Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005032.1 Hibiscus syriacus cultivar Beakdansim tig00011291_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: 65707
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:490 original size:115 final size:117
Alignment explanation
Indices: 200--543 Score: 346
Period size: 118 Copynumber: 2.9 Consensus size: 117
190 TTTGGGTCAA
* * * * * *
200 TCTT-TGGGTACGATATCCTTCATTGTG-AGATGAAATCATGAATGGCTTCTTCGTCGTGATGTT
1 TCTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCATGGATGAC--CTTCGTTGTGAAGTT
* * * *
263 GAGCTTTAAATTGGATATCATTTGTCGTGAAGTTGAAATCCTAGG-GTGCATTGCT
64 GAGCTTTGAATTGGA-ATC-CTTGTCGTGAAGTTGAAATCCAAGGTTTGCATTGCT
* * * * * *
318 GC-TGTGGGCATGATATCATTCATCT-TGAAGTTG-AATCGTGGATGGCTCCTTCTTTGTGAAGT
1 TCTTGTGGGCACGATATCCTTCAT-TGTGAAGTTGAAATCATGGAT-G-ACCTTCGTTGTGAAGT
*
380 TGAGC-TTGAATTGG-ATCCTTCATCGTGAAG-TGAAATCCAAGGTTTGCATTGCT
63 TGAGCTTTGAATTGGAATCCTT-GTCGTGAAGTTGAAATCCAAGGTTTGCATTGCT
** *
433 TCTTGTGGGCACGATATCCTTTGTTGTGAAGTTGAAATCATGGATGACCTTCGTTGTGAAGTTTA
1 TCTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCATGGATGACCTTCGTTGTGAAGTTGA
*
498 GCTTTGAATTGGATATCCTTGTCGTGAAGTTGAAATCTAAGAGTTT
66 GCTTTGAATTGGA-ATCCTTGTCGTGAAGTTGAAATCCAAG-GTTT
544 TTCATGAAAT
Statistics
Matches: 184, Mismatches: 27, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
114 13 0.07
115 40 0.22
116 35 0.19
117 26 0.14
118 59 0.32
119 10 0.05
120 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (117 bp):
TCTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCATGGATGACCTTCGTTGTGAAGTTGA
GCTTTGAATTGGAATCCTTGTCGTGAAGTTGAAATCCAAGGTTTGCATTGCT
Found at i:605 original size:58 final size:58
Alignment explanation
Indices: 498--651 Score: 161
Period size: 58 Copynumber: 2.7 Consensus size: 58
488 GTGAAGTTTA
* * ** *
498 GCTTTGAATTGGATATCCTT-GTCGTGAAGTTGAAATCTAAGAGTTTTTCATGAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATC-AAGAGTTTTTCACCAAATGG
* * *
556 GTTTTGAGTTGGAAATCCTTCGTTGTGAAGTTAAAAT-ACA-AGTTGTTTCACCAAATGG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCA-AGAGTT-TTTCACCAAATGG
* * *
614 GCTTTAAGTTAGATATCCTTCATTGTGAAGTTGAAATC
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATC
652 CAATCTTGTG
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
57 5 0.06
58 59 0.76
59 14 0.18
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (58 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCAAGAGTTTTTCACCAAATGG
Found at i:6801 original size:14 final size:14
Alignment explanation
Indices: 6782--6812 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6772 AAGCATTGAC
6782 TTAAAATAAATAAA
1 TTAAAATAAATAAA
*
6796 TTAAAATAAATCAA
1 TTAAAATAAATAAA
6810 TTA
1 TTA
6813 TTTTAAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TTAAAATAAATAAA
Found at i:13169 original size:42 final size:42
Alignment explanation
Indices: 13113--13262 Score: 158
Period size: 42 Copynumber: 3.5 Consensus size: 42
13103 AAAAACACAA
* * **
13113 CTAAATATCATAACCTTTAGCGACGTTTGGAAAACAATGTCG
1 CTAAATATCATAACCTTTAGCGGCGTTTGAAAAACAACATCG
* *
13155 CTAAATATCATAACCTTTAGCGGCATTTGTAAAAAAAACATCG
1 CTAAATATCATAACCTTTAGCGGCGTTTG-AAAAACAACATCG
