Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001210.1 Hibiscus syriacus cultivar Beakdansim tig00002392_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: 66610
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2545 original size:35 final size:35
Alignment explanation
Indices: 2506--2583 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
2496 GTATAGTCCT
2506 TGAAGATTGGAGGCATGATTAAACTTCATGAGTGG
1 TGAAGATTGGAGGCATGATTAAACTTCATGAGTGG
2541 TGAAGATTGGAGGCATGATTAAACTTCATGAGTGG
1 TGAAGATTGGAGGCATGATTAAACTTCATGAGTGG
*
2576 TGGAGATT
1 TGAAGATT
2584 TGACTGATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.31, C:0.08, G:0.32, T:0.29
Consensus pattern (35 bp):
TGAAGATTGGAGGCATGATTAAACTTCATGAGTGG
Found at i:5203 original size:2 final size:2
Alignment explanation
Indices: 5198--5223 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5188 TGTGTGTGTG
5198 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5224 TCAATGGCTC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9736 original size:49 final size:48
Alignment explanation
Indices: 9639--9736 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 48
9629 GATATGATAA
*
9639 AATTTAATAAAAATATATTATATTGAAACTCGTCACCTCAAAATGACG
1 AATTTAATAAAAATATATTATATTGAAACTCGTCACCTCAAAAGGACG
* * *
9687 AATTTAAATAAAAA-ATATTAT-TTGGAAAACTCGTTACCTTAACAGGACG
1 AATTT-AATAAAAATATATTATATT-G-AAACTCGTCACCTCAAAAGGACG
9736 A
1 A
9737 GTTCCTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
47 2 0.05
48 13 0.30
49 28 0.65
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (48 bp):
AATTTAATAAAAATATATTATATTGAAACTCGTCACCTCAAAAGGACG
Found at i:16714 original size:64 final size:63
Alignment explanation
Indices: 16521--16722 Score: 205
Period size: 65 Copynumber: 3.1 Consensus size: 63
16511 TTTTTCAGAG
** *
16521 CGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCAAATGCATTTCATGC
1 CGATGCACCAA-CCATGCATCGATGCACTC-TGG--TATTTTGAAACATCGAATGCATTTCATGC
*
16584 AC
62 AT
* * * *
16586 CGATACA-CATACTATGCATCGATGCACTCAGAGT-TTTATGAAAACATCGAATGCATTTGATGC
1 CGATGCACCA-ACCATGCATCGATGCACTCTG-GTATTT-TG-AAACATCGAATGCATTTCATGC
16649 AT
62 AT
* *
16651 CGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTTATGCAT
1 CGATGCACCAACCATGCATCGATGCACTCTGG-TATTTTGAAACATCGAATGCATTTCATGCAT
16715 CGATGCAC
1 CGATGCAC
16723 TCTTCGTGCA
Statistics
Matches: 115, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 50 0.43
65 56 0.49
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (63 bp):
CGATGCACCAACCATGCATCGATGCACTCTGGTATTTTGAAACATCGAATGCATTTCATGCAT
Found at i:16968 original size:7 final size:7
Alignment explanation
Indices: 16956--16981 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16946 CAAGAATACA
16956 CAAGAAT
1 CAAGAAT
16963 CAAGAAT
1 CAAGAAT
16970 CAAGAAT
1 CAAGAAT
16977 CAAGA
1 CAAGA
16982 GAGAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (7 bp):
CAAGAAT
Found at i:17937 original size:21 final size:20
Alignment explanation
Indices: 17894--17967 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
17884 ACAGCCTTCG
*
17894 TGCATGGATGCACAACATGA
1 TGCATCGATGCACAACATGA
*
17914 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CATGA
* * *
17935 TGCATCAATACACAGA-AGGA
1 TGCATCGATGCACA-ACATGA
17955 TGCATCGATGCAC
1 TGCATCGATGCAC
17968 TAATTGCATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 27 0.61
21 16 0.36
22 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAACATGA
Found at i:18035 original size:22 final size:23
Alignment explanation
Indices: 18002--18045 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
17992 GTGGATGCAC
18002 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
18025 TGCA-GGTGCATCGATGCACTA
1 TGCATGGTGCATCGATGCACTA
18046 CAGGGGTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:18192 original size:30 final size:30
Alignment explanation
Indices: 18145--18204 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
18135 AAACTTTGAA
*
18145 TAAATTCAATGAAGTCCAAAAA-CATTTTG
1 TAAATTCAATCAAGTCCAAAAACCATTTTG
