Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008842.1 Hibiscus syriacus cultivar Beakdansim tig00112048_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: 52513
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2352 original size:21 final size:21
Alignment explanation
Indices: 2301--2353 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2291 GATTATGACA
*
2301 TCGCAATGTGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
2322 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2343 TCGCAATGCGA
1 TCGCAATGCGA
2354 ATATAAATCG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2414 original size:20 final size:21
Alignment explanation
Indices: 2381--2452 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
2371 ATACTGACTA
* *
2381 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* *
2402 TCGC-ATGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
2421 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
2442 TCGCAATGCGA
1 TCGCAATGCGA
2453 ATTAGGAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 6 0.15
20 20 0.49
21 15 0.37
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:3101 original size:19 final size:19
Alignment explanation
Indices: 3062--3102 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3052 GCAACGAGAG
*
3062 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
* *
3081 AATCGTAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
3100 AAT
1 AAT
3103 TGCATTGCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:3184 original size:52 final size:53
Alignment explanation
Indices: 3107--3239 Score: 207
Period size: 52 Copynumber: 2.5 Consensus size: 53
3097 CAAAATTGCA
**
3107 TTGCGATTTTCA-TTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
3158 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
* *
3211 TTGCGATTCTCATTATCTCGTTGCGATTC
1 TTGCGATTTTCATT-TCGCGTTGCGATTC
3240 ATTTCAACCA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 12 0.16
52 33 0.44
53 17 0.23
54 13 0.17
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
Found at i:3193 original size:33 final size:34
Alignment explanation
Indices: 3156--3221 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
3146 TTTCATTTCG
**
3156 CGTTGCGATTTTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
3189 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
3222 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:3223 original size:20 final size:19
Alignment explanation
Indices: 3107--3239 Score: 117
Period size: 19 Copynumber: 7.5 Consensus size: 19
3097 CAAAATTGCA
*
3107 TTGCGATTTTCA-TTCGCG
1 TTGCGATTCTCATTTCGCG
3125 TTGCGATTCTC---T--CG
1 TTGCGATTCTCATTTCGCG
*
3139 TTGCGATTTTCATTTCGCG
1 TTGCGATTCTCATTTCGCG
*
3158 TTGCGATTTTCATTTCGCG
1 TTGCGATTCTCATTTCGCG
3177 TTGCGATTCTC---T--CG
1 TTGCGATTCTCATTTCGCG
**
3191 TTGCGATAGTCATTTCCGCG
1 TTGCGATTCTCATTT-CGCG
*
3211 TTGCGATTCTCATTATCTCG
1 TTGCGATTCTCATT-TCGCG
3231 TTGCGATTC
1 TTGCGATTC
3240 ATTTCAACCA
Statistics
Matches: 95, Mismatches: 8, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
14 23 0.24
16 2 0.02
17 2 0.02
18 10 0.11
19 31 0.33
20 26 0.27
21 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TTGCGATTCTCATTTCGCG
Found at i:5077 original size:91 final size:90
Alignment explanation
Indices: 4912--5094 Score: 287
Period size: 91 Copynumber: 2.0 Consensus size: 90
4902 TAGATTGCTT
* *
4912 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTATGAAGTTAATATTT
4977 GTCTTTTTGTTTTATCTTTTGGTTGA
66 GTC-TTTTGTTTTATCTTTTGGTTGA
* *
5003 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATTCTTTAACACTATGAAGTTAATAT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGT-TT-ATTAACACTATGAAGTTAATAT
*
5068 TTGTC-TTTGTTTTGTCTTTTGGTTGA
64 TTGTCTTTTGTTTTATCTTTTGGTTGA
5094 A
1 A
5095 AGTTTGAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
91 59 0.69
92 2 0.02
93 24 0.28
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (90 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTATGAAGTTAATATTT
GTCTTTTGTTTTATCTTTTGGTTGA
Found at i:5391 original size:42 final size:42
Alignment explanation
Indices: 5315--5403 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
5305 GACTCGCCTG
* * *
5315 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
* * * * *
5357 TCATTCCTCGAGAGTCCCCTCCCATCATTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
5399 TCATC
1 TCATC
5404 GAAGAGGTCC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
Found at i:6797 original size:14 final size:14
Alignment explanation
Indices: 6778--6813 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6768 ATTGTTTAAT
6778 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
6792 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
6806 TGATTTGT
1 TGATTTGT
6814 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:9511 original size:24 final size:24
Alignment explanation
Indices: 9477--9530 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
9467 CTAAAACATC
*
9477 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
9501 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
9525 ATCAAA
1 ATCAAA
9531 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:10414 original size:20 final size:20
Alignment explanation
Indices: 10367--10416 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
10357 ACGAGAATAC
10367 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
