Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 94 of 143
Found at i:29149730 original size:87 final size:87
Alignment explanation
Indices: 29149567--29149848 Score: 327
Period size: 87 Copynumber: 3.3 Consensus size: 87
29149557 AAAACACTCT
* * * *
29149567 AGTTTGTGAATGAAAC-ACCAGTATTTGCAGAT-AACTTCTAGTAGGTTGTGGATGCACAACATA
1 AGTTTGTGGAT-AAACAACCAATATTTGCAGATAAACTTCCAGTAGGTTGTGAATGCACAACATA
*
29149630 TTTGCAGATAAAAGCTGCTAGTA
65 TTTACAGATAAAAGCTGCTAGTA
* * * * *
29149653 AGTTTGTGGATGAACAACTAATATTTGCAGATAAATTTCCAATAGGTTGTGAATGCTCAACATAT
1 AGTTTGTGGATAAACAACCAATATTTGCAGATAAACTTCCAGTAGGTTGTGAATGCACAACATAT
*
29149718 TTACAAATAAAAGCTGCTAGTA
66 TTACAGATAAAAGCTGCTAGTA
* * * * * * *
29149740 ATTTTGTGTATAAACCACCAGTGTTTGCAGATAAACTGCCAGTAGGTTGTGAGTGCACAACATAT
1 AGTTTGTGGATAAACAACCAATATTTGCAGATAAACTTCCAGTAGGTTGTGAATGCACAACATAT
* *
29149805 TTACAGATAAAAGCTGCCAATA
66 TTACAGATAAAAGCTGCTAGTA
* *
29149827 A-TTTCTTGGATAAACCACCAAT
1 AGTTT-GTGGATAAACAACCAAT
29149849 GTTGCATATT
Statistics
Matches: 164, Mismatches: 29, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
85 3 0.02
86 27 0.16
87 134 0.82
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (87 bp):
AGTTTGTGGATAAACAACCAATATTTGCAGATAAACTTCCAGTAGGTTGTGAATGCACAACATAT
TTACAGATAAAAGCTGCTAGTA
Found at i:29151573 original size:15 final size:16
Alignment explanation
Indices: 29151536--29151577 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
29151526 GTTATAAGAG
29151536 AAGAA-TAATATAATT
1 AAGAATTAATATAATT
*
29151551 AA-ATTTAAT-TAATT
1 AAGAATTAATATAATT
29151565 AAGAATTAATATA
1 AAGAATTAATATA
29151578 CAAATTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.36
15 12 0.55
16 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (16 bp):
AAGAATTAATATAATT
Found at i:29156959 original size:72 final size:72
Alignment explanation
Indices: 29156842--29156984 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 72
29156832 AATGGTGCTA
* * * *
29156842 AGTCCTCTGATCACATTTTTCGCAAGTGCCCTCTTTCCGTAAAAATTTTAGGTTATTTAAATCTT
1 AGTCCTCTGATCACATTTTTCACAAATGCCCTCTGTCCGTAAAAATTTAAGGTTATTTAAATCTT
*
29156907 AGCCATG
66 AACCATG
* *
29156914 AGTCCTCTGATCACATTTTTTACAAATGCCCTGTGTCCGTAAAAATTTAAGGTTATTTAAATCTT
1 AGTCCTCTGATCACATTTTTCACAAATGCCCTCTGTCCGTAAAAATTTAAGGTTATTTAAATCTT
29156979 AACCAT
66 AACCAT
29156985 ATTTTATCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (72 bp):
AGTCCTCTGATCACATTTTTCACAAATGCCCTCTGTCCGTAAAAATTTAAGGTTATTTAAATCTT
AACCATG
Found at i:29158474 original size:35 final size:36
Alignment explanation
Indices: 29158435--29158505 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
29158425 TTAAGTTTGC
29158435 GCTCTCTC-TTTTACATTTTATTTATTTATTGATGT
1 GCTCTCTCTTTTTACATTTTATTTATTTATTGATGT
* *
29158470 GCTCTCTCTTTTTACTTTTTATTTATTTGTTGATGT
1 GCTCTCTCTTTTTACATTTTATTTATTTATTGATGT
29158506 TTATTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 8 0.24
36 25 0.76
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (36 bp):
GCTCTCTCTTTTTACATTTTATTTATTTATTGATGT
Found at i:29160186 original size:3 final size:3
Alignment explanation
Indices: 29160178--29160215 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
29160168 GGATGGATGT
29160178 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
29160216 TTCATGTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:29164005 original size:2 final size:2
Alignment explanation
Indices: 29164000--29164074 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
29163990 TTTTTAAAAA
29164000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
29164042 AT AT AT AT AT AT AT AT AT AC AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29164075 AAGATAAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29177395 original size:40 final size:40
Alignment explanation
Indices: 29177340--29177494 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
29177330 ACGTCAATTC
*
29177340 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAATGAACCT
1 TTATCCTCTTGAAGTTATAGTAAAGCTGGATAATGAACCT
** *
29177380 TTAT-CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATT
1 TTATCCTCT-TGAAGTTATAGTAA-AGCTGGAT-AA---T-GAAC--C---T
*
29177431 CTTATCCTCTTGAAGTTATAGTAAAGCTGGATAACGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGCTGGATAATGAACCT
29177472 TTAT-CTCTCTGAAGTTATAGTAA
1 TTATCCTCT-TGAAGTTATAGTAA
29177495 GAGCAAGATG
Statistics
Matches: 92, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
39 8 0.09
40 36 0.39
41 6 0.07
42 2 0.02
44 1 0.01
45 1 0.01
46 6 0.07
48 1 0.01
50 2 0.02
51 7 0.08
52 18 0.20
53 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (40 bp):
TTATCCTCTTGAAGTTATAGTAAAGCTGGATAATGAACCT
Found at i:29177440 original size:92 final size:92
Alignment explanation
Indices: 29177283--29177784 Score: 887
Period size: 92 Copynumber: 5.5 Consensus size: 92
29177273 AAAAATAGCA
* *
29177283 AACCTTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTTAAACGTCAATTCTTATCCTC
1 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
*
29177348 TTGAAGTTATAGTAAAGTTGGATAATG
66 TTGAAGTTATAGTAAAGTTGGATAACG
29177375 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
1 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
*
29177440 TTGAAGTTATAGTAAAGCTGGATAACG
66 TTGAAGTTATAGTAAAGTTGGATAACG
* *
29177467 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAACTCTTATCCTA
1 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
*
29177532 TTGAAGTTATAGTAAATTTGGATAACG
66 TTGAAGTTATAGTAAAGTTGGATAACG
29177559 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
1 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
*
29177624 TTAAAGTTATAGTAAAGTTGGATAACG
66 TTGAAGTTATAGTAAAGTTGGATAACG
*
29177651 AACCTTTATCTCCCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
1 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
*
29177716 TTGAAGTTATAGTAAAGTTGGATAACA
66 TTGAAGTTATAGTAAAGTTGGATAACG
* * *
29177743 AACCTTTATCTCTCTGAAGTTGTAGTAAGAGAAAGATAAAGC
1 AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
29177785 CTCGACATCA
Statistics
Matches: 391, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 391 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (92 bp):
AACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTC
TTGAAGTTATAGTAAAGTTGGATAACG
Found at i:29177538 original size:52 final size:52
Alignment explanation
Indices: 29177472--29177730 Score: 180
Period size: 52 Copynumber: 5.4 Consensus size: 52
29177462 TAACGAACCT
29177472 TTAT-CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAACTC
1 TTATCCTCT-TGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAACTC
* ** *
29177524 TTATCCTATTGAAGTTATAGT---A--AATTTG--G-AT--AACG--AACCT-
1 TTATCCTCTTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAA-CTC
*
29177564 TTATCTCTC-TGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTC
1 TTATC-CTCTTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAACTC
* * *
29177616 TTATCCTCTTAAAGTTATAGT---A--AAGTTG--G-AT--AACG--AACCT-
1 TTATCCTCTTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAA-CTC
* *
29177656 TTATCTC-CCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTC
1 TTATC-CTCTTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAACTC
29177708 TTATCCTCTTGAAGTTATAGTAA
1 TTATCCTCTTGAAGTTATAGTAA
29177731 AGTTGGATAA
Statistics
Matches: 155, Mismatches: 19, Indels: 66
0.65 0.08 0.28
Matches are distributed among these distances:
40 38 0.25
41 6 0.04
42 8 0.05
43 2 0.01
44 2 0.01
45 11 0.07
47 11 0.07
48 2 0.01
49 2 0.01
50 8 0.05
51 6 0.04
52 56 0.36
53 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (52 bp):
TTATCCTCTTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAACTC
Found at i:29178052 original size:11 final size:11
Alignment explanation
Indices: 29178036--29178096 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
29178026 CAACCAAACC
29178036 ATTTTAAATTT
1 ATTTTAAATTT
*
29178047 ATTTTAAAATTAA
1 ATTTT-AAATT-T
29178060 ATTTATTAAATTT
1 A-TT-TTAAATTT
*
29178073 AAATTTAAATTT
1 -ATTTTAAATTT
*
29178085 AATTTAAATTT
1 ATTTTAAATTT
29178096 A
1 A
29178097 ATAAAATTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 17 0.40
12 13 0.31
13 2 0.05
14 8 0.19
15 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:29178070 original size:26 final size:26
Alignment explanation
Indices: 29178039--29178090 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29178029 CCAAACCATT
*
29178039 TTAAATTT-ATTTTAAAATTAAATTTA
1 TTAAATTTAAATTT-AAATTAAATTTA
*
29178065 TTAAATTTAAATTTAAATTTAATTTA
1 TTAAATTTAAATTTAAATTAAATTTA
29178091 AATTTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAATTTAAATTTAAATTAAATTTA
Found at i:29178074 original size:32 final size:32
Alignment explanation
Indices: 29178038--29178101 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
29178028 ACCAAACCAT
* *
29178038 TTTAAATTT-ATTTTAAAATTAAATTTATTAAA
1 TTTAAATTTAAATTT-AAATTAAATTTAATAAA
*
29178070 TTTAAATTTAAATTTAATTTAAATTTAATAAA
1 TTTAAATTTAAATTTAAATTAAATTTAATAAA
29178102 ATTCCAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TTTAAATTTAAATTTAAATTAAATTTAATAAA
Found at i:29178090 original size:17 final size:17
Alignment explanation
Indices: 29178038--29178098 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
29178028 ACCAAACCAT
*
29178038 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
*
29178055 ATTAAATTT-A-TTAAA
1 TTTAAATTTAATTTAAA
29178070 TTTAAATTTAAATTT-AA
1 TTTAAATTT-AATTTAAA
29178087 TTTAAATTTAAT
1 TTTAAATTTAAT
29178099 AAAATTCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.34
16 3 0.08
17 20 0.53
18 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:29178097 original size:11 final size:11
Alignment explanation
Indices: 29178056--29178098 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
29178046 TATTTTAAAA
29178056 TTAAATTT-A-
1 TTAAATTTAAT
29178065 TTAAATTTAAAT
1 TTAAATTT-AAT
29178077 TTAAATTTAAT
1 TTAAATTTAAT
29178088 TTAAATTTAAT
1 TTAAATTTAAT
29178099 AAAATTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.26
11 15 0.48
12 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:29183992 original size:16 final size:16
Alignment explanation
Indices: 29183971--29184001 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29183961 ATGATTTTTA
*
29183971 TGTTAAAGGACTAAAC
1 TGTTAAAGGAATAAAC
29183987 TGTTAAAGGAATAAA
1 TGTTAAAGGAATAAA
29184002 TTTGTAAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
TGTTAAAGGAATAAAC
Found at i:29193891 original size:6 final size:6
Alignment explanation
Indices: 29193862--29193917 Score: 76
Period size: 6 Copynumber: 8.8 Consensus size: 6
29193852 AGACAGCAAA
*
29193862 CTTCCG CTTCCC TCTTCCC TCTTCCC CTTCCC CTTCCC CTTCCC CTTCCCC
1 CTTCCC CTTCCC -CTTCCC -CTTCCC CTTCCC CTTCCC CTTCCC CTT-CCC
29193913 CTTCC
1 CTTCC
29193918 TTGCTAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 28 0.60
7 19 0.40
ACGTcount: A:0.00, C:0.62, G:0.02, T:0.36
Consensus pattern (6 bp):
CTTCCC
Found at i:29193891 original size:13 final size:12
Alignment explanation
Indices: 29193862--29193917 Score: 76
Period size: 13 Copynumber: 4.4 Consensus size: 12
29193852 AGACAGCAAA
*
29193862 CTTCCGCTTCCC
1 CTTCCCCTTCCC
29193874 TCTTCCCTCTTCCC
1 -CTTCCC-CTTCCC
29193888 CTTCCCCTTCCC
1 CTTCCCCTTCCC
29193900 CTTCCCCTTCCCC
1 CTTCCCCTT-CCC
29193913 CTTCC
1 CTTCC
29193918 TTGCTAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
12 15 0.38
13 19 0.47
14 6 0.15
ACGTcount: A:0.00, C:0.62, G:0.02, T:0.36
Consensus pattern (12 bp):
CTTCCCCTTCCC
Found at i:29195446 original size:26 final size:26
Alignment explanation
Indices: 29195417--29195516 Score: 112
Period size: 26 Copynumber: 3.8 Consensus size: 26
29195407 CAAGCCATTC
*
29195417 CAGAGGTTAGCTCTTACGAGCCTAGA
1 CAGAAGTTAGCTCTTACGAGCCTAGA
* *
29195443 CAG-AGTTAAGCTTTTATGAGCCTAGA
1 CAGAAGTT-AGCTCTTACGAGCCTAGA
* * *
29195469 CAGAAATTAGTTCTTACGAGCCTAAA
1 CAGAAGTTAGCTCTTACGAGCCTAGA
* *
29195495 CAGAATTTAGCTCTTATGAGCC
1 CAGAAGTTAGCTCTTACGAGCC
29195517 CAAAAAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
25 3 0.05
26 55 0.90
27 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (26 bp):
CAGAAGTTAGCTCTTACGAGCCTAGA
Found at i:29195527 original size:26 final size:26
Alignment explanation
