Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005633.1 Hibiscus syriacus cultivar Beakdansim tig00013133_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: 85755
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:787 original size:23 final size:24
Alignment explanation
Indices: 745--797 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
735 CTTTTTTTTT
745 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
769 TTTCTTCTTTT-GAGTGCTTTGAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
792 TTTCTT
1 TTTCTT
798 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:8174 original size:12 final size:12
Alignment explanation
Indices: 8142--8168 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8132 CTTGCTTTCT
8142 TTCACTTTGCAC
1 TTCACTTTGCAC
8154 TTCACTTTGCAC
1 TTCACTTTGCAC
8166 TTC
1 TTC
8169 TTTTTGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.44
Consensus pattern (12 bp):
TTCACTTTGCAC
Found at i:10391 original size:344 final size:347
Alignment explanation
Indices: 9750--10441 Score: 1137
Period size: 344 Copynumber: 2.0 Consensus size: 347
9740 TATGCTTATA
9750 ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
1 ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
*
9815 TCATAAATGATAAATGGAAACATGTAATAATAATGTCCTAAGAAATGATATGTAATCATAGCCTA
66 TCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCCTA
* *
9880 TATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGACGAAATAATATATGATAATTTATA
131 TATTTGAATAACATGAAAAACATGATCAAATAAGCATAGGACGAAATAATATATGATAACTTATA
* *
9945 CTAACATGTGAATGCATGCTTATGATAGAATATAATGTATAAATGATATAGTATAAGATAGGGTA
196 CTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGGTA
* * *
10010 ATGAAGAACTCCCTTAGAAACAGCTATGAAGAACATCCATGGTGTGT-TCAAGTCATGGAGAAAG
261 ATGAAGAACTCCCTTAGAAACAGCAATGAAAAACATCCATGGTGT-TATCAAGTCATGGAGAAAA
* * *
10074 TTGGTGCTTGTTTGGATCGTATC
325 ATGGAGCTAGTTTGGATCGTATC
10097 ACATTGTGTATCAATCATAAAGAT-GTGGTATATGTTGTATGCATGAATATCATATAACATGGTA
1 ACATTGTGTATCAATCATAAAGATAG-GGTATATGTTGTATGCATGAATATCATATAACATGGTA
10161 TTCATAAATGAT-AATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAG-C-
65 TTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCCT
* * * * *
10223 ATATTTGAATGACATGAAAGACTTGATCAACTAAGCATAGGATGAAAATAATA-ATGATAACTTA
130 ATATTTGAATAACATGAAAAACATGATCAAATAAGCATAGGACG-AAATAATATATGATAACTTA
10287 TACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGG
194 TACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGG
* *
10352 TAA-GAAAGAACTCCCTTAGAATCAGCAATGAAAAACATCCATGGTGTTATTAAGTCATGGAGAA
259 TAATG-AAGAACTCCCTTAGAAACAGCAATGAAAAACATCCATGGTGTTATCAAGTCATGGAGAA
10416 AAATGGAGCTAGTTTGGATCGTATC
323 AAATGGAGCTAGTTTGGATCGTATC
10441 A
1 A
10442 TCCTCCCCTT
Statistics
Matches: 323, Mismatches: 18, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
343 2 0.01
344 189 0.59
345 9 0.03
346 49 0.15
347 74 0.23
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.30
Consensus pattern (347 bp):
ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
TCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCCTA
TATTTGAATAACATGAAAAACATGATCAAATAAGCATAGGACGAAATAATATATGATAACTTATA
CTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGGTA
ATGAAGAACTCCCTTAGAAACAGCAATGAAAAACATCCATGGTGTTATCAAGTCATGGAGAAAAA
TGGAGCTAGTTTGGATCGTATC
Found at i:15978 original size:19 final size:21
Alignment explanation
Indices: 15935--15986 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
15925 GAAACCCCTT
*
15935 TGAAAATATATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
15956 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
15975 TGAAGATACATG
1 TGAAAATACATG
15987 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:19210 original size:337 final size:333
Alignment explanation
Indices: 18599--19268 Score: 1241
Period size: 337 Copynumber: 2.0 Consensus size: 333
18589 GATTACTGCT
*
18599 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAATAACCTGCA
1 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
*
18664 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATTGGTAGGCTATT
66 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
* *
18729 TAATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
131 TAATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
18794 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
196 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
18859 CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATATGAAC
261 CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATATGAAC
18924 TAGGAACC
326 TAGGAACC
**
18932 TGATGTAAGGTAATTCTACCTTCTTGTTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
1 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
*
18997 CAAGTGAATGGCTCAAAACATAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
66 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTA-T
19062 TAATAAATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACA
130 T--T-AATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACA
19127 AAAGGATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCA
192 AAAGGATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCA
19192 AAGACCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATAT
257 AAGACCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATAT
19257 GAACTAGGAACC
322 GAACTAGGAACC
19269 AGAAGTATCA
Statistics
Matches: 326, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
333 123 0.38
334 2 0.01
336 1 0.00
337 200 0.61
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (333 bp):
TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
TAATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATATGAAC
TAGGAACC
Found at i:21296 original size:22 final size:20
Alignment explanation
Indices: 21271--21310 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21261 ATGTTTGTTT
21271 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
21293 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
21311 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:22660 original size:13 final size:13
Alignment explanation
Indices: 22638--22667 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
22628 ACTAAACACC
22638 TTTC-ACATACCT
1 TTTCAACATACCT
22650 TTTCAACATACCT
1 TTTCAACATACCT
22663 TTTCA
1 TTTCA
22668 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:25443 original size:21 final size:22
Alignment explanation
Indices: 25419--25464 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
25409 TTCTTTTCTT
*
25419 TGCTTTTTC-TTCTTTTTTGAG
1 TGCTTTTTCAATCTTTTTTGAG
25440 TGC--TTTCAATCTTTTTTGAG
1 TGCTTTTTCAATCTTTTTTGAG
25460 TGCTT
1 TGCTT
25465 CTTTTTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.61
Consensus pattern (22 bp):
TGCTTTTTCAATCTTTTTTGAG
Found at i:26842 original size:22 final size:20
Alignment explanation
Indices: 26817--26856 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26807 ATGTTTGTTT
26817 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
26839 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
26857 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:30339 original size:23 final size:24
Alignment explanation
Indices: 30297--30349 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
30287 TTTCTTTTTT
30297 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
30321 TTTCTTCTTTT-GAGTGCTTTGAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
30344 TTTCTT
1 TTTCTT
30350 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:36908 original size:15 final size:17
Alignment explanation
Indices: 36872--36905 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
36862 TTTGATAACA
36872 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
36888 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
36904 TT
1 TT
36906 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:40023 original size:350 final size:349
Alignment explanation
Indices: 39356--40055 Score: 1152
Period size: 350 Copynumber: 2.0 Consensus size: 349
39346 CATACTTATA
39356 ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
1 ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
* *
39421 TCATAAATGATAAATGGAAACATGTAATAATAATGTCCTAAGAAATGATATGTAATCATAGCATA
66 TCATAAATGATAAATGGAAACATGTAATAACAATATCCTAAGAAATGATATGTAATCATAGCATA
* * *
39486 TATTTGAATAAAATGAAAAACATGATGAAATAAGCATAGGATGAAAATAATAATATGATAATTTA
131 TATTTAAATAAAATGAAAAACATGATCAAATAAGCATAGGATGAAAATAATAATATGATAACTTA
* *
39551 TACTAACATGTGAATGCATGCTTATGATAGAATATAATGTATAAATGATATAGTATAAGATAGGG
196 TACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGG
* *
39616 TAATGAAGAACTCCCTTAGAAACAACTATGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAA
261 TAATGAAGAACTCCCTTAGAAACAACAATGAAAAACATCCATGGTGTGTTCAAGTCATGGAGAAA
* **
39681 GTTGGAGCTTGTTTGGATCGTATC
326 ATTGGAGCTACTTTGGATCGTATC
* *
39705 ACATTGTTTATCAATCATAAAGATGTGGGTATATGTTGTATGCATGAATATCATATAACATGGTA
1 ACATTGTGTATCAATCATAAAGAT-AGGGTATATGTTGTATGCATGAATATCATATAACATGGTA
*
39770 TTCATAAATGATAAATGGAAACATGTAATTACAATATCCTAAGAAATGATATGTAATCATAGCAT
65 TTCATAAATGATAAATGGAAACATGTAATAACAATATCCTAAGAAATGATATGTAATCATAGCAT
