Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005289.1 Hibiscus syriacus cultivar Beakdansim tig00011965_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: 61216
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4778 original size:24 final size:26
Alignment explanation
Indices: 4742--4789 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
4732 ACACATTAAG
*
4742 TGTTGTTACG-AAAATAAA-AAGAAA
1 TGTTGGTACGAAAAATAAAGAAGAAA
*
4766 TGTTGGTATGAAAAATAAAGAAGA
1 TGTTGGTACGAAAAATAAAGAAGA
4790 CGAACATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 8 0.40
26 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.21, T:0.25
Consensus pattern (26 bp):
TGTTGGTACGAAAAATAAAGAAGAAA
Found at i:10401 original size:31 final size:31
Alignment explanation
Indices: 10332--10403 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
10322 ATACTCAATT
*
10332 ATCAAATTAATATTTTATTTAAAATTTAAAA
1 ATCAAATTAATATTTTATCTAAAATTTAAAA
* **
10363 ATTAAATTAATATTTTATCTAAAATTTATTA
1 ATCAAATTAATATTTTATCTAAAATTTAAAA
10394 ATCAAATTAA
1 ATCAAATTAA
10404 AAAATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
ATCAAATTAATATTTTATCTAAAATTTAAAA
Found at i:11272 original size:11 final size:11
Alignment explanation
Indices: 11256--11289 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11246 TGACTTTGTT
11256 TATCATTTTAC
1 TATCATTTTAC
*
11267 TATCA-TTCAC
1 TATCATTTTAC
11277 TATCATTTTAC
1 TATCATTTTAC
11288 TA
1 TA
11290 AAAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (11 bp):
TATCATTTTAC
Found at i:12116 original size:21 final size:21
Alignment explanation
Indices: 12087--12126 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12077 TTTTTATTAT
* *
12087 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
12108 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
12127 CATTTAGACT
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:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:12385 original size:16 final size:16
Alignment explanation
Indices: 12364--12394 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12354 CTTCTAATTT
12364 CTTTTTGAGTTCAAGC
1 CTTTTTGAGTTCAAGC
12380 CTTTTTGAGTTCAAG
1 CTTTTTGAGTTCAAG
12395 TTTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (16 bp):
CTTTTTGAGTTCAAGC
Found at i:16534 original size:22 final size:22
Alignment explanation
Indices: 16509--16569 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 22
16499 AGTATCTAAT
*
16509 AATAACAAAATCGGTAGAAAAA
1 AATAACAAAATCGATAGAAAAA
*
16531 AATAACAAAACCGATAG-AAAA
1 AATAACAAAATCGATAGAAAAA
16552 AATAACAAAATCGATAGA
1 AATAACAAAATCGATAGA
16570 GATGTACCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.13
Consensus pattern (22 bp):
AATAACAAAATCGATAGAAAAA
Found at i:23485 original size:15 final size:16
Alignment explanation
Indices: 23465--23505 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
23455 GTTTATTTCA
*
23465 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
23480 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
23496 GAATGATTCA
1 GAATGATTCA
23506 GAAGTTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:27384 original size:36 final size:37
Alignment explanation
Indices: 27327--27402 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
27317 TTCCGTACTA
27327 CTAGGATTCAAACTCTAAAAAATATGATAGAATTCTG
1 CTAGGATTCAAACTCTAAAAAATATGATAGAATTCTG
*
27364 CTAGGATTC-AACTCCT-AAAAATATGATAGAATTTTG
1 CTAGGATTCAAACT-CTAAAAAATATGATAGAATTCTG
27400 CTA
1 CTA
27403 TATTTTAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 26 0.70
37 11 0.30
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
CTAGGATTCAAACTCTAAAAAATATGATAGAATTCTG
Found at i:27414 original size:37 final size:36
Alignment explanation
Indices: 27327--27419 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 36
27317 TTCCGTACTA
27327 CTAGGATTCAAACT-CTAAAAAATATGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATATGATAGAATTCTG
* *
27364 CTAGGATTCAACTCCTAAAAATATGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATATGATAGAATTCTG
*
27400 CTA-TATTTTAAACTCCTAAA
1 CTAGGA--TTAAACTCCTAAA
27420 GATAGGATCC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
35 1 0.02
36 26 0.53
37 22 0.45
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATATGATAGAATTCTG
Found at i:27897 original size:11 final size:11
Alignment explanation
