Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold279
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: 1516008
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 10
Found at i:165786 original size:60 final size:60
Alignment explanation
Indices: 165684--165875 Score: 228
Period size: 60 Copynumber: 3.2 Consensus size: 60
165674 TAACTAGATT
* ***
165684 TATCGATACATTGACAAAATGTATCGATACATTTTTCA-ATGTATCGATACATT-CATACAAG
1 TATCGATACATTGA-AAGATGTATCGATACA-TTGAAAGATGTATCGATACATTGCA-ACAAG
* * * *
165745 TATCAATACATTGAAAGATGTATCGATACATTGAAAGATGTATCGATACATTGGAAGATG
1 TATCGATACATTGAAAGATGTATCGATACATTGAAAGATGTATCGATACATTGCAACAAG
* * *
165805 TATCGATACATTGGAAGATGTATCGATACATTGGAAGATGTATCGATACATTG-AAAAATG
1 TATCGATACATTGAAAGATGTATCGATACATTGAAAGATGTATCGATACATTGCAACAA-G
165865 TATCGATACAT
1 TATCGATACAT
165876 CTAGGTAAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
59 6 0.05
60 95 0.83
61 14 0.12
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (60 bp):
TATCGATACATTGAAAGATGTATCGATACATTGAAAGATGTATCGATACATTGCAACAAG
Found at i:166725 original size:28 final size:28
Alignment explanation
Indices: 166688--167175 Score: 599
Period size: 28 Copynumber: 17.2 Consensus size: 28
166678 GTGGGCAATA
* *
166688 AAAGGATGCCAATGACTTGTGGGTTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
166716 AGAAGG-TGCCTCTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* *
166744 -AAGAGATGCCGCTGACTCGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
* * * * *
166772 AAATGATGTCGCTGGCTCGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
166800 GACGGATGCCACTGACTTGTGGGCTTT-
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
166827 AAAGAGATGTCACTGACTCGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
*
166856 AAAAAGG-TGCCACTGACTCGTGGGCTTTG
1 --AAAGGATGCCACTGACTTGTGGGCTTTG
*
166885 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1 -AAAGGATGCCACTGACTTGTGGGCTTTG
166914 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
166942 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1 -AAAGGATGCCACTGACTTGTGGGCTTTG
166971 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
166999 AAAGGATGCCACTGACTTGTGGGCTATG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * * *
167027 AAAAGGGTGCCACTGACTTATGCGTTTTA
1 -AAAGGATGCCACTGACTTGTGGGCTTTG
167056 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
167084 AAATGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
167112 AAAGGATGCCACTGACTTGTGAGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
167140 AAAATGG-TGCTACTGACTTTTGAGCTTTG
1 -AAA-GGATGCCACTGACTTGTGGGCTTTG
167169 AAAGGAT
1 AAAGGAT
167176 ATCCTGACTC
Statistics
Matches: 405, Mismatches: 41, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.01
27 5 0.01
28 270 0.67
29 120 0.30
30 3 0.01
31 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:167000 original size:85 final size:85
Alignment explanation
Indices: 166687--167175 Score: 614
Period size: 85 Copynumber: 5.8 Consensus size: 85
166677 TGTGGGCAAT
* * *
166687 AAAAGGATGCCAATGACTTGTGGGTTTTGAGAAGG-TGCCTCTGACTTGTGGGCTTTG-AAGAGA
1 AAAAGGATGCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAAAG-GA
* *
166750 TGCCGCTGACTCGTGGGCTTTG
64 TGCCACTGACTTGTGGGCTTTG
* * * * * * *
166772 -AAATGATGTCGCTGGCTCGTGGGCTTTGGACGGATGCCACTGACTTGTGGGCTTT-AAAGAGAT
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG-GAT
* *
166835 GTCACTGACTCGTGGGCTTTG
65 GCCACTGACTTGTGGGCTTTG
* *
166856 AAAAAGG-TGCCACTGACTCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
1 -AAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA
166920 TGCCACTGACTTGTGGGCTTTG
64 TGCCACTGACTTGTGGGCTTTG
*
166942 AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG
*
167007 CCACTGACTTGTGGGCTATG
66 CCACTGACTTGTGGGCTTTG
* * * * * *
167027 AAAAGGGTGCCACTGACTTATGCGTTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG
167092 CCACTGACTTGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* * * *
167112 -AAAGGATGCCACTGACTTGTGAGCTTTGAAAATGG-TGCTACTGACTTTTGAGCTTTGAAAGGA
1 AAAAGGATGCCACTGACTTGTGGGCTTTG-AAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGA
167175 T
64 T
167176 ATCCTGACTC
Statistics
Matches: 356, Mismatches: 39, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
83 3 0.01
84 90 0.25
85 186 0.52
86 73 0.21
87 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (85 bp):
AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG
CCACTGACTTGTGGGCTTTG
Found at i:167172 original size:57 final size:55
Alignment explanation
Indices: 166688--167175 Score: 566
Period size: 57 Copynumber: 8.6 Consensus size: 55
166678 GTGGGCAATA
* * *
166688 AAAGGATGCCAATGACTTGTGGGTTTTGAGAAGG-TGCCTCTGACTTGTGGGCTTTG
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTG
* * * * * * * *
166744 AAGAGATGCCGCTGACTCGTGGGCTTTGAAATGATGTCGCTGGCTCGTGGGCTTTG
1 AA-AGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
166800 GACGGATGCCACTGACTTGTGGGCTTT-AAAGAGATGTCACTGACTCGTGGGCTTTG
1 AAAGG-TGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTG
* *
166856 AAAAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG
1 --AAAGGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTG
*
166914 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGG-TGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTG
*
166971 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTATG
1 AAAGG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
167027 AAAAGGGTGCCACTGACTTATGCGTTTTAAAAGGATGCCACTGACTTGTGGGCTTTG
1 -AAA-GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* *
167084 AAATGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTG
1 AAA-GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * *
167140 AAAATGGTGCTACTGACTTTTGAGCTTTGAAAGGAT
1 -AAA-GGTGCCACTGACTTGTGGGCTTTGAAAGGAT
167176 ATCCTGACTC
Statistics
Matches: 377, Mismatches: 43, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
55 7 0.02
56 161 0.43
57 179 0.47
58 26 0.07
59 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (55 bp):
AAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:168159 original size:89 final size:89
Alignment explanation
Indices: 168008--168185 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
167998 TTGAAAAGAG
168008 AGGGAATAATTCATAAGTCCTGTGTAAACACCCCATAACAAAATGAGGTAGCAAAAAGAAAGAAC
1 AGGGAATAATTCATAAGTCCTGTGTAAACACCCCATAACAAAATGAGGTAGCAAAAAGAAAGAAC
*
168073 GGCCACCTGTCAATCACTACCCAA
66 GACCACCTGTCAATCACTACCCAA
168097 AGGGAATAATTCATAAGTCCTGTGTAAACACCCCATAACAAAATGAGGTAGCAAAAAGAAAGAAC
1 AGGGAATAATTCATAAGTCCTGTGTAAACACCCCATAACAAAATGAGGTAGCAAAAAGAAAGAAC
168162 GACCACCTGTCAATCACTACCCAA
66 GACCACCTGTCAATCACTACCCAA
168186 GCCCTTATAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.17
Consensus pattern (89 bp):
AGGGAATAATTCATAAGTCCTGTGTAAACACCCCATAACAAAATGAGGTAGCAAAAAGAAAGAAC
GACCACCTGTCAATCACTACCCAA
Found at i:169899 original size:25 final size:25
Alignment explanation
Indices: 169871--169922 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
169861 AATAAACTTT
169871 TTTTTCTCTAGCTCAATTTTATCAA
1 TTTTTCTCTAGCTCAATTTTATCAA
* * *
169896 TTTTTCTCTGGTTCAGTTTTATCAA
1 TTTTTCTCTAGCTCAATTTTATCAA
169921 TT
1 TT
169923 ACAATAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (25 bp):
TTTTTCTCTAGCTCAATTTTATCAA
Found at i:171037 original size:2 final size:2
Alignment explanation
Indices: 171030--171061 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
171020 AATTTATGTC
171030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171062 ATGACGTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171566 original size:6 final size:6
Alignment explanation
Indices: 171555--171597 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
171545 ACATATATAT
* *
171555 ATACAC ATACAC --ACAC ACACAC ATACAC AGACAC ATACAC ATA
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATA
171598 ATAGGGTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 4 0.12
6 28 0.88
ACGTcount: A:0.51, C:0.35, G:0.02, T:0.12
Consensus pattern (6 bp):
ATACAC
Found at i:171578 original size:16 final size:16
Alignment explanation
Indices: 171557--171589 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
171547 ATATATATAT
171557 ACACATACACACACAC
1 ACACATACACACACAC
*
171573 ACACATACACAGACAC
1 ACACATACACACACAC
171589 A
1 A
171590 TACACATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.39, G:0.03, T:0.06
Consensus pattern (16 bp):
ACACATACACACACAC
Found at i:174383 original size:243 final size:243
Alignment explanation
Indices: 173942--174402 Score: 608
Period size: 243 Copynumber: 1.9 Consensus size: 243
173932 CCTTAATAGA
* *
173942 AAAAAAAGGAAAAATATTTTATTTCGTTGTTTGCTAATACAGACAACATTTTCACTTATTTTTTC
1 AAAAAAAGGAAAAATATTTAATTTCGTTATTTGCTAATACAGACAACATTTTCACTTATTTTTTC
* * * **
174007 TTGGTGTTAAAAGTTTTTCTCTACAAATACCGTTTGTGGATAAAAATACATCAAACTCAGACTAT
66 TTGGTGTTAAAAGTTTTTCTATACAAAAAACGTTTACGGATAAAAATACATCAAACTCAGACTAT
* * * * **
174072 AATAAAGATTGAGCATAAAATATAGGTGATAGAGCAACTACTATCACCGTTTAAAACACAAGGCC
131 AATAAAGATTGAGAAAAAAATATAGGCGATAAAGCAACTACTATCACCACTTAAAACACAAGGCC
174137 TCATATT-TTGGGCCAAATTTTGATGCCTACACTGAGAAATAACCTAAT
196 TCATATTCTT-GGCCAAATTTTGATGCCTACACTGAGAAATAACCTAAT
** **
174185 AAAAAAAGGAAAAATATTTAATTTCGTTATTTGCTAATATGGACAATTTTTTCACTTATTTTTTC
1 AAAAAAAGGAAAAATATTTAATTTCGTTATTTGCTAATACAGACAACATTTTCACTTATTTTTTC
* * * *
174250 TTGGTGTTAAAA-TTTTCTCTATACAAAAAATGTTTACGGAT-AAAAT-CATCTAACTTAGAGTA
66 TTGGTGTTAAAAGTTTT-TCTATACAAAAAACGTTTACGGATAAAAATACATCAAACTCAGACTA
* * * *
174312 TGATAAAGATTGAGAAAAAAA-ATTGAGGCGATAAAGCTACTGCTATCACCACTTAAAACAGAAG
130 TAATAAAGATTGAGAAAAAAATA-T-AGGCGATAAAGCAACTACTATCACCACTTAAAACACAAG
*
174376 AGCCTCATATTCTTGGCCAAGTTTTGA
193 -GCCTCATATTCTTGGCCAAATTTTGA
174403 AGTATACACC
Statistics
Matches: 187, Mismatches: 26, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
240 1 0.01
241 32 0.17
242 41 0.22
243 111 0.59
244 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (243 bp):
AAAAAAAGGAAAAATATTTAATTTCGTTATTTGCTAATACAGACAACATTTTCACTTATTTTTTC
TTGGTGTTAAAAGTTTTTCTATACAAAAAACGTTTACGGATAAAAATACATCAAACTCAGACTAT
AATAAAGATTGAGAAAAAAATATAGGCGATAAAGCAACTACTATCACCACTTAAAACACAAGGCC
TCATATTCTTGGCCAAATTTTGATGCCTACACTGAGAAATAACCTAAT
Found at i:179576 original size:28 final size:28
Alignment explanation
Indices: 179544--179597 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