* * * * *
39835 ATATTTAAATGACATGAAAGACTTGATCAACTAAGCATAGGATGAAAATAATAATATGATAACTT
130 ATATTTAAATAAAATGAAAAACATGATCAAATAAGCATAGGATGAAAATAATAATATGATAACTT
39900 ATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGG
195 ATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGG
* * *
39965 GTAA-GAAAGAACTCCCTTAGAATCAGCAATGAAAAACATTCATGGTGTGATT-AAGTCATGGAG
260 GTAATG-AAGAACTCCCTTAGAAACAACAATGAAAAACATCCATGGTGTG-TTCAAGTCATGGAG
40028 AAAATTGGAGCTACTTTGGATCGTATC
323 AAAATTGGAGCTACTTTGGATCGTATC
40055 A
1 A
40056 TCCTCCCCTT
Statistics
Matches: 325, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
349 24 0.07
350 299 0.92
351 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.31
Consensus pattern (349 bp):
ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
TCATAAATGATAAATGGAAACATGTAATAACAATATCCTAAGAAATGATATGTAATCATAGCATA
TATTTAAATAAAATGAAAAACATGATCAAATAAGCATAGGATGAAAATAATAATATGATAACTTA
TACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGG
TAATGAAGAACTCCCTTAGAAACAACAATGAAAAACATCCATGGTGTGTTCAAGTCATGGAGAAA
ATTGGAGCTACTTTGGATCGTATC
Found at i:45886 original size:21 final size:20
Alignment explanation
Indices: 45850--45905 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
45840 GGAGTGCAAA
*
45850 AAGAAAAGAC-AAAAAGAAG
1 AAGAAAAGTCAAAAAAGAAG
*
45869 AAGAAAAATTCAAAAAAGAAG
1 AAG-AAAAGTCAAAAAAGAAG
45890 AAGAAAAGTCAAAAAA
1 AAGAAAAGTCAAAAAA
45906 AGAGAAAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.09
20 17 0.53
21 12 0.38
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.05
Consensus pattern (20 bp):
AAGAAAAGTCAAAAAAGAAG
Found at i:45908 original size:18 final size:19
Alignment explanation
Indices: 45850--45912 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 19
45840 GGAGTGCAAA
*
45850 AAGAAAAGACAAAAAGAAG
1 AAGAAAAGTCAAAAAGAAG
*
45869 AAGAAAAATTCAAAAAAGAAG
1 AAG-AAAAGTC-AAAAAGAAG
45890 AAGAAAAGTCAAAAA-AAG
1 AAGAAAAGTCAAAAAGAAG
45908 -AGAAA
1 AAGAAA
45913 GCAAGCCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.13
18 3 0.08
19 8 0.21
20 11 0.28
21 12 0.31
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (19 bp):
AAGAAAAGTCAAAAAGAAG
Found at i:58634 original size:21 final size:24
Alignment explanation
Indices: 58590--58635 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
58580 GGTTGAAGAT
58590 GATTATTTTAACTTTGAACGTGCA
1 GATTATTTTAACTTTGAACGTGCA
*
58614 GATT-TTTT-ACTTT-AACTTGCA
1 GATTATTTTAACTTTGAACGTGCA
58635 G
1 G
58636 GATGTACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 4 0.19
24 4 0.19
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (24 bp):
GATTATTTTAACTTTGAACGTGCA
Found at i:59154 original size:13 final size:13
Alignment explanation
Indices: 59136--59169 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
59126 GATGATGGTC
59136 TTGATGAAGGATG
1 TTGATGAAGGATG
*
59149 TTGATGATGGATG
1 TTGATGAAGGATG
*
59162 ATGATGAA
1 TTGATGAA
59170 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:67667 original size:11 final size:13
Alignment explanation
Indices: 67635--67664 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
67625 TGGCCAAAGA
67635 TGAAAAGGTATGT
1 TGAAAAGGTATGT
67648 TGAAAAGGTATG-
1 TGAAAAGGTATGT
67660 TGAAA
1 TGAAA
67665 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:71743 original size:13 final size:11
Alignment explanation
Indices: 71702--71787 Score: 68
Period size: 11 Copynumber: 7.3 Consensus size: 11
71692 ACAATCTGTC
71702 CATCACCATTAT
1 CATCACCA-TAT
*
71714 CA-CGCCTATAT
1 CATCACC-ATAT
71725 CATCACCATAGT
1 CATCACCATA-T
71737 CCATCACCATTAT
1 -CATCACCA-TAT
*
71750 CA-CGCCTATAT
1 CATCACC-ATAT
71761 CATCACCATATT
1 CATCACCATA-T
71773 CCATCACCATAT
1 -CATCACCATAT
71785 CAT
1 CAT
71788 GCCTATATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
11 25 0.41
12 15 0.25
13 19 0.31
14 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:71746 original size:36 final size:36
Alignment explanation
Indices: 71699--71803 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
71689 GATACAATCT
71699 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
71735 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
71771 TTCCATCACCA-TATCATGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
71804 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:72006 original size:19 final size:19
Alignment explanation
Indices: 71982--72020 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
71972 TCCTTTCTTA
71982 ATTACTCATTTACTTAACC
1 ATTACTCATTTACTTAACC
72001 ATTACTCATTTACTTAACC
