Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003027.1 Hibiscus syriacus cultivar Beakdansim tig00006298_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: 78911
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3808 original size:35 final size:36
Alignment explanation
Indices: 3769--3841 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 36
3759 TGATCTGATC
*
3769 TTGCTTCACTAGTCTTTTGTGAAGGCTTGA-TTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
*
3804 TTGCTTCACTTCTCTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
3840 TT
1 TT
3842 ACTTGTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 28 0.80
36 7 0.20
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
Found at i:14654 original size:9 final size:9
Alignment explanation
Indices: 14640--14665 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
14630 CAAAAGTTAG
14640 TAAAATAAT
1 TAAAATAAT
14649 TAAAATAAT
1 TAAAATAAT
14658 TAAAATAA
1 TAAAATAA
14666 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAATAAT
Found at i:15289 original size:18 final size:18
Alignment explanation
Indices: 15246--15286 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
15236 TATAAATTCT
*
15246 AATAATAATTAATTATAT
1 AATAATAATTAATTATAA
*
15264 ACTAATAATTAATTATTAA
1 AATAATAATTAATTA-TAA
15283 AATA
1 AATA
15287 TAAAGTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAATAATTAATTATAA
Found at i:17969 original size:38 final size:39
Alignment explanation
Indices: 17938--18095 Score: 166
Period size: 37 Copynumber: 4.2 Consensus size: 39
17928 ATAAATACGT
** *
17938 AATAATATATTCGGTATTTTAATTTAATATAAATTCATA
1 AATAATATATTCTTTATTTTAATTGAATATAAATTCATA
* * *
17977 AATGATATATT-TTTA-TTTAATTAAATATAAATTTATA
1 AATAATATATTCTTTATTTTAATTGAATATAAATTCATA
* *
18014 AATAATATATTC-TTATTTCAATAGAATATAAATTCAT-
1 AATAATATATTCTTTATTTTAATTGAATATAAATTCATA
* * *
18051 AATAATAT-TT-TTATATTTTAATTGAATATACATCCTTA
1 AATAATATATTCTT-TATTTTAATTGAATATAAATTCATA
18089 AATAATA
1 AATAATA
18096 GAACATTATC
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
36 3 0.03
37 60 0.61
38 26 0.26
39 10 0.10
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (39 bp):
AATAATATATTCTTTATTTTAATTGAATATAAATTCATA
Found at i:18031 original size:75 final size:76
Alignment explanation
Indices: 17938--18080 Score: 193
Period size: 75 Copynumber: 1.9 Consensus size: 76
17928 ATAAATACGT
* ** *
17938 AATAATATATTCGGTATTTTAATTTAATATAAATTCATAAATGATATATTTT-TA-TTTAATTAA
1 AATAATATATTCGGTATTTCAATAGAATATAAATTCAT-AATAATAT-TTTTATATTTTAATTAA
18001 ATATAAATTTATA
64 ATATAAATTTATA
* *
18014 AATAATATATTC-TTATTTCAATAGAATATAAATTCATAATAATATTTTTATATTTTAATTGAAT
1 AATAATATATTCGGTATTTCAATAGAATATAAATTCATAATAATATTTTTATATTTTAATTAAAT
18078 ATA
66 ATA
18081 CATCCTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 4 0.07
74 9 0.15
75 34 0.58
76 12 0.20
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (76 bp):
AATAATATATTCGGTATTTCAATAGAATATAAATTCATAATAATATTTTTATATTTTAATTAAAT
ATAAATTTATA
Found at i:19127 original size:2 final size:2
Alignment explanation
Indices: 19120--19149 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19110 TGATTCCTTG
19120 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19150 ACACACACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19154 original size:2 final size:2
Alignment explanation
Indices: 19149--19176 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19139 CTCTCTCTCT
19149 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19177 GTTCTGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:24420 original size:2 final size:2
Alignment explanation
Indices: 24413--24438 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24403 ACAATAATTC
24413 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
24439 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:24443 original size:2 final size:2