179534 GGATGAAACA
179544 ATGAAATATAACAGTTTTACAAGGTACC
1 ATGAAATATAACAGTTTTACAAGGTACC
179572 ATGAAATATAACAGTTTTACAAGGTA
1 ATGAAATATAACAGTTTTACAAGGTA
179598 ATTATAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (28 bp):
ATGAAATATAACAGTTTTACAAGGTACC
Found at i:183805 original size:3 final size:3
Alignment explanation
Indices: 183797--183825 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
183787 ACTTGCTTCT
183797 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
183826 TGGTAGAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:190889 original size:25 final size:25
Alignment explanation
Indices: 190851--190902 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
190841 ATAAACTTTT
*
190851 TTTTTCTCTAGTTCAATTTTGTCAA
1 TTTTTCTCTAGTTCAATTTTATCAA
* *
190876 TTTTTCTCTGGTTCAGTTTTATCAA
1 TTTTTCTCTAGTTCAATTTTATCAA
190901 TT
1 TT
190903 ACAATAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.58
Consensus pattern (25 bp):
TTTTTCTCTAGTTCAATTTTATCAA
Found at i:195721 original size:31 final size:31
Alignment explanation
Indices: 195635--195722 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 31
195625 TTTCCGTATT
* *
195635 ATATATTAA-AAATATTAATAAATAATAATTA
1 ATATA-TAATAAATATTTATAAATAATAACTA
* *
195666 ATATATAATAAAT-TTTAAAAATAATTACTA
1 ATATATAATAAATATTTATAAATAATAACTA
*
195696 A-ATATAATACAATATTTATATATAATA
1 ATATATAATA-AATATTTATAAATAATA
195723 TTTAATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 8 0.17
30 20 0.43
31 19 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
ATATATAATAAATATTTATAAATAATAACTA
Found at i:195733 original size:10 final size:11
Alignment explanation
Indices: 195635--195738 Score: 55
Period size: 10 Copynumber: 9.8 Consensus size: 11
195625 TTTCCGTATT
195635 ATATATTAA-A
1 ATATATTAATA
195645 A-ATATTAATA
1 ATATATTAATA
*
195655 A-ATAATAATTA
1 ATATATTAA-TA
195666 ATATA-TAATA
1 ATATATTAATA
* *
195676 A-ATTTTAAAA
1 ATATATTAATA
*
195686 ATA-ATTACTA
1 ATATATTAATA
195696 A-ATA-TAATA
1 ATATATTAATA
*
195705 CA-ATATTTATA
1 -ATATATTAATA
195716 TATAATATTTAATA
1 -AT-ATA-TTAATA
195730 ATATATTAA
1 ATATATTAA
195739 ACTATAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
9 14 0.19
10 27 0.37
11 16 0.22
12 6 0.08
13 5 0.07
14 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATATTAATA
Found at i:199306 original size:41 final size:41
Alignment explanation
Indices: 199261--199343 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
199251 TATATTTTAT
199261 TTTATTTTTTCACCTATAAATATTCTTATTTTTCTCTCCTC
1 TTTATTTTTTCACCTATAAATATTCTTATTTTTCTCTCCTC
199302 TTTATTTTTTCACCTATAAATATTCTTATTTTTCTCTCCTC
1 TTTATTTTTTCACCTATAAATATTCTTATTTTTCTCTCCTC
199343 T
1 T
199344 CCTTTTGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (41 bp):
TTTATTTTTTCACCTATAAATATTCTTATTTTTCTCTCCTC
Found at i:199624 original size:2 final size:2
Alignment explanation
Indices: 199617--199654 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
199607 GTTTTTGCAA
199617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
199655 GAAGATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208958 original size:57 final size:60
Alignment explanation
Indices: 208895--209007 Score: 160
Period size: 57 Copynumber: 1.9 Consensus size: 60
208885 TTCATCTTTT
*
208895 TTTCTTTTTTAATTTTTATGCTCGC-TTTTTTCTTC-GTTTTT-CTTCAAATTCCCTTCC
1 TTTCTTTTTTAATTTCTATGCTCGCTTTTTTTCTTCAGTTTTTCCTTCAAATTCCCTTCC
* * *
208952 TTTCTTTTTTAATTTCTATTCTCTCTTTTTTTCTTCATTTTTTTCCTTCAAATTCC
1 TTTCTTTTTTAATTTCTATGCTCGCTTTTTTTCTTCA-GTTTTTCCTTCAAATTCC
209008 GTTCTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 22 0.46
58 10 0.21
60 5 0.10
61 11 0.23
ACGTcount: A:0.12, C:0.22, G:0.03, T:0.64
Consensus pattern (60 bp):
TTTCTTTTTTAATTTCTATGCTCGCTTTTTTTCTTCAGTTTTTCCTTCAAATTCCCTTCC
Found at i:213584 original size:20 final size:20
Alignment explanation
Indices: 213517--213586 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
213507 TGAACTCAAA
*
213517 GTATCGATACATTTATAGGAT
1 GTATCGATACATTTATATG-T
*
213538 GTATCGATACATTATGTAT-T
1 GTATCGATACATT-TATATGT
*
213558 GTGTCGATACATTT-TCATGT
1 GTATCGATACATTTAT-ATGT
213578 GTATCGATA
1 GTATCGATA
213587 TAAATGAGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 22 0.52
21 13 0.31
22 3 0.07
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (20 bp):
GTATCGATACATTTATATGT
Found at i:213671 original size:72 final size:72
Alignment explanation
Indices: 213577--213730 Score: 186
Period size: 72 Copynumber: 2.1 Consensus size: 72
213567 CATTTTCATG
* * * * * *
213577 TGTATCGATATAAATGAGGGTTTAAG-ATTTGTTTAACTACTACCAACAAATTGTATCGTTACAT
1 TGTATCGATAAAAATAAGGGTTTAAGCATTT-TGTAACAACTACCAACAAAATGTATCGATACAT
213641 TCACATA-A
65 TCACA-AGA
* * * *
213649 TGTATCGATAAAAATAAGGGTTTTAGCATTTTGTAGCAACTTCTAACAAAATGTATCGATACATT
1 TGTATCGATAAAAATAAGGGTTTAAGCATTTTGTAACAACTACCAACAAAATGTATCGATACATT
213714 CACAAGA
66 CACAAGA
213721 TGTATCGATA
1 TGTATCGATA
213731 CATTTAGTCC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
71 1 0.01
72 65 0.93
73 4 0.06
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (72 bp):
TGTATCGATAAAAATAAGGGTTTAAGCATTTTGTAACAACTACCAACAAAATGTATCGATACATT
CACAAGA
Found at i:213718 original size:21 final size:21
Alignment explanation
Indices: 213694--213734 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
213684 GCAACTTCTA
213694 ACAAAATGTATCGATACATTC
1 ACAAAATGTATCGATACATTC
*
213715 ACAAGATGTATCGATACATT
1 ACAAAATGTATCGATACATT
213735 TAGTCCTTAA
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:0.17, G:0.12, T:0.29
Consensus pattern (21 bp):
ACAAAATGTATCGATACATTC
Found at i:216268 original size:13 final size:13
Alignment explanation
Indices: 216250--216275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
216240 CAATTTTTTG
216250 TGTATCGATACAT
1 TGTATCGATACAT
216263 TGTATCGATACAT
1 TGTATCGATACAT
216276 ACTTGCTGTA
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:217024 original size:21 final size:21
Alignment explanation
Indices: 216983--217025 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
216973 CTCCCCTTTA
* *
216983 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
217004 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
217025 T
1 T
217026 TATATCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.30, G:0.05, T:0.40
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:218848 original size:13 final size:13
Alignment explanation
Indices: 218830--218868 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
218820 ATAATCACCC
218830 TGTATCGATACAA
1 TGTATCGATACAA
218843 TGTATCGATACAA
1 TGTATCGATACAA
218856 TGTATCGATACAA
1 TGTATCGATACAA
218869 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:218879 original size:20 final size:20
Alignment explanation
Indices: 218854--218932 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
218844 GTATCGATAC
218854 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
**
218874 AATGTATCGATACATTGAATTTCTA
1 AATGTATCGATACAAAGAA-----A
*
218899 AATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
218919 CATGTATCGATACA
1 AATGTATCGATACA
218933 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 31 0.63
25 18 0.37
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:220917 original size:15 final size:15
Alignment explanation
Indices: 220897--220927 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
220887 ATTTCGTTTG
*
220897 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
220912 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
220927 G
1 G
220928 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:222759 original size:21 final size:21
Alignment explanation
Indices: 222730--222774 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
222720 AAGTTTTCAT
*
222730 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
222750 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
222772 TTT
1 TTT
222775 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:225001 original size:13 final size:13
Alignment explanation
Indices: 224983--225008 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
224973 CAATTTTTTG
224983 TGTATCGATACAT
1 TGTATCGATACAT
224996 TGTATCGATACAT
1 TGTATCGATACAT
225009 ACTTGCTGTA
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:228917 original size:79 final size:79
Alignment explanation
Indices: 228746--228928 Score: 233
Period size: 79 Copynumber: 2.3 Consensus size: 79
228736 AACCCGGGGT
* * * *
228746 TAGAGTATCCCCAATTGTGAAAAATTAGTGTTTTAAAAATAAAATAGGGGTTGAAGTATCCCCTC
1 TAGAGTATCTCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAATAGAGGTTGAACTATCCCCTC
* *
228811 AAAAATAACGGGGC
66 AAAAATAACGAGAC
* * * * *
228825 TAAAGCATATCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACT-GAGGTTGGACTATCCCCT
1 TAGAGTATCTCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAA-TAGAGGTTGAACTATCCCCT
*
228889 CAAAAATAACGAGAT
65 CAAAAATAACGAGAC
*
228904 TGGAGTATCTCCGATTGTGAAAAAT
1 TAGAGTATCTCCGATTGTGAAAAAT
228929 AAATGTTCTC
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 86 0.99
80 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (79 bp):
TAGAGTATCTCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAATAGAGGTTGAACTATCCCCTC
AAAAATAACGAGAC
Found at i:229034 original size:79 final size:79
Alignment explanation
Indices: 228944--229282 Score: 310
Period size: 79 Copynumber: 4.3 Consensus size: 79
228934 TTCTCCTCGG
* * *
228944 AAATAGCGAGGTTGGAGTAT-CTCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGAGGTT
1 AAATAACGAGGTTGGAGTATCCT-CGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTT
229008 AGAGTATCCCCTCAA
65 AGAGTATCCCCTCAA
* * * * * *
229023 AAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTG
1 AAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTA
*
229088 GAGTATCCCTTCAA
66 GAGTATCCCCTCAA
* * * * * ** * **
229102 AAATAAC-AGGGTTGAAGAATCCCCGATGGTGGAAAATGGGTAGTTTTGGAAATAAAATTGGGGT
1 AAATAACGA-GGTTGGAGTATCCTCGATTGTGAAAAATTAGT-GTTTTAGAAATAAAACCGGGGT
*
229166 T-GCAGTATCCCCTCGA
64 TAG-AGTATCCCCTCAA
* * * * ** *
229182 AAACAATGGGGTTGGAGTATCCTCGATTGT-AGAAAATCTA-TGTTTAAGAAATAAGGCTGGGGT
1 AAATAACGAGGTTGGAGTATCCTCGATTGTGA-AAAAT-TAGTGTTTTAGAAATAAAACCGGGGT
* *
229245 TAGAGTATCCCATCAG
64 TAGAGTATCCCCTCAA
*
229261 AAATAACGGGGTTGGAGTATCC
1 AAATAACGAGGTTGGAGTATCC
229283 CTAATTATGA
Statistics
