Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1943
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: 76323
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:2906 original size:52 final size:52
Alignment explanation
Indices: 2830--2969 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 52
2820 ATTTAACTGG
* ** * *
2830 ATGTATCGATACATTGAATTATGTATTGATACATTTA-AGTCAAAAACCCAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGA-TCAAAAACCCAAA
*
2882 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGATTAAAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGATCAAAAACCCAAA
* *
2934 ATGTATCGATACAATAAAAAACGTATCGATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
2970 TCTTTCCAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 78 0.99
53 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTAGATCAAAAACCCAAA
Found at i:3642 original size:47 final size:48
Alignment explanation
Indices: 3563--3669 Score: 144
Period size: 47 Copynumber: 2.2 Consensus size: 48
3553 ATGCAACATA
* * * *
3563 TATCGATACATCTAAGTTTTTCAGATTGTATCGATATAATGAATAATG
1 TATCGATACATCTAAATTTCTCAGATTGTATCGATACAATCAATAATG
* *
3611 TATTGATACATCTAAATTTCT-AGATTGTATCGATACAATCACTAATG
1 TATCGATACATCTAAATTTCTCAGATTGTATCGATACAATCAATAATG
*
3658 TATCGACACATC
1 TATCGATACATC
3670 CATTACATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 33 0.65
48 18 0.35
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (48 bp):
TATCGATACATCTAAATTTCTCAGATTGTATCGATACAATCAATAATG
Found at i:3854 original size:22 final size:21
Alignment explanation
Indices: 3808--3857 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
3798 ATCCATCAAT
* *
3808 TCTTCTTCTTCCATTAACTCA
1 TCTTCTTCTTCCATAAAATCA
3829 TCTTCATTCTTCCATCAAAATC-
1 TCTTC-TTCTTCCAT-AAAATCA
3851 TCTTCTT
1 TCTTCTT
3858 AACCATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 14 0.56
23 4 0.16
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (21 bp):
TCTTCTTCTTCCATAAAATCA
Found at i:6192 original size:21 final size:21
Alignment explanation
Indices: 6166--6224 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
6156 ATACAAGTGA
6166 AAATGTATCGATACATTATGT
1 AAATGTATCGATACATTATGT
* * *
6187 AAATGTATTGACACATCATGT
1 AAATGTATCGATACATTATGT
* *
6208 GAATATATCGATACATT
1 AAATGTATCGATACATT
6225 TTGTTGGCAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
AAATGTATCGATACATTATGT
Found at i:6318 original size:19 final size:19
Alignment explanation
Indices: 6294--6346 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
6284 GTATCAACAC
6294 AATTCA-AAATGTATCGATA
1 AATTCATAAATGTATC-ATA
6313 AATTCATAAATGTATCATA
1 AATTCATAAATGTATCATA
6332 AATTCATAAATGTAT
1 AATTCATAAATGTAT
6347 TGATTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 24 0.73
20 9 0.27
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (19 bp):
AATTCATAAATGTATCATA
Found at i:9912 original size:144 final size:153
Alignment explanation
Indices: 9758--10077 Score: 343
Period size: 144 Copynumber: 2.1 Consensus size: 153
9748 TACCTTATCA
* * * * *
9758 GAAGCCCGAAAATATATGAAAAATTTTTGAAATCTTTTATACCCCTATAGACGCCCA-TA-AAAA
1 GAAGCCCGAAAAGATACGAAAAACTTTTGAAACCTTTTATACCCCCATAGACGCCCATTAGAAAA
** * *
9821 T-ATAGA-AG-ATTATAATT-TTT-T-TCGAAAGTATTAATTCAATTTAA-TTTTATTTATTTCA
66 TCATAGATAGAAAAATAATTATTTATCTCAAAAGCATTAATTCAATTTAATTTTTATTTATTTCA
*
9879 AAAATACTATTTTATACCCTAAT
131 AAAATACCATTTTATACCCTAAT
* ** * * * * *
9902 GAAGCCCGAAAGGATACGAAATGCTTTTGAAACCTTTTATACCCCCATGGATGTCTATTAGAATA
1 GAAGCCCGAAAAGATACGAAAAACTTTTGAAACCTTTTATACCCCCATAGACGCCCATTAGAAAA
9967 TCATAGATTAGAAAAAATAATTAAAATTTATCTCAAAAGCATTAATTCAATTTAATTTTTATTTA
66 TCATAGA-TAG-AAAAATAATT---ATTTATCTCAAAAGCATTAATTCAATTTAATTTTTATTTA
*
10032 TTTCAAAAATACCATTTTGTACCCTAAT
126 TTTCAAAAATACCATTTTATACCCTAAT
*
10060 GAAAGCCCGAAAGGATAC
1 G-AAGCCCGAAAAGATAC
10078 TGTCGATATA
Statistics
Matches: 142, Mismatches: 19, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
144 45 0.32
145 2 0.01
146 4 0.03
147 5 0.04
149 2 0.01
151 7 0.05
155 3 0.02
156 1 0.01
157 21 0.15
158 36 0.25
159 16 0.11
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (153 bp):
GAAGCCCGAAAAGATACGAAAAACTTTTGAAACCTTTTATACCCCCATAGACGCCCATTAGAAAA
TCATAGATAGAAAAATAATTATTTATCTCAAAAGCATTAATTCAATTTAATTTTTATTTATTTCA
AAAATACCATTTTATACCCTAAT
Found at i:11451 original size:20 final size:20
Alignment explanation
Indices: 11423--11497 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
