Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006494.1 Hibiscus syriacus cultivar Beakdansim tig00015794_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: 55950
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:78 original size:21 final size:20
Alignment explanation
Indices: 47--100 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
37 TAAAAGTAAT
47 TAAAT-AATATTTTAATAAA
1 TAAATAAATATTTTAATAAA
* *
66 TAAAATAAATATTATTATTATA
1 T-AAATAAATATT-TTAATAAA
*
88 TAAATATATATTT
1 TAAATAAATATTT
101 ATGGCTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 16 0.55
22 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATAAATATTTTAATAAA
Found at i:233 original size:26 final size:27
Alignment explanation
Indices: 174--236 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
164 AAACAAGGAC
174 AAAAATCAATAAAATTAAAATGATAGGT
1 AAAAAT-AATAAAATTAAAATGATAGGT
* *
202 ACAAATAATAAAA-TAAAACTTATA-GT
1 AAAAATAATAAAATTAAAA-TGATAGGT
228 AAAAATAAT
1 AAAAATAAT
237 TAGTAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 15 0.48
27 11 0.35
28 5 0.16
ACGTcount: A:0.63, C:0.05, G:0.06, T:0.25
Consensus pattern (27 bp):
AAAAATAATAAAATTAAAATGATAGGT
Found at i:1516 original size:16 final size:19
Alignment explanation
Indices: 1476--1533 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
1466 ATGCAATTTG
*
1476 TAAT-ATATATATATATATT
1 TAATAATATATATATATA-A
1495 TAATAA-ATA-ATA-ATAA
1 TAATAATATATATATATAA
1511 TAATAATATATATATATAA
1 TAATAATATATATATATAA
1530 TAAT
1 TAAT
1534 TATAATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 6 0.18
19 15 0.44
20 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATAATATATATATATAA
Found at i:2038 original size:76 final size:76
Alignment explanation
Indices: 1667--2903 Score: 2117
Period size: 76 Copynumber: 16.5 Consensus size: 76
1657 GATGAAAATA
* * * * *
1667 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
1732 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* * *
1744 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
1808 CCCAAAGGCTT
66 CCCGAAGGCTT
*
1819 TTTGGAAACATCATGCA-TGCAGGACTTATAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1882 CCCGAAGGCTT
66 CCCGAAGGCTT
1893 TTTGGAAACATCATGCACTGCAGGAC-TACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1957 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1968 TTTGGAAACATCATGCACTGCTGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2033 CCCGAAGGCTT
66 CCCGAAGGCTT
2044 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2109 CCCGAAGGCTT
66 CCCGAAGGCTT
2120 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2185 CCCGAAGGCTT
66 CCCGAAGGCTT
2196 TTTGGAAACATCATGCACTGCA-GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2260 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2271 TTTGGAAACATCATGCA-TGCAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2334 CCCAAAGGC-T
66 CCCGAAGGCTT
* *
2344 TTTGGAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGCTTTGAAAACATAAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2409 CCCAAAGGCTT
66 CCCGAAGGCTT
2420 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2485 CCCGAAGGCGT
66 CCCGAAGGCTT
* *
2496 TTTGGAAACGTCATGCACTGCAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2561 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2572 TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2637 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2648 TTTGGAAACATCATGCACTGCAGGACTTACAGAGGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2713 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2724 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2789 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2800 TTTGGAAACATCATGCA-T---TG---TACAGATGACCCTAAGGCTTTGAAAACATCAAAAACCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2858 CCTGAAGGCTT
66 CCCGAAGGCTT
*
2869 TTTGGAAACATCATGTACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
2904 TGGGAAATAG
Statistics
Matches: 1107, Mismatches: 38, Indels: 31
0.94 0.03 0.03
Matches are distributed among these distances:
