Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold514
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: 50061
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2945 original size:40 final size:40
Alignment explanation
Indices: 2815--3035 Score: 236
Period size: 39 Copynumber: 5.6 Consensus size: 40
2805 TTGAATGCTG
* * * * * *
2815 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * *
2855 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAG-TACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
2894 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
2934 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTT-TTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
2973 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
3012 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3036 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 9 0.06
39 84 0.53
40 58 0.36
41 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:2951 original size:79 final size:78
Alignment explanation
Indices: 2815--3037 Score: 250
Period size: 79 Copynumber: 2.8 Consensus size: 78
2805 TTGAATGCTG
* * * * * * *
2815 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGTTAAG-TCCCGAAGGCATT
2879 TGTGCGAGTACTAAA
64 TGTGCGAGTACTAAA
* * *
2894 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTT
**
2959 GTGCGAGTTTTAAA
65 GTGCGAGTACTAAA
* * * * * *
2973 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTTG
3038 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
78 35 0.29
79 83 0.68
80 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTTG
TGCGAGTACTAAA
Found at i:3059 original size:78 final size:79
Alignment explanation
Indices: 2889--3069 Score: 197
Period size: 78 Copynumber: 2.3 Consensus size: 79
2879 TGTGCGAGTA
* * *
2889 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
2954 CAGTCGTGCGAGTT
66 CAGTCGAACGAGAG
* * * *
2968 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
3032 CATTTGAACGAGGAG
66 CAGTCGAACGA-GAG
* *
3047 CTATATCC-GGTTAAAT-CCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
3070 TACGTGATTT
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
77 7 0.08
78 43 0.51
79 34 0.40
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (79 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGAG
Found at i:10904 original size:119 final size:120
Alignment explanation
Indices: 10673--10934 Score: 352
Period size: 119 Copynumber: 2.2 Consensus size: 120
10663 TTGAATGCTG
* * *
10673 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* *
10737 TGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
66 CGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * * * *
10792 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCAT
* *
10855 TCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGTGAGTTACTAAA
65 TCGTGCGAG-TACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
10911 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
10935 TGAACGAGGA
Statistics
Matches: 125, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
118 1 0.01
119 88 0.70
120 36 0.29
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:10925 original size:39 final size:40
Alignment explanation
Indices: 10673--10934 Score: 343
Period size: 40 Copynumber: 6.6 Consensus size: 40
10663 TTGAATGCTG
* * * * * *
10673 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * *
10713 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAG-TACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
10752 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
10792 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
10832 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
10872 TCCGGGTTAAGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
10911 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
10935 TGAACGAGGA
Statistics
Matches: 203, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
38 1 0.00
39 65 0.32
40 129 0.64
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:10955 original size:79 final size:79
Alignment explanation
Indices: 10673--10934 Score: 350
Period size: 79 Copynumber: 3.3 Consensus size: 79
10663 TTGAATGCTG
* * * * * * * *
10673 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGG-CA
10736 TTGTGCGAG-TACTAAA
63 TTGTGCGAGTTACTAAA
10752 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-
*
10817 GTGCGAGTTATTAAA
65 GTGCGAGTTACTAAA
