Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004224.1 Hibiscus syriacus cultivar Beakdansim tig00009246_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: 34927
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:2583 original size:22 final size:24
Alignment explanation
Indices: 2538--2590 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
2528 GCCCTAAATT
*
2538 AAAAAACGAAAAAGAGAAAGAGAAA
1 AAAAAAC-AAAAAGAGAAAAAGAAA
2563 AAAAAAC-AAAAGA-AAAAAGAAA
1 AAAAAACAAAAAGAGAAAAAGAAA
*
2585 AGAAAA
1 AAAAAA
2591 TAAGGTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 13 0.50
23 6 0.23
25 7 0.27
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAACAAAAAGAGAAAAAGAAA
Found at i:3705 original size:106 final size:105
Alignment explanation
Indices: 3515--4407 Score: 924
Period size: 106 Copynumber: 8.7 Consensus size: 105
3505 AAGGGCTTCC
* * *
3515 CAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAGCACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
3580 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTCT
* * * *
3621 CAATCTCAGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
*
3686 TTCACGACGGAGGGACCGCTGGTTGTCAACAAACAATT-T
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTCT
* *
3725 C----T------CAATTTCAACTTCACAATGAAGGATATTGGACTCAAGACAGCACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
* * *
3780 TTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTCT
* * * * *
3821 CGATTTCCGAGCCGATTTCAACTTCACAACGAAGGACATTGGACTCCAA-ACAACGCAAGTTCAA
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT-CAAGACAACACAAGTTCAA
*
3885 ATTCACGACGAAGGGACCGCTGGTTGTCAAC--A-AA----
65 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTCT
* *
3919 CAATTTC----CCAATTTCAACTTCGCAACGAAGGATATTGGACTCAAGACAGCACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
* * * *
3980 TTCACGATGAAGGGACCGCTGGTTGTCAATAAATAATTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTCT
* * * *
4021 CGATTTGAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
* *
4086 TTCACGACGAAGGGACCGCTGGCTGTC-A-ATA-AA----
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTCT
* * * * *
4119 CAATTTC----CCAATTTCAATTTCACAGCGAAGAATATTGGACTCAAGACAGCACAAGCTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
* * *** * *
4180 TTCAC-AGCGAAGGGGCGGCTAACTGTCAACAAACGACTTCC
66 TTCACGA-CGAAGGGACCGCTGGTTGTCAACAAAC-AATTCT
* *
4221 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGTATATTGGACTCCAGACAACACAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
* * *
4286 TTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTT
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTCT
* * * * * * *
4326 CCAGTTCCAGAACCAATTTCAACTTCACAGTCG-AGGATATTGGACTCGAA-ACAATACTTGGAT
1 -CAATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGGACTC-AAGACAACAC---AAG
4389 TTCAACTTCACGACGAAGG
60 TTCAACTTCACGACGAAGG
4408 ATATCCAGTT
Statistics
Matches: 660, Mismatches: 81, Indels: 89
0.80 0.10 0.11
Matches are distributed among these distances:
93 4 0.01
94 221 0.33
95 3 0.00
96 4 0.01
97 2 0.00
98 12 0.02
100 2 0.00
102 12 0.02
103 4 0.01
104 5 0.01
105 6 0.01
106 359 0.54
107 7 0.01
109 19 0.03
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTCT
Found at i:3876 original size:200 final size:200
Alignment explanation
Indices: 3526--4324 Score: 1204
Period size: 200 Copynumber: 4.0 Consensus size: 200
3516 AATTTCAGAG
* *
3526 CCAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAA
* *
3591 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
3656 ACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTCAACAAACA
131 ACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
3721 ATTTC
196 ATTTC
* * *
3726 TCAATTTCAACTTCACAATGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCATGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAA
