Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007413.1 Hibiscus syriacus cultivar Beakdansim tig00020038_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: 67654
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:187 original size:22 final size:23
Alignment explanation
Indices: 132--188 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
122 GGTTTTGTGC
*
132 ATGCACATTCAAGGTGTGCATTG
1 ATGCACATTCAAGGTGTGCATCG
* * * *
155 GTGCACCTTCATGGTG-GTATCG
1 ATGCACATTCAAGGTGTGCATCG
177 ATGCACATTCAA
1 ATGCACATTCAA
189 AGGGATGCAT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATGCACATTCAAGGTGTGCATCG
Found at i:6190 original size:29 final size:29
Alignment explanation
Indices: 6128--6192 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
6118 ATGAAATTAT
*
6128 AAAAATTAGGGACTCTAATTATAAATATA
1 AAAAATTAGGGACTCTAATTATAAATACA
* *
6157 AAAAATTAGGG-TTCCTAATTATATATACA
1 AAAAATTAGGGACT-CTAATTATAAATACA
*
6186 GAAAATT
1 AAAAATT
6193 GGGGCCCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (29 bp):
AAAAATTAGGGACTCTAATTATAAATACA
Found at i:6619 original size:29 final size:30
Alignment explanation
Indices: 6587--6650 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
6577 TTATATTTTA
* *
6587 AATTTAAAATATTGTA-TTTTAAAAAAATC
1 AATTTAAAACATTGAACTTTTAAAAAAATC
** *
6616 AA-TTAAGCCCTTGAACTTTTAAAAAAATC
1 AATTTAAAACATTGAACTTTTAAAAAAATC
6645 AATTTA
1 AATTTA
6651 GGCCACGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 8 0.29
29 17 0.61
30 3 0.11
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (30 bp):
AATTTAAAACATTGAACTTTTAAAAAAATC
Found at i:9399 original size:27 final size:26
Alignment explanation
Indices: 9340--9399 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
9330 GATGAAAATA
* **
9340 AAAATAAAATATTTTTAAATTAAGTT
1 AAAATAAAATATTTATAAATTAACAT
*
9366 AATAATAAAATATTTAATAAGTTAACAT
1 AA-AATAAAATATTT-ATAAATTAACAT
9394 AAAATA
1 AAAATA
9400 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 16 0.57
28 10 0.36
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (26 bp):
AAAATAAAATATTTATAAATTAACAT
Found at i:13571 original size:33 final size:33
Alignment explanation
Indices: 13534--13632 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
13524 ATTTGGCTAG
13534 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
13567 TTGGAAAATTCATCTTGTTTGGTGGGCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
13600 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
13633 TGCATATGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 45 0.75
34 15 0.25
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:15192 original size:22 final size:22
Alignment explanation
Indices: 15164--15211 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
15154 TGATCATTAG
15164 TGTAATTTACCTAATTATTTTC
1 TGTAATTTACCTAATTATTTTC
* *
15186 TGTAATTTACCTGATTATTTTT
1 TGTAATTTACCTAATTATTTTC
15208 TGTA
1 TGTA
15212 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.56
Consensus pattern (22 bp):
TGTAATTTACCTAATTATTTTC
Found at i:15366 original size:30 final size:30
Alignment explanation
Indices: 15330--15405 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
15320 ATATAGATCG
15330 CCAGGTGATCTGGGCGACCAATGAAGGTCA
1 CCAGGTGATCTGGGCGACCAATGAAGGTCA
*
15360 CCAGGTGATCTGGGCGACCAATGAAGGTCG
1 CCAGGTGATCTGGGCGACCAATGAAGGTCA
*
15390 CCAGGTGGTCTGGGCG
1 CCAGGTGATCTGGGCG
15406 CCATGCCGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.17
Consensus pattern (30 bp):
CCAGGTGATCTGGGCGACCAATGAAGGTCA
Found at i:15643 original size:50 final size:50
Alignment explanation
