Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000690.1 Hibiscus syriacus cultivar Beakdansim tig00001346_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: 61087
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1145 original size:12 final size:12
Alignment explanation
Indices: 1128--1176 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
1118 ACTTGGCAAA
*
1128 CATTCTTTCATT
1 CATTCTTCCATT
1140 CATTCTTCCATT
1 CATTCTTCCATT
*
1152 CATTCTTTCATT
1 CATTCTTCCATT
*
1164 CCTTCTTCCATT
1 CATTCTTCCATT
1176 C
1 C
1177 TTTATCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.14, C:0.33, G:0.00, T:0.53
Consensus pattern (12 bp):
CATTCTTCCATT
Found at i:1155 original size:24 final size:24
Alignment explanation
Indices: 1128--1176 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1118 ACTTGGCAAA
1128 CATTCTTTCATTCATTCTTCCATT
1 CATTCTTTCATTCATTCTTCCATT
*
1152 CATTCTTTCATTCCTTCTTCCATT
1 CATTCTTTCATTCATTCTTCCATT
1176 C
1 C
1177 TTTATCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.00, T:0.53
Consensus pattern (24 bp):
CATTCTTTCATTCATTCTTCCATT
Found at i:6484 original size:124 final size:125
Alignment explanation
Indices: 6263--6507 Score: 307
Period size: 124 Copynumber: 2.0 Consensus size: 125
6253 TCCTTAAAGA
* * * * * *
6263 GTAGTGAAATGAATCAAAATTTTCAAATTTGACCTCTCTAAAGAGTAGCAGAGCAAATCTCTTTT
1 GTAGTGAAAAGAATAAAAAATTTCAAATCTGACCTCTCTAAAGAGTAGCAAAACAAATCTCTTTT
** * *
6328 ACAAATTTGATATTCTTGAAGAGTAGTGAAGCAAAT-AATCCACGATTCAATTTTCCATGG
66 ACAAATTTGATATTCTTGAAGAAAAATAAAGCAAATCAA-CCACGATTCAATTTTCCATGG
* * *
6388 GTAGTGAAAAGAATAAAAAATTTCAAATCTGATCTCAT-TAAAGAGTAGTAAAACATATC-CTTT
1 GTAGTGAAAAGAATAAAAAATTTCAAATCTGACCTC-TCTAAAGAGTAGCAAAACAAATCTCTTT
* * *
6451 TACATATTTGATCTTCTTGAAGAAAAATAAAGCAAATCAACCATGATTCAATTTTCC
65 TACAAATTTGATATTCTTGAAGAAAAATAAAGCAAATCAACCACGATTCAATTTTCC
6508 TTGAAGAGCA
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
124 51 0.50
125 50 0.49
126 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (125 bp):
GTAGTGAAAAGAATAAAAAATTTCAAATCTGACCTCTCTAAAGAGTAGCAAAACAAATCTCTTTT
ACAAATTTGATATTCTTGAAGAAAAATAAAGCAAATCAACCACGATTCAATTTTCCATGG
Found at i:6675 original size:252 final size:252
Alignment explanation
Indices: 6172--6675 Score: 522
Period size: 252 Copynumber: 2.0 Consensus size: 252
6162 CAGATCTAGT
* * * * ** *
6172 TTAAAGAGTAGAAAAATAGATCCCTTTTATAGATTTGATCTTCCTGAATAGAGGTGAAGCAAATC
1 TTAAAGAGTAGAAAAACAGATCCCTTTTACAGATTTGATCTTCCTGAAGAAAAATAAAGCAAATC
* * * * * *
6237 AACTAAAATTCAATTTTCCTTAAAGAGTAGTGAAATGAATCAAAATTTTCAAATTTGACCTCTCT
66 AACCAAAATTCAATTTTCCTTAAAGAGCAATGAAATGAATCAAAATTTCCAAATCTGACATCTCT
*
6302 AAAGAGTAGCAGAGCAAATCTCTTTTACAAATTTGATATTCTTGAAGAGTAGTGAAGCAAATAAT
131 AAAGAGTAGCAGAGCAAATCTCTTTTA-AAATTTGATATTCTTAAAGAGTAGTGAAGCAAATAAT
* * * * *
6367 CCACGATTCAATTTTCCATGGGTAGTGAAAAGAATAAAAAATTTCAAATCTGATCTCA
195 CCACGATTCAATTTTCCAAGAGAAATGAAAAGAATAAAAAATTTCAAATATGATCTCA
* * * *
6425 TTAAAGAGTAGTAAAACATAT-CCTTTTACATATTTGATCTTCTTGAAGAAAAATAAAGCAAATC
1 TTAAAGAGTAGAAAAACAGATCCCTTTTACAGATTTGATCTTCCTGAAGAAAAATAAAGCAAATC
** * * *
6489 AACCATGATTCAATTTTCCTTGAAGAGCAATG-AATGAATCAAAATTTCCAGATCTGATATC-CT
66 AACCAAAATTCAATTTTCCTTAAAGAGCAATGAAATGAATCAAAATTTCCAAATCTGACATCTC-
* ** * *
6552 TAAAGAGTGGTGGAGTAGATCT-TTTCT-AAATTTGATATTCTTAAAAGAGTAGT-AAGCAAATC
130 TAAAGAGTAGCAGAGCAAATCTCTTT-TAAAATTTGATATTCTT-AAAGAGTAGTGAAGCAAAT-
* * * *
