Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003765.1 Hibiscus syriacus cultivar Beakdansim tig00008065_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: 77455
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7259 original size:28 final size:28
Alignment explanation
Indices: 7216--7274 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
7206 TAAGTAAGGG
7216 AGGGCGAACTTAAACTTATAAAATTTCA
1 AGGGCGAACTTAAACTTATAAAATTTCA
* * *
7244 AGGGTGAACTTGAACTTATAAAATTTTA
1 AGGGCGAACTTAAACTTATAAAATTTCA
7272 AGG
1 AGG
7275 AGGGCGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (28 bp):
AGGGCGAACTTAAACTTATAAAATTTCA
Found at i:19017 original size:24 final size:24
Alignment explanation
Indices: 18989--19035 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18979 AAAGAGTTAA
**
18989 AATTCTCACCTGAAAAGCAACTGG
1 AATTCTCACCCAAAAAGCAACTGG
19013 AATTCTCACCCAAAAAGCAACTG
1 AATTCTCACCCAAAAAGCAACTG
19036 AGAAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (24 bp):
AATTCTCACCCAAAAAGCAACTGG
Found at i:19155 original size:44 final size:43
Alignment explanation
Indices: 19092--19174 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 43
19082 CTGTAAATAT
* *
19092 GAAATGTTGATAATAGAGAGATTAGGACTTGGAGAGAATTCATA
1 GAAATGTTGAGAATAGAGAGATTAGAACTT-GAGAGAATTCATA
* *
19136 GAAATGTTGAGAATGGAGAGATTTGAACTTGAGAGAATT
1 GAAATGTTGAGAATAGAGAGATTAGAACTTGAGAGAATT
19175 AGAGAGAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 9 0.26
44 26 0.74
ACGTcount: A:0.40, C:0.04, G:0.29, T:0.28
Consensus pattern (43 bp):
GAAATGTTGAGAATAGAGAGATTAGAACTTGAGAGAATTCATA
Found at i:19416 original size:29 final size:29
Alignment explanation
Indices: 19383--19438 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
19373 TCCCAACACA
*
19383 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
19412 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
19439 ACTCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:19540 original size:10 final size:10
Alignment explanation
Indices: 19527--19594 Score: 73
Period size: 10 Copynumber: 6.4 Consensus size: 10
19517 ATGGCCTCGG
19527 TCGGATGGTC
1 TCGGATGGTC
*
19537 TCGGATGCTC
1 TCGGATGGTC
19547 TCGGATGGCCTC
1 TCGGATGG--TC
19559 GGTCGGATGGTC
1 --TCGGATGGTC
*
19571 TCGGATGCTC
1 TCGGATGGTC
*
19581 TCGGATGGCC
1 TCGGATGGTC
19591 TCGG
1 TCGG
19595 TCGGATGGCC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 37 0.76
12 4 0.08
14 8 0.16
ACGTcount: A:0.09, C:0.26, G:0.38, T:0.26
Consensus pattern (10 bp):
TCGGATGGTC
Found at i:19542 original size:24 final size:21
Alignment explanation
Indices: 19513--19594 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 21
19503 CATAGCTCAG
19513 TCGGATGGCCTCGGTCGGATGGTC
1 TCGGATGG-CTC--TCGGATGGTC
19537 TCGGAT-GCTCTCGGATGGCCTC
1 TCGGATGGCTCTCGGATGG--TC
*
19559 GGTCGGATGG-TCTCGGATGCTC
1 --TCGGATGGCTCTCGGATGGTC
19581 TCGGATGGC-CTCGG
1 TCGGATGGCTCTCGG
19595 TCGGATGGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
20 21 0.41
22 7 0.14
23 1 0.02
24 21 0.41
25 1 0.02
ACGTcount: A:0.09, C:0.27, G:0.39, T:0.26
Consensus pattern (21 bp):
TCGGATGGCTCTCGGATGGTC
Found at i:19556 original size:34 final size:34
Alignment explanation
Indices: 19513--19602 Score: 180
Period size: 34 Copynumber: 2.6 Consensus size: 34
19503 CATAGCTCAG
19513 TCGGATGGCCTCGGTCGGATGGTCTCGGATGCTC
1 TCGGATGGCCTCGGTCGGATGGTCTCGGATGCTC
19547 TCGGATGGCCTCGGTCGGATGGTCTCGGATGCTC
1 TCGGATGGCCTCGGTCGGATGGTCTCGGATGCTC
19581 TCGGATGGCCTCGGTCGGATGG
1 TCGGATGGCCTCGGTCGGATGG
19603 CCTCATATGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.09, C:0.26, G:0.40, T:0.26
Consensus pattern (34 bp):
TCGGATGGCCTCGGTCGGATGGTCTCGGATGCTC
Found at i:19601 original size:24 final size:21
Alignment explanation
Indices: 19513--19594 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 21
19503 CATAGCTCAG
*
19513 TCGGATGGCCTCGGTCGGATGGTC
1 TCGGATGG-CTC--TCGGATGCTC
19537 TCGGAT-GCTCTCGGATGGCCTC
1 TCGGATGGCTCTCGGAT-G-CTC
19559 GGTCGGATGG-TCTCGGATGCTC
1 --TCGGATGGCTCTCGGATGCTC
19581 TCGGATGGC-CTCGG
1 TCGGATGGCTCTCGG
19595 TCGGATGGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
20 19 0.37
21 1 0.02
22 8 0.16
23 2 0.04
24 20 0.39
25 1 0.02
ACGTcount: A:0.09, C:0.27, G:0.39, T:0.26
Consensus pattern (21 bp):
TCGGATGGCTCTCGGATGCTC
Found at i:19688 original size:29 final size:29
