Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008007.1 Hibiscus syriacus cultivar Beakdansim tig00110469_pilon, whole genome shotgun sequence
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: 1953294
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1234318 original size:21 final size:21
Alignment explanation
Indices: 1234293--1234335 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1234283 CTTCCGACCG
1234293 CCGTTCGTCGATCCGAAACCA
1 CCGTTCGTCGATCCGAAACCA
*
1234314 CCGTTTGTCGATCCGAAACCA
1 CCGTTCGTCGATCCGAAACCA
1234335 C
1 C
1234336 TATCGTGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
CCGTTCGTCGATCCGAAACCA
Found at i:1234900 original size:23 final size:23
Alignment explanation
Indices: 1234867--1234926 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1234857 AACTCACTAG
* *
1234867 GTCAACTCGTTTACTTTGACCGA
1 GTCAACCCGTTGACTTTGACCGA
1234890 GTCAACCCGTTGACTTTGACCGA
1 GTCAACCCGTTGACTTTGACCGA
*
1234913 GTCAAACCGTTGAC
1 GTCAACCCGTTGAC
1234927 CGTTGACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (23 bp):
GTCAACCCGTTGACTTTGACCGA
Found at i:1235845 original size:27 final size:28
Alignment explanation
Indices: 1235815--1235882 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
1235805 GGAATTATAG
1235815 AAATACCCCTAAAGTGTAAAATGACC-A
1 AAATACCCCTAAAGTGTAAAATGACCTA
* *
1235842 AAATGCCCCTAAAGTGTAAAATGGCCTA
1 AAATACCCCTAAAGTGTAAAATGACCTA
* *
1235870 AAGTACCTCTAAA
1 AAATACCCCTAAA
1235883 CCCTGGAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.21
Consensus pattern (28 bp):
AAATACCCCTAAAGTGTAAAATGACCTA
Found at i:1241758 original size:27 final size:27
Alignment explanation
Indices: 1241704--1241759 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1241694 TATCAATATT
** *
1241704 TAAATAAATAATAGATATTTCTTCAAA
1 TAAATAAATAATAGATATTAATTAAAA
**
1241731 TAAATAAATAATATTTATTAATTAAAA
1 TAAATAAATAATAGATATTAATTAAAA
1241758 TA
1 TA
1241760 TTTAAACTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAATAAATAATAGATATTAATTAAAA
Found at i:1243764 original size:18 final size:18
Alignment explanation
Indices: 1243741--1243783 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1243731 CTTTAAATTA
*
1243741 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1243759 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1243777 TTTATTT
1 TTTATTT
1243784 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1248784 original size:18 final size:18
Alignment explanation
Indices: 1248763--1248798 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1248753 AGTATTTTCA
*
1248763 TTAGGAATTATCTTTTTT
1 TTAGGAATTATATTTTTT
1248781 TTAGGAATTATATTTTTT
1 TTAGGAATTATATTTTTT
1248799 ATTTTTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.61
Consensus pattern (18 bp):
TTAGGAATTATATTTTTT
Found at i:1249573 original size:18 final size:18
Alignment explanation
Indices: 1249550--1249592 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1249540 TTTTAAATTA
*
1249550 TTTATTTAAATATTTTCT
1 TTTATTTAAATATTATCT
*
1249568 TTTATTTAATTATTATCT
1 TTTATTTAAATATTATCT
1249586 TTTATTT
1 TTTATTT
1249593 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAAATATTATCT
Found at i:1255155 original size:18 final size:17
Alignment explanation
Indices: 1255127--1255161 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1255117 TTAAAAATTA
1255127 TTATTTTATATAATTTT
1 TTATTTTATATAATTTT
*
1255144 TTATTATTATATTATTTT
1 TTATT-TTATATAATTTT
1255162 GTCTTAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTATATAATTTT
Found at i:1257325 original size:54 final size:54
Alignment explanation
Indices: 1257255--1257606 Score: 515
Period size: 54 Copynumber: 6.5 Consensus size: 54
1257245 TTTCATGGTT
* * *
1257255 TTGCACTCATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTAGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTACGTAGG
* * * *
1257309 TTGTACACATAGTGTCGATATGGTAATTCACAAACTAATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTACGTAGG
* *
1257363 TTGCACACATAGTGCCGATACGGTAATTCACAAACAAATTATAAATTACGTAGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTACGTAGG
* *
1257417 TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTATGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTACGTAGG
* * * * *
1257471 TTGCACACATAGTGCTGATACGGTAATTCACAAAGTCATTATGAATAACTTAGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTACGTAGG
* * * *
1257525 TTGCACACATAGTGCCAATACGATAATTCACAAACTAATTAGGAATTACTTAGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTACGTAGG
*
1257579 TTGCACACATAGTGCCAATACGGTAATT
1 TTGCACACATAGTGCCGATACGGTAATT
1257607 GCAACATATA
Statistics
Matches: 268, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 268 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (54 bp):
TTGCACACATAGTGCCGATACGGTAATTCACAAACTAATTATGAATTACGTAGG
Found at i:1275911 original size:64 final size:64
Alignment explanation
Indices: 1275843--1275975 Score: 248
Period size: 64 Copynumber: 2.1 Consensus size: 64
1275833 TTTGAATTTG
* *
1275843 ATGAACAAGAGTATACAAATATAAAAGAAAAATGATTAATTCAATAGTTTACCCCAAATAATTA
1 ATGAACAAAAGTATACAAATATAAAAGAAAAATGATTAATTCAATAATTTACCCCAAATAATTA
1275907 ATGAACAAAAGTATACAAATATAAAAGAAAAATGATTAATTCAATAATTTACCCCAAATAATTA
1 ATGAACAAAAGTATACAAATATAAAAGAAAAATGATTAATTCAATAATTTACCCCAAATAATTA
1275971 ATGAA
1 ATGAA
1275976 GGAGGTACAC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (64 bp):
ATGAACAAAAGTATACAAATATAAAAGAAAAATGATTAATTCAATAATTTACCCCAAATAATTA
Found at i:1280555 original size:21 final size:22
Alignment explanation
Indices: 1280516--1280557 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1280506 ATTTGAAAAT
*
1280516 AAAAATAAAACAAAGAACTTTG
1 AAAAAGAAAACAAAGAACTTTG
*
1280538 AAAAAGAAAAGAAA-AACTTT
1 AAAAAGAAAACAAAGAACTTT
1280558 TATTAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAAGAAAACAAAGAACTTTG
Found at i:1280753 original size:24 final size:24
Alignment explanation
Indices: 1280703--1280761 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1280693 AATCCTAATG
* *
1280703 AAAATAATTAAAACAATTTAAACT
1 AAAATAATAAAAACAATATAAACT
*
1280727 AAAATACTAAAAACAATATAAGA-T
1 AAAATAATAAAAACAATATAA-ACT
1280751 AAATATAATAA
1 AAA-ATAATAA
1280762 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAATAATAAAAACAATATAAACT
Found at i:1285101 original size:21 final size:21
Alignment explanation
Indices: 1285059--1285111 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1285049 ATTCTGACTA
1285059 TCGCATTGCGATTTCACAAAT
1 TCGCATTGCGATTTCACAAAT
* *
1285080 TCGCGTTGCGATTTTC-CTAAT
1 TCGCATTGCGA-TTTCACAAAT
*
1285101 TCGCAATGCGA
1 TCGCATTGCGA
1285112 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCACAAAT
Found at i:1285139 original size:20 final size:20
Alignment explanation
Indices: 1285101--1285301 Score: 181
Period size: 20 Copynumber: 10.4 Consensus size: 20
1285091 TTTTCCTAAT
* *
1285101 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGATTACGTAAA
* *
1285121 TCGTAACGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* * *
1285141 TCGCAATACGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
* *
1285162 TTGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
1285182 TCGCAATGCGATTACGT--A
1 TCGCAATGCGATTACGTAAA
1285200 TCGC-ATGCGATTACGT--A
1 TCGCAATGCGATTACGTAAA
*
1285217 -CGCAATGCGAATTA-GGAAA
1 TCGCAATGCG-ATTACGTAAA
*
1285236 TACGCAATGCGAATACGTAAA
1 T-CGCAATGCGATTACGTAAA
*
1285257 TCGCAAAGCGA-TA---AAA
1 TCGCAATGCGATTACGTAAA
*
1285273 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
1285293 TCGCAATGC
1 TCGCAATGC
1285302 AATCTGACTA
Statistics
Matches: 148, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
16 16 0.11
17 21 0.14
18 9 0.06
19 3 0.02
20 69 0.47
21 30 0.20
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:1285209 original size:17 final size:18
Alignment explanation
Indices: 1285164--1285324 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 18
1285154 TAGGAAAATT
*
1285164 GCAATGCGAATACGTAAATC
1 GCAATGCGATTACGT--ATC
1285184 GCAATGCGATTACGTATC
1 GCAATGCGATTACGTATC
1285202 GC-ATGCGATTACGTA-C
1 GCAATGCGATTACGTATC
* *
1285218 GCAATGCGAATTAGGAAATAC
1 GCAATGCG-ATTACG-TAT-C
*
1285239 GCAATGCGAATACGTAAATC
1 GCAATGCGATTACGT--ATC
* **
1285259 GCAAAGCGA-TA-AAATC
1 GCAATGCGATTACGTATC
*
1285275 GCAATGCGAATACGTAAATC
1 GCAATGCGATTACGT--ATC
*
1285295 GCAATGCAATCTGAC-TATC
1 GCAATGCGAT-T-ACGTATC
1285314 GCAATGCGATT
1 GCAATGCGATT
1285325 TACATAGCGC
Statistics
Matches: 113, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
16 14 0.12
17 20 0.18
18 11 0.10
19 15 0.13
20 38 0.34
21 13 0.12
22 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (18 bp):
GCAATGCGATTACGTATC
Found at i:1285322 original size:75 final size:74
Alignment explanation
Indices: 1285142--1285290 Score: 187
Period size: 75 Copynumber: 2.0 Consensus size: 74
1285132 TTACGTAAAT
* * * **
1285142 CGCAATACGAATTAGGAAA-ATTGCAATGCGAATACGTAAATCGCAATGCGATTACGTATCGCAT
