Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1520
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: 65914
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2262 original size:51 final size:52
Alignment explanation
Indices: 2198--2330 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 52
2188 AAGAAAATGT
* *
2198 ATCGATACATTTTTCATTGTATTGATACATTCTGAGTTTTAG-CCCAAATAT
1 ATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTAGACCCAAATAC
* * * *
2249 ATC-AGTACATTTTTCATTTTATCGATACATTTTGGGTTTTTGACCCAAATAC
1 ATCGA-TACATTTTTCATTGTATCGATACATTCTGAGTTTTAGACCCAAATAC
* *
2301 ATCGATACATTCTTCAATGTATCGATACAT
1 ATCGATACATTTTTCATTGTATCGATACAT
2331 GCAGGCTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.01
51 35 0.50
52 33 0.47
53 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (52 bp):
ATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTAGACCCAAATAC
Found at i:4268 original size:38 final size:38
Alignment explanation
Indices: 4226--4303 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
4216 CTTATAACTT
*
4226 ATAGGGTGAAGCTTTATTGACGGCCTGTTATATCCATA
1 ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
4264 ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
1 ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
4302 AT
1 AT
4304 GGAAGGTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (38 bp):
ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
Found at i:5857 original size:1 final size:1
Alignment explanation
Indices: 5851--5875 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5841 AAATGCTCAG
5851 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5876 GAGTACCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8781 original size:74 final size:73
Alignment explanation
Indices: 8474--8813 Score: 324
Period size: 72 Copynumber: 4.7 Consensus size: 73
8464 TTATTTTGCG
* * * * *
8474 AAACTTTTATAAATAAAAA-AAATTATAGCTTAAAAAATTTAAACTTATATGATTATATCCAAAA
1 AAACTTCTATAAATAAAAATAAATTATA-TTTAAAAAATTTAAACTCATATAATTATACCCAAAA
8538 AATAAATTT
65 AATAAATTT
* * *
8547 AAAC-TCGTACAAAT-AAAA-AAA-TAT-TTTAAAAAATTTAAACTCATATAATTA-AACCAGAA
1 AAACTTC-TATAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATTATACCCAAAA
* *
8606 AACAAATAT
65 AATAAATTT
* * * * ** *
8615 AAAGTTCAATAAATGAAAATAAATCATATATT-AAAAATTTAAA-TTTTATAATTATACTCAAAA
1 AAACTTCTATAAATAAAAATAAATTATAT-TTAAAAAATTTAAACTCATATAATTATACCCAAAA
8678 AATAAA-TT
65 AATAAATTT
* * * **
8686 AATACTTCTATAAATAGAAATAAATTATAGTTTAAAAAATTTAAACTCGTATACTCGTACCCAAA
1 AA-ACTTCTATAAATAAAAATAAATTATA-TTTAAAAAATTTAAACTCATATAATTATACCCAAA
*
8751 AAATAAGTTT
64 AAATAAATTT
* *
8761 AAACTTTTACAAATAAAAATAAATTATATTCT-AAAAATTTAAACTCATATAAT
1 AAACTTCTATAAATAAAAATAAATTATATT-TAAAAAATTTAAACTCATATAAT
8814 CATATTTAAA
Statistics
Matches: 216, Mismatches: 37, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
68 21 0.10
69 30 0.14
70 3 0.01
71 17 0.08
72 53 0.25
73 45 0.21
74 43 0.20
75 4 0.02
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.33
Consensus pattern (73 bp):
AAACTTCTATAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATTATACCCAAAAA
ATAAATTT
Found at i:8823 original size:60 final size:60
Alignment explanation
Indices: 8758--8883 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 60
8748 AAAAAATAAG
*
8758 TTTAAACTTTTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
* * *
8818 TTTAAACTTCTACAGATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
*
8878 TCTAAA
1 TTTAAA
8884 AACAAATTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.39
Consensus pattern (60 bp):
TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
Found at i:8847 original size:134 final size:129
