTTTTGA
Found at i:2349143 original size:59 final size:59
Alignment explanation
Indices: 2349049--2349175 Score: 134
Period size: 60 Copynumber: 2.2 Consensus size: 59
2349039 TAAAATGTTC
* * *
2349049 AAAAGTTTGA-GATCAATTTAGAATGAAGATCATAG-TAGGGGATGAAACTGAAATATAT
1 AAAAGTTTAAGGACCAATTTAGAATGAAGATCATAGTTA-GGGATCAAACTGAAATATAT
* * * * *
2349107 AGAAGTTTAAGGACCAATTTAGAAT-AATGGTTATAGTTTAGGGATCAAATTGAAATATTT
1 AAAAGTTTAAGGACCAATTTAGAATGAA-GATCATAG-TTAGGGATCAAACTGAAATATAT
2349167 AAAAGTTTA
1 AAAAGTTTA
2349176 GGAATTAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
58 10 0.18
59 19 0.34
60 25 0.45
61 2 0.04
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.31
Consensus pattern (59 bp):
AAAAGTTTAAGGACCAATTTAGAATGAAGATCATAGTTAGGGATCAAACTGAAATATAT
Found at i:2357587 original size:12 final size:12
Alignment explanation
Indices: 2357570--2357678 Score: 80
Period size: 12 Copynumber: 8.8 Consensus size: 12
2357560 GACCAAGTTC
2357570 CTCATCATCAAA
1 CTCATCATCAAA
**
2357582 CTCATCATC-TT
1 CTCATCATCAAA
2357593 CTTCATCATCATCGAA
1 C-TCATCATCA---AA
*
2357609 CTCGTCATCAAA
1 CTCATCATCAAA
*
2357621 TTCATCATCAAA
1 CTCATCATCAAA
*
2357633 ATCATCATC--A
1 CTCATCATCAAA
2357643 CTTCCATCATCAAA
1 C-T-CATCATCAAA
*
2357657 ATCATCATCAAA
1 CTCATCATCAAA
*
2357669 ATCATCATCA
1 CTCATCATCA
2357679 CTTCCATCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
10 1 0.01
11 2 0.03
12 64 0.82
13 1 0.01
14 1 0.01
15 8 0.10
16 1 0.01
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.30
Consensus pattern (12 bp):
CTCATCATCAAA
Found at i:2357603 original size:24 final size:23
Alignment explanation
Indices: 2357571--2357666 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 23
2357561 ACCAAGTTCC
* *
2357571 TCATCATCAAACTCATCATCTTCT
1 TCATCATCAAAATCATCATC-ACT
* * *
2357595 TCATCATCATCGAACTCGTCATCAAAT
1 TCATCATCA---AAATCATCATC-ACT
2357622 TCATCATCAAAATCATCATCACT
1 TCATCATCAAAATCATCATCACT
2357645 TCCATCATCAAAATCATCATCA
1 T-CATCATCAAAATCATCATCA
2357667 AAATCATCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.05
24 38 0.62
27 20 0.33
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (23 bp):
TCATCATCAAAATCATCATCACT
Found at i:2357624 original size:27 final size:27
Alignment explanation
Indices: 2357571--2357678 Score: 102
Period size: 27 Copynumber: 4.2 Consensus size: 27
2357561 ACCAAGTTCC
***
2357571 TCATCATCAAACTCATCATCTTCTTCA
1 TCATCATCAAACTCATCATCAAATTCA
* *
2357598 TCATCATCGAACTCGTCATCAAATTCA
1 TCATCATCAAACTCATCATCAAATTCA
*
2357625 TCATCA--AAA-TCATCATC-ACTTC-
1 TCATCATCAAACTCATCATCAAATTCA
* *
2357647 -CATCATCAAAATCATCATCAAAATCA
1 TCATCATCAAACTCATCATCAAATTCA
2357673 TCATCA
1 TCATCA
2357679 CTTCCATCAT
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 5 0.08
23 7 0.11
24 15 0.23
25 5 0.08
27 33 0.51
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.31
Consensus pattern (27 bp):
TCATCATCAAACTCATCATCAAATTCA
Found at i:2357637 original size:36 final size:36
Alignment explanation
Indices: 2357613--2357689 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
2357603 ATCGAACTCG
*
2357613 TCATCAAATTCATCATCAAAATCATCATCACTTCCA
1 TCATCAAAATCATCATCAAAATCATCATCACTTCCA
2357649 TCATCAAAATCATCATCAAAATCATCATCACTTCCA
1 TCATCAAAATCATCATCAAAATCATCATCACTTCCA
2357685 TCATC
1 TCATC
2357690 CTCAGGCAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.39, C:0.31, G:0.00, T:0.30
Consensus pattern (36 bp):
TCATCAAAATCATCATCAAAATCATCATCACTTCCA
Found at i:2357674 original size:24 final size:24
Alignment explanation
Indices: 2357597--2357678 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
2357587 CATCTTCTTC
* * *
2357597 ATCATCATCGAACTCGTCATCAAA
1 ATCATCATCAAAATCATCATCAAA
* *
2357621 TTCATCATCAAAATCATCATC-AC
1 ATCATCATCAAAATCATCATCAAA
*
2357644 TTCCATCATCAAAATCATCATCAAA
1 AT-CATCATCAAAATCATCATCAAA
2357669 ATCATCATCA
1 ATCATCATCA
2357679 CTTCCATCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
23 3 0.06
24 44 0.90
25 2 0.04
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.28
