Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2291462 original size:14 final size:14
Alignment explanation
Indices: 2291416--2291466 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2291406 ATATTTTATA
2291416 ATATATAGTTTGTAC
1 ATAT-TAGTTTGTAC
* * *
2291431 ATA-TAGTATATAAT
1 ATATTAGTTTGT-AC
2291445 ATATTAGTTTGTAC
1 ATATTAGTTTGTAC
2291459 ATATTAGT
1 ATATTAGT
2291467 ATTAGTTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
13 6 0.21
14 13 0.46
15 9 0.32
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (14 bp):
ATATTAGTTTGTAC
Found at i:2291597 original size:25 final size:25
Alignment explanation
Indices: 2291538--2291607 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 25
2291528 ACATTCCATG
*
2291538 GTATTTCATGTTATTAATTCATATT
1 GTATTGCATGTTATTAATTCATATT
* *
2291563 G---TGC--GGTATTAATTCATGTT
1 GTATTGCATGTTATTAATTCATATT
2291583 GTATTGCATGTTATTAATTCATATT
1 GTATTGCATGTTATTAATTCATATT
2291608 ACATTAGATG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
20 15 0.43
22 2 0.06
23 3 0.09
25 15 0.43
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (25 bp):
GTATTGCATGTTATTAATTCATATT
Found at i:2293895 original size:189 final size:191
Alignment explanation
Indices: 2293574--2293953 Score: 728
Period size: 189 Copynumber: 2.0 Consensus size: 191
2293564 AACCACATGG
2293574 ATACAAATTCATAATTAATTACAAAAAAAAGATATTCTTTTATTCTTAAATATTGAAAGGGGTGA
1 ATACAAATTCATAATTAATTACAAAAAAAAGATATTCTTTTATTCTTAAATATTGAAAGGGGTGA
2293639 TCTTAAAATAACTAGACATCCCTATTCAATATTTTTTTGAATAAATATATATTCTATCAAGTGAT
66 TCTTAAAATAACTAGACATCCCTATTCAATATTTTTTTGAATAAATATATATTCTATCAAGTGAT
2293704 CACCCTAAAAATTAAATAGGCTCACTAATTAAAATAAAAGGGTGGAGGTTTGTT-CTACGT
131 CACCCTAAAAATTAAATAGGCTCACTAATTAAAATAAAAGGGTGGAGGTTTGTTCCTACGT
*
2293764 ATACAAATTCATAATTAATTA-AAAAAAAAGATATTCTTTTATTCTTAAATATTGAAAGGGGTGG
1 ATACAAATTCATAATTAATTACAAAAAAAAGATATTCTTTTATTCTTAAATATTGAAAGGGGTGA
2293828 TCTTAAAATAACTAGACATCCCTATTCAATATTTTTTTGAATAAATATATATTCTATCAAGTGAT
66 TCTTAAAATAACTAGACATCCCTATTCAATATTTTTTTGAATAAATATATATTCTATCAAGTGAT
*
2293893 CACCTTAAAAATTAAATAGGCTCACTAATTAAAATAAAAGGGTGGAGGTTTGTTCCTACGT
131 CACCCTAAAAATTAAATAGGCTCACTAATTAAAATAAAAGGGTGGAGGTTTGTTCCTACGT
2293954 TTAAATTGAT
Statistics
Matches: 187, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
189 160 0.86
190 27 0.14
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (191 bp):
ATACAAATTCATAATTAATTACAAAAAAAAGATATTCTTTTATTCTTAAATATTGAAAGGGGTGA
TCTTAAAATAACTAGACATCCCTATTCAATATTTTTTTGAATAAATATATATTCTATCAAGTGAT
CACCCTAAAAATTAAATAGGCTCACTAATTAAAATAAAAGGGTGGAGGTTTGTTCCTACGT
Found at i:2294461 original size:43 final size:43
Alignment explanation
Indices: 2294414--2294512 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 43
2294404 GATTCAACTT
2294414 CTTCTGTGAAGAACCAAGCGAAAGATT-TTCACTAATCCGACTC
1 CTTCTGTGAAGAACCAAGCGAAAGATTGTT-ACTAATCCGACTC
* * * *
2294457 CTTCTGTGAA-AGATCAAGTGAAAGGTTGTTACTGATCCGACTC
1 CTTCTGTGAAGA-ACCAAGCGAAAGATTGTTACTAATCCGACTC
2294500 CTTCTGTGAAGAA
1 CTTCTGTGAAGAA
2294513 TCGAGTAACA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.02
43 45 0.92
44 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
CTTCTGTGAAGAACCAAGCGAAAGATTGTTACTAATCCGACTC
Found at i:2295352 original size:14 final size:14
Alignment explanation
Indices: 2295335--2295374 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2295325 CTTTTCCTTT
2295335 TCTTTCTTCTTCTC
1 TCTTTCTTCTTCTC
*
2295349 TCTTTCTTTTTCTC
1 TCTTTCTTCTTCTC
*
2295363 T-TTTTTTCTTCT
1 TCTTTCTTCTTCT
2295375 TCTAAACTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTCTTCTTCTC
Found at i:2295364 original size:12 final size:13
Alignment explanation
Indices: 2295335--2295375 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
2295325 CTTTTCCTTT
2295335 TCTTTCTTCTTCTC
1 TCTTTCTT-TTCTC
2295349 TCTTTCTTTT-TC
1 TCTTTCTTTTCTC
2295361 TCTTT-TTTTCT-
1 TCTTTCTTTTCTC
2295372 TCTT
1 TCTT
2295376 CTAAACTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.31
12 8 0.31
13 2 0.08
14 8 0.31
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TCTTTCTTTTCTC
Found at i:2295992 original size:1 final size:1
Alignment explanation
Indices: 2295986--2296064 Score: 77
Period size: 1 Copynumber: 79.0 Consensus size: 1
2295976 TTTATTTCTC
* * * * * * *
2295986 TTTTTTTCTTTTTCTTTTTTTCTTTTTTCTTTTTTTTCTTTTTTTTTCTTTTTTTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
2296051 TATTCTTTTTTTTT
1 TTTTTTTTTTTTTT
2296065 CTTATTCAAG
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.01, C:0.10, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:2296003 original size:14 final size:14
Alignment explanation
Indices: 2295984--2296062 Score: 92
Period size: 14 Copynumber: 5.6 Consensus size: 14
2295974 AATTTATTTC
2295984 TCTTTTTTTCTTTT
1 TCTTTTTTTCTTTT
2295998 TCTTTTTTTCTTTT
1 TCTTTTTTTCTTTT
*
2296012 T-TCTTTTTT-TTCT
1 TCT-TTTTTTCTTTT
2296025 T-TTTTTTTCTTTT
1 TCTTTTTTTCTTTT
*
2296038 TTTTTTTTTCTTTTAT
1 TCTTTTTTTC-TTT-T
2296054 TCTTTTTTT
1 TCTTTTTTT
2296063 TTCTTATTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.11
13 10 0.18
14 29 0.51
15 3 0.05
16 9 0.16
ACGTcount: A:0.01, C:0.11, G:0.00, T:0.87
Consensus pattern (14 bp):
TCTTTTTTTCTTTT
Found at i:2296024 original size:40 final size:41
Alignment explanation
Indices: 2295980--2296067 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 41
2295970 ACTTAATTTA
2295980 TTTCTCTTTTTTTCTTTTTCTTTTTTTCTTTT-TTCTTTTT
1 TTTCTCTTTTTTTCTTTTTCTTTTTTTCTTTTATTCTTTTT
* *
2296020 TTTCTTTTTTTTTCTTTTTTTTTTTTTCTTTTATTCTTTTT
1 TTTCTCTTTTTTTCTTTTTCTTTTTTTCTTTTATTCTTTTT
2296061 TTT-TCTT
1 TTTCTCTT
2296068 ATTCAAGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 33 0.75
41 11 0.25
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.86
Consensus pattern (41 bp):
TTTCTCTTTTTTTCTTTTTCTTTTTTTCTTTTATTCTTTTT
Found at i:2296407 original size:13 final size:14
Alignment explanation
Indices: 2296389--2296417 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2296379 CGGAACAAAT
2296389 TTAAAA-ATTAGAA
1 TTAAAAGATTAGAA
2296402 TTAAAAGATTAGAA
1 TTAAAAGATTAGAA
2296416 TT
1 TT
2296418 TTAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (14 bp):
TTAAAAGATTAGAA
Found at i:2296855 original size:37 final size:36
Alignment explanation
Indices: 2296795--2296865 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
2296785 TTCTTATGTT
*
2296795 TTTAATAGAAGTAATGAAATATTACCAACCCTAAAAAA
1 TTTAATAGAAGTAATCAAATATTA--AACCCTAAAAAA
* *
2296833 TTTAA-AGAATTAATCAATTATTAAACCCTAAAA
1 TTTAATAGAAGTAATCAAATATTAAACCCTAAAA
2296866 GAGAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 10 0.33
37 15 0.50
38 5 0.17
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.30
Consensus pattern (36 bp):
TTTAATAGAAGTAATCAAATATTAAACCCTAAAAAA
Found at i:2307538 original size:21 final size:21
Alignment explanation
Indices: 2307512--2307567 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2307502 ATAATCACTC
2307512 AAAATTATGATAATTAATC-AA
1 AAAATTATGATAATTAA-CGAA
*
2307533 AAAATTATGATAATTAACGCA
1 AAAATTATGATAATTAACGAA
*
2307554 ATAATTATGATAAT
1 AAAATTATGATAAT
2307568 CGTCATCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAATTATGATAATTAACGAA
Found at i:2322330 original size:82 final size:82
Alignment explanation
Indices: 2322148--2322417 Score: 346
Period size: 82 Copynumber: 3.3 Consensus size: 82
2322138 TTTAGTGACG
* * * * * *
2322148 TTTTTTCAACAAACGCCGTAATAGAGAAGTATTTTAGCGGCGTTTTTATACAAAAGTCGCAATAG
1 TTTTTTCAACAAACACCGCAATAGAGTAGTACTTTAGCGACGTTTTTATACAAAAGTCGTAATAG
*
2322213 GG-TCATCTATAGTGGC
66 GGTTCATCTATAATGGC
* * * * *
2322229 TTTTTTCAACAACCACCGCAACAGAGTAGTACTTTAGCGACATTTTCATACAAAAGTTGTAATAG
1 TTTTTTCAACAAACACCGCAATAGAGTAGTACTTTAGCGACGTTTTTATACAAAAGTCGTAATAG
*
2322294 GGTTAATCTATAATGGC
66 GGTTCATCTATAATGGC
* * *
2322311 GTTTTTCAACAAACACCGCAATAGAGTGGTACTTTAGCGACGTTTTTATATAAACA-TCGTAATA
1 TTTTTTCAACAAACACCGCAATAGAGTAGTACTTTAGCGACGTTTTTATACAAA-AGTCGTAATA
2322375 GGGTTCATCTATAATGGC
65 GGGTTCATCTATAATGGC
* *
2322393 TTTTTTTCAACAAACGCCGTAATAG
1 -TTTTTTCAACAAACACCGCAATAG
2322418 TTTGGTATGT
Statistics
Matches: 161, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
81 56 0.35
82 83 0.52
83 22 0.14
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (82 bp):
TTTTTTCAACAAACACCGCAATAGAGTAGTACTTTAGCGACGTTTTTATACAAAAGTCGTAATAG
GGTTCATCTATAATGGC
Found at i:2322334 original size:41 final size:40
Alignment explanation
Indices: 2322287--2322417 Score: 104
Period size: 41 Copynumber: 3.2 Consensus size: 40
2322277 TACAAAAGTT
2322287 GTAATAGGGTTAATCTATAATGGCGTTTTTCAACAAACACC
1 GTAATAGGGTT-ATCTATAATGGCGTTTTTCAACAAACACC
* * * ** * * *
2322328 GCAATAGAGTGGTA-CTTTAGCGACGTTTTT-ATATAAACATC
1 GTAATAG-G-GTTATCTATAATGGCGTTTTTCA-ACAAACACC
* *
2322369 GTAATAGGGTTCATCTATAATGGCTTTTTTTCAACAAACGCC
1 GTAATAGGGTT-ATCTATAATGGC-GTTTTTCAACAAACACC
2322411 GTAATAG
1 GTAATAG
2322418 TTTGGTATGT
Statistics
Matches: 65, Mismatches: 18, Indels: 13
0.68 0.19 0.14
Matches are distributed among these distances:
39 2 0.03
40 3 0.05
41 37 0.57
42 20 0.31
43 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (40 bp):
GTAATAGGGTTATCTATAATGGCGTTTTTCAACAAACACC
Found at i:2322766 original size:41 final size:41
Alignment explanation
Indices: 2322655--2322806 Score: 187
Period size: 41 Copynumber: 3.7 Consensus size: 41
2322645 CGTTTTTTGA
* * *
2322655 ACAAACGCCGCTATAGACTCGTACTTTAACGACATTTTTAT
1 ACAAACGCCGCTATAGACTCATACTTTAATGACGTTTTTAT
* *
2322696 ACAAACGCTGCTATAGACTCGTACTTTAATGACGTTTTTAT
1 ACAAACGCCGCTATAGACTCATACTTTAATGACGTTTTTAT
* * *
2322737 ACAAACGCCGCTATAGACTAATACTTTAATGGCGTTTGTATTT
1 ACAAACGCCGCTATAGACTCATACTTTAATGACGTTT-T-TAT
* * *
2322780 AAAAACACCGCTAAAGACTCATACTTT
1 ACAAACGCCGCTATAGACTCATACTTT
2322807 GGTGGTGGTG
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 71 0.73
42 1 0.01
43 25 0.26
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (41 bp):
ACAAACGCCGCTATAGACTCATACTTTAATGACGTTTTTAT
Found at i:2322886 original size:16 final size:16
Alignment explanation
Indices: 2322865--2322908 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
2322855 TCCAACTCCC
2322865 TTTTTCATTTTTATAT
1 TTTTTCATTTTTATAT
2322881 TTTTTCATTTTTATAT
1 TTTTTCATTTTTATAT
2322897 TTTTTCATTTTT
1 TTTTTCATTTTT
2322909 TCCTCCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTCATTTTTATAT
Found at i:2322906 original size:8 final size:8
Alignment explanation
Indices: 2322865--2322910 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
2322855 TCCAACTCCC
2322865 TTTTTCAT
1 TTTTTCAT
2322873 TTTTAT-AT
1 TTTT-TCAT
2322881 TTTTTCAT
1 TTTTTCAT
2322889 TTTTAT-AT
1 TTTT-TCAT
2322897 TTTTTCAT
1 TTTTTCAT
2322905 TTTTTC
1 TTTTTC
2322911 CTCCAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.06
8 30 0.88
9 2 0.06
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTCAT
Found at i:2326420 original size:24 final size:20
Alignment explanation
Indices: 2326393--2326450 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
2326383 GCATGAGTAG
2326393 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
2326417 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
2326437 TGCATCGATGCACT
1 TGCATCGATGCACT
2326451 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:2328085 original size:5 final size:5
