Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004945.1 Hibiscus syriacus cultivar Beakdansim tig00011117_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: 60268
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:9241 original size:42 final size:42
Alignment explanation
Indices: 9177--9280 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 42
9167 GTTTATATTA
* * ** *
9177 AAACTCCACTAAGGGACCAAACTTCTACGGCATTTATTACAA-
1 AAACACCACTAAAGGAAAAAACTACTACGGCATTTATTA-AAG
* * *
9219 AAACACCCCTAAAGGAAAAAACTACTGCGGCGTTTATTAAAG
1 AAACACCACTAAAGGAAAAAACTACTACGGCATTTATTAAAG
* *
9261 AAACGCCACTAAATGAAAAA
1 AAACACCACTAAAGGAAAAA
9281 TTATTATGGT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
41 2 0.04
42 48 0.96
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.19
Consensus pattern (42 bp):
AAACACCACTAAAGGAAAAAACTACTACGGCATTTATTAAAG
Found at i:9397 original size:41 final size:41
Alignment explanation
Indices: 9352--9430 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
9342 AACACAGCTA
*
9352 AAGTACATGGATATTGAGGCGTTTGATCACAAACGCCAGAT
1 AAGTACAAGGATATTGAGGCGTTTGATCACAAACGCCAGAT
* * **
9393 AAGTACAAGGCTATTGTGGCGTTTTCTCACAAACGCCA
1 AAGTACAAGGATATTGAGGCGTTTGATCACAAACGCCA
9431 CTAAATTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
AAGTACAAGGATATTGAGGCGTTTGATCACAAACGCCAGAT
Found at i:16456 original size:13 final size:13
Alignment explanation
Indices: 16438--16472 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
16428 TACAATCACT
16438 CAAAAAGAAGAAA
1 CAAAAAGAAGAAA
16451 CAAAAAGAAGAAA
1 CAAAAAGAAGAAA
16464 -AGAAAAGAA
1 CA-AAAAGAA
16473 ATTGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (13 bp):
CAAAAAGAAGAAA
Found at i:23750 original size:59 final size:59
Alignment explanation
Indices: 23658--23784 Score: 227
Period size: 59 Copynumber: 2.2 Consensus size: 59
23648 ACATGTGATA
*
23658 ATTCCACCTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
1 ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
23717 ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
1 ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
* *
23776 TTTGCACTT
1 ATTCCACTT
23785 TACATTTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (59 bp):
ATTCCACTTAAAGTCAAGTCCTCACTTGCCATTATATTGTCGTCAGAAGTCACTAGGAG
Found at i:35908 original size:42 final size:41
Alignment explanation
Indices: 35862--36026 Score: 151
Period size: 42 Copynumber: 4.0 Consensus size: 41
35852 AAATTAACGG
35862 CGTTTATACCACAAACGCCGCAATAG-ATTACA-CATATAGTGA
1 CGTTTATACCACAAACGCCGCAATAGTA-TA-ATCA-ATAGTGA
* * * *
35904 CGTTTATTCCTCAAATGCCGCAATAGTGATAATCAATAGTGG
1 CGTTTATACCACAAACGCCGCAATAGT-ATAATCAATAGTGA
* * * *
35946 CGTTTTTA-GACAAACGCCGCAATAGTTTTAATCAATAGTGG
1 CGTTTATACCACAAACGCCGCAATAG-TATAATCAATAGTGA
* * *
35987 CGTTTTTA--ACAAACGCCACAATAGTGTAATCAATAGTGA
1 CGTTTATACCACAAACGCCGCAATAGTATAATCAATAGTGA
36026 C
1 C
36027 TTTTTTTGTA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
39 14 0.13
40 15 0.14
41 35 0.33
42 37 0.35
43 4 0.04
44 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (41 bp):
CGTTTATACCACAAACGCCGCAATAGTATAATCAATAGTGA
Found at i:35971 original size:41 final size:40
Alignment explanation
Indices: 35872--36048 Score: 171
