Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004443.1 Hibiscus syriacus cultivar Beakdansim tig00009743_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: 45757
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:2193 original size:3 final size:3
Alignment explanation
Indices: 2185--2209 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2175 GAGGAATGAA
2185 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2210 GTGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4255 original size:31 final size:33
Alignment explanation
Indices: 4185--4255 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 33
4175 AGAAAAAACA
* *
4185 TATATATATATATATATATATCAAGGTAAATGG
1 TATATATATACATATATATATCAAGGTAAATAG
* *
4218 TGTATATATACATA-ATATA-C-ATGTAAAATAG
1 TATATATATACATATATATATCAAGGT-AAATAG
4249 TATATAT
1 TATATAT
4256 CAAGGTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 3 0.09
31 12 0.38
32 5 0.16
33 12 0.38
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.39
Consensus pattern (33 bp):
TATATATATACATATATATATCAAGGTAAATAG
Found at i:6394 original size:21 final size:21
Alignment explanation
Indices: 6370--6409 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6360 GTGATTGCGA
*
6370 CCGTCGCGGGCGCTATTGCTG
1 CCGTCGCGGACGCTATTGCTG
*
6391 CCGTCGCGGATGCTATTGC
1 CCGTCGCGGACGCTATTGC
6410 GGCCATTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.33, G:0.35, T:0.25
Consensus pattern (21 bp):
CCGTCGCGGACGCTATTGCTG
Found at i:6420 original size:21 final size:21
Alignment explanation
Indices: 6363--6420 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
6353 ATTTATCGTG
* * **
6363 ATTGCGACCGTCGCGGGCGCT
1 ATTGCGGCCATCGCGGATGCT
* *
6384 ATTGCTGCCGTCGCGGATGCT
1 ATTGCGGCCATCGCGGATGCT
*
6405 ATTGCGGCCATTGCGG
1 ATTGCGGCCATCGCGG
6421 GTAACTCGGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.29, G:0.36, T:0.24
Consensus pattern (21 bp):
ATTGCGGCCATCGCGGATGCT
Found at i:7337 original size:3 final size:3
Alignment explanation
Indices: 7331--7381 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
7321 TTTTTTCATT
* * *
7331 TTA TTA TTA TTA CTA TTA -TA TTTA TTT TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
7376 TTA TTA
1 TTA TTA
7382 CAAACAGGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:8807 original size:15 final size:14
Alignment explanation
Indices: 8787--8831 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
8777 AAGCTTTATT
8787 ATTTTATTCATTTTA
1 ATTTTATT-ATTTTA
8802 ATTTTA-TAGTTTTA
1 ATTTTATTA-TTTTA
8816 ATTTTATTTATTTTA
1 ATTTTA-TTATTTTA
8831 A
1 A
8832 ACATTGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 12 0.44
15 12 0.44
16 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTTTATTATTTTA
Found at i:9807 original size:21 final size:24
Alignment explanation
Indices: 9745--9795 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
9735 CTTTTCAAAA
9745 TTTATATATATTATTTTATTAATG
1 TTTATATATATTATTTTATTAATG
9769 TTTATATATATTATTTTATTAATG
1 TTTATATATATTATTTTATTAATG
9793 TTT
1 TTT
9796 TAGTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTATATATATTATTTTATTAATG
Found at i:14469 original size:10 final size:9
Alignment explanation
Indices: 14444--14468 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14434 CTCATTCATC
14444 AAAAAAATT
1 AAAAAAATT
14453 AAAAAAATT
1 AAAAAAATT
14462 AAAAAAA
1 AAAAAAA
14469 AAAGGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:18177 original size:198 final size:198
Alignment explanation
Indices: 17839--18238 Score: 728
Period size: 198 Copynumber: 2.0 Consensus size: 198
17829 AGCAAGTATG
*
17839 GTTTCAAATACCCAATCTTCTTAACCATGTGTCACATGACAGCGTGTTCTTTAAGCTACATCACA
1 GTTTCAAATACCCAATCTTCTTAACCATGTATCACATGACAGCGTGTTCTTTAAGCTACATCACA
* * *
17904 GTTGCATGGATAAAGATGATCCCCAGGCAGACCATTCGATCTAGTGTTCAGTTCCTCAAGATCTC
66 GTTGCATGGATAAAGATGACCCCCAGGAAGACCATTCGATCTAGGGTTCAGTTCCTCAAGATCTC
17969 AGCTTTGAAGTTTGCATTCTCTGTGTTGGTGATGATTGGAAATATTTCTTTGAGATTCCTGGTAG
131 AGCTTTGAAGTTTGCATTCTCTGTGTTGGTGATGATTGGAAATATTTCTTTGAGATTCCTGGTAG
18034 TTA
196 TTA
*
