Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004328.1 Hibiscus syriacus cultivar Beakdansim tig00009487_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: 80910
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5011 original size:22 final size:22
Alignment explanation
Indices: 4968--5023 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
4958 GATGCACTGT
*
4968 TCACTATTCACGGGGTATTGTTCA
1 TCACTATTCAC--GGTACTGTTCA
*
4992 TCACTGTTCACGGTACTGTTCA
1 TCACTATTCACGGTACTGTTCA
5014 TCACTATTCA
1 TCACTATTCA
5024 TAAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.66
24 10 0.34
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (22 bp):
TCACTATTCACGGTACTGTTCA
Found at i:5747 original size:23 final size:23
Alignment explanation
Indices: 5715--5772 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
5705 GAGATCAGCG
*
5715 CCACGAAGAATTTGAC-CGAAGGA
1 CCACGTAGAATTTGACTC-AAGGA
**
5738 CCACGTAGAATTTTTCTCAAGGA
1 CCACGTAGAATTTGACTCAAGGA
5761 CCACGTAGAATT
1 CCACGTAGAATT
5773 ATCTCGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (23 bp):
CCACGTAGAATTTGACTCAAGGA
Found at i:10566 original size:20 final size:20
Alignment explanation
Indices: 10541--10589 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
10531 TTGAAGAAGT
* * *
10541 ATCGATACTAAGATGTAGGA
1 ATCGATACCAAGAGGAAGGA
*
10561 ATCGATACCAAGAGGAAGGT
1 ATCGATACCAAGAGGAAGGA
10581 ATCGATACC
1 ATCGATACC
10590 GTAATCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (20 bp):
ATCGATACCAAGAGGAAGGA
Found at i:11120 original size:17 final size:17
Alignment explanation
Indices: 11076--11110 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11066 TGTGCTAAAC
11076 GAAAGTGA--TATATGT
1 GAAAGTGACCTATATGT
11091 GAAAGTGACCTATATGT
1 GAAAGTGACCTATATGT
11108 GAA
1 GAA
11111 TGTACTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.29
Consensus pattern (17 bp):
GAAAGTGACCTATATGT
Found at i:11188 original size:2 final size:2
Alignment explanation
Indices: 11181--11227 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
11171 AAGCCCAAGG
11181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11223 TA TA T
1 TA TA T
11228 TAGAGGTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11294 original size:23 final size:23
Alignment explanation
Indices: 11263--11353 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
11253 GTTGAGGGTT
* **
11263 CTATATGGTCCTTCGGGATGAAC
1 CTATGTGGTCCTTCGGGACAAAC
*
11286 CTATGTGGTCCTTCGGAACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* *
11309 CTATGTGGTCCTTTGGGACAAAT
1 CTATGTGGTCCTTCGGGACAAAC
11332 CTATGTGGTCCTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
11354 TATGTGCACT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:11367 original size:20 final size:21
Alignment explanation
Indices: 11342--11380 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
11332 CTATGTGGTC
11342 CTTCGG-GACAAA-TATGTGCA
1 CTTCGGTG-CAAATTATGTGCA
11362 CTTCGGTGCAAATTATGTG
1 CTTCGGTGCAAATTATGTG
11381 AGCAGTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
CTTCGGTGCAAATTATGTGCA
Found at i:17515 original size:21 final size:21
