Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1484
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: 61885
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6312 original size:14 final size:15
Alignment explanation
Indices: 6285--6318 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6275 TGTTCATATC
6285 TTTTATTGTTATTTA
1 TTTTATTGTTATTTA
*
6300 TTTTATT-TTATTTT
1 TTTTATTGTTATTTA
6314 TTTTA
1 TTTTA
6319 AGGCTGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTGTTATTTA
Found at i:6968 original size:15 final size:14
Alignment explanation
Indices: 6946--6981 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
6936 TGGCAATTGG
6946 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
6960 AAGAAAAAAAACAAA
1 AA-AAAAAAAACAAA
6975 AAAAAAA
1 AAAAAAA
6982 GTGAAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.92, C:0.06, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:10814 original size:13 final size:13
Alignment explanation
Indices: 10796--10820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10786 ATAATGCACA
10796 GTATCGATACATT
1 GTATCGATACATT
10809 GTATCGATACAT
1 GTATCGATACAT
10821 GACCACTGTA
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):
GTATCGATACATT
Found at i:10817 original size:33 final size:32
Alignment explanation
Indices: 10775--10837 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
10765 CACCTTTAGA
*
10775 TGTATCGATACATAATGCACAGTATCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
10808 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
10838 TTGCAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:10938 original size:13 final size:13
Alignment explanation
Indices: 10920--10945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10910 ACATACAAGA
10920 TGTATCGATACAT
1 TGTATCGATACAT
10933 TGTATCGATACAT
1 TGTATCGATACAT
10946 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10961 original size:33 final size:32
Alignment explanation
Indices: 10900--10967 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
10890 CCTTAACTGT
10900 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
10932 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
10965 TTG
1 TTG
10968 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:13020 original size:79 final size:79
Alignment explanation
Indices: 12937--13119 Score: 253
Period size: 79 Copynumber: 2.3 Consensus size: 79
12927 TATTTTGGAG
*
12937 ATAAAATCGGAGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAA
1 ATAAAATCGGAGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAA
* * *
13002 TTAGTGTTTTAGAA
66 TCAATGTTCTAGAA
* * *
13016 ATAAAATCGG-GATTGGAGTATCCCTTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAA
1 ATAAAATCGGAG-TTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAA
*
13080 ATCAATGTTCTGGAA
65 ATCAATGTTCTAGAA
*
13095 ATAAAATC-AAGGTTGGAGTATCCCC
1 ATAAAATCGGA-GTTGGAGTATCCCC
13120 AATGGTGGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
78 1 0.01
79 89 0.98
80 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
ATAAAATCGGAGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAA
TCAATGTTCTAGAA
Found at i:13118 original size:51 final size:51
Alignment explanation
Indices: 13054--13169 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
13044 AAAATAACGG
* * * *
13054 GGTTGGAGTATCCCCGATTGTGGAAAATCAATGTTCTGGAAATAAAATCAA
1 GGTTGGAGTATCCCCAATGGTGGAAAATCAATGTTCTGAAAATAAAACCAA
*** * *
13105 GGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTGAAAATAAAACCAG
1 GGTTGGAGTATCCCCAATGGTGGAAAATCAATGTTCTGAAAATAAAACCAA
*
13156 GGTTAGAGTATCCC
1 GGTTGGAGTATCCC
13170 TTCAAAAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATGGTGGAAAATCAATGTTCTGAAAATAAAACCAA
Found at i:13211 original size:130 final size:130
Alignment explanation
Indices: 12975--13211 Score: 343
Period size: 130 Copynumber: 1.8 Consensus size: 130
12965 GAAATAACAG
* * * *
12975 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGATTGGAGTATCCC
1 GGTTGGAGTATCCCCAATGGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGATTAGAGTATCCC
* **
13040 TTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATGTTCTGGAAATAAAATCAA
66 TTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATCAATGTTCTGGAAATAAAATCAA
* *