Matches: 206, Mismatches: 46, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
78 1 0.00
79 145 0.70
80 60 0.29
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (79 bp):
AAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTA
GAGTATCCCCTCAA
Found at i:229297 original size:159 final size:158
Alignment explanation
Indices: 228943--229311 Score: 404
Period size: 159 Copynumber: 2.3 Consensus size: 158
228933 GTTCTCCTCG
* * **
228943 GAAATAGCGAGGTTGGAGTATCTCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCGAGGT
1 GAAATAACGGGGTTGGAGTATC-CCGATTGTGAAAAATCGGTAGTTTTGGAAATAAAACCGAGGT
* *
229007 TAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTAGA
65 TAGAGTATCCCCTCAAAAACAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTAAGA
* *
229072 AATAAAGCCGGGGTTGGAGTATCCCTTCA
130 AATAAAGCCGGGGTTAGAGTATCCCATCA
* * * * * * * ** *
229101 AAAATAACAGGGTTGAAGAATCCCCGATGGTGGAAAATGGGTAGTTTTGGAAATAAAATTGGGGT
1 GAAATAACGGGGTTGGAGTAT-CCCGATTGTGAAAAATCGGTAGTTTTGGAAATAAAACCGAGGT
* * * * * *
229166 T-GCAGTATCCCCTCGAAAACAATGGGGTTGGAGTATCCTCGATTGT-AGAAAATCTATGTTTAA
65 TAG-AGTATCCCCTCAAAAACAACGAGGTTGGAGTATCCTCGATTATGA-AAAATCAATATTTAA
* *
229229 GAAATAAGGCTGGGGTTAGAGTATCCCATCA
128 GAAATAAAGCCGGGGTTAGAGTATCCCATCA
* * *
229260 GAAATAACGGGGTTGGAGTATCCCTAATTATGAAAAATCGATA-TTTTGGAAA
1 GAAATAACGGGGTTGGAGTATCCC-GATTGTGAAAAATCGGTAGTTTTGGAAA
229312 AATCAATGCA
Statistics
Matches: 171, Mismatches: 35, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
158 44 0.26
159 127 0.74
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (158 bp):
GAAATAACGGGGTTGGAGTATCCCGATTGTGAAAAATCGGTAGTTTTGGAAATAAAACCGAGGTT
AGAGTATCCCCTCAAAAACAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTAAGAA
ATAAAGCCGGGGTTAGAGTATCCCATCA
Found at i:230933 original size:13 final size:13
Alignment explanation
Indices: 230915--230940 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
230905 TACACCAAGT
230915 ATGTATCGATACA
1 ATGTATCGATACA
230928 ATGTATCGATACA
1 ATGTATCGATACA
230941 CCAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:230938 original size:32 final size:33
Alignment explanation
Indices: 230897--230960 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
230887 TAGCCAAACT
**
230897 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
230929 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
230961 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:233711 original size:20 final size:20
Alignment explanation
Indices: 233686--233733 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
233676 TTACAGGATG
*
233686 TCGATACATTTTGTAT-TGTA
1 TCGATACATTTT-CATGTGTA
233706 TCGATACATTTTCATGTGTA
1 TCGATACATTTTCATGTGTA
233726 TCGATACA
1 TCGATACA
233734 AATGAAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TCGATACATTTTCATGTGTA
Found at i:234825 original size:13 final size:13
Alignment explanation
Indices: 234807--234832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
234797 CAATTTTTTG
234807 TGTATCGATACAT
1 TGTATCGATACAT
234820 TGTATCGATACAT
1 TGTATCGATACAT
234833 ACTTGCTGTA
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:234897 original size:21 final size:21
Alignment explanation
Indices: 234871--234946 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
234861 CTGCGAAGAA
*
234871 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
234892 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
234912 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
234933 ATGTATCGATACAT
1 ATGTATCGATACAT
234947 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:234917 original size:20 final size:20
Alignment explanation
Indices: 234892--234964 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
234882 CATCTTTTTT
234892 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
234912 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
234933 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
234953 ATGTATCGATAC
1 ATGTATCGATAC
234965 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:234928 original size:41 final size:41
Alignment explanation
Indices: 234871--234964 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
234861 CTGCGAAGAA
*
234871 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
234912 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
234953 ATGTATCGATAC
1 ATGTATCGATAC
234965 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:237412 original size:13 final size:13
Alignment explanation
Indices: 237394--237431 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
237384 ATAAACACCC
237394 TGTATCGATACAG
1 TGTATCGATACAG
*
237407 TGTATCGATACAT
1 TGTATCGATACAG
237420 TGTATCGATACA
1 TGTATCGATACA
237432 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:239531 original size:15 final size:15
Alignment explanation
Indices: 239511--239541 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
239501 ATTTCGTTTG
*
239511 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
239526 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
239541 G
1 G
239542 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:243621 original size:13 final size:13
Alignment explanation
Indices: 243603--243628 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243593 CAATTTTTTG
243603 TGTATCGATACAT
1 TGTATCGATACAT
243616 TGTATCGATACAT
1 TGTATCGATACAT
243629 ACTTGCTGTA
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:243693 original size:21 final size:21
Alignment explanation
Indices: 243667--243742 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
243657 CTGCGAAGAA
*
243667 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
* **
243688 ATGTATCGATACAT-TGTAAC
1 ATGTATCGATACATCTTTTTC
243708 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
243729 ATGTATCGATACAT
1 ATGTATCGATACAT
243743 TGCAACATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:243713 original size:20 final size:20
Alignment explanation
Indices: 243688--243760 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
243678 CATCTTTTTT
243688 ATGTATCGATACATTGTAAC
1 ATGTATCGATACATTGTAAC
* **
243708 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGTAAC
*
243729 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGTAAC
243749 ATGTATCGATAC
1 ATGTATCGATAC
243761 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGTAAC
Found at i:243724 original size:41 final size:41
Alignment explanation
Indices: 243667--243760 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
243657 CTGCGAAGAA
* *
243667 ATGTATCGATACATCTTTTTTATGTATCGATACATTGTAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
243708 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
243749 ATGTATCGATAC
1 ATGTATCGATAC
243761 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:246732 original size:169 final size:169
Alignment explanation
Indices: 246448--246793 Score: 665
Period size: 169 Copynumber: 2.0 Consensus size: 169
246438 AAGCTAAACG
*
246448 AAAAGGGGAAAGAAAAGTGTAATAGTCATGATGTATCTCGTAATTGCCACCGATTATCTTAAGAT
1 AAAATGGGAAAGAAAAGTGTAATAGTCATGATGTATCTCGTAATTGCCACCGATTATCTTAAGAT
*
246513 AACTGAATTGACAATTTAAAGATTTATCTGGATTTTTCGATTAATTGAAGTAAGAAAAATGGATT
66 AACTGAATTGAAAATTTAAAGATTTATCTGGATTTTTCGATTAATTGAAGTAAGAAAAATGGATT
246578 ACTCAAAATTTGAGAAAAAAAGATTCAATTTTTGTTTAA
131 ACTCAAAATTTGAGAAAAAAAGATTCAATTTTTGTTTAA
246617 AAAATGGGAAAGAAAAGTGTAATAGTCATGATGTATCTCGTAATTGCCACCGATTATCTTAAGAT
1 AAAATGGGAAAGAAAAGTGTAATAGTCATGATGTATCTCGTAATTGCCACCGATTATCTTAAGAT
*
246682 AACTGAATTGAAAATTTAAAGATTTATCTGGATTTTTCGATTAATTGAAGTAATAAAAATGGATT
66 AACTGAATTGAAAATTTAAAGATTTATCTGGATTTTTCGATTAATTGAAGTAAGAAAAATGGATT
246747 ACTCAAAATTTGAGAAAAAAAGATTCAATTTTTGTTTAA
131 ACTCAAAATTTGAGAAAAAAAGATTCAATTTTTGTTTAA
246786 AAAATGGG
1 AAAATGGG
246794 GTTGGAGTAT
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
169 174 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.33
Consensus pattern (169 bp):
AAAATGGGAAAGAAAAGTGTAATAGTCATGATGTATCTCGTAATTGCCACCGATTATCTTAAGAT
AACTGAATTGAAAATTTAAAGATTTATCTGGATTTTTCGATTAATTGAAGTAAGAAAAATGGATT
ACTCAAAATTTGAGAAAAAAAGATTCAATTTTTGTTTAA
Found at i:246889 original size:96 final size:96
Alignment explanation
Indices: 246780--246998 Score: 223
Period size: 96 Copynumber: 2.3 Consensus size: 96
246770 TTCAATTTTT
* *
246780 GTTTAAAAAATGGGGTTGGAGTATCCTCTCAAAGGAAT-GAGATTGAAGTGTCCCCG-TGATGAC
1 GTTT-AAAAATGGGGTTGGAGTATCC-CTCAAAAGAATAGAGATTGAAGTAT-CCCGATGATGAC
* * *
246843 AATTTG-GGTGAAAA-TAAGATTTAAATCTTGACAA
63 AA-TTGAAG-CAAAACTAAAATTTAAATCTTGACAA
** * * * * * *
246877 GTTTAAAAATGGGGTTAAAGTGTTCCTCAAAAGAATAGGGGTTGGAGTATCCCGATGATGATAAT
1 GTTTAAAAATGGGGTTGGAGTATCCCTCAAAAGAATAGAGATTGAAGTATCCCGATGATGACAAT
*
246942 TGAAGCAAAACTAAAATTTAAATCTTGACGA
66 TGAAGCAAAACTAAAATTTAAATCTTGACAA
*
246973 G-TTACAAATGGGGTTGGAGTATCCCT
1 GTTTAAAAATGGGGTTGGAGTATCCCT
246999 TTGGAAGATG
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
95 41 0.41
96 54 0.55
97 4 0.04
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (96 bp):
GTTTAAAAATGGGGTTGGAGTATCCCTCAAAAGAATAGAGATTGAAGTATCCCGATGATGACAAT
TGAAGCAAAACTAAAATTTAAATCTTGACAA
Found at i:248306 original size:42 final size:42
Alignment explanation
Indices: 248197--248309 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 42
248187 AAAGGAAAAA
* * * * * *
248197 AAATGAAATGGGTCCTGCTCCTTGTGGACATAGAAAAAAAAAGA
1 AAATGAAATGCGTCATGCTCTTTGAGGACATAG--GAAAAAAGG
* * *
248241 AAAT-AAATGTGTCTTGCTTTTTGAGGACATAGGAAAAAAGG
1 AAATGAAATGCGTCATGCTCTTTGAGGACATAGGAAAAAAGG
*
248282 AAATGAAGTGCGTCATGCTCTTTGAGGA
1 AAATGAAATGCGTCATGCTCTTTGAGGA
248310 GAAAAGGAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 11 0.19
42 19 0.33
43 23 0.40
44 4 0.07
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.26
Consensus pattern (42 bp):
AAATGAAATGCGTCATGCTCTTTGAGGACATAGGAAAAAAGG
Found at i:248480 original size:61 final size:61
Alignment explanation
Indices: 248340--248657 Score: 290
Period size: 61 Copynumber: 5.2 Consensus size: 61
248330 GTGCGTTCTA
* * *
248340 CTCTTTGGGGACT-AGAAGGTGCCACCAACTTG-G-GGGTTTTGAAAA-GAAAAAGTGTCCTG
1 CTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAAGCGTCCTG
* * * * * *
248399 CTCTTTAAGAACTGAAAGGTGCCGCCAACTTGT-TAAGGCTTTAAAAGGAAAAGGCGTCTTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGT-GGGCTTTAAAAGGAAAAAGCGTCCTG
* * * *
