Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005809.1 Hibiscus syriacus cultivar Beakdansim tig00013619_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: 65256
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:605 original size:20 final size:20
Alignment explanation
Indices: 577--614 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
567 GTGAAATTTG
577 TCCCCAAGGACCTATGAATA
1 TCCCCAAGGACCTATGAATA
*
597 TCCCGAAGGACCTATGAA
1 TCCCCAAGGACCTATGAA
615 ACCCTCGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (20 bp):
TCCCCAAGGACCTATGAATA
Found at i:623 original size:20 final size:20
Alignment explanation
Indices: 578--623 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
568 TGAAATTTGT
578 CCCC-AAGGACCTATGAATA
1 CCCCGAAGGACCTATGAATA
*
597 TCCCGAAGGACCTATGAA-A
1 CCCCGAAGGACCTATGAATA
616 CCCTCGAA
1 CCC-CGAA
624 TCTTGGCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.35, C:0.33, G:0.17, T:0.15
Consensus pattern (20 bp):
CCCCGAAGGACCTATGAATA
Found at i:9963 original size:24 final size:25
Alignment explanation
Indices: 9936--9991 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
9926 GTATAACTAC
* *
9936 ATTTTTGGACCTCAGACTTT-TCAA
1 ATTTTTAGACCTCAGAATTTATCAA
* *
9960 ATTTTTAGACCTTATAATTTATCAA
1 ATTTTTAGACCTCAGAATTTATCAA
9985 ATTTTTA
1 ATTTTTA
9992 TAAAATGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (25 bp):
ATTTTTAGACCTCAGAATTTATCAA
Found at i:10617 original size:29 final size:29
Alignment explanation
Indices: 10575--10632 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
10565 AAAGAGTCCC
*
10575 ATGCTTTTCCAATCAAGTCCATACATTGT
1 ATGCTTTTCCAATCAAGGCCATACATTGT
*
10604 ATGCTTTTCCAATCAGGGCCATACATTGT
1 ATGCTTTTCCAATCAAGGCCATACATTGT
10633 CCGATCATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (29 bp):
ATGCTTTTCCAATCAAGGCCATACATTGT
Found at i:12831 original size:21 final size:21
Alignment explanation
Indices: 12802--12848 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12792 ATTCTGACTA
*
12802 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
* *
12823 TCGCGTTGCAATTTTCCTAAT
1 TCGCATTGCAATTTTCCAAAT
12844 TCGCA
1 TCGCA
12849 ATGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCAATTTTCCAAAT
Found at i:12869 original size:20 final size:20
Alignment explanation
Indices: 12844--12937 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
12834 TTTTCCTAAT
12844 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
12864 TCGCAACGCAAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
12885 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
12905 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
12925 TCGCAATGCGAAT
1 TCGCAATGCGAAT
12938 CTGACTATCG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:12894 original size:41 final size:40
Alignment explanation
Indices: 12844--12937 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
12834 TTTTCCTAAT
**
12844 TCGCAATGCGAATACGTAAATCGCAACGCAAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAA-TACGAAAA
* * * *
12885 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATACGAAAA
12925 TCGCAATGCGAAT
1 TCGCAATGCGAAT
12938 CTGACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 17 0.37
41 29 0.63
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCAAATACGAAAA
Found at i:12913 original size:61 final size:60
Alignment explanation
Indices: 12844--12957 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
12834 TTTTCCTAAT
*
12844 TCGCAATGCGAATACGTAAATCGCAACGCAAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATCT-GAAAATCGCAATGCGATTACGTAAA
* * **
12905 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATCTGAAAATCGCAATGCGATT
12958 TACATAGCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 16 0.33
61 32 0.67
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCAAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:13163 original size:22 final size:22
Alignment explanation
Indices: 13137--13198 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
13127 ACATCCGTCC
* *
13137 CCATCTCTGACGAAATCAGTCT
1 CCATCTCCGACGAAATCACTCT
*
13159 CCATCTCCGACGATATCACTCT
1 CCATCTCCGACGAAATCACTCT
*
13181 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
13199 TTCACGGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (22 bp):
CCATCTCCGACGAAATCACTCT
Found at i:13574 original size:20 final size:20
Alignment explanation
Indices: 13549--13601 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
13539 AGATTTTCAT
13549 TTCGCGTTACGATAGTCAAA
1 TTCGCGTTACGATAGTCAAA
* **
13569 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTACGATAGTCAAA
*
13589 TTCGTGTTACGAT
1 TTCGCGTTACGAT
13602 TTTCATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
TTCGCGTTACGATAGTCAAA
Found at i:13607 original size:20 final size:20
Alignment explanation
