Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001698.1 Hibiscus syriacus cultivar Beakdansim tig00003391_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: 82498
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3652 original size:21 final size:20
Alignment explanation
Indices: 3609--3658 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3599 CCGTTAAATA
3609 GGGGGAATCGGTACCCTTGG
1 GGGGGAATCGGTACCCTTGG
3629 GGGGGAATCGGTACCCCCTT-G
1 GGGGGAATCGGTA--CCCTTGG
3650 GGGGGAATC
1 GGGGGAATC
3659 AGTTCCCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.46
21 10 0.36
22 5 0.18
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCTTGG
Found at i:6261 original size:22 final size:23
Alignment explanation
Indices: 6236--6295 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
6226 GAACCCCAGA
*
6236 GGGGTATCGATTCCCCTAC-TGG
1 GGGGTATCGATTCCCCTACAAGG
* * *
6258 GGGGAATCGGTTCCCCTTCAAGG
1 GGGGTATCGATTCCCCTACAAGG
6281 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
6296 TTTACACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.25
Consensus pattern (23 bp):
GGGGTATCGATTCCCCTACAAGG
Found at i:19168 original size:15 final size:17
Alignment explanation
Indices: 19138--19169 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19128 CTCGAGAAAA
19138 GAGACGAGGCAAAGAAG
1 GAGACGAGGCAAAGAAG
19155 GAGACG-GG-AAAGAAG
1 GAGACGAGGCAAAGAAG
19170 AAGAATGTGG
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:0.47, C:0.09, G:0.44, T:0.00
Consensus pattern (17 bp):
GAGACGAGGCAAAGAAG
Found at i:19643 original size:21 final size:21
Alignment explanation
Indices: 19618--19657 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19608 AAGACTTTAT
19618 TTTCAAAATAAAAAAATGATA
1 TTTCAAAATAAAAAAATGATA
**
19639 TTTCAAAATTGAAAAATGA
1 TTTCAAAATAAAAAAATGA
19658 AAATAGTCTT
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:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATAAAAAAATGATA
Found at i:23421 original size:23 final size:22
Alignment explanation
Indices: 23389--23471 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
23379 TGGTGCAGGA
* *
23389 GGTATCGATACCCCATTTGTATG
1 GGTACCGATACCCC-TTTGAATG
* *
23412 GGTACTGATACCCTTCTTGAATG
1 GGTACCGATACCCCT-TTGAATG
*
23435 GGTACCGATACCCTCCTTGAATG
1 GGTACCGATACCC-CTTTGAATG
23458 GGTACCGATACCCC
1 GGTACCGATACCCC
23472 CACATGAGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.04
23 49 0.96
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (22 bp):
GGTACCGATACCCCTTTGAATG
Found at i:24767 original size:40 final size:40
Alignment explanation
Indices: 24710--24799 Score: 162
Period size: 40 Copynumber: 2.2 Consensus size: 40
24700 GAGAATTTAT
24710 TTTCAAAGTATTAGAGTAAGGGGGAGTAATTTCAAAACTTGA
1 TTTCAAA--ATTAGAGTAAGGGGGAGTAATTTCAAAACTTGA
24752 TTTCAAAATTAGAGTAAGGGGGAGTAATTTCAAAACTTGA
1 TTTCAAAATTAGAGTAAGGGGGAGTAATTTCAAAACTTGA
24792 TTTCAAAA
1 TTTCAAAA
24800 ATGATTTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 41 0.85
42 7 0.15
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (40 bp):
TTTCAAAATTAGAGTAAGGGGGAGTAATTTCAAAACTTGA
Found at i:28577 original size:14 final size:15
Alignment explanation
Indices: 28558--28586 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28548 TCAAGCATTT
28558 AACAATCCA-AAACA
1 AACAATCCAGAAACA
28572 AACAATCCAGAAACA
1 AACAATCCAGAAACA
28587 TAAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:36453 original size:19 final size:19
Alignment explanation
Indices: 36429--36481 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
36419 AAAATCCTCA
36429 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
36448 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
* *
36467 GTGTATTGATGCATG
1 GTGCATCGATGCATG
36482 AAATGCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:36457 original size:65 final size:64
