Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004554.1 Hibiscus syriacus cultivar Beakdansim tig00010116_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: 75315
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:5795 original size:19 final size:19
Alignment explanation
Indices: 5753--5800 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5743 CAAATTTAAA
* *
5753 GGGTCGGGTCAATGTTAAC
1 GGGTCGGGTCAAAGTCAAC
* *
5772 AGGTCGGGTTAAAGTCAAC
1 GGGTCGGGTCAAAGTCAAC
*
5791 GGGTCAGGTC
1 GGGTCGGGTC
5801 GGGTTGACTC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (19 bp):
GGGTCGGGTCAAAGTCAAC
Found at i:10959 original size:29 final size:30
Alignment explanation
Indices: 10929--10985 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
10919 AACATATTTA
*
10929 AAAAAT-AAAACTT-AAAATAAAATAAAAT
1 AAAAATGAAAACTTGAAAAGAAAATAAAAT
*
10957 AAAATTGAAAACTTGAAAAGAAAATAAAA
1 AAAAATGAAAACTTGAAAAGAAAATAAAA
10986 GAAATAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 7 0.28
30 13 0.52
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.19
Consensus pattern (30 bp):
AAAAATGAAAACTTGAAAAGAAAATAAAAT
Found at i:14615 original size:54 final size:54
Alignment explanation
Indices: 14495--14895 Score: 500
Period size: 54 Copynumber: 7.5 Consensus size: 54
14485 ATAAGTTCTT
* * * * *
14495 TGGGGTGCACACGTAGTGCCGATACGGTTGTTCATAAAC-CATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* * * *
14548 TGGGTTGCACACTTAGTGCCGACACGGTCATTCATAAACTTATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* * * * *
14602 TGGGTTGAACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAGTTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* * * * *
14656 T-GGTTGCACAGTTAGTGCTGACACGGTCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* * *
14709 TGGGTTGCACACTTAGTGCCGATACGATCGTTCATAAACATATTATTAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* ** * *
14763 TGGGTTGCACACTTACTATCGATACGGTCATTCATAAACATATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* * *
14817 TGGGTTGCACACTTAGTGTCGATACAGTCGTTCATAAACATATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* *
14871 TGGGTAGCTCACTTAGTGCCGATAC
1 TGGGTTGCACACTTAGTGCCGATAC
14896 TACATATAGT
Statistics
Matches: 300, Mismatches: 46, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
53 81 0.27
54 219 0.73
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
Found at i:14895 original size:108 final size:108
Alignment explanation
Indices: 14495--14892 Score: 516
Period size: 107 Copynumber: 3.7 Consensus size: 108
14485 ATAAGTTCTT
* * * *
14495 TGGGGTGCACACGTAGTGCCGATACGGTTGTTCATAAAC-CATTATGAATTTCGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACA
* *
14559 CTTAGTGCCGACACGGTCATTCATAAACTTATTATGAATTCCA
66 CTTAGTGCCGACACGGTCATTCATAAACTTATTATGAATTTCG
* * * *
14602 TGGGTTGAACACTTAGTGCTGATACGGTCGTTCATAAACTTATTATGAGTTTCGT-GGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACA
* * *
14666 GTTAGTGCTGACACGGTCGTTCATAAACTTATTATGAA-TTCTG
66 CTTAGTGCCGACACGGTCATTCATAAACTTATTATGAATTTC-G
* * * *
14709 TGGGTTGCACACTTAGTGCCGATACGATCGTTCATAAACATATTATTAATTCCATGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACA
* ** * *
14774 CTTACTATCGATACGGTCATTCATAAACATATTATGAATTTCG
66 CTTAGTGCCGACACGGTCATTCATAAACTTATTATGAATTTCG
* * * *
14817 TGGGTTGCACACTTAGTGTCGATACAGTCGTTCATAAACATATTATGAA-TTCTGTGGGTAGCTC
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTC-GTGGGTTGCAC
