Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 89 of 186
Found at i:28892852 original size:13 final size:13
Alignment explanation
Indices: 28892834--28892860 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28892824 ACCTACTTAA
28892834 AATTTTAGTTTAG
1 AATTTTAGTTTAG
28892847 AATTTTAGTTTAG
1 AATTTTAGTTTAG
28892860 A
1 A
28892861 TGTAGAGATT
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:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
AATTTTAGTTTAG
Found at i:28901966 original size:176 final size:176
Alignment explanation
Indices: 28901672--28902152 Score: 737
Period size: 176 Copynumber: 2.7 Consensus size: 176
28901662 GAAGTTGTAG
*
28901672 GAAGCAGGCTAAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCGAGGATGGCG
1 GAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCGAGGATGGCG
* *
28901737 AGCCTTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCTTTGAAGTTG
66 AGCCTTATCTCTATGTATTGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCTTTGAAGTTG
*
28901802 CAGAGAGTAGGTTGAAGATACAAGTCTTATCTTCCTAAAGTTACAA
131 CAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTAAAGTTACAA
28901848 GAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCGAGGATGGCG
1 GAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCGAGGATGGCG
*
28901913 AGCCTTATCTCTATGCATTGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCTTTGAAGTTG
66 AGCCTTATCTCTATGTATTGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCTTTGAAGTTG
* * * *
28901978 CAGAGAGCAGGTTGAAGTTACAAGTCTTATCTTCCTGAAGTTGCAG
131 CAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTAAAGTTACAA
* * * * *
28902024 GAAGCAGACTGAAAACTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAGACGGCG
1 GAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCGAGGATGGCG
** * ** * ** * **
28902089 AATCTTATCTGTATGTATTGGCAATGGAGCAGATTTAAGTTACTAGCCTTATCTCCCTGAAGTT
66 AGCCTTATCTCTATGTATTGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCTTTGAAGTT
28902153 TCAGTGGAGC
Statistics
Matches: 279, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
176 279 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (176 bp):
GAAGCAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTATTGAGCAGATCGAGGATGGCG
AGCCTTATCTCTATGTATTGGTTATGGAGCAGATTTTAGCCACTAACCTTATCTCTTTGAAGTTG
CAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTAAAGTTACAA
Found at i:28903700 original size:23 final size:23
Alignment explanation
Indices: 28903645--28903704 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
28903635 TTCTCGTATT
* *
28903645 ATTTTATGTAAATATTTTCTTAA
1 ATTTTATATATATATTTTCTTAA
28903668 ATTTTATATATATATTTT-TTAA
1 ATTTTATATATATATTTTCTTAA
*
28903690 ATTTATTTATATATA
1 ATTT-TATATATATA
28903705 ATTTGGTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTTATATATATATTTTCTTAA
Found at i:28907001 original size:7 final size:7
Alignment explanation
Indices: 28906991--28907016 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28906981 ATTCTAACTC
28906991 TTAAATA
1 TTAAATA
28906998 TTAAATA
1 TTAAATA
28907005 TTAAATA
1 TTAAATA
28907012 TTAAA
1 TTAAA
28907017 GTTTAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATA
Found at i:28907015 original size:21 final size:21
Alignment explanation
Indices: 28906966--28907016 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
28906956 TTAAAATTTA
*
28906966 AAATA-TAAATGTTAAATTCT
1 AAATATTAAATATTAAATTCT
* *
28906986 AACTCTTAAATATTAAATAT-T
1 AAATATTAAATATTAAAT-TCT
28907007 AAATATTAAA
1 AAATATTAAA
28907017 GTTTAATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATATTAAATATTAAATTCT
Found at i:28907942 original size:22 final size:21
Alignment explanation
Indices: 28907899--28907943 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
28907889 TAATATTATT
* *
28907899 ATATTAATTTATAATTTTAAA
1 ATATTAATTTATAATATCAAA
28907920 ATATTAATATTATAATATCAAA
1 ATATTAAT-TTATAATATCAAA
28907942 AT
1 AT
28907944 TCTTCAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTAATTTATAATATCAAA
Found at i:28908518 original size:23 final size:26
Alignment explanation
Indices: 28908465--28908525 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 26
28908455 TGCAGAAACT
*
28908465 TATGACATATTTTAACTTGATATAGAA
1 TATGA-ATATTTCAACTTGATATAGAA
28908492 TATGAATATTTCAA-TT-ATATA-AA
1 TATGAATATTTCAACTTGATATAGAA
*
28908515 TATGAGTATTT
1 TATGAATATTT
28908526 GTTTAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 12 0.38
24 5 0.16
25 2 0.06
26 8 0.25
27 5 0.16
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (26 bp):
TATGAATATTTCAACTTGATATAGAA
Found at i:28916408 original size:8 final size:8
Alignment explanation
Indices: 28916387--28916416 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
28916377 ATTTCTAGGA
28916387 AAAAAATT
1 AAAAAATT
28916395 ATAAAAATT
1 A-AAAAATT
28916404 AAAAAATT
1 AAAAAATT
28916412 AAAAA
1 AAAAA
28916417 TATGTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:28917206 original size:24 final size:23
Alignment explanation
Indices: 28917179--28917237 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
28917169 TTATATAATT
*
28917179 ATTTTATATTCATATTATACTTTAA
1 ATTTTATATTCAT-TCATA-TTTAA
* *
28917204 TTTTTTTATTCATTCATATTTAAA
1 ATTTTATATTCATTCATATTT-AA
28917228 ATTTTATATT
1 ATTTTATATT
28917238 TATAAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.11
24 14 0.50
25 11 0.39
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTATATTCATTCATATTTAA
Found at i:28924045 original size:76 final size:76
Alignment explanation
Indices: 28923912--28924059 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 76
28923902 AACAAAGAGA
* * * * **
28923912 TTGAACCAATTGTATTAGAAACTACACGAAATAGATAAAAATTGAAATTTGGAACAAAAATCGGT
1 TTGAACCAATTGTATTAGAAACTACACGAAAAAGATAAAAATCGAAACTAGGAACAAAAATCAAT
28923977 AGTTGAAGGGG
66 AGTTGAAGGGG
* *
28923988 TTGAACCAATTGTATTA-AAAGCTGCTCGAAACAAG-TAAAAATCGAAAACTAGG-ACAAAAATC
1 TTGAACCAATTGTATTAGAAA-CTACACGAAA-AAGATAAAAATCG-AAACTAGGAACAAAAATC
28924050 AATAGTTGAA
63 AATAGTTGAA
28924060 CAGGTTGTAC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 3 0.05
76 50 0.82
77 8 0.13
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (76 bp):
TTGAACCAATTGTATTAGAAACTACACGAAAAAGATAAAAATCGAAACTAGGAACAAAAATCAAT
AGTTGAAGGGG
Found at i:28930363 original size:30 final size:31
Alignment explanation
Indices: 28930329--28930386 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28930319 AAAAATTGAA
28930329 ATGATTAGAATA-CCTTAAAAGAATCTAGCT
1 ATGATTAGAATACCCTTAAAAGAATCTAGCT
**
28930359 ATGATTAGAATACCCTTAGCAGAATCTA
1 ATGATTAGAATACCCTTAAAAGAATCTA
28930387 CATAAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (31 bp):
ATGATTAGAATACCCTTAAAAGAATCTAGCT
Found at i:28930454 original size:13 final size:13
Alignment explanation
Indices: 28930436--28930460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28930426 TTAATCATAT
28930436 TTTAATATAATTA
1 TTTAATATAATTA
28930449 TTTAATATAATT
1 TTTAATATAATT
28930461 TAATAAAAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAATATAATTA
Found at i:28943413 original size:46 final size:46
Alignment explanation
Indices: 28943346--28943480 Score: 182
Period size: 46 Copynumber: 2.9 Consensus size: 46
28943336 GTGTGCTCTC
*
28943346 TGATATGAAATGTATAAGATCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
28943392 TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
* * * * * * *
28943438 TGACA-GAAAATGAGTAAGACCATAGTTGGAAGACACTATGGCA
1 TGATATG-AAATGAATAAGATCATGGTTGAAAGATACCATGGCA
28943481 TCATATCAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 79 0.99
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (46 bp):
TGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACG
Found at i:28948035 original size:23 final size:21
Alignment explanation
Indices: 28947984--28948037 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
28947974 TATTAAATAA
*
28947984 TAATTTAATTTAATTTTTATT
1 TAATTAAATTTAATTTTTATT
28948005 TAATATTAAATTTAAATTTTTTATT
1 T-A-ATTAAATTT-AA-TTTTTATT
28948030 TAATTAAA
1 TAATTAAA
28948038 AATGAAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 1 0.04
23 14 0.50
24 3 0.11
25 9 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTAAATTTAATTTTTATT
Found at i:28948040 original size:25 final size:23
Alignment explanation
Indices: 28947990--28948038 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
28947980 ATAATAATTT
*
28947990 AATTTAATTTTTATTTAATATTA
1 AATTTAATTTTTATTTAATATAA
28948013 AATTTAAATTTTTTATTTAAT-TAA
1 AATTT-AA-TTTTTATTTAATATAA
28948037 AA
1 AA
