Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold306
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: 53263
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:1888 original size:85 final size:85
Alignment explanation
Indices: 1745--1923 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
1735 TGGCCGCCAT
1745 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1810 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
1830 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1895 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
1915 GGGCATGGG
1 GAGCATGGG
1924 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:3235 original size:47 final size:47
Alignment explanation
Indices: 3181--3863 Score: 1019
Period size: 47 Copynumber: 14.6 Consensus size: 47
3171 TATTTGAATA
*
3181 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3228 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3275 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
3322 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
3369 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
3418 AATGTGAAAGTG--TATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
3463 AATGTGAACA-TG--TATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3508 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3555 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3602 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3649 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3696 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
3743 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
3790 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
3837 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
3864 TCCCGAAGGG
Statistics
Matches: 607, Mismatches: 23, Indels: 12
0.95 0.04 0.02
Matches are distributed among these distances:
45 87 0.14
46 2 0.00
47 471 0.78
49 47 0.08
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:3416 original size:22 final size:22
Alignment explanation
Indices: 3388--3461 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
3378 GTGTATATAT
3388 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * * *
3410 ATGTGATGAATG-TGAAAGTG-TA
1 ATGTGAT-AAGGCCGAATG-GCCA
3432 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
3455 ATGTGAT
1 ATGTGAT
3462 GAATGTGAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
22 23 0.59
23 16 0.41
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:3741 original size:22 final size:22
Alignment explanation
Indices: 3714--3835 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
3704 CATGTGTATG
3714 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
3736 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
3761 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
3783 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
3808 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
3830 TGTGAT
1 TGTGAT
3836 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:6356 original size:38 final size:38
Alignment explanation
Indices: 6292--6366 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
6282 AATCCGAGTT
*
6292 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
6330 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
6367 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:6480 original size:40 final size:40
Alignment explanation
Indices: 6425--6737 Score: 484
Period size: 40 Copynumber: 7.8 Consensus size: 40
6415 TCACGATGAT
6425 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
6465 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
6505 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* *
6545 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
6585 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * * *
6625 CGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * * * * *
6665 CGTGCTAA-ACCCGAAGAGCATTCGTGCTGGTGTTATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * *
6704 CGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
6738 CGTGTATTCG
Statistics
Matches: 252, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 32 0.13
40 220 0.87
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
Found at i:8136 original size:85 final size:85
Alignment explanation
Indices: 7993--8170 Score: 347
Period size: 85 Copynumber: 2.1 Consensus size: 85
7983 GGCCGGCCAT
7993 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
8058 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
8078 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
8143 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
8163 GGGCATGG
1 GAGCATGG
8171 CAATAAAATA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:9487 original size:47 final size:47
Alignment explanation
Indices: 9433--10026 Score: 876
Period size: 47 Copynumber: 12.6 Consensus size: 47
9423 TATTTGAATA
*
9433 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9480 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9529 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
9576 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
9623 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATATGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9672 AATGTGAAA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9718 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9765 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9812 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9859 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
9906 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
9953 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
10000 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
10027 TCCCGAAGGG
Statistics
Matches: 517, Mismatches: 24, Indels: 12
0.93 0.04 0.02
Matches are distributed among these distances:
46 41 0.08
47 385 0.74
48 2 0.00
49 89 0.17
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:9904 original size:22 final size:22
Alignment explanation
Indices: 9877--9998 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
9867 CATGTGTATG
9877 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
9899 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
9924 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
9946 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