14881 ACTTAGTGCCGA
65 ACTTAGTGCCGA
14893 TACTACATAT
Statistics
Matches: 247, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
106 2 0.01
107 127 0.51
108 115 0.47
109 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (108 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACA
CTTAGTGCCGACACGGTCATTCATAAACTTATTATGAATTTCG
Found at i:25653 original size:23 final size:23
Alignment explanation
Indices: 25627--25676 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
25617 TTATTTTATG
25627 AATTTAATATTA-ATAAAATATTT
1 AATTTAATATTATATAAAATA-TT
* * *
25650 AATTTTATTTTATTTAAAATATT
1 AATTTAATATTATATAAAATATT
25673 AATT
1 AATT
25677 ATTAGAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTAATATTATATAAAATATT
Found at i:25687 original size:24 final size:21
Alignment explanation
Indices: 25660--25716 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
25650 AATTTTATTT
25660 TATTTAAAATATTAATTATTAGAA
1 TATTTAAAATA-TAATTATT--AA
*
25684 TATTTTAAAATATATTTATTAA
1 TA-TTTAAAATATAATTATTAA
*
25706 TATTTATAATA
1 TATTTAAAATA
25717 ACATAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.27
22 4 0.13
24 9 0.30
25 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTAAAATATAATTATTAA
Found at i:25831 original size:18 final size:18
Alignment explanation
Indices: 25782--25833 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 18
25772 ATAAGATTTT
*
25782 ATATTTTTATT-TTAATA
1 ATATTTATATTATTAATA
*
25799 ATATATAATAAATTATTAATA
1 ATAT-T--TATATTATTAATA
25820 ATATTTATATTATT
1 ATATTTATATTATT
25834 TCTTAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
20 5 0.18
21 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTATATTATTAATA
Found at i:27221 original size:19 final size:19
Alignment explanation
Indices: 27193--27236 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
27183 ACCCGAAATA
*
27193 ACATTCATGGAAAAATATC
1 ACATTTATGGAAAAATATC
27212 ACATTTATGGAAAAATATC
1 ACATTTATGGAAAAATATC
27231 ACATTT
1 ACATTT
27237 TTATATAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (19 bp):
ACATTTATGGAAAAATATC
Found at i:31236 original size:13 final size:14
Alignment explanation
Indices: 31203--31236 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
31193 TAAGATTTTC
31203 TTTGAAA-ATAAAT
1 TTTGAAATATAAAT
31216 TTTGAAATA-AAAT
1 TTTGAAATATAAAT
31229 TTTGAAAT
1 TTTGAAAT
31237 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.95
14 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (14 bp):
TTTGAAATATAAAT
Found at i:33615 original size:21 final size:23
Alignment explanation
Indices: 33551--33616 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
33541 ATGCATGGCA
33551 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
33574 GAGTGCATCGGTGTATC-TTCAA-
1 GAGTGCATCGATGCA-CATTCAAG
*
33596 GA-TGTATCGATGCACATTCAA
1 GAGTGCATCGATGCACATTCAA
33617 AGGGATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 2 0.06
23 18 0.50
24 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:39507 original size:64 final size:66
Alignment explanation
Indices: 39439--39585 Score: 196
Period size: 66 Copynumber: 2.3 Consensus size: 66
39429 ACTAAGAGTT
*
39439 CATCGATGTATAAAATGCATTCGATG-TTTT-A-AAATAGT-CTGAGTGCATCGATGCATGGCT-
1 CATCGATGCATAAAATGCATTCGATGTTTTTCATAAA-A-TCCTGAGTGCATCGATGCATGG-TA
39499 TATA
63 TATA
**
39503 CATCGATGCATTTAATGCATTCGATGTTTTTCATAAAATCCTGAGTGCATCGATGCATGGTATAT
