Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008444.1 Hibiscus syriacus cultivar Beakdansim tig00111248_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: 85961
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2655 original size:18 final size:18
Alignment explanation
Indices: 2622--2656 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2612 GAACTTGATA
*
2622 CATTTGTACATGTTTTTG
1 CATTTGTACATATTTTTG
*
2640 CATTTGTATATATTTTT
1 CATTTGTACATATTTTT
2657 ACACACTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (18 bp):
CATTTGTACATATTTTTG
Found at i:10852 original size:16 final size:15
Alignment explanation
Indices: 10819--10863 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
10809 ATTTTTTTTG
*
10819 ATAAAATAATTAAAT
1 ATAAAATAAATAAAT
10834 ATAAAATAAATATAAT
1 ATAAAATAAATA-AAT
*
10850 ATAATAAGAAATAA
1 ATAA-AATAAATAA
10864 TTTTACCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 11 0.42
16 8 0.31
17 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAATAAATAAAT
Found at i:17142 original size:30 final size:29
Alignment explanation
Indices: 17108--17191 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 29
17098 GAGAGTTTAT
*
17108 AATTTTGGCAATATTTTTTTATTTAATCAC
1 AATTTTGG-AATATTTTTTAATTTAATCAC
* *
17138 AATTTT-GAA-A--TTTTAATTTAATTAT
1 AATTTTGGAATATTTTTTAATTTAATCAC
*
17163 AATTTTGAGAATATTTTTTGATTTAATCA
1 AATTTTG-GAATATTTTTTAATTTAATCA
17192 ATTTGTGGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
25 18 0.41
27 4 0.09
28 3 0.07
29 1 0.02
30 18 0.41
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.54
Consensus pattern (29 bp):
AATTTTGGAATATTTTTTAATTTAATCAC
Found at i:17845 original size:14 final size:14
Alignment explanation
Indices: 17826--17857 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
17816 ATTTTTTTTT
17826 TAAAAATTGATCTC
1 TAAAAATTGATCTC
17840 TAAAAATTGATCTC
1 TAAAAATTGATCTC
17854 TAAA
1 TAAA
17858 TTATTTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (14 bp):
TAAAAATTGATCTC
Found at i:18588 original size:21 final size:20
Alignment explanation
Indices: 18564--18741 Score: 111
Period size: 21 Copynumber: 8.7 Consensus size: 20
18554 CATATTCGCA
*
18564 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATATTCCAAGTT-GCG
18585 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA--TATTCCAAGTTGCG
* * *
18606 TTGCGATAGTCGAAGTTCGCT
1 TTGCGATATTCCAAGTT-GCG
*
18627 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TATTCCAAGTTGCG
18648 TTGCGATTTATTCCAAGTTGCG
1 TTGCGA--TATTCCAAGTTGCG
*
18670 ATT----TATTCCAAATT-CG
1 -TTGCGATATTCCAAGTTGCG
* *
18686 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATATTCCAAGTT-GCG
18707 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA--TATTCCAAGTTGCG
*
18728 TTGCGATAGTCCAA
1 TTGCGATATTCCAA
18742 AATCGCAACG
Statistics
Matches: 125, Mismatches: 16, Indels: 34
0.71 0.09 0.19
Matches are distributed among these distances:
15 2 0.02
16 2 0.02
17 10 0.08
19 24 0.19
21 56 0.45
22 2 0.02
23 29 0.23
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATATTCCAAGTTGCG
Found at i:18615 original size:42 final size:42
Alignment explanation
Indices: 18564--18741 Score: 242
Period size: 42 Copynumber: 4.3 Consensus size: 42
18554 CATATTCGCA
*
18564 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
18606 TTGCGATAGTCGAAGTTCGCTTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
18648 TTGCGAT--T--TA-TTC-CAAGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGC--GTTGCGATTTATTCCAAATTCG
* *
18686 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
18728 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
18742 AATCGCAACG
Statistics
Matches: 120, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
36 1 0.01
37 3 0.03
38 29 0.24
40 2 0.02
42 81 0.68
43 3 0.03
44 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:18669 original size:17 final size:18
Alignment explanation
Indices: 18627--18680 Score: 74
Period size: 17 Copynumber: 2.9 Consensus size: 18
18617 GAAGTTCGCT
