Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007107.1 Hibiscus syriacus cultivar Beakdansim tig00018571_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: 64981
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4284 original size:13 final size:14
Alignment explanation
Indices: 4266--4294 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4256 CGAAAATCAG
4266 AATAAATTTT-GAA
1 AATAAATTTTAGAA
4279 AATAAATTTTAGAA
1 AATAAATTTTAGAA
4293 AA
1 AA
4295 GATTTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
AATAAATTTTAGAA
Found at i:6878 original size:31 final size:32
Alignment explanation
Indices: 6843--6916 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
6833 GATTGGGCCT
6843 ATGCAATGGACTATAT-AATGGACTCTTTTAA
1 ATGCAATGGACTATATAAATGGACTCTTTTAA
** *
6874 ATGCAATATACTATGTAAATGGACTCTTTTAA
1 ATGCAATGGACTATATAAATGGACTCTTTTAA
6906 ATGCAATGGAC
1 ATGCAATGGAC
6917 CTTTATTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 13 0.35
32 24 0.65
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (32 bp):
ATGCAATGGACTATATAAATGGACTCTTTTAA
Found at i:17538 original size:20 final size:19
Alignment explanation
Indices: 17487--17543 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
17477 AACCAATAAT
17487 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
17506 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
17527 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
17544 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:17659 original size:22 final size:21
Alignment explanation
Indices: 17628--17745 Score: 71
Period size: 22 Copynumber: 5.3 Consensus size: 21
17618 CAAAGAAACT
17628 AAAA-ATATAATGAAAATAA-A
1 AAAATATATAAT-AAAATAATA
*
17648 GAAATAGTATAAATAAAATAATA
1 AAAATA-TAT-AATAAAATAATA
17671 AAAATATATATATAAAA-ATATA
1 AAAATATATA-ATAAAATA-ATA
* * *
17693 AAAATGTATGTATAATATAATA
1 AAAATATAT-AATAAAATAATA
* *
17715 AAATACTAAATAGTAATAATAATA
1 AAA-A-TATATAATAA-AATAATA
17739 ATAAATA
1 A-AAATA
17746 AATGAAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
20 3 0.04
21 3 0.04
22 41 0.54
23 16 0.21
24 11 0.14
25 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAATATATAATAAAATAATA
Found at i:17867 original size:16 final size:17
Alignment explanation
Indices: 17848--17893 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
17838 TTAGGAAAAT
17848 ATAGTAAAAAAAG-AAC
1 ATAGTAAAAAAAGAAAC
*
17864 ATAGT-AAATAAGTAAAC
1 ATAGTAAAAAAAG-AAAC
17881 ATAGATAAAAAAA
1 ATAG-TAAAAAAA
17894 TAATAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 6 0.25
16 5 0.21
17 7 0.29
18 1 0.04
19 5 0.21
ACGTcount: A:0.67, C:0.04, G:0.11, T:0.17
Consensus pattern (17 bp):
ATAGTAAAAAAAGAAAC
Found at i:17906 original size:5 final size:5
Alignment explanation
Indices: 17896--17946 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
17886 TAAAAAAATA
* *
17896 ATAAT ATAAT AT-AT ATATAT AATAAT AGGAAA ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATA-AT -ATAAT A-TAAT ATAAT ATAAT ATAAT
17943 ATAA
1 ATAA
17947 CGCAAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.11
5 24 0.63
6 7 0.18
7 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:17934 original size:21 final size:21
Alignment explanation
Indices: 17893--17943 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
17883 AGATAAAAAA
* *
17893 ATAATAATATAATATATATAT
1 ATAATAATAGAAAATATATAT
17914 ATAATAATAGGAAAATAATATAAT
1 ATAATAATA-GAAAAT-ATAT-AT
17938 ATAATA
1 ATAATA
17944 TAACGCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 4 0.16
23 4 0.16
24 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATAATAGAAAATATATAT
Found at i:17996 original size:10 final size:10
Alignment explanation
Indices: 17970--18001 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17960 GAAAAACAAT
17970 TATAAT-AAA
1 TATAATAAAA
17979 TA-AATAAAA
1 TATAATAAAA
17988 TATAATAAAA
1 TATAATAAAA
17998 TATA
1 TATA
18002 CATATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.14
9 7 0.33
10 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TATAATAAAA
Found at i:18500 original size:37 final size:37
Alignment explanation
Indices: 18407--18504 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
18397 ATGCTTGTGG
* * * * *
18407 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
* *
18444 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
18481 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
