Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001283.1 Hibiscus syriacus cultivar Beakdansim tig00002517_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: 94573
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4950 original size:5 final size:5
Alignment explanation
Indices: 4940--4969 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4930 TAAATAAATG
*
4940 TTTAT TTTAT TTTAT TTTAT TTTAC TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
4970 CTTCAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:8025 original size:233 final size:234
Alignment explanation
Indices: 7615--8084 Score: 888
Period size: 233 Copynumber: 2.0 Consensus size: 234
7605 GTGATATTCA
*
7615 CATGTGCTATTTGGATCACAACCATAGGCAGAGGGGCTTTTCAATACTCTTGAAGGTTTAGGAGT
1 CATGTGCTATTTGGATCACAACCATAGGCAGAGGGGCTTGTCAATACTCTTGAAGGTTTAGGAG-
7680 TAGGTATCGACCATTAGTCAAATGTGGAACCAATTTTGAAATAGGCACTTGAAACACCTTGAGAT
65 T-GGTATCGACCATTAGTCAAATGTGGAACCAATTTTGAAATAGGCACTTGAAACACCTTGAGAT
7745 TTGTGTTGGCCCAAGACCTCTTTCTTGGTGGATGAATATTAAATTCTCTTAGATCTACTCCATCA
129 TTGTGTTGGCCCAAGACCTCTTTCTTGGTGGATGAATATTAAATTCTCTTAGATCTACTCCATCA
7810 TTCATTAAATGCTTAGACATTTGGTTTGATCAAATTCTAGT
194 TTCATTAAATGCTTAGACATTTGGTTTGATCAAATTCTAGT
*
7851 CATGTGCTATTTGGATCACAACCATAGGTAGAGGGGCTTGTCAATACTCTTGAAGGTTTAGGAG-
1 CATGTGCTATTTGGATCACAACCATAGGCAGAGGGGCTTGTCAATACTCTTGAAGGTTTAGGAGT
7915 GGTATCGACCATTAGTCAAATGTGGAACCAATTTTGAAATAGGCACTTGAAACACCTTGAGATTT
66 GGTATCGACCATTAGTCAAATGTGGAACCAATTTTGAAATAGGCACTTGAAACACCTTGAGATTT
*
7980 GTGTTGGCCCAAGACCTCTTTCTTGGTGGATGAATATTAAATTCTCTTAGATCTACTCCATCGTT
131 GTGTTGGCCCAAGACCTCTTTCTTGGTGGATGAATATTAAATTCTCTTAGATCTACTCCATCATT
8045 CATTAAATGCTTAGACATTTGGTTTGATCAAATTCTAGT
196 CATTAAATGCTTAGACATTTGGTTTGATCAAATTCTAGT
8084 C
1 C
8085 CTCGCGTTTA
Statistics
Matches: 231, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
233 169 0.73
236 62 0.27
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (234 bp):
CATGTGCTATTTGGATCACAACCATAGGCAGAGGGGCTTGTCAATACTCTTGAAGGTTTAGGAGT
GGTATCGACCATTAGTCAAATGTGGAACCAATTTTGAAATAGGCACTTGAAACACCTTGAGATTT
GTGTTGGCCCAAGACCTCTTTCTTGGTGGATGAATATTAAATTCTCTTAGATCTACTCCATCATT
CATTAAATGCTTAGACATTTGGTTTGATCAAATTCTAGT
Found at i:10889 original size:15 final size:16
Alignment explanation
Indices: 10865--10897 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10855 TCGTAATTTC
10865 ATCAAAATC-ACAATA
1 ATCAAAATCAACAATA
*
10880 ATCAACATCAACAATA
1 ATCAAAATCAACAATA
10896 AT
1 AT
10898 ATACTTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (16 bp):
ATCAAAATCAACAATA
Found at i:12252 original size:18 final size:18
Alignment explanation
Indices: 12229--12263 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12219 TACAGTAATT
12229 GCTACAGTGCATCGATAC
1 GCTACAGTGCATCGATAC
12247 GCTACAGTGCATCGATA
1 GCTACAGTGCATCGATA
12264 GTGTATCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (18 bp):
GCTACAGTGCATCGATAC
Found at i:12760 original size:20 final size:20
Alignment explanation
Indices: 12735--12775 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12725 ATTATTCCAA
*
12735 AACCATATACCATAGACAAT
1 AACCATAAACCATAGACAAT
12755 AACCATAAACCATAGACAAT