Alignment explanation
Indices: 19651--19708 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
19641 GCAATCTCTT
* *
19651 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGATCGCCCGGAAGACATGGCGACCTA
*
19680 GTAGATCGCCCGGAAGGCATGGCGACCTA
1 GTAGATCGCCCGGAAGACATGGCGACCTA
19709 CGGCTAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGATCGCCCGGAAGACATGGCGACCTA
Found at i:19837 original size:6 final size:6
Alignment explanation
Indices: 19829--19878 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
19819 CGTCCATTCT
* * *
19829 CACTCT CACTCC CACTCG CACTCT CACTCC CACTCC CACTCC CACTCC
1 CACTCC CACTCC CACTCC CACTCC CACTCC CACTCC CACTCC CACTCC
19877 CA
1 CA
19879 TTGACCACTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.18, C:0.60, G:0.02, T:0.20
Consensus pattern (6 bp):
CACTCC
Found at i:19852 original size:18 final size:18
Alignment explanation
Indices: 19829--19878 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
19819 CGTCCATTCT
*
19829 CACTCTCACTCCCACTCG
1 CACTCTCACTCCCACTCC
19847 CACTCTCACTCCCACTCC
1 CACTCTCACTCCCACTCC
*
19865 CACTCCCACTCCCA
1 CACTCTCACTCCCA
19879 TTGACCACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.60, G:0.02, T:0.20
Consensus pattern (18 bp):
CACTCTCACTCCCACTCC
Found at i:22059 original size:31 final size:31
Alignment explanation
Indices: 22021--22128 Score: 162
Period size: 31 Copynumber: 3.5 Consensus size: 31
22011 AGTTACATCA
*
22021 GGGACCATATTGCAAATGGACTAAATGTTGG
1 GGGACCATATTGCAAATAGACTAAATGTTGG
*
22052 GGGACCATATTGCAAATAGACTAAATGTTGA
1 GGGACCATATTGCAAATAGACTAAATGTTGG
* *
22083 GGGACCATATTGAAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAATAGACTAAATGTTGG
**
22114 GGGACTGTATTGCAA
1 GGGACCATATTGCAA
22129 GTTTTAAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (31 bp):
GGGACCATATTGCAAATAGACTAAATGTTGG
Found at i:22864 original size:23 final size:24
Alignment explanation
Indices: 22819--22873 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
22809 TTATCAAATA
*
22819 ATTTAATTATATTCAATATTCAAT
1 ATTTAATTATATTCAATAATCAAT
*
22843 -TTTAATTATACTTTAA-AATCAAT
1 ATTTAATTATA-TTCAATAATCAAT
22866 ATTTAATT
1 ATTTAATT
22874 TTTCATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTAATTATATTCAATAATCAAT
Found at i:23006 original size:19 final size:20
Alignment explanation
Indices: 22984--23025 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
22974 ACTTATAAAG
22984 AAACAATAAAAAAATA-ATA
1 AAACAATAAAAAAATATATA
*
23003 AAACAATAAAAACATATATA
1 AAACAATAAAAAAATATATA
23023 AAA
1 AAA
23026 TTAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
AAACAATAAAAAAATATATA
Found at i:23131 original size:29 final size:29
Alignment explanation
Indices: 23081--23143 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
23071 CACTGAAATT
* *
23081 TTTTAAAACTTTCATTTAAGTCCCCCAAC
1 TTTTAAAACTTGCATATAAGTCCCCCAAC
*
23110 TTTTAAAACTTGCA-ATATAGTCCCCTAAC
1 TTTTAAAACTTGCATATA-AGTCCCCCAAC
*
23139 ATTTA
1 TTTTA
23144 GTCTATTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTTAAAACTTGCATATAAGTCCCCCAAC
Found at i:23164 original size:31 final size:31
Alignment explanation
Indices: 23119--23258 Score: 219
Period size: 31 Copynumber: 4.5 Consensus size: 31
23109 CTTTTAAAAC
*
23119 TTGCAATATAGTCCCCTAACATTTAGTCTAT
1 TTGCAATATGGTCCCCTAACATTTAGTCTAT
*
23150 TTTCAATATGGTCCCCTAACATTTAGTCTAT
1 TTGCAATATGGTCCCCTAACATTTAGTCTAT
*
23181 TTGCAATATGAT-CCCTCAACATTTAGTCTAT
1 TTGCAATATGGTCCCCT-AACATTTAGTCTAT
* *
23212 TTGCAATATGGTCCCCCAACATTTAGTCTGT
1 TTGCAATATGGTCCCCTAACATTTAGTCTAT
23243 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
23259 GACGTAACTA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
30 4 0.04
31 93 0.93
32 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (31 bp):
TTGCAATATGGTCCCCTAACATTTAGTCTAT
Found at i:27039 original size:3 final size:3
Alignment explanation
Indices: 27031--27061 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
27021 TATATAATAT
27031 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27062 ATTTATCTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28246 original size:2 final size:2
Alignment explanation
Indices: 28239--28271 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
28229 TCGTCTCACT
*