11413 TCATACCCTG
11423 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
11443 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
11463 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
11483 ATGTATCGATACATT
1 ATGTATCGATACATT
11498 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:11490 original size:40 final size:39
Alignment explanation
Indices: 11423--11500 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
11413 TCATACCCTG
* *
11423 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
11463 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
11501 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:23459 original size:21 final size:21
Alignment explanation
Indices: 23435--23476 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
23425 CCGTTACACC
23435 CAAAAAAAAAAAAAAACAAAA
1 CAAAAAAAAAAAAAAACAAAA
*
23456 CAAAAAAAAAAAAAAGCAAAA
1 CAAAAAAAAAAAAAAACAAAA
23477 AATAGAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAAAAAACAAAA
Found at i:23460 original size:16 final size:16
Alignment explanation
Indices: 23435--23478 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
23425 CCGTTACACC
*
23435 CAAAAAAAAAAAAAAA
1 CAAAACAAAAAAAAAA
23451 CAAAACAAAAAAAAAA
1 CAAAACAAAAAAAAAA
23467 -AAAAGCAAAAAA
1 CAAAA-CAAAAAA
23479 TAGAAGGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (16 bp):
CAAAACAAAAAAAAAA
Found at i:23478 original size:1 final size:1
Alignment explanation
Indices: 23436--23470 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
23426 CGTTACACCC
* *
23436 AAAAAAAAAAAAAAACAAAACAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23471 GCAAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24944 original size:32 final size:32
Alignment explanation
Indices: 24701--25613 Score: 1309
Period size: 32 Copynumber: 29.2 Consensus size: 32
24691 TGTTCATCCC
*
24701 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
24730 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
24759 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
24787 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* ** * *
24816 TTTCAAAG-CC-TACAAGTTAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
24845 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
24874 TTTTAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
24903 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
24935 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
24967 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
24999 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
25031 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25063 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25095 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25127 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
25159 TTCCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25191 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
25223 TTTCAAACCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
25255 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
25287 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
25319 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
25351 TTCCAAAGCCCACACAAGTCGGTGGTAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25383 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25415 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25447 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
25479 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
25511 TTCCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25543 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** * *
25575 TTTAAAAGCCCATGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
25607 TTTCAAA
1 TTTCAAA
25614 TCACCATATT
Statistics
Matches: 832, Mismatches: 36, Indels: 29
0.93 0.04 0.03
Matches are distributed among these distances:
27 4 0.00
28 36 0.04
29 107 0.13
30 11 0.01
31 18 0.02
32 656 0.79
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:26170 original size:20 final size:20
Alignment explanation
Indices: 26142--26216 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
26132 TCATACCCTG
26142 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
26162 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
26182 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
26202 ATGTATCGATACATT
1 ATGTATCGATACATT