18037 GTTTCAAATACCCAATCTTCTTAACCATGTATCACATGACAGCGTGTTCTTTAAGCTACATCACG
1 GTTTCAAATACCCAATCTTCTTAACCATGTATCACATGACAGCGTGTTCTTTAAGCTACATCACA
*
18102 GTTGCATGGATCAAGATGACCCCCAGGAAGACCATTCGATCTAGGGTTCAGTTCCTCAAGATCTC
66 GTTGCATGGATAAAGATGACCCCCAGGAAGACCATTCGATCTAGGGTTCAGTTCCTCAAGATCTC
* *
18167 GGCTTTGAAGTTTGCATTTTCTGTGTTGGTGATGATTGGAAATATTTCTTTGAGATTCCTGGTAG
131 AGCTTTGAAGTTTGCATTCTCTGTGTTGGTGATGATTGGAAATATTTCTTTGAGATTCCTGGTAG
18232 TTA
196 TTA
18235 GTTT
1 GTTT
18239 TAACCATACT
Statistics
Matches: 194, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 194 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (198 bp):
GTTTCAAATACCCAATCTTCTTAACCATGTATCACATGACAGCGTGTTCTTTAAGCTACATCACA
GTTGCATGGATAAAGATGACCCCCAGGAAGACCATTCGATCTAGGGTTCAGTTCCTCAAGATCTC
AGCTTTGAAGTTTGCATTCTCTGTGTTGGTGATGATTGGAAATATTTCTTTGAGATTCCTGGTAG
TTA
Found at i:18798 original size:54 final size:54
Alignment explanation
Indices: 18729--18832 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
18719 CCTGACTAAA
* * * *
18729 CATCTGAGAATAAGCCACATGAGATGATGAATGTGTTGTCAAATGTTTTACAAG
1 CATCTGAGAAGAAGCCACAAGAAATAATGAATGTGTTGTCAAATGTTTTACAAG
* *
18783 CATCTGAGCAGAAGCCACAAGAAATAATGAATGTGTTGTCAAGTGTTTTA
1 CATCTGAGAAGAAGCCACAAGAAATAATGAATGTGTTGTCAAATGTTTTA
18833 GGAACCAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (54 bp):
CATCTGAGAAGAAGCCACAAGAAATAATGAATGTGTTGTCAAATGTTTTACAAG
Found at i:19785 original size:113 final size:113
Alignment explanation
Indices: 19587--20149 Score: 803
Period size: 113 Copynumber: 5.0 Consensus size: 113
19577 GCAAAGATTT
*
19587 GAATTCATCACTTGATGGATCAACTTTTCCAGAG-GAAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATTCATCACTTGATGGATCAACTTTTCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAA
19651 GAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
65 GAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * *
19700 GAATTCATCACTTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCTGAAG
1 GAATTCATCACTTGATGGATCAACTTTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
19765 AATGAAGAAGAATTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
66 AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
19813 GAATTCATCACTTGATGGATCAACTTTTCCA--TAGGAAGTTCATAATGAGAAGAACTCATCTGA
1 GAATTCATCACTTGATGGATCAACTTTTCCAGGTA--AAGTTCATAATGAGAAGAACTCATCTGA
*
19876 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
64 AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * *
19926 GAATTCATCACTTGATGGATTAGCATTGCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCACTTGATGGATCAACTTTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * * *
19991 AATGAAGAAGAAATTCATAATAAGAAAAATTTGTTCAAACCTTTTGTTT
66 AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGCTC
** *
20040 GAATTCATCACTCAATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAA
1 GAATTCATCACTTGATGGATCAACTTTTCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
20104 G-AGGAAGAAGAAGTTTATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 GAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
20150 ACGACTCTAT
Statistics
Matches: 398, Mismatches: 45, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
111 2 0.01
112 10 0.03
113 318 0.80
114 66 0.17
115 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (113 bp):
GAATTCATCACTTGATGGATCAACTTTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAG
AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:19979 original size:226 final size:227
Alignment explanation
Indices: 19585--20149 Score: 954
Period size: 226 Copynumber: 2.5 Consensus size: 227
19575 TAGCAAAGAT
19585 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
*
19650 AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
* * * *
19715 TGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCTGAAGAATGAAGAAGAATTT
131 TGGATCAGCATTGCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAATT
* * *
19780 CATAATGAGAAGAACTTGTT-TAACCTTTTGC
196 CATAATAAGAAAAACTTGTTCAAACCTTTTGC
*
19811 TTGAATTCATCACTTGATGGATCAACTTTTCCATAGGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
19876 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
