Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1268
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: 34924
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Found at i:3208 original size:19 final size:19
Alignment explanation
Indices: 3164--3217 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
3154 GGCCAGTTTT
**
3164 ATGTATCGATACAATTTGTCC
1 ATGTATCGATAC-A-TTGAAC
3185 ATGTATCGATACATTGAAC
1 ATGTATCGATACATTGAAC
3204 ATGTATCGATACAT
1 ATGTATCGATACAT
3218 GTATGATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.58
20 1 0.03
21 12 0.39
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATTGAAC
Found at i:15935 original size:79 final size:78
Alignment explanation
Indices: 15746--16052 Score: 255
Period size: 79 Copynumber: 3.9 Consensus size: 78
15736 GGAGAAAACA
* ** * * *
15746 ACGGGGGTGGAGTATCCATGATTATGGAAAATCGGTATTCTGAAAATAAAATCAGGGTTGGAGTA
1 ACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGAAAATAAAATCAGGGTTGGAGTA
*
15811 TCCCCTCGAAAAT
66 TCCCCTCAAAAAT
* * * * * *
15824 AACAGGGTTTGAGTATCTCTGATTAT-AGAAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAA
1 -ACGGGGTTGGAGTATCCCCGATTATGA-AAAATCGGTGTTTTGAAAATAAAATCAGGGTTGGAG
15888 TATCCCCTCAAAAAT
64 TATCCCCTCAAAAAT
* *** * *** *
15903 AGCGGGGTTGGAGTATCCCCGATTGTGAAAAATCAACGCTTT-AGAAATAAGGCCGGGGTTGGAG
1 A-CGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGA-AAATAAAATCAGGGTTGGAG
* *
15967 TATCCTCGTGATAACAAT
64 TATCC-CCTCA-AA-AAT
* * * *
15985 --GGGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATC-GGAGTTGGAGT
1 ACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGAAAATAAAATCAGG-GTTGGAGT
16047 ATCCCC
65 ATCCCC
16053 GATTATGAAA
Statistics
Matches: 180, Mismatches: 39, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
78 5 0.03
79 166 0.92
80 4 0.02
81 2 0.01
82 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (78 bp):
ACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGAAAATAAAATCAGGGTTGGAGTA
TCCCCTCAAAAAT
Found at i:16066 original size:51 final size:51
Alignment explanation
Indices: 15988--16103 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
15978 TAACAATGGG
* * * **
15988 GTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGA
*
16039 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGA
16090 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
16104 TTGGAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGA
Found at i:16169 original size:107 final size:107
Alignment explanation
Indices: 16042--16319 Score: 340
Period size: 109 Copynumber: 2.6 Consensus size: 107
16032 AATCGGAGTT
* *
16042 GGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGGGTTGGAGTATCCCCTTG
1 GGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCG
*
16107 GAAATAACGGGATTGGACTATCCCCGATAACATAACGGGGTC
66 GAAATAACGGGATTGGACTATCCCCAATAACATAACGGGGTC
* *** * **
16149 GGAGTACCCCCGATTATGAAAAAAATCAATATTTTAGACATAAAGCCGGGGTTGGAGTATCCCCT
1 GGAGTATCCCCGATTATG--AAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCT
* * * *
16214 CGGAAATAACGTGATTGGAGTATCCCCAATGACATAACGGGGTT
64 CGGAAATAACGGGATTGGACTATCCCCAATAACATAACGGGGTC
*** * * * **
16258 GGAGTATTTTCAATTAAGAAAAATTGGTATTTTGGAAATAAAATCGAAGTTGGAGTATCCCC