6614 AA-CCATGATTCCATTTTACCTAAAGAGAAAT-AAAATGAAT-CAAAATTTCTAGATATGATCTC
192 AATCCACGATTCAATTTT-CC--AAGAGAAATGAAAA-GAATAAAAAATTTC-AAATATGATCTC
6676 CATAAGAGTA
Statistics
Matches: 205, Mismatches: 37, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
249 36 0.18
250 17 0.08
251 54 0.26
252 80 0.39
253 18 0.09
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (252 bp):
TTAAAGAGTAGAAAAACAGATCCCTTTTACAGATTTGATCTTCCTGAAGAAAAATAAAGCAAATC
AACCAAAATTCAATTTTCCTTAAAGAGCAATGAAATGAATCAAAATTTCCAAATCTGACATCTCT
AAAGAGTAGCAGAGCAAATCTCTTTTAAAATTTGATATTCTTAAAGAGTAGTGAAGCAAATAATC
CACGATTCAATTTTCCAAGAGAAATGAAAAGAATAAAAAATTTCAAATATGATCTCA
Found at i:15890 original size:14 final size:14
Alignment explanation
Indices: 15868--15897 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15858 AAAATATCGT
15868 ATAGAATTTTCTGC
1 ATAGAATTTTCTGC
*
15882 ATAGGATTTTCTGC
1 ATAGAATTTTCTGC
15896 AT
1 AT
15898 GCACCGTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (14 bp):
ATAGAATTTTCTGC
Found at i:18593 original size:26 final size:23
Alignment explanation
Indices: 18563--18605 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
18553 AGTCGCATTA
18563 ATTAA-TAAGTTAATGAAGGCAT
1 ATTAATTAAGTTAATGAAGGCAT
*
18585 ATTAGTTAAGTTAATGAAGGC
1 ATTAATTAAGTTAATGAAGGC
18606 TTCAGTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (23 bp):
ATTAATTAAGTTAATGAAGGCAT
Found at i:20317 original size:2 final size:2
Alignment explanation
Indices: 20310--20338 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20300 ATACGTAAAT
20310 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 T
20339 TCGTATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21800 original size:3 final size:3
Alignment explanation
Indices: 21792--21817 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21782 GCATGTAAAT
21792 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
21818 TATTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:22064 original size:37 final size:36
Alignment explanation
Indices: 22007--22082 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 36
21997 TAAAATGGAG
*
22007 AAAATATTAAAT-TTTAAA-AGAAATAAAAAATAGAAA
1 AAAATATTAAATGTTAAAAGAGAAAT-AAAAATA-AAA
22043 AAAATATATAAATGTTAAAAGAGAAATAAAAATAAAA
1 AAAATAT-TAAATGTTAAAAGAGAAATAAAAATAAAA
22080 AAA
1 AAA
22083 GATTGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 7 0.19
37 11 0.31
38 12 0.33
39 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (36 bp):
AAAATATTAAATGTTAAAAGAGAAATAAAAATAAAA
Found at i:23196 original size:20 final size:21
Alignment explanation
Indices: 23147--23198 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
23137 AACCAAAAAT
* *
23147 AATAT-TAATAAATAGATACT
1 AATATATAATAAATAAATACA
23167 AATAATATAATAAATAAATA-A
1 AAT-ATATAATAAATAAATACA
23188 AATATATAATA
1 AATATATAATA
23199 GTATATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 11 0.39
21 5 0.18
22 12 0.43
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AATATATAATAAATAAATACA
Found at i:23285 original size:14 final size:14
Alignment explanation
Indices: 23266--23411 Score: 108
Period size: 14 Copynumber: 10.4 Consensus size: 14
23256 ACACTATAAC
*
23266 ACTATAACATATAT
1 ACTATAATATATAT
23280 ACTATAATATATAAT
1 ACTATAATATAT-AT
*
23295 ATTATAA-ATATAT
1 ACTATAATATATAT
* *
23308 ATTATACTATTATAAT
1 ACTATAATA-TAT-AT
* *
23324 A-TCTAATATCTAAT
1 ACTATAATATAT-AT
23338 AC-ATAATATATAT
1 ACTATAATATATAT
*