1 CGCAATGCGAATTA-GAAATA-CGCAATGCGAATACGTAAATCGCAAAGCGATTACAAATCGCAT
*
1285206 GCGATTACGTA
64 GCGAATACGTA
1285217 CGCAATGCGAATTAGGAAATACGCAATGCGAATACGTAAATCGCAAAGCGA-TA-AAATCGCAAT
1 CGCAATGCGAATTA-GAAATACGCAATGCGAATACGTAAATCGCAAAGCGATTACAAATCGC-AT
1285280 GCGAATACGTA
64 GCGAATACGTA
1285291 AATCGCAATG
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
73 5 0.08
74 14 0.21
75 46 0.70
76 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (74 bp):
CGCAATGCGAATTAGAAATACGCAATGCGAATACGTAAATCGCAAAGCGATTACAAATCGCATGC
GAATACGTA
Found at i:1285938 original size:19 final size:18
Alignment explanation
Indices: 1285911--1285962 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
1285901 CGAAACCAAA
* *
1285911 TCGCATTGCAATTTTCATT
1 TCGCGTTGCGATTTTCA-T
1285930 TCGCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
1285948 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1285963 TTGCGATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:1286013 original size:20 final size:19
Alignment explanation
Indices: 1285911--1286016 Score: 90
Period size: 19 Copynumber: 6.1 Consensus size: 19
1285901 CGAAACCAAA
* *
1285911 TCGCATTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
1285930 TCGCGTTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
1285948 TCGCGTTGCGA---T--TT
1 TCGCGTTGCGATTTTCATT
1285962 T----TTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
**
1285976 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1285995 TCTGCGTTGCGATTTTCATT
1 TC-GCGTTGCGATTTTCATT
1286015 TC
1 TC
1286017 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
10 6 0.09
12 1 0.01
14 5 0.07
15 1 0.01
18 18 0.26
19 22 0.31
20 17 0.24
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1288014 original size:94 final size:93
Alignment explanation
Indices: 1287682--1288052 Score: 596
Period size: 94 Copynumber: 4.1 Consensus size: 93
1287672 TAGATTGCTT
* *
1287682 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1287743 ATTTGTC-TT-TTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1287769 AGTAAATTTATTCGGTTG-TGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1287833 ATTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
1287861 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1287926 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
1287955 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1288020 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1288048 AGTAA
1 AGTAA
1288053 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 8, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
86 16 0.06
87 18 0.07
88 3 0.01
89 2 0.01
90 26 0.10
91 10 0.04
92 25 0.09
93 69 0.26
94 98 0.37
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1288016 original size:187 final size:179
Alignment explanation
Indices: 1287682--1288052 Score: 582
Period size: 187 Copynumber: 2.0 Consensus size: 179
1287672 TAGATTGCTT
1287682 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
*
1287747 GTCTTTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGTGCCAATTCTGCTAAACTGTGTATT
66 GTCTTTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGTGCCAATTCTGCTAAACTGTGTATT
*
1287812 CTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
131 CTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
1287861 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
* *
1287926 ATTTGTCTTTGTTTTATCTTTTGGTTGAAAGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAAC
62 ATTTGTC-TT-TTTTATCTTTTGGTTG-AAGTAAATTTATTCGGTTG-TGCCAATTCTGCTAAAC
*
1287991 TGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
123 TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
1288048 AGTAA
1 AGTAA
1288053 TGCAATCCAT
Statistics
Matches: 175, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
179 34 0.19
181 3 0.02
182 2 0.01
183 26 0.15
184 2 0.01
185 15 0.09
186 17 0.10
187 68 0.39
188 8 0.05
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (179 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGTGCCAATTCTGCTAAACTGTGTATT
CTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1288187 original size:19 final size:19
Alignment explanation
Indices: 1288138--1288253 Score: 116
Period size: 19 Copynumber: 6.3 Consensus size: 19
1288128 TCTTTTGGTT
* *
1288138 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
*
1288157 GAGAATGAAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
1288177 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
* *
1288196 GAAATGAAATTCGCAA--C
1 GAAACGAAAATCGCAACGC
*
1288213 G--AC-AAAATCGCAACGT
1 GAAACGAAAATCGCAACGC
*
1288229 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
1288249 GAAAC
1 GAAAC
1288254 TATAATCACG
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 34 0.41
20 34 0.41
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.09
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:1288220 original size:33 final size:36
Alignment explanation
Indices: 1288143--1288251 Score: 107
Period size: 33 Copynumber: 3.0 Consensus size: 36
1288133 TGGTTGAAAT
1288143 GAAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAAC
1 GAAAATCGCAACGAGA-AATGAAAATCGCAAC-CG-AAC
* *
1288182 GAAAATCGCAACGCGAAATGAAATTCGCAA-CG-AC
1 GAAAATCGCAACGAGAAATGAAAATCGCAACCGAAC
* **
1288216 -AAAATCGCAACGTGAAACCAAAAATCGCAACGCGAA
1 GAAAATCGCAACGAGAAA-TGAAAATCGCAAC-CGAA
1288252 ACTATAATCA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
33 16 0.27
34 11 0.18
36 4 0.07
37 1 0.02
38 13 0.22
39 15 0.25
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.09
Consensus pattern (36 bp):
GAAAATCGCAACGAGAAATGAAAATCGCAACCGAAC
Found at i:1288239 original size:20 final size:20
Alignment explanation
Indices: 1288216--1288253 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1288206 TCGCAACGAC
*
1288216 AAAATCGCAACGTGAAACCA
1 AAAATCGCAACGCGAAACCA
1288236 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1288254 TATAATCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:1288319 original size:33 final size:34
Alignment explanation
Indices: 1288262--1288326 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
1288252 ACTATAATCA
**
1288262 CGTTGCGATTTTTGGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTTCATTTCACGTTGCGATTTTGT
1288296 CGTTGCGA-TTTTCATTTCACGTTGCGATTTT
1 CGTTGCGATTTTTCATTTCACGTTGCGATTTT
1288327 CATTTCGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (34 bp):
CGTTGCGATTTTTCATTTCACGTTGCGATTTTGT
Found at i:1288320 original size:19 final size:19
Alignment explanation
Indices: 1288259--1288342 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
1288249 GAAACTATAA
**
1288259 TCACGTTGCGATTTTTGGTT
1 TCACGTTGCGA-TTTTCATT
*
1288279 TCACGTTGCGA-TTT--TG
1 TCACGTTGCGATTTTCATT
1288295 T--CGTTGCGATTTTCATT
1 TCACGTTGCGATTTTCATT
1288312 TCACGTTGCGATTTTCATT
1 TCACGTTGCGATTTTCATT
* *
1288331 TCGCATTGCGAT
1 TCACGTTGCGAT
1288343 AGTCTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
14 8 0.15
15 3 0.05
16 2 0.04
17 2 0.04
18 3 0.05
19 26 0.47
20 11 0.20
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (19 bp):
TCACGTTGCGATTTTCATT
Found at i:1290159 original size:14 final size:14
Alignment explanation
Indices: 1290140--1290175 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1290130 ATTGTTTAAT
1290140 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1290154 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1290168 TGATTTGT
1 TGATTTGT
1290176 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1290298 original size:19 final size:19
Alignment explanation
Indices: 1290282--1290343 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
1290272 AAAAATGACT
*
1290282 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1290301 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1290320 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
1290339 ATCGC
1 ATCGC
1290344 CACTCGAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 40 0.98
20 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1290351 original size:19 final size:19
Alignment explanation
Indices: 1290282--1290357 Score: 93
Period size: 19 Copynumber: 4.0 Consensus size: 19
1290272 AAAAATGACT
*
1290282 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
1290301 ATCGCAACGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
1290320 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
* *
1290339 ATCGCCACTCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
1290358 TTCACGTTGC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
19 52 0.98
20 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:1290388 original size:19 final size:17
Alignment explanation
Indices: 1290362--1290479 Score: 83
Period size: 17 Copynumber: 7.1 Consensus size: 17
1290352 ACTAAATTCA
1290362 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
**
1290379 CGTTTTGCGA--TTC-CCT
1 CG--TTGCGATTTTCATTT
1290395 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
*
1290412 CGCATTGCGA--TTC-TCT
