Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003529.1 Hibiscus syriacus cultivar Beakdansim tig00007451_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: 57037
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Found at i:943 original size:12 final size:12
Alignment explanation
Indices: 926--950 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
916 ACAAAGGGAT
926 TTTACAACACTA
1 TTTACAACACTA
938 TTTACAACACTA
1 TTTACAACACTA
950 T
1 T
951 GCTCAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTACAACACTA
Found at i:1328 original size:17 final size:17
Alignment explanation
Indices: 1302--1341 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
1292 ACCAAATAAC
1302 AATTTTTATA-ATTTTA
1 AATTTTTATATATTTTA
1318 AATTGTTTATATATTTTA
1 AATT-TTTATATATTTTA
1336 AGATTT
1 A-ATTT
1342 AAAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 8 0.38
19 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
AATTTTTATATATTTTA
Found at i:2167 original size:2 final size:2
Alignment explanation
Indices: 2115--2150 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2105 TGTCCATGTG
2115 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2151 AAAGGCGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3408 original size:35 final size:36
Alignment explanation
Indices: 3365--3434 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
3355 GCCTTAGGTC
3365 TATAAGGAATTACCAG-TTGAT-CGATGTTGAACCTA
1 TATAAGGAATTACCAGCTTGATCCGA-GTTGAACCTA
*
3400 TATAAGGAATTACCAGCTTGGTCCGAGTTGAACCT
1 TATAAGGAATTACCAGCTTGATCCGAGTTGAACCT
3435 GCAGAGACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 16 0.50
36 13 0.41
37 3 0.09
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (36 bp):
TATAAGGAATTACCAGCTTGATCCGAGTTGAACCTA
Found at i:3651 original size:19 final size:20
Alignment explanation
Indices: 3627--3665 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3617 TAAATCATAG
3627 GAAACAATT-CAAA-CAGATA
1 GAAAC-ATTCCAAATCAGATA
3646 GAAACATTCCAAATCAGATA
1 GAAACATTCCAAATCAGATA
3666 AAATAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (20 bp):
GAAACATTCCAAATCAGATA
Found at i:4203 original size:18 final size:18
Alignment explanation
Indices: 4163--4212 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
4153 TAACTTTTTT
* *
4163 GTCAAAGTTAACGGTCAA
1 GTCAAAGTCAACGGGCAA
4181 GTCAAAGTCAACGGGC-A
1 GTCAAAGTCAACGGGCAA
*
4198 GATCAAGGTCAACGG
1 G-TCAAAGTCAACGG
4213 TTCGGTCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (18 bp):
GTCAAAGTCAACGGGCAA
Found at i:24297 original size:46 final size:45
Alignment explanation
Indices: 24244--24519 Score: 435
Period size: 46 Copynumber: 6.0 Consensus size: 45
24234 AAAACGAATC
*
24244 CATAAATGAAATGCATTAAATGATGCATTAAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
24289 ACATAAATGAAATGCATGAAAATGATGCATTAAGGCATGAAATGATG
1 -CATAAATGAAATGCATG-AAATGATGCATTAAGGCATGAAAGGATG
* *
24336 CCATAAATGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
24382 TCAAAAATCAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
24428 CTATAAATGAAATGCATAAAATGATGCATTAAGGCATGAAAGGATGG
1 C-ATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGAT-G
24475 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
24520 TTGATAACTC
Statistics
Matches: 212, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
45 2 0.01
46 165 0.78
47 45 0.21
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
Found at i:36116 original size:46 final size:46
Alignment explanation
Indices: 36063--36180 Score: 191
Period size: 46 Copynumber: 2.6 Consensus size: 46
36053 TAAAACGAAT
* *
36063 CCATAAATGAAATGCATGAAAGGATGCATTATGGCATGAAATGATA
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
* * *
36109 CCATAAATGAAATGCATGAAAGTATGCATTAAGGTATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
36155 CCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
36181 ACATAAATGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
