Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002759.1 Hibiscus syriacus cultivar Beakdansim tig00005687_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: 72889
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:2777 original size:35 final size:35
Alignment explanation
Indices: 2738--2805 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
2728 TTCATGCATC
2738 TAGTTCATTGAAT-AAAGTTAGTTCA-TTAATTAAAG
1 TAGTTCATT-AATCAAAG-TAGTTCATTTAATTAAAG
*
2773 TAGTTCATTCATCAAAGTAGTTCATTTAATTAA
1 TAGTTCATTAATCAAAGTAGTTCATTTAATTAA
2806 CTAACTCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (35 bp):
TAGTTCATTAATCAAAGTAGTTCATTTAATTAAAG
Found at i:2778 original size:17 final size:17
Alignment explanation
Indices: 2738--2805 Score: 84
Period size: 17 Copynumber: 3.9 Consensus size: 17
2728 TTCATGCATC
2738 TAGTTCATTGAA-TAAAG
1 TAGTTCATT-AATTAAAG
2755 TTAGTTCATTAATTAAAG
1 -TAGTTCATTAATTAAAG
* *
2773 TAGTTCATTCATCAAAG
1 TAGTTCATTAATTAAAG
2790 TAGTTCATTTAATTAA
1 TAGTTCA-TTAATTAA
2806 CTAACTCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
17 24 0.55
18 20 0.45
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAG
Found at i:4077 original size:22 final size:22
Alignment explanation
Indices: 4049--4098 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
4039 CCACACTTCT
4049 TTCATTTACAATACACTTCAAC
1 TTCATTTACAATACACTTCAAC
4071 TTCATTTACAATACACTTCAAC
1 TTCATTTACAATACACTTCAAC
4093 TTCATT
1 TTCATT
4099 CTATCATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATTTACAATACACTTCAAC
Found at i:5218 original size:246 final size:246
Alignment explanation
Indices: 4777--5802 Score: 1060
Period size: 246 Copynumber: 4.3 Consensus size: 246
4767 GGGTATCGCC
* * * *
4777 TCCATCGACATTGTCGAAATTGAAATCTTTAGATGACCCGAGAGTGATGGTTCGGTTCTTGTGGT
1 TCCATCAACATTGTCAAAATTGAAATCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGGT
* * * * * *
4842 GCTGTGGTCTGCCTTCTGTATCGGCTGGAGGCCTTTCTGGTGTTTCGATGTATGTTTCACCAACA
66 GCTGTGGTCTGCCTTCTGTATCAGCTGGAAGTCTTTCTGGTCTTTCAATGTATATTTCACCAACA
** *
4907 TGACATTCGTAAGTTTCCACCAACTTAGTAGCGTTTTCTTCTTTCTGTCTTGCTGCTTCATTCCG
131 CAACATTCATAAGTTTCCACCAACTTAGTAGCGTTTTCTTCTTTCTGTCTTGCTGCTTCATTCCG
* **
4972 TAGAGATTCTGCTGCAGCTTCATACAG-TGTCGAAGTCTCGATTTCCACACA
196 TAGAGATTCTGCTGCAGCTTCAGA-AGATGTCGCTGTCTCGATTTCCACACA
*
5023 TCCATCAACATTGTCAAAATTGAAATCTTTAGATGACCCAAGAGTGATGGATCGGTTCTTATGGT
1 TCCATCAACATTGTCAAAATTGAAATCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGGT
* * *
5088 GATGTGGTCTGCCTTCGGTATCAGCTGGAAGTCTTTCTGTTCTTTCAATGTATATTTCACCAACA
66 GCTGTGGTCTGCCTTCTGTATCAGCTGGAAGTCTTTCTGGTCTTTCAATGTATATTTCACCAACA
*
5153 CAACATTCATAAGTTTCCACCAACTTAGTAGCGTTTTCTTCTTTCCGTCTTGCTGCTTCATTCCG
131 CAACATTCATAAGTTTCCACCAACTTAGTAGCGTTTTCTTCTTTCTGTCTTGCTGCTTCATTCCG
* *
5218 TAGAGATTCCGCTGCAGCTTCAGATGATGTCGCTGTCTCGATTTCCACACA
196 TAGAGATTCTGCTGCAGCTTCAGAAGATGTCGCTGTCTCGATTTCCACACA
* *
5269 TCCATCAACATTGTCAAAATTGAAATCTTTAGAAGATCCGAGAGTGATGGATCGGTTCTTATGGT
1 TCCATCAACATTGTCAAAATTGAAATCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGGT
* * * * * *
5334 GCTGTGGTCTGCCTTCCGTATCAGCTTGAGGTATTTCTGGTCTTTCAATGAACATTT--CC-AC-
66 GCTGTGGTCTGCCTTCTGTATCAGCTGGAAGTCTTTCTGGTCTTTCAATGTATATTTCACCAACA
* * * * *
5395 CATC-TT--T--G--T--AGC-A-TT--T-TCTTCTTTCTGTCTTTCTG-CTT--T-ATTCA---
131 CAACATTCATAAGTTTCCACCAACTTAGTAGCGT-TTTCT-TCTTTCTGTCTTGCTGCTTCATTC
* *
5439 -GTAGAGATTCTGCTGCAGCTTCAG-AGAGTATCGCTGTCTC-AGTTTCTACACA
194 CGTAGAGATTCTGCTGCAGCTTCAGAAGA-TGTCGCTGTCTCGA-TTTCCACACA
5491 TCCATCAACATAT-TCAAAATTGAAATCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGG
1 TCCATCAACAT-TGTCAAAATTGAAATCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGG
* ** * * * ** * *
5555 TGCCGAAGTCTGCCTTCTGTATTAGCTAG-AGTTTTTTCTCCTCTTTCGATGTATGTTTCACCAA
65 TGCTGTGGTCTGCCTTCTGTATCAGCTGGAAG-TCTTTCTGGTCTTTCAATGTATATTTCACCAA
** * * * * * * *
5619 TTCGACATTCATAAATTTCCACCAAATTGGTAGCGTTTTCTCCTTTCTGTTTTGCAG-TTGCATT
129 CACAACATTCATAAGTTTCCACCAACTTAGTAGCGTTTTCTTCTTTCTGTCTTGCTGCTT-CATT
** * ** * * *
5683 CCGTAGAGATTCTGCCACGGCTTTGGATAGGCT-TC-CTGTCTCAACTTCCACACA
193 CCGTAGAGATTCTGCTGCAGCTTCAGA-A-GATGTCGCTGTCTCGATTTCCACACA
* * * * * **
5737 TCCATGAACGTTATCAAAATTGAATTCTTTAGCA-GACCCAAGAGTGATGGATATGTTCTTATGG
1 TCCATCAACATTGTCAAAATTGAAATCTTTAG-ATGACCCGAGAGTGATGGATCGGTTCTTATGG
5801 TG
65 TG
5803 TTGCGGTTTT
Statistics
Matches: 656, Mismatches: 84, Indels: 80
0.80 0.10 0.10
Matches are distributed among these distances:
221 4 0.01
222 145 0.22
223 1 0.00
224 2 0.00
225 1 0.00
226 6 0.01
227 3 0.00
228 2 0.00
229 10 0.02
230 7 0.01
231 2 0.00
232 1 0.00
233 3 0.00
235 3 0.00
236 1 0.00
237 3 0.00
238 7 0.01
239 9 0.01
240 2 0.00
241 4 0.01
242 5 0.01
243 2 0.00
244 2 0.00
245 2 0.00
246 422 0.64
247 4 0.01
248 2 0.00
249 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (246 bp):
TCCATCAACATTGTCAAAATTGAAATCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGGT
GCTGTGGTCTGCCTTCTGTATCAGCTGGAAGTCTTTCTGGTCTTTCAATGTATATTTCACCAACA
CAACATTCATAAGTTTCCACCAACTTAGTAGCGTTTTCTTCTTTCTGTCTTGCTGCTTCATTCCG
TAGAGATTCTGCTGCAGCTTCAGAAGATGTCGCTGTCTCGATTTCCACACA
Found at i:5552 original size:222 final size:222
Alignment explanation
Indices: 5166--5581 Score: 631
Period size: 222 Copynumber: 1.9 Consensus size: 222
5156 CATTCATAAG
* *
5166 TTTCCACCAACTTAGTAGCGTTTTCTTCTTTCCGTCTTGCTGCTTCATTCCGTAGAGATTCCGCT
1 TTTCCACCAACTTAGTAGCATTTTCTTCTTTCCGTCTTGCTGCTTCATTCAGTAGAGATTCCGCT
*
5231 GCAGCTTCAGATGATGTCGCTGTCTCGATTTCCACACATCCATCAACATTGTCAAAATTGAAATC
66 GCAGCTTCAGATGATATCGCTGTCTCGATTTCCACACATCCATCAACATTGTCAAAATTGAAATC
* * **
5296 TTTAGAAGATCCGAGAGTGATGGATCGGTTCTTATGGTGCTGTGGTCTGCCTTCCGTATCAGCTT
131 TTTAGAAGACCCGAGAGTGATGGATCGGTTCTTATGGTGCCGAAGTCTGCCTTCCGTATCAGCTT
5361 GAGGTATTTCTGGTCTTTCAATGAACA
196 GAGGTATTTCTGGTCTTTCAATGAACA
* * * * * *
5388 TTTCCACCATCTTTGTAGCATTTTCTTCTTTCTGTCTTTCTGCTTTATTCAGTAGAGATTCTGCT
1 TTTCCACCAACTTAGTAGCATTTTCTTCTTTCCGTCTTGCTGCTTCATTCAGTAGAGATTCCGCT
*
5453 GCAGCTTCAGA-GAGTATCGCTGTCTC-AGTTTCTACACATCCATCAACATAT-TCAAAATTGAA
66 GCAGCTTCAGATGA-TATCGCTGTCTCGA-TTTCCACACATCCATCAACAT-TGTCAAAATTGAA
