Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003197.1 Hibiscus syriacus cultivar Beakdansim tig00006728_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: 66051
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3020 original size:21 final size:21
Alignment explanation
Indices: 2972--3027 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
2962 GTAATTTTCC
*
2972 TAATTCGCATTGCGATTTACG
1 TAATTCGCATTGCGATTTACA
* **
2993 T-ATTCGCGTTGCGATTTTTA
1 TAATTCGCATTGCGATTTACA
*
3013 TAATTCGCAATGCGA
1 TAATTCGCATTGCGA
3028 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (21 bp):
TAATTCGCATTGCGATTTACA
Found at i:3610 original size:20 final size:20
Alignment explanation
Indices: 3582--3648 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 20
3572 TTCGAGAATG
3582 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGCGGAAATA
** *
3602 ATTATCGCAACG-AGAAATA
1 AAAATCGCAACGCGGAAATA
**
3621 AAAATCGCAACGC-GAAACC
1 AAAATCGCAACGCGGAAATA
3640 AAAATCGCA
1 AAAATCGCA
3649 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAATA
Found at i:3647 original size:38 final size:38
Alignment explanation
Indices: 3574--3648 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
3564 GAAGAAGTTT
* * *
3574 CGAGAATGAAAATCGCAACGCGGAAATAATTATCGCAA
1 CGAGAATAAAAATCGCAACGCGGAAACAATAATCGCAA
3612 CGAGAAATAAAAATCGCAACGC-GAAACCAA-AATCGCA
1 CGAG-AATAAAAATCGCAACGCGGAAA-CAATAATCGCA
3649 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 14 0.44
39 18 0.56
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (38 bp):
CGAGAATAAAAATCGCAACGCGGAAACAATAATCGCAA
Found at i:3666 original size:19 final size:19
Alignment explanation
Indices: 3644--3808 Score: 152
Period size: 19 Copynumber: 9.1 Consensus size: 19
3634 GAAACCAAAA
*
3644 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3663 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3677 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3696 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
**
3715 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
3734 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
3748 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
3767 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
3787 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3807 TC
1 TC
3809 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
14 20 0.17
16 5 0.04
17 5 0.04
19 57 0.48
20 31 0.26
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3691 original size:33 final size:33
Alignment explanation
Indices: 3649--3783 Score: 162
Period size: 33 Copynumber: 3.9 Consensus size: 33
3639 CAAAATCGCA
**
3649 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
** * *
3682 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCG
1 TTGCGATAGTCATTTCGCGTTGCGA----T-TCTCTCG
3720 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
3753 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
3784 ATTATCTCGT
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 45 0.50
34 16 0.18
37 1 0.01
38 28 0.31
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:3733 original size:38 final size:37
Alignment explanation
Indices: 3649--3808 Score: 138
Period size: 33 Copynumber: 4.4 Consensus size: 37
3639 CAAAATCGCA
** *
3649 TTGCGATTTTCATTTCGCGTTGCGA---T-TCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTTTATTTCTCG
** *
3682 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCG
1 TTGCGATAGTCATTTCGCGTTGCGA-TTTTATTTCTCG
*
3720 TTGCGATAGTCATTTCGCGTTGCGA---T-TCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTTTATTTCTCG
*
3753 TTGCGATAGTCATTTCCGCGTTGCGATTCTCATTATCTCG
1 TTGCGATAGTCATTT-CGCGTTGCGATT-TTATT-TCTCG
**
3793 TTGCGATTTTCATTTC
1 TTGCGATAGTCATTTC
3809 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
33 45 0.43
34 11 0.10
37 1 0.01
38 28 0.27
39 2 0.02
40 18 0.17
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (37 bp):
TTGCGATAGTCATTTCGCGTTGCGATTTTATTTCTCG
Found at i:3766 original size:71 final size:73
Alignment explanation
Indices: 3643--3808 Score: 246
Period size: 71 Copynumber: 2.3 Consensus size: 73
3633 CGAAACCAAA
* **
3643 ATCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTT-CGCGTTGCGA
1 ATCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGA
* *
3707 TTTTTATT
66 TTCTCATT
**
3715 -TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGA
1 ATCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGA
3779 TTCTCATT
66 TTCTCATT
*
3787 ATCTCGTTGCGATTTTCATTTC
1 ATCGCGTTGCGATTTTCATTTC
3809 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 48 0.59
72 16 0.20
73 18 0.22
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (73 bp):
ATCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGA
TTCTCATT
Found at i:5998 original size:21 final size:20
Alignment explanation
Indices: 5939--5999 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
5929 TCCTCGAGTC
5939 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
5959 CCACTGTCATCGTTAAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
5980 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
6000 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.25, C:0.38, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:6922 original size:19 final size:19
Alignment explanation
Indices: 6895--7031 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
6885 ATTAAACAAA
*
6895 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6914 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
6930 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6947 TCGCATTGCGATTTT--TT
1 TCGCGTTGCGATTTTCATT
*
6964 T--CGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * ***
6981 TCACATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
7000 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATTTTCA-TT
*
7021 TCGTGTTGCGA
1 TCGCGTTGCGA
7032 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
14 8 0.09
15 13 0.14
16 2 0.02
17 8 0.09
18 3 0.03
19 33 0.36
20 22 0.24
21 3 0.03
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6942 original size:33 final size:33
Alignment explanation
Indices: 6900--6992 Score: 141
Period size: 34 Copynumber: 2.8 Consensus size: 33
6890 ACAAATCGCA
*
6900 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
6933 TTGCGATTTTCATTTCGCATTGCGATTTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTTTGTCG
* *
6967 TTACGATTTTCATTTCACATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
6993 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 25 0.45
34 30 0.55
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:7011 original size:20 final size:20
Alignment explanation
Indices: 6986--7031 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
6976 TCATTTCACA
6986 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
7006 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
7026 TTGCGA
1 TTGCGA
7032 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:7531 original size:18 final size:18
Alignment explanation
Indices: 7505--7549 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
7495 GGTCGATCAA
*
7505 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
7523 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
7541 TGATGGCTC
1 TGATGGCTC
7550 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:8888 original size:20 final size:20
Alignment explanation
Indices: 8863--8903 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8853 ATAGTTTCTG
8863 AAATGAAAATCGCAACACGA
1 AAATGAAAATCGCAACACGA
** *
8883 AAATGACTATCGCAACGCGA
1 AAATGAAAATCGCAACACGA
8903 A
1 A
8904 TTTGACTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (20 bp):
AAATGAAAATCGCAACACGA
Found at i:8909 original size:20 final size:20
Alignment explanation
Indices: 8871--8919 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
8861 TGAAATGAAA
*
8871 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
8891 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
8911 ATCGCAACG
1 ATCGCAACG
8920 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:9478 original size:20 final size:20
Alignment explanation
Indices: 9453--9506 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
9443 GATTTTGTAT
9453 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
9473 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
9493 TATCGCATTGCGAT
1 TATCGCATTGCGAT
9507 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:9484 original size:41 final size:41
Alignment explanation
Indices: 9392--9505 Score: 135
Period size: 41 Copynumber: 2.8 Consensus size: 41
9382 CGCTTTGAAA
*
9392 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAAT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAAT
* * * *
