Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002087.1 Hibiscus syriacus cultivar Beakdansim tig00004259_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: 78744
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2689 original size:30 final size:31
Alignment explanation
Indices: 2648--2705 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
2638 GTAACTTTTG
2648 TTTATTTATGTTTATTAAATTAAATTTTATA
1 TTTATTTATGTTTATTAAATTAAATTTTATA
*
2679 TTTA-TTATGTTTATTAAATTAATTTTT
1 TTTATTTATGTTTATTAAATTAAATTTT
2706 CGATAAGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTATTTATGTTTATTAAATTAAATTTTATA
Found at i:3721 original size:16 final size:16
Alignment explanation
Indices: 3698--3740 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
3688 TAATATATAT
3698 TCAGGTAAATATCAAA
1 TCAGGTAAATATCAAA
* *
3714 TCATGTAAATATCATA
1 TCAGGTAAATATCAAA
3730 TCAGGTAAATA
1 TCAGGTAAATA
3741 ACAAGTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (16 bp):
TCAGGTAAATATCAAA
Found at i:4295 original size:27 final size:27
Alignment explanation
Indices: 4257--4340 Score: 159
Period size: 27 Copynumber: 3.1 Consensus size: 27
4247 GTGGTGGCCG
*
4257 GGTAAAACGGAGTGTTTTGAGCTAGCT
1 GGTAAAACGGAGTGTTTTGAGGTAGCT
4284 GGTAAAACGGAGTGTTTTGAGGTAGCT
1 GGTAAAACGGAGTGTTTTGAGGTAGCT
4311 GGTAAAACGGAGTGTTTTGAGGTAGCT
1 GGTAAAACGGAGTGTTTTGAGGTAGCT
4338 GGT
1 GGT
4341 TGAGCGAAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.25, C:0.08, G:0.37, T:0.30
Consensus pattern (27 bp):
GGTAAAACGGAGTGTTTTGAGGTAGCT
Found at i:24094 original size:23 final size:23
Alignment explanation
Indices: 24061--24112 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
24051 TCTAGGATAA
* * *
24061 ATATAATATTTTTTATATTAATGAT
1 ATATAAT-TTATTTAAAATAAT-AT
24086 ATATAATTTATTTAAAATAATAT
1 ATATAATTTATTTAAAATAATAT
24109 ATAT
1 ATAT
24113 TTTAGATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 11 0.46
25 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATAATTTATTTAAAATAATAT
Found at i:24122 original size:21 final size:21
Alignment explanation
Indices: 24084--24123 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24074 TATATTAATG
**
24084 ATATATAATTTATTTAAAATA
1 ATATATAATTTAGATAAAATA
*
24105 ATATATATTTTAGATAAAA
1 ATATATAATTTAGATAAAA
24124 GTAGAAGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATATAATTTAGATAAAATA
Found at i:24786 original size:41 final size:40
Alignment explanation
Indices: 24719--24817 Score: 153
Period size: 41 Copynumber: 2.5 Consensus size: 40
24709 TTGGGTAAGC
* *
24719 AGTACCGATATTGTTCTTATAGGATCGATACCTCCTGAAT
1 AGTACCGATATTGTTCTTACAGGATCGATACCGCCTGAAT
* *
24759 TGTACACGATATTGTTCTTACATGATCGATACCGCCTGAAT
1 AGTAC-CGATATTGTTCTTACAGGATCGATACCGCCTGAAT
24800 AGTACCGATATTGTTCTT
1 AGTACCGATATTGTTCTT
24818 GCAGTATCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 17 0.32
41 36 0.68
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (40 bp):
AGTACCGATATTGTTCTTACAGGATCGATACCGCCTGAAT
Found at i:27729 original size:39 final size:39
Alignment explanation
Indices: 27670--27771 Score: 109
Period size: 39 Copynumber: 2.7 Consensus size: 39
27660 TAGATTTTTT
* ** **
27670 ATTCTTAA-TTCCTAAATTATTTCACTCTAGCATTATAA
1 ATTCTTAATTTCTTAAATTATTTCACAATAAAATTATAA
* * *
27708 TTTCTTAATTTCTTAAATTATTTAACAATAAAATTCTAA
1 ATTCTTAATTTCTTAAATTATTTCACAATAAAATTATAA
*
27747 ATTATTAATTTCTT-AATTATTTCAC
1 ATTCTTAATTTCTTAAATTATTTCAC
27772 CCTAAAAATC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 17 0.33
39 35 0.67