Alignment explanation
Indices: 2328075--2328265 Score: 382
Period size: 5 Copynumber: 38.2 Consensus size: 5
2328065 ATGTGTTTTG
2328075 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
2328125 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
2328175 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
2328225 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA T
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA T
2328266 ATGTGTGTTA
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 186 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TGATA
Found at i:2330067 original size:25 final size:24
Alignment explanation
Indices: 2330034--2330093 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2330024 ATTAGTTAAG
* *
2330034 CATATTATATAAACTATAGTATTTA
1 CATATTATATAAACCATA-TATATA
2330059 CATATTATA-AAACCATATATATA
1 CATATTATATAAACCATATATATA
*
2330082 TATATATATATA
1 CATAT-TATATA
2330094 TATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 9 0.30
24 11 0.37
25 10 0.33
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (24 bp):
CATATTATATAAACCATATATATA
Found at i:2330080 original size:2 final size:2
Alignment explanation
Indices: 2330073--2330107 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2330063 TTATAAAACC
2330073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2330108 ACTAAGCCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2332593 original size:28 final size:28
Alignment explanation
Indices: 2332553--2332613 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
2332543 GGTTTATTTT
2332553 TGTTCGATCCGCAGAAGCTTTTTCATTA
1 TGTTCGATCCGCAGAAGCTTTTTCATTA
*
2332581 TGTTCGATCCGCAGAAGGTTTTTCATTA
1 TGTTCGATCCGCAGAAGCTTTTTCATTA
2332609 TGTTC
1 TGTTC
2332614 TTCGGTTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (28 bp):
TGTTCGATCCGCAGAAGCTTTTTCATTA
Found at i:2335271 original size:15 final size:15
Alignment explanation
Indices: 2335251--2335337 Score: 101
Period size: 15 Copynumber: 6.1 Consensus size: 15
2335241 TATCGATGAA
2335251 TTTTATATAAATAAT
1 TTTTATATAAATAAT
*
2335266 TTTTATTTAAAT-A-
1 TTTTATATAAATAAT
* * *
2335279 TATTATA-GAAGAAT
1 TTTTATATAAATAAT
2335293 TTTTATATAAATAAT
1 TTTTATATAAATAAT
2335308 TTTTATATAAATAAT
1 TTTTATATAAATAAT
*
2335323 TTTTAT-TTAATAAT
1 TTTTATATAAATAAT
2335337 T
1 T
2335338 AGAATTTCAC
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
12 2 0.03
13 6 0.10
14 15 0.25
15 37 0.62
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTTATATAAATAAT
Found at i:2335279 original size:41 final size:42
Alignment explanation
Indices: 2335234--2335320 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
2335224 ATAATAAAAT
* * *
2335234 AATATATTATCGATGAA-TTTTATATAAATAATTTTTATTTA
1 AATATATTATAGAAGAATTTTTATATAAATAATTTTTATATA
2335275 AATATATTATAGAAGAATTTTTATATAAATAATTTTTATATA
1 AATATATTATAGAAGAATTTTTATATAAATAATTTTTATATA
2335317 AATA
1 AATA
2335321 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.36
42 27 0.64
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (42 bp):
AATATATTATAGAAGAATTTTTATATAAATAATTTTTATATA
Found at i:2335761 original size:74 final size:73
Alignment explanation
Indices: 2335681--2335826 Score: 238
Period size: 74 Copynumber: 2.0 Consensus size: 73
2335671 TTTTATTTTT
*
2335681 TAAAGATCAAAATTCGAACAGTAAAGATATCAAAAGTAAGAATATTTAATATGATAAGATTGAAA
1 TAAAGATCAAAATTCGAACAGTAAAGATATCAAAAGTAAGAATATTTAATATGAAAAGATTGAAA
2335746 TATATTTAA
66 TAT-TTTAA
** * *
2335755 TAAAGATTGAAATTTGAACATTAAAGATATCAAAAGTAAGAATATTTAATATGAAAAGATTGAAA
1 TAAAGATCAAAATTCGAACAGTAAAGATATCAAAAGTAAGAATATTTAATATGAAAAGATTGAAA
2335820 TATTTTA
66 TATTTTA
2335827 TTACTTTGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 4 0.06
74 63 0.94
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (73 bp):
TAAAGATCAAAATTCGAACAGTAAAGATATCAAAAGTAAGAATATTTAATATGAAAAGATTGAAA
TATTTTAA
Found at i:2337480 original size:17 final size:17
Alignment explanation
Indices: 2337458--2337508 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
2337448 AATTAAGAGT
2337458 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
2337475 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
*
2337492 TACTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
2337509 CAACTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2340647 original size:17 final size:17
Alignment explanation
Indices: 2340625--2340675 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
2340615 AATTAAGATT
2340625 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
2340642 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
*
2340659 TACTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
2340676 CAACTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2355349 original size:21 final size:23
Alignment explanation
Indices: 2355319--2355365 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2355309 TAAAAATTGT
2355319 TTTCATTTTGATTT-AGTTCTTC
1 TTTCATTTTGATTTAAGTTCTTC
* *
2355341 TTTC-TTTTGTTTTAAGTTTTTC
1 TTTCATTTTGATTTAAGTTCTTC
2355363 TTT
1 TTT
2355366 AACTTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTCATTTTGATTTAAGTTCTTC
Found at i:2356379 original size:21 final size:21
Alignment explanation
Indices: 2356355--2356409 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2356345 ATAGAAAATT
*
2356355 TCTCGAAGGACCTCATATATG
1 TCTCGAAGGACCACATATATG
*
2356376 TCTCGAATGACCACATATATG
1 TCTCGAAGGACCACATATATG
*
2356397 TCCCGAAGGACCA
1 TCTCGAAGGACCA
2356410 TATAGAACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (21 bp):
TCTCGAAGGACCACATATATG
Found at i:2365788 original size:31 final size:31
Alignment explanation
Indices: 2365729--2365789 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2365719 CCCTTTCCAA
*
2365729 AAAAAGAAAATTAAAAAAAACATCAAAAATG
1 AAAAAGAAAATTAAAAAAAACAACAAAAATG
* * *
2365760 AAAAAGAAAATTGAAAAAAAGAAGAAAAAT
1 AAAAAGAAAATTAAAAAAAACAACAAAAAT
2365790 CCCAACATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.75, C:0.03, G:0.10, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAATTAAAAAAAACAACAAAAATG
Found at i:2366713 original size:12 final size:15
Alignment explanation
Indices: 2366682--2366718 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 15
2366672 GCAATTGGAG
2366682 TTGAAAATGAGAGAA
1 TTGAAAATGAGAGAA
2366697 TTGAAAA-GA-AG-A
1 TTGAAAATGAGAGAA
2366709 TTGAAAATGA
1 TTGAAAATGA
2366719 AATTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.38
13 4 0.19
14 2 0.10
15 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (15 bp):
TTGAAAATGAGAGAA
Found at i:2374351 original size:20 final size:19
Alignment explanation
Indices: 2374287--2374362 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
2374277 ATACTATAGT
2374287 AGTATCGATACCATGGTGAG
1 AGTATCGATACCATGGT-AG
* * **
2374307 GGTAACGATACCATGAAAAG
1 AGTATCGATACCATG-GTAG
*
2374327 GGTATCGATACCATGGTAG
1 AGTATCGATACCATGGTAG
*
2374346 TAGTATCGATACTATGG
1 -AGTATCGATACCATGG
2374363 AGCCAGAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 2 0.04
20 43 0.96
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTATCGATACCATGGTAG
Found at i:2374759 original size:59 final size:59
Alignment explanation
Indices: 2374669--2374899 Score: 326
Period size: 59 Copynumber: 3.9 Consensus size: 59
2374659 TTACCAAATA
* * * *
2374669 GCACTTTGTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATTAATTTCCGTATAGG
1 GCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGG
*
2374727 GCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGG
1 GCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGG
* * * * *
2374786 GCACTTCGTGTGCTAACATGATAAGAAATTCATATTAAGTGTTTTAATTTCTGTATTGG
1 GCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGG
2374845 GCACCTT-GTGTGCTAA-A-GAATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1 GCA-CTTCGTGTGCTAACATG-ATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
2374900 GGGAAATATA
Statistics
Matches: 155, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
57 1 0.01
58 45 0.29
59 106 0.68
60 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (59 bp):
GCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGG
Found at i:2375383 original size:68 final size:68
Alignment explanation
Indices: 2375270--2375534 Score: 352
Period size: 68 Copynumber: 3.9 Consensus size: 68
2375260 AAAGATCAAA
* * * **
2375270 AGGCCTAACTATGCATATGACAGAAATGTGTCATTTATTTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2375335 TTG
66 TTG
* * * * * *
2375338 AGGACTAACTGTGCATGTGACAGAACA-ATGTCAATTATGCCAGTTATATGAAAGACTAAGTGTC
1 AGGCCTAACTGTGCATATGACAGAA-AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
2375402 TTTG
65 TTTG
*
2375406 AGGCCTAATTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
2375471 TTG
66 TTG
* * * * * *
2375474 AGGCCTAACTGTGCATATGACAGAATGTTGTCATTTATGCCAGTTAAATGAACGGTTAAGT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
2375535 ACTGTTGAGT
Statistics
Matches: 171, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
67 1 0.01
68 169 0.99
69 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:2375534 original size:136 final size:136
Alignment explanation
Indices: 2375270--2375525 Score: 395
Period size: 136 Copynumber: 1.9 Consensus size: 136
2375260 AAAGATCAAA
* * **
2375270 AGGCCTAACTATGCATATGACAGAAATGTGTCATTTATTTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* *
2375335 TTGAGGACTAACTGTGCATGTGACAGAACAATGTCAATTATGCCAGTTATATGAAAGACTAAGTG
66 TTGAGGACTAACTGTGCATATGACAGAACAATGTCAATTATGCCAGTTAAATGAAAGACTAAGTG
2375400 TCTTTG
131 TCTTTG
* *
2375406 AGGCCTAATTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* *** *
2375471 TTGAGGCCTAACTGTGCATATGACAGAATGTTGTCATTTATGCCAGTTAAATGAA
66 TTGAGGACTAACTGTGCATATGACAGAACAATGTCAATTATGCCAGTTAAATGAA
2375526 CGGTTAAGTA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
136 107 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (136 bp):
AGGCCTAACTATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTGAGGACTAACTGTGCATATGACAGAACAATGTCAATTATGCCAGTTAAATGAAAGACTAAGTG
TCTTTG
Found at i:2375611 original size:81 final size:81
Alignment explanation
Indices: 2375497--2375730 Score: 317
Period size: 81 Copynumber: 2.9 Consensus size: 81
2375487 CATATGACAG
* *
2375497 AATGTTGTCATTTATGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAATTGCCTA
1 AATG-TGTCAATTATGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAATGGCCTA
*
2375562 GCTGTGCAATCGGTACA
65 GCTGTGCAATCGGCACA
* * * *
2375579 AATGTGTCAATTATGTCAGATATATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAG
1 AATGTGTCAATTATGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAATGGCCTAG
* * *
2375644 CTGTTCAATTGGCATA
66 CTGTGCAATCGGCACA
* * * *
2375660 AAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTA-TCGTTGAGTAAAAGAATAATGGCGTA
1 AATGTGTCAATTATGCCAGTTAAATGAACGGTTAAGTACT-GTTGAGTAAAAGAATAATGGCCTA
2375724 GCTGTGC
65 GCTGTGC
2375731 CAGTTAGATG
Statistics
Matches: 133, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
81 129 0.97
82 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (81 bp):
AATGTGTCAATTATGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAATGGCCTAG
CTGTGCAATCGGCACA