26217 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:26209 original size:40 final size:39
Alignment explanation
Indices: 26142--26219 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
26132 TCATACCCTG
* *
26142 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
26182 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
26220 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:35868 original size:1 final size:1
Alignment explanation
Indices: 35862--36002 Score: 129
Period size: 1 Copynumber: 141.0 Consensus size: 1
35852 CGTCCTCCAC
* * ** * * *
35862 AAAAAAAAAAAACAAAAAAAAAAAACAAAAAAAAATTAAAAAAAAAACAAAAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
35927 CAAAAAAAAACAAAAACAAAAAAAAACAAAAAAAAAACAAAAACAACAAAAAAACAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
35992 AACAAAAAAAA
1 AAAAAAAAAAA
36003 GGTTCGGATG
Statistics
Matches: 108, Mismatches: 32, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 108 1.00
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:35886 original size:21 final size:21
Alignment explanation
Indices: 35862--36002 Score: 156
Period size: 21 Copynumber: 6.4 Consensus size: 21
35852 CGTCCTCCAC
35862 AAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAC-AAAAAAAA
*
35884 AAACAAAAAAAAATTAAAAAAAAA
1 AAA-AAAAAAAAA--CAAAAAAAA
*
35908 ACAAAAAAACAAAACAAAACAAA
1 A-AAAAAAA-AAAACAAAAAAAA
*
35931 AAAAAACAAAAACAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAA
* *
35952 ACAAAAAAAAAACAAAAACAA
1 AAAAAAAAAAAACAAAAAAAA
* *
35973 CAAAAAAACAAACAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAA
*
35994 CAAAAAAAA
1 AAAAAAAAA
36003 GGTTCGGATG
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
21 55 0.54
22 9 0.09
23 17 0.17
24 14 0.14
25 6 0.06
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAAAACAAAAAAAA
Found at i:35922 original size:48 final size:46
Alignment explanation
Indices: 35860--36002 Score: 180
Period size: 48 Copynumber: 3.0 Consensus size: 46
35850 GGCGTCCTCC
*
35860 ACAAAAAAAAAAAACAAAAAAAAAAAACAAAAAAAAATTAAAAAAAAA
1 ACAAAAAAACAAAACAAAAAAAAAAAACAAAAAAAAA--AAAAAAAAA
* *
35908 ACAAAAAAACAAAACAAAACAAAAAAAAACAAAAACAAAAAAAAACAA
1 ACAAAAAAACAAAAC-AAA-AAAAAAAAACAAAAAAAAAAAAAAAAAA
*
35956 A-AAAAAAACAAAAACAACAAAAAAACAAACAAAAAAAACAAAAAAAA
1 ACAAAAAAAC-AAAACAA-AAAAAAA-AAACAAAAAAAAAAAAAAAAA
36003 GGTTCGGATG
Statistics
Matches: 84, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
47 16 0.19
48 47 0.56
49 3 0.04
50 18 0.21
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.01
Consensus pattern (46 bp):
ACAAAAAAACAAAACAAAAAAAAAAAACAAAAAAAAAAAAAAAAAA
Found at i:37475 original size:27 final size:28
Alignment explanation
Indices: 37434--37492 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
37424 CATTCCTCAC
* * *
37434 CCTTCAAAAGTCCACAAGTTAGTGGCAA
1 CCTTCAAAAGCCCACAAATCAGTGGCAA
*
37462 CCTTC-AAAGCCCACAAATCAGTGGCAC
1 CCTTCAAAAGCCCACAAATCAGTGGCAA
37489 CCTT
1 CCTT
37493 TTTCGAAGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.20
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAATCAGTGGCAA
Found at i:37633 original size:32 final size:31
Alignment explanation
Indices: 37592--37728 Score: 186
Period size: 32 Copynumber: 4.4 Consensus size: 31
37582 CTCTTTTTCT
*
37592 TCTAAAGCCCACACAAGTTGGTGGCAATCCCC
1 TCTAAAGCCCACACAAGTCGGTGGCAA-CCCC
* * *
37624 TCTAAAGCCCACACAAGGCGGTGGCAGCCCT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCC
37655 TCTCAAAGCCCACACAAGTCGGTGGCAACCCTC
1 TCT-AAAGCCCACACAAGTCGGTGGCAACCC-C
* *
37688 TCTAAAGCCCACACAAGTCAGTGGCAACCCT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCC
37719 TCT-AAGCCCA
1 TCTAAAGCCCA
37729 ATATCGCTGG
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
30 7 0.07
31 9 0.10
32 75 0.80
33 3 0.03
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.16
Consensus pattern (31 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCCC
Found at i:37696 original size:64 final size:63
Alignment explanation
Indices: 37590--37728 Score: 210
Period size: 64 Copynumber: 2.2 Consensus size: 63
37580 CACTCTTTTT
* * *
37590 CTTCTAAAGCCCACACAAGTTGGTGGCAATCCCCTCTAAAGCCCACACAAGGCGGTGGCAGCC
1 CTTCTAAAGCCCACACAAGTCGGTGGCAATCCCCTCTAAAGCCCACACAAGGCAGTGGCAACC
*
37653 CTTCTCAAAGCCCACACAAGTCGGTGGCAA-CCCTCTCTAAAGCCCACACAAGTCAGTGGCAACC
1 CTTCT-AAAGCCCACACAAGTCGGTGGCAATCCC-CTCTAAAGCCCACACAAGGCAGTGGCAACC
37717 CTTCT-AAGCCCA
1 CTTCTAAAGCCCA
37729 ATATCGCTGG