28239 TA TA TA TA TA GA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28272 GTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28383 original size:36 final size:35
Alignment explanation
Indices: 28254--28519 Score: 255
Period size: 36 Copynumber: 7.3 Consensus size: 35
28244 ATATAGATAT
* *
28254 ATATATATATATATTATAGTTTTAAAATATTTTTAAA
1 ATATATATA-ATA-TATAGTTTTTAAATATTTTGAAA
* *
28291 ACCTATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 A--TATATATAATATATAGTTTT-TAAATAT-TTTGAAA
*
28330 ATATTTATATATTATATAGTTTTTAAAGTATTTTGAAA
1 ATA--TATATAATATATAGTTTTTAAA-TATTTTGAAA
* **
28368 ATAAATATAATATATAGTTTTTGCATATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAATA-TTTTGAAA
* *
28404 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAA
1 ATATATATAATATATAGTTTTTAAA-TATTTTGAAA
* * * * *
28440 ATAAATATACTATATAATTTTTAAAACTTTTTTTAAA
1 ATATATATAATATATAGTTTTT-AAA-TATTTTGAAA
* *
28477 A-ATATATATTATATAGTTTTTAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTAAATATTTTGAAA
28511 ATATATATA
1 ATATATATA
28520 GTTTTTAAAA
Statistics
Matches: 191, Mismatches: 27, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
34 8 0.04
35 12 0.06
36 89 0.47
37 26 0.14
38 22 0.12
39 34 0.18
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (35 bp):
ATATATATAATATATAGTTTTTAAATATTTTGAAA
Found at i:28433 original size:72 final size:72
Alignment explanation
Indices: 28254--28519 Score: 299
Period size: 72 Copynumber: 3.6 Consensus size: 72
28244 ATATAGATAT
* * *
28254 ATATATATATATATTATAG-TTTTAAAATATTTTTAAAACCTATATATAATATATAG-TTTTGAA
1 ATATATATAT-TA-TATAGTTTTTAAAGTATTTTGAAAA--TAAATATAATATATAGTTTTTG-A
*
28317 AACATGTTTGAAA
61 AA-ATTTTTGAAA
* *
28330 ATATTTATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTGCATA
1 ATA--TATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTGAAAA
28395 TTTTTGAAA
64 TTTTTGAAA
* * *
28404 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAAATAAATATACTATATAATTTTT-AAAACT
1 ATATATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTGAAAA--
*
28468 TTTTTTAAA
64 TTTTTGAAA
* *
28477 A-ATATATATTATATAGTTTTTAAA-CATTTTGAAAATATATATA
1 ATATATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATA
28520 GTTTTTAAAA
Statistics
Matches: 169, Mismatches: 15, Indels: 17
0.84 0.07 0.08
Matches are distributed among these distances:
71 19 0.11
72 74 0.44
73 9 0.05
74 12 0.07
75 16 0.09
76 13 0.08
77 19 0.11
78 7 0.04
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (72 bp):
ATATATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTGAAAATT
TTTGAAA
Found at i:28598 original size:34 final size:37
Alignment explanation
Indices: 28553--28631 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 37
28543 GAAGAACATA
* * * *
28553 TATATATTATATAGTTTT-TAAATCA-TTTCAAAAAC
1 TATATAATATATAATTTTAAAAAACATTTTCAAAAAC
*
28588 T-TATAATATATAATTTTAAAAAACATTTTTAAAAAC
1 TATATAATATATAATTTTAAAAAACATTTTCAAAAAC
28624 TATATAAT
1 TATATAAT
28632 TTTGGAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 14 0.39
35 6 0.17
36 10 0.28
37 6 0.17
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (37 bp):
TATATAATATATAATTTTAAAAAACATTTTCAAAAAC
Found at i:28665 original size:37 final size:37
Alignment explanation
Indices: 28624--28720 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 37
28614 TTTTAAAAAC
28624 TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
1 TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
* * * * *
28661 TATATAATTTT-AAAATATTTTTAAAAATATATATTA
1 TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
* *
28697 TATAGATTTTTGGAAAATGTTTTT
1 TATATAATTTTGG-AAATGTTTTT
28721 TATTTATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 29 0.59
37 11 0.22
38 9 0.18
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (37 bp):
TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
Found at i:28792 original size:20 final size:20
Alignment explanation
Indices: 28742--28792 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
28732 TTACCTTTTG
*
28742 TTATTTATTTATTATTTATT
1 TTATTTTTTTATTATTTATT
*
28762 TTACTTATTTTATT-TTTATTT
1 TTA-TTTTTTTATTATTTA-TT
28783 TTATTTTTTT
1 TTATTTTTTT
28793 TGTTGCAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
TTATTTTTTTATTATTTATT
Found at i:28792 original size:29 final size:31
Alignment explanation
Indices: 28717--28792 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