Found at i:2375767 original size:217 final size:217
Alignment explanation
Indices: 2375511--2375932 Score: 616
Period size: 217 Copynumber: 1.9 Consensus size: 217
2375501 TTGTCATTTA
2375511 TGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAATTG-CCTAGCTGTGCAATCGG
1 TGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAA-TGACCTAGCTGTGCAATCGG
* * *
2375575 TACAAATGTGTCAATTATG-TCAGATATATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGG
65 CACAAAGGTGTCAATTATGCT-AGATAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGG
* * * * * *
2375639 CCTAGCTGTTCAATTGGCATAAAGG-TGTCAATTATGCCAGTTAGATGAATGGTTAAGTATCGTT
129 CCTAGCTATGCAATTGGCA-AAAGGATATCAATTATGCCAGTTAGATGAACGGTTAAGTACCATT
2375703 GAGTAAAAGAATAATGGCGTAGCTG
193 GAGTAAAAGAATAATGGCGTAGCTG
* * * *
2375728 TGCCAGTTAGATGAACGGTTAGGTACTGTTGAGTAAAAGAATAATGACCTAGTTGTGCAATTGGC
1 TGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAATGACCTAGCTGTGCAATCGGC
* * *
2375793 AGAAAGGTGTCAATTATGCTAGTTAGATGAACGGTTAAGTACCGTTGAGTAAACGAATAATGGCC
66 ACAAAGGTGTCAATTATGCTAGATAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCC
* **
2375858 TAGCTATGCAATTGGCAGAAGGATATCAATTATGTTAGTTAGATGAACGGTTAAGTACCATTGAG
131 TAGCTATGCAATTGGCAAAAGGATATCAATTATGCCAGTTAGATGAACGGTTAAGTACCATTGAG
*
2375923 TAAACGAATA
196 TAAAAGAATA
2375933 GCATAGTTGT
Statistics
Matches: 182, Mismatches: 20, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
216 6 0.03
217 175 0.96
218 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (217 bp):
TGCCAGTTAAATGAACGGTTAAGTACTGTTGAGTAAAAGAATAATGACCTAGCTGTGCAATCGGC
ACAAAGGTGTCAATTATGCTAGATAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCC
TAGCTATGCAATTGGCAAAAGGATATCAATTATGCCAGTTAGATGAACGGTTAAGTACCATTGAG
TAAAAGAATAATGGCGTAGCTG
Found at i:2375785 original size:55 final size:55
Alignment explanation
Indices: 2375673--2375785 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 55
2375663 GTGTCAATTA
* * *
2375673 TGCCAGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGCGTAGCTG
1 TGCCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATGACCTAGCTG
* *
2375728 TGCCAGTTAGATGAACGGTTAGGTA-CTGTTGAGTAAAAGAATAATGACCTAGTTG
1 TGCCAGTTAGATGAACGGTTAAGTATC-GTTGAGTAAAAGAATAATGACCTAGCTG
2375783 TGC
1 TGC
2375786 AATTGGCAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 1 0.02
55 51 0.98
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (55 bp):
TGCCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATGACCTAGCTG
Found at i:2375851 original size:136 final size:136
Alignment explanation
Indices: 2375602--2375862 Score: 423
Period size: 136 Copynumber: 1.9 Consensus size: 136
2375592 TGTCAGATAT
* * *
2375602 ATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTTCAATTGGCATAAAGGTGT
1 ATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGACCTAGCTGTGCAATTGGCAGAAAGGTGT
* * *
2375667 CAATTATGCCAGTTAGATGAATGGTTAAGTATCGTTGAGTAAAAGAATAATGGCGTAGCTGTGCC
66 CAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCC
2375732 AGTTAG
131 AGTTAG
* * *
2375738 ATGAACGGTTAGGTACTGTTGAGTAAAAGAATAATGACCTAGTTGTGCAATTGGCAGAAAGGTGT
1 ATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGACCTAGCTGTGCAATTGGCAGAAAGGTGT
* *
2375803 CAATTATGCTAGTTAGATGAACGGTTAAGTACCGTTGAGTAAACGAATAATGGCCTAGCT
66 CAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCT
2375863 ATGCAATTGG
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
136 114 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (136 bp):
ATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGACCTAGCTGTGCAATTGGCAGAAAGGTGT
CAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCC
AGTTAG
Found at i:2375868 original size:81 final size:81
Alignment explanation
Indices: 2375728--2376058 Score: 411
Period size: 81 Copynumber: 4.1 Consensus size: 81
2375718 GGCGTAGCTG
* * * *
2375728 TGCCAGTTAGATGAACGGTTAGGTACTGTTGAGTAAAAGAATAATGACCTAGTTGTGCAATTGGC
1 TGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTGGC
2375793 AGAAAGGTGTCAATTA
66 AGAAAGGTGTCAATTA
* * *
2375809 TGCTAGTTAGATGAACGGTTAAGTACCGTTGAGTAAACGAATAATGGCCTAGCTATGCAATTGGC
1 TGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTGGC
*
2375874 AG-AAGGATATCAATTA
66 AGAAAGG-TGTCAATTA
** * * * * * *
2375890 TGTTAGTTAGATGAACGGTTAAGTACCATTGAGTAAACGAAT-A--GCATAGTTGTGCAATTAGA
1 TGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTGGC
2375952 AGAAAGGTGTCAATTA
66 AGAAAGGTGTCAATTA
* * * * * *
2375968 TTCCAGTTAGATGAACGATTAAGTATCGTTGAGTAAAAGAATAATGGTCTAACTTTGC-ATTGGC
1 TGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTGGC
*
2376032 AGAAAGGAGTCAATTA
66 AGAAAGGTGTCAATTA
2376048 TGCCAGTTAGA
1 TGCCAGTTAGA
2376059 CCAATGTTAA
Statistics
Matches: 213, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
78 59 0.28
79 5 0.02
80 34 0.16
81 115 0.54
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (81 bp):
TGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTGGC
AGAAAGGTGTCAATTA
Found at i:2376039 original size:159 final size:161
Alignment explanation
Indices: 2375728--2376058 Score: 454
Period size: 159 Copynumber: 2.1 Consensus size: 161
2375718 GGCGTAGCTG
* ** * * *
2375728 TGCCAGTTAGATGAACGGTTAGGTACTGTTGAGTAAAAGAATAATGACCTAGTTGTGCAATTGGC
1 TGCCAGTTAGATGAACGGTTAAGTACCATTGAGTAAAAGAATAATGACATAGTTGTGCAATTAGA
* * *
2375793 AGAAAGGTGTCAATTATGCTAGTTAGATGAACGGTTAAGTACCGTTGAGTAAACGAATAATGGCC
66 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCC
*
2375858 TAGCTATGCAATTGGCAGAAGGATATCAATTA
131 TAACTATGCAATTGGCAGAAGGA-ATCAATTA
** *
2375890 TGTTAGTTAGATGAACGGTTAAGTACCATTGAGTAAACGAAT-A-G-CATAGTTGTGCAATTAGA
1 TGCCAGTTAGATGAACGGTTAAGTACCATTGAGTAAAAGAATAATGACATAGTTGTGCAATTAGA
* * *
2375952 AGAAAGGTGTCAATTATTCCAGTTAGATGAACGATTAAGTATCGTTGAGTAAAAGAATAATGGTC
66 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCC
* *
2376017 TAACTTTGC-ATTGGCAGAAAGGAGTCAATTA
131 TAACTATGCAATTGGCAG-AAGGAATCAATTA
2376048 TGCCAGTTAGA
1 TGCCAGTTAGA
2376059 CCAATGTTAA
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
158 24 0.16
159 86 0.58
160 1 0.01
161 1 0.01
162 36 0.24
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (161 bp):
TGCCAGTTAGATGAACGGTTAAGTACCATTGAGTAAAAGAATAATGACATAGTTGTGCAATTAGA
AGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCC
TAACTATGCAATTGGCAGAAGGAATCAATTA
Found at i:2376132 original size:2 final size:2
Alignment explanation
Indices: 2376125--2376169 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2376115 GAAGGGATGT
*
2376125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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
2376167 TA T
1 TA T
2376170 TGTACAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2376285 original size:44 final size:45
Alignment explanation
Indices: 2376236--2376321 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
2376226 TATCAAAAGC
*
2376236 ATGAAAGGATTCCATAAATG-AAGGTATAATAATGTATAAAAATG
1 ATGAAAGGATGCCATAAATGAAAGGTATAATAATGTATAAAAATG
2376280 ATGAAAGGATGCCATAAATGAAAGGTATAATAATGTATAAAA
1 ATGAAAGGATGCCATAAATGAAAGGTATAATAATGTATAAAA
2376322 GGCATTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.26
Consensus pattern (45 bp):
ATGAAAGGATGCCATAAATGAAAGGTATAATAATGTATAAAAATG
Found at i:2379937 original size:95 final size:93
Alignment explanation
Indices: 2379721--2379939 Score: 239
Period size: 93 Copynumber: 2.3 Consensus size: 93
2379711 TGATTCAATC
* * * * *
2379721 AGTATCGATACCATAGTAAGTGTATCGATACTAAGCAATATCGAACCTAATTTCGGTATCGATAT
1 AGTATCGATACCATGGTAAGTGTATCGATACCAAGAAACATCGAACCTAATTTCGGTATCGATAC
*
2379786 CATAGGGGGTATCAATACCATAGATAGT
66 CATAGGGGGTATCAATACCATAGATAGA
* * * *
2379814 AGTATCGATACCATGGTGAGGGTATCGATACCATGAAACATCGAACTTAACTTT-GGTATCGATA
1 AGTATCGATACCATGGTAAGTGTATCGATACCAAGAAACATCGAACCTAA-TTTCGGTATCGATA
** *
2379878 CCGGA-AGGGGGTATCGGTACTATAGTATAGA
65 CC--ATAGGGGGTATCAATACCATAG-ATAGA
2379909 AGTATC-AGTACCATGGT-AGTAGTATCGATAC
1 AGTATCGA-TACCATGGTAAGT-GTATCGATAC
2379940 TATGGAGCCA
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
93 53 0.50
94 23 0.22
95 30 0.28
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (93 bp):
AGTATCGATACCATGGTAAGTGTATCGATACCAAGAAACATCGAACCTAATTTCGGTATCGATAC
CATAGGGGGTATCAATACCATAGATAGA
Found at i:2380351 original size:59 final size:58
Alignment explanation
Indices: 2380259--2380422 Score: 237
Period size: 59 Copynumber: 2.8 Consensus size: 58
2380249 TACCAAATGA
* * *
2380259 CACTTCGTGTACAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGG
1 CACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGG
*
2380317 CACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGG
1 CACTTCGTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGG
2380376 CACCTT--TGTGCTAAA-GAATAAGAAA-TCATACTAAGTGTATGAATTTC
1 CA-CTTCGTGTGCTAAATG-ATAAGAAATTCATACTAAGTGTATGAATTTC
2380423 CATATGTGAA
Statistics
Matches: 99, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
56 23 0.23
57 9 0.09
58 21 0.21
59 43 0.43
60 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (58 bp):
CACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGG
Found at i:2380906 original size:68 final size:68
Alignment explanation
Indices: 2380797--2381024 Score: 402
Period size: 68 Copynumber: 3.4 Consensus size: 68
2380787 AAAAGATCAA
*
2380797 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
2380862 TTT
66 TTT
* * * * *
2380865 GAGGCCTAACTGTCCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAATGTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
2380930 TTT
66 TTT
2380933 GAGGCCTAACTGTGCATATGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
2380998 TTT
66 TTT
2381001 GAGGCCTAACTGTGCATATGACAG
1 GAGGCCTAACTGTGCATATGACAG
2381025 TATGCTAGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 149 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATATGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
TTT
Found at i:2381177 original size:81 final size:81
Alignment explanation
Indices: 2381025--2381633 Score: 764
Period size: 81 Copynumber: 7.6 Consensus size: 81
2381015 CATATGACAG
* * * * * *
2381025 TATGCTAGTTAGATGAACGATTAAGTACCATTGAGTAAAAGAATAATAGCCTAGCTATGCAGTTG
1 TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
* *
2381090 GCAGAAATGTGTCAAT
66 GAAGAAAGGTGTCAAT
*
2381106 TATGCCAGTTAGAAT-AACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGATGTGCAATT
1 TATGCCAGTTAG-ATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATT
*
2381170 GGAAGAAAGGTGACAAT
65 GGAAGAAAGGTGTCAAT
* * * *
2381187 TATGCCAGCTAGATGAATGGTTAAGTATCGTTGAGTAAAATAATAATGGCCTAGCTGTGCAATTG
1 TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
*
2381252 GCAGAAAGGTGTCAAT
66 GAAGAAAGGTGTCAAT
* * * *
2381268 TATG-TAGTTAGATGAACGGTTAAGTGCCGTTGAGTAAAAGAACAATGGCCTAGCTGTACAATTA
1 TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATT-
* *
2381332 GCAA-AAAGGTTTCAAT
65 GGAAGAAAGGTGTCAAT
* * * * * *
2381348 TATGCCAGTTAGATGAA-TGATAAGTATCGTTGGGTAAACGAATAATGTCCTAGCTGTGCAATTG
1 TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
**
2381412 TCAGAAAGGTGTCAAT
66 GAAGAAAGGTGTCAAT
* * * *
2381428 TATACCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTATGTAATTG
1 TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
**
2381493 GTTGAAAGGTGTCAAT
66 GAAGAAAGGTGTCAAT
* *