* * * *
13198 CTAAATAGT-ATTACCTTTAGCGGCGTTTGTAAAACAACACCA
1 CTAAATA-TCATAACCTTTAGCGGCGTTTGAAAAACAACATCG
* * *
13240 CCAAAAAACATAACCTTTAGCGG
1 CTAAATATCATAACCTTTAGCGG
13263 TATTTGTGGT
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
42 54 0.61
43 34 0.38
44 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.27
Consensus pattern (42 bp):
CTAAATATCATAACCTTTAGCGGCGTTTGAAAAACAACATCG
Found at i:21524 original size:199 final size:199
Alignment explanation
Indices: 21217--21997 Score: 528
Period size: 199 Copynumber: 3.8 Consensus size: 199
21207 GAACACAAAA
** * * *
21217 AAAGTATCGATACACGTATAACAAGTATCGGTACTTATAATTTCGAAACCTATTATTTTAAATGA
1 AAAGTATCGATACACGTATAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAAATGA
* * * * * *
21282 ATTGCTAATTTTACAATGAAAACGGTAAAAATCTACCGGTTTAATGATAATGGGCTTAAATATAA
66 ATAGCTAAATTTACAATGAAAACAGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATAA
* *
21347 AGTATTGATAC-TCTTTGTATGGGTATCGATACTTTTAGTCCAGTATGCTTCTCATCAATTTGCC
131 AGTATCGATACAT-TTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCATCAATTTGCC
21411 CGCAC
195 CGCAC
* *
21416 AAAGTATCGATACATGTATAACCAGTATCAATACTTATAATTTCAAAACCGATTACTTT-AATGT
1 AAAGTATCGATACACGTATAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAAATG-
* * * ** * * * *
21480 TATAGGTAAATTTATAATGTCAATAGTAAAAGTCTACTGGTTTAATGATATTAGGCGTAAACATA
65 AATAGCTAAATTTACAATGAAAACAGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATA
* * ** *
21545 GAGTATCGATACATTTTGTATAGGTATCGATACTTTTTGTATAGGTATCGATACTT-TTAGTCCA
130 AAGTATCGATACATTTTGTATAGGTATCGATACTTTTAGTCCA-GTAT-G---CTTCTCA-T-CA
* * **
21609 GTATGCTTCTCAAAC
188 ATTTGC--C-CGCAC
* * * * * * *** *
21624 AACATGCATGCAGAAAGAATCG-AT-ACACGTGCCA-CAAGTATCAATACTTATAATTTCGAAAC
1 AA-A-GTAT-C-GATA-CA-CGTATAACAAGT---ATCAA-TA-C-TTA--TA-ATTTCAAAACC
* * * * *
21686 GATTACTTTATA-GTAATAGGTAATTTTACAATGAAAA-TGATAAAAATTTACCGGTTTAATGAT
51 GATTACTTTAAATG-AATAGCTAAATTTACAATGAAAACAG-TAAAAATCTACCGGTTTAATGAT
* * *
21749 AATAGGCGTAAACATAAAGTA-CCA-ACACTCTTTCTATAGGTATCGATACTTTTAGTCCAATAT
114 AATAGGCGTAAACATAAAGTATCGATACA-T-TTTGTATAGGTATCGATACTTTTAGTCCAGTAT
* ** * ** *
21812 GCTTCTCAAACAACATACAAGCAG
177 GCTTCTC-ATCAATTTGCCCGCAC
* * * *
21836 AAAGTATTGATACACGTATCAC-A--ATCGATACTTATAATTTGAAAACCGATTACTTTAAA-GT
1 AAAGTATCGATACACGTATAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAAATG-
* * * * *
21897 AATAGGTAAATTTACAATGTAAACGGTAAAAATATAGCGGTTTAATGATAATAGGCGTAAACATA
65 AATAGCTAAATTTACAATGAAAACAGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATA
** * *
21962 AAGTATCGATATTTTTTATATAGGTATCAATACTTT
130 AAGTATCGATACATTTTGTATAGGTATCGATACTTT
21998 CAATCTAAAC
Statistics
Matches: 447, Mismatches: 96, Indels: 80
0.72 0.15 0.13
Matches are distributed among these distances:
197 102 0.23
198 10 0.02
199 138 0.31
200 7 0.02
201 2 0.00
202 3 0.01
203 4 0.01
204 4 0.01
205 6 0.01
206 2 0.00
207 4 0.01
208 10 0.02
209 1 0.00
210 6 0.01
211 2 0.00
212 10 0.02
213 3 0.01
214 4 0.01
215 11 0.02
216 2 0.00
217 3 0.01
218 4 0.01
219 9 0.02
220 99 0.22
221 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (199 bp):
AAAGTATCGATACACGTATAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAAATGA
ATAGCTAAATTTACAATGAAAACAGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATAA
AGTATCGATACATTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCATCAATTTGCCC
GCAC
Found at i:21612 original size:20 final size:20
Alignment explanation
Indices: 21542--21602 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 20
21532 AGGCGTAAAC
21542 ATAGAGTATCGATACATTTTGT
1 ATAG-GTATCGATAC-TTTTGT
21564 ATAGGTATCGATACTTTTTGT
1 ATAGGTATCGATAC-TTTTGT
21585 ATAGGTATCGATACTTTT
1 ATAGGTATCGATACTTTT
21603 AGTCCAGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 4 0.11
21 30 0.79
22 4 0.11
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (20 bp):
ATAGGTATCGATACTTTTGT
Found at i:21744 original size:220 final size:220
Alignment explanation
Indices: 21348--21966 Score: 585
Period size: 220 Copynumber: 2.9 Consensus size: 220
21338 TAAATATAAA
* * * * ** *
21348 GTATTGATACTCTTTGTATGGGTATCGATACTTTTAGTCCAGTATGCTTCTCATCAATTTGCCCG
1 GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAACAACATGCACG
* * * *
21413 CACAAAGTATCGATACATGTATAACCAGTATCAATACTTATAATTTCAAAACCGATTACTTTAAT
66 CACAAAGAATCGATACACGTACAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAAT
* * ** * * *
21478 GTTATAGGTAAATTTATAATGTCAATAGTAAAAGTCTACTGGTTTAATGATATTAGGCGTAAACA
131 GTAATAGGTAAATTTACAATGAAAATAGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACA
* * *
21543 TAGAGTATCGATACA-T-TTTGTATAG
196 TAAAGTA-CCA-ACACTCTTTCTATAG
*
21568 GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACATGCAT
1 GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTC-AACAACATGCAC
* * * *
21633 GCAGAAAGAATCGATACACGTGCCACAAGTATCAATACTTATAATTTCGAAA-CGATTACTTT-A
65 GCACAAAGAATCGATACACGTACAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAA
* *
21696 TAGTAATAGGTAATTTTACAATGAAAAT-GATAAAAATTTACCGGTTTAATGATAATAGGCGTAA
130 T-GTAATAGGTAAATTTACAATGAAAATAG-TAAAAATCTACCGGTTTAATGATAATAGGCGTAA
21760 ACATAAAGTACCAACACTCTTTCTATAG
193 ACATAAAGTACCAACACTCTTTCTATAG
* * * * *
21788 GTATCGATAC---TT-T-TA-G--TCCA-A----TA-TGC--T-T-C-TC-AAACAACATACAAG
1 GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAACAACATGCACG
* * * * *
21833 CAGAAAGTATTGATACACGTATC-AC-A--ATCGATACTTATAATTTGAAAACCGATTACTTTAA
66 CACAAAGAATCGATACACGTA-CAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAA
* * ** * *
21894 AGTAATAGGTAAATTTACAATGTAAACGGTAAAAATATAGCGGTTTAATGATAATAGGCGTAAAC
130 TGTAATAGGTAAATTTACAATGAAAATAGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAAC
21959 ATAAAGTA
195 ATAAAGTA
21967 TCGATATTTT
Statistics
Matches: 345, Mismatches: 45, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
196 19 0.06
197 75 0.22
198 3 0.01
199 31 0.09
200 1 0.00
201 2 0.01
202 1 0.00
203 1 0.00
204 1 0.00
206 2 0.01
207 2 0.01
211 1 0.00
212 3 0.01
214 1 0.00
215 2 0.01
216 1 0.00
217 2 0.01
218 3 0.01
219 6 0.02
220 137 0.40
221 51 0.15
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (220 bp):
GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAACAACATGCACG
CACAAAGAATCGATACACGTACAACAAGTATCAATACTTATAATTTCAAAACCGATTACTTTAAT
GTAATAGGTAAATTTACAATGAAAATAGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAACA
TAAAGTACCAACACTCTTTCTATAG
Found at i:21986 original size:197 final size:198
Alignment explanation
Indices: 21568--21997 Score: 605
Period size: 197 Copynumber: 2.2 Consensus size: 198
21558 TTTTGTATAG
* * * *
21568 GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACATGCAT
1 GTATCGATACTTTTTATATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAAACAACATACAA
* *
21633 GCAGAAAGAATCGATACACGTGCCACAAGTATCAATACTTATAATTTCGAAACGATTACTTTATA
66 GCAGAAAGAATCGATACACGTACCACAAG-ATCAATACTTATAATTTCGAAACGATTACTTTAAA
* * *
21698 GTAATAGGTAATTTTACAATGAAAATGATAAAAATTTACCGGTTTAATGATAATAGGCGTAAACA
130 GTAATAGGTAAATTTACAATGAAAACGATAAAAATATACCGGTTTAATGATAATAGGCGTAAACA
21763 TAAA
195 TAAA
* * * * *
21767 GTACCAACACTCTTTCTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAAACAACATACAA
1 GTATCGATACTTTTTATATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAAACAACATACAA
* * * *
21832 GCAGAAAGTATTGATACACGTATCAC-A-ATCGATACTTATAATTT-GAAAACCGATTACTTTAA
66 GCAGAAAGAATCGATACACGTACCACAAGATCAATACTTATAATTTCG-AAA-CGATTACTTTAA
* * *
21894 AGTAATAGGTAAATTTACAATGTAAACGGTAAAAATATAGCGGTTTAATGATAATAGGCGTAAAC
129 AGTAATAGGTAAATTTACAATGAAAACGATAAAAATATACCGGTTTAATGATAATAGGCGTAAAC
21959 ATAAA
194 ATAAA
* *
21964 GTATCGATATTTTTTATATAGGTATCAATACTTT
1 GTATCGATACTTTTTATATAGGTATCGATACTTT
21998 CAATCTAAAC
Statistics
Matches: 202, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
195 1 0.00
196 19 0.09
197 102 0.50
198 1 0.00
199 79 0.39
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (198 bp):
GTATCGATACTTTTTATATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAAACAACATACAA
GCAGAAAGAATCGATACACGTACCACAAGATCAATACTTATAATTTCGAAACGATTACTTTAAAG
TAATAGGTAAATTTACAATGAAAACGATAAAAATATACCGGTTTAATGATAATAGGCGTAAACAT
AAA
Found at i:22878 original size:2 final size:2
Alignment explanation
Indices: 22871--22918 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
22861 ATAGTGAATG
22871 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
22913 AT AT AT
1 AT AT AT
22919 CTAGAATCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24766 original size:15 final size:15
Alignment explanation
Indices: 24736--24782 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
24726 TATGAAATAA
24736 GAAATGGAAGAAGAAAT
1 GAAATGG-A-AAGAAAT
*
24753 GAAAT-GATAAGAAAG
1 GAAATGGA-AAGAAAT
24768 GAAATGGAAAGAAAT
1 GAAATGGAAAGAAAT
24783 TATATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 18 0.69
16 3 0.12
17 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.13
Consensus pattern (15 bp):
GAAATGGAAAGAAAT
Found at i:29962 original size:3 final size:3
Alignment explanation
Indices: 29954--30033 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
29944 TTATGTATGT
29954 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30002 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30034 TGGTCTTTGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34990 original size:16 final size:17
Alignment explanation
Indices: 34954--34991 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
34944 AGAATATAGG
*
34954 TTTGAGAGTTTTGAGAA
1 TTTGAGAGTTATGAGAA
*
34971 TTTGAGAG-TATGAGAT
1 TTTGAGAGTTATGAGAA
34987 TTTGA
1 TTTGA