18505 TAGTAGGACG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:19446 original size:106 final size:106
Alignment explanation
Indices: 19260--20536 Score: 1863
Period size: 106 Copynumber: 12.0 Consensus size: 106
19250 GCATTGTTTC
* * * *
19260 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCCGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
19324 ACCAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19366 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
**
19431 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
19472 GAGACCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
19537 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
19578 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
*
19643 ACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19685 GAATCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
19750 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
19791 GAGTCCAATATCTTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
19856 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTCTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19897 GAGTCCAATATCCTTCACTGTGAAATTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
19962 CCAGCGGTCACTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20003 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
20068 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
20109 TAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
20174 CCAGCGGTCCCTTCATCATGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20215 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTTTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
20280 CCTGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20321 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* ** * *
20386 CTAGATGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
20427 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATTTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
20492 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
20533 GAGT
1 GAGT
20537 GGCACGATAT
Statistics
Matches: 1065, Mismatches: 104, Indels: 4
0.91 0.09 0.00
Matches are distributed among these distances:
106 965 0.91
107 100 0.09
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:21418 original size:22 final size:22
Alignment explanation
Indices: 21392--21468 Score: 154
Period size: 22 Copynumber: 3.5 Consensus size: 22
21382 TTGTGTTTGG
21392 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
21414 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
21436 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
21458 TCAAAGGTTTG
1 TCAAAGGTTTG
21469 ATGGGGTAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:22106 original size:11 final size:11
Alignment explanation
Indices: 22085--22143 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
22075 TCTTTTTGAT
22085 TTTTGTTCTTTC
1 TTTT-TTCTTTC
22097 TTTTTTCTTT-
1 TTTTTTCTTTC
*
22107 TGTTTTC-TTC
1 TTTTTTCTTTC
22117 TTTTTTGC-TTC
1 TTTTTT-CTTTC
* *
22128 TTTTTTTTTTG
1 TTTTTTCTTTC
22139 TTTTT
1 TTTTT
22144 GCCCTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 2 0.05
10 11 0.28
11 23 0.57
12 4 0.10
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:22114 original size:10 final size:10
Alignment explanation
Indices: 22094--22133 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
22084 TTTTTGTTCT
22094 TTCTTTTTTC
1 TTCTTTTTTC
22104 TT-TTGTTTTC
1 TTCTT-TTTTC
22114 TTCTTTTTTGC
1 TTCTTTTTT-C
22125 TTCTTTTTT
1 TTCTTTTTT
22134 TTTTGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.07
10 13 0.48
11 12 0.44
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:22114 original size:21 final size:20
Alignment explanation
Indices: 22073--22122 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
22063 TTTGTCCCTT
*
22073 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTATTTTTGTTC
* *
22093 TTTCTTTTTT-CTTTTGTTT
1 TTTCTTTTTTATTTTTGTTC
22112 TCTTCTTTTTT
1 T-TTCTTTTTT
22123 GCTTCTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTATTTTTGTTC
Found at i:22117 original size:24 final size:23
Alignment explanation
Indices: 22071--22143 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 23
22061 TTTTTGTCCC
*
22071 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTC-TTTTG--TTTTCTTCTTT-T
22098 TTTTTCTTTTGTTTTCTTCTTTT
1 TTTTTCTTTTGTTTTCTTCTTTT
* *
22121 TTGCTTCTTTT-TTTT-TTGTTTT
1 TT-TTTCTTTTGTTTTCTTCTTTT
22143 T
1 T