9971 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
9993 TGTGAT
1 TGTGAT
9999 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:27545 original size:18 final size:18
Alignment explanation
Indices: 27524--27560 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27514 TTTGTTTCTG
*
27524 AAAATTATTCATTTTCAA
1 AAAATTATTCAATTTCAA
*
27542 AAAATTATTTAATTTCAA
1 AAAATTATTCAATTTCAA
27560 A
1 A
27561 TCGTTATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTATTCAATTTCAA
Found at i:28045 original size:18 final size:18
Alignment explanation
Indices: 28022--28074 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
28012 TGGCCCATTA
*
28022 CAGTAACAGTAAATAGTG
1 CAGTAACAGTAAACAGTG
*
28040 CAGTAATAGTAAACAGTG
1 CAGTAACAGTAAACAGTG
*
28058 CGGTAACAGTAAACAGT
1 CAGTAACAGTAAACAGT
28075 ATGCAATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (18 bp):
CAGTAACAGTAAACAGTG
Found at i:32785 original size:55 final size:54
Alignment explanation
Indices: 32717--32851 Score: 182
Period size: 55 Copynumber: 2.5 Consensus size: 54
32707 TGTGCCCTTA
* * *
32717 ACCCGTGTGCAACACTGACTTTAAAACACGGCCATGACACA-CTCCAGTGTGGCCT
1 ACCCGTGTACAACACTGACTTTAAAACACGACCATGACACATC-CCA-TGTGGCAT
*
32772 ACCCGTGTACAACACTGGCTTTAAAACACGACCATGACACATGCCCATGTGGCAT
1 ACCCGTGTACAACACTGACTTTAAAACACGACCATGACACAT-CCCATGTGGCAT
**
32827 GTCCGTGTACAACACTGACTTTAAA
1 ACCCGTGTACAACACTGACTTTAAA
32852 TTTTAAGTGC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
55 67 0.94
56 3 0.04
57 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (54 bp):
ACCCGTGTACAACACTGACTTTAAAACACGACCATGACACATCCCATGTGGCAT
Found at i:33819 original size:47 final size:46
Alignment explanation
Indices: 33756--33926 Score: 171
Period size: 47 Copynumber: 3.6 Consensus size: 46
33746 ACAACTCTTA
*
33756 GCCAATGCATGTCCCAGACACGTCTTACAATGGCTATCATCGTCGAG
1 GCCAATGCATGTCCCAGACACGTCTTACATTGGCTATCATC-TCGAG
* ** * *
33803 GCCAATGCATGTCCCAGACATGTCTTACATTGGCGCTCATTCTCTAC
1 GCCAATGCATGTCCCAGACACGTCTTACATTGGCTATCA-TCTCGAG
** * * * *
33850 GCTGATGCCATGTCCCAGACACGGTCTTACATTAGCTATCATATTGTG
1 GCCAATG-CATGTCCCAGACAC-GTCTTACATTGGCTATCATCTCGAG
** *
33898 GCTGATGCATGTCCCAGACATGTCTTACA
1 GCCAATGCATGTCCCAGACACGTCTTACA
33927 CTAGCACACA
Statistics
Matches: 103, Mismatches: 18, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
46 8 0.08
47 56 0.54
48 24 0.23
49 15 0.15
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
GCCAATGCATGTCCCAGACACGTCTTACATTGGCTATCATCTCGAG
Found at i:33869 original size:48 final size:46
Alignment explanation
Indices: 33807--33931 Score: 144
Period size: 48 Copynumber: 2.7 Consensus size: 46
33797 GTCGAGGCCA
* *
33807 ATGCATGTCCCAGACATGTCTTACATTGGCGCTCAT-TCTCTACGCTG
1 ATGCATGTCCCAGACATGTCTTACATTAGCGATCATAT-TCT-CGCTG
* * * *
33854 ATGCCATGTCCCAGACACGGTCTTACATTAGCTATCATATTGTGGCTG
1 ATG-CATGTCCCAGACA-TGTCTTACATTAGCGATCATATTCTCGCTG
*
33902 ATGCATGTCCCAGACATGTCTTACACTAGC
1 ATGCATGTCCCAGACATGTCTTACATTAGC
33932 ACACAAGTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
46 12 0.18
47 16 0.24
48 20 0.30
49 18 0.27
50 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACATTAGCGATCATATTCTCGCTG
Found at i:36610 original size:28 final size:27
Alignment explanation
Indices: 36585--36641 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
36575 TTCGTGGCGG
36585 ACCCTAAAAGAAATAATGA-GTATGGCAA
1 ACCCT-AAAGAAATAA-GATGTATGGCAA
*
36613 ACCCTGAAGAAATAAGATGTATGGCAA
1 ACCCTAAAGAAATAAGATGTATGGCAA
36640 AC
1 AC
36642 TCGTAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 2 0.07
27 20 0.74
28 5 0.19
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (27 bp):
ACCCTAAAGAAATAAGATGTATGGCAA
Found at i:41289 original size:28 final size:28
Alignment explanation
Indices: 41257--41384 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
41247 ATAGTAAGTC
*
41257 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41285 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
41314 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
41342 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41371 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41385 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41347 original size:57 final size:57
Alignment explanation
Indices: 41256--41384 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
41246 TATAGTAAGT
*
41256 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
41313 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
41370 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
41385 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:49330 original size:28 final size:28
Alignment explanation
Indices: 49298--49421 Score: 155
Period size: 28 Copynumber: 4.5 Consensus size: 28
49288 ATAGTAAGTC
*
49298 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
49326 CGCACACTT-GT--TACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
49351 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
49379 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
49408 CGCACACTTAGTGC
1 CGCACACTTAGTGC
49422 CAATCTCATG
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
25 22 0.26
26 2 0.02
27 2 0.02
28 40 0.48
29 18 0.21
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:49337 original size:25 final size:25
Alignment explanation
Indices: 49309--49387 Score: 113
Period size: 25 Copynumber: 3.0 Consensus size: 25
49299 GCACACTTAG
49309 TGTTATATAATCAAACTCGCACACT
1 TGTTATATAATCAAACTCGCACACT
*
49334 TGTTACATAATCAAACTCGCACACT
1 TGTTATATAATCAAACTCGCACACT
*
49359 TAGTGCTATATAATCAAACTTGCACACT
1 T-GT--TATATAATCAAACTCGCACACT
49387 T
1 T
49388 AGTGCTATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
25 25 0.52
26 2 0.04
28 21 0.44
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (25 bp):
TGTTATATAATCAAACTCGCACACT
Found at i:51336 original size:44 final size:44
Alignment explanation
Indices: 51262--51361 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
51252 ATACACCTAC
*
51262 AATGTGTAAGACCATAGTTGAAAGATGCTATGGCATCATAATAGA
1 AATGAGTAAGACCATAGTTGAAAGATGCTATGGCATCATAA-AGA
* * *
51307 AATGAGTAAGACCATGGTTG-AATATGCTATGGCATCATAAATA
1 AATGAGTAAGACCATAGTTGAAAGATGCTATGGCATCATAAAGA
51350 AA-GAGTAAGACC
1 AATGAGTAAGACC
51362 CTGACTGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 10 0.20
43 4 0.08
44 19 0.37
45 18 0.35
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (44 bp):
AATGAGTAAGACCATAGTTGAAAGATGCTATGGCATCATAAAGA
Done.