Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000242.1 Hibiscus syriacus cultivar Beakdansim tig00000426_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: 43045
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:201 original size:2 final size:2
Alignment explanation
Indices: 194--248 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
184 AATGTTATGA
194 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
236 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
249 AGAAATAGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1416 original size:96 final size:98
Alignment explanation
Indices: 1203--1564 Score: 456
Period size: 96 Copynumber: 3.8 Consensus size: 98
1193 TATCATGAAA
* *
1203 AACATGTTTTGTCTTAC-TTTACATAATATAAAC-GTTTCATACTTATAACTTAAA-TGATTAAC
1 AACATGTTTTGTCTTACTTTTGCATAATATAAACAGTTTCATACTTATAACTTAAACTGATTGAC
* *
1265 ATTTTAAAAAGGTGTTACCTAGTATGTTCATAAGC
66 A--TTAAAAAAGTGTTACCTAGTACGTTCATAAGC
* * * *
1300 AACATGTATTGTCTTACTTTTGCATAATATTAACAGTTTCATCCTTATAATTTAAACTG-TTGAC
1 AACATGTTTTGTCTTACTTTTGCATAATATAAACAGTTTCATACTTATAACTTAAACTGATTGAC
*
1364 ATTAAAAAAGTGTTACCTAGTACG-TCATAATC
66 ATTAAAAAAGTGTTACCTAGTACGTTCATAAGC
* *
1396 AACATGTTTTGTCTTACTTTTGCATAATATAAATAGTTTCATACTTAT-ACTTAAAC-GACTGAC
1 AACATGTTTTGTCTTACTTTTGCATAATATAAACAGTTTCATACTTATAACTTAAACTGATTGAC
* * *
1459 A-TAAAAAA-TGTGTACCTACTACGTATCATGAGA
66 ATTAAAAAAGTGT-TACCTAGTACGT-TCATAAGC
* * * *
1492 AACATGTTTTATCTTACTTTTGCATCATATAAACAATTTCATACTTATAACTTAAACAG-TTGAC
1 AACATGTTTTGTCTTACTTTTGCATAATATAAACAGTTTCATACTTATAACTTAAACTGATTGAC
1556 ATTAAAAAA
66 ATTAAAAAA
1565 AAAGGTGTTA
Statistics
Matches: 231, Mismatches: 24, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
93 3 0.01
94 18 0.08
95 12 0.05
96 100 0.43
97 50 0.22
98 22 0.10
99 24 0.10
100 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (98 bp):
AACATGTTTTGTCTTACTTTTGCATAATATAAACAGTTTCATACTTATAACTTAAACTGATTGAC
ATTAAAAAAGTGTTACCTAGTACGTTCATAAGC
Found at i:1706 original size:19 final size:19
Alignment explanation
Indices: 1669--1722 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1659 ATATTTGTGG
*
1669 AAAAATATAGATACTTTTCC
1 AAAAATATACATAC-TTTCC
* *
1689 AAAAATATCCATACTTTCG
1 AAAAATATACATACTTTCC
* *
1708 AAAAGTATTCATACT
1 AAAAATATACATACT
1723 CAAATTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (19 bp):
AAAAATATACATACTTTCC
Found at i:2017 original size:19 final size:20
Alignment explanation
Indices: 1993--2048 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1983 TTTAAATTCT
* *
1993 AAAGTATCTATACTTTTG-A
1 AAAGTATCCATACTTTCGAA
*
2012 AAAGTATCCATACATTCGAA
1 AAAGTATCCATACTTTCGAA
2032 AAAGTATCCATACTTTC
1 AAAGTATCCATACTTTC
2049 ACATTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (20 bp):
AAAGTATCCATACTTTCGAA
Found at i:2036 original size:20 final size:19
Alignment explanation
Indices: 1993--2044 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1983 TTTAAATTCT
* * *
1993 AAAGTATCTATACTTTTGA
1 AAAGTATCCATACATTCGA
2012 AAAGTATCCATACATTCGAA
1 AAAGTATCCATACATTCG-A
2032 AAAGTATCCATAC
1 AAAGTATCCATAC