1 AACCATAAACCATAGACAAT
12775 A
1 A
12776 GCCCAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.54, C:0.24, G:0.05, T:0.17
Consensus pattern (20 bp):
AACCATAAACCATAGACAAT
Found at i:12877 original size:33 final size:33
Alignment explanation
Indices: 12835--12901 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
12825 ACCATAGTGC
* *
12835 TAATCCGTATGACACATAAGTTCGTGTCCACCA
1 TAATCCGTATAACACATAAGGTCGTGTCCACCA
*
12868 TAATTCGTATAACACATAAGGTCGTGTCCACCA
1 TAATCCGTATAACACATAAGGTCGTGTCCACCA
12901 T
1 T
12902 CTGTACTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (33 bp):
TAATCCGTATAACACATAAGGTCGTGTCCACCA
Found at i:15155 original size:95 final size:95
Alignment explanation
Indices: 14992--15181 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 95
14982 ATACTGACAA
* * * *
14992 GGTAGTATCGATACCATGGTAAGGGTGTCGATACCAGGCAACATCGAATCTAAAATTGGTATCGA
1 GGTAGCATCGATACCATGGTAAGGATATCGATACCAGGAAACATCGAATCTAAAATTGGTATCGA
* *
15057 TACCG-GAATGGGGTATCGGTACCATAGTAT
66 TACCGAAAAT-GGGTATCAGTACCATAGTAT
*
15087 GGTAGCATCGATACCATGGTAAGGATATCGATACCAGGAAACATCGAATCTAAAATTTGTATCGA
1 GGTAGCATCGATACCATGGTAAGGATATCGATACCAGGAAACATCGAATCTAAAATTGGTATCGA
15152 TACCGAAAATGGGTATCAGTACCATAGTAT
66 TACCGAAAATGGGTATCAGTACCATAGTAT
15182 AGAAGTATCG
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 84 0.97
96 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (95 bp):
GGTAGCATCGATACCATGGTAAGGATATCGATACCAGGAAACATCGAATCTAAAATTGGTATCGA
TACCGAAAATGGGTATCAGTACCATAGTAT
Found at i:15728 original size:46 final size:46
Alignment explanation
Indices: 15678--15960 Score: 395
Period size: 46 Copynumber: 6.0 Consensus size: 46
15668 ATGCATTAAG
* * *
15678 GCATGAAATAATGCATTAAGGCATGAAATGATGTCATAAATAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
15724 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* *
15770 GTATGAAATGATGCATTAAGGCATAAAAGGATGCCATAAATAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* * * * *
15816 GCATGAAAGGATTCATTAAGGCAGGAACGAATGCCATAAATAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
*
15862 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* *
15908 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAATGATG-CAT---T--AAGGCATGAAAGGATGCCATAAATAAAAT
15960 G
1 G
15961 AAATTTAACG
Statistics
Matches: 214, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
46 181 0.85
47 3 0.01
50 1 0.00
52 29 0.14
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.22
Consensus pattern (46 bp):
GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
Found at i:15729 original size:26 final size:25
Alignment explanation
Indices: 15620--15960 Score: 156
Period size: 26 Copynumber: 14.5 Consensus size: 25
15610 AAACCGAATA
*
15620 CATAAATAAAATGCATGAAAGGATG
1 CATAAATAAAATGCATGAAATGATG
* *
15645 CCATAAATAAAATTCATGAAAGGATG
1 -CATAAATAAAATGCATGAAATGATG
* *
15671 CAT---T--AAGGCATGAAATAATG
1 CATAAATAAAATGCATGAAATGATG
*
15691 CAT---T--AAGGCATGAAATGATG
1 CATAAATAAAATGCATGAAATGATG
15711 TCATAAATAAAATGCATGAAATGATG
1 -CATAAATAAAATGCATGAAATGATG
* *
15737 CAT---T--AAGGCATGAAAGGATG
1 CATAAATAAAATGCATGAAATGATG
*
15757 CCATAAATAAAATGTATGAAATGATG
1 -CATAAATAAAATGCATGAAATGATG
