Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001785.1 Hibiscus syriacus cultivar Beakdansim tig00003604_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: 274370
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:247192 original size:19 final size:19
Alignment explanation
Indices: 247168--247221 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
247158 AATATAATTA
247168 ATTATTTATTTGAAATAAT
1 ATTATTTATTTGAAATAAT
247187 ATTA-TT-TTT-AAAT--T
1 ATTATTTATTTGAAATAAT
247201 ATCTATTTAATTTGAAATAAT
1 AT-TATTT-ATTTGAAATAAT
247222 TTAAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 6 0.21
17 3 0.11
18 5 0.18
19 8 0.29
21 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
ATTATTTATTTGAAATAAT
Found at i:247366 original size:23 final size:23
Alignment explanation
Indices: 247317--247367 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
247307 AAAATGATAT
*
247317 TATTTCAAATAAATAATTAATAT
1 TATTTCAAATAAATAATTAATAA
*
247340 TATTTCAAATAAAT-TTTAAATAA
1 TATTTCAAATAAATAATT-AATAA
247363 TATTT
1 TATTT
247368 TAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTCAAATAAATAATTAATAA
Found at i:247366 original size:26 final size:23
Alignment explanation
Indices: 247308--247353 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
247298 GATAATTTAA
*
247308 AAATGATATTATTTCAAATAAAT
1 AAATAATATTATTTCAAATAAAT
*
247331 AATTAATATTATTTCAAATAAAT
1 AAATAATATTATTTCAAATAAAT
247354 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
AAATAATATTATTTCAAATAAAT
Found at i:247380 original size:34 final size:34
Alignment explanation
Indices: 247342--247425 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
247332 ATTAATATTA
247342 TTTCAAATAAATTTTAAATAATA-TTTTAAAATAT
1 TTTCAAATAAATTTTAAATAA-ACTTTTAAAATAT
* *
247376 TTTCATAATAAA--ATAAATAAACTTTTTAGAATAT
1 TTTCA-AATAAATTTTAAATAAAC-TTTTAAAATAT
247410 TTT-AATATAAATTTTA
1 TTTCAA-ATAAATTTTA
247426 TAAATACATA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
32 2 0.05
33 13 0.32
34 18 0.44
35 8 0.20
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTCAAATAAATTTTAAATAAACTTTTAAAATAT
Found at i:247429 original size:33 final size:34
Alignment explanation
Indices: 247340--247429 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 34
247330 TAATTAATAT
*
247340 TATTTCAA-ATAAATTTTA-AATAATATTTTAAAA
1 TATTTTAATATAAATTTTATAA-AATATTTTAAAA
* * ** * *
247373 TATTTTCATAATAAAATAAATAAACT-TTTTAGAA
1 TATTTTAAT-ATAAATTTTATAAAATATTTTAAAA
247407 TATTTTAATATAAATTTTATAAA
1 TATTTTAATATAAATTTTATAAA
247430 TACATAAAAG
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
33 17 0.40
34 15 0.35
35 9 0.21
36 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (34 bp):
TATTTTAATATAAATTTTATAAAATATTTTAAAA
Found at i:248613 original size:10 final size:11
Alignment explanation
Indices: 248579--248610 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
248569 ATAATCCTAT
*
248579 TATTTCAAAAA
1 TATTTAAAAAA
248590 TATTTAAAAAA
1 TATTTAAAAAA
248601 TATTTAAAAA
1 TATTTAAAAA
248611 TATCGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TATTTAAAAAA
Found at i:250001 original size:3 final size:3
Alignment explanation
Indices: 249971--250072 Score: 105
Period size: 3 Copynumber: 33.3 Consensus size: 3
249961 TTTGGGTTTT
* * *