28948039 ATGAAAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 6 0.26
25 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTTAATTTTTATTTAATATAA
Found at i:28949223 original size:59 final size:62
Alignment explanation
Indices: 28949157--28949317 Score: 161
Period size: 59 Copynumber: 2.7 Consensus size: 62
28949147 TTATTATAAC
* * * * * *
28949157 ATTTGGTACTTAAACTTGACATTTTTTTTTCTAATTTTGTGCATAAA-TTTTTT-TGTCC-A
1 ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTACATAAACTTTTTTGGGGCCTA
* * *
28949216 ATTTGGTACTTTAACTTGACA--CTTTTTCCTAATATGGTACCTAAACTTTTTTGGGGCCTA
1 ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTACATAAACTTTTTTGGGGCCTA
* * * * *
28949276 ATTTGGTACTTGAACTTGGCATTTTTTTCCCTAGTTTGGTAC
1 ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTAC
28949318 CTAAGCTATT
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
57 18 0.22
58 6 0.07
59 23 0.28
60 20 0.24
62 15 0.18
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (62 bp):
ATTTGGTACTTAAACTTGACATTTTTTTTCCTAATATGGTACATAAACTTTTTTGGGGCCTA
Found at i:28949292 original size:60 final size:63
Alignment explanation
Indices: 28949215--28949330 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 63
28949205 TTTTTTGTCC
*
28949215 AATTTGGTACTTTAACTTGACA-CTTTTT-CCTAATATGGTACCTAAACT-TTTTTGGGGCCT
1 AATTTGGTACTTGAACTTGACATCTTTTTCCCTAATATGGTACCTAAACTATTTTTGGGGCCT
* * * * *
28949275 AATTTGGTACTTGAACTTGGCATTTTTTTCCCTAGTTTGGTACCTAAGCTATTTTT
1 AATTTGGTACTTGAACTTGACATCTTTTTCCCTAATATGGTACCTAAACTATTTTT
28949331 TAGGTTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 20 0.43
61 5 0.11
62 17 0.36
63 5 0.11
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46
Consensus pattern (63 bp):
AATTTGGTACTTGAACTTGACATCTTTTTCCCTAATATGGTACCTAAACTATTTTTGGGGCCT
Found at i:28949808 original size:60 final size:61
Alignment explanation
Indices: 28949730--28949845 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 61
28949720 ATCGAACAAA
* * *
28949730 AAAAGAAGATTAGATACCAAATTAGGAAAAAGAGTTAAGTTTAGGTATCAAATTAGACACC
1 AAAAGAAGATTAGATACCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTAGACACC
* ** **
28949791 AAAA-AAGATTA-ACTACCAACTTTTAAAAAATTGTCAAGTTTAGGTACCAAATTAG
1 AAAAGAAGATTAGA-TACCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTAG
28949846 GAAGTGTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.02
60 41 0.89
61 4 0.09
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (61 bp):
AAAAGAAGATTAGATACCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTAGACACC
Found at i:28949885 original size:31 final size:31
Alignment explanation
Indices: 28949816--28949901 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 31
28949806 CCAACTTTTA
*
28949816 AAAAATTGTCAAGTTTAGGTACCAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
*
28949847 ---AAGTGTCAAGTTTAGGTACTAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
**
28949875 AAAAAGTGTCAAGTTTATATACCAAAT
1 AAAAAGTGTCAAGTTTAGGTACCAAAT
28949902 GTTATATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 26 0.55
31 21 0.45
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
Found at i:28950291 original size:19 final size:17
Alignment explanation
Indices: 28950267--28950301 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
28950257 ATTGTTAGGA
28950267 TATTGTATAACTTTTATTT
1 TATTGT-TAA-TTTTATTT
28950286 TATTGTTAATTTTATT
1 TATTGTTAATTTTATT
28950302 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTATTT
Found at i:28954555 original size:30 final size:30
Alignment explanation
Indices: 28954504--28954560 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
28954494 GAAAATTTGA
28954504 AATTTAGTTCCTATATTTTTAT-TTTTAGG
1 AATTTAGTTCCTATATTTTTATATTTTAGG
* *
28954533 AATTTAGTTGCTCTACTTTTTATATTTT
1 AATTTAGTTCCTATA-TTTTTATATTTT
28954561 TAAATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.54
30 7 0.29
31 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (30 bp):
AATTTAGTTCCTATATTTTTATATTTTAGG
Found at i:28957096 original size:7 final size:7
Alignment explanation
Indices: 28957084--28957109 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28957074 TAGTCGTTTT
28957084 GTATTTA
1 GTATTTA
28957091 GTATTTA
1 GTATTTA
28957098 GTATTTA
1 GTATTTA
28957105 GTATT
1 GTATT
28957110 ATGTATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:28957115 original size:14 final size:13
Alignment explanation
Indices: 28957081--28957115 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
28957071 AAATAGTCGT
28957081 TTTGTATTTAGTA
1 TTTGTATTTAGTA
28957094 TTTAGTATTTAGTA
1 TTT-GTATTTAGTA
28957108 TTATGTAT
1 TT-TGTAT
28957116 ATCAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (13 bp):
TTTGTATTTAGTA
Found at i:28958020 original size:21 final size:21
Alignment explanation
Indices: 28957971--28958022 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
28957961 CACCCACAAC
*
28957971 CGAAGCAATCACAACCCCCGT
1 CGAAGCAACCACAACCCCCGT
*
28957992 CG-AGCAACCACAACCTCCGT
1 CGAAGCAACCACAACCCCCGT
28958012 CGAAGCAACCA
1 CGAAGCAACCA
28958023 ATGAGGAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.35, C:0.42, G:0.15, T:0.08
Consensus pattern (21 bp):
CGAAGCAACCACAACCCCCGT
Found at i:28960194 original size:13 final size:13
Alignment explanation
Indices: 28960176--28960200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28960166 TTTTATGTTT
28960176 TATTATATTATAC
1 TATTATATTATAC
28960189 TATTATATTATA
1 TATTATATTATA
28960201 TACTTAAATA
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATTATAC
Found at i:28963943 original size:125 final size:126
Alignment explanation
Indices: 28963718--28964095 Score: 463
Period size: 126 Copynumber: 3.0 Consensus size: 126
28963708 GGCCAATCAT
* * * * * *
28963718 GAACTACTGTAGAAAAAGAGCGTCTATGTGGGAGCTTTTTTCAAAAATTTTGGTGACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCATC
* * * *
28963783 CTGCTTGAAGCATTTTTCACACTATTTGTTCAGAAACATCTTCTTAAAAATA-TTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTCAG
* * * *
28963843 GAACTACTATAGAAAAAGAACGTCCACGTGGGAGCCTTTTTCTATAATTTTGCTGACAGTGTATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCATC
* * *
28963908 CTGCTTGAAGCGTTTTTGACACTATTTATTTAGAAACGTCTT-TTCAAAATTATTTTTTCAC
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTT-AAAATTATTTTTTCAG
* *** * * * *
28963969 GAACTACTGTAGAAAAAGAGCGTCCACATAAAAGATTTTTTCTGTAATTTTGTTGATAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCATC
* * * * *
28964034 TTGCTTGAAACGTTTTTGACATTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTCAG
28964095 G
1 G
28964096 GTACAAAATA
Statistics
Matches: 213, Mismatches: 37, Indels: 5
0.84 0.15 0.02
Matches are distributed among these distances:
124 2 0.01
125 98 0.46
126 112 0.53
127 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTCAG
Found at i:28964226 original size:30 final size:29
Alignment explanation
Indices: 28964181--28964277 Score: 86
Period size: 34 Copynumber: 3.1 Consensus size: 29
28964171 ATTTAACCCT
* *
28964181 AAACCCTACACCCTAATTTAATTTATTTA
1 AAACCATAAACCCTAATTTAATTTATTTA
* *
28964210 AAACCCTAGAATCCTAATTTACTTAATTTATTTA
1 AAACCATA-AACCCTAA--T--TTAATTTATTTA
* *
28964244 GAAATCATAAACCCTAATTTAACTTATTTA
1 -AAACCATAAACCCTAATTTAATTTATTTA
28964274 AAAC
1 AAAC
28964278 ACTAATTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
29 11 0.20
30 17 0.31
32 2 0.04
34 19 0.35
35 6 0.11
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (29 bp):
AAACCATAAACCCTAATTTAATTTATTTA
Found at i:28964236 original size:34 final size:35
Alignment explanation
Indices: 28964198--28964273 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
28964188 ACACCCTAAT
* *
28964198 TTAATTTATTTA-AAACCCTAGAATCCTAATTT-AC
1 TTAATTTATTTAGAAACCATA-AACCCTAATTTAAC
*
28964232 TTAATTTATTTAGAAATCATAAACCCTAATTTAAC
1 TTAATTTATTTAGAAACCATAAACCCTAATTTAAC
28964267 TT-ATTTA
1 TTAATTTA
28964274 AAACACTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 27 0.73
35 10 0.27
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.43
Consensus pattern (35 bp):
TTAATTTATTTAGAAACCATAAACCCTAATTTAAC
Found at i:28964408 original size:34 final size:34
Alignment explanation
Indices: 28964340--28964409 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 34
28964330 TAGAACCCTA
*
28964340 ACTTAATTTATTTAAAACCTTAAAAACCCCAATTT
1 ACTTAATTTATTTAAAACCCT-AAAACCCCAATTT
*
28964375 ACTTAATTTATTTAACAACCCT-AAACCCTAATTT
1 ACTTAATTTATTTAA-AACCCTAAAACCCCAATTT
28964409 A
1 A
28964410 AATAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 12 0.38
35 15 0.47
36 5 0.16
