Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009231.1 Hibiscus syriacus cultivar Beakdansim tig00112838_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: 45408
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:9523 original size:7 final size:7
Alignment explanation
Indices: 9501--9563 Score: 60
Period size: 7 Copynumber: 9.1 Consensus size: 7
9491 AAAAGGGAAC
*
9501 AAATAAA
1 AAATGAA
9508 AAGATGAA
1 AA-ATGAA
9516 AAATGAAA
1 AAATG-AA
9524 AAATG-A
1 AAATGAA
*
9530 AAAGGAA
1 AAATGAA
9537 AAA--AA
1 AAATGAA
9542 AAATGAA
1 AAATGAA
9549 AAATGAA
1 AAATGAA
*
9556 AAAAGAA
1 AAATGAA
9563 A
1 A
9564 TGAAAAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
5 5 0.10
6 5 0.10
7 25 0.52
8 13 0.27
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:9551 original size:19 final size:19
Alignment explanation
Indices: 9521--9570 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
9511 ATGAAAAATG
9521 AAAAAATG-AAAAGGAAAA
1 AAAAAATGAAAAAGGAAAA
*
9539 AAAAAATGAAAAATGAAAA
1 AAAAAATGAAAAAGGAAAA
*
9558 AAGAAATGAAAAA
1 AAAAAATGAAAAA
9571 ATAAAAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 8 0.28
19 21 0.72
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAATGAAAAAGGAAAA
Found at i:9558 original size:26 final size:27
Alignment explanation
Indices: 9514--9588 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 27
9504 TAAAAAGATG
9514 AAAAATGAAAAAATG-AAAAGGAAA-AA
1 AAAAATG-AAAAATGAAAAAGGAAATAA
* *
9540 AAAAATGAAAAATGAAAAAAGAAATGA
1 AAAAATGAAAAATGAAAAAGGAAATAA
*
9567 AAAAAT-AAAAAGAGAAAAAGGA
1 AAAAATGAAAAA-TGAAAAAGGA
9589 GGGTTTGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 7 0.17
26 20 0.48
27 15 0.36
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (27 bp):
AAAAATGAAAAATGAAAAAGGAAATAA
Found at i:9572 original size:8 final size:8
Alignment explanation
Indices: 9501--9563 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
9491 AAAAGGGAAC
9501 AAAT-AAA
1 AAATGAAA
9508 AAGATG-AA
1 AA-ATGAAA
9516 AAATGAAA
1 AAATGAAA
9524 AAATGAAA
1 AAATGAAA
**
9532 AGGAAAAAAA
1 A--AATGAAA
9542 AAATG-AA
1 AAATGAAA
9549 AAATGAAA
1 AAATGAAA
9557 AAA-GAAA
1 AAATGAAA
9564 TGAAAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
7 16 0.35
8 24 0.52
10 6 0.13
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:9576 original size:19 final size:19
Alignment explanation
Indices: 9524--9583 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
9514 AAAAATGAAA
* *
9524 AAATG-AAAAGGAAAAAAA
1 AAATGAAAAATGAAAAAAG
9542 AAATGAAAAATGAAAAAAG
1 AAATGAAAAATGAAAAAAG
9561 AAATGAAAAAAT-AAAAAGAG
1 AAATG-AAAAATGAAAAA-AG
9581 AAA
1 AAA
9584 AAGGAGGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.14
19 21 0.57
20 11 0.30
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAATGAAAAATGAAAAAAG
Found at i:9577 original size:33 final size:34
Alignment explanation
Indices: 9501--9577 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
9491 AAAAGGGAAC
*
9501 AAATAAAAAGATGAAAAATGAAAAAATGAAAAGGAA
1 AAAT-AAAA-ATGAAAAATGAAAAAATGAAAAGAAA
*
9537 AAA-AAAAATGAAAAATGAAAAAA-GAAATGAAA
1 AAATAAAAATGAAAAATGAAAAAATGAAAAGAAA
9569 AAATAAAAA
1 AAATAAAAA
9578 GAGAAAAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 10 0.26
33 21 0.55
34 4 0.11
36 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (34 bp):
AAATAAAAATGAAAAATGAAAAAATGAAAAGAAA
Found at i:10703 original size:136 final size:136
Alignment explanation
Indices: 10457--10806 Score: 558
Period size: 136 Copynumber: 2.6 Consensus size: 136
10447 GGTGAACCAG
*
10457 CATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * *
10522 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
10587 GATCAG
131 GATCAA
*
10593 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* *
10658 AGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
10723 GATCAA
131 GATCAA
* ** ** *
10729 CATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCAAAC-GAGGAAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
*
10793 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
