Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006912.1 Hibiscus syriacus cultivar Beakdansim tig00017701_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: 78107
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2486 original size:14 final size:13
Alignment explanation
Indices: 2467--2540 Score: 85
Period size: 14 Copynumber: 5.5 Consensus size: 13
2457 AAGGTCTGTT
2467 TATTTTATTGAAAA
1 TATTTT-TTGAAAA
**
2481 TATTTTTAAAAAA
1 TATTTTTTGAAAA
2494 TATTTTTTGAAAAA
1 TATTTTTTG-AAAA
**
2508 TATTTTTAAAAAA
1 TATTTTTTGAAAA
2521 TATTTTTTGAAAAA
1 TATTTTTTG-AAAA
2535 TATTTT
1 TATTTT
2541 AAGTTATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
13 23 0.46
14 27 0.54
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (13 bp):
TATTTTTTGAAAA
Found at i:2495 original size:13 final size:13
Alignment explanation
Indices: 2477--2540 Score: 92
Period size: 14 Copynumber: 4.8 Consensus size: 13
2467 TATTTTATTG
2477 AAAATATTTTTAA
1 AAAATATTTTTAA
*
2490 AAAATATTTTTTGA
1 AAAATA-TTTTTAA
2504 AAAATATTTTTAA
1 AAAATATTTTTAA
*
2517 AAAATATTTTTTGA
1 AAAATA-TTTTTAA
2531 AAAATATTTT
1 AAAATATTTT
2541 AAGTTATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
13 22 0.48
14 24 0.52
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
AAAATATTTTTAA
Found at i:2499 original size:27 final size:27
Alignment explanation
Indices: 2467--2540 Score: 132
Period size: 27 Copynumber: 2.7 Consensus size: 27
2457 AAGGTCTGTT
2467 TATTTTATTG-AAAATATTTTTAAAAAA
1 TATTTT-TTGAAAAATATTTTTAAAAAA
2494 TATTTTTTGAAAAATATTTTTAAAAAA
1 TATTTTTTGAAAAATATTTTTAAAAAA
2521 TATTTTTTGAAAAATATTTT
1 TATTTTTTGAAAAATATTTT
2541 AAGTTATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 3 0.07
27 43 0.93
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (27 bp):
TATTTTTTGAAAAATATTTTTAAAAAA
Found at i:3748 original size:16 final size:16
Alignment explanation
Indices: 3724--3765 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
3714 ACGAAGCATA
*
3724 GAGGTTGGGCCAATCG
1 GAGGATGGGCCAATCG
3740 GAGGATGGGCCAATCG
1 GAGGATGGGCCAATCG
3756 GAGGATGGGC
1 GAGGATGGGC
3766 AGTACGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.48, T:0.14
Consensus pattern (16 bp):
GAGGATGGGCCAATCG
Found at i:4164 original size:23 final size:24
Alignment explanation
Indices: 4138--4188 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
4128 TTCAAAACTT
*
4138 AATTAATCCTTTA-ATTTTATAAA
1 AATTAATCCTTTATATTATATAAA
* **
4161 AATTGATTTTTTATATTATATAAA
1 AATTAATCCTTTATATTATATAAA
4185 AATT
1 AATT
4189 GAAAGCTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
AATTAATCCTTTATATTATATAAA
Found at i:5387 original size:33 final size:32
Alignment explanation
Indices: 5345--5413 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
5335 TTGGGTGGTT
5345 GAAAATGTTTA-ATACGAAGATGGAGACCTGTGG
1 GAAAATGTTTAGAT--GAAGATGGAGACCTGTGG
* * *
5378 GAAAATGTTTAGGTGAAGCTGGAGACTTGTGG
1 GAAAATGTTTAGATGAAGATGGAGACCTGTGG
5410 GAAA
1 GAAA
5414 TAAATTTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 20 0.62
33 11 0.34
34 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (32 bp):
GAAAATGTTTAGATGAAGATGGAGACCTGTGG
Found at i:6860 original size:26 final size:26
Alignment explanation
Indices: 6824--6876 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
6814 AAATAATAAT
6824 AACAAAACCAGTAACATATTTCATTA
1 AACAAAACCAGTAACATATTTCATTA
6850 AACAAAACCAGTAACATATTTCATTA
1 AACAAAACCAGTAACATATTTCATTA
6876 A
1 A
6877 TCGTATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (26 bp):
AACAAAACCAGTAACATATTTCATTA
Found at i:8445 original size:33 final size:32
Alignment explanation
Indices: 8403--8468 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
8393 AAACACACTT
8403 TCTACAAAAGGCAAGTTCCATTGACAACTCATA