* * * * *
3791 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCCGAGCCGATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* * *
3856 ACATTGGACTCCAAACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
131 ACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
3921 ATTTC
196 ATTTC
* *
3926 CCAATTTCAACTTCGCAACGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGATGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAA
* * * * *
3991 GGGACCGCTGGTTGTCAATAAATAATTTCCCGATTTGAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* * * *
4056 ATATTGGACTCCAGACAATACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACA
131 ACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
4121 ATTTC
196 ATTTC
* * * *
4126 CCAATTTCAATTTCACAGCGAAGAATATTGGACTCAAGACAGCACAAGCTCAACTTCAC-AGCGA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGA-CGA
* * *** *
4190 AGGGGCGGCTAACTGTCAACAAACGACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
65 AGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
* * * *
4255 TATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAC
130 GACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
4320 AATTT
195 AATTT
4325 TCCAGTTCCA
Statistics
Matches: 544, Mismatches: 54, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
199 1 0.00
200 543 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (200 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
ACATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
ATTTC
Found at i:4082 original size:306 final size:298
Alignment explanation
Indices: 3511--4324 Score: 845
Period size: 306 Copynumber: 2.7 Consensus size: 298
3501 GCGAAAGGGC
* * *
3511 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAGCACAAGTT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGACATTGGACTCAAGACAACACAAGTT
*
3576 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATCTCAGAGCCAATTTCA
66 CAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA---CT--ATCTC--A-CCAATTTCA
* * *
3641 ACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGGAGGGACCGCT
123 ACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCT
* *
3706 GGTTGTCAACAAACAATTTCTCAATTTCAACTTCACAATGAAGGATATTGGACTCAAGACAGCAC
188 GGTTGTCAACAAACAATTTCTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACAC
* *
3771 AAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAAT
253 AAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAAT
* * * * *
3817 TTCCCGATTTCCGAGCCGATTTCAACTTCACAACGAAGGACATTGGACTCCAA-ACAACGCAAGT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGACATTGGACT-CAAGACAACACAAGT
*
3881 TCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-T-T-TC-CCAATTTCAACTTCGC
65 TCAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTATCTCACCAATTTCAACTTCAC
* * *
3942 AACGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTC
130 AACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
* * *
4007 AATAAATAATTTCCCGATTTGAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
195 AACAAACAATTT--C----T------CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGAC
*
4072 AATACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAAT
248 AACACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAAT
* * * * * *
4123 TTCCCAATTT------CAA--T----TTCACAGCGAAGAATATTGGACTCAAGACAGCACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGACATTGGACTCAAGACAACACAAGTT
* * * *** * *
4176 CAACTTCAC-AGCGAAGGGGCGGCTAACTGTCAACAAACGACTTCCCAATTTCAGAGCCAATTTC
66 CAAATTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAAC-T----ATCTC--A-CCAATTTC
* * * * *
4240 AACTTCACAACGAAGTATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
122 AACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGC
4305 TGGTTGTCAACAAACAATTT
187 TGGTTGTCAACAAACAATTT
4325 TCCAGTTCCA
Statistics
Matches: 433, Mismatches: 48, Indels: 54
0.81 0.09 0.10
Matches are distributed among these distances:
293 4 0.01
294 144 0.33
296 2 0.00
298 3 0.01
299 1 0.00
300 3 0.01
301 1 0.00
302 3 0.01
306 269 0.62
307 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (298 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGACATTGGACTCAAGACAACACAAGTT
CAAATTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTATCTCACCAATTTCAACTTCACA
ACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ACAAACAATTTCTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAA
CTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAAT
Found at i:6210 original size:2 final size:2
Alignment explanation
Indices: 6203--6315 Score: 108
Period size: 2 Copynumber: 57.5 Consensus size: 2
6193 TTATTATTAT
* * * *
6203 TA TA TA TA TA TA TT TA TA TT TA -A GA TCA TA T- TA T- TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* * * *
6243 TG TA TA TT TA TA TT TCC TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
6285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6316 TTACTTTGGA
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
1 4 0.04
2 84 0.92
3 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6240 original size:34 final size:32
Alignment explanation
Indices: 6189--6318 Score: 122
Period size: 34 Copynumber: 3.9 Consensus size: 32
6179 TTTTCTTAAT
6189 TTTAT-TATTATTATTATATATATATATTTATA
1 TTTATATA-TATTATTATATATATATATTTATA
* * *
6221 TTTAAGATCATATTATTATACATGTATATTTATA
1 TTT-ATAT-ATATTATTATATATATATATTTATA
* *
6255 TTTCCTAT-TA-TATATATATATATATATATATA
1 TTT-ATATATATTAT-TATATATATATATTTATA
*
6287 TATATATATATATATATATATATATATATTTA
1 TTTATATATAT-TAT-TATATATATATATTTA
6319 CTTTGGATCT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
31 6 0.08
32 24 0.30
33 1 0.01
34 47 0.59
35 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (32 bp):
TTTATATATATTATTATATATATATATTTATA
Found at i:6624 original size:15 final size:17
Alignment explanation
Indices: 6594--6625 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
6584 TGTTCTATTC
6594 ATTTTTATATTTACTTT
1 ATTTTTATATTTACTTT
6611 ATTTTT-TA-TTACTTT
1 ATTTTTATATTTACTTT
6626 CCTTATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTATATTTACTTT
Found at i:6666 original size:23 final size:22
Alignment explanation
Indices: 6609--6666 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
6599 TATATTTACT
6609 TTATTTTTTATTACTTTCCTTA
1 TTATTTTTTATTACTTTCCTTA
* *
6631 TT-TCATTTGTATTACTTTCTTTA
1 TTAT--TTTTTATTACTTTCCTTA
6654 TTATTTATTTATT
1 TTATTT-TTTATT
6667 TCATCTCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.03
22 4 0.14
23 23 0.79
24 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTTTATTACTTTCCTTA
Found at i:9101 original size:2 final size:2
Alignment explanation
Indices: 9094--9132 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9084 ATTAAATAAT
9094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9133 TTAATTCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10233 original size:15 final size:15
Alignment explanation
Indices: 10213--10267 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
10203 AACCGGGTAT
10213 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* **
10228 CGGGTATCCGCAAAATC
1 CGGGTACCCG-ATTA-C
10245 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
10260 C-GGTACCC
1 CGGGTACCC
10268 ATAACATCCG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 7 0.22
15 11 0.34
16 4 0.12
17 10 0.31
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:10338 original size:15 final size:16
Alignment explanation
Indices: 10306--10360 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
10296 GAAATCGTCG
*