* * *
5515 ATCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGGTGCCGAAGTCTGCCTTCTGTATTAG
128 ATCTTTAGAAGACCCGAGAGTGATGGATCGGTTCTTATGGTGCCGAAGTCTGCCTTCCGTATCAG
5580 CT
193 CT
5582 AGAGTTTTTT
Statistics
Matches: 174, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
221 3 0.02
222 170 0.98
223 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (222 bp):
TTTCCACCAACTTAGTAGCATTTTCTTCTTTCCGTCTTGCTGCTTCATTCAGTAGAGATTCCGCT
GCAGCTTCAGATGATATCGCTGTCTCGATTTCCACACATCCATCAACATTGTCAAAATTGAAATC
TTTAGAAGACCCGAGAGTGATGGATCGGTTCTTATGGTGCCGAAGTCTGCCTTCCGTATCAGCTT
GAGGTATTTCTGGTCTTTCAATGAACA
Found at i:5797 original size:468 final size:468
Alignment explanation
Indices: 4920--5802 Score: 1193
Period size: 468 Copynumber: 1.9 Consensus size: 468
4910 CATTCGTAAG
* *
4920 TTTCCACCAACTTAGTAGCGTTTTCTTCTTTCTGTCTTGCTGCTTCATTCCGTAGAGATTCTGCT
1 TTTCCACCAACTTAGTAGCATTTTCTTCTTTCTGTCTTGCTGCTTCATTCAGTAGAGATTCTGCT
* *
4985 GCAGCTTCATACAGTGTCGAAGTCTCGATTTCCACACATCCATCAACATTGTCAAAATTGAAATC
66 GCAGCTTCAGACAGTATCGAAGTCTCGATTTCCACACATCCATCAACATTGTCAAAATTGAAATC
* ** *
5050 TTTAGATGACCCAAGAGTGATGGATCGGTTCTTATGGTGATGTGGTCTGCCTTCGGTATCAGCTG
131 TTTAGATGACCCAAGAGTGATGGATCGGTTCTTATGGTGACGAAGTCTGCCTTCGGTATCAGCTA
** * *
5115 GAAGTCTTTCTGTTCTTTCAATGTATATTTCACCAACACAACATTCATAAGTTTCCACCAACTTA
196 GAAGTCTTTCTCCTCTTTCAATGTATATTTCACCAACACAACATTCATAAATTTCCACCAAATTA
* * **
5180 GTAGCGTTTTCTTCTTTCCGTCTTGCTGCTTCATTCCGTAGAGATTCCGCTGCAGCTTCAGATGA
261 GTAGCGTTTTCTCCTTTCCGTCTTGCAGCTTCATTCCGTAGAGATTCCGCCACAGCTTCAGATGA
* * * * *
5245 TGTCGCTGTCTCGATTTCCACACATCCATCAACATTGTCAAAATTGAAATCTTTAGAAGATCCGA
326 TGTCGCTGTCTCAACTTCCACACATCCATCAACATTATCAAAATTGAAATCTTTAGAAGACCCAA
*
5310 GAGTGATGGATCGGTTCTTATGGTGCTGTGGTCTGCCTTCCGTATCAGCTTGAGGTATTTCTGGT
391 GAGTGATGGATAGGTTCTTATGGTGCTGTGGTCTGCCTTCCGTATCAGCTTGAGGTATTTCTGGT
5375 CTTTCAATGAACA
456 CTTTCAATGAACA
* * * *
5388 TTTCCACCATCTTTGTAGCATTTTCTTCTTTCTGTCTTTCTGCTTTATTCAGTAGAGATTCTGCT
1 TTTCCACCAACTTAGTAGCATTTTCTTCTTTCTGTCTTGCTGCTTCATTCAGTAGAGATTCTGCT
* ** *
5453 GCAGCTTCAGAGAGTATCGCTGTCTC-AGTTTCTACACATCCATCAACATAT-TCAAAATTGAAA
66 GCAGCTTCAGACAGTATCGAAGTCTCGA-TTTCCACACATCCATCAACAT-TGTCAAAATTGAAA
* * * *
5516 TCTTTAGATGACCCGAGAGTGATGGATCGGTTCTTATGGTGCCGAAGTCTGCCTTCTGTATTAGC
129 TCTTTAGATGACCCAAGAGTGATGGATCGGTTCTTATGGTGACGAAGTCTGCCTTCGGTATCAGC
* * * ** *
5581 TAG-AGTTTTTTCTCCTCTTTCGATGTATGTTTCACCAATTCGACATTCATAAATTTCCACCAAA
194 TAGAAG-TCTTTCTCCTCTTTCAATGTATATTTCACCAACACAACATTCATAAATTTCCACCAAA
* * * * * **
5645 TTGGTAGCGTTTTCTCCTTTCTGTTTTGCAG-TTGCATTCCGTAGAGATTCTGCCACGGCTTTGG
258 TTAGTAGCGTTTTCTCCTTTCCGTCTTGCAGCTT-CATTCCGTAGAGATTCCGCCACAGCTTCAG
* * * * *
5709 AT-AGGCTTC-CTGTCTCAACTTCCACACATCCATGAACGTTATCAAAATTGAATTCTTTAGCAG
322 ATGATG--TCGCTGTCTCAACTTCCACACATCCATCAACATTATCAAAATTGAAATCTTTAGAAG
*
5772 ACCCAAGAGTGATGGATATGTTCTTATGGTG
385 ACCCAAGAGTGATGGATAGGTTCTTATGGTG
5803 TTGCGGTTTT
Statistics
Matches: 356, Mismatches: 53, Indels: 12
0.85 0.13 0.03
Matches are distributed among these distances:
467 7 0.02
468 346 0.97