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.37
Consensus pattern (34 bp):
ACTTAATTTATTTAAAACCCTAAAACCCCAATTT
Found at i:28964416 original size:34 final size:34
Alignment explanation
Indices: 28964343--28964425 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 34
28964333 AACCCTAACT
* **
28964343 TAATTTATTTAAAACCTTAAAAACCCCAATTTACT
1 TAATTTATTTAAAACCCT-AAAACCCCAATTTAAA
*
28964378 TAATTTATTTAACAACCCT-AAACCCTAATTTAAA
1 TAATTTATTTAA-AACCCTAAAACCCCAATTTAAA
28964412 TAATTT-TTATAAAA
1 TAATTTATT-TAAAA
28964426 TAATACTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
33 4 0.10
34 21 0.50
35 12 0.29
36 5 0.12
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.39
Consensus pattern (34 bp):
TAATTTATTTAAAACCCTAAAACCCCAATTTAAA
Found at i:28965770 original size:24 final size:24
Alignment explanation
Indices: 28965743--28965794 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
28965733 ATAAAAGAAG
28965743 TAGAGATCTAATTCTAATAACTAT
1 TAGAGATCTAATTCTAATAACTAT
28965767 TAGAGATCTAATTCTAATAACTAT
1 TAGAGATCTAATTCTAATAACTAT
28965791 TAGA
1 TAGA
28965795 ATTTAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (24 bp):
TAGAGATCTAATTCTAATAACTAT
Found at i:28969801 original size:28 final size:27
Alignment explanation
Indices: 28969764--28969874 Score: 90
Period size: 26 Copynumber: 4.1 Consensus size: 27
28969754 AAATTTGTTA
*
28969764 TTTTATTTTTCAATTTATTTATATTCATT
1 TTTTA-TTTTCAATTT-TATATATTCATT
28969793 TTTTATTTTC-ATTTTATATATTC-TT
1 TTTTATTTTCAATTTTATATATTCATT
*
28969818 TATTTTTATTTCAA-TTT-TATA-T-ATT
1 T-TTTAT-TTTCAATTTTATATATTCATT
* * *
28969843 TTTTATTTTCAATATATATACATTAATT
1 TTTTATTTTCAAT-TTTATATATTCATT
28969871 TTTT
1 TTTT
28969875 TGAAGTTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
23 6 0.09
24 4 0.06
25 9 0.13
26 19 0.28
27 12 0.18
28 13 0.19
29 5 0.07
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTATTTTCAATTTTATATATTCATT
Found at i:28969860 original size:22 final size:22
Alignment explanation
Indices: 28969820--28969862 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28969810 ATATTCTTTA
*
28969820 TTTTTATTTCAATTTTATATAT
1 TTTTTATTTCAATTATATATAT
28969842 TTTTTATTTTCAA-TATATATA
1 TTTTTA-TTTCAATTATATATA
28969863 CATTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTATTTCAATTATATATAT
Found at i:28971853 original size:43 final size:43
Alignment explanation
Indices: 28971792--28971879 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
28971782 TAAAATAGAC
* *
28971792 TAAAATTAGAGTTCTAATATGATTATAATATTGCTAGAATAAT
1 TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
28971835 TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
1 TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
28971878 TA
1 TA
28971880 GAGTTTAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (43 bp):
TAAAACTAGAGTTCTAATATGATTATAATATTCCTAGAATAAT
Found at i:28971859 original size:23 final size:22
Alignment explanation
Indices: 28971792--28971864 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
28971782 TAAAATAGAC
28971792 TAAAATTAGAGTTCTAATATGAT
1 TAAAA-TAGAGTTCTAATATGAT
* *
28971815 TATAAT--A-TTGCTAGA-ATAAT
1 TAAAATAGAGTT-CTA-ATATGAT
28971835 TAAAACTAGAGTTCTAATATGAT
1 TAAAA-TAGAGTTCTAATATGAT
*
28971858 TATAATA
1 TAAAATA
28971865 TTCCTAGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 15
0.66 0.09 0.26
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 2 0.05
22 4 0.11
23 16 0.42
24 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (22 bp):
TAAAATAGAGTTCTAATATGAT
Found at i:28982266 original size:25 final size:26
Alignment explanation
Indices: 28982227--28982278 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
28982217 TCCGAGCTAT
28982227 ATTATATTGGGAAGCTCAAGAGAGCC
1 ATTATATTGGGAAGCTCAAGAGAGCC
*
28982253 ATTA-ATTGGGAAGCTCATGAGAGCC
1 ATTATATTGGGAAGCTCAAGAGAGCC
28982278 A
1 A
28982279 AACATCGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
ATTATATTGGGAAGCTCAAGAGAGCC
Found at i:28982293 original size:25 final size:25
Alignment explanation
Indices: 28982236--28982328 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
28982226 TATTATATTG
* * *
28982236 GGAAGCTCAAGAGAGCC-ATTAATTG
1 GGAAGCTCATGAGAGCCAAATAA-TA
* *
28982261 GGAAGCTCATGAGAGCCAAA-CATC
1 GGAAGCTCATGAGAGCCAAATAATA
* *
28982285 GGAATGCTCATAAGAGCTAAATAATA
1 GGAA-GCTCATGAGAGCCAAATAATA
*
28982311 GGAAGCTCGTGAGAGCCA
1 GGAAGCTCATGAGAGCCA
28982329 TTGTGTGTCT
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
24 5 0.09
25 42 0.78
26 7 0.13
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCAAATAATA
Found at i:28984324 original size:63 final size:63
Alignment explanation
Indices: 28984225--28984348 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
28984215 CTAATAACTA
* * * * *
28984225 TTATTATATGAGAATTTGATTAACGACAGATATTTCTCCCAATTGCCTTCGAACTCTAAAATG
1 TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCCAATTACCTTCAAACTCTAAAATG
*
28984288 TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCTAATTACCTTCAAACTCTAAAA
1 TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCCAATTACCTTCAAACTCTAAAA
28984349 CACAACACCG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (63 bp):
TTATTATATGAGAATTCGATTAACAACAAATATTTCTCCCAATTACCTTCAAACTCTAAAATG
Found at i:28991578 original size:16 final size:17
Alignment explanation
Indices: 28991550--28991583 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
28991540 CCAATTTGTG
28991550 AAAATAAATAAAAATAA
1 AAAATAAATAAAAATAA
28991567 AAAATAAA-AAAAATAA
1 AAAATAAATAAAAATAA
28991583 A
1 A
28991584 GAACAGACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAATAAAAATAA
Found at i:29008875 original size:28 final size:29
Alignment explanation
Indices: 29008834--29008888 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
29008824 AGTCATTTAT
*
29008834 TATTTTTCTATGTTAGTATAATTTGATTA
1 TATTTTTCTATGTTAATATAATTTGATTA
* *
29008863 TATTTTT-TTTGTTAATATAGTTTGAT
1 TATTTTTCTATGTTAATATAATTTGAT
29008889 GGCATGTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.25, C:0.02, G:0.11, T:0.62
Consensus pattern (29 bp):
TATTTTTCTATGTTAATATAATTTGATTA
Found at i:29008934 original size:81 final size:82
Alignment explanation
Indices: 29008799--29008961 Score: 274
Period size: 81 Copynumber: 2.0 Consensus size: 82
29008789 GTTCTTTTGT
* * *
29008799 TAGTTTCATGTCATGTACCTAAGAGAGTCATTTATTATTTTTCTATGTTAGTATAATTTGATTAT
1 TAGTTTCATGGCATGTACCTAAGAGAGTCATTTAGTATTTTGCTATGTTAGTATAATTTGATTAT
*
29008864 AT-TTTTTTTGTTAATA
66 ATGTTTTGTTGTTAATA
*
29008880 TAGTTTGATGGCATGTACCTAAGAGAGTCATTTAGTATTTTGCTATGTTAGTATAATTTGATTAT
1 TAGTTTCATGGCATGTACCTAAGAGAGTCATTTAGTATTTTGCTATGTTAGTATAATTTGATTAT
29008945 ATGTTTTGTTGTTAATA
66 ATGTTTTGTTGTTAATA
29008962 GACAATATGC
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
81 63 0.83
82 13 0.17
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (82 bp):
TAGTTTCATGGCATGTACCTAAGAGAGTCATTTAGTATTTTGCTATGTTAGTATAATTTGATTAT
ATGTTTTGTTGTTAATA
Found at i:29011091 original size:23 final size:23
Alignment explanation
Indices: 29011028--29011117 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
29011018 TAAATGCTAG
*
29011028 CAAAAGTATGTTTCAAATGTTGT-
1 CAAAA-TATGTTTTAAATGTTGTC
* * * *
29011051 TAAACTAAGATTTAAATGTTGTC
1 CAAAATATGTTTTAAATGTTGTC
**
29011074 CAAAATATGTTTTAAATGTCATC
1 CAAAATATGTTTTAAATGTTGTC
** *
29011097 CAAAACGTGTTTTAAGTGTTG
1 CAAAATATGTTTTAAATGTTG
29011118 CCTAACCTAG
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
22 14 0.28
23 36 0.72
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (23 bp):
CAAAATATGTTTTAAATGTTGTC
Found at i:29011747 original size:72 final size:72
Alignment explanation
Indices: 29011635--29011859 Score: 252
Period size: 72 Copynumber: 3.1 Consensus size: 72
29011625 TTATTTTTTG
** * * * *
29011635 ATTTTACCGACCAGCGCAGAACACACTTATTTGTCAGTTATACTAACTAGTGCTGGGCATACTCA
1 ATTTTACCGACCAGCGCAGGGCACACTTATTTGTCAGTTATACTAACCAATGCTGGGCACAATCA
29011700 TTTTTCA
66 TTTTTCA
* * * * * *
29011707 ATTTTACCGACCAGCGCAGGGTACACTTATTTGTCGGTTATACCAACCAATACTGGGCACATTTA
1 ATTTTACCGACCAGCGCAGGGCACACTTATTTGTCAGTTATACTAACCAATGCTGGGCACAATCA
**
29011772 TTTTTTG
66 TTTTTCA
* ** * * * * *
29011779 GTTTTACCGACCAATGCAAGGCGCAATTATTTGTCAGTTATACTGACCAATGTTGGGCACAATCA
1 ATTTTACCGACCAGCGCAGGGCACACTTATTTGTCAGTTATACTAACCAATGCTGGGCACAATCA
29011844 TTTTTCA
66 TTTTTCA
29011851 ATTTTACCG
1 ATTTTACCG
29011860 GCTAGCCCAA
Statistics
Matches: 123, Mismatches: 30, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
72 123 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (72 bp):
