Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006843.1 Hibiscus syriacus cultivar Beakdansim tig00017395_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: 67233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9151 original size:19 final size:19
Alignment explanation
Indices: 9129--9168 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
9119 GAAATATTAT
*
9129 TTTTTGGAGGGAAAATTTA
1 TTTTTAGAGGGAAAATTTA
9148 TTTTTAGAGGGAAAATTTA
1 TTTTTAGAGGGAAAATTTA
9167 TT
1 TT
9169 AAAAGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (19 bp):
TTTTTAGAGGGAAAATTTA
Found at i:9479 original size:2 final size:2
Alignment explanation
Indices: 9472--9687 Score: 121
Period size: 2 Copynumber: 107.5 Consensus size: 2
9462 ATGTTTAATG
* * * * *
9472 AT AT AT AT AT AT AT AT AC ACT -T AT TT AC AT AC AT CAT AC AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT -AT AT AT AT
* *
9515 AT ACT TT AT AT AT AT AT AT AT AT AT -T AT ACT AT AG AT -T AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
9557 ACT CAT AC GT -T AT AT AT AT GT AT -T AT AT AT AT AT AT AT AT AT
1 A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
9599 AT ACT -T AT AT AT ACT -T AT GT AT AT ACT -T TT AT AT AT AT AT
1 AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
9639 AT AT AT AT -T AT ACT -T AT ACT TT AT AT AT AT AT AT GT ACT -T
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T AT
9679 AT AT AT AT A
1 AT AT AT AT A
9688 CACATCATAC
Statistics
Matches: 165, Mismatches: 26, Indels: 46
0.70 0.11 0.19
Matches are distributed among these distances:
1 11 0.07
2 140 0.85
3 13 0.08
4 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9682 original size:46 final size:45
Alignment explanation
Indices: 9475--9687 Score: 154
Period size: 46 Copynumber: 4.6 Consensus size: 45
9465 TTTAATGATA
* * * *
9475 TATATATATATATACACTTAT-T-TACATACATCATACATATATACTT
1 TATATATATATATATA-TTATATATATATATATTATAC-T-TATACTT
* *
9521 TATATATATATATATA-TAT-TATACTATAGATTATATACTCATACGTT
1 TATATATATATATATATTATATATA-TATATA-T-TATACTTATAC-TT
*
9568 ATATATATGTATTATATATATATATATATATATACTTATA--TATAC-T
1 -TATATATATA-TATATAT-TATATATATATATA-TTATACTTATACTT
* *
9614 TATGTATATACT-TTTATATATATATATATATATTATACTTATACTT
1 TATATATATA-TATATAT-TATATATATATATATTATACTTATACTT
*
9660 TATATATATATATGTACTTATATATATA
1 TATATATATATATATA-TTATATATATA
9688 CACATCATAC
Statistics
Matches: 137, Mismatches: 15, Indels: 30
0.75 0.08 0.16
Matches are distributed among these distances:
43 5 0.04
44 23 0.17
45 17 0.12
46 47 0.34
47 5 0.04
48 17 0.12
49 6 0.04
50 4 0.03
51 9 0.07
52 4 0.03
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (45 bp):
TATATATATATATATATTATATATATATATATTATACTTATACTT
Found at i:26858 original size:20 final size:20
Alignment explanation
Indices: 26822--26975 Score: 113
Period size: 20 Copynumber: 8.0 Consensus size: 20
26812 GAGGGATTAT
* *
26822 CAGTGGTCATTCAGGACAAA
1 CAGTGGTCCTTCGGGACAAA
*
26842 CAGTGGTCCTTTGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
* * * * * *
26860 TAGTGGTTCTTTGGAATAAT
1 CAGTGGTCCTTCGGGACAAA
26880 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
26900 CAGTGGTCCTTCGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
* * * * *
26918 TAGTGGTTCTTCAGAACAAT
1 CAGTGGTCCTTCGGGACAAA
*
26938 CAGTGGTTCTTCGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
* *
26956 TAGTGGTCATTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
26976 TATTTAGTGC
Statistics
Matches: 102, Mismatches: 26, Indels: 12