1 CG--TTGCGATTTTCATTT
1290428 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
*
1290445 CGTATTGCGA--TTC-TCT
1 CG--TTGCGATTTTCATTT
1290461 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
1290478 CG
1 CG
1290480 CATTGCGATA
Statistics
Matches: 78, Mismatches: 8, Indels: 30
0.67 0.07 0.26
Matches are distributed among these distances:
14 18 0.23
16 20 0.26
17 22 0.28
19 18 0.23
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (17 bp):
CGTTGCGATTTTCATTT
Found at i:1290404 original size:33 final size:33
Alignment explanation
Indices: 1290362--1290488 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
1290352 ACTAAATTCA
** *
1290362 CGTTGCGATTTTCATTTCGTTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1290395 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1290428 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1290461 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1290489 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1290435 original size:14 final size:14
Alignment explanation
Indices: 1290383--1290470 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
1290373 TCATTTCGTT
*
1290383 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
1290397 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1290414 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1290430 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1290447 TATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1290463 TTGCGATT
1 TTGCGATT
1290471 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 13 0.22
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1290487 original size:19 final size:19
Alignment explanation
Indices: 1290397--1290508 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 19
1290387 GATTCCCTCG
1290397 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1290416 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1290430 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1290449 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1290463 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
1290482 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1290502 TTGCGAT
1 TTGCGAT
1290509 AGACATTAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
14 12 0.16
16 14 0.19
17 14 0.19
19 25 0.33
20 10 0.13
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1290507 original size:20 final size:19
Alignment explanation
Indices: 1290461--1290515 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1290451 GCGATTCTCT
**
1290461 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1290480 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1290500 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
1290516 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1293080 original size:24 final size:24
Alignment explanation
Indices: 1293029--1293080 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1293019 ATCTGAGTAT
** *
1293029 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
1293053 TGACCAAGATCAAATGT-CGAATAC
1 TGACCAAGATCAAA-GTCCGAATAC
1293077 TGAC
1 TGAC
1293081 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1293937 original size:20 final size:19
Alignment explanation
Indices: 1293914--1294301 Score: 214
Period size: 21 Copynumber: 19.3 Consensus size: 19
1293904 AGAATCTCGT
1293914 TGCGATTTACTAAATCGCAA
1 TGCGA-TTACTAAATCGCAA
*
1293934 TGCGATTAGTAAATCG-AA
1 TGCGATTACTAAATCGCAA
**
1293952 -GCGAATTAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
1293972 TGCGATTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
* *
1293992 TGCGAAATAGTAAAATCGCAA
1 TGCG-ATTACT-AAATCGCAA
1294013 TGCGATTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
*
1294033 TGCGGTTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
**
1294053 TGCGAATTAGAAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
* **
1294074 TGCGAATCAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
* **
1294095 TGCGAATCAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
*
1294116 TGAGATTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
**
1294136 TGCGTATTAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
*
1294157 TGTGATTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
**
1294177 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
* *
1294198 T--GAATACGT-AATCGCAT
1 TGCGATTAC-TAAATCGCAA
* * *
1294215 TGCGATTTTCCTAATTCGCAT
1 TGCGA--TTACTAAATCGCAA
*
1294236 TGCGATTACGT-AATCGCAT
1 TGCGATTAC-TAAATCGCAA
* * *
1294255 TGCGATTTTCCTAATTCGCAT
1 TGCGA--TTACTAAATCGCAA
1294276 TGCGATTTACGT-AATCGCAA
1 TGCGA-TTAC-TAAATCGCAA
1294296 TGCGAT
1 TGCGAT
1294302 AGTCAGAATC
Statistics
Matches: 300, Mismatches: 41, Indels: 55
0.76 0.10 0.14
Matches are distributed among these distances:
17 11 0.04
18 9 0.03
19 36 0.12
20 109 0.36
21 135 0.45
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (19 bp):
TGCGATTACTAAATCGCAA
Found at i:1294009 original size:21 final size:20
Alignment explanation
Indices: 1293925--1294199 Score: 278
Period size: 21 Copynumber: 13.6 Consensus size: 20
1293915 GCGATTTACT
1293925 AAATCGCAATGCGATTAGT-
1 AAATCGCAATGCGATTAGTA
*
1293944 AAATCG-AA-GCGAATTAGGA
1 AAATCGCAATGCG-ATTAGTA
1293963 AAATCGCAATGCGATTACGT-
1 AAATCGCAATGCGATTA-GTA
*
1293983 AAATCGCAATGCGAAATAGTA
1 AAATCGCAATGCG-ATTAGTA
1294004 AAATCGCAATGCGATTACGT-
1 AAATCGCAATGCGATTA-GTA
*
1294024 AAATCGCAATGCGGTTACGT-
1 AAATCGCAATGCGATTA-GTA
*
1294044 AAATCGCAATGCGAATTAGAA
1 AAATCGCAATGCG-ATTAGTA
* *
1294065 AAATCGCAATGCGAATCAGGA
1 AAATCGCAATGCG-ATTAGTA
* *
1294086 AAATCGCAATGCGAATCAGGA
1 AAATCGCAATGCG-ATTAGTA
*
1294107 AAATCGCAATGAGATTACGT-
1 AAATCGCAATGCGATTA-GTA
*
1294127 AAATCGCAATGCGTATTAGGA
1 AAATCGCAATGCG-ATTAGTA
*
1294148 AAATCGCAATGTGATTACGT-
1 AAATCGCAATGCGATTA-GTA
*
1294168 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCG-ATTAGTA
1294189 AAATCGCAATG
1 AAATCGCAATG
1294200 AATACGTAAT
Statistics
Matches: 222, Mismatches: 18, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.01
18 7 0.03
19 12 0.05
20 90 0.41
21 110 0.50
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.21
Consensus pattern (20 bp):
AAATCGCAATGCGATTAGTA
Found at i:1294009 original size:41 final size:41
Alignment explanation
Indices: 1293914--1294300 Score: 323
Period size: 41 Copynumber: 9.6 Consensus size: 41
1293904 AGAATCTCGT
*
1293914 TGCGATTTAC-TAAATCGCAATGCG-ATTA-GTAAATCG-AA
1 TGCGA-TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* * * *
1293952 -GCGAATTAGGAAAATCGCAATGCG-ATTACGTAAATCGCAA
1 TGCG-ATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* * *
1293992 TGCGAAATA-GTAAAATCGCAATGCG-ATTACGTAAATCGCAA
1 TGCG-ATTACGT-AAATCGCAATGCGAATTAGGAAAATCGCAA
* *
1294033 TGCGGTTACGTAAATCGCAATGCGAATTAGAAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* * * *
1294074 TGCGAATCAGGAAAATCGCAATGCGAATCAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* *
1294116 TGAGATTACGTAAATCGCAATGCGTATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
*
1294157 TGTGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* * * **** * *
1294198 T--GAATACGT-AATCGCATTGCGATTTTCCTAATTCGCAT
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* * **** * *
1294236 TGCGATTACGT-AATCGCATTGCGATTTTCCTAATTCGCAT
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1294276 TGCGATTTACGT-AATCGCAATGCGA
1 TGCGA-TTACGTAAATCGCAATGCGA
1294301 TAGTCAGAAT
Statistics
Matches: 303, Mismatches: 34, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
37 6 0.02
38 40 0.13
39 15 0.05
40 59 0.19
41 149 0.49
42 34 0.11
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
Found at i:1294251 original size:40 final size:41
Alignment explanation
Indices: 1294202--1294301 Score: 184
Period size: 40 Copynumber: 2.5 Consensus size: 41
1294192 TCGCAATGAA
1294202 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGA-T
1 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1294242 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
*
1294283 TACGTAATCGCAATGCGAT
1 TACGTAATCGCATTGCGAT
1294302 AGTCAGAATC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
40 39 0.67
41 19 0.33
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (41 bp):
TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
Found at i:1297836 original size:13 final size:13
Alignment explanation
Indices: 1297804--1297828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1297794 GATAAAATAT
1297804 ATCAATTGTGGGA
1 ATCAATTGTGGGA
1297817 ATCAATTGTGGG
1 ATCAATTGTGGG
1297829 TGACAATTCG
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:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (13 bp):
ATCAATTGTGGGA
Found at i:1307162 original size:65 final size:64
Alignment explanation
Indices: 1307046--1307171 Score: 218
Period size: 65 Copynumber: 2.0 Consensus size: 64
1307036 AATGTTAAGC
*
1307046 CGAGCGACCTTTAACAAATGTTTATGTTTTTTTTATCTCCCCATTTTGCTGGGGTGTACCAGCA
