Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold308
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: 47394
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:10883 original size:17 final size:17
Alignment explanation
Indices: 10861--10893 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10851 TTTAATTAAA
10861 ATTAAAACTAATTGTTT
1 ATTAAAACTAATTGTTT
*
10878 ATTAAAATTAATTGTT
1 ATTAAAACTAATTGTT
10894 AGTAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTAAAACTAATTGTTT
Found at i:10885 original size:23 final size:24
Alignment explanation
Indices: 10830--10888 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
10820 TTTAAATTAA
* * *
10830 AATTAAAATTAAAATTATTTTTTT
1 AATTAAAATTAAAACTAATTGTTT
10854 AATTAAAATTAAAACTAATTGTTT
1 AATTAAAATTAAAACTAATTGTTT
10878 -ATTAAAATTAA
1 AATTAAAATTAA
10889 TTGTTAGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
AATTAAAATTAAAACTAATTGTTT
Found at i:10901 original size:16 final size:17
Alignment explanation
Indices: 10863--10903 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
10853 TAATTAAAAT
* *
10863 TAAAACTAATTGTTTAT
1 TAAAATTAATTGTTTAG
10880 TAAAATTAATTG-TTAG
1 TAAAATTAATTGTTTAG
10896 TAAAATTA
1 TAAAATTA
10904 TCAAATCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (17 bp):
TAAAATTAATTGTTTAG
Found at i:11020 original size:59 final size:58
Alignment explanation
Indices: 10928--11038 Score: 179
Period size: 60 Copynumber: 1.9 Consensus size: 58
10918 TGTAATTGTA
*
10928 ATTAATGTTTTAATAAAATCTAACATTTGATTAGTAAAATTTATCAAAATTATTAATGT
1 ATTAATGTTGTAATAAAATCTAACATTTGATTAGT-AAATTTATCAAAATTATTAATGT
*
10987 ATTAATTGTTGTAATAAAATCTAGCA-TTGATTAGTAAATTTATCAAAATTAT
1 ATTAA-TGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAAATTAT
11039 ATTTTGTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
58 17 0.35
59 14 0.29
60 18 0.37
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (58 bp):
ATTAATGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAAATTATTAATGT
Found at i:11047 original size:59 final size:59
Alignment explanation
Indices: 10922--11049 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 59
10912 ATTAATTGTA
*
10922 ATTGTAATTAATGTTTTAATAAAATCTAACATTTGATTAGTAAAATTTATCAAAATTATT
1 ATTGT-ATTAATGTTGTAATAAAATCTAACATTTGATTAGTAAAATTTATCAAAATTATT
* *
10982 AATGTATTAATTGTTGTAATAAAATCTAGCA-TTGATTAGT-AAATTTATCAAAATTATAT
1 ATTGTATTAA-TGTTGTAATAAAATCTAACATTTGATTAGTAAAATTTATCAAAATTAT-T
*
11041 TTTGTATTA
1 ATTGTATTA
11050 TGATTTTAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
58 17 0.28
59 22 0.36
60 22 0.36
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
ATTGTATTAATGTTGTAATAAAATCTAACATTTGATTAGTAAAATTTATCAAAATTATT
Found at i:11183 original size:24 final size:23
Alignment explanation
Indices: 11155--11199 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
11145 AATTAAACTT
*
11155 AAAATAAAAAACTATTATATTTCA
1 AAAATAAAAAA-TAATATATTTCA
11179 AAAATAAAAAATAATATATTT
1 AAAATAAAAAATAATATATTT
11200 AAATTTTCGG
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:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAAAAAATAATATATTTCA
Found at i:11187 original size:23 final size:24
Alignment explanation
Indices: 11155--11199 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
11145 AATTAAACTT
* *
11155 AAAATAAAAAACTATTATATTTCA
1 AAAATAAAAAAATAATATATTTCA
11179 AAAAT-AAAAAATAATATATTT
1 AAAATAAAAAAATAATATATTT
11200 AAATTTTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATAAAAAAATAATATATTTCA
Found at i:16142 original size:42 final size:42
Alignment explanation
Indices: 16052--16162 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
16042 TACCGTATCA
* *
16052 ATGCCATATCCCAGATATGGTCTTATATGAAATACCATATTG
1 ATGCCATATCCCAGATATGGTCTTATATGAAATACCACACTG
* * * *
16094 ACGCCATGTCCCTGACATGGTCTTATATGAAAT-CACACACTG
1 ATGCCATATCCCAGATATGGTCTTATATGAAATAC-CACACTG
*
16136 ATGCCATATCCCAGATATGGTTTTATA
1 ATGCCATATCCCAGATATGGTCTTATA
16163 CGGAATCTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTATATGAAATACCACACTG
Found at i:21825 original size:20 final size:19
Alignment explanation
Indices: 21800--21838 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21790 AAGCTAATAT
*
21800 AAATAAAATATCAATTTAAA
1 AAAT-AAATATCAAGTTAAA
*
21820 AAATAATTATCAAGTTAAA
