Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003034.1 Hibiscus syriacus cultivar Beakdansim tig00006314_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: 72493
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1252 original size:10 final size:10
Alignment explanation
Indices: 1237--1266 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1227 CTTGATTCTA
1237 GTTTCTTGTT
1 GTTTCTTGTT
1247 GTTTCTTGTT
1 GTTTCTTGTT
1257 GTTTCTTGTT
1 GTTTCTTGTT
1267 ATTGATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.20, T:0.70
Consensus pattern (10 bp):
GTTTCTTGTT
Found at i:1442 original size:19 final size:19
Alignment explanation
Indices: 1418--1465 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1408 AGGGCTAGTG
1418 CATCGGTGCACTAAGAGTA
1 CATCGGTGCACTAAGAGTA
*
1437 CATCGGTGCACTAAGAGTG
1 CATCGGTGCACTAAGAGTA
*
1456 CATCGATGCA
1 CATCGGTGCA
1466 TAAAATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (19 bp):
CATCGGTGCACTAAGAGTA
Found at i:1592 original size:72 final size:71
Alignment explanation
Indices: 1470--1611 Score: 189
Period size: 72 Copynumber: 2.0 Consensus size: 71
1460 GATGCATAAA
** * * * *
1470 ATGCATTCGATGTTTTAAAATAGTCTGAGTGTATCGATGCTTGGCTTGTGCATTGATGTATAAAA
1 ATGCATTCGATGTTTTAAAATACCCTGAGTGCATCGATGCATGGCTTGTGCATCGATGCATAAAA
1535 TGCATT
66 TGCATT
1541 ATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGG-TATGTGCATCGATGCATA
1 ATGCATTCGATGTTTT-A-AAATACCCTGAGTGCATCGATGCATGGCT-TGTGCATCGATGCATA
1604 AAATGCAT
63 AAATGCAT
1612 ACGATGTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 17 0.27
72 42 0.68
73 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (71 bp):
ATGCATTCGATGTTTTAAAATACCCTGAGTGCATCGATGCATGGCTTGTGCATCGATGCATAAAA
TGCATT
Found at i:3719 original size:16 final size:16
Alignment explanation
Indices: 3698--3732 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3688 AAAGTTCGAT
3698 GAGCTTAACGAGCATC
1 GAGCTTAACGAGCATC
3714 GAGCTTAACGAGCATC
1 GAGCTTAACGAGCATC
3730 GAG
1 GAG
3733 TAGAGCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (16 bp):
GAGCTTAACGAGCATC
Found at i:6848 original size:45 final size:45
Alignment explanation
Indices: 6784--6870 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
6774 TCTTCATTCC
* * *
6784 CGTCTCGGAAATAGGTTTAATCTCTCTCTCTCTCTTTCTCTCTCT
1 CGTCTCGGAAAGAGGTTTAATCACTCTCTCTCTCTCTCTCTCTCT
6829 CGTCTCGGAAAGAGGTTTAATCACTCTCTCTCTCTCTCTCTC
1 CGTCTCGGAAAGAGGTTTAATCACTCTCTCTCTCTCTCTCTC
6871 GTCGAAGCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.15, C:0.32, G:0.13, T:0.40
Consensus pattern (45 bp):
CGTCTCGGAAAGAGGTTTAATCACTCTCTCTCTCTCTCTCTCTCT
Found at i:9684 original size:26 final size:26
Alignment explanation
Indices: 9617--9677 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
9607 CTAAATCACT
* *
9617 TTCTAGAAGCTGCTAACTGGACCGTC
1 TTCTAGAAGCTGCTGACTGGACCGCC
9643 TTCTAGAAGCTGCTGACTGGACCGCC
1 TTCTAGAAGCTGCTGACTGGACCGCC
9669 TTCTAGAAG
1 TTCTAGAAG
9678 TTACTGATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (26 bp):
TTCTAGAAGCTGCTGACTGGACCGCC
Found at i:11647 original size:14 final size:17
Alignment explanation
Indices: 11604--11640 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11594 AGTCAAATAC
11604 TTAATC-ATCAAAAATTA