1 GGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
16320 GATTGCAGTA
Statistics
Matches: 140, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
107 52 0.37
109 88 0.63
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (107 bp):
GGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCG
GAAATAACGGGATTGGACTATCCCCAATAACATAACGGGGTC
Found at i:16250 original size:28 final size:28
Alignment explanation
Indices: 16195--16264 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
16185 GACATAAAGC
* **
16195 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGATTGGAGTATCCCCAAGGAAATAA
* * *
16223 CGTGATTGGAGTATCCCCAATGACATAA
1 CGGGATTGGAGTATCCCCAAGGAAATAA
*
16251 CGGGGTTGGAGTAT
1 CGGGATTGGAGTAT
16265 TTTCAATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (28 bp):
CGGGATTGGAGTATCCCCAAGGAAATAA
Found at i:16398 original size:51 final size:51
Alignment explanation
Indices: 16272--16398 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 51
16262 TATTTTCAAT
* * *
16272 TAAGAAAAATTGGTATTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGAT
1 TAAGAAAAATTGATGTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGAA
* * * * *
16323 TGCAG-TAAATCGATGCTTTAGAAATAAAATC-AGAGTTGGAGTATCCCCGAA
1 T-AAGAAAAATTGATGTTTTGGAAATAAAATCGA-AGTTGGAGTATCCCCGAA
16374 TAAGAAAAATTGATGTTTTGGAAAT
1 TAAGAAAAATTGATGTTTTGGAAAT
16399 GGAACCGGGA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
50 3 0.05
51 55 0.92
52 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.29
Consensus pattern (51 bp):
TAAGAAAAATTGATGTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGAA
Found at i:18795 original size:13 final size:13
Alignment explanation
Indices: 18777--18806 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
18767 GTAAATCTAG
18777 AATGTATCGATAC
1 AATGTATCGATAC
18790 AATGTATCGATAC
1 AATGTATCGATAC
18803 AATG
1 AATG
18807 AGCAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:18814 original size:20 final size:20
Alignment explanation
Indices: 18789--18904 Score: 164
Period size: 20 Copynumber: 5.8 Consensus size: 20
18779 TGTATCGATA
**
18789 CAATGTATCGATACAATGAG
1 CAATGTATCGATACAACAAG
*
18809 CAATGTATTGATACAACAAG
1 CAATGTATCGATACAACAAG
18829 CAATGTATCGATACAACAAG
1 CAATGTATCGATACAACAAG
18849 CAATGTATCGATACAATGCAA-
1 CAATGTATCGATACAA--CAAG
*
18870 -AATGTATCAATACAACAAG
1 CAATGTATCGATACAACAAG
18889 CAATGTATCGATACAA
1 CAATGTATCGATACAA
18905 TGCAAAATGT
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
18 3 0.03
20 80 0.93
22 3 0.03
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (20 bp):
CAATGTATCGATACAACAAG
Found at i:18842 original size:40 final size:40
Alignment explanation
Indices: 18788--18923 Score: 179
Period size: 40 Copynumber: 3.4 Consensus size: 40
18778 ATGTATCGAT
** *
18788 ACAATGTATCGATACAATGAGCAATGTATTGATACAA-CA
1 ACAATGTATCGATACAACAAGCAATGTATCGATACAAGCA
18827 AGCAATGTATCGATACAACAAGCAATGTATCGATACAATGCA
1 A-CAATGTATCGATACAACAAGCAATGTATCGATACAA-GCA
*
18869 A-AATGTATCAATACAACAAGCAATGTATCGATACAATGCA
1 ACAATGTATCGATACAACAAGCAATGTATCGATACAA-GCA
*
18909 A-AATGTATCAATACA
1 ACAATGTATCGATACA