10387 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
10407 AAAATCGCAA
1 AAAATCGCAA
10417 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:10684 original size:20 final size:20
Alignment explanation
Indices: 10629--10675 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
10619 CAACGGGGAA
10629 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
10649 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
10669 ATCGCAA
1 ATCGCAA
10676 TGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:12711 original size:26 final size:24
Alignment explanation
Indices: 12664--12711 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
12654 AGTAAGCACT
* *
12664 TATATAAACATTTAAAGGAGAACA
1 TATATAAACATTCAAAGAAGAACA
12688 TATATAAACATTCCAGAAGAAGAA
1 TATATAAACATT-CA-AAGAAGAA
12712 TAGTTTACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 1 0.05
26 7 0.35
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.23
Consensus pattern (24 bp):
TATATAAACATTCAAAGAAGAACA
Found at i:12764 original size:20 final size:20
Alignment explanation
Indices: 12741--12794 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
12731 GAAACTTAAA
*
12741 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
12761 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
12781 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
12795 TGCAAATCGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:12803 original size:19 final size:16
Alignment explanation
Indices: 12781--12907 Score: 88
Period size: 19 Copynumber: 7.8 Consensus size: 16
12771 GGAAATGGCT
12781 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAA---AA
12800 ATCGCAA--C-AAAAA
1 ATCGCAATGCGAAAAA
12813 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAA---AA
*
12832 ATCGCAA--CGACAAA
1 ATCGCAATGCGAAAAA
12846 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCG-AA--AAA
*
12865 ATCGCAA--CGACAAA
1 ATCGCAATGCGAAAAA
12879 ATCGCAATGCGAAACAA
1 ATCGCAATGCGAAA-AA
*
12896 ATCGCATTGCGA
1 ATCGCAATGCGA
12908 CTTTCATTTC
Statistics
Matches: 89, Mismatches: 5, Indels: 30
0.72 0.04 0.24
Matches are distributed among these distances:
13 9 0.10
14 19 0.21
15 1 0.01
16 13 0.15
17 21 0.24
19 26 0.29
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (16 bp):
ATCGCAATGCGAAAAA
Found at i:12849 original size:14 final size:14
Alignment explanation
Indices: 12830--12885 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
12820 TGCGAAATGC
12830 AAATCGCAACGACA
1 AAATCGCAACGACA
*
12844 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
12863 AAATCGCAACGACA
1 AAATCGCAACGACA
12877 AAATCGCAA
1 AAATCGCAA
12886 TGCGAAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:12852 original size:33 final size:33
Alignment explanation
Indices: 12781--12901 Score: 203
Period size: 33 Copynumber: 3.8 Consensus size: 33
12771 GGAAATGGCT
*
12781 ATCGCAATGCGAAATGCAAATCGCAAC-AAAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
12813 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
*
12846 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
12879 ATCGCAATGCGAAA--CAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
12902 TTGCGACTTT
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
31 8 0.09
32 27 0.32
33 50 0.59
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:12921 original size:19 final size:18
Alignment explanation
Indices: 12897--12960 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
12887 GCGAAACAAA
12897 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
12916 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
12932 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
12949 TCGCATTGCGAT
1 TCGCATTGCGAT
12961 AGCTATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 4 0.11
19 17 0.45
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:12988 original size:20 final size:19
Alignment explanation
Indices: 12944--12988 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
12934 GTTGCGATTT
12944 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
*
12963 -CTATTTCCGCTTTGCGATAG
1 TC-ATTT-CGCATTGCGATAG
12983 TCATTT
1 TCATTT
12989 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 1 0.05
19 4 0.18
20 16 0.73
21 1 0.05
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:13494 original size:18 final size:18
Alignment explanation
Indices: 13468--13512 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
13458 GTCGATCAGA
**
13468 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGACGAGG
*
13486 TGATAGCTCTGGACGAGG
1 TGATGGCTCTGGACGAGG
13504 TGATGGCTC
1 TGATGGCTC
13513 CCGAAGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:15171 original size:20 final size:21
Alignment explanation
Indices: 15146--15197 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
15136 TTTTCCCAAT
*
15146 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
15166 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
15187 TCGCAATGCGA
1 TCGCAATGCGA
15198 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:15211 original size:20 final size:20
Alignment explanation
Indices: 15186--15300 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
15176 AATTGGGAAA
*
15186 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
15206 ATCGCAATGAGATACTTATT
1 ATCGCAACGCGATACTGACT
* * *
15226 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
