Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004903.1 Hibiscus syriacus cultivar Beakdansim tig00011032_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: 69077
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:9205 original size:28 final size:28
Alignment explanation
Indices: 9171--9227 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 28
9161 AAATTTACAA
9171 AATAATAAATATATAAACATATAATAATAGT
1 AATAA-AAA-ATATAAACA-ATAATAATAGT
*
9202 AATAAAAAATATAAATAATAATAATA
1 AATAAAAAATATAAACAATAATAATA
9228 AAGGCAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 8 0.32
30 3 0.12
31 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
AATAAAAAATATAAACAATAATAATAGT
Found at i:9220 original size:16 final size:17
Alignment explanation
Indices: 9169--9222 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
9159 TGAAATTTAC
9169 AAAATAATAAATATATAA
1 AAAATAATAAATA-ATAA
*
9187 ACATATAATAATAGTAATAA
1 A-AAATAATAA-A-TAATAA
9207 AAAAT-ATAAATAATAA
1 AAAATAATAAATAATAA
9223 TAATAAAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 5 0.16
19 11 0.35
20 6 0.19
21 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
AAAATAATAAATAATAA
Found at i:9259 original size:23 final size:24
Alignment explanation
Indices: 9215--9277 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
9205 AAAAAATATA
* * *
9215 AATAATAATAATAAAG-GCAAAAG
1 AATAATAAAAATATAGTGAAAAAG
*
9238 AATAATAAAAATATAGTGAAAAAT
1 AATAATAAAAATATAGTGAAAAAG
*
9262 AAAAAT-AAAATATAGT
1 AATAATAAAAATATAGT
9278 ATGATATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.22
Consensus pattern (24 bp):
AATAATAAAAATATAGTGAAAAAG
Found at i:13357 original size:2 final size:2
Alignment explanation
Indices: 13350--13376 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13340 ATAGCCCATC
13350 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
13377 GTTCGGCTAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:15770 original size:23 final size:23
Alignment explanation
Indices: 15740--15795 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
15730 GACATATGGT
15740 TGATTCCCTTCCATCAAATGTGC
1 TGATTCCCTTCCATCAAATGTGC
*
15763 TGATTCCCTTCTATCAAATGTGC
1 TGATTCCCTTCCATCAAATGTGC
*
15786 TCATTACCCT
1 TGATT-CCCT
15796 CACCTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.38
Consensus pattern (23 bp):
TGATTCCCTTCCATCAAATGTGC
Found at i:20677 original size:3 final size:3
Alignment explanation
Indices: 20669--20712 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
20659 TCCAGAGAAC
* * *
20669 TCT TCT TCT TCT TCT TCT TCT TTT TCT TTT TCT TAT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
20713 CAGTCGTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:28470 original size:2 final size:2
Alignment explanation
Indices: 28463--28489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28453 TGAACAGATA
28463 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
28490 AATGTTGAAG
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
Found at i:29415 original size:24 final size:24
Alignment explanation
Indices: 29383--29438 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
29373 CTATTCTTTC
29383 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
29407 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
29431 GCTTCAAT
1 GCTTCAAT
29439 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:31196 original size:19 final size:19
Alignment explanation
Indices: 31154--31196 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
31144 TTATTATTAG
* * *
31154 AAAAACTCAAAATATTTTT
1 AAAATCTCAAAAAATTCTT
31173 AAAATCTCAAAAAATTCTT
1 AAAATCTCAAAAAATTCTT
31192 AAAAT
1 AAAAT
31197 ATATAATCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATCTCAAAAAATTCTT
Found at i:33601 original size:17 final size:17
Alignment explanation
Indices: 33567--33599 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33557 TTTAATTATA
33567 ATTATATAATTATATTT
1 ATTATATAATTATATTT
*
33584 ATTATTTAA-TATATTT
1 ATTATATAATTATATTT
33600 TACCTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATAATTATATTT
Found at i:36559 original size:16 final size:16
Alignment explanation
Indices: 36538--36576 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
36528 AATTAATGAT
36538 TATTATTAATTAAAAA
1 TATTATTAATTAAAAA
36554 TATTA-TAA-TAAAAA
1 TATTATTAATTAAAAA
36568 TATT-TTAAT
1 TATTATTAAT
36577 ATTTTTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 13 0.62
15 3 0.14
16 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTATTAATTAAAAA
Found at i:45368 original size:13 final size:13
Alignment explanation
Indices: 45350--45377 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
45340 TTTTTAAGTG
45350 TTTAAATATAAAT
1 TTTAAATATAAAT
45363 TTTAAATATAAAT
1 TTTAAATATAAAT
45376 TT
1 TT