28707 TGGAAAATGT
* * *
28717 TTTTTATTTATTTATTTACCTTTTGTTATTTA
1 TTTTTATTTTTTTACTTA-CTTTTATTATTTA
28749 TTTATTATTTATTTTACTTA-TTTTATT-TTTA
1 TTT-TTATTT-TTTTACTTACTTTTATTATTTA
28780 TTTTTATTTTTTT
1 TTTTTATTTTTTT
28793 TGTTGCAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 4 0.10
30 6 0.15
31 7 0.18
32 9 0.23
33 6 0.15
34 7 0.18
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (31 bp):
TTTTTATTTTTTTACTTACTTTTATTATTTA
Found at i:30252 original size:12 final size:13
Alignment explanation
Indices: 30235--30264 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
30225 TCGAATCGAG
30235 TAATTTAAA-TTT
1 TAATTTAAATTTT
30247 TAATTTAAATTTT
1 TAATTTAAATTTT
30260 TAATT
1 TAATT
30265 CTTCGCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATTTAAATTTT
Found at i:33531 original size:23 final size:23
Alignment explanation
Indices: 33505--33565 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
33495 TTATATATGC
33505 CACTACGGTGCATTTCTACGCCG
1 CACTACGGTGCATTTCTACGCCG
* * * **
33528 CACTTCGGTGTAATTCTACGTGG
1 CACTACGGTGCATTTCTACGCCG
33551 CAC-ATCGGTGCATTT
1 CACTA-CGGTGCATTT
33566 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (23 bp):
CACTACGGTGCATTTCTACGCCG
Found at i:39521 original size:21 final size:21
Alignment explanation
Indices: 39426--39521 Score: 70
Period size: 21 Copynumber: 4.5 Consensus size: 21
39416 AACAATTCTC
* *
39426 TTCATGAAAAGATTAAATCCT
1 TTCATCAAAAGATTAAGTCCT
* * *
39447 TTCGTGAAAAGGTTAAG-CACTT
1 TTCATCAAAAGATTAAGTC-C-T
39469 TTCATCAAAAGGA-TAAGTCCT
1 TTCATCAAAA-GATTAAGTCCT
* **
39490 TTAATTGAAAGATTAAGTCCT
1 TTCATCAAAAGATTAAGTCCT
*
39511 TTCATCTAAAG
1 TTCATCAAAAG
39522 GTATTAACCC
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 3 0.05
21 39 0.67
22 14 0.24
23 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCATCAAAAGATTAAGTCCT
Found at i:45054 original size:22 final size:22
Alignment explanation
Indices: 45029--45070 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45019 TTTTTAACAA
45029 ATTTTTAGTATTTTATTTTTAG
1 ATTTTTAGTATTTTATTTTTAG
* *
45051 ATTTTTATTATTTTCTTTTT
1 ATTTTTAGTATTTTATTTTT
45071 TCCTCAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (22 bp):
ATTTTTAGTATTTTATTTTTAG
Found at i:45576 original size:55 final size:56
Alignment explanation
Indices: 45481--45619 Score: 174
Period size: 55 Copynumber: 2.5 Consensus size: 56
45471 CAGGGCCCAA
* * * * * *
45481 AAAAATAGGGATCCCGAAATTGAATATATCTATCAGTTGTTGTCATTAAGAAGCAT
1 AAAAATAGAGATCCCAAAATCGAATATATATATCAATTGTTGCCATTAAGAAGCAT
*
45537 AAAAATAGAGA-CCCAAAATCGAGTATATATATCAATTGTTGCCATTAAGAAGCAT
1 AAAAATAGAGATCCCAAAATCGAATATATATATCAATTGTTGCCATTAAGAAGCAT
* * *
45592 AAAAATAG-GAGCCCGAAATTGAATATAT
1 AAAAATAGAGATCCCAAAATCGAATATAT
45620 CTAGAAAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
54 2 0.03
55 60 0.83
56 10 0.14
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.27
Consensus pattern (56 bp):
AAAAATAGAGATCCCAAAATCGAATATATATATCAATTGTTGCCATTAAGAAGCAT
Found at i:46161 original size:25 final size:25
Alignment explanation
Indices: 46133--46181 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
46123 TTATGACACG
* * *
46133 TTTTTTATGTTCTTGTGGCATGTTC
1 TTTTCTATGCTCTTATGGCATGTTC
*
46158 TTTTCTCTGCTCTTATGGCATGTT
1 TTTTCTATGCTCTTATGGCATGTT
46182 TCTTATGGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.18, T:0.57
Consensus pattern (25 bp):
TTTTCTATGCTCTTATGGCATGTTC
Found at i:48410 original size:23 final size:24
Alignment explanation
Indices: 48373--48434 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
48363 GGTACGAGAC
48373 AAATATATTGTAAATGATGAT-AA-AA
1 AAATA-ATT-TAAAT-ATGATAAATAA
* *
48398 AAATAATTTAAATTTTATAAATAA
1 AAATAATTTAAATATGATAAATAA
48422 AAATAATTTAAAT
1 AAATAATTTAAAT
48435 TTTATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 3 0.09
23 7 0.21
24 18 0.55
25 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (24 bp):
AAATAATTTAAATATGATAAATAA
Found at i:51662 original size:23 final size:23
Alignment explanation
Indices: 51635--51681 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
51625 AGGGCTAACA
51635 GGGAAACCGGAATAGCGGCAGGG
1 GGGAAACCGGAATAGCGGCAGGG
51658 GGGAAACCGGAATAGCGGCAGGG
1 GGGAAACCGGAATAGCGGCAGGG
51681 G
1 G
51682 CAAACCAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.49, T:0.04
Consensus pattern (23 bp):