Alignment explanation
Indices: 8684--8940 Score: 320
Period size: 133 Copynumber: 2.0 Consensus size: 129
8674 AAAAAATAAA
* * * * *
8684 TTAATACTTCTATAAATAGAAATAAATTATAGTTTAAAAAATTTAAACTCGTATACTCGTACCCA
1 TTAATACTTCTACAAATAAAAATAAATTATA-TTTAAAAAATTTAAACTCATATAATCATACCCA
8749 AAAA-ATAAGTTTAAACTTTTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAA
65 AAAACA-AA-TTTAAACTTTTACAAAT-AAAA-AAATTAT-TT-TAAAAATTTAAACTCATATAA
8813 TCATAT
124 TCATAT
* * * * *
8819 TTAA-ACTTCTACAGATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATATCTAA
1 TTAATACTTCTACAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATCATACCCAA
* * *
8883 AAACAAATTTAAACTTTTACAAATAAAAAAATTATTTTTAAAATTTAAATTCGTATAA
66 AAACAAATTTAAACTTTTACAAATAAAAAAATTATTTTAAAAATTTAAACTCATATAA
8941 CTATATAATT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
128 18 0.17
129 2 0.02
130 7 0.06
131 4 0.04
132 17 0.16
133 32 0.30
134 24 0.22
135 4 0.04
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (129 bp):
TTAATACTTCTACAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATCATACCCAA
AAACAAATTTAAACTTTTACAAATAAAAAAATTATTTTAAAAATTTAAACTCATATAATCATAT
Found at i:12182 original size:28 final size:28
Alignment explanation
Indices: 12122--12183 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
12112 AAATGTCACC
*
12122 CTTTGTATTTGTCAAATATGGTGGTTTT
1 CTTTGTATTTGTCAAATATGGTAGTTTT
12150 CTTTGTATTTGTCAAATATGGTAGTTATT
1 CTTTGTATTTGTCAAATATGGTAGTT-TT
12179 -TTTGT
1 CTTTGT
12184 TTGTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (28 bp):
CTTTGTATTTGTCAAATATGGTAGTTTT
Found at i:12216 original size:24 final size:24
Alignment explanation
Indices: 12180--12225 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
12170 GTAGTTATTT
12180 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
12204 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
12226 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:13329 original size:72 final size:71
Alignment explanation
Indices: 13191--13529 Score: 271
Period size: 72 Copynumber: 4.7 Consensus size: 71
13181 TTATTTTGCG
* * * * *
13191 AAACTTTTATAAATAAAAAAATTATAGCTTAAAAAATTTAAACTTATATGATTATATCCAAAAAA
1 AAACTTGTACAAATAAAAAAATTATA-CTTAAAAAATTTAAACTCATATAATTATAACCAAAAAA
13256 TAAATTT
65 TAAATTT
* * *
13263 AAACTTGTACAAATAAAAAAA-TAT-TTTAAAAAATTTAAACTCATATAATTA-AACCAGAAAAC
1 AAACTTGTACAAATAAAAAAATTATACTTAAAAAATTTAAACTCATATAATTATAACCAAAAAAT
*
13325 AAATAT
66 AAATTT
* ** * * ** *
13331 AAAGTTCAATAAATGAAAATAAATCATACATT-AAAAATTTAAA-TTTTATAATTAT-ACTAAAA
1 AAACTTGTACAAAT-AAAA-AAATTATAC-TTAAAAAATTTAAACTCATATAATTATAAC-CAAA
13393 AAATAAA-TT
62 AAATAAATTT
* * * * ** *
13402 AATACTTCTATAAATAGAAATAAATTATAGCTTAAAAAATTTAAACTCGTATACTCGTACCCAAA
1 AA-ACTTGTACAAATA-AAA-AAATTATA-CTTAAAAAATTTAAACTCATATAATTATAACCAAA
*
13467 AAATAAGTTT
62 AAATAAATTT
* *
13477 AAACTTTTACAAATAAAAATAAATTATA-TTCTAAAAATTTAAACTCATATAAT
1 AAACTTGTACAAAT-AAAA-AAATTATACTT-AAAAAATTTAAACTCATATAAT
13530 CATATTTAAA
Statistics
Matches: 214, Mismatches: 37, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
68 23 0.11
69 28 0.13
70 3 0.01
71 20 0.09
72 63 0.29
73 33 0.15
74 38 0.18
75 6 0.03
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (71 bp):
AAACTTGTACAAATAAAAAAATTATACTTAAAAAATTTAAACTCATATAATTATAACCAAAAAAT
AAATTT
Found at i:13539 original size:60 final size:60
Alignment explanation
Indices: 13474--13599 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 60
13464 AAAAAATAAG
*
13474 TTTAAACTTTTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
* * *
13534 TTTAAACTTCTACAGATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
*
13594 TCTAAA
1 TTTAAA
13600 AACAAATTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.39
