Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008261.1 Hibiscus syriacus cultivar Beakdansim tig00110914_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: 103319
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3474 original size:29 final size:28
Alignment explanation
Indices: 3442--3499 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
3432 GGATGTTTAA
3442 ATTTGATGGTTGT-TGGATGTTTTGAACTT
1 ATTTG-TGGTTGTATGGAT-TTTTGAACTT
* *
3471 ATTTGTTGTTTTATGGATTTTTGAACTT
1 ATTTGTGGTTGTATGGATTTTTGAACTT
3499 A
1 A
3500 ATATTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.55
Consensus pattern (28 bp):
ATTTGTGGTTGTATGGATTTTTGAACTT
Found at i:4277 original size:65 final size:64
Alignment explanation
Indices: 4199--4343 Score: 152
Period size: 65 Copynumber: 2.2 Consensus size: 64
4189 CATCGAATGC
* ** *
4199 ATTTCATGCATCGATGC-ACATATTATGCATCGATGCACTCAGAG-TTTTATGAAAACATCGAAA
1 ATTTCATGAATCGATGCAACA-ACCATGCATCGATGCACTCAG-GCTATTATG-AAACATCGAAA
4262 TA
63 TA
* * * *
4264 ATTTGATGAATCGATGCAACAGCCATGCATCGATGCACTCTGGCTATTATGAAACATCG-AATGC
1 ATTTCATGAATCGATGCAACAACCATGCATCGATGCACTCAGGCTATTATGAAACATCGAAAT-A
*
4328 ATTTCATGCATCGATG
1 ATTTCATGAATCGATG
4344 ACACTTGATG
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
63 3 0.04
64 23 0.34
65 38 0.57
66 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (64 bp):
ATTTCATGAATCGATGCAACAACCATGCATCGATGCACTCAGGCTATTATGAAACATCGAAATA
Found at i:4354 original size:18 final size:18
Alignment explanation
Indices: 4333--4384 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
4323 AATGCATTTC
*
4333 ATGCATCGATGACACTTG-
1 ATGCATCGATG-CACTGGT
* *
4351 ATGCACCGATGCACGGGT
1 ATGCATCGATGCACTGGT
4369 ATGCATCGATGCACTG
1 ATGCATCGATGCACTG
4385 ACGCTCCCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (18 bp):
ATGCATCGATGCACTGGT
Found at i:6059 original size:67 final size:69
Alignment explanation
Indices: 5958--6109 Score: 166
Period size: 69 Copynumber: 2.2 Consensus size: 69
5948 ACAAAAGGTG
* * * * *
5958 TAAGGGTGAAATAAATTGAAGTGGAGATAAAACGG-A-TGGGTGCT-AGTAGAGATTATGATGGA
1 TAAGGGTGAAATAGATTGAAATAGAGATAAAACGGAAGAGGGTGCTGA-TAGAGATAATGATGGA
*
6020 ATTCA
65 AGTCA
** *
6025 TAAGGGTGAAATAGATTGAAATAGAGATGGAACGGAAGAGGGTGCTGATAGAGATAATGGTGGAA
1 TAAGGGTGAAATAGATTGAAATAGAGATAAAACGGAAGAGGGTGCTGATAGAGATAATGATGGAA
*
6090 GTCG
66 GTCA
* *
6094 TGAGGATGAAATAGAT
1 TAAGGGTGAAATAGAT
6110 GTGATGTAGA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
67 30 0.43
68 1 0.01
69 38 0.54
70 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.34, T:0.23
Consensus pattern (69 bp):
TAAGGGTGAAATAGATTGAAATAGAGATAAAACGGAAGAGGGTGCTGATAGAGATAATGATGGAA
GTCA
Found at i:7555 original size:23 final size:23
Alignment explanation
Indices: 7514--7557 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
7504 TGCCATATAA
**
7514 TTGTCCCGAATTACCACATAAGT
1 TTGTCCCGAAGGACCACATAAGT
*
7537 TTGTCCCGAAGGACTACATAA
1 TTGTCCCGAAGGACCACATAA
7558 TTTTATCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAAGT
Found at i:7814 original size:15 final size:15
Alignment explanation
Indices: 7794--7835 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
7784 CCATATACAT
*
7794 ATTCACTTAGCACAG
1 ATTCACATAGCACAG
7809 ATTCACATAGCACA-
1 ATTCACATAGCACAG
*
7823 TTATCACATAGCA
1 AT-TCACATAGCA
7836 TTATCAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (15 bp):
ATTCACATAGCACAG
Found at i:8834 original size:20 final size:20
Alignment explanation
Indices: 8805--8853 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
8795 ATATATAGTT
*
8805 GTTGGTGATGTTTTAGAGCC
1 GTTGGGGATGTTTTAGAGCC
*
8825 GTTGGGGATGTTTTGGAGCC
1 GTTGGGGATGTTTTAGAGCC
*
8845 GTTGAGGAT
1 GTTGGGGAT
8854 TCATTTTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.14, C:0.08, G:0.41, T:0.37
Consensus pattern (20 bp):
GTTGGGGATGTTTTAGAGCC
Found at i:9063 original size:20 final size:20
Alignment explanation
Indices: 9012--9081 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
9002 TTAGCAACGA
* * *
9012 TACTGTTCACACAATATCGG
1 TACTATTCATACAATATCAG
* *
9032 TACTATACATACAGTATCAG
1 TACTATTCATACAATATCAG
*
9052 TACTATTTATACAATA-CAG
1 TACTATTCATACAATATCAG
9071 TACTATTCATA
1 TACTATTCATA
9082 AAACATTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.32
20 28 0.68
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAATATCAG
Found at i:17028 original size:23 final size:21
Alignment explanation
Indices: 16991--17050 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 21
16981 ACCGAAGTGT
16991 CACATAATTATCCCAAATGAC
1 CACATAATTATCCCAAATGAC
17012 CACATAATTTTATCCCAAATGAC
1 CACATAA--TTATCCCAAATGAC
17035 CACATAGGATTATCCC
1 CACATA--ATTATCCC
17051 GTAGGACCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.20
23 27 0.77
25 1 0.03
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.27
Consensus pattern (21 bp):
CACATAATTATCCCAAATGAC
Found at i:17294 original size:27 final size:27
Alignment explanation