GGGAAACCGGAATAGCGGCAGGG
Found at i:51686 original size:22 final size:23
Alignment explanation
Indices: 51638--51687 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
51628 GCTAACAGGG
*
51638 AAACCGGAATAGCGGCAGGGGGG
1 AAACCGGAATAGCGGCAGGGGGC
51661 AAACCGGAATAGCGGCA-GGGGC
1 AAACCGGAATAGCGGCAGGGGGC
51683 AAACC
1 AAACC
51688 AACGACAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.34, C:0.22, G:0.40, T:0.04
Consensus pattern (23 bp):
AAACCGGAATAGCGGCAGGGGGC
Found at i:55552 original size:3 final size:3
Alignment explanation
Indices: 55544--55583 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
55534 TGGATATGAA
55544 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55584 TCGAATGGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55986 original size:133 final size:133
Alignment explanation
Indices: 55736--56166 Score: 470
Period size: 133 Copynumber: 3.2 Consensus size: 133
55726 GTTGTCACTC
* * * * * *
55736 AGGGAATATCATATCT-GGGGATGTTGATCTATTTCACTGTCACTCAAGAAAGATTGAATCGGGG
1 AGGGAATATCAGATCTGGGGGA-GTTGATCCATTCCACTGTCACTCAGGGAAGATTGAAT-TGGG
* *
55800 CAGACTTGTTCCACTGTCACTCAAAGAATATCAAATCTTGAAAAAAAGGGATATGTTCCACTTCT
64 TAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAAAAAGGGATATGTTCCACTTCT
* *
55865 TTTGA
129 TCTCA
* * *
55870 AGGGATTATCAGATCTGGGGGAGTTGATCCATTCCATTGTCACACAGGGAAGATTGAATTGGGTA
1 AGGGAATATCAGATCTGGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATTGGGTA
* * * * * * * *
55935 GACTTATTCCGCTGTTACTCAAGGAATATCAAATCTTGGAAGAGAGTGATATGTTCCGCTTCTTC
66 GACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAAAAAGGGATATGTTCCACTTCTTC
56000 TCA
131 TCA
* ** * *
56003 AGGGAATACCAGATCTGGGGTTGTTGATCCATTCCGCTGTCACTTAGGGAAGATTGAATTGGGGT
1 AGGGAATATCAGATCTGGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATT-GGGT
* * * ** ** *
56068 AGACTTGTTCTACTGTCACTCAGGGAATATCAAATCTT-AAAAAAGATGGACCTGTTCCGTTTTT
65 AGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAAAA-AGGGATATGTTCCACTTCT
*
56132 TCTAA
129 TCTCA
* *
56137 AGGGAATATCAGATCTAGGAGAGGTTGATC
1 AGGGAATATCAGATCTGGGGGA-GTTGATC
56167 TATTGAATCG
Statistics
Matches: 244, Mismatches: 49, Indels: 7
0.81 0.16 0.02
Matches are distributed among these distances:
133 116 0.48
134 116 0.48
135 12 0.05
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (133 bp):
AGGGAATATCAGATCTGGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATTGGGTA
GACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAAAAAGGGATATGTTCCACTTCTTC
TCA
Found at i:56329 original size:111 final size:112
Alignment explanation
Indices: 56055--56387 Score: 470
Period size: 111 Copynumber: 3.0 Consensus size: 112
56045 CTTAGGGAAG
* * ** * *
56055 ATTGAATTGGGGTAGACTTGTTCTACTGTCACTCAGGGAATATCAAATCTTAAAAAAGATGGACC
1 ATTGAATCGGGGCAGACTTGTTCTACTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
* * * *
56120 TGTTCCGTTTTTTCTAAAGGGAATATCAGATCTAGGAGAGGTTGATCT
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTAGGGGA-GTTGATCT
* *
56168 ATTGAATCGGGGCAGACTTGTTCTAGTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGATA
1 ATTGAATCGGGGCAGACTTGTTCTACTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
* * *
56233 TGTTTCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTTATC-
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTAGGGGAGTTGATCT
* * *
56279 ATTGAATCGGGGCACACTTGTTCTACTGTCACTCAAGGAATATCAAATCTTGGAAAAGTGGGACA
1 ATTGAATCGGGGCAGACTTGTTCTACTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
**
56344 TGACCCGCTTCTTCTGAAGGGAATATCAGATCTAGGGGAGTTGA
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTAGGGGAGTTGA
56388 CCCATTCCGT
Statistics
Matches: 195, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
111 99 0.51
112 6 0.03
113 90 0.46
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (112 bp):
ATTGAATCGGGGCAGACTTGTTCTACTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTAGGGGAGTTGATCT
Found at i:56519 original size:134 final size:134
Alignment explanation
Indices: 56279--56626 Score: 454
Period size: 134 Copynumber: 2.6 Consensus size: 134
56269 GGAGTTTATC
* * * * * *
56279 ATTGAATCGGGGCACACTTGTTCTACTGTCACTCAAGGAATATCAAATCTTGGAAAAGTGGGACA
1 ATTGAATCGAGGAAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
* * * * *
56344 TGA-CCCGCTTCTTCTGAAGGGAATATCAGATCTAGGGGAGTTGACCCATTCCGTTGTTACTCAA
