Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1947
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: 76838
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:602 original size:70 final size:70
Alignment explanation
Indices: 472--659 Score: 333
Period size: 70 Copynumber: 2.7 Consensus size: 70
462 TACCTAAAAG
* * *
472 TAAAAACAAAGAGTGACCTAAGTTTCAAAC-TTTTAAGTTCATGAATTTAATATTACAAGTCACA
1 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
536 TATAC
66 TATAC
541 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
1 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
606 TATAC
66 TATAC
*
611 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTGTAAGTTCATGAATTT
1 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTT
660 GGTATTAAAC
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 27 0.24
70 87 0.76
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (70 bp):
TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
TATAC
Found at i:6660 original size:68 final size:67
Alignment explanation
Indices: 6581--6714 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 67
6571 AGAAAGCAAT
* * * *
6581 GCGTTTCCCTTTGCTGAAACTTTAAAATTTGGGTTTGGTTTTTAGTCCATAACTGTCCAACAATG
1 GCGTTTCCCTTTGCTCAAACTCTAAAATTTGGGCTTGGCTTTTAGTCCA-AACTGTCCAACAATG
6646 TAC
65 TAC
* * * *
6649 GCGTTTGCCTTTGCTCAAACTCTAATATTTGGGCTTGGCTTTTAGTCCAAAGTGTCCAACATTGT
1 GCGTTTCCCTTTGCTCAAACTCTAAAATTTGGGCTTGGCTTTTAGTCCAAACTGTCCAACAATGT
6714 A
66 A
6715 GGGTTTAGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 15 0.26
68 43 0.74
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (67 bp):
GCGTTTCCCTTTGCTCAAACTCTAAAATTTGGGCTTGGCTTTTAGTCCAAACTGTCCAACAATGT
AC
Found at i:8038 original size:18 final size:19
Alignment explanation
Indices: 8015--8052 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
8005 AAATAAATGT
*
8015 AAAAAA-TAATATTTTAAA
1 AAAAAATTAAAATTTTAAA
8033 AAAAAATTAAAATTTTAAA
1 AAAAAATTAAAATTTTAAA
8052 A
1 A
8053 TGATTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATTAAAATTTTAAA
Found at i:8931 original size:2 final size:2
Alignment explanation
Indices: 8919--8953 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
8909 TTATTCTTAA
* *
8919 AT AT CT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8954 ACATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9801 original size:19 final size:20
Alignment explanation
Indices: 9779--9818 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9769 TTTTTAAGAA
*
9779 TTATA-TTTTTATTTAATTT
1 TTATAGTTTTTATTAAATTT
9798 TTATAGTTTTTATTAAATTT
1 TTATAGTTTTTATTAAATTT
9818 T
1 T
9819 ATAATATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTATAGTTTTTATTAAATTT
Found at i:9819 original size:19 final size:19
Alignment explanation
Indices: 9779--9821 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
9769 TTTTTAAGAA
*
9779 TTATATTTTTATTTAATTT
1 TTATATTTTTATTTAAATT
9798 TTATAGTTTTTA-TTAAATT
1 TTATA-TTTTTATTTAAATT
9817 TTATA
1 TTATA
9822 ATATGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATTTTTATTTAAATT
Found at i:9881 original size:37 final size:36
Alignment explanation
Indices: 9794--9882 Score: 85
Period size: 37 Copynumber: 2.4 Consensus size: 36
9784 TTTTTATTTA
* *
9794 ATTTT-TATAGTTTTTATTAAATTTTATAATATGAAT
1 ATTTTATATAATTTTTATTAAATATTATAATAT-AAT
* *
9830 AATTTA-AAATATTTTTATTACAATATTAT-ATATATAT
1 ATTTTATATA-ATTTTTATTA-AATATTATAATATA-AT
9867 ATTTTATATAATTTTT
1 ATTTTATATAATTTTT
9883 CATCAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
36 7 0.17
37 26 0.62
38 9 0.21