1 TCTACAAAAGGCAAGTTCCATTGACAAC-CATA
8436 TCTACAAAAGGCAAGTTCCATTGACAACCATA
1 TCTACAAAAGGCAAGTTCCATTGACAACCATA
8468 T
1 T
8469 GTAGAGCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (32 bp):
TCTACAAAAGGCAAGTTCCATTGACAACCATA
Found at i:10473 original size:2 final size:2
Alignment explanation
Indices: 10466--10491 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10456 AATAAATTAA
10466 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
10492 GAGTATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11949 original size:34 final size:34
Alignment explanation
Indices: 11906--11970 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
11896 TTTGTCATTC
11906 GACCGTTGAATAATTAACGATGTTAAAATAAGTT
1 GACCGTTGAATAATTAACGATGTTAAAATAAGTT
11940 GACCGTTGAATAATTAACGATGTTAAAATAA
1 GACCGTTGAATAATTAACGATGTTAAAATAA
11971 ATTGTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (34 bp):
GACCGTTGAATAATTAACGATGTTAAAATAAGTT
Found at i:12483 original size:21 final size:21
Alignment explanation
Indices: 12454--12506 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12444 ATTCTGACTA
12454 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
12475 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
12496 TCGCAATGCGA
1 TCGCATTGCGA
12507 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:12521 original size:20 final size:20
Alignment explanation
Indices: 12496--12583 Score: 124
Period size: 20 Copynumber: 4.4 Consensus size: 20
12486 TTTTCCTAAT
*
12496 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
12516 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
12536 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
**
12556 TCGCAATACGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
12576 TCGCAACG
1 TCGCAACG
12584 AGATTCTGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.02
20 59 0.98
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:13475 original size:24 final size:24
Alignment explanation
Indices: 13443--13496 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
13433 GTATTCGAAA
13443 TTTGATCTTGGACAATACCCGGAC
1 TTTGATCTTGGACAATACCCGGAC
* * *
13467 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGACAATACCCGGAC
13491 TTTGAT
1 TTTGAT
13497 GAATTTTCAG
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:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGACAATACCCGGAC
Found at i:15953 original size:20 final size:20
Alignment explanation
Indices: 15928--15993 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
15918 AAACGCGGAA
*
15928 ATCGCATCACGGAAATGACT
1 ATCGCATCGCGGAAATGACT
*
15948 ATCGCAAT-GCGGAATTGACT
1 ATCGC-ATCGCGGAAATGACT
*
15968 ATCGCAACGCGGAAATGACT
1 ATCGCATCGCGGAAATGACT
15988 ATCGCA
1 ATCGCA
15994 ACGAGAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.93
21 2 0.05
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (20 bp):
ATCGCATCGCGGAAATGACT
Found at i:15994 original size:20 final size:20
Alignment explanation
Indices: 15937--15996 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
15927 AATCGCATCA
*
15937 CGGAAATGACTATCGCAATG
1 CGGAAATGACTATCGCAACG
*
15957 CGGAATTGACTATCGCAACG
1 CGGAAATGACTATCGCAACG
15977 CGGAAATGACTATCGCAACG
1 CGGAAATGACTATCGCAACG
15997 AGAGAATCGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.18
Consensus pattern (20 bp):
CGGAAATGACTATCGCAACG
Found at i:16029 original size:19 final size:19
Alignment explanation
Indices: 16005--16041 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
15995 CGAGAGAATC
16005 GCAATGCGAAATGAAAATT
1 GCAATGCGAAATGAAAATT
16024 GCAATGCGAAATGAAAAT
1 GCAATGCGAAATGAAAAT
16042 CGAAACGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATT
Found at i:16155 original size:20 final size:20
