Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002750.1 Hibiscus syriacus cultivar Beakdansim tig00005666_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: 87723
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2193 original size:15 final size:15
Alignment explanation
Indices: 2173--2209 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2163 TAAGGTTGTT
*
2173 GTTGCCTCTGTTAAA
1 GTTGCCTCGGTTAAA
*
2188 GTTGCCTCGGTTGAA
1 GTTGCCTCGGTTAAA
2203 GTTGCCT
1 GTTGCCT
2210 ACATAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (15 bp):
GTTGCCTCGGTTAAA
Found at i:9539 original size:14 final size:14
Alignment explanation
Indices: 9520--9546 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9510 GTGATGGACT
9520 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
9534 ATGGTGATGGAAA
1 ATGGTGATGGAAA
9547 TAGTATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:13330 original size:16 final size:17
Alignment explanation
Indices: 13305--13338 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13295 TAGATGAAAG
*
13305 AAAAGGAAATGAA-ATA
1 AAAAGAAAATGAATATA
13321 AAAAGAAAATGAATATA
1 AAAAGAAAATGAATATA
13338 A
1 A
13339 CTTACAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (17 bp):
AAAAGAAAATGAATATA
Found at i:13993 original size:13 final size:13
Alignment explanation
Indices: 13975--14021 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
13965 TAGTCGTGAA
13975 GGTGATGAACTAT
1 GGTGATGAACTAT
*
13988 GGTGATGGACTAT
1 GGTGATGAACTAT
**
14001 GGTGATGGAAAGAT
1 GGTGAT-GAACTAT
14015 GGTGATG
1 GGTGATG
14022 GAAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.28, C:0.04, G:0.40, T:0.28
Consensus pattern (13 bp):
GGTGATGAACTAT
Found at i:14018 original size:14 final size:14
Alignment explanation
Indices: 13986--14025 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
13976 GTGATGAACT
**
13986 ATGGTGATGG-ACT
1 ATGGTGATGGAAAG
13999 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
14013 ATGGTGATGGAAA
1 ATGGTGATGGAAA
14026 TAATATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.33, C:0.03, G:0.40, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:18486 original size:27 final size:26
Alignment explanation
Indices: 18433--18495 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
18423 TGGGGTTACC
18433 TTGGTCA-TTTACACTCCAAGGACATT
1 TTGGTCATTTTACACTCCAAGGACA-T
* * **
18459 TTGGTCATTTTACAGTTCAAGGGTAT
1 TTGGTCATTTTACACTCCAAGGACAT
*
18485 TTAGTCATTTT
1 TTGGTCATTTT
18496 CTTAATTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (26 bp):
TTGGTCATTTTACACTCCAAGGACAT
Found at i:19382 original size:22 final size:22
Alignment explanation
Indices: 19334--19396 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
19324 GGGGTCAAAT
* *
19334 TCAAAGGTCAACGGTCAGACCGG
1 TCAAA-GTCAACGGTCACACCGA
*
19357 TCAAAGTCAACGGTCACACTGA
1 TCAAAGTCAACGGTCACACCGA
*
19379 TCAACAGTTAACGAGTCA
1 TCAA-AGTCAACG-GTCA
19397 GGTCAAAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.53
23 12 0.35
24 4 0.12
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.17
Consensus pattern (22 bp):
TCAAAGTCAACGGTCACACCGA
Found at i:26144 original size:26 final size:27
Alignment explanation
