Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold541
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: 74348
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.31
Warning! 6034 characters in sequence are not A, C, G, or T
Found at i:1963 original size:9 final size:9
Alignment explanation
Indices: 1851--1973 Score: 62
Period size: 9 Copynumber: 13.4 Consensus size: 9
1841 TTTTATATTA
1851 AAAATA-AT
1 AAAATATAT
1859 ACAAATA-AT
1 A-AAATATAT
1868 ACAAATATAT
1 A-AAATATAT
1878 ACAAAT-TA-
1 A-AAATATAT
1886 AAAATAT-T
1 AAAATATAT
*
1894 ATAAATTTAT
1 A-AAATATAT
1904 AAAAGTATAT
1 AAAA-TATAT
* *
1914 AAAAGTACAA
1 AAAA-TATAT
1924 AAAATATA-
1 AAAATATAT
*
1932 AAAACATATT
1 AAAATATA-T
*
1942 ATAAATGAAAT
1 A-AAAT-ATAT
1953 AAAATATAT
1 AAAATATAT
*
1962 AAATTAT-T
1 AAAATATAT
1970 AAAA
1 AAAA
1974 ATTGTCAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
7 4 0.04
8 15 0.16
9 36 0.39
10 31 0.33
11 5 0.05
12 2 0.02
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATATAT
Found at i:9515 original size:22 final size:22
Alignment explanation
Indices: 9474--9516 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
9464 AAAATAATAA
9474 AATACTTATAACGTTTTTATGTC
1 AATACTTATAAC-TTTTTATGTC
9497 AATACTTATATA-TTTTTATG
1 AATACTTATA-ACTTTTTATG
9517 AATTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 10 0.53
24 1 0.05
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (22 bp):
AATACTTATAACTTTTTATGTC
Found at i:14785 original size:17 final size:17
Alignment explanation
Indices: 14757--14790 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
14747 AGGTCATACC
14757 ATTTTATATTTATATAAT
1 ATTTTATATTTAT-TAAT
14775 ATTTT-TATTTATTAAT
1 ATTTTATATTTATTAAT
14791 TACTTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATATTTATTAAT
Found at i:17400 original size:23 final size:23
Alignment explanation
Indices: 17368--17413 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
17358 CAACCAAACT
*
17368 GATAGTTTTAGCTTCTCATCTGG
1 GATAGCTTTAGCTTCTCATCTGG
17391 GATAGCTTTAGCTTCTCATCTGG
1 GATAGCTTTAGCTTCTCATCTGG
17414 TACTTGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (23 bp):
GATAGCTTTAGCTTCTCATCTGG
Found at i:22208 original size:16 final size:17
Alignment explanation
Indices: 22177--22209 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22167 CATGTTGGAT
*
22177 ACATATCCATATCCAAG
1 ACATATCCATAACCAAG
22194 ACATA-CCATAACCAAG
1 ACATATCCATAACCAAG
22210 TAACATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.30, G:0.06, T:0.18
Consensus pattern (17 bp):
ACATATCCATAACCAAG
Found at i:25219 original size:7 final size:7
Alignment explanation
Indices: 25207--25233 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25197 TTTTCAACAA
25207 ATTTAAT
1 ATTTAAT
25214 ATTTAAT
1 ATTTAAT
25221 ATTTAAT
1 ATTTAAT
25228 ATTTAA
1 ATTTAA
25234 CAATGTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTAAT
Found at i:30338 original size:24 final size:24
Alignment explanation
