Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001040.1 Hibiscus syriacus cultivar Beakdansim tig00002066_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: 75899
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2730 original size:44 final size:43
Alignment explanation
Indices: 2672--3283 Score: 202
Period size: 44 Copynumber: 13.9 Consensus size: 43
2662 TGAAATAAAA
* * *
2672 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGCCG
1 ATGT-GATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
* * * * * *
2716 ATGCTGATCTACCTCCTTTTGCGATAGAATCGAGCAAAATGTTG
1 ATG-TGATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
* * * * * * ****
2760 GTGATAATCCAACTCCTTCTGTGATGGATTTGAGCAAAATAAAA
1 ATG-TGATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
* *
2804 ATGTCGATCCACCTCCTT-TGTGATGGAATCGAACGAGATGTCG
1 ATGT-GATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
* * * ** * * * *
2847 ATGTTGATCTACCTCATTATGTGATATAATCTAGCAAAAAGTTG
1 ATG-TGATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
* * * * * * ****
2891 AATATGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAA
1 -ATGTGATCCACCTCCTTCTGTGATGGAATCGAAC-AAAATGTCG
* * * *
2936 ATGTCGATCCACCTCCTTCTATGATGGAAATCAAACGATATGTCG
1 ATGT-GATCCACCTCCTTCTGTGATGG-AATCGAACAAAATGTCG
* ** * * * * *
2981 ATAGTGATCTATATCCTTCTGTGGTAGAATCGAGCTAAA-GTTG
1 AT-GTGATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
** * * * * * ****
3024 ACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAA
1 A-TGTGATCCACCTCCTTCTGTGATGGAATCGAAC-AAAATGTCG
* * * * *
3069 AGGTCGATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTTG
1 ATGT-GATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
* * * * * * *
3113 GTGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTG
1 ATG-TGATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
** * * * * ****
3157 CCGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAA
1 ATG-TGATCCACCTCCTTCTGTGATGGAATCGAAC-AAAATGTCG
* * * *
3202 ATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTG
1 ATGT-GATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
* * * * *
3246 GTGCTGGTCTACCTCCTTCTGTGATAGAATCGACCAAA
1 ATG-TGATCCACCTCCTTCTGTGATGGAATCGAACAAA
3284 CAGTTGAACA
Statistics
Matches: 392, Mismatches: 159, Indels: 34
0.67 0.27 0.06
Matches are distributed among these distances:
43 58 0.15
44 224 0.57
45 104 0.27
46 6 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (43 bp):
ATGTGATCCACCTCCTTCTGTGATGGAATCGAACAAAATGTCG
Found at i:3039 original size:133 final size:133
Alignment explanation
Indices: 2634--3290 Score: 896
Period size: 133 Copynumber: 5.0 Consensus size: 133
2624 GATGATGCTT
* *
2634 ATCCAACTCATTCTGCGATGGATTTGAGTG-AAATAAAAATGTCGATCCACCTCCTTCTGTGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * * **
2698 GAATCGAACGAGATGCCGATGCTGATCTACCTCCTTTTGCGATAGAATCGAGCAAAATGTTGGTG
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTT-GAC
*
2763 A-TA
130 ACTG
*
2766 ATCCAACTCCTTCTGTGATGGATTTGAGC-AAAATAAAAATGTCGATCCACCTCCTT-TGTGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * * *
2829 GAATCGAACGAGATGTCGATGTTGATCTACCTCATTATGTGATATAATCTAGCAAAAAGTTGA-A
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACA
*
2893 TATG
131 -CTG
*
2897 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTATGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * ** * *
2962 GAAATCAAACGATATGTCGATAG-TGATCTATATCCTTCTGTGGTAGAATCGAGC-TAAAGTTGA
66 G-AATCGAACGAGATGTCGAT-GCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGA
3025 CACTG
129 CACTG
* *
3030 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAAGGTCGATCCACCTCCTTTTGTGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * * *
3095 GAATCGAACGAGATGTTGGTGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGCCG
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACA
3160 CTG
131 CTG
* *
3163 ATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATG
1 ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
* * * * *
3228 GAATCGAACGAGATGTTGGTGCTGGTCTACCTCCTTCTGTGATAGAATCGACCAAACAGTTGA
66 GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGA
3291 ACAATCTCTT
Statistics
Matches: 466, Mismatches: 49, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
129 1 0.00
130 1 0.00
131 90 0.19
132 121 0.26
133 210 0.45
134 42 0.09
135 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (133 bp):
ATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATG
GAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACA
CTG
Found at i:3167 original size:266 final size:265
Alignment explanation
Indices: 2536--3283 Score: 975
Period size: 266 Copynumber: 2.8 Consensus size: 265
2526 AAAAATATCT
* * * * *
2536 ATCCACCTCCTTCTGTGATGGAATCGAATGAGATGTCGATGATGATCTTCCTCCTTCTGTAATAG
1 ATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
* * *
2601 AATCGAGCAAAAATGACAATGTTGATGATGCTTATCCAACTCATTCTGCGATGGATTTGAGTG-A
66 AATCGAGC---AA--A-AA-GTTGA--A-GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAA
*
2665 AATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGCCGATGCTGATCTACCT
121 AATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCT
* * ** *
2730 CCTTTTGCGATAGAATCGAGCAAAATGTTGGTGATAATCCAACTCCTTCTGTGATGGATTTGAGC
186 CCTTCTGTGATAGAATCGAGCAAAATGTTGGACATAATCCAACTCCTTCTGCGATGGATTTGAGC
*
2795 AAAATAAAAATGTCG
251 AAAATAAAAAGGTCG
* * *
2810 ATCCACCTCC-TTTGTGATGGAATCGAACGAGATGTCGATGTTGATCTACCTCATTATGTGATAT
1 ATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
* **
2874 AATCTAGCAAAAAGTTGAATATGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
66 AATCGAGCAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
* * * **
2939 TCGATCCACCTCCTTCTATGATGGAAATCAAACGATATGTCGATAG-TGATCTATATCCTTCTGT
131 TCGATCCACCTCCTTCTGTGATGG-AATCGAACGAGATGTCGAT-GCTGATCTACCTCCTTCTGT
* * *
3003 GGTAGAATCGAGCTAAA-GTT-GACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATA
194 GATAGAATCGAGCAAAATGTTGGACA-TAATCCAACTCCTTCTGCGATGGATTTGAGC-AAAATA
3066 AAAAGGTCG
257 AAAAGGTCG
* * *
3075 ATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCATTCTGTGATAG
1 ATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
** *
3140 AATCGAGCAAAAAGTTGCCGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAATAAAAATG
66 AATCGAGCAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
* * * *
3205 TCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTGCTGGTCTACCTCCTTCTGTGA
131 TCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
*
3270 TAGAATCGACCAAA
196 TAGAATCGAGCAAA
3284 CAGTTGAACA
Statistics
Matches: 415, Mismatches: 52, Indels: 23
0.85 0.11 0.05
Matches are distributed among these distances:
263 31 0.07
264 68 0.16
265 112 0.27
266 136 0.33
267 2 0.00
268 1 0.00
270 2 0.00
273 53 0.13
274 10 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (265 bp):
ATCCACCTCCTTTTGTGATGGAATCGAACGAGATGTCGATGATGATCTACCTCATTCTGTGATAG
AATCGAGCAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG
TCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
TAGAATCGAGCAAAATGTTGGACATAATCCAACTCCTTCTGCGATGGATTTGAGCAAAATAAAAA
GGTCG
Found at i:3717 original size:36 final size:36
Alignment explanation
Indices: 3660--4177 Score: 257
Period size: 39 Copynumber: 13.9 Consensus size: 36
3650 CAAAGATTGA
*
3660 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
* * *
3695 TCATTTTAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 T-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
* *
3732 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
* *
3768 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-AT
* * ***
3805 TGTTTCAAAGGG-GAC-GTTTTC-A-A-AG---TTTA-
1 TGTTTC-AAGGGAAACTG-TCTCAAGAGAGACAAAAAT
* * * *