10832 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
*
10897 TGTGAGTTACTAAA
66 TGCGAGTTACTAAA
* * *
10911 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
10935 TGAACGAGGA
Statistics
Matches: 165, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
78 4 0.02
79 85 0.52
80 76 0.46
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
TGCGAGTTACTAAA
Found at i:19282 original size:18 final size:19
Alignment explanation
Indices: 19259--19294 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19249 AATTTTCCAA
19259 CCTTAA-CTCTAAAAAAAC
1 CCTTAACCTCTAAAAAAAC
*
19277 CCTTAACCTTTAAAAAAA
1 CCTTAACCTCTAAAAAAA
19295 AGGTCGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (19 bp):
CCTTAACCTCTAAAAAAAC
Found at i:22540 original size:18 final size:19
Alignment explanation
Indices: 22517--22557 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
22507 AAAATATAAG
* *
22517 TTTTG-ATTTTTATAATTA
1 TTTTGAATTTTAAAAATTA
22535 TTTTGAATTTTAAAAATTA
1 TTTTGAATTTTAAAAATTA
22554 TTTT
1 TTTT
22558 AAAAGTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTGAATTTTAAAAATTA
Found at i:24079 original size:40 final size:40
Alignment explanation
Indices: 24035--24295 Score: 396
Period size: 40 Copynumber: 6.5 Consensus size: 40
24025 CAAATTGTTA
* *
24035 ATGTATGGAACTTAGTGTGCGATTCGAGATAGCTTTGGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
* *
24075 ATGTATGGCACTTAGTGTACGATTCGACATAGCTTCGGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
* *
24115 ATGTATGACACTTAGTGTGCGATTCGAGATAGCTTTGGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
24155 ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
* * * * *
24195 ATATGTGGAACTTAGTGTGCGATTCAAGATAGCTTCAGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
* * *
24235 ATGTATAGCACTTAGTGTGCGATTCGTGATAGCTTTGGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
24275 ATGTATGGCACTTAGTGTGCG
1 ATGTATGGCACTTAGTGTGCG
24296 CTATTTTGAG
Statistics
Matches: 197, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 197 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (40 bp):
ATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGCT
Found at i:27552 original size:20 final size:19
Alignment explanation
Indices: 27516--27566 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
27506 AAGGGCTATT
*
27516 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
27535 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
27555 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
27567 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:28253 original size:48 final size:47
Alignment explanation
Indices: 28148--28360 Score: 144
Period size: 46 Copynumber: 4.5 Consensus size: 47
28138 TATGTGTGCT
* * * * * * *
28148 AGTGTAAGACATGCCTAGGACATGCATCGGCCAC-A-TTATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATAT-AAAGCC
28194 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATA-AAGCC
* * * * * *** *
28242 AGTGTAAGACATATCTGAGACATGCATCAACATTGAG-GCGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATAAAGCC
* * * * * * *
28288 AGTTTAAGACCTGTCTGGGACATGGCATCGGCCACGATATATGGAAGTC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGACCTCGAGATAT-AAAGCC
* *
28337 AGTGTAAGACCTTTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
28361 GTCTCAACTT
Statistics
Matches: 127, Mismatches: 34, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
46 53 0.42
47 11 0.09
48 39 0.31
49 24 0.19
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATAAAGCC
Found at i:28297 original size:94 final size:95
Alignment explanation
Indices: 28187--28360 Score: 233
Period size: 95 Copynumber: 1.8 Consensus size: 95
28177 GCCACATTAT
* *
28187 GAGAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGACCTCGAGATATACAAGCCAGTGTAAGA
1 GAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACCACGAGATATACAAGCCAGTGTAAGA
28251 CATATCTGAGACATGCATCAACATTGAGGC
66 CATATCTGAGACATGCATCAACATTGAGGC
* * * * ** *
28281 GAGAGCCAGTTTAAGACCTGTCTGGGACATGGCATCGGCCACGATATATGGAAGTCAGTGTAAGA
1 GAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACCACGAGATATACAAGCCAGTGTAAGA
* * *
28346 CCTTTCTGGGACATG
66 CATATCTGAGACATG
28361 GTCTCAACTT
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
94 27 0.40
95 40 0.60
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (95 bp):
GAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACCACGAGATATACAAGCCAGTGTAAGA
CATATCTGAGACATGCATCAACATTGAGGC
