Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001623.1 Hibiscus syriacus cultivar Beakdansim tig00003227_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: 80616
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1127 original size:35 final size:36
Alignment explanation
Indices: 1088--1179 Score: 100
Period size: 35 Copynumber: 2.6 Consensus size: 36
1078 TAAAACACGA
* * * *
1088 TTTGTCTCGATTGAGACCGTTTTCACTAG-AAGAGT
1 TTTGTCTCCATTGAGACAGTTTTCACTAGAAACAAT
* *
1123 TTTGTCTCTC-TTGAGACAG-TTTCCCTTGAAACAAT
1 TTTGTCTC-CATTGAGACAGTTTTCACTAGAAACAAT
1158 TTTGTCTCCATTGAGACAGTTT
1 TTTGTCTCCATTGAGACAGTTT
1180 CTCTTGAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
34 8 0.17
35 37 0.79
36 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (36 bp):
TTTGTCTCCATTGAGACAGTTTTCACTAGAAACAAT
Found at i:1180 original size:35 final size:35
Alignment explanation
Indices: 1122--1190 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
1112 ACTAGAAGAG
1122 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
*
1157 TTTTGTCTC-CATTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCTC-TTGAGACAGTTTCCCTTGAAACA
1191 TAAACATTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (35 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
Found at i:1300 original size:36 final size:37
Alignment explanation
Indices: 1215--1325 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 37
1205 ATTTCCCTTC
*
1215 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT
*
1252 G--TCTCTTGAGACAGTTTCCCTTGAAA-TAAATTTT
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT
1286 GTCTCTCTTGAGACAGTTTCCCTTGAAAACAAAATATTT
1 GTCTCTCTTGAGACAGTTTCCCTTG-AAACAAAAT-TTT
1325 G
1 G
1326 AATATGTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
34 8 0.12
35 24 0.36
36 22 0.33
37 4 0.06
38 4 0.06
39 4 0.06
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (37 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT
Found at i:1470 original size:101 final size:101
Alignment explanation
Indices: 1231--1480 Score: 326
Period size: 101 Copynumber: 2.5 Consensus size: 101
1221 CTTGAGATAG
1231 TTTCCCTTGAAACAAAATTTTGTCT--CTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCT
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG-TTCCCTTGAAATAAATTTTGTCTCTCT
*
1294 TGAGACAGTTTCCCTTGAAAACAAAATATTTGAATATG
64 TGAGACAGTTTCCCTTGAAAACAAAATATTTGAATATA
* * * ** * *
1332 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTCTTTTGGAACTAAGTTTTGTCTCTCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCCCTT-GAAATAAATTTTGTCTCTCTT
* *
1397 GAGACAGTTTCCCTTG-AAACAAAATCTTTGAATTTA
65 GAGACAGTTTCCCTTGAAAACAAAATATTTGAATATA
* * *
1433 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT-CCCTTGAAA
1481 CAGAAAATCT
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
100 10 0.08
101 69 0.54
102 49 0.38
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCCCTTGAAATAAATTTTGTCTCTCTTG
AGACAGTTTCCCTTGAAAACAAAATATTTGAATATA
Found at i:1527 original size:67 final size:66
Alignment explanation
Indices: 1384--1550 Score: 221
Period size: 67 Copynumber: 2.5 Consensus size: 66
1374 TGGAACTAAG
* * **