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
62 7 0.10
63 8 0.11
64 55 0.79
ACGTcount: A:0.28, C:0.37, G:0.19, T:0.17
Consensus pattern (63 bp):
CTTCTAAAGCCCACACAAGTCGGTGGCAATCCCCTCTAAAGCCCACACAAGGCAGTGGCAACC
Found at i:37842 original size:49 final size:49
Alignment explanation
Indices: 37721--38231 Score: 503
Period size: 49 Copynumber: 10.7 Consensus size: 49
37711 GCAACCCTTC
* * *
37721 TAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGACATCCTTTCTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA--C---CT-TCATCTT
* * *
37776 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
37825 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T--TC--
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
37869 -AAGTCCAATATCGCTGGCCTTGAATCCGCATATTGGCAACTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
37917 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A----CACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* ** *
37960 TAAGCCCAATATCTCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
38009 TAAATCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T--TC--
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
38053 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
38101 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
38144 TAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCATCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-CTT-CATCTT
* *
38196 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
38232 ACATCCTTTT
Statistics
Matches: 385, Mismatches: 44, Indels: 57
0.79 0.09 0.12
Matches are distributed among these distances:
43 143 0.37
44 3 0.01
45 2 0.01
46 8 0.02
47 1 0.00
48 3 0.01
49 149 0.39
50 3 0.01
52 35 0.09
53 1 0.00
55 37 0.10
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:37887 original size:43 final size:43
Alignment explanation
Indices: 37826--38182 Score: 381
Period size: 43 Copynumber: 7.9 Consensus size: 43
37816 CTTCATCTTT
*
37826 AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC
* * *
37869 AAGTCCAATATCGCTGGCCTTGAATCCGCATATTGGCAACTTCTTC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC-AC--CTTC
* * *
37915 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTT
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC
* ** *
37961 AAGCCCAATATCTCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-T--TC
* *
38007 TTTAAATCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTC
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC
* *
38053 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCTTC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC-AC--CTTC
* *
38099 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC
* *
38145 AAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCA
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
38183 TCTTTTCCAT
Statistics
Matches: 262, Mismatches: 34, Indels: 36
0.79 0.10 0.11
Matches are distributed among these distances:
43 135 0.52
44 5 0.02
46 17 0.06
48 5 0.02
49 100 0.38
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC
Found at i:37938 original size:92 final size:92
Alignment explanation
Indices: 37781--38231 Score: 740
Period size: 92 Copynumber: 4.9 Consensus size: 92
37771 ATCTTTAAGC
*
37781 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGTCCAATGTAGCTGGCCT
37846 TGAATCAGCACATTGGCACCTTCAAGT
66 TGAATCAGCACATTGGCACCTTCAAGT
* *
37873 CCAATATCGCTGGCCTTGAATCCGCATATTGGCAACTTCTTCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGTCCAATGTAGCTGGCCT
* * *
37938 TGAATCAGCACATTGACACCTTTAAGC
66 TGAATCAGCACATTGGCACCTTCAAGT
* * *
37965 CCAATATCTCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAATCCAATGTAGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGTCCAATGTAGCTGGCCT
38030 TGAATCAGCACATTGGCACCTTCAAGT
66 TGAATCAGCACATTGGCACCTTCAAGT
*
38057 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCTTCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGTCCAATGTAGCTGGCCT
*
38122 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTCAAGT
* * * *
38149 CCAATATAGCTAGCCTTGAATCAGCATATTGGCATCTTTTCCATCTTTAAGTTCAATGTAGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAAC--TT-CATCTTTAAGTCCAATGTAGCTGG
38214 CCTTGAATCAGCACATTG
63 CCTTGAATCAGCACATTG
38232 ACATCCTTTT
Statistics
Matches: 332, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
92 290 0.87
94 2 0.01
95 40 0.12
