Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006074.1 Hibiscus syriacus cultivar Beakdansim tig00014380_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: 63818
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:979 original size:14 final size:14
Alignment explanation
Indices: 962--989 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
952 CGAGTTCTTC
962 TTAACGAGCCGAAA
1 TTAACGAGCCGAAA
976 TTAACGAGCCGAAA
1 TTAACGAGCCGAAA
990 CGAGCTACTT
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:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TTAACGAGCCGAAA
Found at i:4879 original size:160 final size:161
Alignment explanation
Indices: 4575--4880 Score: 447
Period size: 160 Copynumber: 1.9 Consensus size: 161
4565 TCCCTTAATA
* *
4575 TATAAGAGATGATTATAATATTATATTGAGTCAAATTGAATTTTTTTTCATCCTAAACTTCTCTA
1 TATAAGAGATGATTATAATATTATATCGAGTCAAATCGAA-TTTTTTTCATCCTAAACTTCTCTA
*
4640 CTGTTAGTATTACTACTATTATTTTATCAATCTTTATTAGAGATAATTTATCAGTAGAACTATCT
65 C---T--TATTACTACTATTATTTTATCAATCTTTATTAGAGAAAATTTATCAGTAGAACTATCT
***
4705 AATATTTTTATTGATAGATTTTATTGTAATTATCCCT
125 AATATACGTATTGATAGATTTTATTGTAATTATCCCT
4742 TATAAG-GAATGATTATAATATTATATCGAGTCAAATCGAA-TTTTTTCATCCTAAACTTCTCTA
1 TATAAGAG-ATGATTATAATATTATATCGAGTCAAATCGAATTTTTTTCATCCTAAACTTCTCTA
* *
4805 C-TATTACTACTATTATTTTATCAAGTCTTTATTAGAGAAAATTTATTAGTATAACTATCTAATA
65 CTTATTACTACTATTATTTTATCAA-TCTTTATTAGAGAAAATTTATCAGTAGAACTATCTAATA
4869 TACGTATTGATA
129 TACGTATTGATA
4881 AATATTTTGC
Statistics
Matches: 129, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
159 23 0.18
160 45 0.35
165 24 0.19
166 1 0.01
167 36 0.28
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (161 bp):
TATAAGAGATGATTATAATATTATATCGAGTCAAATCGAATTTTTTTCATCCTAAACTTCTCTAC
TTATTACTACTATTATTTTATCAATCTTTATTAGAGAAAATTTATCAGTAGAACTATCTAATATA
CGTATTGATAGATTTTATTGTAATTATCCCT
Found at i:4931 original size:29 final size:29
Alignment explanation
Indices: 4898--4954 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
4888 TGCATGTATG
* *
4898 TCTACATGTATATATTGATAGATAGATAT
1 TCTACATGTATATATAGATAAATAGATAT
*
4927 TCTACATGTGTATATAGATAAATAGATA
1 TCTACATGTATATATAGATAAATAGATA
4955 GATATTCTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (29 bp):
TCTACATGTATATATAGATAAATAGATAT
Found at i:5021 original size:37 final size:38
Alignment explanation
Indices: 4877--5048 Score: 131
Period size: 37 Copynumber: 4.6 Consensus size: 38
4867 TATACGTATT
* * *
4877 GATAAATATTTTGCATGTATGTCTACATGTATATATTGATA
1 GATAGATATTCTGCATG--TGTGTACATGTATATATT-ATA
* * *
4918 GATAGATATTCTACATGTGTATATA-G-ATA-A--ATA
1 GATAGATATTCTGCATGTGTGTACATGTATATATTATA
* * ** * *
4951 GATAGATATTCTGCATATATGTGTATCTGTATA-TATA
1 GATAGATATTCTGCATGTGTGTACATGTATATATTATA
*
4988 GATAGATATTTTGCATGTGTGTACATGTATATATATTATA
1 GATAGATATTCTGCATGTGTGTACATG--TATATATTATA
*
5028 GATAGATATTATGCATGTGTG
1 GATAGATATTCTGCATGTGTG
5049 AAAGTTAAAT
Statistics
Matches: 104, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
33 23 0.22
35 2 0.02
36 2 0.02
37 27 0.26
38 1 0.01
39 11 0.11
40 24 0.23
41 14 0.13
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.42
Consensus pattern (38 bp):
GATAGATATTCTGCATGTGTGTACATGTATATATTATA
Found at i:8824 original size:23 final size:25
Alignment explanation
Indices: 8797--8844 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
8787 ATTTTGAAAT
8797 TTAATA-AAAATTATAA-ATATTTA
1 TTAATATAAAATTATAATATATTTA
* *
8820 TTAATATGAAATTCTAATATATTTA
1 TTAATATAAAATTATAATATATTTA
8845 AACGTCTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TTAATATAAAATTATAATATATTTA
Found at i:11729 original size:81 final size:81
Alignment explanation