1384 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAATCTTTGAATTTATTTCCCCTAAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTCAAATTTATTTCCCCTAAAACAA
1448 A
66 A
* *
1449 TTTTGTCTCCCTTGAGACAGTTACTCTTGAAACAGAAAATCTTCAAATTTA-TTCCCTTAAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAAATCTTCAAATTTATTTCCCCTAAAACA
1513 TAA
65 -AA
* * *
1516 TTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1551 CAGATATCTT
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
65 30 0.34
66 13 0.15
67 46 0.52
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.38
Consensus pattern (66 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTCAAATTTATTTCCCCTAAAACAA
A
Found at i:2475 original size:207 final size:203
Alignment explanation
Indices: 2194--2703 Score: 668
Period size: 207 Copynumber: 2.5 Consensus size: 203
2184 TCGAGACAAC
* ** *
2194 ACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTTAACAAACAACTTCTTAATTTTAGAGC
1 ACAAGTTCAACTTCACAACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAA-TTCAGAGC
*
2258 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAATGCAAGTTCAACTTCACAACGAAG
64 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACAACGAAG
*
2323 GGACCGCTGCTTGTC-ACACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG-TA
129 GGACCGCTGCTTGTCAACA-AAATT-CC-A-TTCAGAGCCAATTTCAACTTCACAACGAAGGATA
2386 TTAGACTCCAGACA
190 TTAGACTCCAGACA
* *
2400 ATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAG
1 A--CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT-TCAGAG
* * * *
2464 CCAATTTCAACTTCACACCGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
63 CCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACAACGAA
* ** *
2529 GGGACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTG
128 GGGACCGCTGCTTGTCAACAAAATTCCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTA
*
2594 GACTCGAGACA
193 GACTCCAGACA
* * **
2605 ACACAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGC
1 ACA-AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATT-CAGAGC
* * * *
2670 AAATTTCAACTTCACGACGGAGGATTTTGGACTT
64 CAATTTCAACTTCACAACGAAGGATATTGGACTT
2704 GGAACAATGC
Statistics
Matches: 265, Mismatches: 30, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
203 2 0.01
204 65 0.25
205 60 0.23
206 3 0.01
207 96 0.36
208 37 0.14
209 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (203 bp):
ACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACAACGAAGGG
ACCGCTGCTTGTCAACAAAATTCCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGAC
TCCAGACA
Found at i:2531 original size:105 final size:104
Alignment explanation
Indices: 2182--2694 Score: 648
Period size: 105 Copynumber: 5.0 Consensus size: 104
2172 GGATCGTGGC
* * * * *
2182 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTTAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
* * *
2246 TAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
64 CAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
* *
2288 ACTTCAGACAATGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTC-AC-ACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
2351 ATTTCAGAGCCAATTTCAACTTCACAACGAAGG-TATTAG
66 A-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
* *
2390 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
