Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001353.1 Hibiscus syriacus cultivar Beakdansim tig00002636_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: 68974
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:946 original size:3 final size:3
Alignment explanation
Indices: 933--971 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
923 ATTAATCAAT
933 ATA AT- ATA ATA ATA ATA ATA ATA AT- ATA ATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A
972 AGTAACAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1777 original size:17 final size:17
Alignment explanation
Indices: 1744--1777 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1734 ATAATTTAAT
*
1744 TTTAAAAAAATTAAAAA
1 TTTAAAAAAATAAAAAA
*
1761 TTTAAAACAATAAAAAA
1 TTTAAAAAAATAAAAAA
1778 ATAGTTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TTTAAAAAAATAAAAAA
Found at i:4643 original size:54 final size:54
Alignment explanation
Indices: 4521--4645 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 54
4511 TTGAAAGATA
* * *
4521 GTATCGATACCCTTAAAACATCGATTGCCAGATTGATATCGGTACCTTGAGGAG
1 GTATCGATACCCTTGAAACATCGAATGCCAGATTGATATCGGTACCATGAGGAG
* * * *
4575 GTATAGATACCCTTGAAACATCGAATGCTA-TTTCGGTATCGGTACCATGAGGAG
1 GTATCGATACCCTTGAAACATCGAATGCCAGATT-GATATCGGTACCATGAGGAG
*
4629 GTATCGATGCCCTTGAA
1 GTATCGATACCCTTGAA
4646 TGGTAGTATC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 2 0.03
54 59 0.97
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (54 bp):
GTATCGATACCCTTGAAACATCGAATGCCAGATTGATATCGGTACCATGAGGAG
Found at i:5054 original size:21 final size:21
Alignment explanation
Indices: 5028--5078 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
5018 TTATTATGGA
5028 AATGTGAACTATGAATAAGTG
1 AATGTGAACTATGAATAAGTG
* * *
5049 AATGTGAACTTTGAATCATTG
1 AATGTGAACTATGAATAAGTG
5070 AATGTGAAC
1 AATGTGAAC
5079 AAACTCTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (21 bp):
AATGTGAACTATGAATAAGTG
Found at i:6221 original size:2 final size:2
Alignment explanation
Indices: 6214--6299 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
6204 TAGTATATGG
6214 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
6256 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
6298 AT
1 AT
6300 TACATGATTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8214 original size:21 final size:21
Alignment explanation
Indices: 8190--8234 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8180 GGGTCTTATA
*
8190 TGGTCCTTCGAGACAAATATG
1 TGGTCCTCCGAGACAAATATG
* *
8211 TGGTCCTCCGGGATAAATATG
1 TGGTCCTCCGAGACAAATATG
8232 TGG
1 TGG
8235 CACTTCGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (21 bp):
TGGTCCTCCGAGACAAATATG
Found at i:8249 original size:21 final size:22
Alignment explanation
Indices: 8228--8295 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 22
8218 CCGGGATAAA
8228 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
*
8250 CTATATGGTCA-TTCGG-G-ATAAT
1 -TATGTGG-CACTTCGGTGCA-AAT
8272 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
8294 TA
1 TA
8296 CGAGCTGTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 10 0.26
23 12 0.32
24 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Found at i:8585 original size:68 final size:67
Alignment explanation
Indices: 8472--8607 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 67
8462 CTAAATAAGA
*
8472 TTTTTGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTTTTT
1 TTTTTGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTGTTT
8537 TT
66 TT
*
8539 TTTTCTGTTAATAAGTTAGCACTATTAGTATTGCTTCACTAAGTCATCGACTTAGCGTGTGTGTT
1 TTTT-TGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTGTT
8604 TTT
65 TTT
8607 T
1 T
8608 CATGCGTAGG
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 4 0.06