34992 AAGCTTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (17 bp):
TTTGAGAGTTATGAGAA
Found at i:35396 original size:138 final size:137
Alignment explanation
Indices: 35143--35471 Score: 403
Period size: 138 Copynumber: 2.4 Consensus size: 137
35133 CTATTATGTG
* * * *
35143 TATTCATATCAGTACCTATCATGTGTGAGGGGACGAAACAATGTGGTTAAAGCGTATTTCAGGGG
1 TATTCATGTCAGTACCTATCATGTTTGAGGGGACGAAGCAATGTGGTTAAAGCGCATTTCAGGGG
* * * * *
35208 GCGCCTTCCCTTTTTTTTTATTAGAGAATATGTTAAATTTTCCTATTATGTGTGATGTCCCCCGG
66 GCGCC-TACCTTTTTTTTTATCAGAGAATAGGTTAAATTATCCTAGTATGTGTGATGTCCCCCGG
* **
35273 TAGGGTAC
130 AAGGACAC
* * * *
35281 TATTCATGTCAGTACCTATCATGTTTGAGGGGACGTAGTAATGTGGTTAAAGCGCGTTTTAGGGG
1 TATTCATGTCAGTACCTATCATGTTTGAGGGGACGAAGCAATGTGGTTAAAGCGCATTTCAGGGG
* *
35346 GCG-C-ACCTTTCATTTTTTGTCAGAGAATAGGTTATAATTATCCTAGTATGTGTGATGTCCCTC
66 GCGCCTACCTTT--TTTTTTATCAGAGAATAGGTTA-AATTATCCTAGTATGTGTGATGTCCCCC
*
35409 GGAATGACAC
128 GGAAGGACAC
* *
35419 TATTCATGTCAATACCTATCATGTTTGAGGGGA-TACAGCAATGTGGTTAAAGC
1 TATTCATGTCAGTACCTATCATGTTTGAGGGGACGA-AGCAATGTGGTTAAAGC
35472 ATGTTTGAGG
Statistics
Matches: 164, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
135 5 0.03
137 20 0.12
138 139 0.85
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (137 bp):
TATTCATGTCAGTACCTATCATGTTTGAGGGGACGAAGCAATGTGGTTAAAGCGCATTTCAGGGG
GCGCCTACCTTTTTTTTTATCAGAGAATAGGTTAAATTATCCTAGTATGTGTGATGTCCCCCGGA
AGGACAC
Found at i:35475 original size:33 final size:33
Alignment explanation
Indices: 35438--35516 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
35428 CAATACCTAT
35438 CATGTTTGAGGGGATACAGCAATGTGGTTAAAG
1 CATGTTTGAGGGGATACAGCAATGTGGTTAAAG
*
35471 CATGTTTGAGGGGATGCAGCAATGTGGTTAAAG
1 CATGTTTGAGGGGATACAGCAATGTGGTTAAAG
35504 CATGTTTGAGGGG
1 CATGTTTGAGGGG
35517 GTGTGCCTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.27, C:0.09, G:0.37, T:0.28
Consensus pattern (33 bp):
CATGTTTGAGGGGATACAGCAATGTGGTTAAAG
Found at i:36302 original size:35 final size:34
Alignment explanation
Indices: 36257--36322 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
36247 AATTGGAATA
* **
36257 TTAAGTTGAATTTGGATTTGCATTTTAAAAACAT
1 TTAAGTTGAATTTGAATTTAAATTTTAAAAACAT
36291 TTAATGTTGAATTTGAATTTAAATTTTAAAAA
1 TTAA-GTTGAATTTGAATTTAAATTTTAAAAA
36323 TATTATTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.45
Consensus pattern (34 bp):
TTAAGTTGAATTTGAATTTAAATTTTAAAAACAT
Found at i:36895 original size:42 final size:42
Alignment explanation
Indices: 36828--36917 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
36818 TAGGAATGTA
*
36828 ACCC-TGCGGAGATGACATATGAACTGGTGGGCTT-GGCATAT
1 ACCCTTGCGGAGATGACATATAAACTGGTGGG-TTGGGCATAT
* * *
36869 ACCCTTGCGGAGATGGCATCTAAACTGGTGGGTTGGGCATGT
1 ACCCTTGCGGAGATGACATATAAACTGGTGGGTTGGGCATAT
36911 ACCCTTG
1 ACCCTTG
36918 TGGCATCATC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 6 0.14
42 37 0.86
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (42 bp):
ACCCTTGCGGAGATGACATATAAACTGGTGGGTTGGGCATAT
Found at i:37495 original size:17 final size:17
Alignment explanation
Indices: 37473--37508 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
37463 AAACTGAAAC
37473 ATAAATAT-ATAATTCTA