249971 ATA ATA TTA ATAA ATA ATA TATA TTA ATA ATA ATA ATA ATA ATT ATA
1 ATA ATA ATA AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
250018 ATA ATA ATA ATA ATT ATT ATT ATT ATT ATT ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
250066 ATA ATA A
1 ATA ATA A
250073 ATTTTAAAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
3 83 0.93
4 6 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:251511 original size:14 final size:14
Alignment explanation
Indices: 251492--251521 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
251482 ATTCTCTAAA
251492 AATTATAATTAATT
1 AATTATAATTAATT
*
251506 AATTATAATTTATT
1 AATTATAATTAATT
251520 AA
1 AA
251522 CTGTTAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATAATTAATT
Found at i:255774 original size:17 final size:16
Alignment explanation
Indices: 255752--255812 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
255742 AAAAAGAAAT
255752 AAAAAAATAAATTAATA
1 AAAAAAATAAA-TAATA
255769 AAAAAAATAAATAATA
1 AAAAAAATAAATAATA
*
255785 ATAATAATAATAAA-GATA
1 A-AA-AA-AATAAATAATA
255803 AAATAAAATA
1 AAA-AAAATA
255813 TTTTCCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 10 0.25
17 18 0.45
18 6 0.15
19 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAAAATAAATAATA
Found at i:255884 original size:35 final size:36
Alignment explanation
Indices: 255807--256189 Score: 150
Period size: 35 Copynumber: 10.8 Consensus size: 36
255797 AAGATAAAAT
255807 AAAATATTTTCCAAAAACCTATATAATATATATTTCACA
1 AAAATATTTT-C-AAAA-CTATATAATATATATTTCACA
* * ***
255846 AAAATATTTT-AAAATTATATATTATATATTTTTGA
1 AAAATATTTTCAAAACTATATAATATATATTTCACA
*
255881 AAAATGTTTTCAAAAC--TAT-ATA-AT-TTT--CA
1 AAAATATTTTCAAAACTATATAATATATATTTCACA
* * *
255910 AAAATGTTTTTAAAACTATATACTATATAAGTTTTCAC-
1 AAAATATTTTCAAAACTATATAATATAT-A--TTTCACA
**
255948 --AATGA-TTTCAAAACTATATAATATATATGTTTTC-
1 AAAAT-ATTTTCAAAACTATATAATATATAT-TTCACA
* *
255982 AAAATGTTTTTAAAAAACTATAT--T-TAT-TTT--C-
1 AAAAT-ATTTT-CAAAACTATATAATATATATTTCACA
* * * *
256013 AAAATGTTTTAAAAACTATATAATATACATTT-TCA
1 AAAATATTTTCAAAACTATATAATATATATTTCACA
** * * * *
256048 AAAACGTTTTAAAAAATATATATTATATTTATTT-TC-
1 AAAATATTTTCAAAACTATATA--ATATATATTTCACA
* * **
256084 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTCA
1 AAAATATTTTCAAAACTATATAATATAT--AT-TTCACA
* * *
256123 AACATGTTTTCAAAACTATATATTATATATATATTTA-A
1 AAAATATTTTCAAAACTATATA--ATATATAT-TTCACA
*
256161 AAAATGTTTTC-AAACTATATAATATATAT
1 AAAATATTTTCAAAACTATATAATATATAT
256190 ATATATATAT
Statistics
Matches: 280, Mismatches: 32, Indels: 68
0.74 0.08 0.18
Matches are distributed among these distances:
29 27 0.10
30 4 0.01
31 13 0.05
32 6 0.02
33 10 0.04
34 13 0.05
35 57 0.20
36 57 0.20
37 28 0.10
38 23 0.08
39 36 0.13
41 6 0.02
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (36 bp):
AAAATATTTTCAAAACTATATAATATATATTTCACA
Found at i:255912 original size:29 final size:29
Alignment explanation
Indices: 255868--255931 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
255858 AATTATATAT
* *
255868 TATATATTTTTGAAAAATGTTTTCAAAAC
1 TATATAATTTTCAAAAATGTTTTCAAAAC
*
255897 TATATAATTTTCAAAAATGTTTTTAAAAC
1 TATATAATTTTCAAAAATGTTTTCAAAAC
255926 TATATA
1 TATATA
255932 CTATATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAATTTTCAAAAATGTTTTCAAAAC
Found at i:255925 original size:101 final size:97