*
15783 CATTAAGGCATAAAA-G---G--ATG--C
1 CA-TAA---ATAAAATGCATGAAATGATG
* *
15804 CATAAATAAAATGCATGAAAGGATT
1 CATAAATAAAATGCATGAAATGATG
* * *
15829 CAT---T--AAGGCA-GGAACGAATG
1 CATAAATAAAATGCATGAAATG-ATG
*
15849 CCATAAATAAAATGCATGAAAGGATG
1 -CATAAATAAAATGCATGAAATGATG
* *
15875 CAT---T--AAGGCATGAAAGGATG
1 CATAAATAAAATGCATGAAATGATG
*
15895 CCATAAATAAAATGCATGAAAGGATG
1 -CATAAATAAAATGCATGAAATGATG
*
15921 CCATAAATAAAATGCATGAAAGGATG
1 -CATAAATAAAATGCATGAAATGATG
15947 CCATAAATAAAATG
1 -CATAAATAAAATG
15961 AAATTTAACG
Statistics
Matches: 253, Mismatches: 24, Indels: 76
0.72 0.07 0.22
Matches are distributed among these distances:
17 6 0.02
18 1 0.00
19 4 0.02
20 70 0.28
21 15 0.06
22 4 0.02
23 5 0.02
24 4 0.02
25 15 0.06
26 118 0.47
27 4 0.02
28 1 0.00
29 6 0.02
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (25 bp):
CATAAATAAAATGCATGAAATGATG
Found at i:17236 original size:12 final size:12
Alignment explanation
Indices: 17219--17250 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17209 TCCAAATCTC
17219 GTATACGGAAAG
1 GTATACGGAAAG
*
17231 GTATACAGAAAG
1 GTATACGGAAAG
17243 GTATACGG
1 GTATACGG
17251 GAGATAGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (12 bp):
GTATACGGAAAG
Found at i:23997 original size:29 final size:29
Alignment explanation
Indices: 23952--24009 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
23942 ATTTTCACCT
23952 AACTAAATTGATATAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
*
23981 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
24010 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATATAAGCAATGACATCAA
Found at i:28524 original size:29 final size:29
Alignment explanation
Indices: 28482--28538 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
28472 ATTTTCACCT
28482 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
28511 AACTAAATTGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
28539 CTTAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:33664 original size:18 final size:18
Alignment explanation
Indices: 33641--33713 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
33631 ACTGAATATT
33641 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
33659 TGTCCCGAAGGACCACTTA
1 TGTCCCGAAGGACCAC-TA
* * *
33678 TTATTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
33697 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
33714 GATTATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:33696 original size:38 final size:38
Alignment explanation
Indices: 33645--33719 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
33635 AATATTTGTC
* *
33645 CCGAAGGACCACTATGTCCCGAAGGACCACTTATTATT
1 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTATT
33683 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTAT
1 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTAT
33720 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (38 bp):
CCGAAGAACCACTATGTCCCGAAGGACCACTGATTATT
Found at i:42445 original size:26 final size:26
Alignment explanation
Indices: 42416--42482 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
42406 TTACTATGAA
42416 ACTATAAAATTTTATACAATCTATTT
