Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3280.1
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: 146238
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 449 characters in sequence are not A, C, G, or T
Found at i:3951 original size:20 final size:20
Alignment explanation
Indices: 3928--3974 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3918 GGGTTAAGAT
*
3928 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
3948 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
3968 TGAGCTG
1 TGAGCTG
3975 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:13654 original size:23 final size:22
Alignment explanation
Indices: 13603--13654 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
13593 CCTCGTCTTT
*
13603 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
13625 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
13648 TTCTTTT
1 TTCTTTT
13655 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:18828 original size:47 final size:47
Alignment explanation
Indices: 18776--19269 Score: 771
Period size: 47 Copynumber: 10.6 Consensus size: 47
18766 GATAATTGTG
* *
18776 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
18823 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
18870 ATGTGAAAGTGTATATATGTGAT-A---CTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
18913 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
18960 GTGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
19009 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAAGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
19056 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
19103 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAAGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
19150 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
19197 ATGTGAAAGTGTATATATGTGACAGGGCCGACTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
19244 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
19270 TCCCGAAGGG
Statistics
Matches: 415, Mismatches: 26, Indels: 12
0.92 0.06 0.03
Matches are distributed among these distances:
43 42 0.10
44 1 0.00
46 1 0.00
47 327 0.79
49 44 0.11
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:20948 original size:30 final size:31
Alignment explanation
Indices: 20876--20949 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
20866 ACTTAAGCCA
20876 AGCTCAAAT-GAGCTAAAGTAAGCTAAATTG
1 AGCTCAAATCGAGCTAAAGTAAGCTAAATTG
* *
20906 AGCTCAAA-CGAGCTAAATTAAGCT-CATGTG
1 AGCTCAAATCGAGCTAAAGTAAGCTAAAT-TG
20936 AGCT-AAATCGAGCT
1 AGCTCAAATCGAGCT
20950 GGGAAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (31 bp):
AGCTCAAATCGAGCTAAAGTAAGCTAAATTG
Found at i:24016 original size:42 final size:42
Alignment explanation
Indices: 23913--24022 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 42
23903 CTTACCAATG
** *
23913 CCATATCCCAGATATGGTCTTACATGTAATCTCGTATCGATA
1 CCATATCCCAGATATGGTCTTACATCAAATCTCATATCGATA
* * *
23955 CCAATAACCCAGCTATGGTCTTACA-CAAAGTCTCATATTGATGA
1 CC-ATATCCCAGATATGGTCTTACATCAAA-TCTCATATCGAT-A
23999 -CATATCCCAGATATGGTCTTACAT
1 CCATATCCCAGATATGGTCTTACAT
24023 GTAGCCTCAG
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
42 24 0.43
43 31 0.55
44 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (42 bp):
CCATATCCCAGATATGGTCTTACATCAAATCTCATATCGATA
Found at i:30346 original size:24 final size:25
Alignment explanation
Indices: 30301--30347 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
30291 ATTTTTGATT
*
30301 TTGATGAATATTTTGAGTTATGTCA
1 TTGATGAATATTTTGAGCTATGTCA
30326 TTGATGAATA-TTTGAGCTATGT
1 TTGATGAATATTTTGAGCTATGT
30348 GATGTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (25 bp):
TTGATGAATATTTTGAGCTATGTCA
Found at i:37430 original size:26 final size:26
Alignment explanation
Indices: 37401--37508 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
37391 TGGTACAAAT
37401 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
** *
37427 TGATAATGAATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
37453 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
37479 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
37505 TGAT
1 TGAT
37509 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:44533 original size:26 final size:26
Alignment explanation
Indices: 44504--44611 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
44494 TGGTACAAAT
44504 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