2045 TTTCACATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (19 bp):
AAAGTATCCATACATTCGA
Found at i:2150 original size:77 final size:77
Alignment explanation
Indices: 2059--2793 Score: 449
Period size: 77 Copynumber: 9.6 Consensus size: 77
2049 ACATTTTTAA
* * * * * *
2059 TAATAGAAAA-ATTAACATTCCAAATCGTAACTTGCTTTTTTAGTGCACTATAACATT-TTGTGT
1 TAATA-AAAATATTAACATTCCAAATCGTAACTT-ATTTCTTAGTGAACCATAACATTCTTGGGA
** *
2122 GTGACCCATTTTAT
64 GAAACCCATATTAT
* * * * * *
2136 TAATAAAATTATTAAAATTTCAGATCCTAACTTATTTCTTAGTGAACCATGACATTCTTGGGAGA
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGAGA
**
2201 AACTTATATTAT
66 AACCCATATTAT
* ** * *
2213 TAATAAAAATATTAACATTCCAAATCGCAACACATTTCTTAGTGAATCATGACATTCTT--GAGC
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGAG-
* *
2276 ACAACTCGT-TTAT
65 A-AACCCATATTAT
** * * ** *
2289 TAA-AAAAATATTAACATT-C-AATCACAACATA-TTATTA-TGAACCATGGCATTCTTGGGCGA
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGAGA
* *
2349 AACTCATTTTAT
66 AACCCATATTAT
* * * * * ** * *
2361 TAAT-AAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAATCATGACATTCTTAAGCGC
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGAGA
* *
2425 AACTCATTTTAT
66 AACCCATATTAT
* * *** * * * ** *
2437 TAATATAAATATGAACATT-CAAGATTACAACATATTTATTAGTGAATCATGGCATTCTTGGGTG
1 TAATAAAAATATTAACATTCCAA-ATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGAG
** *
2501 AAACTTATTTTAT
65 AAACCCATATTAT
* * * * *
2514 TAATAAAAATATTAACATTCTAGATCGCAACCTATTTCTTAGTGAACCATGACACTT-TT-GGAT
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACA-TTCTTGGGA-
* * *
2577 GCAACTCATTTTAT
64 GAAACCCATATTAT
* ** * *** * * * * *** * * *
2591 TAATAAAAATATTAGCATTTGATATTACAACATATTTATTAGTAAACTAGGCCATTCATGGGCGT
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGAGA
*
2656 AACCCATTTTAT
66 AACCCATATTAT
*
2668 TAATAAAAATATTAACATTCCAAATCGTACCTTATTTCTTAGTGAACCATAACATTCTT-GGACG
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGA-G
* * *
2732 CAACCTATTTTAT
65 AAACCCATATTAT
* * * * *
2745 TAAT-AAAATATTAACATTACATATCGCAACATGTTTCTTAGTGAACCAT
1 TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCAT
2794 GATATTTTTA
Statistics
Matches: 529, Mismatches: 109, Indels: 41
0.78 0.16 0.06
Matches are distributed among these distances:
71 21 0.04
72 27 0.05
73 13 0.02
74 11 0.02
75 23 0.04
76 110 0.21
77 319 0.60
78 5 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (77 bp):
TAATAAAAATATTAACATTCCAAATCGTAACTTATTTCTTAGTGAACCATAACATTCTTGGGAGA
AACCCATATTAT
Found at i:2556 original size:154 final size:152
Alignment explanation
Indices: 2128--2794 Score: 741
Period size: 154 Copynumber: 4.4 Consensus size: 152
2118 GTGTGTGACC
* * * * * *
2128 CATTTTATTAATAAAATTATTAAAATTTCAGA-TCCTAACTTATTTCTTAGTGAACCATGACATT
1 CATTTTATTAATAAAAATATTAACA-TTCA-ATTAC-AACATATTTATTAGTGAACCATGGCATT
* * *
2192 CTTGGGAGAAACTTATATTATTAATAAAAATATTAACATTCCAAATCGCAACAC-ATTTCTTAGT
63 CTTGGGCGAAACTCATTTTATTAATAAAAATATTAACATTCCAAATCGCAAC-CTATTTCTTAGT
* *
2256 GAATCATGACATTCTT-GAGCACAACT
127 GAACCATGACATTCTTAGA-CGCAACT
* *
2282 C-GTTTATTAA-AAAAATATTAACATTCAATCACAACATA-TTATTA-TGAACCATGGCATTCTT