Alignment explanation
Indices: 255820--256107 Score: 296
Period size: 102 Copynumber: 2.9 Consensus size: 97
255810 ATATTTTCCA
* *
255820 AAAACCTATATAATATATATTTCACAAAAATATTTTAAAATTATATATTATATATTTTTGAAAAA
1 AAAA-CTATATAATATATATTTCACAAAAATATTTTAAAAATATATATTATATATTTTT-CAAAA
*
255885 TGTTTTCAAAACTATATAATTTTCAAAAATGTTTTT
64 TGTTTTAAAAACTATATAATTTTC-AAAATG-TTTT
* * * *
255921 AAAACTATATACTATATAAGTTTTCAC---AATGATTTCAAAACTATATAATATATATGTTTTCA
1 AAAACTATATAATATAT-A--TTTCACAAAAAT-ATTTTAAAAATATATATTATATAT-TTTTCA
*
255983 AAATGTTTTTAAAAAACTATATTTATTTTCAAAATGTTTT
61 AAATG-TTTT-AAAAACTATA-TAATTTTCAAAATGTTTT
* * ** *
256023 AAAAACTATATAATATACATTT-TCAAAAACGTTTTAAAAAATATATATTATATTTATTTTCAAA
1 -AAAACTATATAATATATATTTCACAAAAATATTTT-AAAAATATATATTATATAT-TTTTCAAA
256087 ATGTTTTAAAAACTATATAAT
63 ATGTTTTAAAAACTATATAAT
256108 ATATAAATGT
Statistics
Matches: 156, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
99 4 0.03
100 28 0.18
101 39 0.25
102 42 0.27
103 36 0.23
104 7 0.04
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (97 bp):
AAAACTATATAATATATATTTCACAAAAATATTTTAAAAATATATATTATATATTTTTCAAAATG
TTTTAAAAACTATATAATTTTCAAAATGTTTT
Found at i:256004 original size:31 final size:29
Alignment explanation
Indices: 255969--256070 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 29
255959 AACTATATAA
*
255969 TATATATGTTTTCAAAATGTTTTTAAAAAAC
1 TATATATATTTTCAAAATG-TTTT-AAAAAC
*
256000 TATATTTATTTTCAAAATGTTTTAAAAAC
1 TATATATATTTTCAAAATGTTTTAAAAAC
* *
256029 TATATAATATACATTTTCAAAAACGTTTTAAAAAA
1 --TAT-ATAT--ATTTTC-AAAATGTTTTAAAAAC
256064 TATATAT
1 TATATAT
256071 TATATTTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
29 6 0.10
30 4 0.07
31 20 0.33
32 7 0.12
33 3 0.05
34 6 0.10
35 14 0.23
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (29 bp):
TATATATATTTTCAAAATGTTTTAAAAAC
Found at i:256082 original size:37 final size:37
Alignment explanation
Indices: 255897--256191 Score: 269
Period size: 36 Copynumber: 8.2 Consensus size: 37
255887 TTTTCAAAAC
* *
255897 TATATA-ATTTTCAAAAATGTTTTTAAAACTATATAC
1 TATATATATTTTCAAAAATGTTTTAAAAACTATATAT
* * * *
255933 TATATA-AGTTTTC-ACAATGATTTCAAAACTATATAA
1 TATATATA-TTTTCAAAAATGTTTTAAAAACTATATAT
* *
255969 TATATATGTTTTC-AAAATGTTTTTAAAAA--A-CTA-
1 TATATATATTTTCAAAAATG-TTTTAAAAACTATATAT
256002 TAT-T-TATTTTC-AAAATGTTTTAAAAACTATATA-
1 TATATATATTTTCAAAAATGTTTTAAAAACTATATAT
* * *
256035 -ATATACATTTTCAAAAACGTTTTAAAAAATATATAT
1 TATATATATTTTCAAAAATGTTTTAAAAACTATATAT
*
256071 TATATTTATTTTC-AAAATGTTTTAAAAACTATATAAT
1 TATATATATTTTCAAAAATGTTTTAAAAACTATAT-AT
* * * *
256108 ATATAAATGTTTTCAAACATGTTTTCAAAACTATATAT
1 -TATATATATTTTCAAAAATGTTTTAAAAACTATATAT
* * *
256146 TATATATATATTTAAAAAATGTTTT-CAAACTATATAA
1 TATATATAT-TTTCAAAAATGTTTTAAAAACTATATAT
256183 TATATATAT
1 TATATATAT
256192 ATATATATAT
Statistics
Matches: 215, Mismatches: 29, Indels: 29
0.79 0.11 0.11
Matches are distributed among these distances:
30 9 0.04
31 12 0.06
32 4 0.02
33 6 0.03
34 8 0.04
35 21 0.10
36 61 0.28
37 50 0.23
38 25 0.12
39 19 0.09
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATATATTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:256181 original size:2 final size:2
Alignment explanation
Indices: 256176--256208 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
