Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002940.1 Hibiscus syriacus cultivar Beakdansim tig00006070_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: 47938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:390 original size:12 final size:13
Alignment explanation
Indices: 373--407 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
363 ATTCAACTTA
373 TTTTTTTTT-CTT
1 TTTTTTTTTCCTT
385 TTTTTTTTTCCTT
1 TTTTTTTTTCCTT
398 TTTCTTTTTT
1 TTT-TTTTTT
408 TTAAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 6 0.29
14 6 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTCCTT
Found at i:391 original size:13 final size:13
Alignment explanation
Indices: 373--408 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
363 ATTCAACTTA
373 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
*
386 TTTTTTTTCCTTT
1 TTTTTTTTTCTTT
399 TTCTTTTTTT
1 TT-TTTTTTT
409 TAAATAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:7114 original size:10 final size:10
Alignment explanation
Indices: 7101--7141 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
7091 AAAACACGCT
7101 AAAATAATAA
1 AAAATAATAA
7111 AAAATAAT-A
1 AAAATAATAA
*
7120 AAAATAA-AC
1 AAAATAATAA
7129 AAAATGAATAA
1 AAAAT-AATAA
7140 AA
1 AA
7142 TGTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 13 0.50
10 10 0.38
11 3 0.12
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (10 bp):
AAAATAATAA
Found at i:7123 original size:19 final size:19
Alignment explanation
Indices: 7101--7141 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
7091 AAAACACGCT
7101 AAAATAATAAAAAAT-AATA
1 AAAATAA-AAAAAATGAATA
*
7120 AAAATAAACAAAATGAATA
1 AAAATAAAAAAAATGAATA
7139 AAA
1 AAA
7142 TGTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAATAAAAAAAATGAATA
Found at i:7290 original size:32 final size:33
Alignment explanation
Indices: 7254--7318 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
7244 AAGTAGTATT
*
7254 TACTAA-AAAA-AATAAAAAAAATAAATATATAA
1 TACTAAGAAAACAA-AAAAAAAATAAAGATATAA
*
7286 TACTAAGTAAAACAAATAAAAAATAAAGATATA
1 TACTAAG-AAAACAAAAAAAAAATAAAGATATA
7319 CATGATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 6 0.21
34 20 0.71
35 2 0.07
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.22
Consensus pattern (33 bp):
TACTAAGAAAACAAAAAAAAAATAAAGATATAA
Found at i:7297 original size:36 final size:36
Alignment explanation
Indices: 7257--7352 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 36
7247 TAGTATTTAC
*
7257 TAAAAAAAATAAAAAAAATAAATATATAATACTAAG
1 TAAAAAAAATAAAAAAAATAAATACATAATACTAAG
* * *
7293 TAAAACAAATAAAAAATAA-AGATATACATGATATTAAG
1 TAAAAAAAATAAAAAA-AATA-A-ATACATAATACTAAG
7331 -AAAAAAAATAGAAAAAAATAAA
1 TAAAAAAAATA-AAAAAAATAAA
7353 ATAAAGTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
36 17 0.34
37 15 0.30
38 18 0.36
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (36 bp):
TAAAAAAAATAAAAAAAATAAATACATAATACTAAG
Found at i:7434 original size:33 final size:35
Alignment explanation
Indices: 7387--7465 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 35
7377 ATATATAAAT
*
7387 AAATAAATAAAAACA-AAAATAGAATATTAAG-AA
1 AAATATATAAAAACATAAAATAGAATATTAAGAAA
* *
7420 ATATATATAAAAACATCTAAAATATAATATTAAGAAA
1 AAATATATAAAAACA--TAAAATAGAATATTAAGAAA
7457 AAATATATA
1 AAATATATA
7466 CATAGTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 13 0.34
36 15 0.39
37 10 0.26
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (35 bp):
AAATATATAAAAACATAAAATAGAATATTAAGAAA
Found at i:7557 original size:21 final size:22
Alignment explanation
Indices: 7506--7566 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
7496 TTACATATAT
* *
7506 ATATATATATATAAT-GATATA
1 ATATATATATATAATAAAAATA
*
7527 AGATATATATATAATAAAAATA
1 ATATATATATATAATAAAAATA
7549 ATATA-ATATA-AATAAAAA
1 ATATATATATATAATAAAAA
7567 AAGAGGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.23
21 19 0.54
22 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (22 bp):
ATATATATATATAATAAAAATA
Found at i:7558 original size:25 final size:29
Alignment explanation
Indices: 7500--7554 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
7490 ATATCTTTAC
* *
7500 ATATATATATATATATATAATGATATAAG
1 ATATATATATATATATAAAATAATATAAG
7529 ATATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATATAAAATAATATAA
7555 TATAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 3 0.12
29 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (29 bp):
