Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005012.1 Hibiscus syriacus cultivar Beakdansim tig00011252_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: 57733
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:23 original size:1 final size:1
Alignment explanation
Indices: 17--56 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
7 ATGCTTGAAG
* * *
17 AAAAAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
57 GGGGTCAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:37 original size:18 final size:18
Alignment explanation
Indices: 14--56 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
4 ATTATGCTTG
14 AAGAAAAAAAAAAAAAAA
1 AAGAAAAAAAAAAAAAAA
*
32 AAG-AAAAAAAAAGAAAA
1 AAGAAAAAAAAAAAAAAA
49 AAGAAAAA
1 AAGAAAAA
57 GGGGTCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAAAAAAA
Found at i:1190 original size:94 final size:94
Alignment explanation
Indices: 1027--1317 Score: 464
Period size: 94 Copynumber: 3.1 Consensus size: 94
1017 CAAGTGTTCG
*
1027 TGTGCTCATAGCATCTTCTTGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
*
1092 AAAACCAATCATTGAATTTGAAAAATAAA
66 AAAACCAATCATTGGATTTGAAAAATAAA
*
1121 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1186 AAAACCAATCATTGGATTTG--AAATAAA
66 AAAACCAATCATTGGATTTGAAAAATAAA
** *
1213 -GAAACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 TG-TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC
* *
1277 -AAAAACCAATCATTGGATTTGAAAGATGAA
64 GAAAAACCAATCATTGGATTTGAAAAATAAA
1307 TGTGCTCATAG
1 TGTGCTCATAG
1318 TAGAAATAAG
Statistics
Matches: 181, Mismatches: 11, Indels: 11
0.89 0.05 0.05
Matches are distributed among these distances:
91 1 0.01
92 30 0.17
93 59 0.33
94 90 0.50
95 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (94 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
AAAACCAATCATTGGATTTGAAAAATAAA
Found at i:1445 original size:115 final size:115
Alignment explanation
Indices: 1205--1420 Score: 346
Period size: 115 Copynumber: 1.9 Consensus size: 115
1195 CATTGGATTT
* *
1205 GAAATAAAGAA-ACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAT-AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTA
* * * *
1269 TGAACCACAAAAACCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTA
65 GGAACCACAAAAACCAATCATTGGAATTAAAAGATGAATGTGATCATAGTA
1320 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTAG
1 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTAG
*
1385 GAACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
66 GAACCACAAAAACCAATCATTGGAATTAAAAGATGAA
1421 CTGTATGATC
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 31 0.33
115 63 0.67
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (115 bp):
GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTAG
GAACCACAAAAACCAATCATTGGAATTAAAAGATGAATGTGATCATAGTA
Found at i:2501 original size:222 final size:220
Alignment explanation
Indices: 2115--2989 Score: 1109
Period size: 222 Copynumber: 3.9 Consensus size: 220
2105 ATCATTCTTA
2115 GATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
2180 TAATGAGAA-AACTTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATTACCAGG
66 TAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTC-ATGGATCAACATTACCAAG
** * *
2243 TCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTC
130 -AAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
2308 AACTTTTCGCTTGAATTCATCATTCGATG
194 AACTTTT-GCTTAAATCCATCATT-GATG
**
2337 GATCAGCATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
1 GATCAGCATTACCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* * * * * *
2401 ATAATGAGAAGAATTTGTTCAACTTTCCGCTTGAATTCATCA-TTCATGGATCAGCATTACCAGG
65 ATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTCATGGATCAACATTACCAAG
**
2465 TCGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
130 -AAAGTTCATAATGAGAAGAACTCATCTAAAGAA-G--GAAGAAGTTCATAATGAGAAGAACTTG
* *
2530 TTCAACCTTTGCTCAAATCCATCACTTGATG
191 TTCAACTTTTGCTTAAATCCATCA-TTGATG
* * *
2561 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAGAAGAAGTT
1 GATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG--GAAGAAGAAGTT
* * * * *
2626 CATAATGAGAAGAACTTGTTCAACTTTTTG-TTCAAATCCATCATTTGATGGATCAACTTTTCCA
64 CATAATGAGAAGAACTTGTTCAACTTTTCGCTT-AAATCCATCACTTCATGGATCAACATTACCA
*
2690 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAGTTCATAATGAGAAGAACTTGT
128 AGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAG-AAGTTCATAATGAGAAGAACTTGT
2755 TCAACTTTTTG-TTCAAATCCATCATTTGATG
192 TCAAC-TTTTGCTT-AAATCCATCA-TTGATG
* * *
2786 GATCAACATTTCCAG-GTAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTC
1 GATCAGCATTACCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* * * * * *
2850 ATAATGAGAAGAATTTGTTCAA-TTTTTGCTCAAATCCATCACTTGATGGATCAACCTTTCCAAG
65 ATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTCATGGATCAACATTACCAAG
* * *
2914 AAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTAT
130 AAAGTTCATAATGAGAAGAACTCATCT---AAAGAAGGAAGAAGTTCATAATGAGAAGAACTTGT
2979 TCAACCTTTTG
192 TCAA-CTTTTG
2990 AATGACTCTA
Statistics
Matches: 590, Mismatches: 43, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
221 1 0.00
222 186 0.32
223 72 0.12
224 121 0.21
225 116 0.20
226 77 0.13
227 17 0.03
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (220 bp):
GATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTCATGGATCAACATTACCAAGA
AAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CTTTTGCTTAAATCCATCATTGATG
Found at i:2504 original size:112 final size:112
Alignment explanation
Indices: 2115--2988 Score: 1117
Period size: 112 Copynumber: 7.8 Consensus size: 112
2105 ATCATTCTTA
2115 GATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAGCATTACCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
2180 TAATGAGAA-AACTTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATG
65 TAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTC-ATG
**
2227 GATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCA
1 GATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
2289 TAATGAGAAGAATTTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATG
65 TAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTC-ATG
**
2337 GATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
2402 TAATGAGAAGAATTTGTTCAACTTTCCGCTTGAATTCATCA-TTCATG
65 TAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTCATG
** *
2449 GATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCA
1 GATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
2514 TAATGAGAAGAACTTGTTCAACCTTT-GCTCAAATCCATCACTTGATG
65 TAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTCATG
* * *
2561 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAGAAGAAGTT
1 GATCAGCATTACCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG--GAAGAAGAAGTT
* * *
2626 CATAATGAGAAGAACTTGTTCAACTTTTTG-TTCAAATCCATCATTTGATG
63 CATAATGAGAAGAACTTGTTCAACTTTTCGCTT-AAATCCATCACTTCATG
* * * *
2676 GATCAACTTTTCCAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-A-AAGTTCAT
1 GATCAGCATTACCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
2739 AATGAGAAGAACTTGTTCAACTTTTTG-TTCAAATCCATCATTTGATG
66 AATGAGAAGAACTTGTTCAACTTTTCGCTT-AAATCCATCACTTCATG
* * *
2786 GATCAACATTTCCAGGTAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
2851 TAATGAGAAGAATTTGTTCAA-TTTTTGCTCAAATCCATCACTTGATG
65 TAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTCATG
* * * * * *
2898 GATCAACCTTTCCAAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAT
1 GATCAGCATTACCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
2963 AATGAGAAGAGCTTATTCAACCTTTT
66 AATGAGAAGAACTTGTTCAA-CTTTT
2989 GAATGACTCT
Statistics
Matches: 709, Mismatches: 36, Indels: 33
0.91 0.05 0.04
Matches are distributed among these distances:
109 20 0.03
110 156 0.22
111 115 0.16
112 227 0.32
113 87 0.12
114 74 0.10
115 30 0.04
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
GATCAGCATTACCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTTTTCGCTTAAATCCATCACTTCATG
Found at i:2859 original size:24 final size:23
Alignment explanation
Indices: 2816--2860 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2806 GTTCATAATG