1 CATTTTATTAATAAAAATATTAACATTCAATTACAACATATTTATTAGTGAACCATGGCATTCTT
* * *
2343 GGGCGAAACTCATTTTATTAAT-AAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAAT
66 GGGCGAAACTCATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTATTTCTTAGTGAAC
2407 CATGACATTCTTA-AGCGCAACT
131 CATGACATTCTTAGA-CGCAACT
* * *
2429 CATTTTATTAATATAAATATGAACATTCAAGATTACAACATATTTATTAGTGAATCATGGCATTC
1 CATTTTATTAATAAAAATATTAACATTC-A-ATTACAACATATTTATTAGTGAACCATGGCATTC
* * * *
2494 TTGGGTGAAACTTATTTTATTAATAAAAATATTAACATTCTAGATCGCAACCTATTTCTTAGTGA
64 TTGGGCGAAACTCATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTATTTCTTAGTGA
* *
2559 ACCATGACACTT-TTGGATGCAACT
129 ACCATGACA-TTCTTAGACGCAACT
* * * *
2583 CATTTTATTAATAAAAATATTAGCATTTGATATTACAACATATTTATTAGTAAACTA-GGCCATT
1 CATTTTATTAATAAAAATATTAACA-TTCA-ATTACAACATATTTATTAGTGAACCATGG-CATT
* * * *
2647 CATGGGCGTAACCCATTTTATTAATAAAAATATTAACATTCCAAATCG-TACCTTATTTCTTAGT
63 CTTGGGCGAAACTCATTTTATTAATAAAAATATTAACATTCCAAATCGCAACC-TATTTCTTAGT
* *
2711 GAACCATAACATTCTTGGACGCAAC-
127 GAACCATGACATTCTTAGACGCAACT
** * *
2736 CTATTTTATTAAT-AAAATATTAACATTACATATCGCAACATGTTTCTTAGTGAACCATG
1 C-ATTTTATTAATAAAAATATTAACATT-CA-ATTACAACATATTTATTAGTGAACCATG
2795 ATATTTTTAG
Statistics
Matches: 442, Mismatches: 52, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
147 60 0.14
148 43 0.10
149 19 0.04
150 7 0.02
151 15 0.03
152 19 0.04
153 85 0.19
154 189 0.43
155 5 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (152 bp):
CATTTTATTAATAAAAATATTAACATTCAATTACAACATATTTATTAGTGAACCATGGCATTCTT
GGGCGAAACTCATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTATTTCTTAGTGAAC
CATGACATTCTTAGACGCAACT
Found at i:2669 original size:231 final size:226
Alignment explanation
Indices: 2128--2795 Score: 627
Period size: 231 Copynumber: 2.9 Consensus size: 226
2118 GTGTGTGACC
* * * * * * *
2128 CATTTTATTAATAAAATTATTAAAATTTCAGATC-CTAACTTATTTCTTAGTGAACCATGACATT
1 CATTTTATTAATAAAA-TATTAACATTCCAGATCAC-AACATATTTATTAGTAAATCAGGACATT
* ** * * ** * ** *
2192 CTTGGGAGAAACTTATATTATTAATAAAAATATTAACATTCCAAATCGCAACACATTTCTTAGTG
64 CATAAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCAAATTACAACATATTTCTTAGTG
* * ** *
2257 AATCATGACATTCTTGAGCACAACTCGTTTATTAA-AAAAATATTAACATTCAATCACAACATA-
129 AATCATGACATTCTTGGGGA-AACTATTTTATTAATAAAAATATTAACATTCAATCGCAACATAT
* * *
2320 TTATTA-TGAACCATGGCATTCTTGGGCGAAACT
193 TTCTTAGTGAACCATGACATTCTTGGACGAAACT
* * * * *
2353 CATTTTATTAATAAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAATCATGACATTCT
1 CATTTTATTAATAAAATATTAACATTCCAGATCACAACATATTTATTAGTAAATCAGGACATTCA
* * * *
2418 TAAGCGCAACTCATTTTATTAATATAAATATGAACATT-CAAGATTACAACATATTTATTAGTGA
66 TAAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCAA-ATTACAACATATTTCTTAGTGA
* *
2482 ATCATGGCATTCTTGGGTGAAACTTATTTTATTAATAAAAATATTAACATTCTAGATCGCAACCT
130 ATCATGACATTCTTGGG-GAAAC-TATTTTATTAATAAAAATATTAACATTC-A-ATCGCAACAT
* *
2547 ATTTCTTAGTGAACCATGACACTT-TTGGATGCAACT
191 ATTTCTTAGTGAACCATGACA-TTCTTGGACGAAACT
* ** * * *
2583 CATTTTATTAATAAAAATATTAGCATTTGATATTACAACATATTTATTAGTAAA-CTAGGCCATT