15247 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
15267 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
15287 TTCGCAACGCGATA
1 ATCGCAACGCGATA
15301 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.01
20 61 0.79
21 13 0.17
22 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:15292 original size:61 final size:61
Alignment explanation
Indices: 15183--15314 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 61
15173 GCGAATTGGG
* * * * *
15183 AAAATCGCAATGCGATACTGACTATCGCAATGAGATACTTATTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGATTATCGCAACGCGATAATAC
* * *
15244 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTT-TCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGA-TTATCGCAACGCGATAATAC
*
15305 ATAATCGCAA
1 AAAATCGCAA
15315 TGCAATTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGATTATCGCAACGCGATAATAC
Found at i:16069 original size:18 final size:18
Alignment explanation
Indices: 16046--16081 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16036 TTATTACTTA
*
16046 CAAAATCTATCAAAATGG
1 CAAAATATATCAAAATGG
16064 CAAAATATATCAAAATGG
1 CAAAATATATCAAAATGG
16082 TCATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.22
Consensus pattern (18 bp):
CAAAATATATCAAAATGG
Found at i:26449 original size:74 final size:75
Alignment explanation
Indices: 26322--26505 Score: 243
Period size: 74 Copynumber: 2.5 Consensus size: 75
26312 GTTAAATGAC
* *
26322 TAGGGGTATCAGTACCTCTA--AGGGGTATC-AGTACCCATTGGGCATTCTATTTTTCTAGGAGC
1 TAGGGGTATCGGTACC-CTATGAGGGGTATCGAGTACCCATTGGGCATTATATTTTTCTAGGAGC
*
26384 TAAAATTGGCA
65 CAAAATTGGCA
* * *
26395 TAGGGGTATCGGTACCCTATGAGGGGTATCGA-TACCCATTTGGCATTATGTTTTTCTCGGAGCC
1 TAGGGGTATCGGTACCCTATGAGGGGTATCGAGTACCCATTGGGCATTATATTTTTCTAGGAGCC
26459 AAAATTGGCA
66 AAAATTGGCA
*
26469 TAGGGGTATCGGTACACCCTATGAGGAGTATCG-GTAC
1 TAGGGGTATCGGT--ACCCTATGAGGGGTATCGAGTAC
26506 ATCCCTATTT
Statistics
Matches: 98, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
72 3 0.03
73 15 0.15
74 59 0.60
75 1 0.01
76 20 0.20
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (75 bp):
TAGGGGTATCGGTACCCTATGAGGGGTATCGAGTACCCATTGGGCATTATATTTTTCTAGGAGCC
AAAATTGGCA
Found at i:29101 original size:28 final size:27
Alignment explanation
Indices: 29048--29102 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
29038 ACGACACGAG
* ** *
29048 TGAAATTTTGGGGATTTTTCGGCTAAA
1 TGAAATTTTAGGGATTTTAAGCCTAAA
29075 TGAAGATTTTAGGGATTTTAAGCCTAAA
1 TGAA-ATTTTAGGGATTTTAAGCCTAAA
29103 ACCGACAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (27 bp):
TGAAATTTTAGGGATTTTAAGCCTAAA
Found at i:29184 original size:21 final size:20
Alignment explanation
Indices: 29112--29187 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
29102 AACCGACAGG
* * *
29112 GGGTATCGGTACCCATCGAA
1 GGGTATCGATACACATTGAA
* *
29132 GGGTATCAATACACATTCAAAGA
1 GGGTATCGATACACATT--GA-A
29155 GGGTATCGATACACATTGAA
1 GGGTATCGATACACATTGAA
29175 GGGTTATCGATAC
1 GGG-TATCGATAC
29188 CTGGTGCACA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.38
21 10 0.22
22 1 0.02
23 17 0.38
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACACATTGAA
Found at i:34613 original size:54 final size:54
Alignment explanation
Indices: 34531--34642 Score: 197
Period size: 54 Copynumber: 2.1 Consensus size: 54
34521 GGGGGCATCG
*
34531 GTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
1 GTACCCATTGGACATTCTGTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
* *
34585 GTACCCATTTGACATTCTGTTTTTCTCGGAGCCAAAATTGGCATAGGGGTATCA
1 GTACCCATTGGACATTCTGTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
34639 GTAC
1 GTAC
34643 ACCCTATGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (54 bp):
GTACCCATTGGACATTCTGTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
Found at i:34933 original size:12 final size:12
Alignment explanation
Indices: 34916--34947 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34906 CAACAATAAT
*
34916 CACCACCATGAC
1 CACCACCATCAC
34928 CACCACCATCAC
1 CACCACCATCAC
34940 CACCACCA
1 CACCACCA
34948 CCACTTGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.56, G:0.03, T:0.06
Consensus pattern (12 bp):
CACCACCATCAC
Found at i:35876 original size:30 final size:30
Alignment explanation
Indices: 35837--35898 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
35827 GAGTTTAAGT
* *
35837 ATGACTCTCGTTAATTGTTTAACAAATTTC
1 ATGAATCTCGTTAATTGTATAACAAATTTC
35867 ATGAATCTCGTTAATTGTATAACAAATTTC
1 ATGAATCTCGTTAATTGTATAACAAATTTC
35897 AT
1 AT
35899 CAAGTGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (30 bp):
ATGAATCTCGTTAATTGTATAACAAATTTC
Found at i:43630 original size:21 final size:21
Alignment explanation
Indices: 43604--43643 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43594 CCCCCTTTGA
*
43604 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
43625 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
43644 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:49825 original size:23 final size:23
Alignment explanation
Indices: 49792--49845 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
49782 GAGATGTTTG
* **
49792 ATAAAAAATTAAAACATTGAATAT
1 ATAAAATATTAAAA-AAAGAATAT
49816 -TAAAATATTAAAAAAAGAATAT
1 ATAAAATATTAAAAAAAGAATAT
49838 ATAAAATA
1 ATAAAATA
49846 ATCATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
ATAAAATATTAAAAAAAGAATAT
Done.