0.73 0.19 0.09
Matches are distributed among these distances:
18 42 0.41
20 60 0.59
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:26897 original size:58 final size:58
Alignment explanation
Indices: 26820--26973 Score: 213
Period size: 58 Copynumber: 2.7 Consensus size: 58
26810 TCGAGGGATT
* * * ** *
26820 ATCAGTGGTCATTCAGGACAAACAGTGGTCCTTTGGGACATAGTGGTTCTTTGGAATA
1 ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGGTTCTTCAGAACA
26878 ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGGTTCTTCAGAACA
1 ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGGTTCTTCAGAACA
* * *
26936 ATCAGTGGTTCTTCGGGAC--ATAGTGGTCATTCGGGACA
1 ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACA
26974 AATATTTAGT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
56 17 0.20
58 70 0.80
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (58 bp):
ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGGTTCTTCAGAACA
Found at i:26923 original size:38 final size:38
Alignment explanation
Indices: 26881--26975 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
26871 TGGAATAATC
26881 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
* * * * *
26919 AGTGGTTCTTCAGAACAATCAGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
*
26957 AGTGGTCATTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
26976 TATTTAGTGC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
Found at i:29097 original size:31 final size:31
Alignment explanation
Indices: 29049--29204 Score: 235
Period size: 31 Copynumber: 5.0 Consensus size: 31
29039 CCTGAATGAC
* *
29049 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
29080 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
29111 CAGTCCATATATCCCG-AGAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAG-AACATAGGTAAA
*
29142 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
29173 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
29204 C
1 C
29205 CCTCGACCCT
Statistics
Matches: 114, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
30 2 0.02
31 109 0.96
32 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:29969 original size:64 final size:64
Alignment explanation
Indices: 29861--30078 Score: 217
Period size: 64 Copynumber: 3.4 Consensus size: 64
29851 TAATGAAGGT
* * ** ** * * **
29861 ATGCATCGATGCATTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGTTGAG
1 ATGCATCGATGCACTACTTATGCATCAATGCACCAATTGCATTCGATGTT-TCATTATTAATGAG
* *
29925 ATGCATCGATGCACTCCTTATGCATCAATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCAATGCACCAATTGCATTCGATGTTTCATTATTAATGAG
* ** * *
29989 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCAATGCACCAATTGCATTCGATGT-TTCATTATTAATGAG
**
30052 AGTGCATCGATGCACTACCAATGCATC
1 A-TGCATCGATGCACTACTTATGCATC
30079 GGTGCACATT
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 122 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCAATGCACCAATTGCATTCGATGTTTCATTATTAATGAG
Found at i:33295 original size:31 final size:31
Alignment explanation
Indices: 33257--33412 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
33247 CCCGAAGGAC
* *
33257 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
33288 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
33319 CAGTCCATATGTCCCGAGGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
33350 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
33381 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
33412 C
1 C
