Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2616.1
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: 218542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 400 characters in sequence are not A, C, G, or T
Found at i:1771 original size:21 final size:21
Alignment explanation
Indices: 1717--1775 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
1707 TCTATACGCA
*
1717 AAAAAATCTGAACCGAACACC
1 AAAAAATCTGAACCGGACACC
*
1738 AAAACAA-CCGAACCGGACA-C
1 AAAA-AATCTGAACCGGACACC
1758 AAAAAATTCTGAACCGGA
1 AAAAAA-TCTGAACCGGA
1776 ACGGAATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 23 0.72
22 2 0.06
ACGTcount: A:0.51, C:0.27, G:0.14, T:0.08
Consensus pattern (21 bp):
AAAAAATCTGAACCGGACACC
Found at i:5914 original size:39 final size:39
Alignment explanation
Indices: 5860--5934 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5850 AGCGATTGAC
*
5860 TGGTGGACCGATGGTGACTACCTGACTGGTGAACGATGA
1 TGGTGGACCGATGGTGACTACCTGACTCGTGAACGATGA
* *
5899 TGGTGGACCGTTGGTGACTGCCTGACTCGTGAACGA
1 TGGTGGACCGATGGTGACTACCTGACTCGTGAACGA
5935 CAATGGAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (39 bp):
TGGTGGACCGATGGTGACTACCTGACTCGTGAACGATGA
Found at i:14728 original size:24 final size:24
Alignment explanation
Indices: 14696--14747 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
14686 ACAATCATTT
14696 CTTAAATATTACTATCATGATGTG
1 CTTAAATATTACTATCATGATGTG
14720 CTTAAATATTACTATCATGATGTG
1 CTTAAATATTACTATCATGATGTG
14744 CTTA
1 CTTA
14748 GCTCCAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (24 bp):
CTTAAATATTACTATCATGATGTG
Found at i:20827 original size:6 final size:6
Alignment explanation
Indices: 20818--20844 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20808 CAATGATGAT
20818 GATCTG GATCTG GATCTG GATCTG GAT
1 GATCTG GATCTG GATCTG GATCTG GAT
20845 GTTTTGGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (6 bp):
GATCTG
Found at i:27636 original size:18 final size:18
Alignment explanation
Indices: 27611--27662 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
27601 GATATGGCAA
27611 AAATGAGAAATGAACATG
1 AAATGAGAAATGAACATG
* *
27629 ATATGAGAAATGAAATATG
1 AAATGAGAAATG-AACATG
27648 AAATGATGAAATGAA
1 AAATGA-GAAATGAA
27663 ATGTGAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 12 0.41
20 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (18 bp):
AAATGAGAAATGAACATG
Found at i:27681 original size:32 final size:33
Alignment explanation
Indices: 27620--27683 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
27610 AAAATGAGAA
* *
27620 ATGAACATGATATGAGAAATGAAATATGAAATG
1 ATGAACATGAAATGAGAAATGAAAAATGAAATG
* *
27653 ATGAA-ATGAAATGTGAATTGAAAAATGAAAT
1 ATGAACATGAAATGAGAAATGAAAAATGAAAT
27684 CAAGTATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.20, T:0.25
Consensus pattern (33 bp):
ATGAACATGAAATGAGAAATGAAAAATGAAATG
Found at i:32768 original size:34 final size:34
Alignment explanation
Indices: 32725--32800 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
32715 ATTCATGACT
32725 CAAGCTAACAAACTCAACTTCCTACTCCTATTAC
1 CAAGCTAACAAACTCAACTTCCTACTCCTATTAC
* * *
32759 CAAGCTAACAAACTTAGCTTCCTACTCCTATTAG
1 CAAGCTAACAAACTCAACTTCCTACTCCTATTAC
32793 CAAGCTAA
1 CAAGCTAA
32801 AAATCTCCCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.36, C:0.32, G:0.07, T:0.26
Consensus pattern (34 bp):
CAAGCTAACAAACTCAACTTCCTACTCCTATTAC
Found at i:33070 original size:19 final size:19
Alignment explanation
Indices: 33046--33083 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
33036 GAATGTTTTT
33046 ATAGGCTCAAACTTGGTGC
1 ATAGGCTCAAACTTGGTGC
33065 ATAGGCTCAAACTTGGTGC
1 ATAGGCTCAAACTTGGTGC
33084 CTTGATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (19 bp):