Found at i:36129 original size:26 final size:26
Alignment explanation
Indices: 36063--36201 Score: 106
Period size: 26 Copynumber: 5.8 Consensus size: 26
36053 TAAAACGAAT
36063 CCATAAATGAAATGCATGAAAGGAT-
1 CCATAAATGAAATGCATGAAAGGATA
* * *
36088 GCAT-TATG----GCATGAAATGATA
1 CCATAAATGAAATGCATGAAAGGATA
*
36109 CCATAAATGAAATGCATGAAAGTAT-
1 CCATAAATGAAATGCATGAAAGGATA
* * * *
36134 GCAT---T--AAGGTATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATA
36155 CCATAAATGAAATGCATGAAAGGATGA
1 CCATAAATGAAATGCATGAAAGGAT-A
36182 -CATAAATGAAATGCATGAAA
1 CCATAAATGAAATGCATGAAA
36202 TAATGCATTA
Statistics
Matches: 86, Mismatches: 15, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
20 23 0.27
21 6 0.07
22 4 0.05
24 4 0.05
25 6 0.07
26 43 0.50
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (26 bp):
CCATAAATGAAATGCATGAAAGGATA
Found at i:36187 original size:72 final size:73
Alignment explanation
Indices: 36096--36252 Score: 232
Period size: 72 Copynumber: 2.2 Consensus size: 73
36086 ATGCATTATG
* *
36096 GCATGAAATGAT-ACCATAAATGAAATGCATGAAAGT-ATGCATTAAGGTA-TGAAAGGATGCCA
1 GCATGAAATGATGACCATAAATGAAATGCATGAAA-TAATGCATTAAGGCACAG-AAGGATGCCA
36158 TAAATGAAAT
64 TAAATGAAAT
* *
36168 GCATGAAAGGATGA-CATAAATGAAATGCATGAAATAATGCATTAAGGCACAGATGGATGCCATA
1 GCATGAAATGATGACCATAAATGAAATGCATGAAATAATGCATTAAGGCACAGAAGGATGCCATA
36232 AATGAAAT
66 AATGAAAT
36240 GCATGAAATGATG
1 GCATGAAATGATG
36253 CATTAAGGAA
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
71 1 0.01
72 74 0.96
73 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.22
Consensus pattern (73 bp):
GCATGAAATGATGACCATAAATGAAATGCATGAAATAATGCATTAAGGCACAGAAGGATGCCATA
AATGAAAT
Found at i:36232 original size:46 final size:47
Alignment explanation
Indices: 36168--36318 Score: 193
Period size: 46 Copynumber: 3.3 Consensus size: 47
36158 TAAATGAAAT
* * *
36168 GCATGAAA-GGATGACATAAATGAAATGCATGAAATAATGCATTAAG
1 GCATCAAATGGATGCCATAAATGAAATGCATGAAATGATGCATTAAG
*
36214 GCA-CAGATGGATGCCATAAATGAAATGCATGAAATGATGCATTAAG
1 GCATCAAATGGATGCCATAAATGAAATGCATGAAATGATGCATTAAG
* * * *
36260 GAATGAAAT-GATGCCATAAATAAAATACATGAAATGATGCATTAAG
1 GCATCAAATGGATGCCATAAATGAAATGCATGAAATGATGCATTAAG
*
36306 GCATGAAA-GGATG
1 GCATCAAATGGATG
36319 TTGGTAACTC
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
45 2 0.02
46 87 0.95
47 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.22
Consensus pattern (47 bp):
GCATCAAATGGATGCCATAAATGAAATGCATGAAATGATGCATTAAG
Found at i:36252 original size:26 final size:25
Alignment explanation
Indices: 36096--36299 Score: 109
Period size: 26 Copynumber: 8.6 Consensus size: 25
36086 ATGCATTATG
*
36096 GCATGAAATGATACCATAAATGAAAT
1 GCATGAAATGATGCCATAAAT-AAAT
*
36122 GCATGAAA-GTATG-CAT---T-AAG
1 GCATGAAATG-ATGCCATAAATAAAT
* *
36142 GTATGAAAGGATGCCATAAATGAAAT
1 GCATGAAATGATGCCATAAAT-AAAT
* *
36168 GCATGAAAGGATGACATAAATGAAAT
1 GCATGAAATGATGCCATAAAT-AAAT
* *
36194 GCATGAAATAATG-CAT---T-AAG
1 GCATGAAATGATGCCATAAATAAAT
* *
36214 GCA-CAGATGGATGCCATAAATGAAAT
1 GCATGAAAT-GATGCCATAAAT-AAAT
*
36240 GCATGAAATGATG-CAT---T-AAG
1 GCATGAAATGATGCCATAAATAAAT
*
36260 GAATGAAATGATGCCATAAATAAAAT
1 GCATGAAATGATGCCATAAAT-AAAT
*
36286 ACATGAAATGATGC
1 GCATGAAATGATGC
36300 ATTAAGGCAT
Statistics
Matches: 136, Mismatches: 20, Indels: 44
0.68 0.10 0.22
Matches are distributed among these distances:
19 3 0.02
20 34 0.25
21 10 0.07
22 3 0.02
24 3 0.02
25 10 0.07
26 70 0.51
27 3 0.02
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (25 bp):
GCATGAAATGATGCCATAAATAAAT
Found at i:36273 original size:118 final size:118
Alignment explanation
Indices: 36064--36298 Score: 339
Period size: 118 Copynumber: 2.0 Consensus size: 118
36054 AAAACGAATC
* * *
36064 CATAAATGAAATGCATGAAAGGATGCATTATGGCATGAAATGATACCATAAATGAAATGCATGAA
1 CATAAATGAAATGCATGAAAGAATGCATTAAGGCATCAAATGATACCATAAATGAAATGCATGAA
* * *
36129 AGTATGCATTAAGGTATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGA
66 AGTATGCATTAAGGAATGAAAGGATGCCATAAATAAAATACATGAAAGGATGA
* * *
36182 CATAAATGAAATGCATGAAATAATGCATTAAGGCA-CAGATGGATGCCATAAATGAAATGCATGA
1 CATAAATGAAATGCATGAAAGAATGCATTAAGGCATCAAAT-GATACCATAAATGAAATGCATGA
* *
36246 AA-TGATGCATTAAGGAATGAAATGATGCCATAAATAAAATACATGAAATGATG
65 AAGT-ATGCATTAAGGAATGAAAGGATGCCATAAATAAAATACATGAAAGGATG
36299 CATTAAGGCA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
117 4 0.04
118 100 0.96
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (118 bp):
CATAAATGAAATGCATGAAAGAATGCATTAAGGCATCAAATGATACCATAAATGAAATGCATGAA
AGTATGCATTAAGGAATGAAAGGATGCCATAAATAAAATACATGAAAGGATGA
Found at i:36312 original size:20 final size:20
Alignment explanation
Indices: 36240--36318 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
36230 TAAATGAAAT
36240 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
36260 GAATGAAATGATGCCATAAATAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
36286 ACATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
36306 GCATGAAAGGATG
1 GCATGAAATGATG
36319 TTGGTAACTC
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 25 0.54
21 3 0.07
22 1 0.02
24 1 0.02
25 3 0.07
26 13 0.28
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:36410 original size:20 final size:20
Alignment explanation
Indices: 36385--36427 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
36375 CCTAATAGCC
*
36385 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
36405 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
36425 CAT
1 CAT
36428 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:43847 original size:17 final size:17
Alignment explanation
Indices: 43825--43870 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
43815 GGGTTGCTCT
43825 TGTAAGATTAAGTGATA
1 TGTAAGATTAAGTGATA
*
43842 TGTAAGATTAAATGATA
1 TGTAAGATTAAGTGATA
43859 TGTAAGATTAAG
1 TGTAAGATTAAG
43871 GAAGGATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (17 bp):
TGTAAGATTAAGTGATA
Found at i:44952 original size:46 final size:46
Alignment explanation
Indices: 44899--45279 Score: 627
Period size: 46 Copynumber: 8.3 Consensus size: 46
44889 TAAAATGAAT
44899 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
44945 CCATAAATAAAATGCATGAAATGATGCATTAAGGCGTGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * * *
44991 TCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATA
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
45037 CCATAAATGAAATGCATGAAATGATGCATTAAAGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
45083 TCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * * *
45129 TCATATATGAAATGCATAAAATGATGCATTAAGGTATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
45175 ACATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
45221 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGTATG
1 CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
45267 CCATAAATGAAAT
1 CCATAAATGAAAT
45280 TAATGAGTAA
Statistics
Matches: 309, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 309 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.23
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
Found at i:45267 original size:20 final size:20
Alignment explanation
Indices: 44912--45267 Score: 154
Period size: 20 Copynumber: 15.7 Consensus size: 20
44902 TAAATGAAAT
*
44912 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
44932 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
44958 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
44978 GCGTGAAAGGATGTCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
45004 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
45024 GCATGAAATGATACCATAAATGAAAT
1 GCATGAAAGGAT-GCAT---T--AAG
* *
45050 GCATGAAATGATGCATTAAA
1 GCATGAAAGGATGCATTAAG
*
45070 GCATGAAAGGATGTCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
45096 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
45116 GCATGAAAGGATGTCATATATGAAAT
1 GCATGAAAGGATG-C--AT-T--AAG