2381509 TATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAACTGTGC-ATT-
1 TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
2381572 GACAGAAAGGTGTCAAT
66 GA-AGAAAGGTGTCAAT
* ** * *
2381589 TATGCCAGTTAGACGAAC-GTTAAACACTGTTGAGTAAGAGAATAA
1 TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAA
2381634 AGAAATTTTA
Statistics
Matches: 455, Mismatches: 66, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
79 25 0.05
80 165 0.36
81 263 0.58
82 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (81 bp):
TATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
GAAGAAAGGTGTCAAT
Found at i:2381354 original size:161 final size:161
Alignment explanation
Indices: 2381025--2381633 Score: 796
Period size: 161 Copynumber: 3.8 Consensus size: 161
2381015 CATATGACAG
* * * * *
2381025 TATGCTAGTTAGATGAACGATTAAGTACCATTGAGTAAAAGAATAATAGCCTAGCTATGCAGTTG
1 TATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
*
2381090 GCAGAAATGTGTCAATTATGCCAGTTAGAAT-AACGGTTAAGTACCGTTGAGTAAAAGAATAATG
66 GCAGAAAGGTGTCAATTATGCCAGTTAG-ATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATG
* * *
2381154 GCCTAGATGTGCAATTGGAAGAAAGGTGACAAT
130 GCCTAGCTGTGCAATTGCAA-AAAGGTGTCAAT
* * * * *
2381187 TATGCCAGCTAGATGAATGGTTAAGTATCGTTGAGTAAAATAATAATGGCCTAGCTGTGCAATTG
1 TATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
* * *
2381252 GCAGAAAGGTGTCAATTATG-TAGTTAGATGAACGGTTAAGTGCCGTTGAGTAAAAGAACAATGG
66 GCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGG
* *
2381316 CCTAGCTGTACAATTAGCAAAAAGGTTTCAAT
131 CCTAGCTGTGCAATT-GCAAAAAGGTGTCAAT
* * * * *
2381348 TATGCCAGTTAGATGAATGA-TAAGTATCGTTGGGTAAACGAATAATGTCCTAGCTGTGCAATTG
1 TATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
* * *
2381412 TCAGAAAGGTGTCAATTATACCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGG
66 GCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGG
* * ***
2381477 CCTAGCTATGTAATTGGTTGAAAGGTGTCAAT
131 CCTAGCTGTGCAATT-GCAAAAAGGTGTCAAT
*
2381509 TATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAACTGTGC-ATTG
1 TATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
* * ** * *
2381573 ACAGAAAGGTGTCAATTATGCCAGTTAGACGAAC-GTTAAACACTGTTGAGTAAGAGAATAA
66 GCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAA
2381634 AGAAATTTTA
Statistics
Matches: 390, Mismatches: 53, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
160 82 0.21
161 197 0.51
162 111 0.28
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (161 bp):
TATGCCAGTTAGATGAACGATTAAGTACCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCAATTG
GCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATGG
CCTAGCTGTGCAATTGCAAAAAGGTGTCAAT
Found at i:2381675 original size:2 final size:2
Alignment explanation
Indices: 2381668--2381746 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
2381658 GAAGGGATGT
2381668 TA TA TA 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
2381710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2381747 TGTACAACAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2381877 original size:45 final size:45
Alignment explanation
Indices: 2381789--2381931 Score: 153
Period size: 45 Copynumber: 3.2 Consensus size: 45
2381779 TTATAAAGGA
* * * * *
2381789 AAAGGTA-AACAAAATATCAAAGGCATGAAAGGATTCCATAAATG
1 AAAGGTATAATAATATATAAAAGGCATGAAAGGATGCCAAAAATG
* *
2381833 AAAGGTATAATAATATATAAAAGTCATGAAATGATGCCAAAAATG
1 AAAGGTATAATAATATATAAAAGGCATGAAAGGATGCCAAAAATG
* * * * * *
2381878 ATAGGTATAATAATGTATAAAAGGCATGTAAGGATGACATAATTG
1 AAAGGTATAATAATATATAAAAGGCATGAAAGGATGCCAAAAATG
*
2381923 AAATGTATA
1 AAAGGTATA
2381932 TAGGTGCATT
Statistics
Matches: 81, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
44 7 0.09
45 74 0.91
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.24
Consensus pattern (45 bp):
AAAGGTATAATAATATATAAAAGGCATGAAAGGATGCCAAAAATG
Found at i:2389872 original size:17 final size:17
Alignment explanation
Indices: 2389852--2389885 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2389842 AAAATGAAAT
2389852 AAAAATTAAACTTTAGG
1 AAAAATTAAACTTTAGG
2389869 AAAAATTAAACTTTAGG
1 AAAAATTAAACTTTAGG
2389886 TATAACTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
AAAAATTAAACTTTAGG
Found at i:2391871 original size:95 final size:94
Alignment explanation
Indices: 2391734--2391921 Score: 261
Period size: 95 Copynumber: 2.0 Consensus size: 94
2391724 TACCAATGAG
* *
2391734 ATAGTATTGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAA-TCTAAAATTGGTATCAA
1 ATAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACT-TAAAATTGGTATCAA
*
2391798 TACTAGAAAGGGGTCTCGGTACCATAGTATT
65 -ACTAGAAAGGGGTATCGGTACCATAGTATT
* * * * *
2391829 ATAGTATCGATACTATGGTAAGGGTATCGATACTAGGAAACATCGAACTTAAATTTGGTATCGAA
1 ATAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACTTAAAATTGGTATCAAA
* *
2391894 CTAGAAGGGGGTATCGGTGCCATAGTAT
66 CTAGAAAGGGGTATCGGTACCATAGTAT
2391922 AAAGTGTCGG
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
94 26 0.32
95 55 0.67
96 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (94 bp):
ATAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAACTTAAAATTGGTATCAAA
CTAGAAAGGGGTATCGGTACCATAGTATT
Found at i:2392348 original size:59 final size:59
Alignment explanation
Indices: 2392283--2392819 Score: 799
Period size: 59 Copynumber: 9.1 Consensus size: 59
2392273 ATGACACTAA
* * * *
2392283 GTGTGCTAAAATGTTAAGAAATTTATACTAAGTGTATGAATTTTCGTATAAGGCATTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
2392342 GTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCTGTATACGGCGCTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
**
2392401 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
2392460 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCATTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* **
2392519 GCGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATGACCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
2392578 GTGTGCTAAAATATTAAGAAATTCTTACTAAGTTTATGAATTCCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
2392637 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATAGGGAACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
2392696 ATGTGCTAAAATATTAAGAAATTCATACTAAGTTTATGAATTTCCGTAT-GGGACACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG-CACTTC
** *
2392755 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCACTAT-
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACT-TC
2392814 GTGTGC
1 GTGTGC
2392820 ATAACACGGA
Statistics
Matches: 433, Mismatches: 42, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
58 3 0.01
59 426 0.98
60 4 0.01
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:2393257 original size:45 final size:45
Alignment explanation
Indices: 2393188--2393325 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
2393178 GATGTATAAC
* * *
2393188 AATGTATAATAATGTATAGAAGGCATGAAAGGATGCCATAAATGA
1 AATGCATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* *
2393233 AATGCATAATAGTGTATAAAAGGCATGAAAGAATTCCA-AAATGGA
1 AATGCATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAAT-GA
* * * * * *
2393278 AACGGCATAATGGTGCATTATAA-GCATGAAGGGATGCTATAAATGA
1 AA-TGCATAATAGTGTA-TAAAAGGCATGAAAGGATGCCATAAATGA
2393324 AA
1 AA
2393326 ATAAAGAATA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
44 4 0.05
45 37 0.49
46 27 0.36
47 8 0.11
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (45 bp):
AATGCATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:2395071 original size:2 final size:2
Alignment explanation
Indices: 2395066--2395090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2395056 AATGTCAGAA
2395066 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2395091 GCTTTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2397768 original size:94 final size:95
Alignment explanation
Indices: 2397600--2397806 Score: 258
Period size: 95 Copynumber: 2.2 Consensus size: 95
2397590 TGATTCAATC
* * **
2397600 AGTATCGATACCATGGTAATGGTATCATACCAAGTATTATCGAATCTAAATTTGGAATCGATACC
1 AGTATCGATACCATGGTAAGGGTATCATACCAAGAAACATCGAATCTAAATTTGGAATCGATACC
* * *
2397665 GGAATGGGG-TATTGGTACCATAATATTGT
66 GGAATGGGGTTATCGGTACCATAATATAGA
* * *
2397694 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATTGAA-CTTAAATTTGGTATTGATA
1 AGTATCGATACCATGGTAAGGGTATC-ATACCAAGAAACATCGAATC-TAAATTTGGAATCGATA
*
2397758 CCGGAA-GGGGTTATCGGTACCATAGTATAGA
64 CCGGAATGGGGTTATCGGTACCATAATATAGA
* *
2397789 AGTATCGGTACCAGGGTA
1 AGTATCGATACCATGGTA
2397807 GCACTATCGA
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
94 30 0.31
95 67 0.69
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCATACCAAGAAACATCGAATCTAAATTTGGAATCGATACC
GGAATGGGGTTATCGGTACCATAATATAGA
Found at i:2398919 original size:59 final size:59
Alignment explanation
Indices: 2398148--2398918 Score: 1001
Period size: 59 Copynumber: 13.1 Consensus size: 59
2398138 ATGGCACTAA
* * * *
2398148 GTGTGTTAAAATGTCAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
** * *
2398207 GTGTGCTAAAATGTTAAGAAATTCATTTTAAGTGTATGAATTTCCGTATAAGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* ** *
2398266 GTGTGCTAAATTGTTAAGAAATTCATTTTAAGTGTATGAATTTCCGTATATGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
2398325 GTGCGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAAGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
** * *
2398384 GTGTGCTAAAATGTTAAGAAATTCATGTTAAGTGTATGAATTTCTGTATAAGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
2398443 GTGCGCTAAAATGTTAAGAAATTCAAACTAAGTGTATGGATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
2398502 GTGTGTTAAAATTTTAAGAAATTCCTACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * * *
2398561 GTGTGCTAAAATATTAATAAATTCATACTAAGTTTATTAATTTCTGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
2398620 GTGTGCTAAAATGTTAATAAATTCATACTAAGTGTATGAATTTCCGTATAAGGTACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
** ** * *
2398679 GCATGCTAAAATGTTAAGAAATTCATGTTAAGTGTATGAATTTTCATATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
**
2398738 -TCGTGCTAAAATGTTAAGAAATTCATACT-A-TGTATGAATTTCTATATAGGGCACTTC
1 GT-GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* ** * *
2398795 GTGTGCTAAAATATTAAGAAATTCATACTAAGTGTACAAATTTCCATATAGAGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * ** * * *
2398854 GTGTGCAAAAATGTTAAGAAATTCATAGTATTTGTATAAATTTCTGTATTGGGCACTAT-
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACT-TC
2398913 GTGTGC
1 GTGTGC
2398919 ATAACACGGA
Statistics
Matches: 629, Mismatches: 78, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
57 51 0.08
58 3 0.00
59 574 0.91
60 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:2403693 original size:22 final size:20
Alignment explanation
Indices: 2403668--2403714 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
2403658 GGGGTATTGG
*
2403668 TACCATAGTATTGTAGTATCGA
1 TACCATAGTA-AG-AGTATCGA
*
2403690 TACCATGGTAAGAGTATCGA
1 TACCATAGTAAGAGTATCGA
2403710 TACCA
1 TACCA
2403715 GGAAACATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 9 0.39
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
TACCATAGTAAGAGTATCGA
Found at i:2403749 original size:95 final size:95
Alignment explanation
Indices: 2403586--2403794 Score: 276