Indices: 26106--26158 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
26096 TTAATTTTCA
* *
26106 AAAAAATTGAAAATAA-AAACTATTTTT
1 AAAAAATT-AAAAAAATAAAATATTTTT
26133 AAAAAA-TAAAAAAATAAAATATTTTT
1 AAAAAATTAAAAAAATAAAATATTTTT
26159 TAGGATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.26
26 11 0.48
27 6 0.26
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAAATTAAAAAAATAAAATATTTTT
Found at i:26799 original size:2 final size:2
Alignment explanation
Indices: 26792--26816 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26782 TAAACATACT
26792 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
26817 TAAATACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26987 original size:37 final size:38
Alignment explanation
Indices: 26915--26998 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 38
26905 AATATTTATC
* * ** *
26915 ATATATATTAAATTATTAAGTTTGGCTTCT-CAAAAAT
1 ATATATAATAAATTATTAAATTTAACTTCTAAAAAAAT
*
26952 ATATATAATAAATTATTAAATTTAATTTCTAAAAAAAT
1 ATATATAATAAATTATTAAATTTAACTTCTAAAAAAAT
*
26990 ATGTATAAT
1 ATATATAAT
26999 GCTTTGAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 25 0.64
38 14 0.36
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (38 bp):
ATATATAATAAATTATTAAATTTAACTTCTAAAAAAAT
Found at i:33176 original size:108 final size:111
Alignment explanation
Indices: 32983--33183 Score: 304
Period size: 108 Copynumber: 1.8 Consensus size: 111
32973 GAAAAAGAAA
*
32983 AAAAATACTAGATGAATTTAATTATTTTTTTAATTATTTACGTGAACATATGAATTTTAAAGATT
1 AAAAATACTAGATGAATTTAA-TATTTTTTTAATTATTTACGTGAACATATAAATTTTAAAGATT
33048 TAAATTTTTTTACTTGTATGATATTTTGACATATGATTTATATTAAT
65 TAAATTTTTTTACTTGTATGATATTTTGACATATGATTTATATTAAT
* * *
33095 AAAAATATTAGATGAATTT-A-GTTTTTTTAA-TATTTATGTGAACATATAAATTTTAAAGATTT
1 AAAAATACTAGATGAATTTAATATTTTTTTAATTATTTACGTGAACATATAAATTTTAAAGATTT
33157 ATAA-TTTTTTA-TTAGTATGATATTTTG
66 A-AATTTTTTTACTT-GTATGATATTTTG
33184 TTATATAAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
107 2 0.02
108 51 0.61
109 11 0.13
111 1 0.01
112 18 0.22
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (111 bp):
AAAAATACTAGATGAATTTAATATTTTTTTAATTATTTACGTGAACATATAAATTTTAAAGATTT
AAATTTTTTTACTTGTATGATATTTTGACATATGATTTATATTAAT
Found at i:33229 original size:108 final size:109
Alignment explanation
Indices: 33008--33230 Score: 240
Period size: 108 Copynumber: 2.1 Consensus size: 109
32998 ATTTAATTAT
*
33008 TTTTTTAATTATTTACGTGAACATATGAATTTTAAAGATTTAAATTTTTTTACTTGTATGATATT
1 TTTTTTAATTATTTACGTGAACATATAAATTTTAAAGATTTAAATTTTTTTACTTGTATGATATT
* * * * * ** * *
33073 TTGACATATGATTTATATTAATAAAAATATTAGATGAATTTAGT
66 TTGACATATAAATCAAATCAATAAAAATAAAAGATGAATATAGA
*
33117 TTTTTTAA-TATTTATGTGAACATATAAATTTTAAAGATTTATAA-TTTTTTA-TTAGTATGATA
1 TTTTTTAATTATTTACGTGAACATATAAATTTTAAAGATTTA-AATTTTTTTACTT-GTATGATA
** * *
33179 TTTTGTTATATAAATCAAATCAATAACACATAAAATAT-ATATATA-A
64 TTTTGACATATAAATCAAATCAATAA-AAATAAAAGATGA-ATATAGA
33225 TTTTTT
1 TTTTTT
33231 TAAATGGTCC
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
107 2 0.02
108 72 0.76
109 21 0.22
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (109 bp):
TTTTTTAATTATTTACGTGAACATATAAATTTTAAAGATTTAAATTTTTTTACTTGTATGATATT
