Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003573.1 Hibiscus syriacus cultivar Beakdansim tig00007542_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: 85273
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:5402 original size:213 final size:215
Alignment explanation
Indices: 5021--5457 Score: 695
Period size: 214 Copynumber: 2.0 Consensus size: 215
5011 TCATATATTT
* *
5021 GGGTCGGGACGGGTCGGGTTTAGGGTGAAAAAAATTAGACCGACCCGAAAATATATATAATTCGG
1 GGGTCGGGTCGGGTCGGGTTTAGGGTGAAAAAAATCAGACCGACCCGAAAATATATATAATTCGG
*
5086 ATCAGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATATTTTTTATTATTTCGGGTTGGC
66 ATCAGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATATTTTTTATTATTTCGGGTGGGC
* *
5151 CGGATTTCTAATTCATATATTTGGGTCGGTCAGATGAAACTTTATTTTGTTCTGGTCGGG-TTTT
131 CGGATTTCTAATTCATATATTCGGGTCGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTTTTT
*
5215 TTAAGTGTGATATTTGGGTC
196 TTAAGTGTGATATTCGGGTC
* * * *
5235 GGGTTGGGTCGGGTTCGGGTTTAGGGTGAAAAAAA-CCGGCCGACCCGAAAATATATATAATTTG
1 GGGTCGGGTCGGG-TCGGGTTTAGGGTGAAAAAAATCAGACCGACCCGAAAATATATATAATTCG
*
5299 GGTC-GGTCGGATTAAGTCACTGTTTTTATTAAAT-AAAA-ATATTTTTTATTATTTCGGGTCGG
65 GATCAGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATATTTTTTATTATTTCGGGT-GG
* *
5361 GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTT
129 GCCGGATTTCTAATTCATATATTCGGGTC-GGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTT
5426 TTTTTAAGTGTGATATTCGGGTC
193 TTTTTAAGTGTGATATTCGGGTC
5449 GGGTCGGGT
1 GGGTCGGGT
5458 TTAGGGTAAA
Statistics
Matches: 205, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
211 21 0.10
212 32 0.16
213 61 0.30
214 70 0.34
215 21 0.10
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (215 bp):
GGGTCGGGTCGGGTCGGGTTTAGGGTGAAAAAAATCAGACCGACCCGAAAATATATATAATTCGG
ATCAGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATATTTTTTATTATTTCGGGTGGGC
CGGATTTCTAATTCATATATTCGGGTCGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTTTTT
TTAAGTGTGATATTCGGGTC
Found at i:6005 original size:20 final size:20
Alignment explanation
Indices: 5938--6066 Score: 109
Period size: 21 Copynumber: 6.3 Consensus size: 20
5928 ATTTCCAGAT
* *
5938 TCGCAATGCGATTTCCTAAA
1 TCGCAATGCGATTACGTAAA
** * * *
5958 TTCGCGTTGCGATTTTCCTAAT
1 -TCGCAATGCGA-TTACGTAAA
5980 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
6000 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
*
6021 TCGCAATGCGATTACGT-AT
1 TCGCAATGCGATTACGTAAA
*
6040 TCGCATTGCGATTTACGT-AA
1 TCGCAATGCGA-TTACGTAAA
6060 TCGCAAT
1 TCGCAAT
6067 ACTGAATTTC
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
19 11 0.12
20 34 0.38
21 36 0.40
22 8 0.09
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:6927 original size:23 final size:24
Alignment explanation
Indices: 6900--6952 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6890 GTATTCAAAA
6900 TTTGATCTTGGTC-ATACCCGGAT
1 TTTGATCTTGGTCAATACCCGGAT
*
6923 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAT
6947 TTTGAT
1 TTTGAT
6953 GATTTTCAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAT
Found at i:9473 original size:20 final size:19
Alignment explanation
Indices: 9445--9499 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
9435 CAATCATCTT
*
9445 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
9465 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
9484 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
9500 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:9514 original size:33 final size:33
Alignment explanation
Indices: 9472--9598 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
9462 GGAAATGACT
9472 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
9505 ATCGCAATGCGAAATGAAAATCGCAAAGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
9538 ATCGCAATGCGAAATAAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
9571 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