ATATATATATATATATAAAATAATATAAG
Found at i:7562 original size:20 final size:20
Alignment explanation
Indices: 7529--7566 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7519 ATGATATAAG
7529 ATATATATATAATAAAAATA
1 ATATATATATAATAAAAATA
7549 ATATA-ATATAAATAAAAA
1 ATATATATAT-AATAAAAA
7567 AAGAGGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATATATAATAAAAATA
Found at i:8940 original size:36 final size:36
Alignment explanation
Indices: 8891--9000 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 36
8881 AAAGATTGAA
*
8891 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * *
8927 GTTTCAAGAGAAACTGTCTCAAGAGATATAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
8961 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
8997 GTTT
1 GTTT
9001 AACGTAAAAC
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
34 25 0.44
36 32 0.56
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:9050 original size:30 final size:30
Alignment explanation
Indices: 9014--9072 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9004 GTAAAACATA
*
9014 TTCAAAGATTT-TGTTTCAA-ATGAAACTGTT
1 TTCAAAG-TTTATGCTTCAAGA-GAAACTGTT
9044 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGT
9073 CTCAAGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 22 0.85
31 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (30 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTT
Found at i:9105 original size:36 final size:35
Alignment explanation
Indices: 9058--9225 Score: 98
Period size: 36 Copynumber: 4.9 Consensus size: 35
9048 AAGTTTATGC
* *
9058 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATT-GT
* * * **
9094 TTCAAGGGAAACTATCTCATGAGTGACAAAATACAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-TGT
* * ***
9130 TTCAAGGGAAA-TGTTTTC-A-A-TG--TTTA-TGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTGT
* *
9159 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TTGT
* *
9196 TTCAAGGGAACCTATCTCAAGAGAGACAAA
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAA
9226 TTCATCTAAA
Statistics
Matches: 95, Mismatches: 26, Indels: 21
0.67 0.18 0.15
Matches are distributed among these distances:
29 14 0.15
30 3 0.03
31 1 0.01
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 42 0.44
37 29 0.31
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (35 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTGT
Found at i:9163 original size:101 final size:101
Alignment explanation
Indices: 9035--9404 Score: 388
Period size: 101 Copynumber: 3.7 Consensus size: 101
9025 TGTTTCAAAT
* * * *
9035 GAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTGGTTTCAA
1 GAAA-TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTCAA
* * *
9099 GGGAAACTATCTCATGAGTGACAAAATACATTTCAAGG
65 GGGAAACTATCTCAAGAGAGAC-AAATTCATTTCAAGG
* * * * *
9137 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
1 GAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTCAAG
* * *
9202 GGAACCTATCTCAAGAGAGACAAATTCATCTAAAGG
66 GGAAACTATCTCAAGAGAGACAAATTCATTTCAAGG
* * * * * *
9238 GTAATGTTTTCAATGTTTATTTTTCAAGAGAAACTATCTCTAGAGAGACAAAACTTAGTTCCAAA
1 GAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTCAAG
* * * * **
9303 AGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGG
66 GGAAACTATCTCAAGAGAGAC-AAATTCATTTCAAGG
****
9340 GAAACAAATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTCA-TTTCA
1 GAAATGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT-AGTTTCA
9402 AGG
64 AGG
9405 TAAATGTTTT
Statistics
Matches: 226, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
101 138 0.61
102 85 0.38
103 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (101 bp):
GAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTCAAG
GGAAACTATCTCAAGAGAGACAAATTCATTTCAAGG
Found at i:9443 original size:167 final size:167
Alignment explanation
Indices: 9185--9708 Score: 856
Period size: 167 Copynumber: 3.1 Consensus size: 167
9175 TCAAGGGAGA
* * * *
9185 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGAC-AAATTCATCTAAAGGGT-AATGTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAA-GGTAAATGTTT
* *
9247 TCAATGTTTATTTTTCAAGAGAAACTATCTCTAGAGAGACAAAACTTAGTTCCAAAAGAAAATGT
65 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGT
9312 CTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
130 CTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
9350 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTT
*
9415 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* *
9480 TCAAGGGAGACGAAATTTGTTTCAAGGGAAATAGATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
*
9517 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTT
* *
9582 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* * *
9647 TCAAGGGAGACGAAATTAGTTTCAATGAAAACAAATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
* * *
9684 TAAATATTTTGTTTCAAGGGAAACT
1 CAAAGATTTTGTTTCAAGAGAAACT
9709 TGGAAAATGT
Statistics
Matches: 335, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
165 4 0.01
166 35 0.10
167 296 0.88
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (167 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
Found at i:9466 original size:102 final size:102
Alignment explanation
Indices: 9360--9575 Score: 278
Period size: 102 Copynumber: 2.1 Consensus size: 102
9350 CAAAGATTTT
* * * *
9360 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAAT-GTTTTCAATG-TTT
1 GTTTCAAGAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATAG-ATTCAAAGATTT
9423 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT-A
65 -TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTCA
* * * * **
9462 GTTTCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATAGATTCAAAGATTTT
1 GTTTCAAGAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATAGATTCAAAGATTTT
9527 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCA
*
9564 -TTTCAAGGGAAA
1 GTTTCAAGAGAAA
9576 TGTTTTCAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
101 12 0.12
102 83 0.84
103 4 0.04
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (102 bp):
GTTTCAAGAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATAGATTCAAAGATTTT
GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:9482 original size:37 final size:36
Alignment explanation
Indices: 9425--9504 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
9415 CAATGTTTAT
* *
9425 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAA-TTA
* * * *
9462 GTTTCAAAAGAAAATGTCTCAAGGGAGACGAAATTT
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTA
9498 GTTTCAA
1 GTTTCAA
9505 GGGAAATAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 9 0.24
37 28 0.76
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (36 bp):
GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTA
Found at i:9568 original size:65 final size:65
Alignment explanation
Indices: 9462--9626 Score: 217
Period size: 65 Copynumber: 2.5 Consensus size: 65
9452 ACAAAACTTA
* * * * **
9462 GTTTCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATAG-ATTCAAAGATTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGGAAAT-GTATTCAAAG-TTT
9526 -T
64 AT
* * *
9527 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTATTCAAAGTTTAT
9592 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
9627 TAGTTCCAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
64 4 0.05
65 84 0.95
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (65 bp):
GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTATTCAAAGTTTAT
Found at i:10048 original size:106 final size:104
Alignment explanation
Indices: 9856--10164 Score: 375
Period size: 105 Copynumber: 2.9 Consensus size: 104
9846 TGTATTGTTC
* * * * **
9856 CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
9921 GCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTTTACTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGA-CTTGTACTGTCT
** *
9962 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCCAAAATTGGGATATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* **
10027 ACTAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGACTTGTACTGTCT
*
10067 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*** *
10132 ACCAGGTATCCCTTCGTTGTGGAGTTGAACTTG
65 ACCAGCCGTCCCTTCGTTGTGAAGTTG-ACTTG
10165 GGTTGTCTCG
Statistics
Matches: 174, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
105 91 0.52
106 82 0.47
107 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGACTTGTACTGTCT
Found at i:10122 original size:105 final size:105
Alignment explanation
Indices: 9856--10177 Score: 394
Period size: 106 Copynumber: 3.0 Consensus size: 105
9846 TGTATTGTTC
* * * * **
9856 CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAA-CTAAGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATC-GGGAAATTGTTTGTTGAC
* * * * * **