1 ACTATAAAATTTTATACAATCTATTT
*
42442 ACTATAAAATTTTATATAATCTATTT
1 ACTATAAAATTTTATACAATCTATTT
42468 ACTATAAAATTTTAT
1 ACTATAAAATTTTAT
42483 CATACAACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (26 bp):
ACTATAAAATTTTATACAATCTATTT
Found at i:42473 original size:14 final size:14
Alignment explanation
Indices: 42433--42474 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
42423 AATTTTATAC
42433 AATCTATTTACTAT
1 AATCTATTTACTAT
**
42447 AAAAT-TTTA-TAT
1 AATCTATTTACTAT
42459 AATCTATTTACTAT
1 AATCTATTTACTAT
42473 AA
1 AA
42475 AATTTTATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 8 0.36
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (14 bp):
AATCTATTTACTAT
Found at i:45444 original size:3 final size:3
Alignment explanation
Indices: 45436--45477 Score: 66
Period size: 3 Copynumber: 13.3 Consensus size: 3
45426 TATGTAAAAT
45436 TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TTAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA T
45478 TAAAAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:45463 original size:10 final size:10
Alignment explanation
Indices: 45433--45480 Score: 78
Period size: 10 Copynumber: 4.6 Consensus size: 10
45423 TAATATGTAA
45433 AATTAATAAT
1 AATTAATAAT
45443 AATAATAATAAT
1 AAT--TAATAAT
45455 AATTAATAAT
1 AATTAATAAT
45465 AATTAATAAT
1 AATTAATAAT
45475 AATTAA
1 AATTAA
45481 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 26 0.72
12 10 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTAATAAT
Found at i:45492 original size:20 final size:20
Alignment explanation
Indices: 45449--45492 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
45439 TAATAATAAT
* * *
45449 AATAATAATTAATAATAATT
1 AATAATAATTAAAAAAAATA
45469 AATAATAATTAAAAAAAATA
1 AATAATAATTAAAAAAAATA
45489 AATA
1 AATA
45493 TAAAAGACCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAATAATTAAAAAAAATA
Found at i:45963 original size:130 final size:134
Alignment explanation
Indices: 45680--45986 Score: 344
Period size: 130 Copynumber: 2.3 Consensus size: 134
45670 TCGGGTCGTT
* * * * * *
45680 TAAGGGTGACAC-AGTTCATACGTGACGAGGAAATCTGGTC-GAAGGATGACACGACTCATACAT
1 TAAGGGTGACACGA-CTCCTACGTGATGAGGAGATCTAGTCAG-GGGATGACACGACTCATACAT
*
45743 GATGAAGAGTTCTTGGCCATCTTTAAGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGGCT
64 GATGAAGAGTTCTTGGCCATCTTTAAGAA-GGTGATAACTCAGTTCCTACGCAATGAGGACGGCT
45808 GGTTATC
128 GGTTATC
* * *
45815 TAAGGGTGACACGACTCCTACGTGATGAGGATATCTAGTCAGGGGATGACACTG-CTCCTACGTG
1 TAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAGTCAGGGGATGACAC-GACTCATACATG
* *
45879 ATGAAGAGTTCTTGGCCAT-TTT-A-TA-GTGATAACAT-AGTTCCTACGTAATGAGGACGGCTG
65 ATGAAGAGTTCTTGGCCATCTTTAAGAAGGTGATAAC-TCAGTTCCTACGCAATGAGGACGGCTG
45939 GTTATC
129 GTTATC
* * ** *
45945 TAATGTTGACGTTG-CTCCTACGTGATGAGGAGATCTGGTCAG
1 TAAGGGTGAC-ACGACTCCTACGTGATGAGGAGATCTAGTCAG
45987 CTAATGTTGA
Statistics
Matches: 150, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
130 71 0.47
131 2 0.01
132 1 0.01
133 1 0.01
134 3 0.02
135 69 0.46
136 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (134 bp):
TAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAGTCAGGGGATGACACGACTCATACATGA