44530 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
44556 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
44582 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
44608 TGAT
1 TGAT
44612 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:48513 original size:24 final size:25
Alignment explanation
Indices: 48468--48514 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
48458 ATTTTTGATT
*
48468 TTGATGAATATTTTGAGTTATGTCA
1 TTGATGAATATTTTGAGCTATGTCA
48493 TTGATGAATA-TTTGAGCTATGT
1 TTGATGAATATTTTGAGCTATGT
48515 GTTGTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (25 bp):
TTGATGAATATTTTGAGCTATGTCA
Found at i:49178 original size:45 final size:45
Alignment explanation
Indices: 49117--49237 Score: 127
Period size: 45 Copynumber: 2.7 Consensus size: 45
49107 TAGGATTCCA
* *
49117 ATATGTGTTTTTGTGTAAGACCATCTCTGGGACGTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCATCTCTGGGACATTGGCATCAAT
* * *
49162 ATATGTGTTTTCGTGTAAGACCA-CATTTGAGACATTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCATC-TCTGGGACATTGGCATCAAT
* * * * * *
49207 ATATTTGGTTACATATAAGACCATGTCTGGG
1 ATATGTGTTTTCGTGTAAGACCATCTCTGGG
49238 TCATCAGCAT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCATCTCTGGGACATTGGCATCAAT
Found at i:50067 original size:16 final size:16
Alignment explanation
Indices: 50043--50092 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
50033 GCTTAACTTC
*
50043 TATGCTTGAATTTGGT
1 TATGTTTGAATTTGGT
*
50059 TATGTTTGAATATGGTT
1 TATGTTTGAATTTGG-T
*
50076 TAAGTTT--ATTTGGT
1 TATGTTTGAATTTGGT
50090 TAT
1 TAT
50093 AATGCTACGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 3 0.11
15 5 0.18
16 13 0.46
17 7 0.25
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (16 bp):
TATGTTTGAATTTGGT
Found at i:53795 original size:54 final size:52
Alignment explanation
Indices: 53729--54040 Score: 293
Period size: 54 Copynumber: 5.8 Consensus size: 52
53719 AGTGGTTTTA
* * * * * *
53729 CGGTCATTTTACACTATAGGGGTATTATGATCATTTTACAAATCGGGGGTATTT
1 CGGTAATTTTACA-AATAGGGGTATT-TGGTAATCTTACAAACCGGGGGTATTT
* * ** *
53783 CGGTAGTCTTACAAACCGGGGGTATTTCGGTAGTCTTACAAACCGGGGGTATTT
1 CGGTAATTTTACAAA-TAGGGGTATTT-GGTAATCTTACAAACCGGGGGTATTT
* ** *
53837 CGATAATTTTACAAACTAGGGGTATTTCGGTAATCTTACAAACTAGAGGTATTT
1 CGGTAATTTTACAAA-TAGGGGTATTT-GGTAATCTTACAAACCGGGGGTATTT
* * * *
53891 CGGTAATTTTACAAATTGGGGTATTTCAGTAATTTTACAAATCGGGGGTATTT
1 CGGTAATTTTACAAATAGGGGTATTT-GGTAATCTTACAAACCGGGGGTATTT
* *
53944 CGGTAAGTTTACAAATCGAGGGTATTTTGGTAATCTTACAAACCGGGGGTATTT
1 CGGTAATTTTACAAATAG-GGGTA-TTTGGTAATCTTACAAACCGGGGGTATTT
* * *
53998 CGATAATTTTATAAACT-GAGGGTATTTCGGTAATTTTACAAAC
1 CGGTAATTTTACAAA-TAG-GGGTATTT-GGTAATCTTACAAAC
54041 AAAGGTCTTA
Statistics
Matches: 215, Mismatches: 37, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
53 52 0.24
54 159 0.74
55 4 0.02
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (52 bp):
CGGTAATTTTACAAATAGGGGTATTTGGTAATCTTACAAACCGGGGGTATTT
Found at i:54040 original size:27 final size:27
Alignment explanation
Indices: 53761--54040 Score: 316
Period size: 27 Copynumber: 10.4 Consensus size: 27
53751 TATTATGATC
53761 ATTTTACAAA-TCGGGGGTATTTCGGTA
1 ATTTTACAAACT-GGGGGTATTTCGGTA
* * *
53788 GTCTTACAAACCGGGGGTATTTCGGTA
1 ATTTTACAAACTGGGGGTATTTCGGTA
* * * *
53815 GTCTTACAAACCGGGGGTATTTCGATA
1 ATTTTACAAACTGGGGGTATTTCGGTA
*
53842 ATTTTACAAACTAGGGGTATTTCGGTA
1 ATTTTACAAACTGGGGGTATTTCGGTA
* * *
53869 ATCTTACAAACTAGAGGTATTTCGGTA
1 ATTTTACAAACTGGGGGTATTTCGGTA
* *
53896 ATTTTACAAA-TTGGGGTATTTCAGTA
1 ATTTTACAAACTGGGGGTATTTCGGTA
53922 ATTTTACAAA-TCGGGGGTATTTCGGTA
1 ATTTTACAAACT-GGGGGTATTTCGGTA
* * *
53949 AGTTTACAAA-TCGAGGGTATTTTGGTA
1 ATTTTACAAACT-GGGGGTATTTCGGTA
* * *
53976 ATCTTACAAACCGGGGGTATTTCGATA
1 ATTTTACAAACTGGGGGTATTTCGGTA
* *
54003 ATTTTATAAACTGAGGGTATTTCGGTA
1 ATTTTACAAACTGGGGGTATTTCGGTA
54030 ATTTTACAAAC
1 ATTTTACAAAC
54041 AAAGGTCTTA
Statistics
Matches: 218, Mismatches: 32, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
26 24 0.11
27 194 0.89
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (27 bp):
ATTTTACAAACTGGGGGTATTTCGGTA
Found at i:63422 original size:37 final size:37
Alignment explanation
Indices: 63372--63450 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
63362 TTATTACGAA
* * *
63372 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
63409 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
63446 GTCTT
1 GTCTT