*
19941 TGGATTAGCATTGCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAATT
131 TGGATCAGCATTGCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAATT
* *
20006 CATAATAAGAAAAATTTGTTCAAACCTTTTGT
196 CATAATAAGAAAAACTTGTTCAAACCTTTTGC
** * *
20038 TTGAATTCATCACTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
* *
20103 AG-AGGAAGAAGAAGTTTATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
20150 ACGACTCTAT
Statistics
Matches: 319, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
226 248 0.78
227 71 0.22
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (227 bp):
TTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
TGGATCAGCATTGCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAATT
CATAATAAGAAAAACTTGTTCAAACCTTTTGC
Found at i:20588 original size:3 final size:3
Alignment explanation
Indices: 20577--20642 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
20567 ACTAGTTTTT
*
20577 TTA TT- TTA TTA TTA TTA TTA CTA TTA -TA TTA TTA TTTA TT- TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* *
20619 TTA TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
20643 CAAACAGACC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 8 0.15
3 42 0.79
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:25051 original size:18 final size:18
Alignment explanation
Indices: 25014--25051 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25004 AAATGCTAAG
*
25014 TATGATTTCTACCATGCT
1 TATGATTTCTACCATACT
*
25032 TATGATTTCTATCATACT
1 TATGATTTCTACCATACT
25050 TA
1 TA
25052 GCTAAGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.47
Consensus pattern (18 bp):
TATGATTTCTACCATACT
Found at i:25070 original size:15 final size:15
Alignment explanation
Indices: 25050--25083 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
25040 CTATCATACT
25050 TAGCTAAGTTTTCTA
1 TAGCTAAGTTTTCTA
25065 TAGCTAAGTTTTCTA
1 TAGCTAAGTTTTCTA
25080 TAGC
1 TAGC
25084 CAAGGGCTAG
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:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (15 bp):
TAGCTAAGTTTTCTA
Found at i:26746 original size:15 final size:15
Alignment explanation
Indices: 26726--26756 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26716 CAACAAATAG
26726 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
26741 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
26756 A
1 A
26757 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:27264 original size:5 final size:5
Alignment explanation
Indices: 27256--27297 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
27246 TACCAATTGA
*
27256 ATTTT ATTTT -CTTT ATTTACT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTT--T ATTTT ATTTT ATTTT ATTTT A
27298 ATCAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
7 5 0.16
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:27628 original size:3 final size:3
Alignment explanation
Indices: 27622--27731 Score: 184
Period size: 3 Copynumber: 36.7 Consensus size: 3
27612 TTTTTATCCA
* *
27622 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
27670 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27718 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
27732 AATATATTAA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:29170 original size:20 final size:21
Alignment explanation
Indices: 29133--29173 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29123 GATATTTTTA
**
29133 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
29154 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
29174 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:29892 original size:18 final size:17
Alignment explanation
Indices: 29869--29919 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
29859 TTCTTTTCAA
29869 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
29886 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
29904 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
29920 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:29941 original size:13 final size:15
Alignment explanation