1 CATTTTATTAAT-AAAATATTAACATTCCAGATCACAACATATTTATTAGTAAATC-AGGACATT
** * *
2647 CATGGGCGTAACCCATTTTATTAATAAAAATATTAACATTCCAAATCGTAC--CTTATTTCTTAG
64 CATAAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCAAAT--TACAACATATTTCTTAG
* * * *
2710 TGAACCATAACATTCTTGGACGCAACCTATTTTATTAAT-AAAATATTAACATTACATATCGCAA
127 TGAATCATGACATTCTTGG--GGAAACTATTTTATTAATAAAAATATTAACATT-CA-ATCGCAA
*
2774 CATGTTTCTTAGTGAACCATGA
188 CATATTTCTTAGTGAACCATGA
2796 TATTTTTAGG
Statistics
Matches: 370, Mismatches: 55, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
223 3 0.01
224 109 0.29
225 27 0.07
226 16 0.04
227 1 0.00
228 9 0.02
229 5 0.01
230 75 0.20
231 115 0.31
232 6 0.02
233 4 0.01
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (226 bp):
CATTTTATTAATAAAATATTAACATTCCAGATCACAACATATTTATTAGTAAATCAGGACATTCA
TAAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCAAATTACAACATATTTCTTAGTGAA
TCATGACATTCTTGGGGAAACTATTTTATTAATAAAAATATTAACATTCAATCGCAACATATTTC
TTAGTGAACCATGACATTCTTGGACGAAACT
Found at i:7030 original size:3 final size:3
Alignment explanation
Indices: 7015--7072 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
7005 AGTTAAAAAA
*
7015 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
7062 TAG TAT TAT TA
1 TAT TAT TAT TA
7073 AGTGTATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:20159 original size:33 final size:32
Alignment explanation
Indices: 20132--20201 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 32
20122 AAAAAGATGA
* *
20132 AAAATGAAAAAAAATGAAAAAGAAAAAAAATGA
1 AAAATGAAAAAAAATGAAAAA-TAAAAAGATGA
20165 AAAATGAAAAAAGAAATGAAAAATAAAAAGA-GA
1 AAAATG-AAAAA-AAATGAAAAATAAAAAGATGA
20198 AAAA
1 AAAA
20202 GGAGGGTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 12 0.36
34 11 0.33
35 10 0.30
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (32 bp):
AAAATGAAAAAAAATGAAAAATAAAAAGATGA
Found at i:20195 original size:17 final size:16
Alignment explanation
Indices: 20106--20193 Score: 99
Period size: 16 Copynumber: 5.3 Consensus size: 16
20096 ATGCTTGAAG
20106 AAAAAAAA-GAACAAAT
1 AAAAAAAATGAA-AAAT
*
20122 -AAAAAGATGAAAAAT
1 AAAAAAAATGAAAAAT
*
20137 GAAAAAAAATGAAAAAG
1 -AAAAAAAATGAAAAAT
20154 AAAAAAAATGAAAAAT
1 AAAAAAAATGAAAAAT
20170 GAAAAAAGAAATGAAAAAT
1 --AAAAA-AAATGAAAAAT
20189 AAAAA
1 AAAAA
20194 GAGAAAAAGG
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
15 10 0.16
16 18 0.29
17 18 0.29
18 5 0.08
19 11 0.18
ACGTcount: A:0.78, C:0.01, G:0.11, T:0.09
Consensus pattern (16 bp):
AAAAAAAATGAAAAAT
Found at i:21636 original size:105 final size:105
Alignment explanation
Indices: 21416--21670 Score: 341
Period size: 105 Copynumber: 2.4 Consensus size: 105
21406 CTCGCTTGAG
*
21416 GGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * *
21481 TGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
* * * *
21523 GAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* * **
21588 AGAAAAACATGTT-CTTTCTAAGTCCACCGCAAAAGGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAGGAGGT
*
21628 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATC
21671 CACGAGAAAA
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
104 5 0.04
105 112 0.87
106 1 0.01
107 11 0.09
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (105 bp):
GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
Found at i:28773 original size:15 final size:15
Alignment explanation
Indices: 28753--28783 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28743 GCAAAATTGG
28753 ATTTTGAAAAGAAAA
1 ATTTTGAAAAGAAAA
28768 ATTTTGAAAAGAAAA
1 ATTTTGAAAAGAAAA
28783 A
1 A
28784 AATGAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (15 bp):
ATTTTGAAAAGAAAA
Found at i:29313 original size:194 final size:194
Alignment explanation
Indices: 29071--29459 Score: 733
Period size: 194 Copynumber: 2.0 Consensus size: 194
29061 ACCAAAATTA
* *
29071 AAATGAATGTCTCTTGTAGGTGTGTGGGAGCAATGGTGATGAAAGTGAAGATGTTCAAATGCTCT
1 AAATGAATGTCTCTCGTAGGTGTGTGAGAGCAATGGTGATGAAAGTGAAGATGTTCAAATGCTCT
29136 AGCCACACTTGAAAAGGAATGGACAACCTTTAAGCTTATTTTAATTATCTTGCATAATTGGTTGC
66 AGCCACACTTGAAAAGGAATGGACAACCTTTAAGCTTATTTTAATTATCTTGCATAATTGGTTGC
29201 TCATTTAGTTTTAAGCATGCATAAGTTTTGATTTTAAATTAATTTTATGTTTTTCATCTCATGT
131 TCATTTAGTTTTAAGCATGCATAAGTTTTGATTTTAAATTAATTTTATGTTTTTCATCTCATGT
*
29265 AAATGAATGTCTCTCGTAGGTGTGTGAGAGCAATGGTGATGAAAGTGAAGATGTTTAAATGCTCT
1 AAATGAATGTCTCTCGTAGGTGTGTGAGAGCAATGGTGATGAAAGTGAAGATGTTCAAATGCTCT
**
29330 AGCCACACTTGAAAAGGAATGGGTAACCTTTAAGCTTATTTTAATTATCTTGCATAATTGGTTGC
66 AGCCACACTTGAAAAGGAATGGACAACCTTTAAGCTTATTTTAATTATCTTGCATAATTGGTTGC
29395 TCATTTAGTTTTAAGCATGCATAAGTTTTGATTTTAAATTAATTTTATGTTTTTCATCTCATGT
131 TCATTTAGTTTTAAGCATGCATAAGTTTTGATTTTAAATTAATTTTATGTTTTTCATCTCATGT
29459 A
1 A
29460 TGTTGAAAAG
Statistics
Matches: 190, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
194 190 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.39
Consensus pattern (194 bp):
AAATGAATGTCTCTCGTAGGTGTGTGAGAGCAATGGTGATGAAAGTGAAGATGTTCAAATGCTCT
AGCCACACTTGAAAAGGAATGGACAACCTTTAAGCTTATTTTAATTATCTTGCATAATTGGTTGC
TCATTTAGTTTTAAGCATGCATAAGTTTTGATTTTAAATTAATTTTATGTTTTTCATCTCATGT
Found at i:30577 original size:21 final size:22
Alignment explanation
Indices: 30544--30584 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
30534 TTAAAAATTA
30544 TAAAGATAGTATTGATACTCAT
1 TAAAGATAGTATTGATACTCAT
30566 TAAAGA-AGTATTGATACTC
1 TAAAGATAGTATTGATACTC
30585 CCTGTCTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TAAAGATAGTATTGATACTCAT
Found at i:33671 original size:131 final size:129
Alignment explanation
Indices: 33328--33690 Score: 424
Period size: 130 Copynumber: 2.8 Consensus size: 129
33318 TTAAGATTGA
* * ** *
33328 AAATGATAATATCTAATTATTTCTAATCGAGAATAAATGATTTCTCATACCTTAAAGCATTCATT
1 AAATGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATACCTTAAAGCA-ACATT
*** * * * *
33393 TATTACTATGATCGAAATGATGAGATATCACTATTCTGTCTTAAAATTCAATATAGATTCGAGTG
65 TATTACTCCAATCGAAATGAAGAGATATCACTATTCTATCTTAAAAATCAATATAGATTCGAGAG
* * *
33458 AAACGATAATATCTAATGATTTCCAATCGAAAATAAATAACCTCTCATACCTTAAAGCAATCATT
1 AAATGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATACCTTAAAGCAA-CATT
* *