ATTTTACCGACCAGCGCAGGGCACACTTATTTGTCAGTTATACTAACCAATGCTGGGCACAATCA
TTTTTCA
Found at i:29015023 original size:49 final size:49
Alignment explanation
Indices: 29014966--29015197 Score: 221
Period size: 49 Copynumber: 4.7 Consensus size: 49
29014956 CTGGTACGCA
* * *
29014966 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGCACACG
1 TAGTAGCCTACACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* * ** * *
29015015 TAGTAGCCTGCACTTAGTACTACACATATGACCTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACATGTGACC-AATTATCCGGTACACG
* * * * * * *
29015065 TAGTAGCCTATACTTAGTACTACGCACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTACACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACACG
* * * *
29015116 TAGTAGCCTCCACTTAGTACTACACATGAGACTAATTATTCGGTACACG
1 TAGTAGCCTACACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* * * *
29015165 TACTAGCCCACATTTAGTACTACACACGTGACC
1 TAGTAGCCTACACTTAGTACTACACATGTGACC
29015198 TCACAACAGA
Statistics
Matches: 144, Mismatches: 36, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
49 67 0.47
50 42 0.29
51 35 0.24
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTACACTTAGTACTACACATGTGACCAATTATCCGGTACACG
Found at i:29015085 original size:50 final size:49
Alignment explanation
Indices: 29014966--29015087 Score: 154
Period size: 50 Copynumber: 2.5 Consensus size: 49
29014956 CTGGTACGCA
* ** *
29014966 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGCACACG
1 TAGTAGCCTGCACTTAGTACTACACATACGACCAACCATCCGACACACG
* * *
29015015 TAGTAGCCTGCACTTAGTACTACACATATGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATACGACC-AACCATCCGACACACG
**
29015065 TAGTAGCCTATACTTAGTACTAC
1 TAGTAGCCTGCACTTAGTACTAC
29015088 GCACGTGATC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
49 31 0.49
50 32 0.51
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATACGACCAACCATCCGACACACG
Found at i:29015474 original size:27 final size:27
Alignment explanation
Indices: 29015444--29015497 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
29015434 TCATACAACC
* *
29015444 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
29015471 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
29015498 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:29025280 original size:13 final size:13
Alignment explanation
Indices: 29025262--29025287 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29025252 ACGGAATTGG
29025262 ATTTCGAGTTTCA
1 ATTTCGAGTTTCA
29025275 ATTTCGAGTTTCA
1 ATTTCGAGTTTCA
29025288 TAACTCGAGA
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:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTTCGAGTTTCA
Found at i:29034130 original size:25 final size:25
Alignment explanation
Indices: 29034085--29034145 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
29034075 ATTTTCGAAC
* *
29034085 AAAATTTT-CACTAAATCATCTTGT
1 AAAATTTTAGACTAAATAATCTTGT
29034109 AAAATTTTAGACTAAATAATCTTGT
1 AAAATTTTAGACTAAATAATCTTGT
29034134 AAAATTTTAGAC
1 AAAATTTTAGAC
29034146 CATAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 8 0.24
25 26 0.76
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (25 bp):
AAAATTTTAGACTAAATAATCTTGT
Found at i:29034163 original size:27 final size:25
Alignment explanation
Indices: 29034108--29034164 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
29034098 AATCATCTTG
* * **
29034108 TAAAATTTTAGACTAAATAATCTTG
1 TAAAATTTTAGACTAAAAAATATAA
29034133 TAAAATTTTAGACCATAAAAAATATAA
1 TAAAATTTTAGA-C-TAAAAAATATAA
29034160 TAAAA
1 TAAAA
29034165 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 12 0.46
26 1 0.04
27 13 0.50
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.33
Consensus pattern (25 bp):
TAAAATTTTAGACTAAAAAATATAA
Found at i:29034456 original size:23 final size:23
Alignment explanation
Indices: 29034426--29034470 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
29034416 CCAACATAAA
29034426 ACGTACTCTCCTTTGATTGCAAT
1 ACGTACTCTCCTTTGATTGCAAT
29034449 ACGTACTCTCCTTTGATTGCAA
1 ACGTACTCTCCTTTGATTGCAA
29034471 ATCATATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (23 bp):
ACGTACTCTCCTTTGATTGCAAT
Found at i:29038849 original size:46 final size:46
Alignment explanation
Indices: 29038787--29038899 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 46
29038777 TTTGACATGA
* * * * *
29038787 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACTATGGTCTTACACA-TTTCATATCAGGT
* *
29038833 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
*
29038879 TGCCATGGTATATTTCAACTA
1 TGCCATGGTATCTTTCAACTA
29038900 GAGCTGATCA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
Found at i:29039100 original size:38 final size:38
Alignment explanation
Indices: 29039024--29039107 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
29039014 GTTTAGAAAA
* *
29039024 CGGGCCGGGCCTCGAGTAAGAGTTTTTTTGCCTAGGCC
1 CGGGCCGGGCCTCGAGTAAGAGTTTTTTTACCCAGGCC
*
29039062 CGGGCCGGGCCTC-AGGTAAGAGTTTTTTTACCCGGGCC
1 CGGGCCGGGCCTCGA-GTAAGAGTTTTTTTACCCAGGCC
*
29039100 CGGCCCGG
1 CGGGCCGG
29039108 CCCGGCCCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 40 0.98
ACGTcount: A:0.12, C:0.30, G:0.36, T:0.23
Consensus pattern (38 bp):
CGGGCCGGGCCTCGAGTAAGAGTTTTTTTACCCAGGCC
Found at i:29039246 original size:21 final size:22
Alignment explanation
Indices: 29039220--29039262 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
29039210 GTTTTAAGAA
*
29039220 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
29039241 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
29039263 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:29039253 original size:12 final size:12
Alignment explanation
Indices: 29039208--29039266 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
29039198 AATTTGTGTA
* *
29039208 TTGTTTTAAGAA
1 TTGTTTTAATAT
*
29039220 TTGTTTTAGTA-
1 TTGTTTTAATAT
*
29039231 TTATTTT--TAT
1 TTGTTTTAATAT
29039241 TTGTTTTAATAT
1 TTGTTTTAATAT
*
29039253 TTGTTTTTATAT
1 TTGTTTTAATAT
29039265 TT
1 TT
29039267 TAAAATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 2 0.05
10 6 0.15
11 6 0.15
12 25 0.64
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:29039276 original size:24 final size:26
Alignment explanation
Indices: 29039249--29039298 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
29039239 ATTTGTTTTA
29039249 ATATTTG-TTT-TTATATTTTAAAAT
1 ATATTTGATTTATTATATTTTAAAAT
*
29039273 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTAAAAT
29039299 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTAAAAT
Found at i:29039568 original size:46 final size:46
Alignment explanation
Indices: 29039496--29039591 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
29039486 ATCACCTCTA
* *
29039496 CTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATAGTAT
1 CTTTCAACCATGATCTTACACATTTCATATCAAGCTGCCATAGTAT
* *
29039542 CTTTGAACCATGATCTTACACATTTCATATCAAGCTGCCATGGTAT
1 CTTTCAACCATGATCTTACACATTTCATATCAAGCTGCCATAGTAT
29039588 CTTT
1 CTTT
29039592 ATAAATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (46 bp):
CTTTCAACCATGATCTTACACATTTCATATCAAGCTGCCATAGTAT
Found at i:29041528 original size:30 final size:30
Alignment explanation
Indices: 29041461--29041528 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
29041451 CACCCTTAAA
* * *
29041461 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
29041491 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
29041520 AGTATTTAC
1 A-TATTTAC
29041529 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:29045653 original size:26 final size:24
Alignment explanation
Indices: 29045624--29045706 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 24
29045614 GCTATGATCG
29045624 GTAAGCTCCT-TCTAAGCTGATGAACA
1 GTAAGCT-CTATC-AAGCTGA-GAACA
* *
29045650 GTAAGCTCTATCGAGCTGAAAACA
1 GTAAGCTCTATCAAGCTGAGAACA
*
29045674 GTAAGCTCTGA-CAAGCTGAGAATA
1 GTAAGCTCT-ATCAAGCTGAGAACA
29045698 GTAAGCTCT
1 GTAAGCTCT
29045707 TACGAGTTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 32 0.64
25 9 0.18
26 9 0.18
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (24 bp):
GTAAGCTCTATCAAGCTGAGAACA
Found at i:29045677 original size:24 final size:25
Alignment explanation
Indices: 29045646--29045741 Score: 92
Period size: 24 Copynumber: 3.9 Consensus size: 25
29045636 TAAGCTGATG
29045646 AACAGTAAGCTCTAT-CGAGCTGAA
1 AACAGTAAGCTCTATACGAGCTGAA
* * *
29045670 AACAGTAAGCTCT-GACAAGCTGAG
1 AACAGTAAGCTCTATACGAGCTGAA
* *
29045694 AATAGTAAGCTCT-TACGAGTTGATA
1 AACAGTAAGCTCTATACGAGCTGA-A
*
