Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 123 of 332
Found at i:39995295 original size:50 final size:51
Alignment explanation
Indices: 39995153--39995295 Score: 236
Period size: 50 Copynumber: 2.8 Consensus size: 51
39995143 AGTTTCAATA
* *
39995153 TGAATCCCATGTAAAACCATGTCTGGGACATGGCATTGGCATAGATATGTG
1 TGAATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
39995204 TG-ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
1 TGAATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
* *
39995254 TGAAT-CCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 TGAATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
39995296 TCACTATGTG
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
50 83 0.95
51 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (51 bp):
TGAATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
Found at i:39995922 original size:20 final size:21
Alignment explanation
Indices: 39995887--39995925 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39995877 CTGATTTGAT
*
39995887 AAAATCATTATAAGTTATACA
1 AAAATAATTATAAGTTATACA
39995908 AAAATAATTAT-AGTTATA
1 AAAATAATTATAAGTTATA
39995926 ATTTATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATAATTATAAGTTATACA
Found at i:40005625 original size:24 final size:24
Alignment explanation
Indices: 40005592--40005690 Score: 144
Period size: 24 Copynumber: 4.1 Consensus size: 24
40005582 AGGCATCCTC
40005592 GAATACGCCACAAAGGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* *
40005616 GAATATGCCACAAAGGCACATACA
1 GAATACGCCACAAAGGCACTTACA
40005640 GAATACGCCACAAAGGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* * * *
40005664 GAAGACACCATAAAGGCACTTATA
1 GAATACGCCACAAAGGCACTTACA
40005688 GAA
1 GAA
40005691 CATGTGTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.13
Consensus pattern (24 bp):
GAATACGCCACAAAGGCACTTACA
Found at i:40008267 original size:20 final size:20
Alignment explanation
Indices: 40008244--40008341 Score: 67
Period size: 20 Copynumber: 4.9 Consensus size: 20
40008234 GTGCCCTTAT
40008244 TTGTACTTCGGTACCCTTGA
1 TTGTACTTCGGTACCCTTGA
* * *
40008264 TTGTACATAC-GT-GCCTCTGT
1 TTGTAC-TTCGGTACCCT-TGA
*
40008284 TTGTACTTCGGTACCCCTGA
1 TTGTACTTCGGTACCCTTGA
* * * * *
40008304 TTGCACATAC-GTGCCCCTGT
1 TTGTAC-TTCGGTACCCTTGA
40008324 TTGTACTTCGGTACCCTT
1 TTGTACTTCGGTACCCTT
40008342 AAATGCATTT
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
19 7 0.12
20 44 0.77
21 6 0.11
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGTACTTCGGTACCCTTGA
Found at i:40008356 original size:40 final size:40
Alignment explanation
Indices: 40008221--40008341 Score: 197
Period size: 40 Copynumber: 3.0 Consensus size: 40
40008211 AATAATTGAA
* *
40008221 TGATTGCACATACGTGCCCTTATTTGTACTTCGGTACCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
* * *
40008261 TGATTGTACATACGTGCCTCTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
40008301 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
40008341 T
1 T
40008342 AAATGCATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
Found at i:40010286 original size:26 final size:26
Alignment explanation
Indices: 40010256--40010307 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40010246 CACCACTGAA
*
40010256 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40010282 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40010308 CTTTTATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:40010490 original size:26 final size:26
Alignment explanation
Indices: 40010460--40010511 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40010450 CACCAATGAA
*
40010460 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40010486 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40010512 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:40010498 original size:102 final size:102
Alignment explanation
Indices: 40010225--40010589 Score: 610
Period size: 103 Copynumber: 3.6 Consensus size: 102
40010215 TTACCGTTAT
* *
40010225 TGGTGGAT-CCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
40010289 ATCAGCACATAGCAACCCCCTTTT-ATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
40010325 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
40010390 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
40010428 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
*
40010493 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
40010531 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
40010590 TTTATATACA
Statistics
Matches: 252, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
100 8 0.03
101 49 0.19
102 57 0.23
103 137 0.54
104 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:40017397 original size:26 final size:26
Alignment explanation
Indices: 40017367--40017418 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40017357 CACCACTGAA
*
40017367 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40017393 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40017419 CTTTTATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:40017550 original size:102 final size:101
Alignment explanation
Indices: 40017336--40017699 Score: 606
Period size: 102 Copynumber: 3.6 Consensus size: 101
40017326 TAACCGTTAT
* *
40017336 TGGTGGAT-CCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
*
40017400 ATCAGCACATAGCAACCCCCTTTTATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
40017436 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
40017501 AATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
40017538 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
40017603 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTT--CATTTCAAAGATA
* * * **
40017641 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
40017700 TTTATATACA
Statistics
Matches: 251, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
100 8 0.03
101 77 0.31
102 100 0.40
103 65 0.26
104 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (101 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
Found at i:40017600 original size:26 final size:26
Alignment explanation
Indices: 40017570--40017621 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40017560 CACCAATGAA
*
40017570 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40017596 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
40017622 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:40023144 original size:22 final size:22
Alignment explanation
Indices: 40023119--40023185 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
40023109 AAAACAGTAG
* * *
40023119 GCACCGAAGTGTGGAACGATAA
1 GCACCAAAGTGCGAAACGATAA
*
40023141 GCACCAAAGTGCGAAACGGTAA
1 GCACCAAAGTGCGAAACGATAA
*
40023163 GCACTAAAGTGC-AAGACGATAA
1 GCACCAAAGTGCGAA-ACGATAA
40023185 G
1 G
40023186 TGCGCTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 2 0.05
22 36 0.95
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.12
Consensus pattern (22 bp):
GCACCAAAGTGCGAAACGATAA
Found at i:40028308 original size:15 final size:15
Alignment explanation
Indices: 40028268--40028311 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40028258 TTAGTTAAAT
* *
40028268 ATTAATTAATATGAC
1 ATTAATTAATGTGAA
*
40028283 AGTATATTAATGTGAA
1 ATTA-ATTAATGTGAA
40028299 ATTAATTAATGTG
1 ATTAATTAATGTG
40028312 GCCATATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (15 bp):
ATTAATTAATGTGAA
Found at i:40028448 original size:27 final size:27
Alignment explanation
Indices: 40028409--40028488 Score: 67
Period size: 32 Copynumber: 2.9 Consensus size: 27
40028399 TAATTGGATA
*
40028409 AATTAAA-ATAATAATTTTTAAATTTTT
1 AATTAAATA-AATAATTTTTAAATATTT
40028436 AATTAAATAAATATAATTTATTTTAAATATTT
1 AATTAAAT-AA-ATAA--T-TTTTAAATATTT
*
40028468 AA-T-AATAAATAATTTTAAAAT
1 AATTAAATAAATAATTTTTAAAT
40028489 CAAATTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
25 7 0.16
26 1 0.02
27 7 0.16
28 5 0.11
29 7 0.16
30 3 0.07
31 2 0.04
32 13 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTAAATAAATAATTTTTAAATATTT
Found at i:40028452 original size:32 final size:31
Alignment explanation
Indices: 40028406--40028478 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
40028396 ATATAATTGG
*
40028406 ATAAATTAAA-ATAATA-ATTTTTAAATTTTTA
1 ATAAA-TAAATATAATATA-TTTTAAATATTTA
*
40028437 ATTAAATAAATATAATTTATTTTAAATATTTA
1 A-TAAATAAATATAATATATTTTAAATATTTA
40028469 AT-AATAAATA
1 ATAAATAAATA
40028479 ATTTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
30 8 0.22
31 6 0.16
32 22 0.59
33 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATAAATAAATATAATATATTTTAAATATTTA
Found at i:40028641 original size:5 final size:5
Alignment explanation
Indices: 40028629--40028739 Score: 197
Period size: 5 Copynumber: 22.2 Consensus size: 5
40028619 CTCAAAGAAA
*
40028629 ATAA- ATAAA ATAAT ATAAT ATATAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT
40028679 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
40028729 ATAAT ATAAT A
1 ATAAT ATAAT A
40028740 ATGTTTCTAT
Statistics
Matches: 104, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
4 4 0.04
5 95 0.91
6 5 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:40029137 original size:25 final size:25
Alignment explanation
Indices: 40029102--40029154 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
40029092 GCTTAGTTAT
40029102 TATTATGTGATATTCAATAAT-TTTA
1 TATTATGTGAT-TTCAATAATATTTA
* *
40029127 TATTATTTGATTTTAATAATATTTA
1 TATTATGTGATTTCAATAATATTTA
40029152 TAT
1 TAT
40029155 AATTGAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (25 bp):
TATTATGTGATTTCAATAATATTTA
Found at i:40032685 original size:46 final size:45
Alignment explanation
Indices: 40032587--40032749 Score: 163
Period size: 46 Copynumber: 3.6 Consensus size: 45
40032577 GTGCCAATGC
* * *
40032587 CATGTCCCAGACATGGTTTTACACTAAC-ACATCTCGTAGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTACGTCTCG-AGCCGATG
*
40032632 CATGTCCCAGACAT-GTCTTACACTAGCTTACGTCTCGAGGCCGGTG
1 CATGTCCCAGACATGGTCTTACACTAGC-TACGTCTCGA-GCCGATG
* * * *
40032678 CATGTCCCAAACAT-GTCTTACACTAGC-ACTCGTCTCAATGTCAATG
1 CATGTCCCAGACATGGTCTTACACTAGCTA--CGTCTCGA-GCCGATG
40032724 CCATGTCCCAGACATGGTCTTACACT
1 -CATGTCCCAGACATGGTCTTACACT
40032750 GGCTCACACA
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
44 12 0.12
45 15 0.15
46 50 0.50
47 13 0.13
48 10 0.10
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.27
Consensus pattern (45 bp):
CATGTCCCAGACATGGTCTTACACTAGCTACGTCTCGAGCCGATG
Found at i:40034121 original size:46 final size:46
Alignment explanation
Indices: 40034001--40034121 Score: 206