2455 ATCTCAGAGCCAATTTCAACTTCACACCGAAGGATATTAG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
* *
2495 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
** *
2556 ATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
* * * * *
2595 ACTCGAGACAACAC-AGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * * *
2659 GGTTCCAGAGCAAATTTCAACTTCACGACGGAGGAT
65 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGAT
2695 TTTGGACTTG
Statistics
Matches: 365, Mismatches: 31, Indels: 23
0.87 0.07 0.05
Matches are distributed among these distances:
99 35 0.10
100 47 0.13
101 4 0.01
102 56 0.15
103 47 0.13
104 45 0.12
105 88 0.24
106 41 0.11
107 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
Found at i:3293 original size:33 final size:35
Alignment explanation
Indices: 3242--3375 Score: 157
Period size: 37 Copynumber: 3.8 Consensus size: 35
3232 TTTCGTCCTG
3242 CTAGGATTC-AACTCCTAAAAATAGGATAGA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGATTTT
*
3275 -TAGGATTCAAACTCCTAAAAATAGGATAACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGAT-AGATTTT
*
3310 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA-TT-TT
* * * *
3348 CTAAGATTTAAATTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
3376 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
32 8 0.09
33 18 0.21
34 2 0.02
35 3 0.03
36 2 0.02
37 53 0.61
38 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGATTTT
Found at i:3528 original size:9 final size:9
Alignment explanation
Indices: 3514--3539 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3504 TAGTATCTTT
3514 TTTTTTTTA
1 TTTTTTTTA
3523 TTTTTTTTA
1 TTTTTTTTA
3532 TTTTTTTT
1 TTTTTTTT
3540 TGCATGTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:4060 original size:23 final size:23
Alignment explanation
Indices: 4008--4060 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
3998 TTATGTGTAT
*
4008 TTTATTTATTTATATATATTACC
1 TTTATTTATTTATATATATTAAC
4031 TTT-TTTATTT-TATAT-TTATAC
1 TTTATTTATTTATATATATTA-AC
4052 TATTATTTA
1 T-TTATTTA
4061 CTATCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 9 0.35
23 7 0.27
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTATTTATATATATTAAC
Found at i:4101 original size:10 final size:10
Alignment explanation
Indices: 4078--4122 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
4068 TTTTCTATGC
4078 TTTATTTA--
1 TTTATTTATT
4086 TTTATTTATT
1 TTTATTTATT
4096 TTTATTT-TAT
1 TTTATTTAT-T
4106 TTTATTTATT
1 TTTATTTATT
4116 TTTATTT
1 TTTATTT
4123 TGGTTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.24
9 1 0.03
10 23 0.70
11 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTATT
Found at i:11119 original size:24 final size:24
Alignment explanation
Indices: 11092--11146 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
11082 TAAGTTGTTG
11092 AATATTTTTATATTTTGAATTTAA
1 AATATTTTTATATTTTGAATTTAA
11116 AATATTTTTATATTTTGAATTTAA
1 AATATTTTTATATTTTGAATTTAA
11140 AATATTT
1 AATATTT
11147 AAAAAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
AATATTTTTATATTTTGAATTTAA
Found at i:11981 original size:20 final size:20
Alignment explanation
Indices: 11956--11999 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
11946 ATAAGCCATG
11956 ATATATCAAATACGTATAAT