1 TTAATCTAT-AAAAATTA
11621 TTAATCTATAAAAATTA
1 TTAATCTATAAAAATTA
11638 TTA
1 TTA
11641 CTTAAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAATCTATAAAAATTA
Found at i:12490 original size:46 final size:46
Alignment explanation
Indices: 12382--12490 Score: 121
Period size: 46 Copynumber: 2.4 Consensus size: 46
12372 TTCTCTCACT
* * * * *
12382 AAAACGACGTCGTTTTGACGCAATTGTTTTAATACTAAAAAGACTC
1 AAAACTACATCGTTTTGACGCAACTATTTTAATACTAAAAAAACTC
* *
12428 AAAACTACGTCATTTTGACGCAACTATTTTAATACTAAAAAAA-TC
1 AAAACTACATCGTTTTGACGCAACTATTTTAATACTAAAAAAACTC
* *
12473 TAAAATTATATCGTTTTG
1 -AAAACTACATCGTTTTG
12491 TTAGAATTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 2 0.04
46 51 0.96
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (46 bp):
AAAACTACATCGTTTTGACGCAACTATTTTAATACTAAAAAAACTC
Found at i:17071 original size:60 final size:60
Alignment explanation
Indices: 16959--17073 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
16949 TAGTCGGGTG
* ** *
16959 ACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAACAATATCCTATAGTTGGAGA
1 ACCATTTTATAACTTTTAATAGTCGATGGACAAAACAAAACAACATCCTATAGTTGGAGA
*
17019 ACCATTTTATAACTTTTAATAGTCGAAT-GACAAAATAAAACAACA-CCGTATAGTT
1 ACCATTTTATAACTTTTAATAGTCG-ATGGACAAAACAAAACAACATCC-TATAGTT
17074 AGGGGACCGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.04
60 44 0.92
61 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (60 bp):
ACCATTTTATAACTTTTAATAGTCGATGGACAAAACAAAACAACATCCTATAGTTGGAGA
Found at i:19949 original size:24 final size:24
Alignment explanation
Indices: 19922--19968 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19912 ATGTAACTGA
*
19922 ACGGAGAGAGAGAGAGATGAAGAG
1 ACGGAGAGAAAGAGAGATGAAGAG
*
19946 ACGGTGAGAAAGAGAGATGAAGA
1 ACGGAGAGAAAGAGAGATGAAGA
19969 AATGAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.43, T:0.06
Consensus pattern (24 bp):
ACGGAGAGAAAGAGAGATGAAGAG
Found at i:21386 original size:30 final size:30
Alignment explanation
Indices: 21356--21415 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
21346 GATGATTGAC
* * *
21356 CCAAAAA-CTAATTTTATTAAGTTTAGTGA
1 CCAAAAACCTAAATGTATAAAGTTTAGTGA
21385 CCAAAAACGCTAAATGTATAAAGTTTAGTGA
1 CCAAAAAC-CTAAATGTATAAAGTTTAGTGA
21416 GAAAATTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
31 19 0.73
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (30 bp):
CCAAAAACCTAAATGTATAAAGTTTAGTGA
Found at i:23111 original size:14 final size:14
Alignment explanation
Indices: 23083--23119 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
23073 GGGTTAAAAA
*
23083 ATATAAC-AAAATT
1 ATATAACTATAATT
23096 ATATAACTATAATT
1 ATATAACTATAATT
23110 ATATAACTAT
1 ATATAACTAT
23120 TCTTTCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAACTATAATT
Found at i:23506 original size:28 final size:28
Alignment explanation
Indices: 23474--23538 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
23464 CCGATTTAGA
23474 TTGAACCGGACTAAGCAACGGTTCCCGG
1 TTGAACCGGACTAAGCAACGGTTCCCGG
23502 TTGAACCGGACTAAGCAACGGTTCCCGG
1 TTGAACCGGACTAAGCAACGGTTCCCGG
23530 TTGAACCGG
1 TTGAACCGG
23539 TTGAACCGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.18
Consensus pattern (28 bp):
TTGAACCGGACTAAGCAACGGTTCCCGG