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGTCCAATGTAGCTGGCCT
TGAATCAGCACATTGGCACCTTCAAGT
Found at i:38219 original size:52 final size:53
Alignment explanation
Indices: 38141--38294 Score: 193
Period size: 52 Copynumber: 2.9 Consensus size: 53
38131 ACATTGGCAC
*
38141 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCATCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTCTCAT
* * * *
38193 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAT-C-TTTTCTCAT
* * * * *
38248 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTT
38295 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
52 38 0.45
53 4 0.05
54 6 0.07
55 37 0.44
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTCTCAT
Found at i:38855 original size:9 final size:8
Alignment explanation
Indices: 38827--38856 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
38817 GTCCGGGCCA
38827 ATTTTT-G
1 ATTTTTAG
38834 ATTTTTAG
1 ATTTTTAG
38842 ATTTTTAG
1 ATTTTTAG
38850 ATTTTTA
1 ATTTTTA
38857 TAACTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (8 bp):
ATTTTTAG
Found at i:39063 original size:13 final size:13
Alignment explanation
Indices: 39045--39069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39035 CATAAAGTGT
39045 TGTATCGATACAA
1 TGTATCGATACAA
39058 TGTATCGATACA
1 TGTATCGATACA
39070 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:39067 original size:33 final size:33
Alignment explanation
Indices: 39025--39091 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
39015 TTCAACGATT
39025 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
39058 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
39091 T
1 T
39092 TCAAGCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:39150 original size:13 final size:13
Alignment explanation
Indices: 39132--39156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39122 ATCACTTAAA
39132 TGTATCGATACAT
1 TGTATCGATACAT
39145 TGTATCGATACA
1 TGTATCGATACA
39157 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:43757 original size:196 final size:196
Alignment explanation
Indices: 43423--43816 Score: 779
Period size: 196 Copynumber: 2.0 Consensus size: 196
43413 CTGAATAGGG
*
43423 TGGTTGGAGTAAATGCTCAACAACCCATGATGACAATGTGTTCTATCATGCCATTTCTCATTAAT
1 TGGTTGGAGTAAATGCTCAACAACCCATGATGACAATGTGTTCCATCATGCCATTTCTCATTAAT
43488 GCAATGTTTTGGGCTCCCAAAATGATTAAAGTGTGAATTTAAAGCTTGACATTTAACATTGACAT
66 GCAATGTTTTGGGCTCCCAAAATGATTAAAGTGTGAATTTAAAGCTTGACATTTAACATTGACAT
43553 AAGTCTAATCATTTGTGATACAAAAAACTTATTTGAATTGGGCATTGAATGTGGTATAGCAATGG
131 AAGTCTAATCATTTGTGATACAAAAAACTTATTTGAATTGGGCATTGAATGTGGTATAGCAATGG
43618 A
196 A
43619 TGGTTGGAGTAAATGCTCAACAACCCATGATGACAATGTGTTCCATCATGCCATTTCTCATTAAT
1 TGGTTGGAGTAAATGCTCAACAACCCATGATGACAATGTGTTCCATCATGCCATTTCTCATTAAT
43684 GCAATGTTTTGGGCTCCCAAAATGATTAAAGTGTGAATTTAAAGCTTGACATTTAACATTGACAT
66 GCAATGTTTTGGGCTCCCAAAATGATTAAAGTGTGAATTTAAAGCTTGACATTTAACATTGACAT
43749 AAGTCTAATCATTTGTGATACAAAAAACTTATTTGAATTGGGCATTGAATGTGGTATAGCAATGG
131 AAGTCTAATCATTTGTGATACAAAAAACTTATTTGAATTGGGCATTGAATGTGGTATAGCAATGG
43814 A
196 A
43815 TG
1 TG
43817 AAAATATCAC
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 197 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (196 bp):
TGGTTGGAGTAAATGCTCAACAACCCATGATGACAATGTGTTCCATCATGCCATTTCTCATTAAT
GCAATGTTTTGGGCTCCCAAAATGATTAAAGTGTGAATTTAAAGCTTGACATTTAACATTGACAT
AAGTCTAATCATTTGTGATACAAAAAACTTATTTGAATTGGGCATTGAATGTGGTATAGCAATGG
A
Found at i:51506 original size:12 final size:12
Alignment explanation
Indices: 51491--51515 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51481 AGAATATTGG
51491 TAATTTCTAAAA
1 TAATTTCTAAAA
51503 TAATTTCTAAAA
1 TAATTTCTAAAA
51515 T
1 T
51516 TATGTCTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTTCTAAAA
Found at i:53073 original size:281 final size:281
Alignment explanation
Indices: 52570--53131 Score: 991
Period size: 281 Copynumber: 2.0 Consensus size: 281
52560 AATCTATCTA
* *
52570 TGTTTACAAGCTATGTCCACCTTAAACTTGGTGACAAAGGTTAGAAGTCATAACAAAAACTGCAA
1 TGTTTACAAGCTATGTCCACCTTAAACCTGGTGACAAAGGTTAGAAGTCATAACAAAAACTACAA
52635 TTAACACCAGTGACATGGGTCAAAATATATTGAAAGAAACCAATGATTGTGCAAATCAAATATTA
66 TTAACACCAGTGACATGGGTCAAAATATATTGAAAGAAACCAATGATTGTGCAAATCAAATATTA
*
52700 CAAAAACCATAATTTTAAATCGATGGCATGGCTTGAGATCTATTTCTAATCACAAAATACACGTC
131 CAAAAACCATAATTTTAAATCGATGGCATAGCTTGAGATCTATTTCTAATCACAAAATACACGTC
* * * *