TGAAGAGTTCTTGGCCATCTTTAAGAAGGTGATAACTCAGTTCCTACGCAATGAGGACGGCTGGT
TATC
Found at i:46979 original size:19 final size:18
Alignment explanation
Indices: 46944--46978 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46934 TCCTTTATTT
46944 ATTTTTTTCTTCTTTTTC
1 ATTTTTTTCTTCTTTTTC
46962 ATTTTTCTTC-TCTTTTT
1 ATTTTT-TTCTTCTTTTT
46979 TTTTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTTTCTTCTTTTTC
Found at i:46982 original size:16 final size:15
Alignment explanation
Indices: 46945--46998 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
46935 CCTTTATTTA
46945 TTTTTTTCTTCTTTT
1 TTTTTTTCTTCTTTT
* *
46960 TCATTTTTCTTCTCTT
1 T-TTTTTTCTTCTTTT
* *
46976 TTTTTTTATTATTATT
1 TTTTTTTCTTCTT-TT
46992 TTTTTTT
1 TTTTTTT
46999 AAGTGTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 9 0.29
16 22 0.71
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTCTTCTTTT
Found at i:60283 original size:3 final size:3
Alignment explanation
Indices: 60275--60316 Score: 66
Period size: 3 Copynumber: 13.3 Consensus size: 3
60265 TATGTAAAAT
60275 TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TTAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA T
60317 TAAAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:60302 original size:10 final size:10
Alignment explanation
Indices: 60272--60319 Score: 78
Period size: 10 Copynumber: 4.6 Consensus size: 10
60262 TAATATGTAA
60272 AATTAATAAT
1 AATTAATAAT
60282 AATAATAATAAT
1 AAT--TAATAAT
60294 AATTAATAAT
1 AATTAATAAT
60304 AATTAATAAT
1 AATTAATAAT
60314 AATTAA
1 AATTAA
60320 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 26 0.72
12 10 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTAATAAT
Found at i:63455 original size:93 final size:93
Alignment explanation
Indices: 63296--63484 Score: 369
Period size: 93 Copynumber: 2.0 Consensus size: 93
63286 AATTACGAAA
*
63296 ACTATCACTTGTGCAACTAATTTGAGTTCATATTGCAGGATTTGCCTTCATTTATTTTGAGGAAT
1 ACTATCACTTGTGCAACTAATTTGAGTTCAAATTGCAGGATTTGCCTTCATTTATTTTGAGGAAT
63361 AACGTGATGCTGAAGATGCTATTCGTGG
66 AACGTGATGCTGAAGATGCTATTCGTGG
63389 ACTATCACTTGTGCAACTAATTTGAGTTCAAATTGCAGGATTTGCCTTCATTTATTTTGAGGAAT
1 ACTATCACTTGTGCAACTAATTTGAGTTCAAATTGCAGGATTTGCCTTCATTTATTTTGAGGAAT
63454 AACGTGATGCTGAAGATGCTATTCGTGG
66 AACGTGATGCTGAAGATGCTATTCGTGG
63482 ACT
1 ACT
63485 TGATAATATT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 95 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (93 bp):
ACTATCACTTGTGCAACTAATTTGAGTTCAAATTGCAGGATTTGCCTTCATTTATTTTGAGGAAT
AACGTGATGCTGAAGATGCTATTCGTGG
Found at i:68378 original size:23 final size:23
Alignment explanation
Indices: 68352--68397 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
68342 ATTTATCTTT
*
68352 TAAATTTTATAAAAAATTATATA
1 TAAATTTTATAAAAAAGTATATA
*
68375 TAAATTTTATTAAAAAGTATATA
1 TAAATTTTATAAAAAAGTATATA
68398 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTTTATAAAAAAGTATATA
Found at i:68670 original size:3 final size:3
Alignment explanation
Indices: 68662--68690 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
68652 ATGGTATTTC
68662 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
