Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006131.1 Hibiscus syriacus cultivar Beakdansim tig00014541_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: 74000
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:21313 original size:13 final size:13
Alignment explanation
Indices: 21297--21330 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21287 TTTAATAATG
*
21297 TATTTTTATATTA
1 TATTTGTATATTA
21310 TATTTGTATATTA
1 TATTTGTATATTA
*
21323 AATTTGTA
1 TATTTGTA
21331 AGATTGTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TATTTGTATATTA
Found at i:21924 original size:2 final size:2
Alignment explanation
Indices: 21912--21946 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
21902 AATTTCACTA
21912 AT AT A- 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
21947 GACTTGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23688 original size:2 final size:2
Alignment explanation
Indices: 23681--23712 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
23671 TTAGAAATGT
*
23681 CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
23713 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:23717 original size:2 final size:2
Alignment explanation
Indices: 23712--23741 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23702 ACACACACAC
23712 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
23742 TGAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24644 original size:21 final size:22
Alignment explanation
Indices: 24620--24672 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
24610 CGACCCCAAA
24620 TTTCAAATTAAAA-A-AATTATT
1 TTTCAAATTAAAAGATAATTA-T
*
24641 TTTCAAAATAAAAGTATAATTAT
1 TTTCAAATTAAAAG-ATAATTAT
24664 TTTCAAATT
1 TTTCAAATT
24673 TAATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 12 0.44
23 10 0.37
24 5 0.19
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTCAAATTAAAAGATAATTAT
Found at i:25260 original size:10 final size:10
Alignment explanation
Indices: 25221--25260 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
25211 TTCATCACAC
25221 CAAATTCTCT
1 CAAATTCTCT
*
25231 CAATTTCTCT
1 CAAATTCTCT
*
25241 CAACTTCTCT
1 CAAATTCTCT
*
25251 CAAATACTCT
1 CAAATTCTCT
25261 TATATTATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:25316 original size:21 final size:22
Alignment explanation
Indices: 25272--25346 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 22
25262 ATATTATCTG
*
25272 TTTAAGGTATATTTTA-TTATATT
1 TTTAA-GTATTTTTTATTTA-ATT
25295 TTTAA-TATTTTTTATTTAATT
1 TTTAAGTATTTTTTATTTAATT
25316 TATTGAAGTATTTAATTTATTTAATAT
1 T-TT-AAGTATTT--TTTATTTAAT-T
25343 TTTA
1 TTTA
25347 CTTATATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
21 12 0.27
22 5 0.11
23 7 0.16
24 5 0.11
25 1 0.02
26 12 0.27
27 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTAAGTATTTTTTATTTAATT
Found at i:30475 original size:16 final size:15
Alignment explanation
Indices: 30419--30483 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
30409 GTTTTTTCAT
* *
30419 ATAATCATAATAAACA
1 ATAATTATAACAAA-A
*
30435 ATAAGTATAACAAAA
1 ATAATTATAACAAAA
30450 ATAATTATAACAAAA
1 ATAATTATAACAAAA
* *
30465 TTACCTTATAACGAAAA
1 ATA-ATTATAAC-AAAA
30482 AT
1 AT
30484 CGAACAAACT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 17 0.43
16 18 0.45
17 5 0.12
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATTATAACAAAA
Found at i:34403 original size:19 final size:20
Alignment explanation
Indices: 34381--34418 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34371 ATCTAACAAA
*
34381 CTAACAAA-TTAATAACTGC
1 CTAACAAACTAAATAACTGC
34400 CTAACAAACTAAATAACTG
1 CTAACAAACTAAATAACTG
34419 AAATCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (20 bp):
CTAACAAACTAAATAACTGC
Found at i:38931 original size:19 final size:20
Alignment explanation
Indices: 38909--38946 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38899 ATCTAACAAA
*
38909 CTAACAAA-TTAATAACTGC
1 CTAACAAACTAAATAACTGC
38928 CTAACAAACTAAATAACTG
1 CTAACAAACTAAATAACTG
38947 AAATCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (20 bp):
CTAACAAACTAAATAACTGC
Found at i:60917 original size:14 final size:14
Alignment explanation
Indices: 60879--60910 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
60869 AATTCATCTT
60879 TTCTATTAAATATA
1 TTCTATTAAATATA
*
60893 TTCTATTAAATCTA
1 TTCTATTAAATATA
60907 TTCT
1 TTCT
60911 TCTAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (14 bp):
TTCTATTAAATATA
Found at i:62301 original size:26 final size:26
Alignment explanation
Indices: 62272--62330 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
62262 ATTGGGATGA
62272 TGAAGCAGAAAAAGCTTTTATGAAAT
1 TGAAGCAGAAAAAGCTTTTATGAAAT
62298 TGAAGCAGAAAAAGCTTTTATGAAAT
1 TGAAGCAGAAAAAGCTTTTATGAAAT
62324 TGAAGCA
1 TGAAGCA
62331 AGCTATGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.25
Consensus pattern (26 bp):
TGAAGCAGAAAAAGCTTTTATGAAAT
Found at i:64546 original size:22 final size:22