Alignment explanation
Indices: 36319--36461 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 64
36309 TGCACTAAGA
* * *
36319 GTGCATCGATGCATCAAGTGCATTCGATGTTTTAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATATTTTAAAATAGCCACAGTGCATCGATGCATGGCTG
* *
36383 GTGCATCGATGCATCAAATGCATTCGATATTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATATTTT-A-AAATAGCCACAGTGCATCGATGCATGGCT
*
36446 AT
64 -G
36448 GTGCATCGATGCAT
1 GTGCATCGATGCAT
36462 GGTATGTGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
64 32 0.46
65 35 0.50
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATATTTTAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:37291 original size:34 final size:34
Alignment explanation
Indices: 37253--37362 Score: 80
Period size: 34 Copynumber: 3.1 Consensus size: 34
37243 CTAAACTATG
37253 AAAACAAACAATACCCAAATAACCATTTGAAGTA
1 AAAACAAACAATACCCAAATAACCATTTGAAGTA
* * * * * *
37287 AAAACTAAA-AAAACTCAAATTTA-CATACTAAACTA
1 AAAAC-AAACAATACCCAAA-TAACCAT-TTGAAGTA
* * *
37322 TGAAAACAAACAATACCCAAATCACCAATTGGAGTA
1 --AAAACAAACAATACCCAAATAACCATTTGAAGTA
37358 AAAAC
1 AAAAC
37363 TATGAAAATA
Statistics
Matches: 55, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
34 21 0.38
35 10 0.18
36 9 0.16
37 15 0.27
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.18
Consensus pattern (34 bp):
AAAACAAACAATACCCAAATAACCATTTGAAGTA
Found at i:37333 original size:71 final size:72
Alignment explanation
Indices: 37085--37364 Score: 402
Period size: 73 Copynumber: 3.9 Consensus size: 72
37075 AATAAATAAA
* * * * ** *
37085 ACAAATTTATATTCTAAACCATGAAAACAAATAATACTTAAATCACCATTTGGGGTAAAAACTAA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
37150 AAAAAAT
66 AAAAAAT
* *
37157 ACAAATTTACATACTAAACTATGAAAACAAATAATACCCAAATC-CTCATTTGGAGTAAAACCTA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCAC-CATTTGGAGTAAAAACT-
37221 AAAAAAAAT
64 AAAAAAAAT
* * *
37230 ACAAACTTACATACTAAACTATGAAAACAAACAATACCCAAATAACCATTTGAAGTAAAAACTAA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
*
37295 AAAAACT
66 AAAAAAT
*
37302 -CAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCAATTGGAGTAAAAACTA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTA
37365 TGAAAATAAG
Statistics
Matches: 188, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
71 60 0.32
72 62 0.33
73 65 0.35
74 1 0.01
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.23
Consensus pattern (72 bp):
ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
AAAAAAT
Found at i:37354 original size:144 final size:145
Alignment explanation
Indices: 37098--37360 Score: 413
Period size: 144 Copynumber: 1.8 Consensus size: 145
37088 AATTTATATT
* ** * **
37098 CTAAACCATGAAAACAAATAATACTTAAATCACCATTTGGGGTAAAAACTAAAAAAAATACAAAT
1 CTAAACCATGAAAACAAACAATACCCAAATAACCATTTGAAGTAAAAACTAAAAAAAATACAAAT
* *
37163 TTACATACTAAACTATGAAAACAAATAATACCCAAATCCTCATTTGGAGTAAAACCTAAAAAAAA
66 TTACATACTAAACTATGAAAACAAACAATACCCAAATCCTCAATTGGAGTAAAACCTAAAAAAAA
37228 ATACAAACTTACATA
131 ATACAAACTTACATA
* *
37243 CTAAACTATGAAAACAAACAATACCCAAATAACCATTTGAAGTAAAAACTAAAAAAACT-CAAAT
1 CTAAACCATGAAAACAAACAATACCCAAATAACCATTTGAAGTAAAAACTAAAAAAAATACAAAT
37307 TTACATACTAAACTATGAAAACAAACAATACCCAAATCAC-CAATTGGAGTAAAA
66 TTACATACTAAACTATGAAAACAAACAATACCCAAATC-CTCAATTGGAGTAAAA
37361 ACTATGAAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
144 55 0.51
145 52 0.49
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.21
Consensus pattern (145 bp):
CTAAACCATGAAAACAAACAATACCCAAATAACCATTTGAAGTAAAAACTAAAAAAAATACAAAT
TTACATACTAAACTATGAAAACAAACAATACCCAAATCCTCAATTGGAGTAAAACCTAAAAAAAA
ATACAAACTTACATA
Found at i:48926 original size:18 final size:19
Alignment explanation
Indices: 48892--48931 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
