Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001669.1 Hibiscus syriacus cultivar Beakdansim tig00003341_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: 89791
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:2975 original size:17 final size:18
Alignment explanation
Indices: 2945--2979 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2935 CTAGCTCTTC
2945 AGGGACCACACCTCCGTA
1 AGGGACCACACCTCCGTA
2963 AGGGACC-CACCTCCGTA
1 AGGGACCACACCTCCGTA
2980 CTTAGGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.26, C:0.40, G:0.23, T:0.11
Consensus pattern (18 bp):
AGGGACCACACCTCCGTA
Found at i:8691 original size:39 final size:40
Alignment explanation
Indices: 8637--8714 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
8627 CTAGTCAAAT
*
8637 ATATGCACCGTAGTGC-TAACACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTGCATAACACATAAGGTCGTGCCCACC
*
8676 ATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCAC
1 ATATGCACCGAAGTGCATAACACATAAGGTCGTGCCCAC
8715 AAATGTGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (40 bp):
ATATGCACCGAAGTGCATAACACATAAGGTCGTGCCCACC
Found at i:21454 original size:40 final size:40
Alignment explanation
Indices: 21394--21471 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
21384 ACCATAGTGC
* * * *
21394 TTACACATAAGGTTGTGCCCACCATATGCAATGAAGTGTA
1 TTACACACAAGGTCGAGCCCACCACATGCAATGAAGTGTA
*
21434 TTACACACAAGGTCGAGCCCACCACATGCACTGAAGTG
1 TTACACACAAGGTCGAGCCCACCACATGCAATGAAGTG
21472 CTTAATCGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (40 bp):
TTACACACAAGGTCGAGCCCACCACATGCAATGAAGTGTA
Found at i:25212 original size:2 final size:2
Alignment explanation
Indices: 25205--25230 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25195 TTGAGATCCG
25205 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
25231 GTGTCACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27896 original size:13 final size:13
Alignment explanation
Indices: 27878--27936 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
27868 GTCATAAATC
*
27878 TATGACGCGCATT
1 TATGACGCACATT
*
27891 TATGACACACATT
1 TATGACGCACATT
* *
27904 TATGACACATATT
1 TATGACGCACATT
*
27917 TATGACGCGCATT
1 TATGACGCACATT
*
27930 AATGACG
1 TATGACG
27937 TTCATTGAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:28006 original size:85 final size:85
Alignment explanation
Indices: 27914--28127 Score: 272
Period size: 85 Copynumber: 2.5 Consensus size: 85
27904 TATGACACAT
* *
27914 ATTTATGACGCGCAT-TAATGACGTT-CATTGAGTGTCATTGAAGCCCCCATCATAAATTAAG-A
1 ATTTATGACACGCATGT-ATGAC-TTACATTGCGTGTCATTGAAGCCCCCATCATAAA-TAAGCA
27976 TGACACACATTTGTGCGTCATAA
63 TGACACACATTTGTGCGTCATAA
* * * * * *
27999 ATTTATGACACGCATGTATGACTTACATTGCGCGTCGTTAAAGCCCCCGTCATAAATATGCTTGA
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCATCATAAATAAGCATGA
* * *
28064 CATACATTTGTGTGTCCTAA
66 CACACATTTGTGCGTCATAA
*
28084 ATTTATGACACGCATGTATGAATTACATTGCGTGTCATTGAAGC
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGC
28128 ACATATCATT
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 5 0.05
85 105 0.95
86 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCATCATAAATAAGCATGA
CACACATTTGTGCGTCATAA
Found at i:28150 original size:85 final size:84
Alignment explanation
Indices: 27914--28164 Score: 263
Period size: 85 Copynumber: 3.0 Consensus size: 84
27904 TATGACACAT
* * *
27914 ATTTATGACGCGCAT-TAATGACGTT-CATTGAGTGTCATTGAAGCCCCCATCATAAATTAAGAT
1 ATTTATGACACGCATGT-ATGA-ATTACATTGCGTGTCATTGAAGCCCCCATCATAAA-TAAGAT
* *
27977 GACACACATTTGTGCGTCATAA
63 GACAAACATTTGTGTGTCATAA
* * * * * * *
27999 ATTTATGACACGCATGTATGACTTACATTGCGCGTCGTTAAAGCCCCCGTCATAAATATGCTTGA
1 ATTTATGACACGCATGTATGAATTACATTGCGTGTCATTGAAGCCCCCATCATAAATAAG-ATGA
* *
28064 CATACATTTGTGTGTCCTAA
65 CAAACATTTGTGTGTCATAA
* ** *
28084 ATTTATGACACGCATGTATGAATTACATTGCGTGTCATTGAAGCACATATCATTAAAAAAGATGA
1 ATTTATGACACGCATGTATGAATTACATTGCGTGTCATTGAAGCCCCCATCA-TAAATAAGATGA
* *
28149 CAAACGTTCGTGTGTC
65 CAAACATTTGTGTGTC
28165 GTGATTGTAT
Statistics
Matches: 136, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
84 5 0.04
85 124 0.91
86 7 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGAATTACATTGCGTGTCATTGAAGCCCCCATCATAAATAAGATGAC
AAACATTTGTGTGTCATAA
Found at i:30677 original size:51 final size:50
Alignment explanation
Indices: 30604--30699 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 50
30594 TCTCCTCTTC
30604 CTTTTTCCTTTGCGGTGTCCCTTCTCCTTTAC-CCTCTTCCTTTTCTTTCT
1 CTTTTTCCTTTGCGGTGTCCCTTCT-CTTTACTCCTCTTCCTTTTCTTTCT
*
30654 CTTTTTCCATCTT-CGGTGTCCCTTCTCTTTTCTCCTCTTCCTTTTC
1 CTTTTTCC-T-TTGCGGTGTCCCTTCTCTTTACTCCTCTTCCTTTTC
30700 AACAAGTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
50 13 0.31
51 27 0.64
52 2 0.05
ACGTcount: A:0.02, C:0.36, G:0.07, T:0.54
Consensus pattern (50 bp):
CTTTTTCCTTTGCGGTGTCCCTTCTCTTTACTCCTCTTCCTTTTCTTTCT
Found at i:30680 original size:26 final size:25
Alignment explanation
Indices: 30600--30693 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 25
30590 CCTTTCTCCT
30600 CTTC-CTTTTTCCT-TTGCGGTGTCC
1 CTTCTCTTTTTCCTCTT-CGGTGTCC
** * * *
30624 CTTCTCCTTTACCCTCTTC-CTTTTC
1 CTTCT-CTTTTTCCTCTTCGGTGTCC
*
30649 TTTCTCTTTTTCCATCTTCGGTGTCC
1 CTTCTCTTTTTCC-TCTTCGGTGTCC
30675 CTTCTCTTTTCTCCTCTTC
1 CTTCTCTTTT-TCCTCTTC
30694 CTTTTCAACA
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
24 10 0.19
25 12 0.23
26 25 0.48
27 5 0.10
ACGTcount: A:0.02, C:0.37, G:0.07, T:0.53
Consensus pattern (25 bp):
CTTCTCTTTTTCCTCTTCGGTGTCC
Found at i:34553 original size:15 final size:15
Alignment explanation
Indices: 34528--34584 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
34518 GATGCTTTCT
*
34528 TTTTCCTTCTTTGACG
1 TTTT-CTTCTTAGACG
*
34544 TTTTCTTCTTCGACG
1 TTTTCTTCTTAGACG
*
34559 TTTTCTTCTTAGACA
1 TTTTCTTCTTAGACG
*
34574 TTGTCTTCTTA
1 TTTTCTTCTTA
34585 CCCCATGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.11, C:0.23, G:0.11, T:0.56
Consensus pattern (15 bp):
TTTTCTTCTTAGACG
Found at i:40136 original size:40 final size:40