ATAGGCTCAAACTTGGTGC
Found at i:33695 original size:31 final size:31
Alignment explanation
Indices: 33657--33722 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
33647 CAAAATAGTG
* *
33657 ATTAAACTATTCGAGAGTTTTTATTTTAA-TC
1 ATTAAACTATTCAAAAGTTTTTA-TTTAAGTC
33688 ATTAAACTATTCAAAAGTTTTTATTTAAGTC
1 ATTAAACTATTCAAAAGTTTTTATTTAAGTC
33719 ATTA
1 ATTA
33723 GGTTGTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (31 bp):
ATTAAACTATTCAAAAGTTTTTATTTAAGTC
Found at i:44869 original size:53 final size:53
Alignment explanation
Indices: 44812--44920 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
44802 TAAATTGGTT
* *
44812 AATTTATGAGAATGCACCACTAATTTTGCCATATTTATTGAATTTTGTGCAGG
1 AATTTATGAGAATGCACCACTAATTTTGCCATATTTATTAAATTTTGTACAGG
44865 AATTTATGAGAATGCACCACTAATTTTGCCATATTTATTAAATTTTGTACAGG
1 AATTTATGAGAATGCACCACTAATTTTGCCATATTTATTAAATTTTGTACAGG
44918 AAT
1 AAT
44921 GCAATTTGGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (53 bp):
AATTTATGAGAATGCACCACTAATTTTGCCATATTTATTAAATTTTGTACAGG
Found at i:46865 original size:11 final size:11
Alignment explanation
Indices: 46845--46884 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
46835 GGAAGATGAC
46845 CACTTTATTTT
1 CACTTTATTTT
* *
46856 CACTTAATTTA
1 CACTTTATTTT
46867 CACTTTATTTT
1 CACTTTATTTT
*
46878 CAATTTA
1 CACTTTA
46885 CCATTTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (11 bp):
CACTTTATTTT
Found at i:47991 original size:16 final size:16
Alignment explanation
Indices: 47965--48003 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
47955 TTATTTCTCA
47965 ATTTAATTTAATT-TTT
1 ATTT-ATTTAATTGTTT
47981 GATTTATTTAATTGTTT
1 -ATTTATTTAATTGTTT
47998 ATTTAT
1 ATTTAT
48004 GCTATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (16 bp):
ATTTATTTAATTGTTT
Found at i:49109 original size:20 final size:20
Alignment explanation
Indices: 49084--49121 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49074 CCTTGTGGGT
49084 TTGGTACCGCGATACCATCA
1 TTGGTACCGCGATACCATCA
*
49104 TTGGTATCGCGATACCAT
1 TTGGTACCGCGATACCAT
49122 TGTAGGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (20 bp):
TTGGTACCGCGATACCATCA
Found at i:51729 original size:40 final size:40
Alignment explanation
Indices: 51654--51732 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
51644 CCCATATATA
* * * *
51654 TTTTCTGAATAATAATATCCATAAAAGAAATATAATTATC
1 TTTTCTAAATAATAATATCAATAAAACAAACATAATTATC
*
51694 TTTTCTAAATAATAATATCAATAAAACAGACATAATTAT
1 TTTTCTAAATAATAATATCAATAAAACAAACATAATTAT
51733 ACATAATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (40 bp):
TTTTCTAAATAATAATATCAATAAAACAAACATAATTATC
Found at i:72273 original size:50 final size:50
Alignment explanation
Indices: 72172--72300 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 50
72162 AAGCTACAGT
* * * * *
72172 GAAGTAAATGTAGAAAAATAAGC-CTAA-CACTAAGAACAATAAGAACAA
1 GAAGTAAATGCAGAAAAATAAACTTTAAGCTCTAAGAACAATAAAAACAA
* *
72220 GAAGTAAATGCAGAAAAATAAACTTTAAGCTTTAAGAATAATAAAAACAA
1 GAAGTAAATGCAGAAAAATAAACTTTAAGCTCTAAGAACAATAAAAACAA
72270 GAAGTAAATGCAGAAAAATAAACTTTAAGCT
1 GAAGTAAATGCAGAAAAATAAACTTTAAGCT
72301 AAGGTAGAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 21 0.29
49 3 0.04
50 48 0.67
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (50 bp):
GAAGTAAATGCAGAAAAATAAACTTTAAGCTCTAAGAACAATAAAAACAA
Found at i:82118 original size:21 final size:21
Alignment explanation
Indices: 82094--82134 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
82084 GAAAACACTA
*
82094 TAATTGAAATTGGAAACTTGT
1 TAATTGAAATTGAAAACTTGT
82115 TAATTGAAATTGAAAACTTG
1 TAATTGAAATTGAAAACTTG
82135 AAAATGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (21 bp):
