Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002101.1 Hibiscus syriacus cultivar Beakdansim tig00004299_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: 128084
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1885 original size:16 final size:16
Alignment explanation
Indices: 1848--1900 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1838 AAAATATGGC
1848 AATGAAAT-A-AAAAA
1 AATGAAATGATAAAAA
*
1862 AGATGAAA-GAATAAAGA
1 A-ATGAAATG-ATAAAAA
1879 AATGAAATGATAAAAA
1 AATGAAATGATAAAAA
1895 AATGAA
1 AATGAA
1901 GATACTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 19 0.59
17 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (16 bp):
AATGAAATGATAAAAA
Found at i:2539 original size:13 final size:12
Alignment explanation
Indices: 2520--2605 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
2510 ATATAGGCGT
2520 GATATGGTGATG
1 GATATGGTGATG
2532 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2544 GATATAGGCG-T-
1 GATAT-GGTGATG
2555 GATAATGGTGATG
1 GAT-ATGGTGATG
2568 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2580 GATATAGGCG-T-
1 GATAT-GGTGATG
2591 GATAATGGTGATG
1 GAT-ATGGTGATG
2604 GA
1 GA
2606 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2575 original size:36 final size:36
Alignment explanation
Indices: 2502--2606 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
2492 ATTTATAAGT
* *
2502 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2537 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2573 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
2607 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:2991 original size:19 final size:20
Alignment explanation
Indices: 2944--2992 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2934 GAAACCCCTT
**
2944 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2964 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2983 TGAAGATACA
1 TGAAAATACA
2993 GCTCTTGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:7282 original size:18 final size:18
Alignment explanation
Indices: 7259--7301 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
7249 CCTTATTAAG
7259 GATGAAGGATAATTCAAA
1 GATGAAGGATAATTCAAA
7277 GATGAAGGATAATTCAAA
1 GATGAAGGATAATTCAAA
7295 GATGAAG
1 GATGAAG
7302 AAATGGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.21
Consensus pattern (18 bp):
GATGAAGGATAATTCAAA
Found at i:7354 original size:13 final size:12
Alignment explanation
Indices: 7335--7422 Score: 62
Period size: 13 Copynumber: 7.3 Consensus size: 12
7325 ATATAGGCGT
7335 GATATGGTGATG
1 GATATGGTGATG
7347 GAATATGGTGAT-
1 G-ATATGGTGATG
*
7359 GATATAGGCG-T-
1 GATAT-GGTGATG
7370 GATAATGGTGATG
1 GAT-ATGGTGATG
7383 GACTATGGTGAT-
1 GA-TATGGTGATG
*
7395 GATATAGGCG-T-
1 GATAT-GGTGATG
7406 GATAATGGTGATG
1 GAT-ATGGTGATG
7419 GATA
1 GATA
7423 AATTGTATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.34
12 17 0.27
13 23 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:7390 original size:36 final size:36
Alignment explanation
Indices: 7323--7420 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
7313 TATAAGTTGG
7323 TGATATAGGCGTGAT-ATGGTGATGGAATATGGTGA
1 TGATATAGGCGTGATAATGGTGATGGAATATGGTGA
*
7358 TGATATAGGCGTGATAATGGTGATGGACTATGGTGA
1 TGATATAGGCGTGATAATGGTGATGGAATATGGTGA
7394 TGATATAGGCGTGATAATGGTGATGGA
1 TGATATAGGCGTGATAATGGTGATGGA
7421 TAAATTGTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
35 15 0.25
36 46 0.75
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (36 bp):
TGATATAGGCGTGATAATGGTGATGGAATATGGTGA
Found at i:19865 original size:22 final size:20
Alignment explanation
Indices: 19822--19866 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
19812 TGTAGGAGTC
* *
19822 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGCTT
19842 TTTTTCTTCTTTCTTGTTGCTT
1 TTTTTC-T-TTTCTTGTTGCTT
19864 TTT
1 TTT
19867 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGCTT
Found at i:20225 original size:18 final size:18
Alignment explanation
Indices: 20202--20246 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
20192 CCTTGTTGAG
*
20202 GATGAAGGATAATTCAAA
1 GATGAAGAATAATTCAAA
20220 GATGAAGAATAATTCAAA
1 GATGAAGAATAATTCAAA
20238 GATGAAGAA
1 GATGAAGAA
20247 ATGGAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (18 bp):
GATGAAGAATAATTCAAA
Found at i:20300 original size:13 final size:12
Alignment explanation
Indices: 20281--20366 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
20271 ATATAGGCGT
20281 GATATGGTGATG
1 GATATGGTGATG
20293 GAATATGGTGAT-
1 G-ATATGGTGATG
*
20305 GATATAGGCG-T-
1 GATAT-GGTGATG
20316 GATAATGGTGATG
1 GAT-ATGGTGATG
20329 GACTATGGTGAT-