29045719 TATCAGTAAGCTC-ATACGAGCTG
1 -AACAGTAAGCTCTATACGAGCTG
29045742 CGGTGGGTCC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
24 39 0.68
26 18 0.32
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (25 bp):
AACAGTAAGCTCTATACGAGCTGAA
Found at i:29047181 original size:19 final size:19
Alignment explanation
Indices: 29047157--29047194 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29047147 CTCAATAACA
*
29047157 TAGCTCATTTCATGTACAC
1 TAGCTCATTTCATATACAC
29047176 TAGCTCATTTCATATACAC
1 TAGCTCATTTCATATACAC
29047195 ACCTTTTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (19 bp):
TAGCTCATTTCATATACAC
Found at i:29047524 original size:45 final size:43
Alignment explanation
Indices: 29047460--29047579 Score: 143
Period size: 45 Copynumber: 2.7 Consensus size: 43
29047450 TTGAAGGATC
* *
29047460 TCATAGTGTCTTTCAACCATGGTCCTATTCATTCTCGACTTAATG-
1 TCATAGTGTCTTTCAACCATGGTCTTATT-ATT-T-GACATAATGT
* *
29047505 TCATAGTGTCTTTCAACCATGGTCTTATATATTTTACATCATGT
1 TCATAGTGTCTTTCAACCATGGTCTTAT-TATTTGACATAATGT
29047549 TGCCATAGTGTCTTTCAACCATGGTCTTATT
1 T--CATAGTGTCTTTCAACCATGGTCTTATT
29047580 TGTCTGATTC
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
43 6 0.09
44 2 0.03
45 31 0.46
46 28 0.42
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (43 bp):
TCATAGTGTCTTTCAACCATGGTCTTATTATTTGACATAATGT
Found at i:29051204 original size:42 final size:42
Alignment explanation
Indices: 29051111--29051204 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
29051101 GAGTTATATG
* * * * *
29051111 GCCTAGACACACGCCCATGTCCTTGCCCGTGTGGCTCACACG
1 GCCTAGGCACACACCCATGTCCTTACCCGTATGGCTCACACA
*
29051153 GCCTCGGCACACACCCATGTCCTTACCTC-TATGGCTCACACA
1 GCCTAGGCACACACCCATGTCCTTACC-CGTATGGCTCACACA
**
29051195 GTTTAGGCAC
1 GCCTAGGCAC
29051205 TCGTTGATGT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.39, G:0.20, T:0.21
Consensus pattern (42 bp):
GCCTAGGCACACACCCATGTCCTTACCCGTATGGCTCACACA
Found at i:29054411 original size:26 final size:26
Alignment explanation
Indices: 29054375--29054458 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
29054365 CATGAAATTC
29054375 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29054401 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
29054427 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29054453 TTATCA
1 TTATCA
29054459 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29055164 original size:30 final size:31
Alignment explanation
Indices: 29055129--29055187 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
29055119 TTTCGGGATG
29055129 TTACAAT-TTTTTAAAATTT-TAATAATTTTT
1 TTACAATCTTTTT-AAATTTCTAATAATTTTT
*
29055159 TTACAATCTTTTTCAATTTCTAATAATTT
1 TTACAATCTTTTTAAATTTCTAATAATTT
29055188 ATTATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (31 bp):
TTACAATCTTTTTAAATTTCTAATAATTTTT
Found at i:29055321 original size:21 final size:21
Alignment explanation
Indices: 29055297--29055338 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29055287 ATATTAATAA
*
29055297 ATTTAGAATTTTTATAATTTT
1 ATTTAGAATTTTTAAAATTTT
* *
29055318 ATTTATATTTTTTAAAATTTT
1 ATTTAGAATTTTTAAAATTTT
29055339 TACAATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTAGAATTTTTAAAATTTT
Found at i:29065760 original size:21 final size:21
Alignment explanation
Indices: 29065736--29065777 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29065726 AAAAACAATC
29065736 ATGTTGAAATGGAGTTTCATA
1 ATGTTGAAATGGAGTTTCATA
29065757 ATGTTGAAATGGAGTTTCATA
1 ATGTTGAAATGGAGTTTCATA
29065778 TTTCATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (21 bp):
ATGTTGAAATGGAGTTTCATA
Found at i:29067608 original size:16 final size:16
Alignment explanation
Indices: 29067584--29067616 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29067574 TGTATTGGGT
*
29067584 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
29067600 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
29067616 T
1 T
29067617 AGCAAATCAA
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:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:29067661 original size:45 final size:44
Alignment explanation
Indices: 29067595--29067689 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
29067585 GGATTAGAGG
* *
29067595 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
29067640 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
29067684 TGTAAT
1 TGTAAT
29067690 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:29067872 original size:18 final size:17
Alignment explanation
Indices: 29067851--29067885 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29067841 TTATTATTTA
*
29067851 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29067869 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29067886 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29067879 original size:28 final size:27
Alignment explanation
Indices: 29067809--29067881 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
29067799 TTTATTATCA
*
29067809 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
29067837 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
29067864 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
29067882 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:29067998 original size:144 final size:147
Alignment explanation
Indices: 29067770--29068041 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
29067760 ATGATTATTG
29067770 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
29067835 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
29067900 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
29067919 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
29067981 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
29068042 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:29068016 original size:18 final size:17
Alignment explanation
Indices: 29067995--29068029 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29067985 TTATTATTAA
*
29067995 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29068013 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29068030 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29068073 original size:54 final size:54
Alignment explanation
Indices: 29068015--29068193 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
29068005 ATTAAAATAT
*
29068015 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
29068069 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
29068132 TAT
53 -AC
*
29068135 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
29068189 ATAAT
1 ATAAT
29068194 ATATGATTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:29068075 original size:61 final size:61
Alignment explanation
Indices: 29068010--29068197 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
29068000 TTTTAATTAA
*
29068010 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
29068071 AATATATGATACT-GTAAAA-T-ATAA-AATAACATAATTATTAT-TAAATATAAT-ATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATTA-AT-ATTCTTATATGAATTTACTCA-AATCAT
29068130 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
29068191 AATATAT
1 AATATAT
29068198 GATTATAACT
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 29 0.31
60 16 0.17
61 37 0.39
62 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:29068108 original size:120 final size:120
Alignment explanation
Indices: 29067978--29068200 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
29067968 ATCATATTTA
* *
29067978 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
29068043 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
29068098 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
29068163 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGAT
29068201 TATAACTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
Found at i:29068136 original size:18 final size:17
Alignment explanation
Indices: 29068115--29068149 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29068105 TTATTATTAA
29068115 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
29068133 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
29068150 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:29068212 original size:17 final size:16
Alignment explanation
Indices: 29068190--29068236 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
29068180 ACTCAAATCA
29068190 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
29068207 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
29068221 TAAATATATGATTTAA
1 T-AATATATGATTTAA