Indices: 17258--17321 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
17248 ATAGAAGATA
*
17258 TTCACTTATCACA-TATTCACATAACAT
1 TTCACATATCACATTA-TCACATAACAT
*
17285 TTCACATATCACATTATCACATATCAT
1 TTCACATATCACATTATCACATAACAT
*
17312 TATCAAATAT
1 T-TCACATAT
17322 TATTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (27 bp):
TTCACATATCACATTATCACATAACAT
Found at i:17296 original size:7 final size:7
Alignment explanation
Indices: 17259--17310 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
17249 TAGAAGATAT
*
17259 TCACTTA
1 TCACATA
17266 TCACATA
1 TCACATA
17273 TTCACATA
1 -TCACATA
*
17281 --ACATT
1 TCACATA
17286 TCACATA
1 TCACATA
17293 TCACATTA
1 TCACA-TA
17301 TCACATA
1 TCACATA
17308 TCA
1 TCA
17311 TTATCAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 4 0.11
7 20 0.53
8 14 0.37
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (7 bp):
TCACATA
Found at i:17306 original size:15 final size:15
Alignment explanation
Indices: 17259--17310 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
17249 TAGAAGATAT
*
17259 TCACTTATCACA-TA
1 TCACATATCACATTA
17273 TTCACATA--ACATT-
1 -TCACATATCACATTA
17286 TCACATATCACATTA
1 TCACATATCACATTA
17301 TCACATATCA
1 TCACATATCA
17311 TTATCAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 6 0.19
15 16 0.50
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (15 bp):
TCACATATCACATTA
Found at i:17314 original size:13 final size:13
Alignment explanation
Indices: 17274--17327 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
17264 TATCACATAT
*
17274 TCACATAACATT-
1 TCACATATCATTA
17286 TCACATATCACATTA
1 TCACATAT--CATTA
17301 TCACATATCATTA
1 TCACATATCATTA
* *
17314 TCAAATATTATTA
1 TCACATATCATTA
17327 T
1 T
17328 TATTATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.19
13 17 0.47
14 4 0.11
15 8 0.22
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (13 bp):
TCACATATCATTA
Found at i:17461 original size:2 final size:2
Alignment explanation
Indices: 17454--17506 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
17444 TAAAAACTTC
17454 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
17496 AT AT AT AT AT A
1 AT AT AT AT AT A
17507 CTAATAGCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21984 original size:27 final size:27
Alignment explanation
Indices: 21954--22036 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
21944 ATTGAGTTAA
21954 AACTAAAACTAAATTGATAGAATATAT
1 AACTAAAACTAAATTGATAGAATATAT
*** * * *
21981 AACT---ACTTTTTTGAATTGAGT-TAA
1 AACTAAAACTAAATTG-ATAGAATATAT
*
22005 AACTAAAACTAAATTGATAGAATATGT
1 AACTAAAACTAAATTGATAGAATATAT
22032 AACTA
1 AACTA
22037 CTGAGGACCA
Statistics
Matches: 38, Mismatches: 13, Indels: 10
0.62 0.21 0.16
Matches are distributed among these distances:
24 12 0.32
25 5 0.13
26 5 0.13
27 16 0.42
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (27 bp):
AACTAAAACTAAATTGATAGAATATAT
Found at i:22001 original size:51 final size:51
Alignment explanation
Indices: 21936--22038 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
21926 CTACTCTTTA
21936 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTAC
1 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTAC
*
21987 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATGTAACTAC
1 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTAC
22038 T
1 T
22039 GAGGACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (51 bp):
TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTAC
Found at i:28781 original size:26 final size:27
Alignment explanation
Indices: 28747--28809 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
28737 CAAGTAAAAG
*
28747 AATATAAAAACATA-AAATATAGGA-TA
1 AATATAAAAACAGATAAATA-AGGAGTA
* *
28773 AATATAAAAATAGATAAATAATGAGTA
1 AATATAAAAACAGATAAATAAGGAGTA
28800 AATATAAAAA
1 AATATAAAAA
28810 AGTAAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (27 bp):
AATATAAAAACAGATAAATAAGGAGTA
Found at i:28790 original size:16 final size:18
Alignment explanation
Indices: 28758--28792 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
28748 ATATAAAAAC
28758 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
28776 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
28792 A
1 A
28793 ATGAGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:28824 original size:2 final size:2
Alignment explanation
Indices: 28819--28843 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28809 AAGTAAAAAC
28819 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
28844 AGTAAAATAA
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:28925 original size:2 final size:2
Alignment explanation
Indices: 28912--28974 Score: 83
Period size: 2 Copynumber: 31.5 Consensus size: 2
28902 AAAATAGGAA
*
28912 AT AT AT AA AT AT AT AT 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 AT AT AT AT AT AT AT AT AT
* *
28953 AT AA ACT AT AT AT AC AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT A
28975 ATAAAATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