63451 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:63645 original size:49 final size:49
Alignment explanation
Indices: 63568--63921 Score: 699
Period size: 49 Copynumber: 7.2 Consensus size: 49
63558 GCCCTTCGGG
63568 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
63618 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
63667 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
63716 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
63765 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
63814 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
63863 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
63912 ACTTTCACAT
1 ACTTTCACAT
63922 ACACTATCAT
Statistics
Matches: 304, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
49 300 0.99
50 4 0.01
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (49 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
Found at i:64901 original size:55 final size:55
Alignment explanation
Indices: 64834--64942 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
64824 CCCATCCAAC
*
64834 TTTGATCCTCTTTGCTCTTAAGCAACTTAGGATACAACTCTTAAACAAGCTAAAA
1 TTTGATCATCTTTGCTCTTAAGCAACTTAGGATACAACTCTTAAACAAGCTAAAA
64889 TTTGATCATCTTTGCTCTTAAGCAACTTAGGATACAACTCTTAAACAAGCTAAA
1 TTTGATCATCTTTGCTCTTAAGCAACTTAGGATACAACTCTTAAACAAGCTAAA
64943 TCCTTAGTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (55 bp):
TTTGATCATCTTTGCTCTTAAGCAACTTAGGATACAACTCTTAAACAAGCTAAAA
Found at i:68084 original size:41 final size:41
Alignment explanation
Indices: 68018--68191 Score: 170
Period size: 41 Copynumber: 4.2 Consensus size: 41
68008 CAATACATTG
** * * * * *
68018 GCACGAAAACTGCTAAGCTCAAAGCCTAATATAACACACCG
1 GCACGAAGCCTGCTAGGCACAAAGCCTGATATAATACACCA
* * *
68059 GCGCGAAGCCTGCTAGGCCCAAAGCCTGATATAATA-ATTCAA
1 GCACGAAGCCTGCTAGGCACAAAGCCTGATATAATACA--CCA
** * *
68101 AAACGAAGCCTACTAGGCACAAAGCCTGATATAATACACTA
1 GCACGAAGCCTGCTAGGCACAAAGCCTGATATAATACACCA
* * *
68142 GCACGAAGCCTGCTAGGCACAAAGCCTGATGTAGTACACCG
1 GCACGAAGCCTGCTAGGCACAAAGCCTGATATAATACACCA
68183 GCACGAAGC
1 GCACGAAGC
68192 GGCACAAAGC
Statistics
Matches: 108, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 74 0.69
42 32 0.30
43 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.16
Consensus pattern (41 bp):
GCACGAAGCCTGCTAGGCACAAAGCCTGATATAATACACCA
Found at i:70723 original size:12 final size:12
Alignment explanation
Indices: 70706--70747 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
70696 GAATTGGAAC
*
70706 CAAAATGAGAAT
1 CAAAATCAGAAT
70718 CAAAATCAGAAT
1 CAAAATCAGAAT
* *
70730 CAGAATCAAAAT
1 CAAAATCAGAAT
70742 CAAAAT
1 CAAAAT
70748 TACGTGACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.60, C:0.14, G:0.10, T:0.17
Consensus pattern (12 bp):
CAAAATCAGAAT
Found at i:70730 original size:6 final size:6
Alignment explanation
Indices: 70713--70772 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
70703 AACCAAAATG
* * * * *
70713 AGAATC AAAATC AGAATC AGAATC AAAATC AAAATT ACGTGA-C AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
70762 AGAATC AGAAT
1 AGAATC AGAAT
70773 GTGAATGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
5 1 0.02
6 40 0.93
7 1 0.02
8 1 0.02
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:70927 original size:27 final size:26
Alignment explanation
Indices: 70890--70955 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
70880 AGCATGGTTG
*
70890 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
70916 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
70943 CCAGAATCAGATA
1 CCAGAA-CAGATA
70956 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:70960 original size:27 final size:27
Alignment explanation
Indices: 70890--70963 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
70880 AGCATGGTTG
* *
70890 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
70916 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
70943 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
70964 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:70970 original size:27 final size:27
Alignment explanation
Indices: 70914--70971 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
70904 GTGACAGAGT
* * *
70914 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
70941 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
70968 CACC
1 CACC
70972 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:71176 original size:22 final size:22