22144 GCCCTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 7 0.17
23 7 0.17
24 17 0.40
26 5 0.12
27 6 0.14
ACGTcount: A:0.01, C:0.11, G:0.07, T:0.81
Consensus pattern (23 bp):
TTTTTCTTTTGTTTTCTTCTTTT
Found at i:22152 original size:30 final size:31
Alignment explanation
Indices: 22094--22152 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
22084 TTTTTGTTCT
* *
22094 TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
1 TTCTTTTTTCTTTTGTTTTCTCCCTTTTTGC
22125 TTCTTTTTT-TTTTGTTTT-TGCCCTTTTT
1 TTCTTTTTTCTTTTGTTTTCT-CCCTTTTT
22153 TTCTGATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 15 0.60
31 9 0.36
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (31 bp):
TTCTTTTTTCTTTTGTTTTCTCCCTTTTTGC
Found at i:26485 original size:20 final size:19
Alignment explanation
Indices: 26434--26490 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
26424 AACCAATAAT
26434 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
26453 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
26474 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
26491 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:26633 original size:22 final size:22
Alignment explanation
Indices: 26574--26702 Score: 72
Period size: 21 Copynumber: 5.9 Consensus size: 22
26564 CAAAGAAACT
*
26574 AAAAATATA-ATGAAAATAAATA
1 AAAAATATATATAAAAAT-AATA
* * *
26596 AATAGTATAAAT-AAAATAATA
1 AAAAATATATATAAAAATAATA
26617 AAAAATATATATAAAAAT-AT-
1 AAAAATATATATAAAAATAATA
* * *
26637 AAAAATGTATGTATAATATAATA
1 AAAAATATATATA-AAAATAATA
* * *
26660 AAATACTAAATAGTAATAATAATA
1 AAA-AATATATA-TAAAAATAATA
*
26684 ATAAATA-A-ATGAAAAATAA
1 AAAAATATATAT-AAAAATAA
26703 ATATACATAT
Statistics
Matches: 82, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
20 12 0.15
21 27 0.33
22 20 0.24
23 8 0.10
24 13 0.16
25 2 0.02
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (22 bp):
AAAAATATATATAAAAATAATA
Found at i:26850 original size:2 final size:2
Alignment explanation
Indices: 26840--26879 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
26830 AAAAATAATA
26840 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26880 GGAAAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27466 original size:37 final size:37
Alignment explanation
Indices: 27373--27474 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
27363 ATGCTTGTGG
* * ** * *
27373 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCC
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCC
* *
27410 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCC
27447 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
27475 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCC
Found at i:30453 original size:23 final size:23
Alignment explanation
Indices: 30427--30491 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
30417 TTCTACGCGC
*
30427 TCCTTTGGGACAATTCTATGTTG
1 TCCTTTGGGACAATTCTATGTGG
* *
30450 TCCTTCGGGACAATTCTACGTGG
1 TCCTTTGGGACAATTCTATGTGG
*
30473 TCCTTTGGGACAAATCTAT
1 TCCTTTGGGACAATTCTAT
30492 ATGTCACTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (23 bp):
TCCTTTGGGACAATTCTATGTGG
Found at i:31374 original size:15 final size:17
Alignment explanation
Indices: 31345--31387 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
31335 TTTAATTACT
*
31345 TTTTATATGTTTTTAATA
1 TTTTATAT-TTTTAAATA
31363 TTTT-TATTTTTAAATA
1 TTTTATATTTTTAAATA
31379 TTTTATATT
1 TTTTATATT
31388 GCACCATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 12 0.52
17 7 0.30
18 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTATATTTTTAAATA
Found at i:35199 original size:45 final size:45
Alignment explanation
Indices: 35138--35269 Score: 201
Period size: 45 Copynumber: 2.9 Consensus size: 45
35128 AATTTTGTAT
* *
35138 CAATATCCTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
35183 CAATATACTTATCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * * *
35228 TAATATACTTGCCATTTATACCATAAGCTCGTAAGCTAATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
35270 GCCAGTTTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:39004 original size:45 final size:45
Alignment explanation
Indices: 38953--39084 Score: 228
Period size: 45 Copynumber: 2.9 Consensus size: 45
38943 AATTTTGTAT
*
38953 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
38998 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
39043 CAATATACTTGCCATTTATACCATAAGCTCATAAGCTTATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