3834 TGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-AT
* *
3871 TGTTTCAAGGGAAACTGTCTCAAGCGAGACAAAATCTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * *
3909 CTGTTT-ATAGGGAAACTATCTCAAGCGAGACAAAATCTT
1 -TGTTTCA-AGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * *
3948 CTGTTTCTAGGGAAACTATCTCAAGCGAGACAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * * *
3987 CTGTTTCGAGGAAAACTATCTCAAGCGAGACAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * * *
4026 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * * * *
4065 CTGTTTCGAGGGAAACTATCTAAAGTGAGATAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * * *
4104 ATGTTTCGAGTGAAACTATCTCAAGTGAGACAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--AT
* * * *
4143 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAA
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
4178 TCTTTTGTTT
Statistics
Matches: 420, Mismatches: 44, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.01
29 10 0.02
30 2 0.00
32 2 0.00
34 2 0.00
35 1 0.00
36 93 0.22
37 49 0.12
38 8 0.02
39 249 0.59
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAAT
Found at i:3756 original size:15 final size:15
Alignment explanation
Indices: 3702--3794 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
3692 AATTCATTTT
3702 AAGGGAAACTGTCTC
1 AAGGGAAACTGTCTC
*
3717 AAGAGAGACAAAACTTGTTTC
1 AAG-G-G---AAAC-TGTCTC
3738 AAGGGAAACTGTCTC
1 AAGGGAAACTGTCTC
*
3753 AAGGGAGACAAAACTTGTTTC
1 AA-GG-G---AAAC-TGTCTC
3774 AAGGGAAACTGTCTC
1 AAGGGAAACTGTCTC
3789 AAGGGA
1 AAGGGA
3795 GACAAAACTT
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
15 21 0.34
16 11 0.18
17 2 0.03
19 2 0.03
20 11 0.18
21 15 0.24
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (15 bp):
AAGGGAAACTGTCTC
Found at i:3925 original size:39 final size:39
Alignment explanation
Indices: 3851--4377 Score: 738
Period size: 39 Copynumber: 13.6 Consensus size: 39
3841 AGAGAAAATG
* * *
3851 TCTCAAGGGAGACAAAAT-TT-TGTTTCAAGGGAAACTG
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
**
3888 TCTCAAGCGAGACAAAATCTTCTGTTTATAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
3927 TCTCAAGCGAGACAAAATCTTCTGTTTCTAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
3966 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGAAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
4005 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
4044 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * * * *
4083 TCTAAAGTGAGATAAAATCTTATGTTTCGAGTGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
4122 TCTCAAGTGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * * *
4161 TCTCAAGCGAGATAAAATCTTTTGTTTCGAGTGAATCTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * *
4200 TCTCAAGCGAGATAAAAAT-TTCTATTTCGAGTGAAACTA
1 TCTCAAGCGAGA-CAAAATCTTCTGTTTCGAGGGAAACTA
*
4239 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* *
4278 TCTCAAGCGAGA-TAAATCTTCTGTTTCGAGTGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * * * * *
4316 TCTCAAGCAAAATAAAATCTTATATTTCGAGTGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
4355 TCTCAAGCGAGATAAAATCTTCT
1 TCTCAAGCGAGACAAAATCTTCT
4378 TTAAAAACAA
Statistics
Matches: 446, Mismatches: 39, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
37 17 0.04
38 41 0.09
39 383 0.86
40 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (39 bp):
TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
Found at i:4035 original size:20 final size:20
Alignment explanation
Indices: 3973--4035 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
3963 CTATCTCAAG
3973 CGAGACAAAATCTTCTGTTT
1 CGAGACAAAATCTTCTGTTT
* ****
3993 CGAG-GAAAA-CTATCTCAAG
1 CGAGACAAAATCT-TCTGTTT
4012 CGAGACAAAATCTTCTGTTT
1 CGAGACAAAATCTTCTGTTT
4032 CGAG
1 CGAG
4036 GGAAACTATC
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 15 0.50
21 2 0.07