Consensus pattern (24 bp):
ATCATCATCAAAATCATCATCAAA
Found at i:2358681 original size:2 final size:2
Alignment explanation
Indices: 2358670--2358744 Score: 98
Period size: 2 Copynumber: 38.0 Consensus size: 2
2358660 TGGAAGAAAT
* * *
2358670 AG AG AG -G AG AG AG AG AG AT AG AG AG AG AG AG GG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
2358711 AG AG AG GG AG AG AG AG AT AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2358745 GAGGCAGTAG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (2 bp):
AG
Found at i:2361590 original size:57 final size:57
Alignment explanation
Indices: 2361525--2361640 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
2361515 TAAAATATAC
*
2361525 ATAAAATAAATTGTTAAATTATATGTTAGATTAATTAACTAAACTTGTTATTAATTA
1 ATAAAATAAATTGTTAAATTATATGTTAGATTAATTAACTAAACTTATTATTAATTA
* *
2361582 ATAAAATAAATTGTTAAATTGTATGTTAGATTAATTAAGTAAACTTATTATTAATTA
1 ATAAAATAAATTGTTAAATTATATGTTAGATTAATTAACTAAACTTATTATTAATTA
2361639 AT
1 AT
2361641 TTTAATTGGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (57 bp):
ATAAAATAAATTGTTAAATTATATGTTAGATTAATTAACTAAACTTATTATTAATTA
Found at i:2363187 original size:20 final size:20
Alignment explanation
Indices: 2363164--2363202 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2363154 AAAAATTATT
*
2363164 TTAAATTAATAATATTTTAC
1 TTAAAGTAATAATATTTTAC
*
2363184 TTAAAGTATTAATATTTTA
1 TTAAAGTAATAATATTTTA
2363203 ACTTCGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTAAAGTAATAATATTTTAC
Found at i:2363648 original size:27 final size:27
Alignment explanation
Indices: 2363617--2363668 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2363607 TATTTTTATC
*
2363617 ATCTATAATTTTATAAATTTAAATTGT
1 ATCTAAAATTTTATAAATTTAAATTGT
2363644 ATCTAAAATTTTATAAATTTAAATT
1 ATCTAAAATTTTATAAATTTAAATT
2363669 CGTCTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
ATCTAAAATTTTATAAATTTAAATTGT
Found at i:2364362 original size:14 final size:14
Alignment explanation
Indices: 2364343--2364369 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2364333 TTTAGATTTT
2364343 TTAAAATTATATTG
1 TTAAAATTATATTG
2364357 TTAAAATTATATT
1 TTAAAATTATATT
2364370 AAAAATACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
TTAAAATTATATTG
Found at i:2365687 original size:3 final size:3
Alignment explanation
Indices: 2365681--2365705 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2365671 TAATTTCTTT
2365681 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2365706 CATAATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2372537 original size:21 final size:21
Alignment explanation
Indices: 2372513--2372558 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2372503 GGTTCGATGG
* *
2372513 CATCTGAAATGGTTGTTGTGC
1 CATCTAAAATGGTTGATGTGC
2372534 CATCTAAAATGGTTGATGTGC
1 CATCTAAAATGGTTGATGTGC
2372555 CATC
1 CATC
2372559 ATAACGCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (21 bp):
CATCTAAAATGGTTGATGTGC
Found at i:2373140 original size:2 final size:2
Alignment explanation
Indices: 2373133--2373164 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2373123 CCATTCAAAT
2373133 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
2373165 ATTCTTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2375237 original size:17 final size:17
Alignment explanation
Indices: 2375215--2375250 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2375205 AATTGTCTAT
2375215 TTTTAATC-ATCTAATAA
1 TTTTAATCTATCTAA-AA
2375232 TTTTAATCTATCTAAAA
1 TTTTAATCTATCTAAAA
2375249 TT
1 TT
2375251 AAAATAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAATCTATCTAAAA
Found at i:2375293 original size:2 final size:2
Alignment explanation
Indices: 2375286--2375323 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2375276 TATCTTATCC
2375286 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
2375324 CAAAGTCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2381061 original size:18 final size:18