Indices: 15580--15681 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
15570 TTTATCCTAT
*
15580 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
15630 TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
15680 TT
1 TT
15682 CAATAATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
Found at i:16939 original size:31 final size:31
Alignment explanation
Indices: 16902--16965 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
16892 AAAAAACACA
*
16902 TAAGATATGGTCACCTTCGTATTTATTTAAT
1 TAAGATATAGTCACCTTCGTATTTATTTAAT
* *
16933 TAAGATATAGTCACTTTCGTTTTTATTTAAT
1 TAAGATATAGTCACCTTCGTATTTATTTAAT
16964 TA
1 TA
16966 GGATGTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (31 bp):
TAAGATATAGTCACCTTCGTATTTATTTAAT
Found at i:17142 original size:27 final size:27
Alignment explanation
Indices: 17112--17173 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
17102 TAAATCATAA
*
17112 ATTTTTAGATGAAAATAAAAATAAAAT
1 ATTTTTAAATGAAAATAAAAATAAAAT
* ** *
17139 ATTTTTAAATTAAGTTAATAATAAAAT
1 ATTTTTAAATGAAAATAAAAATAAAAT
*
17166 ATATTTAA
1 ATTTTTAA
17174 TAAGTTAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (27 bp):
ATTTTTAAATGAAAATAAAAATAAAAT
Found at i:17191 original size:24 final size:25
Alignment explanation
Indices: 17131--17207 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 25
17121 TGAAAATAAA
*
17131 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
17158 AATAAAATATATTTAATAAGTTAA-
1 AATAAAATATATTTAATAAGTTAAT
* * **
17182 CATAAAATATGTTTTTTAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
17207 A
1 A
17208 TATTTAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
24 20 0.47
25 8 0.19
26 2 0.05
27 13 0.30
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:24455 original size:71 final size:71
Alignment explanation
Indices: 24304--24444 Score: 200
Period size: 71 Copynumber: 2.0 Consensus size: 71
24294 GACTAAATCG
* * *
24304 AAATATAAATAAGTATGGGCGAATTTCATATACAAATATAACTTTAAGGACAAAGTTGAAGTAAA
1 AAATATAAATAAGTATGGGCGAATTTCATAGACAAATATAACTTTAAGGACAAAATTGAAGCAAA
24369 TTGAAA
66 TTGAAA
*
24375 AAATATAAATAAGTATGGGTC-AATTTCATAGACAAATATAATTTTAAGGACTAAAATT-AA-CA
1 AAATATAAATAAGTATGGG-CGAATTTCATAGACAAATATAACTTTAAGGAC-AAAATTGAAGCA
24437 AATT-AAA
64 AATTGAAA
24444 A
1 A
24445 TTTAAATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
69 4 0.06
70 5 0.08
71 49 0.77
72 6 0.09
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (71 bp):
AAATATAAATAAGTATGGGCGAATTTCATAGACAAATATAACTTTAAGGACAAAATTGAAGCAAA
TTGAAA
Found at i:24681 original size:33 final size:32
Alignment explanation
Indices: 24638--24699 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
24628 ATAATATTTA
*
24638 TATAAGTATACATTATACATTATAAGTATAATT
1 TATAACTATACATTATACA-TATAAGTATAATT
24671 TATAACTATACATTATACATATAAGTATA
1 TATAACTATACATTATACATATAAGTATA
24700 TAATATACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (32 bp):
TATAACTATACATTATACATATAAGTATAATT
Found at i:24706 original size:19 final size:19
Alignment explanation
Indices: 24625--24725 Score: 61
Period size: 19 Copynumber: 5.6 Consensus size: 19
24615 TTTAAGTTTA
**
24625 TATATAATATTTATATAAG
1 TATATAATATACATATAAG
* *
24644 TATACATTATACATTATAAG
1 TATATAATATACA-TATAAG
*
24664 --TATAAT-T---TATAAC
1 TATATAATATACATATAAG
* *
24677 TATACATTATACATATAAG
1 TATATAATATACATATAAG
* * *
24696 TATATAATATACTTCTAAA
1 TATATAATATACATATAAG
24715 TATATAATATA
1 TATATAATATA
24726 AGTATTTAAG
Statistics
Matches: 60, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
13 5 0.08
15 4 0.07
16 1 0.02
17 1 0.02
18 4 0.07
19 39 0.65
20 6 0.10