69 62 0.06
70 1 0.00
72 1 0.00
73 19 0.02
74 142 0.13
75 227 0.21
76 614 0.55
77 41 0.04
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2557 original size:452 final size:453
Alignment explanation
Indices: 1667--2903 Score: 2134
Period size: 452 Copynumber: 2.7 Consensus size: 453
1657 GATGAAAATA
* * * *
1667 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
* * *
1732 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTTTGAAAAT
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTGAAAAC
* *
1797 ATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCATGCAGGACTTATAGATGACCCTAAGG
130 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATGCAGGACTTACAGATGACCCTAAGG
1862 CTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTACAGAT
195 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTACAGAT
*
1926 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCTG
260 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
*
1991 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
325 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACATC
2056 ATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
390 ATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
2120 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2185 CCCGAAGGCTTTTTGGAAACATCATGCACTGCA-GACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGAAAAC
*
2249 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATGCAGGACTTACAGATGACCCGAAGG
130 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATGCAGGACTTACAGATGACCCTAAGG
* *
2314 -TTTGAAAACATCAAAAAGCTCCCAAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTATAGA
195 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGAC-TACAGA
* *
2377 TGACCCTAAGGCTTTGAAAACATAAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCA
259 TGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCA
*
2442 GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACGT
324 GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACAT
*
2507 CATGCACTGCAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
389 CATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
2572 TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2637 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAGGACCCTAAGGTTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGAAAAC
2702 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
130 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA-TGCAGGACTTACAGATGACCCTAAG
* *
2767 GTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA-T---TG--TACAGA
194 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTACAGA
* * *
2826 TGACCCTAAGGCTTTGAAAACATCAAAAACCTCCTGAAGGCTTTTTGGAAACATCATGTACTGCA
259 TGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCA
2891 GGACTTACAGATG
324 GGACTTACAGATG
2904 TGGGAAATAG
Statistics
Matches: 746, Mismatches: 31, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
449 78 0.10
451 59 0.08
452 429 0.58
453 108 0.14
454 25 0.03
455 29 0.04
456 18 0.02
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (453 bp):
TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTGAAAACA
TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATGCAGGACTTACAGATGACCCTAAGGC
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTACAGATG
ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
ACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCA
TGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:3777 original size:22 final size:22
Alignment explanation
Indices: 3749--3803 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3739 CATAAAGCTT
3749 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3771 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3793 TCATCTTTGAA
1 TCATCTTTGAA
3804 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:4253 original size:54 final size:54
Alignment explanation
Indices: 4171--4326 Score: 240
Period size: 54 Copynumber: 2.9 Consensus size: 54
4161 AGAATAGCAG
* * *
4171 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAC
* *