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (36 bp):
ATTTTATATAATTTTTATTAAATATTATAATATAAT
Found at i:10986 original size:39 final size:35
Alignment explanation
Indices: 10920--11001 Score: 87
Period size: 39 Copynumber: 2.3 Consensus size: 35
10910 ATTTATAAAA
10920 TATAA-TTATATAAATAATAAAATTTTAAATTAAATT
1 TATAATTTATATAAATAATAAAATTTT-AA-TAAATT
* *
10956 TAATTAATTTATATAAATAAT-TATTATTTAATAAATT
1 T-A-TAATTTATATAAATAATAAAAT-TTTAATAAATT
10993 TATAATTTA
1 TATAATTTA
11002 AATTTAACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
35 7 0.17
36 2 0.05
37 8 0.20
38 7 0.17
39 16 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TATAATTTATATAAATAATAAAATTTTAATAAATT
Found at i:11003 original size:50 final size:52
Alignment explanation
Indices: 10910--11008 Score: 132
Period size: 50 Copynumber: 1.9 Consensus size: 52
10900 ATATTTTTAT
10910 ATTTATAAAATATAATTATATAAATAATAAAATTTTAAATTAAATTTAATTA
1 ATTTATAAAATATAATTATATAAATAATAAAATTTTAAATTAAATTTAATTA
* ** *
10962 ATTTATATAA-ATAATTAT-TATTTAAT-AAATTTATAATTTAAATTTAA
1 ATTTATAAAATATAATTATATAAATAATAAAATTT-TAAATTAAATTTAA
11009 CATATATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 6 0.14
50 19 0.45
51 8 0.19
52 9 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (52 bp):
ATTTATAAAATATAATTATATAAATAATAAAATTTTAAATTAAATTTAATTA
Found at i:11005 original size:28 final size:26
Alignment explanation
Indices: 10943--11005 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
10933 ATAATAAAAT
*
10943 TTTAAATTAAATTTAATTAATTTATA
1 TTTAAATTAAATTTAATAAATTTATA
** *
10969 TAAATAATTATTATTTAATAAATTTATAA
1 TTTA-AATTA-AATTTAATAAATTTAT-A
10998 TTTAAATT
1 TTTAAATT
11006 TAACATATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
26 2 0.07
27 5 0.18
28 18 0.64
29 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTAAATTAAATTTAATAAATTTATA
Found at i:11943 original size:2 final size:2
Alignment explanation
Indices: 11938--11962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11928 AAATAAATAA
11938 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
11963 CTCCCCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12571 original size:2 final size:2
Alignment explanation
Indices: 12520--12553 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12510 TCCTCCCTTT
12520 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12554 AATCTACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:15322 original size:18 final size:18
Alignment explanation
Indices: 15299--15336 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15289 TATGATCTAA
15299 AATTTTTAAATATATTTT
1 AATTTTTAAATATATTTT
**
15317 AATTTTTTTATATATTTT
1 AATTTTTAAATATATTTT
15335 AA
1 AA
15337 AAGAGTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTTTAAATATATTTT
Found at i:16394 original size:20 final size:21
Alignment explanation
Indices: 16369--16425 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
16359 GAAATTATAA
*
16369 AAAAATTAT-AATTTTAAAAT
1 AAAAATTATAAATATTAAAAT
*
16389 AAAAATTGTAAATATTAAAATT
1 AAAAATTATAAATATTAAAA-T
*
16411 TAAAATT-TAAA-ATTA
1 AAAAATTATAAATATTA
16426 TTAAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 12 0.38
21 13 0.41
22 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATTATAAATATTAAAAT
Found at i:17218 original size:2 final size:2
Alignment explanation
Indices: 17171--17202 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17161 TCAATTAGTG
17171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17203 TTAACCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17532 original size:18 final size:19