1 ATATATCAAATACGTATAAT
11976 ATATATCAAATACGTATAAT
1 ATATATCAAATACGTATAAT
11996 ATAT
1 ATAT
12000 TCGTGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (20 bp):
ATATATCAAATACGTATAAT
Found at i:12467 original size:29 final size:29
Alignment explanation
Indices: 12425--12483 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
12415 ACGTCCGATG
12425 GGTAGGTCGCCAGGGCATCCAAGCGACAT
1 GGTAGGTCGCCAGGGCATCCAAGCGACAT
*
12454 GGTAGGTCGCCAGGGCATCCTAGCGACAT
1 GGTAGGTCGCCAGGGCATCCAAGCGACAT
12483 G
1 G
12484 CATTCTGGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.36, T:0.15
Consensus pattern (29 bp):
GGTAGGTCGCCAGGGCATCCAAGCGACAT
Found at i:13402 original size:27 final size:26
Alignment explanation
Indices: 13339--13407 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
13329 TCGAATTAAC
13339 CAAAAAAAT--TTAAATTTTTTTAATT
1 CAAAAAAATAATT-AATTTTTTTAATT
* * *
13364 TATATAAA-AATTAATTGTTTTTAATT
1 CAAAAAAATAATTAATT-TTTTTAATT
13390 CAAAAAAATAATTAATTT
1 CAAAAAAATAATTAATTT
13408 AAATAATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
25 9 0.26
26 17 0.50
27 8 0.24
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (26 bp):
CAAAAAAATAATTAATTTTTTTAATT
Found at i:13706 original size:183 final size:182
Alignment explanation
Indices: 13399--13742 Score: 575
Period size: 183 Copynumber: 1.9 Consensus size: 182
13389 TCAAAAAAAT
13399 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAATTTTTAATTAATTAATATT
1 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAATTTTTAATTAATTAATATT
* *
13464 GATTTAGGTTTAAAAGTTATTGGATATTAAATTATTAATTAGGTTTTAAATGGTTTGGGTTTAG-
66 GATTTAGGTTTAAAAGTTATTGAATATTAAATTATTAATTAGGTTTTAAATGGTTTGGGTTGAGC
*
13528 CTCATATGTTATATATAATATATATAATATTTTTTAATTAAAAAACAGTTTAC
131 CT-ATATATTATATATAATATATATAATATTTTTTAATTAAAAAACAGTTTAC
*
13581 AATTAATTTAAATAATATATAATTATAAAATAAAAATTT-ATATAAAATTTTTAATTAATTAATA
1 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGAT--AATTTTTAATTAATTAATA
* * *
13645 TTGATTTAGGTTTAAAAGTTATTGAATCTTAAATTATTACTTGGGTTTTAAATGGTTTGGGTTGA
64 TTGATTTAGGTTTAAAAGTTATTGAATATTAAATTATTAATTAGGTTTTAAATGGTTTGGGTTGA
*
13710 GCCTATATATTATATATAATATATTTAATATTT
129 GCCTATATATTATATATAATATATATAATATTT
13743 AAAATTTAAT
Statistics
Matches: 151, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
181 3 0.02
182 39 0.26
183 107 0.71
184 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (182 bp):
AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAATTTTTAATTAATTAATATT
GATTTAGGTTTAAAAGTTATTGAATATTAAATTATTAATTAGGTTTTAAATGGTTTGGGTTGAGC
CTATATATTATATATAATATATATAATATTTTTTAATTAAAAAACAGTTTAC
Found at i:16391 original size:20 final size:20
Alignment explanation
Indices: 16349--16393 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16339 CCTAAGGCAA
* * * *
16349 AGTATTGATACTTAGAGGTC
1 AGTATCGATACTAAAAGGCC
16369 AGTATCGATACTAAAAGGCC
1 AGTATCGATACTAAAAGGCC
16389 AGTAT
1 AGTAT
16394 ATGTACCTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTAAAAGGCC
Found at i:17462 original size:21 final size:21
Alignment explanation
Indices: 17436--17484 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
17426 GGGTGCCAAT
17436 ATCGATAATGTATGAGTCAAC
1 ATCGATAATGTATGAGTCAAC
**
17457 ATCGATAATGTATGAGTCAGT