1 ATAAATATAAT-ATTCTA
37490 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
37507 AT
1 AT
37509 TATAGCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:38707 original size:24 final size:23
Alignment explanation
Indices: 38668--38717 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
38658 AATAATAATT
38668 ATATAAATATTATTTTAATAAAAA
1 ATATAAATATTATTTTAA-AAAAA
*
38692 ATAT-AATATTATTTTTAAAAAA
1 ATATAAATATTATTTTAAAAAAA
38714 ATAT
1 ATAT
38718 TTATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
23 12 0.48
24 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATAAATATTATTTTAAAAAAA
Found at i:39788 original size:6 final size:6
Alignment explanation
Indices: 39777--39820 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
39767 AACATACATT
39777 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CC
39821 GTCCTCTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTC
Found at i:41015 original size:50 final size:50
Alignment explanation
Indices: 40956--41075 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
40946 TACGCGAATT
* * *
40956 TGGACTGCCACCTGGGAAACGTGTCCTAGGGATCGCACTTTACATTGAGT
1 TGGAGTGCCACCTGGGAAACGTGTCCTAGGGATCGCACTTTACATTAAGC
** * * *
41006 TGGCTTGCCACCT-GGAAAGCGTGTCCTATGGATCGCGCTTTACGTTAAGC
1 TGGAGTGCCACCTGGGAAA-CGTGTCCTAGGGATCGCACTTTACATTAAGC
*
41056 TGGAGTGCCAACTGGGAAAC
1 TGGAGTGCCACCTGGGAAAC
41076 ACATCCTGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
49 5 0.09
50 48 0.83
51 5 0.09
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (50 bp):
TGGAGTGCCACCTGGGAAACGTGTCCTAGGGATCGCACTTTACATTAAGC
Found at i:41291 original size:13 final size:13
Alignment explanation
Indices: 41273--41297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41263 TTTTTATTCT
41273 TTTAATATTTTTA
1 TTTAATATTTTTA
41286 TTTAATATTTTT
1 TTTAATATTTTT
41298 GCTTAATTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTAATATTTTTA
Found at i:43255 original size:40 final size:40
Alignment explanation
Indices: 43200--43321 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
43190 TGCAGGTTTA
43200 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
43240 TAATACACTTCGGTGTATATGGTGGACACGACTTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
43280 TAATACACTTCGGTGTATATGGTAGGCACTACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
43320 TA
1 TA
43322 GCACTATGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:44435 original size:18 final size:18
Alignment explanation
Indices: 44412--44451 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
44402 GAGGATGTTG
44412 CAATGCATTTGGGACTTC
1 CAATGCATTTGGGACTTC
44430 CAATGCATTTGGGACTTC
1 CAATGCATTTGGGACTTC
44448 CAAT
1 CAAT
44452 AGATGGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (18 bp):
CAATGCATTTGGGACTTC
Found at i:46842 original size:15 final size:15
Alignment explanation
Indices: 46824--46872 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
46814 TATTGAAATA
* *
46824 TATGTTATTTTAATT
1 TATGTTATTATATTT
** *
46839 TATGGCATTGTATTT
1 TATGTTATTATATTT
46854 TATGTTATTATATTT
1 TATGTTATTATATTT
46869 TATG
1 TATG
46873 GCCATCTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (15 bp):