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (19 bp):
TATATAATATACATATAAG
Found at i:24706 original size:26 final size:25
Alignment explanation
Indices: 24637--24707 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
24627 TATAATATTT
* *
24637 ATATAAGTATACATTATACATTATA
1 ATATAAGTATATAATATACATTATA
*
24662 AGTATAA-TTTATAACTATACATTATA
1 A-TATAAGTATATAA-TATACATTATA
24688 CATATAAGTATATAATATAC
1 -ATATAAGTATATAATATAC
24708 TTCTAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.13
26 26 0.68
27 7 0.18
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.39
Consensus pattern (25 bp):
ATATAAGTATATAATATACATTATA
Found at i:25686 original size:24 final size:24
Alignment explanation
Indices: 25659--25723 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
25649 AATAAAACAT
25659 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
25683 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
25707 AATCCAGGTCAGGTATT
1 AATCCAGGTCAAGTATT
25724 ATAATATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTCGATCAG
Found at i:26881 original size:18 final size:18
Alignment explanation
Indices: 26860--26900 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
26850 CTTTCATCCG
*
26860 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
26878 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
*
26896 GTCTT
1 ATCTT
26901 TTCGAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:28174 original size:20 final size:21
Alignment explanation
Indices: 28137--28176 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28127 AAATTAAGTT
28137 AAATGAATTTTAATATTTTAC
1 AAATGAATTTTAATATTTTAC
28158 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-ATATTTTA
28177 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
AAATGAATTTTAATATTTTAC
Found at i:28411 original size:19 final size:19
Alignment explanation
Indices: 28387--28425 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28377 TTTTATGCAT
28387 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
28406 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
28425 T
1 T
28426 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:28527 original size:64 final size:65
Alignment explanation
Indices: 28381--28533 Score: 202
Period size: 65 Copynumber: 2.4 Consensus size: 65
28371 TGAACATTTT
* * *** *
28381 ATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGA
1 ATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGA
* **
28446 ATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCG
1 ATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCAAAACATCG
28509 A
65 A
28510 ATGCATTTCATGCATCGATGCACA
1 ATGCATTTCATGCATCGATGCACA
28534 CTTGGTGCAC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.47
65 41 0.53
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
ATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGA
Found at i:29487 original size:17 final size:17
Alignment explanation
Indices: 29465--29508 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
29455 AATAGTCAAG
*
29465 CATCCAAATATCATAAA
1 CATCCAAATAACATAAA
*
29482 CATCCAAACAAACATAAA
1 CATCCAAA-TAACATAAA
29500 CATCCAAAT
1 CATCCAAAT
29509 CAAAAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (17 bp):
CATCCAAATAACATAAA
Found at i:29499 original size:18 final size:19
Alignment explanation
Indices: 29476--29512 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
29466 ATCCAAATAT
29476 CATAAACATCCAAA-CAAA
1 CATAAACATCCAAATCAAA
29494 CATAAACATCCAAATCAAA
1 CATAAACATCCAAATCAAA
29513 AAGTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (19 bp):
CATAAACATCCAAATCAAA