45378 ACGAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAATATAAAT
Found at i:49188 original size:3 final size:3
Alignment explanation
Indices: 49180--49207 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49170 GAAAAATGCA
49180 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
49208 CACAACCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49528 original size:44 final size:44
Alignment explanation
Indices: 49478--49563 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
49468 GTTGTGGAAA
* * * *
49478 AAATGATTGTCTTGTGTAGAGTCTCGTCGGAATTACATTTTGGT
1 AAATGATTGGCTCGTATAGAGTCTCATCGGAATTACATTTTGGT
* *
49522 AAATGATTGGCTCGTATAGGGTCTCATCGGAATTACTTTTTG
1 AAATGATTGGCTCGTATAGAGTCTCATCGGAATTACATTTTG
49564 ATTTAATGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (44 bp):
AAATGATTGGCTCGTATAGAGTCTCATCGGAATTACATTTTGGT
Found at i:50123 original size:15 final size:15
Alignment explanation
Indices: 50111--50140 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
50101 TTTGAAAATT
50111 TTATTTTTAAAAAAAA
1 TTATTTTT-AAAAAAA
50127 TTATTTTTAAAAAA
1 TTATTTTTAAAAAA
50141 CCCTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATTTTTAAAAAAA
Found at i:50390 original size:20 final size:20
Alignment explanation
Indices: 50365--50419 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
50355 TTTGGTTCAC
*
50365 GGAATGTAAGATTACCAATG
1 GGAATGTAAGATTACCAATA
*
50385 GGAATGTAAGATTACCAGTA
1 GGAATGTAAGATTACCAATA
50405 GGAATGTAAGATTAC
1 GGAATGTAAGATTAC
50420 TAGGGAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (20 bp):
GGAATGTAAGATTACCAATA
Found at i:52969 original size:6 final size:6
Alignment explanation
Indices: 52958--52983 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52948 GTGACAATGC
52958 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
52984 TTTATTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:55321 original size:95 final size:95
Alignment explanation
Indices: 55192--55450 Score: 317
Period size: 95 Copynumber: 2.7 Consensus size: 95
55182 TATAATATTA
* *
55192 TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACACCCCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGA
* *
55257 TAAGAGTCAGCTAGCCTGATAAA-GGTGAT
66 TAAGAGTCAGCTAGCATGATAAATGGTAAT
* * * * *
55286 TATACTATACAATAAAGCTTGAGTTGCCCCCCTAAAGCAATTAGTTAAACGCCCTGGCTTTATGG
1 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
** *
55351 ATATTATTCAGCTAGCATGATAAATGTGGTAAT
65 ATAAGAGTCAGCTAGCATGATAAA--TGGTAAT
* *
55384 TATATTTATACAATAATA--TTGAGTAGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
1 TATA--TATACAATAA-AGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTAT
55447 GGAT
63 GGAT
55451 TTAGCTAGCC
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
94 4 0.03
95 73 0.53
98 51 0.37
99 10 0.07
100 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (95 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGA
TAAGAGTCAGCTAGCATGATAAATGGTAAT
Found at i:56748 original size:84 final size:84
Alignment explanation
Indices: 56556--57064 Score: 477
Period size: 84 Copynumber: 6.2 Consensus size: 84
56546 TAAACAAACT
* * * *
56556 ATTTGCAGCATAGCTTAAGTCAAGAAGGGATAT-C-T-ACC-AAAGACCCTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
*
56617 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCGAAGGCACATC
* * * *
56637 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* * *
56702 CTCAGCTCTAAGACATATC
66 CTCAGCTCGAAGGCACATC
** * ** *
56721 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCCAATAAAAGACCTTCGAGTTCGACTATG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* *
56786 CTCAACTCCAAGGCACATC
66 CTCAGCTCGAAGGCACATC
* ** * * * *
56805 ATTTGCAGTATAGTTTAAGTCGAGAAGGGCTAT--AT-GCC-AAAGACCCTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* *
56866 CTTAGCTTCGAGGGCACATC
66 CTCAGC-TCGAAGGCACATC
* * * * * *
56886 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* *
56951 CTCAGCTCTAAGGCATATC
66 CTCAGCTCGAAGGCACATC
* * * * * * * *
56970 A-TTGTAGCATAGCTTAAGTCGAGAAGGGCTAT-C-T-GCC-AAAGGCTTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
*
57030 CTCAGCTCCGAGGGCACATC
66 CTCAGCT-CGAAGGCACATC
*
57050 ATTTACAGCATAACT
1 ATTTGCAGCATAACT
57065 CAAGGCTAGA
Statistics
Matches: 341, Mismatches: 76, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
79 26 0.08
80 37 0.11
81 73 0.21
82 1 0.00
83 25 0.07
84 124 0.36
85 55 0.16
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCGAAGGCACATC
Found at i:57009 original size:164 final size:164
Alignment explanation
Indices: 56594--57099 Score: 559
Period size: 164 Copynumber: 3.1 Consensus size: 164
56584 GATATCTACC
* * * * * *
56594 AAAGACCCTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATT-TACAGCATAACTCAAGGC
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTGT--AGCATAGCTTAAGTC
* * * * * * *