4225 GTTCGTAAAACATTTGACAACACATTCATCCTTTTTTGTGGTTTCTGCTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAC
* * *
4279 GTTCGTAAAGCGTTTGACAACATATTCATCCTTTTCTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
4327 CAAGATTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAC
Found at i:6638 original size:114 final size:113
Alignment explanation
Indices: 6442--6661 Score: 332
Period size: 114 Copynumber: 1.9 Consensus size: 113
6432 ACGATCATGC
* * * * *
6442 ATTCATCTTTTAATTCCAATGATTGGTTCTGGGGTTCTACCGAACCAGATCAGATAACTCAAAGA
1 ATTCATCTTTCAAATACAATGATTGGTTCTGGGGTTATACCAAACCAGATCAGATAACTCAAAGA
* * *
6507 ATACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAA
* * *
6555 ATTCATCTTTCAAATACAATGATTGGTTTTGGGGTTTATACTAAACTAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATACAATGATTGGTTCTGGGG-TTATACCAAACCAGATCAGATAACTCAAAG
6620 AACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
65 AACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
6662 CGAGAACATG
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
113 30 0.32
114 65 0.68
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (113 bp):
ATTCATCTTTCAAATACAATGATTGGTTCTGGGGTTATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAA
Found at i:10924 original size:14 final size:14
Alignment explanation
Indices: 10907--10945 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
10897 TAAAAGTATG
10907 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
10921 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
10936 AATG-AAAATG
1 AATGCAAAATG
10946 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:13809 original size:27 final size:29
Alignment explanation
Indices: 13774--13828 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
13764 ATTTCAAAAT
13774 TATAATTAT-AA-AAAATATTAATTTATA
1 TATAATTATAAATAAAATATTAATTTATA
* *
13801 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
13829 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:13923 original size:20 final size:19
Alignment explanation
Indices: 13884--13925 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
13874 TTTCTTCGAT
13884 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
13903 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
13923 ATT
1 ATT
13926 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:13998 original size:120 final size:117
Alignment explanation
Indices: 13792--14017 Score: 283
Period size: 120 Copynumber: 1.9 Consensus size: 117
13782 TAAAAAATAT
* * * * *
13792 TAATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCATAAAAGGACTTCTAGG
1 TAATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGG
* *
13857 TGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAA
66 TGCCTTAAGACAGCTCCTTTCTT-AATATTAAAAAATAAATAAATAATTAAAA
**
13910 TAATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCC
1 TAATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCC
* ** * *
13975 AGTTGTTTTAAGACTGC-CCTTTCTTAATATTGAAAAATAAATA
63 AGGTGCCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATA
14018 TTAAAACAGG
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
118 11 0.12
119 22 0.24
120 39 0.43
121 19 0.21
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (117 bp):
TAATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGG
TGCCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATAATTAAAA
Found at i:14116 original size:22 final size:18
Alignment explanation
Indices: 14071--14106 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14061 TTAATAAATA
14071 AAATAAATAATATTTATT
1 AAATAAATAATATTTATT
*
14089 ATATAAATATATATTTAT
1 AAATAAATA-ATATTTAT
14107 GGCTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAAATAATATTTATT
Found at i:14227 original size:27 final size:27
Alignment explanation
Indices: 14181--14244 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
14171 AAACAATGAC
*
14181 AAAAATCAATAAAATTAAAA-TGATAGGT
1 AAAAAT-AATAAAATAAAAACTGATA-GT
* *
14209 ACAAATAATAAAATAAAAACTTATAGT
1 AAAAATAATAAAATAAAAACTGATAGT
14236 AAAAATAAT
1 AAAAATAAT
14245 TAGTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (27 bp):