66 T-ATTCCGCTTCTTCTAAAGGGAATATCAGATATAGGGGAGTTGACCCATTCCGCTGTCACTC-A
56408 GG-AAG
129 GGAAAG
* *
56413 ATTGAATCAGAGTAA-ACTTGTT-TCGCTGTCACTCAGGGAATATCAAGTCTTGGAAAAGAGGGA
1 ATTGAATC-GAGGAAGACTTGTTCT-GCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGA
* *
56476 CATATTCCGCTTCTTCTAAAGGGAATATCATATAT-GGAGGAGTTGATCCATTCCGCTGTCACTC
64 CATATTCCGCTTCTTCTAAAGGGAATATCAGATATAGG-GGAGTTGACCCATTCCGCTGTCACTC
56540 AGGAAAG
128 AGGAAAG
*
56547 ATTGAATCGGGGAAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
1 ATTGAATCGAGGAAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
* *
56612 TGTTTCGCTTCTTCT
66 TATTCCGCTTCTTCT
56627 TAATGGGATA
Statistics
Matches: 188, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
133 11 0.06
134 173 0.92
135 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (134 bp):
ATTGAATCGAGGAAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACA
TATTCCGCTTCTTCTAAAGGGAATATCAGATATAGGGGAGTTGACCCATTCCGCTGTCACTCAGG
AAAG
Found at i:58609 original size:8 final size:7
Alignment explanation
Indices: 58555--58642 Score: 59
Period size: 7 Copynumber: 11.7 Consensus size: 7
58545 ATTTTCTCTC
58555 TTTTTCT
1 TTTTTCT
58562 TTTTTCT
1 TTTTTCT
* *
58569 CTATTCT
1 TTTTTCT
58576 TTTATTCT
1 TTT-TTCT
*
58584 TTTTCTAT
1 TTTT-TCT
58592 CTTTTTCT
1 -TTTTTCT
58600 TTTCTTCTTT
1 TTT-TTC--T
58610 TTTTTCT
1 TTTTTCT
58617 TTTTTCT
1 TTTTTCT
*** *
58624 CGATTAT
1 TTTTTCT
58631 TTTTTCT
1 TTTTTCT
58638 TTTTT
1 TTTTT
58643 TTATTTTTAT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
7 36 0.59
8 14 0.23
9 7 0.11
10 4 0.07
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTCT
Found at i:58617 original size:23 final size:23
Alignment explanation
Indices: 58561--58620 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
58551 TCTCTTTTTC
*
58561 TTTTTTCTCTATTCTTTTATTCTT
1 TTTTTTCT-TTTTCTTTTATTCTT
* *
58585 TTTCTATCTTTTTCTTTTCTTCTT
1 TTT-TTTCTTTTTCTTTTATTCTT
58609 TTTTTTCTTTTT
1 TTTTTTCTTTTT
58621 TCTCGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 8 0.26
24 19 0.61
25 4 0.13
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTCTTTTTCTTTTATTCTT
Found at i:58635 original size:21 final size:19
Alignment explanation
Indices: 58555--58664 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 19
58545 ATTTTCTCTC
58555 TTTTTCTTTTTTCTCTATTCT
1 TTTTTCTTTTTTCTC-ATT-T
*
58576 TTTATTC-TTTTTCT-A-TC
1 TTT-TTCTTTTTTCTCATTT
*
58593 TTTTTCTTTTCT-TC-TTT
1 TTTTTCTTTTTTCTCATTT
58610 TTTTTCTTTTTTCTCGATTAT
1 TTTTTCTTTTTTCTC-ATT-T
*
58631 TTTTTCTTTTTT-TTATTT
1 TTTTTCTTTTTTCTCATTT
* *
58649 TTATATCTTCTTTCTC
1 TT-TTTCTTTTTTCTC
58665 TCTCTTATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
16 4 0.06
17 19 0.27
18 6 0.08
19 12 0.17
20 4 0.06
21 23 0.32
22 3 0.04
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTTCTTTTTTCTCATTT
Found at i:58643 original size:8 final size:8
Alignment explanation
Indices: 58555--58621 Score: 53
Period size: 9 Copynumber: 7.5 Consensus size: 8
58545 ATTTTCTCTC
58555 TTTTTCTT
1 TTTTTCTT
58563 TTTTCTCTAT
1 TTTT-TCT-T
*
58573 TCTTTTATT
1 T-TTTTCTT
58582 CTTTTTCTAT
1 -TTTTTCT-T
58592 CTTTTTCTT
1 -TTTTTCTT
*
58601 TTCTTCTTT
1 TTTTTC-TT
58610 TTTTTCTT
1 TTTTTCTT
58618 TTTT
1 TTTT
58622 CTCGATTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
8 15 0.31
9 17 0.35
10 14 0.29
11 3 0.06
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTCTT
Found at i:58660 original size:55 final size:55
Alignment explanation
Indices: 58555--58660 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
58545 ATTTTCTCTC
* * * *
58555 TTTTTCTTTTTTCTCTATTCTTTTATTCTTTTTCTATCTTTTTCTTTTCTTCTTT
1 TTTTTCTTTTTTCTCGATTATTTTATTCTTTTTCTATCTTTTTATCTTCTTCTTT
*
58610 TTTTTCTTTTTTCTCGATTATTTT-TTCTTTTTTTTAT-TTTTATATCTTCTT
1 TTTTTCTTTTTTCTCGATTATTTTATTC-TTTTTCTATCTTTT-TATCTTCTT
58661 TCTCTCTCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
54 7 0.16
55 37 0.84
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (55 bp):
TTTTTCTTTTTTCTCGATTATTTTATTCTTTTTCTATCTTTTTATCTTCTTCTTT
Found at i:59578 original size:20 final size:21
Alignment explanation
Indices: 59553--59624 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
59543 TTGTGCTTAA
59553 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
*
59573 TGCATCGATGCATCCTTGAAAG
1 TGCATCGATACA-CCTTGAAAG
* *