Indices: 13584--13623 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13574 GTTGCGATAG
13584 TCATTTTCGTGTTACGATTT
1 TCATTTTCGTGTTACGATTT
13604 TCATTTTCGTGTTACGATTT
1 TCATTTTCGTGTTACGATTT
13624 AAAATTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (20 bp):
TCATTTTCGTGTTACGATTT
Found at i:13631 original size:20 final size:20
Alignment explanation
Indices: 13588--13631 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13578 CGATAGTCAT
** *
13588 TTTCGTGTTACGATTTTCAT
1 TTTCGTGTTACGATTTAAAA
13608 TTTCGTGTTACGATTTAAAA
1 TTTCGTGTTACGATTTAAAA
13628 TTTC
1 TTTC
13632 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTACGATTTAAAA
Found at i:15534 original size:34 final size:34
Alignment explanation
Indices: 15487--15637 Score: 144
Period size: 34 Copynumber: 4.3 Consensus size: 34
15477 ATAGTTTATT
15487 ATCGCAATGCGAAAATGACTATCGCAACGACAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGACAGA
* ** * *
15521 ATCGCAATACG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGACAGA
* *
15554 ATCGC-ATCGTGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAAT-GCGAAAATGACTATCGCAA--CG-ACA-GA
* *
15592 CTATCGCAATGCGAAAATGATTATCGCAACGAGAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGACAGA
15628 ATCGCAATGC
1 ATCGCAATGC
15638 AATTTTCATT
Statistics
Matches: 93, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
32 2 0.02
33 24 0.26
34 33 0.35
36 3 0.03
37 4 0.04
38 3 0.03
40 22 0.24
41 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGACAGA
Found at i:15544 original size:33 final size:34
Alignment explanation
Indices: 15487--15559 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 34
15477 ATAGTTTATT
* ** * *
15487 ATCGCAATGCGAAAATGACTATCGCAACGACAGA
1 ATCGCAATACGAAAATGAAAATCGCAACAACAAA
15521 ATCGCAATACG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATACGAAAATGAAAATCGCAACAACAAA
15554 ATCGCA
1 ATCGCA
15560 TCGTGAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 24 0.71
34 10 0.29
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (34 bp):
ATCGCAATACGAAAATGAAAATCGCAACAACAAA
Found at i:15579 original size:20 final size:20
Alignment explanation
Indices: 15564--15620 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
15554 ATCGCATCGT
15564 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
15584 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
*
15604 GAAAATGATTATCGCAA
1 GAAAATGACTATCGCAA
15621 CGAGAGAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (20 bp):
GAAAATGACTATCGCAATGC
Found at i:15759 original size:20 final size:20
Alignment explanation
Indices: 15667--15764 Score: 142
Period size: 20 Copynumber: 4.9 Consensus size: 20
15657 GATTCTCTCG
* **
15667 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
15687 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
15707 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
15727 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
15747 TTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCG
15765 TGTTACGATT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:16348 original size:21 final size:21
Alignment explanation
Indices: 16257--16361 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
16247 GACTCACCTG
*
16257 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
16279 T-ATTGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
16299 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
16320 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
16341 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
16362 CCAACATTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
20 3 0.05
21 57 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:16354 original size:42 final size:42
Alignment explanation
Indices: 16283--16364 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
16273 CTCCCCTATT
*
16283 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACC
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACC
* ** *
16325 GTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
16365 ACATTCTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.21
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACC
Found at i:17768 original size:14 final size:14
Alignment explanation
Indices: 17749--17784 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17739 ATTGTTTAAT
17749 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
17763 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
17777 TGATTTGT
1 TGATTTGT
17785 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:17986 original size:20 final size:20
Alignment explanation
Indices: 17961--18029 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
17951 GCGATTCTCT
*
17961 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCA
17981 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCA
*
18001 TGTTGCGATAGTCATATT-CA