9433 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGT-AAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAA-T
*
9474 ATCGCATTGCGA-TA-GTCAGTATCGCATTGCGA
1 ATCGCATTGCGATTATGT-ATTATCGCATTGCGA
9506 TTTTCCCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
39 2 0.03
40 17 0.27
41 43 0.69
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAAT
Found at i:9491 original size:61 final size:62
Alignment explanation
Indices: 9392--9509 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
9382 CGCTTTGAAA
* * * *
9392 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAATATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
* *
9454 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT
9510 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 2 0.04
61 35 0.71
62 12 0.24
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
Found at i:9617 original size:21 final size:21
Alignment explanation
Indices: 9577--9617 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9567 ACTGTAGACC
** *
9577 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
9598 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
9618 ACGAATTTGC
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:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:12257 original size:13 final size:13
Alignment explanation
Indices: 12239--12271 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12229 TATATTTTAC
*
12239 CCCTAACTTAAAA
1 CCCTAAATTAAAA
12252 CCCTAAATTAAAA
1 CCCTAAATTAAAA
12265 CCCTAAA
1 CCCTAAA
12272 ATCTATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (13 bp):
CCCTAAATTAAAA
Found at i:14316 original size:21 final size:22
Alignment explanation
Indices: 14292--14340 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
14282 GGATTATTAC
14292 GTCAACAAC-GTGAATTATCAT
1 GTCAACAACTGTGAATTATCAT
*
14313 GTCAGC-ACTGTGAATTATCAT
1 GTCAACAACTGTGAATTATCAT
*
14334 ATCAACA
1 GTCAACA
14341 CATAACTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (22 bp):
GTCAACAACTGTGAATTATCAT
Found at i:15123 original size:23 final size:24
Alignment explanation
Indices: 15093--15137 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
15083 ATATATAATT
*
15093 GTAAATTAGTT-ATAAAATTAAAG
1 GTAAATTAGTTAAAAAAATTAAAG
*
15116 GTAAATTATTTAAAAAAATTAA
1 GTAAATTAGTTAAAAAAATTAA
15138 TTACATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (24 bp):
GTAAATTAGTTAAAAAAATTAAAG
Found at i:21186 original size:112 final size:111
Alignment explanation
Indices: 21066--21282 Score: 242
Period size: 112 Copynumber: 1.9 Consensus size: 111
21056 TGAGAAAAAA
* * * * *
21066 AATAATTTATATATATTTATAAATAAAATGTTTAT-T-TATTTAGAAATATCAGAAAAGGACTTC
1 AATAATTTAAATAAAATTA-AAATAAAAT-TTTATATATATTTA-AAATACCAGAAAAGGACATC
* * * *
21129 TAGGTGTCTTAAGACAGCTCTTTTCTTCGATATT-AATAAATATTGATAT
63 CAGGTGTATTAAGACAGCCCTTTTCCTCGATATTGAA-AAATATTGATAT
* * *
21178 AATAATTTAAATAAAATTAAATTATAATTTTATATAATATTTAAAATACCAGAATAGGACATCCA
1 AATAATTTAAATAAAATTAAAATAAAATTTTATAT-ATATTTAAAATACCAGAAAAGGACATCCA
* *
21243 GTTGTATTAAGACTGCCCTTTTCCTCGATATTGAAAAATA
65 GGTGTATTAAGACAGCCCTTTTCCTCGATATTGAAAAATA
21283 AATATTAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
110 5 0.06
111 8 0.09
112 66 0.76
113 8 0.09
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (111 bp):
AATAATTTAAATAAAATTAAAATAAAATTTTATATATATTTAAAATACCAGAAAAGGACATCCAG
GTGTATTAAGACAGCCCTTTTCCTCGATATTGAAAAATATTGATAT
Found at i:21187 original size:23 final size:22
Alignment explanation
Indices: 21161--21218 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
21151 TTCTTCGATA
*
21161 TTAATAAATATTGATATAATAAT
1 TTAATAAATATT-AAATAATAAT
*
21184 TTAAATAAA-ATTAAATTATAAT
1 TT-AATAAATATTAAATAATAAT
*
21206 TTTATATAATATT
1 TTAATA-AATATT
21219 TAAAATACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 3 0.10
22 12 0.41
23 8 0.28
24 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATAAATATTAAATAATAAT
Found at i:22692 original size:3 final size:3
Alignment explanation
Indices: 22673--22740 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
22663 TTATAATATT
* *
22673 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAC TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
22720 TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
22741 ATTTAAATGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:22745 original size:15 final size:14
Alignment explanation
Indices: 22665--22746 Score: 82