33413 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:34177 original size:64 final size:64
Alignment explanation
Indices: 34069--34292 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
34059 TAATAAAGGT
* * * * ***
34069 ATGCATCGATGCACTACTAATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGTTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATCAATGAG
* ** *
34133 ATGCATCGATGCACTTCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATCAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATCAATGAG
* * * * *
34197 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATTTTAAAAGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATCAATGAG
** *
34262 -TGCATCGATGCACTACCAATGCATCGGTGCA
1 ATGCATCGATGCACTACTTATGCATCGATGCA
34293 CATTCAAACA
Statistics
Matches: 136, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
63 1 0.01
64 125 0.92
65 10 0.07
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATCAATGAG
Found at i:37546 original size:24 final size:20
Alignment explanation
Indices: 37514--37569 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
37504 GCACAGGTAG
37514 TGCATCGATGCACATGTTAATGAA
1 TGCATCGATGCAC-TG-T-A-GAA
* *
37538 TGCATCGATACACTGTAGAG
1 TGCATCGATGCACTGTAGAA
37558 TGCATCGATGCA
1 TGCATCGATGCA
37570 TACCTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 1 0.03
23 2 0.07
24 12 0.41
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:38919 original size:20 final size:20
Alignment explanation
Indices: 38896--38991 Score: 124
Period size: 20 Copynumber: 4.9 Consensus size: 20
38886 GAGGGATTAT
*
38896 CAGTAGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
*
38916 CAGTGGTCCTTCGGG--ATA
1 CAGTGGTCCTTCGGGACAAA
* * * *
38934 TAGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGACAAA
38954 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
38974 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
38992 TAGTGATTCT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 14 0.22
20 49 0.78
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:38984 original size:58 final size:58
Alignment explanation
Indices: 38894--39029 Score: 227
Period size: 58 Copynumber: 2.3 Consensus size: 58
38884 TCGAGGGATT
* * *
38894 ATCAGTAGTCCTTCGGGACAAACAGTGGTCCTTCGGGATATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGATTCTTCGGAACA
38952 ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGATTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGATTCTTCGGAACA
* *
39010 ATCAGGGGTCCTTTGGGACA
1 ATCAGTGGTCCTTCGGGACA
39030 TAGTGGTTCT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (58 bp):
ATCAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACATAGTGATTCTTCGGAACA
Found at i:39004 original size:38 final size:38
Alignment explanation
Indices: 38896--39047 Score: 128
Period size: 38 Copynumber: 3.9 Consensus size: 38
38886 GAGGGATTAT
* * * *
38896 CAGTAGTCCTTCGGGACAAACAGTGGTCCTTCGGG--ATA
1 CAGTGGTCCTTCGGGAC--ATAGTGGTTCTTCGGGACAAA
* * * *
38934 TAGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGAC-AT-AGTGGTTCTTCGGGACAAA
* * *
38974 CAGTGGTCCTTCGGGACATAGTGATTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGACATAGTGGTTCTTCGGGACAAA
* * *
39012 CAGGGGTCCTTTGGGACATAGTGGTTCTTTGGGACA
1 CAGTGGTCCTTCGGGACATAGTGGTTCTTCGGGACA
39048 TGAGAGATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
37 2 0.02
38 73 0.78
39 2 0.02
40 16 0.17
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (38 bp):
CAGTGGTCCTTCGGGACATAGTGGTTCTTCGGGACAAA