Alignment explanation
Indices: 40043--40125 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
40033 TTCGAGTAAA
* * *
40043 ATATGCACCATAGTGC-TTACACATAAGGTCGTGCCCACC
1 ATATGAACCAAAGTGCATTACACATAAGGTCATGCCCACC
*
40082 ATATGAACCAAAGTGCATTACACATAAGGTTATGCCCACC
1 ATATGAACCAAAGTGCATTACACATAAGGTCATGCCCACC
40122 ATAT
1 ATAT
40126 ACACTGAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 14 0.36
40 25 0.64
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
ATATGAACCAAAGTGCATTACACATAAGGTCATGCCCACC
Found at i:56420 original size:213 final size:213
Alignment explanation
Indices: 56015--56441 Score: 588
Period size: 213 Copynumber: 2.0 Consensus size: 213
56005 AACAACCAAA
*
56015 TTCACGCATCCCTTCTTGTCTTTGAATACCAAATTGAATTCTTAAAGAAGTAAAATCCAACGGAT
1 TTCACGCATCCCTTCTTGTCTTTGAATACCAAATTGAATTCTTAAAGAAGTAAAATCCAACAGAT
** * *
56080 AAGCCTCAGTTTTGCTTCTTTCTTGCTAATTAAATATTGTAACGCTGCATTATAAGAAAAAACAA
66 AAGCCTCAGTTTTGCTTCTTTCTTGCTAATTAAATATCCTAACGATGCATGATAAGAAAAAACAA
* ** * * *
56145 CAATATTAGTCCCAAATAAATATTATCTATTTTTTTAAAGCAAATACTATGGCAAGAAGCTCTTT
131 CAATATTAGTCCCAAATAAATATAATAAATTTTTTTAAAGAAAATACTATGGAAAAAAGCTCTTT
56210 TTAGGCTGTAGAGTAATT
196 TTAGGCTGTAGAGTAATT
* * *
56228 TTCACGCATCGCTTCTTGTCTTTGATTTCCAAATTGAATT-TTAAAGAAGTAAAATCCAACAGAT
1 TTCACGCATCCCTTCTTGTCTTTGAATACCAAATTGAATTCTTAAAGAAGTAAAATCCAACAGAT
** * * * *
56292 AAGCCTTGGTTTTGCTTCTTTCTTTCTCATTAAATGTCCTAACGATGCATGCTAAG-AAAAACAA
66 AAGCCTCAGTTTTGCTTCTTTCTTGCTAATTAAATATCCTAACGATGCATGATAAGAAAAAACAA
* * *
56356 CGATATTAGTTCCAAGTAAATATGAAATAAATTTTTTTAAAGAAAATACTATGGAAAAAAGCTCT
131 CAATATTAGTCCCAAATAAATAT--AATAAATTTTTTTAAAGAAAATACTATGGAAAAAAGCTCT
* * *
56421 TTTTTGGTTGTTGAGTAATT
194 TTTTAGGCTGTAGAGTAATT
56441 T
1 T
56442 CTCTATGCTG
Statistics
Matches: 186, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
211 28 0.15
212 69 0.37
213 89 0.48
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (213 bp):
TTCACGCATCCCTTCTTGTCTTTGAATACCAAATTGAATTCTTAAAGAAGTAAAATCCAACAGAT
AAGCCTCAGTTTTGCTTCTTTCTTGCTAATTAAATATCCTAACGATGCATGATAAGAAAAAACAA
CAATATTAGTCCCAAATAAATATAATAAATTTTTTTAAAGAAAATACTATGGAAAAAAGCTCTTT
TTAGGCTGTAGAGTAATT
Found at i:57916 original size:22 final size:20
Alignment explanation
Indices: 57883--57926 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
57873 ACATTGAGTG
57883 AAAATAATGAATGAAAATAA
1 AAAATAATGAATGAAAATAA
*
57903 AAAATTAACTGAATTAAAATAA
1 AAAA-TAA-TGAATGAAAATAA
57925 AA
1 AA
57927 CGAAATGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 3 0.14
22 14 0.67
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAATAATGAATGAAAATAA
Found at i:71424 original size:107 final size:107
Alignment explanation
Indices: 71235--71451 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 107
71225 ACAGGATTAA
*
71235 CAAGTTTAGCAATAAGTACAATCACTGTCTTATTAAATGTTGACATGGACTCGCGACCCTCTAAT
1 CAAGTTTAGCAATAAGTACAATCACTGTCTTATTAAATGTTGACATGGACTCACGACCCTCTAAT
71300 AAAGCAAGACAAAGATTAATAACATCGCTTCCAACCAACAGC