Indices: 30311--30358 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
30301 AAATTAGAAA
30311 AACAAAAAGGCTTAATTTTTAACT
1 AACAAAAAGGCTTAATTTTTAACT
30335 AACAAAAAGGCTTAATTTTTAACT
1 AACAAAAAGGCTTAATTTTTAACT
30359 TTTTTTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (24 bp):
AACAAAAAGGCTTAATTTTTAACT
Found at i:32200 original size:16 final size:17
Alignment explanation
Indices: 32167--32208 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
32157 ATTTTTATTA
*
32167 AATTATATT-TAATAAT
1 AATTATATTAAAATAAT
32183 AATTATATTAAAAT-AT
1 AATTATATTAAAATAAT
*
32199 AATTAAATTA
1 AATTATATTA
32209 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATATTAAAATAAT
Found at i:32217 original size:60 final size:61
Alignment explanation
Indices: 32144--32261 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 61
32134 ATTTTCTAAT
32144 ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
1 ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
* * * *
32205 ATTAT-TTTTATTATTTTTATTAAATTATGTTTAATAATAATTTTATTAAAATTTAAT
1 ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT
32262 AACAATAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 48 0.91
61 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (61 bp):
ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
Found at i:32385 original size:16 final size:15
Alignment explanation
Indices: 32364--32405 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
32354 ATTAAATTAC
32364 TTATTACAATTATATT
1 TTATTACAATT-TATT
32380 TTATTACAACTTTATT
1 TTATTACAA-TTTATT
*
32396 CTATTACAAT
1 TTATTACAAT
32406 GGACCGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 21 0.88
17 2 0.08
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTACAATTTATT
Found at i:38723 original size:16 final size:16
Alignment explanation
Indices: 38698--38735 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
38688 TGATAGGAAT
38698 GAAAGAAAAGAAAGAA
1 GAAAGAAAAGAAAGAA
*
38714 GAAAGGAAAGAAAGAA
1 GAAAGAAAAGAAAGAA
38730 GAAAGA
1 GAAAGA
38736 GATGGGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAGAAAGAA
Found at i:39456 original size:16 final size:17
Alignment explanation
Indices: 39425--39467 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
39415 TTGTACTTTC
39425 ATATAT-TTTATAAATTT
1 ATATATATTT-TAAATTT
39442 ATA-ATATTTTAAATTT
1 ATATATATTTTAAATTT
*
39458 GTATATATTT
1 ATATATATTT
39468 GTATTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATATATTTTAAATTT
Found at i:39467 original size:26 final size:25
Alignment explanation
Indices: 39429--39477 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
39419 ACTTTCATAT
39429 ATTTTATAAATTTATAATATTTTAA
1 ATTTTATAAATTTATAATATTTTAA
* * *
39454 ATTTGTATATATTTGTATTATTTT
1 ATTT-TATAAATTTATAATATTTT
39478 TAATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (25 bp):
ATTTTATAAATTTATAATATTTTAA
Found at i:41198 original size:16 final size:17
Alignment explanation
Indices: 41167--41209 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41157 TTGTACTTTC