68 62 0.94
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (67 bp):
TTTTTGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTGTTT
TT
Found at i:14552 original size:20 final size:20
Alignment explanation
Indices: 14505--14561 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
14495 ATACATGTTG
*
14505 ATGATGGTATCGATACCGTA
1 ATGATAGTATCGATACCGTA
* *
14525 AGGGTAGTATCGATACC-TGA
1 ATGATAGTATCGATACCGT-A
*
14545 ATGATAGTATTGATACC
1 ATGATAGTATCGATACC
14562 CTTGAAACAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (20 bp):
ATGATAGTATCGATACCGTA
Found at i:14560 original size:40 final size:41
Alignment explanation
Indices: 14480--14561 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 41
14470 TGAGTATTTT
* * *
14480 GTAAGGGTTGTATCGATACATGTTGATGATGGTATCGATACC
1 GTAAGGGTAGTATCGATACATG-TAATGATAGTATCGATACC
* *
14522 GTAAGGGTAGTATCGATACCTG-AATGATAGTATTGATACC
1 GTAAGGGTAGTATCGATACATGTAATGATAGTATCGATACC
14562 CTTGAAACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 15 0.43
42 20 0.57
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (41 bp):
GTAAGGGTAGTATCGATACATGTAATGATAGTATCGATACC
Found at i:14637 original size:22 final size:20
Alignment explanation
Indices: 14605--14657 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
14595 CCATGAGGAG
*
14605 GTATCGATACCCTTGAAGGGTA
1 GTATCGATACCATT--AGGGTA
*
14627 GTATCGGTACCATTAGGGTA
1 GTATCGATACCATTAGGGTA
*
14647 GTACCGATACC
1 GTATCGATACC
14658 TCCAAGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
22 12 0.44
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
GTATCGATACCATTAGGGTA
Found at i:14646 original size:20 final size:20
Alignment explanation
Indices: 14585--14649 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 20
14575 ATGTTATTTC
*
14585 AGTATCGGTACCATGA-GG-
1 AGTATCGGTACCATTAGGGT
* *
14603 AGGTATCGATACCCTTGAAGGGT
1 A-GTATCGGTACCATT--AGGGT
14626 AGTATCGGTACCATTAGGGT
1 AGTATCGGTACCATTAGGGT
14646 AGTA
1 AGTA
14650 CCGATACCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 11 0.30
20 9 0.24
21 1 0.03
22 14 0.38
23 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (20 bp):
AGTATCGGTACCATTAGGGT
Found at i:15032 original size:21 final size:21
Alignment explanation
Indices: 15006--15056 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
14996 ATATTATGGA
15006 AATGTGAACTTTGAATAAGTG
1 AATGTGAACTTTGAATAAGTG
* *
15027 AATGTGAACTTTGAATCATTG
1 AATGTGAACTTTGAATAAGTG
*
15048 AATATGAAC
1 AATGTGAAC
15057 AAACTCTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (21 bp):
AATGTGAACTTTGAATAAGTG
Found at i:15216 original size:21 final size:21
Alignment explanation
Indices: 15190--15259 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
15180 TCGAGGGTCT
15190 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
*
15211 TATGTGGTCCTTCGGGATAAA
1 TATGTGGTCCTTCGGGACAAA
* * *
15232 TATGTGGTTCTCCGGAACAAA
1 TATGTGGTCCTTCGGGACAAA
15253 TATGTGG
1 TATGTGG
15260 CACTTCAGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:15274 original size:42 final size:41
Alignment explanation
Indices: 15190--15318 Score: 109
Period size: 42 Copynumber: 3.0 Consensus size: 41
15180 TCGAGGGTCT
* * * *
15190 TATGTGGTCCTTCGGGACAAATATGTGGTC-CTTCGGGATAAA
1 TATGTGGTTCTCCGGAACAAATATGTGG-CACTTCGTG-TAAA
15232 TATGTGGTTCTCCGGAACAAATATGTGGCACTTCAGTGTAAA
1 TATGTGGTTCTCCGGAACAAATATGTGGCACTTC-GTGTAAA
* * * *
15274 TCTATGTGGTCTTTCGGGAA-AATTATATGGCACTTCGGTGTAAA
1 --TATGTGGT-TCTCCGGAACAAATATGTGGCACTTC-GTGTAAA
15318 T
1 T
15319 TACGAGCTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 34 0.47
43 2 0.03
44 29 0.40
45 7 0.10
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (41 bp):
TATGTGGTTCTCCGGAACAAATATGTGGCACTTCGTGTAAA
