Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007296.1 Hibiscus syriacus cultivar Beakdansim tig00019408_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: 76119
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Found at i:2734 original size:17 final size:17
Alignment explanation
Indices: 2714--2769 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
2704 AGTAGCTTAT
* *
2714 TGAATGAACTAAGTGCA
1 TGAATGAAATAAATGCA
* *
2731 TGAATGAAAT-ACTTCA
1 TGAATGAAATAAATGCA
2747 TTGAATGAAATAAATGCA
1 -TGAATGAAATAAATGCA
2765 TGAAT
1 TGAAT
2770 AAACTACTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 4 0.12
17 24 0.75
18 4 0.12
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.29
Consensus pattern (17 bp):
TGAATGAAATAAATGCA
Found at i:2753 original size:34 final size:34
Alignment explanation
Indices: 2712--2794 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
2702 GAAGTAGCTT
* *
2712 ATTGAATGAACTAAGTGCATGAATGAAA-TACTTC
1 ATTGAATGAAATAAATGCATGAAT-AAACTACTTC
2746 ATTGAATGAAATAAATGCATGAATAAACTACTTC
1 ATTGAATGAAATAAATGCATGAATAAACTACTTC
* * *
2780 CTTAAATGAAGTAAA
1 ATTGAATGAAATAAA
2795 AGCTTAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 3 0.07
34 40 0.93
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (34 bp):
ATTGAATGAAATAAATGCATGAATAAACTACTTC
Found at i:2816 original size:17 final size:17
Alignment explanation
Indices: 2780--2834 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2770 AAACTACTTC
*
2780 CTTAAATGAAGTAA-AAG
1 CTTAAATGAA-TAACATG
*
2797 CTTAAATGCAAT-GCATG
1 CTTAAATG-AATAACATG
*
2814 CTTTAATGAATAACATG
1 CTTAAATGAATAACATG
2831 CTTA
1 CTTA
2835 TTAAATGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 3 0.10
17 25 0.83
18 2 0.07
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (17 bp):
CTTAAATGAATAACATG
Found at i:5723 original size:23 final size:22
Alignment explanation
Indices: 5697--5758 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
5687 AGCCGCACTC
* *
5697 TTTTCTCTCTTTTCTTCTATTT
1 TTTTCTCTTTTTTCTTCTAATT
*
5719 TTTTTTCCTTTTTTCTTCTAATT
1 TTTTCT-CTTTTTTCTTCTAATT
*
5742 TTTTCCCTTTTTTCTTC
1 TTTTCTCTTTTTTCTTC
5759 ATCGTTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCTCTTTTTTCTTCTAATT
Found at i:5731 original size:22 final size:22
Alignment explanation
Indices: 5697--5758 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
5687 AGCCGCACTC
* *
5697 TTTTCTCTCTTTTCTTCTATTTTT
1 TTTTC-CTTTTTTCTTCTA-ATTT
5721 TTTTCCTTTTTTCTTCTAATTT
1 TTTTCCTTTTTTCTTCTAATTT
*
5743 TTTCCCTTTTTTCTTC
1 TTTTCCTTTTTTCTTC
5759 ATCGTTTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 18 0.51
23 12 0.34
24 5 0.14
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCCTTTTTTCTTCTAATTT
Found at i:6625 original size:27 final size:29
Alignment explanation
Indices: 6565--6641 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
6555 AGATTACATA
*
6565 TTTATTCTGATTTATAAAAAAATTTAGGTG