Indices: 11576--12071 Score: 675
Period size: 81 Copynumber: 6.2 Consensus size: 81
11566 TATGCTCTAA
* * * *
11576 AGTAAAAGATTAATGACCTAGCTGTGTATTTGACAGAAAGGAGTCAATTATGCCATTTAGATTG-
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA-TGA
11640 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * * *
11657 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGTCAGTTAAATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
11722 AGTTTAAATACCTTT-
66 AGGTTAAATACCTTTG
* * *
11737 --T-AATGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGCCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
11799 ATGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
11815 AGTAAAAGATTAAAGACCTAAC--TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGGA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
11878 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
*
11894 AGTAAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATG-A
11959 AAGGTT-AATACCTTTG
65 AAGGTTAAATACCTTTG
* * * * ** *
11975 AGTAAAAGATTAATCGCCTAGTTGTGCATTTGATATAAATATGTCAATTATGACAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
12040 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
*
12056 AGTGAAAGATTAATGG
1 AGTAAAAGATTAATGG
12072 TCTAATTGTG
Statistics
Matches: 365, Mismatches: 41, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
77 67 0.18
78 1 0.00
79 72 0.20
80 10 0.03
81 209 0.57
82 6 0.02
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:12269 original size:14 final size:14
Alignment explanation
Indices: 12230--12270 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12220 ATGAATTACA
* *
12230 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
12244 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
12258 TTTCCGTAAAATG
1 TTTCCGGAAAATG
12271 AATTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:12468 original size:26 final size:27
Alignment explanation
Indices: 12422--12472 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
12412 TCATAAAACT
*
12422 TAATATTATTATTTTTAAAATATTAAA
1 TAATATTATTATTATTAAAATATTAAA
12449 TAAT-TTATTTATTATT-AAATATTA
1 TAATATTA-TTATTATTAAAATATTA
12473 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TAATATTATTATTATTAAAATATTAAA
Found at i:12478 original size:19 final size:19
Alignment explanation
Indices: 12428--12479 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
12418 AACTTAATAT
*
12428 TATTATTTTTAAAATATTAAA
1 TATTATTTTT--ATTATTAAA
*
12449 TAATT-TATTTATTATTAAA
1 T-ATTATTTTTATTATTAAA
12468 TATTATTTTTAT
1 TATTATTTTTAT
12480 AATTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.12
19 15 0.58
21 5 0.19
22 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTTTTATTATTAAA
Found at i:12659 original size:19 final size:19
Alignment explanation
Indices: 12591--12671 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
12581 TTAAATATCT
12591 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
12610 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
12629 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
12649 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
12667 -TATTA
1 TTATTA
12672 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:12742 original size:54 final size:54
Alignment explanation
Indices: 12616--12742 Score: 127
Period size: 54 Copynumber: 2.4 Consensus size: 54
12606 TAGATTATTA
* * *
12616 TATTAATATTAAATAT-ATAAATAATATTATTCATTATTAATAATTTAATAATAT
1 TATTAAAATGAAATATAATAAATAATATTA-TAATTATTAATAATTTAATAATAT
*** * *
12670 TATTTCTATGAAAT-TAATAAATAATA-TA-AATTTTTAATAATTTATTATATAT
1 TATTAAAATGAAATATAATAAATAATATTATAATTATTAATAATTTAATA-ATAT