66 AAAGCAAGACAAAGATTAATAACATCGCTTCCAACCAACAGC
*
71342 CAAGTTTAGCAATAAGTACAATCACTGTCTTATTAATTGTTGACATGGACTCACGACCCTCTAAT
1 CAAGTTTAGCAATAAGTACAATCACTGTCTTATTAAATGTTGACATGGACTCACGACCCTCTAAT
*
71407 AAAGCAAGACAATGATTAATAACATCGCTTCCAACCAACAGC
66 AAAGCAAGACAAAGATTAATAACATCGCTTCCAACCAACAGC
71449 CAA
1 CAA
71452 AACGACCGAT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (107 bp):
CAAGTTTAGCAATAAGTACAATCACTGTCTTATTAAATGTTGACATGGACTCACGACCCTCTAAT
AAAGCAAGACAAAGATTAATAACATCGCTTCCAACCAACAGC
Found at i:74364 original size:38 final size:36
Alignment explanation
Indices: 74320--74771 Score: 346
Period size: 36 Copynumber: 12.3 Consensus size: 36
74310 TTTTATTTAT
74320 ATATATATATATATATTATAG-TTTACAAATGATGTTTGAA
1 ATATATATATA-ATA-TATAGTTTTA-AAAT-AT-TTTGAA
74360 ATATATATATAATATATAGTTTTTAAAATATTTTGAA
1 ATATATATATAATATATAG-TTTTAAAATATTTTGAA
*
74397 A-ATAAATATAATATATAGTTTTTTGAAAATATTTTG-A
1 ATATATATATAATATATAG--TTTT-AAAATATTTTGAA
* *
74434 A-ATATATATAATATATAGTTTTTGAAAACATTTTTAA
1 ATATATATATAATATATAG-TTTT-AAAATATTTTGAA
* * * *
74471 A-AAACTTATATAGTATATAGTATTGAAATCATTTTGAA
1 ATATA--TATATAATATATAGTTTTAAAAT-ATTTTGAA
* * *
74509 A-ACATATGTAATATATAGTTTTGAAATTATTTTGAA
1 ATATATATATAATATATAGTTTT-AAAATATTTTGAA
*
74545 A-ACT-TATATAATATATAGTTTTAAAAACATTTTTG-A
1 ATA-TATATATAATATATAGTTTT-AAAATA-TTTTGAA
* *
74581 A-ACATATATAATATATAGTTTGAAAATATTTTTTG-A
1 ATATATATATAATATATAGTTTTAAAATA--TTTTGAA
*
74617 A-A-ATATATAATATATAGTTTTAAAACATTTTCGAA
1 ATATATATATAATATATAGTTTTAAAATATTTT-GAA
* *
74652 A-A-CTATATAATATATAGTTTTGAAAATATTTTTAA
1 ATATATATATAATATATAGTTTT-AAAATATTTTGAA
* *
74687 AAATATTATATAATATATAGTTTTAAAACATTTTTGAA
1 ATATA-TATATAATATATAGTTTTAAAATA-TTTTGAA
* * *
74725 A-ATATATAT--TATATAGTTTTTGGAAATATTTTTAT
1 ATATATATATAATATATAG-TTTT-AAAATATTTTGAA
74760 ATATAATATATA
1 ATAT-ATATATA
74772 TTATTATTGT
Statistics
Matches: 351, Mismatches: 36, Indels: 52
0.80 0.08 0.12
Matches are distributed among these distances:
33 4 0.01
34 8 0.02
35 62 0.18
36 127 0.36
37 59 0.17
38 56 0.16
39 20 0.06
40 15 0.04
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
ATATATATATAATATATAGTTTTAAAATATTTTGAA
Found at i:74764 original size:25 final size:24
Alignment explanation
Indices: 74717--74762 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
74707 TTTTAAAACA
74717 TTTTTGAAAATATATATTATATAG
1 TTTTTGAAAATATATATTATATAG
* *
74741 TTTTTGGAAATAT-TTTTATATA
1 TTTTTGAAAATATATATTATATA
74763 TAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (24 bp):
TTTTTGAAAATATATATTATATAG
Found at i:74770 original size:73 final size:71
Alignment explanation
Indices: 74364--74771 Score: 436
Period size: 73 Copynumber: 5.6 Consensus size: 71
74354 TTTGAAATAT
* * *
74364 ATATATAATATATAGTTTTTAAAATATTTTGAAAATAA-ATATAATATATAGTTTTTTGAAA-AT
1 ATATATAATATATAGTTTTGAAAATATTTT-TAAATAATATATAATATATAG--TTTTAAAACAT
*
74427 ATTTTGAAAT
63 -TTTTGAAAC
* * * * *
74437 ATATATAATATATAGTTTTTGAAAACATTTTTAAAAAACTTATATAGTATATAGTATTGAAATCA
1 ATATATAATATATAG-TTTTGAAAATATTTTTAAATAA--TATATAATATATAGT-TTTAAAACA