1 CGAGCGACCTTTAACAAATGTTTATGTTTTTTTTATCTACCCATTTTGCTGGGGTGTACCAGCA
1307110 CGAGCGACCTTTAACAAA-GTTTATGTTTTTTTCTTATCTACCCATTTTGCTGGGGTGTACCA
1 CGAGCGACCTTTAACAAATGTTTATG-TTTTTT-TTATCTACCCATTTTGCTGGGGTGTACCA
1307172 ACACAAGAAC
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
63 7 0.12
64 24 0.41
65 28 0.47
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (64 bp):
CGAGCGACCTTTAACAAATGTTTATGTTTTTTTTATCTACCCATTTTGCTGGGGTGTACCAGCA
Found at i:1309859 original size:46 final size:45
Alignment explanation
Indices: 1309764--1309866 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
1309754 CACTAAGAGA
* *
1309764 GCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGT
1 GCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGT
* *
1309809 GCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGT
1 GCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGT
*
1309855 GCATCGGTGCAT
1 GCATCGATGCAT
1309867 GGTATGTGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
45 26 0.51
46 22 0.43
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
GCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGT
Found at i:1309944 original size:65 final size:63
Alignment explanation
Indices: 1309807--1309932 Score: 148
Period size: 65 Copynumber: 2.0 Consensus size: 63
1309797 AATAGCCAGA
* *
1309807 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTACATCGATGCATGGTAT
* **
1309872 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTACATCGATGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTACATCGATGCATGG
1309933 ATTGGTGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
62 3 0.06
63 3 0.06
64 19 0.36
65 28 0.53
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTACATCGATGCATGGTAT
Found at i:1318485 original size:65 final size:65
Alignment explanation
Indices: 1318352--1318509 Score: 205
Period size: 65 Copynumber: 2.4 Consensus size: 65
1318342 AACTAAGAGT
* * *
1318352 GCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGT
1 GCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGA
* * * *
1318416 GCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TAT
1 GCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-G
1318479 GA
64 GA
*
1318481 GCATCGATGCATGAAATGCATTCGATGTT
1 GCATCGATGCATCAAATGCATTCGATGTT
1318510 CAATTAATTC
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
64 27 0.33
65 53 0.64
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (65 bp):
GCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGA
Found at i:1327316 original size:25 final size:27
Alignment explanation
Indices: 1327270--1327322 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1327260 GGGCTGGTCC
1327270 ACACCATTTCATAATTGCAGA-TATTTT
1 ACACCATTTCA-AATTGCAGATTATTTT
1327297 ACACCATTTC-AATT-CAAGATTATTTT
1 ACACCATTTCAAATTGC-AGATTATTTT
1327323 TCAAAACCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.04
25 7 0.29
26 6 0.25
27 10 0.42
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (27 bp):
ACACCATTTCAAATTGCAGATTATTTT
Found at i:1332541 original size:17 final size:16
Alignment explanation
Indices: 1332510--1332543 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1332500 AATCATATGC
1332510 ATATTTTTATAATAAA
1 ATATTTTTATAATAAA
*
1332526 ATATTATTTTTAATAAA
1 ATATT-TTTATAATAAA
1332543 A
1 A
1332544 CCATCTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTTTATAATAAA
Found at i:1339040 original size:26 final size:27
Alignment explanation
Indices: 1338988--1339041 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
1338978 TTTTAAGGAC
1338988 TAAATGATTTGTTTGTAACAATATTTTAAT
1 TAAATGATTTGTTTGTAAC---ATTTTAAT
1339018 TAAATGATTTGTTTGTAAC-TTTTA
1 TAAATGATTTGTTTGTAACATTTTA
1339042 GGAAAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.21
30 19 0.79
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (27 bp):
TAAATGATTTGTTTGTAACATTTTAAT
Found at i:1339444 original size:2 final size:2
Alignment explanation
Indices: 1339437--1339461 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1339427 ATTTAACGTG
1339437 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1339462 TTTTATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1340944 original size:14 final size:14
Alignment explanation
Indices: 1340925--1340952 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1340915 TTTGTTTTTT
1340925 ATTTTCTTTATTTA
1 ATTTTCTTTATTTA
1340939 ATTTTCTTTATTTA
1 ATTTTCTTTATTTA
1340953 TTTCTTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTCTTTATTTA
Found at i:1345785 original size:60 final size:60
Alignment explanation
Indices: 1345678--1345791 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
1345668 TTTGGGGATG
* * * *
1345678 TAGAAAGAGGGTCATAGTTTAGGGATGGAATTAGAATGTTCAAAAGTTTAAGGACTAAAT
1 TAGAAAGAGAGTCATAATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAAAT
*
1345738 TAGAATGAGAGTCATAATTTAGGGATGAAATT-GAAATATT-AAGAAGTTTAAGGA
1 TAGAAAGAGAGTCATAATTTAGGGATGAAATTAG-AATATTCAA-AAGTTTAAGGA
1345792 ACAATTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.29
Consensus pattern (60 bp):
TAGAAAGAGAGTCATAATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAAAT
Found at i:1345805 original size:60 final size:60
Alignment explanation
Indices: 1345688--1345806 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
1345678 TAGAAAGAGG
* * * *
1345688 GTCATAGTTTAGGGATGGAATTAGAATGTTCAAAAGTTTAAGGACTAAATTAGAATGAGA
1 GTCATAATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAAATTAAAATGAGA
*
1345748 GTCATAATTTAGGGATGAAATT-GAAATATT-AAGAAGTTTAAGGAAC-AATTTAAAATGAG
1 GTCATAATTTAGGGATGAAATTAG-AATATTCAA-AAGTTTAAGG-ACTAAATTAAAATGAG
1345807 GGTTATAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 3 0.06
60 46 0.90
61 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (60 bp):
GTCATAATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAAATTAAAATGAGA
Found at i:1348999 original size:21 final size:21
Alignment explanation
Indices: 1348975--1349072 Score: 79
Period size: 21 Copynumber: 4.7 Consensus size: 21
1348965 ATCCTGCAAT
*
1348975 GGTGGCATCTGAACCGACTGC
1 GGTGGCATCTGAAACGACTGC
* *
1348996 GGTGGCATCTGAAATGACTGT
1 GGTGGCATCTGAAACGACTGC
* * ** *
1349017 GGTGCCATCTGAAATGGTTGT
1 GGTGGCATCTGAAACGACTGC
* * *
1349038 TGTGCCATCTGAAACGAATGC
1 GGTGGCATCTGAAACGACTGC
* *
1349059 GGTGCCATATGAAA
1 GGTGGCATCTGAAA
1349073 TGGCTACGAG
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (21 bp):
GGTGGCATCTGAAACGACTGC
Found at i:1350234 original size:21 final size:21
Alignment explanation
Indices: 1350208--1350259 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1350198 GGACCTATCA
*
1350208 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTAATCTGTG
1350229 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTAATCTGTG
*
1350250 TCCCGTAGGA
1 TCCCGAAGGA
1350260 CCTATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (21 bp):
TCCCGAAGGATGTAATCTGTG
Found at i:1350445 original size:23 final size:24
Alignment explanation
Indices: 1350418--1350503 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 24
1350408 GTGTAACCAT
1350418 GTATTTCATA-TCATATGTATCTC
1 GTATTTCATATTCATATGTATCTC
* *
1350441 GTATTACATATTCATATGTCATTTC
1 GTATTTCATATTCATATGT-ATCTC
* * * *
1350466 --ATATCATA-TCACATATATCAC
1 GTATTTCATATTCATATGTATCTC
*
1350487 GTATTGCATATTCATAT
1 GTATTTCATATTCATAT
1350504 ATCATTTCAT
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
21 3 0.06
22 6 0.13
23 21 0.45
24 13 0.28
25 4 0.09
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.44
Consensus pattern (24 bp):
GTATTTCATATTCATATGTATCTC
Found at i:1350476 original size:46 final size:46
Alignment explanation
Indices: 1350423--1350515 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
1350413 ACCATGTATT
* * * *
1350423 TCATATCATATGTATCTCGTATTACATATTCATATGTCATTTCATA
1 TCATATCACATATATCACGTATTACATATTCATATATCATTTCATA
*
1350469 TCATATCACATATATCACGTATTGCATATTCATATATCATTTCATA
1 TCATATCACATATATCACGTATTACATATTCATATATCATTTCATA
1350515 T
1 T
1350516 AGTCACATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (46 bp):
TCATATCACATATATCACGTATTACATATTCATATATCATTTCATA
Found at i:1356951 original size:15 final size:16
Alignment explanation
Indices: 1356919--1356952 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1356909 CGTACAAATG
1356919 TCCCGAAGGACCTATCA
1 TCCCGAAGGA-CTATCA
1356936 TCCCGAAGGA-TATCA
1 TCCCGAAGGACTATCA
1356951 TC
1 TC
1356953 TGTGTCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (16 bp):
TCCCGAAGGACTATCA
Found at i:1356965 original size:21 final size:21
Alignment explanation
Indices: 1356936--1356981 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1356926 GGACCTATCA
* *
1356936 TCCCGAAGGATATCATCTGTG
1 TCCCAAAGGATATAATCTGTG
*
1356957 TCCCAAAGGATGTAATCTGTG
1 TCCCAAAGGATATAATCTGTG
1356978 TCCC
1 TCCC
1356982 GTGGGACCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (21 bp):
TCCCAAAGGATATAATCTGTG
Found at i:1357201 original size:46 final size:46
