Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009454.1 Hibiscus syriacus cultivar Beakdansim tig00113688_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: 170847
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
File 2 of 2
Found at i:135682 original size:17 final size:17
Alignment explanation
Indices: 135660--135726 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
135650 ACAGTTCTTT
135660 TCTTTCTATTATATTAG
1 TCTTTCTATTATATTAG
135677 TCTTTCTATTATATTAG
1 TCTTTCTATTATATTAG
*
135694 TCTTTTCTATTCTATT--
1 TC-TTTCTATTATATTAG
*
135710 T-TTTCTATTCTATTAG
1 TCTTTCTATTATATTAG
135726 T
1 T
135727 ATTAGATTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 13 0.28
16 2 0.04
17 19 0.41
18 12 0.26
ACGTcount: A:0.19, C:0.13, G:0.04, T:0.63
Consensus pattern (17 bp):
TCTTTCTATTATATTAG
Found at i:135715 original size:14 final size:14
Alignment explanation
Indices: 135696--135723 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
135686 TATATTAGTC
135696 TTTTCTATTCTATT
1 TTTTCTATTCTATT
135710 TTTTCTATTCTATT
1 TTTTCTATTCTATT
135724 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:143932 original size:32 final size:32
Alignment explanation
Indices: 143891--143952 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
143881 CATCTATTTT
143891 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
143923 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
143953 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:144724 original size:15 final size:14
Alignment explanation
Indices: 144699--144731 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
144689 TTTACTTTTA
144699 TATTTTATATATAG
1 TATTTTATATATAG
144713 TATTTATATATATAG
1 TATTT-TATATATAG
144728 TATT
1 TATT
144732 CCCGGCCAAA
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:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
TATTTTATATATAG
Found at i:145189 original size:17 final size:17
Alignment explanation
Indices: 145167--145201 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
145157 TGAATTCTTT
145167 AATTCGGAATGAATCAA
1 AATTCGGAATGAATCAA
145184 AATTCGGAATGAATCAA
1 AATTCGGAATGAATCAA
145201 A
1 A
145202 TCTCCTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (17 bp):
AATTCGGAATGAATCAA
Found at i:146218 original size:5 final size:5
Alignment explanation
Indices: 146202--146376 Score: 72
Period size: 5 Copynumber: 37.6 Consensus size: 5
146192 AATAATCTAA
* * * *
146202 TAAAT T-AA- TAAAT TAAAAT AAAAT T-AA- TAAAT TAAAA TAAAA TAAAG
1 TAAAT TAAAT TAAAT T-AAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
* * * * * *
146249 TAAAT TAAAA TAAAG TAAAT TAAAA TAAAA TAAAG TAAA- TAAAG T-AA-
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
* * * * * *
146296 TAAAT TAAA- AAAAT TAAAA TAAAA TAAAG TAAA- TAAAG TAAA- TAAAG
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
* * *
146343 T-AA- TAAAT TAAAA TAAAA TAAAG T-AA- TAAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAA
146377 TAACAAAATA
Statistics
Matches: 139, Mismatches: 16, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
3 5 0.04
4 35 0.25
5 95 0.68
6 4 0.03
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.27
Consensus pattern (5 bp):
TAAAT
Found at i:146246 original size:50 final size:45
Alignment explanation
Indices: 146199--146376 Score: 157