39085 GCCAGCTTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:42746 original size:13 final size:13
Alignment explanation
Indices: 42728--42753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42718 GTCACTTCCA
42728 CTGATTTTAAAAT
1 CTGATTTTAAAAT
42741 CTGATTTTAAAAT
1 CTGATTTTAAAAT
42754 AAAAGTGTAT
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
CTGATTTTAAAAT
Found at i:46554 original size:16 final size:16
Alignment explanation
Indices: 46533--46612 Score: 71
Period size: 16 Copynumber: 5.1 Consensus size: 16
46523 AGATTAAAAT
46533 AATCTAAGAAATTAAA
1 AATCTAAGAAATTAAA
*
46549 AATCTAAGAAATT-AT
1 AATCTAAGAAATTAAA
*
46564 AATGGATAA-AAA-T-AA
1 AAT--CTAAGAAATTAAA
46579 AATCTAAGAAATTAAAA
1 AATCTAAGAAATT-AAA
46596 AAT-TAAGAAACTTAAA
1 AATCTAAGAAA-TTAAA
46612 A
1 A
46613 TTTATAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 10 0.19
16 27 0.51
17 10 0.19
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (16 bp):
AATCTAAGAAATTAAA
Found at i:55269 original size:42 final size:45
Alignment explanation
Indices: 55222--55322 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 45
55212 CACAAGTGCG
* *
55222 ACGTTTGTTCTAAAAAAAC-CA-CTAAATGACTTAA-ATTTTGCA
1 ACGTTTGTTCTAAAAAAACACAGCTAAAAGACCTAACATTTTGCA
* * *
55264 GCGTTTG-T-TACAAAAACATAGCTAAAAGACCTAACATTTTGCA
1 ACGTTTGTTCTAAAAAAACACAGCTAAAAGACCTAACATTTTGCA
55307 ACGTTTGTTACTAAAA
1 ACGTTTGTT-CTAAAA
55323 TGCGCTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
40 8 0.17
41 2 0.04
42 17 0.37
43 14 0.30
44 1 0.02
46 4 0.09
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (45 bp):
ACGTTTGTTCTAAAAAAACACAGCTAAAAGACCTAACATTTTGCA
Found at i:55343 original size:42 final size:43
Alignment explanation
Indices: 55243--55362 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 43
55233 AAAAAAACCA
* *
55243 CTAAATGACTTAA-ATTTTGCAGCGTTTGTTACAAAAACATAG
1 CTAAAAGACATAACATTTTGCAGCGTTTGTTACAAAAACATAG
* * * *
55285 CTAAAAGACCTAACATTTTGCAACGTTTGTTAC-TAAA-ATGCG
1 CTAAAAGACATAACATTTTGCAGCGTTTGTTACAAAAACAT-AG
* *
55327 CTAAAAGACATAACATTTTGTAGCGTTTGTTTCAAA
1 CTAAAAGACATAACATTTTGCAGCGTTTGTTACAAA
55363 TCGTTACTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 44 0.68
43 19 0.29
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (43 bp):
CTAAAAGACATAACATTTTGCAGCGTTTGTTACAAAAACATAG
Found at i:55373 original size:42 final size:41
Alignment explanation
Indices: 55242--55398 Score: 124
Period size: 42 Copynumber: 3.8 Consensus size: 41
55232 TAAAAAAACC
* * * * *
55242 ACTAAATGACTTAA-ATTTTGCAGCGTTTGTTACAAAAACAT
1 ACTAAAAGACCTAACATTTTGCAGCGTTTGTTTC-AAATCGT
* *
55283 AGCTAAAAGACCTAACATTTTGCAACGTTTGTTACTAAAATGCG-
1 A-CTAAAAGACCTAACATTTTGCAGCGTTTGTT--TCAAAT-CGT
* *
55327 -CTAAAAGACATAACATTTTGTAGCGTTTGTTTCAAATCGTT
1 ACTAAAAGACCTAACATTTTGCAGCGTTTGTTTCAAATCG-T
* **
55368 ACTAAAA-CCCTAACATTTTGTGGCGTTTGTT
1 ACTAAAAGACCTAACATTTTGCAGCGTTTGTT
55399 AAAAAAAGCC
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 22 0.23
42 45 0.48
43 16 0.17
44 3 0.03
45 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (41 bp):
ACTAAAAGACCTAACATTTTGCAGCGTTTGTTTCAAATCGT
Found at i:55412 original size:83 final size:85
Alignment explanation
Indices: 55222--55429 Score: 203
Period size: 83 Copynumber: 2.5 Consensus size: 85
55212 CACAAGTGCG
* * *
55222 ACGTTTGTTCTAAAAAAA-CCACTAAATGACTTAA-ATTTTGCAGCGTTTGTTACAAAAACATAG
1 ACGTTTG-T-TAAAAAAAGCCGCTAAAAGACATAACATTTTGCAGCGTTTGTTACAAAAACATAG
55285 CTAAAAGACCTAACATTTTGCA
64 CTAAAAGACCTAACATTTTGCA
* * * * * *
55307 ACGTTTGTTACTAAAATG-CGCTAAAAGACATAACATTTTGTAGCGTTTGTTTC-AAATCGTTA-
1 ACGTTTGTTA-AAAAAAGCCGCTAAAAGACATAACATTTTGCAGCGTTTGTTACAAAAAC-ATAG
* **
55369 CTAAAA-CCCTAACATTTTGTG
64 CTAAAAGACCTAACATTTTGCA
* * *
55390 GCGTTTGTTAAAAAAAGCCGCTAAAAGACCTAACCTTTTG
1 ACGTTTGTTAAAAAAAGCCGCTAAAAGACATAACATTTTG
55430 AAAAAAAAAC
Statistics
Matches: 101, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
82 5 0.05
83 43 0.43
84 27 0.27
85 26 0.26
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (85 bp):
ACGTTTGTTAAAAAAAGCCGCTAAAAGACATAACATTTTGCAGCGTTTGTTACAAAAACATAGCT
AAAAGACCTAACATTTTGCA
Found at i:56418 original size:13 final size:13
Alignment explanation
Indices: 56400--56426 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56390 AGAAATTTAA
56400 AATGAATCTATTG
1 AATGAATCTATTG
56413 AATGAATCTATTG
1 AATGAATCTATTG
56426 A
1 A
56427 CTGTTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AATGAATCTATTG
Done.