469 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (468 bp):
TTTCCACCAACTTAGTAGCATTTTCTTCTTTCTGTCTTGCTGCTTCATTCAGTAGAGATTCTGCT
GCAGCTTCAGACAGTATCGAAGTCTCGATTTCCACACATCCATCAACATTGTCAAAATTGAAATC
TTTAGATGACCCAAGAGTGATGGATCGGTTCTTATGGTGACGAAGTCTGCCTTCGGTATCAGCTA
GAAGTCTTTCTCCTCTTTCAATGTATATTTCACCAACACAACATTCATAAATTTCCACCAAATTA
GTAGCGTTTTCTCCTTTCCGTCTTGCAGCTTCATTCCGTAGAGATTCCGCCACAGCTTCAGATGA
TGTCGCTGTCTCAACTTCCACACATCCATCAACATTATCAAAATTGAAATCTTTAGAAGACCCAA
GAGTGATGGATAGGTTCTTATGGTGCTGTGGTCTGCCTTCCGTATCAGCTTGAGGTATTTCTGGT
CTTTCAATGAACA
Found at i:16707 original size:2 final size:2
Alignment explanation
Indices: 16700--16755 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
16690 ATTCTTATGA
16700 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
16742 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
16756 GGTCGCTACC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25168 original size:23 final size:23
Alignment explanation
Indices: 25122--25169 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
25112 ATAACCATAC
*
25122 CCCAAACAAAACCCGACCTAGAG
1 CCCAAACAAAACCCGACCCAGAG
* * *
25145 CCCAAACCAAACCTGACCCGGAG
1 CCCAAACAAAACCCGACCCAGAG
25168 CC
1 CC
25170 TAACCTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.44, G:0.15, T:0.04
Consensus pattern (23 bp):
CCCAAACAAAACCCGACCCAGAG
Found at i:31084 original size:2 final size:2
Alignment explanation
Indices: 31077--31138 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
31067 AGGAAAAATG
31077 AT AT AT AT A- 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
31118 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
31139 GGAAGATGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31630 original size:23 final size:23
Alignment explanation
Indices: 31562--31630 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
31552 CAACCTTATA
*
31562 TGGAACTTCGATGCATTTCTACG
1 TGGAACTTCGGTGCATTTCTACG
* * * * *
31585 CGGCACTACGGTGTAATTCTACG
1 TGGAACTTCGGTGCATTTCTACG
*
31608 TGGAACTTCGGTGCATTTATACG
1 TGGAACTTCGGTGCATTTCTACG
31631 AGCTATGGTG
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGAACTTCGGTGCATTTCTACG
Found at i:35044 original size:19 final size:18
Alignment explanation
Indices: 35020--35071 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
35010 ATTGTTCAGT
35020 GTGCATCGATGCACAGGAA
1 GTGCATCGATGCACAGG-A
* *
35039 GTGCATTGATGCATAAGGA
1 GTGCATCGATGCA-CAGGA
35058 GTGCATCGATGCAC
1 GTGCATCGATGCAC
35072 CTCCTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 25 0.89
20 3 0.11
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (18 bp):
GTGCATCGATGCACAGGA
Found at i:36265 original size:2 final size:2
Alignment explanation
Indices: 36252--36285 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
36242 AGGTAAAATG
*
36252 AT AT AA 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
36286 GAAGATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36742 original size:23 final size:23
Alignment explanation
Indices: 36709--36776 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