41167 ATATAT-TTTATAAATTT
1 ATATATATTT-TAAATTT
41184 ATA-ATATTTTAAATTT
1 ATATATATTTTAAATTT
*
41200 GTATATATTT
1 ATATATATTT
41210 GTATTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATATATTTTAAATTT
Found at i:41209 original size:26 final size:25
Alignment explanation
Indices: 41171--41219 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
41161 ACTTTCATAT
41171 ATTTTATAAATTTATAATATTTTAA
1 ATTTTATAAATTTATAATATTTTAA
* * *
41196 ATTTGTATATATTTGTATTATTTT
1 ATTT-TATAAATTTATAATATTTT
41220 TAATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (25 bp):
ATTTTATAAATTTATAATATTTTAA
Found at i:42250 original size:9 final size:9
Alignment explanation
Indices: 42229--42351 Score: 62
Period size: 9 Copynumber: 13.4 Consensus size: 9
42219 TTTTGACAAT
42229 TTTTA-ATA
1 TTTTATATA
*
42237 ATTTATATA
1 TTTTATATA
*
42246 TTTTATTTCA
1 TTTTATAT-A
42256 -TTTATAATA
1 TTTTAT-ATA
*
42265 TGTTTTTATA
1 T-TTTATATA
* *
42275 TTTTTTGTA
1 TTTTATATA
42284 CTTTTATATA
1 -TTTTATATA
42294 CTTTTATA-A
1 -TTTTATATA
*
42303 ATTTATAATA
1 TTTTAT-ATA
42313 TTTT-TA-A
1 TTTTATATA
42320 TTTGTATATA
1 TTT-TATATA
42330 TTTGTAT-TA
1 TTT-TATATA
42339 TTTGTAT-TA
1 TTT-TATATA
42348 TTTT
1 TTTT
42352 TAATATAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.04
8 12 0.13
9 41 0.44
10 33 0.35
11 4 0.04
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTATATA
Found at i:42652 original size:17 final size:18
Alignment explanation
Indices: 42619--42664 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
42609 AATTTTAATA
*
42619 ATTTGTATATATTTTATT
1 ATTTTTATATATTTTATT
*
42637 GTTTTTATAT-TTTTATT
1 ATTTTTATATATTTTATT
42654 ATTTTTA-ATAT
1 ATTTTTATATAT
42665 AAAATATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 14 0.58
18 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
ATTTTTATATATTTTATT
Found at i:42897 original size:307 final size:307
Alignment explanation
Indices: 42337--42924 Score: 1005
Period size: 307 Copynumber: 1.9 Consensus size: 307
42327 ATATTTGTAT
*
42337 TATTTGTATTATTTTTAATATAAAATATCACATTTTGCTGCATAGCACAATTCTCGTGTACCACG
1 TATTTGTATTATTTTTAATATAAAATATCACATTTTGCTGCATAGCACAATCCTCGTGTACCACG
* * * * * *
42402 TGACGAAAACAACCTTTAAAAATATTTATTGTTACTCTTTAACGATTGACTGTTAACTTTAACGG
66 TGACAAAAACAACCTTTAAAAATAGTCATCGTTACTCTTTAAAGATTGACCGTTAACTTTAACGG
*
42467 TTAAATAGTTTAATAAATTGAAATTTTAACGTTCAATAACTCAATTGAATTCAAAAAAAGTATAA
131 TTAAATAGTTTAATAAATTGAAATTTTAACGTTCAATAACTCAATTGAACTCAAAAAAAGTATAA
* * * *
42532 GGGCTTAATTGCTCTTTTTGGAAAAATTCAAGGGCTTTAAAGACTCTTTAGCCTTAATTTTTACA
196 GGGCTTAATTGATCTTTTTAGAAAAATTCAAGGACTTTAAAGACTCTTTAACCTTAATTTTTACA
42597 TCATAGCTAACAAATTTTAATAATTTGTATATATTTTATTGTTTTTA
261 TCATAGCTAACAAATTTTAATAATTTGTATATATTTTATTGTTTTTA
* * *
42644 TATTTTTATTATTTTTAATATAAAATATCATATTTTGCTGCATAGCACAATCCTCGTGTGCCACG
1 TATTTGTATTATTTTTAATATAAAATATCACATTTTGCTGCATAGCACAATCCTCGTGTACCACG
*
42709 TGACAAAAATAACCTTTAAAAATAGTCATCGTTACTCTTTAAAGATTGACCGTTAACTTTAACGG
66 TGACAAAAACAACCTTTAAAAATAGTCATCGTTACTCTTTAAAGATTGACCGTTAACTTTAACGG