33523 TATTGCTCCAATAGAAATGAAGAGATATCACTATTCTATCTTAAAAATCAATATTA-ATTCGAGA
65 TATTACTCCAATCGAAATGAAGAGATATCACTATTCTATCTTAAAAATCAATA-TAGATTCGAGA
33587 G
129 G
* * * *
33588 AGAATGATAATAT-TGAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAGAGTAGACA
1 A-AATGATAATATCT-AATTATTTCCAATCGAAAATAAATGACCTCTCATACCTTAAAGCA-ACA
* * * * *
33652 TTCATTACCCCAACCGAAATGAAAAGATATTACTATTCT
63 TTTATTACTCCAATCGAAATGAAGAGATATCACTATTCT
33691 CAATATCGAT
Statistics
Matches: 197, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
130 111 0.56
131 85 0.43
132 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (129 bp):
AAATGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATACCTTAAAGCAACATTT
ATTACTCCAATCGAAATGAAGAGATATCACTATTCTATCTTAAAAATCAATATAGATTCGAGAG
Found at i:34845 original size:22 final size:21
Alignment explanation
Indices: 34804--34851 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
34794 TAAATACAAT
*
34804 ATTTTTTCTTTTTTCTTTTTA
1 ATTTTTTCTTTTTTCATTTTA
34825 ATTTTCTTCATTTTTT-ATTTT-
1 ATTTT-TTC-TTTTTTCATTTTA
34846 ATTTTT
1 ATTTTT
34852 AGAGAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 7 0.29
23 6 0.25
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.79
Consensus pattern (21 bp):
ATTTTTTCTTTTTTCATTTTA
Found at i:35796 original size:14 final size:14
Alignment explanation
Indices: 35773--35802 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35763 AAAAAAAGCA
35773 ATAATAATAATAAT
1 ATAATAATAATAAT
*
35787 ATAATGATAATAAT
1 ATAATAATAATAAT
35801 AT
1 AT
35803 TAAAAATGAG
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:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:36138 original size:134 final size:134
Alignment explanation
Indices: 35973--37194 Score: 1514
Period size: 134 Copynumber: 9.2 Consensus size: 134
35963 AGATTGAGAA
* * *
35973 ACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATTGAGGGAGACTTGTTCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* *
36038 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCACTTTTTCTTGAGGGAAAATCAGATAT
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTTTTCTTGAGGGAAAATCAGATCT
36103 GGGG
131 GGGG
* * * *
36107 ACGTTGATTCATTCCACTATTCTCCAGGGAAGATTGAATCGAGTCAGACTTGTTCTACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* *
36172 CAGGGAATACCAAATCTTGAAAGAGAGGGATATGTTCCGCTTTTTCTTGA-GGAAGAATCAGATC
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTTTTCTTGAGGGAA-AATCAGATC
*
36236 TGCGG
130 TGGGG
36241 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * * * * *
36306 CTGGGAATATC--A-----AAAGATATGGAT-T-TTTCTGCTTTTTCTTGATGAAAAATTAGATA
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTC-GCTTTTTCTTGAGGGAAAATCAGATC
36362 TGGGG
130 TGGGG
* * * *
36367 ATGTTGATTCATTCTACTGTTCTCCAGGGAATATTGAATCGAGGCAGACTTGTTCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* *
36432 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGCTCT
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTTTTCTTGAGGGAAAATCAGATCT
**
36497 GAAG
131 GGGG
* * * * * *
36501 ACATTGATTCATTTCACTATTCTTCAGGGAAGATTGAATCGAGGCAAACGTGTTCCACTATTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * ** * *