74502 -TTTTGAAAAC
62 TTTTTG-AAAC
* * * *
74512 ATATGTAATATATAGTTTTGAAATTATTTTGAAA-ACTTATATAATATATAGTTTTAAAAACATT
1 ATATATAATATATAGTTTTGAAAATATTTTTAAATA-ATATATAATATATAGTTTT-AAAACATT
74576 TTTGAAAC
64 TTTGAAAC
*
74584 ATATATAATATATAG-TTTGAAAATATTTTTTGAA-AATATATAATATATAGTTTTAAAACATTT
1 ATATATAATATATAGTTTTGAAAATA-TTTTTAAATAATATATAATATATAGTTTTAAAACATTT
*
74647 TCGAAA-
65 TTGAAAC
*
74653 ACTATATAATATATAGTTTTGAAAATATTTTTAAAAATATTATATAATATATAGTTTTAAAACAT
1 A-TATATAATATATAGTTTTGAAAATATTTTT--AAATAATATATAATATATAGTTTTAAAACAT
74718 TTTTGAAA-
63 TTTTGAAAC
* *
74726 ATATATATTATATAGTTTTTGGAAATATTTTTATATATAATATATA
1 ATATATAATATATAG-TTTTGAAAATATTTTTA-A-ATAATATATA
74772 TTATTATTGT
Statistics
Matches: 287, Mismatches: 29, Indels: 38
0.81 0.08 0.11
Matches are distributed among these distances:
69 1 0.00
70 33 0.11
71 40 0.14
72 60 0.21
73 84 0.29
74 35 0.12
75 21 0.07
76 13 0.05
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (71 bp):
ATATATAATATATAGTTTTGAAAATATTTTTAAATAATATATAATATATAGTTTTAAAACATTTT
TGAAAC
Found at i:74778 original size:3 final size:3
Alignment explanation
Indices: 74770--74851 Score: 51
Period size: 3 Copynumber: 26.3 Consensus size: 3
74760 ATATAATATA
* * *
74770 TAT TAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TA- TATT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT
* * *
74816 TTT TCAT TA- TAT GTTT TTT TAT TAT TAT TAAT TAT T
1 TAT T-AT TAT TAT -TAT TAT TAT TAT TAT T-AT TAT T
74852 TTTTGTTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.06
3 50 0.75
4 13 0.19
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:74854 original size:22 final size:21
Alignment explanation
Indices: 74770--74855 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 21
74760 ATATAATATA
* * * *
74770 TATTATTATTGTTGTTGTTAT
1 TATTATTATTATTATTTTTTT
*
74791 TATTATTATTATTATATTTATT
1 TATTATTATTATTAT-TTTTTT
*
74813 TATTTTTCATTA-TATGTTTTTT
1 TATTATT-ATTATTAT-TTTTTT
74835 TATTATTATTAATTATTTTTT
1 TATTATTATT-ATTATTTTTT
74856 GTTTTAATTC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 16 0.31
22 29 0.56
23 7 0.13
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (21 bp):
TATTATTATTATTATTTTTTT
Found at i:78895 original size:45 final size:45
Alignment explanation
Indices: 78832--79199 Score: 292
Period size: 45 Copynumber: 8.2 Consensus size: 45
78822 TGAAAATACT
* ** *
78832 AATGCATATGGGTGCATTATTGGCATTAAAAG-ATGCCATAGTTGA
1 AATGCATATGGGTACATTATTAACA-TAAAAGTATGCTATAGTTGA
* * * * *
78877 AATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGA
1 AATGCATATGGGTACATTATTAACATAAAAGTATGCTATAGTTGA
* * * * *
78922 AATGTATTTGGGTACATTATCAAAATAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTACATTATTAACATAAAAGTATGCTATAGTTGA
* * * * * *
78967 AATGCATATGGGTGCATTATCAACAGAAATGTATGTTAGAGTTGA
1 AATGCATATGGGTACATTATTAACATAAAAGTATGCTATAGTTGA
* * * * * * *
79012 AATGCATATAGGTGCATTATCAACAGAAGAGCATGCTACAGTTGA
1 AATGCATATGGGTACATTATTAACATAAAAGTATGCTATAGTTGA
* * * * * *