18174 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAA-TCAAGTCCAAAAACCATTTTG
18205 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 12 0.43
31 7 0.25
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (30 bp):
TAAATTCAATCAAGTCCAAAAACCATTTTG
Found at i:21057 original size:34 final size:32
Alignment explanation
Indices: 20995--21058 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
20985 ACCTTACAAC
* *
20995 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
21027 TCCCTAGCTTTTACACGGGATAAGCTAGAACC
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACC
21059 CCCCTTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 7 0.26
33 5 0.19
34 15 0.56
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:21302 original size:20 final size:22
Alignment explanation
Indices: 21277--21316 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21267 TGTTGTATAT
21277 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
21297 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
21317 TTACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:21365 original size:21 final size:22
Alignment explanation
Indices: 21331--21372 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
21321 TCAAAAAGGT
21331 TGCACATAACATGGTGCATCGG
1 TGCACATAACATGGTGCATCGG
*
21353 TGCAC-TATCATGGTGCATCG
1 TGCACATAACATGGTGCATCG
21373 ATACCCCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
TGCACATAACATGGTGCATCGG
Found at i:21447 original size:20 final size:19
Alignment explanation
Indices: 21418--21490 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
21408 ACAGCCTTCG
*
21418 TGCATTGATGCATAGCAGGA
1 TGCATCGATGCA-AGCAGGA
**
21438 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCA-AG-CAGGA
* *
21459 TACATCGATGCAACGAAGGA
1 TGCATCGATGCAA-GCAGGA
21479 TGCATCGATGCA
1 TGCATCGATGCA
21491 CTAATTGCAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (19 bp):
TGCATCGATGCAAGCAGGA
Found at i:21563 original size:42 final size:41
Alignment explanation
Indices: 21517--21631 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 41
21507 TTTGAGTGCG
* * *
21517 TGGATGCACTGCATGGTGCATTGATGCACTAGTGCA-GG-TTCA
1 TGGATGCACTGCAGGGTGCATGGATGCACT-GT--ATGGATGCA
*
21559 TGGATGCACTACAGGGATGCATGGATGCACTGTATGGATGCA
1 TGGATGCACTGCAGGG-TGCATGGATGCACTGTATGGATGCA
21601 TGGATGCACTGCAGGGGTGCATGGATGCACT
1 TGGATGCACTGCA-GGGTGCATGGATGCACT
21632 TTGACACCCT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
40 1 0.02
41 2 0.03
42 45 0.70
43 16 0.25
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (41 bp):
TGGATGCACTGCAGGGTGCATGGATGCACTGTATGGATGCA
Found at i:21583 original size:21 final size:21
Alignment explanation
Indices: 21517--21631 Score: 119
Period size: 21 Copynumber: 5.5 Consensus size: 21
21507 TTTGAGTGCG
*
21517 TGGATGCACTGCATGG-TGCA
1 TGGATGCACTGCAGGGATGCA
* *
21537 TTGATGCACTAGTGCA-GG-TTCA
1 TGGATGCAC---TGCAGGGATGCA
*
21559 TGGATGCACTACAGGGATGCA
1 TGGATGCACTGCAGGGATGCA
* *
21580 TGGATGCACTGTATGGATGCA
1 TGGATGCACTGCAGGGATGCA
*
21601 TGGATGCACTGCAGGGGTGCA
1 TGGATGCACTGCAGGGATGCA
21622 TGGATGCACT
1 TGGATGCACT
21632 TTGACACCCT
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.04
20 10 0.13
21 49 0.62
22 13 0.16
23 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (21 bp):
TGGATGCACTGCAGGGATGCA
Found at i:21742 original size:29 final size:31
Alignment explanation
Indices: 21710--21768 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
21700 AAACTTTGAA
*
21710 TAAATTCAA-TGAAGTCCAAAAA-CATTTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTTT
21739 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
21769 GTCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.33
30 12 0.44
31 6 0.22
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTT
Found at i:24596 original size:32 final size:34
Alignment explanation
Indices: 24560--24630 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
24550 ACCTTACAAC
* *
24560 TCCCTAG-TTTTTC-CGGGATAAACTAGAACATT
1 TCCCTAGCTTTTACACGAGATAAACTAGAACATT
** *
24592 TCCCTAGCTTTTACACGAGATAAGTTAGAACCTT