36566 CAGGGAATATCAAATTTTGAAAGAGA-AGAGTATGTTTATCTTCTTCTTGAGGGAAAATCATATC
66 CAGGGAATATCAAATCTTGAAAGAGAGGGA-TATGTTTCGCTTTTTCTTGAGGGAAAATCAGATC
36630 TGAGGG
130 TG-GGG
* * * * * * * * *
36636 -CATTGATTCATTCCAGTGTTCTTTAGAGAATACTGAATCTAGTTC-GACTTGTTCCACTATTAC
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG-GCAGACTTGTTCCACTGTTAC
* *
36699 TCAGAGAATATCAAATATTGAAAGAGAGGGATATG-TTCTGCTTTTTCTTGAGGG-AAATCAGAT
65 TCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTC-GCTTTTTCTTGAGGGAAAATCAGAT
* *
36762 TTGAGG
129 CTGGGG
* * * *
36768 ACGTTGATTCATTCCAGTGTTCTTCAGGGAAGATTGAATCAAGACAGACTTATTCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * * * *
36833 CAGGGAATACCAAATCTTGAAATAGAGGGATATG-TTCTTCTTCTTCTAGAGGGAAAATCATATC
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTC-GCTTTTTCTTGAGGGAAAATCAGATC
36897 TGGGG
130 TGGGG
* * *
36902 ACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAGTTC-GACTTGTTCCATTGTTAC
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG-GCAGACTTGTTCCACTGTTAC
* * *
36966 TCAGGGAATATCAAATCTTGAAAGAGAGGGATCTATTAT-ACTTTTTCTTGAGGGAAAATCAGAT
65 TCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTT-TCGCTTTTTCTTGAGGGAAAATCAGAT
*
37030 ATGGGG
129 CTGGGG
* * * * *
37036 ACATTGATTCATTCCACTATTCTTCAGGGAAAATTGAATCGAGGCAGACTTGTTCTACTGTTATT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* *
37101 CAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTAT-GCTTCTTCTTGAGGGAAAATCAGATC
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTT-TCGCTTTTTCTTGAGGGAAAATCAGATC
37165 TGGGG
130 TGGGG
37170 -CGTTGATTCATTCCACTAG-TCTTCA
1 ACGTTGATTCATTCCACT-GTTCTTCA
37195 CTAAAGATTA
Statistics
Matches: 936, Mismatches: 127, Indels: 51
0.84 0.11 0.05
Matches are distributed among these distances:
125 3 0.00
126 95 0.10
127 13 0.01
128 1 0.00
132 4 0.00
133 150 0.16
134 659 0.70
135 10 0.01
136 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (134 bp):
ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
CAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTTTTCTTGAGGGAAAATCAGATCT
GGGG
Found at i:36911 original size:401 final size:398
Alignment explanation
Indices: 35946--37194 Score: 1556
Period size: 401 Copynumber: 3.1 Consensus size: 398
35936 TACTCTACTG
* * * * *
35946 TTTCTTTAGGGTATATCAGA-TTGAGAAACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGA
1 TTTCTTGAGGGAAAATCAGATTTGAG-GACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGA
* *
36010 ATTGAGGGAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTT
65 ATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTT
* * *
36075 CACTTTTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTATTCTCCAGGGAAGA
130 CACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTATTCTTCAGGGAAGA
* *
36140 TTGAATCGAGTCAGACTTGTTCTACTGTTACTCAGGGAATACCAAATCTTGAAAGAGAGGGATAT
195 TTGAATCGAGTCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGA-GG-TAT
*** * *
36205 GTTCCGCTTTTTCTTGA-GGAAGAATCAGATCTGCGGACGTTGATTCATTCCACTGTTCTTCAGG
258 GTTTATCTTTTTCTTGAGGGAA-AATCAGATCTG-GGGCATTGATTCATTCCACTGTTCTTCAGG