TATGTTATTATATTT
Found at i:46883 original size:30 final size:30
Alignment explanation
Indices: 46824--46886 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
46814 TATTGAAATA
* *
46824 TATGTTATTTTAATTTATGGCATTGTATTT
1 TATGTTATTATAATTTATGGCATTCTATTT
*
46854 TATGTTATTATATTTTATGGCCA-TCTATTT
1 TATGTTATTATAATTTATGG-CATTCTATTT
46884 TAT
1 TAT
46887 ATAATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.59
Consensus pattern (30 bp):
TATGTTATTATAATTTATGGCATTCTATTT
Found at i:47293 original size:41 final size:41
Alignment explanation
Indices: 47248--47347 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
47238 TATTTTTTGC
*
47248 ATTTAGGGTTTAAAGTTTAGGGTTTATA-TTATATGGTTGAT
1 ATTTAGGGTTTAAAGTTTAAGGTTTATAGTT-TATGGTTGAT
*** ** * *
47289 ATTTATATTTTAGTGTTTAAGGTTTATAGTTTATGTTTTAT
1 ATTTAGGGTTTAAAGTTTAAGGTTTATAGTTTATGGTTGAT
47330 AGTTTAGGGTTTAAAGTT
1 A-TTTAGGGTTTAAAGTT
47348 AAGTGTTGAA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
41 31 0.70
42 13 0.30
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (41 bp):
ATTTAGGGTTTAAAGTTTAAGGTTTATAGTTTATGGTTGAT
Found at i:47320 original size:14 final size:14
Alignment explanation
Indices: 47303--47347 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
47293 ATATTTTAGT
47303 GTTTAAGGTTTATA
1 GTTTAAGGTTTATA
* *
47317 GTTTATGTTTTATA
1 GTTTAAGGTTTATA
* *
47331 GTTTAGGGTTTAAA
1 GTTTAAGGTTTATA
47345 GTT
1 GTT
47348 AAGTGTTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.53
Consensus pattern (14 bp):
GTTTAAGGTTTATA
Found at i:47327 original size:28 final size:28
Alignment explanation
Indices: 47282--47347 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
47272 TATATTATAT
*
47282 GGTTGATA-TTTATATTTTAGT-GTTTAA
1 GGTTTATAGTTTATATTTTA-TAGTTTAA
* *
47309 GGTTTATAGTTTATGTTTTATAGTTTAG
1 GGTTTATAGTTTATATTTTATAGTTTAA
*
47337 GGTTTAAAGTT
1 GGTTTATAGTT
47348 AAGTGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 8 0.24
28 25 0.76
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (28 bp):
GGTTTATAGTTTATATTTTATAGTTTAA
Found at i:47775 original size:65 final size:64
Alignment explanation
Indices: 47645--47800 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 64
47635 AATTAAATTG
* * *
47645 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCAATGCACATACCATGCACCGATGCACTCAGGATTTTATG-A
* * * *
47710 AACATCGAATGCATTTGATGCATCAATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCAATGCA-CATACCATGCACCGATGCACTCAGGAT-TTTATG
47773 A
64 A
* * *
47774 AACATCAAATACACTTGATGCATCAAT
1 AACATCGAATGCATTTGATGCATCAAT
47801 ACACTCTTAG
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 25 0.32
65 49 0.62
66 5 0.06
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCAATGCACATACCATGCACCGATGCACTCAGGATTTTATGA
Found at i:56428 original size:65 final size:64
Alignment explanation
Indices: 56298--56453 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 64
56288 AATTAAATTG
* * * *
56298 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCATTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCAATGCACATACCATGCACCGATGCACTCAGGATTTTATG-A
* * * * *
56363 AACATCGAATGCATTTGATTCATCAATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCAATGCA-CATACCATGCACCGATGCACTCAGGAT-TTTATG