1 AAATAAATATCAAGTTAAA
21839 TTAAGTAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATAAATATCAAGTTAAA
Found at i:21940 original size:21 final size:22
Alignment explanation
Indices: 21916--21956 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21906 AAATCAATTT
*
21916 TATTTATCAAA-TTTAAGTTAA
1 TATTTATAAAATTTTAAGTTAA
*
21937 TATTTGTAAAATTTTAAGTT
1 TATTTATAAAATTTTAAGTT
21957 TAAGATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
TATTTATAAAATTTTAAGTTAA
Found at i:25199 original size:42 final size:43
Alignment explanation
Indices: 25102--25299 Score: 265
Period size: 43 Copynumber: 4.7 Consensus size: 43
25092 TTATGTGGAA
* * *
25102 AAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * * *
25145 AAACGCCACTATAGGACATGAGCTTTAGCAGCAC-TTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
*
25187 AAATGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * * *
25230 AAACGCCTCTATAAAACATGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
*
25273 AAACG-TGCTATAGAACATGACCTTTAG
1 AAACGCCGCTATAGAACATGACCTTTAG
25300 AGGCGATTTG
Statistics
Matches: 138, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
42 56 0.41
43 82 0.59
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
Found at i:25256 original size:85 final size:85
Alignment explanation
Indices: 25100--25299 Score: 276
Period size: 85 Copynumber: 2.3 Consensus size: 85
25090 GTTTATGTGG
* * **
25100 AAAAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCACAAACGCCACTATAGGACATG
1 AAAAACGC-GCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCACTATAAAACATG
*
25165 AGCTTTAGCAGCAC-TTTCCC
65 ACCTTTAGCAGCACTTTTCCC
* * *
25185 ACAAATGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCTCTATAAAACATG
1 AAAAACG-CGCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCACTATAAAACATG
* *
25250 ACCTTTAGCGGCGCTTTTCCC
65 ACCTTTAGCAGCACTTTTCCC
*
25271 AAAAACGTGCTATAGAACATGACCTTTAG
1 AAAAACGCGCTATAGAACATGACCTTTAG
25300 AGGCGATTTG
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
85 88 0.88
86 12 0.12
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (85 bp):
AAAAACGCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCACTATAAAACATGA
CCTTTAGCAGCACTTTTCCC
Found at i:25478 original size:281 final size:281
Alignment explanation
Indices: 25024--25552 Score: 986
Period size: 281 Copynumber: 1.9 Consensus size: 281
25014 TACTAAAACT
*
25024 ATTTGCGGCGTTTTGATAAGTGCTACAAAAAAAACAGCTATAGTTAACGCCGCTGAAATTTGTGG
1 ATTTGCGGCGTTTTGATAAGTGCTACAAAAAAAACAGCTATAGTTAACGCCGCTAAAATTTGTGG
25089 CGTTTATGTGGAAAAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCACAAACGCCAC
66 CGTTTATGTGGAAAAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCACAAACGCCAC
*
25154 TATAGGACATGAGCTTTAGCAGCACTTTCCCACAAATGCCGCTATAGAACATGACCTTTAGCGGC
131 TATAGGACATGAGCTTTAGCAGCACTTTCCCACAAACGCCGCTATAGAACATGACCTTTAGCGGC
25219 ACTTTTCCCACAAACGCCTCTATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGTGCTAT
196 ACTTTTCCCACAAACGCCTCTATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGTGCTAT
25284 AGAACATGACCTTTAGAGGCG
261 AGAACATGACCTTTAGAGGCG
* * * *
25305 ATTTGCGGCTTTTTGATAAGTGCTGCAACAAAAATAGCTATAGTTAACGCCGCTAAAATTTGTGG
1 ATTTGCGGCGTTTTGATAAGTGCTACAAAAAAAACAGCTATAGTTAACGCCGCTAAAATTTGTGG
25370 CGTTTATGTGGAAAAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCACAAACGCCAC
66 CGTTTATGTGGAAAAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCACAAACGCCAC
25435 TATAGGACATGAGCTTTAGCAGCACTTTCCCACAAACGCCGCTATAGAACATGACCTTTAGCGGC
131 TATAGGACATGAGCTTTAGCAGCACTTTCCCACAAACGCCGCTATAGAACATGACCTTTAGCGGC
* *
25500 ACTTTTCCCACAAACGCCTCTATAAAACATGACCTTTAGTGGCGTTTTTCCCA
196 ACTTTTCCCACAAACGCCTCTATAAAACATGACCTTTAGCGGCGCTTTTCCCA
25553 CAAATGCCGT
Statistics
Matches: 240, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
281 240 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (281 bp):
ATTTGCGGCGTTTTGATAAGTGCTACAAAAAAAACAGCTATAGTTAACGCCGCTAAAATTTGTGG
CGTTTATGTGGAAAAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCACAAACGCCAC
TATAGGACATGAGCTTTAGCAGCACTTTCCCACAAACGCCGCTATAGAACATGACCTTTAGCGGC
ACTTTTCCCACAAACGCCTCTATAAAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGTGCTAT
AGAACATGACCTTTAGAGGCG
Found at i:25480 original size:42 final size:43
Alignment explanation
Indices: 25383--25580 Score: 245