Found at i:31429 original size:43 final size:43
Alignment explanation
Indices: 31291--31614 Score: 329
Period size: 43 Copynumber: 7.6 Consensus size: 43
31281 TTTATGAAAA
* ** * *
31291 AAACGCCGCTATAGAACATGATTTTTAGCAGCTC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
31333 AAATGCCGCTAAAGAACA-AACCTTTAGCAGCGCTTCTCCTA-
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
31374 AAATCGCTGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCAC
1 AAA-CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
31418 AAACGCCGCTAAAGAACATGACCTTTAGTGACGCTTTTCCCA-
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
31460 AAACAG-CACTAAAGAACATGACCTTTAGCAGTGTTTTTCCCAC
1 AAAC-GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
31503 AAACGCCGCTAAAGAACATGACCTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* ** * *
31546 AAACCCCATTATAA-AA-TTGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTA-AAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
31588 AAACACCGATAAAAAACATGACCTTTA
1 AAACGCCGCTAAAGAACATGACCTTTA
31615 AAAAATATTT
Statistics
Matches: 232, Mismatches: 40, Indels: 19
0.80 0.14 0.07
Matches are distributed among these distances:
41 16 0.07
42 102 0.44
43 109 0.47
44 5 0.02
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:31615 original size:85 final size:85
Alignment explanation
Indices: 31303--31615 Score: 312
Period size: 85 Copynumber: 3.7 Consensus size: 85
31293 ACGCCGCTAT
** * * * * *
31303 AGAACATGATTTTTAGCAGCTC-TTTCCCACAAATGCCGCTAAAGAACA-AACCTTTAGC-AGCG
1 AGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAACGA-CG
* * * **
31365 CTTCTCCTAAAATCGCTGCTAA
65 CTTTTCCCAAAA-CACCACTAA
* **
31387 AGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGTGACGC
1 AGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAACGACGC
*
31452 TTTTCCCAAAACAGCACTAA
66 TTTTCCCAAAACACCACTAA
* * * *
31472 AGAACATGACCTTTAGCAGTGTTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAACGGCGC
1 AGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAACGACGC
* *
31537 TTTTCCCACAAACCCCATTATA
66 TTTTCCCA-AAACACCACTA-A
* * * * *
31559 A-AA-TTGACCTTTAGCGGCGCTTTTCTCACAAACACCGATAAAAAACATGACCTTTAA
1 AGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAA
31616 AAAATATTTT
Statistics
Matches: 193, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
84 18 0.09
85 142 0.74
86 30 0.16
87 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (85 bp):
AGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAACGACGC
TTTTCCCAAAACACCACTAA
Found at i:37631 original size:23 final size:23
Alignment explanation
Indices: 37605--37648 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
37595 CATGCCAATA
* *
37605 ATAAATGAAATCATCATGCATTC
1 ATAAATCAAATAATCATGCATTC
*
37628 ATAAATCAAATAATTATGCAT
1 ATAAATCAAATAATCATGCAT
37649 ATTAAGGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.32
Consensus pattern (23 bp):
ATAAATCAAATAATCATGCATTC
Found at i:40148 original size:37 final size:37
Alignment explanation
Indices: 40098--40169 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
40088 AGCTCAGACG
*
40098 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
40135 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGA
40170 ATATATTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:40432 original size:98 final size:96
Alignment explanation
Indices: 40316--40499 Score: 298
Period size: 98 Copynumber: 1.9 Consensus size: 96
40306 GCACATCGCC
*
40316 TACATATTTCACACTAGCCATTAGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCATTAGGCTTTACCACATATACATATCTC--ATACATATTTCACATT
40381 -GACCATTCGGCTTTACCACATATGCATATCTCA
64 AG-CCATTCGGCTTTACCACATATGCATATCTCA
* * *
40414 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCGCATTAG
1 TACATATTTCACACTAGCCATTAGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
40479 CCATTCGGCTTTACCACATAT
66 CCATTCGGCTTTACCACATAT
40500 ATACATGTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
96 35 0.43
97 1 0.01
98 45 0.56
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (96 bp):
TACATATTTCACACTAGCCATTAGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCGGCTTTACCACATATGCATATCTCA
Found at i:40440 original size:48 final size:48
Alignment explanation
Indices: 40316--40500 Score: 291
Period size: 48 Copynumber: 3.8 Consensus size: 48
40306 GCACATCGCC
* *
40316 TACATATTTCACACTAGCCATTAGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