Consensus pattern (60 bp):
TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
Found at i:13621 original size:132 final size:134
Alignment explanation
Indices: 13400--13642 Score: 332
Period size: 133 Copynumber: 1.8 Consensus size: 134
13390 AAAAAATAAA
* * * * *
13400 TTAATACTTCTATAAATAGAAATAAATTATAGCTTAAAAAATTTAAACTCGTATACTCGTACCCA
1 TTAATACTTCTACAAATAAAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCATACCCA
13465 AAAAATAAGTTTAAACTTTTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAAT
66 AAAAATAAGTTTAAACTTTTACAAATAAAAA-AAATTATATTCTAAAAATTTAAACTCATATAAT
13530 CATAT
130 CATAT
* * * * * *
13535 TTAA-ACTTCTACAGATAAAAATAAATTATA-TTTTAAAAATTTAAACTCATATAATTATATCTA
1 TTAATACTTCTACAAATAAAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCATACCCA
*
13598 AAAACA-AA-TTTAAACTTTTACAAATAAAAAAAATTATATTTTAAA
66 AAAA-ATAAGTTTAAACTTTTACAAATAAAAAAAATTATATTCTAAA
13643 TTTAAATTCG
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
131 14 0.15
132 22 0.23
133 31 0.33
134 24 0.25
135 4 0.04
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.36
Consensus pattern (134 bp):
TTAATACTTCTACAAATAAAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCATACCCA
AAAAATAAGTTTAAACTTTTACAAATAAAAAAAATTATATTCTAAAAATTTAAACTCATATAATC
ATAT
Found at i:13665 original size:71 final size:71
Alignment explanation
Indices: 13533--13672 Score: 194
Period size: 71 Copynumber: 2.0 Consensus size: 71
13523 ATATAATCAT
*
13533 ATTTAAACTTCTACAGATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATATCTA
1 ATTTAAACTTCTACAAATAAAAATAAATTATATTTT-AAAATTTAAACTCATATAATTATATCTA
13598 AAAACAA
65 AAAACAA
* * * *
13605 ATTTAAACTTTTACAAATAAAAA-AAATTATATTTT-AAATTTAAATTCGTATAACTATATATTT
1 ATTTAAACTTCTACAAATAAAAATAAATTATATTTTAAAATTTAAACTCATATAA-T-TATATCT
13668 AAAAA
64 AAAAA
13673 TACTATAACA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
69 16 0.26
70 1 0.02
71 23 0.38
72 21 0.34
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (71 bp):
ATTTAAACTTCTACAAATAAAAATAAATTATATTTTAAAATTTAAACTCATATAATTATATCTAA
AAACAA
Found at i:13692 original size:69 final size:71
Alignment explanation
Indices: 13549--13694 Score: 156
Period size: 69 Copynumber: 2.1 Consensus size: 71
13539 ACTTCTACAG
* *
13549 ATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATATCTAAAAACAAATTTAAACT
1 ATAAAAATAAATTATATTTT-AAAATTTAAACTCATATAATTATATCTAAAAACAAATATAAACA
* *
13614 TTTACAA
65 ATTAAAA
* * * * *
13621 ATAAAAA-AAATTATATTTT-AAATTTAAATTCGTATAACTATATATTTAAAAA-TACTAT-AAC
1 ATAAAAATAAATTATATTTTAAAATTTAAACTCATATAA-T-TATATCTAAAAACAAATATAAAC
13682 AATTAAAA
64 AATTAAAA
13690 ATAAA
1 ATAAA
13695 TCATACCTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
69 29 0.46
70 4 0.06
71 23 0.37
72 7 0.11
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (71 bp):
ATAAAAATAAATTATATTTTAAAATTTAAACTCATATAATTATATCTAAAAACAAATATAAACAA
TTAAAA
Found at i:14200 original size:25 final size:26
Alignment explanation
Indices: 14158--14208 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
14148 ATCATACTCA
*
14158 AAAAATAAATTTAAACTTTTACAAAT
1 AAAAATAAATTTAAACTTTTAAAAAT
*
14184 AAAAATAAA-TTATACTTTTAAAAAT
1 AAAAATAAATTTAAACTTTTAAAAAT
14209 TTAAACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAATAAATTTAAACTTTTAAAAAT
Found at i:14212 original size:74 final size:73
Alignment explanation
Indices: 14116--14308 Score: 286
Period size: 74 Copynumber: 2.7 Consensus size: 73
14106 TCAATAATAC
**
14116 TAAATTATA-TTTTAAAAATTTAAACTCGTATAATCATACTCAAAAAATAAATTTAAACTTTTAC
1 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATAAATTTAAACTTTTAC
14180 AAATAAAAA
66 AAAT-AAAA
* *
