Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005154.1 Hibiscus syriacus cultivar Beakdansim tig00011623_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: 47365
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:9881 original size:11 final size:11
Alignment explanation
Indices: 9861--9898 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
9851 TAGATAAAAT
*
9861 TTTTAGAATTC
1 TTTTAAAATTC
9872 TTTTAAAATTC
1 TTTTAAAATTC
9883 TTTT-AAATTC
1 TTTTAAAATTC
9893 TTTTAA
1 TTTTAA
9899 CCAATTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (11 bp):
TTTTAAAATTC
Found at i:11218 original size:43 final size:42
Alignment explanation
Indices: 11102--11221 Score: 109
Period size: 43 Copynumber: 2.8 Consensus size: 42
11092 ATCTCTTTTT
* * * * *
11102 TTTTACATTAATAATTGATGATCCTAAGTTTTTCAATCCACC
1 TTTTACATTTATAATTGAAGCTCCTAATTTTTTCAATCCACA
* * **
11144 TTGTATC-TTTATAATT-AAGCTCTTGTTTTTTTTCAATCTCACA
1 TTTTA-CATTTATAATTGAAGCTCCT-AATTTTTTCAATC-CACA
*
11187 TTTTACATTTATAATTGAAGCCCCTAATTTTTTCA
1 TTTTACATTTATAATTGAAGCTCCTAATTTTTTCA
11222 CCCATTTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
41 5 0.08
42 23 0.39
43 25 0.42
44 6 0.10
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (42 bp):
TTTTACATTTATAATTGAAGCTCCTAATTTTTTCAATCCACA
Found at i:12767 original size:17 final size:17
Alignment explanation
Indices: 12723--12769 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
12713 CTTAAATGAC
12723 TAAAATTAGGACTAAAT
1 TAAAATTAGGACTAAAT
12740 T-AAA-TA--A--AAAT
1 TAAAATTAGGACTAAAT
12751 TAAAATTAGGACTAAAT
1 TAAAATTAGGACTAAAT
12768 TA
1 TA
12770 GGATAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
11 5 0.21
12 3 0.12
13 3 0.12
15 3 0.12
16 3 0.12
17 7 0.29
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (17 bp):
TAAAATTAGGACTAAAT
Found at i:21492 original size:19 final size:21
Alignment explanation
Indices: 21451--21492 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
21441 CTCATGATTT
*
21451 TTATCAAAATAATGATAAACA
1 TTATCAAAATAATAATAAACA
*
21472 TTATC-AAATAA-AATAAGCA
1 TTATCAAAATAATAATAAACA
21491 TT
1 TT
21493 TCATATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (21 bp):
TTATCAAAATAATAATAAACA
Found at i:24446 original size:21 final size:20
Alignment explanation
Indices: 24412--24458 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
24402 CCACTGGTGC
*
24412 CGATATTGAACCCTTCAGTAT
1 CGATACTGAACCC-TCAGTAT
* *
24433 CGATACTGACCCCTGAGTAT
1 CGATACTGAACCCTCAGTAT
24453 CGATAC
1 CGATAC
24459 CAATCTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
CGATACTGAACCCTCAGTAT
Found at i:26235 original size:20 final size:20
Alignment explanation
Indices: 26170--26241 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
26160 ATCAAAAGTT
26170 GGTATCGATACCA-GA-AGGG
1 GGTATCGATACCATGATA-GG
*
26189 GGTATC-AGTACCATAGTATAGT
1 GGTATCGA-TACCAT-G-ATAGG
*
26211 AGTATCGATACCATGATAGG
1 GGTATCGATACCATGATAGG
26231 GGTATCGATAC
1 GGTATCGATAC
26242 TATAGAGCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.02
19 11 0.26
20 14 0.33
21 2 0.05
22 13 0.30
23 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCATGATAGG
Found at i:26237 original size:95 final size:95
Alignment explanation
Indices: 26018--26241 Score: 290
Period size: 96 Copynumber: 2.3 Consensus size: 95
26008 TACCAAAATG
* * * *
26018 GTAGTATCAATACCATGGTAAGGGTATAGATACCATACTACATCGAATCTAAAATGGGTATCAAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGACAACATCGAATCTAAAATGGGTATCAAT
*
26083 ACCGGAAAGGGTATCAGTACCATAATAAATA
66 ACCAGAAAGGGTATCAGTACCATAAT-AATA
* * * *