13105 GGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTT-GAAAATAAAACCAGGG-TTAGAGTATC
1 GGTTGGAGTATCCCCAATGGTGAAAAATTAGTGTTTTAG-AAATAAAACC-GGGATTAGAGTATC
* *
13168 CCTTCAAAAATAATAGGTTTGGAGTATCCCCGATTGTAAAAAAT
64 CCTTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAAT
13212 TGGTATTTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
129 1 0.01
130 90 0.96
131 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (130 bp):
GGTTGGAGTATCCCCAATGGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGATTAGAGTATCCC
TTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATCAATGTTCTGGAAATAAAATCAA
Found at i:13226 original size:130 final size:129
Alignment explanation
Indices: 12975--13249 Score: 329
Period size: 130 Copynumber: 2.1 Consensus size: 129
12965 GAAATAACAG
* * * *
12975 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGATTGGAGTATCCC
1 GGTTGGAGTATCCCCAATGGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGATTAGAGTATCCC
* ** * *
13040 TTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATGTTCTGGAAATAAAATCAA
66 TTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATCAATATTCTAGAAATAAAATC-A
* *
13105 GGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTT-GAAAATAAAACCAGGG-TTAGAGTATC
1 GGTTGGAGTATCCCCAATGGTGAAAAATTAGTGTTTTAG-AAATAAAACC-GGGATTAGAGTATC
* * *** *
13168 CCTTCAAAAATAATAGGTTTGGAGTATCCCCGATTGTAAAAAATTGGTATTTTAGAAATAAAATC
64 CCTTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATCAATATTCTAGAAATAAAATC
*
13233 G
129 A
*
13234 GGATTAGAGTATCCCC
1 GG-TTGGAGTATCCCC
13250 TCGAAAATAA
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
129 3 0.02
130 117 0.95
131 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (129 bp):
GGTTGGAGTATCCCCAATGGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGATTAGAGTATCCC
TTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATCAATATTCTAGAAATAAAATCA
Found at i:13320 original size:209 final size:209
Alignment explanation
Indices: 12952--13328 Score: 567
Period size: 209 Copynumber: 1.8 Consensus size: 209
12942 ATCGGAGTTG
* * *
12952 GAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAA
1 GAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATTAGTATTTTAGAAA
* * * *
13017 TAAAATCGGGATTGGAGTATCCCTTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAAT
66 TAAAATCGGGATTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAAT
* *
13082 CAATGTTCTGGAAATAAAATCAAGGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTGAAAA
131 CAATGTTCTGAAAATAAAATCAAGGTTGGAATATCCCCAATGGTGGAAAATTGGTGTTTTGAAAA
13147 TAAAACCAGGGTTA
196 TAAAACCAGGGTTA
* * * *
13161 GAGTATCCCTTCAAAAATAATAGGTTTGGAGTATCCCCGATTGTAAAAAATTGGTATTTTAGAAA
1 GAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATTAGTATTTTAGAAA
* *
13226 TAAAATCGGGATTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAAT
66 TAAAATCGGGATTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAAT
* * **
13291 CGATGTTTTGAAAATAAAA-CTGGGGTTGGAATATCCCC
131 CAATGTTCTGAAAATAAAATC-AAGGTTGGAATATCCCC
13329 TTAGAAATAA
Statistics
Matches: 148, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
208 1 0.01
209 147 0.99
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (209 bp):
GAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTAAAAAATTAGTATTTTAGAAA
TAAAATCGGGATTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAAT
CAATGTTCTGAAAATAAAATCAAGGTTGGAATATCCCCAATGGTGGAAAATTGGTGTTTTGAAAA
TAAAACCAGGGTTA
Found at i:13430 original size:157 final size:154
Alignment explanation
Indices: 13105--13624 Score: 537
Period size: 158 Copynumber: 3.3 Consensus size: 154
13095 ATAAAATCAA
* ** * * * * *
13105 GGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTAGAGTAT-CC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTAGGGTT-GAATATCCC
* * * * * *
13169 CTTCAAAAATAATAGGTTTGGAGTATCCCCGATTGTAAAAAATTGGTATTTTAGAAATAAAATCG
65 CTT-AGAAATAA-CGGGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTTAGAAATAAAATCG
*
13234 GGATTAGAGTATCCCCTC-GAAAATAATGG
128 GG-TTAGAGTAT-CCCTCAGAAAA-AACGG
*
13263 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTGGAATATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTAGGGTT-GAATATCCC
13328 CTTAGAAATAACGGGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTTAGAAATAAAATCGAG
65 CTTAGAAATAACGGGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTTAGAAATAAAATCG-G
* *
13393 GTTGGAGTATCCTCTCAGAAAAAACAG
129 GTTAGAGTATCC-CTCAGAAAAAACGG
* * * * *
13420 TGTTAGAGTATCCCCGATTATGAAAAATTGATATTTTGAAAATAAAACTAGGGTTGAAGTGTCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTAGGGTTGAA-TATCCC
* * * ** *
13485 CTT-GAAAATAACGGGGTTGGAGTATTCTCGATTATGTAAAATCAATGTTTT-GAAAATAAAACT
65 CTTAG-AAATAAC-GGGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTTAG-AAATAAAA-T
* * *
13548 GGGGTTAGAATATCCCTTCAGAAATAACGG
126 CGGGTTAGAGTATCCC-TCAGAAAAAACGG
* * * *
13578 GGTTGGAGTATCCTCGATTGTAAAAAATCGGTGTTTT-AGAAATAAAA
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGA-AAATAAAA
13625 GCATGAATGG
Statistics
Matches: 307, Mismatches: 44, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
156 6 0.02
157 129 0.42
158 165 0.54
159 7 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (154 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTAGGGTTGAATATCCCC
TTAGAAATAACGGGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTTAGAAATAAAATCGGGT
TAGAGTATCCCTCAGAAAAAACGG
Found at i:13431 original size:236 final size:237
Alignment explanation
Indices: 13189--13624 Score: 657
Period size: 236 Copynumber: 1.8 Consensus size: 237
13179 AATAGGTTTG
* * *
13189 GAGTATCCCCGATTGTAAAAAATTGGTATTTT-AGAAATAAAA-TCGGGATT-AGAGTATCCCCT
1 GAGTATCCCCGATTATAAAAAATTGATATTTTGA-AAATAAAACTAGGG-TTGA-AGTATCCCCT
* *
13251 CGAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGG
63 CGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGTTTTGAAAATAAAACTGGGG
* * *
13316 TTGGAATATCCCCTT-AGAAATAAC-GGGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTTA
128 TTAGAATAT-CCCTTCAGAAATAACGGGGTTGGAGTATCCTCGATTGTAAAAAATCGATATTTTA
13379 GAAATAAAATCGAGGTTGGAGTATCCTCTCAGAAAAAACAGTGTTA
192 GAAATAAAATCGAGGTTGGAGTATCCTCTCAGAAAAAACAGTGTTA
* * *
13425 GAGTATCCCCGATTATGAAAAATTGATATTTTGAAAATAAAACTAGGGTTGAAGTGTCCCCTTGA
1 GAGTATCCCCGATTATAAAAAATTGATATTTTGAAAATAAAACTAGGGTTGAAGTATCCCCTCGA
* * *
13490 AAATAACGGGGTTGGAGTATTCTCGATTATGTAAAATCAATGTTTTGAAAATAAAACTGGGGTTA
66 AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGTTTTGAAAATAAAACTGGGGTTA
* *
13555 GAATATCCCTTCAGAAATAACGGGGTTGGAGTATCCTCGATTGTAAAAAATCGGTGTTTTAGAAA
131 GAATATCCCTTCAGAAATAACGGGGTTGGAGTATCCTCGATTGTAAAAAATCGATATTTTAGAAA
13620 TAAAA
196 TAAAA
13625 GCATGAATGG
Statistics
Matches: 179, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
235 5 0.03
236 124 0.69
237 50 0.28
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (237 bp):
GAGTATCCCCGATTATAAAAAATTGATATTTTGAAAATAAAACTAGGGTTGAAGTATCCCCTCGA
AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGTTTTGAAAATAAAACTGGGGTTA
GAATATCCCTTCAGAAATAACGGGGTTGGAGTATCCTCGATTGTAAAAAATCGATATTTTAGAAA
TAAAATCGAGGTTGGAGTATCCTCTCAGAAAAAACAGTGTTA
Found at i:13606 original size:79 final size:79
Alignment explanation
Indices: 13105--13624 Score: 450
Period size: 79 Copynumber: 6.6 Consensus size: 79
13095 ATAAAATCAA
* ** * * * ** *
13105 GGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAATATCCC
* **
13170 TTCAAAAATAATAG
66 TTCAGAAATAACGG
* * * * * * * *
13184 GTTTGGAGTATCCCCGATTGTAAAAAATTGGTATTTT-AGAAATAAAA-TCGGGATTAGAGTATC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGA-AAATAAAACT-GGGGTTAGAATATC
* *
13247 CCCTC-GAAAATAATGG
64 CCTTCAG-AAATAACGG
*
13263 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTGGAATATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAATAT-CC
13328 CTT-AGAAATAAC-G
65 CTTCAGAAATAACGG
* * * * * * *
13341 GGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTT-AGAAATAAAA-TCGAGGTTGGAGTAT-
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGA-AAATAAAACT-GGGGTTAGAATATC
* *
13403 CCTCTCAGAAAAAACAG
64 CCT-TCAGAAATAACGG
* * * * * *
13420 TGTTAGAGTATCCCCGATTATGAAAAATTGATATTTTGAAAATAAAACTAGGGTT-GAAGTGTCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAA-TAT-C
*
13484 CCTTGA-AAATAACGG
64 CCTTCAGAAATAACGG
* * * *
13499 GGTTGGAGTATTCTCGATTATGTAAAATCAATGTTTTGAAAATAAAACTGGGGTTAGAATATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAATATCCC
13564 TTCAGAAATAACGG
66 TTCAGAAATAACGG
* * * *
13578 GGTTGGAGTATCCTCGATTGTAAAAAATCGGTGTTTT-AGAAATAAAA
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGA-AAATAAAA