48882 AAACAAAGCC
*
48892 AAATAAATATTAAATAATA
1 AAATAAATATAAAATAATA
48911 AAATAAA-ATAAAATAATA
1 AAATAAATATAAAATAATA
48929 AAA
1 AAA
48932 AAGATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATAAATATAAAATAATA
Found at i:51042 original size:57 final size:57
Alignment explanation
Indices: 50780--51148 Score: 607
Period size: 57 Copynumber: 6.5 Consensus size: 57
50770 TCCAATATAT
* *
50780 ATTCATACACTTAATATGAATTTCTTAACATTTTAGCGTACGAAACGCCCTATCGGGAA
1 ATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAACGCCCTATC-TGAA
*
50839 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
* *
50896 ATTCATACACTTAATATGATTTTCTTAACATTTTAGCGTACGAAATGCCCTATCTGAA
1 ATTCATACACTTAGTATGA-TTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
* *
50954 ATTC--ACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATATGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
* *
51009 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAAGCCCTATATGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
*
51066 ATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
51123 ATTCATACACTTAGTATGATTTCTTA
1 ATTCATACACTTAGTATGATTTCTTA
51149 TATTTTGCAC
Statistics
Matches: 291, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
55 39 0.13
56 12 0.04
57 149 0.51
58 74 0.25
59 17 0.06
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (57 bp):
ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
Found at i:55238 original size:45 final size:45
Alignment explanation
Indices: 55150--55264 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 45
55140 CACCTATATG
* * * *
55150 CATTTCAATTATGTCATCATTAT-ATGTCTTTTATACGCTATTATA
1 CATTTCAATTATGGCATCATT-TCATGCCTTTGATACACTATTATA
* * * * *
55195 CCTTTTATTTATGGCTTCCTTTCATGCCTTTGATACACTATTATA
1 CATTTCAATTATGGCATCATTTCATGCCTTTGATACACTATTATA
55240 CATTTCAATTATGGCATCATTTCAT
1 CATTTCAATTATGGCATCATTTCAT
55265 ACAATTATGC
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
44 1 0.02
45 54 0.98
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (45 bp):
CATTTCAATTATGGCATCATTTCATGCCTTTGATACACTATTATA
Found at i:55882 original size:57 final size:57
Alignment explanation
Indices: 55815--56226 Score: 686
Period size: 57 Copynumber: 7.3 Consensus size: 57
55805 CAATACATAT
* * *
55815 ATTCATACACTTAATATGAATTTCTTAACATTTTAGCATACGAAA-GCCCTATCAGAA
1 ATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
*
55872 ATTCATACACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACGCCCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
* *
55929 ATTCATACACTTAATATGATTTCTTAACATTTTAGCGTACGAAACGCTCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
* *
55986 ATTC--ACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAAAGCCCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
* *
56041 ATTCATACACTTAGTATGATTTCTTAACATTTTAGTGTACGAAACACCCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
*
56098 ATTTATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
*
56155 ATTCATACACTTAGTATGATTTCTTAACATTTTACCGTACGAAACGCCCTATCTGAA
1 ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
56212 ATTCATACACTTAGT
1 ATTCATACACTTAGT
56227 GCCCTTTGGA
Statistics
Matches: 332, Mismatches: 20, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
55 51 0.15
56 24 0.07
57 257 0.77
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (57 bp):
ATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
Found at i:56044 original size:169 final size:170
Alignment explanation
Indices: 55815--56226 Score: 684
Period size: 169 Copynumber: 2.4 Consensus size: 170
55805 CAATACATAT
* * *
55815 ATTCATACACTTAATATGAATTTCTTAACATTTTAGCATACG-AAAGCCCTATCAGAAATTCATA
1 ATTCA-ACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAAAGCCCTATCTGAAATTCATA
*