TAATTGAAATTGAAAACTTGT
Found at i:84857 original size:10 final size:10
Alignment explanation
Indices: 84836--84879 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
84826 TTAATTGGTT
84836 ATTAAGGTTTA
1 ATTAA-GTTTA
84847 ATTAAGTTTA
1 ATTAAGTTTA
84857 AGTTAA--TTA
1 A-TTAAGTTTA
84866 ATTAAGTTTA
1 ATTAAGTTTA
84876 ATTA
1 ATTA
84880 TAATTAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 13 0.43
11 9 0.30
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (10 bp):
ATTAAGTTTA
Found at i:84868 original size:19 final size:20
Alignment explanation
Indices: 84844--84886 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
84834 TTATTAAGGT
84844 TTAATTAAGTTTAAGT-TAA
1 TTAATTAAGTTTAAGTATAA
*
84863 TTAATTAAGTTTAATTATAA
1 TTAATTAAGTTTAAGTATAA
84883 TTAA
1 TTAA
84887 ACTAACTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
TTAATTAAGTTTAAGTATAA
Found at i:95160 original size:118 final size:118
Alignment explanation
Indices: 94952--95897 Score: 1892
Period size: 118 Copynumber: 8.0 Consensus size: 118
94942 CAGATCAACT
94952 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95017 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95070 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95135 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95188 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95253 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95306 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95371 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95424 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95489 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95542 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95607 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95660 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95725 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95778 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
1 CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
95843 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
66 ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
95896 CC
1 CC
95898 GTGCCAGGTT
Statistics
Matches: 828, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 828 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (118 bp):
CCTGAGATGTCGATTAGATATGCATCAAATTCAAGCATGATACTTTTGAATTAAGCAGTAGAAGT
ATAGTATTAATATTAGAAGTGACAAGTATAAAAATACACCTGGGAAAGAAGCA
Found at i:107391 original size:46 final size:46
Alignment explanation
Indices: 107324--107420 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
107314 TTACACAACT
107324 AGAATGCAGCAGAAAATGAAAGCAAGGAAGTAAAAGAATGGTTTCC
1 AGAATGCAGCAGAAAATGAAAGCAAGGAAGTAAAAGAATGGTTTCC
*
107370 AGAATGCAGCAGAAAATGAAAGCAAGGAAGTAAAAGCATGGTTTCC
1 AGAATGCAGCAGAAAATGAAAGCAAGGAAGTAAAAGAATGGTTTCC
107416 AGAAT
1 AGAAT
107421 CCTTGTGCAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.15
Consensus pattern (46 bp):
AGAATGCAGCAGAAAATGAAAGCAAGGAAGTAAAAGAATGGTTTCC
Found at i:125830 original size:22 final size:22
Alignment explanation
Indices: 125802--125845 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
125792 ATCATCTTTG
125802 ATCCCCATCAAACAGAAGTATT
1 ATCCCCATCAAACAGAAGTATT
**
125824 ATCCCCATCGCACAGAAGTATT
1 ATCCCCATCAAACAGAAGTATT
125846 GTTCCGTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (22 bp):
ATCCCCATCAAACAGAAGTATT
Found at i:136026 original size:18 final size:19
Alignment explanation
Indices: 136003--136038 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
135993 TTAACTTTCG
*
136003 ATTTTTTATA-TTATTTTT
1 ATTTTTTAGATTTATTTTT
136021 ATTTTTTAGATTTATTTT
1 ATTTTTTAGATTTATTTT