1 TTTATTATGATTTATAAAAAAATTTA-GTG
* *
6595 TTTATTGTGATTAATAAAAAAATTT-GT-
1 TTTATTATGATTTATAAAAAAATTTAGTG
*
6622 TTTATTATAATTTATAAAAA
1 TTTATTATGATTTATAAAAA
6642 TTGAGACACT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 17 0.40
28 2 0.05
30 23 0.55
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTATTATGATTTATAAAAAAATTTAGTG
Found at i:9871 original size:32 final size:32
Alignment explanation
Indices: 9835--9909 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
9825 CTTTTGTTCT
* * ** * *
9835 TTATCTGATTGTGACATTGACAGTGTTGTGCC
1 TTATCTGAATGCGACACCGACAGTATTGTGCA
*
9867 TTATCTGAATGCGACACCGACATTATTGTGCA
1 TTATCTGAATGCGACACCGACAGTATTGTGCA
9899 TTATCTGAATG
1 TTATCTGAATG
9910 TAACACTCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (32 bp):
TTATCTGAATGCGACACCGACAGTATTGTGCA
Found at i:11476 original size:16 final size:16
Alignment explanation
Indices: 11455--11492 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
11445 TCGAGTGTCG
11455 AAAGAGCATTATGCTA
1 AAAGAGCATTATGCTA
**
11471 AAAGAGTTTTATGCTA
1 AAAGAGCATTATGCTA
11487 AAAGAG
1 AAAGAG
11493 TTATGACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (16 bp):
AAAGAGCATTATGCTA
Found at i:11493 original size:16 final size:16
Alignment explanation
Indices: 11463--11494 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11453 CGAAAGAGCA
11463 TTATGCTAAAAGAGTT
1 TTATGCTAAAAGAGTT
11479 TTATGCTAAAAGAGTT
1 TTATGCTAAAAGAGTT
11495 ATGACCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
TTATGCTAAAAGAGTT
Found at i:12409 original size:2 final size:2
Alignment explanation
Indices: 12402--12445 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12392 TATGTAATCG
12402 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
12444 TA
1 TA
12446 AAATAATGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14186 original size:55 final size:54
Alignment explanation
Indices: 14096--14492 Score: 408
Period size: 55 Copynumber: 7.2 Consensus size: 54
14086 TTTATTAGCA
* *
14096 TGCACA-AGTAGTGCCTATACGG-TAATTCATTAACTCATGATGAATTTCGT-AGTT
1 TGCACACA-TAGTGCCTGTACGGCT-ATTCATCAACTCATGATGAATTTCGTGA-TT
* * * * *
14150 ATGCACACATAGTTCTTGCACGGCTATTCATCAACTCGTGATGAATTTCGTGTAAT
1 -TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGTG-ATT
* * *
14206 TGCACACATAGTGCCTGTATGGCTATTCATCAACACATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGT-GATT
*** * *
14261 TGCACACATAGTGCCTGTAATTCTATTCATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGT-GATT
* * * *
14316 TGCACACATAGTGCCTGTACGACTATTCATCAACTCCTGATTAATTACGTAGAATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGT-G-ATT
* * *
14372 T-CACACATAGTGCATGTATGGCTATTCATCAACTCATGATGAATTAT-GTGGAAT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATT-TCGT-GATT
* * * *
14426 TGCACACATAGTGCATGTACGGCTATTCATCAACTCACGATGAATTCCGTGGAAT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGT-GATT
*
14481 TGCACATATAGT