26114 GTAGTATCGATATCATGGTAAGGGTATCGATACCAGCCAACATCGAATC-AAAAGTTGGTATCGA
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGACAACATCGAATCTAAAA-TGGGTATCAA
* *
26178 TACCAGAAGGGGGTATCAGTACCATAGT-ATA
65 TACCAGAA-AGGGTATCAGTACCATAATAATA
* *
26209 GTAGTATCGATACCATGATAGGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
26242 TATAGAGCCA
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
95 37 0.33
96 58 0.52
97 17 0.15
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAGACAACATCGAATCTAAAATGGGTATCAAT
ACCAGAAAGGGTATCAGTACCATAATAATA
Found at i:26716 original size:57 final size:57
Alignment explanation
Indices: 26576--27174 Score: 896
Period size: 57 Copynumber: 10.5 Consensus size: 57
26566 GTGCAAAATA
* * *
26576 TAAGAAATCATACTAAGTGTATGAATTTCAGATAAGGGC-TTTCATATAGGTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGAT-AGGGCGTTTCGTA-CGCTAAAATGT
* *
26634 TAAGAAATCATACTAAGTGTGTGAATTTCAGATAGGACGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
26691 TAAGAAATCATACTAAGTGTATGAATTTCAGATAAGGCGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * **
26748 TAAGAAATCATACTAAATGTATGAATTTTAGATAGGGCGTTTTGTATACTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
26805 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCATACGCTAAAATAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* ** *
26862 TAAGAAATCATACTAAGGGTATGAATTTCAGATAGGGCGTTTTATACGATAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
26919 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGAGTTTCGTACACTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
26976 TAAGAAATC-TACTAAGTGTATGAATTTTAGATAGGGCGTTTCATATGCTAAAATAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
27032 TAAGAAATCATACTAAGTGTATGAATTTCAGATAAGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
27089 TAAGAAATCATACTAAGTGTATGAATTTCATATAGGGCGTTTCGTTCGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
27146 TAAGAAACCATACTAAGTGTATGAATTTC
1 TAAGAAATCATACTAAGTGTATGAATTTC
27175 TGGATTGGAT
Statistics
Matches: 489, Mismatches: 50, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
56 50 0.10
57 401 0.82
58 38 0.08
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:27748 original size:68 final size:68
Alignment explanation
Indices: 27610--27748 Score: 154
Period size: 68 Copynumber: 2.0 Consensus size: 68
27600 AAAAGATTAA
* * **
27610 GAGGCCTAACTGAGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGAGAATATGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTACC
*
27675 TTT
66 ATT
* * * * * **
27678 GAGGCCTAGCTGGGAATTTGACAGAAA-GATGTCAATTATGCCATTTAGATGAACGGTTAAGTAC
1 GAGGCCTAACTGAGAATATGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAAGACTAAGTAC
27742 CATT
65 CATT
27746 GAG
1 GAG
27749 TAAAAAAATA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
67 1 0.02
68 57 0.98
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (68 bp):
GAGGCCTAACTGAGAATATGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTACC
ATT
Found at i:27958 original size:45 final size:45
Alignment explanation
Indices: 27908--28020 Score: 163
Period size: 45 Copynumber: 2.5 Consensus size: 45
27898 GTATAATTGT
* * *
27908 ATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCCATAAATGAAACGTATAATAATGTATAAAAGAC
*
27953 ATGAAAGGATGCCATAAATGAAAGGTATAATAATGTATAAAAGAC
1 ATGAAAGGATGCCATAAATGAAACGTATAATAATGTATAAAAGAC
* * *
27998 ATGTAAGGATGACATAATTGAAA
1 ATGAAAGGATGCCATAAATGAAA
28021 TGCATATAGC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (45 bp):
ATGAAAGGATGCCATAAATGAAACGTATAATAATGTATAAAAGAC
Found at i:31571 original size:17 final size:18
Alignment explanation