256166 GTTTTCAAAC
256176 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256209 AATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:256192 original size:37 final size:37
Alignment explanation
Indices: 255820--256193 Score: 239
Period size: 36 Copynumber: 10.6 Consensus size: 37
255810 ATATTTTCCA
** *
255820 AAAACCTATATAATATATAT-T-TCACAAAAATATTTT
1 AAAA-CTATATAATATATATATATTTCAAAAATGTTTT
* * *
255856 AAAATTATAT-AT-TATATATTTTTGAAAAATGTTTT
1 AAAACTATATAATATATATATATTTCAAAAATGTTTT
255891 ----C-A-A-AACTATATA-AT-TTTCAAAAATGTTTTT
1 AAAACTATATAA-TATATATATATTTCAAAAATG-TTTT
* * *
255921 AAAACTATATACTATATA-AGT-TTTC-ACAATGATTTC
1 AAAACTATATAATATATATA-TATTTCAAAAATG-TTTT
*
255957 AAAACTATATAATATATATGT-TTTC-AAAATGTTTT
1 AAAACTATATAATATATATATATTTCAAAAATGTTTT
* * *
255992 TAAA--A-A-ACTATATTTAT-TTTC-AAAATGTTTT
1 AAAACTATATAATATATATATATTTCAAAAATGTTTT
* *
256023 AAAAACTATAT-A-ATATACAT-TTTCAAAAACGTTTT
1 -AAAACTATATAATATATATATATTTCAAAAATGTTTT
* * *
256058 AAAAAATATATATTATATTTAT-TTTC-AAAATGTTTT
1 -AAAACTATATAATATATATATATTTCAAAAATGTTTT
* * *
256094 AAAAACTATATAATATATAAATGTTTTCAAACATGTTTT
1 -AAAACTATATAATATATATAT-ATTTCAAAAATGTTTT
* *
256133 CAAAACTATATATTATATATATATTTAAAAAATGTTTT
1 -AAAACTATATAATATATATATATTTCAAAAATGTTTT
*
256171 CAAACTATATAATATATATATAT
1 AAAACTATATAATATATATATAT
256194 ATATATATAT
Statistics
Matches: 270, Mismatches: 42, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
29 12 0.04
30 8 0.03
31 26 0.10
32 4 0.01
33 6 0.02
34 15 0.06
35 43 0.16
36 74 0.27
37 37 0.14
38 17 0.06
39 28 0.10
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAACTATATAATATATATATATTTCAAAAATGTTTT
Found at i:256871 original size:84 final size:84
Alignment explanation
Indices: 256775--257504 Score: 707
Period size: 84 Copynumber: 8.8 Consensus size: 84
256765 GCTATGTTGT
* *
256775 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGATAGATAACCCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
* * * *
256840 TAGCCCTGAGTTATGCTAC
66 TAGACTTAAGTTATGCTGC
*
256859 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACTCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
* * *
256923 TAGCCTTGAGTTATGCTGT
66 TAGACTTAAGTTATGCTGC
* * * * ** * ** *
256942 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGTAGACAACCCTT
1 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
*
257007 CTTAGACTTAAGTTGTGCTGC
65 C-TAGACTTAAGTTATGCTGC
* * *
257028 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAATTCGTAGG--TATTGGTGACAGATAACCCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
* * *
257091 TAGCCTTGAGTTATGCTGT
66 TAGACTTAAGTTATGCTGC
* * * * * * ** *
257110 AAATGATATGCCCTCGAAGCTGAGTGTAATCAAAATCGGGGGTC-TTT-G-G-CAGATAGCCCTT
1 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
* * *
257171 CTCGACTTAAGCTATGCTAC
65 CTAGACTTAAGTTATGCTGC
* * * * * *
257191 AAATGATGTGTCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTT-GTTAGCAGACAACCCT
1 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGA-CAGATAACCCT
*
257254 TCTAGACTTAAGTTGTGCTGC
64 TCTAGACTTAAGTTATGCTGC
* * *
257275 AAATAATATGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGAC-TTTGGTGACAGATAACCCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
* * **
257339 TAGCCTTGAGTTATGCTAT
66 TAGACTTAAGTTATGCTGC
* * * * **