Alignment explanation
Indices: 64520--64575 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
64510 AAACCATTCA
*
64520 GGGGGAATCGGTATCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
64542 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
64564 GGGGGAATCGGT
1 GGGGGAATCGGT
64576 TCCTCTAGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.14, C:0.21, G:0.45, T:0.20
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:66555 original size:230 final size:229
Alignment explanation
Indices: 66099--66595 Score: 906
Period size: 231 Copynumber: 2.2 Consensus size: 229
66089 GTTATATTGT
* * * *
66099 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCATTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
* *
66164 TCTTTGGTTAAAATTTTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
66 TATTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
66229 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
66294 AAAAAATTGAAACATAAATTACATAACTTTAAAAA
196 AAAAAATTGAAACATAAATTACATAACTTT-AAAA
66329 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAACATATTTATTATT
*
66394 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
65 ATATTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
66459 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-
130 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
66523 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
66558 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTAT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTAT
66596 AAAAGTAGCT
Statistics
Matches: 259, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
229 42 0.16
230 74 0.29
231 143 0.55
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
TATTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:66903 original size:20 final size:20
Alignment explanation
Indices: 66871--66917 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
66861 CAATATACCA
66871 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
66891 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
66911 GGTAAAA
1 GGTAAAA
66918 TGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:66994 original size:181 final size:181
Alignment explanation
Indices: 66663--67079 Score: 601
Period size: 182 Copynumber: 2.3 Consensus size: 181
66653 GATCCAAATT
* * *
66663 AAAAATG--TCGATCCAAAACGATATACAGGT-AAACTATGACAAAACCGGTATAGAAATGATAA
1 AAAAATGTATCGATCCAAAACGATATACAGGTAAAAATATGATAAAACCGGTA-AAAAATGATAA
* *
66725 AACCGGTAAAACGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCA
65 AACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCA
* *
66790 TGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTT-TA
130 TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
*
66841 AAAAATGTATCGATCCAAAACAATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATA-CAGGTAAAAATATGATAAAACCGGTAA-AAAATGATA
* * * *
66906 AAACCGGTAAAATGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
64 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
66970 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAA
129 ATGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
* *
67023 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAA
1 AAAAATGTATCGATCCAAAACGATAT-ACAGGTAAAAATATGATAAAACCGGTAAAA
67080 TGATACCGGA
Statistics
Matches: 213, Mismatches: 19, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
178 7 0.03
180 17 0.08
181 71 0.33
182 117 0.55
183 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATACAGGTAAAAATATGATAAAACCGGTAAAAAATGATAAA
ACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCAT
GAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
Found at i:69284 original size:21 final size:21
Alignment explanation
Indices: 69258--69322 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
69248 AAGACAATCA
*
69258 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
69279 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
69300 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
69321 AG
1 AG
69323 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:69396 original size:33 final size:32
Alignment explanation
Indices: 69354--69420 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
69344 AAAATAGATG
*
69354 GAGTGGTGAAAGAAGTAGAGGTGTTTGAGGGGT
1 GAGTGGTGAAAGAAGTAGAGGTG-TTAAGGGGT
* *
69387 GAGTGGTGAAAGAAGTTGGGGTGTTAAGGGGT
1 GAGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
69419 GA
1 GA
69421 TATTAAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 10 0.32
33 21 0.68
ACGTcount: A:0.27, C:0.00, G:0.49, T:0.24
Consensus pattern (32 bp):
GAGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
Found at i:71200 original size:17 final size:18
Alignment explanation
Indices: 71178--71219 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
71168 TAGGGTTAAT
71178 TTTGTATAAGATTTAT-A
1 TTTGTATAAGATTTATAA
*
71195 TTTGTATACGATTTATAA
1 TTTGTATAAGATTTATAA