1 1 0.02
2 51 0.96
3 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:30503 original size:105 final size:105
Alignment explanation
Indices: 29992--30963 Score: 1396
Period size: 105 Copynumber: 9.3 Consensus size: 105
29982 CATTGTTCTA
* * **
29992 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAA-TTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-A-TTGGAAAGTTG-TTGTTGACA
* * * *
30055 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
63 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
30098 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T-GAAA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
*
30158 AGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
30198 AGTCCAATATATTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGG-AAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
*
30262 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
30302 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T-GAAA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
30362 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
30402 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
* *
30467 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
30507 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGGTTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
30572 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
30612 AGTCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
30677 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
30717 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTG-TTGTTGACAA
*
30782 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
30824 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAGTTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGA-AAGTTG-TTGTTGACAA
* * * *
30888 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
30930 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
30964 CGCGGATGGC
Statistics
Matches: 794, Mismatches: 54, Indels: 33
0.90 0.06 0.04
Matches are distributed among these distances:
100 171 0.22
101 5 0.01
102 13 0.02
103 8 0.01
104 87 0.11
105 297 0.37
106 97 0.12
107 95 0.12
109 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:31079 original size:415 final size:408
Alignment explanation
Indices: 29992--30963 Score: 1044
Period size: 415 Copynumber: 2.3 Consensus size: 408
29982 CATTGTTCTA
* * ***
29992 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAA-TTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGAAAGTTG-TTGTTGACAA
** ** * * *
30056 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCCGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTCCGTCGTGAA
*** * * * *
30121 GTTGAAATTGAATCTGA--AT--GAAATT-TTGTTGACAAGCAGCAG-TCCCTTCGTCGTGAAGT
129 GTTGAAATTGGCCCTGACGTTGGGAAGTTGTAGTTGACAACCAG-AGATCCCTTCGTCGTGAAGT
* *** * * * * * * * **
30180 TGAACTTGCGTTGTCTGGAGTCCAATATATTTCGTTGTGAAGTTGAAATTGGCTCTGGGA-TTGG
193 TGAACATGCCAAGTAT-GAGT-C-ATAT-CTGCGGTGTGAA-AT-AAATT-GCCCTGAGACCGGG
30244 AAGTTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAA
251 AAGTTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAA
* *
30309 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTC
316 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTATTGACAACCAGCGGTCCCTTC
30374 GTCGTGAAGTTGAACTTGCGTTGTCTGG
381 GTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
30402 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTGTTGACAACC
* * *
30467 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCCGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTCCGTCGTGAAGT
* * * * *
30532 TGAAATTGGCTCTGAGGTTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCCCTGACGTTGGGAAGTTGTAGTTGACAACCAGAGATCCCTTCGTCGTGAAGTTGA
* *** * * * * **
30597 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAG
196 ACATGCCAAGTAT-GAGT-C-ATAT-CTGCGGTGTGAAA-T-AAATT-GCCCTGAGACCGGGAAG
* *
30662 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
254 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
30727 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCC
319 CCTTCGCTGTGAAGTTGAAATTGGCTCTG-AA-T--G-AAA-T-TTTATTGACAACCAGCGGTCC
*
30792 CTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
377 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
30824 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAGTTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGA-AAGTTG-TTGTTGACAA
** ** *
30888 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGCCACGATATCCTCCGTCGT
64 CCAGCCGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGT-CCA--ATATCCTCCGTCGT
*
30953 GGAGTTGAAAT
126 GAAGTTGAAAT
30964 CGCGGATGGC
Statistics
Matches: 500, Mismatches: 41, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
409 90 0.18
410 39 0.08
411 1 0.00
413 6 0.01
414 85 0.17
415 98 0.20
416 2 0.00
417 1 0.00
419 1 0.00
420 3 0.01
421 3 0.01
422 98 0.20
423 48 0.10
424 3 0.01