9599 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:9528 original size:19 final size:18
Alignment explanation
Indices: 9452--9602 Score: 83
Period size: 19 Copynumber: 8.7 Consensus size: 18
9442 CTTAATGTCT
**
9452 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
9472 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
9491 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
9505 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
9524 ATCGCAA---AGA-GAGA
1 ATCGCAAGCGAAATGAAA
*
9538 ATCGCAATGCGAAATAAAA
1 ATCGCAA-GCGAAATGAAA
**
9557 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
9571 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
9590 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
9603 TTTAGTTTCG
Statistics
Matches: 100, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
14 26 0.26
15 6 0.06
16 4 0.04
17 4 0.04
18 6 0.06
19 45 0.45
20 9 0.09
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:9946 original size:25 final size:25
Alignment explanation
Indices: 9918--9965 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
9908 CAACATTTGC
9918 TCAAACAACACTTTCTACACATCCT
1 TCAAACAACACTTTCTACACATCCT
*
9943 TCAAACAACACTTTCTATACATC
1 TCAAACAACACTTTCTACACATC
9966 TAAAACCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (25 bp):
TCAAACAACACTTTCTACACATCCT
Found at i:10025 original size:20 final size:20
Alignment explanation
Indices: 10000--10061 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
9990 TTTCACGCGA
10000 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
10020 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
10039 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
10059 AAT
1 AAT
10062 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:10047 original size:19 final size:19
Alignment explanation
Indices: 9994--10123 Score: 118
Period size: 19 Copynumber: 7.3 Consensus size: 19
9984 AATCATTTTC
9994 ACGCGAAATGAAAATCGCA
1 ACGCGAAATGAAAATCGCA
*
10013 ACGAGAGAATGAAAATCGCA
1 ACGCGA-AATGAAAATCGCA
*
10033 ACGCGAAACGAAAATCGCA
1 ACGCGAAATGAAAATCGCA
*
10052 A--CG--A-GAGAATCGCA
1 ACGCGAAATGAAAATCGCA
*
10066 ACGCGAAATGAAAATCACA
1 ACGCGAAATGAAAATCGCA
*
10085 A--CG--A-GAGAATCGCA
1 ACGCGAAATGAAAATCGCA
**
10099 ATACGAAATGAAAATCGCA
1 ACGCGAAATGAAAATCGCA
10118 ACGCGA
1 ACGCGA
10124 TTATAGTTTC
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 40 0.45
20 18 0.20
ACGTcount: A:0.48, C:0.21, G:0.22, T:0.09
Consensus pattern (19 bp):
ACGCGAAATGAAAATCGCA
Found at i:10068 original size:33 final size:33
Alignment explanation
Indices: 9994--10120 Score: 164
Period size: 33 Copynumber: 3.7 Consensus size: 33
9984 AATCATTTTC
9994 ACGCGAAATGAAAATCGCAACGAGAGAATGAAAATCGCA
1 ACGCGAAATGAAAATCGCAAC--GAG-A-G--AATCGCA
*
10033 ACGCGAAACGAAAATCGCAACGAGAGAATCGCA
1 ACGCGAAATGAAAATCGCAACGAGAGAATCGCA
*
10066 ACGCGAAATGAAAATCACAACGAGAGAATCGCA
1 ACGCGAAATGAAAATCGCAACGAGAGAATCGCA
**
10099 ATACGAAATGAAAATCGCAACG
1 ACGCGAAATGAAAATCGCAACG
10121 CGATTATAGT
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
33 57 0.70
35 1 0.01
36 1 0.01
37 3 0.04
39 20 0.24
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.09
Consensus pattern (33 bp):
ACGCGAAATGAAAATCGCAACGAGAGAATCGCA
Found at i:10191 original size:33 final size:33
Alignment explanation
Indices: 10150--10233 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
10140 CGATTTTTGG
*
10150 TTTCGCGTTGCGATTTTGTCGTTGCGATCTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATCTTCA
* * *
10183 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCTCGTTGCGATCTTCA
10216 TTTCGCGTTGCGATTTTC
1 TTTCGCGTTGCGATTTTC
10234 ATTCTCTCGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.07, C:0.23, G:0.24, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCGTTGCGATCTTCA
Found at i:10193 original size:19 final size:19
Alignment explanation
Indices: 10130--10258 Score: 98
Period size: 20 Copynumber: 7.2 Consensus size: 19
10120 GCGATTATAG
**
10130 TTTCGCGTTGCGATTTTTGG