Period size: 41 Copynumber: 4.3 Consensus size: 40
35862 CGTTTATACC
* **
35872 ACAAACGCCGCAATAGAT-TACA-CATATAGTGACGTTTATTCC
1 ACAAACGCCGCAATAG-TGTA-ATCA-ATAGTGGCGTTT-TTAG
* *
35914 TCAAATGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAG
1 ACAAACGCCGCAATAGTG-TAATCAATAGTGGCGTTTTTAG
*
35955 ACAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTA-
1 ACAAACGCCGCAATAG-TGTAATCAATAGTGGCGTTTTTAG
* * * *
35995 ACAAACGCCACAATAGTGTAATCAATAGTGACTTTTTTTG
1 ACAAACGCCGCAATAGTGTAATCAATAGTGGCGTTTTTAG
*
36035 TATAAACGCCGCAA
1 -ACAAACGCCGCAA
36049 AATGTTAAAT
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
39 19 0.17
40 15 0.13
41 49 0.43
42 27 0.24
43 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (40 bp):
ACAAACGCCGCAATAGTGTAATCAATAGTGGCGTTTTTAG
Found at i:35984 original size:83 final size:81
Alignment explanation
Indices: 35872--36048 Score: 198
Period size: 83 Copynumber: 2.2 Consensus size: 81
35862 CGTTTATACC
** * *
35872 ACAAACGCCGCAATAGATTACACATATAGTGACGTTTATTCCTCAAATGCCGCAATAGTGATAAT
1 ACAAACGCCGCAATAGATTACACATATAGTGACGTTT-TT-AACAAACGCCACAATAGTG-TAAT
*
35937 CAATAGTGGCGTTTTTAG-
63 CAATAGTGACGTTTTTAGT
* *
35955 ACAAACGCCGCAATAGTTTTA-ATCA-ATAGTGGCGTTTTTAACAAACGCCACAATAGTGTAATC
1 ACAAACGCCGCAATAG-ATTACA-CATATAGTGACGTTTTTAACAAACGCCACAATAGTGTAATC
* *
36018 AATAGTGACTTTTTTTGT
64 AATAGTGACGTTTTTAGT
*
36036 ATAAACGCCGCAA
1 ACAAACGCCGCAA
36049 AATGTTAAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
80 19 0.23
81 27 0.33
82 2 0.02
83 28 0.35
84 5 0.06
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (81 bp):
ACAAACGCCGCAATAGATTACACATATAGTGACGTTTTTAACAAACGCCACAATAGTGTAATCAA
TAGTGACGTTTTTAGT
Found at i:46177 original size:21 final size:21
Alignment explanation
Indices: 46159--46255 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 21
46149 TTGAAGCAAG
46159 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* **
46180 GAAAGCAGCCAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
46201 GGAAGCAGAGAAAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * * *
46222 GGCAGCACAGAGAGAAGAAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
46243 GGTAGCACAGAGA
1 GGAAGCAGAGAGA
46256 AAAGCAGCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.41, C:0.20, G:0.38, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:46766 original size:43 final size:43
Alignment explanation
Indices: 46684--46787 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
46674 TGTTTATAAG
* ** *
46684 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTTCAAT
1 AAAAACGCCGCTAAATCTCAACACCTATTACAACATTTTCAAT
* * *
46727 AAAAACGTCGCTAATTCTCAAC-CCTGATTACAACATTTTCGAT
1 AAAAACGCCGCTAAATCTCAACACCT-ATTACAACATTTTCAAT
* *
46770 ACAAACACCGCTAAATCT
1 AAAAACGCCGCTAAATCT
46788 GAAAATCTAC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 3 0.06
43 46 0.94
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.26
Consensus pattern (43 bp):
AAAAACGCCGCTAAATCTCAACACCTATTACAACATTTTCAAT
Found at i:46850 original size:43 final size:43
Alignment explanation
Indices: 46803--47064 Score: 208
Period size: 43 Copynumber: 6.1 Consensus size: 43
46793 TCTACTACGA
* * * *
46803 CGTTTGTGGGGAAAACACTGCTAAACATCATCACCTATTGCGG
1 CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
