Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002547.1 Hibiscus syriacus cultivar Beakdansim tig00005171_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: 66830
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:7004 original size:30 final size:30
Alignment explanation
Indices: 6968--7024 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6958 AAAATGGCTT
*
6968 CCTTCAAGAAGGACTATC-CGAAGAAGGATA
1 CCTTCAAGAAGGACCATCTC-AAGAAGGATA
*
6998 CCTTCAAGAGGGACCATCTCAAGAAGG
1 CCTTCAAGAAGGACCATCTCAAGAAGG
7025 TGCTTGTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.23, G:0.25, T:0.16
Consensus pattern (30 bp):
CCTTCAAGAAGGACCATCTCAAGAAGGATA
Found at i:7087 original size:30 final size:30
Alignment explanation
Indices: 7016--7174 Score: 218
Period size: 30 Copynumber: 5.4 Consensus size: 30
7006 AGGGACCATC
*
7016 TCAAGAAGGT-GCTTGTCGTGAAATGCCCCA
1 TCAAGAA-GTAGCTTGTCATGAAATGCCCCA
* *
7046 T---GAAGTTGCTTGTCAGGAAATGCCCCA
1 TCAAGAAGTAGCTTGTCATGAAATGCCCCA
* *
7073 TCAAGAAGTAGCTTGTCATGAAGTGCCGCA
1 TCAAGAAGTAGCTTGTCATGAAATGCCCCA
*
7103 TCAAGAAGTAGCTTGTCATGAAATGCCGCA
1 TCAAGAAGTAGCTTGTCATGAAATGCCCCA
*
7133 TCAAGAAGTAACTTGTCATGAAATGCCCCA
1 TCAAGAAGTAGCTTGTCATGAAATGCCCCA
7163 TCAAGAAGTAGC
1 TCAAGAAGTAGC
7175 CTCTCAAGAA
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.02
27 22 0.19
30 91 0.79
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (30 bp):
TCAAGAAGTAGCTTGTCATGAAATGCCCCA
Found at i:16726 original size:59 final size:63
Alignment explanation
Indices: 16663--16802 Score: 146
Period size: 64 Copynumber: 2.3 Consensus size: 63
16653 AGTTTAACTC
**
16663 ACTCAAATGGAAATTATT-T-AT-GTTTTA-TTATACAATGTTTATAATTTAATTAATTTCTA
1 ACTCAAATGGAAATTATTCTGATAGTTTTATTTATACAATGTGCATAATTTAATTAATTTCTA
* * * *
16722 ACTCAAAT-GAAAGATATTCGTGTTAGTTTTATTTATGCAATGTGCATAATTTATTTAATTTCTA
1 ACTCAAATGGAAA-TTATTC-TGATAGTTTTATTTATACAATGTGCATAATTTAATTAATTTCTA
** *
16786 TTTCAAATGAAAATTAT
1 ACTCAAATGGAAATTAT
16803 GCCAGCTAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
58 4 0.06
59 12 0.19
61 1 0.02
62 1 0.02
63 6 0.09
64 37 0.58
65 3 0.05
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.46
Consensus pattern (63 bp):
ACTCAAATGGAAATTATTCTGATAGTTTTATTTATACAATGTGCATAATTTAATTAATTTCTA
Found at i:20455 original size:6 final size:6
Alignment explanation
Indices: 20444--20468 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20434 ACTGCAGCTG
20444 GGGTTA GGGTTA GGGTTA GGGTTA G
1 GGGTTA GGGTTA GGGTTA GGGTTA G
20469 TTAGATGCCG
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:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGGTTA
Found at i:22501 original size:18 final size:17
Alignment explanation
Indices: 22474--22517 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
22464 ATTATCTATG
*
22474 TCCCGTAGGACCACTACA
1 TCCCGAAGGA-CACTACA
22492 TCCCGAAGG--ACTACA
1 TCCCGAAGGACACTACA
22507 TCCCGAAGGAC
1 TCCCGAAGGAC
22518 TATTATACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
18 8 0.35
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (17 bp):
TCCCGAAGGACACTACA
Found at i:22506 original size:15 final size:15
Alignment explanation
Indices: 22486--22519 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
22476 CCGTAGGACC
22486 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
22501 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
22516 ACTA
1 ACTA
22520 TTATACCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:22668 original size:23 final size:26
Alignment explanation
Indices: 22631--22681 Score: 81
Period size: 23 Copynumber: 2.1 Consensus size: 26
22621 TTCTCTTGTG
22631 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