Found at i:32296 original size:18 final size:18
Alignment explanation
Indices: 32275--32330 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
32265 GTACCAATCC
*
32275 TTTCACTATATTATTCTT
1 TTTCACTATATTGTTCTT
* *
32293 TTTC-CCATATCGTTC-T
1 TTTCACTATATTGTTCTT
32309 TTTCACTATATTGTTCCTT
1 TTTCACTATATTGTT-CTT
32328 TTT
1 TTT
32331 TCTATACTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 5 0.17
17 16 0.53
18 5 0.17
19 4 0.13
ACGTcount: A:0.16, C:0.21, G:0.04, T:0.59
Consensus pattern (18 bp):
TTTCACTATATTGTTCTT
Found at i:32735 original size:65 final size:65
Alignment explanation
Indices: 32601--32905 Score: 393
Period size: 65 Copynumber: 4.7 Consensus size: 65
32591 TATCATATAG
* ** * *
32601 TCACTCCACCTTATGCACCACAAAGGTACACAAGTCTTGTTGAGTGATCTT-TGCAGTATTCAAT
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCAT-ATGAGTGAT-TTGTGCAGTATTCAAT
*
32665 AA
64 TA
* * *
32667 TCATTCCACCTCATACACCACAAAGGTACATGAGTCATATGAGTGATTTGTGCAGTATTTAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATTTGTGCAGTATTCAATTA
* * * *
32732 TCATTCCATCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTGTAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATTTGTGCAGTATTCAATTA
* * * * *
32797 TCACTCCAACTCATGCACCACAAAGATACATGAGTC--A-GAGTAATATGTGCAATATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATTTGTGCAGTATTCAATTA
*
32859 TCACTCCACCTCATGCACCACAAAGGTACATAAGTCATATGAGTGAT
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGAT
32906 CTATACTGGT
Statistics
Matches: 210, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
62 54 0.26
63 1 0.00
64 3 0.01
65 120 0.57
66 32 0.15
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (65 bp):
TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATTTGTGCAGTATTCAATTA
Found at i:32900 original size:127 final size:129
Alignment explanation
Indices: 32601--32907 Score: 420
Period size: 127 Copynumber: 2.4 Consensus size: 129
32591 TATCATATAG
* * * * *
32601 TCACTCCACCTTATGCACCACAAAGGTACACAAGTCTTGTTGAGTGATCTTTGCAGTATTCAATA
1 TCACTCCACCTCATGCACCACAAAGGTACATAAGTCAT-ATGAGTGATCTGTGCAGTATTCAATA
* * * * * * *
32666 ATCATTCCACCTCATACACCACAAAGGTACATGAGTCATATGAGTGATTTGTGCAGTATTTAATT
65 ATCACTCCAACTCATACACCACAAAGATACATGAGTCA-ATGAGTAATATGTGCAATATTCAATT
32731 A
129 A
* * * * *
32732 TCATTCCATCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTGTAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATAAGTCATATGAGTGATCTGTGCAGTATTCAATAA
*
32797 TCACTCCAACTCATGCACCACAAAGATACATGAGTC-A-GAGTAATATGTGCAATATTCAATTA
66 TCACTCCAACTCATACACCACAAAGATACATGAGTCAATGAGTAATATGTGCAATATTCAATTA
32859 TCACTCCACCTCATGCACCACAAAGGTACATAAGTCATATGAGTGATCT
1 TCACTCCACCTCATGCACCACAAAGGTACATAAGTCATATGAGTGATCT
32908 ATACTGGTGT
Statistics
Matches: 155, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
127 67 0.43
128 1 0.01
130 55 0.35
131 32 0.21
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (129 bp):
TCACTCCACCTCATGCACCACAAAGGTACATAAGTCATATGAGTGATCTGTGCAGTATTCAATAA
TCACTCCAACTCATACACCACAAAGATACATGAGTCAATGAGTAATATGTGCAATATTCAATTA
Found at i:36922 original size:29 final size:29
Alignment explanation
Indices: 36834--37079 Score: 246
Period size: 29 Copynumber: 8.6 Consensus size: 29
36824 TGCATTCTTA
* *