Alignment explanation
Indices: 17505--17548 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
17495 TATAATTAAA
17505 TTTAAATAAAAA-TATTAT
1 TTTAAATAAAAATTATTAT
*
17523 TTTAATTAAAAATTATTAT
1 TTTAAATAAAAATTATTAT
*
17542 TTAAAAT
1 TTTAAAT
17549 CGAATCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAT
Found at i:17704 original size:19 final size:19
Alignment explanation
Indices: 17680--17718 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17670 ATAATATATC
*
17680 ATTTTAACATAATTTA-TAA
1 ATTTTAA-AAAATTTACTAA
17699 ATTTTAAAAAATTTACTAA
1 ATTTTAAAAAATTTACTAA
17718 A
1 A
17719 AACATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTAAAAAATTTACTAA
Found at i:18114 original size:16 final size:16
Alignment explanation
Indices: 18093--18194 Score: 58
Period size: 16 Copynumber: 6.5 Consensus size: 16
18083 GTAAACATAT
18093 TTTATATTATATTATA
1 TTTATATTATATTATA
*
18109 TTTATATT-TA-AATA
1 TTTATATTATATTATA
*
18123 TTT-TATTATTATATAAA
1 TTTATATTA-TAT-TATA
**
18140 TTT-TAAAATATTA-A
1 TTTATATTATATTATA
18154 TTTATA-TA-ATTAATAA
1 TTTATATTATATT-AT-A
18170 TTT-TATATATATGTATA
1 TTTATAT-TATAT-TATA
18187 TTTATATT
1 TTTATATT
18195 TTTAATATGT
Statistics
Matches: 67, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
13 7 0.10
14 12 0.18
15 10 0.15
16 15 0.22
17 15 0.22
18 7 0.10
19 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTATATTATATTATA
Found at i:18306 original size:24 final size:24
Alignment explanation
Indices: 18279--18334 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
18269 ATAAAGTTCA
**
18279 TAATAATATTTATATGTTTAATTG
1 TAATAATATTTATATAATTAATTG
* *
18303 TAATTATATTTATATAATTAATTT
1 TAATAATATTTATATAATTAATTG
18327 TAA-AATAT
1 TAATAATAT
18335 AATTTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TAATAATATTTATATAATTAATTG
Found at i:18561 original size:16 final size:16
Alignment explanation
Indices: 18527--18564 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18517 TTTATTAAAA
*
18527 TTAAAAAAAATTATTT
1 TTAAAAAAAATTATAT
18543 TTAAAAAATAATTA-AT
1 TTAAAAAA-AATTATAT
18559 TTAAAA
1 TTAAAA
18565 TTTAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAAAAAATTATAT
Found at i:20278 original size:51 final size:51
Alignment explanation
Indices: 20202--20306 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 51
20192 ACCCTTGTGT
* *
20202 GAACAGTAATTAATAAAAGAAGGTATAGATGAGGCAACGGGGAAGTTTCGC
1 GAACACTAATTAATAAAAGAAGGTATAGAAGAGGCAACGGGGAAGTTTCGC
* *
20253 GAACACTAATTAATAAAAGAAGGTATGGAAGATGCAACGGGGAAGTTTCGC
1 GAACACTAATTAATAAAAGAAGGTATAGAAGAGGCAACGGGGAAGTTTCGC
20304 GAA
1 GAA
20307 ATTTCCCATC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.19
Consensus pattern (51 bp):
GAACACTAATTAATAAAAGAAGGTATAGAAGAGGCAACGGGGAAGTTTCGC
Found at i:22032 original size:2 final size:2
Alignment explanation
Indices: 22025--22061 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
22015 GACTTGAAGA
*
22025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22062 ACTATTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:22749 original size:1 final size:1
Alignment explanation
Indices: 22743--22769 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
22733 ACATACAGCG
22743 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
22770 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:30664 original size:14 final size:14
Alignment explanation
Indices: 30645--30682 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
30635 TGTTAATATT
30645 AAATATAATTATAA
1 AAATATAATTATAA
*
30659 AAATATAA-AATAA
1 AAATATAATTATAA
30672 AAA-ATAATTAT