52765 GGCATAGCTAATAATTAACCCCCATTGGTAGAGTCTAAACATAGCGTATTAAGAGAAAATTCACA
196 GACATAGCTAACAATTAACCCCCATTGGTAGAGTCTAAACATAACGTATCAAGAGAAAATTCACA
52830 ACACAAAAAATTAGATTACTC
261 ACACAAAAAATTAGATTACTC
52851 TGTTTACAAGCTATGTCCACCTTAAACCTGGTGACAAAGGTTAGAAGTCATAACAAAAACTACAA
1 TGTTTACAAGCTATGTCCACCTTAAACCTGGTGACAAAGGTTAGAAGTCATAACAAAAACTACAA
*
52916 TTAACACCAGTGACATGGGTTAAAATATATTGAAAGAAACCAATGATTGTGCAAATCAAATATTA
66 TTAACACCAGTGACATGGGTCAAAATATATTGAAAGAAACCAATGATTGTGCAAATCAAATATTA
52981 CAAAAACCATAATTTTAAATCGATGGCATAGCTTG-GAATCTATTTCTAATCACAAAATACACGT
131 CAAAAACCATAATTTTAAATCGATGGCATAGCTTGAG-ATCTATTTCTAATCACAAAATACACGT
* ** * *
53045 CGACATGGCTAACAATTAACTTCCATTGGTAGAGTTTGAACATAACGTATCAAGAGAAAATTCAC
195 CGACATAGCTAACAATTAACCCCCATTGGTAGAGTCTAAACATAACGTATCAAGAGAAAATTCAC
53110 AACACAAAAAATTAGATTACTC
260 AACACAAAAAATTAGATTACTC
53132 ATAGTGTATC
Statistics
Matches: 267, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
280 1 0.00
281 266 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (281 bp):
TGTTTACAAGCTATGTCCACCTTAAACCTGGTGACAAAGGTTAGAAGTCATAACAAAAACTACAA
TTAACACCAGTGACATGGGTCAAAATATATTGAAAGAAACCAATGATTGTGCAAATCAAATATTA
CAAAAACCATAATTTTAAATCGATGGCATAGCTTGAGATCTATTTCTAATCACAAAATACACGTC
GACATAGCTAACAATTAACCCCCATTGGTAGAGTCTAAACATAACGTATCAAGAGAAAATTCACA
ACACAAAAAATTAGATTACTC
Found at i:59886 original size:156 final size:155
Alignment explanation
Indices: 59577--60171 Score: 571
Period size: 156 Copynumber: 3.8 Consensus size: 155
59567 AAAGGGTTAA
* * * *
59577 GTTA-AAAAAATTACGAAAATACCCTTAAGAG-ATACCTTCGACGTAAAAGTA-CTTGATACCCT
1 GTTATAAAAAATTACAAAAATACCCCTAAGAGTATACCTTCGACGTAAAAGTATCTCGGTACCC-
* * * * *
59639 TAAAAGACCTAAAAAGGA-TAGAAATGAGATGAACCTATCTTAAATGCTCACCTTCGGCATAAAA
65 TAAAGGACCTAAAAA-GATTAGAAAAGTGATGAACCTATCCTAAATACTCACCTTCGGCATAAAA
* *
59703 G-TGAACCTAGTGACGACCTAAGAGTTG
129 GCAG-ACCTGGTGACGACCTAAGAGTTG
* * * * * *
59730 GTTCTAAAAAATTATAAAAATGCCCCTATGAGTATACTTTCGATGTAAAAGTATCTCGGTAACCC
1 GTTATAAAAAATTACAAAAATACCCCTAAGAGTATACCTTCGACGTAAAAGTATCTCGGT-ACCC
* * *
59795 TAAAGGACCTAAAAAGATTAGAAAAGTGATGAACCTATCCTAATTACTTACTTTCGGCATAAAAG
65 TAAAGGACCTAAAAAGATTAGAAAAGTGATGAACCTATCCTAAATACTCACCTTCGGCATAAAAG
* * *
59860 CAGACCTGGTGATGACTTAAGTGTTG
130 CAGACCTGGTGACGACCTAAGAGTTG
* * * *
59886 GTTATAAAAAAATTACGAAAAT-GCCCTGAAG-GGATACCTTCGACGTGAAAGTATCTCGGTACC
1 GTTAT-AAAAAATTACAAAAATACCCCT-AAGAGTATACCTTCGACGTAAAAGTATCTCGGTACC
* * *
59949 CTAAAGGACTTAAAAAGATTA-AAAATGGTGATGAACCTATCCTAAATACCCACCTTCAGCATAA
64 CTAAAGGACCTAAAAAGATTAGAAAA--GTGATGAACCTATCCTAAATACTCACCTTCGGCAT-A
* * * * *
60013 AAAGCGGACCCGGTGACAACCTAAGACTCG
126 AAAGCAGACCTGGTGACGACCTAAGAGTTG
* * * * * ** * * * *
60043 ATTTTAAAAAATTACAAAAATATCCTTATGAGTATACCTTCGGTGTAAAAGTACCTTGGCAACCT
1 GTTATAAAAAATTACAAAAATACCCCTAAGAGTATACCTTCGACGTAAAAGTATCTCGG-TACCC
* * * * *
60108 TAAAGGACCTAAAAAGACTAAAAAAGGGATGAACCTATCCT--ATACCCACCTTCGACATAAAAG
65 TAAAGGACCTAAAAAGATTAGAAAAGTGATGAACCTATCCTAAATACTCACCTTCGGCATAAAAG
60171 C
130 C
60172 GAACCCAGTG
Statistics
Matches: 362, Mismatches: 65, Indels: 29
0.79 0.14 0.06
Matches are distributed among these distances:
153 3 0.01
154 32 0.09
155 58 0.16
156 157 0.43
157 87 0.24
158 21 0.06
159 4 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (155 bp):
GTTATAAAAAATTACAAAAATACCCCTAAGAGTATACCTTCGACGTAAAAGTATCTCGGTACCCT
AAAGGACCTAAAAAGATTAGAAAAGTGATGAACCTATCCTAAATACTCACCTTCGGCATAAAAGC
AGACCTGGTGACGACCTAAGAGTTG
Found at i:60145 original size:313 final size:311
Alignment explanation
Indices: 59579--60149 Score: 768
Period size: 313 Copynumber: 1.8 Consensus size: 311
59569 AGGGTTAAGT
* *
59579 TAAAAAAATTACGAAAATACCCTTAAGAGATACCTTCGACGTAAAAGTACTTGATACCCTTAAAA
1 TAAAAAAATTACGAAAATACCCTGAAGAGATACCTTCGACGTAAAAGTACTCGATACCCTTAAAA
* * * * * *
59644 GACCTAAAAAGGATAGAAATGAGATGAACCTATCTTAAATGCTCACCTTCGGCATAAAAGTGAAC
66 GACCTAAAAAGGATAAAAATGAGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAGCGAAC
* * * * * * * *
59709 CTAGTGACGACCTAAGAGTTGGTTCTAAAAAATTATAAAAATGCCCCTATGAGTATACTTTCGAT
131 CCAGTGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCCTATGAGTATACCTTCGAT
* * * * *
59774 GTAAAAGTATCTCGGTAACCCTAAAGGACCTAAAAAGATTAGAAAAGTGATGAACCTATCCTAAT
196 GTAAAAGTACCTCGGCAACCCTAAAGGACCTAAAAAGACTAAAAAAGGGATGAACCTATCCTAAT
59839 TACTTACTTTCGGCATAAAAGCAGACCTGGTGATGACTTAAGTGTTGGTTA
261 TACTTACTTTCGGCATAAAAGCAGACCTGGTGATGACTTAAGTGTTGGTTA
* * * *
59890 TAAAAAAATTACGAAAATGCCCTGAAGGGATACCTTCGACGTGAAAGTATCTCGGTACCC-TAAA