426 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (408 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTGTTGACAACC
AGCCGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTCCGTCGTGAAGT
TGAAATTGGCCCTGACGTTGGGAAGTTGTAGTTGACAACCAGAGATCCCTTCGTCGTGAAGTTGA
ACATGCCAAGTATGAGTCATATCTGCGGTGTGAAATAAATTGCCCTGAGACCGGGAAGTTGTTGT
TGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGC
TGTGAAGTTGAAATTGGCTCTGAATGAAATTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGG
Found at i:31877 original size:67 final size:67
Alignment explanation
Indices: 31797--31954 Score: 205
Period size: 67 Copynumber: 2.4 Consensus size: 67
31787 GAAATGAAAT
* * *
31797 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGCGTTTCAAGAGAAACTGTCTCAAGGGAGAC
31860 AAAA
64 AAAA
* * *
31864 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGCGTTTCAAGAGAAGCTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGCGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
31929 AA
66 AA
**
31931 TTT-TTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
31955 GAGAGACGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 22 0.28
67 57 0.71
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGCGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
AA
Found at i:31939 original size:35 final size:35
Alignment explanation
Indices: 31899--31967 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
31889 AGGTTTTGCG
* * *
31899 TTTCAAGAGAAGCTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* * *
31934 TTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
31968 CATTTCTAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (35 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:32041 original size:102 final size:102
Alignment explanation
Indices: 31898--32287 Score: 613
Period size: 102 Copynumber: 3.8 Consensus size: 102
31888 AAGGTTTTGC
* * *
31898 GTTTCAAGAGAAGCTGTCTCAAGGGAGACAAAA-TTT-TTTCAAGGGAAATTATCTCAAGAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* *
31961 CGAAATTCATTTCTAGGGAAATGTTTTCAATGTTTAT
66 CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
* *
31998 GTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
*
32063 CAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTAT
66 CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
* **
32100 GTTTTAAGAGAAACTGTCTCAAGGGAGAAAAAAAATTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* *
32165 CAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTAA
66 CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
*
32202 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* **
32267 CAAAGTTTGTTTCAAGGGAAA
66 CAAAATTCATTTCAAGGGAAA
32288 CTGTCTCAAG
Statistics
Matches: 266, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
100 31 0.12
101 3 0.01
102 232 0.87
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (102 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
Found at i:32048 original size:37 final size:37
Alignment explanation
Indices: 31997--32305 Score: 205
Period size: 37 Copynumber: 8.9 Consensus size: 37
31987 TCAATGTTTA
*
31997 TGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAATTT
*
32034 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
32070 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * * **
32098 ATGTTTTAAGAGAAACTGTCTCAAGGGAGAAAAAAAAT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
32136 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
32172 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * * *
32200 AAGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
32238 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
32274 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
32306 TGGTGAGCAC
Statistics
Matches: 205, Mismatches: 41, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 24 0.12
30 8 0.04
32 1 0.00
33 1 0.00
34 1 0.00
35 6 0.03
36 65 0.32
37 84 0.41
38 9 0.04
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:33824 original size:20 final size:21
Alignment explanation
Indices: 33800--33861 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
33790 TTTTTTGTTC
*
33800 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
33821 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
33841 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
33862 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:33872 original size:22 final size:22
Alignment explanation
Indices: 33818--33870 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
33808 ATTTTTGTTC
33818 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
33839 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
33862 TTTCTTTTT
1 TTTCTTTTT
33871 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:35040 original size:8 final size:8
Alignment explanation
Indices: 35027--35062 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
35017 GTAGATGAAG
35027 ATGCAAAA
1 ATGCAAAA
35035 ATGCAAAA
1 ATGCAAAA
35043 ATGC-AAA
1 ATGCAAAA
*
35050 ATGCAAGA