257358 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-G-CAGATAACCCTT
1 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
* *
257419 CTCGACTTAAGCTATGCTGC
65 CTAGACTTAAGTTATGCTGC
* * * *
257439 AAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTC-TTTGGTTGGCAAATAACCCTT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTT
257503 CT
65 CT
257505 TGTCTTGAGC
Statistics
Matches: 520, Mismatches: 109, Indels: 34
0.78 0.16 0.05
Matches are distributed among these distances:
80 50 0.10
81 76 0.15
82 27 0.05
83 129 0.25
84 173 0.33
85 40 0.08
86 25 0.05
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
TAGACTTAAGTTATGCTGC
Found at i:257337 original size:248 final size:246
Alignment explanation
Indices: 256783--257504 Score: 971
Period size: 248 Copynumber: 2.9 Consensus size: 246
256773 GTAAATGATG
* *
256783 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGATAGATAACCCTTCTAGCCCTG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-C-TTTGGTGACAGATAACCCTTCTAGCCTTG
* * * * * **
256848 AGTTATGCTACAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACA
64 AGTTATGCTATAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CA
* * * * * * * * * *
256912 GATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC
126 GATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGAAC
** * *
256977 TCGGGGGTCTTTTGTTGGTAGACAACCCTTCTTAGACTTAAGTTGTGCTGCAAATGATA
189 TCGAAGGTCTTTTGTTGGCAGACAACCCTTC-TAGACTTAAGTTGTGCTGCAAATAATA
* *
257036 TGCCTTGGAGCTGAGCGTAGTCGAATTCGTAGG-TATTGGTGACAGATAACCCTTCTAGCCTTGA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCT-TTGGTGACAGATAACCCTTCTAGCCTTGA
* * *
257100 GTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAAAATCGGGGGTCTTTGGCAGATA
65 GTTATGCTATAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
* * * * *
257165 GCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGTCGTTGAGCTGAGCGTAGTCAAACTCAAA
130 ACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAGCTGAGCGTAGTCGAACTCGAA
*
257230 GGTCTTTTGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATAATA
194 GGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATAATA
*
257283 TGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGACTTTGGTGACAGATAACCCTTCTAGCCTTGA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-CTTTGGTGACAGATAACCCTTCTAGCCTTGA
257348 GTTATGCTATAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
65 GTTATGCTATAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
*
257413 ACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAA
130 ACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAA
* * *
257478 GGTCTTTGGTTGGCAAATAACCCTTCT
194 GGTCTTTTGTTGGCAGACAACCCTTCT
257505 TGTCTTGAGC
Statistics
Matches: 413, Mismatches: 51, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
247 59 0.14
248 210 0.51
249 37 0.09
250 2 0.00
251 46 0.11
252 28 0.07
253 31 0.08
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (246 bp):
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
TTATGCTATAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAA
CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGG
TCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATAATA
Found at i:262856 original size:16 final size:15
Alignment explanation