* *
45142 GCATAAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
45162 GTATGAAAGGATGACATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
45188 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
45208 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
45234 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
45254 GCATGAAAGTATGC
1 GCATGAAAGGATGC
45268 CATAAATGAA
Statistics
Matches: 260, Mismatches: 34, Indels: 84
0.69 0.09 0.22
Matches are distributed among these distances:
20 107 0.41
21 19 0.07
22 7 0.03
23 4 0.02
24 7 0.03
25 19 0.07
26 97 0.37
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.23
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:47555 original size:17 final size:17
Alignment explanation
Indices: 47533--47568 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
47523 AGAAGTTTAT
47533 TTTATGTTTACTAAAGA
1 TTTATGTTTACTAAAGA
47550 TTTATGTTTACTAAAGA
1 TTTATGTTTACTAAAGA
47567 TT
1 TT
47569 ATCTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTATGTTTACTAAAGA
Found at i:49685 original size:160 final size:157
Alignment explanation
Indices: 49211--49767 Score: 666
Period size: 157 Copynumber: 3.5 Consensus size: 157
49201 GTTACGTGGA
* * * * * *
49211 TATTCTATTATGGTATATGAGAATGTGACTCAAATTTGGTAAAAAAAAATTTTAAAAT-AA-GAA
1 TATTCTATGATGGTTTAGGAGCATGTG-TTCAAATTTGGTAAAAAAAAA-CTTAAAATAAAGGAA
* *
49274 TGAAGTG-AAGAAATAAGGAAATTATAAAAAATTGAGGGACTAAATTAAAAAAATAGAAAATTTG
64 -GAATTGAAAGAAATAAGGAAATTATAAAAAATTGAGGGACTAAATT-GAAAAATAGAAAATTTG
49338 TTATC-AAAAGAGGAATTGAAAGTACATATG
127 TTATCAAAAAGAGGAATTGAAAGTACATATG
* * * * *
49368 TATTCTATGATGATTTATGAGCATGTGGTTCAAATTTGGTAAAAACATACTTAAAATATAGGATA
1 TATTCTATGATGGTTTAGGAGCATGT-GTTCAAATTTGGTAAAAAAAAACTTAAAATAAAGGA-A
* * * * *
49433 -AGTT-AAAGAAACAAAGAAACTATAAAAAATTGAGGGACTAAATTGAAAAATATAAAATTTGTT
64 GAATTGAAAGAAATAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTT
* *
49496 ATCAAAAAAAGGAATGGAAAGTACATATG
129 ATCAAAAAGAGGAATTGAAAGTACATATG
*
49525 TATT-TTTCGATGGTTTAGGAGCATGTGTTTCAAATTTGGTAAAAAAAAGAGACTTAAAATAAAG
1 TATTCTAT-GATGGTTTAGGAGCATGTG-TTCAAATTTGGT-AAAAAAA-A-ACTTAAAATAAAG
* *
49589 GAAGAATTGAAAAAAATAAGGAAATTATAAAAAATTGAGGGGCTAAATTGAAAAATAGAAAA-TT
61 GAAGAATTGAAAGAAATAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTT
*
49653 GTTATCAAAAAGTGGAATTGAAAGTACATATG
126 GTTATCAAAAAGAGGAATTGAAAGTACATATG
* * * * *
49685 TATTCTATAATGGTTTAGGAGCATGTAGATCAAA-TTGGTAAAAACAAACTTAAAATAAATGATG
1 TATTCTATGATGGTTTAGGAGCATGT-GTTCAAATTTGGTAAAAAAAAACTTAAAATAAAGGAAG
*
49749 AATTG-AAGAAATAATGAAA
65 AATTGAAAGAAATAAGGAAA
49768 GCAATGACTA
Statistics
Matches: 343, Mismatches: 42, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
155 12 0.03
156 50 0.15
157 135 0.39
158 15 0.04
159 7 0.02
160 74 0.22
161 50 0.15
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.29
Consensus pattern (157 bp):
TATTCTATGATGGTTTAGGAGCATGTGTTCAAATTTGGTAAAAAAAAACTTAAAATAAAGGAAGA
ATTGAAAGAAATAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTTAT
CAAAAAGAGGAATTGAAAGTACATATG
Found at i:49908 original size:14 final size:14
Alignment explanation
Indices: 49889--49915 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49879 ATTCAAGTTA
49889 ACTCAAATAACTCG
1 ACTCAAATAACTCG
49903 ACTCAAATAACTC
1 ACTCAAATAACTC
49916 AAAATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.04, T:0.22
Consensus pattern (14 bp):
ACTCAAATAACTCG
Found at i:52416 original size:26 final size:26
Alignment explanation
Indices: 52391--52450 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
52381 TATGAATTAT
*
52391 TTAATTTTGCA-CCCCTAAGATTTTA
1 TTAATTTTGCACCCCCTAAAATTTTA
* *
52416 -TAATATCGCACCCCCTAAAATTTTAA
1 TTAATTTTGCACCCCCTAAAATTTT-A
52442 TATAATTTT
1 T-TAATTTT
52451 TTATGTTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
24 8 0.31
25 12 0.46
26 1 0.04
28 5 0.19
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (26 bp):
TTAATTTTGCACCCCCTAAAATTTTA
Done.