Alignment explanation
Indices: 71128--71186 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
71118 GTAAATACGT
*
71128 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
71150 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
71172 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
71187 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:71353 original size:27 final size:26
Alignment explanation
Indices: 71274--71356 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
71264 TCGATCGGTC
* * *
71274 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
71300 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
71327 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
71354 AAC
1 AAC
71357 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:71585 original size:27 final size:27
Alignment explanation
Indices: 71555--71750 Score: 248
Period size: 27 Copynumber: 7.3 Consensus size: 27
71545 GGGGCAAAAT
* * * *
71555 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
71582 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
71609 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
71636 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
71663 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
71690 TGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
71717 GGAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
71744 AGTAATT
1 GGTAATT
71751 TCTCAATCAA
Statistics
Matches: 144, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:71785 original size:27 final size:27
Alignment explanation
Indices: 71755--72382 Score: 763
Period size: 27 Copynumber: 23.3 Consensus size: 27
71745 GTAATTTCTC
*
71755 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
71782 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
71809 AA-CTGAGGGTAAACCAGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
71836 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
71863 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
71890 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
71917 AA-CTGAGGGTAAAATGATAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
71944 AATTGAGGGTAAAATAGTAATTCTGT-
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
71970 AACCTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* *
71998 AATCGAGGGTAAAACGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** *
72025 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
72052 AA-CTGAGGGTAAAACGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
72079 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
72106 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
72133 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
72160 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
**
72187 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
72214 AA-CTGA-GGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
72240 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
72267 AA-CTGAGGGTAAAATGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
**
72294 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
72321 AA-CTGA-GGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
72347 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
72374 AATCGAGGG
1 AATCGAGGG
72383 CATTTTAGTA
Statistics
Matches: 525, Mismatches: 58, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
26 53 0.10
27 465 0.89
28 7 0.01
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:73089 original size:82 final size:82
Alignment explanation
Indices: 72952--73856 Score: 1765
Period size: 82 Copynumber: 11.0 Consensus size: 82
72942 CTCAAATGCT
*
72952 CCACACGCCATTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
* *
73017 AGGCCTACCTACTACAC
66 AGGCCTCCCTACTACCC
73034 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73099 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73116 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73181 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73198 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73263 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73280 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73345 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73362 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73427 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73444 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73509 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73526 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73591 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73608 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73673 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73690 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