Found at i:40019 original size:30 final size:30
Alignment explanation
Indices: 39985--40042 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39975 TCGGATGACC
* *
39985 ATTTTGTAACAAATAATAATGTTAGTGATA
1 ATTTTGTAACAAACAATAACGTTAGTGATA
*
40015 ATTTTGTAACAAACGATAACGTTAGTGA
1 ATTTTGTAACAAACAATAACGTTAGTGA
40043 CCGATTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (30 bp):
ATTTTGTAACAAACAATAACGTTAGTGATA
Found at i:40252 original size:16 final size:16
Alignment explanation
Indices: 40233--40279 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
40223 ATCTTTGATC
40233 ATTCATTTAAAGAAAT
1 ATTCATTTAAAGAAAT
40249 ATTCATTTAAAGAAAT
1 ATTCATTTAAAGAAAT
40265 ATTCATTTAAAGAAA
1 ATTCATTTAAAGAAA
40280 ATAACCGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTCATTTAAAGAAAT
Found at i:41018 original size:23 final size:23
Alignment explanation
Indices: 40992--41066 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
40982 TGAACGGGTG
*
40992 TAAATGAACGTTAACGAACATAA
1 TAAATGAACGTTAACGAACAAAA
41015 TAAATGAACGTTAACGAACACAAA
1 TAAATGAACGTTAACGAACA-AAA
* * * *
41039 CAAACGAACGTAAACGAACACAA
1 TAAATGAACGTTAACGAACAAAA
41062 TAAAT
1 TAAAT
41067 TAATATAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 25 0.57
24 19 0.43
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.16
Consensus pattern (23 bp):
TAAATGAACGTTAACGAACAAAA
Found at i:41054 original size:24 final size:24
Alignment explanation
Indices: 40997--41061 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
40987 GGGTGTAAAT
* * *
40997 GAACGTTAACGAACA-TAATAAAT
1 GAACGTTAACGAACACAAACAAAC
41020 GAACGTTAACGAACACAAACAAAC
1 GAACGTTAACGAACACAAACAAAC
*
41044 GAACGTAAACGAACACAA
1 GAACGTTAACGAACACAA
41062 TAAATTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 15 0.41
24 22 0.59
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.12
Consensus pattern (24 bp):
GAACGTTAACGAACACAAACAAAC
Found at i:45383 original size:27 final size:27
Alignment explanation
Indices: 45351--45539 Score: 155
Period size: 27 Copynumber: 6.7 Consensus size: 27
45341 ATTAATATCC
*
45351 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTAATTCAAATATTGATATTA
*
45378 ATCACATTAATTCAACTATTGATATTA
1 ATCACATTAATTCAAATATTGATATTA
* * * **
45405 ATCACA-TCATTAAAATATAGCGTCAACAAATATCC
1 ATCACATTAATTCAAATAT----T-----GATATTA
*
45440 ATCATATTAATTCAAATATTGATATTA
1 ATCACATTAATTCAAATATTGATATTA
*
45467 ATCACATTAATTCAACTATTGATATTA
1 ATCACATTAATTCAAATATTGATATTA
* * *
45494 TTCACATTCATTCAACTATTGATATTA
1 ATCACATTAATTCAAATATTGATATTA
* * *
45521 ATCATATTCATTAAAATAT
1 ATCACATTAATTCAAATAT
45540 AGCGTTAACA
Statistics
Matches: 130, Mismatches: 22, Indels: 20
0.76 0.13 0.12
Matches are distributed among these distances:
26 9 0.07
27 100 0.77
30 1 0.01
32 1 0.01
35 9 0.07
36 10 0.08
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (27 bp):
ATCACATTAATTCAAATATTGATATTA
Found at i:45581 original size:27 final size:27
Alignment explanation
Indices: 45551--45629 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
45541 GCGTTAACAA
* *
45551 ATATCCATCATATTAATTCAAATATTG
1 ATATCAATCACATTAATTCAAATATTG
* *
45578 ATATTAATCACATTAATTCAACTATTG
1 ATATCAATCACATTAATTCAAATATTG
* *
45605 ATAT-ATATCACATTCATTAAAATAT
1 ATATCA-ATCACATTAATTCAAATAT
45630 ATCGTCAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (27 bp):
ATATCAATCACATTAATTCAAATATTG
Found at i:45582 original size:90 final size:90
Alignment explanation
Indices: 45467--45662 Score: 313