1 ATCGATAATGTATGAGTCAAC
17478 ATCGATA
1 ATCGATA
17485 TTGTTCGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGATAATGTATGAGTCAAC
Found at i:23463 original size:85 final size:80
Alignment explanation
Indices: 23323--23476 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 80
23313 AATACTACAA
23323 CATGTAATCATACTAGATTAATTAAAAAAATTATAATCTATTAATAATTATAAAAAATATATATT
1 CATGTAATCATACTAGATTAATTAAAAAAATTATAATCTATTAATAATTAT--AAAA-ATATATT
23388 TTAGTTTAAATGTTACCG
63 TTAGTTTAAATGTTACCG
* * *
23406 CATGTAATTATCCTAGATTAATTTAAAAAATATTATAATCTATTAGTAATTATAAAAATATATTT
1 CATGTAATCATACTAGATTAA-TTAAAAAA-ATTATAATCTATTAATAATTATAAAAATATATTT
23471 TAGTTT
64 TAGTTT
23477 CATATACTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
82 14 0.21
83 23 0.35
84 8 0.12
85 21 0.32
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (80 bp):
CATGTAATCATACTAGATTAATTAAAAAAATTATAATCTATTAATAATTATAAAAATATATTTTA
GTTTAAATGTTACCG
Found at i:29188 original size:36 final size:35
Alignment explanation
Indices: 29148--29369 Score: 176
Period size: 36 Copynumber: 5.9 Consensus size: 35
29138 AAATGTTTTT
* * *
29148 AAAATATATGTACTATATAGTTTCAAAAACATTTCG
1 AAAATATATATAATATATAGTTTAAAAAACATTT-G
* *
29184 AAAATATATATAGTATATAGTTTTTTAAAAAAAATTTG
1 AAAATATATATAATATATAG---TTTAAAAAACATTTG
* * **
29222 AAAACATATATAATGTATAGTTTTTGAAAATGCATTTG
1 AAAATATATATAATATATAG--TTT-AAAAAACATTTG
** *
29260 AAAATATATATAATATATAGTTTTGAAATCATTTTG
1 AAAATATATATAATATATAGTTTAAAAAACA-TTTG
29296 AAAATATATATAATATATAGTTTTTTAAAAAAAACATTTTTG
1 AAAATATATATAATATATAG---TTT--AAAAAACA--TTTG
*
29338 AAAA-ATTATATAATATATAGTTTTAAAAACAT
1 AAAATA-TATATAATATATAGTTTAAAAAACAT
29370 ATTTTGGAAT
Statistics
Matches: 154, Mismatches: 20, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
35 5 0.03
36 45 0.29
37 12 0.08
38 45 0.29
39 18 0.12
41 6 0.04
42 23 0.15
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (35 bp):
AAAATATATATAATATATAGTTTAAAAAACATTTG
Found at i:29214 original size:38 final size:35
Alignment explanation
Indices: 29148--29369 Score: 203
Period size: 38 Copynumber: 5.9 Consensus size: 35
29138 AAATGTTTTT
* * *
29148 AAAATATATGTACTATATAGTTTCAAAAACATTTCG
1 AAAATATATATAATATATAGTTTTAAAAACATTT-G
* *
29184 AAAATATATATAGTATATAGTTTTTTAAAAAAAATTTG
1 AAAATATATATAATATATAG--TTTT-AAAAACATTTG
* * *
29222 AAAACATATATAATGTATAGTTTTTGAAAATGCATTTG
1 AAAATATATATAATATATAG-TTTT-AAAA-ACATTTG
* *
29260 AAAATATATATAATATATAGTTTTGAAATCATTTTG
1 AAAATATATATAATATATAGTTTTAAAAACA-TTTG
29296 AAAATATATATAATATATAGTTTTTTAAAAAAAACATTTTTG
1 AAAATATATATAATATATAG--TTTT---AAAAACA--TTTG
29338 AAAA-ATTATATAATATATAGTTTTAAAAACAT
1 AAAATA-TATATAATATATAGTTTTAAAAACAT
29370 ATTTTGGAAT
Statistics
Matches: 158, Mismatches: 16, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
35 3 0.02
36 45 0.28
37 20 0.13
38 48 0.30
39 9 0.06
40 4 0.03
41 6 0.04
42 23 0.15
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (35 bp):
AAAATATATATAATATATAGTTTTAAAAACATTTG
Found at i:29334 original size:76 final size:74
Alignment explanation
Indices: 29172--29366 Score: 221
Period size: 74 Copynumber: 2.5 Consensus size: 74
29162 ATATAGTTTC
* *
29172 AAAAACATTTCGAAAATATATATAGTATATAGTTTTTTAAAAAAAATTTGAAAACATATATAATG