68691 GATAGCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:70054 original size:24 final size:24
Alignment explanation
Indices: 70027--70082 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
70017 TGGTCCTGCT
* * *
70027 TATGACAGGTACCGGAGTCCTGAA
1 TATGACAGGCACAGGAGTCCCGAA
** *
70051 TATGGGAGGCACAGGAGTCCCGAG
1 TATGACAGGCACAGGAGTCCCGAA
70075 TATGACAG
1 TATGACAG
70083 ATTCCACAGG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.34, T:0.18
Consensus pattern (24 bp):
TATGACAGGCACAGGAGTCCCGAA
Found at i:77270 original size:8 final size:8
Alignment explanation
Indices: 77257--77300 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
77247 AAATAAGAAG
77257 AAAAAAGA
1 AAAAAAGA
77265 AAAAAAGA
1 AAAAAAGA
77273 GAAAGAAAGA
1 -AAA-AAAGA
*
77283 AAAGAAG-
1 AAAAAAGA
77290 AAAAAAGA
1 AAAAAAGA
77298 AAA
1 AAA
77301 CTGAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 6 0.19
8 14 0.45
9 6 0.19
10 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:77270 original size:10 final size:10
Alignment explanation
Indices: 77241--77300 Score: 57
Period size: 10 Copynumber: 5.6 Consensus size: 10
77231 GAATTACACC
77241 AGAAAAAAATA
1 AGAAAAAAA-A
*
77252 AGAAGAAAAA
1 AGAAAAAAAA
*
77262 AGAAAAAAAG
1 AGAAAAAAAA
77272 AGAAAGAAAGAAA
1 AG-AA-AAA-AAA
*
77285 AGAAGAAAAA
1 AGAAAAAAAA
77295 AGAAAA
1 AGAAAA
77301 CTGAAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
10 19 0.47
11 12 0.30
12 5 0.12
13 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:77272 original size:15 final size:15
Alignment explanation
Indices: 77241--77300 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 15
77231 GAATTACACC
*
77241 AGAAAAAA-ATAAGA
1 AGAAAAAAGAAAAGA
*
77255 AGAAAAAAGAAAAAAA
1 AGAAAAAAG-AAAAGA
77271 GAGAAAGAAAGAAAAGA
1 -AGAAA-AAAGAAAAGA
77288 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
77301 CTGAAATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 8 0.21
15 8 0.21
16 9 0.23
17 10 0.26
18 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (15 bp):
AGAAAAAAGAAAAGA
Found at i:79519 original size:66 final size:66
Alignment explanation
Indices: 79398--79657 Score: 313
Period size: 66 Copynumber: 3.9 Consensus size: 66
79388 GTCTGTCTTA
* * *
79398 TTTGAGATTGTTTCTCTTGAAACAAAGATTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAA
1 TTTGAGATTATTTCTCTCGAAACAAA-TTTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAA
79463 CC
65 CC
* * * * *
79465 TATGAGATTATTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATCAAC
1 TTTGAGATTATTTCTCTCGAAACAAATTTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
*
79530 T
66 C
* * * *
79531 TTTAAGATTATTTCTCTCGAAACAAATTTCATCTTGCTTGAGACAATTTCTCTTGAAACAAAAAC
1 TTTGAGATTATTTCTCTCGAAACAAATTTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
79596 C
66 C
* * * * * * * *
79597 TTTGAGATTGTTTCACTCAAAACAAAATTTTATCTCACCTCAGATAGTTTCTCTTGAAACA
1 TTTGAGATTATTTCTCTCGAAAC-AAATTTTATCTCGCTTGAGACAATTTCTCTTGAAACA
79658 AATTTCTTTC
Statistics
Matches: 164, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
66 110 0.67
67 54 0.33
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (66 bp):