Indices: 29195475--29195543 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
29195465 TAGACAGAAA
* * * *
29195475 TTAGTTCTTACGAGCCTAAACAGAAT
1 TTAGCTCTTACGAGCCCAAAAAAAAT
*
29195501 TTAGCTCTTATGAGCCCAAAAAAAAT
1 TTAGCTCTTACGAGCCCAAAAAAAAT
*
29195527 TTAGCTCATACGAGCCC
1 TTAGCTCTTACGAGCCC
29195544 GGATAGAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (26 bp):
TTAGCTCTTACGAGCCCAAAAAAAAT
Found at i:29195539 original size:52 final size:52
Alignment explanation
Indices: 29195423--29195542 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
29195413 ATTCCAGAGG
* * * * * *
29195423 TTAGCTCTTACGAGCCTAGACAGAGTTAAGCTTTTATGAGCCTAGACAGAAA
1 TTAGCTCTTACGAGCCTAAACAGAATTAAGCTCTTATGAGCCCAGAAAAAAA
* *
29195475 TTAGTTCTTACGAGCCTAAACAGAATTTAGCTCTTATGAGCCCA-AAAAAAA
1 TTAGCTCTTACGAGCCTAAACAGAATTAAGCTCTTATGAGCCCAGAAAAAAA
*
29195526 TTTAGCTCATACGAGCC
1 -TTAGCTCTTACGAGCC
29195543 CGGATAGAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 5 0.09
52 52 0.91
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (52 bp):
TTAGCTCTTACGAGCCTAAACAGAATTAAGCTCTTATGAGCCCAGAAAAAAA
Found at i:29199431 original size:15 final size:16
Alignment explanation
Indices: 29199405--29199434 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29199395 CATTTATGAC
29199405 GATATCTATGAAGATG
1 GATATCTATGAAGATG
29199421 GATAT-TATGAAGAT
1 GATATCTATGAAGAT
29199435 TGGGAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (16 bp):
GATATCTATGAAGATG
Found at i:29203407 original size:7 final size:7
Alignment explanation
Indices: 29203397--29203426 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29203387 AAAAATAGTG
29203397 AAAAAGA
1 AAAAAGA
29203404 AAAAAGA
1 AAAAAGA
29203411 AAAAAG-
1 AAAAAGA
29203417 AAAAAGA
1 AAAAAGA
29203424 AAA
1 AAA
29203427 TGAGTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:29203414 original size:13 final size:14
Alignment explanation
Indices: 29203397--29203426 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
29203387 AAAAATAGTG
29203397 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
29203411 AAAAAG-AAAAAGA
1 AAAAAGAAAAAAGA
29203424 AAA
1 AAA
29203427 TGAGTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:29203638 original size:23 final size:24
Alignment explanation
Indices: 29203595--29203639 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29203585 TTCCTAAAAT
29203595 GGAGAAATAAGAAAGGTGAGATAA
1 GGAGAAATAAGAAAGGTGAGATAA
*
29203619 GGAGAAATAAG-GAGGTGAGAT
1 GGAGAAATAAGAAAGGTGAGAT
29203640 GGAATAGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (24 bp):
GGAGAAATAAGAAAGGTGAGATAA
Found at i:29207382 original size:32 final size:32
Alignment explanation
Indices: 29207346--29207423 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
29207336 TTATTTTGTT
* *
29207346 TTGGATTTTGAAATTATTATGTTTAAAGGTTG
1 TTGGATATTGAAATTATTATGTTTAAAGCTTG
* *
29207378 TTGGATATTGAATTTATTATGTTTCAAGCTTG
1 TTGGATATTGAAATTATTATGTTTAAAGCTTG
29207410 TTGGATATTGAAAT
1 TTGGATATTGAAAT
29207424 GATTGACAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (32 bp):
TTGGATATTGAAATTATTATGTTTAAAGCTTG
Found at i:29208394 original size:19 final size:19
Alignment explanation
Indices: 29208370--29208406 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29208360 TGCTTTAATG
*
29208370 TGGTGTATTACTACTTATA
1 TGGTGTAATACTACTTATA
*
29208389 TGGTGTAATACTAGTTAT
1 TGGTGTAATACTACTTAT
29208407 GCACTTGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (19 bp):
TGGTGTAATACTACTTATA
Found at i:29209378 original size:18 final size:20
Alignment explanation
Indices: 29209346--29209397 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
29209336 TATTTTTTTT
*
29209346 AAAAATTATA-AAAA-AACA
1 AAAAATTATATAAAAGAGCA
* *
29209364 TAAACTTATATAAAAGAGCA
1 AAAAATTATATAAAAGAGCA
29209384 AAAAATTATATAAA
1 AAAAATTATATAAA
29209398 TTATTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 8 0.30
19 4 0.15
20 15 0.56
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (20 bp):
AAAAATTATATAAAAGAGCA
Found at i:29209521 original size:19 final size:19
Alignment explanation
Indices: 29209496--29209547 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
29209486 AAAATTGTAA
29209496 AAAATATTTAAAAAA-TA-
1 AAAATATTTAAAAAATTAC
* *
29209513 TAAATATATAAAAAAATTAC
1 AAAATAT-TTAAAAAATTAC
29209533 AAAATATTATAAAAA
1 AAAATATT-TAAAAA
29209548 TCATACAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 6 0.22
18 7 0.26
19 3 0.11
20 11 0.41
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATATTTAAAAAATTAC
Found at i:29209526 original size:39 final size:38
Alignment explanation
Indices: 29209481--29209578 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 38
29209471 GTTATGAAAA
29209481 ATAAAAAAATTGTAAAAAATATT-TAAAAAAT-ATA-AATAT
1 ATAAAAAAA-T-TAAAAAATATTAT-AAAAATCATACAAT-T
*
29209520 ATAAAAAAATTACAAAATATTATAAAAATCATACAATT
1 ATAAAAAAATTAAAAAATATTATAAAAATCATACAATT
* *
29209558 ATAAAACAACTTAAAATATAT
1 ATAAAA-AAATTAAAAAATAT
29209579 GAAAAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
37 16 0.31
38 12 0.24
39 23 0.45
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (38 bp):
ATAAAAAAATTAAAAAATATTATAAAAATCATACAATT
Found at i:29209537 original size:37 final size:40
Alignment explanation
Indices: 29209481--29209563 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 40
29209471 GTTATGAAAA
29209481 ATAAAAAAATTGTAAAAAATATT-TAAAAAAT-ATA-AATAT
1 ATAAAAAAATTGTAAAAAATATTAT-AAAAATCATACAAT-T
*
29209520 ATAAAAAAA-T-TACAAAATATTATAAAAATCATACAATT
1 ATAAAAAAATTGTAAAAAATATTATAAAAATCATACAATT
29209558 ATAAAA
1 ATAAAA
29209564 CAACTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
37 16 0.40
38 12 0.30
39 12 0.30
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (40 bp):
ATAAAAAAATTGTAAAAAATATTATAAAAATCATACAATT
Found at i:29209539 original size:18 final size:18
Alignment explanation
Indices: 29209421--29209563 Score: 53
Period size: 18 Copynumber: 7.8 Consensus size: 18
29209411 GTAAAAAGCA
* *
29209421 ATAAAAATATTAAAATAAC
1 ATAAAAATA-TAAAAAAAT
* *
29209440 A-AAAAATTTAAAAATCAT
1 ATAAAAATATAAAAA-AAT
* **
29209458 AT-AAAATAT-AAGAGTT
1 ATAAAAATATAAAAAAAT
*
29209474 ATGAAAAATA-AAAAAATT
1 AT-AAAAATATAAAAAAAT
* *
29209492 GTAAAAAATATTTAAAAAAT
1 AT-AAAAATA-TAAAAAAAT
*
29209512 ATAAATATATAAAAAAAT
1 ATAAAAATATAAAAAAAT
*
29209530 -TACAAAATATTATAAAAAT
1 ATA-AAAATA-TAAAAAAAT
* *
29209549 CATACAATTATAAAA
1 -ATAAAAATATAAAA
29209564 CAACTTAAAA
Statistics
Matches: 91, Mismatches: 22, Indels: 22
0.67 0.16 0.16
Matches are distributed among these distances:
16 3 0.03
17 10 0.11
18 46 0.51
19 19 0.21
20 11 0.12
21 2 0.02
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
ATAAAAATATAAAAAAAT
Found at i:29209548 original size:19 final size:18
Alignment explanation
Indices: 29209495--29209548 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
29209485 AAAAATTGTA
*
29209495 AAAAATATT-TAAAAAAT
1 AAAAATATTATAAAAATT
* *
29209512 ATAAATATATAAAAAAATT
1 AAAAATAT-TATAAAAATT
29209531 ACAAAATATTATAAAAAT
1 A-AAAATATTATAAAAAT
29209549 CATACAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.24
18 1 0.03
19 15 0.52
20 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATATTATAAAAATT
Found at i:29209574 original size:37 final size:37
Alignment explanation
Indices: 29209481--29209592 Score: 99
Period size: 37 Copynumber: 3.0 Consensus size: 37
29209471 GTTATGAAAA
29209481 ATAAAAAAATTGTAAAAAATATT-TAAAAAATATAAATAT
1 ATAAAAAAA-T-T-AAAAATATTATAAAAAATATAAATAT
29209520 ATAAAAAAATTACAAAATATTAT-AAAAATCATACAAT-T
1 ATAAAAAAATTA-AAAATATTATAAAAAAT-ATA-AATAT
* * *
29209558 ATAAAACAACTT-AAAATA-TATGAAAAATATTAATA
1 ATAAAA-AAATTAAAAATATTATAAAAAATATAAATA
29209593 AAACATTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 17
0.77 0.02 0.20
Matches are distributed among these distances:
35 3 0.05
36 6 0.09
37 27 0.42
38 12 0.19
39 16 0.25
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (37 bp):
ATAAAAAAATTAAAAATATTATAAAAAATATAAATAT
Found at i:29209819 original size:24 final size:24
Alignment explanation
Indices: 29209791--29209876 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 24
29209781 GATATCTTTT
29209791 TAATTTTTTTTTTGTAATTTTATA
1 TAATTTTTTTTTTGTAATTTTATA
29209815 TAATTTTCCTATTTTTGT-ATTTTAT-
1 TAATTTT--T-TTTTTGTAATTTTATA
*
29209840 TATTTTCAATTTTTTTTGTAATTTTATA
1 TA-ATT---TTTTTTTTGTAATTTTATA
*
29209868 TAAATTTTT
1 TAATTTTTT
29209877 ATAAACTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
24 11 0.22
25 2 0.04
26 17 0.34
27 16 0.32
28 2 0.04
29 2 0.04
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (24 bp):
TAATTTTTTTTTTGTAATTTTATA
Found at i:29209829 original size:26 final size:28
Alignment explanation
Indices: 29209799--29209875 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 28
29209789 TTTAATTTTT
29209799 TTTTTGTAATTTTATATAATTTTC-CTA
1 TTTTTGTAATTTTATATAATTTTCACTA
* *
29209826 TTTTTGT-ATTTTAT-T-ATTTTCAATTT
1 TTTTTGTAATTTTATATAATTTTC-ACTA
29209852 TTTTTGTAATTTTATATAAATTTT
1 TTTTTGTAATTTTATAT-AATTTT
29209876 TATAAACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 6 0.14
25 1 0.02
26 15 0.36
27 14 0.33
28 1 0.02
30 5 0.12
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (28 bp):
TTTTTGTAATTTTATATAATTTTCACTA
Found at i:29209927 original size:18 final size:18
Alignment explanation
Indices: 29209906--29210010 Score: 58
Period size: 18 Copynumber: 5.8 Consensus size: 18
29209896 ACTTTTCTAT
29209906 ATTTTTAA-AATTTTTACA
1 ATTTTTAATAATTTTT-CA
**
29209924 ATTTTTTAA-AAAATTTCA
1 A-TTTTTAATAATTTTTCA
* * *
29209942 TAATTGTAATTATTTTTCA
1 -ATTTTTAATAATTTTTCA
*
29209961 ATTTTTAATAATTTTTATA
1 ATTTTTAATAATTTTT-CA
* *
29209980 ATTTAT-ATTA-TTTTC-
1 ATTTTTAATAATTTTTCA
29209995 ATTTTGTAATAATTTT
1 ATTTT-TAATAATTTT
29210011 AATAATTCTT
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
15 4 0.06
16 1 0.02
17 7 0.11
18 27 0.42
19 25 0.39
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTTTTAATAATTTTTCA
Found at i:29209994 original size:35 final size:36
Alignment explanation
Indices: 29209915--29210017 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 36
29209905 TATTTTTAAA
* * *
29209915 ATTTTTACAATTTTTTAAAAAATTTCATAATTGTAATT
1 ATTTTT-CAA-TTTTTAATAATTTTAATAATTGTAATT
*
29209953 ATTTTTCAATTTTTAATAATTTTTATAATT-TATATT
1 ATTTTTCAATTTTTAATAATTTTAATAATTGTA-ATT
29209989 A-TTTTC-ATTTTGTAATAATTTTAATAATT
1 ATTTTTCAATTTT-TAATAATTTTAATAATT
29210018 CTTTTTTCGC
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
34 5 0.08
35 23 0.39
36 22 0.37
37 3 0.05
38 6 0.10
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (36 bp):
ATTTTTCAATTTTTAATAATTTTAATAATTGTAATT
Found at i:29212803 original size:120 final size:120
Alignment explanation
Indices: 29212585--29212830 Score: 483
Period size: 120 Copynumber: 2.0 Consensus size: 120
29212575 ATTTCGTATT
*
29212585 GAATTTAAAATGCAACCCTCGGACATATAGTTTAAAAAATTCAAATATGGAATACCCGTTTACTT
1 GAATCTAAAATGCAACCCTCGGACATATAGTTTAAAAAATTCAAATATGGAATACCCGTTTACTT
29212650 CGATTTTCGCAGAGAATTAAAATCGTGTCCAACGCGTTAGAACACGATGTTCTCG
66 CGATTTTCGCAGAGAATTAAAATCGTGTCCAACGCGTTAGAACACGATGTTCTCG
29212705 GAATCTAAAATGCAACCCTCGGACATATAGTTTAAAAAATTCAAATATGGAATACCCGTTTACTT
1 GAATCTAAAATGCAACCCTCGGACATATAGTTTAAAAAATTCAAATATGGAATACCCGTTTACTT
29212770 CGATTTTCGCAGAGAATTAAAATCGTGTCCAACGCGTTAGAACACGATGTTCTCG
66 CGATTTTCGCAGAGAATTAAAATCGTGTCCAACGCGTTAGAACACGATGTTCTCG
29212825 GAATCT
1 GAATCT
29212831 CGGAGTTAAC
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 125 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (120 bp):
GAATCTAAAATGCAACCCTCGGACATATAGTTTAAAAAATTCAAATATGGAATACCCGTTTACTT
CGATTTTCGCAGAGAATTAAAATCGTGTCCAACGCGTTAGAACACGATGTTCTCG
Found at i:29213358 original size:30 final size:28
Alignment explanation
Indices: 29213197--29213355 Score: 133
Period size: 29 Copynumber: 5.5 Consensus size: 28
29213187 CTTGATGGCA
** * *
29213197 AAAATGTAATTTCGGGAAAATTTGGGGTT
1 AAAATGTAATTT-TAGAAAGTTTAGGGTT
* *
29213226 AAAATGGAATTTTAGAAAGTTTAGGGGT
1 AAAATGTAATTTTAGAAAGTTTAGGGTT
*
29213254 AAAATGGTAATTTTGGGTGAAA--TTAGGGTT
1 AAAAT-GTAATTTT---AGAAAGTTTAGGGTT
* *
29213284 AAAAATGGAATTTTAGAAAGTTTAGGGGT
1 -AAAATGTAATTTTAGAAAGTTTAGGGTT
* *
29213313 AAAATGGTAATTTTTGGAAGTTTTAGGGTT
1 AAAAT-GTAATTTTAGAAAG-TTTAGGGTT