1 GA-TATGGTGATG
*
20341 GATATAGGCG-T-
1 GATAT-GGTGATG
20352 GATAATGGTGATG
1 GAT-ATGGTGATG
20365 GA
1 GA
20367 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:20336 original size:36 final size:36
Alignment explanation
Indices: 20263--20367 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
20253 ATTTATAAGT
* *
20263 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
20298 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
20334 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
20368 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:27421 original size:18 final size:18
Alignment explanation
Indices: 27400--27442 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
27390 TTTTGGCTTT
**
27400 TTTTTTTGTTTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
27418 TTTTTTTGCCTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
27436 TTTTTTT
1 TTTTTTT
27443 TTTGGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTG
Found at i:27431 original size:31 final size:30
Alignment explanation
Indices: 27388--27445 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
27378 AAATTTTGGC
* *
27388 TTTTTTGGCTTTTTTTTTTGTTTTTTTTTGT
1 TTTTTTGCCTTTTTTTGTT-TTTTTTTTTGT
27419 TTTTTTGCCTTTTTTTGTTTTTTTTTT
1 TTTTTTGCCTTTTTTTGTTTTTTTTTT
27446 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.84
Consensus pattern (30 bp):
TTTTTTGCCTTTTTTTGTTTTTTTTTTTGT
Found at i:27441 original size:10 final size:10
Alignment explanation
Indices: 27398--27444 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
27388 TTTTTTGGCT
27398 TTTTTTTTTG
1 TTTTTTTTTG
27408 TTTTTTTTTG
1 TTTTTTTTTG
27418 --TTTTTTTG
1 TTTTTTTTTG
**
27426 CCTTTTTTTG
1 TTTTTTTTTG
27436 TTTTTTTTT
1 TTTTTTTTT
27445 TGGAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 8 0.24
10 25 0.76
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:30172 original size:13 final size:11
Alignment explanation
Indices: 30131--30215 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
30121 ACAATCTGTC
30131 CATCACCATTAT
1 CATCACCA-TAT
*
30143 CA-CGCCTATAT
1 CATCACC-ATAT
30154 CATCACCATAGT
1 CATCACCATA-T
30166 CCATCACCATTAT
1 -CATCACCA-TAT
*
30179 CATGC-CTATAT
1 CAT-CACCATAT
30190 CATCACCATATT
1 CATCACCATA-T
30202 CCATCACCATAT
1 -CATCACCATAT
30214 CA
1 CA
30216 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:30175 original size:36 final size:36
Alignment explanation
Indices: 30128--30232 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
30118 GATACAATCT
30128 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
30164 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
30200 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
30233 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:30714 original size:14 final size:15
Alignment explanation
Indices: 30680--30726 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
30670 AATTTGGAGT
30680 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
30695 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
30709 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
30726 G
1 G
30727 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:36978 original size:35 final size:36
Alignment explanation
Indices: 36884--36988 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
36874 GATACAATCT
36884 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
36920 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
36956 TTCCTTCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
36989 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:56776 original size:26 final size:26
Alignment explanation
Indices: 56738--56792 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
56728 CTCAATTATT
56738 GAAGAAGCCTGGTTAGCCA-TACATCA
1 GAAGAAGCCTGGTTAG-CAGTACATCA
** *
56764 GAAGAAGTTTGGTTAGTAGTACATCA
1 GAAGAAGCCTGGTTAGCAGTACATCA
56790 GAA
1 GAA
56793 CCACAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (26 bp):
GAAGAAGCCTGGTTAGCAGTACATCA
Found at i:63158 original size:13 final size:11
Alignment explanation
Indices: 63117--63201 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
63107 ACAATCTGTC
63117 CATCACCATTAT
1 CATCACCA-TAT
*
63129 CATGC-CTATAT
1 CAT-CACCATAT
63140 CATCACCATAGT
1 CATCACCATA-T
63152 CCATCACCATTAT
1 -CATCACCA-TAT
*
63165 CA-CGCCTATAT
1 CATCACC-ATAT
63176 CATCACCATATT
1 CATCACCATA-T
63188 CCATCACCATAT
1 -CATCACCATAT
63200 CA
1 CA
63202 CGCCGATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:63161 original size:36 final size:36
Alignment explanation
Indices: 63114--63218 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
63104 GATACAATCT
*