** * * * * *
46846 CGTTTGT-GAAAAAATGCCACAAAATATCAACACCTATTGTGG
1 CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
* * * * *
46888 TGTTTGTAAGTAAAACGCCGCTAAATC-TCAAAACCTACTGCGG
1 CGTTTGTAGGGAAAACGCCGCTAAA-CATCAACACCTATTGCGG
* * *
46931 CGTTTGTAGGGAAAACTCCGCTAAACATCAACACTTATTGCAG
1 CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
* * * * *
46974 CGTTT-TTGTGACAAACGCCGCTATATAACAACACCTATTGCGG
1 CGTTTGTAGGGA-AAACGCCGCTAAACATCAACACCTATTGCGG
* * * *
47017 C-TTTGTTGTGGCAAACGCCGCTAAATAACAACACCTATTGCGG
1 CGTTTGTAG-GGAAAACGCCGCTAAACATCAACACCTATTGCGG
*
47060 TGTTT
1 CGTTT
47065 TTTGTTAAAA
Statistics
Matches: 171, Mismatches: 41, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
42 39 0.23
43 128 0.75
44 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (43 bp):
CGTTTGTAGGGAAAACGCCGCTAAACATCAACACCTATTGCGG
Found at i:47022 original size:128 final size:128
Alignment explanation
Indices: 46772--47022 Score: 299
Period size: 128 Copynumber: 2.0 Consensus size: 128
46762 TTTTCGATAC
* * * * *
46772 AAACACCGCTAAATCTGAAAATCTACTACGACGTTTGTGGGGAAAACACTGCTAAACATCATCAC
1 AAACACCGCTAAATCTCAAAACCTACTACGACGTTTGTAGGGAAAACACCGCTAAACATCAACAC
* * * * *
46837 CTATTGCGGCGTTTGTGAAAAAATGCCACAAAATATCAACACCTATTGTGGTGTTTGTAAGTA
66 CTATTGCAGCGTTTGTGAAAAAACGCCACAAAATAACAACACCTATTGCGGTCTTTGTAAGTA
* * * *
46900 AAACGCCGCTAAATCTCAAAACCTACTGCGGCGTTTGTAGGGAAAACTCCGCTAAACATCAACAC
1 AAACACCGCTAAATCTCAAAACCTACTACGACGTTTGTAGGGAAAACACCGCTAAACATCAACAC
* * * * *
46965 TTATTGCAGCGTTTTTGTG-ACAAACGCCGCTATATAACAACACCTATTGCGG-CTTTGT
66 CTATTGCAGCG--TTTGTGAAAAAACGCCACAAAATAACAACACCTATTGCGGTCTTTGT
47023 TGTGGCAAAC
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
128 70 0.69
129 26 0.25
130 6 0.06
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (128 bp):
AAACACCGCTAAATCTCAAAACCTACTACGACGTTTGTAGGGAAAACACCGCTAAACATCAACAC
CTATTGCAGCGTTTGTGAAAAAACGCCACAAAATAACAACACCTATTGCGGTCTTTGTAAGTA
Found at i:52461 original size:16 final size:18
Alignment explanation
Indices: 52432--52472 Score: 68
Period size: 16 Copynumber: 2.4 Consensus size: 18
52422 TATTAAAATA
52432 AAATATATATATAGTAAT
1 AAATATATATATAGTAAT
52450 AAATAT-TA-ATAGTAAT
1 AAATATATATATAGTAAT
52466 AAATATA
1 AAATATA
52473 AAAGGGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.64
17 2 0.09
18 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATATATATATAGTAAT
Found at i:55637 original size:16 final size:16
Alignment explanation
Indices: 55612--55653 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55602 TGATCTTTAA
*
55612 ATTTATTATTTTTATT
1 ATTTAATATTTTTATT
55628 ATTTAATA-TTTTATT
1 ATTTAATATTTTTATT
55643 -TTTATATATTT
1 ATTTA-ATATTT
55654 ATTGTATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 10 0.43
16 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTAATATTTTTATT
Found at i:57796 original size:23 final size:25
Alignment explanation
Indices: 57770--57815 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
57760 AATAAAAATG
57770 TATTTAAT-AAGTTAATA-ATATGA
1 TATTTAATAAAGTTAATATATATGA
**
57793 TATTTCTTAAAGTTAATATATAT
1 TATTTAATAAAGTTAATATATAT
57816 AAAATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 9 0.47
25 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (25 bp):