29213343 AAAATGTAATTTT
1 AAAATGTAATTTT
29213356 TTGAATTTTT
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
27 4 0.04
28 21 0.20
29 44 0.42
30 27 0.26
31 5 0.05
32 4 0.04
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTAGAAAGTTTAGGGTT
Found at i:29213886 original size:2 final size:2
Alignment explanation
Indices: 29213876--29213924 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
29213866 AATAAAAAAA
* * *
29213876 TC TC CC TC TC TC TC TC TC TC TC TC TC TC AC CC TC TC -C TC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29213916 TC T- TC TC TC
1 TC TC TC TC TC
29213925 ATTGGCTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.02, C:0.53, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:29222465 original size:59 final size:59
Alignment explanation
Indices: 29222127--29222512 Score: 506
Period size: 59 Copynumber: 6.6 Consensus size: 59
29222117 ATTTTGGGAA
* * * ** * **
29222127 AAAAATGGGATTTTGGAAGGTTCGGGGGTAAAATAATAATTTTTAGTGAAATTGGGGCC
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
* * * * * *
29222186 AAAAAT-GAGATTTTGGAAAGCTCGGGGGTAAAATTGTAATTTTTGGTAAAATCGAGGTT
1 AAAAATGGA-ATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
* * *
29222245 AAAAATGAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATTGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
* * *
29222304 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAACGGTAATTTTTGGTGAAACTGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
* *
29222363 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATTGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
* * *
29222422 AAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
* *
29222481 -AAAATGGAATTTTAGAAAGTTCGGGGGTAAAA
1 AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAA
29222513 ATATGATTTT
Statistics
Matches: 292, Mismatches: 33, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
58 30 0.10
59 261 0.89
60 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (59 bp):
AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT
Found at i:29222507 original size:29 final size:28
Alignment explanation
Indices: 29222187--29222512 Score: 176
Period size: 30 Copynumber: 11.1 Consensus size: 28
29222177 ATTGGGGCCA
* *
29222187 AAAAT-GAGATTTTGGAAAGCTCGGGGGT
1 AAAATGGA-ATTTTGGAAAGTTCGGGGTT
* * *
29222215 AAAATTGTAATTTTTGGTAAA-ATCGAGGTT
1 AAAA-TGGAA-TTTTGG-AAAGTTCGGGGTT
* *
29222245 AAAAATGAAATTTTGGAAAGTTTAGGGG-T
1 -AAAATGGAATTTTGGAAAG-TTCGGGGTT
29222274 AAAATGGTAATTTTTGATGAAA-TT-GGGGTT
1 AAAATGG-AA-TTTTG--GAAAGTTCGGGGTT
*
29222304 AAAAATGGAATTTTGGAAAGTTTAGGGG-T
1 -AAAATGGAATTTTGGAAAG-TTCGGGGTT
* *
29222333 AAAACGGTAATTTTTGGTGAAA-CT-GGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTCGGGGTT
*
29222363 AAAAATGGAATTTTGGAAAGTTTAGGGG-T
1 -AAAATGGAATTTTGGAAAG-TTCGGGGTT
29222392 AAAATGGTAATTTTGGGTGAAA-TT-GGGGTT
1 AAAATGG-AATTTT--G-GAAAGTTCGGGGTT
*
29222422 AAAAATGGAATTTTGGAAAGTTCAAGGG-T
1 -AAAATGGAATTTTGGAAAGTTC-GGGGTT
29222451 AAAATGGTAATTTTGGGTGAAA--TCGGGGTT
1 AAAATGG-AATTTT--G-GAAAGTTCGGGGTT
* *
29222481 AAAATGGAATTTTAGAAAGTTCGGGGGT
1 AAAATGGAATTTTGGAAAGTTCGGGGTT
29222509 AAAA
1 AAAA
29222513 ATATGATTTT
Statistics
Matches: 240, Mismatches: 17, Indels: 82
0.71 0.05 0.24
Matches are distributed among these distances:
26 4 0.02
27 12 0.05
28 48 0.20
29 61 0.25
30 69 0.29
31 30 0.12
32 16 0.07
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTCGGGGTT
Found at i:29224499 original size:6 final size:6
Alignment explanation
Indices: 29224490--29224566 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
29224480 TTGAATTTGA
* * *
29224490 TTAAAT TTAAAT CTAAA- ATAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
** *
29224538 ACAAAT TTAAAA TT-AAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
29224567 AGCCCAAGCC
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
5 11 0.20
6 32 0.59
7 6 0.11
8 5 0.09
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:29224511 original size:17 final size:16
Alignment explanation
Indices: 29224491--29224553 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
29224481 TGAATTTGAT
29224491 TAAATTTAAATCTAAAA
1 TAAATTTAAAT-TAAAA
*
29224508 TAAATTTAAA-T-AAG
1 TAAATTTAAATTAAAA
29224522 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTAAAA
*
29224539 CAAATTTAAAATTAA
1 TAAATTT-AAATTAA
29224554 TTTAAACTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 12 0.31
15 1 0.03
16 1 0.03
17 22 0.56
18 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAATTTAAATTAAAA
Found at i:29224517 original size:11 final size:11
Alignment explanation
Indices: 29224497--29224559 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
29224487 TGATTAAATT
*
29224497 TAAATCTAAAA
1 TAAATTTAAAA
29224508 TAAATTT-AAA
1 TAAATTTAAAA
* *
29224518 T-AA-GTAAATT
1 TAAATTTAAA-A
29224528 TAAATTTAAAA
1 TAAATTTAAAA
*
29224539 CAAATTTAAAA
1 TAAATTTAAAA
*
29224550 TTAATTTAAA
1 TAAATTTAAA
29224560 CTTTAAAAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
8 1 0.03
9 4 0.10
10 5 0.12
11 26 0.65
12 4 0.10
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:29225097 original size:24 final size:24
Alignment explanation
Indices: 29225036--29225100 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
29225026 TGAGAAATAA
* *
29225036 TATTTCAATCAAACTCTGTTTATT
1 TATTTGAATCAAACTCTATTTATT
* * *
29225060 TGTTTTAATTAAACTCTATTTATT
1 TATTTGAATCAAACTCTATTTATT
*
29225084 TATTTGAGTCAAACTCT
1 TATTTGAATCAAACTCT
29225101 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (24 bp):
TATTTGAATCAAACTCTATTTATT
Found at i:29226828 original size:116 final size:117
Alignment explanation
Indices: 29226671--29226913 Score: 461
Period size: 116 Copynumber: 2.1 Consensus size: 117
29226661 TAAGACTAAC
*
29226671 GCTCTATCCCGCTGAGCTACGGGAGTCGCCGACTGTTTAAAACAAATTCTGATTTATTGGCTTAA
1 GCTCTAACCCGCTGAGCTACGGGAGTCGCCGACTGTTTAAAACAAATTCTGATTTATTGGCTTAA
29226736 AAAAGGTCTAAGAATTAAAAAGATTTTATGGGCTTTGGGTGGTCCCTGCGGG
66 AAAAGGTCTAAGAATTAAAAAGATTTTATGGGCTTTGGGTGGTCCCTGCGGG
29226788 GCTCTAACCCGCTGAGCTAC-GGAGTCGCCGACTGTTTAAAACAAATTCTGATTTATTGGCTTAA
1 GCTCTAACCCGCTGAGCTACGGGAGTCGCCGACTGTTTAAAACAAATTCTGATTTATTGGCTTAA
29226852 AAAAGGTCTAAGAATTAAAAAGATTTTATGGGCTTTGGGTGGTCCCTGCGGG
66 AAAAGGTCTAAGAATTAAAAAGATTTTATGGGCTTTGGGTGGTCCCTGCGGG
*
29226904 GCTCGAACCC
1 GCTCTAACCC
29226914 ACGACCTTCG
Statistics
Matches: 124, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
116 105 0.85
117 19 0.15
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (117 bp):
GCTCTAACCCGCTGAGCTACGGGAGTCGCCGACTGTTTAAAACAAATTCTGATTTATTGGCTTAA
AAAAGGTCTAAGAATTAAAAAGATTTTATGGGCTTTGGGTGGTCCCTGCGGG
Found at i:29227508 original size:29 final size:29
Alignment explanation
Indices: 29227449--29227508 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
29227439 TATAGTTTAA
* * *
29227449 TGTGCAATTGTATACATGAACTTTGGTTT
1 TGTGCAATTGTATACATAAAATTTGGATT
* * *
29227478 TGTGTAATTTTATACATAAAATTTTGATT
1 TGTGCAATTGTATACATAAAATTTGGATT
29227507 TG
1 TG
29227509 ATCCAATTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (29 bp):
TGTGCAATTGTATACATAAAATTTGGATT
Found at i:29236564 original size:31 final size:30
Alignment explanation
Indices: 29236529--29236596 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
29236519 TTGTTAATCC
*
29236529 GTGATTGTTTTGTTACTTTTTGATAACGTT-A
1 GTGATTGTTTTGTTACTTTTTCA-AA-GTTGA
*
29236560 GTGATAGTTTTGTTACTTTTTCAAAGTTGA
1 GTGATTGTTTTGTTACTTTTTCAAAGTTGA
29236590 GTGATTG
1 GTGATTG
29236597 AAATGAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 9 0.27
31 21 0.64
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (30 bp):
GTGATTGTTTTGTTACTTTTTCAAAGTTGA
Found at i:29250488 original size:78 final size:77
Alignment explanation
Indices: 29250389--29252322 Score: 1555
Period size: 78 Copynumber: 24.6 Consensus size: 77
29250379 TTAATCAGAA
* **
29250389 GGCAGATTGAAGACA-CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACACCAATCTCT
1 GGCAGATTGAAG-CATCCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGACACACCAATCTCT
29250453 TACCCCGATCATAG
64 TACCCCGATCATAG
* * * *
29250467 GGCAAATTAAAGCACCCAATCTTTTACCCTAATCAGAAGGCAGATTGAAGACACACCAATCTCTT
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCTT
*
29250532 ACCCCGATCATTG
65 ACCCCGATCATAG
* * * * * *
29250545 GGCAAATTGAAGCATCCGATCTTTTACCCTAATCAGAAGGTAGATTGAAGACATAACAATCTCTT
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCTT
* * *
29250610 ACCTCAATCATGG
65 ACCCCGATCATAG
* * * * * *
29250623 GGCAGATTGAAGCATCCAATTTTTTTACCCTAATCAGAAGGTAGATTGAAG-CA-TCTAATCTTT
1 GGCAGATTGAAGCATCCAA-TCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCT
** *
29250686 TACCCTAATCAAAG
64 TACCCCGATCATAG
* * ** * *
29250700 GGCAAATTGAAGACA-CAGTAATCTTTTACCCCGATCATGGGGCA-ATTGAAG-CA-TCTAATCT
1 GGCAGATTGAAG-CATC--CAATCTTTTACCCTAATCA-GGGGCAGATTGAAGACACACCAATCT
* ** * *
29250761 TTTACCCTAATTAGAG
62 CTTACCCCGATCATAG
* * * * * * * *
29250777 GGTAGATTGAAGACACACCAATCTCTTACCCTAATCATGTGGTAGATTGAAG-CA-TCCGATCTT
1 GGCAGATTGAAG-CA-TCCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGACACACCAATCTC
** *
29250840 TTACCCTAATCAGAG
63 TTACCCCGATCATAG
* ** * * *
29250855 GGTAGATTGAAGACATACCAATCTTTTACCCCGATCATAGGGCAGATTGAAG-CA-TCCAATCTT
1 GGCAGATTGAAG-CAT-CCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGACACACCAATCTC
** * *
29250918 TTACCCTAATTAGAG
63 TTACCCCGATCATAG
* * * * * * * *
29250933 GGTAGATTAAAGACATACCAATCTCTTACCTTGATCATAGGGCAGATTGAA-ACA-TCCAATCTT
1 GGCAGATTGAAG-CAT-CCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGACACACCAATCTC
** *
29250996 TTACCCTAATCAGAG
63 TTACCCCGATCATAG
* * * * * * **** *
29251011 GGCAAATTAAAGACACACCAATCTCTTACCCCAATCATGGGGTAGATTGAAG-CA-TTTGATCTT
1 GGCAGATTGAAG-CA-TCCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGACACACCAATCTC
** *
29251074 TTACCCTAATCAGAG
63 TTACCCCGATCATAG
* * * **
29251089 GGCAGATTGAAGACACACCAATCTCTTACCC-AGATCATGGGGCAGATTGAAG-CA-TCTGATCT
1 GGCAGATTGAAG-CA-TCCAATCTTTTACCCTA-ATCA-GGGGCAGATTGAAGACACACCAATCT
* ** *
29251151 TTTACCCTAATCAGAG
62 CTTACCCCGATCATAG
* * ** * *
29251167 GGCAAATTGAAGACATACCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACACACTAATCTC
1 GGCAGATTGAAG-CAT-CCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGACACACCAATCTC
29251232 TTACCCCGATCATAG
63 TTACCCCGATCATAG
* * * * *
29251247 GACAAATTGAAGCATCCAATCTTTTACCCTAATTAGAAGGCAAATTGAAGACACACCAATCTCTT
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCTT
29251312 ACCCCGATCATAG
65 ACCCCGATCATAG
* * * ** * **
29251325 AGTAGATTGAAGCATCCGATCTTTTACCCTAATCAAAAGGTAGATTGAAGACACAGTAATCTCTT
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATC-AGGGGCAGATTGAAGACACACCAATCTCTT
29251390 ACCCCGATCATAG
65 ACCCCGATCATAG
* * * * *
29251403 GGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGATACAGCAATCTCTC
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCTT
*
29251468 ACCCCGATCATGG
65 ACCCCGATCATAG
* * ** * **
29251481 GGCAGATTGAAGCATTCAATATTTTACCCTAATCAGAAAGTAGATTGAAGACACAATAATCTCTT
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCTT
*
29251546 ACCCTGATCAT-G
65 ACCCCGATCATAG
* * * * **
29251558 AAGCAGATTGAAGCATCTAATCTTTTACCCTAATTAGAGGGCAAATTGAAGACACAATAATCTCT
1 -GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCT
29251623 TACCCCGATCAT-G
64 TACCCCGATCATAG
** * *
29251636 AGGCAGATTGAAGCATTTAATCTTTTACCCTAATTAGAGGGCAAATTGAAGACACACCAATCTCT
1 -GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCT
* *
29251701 TACTCGGATCAT-G
64 TACCCCGATCATAG
* * *
29251714 AGGCAGATTGAAGCATCCGATCTTTTACCCTAATCAGAAGGTAGATTGAAGACACACCAATCTCT
1 -GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCT
** *
29251779 TACCTTGATCATGG
64 TACCCCGATCATAG
* * * *
29251793 GGTAGATTAAAGCATCCAATCTTTTGCCCTAATCAAAGGGCAGATTGAAGACACACCAATCTCTT
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATC-AGGGGCAGATTGAAGACACACCAATCTCTT
29251858 ACCCCGATCAT-G
65 ACCCCGATCATAG
* *
29251870 AGGTAGATTGAAGCATCCGATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACACCAATCTCT
1 -GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCT
*
29251935 TACCCTGATCAT-G
64 TACCCCGATCATAG
* * * ** * *
29251948 GAGCAGATTGAAGTATTCGATCTTTTACCCTAATCAGAGCCCAAATTGAAAACACACCAATCTCT