63114 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
63150 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
63186 TTCCATCACCA-TATCACGCCGATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
63219 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:63687 original size:14 final size:15
Alignment explanation
Indices: 63653--63699 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
63643 AATTTGGAGT
63653 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
63668 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
63682 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
63699 G
1 G
63700 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:68797 original size:13 final size:11
Alignment explanation
Indices: 68756--68840 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
68746 ACAATCTGTC
68756 CATCACCATTAT
1 CATCACCA-TAT
*
68768 CA-CGCCTATAT
1 CATCACC-ATAT
68779 CATCACCATAGT
1 CATCACCATA-T
68791 CCATCACCATTAT
1 -CATCACCA-TAT
*
68804 CA-CGCCTATAT
1 CATCACC-ATAT
68815 CATCACCATATT
1 CATCACCATA-T
68827 CCATCACCATAT
1 -CATCACCATAT
68839 CA
1 CA
68841 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:68800 original size:36 final size:36
Alignment explanation
Indices: 68753--68857 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
68743 GATACAATCT
68753 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
68789 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
68825 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
68858 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:71465 original size:90 final size:91
Alignment explanation
Indices: 71310--71483 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 91
71300 CCTAGAACAC
* * *
71310 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTTCATGAGGATCATTTAGGCGCCAGGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
71375 AAGAGT-TATCTCCCTATTCGGCCAAG
66 AAGA-TCTATCTCCCTATTCGGCCAAG
** * * * *
71401 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
71465 AAGATCTCTCTCCCTATTC
66 AAGATCTATCTCCCTATTC
71484 AGCTAAGCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
89 1 0.01
90 52 0.72
91 19 0.26
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGATCTATCTCCCTATTCGGCCAAG
Found at i:72300 original size:23 final size:24
Alignment explanation
Indices: 72272--72325 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
72262 AAAATCAGCA
72272 AAGAAAATAAAAGCACT-CAAAAG
1 AAGAAAATAAAAGCACTCCAAAAG
* * *
72295 AAGAAATTGAGAGCACTCCAAAAG
1 AAGAAAATAAAAGCACTCCAAAAG
*
72319 AATAAAA
1 AAGAAAA
72326 AGAAAGAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.61, C:0.13, G:0.15, T:0.11
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCCAAAAG
Found at i:75723 original size:26 final size:26
Alignment explanation
Indices: 75687--75752 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
75677 CTAGAATATA
75687 CATGTGCCTTGCATATGACCAGCCCC
1 CATGTGCCTTGCATATGACCAGCCCC
75713 CATGTGCCTTGCATATGACCAGCCCC
1 CATGTGCCTTGCATATGACCAGCCCC
75739 CATGTGCCTTGCAT
1 CATGTGCCTTGCAT
75753 GAGGATCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.18, C:0.36, G:0.20, T:0.26
Consensus pattern (26 bp):
CATGTGCCTTGCATATGACCAGCCCC
Found at i:75867 original size:90 final size:91
Alignment explanation
Indices: 75721--75892 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 91
75711 CCCATGTGCC
* *
75721 TTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAG-TTC
1 TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTT-
*
75785 TCTCCCTATTTGGCCAAGACATGTGTT
65 TCTCCCTATTCGGCCAAGACATGTGTT
* * * *
75812 TTGCATGTGAACAG-CCCCATATGCCTTGCATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTTT
1 TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTTT
75876 CTCCCTATTCGGCCAAG
66 CTCCCTATTCGGCCAAG
75893 CATCATTTCC
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
90 59 0.81
91 14 0.19
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (91 bp):
TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTTT
CTCCCTATTCGGCCAAGACATGTGTT
Found at i:78150 original size:36 final size:36
Alignment explanation
Indices: 78103--78207 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
78093 GATACAATCT
78103 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
78139 GTCCATCACCATTATCACGCCTACATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
78175 TTCCATCACCA-AATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
78208 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.31, C:0.37, G:0.05, T:0.27
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:78686 original size:14 final size:15
Alignment explanation