Period size: 95 Copynumber: 2.2 Consensus size: 95
2403576 ACTAATGAGA
* * * * *
2403586 TAGTATCAATACCATGGTAAGGGTATCGATACCAAGTAACATCGAATCTAAAGTTGGTGTCGATA
1 TAGTATCGATACCATGGTAAGAGTATCGATACCAAGAAACATCAAATCTAAAGTTGGTATCGATA
* * * *
2403651 CCGGAATGGGGTATTGGTACCATAGTATTG
66 CCGGAAGGGGGTATCGGTACCATAATATAG
* * *
2403681 TAGTATCGATACCATGGTAAGAGTATCGATACCAGGAAACATCAAA-CTTAAATTTGGTATCTAT
1 TAGTATCGATACCATGGTAAGAGTATCGATACCAAGAAACATCAAATC-TAAAGTTGGTATCGAT
2403745 ACCGGAAGGGGGTATCGGTACCATAATATAG
65 ACCGGAAGGGGGTATCGGTACCATAATATAG
* *
2403776 AAGTATCGGTACCATGGTA
1 TAGTATCGATACCATGGTA
2403795 GCACAATCGA
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 1 0.01
95 98 0.99
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (95 bp):
TAGTATCGATACCATGGTAAGAGTATCGATACCAAGAAACATCAAATCTAAAGTTGGTATCGATA
CCGGAAGGGGGTATCGGTACCATAATATAG
Found at i:2404173 original size:59 final size:58
Alignment explanation
Indices: 2404135--2404821 Score: 931
Period size: 59 Copynumber: 11.8 Consensus size: 58
2404125 ATGGCACTAA
* *
2404135 GTGTGCTAATATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
*
2404194 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCATTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
* * * * *
2404253 GTGTGCTAAAATGCTAAGAAATTCATACTGAGTGTATGCA-TTCCATATAAGGCAC--C
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC-GATAGGGCACTTC
* *
2404309 -----CTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCATTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
* * *
2404363 GTGTGTTAGAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
* * *
2404422 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTAAGAATTTCCATATAGGGCACATC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC-GATAGGGCACTTC
* *
2404481 GTGTACTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
2404540 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
** * *
2404599 ACGTGCTAAAATGTTAAGAAAATCATACTAAGTGTACGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
* * *
2404658 GCGTGCTAAAATGATAAGAAATTCATACTAAGTGTGTGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG-ATAGGGCACTTC
* * * * *
2404717 ATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGACAGTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC-GATAGGGCACTTC
* *
2404776 GTGTGGTAAAATGTTAAGAAATTCATACTAATTGTATGAATTTCCG
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
2404822 TATTGGGTAC
Statistics
Matches: 560, Mismatches: 55, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
51 32 0.06
52 10 0.02
54 1 0.00
56 1 0.00
58 11 0.02
59 505 0.90
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (58 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGATAGGGCACTTC
Found at i:2404564 original size:177 final size:176
Alignment explanation
Indices: 2404135--2404820 Score: 1035
Period size: 177 Copynumber: 3.9 Consensus size: 176
2404125 ATGGCACTAA
* *
2404135 GTGTGCTAATATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGGCACTTCGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
*
2404200 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCATTTCGTGTGCTAAAAT
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAAT
* * * *
2404265 GCTAAGAAATTCATACTGAGTGTATGCA-TTCCATATAAGGCAC-C
131 GTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTC
* * *
2404309 -----CTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCATTTCGTGTGT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
* *
2404369 TAGAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAAT
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAAT
*
2404434 GTTAAGAAATTCATACTAAGTGTAAGAATTTCCATATAGGGCACATC
131 GTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCAC-TC
* *
2404481 GTGTACTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTCGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
**
2404546 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCACGTGCTAAAAT
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAAT
* * *
2404611 GTTAAGAAAATCATACTAAGTGTACGAATTTCCGTATAGGGCACTTC
131 GTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCAC-TC
* * * *
2404658 GCGTGCTAAAATGATAAGAAATTCATACTAAGTGTGTGAATTTCCGTATAGGGCACTTCATGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
* * * * *
2404723 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGACAGTTTGTGTGGTAAAAT
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAAT
*
2404788 GTTAAGAAATTCATACTAATTGTATGAATTTCC
131 GTTAAGAAATTCATACTAAGTGTATGAATTTCC
2404821 GTATTGGGTA
Statistics
Matches: 463, Mismatches: 41, Indels: 13
0.90 0.08 0.03
Matches are distributed among these distances:
169 141 0.30
170 14 0.03
172 1 0.00
177 307 0.66
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (176 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAAT
GTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTC
Found at i:2404840 original size:118 final size:118
Alignment explanation
Indices: 2404135--2404824 Score: 1036
Period size: 118 Copynumber: 5.9 Consensus size: 118
2404125 ATGGCACTAA
* *
2404135 GTGTGCTAATATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGGCACTTCGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
*
2404200 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCATTTC
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * * *
2404253 GTGTGCTAAAATGCTAAGAAATTCATACTGAGTGTATGCA-TTCCATATAAGGCAC--C-----C
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
* *
2404310 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCATTTC
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
2404363 GTGTGTTAGAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
* * *
2404428 TAAAATGTTAAGAAATTCATACTAAGTGTAAGAATTTCCATATAGGGCACATC
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
2404481 GTGTACTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTCGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
2404546 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
** * * *
2404599 ACGTGCTAAAATGTTAAGAAAATCATACTAAGTGTACGAATTTCCGTATAGGGCACTTCGCGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
* *
2404664 TAAAATGATAAGAAATTCATACTAAGTGTGTGAATTTCCGTATAGGGCACTTC
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * * * *
2404717 ATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGACAGTTTGTGTGG
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
*
2404782 TAAAATGTTAAGAAATTCATACTAATTGTATGAATTTCCGTAT
66 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
2404825 TGGGTACTAT
Statistics
Matches: 516, Mismatches: 48, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
110 87 0.17
111 13 0.03
113 1 0.00
115 1 0.00
117 14 0.03
118 400 0.78
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (118 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:2405307 original size:45 final size:46
Alignment explanation
Indices: 2405243--2405376 Score: 157
Period size: 45 Copynumber: 2.9 Consensus size: 46
2405233 TATAACAACG
* * *
2405243 TATAATATTATATAAAAGGCATGAAAGGATGCCATAAATGAAAT-A
1 TATAATAGTGTATTAAAGGCATGAAAGGATGCCATAAATGAAATGA
2405288 TATAATAGTGTATTAAAGGCATGAAAGGATGCCA-AAATGGAAATGA
1 TATAATAGTGTATTAAAGGCATGAAAGGATGCCATAAAT-GAAATGA
* * * * *
2405334 CATAATGGTGCATTATAA-GCATGAAGGGATGCTATAAATGAAA
1 TATAATAGTGTATTA-AAGGCATGAAAGGATGCCATAAATGAAA
2405377 ATAAAGAATA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
44 4 0.05
45 36 0.47
46 31 0.40
47 6 0.08
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.25
Consensus pattern (46 bp):
TATAATAGTGTATTAAAGGCATGAAAGGATGCCATAAATGAAATGA
Found at i:2405364 original size:46 final size:45
Alignment explanation
Indices: 2405257--2405376 Score: 154
Period size: 46 Copynumber: 2.6 Consensus size: 45
2405247 ATATTATATA
* *
2405257 AAAGGCATGAAAGGATGCCATAAATGAAATATATAATAGTGTATT
1 AAAGGCATGAAAGGATGCCATAAATGAAATACATAATAGTGCATT
*
2405302 AAAGGCATGAAAGGATGCCA-AAATGGAAATGACATAATGGTGCATT
1 AAAGGCATGAAAGGATGCCATAAAT-GAAAT-ACATAATAGTGCATT
* *
2405348 ATAA-GCATGAAGGGATGCTATAAATGAAA
1 A-AAGGCATGAAAGGATGCCATAAATGAAA
2405377 ATAAAGAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
44 4 0.06
45 25 0.38
46 31 0.47
47 6 0.09
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (45 bp):
AAAGGCATGAAAGGATGCCATAAATGAAATACATAATAGTGCATT
Found at i:2406746 original size:23 final size:23
Alignment explanation
Indices: 2406720--2406763 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2406710 ATCATTAAGA
2406720 ATCAATTTGATTATTATATACTT
1 ATCAATTTGATTATTATATACTT
2406743 ATCAATTTGATTATTATATAC
1 ATCAATTTGATTATTATATAC
2406764 ATTTGTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (23 bp):
ATCAATTTGATTATTATATACTT
Found at i:2422688 original size:24 final size:22
Alignment explanation
Indices: 2422653--2422713 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
2422643 AAATTAAAAC
*
2422653 ACTTAAATTCCTAATAAATAGTAA-
1 ACTTAAAATCCTAAT-AATA--AAT
2422677 ACTTAAAATCCTAATAATAAAT
1 ACTTAAAATCCTAATAATAAAT
*
2422699 AATTAAAATCCTAAT
1 ACTTAAAATCCTAAT
2422714 CGAAATTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 14 0.41
23 4 0.12
24 14 0.41
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
ACTTAAAATCCTAATAATAAAT
Found at i:2426853 original size:360 final size:365
Alignment explanation
Indices: 2426170--2426894 Score: 1381
Period size: 360 Copynumber: 2.0 Consensus size: 365
2426160 ATTGAACAAC
* *
2426170 TCCCCACTTAAGATGAGAAAGTATTATGAAAGAACCAACTCAACAACCTCAAAGAACAAGTGTAA
1 TCCCCACTTAAGATGAGAAAGTATTATGAAAGAACAAACACAACAACCTCAAAGAACAAGTGTAA
2426235 TTAAGAAGATCCACGAGATGAGAAAATGTTATTTAGATTATCATGTTGTATTTCTCCAAGAAATA
66 TTAAGAAGATCCACGAGATGAGAAAATGTTATTTAGATTATCATGTTGTATTTCTCCAAGAAATA
2426300 AGGATGACAATGGAGTGATGGAGGATGATCTAATCAACTTTCGTAATGTCATAAAAGTTATAACT
131 AGGATGACAATGGAGTGATGGAGGATGATCTAATCAACTTTCGTAATGTCATAAAAGTTATAACT
2426365 CCCAAAAGTGGATTAATGCCATGTAAGAAGAGTATAATTTCTACAGAAGATAATAAAATTTGAAA
196 CCCAAAAGTGGATTAATGCCATGTAAGAAGAGTATAATTTCTACAGAAGATAATAAAATTTGAAA
2426430 ACTTATCTCATCATCTAAGGCTAAAAAGTTGATTGGTTGCAAATGGAAATTTAAAACCAAGATGG
261 ACTTATCTCATCATCTAAGGCTAAAAAGTTGATTGGTTGCAAATGGAAATTTAAAACCAAGATGG
2426495 ATACAAATGGTGGCGTTGACATGTATAAGGCATGTCTTGT
326 ATACAAATGGTGGCGTTGACATGTATAAGGCATGTCTTGT
2426535 TCCCCACTTAAGATGAG-AAGTATTATGAAAG-ACAAACAACAACAACCTCAAAGAACAAGTGTA
1 TCCCCACTTAAGATGAGAAAGTATTATGAAAGAACAAAC-ACAACAACCTCAAAGAACAAGTGTA
2426598 ATTAAGAAGATCCACGAGATGAGAAAATGTTATTTAGATTATCATGTTGTATTTCTCCAAGAAAT
65 ATTAAGAAGATCCACGAGATGAGAAAATGTTATTTAGATTATCATGTTGTATTTCTCCAAGAAAT
2426663 AA-GATGACAATGGAGTGATGGAGGATGATCTAATCAACTTTCGT-ATGTCAT-AAAGTTATAAC
130 AAGGATGACAATGGAGTGATGGAGGATGATCTAATCAACTTTCGTAATGTCATAAAAGTTATAAC
2426725 TCCCAAAAGTGGATTAATG-CATGTAAGAAGAGTATAATTTCTACAGAAGATAATAAAATTTGAA
195 TCCCAAAAGTGGATTAATGCCATGTAAGAAGAGTATAATTTCTACAGAAGATAATAAAATTTGAA
2426789 AACTTATCTCATCATCTAAGGCTAAAAAGTTGATTGGTTGCAAATGGAAATTTAAAACCAAGATG
260 AACTTATCTCATCATCTAAGGCTAAAAAGTTGATTGGTTGCAAATGGAAATTTAAAACCAAGATG
2426854 GATACAAATGGTGGCGTTGACATGTATAAGGCATGTCTTGT
325 GATACAAATGGTGGCGTTGACATGTATAAGGCATGTCTTGT
2426895 ATCTTAAGTA
Statistics
Matches: 357, Mismatches: 2, Indels: 7
0.98 0.01 0.02
Matches are distributed among these distances:
360 151 0.42
361 30 0.08
362 7 0.02