Indices: 262831--262861 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
262821 TAATAATGCT
262831 AAAAAAATAAAAATA
1 AAAAAAATAAAAATA
262846 AAAACAAATAAAAATA
1 AAAA-AAATAAAAATA
262862 TATAGTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:264222 original size:12 final size:12
Alignment explanation
Indices: 264205--264255 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
264195 ACCTGGAAAG
264205 AAAAATGAAATA
1 AAAAATGAAATA
264217 AAAAATGAAATTA
1 AAAAATGAAA-TA
*
264230 ATAAAATAAAATA
1 A-AAAATGAAATA
264243 AAAAA-GAAATA
1 AAAAATGAAATA
264254 AA
1 AA
264256 TAATAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 7 0.20
12 14 0.40
13 6 0.17
14 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (12 bp):
AAAAATGAAATA
Found at i:264279 original size:6 final size:5
Alignment explanation
Indices: 264229--264288 Score: 57
Period size: 6 Copynumber: 10.8 Consensus size: 5
264219 AAATGAAATT
*
264229 AATAA AATAA AATAA AAAAGA AATAAA TAATAA TAATAA TAATAA AGATAA
1 AATAA AATAA AATAA AATA-A AAT-AA -AATAA -AATAA -AATAA A-ATAA
264280 AATAA AATA
1 AATAA AATA
264289 TTTTCCAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
5 22 0.45
6 23 0.47
7 4 0.08
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:264360 original size:35 final size:36
Alignment explanation
Indices: 264283--264588 Score: 127
Period size: 36 Copynumber: 8.8 Consensus size: 36
264273 AAGATAAAAT
264283 AAAATATTTTCCAAAAACCTATATAATATATATTTCACA
1 AAAATATTTT-C-AAAA-CTATATAATATATATTTCACA
* * ***
264322 AAAATATTTT-AAAATTATATATTATATATTTTTGA
1 AAAATATTTTCAAAACTATATAATATATATTTCACA
*
264357 AAAATGTTTTCAAAAC--TAT-ATA-AT-TTT--CA
1 AAAATATTTTCAAAACTATATAATATATATTTCACA
* * *
264386 AAAATGTTTTTAAAACTATATACTATATAAGTTTTCAC-
1 AAAATATTTTCAAAACTATATAATATAT-A--TTTCACA
**
264424 --AATGA-TTTCAAAACTATATAATATATATGTTTTC-
1 AAAAT-ATTTTCAAAACTATATAATATATAT-TTCACA
* *
264458 AAAATGTTTTTAAAAAACTATAT--T-TAT-TTT--C-
1 AAAAT-ATTTT-CAAAACTATATAATATATATTTCACA
* * *
264489 AAAATATTTTAAAAACTATATAATATACATTT-TCA
1 AAAATATTTTCAAAACTATATAATATATATTTCACA
** * * * *
264524 AAAACGTTTTAAAAAATATATATTATATTTATTT-TC-
1 AAAATATTTTCAAAACTATATA--ATATATATTTCACA
* *
264560 AAAATGTTTTAAAAACTATATAATATATA
1 AAAATATTTTCAAAACTATATAATATATA
264589 ATGTCCGTCG
Statistics
Matches: 214, Mismatches: 28, Indels: 55
0.72 0.09 0.19
Matches are distributed among these distances:
29 27 0.13
30 4 0.02
31 13 0.06
32 6 0.03
33 10 0.05
34 14 0.07
35 48 0.22
36 55 0.26
37 16 0.07
38 10 0.05
39 11 0.05
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (36 bp):
AAAATATTTTCAAAACTATATAATATATATTTCACA
Found at i:264388 original size:29 final size:29
Alignment explanation
Indices: 264344--264407 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
264334 AATTATATAT
* *
264344 TATATATTTTTGAAAAATGTTTTCAAAAC
1 TATATAATTTTCAAAAATGTTTTCAAAAC
*
264373 TATATAATTTTCAAAAATGTTTTTAAAAC
1 TATATAATTTTCAAAAATGTTTTCAAAAC
264402 TATATA
1 TATATA
264408 CTATATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAATTTTCAAAAATGTTTTCAAAAC
Found at i:264406 original size:65 final size:64
Alignment explanation
Indices: 264320--264445 Score: 164
Period size: 65 Copynumber: 2.0 Consensus size: 64
264310 ATATATTTCA
* * * *
264320 CAAAAATATTTTAAAATTATATATTATAT-ATTTTTGAAAAATGTTTTCAAAACTATATAATTTT