18924 TCTGGGTAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
39 1 0.01
40 86 0.96
42 3 0.03
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (40 bp):
ACAATGTATCGATACAACAAGCAATGTATCGATACAAGCA
Found at i:18865 original size:60 final size:60
Alignment explanation
Indices: 18789--18904 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
18779 TGTATCGATA
* **
18789 CAATGTATCGATACAATG-AGCAATGTATTGATACAACAAGCAATGTATCGATACAACAAG
1 CAATGTATCGATACAATGCA-AAATGTATCAATACAACAAGCAATGTATCGATACAACAAG
18849 CAATGTATCGATACAATGCAAAATGTATCAATACAACAAGCAATGTATCGATACAA
1 CAATGTATCGATACAATGCAAAATGTATCAATACAACAAGCAATGTATCGATACAA
18905 TGCAAAATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (60 bp):
CAATGTATCGATACAATGCAAAATGTATCAATACAACAAGCAATGTATCGATACAACAAG
Found at i:18913 original size:20 final size:19
Alignment explanation
Indices: 18788--18923 Score: 141
Period size: 20 Copynumber: 6.8 Consensus size: 19
18778 ATGTATCGAT
*
18788 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAA-CA
* *
18808 GCAATGTATTGATACAACA
1 ACAATGTATCGATACAACA
18827 AGCAATGTATCGATACAACA
1 A-CAATGTATCGATACAACA
18847 AGCAATGTATCGATACAATGCA
1 A-CAATGTATCGATACAA--CA
*
18869 A-AATGTATCAATACAACA
1 ACAATGTATCGATACAACA
18887 AGCAATGTATCGATACAATGCA
1 A-CAATGTATCGATACAA--CA
*
18909 A-AATGTATCAATACA
1 ACAATGTATCGATACA
18924 TCTGGGTAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.03
19 1 0.01
20 91 0.90
22 6 0.06
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (19 bp):
ACAATGTATCGATACAACA
Found at i:18914 original size:60 final size:59
Alignment explanation
Indices: 18788--18923 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 59
18778 ATGTATCGAT
* **
18788 ACAATGTATCGATACAATGAGCAATGTATTGATACAACAAGCAATGTATCGATACAACA
1 ACAATGTATCGATACAATGAGAAATGTATCAATACAACAAGCAATGTATCGATACAACA
18847 AGCAATGTATCGATACAATGCA-AAATGTATCAATACAACAAGCAATGTATCGATACAATGCA
1 A-CAATGTATCGATACAATG-AGAAATGTATCAATACAACAAGCAATGTATCGATACAA--CA
*
18909 A-AATGTATCAATACA
1 ACAATGTATCGATACA
18924 TCTGGGTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
59 1 0.01
60 64 0.93
61 1 0.01
62 3 0.04
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (59 bp):
ACAATGTATCGATACAATGAGAAATGTATCAATACAACAAGCAATGTATCGATACAACA
Found at i:18957 original size:13 final size:13
Alignment explanation
Indices: 18939--18966 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18929 GTAAACCTAG
18939 AATGTATCGATAC
1 AATGTATCGATAC
18952 AATGTATCGATAC
1 AATGTATCGATAC
18965 AA
1 AA
18967 ATTGTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:19632 original size:41 final size:43
Alignment explanation
Indices: 19557--19643 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 43
19547 AAGTCAAAGG
*
19557 AAAAGAGAATGAAATAGGTCTTGCTCCTTAAGGACAAAG-GAA
1 AAAAGAGAAGGAAATAGGTCTTGCTCCTTAAGGACAAAGTGAA
* * *
19599 AAAAGAGAAGGAAA-ATGTCTTGCTTCTTGAGGACAAAGTGAA
1 AAAAGAGAAGGAAATAGGTCTTGCTCCTTAAGGACAAAGTGAA
19641 AAA
1 AAA
19644 GAGTACGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 21 0.52
42 19 0.47
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (43 bp):
AAAAGAGAAGGAAATAGGTCTTGCTCCTTAAGGACAAAGTGAA
Found at i:19790 original size:45 final size:43
