Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006948.1 Hibiscus syriacus cultivar Beakdansim tig00017853_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: 63549
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:6287 original size:77 final size:74
Alignment explanation
Indices: 6157--6372 Score: 283
Period size: 77 Copynumber: 2.9 Consensus size: 74
6147 ATTTTAAACA
* *
6157 TTATATTTTATCTTTGTTTTAGGCATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTA
*
6222 GTATATTATTT
65 GAATATTA-TT
*
6233 TTATATTTTATCTTTGTTTTAGGTATTTTTAGTTTAAATATGTTTTAGTATTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGGTA-TTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTT
6298 AGAATATTATT
64 AGAATATTATT
* * * * *
6309 TTAAATATTAT-TATT-TTTTAGATATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCT-TTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAAGATTT
6372 A
64 A
6373 AGATGTTTTA
Statistics
Matches: 128, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
73 5 0.04
74 33 0.26
75 9 0.07
76 37 0.29
77 44 0.34
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (74 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGATTTAG
AATATTATT
Found at i:8052 original size:21 final size:21
Alignment explanation
Indices: 8010--8052 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
8000 TTTCTGGGCT
*
8010 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
8031 AGGGGAATCGATACGCC-CTCA
1 AGGGGAATCGATAC-CCACTCA
8052 A
1 A
8053 ACGAATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:8104 original size:19 final size:19
Alignment explanation
Indices: 8080--8116 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8070 GAACGCTAGA
*
8080 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
8099 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
8117 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:8922 original size:103 final size:103
Alignment explanation
Indices: 8594--8914 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
8584 GTAGAGGGTC
8594 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
8659 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
8697 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
8762 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
8800 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTATGAATTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
8865 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGG
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
8903 TATGTGGTCCTT
1 TATGTGGTCCTT
8915 ATGGACATTA
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:8964 original size:23 final size:23
Alignment explanation
Indices: 8931--8993 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
8921 ATTATTATAT
8931 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
8954 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
8977 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
8994 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:14997 original size:21 final size:21
Alignment explanation
Indices: 14955--14997 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
14945 TTTCTGGGCT
*
14955 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
14976 AGGGGAATCGATACGCC-CTCA
1 AGGGGAATCGATAC-CCACTCA
14997 A
1 A
14998 ACGAATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:15050 original size:20 final size:20
Alignment explanation
Indices: 15025--15062 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15015 GAACGCTAGA
*
15025 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
15045 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
15063 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:15870 original size:103 final size:103
Alignment explanation
Indices: 15542--15858 Score: 598