1 ATGCAAAA
35058 ATGCA
1 ATGCA
35063 TGAAATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (8 bp):
ATGCAAAA
Found at i:35052 original size:15 final size:15
Alignment explanation
Indices: 35027--35062 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
35017 GTAGATGAAG
35027 ATGCAAAAATGCAAAA
1 ATGC-AAAATGCAAAA
*
35043 ATGCAAAATGCAAGA
1 ATGCAAAATGCAAAA
35058 ATGCA
1 ATGCA
35063 TGAAATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:37035 original size:16 final size:18
Alignment explanation
Indices: 37003--37037 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
36993 ATATAAAAAC
37003 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
37021 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
37037 A
1 A
37038 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:37757 original size:3 final size:3
Alignment explanation
Indices: 37745--37818 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
37735 TGTCACCTAC
37745 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
37792 CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
37819 CAGTCCACAT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43291 original size:65 final size:63
Alignment explanation
Indices: 43094--43302 Score: 208
Period size: 65 Copynumber: 3.3 Consensus size: 63
43084 TGGACCCTTA
* **
43094 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAA-AATAGCATAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAATTCCATAGTGCATCGATGCATGG-TG
* * ** * *
43157 ATGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCCCAGTGCATCAATTCATGGTG
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAT-AATTCCATAGTGCATCGATGCATGGTG
* * *
43221 TGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATGGTGCATCGATGCATGGAT
1 -GTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TAATTCCATAGTGCATCGATGCATGG--
43285 TG
62 TG
* *
43287 GTGCATTGGTGCATCA
1 GTGCATCGATGCATCA
43303 CTTTGAAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
63 31 0.26
64 25 0.21
65 59 0.50
66 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAATTCCATAGTGCATCGATGCATGGTG
Found at i:45569 original size:7 final size:8
Alignment explanation
Indices: 45540--45567 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
45530 AAAATTTTAA
45540 AAAAATTG
1 AAAAATTG
45548 AAAAATTG
1 AAAAATTG
45556 AAAAATTG
1 AAAAATTG
45564 AAAA
1 AAAA
45568 TTTGTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (8 bp):
AAAAATTG
Found at i:45981 original size:21 final size:20
Alignment explanation
Indices: 45951--46017 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
45941 TATGCATTGG
*
45951 TGCACCTTCATGGTGTATCGA
1 TGCACATTCA-GGTGTATCGA
*
45972 TGCACATTCAAGGATGCATCGA
1 TGCACATTC-AGG-TGTATCGA
*
45994 TGCACTATT-AGGTGTATTGA
1 TGCAC-ATTCAGGTGTATCGA
46014 TGCA
1 TGCA
46018 TTAAGCACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 10 0.26
21 13 0.33
22 13 0.33
23 3 0.08
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TGCACATTCAGGTGTATCGA
Found at i:51870 original size:56 final size:57
Alignment explanation
Indices: 51798--51909 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
51788 AAGAGTGCAT
* *
51798 TGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGC
1 TGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGGC
* *
51854 TGATGCATCAAATGCATTCGATGTTTTCATAAAATCCCCAGTGCATCGATGCATGG
1 TGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGG
51910 TGTGTGCATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 22 0.44
57 25 0.50
58 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (57 bp):
TGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGC
Found at i:60247 original size:21 final size:21
Alignment explanation
Indices: 60218--60267 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
60208 TATTTGTTAG
*
60218 TATTT-ATTTAATTATTGTAT
1 TATTTAATTTAATTATTATAT
** *
60238 TATTTAATTTTTTTATTATTT
1 TATTTAATTTAATTATTATAT
60259 TATTTAATT
1 TATTTAATT
60268 ATTTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TATTTAATTTAATTATTATAT
Found at i:60263 original size:16 final size:16
Alignment explanation
Indices: 60221--60263 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
60211 TTGTTAGTAT
* *
60221 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
60237 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
60253 TTATTTTATTT
1 TTATTTAATTT
60264 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:60272 original size:21 final size:20
Alignment explanation
Indices: 60237--60279 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
60227 AATTATTGTA
*
60237 TTATTTAATTTTTTTATTATT
1 TTATTTAATTATTTTATT-TT
60258 TTATTTAATTATTTTATTTT
1 TTATTTAATTATTTTATTTT
60278 TT
1 TT
60280 CACAGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TTATTTAATTATTTTATTTT
Found at i:62861 original size:7 final size:7
Alignment explanation
Indices: 62851--62882 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
62841 ACGAGAAAGC
62851 AAGCATG