12722 TATTAAAATGAAAATATAATA
1 TATTAAAATG-AAATATAATA
12743 TCTTATATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
51 16 0.27
52 11 0.18
53 7 0.12
54 26 0.43
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (54 bp):
TATTAAAATGAAATATAATAAATAATATTATAATTATTAATAATTTAATAATAT
Found at i:12821 original size:10 final size:10
Alignment explanation
Indices: 12780--12825 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
12770 ATTTTATTAT
12780 AATATTAA-A
1 AATATTAATA
12789 AATA-TAATA
1 AATATTAATA
12798 TAATATTATTATA
1 -AATATTA--ATA
12811 AATATTAATA
1 AATATTAATA
12821 AATAT
1 AATAT
12826 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:12828 original size:21 final size:22
Alignment explanation
Indices: 12781--12837 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
12771 TTTTATTATA
*
12781 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATATAAT
12802 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
12824 ATATTTTAAATATT
1 ATATTATAAATATT
12838 TTAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:12842 original size:23 final size:21
Alignment explanation
Indices: 12788--12837 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
12778 ATAATATTAA
*
12788 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
12810 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
12831 AAATATT
1 AAATATT
12838 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:13114 original size:42 final size:42
Alignment explanation
Indices: 13053--13147 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
13043 TTCCTCCAAC
* *
13053 CAAACACTGGAAAACATTTTTCGGAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
* *
13095 CAAACACGGGAAAATATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
*
13137 CAAATACGGGA
1 CAAACACGGGA
13148 TTTTGGGGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.19
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
Found at i:14224 original size:18 final size:17
Alignment explanation
Indices: 14170--14218 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
14160 TTAGACCCTT
* *
14170 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
14188 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
14206 AGTGCATTCGATG
1 AGTGCA-TCGATG
14219 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:14786 original size:28 final size:28
Alignment explanation
Indices: 14746--14809 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
14736 CCCCTTACTA
14746 TAACACTTCTCCCCTTTTAAAAACATTT
1 TAACACTTCTCCCCTTTTAAAAACATTT
*
14774 TAACGCTTCTCCCCTTTTAAAAACATTT
1 TAACACTTCTCCCCTTTTAAAAACATTT
14802 TAACACTT
1 TAACACTT
14810 AACACACTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.02, T:0.39
Consensus pattern (28 bp):
TAACACTTCTCCCCTTTTAAAAACATTT
Found at i:14976 original size:13 final size:13
Alignment explanation
Indices: 14958--14982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14948 AGCCATTGGT
14958 TTCATAATCAATA
1 TTCATAATCAATA
14971 TTCATAATCAAT
1 TTCATAATCAAT
14983 GTGACATGGT
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:15586 original size:21 final size:21
Alignment explanation
Indices: 15561--15604 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
15551 CCGGAGTAGG
*
15561 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
15582 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
15603 AG
1 AG
15605 CTCCCGAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:16634 original size:11 final size:11
Alignment explanation
Indices: 16618--16647 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
16608 TGGGCAAGGT
16618 TTTGAAAACTA
1 TTTGAAAACTA
16629 TTTGAAAACTA