* * * *
36269 GAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCTGGGAATATC----A---AAAGATATG
321 GAAAATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAAAGAGAGG
*
36327 GATTTTTCTGCTT
386 GATTGTTCTGCTT
* * * * * * * * *
36340 TTTCTTGATGAAAAATTAGATATGGGGATGTTGATTCATTCTACTGTTCTCCAGGGAATATTGAA
1 TTTCTTGAGGGAAAATCAGATTTGAGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
36405 TCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTC
66 TCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTC
* * ** * *
36470 GCTTCTTCTTGAGGGAAAATCAGCTCTGAAGACATTGATTCATTTCACTATTCTTCAGGGAAGAT
131 ACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTATTCTTCAGGGAAGAT
* * * * *
36535 TGAATCGAGGCAAACGTGTTCCACTATTACTCAGGGAATATCAAATTTTGAAAGAGAAGAGTATG
196 TGAATCGAGTCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAG-AG-GTATG
* * * * *
36600 TTTATCTTCTTCTTGAGGGAAAATCATATCTGAGGGCATTGATTCATTCCAGTGTTCTTTAGAGA
259 TTTATCTTTTTCTTGAGGGAAAATCAGATCTG-GGGCATTGATTCATTCCACTGTTCTTCAGGGA
* * * * * *
36665 ATACTGAATCTAGTTC-GACTTGTTCCACTATTACTCAGAGAATATCAAATATTGAAAGAGAGGG
323 AAATTGAATCGAG-GCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAAAGAGAGGG
36729 ATATGTTCTGCTT
387 AT-TGTTCTGCTT
*
36742 TTTCTTGAGGG-AAATCAGATTTGAGGACGTTGATTCATTCCAGTGTTCTTCAGGGAAGATTGAA
1 TTTCTTGAGGGAAAATCAGATTTGAGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
* * * * *
36806 TCAAGACAGACTTATTCCACTGTTACTCAGGGAATACCAAATCTTGAAATAGAGGGATATG-TTC
66 TCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTC
* * * * *
36870 TTCTTCTTCTAGAGGGAAAATCATATCTGGGGACGTTGATTCATTCCACTGTTCTTTAGGGAAGA
131 -ACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTATTCTTCAGGGAAGA
* * *
36935 TTGAATCGAGTTC-GACTTGTTCCATTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
195 TTGAATCGAG-TCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGTATG
* *
36999 TATTATACTTTTTCTTGAGGGAAAATCAGATATGGGGACATTGATTCATTCCACTATTCTTCAGG
259 T-TTAT-CTTTTTCTTGAGGGAAAATCAGATCTGGGG-CATTGATTCATTCCACTGTTCTTCAGG
* * *
37064 GAAAATTGAATCGAGGCAGACTTGTTCTACTGTTATTCAGGGAATATCAAATCTTGAAAGAGAGG
321 GAAAATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAAAGAGAGG
*
37129 GATTTGTTATGCTT
386 GA-TTGTTCTGCTT
* * *
37143 CTTCTTGAGGGAAAATCAGATCTG-GGGCGTTGATTCATTCCACTAG-TCTTCA
1 TTTCTTGAGGGAAAATCAGATTTGAGGACGTTGATTCATTCCACT-GTTCTTCA
37195 CTAAAGATTA
Statistics
Matches: 726, Mismatches: 107, Indels: 37
0.83 0.12 0.04
Matches are distributed among these distances:
394 306 0.42
395 10 0.01
398 1 0.00
399 4 0.01
400 13 0.02
401 360 0.50
402 32 0.04
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (398 bp):
TTTCTTGAGGGAAAATCAGATTTGAGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
TCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTTC
ACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTATTCTTCAGGGAAGAT
TGAATCGAGTCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGTATGTT
TATCTTTTTCTTGAGGGAAAATCAGATCTGGGGCATTGATTCATTCCACTGTTCTTCAGGGAAAA
TTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAAAGAGAGGGATTG
TTCTGCTT
Done.