1 G-GCAGATTGAAGCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAGACACACCAATCTCT
*
29252013 TACCCCGATCATGG
64 TACCCCGATCATAG
* * *
29252027 GGCAGATTGAAGCACCCAATCTTTTACCCTAATCAAAGGGTAGATTGAAGACACACCAATCTCTT
1 GGCAGATTGAAGCATCCAATCTTTTACCCTAATC-AGGGGCAGATTGAAGACACACCAATCTCTT
* *
29252092 ACCACGATCATGG
65 ACCCCGATCATAG
* * *
29252105 GGCAGATTGAAGCATCCGAA-CTTTTACCCTAATCATGGGGCAAATTAAAAACATCATCCAATCT
1 GGCAGATTGAAGCATCC-AATCTTTTACCCTAATCA-GGGGCAGATTGAAGACA-CA-CCAATCT
*
29252169 CTTATCCCGATCAT-G
62 CTTACCCCGATCATAG
* * * *
29252184 GAGCATATTGCAGTCATCCAAT-TTCTTACCC-AGATCATGAGGCAGATTAAAGACATCATCCAA
1 G-GCAGATTGAAG-CATCCAATCTT-TTACCCTA-ATCA-GGGGCAGATTGAAGACA-CA-CCAA
*
29252247 TCTCTTACCCCGATCATGG
59 TCTCTTACCCCGATCATAG
29252266 GGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAAAGGGGCAGATTGAAG
1 GGCAGATTGAAG----CATCCAATCTTTTA-CCCTAATC---AGGGGCAGATTGAAG
29252323 CCATCTTCTC
Statistics
Matches: 1601, Mismatches: 206, Indels: 89
0.84 0.11 0.05
Matches are distributed among these distances:
77 102 0.06
78 1288 0.80
79 51 0.03
80 62 0.04
81 63 0.04
82 2 0.00
84 11 0.01
85 8 0.00
86 1 0.00
87 12 0.01
88 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (77 bp):
GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGGGGCAGATTGAAGACACACCAATCTCTTA
CCCCGATCATAG
Found at i:29252183 original size:42 final size:40
Alignment explanation
Indices: 29251989--29252298 Score: 169
Period size: 42 Copynumber: 7.8 Consensus size: 40
29251979 AATCAGAGCC
29251989 CAAATTGAAAACA-CA-CCAATCTCTTACCCCGATCATGGGG
1 CAAATT-AAAACATCATCCAATCTCTTA-CCCGATCATGGGG
* * * * * **
29252029 CAGATTGAAGCA-C--CCAATCTTTTACCCTAATCAAAGGG
1 CAAATTAAAACATCATCCAATCTCTTACCC-GATCATGGGG
* * *
29252067 TAGATTGAAGACA-CA-CCAATCTCTTACCACGATCATGGGG
1 CAAATT-AAAACATCATCCAATCTCTTACC-CGATCATGGGG
* * * * * *
29252107 CAGATTGAAGCATC--CGAA-CTTTTACCCTAATCATGGGG
1 CAAATTAAAACATCATCCAATCTCTTACCC-GATCATGGGG
*
29252145 CAAATTAAAAACATCATCCAATCTCTTATCCCGATCATGGAG
1 CAAATT-AAAACATCATCCAATCTCTTA-CCCGATCATGGGG
* * * *
29252187 CATATT---GCAGTCATCCAATTTCTTACCCAGATCATGAGG
1 CAAATTAAAACA-TCATCCAATCTCTTACCC-GATCATGGGG
*
29252226 CAGATTAAAGACATCATCCAATCTCTTACCCCGATCATGGGG
1 CAAATTAAA-ACATCATCCAATCTCTTA-CCCGATCATGGGG
* ** * *
29252268 CAGATTGAAGCCACCATCCAATCTTTTACCC
1 CAAATT-AAAACATCATCCAATCTCTTACCC
29252299 CTAATCAAAA
Statistics
Matches: 209, Mismatches: 42, Indels: 37
0.73 0.15 0.13
Matches are distributed among these distances:
37 4 0.02
38 48 0.23
39 48 0.23
40 30 0.14
41 7 0.03
42 62 0.30
43 10 0.05
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (40 bp):
CAAATTAAAACATCATCCAATCTCTTACCCGATCATGGGG
Found at i:29252205 original size:39 final size:38
Alignment explanation
Indices: 29251848--29252298 Score: 162
Period size: 38 Copynumber: 11.4 Consensus size: 38
29251838 TGAAGACACA
* *
29251848 CCAATCTCTTACCCCGATCAT-GAGGTAGATTGA-AGCAT
1 CCAATCTCTTA-CCCGATCATGGA-GCAGATTGACATCAT
* * * *
29251886 CCGATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACA-CA-
1 CCAATCTCTTACCC-GATCATG-GAGCAGATT---GACATCAT
29251926 CCAATCTCTTACCCTGATCATGGAGCAGATTGA-AGT-AT
1 CCAATCTCTTACCC-GATCATGGAGCAGATTGACA-TCAT
* * * * * * * *
29251964 TCGATCTTTTACCCTAATCA--GAGCCCAAATTGAAAACACA
1 CCAATCTCTTACCC-GATCATGGAG--CAGATTGACATCA-T
* * *
29252004 CCAATCTCTTACCCCGATCATGGGGCAGATTGA-AGCAC
1 CCAATCTCTTA-CCCGATCATGGAGCAGATTGACATCAT
* * * *
29252042 CCAATCTTTTACCCTAATCAAAGG-GTAGATTGAAGACA-CA-
1 CCAATCTCTTACCC-GATC-ATGGAGCAGATT---GACATCAT
* *
29252082 CCAATCTCTTACCACGATCATGGGGCAGATTGA-AGCAT
1 CCAATCTCTTACC-CGATCATGGAGCAGATTGACATCAT
* * * * *
29252120 CCGAA-CTTTTACCCTAATCATGGGGCAAATTAAAAACATCAT
1 CC-AATCTCTTACCC-GATCATGGAGCAGATT---GACATCAT
*
29252162 CCAATCTCTTATCCCGATCATGGAGCATATTG-CAGTCAT
1 CCAATCTCTTA-CCCGATCATGGAGCAGATTGACA-TCAT
*
29252201 CCAATTTCTTACCCAGATCAT-GAGGCAGATTAAAGACATCAT
1 CCAATCTCTTACCC-GATCATGGA-GCAGATT---GACATCAT
* *
29252243 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCACCAT
1 CCAATCTCTTA-CCCGATCATGGAGCAGATTG-A--CATCAT
*
29252285 CCAATCTTTTACCC
1 CCAATCTCTTACCC
29252299 CTAATCAAAA
Statistics
Matches: 316, Mismatches: 48, Indels: 95
0.69 0.10 0.21
Matches are distributed among these distances:
36 5 0.02
37 14 0.04
38 91 0.29
39 41 0.13
40 66 0.21
41 19 0.06
42 71 0.22
43 9 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (38 bp):
CCAATCTCTTACCCGATCATGGAGCAGATTGACATCAT
Found at i:29252325 original size:45 final size:42
Alignment explanation
Indices: 29250389--29252325 Score: 341
Period size: 40 Copynumber: 49.4 Consensus size: 42
29250379 TTAATCAGAA
* *
29250389 GGCAGATTGAAG--A-CA-CCAATCTCTTACCCCGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* *
29250427 GGCAGATTGAAGACA-CA-CCAATCTCTTACCCCGATCATA-G
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCA-AGG
* * * * *
29250467 GGCAAATTAAAG-CA-C--CCAATCTTTTACCCTAATC-AGAA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * **
29250505 GGCAGATTGAAGACA-CA-CCAATCTCTTACCCCGATCATTG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * *
29250545 GGCAAATTGAAG----CATCCGATCTTTTACCCTAATC-AGAA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * * *
29250583 GGTAGATTGAAG--A-CATAACAATCTCTTACCTCAATCATGG
1 GGCAGATTGAAGCCACCAT-CCAATCTCTTACCCCAATCAAGG
* * * *
29250623 GGCAGATTGAAG----CATCCAATTTTTTTACCCTAATC-AGAA
1 GGCAGATTGAAGCCACCATCCAA-TCTCTTACCCCAATCAAG-G
* * * * *
29250662 GGTAGATTGAAG----CATCTAATCTTTTACCCTAATCAAAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * *
29250700 GGCAAATTGAAGACA-CAGT--AATCTTTTACCCCGATCATGG
1 GGCAGATTGAAGCCACCA-TCCAATCTCTTACCCCAATCAAGG
* * * *
29250740 GGCA-ATTGAAG----CATCTAATCTTTTACCCTAAT-TAGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * * * *
29250777 GGTAGATTGAAGACA-CA-CCAATCTCTTACCCTAATCATGT
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * *
29250817 GGTAGATTGAAG----CATCCGATCTTTTACCCTAATC-AGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * *
29250855 GGTAGATTGAAG--A-CATACCAATCTTTTACCCCGATCATA-G
1 GGCAGATTGAAGCCACCAT-CCAATCTCTTACCCCAATCA-AGG
* * *
29250895 GGCAGATTGAAG----CATCCAATCTTTTACCCTAAT-TAGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * ***
29250933 GGTAGATTAAAG--A-CATACCAATCTCTTACCTTGATCATA-G
1 GGCAGATTGAAGCCACCAT-CCAATCTCTTACCCCAATCA-AGG
* *
29250973 GGCAGATTGAA---A-CATCCAATCTTTTACCCTAATC-AGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * * *
29251011 GGCAAATTAAAGACA-CA-CCAATCTCTTACCCCAATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* *** * *
29251051 GGTAGATTGAAG----CATTTGATCTTTTACCCTAATC-AGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* *
29251089 GGCAGATTGAAGACA-CA-CCAATCTCTTA-CCCAGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCA-ATCAAGG
** * *
29251129 GGCAGATTGAAG----CATCTGATCTTTTACCCTAATC-AGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* *
29251167 GGCAAATTGAAG--A-CATACCAATCTCTTACCCCGATCATA-G
1 GGCAGATTGAAGCCACCAT-CCAATCTCTTACCCCAATCA-AGG
* * *
29251207 GGCAGATTGAAGACA-CA-CTAATCTCTTACCCCGATCATA-G
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCA-AGG
* * * * * *
29251247 GACAAATTGAAG----CATCCAATCTTTTACCCTAAT-TAGAA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * *
29251285 GGCAAATTGAAGACA-CA-CCAATCTCTTACCCCGATCATA-G
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCA-AGG
* * * * * **
29251325 AGTAGATTGAAG----CATCCGATCTTTTACCCTAATCAAAA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * *
29251363 GGTAGATTGAAGACA-CAGT--AATCTCTTACCCCGATCATA-G
1 GGCAGATTGAAGCCACCA-TCCAATCTCTTACCCCAATCA-AGG
* * *
29251403 GGTAGATTGAAG----CATCCAATCTTTTACCCTAATC-AGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* ** * * * *
29251441 GGCAAATTGAAGATA-CA-GCAATCTCTCACCCCGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * *
29251481 GGCAGATTGAAG----CATTCAATATTTTACCCTAATC-AGAA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * * * ** * *
29251519 AGTAGATTGAAGACACAAT--AATCTCTTACCCTGATCATGA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * *
29251559 AGCAGATTGAAG----CATCTAATCTTTTACCCTAAT-TAGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * * * * *
29251597 GGCAAATTGAAGACACAAT--AATCTCTTACCCCGATCATGA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
** * * *
29251637 GGCAGATTGAAG----CATTTAATCTTTTACCCTAAT-TAGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * * ** * *
29251675 GGCAAATTGAAGACA-CA-CCAATCTCTTACTCGGATCATGA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * *
29251715 GGCAGATTGAAG----CATCCGATCTTTTACCCTAATC-AGAA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* * *** *
29251753 GGTAGATTGAAGACA-CA-CCAATCTCTTACCTTGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * * *
29251793 GGTAGATT-AA---AGCATCCAATCTTTTGCCCTAATCAAAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * *
29251831 GGCAGATTGAAGACA-CA-CCAATCTCTTACCCCGATCATGA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * *
29251871 GGTAGATTGAAG----CATCCGATCTTTTACCCTAATC-AGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
* ** *
29251909 GGCAGATTGAAGACA-CA-CCAATCTCTTACCCTGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * * *
29251949 AGCAGATTGAAG----TATTCGATCTTTTACCCTAATC-AGAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAG-G
** * ** * *
29251987 CCCAAATTGAAAACA-CA-CCAATCTCTTACCCCGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * *
29252027 GGCAGATTGAAG-CA-C--CCAATCTTTTACCCTAATCAAAG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * *
29252065 GGTAGATTGAAGACA-CA-CCAATCTCTTACCACGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * *
29252105 GGCAGATTGAAG----CATCCGAA-CTTTTACCCTAATCATGG
1 GGCAGATTGAAGCCACCATCC-AATCTCTTACCCCAATCAAGG
* * ** * * * *
29252143 GGCAAATTAAAAACATCATCCAATCTCTTATCCCGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
* * * * * * *
29252185 AGCATATTGCAG---TCATCCAATTTCTTA-CCCAGATCATGA
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCA-ATCAAGG
* * * * *
29252224 GGCAGATTAAAGACATCATCCAATCTCTTACCCCGATCATGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
*
29252266 GGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAAAGG
1 GGCAGATTGAAGCCACCATCCAATCTCTTACCCC-AATC--AAGG
29252311 GGCAGATTGAAGCCA
1 GGCAGATTGAAGCCA
29252326 TCTTCTCACA
Statistics
Matches: 1438, Mismatches: 313, Indels: 289
0.70 0.15 0.14
Matches are distributed among these distances:
35 1 0.00
36 14 0.01
37 53 0.04
38 534 0.37
39 110 0.08
40 574 0.40
41 38 0.03
42 90 0.06
43 6 0.00
45 18 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (42 bp):
GGCAGATTGAAGCCACCATCCAATCTCTTACCCCAATCAAGG
Found at i:29255852 original size:31 final size:30
Alignment explanation
Indices: 29255796--29255936 Score: 135
Period size: 31 Copynumber: 4.5 Consensus size: 30
29255786 TATATCAAAA
*
29255796 ATTAAATTATTTTATAATTTATATATCATTAT
1 ATTAAATTA-TTTA-AATTTTTATATCATTAT
29255828 ATTAAATTATTTAAATATTTTATATATCATTAT
1 ATTAAATTATTT-AA-ATTTT-TATATCATTAT
29255861 ATTAAATTATTTAAATGTCATTTAT-T-ATTAT
1 ATTAAATTATTTAAAT-T--TTTATATCATTAT
* * *
29255892 ATCAAATTATTTAAATTTTAATTATTATTAT
1 ATTAAATTATTTAAATTTTTA-TATCATTAT
*
29255923 ATTAACTT-TTTAAA
1 ATTAAATTATTTAAA
29255937 AATATTTTAT
Statistics
Matches: 95, Mismatches: 5, Indels: 20
0.79 0.04 0.17
Matches are distributed among these distances:
28 3 0.03
29 1 0.01
30 8 0.08
31 37 0.39
32 18 0.19
33 26 0.27
34 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.55
Consensus pattern (30 bp):
ATTAAATTATTTAAATTTTTATATCATTAT
Found at i:29255855 original size:33 final size:33
Alignment explanation
Indices: 29255796--29255953 Score: 168
Period size: 33 Copynumber: 4.9 Consensus size: 33
29255786 TATATCAAAA
* *
29255796 ATTAAATTATTT-TATAATTTATATATCATTAT
1 ATTAAATTATTTAAATATTTTATATATCATTAT
29255828 ATTAAATTATTTAAATATTTTATATATCATTAT
1 ATTAAATTATTTAAATATTTTATATATCATTAT
* *
29255861 ATTAAATTATTTAAATGTCATT-TAT-T-ATTAT
1 ATTAAATTATTTAAATAT-TTTATATATCATTAT
* * *
29255892 ATCAAATTATTTAAAT-TTTAAT-TATTATTAT
1 ATTAAATTATTTAAATATTTTATATATCATTAT
*
29255923 ATTAACTT-TTTAAAAATATTTTATATATCAT
1 ATTAAATTATTT--AAATATTTTATATATCAT
29255954 AAAATTTTAC
Statistics
Matches: 106, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.02
30 6 0.06
31 31 0.29
32 17 0.16
33 43 0.41
34 7 0.07
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (33 bp):