23351 AACTATATTATATAT
1 -ACTATAATATATAT
23366 ACTAT-ATGATATAT
1 ACTATAAT-ATATAT
*
23380 AATATAATATATAT
1 ACTATAATATATAT
23394 AC-A-AATATACTAT
1 ACTATAATATA-TAT
23407 A-TATA
1 ACTATA
23412 TCCGGACGAA
Statistics
Matches: 108, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
12 6 0.06
13 17 0.16
14 54 0.50
15 28 0.26
16 3 0.03
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.42
Consensus pattern (14 bp):
ACTATAATATATAT
Found at i:23291 original size:2 final size:2
Alignment explanation
Indices: 23274--23412 Score: 79
Period size: 2 Copynumber: 73.0 Consensus size: 2
23264 ACACTATAAC
*
23274 AT AT AT ACT AT A- AT AT AT A- AT AT -T AT AA AT AT AT AT -T AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
23313 ACT AT -T AT A- AT AT CT A- AT AT CT A- AT AC AT A- AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23351 A- ACT AT AT -T AT AT AT ACT AT AT GAT AT AT A- AT AT A- AT AT
1 AT A-T AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT
* *
23390 AT AT AC AA AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT
23413 CCGGACGAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 38
0.69 0.07 0.24
Matches are distributed among these distances:
1 13 0.12
2 83 0.78
3 11 0.10
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:23408 original size:43 final size:41
Alignment explanation
Indices: 23275--23409 Score: 112
Period size: 43 Copynumber: 3.1 Consensus size: 41
23265 CACTATAACA
* * * *
23275 TATATACTATA-ATATATAATATTATAAATATATATTATAC
1 TATATACTATATATATATAATATAATATATATAAAATATAC
* * * *
23315 TATTATAATATCTAATATCTAATACATAATATATATAACTATATTA-
1 TA-TATACTATAT-ATATATAAT--ATAATATATATAA-AATA-TAC
23361 TATATACTATATGATATATAATATAATATATATACAAATATAC
1 TATATACTATAT-ATATATAATATAATATATATA-AAATATAC
23404 TATATA
1 TATATA
23410 TATCCGGACG
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
40 2 0.03
41 7 0.10
42 2 0.03
43 29 0.40
44 1 0.01
45 26 0.36
46 4 0.05
47 2 0.03
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.43
Consensus pattern (41 bp):
TATATACTATATATATATAATATAATATATATAAAATATAC
Found at i:25140 original size:15 final size:15
Alignment explanation
Indices: 25122--25210 Score: 57
Period size: 15 Copynumber: 6.0 Consensus size: 15
25112 TAATTATTTA
25122 AATATAATATTATAT
1 AATATAATATTATAT
*
25137 AATATAATTTTA-AT
1 AATATAATATTATAT
25151 AAT-T-ATATT-T-T
1 AATATAATATTATAT
*
25162 AATATTATATTA-AT
1 AATATAATATTATAT
25176 ATATACTCAATA-TATAAT
1 A-ATA-T-AATATTAT-AT
25194 AATATATGATATTATAT
1 AATATA--ATATTATAT
25211 TTAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 24
0.68 0.04 0.28
Matches are distributed among these distances:
11 4 0.07
12 5 0.09
13 6 0.10
14 7 0.12
15 15 0.26
16 4 0.07
17 11 0.19
18 6 0.10
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (15 bp):
AATATAATATTATAT
Found at i:25170 original size:13 final size:13
Alignment explanation
Indices: 25116--25172 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
25106 AAATATTAAT
* *
25116 TATTTAAATATAA
1 TATTTTAATATTA
25129 TATTATATAATA-TA
1 TATT-T-TAATATTA
25143 -ATTTTAATAATTA
1 TATTTTAAT-ATTA
25156 TATTTTAATATTA
1 TATTTTAATATTA
25169 TATT
1 TATT
25173 AATATATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 4 0.11
12 2 0.05
13 17 0.46
14 10 0.27
15 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTTTAATATTA
Found at i:25470 original size:26 final size:26
Alignment explanation