Period size: 46 Copynumber: 2.6 Consensus size: 46
40033991 TATACCAGCC
* * *
40034001 AGTGTAAGACATGTCTGGGACATGCATCAACATTAAGACGAGAGCT
1 AGTGTAAGACATATCTGGGACATGCATCGACATTAAGACCAGAGCT
40034047 AGTGTAAGACATATCTGGGACATGCATCGACATTAAGACCAGAGCT
1 AGTGTAAGACATATCTGGGACATGCATCGACATTAAGACCAGAGCT
*
40034093 AGTGTAAGACATATCCGGGACATGCATCG
1 AGTGTAAGACATATCTGGGACATGCATCG
40034122 GCCTCGAGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATATCTGGGACATGCATCGACATTAAGACCAGAGCT
Found at i:40041335 original size:19 final size:20
Alignment explanation
Indices: 40041294--40041336 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
40041284 TTTTGTAAAG
* *
40041294 TTTGTAAAATAGATGGTACT
1 TTTGTAAAATAGATGGAAAT
*
40041314 TTTGTGAAATA-ATGGAAAT
1 TTTGTAAAATAGATGGAAAT
40041333 TTTG
1 TTTG
40041337 GGTTGCTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGTAAAATAGATGGAAAT
Found at i:40041843 original size:48 final size:48
Alignment explanation
Indices: 40041788--40041956 Score: 175
Period size: 48 Copynumber: 3.6 Consensus size: 48
40041778 TGATATGTGT
* *
40041788 GCTAGTGTAAAACATTTCTGGGACATGCATCGGCCTCGAGATATACCA
1 GCTAGTGTAAGACATTTCTGGGACATGCATCGGCCTCGAGATATACAA
* * * * ** *
40041836 GCCAGTGTAAGACATGTCTGGGACATGCATCGACATTC-AGA-CGA-GA
1 GCTAGTGTAAGACATTTCTGGGACATGCATCGGC-CTCGAGATATACAA
* *
40041882 GCTAGTGTAAGACATGTT-TGGGACATGCATCAGCCTTGAGATATACAA
1 GCTAGTGTAAGACAT-TTCTGGGACATGCATCGGCCTCGAGATATACAA
* *
40041930 GCTAGTGTAAGACCTATCTGGGACATG
1 GCTAGTGTAAGACATTTCTGGGACATG
40041957 GCGTCAGCTT
Statistics
Matches: 96, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
45 1 0.01
46 32 0.33
47 4 0.04
48 57 0.59
49 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACATTTCTGGGACATGCATCGGCCTCGAGATATACAA
Found at i:40042615 original size:54 final size:55
Alignment explanation
Indices: 40042555--40042672 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 55
40042545 CGTGTATAAC
* * ** **
40042555 ACTGACTT-TAGGGCACGACCATGACACACGCCTGTG-GGGTTACCTGTGGACAAT
1 ACTGACTTATA-GACACGACCATGACACACGCCCGTGTGGCCTACCCATGGACAAT
* *
40042609 ACTGACTTATAGACACGGCTATGACACACGCCCGTGTGGCCTACCCATGGACAAT
1 ACTGACTTATAGACACGACCATGACACACGCCCGTGTGGCCTACCCATGGACAAT
40042664 ACTGACTTA
1 ACTGACTTA
40042673 AAAGTTTAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 29 0.54
55 25 0.46
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (55 bp):
ACTGACTTATAGACACGACCATGACACACGCCCGTGTGGCCTACCCATGGACAAT
Found at i:40043623 original size:47 final size:46
Alignment explanation
Indices: 40043422--40043785 Score: 186
Period size: 47 Copynumber: 7.7 Consensus size: 46
40043412 TTAAGTTGCC
* * * *
40043422 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCTTCATCGAGGCC
1 GATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATC-TCTAGGCG
* * * * * * * * *
40043471 GATGCCATGTCCCAAACATGGTCTTCCACTAGCTCTCGTGTATACGTGCT
1 GATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATCTCTA-G-GCG
* * * * * *
40043521 GATGCATGTCCTAAACATGTCTTACACTAGC-A-CGAAGCT-TA-GCT
1 GATGCATGTCCCAGACACGTCTTACACTGGCTATC--ATCTCTAGGCG
*
40043565 GATGCAGGTCCCAGACACGTCTTACACTGGCTATCATCAT-TAAGGCG
1 GATGCATGTCCCAGACACGTCTTACACTGGCTATCATC-TCT-AGGCG
* * * *
40043612 GATGCATGTCCCACACATGTCTTACACTGGC-ACTCATCTCTATGCC
1 GATGCATGTCCCAGACACGTCTTACACTGGCTA-TCATCTCTAGGCG
* * * * *
40043658 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCGTAATGT-GGCT
1 GATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCAT-CTCTAGGCG
* ** * * *
40043706 GATGCATGTCCCAGACACGTCTTACACTAGCCCTCGTCTCAATGCCG
1 GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCTCTA-GGCG
*
40043753 G-TGCCATGTCCCAGACATGGTCTTACACTGGCT
1 GATG-CATGTCCCAGACA-CGTCTTACACTGGCT
40043786 CTCACATAAC
Statistics
Matches: 249, Mismatches: 47, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
44 31 0.12
45 4 0.02
46 30 0.12
47 79 0.32
48 49 0.20
49 50 0.20
50 6 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCTCTAGGCG
Found at i:40043707 original size:141 final size:139
Alignment explanation
Indices: 40043430--40043781 Score: 363
Period size: 141 Copynumber: 2.5 Consensus size: 139
40043420 CCGATGCCAT
* * *
40043430 GTCCCAGACATGGTCTTACACTGGCTATCTTCATCGAGGCCGATGCCATGTCCCAAACATGGTCT
1 GTCCCAGACA-CGTCTTACACTGGCTATCATCATCAAGGCCGATGCCATGTCCCAAACATGGTCT
* * * * * *
40043495 TCCACTAGCTCTCGTGTATACGTGCTGATGCATGTCCTAAACATGTCTTACACTAGCACGAAGCT
65 TACACTAGCACTCATCTATAC-TGCCGATGCATGTCCCAAACATGTCTTACACTAGCACGAAGC-
40043560 TAGCTGATGCAG
128 TAGCTGATGCAG
* * *
40043572 GTCCCAGACACGTCTTACACTGGCTATCATCATTAAGGCGGATG-CATGTCCCACACAT-GTCTT
1 GTCCCAGACACGTCTTACACTGGCTATCATCATCAAGGCCGATGCCATGTCCCAAACATGGTCTT
* * * *
40043635 ACACTGGCACTCATCTCTA-TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCGTAA
66 ACACTAGCACTCATCTATACTGCCGATG-CATGTCCCAAACAT-GTCTTACACTAGC-A-CG-AA
* *
40043699 TG-TGGCTGATGCAT
126 -GCTAGCTGATGCAG
* ** * * * *
40043713 GTCCCAGACACGTCTTACACTAGCCCTCGTC-TCAATGCCGGTGCCATGTCCCAGACATGGTCTT
1 GTCCCAGACACGTCTTACACTGGCTATCATCATCAAGGCCGATGCCATGTCCCAAACATGGTCTT
40043777 ACACT
66 ACACT
40043782 GGCTCTCACA
Statistics
Matches: 175, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
137 7 0.04
138 12 0.07
139 30 0.17
140 22 0.13
141 81 0.46
142 22 0.13
143 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (139 bp):
GTCCCAGACACGTCTTACACTGGCTATCATCATCAAGGCCGATGCCATGTCCCAAACATGGTCTT
ACACTAGCACTCATCTATACTGCCGATGCATGTCCCAAACATGTCTTACACTAGCACGAAGCTAG
CTGATGCAG
Found at i:40043713 original size:94 final size:94
Alignment explanation
Indices: 40043422--40043785 Score: 355
Period size: 94 Copynumber: 3.9 Consensus size: 94
40043412 TTAAGTTGCC
* * * * *
40043422 GATGCCATGTCCCAGACATGGTCTTACACTGGCTA-TCTTCATCGAGGCCGATGCCATGTCCCAA
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATC-TCTATGCCGATGCCATGTCCCAG
* * * *
40043486 ACATGGTCTTCCACTAGCTCTCGTGTATACGT-GCT
62 ACATGGTCTTACACTGGCTATC--GTA-ATGTGGCT
* * ** * * *
40043521 GATGCATGTCCTAAACATGTCTTACACTAGCACGAAGCT-TA-GCTGATG-CAGGTCCCAGACA-
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
* * * *
40043582 CGTCTTACACTGGCTATCATCAT-TAAGGCG
66 GGTCTTACACTGGCTATCGTAATGT--GGCT
* *
40043612 GATGCATGTCCCACACATGTCTTACACTGGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
40043677 GGTCTTACACTGGCTATCGTAATGTGGCT
66 GGTCTTACACTGGCTATCGTAATGTGGCT
* * * * *
40043706 GATGCATGTCCCAGACACGTCTTACACTAGCCCTCGTCTCAATGCCGGTGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
40043771 GGTCTTACACTGGCT
66 GGTCTTACACTGGCT
40043786 CTCACATAAC
Statistics
Matches: 218, Mismatches: 38, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
88 1 0.00
89 1 0.00
90 1 0.00
91 35 0.16
92 16 0.07
93 17 0.08
94 94 0.43
95 21 0.10
96 3 0.01
97 13 0.06
98 12 0.06
99 4 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (94 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
GGTCTTACACTGGCTATCGTAATGTGGCT
Found at i:40051022 original size:47 final size:47
Alignment explanation
Indices: 40050823--40051137 Score: 199
Period size: 47 Copynumber: 6.7 Consensus size: 47
40050813 TTAAGTTGCC
* * * * *
40050823 GATGCCATGTCCCAGACATGGTTTTCCACTGGCTATCT-TCATCGAGGCT
1 GATG-CATGTCCCAGACA-AGTCTTACACTAGCTA-CTATCATTGAGGCT
* * *
40050872 GATGCCATGTCCCAAACATAGTCTTACACTAGCT-C--TCGTGTATACGTGCT
1 GATG-CATGTCCCAGACA-AGTCTTACACTAGCTACTATCAT-T-GA-G-GCT
* * * *
40050922 GATGCATGTCCTAGA-AATGTCTTACACTAG-TACAAACCTT-A-GCT
1 GATGCATGTCCCAGACAA-GTCTTACACTAGCTACTATCATTGAGGCT
* *
40050966 GATGCATGTCCCAGACAAGTCTTACACTGGCTACTATCATTGAGGCC
1 GATGCATGTCCCAGACAAGTCTTACACTAGCTACTATCATTGAGGCT
* * *
40051013 GATGCATGTCCCAGACATGTCTTACACTCGC-ACTCATC-TCT-ACGCT
1 GATGCATGTCCCAGACAAGTCTTACACTAGCTACT-ATCAT-TGAGGCT
* * *
40051059 GATGCCATGTCCCAGACATGGTCTTACACTTGCTATCGTA--A-TGTGGCT
1 GATG-CATGTCCCAGACA-AGTCTTACACTAGCTA-C-TATCATTGAGGCT
*
40051107 GATGCATGTCCCAGACACGTCTTACACTAGC
1 GATGCATGTCCCAGACAAGTCTTACACTAGC
40051138 CCTCGTCTTA
Statistics
Matches: 217, Mismatches: 28, Indels: 45
0.75 0.10 0.16
Matches are distributed among these distances:
44 28 0.13
45 9 0.04
46 27 0.12
47 66 0.30
48 34 0.16
49 41 0.19
50 11 0.05
51 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
GATGCATGTCCCAGACAAGTCTTACACTAGCTACTATCATTGAGGCT
Found at i:40051108 original size:141 final size:139
Alignment explanation
Indices: 40050823--40051134 Score: 337
Period size: 141 Copynumber: 2.2 Consensus size: 139
40050813 TTAAGTTGCC
* * * *
40050823 GATGCCATGTCCCAGACATGGTTTTCCACTGGCTATCTTCATCGAGGCTGATGCCATGTCCCAAA
1 GATG-CATGTCCCAGACA-AGTCTTACACTGGCTATCTTCATCGAGGCCGATGCCATGTCCCAAA
* * * *
40050888 CATAGTCTTACACTAGCTCTCGTGTATACGTGCTGATGCATGTCCTAGAAATGTCTTACACTAGT
64 CATAGTCTTACACTAGCACTCATCTATACG-GCTGATGCATGTCCCAGAAATGTCTTACACTAGT
40050953 ACAAACCTTAGCT
128 ACAAA-CTTAGCT
* *
40050966 GATGCATGTCCCAGACAAGTCTTACACTGGCTA-CTATCATTGAGGCCGATG-CATGTCCCAGAC
1 GATGCATGTCCCAGACAAGTCTTACACTGGCTATCT-TCATCGAGGCCGATGCCATGTCCCAAAC
* * * *
40051029 AT-GTCTTACACTCGCACTCATCTCTAC-GCTGATGCCATGTCCCAGACATGGTCTTACACTTGC
65 ATAGTCTTACACTAGCACTCATCTATACGGCTGATG-CATGTCCCAGAAAT-GTCTTACACTAG-
* *
40051092 TATCGTAA-TGTGGCT
127 TA-C-AAACT-TAGCT
*
40051107 GATGCATGTCCCAGACACGTCTTACACT
1 GATGCATGTCCCAGACAAGTCTTACACT
40051135 AGCCCTCGTC
Statistics
Matches: 145, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
137 7 0.05
138 12 0.08
139 31 0.21
140 18 0.12
141 58 0.40
142 15 0.10
143 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (139 bp):
GATGCATGTCCCAGACAAGTCTTACACTGGCTATCTTCATCGAGGCCGATGCCATGTCCCAAACA
TAGTCTTACACTAGCACTCATCTATACGGCTGATGCATGTCCCAGAAATGTCTTACACTAGTACA
AACTTAGCT
Found at i:40051114 original size:94 final size:94
Alignment explanation
Indices: 40050869--40051182 Score: 313
Period size: 94 Copynumber: 3.4 Consensus size: 94
40050859 CTTCATCGAG
* * *
40050869 GCTGATGCCATGTCCCAAACATAGTCTTACACTAGCTCTCGTGTATACGT-GCTGATGCATGTCC
1 GCTGATGCCATGTCCCAGACATAGTCTTACACTAGCTATC--GTATATGTGGCTGATGCATGTCC
* * * ** *
40050933 TAGAAATGTCTTACACTAGTACAAACCTTA-
64 CAGACATGTCTTACACTAGCACTCATCTTAC
* * *
40050963 GCTGATG-CATGTCCCAGACA-AGTCTTACACTGGCTA-C-TATCATTGAGGCCGATGCATGTCC
1 GCTGATGCCATGTCCCAGACATAGTCTTACACTAGCTATCGTAT-A-TGTGGCTGATGCATGTCC
*
40051024 CAGACATGTCTTACACTCGCACTCATCTCTAC
64 CAGACATGTCTTACACTAGCACTCATCT-TAC
* *
40051056 GCTGATGCCATGTCCCAGACATGGTCTTACACTTGCTATCGTA-ATGTGGCTGATGCATGTCCCA
1 GCTGATGCCATGTCCCAGACATAGTCTTACACTAGCTATCGTATATGTGGCTGATGCATGTCCCA
* * *
40051120 GACACGTCTTACACTAGCCCTCGTCTTAATTC
66 GACATGTCTTACACTAGCACTCATCTT-A--C
* *
40051152 -CAG-TGCCATGTCCCAGACATGGTCTTACACT
1 GCTGATGCCATGTCCCAGACATAGTCTTACACT
40051183 GGTTCTCACA
Statistics
Matches: 186, Mismatches: 22, Indels: 24
0.80 0.09 0.10
Matches are distributed among these distances:
88 3 0.02
89 1 0.01
90 1 0.01
91 35 0.19
92 16 0.09
93 20 0.11
94 89 0.48
95 17 0.09
96 2 0.01
97 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (94 bp):
GCTGATGCCATGTCCCAGACATAGTCTTACACTAGCTATCGTATATGTGGCTGATGCATGTCCCA
GACATGTCTTACACTAGCACTCATCTTAC
Found at i:40054624 original size:23 final size:24
Alignment explanation
Indices: 40054558--40054624 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 24
40054548 AGTTAATTCT
*
40054558 ATTTTA-TTTTTTTTTATTTATTA
1 ATTTTACTTTTTATTTATTTATTA
40054581 ATTTTAATTCTATTTTA-TTATTTATTA
1 ATTTT-A--CT-TTTTATTTATTTATTA
40054608 A-TTTACTTTTTATTTAT
1 ATTTTACTTTTTATTTAT
40054625 CTTGGCAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
22 5 0.14
23 11 0.30
24 1 0.03
25 1 0.03
26 3 0.08
27 12 0.32
28 4 0.11
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTTTACTTTTTATTTATTTATTA
Found at i:40063471 original size:23 final size:22
Alignment explanation
Indices: 40063419--40063471 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40063409 TCCACGTCTT
*
40063419 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40063441 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40063464 TTTCTTTT
1 TTTCTTTT
40063472 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40072752 original size:46 final size:45
Alignment explanation
Indices: 40072668--40072834 Score: 149
Period size: 46 Copynumber: 3.6 Consensus size: 45
40072658 TCTCGTAGTC
* * * *
40072668 GATGCAAGTCCCA-AGCATGTCTTATACTAGCTTACGTCTCGAGGCC
1 GATGCATGTCCCAGA-CATGTCTTACACTAGCCT-CGTCTCGAGGCT
* * *
40072714 GATGCATGTCCTAGACATGTCTTACACTAGCACTCGTCTCAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGC-CTCGTCTCGAGGCT
* * * * *
40072760 GATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCATAAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTAG-CCTCGT-CTCGAGGCT
40072808 GATGCATGTCCCAGACATGTCTTACAC
1 GATGCATGTCCCAGACATGTCTTACAC
40072835 CAGCTCACAA
Statistics
Matches: 100, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
46 48 0.48
47 29 0.29
48 22 0.22
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCTCGTCTCGAGGCT
Found at i:40078824 original size:19 final size:19
Alignment explanation
Indices: 40078800--40078838 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40078790 TTGAGTAAGC
40078800 TACTTCCATTTTTCATCAA
1 TACTTCCATTTTTCATCAA
40078819 TACTTCCATTTTTCATCAA
1 TACTTCCATTTTTCATCAA
40078838 T
1 T
40078839 GCCAATGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (19 bp):
TACTTCCATTTTTCATCAA
Found at i:40082358 original size:23 final size:23
Alignment explanation
Indices: 40082314--40082358 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40082304 CCAATTCCAA
*
40082314 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
40082337 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
40082359 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:40093466 original size:16 final size:15
Alignment explanation
Indices: 40093433--40093498 Score: 66
Period size: 15 Copynumber: 4.3 Consensus size: 15
40093423 TGGAACTAAT
40093433 TAAAGAAAT-AAATAAA
1 TAAA-AAATAAAAT-AA
40093449 TAAAAAATAAGAATAA
1 TAAAAAATAA-AATAA
40093465 TAAAAAATAAAATAA
1 TAAAAAATAAAATAA
*
40093480 -AATAAAGTAAAATAA
1 TAA-AAAATAAAATAA
40093495 -AAAA
1 TAAAA
40093499 TAGGATAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
14 4 0.09
15 22 0.48
16 17 0.37
17 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
TAAAAAATAAAATAA
Found at i:40093468 original size:20 final size:20
Alignment explanation
Indices: 40093438--40093500 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
40093428 CTAATTAAAG
40093438 AAATAAATAAATAAAAAATA
1 AAATAAATAAATAAAAAATA
*
40093458 AGAAT-AATAAAAAATAAAATA
1 A-AATAAATAAATAA-AAAATA
40093479 AAATAAAGTAAAATAAAAAATA
1 AAATAAA-T-AAATAAAAAATA
40093501 GGATAATGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 12 0.33
21 12 0.33
22 7 0.19
23 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (20 bp):
AAATAAATAAATAAAAAATA
Found at i:40093474 original size:27 final size:27
Alignment explanation
Indices: 40093442--40093500 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
40093432 TTAAAGAAAT
40093442 AAATAAATAAAAAAT-AAG-AATAATAAA
1 AAATAAA-AAAAAATAAAGTAA-AATAAA
*
40093469 AAATAAAATAAAATAAAGTAAAATAAA
1 AAATAAAAAAAAATAAAGTAAAATAAA
40093496 AAATA
1 AAATA
40093501 GGATAATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 21 0.72
28 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (27 bp):
AAATAAAAAAAAATAAAGTAAAATAAA
Found at i:40093481 original size:10 final size:10
Alignment explanation
Indices: 40093438--40093496 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
40093428 CTAATTAAAG
40093438 AAAT-AAATA
1 AAATAAAATA
*
40093447 AATAAAAAATA
1 AA-ATAAAATA
40093458 AGAATAATAA-A
1 A-AATAA-AATA
40093469 AAATAAAATA
1 AAATAAAATA
*
40093479 AAATAAAGTA
1 AAATAAAATA
40093489 AAATAAAA
1 AAATAAAA
40093497 AATAGGATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.10
10 23 0.56
11 11 0.27
12 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
AAATAAAATA
Found at i:40093500 original size:7 final size:7
Alignment explanation
Indices: 40093433--40093476 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 7
40093423 TGGAACTAAT
40093433 TAAAGAAA
1 TAAA-AAA
40093441 TAAATAAA
1 TAAA-AAA
40093449 TAAAAAA
1 TAAAAAA
40093456 TAAGAATAA
1 TAA-AA-AA
40093465 TAAAAAA
1 TAAAAAA
40093472 TAAAA
1 TAAAA
40093477 TAAAATAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 13 0.39
8 15 0.45
9 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (7 bp):
TAAAAAA
Found at i:40093757 original size:7 final size:7
Alignment explanation
Indices: 40093745--40093775 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
40093735 TGGTTCGGTC
40093745 AAGGGAG
1 AAGGGAG
40093752 AAGGGAG
1 AAGGGAG
40093759 AAGGGAG
1 AAGGGAG
40093766 AAGGG-G
1 AAGGGAG
40093772 AAGG
1 AAGG
40093776 CGGGCTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (7 bp):
AAGGGAG
Found at i:40094211 original size:20 final size:20
Alignment explanation
Indices: 40094186--40094237 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
40094176 TCGCTTCTTC
40094186 CACGCCCGTGTGACCT-CCCA
1 CACGCCCGTGTGA-CTGCCCA
40094206 CACGCCCGTGTGACTGCCCA
1 CACGCCCGTGTGACTGCCCA
*
40094226 CACGACCGTGTG
1 CACGCCCGTGTG
40094238 CCTTGCCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.15, C:0.44, G:0.25, T:0.15
Consensus pattern (20 bp):
CACGCCCGTGTGACTGCCCA
Found at i:40097059 original size:94 final size:94
Alignment explanation
Indices: 40096898--40097461 Score: 993
Period size: 94 Copynumber: 6.0 Consensus size: 94
40096888 AATTTGACCG
* * *
40096898 TATATGCTATTTGAATTAAGTAAGTTGCCATATTATAATGAGCTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
*
40096963 GAATGAAATCTCACTTTGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
40096992 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
*
40097057 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
*
40097086 TATATGCTATTTGGATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
*
40097151 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
*
40097180 TATATGCTATTTGAGTTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
40097245 GAATTAAATCTCACTTTGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
*
40097274 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGACTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
40097339 GAATTAAATCTCACTTTGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
* * *
40097368 TATATGCTATTTGAATCAAGTAAATTGCTTTATTATAATGAGTCAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
** *
40097433 GAATTAAATGGCACTATGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
40097462 GAATGTCGAT
Statistics
Matches: 452, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 452 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (94 bp):
TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
GAATTAAATCTCACTTTGTGTGCAGATTT
Found at i:40097525 original size:24 final size:24
Alignment explanation
Indices: 40097493--40097553 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
40097483 AATTTCAGGT
* * *
40097493 ACTATGTGTGCG-GTTTAGTATGGC
1 ACTATGTGTGCGAGCTTAATA-AGC
40097517 ACTATGTGTGCGAGCTTAATAAGC
1 ACTATGTGTGCGAGCTTAATAAGC
40097541 ACTATGTGTGCGA
1 ACTATGTGTGCGA
40097554 ATTTGGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (24 bp):
ACTATGTGTGCGAGCTTAATAAGC
Found at i:40105156 original size:94 final size:94
Alignment explanation
Indices: 40104995--40105276 Score: 501
Period size: 94 Copynumber: 3.0 Consensus size: 94
40104985 AATGTGACCG
* * * *
40104995 TATATGCTATTTGAATTAAGTAAGTTGCCATATTATAATGAGTTAACATTGACATTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
*
40105060 GAATTAAATCTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
40105089 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
40105154 GAATTAAATGTCACTTTGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
40105183 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
* *
40105248 GAATTAAATGGCACTATGTGTGCAGATTT
66 GAATTAAATGTCACTTTGTGTGCAGATTT
40105277 GAATGTCGAT
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 181 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (94 bp):
TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
GAATTAAATGTCACTTTGTGTGCAGATTT
Found at i:40105337 original size:24 final size:24
Alignment explanation
Indices: 40105304--40105367 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
40105294 TGAAAATTTC
* *
40105304 AGCACTATGTGTGCG-GTTTAGTAT
1 AGCACTATGTGTGCGAGCTTAAT-T
*
40105328 GGCACTATGTGTGCGAGCTTAATT
1 AGCACTATGTGTGCGAGCTTAATT
40105352 AGCACTATGTGTGCGA
1 AGCACTATGTGTGCGA
40105368 ATTTGGTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.33
Consensus pattern (24 bp):
AGCACTATGTGTGCGAGCTTAATT
Found at i:40108329 original size:35 final size:38
Alignment explanation
Indices: 40108213--40108356 Score: 188
Period size: 39 Copynumber: 3.8 Consensus size: 38
40108203 AGCCCGGTTA
40108213 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG-AT
1 TAGTAACTCGCACAAATG-CTTC-GGACTTAACCCGGAAT
*
40108252 TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATG-CTTCGGACTTAACCCGGAAT
*
40108291 TAGTAACTCGCAC-AATG-TTCGG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCTTCGGACTTAACCCGGAAT
*
40108326 TAGTATCTCGCACAAATGCCTTCGGATCTTA
1 TAGTAACTCGCACAAATG-CTTCGGA-CTTA
40108357 GTCCGGATAT
Statistics
Matches: 95, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
35 23 0.24
36 9 0.09
38 22 0.23
39 37 0.39
40 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (38 bp):