10306 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
10323 ACCCGGAAAT-CGGGT
1 ACCCGGAAATCCGGGT
*
10338 ACCCGAAAATCCGGGT
1 ACCCGGAAATCCGGGT
*
10354 ACTCGGA
1 ACCCGGA
10361 TTTACACACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 14 0.42
16 11 0.33
17 8 0.24
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:14416 original size:29 final size:29
Alignment explanation
Indices: 14383--14442 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
14373 TAACTTTCTC
14383 AAATATTTTTCTTTATATATTCTTCAACA
1 AAATATTTTTCTTTATATATTCTTCAACA
*
14412 AAATATTTTTGTTTATATATTCTTCAACA
1 AAATATTTTTCTTTATATATTCTTCAACA
14441 AA
1 AA
14443 TCGTTTATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (29 bp):
AAATATTTTTCTTTATATATTCTTCAACA
Found at i:18102 original size:18 final size:18
Alignment explanation
Indices: 18081--18143 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 18
18071 TATTTTAATT
*
18081 AATGAACCAGCTTTATTA
1 AATGAACTAGCTTTATTA
18099 AATGAAACTAGC-TTACTTA
1 AATG-AACTAGCTTTA-TTA
*
18118 AATGAAGTAGCTTT-TTA
1 AATGAACTAGCTTTATTA
18135 AATGAACTA
1 AATGAACTA
18144 TATGTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 11 0.28
18 13 0.33
19 15 0.38
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (18 bp):
AATGAACTAGCTTTATTA
Found at i:18118 original size:19 final size:18
Alignment explanation
Indices: 18096--18140 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
18086 ACCAGCTTTA
18096 TTAAATGAAACTAGCTTAC
1 TTAAATGAAACTAGCTT-C
* *
18115 TTAAATG-AAGTAGCTTT
1 TTAAATGAAACTAGCTTC
18132 TTAAATGAA
1 TTAAATGAA
18141 CTATATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 7 0.30
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (18 bp):
TTAAATGAAACTAGCTTC
Found at i:22817 original size:635 final size:635
Alignment explanation
Indices: 21607--22882 Score: 2241
Period size: 635 Copynumber: 2.0 Consensus size: 635
21597 TCATGGTGGG
*
21607 GTTCGAAATAAACAAGCACAAAACAAGTTTCATTCGTTCCTTACAACCCAATAATAAAATATGAA
1 GTTCGAAATAAACAAGCACAAAACAAGTTTCATTCGTTCCTTACAACCCAATAACAAAATATGAA
*
21672 AGCAAAGAACTAAGAGGAGGAGAGAAAGCCTTCGACGTGCACTGCCCAATGCTTCCCGGCCACCA
66 AGCAAAAAACTAAGAGGAGGAGAGAAAGCCTTCGACGTGCACTGCCCAATGCTTCCCGGCCACCA
*
21737 AGCACTGCTCCTAGAGAACTGGCTCCTCTCAGATGCTCAGGATGCTACTCCCTCAGGCTTGTCAA
131 AGCACTGCTCCTAGAGAACTGGCTCCTCTCAGATGCTCAGGATGCCACTCCCTCAGGCTTGTCAA
*
21802 GGAAAAATGCCTCGGCAAGTAGGATTGACGGAGACAGATGACACATTCTCTCTCTAACTTTTTAA
196 GGAAAAATGCCTCGGCAAGTAGGATTGACGGAGAAAGATGACACATTCTCTCTCTAACTTTTTAA
*
21867 GCTCAAATCTGCATGGAACCAAAGTCCTCTTCATTGTGGCTTCATCCTCTATTTATAGGGGAAAA
261 GCTCAAATCTGCATGGAACCAAAGTCCTCTTCATTGTGGCTTCATCCTCTATTTATAAGGGAAAA
*
21932 TTAACCCTAGGACTTGGTGTTGAAATTCCTAGAAAACCCTAAACCATGCTTAAATCACATGAGTA
326 TTAACCCTAGGACTTGGTGTTGAAATTCCTAGAAAACCCCAAACCATGCTTAAATCACATGAGTA
* *
21997 TCGGGTAGAGCATAGTAGTGATCCAGTCTGGGTTACCGACTGAGTACCCAGCATAATCCCACTGC
391 TCGGGCAGAGCATAGTAGTGATCCAGTCTGGGTTACCGACTGAGTACCCAGCATAATCCCACTAC
* * *
22062 AGACGCCTAAGGACAGACAAGATCTGCAGAGTAGGCTGCATGGTCAACAGGATCGGTTATAGCAG
456 AGACGCCTAAGGACAGACAAGATCTACAGAGTAGGATGCATGGTCAACAGGATCGGCTATAGCAG
* *
22127 TGCCCACCCCTCCAGGCGGATCTTCGAGGCAGATTTATCGGGCAGAGCTCTCGGAAAGTCGGATA
521 TGCCCACCCCTCCAGGCGGATCTTCGAGGCAGATTTATCGGGCAGAGCTCTCGGAAAGTCAGAGA
* *
22192 TAGTTGGCTTCAAAATATCTTCTCACACTTTAAGCGCTATCGAAATGATA
586 TAGTTGGCTTCAAAATATCTTCTCACACTTTAAGCACTATCAAAATGATA
*
22242 GTTCGAAATAAACAAGCACAAAGCAAGTTTCATTCGTTCCTTACAACCCAATAACAAAATATGAA
1 GTTCGAAATAAACAAGCACAAAACAAGTTTCATTCGTTCCTTACAACCCAATAACAAAATATGAA
* *
22307 AGCAAAAAACTAAGAGGAGGAGAGAAAGCCTTTGACGTGCACTGCCCAATGTTTCCCGGCCACCA
66 AGCAAAAAACTAAGAGGAGGAGAGAAAGCCTTCGACGTGCACTGCCCAATGCTTCCCGGCCACCA
* *
22372 AGCACTGCTCCTAGAGAACTGGCTCCTCTCGGATGCTCATGATGCCACTCCCTCAGGCTTGTCAA
131 AGCACTGCTCCTAGAGAACTGGCTCCTCTCAGATGCTCAGGATGCCACTCCCTCAGGCTTGTCAA