29068237 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:29068237 original size:17 final size:17
Alignment explanation
Indices: 29068209--29068242 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29068199 ATTATAACTA
*
29068209 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
29068226 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
29068243 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:29068385 original size:93 final size:92
Alignment explanation
Indices: 29068275--29068469 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
29068265 GATTATAGTT
* * *
29068275 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
29068338 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
29068368 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
29068433 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
29068460 TATGAATTTA
1 TATGAATTTA
29068470 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:29069884 original size:11 final size:11
Alignment explanation
Indices: 29069870--29069896 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29069860 AAAAATCAAT
29069870 ACAAAAGTTTC
1 ACAAAAGTTTC
29069881 ACAAAAGTTTC
1 ACAAAAGTTTC
29069892 ACAAA
1 ACAAA
29069897 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:29088357 original size:11 final size:11
Alignment explanation
Indices: 29088341--29088365 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29088331 ATATCTAGAA
29088341 TTCTCTTCATT
1 TTCTCTTCATT
29088352 TTCTCTTCATT
1 TTCTCTTCATT
29088363 TTC
1 TTC
29088366 ATCAGCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:29089645 original size:25 final size:25
Alignment explanation
Indices: 29089616--29089667 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
29089606 AAGAATAATT
**
29089616 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
29089641 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
29089666 TG
1 TG
29089668 TTAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:29090335 original size:10 final size:10
Alignment explanation
Indices: 29090320--29090347 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
29090310 ATATTACATG
29090320 TTTACTTTGT
1 TTTACTTTGT
29090330 TTTACTTTGT
1 TTTACTTTGT
29090340 TTTACTTT
1 TTTACTTT
29090348 TTCCCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Found at i:29095104 original size:17 final size:18
Alignment explanation
Indices: 29095066--29095108 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
29095056 TGGCCAATAT
29095066 CCCACACGCCCGTGTGGG
1 CCCACACGCCCGTGTGGG
* *
29095084 CCCACATGCCCTTGT-GG
1 CCCACACGCCCGTGTGGG
29095101 CCCACACG
1 CCCACACG
29095109 ACCCAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.14, C:0.47, G:0.26, T:0.14
Consensus pattern (18 bp):
CCCACACGCCCGTGTGGG
Found at i:29098792 original size:30 final size:30
Alignment explanation
Indices: 29098756--29098813 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
29098746 TGGCAAACAT
29098756 TGCCCTGACGTATAGAATTATTATTTAATA
1 TGCCCTGACGTATAGAATTATTATTTAATA
29098786 TGCCCTGACGTATAGAATTATTATTTAA
1 TGCCCTGACGTATAGAATTATTATTTAA
29098814 CATCGCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (30 bp):
TGCCCTGACGTATAGAATTATTATTTAATA
Found at i:29099056 original size:27 final size:26
Alignment explanation
Indices: 29099022--29099078 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 26
29099012 AATTAATATC
*
29099022 AATTTTTATAATATTTAAATTTATAAAAA
1 AATTTATATAA-ATTT-AATTT-TAAAAA
29099051 AATTTATATAAATTTAATTTTAAAAA
1 AATTTATATAAATTTAATTTTAAAAA
29099077 AA
1 AA
29099079 CTTAATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.30
27 5 0.19
28 4 0.15
29 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTTATATAAATTTAATTTTAAAAA
Found at i:29099077 original size:28 final size:29
Alignment explanation
Indices: 29099022--29099078 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
29099012 AATTAATATC
* *
29099022 AATTTTTATAATATTTAAATTTATAAAAA
1 AATTTATATAATATTTAAATTTAAAAAAA
*
29099051 AATTTATATAA-ATTTAATTTTAAAAAAA
1 AATTTATATAATATTTAAATTTAAAAAAA
29099079 CTTAATACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTATATAATATTTAAATTTAAAAAAA
Found at i:29102421 original size:3 final size:3
Alignment explanation
Indices: 29102413--29102440 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29102403 TTGCAGCTCT
29102413 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29102441 GATGATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29105436 original size:11 final size:11
Alignment explanation
Indices: 29105422--29105446 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29105412 TCTTTCTAAA
29105422 TTCTCTCAAAT
1 TTCTCTCAAAT
29105433 TTCTCTCAAAT
1 TTCTCTCAAAT
29105444 TTC
1 TTC
29105447 ATCAAAGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:29105436 original size:22 final size:21
Alignment explanation
Indices: 29105398--29105452 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
29105388 GTCCTTTCAC
* * *
29105398 AATTCTCTTTAAATTCTTTCTA
1 AATTCTCATCAAATTCTCTC-A
29105420 AATTCTC-TCAAATTTCTCTCA
1 AATTCTCATCAAA-TTCTCTCA
29105441 AATT-TCATCAAA
1 AATTCTCATCAAA
29105453 GCTGTCTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 14 0.48
22 13 0.45
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTCTCATCAAATTCTCTCA
Found at i:29108755 original size:7 final size:7
Alignment explanation
Indices: 29108742--29108774 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
29108732 TAGTTGTTTC
29108742 GTATTTA
1 GTATTTA
*
29108749 ATATTTA
1 GTATTTA
29108756 GTATTTA
1 GTATTTA
29108763 GTATTTA
1 GTATTTA
29108770 GTATT
1 GTATT
29108775 ACCTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:29109623 original size:22 final size:21
Alignment explanation
Indices: 29109591--29109641 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
29109581 CCAACACCCA
29109591 CAACCA-AATCCCCTACCGGAG
1 CAACCACAATCCCC-ACCGGAG
* *
29109612 GAACCACAATCCCCACTGGAG
1 CAACCACAATCCCCACCGGAG
29109633 CAACCACAA
1 CAACCACAA
29109642 CCCTCGCCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.37, C:0.41, G:0.14, T:0.08
Consensus pattern (21 bp):
CAACCACAATCCCCACCGGAG
Found at i:29109975 original size:127 final size:128
Alignment explanation
Indices: 29109756--29110128 Score: 660
Period size: 127 Copynumber: 2.9 Consensus size: 128
29109746 TTGTAGAAAC
29109756 ATTTTTATATAGTTTT-ATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
1 ATTTTTATATAGTTTTAAT-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
*
29109820 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATGTTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
*
29109884 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTT-TTTTTAATATTTTAATTGTACTTTAATTT
1 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* *
29109948 TTTTAATTTTATTAAAATAAATATTCTTTTAAATTGGCCAATATTTTTATTATTTTTATATTT
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
29110011 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* *
29110076 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGCCAATAATTTTTATTA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAAT-ATTTTTATTA
29110129 AAATAAATGT
Statistics
Matches: 233, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
127 123 0.53
128 98 0.42
129 12 0.05
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (128 bp):
ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
Found at i:29110134 original size:39 final size:38
Alignment explanation
Indices: 29110082--29110166 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 38
29110072 CTTTTTTTAA
* *
29110082 TTTTAATACAATAAATGTTCTTTTAAAT-TAGCCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATATAG-CAAT-AT
* *
29110121 TTTTATTAAAATAAATGTTATTTTGAATATAGCAATAT
1 TTTTAATAAAATAAATGTTATTTTAAATATAGCAATAT
29110159 TTTTAATA
1 TTTTAATA
29110167 TTTTTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
38 9 0.22
39 28 0.70
40 3 0.08
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (38 bp):
TTTTAATAAAATAAATGTTATTTTAAATATAGCAATAT
Found at i:29110168 original size:9 final size:9
Alignment explanation
Indices: 29110154--29110184 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29110144 TGAATATAGC
29110154 AATATTTTT
1 AATATTTTT
29110163 AATATTTTT
1 AATATTTTT
*
29110172 TATATTTTT
1 AATATTTTT
29110181 AATA
1 AATA
29110185 AAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AATATTTTT
Found at i:29113447 original size:126 final size:125
Alignment explanation
Indices: 29113218--29113524 Score: 506