36699 AACCTTATAT
36709 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
36732 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
36755 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
36777 AGATGTGGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:40776 original size:30 final size:30
Alignment explanation
Indices: 40659--40778 Score: 181
Period size: 30 Copynumber: 4.1 Consensus size: 30
40649 GTTCTTTGTG
* *
40659 AGTTGT-T-TGTCTCCCAAATGCTCCACCT
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
* * *
40687 AGTTGTATATGTCATCCGAATGCTCCACTA
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
40717 AGTTGTATATGTCTTCCAAATGCTCCACCA
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
40747 AGTTGTATATGTCTTCCAAATGCTCCACCA
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
40777 AG
1 AG
40779 ATGTCTAAAC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 6 0.07
29 1 0.01
30 75 0.91
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (30 bp):
AGTTGTATATGTCTTCCAAATGCTCCACCA
Found at i:40803 original size:60 final size:59
Alignment explanation
Indices: 40675--40790 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 59
40665 TTGTCTCCCA
* * * * * *
40675 AATGCTCCACCTAGTTGTATATGTCATCCGAATGCTCCACTAAGTTGTATATGTCTTCC
1 AATGCTCCACCAAGTTGTATATGTCATCCAAATGCTCCACCAAGTTCTAAACGTCTTCC
*
40734 AAATGCTCCACCAAGTTGTATATGTCTTCCAAATGCTCCACCAAGATGTCTAAACGT
1 -AATGCTCCACCAAGTTGTATATGTCATCCAAATGCTCCACCAAG-T-TCTAAACGT
40791 GTATCATGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 40 0.85
61 1 0.02
62 6 0.13
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (59 bp):
AATGCTCCACCAAGTTGTATATGTCATCCAAATGCTCCACCAAGTTCTAAACGTCTTCC
Found at i:47105 original size:21 final size:21
Alignment explanation
Indices: 47066--47105 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
47056 AAGGAAGATT
*
47066 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
47087 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
47106 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:47154 original size:22 final size:21
Alignment explanation
Indices: 47128--47168 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
47118 GCTGCAAAAT
*
47128 TGATGGTTTTGATGGATGAAGA
1 TGATGGTGTTGAT-GATGAAGA
47150 TGATGGTGTTGATGATGAA
1 TGATGGTGTTGATGATGAA
47169 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTGTTGATGATGAAGA
Found at i:56052 original size:264 final size:264
Alignment explanation
Indices: 55582--56115 Score: 942
Period size: 264 Copynumber: 2.0 Consensus size: 264
55572 TTCTTCTTTG
* * * *
55582 GCGTGTTTGAGATACAACAACAACACCATCTCTATTTCATCATTAACACCATCATCTTCATCCAT
1 GCGTGTTTGAGATACAACAACAAAACCATATCCATTTCATCATCAACACCATCATCTTCATCCAT
* * *
55647 CAAGACCATTCATTCCGCATCCATCTCTATCCTTTATTTATTTCATTTCATTCCTTATCTCTATC
66 CAAGACCATACATTCCGCAACCATCTCTATCCTTTATTTATTTCATTTAATTCCTTATCTCTATC
55712 ATTTCATTAATCTTCCTTTATTAATCATTTTCCTTTTATTATCTATGTTGCAGCCAAGCTTATAA
131 ATTTCATTAATCTTCCTTTATTAATCATTTTCCTTTTATTATCTATGTTGCAGCCAAGCTTATAA
* *