*
2816 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
2839 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
2861 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:3203 original size:3 final size:3
Alignment explanation
Indices: 3197--3256 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
3187 TAACCCATTT
* *
3197 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
3245 TTA TTA TTA TTA
1 TTA TTA TTA TTA
3257 AAAAAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:7054 original size:23 final size:23
Alignment explanation
Indices: 7028--7096 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
7018 CACCACAGCT
* *
7028 CGTATAATTGCACCGAAGTTCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
7051 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
7074 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
7097 TATAAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:9375 original size:20 final size:21
Alignment explanation
Indices: 9352--9395 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9342 TATTAAAAAT
*
9352 AAAAATAAATT-ATATATTTA
1 AAAAATAAATTAAAATATTTA
* *
9372 AAAAGTTAATTAAAATATTTA
1 AAAAATAAATTAAAATATTTA
9393 AAA
1 AAA
9396 TATTTAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATAAATTAAAATATTTA
Found at i:22682 original size:30 final size:31
Alignment explanation
Indices: 22608--22684 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
22598 CAGTTATGTC
*
22608 AGGGACTATATTGAAAAAGGACTAAATGTTG
1 AGGGACTATATTGCAAAAGGACTAAATGTTG
* *
22639 AGGGACCATATTGCAAACGGACTAAATG-TG
1 AGGGACTATATTGCAAAAGGACTAAATGTTG
* *
22669 GGGGATTATATTGCAA
1 AGGGACTATATTGCAA
22685 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 15 0.38
31 25 0.62
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (31 bp):
AGGGACTATATTGCAAAAGGACTAAATGTTG
Found at i:24506 original size:31 final size:31
Alignment explanation
Indices: 24468--24538 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
24458 CTTTTAAAAC
* *
24468 TTGCAATATAATCACC-TAATATTTAGTTCGT
1 TTGCAATATAATC-CCTTAACATTTAGTCCGT
**
24499 TTGCAATATGGTCCCTTAACATTTAGTCCGT
1 TTGCAATATAATCCCTTAACATTTAGTCCGT
24530 TTGCAATAT
1 TTGCAATAT
24539 GGTCCCTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (31 bp):
TTGCAATATAATCCCTTAACATTTAGTCCGT
Found at i:27990 original size:50 final size:50
Alignment explanation
Indices: 27915--28012 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
27905 TAATTAAAGT
*
27915 CTTTGAAAATCCATATCCTCCAACTAGATACAATCCTTTAATAAAAATGC
1 CTTTGAAAATCCATATCCTCCAACTAAATACAATCCTTTAATAAAAATGC
* * *
27965 CTTTGAAAATCCGTATCCTCCAACTAAATATAATCCTTTAGTAAAAAT
1 CTTTGAAAATCCATATCCTCCAACTAAATACAATCCTTTAATAAAAAT
28013 ACTGACAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (50 bp):
CTTTGAAAATCCATATCCTCCAACTAAATACAATCCTTTAATAAAAATGC
Found at i:28229 original size:99 final size:98
Alignment explanation
Indices: 28082--28278 Score: 358
Period size: 99 Copynumber: 2.0 Consensus size: 98
28072 TTCTACCATT
*
28082 TAGTTCATTAAAAATCAATATATAAACCTCTTAGGCAAGTCTAATAGAGAGATCTGAATTAAATA
1 TAGTTCATTAAAAATCAATATATAAACCTCTTAGGCAAGTCTAATAGAGAGATCTGAATTAAAAA
**
28147 TCAATATATAAATCTTTTTGACAAGTCTAAGAGA
66 TCAATATATAAATC-TTTAAACAAGTCTAAGAGA
28181 TAGTTCATTAAAAATCAATATATAAACCTCTTAGGCAAGTCTAATAGAGAGATCTGAATTAAAAA
1 TAGTTCATTAAAAATCAATATATAAACCTCTTAGGCAAGTCTAATAGAGAGATCTGAATTAAAAA
28246 TCAATATATAAATCTTTAAACAAGTCTAAGAGA
66 TCAATATATAAATCTTTAAACAAGTCTAAGAGA
28279 GACCTGAATT
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
98 17 0.18
99 78 0.82
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (98 bp):
TAGTTCATTAAAAATCAATATATAAACCTCTTAGGCAAGTCTAATAGAGAGATCTGAATTAAAAA
TCAATATATAAATCTTTAAACAAGTCTAAGAGA
Found at i:28288 original size:48 final size:51
Alignment explanation
Indices: 28088--28288 Score: 252
Period size: 51 Copynumber: 4.1 Consensus size: 51
28078 CATTTAGTTC
*
28088 ATTAAAAATCAATATATAAACCTCTTAGGCAAGTCTAATAGAGAGATCTGA
1 ATTAAAAATCAATATATAAACCTCTTAGACAAGTCTAATAGAGAGATCTGA
* * * * * * *