13625 GCATGAATGG
Statistics
Matches: 363, Mismatches: 58, Indels: 40
0.79 0.13 0.09
Matches are distributed among these distances:
76 3 0.01
77 3 0.01
78 71 0.20
79 269 0.74
80 14 0.04
81 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAATATCCC
TTCAGAAATAACGG
Found at i:16644 original size:42 final size:41
Alignment explanation
Indices: 16597--16691 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
16587 GTTAAATGTG
16597 TCTTACTCTTTGAGGACAAAGGAGAAAAGGAAATAAAATGCA
1 TCTTACTCTTTGAGGACAAAGG-GAAAAGGAAATAAAATGCA
* *
16639 TCTTACTCTTTGAGGACAAAGGGAAAAGGAAATAAAGTGCG
1 TCTTACTCTTTGAGGACAAAGGGAAAAGGAAATAAAATGCA
*
16680 TCCTACTCTTTG
1 TCTTACTCTTTG
16692 GAGACTAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
41 28 0.56
42 22 0.44
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (41 bp):
TCTTACTCTTTGAGGACAAAGGGAAAAGGAAATAAAATGCA
Found at i:16890 original size:61 final size:61
Alignment explanation
Indices: 16700--17187 Score: 604
Period size: 61 Copynumber: 8.1 Consensus size: 61
16690 TGGAGACTAG
* * * *
16700 AAGGTGCCACCAACTT-TGTGGGCTTTACAAGGAGAAA-GCATCCTACTTTTTGAAGACTAGA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCATCCTGCTCTTTGAGGACT-GA
* *
16761 AA-GTGCCACCAACTTGTGTAGGCTTTGAAAGG-AAA-GCATCCTGCTCTTTGAGGACT-A
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGA
* *
16818 GAAGGTCCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGATTGA
1 -AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGA
* * *
16880 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTTCTGCT-TTCTAAGGACTGA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTT-TGAGGACTGA
*
16941 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTT-AGGGACTGAA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGA-GGACTG-A
* ** *
17003 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGTGTCCTGCTCTTTGAGGAAT-A
1 AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGA
* * * *
17064 GAAGGTGCCACCAACTTGTGTGCGCTTTGAAAGG-AAA-GCATCCTGCTCTTTAAGGACTGG
1 -AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGA
* * * *
17124 AAGGTGCCACCAACTTGTGTGGG-TTTAAAAGGAAAAGGTACCCTGCTCCTTGAGGAATGA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGA
17184 AAGG
1 AAGG
17188 ATAAAAAGTT
Statistics
Matches: 372, Mismatches: 39, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
57 1 0.00
58 10 0.03
59 90 0.24
60 43 0.12
61 145 0.39
62 57 0.15
63 25 0.07
64 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (61 bp):
AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGA
Found at i:16973 original size:29 final size:29
Alignment explanation
Indices: 16940--17033 Score: 68
Period size: 29 Copynumber: 3.1 Consensus size: 29
16930 CTAAGGACTG
16940 AAAGGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * *
16969 AAAGGAAAAGGCATCCTACTCT-T-TAGGGAC-TGA
1 AAAGG---TGCCA-CCAACT-TGTGT-GGG-CTTTA
17002 AAAGGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGTGCCACCAACTTGTGTGGGCTTTA
17031 AAA
1 AAA
17034 AAGAAAAGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 20
0.63 0.11 0.27
Matches are distributed among these distances:
28 2 0.04
29 19 0.40
30 4 0.09
32 4 0.09
33 16 0.34
34 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (29 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTTA
Found at i:18178 original size:23 final size:21
Alignment explanation
Indices: 18151--18192 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
18141 CTTAAGTAGG
18151 CTCTTTTCTTTTCTCTTTTTTAT
1 CTCTTTT-TTTTCT-TTTTTTAT
*
18174 CTCTTTTTTTTGTTTTTTT
1 CTCTTTTTTTTCTTTTTTT
18193 GTTTTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (21 bp):
CTCTTTTTTTTCTTTTTTTAT
Found at i:18181 original size:1 final size:1
Alignment explanation
Indices: 18177--18235 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
18167 TTTTTATCTC
* * * * ** *
18177 TTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTGGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18236 AGAAAAAGTA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:18210 original size:24 final size:24
Alignment explanation
Indices: 18178--18233 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
18168 TTTTATCTCT
*
18178 TTTTTTTGTTTTTTTGTTTTTTTG
1 TTTTTTTGTTTTTTGGTTTTTTTG
*
18202 TTTTTTTGTTTTTTGGTTTTTTTT