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.49
Consensus pattern (39 bp):
ATTCTTAATTTCTTAAATTATTTCACAATAAAATTATAA
Found at i:27778 original size:38 final size:38
Alignment explanation
Indices: 27674--27790 Score: 117
Period size: 38 Copynumber: 3.1 Consensus size: 38
27664 TTTTTTATTC
* * * ** * * *
27674 TTAATTCCTAAATTATTTCACTCTAGCATTATAATTTC
1 TTAATTTCTTAATTATTTCACACTAAAATTCTAAATTA
* *
27712 TTAATTTCTTAAATTATTTAACAATAAAATTCTAAATTA
1 TTAATTTCTT-AATTATTTCACACTAAAATTCTAAATTA
* *
27751 TTAATTTCTTAATTATTTCACCCTAAAAATCTAAATTA
1 TTAATTTCTTAATTATTTCACACTAAAATTCTAAATTA
27789 TT
1 TT
27791 CCTCAAATTA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 34 0.53
39 30 0.47
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (38 bp):
TTAATTTCTTAATTATTTCACACTAAAATTCTAAATTA
Found at i:29080 original size:2 final size:2
Alignment explanation
Indices: 29073--29110 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
29063 CCGTCAGTAC
29073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
29111 AAAGAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30061 original size:31 final size:31
Alignment explanation
Indices: 29984--30054 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
29974 GTTTTAAAAA
* *
29984 TAACAAATTAGTCATTAACATTAACGATTTG
1 TAACAAAATAGTCACTAACATTAACGATTTG
* * *
30015 TAATAAAATAGTCACTAACGTTATCGATTTG
1 TAACAAAATAGTCACTAACATTAACGATTTG
30046 TAACAAAAT
1 TAACAAAAT
30055 GATCACTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
TAACAAAATAGTCACTAACATTAACGATTTG
Found at i:30685 original size:31 final size:31
Alignment explanation
Indices: 30650--30708 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
30640 ATAAAGGTGA
*
30650 AGTGACCA-TTTTGTTACAAATTGATAACTGT
1 AGTGA-CAGTTTTGTTACAAATCGATAACTGT
30681 AGTGACAGTTTTGTTACAAATCGATAAC
1 AGTGACAGTTTTGTTACAAATCGATAAC
30709 GTTAGTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (31 bp):
AGTGACAGTTTTGTTACAAATCGATAACTGT
Found at i:32599 original size:92 final size:92
Alignment explanation
Indices: 32442--32614 Score: 267
Period size: 92 Copynumber: 1.9 Consensus size: 92
32432 ATTTTCTTGA
32442 GATAGATTTTCGACGACTCCTTACGTATTCAAGATCTTTTGGTCACCTGTATCCTTAAATACAAC
1 GATAGATTTTCGACGACTCCTTACGTATTCAAGATCTTTTGGTCACCTGTATCCTTAAATACAAC
32507 AACTCGATTCGAGATCGTTTGCATATT
66 AACTCGATTCGAGATCGTTTGCATATT
* * * * * * *
32534 GATAGATTTTTGGCGACTCCTTAGGTGTTCAAGATCTTTTGGTTATCTGTCTCC-TAAGATACAA
1 GATAGATTTTCGACGACTCCTTACGTATTCAAGATCTTTTGGTCACCTGTATCCTTAA-ATACAA
32598 CAACTCGATTCGAGATC
65 CAACTCGATTCGAGATC
32615 ACAAACTATT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 3 0.04
92 70 0.96
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (92 bp):
GATAGATTTTCGACGACTCCTTACGTATTCAAGATCTTTTGGTCACCTGTATCCTTAAATACAAC
AACTCGATTCGAGATCGTTTGCATATT
Found at i:32819 original size:34 final size:34
Alignment explanation
Indices: 32774--32838 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
32764 AGTCAAACAT
*
32774 ATATTTTTTAATATTCAAAT-TTAAAAAGATAATA
1 ATATCTTTTAAT-TTCAAATATTAAAAAGATAATA
* *
32808 ATATCTTTTAATTTGAAATATTCAAAAGATA
1 ATATCTTTTAATTTCAAATATTAAAAAGATA
32839 TAAACAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 21 0.78
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (34 bp):
ATATCTTTTAATTTCAAATATTAAAAAGATAATA
Found at i:32860 original size:63 final size:65
Alignment explanation
Indices: 32792--32927 Score: 145
Period size: 65 Copynumber: 2.1 Consensus size: 65
32782 TAATATTCAA
*