36834 ATTCTGCATGAGATTACATCC-CGTCTTG
1 ATTCTGCATGGGATTACATCCTCGTCCTG
*
36862 ATTCTGCATGGGATTATAT-CTCGTCCTG
1 ATTCTGCATGGGATTACATCCTCGTCCTG
* *
36890 ATTCTACATGGGATTACATCCTTGTCCTG
1 ATTCTGCATGGGATTACATCCTCGTCCTG
* * * * *
36919 ATTCTGCACGTGAATACATCCCCATCCTG
1 ATTCTGCATGGGATTACATCCTCGTCCTG
* * * * *
36948 ATTCTACAAGGGAGTACATCCCCGTCCTA
1 ATTCTGCATGGGATTACATCCTCGTCCTG
**
36977 ATTCTGCATGGGATTGA-ATCCTAATCCTG
1 ATTCTGCATGGGATT-ACATCCTCGTCCTG
** * *
37006 ATTCTGCATGAAATTACATCCACGTCCCG
1 ATTCTGCATGGGATTACATCCTCGTCCTG
* * *
37035 ATTCTGCGTGGGATTAAATCCTCGTCGTG
1 ATTCTGCATGGGATTACATCCTCGTCCTG
37064 ATTCTGCATGGGATTA
1 ATTCTGCATGGGATTA
37080 TATTAGCGTC
Statistics
Matches: 174, Mismatches: 40, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
27 1 0.01
28 41 0.24
29 131 0.75
30 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (29 bp):
ATTCTGCATGGGATTACATCCTCGTCCTG
Found at i:45788 original size:14 final size:14
Alignment explanation
Indices: 45769--45808 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
45759 AACGAACATA
45769 AACGAACACAAACG
1 AACGAACACAAACG
*
45783 AACGAACATAAACG
1 AACGAACACAAACG
45797 AAC-AACACAAAC
1 AACGAACACAAAC
45809 ACAAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.60, C:0.28, G:0.10, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:45800 original size:10 final size:10
Alignment explanation
Indices: 45756--45785 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
45746 CATTTAAATG
45756 ATAAACGAAC
1 ATAAACGAAC
45766 ATAAACGAAC
1 ATAAACGAAC
*
45776 ACAAACGAAC
1 ATAAACGAAC
45786 GAACATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:46083 original size:14 final size:14
Alignment explanation
Indices: 46062--46107 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
46052 GCCCTCTTTT
46062 CGAACATAAATGAA
1 CGAACATAAATGAA
*
46076 CTAACATAAATGAA
1 CGAACATAAATGAA
46090 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
46106 CG
1 CG
46108 TTCACGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 20 0.71
15 3 0.11
16 5 0.18
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.17
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:61546 original size:11 final size:11
Alignment explanation
Indices: 61519--61575 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
61509 AGATTCAATC
*
61519 AGAACAAAAAG
1 AGAAAAAAAAG
*
61530 AGAAAAAAGAG
1 AGAAAAAAAAG
*
61541 AAAAAAAGCAAAG
1 AGAAAAA--AAAG
61554 AGAAAATAAAAAG
1 AG-AAA-AAAAAG
61567 AGAAAAAAA
1 AGAAAAAAA
61576 GGGAAAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 19 0.51
12 3 0.08
13 10 0.27
14 3 0.08
15 2 0.05
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:61566 original size:13 final size:13
Alignment explanation
Indices: 61532--61575 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
61522 ACAAAAAGAG
61532 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
61545 AAAGCAAAGAGAAAA
1 AAA--AAAGAGAAAA
*
61560 TAAAAAGAGAAAA
1 AAAAAAGAGAAAA
61573 AAA
1 AAA
61576 GGGAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 15 0.56
15 12 0.44
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:61746 original size:69 final size:69
Alignment explanation
Indices: 61655--61792 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