Alignment explanation
Indices: 17491--17530 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
17481 GAAACGAGAG
17491 TTGAAAA-AGACATTGAGAGCA
1 TTGAAAATAGA-ATTGAGAGCA
17512 TTGAAAATAGAATTGAGAG
1 TTGAAAATAGAATTGAGAG
17531 TGAAAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGAAAATAGAATTGAGAGCA
Found at i:20795 original size:26 final size:26
Alignment explanation
Indices: 20759--20820 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
20749 AGTAATTCTT
20759 TTCATCTTTAAAGAAAAAATATTTAC
1 TTCATCTTTAAAGAAAAAATATTTAC
20785 TTCATCTTTAAAGAAAAAATATTTAC
1 TTCATCTTTAAAGAAAAAATATTTAC
20811 TTCATCTTTA
1 TTCATCTTTA
20821 TATTCCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (26 bp):
TTCATCTTTAAAGAAAAAATATTTAC
Found at i:21441 original size:30 final size:31
Alignment explanation
Indices: 21407--21484 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
21397 ATATTTATCC
21407 AAAATTAAAACACACATCATTC-AAAAAAAA
1 AAAATTAAAACACACATCATTCAAAAAAAAA
21437 AAAATTAAAACACACATCATTCAAAAAAAAA
1 AAAATTAAAACACACATCATTCAAAAAAAAA
21468 AAAATTAAAACACACAT
1 AAAATTAAAACACACAT
21485 TTAATTGATT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 22 0.47
31 25 0.53
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (31 bp):
AAAATTAAAACACACATCATTCAAAAAAAAA
Found at i:21686 original size:12 final size:11
Alignment explanation
Indices: 21663--21697 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21653 AACAATTTAA
21663 TTAAATATTTT
1 TTAAATATTTT
21674 TTAAATATATTT
1 TTAAATAT-TTT
*
21686 TTACATATTTT
1 TTAAATATTTT
21697 T
1 T
21698 ATCAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
TTAAATATTTT
Found at i:22054 original size:20 final size:20
Alignment explanation
Indices: 22026--22070 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
22016 TTAGAATTTT
*
22026 TAAAATTTATATTTTAAAAA
1 TAAATTTTATATTTTAAAAA
*
22046 TAAATTTTATTTTTTAAAAA
1 TAAATTTTATATTTTAAAAA
22066 -AAATT
1 TAAATT
22071 CAAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATTTTATATTTTAAAAA
Found at i:25059 original size:29 final size:29
Alignment explanation
Indices: 25023--25098 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
25013 AACTAAATTT
25023 ATGTAAGCAATGACATCATTAATTAAATG
1 ATGTAAGCAATGACATCATTAATTAAATG
*
25052 ATGTAAGCAATGACATCTTTAATTAAATG
1 ATGTAAGCAATGACATCATTAATTAAATG
*
25081 ATGTAAGTAATGACATCA
1 ATGTAAGCAATGACATCA
25099 ATTTAGTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (29 bp):
ATGTAAGCAATGACATCATTAATTAAATG
Found at i:29815 original size:29 final size:29
Alignment explanation
Indices: 29779--29854 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
29769 AACTAAATTT
29779 ATGTAAGCAATGACATCATTAATTAAATG
1 ATGTAAGCAATGACATCATTAATTAAATG
*
29808 ATGTAAGCAATGACATCTTTAATTAAATG
1 ATGTAAGCAATGACATCATTAATTAAATG
*
29837 ATGTAAGTAATGACATCA
1 ATGTAAGCAATGACATCA
29855 ATTTAGTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (29 bp):
ATGTAAGCAATGACATCATTAATTAAATG
Found at i:34405 original size:18 final size:16
Alignment explanation
Indices: 34379--34419 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