Alignment explanation
Indices: 1357144--1357248 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
1357134 ATGTGTAACC
1357144 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
1357189 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
1357235 ATATCATTTCATAT
1 ATGTCATTTCATAT
1357249 AGTCACATAG
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:1359580 original size:24 final size:23
Alignment explanation
Indices: 1359526--1359580 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
1359516 ACTAAAAAAT
*
1359526 AAATAAAT-AAATAAAACATTTA
1 AAATAATTAAAATAAAACATTTA
* *
1359548 CAATAATTAAAATAACACAATTTA
1 AAATAATTAAAATAAAAC-ATTTA
*
1359572 AAATTATTA
1 AAATAATTA
1359581 TTGTATCGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 6 0.23
23 8 0.31
24 12 0.46
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATAATTAAAATAAAACATTTA
Found at i:1367922 original size:6 final size:6
Alignment explanation
Indices: 1367911--1367974 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
1367901 CATGCACCAA
1367911 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1367959 ACGACC ACGACC ACGA
1 ACGACC ACGACC ACGA
1367975 GCCGAGCCGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.34, C:0.48, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:1368023 original size:5 final size:5
Alignment explanation
Indices: 1367972--1368020 Score: 80
Period size: 5 Copynumber: 9.8 Consensus size: 5
1367962 ACCACGACCA
* *
1367972 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1368021 ACGGACGGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.24, C:0.35, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:1373873 original size:6 final size:6
Alignment explanation
Indices: 1373862--1373904 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1373852 GACACGTATT
*
1373862 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1373905 GCCGAGCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:1383710 original size:44 final size:44
Alignment explanation
Indices: 1383660--1383761 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
1383650 TGCACAGGGA
* **
1383660 GTGCATCGATGCA-CCCATTAAAATGGAAACATCGAATGGGATTG
1 GTGCATCGATGCATCCC-CTAAAATACAAACATCGAATGGGATTG
* *
1383704 GTGCATCGATACATCCCCTAAAATACAAACATCGAATGGGATTT
1 GTGCATCGATGCATCCCCTAAAATACAAACATCGAATGGGATTG
*
1383748 GTGCACCGATGCAT
1 GTGCATCGATGCAT
1383762 AGATAGTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 47 0.94
45 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (44 bp):
GTGCATCGATGCATCCCCTAAAATACAAACATCGAATGGGATTG
Found at i:1386503 original size:18 final size:18
Alignment explanation
Indices: 1386480--1386520 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1386470 AGAGATGATA
1386480 AAGAATAAAATTCTGTAT
1 AAGAATAAAATTCTGTAT
* *
1386498 AAGAATAAAGTTTTGTAT
1 AAGAATAAAATTCTGTAT
1386516 AAGAA
1 AAGAA
1386521 ATAGGGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGAATAAAATTCTGTAT
Found at i:1387968 original size:44 final size:44
Alignment explanation
Indices: 1387918--1388019 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
1387908 TGCACAGGGA
* **
1387918 GTGCATCGATGCA-CCCATTAAAATGGAAACATCGAATGGGATTG
1 GTGCATCGATGCATCCC-CTAAAATACAAACATCGAATGGGATTG
* *
1387962 GTGCATCGATACATCCCCTAAAATACAAACATCGAATGGGATTT
1 GTGCATCGATGCATCCCCTAAAATACAAACATCGAATGGGATTG
*
1388006 GTGCACCGATGCAT
1 GTGCATCGATGCAT
1388020 AGATAGTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 47 0.94
45 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (44 bp):
GTGCATCGATGCATCCCCTAAAATACAAACATCGAATGGGATTG
Found at i:1390746 original size:18 final size:18
Alignment explanation
Indices: 1390723--1390763 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1390713 CAAGATGATA
1390723 AAGAATAAAATTCTGTAT
1 AAGAATAAAATTCTGTAT
* *
1390741 AAGAATAAAGTTTTGTAT
1 AAGAATAAAATTCTGTAT
1390759 AAGAA
1 AAGAA
1390764 ATAGGGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGAATAAAATTCTGTAT
Found at i:1392225 original size:63 final size:62
Alignment explanation
Indices: 1392158--1392296 Score: 179
Period size: 63 Copynumber: 2.2 Consensus size: 62
1392148 ACAGGAAGTA
* ** *
1392158 CATCGATGCACCCATTAAAATGGAAACATCGAATGCGATTGGTGCATCGATGCATAAAGAGTG
1 CATCGATGCACCC-CTAAAATACAAACATCGAATGCGATTGGTGCACCGATGCATAAAGAGTG
* * * *
1392221 CATCGATGCATCCCCTAAAATACAAACATCGAATGGGATTTGTGCACCGATGCATAGATAGTG
1 CATCGATGCA-CCCCTAAAATACAAACATCGAATGCGATTGGTGCACCGATGCATAAAGAGTG
*
1392284 CTTCGATGCACCC
1 CATCGATGCACCC
1392297 GTCTAGGGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
62 3 0.05
63 60 0.91
64 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (62 bp):
CATCGATGCACCCCTAAAATACAAACATCGAATGCGATTGGTGCACCGATGCATAAAGAGTG
Found at i:1393911 original size:23 final size:23
Alignment explanation
Indices: 1393854--1393914 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1393844 CTCGTATAAA
*
1393854 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1393877 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1393900 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
1393915 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1400800 original size:23 final size:23
Alignment explanation
Indices: 1400768--1400874 Score: 178
Period size: 23 Copynumber: 4.7 Consensus size: 23
1400758 CTCGTATAAA
*
1400768 TGCACAGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1400791 TACACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1400814 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1400837 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1400860 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1400875 TATAAGATTG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1404668 original size:11 final size:11
Alignment explanation
Indices: 1404635--1404660 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1404625 TATTAAGCTT
1404635 AAATGAATTTA
1 AAATGAATTTA
1404646 AAATGAATTTA
1 AAATGAATTTA
1404657 AAAT
1 AAAT
1404661 TCATTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (11 bp):
AAATGAATTTA
Found at i:1405140 original size:7 final size:7
Alignment explanation
Indices: 1405124--1405169 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
1405114 CTTTTAAAAT
1405124 TTTTAAA
1 TTTTAAA
*
1405131 TTTTATA
1 TTTTAAA
1405138 TTTTAAA
1 TTTTAAA
*
1405145 TTTTATA
1 TTTTAAA
*
1405152 CTTTAAA
1 TTTTAAA
*
1405159 TTTTATA
1 TTTTAAA
1405166 TTTT
1 TTTT
1405170 GACCACTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTTAAA
Found at i:1405143 original size:14 final size:14
Alignment explanation
Indices: 1405124--1405169 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
1405114 CTTTTAAAAT
1405124 TTTTAAATTTTATA
1 TTTTAAATTTTATA
1405138 TTTTAAATTTTATA
1 TTTTAAATTTTATA
*
1405152 CTTTAAATTTTATA
1 TTTTAAATTTTATA
1405166 TTTT
1 TTTT
1405170 GACCACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTAAATTTTATA
Found at i:1406862 original size:21 final size:21
Alignment explanation
Indices: 1406836--1406880 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1406826 ATACAAATCG
*
1406836 ATTTTTCTTTGAAATATAATAA
1 ATTTTACTTTGAAATA-AATAA
* *
1406858 ATTTTATTTTGAATTAAATAA
1 ATTTTACTTTGAAATAAATAA
1406879 AT
1 AT
1406881 AATTCAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTTACTTTGAAATAAATAA
Found at i:1410471 original size:17 final size:18
Alignment explanation
Indices: 1410445--1410485 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1410435 TAAATTTAAA
*
1410445 ATTTTATTAA-TTATTTC
1 ATTTTTTTAACTTATTTC
*
1410462 ATTTTTTTAACTTATTTT
1 ATTTTTTTAACTTATTTC
1410480 ATTTTT
1 ATTTTT
1410486 ATTTAGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTTAACTTATTTC
Found at i:1416497 original size:17 final size:19
Alignment explanation
Indices: 1416475--1416516 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1416465 ATTAGTATTT
1416475 TGTTAA-GTA-GTATGAAA
1 TGTTAAGGTATGTATGAAA
*
1416492 TGTTAAGGTATTTATGAAA
1 TGTTAAGGTATGTATGAAA
1416511 TGTTAA
1 TGTTAA
1416517 ATTGTTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 3 0.14
19 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (19 bp):
TGTTAAGGTATGTATGAAA
Found at i:1422077 original size:13 final size:13
Alignment explanation
Indices: 1422059--1422093 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1422049 TTCAATTTCA
1422059 GTATGTGTTTAAT
1 GTATGTGTTTAAT
*
1422072 GTATGTGTTTCAT
1 GTATGTGTTTAAT
1422085 GTATGTGTT
1 GTATGTGTT
1422094 CCAAGGCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (13 bp):
GTATGTGTTTAAT
Found at i:1423539 original size:17 final size:18
Alignment explanation
Indices: 1423519--1423557 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1423509 AAAAATTTTG
1423519 AAAAAAT-AAATAG-TTGA
1 AAAAAATGAAA-AGATTGA
1423536 AAAAAATGAAAAGATTGA
1 AAAAAATGAAAAGATTGA
1423554 AAAA
1 AAAA
1423558 GTTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (18 bp):
AAAAAATGAAAAGATTGA