Period size: 50 Copynumber: 3.8 Consensus size: 45
146189 TCTAATAATC
146199 TAATAAATTAATAAATTAAAATAAAATTAATAAATTAAAATAAAATAAAG
1 TAATAAATT-A-AAA-TAAAAT-AAATTAATAAATTAAAAT-AAATAAAG
* * *
146249 ---TAAATTAAAATAAAGTAAATTAAAATAAAATAAAGTAAATAAAG
1 TAATAAATTAAAATAAAATAAATT--AATAAATTAAAATAAATAAAG
* *
146293 TAATAAATTAAAAAAATTAAAATAAAATAAAGTAAA-TAAAGTAAATAAAG
1 TAATAAATT---AAAA-TAAAAT-AAATTAA-TAAATTAAAATAAATAAAG
*
146343 TAATAAATTAAAATAAAATAAAGTAATAAATTAA
1 TAATAAATTAAAATAAAATAAATTAATAAATTAA
146377 TAACAAAATA
Statistics
Matches: 109, Mismatches: 7, Indels: 29
0.75 0.05 0.20
Matches are distributed among these distances:
43 5 0.05
44 17 0.16
45 22 0.20
46 7 0.06
47 16 0.15
50 29 0.27
51 9 0.08
52 4 0.04
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (45 bp):
TAATAAATTAAAATAAAATAAATTAATAAATTAAAATAAATAAAG
Found at i:146268 original size:9 final size:9
Alignment explanation
Indices: 146217--146364 Score: 99
Period size: 9 Copynumber: 16.3 Consensus size: 9
146207 TAATAAATTA
*
146217 AAATAAAAT
1 AAATAAAGT
* *
146226 TAATAAATT
1 AAATAAAGT
*
146235 AAAATAAAAT
1 -AAATAAAGT
*
146245 AAAGTAAATT
1 AAA-TAAAGT
146255 AAAATAAAGT
1 -AAATAAAGT
*
146265 AAATTAAAAT
1 AAA-TAAAGT
146275 AAAATAAAGT
1 -AAATAAAGT
146285 AAATAAAGT
1 AAATAAAGT
*
146294 -AATAAATT
1 AAATAAAGT
* *
146302 AAAAAAATT
1 AAATAAAGT
*
146311 AAA-ATA--
1 AAATAAAGT
146317 AAATAAAGT
1 AAATAAAGT
146326 AAATAAAGT
1 AAATAAAGT
146335 AAATAAAGT
1 AAATAAAGT
*
146344 -AATAAATT
1 AAATAAAGT
*
146352 AAAATAAAAT
1 -AAATAAAGT
146362 AAA
1 AAA
146365 GTAATAAATT
Statistics
Matches: 114, Mismatches: 14, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
6 3 0.03
7 2 0.02
8 16 0.14
9 53 0.46
10 34 0.30
11 6 0.05
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (9 bp):
AAATAAAGT
Found at i:146316 original size:41 final size:41
Alignment explanation
Indices: 146200--146379 Score: 179
Period size: 41 Copynumber: 4.3 Consensus size: 41
146190 CTAATAATCT
* *
146200 AATAAATTAATAAATTAAAATAAAATT--AATAAATTAAAATAA
1 AATAAAGTAATAAATT-AAA-AAAATTAAAATAAAATAAAAT-A
* * *
146242 AATAAAGTAAATTAAAATAAAGTAAATTAAAATAAAATAAAGTA
1 AATAAAGT-AA-TAAATTAAA-AAAATTAAAATAAAATAAAATA
*
146286 AATAAAGTAATAAATTAAAAAAATTAAAATAAAATAAAGTA
1 AATAAAGTAATAAATTAAAAAAATTAAAATAAAATAAAATA
* * *
146327 AATAAAGTAAATAAAGT-AATAAATTAAAATAAAATAAAGT-
1 AATAAAGT-AATAAATTAAAAAAATTAAAATAAAATAAAATA
*
146367 AATAAATTAATAA
1 AATAAAGTAATAA
146380 CAAAATAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
39 5 0.04
40 7 0.06
41 51 0.42
42 22 0.18
43 12 0.10
44 14 0.11
45 11 0.09
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (41 bp):
AATAAAGTAATAAATTAAAAAAATTAAAATAAAATAAAATA
Found at i:146405 original size:13 final size:12
Alignment explanation
Indices: 146200--146403 Score: 83
Period size: 13 Copynumber: 16.7 Consensus size: 12
146190 CTAATAATCT
146200 AATAAATTAAT-A
1 AATAAA-TAATAA
*
146212 AATTAA-AATAA
1 AATAAATAATAA
*
146223 AATTAATAAATTAA
1 AATAAAT-AA-TAA
146237 AAT-AA-AATAA
1 AATAAATAATAA
*
146247 AGTAAAT--TAA
1 AATAAATAATAA
146257 AATAAAGTAAATTAA
1 AATAAA-T-AA-TAA
146272 AATAAAATAA-AGTA
1 AAT-AAATAATA--A
146286 AATAAAGTAATAA
1 AATAAA-TAATAA
* *
146299 ATTAAAAAAATTAA
1 AAT-AAATAA-TAA
146313 AAT-AA-AATAA
1 AATAAATAATAA
*
146323 AGTAAATAA-AGTA
1 AATAAATAATA--A
146336 AATAAAGTAAT-A
1 AATAAA-TAATAA
*
146348 AATTAA-AATAA
1 AATAAATAATAA