71213 TTTGTAT
1 TTTGTAT
71220 GTGAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (18 bp):
TTTGTATAAGATTTATAA
Found at i:71689 original size:198 final size:200
Alignment explanation
Indices: 71310--73431 Score: 3522
Period size: 198 Copynumber: 10.9 Consensus size: 200
71300 ATACACATTA
*
71310 AGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
71375 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
*
71440 TATGTCTAAA-ATATG-GATCGATACTTTTTTAGTTTGTGTCGATA-TTTTGGTCCAGAATGAAT
131 TATGTCTAAATA-ATGTG-TCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
71502 GGAAAAC
194 GGAAAAC
*
71509 AGGGTGCAACCATAAAGTCTCGATCCATATAT-AAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
71573 AAAGTATAATGTAATAT-TAATTTTTTAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
71637 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
71702 AAAAC
196 AAAAC
* * *
71707 ATGGTGCAACCACAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATTGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
71772 AAAGTATAATGTAATATGTAGTTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
66 AAAGTATAATGTAATATGTA-ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
*
71837 ATATGTCT-AATAA-GTGTCGACA--TTTTTAGTTTCTGTCGAT-TTTTTGGTCCAGAATGAATG
130 ATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
71897 GAAAAC
195 GAAAAC
71903 AGGGTGC-A--A-AAA---TCGATCC--ATATAAAAAGTGTCGATCCCAAAAACATCG-AAACC-
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
71957 AAAGTATAATGTAATATGT-ATTTTTCAATCTAACC-GTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
72020 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCA-AATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
72084 AAAAAC
196 -AAAAC
* *
72090 AGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTTTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
72155 AAAGT-TAATGTAATATGTAATTTTTCAATCTAACC-GTACAAGTATACCGGTTTGATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
72218 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
72283 AAAAC
196 AAAAC
* *
72288 AGGGTGCAACCATAAAGTGTCGATCCATATA-AAAACGT-TAGATCCCAAAAAC-TCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
72350 AAAGTAT-ATGTAATATGTAGTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
*
72414 TATGTCTAAATAA-GTGTCGACACCTTTTTTAGTTTGTGTCGATATTTTTTGGTCCATAATGAAT
131 TATGTCTAAATAATGTGTCGACA-CTTTTTTAGTTTGTGTCGATA-TTTTTGGTCCAGAATGAAT
72478 GGAAAAC
194 GGAAAAC
72485 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
72549 AAAGTATAATGTAATATGT-A-TTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAT
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
72612 TATG--TAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGAT-TTTTTGGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
72674 -AAAC
196 AAAAC
72678 AGGGTGCAACCATAAAGTGTCGATCC--ATAT-AAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
72740 AAAGTATAATGTAATATGTATTTTTTTTTCAATCT-ACCGGTACAAG-ATACCGGTTTTAT--GA
66 AAAGTATAATGTAATATGTA---ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
72801 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
128 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
72866 TGGAAAAC
193 TGGAAAAC
*
72874 AGGGTGCAACCATAAAGTGTCGATCC--ATATAAAACGTGTCGATCCCAAAAACATCGAAAACC-
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
72936 AAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
*
73000 TATGTCTAAATAATGTGTCGAC-CCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
73064 AAAAC
196 AAAAC
*
73069 AGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
73133 AAAG--T-ATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACC-GTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
73194 TATGTCTAAAT-ATGTGTCGACACTTTTTTAGTTTTGTGTCGATA-TTTTGGTCCAGAATGAATG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAG-TTTGTGTCGATATTTTTGGTCCAGAATGAATG
73257 GAAAAC
195 GAAAAC
73263 A-GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
73326 AAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAAGTATACC-GTTTTATGAGAGAT
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
73389 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTT-TGTCGATA
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
73432 CTAATTTAAA
Statistics
Matches: 1825, Mismatches: 39, Indels: 123
0.92 0.02 0.06
Matches are distributed among these distances:
182 35 0.02
183 20 0.01
184 9 0.00
185 19 0.01
186 31 0.02
187 51 0.03
188 1 0.00
189 7 0.00
190 16 0.01
191 42 0.02
192 22 0.01
193 117 0.06
194 168 0.09
195 256 0.14
196 299 0.16
197 244 0.13
198 300 0.16
199 120 0.07
200 18 0.01
201 50 0.03
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (200 bp):
AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
AAAAC
Found at i:72452 original size:196 final size:199
Alignment explanation
Indices: 71310--73431 Score: 3514
Period size: 196 Copynumber: 10.9 Consensus size: 199
71300 ATACACATTA
*