Indices: 31549--31583 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31539 CAATACCATA
31549 GGAAGGG-TATCGATACC
1 GGAAGGGATATCGATACC
*
31566 GGAAGGGATATCGGTACC
1 GGAAGGGATATCGATACC
31584 ATAATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.17, G:0.37, T:0.17
Consensus pattern (18 bp):
GGAAGGGATATCGATACC
Found at i:31715 original size:20 final size:22
Alignment explanation
Indices: 31667--31726 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
31657 ATAACAGAAG
*
31667 GGGGTATCGGTACCATAGTATA
1 GGGGTATCGATACCATAGTATA
**
31689 GTAGTATCGATACCAT-G-ATA
1 GGGGTATCGATACCATAGTATA
*
31709 GGGGTATCGATACTATAG
1 GGGGTATCGATACCATAG
31727 AGCCAGAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 16 0.52
21 2 0.06
22 13 0.42
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (22 bp):
GGGGTATCGATACCATAGTATA
Found at i:32131 original size:57 final size:57
Alignment explanation
Indices: 32063--32603 Score: 764
Period size: 57 Copynumber: 9.5 Consensus size: 57
32053 GTGCAAAATA
* *
32063 TAAGAAATCATACTAAGGGTATGAATTTCAGATAGGGCGTTTCATATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
* * * * * ** * *
32120 TAATAAATCATACTAAGTGTACGAGTTTTAGAAATTGTGTTTCGTACT-ATAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTA-TGCTAAAATGT
* * *
32177 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
* * *
32234 TAAGAAATCATACTAAGTGTATGAATTTCATG-TAGGGCGTTTGGTACT-TTAAACTGT
1 TAAGAAATCATACTAAGTGTATGAATTTCA-GATAGGGCGTTTCGTA-TGCTAAAATGT
* *
32291 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
* *
32348 TAAGAAATCATACTAAGTGTATGAATTTCAGAGAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
* * *
32405 TAATAAATCATACTGAGTGTATGAATTTCAGATAGGGTGTTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
* *
32462 TACGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
* *
32519 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTATGCTATAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
* *
32576 TAAGAAATCATACTAATTGTTTGAATTT
1 TAAGAAATCATACTAAGTGTATGAATTT
32604 TTGTATTGGA
Statistics
Matches: 428, Mismatches: 50, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
56 1 0.00
57 425 0.99
58 2 0.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
Found at i:33308 original size:45 final size:45
Alignment explanation
Indices: 33257--33371 Score: 169
Period size: 45 Copynumber: 2.6 Consensus size: 45
33247 GCATAATTGT
*
33257 ATGAAAGGATGCAATAAATGAAATGTATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCAATAAATGAAATGTATAATAGTGTATAAAAGGC
* *
33302 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATAAAAGGC
1 ATGAAAGGATGCAATAAATGAAATGTATAATAGTGTATAAAAGGC
* *
33347 ATGTAAGGATG-ACATAATTGAAATG
1 ATGAAAGGATGCA-ATAAATGAAATG
33372 CATATAGGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.24
Consensus pattern (45 bp):
ATGAAAGGATGCAATAAATGAAATGTATAATAGTGTATAAAAGGC
Found at i:35221 original size:29 final size:30
Alignment explanation
Indices: 35165--35222 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
35155 GTGAATCCAC
* *
35165 AACTTTTCCAAAATTACTAATTGTTCCCCG
1 AACTTTTCCAAAATTACTAAATGGTCCCCG
35195 AACTTTT-CAAAATTAC-AGAATGGTCCCC
1 AACTTTTCCAAAATTACTA-AATGGTCCCC
35223 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 17 0.68
30 7 0.28
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (30 bp):
AACTTTTCCAAAATTACTAAATGGTCCCCG
Found at i:37715 original size:95 final size:95
Alignment explanation
Indices: 37515--37708 Score: 223
Period size: 95 Copynumber: 2.0 Consensus size: 95
37505 GTTAAGGCAA
*
37515 TATCGATACCATTGTAAGGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCGATATC
1 TATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCGATATC
** * * * *
37580 GTAAGGGGTATTGATTCCATAGTATAGTAG
66 CCAAGGAGTATCGATACCATAGTATAGAAG
* * *
37610 TATCGATACCATGGTACGGGTATCGATACC-AGGAAACATCG-AGCTTAATTTTGGTATCGATA-
1 TATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAATC-TAATTTTGGTATCGATAT
* * *
37672 CCCAGAGGAAGTATCGGTACTATAGTATTGAAG
65 CCCA-AGG-AGTATCGATACCATAGTATAGAAG
37705 TATC
1 TATC
37709 AGTACCAAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
93 4 0.05
94 30 0.36
95 49 0.59
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (95 bp):
TATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCGATATC
CCAAGGAGTATCGATACCATAGTATAGAAG
Found at i:38242 original size:45 final size:45
Alignment explanation
Indices: 38142--38463 Score: 405
Period size: 45 Copynumber: 7.2 Consensus size: 45
38132 TGAACATAAT
* * * * * *
38142 AATGTATATGGGTGCATTATCGACA-TAAAGGATGCCATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* * * *
38186 AATGTATATGGGTACATTATCAACAGAAAAATTTACTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* * *
38231 AATGCATATGGGTGCATTATCAAGAGAAAAGTATGCCATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* *
38276 AATGCATATGGGTGCATTATCAACAGAAAAGTATGTTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
**
38321 AATATATATGGGTACATTATCAACA-AAAAGTATGCTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* * * * *
38365 ATTGTATATGGGTACATTATCAACATAAAAGTATGATATAGTTAA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* *
38410 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTAAA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTT-GA
38456 AATGCATA
1 AATGCATA
38464 ATGGTGCATT
Statistics
Matches: 244, Mismatches: 31, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
44 64 0.26
45 170 0.70
46 10 0.04
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
Found at i:38387 original size:134 final size:135
Alignment explanation
Indices: 38142--38452 Score: 446
Period size: 134 Copynumber: 2.3 Consensus size: 135
38132 TGAACATAAT
* * * * * *
38142 AATGTATATGGGTGCATTATCGACA-TAAAGGATGCCATAGTTGAAATGTATATGGGTACATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATATATATGGGTACATTAT
* * * *
38206 CAACAGAAAAATTTACTATAGTTGAAATGCATATGGGTGCATTATCAAGAGAAAAGTATGCCATA
66 CAACAGAAAAATATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGACATA
*
38271 GTTGA
131 GTTAA
*
38276 AATGCATATGGGTGCATTATCAACAGAAAAGTATGTTATAGTTGAAATATATATGGGTACATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATATATATGGGTACATTAT
* * * * * *
38341 CAACA-AAAAGTATGCTATAGTTGAATTGTATATGGGTACATTATCAACATAAAAGTATGATATA
66 CAACAGAAAAATATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGACATA
38405 GTTAA
131 GTTAA
38410 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTT
38453 AAAAATGCAT
Statistics
Matches: 157, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
134 118 0.75
135 39 0.25
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (135 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATATATATGGGTACATTAT
CAACAGAAAAATATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGACATA
GTTAA
Found at i:41809 original size:11 final size:12
Alignment explanation
Indices: 41770--41811 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
41760 CTTTACTTAG
*
41770 GAAGAGGAAGAT
1 GAAGAGGAAAAT
41782 GAAGAGAGAAAAT
1 GAAGAG-GAAAAT
*
41795 GAAG-GGAACAT
1 GAAGAGGAAAAT
41806 GAAGAG
1 GAAGAG
41812 TGTTAGGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.35
12 8 0.31
13 9 0.35
ACGTcount: A:0.52, C:0.02, G:0.38, T:0.07
Consensus pattern (12 bp):
GAAGAGGAAAAT
Done.