1 AAGCATG
62858 AAGCATG
1 AAGCATG
62865 AAGCATG
1 AAGCATG
62872 AAGCATG
1 AAGCATG
62879 AAGC
1 AAGC
62883 CCAGCATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (7 bp):
AAGCATG
Found at i:64084 original size:314 final size:314
Alignment explanation
Indices: 63515--64145 Score: 1219
Period size: 314 Copynumber: 2.0 Consensus size: 314
63505 TAGTGATTTT
*
63515 CCCATCATGATAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
1 CCCATCATGACAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
63580 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTGAAAGGGGTCTATTTTTAAAAATATTGTT
66 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTGAAAGGGGTCTATTTTTAAAAATATTGTT
63645 AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCGAAAGTATGGTA
131 AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCGAAAGTATGGTA
*
63710 ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAATAAACTCGAAAA
196 ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAACTCGAAAA
63775 TATGGTGATCTAATGGGTCTCATTTTAATGATTAGAAGGGAAATTAAGTATGAG
261 TATGGTGATCTAATGGGTCTCATTTTAATGATTAGAAGGGAAATTAAGTATGAG
63829 CCCATCATGACAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
1 CCCATCATGACAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
63894 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTTG-AAGGGGTCTATTTTTAAAAATATTGT
66 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAG-TTGAAAGGGGTCTATTTTTAAAAATATTGT
63958 TAAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCGAAAGTATGGT
130 TAAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCGAAAGTATGGT
64023 AATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAACTCGAAA
195 AATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAACTCGAAA
*
64088 ATATGGTGATCTAATGGGTCTCATTTTAATGATTGGAAGGGAAATTAAGTATGAG
260 ATATGGTGATCTAATGGGTCTCATTTTAATGATTAGAAGGGAAATTAAGTATGAG
64143 CCC
1 CCC
64146 TCACTTATCT
Statistics
Matches: 313, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
314 310 0.99
315 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (314 bp):
CCCATCATGACAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTGAAAGGGGTCTATTTTTAAAAATATTGTT
AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCGAAAGTATGGTA
ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAACTCGAAAA
TATGGTGATCTAATGGGTCTCATTTTAATGATTAGAAGGGAAATTAAGTATGAG
Found at i:65697 original size:54 final size:54
Alignment explanation
Indices: 65612--66038 Score: 588
Period size: 54 Copynumber: 7.9 Consensus size: 54
65602 AATACGGTCG
** * * ** ** *
65612 TTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCAATACGTAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
65666 TTCATAAACTCATTATGAATTTCTTAAGTTGCACATACAGTGCCAATATGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
*
65720 TTCATAAACTTATTATGAATTTCTTAAGTTG--CACACAGTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
** * *
65772 TTCATAAACTTATTATGAATTTCTTAAGTTGCAGGCACATTGCCAATACAGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
65826 TTCATAAACTTATTATGATTTTCTTAAGTTGCACACACACAGTGCAAATATGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTG--CACACACAGTGCCAATACGGAAA
65882 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
65936 TTCATAAATTTATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
65990 TTTATAAACTTATTATGAATTTCTTAAGTTGCACATACAATGCCAATAC
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
66039 ATACATTAAG
Statistics
Matches: 332, Mismatches: 37, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
52 49 0.15
54 236 0.71
56 47 0.14
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (54 bp):
TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
Found at i:65906 original size:110 final size:108
Alignment explanation
Indices: 65612--66038 Score: 597
Period size: 110 Copynumber: 4.0 Consensus size: 108
65602 AATACGGTCG
** * * ** ** * *
65612 TTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCAATACGTAAATTCATAAACTC
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTT
* *
65677 ATTATGAATTTCTTAAGTTGCACATACAGTGCCAATATGGAAA
66 ATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
65720 TTCATAAACTTATTATGAATTTCTTAAGTTG--CACACAGTGCCAATACGAAAATTCATAAACTT
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTT
** * *
65783 ATTATGAATTTCTTAAGTTGCAGGCACATTGCCAATACAGAAA
66 ATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * * *
65826 TTCATAAACTTATTATGATTTTCTTAAGTTGCACACACACAGTGCAAATATGGAAATTCATAAAC
1 TTCATAAACTTATTATGAATTTCTTAAGTTG--CACACACAGTGCCAATACGAAAATTCATAAAC
65891 TTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
64 TTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
65936 TTCATAAATTTATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAATTTATAAACTT
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTT
* *
66001 ATTATGAATTTCTTAAGTTGCACATACAATGCCAATAC
66 ATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
66039 ATACATTAAG
Statistics