71310 AGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
71375 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
*
71440 TATGTCTAAA-ATATG-GATCGATACTTTTTTAGTTTGTGTCGATA-TTTTGGTCCAGAATGAAT
130 TATGTCTAAATA-ATGTG-TCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
71502 GGAAAAC
193 GGAAAAC
*
71509 AGGGTGCAACCATAAAGTCTCGATCCATATAT-AAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
71573 AAAGTATAATGTAATAT-TAATTTTTTAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
71637 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
130 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
71702 AAAAC
195 AAAAC
* * *
71707 ATGGTGCAACCACAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATTGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
71772 AAAGTATAATGTAATATGTAGTTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
66 AAAGTATAATGTAATATGTA--TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
*
71837 ATATGTCT-AATAA-GTGTCGACA--TTTTTAGTTTCTGTCGAT-TTTTTGGTCCAGAATGAATG
129 ATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
71897 GAAAAC
194 GAAAAC
71903 AGGGTGC-A--A-AAA---TCGATCC--ATATAAAAAGTGTCGATCCCAAAAACATCG-AAACC-
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
71957 AAAGTATAATGTAATATGTATTTTTCAATCTAACC-GTACAAGTATACCGGTTTTATGAGAGAAT
66 AAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
72021 ATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCA-AATGAATGGA
131 ATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG-
72085 AAAAC
195 AAAAC
* *
72090 AGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTTTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
72155 AAAGT-TAATGTAATATGTAATTTTTCAATCTAACC-GTACAAGTATACCGGTTTGATGAGAGAA
66 AAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
72218 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
130 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
72283 AAAAC
195 AAAAC
* *
72288 AGGGTGCAACCATAAAGTGTCGATCCATATA-AAAACGT-TAGATCCCAAAAAC-TCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
72350 AAAGTAT-ATGTAATATGTAGTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTA-TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
*
72414 TATGTCTAAATAA-GTGTCGACACCTTTTTTAGTTTGTGTCGATATTTTTTGGTCCATAATGAAT
130 TATGTCTAAATAATGTGTCGACA-CTTTTTTAGTTTGTGTCGATA-TTTTTGGTCCAGAATGAAT
72478 GGAAAAC
193 GGAAAAC
72485 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
72549 AAAGTATAATGTAATATGTA-TTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGATT
66 AAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
72613 ATG--TAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGAT-TTTTTGGTCCAGAATGAATGG-
131 ATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGA
72674 AAAC
196 AAAC
72678 AGGGTGCAACCATAAAGTGTCGATCC--ATAT-AAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
72740 AAAGTATAATGTAATATGTATTTTTTTTTCAATCT-ACCGGTACAAG-ATACCGGTTTTAT--GA
66 AAAGTATAATGTAATATGTA----TTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
72801 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
127 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
72866 TGGAAAAC
192 TGGAAAAC
*
72874 AGGGTGCAACCATAAAGTGTCGATCC--ATATAAAACGTGTCGATCCCAAAAACATCGAAAACC-
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
72936 AAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
66 AAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
*
73001 ATGTCTAAATAATGTGTCGAC-CCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGA
131 ATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGA
73065 AAAC
196 AAAC
*
73069 AGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
73133 AAAG--T-ATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACC-GTTTTATGAGAGAA
66 AAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
73194 TATGTCTAAAT-ATGTGTCGACACTTTTTTAGTTTTGTGTCGATA-TTTTGGTCCAGAATGAATG
130 TATGTCTAAATAATGTGTCGACACTTTTTTAG-TTTGTGTCGATATTTTTGGTCCAGAATGAATG
73257 GAAAAC
194 GAAAAC
73263 A-GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
73326 AAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAAGTATACC-GTTTTATGAGAGATT
66 AAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
73390 ATGTCTAAATAATGTGTCGACACTTTTTTAGTTT-TGTCGATA
131 ATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
73432 CTAATTTAAA
Statistics
Matches: 1829, Mismatches: 33, Indels: 127
0.92 0.02 0.06
Matches are distributed among these distances:
182 35 0.02
183 20 0.01
184 9 0.00
185 20 0.01
186 31 0.02
187 51 0.03
188 1 0.00
189 7 0.00
190 16 0.01
191 43 0.02
192 22 0.01
193 117 0.06
194 169 0.09
195 255 0.14
196 300 0.16
197 244 0.13
198 300 0.16
199 121 0.07
200 18 0.01
201 50 0.03
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (199 bp):
AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
AAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
ATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGA
AAAC
Done.