Period size: 43 Copynumber: 4.6 Consensus size: 43
25373 TTATGTGGAA
* * *
25383 AAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * * *
25426 AAACGCCACTATAGGACATGAGCTTTAGCAGCAC-TTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
25468 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * * **
25511 AAACGCCTCTATAAAACATGACCTTTAGTGGCGTTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
* * * *
25554 AAATGCCGTTAAAGAACATAACCTTTA
1 AAACGCCGCTATAGAACATGACCTTTA
25581 AAAAAATTAT
Statistics
Matches: 136, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 38 0.28
43 98 0.72
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCAC
Found at i:25530 original size:85 final size:86
Alignment explanation
Indices: 25383--25580 Score: 254
Period size: 85 Copynumber: 2.3 Consensus size: 86
25373 TTATGTGGAA
* * * ** *
25383 AAACGCTGCTATAGGACATGAGCTTTAGCGGCACTTTTCCCACAAACGCCACTATAGGACATGAG
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCACTATAAAACATGAC
25448 CTTTAGCAGC-ACTTTCCCAC
66 CTTTAGCAGCGACTTTCCCAC
*
25468 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCTCTATAAAACATGAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCACTATAAAACATGAC
** **
25533 CTTTAGTGGCGTTTTTCCCAC
66 CTTTAGCAGCGACTTTCCCAC
* * * *
25554 AAATGCCGTTAAAGAACATAACCTTTA
1 AAACGCCGCTATAGAACATGACCTTTA
25581 AAAAAATTAT
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
85 66 0.68
86 31 0.32
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (86 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCACTATAAAACATGAC
CTTTAGCAGCGACTTTCCCAC
Found at i:26051 original size:15 final size:15
Alignment explanation
Indices: 26031--26061 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26021 ATTGATTAAG
26031 CTGCTAATGAATATT
1 CTGCTAATGAATATT
26046 CTGCTAATGAATATT
1 CTGCTAATGAATATT
26061 C
1 C
26062 CTTTGACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (15 bp):
CTGCTAATGAATATT
Found at i:26333 original size:43 final size:42
Alignment explanation
Indices: 26263--26351 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 42
26253 CATTGCAAGA
* * * * *
26263 TAATAAAACATACAATGCATTTTCTTAATTAAGTAAATCTTGG
1 TAATAAAACATACAATACATGTACTTAATCAAGGAAATCTT-G
* *
26306 TAATAAAAGATATAATACATGTACTTAATCAAGGAAATCTTG
1 TAATAAAACATACAATACATGTACTTAATCAAGGAAATCTTG
26348 TAAT
1 TAAT
26352 GAACTCAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 5 0.13
43 34 0.87
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (42 bp):
TAATAAAACATACAATACATGTACTTAATCAAGGAAATCTTG
Found at i:28794 original size:40 final size:40
Alignment explanation
Indices: 28732--28818 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
28722 TTTTTTGCCA
28732 CATTTTTCAAAAAGTGTCGCTAAT-ACTCGATCTATAGTGG
1 CATTTTTCAAAAAGTGTCGCTAATGA-TCGATCTATAGTGG
*
28772 CGTTTTTCAAAAAGTG-CAGCTAATGATCGATCTATAGTGG
1 CATTTTTCAAAAAGTGTC-GCTAATGATCGATCTATAGTGG
28812 CATTTTT
1 CATTTTT
28819 TTCATAAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
39 1 0.02
40 41 0.95
41 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (40 bp):
CATTTTTCAAAAAGTGTCGCTAATGATCGATCTATAGTGG
Found at i:29450 original size:22 final size:22
Alignment explanation
Indices: 29425--29475 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
29415 AAATTCTATA
*
29425 TTATTGAAATAAAATGTGAATG
1 TTATTGAAATAAAATATGAATG
29447 TTATTGAAATAAAATATGAATG
1 TTATTGAAATAAAATATGAATG
29469 TTATTGA
1 TTATTGA
29476 GTACGACACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATTGAAATAAAATATGAATG
Found at i:29654 original size:42 final size:42
Alignment explanation
Indices: 29579--29697 Score: 161
Period size: 42 Copynumber: 2.8 Consensus size: 42
29569 AGGGTTACTA
* *
29579 AGATGACGTGTAAGACCATATCTGGGATATGGCATTGATATG
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
* *
29621 AGACTT-CGTGTAAGACCATAGCT-GGCTATTGGCATCGATATG
1 AGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATG
*
29663 AGATTACATGTAAGACCATATCTGGGATATGGCAT
1 AGATTACGTGTAAGACCATATCTGGGATATGGCAT
29698 TGGTACGGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
41 6 0.09
42 55 0.83
43 5 0.08
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
Found at i:40767 original size:37 final size:36
Alignment explanation
Indices: 40707--40784 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 36