Indices: 78652--78698 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
78642 AATTTGGAGT
78652 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
78667 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
78681 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
78698 G
1 G
78699 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:83866 original size:36 final size:36
Alignment explanation
Indices: 83819--83923 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
83809 GATACAATCT
83819 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
83855 GTCCATCACCATTATCACGCCTACATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
83891 TTCCATCACCA-AATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
83924 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.31, C:0.37, G:0.05, T:0.27
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:86007 original size:91 final size:91
Alignment explanation
Indices: 85832--86012 Score: 240
Period size: 91 Copynumber: 2.0 Consensus size: 91
85822 CCTAGAACAC
* *
85832 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTTCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATG
** *
85897 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGACATCTATCCCTATTCGGCCAAG
** * * *
85923 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATG
85988 AATGACCATCTAT-CC-ATTCGGCCAA
66 AA-GA-CATCTATCCCTATTCGGCCAA
86013 ACATCATTAC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
91 70 0.90
92 4 0.05
93 4 0.05
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATG
AAGACATCTATCCCTATTCGGCCAAG
Found at i:91629 original size:14 final size:13
Alignment explanation
Indices: 91612--91661 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
91602 GTGCAAAAAG
91612 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
91626 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
91639 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
91650 AAAGAAAAAGAA
1 AAAGAAAAAGAA
91662 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:91658 original size:19 final size:18
Alignment explanation
Indices: 91606--91661 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
91596 ATTGGAGTGC
91606 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
91623 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
91642 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
91661 A
1 A
91662 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:91659 original size:11 final size:11
Alignment explanation
Indices: 91606--91661 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
91596 ATTGGAGTGC
91606 AAAAAG-AAAG
1 AAAAAGAAAAG
91616 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
91630 AAGAAGAAAAG
1 AAAAAGAAAAG
91641 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
91654 AAAAAGAA
1 AAAAAGAA
91662 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:100252 original size:24 final size:21
Alignment explanation
Indices: 100218--100260 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
100208 TGCACAAGAT
*
100218 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
100240 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
100261 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:102126 original size:91 final size:91
Alignment explanation
Indices: 101960--102128 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 91
101950 CACATGTGCC
* ** **
101960 TTGCATATGACCAGCCCCCATGTGTCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATACGGATCATTTAGGCGCCAAGATGAAGACATCT
*
102025 CTCCCTATTCGGCCAAGCCATGTGTT
66 ATCCCTATTCGGCCAAGCCATGTGTT
* * *
102051 TTGCATGTGATCAGCCCCCATGTGCCTTGCATACGGTTCATTTAGGCGCCAAGATGAATGGACAT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATACGGATCATTTAGGCGCCAAGATGAA--GACAT
102116 CTAT-CC-ATTCGGC
64 CTATCCCTATTCGGC
102129 AAAACACCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
91 59 0.88
92 2 0.03
93 6 0.09
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCATACGGATCATTTAGGCGCCAAGATGAAGACATCT
ATCCCTATTCGGCCAAGCCATGTGTT
Found at i:103431 original size:19 final size:20
Alignment explanation
Indices: 103390--103440 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
103380 GAAACCCCTT
*
103390 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
103410 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
103429 TGAAGATACATG
1 TGAAAATACATG
103441 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:104389 original size:30 final size:31
Alignment explanation
Indices: 104349--104408 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
104339 ACATGCTGCC
**
104349 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