Period size: 103 Copynumber: 3.1 Consensus size: 103
15532 GTAGAGGGTC
15542 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
15607 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
15645 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
15710 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
15748 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
15813 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
15851 TATGTGGT
1 TATGTGGT
15859 TCTTATGGAC
Statistics
Matches: 208, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:15912 original size:23 final size:23
Alignment explanation
Indices: 15879--15941 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
15869 ATTATTATAT
15879 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
15902 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
15925 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
15942 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:20213 original size:2 final size:2
Alignment explanation
Indices: 20208--20238 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20198 TTTGTGTGTG
*
20208 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20239 TAAAGACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20919 original size:115 final size:114
Alignment explanation
Indices: 20713--20946 Score: 414
Period size: 115 Copynumber: 2.0 Consensus size: 114
20703 TAAAAGGGTG
20713 AAAATTTGATAGATCCATTTACTATGTTGCTTTATTCCATTACATTTGAAAAGTTAGTCTTCAAC
1 AAAATTTGATAGATCCATTTACTATGTTGCTTTATTCCATTACATTTGAAAAGTTAGTCTTCAAC
*
20778 AATATATTATGTCATTTCAGAGGTCTTGAATGATACATTCATGAGATGAT
66 AATATATTATGTCATTTCAGAAGTCTTGAATGATACA-TCATGAGATGAT
* * *
20828 AAAATTTGATAGATCCATTTAGTATGTTGCTTTATTTCATTACATTTGAGAAGTTAGTCTTCAAC
1 AAAATTTGATAGATCCATTTACTATGTTGCTTTATTCCATTACATTTGAAAAGTTAGTCTTCAAC
*
20893 GATATATTATGTCATTTCAGAAGTCTTGAATGATACATCATGAGATGAT
66 AATATATTATGTCATTTCAGAAGTCTTGAATGATACATCATGAGATGAT
20942 AAAAT
1 AAAAT
20947 ACATGATGTA
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
114 17 0.15
115 97 0.85
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (114 bp):
AAAATTTGATAGATCCATTTACTATGTTGCTTTATTCCATTACATTTGAAAAGTTAGTCTTCAAC
AATATATTATGTCATTTCAGAAGTCTTGAATGATACATCATGAGATGAT
Found at i:26033 original size:43 final size:43
Alignment explanation
Indices: 25944--26172 Score: 128
Period size: 43 Copynumber: 5.3 Consensus size: 43
25934 TTCAACAAAA
** * * * **
25944 AAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAGC-C
1 AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTT-TCTTCAC
* *
25987 AAACGCCGCAATAGGCGTTGATGTTTAGCGGCGTTTTCTTCAC
1 AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTTTCTTCAC
* * * * * * * *
26030 AAACGCCGCAGTAGATGTTTATTTTTACCGTCGTTTT-TCCTAC
1 AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTTTCTTC-AC
* * * *
26073 AAACTCCGCAGA-AGATGTTGATATTTAGCGGCATTTTCCT-AC
1 AAACGCCGCA-ATAGACGTTGATGTTTAGCGGCATTTTCTTCAC
* * * *
26115 AAACGCCGTAGAATATGTC-TTGA-GATTTAGCGGCATTTTCGTCAA
1 AAACGCCG--CAATA-GACGTTGATG-TTTAGCGGCATTTTCTTCAC
26160 AAACGCCGCAATA
1 AAACGCCGCAATA
26173 TGTCTTGAGA
Statistics
Matches: 144, Mismatches: 32, Indels: 20
0.73 0.16 0.10
Matches are distributed among these distances:
42 13 0.09
43 99 0.69
44 22 0.15
45 10 0.07
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTTTCTTCAC
Found at i:26184 original size:43 final size:43
Alignment explanation
Indices: 26090--26196 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
26080 GCAGAAGATG
* * *
26090 TTGATATTTAGCGGCATTTTCCTACAAACGCCGTAGAATATGTC
1 TTGAGATTTAGCGGCATTTTCCTAAAAACGCCG-ACAATATGTC
*
26134 TTGAGATTTAGCGGCATTTTCGTCAAAAACGCCG-CAATATGTC
1 TTGAGATTTAGCGGCATTTTCCT-AAAAACGCCGACAATATGTC
* *
26177 TTGAGATTTCGCGGCGTTTT
1 TTGAGATTTAGCGGCATTTT
26197 TATCACAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 26 0.46