AAAAATAATAAAATAAAAACTGATAGT
Found at i:15502 original size:29 final size:30
Alignment explanation
Indices: 15470--15546 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
15460 ATGTAATTTG
15470 TAATATATATATA-TATATT-TAATAATAAA
1 TAATATATATATATTATATTATAATAAT-AA
*
15499 TAATAATAATATATATTATATTATATTAATAA
1 TAAT-AT-ATATATATTATATTATAATAATAA
15531 TAAT-TATA-ATTATTAT
1 TAATATATATA-TATTAT
15547 TATGAAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.02
29 13 0.31
30 3 0.07
31 7 0.17
32 12 0.29
33 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAATATATATATATTATATTATAATAATAA
Found at i:24185 original size:81 final size:81
Alignment explanation
Indices: 24098--24470 Score: 491
Period size: 81 Copynumber: 4.6 Consensus size: 81
24088 CATTTAACTT
* * * **
24098 TTCATCTAACTTGCATGATTGAAACTTTTCTGCCAAATGCATAGTTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCATAACTAGGCCATTTATCTTTTACT
24163 CAACGGTCTTTAACCA
66 CAACGGTCTTTAACCA
* * * * *
24179 TCCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGTCATTTATATTTTACT
1 TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCATAACTAGGCCATTTATCTTTTACT
24244 CAACGGTCTTTAACCA
66 CAACGGTCTTTAACCA
* * *
24260 TTCATCTAATTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCATAACTAGGCCATTTATCTTTTACT
* *
24325 CAACGGTATTTAACCG
66 CAACGGTCTTTAACCA
* * *
24341 TTCATCTAACTGGCATAATTGATACCTTTT-TGCCAAATGC-TCAGCTAGGCAATTTATCTTTTA
1 TTCATCTAACTGGCATAATTGACA-CTTTTCTGCCAAATGCAT-AACTAGGCCATTTATCTTTTA
* *
24404 CTCAATGGTCTTTAACCG
64 CTCAACGGTCTTTAACCA
* * *
24422 TTCATCTAACTAGCATAATTGACACATTTT-TTCCAAATGCATATCTAGG
1 TTCATCTAACTGGCATAATTGACAC-TTTTCTGCCAAATGCATAACTAGG
24471 TCTCAAAGAC
Statistics
Matches: 260, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.00
81 254 0.98
82 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCATAACTAGGCCATTTATCTTTTACT
CAACGGTCTTTAACCA
Found at i:26738 original size:24 final size:24
Alignment explanation
Indices: 26706--26762 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
26696 ATTAAATGTG
26706 AAAGTGCTATACATGTATTTCACC
1 AAAGTGCTATACATGTATTTCACC
26730 AAAGTGCTATACATGTATTTCACC
1 AAAGTGCTATACATGTATTTCACC
26754 AAAGTGCTA
1 AAAGTGCTA
26763 ATTGATCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (24 bp):
AAAGTGCTATACATGTATTTCACC
Found at i:26924 original size:2 final size:2
Alignment explanation
Indices: 26917--26966 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
26907 TTGTTGTACA
26917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26959 AT AT AT AT
1 AT AT AT AT
26967 CATCCTTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27270 original size:81 final size:81
Alignment explanation
Indices: 27150--28005 Score: 1128
Period size: 81 Copynumber: 10.7 Consensus size: 81
27140 CACAACAGTG
* * * *
27150 TTTAACCGTTCATCTAACTGGTATAACTGACACATTTCTGTC-ATGTGCACAGTTAGACCATTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAT-TGCACAGTTAGGCCATTAT
**
27214 TCTTTTACTCAAAAGTA
65 TCTTTTACTCAATGGTA
* * * *
27231 TTTAACTGTTCATGTAATTGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGCCATTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
27296 CTTTTACTCAATGGTA
66 CTTTTACTCAATGGTA
* * * *
27312 TTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCATAGTTAGGCCGTTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
*
27377 -TTTTACTCAACGGTA
66 CTTTTACTCAATGGTA
* * * * *
27392 TTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGCCAATTTCGCAGTTAGGCTATTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
27457 CTTTTACTCAATGGTA
66 CTTTTACTCAATGGTA
** * * *
27473 TTTAACTATTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGTCGTTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
*
27538 CTTTTACTCAATGGAA
66 CTTTTACTCAATGGTA
* * * * *
27554 TTTAACCGTTCATATAACTAGCAT-ATTGACACATTTCTGCCAATTGCATAGTTAAGCCGTTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
* *
27618 CTTTTACTCAACGATA
66 CTTTTACTCAATGGTA
** * * *
27634 TTTAACCGTTCATCTAACTAACATAATTGACACATTTCTACCAATTGCACAATTAGGCTATTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