Found at i:15319 original size:22 final size:22
Alignment explanation
Indices: 15257--15320 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
15247 AACAAATATG
* *
15257 TGGCACTTCAGTGTAAATCTATG
1 TGGCACTTCGGTGTAAAT-TATA
* *
15280 TGGTC-TTTCGG-GAAAATTATA
1 TGG-CACTTCGGTGTAAATTATA
15301 TGGCACTTCGGTGTAAATTA
1 TGGCACTTCGGTGTAAATTA
15321 CGAGCTGTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.03
21 11 0.34
22 12 0.38
23 7 0.22
24 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (22 bp):
TGGCACTTCGGTGTAAATTATA
Found at i:20071 original size:16 final size:16
Alignment explanation
Indices: 20052--20082 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20042 ATATAATATA
20052 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
20068 ATATTATGAATTATT
1 ATATAATGAATTATT
20083 AGATTTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:23622 original size:29 final size:29
Alignment explanation
Indices: 23580--23639 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
23570 AAACCCTAAT
23580 TTCAATTATTATATATATAAAAATCATTG
1 TTCAATTATTATATATATAAAAATCATTG
*
23609 TTCAATTATTATATATATAAAGATCATTG
1 TTCAATTATTATATATATAAAAATCATTG
23638 TT
1 TT
23640 TTATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (29 bp):
TTCAATTATTATATATATAAAAATCATTG
Found at i:24339 original size:21 final size:21
Alignment explanation
Indices: 24313--24360 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
24303 GCCCTGCAAA
*
24313 TAACGGAATTAA-TGGATTTTC
1 TAACGGAAGTAACT-GATTTTC
*
24334 TAACGGAAGTAACTGATTTTG
1 TAACGGAAGTAACTGATTTTC
24355 TAACGG
1 TAACGG
24361 GATTTTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (21 bp):
TAACGGAAGTAACTGATTTTC
Found at i:27998 original size:18 final size:18
Alignment explanation
Indices: 27967--28001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27957 GATTAGGGAA
*
27967 TATTTTATTAATTTTAAT
1 TATTTAATTAATTTTAAT
*
27985 TATTTAATTTATTTTAA
1 TATTTAATTAATTTTAA
28002 CTTGTATCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTAATTAATTTTAAT
Found at i:29375 original size:60 final size:60
Alignment explanation
Indices: 29276--29433 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
29266 TTTTAAATTG
* * * *
29276 GTCCTTAAACTTTTAAATATTTCAATTTTAT-TCTTAAACTATGA-CTATCATTCTAACGTA
1 GTCCTCAAACTTTTAAATATTTCAATTTCATCTC-AAAACTATGACCT-TCATTCTAAAGTA
* * *
29336 GTCCTCAAACTTTTAAATATTTCAATTTCATCTCAAAACTGTGACCTTCATTCTAAATTG
1 GTCCTCAAACTTTTAAATATTTCAATTTCATCTCAAAACTATGACCTTCATTCTAAAGTA
* * * * *
29396 GTCCCCAAACTTTTTGAACATTCCAATTTCATCCCAAA
1 GTCCTCAAAC-TTTTAAATATTTCAATTTCATCTCAAA
29434 CAATACATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 56 0.67
61 27 0.33
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
GTCCTCAAACTTTTAAATATTTCAATTTCATCTCAAAACTATGACCTTCATTCTAAAGTA
Found at i:29643 original size:29 final size:29
Alignment explanation
Indices: 29608--29704 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
29598 AGAGAGTCAT
29608 AGTTTAAGGATGAAATTAGAATGTTCAAA
1 AGTTTAAGGATGAAATTAGAATGTTCAAA
** * * *
29637 AGTTTAAGGACT-ACTTTAAAATGAGTC-AT
1 AGTTTAAGGA-TGAAATTAGAATG-TTCAAA
*
29666 AGTTTAAGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTAGAATGTTCAAA
*
29695 ATTTTAAGGA
1 AGTTTAAGGA
29705 CCAATTTAGA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 3 0.06
29 46 0.88
30 3 0.06
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTAGAATGTTCAAA
Found at i:29681 original size:58 final size:60
Alignment explanation
Indices: 29554--29730 Score: 223
Period size: 58 Copynumber: 3.0 Consensus size: 60
29544 GATGAATTTG
* * **
29554 AGGATGAAAGTAGAATATTAAAAAGTTTGGGGACAAATTTAGAAAGAGAGTCATAGTTTA
1 AGGATGAAATTAGAATATTCAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTTA
* * * *