40366 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
40414 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
40462 TACATATTTCGCATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
40501 TACATGTTCA
Statistics
Matches: 126, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
48 83 0.66
49 2 0.02
50 41 0.33
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:40563 original size:47 final size:47
Alignment explanation
Indices: 40473--40616 Score: 153
Period size: 47 Copynumber: 3.1 Consensus size: 47
40463 ACATATTTCG
* * * * * *
40473 CATTAGCCATTCGGCTTTACCACATATATACATGTTCATATTCACCA
1 CATTGGCCATTCGGCCTTATCACACATATACATGCTCACATTCACCA
* * *
40520 CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATACATGCTCACATTCACCA
* * *** *
40567 CATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATACATGCTCACATTCACCA
40614 CAT
1 CAT
40617 AAAATCCTAA
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 81 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATATACATGCTCACATTCACCA
Found at i:44754 original size:40 final size:40
Alignment explanation
Indices: 44722--45025 Score: 489
Period size: 40 Copynumber: 7.8 Consensus size: 40
44712 CCAGCATGAT
* * *
44722 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
44762 TGCTCTTCGGG-TTTAG-CAGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
44800 TGCTCTTCGGAACTTAGCCCGG--ATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
44838 TGCTCTT--GGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
44876 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
44915 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
44955 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
44995 TGCTCTTC-GGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
45026 CTCAATTCTC
Statistics
Matches: 247, Mismatches: 11, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
36 12 0.05
38 75 0.30
39 69 0.28
40 91 0.37
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:49164 original size:44 final size:45
Alignment explanation
Indices: 49068--49271 Score: 111
Period size: 48 Copynumber: 4.4 Consensus size: 45
49058 ATATGAAGAT
* *
49068 AAGCCGAAT-GCAATGTGATGAATGTGAGCATGCATATGTTGATA
1 AAGCCGAATGGCAATGTGATGAATATGAGCATGCATATATTGATA
* * *
49112 AGAG-CGAATGGC-ATGTGGTGAATATGA-CATGTATATATGTGGTA
1 A-AGCCGAATGGCAATGTGATGAATATGAGCATGCATATAT-TGATA
* * * *
49156 AAGCCGAATGGCTAATGCGAAAT-ATGTATGAGATATG--TATATGTGGTA
1 AAGCCGAATGGC-AATGTG--ATGA-ATATGAG-CATGCATATAT-TGATA
* * *
49204 AAGCCGAATGGCTAATGTGAAAT-ATGTATGAGATATGCATAT-GTGATA
1 AAGCCGAATGGC-AATGTG--ATGA-ATATGAG-CATGCATATATTGATA
49252 AAGCCGAATGGTCAATGTGA
1 AAGCCGAATGG-CAATGTGA
49272 AATATATATA
Statistics
Matches: 134, Mismatches: 12, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
43 11 0.08
44 32 0.24
45 4 0.03
46 5 0.04
47 1 0.01
48 74 0.55
49 1 0.01
50 6 0.04
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (45 bp):
AAGCCGAATGGCAATGTGATGAATATGAGCATGCATATATTGATA
Found at i:49312 original size:98 final size:96
Alignment explanation
Indices: 49146--49329 Score: 289
Period size: 98 Copynumber: 1.9 Consensus size: 96
49136 TGACATGTAT
* *
49146 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGATAAAGCCGAATGGCTAATGCGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
49211 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
*
49242 ATATGTGATAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGATAAAGCCGAATGGCT-AATGCG-AA-ATATATATGAGATATGTATATGTGGTAAAGC
* *
49306 CTAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
49330 GGCGATGTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 1 0.01
96 25 0.31
97 2 0.03
98 52 0.65
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (96 bp):
ATATGTGATAAAGCCGAATGGCTAATGCGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:49345 original size:50 final size:48
Alignment explanation
Indices: 49145--49329 Score: 282
Period size: 48 Copynumber: 3.8 Consensus size: 48
49135 ATGACATGTA
*
49145 TATATGTGGTAAAGCCGAATGGCTAATGCGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
49193 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* * *
49241 CATATGTGATAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
* *
49291 TATATGTGGTAAAGCCTAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
49330 GGCGATGTGC
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
47 1 0.01
48 79 0.64
49 4 0.03
50 39 0.31
51 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Done.