22655 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
22680 AT
1 AT
22682 AACATATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.44
24 8 0.32
25 6 0.24
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:22681 original size:12 final size:12
Alignment explanation
Indices: 22664--22699 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
22654 TATCATGTTC
22664 TCATATCACATG
1 TCATATCACATG
* *
22676 TCATATAACATA
1 TCATATCACATG
22688 TCATATCACATG
1 TCATATCACATG
22700 AACATATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:23912 original size:29 final size:29
Alignment explanation
Indices: 23870--23930 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
23860 TATTCATTCA
23870 TTCTATTTTAATCACCAAAATCTGAAACT
1 TTCTATTTTAATCACCAAAATCTGAAACT
23899 TTCTATTTTAATCACCAAAATCTGAAACT
1 TTCTATTTTAATCACCAAAATCTGAAACT
23928 TTC
1 TTC
23931 CAATTTAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (29 bp):
TTCTATTTTAATCACCAAAATCTGAAACT
Found at i:23937 original size:29 final size:29
Alignment explanation
Indices: 23876--23942 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
23866 TTCATTCTAT
* *
23876 TTTAATCACCAAAATCTGAAACTTTCTAT
1 TTTAATCACCAAAATCTGAAACTTTCCAA
23905 TTTAATCACCAAAATCTGAAACTTTCCAA
1 TTTAATCACCAAAATCTGAAACTTTCCAA
*
23934 TTTAGTCAC
1 TTTAATCAC
23943 TAACCTGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTAATCACCAAAATCTGAAACTTTCCAA
Found at i:25718 original size:2 final size:2
Alignment explanation
Indices: 25711--25744 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25701 AAACTATAAA
25711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25745 TAATTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28605 original size:17 final size:19
Alignment explanation
Indices: 28564--28605 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28554 TTGGAGCCTT
* *
28564 AGTGCATCGGTGCACTAAG
1 AGTGCACCGATGCACTAAG
28583 AGTGCACCGATGCA-TAA-
1 AGTGCACCGATGCACTAAG
28600 AGTGCA
1 AGTGCA
28606 TTTGATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 12 0.57
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (19 bp):
AGTGCACCGATGCACTAAG
Found at i:28651 original size:45 final size:46
Alignment explanation
Indices: 28582--28688 Score: 132
Period size: 46 Copynumber: 2.3 Consensus size: 46
28572 GGTGCACTAA
* * *
28582 GAGTGCACCGATGCATAAAGTGCATTTGATG-TTTCA-AAATA-GTCT
1 GAGTGCATCGATGCATAAAGTGCATTCGATGTTTTCATAAA-ACCT-T
28627 GAGTGCATCGATGCATCAAA-TGCATTCGATGTTTTCATAAAACCTT
1 GAGTGCATCGATGCAT-AAAGTGCATTCGATGTTTTCATAAAACCTT
28673 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
28689 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
45 25 0.45
46 26 0.47
47 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAGTGCATTCGATGTTTTCATAAAACCTT
Found at i:28680 original size:46 final size:45
Alignment explanation
Indices: 28582--28688 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
28572 GGTGCACTAA
* * *
28582 GAGTGCACCGATGCATAAAGTGCATTTGATGTTTCAAAATAGTCT
1 GAGTGCATCGATGCATAAAGTGCATTCGATGTTTCAAAATACTCT
28627 GAGTGCATCGATGCATCAAA-TGCATTCGATGTTTTCATAAA-AC-CTT
1 GAGTGCATCGATGCAT-AAAGTGCATTCGATG-TTTCA-AAATACTC-T
28673 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
28689 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
45 26 0.47
46 26 0.47
47 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAGTGCATTCGATGTTTCAAAATACTCT
Found at i:30690 original size:13 final size:13
Alignment explanation
Indices: 30659--30684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30649 CAAAGACATC
30659 AAATTTAAAATTT
1 AAATTTAAAATTT
30672 AAATTTAAAATTT
1 AAATTTAAAATTT