*
42774 TTAAATAGTTTAATAAATTGAAATTTTAACGTTCAATAATTCAATTGAACTCAAAAAAAGTATAA
131 TTAAATAGTTTAATAAATTGAAATTTTAACGTTCAATAACTCAATTGAACTCAAAAAAAGTATAA
*
42839 GGGCTTAATTGATCTTTTTAGAAAAATTCAAGGACTTTTAAGACTCTTTAACCTTAATTTTTACA
196 GGGCTTAATTGATCTTTTTAGAAAAATTCAAGGACTTTAAAGACTCTTTAACCTTAATTTTTACA
*
42904 TCATAGTTAACAAATTTTAAT
261 TCATAGCTAACAAATTTTAAT
42925 GCATCGAATA
Statistics
Matches: 262, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
307 262 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (307 bp):
TATTTGTATTATTTTTAATATAAAATATCACATTTTGCTGCATAGCACAATCCTCGTGTACCACG
TGACAAAAACAACCTTTAAAAATAGTCATCGTTACTCTTTAAAGATTGACCGTTAACTTTAACGG
TTAAATAGTTTAATAAATTGAAATTTTAACGTTCAATAACTCAATTGAACTCAAAAAAAGTATAA
GGGCTTAATTGATCTTTTTAGAAAAATTCAAGGACTTTAAAGACTCTTTAACCTTAATTTTTACA
TCATAGCTAACAAATTTTAATAATTTGTATATATTTTATTGTTTTTA
Found at i:43241 original size:28 final size:26
Alignment explanation
Indices: 43205--43257 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
43195 TTATTAAAAA
*
43205 ATTCAATTTTTAATAATTTTTATATTTT
1 ATTCAATTTATAAT-ATTTTTA-ATTTT
*
43233 ATTCCATTTATAATATTTTTAATTT
1 ATTCAATTTATAATATTTTTAATTT
43258 GTAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 7 0.30
28 12 0.52
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTCAATTTATAATATTTTTAATTTT
Found at i:47911 original size:18 final size:18
Alignment explanation
Indices: 47888--48026 Score: 107
Period size: 18 Copynumber: 7.7 Consensus size: 18
47878 ATCTCATTCC
* *
47888 CATTCTCGCTCACACTCT
1 CATTCTCACTCTCACTCT
* *
47906 CATTCTCACTCACACTGT
1 CATTCTCACTCTCACTCT
*
47924 CATTCTCAATCTCACTCT
1 CATTCTCACTCTCACTCT
* * *
47942 CACTCTCACCCTCACTCA
1 CATTCTCACTCTCACTCT
* * **
47960 CACTCTCATTCTCAAACT
1 CATTCTCACTCTCACTCT
* * *
47978 CATTCTCGCTCTTATTCT
1 CATTCTCACTCTCACTCT
* *
47996 CATTCTCACTCACACTCA
1 CATTCTCACTCTCACTCT
* *
48014 CACTCTCATTCTC
1 CATTCTCACTCTC
48027 GTTTTTCATC
Statistics
Matches: 93, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 93 1.00
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.35
Consensus pattern (18 bp):
CATTCTCACTCTCACTCT
Found at i:47928 original size:42 final size:42
Alignment explanation
Indices: 47879--48027 Score: 136
Period size: 42 Copynumber: 3.4 Consensus size: 42
47869 GGATGCTGAA
*
47879 TCTCATTCCCATTCTCGCTCACACTCTCATTCTCACTCACAC
1 TCTCATTCCCATTCTCGCTCTCACTCTCATTCTCACTCACAC
* * * * **
47921 TGTCATTCTCAATCTCACTCTCACTCTCACCCTCACTCACAC
1 TCTCATTCCCATTCTCGCTCTCACTCTCATTCTCACTCACAC
* *
47963 TCTCATTCTCAAACTCATTCTCGCTCTTATTCTCATTCTCACTCACAC
1 TCTCA-T-TC---C-CATTCTCGCTCTCACTCTCATTCTCACTCACAC
* * *
48011 TCACACTCTCATTCTCG
1 TCTCATTCCCATTCTCG
48028 TTTTTCATCT
Statistics
Matches: 83, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
42 47 0.57
43 1 0.01
44 2 0.02
46 2 0.02
48 31 0.37
ACGTcount: A:0.20, C:0.42, G:0.03, T:0.35
Consensus pattern (42 bp):
TCTCATTCCCATTCTCGCTCTCACTCTCATTCTCACTCACAC
Found at i:47930 original size:24 final size:24
Alignment explanation
