Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001548.1 Hibiscus syriacus cultivar Beakdansim tig00003044_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: 71690
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:781 original size:208 final size:205
Alignment explanation
Indices: 426--816 Score: 719
Period size: 208 Copynumber: 1.9 Consensus size: 205
416 TACTTGCTAC
* *
426 GTTTGTACAACTTCCTCCATCAATGATCACCACGCAAATTTTATCTTCCTGACATTTGGTATGGA
1 GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTTCCTGACATTTGGTATGGA
*
491 AGATGTTCTCTCTTTGTTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAGATG
66 AGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAGATG
556 TTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGACTTTGAAGATGTT
131 TTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGACTTTGAAGATGTT
621 CAAAGTCCTT
196 CAAAGTCCTT
631 GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTTCCACGTGACATTTGGTAT
1 GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTT-C-C-TGACATTTGGTAT
*
696 GGAAGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACTACAAAG
63 GGAAGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAG
761 ATGTTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGAC
128 ATGTTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGAC
817 CTTATTAGAA
Statistics
Matches: 179, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
205 45 0.25
206 1 0.01
207 1 0.01
208 132 0.74
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (205 bp):
GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTTCCTGACATTTGGTATGGA
AGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAGATG
TTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGACTTTGAAGATGTT
CAAAGTCCTT
Found at i:1250 original size:15 final size:15
Alignment explanation
Indices: 1215--1243 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1205 GTGCTTCAAC
1215 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
1229 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
1244 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:4000 original size:43 final size:45
Alignment explanation
Indices: 3925--4028 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 45
3915 AGGATTAGAT
* *
3925 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAATTATCTTTAG-TTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAA-CATCTTTAGTTTA
* *
3973 TTATTATTTTATTAGGAATT-A-GAGTTAAGACATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACATCTTTAGTTTA
4016 TTATTATTTTATT
1 TTATTATTTTATT
4029 CATTAGTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
42 7 0.14
43 23 0.45
47 1 0.02
48 20 0.39
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACATCTTTAGTTTA
Found at i:6381 original size:16 final size:16
Alignment explanation
Indices: 6360--6398 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6350 AAGATATGGT
6360 AATGAAACAAGAAAAA
1 AATGAAACAAGAAAAA
* * *
6376 AATGAAAGAATAAAGA
1 AATGAAACAAGAAAAA
6392 AATGAAA
1 AATGAAA
6399 TAGTAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (16 bp):
AATGAAACAAGAAAAA
Found at i:6679 original size:21 final size:20
Alignment explanation
Indices: 6617--6679 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
6607 AGTCTCTTCT
* *
6617 TTCTCTTTTTTTTGTTTTTC
1 TTCTTTTTTTTTTGTTTTTG
* *
6637 TTCTTTCTTTTTCTCTTTTTG
1 TTCTTT-TTTTTTTGTTTTTG
*
6658 TTGCTTTTTTTTTTGTTGTTG
1 TT-CTTTTTTTTTTGTTTTTG
6679 T
1 T
6680 AGCACTTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 5 0.15
21 25 0.74
22 4 0.12
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.78
Consensus pattern (20 bp):
TTCTTTTTTTTTTGTTTTTG
Found at i:8265 original size:33 final size:33
Alignment explanation
Indices: 8186--8289 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
8176 ATACAATCTG
* *
8186 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
8222 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
8255 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
8288 TC
1 TC