1 TGCACACATAGT
14493 TTTTGTAGTA
Statistics
Matches: 293, Mismatches: 40, Indels: 18
0.83 0.11 0.05
Matches are distributed among these distances:
54 3 0.01
55 281 0.96
56 8 0.03
57 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (54 bp):
TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTTCGTGATT
Found at i:14289 original size:110 final size:110
Alignment explanation
Indices: 14096--14492 Score: 455
Period size: 110 Copynumber: 3.6 Consensus size: 110
14086 TTTATTAGCA
* * * *
14096 TGCACA-AGTAGTGCCTATACGG-TAATTCATTAACTCATGATGAATTTCGTAG-TTATGCACAC
1 TGCACACA-TAGTGCCTGTACGGCT-ATTCATCAACTCATGATGAATTCCGTGGATT-TGCACAC
* * * ** * *
14158 ATAGTTCTTGCACGGCTATTCATCAACTCGTGATGAATTTCGTGTAAT
63 ATAGTGCATGTAATGCTATTCATCAACTCATGATGAATTTCGTGGAAT
* *
14206 TGCACACATAGTGCCTGTATGGCTATTCATCAACACATGATGAATTCCGTGGATTTGCACACATA
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
* * * * *
14271 GTGCCTGTAATTCTATTCATCAACTCATGATGAATTCCATGGATT
66 GTGCATGTAATGCTATTCATCAACTCATGATGAATTTCGTGGAAT
* * * * *
14316 TGCACACATAGTGCCTGTACGACTATTCATCAACTCCTGATTAATTACGTAGAATTT-CACACAT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGT-GGATTTGCACACAT
14380 AGTGCATGT-ATGGCTATTCATCAACTCATGATGAATTAT-GTGGAAT
65 AGTGCATGTAAT-GCTATTCATCAACTCATGATGAATT-TCGTGGAAT
* * * *
14426 TGCACACATAGTGCATGTACGGCTATTCATCAACTCACGATGAATTCCGTGGAATTGCACATATA
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
14491 GT
66 GT
14493 TTTTGTAGTA
Statistics
Matches: 242, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
109 6 0.02
110 227 0.94
111 9 0.04
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (110 bp):
TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
GTGCATGTAATGCTATTCATCAACTCATGATGAATTTCGTGGAAT
Found at i:14379 original size:165 final size:165
Alignment explanation
Indices: 14120--14492 Score: 498
Period size: 165 Copynumber: 2.3 Consensus size: 165
14110 CTATACGGTA
* * * * * *
14120 ATTCATTAACTCATGATGAATTTCGTAG-TTATGCACACATAGTTCTTGCACGGCTATTCATCAA
1 ATTCATCAACTCATGATGAATTCCGTGGATT-TGCACACATAGTGCCTGCACGACTATTCATCAA
* * *
14184 CTCGTGATGAATTTCGTGTAATTGCACACATAGTGCCTGTATGGCTATTCATCAACACATGATGA
65 CTCCTGATGAATTACGTGTAATTGCACACATAGTGCATGTATGGCTATTCATCAACACATGATGA
* * * **
14249 ATTCCGTGGATTTGCACACATAGTGCCTGTAATTCT
130 ATTACGTGGAATTGCACACATAGTGCATGTAAGGCT
* *
14285 ATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCCTGTACGACTATTCATCAAC
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGCACGACTATTCATCAAC
* * *
14350 TCCTGATTAATTACGTAG-AATTTCACACATAGTGCATGTATGGCTATTCATCAACTCATGATGA
66 TCCTGATGAATTACGT-GTAATTGCACACATAGTGCATGTATGGCTATTCATCAACACATGATGA
* *
14414 ATTATGTGGAATTGCACACATAGTGCATGTACGGCT
130 ATTACGTGGAATTGCACACATAGTGCATGTAAGGCT
* * *
14450 ATTCATCAACTCACGATGAATTCCGTGGAATTGCACATATAGT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGT
14493 TTTTGTAGTA
Statistics
Matches: 181, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