TAGTAACTCGCACAAATGCTTCGGACTTAACCCGGAAT
Found at i:40108344 original size:74 final size:77
Alignment explanation
Indices: 40108185--40108403 Score: 234
Period size: 74 Copynumber: 2.8 Consensus size: 77
40108175 GCTACTCGTT
* *
40108185 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTC-GGACTTAACCCGGTTATAGTAACTCGCACAAATG-CTTCGGGACTTAACCCGG
40108250 ATTAGTAACTCGCA
64 ATTAGTAACTCGCA
*
40108264 CAAATGCCTTCGGACTTAACCCGGATT-TAGTAACTCGCAC-AATG-TTC-GG-CTTAGCCCGGA
1 CAAATGCCTTCGGACTTAACCCGG-TTATAGTAACTCGCACAAATGCTTCGGGACTTAACCCGG-
*
40108324 ATTAGTATCTCGCA
64 ATTAGTAACTCGCA
** * * * * *
40108338 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAACCCGGTTATAGTAAC-TCGCACAAATG-CTTCGGGACTTAACCCG
40108402 GA
63 GA
40108404 CATCATTCAA
Statistics
Matches: 120, Mismatches: 10, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
73 9 0.08
74 30 0.25
75 16 0.13
76 6 0.05
77 6 0.05
78 27 0.22
79 16 0.13
80 10 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGACTTAACCCGGTTATAGTAACTCGCACAAATGCTTCGGGACTTAACCCGGAT
TAGTAACTCGCA
Found at i:40108403 original size:40 final size:39
Alignment explanation
Indices: 40108185--40108403 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 39
40108175 GCTACTCGTT
* *
40108185 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCA
*
40108225 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCA
* *
40108264 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCA
*
40108303 C-AATG--TTCGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
40108338 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATATAGTAAC-TCGCA
40108379 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
40108404 CATCATTCAA
Statistics
Matches: 157, Mismatches: 12, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
35 22 0.14
36 9 0.06
38 24 0.15
39 36 0.23
40 54 0.34
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:40112995 original size:40 final size:40
Alignment explanation
Indices: 40112928--40113104 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
40112918 ACCCAAGTAT
*
40112928 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
40112967 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
40113007 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
40113047 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
40113087 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
40113105 TTATCATCCG
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 104 0.87
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:40121022 original size:40 final size:40
Alignment explanation
Indices: 40120955--40121131 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
40120945 ACCCGAGTAT
*
40120955 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
40120994 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
40121034 CTTTGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
40121074 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
40121114 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
40121132 TTATCATCCG
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 102 0.86
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:40129161 original size:94 final size:94
Alignment explanation
Indices: 40128906--40129182 Score: 474
Period size: 94 Copynumber: 3.0 Consensus size: 94
40128896 TAATGTGACG
* *
40128906 TATATGC-ATTTGAATTAAGTAAGTTGCCATATT-TAATGAGTTAACATT-G-ACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
40128967 GAATTAAATCTCACTTTGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
40128996 TATATGCTATTTGAA-TAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
40129060 GAATTAAATCTCACTTTGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
40129089 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
1 TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
** *
40129154 GAATTAAATGGCACTATGTGTGCAGATTT
66 GAATTAAATCTCACTTTGTGTGCAGATTT
40129183 GAATGTCGAT
Statistics
Matches: 177, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
90 23 0.13
91 22 0.12
92 1 0.01
93 56 0.32
94 75 0.42
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (94 bp):
TATATGCTATTTGAATTAAGTAAATTGCCTTATTATAATGAGTTAACATTGGCACTATGTGTGCG
GAATTAAATCTCACTTTGTGTGCAGATTT
Found at i:40129244 original size:24 final size:24
Alignment explanation
Indices: 40129211--40129274 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
40129201 GAAAATTTCA
* *
40129211 AGCACTATGTGTGCG-GTTTAGTAT
1 AGCACTATGTGTGCGAGCTTAAT-T
*
40129235 GGCACTATGTGTGCGAGCTTAATT
1 AGCACTATGTGTGCGAGCTTAATT
40129259 AGCACTATGTGTGCGA
1 AGCACTATGTGTGCGA
40129275 ATTTGGTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.33
Consensus pattern (24 bp):
AGCACTATGTGTGCGAGCTTAATT
Found at i:40132148 original size:40 final size:40
Alignment explanation
Indices: 40132111--40132333 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
40132101 GCTACTCGTT
* *
40132111 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
40132151 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40132190 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
40132230 CAAATGCCTTC-GG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
40132268 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
40132309 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40132334 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 35 0.21
39 36 0.22
40 82 0.50
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40132293 original size:78 final size:79
Alignment explanation
Indices: 40132111--40132333 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
40132101 GCTACTCGTT
* *
40132111 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGG
*
40132175 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
40132190 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGA
*
40132254 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* * * * *
40132268 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATGCCTTC-GGACTTAGCCC
40132331 GGA
63 GGA
40132334 CATCATTCAA
Statistics
Matches: 128, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
77 3 0.02
78 54 0.42
79 58 0.45
80 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:40140221 original size:77 final size:80
Alignment explanation
Indices: 40140064--40140233 Score: 256
Period size: 77 Copynumber: 2.2 Consensus size: 80
40140054 GCTACTCGTT
* * *
40140064 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
40140129 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* *
40140144 CAAATGCCTTCGGGACTTAACCCGATT-TAGTAACTCGCACAAATG-CTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
40140206 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
40140221 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40140234 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
77 35 0.42
78 7 0.08
79 17 0.20
80 24 0.29
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:40140246 original size:117 final size:119
Alignment explanation
Indices: 40140064--40140284 Score: 281
Period size: 117 Copynumber: 1.9 Consensus size: 119
40140054 GCTACTCGTT
* *
40140064 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
40140129 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGATTTAGTAACTCGCA
* * **
40140183 CAAATG-CTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
40140244 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCG
40140285 GACATCATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
116 4 0.05
117 63 0.72
118 15 0.17
119 6 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGATTTAGTAACTCGCA
Found at i:40140286 original size:40 final size:40
Alignment explanation
Indices: 40140045--40140286 Score: 273
Period size: 40 Copynumber: 6.1 Consensus size: 40
40140035 CGGAATTTAA
** *
40140045 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40140085 CCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40140125 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40140165 CC-GATTTAGTAACTCGCACAAATG-CTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40140202 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40140242 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40140282 CCGGA
1 CCGGA
40140287 CATCATTCAA
Statistics
Matches: 177, Mismatches: 16, Indels: 18
0.84 0.08 0.09
Matches are distributed among these distances:
37 7 0.04
38 28 0.16
39 27 0.15
40 103 0.58
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40148921 original size:22 final size:22
Alignment explanation
Indices: 40148887--40148930 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40148877 CCTCCGTTGC
40148887 CTCTAGCACTGACATTCTCTGT
1 CTCTAGCACTGACATTCTCTGT
* *
40148909 CTCTAGTATTGACATTCTCTGT
1 CTCTAGCACTGACATTCTCTGT
40148931 GGAATCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (22 bp):
CTCTAGCACTGACATTCTCTGT
Found at i:40151871 original size:71 final size:70
Alignment explanation
Indices: 40151640--40151873 Score: 195
Period size: 70 Copynumber: 3.3 Consensus size: 70
40151630 TGGCTGGGGT
* * * * * * *
40151640 TTTTCACTTGCGAGCCTTAATATGACAACT-AGGAGTTTTTAATTCTTGCTAACTGTGTCGTGGC
1 TTTTCACCTACGAGCCTTAATATTACAACTGA-GAGTTTTTAACTCTAGCTAACTGTGTAGAGGC
* **
40151704 TACATT
65 TGCAAA
* * * *
40151710 TTTTCACCTACGAGCCTTAGTATGA-AAGCTGGGAGTTTTTAACTCTCGC-AACTGTGTTAGAGG
1 TTTTCACCTACGAGCCTTAATATTACAA-CTGAGAGTTTTTAACTCTAGCTAACTGTG-TAGAGG
* **
40151773 TTGCGGA
64 CTGCAAA
* * * * *
40151780 TTTTAACCTATGAGCATTAATATTTCAACTGAGAGTTTTTAACTCTAGCTAACTGTGCTGGAGGC
1 TTTTCACCTACGAGCCTTAATATTACAACTGAGAGTTTTTAACTCTAGCTAACTGTG-TAGAGGC
40151845 TGCAAA
65 TGCAAA
* *
40151851 TTTTCACCTGCGAACCTTAATAT
1 TTTTCACCTACGAGCCTTAATAT
40151874 GATAGCTAAT
Statistics
Matches: 128, Mismatches: 31, Indels: 9
0.76 0.18 0.05
Matches are distributed among these distances:
69 9 0.07
70 83 0.65
71 36 0.28
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (70 bp):
TTTTCACCTACGAGCCTTAATATTACAACTGAGAGTTTTTAACTCTAGCTAACTGTGTAGAGGCT
GCAAA
Found at i:40175662 original size:120 final size:119
Alignment explanation
Indices: 40175431--40175688 Score: 292
Period size: 120 Copynumber: 2.2 Consensus size: 119
40175421 TTGAATGATG
* * * *
40175431 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTGACCAAATCCGGACTAAGATCCAAAGGCATTTG
**
40175496 TACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAA
66 TACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAA
* * **
40175550 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCAAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGTGACCAAATCCGGACTAAGAT-CCAAAGGCATT
* * * *