Found at i:1423566 original size:28 final size:28
Alignment explanation
Indices: 1423530--1423596 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
1423520 AAAAATAAAT
* *
1423530 AGTTG-AAAAAAATGAAAAGATTG-AAAA
1 AGTTGAAAAAAAAGGAAAA-AGTGAAAAA
1423557 AGTTGAAAAAAAAGGAAAAAGTGAAAAA
1 AGTTGAAAAAAAAGGAAAAAGTGAAAAA
1423585 AGTTGAAAAAAA
1 AGTTGAAAAAAA
1423597 TAAATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 8 0.22
28 28 0.78
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (28 bp):
AGTTGAAAAAAAAGGAAAAAGTGAAAAA
Found at i:1423592 original size:18 final size:18
Alignment explanation
Indices: 1423530--1423594 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
1423520 AAAAATAAAT
* *
1423530 AGTTGAAAAAAATGAAAAG
1 AGTTG-AAAAAGTGAAAAA
1423549 A-TTGAAAAAGTTGAAAAA
1 AGTTGAAAAAG-TGAAAAA
***
1423567 AAAGGAAAAAGTGAAAAA
1 AGTTGAAAAAGTGAAAAA
1423585 AGTTGAAAAA
1 AGTTGAAAAA
1423595 AATAAATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.14
18 24 0.65
19 8 0.22
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (18 bp):
AGTTGAAAAAGTGAAAAA
Found at i:1423688 original size:19 final size:19
Alignment explanation
Indices: 1423672--1423724 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
1423662 ATAAAAATGG
1423672 AAACAAAAATAAAAAATAT
1 AAACAAAAATAAAAAATAT
*
1423691 AAACAAATA-AAAAAATAT
1 AAACAAAAATAAAAAATAT
1423709 AAA-AACAAATAAAAAA
1 AAACAA-AAATAAAAAA
1423725 AGATAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 14 0.47
19 14 0.47
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (19 bp):
AAACAAAAATAAAAAATAT
Found at i:1423705 original size:20 final size:20
Alignment explanation
Indices: 1423672--1423730 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1423662 ATAAAAATGG
* *
1423672 AAACAAA-AATAAAAAATAT
1 AAACAAATAAAAAAAAATAA
*
1423691 AAACAAATAAAAAAATATAA
1 AAACAAATAAAAAAAAATAA
*
1423711 AAACAAATAAAAAAAGATAA
1 AAACAAATAAAAAAAAATAA
1423731 TATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 7 0.20
20 28 0.80
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (20 bp):
AAACAAATAAAAAAAAATAA
Found at i:1423710 original size:10 final size:9
Alignment explanation
Indices: 1423676--1423730 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
1423666 AAATGGAAAC
1423676 AAAAATAAA
1 AAAAATAAA
*
1423685 AAATAT-AA
1 AAAAATAAA
*
1423693 ACAAATAAA
1 AAAAATAAA
1423702 AAAATATAAA
1 AAAA-ATAAA
1423712 AACAAATAAA
1 AA-AAATAAA
1423722 AAAAGATAA
1 AAAA-ATAA
1423731 TATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 6 0.16
9 12 0.32
10 18 0.47
11 2 0.05
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (9 bp):
AAAAATAAA
Found at i:1425465 original size:19 final size:20
Alignment explanation
Indices: 1425435--1425476 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1425425 TTTAATAATT
*
1425435 TTAATTTATTTTATGACGTG
1 TTAATTTATTTTATCACGTG
*
1425455 TTAATTT-TTTTCTCACGTG
1 TTAATTTATTTTATCACGTG
1425474 TTA
1 TTA
1425477 TAAACGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.57
Consensus pattern (20 bp):
TTAATTTATTTTATCACGTG
Found at i:1426683 original size:24 final size:24
Alignment explanation
Indices: 1426631--1426684 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1426621 AGGACAACCG
* *
1426631 AATAAACAAGCTTATAAATAAATT
1 AATAAACAAGCTTATAAACAAATC
* * *
1426655 GATAAATAAGCTTATAAACAAGTC
1 AATAAACAAGCTTATAAACAAATC
1426679 AATAAA
1 AATAAA
1426685 AGAACTTGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.26
Consensus pattern (24 bp):
AATAAACAAGCTTATAAACAAATC
Found at i:1427961 original size:32 final size:30
Alignment explanation
Indices: 1427914--1427973 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 30
1427904 GGATTAGAAC
1427914 TCAAAAAGAATTAAGAGATTGTGTATAAAATA
1 TCAAAAAGAATT-A-AGATTGTGTATAAAATA
1427946 TCAAAAAGTAA-TAAGATTGTGTATAAAA
1 TCAAAAAG-AATTAAGATTGTGTATAAAA
1427974 ATGAGCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 15 0.56
31 1 0.04
32 9 0.33
33 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.28
Consensus pattern (30 bp):
TCAAAAAGAATTAAGATTGTGTATAAAATA
Found at i:1428179 original size:60 final size:60
Alignment explanation
Indices: 1428014--1428169 Score: 197
Period size: 60 Copynumber: 2.6 Consensus size: 60
1428004 TACGTATTTT
* ** *
1428014 ATTCCAAATTAGTCCTTAAACTTTT-AAATATTTTAAATACATCCCCAAACTATAACTATC
1 ATTCTAAATTAGTCCTTAAACTTTTGAAA-ATTCCAAATACATCCCCAAACTATAACCATC
* * * * *
1428074 ATTCTAAATTGGTCCTTAAACTTTTGAATATTCCAAATTCATCCCCAAACTATGACCCTC
1 ATTCTAAATTAGTCCTTAAACTTTTGAAAATTCCAAATACATCCCCAAACTATAACCATC
* *
1428134 ATTCTATATTAGTCCTCAAACTTTTGAAAATTCCAA
1 ATTCTAAATTAGTCCTTAAACTTTTGAAAATTCCAA
1428170 TAACTTCCCC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 80 0.98
61 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (60 bp):
ATTCTAAATTAGTCCTTAAACTTTTGAAAATTCCAAATACATCCCCAAACTATAACCATC
Found at i:1428377 original size:60 final size:59
Alignment explanation
Indices: 1428201--1428384 Score: 165
Period size: 60 Copynumber: 3.1 Consensus size: 59
1428191 AAAAGTTTGG
* * * * * * * *
1428201 GGATAAAATCAGAATATTCATAAGTTTGGAGATCAATATAGAATGAGGGTCATAGTTTAA
1 GGAT-AAATTAGAATATTTAAAAATTTAGAGATTAATTTAGAATGAGAGTCATAGTTTAA
* * * * * * *
1428261 GGATAGATTCAAAATGTTTAAAATTTTAGGGATTAATTTAGAATAAGAAT-AGTAGTTT-A
1 GGATAAATT-AGAATATTTAAAAATTTAGAGATTAATTTAGAATGAGAGTCA-TAGTTTAA
*
1428320 GAGATGAAATTAGAATATTTAAAAATTTAGAGATTAATTTAGAATGAGAGTCATAGTTTGA
1 G-GAT-AAATTAGAATATTTAAAAATTTAGAGATTAATTTAGAATGAGAGTCATAGTTTAA
1428381 GGAT
1 GGAT
1428385 GTATAGTGCA
Statistics
Matches: 97, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
59 6 0.06
60 84 0.87
61 7 0.07
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (59 bp):
GGATAAATTAGAATATTTAAAAATTTAGAGATTAATTTAGAATGAGAGTCATAGTTTAA
Found at i:1430511 original size:30 final size:30
Alignment explanation
Indices: 1430475--1430535 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1430465 TCATGTAGAC
1430475 GTAGTTGTTCAAACCAGAGACTTCGAGGGA
1 GTAGTTGTTCAAACCAGAGACTTCGAGGGA
1430505 GTAGTTGTTCAAACCAGAGACTTCGAGGGA
1 GTAGTTGTTCAAACCAGAGACTTCGAGGGA
1430535 G
1 G
1430536 AACAAGACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (30 bp):
GTAGTTGTTCAAACCAGAGACTTCGAGGGA
Found at i:1436137 original size:23 final size:24
Alignment explanation
Indices: 1436101--1436166 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1436091 AATAATTATG
1436101 CTTTTAT-AGCACGTTTTCTTCTGC
1 CTTTTATGA-CACGTTTTCTTCTGC
* * *
1436125 C-TTTATGATACGTTTTTTTTTTGC
1 CTTTTATGACACG-TTTTCTTCTGC
1436149 CTTTTATGACACGTTTTC
1 CTTTTATGACACGTTTTC
1436167 GGTCGTTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 8 0.24
24 16 0.47
25 10 0.29
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.55
Consensus pattern (24 bp):
CTTTTATGACACGTTTTCTTCTGC
Found at i:1436858 original size:15 final size:15
Alignment explanation
Indices: 1436835--1436864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1436825 TCAAGGAAAT
1436835 TAAAAATAAAGATAA
1 TAAAAATAAAGATAA
*
1436850 TAAAGATAAAGATAA
1 TAAAAATAAAGATAA
1436865 AATACAATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
TAAAAATAAAGATAA
Found at i:1436926 original size:13 final size:13
Alignment explanation
Indices: 1436908--1436947 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
1436898 CATAGTTGAA
1436908 CAGTCTTCATATG
1 CAGTCTTCATATG
1436921 CAGTCTTCATATG
1 CAGTCTTCATATG
1436934 CAGTCTTCATATG
1 CAGTCTTCATATG
1436947 C
1 C
1436948 GCGTCTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1438633 original size:2 final size:2
Alignment explanation
Indices: 1438626--1438665 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1438616 TCTTTAACTC
1438626 TA TA TA TA 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 TA TA TA TA
1438666 GATCCACGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1445981 original size:13 final size:13
Alignment explanation
Indices: 1445944--1445982 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1445934 AGTAACAATA
1445944 AAATGATTAAATT
1 AAATGATTAAATT
* *
1445957 AAATAATAAAATT
1 AAATGATTAAATT
1445970 AAATGATTAAATT
1 AAATGATTAAATT
1445983 TAATTTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (13 bp):
AAATGATTAAATT
Found at i:1446744 original size:36 final size:36
Alignment explanation
Indices: 1446672--1446743 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
1446662 TTAAGGTTTC
* *
1446672 ACCCGACCCGACCCGACCCGAATATATGACTTAAAA
1 ACCCGACCCGACCCGACCCGAATATATGAATAAAAA
1446708 ACCCGACCCGACCCGACCCGAA-ATAAT-AATAAAAA
1 ACCCGACCCGACCCGACCCGAATAT-ATGAATAAAAA
1446743 A
1 A
1446744 AAATTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.11
Consensus pattern (36 bp):
ACCCGACCCGACCCGACCCGAATATATGAATAAAAA
Found at i:1447089 original size:31 final size:29
Alignment explanation
Indices: 1447052--1447131 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
1447042 ACTATTTGTG
1447052 AAAATAAATATTTAAAATTATTTTCTTAGTC
1 AAAATAAATATTTAAAA-TATTTTCTTA-TC