165 178 0.98
166 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (165 bp):
ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGCACGACTATTCATCAAC
TCCTGATGAATTACGTGTAATTGCACACATAGTGCATGTATGGCTATTCATCAACACATGATGAA
TTACGTGGAATTGCACACATAGTGCATGTAAGGCT
Found at i:19234 original size:55 final size:55
Alignment explanation
Indices: 19166--19480 Score: 358
Period size: 55 Copynumber: 5.9 Consensus size: 55
19156 CTATATGGAA
* * * * * *
19166 ATTCATCAACTCATGATGAATTTTGT-GATTATGGACATATAGTGCATGTACGACT
1 ATTCATCAACTCATGATGAATTTCGTGGAAT-TGCACACATAGTGCCTGTACGGCT
* * * *
19221 ATTCATCAACTCATGATGAATTCCGTGGAATTGCACACAAAGTGCCTGTATGACT
1 ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCTGTACGGCT
* * * *
19276 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTCTACGGCT
1 ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCTGTACGGCT
* * * * *
19331 ATTCATCAACTCATGATGAA-------GATTTGTAAACATAGTGTCTGTAAGGCT
1 ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCTGTACGGCT
19379 ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCTGTACGGCT
* * * *
19434 ATTCATCAACTCGTGATGAATTCCGTGAAATTGTACACATAGTGCCT
1 ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCT
19481 ATAGTACACT
Statistics
Matches: 223, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
48 42 0.19
55 178 0.80
56 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCTGTACGGCT
Found at i:19407 original size:103 final size:104
Alignment explanation
Indices: 19166--19454 Score: 348
Period size: 103 Copynumber: 2.7 Consensus size: 104
19156 CTATATGGAA
* * * *
19166 ATTCATCAACTCATGATGAATTTTGT-GATTATGGACATATAGTGCATGTACGACTATTCATCAA
1 ATTCATCAACTCATGATGAATTTCGTGGATT-TGCACACATAGTGCATGTACGGCTATTCATCAA
* *
19230 CTCATGATGAATTCCGTGGAATTGCACACAAAGTGCCTGTATGACT
65 CTCATGATGAA-----T-GAATTGCAAACAAAGTGCCTGTAAGACT
* * *
19276 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTCTACGGCTATTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCATGTACGGCTATTCATCAAC
* * * * *
19341 TCATGATGAA-GATTTGTAAACATAGTGTCTGTAAGGCT
66 TCATGATGAATGAATTGCAAACAAAGTGCCTGTAAGACT
* *
19379 ATTCATCAACTCATGATGAATTTCGTGGAATTGCACACATAGTGCCTGTACGGCTATTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCATGTACGGCTATTCATCAAC
*
19444 TCGTGATGAAT
66 TCATGATGAAT
19455 TCCGTGAAAT
Statistics
Matches: 158, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
103 91 0.58
110 63 0.40
111 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (104 bp):
ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCATGTACGGCTATTCATCAAC
TCATGATGAATGAATTGCAAACAAAGTGCCTGTAAGACT
Found at i:19872 original size:19 final size:22
Alignment explanation
Indices: 19821--19874 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 22
19811 TACCCCTACC
19821 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACTACTATACT
**
19843 ATGGTGCCGATACT-CT-T-CT
1 ATGGTATCGATACTACTATACT
19862 ATGGTATCGATAC