Indices: 27877--27960 Score: 64
Period size: 11 Copynumber: 7.3 Consensus size: 11
27867 TTAATTATTT
*
27877 TTATTCTAATA
1 TTATTTTAATA
27888 TTATTTTAATA
1 TTATTTTAATA
27899 TT-TTTTAA-A
1 TTATTTTAATA
*
27908 GTTATTATATATA
1 -TTATTTTA-ATA
27921 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
27935 TTATATTTATTA
1 TTAT-TTTAATA
*
27947 TTATTTTACTA
1 TTATTTTAATA
27958 TTA
1 TTA
27961 ACGTATATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
9 1 0.02
10 8 0.13
11 25 0.42
12 8 0.13
13 11 0.18
14 7 0.12
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:27951 original size:15 final size:15
Alignment explanation
Indices: 27909--27951 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
27899 TTTTTTAAAG
27909 TTATTATATATATATAT
1 TTATTAT-TAT-TATAT
* *
27926 TTATAACTATTATAT
1 TTATTATTATTATAT
27941 TTATTATTATT
1 TTATTATTATT
27952 TTACTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:27954 original size:26 final size:25
Alignment explanation
Indices: 27853--27954 Score: 63
Period size: 23 Copynumber: 4.1 Consensus size: 25
27843 TATTATTAAG
* *
27853 TATATATATATATATTAATTATTTTTAT
1 TATA-ATAT-TATATTTATTATTATT-T
* *
27881 TCTAATATTAT-TTTAATATT-TTT
1 TATAATATTATATTTATTATTATTT
*
27904 TA-AAGTTATTATATATA-TA-TA-TT
1 TATAA--TATTATATTTATTATTATTT
27927 TATAACTATTATATTTATTATTATTT
1 TATAA-TATTATATTTATTATTATTT
27953 TA
1 TA
27955 CTATTAACGT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
22 2 0.03
23 17 0.29
24 14 0.24
25 12 0.20
26 7 0.12
27 4 0.07
28 3 0.05
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (25 bp):
TATAATATTATATTTATTATTATTT
Found at i:28149 original size:16 final size:16
Alignment explanation
Indices: 28130--28163 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28120 CATGTATTTA
28130 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
28146 TATTATTTTACTTTAT
1 TATTATATTACATTAT
28162 TA
1 TA
28164 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:28168 original size:21 final size:22
Alignment explanation
Indices: 28144--28194 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
28134 ATATTACATT
*
28144 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
28165 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
28187 ATTATTAT
1 ATTATTAT
28195 ATATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:31496 original size:23 final size:25
Alignment explanation
Indices: 31470--31523 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
31460 TGATTCAATC
*
31470 AAAACAAAAAG-GGCA-AAAAGAAA
1 AAAACAAAAAGAAGCAGAAAAGAAA
* *
31493 AAAA-GAAAAGAAGCAGAAAAGGAA
1 AAAACAAAAAGAAGCAGAAAAGAAA
31517 AAAACAA
1 AAAACAA
31524 GAACAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 5 0.21
23 7 0.29
24 11 0.46
25 1 0.04
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (25 bp):
AAAACAAAAAGAAGCAGAAAAGAAA
Found at i:33133 original size:37 final size:37
Alignment explanation
Indices: 33039--33148 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
33029 GTGCTCACCA
*
33039 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
33075 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
33112 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
33149 ATTGAAAACA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 30 0.45
37 33 0.50
38 3 0.05
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:33234 original size:102 final size:102
Alignment explanation
Indices: 33074--33448 Score: 626
Period size: 102 Copynumber: 3.7 Consensus size: 102
33064 TAAAACAAAC
* *
33074 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
*
33139 AAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
** * *
33176 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGATAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
* *
33241 AAACATAAACATTGGAAACATTTCCTTTGAAATGAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
* *
33278 TTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTTTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
33343 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
66 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
* *
33380 TTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
33444 AAACA
66 AAACA
33449 CAAAACCTTT
Statistics
Matches: 252, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
101 36 0.14
102 216 0.86