10807 AACTTCGCAT
Statistics
Matches: 198, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
135 34 0.17
136 164 0.83
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:11171 original size:91 final size:92
Alignment explanation
Indices: 11056--11222 Score: 275
Period size: 91 Copynumber: 1.8 Consensus size: 92
11046 AAAGAGATGG
11056 ATCAACATTTCCAATGGAGAGTTCATAAT-AAGAAGAACTCATCCAAT-GAGAGAGAAGAAGTTC
1 ATCAACATTTCCAATGGAGAGTTCATAATGAA-AAGAACTCATCCAATAGAGAGAGAAGAAGTTC
11119 ATAATGAGAAGAACTTGTTCAACTTCGC
65 ATAATGAGAAGAACTTGTTCAACTTCGC
* * * *
11147 ATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCAATAGAGAGAGAAGAAGTTCA
11212 TAATGAGAAGA
66 TAATGAGAAGA
11223 GTTTTTTTGA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
91 41 0.59
92 29 0.41
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (92 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCAATAGAGAGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTCGC
Found at i:11411 original size:332 final size:331
Alignment explanation
Indices: 10726--11427 Score: 1057
Period size: 332 Copynumber: 2.1 Consensus size: 331
10716 CTTGAGGGAT
*
10726 CAACATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCAAACGAGGAAGAAGAAGTTCATAA
1 CAACATTTCCA-TGAAGAGTTCATAATGAGAAGAACTCATCAAACGAGGAAGAAGAAGTTCATAA
* *
10791 TGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCG
65 TGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCA
*
10856 TCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGAC
130 TCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGAC
* * * *
10921 ATTTCGAATTAGTGACACCTAGCTTGAGGGATTGATATTTTCAGAAGAGTTCATAATGAGAAGAA
195 ATTTCGAATCAGTGACACCTAGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAA
* * * *
10986 CTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGA
260 CTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAGAAAGA
* *
11051 GATGGAT
325 GATGAAC
* * * *
11058 CAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCAATGA-GAGAGAAGAAGTTCATA
1 CAACATTTCC-ATGAAGAGTTCATAATGAGAAGAACTCATCAAACGAGGA-AGAAGAAGTTCATA
* *
11122 ATGAGAAGAACTTGTTCAACTTCGCATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTC
64 ATGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTC
* * * * *
11187 ATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTTTTTGACCTATCACTTGATTCACGA
129 ATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGA
** *
11252 CATTTCGAATCAGTGATGCCTCGCTTGAGGGATCGACATTTCCAATGAAGAGTTCATAATGAGAA
194 CATTTCGAATCAGTGACACCTAGCTTGAGGGATCGACATTTCC-A-GAAGAGTTCATAATGAGAA
* *
11317 GAACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATTCACCACAGAT
257 GAACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAGAA
* *
11382 GGAGGTGAAC
322 AGAGATGAAC
11392 CAACATTTCC-TGAAGAGTTCATAATGAGAAGAACTC
1 CAACATTTCCATGAAGAGTTCATAATGAGAAGAACTC
11428 GTCCTAAAGG
Statistics
Matches: 332, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
331 2 0.01
332 234 0.70
333 2 0.01
334 94 0.28
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (331 bp):
CAACATTTCCATGAAGAGTTCATAATGAGAAGAACTCATCAAACGAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCAT
CCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACA
TTTCGAATCAGTGACACCTAGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAAC
TCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAGAAAGAG
ATGAAC
Found at i:11610 original size:14 final size:14
Alignment explanation
Indices: 11593--11644 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
11583 GTTAAAAAAA
11593 TATTATTAAATTAT
1 TATTATTAAATTAT
11607 TATTATTAAATTAT
1 TATTATTAAATTAT
* *
11621 TATTATTAATTTTAG
1 TATTATTAA-ATTAT
11636 TATTATTAA
1 TATTATTAA
11645 GTGTGTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TATTATTAAATTAT
Found at i:13299 original size:23 final size:25
Alignment explanation
Indices: 13271--13319 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
13261 ATTTTAGTCA
*
13271 TTAAAG-CTATTATTTTT-CTATTT
1 TTAAAGTCTATGATTTTTGCTATTT
*
13294 TTAAAGTGTATGATTTTTGCTATTT