1 CGTTGCGATAGTCAT-TTCCA
18021 CGTTGCGAT
1 CGTTGCGAT
18030 TTTCGCGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCA
Found at i:20273 original size:3 final size:3
Alignment explanation
Indices: 20265--20297 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20255 ATTTGGGGAT
20265 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20298 AGGGTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:20506 original size:24 final size:24
Alignment explanation
Indices: 20472--20525 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
20462 CTGAAAAATC
20472 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
20496 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
20520 ATCAAA
1 ATCAAA
20526 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:20539 original size:24 final size:24
Alignment explanation
Indices: 20472--20539 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
20462 CTGAAAAATC
* * *
20472 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
20496 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
20520 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
20540 TAGCACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:21364 original size:20 final size:20
Alignment explanation
Indices: 21339--21425 Score: 156
Period size: 20 Copynumber: 4.3 Consensus size: 20
21329 AAATTCAGTA
21339 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
21359 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
21379 TTGCGATAGTCAGATTCTCG
1 TTGCGATAGTCAGAATCTCG
*
21399 TTGCGATAGTCAGATTCTCG
1 TTGCGATAGTCAGAATCTCG
21419 TTGCGAT
1 TTGCGAT
21426 TTACGTATTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:21435 original size:20 final size:20
Alignment explanation
Indices: 21419--21525 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
21409 CAGATTCTCG
21419 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
21439 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
21459 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** **
21479 TTGCGATTTTCCAAATTCGTG
1 TTGCGA-TTTACGTATTCGCA
21500 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
21520 TTGCGA
1 TTGCGA
21526 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 60 0.81
21 14 0.19
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:21443 original size:40 final size:40
Alignment explanation
Indices: 21359--21525 Score: 146
Period size: 40 Copynumber: 4.2 Consensus size: 40
21349 CAGAATCTCG
* * * *
21359 TTGCGATAGTCAGAATCTCGTTGCGATAGT-CAG-ATTCTCG
1 TTGCGATAGTCAGATTCTCGTTGCGAT-TTAC-GTATTCGCA
21399 TTGCGATAGTCAGATTCTCGTTGCGATTTACGTATTCGCA
1 TTGCGATAGTCAGATTCTCGTTGCGATTTACGTATTCGCA
* * * *
21439 TTGCGAT--TTACGTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATAGTCA-G-ATTCTCGTTGCGATTTACGTATTCGCA
** *
21479 TTGCGATTTTCCAAATTCGT-GTTGCGATTTACGTATTCGCA
1 TTGCGATAGT-CAGATTC-TCGTTGCGATTTACGTATTCGCA
21520 TTGCGA
1 TTGCGA
21526 ATTAGGAAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
38 2 0.02
39 3 0.03
40 70 0.66
41 29 0.27
42 1 0.01
43 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCAGATTCTCGTTGCGATTTACGTATTCGCA
Found at i:21509 original size:41 final size:40
Alignment explanation
Indices: 21412--21525 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 40
21402 CGATAGTCAG
* **
21412 ATTCTCGTTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACAA
* * *
21452 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAA
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA-TTTACAA
*
21493 ATTCGTGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA
21526 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 30 0.47
41 34 0.53
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (40 bp):
ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACAA
Found at i:21546 original size:21 final size:21
Alignment explanation
Indices: 21522--21567 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
21512 TATTCGCATT
21522 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
21543 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
21564 GCGA
1 GCGA
21568 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:23959 original size:11 final size:11
Alignment explanation
Indices: 23945--23986 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
23935 TGTGCCATCC
23945 TCGATGAGTCA
1 TCGATGAGTCA
23956 TCGATGAGGTTC-
1 TCGATGA-G-TCA
23968 TCGATGAGTCA
1 TCGATGAGTCA
*
23979 TCGTTGAG
1 TCGATGAG
23987 GTTGTCGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 8 0.30
13 2 0.07
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (11 bp):
TCGATGAGTCA
Found at i:23974 original size:23 final size:23
Alignment explanation
Indices: 23944--24003 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
23934 TTGTGCCATC
23944 CTCGATGAGTCATCGATGAGGTT
1 CTCGATGAGTCATCGATGAGGTT
*