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (102 bp):
TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
Found at i:33409 original size:36 final size:36
Alignment explanation
Indices: 33362--33448 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
33352 CATTGAAAAC
** * *
33362 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
33398 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
33434 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
33449 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:33472 original size:67 final size:66
Alignment explanation
Indices: 33390--33548 Score: 212
Period size: 67 Copynumber: 2.4 Consensus size: 66
33380 TTCGTCTCTC
* * *
33390 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGAT-TTTTCCCTTGAAACAAACTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
33455 CT
65 CT
* * *
33457 TTGAGATTGTTTCCCTCGAAACAAACTTTGTCTCCCATGAGATAGTTTCTCTTGAAACACAAAAT
1 TTGAGATT-TTTCCCTTGAAACAAACTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
33522 CT
65 CT
*
33524 TTGA-ATTTATCTCCCTTAAAACAAA
1 TTGAGATTT-T-TCCCTTGAAACAAA
33549 ATTTCGTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 76 0.94
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (66 bp):
TTGAGATTTTTCCCTTGAAACAAACTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACC
T
Found at i:34461 original size:43 final size:43
Alignment explanation
Indices: 34413--34558 Score: 165
Period size: 43 Copynumber: 3.4 Consensus size: 43
34403 CAGAGCCAAT
34413 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
1 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
* * * * * *
34456 TTCAACTTCACAACGAAGG-GA-CGG-CT-GATTGTCAACAAAAT
1 TTCAACTTCACAGCGAAGGATATTGGACTCGA--GACAACACAAG
* *
34497 TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAG
1 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
*
34540 CTCAACTTCACAGCGAAGG
1 TTCAACTTCACAGCGAAGG
34559 GGCGGCTATT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 28 0.34
42 2 0.02
43 44 0.54
44 2 0.02
45 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (43 bp):
TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
Found at i:34488 original size:106 final size:107
Alignment explanation
Indices: 34129--34498 Score: 446
Period size: 109 Copynumber: 3.4 Consensus size: 107
34119 TAGCTAGAGT
* * * ** *
34129 CAAGTTAAACTTCACAACAAAGGGACGGCTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAC-ATTTTTCAATTTCAGAACCG
* *
34193 ATTTCAACTCCACGACGGAGGATATCATGCTACCCGAGACAACA
65 ATTTCAACTCCACGACGGAGGATATC-TGCCACTCGAGACAACA
* * * **
34237 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAC-ATTTTTCAATTTCAGAAC-C
34301 GATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACA
64 GATTTCAACTCCACGACGGAGGATATC-TGCCACTCGAGACAACA
** * *
34346 CAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTC-AATTTCAGAACCG
* * *
34411 ATTTCAACTTCAC-AGCGAAGGATAT-TG-GACTCGAGACAACA
65 ATTTCAACTCCACGA-CGGAGGATATCTGCCACTCGAGACAACA
*
34452 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-ATTT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTT
34499 CAACTTCACA
Statistics
Matches: 230, Mismatches: 27, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
105 4 0.02
106 53 0.23
107 2 0.01
108 45 0.20
109 125 0.54
110 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (107 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAATTTCAGAACCGA
TTTCAACTCCACGACGGAGGATATCTGCCACTCGAGACAACA
Found at i:34514 original size:84 final size:84
Alignment explanation
Indices: 34410--34565 Score: 267
Period size: 84 Copynumber: 1.9 Consensus size: 84
34400 TTTCAGAGCC
* *
34410 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAACGAAGG
34475 GACGGCTGATTGTCAACAA
66 GACGGCTGATTGTCAACAA
* *
34494 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAACGAAGG
*
34559 GGCGGCT
66 GACGGCT
34566 ATTAGACTCG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (84 bp):
AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAACGAAGG
GACGGCTGATTGTCAACAA
Found at i:35141 original size:36 final size:37
Alignment explanation
Indices: 35084--35159 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
35074 TTTCGTCCTA
35084 CTAGGATTCAAACTCTAAAAAATATGATAGAATTCTG
1 CTAGGATTCAAACTCTAAAAAATATGATAGAATTCTG
*
35121 CTAGGATTC-AACTCCT-AAAAATATGATAGAATTTTG