* *
1447083 AAAATAAGTATTTAAAATATTTTTTTATC
1 AAAATAAATATTTAAAATATTTTCTTATC
* * *
1447112 AAAATAGATACTTATAATAT
1 AAAATAAATATTTAAAATAT
1447132 ACATTTTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 18 0.42
30 9 0.21
31 16 0.37
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (29 bp):
AAAATAAATATTTAAAATATTTTCTTATC
Found at i:1448370 original size:126 final size:127
Alignment explanation
Indices: 1448188--1448439 Score: 497
Period size: 126 Copynumber: 2.0 Consensus size: 127
1448178 AGCTGGGAAT
1448188 TTGCTTCAACAGCACAGAGAACAACAAAGAAAACTATAAAACCCCACTCATAGTTTTGAGTTTTG
1 TTGCTTCAACAGCACAGAGAACAACAAAGAAAACTATAAAACCCCACTCATAGTTTTGAGTTTTG
1448253 ACAAAATATGTTTGAGAACTAAAACAATCTTATCATAGCACTGCAAAAGAACCAAAGCAAAA
66 ACAAAATATGTTTGAGAACTAAAACAATCTTATCATAGCACTGCAAAAGAACCAAAGCAAAA
1448315 TTGCTTCAACAGCACAGAGAACAACAAA-AAAACTATAAAACCCCACTCATAGTTTTGAGTTTTG
1 TTGCTTCAACAGCACAGAGAACAACAAAGAAAACTATAAAACCCCACTCATAGTTTTGAGTTTTG
1448379 ACAAAATATGTTTGAGAACTAAAACAATCTTATCATAGCACTGCAAAAGAACCAAAGCAAA
66 ACAAAATATGTTTGAGAACTAAAACAATCTTATCATAGCACTGCAAAAGAACCAAAGCAAA
1448440 CACATAAATG
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 97 0.78
127 28 0.22
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (127 bp):
TTGCTTCAACAGCACAGAGAACAACAAAGAAAACTATAAAACCCCACTCATAGTTTTGAGTTTTG
ACAAAATATGTTTGAGAACTAAAACAATCTTATCATAGCACTGCAAAAGAACCAAAGCAAAA
Found at i:1448989 original size:2 final size:2
Alignment explanation
Indices: 1448984--1449011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1448974 ACACACACAC
1448984 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
1449012 GAATTTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1454266 original size:22 final size:23
Alignment explanation
Indices: 1454241--1454289 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1454231 ATTATCTATT
*
1454241 TTTAAAATGTA-TTTTAATGAAA
1 TTTAAAATGCAGTTTTAATGAAA
**
1454263 TTTATGATGCAGTTTTAATGAAA
1 TTTAAAATGCAGTTTTAATGAAA
1454286 TTTA
1 TTTA
1454290 TTGAAATACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (23 bp):
TTTAAAATGCAGTTTTAATGAAA
Found at i:1456224 original size:18 final size:18
Alignment explanation
Indices: 1456201--1456250 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
1456191 GTCGAGGGAT
*
1456201 TAGTGGTCATTCGGGACA
1 TAGTGGTCCTTCGGGACA
1456219 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
1456237 TAGTGGTCCTTCGG
1 TAGTGGTCCTTCGG
1456251 ACAAATATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.30
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:1458121 original size:6 final size:6
Alignment explanation
Indices: 1458110--1458148 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1458100 GGCTACCCAG
* *
1458110 AGAGGA AGAGGA AGAGGA AGAGGT AGAGGT AGAGGA AGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGA
1458149 AGTCAATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.05
Consensus pattern (6 bp):
AGAGGA
Found at i:1462994 original size:18 final size:18
Alignment explanation
Indices: 1462961--1463030 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
1462951 GGGATTATCG
1462961 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
1462979 GTTGTCTTTTGGGACATA
1 GTGGTCCTTCGGGACATA
1462997 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1463015 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
1463031 AATATTTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1473984 original size:111 final size:111
Alignment explanation
Indices: 1473787--1473987 Score: 271
Period size: 111 Copynumber: 1.8 Consensus size: 111
1473777 ATTGTTTTAT
* * *
1473787 TTTTTATTTTAAATATATATTAATTAGATTATTTATTTTGATTTTATAGATTAACTATATTTGCG
1 TTTTTATTTTAAATATATAGTAATTAGACTATTTATTTTGATTTTATAGATTAACTATATTTGAG
* * *
1473852 TGGTTTGGTAAGTTTAATTTAAATTTGCGTATAATTTTTAGTGTAA
66 TAGCTTGATAAGTTTAATTTAAATTTGCGTATAATTTTTAGTGTAA
* * * *
1473898 TTTTTGTTTTAAATA-ATAAGT-ATTAGACTATTTATTTTGATTTTATATATTAAGTTGTATTTG
1 TTTTTATTTTAAATATAT-AGTAATTAGACTATTTATTTTGATTTTATAGATTAA-CTATATTTG
*
1473961 AGTAGCTTGATAAGTTTAGTTTAAATT
64 AGTAGCTTGATAAGTTTAATTTAAATT
1473988 ATATTTTTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
110 32 0.42
111 45 0.58
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.54
Consensus pattern (111 bp):
TTTTTATTTTAAATATATAGTAATTAGACTATTTATTTTGATTTTATAGATTAACTATATTTGAG
TAGCTTGATAAGTTTAATTTAAATTTGCGTATAATTTTTAGTGTAA
Found at i:1474303 original size:117 final size:119
Alignment explanation
Indices: 1474107--1474322 Score: 289
Period size: 117 Copynumber: 1.8 Consensus size: 119
1474097 TAAGGTTTAG
*
1474107 GGTTTTTATTGTAAATATAAATTAACTAGACTATTTATTTTGATTTTACAAATTAAACAATATTC
1 GGTTTTTATTGTAAATATAAATTAACTAGACTATTTATTTTGATTATACAAATTAAACAATATTC
* * *
1474172 GAGTGGTTTGGTAAGTTTAATTTATATT-TTTTTGTAATTTTTAGTATAATTTT
66 GAGTAGTTTCGTAAGTTTAATTTAAATTATTTTTGTAATTTTTAGTATAATTTT
* * * *
1474225 GGTTTTTAATT-TAAAT-TATAATT-ATTAGACTATTTATTTTGATTATACATATTAAGTC-GTA
1 GGTTTTT-ATTGTAAATATA-AATTAACTAGACTATTTATTTTGATTATACAAATTAA-ACAATA
*
1474286 TTTGAGTAGTTTCGTAAGTTTAATTTAAATTATTTTT
63 TTCGAGTAGTTTCGTAAGTTTAATTTAAATTATTTTT
1474323 AATATAAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
117 60 0.71
118 22 0.26
119 3 0.04
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (119 bp):
GGTTTTTATTGTAAATATAAATTAACTAGACTATTTATTTTGATTATACAAATTAAACAATATTC
GAGTAGTTTCGTAAGTTTAATTTAAATTATTTTTGTAATTTTTAGTATAATTTT
Found at i:1476873 original size:14 final size:15
Alignment explanation
Indices: 1476854--1476883 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1476844 TAACTACTTA
1476854 TTATTACT-TCTAAT
1 TTATTACTCTCTAAT
1476868 TTATTACTCTCTAAT
1 TTATTACTCTCTAAT
1476883 T
1 T
1476884 CTCAACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTACTCTCTAAT
Found at i:1477063 original size:300 final size:295
Alignment explanation
Indices: 1476420--1477320 Score: 1339
Period size: 300 Copynumber: 3.0 Consensus size: 295
1476410 TTAAATTAAA
* *
1476420 TACTACAATATTATTTAACCTTGCAAAAATGTAAATATATTAACAATATTTTTTTTATAAAATAA
1 TACTACAATATTATTTAACCTTGCAAAAATATAAATATATTAACAATATTTTTTATA-AAAATAA
* *
1476485 -TACTTAAACACTATGATTACATTATAATAATGATTAAATTTATTACTTCGAATTTTTTATAACT
65 TTA-TTAAATACTATGATTACATTATAATAATGATTAAATTTATTACTTCGGA-TTTTTATAACT
* * *
1476549 ACTTATTATTACTTCGAATTTATTAGTCCCTAATTCTCAACCAAAATACCCCATTTTATAACATC
128 ACTTATTATTACTTCTAATTTATTACT-CCTAATTCTCAACCAAAACA-CCCATTTTATAACAT-
* * * *
1476614 CCGGAGTATTCATTATATTTTTCCCGTTCAACCACCAAACTACCTGAGTTATTAATGGATAATTA
190 CTGGAGTATTCATTATACTTTT-CCGTTTAACCACCAACCTACC-GAGTTATTAATGGATAATTA
1476679 ATGGTGCCATTATTTTTCGTCATTATAATAAATATTATTTTTC
253 ATGGTGCCATTATTTTTCGTCATTATAATAAATATTATTTTTC
1476722 TACTACAATATTATTTAACCTTGCAAAAATATAAATATATTAACAATATTTTTTATAAAAATAAT
1 TACTACAATATTATTTAACCTTGCAAAAATATAAATATATTAACAATATTTTTTATAAAAATAAT
1476787 TATTAAATACTATGATTACATTATAATAATGATTAAATTTATTACTTCGGATTTTTATAACTACT
66 TATTAAATACTATGATTACATTATAATAATGATTAAATTTATTACTTCGGATTTTTATAACTACT
1476852 TATTATTACTTCTAATTTATTACTCTCTAATTCTCAACCAAAACACCTCATTTTATAACATCATG
131 TATTATTACTTCTAATTTATTACTC-CTAATTCTCAACCAAAACACC-CATTTTATAACATC-TG
* *
1476917 GAATATTTATTATACTTTTCCGTTTAACCACCAACCTACTCGAGTTATTAATGGATAATTAATGG
193 GAGTATTCATTATACTTTTCCGTTTAACCACCAACCTAC-CGAGTTATTAATGGATAATTAATGG
*
1476982 TGCCATTATTTTTTGTCATTATAATAAATATTATTTTTC
257 TGCCATTATTTTTCGTCATTATAATAAATATTATTTTTC
1477021 TACTACAATATTATTTAACCTTGCAAAAAATATAAATATATTAACAATATTTTTTATAAAAATAA
1 TACTACAATATTATTTAACCTTGC-AAAAATATAAATATATTAACAATATTTTTTATAAAAATAA
* * *
1477086 TGATTAAATACTATGATTTCATTATAATAATGATTAAATTTATTACTTTGGATTTTTATAACTAC
65 TTATTAAATACTATGATTACATTATAATAATGATTAAATTTATTACTTCGGATTTTTATAACTAC
*
1477151 TTATTATTACTT-TAAATTTATTACTCCATAATTTTCAACCAAAACACCCAATTTTATAACATCT
130 TTATTATTACTTCT-AATTTATTACTCC-TAATTCTCAACCAAAACACCC-ATTTTATAACATCT
* * * *
1477215 CAGG-GTATTCATTATAC-CTTCCGGTTCACCAACCACAACCTACCCG-GATTATTAATGTATAA
192 --GGAGTATTCATTATACTTTTCCGTTTAACC-A-C-CAACCTA-CCGAG-TTATTAATGGATAA
*
1477277 TTAATGGTGCCATTATTTTTCGTTATTATAAT-AA-ATTATTTTTC
250 TTAATGGTGCCATTATTTTTCGTCATTATAATAAATATTATTTTTC
1477321 GTCATTATAA
Statistics
Matches: 557, Mismatches: 26, Indels: 34
0.90 0.04 0.06
Matches are distributed among these distances:
299 122 0.22
300 265 0.48
301 60 0.11
302 109 0.20
303 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (295 bp):
TACTACAATATTATTTAACCTTGCAAAAATATAAATATATTAACAATATTTTTTATAAAAATAAT
TATTAAATACTATGATTACATTATAATAATGATTAAATTTATTACTTCGGATTTTTATAACTACT
TATTATTACTTCTAATTTATTACTCCTAATTCTCAACCAAAACACCCATTTTATAACATCTGGAG
TATTCATTATACTTTTCCGTTTAACCACCAACCTACCGAGTTATTAATGGATAATTAATGGTGCC
ATTATTTTTCGTCATTATAATAAATATTATTTTTC
Found at i:1477316 original size:23 final size:23
Alignment explanation
Indices: 1477288--1477335 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1477278 TAATGGTGCC
*
1477288 ATTATTTTTCGTTATTATAATAA
1 ATTATTTTTCGTCATTATAATAA
1477311 ATTATTTTTCGTCATTATAATAA
1 ATTATTTTTCGTCATTATAATAA
1477334 AT
1 AT