23967 CTCGATGAGTCATCGTTGAGGTT
1 CTCGATGAGTCATCGATGAGGTT
* *
23990 GTCGATGAGCCATC
1 CTCGATGAGTCATC
24004 ATCGTCGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (23 bp):
CTCGATGAGTCATCGATGAGGTT
Found at i:26607 original size:2 final size:2
Alignment explanation
Indices: 26600--26635 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26590 ACTTCCTTTC
26600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26636 AAGTTTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29006 original size:12 final size:13
Alignment explanation
Indices: 28988--29019 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28978 TAAATCTCCG
28988 TCCCCGACCCCGA
1 TCCCCGACCCCGA
29001 -CCCCGA-CCCGA
1 TCCCCGACCCCGA
29012 TCCCCGAC
1 TCCCCGAC
29020 GGGTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.16, C:0.62, G:0.16, T:0.06
Consensus pattern (13 bp):
TCCCCGACCCCGA
Found at i:31586 original size:2 final size:2
Alignment explanation
Indices: 31575--31649 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
31565 AAATAATAAA
31575 AT AT -T 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
31616 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
31650 CGGGTCGGGG
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:33399 original size:18 final size:19
Alignment explanation
Indices: 33364--33400 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
33354 CACGGAATGT
33364 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
33384 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
33401 GAATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:48225 original size:12 final size:12
Alignment explanation
Indices: 48208--48232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48198 GTTCAACTAA
48208 TGACTAATATTT
1 TGACTAATATTT
48220 TGACTAATATTT
1 TGACTAATATTT
48232 T
1 T
48233 ATAGACCTTC
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TGACTAATATTT
Found at i:49955 original size:97 final size:98
Alignment explanation
Indices: 49785--50078 Score: 563
Period size: 98 Copynumber: 3.0 Consensus size: 98
49775 CATTTAAGCC
49785 TATTTGTTAATGTGATGACGTTAATGAGTTTGAC-AATTATTTAATTTTATTGTGATTATTGCAA
1 TATTTGTTAATGTGATGACGTTAATGAGTTTGACAAATTATTTAATTTTATTGTGATTATTGCAA
49849 ATAATTTTTTAATAGAGTTATTTTCTTAAAAAT
66 ATAATTTTTTAATAGAGTTATTTTCTTAAAAAT
49882 TATTTGTTAATGTGATGACGTTAATGAGTTTGACAAATTATTTAATTTTATTGTGATTATTGCAA
1 TATTTGTTAATGTGATGACGTTAATGAGTTTGACAAATTATTTAATTTTATTGTGATTATTGCAA
49947 ATAATTTTTTAATAGAGTTATTTTCTTAAAAAT
66 ATAATTTTTTAATAGAGTTATTTTCTTAAAAAT
49980 TATTTGTTAATGTGATGACGTTAATGAGTTTGACAAATTATTTAATTTTATTGTGATTATTGCAA
1 TATTTGTTAATGTGATGACGTTAATGAGTTTGACAAATTATTTAATTTTATTGTGATTATTGCAA
*
50045 ATAATTTTTTTAATGGAGTTATTTTCTTAAAAAT
66 ATAA-TTTTTTAATAGAGTTATTTTCTTAAAAAT
50079 AATTAAGTTT
Statistics
Matches: 194, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
97 34 0.18
98 132 0.68
99 28 0.14
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (98 bp):
TATTTGTTAATGTGATGACGTTAATGAGTTTGACAAATTATTTAATTTTATTGTGATTATTGCAA
ATAATTTTTTAATAGAGTTATTTTCTTAAAAAT
Found at i:51993 original size:20 final size:21
Alignment explanation
Indices: 51968--52008 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
51958 ACATAGTATT
51968 AAATAA-AAATA-ATAATAGAA
1 AAATAAGAAATATAT-ATAGAA
51988 AAATAAGAAATATATATAGAA
1 AAATAAGAAATATATATAGAA
52009 CATATAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 11 0.58
22 2 0.11
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATATATATAGAA
Found at i:52183 original size:2 final size:2
Alignment explanation
Indices: 52178--52202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52168 AGTATACTTA
52178 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52203 CTAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53659 original size:106 final size:107
Alignment explanation
Indices: 53482--53713 Score: 331
Period size: 106 Copynumber: 2.2 Consensus size: 107
53472 ATCTTCTGTC
* * * * **
53482 GTGAAGTTGAAGTTGGTTCTGGAACTGGGAAATTGTTTTGTTGACAGTCAGCCGCCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGCCCCTTCGTTG
* *
53547 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATGCCCTTCAAT
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATACCATTCAAT
* *
53589 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTG-TTTGTTGACAACCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGCCCCTTCGTTG
* * **
53653 TGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCATTCGCT
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATACCATTCAAT
53695 GTGAAGTTGAAATTGGCTC
1 GTGAAGTTGAAATTGGCTC
53714 TAGCTAAAAC
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
106 81 0.73
107 30 0.27
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (107 bp):
GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGCCCCTTCGTTG
TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATACCATTCAAT
Found at i:54159 original size:31 final size:31
Alignment explanation
Indices: 54124--54251 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 31
54114 GGGAAATAAA
54124 CTCAAA-GATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAACGATTTTGTGTTTCAAGAGAAACT-T
** * *
54155 CTCAAGGGAGACGAAATT-TGTTTCAAGGGAAACAAT
1 CTC-A---A-ACGATTTTGTGTTTCAAGAGAAAC-TT
*
54191 CTCAAA-GGTTTTGTGTTTCAAGAGAAACATT
1 CTCAAACGATTTTGTGTTTCAAGAGAAAC-TT
* * *
54222 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAACG-ATTTTGTGTTTCAAGAGAAAC
54252 AATTTCAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
30 3 0.04
31 25 0.33
32 3 0.04
33 20 0.26
35 2 0.03
36 19 0.25
37 4 0.05
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (31 bp):
CTCAAACGATTTTGTGTTTCAAGAGAAACTT
Found at i:54159 original size:67 final size:67
Alignment explanation
Indices: 54027--54218 Score: 258
Period size: 67 Copynumber: 2.8 Consensus size: 67
54017 GTCTTAAAAA
* * * * *
54027 AGACAGAATTCGTTTCAAGGGAAACAATCTTAAAGATATATGTTGTTTCACGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCA
54092 AGGG
64 AGGG
* * * * *
54096 AGACAAAATTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
54161 GG
66 GG
* *
54163 AGACGAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
54219 ATTTTCAAAG
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 74 0.69
68 3 0.03
69 31 0.29
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
GG
Found at i:54278 original size:36 final size:33
Alignment explanation
Indices: 54173--54287 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
54163 AGACGAAATT
* *
54173 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
*
54204 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
54237 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
54273 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
54288 TGTATCAAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
33 30 0.40
35 1 0.01
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:54427 original size:36 final size:36
Alignment explanation
Indices: 54328--54684 Score: 185
Period size: 36 Copynumber: 10.4 Consensus size: 36
54318 CAAGGATTGA
*
54328 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
54365 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAATA
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
54402 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
54438 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
54467 TGTTTCAAGGGAAACTGTTTTC-A-A-AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
54496 ATGTTTCAATAGAAACTGTCTCAA-AGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAATT
* *
54533 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
54569 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
54597 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
54635 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
54671 CATTTCAAGGGAAA
1 TGTTTCAAGAGAAA
54685 TGTTTTCAAT
Statistics
Matches: 251, Mismatches: 39, Indels: 61
0.72 0.11 0.17
Matches are distributed among these distances:
28 3 0.01
29 34 0.14
30 28 0.11
32 3 0.01
33 3 0.01
34 2 0.01
35 5 0.02
36 90 0.36
37 64 0.25
38 19 0.08
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:54492 original size:30 final size:30
Alignment explanation
Indices: 54456--54514 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
54446 GTAAAACATA
*
54456 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
54486 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
54515 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:54660 original size:102 final size:102
Alignment explanation
Indices: 54469--54773 Score: 504
Period size: 102 Copynumber: 3.0 Consensus size: 102
54459 AAAGATTTTG
* * *
54469 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
54533 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
54571 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
54636 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* *
54673 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * *
54738 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
65 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
54774 CTTGTTTTAA
Statistics
Matches: 192, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
101 46 0.24
102 111 0.58
103 3 0.02
104 32 0.17
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:64222 original size:18 final size:18
Alignment explanation
Indices: 64199--64240 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
64189 GTGTGGAAGC
64199 GCAATTGCCGGGCAAAGA
1 GCAATTGCCGGGCAAAGA
64217 GCAATTGCCGGGCAAAGA
1 GCAATTGCCGGGCAAAGA
64235 GCAATT
1 GCAATT
64241 TGATCAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.31, T:0.14
Consensus pattern (18 bp):
GCAATTGCCGGGCAAAGA
Done.