59595 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAAAG
*
59616 TGCACCGAT
1 TGCATCGAT
59625 GCACGCCTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 11 0.25
21 17 0.39
22 14 0.32
23 2 0.05
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:60056 original size:21 final size:21
Alignment explanation
Indices: 60032--60071 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
60022 TTTTTGAAAT
60032 AAAAAAATACCAATTGTTAAC
1 AAAAAAATACCAATTGTTAAC
** *
60053 AAAATGATATCAATTGTTA
1 AAAAAAATACCAATTGTTA
60072 CCAATTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAAATACCAATTGTTAAC
Found at i:61229 original size:19 final size:20
Alignment explanation
Indices: 61186--61233 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
61176 TCTAAATCCT
*
61186 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
61206 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
61225 TTTTCAAAA
1 TTTTCAAAA
61234 GAAAAACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:66576 original size:20 final size:20
Alignment explanation
Indices: 66551--66617 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
66541 TTTTCCAAAT
66551 TCGCAACGCGAATAGTTAAA
1 TCGCAACGCGAATAGTTAAA
**
66571 TCGCAACGATAATA-TGTAAA
1 TCGCAACGCGAATAGT-TAAA
*
66591 TCGCAATGCGAATAGTTAAA
1 TCGCAACGCGAATAGTTAAA
66611 TCGCAAC
1 TCGCAAC
66618 ACATAAGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATAGTTAAA
Found at i:66634 original size:20 final size:20
Alignment explanation
Indices: 66611--66656 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
66601 AATAGTTAAA
*
66611 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
66631 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
66651 TCGCAA
1 TCGCAA
66657 AGCGCATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:66635 original size:40 final size:42
Alignment explanation
Indices: 66546--66637 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 42
66536 TGCAATTTTC
*
66546 CAAATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 CAAATTCGCAACGCGAATAGTTAAATCGCAACGATAATAAGT
* *
66588 -AAA-TCGCAATGCGAATAGTTAAATCGCAAC-A-CATAAGT
1 CAAATTCGCAACGCGAATAGTTAAATCGCAACGATAATAAGT
66626 CAAATTCGCAAC
1 CAAATTCGCAAC
66638 ACAGAAGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
38 5 0.11
39 4 0.09
40 32 0.73
41 3 0.07
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (42 bp):
CAAATTCGCAACGCGAATAGTTAAATCGCAACGATAATAAGT
Found at i:67261 original size:39 final size:41
Alignment explanation
Indices: 67218--67304 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 41
67208 AAAATCACAA
*
67218 CGTTGCGAAAATGAAATTT-GCGTTGCGATTTTCA-TTTCG
1 CGTTGCGAAAATGAAATTTCGCGTTACGATTTTCATTTTCG
** ** *
67257 CGTTGCG-ATTTTCATTTTCGCGTTACGATTTTCATTTTCG
1 CGTTGCGAAAATGAAATTTCGCGTTACGATTTTCATTTTCG
67297 CGTTGCGA
1 CGTTGCGA
67305 TTTTAAGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 6 0.15
39 21 0.54
40 12 0.31
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (41 bp):
CGTTGCGAAAATGAAATTTCGCGTTACGATTTTCATTTTCG
Found at i:67277 original size:20 final size:20
Alignment explanation
Indices: 67237--67308 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
67227 AATGAAATTT
67237 GCGTTGCGATTTTCA-TTTC
1 GCGTTGCGATTTTCATTTTC
67256 GCGTTGCGATTTTCATTTTC
1 GCGTTGCGATTTTCATTTTC
*
67276 GCGTTACGATTTTCATTTTC
1 GCGTTGCGATTTTCATTTTC
67296 GCGTTGCGATTTT
1 GCGTTGCGATTTT
67309 AAGTTTAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 15 0.30
20 35 0.70
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (20 bp):
GCGTTGCGATTTTCATTTTC
Found at i:68847 original size:21 final size:21
Alignment explanation
Indices: 68823--68877 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
68813 CTACAGCTCT
68823 ACAACGAGAGCCATCACCTCC
1 ACAACGAGAGCCATCACCTCC
68844 ACAACGAGAGCCATCACCTCC
1 ACAACGAGAGCCATCACCTCC
68865 ACAACGAGAGCCA
1 ACAACGAGAGCCA
68878 CCCTATTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.40, G:0.16, T:0.07
Consensus pattern (21 bp):
ACAACGAGAGCCATCACCTCC
Found at i:69490 original size:31 final size:31
Alignment explanation
Indices: 69455--69515 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
69445 CACCTGTCAT
* *
69455 CGTTCAAGAGGCCTCT-CCTATCGTTCAAGAC
1 CGTTCAAGAGGCCCCTATC-ATCGTTCAAGAC
69486 CGTTCAAGAGGCCCCTATCATCGTTCAAGA
1 CGTTCAAGAGGCCCCTATCATCGTTCAAGA