73755 AGGCCTCCCTACTACCC
66 AGGCCTCCCTACTACCC
73772 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
1 CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
* *
73837 AGGCCTACCTACTACAC
66 AGGCCTCCCTACTACCC
73854 CCA
1 CCA
73857 GGGTTTGATT
Statistics
Matches: 818, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 818 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (82 bp):
CCACACGCCACTTGCCACTAAGCCATAAGGTTTTTTGTGTCACAATTTCTCCAACAATATTCTTA
AGGCCTCCCTACTACCC
Found at i:77697 original size:27 final size:26
Alignment explanation
Indices: 77636--77747 Score: 116
Period size: 27 Copynumber: 4.1 Consensus size: 26
77626 GGAAGCGTCT
* *
77636 TGGTGGCTATGCCACAAATTATCTGATC
1 TGGTGGCTCTGCCAC--ATTATCTGTTC
77664 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGTTC
** *
77691 TAATGGCTCTGCCATGATTATCTGTATC
1 TGGTGGCTCTGCCA-CATTATCTGT-TC
* *
77719 TGGTGACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGTTC
77745 TGG
1 TGG
77748 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.10
27 36 0.51
28 28 0.39
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGTTC
Found at i:85252 original size:27 final size:26
Alignment explanation
Indices: 85194--85306 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
85184 AGGAAGCGTC
* *
85194 CTGGTGGCTATGCCACAAATTATCTAAT
1 CTGGTGGCTCTGCCAC--ATTATCTATT
*
85222 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTATT
*
85249 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTAT-T
* *
85277 CTGGTGACTCTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTATT
85303 CTGG
1 CTGG
85307 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
26 7 0.09
27 37 0.49
28 32 0.42
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTATT
Found at i:85279 original size:55 final size:54
Alignment explanation
Indices: 85194--85306 Score: 147
Period size: 55 Copynumber: 2.1 Consensus size: 54
85184 AGGAAGCGTC
* *
85194 CTGGTGGCTATGCCACAAATTATCTAATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATTATCTAATCTGGTGACTCTGCCACAT-TATCTATT
* * * *
85249 CTGGTGGCTCTGCCAC-GATTATCTGTATCTGGTGACTCTGTCACATTATCTATT
1 CTGGTGGCTATGCCACAAATTATCT-AATCTGGTGACTCTGCCACATTATCTATT
85303 CTGG
1 CTGG
85307 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
54 18 0.35
55 33 0.65
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATTATCTAATCTGGTGACTCTGCCACATTATCTATT
Found at i:88486 original size:14 final size:15
Alignment explanation
Indices: 88469--88497 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
88459 GCACGAAAAT
88469 TTCACACAA-ATAAA
1 TTCACACAATATAAA
88483 TTCACACAATATAAA
1 TTCACACAATATAAA
88498 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (15 bp):
TTCACACAATATAAA
Found at i:95707 original size:55 final size:55
Alignment explanation
Indices: 95639--95764 Score: 171
Period size: 55 Copynumber: 2.3 Consensus size: 55
95629 TGCGATATGC
* * *
95639 CCATGGTCAAGCCTGTCAAAACAACACGGGCGTACGACACGCCCGTGTGGAAGAA
1 CCATGGTCGAGCCTGTCAAAACAACACGGGCGTACAACACGCCCGTGTGGAACAA
* * * *
95694 CCATGGTCGAGCCTGCCAAAACAGCACGGGCGTTCAACACGCCCGTGTGGAACAC
1 CCATGGTCGAGCCTGTCAAAACAACACGGGCGTACAACACGCCCGTGTGGAACAA
* *
95749 CCGTGGTCGAACCTGT
1 CCATGGTCGAGCCTGT
95765 TAAATTAACA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (55 bp):
CCATGGTCGAGCCTGTCAAAACAACACGGGCGTACAACACGCCCGTGTGGAACAA
Found at i:99496 original size:19 final size:21
Alignment explanation
Indices: 99472--99511 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
99462 CGAAAGGAAT
99472 GAGAAA-TGGGCCAAA-AACG
1 GAGAAACTGGGCCAAAGAACG
99491 GAGAAACTGGGCCAAAGAACG
1 GAGAAACTGGGCCAAAGAACG
99512 AAATTAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.45, C:0.17, G:0.33, T:0.05
Consensus pattern (21 bp):
GAGAAACTGGGCCAAAGAACG
Found at i:102423 original size:25 final size:23
Alignment explanation
Indices: 102391--102452 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
102381 AATAGCCATG
*
102391 AATCGGTAAGCTCTTCTGAGCTGTA
1 AATCGGTAAGCTCTAC-GAGCTG-A
* *
102416 AATTGGTAAGCTAATACGAGCTGA
1 AATCGGTAAGCT-CTACGAGCTGA
102440 AATCGGTAAGCTC
1 AATCGGTAAGCTC