44 21 0.38
45 9 0.16
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (43 bp):
TTGAGATTTAGCGGCATTTTCCTAAAAACGCCGACAATATGTC
Found at i:26643 original size:21 final size:21
Alignment explanation
Indices: 26576--26637 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
26566 GCCACTGCCA
*
26576 CTGCTTCTCTCTCTGCTTCCG
1 CTGCTACTCTCTCTGCTTCCG
* **
26597 CTGCTGCTCTAGCTGCTTCCG
1 CTGCTACTCTCTCTGCTTCCG
26618 CTGCTACTCTCTCTGCTTCC
1 CTGCTACTCTCTCTGCTTCC
26638 ATTGCTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.03, C:0.42, G:0.16, T:0.39
Consensus pattern (21 bp):
CTGCTACTCTCTCTGCTTCCG
Found at i:32780 original size:19 final size:19
Alignment explanation
Indices: 32756--32796 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
32746 ATAAGGGATC
32756 GTTAAGGACAGAAAAGATG
1 GTTAAGGACAGAAAAGATG
32775 GTTAAGGACAGAAAAGATG
1 GTTAAGGACAGAAAAGATG
32794 GTT
1 GTT
32797 CCAACATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.32, T:0.20
Consensus pattern (19 bp):
GTTAAGGACAGAAAAGATG
Found at i:35521 original size:26 final size:28
Alignment explanation
Indices: 35478--35538 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
35468 CATACTTCTT
* * *
35478 CATTGTTAATATTTTAATATTTTT-ATA
1 CATTTTTAATACTCTAATATTTTTAATA
35505 -ATTTTTAATACTCTAATATTTTTAATA
1 CATTTTTAATACTCTAATATTTTTAATA
35532 CATTTTT
1 CATTTTT
35539 CTTATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 20 0.69
27 3 0.10
28 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (28 bp):
CATTTTTAATACTCTAATATTTTTAATA
Found at i:36898 original size:13 final size:14
Alignment explanation
Indices: 36872--36903 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36862 GATTTTAAAA
36872 GTAATTTGAAAATT
1 GTAATTTGAAAATT
36886 GTAATTT-AAAATT
1 GTAATTTGAAAATT
36899 -TAATT
1 GTAATT
36904 GTTTGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 6 0.33
14 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
GTAATTTGAAAATT
Found at i:42577 original size:14 final size:14
Alignment explanation
Indices: 42558--42585 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42548 GGTCAACAAA
42558 GTCACTCAATTATC
1 GTCACTCAATTATC
42572 GTCACTCAATTATC
1 GTCACTCAATTATC
42586 TTTCTAGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
GTCACTCAATTATC
Found at i:43170 original size:23 final size:22
Alignment explanation
Indices: 43085--43171 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 22
43075 ATCAGAACAA
43085 AAAGAAAAAAG--AGAAAAAAC
1 AAAGAAAAAAGTAAGAAAAAAC
* * *
43105 AAAGAAAAAAGCAAAGAGAAAAT
1 AAAGAAAAAAG-TAAGAAAAAAC
43128 AAA-AAAAAAGATAA-ACAAAAAC
1 AAAGAAAAAAG-TAAGA-AAAAAC
*
43150 AAAGGAAAAAGTGAAGAAAAAA
1 AAAGAAAAAAGT-AAGAAAAAA
43172 AGAAAACAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
20 11 0.21
21 1 0.02
22 17 0.32
23 23 0.43
24 1 0.02
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAGAAAAAAGTAAGAAAAAAC
Found at i:45291 original size:60 final size:59
Alignment explanation
Indices: 45154--45432 Score: 294
Period size: 60 Copynumber: 4.6 Consensus size: 59
45144 CAAAAGATTG
* **** ** *
45154 GATTTCAACTTCACAACGAAGGATATCCAACTC-AGGCCAA-ACAAT-ATTCAAGATTA
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATATTA
* *
45210 GATTTCAACTTCAAAATGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATACTTA
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATA-TTA
* *
45270 GATTTCAACTTCACAACGAAGGATATCCAACTCAAATCCAATTTGGTGAAACTTACTCAATATTG
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTG-AA---A--CAATATTA
* * * * * *
45335 GATTTCAACTTCACGATGAAGGATATCCAACTCAAAACCATTTTGGTGAAACAATCCTTG
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAAT-ATTA
*
45395 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGC
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
45433 TCAACTCCAC
Statistics