1 TTTTTTTGTTTTTTGGTTTTTTTG
18226 TTGTTTTT
1 TT-TTTTT
18234 TTAGAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (24 bp):
TTTTTTTGTTTTTTGGTTTTTTTG
Found at i:18235 original size:8 final size:8
Alignment explanation
Indices: 18178--18224 Score: 85
Period size: 8 Copynumber: 5.9 Consensus size: 8
18168 TTTTATCTCT
18178 TTTTTTTG
1 TTTTTTTG
18186 TTTTTTTG
1 TTTTTTTG
18194 TTTTTTTG
1 TTTTTTTG
18202 TTTTTTTG
1 TTTTTTTG
*
18210 TTTTTTGG
1 TTTTTTTG
18218 TTTTTTT
1 TTTTTTT
18225 TTTGTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:30476 original size:79 final size:79
Alignment explanation
Indices: 30406--30558 Score: 184
Period size: 79 Copynumber: 1.9 Consensus size: 79
30396 ATCCCTTCTG
* * * * *
30406 AAATAATGGGGTTGGAGTAT-CCTCGATTGT-GAAAATTTAATGTTTTGGAAATAAAATCAGGGT
1 AAATAATGGGGTTAGAGTATCCCT-AATTGTGGAAAA-TCAATGTTCTGAAAATAAAATCAGGGT
* *
30469 TTAAGTATCCTTTAAA
64 TGAAGTATCCCTTAAA
* *
30485 AAATAATGGGGTTAGAGTATCCCTAATTGTGGAAAATCGATGTTCTGAAAATAAAATCGGGGTTG
1 AAATAATGGGGTTAGAGTATCCCTAATTGTGGAAAATCAATGTTCTGAAAATAAAATCAGGGTTG
*
30550 GAGTATCCC
66 AAGTATCCC
30559 CAATGGTGGA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
79 54 0.87
80 8 0.13
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.32
Consensus pattern (79 bp):
AAATAATGGGGTTAGAGTATCCCTAATTGTGGAAAATCAATGTTCTGAAAATAAAATCAGGGTTG
AAGTATCCCTTAAA
Found at i:30557 original size:51 final size:51
Alignment explanation
Indices: 30492--30610 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
30482 AAAAAATAAT
* * *
30492 GGGGTTAGAGTATCCCTAATTGTGGAAAATCGATGTTCT-GAAAATAAAATC
1 GGGGTTAGAGTATCCCCAATGGTGGAAAATCGATGTTCTCG-AAATAAAACC
* * * *
30543 GGGGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTCGAAATAAAACC
1 GGGGTTAGAGTATCCCCAATGGTGGAAAATCGATGTTCTCGAAATAAAACC
*
30594 AGGGTTAGAGTATCCCC
1 GGGGTTAGAGTATCCCC
30611 TCGAAAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 57 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (51 bp):
GGGGTTAGAGTATCCCCAATGGTGGAAAATCGATGTTCTCGAAATAAAACC
Found at i:30587 original size:130 final size:130
Alignment explanation
Indices: 30413--30689 Score: 319
Period size: 130 Copynumber: 2.1 Consensus size: 130
30403 CTGAAATAAT
* * * * *
30413 GGGGTTGGAGTATCCTCGATTGTGAAAATTTAATGTTTTGGAAATAAAATCAGGGTTTA-AGTAT
1 GGGGTTGGAGTATCCCCAATGGTGAAAATTTAATGTTTTCGAAATAAAACCAGGG-TTAGAGTAT
** * * * *
30477 CCTTTAAAAAATAATGGGGTTAG-AGTATCCCTAATTGTGGAAAATCGATGTTCTGA-AAATAAA
65 CCCCTAAAAAATAATAGGGTT-GTAGTATCCCCAATTGTGAAAAATCGATATT-TGAGAAATAAA
30540 ATC
128 ATC
**
30543 GGGGTTGGAGTATCCCCAATGGTGGAAAA-TTGGTGTTTTCGAAATAAAACCAGGGTTAGAGTAT
1 GGGGTTGGAGTATCCCCAATGGT-GAAAATTTAATGTTTTCGAAATAAAACCAGGGTTAGAGTAT
** * *
30607 CCCCTCGAAAATAATAGGGTTGTAGTATCCCCAATTGTGAAAAATTGATATTTTAGAAATAAAAT
65 CCCCTAAAAAATAATAGGGTTGTAGTATCCCCAATTGTGAAAAATCGATATTTGAGAAATAAAAT
30672 C
130 C
* *
30673 GAGGTTAGAGTATCCCC
1 GGGGTTGGAGTATCCCC
30690 TAGAAAATAA
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
129 6 0.05
130 113 0.91
131 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (130 bp):
GGGGTTGGAGTATCCCCAATGGTGAAAATTTAATGTTTTCGAAATAAAACCAGGGTTAGAGTATC
CCCTAAAAAATAATAGGGTTGTAGTATCCCCAATTGTGAAAAATCGATATTTGAGAAATAAAATC
Found at i:30634 original size:79 final size:79
Alignment explanation
Indices: 30544--30922 Score: 356
Period size: 79 Copynumber: 4.8 Consensus size: 79
30534 AATAAAATCG
* * ** * * *
30544 GGGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTCGAAATAAAA-CCAGGGTTAGAGTATC
1 GGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAAATAAAATCGA-GGTTAGAGTATC
30608 CCCTCGAAAATAATA
65 CCCTCGAAAATAATA
* *
30623 GGGTTGTAGTATCCCCAATTGTGAAAAATTGATATTTTAGAAATAAAATCGAGGTTAGAGTATCC
1 GGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAAATAAAATCGAGGTTAGAGTATCC
*
30688 CCTAGAAAATAATA
66 CCTCGAAAATAATA
* * * * * *
30702 GGGTTGGAGTCTCCCCGATTGTGAAAAATCAATGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAAATAAAATCGAGGTTAGAGTATCC
*
30767 CCTC-AGAAATAACA
66 CCTCGA-AAATAATA
* * * * * *
30781 GGGTTAGAGTATCCCCGATTGTGGAAAATTAGTATTTTAGAAATAAAAT-TAGGGTTAGAGTGTC
1 GGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAAATAAAATCGA-GGTTAGAGTATC
* **
30845 CCTTC-AGAAATAACG
65 CCCTCGA-AAATAATA
* * * ** * * *