102453 ATATGAGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 12 0.39
25 17 0.55
26 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (23 bp):
AATCGGTAAGCTCTACGAGCTGA
Found at i:102447 original size:24 final size:25
Alignment explanation
Indices: 102391--102459 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
102381 AATAGCCATG
* *
102391 AATCGGTAAGCTCTTCTGAGCTGTA
1 AATCGGTAAGCTATACTGAGCTGTA
*
102416 AATTGGTAAGCTAATAC-GAGCTG-A
1 AATCGGTAAGCT-ATACTGAGCTGTA
102440 AATCGGTAAGCTCATA-TGAG
1 AATCGGTAAGCT-ATACTGAG
102460 TTGAGAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 18 0.49
25 17 0.46
26 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (25 bp):
AATCGGTAAGCTATACTGAGCTGTA
Found at i:104538 original size:27 final size:27
Alignment explanation
Indices: 104508--104586 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
104498 ACTTAATCGA
104508 TAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
** **
104535 TAAAATGACTGA-AATG-CCTCTACATGG
1 TAAAATGACT-ATTTTGCCCT-TATGTGG
*
104562 TAAAATGACT-TTTTGCCCCTATGTG
1 TAAAATGACTATTTTGCCCTTATGTG
104587 ATGTATATAT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
26 9 0.23
27 29 0.74
28 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGG
Found at i:107727 original size:14 final size:14
Alignment explanation
Indices: 107710--107737 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
107700 CAAGTATCAC
107710 AAGGTTAGTGAGTT
1 AAGGTTAGTGAGTT
107724 AAGGTTAGTGAGTT
1 AAGGTTAGTGAGTT
107738 CATATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (14 bp):
AAGGTTAGTGAGTT
Found at i:107900 original size:27 final size:26
Alignment explanation
Indices: 107870--107920 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
107860 AAATGTCTCT
**
107870 TTTCACATATCTATATTCATATAAATA
1 TTTCACATAAATAT-TTCATATAAATA
*
107897 TTTCATATAAATATTTCATATAAA
1 TTTCACATAAATATTTCATATAAA
107921 CACTTCTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTCACATAAATATTTCATATAAATA
Found at i:107903 original size:13 final size:13
Alignment explanation
Indices: 107885--107965 Score: 83
Period size: 13 Copynumber: 6.2 Consensus size: 13
107875 CATATCTATA
*
107885 TTCATATAAATAT
1 TTCATATAAACAT
*
107898 TTCATATAAATAT
1 TTCATATAAACAT
*
107911 TTCATATAAACAC
1 TTCATATAAACAT
* *
107924 TTCTTATAACCAT
1 TTCATATAAACAT
*
107937 TTCATAT-ATCTAT
1 TTCATATAAAC-AT
107950 TTCCATATAAACAT
1 TT-CATATAAACAT
107964 TT
1 TT
107966 AATACATCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
12 2 0.04
13 44 0.77
14 9 0.16
15 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
TTCATATAAACAT
Found at i:107977 original size:40 final size:39
Alignment explanation
Indices: 107896--107983 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 39
107886 TCATATAAAT
*
107896 ATTTCATATAAATATTTCATATAAACACTTCTTATAACC
1 ATTTCATATAAATATTTCATATAAACACTTCTAATAACC
**
107935 ATTTCATATATCTATTTCCATATAAACA-TT-TAATACATCC
1 ATTTCATATAAATATTT-CATATAAACACTTCTAATA-A-CC
107975 ATTTCATAT
1 ATTTCATAT
107984 TACCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 4 0.09
39 18 0.42
40 21 0.49
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (39 bp):
ATTTCATATAAATATTTCATATAAACACTTCTAATAACC
Found at i:107992 original size:40 final size:40
Alignment explanation
Indices: 107909--107993 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
107899 TCATATAAAT
* *
107909 ATTT-CATATAAACACTTCTTATAACCATTTCATATATCT
1 ATTTCCATATAAACACTTCTAATAACCATTTCATATATCC
107948 ATTTCCATATAAACA-TT-TAATACATCCATTTCATAT-TACC
1 ATTTCCATATAAACACTTCTAATA-A-CCATTTCATATAT-CC
107988 ATTTCC
1 ATTTCC
107994 GTTTACTCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 4 0.10
39 8 0.20
40 28 0.70
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.42
Consensus pattern (40 bp):
ATTTCCATATAAACACTTCTAATAACCATTTCATATATCC
Found at i:108118 original size:25 final size:25
Alignment explanation
Indices: 108051--108120 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
108041 ACGTAGGAAC
* * * *
108051 AATGCTCACACAAGCTATAATGGTA
1 AATGCTCACACGAGCTGTGATTGTA
* *
108076 AATGCTCACATGATCTGTGATTGTA
1 AATGCTCACACGAGCTGTGATTGTA
108101 AATGCTCA-ACCGAGCTGTGA
1 AATGCTCACA-CGAGCTGTGA
108121 AATGGGCCTG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (25 bp):
AATGCTCACACGAGCTGTGATTGTA
Found at i:110749 original size:38 final size:38
Alignment explanation
Indices: 110701--110909 Score: 262
Period size: 38 Copynumber: 5.5 Consensus size: 38