1 CAAAAATATTTTAAAACTATATACTATATAAGTTTT-AAAAATGATTTCAAAACTATATAATTTT
* * *
264384 CAAAAATGTTTTTAAAACTATATACTATATAAGTTTTCACAATGATTTCAAAACTATATAAT
1 CAAAAAT-ATTTTAAAACTATATACTATATAAGTTTTAAAAATGATTTCAAAACTATATAAT
264446 ATATATGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 7 0.13
65 41 0.77
66 5 0.09
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (64 bp):
CAAAAATATTTTAAAACTATATACTATATAAGTTTTAAAAATGATTTCAAAACTATATAATTTT
Found at i:264411 original size:36 final size:35
Alignment explanation
Indices: 264371--264590 Score: 204
Period size: 36 Copynumber: 6.3 Consensus size: 35
264361 TGTTTTCAAA
*
264371 ACTATATAATTTTCAAAAATGTTTTTAAAACTATAT
1 ACTATATAATTTTC-AAAATGTTTTAAAAACTATAT
* * *
264407 ACTATATAAGTTTTCACAATGATTTCAAAACTATAT
1 ACTATATAA-TTTTCAAAATGTTTTAAAAACTATAT
* *
264443 AATATATATGTTTTCAAAATGTTTTTAAAAA--ACTAT
1 ACTATATA-ATTTTCAAAATG-TTTTAAAAACTA-TAT
*
264479 A-T-T-T-ATTTTCAAAATATTTTAAAAACTATAT
1 ACTATATAATTTTCAAAATGTTTTAAAAACTATAT
* *
264510 A--ATATACATTTTCAAAAACGTTTTAAAAAATATAT
1 ACTATATA-ATTTTC-AAAATGTTTTAAAAACTATAT
* *
264545 ATTATATTTATTTTCAAAATGTTTTAAAAACTATAT
1 ACTATA-TAATTTTCAAAATGTTTTAAAAACTATAT
*
264581 AATATATAAT
1 ACTATATAAT
264591 GTCCGTCGGA
Statistics
Matches: 152, Mismatches: 18, Indels: 29
0.76 0.09 0.15
Matches are distributed among these distances:
30 9 0.06
31 15 0.10
32 2 0.01
33 1 0.01
34 7 0.05
35 24 0.16
36 72 0.47
37 21 0.14
38 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (35 bp):
ACTATATAATTTTCAAAATGTTTTAAAAACTATAT
Found at i:264462 original size:101 final size:98
Alignment explanation
Indices: 264283--264583 Score: 302
Period size: 101 Copynumber: 3.0 Consensus size: 98
264273 AAGATAAAAT
* ** * *
264283 AAAATATTTTCCAAAAACCTATATAATATATA-TTTCACAAAAATATTTTAAAATTATATATTAT
1 AAAATATTTT--AAAAA-CTATATAATATACATTTTCA-AAAACGATTTAAAAAATATATATTAT
* *
264347 ATATTTTTGAAAAATGTTTTCAAAACTATATAATTTTC
62 ATATTTTT-CAAAATGTTTTAAAAACTATATAATTTTC
* * * * * * *
264385 AAAAATGTTTTTAAAACTATATACTATATA-AGTTTTC-ACAATGATTTCAAAACTATATAATAT
1 -AAAATATTTTAAAAACTATATA--ATATACA-TTTTCAAAAACGATTTAAAAAATATATATTAT
*
264448 ATATGTTTTCAAAATGTTTTTAAAAAACTATATTTATTTTC
62 ATAT-TTTTCAAAATG-TTTT-AAAAACTATA-TAATTTTC
* *
264489 AAAATATTTTAAAAACTATATAATATACATTTTCAAAAACGTTTTAAAAAATATATATTATATTT
1 AAAATATTTTAAAAACTATATAATATACATTTTCAAAAACGATTTAAAAAATATATATTATATAT
264554 ATTTTCAAAATGTTTTAAAAACTATATAAT
66 -TTTTCAAAATGTTTTAAAAACTATATAAT
264584 ATATAATGTC
Statistics
Matches: 166, Mismatches: 22, Indels: 24
0.78 0.10 0.11
Matches are distributed among these distances:
99 3 0.02
100 17 0.10
101 49 0.30
102 48 0.29
103 42 0.25
104 7 0.04
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (98 bp):
AAAATATTTTAAAAACTATATAATATACATTTTCAAAAACGATTTAAAAAATATATATTATATAT
TTTTCAAAATGTTTTAAAAACTATATAATTTTC
Found at i:264480 original size:31 final size:29
Alignment explanation
Indices: 264445--264510 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
264435 AACTATATAA
* *
264445 TATATATGTTTTCAAAATGTTTTTAAAAAAC
1 TATATATATTTTCAAAAT-ATTTT-AAAAAC
*
264476 TATATTTATTTTCAAAATATTTTAAAAAC
1 TATATATATTTTCAAAATATTTTAAAAAC
264505 TATATA
1 TATATA
264511 ATATACATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.35
30 4 0.13
31 16 0.52
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (29 bp):