30860 GGGATGGA-TATTCCTCGATTGTGAAAAATCGATGA-TTTGGATATAAAATCGAGGTTGGAGTAT
1 GGGTTGGAGTA-TCCCCAATTGTGAAAAATTAAT-ATTTTAGAAATAAAATCGAGGTTAGAGTAT
30923 ATGCAATTGT
Statistics
Matches: 252, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
78 4 0.02
79 244 0.97
80 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAAATAAAATCGAGGTTAGAGTATCC
CCTCGAAAATAATA
Found at i:30752 original size:209 final size:209
Alignment explanation
Indices: 30392--30768 Score: 508
Period size: 209 Copynumber: 1.8 Consensus size: 209
30382 ATCGAGATTG
* * * * * * *
30392 GAGTATCCCTTCTGAAATAATGGGGTTGGAGTATCCTCGATTGTGAAAATTTAATGTTTTGGAAA
1 GAGTATCCCCTCTGAAATAATAGGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAAA
** * * *
30457 TAAAATCAGGGTTTAAGTATCCTTTAAAAAATAATGGGGTTAGAGTATCCCTAATTGTGGAAAAT
66 TAAAATCAGGGTTTAAGTATCCCCTAAAAAATAATAGGGTTAGAGTATCCCCAATTGTGAAAAAT
* *
30522 CGATGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTCGAAA
131 CAATGTTCTGAAAATAAAATCGAGGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTCGAAA
30587 TAAAACCAGGGTTA
196 TAAAACCAGGGTTA
* *
30601 GAGTATCCCCTC-GAAAATAATAGGGTTGTAGTATCCCCAATTGTGAAAAATTGATATTTTAGAA
1 GAGTATCCCCTCTG-AAATAATAGGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAA
* * * *
30665 ATAAAATC-GAGG-TTAGAGTATCCCCTAGAAAATAATAGGGTTGGAGTCTCCCCGATTGTGAAA
65 ATAAAATCAG-GGTTTA-AGTATCCCCTAAAAAATAATAGGGTTAGAGTATCCCCAATTGTGAAA
* *
30728 AATCAATGTTTTGGAAATAAAATCGAGGTTGGAGTATCCCC
128 AATCAATGTTCTGAAAATAAAATCGAGGTTGGAGTATCCCC
30769 TCAGAAATAA
Statistics
Matches: 143, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
208 5 0.03
209 138 0.97
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (209 bp):
GAGTATCCCCTCTGAAATAATAGGGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTAGAAA
TAAAATCAGGGTTTAAGTATCCCCTAAAAAATAATAGGGTTAGAGTATCCCCAATTGTGAAAAAT
CAATGTTCTGAAAATAAAATCGAGGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTCGAAA
TAAAACCAGGGTTA
Found at i:30763 original size:158 final size:158
Alignment explanation
Indices: 30544--30922 Score: 448
Period size: 158 Copynumber: 2.4 Consensus size: 158
30534 AATAAAATCG
* * * * * * * *
30544 GGGTTGGAGTATCCCCAATGGTGGAAAATTGGTGTTTTCGAAATAAAA-CCAGGGTTAGAGTATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGGAAATAAAATCGA-GGTTGGAGTATC
*
30608 CCCTC-GAAAATAATAGGGTT-GTAGTATCCCCAATTGTGAAAAATT-GATATTTTAGAAATAAA
65 CCCTCAG-AAATAACAGGGTTAG-AGTATCCCCAATTGTGAAAAATTAG-TATTTTAGAAATAAA
*
30670 ATCGA-GGTTAGAGTATCCCCT-AGAAAATAATA
127 AT-GAGGGTTAGAGTATCCCCTCAG-AAATAACA
* *
30702 GGGTTGGAGTCTCCCCGATTGTGAAAAATCAATGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
* * *
30767 CCTCAGAAATAACAGGGTTAGAGTATCCCCGATTGTGGAAAATTAGTATTTTAGAAATAAAATTA
66 CCTCAGAAATAACAGGGTTAGAGTATCCCCAATTGTGAAAAATTAGTATTTTAGAAATAAAATGA
* * *
30832 GGGTTAGAGTGTCCCTTCAGAAATAACG
131 GGGTTAGAGTATCCCCTCAGAAATAACA
* * * *
30860 GGGATGGA-TATTCCTCGATTGTGAAAAATCGATGATTTGGATATAAAATCGAGGTTGGAGTAT
1 GGGTTGGAGTA-TCCCCGATTGTGAAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTAT
30923 ATGCAATTGT
Statistics
Matches: 190, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
157 2 0.01
158 181 0.95
159 7 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (158 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
CCTCAGAAATAACAGGGTTAGAGTATCCCCAATTGTGAAAAATTAGTATTTTAGAAATAAAATGA
GGGTTAGAGTATCCCCTCAGAAATAACA
Found at i:36723 original size:13 final size:13
Alignment explanation
Indices: 36705--36729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36695 CATATTGCTT
36705 TGTATCGATACAG
1 TGTATCGATACAG
36718 TGTATCGATACA
1 TGTATCGATACA
36730 TGATCTTGGT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:37573 original size:9 final size:9
Alignment explanation
Indices: 37561--37589 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
37551 GGAAAAGAGT
37561 AAAAAAATC
1 AAAAAAATC
37570 AAAAAAATC
1 AAAAAAATC
37579 -AAAAAATC
1 AAAAAAATC
37587 AAA
1 AAA
37590 GTGGGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:38287 original size:134 final size:136
Alignment explanation
Indices: 37991--38308 Score: 423
Period size: 134 Copynumber: 2.4 Consensus size: 136
37981 AAAAAATATG
* * *
37991 AAATTG-AGTGGCTTGGGATTTGAACCTAGGCCACTCATGATGAAAGA-AAAAGCCACTAACCAC
1 AAATTGAAGTGGCTTGCGATTTGAACCCAGGCCACCCATGATGAAAGAGAAAAGCCACTAACCAC