1 ATGGTATCGATAC
19875 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
21 2 0.07
22 12 0.43
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (22 bp):
ATGGTATCGATACTACTATACT
Found at i:19926 original size:20 final size:20
Alignment explanation
Indices: 19901--19950 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
19891 TTCAAAATGA
19901 TATCGATACAT-TCCCTTCGG
1 TATCGATAC-TCTCCCTTCGG
*
19921 TATCGATACTCTCCCTTTGG
1 TATCGATACTCTCCCTTCGG
19941 TATCGATACT
1 TATCGATACT
19951 GAATTAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (20 bp):
TATCGATACTCTCCCTTCGG
Found at i:26886 original size:14 final size:14
Alignment explanation
Indices: 26867--26898 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
26857 AATAAGACGA
26867 TTTAGTTTAAATGT
1 TTTAGTTTAAATGT
*
26881 TTTAGTTTAAATTT
1 TTTAGTTTAAATGT
26895 TTTA
1 TTTA
26899 AAGAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (14 bp):
TTTAGTTTAAATGT
Found at i:26968 original size:26 final size:25
Alignment explanation
Indices: 26930--26981 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
26920 TAATGTGTGG
*
26930 AATTAAAAAGGAAAAAGAAAGGGTTT
1 AATTAAAAAGGAAAAA-AAAGAGTTT
* * *
26956 AATTAGAAGGGAAGAAAAAGAGTTT
1 AATTAAAAAGGAAAAAAAAGAGTTT
26981 A
1 A
26982 GGTTCAAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (25 bp):
AATTAAAAAGGAAAAAAAAGAGTTT
Found at i:37022 original size:95 final size:94
Alignment explanation
Indices: 36842--37023 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 94
36832 TCCTTTTTAC
* * * * *
36842 GATTTAATTCTTTCAATTCTTGCTCGTGTCCATCATCATGTATTAGTGAAACGAATGACTCTTTA
1 GATTCAATTCTTTCAATGCTTGCTCATGTCCATCATCATGTATTAGTGAAACGAATAACCCTTTA
36907 ATTCTTCCAATCCTATTGTAGTCATCAAT
66 ATTCTTCCAATCCTATTGTAGTCATCAAT
* * *
36936 GATTCAATTCATTT-AATGCTTGTTCATGTCTATCATCATGTATTAGTGAAATGAATAACCCTTT
1 GATTCAATTC-TTTCAATGCTTGCTCATGTCCATCATCATGTATTAGTGAAACGAATAACCC-TT
37000 TAATTCTTCCAATCCTATTGTAGT
64 TAATTCTTCCAATCCTATTGTAGT
37024 AGTCCATTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 49 0.63
95 29 0.37
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (94 bp):
GATTCAATTCTTTCAATGCTTGCTCATGTCCATCATCATGTATTAGTGAAACGAATAACCCTTTA
ATTCTTCCAATCCTATTGTAGTCATCAAT
Found at i:37541 original size:23 final size:23
Alignment explanation
Indices: 37511--37555 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
37501 GAGATTATAT
* *
37511 TAAATTTACAAGAGTGAAGAATC
1 TAAATTTAAAAGAGTCAAGAATC
37534 TAAATTTAAAAGAGTCAAGAAT
1 TAAATTTAAAAGAGTCAAGAAT
37556 GATTAACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.27
Consensus pattern (23 bp):
TAAATTTAAAAGAGTCAAGAATC
Found at i:38296 original size:90 final size:89
Alignment explanation
Indices: 38142--38318 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
38132 CCTAACACAC
* *
38142 CCTTTTATAGCCAAGTTATCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
* *
38207 TTTAATTAATTGGAATTCAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
38231 CCTTTTATATCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATT-AGGATTTTATTATTTCAAATTAATTAAATCTAT
38296 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
38319 TTCAGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 29 0.35
90 53 0.65
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:47322 original size:12 final size:12
Alignment explanation
Indices: 47302--47335 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
47292 GTTCATTTGG
*
47302 CCCAGGAGCCCA
1 CCCAAGAGCCCA
47314 CCCAAGAGCCCA
1 CCCAAGAGCCCA
47326 CCCAAGAGCC
1 CCCAAGAGCC
47336 ACCTTATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.50, G:0.21, T:0.00
Consensus pattern (12 bp):
CCCAAGAGCCCA
Found at i:53623 original size:136 final size:135
Alignment explanation
Indices: 53085--53730 Score: 355
Period size: 134 Copynumber: 4.8 Consensus size: 135
53075 AAATTTGACC
* * * * * * * *
53085 AAAAAACATAGGATGGAAAATAACTGCTTGTTGTTGACTTAAGCTAGAA-TATAGACT-ACTCC-
1 AAAAAACCTTGGATGGAAAATAGCT-ATTGTAGTTGAGTTAAACTA-AATTGTAGA-TGACTCCA
* * * ** ** *
53147 TCTATTACGAGTTAGGTCAATTTTGGGTG-TTTTCGAGTTTAATATCCTTCTTCGTGAAAATGAA
63 TC-ATTACGAGTTAAGTCAATTTTGGGTGCTCTTAGAGTCCAATATCCTTCTTAATGAAATTGAA
*
53211 ATTTGACTA
127 ATTTAACTA
* * ** * * * * * * ** *
53220 AAAAAACTTTGGCTTTAAAATAGCTCCTCGTTGTTGAGTTCATCTAGATTACAAATGACT-CATC
1 AAAAAACCTTGGATGGAAAATAGCT-ATTGTAGTTGAGTTAAACTAAATTGTAGATGACTCCATC
* * * * * * * *
53284 TATT-CTGAGTTAAGTCAATTTTGAGAGCTCTTAAAGTTCAATATCTTTCATAGTGAAGTTGAAA
65 -ATTAC-GAGTTAAGTCAATTTTGGGTGCTCTTAGAGTCCAATATCCTTCTTAATGAAATTGAAA
*
53348 TTTGACT-
128 TTTAACTA
* * * * * * * ** *
53355 -AAAAATCATGGTTGGATAATAGCTCCTCAT-TA-TTAAGTTAAGCTAAATTACAGACGACTCC-
1 AAAAAACCTTGGATGGAAAATAGCT-AT--TGTAGTTGAGTTAAACTAAATTGTAGATGACTCCA
* * *
53416 T-A-T--GAGTT-AGTCAGTTATGGGTGCTCTTCGAGT-CAATATCCTTCTTAATGAAATTGAAA
63 TCATTACGAGTTAAGTCAATTTTGGGTGCTCTTAGAGTCCAATATCCTTCTTAATGAAATTGAAA
53475 TTTAACTAA
128 TTTAACT-A
* * *
53484 AAAAAACCTTGGAT-GAAAAGTAGTTCATCAT-TA-TTGAGTTAAACTATATTGTAGATGATTCC
1 AAAAAACCTTGGATGGAAAA-TAGCT-AT--TGTAGTTGAGTTAAACTAAATTGTAGATGACTCC
* * * ** * *
53546 -TCTATTACGAGTTAAGTTAATTTTGGGTGCTCTTAGAGTCCAATATCTTTTTTCGTTAAGTTGA
62 ATC-ATTACGAGTTAAGTCAATTTTGGGTGCTCTTAGAGTCCAATATCCTTCTTAATGAAATTGA
* *
53610 TATTTGACT-
126 AATTTAACTA
* * *
53619 AAAAAACCTTGGCTGGAAAATAGCTATTGTAGTTGAGTTAAGCTAAATTGTAGATTACTCCATCA
1 AAAAAACCTTGGATGGAAAATAGCTATTGTAGTTGAGTTAAACTAAATTGTAGATGACTCCATCA
* * * *
53684 TTATGAGTTAAGTCAATTTTAGGTGCTCTTTGAATCCAATATCCTTC
66 TTACGAGTTAAGTCAATTTTGGGTGCTCTTAGAGTCCAATATCCTTC
53731 CTCGTAAAAT
Statistics
Matches: 398, Mismatches: 90, Indels: 47
0.74 0.17 0.09
Matches are distributed among these distances:
127 28 0.07
128 19 0.05
129 9 0.02
130 44 0.11
131 1 0.00
132 3 0.01
133 3 0.01
134 114 0.29
135 92 0.23
136 60 0.15
137 25 0.06
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (135 bp):