Period size: 90 Copynumber: 2.2 Consensus size: 90
45457 ATTGATATTA
* * * * *
45467 ATCACATTAATTCAACTATTGATATTATTCACATTCATTCAACTATTGATAT-TAATCATATTCA
1 ATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATAT-ATCACATTCA
*
45531 TTAAAATATAGCGTTAACAAATATCC
65 TTAAAATATAGCGTCAACAAATATCC
45557 ATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATATATCACATTCAT
1 ATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATATATCACATTCAT
*
45622 TAAAATATATCGTCAACAAATATCC
66 TAAAATATAGCGTCAACAAATATCC
45647 ATCATATTAATTCAAA
1 ATCATATTAATTCAAA
45663 AAATAGATAA
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
90 97 0.99
91 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (90 bp):
ATCATATTAATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATATATCACATTCAT
TAAAATATAGCGTCAACAAATATCC
Found at i:45582 original size:117 final size:116
Alignment explanation
Indices: 45351--45622 Score: 465
Period size: 117 Copynumber: 2.3 Consensus size: 116
45341 ATTAATATCC
* * * *
45351 ATCACATTCATTCAAATATTGATATTAATCACATTAATTCAACTATTGATATTAATCACATCATT
1 ATCACATTAATTCAACTATTGATATTATTCACATTCATTCAACTATTGATATTAATCACATCATT
45416 AAAATATAGCGTCAACAAATATCCATCATATTAATTCAAATATTGATATTA
66 AAAATATAGCGTCAACAAATATCCATCATATTAATTCAAATATTGATATTA
*
45467 ATCACATTAATTCAACTATTGATATTATTCACATTCATTCAACTATTGATATTAATCATATTCAT
1 ATCACATTAATTCAACTATTGATATTATTCACATTCATTCAACTATTGATATTAATCACA-TCAT
*
45532 TAAAATATAGCGTTAACAAATATCCATCATATTAATTCAAATATTGATATTA
65 TAAAATATAGCGTCAACAAATATCCATCATATTAATTCAAATATTGATATTA
45584 ATCACATTAATTCAACTATTGATA-TATATCACATTCATT
1 ATCACATTAATTCAACTATTGATATTAT-TCACATTCATT
45623 AAAATATATC
Statistics
Matches: 148, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
116 58 0.39
117 90 0.61
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (116 bp):
ATCACATTAATTCAACTATTGATATTATTCACATTCATTCAACTATTGATATTAATCACATCATT
AAAATATAGCGTCAACAAATATCCATCATATTAATTCAAATATTGATATTA
Found at i:48505 original size:29 final size:32
Alignment explanation
Indices: 48430--48490 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
48420 AAATTTTAAA
*
48430 AAATGTAAATATTAACAATATTTTTTTATTAT
1 AAATATAAATATTAACAATATTTTTTTATTAT
48462 AAATATAAATATTAACAATATTTTTTTAT
1 AAATATAAATATTAACAATATTTTTTTAT
48491 AAAAATAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (32 bp):
AAATATAAATATTAACAATATTTTTTTATTAT
Found at i:49012 original size:25 final size:25
Alignment explanation
Indices: 48974--49033 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
48964 AATTAGTGTC
*
48974 ATTATTTCTT-GTCATTATAATGAAT
1 ATTATTT-TTCGTCATTATAATAAAT
48999 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCGTCATTATAATAAAT
49024 ATTATTTTTC
1 ATTATTTTTC
49034 TACTACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (25 bp):
ATTATTTTTCGTCATTATAATAAAT
Found at i:49564 original size:191 final size:189
Alignment explanation
Indices: 49233--49603 Score: 575
Period size: 191 Copynumber: 2.0 Consensus size: 189
49223 ACTTGAGAGT
* *
49233 TTCTTCCGACAAGTTGATGTTATAAAAAAACCTTTTCGAATTTCTTACTCACTTCTTTTTACCCG
1 TTCTTCCGACAAGTTGATGTTATAAAAAAACATTTTCGAATTTATTACTCACTTCTTTTTACCCG
* *
49298 CAACAACATATTAAAAATAATATTTCAATAACATTTCCGATATAGAGATATATTATTCGAATATG
66 CAACAACATATTAAAAATAATATTTCAAAAACATTTCCGAAATAGAGATATATTATTCGAATATG
* *
49363 AAGGAAATTTTATTCGAATAATACTTAAAGATTATAGATT-GAAAGAAAATTTTCTCTACTA
131 AAGAAAATTTTATTCGAATAATACTT--ACATTATAGATTAG-AAGAAAATTTTCTCTACTA
* *
49424 TTCTTTCGACAAGTTGATGTTAT-AAAAAACATTTTCGAATTTATTACTCACTTCTTTTTTACCT