1 TTTGAAAACTA
16640 TTTGAAAA
1 TTTGAAAA
16648 TAATCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (11 bp):
TTTGAAAACTA
Found at i:21104 original size:20 final size:20
Alignment explanation
Indices: 21062--21104 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
21052 TTATTTTCAT
* *
21062 TTTTTAATTTTGAAATATCA
1 TTTTTAATTTTGAAAAATAA
21082 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
21102 TTT
1 TTT
21105 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:23061 original size:18 final size:17
Alignment explanation
Indices: 23007--23055 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
22997 TTGGACCCTT
* *
23007 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
23025 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
23043 AGTGCATTCGATG
1 AGTGCA-TCGATG
23056 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:23162 original size:66 final size:66
Alignment explanation
Indices: 23027--23187 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 66
23017 TGCACTAAGA
* * *
23027 GTGCATCGATGCATCAAGTGCATTCGATG--TTTCAAAATAGCCAGAGTGTATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
23090 G
66 G
* * *
23091 GTGCATCGATACATCAAATGCATTCGATGTTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTCA-AAATAGCCACAGTGCATCGATGCATGGC
*
23154 TAT
65 T-G
*
23157 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
23188 CAATTTAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 27 0.32
65 1 0.01
66 53 0.63
67 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (66 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
G
Found at i:24824 original size:14 final size:14
Alignment explanation
Indices: 24788--24826 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
24778 ATTATCTTAT
24788 ATTATTTTATAATAA
1 ATTATTTT-TAATAA
24803 ATTATTTTTAA-AA
1 ATTATTTTTAATAA
24816 ATATATTTTTA
1 AT-TATTTTTA
24827 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 11 0.48
15 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTTTTAATAA
Found at i:32398 original size:17 final size:16
Alignment explanation
Indices: 32376--32409 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
32366 AAAATCGATC
32376 AAAAAAACCGATAACCG
1 AAAAAAACCGA-AACCG
*
32393 AAAAAACCCGAAACCG
1 AAAAAAACCGAAACCG
32409 A
1 A
32410 TTTGGTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.26, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAAACCGAAACCG
Found at i:46997 original size:87 final size:87
Alignment explanation
Indices: 46851--47011 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 87
46841 TTGTTTACCC
* * *
46851 AATTCTCTTTTTCCTTTTATCTTTTTACATTTTAACTATTGGTGAATATAAGGACTAAATTGAAC
1 AATTCTCTTTTTCCTTTTATCTTTTTACATTTTAAATATTGATAAATATAAGGACTAAATTGAAC
46916 ACATGATAAATTTTGGAGTTCA
66 ACATGATAAATTTTGGAGTTCA
* *
46938 AATTCTCTTTTTCCTTTTATCTTTTTACATTTTAAATATTGATAAATGTATA-GATTAAATTGAA
1 AATTCTCTTTTTCCTTTTATCTTTTTACATTTTAAATATTGATAAATATA-AGGACTAAATTGAA
47002 CACATGATAA
65 CACATGATAA
47012 TATAGTTTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
87 67 0.99
88 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (87 bp):
AATTCTCTTTTTCCTTTTATCTTTTTACATTTTAAATATTGATAAATATAAGGACTAAATTGAAC
ACATGATAAATTTTGGAGTTCA
Found at i:47293 original size:23 final size:23
Alignment explanation
Indices: 47257--47323 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
47247 AAGTAAAGAA
* * *
47257 GTTTGTTAACGTTAAATGAATAT
1 GTTTGTGAATGTTAAATGAACAT
*
47280 GTTTGTGAATGTTAAACGAACAT
1 GTTTGTGAATGTTAAATGAACAT
* *
47303 GTTCGTGAATATTAAATGAAC
1 GTTTGTGAATGTTAAATGAAC
47324 CGGACATGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.37