1 TTAAAGTCTATGATTTTTGCTATTT
13319 T
1 T
13320 AGACCCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 9 0.41
25 7 0.32
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.59
Consensus pattern (25 bp):
TTAAAGTCTATGATTTTTGCTATTT
Found at i:15251 original size:35 final size:36
Alignment explanation
Indices: 15204--15278 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 36
15194 AAGATGTACA
* *
15204 TAAATTTTTATGGTAGGATATGAATTTTTAAATTTT
1 TAAATTTTTATGGTAGGAGATGAATTTTTAAAATTT
15240 TAAA-TTTTATGGTAGGAGATGAATTTTTAAAATTT
1 TAAATTTTTATGGTAGGAGATGAATTTTTAAAATTT
15275 TAAA
1 TAAA
15279 AGAAGATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 33 0.89
36 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (36 bp):
TAAATTTTTATGGTAGGAGATGAATTTTTAAAATTT
Found at i:17264 original size:2 final size:2
Alignment explanation
Indices: 17257--17312 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
17247 TCATTCAATA
17257 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
17299 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
17313 TATTAATCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17376 original size:2 final size:2
Alignment explanation
Indices: 17369--17396 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17359 TTATTCAACA
17369 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
17397 CTTGATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18485 original size:2 final size:2
Alignment explanation
Indices: 18480--18532 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
18470 TATATTTAAT
* * *
18480 TC TC TC TC TC TC TC CC TC TC CC TC TC CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18522 TC TC TC TC TC T
1 TC TC TC TC TC T
18533 TAAATATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:19706 original size:158 final size:159
Alignment explanation
Indices: 19410--19753 Score: 530
Period size: 158 Copynumber: 2.2 Consensus size: 159
19400 TTCCTCCTCC
* * *
19410 ATTTTAAGTCTATGTTTTTACAAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
1 ATTTTAAGTCCATTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
19475 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
66 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
* * *
19540 AGTCTCCTTATTTCTTCAATTCATCATTT
131 AATATCCTTATTCCTTCAATTCATCATTT
* * *
19569 -TTTTAAGTTCGTTTTTTTACCAAATTTGAGCCACATGCTCCTAAACCATAGTAGAATACATGTG
1 ATTTTAAGTCCATTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
* * *
19633 TACTTTCAATTCCTCTTTTTGGTAACAAATTTTTTATTTTTCAATTTAGTTCTTCAAATT-TTCA
66 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTC-AATTATTCA
** *
19697 TAATATCCTTATTCCTTCAATTTGTGATTT
130 TAATATCCTTATTCCTTCAATTCATCATTT
19727 ATTTTAAGTCCATTTTTTTACCAAATT
1 ATTTTAAGTCCATTTTTTTACCAAATT
19754 GTTTTTTTAT
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
158 138 0.83
159 28 0.17
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (159 bp):
ATTTTAAGTCCATTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
AATATCCTTATTCCTTCAATTCATCATTT
Found at i:22961 original size:29 final size:29
Alignment explanation
Indices: 22896--22960 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 29
22886 TTCTAATATT
*
22896 TATTTGTTATTACAAGTCTAATTTTTCAG
1 TATTTTTTATTACAAGTCTAATTTTTCAG
* *
22925 TATTTTTTATTAGAGGTCT-ATTTTTCAG
1 TATTTTTTATTACAAGTCTAATTTTTCAG
22953 TATTTTTT
1 TATTTTTT
22961 TTAATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.23, C:0.08, G:0.11, T:0.58
Consensus pattern (29 bp):
TATTTTTTATTACAAGTCTAATTTTTCAG
Found at i:22986 original size:22 final size:22
Alignment explanation
Indices: 22943--22987 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
22933 ATTAGAGGTC
* ***
22943 TATTTTTCAGTATTTTTTTTAA
1 TATTTTTCAATATTTGAGTTAA
22965 TATTTTTCAATATTTGAGTTAA
1 TATTTTTCAATATTTGAGTTAA
22987 T
1 T
22988 TAAAATATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (22 bp):
TATTTTTCAATATTTGAGTTAA
Found at i:23017 original size:11 final size:11
Alignment explanation