Alignment explanation
Indices: 2381038--2381097 Score: 111
Period size: 18 Copynumber: 3.3 Consensus size: 18
2381028 TGTGCAGGTT
2381038 AGGAGCAGGATCCTTTGG
1 AGGAGCAGGATCCTTTGG
2381056 AGGAGCAGGATCCTTTGG
1 AGGAGCAGGATCCTTTGG
2381074 AGGAGCAGGATCCTTTGG
1 AGGAGCAGGATCCTTTGG
*
2381092 TGGAGC
1 AGGAGC
2381098 GTATACTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.22, C:0.17, G:0.40, T:0.22
Consensus pattern (18 bp):
AGGAGCAGGATCCTTTGG
Found at i:2382616 original size:60 final size:60
Alignment explanation
Indices: 2382502--2382617 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
2382492 TGTGAGTTAC
* * **
2382502 TCGAGTTTTAACTTCAATCGAGTTAAGTTTGAGAATGTTTCGAGTTCAGTTTTTTTAAGT
1 TCGAGTTTGAACTTCAATCGAATTAAGTTTGAGAATGTTTCGAGTTCAAATTTTTTAAGT
*
2382562 TCGAGTTTGAGCTTCAATCGAATTAAGTTTGAGAATGTTTCGAGTTCAAATTTTTT
1 TCGAGTTTGAACTTCAATCGAATTAAGTTTGAGAATGTTTCGAGTTCAAATTTTTT
2382618 CAAGCTCAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (60 bp):
TCGAGTTTGAACTTCAATCGAATTAAGTTTGAGAATGTTTCGAGTTCAAATTTTTTAAGT
Found at i:2383449 original size:41 final size:41
Alignment explanation
Indices: 2383392--2383492 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
2383382 ATTCGCGTTG
* **
2383392 CATTTCGCATTGCGATAGTTGAAAACCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAACCGCAATGCGATTTTC
* *
2383433 CATTTCGTGTTGCGATAGTTGAAAATCGCAATGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAACCGCAATGCGATTTTC
2383474 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2383493 CTACAGTTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAACCGCAATGCGATTTTC
Found at i:2383487 original size:20 final size:20
Alignment explanation
Indices: 2383418--2383489 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
2383408 AGTTGAAAAC
2383418 CGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
* * ** **
2383438 CGTGTTGCGATAGTTGAAAAT
1 CGCGTTGCGAT-TTTCCATTT
**
2383459 CGCAATGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
2383479 CGCGTTGCGAT
1 CGCGTTGCGAT
2383490 AGTCTACAGT
Statistics
Matches: 35, Mismatches: 16, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTTCCATTT
Found at i:2384111 original size:6 final size:6
Alignment explanation
Indices: 2384102--2384127 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2384092 CGCCGTCGCC
2384102 GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GT
2384128 AATACGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTCGTG
Found at i:2384244 original size:41 final size:41
Alignment explanation
Indices: 2384192--2384285 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 41
2384182 ATTTTTTTTA
* *
2384192 ACTATCACAACGAATTTGAAAAATCGTAACAACAACTGTAG
1 ACTATCGCAACGAATTTGAAAAATCGCAACAACAACTGTAG
* ** *
2384233 ATTATCGCAACGAATTTGGTAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGAAAAATCGCAACAACAACTGTAG
2384274 ACTATCGCAACG
1 ACTATCGCAACG
2384286 CGAAATGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGAAAAATCGCAACAACAACTGTAG
Found at i:2384283 original size:22 final size:21
Alignment explanation
Indices: 2384214--2384285 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
2384204 AATTTGAAAA
* *
2384214 ATCGTAACAACAACTGTAGATT
1 ATCGCAACGACAACTGTAGA-T
**
2384236 ATCGCAACGA-ATTTGGTA-A-
1 ATCGCAACGACAACT-GTAGAT
2384255 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGA-T
2384277 ATCGCAACG
1 ATCGCAACG
2384286 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 13 0.33
20 3 0.08
21 3 0.08
22 20 0.51
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGACAACTGTAGAT
Found at i:2384328 original size:20 final size:20
Alignment explanation
Indices: 2384277--2384321 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2384267 ACTGTAGACT
*
2384277 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
2384297 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
2384317 ATCGC
1 ATCGC
2384322 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:2384565 original size:2 final size:2