146359 AATAAAGTAAT-A
1 AATAAA-TAATAA
* *
146371 AATTAATAACAA
1 AATAAATAATAA
146383 AATAAATACATAA
1 AATAAATA-ATAA
146396 AATAAATA
1 AATAAATA
146404 CAATAATAGA
Statistics
Matches: 149, Mismatches: 14, Indels: 57
0.68 0.06 0.26
Matches are distributed among these distances:
10 24 0.16
11 26 0.17
12 30 0.20
13 32 0.21
14 26 0.17
15 8 0.05
16 3 0.02
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:146408 original size:9 final size:8
Alignment explanation
Indices: 146200--146409 Score: 86
Period size: 9 Copynumber: 23.1 Consensus size: 8
146190 CTAATAATCT
*
146200 AATAAATT
1 AATAAATA
146208 AATAAATTAA
1 AATAAA-T-A
*
146218 AATAAAATT
1 AAT-AAATA
146227 AATAAATTAA
1 AATAAA-T-A
146237 AATAAAATA
1 AAT-AAATA
146246 AAGTAAATTAA
1 AA-TAAA-T-A
146257 AATAAAGTA
1 AATAAA-TA
146266 AATTAAAATAA
1 AA-T-AAAT-A
146277 AATAAAGTA
1 AATAAA-TA
146286 AATAAAGT-
1 AATAAA-TA
146294 AATAAATTA
1 AATAAA-TA
*
146303 AAAAAATTAA
1 AATAAA-T-A
146313 AATAAAATA
1 AAT-AAATA
146322 AAGTAAATA
1 AA-TAAATA
146331 AAGTAAATA
1 AA-TAAATA
146340 AAGT-AATA
1 AA-TAAATA
146348 AATTAAAATAA
1 AA-T-AAAT-A
146359 AATAAAGT-
1 AATAAA-TA
*
146367 AATAAATT
1 AATAAATA
146375 AATAACA-A
1 AATAA-ATA
146383 AATAAATA
1 AATAAATA
*
146391 CATAAAATA
1 AAT-AAATA
146400 AATACAATA
1 AATA-AATA
146409 A
1 A
146410 TAGATAAAAC
Statistics
Matches: 165, Mismatches: 11, Indels: 51
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.01
8 43 0.26
9 70 0.42
10 29 0.18
11 21 0.13
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (8 bp):
AATAAATA
Found at i:148001 original size:21 final size:20
Alignment explanation
Indices: 147960--148001 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
147950 CCCGTTATCC
*
147960 AATAAAAACCTAAAATTCCT
1 AATAAAAACCTAAAATGCCT
147980 AATAATAAACC-AAAATCGCCT
1 AATAA-AAACCTAAAAT-GCCT
148001 A
1 A
148002 TCCGATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (20 bp):
AATAAAAACCTAAAATGCCT
Found at i:148752 original size:21 final size:21
Alignment explanation
Indices: 148728--148770 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
148718 TTCTATTTAC
148728 ATTTATATTTCCATATAATTA
1 ATTTATATTTCCATATAATTA
148749 ATTTATATTTCCATATAATTA
1 ATTTATATTTCCATATAATTA
148770 A
1 A
148771 AGGAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTATATTTCCATATAATTA
Found at i:149220 original size:21 final size:21
Alignment explanation
Indices: 149196--149238 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
149186 AAGGTACCAA
149196 TAAATTAAATACAAATTCTTC
1 TAAATTAAATACAAATTCTTC
149217 TAAATTAAATACAAATTCTTC
1 TAAATTAAATACAAATTCTTC
149238 T
1 T
149239 TTTTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTAAATACAAATTCTTC
Found at i:149381 original size:11 final size:11
Alignment explanation
Indices: 149365--149404 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
149355 TTTTTTTATG
149365 AAATTTGTATA
1 AAATTTGTATA
149376 AAATTTGTAT-
1 AAATTTGTATA
149386 --A-TTGTATA
1 AAATTTGTATA
149394 AAATTTGTATA
1 AAATTTGTATA
149405 GTAGTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 6 0.24
8 1 0.04
10 1 0.04
11 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (11 bp):
AAATTTGTATA
Found at i:149392 original size:18 final size:18
Alignment explanation
Indices: 149369--149404 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
149359 TTTATGAAAT
149369 TTGTATAAAATTTGTATA
