Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008304.1 Hibiscus syriacus cultivar Beakdansim tig00110990_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: 283871
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:211520 original size:37 final size:37
Alignment explanation
Indices: 211479--211631 Score: 236
Period size: 37 Copynumber: 4.2 Consensus size: 37
211469 GGCCTTCGGG
211479 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
211516 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-GAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
211552 CCATTTTAAGCTTTCACCGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
211589 CCATCTTAAGCCTTCATCGAAGAGTGGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
*
211626 CAATCT
1 CCATCT
211632 CGAGTCTGAT
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 32 0.31
37 72 0.69
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (37 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:211572 original size:73 final size:73
Alignment explanation
Indices: 211479--211621 Score: 243
Period size: 73 Copynumber: 2.0 Consensus size: 73
211469 GGCCTTCGGG
211479 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCA-CAGAAGAGTAG
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCATC-GAAGAGTAG
211543 TGAAGCGAT
65 TGAAGCGAT
* * *
211552 CCATTTTAAGCTTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTGGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTAGT
211617 GAAGC
66 GAAGC
211622 AAATCAATCT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 65 0.98
74 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (73 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTAGT
GAAGCGAT
Found at i:211820 original size:13 final size:13
Alignment explanation
Indices: 211802--211826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211792 GTCCGGGATA
211802 TTATTATTATTAT
1 TTATTATTATTAT
211815 TTATTATTATTA
1 TTATTATTATTA
211827 ATACTATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:211824 original size:19 final size:19
Alignment explanation
Indices: 211800--211844 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
211790 TTGTCCGGGA
* *
211800 TATTATTATTATTATTTAT
1 TATTATTAATACTATTTAT
211819 TATTATTAATACTATTTAT
1 TATTATTAATACTATTTAT
*
211838 TTTTATT
1 TATTATT
211845 TTGTAGCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATTAATACTATTTAT
Found at i:224154 original size:10 final size:10
Alignment explanation
Indices: 224135--224172 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
224125 CTTAAATATA
*
224135 GAGAGTATTT
1 GAGAGAATTT
224145 GAGAGAATTT
1 GAGAGAATTT
*
224155 GATAGAATTT
1 GAGAGAATTT
224165 GAGAGAAT
1 GAGAGAAT
224173 ATGGTGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:224781 original size:29 final size:29
Alignment explanation
Indices: 224749--224805 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
224739 AGAATAATAT
*
224749 TATA-CATTAAATTAATAATTAATATTTTG
1 TATATCATTAAATT-ATAATTAAAATTTTG
* *
224778 TATATCTTTCAATTATAATTAAAATTTT
1 TATATCATTAAATTATAATTAAAATTTT
224806 ATTTTGATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (29 bp):
TATATCATTAAATTATAATTAAAATTTTG
Found at i:234845 original size:22 final size:23
Alignment explanation
Indices: 234820--234902 Score: 57
Period size: 24 Copynumber: 3.5 Consensus size: 23
234810 ATTGTATTCT
234820 TTAA-AAAATATATCCACGTTTA
1 TTAATAAAATATATCCACGTTTA
* **
234842 TTAATTAAAATATTAAAT-TATATTCT-
1 TTAA-TAAAATA-T--ATCCACGTT-TA
234868 TTAA-AAAATATATCCACGTTTA
1 TTAATAAAATATATCCACGTTTA
234890 TTAATTAAAATAT
1 TTAA-TAAAATAT
234903 TAAATTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
21 3 0.07
22 11 0.24
23 1 0.02
24 19 0.42
25 1 0.02
26 7 0.16
27 3 0.07
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.42
Consensus pattern (23 bp):
TTAATAAAATATATCCACGTTTA
Found at i:234866 original size:48 final size:48
Alignment explanation
Indices: 234793--234935 Score: 277
Period size: 48 Copynumber: 3.0 Consensus size: 48
234783 ACGCGAAGTC
*
234793 ATTAATTAAAATATTAAATTGTATTCTTTAAAAAATATATCCACGTTT
1 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
234841 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
1 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
234889 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTT
1 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTT
234936 GAAGAAAACT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (48 bp):
ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
Found at i:234919 original size:22 final size:22
Alignment explanation
Indices: 234846--234921 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 22
234836 CGTTTATTAA
234846 TTAAAATATTAAATTATATTCT
1 TTAAAATATTAAATTATATTCT
** **
234868 TTAAAAAATATATCCACGTT-TATTAA
1 TT--AAAATAT-T--AAATTATATTCT
234894 TTAAAATATTAAATTATATTCT