* * * *
38054 TTTGCCATACCCATTTTTTGGTTAAAATTACCCAAACAATCTTTTAACCTATTGATTTCGTGGGT
66 TTTGCCACACCCATTTTTT-GTTAAAATTACCAAAACAATCATTTAACATATTGATTTCGTGGGT
38119 GATTGAA
130 GATTGAA
* * * * *
38126 AAATTTAAGTGGTTTGCGATTTGAACCCATGCCACCCATGATGAAAGAGGAAA-CCATTAACCAC
1 AAATTGAAGTGGCTTGCGATTTGAACCCAGGCCACCCATGATGAAAGAGAAAAGCCACTAACCAC
* *
38190 TTTGCCACACCCA-TTTTT-TTAAGAATTACCAAAACAATCATTTAACATGTTGATTTTGTGGGT
66 TTTGCCACACCCATTTTTTGTTAA-AATTACCAAAACAATCATTTAACATATTGATTTCGTGGGT
38253 GATTGAA
130 GATTGAA
* *
38260 AAATTGAAGTGGCTTGTGA-TTGAAACCCAGGCCACCCATGTTGAAAGAG
1 AAATTGAAGTGGCTTGCGATTTG-AACCCAGGCCACCCATGATGAAAGAG
38309 TAGCACCTAA
Statistics
Matches: 160, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
133 7 0.04
134 82 0.51
135 10 0.06
136 58 0.36
137 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (136 bp):
AAATTGAAGTGGCTTGCGATTTGAACCCAGGCCACCCATGATGAAAGAGAAAAGCCACTAACCAC
TTTGCCACACCCATTTTTTGTTAAAATTACCAAAACAATCATTTAACATATTGATTTCGTGGGTG
ATTGAA
Found at i:41625 original size:27 final size:28
Alignment explanation
Indices: 41594--41647 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
41584 TGTTATCTCT
41594 CTTTTTATTTCAAAAAT-ATCTCTCCTC
1 CTTTTTATTTCAAAAATAATCTCTCCTC
* *
41621 CTTTTTGTTTCAAAAATAATCTTTCCT
1 CTTTTTATTTCAAAAATAATCTCTCCT
41648 TTCATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.26, C:0.22, G:0.02, T:0.50
Consensus pattern (28 bp):
CTTTTTATTTCAAAAATAATCTCTCCTC
Found at i:42831 original size:522 final size:522
Alignment explanation
Indices: 41840--42859 Score: 1824
Period size: 522 Copynumber: 2.0 Consensus size: 522
41830 ATAGCAAGAC
* *
41840 AAGCATTCATGAAAGCAAACATCTAAGCATATTCAATATATAAACACAAAATCCAAGTACCACAT
1 AAGCATCCATGAAAGCAAACATCAAAGCATATTCAATATATAAACACAAAATCCAAGTACCACAT
*
41905 AGTCACTTAAGCAAAAACAAATACGACTACTCCTAATACAAGGACTAATCCTATGACTCATCGTT
66 AGTCACTTAAGCAAAAACAAATACGACTACTCCTAATACAAGGACTAATCCTATGACTCATCGTC
* * *
41970 ACTAAAGTTAGTCAGAGTTAAGTGGAGATGTTGCTCAATGGTGATGAGTCGAGTGTCCATCGTGT
131 ACTAAAGTTAGTCAGAGTTAAGTAGAGATGTTGCTCAATGGTGATGAGTCGAGTGTCCACCATGT
42035 CAAGGCACTGATTTAAAGAAACGAAGTGTTGATCTACGTGCTAAAAGAAGGAAGTGATCAACTCT
196 CAAGGCACTGATTTAAAGAAACGAAGTGTTGATCTACGTGCTAAAAGAAGGAAGTGATCAACTCT
* *
42100 CGAATCGATGGTGGAAGAGGAGGTTCATCGGCTTCCATTGCTTGTTCTCCTTCAAGCTCGTCGTC
261 CGAATCGATGGTGGAAGAGGAGGCTCATCGACTTCCATTGCTTGTTCTCCTTCAAGCTCGTCGTC
* *
42165 GTATTTTGGAGGCTGAGATGCTTCATCTTGTCATGTTGGTACCAAGGACCCTCTTTGGACTTTAT
326 GCATTGTGGAGGCTGAGATGCTTCATCTTGTCATGTTGGTACCAAGGACCCTCTTTGGACTTTAT
42230 AGCCAATATTTGCCATGGTCTTGGAACCAATGAACTGTGGTCGAGAAATTGGCATCCTAAGGTCG
391 AGCCAATATTTGCCATGGTCTTGGAACCAATGAACTGTGGTCGAGAAATTGGCATCCTAAGGTCG
*
42295 AATGACAAGTCGATTCCACTCTTTTCGAAGAAGTAATTTAGATAGCAAACATCCAAGTACCACAT
456 AATGACAAGTCGATTCCACTCTTTTCGAAGAAGTAACTTAGATAGCAAACATCCAAGTACCACAT
42360 CA
521 CA
42362 AAGCATCCATGAAAGCAAACATCAAAGCATATTCAATATATAAACACAAAATCCAAGTACCACAT
1 AAGCATCCATGAAAGCAAACATCAAAGCATATTCAATATATAAACACAAAATCCAAGTACCACAT
*
42427 AGTCACTTAAGCAAAAACAAGTACGACTACTCCTAATACAAGGACTAATCCTATGACTCATCGTC
66 AGTCACTTAAGCAAAAACAAATACGACTACTCCTAATACAAGGACTAATCCTATGACTCATCGTC
* * *
42492 ACTAAAGTTAGTCGGAGTTAAGTAGAGATGTTGCTCGATGGTGATGATTCGAGTGTCCACCATGT
131 ACTAAAGTTAGTCAGAGTTAAGTAGAGATGTTGCTCAATGGTGATGAGTCGAGTGTCCACCATGT
* * * * *
42557 CAAGGCACTGATTTAAAGAAATGAAGTGTTGATTTATGTGCTGAGAGAAGGAAGTGATCAACTCT
196 CAAGGCACTGATTTAAAGAAACGAAGTGTTGATCTACGTGCTAAAAGAAGGAAGTGATCAACTCT
*
42622 CGAATCGATGGTGGAAGAGGAGGCTCATCGACTTCCATTGCTTTTTCTCCTTCAAGCTCGTCGTC
261 CGAATCGATGGTGGAAGAGGAGGCTCATCGACTTCCATTGCTTGTTCTCCTTCAAGCTCGTCGTC
42687 GCATTGTGGAGGCTGAGATGCTTCATCTTGTCATGTTGGTACCAAGGACCCTCTTTGGACTTTAT
326 GCATTGTGGAGGCTGAGATGCTTCATCTTGTCATGTTGGTACCAAGGACCCTCTTTGGACTTTAT
*
42752 AGCCAATATTTGCCATGGTCTTGGAACCAATGAACTGTGGTCGAGAAATTGGCATCCTAGGGTCG
391 AGCCAATATTTGCCATGGTCTTGGAACCAATGAACTGTGGTCGAGAAATTGGCATCCTAAGGTCG
**
42817 AATGACAAGTCGATTCTGCTCTTTTCGAAGAAGTAACTTAGAT
456 AATGACAAGTCGATTCCACTCTTTTCGAAGAAGTAACTTAGAT
42860 GCATTGCATG
Statistics
Matches: 474, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
522 474 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (522 bp):
AAGCATCCATGAAAGCAAACATCAAAGCATATTCAATATATAAACACAAAATCCAAGTACCACAT
AGTCACTTAAGCAAAAACAAATACGACTACTCCTAATACAAGGACTAATCCTATGACTCATCGTC