27699 CTTTTACTCAATGGTA
66 CTTTTACTCAATGGTA
* * * * * *
27715 TTTAACCGTTCATCTAACTAGCATAATTGATACCTTTATGCCAATTGTACAGTTAGGCAATTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
27780 CTTTTACTCAATGGTA
66 CTTTTACTCAATGGTA
* * *
27796 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCACAGTTAGACCATTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
27861 CTTTTACTC-------
66 CTTTTACTCAATGGTA
* *
27870 ---AA-CGGTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAATTAGGCCATTATT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
*
27931 CTTTTACTCAACGGTA
66 CTTTTACTCAATGGTA
* * *
27947 TTTAACCATTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGCACAGTTAGGCC
1 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCC
28006 TCAAAGGCAC
Statistics
Matches: 677, Mismatches: 84, Indels: 28
0.86 0.11 0.04
Matches are distributed among these distances:
70 63 0.09
71 2 0.00
80 144 0.21
81 466 0.69
82 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (81 bp):
TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
CTTTTACTCAATGGTA
Found at i:27423 original size:161 final size:162
Alignment explanation
Indices: 27150--28005 Score: 1137
Period size: 161 Copynumber: 5.4 Consensus size: 162
27140 CACAACAGTG
** * * *
27150 TTTAACCGTTCATCTAACTGGTATAACTGACACATTTCTGTC-ATGTGCACAGTTAGACCATTAT
1 TTTAACCGTTCATCTAACTGACATAATTGACACATTTCTGCCAAT-TGCACAGTTAGGCCATTAT
** * * * * *
27214 TCTTTTACTCAAAAGTATTTAACTGTTCATGTAATTGGCATAATTGACACCTTTCTGCCAATTGC
65 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGC
27279 ACAGTTAGGCCATTATTCTTTTACTCAATGGTA
130 ACAGTTAGGCCATTATTCTTTTACTCAATGGTA
* * *
27312 TTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCATAGTTAGGCCGTTATT
1 TTTAACCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
* * *
27377 -TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGCCAATTTCG
66 CTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCA
*
27441 CAGTTAGGCTATTATTCTTTTACTCAATGGTA
131 CAGTTAGGCCATTATTCTTTTACTCAATGGTA
** * *
27473 TTTAACTATTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGTCGTTATT
1 TTTAACCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
* * *
27538 CTTTTACTCAATGGAATTTAACCGTTCATATAACTAGCAT-ATTGACACATTTCTGCCAATTGCA
66 CTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCA
* * * * *
27602 TAGTTAAGCCGTTATTCTTTTACTCAACGATA
131 CAGTTAGGCCATTATTCTTTTACTCAATGGTA
* * * *
27634 TTTAACCGTTCATCTAACTAACATAATTGACACATTTCTACCAATTGCACAATTAGGCTATTATT
1 TTTAACCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
* * * * *
27699 CTTTTACTCAATGGTATTTAACCGTTCATCTAACTAGCATAATTGATACCTTTATGCCAATTGTA
66 CTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCA
*
27764 CAGTTAGGCAATTATTCTTTTACTCAATGGTA
131 CAGTTAGGCCATTATTCTTTTACTCAATGGTA
* * * *
27796 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCACAGTTAGACCATTATT
1 TTTAACCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
*
27861 CTTTTACTCAAC-G---------G-TCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCA
66 CTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCA
* *
27915 CAATTAGGCCATTATTCTTTTACTCAACGGTA
131 CAGTTAGGCCATTATTCTTTTACTCAATGGTA
* * * *
27947 TTTAACCATTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGCACAGTTAGGCC
1 TTTAACCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGCC
28006 TCAAAGGCAC
Statistics
Matches: 619, Mismatches: 72, Indels: 17
0.87 0.10 0.02
Matches are distributed among these distances:
151 119 0.19
152 1 0.00
161 291 0.47
162 206 0.33
163 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (162 bp):
TTTAACCGTTCATCTAACTGACATAATTGACACATTTCTGCCAATTGCACAGTTAGGCCATTATT
CTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCA
CAGTTAGGCCATTATTCTTTTACTCAATGGTA
Found at i:27625 original size:242 final size:241
Alignment explanation
Indices: 27135--28004 Score: 1151
Period size: 242 Copynumber: 3.6 Consensus size: 241
27125 ACCTTTCATG
* * * * * * *
27135 TTTTACACAACAGTGTTTAACCGTTCATCTAACTGGTATAACTGACACATTTCTGTC-ATGTGCA
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAAT-TGCA
* * ** ** * * *