248460 CACTTTTAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAACAA-TAAAGAAGTGTCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAGGAAA-AAGCGTCCTG
* ** *
248522 CTCTTTGAGGACT-AAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAATTGCGTCCTA
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCCTG
* * * * * * * *
248582 CTCTTTGAGGACTAAAAGGTGCTATCAACTCGTGTTGGCTTTGAAAAGAAAAAAAGGTGTCATG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAA-GCGTCCTG
248646 CTCTTTGAGGAC
1 CTCTTTGAGGAC
248658 AAAGGAAAAG
Statistics
Matches: 209, Mismatches: 37, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
59 26 0.12
60 26 0.12
61 111 0.53
62 26 0.12
63 3 0.01
64 17 0.08
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (61 bp):
CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCCTG
Found at i:248562 original size:122 final size:121
Alignment explanation
Indices: 248327--248662 Score: 349
Period size: 122 Copynumber: 2.8 Consensus size: 121
248317 AAAAGGAAAT
* * * * * *
248327 AAAGTGCGTTCTACTCTTTGGGGACTAGAAGGTGCCACCAACTTG-G-GGGTTTTGAAAAGAAAA
1 AAAG-GCGTCCTACACTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAA
* * * *
248390 AGTGTCCTGCTCTTTAAGAACTGAAAGGTGCCGCCAACTTGTTAAGGCTTTAAAAGGA
65 AGTGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTATTAAGGCTTTAAAAGGA
* * * * *
248448 AAAGGCGTCTTGCACTTTTAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AACAATAAAG
1 AAAGGCGTCCTACACTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AA-AAAA
*
248512 AAGTGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTATGT-GGGCTTTAAAAGGA
64 AAGTGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTAT-TAAGGCTTTAAAAGGA
** * * * * *
248570 AATTGCGTCCTACTCTTTGAGGACTAAAAGGTGCTATCAACTCGTGTTGGCTTTGAAAAGAAAAA
1 AAAGGCGTCCTACACTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAA-AAAAA
*
248635 AAGGTGTCATGCTCTTTGAGGAC-AAAGG
64 AA-GTGTCCTGCTCTTTGAGGACTAAAGG
248663 AAAAGAAGGA
Statistics
Matches: 177, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
120 32 0.18
121 7 0.04
122 81 0.46
123 35 0.20
124 22 0.12
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (121 bp):
AAAGGCGTCCTACACTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAA
GTGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTATTAAGGCTTTAAAAGGA
Found at i:249156 original size:20 final size:20
Alignment explanation
Indices: 249111--249162 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
249101 GTAGCCAAAC
* **
249111 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
249131 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
249150 TTGTATCGATACA
1 TTGTATCGATACA
249163 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:251365 original size:21 final size:21
Alignment explanation
Indices: 251332--251381 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
251322 TTGCAAGTTG
*
251332 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
251354 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
251375 AAATAAA
1 AAATAAA
251382 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:253199 original size:15 final size:15
Alignment explanation
Indices: 253179--253209 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
253169 TAAAAATGTC
*
253179 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
253194 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
253209 C
1 C
253210 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:255457 original size:20 final size:20
Alignment explanation
Indices: 255414--255459 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
255404 AAATCTTTTA
255414 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
255435 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
255455 CAAAA
1 CAAAA
255460 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:258709 original size:61 final size:61
Alignment explanation
Indices: 258638--258972 Score: 442
Period size: 61 Copynumber: 5.4 Consensus size: 61
258628 AAAGGAAAGA
* *
258638 GTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
* * * *
258699 GTCCTGCTCTTTGAAGACTGAAATGTGTCATCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
*
258760 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGAAAGG
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG---A-G-AAGG
*
258825 T
61 C
* * *
258826 GTCTTGTTCTTTCGA-GACTAGAAA-GTACCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
1 GTCCTGCTCTTT-GAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
* *
258887 GTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
* *
258948 GTCATACTCTTTGAGGACTGAAAGG
1 GTCCTGCTCTTTGAGGACTGAAAGG
258973 ATAAAAGGTT
Statistics
Matches: 240, Mismatches: 25, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
60 6 0.03
61 178 0.74
62 1 0.00
63 1 0.00
64 1 0.00
65 1 0.00
66 46 0.19
67 6 0.03
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
Found at i:258895 original size:127 final size:126
Alignment explanation
Indices: 258638--258946 Score: 443
Period size: 127 Copynumber: 2.5 Consensus size: 126
258628 AAAGGAAAGA
* *
258638 GTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG---A-GAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGAAGGC
** *
258699 GTCCTGCTCTTTGAAGACTGAAATGTGTCATCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
66 GTCCTGCTCTTTGAAGACTGAAATGTACCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
*
258760 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGAAAGG
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG-AAGG
* * *
258825 TGTCTTGTTCTTTCG-AGACTAGAAA-GTACCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
65 CGTCCTGCTCTTT-GAAGACT-GAAATGTACCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
*
258887 GTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGG
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
258947 CGTCATACTC
Statistics
Matches: 168, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
122 51 0.30
125 1 0.01
126 1 0.01
127 106 0.63
128 9 0.05
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (126 bp):
GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGAAGGC
GTCCTGCTCTTTGAAGACTGAAATGTACCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
Found at i:259932 original size:17 final size:15
Alignment explanation
Indices: 259907--259946 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
259897 CTTAAGCAGG
259907 TTTTTTTTTTCTCTTT
1 TTTTTTTTTTC-CTTT
259923 TTTCTTTTTTTCCTTT
1 TTT-TTTTTTTCCTTT
259939 TTTTTTTT
1 TTTTTTTT
259947 GGTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTCCTTT
Found at i:270280 original size:4 final size:4
Alignment explanation
Indices: 270271--270309 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
270261 AAACAAAACA
*
270271 AAAT AAAT AAAT AAAT AAAT GAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
270310 CACCTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:271540 original size:33 final size:34
Alignment explanation
Indices: 271458--271550 Score: 109
Period size: 33 Copynumber: 2.7 Consensus size: 34
271448 ATTGTTTACC
* *
271458 TTTAAGGCTAAGGTATAACCT-TACACCCCTATCTT
1 TTTAAGGCTAAGATAGAACCTCTACA--CCTATCTT
*
271493 TTACAAAGGCTAAGATAGAACCTCTACA-CTATCTT
1 TT--TAAGGCTAAGATAGAACCTCTACACCTATCTT
271528 TTTAAGGCTAAGATAGAACCTCT
1 TTTAAGGCTAAGATAGAACCTCT
271551 CAATCACTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
33 20 0.39
35 11 0.22
37 16 0.31
38 4 0.08
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (34 bp):
TTTAAGGCTAAGATAGAACCTCTACACCTATCTT
Found at i:272036 original size:10 final size:10
Alignment explanation
Indices: 272021--272045 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
272011 GTATTGATAC
272021 ATGAACAGTG
1 ATGAACAGTG
272031 ATGAACAGTG
1 ATGAACAGTG
272041 ATGAA
1 ATGAA
272046 TAGTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.28, T:0.20
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:272100 original size:13 final size:13
Alignment explanation
Indices: 272082--272106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
272072 TACTAGTTTT
272082 ATGTATCGATACA
1 ATGTATCGATACA
272095 ATGTATCGATAC
1 ATGTATCGATAC
272107 TAAGCAAAAT
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):
ATGTATCGATACA
Found at i:273634 original size:77 final size:77
Alignment explanation
Indices: 273538--273788 Score: 276
Period size: 77 Copynumber: 3.2 Consensus size: 77
273528 TAAAACCCGA
* *
273538 GGTTAGAGTATCCCATCGAAAATAACAGGGTTGGAGTATCCCTGATTATGAAAAATCAGTATTTT
1 GGTTAGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCTGATTGTGAAAAATCAGTATTTT
273603 -GAAAAAAATCGG
65 AGAAAAAAATCGG
* ** *
273615 GGTTAGAGTATCCCCTCGAAAATAACGAGCTTGGAGTATCCCCAATTGTGAAAAATCAGTGTTTT
1 GGTTAGAGTATCCCCTCGAAAATAACG-GGTTGGAGTATCCCTGATTGTGAAAAATCAGTATTTT
* *
273680 AAAAATAAAATCGA
65 AGAAA-AAAATCGG
* * *
273694 GATTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTAT-CCTCGATTGTGAAAAATCAGTGTT
1 GGTTAGAGTATCCCCTCGA-AAATAAC-GGGTTGGAGTATCCCT-GATTGTGAAAAATCAGT-AT
* *
273757 CTTCTCGAAAATAA-CGG
62 -TT-TAGAAAAAAATCGG
273774 GGTTAGAGTATCCCC
1 GGTTAGAGTATCCCC
273789 GATTGTGAAA
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
76 1 0.01
77 57 0.39
78 6 0.04
79 55 0.38
80 17 0.12
81 5 0.03
82 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (77 bp):
GGTTAGAGTATCCCCTCGAAAATAACGGGTTGGAGTATCCCTGATTGTGAAAAATCAGTATTTTA
GAAAAAAATCGG
Found at i:273717 original size:79 final size:77
Alignment explanation
Indices: 273535--273756 Score: 277
Period size: 79 Copynumber: 2.9 Consensus size: 77
273525 AGATAAAACC
* * * * *
273535 CGAGGTTAGAGTATCCCATCGAAAATAAC-AGGGTTGGAGTATCCCTGATTATGAAAAATCAGTA
1 CGAGATTAGAGTATCCCCTCGAAAATAACGA-GGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
*
273599 TTTTGAAAAAAAT
65 TTTTAAAAAAAAT
* * * *
273612 CGGGGTTAGAGTATCCCCTCGAAAATAACGAGCTTGGAGTATCCCCAATTGTGAAAAATCAGTGT
1 CGAGATTAGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGT
273677 TTTAAAAATAAAAT
66 TTT-AAAA-AAAAT
* * *
273691 CGAGATTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCAGTG
1 CGAGATTAGAGTATCCCCTCGA-AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
273755 TT
65 TT
273757 CTTCTCGAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
77 59 0.47
78 5 0.04
79 62 0.49
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (77 bp):
CGAGATTAGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGT
TTTAAAAAAAAT
Found at i:273799 original size:131 final size:131
Alignment explanation
Indices: 273629--273882 Score: 375
Period size: 131 Copynumber: 1.9 Consensus size: 131
273619 AGAGTATCCC
*
273629 CTCGAAAATAACGAGCTTGGAGTATCCCCAATTGTGAAAAATCAGTGTTTTAAAAATAAAATCGA
1 CTCGAAAATAACGAGCTTAGAGTATCCCCAATTGTGAAAAATCAGTGTTTTAAAAATAAAATCGA
* * *
273694 GATTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCAGTGTTC
66 GATTAGAGTATCCCCTCGA-AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAGTGTTC
273758 TT
130 TT
* * * * *
273760 CTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAATCGG
1 CTCGAAAATAACGAGCTTAGAGTATCCCCAATTGTGAAAAATCAGTGTTTTAAAAATAAAATCGA
* * * *
273825 GGTTATAGTATCCTCTCGAAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAATCA
66 GATTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCA
273883 ATATTTTAGA
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
131 108 0.99
132 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (131 bp):
CTCGAAAATAACGAGCTTAGAGTATCCCCAATTGTGAAAAATCAGTGTTTTAAAAATAAAATCGA
GATTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAGTGTTCT
T
Found at i:273848 original size:79 final size:79
Alignment explanation
Indices: 273759--273916 Score: 235
Period size: 79 Copynumber: 2.0 Consensus size: 79
273749 TCAGTGTTCT
* * * *
273759 TCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAATCG
1 TCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTTTAAAAATAAAATCA
*
273824 GGGTTATAGTATCC
66 GGGTTAGAGTATCC
* * *
273838 TCTCGAAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGTCA
1 TCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTTTAAAAATAAAATCA
*
273903 GGGTTGGAGTATCC
66 GGGTTAGAGTATCC
273917 CTGACTGGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (79 bp):
TCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTTTAAAAATAAAATCA
GGGTTAGAGTATCC
Found at i:273932 original size:131 final size:131
Alignment explanation
Indices: 273648--273951 Score: 339
Period size: 131 Copynumber: 2.3 Consensus size: 131
273638 AACGAGCTTG
* * *
273648 GAGTATCCCCAATTGTGAAAAATCAGTGTTTTAAAAATAAAATCGAGATTGGAGTATCCCCTCAG
1 GAGTATCCCCGATGGTGAAAAATCAGTGTTTTAAAAATAAAATCGAGATTAGAGTATCCCCTCAG
* * * * * *
273713 AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCAGTGTTCTTCTCGAAAATAACGGGGTT
66 AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATGATCTTCTAGAAAATAACAGGGTT
273778 A
131 A
* * * * * *
273779 GAGTATCCCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAATCGGGGTTATAGTATCCTCTC-G
1 GAGTATCCCCGATGGTGAAAAATCAGTGTTTTAAAAATAAAATCGAGATTAGAGTATCCCCTCAG
*
273843 AAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAATCAAT-AT-TT-TAG-AAATAAAGTCAG
66 -AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATGATCTTCTAGAAAAT-AA--CAG
*
273904 GGTTG
127 GGTTA
* * * *
273909 GAGTATCCCTGACTGGTGGAAAATCGGTGTTTTGAAAATAAAA
1 GAGTATCCCCGA-TGGTGAAAAATCAGTGTTTTAAAAATAAAA
273952 ACATCGATGC
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
127 4 0.03
128 4 0.03
129 2 0.01
130 19 0.13
131 118 0.80
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (131 bp):
GAGTATCCCCGATGGTGAAAAATCAGTGTTTTAAAAATAAAATCGAGATTAGAGTATCCCCTCAG
AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATGATCTTCTAGAAAATAACAGGGTT
A
Found at i:276776 original size:19 final size:18
Alignment explanation
Indices: 276752--276818 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
276742 ATTCAACAAA
276752 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAG-T
276771 TTGTATCGATAC--AA--
1 TTGTATCGATACATAAGT
276785 -TGTATCGATACATAAGT
1 TTGTATCGATACATAAGT
276802 ATTGTATCGATACATAA
1 -TTGTATCGATACATAA
276819 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
TTGTATCGATACATAAGT
Found at i:276789 original size:32 final size:32
Alignment explanation
Indices: 276753--276815 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
276743 TTCAACAAAT
*
276753 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
276785 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
276816 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:276790 original size:13 final size:13
Alignment explanation
Indices: 276772--276796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
276762 ACATAAGTTT
276772 TGTATCGATACAA
1 TGTATCGATACAA
276785 TGTATCGATACA
1 TGTATCGATACA
276797 TAAGTATTGT
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:276873 original size:13 final size:13
Alignment explanation
Indices: 276855--276881 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
276845 ATACATTTTT
276855 TTGTATCGATACA
1 TTGTATCGATACA
276868 TTGTATCGATACA
1 TTGTATCGATACA
276881 T
1 T
276882 GGATCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:276896 original size:33 final size:31
Alignment explanation
Indices: 276838--276902 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 31
276828 GCCAAGGAAA
* *
276838 TGTATCGATACATTTTTTTGTATCGATACAT
1 TGTATCGATACATATCTTTGTATCGATACAT
276869 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACAT--ATCTTTGTATCGATACAT
276902 T
1 T
276903 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.43
33 17 0.57
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (31 bp):
TGTATCGATACATATCTTTGTATCGATACAT
Found at i:277454 original size:55 final size:55
Alignment explanation
Indices: 277259--277832 Score: 609
Period size: 55 Copynumber: 10.1 Consensus size: 55
277249 TGCTTTTTCT
* * * **
277259 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAAGACGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATACC
* ** *
277314 TTTTCTTTTAAAGCCCACACAAGTTAGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCTTTCTT
1 -TTTC----AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA----TAC--
277378 C
55 C
*
277379 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAATCCTCAAAGAGCAGGATACC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATACC
* *
277434 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACT
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATACC
* * * *
277489 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGAATGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATACC
* * ** *
277544 TTTTCTTTTAAAGCCCACATAAGTTAGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCCTTATT
1 -TTTC----AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA-----TA-C
277608 C
55 C
* * * *
277609 TTTCAAAGCCCACACAAGTTGGAGGCATTTTCCAATCCTCAAAGAGCAGGACACC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATACC
* *
277664 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATACC
*
277719 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGA-AGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGATA-CC
* *
277774 TTTCAAAGCCCACACGAGTTGGTGGCACTTTTT-AGTCCTCAATGAGCAGGATACAC
1 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGATAC-C
277830 TTT
1 TTT
277833 ATTTTCCTCT
Statistics
Matches: 444, Mismatches: 47, Indels: 54
0.81 0.09 0.10
Matches are distributed among these distances:
54 1 0.00
55 252 0.57
56 17 0.04
57 2 0.00
59 36 0.08
60 85 0.19
61 39 0.09
63 1 0.00
64 9 0.02
65 2 0.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (55 bp):
TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATACC
Found at i:277614 original size:175 final size:170
Alignment explanation
Indices: 277222--277824 Score: 715
Period size: 175 Copynumber: 3.5 Consensus size: 170
277212 GGCAATGAGG
*
277222 GGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAT
1 GGCACCTTCAGTCCTCAAAGAGCAGGA-GC--TATC-TTTCAAAGCCCACACAAGTTGGTGGCAT
* * * * **
277287 TTTCCAGTCCCCAAAGAGCAAGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-C
62 TTTCCAGTCCTCAAAGAGCAGGAC-ACTTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
*
277351 AGTCCTCAAAGAGCAGGACGCTTTCTTCTTTCAAAGCCCACACAAGTTGGT
122 AGTCCTCAAAGAGCAGGACGCCTT-TTCTTT-AAAGCCCACACAAGTTGGT
** * *
277402 GGCATTTTTCAATCCTCAAAGAGCAGGA--TACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 GGCA-CCTTCAGTCCTCAAAGAGCAGGAGCTATCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* *
277465 TCAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCA
65 CCAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
* * * *
277530 AAGAGCAGAATGCCTTTTCTTTTAAAGCCCACATAAGTTAGT
130 AAGAGCAGGACGCCTTTTC-TTTAAAGCCCACACAAGTTGGT
*
277572 GGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTATTCTTTCAAAGCCCACACAAGTTGGAGGCAT
1 GGCACCTTCAGTCCTCAAAGAGCAGGA-G-C-TA-TCTTTCAAAGCCCACACAAGTTGGTGGCAT
* *
277637 TTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
62 TTTCCAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
*
277702 TCAAAGAGCAGGACACC-TTTC---AAAGCCCACACAAGTTGGT
127 TCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGT
* *
277742 GGCACCTTTTAGTCCTCAAAGAGCAGGAAGC---CTTTCAAAGCCCACACGAGTTGGTGGCACTT
1 GGCACC-TTCAGTCCTCAAAGAGCAGG-AGCTATCTTTCAAAGCCCACACAAGTTGGTGGCA-TT
* *
277804 TT-TAGTCCTCAATGAGCAGGA
63 TTCCAGTCCTCAAAGAGCAGGA
277825 TACACTTTAT
Statistics
Matches: 373, Mismatches: 38, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
165 42 0.11
166 4 0.01
169 20 0.05
170 72 0.19
171 44 0.12
172 1 0.00
174 12 0.03
175 152 0.41
176 2 0.01
180 4 0.01
181 20 0.05
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (170 bp):
GGCACCTTCAGTCCTCAAAGAGCAGGAGCTATCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
CAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
AGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGT
Found at i:277667 original size:230 final size:229
Alignment explanation
Indices: 277257--277824 Score: 898
Period size: 230 Copynumber: 2.5 Consensus size: 229
277247 GATGCTTTTT
*
277257 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAAGACGCCTTTTCTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGC-AGAAGCCTTTTCTTT
* *
277322 TAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTCTTCTTTCAAAG
65 TAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTATTCTTTCAAAG
* * *
277387 CCCACACAAGTTGGTGGCATTTTTCAATCCTCAAAGAGCAGGATACCTTTCAAAGCCCACACAAG
130 CCCACACAAGTTGGAGGCATTTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
*
277452 TTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACA
195 TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
277487 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGAATGCCTTTTCTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGAA-GCCTTTTCTTT