TATATATATTTTCAAAATATTTTAAAAAC
Found at i:265555 original size:30 final size:31
Alignment explanation
Indices: 265510--265570 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
265500 GATGGATCAA
**
265510 AGAGATTTAAGGGATTGGATGTTTTGGGTTTT
1 AGAGATTTAAGGGATT-GAAATTTTGGGTTTT
265542 AGAGA-TT-AGGGATTGAAATTTTGGGTTTT
1 AGAGATTTAAGGGATTGAAATTTTGGGTTTT
265571 CAGATGATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
30 7 0.26
31 2 0.07
32 5 0.19
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.43
Consensus pattern (31 bp):
AGAGATTTAAGGGATTGAAATTTTGGGTTTT
Found at i:266597 original size:11 final size:12
Alignment explanation
Indices: 266580--266605 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
266570 CTTAACAACT
266580 TTTTTTTAACAA
1 TTTTTTTAACAA
266592 TTTTTTTAACAA
1 TTTTTTTAACAA
266604 TT
1 TT
266606 GTTAAAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTTTAACAA
Found at i:268402 original size:4 final size:4
Alignment explanation
Indices: 268393--268452 Score: 66
Period size: 4 Copynumber: 14.0 Consensus size: 4
268383 TATATTTAGG
* *
268393 ATTA ATTA ATTA ATAA ATTA ATAA ATTA TATTTA GGATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA -A-TTA --ATTA ATTA ATTA
268441 ATTA ATTA ATTA
1 ATTA ATTA ATTA
268453 TATTTAGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
4 40 0.83
5 1 0.02
6 6 0.12
7 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:268422 original size:36 final size:34
Alignment explanation
Indices: 268381--268474 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 34
268371 CTCGAAAAGT
268381 ATTATATTTAGGATTAATTAATTAATAAATTAATAA
1 ATTATATTTAGGATTAATTAATT-AT-AATTAATAA
*
268417 ATTATATTTAGGATTAATTAA-T-TAATTAATTA
1 ATTATATTTAGGATTAATTAATTATAATTAATAA
268449 ATTATATTTAGGA-TAATTTAATTATA
1 ATTATATTTAGGATTAA-TTAATTATA
268475 TATGCATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
31 3 0.06
32 25 0.46
33 2 0.04
34 2 0.04
35 1 0.02
36 21 0.39
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (34 bp):
ATTATATTTAGGATTAATTAATTATAATTAATAA
Found at i:268485 original size:20 final size:21
Alignment explanation
Indices: 268441--268485 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
268431 TAATTAATTA
* *
268441 ATTAA-TTAATTATATTTAGG
1 ATTAATTTAATTATATATAGC
268461 A-TAATTTAATTATATAT-GC
1 ATTAATTTAATTATATATAGC
268480 ATTAAT
1 ATTAAT
268486 ATTGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTAATTTAATTATATATAGC
Found at i:271241 original size:28 final size:26
Alignment explanation
Indices: 271190--271241 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
271180 AATTTTAAAA
271190 TTTATATAATACTATATTTAATTTTT
1 TTTATATAATACTATATTTAATTTTT
* *
271216 TTTATATTTATACATATATTTTATTT
1 TTTATA-TAATAC-TATATTTAATTT
271242 AATCTTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 5 0.23
28 11 0.50
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTATATAATACTATATTTAATTTTT
Found at i:272609 original size:16 final size:17
Alignment explanation
Indices: 272576--272611 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
272566 CATTACTATA
*
272576 GATATTCAAAATTTTCG
1 GATATCCAAAATTTTCG
272593 GATATCCAAAA-TTTCG
1 GATATCCAAAATTTTCG
272609 GAT
1 GAT
272612 CGGATGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (17 bp):
GATATCCAAAATTTTCG
Done.