79057 AATGTATGTGGGTACATTATCAACATAAAAGTGTACTATGGTTGA
1 AATGCATATGGGTACATTATTAACATAAAAGTATGCTATAGTTGA
* * * *
79102 AATGTATATGGGTA-AATAGTCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTACATTA-TTAACATAAAAGTATGCTATAGTTGA
* * * * * * *
79147 AGTGCATATGGCTGCATTATCAACATAAAAG-ATGTTATAATTTA
1 AATGCATATGGGTACATTATTAACATAAAAGTATGCTATAGTTGA
79191 AAGTGCATA
1 AA-TGCATA
79200 ATGGTTGATT
Statistics
Matches: 266, Mismatches: 53, Indels: 8
0.81 0.16 0.02
Matches are distributed among these distances:
44 18 0.07
45 245 0.92
46 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTACATTATTAACATAAAAGTATGCTATAGTTGA
Found at i:78965 original size:90 final size:90
Alignment explanation
Indices: 78858--79177 Score: 367
Period size: 90 Copynumber: 3.6 Consensus size: 90
78848 TTATTGGCAT
* *
78858 TAAAAG-ATGCCATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGA
1 TAAAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGA
* *
78922 AATGTATTTGGGTACATTATCAAAA
66 AATGTATATGGGTACATTATCAACA
* * * **
78947 TAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAATGTATGTTA-GAGTTG
1 TAAAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATG-GTTG
* * *
79011 AAATGCATATAGGTGCATTATCAACA
65 AAATGTATATGGGTACATTATCAACA
* * * * * * * *
79037 GAAGAGCATGCTACAGTTGAAATGTATGTGGGTACATTATCAACATAAAAGTGTACTATGGTTGA
1 TAAAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGA
*
79102 AATGTATATGGGTA-AATAGTCAACA
66 AATGTATATGGGTACATTA-TCAACA
* * * * *
79127 TAAAAGTATACTATAGTTGAAGTGCATATGGCTGCATTATCAACATAAAAG
1 TAAAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAG
79178 ATGTTATAAT
Statistics
Matches: 189, Mismatches: 38, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
89 10 0.05
90 178 0.94
91 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (90 bp):
TAAAAGTATGCTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGA
AATGTATATGGGTACATTATCAACA
Found at i:79033 original size:135 final size:134
Alignment explanation
Indices: 78871--79177 Score: 366
Period size: 135 Copynumber: 2.3 Consensus size: 134
78861 AAGATGCCAT
* * * ** *
78871 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATTTGGGTA
1 AGTTGAAATGCATAT-GGTGCATTATCAACAGAAAAGCATACTACAGTTGAAATGTATGTGGGTA
* * * *
78936 CATTATCAAAATAAAAGTATGCTA-GAGTTGAAATGCATATGGGTGCATTA-TCAACAGAAATGT
65 CATTATCAAAATAAAAGTATACTATG-GTTGAAATGCATATGGGT-AAATAGTCAACAGAAAAGT
**
78999 ATGTTAG
128 ATACTAG
* *
79006 AGTTGAAATGCATATAGGTGCATTATCAACAGAAGAGCATGCTACAGTTGAAATGTATGTGGGTA
1 AGTTGAAATGCATAT-GGTGCATTATCAACAGAAAAGCATACTACAGTTGAAATGTATGTGGGTA
* * * *
79071 CATTATCAACATAAAAGTGTACTATGGTTGAAATGTATATGGGTAAATAGTCAACATAAAAGTAT
65 CATTATCAAAATAAAAGTATACTATGGTTGAAATGCATATGGGTAAATAGTCAACAGAAAAGTAT
*
79136 ACTAT
130 ACTAG
* *
79141 AGTTGAAGTGCATATGGCTGCATTATCAACATAAAAG
1 AGTTGAAATGCATATGG-TGCATTATCAACAGAAAAG
79178 ATGTTATAAT
Statistics
Matches: 146, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
134 5 0.03
135 140 0.96
136 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (134 bp):