32792 ATTTAAAAAGATAAT-AATA-TCTTTTAATTTG-AAATATTCAAAAG-ATATAAACAATTTTTTA
1 ATTTAAAAAGA-AATAAATATTATTTTAA-TTGAAAATATTCAAAAGTATATAAACAATTTTTTA
*
32853 TT
64 AT
*** * * **
32855 ATTTAAACTTAAATAAATATTATTTTAATTGAAAATATTTAATAGTATATAATTAATTTTTTAAT
1 ATTTAAAAAGAAATAAATATTATTTTAATTGAAAATATTCAAAAGTATATAAACAATTTTTTAAT
32920 ATTTAAAA
1 ATTTAAAA
32928 TTAAATAGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
62 3 0.05
63 15 0.25
64 18 0.31
65 23 0.39
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (65 bp):
ATTTAAAAAGAAATAAATATTATTTTAATTGAAAATATTCAAAAGTATATAAACAATTTTTTAAT
Found at i:32923 original size:65 final size:64
Alignment explanation
Indices: 32813--32934 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 64
32803 TAATAATATC
* *
32813 TTTTAATTTGAAATATTCAAAAGATATAAACAATTTTTTATTATTTAAACTTAAATAAATATTA
1 TTTTAATTTGAAATATTCAAAAGATATAAACAATTTTTTAATATTTAAAATTAAATAAATATTA
* * **
32877 TTTTAA-TTGAAAATATTTAATAGTATATAATTAATTTTTTAATATTTAAAATTAAATA
1 TTTTAATTTG-AAATATTCAAAAG-ATATAAACAATTTTTTAATATTTAAAATTAAATA
32935 GATAGCAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 3 0.06
64 17 0.34
65 30 0.60
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (64 bp):
TTTTAATTTGAAATATTCAAAAGATATAAACAATTTTTTAATATTTAAAATTAAATAAATATTA
Found at i:39075 original size:19 final size:19
Alignment explanation
Indices: 39051--39095 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
39041 AGAGCAGCTG
39051 AAATGTTTGATGAAATGAC
1 AAATGTTTGATGAAATGAC
*
39070 AAATGTTTGATGAAGTGAC
1 AAATGTTTGATGAAATGAC
39089 AAATGTT
1 AAATGTT
39096 GTAACTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (19 bp):
AAATGTTTGATGAAATGAC
Found at i:40231 original size:6 final size:6
Alignment explanation
Indices: 40222--40246 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40212 ATATCTTAAC
40222 CATGGA CATGGA CATGGA CATGGA C
1 CATGGA CATGGA CATGGA CATGGA C
40247 TTGTGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (6 bp):
CATGGA
Found at i:41032 original size:10 final size:10
Alignment explanation
Indices: 41017--41042 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41007 AATACACATT
41017 CATATATATA
1 CATATATATA
41027 CATATATATA
1 CATATATATA
41037 CATATA
1 CATATA
41043 AGAGGTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (10 bp):
CATATATATA
Found at i:48100 original size:30 final size:30
Alignment explanation
Indices: 48064--48161 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
48054 GTCATGAAAT
48064 TAGAATGTTTTAAAAGTTTGGGGACCAATA
1 TAGAATGTTTTAAAAGTTTGGGGACCAATA
* * * * * **
48094 TAGAATGAATGTCAAAGTTTGAGAATGAA-A
1 TAGAATG-TTTTAAAAGTTTGGGGACCAATA
* * *
48124 TTGAAATGTTTAAAAAGTTTGGGGACTAATA
1 TAG-AATGTTTTAAAAGTTTGGGGACCAATA
48155 TAGAATG
1 TAGAATG
48162 AATGTCAAAG
Statistics
Matches: 48, Mismatches: 17, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
30 27 0.56
31 21 0.44
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (30 bp):
TAGAATGTTTTAAAAGTTTGGGGACCAATA
Found at i:48113 original size:31 final size:31
Alignment explanation
Indices: 48076--48175 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
48066 GAATGTTTTA
48076 AAAGTTTGGGGACCAATATAGAATGAATGTC
1 AAAGTTTGGGGACCAATATAGAATGAATGTC
* * ** * * *
48107 AAAGTTTGAGAATGAA-ATTGAAATG--TTTAA
1 AAAGTTTGGGGACCAATATAG-AATGAATGT-C
*
48137 AAAGTTTGGGGACTAATATAGAATGAATGTC
1 AAAGTTTGGGGACCAATATAGAATGAATGTC
48168 AAAGTTTG
1 AAAGTTTG
48176 AGAATGAAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 10
0.68 0.19 0.14