28139 ATTAAATATCAATATATAAATCTTTTTGACAAGTCTAAGAGATAG-T-T-C
1 ATTAAAAATCAATATATAAACCTCTTAGACAAGTCTAATAGAGAGATCTGA
*
28187 ATTAAAAATCAATATATAAACCTCTTAGGCAAGTCTAATAGAGAGATCTGA
1 ATTAAAAATCAATATATAAACCTCTTAGACAAGTCTAATAGAGAGATCTGA
* * *
28238 ATTAAAAATCAATATATAAATCT-TTAAACAAGTCT-A-AGAGAGACCTGA
1 ATTAAAAATCAATATATAAACCTCTTAGACAAGTCTAATAGAGAGATCTGA
28286 ATT
1 ATT
28289 CTCTGGGAAG
Statistics
Matches: 127, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
48 52 0.41
49 3 0.02
50 12 0.09
51 60 0.47
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (51 bp):
ATTAAAAATCAATATATAAACCTCTTAGACAAGTCTAATAGAGAGATCTGA
Found at i:33659 original size:20 final size:20
Alignment explanation
Indices: 33616--33666 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
33606 TTATCATTAT
*
33616 AAATAATTTTAAATCTTCTT
1 AAATAATTTTAAATCTTCTC
* * *
33636 AAATAATTTTTATTTTTCTC
1 AAATAATTTTAAATCTTCTC
*
33656 AAATAAATTTA
1 AAATAATTTTA
33667 TATAACTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATAATTTTAAATCTTCTC
Found at i:34367 original size:12 final size:12
Alignment explanation
Indices: 34330--34370 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
34320 ACTATATGGT
*
34330 ATGAACAGTACC
1 ATGAACAATACC
*
34342 GTGAACAATA--
1 ATGAACAATACC
34352 ATGAACAATACC
1 ATGAACAATACC
34364 ATGAACA
1 ATGAACA
34371 GTGCTACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.17
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:35098 original size:31 final size:31
Alignment explanation
Indices: 35060--35215 Score: 201
Period size: 31 Copynumber: 5.0 Consensus size: 31
35050 CCGGAAGGAC
* * *
35060 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
*
35091 CAGTCCATATG-TCACGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
35122 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
*
35153 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
* *
35184 CAGTCTATATG-TCCCTAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
35215 C
1 C
35216 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAA
Found at i:35157 original size:62 final size:62
Alignment explanation
Indices: 35060--35215 Score: 233
Period size: 62 Copynumber: 2.5 Consensus size: 62
35050 CCGGAAGGAC
* * * *
35060 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCACGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATATCACGAAGAACATAGGTAAA
*
35122 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATATCACGAAGAACATAGGTAAA
* *
35184 CAGTCTATATGTCCCTAAGAACATAGGTAAAC
1 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
35216 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
62 85 0.99
63 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATATCACGAAGAACATAGGTAAA
Found at i:38707 original size:18 final size:18
Alignment explanation
Indices: 38672--38717 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
38662 TCATGTTTTA
*
38672 TATG-ATGT-TGTGTATG
1 TATGTATGTATGTATATG
38688 TATGTATGTATGTATATG
1 TATGTATGTATGTATATG
*
38706 TATGTATATATG
1 TATGTATGTATG
38718 CACACACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 18 0.69
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (18 bp):
TATGTATGTATGTATATG
Found at i:42307 original size:21 final size:21
Alignment explanation
Indices: 42281--42342 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
42271 TCTGGTTCGG
*
42281 TTGAATGTGTACCGATTCCCA
1 TTGAATGGGTACCGATTCCCA
*
42302 TTGAATGGGTATCGATTCCCA
1 TTGAATGGGTACCGATTCCCA
42323 TTGAATGGGTACCGATTCCC
1 TTGAATGGGTACCGATTCCC
42343 CTAGCCCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCA
Found at i:49030 original size:22 final size:23
Alignment explanation
Indices: 48977--49030 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
48967 ACAAGTTTTG
*
48977 AATGAGCTTTAAATGATTTATCA
1 AATGAGCTTTAAATGATTCATCA
* *
49000 AATGTGCTTTGAACT-ATTCAT-A
1 AATGAGCTTT-AAATGATTCATCA
49022 AATGAGCTT
1 AATGAGCTT
49031 GTTGTGAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.35
23 14 0.54
24 3 0.12
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (23 bp):
AATGAGCTTTAAATGATTCATCA
Done.