34369 AAACAAGATT
34379 AAGACAAAGGATAATATA
1 AAGACAAAGGA-AA-ATA
*
34397 AAGATAAAGGAAAATA
1 AAGACAAAGGAAAATA
34413 AAGACAA
1 AAGACAA
34420 TGAATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 10 0.48
ACGTcount: A:0.66, C:0.05, G:0.17, T:0.12
Consensus pattern (16 bp):
AAGACAAAGGAAAATA
Found at i:36808 original size:20 final size:21
Alignment explanation
Indices: 36757--36809 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
36747 AAAATGTCTC
36757 AGTATCAATACTGACCCTCTG
1 AGTATCAATACTGACCCTCTG
**
36778 AGTATTGATACTGGACCC-C-G
1 AGTATCAATACT-GACCCTCTG
36798 AGTATCAATACT
1 AGTATCAATACT
36810 CCTTAAAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.41
21 11 0.41
22 5 0.19
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
AGTATCAATACTGACCCTCTG
Found at i:37885 original size:66 final size:66
Alignment explanation
Indices: 37779--37915 Score: 229
Period size: 66 Copynumber: 2.1 Consensus size: 66
37769 TTAACTCAAC
* **
37779 AGGTGCCACTAATGAAAATTTTTGATCGATTTTGTTTAATGCATAACTGTGCATTATCGACATAA
1 AGGTGCCACTAATGAAAATTTTTGATCAATTTTGTTTAATGCATAACAATGCATTATCGACATAA
37844 A
66 A
* *
37845 AGGTGCCACTAATGAAAATTTTTGATCAATTTTGTTTAATGCATAACAATGCATTATTGGCATAA
1 AGGTGCCACTAATGAAAATTTTTGATCAATTTTGTTTAATGCATAACAATGCATTATCGACATAA
37910 A
66 A
37911 AGGTG
1 AGGTG
37916 TCGCTCATGG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (66 bp):
AGGTGCCACTAATGAAAATTTTTGATCAATTTTGTTTAATGCATAACAATGCATTATCGACATAA
A
Found at i:47513 original size:23 final size:23
Alignment explanation
Indices: 47485--47529 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47475 ACGTAGAATT
* *
47485 TGTCCCGAAGGACCACGTATAAA
1 TGTCCCAAAGGACCACATATAAA
*
47508 TGTCCCAAATGACCACATATAA
1 TGTCCCAAAGGACCACATATAA
47530 CACATATGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.20
Consensus pattern (23 bp):
TGTCCCAAAGGACCACATATAAA
Found at i:57612 original size:18 final size:18
Alignment explanation
Indices: 57591--57633 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
57581 ACATTACTTA
*
57591 AGAAGAAGACCTTGGTTG
1 AGAAGAAGACCTTGGCTG
57609 AGAAGAAGACCTTGGCTG
1 AGAAGAAGACCTTGGCTG
57627 AGAAGAA
1 AGAAGAA
57634 CTGCGTCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.33, T:0.16
Consensus pattern (18 bp):
AGAAGAAGACCTTGGCTG
Found at i:58487 original size:199 final size:199
Alignment explanation
Indices: 58147--58968 Score: 1068
Period size: 199 Copynumber: 4.1 Consensus size: 199
58137 AAAATATCGA
* * * * * *
58147 ATACCTATATAAAAGTATCGGTACTTGGTATTTACACCTATTATAAATATATCGGTAGACTTTTC
1 ATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTA
* * * *
58212 CCGTTTACATTGTTAATTTACCTATTACTTTAAAGTATTAGGTTTCGAAATTCCAAGTATTGATA
66 CCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCAAAATTCCAAGTATCGATA
* * *
58277 CTTTATATATGTGTATTGATACATTTTGTGCAAAAATTGTTTGAGAAGCATACTGGAACAAAAGT
131 CTTTATATATGTGTATCGATACATTTTGTGCGAAAATTGTTTGAGAAGCATACTGGAATAAAAGT
58342 ATCC
196 ATCC
*
58346 ATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATCATACCGGTAGACTTTTA
1 ATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTA
* * * * * *