363 47 0.13
364 105 0.29
365 17 0.05
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (365 bp):
TCCCCACTTAAGATGAGAAAGTATTATGAAAGAACAAACACAACAACCTCAAAGAACAAGTGTAA
TTAAGAAGATCCACGAGATGAGAAAATGTTATTTAGATTATCATGTTGTATTTCTCCAAGAAATA
AGGATGACAATGGAGTGATGGAGGATGATCTAATCAACTTTCGTAATGTCATAAAAGTTATAACT
CCCAAAAGTGGATTAATGCCATGTAAGAAGAGTATAATTTCTACAGAAGATAATAAAATTTGAAA
ACTTATCTCATCATCTAAGGCTAAAAAGTTGATTGGTTGCAAATGGAAATTTAAAACCAAGATGG
ATACAAATGGTGGCGTTGACATGTATAAGGCATGTCTTGT
Found at i:2428851 original size:24 final size:24
Alignment explanation
Indices: 2428819--2428867 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2428809 AATGTTCATC
2428819 CATATTTAATTTAATTTCTTTTCT
1 CATATTTAATTTAATTTCTTTTCT
2428843 CATATTTAATTTAATTTCTTTTCT
1 CATATTTAATTTAATTTCTTTTCT
2428867 C
1 C
2428868 TTTTGTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.61
Consensus pattern (24 bp):
CATATTTAATTTAATTTCTTTTCT
Found at i:2428954 original size:3 final size:3
Alignment explanation
Indices: 2428946--2429711 Score: 780
Period size: 3 Copynumber: 261.0 Consensus size: 3
2428936 TGAAAGTTAT
*
2428946 AGA AGA AGA AGA AGA AGAA AGA A-A AGA AGA AAA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
2428991 AGA AGA AGA AGG AGA AGA AGA AGA GGA GAGA AGG AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA
2429037 AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AG- AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * *
2429083 A-A GGG AGG AGA AG- AGG AGA AG- AGG AGA AGA AGGA GGA AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA
* * * *
2429126 AGG AGA AG- AGAA AGA AGA AGA AGA AGA AGG AGA AGG AGA AGG AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * * * * *
2429171 AGG AGA AGG AGA AGG AGA AGG AGG AGA AGG ACA AGG AGG AGA AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * * *
2429219 AGG AGA AGA AGG AGG AGA AGG AGG AGG AGA AGG AGG AG- AGA AGGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA
* * * * * *
2429264 GGA AGA AG- AGG AGA AGA AGG AGA AGA AG- AGG AGA AGG AGG AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
2429309 AGA AGG AGA AG- AGA AGA A-A AG- AGA AGA AG- AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
2429353 AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA AGA AGG AGA AGA AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
2429401 AGA AGA AGA GAGA AGA AGG AGA AG- AGAA AGA AG- AGA AGA AG- AGA
1 AGA AGA AGA -AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA
* *
2429445 AGA A-A GGA AGA AGA AGA AGA AGG AGA AGA AGGA AGA AGAA AGA A-A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AG-A AGA AGA
* *
2429490 GAGA AGA AGA AGA AGG A-A AGA AGA AGA AGA AGG AGA AGA AGA GAGA
1 -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA
*
2429536 AGA AGA AGG AGA AG- AGA AG- AGA AGA AGA AGA AG- AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2429581 AGA AGA AG- AGA AGA AGA AG- AGA AG- AGA AGA AGA AGA AG- AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2429625 AGA AGA A-A AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA
2429670 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2429712 GAGCTGACTA
Statistics
Matches: 649, Mismatches: 73, Indels: 82
0.81 0.09 0.10
Matches are distributed among these distances:
2 54 0.08
3 566 0.87
4 29 0.04
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2440696 original size:12 final size:12
Alignment explanation
Indices: 2440679--2440708 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2440669 CAAAATAAGA
2440679 CCCTAAGTAACT
1 CCCTAAGTAACT
2440691 CCCTAAGTAACT
1 CCCTAAGTAACT
2440703 CCCTAA
1 CCCTAA
2440709 ATAAGACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.37, G:0.07, T:0.23
Consensus pattern (12 bp):
CCCTAAGTAACT
Found at i:2442054 original size:69 final size:70
Alignment explanation
Indices: 2441918--2442147 Score: 268
Period size: 70 Copynumber: 3.3 Consensus size: 70
2441908 TTGGGCACAC
* * *
2441918 GCATCCGATGCACGTAAAAGTTTGGATTGCACCCAATGCTCAAGAGCCTACATGTCAACTAGGGA
1 GCATCCGATGCACGTAAAATTTTGGATTGCACCCAATACTCAAGAACCTACATGTCAACTAGGGA
2441983 CGTAA
66 CGTAA
*
2441988 GCATACGATGCACGTAAAATTTTGGATTGCA-CCAATACTCGAA-AACCTACATGTCAACTAGGG
1 GCATCCGATGCACGTAAAATTTTGGATTGCACCCAATACTC-AAGAACCTACATGTCAACTAGGG
2442051 ACGTAA
65 ACGTAA
** ** * * * *
2442057 GCATCCGATGCACGTAAAATTTTATATCACATCCAATACTTAAGAAACTACATGT-AGGCTAGGG
1 GCATCCGATGCACGTAAAATTTTGGATTGCACCCAATACTCAAGAACCTACATGTCA-ACTAGGG
*
2442121 ATGTAA
65 ACGTAA
* ** *
2442127 GCTTTTGATGCATGTAAAATT
1 GCATCCGATGCACGTAAAATT
2442148 CCAGTTCTTA
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
69 62 0.45
70 77 0.55
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (70 bp):
GCATCCGATGCACGTAAAATTTTGGATTGCACCCAATACTCAAGAACCTACATGTCAACTAGGGA
CGTAA
Found at i:2442137 original size:70 final size:69
Alignment explanation
Indices: 2441965--2442147 Score: 208
Period size: 69 Copynumber: 2.6 Consensus size: 69
2441955 GCTCAAGAGC
* **
2441965 CTACATGTCAACTAGGGACGTAAGCATACGATGCACGTAAAATTTTGGATTGCACCAATACTCGA
1 CTACATGTCAACTAGGGACGTAAGCATACGATGCACGTAAAATTTTAGATCACACCAATACTCGA
*
2442030 AAAC
66 AAAA
* * *
2442034 CTACATGTCAACTAGGGACGTAAGCATCCGATGCACGTAAAATTTTATATCACATCCAATACT-T
1 CTACATGTCAACTAGGGACGTAAGCATACGATGCACGTAAAATTTTAGATCACA-CCAATACTCG
2442098 AAGAAA
65 AA-AAA
* * * ** *
2442104 CTACATGT-AGGCTAGGGATGTAAGCTTTTGATGCATGTAAAATT
1 CTACATGTCA-ACTAGGGACGTAAGCATACGATGCACGTAAAATT
2442148 CCAGTTCTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
69 52 0.53
70 46 0.47
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (69 bp):
CTACATGTCAACTAGGGACGTAAGCATACGATGCACGTAAAATTTTAGATCACACCAATACTCGA
AAAA
Found at i:2461847 original size:19 final size:20
Alignment explanation
Indices: 2461823--2461868 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2461813 CAAAATGATC
*
2461823 CAATTTC-ACATTCAAACAT
1 CAATTTCAACACTCAAACAT
*
2461842 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCAAACAT
*
2461862 AAATTTC
1 CAATTTC
2461869 TAGCATAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATTTCAACACTCAAACAT
Found at i:2463096 original size:31 final size:30
Alignment explanation
Indices: 2463031--2463098 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
2463021 CAAAAGACAT
* *
2463031 AACTTTTAAAAATTACACTTTTGGTCTCTG
1 AACTTTTAAAAATTACACTTTTAGTCTCTA
* *
2463061 AACTTTTGGAAAATTACCCTTTTAGTC-CTTA
1 AACTTTT-AAAAATTACACTTTTAGTCTC-TA
2463092 AACTTTT
1 AACTTTT
2463099 CCAATTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (30 bp):
AACTTTTAAAAATTACACTTTTAGTCTCTA
Found at i:2463711 original size:26 final size:27
Alignment explanation
Indices: 2463682--2463742 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
2463672 ATTTTGATTG
2463682 AATGTTGTAGC-AAGGTTAAAATAATA
1 AATGTTGTAGCAAAGGTTAAAATAATA
2463708 AATGTTGTAGCAAAGGTTAAAATAATA
1 AATGTTGTAGCAAAGGTTAAAATAATA
2463735 AATGTTGT
1 AATGTTGT
2463743 GGCGAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.33
Consensus pattern (27 bp):
AATGTTGTAGCAAAGGTTAAAATAATA
Found at i:2465355 original size:6 final size:6
Alignment explanation
Indices: 2465344--2465410 Score: 57
Period size: 6 Copynumber: 10.8 Consensus size: 6
2465334 ATTTTTGTCA
* *
2465344 ATTTTT ATTTTT ATTTTT A-TTTT -TCTTT ATTTATT ATTTATT ATTATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT-TT ATTT-TT ATTTTT
*
2465392 ATTGTT ATTATTTT ATTTT
1 ATTTTT A-T-TTTT ATTTT
2465411 AGGTACCCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
5 7 0.14
6 26 0.51
7 14 0.27
8 4 0.08
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:2468634 original size:20 final size:20
Alignment explanation
Indices: 2468595--2468634 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2468585 TTCAGTGCTA
2468595 AAATTTAATTACTAAATGTTG
1 AAATTTAATTA-TAAATGTTG
2468616 AAATTTAATT-TAGAATGTT
1 AAATTTAATTATA-AATGTT
2468635 TATTTAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 6 0.33
21 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (20 bp):
AAATTTAATTATAAATGTTG
Found at i:2470561 original size:20 final size:20
Alignment explanation
Indices: 2470516--2470565 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2470506 TGATAAGCAA
2470516 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
*
2470537 TATCGATACTGATGTGGAG-G
1 TATCGATACTGAT-TGAAGAG
2470557 TATCGATAC
1 TATCGATAC
2470566 CAAGAGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:2471043 original size:2 final size:2
Alignment explanation
Indices: 2471036--2471088 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
2471026 CATTGTTATG
2471036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2471078 AT -T AT AT AT AT
1 AT AT AT AT AT AT
2471089 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2471093 original size:2 final size:2
Alignment explanation
Indices: 2471088--2471137 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2471078 ATTATATATA
2471088 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2471130 TG TG TG TG
1 TG TG TG TG
2471138 AAATATTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2471609 original size:23 final size:23
Alignment explanation
Indices: 2471579--2471656 Score: 111
Period size: 23 Copynumber: 3.3 Consensus size: 23
2471569 AGTCGAGGGT
2471579 TCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* *
2471602 TCTATGTGGTCCTTTGGCACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* *
2471625 TTTATGTGGTACTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
2471648 TTCTATGTG
1 -TCTATGTG
2471657 CACTTCGGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 40 0.85
24 7 0.15
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:2471661 original size:23 final size:24
Alignment explanation
Indices: 2471578--2471672 Score: 94
Period size: 23 Copynumber: 4.1 Consensus size: 24
2471568 GAGTCGAGGG
2471578 TTCTATGTGGTC-CTTCGGGACAAA
1 TTCTATGTGG-CACTTCGGGACAAA
* *
2471602 -TCTATGTGGTC-CTTTGGCACAAA
1 TTCTATGTGG-CACTTCGGGACAAA
*
2471625 TT-TATGTGGTACTTCGGGACAAA
1 TTCTATGTGGCACTTCGGGACAAA
2471648 TTCTATGT-GCACTTCGGTG-CAAA
1 TTCTATGTGGCACTTCGG-GACAAA
2471671 TT
1 TT
2471673 ATTTGAGCAG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
23 54 0.89
24 7 0.11
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (24 bp):
TTCTATGTGGCACTTCGGGACAAA
Found at i:2476480 original size:20 final size:20
Alignment explanation
Indices: 2476434--2476490 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2476424 CGATACTGAA
*
2476434 GTAG-GTATCGGTACCATAG
1 GTAGAGTATCGGTACTATAG
*
2476453 G-AGAAGTATCGGTACTATGG
1 GTAG-AGTATCGGTACTATAG
* *
2476473 GTAGAGTACCGATACTAT
1 GTAGAGTATCGGTACTAT
2476491 TTGGTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 26 0.84
21 2 0.06
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (20 bp):
GTAGAGTATCGGTACTATAG
Found at i:2476840 original size:2 final size:2
Alignment explanation
Indices: 2476833--2476874 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2476823 TTGTTATGAA
2476833 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2476875 AAATATTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2477331 original size:23 final size:23
Alignment explanation
Indices: 2477267--2477389 Score: 106