TATTTAATAAAGTTAATATATATGA
Found at i:58225 original size:40 final size:40
Alignment explanation
Indices: 58133--58261 Score: 168
Period size: 40 Copynumber: 3.1 Consensus size: 40
58123 CATTTCTAGC
* * *
58133 GGCGTTTTTAGAACAAACACCGCTAAATACTTCGTACTTTAGT
1 GGCGTTTTTA-TACAAATACCGCTAAAGAC-T-GTACTTTAGT
* * * *
58176 GACGCTTTTATACAAATGCCGCTAAAGACTGTATTTTAGT
1 GGCGTTTTTATACAAATACCGCTAAAGACTGTACTTTAGT
58216 GGCGTTTTTATACAAATACCGCTAAAGACTGTACTTTAGT
1 GGCGTTTTTATACAAATACCGCTAAAGACTGTACTTTAGT
58256 GGCGTT
1 GGCGTT
58262 AAAGATTAGT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
40 51 0.68
41 1 0.01
42 15 0.20
43 8 0.11
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (40 bp):
GGCGTTTTTATACAAATACCGCTAAAGACTGTACTTTAGT
Found at i:58275 original size:24 final size:23
Alignment explanation
Indices: 58238--58285 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
58228 CAAATACCGC
58238 TAAAGACTGTACTTTAGTGGCGT
1 TAAAGACTGTACTTTAGTGGCGT
*
58261 TAAAGATTAGTACTTTAGTGGCGT
1 TAAAGACT-GTACTTTAGTGGCGT
58285 T
1 T
58286 TTTATACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (23 bp):
TAAAGACTGTACTTTAGTGGCGT
Found at i:58354 original size:104 final size:104
Alignment explanation
Indices: 58166--58365 Score: 260
Period size: 104 Copynumber: 1.9 Consensus size: 104
58156 TAAATACTTC
* * *
58166 GTACTTTAGTGACGCTTTTATACAAATGCCGCTAAAGACTGTATTTTAGTGGCGTTTTTATACAA
1 GTACTTTAGTGACGCTTTTATACAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTTTATACAA
58231 ATACCGCTAAAGACTGTACTTTAGTGGCGTTAAAGATTA
66 ATACCGCTAAAGACTGTACTTTAGTGGCGTTAAAGATTA
* * * * *
58270 GTACTTTAGTGGCGTTTTTATACAACCGCCGCTAAAGATTGTACTTTAGT-GCATTTTTGA-ATA
1 GTACTTTAGTGACGCTTTTATACAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTTT-ATACA
* * * *
58333 AATACCGCTATATACTAGTACTTTCGTGTCGTT
65 AATACCGCTAAAGACT-GTACTTTAGTGGCGTT
58366 TTTATACAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
103 23 0.28
104 59 0.72
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (104 bp):
GTACTTTAGTGACGCTTTTATACAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTTTATACAA
ATACCGCTAAAGACTGTACTTTAGTGGCGTTAAAGATTA
Found at i:58381 original size:41 final size:41
Alignment explanation
Indices: 58261--58634 Score: 291
Period size: 41 Copynumber: 9.2 Consensus size: 41
58251 TTAGTGGCGT
* *
58261 TAAAGATTAGTACTTTAGTGGCGTTTTTATACAACCGCCGC
1 TAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGC
* * * **
58302 TAAAGA-TTGTACTTTAGT-GCATTTTTGA-ATAAATACCGC
1 TAAAGACTAGTACTTTAGTGGCGTTTTT-ATACAAACGCCGC
* * * * *
58341 TATATACTAGTACTTTCGTGTCGTTTTTATACAAACACCGC
1 TAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGC
* * *
58382 TAAAGA-TTGTACTTTAATGGCGTTTTT-TGAACAAACGCCAC
1 TAAAGACTAGTACTTTAGTGGCGTTTTTAT--ACAAACGCCGC
* * * * *
58423 TATAGACTAGTACTTTCA-TGTCATTTTTATACAAATGCCAC
1 TAAAGACTAGTACTTT-AGTGGCGTTTTTATACAAACGCCGC
* * * *
58464 TAAAGA-TTGTACTTTAGTGGCG-TTTTAGAACAAACACTGC
1 TAAAGACTAGTACTTTAGTGGCGTTTTTA-TACAAACGCCGC
* * * * * *
58504 TATACACTAGTACTTTCGTGGCGTTTTTATACAAGCACCAC
1 TAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGC
* * * *
58545 TAAA-AATTGTACTTTTGTGGCGTTTTTAAAACAAACGCCGC
1 TAAAGACTAGTACTTTAGTGGCGTTTTT-ATACAAACGCCGC
* *
58586 TAAAGACGCA-TATTTTAGTGGCGTTTTTATACAAACGCCGC