58411 CCTTTTACATTGTTAATTTACATATTACTTTAAAATAATAAGTTTCAAAATTTCATGTATCAATA
66 CCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCAAAATTCCAAGTATCGATA
58476 CTTTATATATGTGTATCGATACATTTTGCATGC--AAATTGTTTGAGAAGCATACTGGAATAAAA
131 CTTTATATATGTGTATCGATACATTTTG--TGCGAAAATTGTTTGAGAAGCATACTGGAATAAAA
*
58539 GTATCG
194 GTATCC
* * *
58545 ATACCTACATGAAAGTATC-AGTACTTGGTATTTACGCCTATTGTCATTATACCGGTAGACTTTT
1 ATACCTATATAAAAGTATCGA-TACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTT
* * *
58609 ACCGTTTACATTGTTAATTTACCTATTA-TTTCAATGTAAT-AGATTTCGAAATTCCAAGTATCT
65 ACCGTTTACATTGTTAATTTACCTATTACTTT-AAAGTAATAAG-TTTCAAAATTCCAAGTATCG
* * * * * *
58672 ATACTTTATACA--TGTATCGATATATTTTGTGTGCAAATTGTTTGAGAAACATATTGGAATAAA
128 ATACTTTATATATGTGTATCGATACATTTTGTGCGAAAATTGTTTGAGAAGCATACTGGAATAAA
58735 AGTATCC
193 AGTATCC
* * * * *
58742 ATACCTATATAAAGAGTGTTGATACTTAGTATTTTCGCCTATTATCATTAT-GC-GTAGACTTTT
1 ATACCTATATAAA-AGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTT
* * * *
58805 ACCGTTTACATTGTTAATTTACCTATTACTTTAAGGTAATAGGTTCCAAAATTTCAAGTATCGAT
65 ACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCAAAATTCCAAGTATCGAT
* * * *
58870 ACTTTATATATGTGTAACGATACATTTTGCGTGAAAATTGTTTGAGAATCATACTGGAATAAAAG
130 ACTTTATATATGTGTATCGATACATTTTGTGCGAAAATTGTTTGAGAAGCATACTGGAATAAAAG
58935 TATCC
195 TATCC
* ***
58940 ATATCGGCATAAGAAGTATCGATACTTGG
1 ATACCTATATAA-AAGTATCGATACTTGG
58969 ACATTTTCGT
Statistics
Matches: 543, Mismatches: 66, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
195 2 0.00
196 72 0.13
197 65 0.12
198 108 0.20
199 293 0.54
201 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (199 bp):
ATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTA
CCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAAGTTTCAAAATTCCAAGTATCGATA
CTTTATATATGTGTATCGATACATTTTGTGCGAAAATTGTTTGAGAAGCATACTGGAATAAAAGT
ATCC
Found at i:58926 original size:395 final size:398
Alignment explanation
Indices: 58136--58938 Score: 1168
Period size: 395 Copynumber: 2.0 Consensus size: 398
58126 GTTTAGATAA
* * * *
58136 AAAAATATCGAATACCTATATAAAAGTATCGGTACTTGGTATTTACACCTATTATAAATATATCG
1 AAAAGTATCGAATACCTACATAAAAGTATCAGTACTTGGTATTTACACCTATTATAAATATACCG
* * *
58201 GTAGACTTTTCCCGTTTACATTGTTAATTTACCTATTACTTTAAAGTATTAGGTTTCGAAATTCC
66 GTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGATTTCGAAATTCC
* * *
58266 AAGTATTGATACTTTATATATGTGTATTGATACATTTTGTGCAAAAATTGTTTGAGAAGCATACT
131 AAGTATTGATACTTTATACA-GTGTATCGATACATTTTGTGCAAAAATTGTTTGAGAAACATACT
*
58331 GGAACAAAAGTATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATCAT
195 GGAACAAAAGTATCCATACCTATATAAAAGTATCGATACTTAGTATTTACGCCTATTATCATCAT
* *
58396 ACCGGTAGACTTTTACCTTTTACATTGTTAATTTACATATTACTTTAAAATAATAAGTTTCAAAA
260 ACCGGTAGACTTTTACCGTTTACATTGTTAATTTACATATTACTTTAAAATAATAAGTTCCAAAA
* * *
58461 TTTCATGTATCAATACTTTATATATGTGTATCGATACATTTTGCATGCAAATTGTTTGAGAAGCA
325 TTTCAAGTATCAATACTTTATATATGTGTAACGATACATTTTGCATGAAAATTGTTTGAGAAGCA
58526 TACTGGAAT
390 TACTGGAAT
* * * * *
58535 AAAAGTATCG-ATACCTACATGAAAGTATCAGTACTTGGTATTTACGCCTATTGTCATTATACCG