9920 AGCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTTTACTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGA-CTTGTGTTGTCT
* ** * *
9962 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCCAAAATTGGGATATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
*
10027 ACTAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
10067 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
*** * *
10132 ACCAGGTATCCCTTCGTTGTGGAGTTGAACTTGGGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTG-ACTTGTGTTGTCT
10173 CGAGT
1 CGAGT
10178 GGCACGATAT
Statistics
Matches: 184, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
105 91 0.49
106 93 0.51
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
Found at i:11877 original size:69 final size:69
Alignment explanation
Indices: 11762--11899 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
11752 CGTCTCTCTC
*
11762 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
11827 TCAT
66 TCAT
* * * *
11831 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
11896 TCAT
66 TCAT
11900 AGTTTGAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:11987 original size:13 final size:13
Alignment explanation
Indices: 11971--12011 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
11961 TTTTCTTCAA
11971 TTTTC-CTTTGTTT
1 TTTTCTCTTT-TTT
*
11984 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
11997 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
12010 TT
1 TT
12012 CTTTTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:11995 original size:11 final size:10
Alignment explanation
Indices: 11981--12027 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
11971 TTTTCCTTTG
*
11981 TTTTTTTCTC
1 TTTTTTTTTC
11991 TTTTTATTTTC
1 TTTTT-TTTTC
12002 TCTTTTTTTTC
1 T-TTTTTTTTC
*
12013 TTTTTTTCTC
1 TTTTTTTTTC
12023 TTTTT
1 TTTTT
12028 GCTTTGATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 18 0.55
11 11 0.33
12 4 0.12
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:15213 original size:18 final size:17
Alignment explanation
Indices: 15186--15232 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
15176 AATTAATGGA
15186 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
15203 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
15221 G-AATAAAAATAA
1 GTAA-AAAAATAA
15233 GGTGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:15358 original size:15 final size:13
Alignment explanation
Indices: 15330--15354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15320 CATGATATTA
15330 AGAAAAAAATAAT
1 AGAAAAAAATAAT
15343 AGAAAAAAATAA
1 AGAAAAAAATAA
15355 AATAAAGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:15496 original size:2 final size:2
Alignment explanation
Indices: 15489--15534 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
15479 TTAATACATC
*
15489 TA TA TA TA TA TA TA TA TA TA TGA TA TA -A GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
15531 TA TA
1 TA TA
15535 AAAATAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:15550 original size:28 final size:30
Alignment explanation
Indices: 15489--15546 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
15479 TTAATACATC
* * *
15489 TATATATATATATATATATATGATATAAGA
1 TATATATATATATATAAAAATAATATAAGA
15519 TATATATATATATATAAAAATAATATAA
1 TATATATATATATATAAAAATAATATAA
15547 TATAAATAAA
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:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
TATATATATATATATAAAAATAATATAAGA
Found at i:15555 original size:20 final size:21
Alignment explanation
Indices: 15498--15558 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
15488 CTATATATAT
* *
15498 ATATATATATATGATATAAGAT-
1 ATATATATATA-AATA-AAAATA
*
15520 ATATATATATATATAAAAATA
1 ATATATATATAAATAAAAATA
15541 ATATA-ATATAAATAAAAA
1 ATATATATATAAATAAAAA
15559 AAGGAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.46
21 8 0.23
22 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
ATATATATATAAATAAAAATA
Found at i:15558 original size:21 final size:20
Alignment explanation
Indices: 15520--15596 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 20
15510 GATATAAGAT
* *
15520 ATATATATATATATAAAAATA
1 ATATA-ATATAAATAAAAAAA
15541 ATATAATATAAATAAAAAAA
1 ATATAATATAAATAAAAAAA
15561 GGA-AT-ATAGTAAATAAATAAAAA
1 --ATATAATA-TAAAT-AA-AAAAA
15584 ATATAAT-TAAATA
1 ATATAATATAAATA
15597 TATATATAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
20 17 0.36
21 18 0.38
22 5 0.11
23 7 0.15