TTGACATATAAATCAAATCAATAAAAATAAAAGATGAATATAGA
Found at i:34189 original size:30 final size:30
Alignment explanation
Indices: 34151--34213 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
34141 AAAAATGAAG
*
34151 AAATTTT-AAATATATTAACTATAAAA-TTA
1 AAATTTTAAAATAT-TTAAATATAAAATTTA
*
34180 AAATATTTAAAATATTTAAATTTAAAATTTA
1 AAAT-TTTAAAATATTTAAATATAAAATTTA
34211 AAA
1 AAA
34214 AGTTTACTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 13 0.45
31 12 0.41
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATTTTAAAATATTTAAATATAAAATTTA
Found at i:34193 original size:31 final size:31
Alignment explanation
Indices: 34153--34213 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
34143 AAATGAAGAA
* *
34153 ATTTTAAATATATTAACTATAAAA-TTAAAAT
1 ATTTAAAATAT-TTAAATATAAAATTTAAAAT
*
34184 ATTTAAAATATTTAAATTTAAAATTTAAAA
1 ATTTAAAATATTTAAATATAAAATTTAAAA
34214 AGTTTACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
ATTTAAAATATTTAAATATAAAATTTAAAAT
Found at i:35700 original size:17 final size:17
Alignment explanation
Indices: 35673--35708 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
35663 ATGAAGGCTT
35673 TTATATCTATTCATCTTC
1 TTATATCTATTCAT-TTC
35691 TTAT-TCTATTCATTTC
1 TTATATCTATTCATTTC
35707 TT
1 TT
35709 CTTTCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATCTATTCATTTC
Found at i:36990 original size:17 final size:17
Alignment explanation
Indices: 36968--37003 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36958 AAAATAGAGT
*
36968 AAAGTAATAAACTAGTA
1 AAAGTAATAAACTAATA
*
36985 AAAGTAATAGACTAATA
1 AAAGTAATAAACTAATA
37002 AA
1 AA
37004 CCGTCACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (17 bp):
AAAGTAATAAACTAATA
Found at i:37635 original size:332 final size:332
Alignment explanation
Indices: 37029--37672 Score: 1146
Period size: 332 Copynumber: 1.9 Consensus size: 332
37019 ATAAAAGAGA
* *
37029 GAATGAGTGAGATAGAAACTAGTGAGGAGTTGACCTCACTTTAGCATGTCAAGATACACTAGTGA
1 GAATGAGTGAGATAGAAACTAGTGAGGAGTTGACCTCACTTTAGCATGTAAAGATACACTAGTAA
*
37094 TCTAAGGGTGTTGTACCGTTTAGAATGCAGATCTAGGAAGGAAGCAAAACAATCTGTAAGTGTAA
66 TCTAAGGGTGTTGTACCATTTAGAATGCAGATCTAGGAAGGAAGCAAAACAATCTGTAAGTGTAA
*
37159 GTGAATGGCTTGGTAGTTGATATAGGTGAAGAATGGTGGGTTGTTTTGTTTGAATGGAAATGGAA
131 GTGAATGGCTTGGTAGTTGATATAGGTGAAGAATGGTGGGTTGTTTTGTTTGAATAGAAATGGAA
* *
37224 TTTGATTAAGTGATATGAAGGTGATGGTTTATGAAAGAAAATTATTAAGGTGATAGTATCTTGTA
196 TTTGATTAAGTGATAGGAAGGTGATGGTTTATGAAAGAAAATTATTAAGGTGATAGTATCTTATA
* *
37289 GGACTAATAATAAACCAATGCTATAGATGACCAAATACATGATTCTTATAAGGTGATGGTTTATG
261 GGACTAATAATAAACCAATGCTATAGACGACCAAAGACATGATTCTTATAAGGTGATGGTTTATG
37354 CCTTTTT
326 CCTTTTT
37361 GAATGAGTGAGATAGAAACTAGTGAGGAGTTGACCTCACTTTAGCATGTAAAGATACACTAGTAA
1 GAATGAGTGAGATAGAAACTAGTGAGGAGTTGACCTCACTTTAGCATGTAAAGATACACTAGTAA
* * *
37426 TCTAAGGGTTTTGTACCATTTTGAATGCGGATCTAGGAAGGAAGCAAAACAATCTGTAAGTGTAA
66 TCTAAGGGTGTTGTACCATTTAGAATGCAGATCTAGGAAGGAAGCAAAACAATCTGTAAGTGTAA
37491 GTGAATGGCTTGGTAGTTGATATAGGTGAAGAATGGTGGGTTGTTTTGTTTGAATAGAAATGGAA
131 GTGAATGGCTTGGTAGTTGATATAGGTGAAGAATGGTGGGTTGTTTTGTTTGAATAGAAATGGAA
* * *
37556 TTTGATTAAGTGATAGGAAGGTGATTGTTTATGAAA-AAATTTTGTTAAGGTGATAGTATCTTAT