Period size: 23 Copynumber: 5.3 Consensus size: 23
2477257 AGTCGAGGGT
* *
2477267 TCTATTTGGTCCTTCGAGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* *
2477290 TCTATATAGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* *
2477313 TCTATGTGGTCCTTTGGGACATA
1 TCTATGTGGTCCTTCGGGACAAA
* * * *
2477336 TTTATGTAGTCCTTTGGGATAAA
1 TCTATGTGGTCCTTCGGGACAAA
* *
2477359 TTATATGTGGTACTTCGGTG-CAAA
1 -TCTATGTGGTCCTTCGG-GACAAA
2477383 T-TATGTG
1 TCTATGTG
2477390 AGCAGTGGTG
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
22 6 0.07
23 59 0.72
24 16 0.20
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.38
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:2477346 original size:46 final size:47
Alignment explanation
Indices: 2477266--2477375 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 47
2477256 GAGTCGAGGG
*
2477266 TTCTATTTGGTCCTTCGAGACAAATCTATATAGTCCTTCGGGACAAA
1 TTCTATGTGGTCCTTCGAGACAAATCTATATAGTCCTTCGGGACAAA
* * * * * * *
2477313 -TCTATGTGGTCCTTTGGGACATATTTATGTAGTCCTTTGGGATAAA
1 TTCTATGTGGTCCTTCGAGACAAATCTATATAGTCCTTCGGGACAAA
* *
2477359 TTATATGTGGTACTTCG
1 TTCTATGTGGTCCTTCG
2477376 GTGCAAATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
46 38 0.75
47 13 0.25
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (47 bp):
TTCTATGTGGTCCTTCGAGACAAATCTATATAGTCCTTCGGGACAAA
Found at i:2477870 original size:18 final size:18
Alignment explanation
Indices: 2477847--2477881 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2477837 GATTGTTGGT
2477847 ATGTACTAAAATATGTAC
1 ATGTACTAAAATATGTAC
*
2477865 ATGTACTAAAATGTGTA
1 ATGTACTAAAATATGTA
2477882 AGTCATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (18 bp):
ATGTACTAAAATATGTAC
Found at i:2482910 original size:29 final size:31
Alignment explanation
Indices: 2482877--2482939 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
2482867 CAAATTTTGG
*
2482877 TTAGTGACCAAAATATAAGC-TT-TAAAAGT
1 TTAGTGACCAAAATATAAACTTTGTAAAAGT
* * *
2482906 TTAGTGGCTAAAGTATAAACTTTGTAAAAGT
1 TTAGTGACCAAAATATAAACTTTGTAAAAGT
2482937 TTA
1 TTA
2482940 AGGACTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 2 0.07
31 10 0.36
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (31 bp):
TTAGTGACCAAAATATAAACTTTGTAAAAGT
Found at i:2485962 original size:13 final size:13
Alignment explanation
Indices: 2485944--2485968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2485934 TCTTGATTTA
2485944 AATGTTAATCTTG
1 AATGTTAATCTTG
2485957 AATGTTAATCTT
1 AATGTTAATCTT
2485969 TCAAAAAATT
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:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (13 bp):
AATGTTAATCTTG
Found at i:2490846 original size:29 final size:30
Alignment explanation
Indices: 2490782--2490852 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
2490772 TAAGACGACC
2490782 CTTGGGTAGGCTCTGCGGCCCTGAGATTTT
1 CTTGGGTAGGCTCTGCGGCCCTGAGATTTT
*
2490812 CTTGGGTAGGC-CGTG-GTCCC-GAGAATTTT
1 CTTGGGTAGGCTC-TGCGGCCCTGAG-ATTTT
2490841 CTTGGGTAGGCT
1 CTTGGGTAGGCT
2490853 TACAGGCCCC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 3 0.08
29 21 0.57
30 13 0.35
ACGTcount: A:0.11, C:0.21, G:0.35, T:0.32
Consensus pattern (30 bp):
CTTGGGTAGGCTCTGCGGCCCTGAGATTTT
Found at i:2491681 original size:13 final size:14
Alignment explanation
Indices: 2491658--2491693 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
2491648 CTTTTTAATG
2491658 ATATATATTAAATT
1 ATATATATTAAATT
2491672 ATATAT-TTAAATT
1 ATATATATTAAATT
2491685 ATAT-TATTA
1 ATATATATTA
2491694 TTCTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 14 0.67
14 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATATTAAATT
Found at i:2495506 original size:21 final size:21
Alignment explanation
Indices: 2495480--2495519 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2495470 GGTCATTGAT
*
2495480 ATAATTTACCTTTTATTTTAA
1 ATAATTTACCTTTAATTTTAA
2495501 ATAATTTACCTTTAATTTT
1 ATAATTTACCTTTAATTTT
2495520 TCAACTAATT
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:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAATTTACCTTTAATTTTAA
Found at i:2496580 original size:233 final size:231
Alignment explanation
Indices: 2496121--2496585 Score: 627
Period size: 233 Copynumber: 2.0 Consensus size: 231
2496111 TGTATATTAA
** * *
2496121 TTAAAATATTTTAATACTTTTATATGTGTAAATTGTATATAAAAATATCATATTAATAAATAAAA
1 TTAAAATATTTTAATACTTTTATACATGTAAATTATATATAAAAATATCATACTAATAAATAAAA
* *
2496186 TTTTATAAATCCTTAAAATTCAGCTTTTTCACGTAAAAATTCAAAGAAACAAAATGCATAGTTTT
66 TTTTATAAATCCTTAAAATTCAGCTTGTTCACATAAAAATTCAAAGAAACAAAATGCATAGTTTT
* *
2496251 TTATTTGTTCATTATTTCACACATGTAACATATAATCTTAAAATTATATCAATTTAATTTTATAA
131 TTATTTGTTCATTATTTCACACATGTAACATATAACCATAAAATTATATCAATTTAATTTTATAA
* * *
2496316 TAAATTCATATACTATAAAAATTTAATCAATAAATT
196 AAAAATCATATAATATAAAAATTTAATCAATAAATT
* * * *
2496352 TTAAAATATTTTAATAC-TTTATCCATGTAAATTATATATCAGAATGTCATACTAATAAAATAAA
1 TTAAAATATTTTAATACTTTTATACATGTAAATTATATATAAAAATATCATACTAAT-AAATAAA
* **
2496416 A-TTTATAAATCCTTAAAATTCATC-TGTTCACATAAAAATTCAAA-ATAGA-AAAATTTATAGT
65 ATTTTATAAATCCTTAAAATTCAGCTTGTTCACATAAAAATTCAAAGA-A-ACAAAATGCATAGT
2496477 CTATTTTATTTGTT-ATTATTTCACACAACATGTAACATATAACCATAAAATTATATCAATTTAA
128 -T-TTTTATTTGTTCATTATTT--CAC-ACATGTAACATATAACCATAAAATTATATCAATTTAA
* * *
2496541 TTTTATAAAAAAATCTTATAATATACAAATTTTATCAATAAATT
188 TTTTATAAAAAAATCATATAATATAAAAATTTAATCAATAAATT
2496585 T
1 T
2496586 AAATTTATAT
Statistics
Matches: 205, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
228 1 0.00
229 29 0.14
230 62 0.30
231 36 0.18
232 3 0.01
233 74 0.36
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (231 bp):
TTAAAATATTTTAATACTTTTATACATGTAAATTATATATAAAAATATCATACTAATAAATAAAA
TTTTATAAATCCTTAAAATTCAGCTTGTTCACATAAAAATTCAAAGAAACAAAATGCATAGTTTT
TTATTTGTTCATTATTTCACACATGTAACATATAACCATAAAATTATATCAATTTAATTTTATAA
AAAAATCATATAATATAAAAATTTAATCAATAAATT
Found at i:2496626 original size:2 final size:2
Alignment explanation
Indices: 2496621--2496652 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2496611 AGGCATATTA
2496621 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
2496653 GTTTGCGCGT
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):
AT
Found at i:2498462 original size:2 final size:2
Alignment explanation
Indices: 2498455--2498511 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2498445 ATATTTGGAT
2498455 TA TA TA 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
2498497 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2498512 TAATTAAAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2499335 original size:27 final size:27
Alignment explanation
Indices: 2499305--2499418 Score: 79
Period size: 27 Copynumber: 4.1 Consensus size: 27
2499295 TTGCTCGGAG
2499305 TTATTTTATTTTTTATATATTTTTATT
1 TTATTTTATTTTTTATATATTTTTATT
* * * *
2499332 TTATTTTATTATATATATATATATATAT
1 TTATTTTATTTTTTATATATTTTTAT-T
* *
2499360 ATATTTT-TTATTATTATAATAATTATTATT
1 TTATTTTATT-TT-TTAT-AT-ATTTTTATT
* * *
2499390 ATTATTATATTTATTAT-TTTTTTTATT
1 -TTATTTTATTTTTTATATATTTTTATT
2499417 TT
1 TT
2499419 TTGTATGCCC
Statistics
Matches: 65, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
26 2 0.03
27 31 0.48
28 9 0.14
29 3 0.05
30 7 0.11
31 11 0.17
32 2 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
TTATTTTATTTTTTATATATTTTTATT
Found at i:2499365 original size:33 final size:30
Alignment explanation
Indices: 2499318--2499406 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 30
2499308 TTTTATTTTT
*
2499318 TATATATTTTTATTTTATTTTATTATATATATA
1 TATATA-TATTATTTTATTTTATTATA-ATA-A
2499351 TATATATATATATTTT-TTATTATTATAATAA
1 TATATATAT-TATTTTATT-TTATTATAATAA
2499382 T-TAT-TATTATTATTATATTTATTAT
1 TATATATATTATT-TTAT-TTTATTAT
2499407 TTTTTTTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
28 4 0.08
29 5 0.10
30 11 0.22
31 3 0.06
32 7 0.14
33 20 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TATATATATTATTTTATTTTATTATAATAA
Found at i:2499376 original size:6 final size:6
Alignment explanation
Indices: 2499305--2499407 Score: 60
Period size: 6 Copynumber: 17.3 Consensus size: 6
2499295 TTGCTCGGAG
*
2499305 TTATT- TTATT- TT-TTA TATATTT TTATT- TTATT- TTATTA TATATATA
1 TTATTA TTATTA TTATTA T-TATTA TTATTA TTATTA TTATTA T-TAT-TA
* *
2499351 TATATATA TATATT- TT-TTA TTATTA TAATAA TTATTA TTATTA TTA-TA
1 T-TAT-TA T-TATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
2499399 TTTATTA TT
1 -TTATTA TT
2499408 TTTTTTATTT
Statistics
Matches: 83, Mismatches: 5, Indels: 19
0.78 0.05 0.18
Matches are distributed among these distances:
4 4 0.05
5 23 0.28
6 32 0.39
7 9 0.11
8 15 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATTA
Found at i:2499414 original size:12 final size:12
Alignment explanation
Indices: 2499305--2499420 Score: 53
Period size: 12 Copynumber: 9.6 Consensus size: 12
2499295 TTGCTCGGAG
*
2499305 TTATTTTATTTT
1 TTATTTTATTTA
*
2499317 TTA-TATATTT-
1 TTATTTTATTTA
2499327 TTATTTTATTTTA
1 TTATTTTA-TTTA
* *
2499340 TTATATATATATA
1 TTAT-TTTATTTA
* *
2499353 TATATATATATTTT
1 T-TAT-TTTATTTA
*
2499367 TTATTATTA-TAA
1 TTATT-TTATTTA
*
2499379 TAATTATTA-TTA
1 TTATT-TTATTTA
*
2499391 TTATTATATTTA
1 TTATTTTATTTA
*
2499403 TTATTTTTTTTA
1 TTATTTTATTTA
2499415 TT-TTTT
1 TTATTTT
2499421 GTATGCCCTA
Statistics
Matches: 82, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
10 3 0.04
11 15 0.18
12 37 0.45
13 13 0.16
14 14 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTTTATTTA
Found at i:2503209 original size:24 final size:23
Alignment explanation
Indices: 2503178--2503227 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
2503168 AAAAAGGAAA
2503178 AAAGAGAAAA-AATAAAGAAAAAGC
1 AAAGAGAAAATAA-AAAGAAAAA-C
*
2503202 AAAGAGAAAATAAAAAGAGAAAC
1 AAAGAGAAAATAAAAAGAAAAAC
2503225 AAA
1 AAA
2503228 AACAAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 18 0.75
25 2 0.08
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (23 bp):
AAAGAGAAAATAAAAAGAAAAAC
Found at i:2503218 original size:13 final size:12
Alignment explanation
Indices: 2503175--2503229 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 12
2503165 AACAAAAAGG
2503175 AAAAAAGAGAAA
1 AAAAAAGAGAAA
2503187 AAATAAAGA-AAA
1 AAA-AAAGAGAAA
**
2503199 AGCAAAGAGAAA
1 AAAAAAGAGAAA
2503211 ATAAAAAGAGAAA
1 A-AAAAAGAGAAA
2503224 CAAAAA
1 -AAAAA
2503230 CAAAGGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 5 0.14
12 11 0.31
13 18 0.51
14 1 0.03
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:2504356 original size:32 final size:32
Alignment explanation
Indices: 2504306--2504393 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 32
2504296 GGAATATTGG
** * * *
2504306 GGGCATCTTTAAATATTCAACATTAAATGTTA
1 GGGCATCTTTGGAGATTCAACATCAAATATTA
* * * *
2504338 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATATTA
*
2504370 GGGCATCTTTGGATATTCAACATC
1 GGGCATCTTTGGAGATTCAACATC
2504394 CTAATACGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATATTA
Found at i:2505476 original size:36 final size:36
Alignment explanation
Indices: 2505421--2505638 Score: 256
Period size: 36 Copynumber: 6.2 Consensus size: 36
2505411 AATTTACTCA
2505421 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