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
ATATAATATAAATAAAAAAA
Found at i:23622 original size:73 final size:73
Alignment explanation
Indices: 23457--23732 Score: 256
Period size: 74 Copynumber: 3.7 Consensus size: 73
23447 AAAAAATATA
* * * *
23457 TAATATATGAAATCATTATAATATTTGTTTTCCCACTTGTTTCCTTAATTTAAGTTATAATGGTT
1 TAATATATGGAATCATTATAATATTTGTTTCCCCACATGTTTCCTTAATTTAAGCTATAATGGTT
23522 TAGTTTTT
66 TAGTTTTT
* * *
23530 TAAATATATGGAGTCATTATATTATTTGTTTCCCCACATGCTTT-CTTAATTTAAGCTATAGTGG
1 T-AATATATGGAATCATTATAATATTTGTTTCCCCACATG-TTTCCTTAATTTAAGCTATAATGG
23594 TTTAGTTTTT
64 TTTAGTTTTT
* * * * * *
23604 TAATATATGGAATTATTATAATATTTATTTCTCCAC---TTTCCCTAATTTAAGCAACGT-TTGG
1 TAATATATGGAATCATTATAATATTTGTTTCCCCACATGTTTCCTTAATTTAAGCTA--TAAT-G
*
23665 TGTTTAGCTATTAAT
63 -GTTTAG-T-TT-TT
* * * * *
23680 AATATATATAGAATTATTATAGTATTTGTTTCCCCACTTGTTTCCTTAATTTA
1 TA-ATATATGGAATCATTATAATATTTGTTTCCCCACATGTTTCCTTAATTTA
23733 TTGCTTTGAA
Statistics
Matches: 167, Mismatches: 22, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
69 3 0.02
70 12 0.07
71 1 0.01
72 2 0.01
73 37 0.22
74 63 0.38
75 5 0.03
76 2 0.01
77 30 0.18
80 12 0.07
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.49
Consensus pattern (73 bp):
TAATATATGGAATCATTATAATATTTGTTTCCCCACATGTTTCCTTAATTTAAGCTATAATGGTT
TAGTTTTT
Found at i:28405 original size:13 final size:13
Alignment explanation
Indices: 28387--28411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28377 ATTATAGATG
28387 TGCATATGAAGAC
1 TGCATATGAAGAC
28400 TGCATATGAAGA
1 TGCATATGAAGA
28412 TTGTTCAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
TGCATATGAAGAC
Found at i:29234 original size:37 final size:37
Alignment explanation
Indices: 29184--29255 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
29174 ATGACATTCG
*
29184 ATATTTTGTGTCATGTTGTATACTTCTATCCTTCCAT
1 ATATTTTGTGTCATGTGGTATACTTCTATCCTTCCAT
29221 ATATTTTGTGTCATGTGGTATACTTCTATCCTTCC
1 ATATTTTGTGTCATGTGGTATACTTCTATCCTTCC
29256 CTACTCCATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.18, C:0.19, G:0.12, T:0.50
Consensus pattern (37 bp):
ATATTTTGTGTCATGTGGTATACTTCTATCCTTCCAT
Found at i:32192 original size:13 final size:13
Alignment explanation
Indices: 32174--32205 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
32164 GGACGTCCTG
32174 AGTCTGAATCCGA
1 AGTCTGAATCCGA
32187 AGTCTGAATCCGA
1 AGTCTGAATCCGA
32200 AGTCTG
1 AGTCTG
32206 TTTCACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (13 bp):
AGTCTGAATCCGA
Found at i:34481 original size:29 final size:26
Alignment explanation
Indices: 34452--34503 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
34442 CATCATCTGG
34452 TGGTTTAGTACTACTAAGCTTCCCAA
1 TGGTTTAGTACTACTAAGCTTCCCAA
34478 TGGTTTAGTACTACTAAGCTTCCCAA
1 TGGTTTAGTACTACTAAGCTTCCCAA
34504 AGCTCACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (26 bp):
TGGTTTAGTACTACTAAGCTTCCCAA
Found at i:38387 original size:2 final size:2
Alignment explanation
Indices: 38380--38446 Score: 75
Period size: 2 Copynumber: 34.0 Consensus size: 2
38370 TAGTGCCTCC
*
38380 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
38421 -T CT TT GT GAT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT
38447 GACTGTTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 2 0.03
2 55 0.95
3 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43027 original size:20 final size:20
Alignment explanation
Indices: 43002--43051 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
42992 ACACCTACAT
43002 TTGGTATCGATACCAGGATG
1 TTGGTATCGATACCAGGATG
*
43022 TTGGTATCGATACCGGGATG
1 TTGGTATCGATACCAGGATG
43042 TTGGTATCGA
1 TTGGTATCGA
43052 GATCGAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (20 bp):
TTGGTATCGATACCAGGATG
Found at i:43822 original size:17 final size:17
Alignment explanation
Indices: 43800--43832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43790 TTATAAATAA
43800 AATAATCATTTTATTTG
1 AATAATCATTTTATTTG
*
43817 AATAATGATTTTATTT
1 AATAATCATTTTATTT
43833 ATTTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
AATAATCATTTTATTTG
Found at i:45046 original size:18 final size:17
Alignment explanation
Indices: 45020--45053 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45010 AATAATTTTT
45020 TTATCTTTTATGATTATC
1 TTATCTTTTATG-TTATC
*
45038 TTATTTTTTATGTTAT
1 TTATCTTTTATGTTAT
45054 TTTTTCCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (17 bp):
TTATCTTTTATGTTATC
Done.