Alignment explanation
Indices: 19659--19896 Score: 199
Period size: 42 Copynumber: 5.6 Consensus size: 43
19649 CGTCCTACAT
*
19659 TTTGAGGACAAAGG-AAAAAAGGAAAATGAAATGTGTCTTGCTC
1 TTTGAGGACAAAGGAAAAAAAGG-AAATGAAATGTGTCCTGCTC
* * * *
19702 TTTGAGGACAAA--AGAAAGAGGAAAATAAAATGCGTCCTGCTC
1 TTTGAGGACAAAGGAAAAAAAGG-AAATGAAATGTGTCCTGCTC
* * *
19744 TTTGAGGACAAAGGGAAAAAGAAGGGAATGAAGTGTGTCTTGCTC
1 TTTGAGGACAAA-GGAAAAA-AAGGAAATGAAATGTGTCCTGCTC
* **
19789 TTTGAGGACAAA--AAAGAAAAGG--A--AAAGGCATCCTGCTC
1 TTTGAGGACAAAGGAAA-AAAAGGAAATGAAATGTGTCCTGCTC
* *
19827 TTTAAAGACGAAAGGGAAAAAAAGGAAATGAAATGTGTCCTGCTC
1 TTTGAGGAC-AAA-GGAAAAAAAGGAAATGAAATGTGTCCTGCTC
* * *
19872 TTTGAGGATAAAAG-AGAAAAGGAAA
1 TTTGAGGACAAAGGAAAAAAAGGAAA
19897 AGACGTCCTG
Statistics
Matches: 154, Mismatches: 27, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
38 17 0.11
39 3 0.02
40 1 0.01
41 6 0.04
42 56 0.36
43 16 0.10
44 3 0.02
45 49 0.32
46 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (43 bp):
TTTGAGGACAAAGGAAAAAAAGGAAATGAAATGTGTCCTGCTC
Found at i:19829 original size:38 final size:38
Alignment explanation
Indices: 19697--19925 Score: 138
Period size: 38 Copynumber: 5.6 Consensus size: 38
19687 AAATGTGTCT
** *
19697 TGCTCTTTGAGGACAAAAGAAAGAGGAAAATAAAATGCGTCC
1 TGCTCTTTGAGGAC-AAA-AAAGA--AAAGGAAAAGGCGTCC
* *
19739 TGCTCTTTGAGGACAAAGGGAAA-AAGAAGGGAATGAAGTGTGTCT
1 TGCTCTTTGAGGACAAA---AAAGAA-AA-GGAA--AAG-GCGTCC
*
19784 TGCTCTTTGAGGACAAAAAAGAAAAGGAAAAGGCATCC
1 TGCTCTTTGAGGACAAAAAAGAAAAGGAAAAGGCGTCC
* * * *
19822 TGCTCTTTAAAGACGAAAGGGAAA-AAAAGGAAATGAAATGTGTCC
1 TGCTCTTTGAGGAC-AAA---AAAGAAAAGG--A--AAAGGCGTCC
* * *
19867 TGCTCTTTGAGGATAAAAGAGAAAAGGAAAAGACGTCC
1 TGCTCTTTGAGGACAAAAAAGAAAAGGAAAAGGCGTCC
*
19905 TGCTCTTTGAGGACTAAAAAG
1 TGCTCTTTGAGGACAAAAAAG
19926 TGCCACCAAC
Statistics
Matches: 147, Mismatches: 23, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
38 40 0.27
39 6 0.04
40 2 0.01
41 17 0.12
42 31 0.21
43 7 0.05
44 5 0.03
45 39 0.27
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (38 bp):
TGCTCTTTGAGGACAAAAAAGAAAAGGAAAAGGCGTCC
Found at i:19871 original size:83 final size:82
Alignment explanation
Indices: 19665--19912 Score: 311
Period size: 83 Copynumber: 3.0 Consensus size: 82
19655 ACATTTTGAG
**
19665 GACAAA-GG-AAAAAAGGAAAATGAAATGTGTCTTGCTCTTTGAGGACAAAAGAAAGAGGAAAAT
1 GACAAAGGGAAAAAAAGG-AAATGAAATGTGTCTTGCTCTTTGAGGAC-AAA-AAAGA--AAAGG
* * *
19728 AAAATGCGTCCTGCTCTTTGAG
61 AAAAGGCGTCCTGCTCTTTAAA
* *
19750 GACAAAGGGAAAAAGAAGGGAATGAAGTGTGTCTTGCTCTTTGAGGACAAAAAAGAAAAGGAAAA
1 GACAAAGGGAAAAA-AAGGAAATGAAATGTGTCTTGCTCTTTGAGGACAAAAAAGAAAAGGAAAA
*
19815 GGCATCCTGCTCTTTAAA
65 GGCGTCCTGCTCTTTAAA
* * *
19833 GACGAAAGGGAAAAAAAGGAAATGAAATGTGTCCTGCTCTTTGAGGATAAAAGAGAAAAGGAAAA
1 GAC-AAAGGGAAAAAAAGGAAATGAAATGTGTCTTGCTCTTTGAGGACAAAAAAGAAAAGGAAAA
*
19898 GACGTCCTGCTCTTT
65 GGCGTCCTGCTCTTT
19913 GAGGACTAAA
Statistics
Matches: 144, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
83 82 0.57
84 11 0.08
85 11 0.08
86 5 0.03
87 31 0.22
88 4 0.03
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (82 bp):
GACAAAGGGAAAAAAAGGAAATGAAATGTGTCTTGCTCTTTGAGGACAAAAAAGAAAAGGAAAAG
GCGTCCTGCTCTTTAAA