14189 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACCCAAAAAATAAATTTAAATTTTTAC
1 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATAAATTTAAACTTTTAC
14254 AAATAAAA
66 AAATAAAA
* * *
14262 -AAATTACAC-TTTAAAAATTTAAATTTATATAATCATA-TCTAAAAATA
1 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATA
14309 CTTTAACAAC
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
70 8 0.07
71 27 0.24
72 8 0.07
73 13 0.12
74 55 0.50
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (73 bp):
TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATAAATTTAAACTTTTAC
AAATAAAA
Found at i:14920 original size:70 final size:72
Alignment explanation
Indices: 14732--14921 Score: 181
Period size: 73 Copynumber: 2.6 Consensus size: 72
14722 TTTATAATAC
* * * * *
14732 TAAATTATACATTT-AAAAATTTTTAACTCATATAATTATACTCAAAAATAAATTTTAACTTCTA
1 TAAATTAT--ATTTAAAAAAATTTAAACTCATATAATCATACTAAAAAATAAATTTAAACTTCTA
*
14796 CAAGTAAAA
64 CAAATAAAA
** * * * * *
14805 TAAATTATATTTTCAAAAATTTAAACTCGTATAATCATGCTTAAAAAATCAATTTAAATTTTTAC
1 TAAATTATATTTAAAAAAATTTAAACTCATATAATCATAC-TAAAAAATAAATTTAAACTTCTAC
14870 AAAT-AAA
65 AAATAAAA
* *
14877 -AAATTATA-TTAAAAAAATTTAAATTTATATAATCATATCTAAAAA
1 TAAATTATATTTAAAAAAATTTAAACTCATATAATCATA-CTAAAAA
14922 CACATTAAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
70 29 0.30
71 13 0.14
72 24 0.25
73 30 0.31
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (72 bp):
TAAATTATATTTAAAAAAATTTAAACTCATATAATCATACTAAAAAATAAATTTAAACTTCTACA
AATAAAA
Found at i:15146 original size:50 final size:49
Alignment explanation
Indices: 15072--15170 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
15062 CCTCAATTAC
* * * *
15072 TTGGGGGTGGGGTATTCAGCGACTCCCCTAAATAATAATTGTACCCTAAA
1 TTGGGGGTAGGGTATCCAACGACTCCCAT-AATAATAATTGTACCCTAAA
* * *
15122 TTGGGGGTAGGGTATCCAATGACTCCCATATTAATAATTGTACCTTAAA
1 TTGGGGGTAGGGTATCCAACGACTCCCATAATAATAATTGTACCCTAAA
15171 CCCTATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 18 0.43
50 24 0.57
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (49 bp):
TTGGGGGTAGGGTATCCAACGACTCCCATAATAATAATTGTACCCTAAA
Found at i:18103 original size:18 final size:18
Alignment explanation
Indices: 18080--18135 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
18070 AGAGAATTAG
*
18080 TGCTTGGCAGCGATTACA
1 TGCTTGGCAGAGATTACA
*
18098 TGCTTGGCAGAGACTACA
1 TGCTTGGCAGAGATTACA
18116 TGCTTGGCAGAGATTACA
1 TGCTTGGCAGAGATTACA
18134 TG
1 TG
18136 ATGCTCCTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (18 bp):
TGCTTGGCAGAGATTACA
Found at i:18897 original size:117 final size:117
Alignment explanation
Indices: 18775--18985 Score: 284
Period size: 117 Copynumber: 1.8 Consensus size: 117
18765 TATATATATA
* * * * *
18775 TATATTCAATGAATTATATTCTTAATTTGTAATTTGTGACT-TTTTGTTA-TTCTTAAGGCTAAC
1 TATATTAAATGAATTATATTC-CAATCTGTAATTTGTGA-TATGTTGTTATTTATTAAGGCTAA-
18838 A-TACTAAAGAAATCCTTATATATTTTAAAGTGAACTAAATTTTCACTACCTTTC
63 AGTACTAAAGAAATCCTTATATATTTTAAAGTGAACTAAATTTTCACTACCTTTC
* *
18892 TATATTAAATGAATTATATTCCCATCTGTAATTTGTGATATGTTGTTATTTATTAAGGTTAAAGT
1 TATATTAAATGAATTATATTCCAATCTGTAATTTGTGATATGTTGTTATTTATTAAGGCTAAAGT
* * *
18957 ATTAAAGAAATCCTTGTATGTTTTAAAGT
66 ACTAAAGAAATCCTTATATATTTTAAAGT
18986 TACATTTATA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
115 1 0.01
116 22 0.27
117 58 0.72
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (117 bp):
TATATTAAATGAATTATATTCCAATCTGTAATTTGTGATATGTTGTTATTTATTAAGGCTAAAGT
ACTAAAGAAATCCTTATATATTTTAAAGTGAACTAAATTTTCACTACCTTTC
Found at i:20745 original size:5 final size:5
Alignment explanation
Indices: 20737--20777 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
20727 AAATATTTTA
* *