Matches are distributed among these distances:
29 2 0.04
30 19 0.38
31 27 0.54
32 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (31 bp):
AAAGTTTGGGGACCAATATAGAATGAATGTC
Found at i:48234 original size:60 final size:60
Alignment explanation
Indices: 48057--48213 Score: 253
Period size: 61 Copynumber: 2.6 Consensus size: 60
48047 GTATGCTGTC
*
48057 ATGAAATT-AGAATGTTTTAAAAGTTTGGGGACCAATATAGAATGAATGTCAAAGTTTGAGA
1 ATGAAATTGA-AATG-TTTAAAAGTTTGGGGACTAATATAGAATGAATGTCAAAGTTTGAGA
48118 ATGAAATTGAAATGTTTAAAAAGTTTGGGGACTAATATAGAATGAATGTCAAAGTTTGAGA
1 ATGAAATTGAAATGTTT-AAAAGTTTGGGGACTAATATAGAATGAATGTCAAAGTTTGAGA
**
48179 ATGAAATTGAAATGTTTAAAAGTTTAAGGACTAAT
1 ATGAAATTGAAATGTTTAAAAGTTTGGGGACTAAT
48214 TTATAATAAT
Statistics
Matches: 91, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
60 19 0.21
61 71 0.78
62 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.32
Consensus pattern (60 bp):
ATGAAATTGAAATGTTTAAAAGTTTGGGGACTAATATAGAATGAATGTCAAAGTTTGAGA
Found at i:58910 original size:9 final size:8
Alignment explanation
Indices: 58888--58938 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
58878 TGTTTCAACA
58888 TTTTGGAT
1 TTTTGGAT
58896 ATTTTGGAT
1 -TTTTGGAT
58905 TGTTT-GAT
1 T-TTTGGAT
58913 TTTGTGGAT
1 TTT-TGGAT
*
58922 TGTTGGA-
1 TTTTGGAT
58929 TTTTGGAT
1 TTTTGGAT
58937 TT
1 TT
58939 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:58922 original size:17 final size:17
Alignment explanation
Indices: 58890--58933 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
58880 TTTCAACATT
58890 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
58907 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
58924 TTGGATTTTG
1 TTGGATTTTG
58934 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:65077 original size:17 final size:18
Alignment explanation
Indices: 65055--65110 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
65045 TGAGGGTAGC
* *
65055 AGGTGAG-GGGGAGGGAG
1 AGGTGAGAGGTGAGAGAG
*
65072 AGGTGAGAGGTGAGAGGG
1 AGGTGAGAGGTGAGAGAG
*
65090 AGG-GAGAGGTGAGAGAA
1 AGGTGAGAGGTGAGAGAG
65107 AGGT
1 AGGT
65111 TTTATATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 22 0.69
18 10 0.31
ACGTcount: A:0.30, C:0.00, G:0.61, T:0.09
Consensus pattern (18 bp):
AGGTGAGAGGTGAGAGAG
Found at i:65082 original size:24 final size:24
Alignment explanation
Indices: 65055--65104 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
65045 TGAGGGTAGC
*
65055 AGGTGAGGGGGAGGGAGAGGTGAG
1 AGGTGAGAGGGAGGGAGAGGTGAG
65079 AGGTGAGAGGGAGGGAGAGGTGAG
1 AGGTGAGAGGGAGGGAGAGGTGAG
65103 AG
1 AG
65105 AAAGGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.64, T:0.08
Consensus pattern (24 bp):
AGGTGAGAGGGAGGGAGAGGTGAG
Found at i:65682 original size:23 final size:23
Alignment explanation
Indices: 65650--65710 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
65640 CTGAATGATT
*
65650 CAGTGCTGACTGATTTAGCAAAA
1 CAGTGTTGACTGATTTAGCAAAA
*
65673 TAGTGTTGACTGATTTAGCAAAA
1 CAGTGTTGACTGATTTAGCAAAA
*
65696 CAGTGTTGAATGATT
1 CAGTGTTGACTGATT
65711 CATCACAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (23 bp):
CAGTGTTGACTGATTTAGCAAAA
Found at i:66298 original size:37 final size:37
Alignment explanation
Indices: 66222--66298 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
66212 TTTTTATATT
*
66222 TTTAATTTTGTAAACAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
* * * *
66259 TTTACTTTTTTAAAGAAAA-TATATAAATATTTTTCAA
1 TTTAATTTTGTAAACAAAATTATATAAATA-TTATCAA
66296 TTT
1 TTT