Indices: 25425--25475 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
25415 CCGAATTAAC
* * *
25425 TGATATTTTTTAATTGTTAATCAAAT
1 TGATATTTTTTAAATATTAACCAAAT
*
25451 TGATTTTTTTTAAATATTAACCAAA
1 TGATATTTTTTAAATATTAACCAAA
25476 CAAACTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (26 bp):
TGATATTTTTTAAATATTAACCAAAT
Found at i:33035 original size:6 final size:6
Alignment explanation
Indices: 33026--33065 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
33016 TTTCTTTTTT
33026 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
33066 AGTTATCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTTCCC
Found at i:33291 original size:2 final size:2
Alignment explanation
Indices: 33286--33345 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
33276 ATATTCATCC
33286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33328 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
33346 TAAAAAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35777 original size:21 final size:20
Alignment explanation
Indices: 35747--35799 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
35737 AAAAGATAAG
* *
35747 ATGTATATTATAGATATTATC
1 ATGTAAATTATAAATA-TATC
* *
35768 CTGTAAATTAAAAATATATC
1 ATGTAAATTATAAATATATC
*
35788 ATTTAAATTATA
1 ATGTAAATTATA
35800 TTTACACTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (20 bp):
ATGTAAATTATAAATATATC
Found at i:35928 original size:15 final size:14
Alignment explanation
Indices: 35885--35931 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
35875 AATTCATTAG
35885 TAATAT-TTATATA
1 TAATATATTATATA
*
35898 TAA-ATATTTTAT-
1 TAATATATTATATA
35910 TAATATATATATATA
1 TAATATAT-TATATA
35925 TAATATA
1 TAATATA
35932 AATAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 5 0.18
13 12 0.43
14 4 0.14
15 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATATATTATATA
Found at i:35935 original size:21 final size:21
Alignment explanation
Indices: 35892--35935 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
35882 TAGTAATATT
** *
35892 TATATATAAATATTTTATTAA
1 TATATATAAATATAATATAAA
*
35913 TATATATATATATAATATAAA
1 TATATATAAATATAATATAAA
35934 TA
1 TA
35936 ATTTTTAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATAAATATAATATAAA
Found at i:36411 original size:2 final size:2
Alignment explanation
Indices: 36406--36448 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36396 TTTGGGTCAA
36406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36448 A
1 A
36449 CACACTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37302 original size:32 final size:31
Alignment explanation
Indices: 37266--37353 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 31
37256 TTTTGTTCGA
*
37266 GTCAATATCACATTGGTTGATTTTTGAGTTAG
1 GTCAATATCACATT-GTTGATTTTTGAGTCAG
*
37298 GTCAATATCGAATCATT-TTG-TTTTTGGGTCAG
1 GTCAATATC--A-CATTGTTGATTTTTGAGTCAG
* *
37330 GTCAATACCACATCAGTTGATTTT
1 GTCAATATCACAT-TGTTGATTTT
37354 CAGGTCGGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
29 3 0.07
30 1 0.02
31 3 0.07
32 31 0.67
33 3 0.07
34 1 0.02
35 4 0.09
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (31 bp):
GTCAATATCACATTGTTGATTTTTGAGTCAG
Found at i:41109 original size:106 final size:106
Alignment explanation
Indices: 40921--41194 Score: 413
Period size: 106 Copynumber: 2.6 Consensus size: 106
40911 AATTGAACTA
* * * * * * ***
40921 GGAAATTGTTTGTTGACAGCCAGCCGCCCCTTCGCTCTAAAGTTAAACTTGTGCCATCTCGAGTC