104380 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
104409 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:106814 original size:19 final size:19
Alignment explanation
Indices: 106792--106847 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
106782 TTTGAACTTC
106792 TCTTTTTCTTTTCTTTTCT
1 TCTTTTTCTTTTCTTTTCT
*
106811 TC-TTTTCTGATTT-TTCTCT
1 TCTTTTTCT--TTTCTTTTCT
106830 TCTTTTTGTCTTTTCTTT
1 TC-TTTT-TCTTTTCTTT
106848 CTTTTTGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.21
19 9 0.31
20 6 0.21
21 5 0.17
22 3 0.10
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.75
Consensus pattern (19 bp):
TCTTTTTCTTTTCTTTTCT
Found at i:106847 original size:13 final size:12
Alignment explanation
Indices: 106789--106847 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 12
106779 CTTTTTGAAC
106789 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
106802 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
*
106815 TTCTGATTTTTCTC
1 TTCT--TTTTTCTT
106829 TTCTTTTTGTCTT
1 TTCTTTTT-TCTT
106842 TTCTTT
1 TTCTTT
106848 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.17
13 22 0.55
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:106851 original size:17 final size:18
Alignment explanation
Indices: 106778--106854 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 18
106768 GCTTGCTTTC
* *
106778 TCTTTTTGAACTTCTCTT
1 TCTTTTTGATCTTTTCTT
106796 T-TTCTTT--TCTTTTC-T
1 TCTT-TTTGATCTTTTCTT
106811 TCTTTTCTGAT-TTTTCTCT
1 TCTTTT-TGATCTTTTCT-T
106830 TCTTTTTG-TCTTTTCTT
1 TCTTTTTGATCTTTTCTT
106847 TCTTTTTG
1 TCTTTTTG
106855 CACTCCAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
15 4 0.08
16 8 0.16
17 17 0.35
18 13 0.27
19 7 0.14
ACGTcount: A:0.04, C:0.19, G:0.05, T:0.71
Consensus pattern (18 bp):
TCTTTTTGATCTTTTCTT
Found at i:106852 original size:27 final size:27
Alignment explanation
Indices: 106794--106845 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
106784 TGAACTTCTC
*
106794 TTTTTCTTTTCTTTTCTTCTTTTCTGA
1 TTTTTCTCTTCTTTTCTTCTTTTCTGA
106821 TTTTTCTCTTCTTTT-TGTCTTTTCT
1 TTTTTCTCTTCTTTTCT-TCTTTTCT
106846 TTCTTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTTCTCTTCTTTTCTTCTTTTCTGA
Found at i:107594 original size:19 final size:20
Alignment explanation
Indices: 107553--107603 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
107543 GAAACCTCTT
*
107553 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
107573 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
107592 TGAAGATACATG
1 TGAAAATACATG
107604 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:107944 original size:24 final size:24
Alignment explanation
Indices: 107895--107944 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
107885 TCAAGGTAAG
* *
107895 CTAGGTGAGTGTCTTGGTAGATAA
1 CTAGGTGAGTGTATAGGTAGATAA
*
107919 CTAGGTGAGT-TATAGGTTGATGAA
1 CTAGGTGAGTGTATAGGTAGAT-AA
107943 CT
1 CT
107945 CAAGCTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.26, C:0.08, G:0.32, T:0.34
Consensus pattern (24 bp):
CTAGGTGAGTGTATAGGTAGATAA
Found at i:108553 original size:30 final size:31
Alignment explanation
Indices: 108513--108572 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
108503 ACATGCTGCC
**
108513 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
108544 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
108573 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:109729 original size:20 final size:20
Alignment explanation
Indices: 109704--109752 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
109694 TATATTCATC
109704 TCCATTACCTTCATTCTACT
1 TCCATTACCTTCATTCTACT
109724 TCCATTACCTTCATTCTACT
1 TCCATTACCTTCATTCTACT
109744 TCCATTACC
1 TCCATTACC
109753 ATACTTCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (20 bp):
TCCATTACCTTCATTCTACT
Found at i:113263 original size:20 final size:20
Alignment explanation
Indices: 113238--113286 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
113228 TATATTCATC
113238 TCCATTACCTTCATTCTACT
1 TCCATTACCTTCATTCTACT
113258 TCCATTACCTTCATTCTACT
1 TCCATTACCTTCATTCTACT
113278 TCCATTACC
1 TCCATTACC
113287 ATACTTCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (20 bp):
TCCATTACCTTCATTCTACT
Found at i:116830 original size:24 final size:20
Alignment explanation
Indices: 116775--116821 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
116765 TATTCATCTC
116775 CATTACCTTCATTCTACTTA
1 CATTACCTTCATTCTACTTA
*
116795 CATTACCTTCATTCTACTTC
1 CATTACCTTCATTCTACTTA
116815 CATTACC
1 CATTACC
116822 ATACTTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (20 bp):
CATTACCTTCATTCTACTTA
Done.