2505458 AAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * *
2505494 AAACAAA-----AC-CT-TCGA-ATATGTTTTACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-G-TTTCCCTTG
* * *
2505523 AAACCAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
2505559 AAACAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
2505596 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
2505632 AAACAAA
1 AAACAAA
2505639 ATCTTTGAAT
Statistics
Matches: 152, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
28 2 0.01
29 10 0.07
30 8 0.05
31 1 0.01
34 1 0.01
35 6 0.04
36 81 0.53
37 43 0.28
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:2505651 original size:138 final size:139
Alignment explanation
Indices: 2505421--2505776 Score: 529
Period size: 138 Copynumber: 2.6 Consensus size: 139
2505411 AATTTACTCA
*
2505421 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAAAGT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
* *
2505486 TTCCCTTGAAACAAAACCTTCGAATATGTTTTACATT-AAACCAATTTTGTCTCCCTTGAGACAG
66 TTCCCTTGAAACAAAACCTTCGAATATGTTTT-CATTGAAACAAATTTCGTCTCCCTTGAGACAG
2505550 -TTTCTCTT-G
130 TTTTCT-TTCG
*
2505559 AAACAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
* * *
2505624 TTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGT
66 TTCCCTTGAAACAAAACCTTCGAATATGTTTTCATTGAAACAAATTTCGTCTCCCTTGAGACAGT
2505689 TTTCTTTCG
131 TTTCTTTCG
* * * * * * *
2505698 GAACTAAGTTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2505763 TTTCTCTTGAAACA
65 TTTCCCTTGAAACA
2505777 CAAAAAAAAC
Statistics
Matches: 198, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
137 3 0.02
138 120 0.61
139 42 0.21
140 33 0.17
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (139 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
TTCCCTTGAAACAAAACCTTCGAATATGTTTTCATTGAAACAAATTTCGTCTCCCTTGAGACAGT
TTTCTTTCG
Found at i:2505735 original size:103 final size:102
Alignment explanation
Indices: 2505550--2505747 Score: 283
Period size: 103 Copynumber: 1.9 Consensus size: 102
2505540 CTTGAGACAG
* *
2505550 TTTCTCTTGAAACAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
*
2505615 TGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
66 TAAGACAGTTTCCCTTGAAACAAAAT-TTTGAATATGT
* * * *
2505653 TTTC-CTTGAAACAAA-TTTCGTCTCCCTTGAGACAGTTTTCTTTCGGAACTAAGTTTTGTCTCT
1 TTTCTCTTGAAACAAATTTTCGTCTCCCTTGAGACAGTTTCCCTT-GAAAC-AAATTTTGTCTCT
*
2505716 CTTAAGACAGTTTCTCTTGAAACAAAATTTTG
64 CTTAAGACAGTTTCCCTTGAAACAAAATTTTG
2505748 CCTCCCTTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
101 24 0.28
102 19 0.22
103 42 0.49
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
TAAGACAGTTTCCCTTGAAACAAAATTTTGAATATGT
Found at i:2505747 original size:37 final size:37
Alignment explanation
Indices: 2505653--2505776 Score: 137
Period size: 37 Copynumber: 3.4 Consensus size: 37
2505643 TTGAATATGT
*
2505653 TTTC-CTTGAAAC-AAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
* * * * *
2505688 TTT-TCTTTCGGAACTAAGTTTTGTCTCTCTTAAGACAG
1 TTTCTC-TT-GAAACAAAATTTTGTCTCCCTTGAGACAG
* *
2505726 TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAT
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
2505763 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
2505777 CAAAAAAAAC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
35 4 0.06
36 2 0.03
37 40 0.56
38 24 0.33
39 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:2506240 original size:18 final size:18
Alignment explanation
Indices: 2506214--2506249 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2506204 CCCGGAGTTA
* *
2506214 TTTTGTTTTTTTATATAT
1 TTTTATTTTATTATATAT
2506232 TTTTATTTTATTATATAT
1 TTTTATTTTATTATATAT
2506250 ATATACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTATTTTATTATATAT
Found at i:2506282 original size:18 final size:18
Alignment explanation
Indices: 2506227--2506286 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 18
2506217 TGTTTTTTTA
2506227 TATATTT-TTATT-TTAT
1 TATATTTATTATTATTAT
* *
2506243 TATATATA-TA-TA-CAT
1 TATATTTATTATTATTAT
2506258 ATATATTTATTATTATTAT
1 -TATATTTATTATTATTAT
2506277 TATATTTATT
1 TATATTTATT
2506287 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 3 0.09
16 15 0.44
17 2 0.06
18 12 0.35
19 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATTTATTATTATTAT
Found at i:2508906 original size:16 final size:17
Alignment explanation
Indices: 2508878--2508909 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2508868 AAAAAATACT
2508878 AAGGATGTGTTTGGTTC
1 AAGGATGTGTTTGGTTC
2508895 AAGGAT-TGTTTGGTT
1 AAGGATGTGTTTGGTT
2508910 GGTCCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (17 bp):
AAGGATGTGTTTGGTTC
Found at i:2509298 original size:37 final size:37
Alignment explanation
Indices: 2509222--2509298 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
2509212 TTTTTATATT
*
2509222 TTTAATTTTGTAAAACAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAACAAATTATATAAATATTATCAA
* *
2509259 TTTAATTTTTTAAAGA-AAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-ACAAATTATATAAATATTAT-CAA
2509296 TTT
1 TTT
2509299 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 21 0.60
38 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAACAAATTATATAAATATTATCAA
Found at i:2509799 original size:21 final size:21
Alignment explanation
Indices: 2509759--2509800 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2509749 TAAAGTACTT
*
2509759 AATAATAACATTTTCGATAAA
1 AATAATAACATTTTCAATAAA
* *
2509780 AATAATAATATTTTTAATAAA
1 AATAATAACATTTTCAATAAA
2509801 TTTTTATCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTCAATAAA
Found at i:2510719 original size:3 final size:3
Alignment explanation
Indices: 2510711--2510742 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2510701 TGGGAGAACC
2510711 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2510743 TTGAAAATCA
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:2516661 original size:13 final size:13
Alignment explanation
Indices: 2516625--2516660 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2516615 TATATTGATT
*
2516625 TTTTCAAAAATTG
1 TTTTCAAAAATAG
2516638 TTTTCAAAAATAG
1 TTTTCAAAAATAG
2516651 TCTTTCAAAA
1 T-TTTCAAAA
2516661 TTGCCCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:2519662 original size:55 final size:55
Alignment explanation
Indices: 2519573--2519882 Score: 278
Period size: 55 Copynumber: 5.7 Consensus size: 55
2519563 TTAACTCAAC
* * *
2519573 ATACTCCTTGAAAGAAGAGGGAGCA-GACCCATTTTTAAAAGATTGTTCGAGTCCT
1 ATACTCCCTGAAAGAAGAGGGAGCATGACCCATTTTT-GAAGATTGTTTGAGTCCT
** * * *
2519628 ATACTCCCTGAAAGAAGA-GGAAAATGACCTATTTTCTGAAGATTGTTCGAGTCTT
1 ATACTCCCTGAAAGAAGAGGGAGCATGACCCATTTT-TGAAGATTGTTTGAGTCCT
* * * *
2519683 ATACTTCCTGAAAGAAGAGGGATCA-GA--CATGTTTGCTAAACATTGTTTGAGTCCT
1 ATACTCCCTGAAAGAAGAGGGAGCATGACCCAT-TTT--TGAAGATTGTTTGAGTCCT
* * * * **
2519738 GTACTCCCTGAAAGAAAACGGAG--TGAACACGATTACTGAAGATTGTTTGAGTCCT
1 ATACTCCCTGAAAGAAGAGGGAGCATG-AC-CCATTTTTGAAGATTGTTTGAGTCCT
** *
2519793 ATACTCTTTGAAAGAAGAAGGAGCAT-ACCCATTTTTGAAGATTGTTTGAGTCCT
1 ATACTCCCTGAAAGAAGAGGGAGCATGACCCATTTTTGAAGATTGTTTGAGTCCT
* * *
2519847 ATACTCCCTAAAAGAAAAGGGAGCA-GACCCGTTTTT
1 ATACTCCCTGAAAGAAGAGGGAGCATGACCCATTTTT
2519883 CTTAAGATTT
Statistics
Matches: 204, Mismatches: 38, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
53 2 0.01
54 60 0.29
55 133 0.65
56 5 0.02
57 2 0.01
58 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (55 bp):
ATACTCCCTGAAAGAAGAGGGAGCATGACCCATTTTTGAAGATTGTTTGAGTCCT
Found at i:2519890 original size:110 final size:108
Alignment explanation
Indices: 2519573--2519900 Score: 317
Period size: 110 Copynumber: 3.0 Consensus size: 108
2519563 TTAACTCAAC
* *
2519573 ATACTCCTTGAAAGAAGAGGGAGCAGACCCATTTTTAAAAGATTGTTCGAGTCCTATACTCCCTG
1 ATACTCTTTGAAAGAAGAGGGAGCAGACCCATTTTT-AAAGATTGTTTGAGTCCTATACTCCCTG
* * *
2519638 AAAGAAGAGGAAAATGA-CC-TATTTTCTGAAGATTGTTCGAGTCTT
65 AAAGAAAAGG-AGA-GACCCGT-TTTTCTGAAGATTGTTCGAGTCCT
* * * *
2519683 ATACT-TCCTGAAAGAAGAGGGATCAGA--CATGTTTGCTAAACATTGTTTGAGTCCTGTACTCC
1 ATACTCT-TTGAAAGAAGAGGGAGCAGACCCAT-TTT--TAAAGATTGTTTGAGTCCTATACTCC
* * * * *
2519745 CTGAAAGAAAACGGAGTGAACACG-ATTACTGAAGATTGTTTGAGTCCT
62 CTGAAAGAAAA-GGAGAG-ACCCGTTTTTCTGAAGATTGTTCGAGTCCT
* * * *
2519793 ATACTCTTTGAAAGAAGAAGGAGCATACCCATTTTTGAAGATTGTTTGAGTCCTATACTCCCTAA
1 ATACTCTTTGAAAGAAGAGGGAGCAGACCCATTTTTAAAGATTGTTTGAGTCCTATACTCCCTGA
* * *
2519858 AAGAAAAGGGAGCAGACCCGTTTTTCTTAAGATTTTTCAAGTC
66 AAGAAAA-GGAG-AGACCCGTTTTTCTGAAGATTGTTCGAGTC
2519901 TCACTTATTC
Statistics
Matches: 174, Mismatches: 31, Indels: 26
0.75 0.13 0.11
Matches are distributed among these distances:
108 3 0.02
109 45 0.26
110 115 0.66
111 8 0.05
112 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (108 bp):
ATACTCTTTGAAAGAAGAGGGAGCAGACCCATTTTTAAAGATTGTTTGAGTCCTATACTCCCTGA
AAGAAAAGGAGAGACCCGTTTTTCTGAAGATTGTTCGAGTCCT
Found at i:2527616 original size:2 final size:2
Alignment explanation
Indices: 2527609--2527657 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2527599 TTATTTTCAG
2527609 TA TA TA 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
2527651 TA TA TA T
1 TA TA TA T
2527658 TTGTTTAACG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2541501 original size:45 final size:48
Alignment explanation
Indices: 2541451--2541540 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
2541441 AACTGTCTCT
*
2541451 TATTA-TTAGAAATTA-AA-AATTAAAAATATAT-TTAATTTATAATCC
1 TATTATTTA-AAATTATAATAATGAAAAATATATATTAATTTATAATCC
*
2541496 TATTATTTTAAAATTATAATTATGAAAAATATATATTAATTTATA
1 TATTA-TTTAAAATTATAATAATGAAAAATATATATTAATTTATA
2541541 TATTTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 5 0.13
46 6 0.16
47 5 0.13
48 12 0.32
49 10 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (48 bp):
TATTATTTAAAATTATAATAATGAAAAATATATATTAATTTATAATCC
Found at i:2543285 original size:3 final size:3
Alignment explanation
Indices: 2543277--2543347 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
2543267 GGCCTGTTTG
* * *
2543277 TAA TAA TAA TAA TTA T-T TAT TTAA TAA TAA TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* *
2543320 TAA TAT TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2543348 ATAAAACAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 9 0.16
3 46 0.81
4 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2543321 original size:13 final size:14
Alignment explanation
Indices: 2543298--2543351 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
2543288 ATTATTTATT
2543298 TAATAATAATAATA
1 TAATAATAATAATA
2543312 TAAT-ATAATAATA
1 TAATAATAATAATA
* *
2543325 T--TAA-AACAAAA
1 TAATAATAATAATA
2543336 TAATAATAATAA-A
1 TAATAATAATAATA
2543349 TAA
1 TAA
2543352 AACAAATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.21
12 1 0.03
13 17 0.52
14 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:2543321 original size:16 final size:16
Alignment explanation
Indices: 2543300--2543344 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2543290 TATTTATTTA
* *
2543300 ATAATAATAATATAAT
1 ATAATAATAATAAAAC
*
2543316 ATAATAATATTAAAAC
1 ATAATAATAATAAAAC
*
2543332 AAAATAATAATAA
1 ATAATAATAATAA
2543345 TAAATAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATAATAATAAAAC
Done.