Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000342.1 Hibiscus syriacus cultivar Beakdansim tig00000633_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: 58257
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2343 original size:24 final size:24
Alignment explanation
Indices: 2316--2369 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2306 GTATTCGAAA
* *
2316 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2340 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2364 TTTGAT
1 TTTGAT
2370 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2556 original size:12 final size:12
Alignment explanation
Indices: 2539--2563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2529 TTCATATCCT
2539 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2551 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2563 G
1 G
2564 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4881 original size:33 final size:33
Alignment explanation
Indices: 4839--4964 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
4829 GGAAATTACT
4839 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
4872 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
4904 TTTCGCAATGCGAAATG-AAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4937 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4965 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
32 27 0.33
33 56 0.67
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4945 original size:65 final size:66
Alignment explanation
Indices: 4840--4971 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 66
4830 GAAATTACTA
*
4840 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4905 T
66 T
*
4906 TCGCAATGCGAAATG-AAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
4970 T
66 T
4971 T
1 T
4972 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 49 0.77
66 15 0.23
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:5146 original size:14 final size:14
Alignment explanation
Indices: 5127--5163 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5117 CATCAATTAA
5127 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5141 ACAAATCACCTTTT
1 ACAAATCAACTTTT
5155 ACAAATCAA
1 ACAAATCAA
5164 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:8669 original size:33 final size:33
Alignment explanation
Indices: 8612--8710 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
8602 ACGAGATAAT
* *
8612 GAGAATCGCAACGAGGAAATGACTATCGCAACGA
1 GAGAATCGCAACG-CGAAATGACTATCGCAACCA
*
8646 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
8679 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
8711 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:8752 original size:19 final size:19
Alignment explanation
Indices: 8587--8743 Score: 118
Period size: 20 Copynumber: 8.6 Consensus size: 19
8577 TCTTTTGGTT
*
8587 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
8606 GATAATGAGAATCGCAACGAG
1 GA-AATGAAAATCGCAACG-C
**
8627 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
8644 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
8660 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
8678 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
8693 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
8713 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
8732 GAAATGAAAATC
1 GAAATGAAAATC
8744 ACAATGCGAT
Statistics
Matches: 110, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 2 0.02
17 1 0.01
18 3 0.03
19 35 0.32
20 45 0.41
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:8770 original size:19 final size:18
Alignment explanation
Indices: 8748--8814 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 18
8738 AAAATCACAA
*
8748 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
8767 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTTATTTCGCGT
*
8786 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
8806 TGCGATTTT
1 TGCGATTTT
8815 CATTCTCGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 26 0.62
20 15 0.36
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:9415 original size:20 final size:20
Alignment explanation
Indices: 9330--9463 Score: 144
Period size: 20 Copynumber: 6.7 Consensus size: 20
9320 CGCTATGTAA
* * *
9330 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
9350 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
9370 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
9391 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
9411 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
9431 ATCGCATTACGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
9451 ATCGCATTGCGAT
1 ATCGCATTGCGAT
9464 TTTCCCAATT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 82 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:9496 original size:20 final size:21
Alignment explanation
Indices: 9452--9503 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
9442 ATAGTCAGTA
*
9452 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
9473 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
9493 TCGCATTGCGA
1 TCGCATTGCGA
9504 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:9503 original size:81 final size:81
Alignment explanation
Indices: 9330--9484 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
9320 CGCTATGTAA
* * * * * ** *
9330 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 ATCGCATTGCGAAAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
9395 CATTGCGATAGTAAGT
66 CATTGCGATAGTAAGT
* * *
9411 ATCGCATTGCGATAGTCAGTATCGCATTACGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT-CCAATATC
9475 GCATTGCGAT
65 GCATTGCGAT
9485 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
81 60 0.97
82 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (81 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
CATTGCGATAGTAAGT
Found at i:9574 original size:21 final size:21
Alignment explanation
Indices: 9534--9574 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9524 ATTGTATACC
**
9534 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
9555 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
9575 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:9766 original size:22 final size:22
Alignment explanation
Indices: 9732--9773 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9722 GTTGGGGTTA
*
9732 AAAAATAAGAATTAAATAAAAG
1 AAAAACAAGAATTAAATAAAAG
*
9754 AAAAACAATAATTAAATAAA
1 AAAAACAAGAATTAAATAAA
9774 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAACAAGAATTAAATAAAAG
Found at i:10453 original size:19 final size:19
Alignment explanation