Found at i:19990 original size:61 final size:60
Alignment explanation
Indices: 19888--20253 Score: 388
Period size: 61 Copynumber: 6.1 Consensus size: 60
19878 GATAAAAGAG
* * * * *
19888 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGAGCTTT
1 AAAA-GAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
19949 GAAAAGAAAAGGCGTCATGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 -AAAAGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * * ** *
20010 GCAAAGAGAAA-GCATCCTGCTTTTTGAGGACTGGAAGGTGCCACCAACTCGACTGGTCTTT
1 -AAAAGA-AAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
20071 AAAAAGAGAAA-GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGTGCTTT
1 -AAAAGA-AAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
20132 ----G-AAAGGCGTCTTGCTCTTTGAGGACTAGGAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAGAAAAGGCATCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
*
20187 AAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTT
1 AAAA-GAAAAGGCATCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
20249 AAAAG
1 AAAAG
20254 CCATCTTGCT
Statistics
Matches: 260, Mismatches: 34, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
54 3 0.01
55 41 0.16
56 5 0.02
60 1 0.00
61 177 0.68
62 33 0.13
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (60 bp):
AAAAGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:20165 original size:55 final size:55
Alignment explanation
Indices: 20078--20275 Score: 238
Period size: 55 Copynumber: 3.5 Consensus size: 55
20068 TTTAAAAAGA
* *
20078 GAAA-GCATCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGTGCTTT
1 GAAAGGCATCTTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTT
* *
20132 GAAAGGCGTCTTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAGGCATCTTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* *
20187 AAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTT
1 -----G-AAAGGCATCTTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT
* *
20249 AAAAGCCATCTTGCTCTTTGAGGACTA
1 GAAAGGCATCTTGCTCTTTGAGGACTA
20276 AAGGGCGAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
54 4 0.03
55 44 0.35
56 25 0.20
60 1 0.01
61 28 0.23
62 22 0.18
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (55 bp):
GAAAGGCATCTTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:20435 original size:156 final size:156
Alignment explanation
Indices: 20152--20435 Score: 426
Period size: 156 Copynumber: 1.8 Consensus size: 156
20142 TTGCTCTTTG
*
20152 AGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGA
1 AGGACTAGGAAATGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGA
* *
20217 CTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGCCATCTTGCTCTTTGAGGACTAAAGGGC
66 CTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGCCATCCTACTCTTTGAGGACTAAAGGGC
20282 GAAAGGAGAGAGCGTCCTCCTATTTT
131 GAAAGGAGAGAGCGTCCTCCTATTTT
* * **
20308 AGGACTAGGAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAGAAGGTGTCCTGCTCTTTGAGGA
1 AGGACTAGGAAATGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGA
* * * * * * *
20373 TTGGGAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTATTCTTTGAGGACTGAAAGG
66 CTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGCCATCCTACTCTTTGAGGACT-AAAGG
20436 TGCCACCAAC
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
155 43 0.38
156 70 0.62
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (156 bp):
AGGACTAGGAAATGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGA
CTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGCCATCCTACTCTTTGAGGACTAAAGGGC
GAAAGGAGAGAGCGTCCTCCTATTTT
Found at i:20440 original size:55 final size:55
Alignment explanation
Indices: 20381--20519 Score: 242
Period size: 55 Copynumber: 2.5 Consensus size: 55
20371 GATTGGGAAA
* *
20381 TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTATTCTTTGAGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
* *
20436 TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
20491 TGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGG
20520 AAAAGGCGTC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 79 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (55 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTTTGAGGACTAAAAGG
Found at i:20524 original size:116 final size:111
Alignment explanation
Indices: 20319--20549 Score: 270
Period size: 116 Copynumber: 2.0 Consensus size: 111
20309 GGACTAGGAA
* * *
20319 GTGCCACCAACTTATGTGGGCTTTAAAAGGAGAAGGTGTCCTGCTCTTTGAGGATTGGGAAATGC
1 GTGCCACCAACTTATGTGGGCTTT---A-GAGAAGGCGTCCTGCTCTTTGAGGACT-GAAAATGC
* *
20384 CACCAACTTGTGTGGGCTTTAAAAGGCGTCCTATTCTTTGAGGACTGAAAG
61 CACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTTTGAAGACTGAAAG
*
20435 GTGCCACCAACTTGTGTGGGCTTT-GA-AAGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCAC
1 GTGCCACCAACTTATGTGGGCTTTAGAGAAGGCGTCCTGCTCTTTGAGGACTGAAAA--TGCCAC
20497 CAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTGAAGACTGAAA
64 CAACTTGTGTGGGCTTT------AAAAGGCGTCCTACTCTTTGAAGACTGAAA
20550 AGTGAAAGGA
Statistics
Matches: 101, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
108 3 0.03
110 45 0.45
111 2 0.02
116 51 0.50
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (111 bp):
GTGCCACCAACTTATGTGGGCTTTAGAGAAGGCGTCCTGCTCTTTGAGGACTGAAAATGCCACCA
ACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTTTGAAGACTGAAAG
Found at i:21548 original size:10 final size:9
Alignment explanation
Indices: 21535--21591 Score: 69
Period size: 10 Copynumber: 5.8 Consensus size: 9
21525 CTTTTCTCTC
21535 TTTTTCTTTG
1 TTTTT-TTTG
21545 TTTTGTTTTG
1 TTTT-TTTTG
21555 TTTTTTTTTG
1 -TTTTTTTTG
21565 TTTTGTTTTG
1 TTTT-TTTTG
21575 TTGTTTTTTG
1 TT-TTTTTTG
21585 TTTTTTT
1 TTTTTTT
21592 GAAAAAGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.21
10 27 0.63
11 7 0.16
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:21549 original size:5 final size:5
Alignment explanation
Indices: 21541--21588 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
21531 TCTCTTTTTC
*
21541 TTTGT TTTGT TTTGT TTTTT TTTGT TTTGT TTTGT TGTT-T TTTGT TTT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT T-TTGT TTTGT TTT
21589 TTTGAAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 2 0.05
5 35 0.90
6 2 0.05
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTGT
Found at i:21558 original size:20 final size:19