Matches: 189, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
56 31 0.16
57 6 0.03
58 1 0.01
59 9 0.05
60 85 0.45
61 3 0.02
64 3 0.02
65 46 0.24
66 5 0.03
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.27
Consensus pattern (59 bp):
GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAATATTA
Found at i:45557 original size:124 final size:123
Alignment explanation
Indices: 45392--45735 Score: 526
Period size: 124 Copynumber: 2.8 Consensus size: 123
45382 GAAACAATCC
* *
45392 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTCCACAATGAAGAAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAG-AGCCAT
* ** * *
45457 CCACGATTTCAACTTCACGACGAAGGATATTGTACCTATAAGCAGCATCCATCTCTAGA
65 CCACGATTTTAACTTCACGACGAAGGATATCATACCCACAAGCAGCATCCATCTCTAGA
* *
45516 TTGGATTTTAACTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAA-GAGCCAT
* * * * *
45581 ACACGATTTTAACTTCACGGCAAAGGATATCATGCCCACAAGTAGCATCCATCTCTAGA
65 CCACGATTTTAACTTCACGACGAAGGATATCATACCCACAAGCAGCATCCATCTCTAGA
*
45640 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAA-GAGCCAT
45705 CCACGATTTTAACTTCACGACGAAGGATATC
65 CCACGATTTTAACTTCACGACGAAGGATATC
45736 GTGCCTAACG
Statistics
Matches: 198, Mismatches: 21, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
124 197 0.99
125 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (123 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGAGCCATC
CACGATTTTAACTTCACGACGAAGGATATCATACCCACAAGCAGCATCCATCTCTAGA
Found at i:47672 original size:26 final size:28
Alignment explanation
Indices: 47625--47676 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
47615 CCCTTACTCT
47625 AACACTTCTCAACACTTTTCCCCTTTAA
1 AACACTTCTCAACACTTTTCCCCTTTAA
47653 AACACTT-T-AACA-TTTCTCCCCTTT
1 AACACTTCTCAACACTTT-TCCCCTTT
47677 TTTGTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.13
26 12 0.52
27 1 0.04
28 7 0.30
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (28 bp):
AACACTTCTCAACACTTTTCCCCTTTAA
Found at i:59734 original size:27 final size:27
Alignment explanation
Indices: 59692--59752 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
59682 GCCTGCTTTG
*
59692 GTTGGGTCTTGCTGGGTTAGGCACCC-
1 GTTGGGCCTTGCTGGGTTAGGCACCCA
*
59718 GATTGGGCCTTGTTGGGTTAGGCACCCA
1 G-TTGGGCCTTGCTGGGTTAGGCACCCA
59746 GTTGGGC
1 GTTGGGC
59753 TCCCTTATCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 1 0.03
27 29 0.94
28 1 0.03
ACGTcount: A:0.10, C:0.21, G:0.39, T:0.30
Consensus pattern (27 bp):
GTTGGGCCTTGCTGGGTTAGGCACCCA
Found at i:59815 original size:11 final size:11
Alignment explanation
Indices: 59801--59842 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
59791 CTAAAAATGG
59801 AATAAAAAATA
1 AATAAAAAATA
59812 AATAAACAAAATA
1 AAT-AA-AAAATA
59825 AATAAAAAATA
1 AATAAAAAATA
*
59836 CATAAAA
1 AATAAAA
59843 TAACCGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 15 0.54
12 4 0.14
13 9 0.32
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:59822 original size:13 final size:13
Alignment explanation
Indices: 59806--59830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59796 AATGGAATAA
59806 AAAATAAATAAAC
1 AAAATAAATAAAC
59819 AAAATAAATAAA
1 AAAATAAATAAA
59831 AAATACATAA
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:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAATAAAC
Found at i:59826 original size:20 final size:20
Alignment explanation
Indices: 59801--59845 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
59791 CTAAAAATGG
59801 AATAAA-AAATAAATAAACAA
1 AATAAATAAA-AAATAAACAA
* *
59821 AATAAATAAAAAATACATAA
1 AATAAATAAAAAATAAACAA
59841 AATAA
1 AATAA
59846 CCGATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (20 bp):
AATAAATAAAAAATAAACAA
Found at i:59985 original size:61 final size:60
Alignment explanation
Indices: 59918--60034 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 60