Found at i:29846 original size:21 final size:21
Alignment explanation
Indices: 29822--29865 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29812 GAGGAGGAGG
*
29822 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
* *
29843 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
29864 AG
1 AG
29866 CTCCCGGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.36, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:37344 original size:64 final size:66
Alignment explanation
Indices: 37239--37401 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 66
37229 CGGTGCACCA
*
37239 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
37302 G
66 G
** * ** *
37303 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGTATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
37367 G
66 G
* * * *
37368 AGAGTGCATCGGTGCATGGAATGCATTTGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
37402 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 37 0.45
65 46 0.55
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
G
Found at i:37373 original size:19 final size:19
Alignment explanation
Indices: 37349--37387 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
37339 GAAAATATTC
*
37349 AGAGTGTATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
37368 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
37387 A
1 A
37388 ATGCATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.38, T:0.23
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:37641 original size:20 final size:21
Alignment explanation
Indices: 37618--37657 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
37608 GAATCGAATA
37618 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
37638 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
37658 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:40255 original size:24 final size:24
Alignment explanation
Indices: 40186--40274 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
40176 AACAAAACAT
** *
40186 AATCCAGGTCAAGTATCAAATCAA
1 AATCCAGGTCAAGTATCCGATCAG
* * * *
40210 AATTCAAAGTCAACTATTCGATCAG
1 AA-TCCAGGTCAAGTATCCGATCAG
40235 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
40259 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
40275 TATAATATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 35 0.67
25 17 0.33
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:41437 original size:18 final size:18
Alignment explanation
Indices: 41414--41453 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41404 TTCCATCTGG
*
41414 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
* *
41432 TCTTATCATTTACTTCAG
1 TCTTATCATTTAATTCAA
41450 TCTT
1 TCTT
41454 TTTCGAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:44599 original size:6 final size:6
Alignment explanation
Indices: 44585--44666 Score: 64
Period size: 6 Copynumber: 13.5 Consensus size: 6
44575 TATATATATG
44585 TTTTCTA TTTTTA -TTTTA -TTTTA TTATGTT- TTTTTA TTTTTA TTTTTA
1 TTTT-TA TTTTTA TTTTTA TTTTTA TT-T-TTA TTTTTA TTTTTA TTTTTA
* * *
44633 TTTTTC TTTTT- TTCTTTG TTTTATA TTTATA TTT
1 TTTTTA TTTTTA TT-TTTA TTTT-TA TTTTTA TTT
44667 ATATGTTATC
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
5 14 0.22
6 36 0.55
7 13 0.20
8 2 0.03
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:44655 original size:35 final size:35
Alignment explanation
Indices: 44585--44684 Score: 96
Period size: 35 Copynumber: 2.8 Consensus size: 35
44575 TATATATATG
* * *
44585 TTTTCTATTTTTATTTTAT-TTTATTATGTTTTTTTA
1 TTTTATATTTTTATTTT-TCTTT-TTTTCTTTTTTTA
44621 TTTT-TATTTTTATTTTTCTTTTTTTCTTTGTTTTA