Period size: 126 Copynumber: 2.4 Consensus size: 125
29113208 GTTTAAGGCG
* *
29113218 TTTTCAGATACTACTGTAGCAAAAGAGTGTCCACGTGGGAGCTTTTTCCGTAATTTTGCTGACAG
1 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCGTAATTTTACTGACAG
*
29113283 TGCATCATTCTTAAAGCATTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATT
66 TGCATCATTCTTAAAGCATTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
* * * *
29113343 TTTTCAAATACTACTGTAGCAAAATAGCATCCATGTGGGAGCTTTTTCCTGTAATTTTACTGACA
1 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCC-GTAATTTTACTGACA
* *
29113408 GTGCATCATTCTTGAAGCGTTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
65 GTGCATCATTCTTAAAGCATTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
*
29113469 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTTTTTCCGTAATT
1 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGC-TTTTTCCGTAATT
29113525 AATAGTTAAT
Statistics
Matches: 166, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
125 44 0.27
126 115 0.69
127 7 0.04
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (125 bp):
TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCGTAATTTTACTGACAG
TGCATCATTCTTAAAGCATTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
Found at i:29113679 original size:16 final size:16
Alignment explanation
Indices: 29113650--29113687 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
29113640 CTTAAAAAAT
*
29113650 ACTAAAATCCTAAACC
1 ACTAAAAACCTAAACC
29113666 -CTAAAAACCATAAACC
1 ACTAAAAACC-TAAACC
29113682 ACTAAA
1 ACTAAA
29113688 CCGTAACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (16 bp):
ACTAAAAACCTAAACC
Found at i:29113773 original size:172 final size:171
Alignment explanation
Indices: 29113545--29114047 Score: 735
Period size: 172 Copynumber: 2.9 Consensus size: 171
29113535 TTAATTAATA
*
29113545 AACCCTAAAAAACCCTAAACCCTAATTTAATT-A-TTTTTTAATTTAATAGTTAATTTAATTAAT
1 AACCCT-AAAAACCCTAAACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAAT
*
29113608 TAACCCTCAAGTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAATCCTAAACCCTAAAAA
65 TAACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAA-CCTAAACCCTAAAAA
* * *
29113673 CCATAAACCACTAAACCGTAACCCTAAAATAATAAAAAACCTT
129 CCATAAACCACTAAACCCTAACCCTAAAACAATAAAAAACCCT
* *
29113716 AACCCTAAAACCCCTAAACCCTAATTTAATTGATTTTTTTAATTTCATGGTTAATTTAATTAATT
1 AACCCTAAAAACCCTAAACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAATT
* *
29113781 AACCCTCAACTCTAATTAAATTAATTTTTTCCTTAGAAAACACTAAAACCATAAACCCTAAAAAC
66 AACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAACC-TAAACCCTAAAAAC
** ** *
29113846 TC-TAAACCACTAAACATTAACTTTAAAACAATCAAAAACCCT
130 -CATAAACCACTAAACCCTAACCCTAAAACAATAAAAAACCCT
* *
29113888 AACCTTAAAAACCCTAAACTCTAATTTAATTGATTTTTTTTTAATTTCATAGTTAATTTAATTAA
1 AACCCTAAAAACCCTAAACCCTAATTTAATTGA--TTTTTTTAATTTCATAGTTAATTTAATTAA
* *
29113953 TTAACCCTGAACTCTAATTAAATTAATTTTTCCCTTAAAAAATACTAAAACCCTAAACCCTAAAA
64 TTAACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAA-CCTAAACCCTAAAA
*
29114018 A-CACTAAACCACTAAACCCTAATCCTAAAA
128 ACCA-TAAACCACTAAACCCTAACCCTAAAA
29114048 AAAAGGGTCA
Statistics
Matches: 297, Mismatches: 26, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
170 24 0.08
171 9 0.03
172 152 0.51
173 1 0.00
174 109 0.37
175 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (171 bp):
AACCCTAAAAACCCTAAACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAATT
AACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAACCTAAACCCTAAAAACC
ATAAACCACTAAACCCTAACCCTAAAACAATAAAAAACCCT
Found at i:29114017 original size:24 final size:24
Alignment explanation
Indices: 29113990--29114039 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
29113980 TTTTCCCTTA
*
29113990 AAAAATACTAAAACC-CTAAACCCT
1 AAAAACACT-AAACCACTAAACCCT
29114014 AAAAACACTAAACCACTAAACCCT
1 AAAAACACTAAACCACTAAACCCT
29114038 AA
1 AA
29114040 TCCTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.14
Consensus pattern (24 bp):
AAAAACACTAAACCACTAAACCCT
Found at i:29114024 original size:16 final size:17
Alignment explanation
Indices: 29113999--29114033 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29113989 AAAAAATACT
*
29113999 AAAACCCTAAACC-CTA
1 AAAACACTAAACCACTA
29114015 AAAACACTAAACCACTA
1 AAAACACTAAACCACTA
29114032 AA
1 AA
29114034 CCCTAATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.31, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAACACTAAACCACTA
Found at i:29115120 original size:22 final size:23
Alignment explanation
Indices: 29115081--29115162 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 23
29115071 CACTATTAAA
*
29115081 CAGAGAGTACTGAA-GTGCTATA-
1 CAGAGAGCACT-AATGTGCTATAG
29115103 CAGAGAGCA-TAGATGTGCTA-AG
1 CAGAGAGCACTA-ATGTGCTATAG
* *
29115125 CGGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTAATGTGCT-AT-AG
29115150 CAGAGAGCACTAA
1 CAGAGAGCACTAA
29115163 CGTACTAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 3 0.06
22 29 0.59
23 3 0.06
25 13 0.27
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (23 bp):
CAGAGAGCACTAATGTGCTATAG
Found at i:29115160 original size:25 final size:25
Alignment explanation
Indices: 29115127--29115178 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
29115117 GTGCTAAGCG
* *
29115127 GAGAGCACTAATGTGCTAATAATCA
1 GAGAGCACTAACGTACTAATAATCA
29115152 GAGAGCACTAACGTACTAATAATCA
1 GAGAGCACTAACGTACTAATAATCA
29115177 GA
1 GA
29115179 TAGCGCGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (25 bp):
GAGAGCACTAACGTACTAATAATCA
Found at i:29115450 original size:22 final size:22
Alignment explanation
Indices: 29115417--29115459 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29115407 TCACTTTTCA
* *
29115417 ATTCCAATTTCACTTTCATTTT
1 ATTCCAATTTCAATTTAATTTT
29115439 ATTCACAA-TTCAATTTAATTT
1 ATTC-CAATTTCAATTTAATTT
29115460 CACTTTCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTCCAATTTCAATTTAATTTT
Found at i:29116098 original size:169 final size:170
Alignment explanation
Indices: 29115803--29116109 Score: 402
Period size: 169 Copynumber: 1.8 Consensus size: 170
29115793 TATCTTTAAT
* ** * * *
29115803 CAAATCATGAACCTTTGGTTCAAGCTTTGAATCACATATCTCAATTTCAATTCACATTTCAATTC
1 CAAATCATGAACCTTAGGTTCAAGCTTCAAATCACACATCTCAATTTCAATTCACAATTCAACTC
* * * *
29115868 ATAATTCCACTTTTTCCTACTTTCAATAGTTCAATCGATCAAATTCATTCAATTTTCTCATTTCA
66 ATAATT-CACTTTCTCATACTTTCAATAGTACAATCAATCAAATTCATTCAATTTTCTCATTTCA
*
29115933 TTTATTCAACTGATTTCAATATCAACAATTTGATATTTTAG
130 GTTATTCAACTGATTTCAATATCAACAATTTGATATTTTAG
* * *
29115974 CAAATTCATGAACCTTAGGTTTATGCTTCAAATCTCACATCTCAA-TTCAATTCACAATTCAACT
1 CAAA-TCATGAACCTTAGGTTCAAGCTTCAAATCACACATCTCAATTTCAATTCACAATTCAACT
* * * * * *
29116038 CATAATT-TCTTTCTCATATTTTTAATAGTACGATCAATCAAATTTATTTAATTTTCTCATTTCA
65 CATAATTCACTTTCTCATACTTTCAATAGTACAATCAATCAAATTCATTCAATTTTCTCATTTCA
29116102 GTTATTCA
130 GTTATTCA
29116110 CCCTATTAAC
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
169 54 0.47
171 28 0.24
172 33 0.29
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (170 bp):
CAAATCATGAACCTTAGGTTCAAGCTTCAAATCACACATCTCAATTTCAATTCACAATTCAACTC
ATAATTCACTTTCTCATACTTTCAATAGTACAATCAATCAAATTCATTCAATTTTCTCATTTCAG
TTATTCAACTGATTTCAATATCAACAATTTGATATTTTAG
Found at i:29116277 original size:23 final size:23
Alignment explanation
Indices: 29116232--29116329 Score: 128
Period size: 23 Copynumber: 4.3 Consensus size: 23
29116222 AGTGCATGAA
* *
29116232 ACGACACACGAGGTGCCT--CAT
1 ACGACACACGAGGTGCTTGAAAT
*
29116253 ACGACACACGAGATGCTTGAAAT
1 ACGACACACGAGGTGCTTGAAAT
29116276 ACGACACACGAGGTGCTTGAAAT
1 ACGACACACGAGGTGCTTGAAAT
* *
29116299 ACGACACACGAGGTGCCTAAAAT
1 ACGACACACGAGGTGCTTGAAAT
*
29116322 ATGACACA
1 ACGACACA
29116330 TAAAGTGCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.24
23 52 0.76
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (23 bp):
ACGACACACGAGGTGCTTGAAAT
Found at i:29116699 original size:44 final size:44
Alignment explanation
Indices: 29116609--29116700 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
29116599 CCCATGTAAC
* * * *
29116609 AGTAGCAGTACGACACACATGGTGCCTCATCGACTAGATGTTGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACTAGAGGTCGA
**
29116653 AGTAACAGTACGACACTTATAGTGCCTCATCGACTCA-AGGTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACT-AGAGGTCGA
29116697 AGTA
1 AGTA
29116701 TCCCTGAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 40 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (44 bp):
AGTAACAGTACGACACACATAGTGCCTCATCGACTAGAGGTCGA