1 TTAAAATATTAAATTATATTCT
234916 TTAAAA
1 TTAAAA
234922 AATATATCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
21 3 0.08
22 12 0.30
23 1 0.03
24 14 0.35
25 1 0.03
26 6 0.15
27 3 0.08
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (22 bp):
TTAAAATATTAAATTATATTCT
Found at i:238901 original size:20 final size:20
Alignment explanation
Indices: 238876--238924 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
238866 TCTAGCAAAT
* *
238876 GATCGATTCATTTTCAAAAG
1 GATCGATCCATTTACAAAAG
* *
238896 GATCGATCCCTTTACAAAAT
1 GATCGATCCATTTACAAAAG
238916 GATCGATCC
1 GATCGATCC
238925 TTTCTCTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (20 bp):
GATCGATCCATTTACAAAAG
Found at i:245909 original size:21 final size:21
Alignment explanation
Indices: 245883--245940 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
245873 AGAACCCCAG
*
245883 GGGGGGTATCGATTCCCCT-GT
1 GGGGGG-ATCGATTCCCCTCAT
*
245904 GGGGGGAATCGGTT-CCCTCAT
1 GGGGGG-ATCGATTCCCCTCAT
245925 GGGGGGATCGATTCCC
1 GGGGGGATCGATTCCC
245941 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (21 bp):
GGGGGGATCGATTCCCCTCAT
Found at i:249786 original size:22 final size:21
Alignment explanation
Indices: 249744--249783 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
249734 GAGTTTGTTT
*
249744 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
249765 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
249784 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:253376 original size:37 final size:37
Alignment explanation
Indices: 253323--253396 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
253313 TAGGTTTTGT
*
253323 ATTATTATATACAAATATTATAAAACATATAAGTTGC
1 ATTATTATATAAAAATATTATAAAACATATAAGTTGC
253360 ATTATTATATAAAAATATTATAAAACATATAAGTTGC
1 ATTATTATATAAAAATATTATAAAACATATAAGTTGC
253397 CAAATAGGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (37 bp):
ATTATTATATAAAAATATTATAAAACATATAAGTTGC
Found at i:253699 original size:13 final size:13
Alignment explanation
Indices: 253681--253705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253671 CATAGTTGAA
253681 CAGTCTTCATATG
1 CAGTCTTCATATG
253694 CAGTCTTCATAT
1 CAGTCTTCATAT
253706 ACGCGTCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:258753 original size:58 final size:60
Alignment explanation
Indices: 258640--258765 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 60
258630 ATAGTTGGGC
*
258640 GATCATTTTGTAACTTTTAATAGTTGAGAGACATAAAAAAGTAACATTCTATAGTC-A-G
1 GATCATTTTGTAACTTTTAATAGTTAAGAGACATAAAAAAGTAACATTCTATAGTCGAGG
* * ** *
258698 GATCATTTTGTAACTTTTAATAGTTAAGGGACTTAATAAAA-TAGTA-TCTTGTAGTCGAGG
1 GATCATTTTGTAACTTTTAATAGTTAAGAGACATAA-AAAAGTAACATTC-TATAGTCGAGG
258758 GATCATTT
1 GATCATTT
258766 GTCTACTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
57 2 0.03
58 42 0.72
59 5 0.09
60 9 0.16
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTTAAGAGACATAAAAAAGTAACATTCTATAGTCGAGG
Found at i:264947 original size:28 final size:28
Alignment explanation
Indices: 264907--264963 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
264897 TATAAAAGGA
264907 AAGAAGAACAAAAGTATCATAGGAAAAT
1 AAGAAGAACAAAAGTATCATAGGAAAAT
264935 AAGAAGAACAAAAGTATCATAGGAAAAT
1 AAGAAGAACAAAAGTATCATAGGAAAAT
264963 A
1 A
264964 TGGCAACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.61, C:0.07, G:0.18, T:0.14
Consensus pattern (28 bp):
AAGAAGAACAAAAGTATCATAGGAAAAT
Found at i:267312 original size:3 final size:3
Alignment explanation
Indices: 267304--267344 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
267294 TCAGTTCATT
*
267304 TTA TTA TTA TTAA TTA TTA AT- TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
267345 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:269501 original size:18 final size:17
Alignment explanation
Indices: 269478--269528 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
269468 TTTCTTTCAA
269478 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
269495 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
269513 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
269529 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:274205 original size:6 final size:6
Alignment explanation
Indices: 274189--274239 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
274179 CTCATCCAAC
*
274189 AAAGAA AGAAGAA GAAGAA AAAGAA AAAGAA AAA-AA AAAGAA AAAGGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA
274238 AA
1 AA
274240 TCGAATAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 5 0.12
6 25 0.62
7 10 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:276573 original size:83 final size:83
Alignment explanation
Indices: 276434--276689 Score: 467
Period size: 83 Copynumber: 3.1 Consensus size: 83
276424 CTGAAAGAGA
*
276434 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
276499 ATTTAGAAGATGAATCTG