TTTGAGATTATTTCTCTCGAAACAAATTTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
C
Found at i:79589 original size:36 final size:35
Alignment explanation
Indices: 79408--79592 Score: 124
Period size: 36 Copynumber: 5.5 Consensus size: 35
79398 TTTGAGATTG
79408 TTTCTCTTGAAACAAAGATTTATCTCGCTTGAGACAA
1 TTTCTCTTGAAAC-AA-ATTTATCTCGCTTGAGACAA
**
79445 TTTCTCTTGAAACATAA---A---C-CTATGAGATTA
1 TTTCTCTTGAAACA-AATTTATCTCGCT-TGAGACAA
* *
79475 TTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTATCTCGCTTGAGACAA
* * * * **
79511 TTTCTCTTGAAAC--A-TCAACT--TTTAAGATTA
1 TTTCTCTTGAAACAAATTTATCTCGCTTGAGACAA
* *
79541 TTTCTCTCGAAACAAATTTCATCTTGCTTGAGACAA
1 TTTCTCTTGAAACAAATTT-ATCTCGCTTGAGACAA
79577 TTTCTCTTGAAACAAA
1 TTTCTCTTGAAACAAA
79593 AACCTTTGAG
Statistics
Matches: 110, Mismatches: 22, Indels: 33
0.67 0.13 0.20
Matches are distributed among these distances:
29 4 0.04
30 38 0.35
32 4 0.04
33 2 0.02
34 4 0.04
36 42 0.38
37 16 0.15
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (35 bp):
TTTCTCTTGAAACAAATTTATCTCGCTTGAGACAA
Found at i:79590 original size:132 final size:134
Alignment explanation
Indices: 79402--79657 Score: 356
Period size: 132 Copynumber: 1.9 Consensus size: 134
79392 GTCTTATTTG
* * *
79402 AGATTGTTTCTCTTGAAACAAAGATTTATCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTA
1 AGATTATTTCTCTCGAAACAAAGATTTATCTCGCTTGAGACAATTTCTCTTGAAACAAAAACCTA
* ** * * * *
79467 TGAGATTATTTCTCTTGAAAC-AAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATCAACT
66 TGAGATTATTTCACTCAAAACAAAATTTTATCTCACCTCAGACAGTTTCTCTTGAAACATCAACT
79531 TTTA
131 TTTA
*
79535 AGATTATTTCTCTCGAAAC-AA-ATTTCATCTTGCTTGAGACAATTTCTCTTGAAACAAAAACCT
1 AGATTATTTCTCTCGAAACAAAGATTT-ATCTCGCTTGAGACAATTTCTCTTGAAACAAAAACCT
* * *
79598 TTGAGATTGTTTCACTCAAAACAAAATTTTATCTCACCTCAGATAGTTTCTCTTGAAACA
65 ATGAGATTATTTCACTCAAAACAAAATTTTATCTCACCTCAGACAGTTTCTCTTGAAACA
79658 AATTTCTTTC
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
131 4 0.04
132 54 0.50
133 49 0.46
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (134 bp):
AGATTATTTCTCTCGAAACAAAGATTTATCTCGCTTGAGACAATTTCTCTTGAAACAAAAACCTA
TGAGATTATTTCACTCAAAACAAAATTTTATCTCACCTCAGACAGTTTCTCTTGAAACATCAACT
TTTA
Found at i:81360 original size:3 final size:3
Alignment explanation
Indices: 81352--81423 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
81342 TTATGTATGT
81352 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
81400 TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
81424 CCATTATTTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:81930 original size:25 final size:25
Alignment explanation
Indices: 81894--81979 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
81884 ATTTTAGTAA
*
81894 TTCATTGTATGTTATTAATTCATAT
1 TTCATTGCATGTTATTAATTCATAT
*
81919 TTCATTGCATGTTATTAATTCATGT
1 TTCATTGCATGTTATTAATTCATAT
**
81944 TGAATTGCA---TATTAATTCATAT
1 TTCATTGCATGTTATTAATTCATAT
*
81966 TACATTAG-ATGTTA
1 TTCATT-GCATGTTA
81980 AGTAATCAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 17 0.34
23 1 0.02
25 32 0.64
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.50
Consensus pattern (25 bp):
TTCATTGCATGTTATTAATTCATAT