Indices: 47903--48026 Score: 107
Period size: 24 Copynumber: 5.4 Consensus size: 24
47893 TCGCTCACAC
*
47903 TCTCATTCTCACTCACACTGTCAT
1 TCTCATTCTCACTCACACTCTCAT
* *
47927 TCTCAATCTCACTCTCACTCTCA-
1 TCTCATTCTCACTCACACTCTCAT
47950 -C-C---CTCACTCACACTCTCAT
1 TCTCATTCTCACTCACACTCTCAT
** * * * *
47969 TCTCAAACTCATTCTCGCTCTTAT
1 TCTCATTCTCACTCACACTCTCAT
* *
47993 TCTCATTCTCACTCACACTCACAC
1 TCTCATTCTCACTCACACTCTCAT
48017 TCTCATTCTC
1 TCTCATTCTC
48027 GTTTTTCATC
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
18 15 0.19
20 1 0.01
21 2 0.03
22 1 0.01
24 59 0.76
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.35
Consensus pattern (24 bp):
TCTCATTCTCACTCACACTCTCAT
Found at i:47936 original size:6 final size:6
Alignment explanation
Indices: 47900--48026 Score: 92
Period size: 6 Copynumber: 21.2 Consensus size: 6
47890 TTCTCGCTCA
* * * * *
47900 CACTCT CATTCT CACTCA CACTGT CATTCT CAATCT CACTCT CACTCT
1 CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT
* * * ** * * * *
47948 CACCCT CACTCA CACTCT CATTCT CAAACT CATTCT CGCTCT TATTCT
1 CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT
* * * *
47996 CATTCT CACTCA CACTCA CACTCT CATTCT C
1 CACTCT CACTCT CACTCT CACTCT CACTCT C
48027 GTTTTTCATC
Statistics
Matches: 93, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.21, C:0.43, G:0.02, T:0.35
Consensus pattern (6 bp):
CACTCT
Found at i:48355 original size:5 final size:5
Alignment explanation
Indices: 48345--48370 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
48335 GAAAGCAGTA
48345 TTCTT TTCTT TTCTT TTCTT TTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT T
48371 GCAAACAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:48895 original size:26 final size:26
Alignment explanation
Indices: 48866--48915 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
48856 ACTTTTATAC
*
48866 ATTTTTATAAATTTATAATATTTTAA
1 ATTTGTATAAATTTATAATATTTTAA
* * *
48892 ATTTGTATATATTTGTATTATTTT
1 ATTTGTATAAATTTATAATATTTT
48916 TAATATAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (26 bp):
ATTTGTATAAATTTATAATATTTTAA
Found at i:50628 original size:21 final size:20
Alignment explanation
Indices: 50556--50630 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 20
50546 TAACTTAATT
50556 ATTTTAAATATTTTATTAACA
1 ATTTTAAA-ATTTTATTAACA
*** *
50577 ATTTTATGCTTTT-TATAA-T
1 ATTTTAAAATTTTAT-TAACA
*
50596 ATTTTGTAAATTTTATTAACA
1 ATTTT-AAAATTTTATTAACA
50617 ATTTTAAGAATTTT
1 ATTTTAA-AATTTT
50631 CTGTATTTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
19 6 0.15
20 15 0.38
21 18 0.46
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTAAAATTTTATTAACA
Found at i:52982 original size:39 final size:39
Alignment explanation
Indices: 52826--52982 Score: 183
Period size: 39 Copynumber: 4.0 Consensus size: 39
52816 GACCAAACTG
* * *
52826 ACCTAGAATAATCATCCCTTTTCAGATCATCTT-TCTCCC
1 ACCTAGAATATTCATCCCTATTCTGATCATCTTCTC-CCC
* *
52865 ACCTAGAATATTCATCCCTCTTCTGATCATCTTTTCCCC