20737 TTAAT TTAAA TTAAT TTAAT TTAAT TTAAA TTAAT ATTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT -TTAAT
20778 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:20751 original size:10 final size:10
Alignment explanation
Indices: 20736--20776 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
20726 TAAATATTTT
20736 ATTAATTTAA
1 ATTAATTTAA
20746 ATTAATTTAA
1 ATTAATTTAA
*
20756 TTTAATTTAA
1 ATTAATTTAA
20766 ATTAATATTAA
1 ATTAAT-TTAA
20777 TAATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 24 0.86
11 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:20762 original size:20 final size:21
Alignment explanation
Indices: 20737--20777 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
20727 AAATATTTTA
20737 TTAATTTAAATTAAT-TTAAT
1 TTAATTTAAATTAATATTAAT
20757 TTAATTTAAATTAATATTAAT
1 TTAATTTAAATTAATATTAAT
20778 AATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATTTAAATTAATATTAAT
Found at i:20842 original size:50 final size:51
Alignment explanation
Indices: 20749--20893 Score: 135
Period size: 50 Copynumber: 2.9 Consensus size: 51
20739 AATTTAAATT
**
20749 AATTTAATTTAATT-TAAAT--T-AATATTAATAATTAAAAAATATTTTTATATA
1 AATTTAA-TTAATTATAAATAATAAATATTAATAA-TAAAATTTATTTTT-TA-A
20800 AATTTAATT-A-TAT-AATATATAAATATTAAT-ATAAAATTTATTTTTTAA
1 AATTTAATTAATTATAAATA-ATAAATATTAATAATAAAATTTATTTTTTAA
* * *
20848 TATTTTATTAATTATAAATAATAAATATAAATAATATAAATTTATT
1 AATTTAATTAATTATAAATAATAAATATTAATAATA-AAATTTATT
20894 AAATCAAATC
Statistics
Matches: 79, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
48 12 0.15
49 5 0.06
50 28 0.35
51 16 0.20
52 18 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (51 bp):
AATTTAATTAATTATAAATAATAAATATTAATAATAAAATTTATTTTTTAA
Found at i:22182 original size:26 final size:27
Alignment explanation
Indices: 22134--22184 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
22124 AAAATAATTT
* *
22134 AAATATATTATGATATATAAAAATAAA
1 AAATATAATATGAAATATAAAAATAAA
22161 AAATATAATAT-AAATATAAAAATA
1 AAATATAATATGAAATATAAAAATA
22185 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
AAATATAATATGAAATATAAAAATAAA
Found at i:22191 original size:28 final size:28
Alignment explanation
Indices: 22115--22201 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
22105 ACACATATAC
*
22115 ATAAAGTA-AAAAATAATTT-AAATATATT
1 ATAAA-TATAAAAAT-ATTTAAAATATAAT
* *
22143 ATGATATATAAAAATA--AAAAATATAAT
1 AT-AAATATAAAAATATTTAAAATATAAT
* *
22170 ATAAATATAAAAATATTTAAAATTTTAT
1 ATAAATATAAAAATATTTAAAATATAAT
22198 ATAA
1 ATAA
22202 TACAAATTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
26 12 0.26
27 10 0.21
28 17 0.36
29 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
ATAAATATAAAAATATTTAAAATATAAT
Found at i:22236 original size:13 final size:13
Alignment explanation
Indices: 22210--22258 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
22200 AATACAAATT
**
22210 TAATATATAAATA
1 TAATATATTTATA
22223 TAATATATTTATA
1 TAATATATTTATA
*
22236 TATTATAATTTATA
1 TAATAT-ATTTATA
22250 TAAATATAT
1 T-AATATAT
22259 AACATTGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 16 0.53
14 10 0.33
15 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATATATTTATA
Found at i:22480 original size:92 final size:90
Alignment explanation
Indices: 22313--22483 Score: 218
Period size: 92 Copynumber: 1.9 Consensus size: 90
22303 TTCAAAAAAA
* * * * *
22313 AGTAATAGCAAGTCGTTACCGTTACTAAGAAGTTAATTGCTTCAGTCTGTATTCTTATTCACCTA
1 AGTAATAGCAAGTCGTCACCGTGACTAAAAAGTCAATTGCTTCAGTCTGGATTCTTATTCACCTA
22378 CCCTCTACTAATGACTTTTTGAAGT
66 CCCTCTACTAATGACTTTTTGAAGT
* * * *
22403 AGTAATAGCAAGTCGTCACCGAAGTGAGTAAAAAGTCAATTGCTTCTGTC-GGATTGTTATTTAC
1 AGTAATAGCAAGTCGTCACC---GTGACTAAAAAGTCAATTGCTTCAGTCTGGATTCTTATTCAC