ATTAAATTATTTAAATATTTTATATATCATTAT
Found at i:29255873 original size:24 final size:24
Alignment explanation
Indices: 29255833--29255887 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
29255823 ATTATATTAA
*
29255833 ATTAT-TTAAATATTTTATATATC
1 ATTATATTAAATATTTTAAATATC
*
29255856 ATTATATTAAAT-TATTTAAATGTC
1 ATTATATTAAATAT-TTTAAATATC
29255880 ATT-TATTA
1 ATTATATTA
29255888 TTATATCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTATATTAAATATTTTAAATATC
Found at i:29255891 original size:64 final size:61
Alignment explanation
Indices: 29255796--29255936 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 61
29255786 TATATCAAAA
* * *
29255796 ATTAAATTATTTTATAATTTATATATCATTATATTAAATTATTTAAATATTTTATATATCATTAT
1 ATTAAATTA-TTTA-AATTCATATATCATTATATCAAATTATTTAAAT-TTTAAT-TATCATTAT
* * *
29255861 ATTAAATTATTTAAATGTCATTTATTATTATATCAAATTATTTAAATTTTAATTATTATTAT
1 ATTAAATTATTTAAAT-TCATATATCATTATATCAAATTATTTAAATTTTAATTATCATTAT
*
29255923 ATTAACTT-TTTAAA
1 ATTAAATTATTTAAA
29255937 AATATTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
61 6 0.09
62 15 0.22
63 8 0.12
64 30 0.44
65 9 0.13
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.55
Consensus pattern (61 bp):
ATTAAATTATTTAAATTCATATATCATTATATCAAATTATTTAAATTTTAATTATCATTAT
Found at i:29256744 original size:29 final size:30
Alignment explanation
Indices: 29256708--29256773 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 30
29256698 AATATAAAAA
*
29256708 ATTATATTTAATACAATAAAATATTTATTAT
1 ATTAT-TTTAATACAATAAAATACTTATTAT
*
29256739 ATTATTTTTTAATATAATAAAATACTTATTAT
1 ATTA--TTTTAATACAATAAAATACTTATTAT
29256771 ATT
1 ATT
29256774 TATGGTAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 4 0.13
32 26 0.84
33 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTATTTTAATACAATAAAATACTTATTAT
Found at i:29257567 original size:13 final size:13
Alignment explanation
Indices: 29257549--29257583 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
29257539 TTCGAGCATT
29257549 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
29257562 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
29257575 TGTGTGTGC
1 TGTGTGTGC
29257584 GTTATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.09, G:0.46, T:0.34
Consensus pattern (13 bp):
TGTGTGTGCAAGG
Found at i:29258568 original size:21 final size:21
Alignment explanation
Indices: 29258544--29258597 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
29258534 CTTGAGACAA
29258544 TTCTACCGATACAAGT-ATGAC
1 TTCTACCGATACAAGTCATG-C
* * *
29258565 TTCTACCAAAACATGTCATGC
1 TTCTACCGATACAAGTCATGC
29258586 TTCTACCGATAC
1 TTCTACCGATAC
29258598 TAAAAATTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:29259752 original size:195 final size:194
Alignment explanation
Indices: 29259348--29259795 Score: 544
Period size: 195 Copynumber: 2.3 Consensus size: 194
29259338 TACCAGTACT
* * * *
29259348 CGATGCTGCTCACATGAGCTGTCGAGGACTCACAACGTTTGCGGTACCCCAGCCATCGATACAGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCGATACAGT
* * * *
29259413 GCCTGTCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTATCGAGAGTATGCATA
66 ACCTG-CTGCACTATAAACTGTTCCCTAACAATGCTGCTCACACGAGCTATCGAGAATATGCATA
* * *
29259478 AAGCATAGTCCCAGCCATCGTAGGGCCTACAATCCATTTAGGATCCATTTCTCTTTTCCAAGTCA
130 AAGCATAATCCCAGCCATCGTAGGCCCTACAATCCATTTAGGATCCATTTCTCTTTTCCAACTCA
* * *
29259543 CGGTGTTGCTCACACGAGCTGTCGAGGACTCACAACATATGCGGTATCTCAGCCATCGATAC-GA
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCGATACAG-
* *
29259607 TATCTG-TGCA-TA-AAACTGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCACT
65 TACCTGCTGCACTATAAACTGTTCCCTAACAATGCTGCTCACACGAGCTATCGAGAATATGCA-T
* * * ** * * * ***
29259669 TATGCATAAATCTCAGCCATCGTAGGCCCTGTAATCCATTCTTGGATTCTTTTCTCATTTTTTGA
129 AAAGCAT-AATCCCAGCCATCGTAGGCCCTACAATCCATT-TAGGATCCATTTCTC-TTTTCCAA
29259734 CTCA
191 CTCA
* * *
29259738 CGATGCTACTCACACGAGTTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCG
29259796 CGTCGGTTTC
Statistics
Matches: 215, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
191 45 0.21
192 8 0.04
193 30 0.14
194 13 0.06
195 119 0.55
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (194 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCGATACAGT
ACCTGCTGCACTATAAACTGTTCCCTAACAATGCTGCTCACACGAGCTATCGAGAATATGCATAA
AGCATAATCCCAGCCATCGTAGGCCCTACAATCCATTTAGGATCCATTTCTCTTTTCCAACTCA
Found at i:29264414 original size:20 final size:20
Alignment explanation
Indices: 29264389--29264426 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29264379 CCGCAGTCAC
29264389 TTAGCATTGTTAATTGCACA
1 TTAGCATTGTTAATTGCACA
29264409 TTAGCATTGTTAATTGCA
1 TTAGCATTGTTAATTGCA
29264427 GAAAGCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
TTAGCATTGTTAATTGCACA
Found at i:29266784 original size:1 final size:1
Alignment explanation
Indices: 29266778--29266804 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
29266768 ACGGTATTGT
29266778 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
29266805 GGGGGACGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29271635 original size:7 final size:7
Alignment explanation
Indices: 29271625--29271760 Score: 64
Period size: 7 Copynumber: 19.3 Consensus size: 7
29271615 ATGTATAGAA
*
29271625 TTTAGGG
1 TTTAAGG
29271632 TTTAAGG
1 TTTAAGG
29271639 TTTTAA-G
1 -TTTAAGG
* *
29271646 TCTAAGA
1 TTTAAGG
*
29271653 TTTAAAG
1 TTTAAGG
29271660 TTTAAGG
1 TTTAAGG
29271667 TTTCAA-G
1 TTT-AAGG
*
29271674 TTTAGGG
1 TTTAAGG
*
29271681 TTTAGGG
1 TTTAAGG
29271688 TTTCAA-G
1 TTT-AAGG
* *
29271695 TCTAAAG
1 TTTAAGG
29271702 TTTAAGG
1 TTTAAGG
* *
29271709 TTTATGA
1 TTTAAGG
29271716 TTCTAA-G
1 TT-TAAGG
**
29271723 TTTTGGG
1 TTTAAGG
*
29271730 TTTTAGGG
1 -TTTAAGG
*
29271738 TTTAAGT
1 TTTAAGG
*
29271745 TTTAGGG
1 TTTAAGG
29271752 TTTAAGG
1 TTTAAGG
29271759 TT
1 TT
29271761 ATGAAATTTA
Statistics
Matches: 96, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
6 8 0.08
7 72 0.75
8 16 0.17
ACGTcount: A:0.25, C:0.04, G:0.26, T:0.46
Consensus pattern (7 bp):
TTTAAGG
Found at i:29271655 original size:28 final size:28
Alignment explanation
Indices: 29271624--29271690 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
29271614 CATGTATAGA
*
29271624 ATTTAGGGTTTAAGGTTTTAAGTCTAAG
1 ATTTAGGGTTTAAGGTTTCAAGTCTAAG
** * *
29271652 ATTTAAAGTTTAAGGTTTCAAGTTTAGG
1 ATTTAGGGTTTAAGGTTTCAAGTCTAAG
*
29271680 GTTTAGGGTTT
1 ATTTAGGGTTT
29271691 CAAGTCTAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.25, T:0.45
Consensus pattern (28 bp):
ATTTAGGGTTTAAGGTTTCAAGTCTAAG
Found at i:29271674 original size:14 final size:14
Alignment explanation
Indices: 29271631--29271712 Score: 76
Period size: 14 Copynumber: 5.9 Consensus size: 14
29271621 AGAATTTAGG
*
29271631 GTTTAAGGTTTTAA
1 GTTTAAGGTTTAAA
* *
29271645 GTCTAAGATTTAAA
1 GTTTAAGGTTTAAA
*
29271659 GTTTAAGGTTTCAA
1 GTTTAAGGTTTAAA
* **
29271673 GTTTAGGGTTTAGG
1 GTTTAAGGTTTAAA
*
29271687 GTTTCAA-GTCTAAA
1 GTTT-AAGGTTTAAA
29271701 GTTTAAGGTTTA
1 GTTTAAGGTTTA
29271713 TGATTCTAAG
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
13 2 0.04
14 48 0.94
15 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (14 bp):
GTTTAAGGTTTAAA
Found at i:29271677 original size:21 final size:21
Alignment explanation
Indices: 29271653--29271711 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
29271643 AAGTCTAAGA
29271653 TTTAAAGTTTAAGGTTTCAAG
1 TTTAAAGTTTAAGGTTTCAAG
** *
29271674 TTTAGGGTTTAGGGTTTCAAG
1 TTTAAAGTTTAAGGTTTCAAG
*
29271695 TCTAAAGTTTAAGGTTT
1 TTTAAAGTTTAAGGTTT
29271712 ATGATTCTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (21 bp):
TTTAAAGTTTAAGGTTTCAAG
Found at i:29271681 original size:49 final size:49
Alignment explanation
Indices: 29271625--29271744 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 49
29271615 ATGTATAGAA
*
29271625 TTTAGGGTTTAAGGTTTTAAGTCT-AAGATTTAAAGTTTAAGGTTTC-AAG
1 TTTAGGGTTTAAGGTTTTAAGTCTAAAG-TTTAAAGTTT-AGGATTCTAAG
* * * *
29271674 TTTAGGGTTTAGGGTTTCAAGTCTAAAGTTTAAGGTTTATGATTCTAAG
1 TTTAGGGTTTAAGGTTTTAAGTCTAAAGTTTAAAGTTTAGGATTCTAAG
* * *
29271723 TTTTGGGTTTTAGGGTTTAAGT
1 TTTAGGGTTTAAGGTTTTAAGT
29271745 TTTAGGGTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 5 0.08
49 51 0.86
50 3 0.05
ACGTcount: A:0.26, C:0.04, G:0.25, T:0.45
Consensus pattern (49 bp):
TTTAGGGTTTAAGGTTTTAAGTCTAAAGTTTAAAGTTTAGGATTCTAAG
Found at i:29271998 original size:21 final size:21
Alignment explanation
Indices: 29271972--29272016 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29271962 TAGGGTCCAT
29271972 TTGCCCCAGAGGAGTAAAGTA
1 TTGCCCCAGAGGAGTAAAGTA
** *
29271993 TTGCCCGGGAGGAGTAGAGTA
1 TTGCCCCAGAGGAGTAAAGTA
29272014 TTG
1 TTG
29272017 TGGTGGCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.36, T:0.22
Consensus pattern (21 bp):
TTGCCCCAGAGGAGTAAAGTA
Found at i:29272073 original size:45 final size:45
Alignment explanation
Indices: 29272009--29272100 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
29271999 GGGAGGAGTA
* *
29272009 GAGTATTGTGGTGGCTCGTCAAACTGAGACTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGACTGATATCCTTAGCTT
*
29272054 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTAGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGACTGATATCCTTAGCTT
29272099 GA
1 GA
29272101 TGAGCTATGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTGAGACTGATATCCTTAGCTT
Found at i:29273928 original size:47 final size:47
Alignment explanation
Indices: 29273877--29273966 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
29273867 AATACATAAG
* *
29273877 TTTACCAATATAATACAAAA-ATAATAATTAAATACCAAAATGGATTA
1 TTTACCAAAATAATACAAAATAT-ATAATTAAATAACAAAATGGATTA
* * * *
29273924 TTTACTAAAATGATACAAAATATATATTTATATAACAAAATGG
1 TTTACCAAAATAATACAAAATATATAATTAAATAACAAAATGG
29273967 TATCCATACA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
47 34 0.94
48 2 0.06
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (47 bp):
TTTACCAAAATAATACAAAATATATAATTAAATAACAAAATGGATTA
Found at i:29274069 original size:16 final size:15
Alignment explanation
Indices: 29274048--29274097 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
29274038 TGATGGAGAT
29274048 ATTATTTTGGTAATTA
1 ATTATTTT-GTAATTA
*
29274064 ATTATTTTTTATATT-
1 ATTATTTTGTA-ATTA
29274079 A-TATTTTTGTAATTA
1 ATTA-TTTTGTAATTA
29274094 ATTA
1 ATTA
29274098 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 5 0.18
15 10 0.36
16 13 0.46
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTATTTTGTAATTA
Found at i:29274093 original size:14 final size:15
Alignment explanation
Indices: 29274047--29274093 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
29274037 GTGATGGAGA
*
29274047 TATTATTTTGGTAAT
1 TATTATTTTTGTAAT
29274062 TAATTATTTTT-TATAT
1 T-ATTATTTTTGTA-AT
29274078 TA-TATTTTTGTAAT
1 TATTATTTTTGTAAT
29274092 TA
1 TA
29274094 ATTAGCTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 11 0.39
15 6 0.21
16 11 0.39
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TATTATTTTTGTAAT
Found at i:29274834 original size:20 final size:21
Alignment explanation
Indices: 29274809--29274851 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29274799 TACTTACTAC
29274809 TACTAA-TAACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
29274829 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
29274850 TA
1 TA
29274852 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:29275969 original size:19 final size:18
Alignment explanation
Indices: 29275937--29275972 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29275927 ATCGCTTTAA
*
29275937 ATATAATATTTAAAAAAT
1 ATATAATATATAAAAAAT
29275955 ATATATATATATAAAAAA
1 ATATA-ATATATAAAAAA
29275973 GTAGTTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATAATATATAAAAAAT
Found at i:29276548 original size:23 final size:21
Alignment explanation
Indices: 29276502--29276549 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 21
29276492 TGGGTTTAAA
29276502 TAATTAATTAAAAAATTAATTT
1 TAATTAATTAAAAAA-TAATTT
29276524 TAATTATATTAAATAAA-AATATT
1 TAATTA-ATTAAA-AAATAAT-TT
29276547 TAA
1 TAA
29276550 ATATGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 9 0.39
23 11 0.48
24 3 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTAATTAAAAAATAATTT
Found at i:29277205 original size:16 final size:15
Alignment explanation
Indices: 29277177--29277215 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
29277167 TAAATAATTA
29277177 AAACAACACACAAAAT
1 AAACAA-ACACAAAAT
*
29277193 AAAGCAAACACAATAT
1 AAA-CAAACACAAAAT
29277209 AAACAAA
1 AAACAAA
29277216 AGGATTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 14 0.67
17 3 0.14
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.08
Consensus pattern (15 bp):
AAACAAACACAAAAT
Found at i:29277468 original size:2 final size:2
Alignment explanation
Indices: 29277461--29277487 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29277451 CAATATCTTT
29277461 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29277488 TTTAAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29279243 original size:14 final size:13
Alignment explanation
Indices: 29279186--29279244 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 13
29279176 TACAATGTTA
*
29279186 ATATATTACTTAT
1 ATATAATACTTAT
*
29279199 ATATAAT-TTTAT
1 ATATAATACTTAT
29279211 ATA-AATA-TTAT
1 ATATAATACTTAT
*
29279222 -TTTAATACTTAT
1 ATATAATACTTAT
29279234 AATATAATACT
1 -ATATAATACT
29279245 AAATTTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 1 0.03
11 11 0.30
12 11 0.30
13 6 0.16
14 8 0.22
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATAATACTTAT
Found at i:29283528 original size:22 final size:22
Alignment explanation
Indices: 29283491--29283556 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
29283481 AAGGTCAAAG
*
29283491 TCAATGGGTTGAGTCGGGTTCAA
1 TCAAT-GGTTGGGTCGGGTTCAA
*
29283514 TCAATGGTTGGGTCGAGTTCAA
1 TCAATGGTTGGGTCGGGTTCAA
29283536 TCAATGGTCT-GGTCGGGTTCA
1 TCAATGGT-TGGGTCGGGTTCA
29283557 CGGGTTCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 33 0.85
23 6 0.15
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.32
Consensus pattern (22 bp):
TCAATGGTTGGGTCGGGTTCAA
Found at i:29296701 original size:6 final size:6
Alignment explanation
Indices: 29296663--29296699 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
29296653 TAAAACAACC
*
29296663 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ACAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
29296700 CATAGTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (6 bp):
ATAAAA
Found at i:29298229 original size:3 final size:3
Alignment explanation
Indices: 29298223--29298301 Score: 113
Period size: 3 Copynumber: 26.3 Consensus size: 3
29298213 AATAATAATA
*
29298223 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
* * * *
29298271 GTG GTG ATG GTG ATG GTG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
29298302 AAGGAGGGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.28, C:0.00, G:0.39, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:29301312 original size:24 final size:24
Alignment explanation
Indices: 29301284--29301336 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
29301274 ATTCGTAGGT
*
29301284 TAAATAAATTATGCTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
**
29301308 TAAATTTATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
29301332 TAAAT
1 TAAAT
29301337 TTTCTAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:29301337 original size:24 final size:24
Alignment explanation
Indices: 29301291--29301338 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
29301281 GGTTAAATAA
*
29301291 ATTATGCTAATAAATACTAAATTT
1 ATTATACTAATAAATACTAAATTT
29301315 ATTATACTAATAAATACTAAATTT
1 ATTATACTAATAAATACTAAATTT
29301339 TCTAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATTT
Found at i:29301658 original size:43 final size:43
Alignment explanation
Indices: 29301605--29301796 Score: 240
Period size: 43 Copynumber: 4.5 Consensus size: 43
29301595 TTATGAGGAA
* * *
29301605 AAACGCCGCTAAAGAACATGATTTTTAGCGGCGCTTATCTCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* *
29301648 AAACGACGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* * **
29301691 AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* * * **
29301734 AAACGCCGCTAAAGACCATGATCTTTAGTGGTGCTTTTCCCGT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
**
29301777 AAACGCCTTTAAAGAACATG
1 AAACGCCGCTAAAGAACATG
29301797 GTTTTTAACG
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 130 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
Found at i:29301824 original size:43 final size:43
Alignment explanation
Indices: 29301605--29301826 Score: 228
Period size: 43 Copynumber: 5.2 Consensus size: 43
29301595 TTATGAGGAA
* * * ** * *
29301605 AAACGCCGCTAAAGAACATGATTTTTAGCGGCGCTTATCTCAC
1 AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
* * **
29301648 AAACGACGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
29301691 AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
1 AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
* * * * * **
29301734 AAACGCCGCTAAAGACCATGATCTTTAGTGGTGCTTTTCCCGT
1 AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
* * * ** *
29301777 AAACGCCTTTAAAGAACATGGTTTTTAACGATATTTTTTCCAC
1 AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
29301820 AAACGCC
1 AAACGCC
29301827 ACTAACATTA
Statistics
Matches: 150, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 150 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (43 bp):
AAACGCCGTTAAAGAACATGGTCTTTAGCGATGCTTTTCCCAC
Found at i:29308105 original size:41 final size:41
Alignment explanation
Indices: 29308058--29308296 Score: 291
Period size: 41 Copynumber: 5.9 Consensus size: 41
29308048 GCGTTTTTCA
* * ** *
29308058 CATAAGCGCCGCTAATGCTCTGACCTTTAGTGGTACTTGCT
1 CATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCC
* *
29308099 CATAAGCACCGCTATTGCTCTGACGTTTAGCGGCGCTTGCC
1 CATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCC
** * * *
29308140 CATAAGCTTCGCTATTGTTCTGACCTTTAGCGACGCTTGCA
1 CATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCC
* * *
29308181 CATAAGTGCAGCTATTGCTCTGACCTTTAGCGGCGCTTACC
1 CATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCC
* *
29308222 CATAAGCGCCGCTATTGCTCTGACCTTTAGTGGCGCTTTCC
1 CATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCC
* * *
29308263 GATAAGCGTCGCTATTGCTCT-ACCTTTTGCGGCG
1 CATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
29308297 TTATGTAAAA
Statistics
Matches: 169, Mismatches: 29, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
40 11 0.07
41 158 0.93
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.31
Consensus pattern (41 bp):
CATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCC
Found at i:29308275 original size:123 final size:122
Alignment explanation
Indices: 29308056--29308289 Score: 324
Period size: 123 Copynumber: 1.9 Consensus size: 122
29308046 TGGCGTTTTT
* * * * *
29308056 CACATAAGCGCCGCTAATGCTCTGACCTTTAGTGGTACTTGCTCATAAGCACCGCTATTGCTCTG
1 CACATAAGCGCAGCTAATGCTCTGACCTTTAGCGGCACTTACCCATAAGCACCGCTATTGCTCTG
* * *
29308121 ACGTTTAGCGGCGCTTGCCCATAAGCTTCGCTATTGTTCTGACCTTTAGCGACGCTTG
66 ACCTTTAGCGGCGCTTGCCCATAAGCGTCGCTATTGCTCT-ACCTTTAGCGACGCTTG
* * * *
29308179 CACATAAGTGCAGCTATTGCTCTGACCTTTAGCGGCGCTTACCCATAAGCGCCGCTATTGCTCTG
1 CACATAAGCGCAGCTAATGCTCTGACCTTTAGCGGCACTTACCCATAAGCACCGCTATTGCTCTG
* * *
29308244 ACCTTTAGTGGCGCTTTCCGATAAGCGTCGCTATTGCTCTACCTTT
66 ACCTTTAGCGGCGCTTGCCCATAAGCGTCGCTATTGCTCTACCTTT
29308290 TGCGGCGTTA
Statistics
Matches: 96, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
122 6 0.06
123 90 0.94
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.31
Consensus pattern (122 bp):
CACATAAGCGCAGCTAATGCTCTGACCTTTAGCGGCACTTACCCATAAGCACCGCTATTGCTCTG
ACCTTTAGCGGCGCTTGCCCATAAGCGTCGCTATTGCTCTACCTTTAGCGACGCTTG
Found at i:29313452 original size:23 final size:22
Alignment explanation
Indices: 29313397--29313457 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
29313387 TACATACATT
29313397 TTATT-TAA-TATTTTAATTAA
1 TTATTATAATTATTTTAATTAA
**
29313417 TTA-TAGTGTTTATTTGTAATTAA
1 TTATTA-TAATTATTT-TAATTAA
29313440 TTATTATAATTATATTTA
1 TTATTATAATTAT-TTTA
29313458 GAGAATTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
19 1 0.03
20 3 0.10
21 1 0.03
22 5 0.16
23 17 0.55
24 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
TTATTATAATTATTTTAATTAA
Found at i:29317263 original size:7 final size:7
Alignment explanation
Indices: 29317251--29317297 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
29317241 TGATGTTCGA
29317251 GTTTAAG
1 GTTTAAG
*
29317258 GTTTAAA
1 GTTTAAG
*
29317265 GTTTAGG
1 GTTTAAG
*
29317272 GTTTGA-
1 GTTTAAG
*
29317278 GTTTAAT
1 GTTTAAG
29317285 GTTTAAG
1 GTTTAAG
29317292 GTTTAA
1 GTTTAA
29317298 AGTGAAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:29317283 original size:20 final size:20
Alignment explanation
Indices: 29317258--29317295 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29317248 CGAGTTTAAG
*
29317258 GTTTAAAGTTTAGGGTTTGA
1 GTTTAAAGTTTAAGGTTTGA
*
29317278 GTTTAATGTTTAAGGTTT
1 GTTTAAAGTTTAAGGTTT
29317296 AAAGTGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTTAAAGTTTAAGGTTTGA
Found at i:29327125 original size:21 final size:21
Alignment explanation
Indices: 29327101--29327149 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
29327091 GTTTTAAGTA
*
29327101 TCGGTAGAAG-CATGACATGTT
1 TCGGTAGAAGTCAT-ACATGTG
*
29327122 TCGGTAGAAGTCATACTTGTG
1 TCGGTAGAAGTCATACATGTG
29327143 TCGGTAG
1 TCGGTAG
29327150 TATTGTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (21 bp):
TCGGTAGAAGTCATACATGTG
Found at i:29348836 original size:23 final size:22
Alignment explanation
Indices: 29348794--29348837 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29348784 TCTTTGTTCT
*
29348794 TTTTCTTTTTTGAAATCAAAAG
1 TTTTCTTTTTTGAAAACAAAAG
29348816 TTTTCTTTTGATT-AAAACAAAA
1 TTTTCTTTT--TTGAAAACAAAA
29348838 TCACTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 8 0.42
24 2 0.11
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTTCTTTTTTGAAAACAAAAG
Found at i:29349069 original size:148 final size:149
Alignment explanation
Indices: 29348834--29349206 Score: 499
Period size: 149 Copynumber: 2.5 Consensus size: 149
29348824 TGATTAAAAC
* * *
29348834 AAAATCACTACTTTATTTCAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAGAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* *
29348899 TGTTTAAAATTTTAAACTTTTTCTTTAAAATCACT-AAAAA-ATA-TTTTATTTTTTAAAAAATC
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAACAAATTTTTA-TTTTT-AAAAATC
29348961 TAAACTTTCTT-TTTCTTAATA-
129 TAAACTTT-TTCTTTCTTAA-AG
*
29348982 AAAATCACTACTTTGCTTAAAAATTC-AAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAAC
1 AAAATCACTACTTTACTTAAAAA-TCAAAACTTTTATTTCGAAATAGTT-AAAAAAAATCAAAAC
* *
29349046 TTTGTTTAAAAATTTACAC-TTTTCTTTAAAATGACTAAAAAACAAATTTTTATTTTTAAAAATC
64 TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAACAAATTTTTATTTTTAAAAATC
* *
29349110 TAAAGTTTTTCTTTTTTAAAG
129 TAAACTTTTTCTTTCTTAAAG
* * * * *
29349131 AAAATCACTATTTTACTTAAAAATCTAAATTTTTATTTCGAATTAGTTAAAAAAAATCAAAAGTT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
*
29349196 TGATTAAAAAT
66 TGTTTAAAAAT
29349207 AACTAAAATA
Statistics
Matches: 201, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
148 89 0.44
149 100 0.50
150 7 0.03
151 5 0.02
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (149 bp):
AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAACAAATTTTTATTTTTAAAAATCTA
AACTTTTTCTTTCTTAAAG
Found at i:29349087 original size:53 final size:53
Alignment explanation
Indices: 29348981--29349092 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 53
29348971 TTTTCTTAAT
** * * *
29348981 AAAAATCACTACTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAA
1 AAAAATCAAAACTTTGCTTAAAAATTCAAACTTTTATTTCAAAATACTAAAAA
* * * *
29349034 AAAAATCAAAACTTTGTTTAAAAATTTACACTTTTCTTT-AAAATGACTAAAAA
1 AAAAATCAAAACTTTGCTTAAAAATTCAAACTTTTATTTCAAAAT-ACTAAAAA
*
29349087 ACAAAT
1 AAAAAT
29349093 TTTTATTTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
52 4 0.08
53 44 0.92
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (53 bp):
AAAAATCAAAACTTTGCTTAAAAATTCAAACTTTTATTTCAAAATACTAAAAA
Found at i:29349186 original size:129 final size:129
Alignment explanation
Indices: 29349073--29349325 Score: 352