27199 CAGTTAGACCATTATTCTTTTACTCAAAAGTATTTAACTGTTCATGTAATTGGCATAATTGACAC
65 CAATTAGGCCATTATTCTTTTACTCAATGGTATTTAACCATTCATCTAACTGACATAATTGACAC
* *
27264 CTTTCTGCCAATTGCACAGTTAGGCCATTATTCTTTTACTCAATGGTATTTAACTGTTCATCTAA
130 CTTTATGCCAATTGCACAGTTAGG-CATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAA
*
27329 CTGACATAATTGACACATTTCTGCCAATTGCATAGTTAGGCCGTTATT-
194 CTG-CATAATTGACACATTTCTGCCAATTGCATAGTTAAGCCGTTATTC
* * *
27377 TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGCCAATTTCGC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCAC
* * * *
27442 AGTTAGGCTATTATTCTTTTACTCAATGGTATTTAACTATTCATCTAACTGACATAATTGACACA
66 AATTAGGCCATTATTCTTTTACTCAATGGTATTTAACCATTCATCTAACTGACATAATTGACACC
* * * *
27507 TTTCTGCCAATTGCACAGTTAGGTCGTTATTCTTTTACTCAATGGAATTTAACCGTTCATATAAC
131 TTTATGCCAATTGCACAGTTAGG-CATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAAC
27572 TAGCAT-ATTGACACATTTCTGCCAATTGCATAGTTAAGCCGTTATTC
195 T-GCATAATTGACACATTTCTGCCAATTGCATAGTTAAGCCGTTATTC
* * *
27619 TTTTACTCAACGATATTTAACCGTTCATCTAACTAACATAATTGACACATTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCAC
* * *
27684 AATTAGGCTATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAACT-AGCATAATTGATAC
66 AATTAGGCCATTATTCTTTTACTCAATGGTATTTAACCATTCATCTAACTGA-CATAATTGACAC
*
27748 CTTTATGCCAATTGTACAGTTAGGCAATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAA
130 CTTTATGCCAATTGCACAGTTAGGC-ATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAA
* * * *
27813 CTGGCATAATTGACACCTTTCTACCAATTGCACAGTT-AGACCATTATTC
194 CT-GCATAATTGACACATTTCTGCCAATTGCATAGTTAAG-CCGTTATTC
*
27862 TTTTACTCAAC-G---------G-TCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCAC
* *
27916 AATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACC
66 AATTAGGCCATTATTCTTTTACTCAATGGTATTTAACCATTCATCTAACTGACATAATTGACACC
27981 TTTATGCCAATTGCACAGTTAGGC
131 TTTATGCCAATTGCACAGTTAGGC
28005 CTCAAAGGCA
Statistics
Matches: 564, Mismatches: 56, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
232 120 0.21
233 1 0.00
241 41 0.07
242 354 0.63
243 48 0.09
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (241 bp):
TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGCCAATTGCAC
AATTAGGCCATTATTCTTTTACTCAATGGTATTTAACCATTCATCTAACTGACATAATTGACACC
TTTATGCCAATTGCACAGTTAGGCATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAACT
GCATAATTGACACATTTCTGCCAATTGCATAGTTAAGCCGTTATTC
Found at i:27927 original size:70 final size:70
Alignment explanation
Indices: 27805--27945 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 70
27795 ATTTAACCGT
* *
27805 TCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCACAGTTAGACCATTATTCTTTTACTC
1 TCATCTAACTGGCATAATTGACACATTTCTACCAATTGCACAATTAGACCATTATTCTTTTACTC
27870 AACGG
66 AACGG
* *
27875 TCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTC
1 TCATCTAACTGGCATAATTGACACATTTCTACCAATTGCACAATTAGACCATTATTCTTTTACTC
27940 AACGG
66 AACGG
27945 T
1 T
27946 ATTTAACCAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (70 bp):
TCATCTAACTGGCATAATTGACACATTTCTACCAATTGCACAATTAGACCATTATTCTTTTACTC
AACGG
Found at i:27998 original size:151 final size:151
Alignment explanation
Indices: 27724--28002 Score: 459
Period size: 151 Copynumber: 1.8 Consensus size: 151
27714 ATTTAACCGT
* * * *
27724 TCATCTAACTAGCATAATTGATACCTTTATGCCAATTGTACAGTTAGGCAATTATTCTTTTACTC
1 TCATCTAACTAGCATAATTGACACATTTATGCCAATTGCACAATTAGGCAATTATTCTTTTACTC
* * *
27789 AATGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCACAGTTAGAC
66 AACGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTATACCAATTGCACAGTTAGAC
27854 CATTATTCTTTTACTCAACGG
131 CATTATTCTTTTACTCAACGG
* * *
27875 TCATCTAACTGGCATAATTGACACATTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTC
1 TCATCTAACTAGCATAATTGACACATTTATGCCAATTGCACAATTAGGCAATTATTCTTTTACTC
*
27940 AACGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGCACAGTTAG
66 AACGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTATACCAATTGCACAGTTAG
28003 GCCTCAAAGG
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 117 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (151 bp):