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
CGAGACAAAATCTTCTGTTT
Found at i:6734 original size:30 final size:30
Alignment explanation
Indices: 6687--6745 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
6677 CAAAGATTCA
6687 AAAATGCACATGCAAATGCAATATGCAAAC
1 AAAATGCACATGCAAATGCAATATGCAAAC
* *
6717 AAAATGGA-ATGCAAAATGCGATATGCAAA
1 AAAATGCACATGC-AAATGCAATATGCAAA
6746 TGCAACAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (30 bp):
AAAATGCACATGCAAATGCAATATGCAAAC
Found at i:10334 original size:29 final size:30
Alignment explanation
Indices: 10294--10351 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
10284 CGCAGGAAAC
10294 AATAGATGAT-GG-GTTGGTGTTGAAAAAA
1 AATAGATGATGGGTGTTGGTGTTGAAAAAA
10322 AATAGGATGATGGGTGTTGGTGTTGAAAAA
1 AATA-GATGATGGGTGTTGGTGTTGAAAAA
10352 TGAGGTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 6 0.22
30 2 0.07
31 15 0.56
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.29
Consensus pattern (30 bp):
AATAGATGATGGGTGTTGGTGTTGAAAAAA
Found at i:10344 original size:31 final size:30
Alignment explanation
Indices: 10294--10379 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 30
10284 CGCAGGAAAC
10294 AATA-GATGATGG-GTTGGTGTTGAAAAAA
1 AATAGGATGATGGTGTTGGTGTTGAAAAAA
10322 AATAGGATGATGGGTGTTGGTGTTG---AAA
1 AATAGGATGAT-GGTGTTGGTGTTGAAAAAA
*
10350 AATGAGG-TGATAGGTGTTGATGTTGAAAAA
1 AAT-AGGATGAT-GGTGTTGGTGTTGAAAAA
10380 TGATGTTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
28 26 0.53
29 9 0.18
30 2 0.04
31 12 0.24
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (30 bp):
AATAGGATGATGGTGTTGGTGTTGAAAAAA
Found at i:10381 original size:28 final size:29
Alignment explanation
Indices: 10319--10382 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 29
10309 GGTGTTGAAA
* *
10319 AAAAAT-AGGATGATGGGTGTTGGTGTTG
1 AAAAATGAGGATGATAGGTGTTGATGTTG
10347 AAAAATGAGG-TGATAGGTGTTGATGTTG
1 AAAAATGAGGATGATAGGTGTTGATGTTG
10375 AAAAATGA
1 AAAAATGA
10383 TGTTTACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (29 bp):
AAAAATGAGGATGATAGGTGTTGATGTTG
Found at i:11999 original size:27 final size:27
Alignment explanation
Indices: 11961--12015 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
11951 TAACACTCAA
11961 ACTGTAGAAATAAATAAATGATTAAAT
1 ACTGTAGAAATAAATAAATGATTAAAT
11988 ACTGTAGAAATAAATAAATGATTAAAT
1 ACTGTAGAAATAAATAAATGATTAAAT
12015 A
1 A
12016 TACTGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (27 bp):
ACTGTAGAAATAAATAAATGATTAAAT
Found at i:38209 original size:93 final size:92
Alignment explanation
Indices: 38089--38321 Score: 277
Period size: 87 Copynumber: 2.5 Consensus size: 92
38079 ATACTGCTCG
*
38089 TGGGGTAAATGCATTTCCTATGATTTCCATCTCAAGGGATGTGGGGATTGTTGAAGAAAAGAATG
1 TGGGGTAAATGC-TTGCCTATGATTTCCATCTCAA-GGATGTGGGGA-TGTTGAAGAAAAGAATG
38154 ACATGATACA-A-ACCAAAGATAGTGCTTA
63 ACATGATACACAGACCAAAGATAGTGCTTA
* * *
38182 TGGGGTAAATGTCTTGCCTATGATTTCCATCTCAA-GA------AATGTTGGAGAAAAGACTGAC
1 TGGGGTAAATG-CTTGCCTATGATTTCCATCTCAAGGATGTGGGGATGTTGAAGAAAAGAATGAC
* *
38240 CTGATACAGCAGACCAAAGTTAGTGCTTA
65 ATGATACA-CAGACCAAAGATAGTGCTTA
38269 TGGGGTAAATGCCTTGCCTATGATTTCCATCTCAAGAGATGTGGAGGATGTTG
1 TGGGGTAAATG-CTTGCCTATGATTTCCATCTCAAG-GATGTGG-GGATGTTG
38322 GTGGACAATC
Statistics
Matches: 119, Mismatches: 8, Indels: 23
0.79 0.05 0.15
Matches are distributed among these distances:
84 24 0.20
85 1 0.01
86 1 0.01
87 50 0.42
89 2 0.02
91 2 0.02
93 32 0.27
94 1 0.01
96 6 0.05
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (92 bp):
TGGGGTAAATGCTTGCCTATGATTTCCATCTCAAGGATGTGGGGATGTTGAAGAAAAGAATGACA
TGATACACAGACCAAAGATAGTGCTTA
Found at i:39535 original size:132 final size:125
Alignment explanation
Indices: 39305--39561 Score: 433
Period size: 132 Copynumber: 2.0 Consensus size: 125
39295 TGAATTCAGA
39305 AGTCGTTGGTTTGGTGGCTGGACAGGGGAGGTATATGCTTCATTTTGTTCTATTGATCTTTGAAT