1 TTTTATATTTTTATTTTTCTTTTTTTCTTT-TTTTA
* *
44656 TATTTATATTTATATGTTATCTTTTTTTC
1 T-TTTATATTTTTAT-TTTTCTTTTTTTC
44685 CTGTTTTTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
34 7 0.13
35 21 0.38
36 7 0.13
37 8 0.15
38 12 0.22
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (35 bp):
TTTTATATTTTTATTTTTCTTTTTTTCTTTTTTTA
Found at i:44683 original size:29 final size:29
Alignment explanation
Indices: 44566--44683 Score: 107
Period size: 29 Copynumber: 4.1 Consensus size: 29
44556 ATTTTATTTG
* * *
44566 TTATATATATATATATATGTTTTCTATTT
1 TTATATTTATATTTATATGTTTTCTTTTT
*
44595 TTAT-TTTAT-TTTATTATGTTTTTTTATTT
1 TTATATTTATATTTA-TATGTTTTCTT-TTT
* * * *
44624 TTATTTTTATTTTTCT-TTTTTTCTTTGTT
1 TTATATTTATATTTATATGTTTTCTTT-TT
*
44653 TTATATTTATATTTATATGTTATCTTTTT
1 TTATATTTATATTTATATGTTTTCTTTTT
44682 TT
1 TT
44684 CCTGTTTTTC
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
27 3 0.04
28 14 0.20
29 37 0.52
30 14 0.20
31 3 0.04
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (29 bp):
TTATATTTATATTTATATGTTTTCTTTTT
Found at i:44690 original size:37 final size:37
Alignment explanation
Indices: 44614--44691 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
44604 TTTATTATGT
* * * * *
44614 TTTTTTATTTTTATTTTTATTTTTCTTTTTTTCTTTG
1 TTTTATATTTATATTTATATTTATCTTTTTTTCTCTG
44651 TTTTATATTTATATTTATATGTTATCTTTTTTTC-CTG
1 TTTTATATTTATATTTATAT-TTATCTTTTTTTCTCTG
44688 TTTT
1 TTTT
44692 TCTTGTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 23 0.66
38 12 0.34
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (37 bp):
TTTTATATTTATATTTATATTTATCTTTTTTTCTCTG
Found at i:44716 original size:87 final size:86
Alignment explanation
Indices: 44528--44718 Score: 192
Period size: 87 Copynumber: 2.2 Consensus size: 86
44518 TCTTTTTTAA
* *
44528 TTTTTGTTTTCTTTTTTTATTGGTTTTTATTTTATTTGTTATATATATATATATATGTTTTCTAT
1 TTTTTGTTTTCTATTTTTATT-GTTTTTATTTTATTTGTTATATATATATATATATGTTATCTAT
* *
44593 TTTTATTTTATTTTATTATGTT
65 TTTTACTGTATTTTATTATGTT
* * * * *
44615 TTTTTATTTT-TATTTTTATT-TTTCTTTTTTTCTTTGTTTTATATTTATATTTATATGTTATCT
1 TTTTTGTTTTCTATTTTTATTGTTT-TTATTTTATTTG--TTATATATATATATATATGTTATCT
* * * *
44678 TTTTTTCCTGT-TTTTCTTGT-TT
63 ATTTTTACTGTATTTTATTATGTT
44700 TTATTTGTTTTCTATTTTT
1 TT-TTTGTTTTCTATTTTT
44719 TTTATATATA
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
84 3 0.04
85 14 0.16
86 23 0.27
87 45 0.53
ACGTcount: A:0.15, C:0.05, G:0.06, T:0.75
Consensus pattern (86 bp):
TTTTTGTTTTCTATTTTTATTGTTTTTATTTTATTTGTTATATATATATATATATGTTATCTATT
TTTACTGTATTTTATTATGTT
Found at i:45702 original size:18 final size:18
Alignment explanation
Indices: 45679--45713 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45669 TTCCATCTGG
*
45679 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
45697 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
45714 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:48918 original size:6 final size:6
Alignment explanation
Indices: 48854--48912 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
48844 TATATATATG
48854 TTTTCTA TTTTTA TTTTTA -TTTTA TTATGTT- TTTTTA TTTTTA TTTTTA
1 TTTT-TA TTTTTA TTTTTA TTTTTA TT-T-TTA TTTTTA TTTTTA TTTTTA
*
48903 TTTTTC TTTT
1 TTTTTA TTTT
48913 CTTTTTTTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
5 7 0.15
6 31 0.66
7 7 0.15
8 2 0.04
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:48919 original size:30 final size:30
Alignment explanation
Indices: 48850--48906 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
48840 TATATATATA
*
48850 TATG-TTTTCTATTTTTATTTTTATTTTAT
1 TATGTTTTTTTATTTTTATTTTTATTTTAT