56658 TAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGACATATCA
63 GAGAAGGGCTAT-C-T-GCC-AAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCA
* * * * * * *
56722 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCCAATA
124 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
* * * * *
56763 AAAGACCTTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATTTGCAGTATAGTTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA-TTGTAGCATAGCTTAAGTCGA
* * *
56828 GAAGGGCTATATGCCAAAGACCCTCGAGTTCGACTACGCTTAGCTTCGAGGGCACATCATTTACA
65 GAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACA
* *
56893 ACATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
130 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
* *
56928 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTGTAGCATAGCTTAAGTCGAG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTGTAGCATAGCTTAAGTCGAG
* * * * *
56993 AAGGGCTATCTGCCAAAGGCTTTCGAGTTCGATTACACTCAGCTCCGAGGGCACATCATTTACAG
66 AAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAG
** *
57058 CATAACTCAAGGCTAGAAGAATTATCTGTGAACA
131 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
57092 AAA-ACCTT
1 AAAGACCTT
57100 TGAGATTGTT
Statistics
Matches: 284, Mismatches: 50, Indels: 12
0.82 0.14 0.03
Matches are distributed among these distances:
163 5 0.02
164 135 0.48
165 83 0.29
166 1 0.00
168 32 0.11
169 28 0.10
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (164 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTGTAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAG
CATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
Found at i:57181 original size:35 final size:36
Alignment explanation
Indices: 57107--57367 Score: 231
Period size: 37 Copynumber: 7.4 Consensus size: 36
57097 CTTTGAGATT
* *
57107 GTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
57143 GTTTCCCTTGAAACAAATTTCGTCTC-CTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
57178 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATTTA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA--CA
* * * *
57208 -TTTCCCTTAAAACAAAATTTAT-TTTCCCTTAAGACA
1 GTTTCCCTTGAAAC-AAATTT-TGTCTCTCTTGAGACA
** *
57244 GTTTCTTTTGAAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
57281 GTTTCTC-TGAAACAAATTTTGCCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
57316 TTTTCCCTTGAGACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
57353 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
57368 CCAATCTTTG
Statistics
Matches: 181, Mismatches: 28, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.01
29 18 0.10
30 4 0.02
35 50 0.28
36 42 0.23
37 65 0.36
38 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:57466 original size:36 final size:36
Alignment explanation
Indices: 57420--57548 Score: 195
Period size: 36 Copynumber: 3.6 Consensus size: 36
57410 CTCTAAGACA
57420 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
* * *
57456 GTTTATCTTGAAACACCAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
*
57492 GTTTCTCTTGAAACACAAAAAAAACCCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
* *
57528 ATTTCTCTTTGAAACCCAAAA
1 GTTTCTC-TTGAAACACAAAA
57549 GACCTTCGAG
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 71 0.86
37 12 0.14
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
Found at i:57470 original size:176 final size:172
Alignment explanation
Indices: 57091--57470 Score: 408
Period size: 176 Copynumber: 2.2 Consensus size: 172
57081 ATCTGTGAAC
* * * * * *
57091 AAAAACCTTTGAGATTGTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA
1 AAAAACCTTTGAAAATGTTTCTCTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCCCTTGAAA
* *
57156 CAAATTTCGTCTCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCTTAAAAC
66 CAAATTTCGTCTCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTCCATTAAAAC
* * * **
57221 AAAATTTATTTTCCCTTAAGACAGTTTCTTTTGAAACTAAGT
131 AAAATTTATTCTCCCTTAAGACAGTTTCTCTTGAAACCAAAA
***** * *
57263 TTTGTCTCTCTTGAGACA-GTTTCTC-TGAAACAAATTTTGCCTCTCTTGAGACATTTTCCCTTG
1 AAAAAC-CT-TTGA-AAATGTTTCTCTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
57326 AGACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAATCTTTGAATATGTTTCTAT
63 AAACAAA-TTTCGTCTC-CTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATATATTTCCAT
57391 TAAAACAAAATTT-TGTCT-CCTCTAAGACAGTTTCTCTTGAAACACAAAA
125 TAAAACAAAATTTAT-TCTCCCT-TAAGACAGTTTCTCTTGAAAC-CAAAA
*
57440 AAAAACCTTTGAAAATGTTTATCTTGAAACA
1 AAAAACCTTTGAAAATGTTTCTCTTGAAACA
57471 CCAAAAAAAA
Statistics
Matches: 164, Mismatches: 33, Indels: 18
0.76 0.15 0.08
Matches are distributed among these distances:
172 1 0.01
173 42 0.26
174 20 0.12
175 37 0.23
176 61 0.37
177 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (172 bp):
AAAAACCTTTGAAAATGTTTCTCTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCCCTTGAAA
CAAATTTCGTCTCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTCCATTAAAAC
AAAATTTATTCTCCCTTAAGACAGTTTCTCTTGAAACCAAAA
Found at i:61512 original size:19 final size:19
Alignment explanation
Indices: 61488--61538 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
61478 ACCAACAAAA
61488 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
61507 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
*
61526 TCGCAACGCGATC
1 TCGCAATGCGATC
61539 TCCATTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATCGCTAAT
Found at i:61654 original size:20 final size:20
Alignment explanation
Indices: 61629--61695 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
61619 TTTTCCCAAT
61629 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
61649 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
61669 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
61690 TCGCAA
1 TCGCAA
61696 CGTGAATTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:61671 original size:41 final size:41
Alignment explanation
Indices: 61626--61721 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
61616 CGATTTTCCC
61626 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
61667 AATTCGCAATGCGAATAAGTAAATCGCAACGTGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
61708 AAATCGCAATGCGA
1 AATTCGCAATGCGA
61722 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:61675 original size:21 final size:20
Alignment explanation
Indices: 61629--61721 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
61619 TTTTCCCAAT
*
61629 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
61649 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
61669 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* * **
61690 TCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
61711 TCGCAATGCGA
1 TCGCAATGCGA
61722 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:61735 original size:20 final size:20
Alignment explanation
Indices: 61710--61804 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
61700 AATTGGGAAA
*
61710 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
61730 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
61751 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
61771 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
61791 TTCGCAACGCGATA
1 ATCGCAACGCGATA
61805 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:61752 original size:41 final size:41
Alignment explanation
Indices: 61707--61784 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
61697 GTGAATTGGG
* * *
61707 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
61748 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
61785 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:62020 original size:22 final size:22
Alignment explanation
Indices: 61992--62035 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
61982 CACTCTCTCA
61992 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
62014 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
62036 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:62324 original size:20 final size:20
Alignment explanation
Indices: 62299--62336 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62289 CGATTCTCTC
62299 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
62319 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
62337 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:63667 original size:18 final size:18
Alignment explanation
Indices: 63646--63690 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
63636 TCCACTTCGG
*
63646 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
63664 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
63682 GAGCCATCA
1 GAGCCATCA
63691 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:64255 original size:14 final size:14
Alignment explanation
Indices: 64236--64272 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
64226 CATCAATTAA
64236 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
64250 ACAAATCACCTTTT
1 ACAAATCAACTTTT
64264 ACAAATCAA
1 ACAAATCAA
64273 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:65691 original size:21 final size:21
Alignment explanation
Indices: 65625--65691 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
65615 TGTGAATCGG
*
65625 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
65645 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
65667 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
65688 CTCT
1 CTCT
65692 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:65710 original size:42 final size:41
Alignment explanation
Indices: 65625--65747 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
65615 TGTGAATCGG
* * * * *
65625 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