AGTTGAAATGCATATGGTGCATTATCAACAGAAAAGCATACTACAGTTGAAATGTATGTGGGTAC
ATTATCAAAATAAAAGTATACTATGGTTGAAATGCATATGGGTAAATAGTCAACAGAAAAGTATA
CTAG
Found at i:81973 original size:103 final size:102
Alignment explanation
Indices: 81790--81992 Score: 295
Period size: 103 Copynumber: 2.0 Consensus size: 102
81780 CCAAATTTTA
* * *
81790 ATATTACAATAAAGCTTGAGTTTTCCCTCTAAAGCAATTAGTTAAAAGCCCTGACTTTATGGACA
1 ATATTACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTAGTTAAAAGCCCAGACTTTATGGACA
81855 AGATTCAGCTTGCCTGATAAAGGTGATTATAATATAT
66 AGATTCAGCTTGCCTGATAAAGGTGATTATAATATAT
* *
81892 ATATATACAATAAAGCTTGAGCTGTCCCTC-AAGAGCAATTGGTTAAACGCTCCAG-CTTTATGG
1 ATAT-TACAATAAAGCTTGAGCTGTCCCTCTAA-AGCAATTAGTTAAAAGC-CCAGACTTTATGG
*
81955 ATAAGATTCAG-TTAGCCTGATAAAGGTGATTATAATAT
63 ACAAGATTCAGCTT-GCCTGATAAAGGTGATTATAATAT
81993 TGAGTTGTCC
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
102 8 0.09
103 80 0.88
104 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (102 bp):
ATATTACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTAGTTAAAAGCCCAGACTTTATGGACA
AGATTCAGCTTGCCTGATAAAGGTGATTATAATATAT
Found at i:83708 original size:85 final size:83
Alignment explanation
Indices: 83369--83860 Score: 511
Period size: 85 Copynumber: 5.8 Consensus size: 83
83359 GAATTATTCG
* **
83369 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCTACCAAAAGGTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-AACAAAACCTTCGAGTTCGATT-CATTCAGC
*
83434 TCAAGGGCATATCAATTTTA
64 TCAAGGGCATATCAAATTTA
* * * *
83454 CAGCATAGA-TCAAGGCGAAAAGGGTTATCTATTAGTAAAAAACCTTCGAGTTCGATTTCATTCA
1 CAGCATA-ACTCAAGGCGAGAAGGGTTATCTGTCA--ACAAAACCTTCGAGTTCGA-TTCATTCA
**
83518 GCTCAAGAACATATCAAATTTA
62 GCTCAAGGGCATATCAAATTTA
* * ** * * *
83540 CAGCATAACTCAAGGAGAGAATGACTATATGTTAAC-AAACCTTCGAGTTCGATTCTATTTAGCT
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAACCTTCGAGTTCGATTC-ATTCAGCT
83604 CAAGGGCATATCAAATTTA
65 CAAGGGCATATCAAATTTA
* * * * *
83623 CAGCATAACTTAAGGCGAGAAGGGTTATCTATCAACAAAGACCTTCGTGTTTGATTACATTTAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAA-ACCTTCGAGTTCGATT-CATTCAGC
*
83688 TCAAGGACATATCAAATTTA
64 TCAAGGGCATATCAAATTTA
* * *
83708 CAGCATAAATCAAGGCAAGAAGGGTTATCTGTCAACAAATACCTTCGAGTTTGATTCTATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAA-ACCTTCGAGTTCGATTC-ATTCAGC
*
83773 TCAAGGGCATGTCAAATTTA
64 TCAAGGGCATATCAAATTTA
* * ** * ** * * *
83793 CAGTATAGCTTTAGTCGAGAAAAGCTATCTGTCAATAAAAAACTGTCGAGTTCGATTCCATTCAG
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAAACCT-TCGAGTTCGATT-CATTCAG
83858 CTC
63 CTC
83861 GATGATATAT
Statistics
Matches: 340, Mismatches: 54, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
82 3 0.01
83 68 0.20
84 5 0.01
85 171 0.50
86 90 0.26
87 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (83 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAACCTTCGAGTTCGATTCATTCAGCTC
AAGGGCATATCAAATTTA
Found at i:86417 original size:24 final size:24
Alignment explanation