1 CTAGGATTCAAACT-CTAAAAAATATGATAGAATTCTG
35157 CTA
1 CTA
35160 TGTTTTAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 26 0.70
37 11 0.30
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
CTAGGATTCAAACTCTAAAAAATATGATAGAATTCTG
Found at i:35171 original size:37 final size:36
Alignment explanation
Indices: 35084--35176 Score: 116
Period size: 36 Copynumber: 2.5 Consensus size: 36
35074 TTTCGTCCTA
35084 CTAGGATTCAAACT-CTAAAAAATATGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATATGATAGAATTCTG
* *
35121 CTAGGATTCAACTCCTAAAAATATGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATATGATAGAATTCTG
**
35157 CTATGTTTTAAACTCCTAAA
1 CTA-GGATTAAACTCCTAAA
35177 GATAAGATCC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 26 0.53
37 23 0.47
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATATGATAGAATTCTG
Found at i:35911 original size:21 final size:21
Alignment explanation
Indices: 35881--35937 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
35871 ATTTATATTA
* *
35881 TATTACATTATTATTTTACTT
1 TATTAAATTATTATTTTACGT
* *
35902 TATTAAATTATTTTTTTTCGT
1 TATTAAATTATTATTTTACGT
35923 TATTATAATTATTAT
1 TATTA-AATTATTAT
35938 ATATATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTAAATTATTATTTTACGT
Found at i:43970 original size:32 final size:33
Alignment explanation
Indices: 43929--44017 Score: 92
Period size: 36 Copynumber: 2.7 Consensus size: 33
43919 AGTGTGATAT
*
43929 TCGAG-TCGGGTCGGGTTTTTTT-AAAAAAAAT
1 TCGAGATCGGGTCGGGTTTTTTTAAAAAAAAAA
* * *
43960 TCGGGATCGGGTTGGAATTTTTTTTAAAAAAAAAAA
1 TCGAGATCGGGTCGG--GTTTTTTT-AAAAAAAAAA
*
43996 TCGAGTTCGGGTCGGGTTTTTT
1 TCGAGATCGGGTCGGGTTTTTT
44018 AAGTATGATA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
31 4 0.09
32 8 0.18
34 13 0.29
36 20 0.44
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.37
Consensus pattern (33 bp):
TCGAGATCGGGTCGGGTTTTTTTAAAAAAAAAA
Found at i:45648 original size:20 final size:20
Alignment explanation
Indices: 45623--45668 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
45613 AAGAGCTACC
45623 TAATATGTTATTGTACTTGA
1 TAATATGTTATTGTACTTGA
45643 TAATATGTTATTGTACTTGA
1 TAATATGTTATTGTACTTGA
45663 TAATAT
1 TAATAT
45669 TTCCGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (20 bp):
TAATATGTTATTGTACTTGA
Found at i:48716 original size:19 final size:19
Alignment explanation
Indices: 48688--48725 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
48678 TTCTCTCTGG
48688 AGAGAAAAAGAACAAACCT
1 AGAGAAAAAGAACAAACCT
*
48707 AGAGAGAAAGAACAAACCT
1 AGAGAAAAAGAACAAACCT
48726 TTTATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.16, G:0.18, T:0.05
Consensus pattern (19 bp):
AGAGAAAAAGAACAAACCT
Found at i:54962 original size:26 final size:26
Alignment explanation
Indices: 54923--55002 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
54913 ACAATGACGG
* *
54923 CCCTCCTACGTCACAATCAACGAAGA
1 CCCTCCAACATCACAATCAACGAAGA
54949 CCCTCCAACATCACAATCAACGAAGA
1 CCCTCCAACATCACAATCAACGAAGA
54975 CCCTCCAACATCACAATCAACGAAGA
1 CCCTCCAACATCACAATCAACGAAGA
55001 CC
1 CC
55003 ATCACATCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.39, C:0.40, G:0.09, T:0.12
Consensus pattern (26 bp):
CCCTCCAACATCACAATCAACGAAGA
Found at i:56614 original size:35 final size:36
Alignment explanation
Indices: 56541--56626 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
56531 ATTGTATAAT
56541 ATTACAAATTATAAATATTTATATATTTCTTTAAAAA
1 ATTA-AAATTATAAATATTTATATATTTCTTTAAAAA
* *
56578 A-TAAAATTCAT-AATATTTATA-ATTTTTTTTACAAA
1 ATTAAAATT-ATAAATATTTATATA-TTTCTTTAAAAA
*
56613 ATTAAAAATATAAA
1 ATTAAAATTATAAA
56627 AAAGTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
34 1 0.02
35 28 0.67
36 12 0.29
37 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (36 bp):
ATTAAAATTATAAATATTTATATATTTCTTTAAAAA
Found at i:61130 original size:28 final size:32
Alignment explanation
Indices: 61082--61144 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
61072 GTATTTTTAC
*
61082 ATAGTTATTATATTTTATT-AATATA-ATTAT
1 ATAGTTATTATATTTTATTAAAAATATATTAT
61112 ATAGTTATT-T-TTTTATTAAAAATATATTAT
1 ATAGTTATTATATTTTATTAAAAATATATTAT
61142 ATA
1 ATA
61145 ATATTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
29 6 0.20
30 17 0.57
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (32 bp):
ATAGTTATTATATTTTATTAAAAATATATTAT
Done.