*
22437 GGAGAAATGCCTCGGCAAGTAGGATTGACGGAGAAAGATGACACATTCTCTCTCTAACTTTTTAA
196 GGAAAAATGCCTCGGCAAGTAGGATTGACGGAGAAAGATGACACATTCTCTCTCTAACTTTTTAA
22502 GCTCAAATCTGCATGGAACCAAAGTCCTCTTCATTGTGGCTTCATCCTCTATTTATAAGGGAAAA
261 GCTCAAATCTGCATGGAACCAAAGTCCTCTTCATTGTGGCTTCATCCTCTATTTATAAGGGAAAA
*
22567 TTAACCCTAGGACTTGGTGTTGAAATTCCTA-AGAAACCCCAAACCATGCTTAAATCACATGGGT
326 TTAACCCTAGGACTTGGTGTTGAAATTCCTAGA-AAACCCCAAACCATGCTTAAATCACATGAGT
* * **
22631 ATCGGGCAGAGCATAGTAGTGATCCAGTCTGGGTTACCGACTGAGTACCCGGCGTAATCCTGCTA
390 ATCGGGCAGAGCATAGTAGTGATCCAGTCTGGGTTACCGACTGAGTACCCAGCATAATCCCACTA
* *
22696 CAGACGCCTAAGGACAGACAAGATCTACAGAGTAGGATGCATGGTCAGCAGGATCGGCTGTAGCA
455 CAGACGCCTAAGGACAGACAAGATCTACAGAGTAGGATGCATGGTCAACAGGATCGGCTATAGCA
* *
22761 GTGCCCACCCCTCCAGGCGGATCTTCGAGGTAGATTTCTCGGGCAGAGCTCTCGGAAAGTCAGAG
520 GTGCCCACCCCTCCAGGCGGATCTTCGAGGCAGATTTATCGGGCAGAGCTCTCGGAAAGTCAGAG
* *
22826 ATAGTTGGCTTCAAAATATCTTCTCGCACTTTAAGCACTATCAAAATGCTA
585 ATAGTTGGCTTCAAAATATCTTCTCACACTTTAAGCACTATCAAAATGATA
22877 G-TCGAA
1 GTTCGAA
22883 CTTGGCAATT
Statistics
Matches: 608, Mismatches: 32, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
634 6 0.01
635 602 0.99
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (635 bp):
GTTCGAAATAAACAAGCACAAAACAAGTTTCATTCGTTCCTTACAACCCAATAACAAAATATGAA
AGCAAAAAACTAAGAGGAGGAGAGAAAGCCTTCGACGTGCACTGCCCAATGCTTCCCGGCCACCA
AGCACTGCTCCTAGAGAACTGGCTCCTCTCAGATGCTCAGGATGCCACTCCCTCAGGCTTGTCAA
GGAAAAATGCCTCGGCAAGTAGGATTGACGGAGAAAGATGACACATTCTCTCTCTAACTTTTTAA
GCTCAAATCTGCATGGAACCAAAGTCCTCTTCATTGTGGCTTCATCCTCTATTTATAAGGGAAAA
TTAACCCTAGGACTTGGTGTTGAAATTCCTAGAAAACCCCAAACCATGCTTAAATCACATGAGTA
TCGGGCAGAGCATAGTAGTGATCCAGTCTGGGTTACCGACTGAGTACCCAGCATAATCCCACTAC
AGACGCCTAAGGACAGACAAGATCTACAGAGTAGGATGCATGGTCAACAGGATCGGCTATAGCAG
TGCCCACCCCTCCAGGCGGATCTTCGAGGCAGATTTATCGGGCAGAGCTCTCGGAAAGTCAGAGA
TAGTTGGCTTCAAAATATCTTCTCACACTTTAAGCACTATCAAAATGATA
Found at i:29327 original size:19 final size:19
Alignment explanation
Indices: 29253--29327 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 19
29243 CGATTAGAGT
*
29253 TAGAAAGTGATATTATAGG
1 TAGAAAATGATATTATAGG
* * *
29272 TAGAAAATAAATATCGATACTTG
1 TAGAAAAT-GATAT-TATA--GG
*
29295 TATAAAAT-ATTATTATAGG
1 TAGAAAATGA-TATTATAGG
29314 TAGAAAATGATATT
1 TAGAAAATGATATT
29328 GTATGTTGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 19 0.45
20 5 0.12
21 7 0.17
22 3 0.07
23 8 0.19
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.35
Consensus pattern (19 bp):
TAGAAAATGATATTATAGG
Found at i:31214 original size:65 final size:66
Alignment explanation
Indices: 31113--31263 Score: 225
Period size: 65 Copynumber: 2.3 Consensus size: 66
31103 GCAATTGAGA
*
31113 AACTTAAGGGGG-GAAGTGGGTGCAAAAATAGATGGAGTGGTGAAAGAAGTTGTGGAATTGAGGG
1 AACTTAAGGGGGTG-A-TGGGTGCAAAAATAGATGGAGTGGTGAAAGAAGTTGTGAAATTGAGGG
31177 GTG
64 GTG
* * * *
31180 AACTTAAGGGGGTGATGGGTG-GAAAATTGATGGAGTGGTGAAGGAAGTTGTGAAATTTAGGGGT
1 AACTTAAGGGGGTGATGGGTGCAAAAATAGATGGAGTGGTGAAAGAAGTTGTGAAATTGAGGGGT
31244 G
66 G
31245 AACTTAAGGGGGTGATGGG
1 AACTTAAGGGGGTGATGGG
31264 AGTGATTGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
65 58 0.74
66 6 0.08
67 13 0.17
68 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.44, T:0.23
Consensus pattern (66 bp):
AACTTAAGGGGGTGATGGGTGCAAAAATAGATGGAGTGGTGAAAGAAGTTGTGAAATTGAGGGGT
G
Found at i:33083 original size:27 final size:27
Alignment explanation
Indices: 33047--33109 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
33037 ATATATGGAG
*
33047 ATCGTTGTCTGCATTATTCCAAACGTC
1 ATCGTTGTCTACATTATTCCAAACGTC
* * *
33074 GTCGTTGTCTATATTATTCCAAATGTC
1 ATCGTTGTCTACATTATTCCAAACGTC
33101 ATCGTTGTC
1 ATCGTTGTC
33110 ATAAGACGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (27 bp):
ATCGTTGTCTACATTATTCCAAACGTC
Done.