55879 CACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACGCCCTATCTGAAATTCATACACTTAAT
64 CACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATCTGAAATTCATACACTTAAT
*
55944 ATGATTTCTTAACATTTTAGCGTACGAAACGCTCTATCTGAA
129 ATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
*
55986 ATTC-ACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAAAGCCCTATCTGAAATTCATACA
1 ATTCAACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAAGCCCTATCTGAAATTCATACA
* * *
56050 CTTAGTATGATTTCTTAACATTTTAGTGTACGAAACACCCTATCTGAAATTTATACACTTAGTAT
66 CTTAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATCTGAAATTCATACACTTAATAT
56115 GATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
131 GATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
* *
56155 ATTCATACACTTAGTATGATTTCTTAACATTTTACCGTACGAAACGCCCTATCTGAAATTCATAC
1 ATTCA-ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAAGCCCTATCTGAAATTCATAC
56220 ACTTAGT
65 ACTTAGT
56227 GCCCTTTGGA
Statistics
Matches: 226, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
168 21 0.09
169 138 0.61
171 67 0.30
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (170 bp):
ATTCAACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAAGCCCTATCTGAAATTCATACA
CTTAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATCTGAAATTCATACACTTAATAT
GATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAA
Found at i:56209 original size:226 final size:227
Alignment explanation
Indices: 55815--56226 Score: 702
Period size: 226 Copynumber: 1.8 Consensus size: 227
55805 CAATACATAT
*
55815 ATTCATACACTTAATATGAATTTCTTAACATTTTAGCATACGAAAGCCCTATCAGAAATTCATAC
1 ATTCATACACTTAATATGAATTTCTTAACATTTTAGCATACGAAAACCCTATCAGAAATTCATAC
55880 ACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACGCCCTATCTGAAATTCATACACTTAATA
66 ACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACGCCCTATCTGAAATTCATACACTTAATA
* *
55945 TGATTTCTTAACATTTTAGCGTACGAAACGCTCTATCTGAAATTC-ACACTTAGTATGATTTCTT
131 TGATTTCTTAACATTTTACCGTACGAAACGCCCTATCTGAAATTCAACACTTAGTATGATTTCTT
56009 AACATTTTAGCGTATGAAAAGCCCTATCTGAA
196 AACATTTTAGCGTATGAAAAGCCCTATCTGAA
* ** * *
56041 ATTCATACACTTAGTATG-ATTTCTTAACATTTTAGTGTACGAAACACCCTATCTGAAATTTATA
1 ATTCATACACTTAATATGAATTTCTTAACATTTTAGCATACGAAA-ACCCTATCAGAAATTCATA
* *
56105 CACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAGT
65 CACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACGCCCTATCTGAAATTCATACACTTAAT
56170 ATGATTTCTTAACATTTTACCGTACGAAACGCCCTATCTGAAATTCATACACTTAGT
130 ATGATTTCTTAACATTTTACCGTACGAAACGCCCTATCTGAAATTCA-ACACTTAGT
56227 GCCCTTTGGA
Statistics
Matches: 173, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
225 24 0.14
226 140 0.81
228 9 0.05
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (227 bp):
ATTCATACACTTAATATGAATTTCTTAACATTTTAGCATACGAAAACCCTATCAGAAATTCATAC
ACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACGCCCTATCTGAAATTCATACACTTAATA
TGATTTCTTAACATTTTACCGTACGAAACGCCCTATCTGAAATTCAACACTTAGTATGATTTCTT
AACATTTTAGCGTATGAAAAGCCCTATCTGAA
Found at i:58310 original size:3 final size:3
Alignment explanation
Indices: 58286--58337 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
58276 ATTGAAAATA
* *
58286 AAT AAA AAT AAT GAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
58333 AAT AA
1 AAT AA
58338 AAACGACTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 38 0.88
4 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:58495 original size:35 final size:34
Alignment explanation
Indices: 58452--58570 Score: 125
Period size: 35 Copynumber: 3.4 Consensus size: 34
58442 TTTAAAATTC
58452 TATATTATACGTTTTCAAAATTATCTTAAAAACTA
1 TATATTATACGTTTTCAAAATTAT-TTAAAAACTA
* * *
58487 TATATTATATGTTTTCAAAATTGTTT--TAACTA
1 TATATTATACGTTTTCAAAATTATTTAAAAACTA
* * *
58519 TATAGTATACGTTTTTAAAAATATTTTTTAAAAACTA