1 TTTCGCGTTGCGA-TTTTCA
10150 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
* *
10166 TGT--CGTTGCGATCTTCA
1 TTTCGCGTTGCGATTTTCA
10183 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
10199 --TCTCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCA
10216 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
10235 TTCTCTCGTTGCGATTTTAA
1 TT-TCGCGTTGCGATTTTCA
10255 TTTC
1 TTTC
10259 AACCAAAGAC
Statistics
Matches: 90, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 5 0.06
17 5 0.06
18 3 0.03
19 27 0.30
20 30 0.33
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:10246 original size:20 final size:20
Alignment explanation
Indices: 10195--10252 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 20
10185 TCGCGTTGCG
10195 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
10215 GTT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
10234 ATTCTCTCGTTGCGATTTT
1 ATTCTCTCGTTGCGATTTT
10253 AATTTCAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.09, C:0.22, G:0.19, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:10447 original size:94 final size:94
Alignment explanation
Indices: 10345--10814 Score: 729
Period size: 94 Copynumber: 5.1 Consensus size: 94
10335 ATGGATTGCA
* * * *
10345 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTTAGAGTATTAAAAAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
10409 TTAGCAGAATTGGCAGCAAACGTACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
10438 TTACTTTCAACCAAATGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
10503 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
10532 TTACTTTCAACCAAAAGATAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
10597 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
10626 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
10690 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
10719 TTAC-TTCAACCAAAAGACAAACACAAAAGACAAATACTAACTTCACACTGTT-AATAA-ACA-A
1 TTACTTTCAACCAAAAGACAAA-AC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACA
* * *
10780 -TTTAGCAGTATTGGCAACAACCGAATAAAT
64 GTTTAGCAGAATTGGCAGCAACCGAACAAAT
10810 TTACT
1 TTACT
10815 AAGCAATCTA
Statistics
Matches: 353, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
91 32 0.09
92 8 0.02
93 97 0.27
94 190 0.54
95 26 0.07
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:12564 original size:19 final size:19
Alignment explanation
Indices: 12501--12578 Score: 95
Period size: 19 Copynumber: 4.1 Consensus size: 19
12491 TCTTTTGGTT
* *
12501 GAAATGAAAATCTCAACGA
1 GAAATGAAAATCGCAACGC
12520 G-AATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
12538 GTAAATGACTATCGCAACGC
1 G-AAATGAAAATCGCAACGC
*
12558 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
12577 GA
1 GA
12579 TTTTAGTTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 16 0.32
19 18 0.36
20 16 0.32
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:12622 original size:33 final size:33
Alignment explanation
Indices: 12574--12654 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
12564 AAAATCGCAA
12574 TGCGATTTT-AGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCA-TTTCGCGTTGCGATTATCTCGT
* *
12607 TGTGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
12640 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
12655 TCTCGTTGCG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 43 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:12657 original size:21 final size:20
Alignment explanation
Indices: 12638--12709 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
12628 CGATTCTCTC
12638 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
12658 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
12679 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
12699 GTTGCGATTTT
1 GTTGCGATTTT
12710 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:13287 original size:21 final size:20
Alignment explanation
Indices: 13243--13314 Score: 117