1 CATCGATGCATAAAATGCATTCGATGTTTTTCATAAAATCCTGAGTGCATCGATGCATGGTATAT
*
39568 G
66 A
39569 CATCGATGCATAAAATG
1 CATCGATGCATAAAATG
39586 TTTTCAATGT
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
64 23 0.32
65 6 0.08
66 40 0.56
67 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (66 bp):
CATCGATGCATAAAATGCATTCGATGTTTTTCATAAAATCCTGAGTGCATCGATGCATGGTATAT
A
Found at i:40820 original size:12 final size:13
Alignment explanation
Indices: 40793--40818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40783 TTTTTAATCA
40793 TCTCTCAATTTTT
1 TCTCTCAATTTTT
40806 TCTCTCAATTTTT
1 TCTCTCAATTTTT
40819 CTTTTCTTTT
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:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTCAATTTTT
Found at i:42043 original size:21 final size:21
Alignment explanation
Indices: 42017--42074 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
42007 CGATATCAAG
42017 TAGAATTGAATATTTCTACTT
1 TAGAATTGAATATTTCTACTT
42038 TAGAATTGAATATTTCTACTT
1 TAGAATTGAATATTTCTACTT
**
42059 TAGAATTCTATATTTC
1 TAGAATTGAATATTTC
42075 ATTCTCAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (21 bp):
TAGAATTGAATATTTCTACTT
Found at i:43796 original size:45 final size:46
Alignment explanation
Indices: 43737--43823 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
43727 GTTCTTACCA
*
43737 ATATACATATCATTTA-TCTCATAAGCTCGTAAGCTTATTTTATCC
1 ATATACATACCATTTATTCTCATAAGCTCGTAAGCTTATTTTATCC
* *
43782 ATATACTTACCATTTATTTTCATAAGCTCGTAAGCTTATTTT
1 ATATACATACCATTTATTCTCATAAGCTCGTAAGCTTATTTT
43824 CCTGTTTACC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 14 0.37
46 24 0.63
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (46 bp):
ATATACATACCATTTATTCTCATAAGCTCGTAAGCTTATTTTATCC
Found at i:44009 original size:61 final size:61
Alignment explanation
Indices: 43930--44045 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
43920 CTAAACTTGA
* *
43930 ACTAAGCTTACATCATAGTGCTAATTCGGACAAT-ACACATAAGGTCGTGTCCACCACCTGC
1 ACTAAGCTTACATCATAGTGCTAATCCGGAC-ATGACACATAAGGTCGTATCCACCACCTGC
* *
43991 ACTAAGCTTAC-GCTATAGTGCTAATCCGGACATGATACATAAGGTCGTATCCACC
1 ACTAAGCTTACATC-ATAGTGCTAATCCGGACATGACACATAAGGTCGTATCCACC
44046 TTCCCCGCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 3 0.06
61 46 0.94
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (61 bp):
ACTAAGCTTACATCATAGTGCTAATCCGGACATGACACATAAGGTCGTATCCACCACCTGC
Found at i:49579 original size:38 final size:38
Alignment explanation
Indices: 49537--49616 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
49527 CAAAATTTAA
* **
49537 CGAAATTAAAATCAACCAAAACCAAAATTAACCCGAAC
1 CGAAAATAAAATCAACCAAAACCAAAAGCAACCCGAAC
* * *
49575 CGAAAATGAAATTAACCAAAACCAAAAGCAACTCGAAC
1 CGAAAATAAAATCAACCAAAACCAAAAGCAACCCGAAC
49613 CGAA
1 CGAA
49617 TGCAACTCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.55, C:0.25, G:0.09, T:0.11
Consensus pattern (38 bp):
CGAAAATAAAATCAACCAAAACCAAAAGCAACCCGAAC
Found at i:49597 original size:22 final size:21
Alignment explanation
Indices: 49561--49601 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
49551 ACCAAAACCA
**
49561 AAATTAACCCGAACCGAAAATG
1 AAATTAACCAAAACC-AAAATG
49583 AAATTAACCAAAACCAAAA
1 AAATTAACCAAAACCAAAA
49602 GCAACTCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.22, G:0.07, T:0.12
Consensus pattern (21 bp):
AAATTAACCAAAACCAAAATG
Found at i:51724 original size:47 final size:50
Alignment explanation
Indices: 51655--51756 Score: 156