Indices: 29910--29946 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
29900 TTATATGTTT
29910 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
29925 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
29938 TA-TTTATTT
1 TATTTTATTT
29947 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:33285 original size:14 final size:15
Alignment explanation
Indices: 33256--33287 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
33246 GAATTATTTT
33256 ATTCATTAAGTTAAA
1 ATTCATTAAGTTAAA
33271 ATTCATTAA-TTAAA
1 ATTCATTAAGTTAAA
33285 ATT
1 ATT
33288 TGAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTCATTAAGTTAAA
Found at i:40554 original size:1 final size:1
Alignment explanation
Indices: 40548--40597 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
40538 ATGCTTGAAG
* * * * *
40548 AAAAAAAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40598 GGGGAGTCAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:40560 original size:10 final size:10
Alignment explanation
Indices: 40545--40598 Score: 74
Period size: 10 Copynumber: 5.3 Consensus size: 10
40535 ATTATGCTTG
40545 AAGAAAAAAA
1 AAGAAAAAAA
40555 AAGAAAAAAA
1 AAGAAAAAAA
40565 AAGAAAAAAAA
1 AAG-AAAAAAA
40576 AAGAAAAAGAA
1 AAGAAAAA-AA
*
40587 AA-AAGAAAA
1 AAGAAAAAAA
40596 AAG
1 AAG
40599 GGGAGTCAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
9 4 0.10
10 22 0.55
11 14 0.35
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:40563 original size:7 final size:7
Alignment explanation
Indices: 40551--40598 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
40541 CTTGAAGAAA
40551 AAAAAAG
1 AAAAAAG
40558 AAAAAA-
1 AAAAAAG
*
40564 AAAGAAAA
1 AAA-AAAG
40572 AAAAAAG
1 AAAAAAG
40579 -AAAAAG
1 AAAAAAG
40585 AAAAAAG
1 AAAAAAG
40592 AAAAAAG
1 AAAAAAG
40599 GGGAGTCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 9 0.24
7 25 0.68
8 3 0.08
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:40564 original size:11 final size:11
Alignment explanation
Indices: 40548--40597 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
40538 ATGCTTGAAG
40548 AAAAAAAAAG-
1 AAAAAAAAAGA
40558 AAAAAAAAAGA
1 AAAAAAAAAGA
40569 AAAAAAAAAGAA
1 AAAAAAAAAG-A
40581 AAAGAAAAAAGA
1 AAA-AAAAAAGA
40593 AAAAA
1 AAAAA
40598 GGGGAGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.27
11 12 0.32
12 8 0.22
13 7 0.19
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:40570 original size:20 final size:21
Alignment explanation
Indices: 40545--40598 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
40535 ATTATGCTTG
40545 AAGAAAAAAAAAGAAAAA-AA
1 AAGAAAAAAAAAGAAAAAGAA
40565 AAGAAAAAAAAAAGAAAAAGAA
1 AAG-AAAAAAAAAGAAAAAGAA
*
40587 AA-AAGAAAAAAG
1 AAGAAAAAAAAAG
40599 GGGAGTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 12 0.39
21 15 0.48
22 4 0.13
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAAAAGAA
Found at i:40964 original size:19 final size:20
Alignment explanation
Indices: 40931--40972 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
40921 TTCAAGTTCA
*
40931 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
40951 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
40970 ATT
1 ATT
40973 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:41880 original size:83 final size:83
Alignment explanation
Indices: 41741--42031 Score: 478
Period size: 83 Copynumber: 3.5 Consensus size: 83
41731 TGAAAGAGAC
* *
41741 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTACACAGAACCAATCATCGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGACAGAACCAATCATCGAA
41806 TTTAGAAGATGAATGTGT
66 TTTAGAAGATGAATGTGT
*
41824 TCATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGACAGAACCAATCATCGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGACAGAACCAATCATCGAA
41889 TTTAGAAGATGAATGTGT
66 TTTAGAAGATGAATGTGT
*
41907 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTT-GACAGAACCAATCATTGA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTAGACAGAACCAATCATCGA
*
41971 ATTTAGAAGATGAATTTG-
65 ATTTAGAAGATGAATGTGT
* * *
41989 CCAATAGCATCTTCTAGAAGTGTCCTTTGAGTTATCTGATCTG