30685 TGATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:31116 original size:20 final size:20
Alignment explanation
Indices: 31091--31142 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
31081 ACCCGACGGA
31091 TGCATCGATGCATGGCCTTG
1 TGCATCGATGCATGGCCTTG
*
31111 TGCATCGATGCATGGCTTTG
1 TGCATCGATGCATGGCCTTG
31131 TGCATCGATGCA
1 TGCATCGATGCA
31143 CATTCCAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATGGCCTTG
Found at i:31159 original size:23 final size:24
Alignment explanation
Indices: 31129--31191 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
31119 TGCATGGCTT
31129 TGTGCATCGATGCACATTCCA-GG
1 TGTGCATCGATGCACATTCCATGG
*
31152 TGTGCATC-AGTGCACCTT-CATGG
1 TGTGCATCGA-TGCACATTCCATGG
*
31175 TGT--ATCGATGTACATTC
1 TGTGCATCGATGCACATTC
31192 AAAGGGATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 9 0.27
22 4 0.12
23 20 0.61
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (24 bp):
TGTGCATCGATGCACATTCCATGG
Found at i:35301 original size:117 final size:118
Alignment explanation
Indices: 35081--35301 Score: 250
Period size: 117 Copynumber: 1.9 Consensus size: 118
35071 CTTTCAAATC
* * *
35081 AAAATTTTATTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGAGTT
1 AAAATTTTATTTTTCAAAACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
* *
35146 TATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAATTTTGTTTAATTTG
66 TATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAATTTTGTTTAATTTG
* * * * * * *
35199 AAAA-TTTCTTTTTCAAAATTTTCAGATTTTAGTTTTGAAAGCTCTAACTCTTTTTTCAACA-TT
1 AAAATTTTATTTTTCAAAACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
* * * **
35262 TCATTTTGTTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAA
66 T-ATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
35302 GATCATTTTT
Statistics
Matches: 84, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
116 3 0.04
117 73 0.87
118 8 0.10
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.49
Consensus pattern (118 bp):
AAAATTTTATTTTTCAAAACTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
TATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAATTTTGTTTAATTTG
Found at i:36671 original size:18 final size:19
Alignment explanation
Indices: 36623--36671 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
36613 TTGGAGCCTT
*
36623 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
36642 AGTGCATCGATGCA-TAA-
1 AGTGCATCGATGCACTAAG
36659 AGTGCATTCGATG
1 AGTGCA-TCGATG
36672 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 13 0.46
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:36765 original size:47 final size:47
Alignment explanation
Indices: 36641--36765 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 47
36631 GGTGCACTAA
* *
36641 GAGTGCATCGATGCATAAAGTGCATTCGATG--TTTCAAAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCT
* ** *
36686 GAGTGCATCGATGCATCAAATGCATTTAATGTTTTTTATAAA-ACCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTCA-AAATACCCT
*
36733 GAGTGTATCGATGCATAAAATGCATTCGATGTT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTT
36766 CAATTTAGTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 27 0.40
47 37 0.55
48 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (47 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCT
Found at i:42541 original size:2 final size:2
Alignment explanation
Indices: 42525--42707 Score: 99
Period size: 2 Copynumber: 103.5 Consensus size: 2
42515 TAATATAAAA
* *
42525 AT AT -T AT AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
42562 AT A- AT AT AT A- AT -T A- AT AT AA AG AA AT AT A- AA AT CT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