196 TTTGATTAAGTGATAGGAAGGTGATGGTTTATGAAAGAAA-ATTATTAAGGTGATAGTATCTTAT
37620 AGGACTAATAATAAACCAATGCTATAGACGACCAAAGACATGATTCTTATAAG
260 AGGACTAATAATAAACCAATGCTATAGACGACCAAAGACATGATTCTTATAAG
37673 TCTTTATAAG
Statistics
Matches: 297, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
331 3 0.01
332 294 0.99
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (332 bp):
GAATGAGTGAGATAGAAACTAGTGAGGAGTTGACCTCACTTTAGCATGTAAAGATACACTAGTAA
TCTAAGGGTGTTGTACCATTTAGAATGCAGATCTAGGAAGGAAGCAAAACAATCTGTAAGTGTAA
GTGAATGGCTTGGTAGTTGATATAGGTGAAGAATGGTGGGTTGTTTTGTTTGAATAGAAATGGAA
TTTGATTAAGTGATAGGAAGGTGATGGTTTATGAAAGAAAATTATTAAGGTGATAGTATCTTATA
GGACTAATAATAAACCAATGCTATAGACGACCAAAGACATGATTCTTATAAGGTGATGGTTTATG
CCTTTTT
Found at i:44079 original size:18 final size:18
Alignment explanation
Indices: 44056--44096 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
44046 TTCTCTTTTG
44056 CACACTAGGCACCTCTCA
1 CACACTAGGCACCTCTCA
44074 CACACTAGGCACCTCTCA
1 CACACTAGGCACCTCTCA
44092 CACAC
1 CACAC
44097 CATCTCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.46, G:0.10, T:0.15
Consensus pattern (18 bp):
CACACTAGGCACCTCTCA
Found at i:52042 original size:2 final size:2
Alignment explanation
Indices: 52030--52108 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
52020 TCATAACAAC
*
52030 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52109 GAAATAAGCA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:57940 original size:3 final size:3
Alignment explanation
Indices: 57934--57967 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
57924 TATTATTTAT
*
57934 TAA TAA TAC TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
57968 TAAATGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:57962 original size:14 final size:14
Alignment explanation
Indices: 57943--57970 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57933 TTAATAATAC
57943 TAATAATAATATAA
1 TAATAATAATATAA
57957 TAATAATAATATAA
1 TAATAATAATATAA
57971 ATGCATAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:64896 original size:27 final size:27
Alignment explanation
Indices: 64843--64898 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
64833 TAAGATTGTG
* * **
64843 AAGTGCTTCATCATTGTGGCATTGCTT
1 AAGTACTTCATCATTCTGGCACCGCTT
*
64870 AAGTACTTCATCATTCTGTCACCGCTT
1 AAGTACTTCATCATTCTGGCACCGCTT
64897 AA
1 AA
64899 TCTTTTTCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (27 bp):
AAGTACTTCATCATTCTGGCACCGCTT
Found at i:71763 original size:22 final size:22
Alignment explanation
Indices: 71735--71777 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
71725 GGCTTCAAGC
*
71735 TTGTTTTGTATTTGGGCCCTAG
1 TTGTTTTGAATTTGGGCCCTAG
71757 TTGTTTTGAATTTGGGCCCTA
1 TTGTTTTGAATTTGGGCCCTA
71778 TTTTGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (22 bp):
TTGTTTTGAATTTGGGCCCTAG
Found at i:71823 original size:3 final size:3
Alignment explanation
Indices: 71817--71851 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
71807 ATTTATTATT
71817 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
71852 TAAATGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:72084 original size:14 final size:15
Alignment explanation
Indices: 72065--72094 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