110691 GGCTCAAAGG
* * *
110701 CCCGAATATAATACCAGCACTAGGCCTACGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
*
110739 CCCGGATATAATACTAGCACGAAGCCTACGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
* * * *
110777 CCCGGATAT-ATACCCAGCATGAAGCCTGCAGGATTTAT
1 CCCGGATATAATA-CCAGCACGAAGCCTACGGGATTTAA
*
110815 CCCGGATATAATACTAGCACGAAGCCTGA-GGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCT-ACGGGATTTAA
* *
110853 CCCGGATATATTACCAGCACGAAGCC-AGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTA-CGGGATTTAA
*
110891 CCCGGATATAATTCCAGCA
1 CCCGGATATAATACCAGCA
110910 TATAGCCTGC
Statistics
Matches: 147, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
36 1 0.01
37 3 0.02
38 140 0.95
39 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
Found at i:110908 original size:114 final size:113
Alignment explanation
Indices: 110701--110923 Score: 301
Period size: 114 Copynumber: 2.0 Consensus size: 113
110691 GGCTCAAAGG
* * *
110701 CCCGAATATAATACCAGCACTAGGCCTACGGGATTTAACCCGGATATAATACTAGCACGAAGCCT
1 CCCGAATATAATACCAGCACGAAGCCTACGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
110766 ACGGGATTTAACCCGGATATATACCCAGCATGA-AGCCTGCAGGATTTAT
66 ACGGGATTTAACCCGGATATATACCCAGCAT-ATAGCCTGC-GGATTTAT
* * *
110815 CCCGGATATAATACTAGCACGAAGCCTGA-GGGATTTAACCCGGATATATTACCAGCACGAAGCC
1 CCCGAATATAATACCAGCACGAAGCCT-ACGGGATTTAACCCGGATATAATACCAGCACGAAGCC
* *
110879 -AGCGGGATTTATCCCGGATATA-ATTCCAGCATATAGCCTGCGGAT
65 TA-CGGGATTTAACCCGGATATATA-CCCAGCATATAGCCTGCGGAT
110924 CTTTAAGCCC
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
113 7 0.07
114 89 0.92
115 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (113 bp):
CCCGAATATAATACCAGCACGAAGCCTACGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
ACGGGATTTAACCCGGATATATACCCAGCATATAGCCTGCGGATTTAT
Found at i:119888 original size:20 final size:21
Alignment explanation
Indices: 119833--119890 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
119823 ATTCGAAATT
119833 TGTATATGTATAAG-TATATAA
1 TGTATATG-ATAAGATATATAA
* * *
119854 TGT-TTTGATATGATAT-TTA
1 TGTATATGATAAGATATATAA
119873 TGTATATGATAAGATATA
1 TGTATATGATAAGATATA
119891 CTTGTAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 9 0.31
20 17 0.59
21 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
TGTATATGATAAGATATATAA
Found at i:130038 original size:20 final size:20
Alignment explanation
Indices: 129983--130046 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
129973 ATTCGGCATT
*
129983 TGTATATGTATAAG-TATATAA
1 TGTATATG-ATAAGATAT-TTA
* *
130004 TGT-TTTGATATGATATTTA
1 TGTATATGATAAGATATTTA
*
130023 TGTATATGATAAGATATTTT
1 TGTATATGATAAGATATTTA
130043 TGTA
1 TGTA
130047 ATGTATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 9 0.26
20 23 0.66
21 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TGTATATGATAAGATATTTA
Found at i:133702 original size:38 final size:38
Alignment explanation
Indices: 133651--133812 Score: 261
Period size: 38 Copynumber: 4.3 Consensus size: 38
133641 ATATTCGATG
*
133651 TATATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
133689 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
133727 AATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
133765 TATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
133803 TATATTCGGG
1 TATATCCGGG
133813 CCTTCGTGCC
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 115 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:133866 original size:43 final size:43
Alignment explanation
Indices: 133784--133915 Score: 196
Period size: 43 Copynumber: 3.1 Consensus size: 43
133774 GATAAATCCC
* * *
133784 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
133825 GCAGGCTTCGTGCTGGTGATGTGTATTCAGGCCTTCATGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
133868 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
133911 GCAGG
1 GCAGG
133916 TGTAATGCCG
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 15 0.19
42 2 0.02
43 64 0.79
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.30
Consensus pattern (43 bp):
GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:134313 original size:45 final size:42
Alignment explanation
Indices: 134246--134353 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 42
134236 TTGAGTTGAT
* *
134246 TATTCGGGCCTTTGAGCTTAGCAAACTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGT--GA-AC
**
134291 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