1 AAAAACATTT-GAAAATATATATAATATATAG--TTTTAAAAAAAATTTGAAAACATATATAATA
*
29237 TATAGTTTTTGA
63 TATAGTTTTTAA
** * ** * *
29249 AAATGCATTTGAAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATAT
1 AAAAACATTTGAAAATATATATAATATATAGTTTTAAAAAAAATTTGAAAACATATATAATATAT
29314 AGTTTTTTAAA
66 AG-TTTTT-AA
29325 AAAAACATTTTTGAAAA-ATTATATAATATATAGTTTTAAAAA
1 AAAAACA--TTTGAAAATA-TATATAATATATAGTTTTAAAAA
29367 CATATTTTGG
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
74 30 0.30
75 5 0.05
76 26 0.26
77 9 0.09
78 29 0.29
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (74 bp):
AAAAACATTTGAAAATATATATAATATATAGTTTTAAAAAAAATTTGAAAACATATATAATATAT
AGTTTTTAA
Found at i:29375 original size:38 final size:37
Alignment explanation
Indices: 29143--29499 Score: 191
Period size: 38 Copynumber: 9.7 Consensus size: 37
29133 TTTGAAAATG
* * * *
29143 TTTTTAAAATATATGTACTATATAGTTTCAAAAAC--A
1 TTTTGAAAAT-TATATAATATATAGTTTTAAAAACATA
* *
29179 TTTCGAAAATATATATAGTATATAGTTTTTTAAAAA-A-A
1 TTTTGAAAAT-TATATAATATATAG--TTTTAAAAACATA
* * * **
29217 ATTTGAAAACATATATAATGTATAGTTTTTGAAA-ATGCA
1 TTTTGAAAA-TTATATAATATATAGTTTTAAAAACAT--A
* *
29256 -TTTGAAAATATATATAATATATAGTTTTGAAATC--A
1 TTTTGAAAAT-TATATAATATATAGTTTTAAAAACATA
29291 TTTTGAAAATATATATAATATATAGTTTTTTAAAAAAAACAT-
1 TTTTGAAAAT-TATATAATATATAG--TTTT---AAAAACATA
29333 TTTTGAAAAATTATATAATATATAGTTTTAAAAACATA
1 TTTTG-AAAATTATATAATATATAGTTTTAAAAACATA
* *
29371 TTTTG-GAATCT-TAT-ATA-ATA-TTCTT-AAATCAT-
1 TTTTGAAAAT-TATATAATATATAGTT-TTAAAAACATA
* **
29403 TTTTGAAAACTATATAATATATAGTTTT-GGAA-AT-
1 TTTTGAAAATTATATAATATATAGTTTTAAAAACATA
* * *
29437 TTTT--TAATAATATAATATATAGTTTTAAAAAAATA
1 TTTTGAAAATTATATAATATATAGTTTTAAAAACATA
*
29472 TTTTTG-AAATATATATATTATATAGTTT
1 -TTTTGAAAAT-TATATAATATATAGTTT
29500 ATATTATATT
Statistics
Matches: 255, Mismatches: 34, Indels: 62
0.73 0.10 0.18
Matches are distributed among these distances:
32 25 0.10
33 15 0.06
34 16 0.06
35 10 0.04
36 65 0.25
37 12 0.05
38 79 0.31
39 1 0.00
40 4 0.02
41 4 0.02
42 19 0.07
43 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATTATATAATATATAGTTTTAAAAACATA
Found at i:29486 original size:36 final size:36
Alignment explanation
Indices: 29265--29499 Score: 129
Period size: 36 Copynumber: 6.5 Consensus size: 36
29255 ATTTGAAAAT
* ** ***
29265 ATATATAATATATAGTTTTGAAATCAT-TTTGAAAA
1 ATATATAATATATAGTTTTAAAAAAATATTTTTGAA
*
29300 TATATATAATATATAGTTTTTTAAAAAAAACATTTTTGAAAA
1 -ATATATAATATATAG--TTTT-AAAAAAATATTTTTG--AA
* *
29342 ATTATATAATATATAGTTTTAAAAACATA-TTTTGGA
1 A-TATATAATATATAGTTTTAAAAAAATATTTTTGAA
*
29378 ATCT-T-ATATAATA-TTCTT----AAATCATTTTTGAAA
1 ATATATAATAT-ATAGTT-TTAAAAAAAT-ATTTTTG-AA
**
29411 ACTATATAATATATAGTTTT--GGAAAT-TTTTT--A
1 A-TATATAATATATAGTTTTAAAAAAATATTTTTGAA
29443 ATAATATAATATATAGTTTTAAAAAAATATTTTTGAA
1 AT-ATATAATATATAGTTTTAAAAAAATATTTTTGAA
29480 ATATATATATTATATAGTTT
1 ATATATA-A-TATATAGTTT
29500 ATATTATATT
Statistics
Matches: 157, Mismatches: 16, Indels: 50
0.70 0.07 0.22
Matches are distributed among these distances:
30 3 0.02
31 2 0.01
32 24 0.15
33 8 0.05
34 12 0.08
35 18 0.11
36 28 0.18
37 8 0.05
38 19 0.12
39 11 0.07
40 7 0.04
41 1 0.01
42 16 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATATAATATATAGTTTTAAAAAAATATTTTTGAA