1 GGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTC
40986 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTT
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTT
41027 GGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTC
1 GGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTC
* *
41092 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTT
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTT
* * * *
41133 GGAAATTGTTTGTTGAGAACCAGCCATCCCTTCGTTGTGGAGTTGAACTTATGTTGTCTCGA
1 GGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA
41195 TTGGCACGAT
Statistics
Matches: 153, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 153 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (106 bp):
GGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTC
CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTT
Found at i:41831 original size:32 final size:32
Alignment explanation
Indices: 41795--41880 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
41785 CCAAAGATTT
* *
41795 CCCAATATTCAATGTTGAATCTCAAAAA-ATGC
1 CCCAACATTCAATGTTAAATCT-AAAAATATGC
** *
41827 CCCAACATTTGATGTTAAATCTAAAAATATGT
1 CCCAACATTCAATGTTAAATCTAAAAATATGC
**
41859 CCCAACATTTGATGTTAAATCT
1 CCCAACATTCAATGTTAAATCT
41881 TCAAAGATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 5 0.10
32 43 0.90
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (32 bp):
CCCAACATTCAATGTTAAATCTAAAAATATGC
Found at i:42816 original size:69 final size:69
Alignment explanation
Indices: 42729--42866 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
42719 TGTCTCTCTC
* *
42729 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAAAAATGATTGTGCTTGATCAATC
42794 TCAT
66 TCAT
* * *
42798 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAAAAATGATTGTGCTTGATCAATC
42863 TCAT
66 TCAT
42867 AGTTTAAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:42950 original size:9 final size:8
Alignment explanation
Indices: 42927--42994 Score: 59
Period size: 8 Copynumber: 8.0 Consensus size: 8
42917 TCTTGTCTTC
42927 TTTTTTCT
1 TTTTTTCT
*
42935 TAATTTTCCT
1 T--TTTTTCT
42945 TTTTTTCT
1 TTTTTTCT
42953 TTTTTT-T
1 TTTTTTCT
42960 TTTTCTT-T
1 TTTT-TTCT
42968 GTTTTTTCT
1 -TTTTTTCT
42977 CTTTTTTCT
1 -TTTTTTCT
42986 TTTTGTTCT
1 TTTT-TTCT
42995 GATTGAATCT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
7 5 0.10
8 22 0.43
9 17 0.33
10 7 0.14
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.81
Consensus pattern (8 bp):
TTTTTTCT
Found at i:42962 original size:13 final size:13
Alignment explanation
Indices: 42944--42989 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
42934 TTAATTTTCC
42944 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
*
42957 TTTTTTTCTTTGT
1 TTTTTTTCTTTTT
*
42970 TTTTTCTCTTTTT
1 TTTTTTTCTTTTT
*
42983 TCTTTTT
1 TTTTTTT
42990 GTTCTGATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.87
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:52705 original size:11 final size:11
Alignment explanation
Indices: 52675--52712 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52665 AAAGCGGTTG
* *
52675 AAGATAAAGTA
1 AAGATAAATTC
52686 AAGAT-AATTC
1 AAGATAAATTC
52696 AAGATAAATTC
1 AAGATAAATTC
52707 AAGATA
1 AAGATA
52713 GCATCTGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (11 bp):
AAGATAAATTC
Found at i:55055 original size:24 final size:24
Alignment explanation