Alignment explanation
Indices: 16130--16196 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
16120 TTTTCCTAAT
16130 TCGCAACGCAAATACGTAAA
1 TCGCAACGCAAATACGTAAA
* *
16150 TCGCAACGCGATTACGTAAA
1 TCGCAACGCAAATACGTAAA
* *
16170 TCGCAATGCGAAAT--GAAAA
1 TCGCAACGC-AAATACGTAAA
16189 TCGCAACG
1 TCGCAACG
16197 AGTGAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 11 0.28
20 26 0.67
21 2 0.05
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
TCGCAACGCAAATACGTAAA
Found at i:16275 original size:20 final size:20
Alignment explanation
Indices: 16252--16337 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
16242 ATTTACAGAT
16252 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
16272 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
16292 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
16312 TCGCAATGTGAAT-CTGTAAA
1 TCGCAATGCGATTAC-GTAAA
16332 TCGCAA
1 TCGCAA
16338 CGATTTTCAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 1 0.02
20 62 0.98
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:16380 original size:34 final size:34
Alignment explanation
Indices: 16338--16428 Score: 121
Period size: 33 Copynumber: 2.7 Consensus size: 34
16328 TAAATCGCAA
*
16338 CGATTTTCATTTTCGCATTGCGATTCACTTGTTG
1 CGATTTTCATTTTCGCATTGCGATTCACTCGTTG
*
16372 CGATTTTCA-TTTCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTTCGCATTGCGATTCACTCGTTG
** * *
16405 CGATAGTCATTTCCGCGTTGCGAT
1 CGATTTTCATTTTCGCATTGCGAT
16429 AGTCTGTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
33 29 0.58
34 21 0.42
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
CGATTTTCATTTTCGCATTGCGATTCACTCGTTG
Found at i:16551 original size:14 final size:14
Alignment explanation
Indices: 16532--16566 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16522 TCAATTAAAA
16532 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
16546 AAATCATCTTTTAC
1 AAATCAACATTTAC
16560 AAATCAA
1 AAATCAA
16567 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:18023 original size:42 final size:42
Alignment explanation
Indices: 17916--18027 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
17906 TCTAGAATGT
* *
17916 TAGGAGG-GATCTCTTCAACGATGACAGTGGCCTCTTGAACAG
1 TAGGAGGAGA-CTCTTGAACGATGACAGGGGCCTCTTGAACAG
* * ** *
17958 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC-G
1 TAGGAGGAGACTCTTGAACGATGACAGGGGCCTCTTGAACAG
17999 ATAGG-GGAGACCTCTTGAACGATGACAGG
1 -TAGGAGGAGA-CTCTTGAACGATGACAGG
18028 TGAGTCAGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 5 0.09
42 49 0.88
43 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (42 bp):
TAGGAGGAGACTCTTGAACGATGACAGGGGCCTCTTGAACAG
Found at i:18530 original size:20 final size:20
Alignment explanation
Indices: 18515--18633 Score: 184
Period size: 20 Copynumber: 6.0 Consensus size: 20
18505 AAATCGTAAC
18515 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
18535 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
18555 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
*
18575 GCGAAAATGACTATCACAAT
1 GCGAAAATGACTATCGCAAT
**
18595 GCGAATTTGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
** *
18615 GCGAATTTAACTATCGCAA
1 GCGAAAATGACTATCGCAA
18634 CGAGAGAATC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 94 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:18690 original size:19 final size:18
Alignment explanation
Indices: 18668--18749 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 18
18658 AAATCGCAAC
*
18668 GCGATTATAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
*
18687 GCGATTTTGGTTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
*
18706 ACGATTTTCATTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
* *
18725 ACGATTTTTATTTCTCGTT