136039 AATAAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
ATTTTTTAGATTTATTTTT
Found at i:136181 original size:27 final size:29
Alignment explanation
Indices: 136137--136190 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
136127 AAATTTTTAC
* *
136137 TTATTTTACTATTTTAAATA-TAAAATAT
1 TTATTTTACTATTGTAAAAATTAAAATAT
*
136165 TTATTTT-GTATTGTAAAAATTAAAAT
1 TTATTTTACTATTGTAAAAATTAAAAT
136191 TAATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (29 bp):
TTATTTTACTATTGTAAAAATTAAAATAT
Found at i:143098 original size:49 final size:49
Alignment explanation
Indices: 143041--143138 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
143031 CCTTTTCAAC
143041 CTGCGCACGGAAACAA-TCGTACGCTGAGTATTTTATACTCAGTGGTATT
1 CTGCGCACGGAAACAACT-GTACGCTGAGTATTTTATACTCAGTGGTATT
143090 CTGCGCACGGAAACAACTGTACGCTGAGTATTTTATACTCAGTGGTATT
1 CTGCGCACGGAAACAACTGTACGCTGAGTATTTTATACTCAGTGGTATT
143139 ACTATAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 47 0.98
50 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (49 bp):
CTGCGCACGGAAACAACTGTACGCTGAGTATTTTATACTCAGTGGTATT
Found at i:143991 original size:3 final size:3
Alignment explanation
Indices: 143983--144023 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
143973 TAATCATTAA
* * *
143983 AAT AAT AAT AAT AAT TAT ATT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
144024 AATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:144844 original size:5 final size:5
Alignment explanation
Indices: 144836--144902 Score: 63
Period size: 5 Copynumber: 14.2 Consensus size: 5
144826 TTTTTTACTT
* * *
144836 ATATA ATATA ACACA ATACA ATATA ATATA ATATA ATAT- ATA-A TATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA
144885 ATA-A A-ATA ATAT- ATATA A
1 ATATA ATATA ATATA ATATA A
144903 AGCATAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 1 0.02
4 11 0.21
5 39 0.75
6 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (5 bp):
ATATA
Found at i:144878 original size:7 final size:7
Alignment explanation
Indices: 144866--144899 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
144856 ATATAATATA
144866 ATATAAT
1 ATATAAT
144873 ATATAAT
1 ATATAAT
144880 ATATAAT
1 ATATAAT
*
144887 AAAATAAT
1 -ATATAAT
144895 ATATA
1 ATATA
144900 TAAAGCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
ATATAAT
Found at i:144878 original size:12 final size:12
Alignment explanation
Indices: 144861--144899 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
144851 ATACAATATA
144861 ATATAATATAAT
1 ATATAATATAAT
144873 ATATAATAT-AT
1 ATATAATATAAT
*
144884 A-ATAAAATAAT
1 ATATAATATAAT
144895 ATATA
1 ATATA
144900 TAAAGCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 6 0.25
11 6 0.25
12 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:144878 original size:17 final size:15
Alignment explanation
Indices: 144855--144903 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 15
144845 AACACAATAC
144855 AATATAATATAATATA
1 AATATAATAT-ATATA
144871 ATATATAATATATAATA
1 A-ATATAATATAT-ATA
144888 AA-ATAATATATATA
1 AATATAATATATATA
144902 AA
1 AA
144904 GCATAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.16
15 9 0.29
16 4 0.13
17 13 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATAATATATATA
Found at i:144880 original size:22 final size:22
Alignment explanation
Indices: 144856--144899 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 22
144846 ACACAATACA
144856 ATATAATATAATATAATATATAAT
1 ATATAATA-AA-ATAATATATAAT
144880 ATATAATAAAATAATATATA
1 ATATAATAAAATAATATATA
144900 TAAAGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 2 0.10
24 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATAATAAAATAATATATAAT
Found at i:144892 original size:24 final size:24
Alignment explanation
Indices: 144856--144902 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
144846 ACACAATACA
*
144856 ATATAATATAAT-ATAATATATAAT
1 ATATAATAAAATAAT-ATATATAAT
144880 ATATAATAAAATAATATATATAA
1 ATATAATAAAATAATATATATAA
144903 AGCATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAATAAAATAATATATATAAT
Found at i:153307 original size:82 final size:82
Alignment explanation
Indices: 153164--153326 Score: 265
Period size: 82 Copynumber: 2.0 Consensus size: 82
153154 AAAAATTAAT
* *
153164 CCCTTTTAAAATATGGGTTGGATTCGAGCTTGAACATTCAATGCTTGAGTCCGGCTCGACCCGTT
1 CCCTTTTAAAATATGGGTTGGATTCGAGCTTGAACATTCAAGGCTTGAGTCCAGCTCGACCCGTT
153229 TTTAAGTTTATAATACG
66 TTTAAGTTTATAATACG
* * *
153246 CCCTTTTAAAATCTGGGTTGGGTTCGAGCTTGAACATTCAAGGCTTGAG-CCTAGCTTGACCCGT
1 CCCTTTTAAAATATGGGTTGGATTCGAGCTTGAACATTCAAGGCTTGAGTCC-AGCTCGACCCGT
153310 TTTTAAGTTTATAATAC
65 TTTTAAGTTTATAATAC
153327 CTTATATTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
81 2 0.03
82 73 0.97
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (82 bp):
CCCTTTTAAAATATGGGTTGGATTCGAGCTTGAACATTCAAGGCTTGAGTCCAGCTCGACCCGTT
TTTAAGTTTATAATACG
Found at i:155034 original size:3 final size:3
Alignment explanation
Indices: 155012--155050 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
155002 AAGCATAAAC
* * *
155012 TAA TAA AAA TAA TAA GAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
155051 CATTGGAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:155208 original size:6 final size:6
Alignment explanation
Indices: 155166--155199 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
155156 ATAAAAATAT
155166 ATACTA ATACATA ATACTA ATACTA ATACTA ATA
1 ATACTA ATAC-TA ATACTA ATACTA ATACTA ATA
155200 ATACTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:155211 original size:12 final size:12
Alignment explanation
Indices: 155161--155202 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
155151 ACATAATAAA
155161 AATATATACTAAT
1 AATA-ATACTAAT
155174 ACATAATACTAAT
1 A-ATAATACTAAT
*
155187 ACTAATACTAAT
1 AATAATACTAAT
155199 AATA
1 AATA
155203 CTAATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 13 0.50
13 10 0.38
14 3 0.12
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATACTAAT
Found at i:155699 original size:11 final size:11
Alignment explanation
Indices: 155685--155720 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
155675 AAAAAAAAAA
155685 GAAGAGAGAGG
1 GAAGAGAGAGG
*
155696 GAAGAGAGAAG
1 GAAGAGAGAGG
155707 GAAGAGAGAAGG
1 GAAGAGAG-AGG
155719 GA
1 GA
155721 GGGGGGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:155848 original size:16 final size:17
Alignment explanation
Indices: 155827--155864 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
155817 AGGTAAAAAA
* *
155827 TTTATTTTTTGT-TTTT
1 TTTATTTGTTGTATATT
155843 TTTATTTGTTGTATATT
1 TTTATTTGTTGTATATT
155860 TTTAT
1 TTTAT
155865 GTTAAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTATTTGTTGTATATT
Found at i:156423 original size:6 final size:6
Alignment explanation
Indices: 156409--156447 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
156399 GTAATCAAAA
*
156409 ACCATT ACCAAT ACCAAT ACCAAT ACCAAT ACCAAT ACC
1 ACCAAT ACCAAT ACCAAT ACCAAT ACCAAT ACCAAT ACC
156448 GTTTCCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (6 bp):
ACCAAT
Found at i:166838 original size:4 final size:4
Alignment explanation
Indices: 166831--166871 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
166821 TATATACGTG
166831 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
166872 TGTCTTGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:177289 original size:6 final size:6