1 TTGTATAAAATTTGTATA
149387 TTGTATAAAATTTGTATA
1 TTGTATAAAATTTGTATA
149405 GTAGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
TTGTATAAAATTTGTATA
Found at i:149856 original size:3 final size:3
Alignment explanation
Indices: 149843--149896 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
149833 TAGTGTTAAA
**
149843 ATT ATT AATT ATT ATT AAA ATT ATT AATT ATT ATT A-T ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
149889 ATT ATT AT
1 ATT ATT AT
149897 AATAAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:149862 original size:19 final size:19
Alignment explanation
Indices: 149838--149895 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 19
149828 TATGTTAGTG
149838 TTAAAATTATTAATTATTA
1 TTAAAATTATTAATTATTA
149857 TTAAAATTATTAATTATTA
1 TTAAAATTATTAATTATTA
*
149876 TT-ATATTATT-ATTATTA
1 TTAAAATTATTAATTATTA
149893 TTA
1 TTA
149896 TAATAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
17 9 0.24
18 7 0.19
19 21 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAAAATTATTAATTATTA
Found at i:149886 original size:30 final size:32
Alignment explanation
Indices: 149844--149924 Score: 68
Period size: 30 Copynumber: 2.7 Consensus size: 32
149834 AGTGTTAAAA
* *
149844 TTATTAATTATTATTA-A-AATTATTAAT-TA
1 TTATTAATTATTATTATATTATTAATAATATA
149873 TTATTATATTATTATTATTATTA-TAATAA-ATA
1 TTATTA-ATTATTATTA-TATTATTAATAATATA
*
149905 TTAATAATT-TTATTAT-TTAT
1 TTATTAATTATTATTATATTAT
149925 ACTATAGGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
28 3 0.07
29 7 0.16
30 16 0.37
31 3 0.07
32 13 0.30
33 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TTATTAATTATTATTATATTATTAATAATATA
Found at i:150159 original size:76 final size:76
Alignment explanation
Indices: 150033--150186 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
150023 CTGAATTACT
150033 ATAATATCCTTTCCTTGTTTTCAACCCACTTGAGAAAAACCCTTTCTAATTTAGTGGATATAGAA
1 ATAATATCCTTTCCTTGTTTTCAACCCACTTGAGAAAAACCCTTTCTAATTTAGTGGATATAGAA
150098 ATAATGTATCA
66 ATAATGTATCA
150109 ATAATATCCTTTCCTTGTTTTCAACCCACTTGAGAAAAACCCTTTCTAATTTAGTGGATATAGAA
1 ATAATATCCTTTCCTTGTTTTCAACCCACTTGAGAAAAACCCTTTCTAATTTAGTGGATATAGAA
150174 ATAATGTATCA
66 ATAATGTATCA
150185 AT
1 AT
150187 TTTAAGTGAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (76 bp):
ATAATATCCTTTCCTTGTTTTCAACCCACTTGAGAAAAACCCTTTCTAATTTAGTGGATATAGAA
ATAATGTATCA
Found at i:150745 original size:13 final size:13
Alignment explanation
Indices: 150727--150755 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
150717 AAGATTCCTT
150727 TTGAACCTTCAAA
1 TTGAACCTTCAAA
150740 TTGAACCTTCAAA
1 TTGAACCTTCAAA
150753 TTG
1 TTG
150756 CTATTTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (13 bp):
TTGAACCTTCAAA
Found at i:152240 original size:17 final size:17
Alignment explanation
Indices: 152218--152251 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
152208 TTTTACCTTT
152218 TTTTTTTACTTAACTTA
1 TTTTTTTACTTAACTTA
152235 TTTTTTTACTTAACTTA
1 TTTTTTTACTTAACTTA
152252 AACTTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTTACTTAACTTA
Found at i:152385 original size:21 final size:21
Alignment explanation
Indices: 152359--152400 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
152349 TTTGTTTTAT
152359 TCATGAAAACTATCTATAAAA
1 TCATGAAAACTATCTATAAAA
152380 TCATGAAAACTATCTATAAAA
1 TCATGAAAACTATCTATAAAA