*
22467 CTACCCTTTACTAATGA
63 CTACCCTCTACTAATGA
22484 AAGTAAAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
90 19 0.28
92 27 0.40
93 22 0.32
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (90 bp):
AGTAATAGCAAGTCGTCACCGTGACTAAAAAGTCAATTGCTTCAGTCTGGATTCTTATTCACCTA
CCCTCTACTAATGACTTTTTGAAGT
Found at i:22800 original size:14 final size:14
Alignment explanation
Indices: 22781--22812 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
22771 TCATAGTTTG
22781 ATTTTATAATTGTT
1 ATTTTATAATTGTT
*
22795 ATTTTATAATTTTT
1 ATTTTATAATTGTT
22809 ATTT
1 ATTT
22813 ATTTTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
ATTTTATAATTGTT
Found at i:26836 original size:24 final size:24
Alignment explanation
Indices: 26808--26853 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
26798 AATAAAAATT
26808 AGCCACCAATTT-TGACAAACAACA
1 AGCCACCAATTTGT-ACAAACAACA
26832 AGCCACCAATTTGTACAAACAA
1 AGCCACCAATTTGTACAAACAA
26854 AAATAACCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.46, C:0.28, G:0.09, T:0.17
Consensus pattern (24 bp):
AGCCACCAATTTGTACAAACAACA
Found at i:26891 original size:28 final size:28
Alignment explanation
Indices: 26858--26940 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
26848 AAACAAAAAT
*
26858 AACCACCATATTTGACAAATATAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
26886 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
26914 AACTACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
26941 GTGGCATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:31519 original size:28 final size:28
Alignment explanation
Indices: 31486--31568 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
31476 AAACAAAAAT
*
31486 AACCACCATATTTGACAAATATAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
31514 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
31542 AACTACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
31569 GTGGCATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:31612 original size:19 final size:19
Alignment explanation
Indices: 31588--31626 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31578 GTTGACTAGA
*
31588 GATAGCCACCCACCATAAG
1 GATAGCCACCCACCACAAG
*
31607 GATAGCCATCCACCACAAG
1 GATAGCCACCCACCACAAG
31626 G
1 G
31627 TGCTCCCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.36, G:0.18, T:0.10
Consensus pattern (19 bp):
GATAGCCACCCACCACAAG
Found at i:32011 original size:11 final size:11
Alignment explanation
Indices: 31997--32021 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31987 TTAGAGGTCC
31997 TTTATTATTTT
1 TTTATTATTTT
32008 TTTATTATTTT
1 TTTATTATTTT
32019 TTT
1 TTT
32022 TTGTCTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTATTTT
Found at i:33333 original size:22 final size:22
Alignment explanation
Indices: 33279--33401 Score: 96
Period size: 22 Copynumber: 5.8 Consensus size: 22
33269 TTTTTTAATT
*
33279 TTAATTAATTATATT-AAATTA
1 TTAATTAATTATATTAAAAATA
*
33300 ATAATTAATTATATTAAAAATA
1 TTAATTAATTATATTAAAAATA
*
33322 TTAAGTAATTATATTAATAAATA
1 TTAATTAATTATATTAA-AAATA
* * *
33345 -AAGATTGATTA-ATTAAAAATT
1 TTA-ATTAATTATATTAAAAATA
* * * *
33366 TTACTT--TTTTAAT-CAAATA
1 TTAATTAATTATATTAAAAATA
33385 TTAATTAATTATATTAA
1 TTAATTAATTATATTAA
33402 TTATTATTGT
Statistics
Matches: 76, Mismatches: 18, Indels: 15
0.70 0.17 0.14
Matches are distributed among these distances:
19 11 0.14
20 2 0.03
21 25 0.33
22 27 0.36
23 11 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAATTAATTATATTAAAAATA
Found at i:33418 original size:20 final size:18
Alignment explanation
Indices: 33395--33434 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
33385 TTAATTAATT