Period size: 47 Copynumber: 2.1 Consensus size: 50
51645 GGAGTTACTA
*
51655 TGGTAAGAAGTAACTCCTAATTGTTA-TGT-GC-ATGCATATATGTGCAT
1 TGGTAAGAAGTAACTCCTAATTGTTATTATGGCGATGCATATATGTGCAT
*
51702 TGGTAAGAAGTGACTCCTAATTGTTATTATGGCGTATGCATATATGTGCAT
1 TGGTAAGAAGTAACTCCTAATTGTTATTATGGCG-ATGCATATATGTGCAT
51753 TGGT
1 TGGT
51757 GAGCTTATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
47 25 0.51
48 2 0.04
49 2 0.04
51 20 0.41
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (50 bp):
TGGTAAGAAGTAACTCCTAATTGTTATTATGGCGATGCATATATGTGCAT
Found at i:55397 original size:27 final size:27
Alignment explanation
Indices: 55363--55453 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
55353 ATTTTTCTTA
*
55363 TTCTTCTGGCTCATAGCTTTTACATTC
1 TTCTTCTGGCTCATAGCTTTCACATTC
*
55390 TTCTTCTGGCTCATAGCTTTCACTTTC
1 TTCTTCTGGCTCATAGCTTTCACATTC
*
55417 TTCTTCTTTTGGCTCGTAGCTTTCAC-TTGC
1 TTCTTC---TGGCTCATAGCTTTCACATT-C
55447 TTCTTCT
1 TTCTTCT
55454 TCAATAATTG
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
27 32 0.56
29 2 0.04
30 23 0.40
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (27 bp):
TTCTTCTGGCTCATAGCTTTCACATTC
Found at i:55423 original size:30 final size:30
Alignment explanation
Indices: 55356--55455 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
55346 TCCATTAATT
* *
55356 TTTCTTATTCTTCTGGCTCATAGCTTTTAC
1 TTTCTTCTTCTTCTGGCTCATAGCTTTCAC
*
55386 ---ATTCTTCTTCTGGCTCATAGCTTTCAC
1 TTTCTTCTTCTTCTGGCTCATAGCTTTCAC
* *
55413 TTTCTTCTTCTTTTGGCTCGTAGCTTTCAC
1 TTTCTTCTTCTTCTGGCTCATAGCTTTCAC
*
55443 TTGCTTCTTCTTC
1 TTTCTTCTTCTTC
55456 AATAATTGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
27 24 0.41
30 35 0.59
ACGTcount: A:0.10, C:0.27, G:0.11, T:0.52
Consensus pattern (30 bp):
TTTCTTCTTCTTCTGGCTCATAGCTTTCAC
Found at i:58979 original size:17 final size:17
Alignment explanation
Indices: 58957--59000 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
58947 ATATGCTATT
*
58957 TATTAATTATATAACCA
1 TATTAATTACATAACCA
* *
58974 TATTAATCACATAACTA
1 TATTAATTACATAACCA
58991 TAATTAATTA
1 T-ATTAATTA
59001 AAGTTTGACC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTAATTACATAACCA
Found at i:59133 original size:13 final size:15
Alignment explanation
Indices: 59103--59136 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
59093 AATTAATACA
59103 TAATACAAAGTAAAT
1 TAATACAAAGTAAAT
59118 TAATACAAA-T-AAT
1 TAATACAAAGTAAAT
59131 TAATAC
1 TAATAC
59137 TATTAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 1 0.05
15 9 0.47
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (15 bp):
TAATACAAAGTAAAT
Found at i:69260 original size:15 final size:16
Alignment explanation
Indices: 69242--69271 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
69232 TTACAAATAA
69242 AAAATTTA-ACTTTTG
1 AAAATTTACACTTTTG
69257 AAAATTTACACTTTT
1 AAAATTTACACTTTT
69272 ACTCCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAATTTACACTTTTG
Found at i:69323 original size:29 final size:28
Alignment explanation
Indices: 69247--69333 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
69237 AATAAAAAAT
* *
69247 TTAACTTTTGAAAATTTACACTTTTACTCC
1 TTAACATTT-AAAATTTACAC-TTTAGTCC
* *
69277 TTAAAATTTACAACTTTACACTTTAGTCC
1 TTAACATTTA-AAATTTACACTTTAGTCC
*
69306 TTAACCTTTCAAAATTTACA-TTCTAGTC
1 TTAACATTT-AAAATTTACACTT-TAGTC
69334 ATCAGTCCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 28 0.60
30 17 0.36