Matches: 282, Mismatches: 33, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
106 95 0.34
108 90 0.32
110 97 0.34
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (108 bp):
TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTT
ATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
Found at i:69523 original size:30 final size:30
Alignment explanation
Indices: 69489--69547 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
69479 ATAGAATCGA
69489 CTGAAAACCGGT-AAAACCGGGGTGAACCGG
1 CTGAAAACC-GTCAAAACCGGGGTGAACCGG
**
69519 CTGAAAACCGTCAAAACCGGTTTGAACCG
1 CTGAAAACCGTCAAAACCGGGGTGAACCG
69548 CCGGTTCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.34, C:0.25, G:0.27, T:0.14
Consensus pattern (30 bp):
CTGAAAACCGTCAAAACCGGGGTGAACCGG
Found at i:73142 original size:29 final size:29
Alignment explanation
Indices: 73109--73244 Score: 155
Period size: 29 Copynumber: 4.6 Consensus size: 29
73099 TAAAATATAT
73109 ATATATTTTATTCTTATCTTAACTTAAAA
1 ATATATTTTATTCTTATCTTAACTTAAAA
* * *
73138 GTATATTTTATTCTTATTTTCACTTAAAA
1 ATATATTTTATTCTTATCTTAACTTAAAA
* * * *
73167 ATATATTTTAATATTTTATTAACTTAAAAA
1 ATATATTTTATTCTTATCTTAACTT-AAAA
* *
73197 ATATAATTTATTCTTACCTTAACTTAAATA
1 ATATATTTTATTCTTATCTTAACTTAAA-A
*
73227 TTTATATTTTATTCTTAT
1 -ATATATTTTATTCTTAT
73245 AATATTTTAA
Statistics
Matches: 86, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
29 48 0.56
30 24 0.28
31 14 0.16
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.54
Consensus pattern (29 bp):
ATATATTTTATTCTTATCTTAACTTAAAA
Found at i:73394 original size:30 final size:30
Alignment explanation
Indices: 73359--73435 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
73349 AAGGATAAAT
*
73359 TATATTTAATAATTTAAGGTAAGACTAGAA
1 TATATTTAATAATTTAAGGTAAGAATAGAA
* *
73389 TATATTTAATAATTTAAGTTAAGAATATAA
1 TATATTTAATAATTTAAGGTAAGAATAGAA
* *
73419 TATATGTAATAAGTTAA
1 TATATTTAATAATTTAA
73436 AATAAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.40
Consensus pattern (30 bp):
TATATTTAATAATTTAAGGTAAGAATAGAA
Found at i:73448 original size:36 final size:32
Alignment explanation
Indices: 73408--73540 Score: 100
Period size: 29 Copynumber: 4.2 Consensus size: 32
73398 TAATTTAAGT
73408 TAAGAATATAATATATGTAATAAGTTAAAATAAAAA
1 TAAGAATAT-AT-T-TGTAA-AAGTTAAAATAAAAA
* *
73444 TAAG-ATATATTTTTAAAAGTTAAGATAAAAA
1 TAAGAATATATTTGTAAAAGTTAAAATAAAAA
* * * * *
73475 TAA-AATAT-TTT-TTAAAGTTGAGATAAGAT
1 TAAGAATATATTTGTAAAAGTTAAAATAAAAA
*
73504 TAA-AATATATTT-T-CAAGTTAAAATAAAAA
1 TAAGAATATATTTGTAAAAGTTAAAATAAAAA
*
73533 TAAAAATA
1 TAAGAATA
73541 AAATATATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
29 36 0.43
30 11 0.13
31 21 0.25
32 4 0.05
33 1 0.01
34 2 0.02
35 4 0.05
36 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (32 bp):
TAAGAATATATTTGTAAAAGTTAAAATAAAAA
Found at i:73492 original size:29 final size:29
Alignment explanation
Indices: 73429--73537 Score: 128
Period size: 29 Copynumber: 3.7 Consensus size: 29
73419 TATATGTAAT
*
73429 AAGTTAAAATAAAAATAAGATATATTTTTAA
1 AAGTTAAAATAAAAATAA-A-ATATTTTTTA
*
73460 AAGTTAAGATAAAAATAAAATATTTTTTA
1 AAGTTAAAATAAAAATAAAATATTTTTTA
* * * * * *
73489 AAGTTGAGATAAGATTAAAATATATTTTC
1 AAGTTAAAATAAAAATAAAATATTTTTTA
73518 AAGTTAAAATAAAAATAAAA
1 AAGTTAAAATAAAAATAAAA
73538 ATAAAATATA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 49 0.73
30 1 0.01
31 17 0.25
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (29 bp):
AAGTTAAAATAAAAATAAAATATTTTTTA
Found at i:73617 original size:29 final size:29
Alignment explanation
Indices: 73245--73617 Score: 105
Period size: 30 Copynumber: 12.7 Consensus size: 29
73235 TTATTCTTAT
* *
73245 AATAT-TTTAAAAT-TTAAGATAAAATAA
1 AATATATTTATAATGTTAAAATAAAATAA
* * *
73272 AACATATTT-TCAA-ATTAAAA-AATA-AA
1 AATATATTTAT-AATGTTAAAATAAAATAA
* * *
73298 AATACATTTTTAA-GTAAAAATAATAATAA
1 AATATATTTATAATGTTAAAATAA-AATAA
* *
73327 AATATAGATTT-T-ATGTTACAATAAGGATAA
1 AATAT--ATTTATAATGTTAAAATAA-AATAA
* ** * *
73357 ATTATATTTAATAAT-TTAAGGTAAGACTAG
1 AATATATTT-ATAATGTTAAAATAA-AATAA
** *
73387 AATATATTTAATAAT-TTAAGTTAAGAATAT
1 AATATATTT-ATAATGTTAAAATAA-AATAA
*
73417 AATATATGTAATAA-GTTAAAATAAAAATAA
1 AATATAT-TTATAATGTTAAAAT-AAAATAA
* * * *
73447 GATATATTTTTAAAAGTTAAGATAAAAATAA
1 AATATATTTAT-AATGTTAAAAT-AAAATAA
* * * * *
73478 AATAT-TTTTTAAAGTTGAGATAAGATTAA
1 AATATATTTATAATGTTAAAATAA-AATAA
73507 AATATATTT-TCAA-GTTAAAATAAAAATAAA
1 AATATATTTAT-AATGTTAAAAT-AAAAT-AA
* * * *
73537 AATAAAATATATTTTTAGGTTAGACA-AAAATAA
1 AAT---ATAT-TTATAATGTTA-AAATAAAATAA
* *
73570 AATAGATTTAATACT-TTAAAATAAAATAA
1 AATATATTT-ATAATGTTAAAATAAAATAA
*
73599 AAAATATTTATAATGTTAA
1 AATATATTTATAATGTTAA
73618 TATTTAAATT
Statistics
Matches: 263, Mismatches: 50, Indels: 64
0.70 0.13 0.17
Matches are distributed among these distances:
26 16 0.06
27 10 0.04
28 23 0.09
29 60 0.23
30 102 0.39
31 28 0.11
33 9 0.03
34 8 0.03
35 5 0.02
36 2 0.01
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
AATATATTTATAATGTTAAAATAAAATAA
Found at i:74622 original size:138 final size:140