1477336 ATTATTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTATTTTTCGTCATTATAATAA
Found at i:1482135 original size:17 final size:17
Alignment explanation
Indices: 1482100--1482201 Score: 125
Period size: 17 Copynumber: 5.9 Consensus size: 17
1482090 TATTAATCTG
1482100 TCTGATAACTGTAAAATA
1 TCTGATAACTGT-AAATA
*
1482118 TCTGATATCTGTAAATA
1 TCTGATAACTGTAAATA
*
1482135 TCTTATAACTGT-AATCA
1 TCTGATAACTGTAAAT-A
*
1482152 TCTGATATCTGTAAATA
1 TCTGATAACTGTAAATA
* *
1482169 TCTTATAACTGAAAATCA
1 TCTGATAACTGTAAAT-A
1482187 TCTGATAACTGTAAA
1 TCTGATAACTGTAAA
1482202 CATTTAGAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
16 3 0.04
17 40 0.56
18 28 0.39
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (17 bp):
TCTGATAACTGTAAATA
Found at i:1482193 original size:35 final size:35
Alignment explanation
Indices: 1482104--1482201 Score: 155
Period size: 34 Copynumber: 2.8 Consensus size: 35
1482094 AATCTGTCTG
1482104 ATAACTGTAAAAT-ATCTGATATCTGTAAATATCTT
1 ATAACTG-AAAATCATCTGATATCTGTAAATATCTT
*
1482139 ATAACTG-TAATCATCTGATATCTGTAAATATCTT
1 ATAACTGAAAATCATCTGATATCTGTAAATATCTT
*
1482173 ATAACTGAAAATCATCTGATAACTGTAAA
1 ATAACTGAAAATCATCTGATATCTGTAAA
1482202 CATTTAGAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 3 0.05
34 29 0.50
35 26 0.45
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (35 bp):
ATAACTGAAAATCATCTGATATCTGTAAATATCTT
Found at i:1483127 original size:38 final size:39
Alignment explanation
Indices: 1483076--1483159 Score: 134
Period size: 40 Copynumber: 2.2 Consensus size: 39
1483066 CACTCACCTT
1483076 TATAATAAT-ACACATTTATAAACACAACTGTCTAAATA
1 TATAATAATAACACATTTATAAACACAACTGTCTAAATA
* *
1483114 TATAATAATACACACATTTATAAACACAACTGTTTAAATC
1 TATAATAATA-ACACATTTATAAACACAACTGTCTAAATA
1483154 TATAAT
1 TATAAT
1483160 TGTTAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 9 0.21
40 33 0.79
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.33
Consensus pattern (39 bp):
TATAATAATAACACATTTATAAACACAACTGTCTAAATA
Found at i:1484032 original size:15 final size:15
Alignment explanation
Indices: 1484009--1484042 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1483999 GAAGAAATAG
1484009 ACTACTATATTAACA
1 ACTACTATATTAACA
*
1484024 ACTATTATATTAACA
1 ACTACTATATTAACA
1484039 ACTA
1 ACTA
1484043 GTTAATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (15 bp):
ACTACTATATTAACA
Found at i:1484334 original size:72 final size:72
Alignment explanation
Indices: 1484243--1484383 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
1484233 CAAGTTAATG
* *
1484243 GATTAAATTCCAATAATTAAACGAAAAGAAAAATGTTAAAGTATACAAATGGTCTTCGACTATAA
1 GATTAAATTCCAATAATTAAACCAAAAGAAAAAGGTTAAAGTATACAAATGGTCTTCGACTATAA
1484308 GGTGATA
66 GGTGATA
* * * * *
1484315 GATTAAATTCCAATGATTAAACCAAAATAAAAAGGTTAAAGTATACAAATGGTTTTTGACTATAG
1 GATTAAATTCCAATAATTAAACCAAAAGAAAAAGGTTAAAGTATACAAATGGTCTTCGACTATAA
1484380 GGTG
66 GGTG
1484384 TTGCTTCATT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (72 bp):
GATTAAATTCCAATAATTAAACCAAAAGAAAAAGGTTAAAGTATACAAATGGTCTTCGACTATAA
GGTGATA
Found at i:1485443 original size:5 final size:5
Alignment explanation
Indices: 1485433--1485463 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1485423 GAGGACCTTT
1485433 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
1485464 GGCCCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1487087 original size:2 final size:2
Alignment explanation
Indices: 1487080--1487104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1487070 CTATTTTTAA
1487080 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1487105 ATGTCTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1488320 original size:2 final size:2
Alignment explanation
Indices: 1488313--1488354 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1488303 TTAGCGACTT
1488313 TA TA TA TA TA 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 TA TA TA TA TA
1488355 AGCATTCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1495572 original size:22 final size:22
Alignment explanation
Indices: 1495544--1495608 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
1495534 GACATGTGAA
*
1495544 ATATGTCTCGAAAGACCTATGC
1 ATATGTCCCGAAAGACCTATGC
* * *
1495566 ATATGTCCCGAAGGACCTGTGT
1 ATATGTCCCGAAAGACCTATGC
*
1495588 ATATGTCCCGACAGACCTATG
1 ATATGTCCCGAAAGACCTATG
1495609 TAACCCTCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (22 bp):
ATATGTCCCGAAAGACCTATGC
Found at i:1498533 original size:21 final size:19
Alignment explanation
Indices: 1498496--1498542 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1498486 TTTATAATTT
*
1498496 TTATATTATATAATATTA-
1 TTATATGATATAATATTAG
1498514 TATATATGATATAAATTATTAG
1 T-TATATGATAT-AA-TATTAG
1498536 TTATATG
1 TTATATG
1498543 TGAAGGGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 9 0.38
20 2 0.08
21 11 0.46
22 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
TTATATGATATAATATTAG
Found at i:1510847 original size:118 final size:116
Alignment explanation
Indices: 1510724--1510985 Score: 283
Period size: 118 Copynumber: 2.2 Consensus size: 116
1510714 TCCTATTCAA
* * *
1510724 AAATTCATACATTTAGTATGATTTTGTTACCATTTTAGCACTTGAAATGCCCTATATGAAAATCC
1 AAATTCATACATTTAGTATGATTTTGTTACCATTTTAGCACATAAAATACCCTATATG-AAATCC
* * * * * * * *
1510789 ATAACATT-AGTATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATTTGG
65 AT-ACATTCAATATGATTCCCTTACCATT-TAGCACACTCAGTGCTCTATATGG
** * * * *
1510842 AAATTCATACATTTAGTATGATCCTCTTACCATTTTAGGACATAAAATACCCTATCTGGAATCCA
1 AAATTCATACATTTAGTATGATTTTGTTACCATTTTAGCACATAAAATACCCTATATGAAATCCA
**
1510907 TATTTTCAATATGATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGG
66 TACATTCAATATGATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGG
* * *
1510958 AAATCCATACACTCAGTATGATTCTTGT
1 AAATTCATACATTTAGTATGATT-TTGT
1510986 CGAGACCGTC
Statistics
Matches: 117, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
116 42 0.36
117 25 0.21
118 50 0.43
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (116 bp):
AAATTCATACATTTAGTATGATTTTGTTACCATTTTAGCACATAAAATACCCTATATGAAATCCA
TACATTCAATATGATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGG
Found at i:1510978 original size:58 final size:58
Alignment explanation
Indices: 1510640--1510981 Score: 146
Period size: 59 Copynumber: 5.8 Consensus size: 58
1510630 CCTTTCAATA
* ** * *
1510640 TTAGCACTCTCAA-TGCTCTATATGGAAGAT-CATACACTTGGTATGCTTCCCCTT-TCATT
1 TTAGCACACT-AAGTGCTCTATATGGAA-ATCCATACACTCAGTATGATT-CCCTTACCA-T
* ** * * * ***
1510699 TTAGCACACGAAGTG-TCCTAT-TCAAAAATTCATACATTTAGTATGATTTTGTTACCATT
1 TTAGCACACTAAGTGCT-CTATAT-GGAAATCCATACACTCAGTATGATTCCCTTACCA-T
* * * * * * * *
1510758 TTAGCAC-TTGAAATGCCCTATATGAAAATCCATA-ACATTAGTATGATTTCCTTATCTT
1 TTAGCACACT-AAGTGCTCTATATGGAAATCCATACAC-TCAGTATGATTCCCTTACCAT
* * * * * * *
1510816 TGTAGCACCCTTAGTGCTTTATTTGGAAATTCATACATTTAGTATGA-TCCTCTTACCATT
1 T-TAGCACACTAAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCC-CTTACCA-T
* * * * * *** *
1510876 TTAGGACA-TAAAATACCCTATCTGG-AATCCATATTTTCAATATGATTCCCTTACCAT
1 TTAGCACACT-AAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCCTTACCAT
*
1510933 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTC
1 TTAGCACACTAAGTGCTCTATATGGAAATCCATACACTCAGTATGATTC
1510982 TTGTCGAGAC
Statistics
Matches: 208, Mismatches: 57, Indels: 37
0.69 0.19 0.12
Matches are distributed among these distances:
57 18 0.09
58 56 0.27
59 129 0.62
60 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (58 bp):
TTAGCACACTAAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCCTTACCAT
Found at i:1511387 original size:14 final size:15
Alignment explanation
Indices: 1511354--1511386 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1511344 ATAAAAACAT
1511354 AAAATAAAAGTAAAA
1 AAAATAAAAGTAAAA
*
1511369 AAAATAATAGTAAAA
1 AAAATAAAAGTAAAA
1511384 AAA
1 AAA
1511387 TGTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (15 bp):
AAAATAAAAGTAAAA
Found at i:1512747 original size:16 final size:16
Alignment explanation
Indices: 1512726--1512758 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1512716 AAAATTGAGA
1512726 AATAATAATAAATAAT
1 AATAATAATAAATAAT
1512742 AATAATAATAAATAAT
1 AATAATAATAAATAAT
1512758 A
1 A
1512759 CATATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAAATAAT
Found at i:1512885 original size:32 final size:31
Alignment explanation
Indices: 1512819--1512907 Score: 115
Period size: 32 Copynumber: 2.7 Consensus size: 31
1512809 CTATATATTA
1512819 TATATAAATTTTCAAAAATGCTTTTTTTTAAAAC
1 TATAT-AATTTT-AAAAATG-TTTTTTTTAAAAC
*
1512853 TATATAACTTTTAAAAATGTTTTTTTTGAAAC
1 TATATAA-TTTTAAAAATGTTTTTTTTAAAAC
*
1512885 TATATAATTTCCAAAAATGTTTT
1 TATATAATTT-TAAAAATGTTTT
1512908 AAAAATTATA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
31 3 0.06
32 30 0.59
33 9 0.18
34 9 0.18
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.48
Consensus pattern (31 bp):
TATATAATTTTAAAAATGTTTTTTTTAAAAC
Done.