1 GCGA-TTTTATTTCGCGTT
18744 GCGATT
1 GCGATT
18750 CTCTCGTGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
18 2 0.04
19 48 0.89
20 4 0.07
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (18 bp):
GCGATTTTATTTCGCGTT
Found at i:19009 original size:94 final size:94
Alignment explanation
Indices: 18874--19246 Score: 568
Period size: 94 Copynumber: 4.0 Consensus size: 94
18864 GCATTACTTA
* *
18874 AACCAAAAGACAAAACAAAGACAAATAATAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGA
18939 ATTGGCAGCAACCGAACAAATTTACTTTC
66 ATTGGCAGCAACCGAACAAATTTACTTTC
* *
18968 AACCAAAAGACAAAACAAAGACAAATACTAAATTCACAGTATTAAAGAATACATAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGA
*
19033 ATTGGCAGCAACCGAACAAATTTACTTTT
66 ATTGGCAGCAACCGAACAAATTTACTTTC
* * *
19062 AACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAAA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGA
* *
19127 ATTGGCAGGAACCGAATAAATTTAC-TTC
66 ATTGGCAGCAACCGAACAAATTTACTTTC
* * * *
19155 AACCAAAAGATAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAG
1 AACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAG
* * * *
19220 TATTGACAGCAACCTAATAAATTTACT
65 AATTGGCAGCAACCGAACAAATTTACT
19247 AAGCAATCTA
Statistics
Matches: 255, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
93 17 0.07
94 238 0.93
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (94 bp):
AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGA
ATTGGCAGCAACCGAACAAATTTACTTTC
Found at i:21012 original size:20 final size:20
Alignment explanation
Indices: 20987--21027 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20977 CAATCGATAG
* *
20987 TCATTTTCGTGTTGTGATTT
1 TCATTTTCATGTTGCGATTT
21007 TCATTTTCATGTTGCGATTT
1 TCATTTTCATGTTGCGATTT
21027 T
1 T
21028 AAGTTTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (20 bp):
TCATTTTCATGTTGCGATTT
Found at i:21628 original size:34 final size:34
Alignment explanation
Indices: 21566--21631 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
21556 AAAAATCGCG
* *
21566 TTGCGATTTACGGATACGCGTTGTGATTTACGCA
1 TTGCGATTTACGGATACGCGGTGCGATTTACGCA
* * *
21600 TTGCGATTTACGTATTCTCGGTGCGATTTACG
1 TTGCGATTTACGGATACGCGGTGCGATTTACG
21632 GATACGCGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (34 bp):
TTGCGATTTACGGATACGCGGTGCGATTTACGCA
Found at i:21652 original size:21 final size:20
Alignment explanation
Indices: 21562--21667 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
21552 CTTTAAAAAT
21562 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
21582 CGCGTTGTGA-TT-----TA
1 CGCGTTGCGATTTACGGATA
* * *
21596 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
21616 CTCGGTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
21636 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
21657 CTCGTTGCGAT
1 CGCGTTGCGAT
21668 AGTCAGAATC
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
19 2 0.03
20 34 0.51
21 19 0.28
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:21840 original size:20 final size:20
Alignment explanation
Indices: 21729--21844 Score: 67
Period size: 21 Copynumber: 5.7 Consensus size: 20
21719 ATTTTCATAT
* *
21729 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTAG-AAA
* **
21750 TCGCAATGCGAATTCGTA-CTA
1 TCGCATTGCG-ATTC-TAGAAA
* **
21771 TCGCATTGCGATTATTCATAA
1 TCGCATTGCGATTCTAGA-AA
* *
21792 TCGCGTTGCGATTCTAAGAAC
1 TCGCATTGCGATTCT-AGAAA
21813 T-G-ATTTGCGATTCTAGAAA
1 TCGCA-TTGCGATTCTAGAAA
21832 TCGCATTGCGATT
1 TCGCATTGCGATT
21845 TTTATTTCTC
Statistics
Matches: 70, Mismatches: 17, Indels: 17
0.67 0.16 0.16
Matches are distributed among these distances:
19 6 0.09
20 23 0.33
21 35 0.50
22 5 0.07
23 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTCTAGAAA
Found at i:24800 original size:40 final size:42
Alignment explanation
Indices: 24742--24833 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 42
24732 GATTAAGGTA
* *
24742 ATAAATTA-TTACTACATATTAAACTC-ATA-TATTAAAAAT
1 ATAAATGAGTTACTACATATTAAACGCAATAGTATTAAAAAT
24781 ATAAATGAGTTACTACATATTAAACGCATATAGTATTAAAAAT
1 ATAAATGAGTTACTACATATTAAACGCA-ATAGTATTAAAAAT
*
24824 ATATATGAGT
1 ATAAATGAGT
24834 ATATTATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 7 0.15
40 17 0.37
42 3 0.07
43 19 0.41
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (42 bp):
ATAAATGAGTTACTACATATTAAACGCAATAGTATTAAAAAT
Found at i:24986 original size:40 final size:40
Alignment explanation
Indices: 24942--25025 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
24932 TTTATAACCC
*
24942 TTTAGATAAAATAATATAACATCATACAATAAGAATCAAA
1 TTTAGATAAAATAATATAACATCATACAATAAGAATAAAA
* *
24982 TTTAGATAAAATAATATAACATCATAGATTAAGAATAAAA
1 TTTAGATAAAATAATATAACATCATACAATAAGAATAAAA
25022 TTTA
1 TTTA
25026 TAATTAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (40 bp):
TTTAGATAAAATAATATAACATCATACAATAAGAATAAAA
Found at i:43776 original size:21 final size:21
Alignment explanation
Indices: 43750--43793 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
43740 CATTCATGTA
43750 GATCGTGTAATACACGTATAT
1 GATCGTGTAATACACGTATAT
43771 GATCGTGTAATACACGTATAT
1 GATCGTGTAATACACGTATAT
43792 GA
1 GA
43794 ATGAGAGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (21 bp):
GATCGTGTAATACACGTATAT
Found at i:50410 original size:36 final size:36
Alignment explanation
Indices: 50336--50410 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
50326 TTTTTATATT
*
50336 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
50372 TTTAATTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
50408 TTT
1 TTT
50411 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:56330 original size:38 final size:39
Alignment explanation
Indices: 56269--56346 Score: 106
Period size: 38 Copynumber: 2.0 Consensus size: 39
56259 ACTTAACGTT
*
56269 AAATTTTCAACGGTGATATTAAAAGGAAACAAAAAATAA
1 AAATTTTCAACGGTGATACTAAAAGGAAACAAAAAATAA
* *
56308 AAATTTT-AACGGGTG-TACTAAAATGAAATAAAAAATAA
1 AAATTTTCAAC-GGTGATACTAAAAGGAAACAAAAAATAA
56346 A
1 A
56347 CTTTAGGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 24 0.69
39 11 0.31
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.24
Consensus pattern (39 bp):
AAATTTTCAACGGTGATACTAAAAGGAAACAAAAAATAA
Found at i:57792 original size:12 final size:12
Alignment explanation
Indices: 57769--57801 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57759 CGTTTACATG
57769 ATATAT-AATTT
1 ATATATAAATTT
57780 ATATATAAATTT
1 ATATATAAATTT
*
57792 ATATAAAAAT
1 ATATATAAAT
57802 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATAAATTT
Found at i:59594 original size:31 final size:31
Alignment explanation
Indices: 59525--59596 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
59515 GAAATGAAAC
* * *
59525 TTTCAAAAGTTTAGGGATCAAAGTGTAAAGT
1 TTTCAAAAGTTTAGGAATAAAAGTATAAAGT
* *
59556 TAT-AAAAGTTTAGTAACTAAAAGTATAAA-T
1 TTTCAAAAGTTTAGGAA-TAAAAGTATAAAGT
59586 TTTCAAAAGTT
1 TTTCAAAAGTT
59597 ATATTTTGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (31 bp):
TTTCAAAAGTTTAGGAATAAAAGTATAAAGT
Found at i:65980 original size:19 final size:19
Alignment explanation
Indices: 65938--66008 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
65928 TGACTTCTGT
* * *
65938 GTTGCGAATTTGGAAACCGT
1 GTTGCGAA-TTCGAAATCGA
65958 GTTGCGAATTCGAAATCGA
1 GTTGCGAATTCGAAATCGA
* *
65977 GTTGCAAATTCGAAATTGA
1 GTTGCGAATTCGAAATCGA
*
65996 ATTGCGAATTCGA
1 GTTGCGAATTCGA
66009 TGGTTATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 36 0.82
20 8 0.18
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (19 bp):