29614 AGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTACTTTA-AAA-TGAGTCATAGTTTA
1 AGGATGAAATTAGAATATTCAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTTA
* * * * *
29672 AGGATGAAATTAGAATATTCAAAATTTTAAGGACCAATTTAGAATGAAAGTTATAGTTT
1 AGGATGAAATTAGAATATTCAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTT
29731 GGGGATATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
58 50 0.51
59 5 0.05
60 44 0.44
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (60 bp):
AGGATGAAATTAGAATATTCAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTTA
Found at i:29713 original size:29 final size:29
Alignment explanation
Indices: 29608--29716 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 29
29598 AGAGAGTCAT
** * *
29608 AGTTTAAGGATGAAATTAGAATGTTCAAA
1 AGTTTAAGGACCAATTTAGAATATTCAAA
* * * * *
29637 AGTTTAAGGACTACTTTAAAATGAGTC-AT
1 AGTTTAAGGACCAATTTAGAAT-ATTCAAA
** *
29666 AGTTTAAGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGACCAATTTAGAATATTCAAA
*
29695 ATTTTAAGGACCAATTTAGAAT
1 AGTTTAAGGACCAATTTAGAAT
29717 GAAAGTTATA
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
28 3 0.05
29 54 0.92
30 2 0.03
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.33
Consensus pattern (29 bp):
AGTTTAAGGACCAATTTAGAATATTCAAA
Found at i:32341 original size:76 final size:76
Alignment explanation
Indices: 32252--32404 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
32242 AAAACATATA
32252 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAAAAATAATACTTATACATACTTAC
1 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAAAAATAATACTTATACATACTTAC
32317 ATTAGTGTAAG
66 ATTAGTGTAAG
*
32328 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAGAAATAATACTTATACATACTTAC
1 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAAAAATAATACTTATACATACTTAC
32393 ATTAGTGTAAG
66 ATTAGTGTAAG
32404 T
1 T
32405 ATGATAAAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (76 bp):
TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAAAAATAATACTTATACATACTTAC
ATTAGTGTAAG
Found at i:32497 original size:2 final size:2
Alignment explanation
Indices: 32490--32527 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
32480 GACGCGTGAA
32490 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
32528 TAAGTTTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37731 original size:60 final size:59
Alignment explanation
Indices: 37630--37743 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 59
37620 GTATACACAT
* *
37630 ATAGTTTGGGATGAAATTGAAATGTTCAAAATGTTTGGGACTAATTTAAAATGAAGGTC
1 ATAGTTGGGGATGAAAATGAAATGTTCAAAATGTTTGGGACTAATTTAAAATGAAGGTC
* *
37689 ATAGTTGGAGGATGAAAAT-AAATTGTTTAAAA-GTTTGAGGACTAATTTAGAATGA
1 ATAGTTGG-GGATGAAAATGAAA-TGTTCAAAATGTTTG-GGACTAATTTAAAATGA
37744 CAGCCATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 15 0.31
60 33 0.69
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (59 bp):
ATAGTTGGGGATGAAAATGAAATGTTCAAAATGTTTGGGACTAATTTAAAATGAAGGTC
Found at i:37762 original size:60 final size:59
Alignment explanation
Indices: 37630--37765 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
37620 GTATACACAT
* * *
37630 ATAGTTTGGGATGAAATTGAAATGTTCAAAATGTTTGGGACTAATTTAAAATGAAGGTC
1 ATAGTTAGGGATGAAAATGAAATGTTCAAAATGTTTGGGACTAATTTAAAATGAAGGCC
* * *
37689 ATAGTTGGAGGATGAAAAT-AAATTGTTTAAAA-GTTTGAGGACTAATTTAGAATGACA-GCC
1 ATAGTTAG-GGATGAAAATGAAA-TGTTCAAAATGTTTG-GGACTAATTTAAAATGA-AGGCC
*
37749 ATAATTTAGGGATGAAA
1 AT-AGTTAGGGATGAAA
37766 TTATAACATA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
59 15 0.23
60 45 0.69
61 5 0.08
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.32
Consensus pattern (59 bp):
ATAGTTAGGGATGAAAATGAAATGTTCAAAATGTTTGGGACTAATTTAAAATGAAGGCC
Found at i:43324 original size:20 final size:21
Alignment explanation