1 AGTCGTTGGTTTGGTGGCTGGACAGGGGAGGTATATGCTTCATTTTGTTCTATTGATCTTTGAAT
39370 CACTCAGGCCCTTTTGGTATTTAGTTTGATTTGTAGTATGTATTTGTTGTCTTATAAATG
66 CACTCAGGCCCTTTTGGTATTTAGTTTGATTTGTAGTATGTATTTGTTGTCTTATAAATG
39430 AGTCGTTGGTTTGGTGGCTGGACAGGGGAGGTATTAGGTATATGCTTCATTTTGTTCTATTGATC
1 AGTCGTTGGTTTGGTGGCTGGACA--GG-GG----AGGTATATGCTTCATTTTGTTCTATTGATC
* *
39495 TTTGAATCACTCAGGTCCTTTTGTTATTTAGTTTGATTTGTAGTATGTATTTGTTGTCTTATAAA
59 TTTGAATCACTCAGGCCCTTTTGGTATTTAGTTTGATTTGTAGTATGTATTTGTTGTCTTATAAA
39560 TG
124 TG
39562 CCAAAGTTTA
Statistics
Matches: 123, Mismatches: 2, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
125 24 0.20
127 2 0.02
128 2 0.02
132 95 0.77
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.46
Consensus pattern (125 bp):
AGTCGTTGGTTTGGTGGCTGGACAGGGGAGGTATATGCTTCATTTTGTTCTATTGATCTTTGAAT
CACTCAGGCCCTTTTGGTATTTAGTTTGATTTGTAGTATGTATTTGTTGTCTTATAAATG
Found at i:42213 original size:37 final size:37
Alignment explanation
Indices: 42163--42239 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
42153 CAAATTGGAT
42163 ACTAAAGCATGTAGGAATTAGGAGTAGCCAAGTATAA
1 ACTAAAGCATGTAGGAATTAGGAGTAGCCAAGTATAA
* *
42200 ACTAAAGCATGTAGGGATTAGGTGTAGCCAAGTATAA
1 ACTAAAGCATGTAGGAATTAGGAGTAGCCAAGTATAA
42237 ACT
1 ACT
42240 TATAGCTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (37 bp):
ACTAAAGCATGTAGGAATTAGGAGTAGCCAAGTATAA
Found at i:56387 original size:59 final size:57
Alignment explanation
Indices: 56269--56441 Score: 170
Period size: 59 Copynumber: 2.9 Consensus size: 57
56259 TATTTGGATG
* * *
56269 AATTTGGGGATGAAATTAGGATATTCAAAATTTTAGAGACTAATTAGAAAT-AGGGTCAT
1 AATTT-GGGATGAAATTAGAATATTCAAAATTTAAG-GACTAATTA-AAATGAGAGTCAT
* * * *
56328 AATTTAGGGATGAAATTAGAATGTTCAAAACTTTAAGGAATAATTTAAATGAGATTCAT
1 AATTT-GGGATGAAATTAGAATATTCAAAA-TTTAAGGACTAATTAAAATGAGAGTCAT
* *
56387 AGTTTGAGGATTAAATT-GAAATATTCAAAAGTTTAAGGACTAATCTAAAATGAGA
1 AATTTG-GGATGAAATTAG-AATATTCAAAA-TTTAAGGACTAAT-TAAAATGAGA
56442 AATATTATAG
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
58 6 0.06
59 75 0.79
60 14 0.15
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (57 bp):
AATTTGGGATGAAATTAGAATATTCAAAATTTAAGGACTAATTAAAATGAGAGTCAT
Found at i:60450 original size:33 final size:33
Alignment explanation
Indices: 60405--60468 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
60395 ACACGCTGGG
* *
60405 CATCCGACCGAGCTATGCGAGAGCATCCGAGGC
1 CATCCGAACGAGCTATGCGAGAGCAGCCGAGGC
*
60438 CATCCGAACGAGCTATGCGAGGGCAGCCGAG
1 CATCCGAACGAGCTATGCGAGAGCAGCCGAG
60469 CGAGCTATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.33, T:0.11
Consensus pattern (33 bp):
CATCCGAACGAGCTATGCGAGAGCAGCCGAGGC
Found at i:60458 original size:23 final size:23
Alignment explanation
Indices: 60432--60495 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
60422 CGAGAGCATC
*
60432 CGAGGCCATCCGAACGAGCTATG
1 CGAGGCCAGCCGAACGAGCTATG
* *
60455 CGAGGGCAGCCGAGCGAGCTATG
1 CGAGGCCAGCCGAACGAGCTATG
* *
60478 CGAGGGCAGCCGAGCGAG
1 CGAGGCCAGCCGAACGAG
60496 GGTAGGTCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.28, G:0.41, T:0.08
Consensus pattern (23 bp):
CGAGGCCAGCCGAACGAGCTATG
Found at i:60532 original size:29 final size:29
Alignment explanation
Indices: 60499--60554 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
60489 GAGCGAGGGT
*
60499 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
60528 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
60555 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:74909 original size:13 final size:13
Alignment explanation
Indices: 74888--74920 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
74878 GCATAAAGCG
74888 AGCGCTTTCGCTT
1 AGCGCTTTCGCTT
*
74901 AGTGCTTTCGCTT
1 AGCGCTTTCGCTT
74914 AGCGCTT
1 AGCGCTT
74921 CGGTGTCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.39
Consensus pattern (13 bp):
AGCGCTTTCGCTT
Done.