152401 ATAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (21 bp):
TCATGAAAACTATCTATAAAA
Found at i:154540 original size:20 final size:20
Alignment explanation
Indices: 154515--154601 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 20
154505 TAGAATTAAA
154515 TATTATTAATATATAAATAT
1 TATTATTAATATATAAATAT
* *
154535 TATTATAAATATTATTAATATAAA
1 TATTATTAATA-TA-TAA-AT-AT
154559 TATTATTAATATAATATAA-A-
1 TATTATTAATAT-ATA-AATAT
154579 TATTATT-A-ATATAAATAT
1 TATTATTAATATATAAATAT
154597 TATTA
1 TATTA
154602 ATATAATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
16 2 0.04
17 4 0.07
18 7 0.12
19 1 0.02
20 17 0.30
21 3 0.05
22 3 0.05
23 6 0.11
24 13 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTATTAATATATAAATAT
Found at i:154549 original size:29 final size:31
Alignment explanation
Indices: 154513--154612 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 31
154503 CTTAGAATTA
154513 AATATTATTAATATATAAATATTATT-ATA-
1 AATATTATTAATATATAAATATTATTAATAT
154542 AATATTATT-A-ATATAAATATTATTAATAT
1 AATATTATTAATATATAAATATTATTAATAT
*
154571 AATATAAATATTATTAATATAAATATTATTAATAT
1 AATAT---TATTAAT-ATATAAATATTATTAATAT
154606 AATATTA
1 AATATTA
154613 CTTATTCAAC
Statistics
Matches: 62, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
27 14 0.23
28 4 0.06
29 14 0.23
32 6 0.10
35 24 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
AATATTATTAATATATAAATATTATTAATAT
Found at i:154556 original size:15 final size:15
Alignment explanation
Indices: 154511--154612 Score: 120
Period size: 15 Copynumber: 6.6 Consensus size: 15
154501 ATCTTAGAAT
154511 TAAATATTATTAATA
1 TAAATATTATTAATA
*
154526 TATAA-A-TATTATTA
1 TA-AATATTATTAATA
154540 TAAATATTATTAATA
1 TAAATATTATTAATA
154555 TAAATATTATTAATATAATA
1 T-AA-A-TATT-AT-TAATA
154575 TAAATATTATTAATA
1 TAAATATTATTAATA
154590 TAAATATTATTAATA
1 TAAATATTATTAATA
154605 T-AATATTA
1 TAAATATTA
154613 CTTATTCAAC
Statistics
Matches: 77, Mismatches: 2, Indels: 17
0.80 0.02 0.18
Matches are distributed among these distances:
13 2 0.03
14 17 0.22
15 32 0.42
16 6 0.08
17 5 0.06
18 5 0.06
19 4 0.05
20 6 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATATTATTAATA
Found at i:154561 original size:35 final size:36
Alignment explanation
Indices: 154522--154610 Score: 139
Period size: 35 Copynumber: 2.6 Consensus size: 36
154512 AAATATTATT
* *
154522 AATA-TATAAATATTATTATAAATATTATTAATATA
1 AATATTATTAATATTAATATAAATATTATTAATATA
154557 AATATTATTAATA-TAATATAAATATTATTAATATA
1 AATATTATTAATATTAATATAAATATTATTAATATA
154592 AATATTATTAATA-TAATAT
1 AATATTATTAATATTAATAT
154611 TACTTATTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
35 44 0.86
36 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
AATATTATTAATATTAATATAAATATTATTAATATA
Found at i:154605 original size:44 final size:44
Alignment explanation
Indices: 154511--154605 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
154501 ATCTTAGAAT
* *
154511 TAAATATTATTAATATATAAATATTATTATAAATATTATTAATA
1 TAAATATTATTAATATATAAATATTATTATAAATATAAATAATA
* *
154555 TAAATATTATTAATATAATATAA-A-TATTATTAATATAAATATTA
1 TAAATATTATTAATAT-ATA-AATATTATTATAAATATAAATAATA
*
154599 TTAATAT
1 TAAATAT
154606 AATATTACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
44 38 0.86
45 4 0.09
46 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (44 bp):