1 AAATATAATTAT
30683 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 4 0.19
13 9 0.43
14 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATATAATTATAA
Found at i:31232 original size:15 final size:15
Alignment explanation
Indices: 31185--31269 Score: 52
Period size: 15 Copynumber: 5.7 Consensus size: 15
31175 GAGTAAAATA
*
31185 ATTTAAATAAATTTTAG
1 ATTTAAAT-AA-TTTAT
*
31202 ATTT-ATTAATTATAT
1 ATTTAAATAATT-TAT
31217 ATTTAAATAATTTAT
1 ATTTAAATAATTTAT
* * *
31232 A-AT-ATTAAATT-T
1 ATTTAAATAATTTAT
*
31244 ATTTAAATAATTTAA
1 ATTTAAATAATTTAT
*
31259 ATTTATATAAT
1 ATTTAAATAAT
31270 ATTTATTATG
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
12 2 0.04
13 7 0.13
14 9 0.17
15 22 0.42
16 8 0.15
17 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (15 bp):
ATTTAAATAATTTAT
Found at i:31505 original size:23 final size:25
Alignment explanation
Indices: 31447--31506 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
31437 ATATAAAGAA
31447 AAAATTTATATTTTTATGTAATAAAT
1 AAAATTTATA-TTTTATGTAATAAAT
* *
31473 --ATTTTTTATTTTAT-TAA-AAAT
1 AAAATTTATATTTTATGTAATAAAT
31494 AAAATTTATATTT
1 AAAATTTATATTT
31507 ATTGTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
21 4 0.14
22 3 0.11
23 15 0.54
24 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
AAAATTTATATTTTATGTAATAAAT
Found at i:37972 original size:12 final size:12
Alignment explanation
Indices: 37955--37983 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
37945 TTATAATTTT
37955 TTAAAAATTAAA
1 TTAAAAATTAAA
37967 TTAAAAATTAAA
1 TTAAAAATTAAA
37979 TTAAA
1 TTAAA
37984 TAATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAAAATTAAA
Found at i:38866 original size:9 final size:9
Alignment explanation
Indices: 38852--38877 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38842 AGAAAAAGCC
38852 TTTCTTTTT
1 TTTCTTTTT
38861 TTTCTTTTT
1 TTTCTTTTT
38870 TTTCTTTT
1 TTTCTTTT
38878 GGCTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:38904 original size:2 final size:2
Alignment explanation
Indices: 38897--38931 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38887 TTATGGTAAC
38897 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
38932 ACACACTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:41286 original size:23 final size:23
Alignment explanation
Indices: 41242--41289 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
41232 TTAAAAAATT
* **
41242 TATAATTTTTTATTTATATTAAA
1 TATAATTTTATATAAATATTAAA
*
41265 TATAATTTTATATAAATTTTAAA
1 TATAATTTTATATAAATATTAAA
41288 TA
1 TA
41290 AAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATAATTTTATATAAATATTAAA
Found at i:52778 original size:280 final size:280
Alignment explanation
Indices: 52277--52819 Score: 924
Period size: 280 Copynumber: 1.9 Consensus size: 280
52267 ATCTAACAAT
*
52277 GCACTTAAAATACAGGACACAGTTCATCCTCTTGCATCCAAATTCCTCATGGTCAATTAAAAAGT
1 GCACTTAAAATACAGGACACAGTTCATCCTCTTGCATCCAAATTCCTAATGGTCAATTAAAAAGT
* *
52342 TAAGGATTAAGCTTAATGTGGTTATTAACAGGAACAATAAACATGATAACATCAAAGAGAATAAC
66 TAAGGATTAAGCTTAATGTGGTTAGTAACAGGAACAATAAACATGATAAAATCAAAGAGAATAAC
* * *
52407 TGCTCTATAGGCAAGCCTTCCAGGAAATGGTTAGAAAGATTTAACTTGGAATCCTCCGAGGTCCA
131 TGCTCTATAGGCAAGCCTTCCAGGAAATGGTTAGAAAGATTTAACTCGGAATCCCCCGAGGCCCA
* * *
52472 AGCACATACGATGTAGACAAGTGGTAGCCAAAGATGATTGTAAACACAAGCTCGATGATGATGAT
196 AGCACATAAGATATAGACAAGTGGTAGACAAAGATGATTGTAAACACAAGCTCGATGATGATGAT
52537 GATAAAGATGACTAGCGAGA
261 GATAAAGATGACTAGCGAGA
* * **
52557 GCACTTAAAATACAGTACACAGTTCATTCTCTTGCATCGTAATTCCTAATGGTCAATTAAAAAGT
1 GCACTTAAAATACAGGACACAGTTCATCCTCTTGCATCCAAATTCCTAATGGTCAATTAAAAAGT