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (28 bp):
TTAACATTTAAAATTTACACTTTAGTCC
Found at i:71944 original size:21 final size:21
Alignment explanation
Indices: 71910--71949 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
71900 AGTCGTATAT
71910 AGCCGTTGGAGATG-TTTTGG
1 AGCCGTTGGAGATGATTTTGG
*
71930 AGCCGTTTGGGGATGATTTT
1 AGCCG-TTGGAGATGATTTT
71950 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGATTTTGG
Found at i:72058 original size:15 final size:15
Alignment explanation
Indices: 72040--72092 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
72030 GGGGTATCAG
72040 TACCCAGGGTATGGA
1 TACCCAGGGTATGGA
72055 TACCCTGGAGGGTATAGG-
1 TACCC---AGGGTAT-GGA
*
72073 TACCCGGGGTATGGA
1 TACCCAGGGTATGGA
72088 TACCC
1 TACCC
72093 CTGGAGGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 2 0.06
15 16 0.50
18 12 0.38
19 2 0.06
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.21
Consensus pattern (15 bp):
TACCCAGGGTATGGA
Found at i:72076 original size:33 final size:34
Alignment explanation
Indices: 72031--72111 Score: 130
Period size: 33 Copynumber: 2.4 Consensus size: 34
72021 TGCAGCCAGG
72031 GGGTATCA-GTACCCAGGGTATGGATA-CCCTGGA
1 GGGTAT-AGGTACCCAGGGTATGGATACCCCTGGA
*
72064 GGGTATAGGTACCCGGGGTATGGATACCCCTGGA
1 GGGTATAGGTACCCAGGGTATGGATACCCCTGGA
72098 GGGTATAGGTACCC
1 GGGTATAGGTACCC
72112 TCCGAGCAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 1 0.02
33 23 0.51
34 21 0.47
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.21
Consensus pattern (34 bp):
GGGTATAGGTACCCAGGGTATGGATACCCCTGGA
Found at i:72110 original size:19 final size:18
Alignment explanation
Indices: 72045--72112 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
72035 ATCAGTACCC
72045 AGGGTATGGATACCCTGG
1 AGGGTATGGATACCCTGG
72063 AGGGTATAGG-TACCC--G
1 AGGGTAT-GGATACCCTGG
72079 -GGGTATGGATACCCCTGG
1 AGGGTATGGATA-CCCTGG
72097 AGGGTATAGG-TACCCT
1 AGGGTAT-GGATACCCT
72113 CCGAGCAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.05
15 8 0.19
16 4 0.09
18 17 0.40
19 10 0.23
20 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (18 bp):
AGGGTATGGATACCCTGG
Found at i:72177 original size:20 final size:21
Alignment explanation
Indices: 72135--72176 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
72125 GAATTTGAGT
72135 CTTCAGGGGGTATGGATACCC
1 CTTCAGGGGGTATGGATACCC
72156 CTTCAGGGGGTATCGG-TACCC
1 CTTCAGGGGGTAT-GGATACCC
72177 TGTAGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (21 bp):
CTTCAGGGGGTATGGATACCC
Found at i:72284 original size:31 final size:31
Alignment explanation
Indices: 72249--72307 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
72239 AACTTTGAAT
72249 AAATTCAATTCAAGTCCAAAAACATTTTTGC
1 AAATTCAATTCAAGTCCAAAAACATTTTTGC
72280 AAATTCAATTCAAGTCCAAAAACATTTT
1 AAATTCAATTCAAGTCCAAAAACATTTT
72308 GCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (31 bp):
AAATTCAATTCAAGTCCAAAAACATTTTTGC
Found at i:72474 original size:19 final size:19
Alignment explanation
Indices: 72420--72475 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
72410 TGTTCAATGA
72420 AAAAGATACCAATTGTTAC
1 AAAAGATACCAATTGTTAC
*
72439 AAAAGGATACTAATTGTTA-
1 AAAA-GATACCAATTGTTAC
*
72458 ACAAGATAACCAATTGTT
1 AAAAGAT-ACCAATTGTT
72476 TGAAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 3 0.09
19 16 0.50
20 13 0.41
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (19 bp):
AAAAGATACCAATTGTTAC
Done.