1 ACCTAGAATATTCATCCCTATTCTGATCATCTTCTCCCC
* * * * * *
52904 ATCTAGAGTATTCATCCTTATTCCGGTCATCTTCCCCCC
1 ACCTAGAATATTCATCCCTATTCTGATCATCTTCTCCCC
52943 ACCTAGAATATTCAT-CCTATTCTGATCATCATTCTCCCC
1 ACCTAGAATATTCATCCCTATTCTGATCATC-TTCTCCCC
52982 A
1 A
52983 TTCTCCACAT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
38 12 0.12
39 85 0.86
40 2 0.02
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.36
Consensus pattern (39 bp):
ACCTAGAATATTCATCCCTATTCTGATCATCTTCTCCCC
Found at i:55390 original size:13 final size:13
Alignment explanation
Indices: 55372--55409 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
55362 CTCAAATTTT
*
55372 TCAAAAGTGCTTC
1 TCAAAAGTACTTC
*
55385 TCAAAAGCACTTC
1 TCAAAAGTACTTC
55398 TCAAAAGTACTT
1 TCAAAAGTACTT
55410 TTTCACAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (13 bp):
TCAAAAGTACTTC
Found at i:59422 original size:16 final size:17
Alignment explanation
Indices: 59401--59435 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
59391 AACATTGCTG
*
59401 AAATAATTTAAA-TAAT
1 AAATAATTCAAATTAAT
59417 AAATAATTCAAATTAAT
1 AAATAATTCAAATTAAT
59434 AA
1 AA
59436 CAGTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAATTCAAATTAAT
Found at i:61882 original size:24 final size:24
Alignment explanation
Indices: 61850--61964 Score: 86
Period size: 24 Copynumber: 4.5 Consensus size: 24
61840 CTTGTCGTGT
61850 CTCTCATTCTCATTCTCGCTCACA
1 CTCTCATTCTCATTCTCGCTCACA
* * * *
61874 CTCTCATTCTTATTTTTGCTTACA
1 CTCTCATTCTCATTCTCGCTCACA
* *
61898 CTCTCCTTCTCATTCTCAATCTTACACTCA
1 CTCTCATTCTCATTCTC--GC-T-CA--CA
* * *
61928 CTCTCACTCTCACTCTCACTCACA
1 CTCTCATTCTCATTCTCGCTCACA
*
61952 CTCTCATCCTCAT
1 CTCTCATTCTCAT
61965 CCTCAATCTC
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
24 45 0.66
26 3 0.04
27 2 0.03
28 2 0.03
30 16 0.24
ACGTcount: A:0.18, C:0.40, G:0.02, T:0.40
Consensus pattern (24 bp):
CTCTCATTCTCATTCTCGCTCACA
Found at i:61913 original size:6 final size:6
Alignment explanation
Indices: 61896--61987 Score: 73
Period size: 6 Copynumber: 15.3 Consensus size: 6
61886 TTTTTGCTTA
* * * *
61896 CACTCT C-CTTCT CATTCT CAATCT TACACT CACTCT CACTCT CACTCT
1 CACTCT CAC-TCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT
* * *
61944 CACTCA CACTCT CA-TCCT CA-TCCT CAATCT CATTCT CACTCT CA
1 CACTCT CACTCT CACT-CT CACT-CT CACTCT CACTCT CACTCT CA
61988 TACTTATTCT
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
5 2 0.03
6 68 0.96
7 1 0.01
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.35
Consensus pattern (6 bp):
CACTCT
Found at i:69888 original size:5 final size:5
Alignment explanation
Indices: 69861--69925 Score: 82
Period size: 5 Copynumber: 13.2 Consensus size: 5
69851 TTTTTATGTT
69861 TTATA -TATA TTAT- TT-TA TTATA TAATATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
*
69910 TTGTA TTATA TTATA T
1 TTATA TTATA TTATA T
69926 AAGTAAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 39 0.74
7 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
TTATA
Done.