48879 TATGTTTTTTTATTTTTATTTTTATTTT
1 TATGTTTTTTTATTTTTATTTTTATTTT
48907 TCTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.79
Consensus pattern (30 bp):
TATGTTTTTTTATTTTTATTTTTATTTTAT
Found at i:48935 original size:36 final size:35
Alignment explanation
Indices: 48852--48994 Score: 112
Period size: 36 Copynumber: 3.9 Consensus size: 35
48842 TATATATATA
*
48852 TGTTTTCTATTTTTATTTTTATTTTATTATGTTTT-TT
1 TGTTTT-TATTTTTATTTTTATTTTCTT-T-TTTTCTT
* *
48889 TATTTTTATTTTTATTTTTCTTTTCTTTTTTTCTT
1 TGTTTTTATTTTTATTTTTATTTTCTTTTTTTCTT
* * *
48924 TGTTTTATATTTATATTTATATGTTATCTTTTTTTC-C
1 TGTTTT-TATTTTTATTTTTAT-TT-TCTTTTTTTCTT
* *
48961 TGTTTTTCTTGTTT-TTATTTGTTTTCTATTTTTT
1 TGTTTTTATT-TTTATT-TTTATTTTCT-TTTTTT
48995 TATATATAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
34 4 0.05
35 11 0.13
36 44 0.51
37 18 0.21
38 10 0.11
ACGTcount: A:0.12, C:0.06, G:0.05, T:0.77
Consensus pattern (35 bp):
TGTTTTTATTTTTATTTTTATTTTCTTTTTTTCTT
Found at i:50694 original size:35 final size:35
Alignment explanation
Indices: 50632--50712 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
50622 TTCAAGTTAG
* * * *
50632 TTTTCATAATCATAATTATCTTAATTTTCTTATTT-
1 TTTTCACAATTATAATTATATTAATTTTATT-TTTC
50667 TTTTCACAATTATAATTATAATT-ATTTTATTTTTC
1 TTTTCACAATTATAATTAT-ATTAATTTTATTTTTC
*
50702 TTTTCAGAATT
1 TTTTCACAATT
50713 TTGATGCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
34 3 0.08
35 34 0.87
36 2 0.05
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTTCACAATTATAATTATATTAATTTTATTTTTC
Found at i:53227 original size:16 final size:16
Alignment explanation
Indices: 53184--53239 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
53174 TTGGAATGTT
*
53184 TCTGAGGGAATT-AGAA
1 TCTGAAGGAATTGA-AA
53200 TCTGTAAAGGAATTGAAA
1 TCTG--AAGGAATTGAAA
*
53218 TCTGAAGGAATTGGAA
1 TCTGAAGGAATTGAAA
53234 TCTGAA
1 TCTGAA
53240 TCTGAAACCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 21 0.60
18 13 0.37
19 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
TCTGAAGGAATTGAAA
Found at i:53607 original size:34 final size:34
Alignment explanation
Indices: 53565--53640 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
53555 CCACCCGACT
53565 CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
1 CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
*
53599 CGACCCGAGAACAAGGGAACCTCCACCTGAGACC
1 CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
53633 CGACCCGA
1 CGACCCGA
53641 CCTGAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.32, C:0.41, G:0.24, T:0.04
Consensus pattern (34 bp):
CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
Found at i:53633 original size:29 final size:32
Alignment explanation
Indices: 53554--53640 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 32
53544 GTTGGGTTGG
**
53554 TCCACCCGACTCGACCCGAGAACAAGGGAACC
1 TCCACCCGAGACGACCCGAGAACAAGGGAACC
53586 TCCACCCGAGACCCGACCCGAGAACAAGGGAACC
1 TCCACCCGAGA--CGACCCGAGAACAAGGGAACC
*
53620 TCCACCTGAGACCCGACCCGA
1 TCCACCCGAGA--CGACCCGA
53641 CCTGAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 9 0.18
34 41 0.82
ACGTcount: A:0.30, C:0.43, G:0.22, T:0.06
Consensus pattern (32 bp):
TCCACCCGAGACGACCCGAGAACAAGGGAACC
Found at i:53880 original size:33 final size:35
Alignment explanation
Indices: 53817--53885 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 35
53807 TTTTCACCCT
*
53817 AAACCCGAACCCGACCCGAATATCACACTTAAAAAA
1 AAACCCGAACCCGACCCG-ATATCAAACTTAAAAAA
*
53853 AAACCC-AACCTGACCCG-TATCAAACTTAAAAAA
1 AAACCCGAACCCGACCCGATATCAAACTTAAAAAA
53886 TCCCGACCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 15 0.48