72055 ACTTATTTTG
72065 ACAAAAAGA-ATATT
1 ACAAAAAGATATATT
72079 ACAAAAAGATATATT
1 ACAAAAAGATATATT
72094 A
1 A
72095 TTGCTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (15 bp):
ACAAAAAGATATATT
Found at i:72777 original size:6 final size:6
Alignment explanation
Indices: 72768--72807 Score: 53
Period size: 6 Copynumber: 6.2 Consensus size: 6
72758 ATTATAATTA
72768 TATTTT TATTTT TATTTT TATTTTT TATTTATT TATTTT T
1 TATTTT TATTTT TATTTT TA-TTTT TA-TT-TT TATTTT T
72808 TTTGTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 17 0.53
7 11 0.34
8 4 0.12
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:73239 original size:13 final size:13
Alignment explanation
Indices: 73221--73285 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
73211 CAGATGAATC
73221 AAAAATTTAAATA
1 AAAAATTTAAATA
**
73234 AAAAATAAAAATA
1 AAAAATTTAAATA
* *
73247 AATAA-TTAATCTTA
1 AAAAATTTAA--ATA
*
73261 TAAAATTTAAATA
1 AAAAATTTAAATA
*
73274 TAAAATTTAAAT
1 AAAAATTTAAAT
73286 TTTATGTGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
12 2 0.05
13 29 0.73
14 5 0.12
15 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAATTTAAATA
Found at i:81527 original size:16 final size:16
Alignment explanation
Indices: 81506--81536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
81496 ACTTTTGAGT
81506 ATATTTAAAAGTATAA
1 ATATTTAAAAGTATAA
*
81522 ATATTTGAAAGTATA
1 ATATTTAAAAGTATA
81537 CTAACATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
ATATTTAAAAGTATAA
Found at i:82854 original size:176 final size:175
Alignment explanation
Indices: 82619--82948 Score: 391
Period size: 176 Copynumber: 1.9 Consensus size: 175
82609 TAATTGTCAC
* * *
82619 AAACGTGAATATCATTATTTTTGTGACAATGTTTTTTGTAATAATTAGTAAAACTTATAGTTACA
1 AAACGTGAATATCACTATTTTTGTGACAA-GTTTTTTGTAACAATAAGTAAAACTTATAGTTACA
* * * * *
82684 AAATTTGTCACTATATGAATTT-TTTGGCGTA-ACAATATT-GAGGA-AATCTTTGTGACAATAT
65 AAA--TGTCACTACAT-AATTTCTTT-GCGTACAAAAAATTGGA-GATAATCATTGTGACAATAC
82745 ATTTTGTCACTATAATTAAAACATATAACGACAAACATTATTTTTTACTAA
125 ATTTTGTCACTATAATTAAAACATATAACGACAAACATTATTTTTTACTAA
* * * * *
82796 AAACTTGAATCTCACTATTTGTTGTGACAA-TTTTTTGTAACAATAATTATAGCTTATAGTTACA
1 AAACGTGAATATCACTATTT-TTGTGACAAGTTTTTTGTAACAATAAGTAAAACTTATAGTTACA
* ** *
82860 AAATGTCACTACATTATTTCGTTTTTGTACAAAAAATTGGAGATAATCATTGTGACTATACATTT
65 AAATGTCACTACATAATTTC-TTTGCGTACAAAAAATTGGAGATAATCATTGTGACAATACATTT
*
82925 TGTCACTATAATTAAAATATATAA
129 TGTCACTATAATTAAAACATATAA
82949 TTACAAAAAA
Statistics
Matches: 129, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
173 4 0.03
174 13 0.10
175 11 0.09
176 75 0.58
177 17 0.13
178 9 0.07
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (175 bp):
AAACGTGAATATCACTATTTTTGTGACAAGTTTTTTGTAACAATAAGTAAAACTTATAGTTACAA
AATGTCACTACATAATTTCTTTGCGTACAAAAAATTGGAGATAATCATTGTGACAATACATTTTG
TCACTATAATTAAAACATATAACGACAAACATTATTTTTTACTAA
Found at i:85839 original size:19 final size:20
Alignment explanation
Indices: 85815--85857 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
85805 AGCATTTATC
*
85815 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
85834 TTCATTAAAAATCATGTTTT
1 TTCATTAAAAATCATGTATT