40697 TTATTACGAA
* *
40707 GTCTTACCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCGGACAAAATCTCCACACGAAGTCATCGG
*
40743 GTCTTACCCGGACAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTA-CCGGACAAAATCT-CCACACGAAGTCATCGG
40780 GTCTT
1 GTCTT
40785 TAGAGCTCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 7 0.19
37 30 0.81
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (36 bp):
GTCTTACCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:40981 original size:47 final size:47
Alignment explanation
Indices: 40903--41246 Score: 450
Period size: 47 Copynumber: 7.4 Consensus size: 47
40893 CCCTTCGGGA
* * * * * *
40903 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
40950 CCTGTCACATATATACACTTTCACATTCATCACA-TCGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
40996 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
41043 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
41090 CTTATCAC--ATATACACTTTCACATTCATCACATTAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
41135 CTTATCACACATATAACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT-ACACTTTCACATTCATCACATTGGCCATTAGGC
* *
41183 CTTAT-ACATATAT--ACTTTCACATTTATCAC-TTCGGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATT--GGCCATTAGGC
41228 CTTATCACATATATACACT
1 CTTATCACATATATACACT
41247 GTCTTGGCTG
Statistics
Matches: 263, Mismatches: 25, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.00
44 16 0.06
45 58 0.22
46 49 0.19
47 101 0.38
48 38 0.14
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:41062 original size:93 final size:94
Alignment explanation
Indices: 40903--41246 Score: 477
Period size: 93 Copynumber: 3.7 Consensus size: 94
40893 CCCTTCGGGA
* * * * * * * *
40903 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
40968 TTTCACATTCATCACATC-GCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
40996 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATTACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
*
41061 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * *
41090 CTTATCAC--ATATACACTTTCACATTCATCACATTAGCTATTAGGCCTTATCACACATATAACA
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATAT-ACA
41153 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATCGGCCATTAGGC
* *
41183 CTTAT-ACATATAT--ACTTTCACATTTATCAC-TTCGGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATT--GGCCATTAGGCCTTATCACATATATAC
41244 ACT
64 ACT
41247 GTCTTGGCTG
Statistics
Matches: 227, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
91 2 0.01
92 70 0.31
93 134 0.59
94 21 0.09
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:44812 original size:39 final size:40
Alignment explanation
Indices: 44769--44945 Score: 166
Period size: 39 Copynumber: 4.5 Consensus size: 40
44759 ACAGCATGAT
* *
44769 TGCTCTTCGGGACCTAGCCCGGATATAACAC-AGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** * **
44808 TGCTCTTCGGGGTTTAGCACAAATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
44848 TGCTCTTC-GGAATTAGTCCGGATACATCACTAGCAC-AGA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGA-A
* * *
44887 TGCTCTTCGGAACTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGACTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
44928 AGC-CTTCGGGACTTAGCC
1 TGCTCTTCGGGACTTAGCC
44946 GGACATCATT
Statistics
Matches: 112, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.01
39 54 0.48
40 43 0.38
41 7 0.06
42 7 0.06
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:45448 original size:43 final size:43
Alignment explanation
Indices: 45316--45460 Score: 210
Period size: 41 Copynumber: 3.4 Consensus size: 43
45306 GCAATTTCAA
*
45316 GCCCGC-CACCTTGGTGCCAATCT-ACAACCGTGAACACTTATT
1 GCCCGCACA-CTTAGTGCCAATCTCACAACCGTGAACACTTATT
45358 GCCCGCA-ACTTAGTGCCAATCTCA-AACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
45399 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACCTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACA-CTTATT
45443 G-CCGCAGCACATTAGTGC
1 GCCCGCA-CAC-TTAGTGC
45461 TGAACCAACC
Statistics
Matches: 95, Mismatches: 1, Indels: 11
0.89 0.01 0.10
Matches are distributed among these distances:
41 37 0.39
42 25 0.26
43 16 0.17
44 10 0.11
45 7 0.07
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Done.