69516 GGTCTCTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (31 bp):
CGTTCAAGAGGCCCCTATCATCGTTCAAGAC
Found at i:69532 original size:20 final size:21
Alignment explanation
Indices: 69484--69536 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
69474 ATCGTTCAAG
*
69484 ACCGTTCAAGAGGCCCCTATC
1 ACCGTTCAAGAGGCCCCTACC
* * *
69505 ATCGTTCAAGAGGTCTCT-CC
1 ACCGTTCAAGAGGCCCCTACC
69525 ACCGTTCAAGAG
1 ACCGTTCAAGAG
69537 CCCGATTCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (21 bp):
ACCGTTCAAGAGGCCCCTACC
Found at i:71072 original size:20 final size:20
Alignment explanation
Indices: 71026--71063 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
71016 ACACTTTCGT
71026 AACGCGAAAATCAAATTCAC
1 AACGCGAAAATCAAATTCAC
*
71046 AACGCGAAAGTCAAATTC
1 AACGCGAAAATCAAATTC
71064 GCATTGCGAT
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:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (20 bp):
AACGCGAAAATCAAATTCAC
Found at i:71255 original size:20 final size:20
Alignment explanation
Indices: 71230--71343 Score: 149
Period size: 20 Copynumber: 5.8 Consensus size: 20
71220 CATAAGGTAC
*
71230 ACTTTCGCGTTACGATTTTG
1 ACTTTCGCGTTGCGATTTTG
71250 ACTTTCGCGTTGCGA-TTTG
1 ACTTTCGCGTTGCGATTTTG
*
71269 ATTTTCGCGTTGCGATTTTG
1 ACTTTCGCGTTGCGATTTTG
71289 ACTTTCGCGTTGCGATTTTG
1 ACTTTCGCGTTGCGATTTTG
* ** *
71309 TCTTTCATGTTGCGAATTTG
1 ACTTTCGCGTTGCGATTTTG
* *
71329 ATTTTCGTGTTGCGA
1 ACTTTCGCGTTGCGA
71344 AAGTGTACCT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
19 18 0.22
20 65 0.78
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (20 bp):
ACTTTCGCGTTGCGATTTTG
Found at i:71286 original size:39 final size:40
Alignment explanation
Indices: 71231--71343 Score: 149
Period size: 39 Copynumber: 2.9 Consensus size: 40
71221 ATAAGGTACA
*
71231 CTTTCGCGTTACGATTTTGACTTTCGCGTTGCGA-TTTGAT
1 CTTTCGCGTTGCGATTTTGACTTTCGCGTTGCGATTTTG-T
71271 -TTTCGCGTTGCGATTTTGACTTTCGCGTTGCGATTTTGT
1 CTTTCGCGTTGCGATTTTGACTTTCGCGTTGCGATTTTGT
** * * *
71310 CTTTCATGTTGCGAATTTGATTTTCGTGTTGCGA
1 CTTTCGCGTTGCGATTTTGACTTTCGCGTTGCGA
71344 AAGTGTACCT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.51
40 32 0.49
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (40 bp):
CTTTCGCGTTGCGATTTTGACTTTCGCGTTGCGATTTTGT
Found at i:71322 original size:59 final size:60
Alignment explanation
Indices: 71230--71343 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 60
71220 CATAAGGTAC
*
71230 ACTTTCGCGTTACGATTTTGACTTTCGCGTTGCG-ATTTGATTTTCGCGTTGCGATTTTG
1 ACTTTCGCGTTACGATTTTGACTTTCACGTTGCGAATTTGATTTTCGCGTTGCGATTTTG
* * * *
71289 ACTTTCGCGTTGCGATTTTGTCTTTCATGTTGCGAATTTGATTTTCGTGTTGCGA
1 ACTTTCGCGTTACGATTTTGACTTTCACGTTGCGAATTTGATTTTCGCGTTGCGA
71344 AAGTGTACCT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 30 0.61
60 19 0.39
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (60 bp):
ACTTTCGCGTTACGATTTTGACTTTCACGTTGCGAATTTGATTTTCGCGTTGCGATTTTG
Found at i:71657 original size:17 final size:17
Alignment explanation
Indices: 71635--71669 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
71625 AAGTCGGTTG
*
71635 TGATTGGGATTTTGATT
1 TGATTGCGATTTTGATT
71652 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
71669 T
1 T
71670 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (17 bp):
TGATTGCGATTTTGATT
Found at i:74119 original size:12 final size:12
Alignment explanation
Indices: 74098--74132 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
74088 GGTTGTGGGT
*
74098 TTTGAGATTGTG
1 TTTGATATTGTG
74110 TTTGATATTGTG
1 TTTGATATTGTG
*
74122 TTTGGTATTGT
1 TTTGATATTGT
74133 AAATGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:74952 original size:19 final size:19
Alignment explanation
Indices: 74903--74952 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
74893 AAGTTATTGT
* *
74903 GAAATTAAAATTCGTGTTGC
1 GAAATCAAAA-TCGAGTTGC
* *
74923 GAATTCGAAATCGAGTTGC
1 GAAATCAAAATCGAGTTGC
74942 GAAATCAAAAT
1 GAAATCAAAAT
74953 TCGTGTTGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (19 bp):
GAAATCAAAATCGAGTTGC
Found at i:76329 original size:3 final size:3
Alignment explanation
Indices: 76321--76350 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
76311 CTGAAAAGAA
76321 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
76351 TCGGATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.