8290 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:13943 original size:33 final size:33
Alignment explanation
Indices: 13864--13967 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
13854 ATACAATCTG
* *
13864 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
13900 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
13933 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
13966 TC
1 TC
13968 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:16606 original size:91 final size:91
Alignment explanation
Indices: 16446--16628 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
16436 GGTAGTTGAT
* * *
16446 GCTTGGCCGAATAGGGAGGGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATA
16511 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* *
16537 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCGCATA
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATA
* * **
16602 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGATCACATGCAAAACACATG
16628 G
1 G
16629 GTGTTCTAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATA
GGGGCTGATCACATGCAAAACACATG
Found at i:18445 original size:11 final size:13
Alignment explanation
Indices: 18413--18442 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18403 TGGCCAAAGA
18413 TGAAAAGGTATGT
1 TGAAAAGGTATGT
18426 TGAAAAGGTATG-
1 TGAAAAGGTATGT
18438 TGAAA
1 TGAAA
18443 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:27685 original size:24 final size:23
Alignment explanation
Indices: 27658--27713 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
27648 CAAAGAAAGC
27658 AAGAA-AAATCAGAAAAGCACTCAA
1 AAGAAGAAAT-AG-AAAGCACTCAA
*
27682 AAGAAGAAATTGAAAGCACTCAA
1 AAGAAGAAATAGAAAGCACTCAA
27705 AAGAAGAAA
1 AAGAAGAAA
27714 AAAGAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 20 0.67
24 6 0.20
25 4 0.13
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.09
Consensus pattern (23 bp):
AAGAAGAAATAGAAAGCACTCAA
Found at i:30496 original size:11 final size:13
Alignment explanation
Indices: 30464--30493 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30454 TGCCCAAAGA
30464 TGAAAAGGTATGT
1 TGAAAAGGTATGT
30477 TGAAAAGGTATG-
1 TGAAAAGGTATGT
30489 TGAAA
1 TGAAA
30494 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:33288 original size:11 final size:12
Alignment explanation
Indices: 33267--33315 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
33257 TTGAGAATTT
33267 GGTGATGATATA
1 GGTGATGATATA
33279 GGTG-TGATAT-
1 GGTGATGATATA
*
33289 GATGATGGACTAT-
1 GGTGAT-GA-TATA
33302 GGTGATGATATA
1 GGTGATGATATA
33314 GG
1 GG
33316 CGTGATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 10 0.32
12 10 0.32
13 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:33312 original size:35 final size:37
Alignment explanation
Indices: 33266--33345 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
33256 TTTGAGAATT
* *
33266 TGGTGATGATATAGGTGTGAT-AT-GATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
33301 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
33338 TGGTGATG
1 TGGTGATG
33346 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 2 0.05
37 18 0.45
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:33707 original size:19 final size:19
Alignment explanation
Indices: 33683--33751 Score: 102
Period size: 19 Copynumber: 3.6 Consensus size: 19
33673 GAAACCCCTT
33683 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTGA
33702 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTGA
* **
33721 TGAAAATACACGATTTAAA
1 TGAAAATACATGATTTTGA
*
33740 TGAAGATACATG
1 TGAAAATACATG
33752 CTCTTGGCCG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (19 bp):
TGAAAATACATGATTTTGA
Found at i:36879 original size:20 final size:20
Alignment explanation
Indices: 36841--36878 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36831 TGCTTCACTT
*
36841 TTCTTTTGCTTTTGATTTTC
1 TTCTTTTGCTTTTCATTTTC
*
36861 TTCTTTTTCTTTTC-TTTT
1 TTCTTTTGCTTTTCATTTT
36879 TTTTGCACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (20 bp):
TTCTTTTGCTTTTCATTTTC