65667 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
65709 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
65748 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:67771 original size:20 final size:18
Alignment explanation
Indices: 67739--67898 Score: 84
Period size: 20 Copynumber: 8.8 Consensus size: 18
67729 TCTTTTGGTT
67739 GAAATGAAATCGCAACGA
1 GAAATGAAATCGCAACGA
*
67757 GATAATGAGAATCGCAACGCG
1 GA-AATGA-AATCGCAACG-A
*
67778 GAAATGACTATCGCAACGA
1 GAAATGA-AATCGCAACGA
*
67797 G--A-G-AATCGCAACGC
1 GAAATGAAATCGCAACGA
* * *
67811 GAAATGACTATCGCGACCA
1 GAAATGA-AATCGCAACGA
* *
67830 G--A--CAATCGCAACGC
1 GAAATGAAATCGCAACGA
*
67844 GAAATGAAAATCGCAACCGC
1 GAAATG-AAATCGCAA-CGA
* *
67864 GAAATTAAAATCGCAACGC
1 GAAA-TGAAATCGCAACGA
67883 GAAATGAAAATCGCAA
1 GAAATG-AAATCGCAA
67899 TGCGATTTTG
Statistics
Matches: 108, Mismatches: 18, Indels: 31
0.69 0.11 0.20
Matches are distributed among these distances:
14 18 0.17
16 3 0.03
17 3 0.03
18 3 0.03
19 38 0.35
20 40 0.37
21 3 0.03
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGA
Found at i:67820 original size:33 final size:33
Alignment explanation
Indices: 67763--67861 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
67753 ACGAGATAAT
*
67763 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
67797 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
67830 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
67862 GCGAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:67855 original size:19 final size:19
Alignment explanation
Indices: 67739--67903 Score: 127
Period size: 19 Copynumber: 9.1 Consensus size: 19
67729 TCTTTTGGTT
*
67739 GAAATG-AAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
67757 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
67777 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
67795 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
67811 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
67829 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
67844 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
67864 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
67883 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
67902 GA
1 GA
67904 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 15, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 6 0.05
19 45 0.38
20 40 0.34
21 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:67976 original size:20 final size:19
Alignment explanation
Indices: 67899--67982 Score: 114
Period size: 19 Copynumber: 4.4 Consensus size: 19
67889 AAAATCGCAA
**
67899 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
67918 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
67937 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
67956 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
67976 TGCGATT
1 TGCGATT
67983 CTCATTCTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 47 0.81
20 11 0.19
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.46
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:68521 original size:20 final size:20
Alignment explanation
Indices: 68493--68544 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
68483 CGCTATGTAA
* *
68493 ATCGCGTTGCGAAAGTCAGT
1 ATCGTGTTGCGAAAGTAAGT
68513 ATCGTGTTGCGAAAGTAAGT
1 ATCGTGTTGCGAAAGTAAGT
68533 ATC-TCGTTGCGA
1 ATCGT-GTTGCGA
68545 TTTTATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGTGTTGCGAAAGTAAGT
Found at i:68586 original size:21 final size:21
Alignment explanation
Indices: 68553--68645 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
68543 GATTTTATTA
68553 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * *
68574 TCGCGTTGTGATTTAT---TAT
1 TCGCATTGCGATTT-TCCCAAT
*
68593 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
68614 TCGCGTTGCGATTTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
68635 TCGCATTGCGA
1 TCGCATTGCGA
68646 ATTGGGAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
18 1 0.02
19 13 0.24
21 40 0.73
22 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:68648 original size:42 final size:41
Alignment explanation
Indices: 68537--68648 Score: 183
Period size: 40 Copynumber: 2.8 Consensus size: 41
68527 GTAAGTATCT
*
68537 CGTTGCGATTTTATTA-TCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTTATTATTCGCATTGCGAATTTCCCAATTCG
*
68577 CGTTGTGA-TTTATTATTCGCATTGCGAATTTCCCAATTCG
1 CGTTGCGATTTTATTATTCGCATTGCGAATTTCCCAATTCG
68617 CGTTGCGATTTTACTTATTCGCATTGCGAATT
1 CGTTGCGATTTTA-TTATTCGCATTGCGAATT
68649 GGGAAAATCG
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
39 7 0.11
40 37 0.56
41 4 0.06
42 18 0.27
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.43
Consensus pattern (41 bp):
CGTTGCGATTTTATTATTCGCATTGCGAATTTCCCAATTCG
Done.