66 ATTTAGAAGATGAATCTG
276517 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
*
276582 ATTTAGAAGATGAATGTG
66 ATTTAGAAGATGAATCTG
* *
276600 CTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTATACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
*
276665 ATTTAGAAGATGAATTTG
66 ATTTAGAAGATGAATCTG
276683 CTCATAG
1 CTCATAG
276690 GAGAAATAAG
Statistics
Matches: 168, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 168 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (83 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
ATTTAGAAGATGAATCTG
Found at i:278970 original size:40 final size:40
Alignment explanation
Indices: 278915--278994 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
278905 TGAGCAAAGT
278915 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
* *
278955 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
278995 TAAGCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
Found at i:279425 original size:22 final size:22
Alignment explanation
Indices: 279399--279449 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
279389 TACACTCTTC
* *
279399 AAGATGATAGATTCTCTTTTTA
1 AAGATGACAGATTCTCTTTTCA
279421 AAGATGACAGATTCTCTTTTCA
1 AAGATGACAGATTCTCTTTTCA
279443 AAGATGA
1 AAGATGA
279450 AAACTTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (22 bp):
AAGATGACAGATTCTCTTTTCA
Found at i:280165 original size:113 final size:113
Alignment explanation
Indices: 279849--280514 Score: 895
Period size: 113 Copynumber: 6.0 Consensus size: 113
279839 AGCAAAGTTC
** * **
279849 AATCCATCATTCAATGGATCAACA-TTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
279912 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * * *
279961 AATCCATCATTCGATGGATTGA-CATTTCTATAG-AAGTTCATAATGAGAAGAACTCATATGAAG
1 AATCCATCATTTGATGGA-TCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
280024 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
*
280073 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
280138 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTACTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* * *
280186 AATCTATTATTTGATGGATCATCATTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
280251 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACT-TG
* * * * *
280299 AATTCATCACTTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
280363 AAGGAAGAAGAAGTTCAT-ATAAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * **
280411 AATCCATCACTTGAT-GAACAAC-TTTTTAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
280473 AGGAAGAAGAAGTTCATAAT-AAAAGAATTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
280515 GCATAATTCT
Statistics
Matches: 500, Mismatches: 44, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
109 67 0.13
110 6 0.01
111 8 0.02
112 160 0.32
113 258 0.52
114 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
Found at i:281183 original size:75 final size:76
Alignment explanation
Indices: 280920--281627 Score: 1182
Period size: 75 Copynumber: 9.4 Consensus size: 76
280910 ACTATTTCCC
* *
280920 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTT-
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT-TTC
*
280984 AAAGCCTTCGGG
65 AAAGCCTTAGGG
*
280996 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
281061 AAGCCTTCGGC
66 AAGCCTTAGGG
* *
281072 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATG-TTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
281136 AAGCCTTAGGG
66 AAGCCTTAGGG
* *
281147 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTTGATGTTTTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
281211 AAGCCTTCGGG
66 AAGCCTTAGGG
281222 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
281286 AAGCCTTAGGG
66 AAGCCTTAGGG
281297 TCATCTGTAAGTCCTTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
281361 AAGCCTTCGGG
66 AAGCCTTAGGG
281372 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
281437 AAGCCTT-CGG
66 AAGCCTTAGGG
*
281447 TCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
281510 AAGCCTTAGGA
66 AAGCCTTAGGG
* *
281521 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
281586 AAGCCTTAGGG
66 AAGCCTTAGGG
*
281597 TCATC-GTAAGCCCTTCAGTGCATGATGTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTC
281628 AACATTTCCA
Statistics
Matches: 601, Mismatches: 23, Indels: 17
0.94 0.04 0.03
Matches are distributed among these distances:
73 21 0.03
74 87 0.14
75 284 0.47
76 209 0.35
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGG
Found at i:281764 original size:3 final size:3
Alignment explanation
Indices: 281756--281796 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
281746 TCAGTTCATT
*
281756 TTA TTA TTA TTAA TTA TTA AT- TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
281797 ATAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Done.