1 TCCCTAGCTTTTACACGAGATAAACTAGAACATT
24626 TCCCT
1 TCCCT
24631 TTACAAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGAGATAAACTAGAACATT
Found at i:27142 original size:27 final size:27
Alignment explanation
Indices: 27110--27162 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
27100 TAATTCTTTC
27110 TTTTCAAAAT-TTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
*
27137 TTTTCATAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
27163 TTTATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:31450 original size:19 final size:19
Alignment explanation
Indices: 31426--31471 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
31416 TTACCAGTTA
*
31426 AACCAAATGACCTCAAAAG
1 AACCAAACGACCTCAAAAG
31445 AACCAAACGACCTCAAAAG
1 AACCAAACGACCTCAAAAG
31464 AACCAAAC
1 AACCAAAC
31472 CTTCAATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.54, C:0.30, G:0.09, T:0.07
Consensus pattern (19 bp):
AACCAAACGACCTCAAAAG
Found at i:32823 original size:32 final size:32
Alignment explanation
Indices: 32784--32846 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
32774 TCGGGACACA
*
32784 AGAAGTATCTCTACGAGATGAGCATAACAATG
1 AGAAGTATCTCTACAAGATGAGCATAACAATG
32816 AGAAGTATCTCTACAAGATGAGCATAACAAT
1 AGAAGTATCTCTACAAGATGAGCATAACAAT
32847 CATTTCTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAATG
Found at i:35306 original size:74 final size:75
Alignment explanation
Indices: 35172--35350 Score: 200
Period size: 74 Copynumber: 2.4 Consensus size: 75
35162 ATTAACAAGA
* *** * *
35172 AGCAAATGA-TGGGGCATGTTGAAAGCCCATTTCAATCAGAATTTGGAATATTAATACATTTTGA
1 AGCAAAT-ACTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTAACACATTTTAA
*
35236 ACGTTTATATC
65 ACGTCTATATC
* * * *
35247 AGCAAATACT-GGGCATGCTGAAAGCCCATTTCAATCATAATCAAGAATGTTGACGCATTTTAAA
1 AGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTAACACATTTTAAA
*
35311 CGTCTATATT
66 CGTCTATATC
* * *
35321 AGCAAATGCTGGGGCATGCTAAAACCCCAT
1 AGCAAATACTGGGGCATGCTGAAAGCCCAT
35351 ATCATCTTAC
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
74 62 0.71
75 25 0.29
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (75 bp):
AGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTAACACATTTTAAA
CGTCTATATC
Found at i:36681 original size:22 final size:20
Alignment explanation
Indices: 36627--36681 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 20
36617 TACATCTACA
36627 TTCTTCAAAGATGATAGATT
1 TTCTTCAAAGATGATAGATT
*
36647 TTC-TCAAAAATGATAG-TT
1 TTCTTCAAAGATGATAGATT
36665 TCTCTTTTCAAAGATGA
1 T-TC--TTCAAAGATGA
36682 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 14 0.48
20 3 0.10
22 9 0.31
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
TTCTTCAAAGATGATAGATT
Found at i:37513 original size:73 final size:73
Alignment explanation
Indices: 37345--38605 Score: 1954
Period size: 73 Copynumber: 17.3 Consensus size: 73
37335 TTCTAACATA
*
37345 TGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTT-AAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
*
37409 GGGTCTTC
66 GGGTCATC
** * * * * * *
37417 CATAAGACCTGCAGTACAAGATGTTTTTAAAAAGCCTTCAGGAGCTTTTTTATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
*
37482 GGGTTATC
66 GGGTCATC
*
37490 TGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTC-
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
37554 GGGTCATC
66 GGGTCATC
** *
37562 CATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
37627 GGGTCATC
66 GGGTCATC
*
37635 TGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
37700 GGGTCATC
66 GGGTCATC
** *
37708 CATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTTA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
37773 GGGTCATC
66 GGGTCATC
* * *
37781 TGTAAGACCTTCAATGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
37846 GGGTCATC
66 GGGTCATC
** *
37854 CATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
37919 GGGTCATC
66 GGGTCATC
* * *
37927 TGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATTTTAAAGCCTTA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
37992 GGGTCATC