Alignment explanation
Indices: 24438--24470 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24428 TCTCTCTCTC
24438 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 T
24471 TAACTAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28273 original size:44 final size:44
Alignment explanation
Indices: 28222--28313 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
28212 GTAATTTGTA
*
28222 ATATAGTCATAGTTATACCATTTAGGTCATCAGACAAGATAAAC
1 ATATAGTCATAGTTATACCATTTAGATCATCAGACAAGATAAAC
*
28266 ATATAGTCATAGTTATACCATTTCGATCATCAGACAAGATAAAC
1 ATATAGTCATAGTTATACCATTTAGATCATCAGACAAGATAAAC
28310 ATAT
1 ATAT
28314 TCAATCTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (44 bp):
ATATAGTCATAGTTATACCATTTAGATCATCAGACAAGATAAAC
Found at i:28826 original size:2 final size:2
Alignment explanation
Indices: 28819--28870 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
28809 ACATAAAATC
28819 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
28861 AT AT AT AT AT
1 AT AT AT AT AT
28871 GTAAACTCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31298 original size:165 final size:166
Alignment explanation
Indices: 30929--31635 Score: 918
Period size: 165 Copynumber: 4.2 Consensus size: 166
30919 AATGACTTAG
** *
30929 TTTT-TGAACATTAAATGAGAAACTTTAATAATCGCTTTCTC-ATTGTCATGTGAAAACATCATA
1 TTTTCTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCAATT-TCATGTGAAAACATCCTA
** * * * *
30992 CCCTGAGGTTTTACAGATGGCTTGGAGGACTTATCATCTTTAGGACATTGTTTACTAGGTAAGAA
65 CCCTGAGGTTTTACAGATGGCCCGAAGGACTTATCATCTTTGGGAAATTGTTTACTGGGTAAGAA
*
31057 ACTTTGAAAATTGCTTTCTTACTTTTTAACAATTTCA
130 ACTTTGAAAATTACTTTCTTACTTTTTAACAATTTCA
*
31094 TTTTCTGAACATTAAATTAGAAACTTTGGTAATCGCTTTCTCAATTTCATGTGAAAACATCCTAC
1 TTTTCTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCAATTTCATGTGAAAACATCCTAC
*
31159 CCTGAGGTTTTACAGATGGCCCGAAGGACTTATCATCTTTGGGAAATTGTTTA-TTGGTAAGAAA
66 CCTGAGGTTTTACAGATGGCCCGAAGGACTTATCATCTTTGGGAAATTGTTTACTGGGTAAGAAA
* *
31223 CTTTGGAAATTGCTTTCTTACTTTTTAACAATTTCA
131 CTTTGAAAATTACTTTCTTACTTTTTAACAATTTCA
* * *
31259 TTTTCTGAACATTAAATGAGAAACTTTGGTAACCGCTTTCTCATTTTCATGTAAAAACATCCTAC
1 TTTTCTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCAATTTCATGTGAAAACATCCTAC
* *
31324 CCTGAGGTTTTACAGATGACCCGAATGACTTATCATCTTTGGGAAATTTTTTACTGGGAAATTTT
66 CCTGAGGTTTTACAGATGGCCCGAAGGACTTATCATCTTTGGGAAA-----T--T--G------T
* * *
31389 TTACTGGGTAAGAAACTTTGGAAATTATTTTCTTACTTATTAACAATTTCA
116 TTACTGGGTAAGAAACTTTGAAAATTACTTTCTTACTTTTTAACAATTTCA
* *
31440 TTTTCTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGTGAAAACATCAC-A
1 TTTTCTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCAATTTCATGTGAAAACATC-CTA
* *
31504 CCCTGAGGTTTTACAGATGGCCCGGAGGACTTATCATCTTTGGGAAATAGTTTACTGGGTAAGAA
65 CCCTGAGGTTTTACAGATGGCCCGAAGGACTTATCATCTTTGGGAAATTGTTTACTGGGTAAGAA
* * * * *
31569 ACATTGAAAATCATTTTCTTACTTTTCAATAATTTCA
130 ACTTTGAAAATTACTTTCTTACTTTTTAACAATTTCA
* *
31606 TTTTCAGAAAAGATTAAATGAGAAACTTTG
1 TTTTCTG--AACATTAAATGAGAAACTTTG
31636 AAAATCATTT
Statistics
Matches: 485, Mismatches: 36, Indels: 39
0.87 0.06 0.07
Matches are distributed among these distances:
165 154 0.32
166 152 0.31
167 3 0.01
168 20 0.04
170 1 0.00
172 2 0.00
174 1 0.00
176 1 0.00
180 4 0.01
181 146 0.30
182 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (166 bp):
TTTTCTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCAATTTCATGTGAAAACATCCTAC
CCTGAGGTTTTACAGATGGCCCGAAGGACTTATCATCTTTGGGAAATTGTTTACTGGGTAAGAAA
CTTTGAAAATTACTTTCTTACTTTTTAACAATTTCA
Found at i:31383 original size:15 final size:15
Alignment explanation
Indices: 31363--31396 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
31353 TTATCATCTT
31363 TGGGAAATTTTTTAC
1 TGGGAAATTTTTTAC
31378 TGGGAAATTTTTTAC
1 TGGGAAATTTTTTAC
31393 TGGG
1 TGGG