35 10 0.32
36 6 0.19
ACGTcount: A:0.48, C:0.32, G:0.07, T:0.13
Consensus pattern (35 bp):
AAACCCGAACCCGACCCGATATCAAACTTAAAAAA
Found at i:53968 original size:32 final size:30
Alignment explanation
Indices: 53908--53969 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
53898 CCCAAATTTT
* * *
53908 TTTTAAAAAAAATCCGACCCTATCCCAAAA
1 TTTTAAAAAAAAACCGACCCAATACCAAAA
53938 TTTTAAAAAAAAACCAGACCCGAATACCAAAA
1 TTTTAAAAAAAAACC-GACCC-AATACCAAAA
53970 GATTGATGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 14 0.52
31 5 0.19
32 8 0.30
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (30 bp):
TTTTAAAAAAAAACCGACCCAATACCAAAA
Found at i:54715 original size:58 final size:58
Alignment explanation
Indices: 54632--54773 Score: 223
Period size: 58 Copynumber: 2.4 Consensus size: 58
54622 CAGTTTTCAA
* *
54632 ATTCGCAACTC-GATTCTCCAAATTCGCAACACTAATTACCGATATAGGTAAACTCAACT
1 ATTCGCAACTCAG-TT-TTCAAATTCGCAACACTAATTACCGATATAGGTAAACACAACT
* *
54691 ATTCGCAATTCAGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACT
1 ATTCGCAACTCAGTTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACACAACT
54749 ATTCGCAACTCAGTTTTCAAATTCG
1 ATTCGCAACTCAGTTTTCAAATTCG
54774 TAACTCAGAT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
58 64 0.83
59 12 0.16
60 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.30
Consensus pattern (58 bp):
ATTCGCAACTCAGTTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACACAACT
Found at i:54778 original size:20 final size:20
Alignment explanation
Indices: 54749--54797 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
54739 AAACACAACT
*
54749 ATTCGCAACTCAGTTTTCAA
1 ATTCGCAACTCAGATTTCAA
*
54769 ATTCGTAACTCAGATTTCAA
1 ATTCGCAACTCAGATTTCAA
54789 ATTCGCAAC
1 ATTCGCAAC
54798 ACGAATTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (20 bp):
ATTCGCAACTCAGATTTCAA
Found at i:54805 original size:20 final size:20
Alignment explanation
Indices: 54763--54826 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
54753 GCAACTCAGT
* *
54763 TTTCAAATTCGTAACTC-AGA
1 TTTCAAATTCGCAACACGA-A
54783 TTTCAAATTCGCAACACGAA
1 TTTCAAATTCGCAACACGAA
*** *
54803 TTTCGTTTTCGCAACGCGAA
1 TTTCAAATTCGCAACACGAA
54823 TTTC
1 TTTC
54827 CCATATAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 36 0.97
21 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (20 bp):
TTTCAAATTCGCAACACGAA
Found at i:55365 original size:20 final size:21
Alignment explanation
Indices: 55342--55462 Score: 83
Period size: 20 Copynumber: 6.0 Consensus size: 21
55332 TTGCGAAAAC
*
55342 GAAATTCGCGTTGTGAATTTG
1 GAAATTCGCGTTGCGAATTTG
* *
55363 AAAATT-GTGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
*
55383 GAGAA-TCGCGTTGCAAATTTG
1 GA-AATTCGCGTTGCGAATTTG
* * * **
55404 GAAACT-GTGTTGCGAAATCA
1 GAAATTCGCGTTGCGAATTTG
*
55424 G-AGTTCGCGTTGCGAATTT-
1 GAAATTCGCGTTGCGAATTTG
* *
55443 GAGA-TCGCATTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
55463 TTGGTTATTT
Statistics
Matches: 75, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
19 17 0.23
20 36 0.48
21 22 0.29
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (21 bp):
GAAATTCGCGTTGCGAATTTG
Found at i:55421 original size:21 final size:20
Alignment explanation
Indices: 55357--55421 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
55347 TCGCGTTGTG
*
55357 AATTTGAAAATTGTGTTGCG-
1 AATTTGGAAA-TGTGTTGCGA
*
55377 AATTTGGAGAATCGCGTTGC-A
1 AATTTGGA-AAT-GTGTTGCGA
55398 AATTTGGAAACTGTGTTGCGA
1 AATTTGGAAA-TGTGTTGCGA
55419 AAT
1 AAT
55422 CAGAGTTCGC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (20 bp):
AATTTGGAAATGTGTTGCGA
Done.