18627 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCC-AA-T-G
18648 TTGCGATTTATTCCAA-G
1 TTGCGATTTATTCCAATG
18665 TTGCGATTTATTCCAA
1 TTGCGATTTATTCCAA
18681 ATTCGTTGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.52
20 2 0.06
21 14 0.42
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (18 bp):
TTGCGATTTATTCCAATG
Found at i:18676 original size:80 final size:80
Alignment explanation
Indices: 18584--18734 Score: 275
Period size: 80 Copynumber: 1.9 Consensus size: 80
18574 CCAAGTTCGC
* *
18584 GTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCTTTGCGATTTATTCCAAATTCGT
1 GTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
18649 TGCGATTTATTCCAA
66 TGCGATTTATTCCAA
*
18664 GTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 GTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
18729 TGCGAT
66 TGCGAT
18735 AGTCCAAAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (80 bp):
GTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
TGCGATTTATTCCAA
Found at i:21387 original size:24 final size:24
Alignment explanation
Indices: 21355--21400 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
21345 GGAGATGATA
*
21355 ATGGGGACGACGACGACGACGATG
1 ATGGGGACGAAGACGACGACGATG
* *
21379 ATGGTGACGAAGATGACGACGA
1 ATGGGGACGAAGACGACGACGA
21401 CGAGGGAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.39, T:0.11
Consensus pattern (24 bp):
ATGGGGACGAAGACGACGACGATG
Found at i:21414 original size:24 final size:24
Alignment explanation
Indices: 21360--21415 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
21350 TGATAATGGG
* * * * *
21360 GACGACGACGACGACGATGATGGT
1 GACGAAGATGACGACGACGAGGGA
21384 GACGAAGATGACGACGACGAGGGA
1 GACGAAGATGACGACGACGAGGGA
*
21408 GAGGAAGA
1 GACGAAGA
21416 GGAAGAGGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.41, T:0.07
Consensus pattern (24 bp):
GACGAAGATGACGACGACGAGGGA
Found at i:21428 original size:15 final size:15
Alignment explanation
Indices: 21408--21446 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
21398 CGACGAGGGA
21408 GAGGAAGAGGAAGAG
1 GAGGAAGAGGAAGAG
*
21423 GAGGAAGAGGATGAG
1 GAGGAAGAGGAAGAG
*
21438 GACGAAGAG
1 GAGGAAGAG
21447 CTTCAGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.51, T:0.03
Consensus pattern (15 bp):
GAGGAAGAGGAAGAG
Found at i:24854 original size:17 final size:17
Alignment explanation
Indices: 24834--24866 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
24824 ATCTTCATCA
24834 CAATCAATATCTCTTAT
1 CAATCAATATCTCTTAT
24851 CAATCAATATCTCTTA
1 CAATCAATATCTCTTA
24867 GTTATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (17 bp):
CAATCAATATCTCTTAT
Found at i:28501 original size:16 final size:16
Alignment explanation
Indices: 28476--28508 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28466 ATTGAATTGT
28476 TCAAATAATA-ATAAA
1 TCAAATAATATATAAA
28491 TCAATATAATATATAAA
1 TCAA-ATAATATATAAA
28508 T
1 T
28509 TTTGAGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TCAAATAATATATAAA
Found at i:31775 original size:2 final size:2
Alignment explanation
Indices: 31768--31801 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31758 ATCAATTTGG
31768 AT AT AT AT A- 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 A
31802 GTGTAGATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44736 original size:97 final size:97
Alignment explanation
Indices: 44551--44747 Score: 360
Period size: 97 Copynumber: 2.0 Consensus size: 97
44541 TATTCCCTTA
*
44551 TAAAAGTATAGAGGCTAAATTTCAAATTTGAGCATAGTTGATGGACCAAAATTATAATTTGACCT
1 TAAAAGTATAGAGGCTAAATTTCAAATTTGAGCATAGTTGATGGACCAAAATCATAATTTGACCT
44616 AATAATAAAAGTTAAAGTTCATTGGTCATTAT
66 AATAATAAAAGTTAAAGTTCATTGGTCATTAT
*
44648 TAAAAGTATAGAGGCTAAATTTCAAATTTGAGCATAGTTGATGG-CCATAATCATAATTTGACCT
1 TAAAAGTATAGAGGCTAAATTTCAAATTTGAGCATAGTTGATGGACCAAAATCATAATTTGACCT
44712 AATAATAAAAGTTAAAGTTCCATTGGTCATTAT
66 AATAATAAAAGTTAAAGTT-CATTGGTCATTAT
44745 TAA
1 TAA
44748 GGAGTAAAAT
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
96 37 0.38
97 60 0.62
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (97 bp):