Period size: 20 Copynumber: 3.5 Consensus size: 20
13233 GCTATGTAAA
13243 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
13263 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
13284 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
13304 TCGCATTGCGA
1 TCGCATTGCGA
13315 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:13329 original size:41 final size:41
Alignment explanation
Indices: 13240--13329 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
13230 GGCGCTATGT
* * *
13240 AAATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACCA
* **
13281 AATTCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACCA
13322 AAATCGCA
1 AAATCGCA
13330 ACGCGAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACCA
Found at i:13335 original size:21 final size:21
Alignment explanation
Indices: 13311--13356 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
13301 TATTCGCATT
13311 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
13332 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
13353 GCGA
1 GCGA
13357 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:13751 original size:16 final size:16
Alignment explanation
Indices: 13729--13767 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
13719 AATTGAATTT
13729 CAATTCCTACAGATTC
1 CAATTCCTACAGATTC
*
13745 TAATTCCTACAGATTC
1 CAATTCCTACAGATTC
13761 CAATTCC
1 CAATTCC
13768 CTCATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (16 bp):
CAATTCCTACAGATTC
Found at i:21762 original size:35 final size:35
Alignment explanation
Indices: 21716--21792 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
21706 AAAACAGTCC
* * *
21716 TCAATTTCATTCTAAACCCCAATTTTCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
21751 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
21786 TCAATTT
1 TCAATTT
21793 TCTTATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:22094 original size:2 final size:2
Alignment explanation
Indices: 22087--22124 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
22077 ACGAGTAACG
22087 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
22125 TAAAAGCAAA
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:22213 original size:10 final size:10
Alignment explanation
Indices: 22198--22222 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
22188 ATATTAGATT
22198 TATAAAAATA
1 TATAAAAATA
22208 TATAAAAATA
1 TATAAAAATA
22218 TATAA
1 TATAA
22223 TACAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATAAAAATA
Found at i:22249 original size:42 final size:42
Alignment explanation
Indices: 22168--22249 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 42
22158 ATTTAGTATG
* * * *
22168 TAAAAATATAAAATATAGATATATTAGATTTATAAAAATATA
1 TAAAAATATAAAATACAAATATATTAGATTAAAAAAAATATA
* *
22210 TAAAAATATATAATACAAATATATTTG-TTAAAAATAAATA
1 TAAAAATATAAAATACAAATATATTAGATTAAAAA-AAATA
22250 AAATAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
41 5 0.15
42 28 0.85
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (42 bp):
TAAAAATATAAAATACAAATATATTAGATTAAAAAAAATATA
Found at i:23630 original size:24 final size:24
Alignment explanation
Indices: 23598--23654 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
23588 GTTTGAGTCG
23598 AGTTGAGCTTACTTTTAAAGTTTA
1 AGTTGAGCTTACTTTTAAAGTTTA
*
23622 AGTTGAGCTTACTTTTAAAGTTTG
1 AGTTGAGCTTACTTTTAAAGTTTA
23646 AGTTGAGCT
1 AGTTGAGCT
23655 CAGTAATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (24 bp):
AGTTGAGCTTACTTTTAAAGTTTA
Found at i:39978 original size:37 final size:38
Alignment explanation
Indices: 39905--39978 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 38
39895 TTATATTTTT
* *
39905 AATTTTGTAAAAAAAACTATATAAATATTATGAATTTA
1 AATTTTGTAAAAAAAACTAAATAAATATTATCAATTTA
* *
39943 AATTTT-TAAAGAAAA-TAAATAAATATTTTACAATTT
1 AATTTTGTAAAAAAAACTAAATAAATATTAT-CAATTT
39979 GTAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 12 0.39
37 13 0.42
38 6 0.19