Consensus pattern (23 bp):
GTTTGTGAATGTTAAATGAACAT
Found at i:50304 original size:18 final size:18
Alignment explanation
Indices: 50281--50315 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50271 AAAATCAAGA
50281 AAGAACTTTAAAGATGTT
1 AAGAACTTTAAAGATGTT
*
50299 AAGAACTTTGAAGATGT
1 AAGAACTTTAAAGATGT
50316 GAAGCGCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (18 bp):
AAGAACTTTAAAGATGTT
Found at i:50450 original size:19 final size:19
Alignment explanation
Indices: 50416--50477 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
50406 TTATCATTGC
50416 GAAAAG-AAAATA-ATGAAA
1 GAAAAGTAAAA-AGATGAAA
50434 GAAAAGTAAAAAGATGAAA
1 GAAAAGTAAAAAGATGAAA
50453 GAAAAGTAAAAAAGATGAAA
1 GAAAAGT-AAAAAGATGAAA
50473 GAAAA
1 GAAAA
50478 ATATAACTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.17
19 17 0.41
20 17 0.41
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (19 bp):
GAAAAGTAAAAAGATGAAA
Found at i:50464 original size:20 final size:20
Alignment explanation
Indices: 50416--50477 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
50406 TTATCATTGC
*
50416 GAAAAG-AAAATA-ATGAAA
1 GAAAAGTAAAAAAGATGAAA
50434 GAAAAGT-AAAAAGATGAAA
1 GAAAAGTAAAAAAGATGAAA
50453 GAAAAGTAAAAAAGATGAAA
1 GAAAAGTAAAAAAGATGAAA
50473 GAAAA
1 GAAAA
50478 ATATAACTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 10 0.25
19 13 0.32
20 17 0.43
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (20 bp):
GAAAAGTAAAAAAGATGAAA
Found at i:51316 original size:10 final size:10
Alignment explanation
Indices: 51303--51327 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
51293 TTTTTTTTCG
51303 TTTTTCATTT
1 TTTTTCATTT
51313 TTTTTCATTT
1 TTTTTCATTT
51323 TTTTT
1 TTTTT
51328 GAAATTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:52246 original size:12 final size:12
Alignment explanation
Indices: 52219--52265 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
52209 TAAAGTTCTC
* *
52219 TTTTCTTTTAAG
1 TTTTATTTTTAG
52231 TTTTCATTTTTA-
1 TTTT-ATTTTTAG
*
52243 TTTTATTTTAAG
1 TTTTATTTTTAG
52255 TTTTATTTTTA
1 TTTTATTTTTA
52266 AACAAACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 6 0.21
12 18 0.62
13 5 0.17
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (12 bp):
TTTTATTTTTAG
Found at i:52251 original size:24 final size:23
Alignment explanation
Indices: 52219--52265 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
52209 TAAAGTTCTC
*
52219 TTTTCTTTTAAGTTTTCATTTTTA
1 TTTTATTTTAAGTTTT-ATTTTTA
52243 TTTTATTTTAAGTTTTATTTTTA
1 TTTTATTTTAAGTTTTATTTTTA
52266 AACAAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTATTTTAAGTTTTATTTTTA
Found at i:52603 original size:22 final size:22
Alignment explanation
Indices: 52552--52596 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
52542 TTGCCAAGAG
52552 GGAATTGAGATCAAAATTAGTA
1 GGAATTGAGATCAAAATTAGTA
52574 GGAATTGAGATCAAAATTAGTA
1 GGAATTGAGATCAAAATTAGTA
52596 G
1 G
52597 TTATTGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.27
Consensus pattern (22 bp):
GGAATTGAGATCAAAATTAGTA
Found at i:54989 original size:17 final size:17
Alignment explanation
Indices: 54967--55001 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
54957 TGTGTGATCT
54967 TGGTGCCTCTACTAATG
1 TGGTGCCTCTACTAATG
54984 TGGTGCCTCTACTAATG
1 TGGTGCCTCTACTAATG
55001 T
1 T
55002 AATGCCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (17 bp):
TGGTGCCTCTACTAATG
Found at i:55007 original size:17 final size:17
Alignment explanation
Indices: 54970--55010 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
54960 GTGATCTTGG
**
54970 TGCCTCTACTAATGTGG
1 TGCCTCTACTAATGTAA
54987 TGCCTCTACTAATGTAA
1 TGCCTCTACTAATGTAA