1 TTCTTCCGACAAGTTGATGTTATAAAAAAACATTTTCGAATTTATTACTCACTTC-TTTTTACCC
* * *
49488 GCAACAACATATTAAAAATAATATTTTAAAAACCTTTCCGAAATAGAGATATTTTATTCGAATAT
65 GCAACAACATATTAAAAATAATATTTCAAAAACATTTCCGAAATAGAGATATATTATTCGAATAT
* *
49553 GAATAAAATTTTATTCGAATAATTCTTACATTATAGATTAGAAGAAAATTT
130 GAAGAAAATTTTATTCGAATAATACTTACATTATAGATTAGAAGAAAATTT
49604 CTTTAAAAAT
Statistics
Matches: 165, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
189 21 0.13
190 30 0.18
191 114 0.69
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (189 bp):
TTCTTCCGACAAGTTGATGTTATAAAAAAACATTTTCGAATTTATTACTCACTTCTTTTTACCCG
CAACAACATATTAAAAATAATATTTCAAAAACATTTCCGAAATAGAGATATATTATTCGAATATG
AAGAAAATTTTATTCGAATAATACTTACATTATAGATTAGAAGAAAATTTTCTCTACTA
Found at i:50041 original size:85 final size:85
Alignment explanation
Indices: 49879--50042 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
49869 TAAATCACAT
* * **
49879 AGTCTTCTTCATGGTCAACTTGTCTGAAGATTCCAAGTGATCACAAAGCCTTTAATTTTGCCTGA
1 AGTCTTCTTCATGGCCAACTTGCCTGAAGACGCCAAGTGATCACAAAGCCTTTAATTTTGCCTGA
* **
49944 AGACGCTGAGATTTCTTGGG
66 AAACGCCAAGATTTCTTGGG
* * *
49964 AGTCTT-TTGCATGGCCAACTTGCCTGAAGACGCCAAGTGATCCCAGAGCCTTTAATTTTGTCTG
1 AGTCTTCTT-CATGGCCAACTTGCCTGAAGACGCCAAGTGATCACAAAGCCTTTAATTTTGCCTG
*
50028 AAAATGCCAAGATTT
65 AAAACGCCAAGATTT
50043 TCTGAAATCT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 2 0.03
85 65 0.97
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (85 bp):
AGTCTTCTTCATGGCCAACTTGCCTGAAGACGCCAAGTGATCACAAAGCCTTTAATTTTGCCTGA
AAACGCCAAGATTTCTTGGG
Found at i:65285 original size:21 final size:21
Alignment explanation
Indices: 65259--65303 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
65249 GATTTCTGGG
* *
65259 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
65280 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
65301 CAA
1 CAA
65304 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:66949 original size:150 final size:148
Alignment explanation
Indices: 66751--67035 Score: 502
Period size: 147 Copynumber: 1.9 Consensus size: 148
66741 GGACATATGA
*
66751 ATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATT
1 ATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCC---TATATGTATATGATT
66816 CTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA-TCTACGCGG
63 CTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAATTCTACGCGG
66880 TC-CTTCGGGATATATATATAT
128 -CACTTCGGGATATATATATAT
66901 ATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTATATGTATATGATTCTT
1 ATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTATATGTATATGATTCTT
*
66966 AAGGAATAATATGTGGTCCTTATGGACATTGTTATATGGCACTACGGTGCAATTCTACGCGGCAC
66 AAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAATTCTACGCGGCAC
67031 TTCGG
131 TTCGG
67036 TGCAATTATA
Statistics
Matches: 131, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
147 70 0.53
148 15 0.11
150 46 0.35
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (148 bp):
ATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCCTATATGTATATGATTCTT
AAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAATTCTACGCGGCAC
TTCGGGATATATATATAT
Found at i:67036 original size:23 final size:23
Alignment explanation
Indices: 67003--67047 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
66993 ATTGTTATAT
*
67003 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
67026 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
67048 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Done.