GTTGCGAATTCGAAATCGA
Found at i:66542 original size:17 final size:17
Alignment explanation
Indices: 66511--66562 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
66501 AGAATGAAAA
* *
66511 AAGAAAAGATGAAGAAG
1 AAGAAAAAATAAAGAAG
*
66528 AAGAAAAAATAAAGATG
1 AAGAAAAAATAAAGAAG
*
66545 AAAGAAGAAA-AAAGAAG
1 -AAGAAAAAATAAAGAAG
66562 A
1 A
66563 GTTGACGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 1 0.03
17 20 0.69
18 8 0.28
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (17 bp):
AAGAAAAAATAAAGAAG
Found at i:66551 original size:21 final size:24
Alignment explanation
Indices: 66501--66560 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 24
66491 TATTTGAGAG
66501 AGAATGAAAAAAGAAAAGATGAAGA
1 AGAA-GAAAAAAGAAAAGATGAAGA
*
66526 AGAAGAAAAAA-TAAAGATG-A-A
1 AGAAGAAAAAAGAAAAGATGAAGA
66547 AGAAGAAAAAAGAA
1 AGAAGAAAAAAGAA
66561 GAGTTGACGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 7 0.22
24 7 0.22
25 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (24 bp):
AGAAGAAAAAAGAAAAGATGAAGA
Found at i:68915 original size:7 final size:7
Alignment explanation
Indices: 68905--68965 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
68895 ACCTTAAATC
68905 CTAAACT
1 CTAAACT
68912 CTAAAC-
1 CTAAACT
68918 CATAAACT
1 C-TAAACT
*
68926 CTAAACC
1 CTAAACT
68933 CTAAACT
1 CTAAACT
*
68940 TTAAAC-
1 CTAAACT
68946 CTTAAAC-
1 C-TAAACT
68953 CATAAACT
1 C-TAAACT
68961 CTAAA
1 CTAAA
68966 AGTAAAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
6 1 0.02
7 42 0.93
8 2 0.04
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAAACT
Found at i:68916 original size:14 final size:13
Alignment explanation
Indices: 68899--68965 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 13
68889 CGTAAAACCT
68899 TAAATCCTAAACTC
1 TAAA-CCTAAACTC
68913 TAAACCATAAACTC
1 TAAACC-TAAACTC
*
68927 TAAACCCTAAACTT
1 TAAA-CCTAAACTC
68941 TAAACCTTAAAC-C
1 TAAACC-TAAACTC
68954 ATAAACTCTAAA
1 -TAAAC-CTAAA
68966 AGTAAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
13 4 0.09
14 39 0.85
15 3 0.07
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAACCTAAACTC
Found at i:68918 original size:21 final size:20
Alignment explanation
Indices: 68893--68959 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
68883 AATTATCGTA
*
68893 AAACCTTAAATCCTAAACTCT
1 AAACCTTAAA-CCTAAACCCT
*
68914 AAACCATAAACTCTAAACCCT
1 AAACCTTAAAC-CTAAACCCT
* *
68935 AAACTTTAAACCTTAAACCAT
1 AAACCTTAAACC-TAAACCCT
68956 AAAC
1 AAAC
68960 TCTAAAAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.95
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACCTTAAACCTAAACCCT
Found at i:71349 original size:14 final size:14
Alignment explanation
Indices: 71326--71355 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71316 GGAAATATGA
*
71326 CCTCCGAGGATCCT
1 CCTCCAAGGATCCT
71340 CCTCCAAGGATCCT
1 CCTCCAAGGATCCT
71354 CC
1 CC
71356 AAAGACATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.47, G:0.17, T:0.20
Consensus pattern (14 bp):
CCTCCAAGGATCCT
Found at i:75422 original size:21 final size:20
Alignment explanation
Indices: 75392--75435 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
75382 AATAATACAT
* *
75392 AAAAAATAATTATTATTTTA
1 AAAAAATAATAATAATTTTA
75412 AAAATAATAATAATAATTTTA
1 AAAA-AATAATAATAATTTTA
75433 AAA
1 AAA
75436 TTTTTAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATAATAATAATTTTA
Found at i:77159 original size:15 final size:14
Alignment explanation
Indices: 77131--77157 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
77121 GACTAAAATC
77131 TTTAAAACTTTTTA
1 TTTAAAACTTTTTA
77145 TTTAAAACTTTTT
1 TTTAAAACTTTTT
77158 TAAAGTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAAAACTTTTTA
Done.