1 TATATTATACG-TTTT-CAAA-ATTATTTAAAAACTA
*
58556 TATATTATATGTTTT
1 TATATTATACGTTTT
58571 TGAAAATACG
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
32 14 0.20
33 4 0.06
34 5 0.07
35 28 0.41
36 4 0.06
37 14 0.20
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (34 bp):
TATATTATACGTTTTCAAAATTATTTAAAAACTA
Found at i:69986 original size:13 final size:14
Alignment explanation
Indices: 69961--69989 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
69951 AGCAAAGCCA
69961 AATAAATATTAAAT
1 AATAAATATTAAAT
69975 AATAAA-ATTAAAT
1 AATAAATATTAAAT
69988 AA
1 AA
69990 AATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAAATATTAAAT
Found at i:71575 original size:34 final size:34
Alignment explanation
Indices: 71435--71630 Score: 214
Period size: 34 Copynumber: 5.6 Consensus size: 34
71425 TTTTAAATTT
* *
71435 TATATTATACATTTTCAAAATTATCTTAAAATCTA
1 TATATTATACGTTTTCAAAATTATTTTAAAA-CTA
* * **
71470 TATACTATATGTTTTCAAAATCGTTTT-AAACTA
1 TATATTATACGTTTTCAAAATTATTTTAAAACTA
** *
71503 TATAGAATACGTTTTCAAAACTATTTTTAAAAACTA
1 TATATTATACGTTTTCAAAATTA-TTTT-AAAACTA
*
71539 TATATTATAGGTTTTCAAAATTATTTTAAAACTA
1 TATATTATACGTTTTCAAAATTATTTTAAAACTA
*
71573 TATACTATACGTTTTCAAAACTATATTGTTAAAAACTA
1 TATATTATACGTTTTCAAAA-T-TATT-TT-AAAACTA
*
71611 TATATTATATGTTTTCAAAA
1 TATATTATACGTTTTCAAAA
71631 ATCCGGCTTC
Statistics
Matches: 134, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
33 20 0.15
34 32 0.24
35 26 0.19
36 29 0.22
37 2 0.01
38 25 0.19
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (34 bp):
TATATTATACGTTTTCAAAATTATTTTAAAACTA
Found at i:71613 original size:70 final size:69
Alignment explanation
Indices: 71356--71630 Score: 238
Period size: 72 Copynumber: 3.9 Consensus size: 69
71346 TTTTTCTTTA
* * * * * *
71356 TAAACCATATATTATACG-CTTCAAAACCAT-TTTGAAAAA-ATATATTATATATATTTTCAAAA
1 TAAACTATATACTATACGTTTTCAAAACTATATTTTAAAAACATATA-T-TATATGTTTTCAAAA
*
71418 CCATTTTTTT
64 TCA----TTT
* * * * * * *
71428 TAAATTTTATATTATACATTTTCAAAA-T-TATCTTAAAATCTATATACTATATGTTTTCAAAAT
1 TAAACTATATACTATACGTTTTCAAAACTATATTTTAAAAAC-ATATATTATATGTTTTCAAAAT
*
71491 CGTTT
65 CATTT
** *
71496 TAAACTATATAGAATACGTTTTCAAAACTAT-TTTTAAAAACTATATATTATAGGTTTTCAAAAT
1 TAAACTATATACTATACGTTTTCAAAACTATATTTTAAAAAC-ATATATTATATGTTTTCAAAAT
*
71560 TATTT
65 CATTT
71565 TAAAACTATATACTATACGTTTTCAAAACTATATTGTTAAAAACTATATATTATATGTTTTCAAA
1 T-AAACTATATACTATACGTTTTCAAAACTATATT-TTAAAAAC-ATATATTATATGTTTTCAAA
71630 A
63 A
71631 ATCCGGCTTC
Statistics
Matches: 167, Mismatches: 27, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
68 25 0.15
69 34 0.20
70 29 0.17
71 3 0.02
72 64 0.38
73 7 0.04
74 5 0.03
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (69 bp):
TAAACTATATACTATACGTTTTCAAAACTATATTTTAAAAACATATATTATATGTTTTCAAAATC
ATTT
Found at i:73744 original size:13 final size:14
Alignment explanation
Indices: 73719--73747 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
73709 AACAAAGCCA
73719 AATAAATATTAAAT
1 AATAAATATTAAAT
73733 AATAAA-ATTAAAT
1 AATAAATATTAAAT
73746 AA
1 AA
73748 AATAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAAATATTAAAT
Found at i:73763 original size:18 final size:18
Alignment explanation
Indices: 73729--73763 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73719 AATAAATATT
*
73729 AAATAATAAAATTAAATA
1 AAATAATAAAATGAAATA
*
73747 AAATAATAAAGTGAAAT
1 AAATAATAAAATGAAAT
73764 TTAAAGTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATAATAAAATGAAATA
Found at i:73768 original size:12 final size:12
Alignment explanation
Indices: 73753--73780 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
73743 AATAAAATAA
73753 TAAAGTGAAATT
1 TAAAGTGAAATT
73765 TAAAGTGAAATT
1 TAAAGTGAAATT
73777 TAAA
1 TAAA
73781 AAACATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (12 bp):
TAAAGTGAAATT
Done.