Indices: 55028--55073 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
55018 GCATGACATG
55028 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
55052 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
55074 ATCTGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:56827 original size:31 final size:31
Alignment explanation
Indices: 56746--56831 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 31
56736 ACTCGGCCTG
*
56746 AAATCAACTAATTTGATATTGACCCGACCCAA
1 AAATCAAC-AATGTGATATTGACCCGACCCAA
*
56778 AAA-CAA-AATGATTCGATATTGACCCGA-CTAA
1 AAATCAACAATG--T-GATATTGACCCGACCCAA
56809 AAATCAACCAATGTGATATTGAC
1 AAATCAA-CAATGTGATATTGAC
56832 TCGAATCACA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
29 3 0.07
31 19 0.41
32 20 0.43
34 4 0.09
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (31 bp):
AAATCAACAATGTGATATTGACCCGACCCAA
Found at i:58873 original size:3 final size:3
Alignment explanation
Indices: 58867--58936 Score: 86
Period size: 3 Copynumber: 22.0 Consensus size: 3
58857 TTCATTTCGT
**
58867 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
58913 TATA TATA TATA TTA TTA TTA TTA
1 T-TA T-TA T-TA TTA TTA TTA TTA
58937 ATAATATTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 47 0.76
4 15 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:58944 original size:12 final size:12
Alignment explanation
Indices: 58867--58945 Score: 77
Period size: 12 Copynumber: 6.2 Consensus size: 12
58857 TTCATTTCGT
*
58867 TTATTATTATTA
1 TTATTATTAATA
*
58879 TTATTATTAAAA
1 TTATTATTAATA
*
58891 TTATTATTATTA
1 TTATTATTAATA
58903 TTATTATATATATA
1 TTATTAT-TA-ATA
*
58917 TATATATATTATTA
1 T-TAT-TATTAATA
*
58931 TTATTAATAATA
1 TTATTATTAATA
58943 TTA
1 TTA
58946 CAAGCAAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
12 36 0.65
13 5 0.09
14 6 0.11
15 5 0.09
16 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:60495 original size:116 final size:113
Alignment explanation
Indices: 60284--60499 Score: 249
Period size: 116 Copynumber: 1.9 Consensus size: 113
60274 TTTAATCATG
* * * *
60284 TTTTAATATTTATTTATTTTTCAATATTAAGAAAGGACATCTTAAAACAACTGGATGTCCATTTT
1 TTTTAATATTTATTTATTTTTCAATATGAAGAAAAGACATCTTAAAACAACTAGAAGTCCATTTT
60349 CTGATATTTTAAATAAATAAATATCCTATTTTATAAATTATATCTAATTA
66 CTGATATTTTAAATAAAT-AATATCCTA-TTTATAAATTATATCTAATTA
* * ** *
60399 TTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTTTCTTAAGGCACCTAGAAGT-CA
1 TTTTAA-TATTTATTTATTTTTCAATAT-GAAGAAAAGA-C-ATCTTAAAACAACTAGAAGTCCA
**
60463 TTTTCTGATATTTCTAAAT-AAT-ATATTTTATTTATAA
62 TTTTCTGATATTT-TAAATAAATAATATCCTATTTATAA
60500 TATATTAAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
115 13 0.15
116 26 0.31
117 8 0.09
118 19 0.22
119 19 0.22
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (113 bp):
TTTTAATATTTATTTATTTTTCAATATGAAGAAAAGACATCTTAAAACAACTAGAAGTCCATTTT
CTGATATTTTAAATAAATAATATCCTATTTATAAATTATATCTAATTA
Found at i:61039 original size:21 final size:22
Alignment explanation
Indices: 60992--61047 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
60982 TTTCTTTCAA
60992 ATTTTTTATTACTTATATTTTTAT
1 ATTTTTTATTA--TATATTTTTAT
*
61016 ATTTTTTATTA-ATATTTTTTT
1 ATTTTTTATTATATATTTTTAT
61037 ATTTATTTATT
1 ATTT-TTTATT
61048 CAGGTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 13 0.43
22 6 0.20
24 11 0.37
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
ATTTTTTATTATATATTTTTAT
Done.