40175614 TGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATA
64 TGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAA
* *
40175670 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40175689 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
119 38 0.32
120 78 0.66
121 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTGACCAAATCCGGACTAAGATCCAAAGGCATTTG
TACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAA
Found at i:40175669 original size:40 final size:40
Alignment explanation
Indices: 40175431--40175655 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
40175421 TTGAATGATG
* * * *
40175431 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40175470 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40175510 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40175550 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40175590 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40175631 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40175656 AACGAGTAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 19 0.11
40 148 0.88
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40179979 original size:84 final size:83
Alignment explanation
Indices: 40179884--40180101 Score: 328
Period size: 84 Copynumber: 2.6 Consensus size: 83
40179874 ATAAGCCTGT
*
40179884 TAGACCTTTAAGTCCTATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCCGATAATCT
1 TAGACCTTTAAGT-CTATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCCGATAATAT
* *
40179949 TCACCAGCTTAAATATTGG
65 TCACCAGCTTAAAGATTGC
**
40179968 TAGACCTTTAAGTACGGTATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCCGATAATAT
1 TAGACCTTTAAGT-CTATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCCGATAATAT
*
40180033 TCACCAGCTTAAAGCTTGC
65 TCACCAGCTTAAAGATTGC
* * *
40180052 TAGACCCTTAAGTCTGATATCATTTCACCGGCATTATGCCTGCCAGGCTC
1 TAGACCTTTAAGTCT-ATATCATTTCACCGGCATTACGCCTGCTAGGCTC
40180102 AAAGCTCGAA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
83 1 0.01
84 120 0.99
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (83 bp):
TAGACCTTTAAGTCTATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCCGATAATATT
CACCAGCTTAAAGATTGC
Found at i:40186513 original size:93 final size:93
Alignment explanation
Indices: 40186402--40186572 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
40186392 ACCCTTAAGT
* * *
40186402 GAACTAGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTAGGACTCAACTCAACAAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
40186467 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
40186495 GAACTCGGACTCAACTCAACAAGCTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTAGGACTCAACTCAACAAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
40186560 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40186573 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (93 bp):
GAACTAGGACTCAACTCAACAAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40186560 original size:46 final size:46
Alignment explanation
Indices: 40186397--40186560 Score: 154
Period size: 46 Copynumber: 3.5 Consensus size: 46
40186387 AACCCACCCT
* * * * *
40186397 TAAGTGAACTAGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACAAGCTCAGACATTTGCATCCA
* * * * * *
40186443 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACAAGCTC--A-GAC-ATTTGCATCCA
* *
40186491 TCA-CGAACTCGGACTCAACTCAACAAGCTCAGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACAAGCTCAGACATTTGCATCCA
40186536 TAAGTGAACTCGGACTCAACTCAAC
1 TAAGTGAACTCGGACTCAACTCAAC
40186561 GAGTTCGGAT
Statistics
Matches: 92, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
43 6 0.07
44 3 0.03
45 3 0.03
46 47 0.51
47 24 0.26
48 2 0.02
49 3 0.03
50 4 0.04
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACAAGCTCAGACATTTGCATCCA
Found at i:40192179 original size:48 final size:48
Alignment explanation
Indices: 40192124--40192338 Score: 226
Period size: 46 Copynumber: 4.6 Consensus size: 48
40192114 AAGCTGACGC
*
40192124 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCTGATG
* ** *
40192172 CATGTCCCAGACATGTCTTACACTAGC-TCT-CGTCTCAATGGC-GATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGA-GGCTGATG
* * * * * * *
40192218 CATGTCCTAGTCAAGTCTTACACTGGCTTGTATATTTTGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCTGATG
* * *
40192266 CATGTCCCAGACATGTCTTACACTAGCTCT-CATA-AT-GTGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TGTATATCTCGAGGCTGATG
*
40192312 CATGTCCCAGGCATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
40192339 ACACATATCA
Statistics
Matches: 138, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
46 65 0.47
47 11 0.08
48 61 0.44
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.31
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCTGATG
Found at i:40192247 original size:94 final size:94
Alignment explanation
Indices: 40192124--40192338 Score: 283
Period size: 94 Copynumber: 2.3 Consensus size: 94
40192114 AAGCTGACGC
* *
40192124 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCTAATGCATGTCCCAGACATGTC
1 CATGTCCCAGACAAGTCTTACACTAGCTTGTATATCTCGAGGCCAATGCATGTCCCAGACATGTC
40192189 TTACACTAGCTCTCGTCTCAATGGCGATG
66 TTACACTAGCTCTCGTCTCAATGGCGATG
* * * * * *
40192218 CATGTCCTAGTCAAGTCTTACACTGGCTTGTATATTTTGAGGCCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACAAGTCTTACACTAGCTTGTATATCTCGAGGCCAATGCATGTCCCAGACATGTC
*
40192283 TTACACTAGCTCTC--AT-AATGTGGCTGATG
66 TTACACTAGCTCTCGTCTCAA--TGGC-GATG
* *
40192312 CATGTCCCAGGCATGTCTTACACTAGC
1 CATGTCCCAGACAAGTCTTACACTAGC
40192339 ACACATATCA
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
91 2 0.02
92 1 0.01
93 4 0.04
94 98 0.93
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.31
Consensus pattern (94 bp):
CATGTCCCAGACAAGTCTTACACTAGCTTGTATATCTCGAGGCCAATGCATGTCCCAGACATGTC
TTACACTAGCTCTCGTCTCAATGGCGATG
Found at i:40192320 original size:46 final size:47
Alignment explanation
Indices: 40191977--40192338 Score: 223
Period size: 49 Copynumber: 7.7 Consensus size: 47
40191967 CGTCAAAGTC
* * * ** *
40191977 GATGCAATGTCCTAGACAGGTCTTACACTAACTTTTATATATCGAGGCC
1 GATGC-ATGTCCCAGACATGTCTTACACTAGCTTGCATATAT-GAGGCT
* * *
40192026 GATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CATCTATTG-GTG-T
1 GATG-CATGTCCCAGACATGTCTTACACTAGCT-TGCATATA-TGAG-GCT
* * * * *
40192074 CGATGCCATGTCCCAGATAGGTCTTACAAT-GACATACA-ATA--A-GCT
1 -GATG-CATGTCCCAGACATGTCTTACACTAG-CTTGCATATATGAGGCT
* * *
40192119 GACGCCATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCT
1 GATG-CATGTCCCAGACATGTCTTACACTAGCTTGCATATAT-GAGGCT
*
40192168 AATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTC-TCA-AT--GGC-
1 GATGCATGTCCCAGACATGTCTTACACTAGCT-T-G-CAT-ATATGAGGCT
* * * * * * *
40192214 GATGCATGTCCTAGTCAAGTCTTACACTGGCTTGTATATTTTGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTGCATA-TATGAGGCT
*
40192262 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATA-ATGTGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCT-TGCATATATGAGGCT
*
40192308 GATGCATGTCCCAGGCATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
40192339 ACACATATCA
Statistics
Matches: 249, Mismatches: 38, Indels: 55
0.73 0.11 0.16
Matches are distributed among these distances:
43 1 0.00
44 31 0.12
45 6 0.02
46 62 0.25
47 6 0.02
48 65 0.26
49 71 0.29
50 6 0.02
51 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTGCATATATGAGGCT
Found at i:40197131 original size:12 final size:12
Alignment explanation
Indices: 40197114--40197139 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40197104 CTAAAAATGT
40197114 GAAAATCATCAA
1 GAAAATCATCAA
40197126 GAAAATCATCAA
1 GAAAATCATCAA
40197138 GA
1 GA
40197140 TCACTTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (12 bp):
GAAAATCATCAA
Found at i:40200354 original size:18 final size:17
Alignment explanation
Indices: 40200328--40200362 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40200318 ACACCACTAC
40200328 CACTAATCTTCTCTCTTT
1 CACTAATCTTCT-TCTTT
*
40200346 CACTCATCTTCTTCTTT
1 CACTAATCTTCTTCTTT
40200363 TACTTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.51
Consensus pattern (17 bp):
CACTAATCTTCTTCTTT
Found at i:40202317 original size:30 final size:30
Alignment explanation
Indices: 40202283--40202342 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
40202273 CCTTAACTCT
40202283 AACTTTGGAAAAATTACAATTTTGCCCCTA
1 AACTTTGGAAAAATTACAATTTTGCCCCTA
* * * * *
40202313 AACTTTTGCATATTTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACAATTTTGCCCCTA
40202343 GGCTGGGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACAATTTTGCCCCTA
Found at i:40207965 original size:79 final size:78
Alignment explanation
Indices: 40207832--40208050 Score: 276
Period size: 79 Copynumber: 2.8 Consensus size: 78
40207822 GAGTCACATC
* * * * * * *
40207832 TCATGTAACTGTAGTGAATTAGGATTACCTTTTCAAGTCAAATCCTACCCACCTTAAGTTATCAT
1 TCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTTAAATCCTATCCACCTTAAGTTACCAT
*
40207897 AAGGAATCATGTA
66 AAGGAATCATATA
** * *
40207910 TTGTGTAACCGTAGCGAATCAGGATTATCCTTTTCAGGTTAAATGCTATCCACCTTAGGTTACCA
1 TCATGTAACCGTAGCGAATCAGGATTA-CCTTTTCAGGTTAAATCCTATCCACCTTAAGTTACCA
*
40207975 TAATGAATCATATA
65 TAAGGAATCATATA
* * *
40207989 TCATGTAACCATAGCGAATCAAGATTACCCTTTTCAGATTAAATCCTATCCACCTTAAGTTA
1 TCATGTAACCGTAGCGAATCAGGATTA-CCTTTTCAGGTTAAATCCTATCCACCTTAAGTTA
40208051 ACGTAGTGAA
Statistics
Matches: 119, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
78 22 0.18
79 97 0.82
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (78 bp):
TCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTTAAATCCTATCCACCTTAAGTTACCAT
AAGGAATCATATA
Found at i:40208101 original size:40 final size:40
Alignment explanation
Indices: 40208028--40208165 Score: 114
Period size: 40 Copynumber: 3.5 Consensus size: 40
40208018 CTTTTCAGAT
* * * *
40208028 TAAATCCTATCCACCTTAAGTTAACGTAGTGAATCAAGAA
1 TAAATCCTATCCACTTTAAATTAACATAATGAATCAAGAA
* * *
40208068 TAAATCCTATTCACTTTAAATTACCATAATGAATCAGGAA
1 TAAATCCTATCCACTTTAAATTAACATAATGAATCAAGAA
* * * ** ** * *
40208108 CAAATCTTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 TAAATCCTATCCACTTTAAATTAACATAATGAATCAAGAA
**
40208148 CGAATCCTATCCACTTTA
1 TAAATCCTATCCACTTTA
40208166 TATTCTCGAG
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.31
Consensus pattern (40 bp):
TAAATCCTATCCACTTTAAATTAACATAATGAATCAAGAA
Found at i:40209870 original size:28 final size:28
Alignment explanation
Indices: 40209793--40209870 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
40209783 CTTCCTTATA
*
40209793 TATTAAATAATT-TAATAATAAAATATCT
1 TATTAAATAATTATAATAAT-ATATATCT
* *