Found at i:29124828 original size:25 final size:25
Alignment explanation
Indices: 29124800--29124869 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
29124790 TTTTTAATTC
29124800 TCTTAACAATAATTGTAAAAGAAAA
1 TCTTAACAATAATTGTAAAAGAAAA
* *
29124825 TCTTAAACTAA-AAAT-TAATAGAAAA
1 TCTT-AAC-AATAATTGTAAAAGAAAA
*
29124850 TCTATAAAAATAATTG-AAAA
1 TCT-TAACAATAATTGTAAAA
29124870 TTCATAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
24 2 0.06
25 24 0.69
26 7 0.20
27 2 0.06
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.29
Consensus pattern (25 bp):
TCTTAACAATAATTGTAAAAGAAAA
Found at i:29127649 original size:4 final size:4
Alignment explanation
Indices: 29127640--29127720 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
29127630 GTAAGTTAAA
* * *** * *
29127640 AAAG AAAG AAAA AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
*
29127690 TAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
29127721 TAGAAAAGGG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
4 56 0.92
5 4 0.07
6 1 0.02
ACGTcount: A:0.68, C:0.04, G:0.23, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:29128549 original size:47 final size:47
Alignment explanation
Indices: 29128485--29128595 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
29128475 GACATTGAGT
*
29128485 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
29128532 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
29128579 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
29128596 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:29141123 original size:12 final size:13
Alignment explanation
Indices: 29141087--29141124 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
29141077 AAATATTTGA
29141087 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
29141100 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
29141114 CTTG-TCTTAAT
1 CTTGTTCTTAAT
29141125 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:29159980 original size:34 final size:34
Alignment explanation
Indices: 29159942--29160009 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
29159932 TTGAGGAAGT
*
29159942 ATGTGCAGTGGTGTGGCCGCCTTTGAGTCCCTCG
1 ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
29159976 ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
1 ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
29160010 CAACACCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.10, C:0.26, G:0.34, T:0.29
Consensus pattern (34 bp):
ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
Found at i:29162492 original size:17 final size:17
Alignment explanation
Indices: 29162466--29162499 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29162456 TATATAATTG
*
29162466 AAATATGTTATAATATA
1 AAATAAGTTATAATATA
29162483 AAATAAGTTATAATATA
1 AAATAAGTTATAATATA
29162500 TTAAGTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATAAGTTATAATATA
Found at i:29163669 original size:24 final size:24
Alignment explanation
Indices: 29163637--29163745 Score: 141
Period size: 24 Copynumber: 4.5 Consensus size: 24
29163627 GAAATGACAT
29163637 TGGCACTATGTGTGCGGATTTAAA
1 TGGCACTATGTGTGCGGATTTAAA
*
29163661 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTAAA
* **
29163685 TGGCACTATGTGTGCAGATTTGGA
1 TGGCACTATGTGTGCGGATTTAAA
*
29163709 TGGCACTACGTGTGCGGA-TTAGCAA
1 TGGCACTATGTGTGCGGATTTA--AA
29163734 -GGCACTATGTGT
1 TGGCACTATGTGT
29163746 ACGGGTTAGC
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 2 0.03
24 72 0.96
25 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.31
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTAAA
Found at i:29163693 original size:48 final size:49
Alignment explanation
Indices: 29163637--29163745 Score: 159
Period size: 48 Copynumber: 2.3 Consensus size: 49
29163627 GAAATGACAT
* * *
29163637 TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTG-AA
1 TGGCACTATGTGTGCAGATTTAAATGGCACTACGTGTGCGGATTAGCAA
**
29163685 TGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGATTAGCAA
1 TGGCACTATGTGTGCAGATTTAAATGGCACTACGTGTGCGGATTAGCAA
29163734 -GGCACTATGTGT
1 TGGCACTATGTGT
29163746 ACGGGTTAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 53 0.96
49 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.31
Consensus pattern (49 bp):
TGGCACTATGTGTGCAGATTTAAATGGCACTACGTGTGCGGATTAGCAA
Found at i:29163754 original size:24 final size:24
Alignment explanation
Indices: 29163638--29163770 Score: 101
Period size: 24 Copynumber: 5.5 Consensus size: 24
29163628 AAATGACATT
*
29163638 GGCACTATGTGTGCGGATTTA--AA
1 GGCACTATGTGTACGGA-TTAGCAA
* *
29163661 TGGCACTATGTGTGCGGATTTG-AA
1 -GGCACTATGTGTACGGATTAGCAA
* * * * *
29163685 TGGCACTATGTGTGCAGATTTGGAT
1 -GGCACTATGTGTACGGATTAGCAA
* *
29163710 GGCACTACGTGTGCGGATTAGCAA
1 GGCACTATGTGTACGGATTAGCAA
* *
29163734 GGCACTATGTGTACGGGTTAGCAT
1 GGCACTATGTGTACGGATTAGCAA
*
29163758 GGCAATATGTGTA
1 GGCACTATGTGTA
29163771 TGAATTTCCT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 91 0.97
25 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.30
Consensus pattern (24 bp):
GGCACTATGTGTACGGATTAGCAA
Found at i:29163760 original size:48 final size:48
Alignment explanation
Indices: 29163637--29163761 Score: 146
Period size: 48 Copynumber: 2.6 Consensus size: 48
29163627 GAAATGACAT
* *
29163637 TGGCACTATGTGTGCGGATTTA-AATGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGA-TTAGAATGGCACTACGTGTGCGGATTAGAA
* * *
29163685 TGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGATTAGCAA
1 TGGCACTATGTGTGCGGATTAGAATGGCACTACGTGTGCGGATTAG-AA
* * *
29163734 -GGCACTATGTGTACGGGTTAGCATGGCA
1 TGGCACTATGTGTGCGGATTAGAATGGCA
29163762 ATATGTGTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
47 2 0.03
48 61 0.94
49 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (48 bp):
TGGCACTATGTGTGCGGATTAGAATGGCACTACGTGTGCGGATTAGAA
Found at i:29167371 original size:17 final size:18
Alignment explanation
Indices: 29167345--29167378 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29167335 TTTTTGTTTA
29167345 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
29167362 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
29167379 ATATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:29167387 original size:23 final size:23
Alignment explanation
Indices: 29167360--29167410 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
29167350 ATTAATAGCA
*
29167360 TTAATAATTTAATATGCATATAT
1 TTAATAATGTAATATGCATATAT
29167383 TTAATAATGTAATATGCATATAT
1 TTAATAATGTAATATGCATATAT
29167406 TTAAT
1 TTAAT
29167411 TATTAATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (23 bp):
TTAATAATGTAATATGCATATAT
Found at i:29169910 original size:199 final size:199
Alignment explanation
Indices: 29169570--29169967 Score: 796
Period size: 199 Copynumber: 2.0 Consensus size: 199
29169560 ACAATAAAGA
29169570 CATTATTCATCTTAAGTAAGGGGACCGAAAAATTGAATTTGAATTATTTCCACTCAGAATAAATT
1 CATTATTCATCTTAAGTAAGGGGACCGAAAAATTGAATTTGAATTATTTCCACTCAGAATAAATT
29169635 TTCTTTTAATTATGATTAGGATATATTTTTCAATAATTGGAAATTCTGTTAAGTATGCTCAACTT
66 TTCTTTTAATTATGATTAGGATATATTTTTCAATAATTGGAAATTCTGTTAAGTATGCTCAACTT
29169700 CAGTATAAATAAAGTTATATTATTTCAATAAATTATTATGTTAGCTTAATAATGATATGAATGTA
131 CAGTATAAATAAAGTTATATTATTTCAATAAATTATTATGTTAGCTTAATAATGATATGAATGTA
29169765 TTTC
196 TTTC
29169769 CATTATTCATCTTAAGTAAGGGGACCGAAAAATTGAATTTGAATTATTTCCACTCAGAATAAATT
1 CATTATTCATCTTAAGTAAGGGGACCGAAAAATTGAATTTGAATTATTTCCACTCAGAATAAATT
29169834 TTCTTTTAATTATGATTAGGATATATTTTTCAATAATTGGAAATTCTGTTAAGTATGCTCAACTT
66 TTCTTTTAATTATGATTAGGATATATTTTTCAATAATTGGAAATTCTGTTAAGTATGCTCAACTT
29169899 CAGTATAAATAAAGTTATATTATTTCAATAAATTATTATGTTAGCTTAATAATGATATGAATGTA
131 CAGTATAAATAAAGTTATATTATTTCAATAAATTATTATGTTAGCTTAATAATGATATGAATGTA
29169964 TTTC
196 TTTC
29169968 TAATAAAGCA
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 199 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (199 bp):
CATTATTCATCTTAAGTAAGGGGACCGAAAAATTGAATTTGAATTATTTCCACTCAGAATAAATT
TTCTTTTAATTATGATTAGGATATATTTTTCAATAATTGGAAATTCTGTTAAGTATGCTCAACTT
CAGTATAAATAAAGTTATATTATTTCAATAAATTATTATGTTAGCTTAATAATGATATGAATGTA
TTTC
Found at i:29172348 original size:19 final size:19
Alignment explanation
Indices: 29172317--29172362 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
29172307 GGTATAGAGC
*
29172317 ACACGCCCGTGTGCTAGGG
1 ACACGCCCATGTGCTAGGG
*
29172336 ACATGCCCATGTGCTAGGG
1 ACACGCCCATGTGCTAGGG
29172355 ACACGCCC
1 ACACGCCC
29172363 GTGTCCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (19 bp):
ACACGCCCATGTGCTAGGG
Done.