Period size: 129 Copynumber: 2.0 Consensus size: 129
29349063 ACTTTTCTTT
* *
29349073 AAAATGACTAAAA-AACAAATTTTTATTTTTAAAAATCTAAAGTTTT-TCTTTTTTAAAGAAAAT
1 AAAATAACTAAAATAA-AAATTTTTATTTTTAAAAATCTAAA-TTTTCTCTTTTTAAAAGAAAAT
* * *
29349136 CACTAT-TTTACTTAAAAATCTAAATTTTTATTTCG-AATTAGTTAAAAAAAATCAAAAGTTTGA
64 CACTATATTT-CTTAAAAATCAAAACTTTTATTTCGAAATT-GTTAAAAAAAATCAAAACTTTGA
29349199 TTA
127 TTA
* *
29349202 AAAATAACTAAAATAAAAATTTTTATTTTTAAAAATTTAAATTTTCTCTTTTTAAAATAAAATCA
1 AAAATAACTAAAATAAAAATTTTTATTTTTAAAAATCTAAATTTTCTCTTTTTAAAAGAAAATCA
* * *
29349267 CTATATTTCTTATAAATCAAAACTTTTATTTCGAAATTGTTTAAAAAAACCAAAACTTT
66 CTATATTTCTTAAAAATCAAAACTTTTATTTCGAAATTGTTAAAAAAAATCAAAACTTT
29349326 TCCCAAAAAC
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
128 4 0.04
129 97 0.88
130 9 0.08
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (129 bp):
AAAATAACTAAAATAAAAATTTTTATTTTTAAAAATCTAAATTTTCTCTTTTTAAAAGAAAATCA
CTATATTTCTTAAAAATCAAAACTTTTATTTCGAAATTGTTAAAAAAAATCAAAACTTTGATTA
Found at i:29349237 original size:22 final size:22
Alignment explanation
Indices: 29349210--29349263 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
29349200 TAAAAATAAC
29349210 TAAAATAAAAATTTT-TATTTT
1 TAAAATAAAAATTTTCTATTTT
** *
29349231 TAAAAATTTAAATTTTCTCTTTT
1 T-AAAATAAAAATTTTCTATTTT
29349254 TAAAATAAAA
1 TAAAATAAAA
29349264 TCACTATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 19 0.73
23 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAATAAAAATTTTCTATTTT
Found at i:29350242 original size:42 final size:42
Alignment explanation
Indices: 29350191--29350547 Score: 518
Period size: 42 Copynumber: 8.5 Consensus size: 42
29350181 ACCTCACATT
29350191 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * *
29350233 TGGACCTCTAAATGAAATGAAAAGTAAATGGACCTCCACACA
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * *
29350275 TGGGCCTCTAGATGCGATGAAAAGTAAAGGGACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
29350317 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCATAACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCA-CACC
* * *
29350360 -GGGCCTCTAAATGTAATGAAAAGTAAATGGACATCTACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * * *
29350401 TAGGTCTTTAAATGCGATGAAAAGTAAATGGACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
29350443 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
** *
29350485 TGGAACTCTAAATGCAATGAAAAGTAAATGGACCTCCACAGC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
29350527 TGGACCTTTAAATGCAATGAA
1 TGGGCCTCTAAATGCAATGAA
29350548 TGCTTTCCTT
Statistics
Matches: 278, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
41 3 0.01
42 272 0.98
43 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (42 bp):
TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
Found at i:29359182 original size:4 final size:4
Alignment explanation
Indices: 29359153--29359195 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
29359143 ACAAATGAGC
* * * *
29359153 GAAT GAGT GAAT GGAT GGAT GGAT GAAT GAAT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
29359196 ATTGGGGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:29359283 original size:26 final size:26
Alignment explanation
Indices: 29359247--29359304 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
29359237 TCTTTCATAG
29359247 AAGGTTCAAAAATTATTCGGCTTACA
1 AAGGTTCAAAAATTATTCGGCTTACA
29359273 AAGGTTCAAAAATTATTCGGCTTACA
1 AAGGTTCAAAAATTATTCGGCTTACA
29359299 AAGGTT
1 AAGGTT
29359305 TTTTCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (26 bp):
AAGGTTCAAAAATTATTCGGCTTACA
Found at i:29359445 original size:119 final size:119
Alignment explanation
Indices: 29359303--29359537 Score: 443
Period size: 119 Copynumber: 2.0 Consensus size: 119
29359293 CTTACAAAGG
29359303 TTTTTTCATTTTTCATTCATAATTAAAGAAAATCCTAATTGATCCTATTATCATAGGGGAAATCT
1 TTTTTTCATTTTTCATTCATAATTAAAGAAAATCCTAATTGATCCTATTATCATAGGGGAAATCT
*
29359368 CTACTCGTTGTTCTTCTTCTTCCTCCTCATGAGCTTGATGAACTTTTGGTAGGT
66 CTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGAACTTTTGGTAGGT
*
29359422 TTTTTTCATTTTTCATTCATAATTAAAGAAAATCCTAATTGATCCTATTGTCATAGGGGAAATCT
1 TTTTTTCATTTTTCATTCATAATTAAAGAAAATCCTAATTGATCCTATTATCATAGGGGAAATCT
*
29359487 CTACTCGTCGTTCTTTTTCTTCCTCCTCATGAGCTTGATGAACTTTTGGTA
66 CTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGAACTTTTGGTA
29359538 ATGTGCCTGA
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 113 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (119 bp):
TTTTTTCATTTTTCATTCATAATTAAAGAAAATCCTAATTGATCCTATTATCATAGGGGAAATCT
CTACTCGTCGTTCTTCTTCTTCCTCCTCATGAGCTTGATGAACTTTTGGTAGGT
Found at i:29362213 original size:23 final size:20
Alignment explanation
Indices: 29362172--29362216 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 20
29362162 ATTAGAAAAT
29362172 TAAATAAATTAATGCATAAA
1 TAAATAAATTAATGCATAAA
29362192 TAAATAAATCTAATATGCATAAA
1 TAAATAAAT-T-A-ATGCATAAA
29362215 TA
1 TA
29362217 CTAAAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 1 0.05
23 11 0.50
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAATAAATTAATGCATAAA
Found at i:29363966 original size:19 final size:19
Alignment explanation
Indices: 29363942--29363983 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29363932 AAATAGTTAA
29363942 AAAAATCAAAATTTTGTTT
1 AAAAATCAAAATTTTGTTT
* * *
29363961 AAAAATTAAACTTTTTTTT
1 AAAAATCAAAATTTTGTTT
29363980 AAAA
1 AAAA
29363984 TGACTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAATCAAAATTTTGTTT
Found at i:29364152 original size:146 final size:147
Alignment explanation
Indices: 29363742--29364257 Score: 691
Period size: 146 Copynumber: 3.5 Consensus size: 147
29363732 TCTTTTTATT
* * * *
29363742 AATCACTACTTTACTTCAAAATTAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTGT
1 AATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGT
** *
29363807 TTAAAAATTTAATTTTTTTCTTTAAAATCACTAAAAAATAGATTTTTATTTTTTAAAAAATCTAA
66 TTAAAAATTTAA-ACTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTT--AAAATCTAA
29363872 ACTTTCTTCTTTTTTTAATGAA
128 ACTTTC-TCTTTTTTTAA-GAA
* * * * * *
29363894 AATCATTAGTTTACTTAAAAATCCAAACTTTGATTTCAAAATAGTTAAAAAAATCAAAATTTTGT
1 AATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGT
* *
29363959 TTAAAAA-TTAAACTTTTTTTTAAAATGACTAAAAAATAGATTTTTATTTTTTAAAATCTAAACT
66 TTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAATCTAAACT
29364023 TTCT-TTTTTTTAA-AA
131 TTCTCTTTTTTTAAGAA
* * * * * *
29364038 AATCATTATTTTACTTAAAAATCCAAATTTTTATTTCGTAATAGTTAAAAAAAATCAAAGCTTTA
1 AATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTTTG
* *
29364103 TTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAATTAGATTTTTATTTTTAAAAATCTAAAC
65 TTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAATCTAAAC
*
29364168 TTT-TCTTTTTTAAAGAA
130 TTTCTCTTTTTTTAAGAA
* *
29364185 AATCACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATTATTTAAAAAAATCAAAACTTT-
1 AATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAA-TAGTTAAAAAAATCAAAACTTTG
*
29364249 TTTCAAAAT
65 TTTAAAAAT
29364258 CAAGCTATTT
Statistics
Matches: 327, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
144 43 0.13
145 24 0.07
146 80 0.24
147 55 0.17
148 19 0.06
150 37 0.11
151 4 0.01
152 65 0.20
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.44
Consensus pattern (147 bp):
AATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGT
TTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAATCTAAACT
TTCTCTTTTTTTAAGAA
Found at i:29364666 original size:3 final size:3
Alignment explanation
Indices: 29364658--29364694 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
29364648 CATGAAACCC
29364658 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29364695 TTGTGCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29366656 original size:50 final size:49
Alignment explanation
Indices: 29366586--29366683 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 49
29366576 AAATATTGAA
*
29366586 TTTAAATTATAAAATCAATTGAGTATAATTAGATTATTTGATTATAAAT
1 TTTAAATTATAAAATCAATTGAATATAATTAGATTATTTGATTATAAAT
* *
29366635 TTTAAATTTTGAAAATCAATTGAATATAATTAGATTGTTTGATTATAAA
1 TTTAAATTAT-AAAATCAATTGAATATAATTAGATTATTTGATTATAAA
29366684 ATCAATTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 9 0.20
50 36 0.80
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (49 bp):
TTTAAATTATAAAATCAATTGAATATAATTAGATTATTTGATTATAAAT
Found at i:29370850 original size:30 final size:30
Alignment explanation
Indices: 29370728--29371236 Score: 422
Period size: 30 Copynumber: 17.0 Consensus size: 30
29370718 GAGAATTCGA
29370728 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
* * * *
29370758 GGATATAAATGTAATTTT-GTAATGTTT-GG
1 GGTTA-AAATGTAATTTTGGAAAAGTTTAAG
* *
29370787 GGTTAAAATGTGATTTT--AATGAAGTTT-GG
1 GGTTAAAATGTAATTTTGGAA--AAGTTTAAG
* * *
29370816 GGTTAAAATGTGATTTT-AAAGAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAA-AAGTTTAAG
29370846 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
29370876 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
*
29370906 GGTCAAAATGTAATTTTAGG-AAAGTTT-AG
1 GGTTAAAATGTAATTTT-GGAAAAGTTTAAG
* *
29370935 GGTTAAAATGCAATTTT--AATGAAGTTT-AT
1 GGTTAAAATGTAATTTTGGAA--AAGTTTAAG
* ** *
29370964 GATTAAAAATGCGATTTTAGAGAAA-TTTAAG
1 GGTT-AAAATGTAATTTTGGA-AAAGTTTAAG
*
29370995 GGTTAAAATGTAATTTTGGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
29371025 GGTTAAAATGTAATTTTGGAAAAAG-TTAAG
1 GGTTAAAATGTAATTTTGG-AAAAGTTTAAG
*
29371055 GGTTAAAAT-TGAATTTTGGAAAAGTTTAGG
1 GGTTAAAATGT-AATTTTGGAAAAGTTTAAG
* * **
29371085 GGTAAAAAT-TCAATTTTGGAAAGGTTCGAG
1 GGTTAAAATGT-AATTTTGGAAAAGTTTAAG
* * **
29371115 GATCAAAATACAATTTTGGCAAAA-TTTAAG
1 GGTTAAAATGTAATTTTGG-AAAAGTTTAAG
* * **
29371145 GGTCAAAATGTAATTTTGAAAAAAAATTAAG
1 GGTTAAAATGTAATTTTG-GAAAAGTTTAAG
* * **
29371176 GGTTAAAATGTAATTTTTGAGAAGTTCGAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAAG
* * * *
29371206 GGTCAAAATATGATTTTTGG-AAAGTTCAAG
1 GGTTAAAATGT-AATTTTGGAAAAGTTTAAG
29371236 G
1 G
29371237 ACCTTTTGGG
Statistics
Matches: 399, Mismatches: 56, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
27 2 0.01
28 11 0.03
29 72 0.18
30 255 0.64
31 57 0.14
32 1 0.00
33 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTAAG
Found at i:29370951 original size:119 final size:118
Alignment explanation
Indices: 29370728--29371161 Score: 454
Period size: 119 Copynumber: 3.7 Consensus size: 118
29370718 GAGAATTCGA
* * * * *
29370728 GGTTAAAATGTAATTTTGGAAAAGTTTAAGGGATATAAATGTAATTTT-GTAATGTTT-GGGGTT
1 GGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTA-AAATGTAATTTTGGAAAAGTTTAAGGGTC
* * * *
29370791 AAAATGTGATTTTAATG-AAGTTTGGGGTTAAAATGTGATTTTAAAGAAGTTTAGG
65 AAAATGTAATTTT-AGGAAAGTTTAGGGTTAAAATG-AATTTTAAAGAAGTTTAGG
29370846 GGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTCA
1 GGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTCA
* *
29370911 AAATGTAATTTTAGGAAAGTTTAGGGTTAAAATGCAATTTTAATGAAGTTTA-T
66 AAATGTAATTTTAGGAAAGTTTAGGGTTAAAATG-AATTTTAAAGAAGTTTAGG
* ** * *
29370964 GATTAAAAATGCGATTTTAGAGAAA-TTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGT
1 GGTT-AAAATGTAATTTTGGA-AAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGT
* * *
29371028 TAAAATGTAATTTT-GGAAAAAGTTAAGGGTTAAAATTGAATTTTGGAA-AAGTTTAGG
64 CAAAATGTAATTTTAGG--AAAGTTTAGGGTTAAAA-TGAATTTT-AAAGAAGTTTAGG
* * ** * * **
29371085 GGTAAAAAT-TCAATTTTGGAAAGGTTCGAGGATCAAAATACAATTTTGGCAAAA-TTTAAGGGT
1 GGTTAAAATGT-AATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGG-AAAAGTTTAAGGGT
29371148 CAAAATGTAATTTT
64 CAAAATGTAATTTT
29371162 GAAAAAAAAT
Statistics
Matches: 267, Mismatches: 36, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
117 12 0.04
118 48 0.18
119 114 0.43
120 84 0.31
121 9 0.03
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (118 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTCA
AAATGTAATTTTAGGAAAGTTTAGGGTTAAAATGAATTTTAAAGAAGTTTAGG
Found at i:29372022 original size:29 final size:29
Alignment explanation
Indices: 29371989--29372083 Score: 172
Period size: 29 Copynumber: 3.3 Consensus size: 29
29371979 TAAAAATATG
*
29371989 TTTGTTTTCCTTTTTTACTTTCTTCTTAA
1 TTTGTTTTCCTTTTTTACTTTCTTGTTAA
29372018 TTTGTTTTCCTTTTTTACTTTCTTGTTAA