Indices: 22987--23023 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22977 TTTGAGTTAA
*
22987 TTAAAATATGT
1 TTAAAATGTGT
22998 TT-AAA-GTGT
1 TTAAAATGTGT
23007 TTAAAATGTGT
1 TTAAAATGTGT
23018 TTAAAA
1 TTAAAA
23024 CTTTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 5 0.22
10 6 0.26
11 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (11 bp):
TTAAAATGTGT
Found at i:25422 original size:3 final size:3
Alignment explanation
Indices: 25416--25457 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
25406 AATGACTCGT
25416 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG TATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG -ATG AT
25458 CATAGCTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (3 bp):
ATG
Found at i:25741 original size:68 final size:68
Alignment explanation
Indices: 25656--25993 Score: 465
Period size: 68 Copynumber: 5.0 Consensus size: 68
25646 GTTAGGGTTT
**
25656 TTTAGGGTAAACTACCTATTCAGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
25721 TTA
66 TTA
* * *
25724 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATATTTTGGTCATTAGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
25789 TTA
66 TTA
* *
25792 TTTAGAGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTTACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
25857 TTA
66 TTA
* * ** *
25860 TTTAGGGTAAACTACCTATTTGGTCACTAATATATTATCTAATATAAT-TCAT-AT-A-T--ATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTCACTCGATT
*
25919 TTTA
65 ATTA
* **
25923 TTTAGGGTAAACTACCTATTTGGTCACTTATCTATTATCTAATTTATGTTTTGAG-CACTTTATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTG-GTCACTCGATT
25987 ATTA
65 ATTA
25991 TTT
1 TTT
25994 TTTCAAAATT
Statistics
Matches: 238, Mismatches: 24, Indels: 16
0.86 0.09 0.06
Matches are distributed among these distances:
62 3 0.01
63 49 0.21
65 2 0.01
66 2 0.01
67 1 0.00
68 178 0.75
69 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:25760 original size:37 final size:36
Alignment explanation
Indices: 25705--25897 Score: 115
Period size: 37 Copynumber: 5.6 Consensus size: 36
25695 TAATTTATGT
*
25705 TTTGGTCACTCGAT-TATTATTTAGGGTAAACTACCTA
1 TTTGGTCACT-TATATATTATTTA-GGTAAACTACCTA
* * **
25742 TTTGGTCACTTATATATTATCTA-ATTTA-TA--T-
1 TTTGGTCACTTATATATTATTTAGGTAAACTACCTA
*
25773 TTTGGTCA-TTAGATTATTATTTAGAGTAAACTACCTA
1 TTTGGTCACTTATA-TATTATTTAG-GTAAACTACCTA
* ** **
25810 TTTGGTCACTTATATATTA--T--CTAATTTATGT-
1 TTTGGTCACTTATATATTATTTAGGTAAACTACCTA
* *
25841 TTTGGTTACTCGAT-TATTATTTAGGGTAAACTACCTA
1 TTTGGTCACT-TATATATTATTTA-GGTAAACTACCTA
*
25878 TTTGGTCACTAATATATTAT
1 TTTGGTCACTTATATATTAT
25898 CTAATATAAT
Statistics
Matches: 114, Mismatches: 25, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
30 4 0.04
31 30 0.26
32 9 0.08
33 3 0.03
34 4 0.04
35 3 0.03
36 11 0.10
37 46 0.40
38 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (36 bp):
TTTGGTCACTTATATATTATTTAGGTAAACTACCTA
Found at i:25777 original size:31 final size:31
Alignment explanation
Indices: 25678--25846 Score: 99
Period size: 31 Copynumber: 5.1 Consensus size: 31
25668 TACCTATTCA
*
25678 GTCACTTATATATTATCTAATTTATGTTTTG
1 GTCACTTATATATTATCTAATTTATATTTTG
* * * **
25709 GTCACTCGAT-TATTATTTAGGGTAAACTACCTATTTG
1 GTCACT-TATATATTATCTA--ATTTA-TA--T-TTTG
25746 GTCACTTATATATTATCTAATTTATATTTTG
1 GTCACTTATATATTATCTAATTTATATTTTG
* * **
25777 GTCA-TTAGATTATTATTTAGAGTAAACTACCTATTTG
1 GTCACTTATA-TATTATCTA-A-TTTA-TA--T-TTTG
*
25814 GTCACTTATATATTATCTAATTTATGTTTTG
1 GTCACTTATATATTATCTAATTTATATTTTG
25845 GT
1 GT
25847 TACTCGATTA
Statistics
Matches: 102, Mismatches: 20, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
30 4 0.04
31 36 0.35
32 5 0.05
33 4 0.04
34 6 0.06
35 4 0.04
36 5 0.05
37 34 0.33
38 4 0.04
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (31 bp):
GTCACTTATATATTATCTAATTTATATTTTG
Found at i:26116 original size:32 final size:32
Alignment explanation
Indices: 26072--26135 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
26062 TGCTAACATG
26072 ACATTTTCTAATTATGTTTGGATGTTGGACTA
1 ACATTTTCTAATTATGTTTGGATGTTGGACTA