Indices: 10397--10459 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
10387 CTATTTAAAC
**
10397 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
10417 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
10437 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
10456 TAAA
1 TAAA
10460 CTAAAATTCA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:13866 original size:31 final size:31
Alignment explanation
Indices: 13828--13950 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
13818 CCCGAAGGAC
* *
13828 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
13859 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
13890 CAGTCCGTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
13921 CAGTCCGTATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
13951 CCCTCGACCC
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:15113 original size:13 final size:15
Alignment explanation
Indices: 15082--15117 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
15072 TTCACACGTG
15082 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
15097 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
15109 GAGAAGAGA
1 GAGAAGAGA
15118 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:18195 original size:31 final size:31
Alignment explanation
Indices: 18157--18279 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
18147 CCCGAAGGAC
* *
18157 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
18188 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
18219 CAGTCCGTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
18250 CAGTCCGTATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
18280 CCCTCGACCC
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:19446 original size:13 final size:15
Alignment explanation
Indices: 19415--19450 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
19405 TTCACACGTG
19415 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
19430 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
19442 GAGAAGAGA
1 GAGAAGAGA
19451 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:22561 original size:15 final size:15
Alignment explanation
Indices: 22541--22569 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22531 CTCTTATTCT
22541 TCCTGATGTGCGTCA
1 TCCTGATGTGCGTCA
22556 TCCTGATGTGCGTC
1 TCCTGATGTGCGTC
22570 TTTTTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.28, G:0.28, T:0.34
Consensus pattern (15 bp):
TCCTGATGTGCGTCA
Found at i:24357 original size:21 final size:22
Alignment explanation
Indices: 24324--24364 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
24314 TTGTGGTTAA
24324 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
24346 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
24365 CAAAATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:24364 original size:25 final size:24
Alignment explanation
Indices: 24322--24369 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
24312 AGTTGTGGTT
* *
24322 AAAAAAATAAGAATTAAATAAAAG
1 AAAAAAATAAGAAATAAACAAAAG
*
24346 AAAAAAATAATTAAATAAACAAAA
1 AAAAAAATAA-GAAATAAACAAAA
24370 TAAAGAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAAATAAGAAATAAACAAAAG
Found at i:25079 original size:75 final size:76
Alignment explanation
Indices: 25012--25175 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 76
25002 AAAAAATAAT
* *
25012 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
25076 AAAATATAAAA
66 AAAATATAAAA
*
25087 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
25151 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
25163 ATATTATCCTAAA
1 ATAATATCCTAAA
25176 TTTGAGTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 32 0.40
76 48 0.60
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:34765 original size:14 final size:14
Alignment explanation
Indices: 34746--34777 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
34736 CAATAATTAA
34746 AATAAATATACAAT
1 AATAAATATACAAT
34760 AATAAATATACAAT
1 AATAAATATACAAT
34774 AATA
1 AATA
34778 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAAATATACAAT
Found at i:46718 original size:29 final size:30
Alignment explanation
Indices: 46658--46750 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 30
46648 ATTTAAGTAT
*
46658 CACATT-GAATATTTTGTCAAAGTAGAGGTAC
1 CACATTAG-ATATTTTGT-AAAGTACAGGTAC
46689 CACATTAGATATTTT-TAAAGTACAGGTAC
1 CACATTAGATATTTTGTAAAGTACAGGTAC
* * *
46718 CATATAAGATATTTTGATAAAATACAGGTAC
1 CACATTAGATATTTTG-TAAAGTACAGGTAC
46749 CA
1 CA
46751 AATGCGACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 25 0.45
30 1 0.02
31 28 0.51
32 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
CACATTAGATATTTTGTAAAGTACAGGTAC
Found at i:49099 original size:23 final size:24
Alignment explanation
Indices: 49072--49118 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
49062 AAACCAAAAT
* *
49072 AAATTAAATAAATTATA-AATATA
1 AAATTAAAAAAATGATAGAATATA
49095 AAATTAAAAAAATGATAGAATATA
1 AAATTAAAAAAATGATAGAATATA
49119 TAAGTAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATTAAAAAAATGATAGAATATA
Found at i:49680 original size:38 final size:39
Alignment explanation
Indices: 49638--49723 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
49628 CATTTTCCTT
*
49638 AACATTTTTGGTTGAACA-AAAAATATTACATTCTTCAA
1 AACATTTTCGGTTGAACACAAAAATATTACATTCTTCAA
** * *
49676 AACATTTTCGGTTGCTCATCAAAAATATTATATTCTTCGA
1 AACATTTTCGGTTGAACA-CAAAAATATTACATTCTTCAA
*
49716 TACATTTT
1 AACATTTT
49724 AGGGTTCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
38 15 0.38
40 25 0.62
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (39 bp):
AACATTTTCGGTTGAACACAAAAATATTACATTCTTCAA
Found at i:51763 original size:25 final size:26
Alignment explanation
Indices: 51728--51780 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
51718 CATCCTCCTG
*
51728 AAATGCTTTTGCT-GGATATTCATTTC
1 AAATGCTTTTGCTGGGA-ATCCATTTC
*
51754 AAATG-TTTTGTTGGGAATCCATTTC
1 AAATGCTTTTGCTGGGAATCCATTTC
51779 AA
1 AA
51781 GTAGGGGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (26 bp):
AAATGCTTTTGCTGGGAATCCATTTC
Found at i:57368 original size:31 final size:31
Alignment explanation
Indices: 57310--57394 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
57300 AATTGATCAC
* *
57310 TAACATTATCGATTTATAAC-AAAATGGTCT
1 TAACGTTATTGATTTATAACAAAAATGGTCT
57340 TAACGTTATTGATTTATAACAAAAATGGTCT
1 TAACGTTATTGATTTATAACAAAAATGGTCT
* *
57371 TAACGATATTAATTTATAACAAAA
1 TAACGTTATTGATTTATAACAAAA
57395 TAGTTACTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 18 0.36
31 32 0.64
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (31 bp):
TAACGTTATTGATTTATAACAAAAATGGTCT
Done.