31397 TAAGAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (15 bp):
TGGGAAATTTTTTAC
Found at i:31518 original size:181 final size:180
Alignment explanation
Indices: 31198--31562 Score: 588
Period size: 181 Copynumber: 2.0 Consensus size: 180
31188 TTATCATCTT
* * *
31198 TGGGAAATTGTTTATTGGTAAGAAACTTTGGAAATTGCTTTCTTACTTTTTAACAATTTCATTTT
1 TGGGAAATTGTTTATGGGTAAGAAACTTTGGAAATTACTTTCTTACTTATTAACAATTTCATTTT
*
31263 CTGAACATTAAATGAGAAACTTTGGTAACCGCTTTCTCATTTTCATGTAAAAACATCCTACCCTG
66 CTGAACATTAAATGAGAAACTTTGGTAACCACTTTCTCATTTTCATGTAAAAACATCCTACCCTG
* **
31328 AGGTTTTACAGATGACCCGAATGACTTATCATCTTTGGGAAATTTTTTAC
131 AGGTTTTACAGATGACCCGAAGGACTTATCATCTTTGGGAAATAGTTTAC
* *
31378 TGGGAAATTTTTTACTGGGTAAGAAACTTTGGAAATTATTTTCTTACTTATTAACAATTTCATTT
1 TGGGAAATTGTTTA-TGGGTAAGAAACTTTGGAAATTACTTTCTTACTTATTAACAATTTCATTT
* *
31443 TCTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGTGAAAACATCAC-ACCC
65 TCTGAACATTAAATGAGAAACTTTGGTAACCACTTTCTCATTTTCATGTAAAAACATC-CTACCC
* *
31507 TGAGGTTTTACAGATGGCCCGGAGGACTTATCATCTTTGGGAAATAGTTTAC
129 TGAGGTTTTACAGATGACCCGAAGGACTTATCATCTTTGGGAAATAGTTTAC
31559 TGGG
1 TGGG
31563 TAAGAAACAT
Statistics
Matches: 170, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
180 13 0.08
181 156 0.92
182 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (180 bp):
TGGGAAATTGTTTATGGGTAAGAAACTTTGGAAATTACTTTCTTACTTATTAACAATTTCATTTT
CTGAACATTAAATGAGAAACTTTGGTAACCACTTTCTCATTTTCATGTAAAAACATCCTACCCTG
AGGTTTTACAGATGACCCGAAGGACTTATCATCTTTGGGAAATAGTTTAC
Found at i:31973 original size:29 final size:29
Alignment explanation
Indices: 31939--31996 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
31929 ACTCCAAAGT
31939 GGTGAATGCGATCTTCTTCCACTTGATCA
1 GGTGAATGCGATCTTCTTCCACTTGATCA
** * *
31968 GGTGAATTTGATTTTCTTTCACTTGATCA
1 GGTGAATGCGATCTTCTTCCACTTGATCA
31997 TTCATTTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (29 bp):
GGTGAATGCGATCTTCTTCCACTTGATCA
Found at i:33162 original size:22 final size:21
Alignment explanation
Indices: 33110--33169 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
33100 AATTTCTGGG
33110 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
33131 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
33151 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
33170 CTCAAGTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:33247 original size:23 final size:22
Alignment explanation
Indices: 33203--33247 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
33193 AATCTCATAG
*
33203 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
33225 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
33248 AAAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:34727 original size:103 final size:103
Alignment explanation
Indices: 34543--34760 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
34533 GTCGAGGGTC
*
34543 TATGTGGTCCTTCGGGACATATATGTATTCTTTGTAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
34608 TTGATCCTTGGCATATGTATATGATTCTTAAGAAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
*
34646 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
34711 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
34749 TATGTGGTCCTT
1 TATGTGGTCCTT
34761 ATGGATATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
Found at i:34806 original size:23 final size:23
Alignment explanation
Indices: 34780--34847 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
34770 ATTATTATAT
* *
34780 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTATACGC
* * *
34803 GGCACTCCAGTGCAATTATACGT
1 GGCACTACGGTGCAATTATACGC
*
34826 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
34848 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:38050 original size:9 final size:9
Alignment explanation
Indices: 38036--38079 Score: 54
Period size: 8 Copynumber: 4.7 Consensus size: 9
38026 TTGATTCAAT