66 GGGTCATC
* * * * * *
38000 TATAAGACATGCAGTACAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATTTTAAAGCTTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
38065 GGGTCATC
66 GGGTCATC
*
38073 TGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTT-AAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
*
38137 AGGTCATC
66 GGGTCATC
** * *
38145 CATAAGACCTGCAGTGCAGGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
38210 GGGTCATC
66 GGGTCATC
* * * *
38218 TGTAATACCTTCAATGCAGGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTAATTTTAAAGCCTC
1 TGTAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTC
38283 AGGGTCATC
65 AGGGTCATC
** *
38292 CATAAGACCTACAGTGCAGGATGTTTTTAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
38357 GGGTCATC
66 GGGTCATC
* *
38365 TGTAAGACCTACAGTGCATGATGTTTTTAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
38430 GGGTCATC
66 GGGTCATC
** * * *
38438 CATAAGACCTGCAGTGCAGGATGTTTTCAAAAA-CCTTCGGGAGATTTTTGATTTTAAAGCCTCT
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
38502 GGGTCATC
66 GGGTCATC
* * *
38510 TTTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCA
1 TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
*
38575 GGGTCATT
66 GGGTCATC
*
38583 TGTAAGACCTACAGTGCAAGATG
1 TGTAAGACCTACAGTGCAGGATG
38606 ATAGGACTTC
Statistics
Matches: 1083, Mismatches: 101, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
72 246 0.23
73 772 0.71
74 65 0.06
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (73 bp):
TGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCCTCA
GGGTCATC
Found at i:38780 original size:3 final size:3
Alignment explanation
Indices: 38762--38796 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
38752 TTTCATTTAA
*
38762 ATT ATT TTT AATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A
38797 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.93
4 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41336 original size:20 final size:20
Alignment explanation
Indices: 41311--41404 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
41301 GCAGCCTTCG
* *
41311 TGCATGGATGCACAGCATGA
1 TGCATCGATGCACAGCAGGA
*
41331 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* **
41351 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-AGCAGGA
* *
41372 TGCATCGATGCACTGAAGGA
1 TGCATCGATGCACAGCAGGA
41392 TGCATCGATGCAC
1 TGCATCGATGCAC
41405 TAATTGCATT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 46 0.73
21 17 0.27
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:41382 original size:41 final size:40
Alignment explanation
Indices: 41311--41404 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
41301 GCAGCCTTCG
* * * *
41311 TGCATGGATGCACAGCATGATGCATGGATGCACAGCAGGA
1 TGCATCGATGCACACCATGATGCATCGATGCACAGAAGGA
* *
41351 TGCATCGATGCACAACCTTGATGCATCGATGCACTGAAGGA
1 TGCATCGATGCAC-ACCATGATGCATCGATGCACAGAAGGA
41392 TGCATCGATGCAC
1 TGCATCGATGCAC
41405 TAATTGCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (40 bp):
TGCATCGATGCACACCATGATGCATCGATGCACAGAAGGA
Found at i:41444 original size:12 final size:12
Alignment explanation
Indices: 41427--41451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41417 GTGTTTGAGT
41427 GCATGGTGCATC
1 GCATGGTGCATC
41439 GCATGGTGCATC
1 GCATGGTGCATC
41451 G
1 G
41452 ATGCACTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GCATGGTGCATC
Found at i:41602 original size:29 final size:29
Alignment explanation
Indices: 41581--41638 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
41571 AAACTTTGAA
41581 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
41610 TAAATTCAATTCACGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
41639 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:41630 original size:30 final size:30
Alignment explanation
Indices: 41581--41640 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
41571 AAACTTTGAA
41581 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
41610 TAAATTCAATTCACGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