TCATCTAACTAGCATAATTGACACATTTATGCCAATTGCACAATTAGGCAATTATTCTTTTACTC
AACGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTATACCAATTGCACAGTTAGAC
CATTATTCTTTTACTCAACGG
Found at i:28121 original size:68 final size:68
Alignment explanation
Indices: 27955--28123 Score: 257
Period size: 68 Copynumber: 2.5 Consensus size: 68
27945 TATTTAACCA
* * * * *
27955 TTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
*
28020 TCT
66 CCT
*
28023 TTCATCTAAATGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
28088 CCT
66 CCT
* *
28091 TTCATCTAACTAGCATAAATGACACATTTCTGT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGT
28124 TGGTTGCACA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 91 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:28544 original size:58 final size:57
Alignment explanation
Indices: 28479--28751 Score: 397
Period size: 58 Copynumber: 4.7 Consensus size: 57
28469 TCCCATATAG
* *
28479 AAATTCATACATTTAGTATGAATCTCTTAACGA-TTTGCAC-GCACAGTGCCCAATACAA
1 AAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTGCACAG-A-AGTGCCCAATACAA
* *
28537 AAATTCATACACTTAGTATGGATTTCTTAACATTTTGCACATGAAGTGCCCAATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACA-GAAGTGCCCAATACAA
**
28595 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACA-GAAGTGCCCAATACAA
*
28653 AAATTCATACACTTAGTATGAATTTCTTAACATTTTACACATGAAGTGCCCAATACAA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACA-GAAGTGCCCAATACAA
* *
28711 AAATTCATACAATTAATATGAATTTCTTAACATTTTGCACA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACA
28752 CTTAGTGCCA
Statistics
Matches: 198, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
57 1 0.01
58 195 0.98
59 1 0.01
60 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACAGAAGTGCCCAATACAA
Found at i:29243 original size:95 final size:95
Alignment explanation
Indices: 29101--29302 Score: 298
Period size: 95 Copynumber: 2.1 Consensus size: 95
29091 ACTACCCTGG
* * * * *
29101 TATCGATACTTCTATACTATGGTACCGATACCCCTTTCCGGTATCGATACCAATTTTATG-TTCG
1 TATCGATACTACCATACTATGGTACCGATACCCCATTCCGATATCGATAACAATTTTA-GATTCG
29165 ATGTTGCCTGGTATCGATACCCTTACCATGA
65 ATGTTGCCTGGTATCGATACCCTTACCATGA
29196 TATCGATACTACCATACTATGGTACCGATACCCCATTCCGATATCGATAACAATTTTAGATTCGA
1 TATCGATACTACCATACTATGGTACCGATACCCCATTCCGATATCGATAACAATTTTAGATTCGA
* * * * *
29261 TGTTTCTTGGTTTCGATACCTTTACCATGG
66 TGTTGCCTGGTATCGATACCCTTACCATGA
29291 TATCGATACTAC
1 TATCGATACTAC
29303 ATCCCTGGTA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 95 0.99
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (95 bp):
TATCGATACTACCATACTATGGTACCGATACCCCATTCCGATATCGATAACAATTTTAGATTCGA
TGTTGCCTGGTATCGATACCCTTACCATGA
Found at i:38480 original size:25 final size:22
Alignment explanation
Indices: 38430--38483 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 22
38420 ATATTATTAT
38430 ATTTTTTAATATTTTGTATTTA
1 ATTTTTTAATATTTTGTATTTA
*
38452 ATTTATTTAATATTTTACTTATTTA
1 ATTT-TTTAATATTTT--GTATTTA
38477 ATTTTTT
1 ATTTTTT
38484 TTGCAGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 11 0.39
24 3 0.11
25 10 0.36
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
ATTTTTTAATATTTTGTATTTA
Found at i:40812 original size:10 final size:10
Alignment explanation
Indices: 40797--40842 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
40787 GTTAATTTTG
40797 TTTATTATCA
1 TTTATTATCA
40807 TTTATTATCA
1 TTTATTATCA
* * *
40817 GTTATTGTAA
1 TTTATTATCA
40827 TTTGATTATCA
1 TTT-ATTATCA
40838 TTTAT
1 TTTAT
40843 CATTTAATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (10 bp):
TTTATTATCA
Found at i:44757 original size:30 final size:29
Alignment explanation
Indices: 44695--44757 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
44685 TACTGCTAAG
*
44695 GGTGTTAGATCGAGAAATATAGTCTGACC
1 GGTGTTAGATCGAGAAATATAGTCTCACC
44724 GGTGTTAGATCG-GTAAATATA-TCGATCACC
1 GGTGTTAGATCGAG-AAATATAGTC--TCACC
44754 GGTG
1 GGTG
44758 ATTTTTCAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.10
29 19 0.63
30 8 0.27
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAGTCTCACC
Done.