Alignment explanation
Indices: 2384558--2384595 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2384548 TAATTATGAA
2384558 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
2384596 TCAAGTCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2386969 original size:18 final size:17
Alignment explanation
Indices: 2386948--2386985 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
2386938 TATGTCCTGT
2386948 AGGACCACTACGTCCCGA
1 AGGA-CACTACGTCCCGA
2386966 AGG--ACTACGTCCCGA
1 AGGACACTACGTCCCGA
2386981 AGGAC
1 AGGAC
2386986 TACAATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
15 15 0.83
18 3 0.17
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (17 bp):
AGGACACTACGTCCCGA
Found at i:2386974 original size:15 final size:15
Alignment explanation
Indices: 2386954--2386988 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2386944 CTGTAGGACC
2386954 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
2386969 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
2386984 ACTAC
1 ACTAC
2386989 AATACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:2389382 original size:26 final size:26
Alignment explanation
Indices: 2389347--2389458 Score: 120
Period size: 26 Copynumber: 4.4 Consensus size: 26
2389337 TGGCAGCAGT
2389347 GGTGGCTGTTGAGTGGTCCAAGCGGC
1 GGTGGCTGTTGAGTGGTCCAAGCGGC
* *** *
2389373 GGTGGTTGTTGAGCAATCCAAGCGGT
1 GGTGGCTGTTGAGTGGTCCAAGCGGC
*
2389399 GGTGGCTGATGAGTGGTCCAAGCGGC
1 GGTGGCTGTTGAGTGGTCCAAGCGGC
* * *
2389425 GGTGGC--ATGAGTGGTCCAAGTGGT
1 GGTGGCTGTTGAGTGGTCCAAGCGGC
*
2389449 GGCGGCTGTT
1 GGTGGCTGTT
2389459 CTGGAAACCC
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
24 21 0.30
26 48 0.70
ACGTcount: A:0.14, C:0.17, G:0.45, T:0.24
Consensus pattern (26 bp):
GGTGGCTGTTGAGTGGTCCAAGCGGC
Found at i:2389693 original size:12 final size:11
Alignment explanation
Indices: 2389649--2389695 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 11
2389639 AAATCTGTAA
2389649 AATAAAAT-AT
1 AATAAAATAAT
2389659 AATTATAAATAAT
1 AA-TA-AAATAAT
2389672 AATAATAATAAT
1 AATAA-AATAAT
2389684 AATATAAATAAT
1 AATA-AAATAAT
2389696 GACGGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.69
13 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:2402529 original size:21 final size:23
Alignment explanation
Indices: 2402494--2402553 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
2402484 TTGGTGCAGA
*
2402494 GGGAATCGA-TCCCCCCCTG-A-
1 GGGAACCGATTCCCCCCCTGAAG
* **
2402514 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCCTGAAG
2402537 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
2402554 ACAGGGGAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.20, C:0.37, G:0.25, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCCTGAAG
Found at i:2402561 original size:21 final size:21
Alignment explanation
Indices: 2402535--2402574 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2402525 CCCCCTTTGA
*
2402535 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2402556 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2402575 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2404561 original size:17 final size:17
Alignment explanation
Indices: 2404529--2404572 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2404519 TTTAAACATT
2404529 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
2404546 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
2404563 TTGGATTTTG
1 TTGGATTTTG
2404573 GACTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:2410118 original size:106 final size:106
Alignment explanation
Indices: 2409921--2411791 Score: 2937
Period size: 106 Copynumber: 17.7 Consensus size: 106
2409911 TCCTCCGTCG
* * *
2409921 TGAAGTTGA-AAGTTGTTTATTGACAACCAGCGGTTCCTTCG-CTGTGAAGTTGAACTTGCGTTG
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTG
* * *
2409984 TCTTGG-GTCCAATATCCTTCGCTATGAAGTTGAAATTGACTC
65 TC-TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * *
2410026 TGAAATTGGGAAATTGTTTATTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
2410091 CTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
2410132 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
2410197 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
** *
2410238 TGAAATTGAGAAGTTGTTTGTTGACAACCAATGGTCCCTTCGTCGTGAAGTTGAA-TATGTGTTG
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT-TGCGTTG
*
2410302 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
2410344 TGATATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
2410409 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
2410450 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
2410515 CTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
2410556 TAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
2410621 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
2410662 TGATATTGAGAAGTTGTTTGTTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
2410727 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * *
2410768 TGAAATTGGGAAGTTGTTTATTAACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
2410833 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
2410874 TAAAATTGAGAAGTTGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
2410939 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
2410980 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
2411045 CTGGAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
2411086 TGAAATTGAGAAATTGTTTATTGACAACCAGCGGGCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
2411151 CTGGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * * * * *
2411192 TAAAATT-AGGAAATT-ATTGTTGACAACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTG
1 TGAAATTGA-GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
*
2411255 TCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
2411297 TGAAATTGAGAAGTTGTTTGTTGACAACCAGGGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
2411362 CTGGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
2411403 CGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
2411468 CTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
2411509 TGAAATTGGGAAGTTGTTTGTTGACAACTAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
2411574 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
** * * * *
2411615 TGAAATTGAGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGTTG
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTG
* * *
2411679 TCTTGAGTCCAATGTCCTTCGCTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * * *
2411721 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTCT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
2411786 CTGGAG
66 CTGGAG
2411792 AGAAACTGTC
Statistics
Matches: 1632, Mismatches: 124, Indels: 19
0.92 0.07 0.01
Matches are distributed among these distances:
105 104 0.06
106 1526 0.94
107 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (106 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:2411914 original size:37 final size:36
Alignment explanation
Indices: 2411792--2411929 Score: 147
Period size: 37 Copynumber: 3.8 Consensus size: 36
2411782 TTCTCTGGAG
*
2411792 AGAA-ACTGTCTCAAG-GAAGACAAAATTTGTTTCAA
1 AGAAGACTGTCTCAAGCG-AGACAAAATTTGTTTTAA
* * * *
2411827 GGAAGACTGTCTCAAGGGAGACGAAATTTGTTTCAA
1 AGAAGACTGTCTCAAGCGAGACAAAATTTGTTTTAA
* * *
2411863 AGAAAAACTATCTCAAGCGAGATAAAATCTTGTTTTAA
1 AG-AAGACTGTCTCAAGCGAGACAAAAT-TTGTTTTAA
2411901 ATG-AGACTGTCTCAAGCGAGACAAAATTT
1 A-GAAGACTGTCTCAAGCGAGACAAAATTT
2411930 ATATTGAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
35 3 0.03
36 31 0.36
37 42 0.49
38 9 0.10
39 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
AGAAGACTGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:2420206 original size:20 final size:20
Alignment explanation
Indices: 2420164--2420214 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2420154 ATTATTATTT
* * *
2420164 TTAATATTATATTATAGATA
1 TTAATTTTATATCATAGAAA
*
2420184 TTAATTTTATATCATATAAA