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (38 bp):
AATTTTGTAAAAAAAACTAAATAAATATTATCAATTTA
Found at i:40159 original size:20 final size:20
Alignment explanation
Indices: 40123--40160 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40113 AATCCATTCC
**
40123 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
40143 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
40161 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:43848 original size:2 final size:2
Alignment explanation
Indices: 43841--43882 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
43831 TTGTGTTTTG
43841 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
43883 TGTGAAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46064 original size:14 final size:14
Alignment explanation
Indices: 46045--46072 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46035 TGCTGTTAAG
46045 CCTTTTCTGGGTCA
1 CCTTTTCTGGGTCA
46059 CCTTTTCTGGGTCA
1 CCTTTTCTGGGTCA
46073 TGAATGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.21, T:0.43
Consensus pattern (14 bp):
CCTTTTCTGGGTCA
Found at i:53870 original size:135 final size:135
Alignment explanation
Indices: 53623--53891 Score: 360
Period size: 135 Copynumber: 2.0 Consensus size: 135
53613 GTTCTCTTGA
* * * *
53623 GAAGTGAGGCTCTGGTTGCTGGTCAGGATATGATGAAGTTCTATACAAAGGCTTTGCTCCTGAAA
1 GAAGAGAGGCTCTGGTTGCTGCTCAGGATATGATGAAGTTCTATACAAACGCTTTGCTCCTAAAA
* * * *
53688 AACGAGCAGAAGATGGTTGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAACATCTTCAGTATCA
66 AACAAACAGAAGATGATAGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAACATCTTCAGTATCA
53753 AACAT
131 AACAT
** *
53758 GAAGAGAGGCTCTGGTTGCTGCTGGGGATATGATGAAGTTCTATACAAACGCTTTGAGT-CTAAA
1 GAAGAGAGGCTCTGGTTGCTGCTCAGGATATGATGAAGTTCTATACAAACGCTTTG-CTCCTAAA
* * * * * * *
53822 AAACAAACAGAGGTTGATAGTGGTTGTGAGGACCATCTCTTGCCTTCTTGAGCATCTTCTGTATC
65 AAACAAACAGAAGATGATAGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAACATCTTCAGTATC
53887 AAACA
130 AAACA
53892 CATGCTGATC
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
135 114 0.99
136 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (135 bp):
GAAGAGAGGCTCTGGTTGCTGCTCAGGATATGATGAAGTTCTATACAAACGCTTTGCTCCTAAAA
AACAAACAGAAGATGATAGTGGCTGAGAAGACCATCTCTTGCCTTCTTGAACATCTTCAGTATCA
AACAT
Found at i:60929 original size:25 final size:25
Alignment explanation
Indices: 60901--60948 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
60891 TAATTATCGA
*
60901 AGAAAATTTAAATTTTAAGATAATT
1 AGAAAATTTAAATTTCAAGATAATT
60926 AGAAAATTTAAATTTCAAGATAA
1 AGAAAATTTAAATTTCAAGATAA
60949 GTACGTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (25 bp):
AGAAAATTTAAATTTCAAGATAATT
Found at i:63482 original size:24 final size:24
Alignment explanation
Indices: 63450--63495 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
63440 CAATTGCTCC
63450 TGCTTCCTCATCTCTCTTCTTCGA
1 TGCTTCCTCATCTCTCTTCTTCGA
*
63474 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCATCTCTCTTCTTC
63496 TCCAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.04, C:0.39, G:0.07, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCATCTCTCTTCTTCGA
Found at i:68604 original size:24 final size:24
Alignment explanation
Indices: 68572--68617 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
68562 CAATTGCTCC
68572 TGCTTCCTCATCTCTCTTCTTCGA
1 TGCTTCCTCATCTCTCTTCTTCGA
*
68596 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCATCTCTCTTCTTC
68618 TCCAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.04, C:0.39, G:0.07, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCATCTCTCTTCTTCGA
Found at i:84803 original size:8 final size:8
Alignment explanation
Indices: 84790--84815 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
84780 ACATGTTGTT
84790 GAGCCGAC
1 GAGCCGAC
84798 GAGCCGAC
1 GAGCCGAC
84806 GAGCCGAC
1 GAGCCGAC
84814 GA
1 GA
84816 CCGGTGGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (8 bp):
GAGCCGAC
Done.