Alignment explanation
Indices: 21535--21588 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
21525 CTTTTCTCTC
21535 TTTTTCTTTGTTTTGTTTTG
1 TTTTT-TTTGTTTTGTTTTG
21555 TTTTTTTTTGTTTTGTTTTG
1 -TTTTTTTTGTTTTGTTTTG
21575 TTGTTTTTTGTTTT
1 TT-TTTTTTGTTTT
21589 TTTGAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.06
20 25 0.78
21 5 0.16
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (19 bp):
TTTTTTTTGTTTTGTTTTG
Found at i:29329 original size:25 final size:25
Alignment explanation
Indices: 29295--29350 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
29285 ATCATCACAT
*
29295 ACGTAAACATGGTATATAGGAGTAA
1 ACGTAAACATGGAATATAGGAGTAA
29320 ACGTAAACATGGAATATAGGAGTAA
1 ACGTAAACATGGAATATAGGAGTAA
*
29345 AGGTAA
1 ACGTAA
29351 GAAATGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.21
Consensus pattern (25 bp):
ACGTAAACATGGAATATAGGAGTAA
Found at i:31111 original size:79 final size:78
Alignment explanation
Indices: 30972--31271 Score: 302
Period size: 79 Copynumber: 3.8 Consensus size: 78
30962 TGGAGATAAC
* * * *
30972 AACGGGGGTGGAGTATCCGCGATTATGGAACATCGGTATTTTGAAAATAAAATC-AGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGAAAATAAAATCGA-GGTTGGAG
31036 TATTCCCACAGAAAT
65 TATTCCC-CAGAAAT
* * * *
31051 AACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTTGAAAATAAAATCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGAAAATAAAATCGAGGTTGGAGT
* *
31116 ATCCCCTCAAAAAT
66 ATTCCC-CAGAAAT
* * * *** * *
31130 AACGGGGTTGGAGTATCCCCGATTGTGGAAAATCGATGCTTT-AGAAATAAGGCCGGGGTTAGAG
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGA-AAATAAAATCGAGGTTGGAG
31194 TA-TCCCCATGATAAT
65 TATTCCCCA-GA-AAT
* ** * *
31209 AACGGGGTTGGAGTATCCCCGATTGT-GAGAAATTAGTGTTTTGGAAATAAAATCGAAGTTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGGA-AAATCGGTGTTTTGAAAATAAAATCGAGGTTGGA
31272 ATATCTCCGA
Statistics
Matches: 179, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
77 2 0.01
78 7 0.04
79 169 0.94
80 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.27
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGAAAATAAAATCGAGGTTGGAGT
ATTCCCCAGAAAT
Found at i:31282 original size:51 final size:51
Alignment explanation
Indices: 31215--31312 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
31205 TAATAACGGG
* * * *
31215 GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGGAAATAAAATCGAA
1 GTTGGAATATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAATCGAA
* *
31266 GTTGGAATATCTCCGATTGTGAAAAATTGGTATTTTAGAAATAAAAT
1 GTTGGAATATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAAT
31313 TGGGGTTAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAATCGAA
Found at i:33846 original size:33 final size:33
Alignment explanation
Indices: 33809--33877 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
33799 TAAATCCAGC
** *
33809 ATGTATTGATACAATGAGCAATGTATCGATACA
1 ATGTATTGATACAACAAGCAATGTATCAATACA
33842 ATGTATTGATACAACAAGCAATGTATCAATACA
1 ATGTATTGATACAACAAGCAATGTATCAATACA
33875 ATG
1 ATG
33878 CAAAATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (33 bp):
ATGTATTGATACAACAAGCAATGTATCAATACA
Found at i:33884 original size:102 final size:102