61645 GATTCAAACT
* * *
61655 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTTCACTCG-ATGATCATAGGGC
1 ATGAAATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAT-ATCATAGAGC
61719 ATCAA
65 ATCAA
*
61724 ATGAAATTGATCAAGCATAATCATTTCTGAATCACTGAATCACTCCACTCGAATATCATAGAGCA
1 ATGAAATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAATATCATAGAGCA
61789 TCAA
66 TCAA
61793 GAAAGATACA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 62 0.97
70 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (69 bp):
ATGAAATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAATATCATAGAGCA
TCAA
Found at i:62752 original size:32 final size:31
Alignment explanation
Indices: 62715--62829 Score: 113
Period size: 32 Copynumber: 3.6 Consensus size: 31
62705 GGAACAATGA
*
62715 GGGCATCTTTGAAGATTCAACATCAAATGCTG
1 GGGCATCTTTG-AGATTCAACATCAAATGTTG
* * * *
62747 GGGCATTTTTTATATTTAACATCAAATGTTG
1 GGGCATCTTTGAGATTCAACATCAAATGTTG
* * *
62778 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATGTTG
* *
62810 GGCCATCTTTGGGAATTCAA
1 GGGCATCTTTGAG-ATTCAA
62830 TATCCTGATG
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 28 0.41
32 40 0.59
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATGTTG
Found at i:63480 original size:43 final size:43
Alignment explanation
Indices: 63372--63488 Score: 198
Period size: 44 Copynumber: 2.7 Consensus size: 43
63362 GGGCCATCTG
* *
63372 CGATGTCAACCCCACGACGGAGGATATCGTACCCACACATCCA
1 CGATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCA
63415 CGATTTTCAACTCCACGACGGAGGATATCGTACCCACACATCCA
1 CGA-TTTCAACTCCACGACGGAGGATATCGTACCCACACATCCA
*
63459 CGATTTCAACTCCACAACGGAGGATATCGT
1 CGATTTCAACTCCACGACGGAGGATATCGT
63489 GCCATTTGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 29 0.41
44 41 0.59
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (43 bp):
CGATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCA
Found at i:63717 original size:106 final size:105
Alignment explanation
Indices: 63538--63783 Score: 350
Period size: 106 Copynumber: 2.3 Consensus size: 105
63528 ATTTCATAGT
* * *
63538 CAATTTCAACTTCACAGTGAAGAATATTAGACTCGAGACAACACAAGTTCAACTTCACATCGAAG
1 CAATTTCAACTTCACA-TGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAG
* *
63603 GGATGGCTGGTTGTCAACAAACAATTTCGT-AGTTTCAAAAC
65 GGACGGCTGGTTGTCAACAAACAATTTC-TCAGTTCCAAAAC
63644 CAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAT-GAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAG
* * * *
63709 GGACGGCTGGTTGTCAATAAATAATTTCTCAGTTCCAGAGC
65 GGACGGCTGGTTGTCAACAAACAATTTCTCAGTTCCAAAAC
* *
63750 CAATTTCAACTTCACGGTGGAGGATATTGGACTC
1 CAATTTCAACTTCAC-ATGAAGGATATTGGACTC
63784 AGAACAATAC
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
105 2 0.02
106 123 0.98
107 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (105 bp):
CAATTTCAACTTCACATGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGG
GACGGCTGGTTGTCAACAAACAATTTCTCAGTTCCAAAAC
Found at i:64108 original size:102 final size:102
Alignment explanation
Indices: 63930--64116 Score: 243
Period size: 102 Copynumber: 1.8 Consensus size: 102
63920 GACAGTTTCC
* * *
63930 AAGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATATCTTTTCCTTGAAAC
1 AAGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACAAAATCATTGAATAACTTTCCCTTGAAAC
63995 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
66 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
* * * *
64032 AAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATTGAA-AACATTTCCCTTGAA
1 AAGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACA-AAATCATTGAATAAC-TTTCCCTTGAA
** * *
64095 ATGAATTTTGTCTCTCTTGAGA
64 ACAAATTTCGTCTCCCTTGAGA
64117 TAGTTTCCCT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
101 2 0.03
102 67 0.93
103 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (102 bp):
AAGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACAAAATCATTGAATAACTTTCCCTTGAAAC
AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
Found at i:64332 original size:37 final size:37
Alignment explanation
Indices: 64289--64379 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 37
64279 TTGAATACAA
64289 TTTCTCTTGAAACACACAAAAAAAACCTTTGAA-ATTG
1 TTTCTCTTGAAACACACAAAAAAAACCTTTGAAGA-TG
64326 TTTCTCTTG-AA-ACACAAAAAAAACCTTTGAAGATG
1 TTTCTCTTGAAACACACAAAAAAAACCTTTGAAGATG
64361 TTTCTCTTGAAACAC-CAAA
1 TTTCTCTTGAAACACACAAA
64380 CCCTCAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
35 31 0.61
36 9 0.18
37 11 0.22
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (37 bp):
TTTCTCTTGAAACACACAAAAAAAACCTTTGAAGATG
Found at i:65732 original size:4 final size:4
Alignment explanation
Indices: 65723--65797 Score: 50
Period size: 4 Copynumber: 18.2 Consensus size: 4
65713 CTTTTATGGA
65723 ATTT ATTT ATTT A-TT -TTT ATGTCT -TTT ATTTT ATTTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT AT-T-T ATTT A-TTT A-TTT ATTT ATTT
* *
65768 ATTT CGTTT CTTT ATTT -TTT ATTT AATTT A
1 ATTT -ATTT ATTT ATTT ATTT ATTT -ATTT A
65798 CTTGTTATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
3 8 0.14
4 32 0.54
5 18 0.31
6 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:65737 original size:32 final size:32
Alignment explanation
Indices: 65696--65780 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 32
65686 TTTCTAGTGT
65696 TTTATTTATTTCATTTGCTTTTA-TGGAATTTA
1 TTTATTTATTTC-TTTGCTTTTATTGGAATTTA
** *
65728 TTTATTTATTT-TTATGTCTTTTATTTTATTTTA
1 TTTATTTATTTCTT-TG-CTTTTATTGGAATTTA
65761 TTTATTTATTTCGTTT-CTTT
1 TTTATTTATTTC-TTTGCTTT
65781 ATTTTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
30 2 0.04
31 2 0.04
32 21 0.47
33 17 0.38
34 1 0.02
35 2 0.04
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (32 bp):
TTTATTTATTTCTTTGCTTTTATTGGAATTTA
Found at i:65740 original size:23 final size:24
Alignment explanation
Indices: 65699--65743 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
65689 CTAGTGTTTT
*
65699 ATTTATTTCATTTGCTTTTATGGA
1 ATTTATTTCATTTACTTTTATGGA
*
65723 ATTTATTT-ATTTATTTTTATG
1 ATTTATTTCATTTACTTTTATG
65744 TCTTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.22, C:0.04, G:0.09, T:0.64
Consensus pattern (24 bp):
ATTTATTTCATTTACTTTTATGGA
Found at i:65788 original size:33 final size:33
Alignment explanation
Indices: 65724--65797 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
65714 TTTTATGGAA
*
65724 TTTATTTATTTATTTTTATGTCTTTTATTTTAT
1 TTTATTTATTTATTTGTATGTCTTTTATTTTAT
*