TAAAAGTATAGAGGCTAAATTTCAAATTTGAGCATAGTTGATGGACCAAAATCATAATTTGACCT
AATAATAAAAGTTAAAGTTCATTGGTCATTAT
Found at i:44986 original size:32 final size:31
Alignment explanation
Indices: 44948--45008 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
44938 TTGCAAATTA
44948 TCATTAAACTTGCATAACTATTACAGAAATGG
1 TCATTAAACTTGCATAACTATTACA-AAATGG
**
44980 TCATTAATTTTGCATAACTATTACAAAAT
1 TCATTAAACTTGCATAACTATTACAAAAT
45009 AATCCCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (31 bp):
TCATTAAACTTGCATAACTATTACAAAATGG
Found at i:46430 original size:43 final size:43
Alignment explanation
Indices: 46371--46492 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
46361 TTGTAAATAA
* * * * *
46371 AAAACGCCGTTATATACCATGATATTTCGCGGCGTTTGTGTAT
1 AAAACGCCGCTATATACTATGATATTTAGCGGCGTTTGTGAAC
* * * **
46414 AAAACGCCGCTATATACTATGATATGTAACAGAATTTGTGAAC
1 AAAACGCCGCTATATACTATGATATTTAGCGGCGTTTGTGAAC
* *
46457 AAAATGACGCTATATACTATGATATTTAGCGGCGTT
1 AAAACGCCGCTATATACTATGATATTTAGCGGCGTT
46493 CGTTATACTA
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (43 bp):
AAAACGCCGCTATATACTATGATATTTAGCGGCGTTTGTGAAC
Found at i:48111 original size:15 final size:15
Alignment explanation
Indices: 48091--48124 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48081 GGCAACTTTC
48091 TCCGACCCCGAAGTG
1 TCCGACCCCGAAGTG
* *
48106 TCCGACCTCGACGTG
1 TCCGACCCCGAAGTG
48121 TCCG
1 TCCG
48125 GACCAGGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.41, G:0.26, T:0.18
Consensus pattern (15 bp):
TCCGACCCCGAAGTG
Found at i:48600 original size:22 final size:22
Alignment explanation
Indices: 48572--48619 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
48562 TTGCTGCTTA
48572 AGGAAGTATTGTAGCCTAATTG
1 AGGAAGTATTGTAGCCTAATTG
48594 AGGAAGTATTGTAGCCTAATTG
1 AGGAAGTATTGTAGCCTAATTG
48616 AGGA
1 AGGA
48620 CATTTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (22 bp):
AGGAAGTATTGTAGCCTAATTG
Found at i:55022 original size:18 final size:17
Alignment explanation
Indices: 54995--55031 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
54985 ATCCGCTCTG
*
54995 ACCCCTTCTTCTTCTTC
1 ACCCCTTCTTCTCCTTC
55012 ACCCTCTTCTTCTCCTTC
1 ACCC-CTTCTTCTCCTTC
55030 AC
1 AC
55032 ATTCACCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.08, C:0.49, G:0.00, T:0.43
Consensus pattern (17 bp):
ACCCCTTCTTCTCCTTC
Found at i:57253 original size:16 final size:16
Alignment explanation
Indices: 57234--57286 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
57224 CCATAACCCC
57234 TATCACACATATATCA
1 TATCACACATATATCA
** * *
57250 TATCATGCACACATCA
1 TATCACACATATATCA
57266 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
57284 TAT
1 TAT
57287 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:57775 original size:103 final size:103
Alignment explanation
Indices: 57604--57816 Score: 399
Period size: 103 Copynumber: 2.1 Consensus size: 103
57594 TAATGTCCAT
* *
57604 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
57669 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
*
57707 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
57772 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
57810 AAGGACC
1 AAGGACC
57817 GCGTAGACCC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
Found at i:62463 original size:16 final size:16
Alignment explanation
Indices: 62444--62496 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
62434 CCATAACCCC
62444 TATCACACATATATCA
1 TATCACACATATATCA
** * *
62460 TATCATGCACACATCA
1 TATCACACATATATCA
62476 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
62494 TAT
1 TAT
62497 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:62848 original size:23 final size:23
Alignment explanation
Indices: 62817--62885 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
62807 CACCACAGCT
* *
62817 CGTATAATTGTACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
62840 CGTAGAATTGCACCAAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
62863 CATAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