Alignment explanation
Indices: 74356--74637 Score: 514
Period size: 138 Copynumber: 2.0 Consensus size: 140
74346 TTTTTAATAT
*
74356 ATAATTTAACATTTAATATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
1 ATAATTTAACATTTAACATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
74421 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
66 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
74486 CGAATG-AAG
131 CGAATGAAAG
* *
74495 ATAATTTAACATTTAACATATTAATTACATACAAATCTATATATAATTATACTAATATATTAT-A
1 ATAATTTAACATTTAACATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
*
74559 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAG
66 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
74624 CGAATGAAAG
131 CGAATGAAAG
74634 ATAA
1 ATAA
74638 AACAGGGAGG
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
138 71 0.51
139 67 0.49
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (140 bp):
ATAATTTAACATTTAACATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
CGAATGAAAG
Found at i:76829 original size:13 final size:14
Alignment explanation
Indices: 76813--76841 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
76803 GATGTCTACC
76813 TCAACATTC-TATG
1 TCAACATTCTTATG
76826 TCAACATTCTTATG
1 TCAACATTCTTATG
76840 TC
1 TC
76842 TCATACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (14 bp):
TCAACATTCTTATG
Found at i:90594 original size:21 final size:21
Alignment explanation
Indices: 90555--90594 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
90545 AAATACCTTG
* *
90555 GTATCAATACTCTTTTGAGGA
1 GTATCAATACTCCTATGAGGA
*
90576 GTATCGATACTCCTATGAG
1 GTATCAATACTCCTATGAG
90595 TATCGATACC
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:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GTATCAATACTCCTATGAGGA
Found at i:92526 original size:35 final size:35
Alignment explanation
Indices: 92482--92549 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
92472 GCATTCATGT
*
92482 GGTATCGATACCTGAAGAACAATATCGATACCAAG
1 GGTACCGATACCTGAAGAACAATATCGATACCAAG
* ** *
92517 GGTACCGATACTTTTAGAACGATATCGATACCA
1 GGTACCGATACCTGAAGAACAATATCGATACCA
92550 TCTTTGAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (35 bp):
GGTACCGATACCTGAAGAACAATATCGATACCAAG
Found at i:92987 original size:2 final size:2
Alignment explanation
Indices: 92980--93006 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92970 AACACATGCG
92980 TA 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 TA T
93007 GGTTGTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94352 original size:60 final size:61
Alignment explanation
Indices: 94198--94353 Score: 163
Period size: 61 Copynumber: 2.6 Consensus size: 61
94188 AGATGTTCAA
* * * *
94198 AAAAGTTTGGGGACCAATTTAGAATGAAAATCATAGTTTGGGGATGAAAAATGAAATGTCC
1 AAAAGTTTAGGGACCAATTTAGAATGAAAGTCATAGTTTAGGGATGAAAAATAAAATGTCC
* * ** * * * **
94259 AAAAGTTTAAGAATTAATTTAGAATGATAGTCATAGTTTAGGGATG-TAATTAAAATGTTT
1 AAAAGTTTAGGGACCAATTTAGAATGAAAGTCATAGTTTAGGGATGAAAAATAAAATGTCC
*
94319 AAAAGTTTAGGGACCAATTTAAAAT-AAAGGTCATA
1 AAAAGTTTAGGGACCAATTTAGAATGAAA-GTCATA
94354 ACTGAAGGAC
Statistics
Matches: 75, Mismatches: 19, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
59 2 0.03
60 35 0.47
61 38 0.51
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.31
Consensus pattern (61 bp):
AAAAGTTTAGGGACCAATTTAGAATGAAAGTCATAGTTTAGGGATGAAAAATAAAATGTCC
Found at i:94692 original size:21 final size:21
Alignment explanation
Indices: 94659--94698 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
94649 GGGATTTTTT
94659 TATTTTTATATTATTAAAATA
1 TATTTTTATATTATTAAAATA
94680 TATTCTTTA-ATTATTAAAA
1 TATT-TTTATATTATTAAAA
94699 AACATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTTATATTATTAAAATA
Found at i:95638 original size:16 final size:16
Alignment explanation
Indices: 95617--95658 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
95607 TGTTGCTCGA
95617 CTCGTTGCTCATTAAG
1 CTCGTTGCTCATTAAG
* *
95633 CTCGTTACTCGTTAAG
1 CTCGTTGCTCATTAAG
95649 CTCGTTGCTC
1 CTCGTTGCTC
95659 TTCTCGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (16 bp):
CTCGTTGCTCATTAAG
Found at i:99640 original size:24 final size:24
Alignment explanation
Indices: 99608--99675 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
99598 CGTTCGGTAA
99608 TATGTTCGTTCAGTTATGTTCATT
1 TATGTTCGTTCAGTTATGTTCATT
**
99632 TATGTTCGTTC-GTTTATGTTTGTT
1 TATGTTCGTTCAG-TTATGTTCATT
** *
99656 TATGTGAGTTCATTTATGTT
1 TATGTTCGTTCAGTTATGTT
99676 TAGCTCAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.15, C:0.09, G:0.19, T:0.57
Consensus pattern (24 bp):
TATGTTCGTTCAGTTATGTTCATT
Found at i:102964 original size:2 final size:2
Alignment explanation
Indices: 102959--102997 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
102949 AACTGTGGGT
102959 TA TA TA TA TA TA TA -A 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
102998 ACAGATTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.