134333 TGATATCGGGCC-TCGAGCCTA
1 T-AT-TCGGGCCTTCGAGCCTA
134354 ACAGGCGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 3 0.05
43 13 0.23
44 7 0.12
45 34 0.60
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (42 bp):
TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
Found at i:137380 original size:44 final size:44
Alignment explanation
Indices: 137199--137368 Score: 127
Period size: 43 Copynumber: 4.0 Consensus size: 44
137189 CTCATACAAC
* * * *
137199 GCCAACGTCCCAGACGTGGTCTTACATG-TAATCA-AATATCGAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAAATCACAA-ATCGAT
* ** * * * *
137242 GCCACTGTCTTAGATAGGGTCTTACATG-AAATCA-AAGA-CAAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAAATCACAA-ATCGAT
* * * *
137284 GCCGATGTCCCATACATGGTCTTACACGTAAATCTCAAATCGAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
* *
137328 GCCAATGTCCCAGACGTGGTCTTACAC-AAAATCACATATCG
1 GCCAATGTCCCAGACATGGTCTTACACGAAAATCACAAATCG
137369 GAATCCTATG
Statistics
Matches: 98, Mismatches: 26, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
42 23 0.23
43 46 0.47
44 29 0.30
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
GCCAATGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
Found at i:139950 original size:49 final size:47
Alignment explanation
Indices: 139894--140060 Score: 140
Period size: 49 Copynumber: 3.4 Consensus size: 47
139884 TGTTGTGTGA
*
139894 CAGTGTAAGACTTGTCTAGGACATGGTATCGACACTGATAGATGAGAGC
1 CAGTGTAAGACTTGTCTAGGACATGGCATCGAC-CTGATAGATGA-AGC
* * * * * *
139943 CAGTGTAAGACCTGTCTGGGACACGGCATCGACCTCCATATATGAATGT
1 CAGTGTAAGACTTGTCTAGGACATGGCATCGACCT-GATAGATGAA-GC
* * * * *
139992 CAGTGTAAGACTTTTCTAGGATATGGCATCAACTTTGAT-G-TGCTAGC
1 CAGTGTAAGACTTGTCTAGGACATGGCATCGAC-CTGATAGATG-AAGC
*
140039 CAGTGTAAGACCATGTCTAGGA
1 CAGTGTAAGA-CTTGTCTAGGA
140061 TAAGGCGTCG
Statistics
Matches: 93, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
47 13 0.14
48 13 0.14
49 66 0.71
50 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (47 bp):
CAGTGTAAGACTTGTCTAGGACATGGCATCGACCTGATAGATGAAGC
Found at i:143570 original size:25 final size:25
Alignment explanation
Indices: 143541--143601 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
143531 TAGAATAAAC
143541 ATACATGAAATTCATAAAAATGATG
1 ATACATGAAATTCATAAAAATGATG
143566 ATACATGAAATTCATAAAAATGATG
1 ATACATGAAATTCATAAAAATGATG
143591 ATACATGAAAT
1 ATACATGAAAT
143602 ATTGATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (25 bp):
ATACATGAAATTCATAAAAATGATG
Found at i:144217 original size:40 final size:40
Alignment explanation
Indices: 144180--145163 Score: 1796
Period size: 40 Copynumber: 24.6 Consensus size: 40
144170 GCTACTCGTT
* *
144180 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
144220 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144260 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144300 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144340 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144380 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144420 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144460 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144500 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144540 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144580 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144620 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144660 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144700 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144740 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144780 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144820 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144860 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144900 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144940 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
144980 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
145020 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
145060 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
145099 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
145140 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGG
145164 TCATCATTCG
Statistics
Matches: 924, Mismatches: 15, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
38 2 0.00
39 32 0.03
40 877 0.95
41 13 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Done.