*
26104 ACATTTTTTAATTATGTTTGGATGTTGGACTA
1 ACATTTTCTAATTATGTTTGGATGTTGGACTA
26136 TGTAATTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (32 bp):
ACATTTTCTAATTATGTTTGGATGTTGGACTA
Found at i:27501 original size:20 final size:20
Alignment explanation
Indices: 27476--27525 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
27466 TCCTATTCCA
*
27476 TGGTAATCTTTTATTCTCAC
1 TGGTAATCTTTTATTCCCAC
27496 TGGTAATCTTTTATTCCCAC
1 TGGTAATCTTTTATTCCCAC
*
27516 TAGTAATCTT
1 TGGTAATCTT
27526 ACATTCCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (20 bp):
TGGTAATCTTTTATTCCCAC
Found at i:30385 original size:121 final size:121
Alignment explanation
Indices: 30180--30515 Score: 528
Period size: 121 Copynumber: 2.8 Consensus size: 121
30170 TTGGGCACAT
* * * * * * * *
30180 TATCCTTCTTTGTGAAGTTGAAACCGTGGGTGGCTCATTCGTCGTGAAGTTGAGCTTTGAGTTGG
1 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
*
30245 ATATCCTTCGTCTTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
66 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
*
30301 TATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
1 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
30366 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
66 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
* * *
30422 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGATCCTTCATTGTGAAGTTGAGTTTTGAATTGA
1 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
* * *
30487 ATATCATTCGTTGTGAAGTTAAAATCCAA
66 ATATCCTTCGTCGTGAAGTTGAAATCCAA
30516 TCTTGTGTAA
Statistics
Matches: 198, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 198 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.36
Consensus pattern (121 bp):
TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
Found at i:30739 original size:34 final size:34
Alignment explanation
Indices: 30696--30774 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
30686 GCTCATTCCC
30696 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
1 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
30730 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
1 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
30764 TGTGAAGTTGA
1 TGTGAAGTTGA
30775 AATCCAATCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (34 bp):
TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
Found at i:35814 original size:16 final size:16
Alignment explanation
Indices: 35795--35845 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
35785 ATAAGTATTT
35795 AAATTTATAAAGACCA
1 AAATTTATAAAGACCA
* * *
35811 AAATATAGAAAAACCA
1 AAATTTATAAAGACCA
* *
35827 AAATTT-TAAGGATCA
1 AAATTTATAAAGACCA
35842 AAAT
1 AAAT
35846 AGCAAAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.24
Consensus pattern (16 bp):
AAATTTATAAAGACCA
Found at i:41751 original size:2 final size:2
Alignment explanation
Indices: 41744--41778 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41734 AACTATATTT
41744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41779 CAATTTCGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43478 original size:31 final size:29
Alignment explanation
Indices: 43442--43514 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
43432 ATAGTAAAAC
* *
43442 TTGGTCAAAGTTAAAGTCAAAGTTAACGGGT
1 TTGGTCAAAGTT-AAGTCAAAGTCAAC-AGT
*
43473 TTGGTCAACAGTTAGGTCAAAGTCAACAGT
1 TTGGTCAA-AGTTAAGTCAAAGTCAACAGT
43503 TTGGGTCAAAGT
1 TT-GGTCAAAGT
43515 CAACAAGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 7 0.19
31 26 0.70
32 4 0.11
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (29 bp):
TTGGTCAAAGTTAAGTCAAAGTCAACAGT
Found at i:43499 original size:18 final size:19
Alignment explanation
Indices: 43476--43519 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
43466 AACGGGTTTG
43476 GTCAACAG-TTAGGTCAAA
1 GTCAACAGTTTAGGTCAAA
*
43494 GTCAACAGTTTGGGTCAAA
1 GTCAACAGTTTAGGTCAAA
43513 GTCAACA
1 GTCAACA
43520 AGTCAGACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (19 bp):
GTCAACAGTTTAGGTCAAA
Done.