1 TAAAAAAATTACGAAAATACCCTGAAGAGATACCTTCGACGTAAAAGTA-CTCGATACCCTTAAA
* * *
59954 GGACTTAAAAA-GATTAAAAATGGTGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAAGC
65 AGACCTAAAAAGGA-TAAAAAT-GAGATGAACCTATCCTAAATACCCACCTTCAGCAT-AAAAGC
* * * * *
60018 GGACCCGGTGACAACCTAAGACTCGATTTTAAAAAATTACAAAAATATCCTTATGAGTATACCTT
127 GAACCCAGTGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCCTATGAGTATACCTT
* * *
60083 CGGTGTAAAAGTACCTTGGCAACCTTAAAGGACCTAAAAAGACTAAAAAAGGGATGAACCTATCC
192 CGATGTAAAAGTACCTCGGCAACCCTAAAGGACCTAAAAAGACTAAAAAAGGGATGAACCTATCC
60148 TA
257 TA
60150 TACCCACCTT
Statistics
Matches: 220, Mismatches: 36, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
310 2 0.01
311 64 0.29
312 38 0.17
313 116 0.53
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (311 bp):
TAAAAAAATTACGAAAATACCCTGAAGAGATACCTTCGACGTAAAAGTACTCGATACCCTTAAAA
GACCTAAAAAGGATAAAAATGAGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAGCGAAC
CCAGTGACAACCTAAGACTCGATTCTAAAAAATTACAAAAATACCCCTATGAGTATACCTTCGAT
GTAAAAGTACCTCGGCAACCCTAAAGGACCTAAAAAGACTAAAAAAGGGATGAACCTATCCTAAT
TACTTACTTTCGGCATAAAAGCAGACCTGGTGATGACTTAAGTGTTGGTTA
Found at i:60342 original size:140 final size:139
Alignment explanation
Indices: 60102--60357 Score: 354
Period size: 140 Copynumber: 1.8 Consensus size: 139
60092 AGTACCTTGG
* * *
60102 CAACCTTAAAGGACCTAAAAAGACTAAAAAAGGGATGAACCTATCCTATACCCACCTTCGACATA
1 CAACCCTAAAAGACCTAAAAAGACTAAAAAAGGGATAAACCTATCCTATACCCACCTTCGACATA
* *
60167 AAAGCGAACCCAGTGACAACCTAGGACTCGATTTTAAAAAATTACGAAAATGCCCTTATGTAAAA
66 AAAGCGAACCCAGTGACAACCTAAGACTCGATTTTAAAAAATTACAAAAATGCCCTTATGTAAAA
60232 GTATCCCGA
131 GTATCCCGA
* * *
60241 CAACCCTAAAAGACTTAAAAAGGCTAAAAAAGGG-TAAACCTATCCTAAATACCCATCTTCGACA
1 CAACCCTAAAAGACCTAAAAAGACTAAAAAAGGGATAAACCTATCCT--ATACCCACCTTCGACA
* ** * *
60305 TAGAAGC-AGACCTGGTGATAACCTAAGACTCGGTTTTAAAAAATTACAAAAAT
64 TAAAAGCGA-ACCCAGTGACAACCTAAGACTCGATTTTAAAAAATTACAAAAAT
60358 ACCCCTAAAG
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
138 11 0.11
139 31 0.31
140 59 0.58
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (139 bp):
CAACCCTAAAAGACCTAAAAAGACTAAAAAAGGGATAAACCTATCCTATACCCACCTTCGACATA
AAAGCGAACCCAGTGACAACCTAAGACTCGATTTTAAAAAATTACAAAAATGCCCTTATGTAAAA
GTATCCCGA
Found at i:61246 original size:130 final size:130
Alignment explanation
Indices: 60996--61243 Score: 304
Period size: 129 Copynumber: 1.9 Consensus size: 130
60986 TTTTTCTAAA
* *
60996 AAAATCATTTTGTACCTTAATGGATATCCAAAAAGTTACGAAAAGTTTTTCAAAATCTTTTATAT
1 AAAATCATTTTGTACCTTAATGGATACCCAAAAAGATACGAAAAGTTTTTCAAAATCTTTTATAT
* * * * * *
61061 ACTTGCGTATACCTATAGGAATATAAAAAACTTGAAAATAATTGATATTTATTTAAGTTTTGAAG
66 ACTTACGGATACCCATAAGAATATAAAAAACTTAAAAATAATTAATATTTATTTAAGTTTTGAAG
* * * * *
61126 AAAATTATTTTGTATCTTAATGGATACCCGAAAAGATATGAAAAGTTTTT-GAAATCTTTTATA-
1 AAAATCATTTTGTACCTTAATGGATACCCAAAAAGATACGAAAAGTTTTTCAAAATCTTTTATAT
* * * *
61189 CCTCTACGGATACCCATAAGAATATAAAAGA-TTAAAAAATGATTAATGTTTATTT
66 ACT-TACGGATACCCATAAGAATATAAAAAACTT-AAAAATAATTAATATTTATTT
61244 TAATTAACAA
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
128 4 0.04
129 51 0.52
130 44 0.44
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (130 bp):
AAAATCATTTTGTACCTTAATGGATACCCAAAAAGATACGAAAAGTTTTTCAAAATCTTTTATAT
ACTTACGGATACCCATAAGAATATAAAAAACTTAAAAATAATTAATATTTATTTAAGTTTTGAAG
Found at i:63059 original size:166 final size:164
Alignment explanation
Indices: 62884--63447 Score: 619
Period size: 166 Copynumber: 3.5 Consensus size: 164
62874 ATTTCAATAA
* * *
62884 AAAAATTCAAAAATCATGAAAATGAATTAATTTTTTAAAACTGAATTAATATG-AATCAAATGAT
1 AAAAATTCAAAAATCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAAT-AAATAAT
*
62948 GATATTTGATGAATTCTAAAAAATTGAAAAATGAGAAAAATCCCCTCGAAAAAA-TTACGGAGTA
65 GATATTTGATGAATT-TAAAAAATTGAAAAATAAGAAAAATCCCCTCGAAAAAATTTACGGAGTA
*
63012 GAAAACACTGTATTTAGGAAAAAGGAAAGTTTCAAAG
129 GAAAACACTGTATTTA-GAAAAAGGAAAGTTTCAAGG
* * *
63049 AAAGAATTC-AAAA--ATG--AATG-AT---TTTTTAAAAACCGAATTAATATAAAATAAATAAT
1 AAA-AATTCAAAAATCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* * * ** * *
63105 GATGTTTGATGAATTTAAAAAATT-AAAAACAAGAAAAAT-CTCTTAAAAAAATTTACAGAGTTG
65 GATATTTGATGAATTTAAAAAATTGAAAAATAAGAAAAATCCCCTCGAAAAAATTTACGGAGTAG
*
63168 AAAACACTATATTTCA-AAAAA--AAAGTTTCAAGG
130 AAAACACTGTATTT-AGAAAAAGGAAAGTTTCAAGG
* *
63201 AAAAA-ACTAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGTAATAAATAA
1 AAAAATTC-AAAAA-TCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAA
* * * * *
63265 TTATATTTGATAAATTTTAAAAATTGAAAACTAAGAAAAATCTCCTCGAAAAAATTTACGGAGTA
64 TGATATTTGATGAATTTAAAAAATTGAAAAATAAGAAAAATCCCCTCGAAAAAATTTACGGAGTA
*
63330 TAAAACA-TCGTATTTTAGAAAAATAGG--AGTTTCAAGG
129 GAAAACACT-GTA-TTTAG-AAAA-AGGAAAGTTTCAAGG
* * *
63367 AAAAAATCAAAAGCTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATGAT
1 AAAAATTCAAAA-ATCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* *
63432 AATATTTAATGAATTT
65 GATATTTGATGAATTT
63448 TGATGCTTGA
Statistics
Matches: 333, Mismatches: 40, Indels: 51
0.79 0.09 0.12
Matches are distributed among these distances:
150 1 0.00
151 2 0.01
152 18 0.05
154 14 0.04
155 38 0.11
156 10 0.03
157 44 0.13
158 5 0.02
160 2 0.01
161 54 0.16
162 14 0.04
163 29 0.09
164 3 0.01
165 11 0.03
166 87 0.26
167 1 0.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (164 bp):
AAAAATTCAAAAATCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATG
ATATTTGATGAATTTAAAAAATTGAAAAATAAGAAAAATCCCCTCGAAAAAATTTACGGAGTAGA
AAACACTGTATTTAGAAAAAGGAAAGTTTCAAGG
Found at i:64602 original size:24 final size:22
Alignment explanation
Indices: 64559--64603 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
64549 TAATTTTAAT
*
64559 TATTTATAAAATATATAATAAA
1 TATTTATAAAATATAAAATAAA
*
64581 TATTTTTAAAATAAATAAAATAA
1 TATTTATAAAAT--ATAAAATAA
64604 TAATCATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATTTATAAAATATAAAATAAA
Found at i:64861 original size:16 final size:16
Alignment explanation
Indices: 64840--64870 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64830 TTTAATATTG
*
64840 AAATAATCTAAATTTA
1 AAATAATATAAATTTA
64856 AAATAATATAAATTT
1 AAATAATATAAATTT
64871 TTTTTAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAATATAAATTTA
Found at i:65007 original size:10 final size:10
Alignment explanation
Indices: 64989--65022 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
64979 TAGTTTTTAC
64989 TAATTTAAAT
1 TAATTTAAAT
*
64999 TAATCTAAAT
1 TAATTTAAAT
65009 TAATTTAAAT
1 TAATTTAAAT
65019 TAAT
1 TAAT
65023 ATTTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:65032 original size:20 final size:19
Alignment explanation
Indices: 64983--65032 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
64973 TAGATATAGT
*
64983 TTTTACTAATTTAAATTAA
1 TTTTAATAATTTAAATTAA
* *
65002 TCTAAATTAATTTAAATTAA
1 TTTTAA-TAATTTAAATTAA
65022 TATTTAATAAT
1 T-TTTAATAAT
65033 AAAAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAATAATTTAAATTAA
Found at i:65042 original size:28 final size:29
Alignment explanation
Indices: 64989--65068 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
64979 TAGTTTTTAC
* * * *
64989 TAATTTAAATTAATCTAAATTAATTTAAAT
1 TAATTTTAA-TAATATAAAATATTTTAAAT
* *
65019 TAATATTTAATAATA-AAAATATTTTTATT
1 TAAT-TTTAATAATATAAAATATTTTAAAT
*
65048 TAATTTTAATTATATAAAATA
1 TAATTTTAATAATATAAAATA
65069 AATATTAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
28 9 0.22
29 20 0.49
30 8 0.20
31 4 0.10
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TAATTTTAATAATATAAAATATTTTAAAT
Found at i:68696 original size:71 final size:70
Alignment explanation
Indices: 68575--68710 Score: 236
Period size: 70 Copynumber: 1.9 Consensus size: 70
68565 ATTGACAGCA
*
68575 TTTTTTTTTTTTTTAAATTCATTTTAGTTTTATTGGCATATTCCTATCAAGTTTTTCCTCTACTA
1 TTTTTTTTTTTTTTAAATTCATTTTAGTTTTATTGGCATATTCCTATCAAGTTTTTCCCCTACTA
68640 TAATT
66 TAATT
**
68645 TTTTTTTTTTTTTTAGTTTCATTTTAGTTTTATTGGCATAGTTCCTATCAAGTTTTTCCCCTACT
1 TTTTTTTTTTTTTTAAATTCATTTTAGTTTTATTGGCATA-TTCCTATCAAGTTTTTCCCCTACT
68710 A
65 A
68711 CTCTAATTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
70 38 0.61
71 24 0.39
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (70 bp):
TTTTTTTTTTTTTTAAATTCATTTTAGTTTTATTGGCATATTCCTATCAAGTTTTTCCCCTACTA
TAATT
Found at i:73055 original size:2 final size:2
Alignment explanation
Indices: 73048--73078 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
73038 GGTTTTCTTC
73048 TA TA TA 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 TA TA TA T
73079 TAATATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73294 original size:2 final size:2
Alignment explanation
Indices: 73289--73323 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
73279 ATTACCATTT
*
73289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73324 TGCATTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Done.