Found at i:37373 original size:35 final size:37
Alignment explanation
Indices: 37327--37406 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
37317 TTTGAGAATT
*
37327 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
37362 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
37399 TGGTGATG
1 TGGTGATG
37407 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:40780 original size:8 final size:8
Alignment explanation
Indices: 40767--40822 Score: 69
Period size: 9 Copynumber: 6.8 Consensus size: 8
40757 TATTTTTTTT
40767 AAAAAACA
1 AAAAAACA
*
40775 AAAAAAGGA
1 AAAAAA-CA
40784 AAAAAA-A
1 AAAAAACA
40791 AAAAAACA
1 AAAAAACA
40799 AAAAAACAA
1 AAAAAAC-A
40808 AAAAAACA
1 AAAAAACA
40816 CAAAAAA
1 -AAAAAA
40823 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
7 7 0.16
8 15 0.35
9 21 0.49
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:40796 original size:24 final size:23
Alignment explanation
Indices: 40767--40813 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
40757 TATTTTTTTT
*
40767 AAAAAACAAAAAAAGGAAAAAAAA
1 AAAAAACAAAAAAA-CAAAAAAAA
40791 AAAAAACAAAAAAACAAAAAAAA
1 AAAAAACAAAAAAACAAAAAAAA
40814 CACAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.89, C:0.06, G:0.04, T:0.00
Consensus pattern (23 bp):
AAAAAACAAAAAAACAAAAAAAA
Found at i:40813 original size:17 final size:17
Alignment explanation
Indices: 40767--40822 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
40757 TATTTTTTTT
**
40767 AAAAAAC-AAAAAAAGG
1 AAAAAACAAAAAAAACA
40783 AAAAAA-AAAAAAAACA
1 AAAAAACAAAAAAAACA
40799 AAAAAACAAAAAAAACA
1 AAAAAACAAAAAAAACA
40816 CAAAAAA
1 -AAAAAA
40823 GCCAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 19 0.54
17 10 0.29
18 6 0.17
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAAAAAACA
Found at i:40814 original size:9 final size:9
Alignment explanation
Indices: 40783--40822 Score: 57
Period size: 8 Copynumber: 4.6 Consensus size: 9
40773 CAAAAAAAGG
40783 AAAAAA-AA
1 AAAAAACAA
40791 AAAAAAC-A
1 AAAAAACAA
40799 AAAAAACAA
1 AAAAAACAA
40808 AAAAAACACA
1 AAAAAACA-A
40818 AAAAA
1 AAAAA
40823 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 14 0.48
9 9 0.31
10 6 0.21
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:40828 original size:9 final size:9
Alignment explanation
Indices: 40767--40829 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 9
40757 TATTTTTTTT
40767 AAAAAA-CA
1 AAAAAACCA
**
40775 AAAAAAGGA
1 AAAAAACCA
40784 AAAAAA--A
1 AAAAAACCA
40791 AAAAAA-CA
1 AAAAAACCA
*
40799 AAAAAACAA
1 AAAAAACCA
40808 AAAAAACACA
1 AAAAAAC-CA
*
40818 AAAAAGCCA
1 AAAAAACCA
40827 AAA
1 AAA
40830 TTTCAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
7 7 0.15
8 13 0.28
9 20 0.43
10 7 0.15
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAACCA
Found at i:40829 original size:19 final size:19
Alignment explanation
Indices: 40783--40822 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40773 CAAAAAAAGG
40783 AAAA-AAAAAAAAAACAAA
1 AAAACAAAAAAAAAACAAA
*
40801 AAAACAAAAAAAACACAAA
1 AAAACAAAAAAAAAACAAA
40820 AAA
1 AAA
40823 GCCAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAAAAAACAAA
Found at i:44936 original size:15 final size:16
Alignment explanation
Indices: 44909--44945 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
44899 CTTTATTATC
44909 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
44925 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
44940 TTATTT
1 TTATTT
44946 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:47309 original size:9 final size:9
Alignment explanation
Indices: 47297--47328 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
47287 AAAAAAAGGG
47297 AAAAAACAA
1 AAAAAACAA
47306 AAAAACACAA
1 AAAAA-ACAA
47316 AAAAAACAA
1 AAAAAACAA
47325 AAAA
1 AAAA
47329 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:47317 original size:17 final size:16
Alignment explanation
Indices: 47274--47328 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
47264 GCTATTTTTT
47274 AAAAACAAAAAACAAA