* *
52622 TAAGGATTAAGCTTAATGTGGTTAGTAACAGGAACAATAAACATGTTAAAATCACAGAGAATAAC
66 TAAGGATTAAGCTTAATGTGGTTAGTAACAGGAACAATAAACATGATAAAATCAAAGAGAATAAC
* *
52687 TGCTCTATAGGCAAGCCTTCCAGGAAATGGTTAGAAAGATTTAAGTCGGAATCCCCCGGGGCCCA
131 TGCTCTATAGGCAAGCCTTCCAGGAAATGGTTAGAAAGATTTAACTCGGAATCCCCCGAGGCCCA
*
52752 AGCACATAATATATAGACAAGTGGTAGACAAAGATGATTGTAAACACAAGCTCGATGATGATGAT
196 AGCACATAAGATATAGACAAGTGGTAGACAAAGATGATTGTAAACACAAGCTCGATGATGATGAT
52817 GAT
261 GAT
52820 GATAAAGATA
Statistics
Matches: 245, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
280 245 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (280 bp):
GCACTTAAAATACAGGACACAGTTCATCCTCTTGCATCCAAATTCCTAATGGTCAATTAAAAAGT
TAAGGATTAAGCTTAATGTGGTTAGTAACAGGAACAATAAACATGATAAAATCAAAGAGAATAAC
TGCTCTATAGGCAAGCCTTCCAGGAAATGGTTAGAAAGATTTAACTCGGAATCCCCCGAGGCCCA
AGCACATAAGATATAGACAAGTGGTAGACAAAGATGATTGTAAACACAAGCTCGATGATGATGAT
GATAAAGATGACTAGCGAGA
Found at i:54672 original size:199 final size:193
Alignment explanation
Indices: 54179--54902 Score: 634
Period size: 199 Copynumber: 3.8 Consensus size: 193
54169 TGTAGAACAG
* * * * *
54179 AAAATCTTCTAAAAACTAATAGAAAATTAAC-CAAGAAA-AAGAAAAGAAATCAAAAAGATATTG
1 AAAATCTTCT-AAAACAAACAGAAAAATAACAGAAGAAAGAAGAAAAGAAATAAAAAAGATATTG
* *
54242 ATCAAAACCTGTTGTGCTTGAGACGGCTCTTCCTTTTTGCTGGGCGTTTTCTGATCAAGAAAATA
65 ATCAAAACCTGTTGTGCTTGAGACGGTTCTTCCTTTTTGCTGGGCATTTTCTGATCAAGAAAATA
* * * *
54307 AAAAAAGAGTTAACGTAAAATCTCCGTCAAATCAAAATTTACTTTTTTTCCGTTCCTTAACACC
130 AAAAAAGAATTAACGTAAAATCTCCGTCAAATCAAAATGTACTTTTTTTCAGTTCCTGAACACC
* * * *
54371 AAAATTTTCTAAAACGAACAGAAAATTCACAGAAGAAAGAAGAAAAGAAATAAAAAAGATAATTG
1 AAAATCTTCTAAAACAAACAGAAAAATAACAGAAGAAAGAAGAAAAGAAATAAAAAAGAT-ATTG
* * ** * * *
54436 ATCAAAACCTGTTGTGATTGACACAATTCTTCCTTTTTGCTAGGCATTTTCTGATTAAGATAAT-
65 ATCAAAACCTGTTGTGCTTGAGACGGTTCTTCCTTTTTGCTGGGCATTTTCTGATCAAGAAAATA
* * ** ** *
54500 AAAAAAGAATTAACGTAAAATCTCTGTTAAATCGCAATGTGGTTACTTTTTCAGTTTCTGAACAC
130 AAAAAAGAATTAACGTAAAATCTCCGTCAAATCAAAATGTACTT--TTTTTCAGTTCCTGAACAC
54565 C
193 C
*
54566 AAAATCTTCTACAAACCAAATAGAAAAATAACAGAAGAAAAAGAAATGGAAAA-AAA-AAAAAAG
1 AAAATCTTCTA-AAA-CAAACAGAAAAATAACAGAAG--AAAG-AA--GAAAAGAAATAAAAAAG
* * * *
54629 ATATTTATCAAAACCTGCTGTGCTTGAGATGGTTCTTCCTTTTTGCTGGGCATTCTCTGATCAAG
59 ATATTGATCAAAACCTGTTGTGCTTGAGACGGTTCTTCCTTTTTGCTGGGCATTTTCTGATCAAG
* * * * * *
54694 AAAATTAAAGAAAAAGAATTAAGGTAAAACCT-C--CAAATCACAACGTAGTTTGCTTTTTATGT
124 AAAA-T-AA-AAAAAGAATTAACGTAAAATCTCCGTCAAATCAAAATGTACTTT--TTTTCA-GT
* * **
54756 TTCTAAACAAG
183 TCCTGAACACC
* * **
54767 AAAATGTTCTAAAACGAGTAGAAAAATAAC-------AG--G----G-AA-AAAAAAGATATTGA
1 AAAATCTTCTAAAACAAACAGAAAAATAACAGAAGAAAGAAGAAAAGAAATAAAAAAGATATTGA
* * * * *
54817 TCAAAACCTGTTGTGCTTGAGACAGCTCTTCCTTTCTGCTAGGCATTTTCTGATTAAGAAAAT-A
66 TCAAAACCTGTTGTGCTTGAGACGGTTCTTCCTTTTTGCTGGGCATTTTCTGATCAAGAAAATAA
*
54881 TAAAAGAATT-ACGTAAAATCTC
131 AAAAAGAATTAACGTAAAATCTC
54903 GATTGAATCA
Statistics
Matches: 443, Mismatches: 68, Indels: 57
0.78 0.12 0.10
Matches are distributed among these distances:
176 9 0.02
177 9 0.02
178 1 0.00
180 1 0.00
181 69 0.16
185 1 0.00
190 2 0.00
191 17 0.04
192 15 0.03
193 56 0.13
194 59 0.13
195 27 0.06
196 3 0.01
197 17 0.04
198 1 0.00
199 74 0.17
200 33 0.07
201 23 0.05
202 6 0.01
203 20 0.05
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (193 bp):
AAAATCTTCTAAAACAAACAGAAAAATAACAGAAGAAAGAAGAAAAGAAATAAAAAAGATATTGA
TCAAAACCTGTTGTGCTTGAGACGGTTCTTCCTTTTTGCTGGGCATTTTCTGATCAAGAAAATAA
AAAAAGAATTAACGTAAAATCTCCGTCAAATCAAAATGTACTTTTTTTCAGTTCCTGAACACC