85854 TTCA
1 TTCA
85858 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:86271 original size:34 final size:35
Alignment explanation
Indices: 86201--86275 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
86191 TACTTTCTAT
* *
86201 ACCATCTTTCATCTCCATATCACGCCTATATCATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
*
86236 ACCATCTTCCAAT-TCCATTTC-CGCCTATATAATC
1 ACCATCTTCC-ATCTCCATATCACGCCTATATAATC
86270 ACCATC
1 ACCATC
86276 CCATTATCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 18 0.50
35 16 0.44
36 2 0.06
ACGTcount: A:0.27, C:0.37, G:0.03, T:0.33
Consensus pattern (35 bp):
ACCATCTTCCATCTCCATATCACGCCTATATAATC
Found at i:86484 original size:15 final size:15
Alignment explanation
Indices: 86464--86504 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
86454 CTAATTTCAT
86464 ATTTCCATTTCAATC
1 ATTTCCATTTCAATC
86479 ATTTCCATTTCAATC
1 ATTTCCATTTCAATC
86494 ATTTCCATTTC
1 ATTTCCATTTC
86505 TATTTCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTCCATTTCAATC
Found at i:86497 original size:44 final size:43
Alignment explanation
Indices: 86413--86517 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 43
86403 ATATCATTTC
**
86413 TTTCA-ATTTCCTTTTCTTAATCATTTCCATTCTTTCCATTTCTAA
1 TTTCATATTTCCTTTTC--AATCATTTCCATTCAATCCATTTC-AA
* *
86458 TTTCATATTTCCATTTCAATCATTTCCATTTCAAT-CATTTCCA
1 TTTCATATTTCCTTTTCAATCATTTCCA-TTCAATCCATTTCAA
86501 TTTC-TATTTCCTTTTCA
1 TTTCATATTTCCTTTTCA
86518 TTCTTAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
42 12 0.23
43 5 0.09
44 17 0.32
45 9 0.17
46 10 0.19
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (43 bp):
TTTCATATTTCCTTTTCAATCATTTCCATTCAATCCATTTCAA
Found at i:86517 original size:27 final size:28
Alignment explanation
Indices: 86405--86516 Score: 83
Period size: 27 Copynumber: 3.9 Consensus size: 28
86395 ATAGTTTGAT
* *
86405 ATCATTT-C-TTTCAATTTCCTTTTCTTA
1 ATCATTTCCATTTCTATTTCCATTTC-TA
86432 ATCATTTCCA-TTC--TTTCCATTTCTA
1 ATCATTTCCATTTCTATTTCCATTTCTA
86457 ATTTCATATTTCCATTTCAATCATTTCCATTTC-A
1 A--TC--ATTTCCATTTC--T-ATTTCCATTTCTA
*
86491 ATCATTTCCATTTCTATTTCCTTTTC
1 ATCATTTCCATTTCTATTTCCATTTC
86517 ATTCTTAATT
Statistics
Matches: 71, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
25 3 0.04
26 9 0.13
27 19 0.27
28 5 0.07
29 7 0.10
30 14 0.20
32 2 0.03
34 2 0.03
35 10 0.14
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (28 bp):
ATCATTTCCATTTCTATTTCCATTTCTA
Found at i:86800 original size:11 final size:11
Alignment explanation
Indices: 86784--86817 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
86774 CAAAAGAAAG
86784 AAAAGAAAAAA
1 AAAAGAAAAAA
86795 AAAAGAAAAAA
1 AAAAGAAAAAA
86806 ATCAAAGAAAAA
1 A--AAAGAAAAA
86818 GAAGTGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
13 9 0.43
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:86806 original size:19 final size:20
Alignment explanation
Indices: 86775--86820 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
86765 TTTGGAGTGC
86775 AAAAGAAAGAAAAGAAAAAA
1 AAAAGAAAGAAAAGAAAAAA
** *
86795 AAAAGAAA-AAAATCAAAGA
1 AAAAGAAAGAAAAGAAAAAA
86814 AAAAGAA
1 AAAAGAA
86821 GTGAAGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAAGAAAGAAAAGAAAAAA
Done.