40209821 TATTAAA-ATATTAAAATAATATTTATCT
1 TATTAAATA-ATTATAATAATATATATCT
40209849 TAATTAAATAATTATAA-AATAT
1 T-ATTAAATAATTATAATAATAT
40209871 CATCAACATC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
27 1 0.02
28 22 0.52
29 18 0.43
30 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
TATTAAATAATTATAATAATATATATCT
Found at i:40216039 original size:46 final size:46
Alignment explanation
Indices: 40215962--40216049 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
40215952 CATTAGATGG
*
40215962 TATGTGAGCCAGTGTAAGACATATCTGGGACATGCATCGGCCGTAT
1 TATGAGAGCCAGTGTAAGACATATCTGGGACATGCATCGGCCGTAT
* *
40216008 TATGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
1 TATGAGAGCCAGTGTAAGACATATCTGGGACATGCATCGGCC
40216050 TTGGGATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (46 bp):
TATGAGAGCCAGTGTAAGACATATCTGGGACATGCATCGGCCGTAT
Found at i:40216081 original size:48 final size:46
Alignment explanation
Indices: 40215972--40216089 Score: 141
Period size: 46 Copynumber: 2.5 Consensus size: 46
40215962 TATGTGAGCC
* * *
40215972 AGTGTAAGACATATCTGGGACATGCATCGGCCGTATTATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCGGATTATGAAAGCT
40216018 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGGGA-TAT-ACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC---GGATTATGA-AAGCT
* *
40216066 AGTGTAAGACCTGTCTGAGACATG
1 AGTGTAAGACATGTCTGGGACATG
40216090 GCGTCAGCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
46 31 0.49
47 1 0.02
48 29 0.46
49 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCGGATTATGAAAGCT
Found at i:40236399 original size:27 final size:27
Alignment explanation
Indices: 40236349--40236443 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 27
40236339 CGAAGTCTAA
* * *
40236349 GTCGGTCA-TTTACCCTACAGGGGTAT
1 GTCGGTAATTTTACACTACAAGGGTAT
*
40236375 GTCGGTCATTTTACACTACAAGGGTAT
1 GTCGGTAATTTTACACTACAAGGGTAT
* **
40236402 TTTTGTAATTTTACACTACAAGGGTAT
1 GTCGGTAATTTTACACTACAAGGGTAT
* *
40236429 TTCGATAATTTTACA
1 GTCGGTAATTTTACA
40236444 AATCAGGGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 8 0.14
27 51 0.86
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (27 bp):
GTCGGTAATTTTACACTACAAGGGTAT
Found at i:40236453 original size:27 final size:27
Alignment explanation
Indices: 40236423--40236867 Score: 298
Period size: 27 Copynumber: 16.6 Consensus size: 27
40236413 TACACTACAA
40236423 GGGTATTTCGATAATTTTACAAATCAG
1 GGGTATTTCGATAATTTTACAAATCAG
* *
40236450 GGGTGTTTTGATAATTTTACAAATC-G
1 GGGTATTTCGATAATTTTACAAATCAG
* * *
40236476 AGGGCATTTCGGTAATTTTACAAAT-TG
1 -GGGTATTTCGATAATTTTACAAATCAG
* *
40236503 AGGTTATTTCGGTAATTTTACAAATCTA-
1 -GGGTATTTCGATAATTTTACAAATC-AG
*
40236531 GGGTATTT-GGTAATTTTACAAATCTA-
1 GGGTATTTCGATAATTTTACAAATC-AG
*
40236557 GGGTATTT-GGTAATTTTACAAATCGAG
1 GGGTATTTCGATAATTTTACAAATC-AG
* *
40236584 GGTGT-TTT-GTTAATTTTACAAATCAA
1 GG-GTATTTCGATAATTTTACAAATCAG
* * *
40236610 GGGTGTTACGATAATTTTACAAAT-TG
1 GGGTATTTCGATAATTTTACAAATCAG
* * * * *
40236636 AGGGTGTTTCGGTAATTTCACAAATTAA
1 -GGGTATTTCGATAATTTTACAAATCAG
40236664 GGGTATTTC-AGTAATTTTACAAATC-G
1 GGGTATTTCGA-TAATTTTACAAATCAG
* *
40236690 AGGGTATTTC-AGTAATTTCACAAATCGG
1 -GGGTATTTCGA-TAATTTTACAAATCAG
* * ** *
40236718 GGGTATTCCGGTACGTTTACAAATCAA
1 GGGTATTTCGATAATTTTACAAATCAG
* * * *
40236745 GAGTATTTC-AGTAATTTCACAATTGA-
1 GGGTATTTCGA-TAATTTTACAAATCAG
* *
40236771 GGGTATTTCGGTAATTTTACAAAT-TG
1 GGGTATTTCGATAATTTTACAAATCAG
*
40236797 AGGGTATTTCAATAATTTTAC-AATC-G
1 -GGGTATTTCGATAATTTTACAAATCAG
* * *
40236823 AAGGTATTTAGGTAATTTTACAAATC-G
1 -GGGTATTTCGATAATTTTACAAATCAG
40236850 AGGGTATTTC-AGTAATTT
1 -GGGTATTTCGA-TAATTT
40236868 CTCTTTATTA
Statistics
Matches: 340, Mismatches: 57, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
25 2 0.01
26 89 0.26
27 246 0.72
28 3 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAATCAG
Found at i:40236465 original size:54 final size:53
Alignment explanation
Indices: 40236401--40236867 Score: 365
Period size: 54 Copynumber: 8.8 Consensus size: 53
40236391 TACAAGGGTA
* * *
40236401 TTTTTG-TAATTTTAC-ACTACAAGGGTATTTCGATAATTTTACAAATCAGGGG
1 TTTTTGATAATTTTACAAAT-CGAGGGTATTTCGGTAATTTTACAAATCAGGGG
* * *
40236453 TGTTTTGATAATTTTACAAATCGAGGGCATTTCGGTAATTTTACAAAT-TGAGG
1 T-TTTTGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCAGGGG
* *
40236506 TTATTTCGGTAATTTTACAAATCTAGGGTATTT-GGTAATTTTACAAATCTA-GGG
1 TT-TTT-GATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATC-AGGGG
* * * * * *
40236560 TATTTGGTAATTTTACAAATCGAGGGTGTTTTGTTAATTTTACAAATCAAGGG
1 TTTTTGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCAGGGG
** * * * * *
40236613 TGTTACGATAATTTTACAAATTGAGGGTGTTTCGGTAATTTCACAAATTAAGGG
1 T-TTTTGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCAGGGG
* * * * *
40236667 TATTTCAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAAATCGGGGG
1 TTTTTGA-TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCAGGGG
** * ** * * * * * *
40236721 TATTCCGGTACGTTTACAAATCAAGAGTATTTCAGTAATTTCACAATTGA-GGG
1 T-TTTTGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCAGGGG
* * * ** *
40236774 TATTTCGGTAATTTTACAAATTGAGGGTATTTCAATAATTTTAC-AATC-GAAGG
1 T-TTTTGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCAG-GGG
* * *
40236827 TATTTAGGTAATTTTACAAATCGAGGGTATTTCAGTAATTT
1 T-TTTTGATAATTTTACAAATCGAGGGTATTTCGGTAATTT
40236868 CTCTTTATTA
Statistics
Matches: 341, Mismatches: 60, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
52 29 0.09
53 130 0.38
54 179 0.52
55 3 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (53 bp):
TTTTTGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCAGGGG
Found at i:40238106 original size:25 final size:25
Alignment explanation
Indices: 40238078--40238156 Score: 97
Period size: 25 Copynumber: 3.1 Consensus size: 25
40238068 GCCTAGCCTC
*
40238078 TTTTAATAATTGGGGCAAAGCCCTT
1 TTTTAATAACTGGGGCAAAGCCCTT
*
40238103 TTTTGATTAACTGGGGCAAAGCCC-T
1 TTTT-AATAACTGGGGCAAAGCCCTT
* *
40238128 TTTCAGTAAACTGGGGCAAAGCCCTT
1 TTTTAAT-AACTGGGGCAAAGCCCTT
40238154 TTT
1 TTT
40238157 GCACTTCCTC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 2 0.04
25 24 0.51
26 21 0.45
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (25 bp):
TTTTAATAACTGGGGCAAAGCCCTT
Found at i:40238121 original size:26 final size:25
Alignment explanation
Indices: 40238088--40238156 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
40238078 TTTTAATAAT
* *
40238088 TGGGGCAAAGCCCTTTTTTGATTAAC
1 TGGGGCAAAGCCCTTTTTAG-TAAAC
*
40238114 TGGGGCAAAGCCCTTTTCAGTAAAC
1 TGGGGCAAAGCCCTTTTTAGTAAAC
40238139 TGGGGCAAAGCCCTTTTT
1 TGGGGCAAAGCCCTTTTT
40238157 GCACTTCCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 21 0.54
26 18 0.46
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (25 bp):
TGGGGCAAAGCCCTTTTTAGTAAAC
Found at i:40238239 original size:11 final size:10
Alignment explanation
Indices: 40238223--40238259 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
40238213 CATCTCATAA
40238223 CATATCATGT
1 CATATCATGT
40238233 GCATATCATGT
1 -CATATCATGT
40238244 CATATCATGT
1 CATATCATGT
40238254 -ATATCA
1 CATATCA
40238260 AAATCTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (10 bp):
CATATCATGT
Found at i:40238247 original size:21 final size:21
Alignment explanation
Indices: 40238203--40238253 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
40238193 TATAACGAAT
* *
40238203 ATATCTTGTGCATCTCATAAC
1 ATATCATGTGCATATCATAAC
**
40238224 ATATCATGTGCATATCATGTC
1 ATATCATGTGCATATCATAAC
40238245 ATATCATGT
1 ATATCATGT
40238254 ATATCAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (21 bp):
ATATCATGTGCATATCATAAC
Found at i:40247928 original size:25 final size:25
Alignment explanation
Indices: 40247900--40247972 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
40247890 CCTCTTTTAA
40247900 TAACTGGGGCAAAGCCCTTTTTGAT
1 TAACTGGGGCAAAGCCCTTTTTGAT
* *
40247925 TAACTGGGGCAAAGCCCTTTTCGGT
1 TAACTGGGGCAAAGCCCTTTTTGAT
* *
40247950 AAACTTGGGCAAAGCCCTTTTTG
1 TAACTGGGGCAAAGCCCTTTTTG
40247973 CACTTCCTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (25 bp):
TAACTGGGGCAAAGCCCTTTTTGAT
Found at i:40248054 original size:11 final size:10
Alignment explanation
Indices: 40248038--40248074 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
40248028 CATCTCATAA
40248038 CATATCATGT
1 CATATCATGT
40248048 GCATATCATGT
1 -CATATCATGT
40248059 CATATCATGT
1 CATATCATGT
40248069 -ATATCA
1 CATATCA
40248075 AAATCTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (10 bp):
CATATCATGT
Found at i:40248062 original size:21 final size:21
Alignment explanation
Indices: 40248004--40248068 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
40247994 ACCCAACCCA
* * *
40248004 TGCATATAATGAATATATCTTG
1 TGCATATCAT-AACATATCATG
*
40248026 TGCATCTCATAACATATCATG
1 TGCATATCATAACATATCATG
**
40248047 TGCATATCATGTCATATCATG
1 TGCATATCATAACATATCATG
40248068 T
1 T
40248069 ATATCAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 28 0.78
22 8 0.22
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
TGCATATCATAACATATCATG
Found at i:40250127 original size:28 final size:28
Alignment explanation
Indices: 40250040--40250128 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 28
40250030 TGGCCCCTTT
*
40250040 AGGCCCAATCTCGTTCATATGGCCCATC
1 AGGCCCAATCTCATTCATATGGCCCATC
* * * * *
40250068 GGGCCTAATCTCATTCACATGGCCTATG
1 AGGCCCAATCTCATTCATATGGCCCATC
* * *
40250096 AGGCCCAATCACATTCATATAGCCCCTC
1 AGGCCCAATCTCATTCATATGGCCCATC
40250124 AGGCC
1 AGGCC
40250129 TAACTACTTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCTCATTCATATGGCCCATC
Found at i:40251646 original size:43 final size:42
Alignment explanation
Indices: 40251555--40251663 Score: 112
Period size: 43 Copynumber: 2.6 Consensus size: 42
40251545 TTTAAGATTA
* * *
40251555 CATGTAAGACCATATCTGGGATATGACATCGATATGAGAATT
1 CATGTAAGACCATAACTGGGATATGACATCGATACGAGAATC
* * * *
40251597 CGTGTAAGGCCATAACTGGGCTATTGGCATCGATACGAG-ATCC
1 CATGTAAGACCATAACTGGGATA-TGACATCGATACGAGAAT-C
* *
40251640 CATGTAAAACCATATCTGGGATAT
1 CATGTAAGACCATAACTGGGATAT
40251664 AGAATTGGTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 22 0.42
43 31 0.58
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (42 bp):
CATGTAAGACCATAACTGGGATATGACATCGATACGAGAATC
Found at i:40255772 original size:47 final size:47
Alignment explanation
Indices: 40255672--40255798 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 47
40255662 ATCGATAAGT
* ** **
40255672 ACCTCTACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGGAGT
1 ACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCAAAAC
* * * * *