38036 TTTTTTTTC
1 TTTTTTTTC
38045 -TTTTTTTC
1 TTTTTTTTC
38053 TTTTTTTTCATC
1 -TTTTTTT--TC
38065 TTTTTTTTC
1 TTTTTTTTC
38074 TTTTTT
1 TTTTTT
38080 CCTAATAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.26
9 8 0.26
10 6 0.19
11 7 0.23
12 2 0.06
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:42934 original size:17 final size:17
Alignment explanation
Indices: 42912--42952 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
42902 AGAGAGAAAT
42912 TTTCCCTTCTCTTTAAA
1 TTTCCCTTCTCTTTAAA
42929 TTTCCCTTCTCTTTAAA
1 TTTCCCTTCTCTTTAAA
42946 TTTCCCT
1 TTTCCCT
42953 CGTCGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTCCCTTCTCTTTAAA
Found at i:43814 original size:3 final size:3
Alignment explanation
Indices: 43808--43841 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
43798 GTATTATTTG
43808 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
43842 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43846 original size:3 final size:3
Alignment explanation
Indices: 43840--43880 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
43830 AATAATAATA
43840 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43881 GTAGATATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:43990 original size:29 final size:31
Alignment explanation
Indices: 43958--44021 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
43948 AAAATTTTGG
* *
43958 TTAGTAACCAAAATGTAAA-TTTTG-AAAGT
1 TTAGTAACCAAAATATAAAGTTTAGAAAAGT
* *
43987 TTAGTAGCCAAAGTATAAAGTTTAGAAAAGT
1 TTAGTAACCAAAATATAAAGTTTAGAAAAGT
44018 TTAG
1 TTAG
44022 GGATCAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.55
30 4 0.14
31 9 0.31
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (31 bp):
TTAGTAACCAAAATATAAAGTTTAGAAAAGT
Found at i:46758 original size:24 final size:24
Alignment explanation
Indices: 46652--46760 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
46642 AAACGGAGAT
* * * *
46652 ATCAAAAATCAAAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAA
* * * *
46676 ATTA-AATATCATAACAGAATCCAG
1 ATCAGAA-ATCAGAACAGAATTCAA
* *
46700 GTCAGAAATAAGAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* **
46724 ATAAGGTATCAGAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
46748 ATCAGAAATCAGA
1 ATCAGAAATCAGA
46761 TAAAACATTC
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 61 0.94
25 2 0.03
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:48832 original size:30 final size:29
Alignment explanation
Indices: 48796--48865 Score: 113
Period size: 30 Copynumber: 2.4 Consensus size: 29
48786 TGTCGTTTTG
*
48796 GTCAAAGTCAACGGTCAACGGGTTGACTTA
1 GTCAAAGTCAACGGTCAACGGGTTAAC-TA
*
48826 GTCAAAGTCAACGGTCAACGGGTTAACTC
1 GTCAAAGTCAACGGTCAACGGGTTAACTA
48855 GTCAAAGTCAA
1 GTCAAAGTCAA
48866 TGAGTTGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 12 0.32
30 26 0.68
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (29 bp):
GTCAAAGTCAACGGTCAACGGGTTAACTA
Found at i:50591 original size:13 final size:13
Alignment explanation
Indices: 50575--50620 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
50565 TGAAAGTAAA
50575 TATGAAAAGTGAT
1 TATGAAAAGTGAT
* *
50588 TATG-AAAGTAAA
1 TATGAAAAGTGAT
50600 TATGAAAAAGTGAT
1 TATG-AAAAGTGAT
50614 TATGAAA
1 TATGAAA
50621 GATAAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (13 bp):
TATGAAAAGTGAT
Found at i:50593 original size:25 final size:26
Alignment explanation
Indices: 50565--50621 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
50555 CATTGTGTTT
50565 TGAAAGTAAATATG-AAAAGTGATTA
1 TGAAAGTAAATATGAAAAAGTGATTA
50590 TGAAAGTAAATATGAAAAAGTGATTA
1 TGAAAGTAAATATGAAAAAGTGATTA
50616 TGAAAG
1 TGAAAG
50622 ATAAGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (26 bp):
TGAAAGTAAATATGAAAAAGTGATTA
Found at i:50621 original size:12 final size:12
Alignment explanation