TAAATATTATTAATATATAAATATTATTATAAATATAAATAATA
Found at i:155917 original size:17 final size:17
Alignment explanation
Indices: 155895--155929 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
155885 TTTCGAAATA
155895 ATTACGAATATAGTAAT
1 ATTACGAATATAGTAAT
155912 ATTACGAATATAGTAAT
1 ATTACGAATATAGTAAT
155929 A
1 A
155930 GATTTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (17 bp):
ATTACGAATATAGTAAT
Found at i:156125 original size:22 final size:23
Alignment explanation
Indices: 156097--156154 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 23
156087 GAAATTTATC
156097 TTTACTT-TAATAGAATAGGAGG
1 TTTACTTATAATAGAATAGGAGG
156119 TTTACTTACTCAGTAATAGAATAGGAGG
1 TTTAC-T--T-A-TAATAGAATAGGAGG
156147 TTTACTTA
1 TTTACTTA
156155 CTCAGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 5 0.17
23 1 0.03
24 1 0.03
25 2 0.07
27 1 0.03
28 20 0.67
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (23 bp):
TTTACTTATAATAGAATAGGAGG
Found at i:156157 original size:28 final size:28
Alignment explanation
Indices: 156104--156160 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
156094 ATCTTTACTT
156104 TAATAGAATAGGAGGTTTACTTACTCAG
1 TAATAGAATAGGAGGTTTACTTACTCAG
156132 TAATAGAATAGGAGGTTTACTTACTCAG
1 TAATAGAATAGGAGGTTTACTTACTCAG
156160 T
1 T
156161 TTTTCTTTGA
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:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (28 bp):
TAATAGAATAGGAGGTTTACTTACTCAG
Found at i:160237 original size:18 final size:18
Alignment explanation
Indices: 160214--160251 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
160204 ATGAAAATCT
160214 AATAAATCGACTAATTCA
1 AATAAATCGACTAATTCA
160232 AATAAATCGACTAATTCA
1 AATAAATCGACTAATTCA
160250 AA
1 AA
160252 ATTTGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (18 bp):
AATAAATCGACTAATTCA
Found at i:160819 original size:13 final size:13
Alignment explanation
Indices: 160801--160826 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160791 AATTTCTAAT
160801 TAATATATATTTG
1 TAATATATATTTG
160814 TAATATATATTTG
1 TAATATATATTTG
160827 ATATGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TAATATATATTTG
Found at i:161917 original size:18 final size:18
Alignment explanation
Indices: 161894--161930 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
161884 CCAATCATTT
161894 TTTTTTCGTTCGGTGCTA
1 TTTTTTCGTTCGGTGCTA
161912 TTTTTTCGTTCGGTGCTA
1 TTTTTTCGTTCGGTGCTA
161930 T
1 T
161931 AAGGGGGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (18 bp):
TTTTTTCGTTCGGTGCTA
Found at i:167016 original size:17 final size:17
Alignment explanation
Indices: 166994--167028 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
166984 CTTGAGGAGA
166994 TTTGATTCATTCCGAAT
1 TTTGATTCATTCCGAAT
167011 TTTGATTCATTCCGAAT
1 TTTGATTCATTCCGAAT
167028 T
1 T
167029 AAAGAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTGATTCATTCCGAAT
Found at i:168275 original size:30 final size:30
Alignment explanation
Indices: 168236--168293 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
168226 CTTTTGGTTT
168236 TTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTCATGTTGTCAAAGAGTTGAACAATGGA
*
168266 TTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTCATGTTGTCAAAGAGTTGAACAATG
168294 AAAATAGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (30 bp):
TTTCATGTTGTCAAAGAGTTGAACAATGGA
Done.