40255719 ATCTATACCGTGGCCTGTAGCCAAATCAAGGTAACTTCTCTCAAAAC
1 ACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCAAAAC
* * *
40255766 ACCTATATCATGACCCATAGCCAAATCAAGGTA
1 ACCTATACCATGGCCCGTAGCCAAATCAAGGTA
40255799 TTAGTCGCAC
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (47 bp):
ACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCAAAAC
Found at i:40258162 original size:11 final size:11
Alignment explanation
Indices: 40258146--40258176 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
40258136 CAAAAACATA
40258146 AAAAACGGAGC
1 AAAAACGGAGC
40258157 AAAAACGGAGC
1 AAAAACGGAGC
40258168 AAAAACGGA
1 AAAAACGGA
40258177 CTTACAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.16, G:0.26, T:0.00
Consensus pattern (11 bp):
AAAAACGGAGC
Found at i:40267281 original size:10 final size:10
Alignment explanation
Indices: 40267246--40267281 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
40267236 AATAGACATG
40267246 AAAATAAATA
1 AAAATAAATA
*
40267256 AAAACGAAATA
1 AAAA-TAAATA
40267267 AAAATAAATA
1 AAAATAAATA
40267277 AAAAT
1 AAAAT
40267282 TATACAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (10 bp):
AAAATAAATA
Found at i:40267906 original size:21 final size:21
Alignment explanation
Indices: 40267880--40267927 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
40267870 TTCGAAATAG
*
40267880 TTTAAAAAATTTAAACTTT-G
1 TTTAAAAAATTTAAACTTTCC
* *
40267900 TTTTAAAATTTTAAACTTTCC
1 TTTAAAAAATTTAAACTTTCC
40267921 TTTAAAA
1 TTTAAAA
40267928 CGAATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAAAAAATTTAAACTTTCC
Found at i:40268071 original size:154 final size:153
Alignment explanation
Indices: 40267883--40268292 Score: 452
Period size: 154 Copynumber: 2.7 Consensus size: 153
40267873 GAAATAGTTT
** * *
40267883 AAAAAATTTAAAC-TTTGTTTTAAAATTTTAAACTTTCCTTTAAAACGAATTAAAAAAACGA-AT
1 AAAAAATCAAAACTTTTGTTTTAAAATTTTAAACTTTCCTTTAAAA-TAATTAAAAAAACAAGAT
* *
40267946 TTTTATTTTTCAAAATCTAAACTCTCTCTTTTTAAAAAAAAAAACAAAACACTATTTTTCTTACA
65 TTTTATTTTT-AAAATCTAAACTTTCTCTTTTT-AAAAAAAAAA-AAAACACTATTTTTCATA-A
*
40268011 A-ATTAAAGCTTTTATTTTG-TAGTTGAA
126 AGATT-AAGCTTTTAATTTGATAGTTGAA
* *
40268038 AAAAAAT-AAAA-TTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATAACTAAAAAAAAAAAAAG
1 AAAAAATCAAAACTTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATAA-T--TAAAAAAACAAG
*
40268101 ATTTTTATTTTTTAAAATCTAAACTTTCTCCTTTTT------AAAAAAAATACTATTTTTCATAA
63 ATTTTTA-TTTTTAAAATCTAAACTTTCT-CTTTTTAAAAAAAAAAAAAACACTATTTTTCATAA
*
40268160 AGATTAAGCTTTTAATTTGAAATAGTTGGA
126 AGATTAAGCTTTTAATTTG--ATAGTTGAA
* * *
40268190 AAAAAATCAAAACTTTT-TTTTAAAAATTTAAACTTTCATTTAAAATAACTAAAAAAACAAAGAT
1 AAAAAATCAAAACTTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATAATTAAAAAAAC-AAGAT
* *
40268254 TTTT-TTGTTAAAATCTAAACTTTCTCTTTTTTAAAAAAA
65 TTTTATTTTTAAAATCTAAACTTTCTCTTTTTAAAAAAAA
40268293 TTCAAAAATT
Statistics
Matches: 219, Mismatches: 16, Indels: 41
0.79 0.06 0.15
Matches are distributed among these distances:
148 6 0.03
149 35 0.16
150 26 0.12
151 13 0.06
152 14 0.06
153 35 0.16
154 42 0.19
155 7 0.03
156 8 0.04
157 22 0.10
158 11 0.05
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (153 bp):
AAAAAATCAAAACTTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATAATTAAAAAAACAAGATT
TTTATTTTTAAAATCTAAACTTTCTCTTTTTAAAAAAAAAAAAAACACTATTTTTCATAAAGATT
AAGCTTTTAATTTGATAGTTGAA
Found at i:40268235 original size:153 final size:149
Alignment explanation
Indices: 40267883--40268292 Score: 444
Period size: 149 Copynumber: 2.7 Consensus size: 149
40267873 GAAATAGTTT
* * * * ** *
40267883 AAAAAATTTAAACTTTGTTTTAAAATTTTAAACTTTCCTTT--AA-AACGAATTAAAAAAACGAA
1 AAAAAAATAAAACTTTTTTTTAAAATTTTAAACTTTCCTTTAAAATAACTAAAAAAAAAAAAG-A
* * *
40267945 TTTTTATTTTTCAAAATCTAAACTCTCT-CTTTTTAAAAAAAAAAACAAAACACTATTTTTCTTA
65 TTTTTATTTTTTAAAATCTAAACTTTCTCCTTTTT-------AAAA-AAAACACTATTTTTCATA
*
40268009 CAAATTAAAGCTTTTATTTTGTAGTTGA
122 CAAATTAAAGCTTTTAATTTGTAGTTGA
40268037 AAAAAAATAAAA-TTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATAACTAAAAAAAAAAAAAG
1 AAAAAAATAAAACTTTT-TTTTAAAATTTTAAACTTTCCTTTAAAATAACT-AAAAAAAAAAAAG
*
40268101 ATTTTTATTTTTTAAAATCTAAACTTTCTCCTTTTTAAAAAAAATACTATTTTTCATA-AAGATT
64 ATTTTTATTTTTTAAAATCTAAACTTTCTCCTTTTTAAAAAAAACACTATTTTTCATACAA-ATT
*
40268165 -AAGCTTTTAATTTGAAATAGTTGG
128 AAAGCTTTTAATTTG---TAGTTGA
* * *
40268189 AAAAAAATCAAAACTTTTTTTTAAAAATTTAAACTTTCATTTAAAATAACT-AAAAAAACAAAGA
1 AAAAAAAT-AAAACTTTTTTTTAAAATTTTAAACTTTCCTTTAAAATAACTAAAAAAAAAAAAGA
* *
40268253 -TTTT-TTTGTTAAAATCTAAACTTTCTCTTTTTTAAAAAAA
65 TTTTTATTTTTTAAAATCTAAACTTTCTCCTTTTTAAAAAAA
40268293 TTCAAAAATT
Statistics
Matches: 226, Mismatches: 18, Indels: 29
0.83 0.07 0.11
Matches are distributed among these distances:
149 49 0.22
150 23 0.10
151 16 0.07
152 14 0.06
153 38 0.17
154 38 0.17
156 2 0.01
157 30 0.13
158 16 0.07
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (149 bp):
AAAAAAATAAAACTTTTTTTTAAAATTTTAAACTTTCCTTTAAAATAACTAAAAAAAAAAAAGAT
TTTTATTTTTTAAAATCTAAACTTTCTCCTTTTTAAAAAAAACACTATTTTTCATACAAATTAAA
GCTTTTAATTTGTAGTTGA
Found at i:40269165 original size:15 final size:15
Alignment explanation
Indices: 40269145--40269174 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40269135 AGATGCAATG
40269145 AAAAGTGAATGGACC
1 AAAAGTGAATGGACC
40269160 AAAAGTGAATGGACC
1 AAAAGTGAATGGACC
40269175 TCCACACCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (15 bp):
AAAAGTGAATGGACC
Found at i:40269208 original size:42 final size:42
Alignment explanation
Indices: 40269160--40269452 Score: 417
Period size: 42 Copynumber: 7.0 Consensus size: 42
40269150 TGAATGGACC
*
40269160 AAAAGTGAATGGACCTCCACACCTGGGTCTCTGAATGCAATG
1 AAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAATG
* *
40269202 AAAAGTGAATGGACCTCTACACTTGGGTCTCTAAATGCAATG
1 AAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAATG
** * * *
40269244 AAAAGTGAATGG-CGCTTTACACATAGGTCTCTAAATGAAATG
1 AAAAGTGAATGGAC-CTCCACACCTGGGTCTCTAAATGCAATG
*
40269286 AAAAGTGAATGGACCTCCACACCTAGGTCTCTAAATGCAATG
1 AAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAATG
* *
40269328 AAAAGTGAATAGACCTCCACACCTGGGTCTCTAAATGTAATG
1 AAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAATG
* * * *
40269370 ATAAGTGAATGTACCTCCACACATAGGTCTCTAAATGCAATG
1 AAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAATG
* *
40269412 AAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
1 AAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
40269453 TAATGTTTTC
Statistics
Matches: 223, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
41 1 0.00
42 221 0.99
43 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (42 bp):
AAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAATG
Found at i:40269893 original size:15 final size:13
Alignment explanation
Indices: 40269873--40269908 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
40269863 TTGGTTTCTT
40269873 TATTTTTTCTCTC
1 TATTTTTTCTCTC
40269886 TATTTTTTCTCTC
1 TATTTTTTCTCTC
40269899 TATTTTTTCT
1 TATTTTTTCT
40269909 ATTTAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTTTTCTCTC
Found at i:40274884 original size:28 final size:28
Alignment explanation
Indices: 40274838--40274894 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
40274828 AATCACACTG
40274838 AGTAAAAGGTCTCAAATAGTGGAAGACA
1 AGTAAAAGGTCTCAAATAGTGGAAGACA
* * *
40274866 AGTAAAAGGTCTTAGATAGTGGAGGACA
1 AGTAAAAGGTCTCAAATAGTGGAAGACA
40274894 A
1 A
40274895 ATCAAAGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (28 bp):
AGTAAAAGGTCTCAAATAGTGGAAGACA
Found at i:40274901 original size:28 final size:28
Alignment explanation
Indices: 40274840--40274902 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
40274830 TCACACTGAG
*
40274840 TAAAAGGTCTCAAATAGTGGAAGACAAG
1 TAAAAGGTCTCAAATAGTGGAAGACAAA
* * *
40274868 TAAAAGGTCTTAGATAGTGGAGGACAAA
1 TAAAAGGTCTCAAATAGTGGAAGACAAA
*
40274896 TCAAAGG
1 TAAAAGG
40274903 AGGTTCCACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (28 bp):
TAAAAGGTCTCAAATAGTGGAAGACAAA
Found at i:40276222 original size:21 final size:21
Alignment explanation
Indices: 40276196--40276238 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40276186 GGTTCGCTGT
*
40276196 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
40276217 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
40276238 A
1 A
40276239 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:40276238 original size:16 final size:16
Alignment explanation
Indices: 40276219--40276251 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40276209 TGTATTGGAT
*
40276219 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
40276235 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
40276251 T
1 T
40276252 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:40276296 original size:45 final size:44
Alignment explanation
Indices: 40276230--40276324 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
40276220 GGATTAGAGG
* *
40276230 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
40276275 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
40276319 TGTAAT
1 TGTAAT
40276325 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:40276507 original size:18 final size:17
Alignment explanation
Indices: 40276486--40276520 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40276476 TTATTATTTA
*
40276486 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40276504 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40276521 GGTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40276514 original size:28 final size:27
Alignment explanation
Indices: 40276444--40276516 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
40276434 TTTATTATCA
*
40276444 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
40276472 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
40276499 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
40276517 AAATGGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:40276633 original size:144 final size:147
Alignment explanation
Indices: 40276405--40276676 Score: 469
Period size: 144 Copynumber: 1.9 Consensus size: 147
40276395 ATGATTATTG
40276405 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
40276470 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATGGTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGC
40276535 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
40276554 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
*
40276616 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTA
40276677 ATATTCTTAT
Statistics
Matches: 119, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