ACTAAAGTTAGTCAGAGTTAAGTAGAGATGTTGCTCAATGGTGATGAGTCGAGTGTCCACCATGT
CAAGGCACTGATTTAAAGAAACGAAGTGTTGATCTACGTGCTAAAAGAAGGAAGTGATCAACTCT
CGAATCGATGGTGGAAGAGGAGGCTCATCGACTTCCATTGCTTGTTCTCCTTCAAGCTCGTCGTC
GCATTGTGGAGGCTGAGATGCTTCATCTTGTCATGTTGGTACCAAGGACCCTCTTTGGACTTTAT
AGCCAATATTTGCCATGGTCTTGGAACCAATGAACTGTGGTCGAGAAATTGGCATCCTAAGGTCG
AATGACAAGTCGATTCCACTCTTTTCGAAGAAGTAACTTAGATAGCAAACATCCAAGTACCACAT
CA
Found at i:50153 original size:20 final size:18
Alignment explanation
Indices: 50128--50180 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
50118 TGCCAGTTTA
*
50128 ATGTATCGATACAATTAAC
1 ATGTATCGATACAA-GAAC
*
50147 TATGTATCAATACCAAGAAC
1 -ATGTATCGATA-CAAGAAC
50167 ATGTATCGATACAA
1 ATGTATCGATACAA
50181 AGCAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 10 0.34
20 13 0.45
21 3 0.10
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
ATGTATCGATACAAGAAC
Found at i:50206 original size:33 final size:33
Alignment explanation
Indices: 50169--50232 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
50159 CCAAGAACAT
50169 GTATCGATACAAAGCAATTT-TAATCGATACTAC
1 GTATCGATACAAAGCAATTTGT-ATCGATACTAC
50202 GTATCGATACAAAGCAATTTGTATCGATACT
1 GTATCGATACAAAGCAATTTGTATCGATACT
50233 TTCTAGGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (33 bp):
GTATCGATACAAAGCAATTTGTATCGATACTAC
Found at i:54942 original size:53 final size:51
Alignment explanation
Indices: 54875--55059 Score: 208
Period size: 52 Copynumber: 3.5 Consensus size: 51
54865 GAAATAACGA
* * *
54875 GGTTGGAGTGTCCTCGATTGTGAAAATATTAGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAA-ATTAGTG-TTTTGGAAATAAAATCGG
* * * * * * *
54928 AGCTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * *
54980 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAATCGG
*
55032 GGTTGGAGTATCCCCGATTATGAGAAAT
1 GGTTGGAGTATCCCCGATTATGAAAAAT
55060 CAATATTTTA
Statistics
Matches: 110, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
51 6 0.05
52 78 0.71
53 22 0.20
54 4 0.04
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:54987 original size:52 final size:51
Alignment explanation
Indices: 54875--55097 Score: 202
Period size: 52 Copynumber: 4.3 Consensus size: 51
54865 GAAATAACGA
* * * *
54875 GGTTGGAGTGTCCTCGATTGTGAAAATATTAGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAA-ATTAGTG-TTTTGAAAATAAAATCGG
* * * ** *
54928 AGCTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAATTAGTGTTTTGAAAATAAAATCGG
*
54980 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGG-AAAATTAGTGTTTTGA-AAATAAAATCGG
* * * * *
55032 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTT-AAGAAT-AAAGCAGG
1 GGTTGGAGTATCCCCGATTGTGGA-AAATTAGTGTTTTGAA-AATAAAATC-GG
55083 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
55098 TCAGAAATAA
Statistics
Matches: 143, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
50 5 0.03
51 35 0.24
52 77 0.54
53 22 0.15
54 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTGAAAATAAAATCGG
Found at i:55143 original size:27 final size:27
Alignment explanation
Indices: 55081--55182 Score: 152
Period size: 27 Copynumber: 3.7 Consensus size: 27
55071 GAATAAAGCA
* *
55081 GGGGTTGGAGTATCCCCTCA-GAAATAAC
1 GGGGTTGGAGTATCCCC-GATG-ATTAAC
55109 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGATTAAC
55136 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGATTAAC
*
55163 GGGGTTGGAGTATCTCCGAT
1 GGGGTTGGAGTATCCCCGAT
55183 TGTGAAAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
27 52 0.74
28 18 0.26
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATGATTAAC
Found at i:55235 original size:53 final size:52
Alignment explanation
Indices: 55171--55288 Score: 134
Period size: 51 Copynumber: 2.3 Consensus size: 52
55161 ACGGGGTTGG
* * * *
55171 AGTATCTCCGATTGTGAAAAATTGGTGTTTTTTTG-AAATAAAATCGGAG-TTAA
1 AGTATCCCCGATTGTAAAAAATTAGTG---TTTTGAAAATAAAATCGGAGATGAA
* *
55224 AGTATCCCCGATTATAAAAAATTAGTGTTTTGAAAATAAAATCGGAGATGGA
1 AGTATCCCCGATTGTAAAAAATTAGTGTTTTGAAAATAAAATCGGAGATGAA
55276 A-TATCCCCGATTG
1 AGTATCCCCGATTG
55289 CGGAGAATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
50 5 0.09
51 25 0.45
52 3 0.05
53 23 0.41
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (52 bp):
AGTATCCCCGATTGTAAAAAATTAGTGTTTTGAAAATAAAATCGGAGATGAA
Done.