Alignment explanation
Indices: 177280--177305 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
177270 GGTAGTATCC
177280 CATTGG CATTGG CATTGG CATTGG CA
1 CATTGG CATTGG CATTGG CATTGG CA
177306 AATCCTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (6 bp):
CATTGG
Found at i:182646 original size:17 final size:17
Alignment explanation
Indices: 182596--182647 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
182586 TATCGTCTAT
**
182596 TTTAATTTTTGAATTTA
1 TTTAATTTTTTTATTTA
**
182613 --TAATTTTTTTAAATA
1 TTTAATTTTTTTATTTA
182628 TTTAATTTTTTTATTTA
1 TTTAATTTTTTTATTTA
182645 TTT
1 TTT
182648 TAATCCTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 11 0.41
17 16 0.59
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTAATTTTTTTATTTA
Found at i:199280 original size:28 final size:30
Alignment explanation
Indices: 199227--199303 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 30
199217 AGTTTGTGAG
*
199227 AATTGAA-ACAAATCAAA-TTTCATGTATAA
1 AATTGAACATAAATCAAAGTTT-ATGTATAA
199256 AATTGAACA-AAATCAAAGTTT-TGTATAA
1 AATTGAACATAAATCAAAGTTTATGTATAA
*
199284 AATTGTACATTAAATCAAAG
1 AATTGAACA-TAAATCAAAG
199304 GTCATGGTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
28 15 0.35
29 15 0.35
30 13 0.30
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (30 bp):
AATTGAACATAAATCAAAGTTTATGTATAA
Found at i:201375 original size:20 final size:21
Alignment explanation
Indices: 201341--201381 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
201331 TATTTATATT
201341 TATATATTAAGTTAC-AAAAA
1 TATATATTAAGTTACTAAAAA
* *
201361 TATATATTTATTTACTAAAAA
1 TATATATTAAGTTACTAAAAA
201382 GATTATAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
TATATATTAAGTTACTAAAAA
Found at i:205395 original size:15 final size:16
Alignment explanation
Indices: 205363--205400 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
205353 ATTTTAAATT
* *
205363 TTAAAAATTATACGAA
1 TTAAAAATGATACCAA
205379 TTAAAAATGAT-CCAA
1 TTAAAAATGATACCAA
205394 TTAAAAA
1 TTAAAAA
205401 ATATGGACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
TTAAAAATGATACCAA
Found at i:210756 original size:60 final size:59
Alignment explanation
Indices: 210662--210781 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 59
210652 ATGTATTGTA
210662 GTAGCTAATGATCTACGCTCTTCCGATGCTGATAAATTTGTCTGATTAACACTGAATCG
1 GTAGCTAATGATCTACGCTCTTCCGATGCTGATAAATTTGTCTGATTAACACTGAATCG
* *
210721 GNTAGCTAATGATCTACGCTCTTCTGATTCTGATAAATTTGTCTGATTAACACTGAATCG
1 G-TAGCTAATGATCTACGCTCTTCCGATGCTGATAAATTTGTCTGATTAACACTGAATCG
210781 G
1 G
210782 AAATATTTGA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 1 0.02
60 57 0.98
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (59 bp):
GTAGCTAATGATCTACGCTCTTCCGATGCTGATAAATTTGTCTGATTAACACTGAATCG
Found at i:211336 original size:25 final size:23
Alignment explanation
Indices: 211293--211343 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
211283 ACATTATTCT
*
211293 ATATTTATATATTATATATACAA
1 ATATTTATATATTATATATAAAA
211316 ATATTTATACTTATTCA-ATATAAAA
1 ATATTTATA--TATT-ATATATAAAA
211341 ATA
1 ATA
211344 GACTGATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.38
25 14 0.58
26 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTTATATATTATATATAAAA
Found at i:217191 original size:12 final size:12
Alignment explanation
Indices: 217174--217198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
217164 ATAATTATAC
217174 TTATCTCATTTT
1 TTATCTCATTTT
217186 TTATCTCATTTT
1 TTATCTCATTTT
217198 T
1 T
217199 GTAATGTGAA
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:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATCTCATTTT
Done.