Found at i:38250 original size:21 final size:23
Alignment explanation
Indices: 38224--38269 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
38214 AACATAAAAA
*
38224 TTTTAA-AAT-ATTTTTTAACTT
1 TTTTAATAATCATTTTATAACTT
*
38245 TTTTAATGATCATTTTATAACTT
1 TTTTAATAATCATTTTATAACTT
38268 TT
1 TT
38270 AAAATCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 13 0.62
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTAATAATCATTTTATAACTT
Found at i:39356 original size:2 final size:2
Alignment explanation
Indices: 39349--39373 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39339 CGGGATGCAG
39349 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
39374 TCAACAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39518 original size:214 final size:214
Alignment explanation
Indices: 39149--39563 Score: 821
Period size: 214 Copynumber: 1.9 Consensus size: 214
39139 ATTATTTTAT
39149 TCTCTCTCTCTTCAACAATGGCGGAAATATCGCCTTACCATGTGCGCTTCAACAGATATTATTAT
1 TCTCTCTCTCTTCAACAATGGCGGAAATATCGCCTTACCATGTGCGCTTCAACAGATATTATTAT
*
39214 TAATACCCACTGCTTCTACGCTCCTTATCTTTTCTCTGCTTGTTTCATTTACTAAATACCATTCC
66 TAATACCCACTGCTTCTACGCTCCTTATCTTTTCTCTGCTTGTTTCATTTACTAAATACCATGCC
39279 GCTGATTTTTGGAAGGAATAATGATAATTCTAGTTCAATCAGACGCTCGGGGTTTCTTCACGGGA
131 GCTGATTTTTGGAAGGAATAATGATAATTCTAGTTCAATCAGACGCTCGGGGTTTCTTCACGGGA
39344 TGCAGTCTCTCTCTCTCTC
196 TGCAGTCTCTCTCTCTCTC
39363 TCTCTCTCTCTTCAACAATGGCGGAAATATCGCCTTACCATGTGCGCTTCAACAGATATTATTAT
1 TCTCTCTCTCTTCAACAATGGCGGAAATATCGCCTTACCATGTGCGCTTCAACAGATATTATTAT
39428 TAATACCCACTGCTTCTACGCTCCTTATCTTTTCTCTGCTTGTTTCATTTACTAAATACCATGCC
66 TAATACCCACTGCTTCTACGCTCCTTATCTTTTCTCTGCTTGTTTCATTTACTAAATACCATGCC
39493 GCTGATTTTTGGAAGGAATAATGATAATTCTAGTTCAATCAGACGCTCGGGGTTTCTTCACGGGA
131 GCTGATTTTTGGAAGGAATAATGATAATTCTAGTTCAATCAGACGCTCGGGGTTTCTTCACGGGA
39558 TGCAGT
196 TGCAGT
39564 GTATCTCCGT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 200 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (214 bp):
TCTCTCTCTCTTCAACAATGGCGGAAATATCGCCTTACCATGTGCGCTTCAACAGATATTATTAT
TAATACCCACTGCTTCTACGCTCCTTATCTTTTCTCTGCTTGTTTCATTTACTAAATACCATGCC
GCTGATTTTTGGAAGGAATAATGATAATTCTAGTTCAATCAGACGCTCGGGGTTTCTTCACGGGA
TGCAGTCTCTCTCTCTCTC
Found at i:56284 original size:31 final size:31
Alignment explanation
Indices: 56235--56315 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
56225 AATATATTTA
56235 ACGTGTATATAAA-TAATGATGTGGCACATAAC
1 ACGTGT-T-TAAATTAATGATGTGGCACATAAC
*
56267 ACTTGTTTAAATTAATGATGTGGCACATAAC
1 ACGTGTTTAAATTAATGATGTGGCACATAAC
56298 ACGTGTTTAAATTAATGA
1 ACGTGTTTAAATTAATGA
56316 CATGATACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 4 0.09
31 37 0.80
32 5 0.11
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33
Consensus pattern (31 bp):
ACGTGTTTAAATTAATGATGTGGCACATAAC
Found at i:56326 original size:31 final size:31
Alignment explanation
Indices: 56259--56326 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
56249 AATGATGTGG
* ** *
56259 CACATAACACTTGTTTAAATTAATGATGTGG
1 CACATAACACGTGTTTAAATTAATGACATGA
56290 CACATAACACGTGTTTAAATTAATGACATGA
1 CACATAACACGTGTTTAAATTAATGACATGA
*
56321 TACATA
1 CACATA
56327 CCATCATTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (31 bp):