1 AAAAGTATCGAATACCTACATAAAAGTATCAGTACTTGGTATTTACACCTATTATAAATATACCG
*
58599 GTAGACTTTTACCGTTTACATTGTTAATTTACCTATTA-TTTCAATGTAATAGATTTCGAAATTC
66 GTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTT-AAAGTAATAGATTTCGAAATTC
* *** *
58663 CAAGTATCT-ATACTTTATACA-TGTATCGATATATTTTGTGTGCAAATTGTTTGAGAAACATAT
130 CAAGTAT-TGATACTTTATACAGTGTATCGATACATTTTGTGCAAAAATTGTTTGAGAAACATAC
* * * * *
58726 TGGAATAAAAGTATCCATACCTATATAAAGAGTGTTGATACTTAGTATTTTCGCCTATTATCATT
194 TGGAACAAAAGTATCCATACCTATATAAA-AGTATCGATACTTAGTATTTACGCCTATTATCATC
* * ** *
58791 AT-GC-GTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAGGTAATAGGTTCCAA
258 ATACCGGTAGACTTTTACCGTTTACATTGTTAATTTACATATTACTTTAAAATAATAAGTTCCAA
* * *
58854 AATTTCAAGTATCGATACTTTATATATGTGTAACGATACATTTTGCGTGAAAATTGTTTGAGAAT
323 AATTTCAAGTATCAATACTTTATATATGTGTAACGATACATTTTGCATGAAAATTGTTTGAGAAG
58919 CATACTGGAAT
388 CATACTGGAAT
58930 AAAAGTATC
1 AAAAGTATC
58939 CATATCGGCA
Statistics
Matches: 361, Mismatches: 40, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
395 132 0.37
396 64 0.18
397 35 0.10
398 120 0.33
399 10 0.03
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (398 bp):
AAAAGTATCGAATACCTACATAAAAGTATCAGTACTTGGTATTTACACCTATTATAAATATACCG
GTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGATTTCGAAATTCC
AAGTATTGATACTTTATACAGTGTATCGATACATTTTGTGCAAAAATTGTTTGAGAAACATACTG
GAACAAAAGTATCCATACCTATATAAAAGTATCGATACTTAGTATTTACGCCTATTATCATCATA
CCGGTAGACTTTTACCGTTTACATTGTTAATTTACATATTACTTTAAAATAATAAGTTCCAAAAT
TTCAAGTATCAATACTTTATATATGTGTAACGATACATTTTGCATGAAAATTGTTTGAGAAGCAT
ACTGGAAT
Found at i:59249 original size:147 final size:145
Alignment explanation
Indices: 58851--59251 Score: 529
Period size: 145 Copynumber: 2.8 Consensus size: 145
58841 TAATAGGTTC
* * * *
58851 CAAAATT-TCAAGTATCGATACTTT-ATATATGTGTAACGATACATTTTGCGTGAAAATTGTTTG
1 CAAAATTAT-AAGTATCGATACTTTAATA-ATGTGTATCGATACATTTGGCATGCAAATTGTTTG
* * * * * *
58914 AGAATCATACTGGAATAAAAGTATCCATATCGGCATAAGAAGTATCGATACTTGGACATTTTCGT
64 ACAAACATACTGGAATAAAAGTATCGATATCGGCATAACAAGTATCGATACATGGACATTTTCAT
58979 ACTTTGCATACATGTTT
129 ACTTTGCATACATGTTT
* * *
58996 CAAAATTATAAATATCGATACTATAATAATGTGTATCGATACATTTGGCCTGCAAATTGTTTGAC
1 CAAAATTATAAGTATCGATACTTTAATAATGTGTATCGATACATTTGGCATGCAAATTGTTTGAC
* ** * *
59061 AAGCATACAAGAATAAAAGTATACG-TACCGGCATAATAAGTATCGATACATGGACATTTTCATA
66 AAACATACTGGAATAAAAGTAT-CGATATCGGCATAACAAGTATCGATACATGGACATTTTCATA
*
59125 CTTTGCATACATTTTTTT
130 CTTTGCATACA--TGTTT
*
59143 CAAAATTATAAGTATCAATACTTTAATAATGTGTATCGATACATTTGGCATGCAAATTGTTTGAC
1 CAAAATTATAAGTATCGATACTTTAATAATGTGTATCGATACATTTGGCATGCAAATTGTTTGAC
* * *
59208 AAACACACTGGAATAAAAGTATCGATATCGACACAACAAGTATC
66 AAACATACTGGAATAAAAGTATCGATATCGGCATAACAAGTATC
59252 CATATTTACA
Statistics
Matches: 222, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
145 117 0.53
146 7 0.03
147 98 0.44
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (145 bp):
CAAAATTATAAGTATCGATACTTTAATAATGTGTATCGATACATTTGGCATGCAAATTGTTTGAC
AAACATACTGGAATAAAAGTATCGATATCGGCATAACAAGTATCGATACATGGACATTTTCATAC
TTTGCATACATGTTT
Found at i:59368 original size:14 final size:15
Alignment explanation