Indices: 50565--50606 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
50555 CATTGTGTTT
50565 TGAAAGTAAATA
1 TGAAAGTAAATA
* *
50577 TGAAAAGTGATTA
1 TG-AAAGTAAATA
50590 TGAAAGTAAATA
1 TGAAAGTAAATA
50602 TGAAA
1 TGAAA
50607 AAGTGATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (12 bp):
TGAAAGTAAATA
Found at i:57099 original size:18 final size:20
Alignment explanation
Indices: 57040--57100 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 20
57030 AACAAGTTTA
* * *
57040 TTTTTATAATGAAGTATTTAT
1 TTTTTA-AATAAATTATTTTT
57061 TTTTTAAATAAATTATCTTTTT
1 TTTTTAAATAAATTA--TTTTT
57083 TTTTTAAA-AAA-TATTTTT
1 TTTTTAAATAAATTATTTTT
57101 AAAATCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 5 0.14
20 9 0.26
21 9 0.26
22 12 0.34
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTTAAATAAATTATTTTT
Found at i:58604 original size:20 final size:20
Alignment explanation
Indices: 58579--58629 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
58569 ACCAATAGGC
*
58579 AGTATCGGTACTGCCATGGG
1 AGTATCGATACTGCCATGGG
58599 AGTATCGATACTGCCATGGG
1 AGTATCGATACTGCCATGGG
58619 AGTATCGATAC
1 AGTATCGATAC
58630 CTCCCTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTGCCATGGG
Found at i:60411 original size:20 final size:20
Alignment explanation
Indices: 60386--60437 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
60376 TCTCACCTCT
*
60386 TTCTTTTTCTT-GTTCTTCTC
1 TTCTTTTTCTTCATTCTT-TC
60406 TTCTTTTTCTTCATTCTTTC
1 TTCTTTTTCTTCATTCTTTC
60426 TTCTTTCTTCTT
1 TTCTTT-TTCTT
60438 TCTTTGGAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (20 bp):
TTCTTTTTCTTCATTCTTTC
Found at i:60439 original size:14 final size:13
Alignment explanation
Indices: 60383--60441 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 13
60373 AATTCTCACC
*
60383 TCTTTCTTTTTCT
1 TCTTTCTTCTTCT
*
60396 T-GTTCTTC-TCT
1 TCTTTCTTCTTCT
60407 TCTTT-TTCTTCAT
1 TCTTTCTTCTTC-T
60420 TCTTTCTTCTTTCT
1 TCTTTCTTC-TTCT
60434 TCTTTCTT
1 TCTTTCTT
60442 TGGAGCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.18
12 9 0.24
13 7 0.18
14 12 0.32
15 3 0.08
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (13 bp):
TCTTTCTTCTTCT
Found at i:71066 original size:21 final size:21
Alignment explanation
Indices: 71012--71067 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
71002 CAGTGATATA
*
71012 TGAAATGGATGTGGTACCATC
1 TGAAATGGATGCGGTACCATC
* * * *
71033 TGATACGGCTGCGGTGCCATC
1 TGAAATGGATGCGGTACCATC
*
71054 TGAAATGGTTGCGG
1 TGAAATGGATGCGG
71068 AATGTACAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (21 bp):
TGAAATGGATGCGGTACCATC
Found at i:72782 original size:28 final size:29
Alignment explanation
Indices: 72751--72815 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
72741 TGCAAAAATT
72751 AATAAAAATTTGTATAATAAATT-TAATA-
1 AATAAAAATTTGT-TAATAAATTATAATAC
* * *
72779 AATATAAA-TTGTTGATTAATTATAATAC
1 AATAAAAATTTGTTAATAAATTATAATAC
72807 AATAAAAAT
1 AATAAAAAT
72816 ATTTACCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 7 0.23
27 9 0.30
28 14 0.47
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (29 bp):
AATAAAAATTTGTTAATAAATTATAATAC
Found at i:73997 original size:17 final size:17
Alignment explanation
Indices: 73972--74005 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
73962 ATACATTATT
*
73972 AATAAATTATTTTTTAA
1 AATAAATTATCTTTTAA
*
73989 AATAGATTATCTTTTAA
1 AATAAATTATCTTTTAA
74006 TTATTCATAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
AATAAATTATCTTTTAA
Found at i:76074 original size:15 final size:14
Alignment explanation
Indices: 76049--76081 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
76039 TGATCTGGGG
76049 CTCACCAAATCGGT
1 CTCACCAAATCGGT
76063 CTCACACAAATCGGT
1 CTCAC-CAAATCGGT
76078 CTCA
1 CTCA
76082 TGTGGAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.21
Consensus pattern (14 bp):
CTCACCAAATCGGT
Done.