42598 AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
42634 -T AT AT AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42670 AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42708 ATAGGGGCGG
Statistics
Matches: 145, Mismatches: 12, Indels: 48
0.71 0.06 0.23
Matches are distributed among these distances:
1 24 0.17
2 121 0.83
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:42576 original size:59 final size:57
Alignment explanation
Indices: 42507--42709 Score: 184
Period size: 59 Copynumber: 3.5 Consensus size: 57
42497 TGGTTTGTAT
42507 TATATAATTAATATAAAAATATTATATATTATATATATAATTAATATAAAAATATATAA
1 TATATAATTAATATAAAAATA-TATA-ATTATATATATAATTAATATAAAAATATATAA
*
42566 TATATAATTAATATAAAGAAATATAAAATCT-TATATATAATTAATAT-AAAATATATAA
1 TATATAATTAATAT-AA-AAATATATAAT-TATATATATAATTAATATAAAAATATATAA
* * * * * *
42624 AATATTA-TATTATATATATATATAATTA-ATATA-AAAT-ATATAAAATATTATATATA
1 TATATAATTAATATAAAAATATATAATTATATATATAATTAATATAAAA-A-TATATA-A
* *
42680 TATATATATATATATATATATATATATAAT
1 TATATA-AT-TA-ATATAAAAATATATAAT
42710 AGGGGCGGGG
Statistics
Matches: 121, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
52 4 0.03
53 6 0.05
54 7 0.06
55 15 0.12
56 6 0.05
57 6 0.05
58 16 0.13
59 34 0.28
60 22 0.18
61 5 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.43
Consensus pattern (57 bp):
TATATAATTAATATAAAAATATATAATTATATATATAATTAATATAAAAATATATAA
Found at i:42594 original size:68 final size:68
Alignment explanation
Indices: 42516--42710 Score: 200
Period size: 68 Copynumber: 2.8 Consensus size: 68
42506 TTATATAATT
42516 AATATAAAAATATTATATATTATATATATAATTA-ATATAAAAATATATAATATATAATTAATAT
1 AATAT-AAAATATTATATATTATATATATAATTATATATAAAAATATATAATATATAATTAATAT
42580 AAAGA
65 AAA-A
* * * *
42585 AATATAAAATCTTATATATAAT-TAATATAAAATATATAAAATATTATATTATATATATATATAA
1 AATATAAAATATTATATATTATAT-ATAT-AATTATATATAA-A--A-A-TATATA-ATATATAA
42649 TTAATATAAAA
58 TTAATATAAAA
* * *
42660 TATATAAAATATTATATA-TATATATAT-ATATATATATATATATATATAATA
1 AATATAAAATATTATATATTATATATATAAT-TATATATAAAAATATATAATA
42711 GGGGCGGGGC
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
67 4 0.04
68 25 0.24
69 10 0.10
70 5 0.05
71 1 0.01
72 2 0.02
73 8 0.08
74 7 0.07
75 24 0.23
76 18 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (68 bp):
AATATAAAATATTATATATTATATATATAATTATATATAAAAATATATAATATATAATTAATATA
AAA
Found at i:42653 original size:43 final size:44
Alignment explanation
Indices: 42597--42691 Score: 183
Period size: 43 Copynumber: 2.2 Consensus size: 44
42587 TATAAAATCT
42597 TATATATAATTAATATAAAATATATAAAATATTATAT-TATATA
1 TATATATAATTAATATAAAATATATAAAATATTATATATATATA
42640 TATATATAATTAATATAAAATATATAAAATATTATATATATATA
1 TATATATAATTAATATAAAATATATAAAATATTATATATATATA
42684 TATATATA
1 TATATATA
42692 TATATATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 37 0.73
44 14 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (44 bp):
TATATATAATTAATATAAAATATATAAAATATTATATATATATA
Found at i:47858 original size:3 final size:3
Alignment explanation
Indices: 47850--47893 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
47840 TAATTTTAAT
*
47850 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47894 CAAATTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:48833 original size:2 final size:2
Alignment explanation
Indices: 48826--48855 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48816 TTATAAAATG
48826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48856 TAAATGCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49307 original size:30 final size:29
Alignment explanation
Indices: 49236--49384 Score: 95