1 TC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
42032 GTTTGGTAAG
Statistics
Matches: 197, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
82 2 0.01
83 191 0.97
84 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (83 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGACAGAACCAATCATCGAA
TTTAGAAGATGAATGTGT
Found at i:42885 original size:113 final size:112
Alignment explanation
Indices: 42682--43351 Score: 803
Period size: 113 Copynumber: 5.9 Consensus size: 112
42672 GATTCAATCT
* *** *
42682 ATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATCAACATTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
42747 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCC
65 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* * * **
42795 ATCATTTGATGGATCAGCCTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATCAACATTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
42860 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGTTTGAATTC
65 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTTGCTTGAATTC
* *** *
42909 ATCACTTGATGGATTATTGTTGCCA-GAGGAGGTTCATAATGAG-A-AACTCATCTGAAGAAGGA
1 ATCACTTGATGGATCAACATTTCCAGGA-GA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
42971 AGGAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATC
64 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* *** * *
43019 TATCACTTGATGGATTATTTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 -ATCACTTGATGGATCA-ACATTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
43084 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
63 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* *
43134 ATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCACTTGATGGATCAACATTTCCAGG-AGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG
* * **
43199 AAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATCTTTTGCAAGAATTC
62 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGCTTGAATTC
* * *
43251 ATCAATTGATGGATCAACATTT-CTGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCACTTGATGGATCAACATTTCCAGGAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
43315 GAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTT
65 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
43352 CGCATAATTC
Statistics
Matches: 493, Mismatches: 48, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
110 5 0.01
111 26 0.05
112 73 0.15
113 164 0.33
114 115 0.23
115 8 0.02
116 66 0.13
117 36 0.07
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (112 bp):
ATCACTTGATGGATCAACATTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
Found at i:43671 original size:3 final size:3
Alignment explanation
Indices: 43663--43759 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
43653 TTTTTATCCA
43663 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
43708 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT CAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43755 TAT TA
1 TAT TA
43760 AATATATTAA
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
2 8 0.09
3 78 0.91
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:43689 original size:23 final size:23
Alignment explanation
Indices: 43663--43759 Score: 144
Period size: 23 Copynumber: 4.2 Consensus size: 23
43653 TTTTTATCCA
43663 TATTATTATTA-TATTATTATTAT
1 TATTATTATTACTATTATTA-TAT
43686 TATTATTATTA-TATTATTATAT
1 TATTATTATTACTATTATTATAT
*
43708 TATTATTATTATTATTATTATAT
1 TATTATTATTACTATTATTATAT
*
43731 TATTATCATTACTATTATTATTAT
1 TATTATTATTACTATTATTA-TAT
43755 TATTA
1 TATTA
43760 AATATATTAA
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
22 14 0.20
23 48 0.69
24 8 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTATTACTATTATTATAT
Found at i:45160 original size:19 final size:20
Alignment explanation
Indices: 45122--45163 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
45112 GTGATATTTT
**
45122 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
45142 TATTTTA-TATATTCATAAA
1 TATTTTATTATATTCATAAA
45161 TAT
1 TAT
45164 ACATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Done.