*
277552 TAAAGCCCACATAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTATTCTTTCAAAG
65 TAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTATTCTTTCAAAG
277617 CCCACACAAGTTGGAGGCATTTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
130 CCCACACAAGTTGGAGGCATTTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
277682 TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
195 TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* *
277717 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT--AGTCCTCAAAGAGCAGGAAGCC-TTTC-
1 CTTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCCCAAAGAGCA-GAAGCCTTTTCT
* * * * *
277778 ---AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAATGAGCAGGA
63 TTTAAAGCCCACACAAGTTAGTGGCAC-CTTCAGTCCTCAAAGAGCAGGA
277825 TACACTTTAT
Statistics
Matches: 317, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
225 21 0.07
226 19 0.06
229 7 0.02
230 263 0.83
231 3 0.01
232 4 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (229 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGAAGCCTTTTCTTTT
AAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTATTCTTTCAAAGC
CCACACAAGTTGGAGGCATTTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGT
TGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
Found at i:277748 original size:29 final size:29
Alignment explanation
Indices: 277660--277750 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
277650 AAGAGCAGGA
277660 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
* * * * * **
277689 CA-TTTTC-CAGTCCTCA-AAG-AGCAGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
277714 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTCAAAGCCCACACAAGTTGGTGG
277744 CACCTTT
1 CACCTTT
277751 TAGTCCTCAA
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
25 3 0.07
26 5 0.12
27 10 0.23
28 10 0.23
29 12 0.28
30 3 0.07
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:278635 original size:19 final size:18
Alignment explanation
Indices: 278611--278678 Score: 90
Period size: 19 Copynumber: 3.9 Consensus size: 18
278601 ATTCAACAAA
278611 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAG-T
278630 TTGTATCGATAC--AA--
1 TTGTATCGATACATAAGT
278644 TTGTATCGATACATAAGT
1 TTGTATCGATACATAAGT
278662 ATTGTATCGATACATAA
1 -TTGTATCGATACATAA
278679 TTAGCTACTG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.27
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
TTGTATCGATACATAAGT
Found at i:278649 original size:14 final size:14
Alignment explanation
Indices: 278630--278656 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
278620 TACATAAGTT
278630 TTGTATCGATACAA
1 TTGTATCGATACAA
278644 TTGTATCGATACA
1 TTGTATCGATACA
278657 TAAGTATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TTGTATCGATACAA
Found at i:278651 original size:33 final size:33
Alignment explanation
Indices: 278609--278675 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
278599 AAATTCAACA
*
278609 AATTGTATCGATACATAAGTTTTGTATCGATAC
1 AATTGTATCGATACATAAGTATTGTATCGATAC
278642 AATTGTATCGATACATAAGTATTGTATCGATAC
1 AATTGTATCGATACATAAGTATTGTATCGATAC
278675 A
1 A
278676 TAATTAGCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (33 bp):
AATTGTATCGATACATAAGTATTGTATCGATAC
Found at i:278732 original size:13 final size:13
Alignment explanation
Indices: 278714--278740 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
278704 GATACATTTT
278714 TTGTATCGATACA
1 TTGTATCGATACA
278727 TTGTATCGATACA
1 TTGTATCGATACA
278740 T
1 T
278741 GGATCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:278759 original size:33 final size:30
Alignment explanation
Indices: 278698--278761 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 30
278688 GCCAAGGAAA
* *
278698 TGTATCGATACATTTTTTGTATCGATACAT
1 TGTATCGATACATTCTTTGTATCAATACAT
278728 TGTATCGATACATGGATCTTTGTATCAATACAT
1 TGTATCGATACAT---TCTTTGTATCAATACAT
278761 T
1 T
278762 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 13 0.45
33 16 0.55
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (30 bp):
TGTATCGATACATTCTTTGTATCAATACAT
Found at i:281283 original size:28 final size:27
Alignment explanation
Indices: 281216--281284 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
281206 CTTCACAATC
* **
281216 GGGGATACTCCAACCCTGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
281243 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
281271 GGGGATACTCCAAC
1 GGGGATACTCCAAC
281285 TCTGATTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:281358 original size:28 final size:28
Alignment explanation
Indices: 281325--281396 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
281315 TCATAGTCGA
* * **
281325 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
281353 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
281381 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
281397 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:281367 original size:108 final size:108
Alignment explanation
Indices: 281162--281475 Score: 388
Period size: 107 Copynumber: 2.9 Consensus size: 108
281152 TTCTATAATC
*
281162 GGGGATACTCCAACTCCGATTTTATTTCCAAAAA-ACATCAATTTCTTCACAATCGGGGATACTC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC--CAATTT-TTCATAATCGGGGATACTC
* *
281226 CAACC-CTGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTCCGA
63 CAACCTC-GTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *
281271 GGGGATACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTTTCATAGTCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCAA
281336 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
* ** * *** * *
281379 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCAA
*
281443 CCTCGTTATTT--TCGAGGGGATACTCCAATCCCG
66 CCTCGTTATTTCATC--GGGGATACTCCAACCCCG
281476 ATTTTTTTTC
Statistics
Matches: 181, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
105 2 0.01
107 85 0.47
108 59 0.33
109 33 0.18
110 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (108 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCAA
CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:281528 original size:78 final size:78
Alignment explanation
Indices: 281350--281553 Score: 230
Period size: 78 Copynumber: 2.6 Consensus size: 78
281340 GTTATTTCAT
* * *
281350 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
281415 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * * ** *
281429 TGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
281493 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * *
281507 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
281554 TTATTATCTC
Statistics
Matches: 104, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
77 3 0.03
78 60 0.58
79 41 0.39
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:284793 original size:24 final size:25
Alignment explanation
Indices: 284732--284794 Score: 108
Period size: 25 Copynumber: 2.4 Consensus size: 25
284722 TTTTTTTCCA
284732 AGATCATTCTTTTTTCTTTAAGTTTAG
1 AGATCA-T-TTTTTTCTTTAAGTTTAG
284759 AGATCATTTTTTTCTTTAAGTTTAG
1 AGATCATTTTTTTCTTTAAGTTTAG
284784 AGATCATTTTT
1 AGATCATTTTT
284795 CTATATTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 29 0.81
26 1 0.03
27 6 0.17
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.56
Consensus pattern (25 bp):
AGATCATTTTTTTCTTTAAGTTTAG
Found at i:286871 original size:20 final size:20
Alignment explanation
Indices: 286826--286897 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
286816 TAAACTTAAA
* *
286826 GTATCGATACATTTACAGGAT
1 GTATCGATACATTTTCATG-T
*
286847 GTATCGATACATTTTGTAT-T
1 GTATCGATACATTTT-CATGT
286867 GTATCGATACATTTTCATGT
1 GTATCGATACATTTTCATGT
286887 GTATCGATACA
1 GTATCGATACA
286898 AATGAGGGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 2 0.04
20 28 0.62
21 14 0.31
22 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (20 bp):
GTATCGATACATTTTCATGT
Found at i:287027 original size:21 final size:21
Alignment explanation
Indices: 287003--287044 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
286993 GCTAATGCCA
*
287003 ACAAAATATATCGATACATTC
1 ACAAAATATATCAATACATTC
*
287024 ACAAGATATATCAATACATTC
1 ACAAAATATATCAATACATTC
287045 GGTCTTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (21 bp):
ACAAAATATATCAATACATTC
Found at i:288125 original size:21 final size:20
Alignment explanation
Indices: 288100--288152 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
288090 TACAAACCAA
**
288100 TGTATCGATACAATTTTTTTG
1 TGTATCGATACAA-TACTTTG
288121 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
288140 TGTATCGATACAA
1 TGTATCGATACAA
288153 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:290781 original size:21 final size:20
Alignment explanation
Indices: 290756--290808 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
290746 TACAAACCAA
**
290756 TGTATCAATACAATTTTTTTG
1 TGTATCAATACAA-TACTTTG
*
290777 TGTATCGATAC-ATACTTTG
1 TGTATCAATACAATACTTTG
290796 TGTATCAATACAA
1 TGTATCAATACAA
290809 GTTTGGCTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 15 0.56
20 2 0.07
21 10 0.37
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (20 bp):
TGTATCAATACAATACTTTG
Found at i:294206 original size:21 final size:21
Alignment explanation
Indices: 294165--294208 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
294155 CTCCCCTTTA
* *
294165 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
294186 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
294207 TC
1 TC
294209 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:298113 original size:15 final size:15
Alignment explanation
Indices: 298093--298123 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
298083 ATTTCGTTTG
*
298093 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
298108 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
298123 G
1 G
298124 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:302211 original size:13 final size:13
Alignment explanation
Indices: 302193--302218 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
302183 AATTTTTTTG
302193 TGTATCGATACAT
1 TGTATCGATACAT
302206 TGTATCGATACAT
1 TGTATCGATACAT
302219 ACTTTGTGTA
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:307715 original size:20 final size:21
Alignment explanation