55777 ATCAAGGACATCAGTACTTGTTAATCCTAGATCGGGACACAATAAGTCTATCTACTCTCTTCTCC
196 ATCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATCTACTCTCTTCTCC
55842 CAAA
261 CAAA
55846 GCGTGTTTGAGATACAACAACAAAACCATATCCATTTCATCATCAACACCATCATCTTCATCCAT
1 GCGTGTTTGAGATACAACAACAAAACCATATCCATTTCATCATCAACACCATCATCTTCATCCAT
** *
55911 CAAGACCATAGTTTCCGCAACCATCTCTATCCTTTATTTATTTCATTTAATTCCTTATCTTTATC
66 CAAGACCATACATTCCGCAACCATCTCTATCCTTTATTTATTTCATTTAATTCCTTATCTCTATC
*
55976 ATTTCATTAATCTTCCTTTATTAATCATTTTCCTTTTCTTATCTATGTTGCAGCCAAGCTTATAA
131 ATTTCATTAATCTTCCTTTATTAATCATTTTCCTTTTATTATCTATGTTGCAGCCAAGCTTATAA
*
56041 TTCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATCTACTCTCTTCTCC
196 ATCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATCTACTCTCTTCTCC
56106 CAAA
261 CAAA
56110 GCGTGT
1 GCGTGT
56116 AGATCACCTT
Statistics
Matches: 256, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
264 256 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (264 bp):
GCGTGTTTGAGATACAACAACAAAACCATATCCATTTCATCATCAACACCATCATCTTCATCCAT
CAAGACCATACATTCCGCAACCATCTCTATCCTTTATTTATTTCATTTAATTCCTTATCTCTATC
ATTTCATTAATCTTCCTTTATTAATCATTTTCCTTTTATTATCTATGTTGCAGCCAAGCTTATAA
ATCAAGGACATCAGTACTTGTCAATCCTAGATCGGGACACAATAAGGCTATCTACTCTCTTCTCC
CAAA
Found at i:57570 original size:22 final size:21
Alignment explanation
Indices: 57533--57573 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
57523 CCATCTCCAT
57533 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
57554 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
57574 ATTCCACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:57656 original size:18 final size:17
Alignment explanation
Indices: 57635--57668 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
57625 TCTTTATCAT
*
57635 TTAATTAATCTTCCTTTA
1 TTAATCAAT-TTCCTTTA
57653 TTAATCAATTTCCTTT
1 TTAATCAATTTCCTTT
57669 TCTTATCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATCAATTTCCTTTA
Found at i:62042 original size:22 final size:21
Alignment explanation
Indices: 62005--62045 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
61995 CCATCTCCAT
62005 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
62026 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
62046 ATTTCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:66932 original size:17 final size:17
Alignment explanation
Indices: 66891--66940 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
66881 GCATCATTCC
66891 TTTTCTTCTTTTCTGAAT
1 TTTTCTTCTTTT-TGAAT
* *
66909 ATTTCTTCTTTTTGTAT
1 TTTTCTTCTTTTTGAAT
66926 TTTTCTTTCTTTTTG
1 TTTTC-TTCTTTTTG
66941 CACTCCGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTCTTCTTTTTGAAT
Found at i:68769 original size:22 final size:21
Alignment explanation
Indices: 68732--68772 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
68722 CCATCTCCAT
68732 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
68753 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
68773 ATTCCAGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Done.