1 ATTACTCATTTACTTAACC
72020 A
1 A
72021 ATCATTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTACTCATTTACTTAACC
Found at i:74647 original size:19 final size:20
Alignment explanation
Indices: 74600--74650 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
74590 GAAACCCCTT
**
74600 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
74620 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
74639 TGAAGATACATG
1 TGAAAATACATG
74651 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:78263 original size:24 final size:24
Alignment explanation
Indices: 78234--78296 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 24
78224 CTAGTGACCT
78234 CTTTTTCTTTTGCCTCTTTCTTAA
1 CTTTTTCTTTTGCCTCTTTCTTAA
*
78258 CTTTTTCTTTTTTTGCCTCTTTCTTAG
1 CTTTTTC---TTTTGCCTCTTTCTTAA
78285 CTTTTTTCTTTT
1 C-TTTTTCTTTT
78297 TTGCTTTCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 7 0.21
25 4 0.12
27 17 0.50
28 6 0.18
ACGTcount: A:0.05, C:0.22, G:0.05, T:0.68
Consensus pattern (24 bp):
CTTTTTCTTTTGCCTCTTTCTTAA
Found at i:78278 original size:27 final size:28
Alignment explanation
Indices: 78241--78298 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
78231 CCTCTTTTTC
78241 TTTTGCCTCTTTCTTAAC-TTTTTCTTT
1 TTTTGCCTCTTTCTTAACTTTTTTCTTT
*
78268 TTTTGCCTCTTTCTTAGCTTTTTTCTTT
1 TTTTGCCTCTTTCTTAACTTTTTTCTTT
78296 TTT
1 TTT
78299 GCTTTCCCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.05, C:0.21, G:0.05, T:0.69
Consensus pattern (28 bp):
TTTTGCCTCTTTCTTAACTTTTTTCTTT
Found at i:79550 original size:33 final size:33
Alignment explanation
Indices: 79508--79576 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
79498 GTTGATGAAT
*
79508 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
79541 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
79574 GAA
1 GAA
79577 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:79581 original size:13 final size:12
Alignment explanation
Indices: 79562--79646 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
79552 TTATTGGCGT
79562 GATATGGTGATG
1 GATATGGTGATG
79574 GAATATGGTGAT-
1 G-ATATGGTGATG
*
79586 GATATAGGCG-T-
1 GATAT-GGTGATG
79597 GATAATGGTGATG
1 GAT-ATGGTGATG
79610 GACTATGGTGAT-
1 GA-TATGGTGATG
79622 GATATAGGCTGAT-
1 GATAT-GG-TGATG
79635 -A-ATGGTGATG
1 GATATGGTGATG
79645 GA
1 GA
79647 CAGATTGTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 21
0.73 0.02 0.25
Matches are distributed among these distances:
9 4 0.07
10 2 0.03
11 17 0.28
12 13 0.21
13 24 0.39
14 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:79647 original size:35 final size:36
Alignment explanation
Indices: 79547--79647 Score: 161
Period size: 35 Copynumber: 2.9 Consensus size: 36
79537 AATGGAAGGA
* * *
79547 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
79582 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
79618 TGATGATATAGGC-TGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
79648 AGATTGTATC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 33 0.53
36 29 0.47
ACGTcount: A:0.27, C:0.05, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:83366 original size:33 final size:32
Alignment explanation
Indices: 83303--83366 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
83293 GGATATGGTT
* *
83303 ATGATAAGGTAGGATAGAAAAAGATTAAGAAAG
1 ATGATAAGGTA-GATAAAAAAAGATAAAGAAAG
83336 ATGATAAGGTA-ATGAAAAAAAGATGAAAGAA
1 ATGATAAGGTAGAT-AAAAAAAGAT-AAAGAA
83367 TAAGAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.07
32 9 0.33
33 16 0.59
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (32 bp):
ATGATAAGGTAGATAAAAAAAGATAAAGAAAG
Found at i:84019 original size:33 final size:33
Alignment explanation
Indices: 83977--84045 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
83967 GTTGATGAAT
*
83977 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
84010 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
84043 GAA
1 GAA
84046 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:84090 original size:36 final size:36
Alignment explanation
Indices: 84016--84117 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
84006 AATGGAAGGA
* * * *
84016 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATCG
*
84051 TGATGATATAGGCGTGATAATGGTGATGGACTATCG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATCG
84087 TGATGATATAGGCGTGATAATGGTGATGGAA
1 TGATGATATAGGCGTGATAATGGTGATGGAA
84118 AGATTGTATC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.27
36 44 0.73
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATCG
Done.