62886 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:63072 original size:103 final size:103
Alignment explanation
Indices: 62908--63113 Score: 358
Period size: 103 Copynumber: 2.0 Consensus size: 103
62898 CATAAGGAAT
* * *
62908 ACATATCATTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
62973 CACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
66 CACATGTTCCAAAGAATACATATATATCCCGAAGGACC
*
63011 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
63076 CACATGTTCCAAAGAATACATATATATCCTGAAGGACC
66 CACATGTTCCAAAGAATACATATATATCCCGAAGGACC
63114 GCGTAGACCC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATATATCCCGAAGGACC
Found at i:66294 original size:15 final size:15
Alignment explanation
Indices: 66274--66303 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
66264 ATTAACTTTT
66274 AAGAATGAGATTATA
1 AAGAATGAGATTATA
66289 AAGAATGAGATTATA
1 AAGAATGAGATTATA
66304 GATTTGTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (15 bp):
AAGAATGAGATTATA
Found at i:67536 original size:23 final size:23
Alignment explanation
Indices: 67493--67536 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
67483 TAATTATATT
*
67493 TTAAAATATTAATGTGTTTAAGG
1 TTAAAATATTAATATGTTTAAGG
*
67516 TTAAAAT-TTATTATGTATTAA
1 TTAAAATATTAATATGT-TTAA
67537 TATTTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (23 bp):
TTAAAATATTAATATGTTTAAGG
Found at i:69876 original size:22 final size:24
Alignment explanation
Indices: 69826--69873 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
69816 GACACATACT
*
69826 ACATCATCATTTTAAATCACATGAA
1 ACATCATCATTTTAAATCAAATG-A
*
69851 ACATCATCATTTT-AATGAAATGA
1 ACATCATCATTTTAAATCAAATGA
69874 CATATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 7 0.33
25 13 0.62
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (24 bp):
ACATCATCATTTTAAATCAAATGA
Found at i:76587 original size:21 final size:21
Alignment explanation
Indices: 76562--76603 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
76552 CCAGAATGGG
*
76562 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
76583 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
76604 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:76782 original size:33 final size:35
Alignment explanation
Indices: 76726--76819 Score: 129
Period size: 33 Copynumber: 2.7 Consensus size: 35
76716 GGGGAATCTG
* *
76726 TACCCCCTGGGGAGGAATTTGTTCTCGGGGAATCGA
1 TACCCCCTGGGG-GGAATCTGTTCTCGGGAAATCGA
* *
76762 TA-CCCCT-TGGGGAATCTGTTCCCGGGAAATCGA
1 TACCCCCTGGGGGGAATCTGTTCTCGGGAAATCGA
76795 TACCCCCTGGGGGGAATCTGTTCTC
1 TACCCCCTGGGGGGAATCTGTTCTC
76820 TCTCTGCAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
33 22 0.44
34 7 0.14
35 19 0.38
36 2 0.04
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.26
Consensus pattern (35 bp):
TACCCCCTGGGGGGAATCTGTTCTCGGGAAATCGA
Found at i:80103 original size:21 final size:21
Alignment explanation
Indices: 80077--80118 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
80067 CCAGAATGGG
*
80077 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
80098 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
80119 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:81557 original size:34 final size:34
Alignment explanation
Indices: 81519--81588 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
81509 GACTCACTCT
81519 ATTATTTAATTTTACTAAATTTCAAAAGAGTCAA
1 ATTATTTAATTTTACTAAATTTCAAAAGAGTCAA
81553 ATTATTTAATTTTACTAAATTTCAAAAGAGTCAA
1 ATTATTTAATTTTACTAAATTTCAAAAGAGTCAA
81587 AT
1 AT
81589 ACTGGTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (34 bp):
ATTATTTAATTTTACTAAATTTCAAAAGAGTCAA
Found at i:84226 original size:11 final size:11
Alignment explanation
Indices: 84212--84242 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
84202 CGTCCCTCAG
84212 CCGTCCCCGAA
1 CCGTCCCCGAA
84223 CCGTCCCCGAA
1 CCGTCCCCGAA
84234 CCGTCCCCG
1 CCGTCCCCG
84243 TACCCGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.13, C:0.58, G:0.19, T:0.10
Consensus pattern (11 bp):
CCGTCCCCGAA
Done.