CACATAACACGTGTTTAAATTAATGACATGA
Found at i:58478 original size:2 final size:2
Alignment explanation
Indices: 58471--58495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58461 AGCTTATCCA
58471 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
58496 ATACACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60958 original size:40 final size:41
Alignment explanation
Indices: 60880--60959 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 41
60870 GAAAAATTCG
* *
60880 TTTATGTTCGTTTATTTATTAAACGAATGGACATGAATAATAT
1 TTTATGTTCGTTTA--TATTAAACGAATGAACACGAATAATAT
*
60923 TTTATGTTCGTTTA-ATTAAATGAATGAACACGAATAA
1 TTTATGTTCGTTTATATTAAACGAATGAACACGAATAA
60960 AGAGTTTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 20 0.59
43 14 0.41
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (41 bp):
TTTATGTTCGTTTATATTAAACGAATGAACACGAATAATAT
Found at i:62314 original size:19 final size:19
Alignment explanation
Indices: 62290--62327 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
62280 ACCGAAACCA
*
62290 GTTTTTTGGTTTGGTTCGG
1 GTTTTTTGGTTCGGTTCGG
62309 GTTTTTTGGTTCGGTTCGG
1 GTTTTTTGGTTCGGTTCGG
62328 TTCGGTTTTT
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:0.00, C:0.08, G:0.37, T:0.55
Consensus pattern (19 bp):
GTTTTTTGGTTCGGTTCGG
Found at i:62342 original size:23 final size:24
Alignment explanation
Indices: 62297--62342 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
62287 CCAGTTTTTT
* *
62297 GGTTTGGTTCGGGTTTTTTGGTTC
1 GGTTCGGTTCGGGTTTTTCGGTTC
62321 GGTTCGGTTC-GGTTTTTCGGTT
1 GGTTCGGTTCGGGTTTTTCGGTT
62343 TTTCAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.00, C:0.11, G:0.37, T:0.52
Consensus pattern (24 bp):
GGTTCGGTTCGGGTTTTTCGGTTC
Found at i:65602 original size:23 final size:20
Alignment explanation
Indices: 65576--65629 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 20
65566 TTTTGAATGT
65576 TTTATTTATTTATTTTAGTATA
1 TTTATTTATTTATTTT--TATA
65598 GTTTATATT-TTTATTTTTATA
1 -TTTAT-TTATTTATTTTTATA
65619 -TTATTTATTTA
1 TTTATTTATTTA
65630 ATTAGGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.07
19 8 0.28
21 4 0.14
23 13 0.45
24 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTATTTATTTATTTTTATA
Found at i:65618 original size:14 final size:15
Alignment explanation
Indices: 65599--65628 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
65589 TTTAGTATAG
65599 TTTATATT-TTTATT
1 TTTATATTATTTATT
65613 TTTATATTATTTATT
1 TTTATATTATTTATT
65628 T
1 T
65629 AATTAGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATATTATTTATT
Found at i:68335 original size:22 final size:19
Alignment explanation
Indices: 68305--68344 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
68295 ATTGAATCCC
68305 AAAATAACAATAAATAAAAAT
1 AAAATAACAA-AAA-AAAAAT
68326 AAAATTAACAAAAAAAAAA
1 AAAA-TAACAAAAAAAAAA
68345 CATGTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAATAACAAAAAAAAAAT
Found at i:69288 original size:6 final size:6
Alignment explanation
Indices: 69277--69301 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
69267 GATCTTCTTT
69277 TTCACA TTCACA TTCACA TTCACA T
1 TTCACA TTCACA TTCACA TTCACA T
69302 CATAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (6 bp):
TTCACA
Done.