Period size: 30 Copynumber: 5.0 Consensus size: 29
49226 TTTGTAACTT
* * *
49236 CTATTTTAGTCCTTTAAGTTTCTGTATTTG
1 CTATTTTAGTCC-TTAAATTTATGTTTTTG
* *
49266 -TATTTTGGTCCTTAAATTTATATTTTTTG
1 CTATTTTAGTCCTTAAATTTAT-GTTTTTG
** * *
49295 CTATTTTAGTCCTTTAGGTTTATGTCTTTA
1 CTATTTTAGTCC-TTAAATTTATGTTTTTG
* *
49325 CTGTTTTAGTCCATAAGA-TTATGTTTTTTG
1 CTATTTTAGTCCTTAA-ATTTATG-TTTTTG
* * *
49355 CCATTTTAGGTCCTTTAAGTTTCTGTTTTT
1 CTATTTTA-GTCC-TTAAATTTATGTTTTT
49385 ATTCTAGTCC
Statistics
Matches: 89, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
28 8 0.09
29 22 0.25
30 35 0.39
31 17 0.19
32 7 0.08
ACGTcount: A:0.17, C:0.12, G:0.13, T:0.57
Consensus pattern (29 bp):
CTATTTTAGTCCTTAAATTTATGTTTTTG
Found at i:49352 original size:59 final size:61
Alignment explanation
Indices: 49236--49385 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 61
49226 TTTGTAACTT
* * *
49236 CTATTTTAGTCCTTTAAGTTTCTGTATTT-GTATTTTGGTCCTTAAATTTATA-TTTTTTG
1 CTATTTTAGTCCTTTAAGTTTCTGTATTTACTATTTTAGTCCATAAATTTATAGTTTTTTG
* * * *
49295 CTATTTTAGTCCTTTAGGTTTATGTCTTTACTGTTTTAGTCCATAAGA-TTAT-GTTTTTTG
1 CTATTTTAGTCCTTTAAGTTTCTGTATTTACTATTTTAGTCCATAA-ATTTATAGTTTTTTG
* *
49355 CCATTTTAGGTCCTTTAAGTTTCTGTTTTTA
1 CTATTTTA-GTCCTTTAAGTTTCTGTATTTA
49386 TTCTAGTCCC
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 26 0.34
60 30 0.39
61 20 0.26
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.57
Consensus pattern (61 bp):
CTATTTTAGTCCTTTAAGTTTCTGTATTTACTATTTTAGTCCATAAATTTATAGTTTTTTG
Found at i:51598 original size:57 final size:57
Alignment explanation
Indices: 51535--51648 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
51525 GAGAGATAAA
51535 AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
1 AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
* * *
51592 AATAAAGTTAGATGGGAGTATTTGAGAAGTAGGTGGGCGCTGTTTCCATTTTCAAAT
1 AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
51649 GGTTGAATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.32
Consensus pattern (57 bp):
AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
Found at i:59066 original size:23 final size:24
Alignment explanation
Indices: 59040--59090 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
59030 TAATAATTGT
*
59040 ATTTTAATTAAATTATATTTA-AA
1 ATTTTAATTAAATTATAATTATAA
*
59063 ATTTTAATTAATTTATAATTATAA
1 ATTTTAATTAAATTATAATTATAA
59087 ATTT
1 ATTT
59091 AATACTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTAATTAAATTATAATTATAA
Found at i:59089 original size:18 final size:18
Alignment explanation
Indices: 59047--59089 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
59037 TGTATTTTAA
59047 TTAAATTATATTTAAAAT
1 TTAAATTATATTTAAAAT
* *
59065 TTTAATTA-ATTTATAAT
1 TTAAATTATATTTAAAAT
59082 TATAAATT
1 T-TAAATT
59090 TAATACTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATTATATTTAAAAT
Found at i:62458 original size:18 final size:18
Alignment explanation
Indices: 62431--62468 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
62421 TCGTGCTAAG
*
62431 ACTAGTTAATAATCTTCT
1 ACTAGCTAATAATCTTCT
62449 ACTAGCTAATAATCTTCT
1 ACTAGCTAATAATCTTCT
62467 AC
1 AC
62469 GAAAAGGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (18 bp):
ACTAGCTAATAATCTTCT
Found at i:65448 original size:23 final size:23
Alignment explanation
Indices: 65374--65448 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
65364 CATCTTATAT
* *
65374 GGCACTTCAGTGCATTTCTACGC
1 GGCACTACAGTGCAATTCTACGC
*
65397 AGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
* *
65420 GACACTACAGTGCAATTCTACGT
1 GGCACTACAGTGCAATTCTACGC
65443 GGCACT
1 GGCACT
65449 TTGGTGCAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Done.