AAAAAACCTTGGATGGAAAATAGCTATTGTAGTTGAGTTAAACTAAATTGTAGATGACTCCATCA
TTACGAGTTAAGTCAATTTTGGGTGCTCTTAGAGTCCAATATCCTTCTTAATGAAATTGAAATTT
AACTA
Found at i:53692 original size:134 final size:132
Alignment explanation
Indices: 53517--53775 Score: 322
Period size: 134 Copynumber: 1.9 Consensus size: 132
53507 TTCATCATTA
* * * *
53517 TTGAGTTAAACTATATTGTAGATGATTCCTCTATTACGAGTTAAGTTAATTTTGGGTGCTCTTAG
1 TTGAGTTAAACTAAATTGTAGATGACTCCTCTATTACGAGTTAAGTCAATTTTAGGTGCTCTTAG
* * ** * * * * *
53582 AGTCCAATATCTTTTTTCGTTAAGTTGATATTTGACTAAAAAACCTTGGCTGGAAAATAGCTATT
66 AATCCAATATCCTTCCTCGTAAAATTAAAATTAGACT-AAAAA-CTTGGCTGGAAAATAGCTATT
53647 GTAG
129 GTAG
* * * *
53651 TTGAGTTAAGCTAAATTGTAGATTACTCCATC-ATTATGAGTTAAGTCAATTTTAGGTGCTCTTT
1 TTGAGTTAAACTAAATTGTAGATGACTCC-TCTATTACGAGTTAAGTCAATTTTAGGTGCTCTTA
*
53715 GAATCCAATATCCTTCCTCGTAAAATTAAAATTAGACTAAAAACTTGGTTGGAAAATAGCT
65 GAATCCAATATCCTTCCTCGTAAAATTAAAATTAGACTAAAAACTTGGCTGGAAAATAGCT
53776 CTGCATTATA
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
132 17 0.16
133 5 0.05
134 82 0.77
135 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (132 bp):
TTGAGTTAAACTAAATTGTAGATGACTCCTCTATTACGAGTTAAGTCAATTTTAGGTGCTCTTAG
AATCCAATATCCTTCCTCGTAAAATTAAAATTAGACTAAAAACTTGGCTGGAAAATAGCTATTGT
AG
Found at i:55942 original size:20 final size:20
Alignment explanation
Indices: 55887--55950 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
55877 TCATTTCTTG
*
55887 AAAGGGATCGATCATTTTTCA
1 AAAGGGATCGATC-CTTTTCA
** * * *
55908 TGAGGGATTGGTCCTTTTGA
1 AAAGGGATCGATCCTTTTCA
*
55928 AAAGGGATCGATCCTTTGCA
1 AAAGGGATCGATCCTTTTCA
55948 AAA
1 AAA
55951 CAGAAACTGT
Statistics
Matches: 31, Mismatches: 12, Indels: 1
0.70 0.27 0.02
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (20 bp):
AAAGGGATCGATCCTTTTCA
Found at i:60577 original size:20 final size:20
Alignment explanation
Indices: 60546--60595 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
60536 TATGCTACTT
*
60546 CAACTGCCTTGACGCATAAA
1 CAACTACCTTGACGCATAAA
*
60566 CAATTACCTTGACGCATAAA
1 CAACTACCTTGACGCATAAA
60586 CAACTACCTT
1 CAACTACCTT
60596 TATGTCTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.24
Consensus pattern (20 bp):
CAACTACCTTGACGCATAAA
Found at i:74014 original size:35 final size:34
Alignment explanation
Indices: 73916--74040 Score: 133
Period size: 35 Copynumber: 3.6 Consensus size: 34
73906 TTTAACTCGA
* *
73916 TCAAACTGGTAATTCTTTATATAGGTTCAGACTA
1 TCAAACTGGTAATTCCTTATATAGGTTCAGACTG
* *** *
73950 TAAAACTGGTAATTCCTTACGGCAGGTTCAGCTCTG
1 TCAAACTGGTAATTCCTTA-TATAGGTTCAG-ACTG
* *
73986 TCAAAGTGGTAATTCCTTATATATGTTCAGACTG
1 TCAAACTGGTAATTCCTTATATAGGTTCAGACTG
*
74020 ATCAAGCTGGTAATTCCTTAT
1 -TCAAACTGGTAATTCCTTAT
74041 GGATCTAAGG
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
34 20 0.28
35 33 0.46
36 19 0.26
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (34 bp):
TCAAACTGGTAATTCCTTATATAGGTTCAGACTG
Done.