59908 TTCAAAAGTA
* * * *
59918 TTTTTTAAAAACTATATATTATACGGTTTTTAAAAAATATTTTTTAAAATCTATATTATACG
1 TTTTTAAAAAACCATATATTATAC-GTTTTCAAAAAATATTTTTCAAAA-CTATATTATACG
* *
59980 TTTTTAAAAAAACCATATATTATACGTTTTCAAAAACTGTTTTTCAAAACTATAT
1 TTTTT-AAAAAACCATATATTATACGTTTTCAAAAAATATTTTTCAAAACTATAT
60035 AATATATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 6 0.12
62 25 0.52
63 17 0.35
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.45
Consensus pattern (60 bp):
TTTTTAAAAAACCATATATTATACGTTTTCAAAAAATATTTTTCAAAACTATATTATACG
Found at i:59991 original size:37 final size:38
Alignment explanation
Indices: 59893--59990 Score: 130
Period size: 37 Copynumber: 2.6 Consensus size: 38
59883 CTAATATATA
* * *
59893 TATATATTATAC-TCTTTCAAAAGTATTTTTTAAAAAC
1 TATATATTATACGTTTTTAAAAAATATTTTTTAAAAAC
59930 TATATATTATACGGTTTTTAAAAAATATTTTTT-AAAA-
1 TATATATTATAC-GTTTTTAAAAAATATTTTTTAAAAAC
*
59967 TCTATATTATACGTTTTTAAAAAA
1 TATATATTATACGTTTTTAAAAAA
59991 ACCATATATT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
36 12 0.22
37 23 0.42
38 4 0.07
39 16 0.29
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (38 bp):
TATATATTATACGTTTTTAAAAAATATTTTTTAAAAAC
Found at i:60163 original size:36 final size:36
Alignment explanation
Indices: 60041--60172 Score: 174
Period size: 36 Copynumber: 3.6 Consensus size: 36
60031 ATATAATATA
* * * *
60041 TATATATATATATATATTTCAAAAAATGTTTTTCTAAT
1 TATATA-ATATATGT-TTTCAAAAATTGTTTTTCAAAC
* *
60079 TATATAATATATGTTTGCAAAAATTGTTTTTAAAAC
1 TATATAATATATGTTTTCAAAAATTGTTTTTCAAAC
*
60115 TATATATTATATGTTTTCAAAAATTGTTTTTCAAAC
1 TATATAATATATGTTTTCAAAAATTGTTTTTCAAAC
*
60151 TATATAATATATGTTTTTAAAA
1 TATATAATATATGTTTTCAAAA
60173 CATATTTTCA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
36 70 0.84
37 7 0.08
38 6 0.07
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (36 bp):
TATATAATATATGTTTTCAAAAATTGTTTTTCAAAC
Found at i:60186 original size:72 final size:72
Alignment explanation
Indices: 60041--60242 Score: 214
Period size: 72 Copynumber: 2.8 Consensus size: 72
60031 ATATAATATA
* ** *
60041 TATATATATATATATATTTCAAAAAATGTTTTTCTAATTATATAATATATGTTTGCAAAAATTGT
1 TATATAT-TATATAT-TTTCAAAAAATGTTTTTCAAATTATATAATATATGTTTTTAAAAATTAT
*
60106 TTTTAAAAC
64 TTTCAAAAC
* * *
60115 TATATATTATATGTTTTCAAAAATTGTTTTTCAAACTATATAATATATGTTTTTAAAACA-TATT
1 TATATATTATATATTTTCAAAAAATGTTTTTCAAATTATATAATATATGTTTTTAAAA-ATTATT
60179 TTCAAAAC
65 TTCAAAAC
* ** * * *
60187 --CATATTATATATTTTCAAAAACCGATTTTTAAAATTATATATTATATG-ATTTAAAA
1 TATATATTATATATTTTCAAAAAATG-TTTTTCAAATTATATAATATATGTTTTTAAAA
60243 TGTTTAAATT
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
70 27 0.25
71 20 0.18
72 49 0.45
73 7 0.06
74 7 0.06
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (72 bp):
TATATATTATATATTTTCAAAAAATGTTTTTCAAATTATATAATATATGTTTTTAAAAATTATTT
TCAAAAC
Found at i:61813 original size:2 final size:2
Alignment explanation
Indices: 61806--61836 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61796 TTTACTAGTT
61806 TC TC TC 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 TC TC TC T
61837 TTGTTTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:61976 original size:3 final size:3
Alignment explanation
Indices: 61968--62015 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
61958 AATCTTCATA
61968 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
62013 AAT
1 AAT
62016 GTAAAACAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:61997 original size:20 final size:20
Alignment explanation
Indices: 61972--62010 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
61962 TTCATAAATA
61972 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
61992 ATAATAATAATAATAATAA
1 ATAATAATAATAATAATAA
62011 CTAATGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Done.