55004 TGCCTCT
1 TGCCTCT
55011 CTCTGTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (17 bp):
TGCCTCTACTAATGTAA
Found at i:58824 original size:13 final size:13
Alignment explanation
Indices: 58808--58853 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
58798 CTCTTTTTTC
*
58808 TTTTCTTTTTAAG
1 TTTTCATTTTAAG
*
58821 TTTTCATTTTCA-
1 TTTTCATTTTAAG
58833 TTTT-ATTTTAAG
1 TTTTCATTTTAAG
58845 TTTT-ATTTT
1 TTTTCATTTT
58854 TAAACATGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 6 0.21
12 13 0.45
13 10 0.34
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTCATTTTAAG
Found at i:58856 original size:13 final size:12
Alignment explanation
Indices: 58814--58853 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
58804 TTTCTTTTCT
58814 TTTTAAGTTTTCA
1 TTTTAAGTTTT-A
*
58827 TTTTCA-TTTTA
1 TTTTAAGTTTTA
58838 TTTTAAGTTTTA
1 TTTTAAGTTTTA
58850 TTTT
1 TTTT
58854 TAAACATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTAAGTTTTA
Found at i:60505 original size:19 final size:20
Alignment explanation
Indices: 60463--60504 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
60453 AATCCAGATT
60463 CCCC-AGAGGGTACTGATAC
1 CCCCAAGAGGGTACTGATAC
60482 CCCCAAGAGGGTACTGATAC
1 CCCCAAGAGGGTACTGATAC
60502 CCC
1 CCC
60505 ATGTAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.26, C:0.36, G:0.24, T:0.14
Consensus pattern (20 bp):
CCCCAAGAGGGTACTGATAC
Found at i:60603 original size:76 final size:74
Alignment explanation
Indices: 60469--60630 Score: 263
Period size: 76 Copynumber: 2.2 Consensus size: 74
60459 GATTCCCCAG
* *
60469 AGGGTACTGATACCCCCAAGAGGGTACTGATACCCCATGTAAGATTTGGCTCCGAGAAATAACAG
1 AGGGTACCGATACCCCCAAGAGGGTACTGATACCCCATGTAAGATCTGGCTCCGAGAAATAACAG
60534 ATTGCTCGA
66 ATTGCTCGA
60543 AGGGTACCGATACCCCCTAAGAGGGTA-TCGATACCCCAATGTAAGATCTGGCTCCGAGAAATAA
1 AGGGTACCGATACCCCC-AAGAGGGTACT-GATACCCC-ATGTAAGATCTGGCTCCGAGAAATAA
*
60607 CAGATTGCTCGG
63 CAGATTGCTCGA
60619 AGGGTACCGATA
1 AGGGTACCGATA
60631 AGCCCCAGGA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
74 17 0.21
75 17 0.21
76 48 0.59
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (74 bp):
AGGGTACCGATACCCCCAAGAGGGTACTGATACCCCATGTAAGATCTGGCTCCGAGAAATAACAG
ATTGCTCGA
Found at i:60646 original size:20 final size:20
Alignment explanation
Indices: 60621--60697 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
60611 TTGCTCGGAG
* *
60621 GGTACCGATAAGCCCCAGGA
1 GGTACCAATAACCCCCAGGA
*
60641 GGTACCAATACCCCCCAGGA
1 GGTACCAATAACCCCCAGGA
*
60661 GGTACCAA-AACCCCCCCAGAA
1 GGTACCAATAA--CCCCCAGGA
60682 GGTACCAAT-ACCCCCA
1 GGTACCAATAACCCCCA
60698 TCTCATAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 7 0.14
20 25 0.51
21 17 0.35
ACGTcount: A:0.32, C:0.39, G:0.19, T:0.09
Consensus pattern (20 bp):
GGTACCAATAACCCCCAGGA
Found at i:60677 original size:21 final size:21
Alignment explanation
Indices: 60633--60696 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
60623 TACCGATAAG
60633 CCCCAGGAGGTACCAATA-CC
1 CCCCAGGAGGTACCAATACCC
*
60653 CCCCAGGAGGTACCAAAACCC
1 CCCCAGGAGGTACCAATACCC
*
60674 CCCCAGAAGGTACCAATACCC
1 CCCCAGGAGGTACCAATACCC
60695 CC
1 CC
60697 ATCTCATAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.31, C:0.44, G:0.17, T:0.08
Consensus pattern (21 bp):
CCCCAGGAGGTACCAATACCC
Found at i:62633 original size:21 final size:21
Alignment explanation
Indices: 62609--62648 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62599 AAGACTTTAT
62609 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
*
62630 TTTCGAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
62649 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Done.