144 90 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:40276651 original size:18 final size:17
Alignment explanation
Indices: 40276630--40276664 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40276620 TTATTATTAA
*
40276630 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40276648 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40276665 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40282215 original size:27 final size:27
Alignment explanation
Indices: 40282185--40282362 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40282175 ATATTGAGTC
* * * *
40282185 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40282212 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40282239 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40282267 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40282294 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40282321 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40282348 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40282363 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40282324 original size:82 final size:81
Alignment explanation
Indices: 40282206--40282361 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40282196 TGCTATATAA
* *
40282206 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40282271 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40282288 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40282352 CACTTAGTGC
65 CACTTAGTGC
40282362 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40290406 original size:27 final size:27
Alignment explanation
Indices: 40290376--40290553 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40290366 ATATTGAGTC
* * * *
40290376 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40290403 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40290430 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40290458 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40290485 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40290512 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40290539 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40290554 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40290515 original size:82 final size:81
Alignment explanation
Indices: 40290397--40290552 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40290387 TGCTATATAA
* *
40290397 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40290462 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40290479 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40290543 CACTTAGTGC
65 CACTTAGTGC
40290553 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40294223 original size:32 final size:32
Alignment explanation
Indices: 40294187--40294251 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
40294177 ATTGACTTAA
*
40294187 TGTGGCGAAAATAGAACTGTTCCAGGCTTTAG
1 TGTGGCGAAAAGAGAACTGTTCCAGGCTTTAG
*
40294219 TGTGGCGAAAAGGGAACTGTTCCAGGCTTTAG
1 TGTGGCGAAAAGAGAACTGTTCCAGGCTTTAG
40294251 T
1 T
40294252 ATAAGCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (32 bp):
TGTGGCGAAAAGAGAACTGTTCCAGGCTTTAG
Found at i:40303259 original size:27 final size:27
Alignment explanation
Indices: 40303229--40303313 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 27
40303219 TTGAGTTAAG
*
40303229 TCCGAGTTCGTGAGATTTAACTAGGCA
1 TCCGAGCTCGTGAGATTTAACTAGGCA
*
40303256 TCCGAGCTCGTTGAG--TT---GA-G--
1 TCCGAGCTCG-TGAGATTTAACTAGGCA
* *
40303276 TCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAGCTCGTGAGATTTAACTAGGCA
40303303 TCCGAGCTCGT
1 TCCGAGCTCGT
40303314 TAAGTTGAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
19 4 0.09
20 9 0.21
21 1 0.02
22 1 0.02
23 1 0.02
24 1 0.02
25 1 0.02
26 2 0.05
27 19 0.44
28 4 0.09
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (27 bp):
TCCGAGCTCGTGAGATTTAACTAGGCA
Found at i:40303278 original size:47 final size:47
Alignment explanation
Indices: 40303209--40303333 Score: 214
Period size: 47 Copynumber: 2.7 Consensus size: 47
40303199 ATGGTTGAGT
* * *
40303209 TCCGAACTCGTTGAGTTAAGTCCGAGTTCGTGAGATTTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
40303256 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
*
40303303 TCCGAGCTCGTTAAGTTGAGTCCGAGTTCGT
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGT
40303334 TTATGGCCGG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (47 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:40310070 original size:20 final size:20
Alignment explanation
Indices: 40310045--40310095 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
40310035 AGTTACAGTA
40310045 GTTGACACATATAGTGTCTC
1 GTTGACACATATAGTGTCTC
40310065 GTTGACACATATAGTGTCTC
1 GTTGACACATATAGTGTCTC
* *
40310085 ATCGACACATA
1 GTTGACACATA
40310096 GTCAGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (20 bp):
GTTGACACATATAGTGTCTC
Found at i:40310982 original size:14 final size:15
Alignment explanation
Indices: 40310946--40310982 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
40310936 TTTCTTTTAT
*
40310946 TTATTATAACTATTA
1 TTATTATATCTATTA
40310961 -TATTATATC-ATTA
1 TTATTATATCTATTA
40310974 TTATTATAT
1 TTATTATAT
40310983 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATATCTATTA
Found at i:40310999 original size:21 final size:21
Alignment explanation
Indices: 40310948--40311010 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
40310938 TCTTTTATTT
* *
40310948 ATTATAACTATTATA--TTAT
1 ATTATAATTATTATATTTTAA
* *
40310967 ATCATTATTATTATATTTTAA
1 ATTATAATTATTATATTTTAA
40310988 ATTATAATTATTAT-TTCTTAA
1 ATTATAATTATTATATT-TTAA
40311009 AT
1 AT
40311011 ATTAAGTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 12 0.34
20 2 0.06
21 21 0.60
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATAATTATTATATTTTAA
Found at i:40321542 original size:106 final size:109
Alignment explanation
Indices: 40321360--40321586 Score: 354
Period size: 107 Copynumber: 2.1 Consensus size: 109
40321350 AAAAAAATAC
* * *
40321360 TATTTTTCTTAAAGATTAAAGCTTTTATTTTGAAGTAGTTGAAAAAGAATCAAAATTTTGTTTTA
1 TATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAGAATCAAAACTTTGTTTTA
*
40321425 AAAATTTAAACTTTCCTTTAAAATGA-CTAAAAAAATAGATTTT
66 AAAATTTAAACTTTCCTTTAAAATAATCTAAAAAAATAGATTTT
* *
40321468 TATTTTT-TTAAAGGTTAAATCTTTTACTTTGAAATAGTTGAAAAA-AATCAAAACTTTGTTTTA
1 TATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAGAATCAAAACTTTGTTTTA
*
40321531 AAAATTTAAACTTTCCTTTAAAATAATTTAAAAAAATAGATTTT
66 AAAATTTAAACTTTCCTTTAAAATAATCTAAAAAAATAGATTTT
*
40321575 T-TTTTTGTTAAA
1 TATTTTTCTTAAA
40321587 ATCAAAACTT
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
106 47 0.43
107 56 0.51
108 7 0.06
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.44
Consensus pattern (109 bp):
TATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAGAATCAAAACTTTGTTTTA
AAAATTTAAACTTTCCTTTAAAATAATCTAAAAAAATAGATTTT
Found at i:40321595 original size:53 final size:52
Alignment explanation
Indices: 40321415--40321617 Score: 158
Period size: 52 Copynumber: 3.8 Consensus size: 52
40321405 AGAATCAAAA
* * * * *
40321415 TTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGA-CTAAAAAAATAGATT
1 TTTTTTTTTTAAAATTAAAACTTTCCTTTAAAATAATTTAAAAAAATAGATT
* * * * * * **
40321466 TTTATTTTTTTAAAGGTTAAATCTTTTACTTTGAAATAGTTGAAAAAAATCA-AAA
1 TTT-TTTTTTTAAA-ATTAAAAC-TTTCCTTTAAAATAATTTAAAAAAAT-AGATT
* * * *
40321521 CTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAATTTAAAAAAATAGATT
1 TTTTTTTTTTAAAATTAAAACTTTCCTTTAAAATAATTTAAAAAAATAGATT
* * *
40321573 TTTTTTTTGTTAAAATCAAAACTTTCTCTTTAAAAAAAATTAAAA
1 TTTTTTTT-TTAAAATTAAAACTTTC-CTTTAAAATAATTTAAAA
40321618 CTTTCTCTTT
Statistics
Matches: 112, Mismatches: 32, Indels: 13
0.71 0.20 0.08
Matches are distributed among these distances:
51 4 0.04
52 37 0.33
53 24 0.21
54 35 0.31
55 11 0.10
56 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (52 bp):
TTTTTTTTTTAAAATTAAAACTTTCCTTTAAAATAATTTAAAAAAATAGATT
Found at i:40321611 original size:24 final size:25
Alignment explanation
Indices: 40321584--40321646 Score: 110
Period size: 24 Copynumber: 2.6 Consensus size: 25
40321574 TTTTTTTGTT
40321584 AAAATCAAAACTTTCTCTTT-AAAA
1 AAAATCAAAACTTTCTCTTTAAAAA
*
40321608 AAAATTAAAACTTTCTCTTTAAAAA
1 AAAATCAAAACTTTCTCTTTAAAAA
40321633 AAAATCAAAACTTT
1 AAAATCAAAACTTT
40321647 TCCCAAAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 19 0.53
25 17 0.47
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATCAAAACTTTCTCTTTAAAAA
Found at i:40322948 original size:54 final size:54
Alignment explanation
Indices: 40322866--40322974 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
40322856 CATGGGCTTC
*
40322866 ATCCCATTAGTACTTTAAACAACTTGTATGCTATTCGTACCAATACGAAGGAAA
1 ATCCCATTAGTACTTTAAACAACTTGTATGCAATTCGTACCAATACGAAGGAAA
40322920 ATCCCATTAGTACTTTAAACAACTTGTATGCAATTCGTACCAATACGAAGGAAA
1 ATCCCATTAGTACTTTAAACAACTTGTATGCAATTCGTACCAATACGAAGGAAA
40322974 A
1 A
40322975 CCGTTGGTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (54 bp):
ATCCCATTAGTACTTTAAACAACTTGTATGCAATTCGTACCAATACGAAGGAAA
Found at i:40326477 original size:134 final size:134
Alignment explanation
Indices: 40326237--40326508 Score: 490
Period size: 134 Copynumber: 2.0 Consensus size: 134
40326227 TTTTTTCTTT
* * *
40326237 ACATATACAGTCCTTGCAGAGACAATACTCTTTACTCACTACTTTGTTACTTGTTGACGACTGTG
1 ACATATAAAGTCCTTGCAGAAACAATACTCTTTACTCACTACTTTGTTACTTGTTGACGACTGGG
*
40326302 TACACTTGCACATCATTCAATTACTTTCGGGACAAGTTTTTGACGCTGTTGTTAGGGATTGTGTT
66 TACACTTGCACATCATTCAATTACTTTCAGGACAAGTTTTTGACGCTGTTGTTAGGGATTGTGTT
40326367 TTAA
131 TTAA
* *
40326371 ACATATAAAGTCCTTGCAGAAACGATACTCTTTACTCACTACTTTGTTACTTGTTGATGACTGGG
1 ACATATAAAGTCCTTGCAGAAACAATACTCTTTACTCACTACTTTGTTACTTGTTGACGACTGGG
40326436 TACACTTGCACATCATTCAATTACTTTCAGGACAAGTTTTTGACGCTGTTGTTAGGGATTGTGTT
66 TACACTTGCACATCATTCAATTACTTTCAGGACAAGTTTTTGACGCTGTTGTTAGGGATTGTGTT
40326501 TTAA
131 TTAA
40326505 ACAT
1 ACAT
40326509 TATTTGTGAA
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (134 bp):
ACATATAAAGTCCTTGCAGAAACAATACTCTTTACTCACTACTTTGTTACTTGTTGACGACTGGG
TACACTTGCACATCATTCAATTACTTTCAGGACAAGTTTTTGACGCTGTTGTTAGGGATTGTGTT
TTAA
Found at i:40326689 original size:15 final size:15
Alignment explanation
Indices: 40326669--40326702 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
40326659 GGAGAAGAAA
40326669 ACAAACAACTGTGAG
1 ACAAACAACTGTGAG
40326684 ACAAACAACTGTGAG
1 ACAAACAACTGTGAG
40326699 ACAA
1 ACAA
40326703 TTTGAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.12
Consensus pattern (15 bp):
ACAAACAACTGTGAG
Done.