Indices: 86390--86441 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
86380 AACGGATATA
*
86390 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
86414 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
86438 TCAA
1 TCAA
86442 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:86442 original size:24 final size:24
Alignment explanation
Indices: 86410--86528 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 24
86400 AAACATAAAT
*
86410 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
86434 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
86458 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
86482 CATGTC-AGATATCAAATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
86506 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
86529 TCAAATCAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 78 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:86537 original size:24 final size:24
Alignment explanation
Indices: 86413--86546 Score: 146
Period size: 24 Copynumber: 5.6 Consensus size: 24
86403 CATAAATCAG
* *
86413 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAA
*
86437 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
86461 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
86485 GTC-AGATATCAAATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
*
86509 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
86533 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
86547 AAAATATTCA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 5 0.05
24 88 0.93
25 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:89008 original size:15 final size:15
Alignment explanation
Indices: 88974--89022 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
88964 GGTCAACAGT
88974 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
* *
88991 GGTCAATGGGTTAAC
1 GGTCAACGGGTCAAC
89006 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
89021 GG
1 GG
89023 GTCGGGTCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 21 0.75
17 7 0.25
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:89035 original size:18 final size:18
Alignment explanation
Indices: 89012--89052 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
89002 TAACGGTCAA
89012 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
89030 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
89048 CGGGT
1 CGGGT
89053 TCTGACCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:89043 original size:8 final size:8
Alignment explanation
Indices: 88964--89025 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
88954 TCAAAGTTTT
88964 GGTCAACAG
1 GGTCAAC-G
88973 TGGTCAACG
1 -GGTCAACG
88982 CCGGTCAAC-
1 --GGTCAACG
*
88991 GGTCAATG
1 GGTCAACG
*
88999 GGTTAAC-
1 GGTCAACG
89006 GGTCAACG
1 GGTCAACG
89014 GGTCAACG
1 GGTCAACG
89022 GGTC
1 GGTC
89026 GGGTCGGGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 12 0.27
8 17 0.39
9 1 0.02
10 14 0.32
ACGTcount: A:0.24, C:0.24, G:0.34, T:0.18
Consensus pattern (8 bp):
GGTCAACG
Done.