1 TTTGTTTTCCTTTTTTACTTTCTTGTTAA
29372047 TTTGTTTTCCTTTTTTACTTTCTTGTTAA
1 TTTGTTTTCCTTTTTTACTTTCTTGTTAA
*
29372076 TTTCTTTT
1 TTTGTTTT
29372084 TTTAAAAAGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.71
Consensus pattern (29 bp):
TTTGTTTTCCTTTTTTACTTTCTTGTTAA
Found at i:29373627 original size:39 final size:39
Alignment explanation
Indices: 29373574--29373982 Score: 324
Period size: 39 Copynumber: 10.5 Consensus size: 39
29373564 TTTGCTCCAA
* * * * *
29373574 GCTC-GGGTAAGAGATTGGGTGATGATGATCTGCCTCTG
1 GCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAG
* * **
29373612 GCTCGAGGTAAGAGATAGGATGACT-GCAATCTACCCCAG
1 GCTCGGGGTAAGAGATTGGATGA-TGGTGATCTACCCCAG
* * * *
29373651 GCTCGGGGTAAGAGGTTAGCTGATGGTGATCTGCCCCAG
1 GCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAG
* * * * *
29373690 GCTCGGGGTAAAAGATCGAATGGAT-ATAATCTACCCCAG
1 GCTCGGGGTAAGAGATTGGAT-GATGGTGATCTACCCCAG
* *
29373729 GCTCTGGGTAAGAGATTGGCTGATGGTGATCTACCCCAG
1 GCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAG
* * * * * ** * *
29373768 GCTCAGGGTAAAAGATTGAATGGTTGCAATCTGCCTCAG
1 GCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAG
* * *
29373807 GCTCGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAA
1 GCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAG
* * * * **
29373846 GCTCGGGGTAAGAGATCGAATGGAT-GTAATCTGCCTTAG
1 GCTCGGGGTAAGAGATTGGAT-GATGGTGATCTACCCCAG
*
29373885 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTACCCCAG
1 GCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAG
* * * * * * *
29373924 GCTCGAGATAAAAGATTGGATGGCT-GTAATTTGCCCCAG
1 GCTCGGGGTAAGAGATTGGAT-GATGGTGATCTACCCCAG
*
29373963 ACTCGGGGTAAGAGATTGGA
1 GCTCGGGGTAAGAGATTGGA
29373983 ATCTTCAATC
Statistics
Matches: 280, Mismatches: 83, Indels: 15
0.74 0.22 0.04
Matches are distributed among these distances:
38 11 0.04
39 260 0.93
40 9 0.03
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (39 bp):
GCTCGGGGTAAGAGATTGGATGATGGTGATCTACCCCAG
Found at i:29373681 original size:78 final size:77
Alignment explanation
Indices: 29373499--29373981 Score: 495
Period size: 78 Copynumber: 6.2 Consensus size: 77
29373489 CCCCTTGTCG
* * * * *
29373499 CGGGGTAAGAAAATGGCTAATGGTGATCTACCCCAGGCTC-AGGATAAAAGATCGAATTGTTGCA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGG-TAAAAGATCGAA-TGATGTA
* * *
29373563 ATTTGCTCCAAGCT
64 ATCTGCCCCAGGCT
* * * * * * * * *
29373577 C-GGGTAAGAGATTGGGTGATGATGATCTGCCTCTGGCTCGAGGTAAGAGATAGGATGACTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGATCGAATGA-TGTAA
*
29373641 TCTACCCCAGGCT
65 TCTGCCCCAGGCT
* * * * *
29373654 CGGGGTAAGAGGTTAGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGATATAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGATCGAAT-GATGTAA
*
29373719 TCTACCCCAGGCT
65 TCTGCCCCAGGCT
* * * *
29373732 CTGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTC-AGGGTAAAAGATTGAATGGTTGCA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGA-GGTAAAAGATCGAAT-GATGTA
*
29373796 ATCTGCCTCAGGCT
64 ATCTGCCCCAGGCT
* * * *
29373810 CGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAAGCTCGGGGTAAGAGATCGAATGGATGTAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGATCGAAT-GATGTAA
**
29373875 TCTGCCTTAGGCT
65 TCTGCCCCAGGCT
* * * * *
29373888 CGGGGTAAGAGATTGGTTGATGGTGATCTACCCCAGGCTCGAGATAAAAGATTGGATGGCTGTAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGATCGAAT-GATGTAA
* *
29373953 TTTGCCCCAGACT
65 TCTGCCCCAGGCT
29373966 CGGGGTAAGAGATTGG
1 CGGGGTAAGAGATTGG
29373982 AATCTTCAAT
Statistics
Matches: 338, Mismatches: 61, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
76 2 0.01
77 54 0.16
78 280 0.83
79 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (77 bp):
CGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGATCGAATGATGTAAT
CTGCCCCAGGCT
Found at i:29373799 original size:156 final size:155
Alignment explanation
Indices: 29373499--29373979 Score: 595
Period size: 156 Copynumber: 3.1 Consensus size: 155
29373489 CCCCTTGTCG
* * * * * * * * *
29373499 CGGGGTAAGAAAATGGCTAATGGTGATCTACCCCAGGCTCAGGATAAAAGATCGAATTGTTGCAA
1 CGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGATGTAA
* * * * * * * * * *
29373564 TTTGCTCCAAGCTCGGGTAAGAGATTGGGTGATGATGATCTGCCTCTGGCTCGAGGTAAGAGATA
66 TCTGCCCCAGGCTCGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGATT
* *
29373629 GGATGACTGCAATCTACCCCAGGCT
131 GGATGGCTGCAATCTGCCCCAGGCT
* * *
29373654 CGGGGTAAGAGGTTAGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGATATAA
1 CGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGATGTAA
*
29373719 TCTACCCCAGGCTCTGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTC-AGGGTAAAAGA
66 TCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGA-GGTAAAAGA
* * *
29373783 TTGAATGGTTGCAATCTGCCTCAGGCT
129 TTGGATGGCTGCAATCTGCCCCAGGCT
* *
29373810 CGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAAGCTCGGGGTAAGAGATCGAATGGATGTAA
1 CGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGATGTAA
** * *
29373875 TCTGCCTTAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTACCCCAGGCTCGAGATAAAAGAT
66 TCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGAT
* * *
29373940 TGGATGGCTGTAATTTGCCCCAGACT
130 TGGATGGCTGCAATCTGCCCCAGGCT
29373966 CGGGGTAAGAGATT
1 CGGGGTAAGAGATT
29373980 GGAATCTTCA
Statistics
Matches: 278, Mismatches: 45, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
155 64 0.23
156 213 0.77
157 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (155 bp):
CGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGATGTAA
TCTGCCCCAGGCTCGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGAGGTAAAAGATT
GGATGGCTGCAATCTGCCCCAGGCT
Found at i:29386228 original size:29 final size:28
Alignment explanation
Indices: 29386157--29386278 Score: 82
Period size: 29 Copynumber: 4.2 Consensus size: 28
29386147 AAAATGTAAT
* * ** *
29386157 TTTTGAAAAGTTTGGGGTGTAAATGTGA
1 TTTTGAGAACTTTGGGGTCAAAATATGA
* *
29386185 TTTTAAGAAAGTTTGGGGTCAAAATATGA
1 TTTTGAG-AACTTTGGGGTCAAAATATGA
* **
29386214 TTTTGATGAACTTTGGGGTTAAAATGCGA
1 TTTTGA-GAACTTTGGGGTCAAAATATGA
* * *
29386243 TTTTTGGAGAAGTTTAAGGGTCAAAATATAA
1 -TTTT-GAGAACTTT-GGGGTCAAAATATGA
29386274 TTTTG
1 TTTTG
29386279 GTAAAGTTTA
Statistics
Matches: 73, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
28 5 0.07
29 41 0.56
30 15 0.21
31 12 0.16
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.39
Consensus pattern (28 bp):
TTTTGAGAACTTTGGGGTCAAAATATGA
Found at i:29386286 original size:30 final size:29
Alignment explanation
Indices: 29386244--29386528 Score: 241
Period size: 30 Copynumber: 9.6 Consensus size: 29
29386234 AAAATGCGAT
29386244 TTTTGGAGAAGTTTAAGGGTCAAAATATAA
1 TTTTGGA-AAGTTTAAGGGTCAAAATATAA
* * *
29386274 TTTTGGTAAAGTTTAAGGGTTAAATTGTAA
1 TTTTGG-AAAGTTTAAGGGTCAAAATATAA
* * *
29386304 TTTAGGAAAAGTTT-AGGGTAAAAATTTAA
1 TTTTGG-AAAGTTTAAGGGTCAAAATATAA
* * **
29386333 TTTTGGAAAGGTTT-GGGGGCAAAATGCAA
1 TTTTGGAAA-GTTTAAGGGTCAAAATATAA
* * * *
29386362 TTTTAGCAAAATTTAAGTGTCAAAATGTAA
1 TTTT-GGAAAGTTTAAGGGTCAAAATATAA
* *
29386392 TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
1 TTTTGG-AAAGTTTAAGGGTCAAAATATAA
* * *
29386422 TTTTGGAAAAATTTAAGGGTTATAATATAA
1 TTTTGG-AAAGTTTAAGGGTCAAAATATAA
* **
29386452 TTTTGGAAAATTCGAGGGTCAAAATATAA
1 TTTTGGAAAGTTTAAGGGTCAAAATATAA
* * *
29386481 TTTTGAAGAAGTTCAAGGGTCAAAATATGAT
1 TTTTGGA-AAGTTTAAGGGTCAAAATAT-AA
*
29386512 TTTTGGAAAGTTCAAGG
1 TTTTGGAAAGTTTAAGG
29386529 ACCTTCTAGG
Statistics
Matches: 210, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.01
29 64 0.30
30 135 0.64
31 8 0.04
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTTAAGGGTCAAAATATAA
Found at i:29386334 original size:59 final size:59
Alignment explanation
Indices: 29386147--29386523 Score: 270
Period size: 59 Copynumber: 6.4 Consensus size: 59
29386137 ATTCGAGGTT
* * ** * * *
29386147 AAAATGTAATTTTTGAAAAGTTT-GGGGTGTAAATGTGATTTTAAG-AAAGTTT-GGGGTC
1 AAAATATAA-TTTTGGAAAGTTTAGGGGTCAAAATGT-AATTTAGGAAAAGTTTAAGGGTC
* * * * * * *
29386205 AAAATATGATTTT-GATGAACTTT-GGGGTTAAAATGCGATTTTTGGAGAAGTTTAAGGGTC
1 AAAATATAATTTTGGA--AAGTTTAGGGGTCAAAATG-TAATTTAGGAAAAGTTTAAGGGTC
* * * *
29386265 AAAATATAATTTTGGTAAAGTTTAAGGGTTAAATTGTAATTTAGGAAAAGTTT-AGGGTA
1 AAAATATAATTTTGG-AAAGTTTAGGGGTCAAAATGTAATTTAGGAAAAGTTTAAGGGTC
* * * * *
29386324 AAAATTTAATTTTGGAAAGGTTT-GGGGGCAAAATGCAATTTTAGCAAAA-TTTAAGTGTC
1 AAAATATAATTTTGGAAA-GTTTAGGGGTCAAAATGTAA-TTTAGGAAAAGTTTAAGGGTC
* * * *
29386383 AAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAATTTAAGGGTT
1 AAAATATAATTTTGG-AAAGTTTAGGGGTCAAAATGTAATTTAGGAAAAGTTTAAGGGTC
* * * * * *
29386443 ATAATATAATTTTGGAAA-ATTCGAGGGTCAAAATATAATTT-TGAAGAAGTTCAAGGGTC
1 AAAATATAATTTTGGAAAGTTTAG-GGGTCAAAATGTAATTTAGGAA-AAGTTTAAGGGTC
*
29386502 AAAATATGATTTTTGGAAAGTT
1 AAAATAT-AATTTTGGAAAGTT
29386524 CAAGGACCTT
Statistics
Matches: 253, Mismatches: 48, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
56 1 0.00
57 4 0.02
58 50 0.20
59 103 0.41
60 82 0.32
61 12 0.05
62 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.36
Consensus pattern (59 bp):
AAAATATAATTTTGGAAAGTTTAGGGGTCAAAATGTAATTTAGGAAAAGTTTAAGGGTC
Found at i:29386473 original size:89 final size:88
Alignment explanation
Indices: 29386244--29386528 Score: 279
Period size: 89 Copynumber: 3.2 Consensus size: 88
29386234 AAAATGCGAT
* * * * *
29386244 TTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTGGTAAAGTTTAAGGGTTAAATTGTAATTTAG
1 TTTTGGAAAAGTTTAAGGGTCAAAATATAATTTTGG-AAAATTTAAGGGTCAAAATGTAATTTTG
* *
29386309 GAAAAGTTTAGGGTAAAAATTTAA
65 GAAAAGTTTAGGGTCAAAATATAA
* * * ** * *
29386333 TTTTGGAAAGGTTT-GGGGGCAAAATGCAATTTTAGCAAAATTTAAGTGTCAAAATGTAATTTTG
1 TTTTGGAAAAGTTTAAGGGTCAAAATATAATTTT-GGAAAATTTAAGGGTCAAAATGTAATTTTG
*
29386397 GAAAAGTTTAGGGGTCAAAATGTAA
65 GAAAAGTTTA-GGGTCAAAATATAA
* * * ** *
29386422 TTTTGGAAAAATTTAAGGGTTATAATATAATTTTGGAAAATTCGAGGGTCAAAATATAATTTT-G
1 TTTTGGAAAAGTTTAAGGGTCAAAATATAATTTTGGAAAATTTAAGGGTCAAAATGTAATTTTGG
* *
29386486 AAGAAGTTCAAGGGTCAAAATATGAT
66 AA-AAGTT-TAGGGTCAAAATAT-AA
*
29386512 TTTTGG-AAAGTTCAAGG
1 TTTTGGAAAAGTTTAAGG
29386529 ACCTTCTAGG
Statistics
Matches: 158, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
88 51 0.32
89 86 0.54
90 21 0.13
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (88 bp):
TTTTGGAAAAGTTTAAGGGTCAAAATATAATTTTGGAAAATTTAAGGGTCAAAATGTAATTTTGG
AAAAGTTTAGGGTCAAAATATAA
Found at i:29422205 original size:3 final size:3
Alignment explanation
Indices: 29422197--29422228 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
29422187 TTAGCACATG
29422197 TTC TTC TTC TTC TTC TTC TTC TTC TTCC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC T
29422229 CTTGGCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:29429790 original size:28 final size:27
Alignment explanation
Indices: 29429757--29429831 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
29429747 AGAATGGTTA
*
29429757 GCTCTTACAAGCCCAGAATCAGAATAAT
1 GCTCTTACAAG-CCAGAATCAGAATAAC
* *
29429785 GCTCTTTCGAGCCAGAATCAGAATAAC
1 GCTCTTACAAGCCAGAATCAGAATAAC
* * *
29429812 GCTCTTTCGAGACAGAATCA
1 GCTCTTACAAGCCAGAATCA
29429832 AATTACTCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 34 0.79
28 9 0.21
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (27 bp):
GCTCTTACAAGCCAGAATCAGAATAAC
Found at i:29429805 original size:27 final size:27
Alignment explanation
Indices: 29429769--29429831 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
29429759 TCTTACAAGC
*
29429769 CCAGAATCAGAATAATGCTCTTTCGAG
1 CCAGAATCAGAATAACGCTCTTTCGAG
29429796 CCAGAATCAGAATAACGCTCTTTCGAG
1 CCAGAATCAGAATAACGCTCTTTCGAG
*
29429823 ACAGAATCA
1 CCAGAATCA
29429832 AATTACTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (27 bp):
CCAGAATCAGAATAACGCTCTTTCGAG
Found at i:29443245 original size:26 final size:26
Alignment explanation
Indices: 29443185--29443245 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
29443175 TTTCGGGAAA
29443185 AATTTTGGACATGCTCATACAGCGAC
1 AATTTTGGACATGCTCATACAGCGAC
* * * * *
29443211 AACTCTGGACATGTTCATGCAGCGAT
1 AATTTTGGACATGCTCATACAGCGAC
29443237 AATTTTGGA
1 AATTTTGGA
29443246 TAAGTTTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (26 bp):
AATTTTGGACATGCTCATACAGCGAC
Done.