41641 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:42062 original size:13 final size:13
Alignment explanation
Indices: 42044--42068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42034 TCTGAAGTGT
42044 TTGTGGTATTGCC
1 TTGTGGTATTGCC
42057 TTGTGGTATTGC
1 TTGTGGTATTGC
42069 TGCTTCGACC
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:0.08, C:0.12, G:0.32, T:0.48
Consensus pattern (13 bp):
TTGTGGTATTGCC
Found at i:52356 original size:44 final size:44
Alignment explanation
Indices: 52308--52395 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
52298 TTGAGAAAAA
*
52308 GGATTTAAAAACTTGCTGAATTGAAGAAAAATAACACATCGGAT
1 GGATTAAAAAACTTGCTGAATTGAAGAAAAATAACACATCGGAT
52352 GGATTAAAAAACTTGCTGAATTGAAGAAAAATAACACATCGGAT
1 GGATTAAAAAACTTGCTGAATTGAAGAAAAATAACACATCGGAT
52396 AACAAAGGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (44 bp):
GGATTAAAAAACTTGCTGAATTGAAGAAAAATAACACATCGGAT
Found at i:53780 original size:16 final size:15
Alignment explanation
Indices: 53760--53806 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
53750 ATTTTGTTAG
53760 TAATTTATTTAAATT
1 TAATTTATTTAAATT
53775 TAAATTT-TTTAATATT
1 T-AATTTATTTAA-ATT
* *
53791 TTATTTAATTAAATT
1 TAATTTATTTAAATT
53806 T
1 T
53807 TTTTTTGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTTATTTAAATT
Found at i:56303 original size:16 final size:16
Alignment explanation
Indices: 56284--56319 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
56274 TTTTTAGAAA
56284 AAAATAAAAAAAAATG
1 AAAATAAAAAAAAATG
* *
56300 AAAATTAAAAAAAATT
1 AAAATAAAAAAAAATG
56316 AAAA
1 AAAA
56320 ATATATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAAAAATG
Found at i:56320 original size:17 final size:17
Alignment explanation
Indices: 56282--56321 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
56272 TGTTTTTAGA
*
56282 AAAAAATAAAAAAAAAT
1 AAAAATTAAAAAAAAAT
* *
56299 GAAAATTAAAAAAAATT
1 AAAAATTAAAAAAAAAT
56316 AAAAAT
1 AAAAAT
56322 ATATATAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAATTAAAAAAAAAT
Found at i:56553 original size:15 final size:16
Alignment explanation
Indices: 56524--56556 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56514 TCCTTAAATC
*
56524 ATTTTTTAATAATTTA
1 ATTTTGTAATAATTTA
56540 ATTTTGTAAT-ATTTA
1 ATTTTGTAATAATTTA
56555 AT
1 AT
56557 GTATTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTTGTAATAATTTA
Found at i:57935 original size:2 final size:2
Alignment explanation
Indices: 57928--57977 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
57918 GGTGGGTCGG
* * * *
57928 AT AT AT AT AT TT AA AT -T AA AT AT AT AA AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57968 AT AT AT AT AT
1 AT AT AT AT AT
57978 TAATTTAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57987 original size:44 final size:42
Alignment explanation
Indices: 57928--58014 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 42
57918 GGTGGGTCGG
57928 ATATATATATTTAAATTAAATATATAAATATTATATATATAT
1 ATATATATATTTAAATTAAATATATAAATATTATATATATAT
* *
57970 ATATATATTAATTTAAATTAAATTTATTAATATTATATATATAT
1 ATATATA-T-ATTTAAATTAAATATATAAATATTATATATATAT
58014 A
1 A
58015 ATTATTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 7 0.17
43 1 0.02
44 33 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
ATATATATATTTAAATTAAATATATAAATATTATATATATAT
Found at i:59523 original size:24 final size:24
Alignment explanation
Indices: 59495--59557 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
59485 CTTAGGAACA
59495 AGCTGCATCCCCCATAGGAGTGGC
1 AGCTGCATCCCCCATAGGAGTGGC
59519 AGCTGCATCCCCCATAGGAGTGGC
1 AGCTGCATCCCCCATAGGAGTGGC
59543 AGCTGCATCCCCCAT
1 AGCTGCATCCCCCAT
59558 TGATACAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (24 bp):
AGCTGCATCCCCCATAGGAGTGGC
Found at i:65702 original size:2 final size:2
Alignment explanation
Indices: 65697--65723 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65687 GTTTTAAGAA
65697 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 A
65724 GTACCCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.