Indices: 59335--59374 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
59325 ATGAATTACA
59335 TTTCTGGAAAACAGT
1 TTTCTGGAAAACAGT
59350 TTTCTGGAAAACA-T
1 TTTCTGGAAAACAGT
*
59364 TTTCTAGAAAA
1 TTTCTGGAAAA
59375 TGTTTTCCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (15 bp):
TTTCTGGAAAACAGT
Found at i:61262 original size:92 final size:92
Alignment explanation
Indices: 61099--61281 Score: 287
Period size: 92 Copynumber: 2.0 Consensus size: 92
61089 TAAACATTTT
* * * *
61099 ATAAACTGAACTTAACAGATGTTTTAACCCTGTACATCTGCAACTCCCATTTCTACCACAATAAA
1 ATAAAATGAACTTAACAGATGTTTTAAACCTGTACATCTGCAACTCCCATTTCTAACAAAATAAA
*
61164 CTAGCTTTATACAAAAAGAGAACTCTC
66 CAAGCTTTATACAAAAAGAGAACTCTC
* *
61191 ATAAAATGAACTTAACCA-ATGTTTTAAACCTGTACATCTGCACCTCCCATTTCTAACAAAATAG
1 ATAAAATGAACTTAA-CAGATGTTTTAAACCTGTACATCTGCAACTCCCATTTCTAACAAAATAA
61255 ACAAGCTTTATACAAAAAGAGAACTCT
65 ACAAGCTTTATACAAAAAGAGAACTCT
61282 TCCAGAAAAG
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 81 0.98
93 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (92 bp):
ATAAAATGAACTTAACAGATGTTTTAAACCTGTACATCTGCAACTCCCATTTCTAACAAAATAAA
CAAGCTTTATACAAAAAGAGAACTCTC
Found at i:67001 original size:20 final size:20
Alignment explanation
Indices: 66959--67001 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
66949 CTCTTTACTA
* *
66959 GTTTTATCAAATTGAAATAT
1 GTTTTATCAAATTCAAACAT
* *
66979 GTTTTGTCAAATTCAAACCT
1 GTTTTATCAAATTCAAACAT
66999 GTT
1 GTT
67002 ATATTATCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (20 bp):
GTTTTATCAAATTCAAACAT
Found at i:67003 original size:196 final size:194
Alignment explanation
Indices: 66676--67366 Score: 820
Period size: 198 Copynumber: 3.5 Consensus size: 194
66666 ATTTTTTATA
* * *
66676 TCTTTTAAATTCCTAAAGTACCGATACTATGGTACATATACTTATAAATGTATCGAT---AAGTT
1 TCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTT
* * * * * * * *
66738 CAATAATTCCGATAGCACTTTATCGGTTATGTCAAAGTGAAACTGGTTTTGTCAAATTTCAATCT
66 CAACAATTCCGATAGCTCTTTACCAGTTTTGTCAAATTGAAA-TTGTTTTGTCAAATTTCAACCT
* * *
66803 GTTATATTGTCATGTATTGATACATGTGTCTAGGGTATTGATACTTTATAGATGCTATTATTGCA
130 GTTATATTGTCATGTATCGATACATGTGTGTAAGGTATTGATACTTTATAG--GCTATTATTGCA
66868 AT
193 AT
* *
66870 TCTTTTAAATTCCTAAAGTACCGATA-TTTTGTACATATACTTATAAAAGTGTCGATACAAATTT
1 TCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTT
* * * * *
66934 CAACCATTTCGTTAGCTCTTTACTAGTTTTATCAAATTGAAATATGTTTTGTCAAA-TTCAAACC
66 CAACAATTCCGATAGCTCTTTACCAGTTTTGTCAAATTGAAAT-TGTTTTGTCAAATTTC-AACC
* *
66998 TGTTATATTATCATGTATCGATACATGTGTGTAAGGTATCGATACTTTATAGGCATTATTATTGC
129 TGTTATATTGTCATGTATCGATACATGTGTGTAAGGTATTGATACTTTATAGGC--TATTATTGC
67063 AAT
192 AAT
* * ** * *
67066 TATTTTAAATTCATAAAGTAATGATACTTTGGTGCATATACTTATAAACGTATCGATACAAATTT
1 TCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTT
* * * * * * * *
67131 CAACAATTCCGGTAGATCTTTACCGGTTTTTTTAAAAATGAAACCTGGTTTGTCAAATTTCAACC
66 CAACAATTCCGATAGCTCTTTACCAG-TTTTGTCAAATTGAAA-TTGTTTTGTCAAATTTCAACC
* * *
67196 TGTTATATTGTCATGTATCGATACATGTGTGTAAGGTA-TGAATACTTTATAGCCACTACTATTT
129 TGTTATATTGTCATGTATCGATACATGTGTGTAAGGTATTG-ATACTTTATAG--GCTATTATTG