1 TTAATTTTATATCATAGAAA
2420204 TT-ATTTTATAT
1 TTAATTTTATAT
2420215 ATTATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATTTTATATCATAGAAA
Found at i:2423116 original size:22 final size:23
Alignment explanation
Indices: 2423082--2423124 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2423072 ATATAATAAA
2423082 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
2423105 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
2423125 TACTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:2423527 original size:25 final size:25
Alignment explanation
Indices: 2423482--2423574 Score: 68
Period size: 25 Copynumber: 3.7 Consensus size: 25
2423472 TATAATTGAG
* * *
2423482 TATATTAT-TGTAATAATAATATTAT
1 TATATTATAT-TATTAAAAATATTAA
2423507 TATATTATATTATTAAAAATATTAA
1 TATATTATATTATTAAAAATATTAA
* * *
2423532 TA-AATATATT-TTAAATATGTTAA
1 TATATTATATTATTAAAAATATTAA
2423555 TA-ATTAATATTTTATTAAAA
1 TATATT-ATA--TTATTAAAA
2423575 TGATACTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
23 15 0.27
24 10 0.18
25 22 0.40
26 3 0.05
27 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TATATTATATTATTAAAAATATTAA
Found at i:2423554 original size:23 final size:23
Alignment explanation
Indices: 2423512--2423568 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2423502 ATTATTATAT
2423512 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
2423536 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
2423559 TAATATTTTA
1 T-ATATTTTA
2423569 TTAAAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:2423963 original size:24 final size:24
Alignment explanation
Indices: 2423935--2423988 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2423925 ATTTTATGTC
2423935 CTTGTGACACG-ATTTCTCTCTGCT
1 CTTGTGACACGCATTT-TCTCTGCT
* *
2423959 CTTGTGGCACGCGTTTTCTCTGCT
1 CTTGTGACACGCATTTTCTCTGCT
*
2423983 CCTGTG
1 CTTGTG
2423989 GCATAATCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.07, C:0.30, G:0.22, T:0.41
Consensus pattern (24 bp):
CTTGTGACACGCATTTTCTCTGCT
Found at i:2428681 original size:2 final size:2
Alignment explanation
Indices: 2428674--2428698 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2428664 ATCATCCTAT
2428674 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
2428699 CAATTATAAC
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:2429587 original size:2 final size:2
Alignment explanation
Indices: 2429580--2429644 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
2429570 ATGTACATAC
*
2429580 AT AT AT AT AT AC 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
2429622 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2429645 GGTATTTAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2429777 original size:43 final size:43
Alignment explanation
Indices: 2429729--2429811 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
2429719 GGTTCGAGCA
2429729 CGCCATCTACAATGATATTTGAATATTCACTATCAAATGGGCT
1 CGCCATCTACAATGATATTTGAATATTCACTATCAAATGGGCT
2429772 CGCCATCTACAATGATATTTGAATATTCACTATCAAATGG
1 CGCCATCTACAATGATATTTGAATATTCACTATCAAATGG
2429812 TTAACAGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (43 bp):
CGCCATCTACAATGATATTTGAATATTCACTATCAAATGGGCT
Found at i:2431146 original size:19 final size:19
Alignment explanation
Indices: 2431122--2431165 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2431112 AAAAATTTTA
2431122 AAAATTCAT-TCTCTAACAT
1 AAAATT-ATGTCTCTAACAT
*
2431141 AAAATTTTGTCTCTAACAT
1 AAAATTATGTCTCTAACAT
2431160 AAAATT
1 AAAATT
2431166 TTGTGTATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATTATGTCTCTAACAT
Found at i:2431166 original size:19 final size:19
Alignment explanation
Indices: 2431131--2431169 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2431121 AAAAATTCAT
2431131 TCTCTAACATAAAATTTTG
1 TCTCTAACATAAAATTTTG
2431150 TCTCTAACATAAAATTTTG
1 TCTCTAACATAAAATTTTG
2431169 T
1 T
2431170 GTATGCGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
TCTCTAACATAAAATTTTG
Done.