*
33395 ATATTAATTATTATTGTTAA
1 ATATGAATTATT-TT-TTAA
33415 ATATGAATTATTTTTTAA
1 ATATGAATTATTTTTTAA
33433 AT
1 AT
33435 TATATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATATGAATTATTTTTTAA
Found at i:36774 original size:32 final size:32
Alignment explanation
Indices: 36733--36795 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
36723 AGTGGGACAT
* *
36733 GTAGGAAGCGCTAATGCGC-TTAGCGCATCCAC
1 GTAGGAAGCGCT-AGGCGCATTAGCACATCCAC
36765 GTAGGAAGCGCTAGGCGCATTAGCACATCCA
1 GTAGGAAGCGCTAGGCGCATTAGCACATCCA
36796 ATGTGGCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (32 bp):
GTAGGAAGCGCTAGGCGCATTAGCACATCCAC
Found at i:37108 original size:29 final size:29
Alignment explanation
Indices: 37063--37122 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
37053 AGTTAACAGC
*
37063 AAAACAATAATAGTTTGATAAATTATTTT
1 AAAAAAATAATAGTTTGATAAATTATTTT
* *
37092 AAAAAAATAATATTTTGATAATTTATTTT
1 AAAAAAATAATAGTTTGATAAATTATTTT
37121 AA
1 AA
37123 TTTTAACAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (29 bp):
AAAAAAATAATAGTTTGATAAATTATTTT
Found at i:37816 original size:13 final size:13
Alignment explanation
Indices: 37784--37844 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
37774 AGGTAACCTC
*
37784 TATATACATA-TA
1 TATATATATACTA
37796 TATATATATACTA
1 TATATATATACTA
*
37809 TTTATATATACTA
1 TATATATATACTA
* *
37822 TAAATATATAGTA
1 TATATATATACTA
37835 TATATATATA
1 TATATATATA
37845 TTAATGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
12 9 0.21
13 33 0.79
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (13 bp):
TATATATATACTA
Found at i:37858 original size:2 final size:2
Alignment explanation
Indices: 37784--37845 Score: 70
Period size: 2 Copynumber: 29.5 Consensus size: 2
37774 AGGTAACCTC
* * *
37784 TA TA TA CA TA TA TA TA TA TA TA CTA TT TA TA TA TA CTA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
37828 TA TA GTA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA T
37846 TAATGAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 45 0.88
3 6 0.12
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:40340 original size:24 final size:24
Alignment explanation
Indices: 40312--40361 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
40302 AAATGAAACT
* *
40312 GAGGCCTGCAGAGAAAGGACTGAA
1 GAGGCCTACAGAGAAAGGACCGAA
*
40336 GAGGCCTACAGTGAAAGGACCGAA
1 GAGGCCTACAGAGAAAGGACCGAA
40360 GA
1 GA
40362 TGAAGAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.36, T:0.08
Consensus pattern (24 bp):
GAGGCCTACAGAGAAAGGACCGAA
Found at i:43285 original size:50 final size:50
Alignment explanation
Indices: 43210--43469 Score: 414
Period size: 50 Copynumber: 5.2 Consensus size: 50
43200 AAGTTGTTGC
* * *
43210 AATTGTTAACTATCCTTCACCAACCTTTGACAATA-AAGAGAGGTGGCCAT
1 AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAG-GAGGTGGCCAT
43260 AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCAT
1 AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCAT
* * * *
43310 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGGGAGGTAGTCAT
1 AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCAT
* *
43360 AATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGACCAT
1 AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCAT
*
43410 AATTGTTGACGATTCTTCACCCACCTTTGACAATAGAAGGAGGTGGCCAT
1 AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCAT
43460 AATTGTTGAC
1 AATTGTTGAC
43470 TCTAAGTATA
Statistics
Matches: 194, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 191 0.98
51 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (50 bp):
AATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCAT
Found at i:47036 original size:20 final size:20