67260 CAAT
191 CAAT
* * *
67264 TCTTTTAAATTCCTACAGTACCGATACTTTGGTACATATACCTATAAACA-TATCGAAACAAATT
1 TCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAA-AGTATCGATACAAATT
*
67328 TCAACAATTTCGATAGCTCTTTACCAGTTTTGTCAAATT
65 TCAACAATTCCGATAGCTCTTTACCAGTTTTGTCAAATT
67367 TCATCCGGTT
Statistics
Matches: 419, Mismatches: 63, Indels: 27
0.82 0.12 0.05
Matches are distributed among these distances:
193 26 0.06
194 28 0.07
195 4 0.01
196 130 0.31
197 64 0.15
198 163 0.39
199 3 0.01
200 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (194 bp):
TCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTT
CAACAATTCCGATAGCTCTTTACCAGTTTTGTCAAATTGAAATTGTTTTGTCAAATTTCAACCTG
TTATATTGTCATGTATCGATACATGTGTGTAAGGTATTGATACTTTATAGGCTATTATTGCAAT
Found at i:67561 original size:26 final size:25
Alignment explanation
Indices: 67514--67562 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
67504 TTTTAAATCA
* * *
67514 ATAAAGTATTGATACTTTTATACAT
1 ATAAAGTATCGATACATGTATACAT
67539 ATAAAGGTATCGATACATGTATAC
1 ATAAA-GTATCGATACATGTATAC
67563 TTTTAACGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (25 bp):
ATAAAGTATCGATACATGTATACAT
Found at i:70536 original size:14 final size:14
Alignment explanation
Indices: 70517--70552 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
70507 AAAATCGGAC
70517 AACAGATTCTGCAA
1 AACAGATTCTGCAA
70531 AACAGATTCTGCAA
1 AACAGATTCTGCAA
*
70545 ATCAGATT
1 AACAGATT
70553 ATGTTGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (14 bp):
AACAGATTCTGCAA
Found at i:71885 original size:47 final size:45
Alignment explanation
Indices: 71791--71916 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
71781 ATAACCATGC
* * *
71791 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
*
71835 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGAA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
*
71882 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
71917 AGATTTTATA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 22 0.30
45 11 0.15
46 1 0.01
47 40 0.54
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:74729 original size:3 final size:3
Alignment explanation
Indices: 74721--74756 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
74711 CAGAAGGAAA
74721 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
74757 TCAAGCAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:79151 original size:45 final size:43
Alignment explanation
Indices: 79054--79164 Score: 134
Period size: 45 Copynumber: 2.5 Consensus size: 43
79044 GGTAACCATG
* *
79054 AAAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGA
1 AAAATAAGCTTACGAGCTTA-TGAATAATGGCAAGTATATTGGA
* * *
79098 AAAATAAGCTTACGAGCTTATGAATTTAAATGG-TAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGAA--T-AATGGCAAGTATATTGGA
79143 AAAATAAGCTTACGAGCTTATG
1 AAAATAAGCTTACGAGCTTATG
79165 GGTAAATGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
43 3 0.05
44 19 0.32
45 32 0.54
46 5 0.08
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (43 bp):
AAAATAAGCTTACGAGCTTATGAATAATGGCAAGTATATTGGA
Done.