65757 TTTATTTATTTATTTCGT-T-TCTTTATTTTTTAT
1 TTTATTTATTTATTT-GTATGTCTTT-TATTTTAT
*
65790 TTAATTTA
1 TTTATTTA
65798 CTTGTTATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 5 0.14
33 30 0.83
34 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (33 bp):
TTTATTTATTTATTTGTATGTCTTTTATTTTAT
Found at i:65823 original size:33 final size:31
Alignment explanation
Indices: 65747--65823 Score: 73
Period size: 33 Copynumber: 2.4 Consensus size: 31
65737 TTTTATGTCT
* * **
65747 TTTATTTTATTTTATTTATTTATTTCGTTTC
1 TTTATTTTATTTAATTTACTTATTTCGTTAA
*
65778 TTTATTTTTTATTTAATTTACTTGTTATCGTTAA
1 TTTA--TTTTATTTAATTTACTTATT-TCGTTAA
65812 TTTATTATTATT
1 TTTATT-TTATT
65824 CTTTCCTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
31 4 0.11
32 2 0.05
33 22 0.59
34 9 0.24
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (31 bp):
TTTATTTTATTTAATTTACTTATTTCGTTAA
Found at i:68792 original size:20 final size:20
Alignment explanation
Indices: 68763--68800 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
68753 TTTGGTTCAC
*
68763 GGAATGTAAGATTACCAGTA
1 GGAATATAAGATTACCAGTA
68783 GGAATATAAGATTACCAG
1 GGAATATAAGATTACCAG
68801 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTA
Found at i:68806 original size:18 final size:19
Alignment explanation
Indices: 68763--68806 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
68753 TTTGGTTCAC
*
68763 GGAATGTAAGATTACCAGTA
1 GGAATATAAGATTACCAG-A
68783 GGAATATAAGATTACCAG-
1 GGAATATAAGATTACCAGA
68801 GGAATA
1 GGAATA
68807 GGATTATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATATAAGATTACCAGA
Found at i:70677 original size:9 final size:9
Alignment explanation
Indices: 70663--70700 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
70653 TGATATTAAT
70663 TTAATTGGA
1 TTAATTGGA
*
70672 TTAATTTG-
1 TTAATTGGA
70680 -TAATTGGA
1 TTAATTGGA
70688 TTAATTGGA
1 TTAATTGGA
70697 TTAA
1 TTAA
70701 GTTTTGATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 6 0.24
9 19 0.76
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (9 bp):
TTAATTGGA
Found at i:71503 original size:28 final size:28
Alignment explanation
Indices: 71472--71531 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
71462 TTATGTCGTC
*
71472 GAGCTAGTGCTGGAAACAATATGTTATT
1 GAGCCAGTGCTGGAAACAATATGTTATT
* *
71500 GAGCCAGTGCTTGAAACATTATGTTATT
1 GAGCCAGTGCTGGAAACAATATGTTATT
71528 GAGC
1 GAGC
71532 AAATGCTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (28 bp):
GAGCCAGTGCTGGAAACAATATGTTATT
Found at i:71548 original size:28 final size:28
Alignment explanation
Indices: 71479--71542 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
71469 GTCGAGCTAG
* * * *
71479 TGCTGGAAACAATATGTTATTGAGCCAG
1 TGCTTGAAACATTATGTTATTGAGCAAA
71507 TGCTTGAAACATTATGTTATTGAGCAAA
1 TGCTTGAAACATTATGTTATTGAGCAAA
71535 TGCTTGAA
1 TGCTTGAA
71543 CTATTAGTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (28 bp):
TGCTTGAAACATTATGTTATTGAGCAAA
Found at i:72117 original size:2 final size:2
Alignment explanation
Indices: 72110--72155 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
72100 GTATTTTACA
72110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
72152 AT AT
1 AT AT
72156 TTAATATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.