Alignment explanation
Indices: 47008--47082 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
46998 TCATACCCTG
47008 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
47028 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
47048 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
47068 ATGTATCGATACATT
1 ATGTATCGATACATT
47083 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:47075 original size:40 final size:39
Alignment explanation
Indices: 47008--47085 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
46998 TCATACCCTG
* *
47008 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
47048 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
47086 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:50597 original size:32 final size:32
Alignment explanation
Indices: 50552--51009 Score: 740
Period size: 32 Copynumber: 14.3 Consensus size: 32
50542 TGGTGATTTG
* *
50552 GAAA-GGGTTGCCACTGACTTGCGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* *
50583 TAAATGGGTTGCCACCGACTTGCGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* * * *
50615 TAAATGGGTTGCCACCAACTTCTGGGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
**
50647 GAAAAAGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
50679 GAAATGGGTTGCCACCTACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
50711 -AGAATGGGTTGCCACCGGCTTGTGTGGGCTTT
1 GA-AATGGGTTGCCACCGACTTGTGTGGGCTTT
50743 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
50775 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* *
50807 GAAATGGGTTGCCACCGACTTGTATAGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
50839 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
50871 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
50903 GAAATGGGTTGCCACCAACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
50935 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
50967 GGAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
*
50999 GGAATGGGTTG
1 GAAATGGGTTG
51010 TAAGTTGCAG
Statistics
Matches: 399, Mismatches: 25, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
31 4 0.01
32 394 0.99
33 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
GAAATGGGTTGCCACCGACTTGTGTGGGCTTT
Found at i:56006 original size:13 final size:13
Alignment explanation
Indices: 55988--56012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55978 CATAAAGTGT
55988 TGTATCGATACAA
1 TGTATCGATACAA
56001 TGTATCGATACA
1 TGTATCGATACA
56013 TGTTTTTTTG
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:56093 original size:13 final size:13
Alignment explanation
Indices: 56075--56099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56065 ATCACTTAAA
56075 TGTATCGATACAT
1 TGTATCGATACAT
56088 TGTATCGATACA
1 TGTATCGATACA
56100 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:56152 original size:52 final size:52
Alignment explanation
Indices: 56108--56288 Score: 344
Period size: 52 Copynumber: 3.5 Consensus size: 52
56098 CACTGATCTT
56108 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
56160 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
56212 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
56264 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
56289 TCATATTTCG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 127 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:60434 original size:10 final size:10
Alignment explanation
Indices: 60419--60445 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
60409 TGCTAACTAA
60419 GTTTTTGTTT
1 GTTTTTGTTT
60429 GTTTTTGTTT
1 GTTTTTGTTT
60439 GTTTTTG
1 GTTTTTG
60446 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Done.