56426 A
64 A
**
56427 AACATCGAATGCGCTTGATGCATCAAT
1 AACATCGAATGCATTTGATGCATCAAT
56454 ATACTCTTAG
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 25 0.32
65 47 0.61
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCAATGCACATACCATGCACCGATGCACTCAGGATTTTATGA
Found at i:57309 original size:28 final size:28
Alignment explanation
Indices: 57277--57343 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
57267 ATGACTTAGG
* * *
57277 GTTTATATTTTACTATTAAGGGTTTATT
1 GTTTATATTTTAATATTAAGGATTTATA
* * *
57305 GTTTATAATTTAATGTTTAGGATTTATA
1 GTTTATATTTTAATATTAAGGATTTATA
57333 GTTTATATTTT
1 GTTTATATTTT
57344 TGAGTTTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.58
Consensus pattern (28 bp):
GTTTATATTTTAATATTAAGGATTTATA
Found at i:57350 original size:28 final size:28
Alignment explanation
Indices: 57306--57394 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
57296 GGGTTTATTG
* *
57306 TTTATAATTTA-ATGTTTAGGATTTATAG
1 TTTATATTTTAGA-GTTTAGGATTTATAA
* * *
57334 TTTATATTTTTGAGTTTAAGG-TCTAGAA
1 TTTATATTTTAGAGTTT-AGGATTTATAA
* *
57362 TTTATGTTTTAGAGTTTATGATTTATAA
1 TTTATATTTTAGAGTTTAGGATTTATAA
57390 TTTAT
1 TTTAT
57395 GGTGTATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
27 2 0.04
28 42 0.88
29 4 0.08
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (28 bp):
TTTATATTTTAGAGTTTAGGATTTATAA
Found at i:57374 original size:14 final size:14
Alignment explanation
Indices: 57357--57395 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
57347 GTTTAAGGTC
*
57357 TAGAATTTATGTTT
1 TAGAATTTATGATT
*
57371 TAGAGTTTATGATT
1 TAGAATTTATGATT
*
57385 TATAATTTATG
1 TAGAATTTATG
57396 GTGTATTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (14 bp):
TAGAATTTATGATT
Found at i:63313 original size:19 final size:19
Alignment explanation
Indices: 63289--63374 Score: 154
Period size: 19 Copynumber: 4.5 Consensus size: 19
63279 GGTATTCTCT
*
63289 CATCTCTCTTCGTTAGGTG
1 CATCTCTCTTCGTTTGGTG
*
63308 CATCTCTCTTCGTTGGGTG
1 CATCTCTCTTCGTTTGGTG
63327 CATCTCTCTTCGTTTGGTG
1 CATCTCTCTTCGTTTGGTG
63346 CATCTCTCTTCGTTTGGTG
1 CATCTCTCTTCGTTTGGTG
63365 CATCTCTCTT
1 CATCTCTCTT
63375 TTGCTTCTGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.07, C:0.28, G:0.20, T:0.45
Consensus pattern (19 bp):
CATCTCTCTTCGTTTGGTG
Found at i:63922 original size:16 final size:16
Alignment explanation
Indices: 63885--63925 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
63875 TAGCACCACA
63885 TCCCC-TCTCGCAACG
1 TCCCCTTCTCGCAACG
*
63900 CCACCCTTCTCGCAACG
1 TC-CCCTTCTCGCAACG
63917 TCCCCTTCT
1 TCCCCTTCT
63926 AGTCGCGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 1 0.05
16 10 0.45
17 11 0.50
ACGTcount: A:0.12, C:0.54, G:0.10, T:0.24
Consensus pattern (16 bp):
TCCCCTTCTCGCAACG
Found at i:65350 original size:20 final size:21
Alignment explanation
Indices: 65321--65360 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
65311 TAGTTTAGGA
65321 ATTATCTTTA-GAATTTATCTC
1 ATTATCTTTAGGAA-TTATCTC
65342 ATTAT-TTTAGGAATTATCT
1 ATTATCTTTAGGAATTATCT
65361 TTTCCTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTATCTTTAGGAATTATCTC
Done.