Found at i:90631 original size:17 final size:18
Alignment explanation
Indices: 90604--90640 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
90594 TTAAATAATA
90604 ATTGCATGTTAGTAATTC
1 ATTGCATGTTAGTAATTC
*
90622 ATTGCA-GTTATTAATTC
1 ATTGCATGTTAGTAATTC
90639 AT
1 AT
90641 GTGTCATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
ATTGCATGTTAGTAATTC
Found at i:90660 original size:25 final size:24
Alignment explanation
Indices: 90619--90677 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 24
90609 ATGTTAGTAA
90619 TTCATTGCA-GTTATTAATTCATG
1 TTCATTGCATGTTATTAATTCATG
90642 TGTCATTGCATGTTATTAATTCATG
1 T-TCATTGCATGTTATTAATTCATG
90667 TTGCATTGCAT
1 TT-CATTGCAT
90678 ATTAATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 1 0.03
24 9 0.27
25 23 0.70
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (24 bp):
TTCATTGCATGTTATTAATTCATG
Found at i:90683 original size:22 final size:23
Alignment explanation
Indices: 90620--90687 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 23
90610 TGTTAGTAAT
90620 TCATTGCAGTTATTAATTCATGTG
1 TCATTGCA-TTATTAATTCATGTG
90644 TCATTGCATGTTATTAATTCATGT-
1 TCATTGCA--TTATTAATTCATGTG
90668 TGCATTGCA-TATTAATTCAT
1 T-CATTGCATTATTAATTCAT
90688 ATTACATTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.26
24 9 0.21
25 22 0.52
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (23 bp):
TCATTGCATTATTAATTCATGTG
Found at i:90702 original size:47 final size:49
Alignment explanation
Indices: 90621--90731 Score: 113
Period size: 47 Copynumber: 2.2 Consensus size: 49
90611 GTTAGTAATT
* * *
90621 CATTGCAGTTATTAATTCATGTGTCATTGCATGTT-ATTAATT-CATGTTG
1 CATTGCA--TATTAATTCATATGTCATTGCATGTTAAGTAATTACATGTTA
90670 CATTGCATATTAATTCATAT-TACATTAG-ATGTTAAGTAATTAGCATGTTA
1 CATTGCATATTAATTCATATGT-CATT-GCATGTTAAGTAATTA-CATGTTA
*
90720 CATTGCACATTA
1 CATTGCATATTA
90732 GTATTTTAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
46 1 0.02
47 21 0.40
48 7 0.13
49 7 0.13
50 17 0.32
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.43
Consensus pattern (49 bp):
CATTGCATATTAATTCATATGTCATTGCATGTTAAGTAATTACATGTTA
Found at i:91488 original size:11 final size:12
Alignment explanation
Indices: 91463--91488 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
91453 TTAAGCATGC
91463 AAAAATCAAGAA
1 AAAAATCAAGAA
91475 AAAAATCAAGAA
1 AAAAATCAAGAA
91487 AA
1 AA
91489 TTCGATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAATCAAGAA
Found at i:93506 original size:16 final size:17
Alignment explanation
Indices: 93474--93507 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
93464 ATTTCAAATC
93474 TTTTCTAAATTTGATTT
1 TTTTCTAAATTTGATTT
93491 TTTTCTAAATTT-ATTT
1 TTTTCTAAATTTGATTT
93507 T
1 T
93508 GATTTTCGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTCTAAATTTGATTT
Found at i:93536 original size:18 final size:18
Alignment explanation
Indices: 93513--93551 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
93503 ATTTTGATTT
93513 TCGTCACTTCGAAAAAAG
1 TCGTCACTTCGAAAAAAG
93531 TCGTCACTTCGAAAAAAG
1 TCGTCACTTCGAAAAAAG
93549 TCG
1 TCG
93552 CCGCGACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (18 bp):
TCGTCACTTCGAAAAAAG
Done.