Indices: 307670--307723 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
307660 ATAATAAAAA
307670 ATGTATCGATACATTGCAAGC
1 ATGTATCGATACATTGCAAGC
**
307691 ATGTATCGATACATT-CATTC
1 ATGTATCGATACATTGCAAGC
307711 ATGTATCGATACA
1 ATGTATCGATACA
307724 ATTTTTCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTGCAAGC
Found at i:308821 original size:27 final size:28
Alignment explanation
Indices: 308790--308854 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
308780 AATAAAATTG
* *
308790 GGGTTGGAGC-ATCCCTTCGGAAATAAA
1 GGGTTGGAGCTATCCCCTCAGAAATAAA
*
308817 GGGTTTGGA-CTATCCCCTCAGAAATAAC
1 GGG-TTGGAGCTATCCCCTCAGAAATAAA
308845 GGAGTTGGAG
1 GG-GTTGGAG
308855 TTTCCCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.13
28 26 0.84
29 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (28 bp):
GGGTTGGAGCTATCCCCTCAGAAATAAA
Found at i:310000 original size:13 final size:13
Alignment explanation
Indices: 309982--310007 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
309972 CAATTTTTTG
309982 TGTATCGATACAT
1 TGTATCGATACAT
309995 TGTATCGATACAT
1 TGTATCGATACAT
310008 ACTTGCTGTA
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:312546 original size:13 final size:13
Alignment explanation
Indices: 312528--312566 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
312518 ATAATCACCC
*
312528 TGTATCGATACAG
1 TGTATCGATACAA
312541 TGTATCGATACAA
1 TGTATCGATACAA
312554 TGTATCGATACAA
1 TGTATCGATACAA
312567 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:312577 original size:20 final size:20
Alignment explanation
Indices: 312552--312630 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
312542 GTATCGATAC
312552 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
312572 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
312597 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
312617 CATGTATCGATACA
1 AATGTATCGATACA
312631 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:314666 original size:15 final size:15
Alignment explanation
Indices: 314646--314676 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
314636 ATTTCGTTTG
*
314646 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
314661 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
314676 G
1 G
314677 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:316508 original size:21 final size:21
Alignment explanation
Indices: 316479--316523 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
316469 AAGTTTTCAT
*
316479 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
316499 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
316521 TTT
1 TTT
316524 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:318760 original size:13 final size:13
Alignment explanation
Indices: 318742--318767 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
318732 CAATTTTTTG
318742 TGTATCGATACAT
1 TGTATCGATACAT
318755 TGTATCGATACAT
1 TGTATCGATACAT
318768 ACTTGCTGTA
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:319650 original size:20 final size:20
Alignment explanation
Indices: 319625--319678 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
319615 GTTACAAGCA
*
319625 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
319645 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
319665 ATGTATCGATACAA
1 ATGTATCGATACAA
319679 ACAATGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:319751 original size:19 final size:18
Alignment explanation
Indices: 319706--319763 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
319696 ACTGCCAGTT
319706 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
319725 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
*
319744 ATCATGTATCGATATAATG
1 -TCATGTATCGATACAATG
319763 T
1 T
319764 ATCGATACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.53
20 16 0.44
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:319769 original size:32 final size:33
Alignment explanation
Indices: 319728--319790 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
319718 ACAATTGTCC
* *
319728 ATGTATCGATACAATG-ATCATGTATCGATATA
1 ATGTATCGATACAAAGCATAATGTATCGATATA
319760 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
319791 CTTCTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:328516 original size:20 final size:20
Alignment explanation
Indices: 328491--328544 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
328481 GTTACAAGCA
*
328491 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
328511 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
328531 ATGTATCGATACAA
1 ATGTATCGATACAA
328545 ATAATGGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:329073 original size:79 final size:78
Alignment explanation
Indices: 328919--329616 Score: 559
Period size: 79 Copynumber: 8.8 Consensus size: 78
328909 CATAGTTGAC
** * *
328919 GTATCCCCTTAAAAATAAC-GAGATTGGAGTATCCCCGATAGTGAAAAATT-GATGTTTTAGAAA
1 GTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCCCGATGGTGAAAAATTAG-TGTTTTAGAAA
328982 TAAAACCAGGGTTAGA
64 TAAAA-CAGGGTTAGA
* * * * * * *
328998 ATATCCCATCGGAAATAACAGGGTTGGAGTATACCCGATGGTGAAAAAATTAGTGCTTTATAGAT
1 GTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGGTG-AAAAATTAGTGTTTTAGAAAT
* * *
329063 AATACCGGGTTTAAA
65 AAAACAGGG-TTAGA
* * * * *
329078 GTATCCCCTCAAAAATAAC-GAGGTTGGAGTATCCTTC-ATGGCGAAAAA-TCGATATTTTAGAA
1 GTATCCCCTCGAAAATAACAG-GGTTGGAGTATCC-CCGATGGTGAAAAATTAG-TGTTTTAGAA
*
329140 ATAAAACTGAGGTTAGA
63 ATAAAACAG-GGTTAGA
* * * *
329157 GTATCCCTTCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATA
1 GTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAATA
*
329222 AAACTATGGTTAGA
66 AAAC-AGGGTTAGA
* * * * * *
329236 GTATCCTCTCGAAAATAA-TGGGATTGGAGTATCCTCGATGGTGGAAAATCAATGTTTTAGAAAT
1 GTATCCCCTCGAAAATAACAGGG-TTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAAT
* *
329300 AAAATCAGGATTAAA
65 AAAA-CAGGGTTAGA
* * * * * * * * * ** *
329315 GTATCCCTTCGAAAATAACAAGGTTAGAATATTCCTGAGGGTGGAAAATTGGTACTTTAGAGATA
1 GTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAATA
* *
329380 AAACCGGGGTTGGA
66 AAA-CAGGGTTAGA
* ** * *
329394 GTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCGAT-GTGGAAAAATCGGTGCTTTAGAGA
1 GTATCCCCTCGA-AAATAACAGGGTTGGAGTATCCCCGATGGT-GAAAAATTAGTGTTTTAGAAA
* * *
329457 TTAAACTGGGATTTGA
64 TAAAACAGGG-TTAGA
* * * * ** * *
329473 GTCTCCCTTC-AGAAATAACAAGATTGGAGTATCTTCGATGGCGAAAAATTAGTGTTTTAGAAAG
1 GTATCCCCTCGA-AAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAAT
* *
329537 AAAACTAGAGTTGGA
65 AAAAC-AGGGTTAGA
* * *
329552 GTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGGTGGAAAATTGGTGTTTTAGAAATA
1 GTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAATA
329617 TGAAAGCTCA
Statistics
Matches: 486, Mismatches: 112, Indels: 42
0.76 0.17 0.07
Matches are distributed among these distances:
78 13 0.03
79 405 0.83
80 66 0.14
81 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (78 bp):
GTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAATA
AAACAGGGTTAGA
Found at i:329318 original size:158 final size:157
Alignment explanation
Indices: 328919--329616 Score: 629
Period size: 158 Copynumber: 4.4 Consensus size: 157
328909 CATAGTTGAC
** * * * *
328919 GTATCCCCTTAAAAATAACGAGATTGGAGTATCCCCGATAGTGAAAAATTGATGTTTTAGAAATA
1 GTATCCCCTCGAAAATAACG-GGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATA
* * * * * * *
328984 AAACCAGGGTTAGAA-TATCCCATCGGAAATAACAGGGTTGGAGTATACCCGATGGTGAAAAAAT
65 AAATCAGGATTA-AAGTATCCCTTCGAAAATAACAAGGTTAGAGTATCCCCGATGGTG-AAAAAT
* * * * *
329048 TAGTGCTTTATAGATAATAC-CGGGTTTAAA
128 TAGTGCTTTAGAAATAAAACTAGGG-TTAGA
* * * * *
329078 GTATCCCCTCAAAAATAACGAGGTTGGAGTATCCTTC-ATGGCGAAAAATCGATATTTTAGAAAT
1 GTATCCCCTCGAAAATAACG-GGTTGGAGTATCC-CCGATGGTGGAAAATCGATGTTTTAGAAAT
* * **
329142 AAAACTGAGG-TTAGAGTATCCCTTCGAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAAT
64 AAAA-TCAGGATTAAAGTATCCCTTCGAAAATAACAAGGTTAGAGTATCCCCGATGGTGAAAAAT
* * *
329206 CAGTGTTTTAGAAATAAAACTATGGTTAGA
128 TAGTGCTTTAGAAATAAAACTAGGGTTAGA
* * * *
329236 GTATCCTCTCGAAAATAATGGGATTGGAGTATCCTCGATGGTGGAAAATCAATGTTTTAGAAATA
1 GTATCCCCTCGAAAATAACGGG-TTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATA
* * * * * *
329301 AAATCAGGATTAAAGTATCCCTTCGAAAATAACAAGGTTAGAATATTCCTGAGGGTGGAAAATTG
65 AAATCAGGATTAAAGTATCCCTTCGAAAATAACAAGGTTAGAGTATCCCCGATGGTGAAAAATTA
* * ** *
329366 GTACTTTAGAGATAAAACCGGGGTTGGA
130 GTGCTTTAGAAATAAAACTAGGGTTAGA
* * *
329394 GTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCGAT-GTGGAAAAATCGGTGCTTTAGAGA
1 GTATCCCCTCGA-AAATAAC-GGGTTGGAGTATCCCCGATGGTGG-AAAATCGATGTTTTAGAAA
* * ** * * * ** *
329457 TTAAA-CTGGGATTTGAGTCTCCCTTC-AGAAATAACAAGATTGGAGTATCTTCGATGGCGAAAA
63 TAAAATC-AGGATTAAAGTATCCCTTCGA-AAATAACAAGGTTAGAGTATCCCCGATGGTGAAAA
* * * *
329520 ATTAGTGTTTTAGAAAGAAAACTAGAGTTGGA
126 ATTAGTGCTTTAGAAATAAAACTAGGGTTAGA
* * *
329552 GTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGGTGGAAAATTGGTGTTTTAGAAATA
1 GTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATA
329617 TGAAAGCTCA
Statistics
Matches: 441, Mismatches: 84, Indels: 29
0.80 0.15 0.05
Matches are distributed among these distances:
157 15 0.03
158 314 0.71
159 108 0.24
160 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (157 bp):
GTATCCCCTCGAAAATAACGGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAA
AATCAGGATTAAAGTATCCCTTCGAAAATAACAAGGTTAGAGTATCCCCGATGGTGAAAAATTAG
TGCTTTAGAAATAAAACTAGGGTTAGA
Found at i:329433 original size:237 final size:235
Alignment explanation
Indices: 328919--329616 Score: 669
Period size: 237 Copynumber: 2.9 Consensus size: 235
328909 CATAGTTGAC
* * * * *
328919 GTATCCCCTTAAAAATAACGAGATTGGAGTATCCCCGATAGTGAAAAAT-TGATGTTTTAGAAAT
1 GTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT-GTGAAAAATCAG-TGTTTTAGAAAT
* * *
328983 AAAACCAGGGTTAGAATATCCCATCGGAAATAACAGGG-TTGGAGTATACC-CGATGGTGAAAAA
64 AAAACTAGGGTTAGAGTATCCCATCGAAAATAA-AGGGATTGGAGTAT-CCTCGATGGTG-AAAA
* * * * * * * *
329046 ATTAGTGCTTTATAGATAATACCGGGTTTAAAGTATCCCCTCAAAAATAACGAGGTTGGAGTA-T
126 ATTAGTGTTTTAGAAATAA-AACAGGATTAAAGTATCCCCTCGAAAATAACAAGGTTGGAGTATT
* * * * * * *
329110 CCTTCATGGCGAAAAATCGATATTTTAGAAATAAAACTGAGGTTAGA
190 CC-TGATGGTGGAAAATTGGTACTTTAGAAATAAAACCGAGGTTAGA
* *
329157 GTATCCCTTC-GAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAAT
1 GTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGAT-GTGAAAAATCAGTGTTTTAGAAAT
* * *
329221 AAAACTATGGTTAGAGTATCCTC-TCGAAAATAATGGGATTGGAGTATCCTCGATGGTGGAAAAT
64 AAAACTAGGGTTAGAGTATCC-CATCGAAAATAAAGGGATTGGAGTATCCTCGATGGTGAAAAAT
* * * * *
329285 CAATGTTTTAGAAATAAAATCAGGATTAAAGTATCCCTTCGAAAATAACAAGGTTAGAATATTCC
128 TAGTGTTTTAGAAATAAAA-CAGGATTAAAGTATCCCCTCGAAAATAACAAGGTTGGAGTATTCC
* * * *
329350 TGAGGGTGGAAAATTGGTACTTTAGAGATAAAACCGGGGTTGGA
192 TGATGGTGGAAAATTGGTACTTTAGAAATAAAACCGAGGTTAGA
* * * *
329394 GTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGTGGAAAAATCGGTGCTTTAGAGATT
1 GTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGT-GAAAAATCAGTGTTTTAGAAATA
* * * * * *
329459 AAACT-GGGATTTGAGTCTCCCTTC-AGAAATAACA-AGATTGGAGTATCTTCGATGGCGAAAAA
65 AAACTAGGG-TTAGAGTATCCCATCGA-AAATAA-AGGGATTGGAGTATCCTCGATGGTGAAAAA
* ** * * *
329521 TTAGTGTTTTAGAAAGAAAACTA-GAGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATC
127 TTAGTGTTTTAGAAATAAAAC-AGGA-TTAAAGTATCCCCTCGAAAATAACAAGGTTGGAGTATT
* **
329585 CCCGATGGTGGAAAATTGGTGTTTTAGAAATA
190 CCTGATGGTGGAAAATTGGTACTTTAGAAATA
329617 TGAAAGCTCA
Statistics
Matches: 377, Mismatches: 68, Indels: 31
0.79 0.14 0.07
Matches are distributed among these distances:
236 10 0.03
237 264 0.70
238 101 0.27
239 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (235 bp):
GTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGTGAAAAATCAGTGTTTTAGAAATAA
AACTAGGGTTAGAGTATCCCATCGAAAATAAAGGGATTGGAGTATCCTCGATGGTGAAAAATTAG
TGTTTTAGAAATAAAACAGGATTAAAGTATCCCCTCGAAAATAACAAGGTTGGAGTATTCCTGAT
GGTGGAAAATTGGTACTTTAGAAATAAAACCGAGGTTAGA
Found at i:330567 original size:22 final size:23
Alignment explanation
Indices: 330519--330567 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
330509 ACTTTTTACT
***
330519 TAAAAACATTTGAATTATGGTTC
1 TAAAAACATTTGAATTATAACTC
330542 -AAAAACATTTG-ATTATAACTC
1 TAAAAACATTTGAATTATAACTC
330563 TAAAA
1 TAAAA
330568 CTTTCATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (23 bp):
TAAAAACATTTGAATTATAACTC
Found at i:332762 original size:21 final size:22
Alignment explanation
Indices: 332720--332769 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
332710 TTTGTTGATG
332720 ATTTTG-A-TGTAAAATGAAGA
1 ATTTTGAAGTGTAAAATGAAGA
332740 ATTTTGAAGTGTAAAAT-AAGA
1 ATTTTGAAGTGTAAAATGAAGA
*
332761 ATTTCGAAG
1 ATTTTGAAG
332770 AAGATTTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.22
21 13 0.48
22 8 0.30
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (22 bp):
ATTTTGAAGTGTAAAATGAAGA
Found at i:332895 original size:13 final size:13
Alignment explanation
Indices: 332877--332903 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
332867 ATAGTAACCT
332877 TTGTATCGATACA
1 TTGTATCGATACA
332890 TTGTATCGATACA
1 TTGTATCGATACA
332903 T
1 T
332904 CTTTAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:338992 original size:33 final size:32
Alignment explanation
Indices: 338934--339002 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
338924 CCGTTAGAAG
338934 CAATGCATCGATACAATTCATCATGTATCAATA
1 CAATGCATCGATACAATTCA-CATGTATCAATA
* *
338967 CAATGTATCGATACAATATGC-CATGTATCGATA
1 CAATGCATCGATACAAT-T-CACATGTATCAATA
339000 CAA
1 CAA
339003 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (32 bp):
CAATGCATCGATACAATTCACATGTATCAATA
Found at i:339075 original size:19 final size:20
Alignment explanation
Indices: 339031--339085 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
339021 CTATCAGTTT
* * *
339031 CATGTATCGATAAAATTATC
1 CATGTATCGATACAATGATA
339051 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
*
339070 CATGTATTGATACAAT
1 CATGTATCGATACAAT
339086 ATATAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:341630 original size:79 final size:78
Alignment explanation
Indices: 341534--341832 Score: 271
Period size: 78 Copynumber: 3.8 Consensus size: 78
341524 ACAACGGGGC
* * *
341534 TGGAGTATCCCCGATTATGGAAAATCGGTGTTCTGGAAATAAAACCGAGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCTC
*
341599 GAAAATAACAGGTT
66 GAAAATAAC-GGAT
* * * *** * * *
341613 TGGAGTATCCCTGATTAT-AAAAATCGATGCTTTAGAAATAAGGTCGGGGTTAGAGTATCCCGTC
1 TGGAGTATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCTC
* *
341677 GAATATAACGGGGT
66 GAAAATAAC-GGAT
* * * ** * *
341691 TGGAGTATCCCCAATTGTGAAAAAACTGGCGTTTTGGGAATAAAATC-AGGGTTGGAGTATCCCC
1 TGGAGTATCCCCGATTATGAAAAATC-GATGTTTTGGAAATAAAACCGA-GGTTGGAGTATCCCC
*
341755 TCGGAAATAACGAGAT
64 TCGAAAATAACG-GAT
* * ** *
341771 TAGAGCATCCCCGATTATGAAAAAATC-ATGTTTTCAAAATAAAACCGGGGTTGGAGTATCCC
1 TGGAGTATCCCCGATTATG-AAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGAGTATCCC
341833 TGAGATGAAG
Statistics
Matches: 170, Mismatches: 44, Indels: 12
0.75 0.19 0.05
Matches are distributed among these distances:
78 61 0.36
79 51 0.30
80 52 0.31
81 6 0.04
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (78 bp):
TGGAGTATCCCCGATTATGAAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCTC
GAAAATAACGGAT
Found at i:341751 original size:80 final size:78
Alignment explanation
Indices: 341526--341832 Score: 269
Period size: 79 Copynumber: 3.9 Consensus size: 78
341516 TGGAGATAAC
* * * * *
341526 AACGGGGCTGGAGTATCCCCGATTATGGAAAATCGGTGTTCTGGAAATAAAA-CCGAGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAAACGGTGTTTTGGAAATAAAATCAG-GGTTGGAG
341590 TATCCCCTCGAAAAT
65 TATCCCCTCG-AAAT
* * * * * * * ** * *
341605 AACAGGTTTGGAGTATCCCTGATTAT-AAAAATCGATGCTTTAGAAATAAGGTCGGGGTTAGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAAACGGTGTTTTGGAAATAAAATCAGGGTTGGAGT
*
341669 ATCCCGTCGAATAT
66 ATCCCCTCGAA-AT
* * * *
341683 AACGGGGTTGGAGTATCCCCAATTGTGAAAAAACTGGCGTTTTGGGAATAAAATCAGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAAAC-GGTGTTTTGGAAATAAAATCAGGGTTGGAG
341748 TATCCCCTCGGAAAT
65 TATCCCCTC-GAAAT
* * * * * ** * *
341763 AACGAGATTAGAGCATCCCCGATTATGAAAAAATC-ATGTTTTCAAAATAAAACCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAAA-CGGTGTTTTGGAAATAAAATCAGGGTTGGAG
341827 TATCCC
65 TATCCC
341833 TGAGATGAAG
Statistics
Matches: 179, Mismatches: 43, Indels: 12
0.76 0.18 0.05
Matches are distributed among these distances:
77 2 0.01
78 57 0.32
79 58 0.32
80 58 0.32
81 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAAACGGTGTTTTGGAAATAAAATCAGGGTTGGAGT
ATCCCCTCGAAAT
Found at i:344540 original size:13 final size:13
Alignment explanation
Indices: 344522--344547 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
344512 TACAGCAAGT
344522 ATGTATCGATACA
1 ATGTATCGATACA
344535 ATGTATCGATACA
1 ATGTATCGATACA
344548 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:346217 original size:21 final size:21
Alignment explanation
Indices: 346184--346228 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
346174 TTGCAAGTTG
*
346184 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
346206 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
346226 AAA
1 AAA
346229 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:348052 original size:15 final size:15
Alignment explanation
Indices: 348032--348062 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
348022 TAAAAATGTC
*
348032 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
348047 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
348062 C
1 C
348063 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:350157 original size:20 final size:20
Alignment explanation
Indices: 350078--350157 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
350068 AATGTCCAAA
*
350078 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
350098 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
350123 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
350143 TTGTATCGATACATT
1 ATGTATCGATACATT
350158 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:350161 original size:13 final size:13
Alignment explanation
Indices: 350143--350181 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
350133 ACATTTTTCT
350143 TTGTATCGATACA
1 TTGTATCGATACA
350156 TTGTATCGATACA
1 TTGTATCGATACA
*
350169 CTGTATCGATACA
1 TTGTATCGATACA
350182 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:353232 original size:13 final size:13
Alignment explanation
Indices: 353214--353239 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
353204 TACAGCAAGT
353214 ATGTATCGATACA
1 ATGTATCGATACA
353227 ATGTATCGATACA
1 ATGTATCGATACA
353240 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:356043 original size:64 final size:60
Alignment explanation
Indices: 355967--356527 Score: 495
Period size: 60 Copynumber: 9.3 Consensus size: 60
355957 GAAAGAGCAA
* * *
355967 TCCTACTTTTTGAGGACTAGAAA-GTGCCACTAGCTTGTG-GGGTTTTCAAAGAAAAGAGGAAGT
1 TCCTACTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGTTTT-AAA-AAAA-A--AAGT
356030 G
60 G
* *
356031 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTGAAAAAAAATGTG
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAAAAAAAGTG
* * * *
356091 TCTTACTCTTTGAGGACTAAAAGGTGCCACCAACGTGTGTGGGCTTTAAAAAGAAAAG-G
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAAAAAAAGTG
* * * * **
356150 CATCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTT-AAAAGGAAAGTG
1 --TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAAAAAAAGTG
* * * * * * *
356211 TCTTGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAAAAAGGCG
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAAAAAAAGTG
* * * * * * *
356271 TCCTGCTCTTTAAGGACTGAAAGATGCCACCAACTCGTGTGGGTTTTAAAAGAAAAAGGCG
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAA-AAAAAAGTG
* ** * * ** * *
356332 TCATGTTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCG
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGG-TTTTAAAAAAAAAAGTG
* * * * * **
356393 TCCTGCTCTTTGAGGACTGAAAGGTGCCACTAACCTGTGTGGGCTTTAAAAGGAAAA-TG
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAAAAAAAGTG
* * * * * * * *
356452 TCTTGCTCTTTAAGGATTGAAAGGTGCCACCAATTTGTGTGGGCTTTAAAAAGGAAAA-TG
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAA-AAAAAGTG
*
356512 TCCTGCTCTTTGAGGA
1 TCCTACTCTTTGAGGA
356528 TTGAAAGGAT
Statistics
Matches: 433, Mismatches: 55, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
59 91 0.21
60 148 0.34
61 139 0.32
62 7 0.02
63 7 0.02
64 34 0.08
65 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (60 bp):
TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAAAAAAAGTG
Done.