1 AAAAACAAAAAACAAA
**
47290 AAAAGGGAAAAAACAAA
1 AAAA-ACAAAAAACAAA
47307 AAAACACAAAAAA-AACA
1 AAAA-ACAAAAAACAA-A
47324 AAAAA
1 AAAAA
47329 GCCAAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 7 0.22
17 25 0.78
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAACAAA
Found at i:50764 original size:12 final size:11
Alignment explanation
Indices: 50749--50802 Score: 72
Period size: 12 Copynumber: 4.7 Consensus size: 11
50739 AAATTTTGGC
50749 TTTTTTTGCTT
1 TTTTTTTGCTT
*
50760 TTTTTTGTGCCT
1 TTTTTT-TGCTT
*
50772 TTTTTTTACTT
1 TTTTTTTGCTT
50783 TTTTTTTGCCTT
1 TTTTTTTG-CTT
50795 TTTTTTTG
1 TTTTTTTG
50803 AAAAAAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 16 0.43
12 21 0.57
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:50773 original size:22 final size:21
Alignment explanation
Indices: 50742--50799 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 21
50732 TTTTTTGAAA
* *
50742 TTTTGGCTTTTTTTGCTTTTT
1 TTTTGCCTTTTTTTACTTTTT
50763 TTTGTGCCTTTTTTTTACTTTTT
1 TTT-TGCC-TTTTTTTACTTTTT
50786 TTTTGCCTTTTTTT
1 TTTTGCCTTTTTTT
50800 TTGAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.30
22 7 0.21
23 16 0.48
ACGTcount: A:0.02, C:0.12, G:0.10, T:0.76
Consensus pattern (21 bp):
TTTTGCCTTTTTTTACTTTTT
Found at i:50800 original size:22 final size:23
Alignment explanation
Indices: 50749--50800 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
50739 AAATTTTGGC
*
50749 TTTTTTTGCTTTTTTTTGTGCCT
1 TTTTTTTACTTTTTTTTGTGCCT
50772 TTTTTTTACTTTTTTTT-TGCCT
1 TTTTTTTACTTTTTTTTGTGCCT
50794 TTTTTTT
1 TTTTTTT
50801 TGAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.79
Consensus pattern (23 bp):
TTTTTTTACTTTTTTTTGTGCCT
Found at i:56600 original size:22 final size:22
Alignment explanation
Indices: 56575--56616 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56565 CAAAAAAAAA
*
56575 ACAAAAAAAGGAAAAAAAAGGC
1 ACAAAAAAAAGAAAAAAAAGGC
*
56597 ACAAAAAAAAGCAAAAAAAG
1 ACAAAAAAAAGAAAAAAAAG
56617 CCAAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (22 bp):
ACAAAAAAAAGAAAAAAAAGGC
Found at i:66383 original size:10 final size:10
Alignment explanation
Indices: 66368--66407 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
66358 GGCTTTCTTT
66368 CTTTTTTTGC
1 CTTTTTTTGC
66378 CTTTTTTTTTGC
1 C--TTTTTTTGC
*
66390 TTTTTTTTGC
1 CTTTTTTTGC
66400 CTTTTTTT
1 CTTTTTTT
66408 TGTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 17 0.65
12 9 0.35
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (10 bp):
CTTTTTTTGC
Found at i:66397 original size:22 final size:20
Alignment explanation
Indices: 66369--66417 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 20
66359 GCTTTCTTTC
66369 TTTTTTTGCCTTTTTTTTTGCT
1 TTTTTTTGCC-TTTTTTTTG-T
66391 TTTTTTTGCCTTTTTTTTGT
1 TTTTTTTGCCTTTTTTTTGT
66411 TTTTTTT
1 TTTTTTT
66418 AAAATAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 8 0.30
21 9 0.33
22 10 0.37
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (20 bp):
TTTTTTTGCCTTTTTTTTGT
Found at i:66414 original size:10 final size:11
Alignment explanation
Indices: 66369--66417 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
66359 GCTTTCTTTC
66369 TTTTTTTGCCTT
1 TTTTTTTGCC-T
66381 TTTTTTTG-CT
1 TTTTTTTGCCT
66391 TTTTTTTGCCT
1 TTTTTTTGCCT
66402 TTTTTTTG--T
1 TTTTTTTGCCT
66411 TTTTTTT
1 TTTTTTT
66418 AAAATAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.22
10 9 0.25
11 11 0.31
12 8 0.22
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:67496 original size:10 final size:10
Alignment explanation
Indices: 67473--67532 Score: 59
Period size: 11 Copynumber: 5.7 Consensus size: 10
67463 TTTTTTCAAA
**
67473 AAAAAAAACA
1 AAAAAAAAGG
67483 AAAAAAAAGG
1 AAAAAAAAGG
67493 -AAAAAAAGG
1 AAAAAAAAGG
67502 TAAAAAAAAGG
1 -AAAAAAAAGG
67513 CACAAAAAAATGG
1 -A-AAAAAAA-GG
67526 AAAAAAA
1 AAAAAAA
67533 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
9 9 0.21
10 8 0.19
11 16 0.37
12 8 0.19
13 2 0.05
ACGTcount: A:0.78, C:0.05, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGG
Done.