Alignment explanation
Indices: 33759--33944 Score: 248
Period size: 102 Copynumber: 1.8 Consensus size: 102
33749 AAAATGCCTA
* * * * * * *
33759 AATGTATCGATACATTATAAAATGTATCGATATATTTGGGTAAATCC-AGCATGTATTGATACAA
1 AATGTATCAATACAATACAAAATGTATCGATACATCTGGGTAAA-CCTAGAATGTATCGATACAA
* *
33823 TGAGCAATGTATCGATACAATGTATTGATACAACAAGC
65 TAAACAATGTATCGATACAATGTATTGATACAACAAGC
*
33861 AATGTATCAATACAATGCAAAATGTATCGATACATCTGGGTAAACCTAGAATGTATCGATACAAT
1 AATGTATCAATACAATACAAAATGTATCGATACATCTGGGTAAACCTAGAATGTATCGATACAAT
* *
33926 AAATAATGTATTGATACAA
66 AAACAATGTATCGATACAA
33945 ATTGTGAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 2 0.03
102 69 0.97
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (102 bp):
AATGTATCAATACAATACAAAATGTATCGATACATCTGGGTAAACCTAGAATGTATCGATACAAT
AAACAATGTATCGATACAATGTATTGATACAACAAGC
Found at i:33934 original size:49 final size:48
Alignment explanation
Indices: 33755--33943 Score: 141
Period size: 49 Copynumber: 3.8 Consensus size: 48
33745 GTCAAAAATG
* * *
33755 CCTA-AATGTATCGATACATTATAAAATGTATCGATATATTTGGGTAAA
1 CCTAGAATGTATCGATACAATA-AAAATGTATCGATACATATGGGTAAA
* * ** * *
33803 TCC-AGCATGTATTGATACAATGAGCAATGTATCGATACAATGTATTGATACAA
1 -CCTAGAATGTATCGATACAAT-AAAAATGTATCGATAC-A--TATGGGTA-AA
* * * *
33856 -CAAGCAATGTATCAATACAATGCAAAATGTATCGATACATCTGGGTAAA
1 CCTAG-AATGTATCGATACAAT-AAAAATGTATCGATACATATGGGTAAA
*
33905 CCTAGAATGTATCGATACAATAAATAATGTATTGATACA
1 CCTAGAATGTATCGATACAATAAA-AATGTATCGATACA
33944 AATTGTGAAA
Statistics
Matches: 108, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
48 3 0.03
49 57 0.53
50 10 0.09
51 1 0.01
52 8 0.07
53 29 0.27
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (48 bp):
CCTAGAATGTATCGATACAATAAAAATGTATCGATACATATGGGTAAA
Found at i:34626 original size:41 final size:41
Alignment explanation
Indices: 34526--34628 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 41
34516 ATCCCACTTT
*
34526 TTGAGGACAAAGGAAAAA-AGAATGAAATAGGTCTTGCTCC
1 TTGAGGACAAAGGAAAAAGAGAAGGAAATAGGTCTTGCTCC
* * *
34566 TTAAGGACAAAGGAAAAAAGAGAAGGAAA-ATGTCTTGCTTC
1 TTGAGGACAAAGG-AAAAAGAGAAGGAAATAGGTCTTGCTCC
34607 TTGAGGACAAAGTGAAAAAGAG
1 TTGAGGACAAAG-GAAAAAGAG
34629 TACATCCTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
40 12 0.22
41 34 0.62
42 9 0.16
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.18
Consensus pattern (41 bp):
TTGAGGACAAAGGAAAAAGAGAAGGAAATAGGTCTTGCTCC
Found at i:34768 original size:45 final size:43
Alignment explanation
Indices: 34641--34783 Score: 175
Period size: 42 Copynumber: 3.3 Consensus size: 43
34631 CATCCTGTTT
* * *
34641 TTTGAGGA-TAAAGGAAAAAGGAAAATGAAATGCGTCCTGCTC
1 TTTGAGGACAAAAGGAAAGAGGAAAATGAAGTGCGTCCTGCTC
* *
34683 TTTGAGGACAAAA-GAAAGAGGAAAATAAAGTGCGTTCTGCTC
1 TTTGAGGACAAAAGGAAAGAGGAAAATGAAGTGCGTCCTGCTC
* *
34725 TTTGAGGACAAAAGGGAAAAGAAGG-GAATGAAGTGTGTCCTGCTC
1 TTTGAGGACAAAA-GG-AAAG-AGGAAAATGAAGTGCGTCCTGCTC
34770 TTTGAGGACAAAAG
1 TTTGAGGACAAAAG
34784 TGTGATTTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
42 46 0.53
43 3 0.03
44 2 0.02
45 33 0.38
46 3 0.03
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (43 bp):
TTTGAGGACAAAAGGAAAGAGGAAAATGAAGTGCGTCCTGCTC
Done.