1 TAAAGAC-TAGTACTTTAGTGGCGTTTTTATACAAACGCCGC
58627 TAAAGACT
1 TAAAGACT
58635 CGTAGGCGTT
Statistics
Matches: 258, Mismatches: 59, Indels: 33
0.74 0.17 0.09
Matches are distributed among these distances:
39 25 0.10
40 82 0.32
41 111 0.43
42 38 0.15
43 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (41 bp):
TAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGC
Found at i:58453 original size:82 final size:82
Alignment explanation
Indices: 58268--58632 Score: 400
Period size: 82 Copynumber: 4.5 Consensus size: 82
58258 CGTTAAAGAT
* *
58268 TAGTACTTT-AGTGGCGTTTTTATACAACCGCCGCTAAAGATTGTACTTTAGT-GCATTTTT-GA
1 TAGTACTTTCA-TGGCGTTTTTATACAAACGCCGCTAAAGATTGTACTTTAGTGGCGTTTTTAGA
* * *
58330 ATAAATACCGCTATATAC
65 ACAAACACCGCTATAGAC
* * * * *
58348 TAGTACTTTCGTGTCGTTTTTATACAAACACCGCTAAAGATTGTACTTTAATGGCGTTTTTTGAA
1 TAGTACTTTCATGGCGTTTTTATACAAACGCCGCTAAAGATTGTACTTTAGTGGCGTTTTTAGAA
* *
58413 CAAACGCCACTATAGAC
66 CAAACACCGCTATAGAC
* * * *
58430 TAGTACTTTCATGTCATTTTTATACAAATGCCACTAAAGATTGTACTTTAGTGGCG-TTTTAGAA
1 TAGTACTTTCATGGCGTTTTTATACAAACGCCGCTAAAGATTGTACTTTAGTGGCGTTTTTAGAA
* *
58494 CAAACACTGCTATACAC
66 CAAACACCGCTATAGAC
* * * * * * *
58511 TAGTACTTTCGTGGCGTTTTTATACAAGCACCACTAAAAATTGTACTTTTGTGGCGTTTTTAAAA
1 TAGTACTTTCATGGCGTTTTTATACAAACGCCGCTAAAGATTGTACTTTAGTGGCGTTTTTAGAA
* *
58576 CAAACGCCGCTAAAGAC
66 CAAACACCGCTATAGAC
* *
58593 GCA-TA-TTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA
1 -TAGTACTTTCA-TGGCGTTTTTATACAAACGCCGCTAAAGA
58633 CTCGTAGGCG
Statistics
Matches: 237, Mismatches: 42, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
80 46 0.19
81 78 0.33
82 112 0.47
83 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (82 bp):
TAGTACTTTCATGGCGTTTTTATACAAACGCCGCTAAAGATTGTACTTTAGTGGCGTTTTTAGAA
CAAACACCGCTATAGAC
Found at i:58568 original size:163 final size:162
Alignment explanation
Indices: 58261--58632 Score: 444
Period size: 163 Copynumber: 2.3 Consensus size: 162
58251 TTAGTGGCGT
* * * * *
58261 TAAAGATTAGTACTTT-AGTGGCGTTTTTATACAACCGCCGCTAAAGATTGTACTTTAGTGCATT
1 TAAAGACTAGTACTTTCA-TGTCATTTTTATACAAACGCCACTAAAGATTGTACTTTAGTGCATT
* * * * * * *
58325 TTTGAATAAATACCGCTATATACTAGTACTTTCGTGTCGTTTTTATACAAACACCGCTAAAGATT
65 TTAGAACAAACACCGCTATACACTAGTACTTTCGTGGCGTTTTTATACAAACACCACTAAAAATT
**
58390 GTACTTTAATGGCGTTTTTTGAACAAACGCCAC
130 GTACTTTAATGGCGTTTTTAAAACAAACGCCAC
* * *
58423 TATAGACTAGTACTTTCATGTCATTTTTATACAAATGCCACTAAAGATTGTACTTTAGTGGCGTT
1 TAAAGACTAGTACTTTCATGTCATTTTTATACAAACGCCACTAAAGATTGTACTTTAGT-GCATT
* *
58488 TTAGAACAAACACTGCTATACACTAGTACTTTCGTGGCGTTTTTATACAAGCACCACTAAAAATT
65 TTAGAACAAACACCGCTATACACTAGTACTTTCGTGGCGTTTTTATACAAACACCACTAAAAATT
** *
58553 GTACTTTTGTGGCGTTTTTAAAACAAACGCCGC
130 GTACTTTAATGGCGTTTTTAAAACAAACGCCAC
* * * * *
58586 TAAAGACGCA-TA-TTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA
1 TAAAGAC-TAGTACTTTCA-TGTCATTTTTATACAAACGCCACTAAAGA
58633 CTCGTAGGCG
Statistics
Matches: 177, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
162 54 0.31
163 122 0.69
164 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (162 bp):
TAAAGACTAGTACTTTCATGTCATTTTTATACAAACGCCACTAAAGATTGTACTTTAGTGCATTT
TAGAACAAACACCGCTATACACTAGTACTTTCGTGGCGTTTTTATACAAACACCACTAAAAATTG
TACTTTAATGGCGTTTTTAAAACAAACGCCAC
Done.