66299 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 10 0.29
37 24 0.71
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
Found at i:67468 original size:45 final size:44
Alignment explanation
Indices: 67405--67493 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 44
67395 GTTTGGTTCG
67405 CGAAAAAAATATTATCAA-GAGGAATAATATTTTCTGAAATTGCA
1 CGAAAAAAATATTATCAAGGA-GAATAATATTTTCTGAAATTGCA
67449 CGAAAAAGAATATTATCAAGGAGAATAATATTTTCTGAAATTGCA
1 CGAAAAA-AATATTATCAAGGAGAATAATATTTTCTGAAATTGCA
67494 TTTTTACGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
44 7 0.16
45 34 0.79
46 2 0.05
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (44 bp):
CGAAAAAAATATTATCAAGGAGAATAATATTTTCTGAAATTGCA
Found at i:71234 original size:73 final size:72
Alignment explanation
Indices: 71104--71241 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 72
71094 AGTTAATTAG
* * * *
71104 GAAATTAAAATATCGATAGTTATGCTTTAATGTTCAATACATTTAAATTTTAAAAAGTTTATGAA
1 GAAATTAAAATATCGATACTTATGCTTTAATGTTCAATAAATTTAAATTTGAAAAAGTATATGAA
71169 AGTAATC
66 AGTAATC
* * *
71176 GAAAGTTAAAATATTGATACTTATGCTTTAATGTTCAATAAATTTACATTTGACAAAGTATATGA
1 GAAA-TTAAAATATCGATACTTATGCTTTAATGTTCAATAAATTTAAATTTGAAAAAGTATATGA
71241 A
65 A
71242 TATAATACTG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
72 4 0.07
73 54 0.93
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (72 bp):
GAAATTAAAATATCGATACTTATGCTTTAATGTTCAATAAATTTAAATTTGAAAAAGTATATGAA
AGTAATC
Found at i:76577 original size:23 final size:23
Alignment explanation
Indices: 76533--76577 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
76523 CTCGATTTGA
*
76533 AAAAAATAAATGATTTATAAATT
1 AAAAAATAAATGATTTAAAAATT
*
76556 AAAAATTAAATCGA-TTAAAAAT
1 AAAAAATAAAT-GATTTAAAAAT
76578 ATTATCTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
AAAAAATAAATGATTTAAAAATT
Found at i:77083 original size:5 final size:5
Alignment explanation
Indices: 77063--77119 Score: 51
Period size: 5 Copynumber: 10.4 Consensus size: 5
77053 CAAATTACTG
* *
77063 ATAAA ATTATA ATAAA ATAAA ATAAA ATTTCAAA ATTATA ATAAA ATAAA
1 ATAAA A-TAAA ATAAA ATAAA ATAAA A--T-AAA A-TAAA ATAAA ATAAA
77113 ATAAA AT
1 ATAAA AT
77120 TTCAAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 30 0.68
6 7 0.16
7 3 0.07
8 4 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (5 bp):
ATAAA
Found at i:77101 original size:29 final size:29
Alignment explanation
Indices: 77065--77144 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
77055 AATTACTGAT
77065 AAAATTATAATAAAATAAAATAAAATTTC
1 AAAATTATAATAAAATAAAATAAAATTTC
77094 AAAATTATAATAAAATAAAATAAAATTTC
1 AAAATTATAATAAAATAAAATAAAATTTC
*
77123 AAAATTA-AA-AAAATATAATAAA
1 AAAATTATAATAAAATAAAATAAA
77145 TAATCATAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 12 0.24
28 2 0.04
29 36 0.72
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (29 bp):
AAAATTATAATAAAATAAAATAAAATTTC
Found at i:77140 original size:37 final size:34
Alignment explanation
Indices: 77073--77160 Score: 90
Period size: 37 Copynumber: 2.5 Consensus size: 34
77063 ATAAAATTAT
** *
77073 AATAAAATAAAATAAAATTTCAAAATTATAATAA
1 AATAAAATAAAATAAAATTAAAAAAATATAATAA
77107 AATAAAATAAAATTTCAAAATTAAAAAAATATAAT-A
1 AATAAAATAAAA--T-AAAATTAAAAAAATATAATAA
*
77143 AATAATCAT-AAATAAAAT
1 AATAA-AATAAAATAAAAT
77161 ATATATTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
33 5 0.11
34 13 0.28
36 10 0.22
37 18 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (34 bp):
AATAAAATAAAATAAAATTAAAAAAATATAATAA
Done.