Found at i:56218 original size:23 final size:22
Alignment explanation
Indices: 56181--56223 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
56171 ATATCTTAAC
56181 TTTTAAATATAATTTTAAAAATA
1 TTTTAAATATAA-TTTAAAAATA
* *
56204 TTTTAAATTTTATTTAAAAA
1 TTTTAAATATAATTTAAAAA
56224 CTCGATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAATATAATTTAAAAATA
Found at i:61318 original size:34 final size:34
Alignment explanation
Indices: 61280--61344 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
61270 AATATTAATA
*
61280 ATAGAAAGTGAAAAGAATTAAAATCATGAATATG
1 ATAGAAAGTGAAAAGAATCAAAATCATGAATATG
61314 ATAGAAAGTGAAAAGAATCAAAATCATGAAT
1 ATAGAAAGTGAAAAGAATCAAAATCATGAAT
61345 TACGATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.22
Consensus pattern (34 bp):
ATAGAAAGTGAAAAGAATCAAAATCATGAATATG
Found at i:62152 original size:1 final size:1
Alignment explanation
Indices: 62146--62170 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
62136 TTGAAACCAA
62146 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
62171 AAGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:70106 original size:2 final size:2
Alignment explanation
Indices: 70101--70132 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
70091 CTCATATTAA
70101 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
70133 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:70137 original size:2 final size:2
Alignment explanation
Indices: 70132--70156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70122 TCTCTCTCTC
70132 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
70157 GACATTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72267 original size:15 final size:16
Alignment explanation
Indices: 72236--72270 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
72226 GTTATATATT
*
72236 TTTATATTTAGTTATA
1 TTTATATTTAATTATA
72252 TTTATA-TTAATTATA
1 TTTATATTTAATTATA
72267 TTTA
1 TTTA
72271 AAATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTATATTTAATTATA
Found at i:72400 original size:16 final size:16
Alignment explanation
Indices: 72379--72410 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
72369 TATTTTTAAT
72379 AAAAAATTATTAATTA
1 AAAAAATTATTAATTA
*
72395 AAAAAATTATTTATTA
1 AAAAAATTATTAATTA
72411 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAAATTATTAATTA
Found at i:72913 original size:10 final size:10
Alignment explanation
Indices: 72892--72922 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
72882 ACGTGATATA
72892 ATATTAAAAAT
1 ATATT-AAAAT
72903 ATATTAAAAT
1 ATATTAAAAT
72913 ATATTAAAAT
1 ATATTAAAAT
72923 TTTATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATTAAAAT
Found at i:72961 original size:24 final size:25
Alignment explanation
Indices: 72899--72983 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 25
72889 ATAATATTAA
*
72899 AAATATATTA-AAATATATTAAAATT
1 AAATATAATATAAATA-ATTAAAATT
** *
72924 TTATATAATGTAAATAATTAAAA-T
1 AAATATAATATAAATAATTAAAATT
* *
72948 AAATATAATATAAATATTTAAATTGTT
1 AAATATAATATAAATAATTAAA--ATT
72975 AAATATAAT
1 AAATATAAT
72984 TTTACGATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
24 19 0.40
25 13 0.28
26 5 0.11
27 10 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATATAATATAAATAATTAAAATT
Found at i:75520 original size:2 final size:2
Alignment explanation
Indices: 75513--75537 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75503 ACTGACCAGC
75513 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
75538 CACACCCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.