Indices: 43278--43324 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
43268 TAAAAATAAT
* * *
43278 TTATTTGTATTAAAATTTATA
1 TTATTTTTATTAAAATTAAAA
43299 TT-TTTTTATT-AAATTAAAA
1 TTATTTTTATTAAAATTAAAA
43318 TTATTTT
1 TTATTTT
43325 CTCTTTTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.41
20 11 0.50
21 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATTTTTATTAAAATTAAAA
Found at i:47200 original size:137 final size:138
Alignment explanation
Indices: 46965--47224 Score: 380
Period size: 137 Copynumber: 1.9 Consensus size: 138
46955 ATAAATTGTA
* * *
46965 TATACAAGTTATCGATCAATTTTGTTTAATGCATAATGGTGTATTTTCGTATCAGTACTATGTGT
1 TATAAAAGTTATCGATCAATTTTGTTTAATGCATAATGGTGTATTTTCGTATCAGTACTATATAT
** * *
47030 TCTTTCGGCACTAGATGTGCAACTATGGTATTCATAATGAGTTTGTGAATTACCATTTCGATATA
66 AATTTCGGCACTAGATGTGCAACCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGATATA
47095 CAATTATG
131 CAATTATG
* * *
47103 TATAAAAG-TATCGATCGATTTTTTTTAATGCATAATGGTGTATTTTTGTATCAGTACTATATAT
1 TATAAAAGTTATCGATCAATTTTGTTTAATGCATAATGGTGTATTTTCGTATCAGTACTATATAT
* * *
47167 AATTTCGGCACTATG-TGTGCATCCATGGAATTCATAATGGGTTTGTGAATTTCCATTT
66 AATTTCGGCACTA-GATGTGCAACCATGGAATTCATAATGAGTTTGTGAATTACCATTT
47225 TGGCACTTAG
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
137 100 0.93
138 8 0.07
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (138 bp):
TATAAAAGTTATCGATCAATTTTGTTTAATGCATAATGGTGTATTTTCGTATCAGTACTATATAT
AATTTCGGCACTAGATGTGCAACCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGATATA
CAATTATG
Found at i:54100 original size:20 final size:19
Alignment explanation
Indices: 54075--54115 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
54065 GAGTCGGGTT
*
54075 GACCGGTTCGAGTCGGTCCA
1 GACCGGTTCGA-CCGGTCCA
*
54095 GACCGGTTGGACCGGTCCA
1 GACCGGTTCGACCGGTCCA
54114 GA
1 GA
54116 AGCTCCAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.17, C:0.29, G:0.37, T:0.17
Consensus pattern (19 bp):
GACCGGTTCGACCGGTCCA
Found at i:56469 original size:19 final size:19
Alignment explanation
Indices: 56414--56472 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
56404 CAGATATTAG
* * *
56414 AGATAATAAAAGAAATCAG
1 AGATCATAACAGAAATCAA
* *
56433 AGATCATAACATATATCAA
1 AGATCATAACAGAAATCAA
*
56452 AGTTCATAACAGAAATCAA
1 AGATCATAACAGAAATCAA
56471 AG
1 AG
56473 GTCAGACTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (19 bp):
AGATCATAACAGAAATCAA
Found at i:59113 original size:23 final size:23
Alignment explanation
Indices: 59086--59153 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
59076 CCACATAGAA
59086 TATCCCGAGGACCGCGTAGAAAT
1 TATCCCGAGGACCGCGTAGAAAT
* *
59109 TATCCCCAAGGACCACGTA-AAAT
1 TAT-CCCGAGGACCGCGTAGAAAT
*
59132 TATCCCGAAGGACCGCATAGAA
1 TATCCCG-AGGACCGCGTAGAA
59154 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 3 0.08
23 19 0.51
24 15 0.41
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (23 bp):
TATCCCGAGGACCGCGTAGAAAT
Found at i:59122 original size:24 final size:24
Alignment explanation
Indices: 59093--59153 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
59083 GAATATCCCG
59093 AGGACCGCGTAGAAATTATCCCCA
1 AGGACCGCGTAGAAATTATCCCCA
* *
59117 AGGACCACGTA-AAATTATCCCGA
1 AGGACCGCGTAGAAATTATCCCCA
*
59140 AGGACCGCATAGAA
1 AGGACCGCGTAGAA
59154 CCCTCGACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (24 bp):
AGGACCGCGTAGAAATTATCCCCA
Found at i:65264 original size:23 final size:23
Alignment explanation
Indices: 65237--65281 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
65227 GAAAATTCAA
*
65237 AATTT-CATTAAATAAACTAAAAT
1 AATTTACA-TAAATAAAATAAAAT
65260 AATTTACATAAATAAAATAAAA
1 AATTTACATAAATAAAATAAAA
65282 AAAAAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AATTTACATAAATAAAATAAAAT
Done.