Period size: 15 Copynumber: 5.9 Consensus size: 14
22655 ATTGGGCTTT
22665 ATAAT-ATTTAAT-
1 ATAATAATTTAATA
*
22677 A-AATAATAT-ATA
1 ATAATAATTTAATA
22689 ATAATAATTATAATA
1 ATAATAATT-TAATA
*
22704 ATAATAATACTAATA
1 ATAATAAT-TTAATA
22719 ATAATAATTTTAATA
1 ATAATAA-TTTAATA
22734 ATAATAAATTTAA
1 ATAAT-AATTTAA
22747 ATGAAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
11 5 0.09
12 5 0.09
13 6 0.10
14 1 0.02
15 38 0.66
16 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATAATTTAATA
Found at i:24221 original size:76 final size:76
Alignment explanation
Indices: 22872--24194 Score: 2468
Period size: 76 Copynumber: 17.4 Consensus size: 76
22862 GAAATGTTGA
* *
22872 AAACATCAGGCACTGAAGGGA-TTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCC
1 AAACATCATGCACTGAA-GGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCC
22936 GAAGGCTTTTTGG
64 GAAGGCTTTTTGG
* *
22949 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
23014 AGTCTTTTTGG
66 AGGCTTTTTGG
23025 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23090 AGGCTTTTTGG
66 AGGCTTTTTGG
23101 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23166 AGGCTTTTTGG
66 AGGCTTTTTGG
23177 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23242 AGGCTTTTTGG
66 AGGCTTTTTGG
23253 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23318 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
23329 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23394 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
23405 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
23470 AGTCTTTTTGG
66 AGGCTTTTTGG
*
23481 AAACATCATGCACTGAATGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23546 AGGCTTTTTGG
66 AGGCTTTTTGG
23557 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23622 AGGCTTTTTGG
66 AGGCTTTTTGG
23633 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23698 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
23709 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23774 AGGCTTTTTGG
66 AGGCTTTTTGG
23785 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23850 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
23861 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23926 AGGCTTTTTGG
66 AGGCTTTTTGG
23937 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
24002 AGGCTTTTTGG
66 AGGCTTTTTGG
24013 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
24078 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
24089 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
24154 AGGCTTTTTGG
66 AGGCTTTTTGG
24165 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
24195 TGGGAAATAG
Statistics
Matches: 1217, Mismatches: 28, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
76 1185 0.97
77 32 0.03
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:24897 original size:22 final size:22
Alignment explanation
Indices: 24872--24927 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
24862 CATAAAGCTT
* *
24872 TCATCTTTGAAAAGAGAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* *
24894 TCATCTTTTAAAAAGGGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
24917 TCATCTTTGAA
1 TCATCTTTGAA
24928 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:29333 original size:7 final size:7
Alignment explanation
Indices: 29321--29370 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
29311 TGATTCAATT
29321 TTTTTTC
1 TTTTTTC
29328 TTTTTTC
1 TTTTTTC
29335 TTTTTT-
1 TTTTTTC
29341 TTTTTGT-
1 TTTTT-TC
*
29348 TTTGTT-
1 TTTTTTC
29354 TTTTTTC
1 TTTTTTC
*
29361 TTCTTTC
1 TTTTTTC
29368 TTT
1 TTT
29371 GCTGGATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 11 0.30
7 26 0.70
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:29341 original size:17 final size:17
Alignment explanation
Indices: 29319--29370 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
29309 CTTGATTCAA
29319 TTTTTTTTCTTTTTTCT
1 TTTTTTTTCTTTTTTCT
*
29336 TTTTTTTT-TTGTTTT-G
1 TTTTTTTTCTT-TTTTCT
*
29352 TTTTTTTTCTTCTTTCT
1 TTTTTTTTCTTTTTTCT
29369 TT
1 TT
29371 GCTGGATGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.87
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTCT
Found at i:34643 original size:23 final size:22
Alignment explanation
Indices: 34617--34674 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
34607 TTCTTCGATA
*
34617 TTAATAAATATTGATATAATAAT
1 TTAATAAATATT-AAATAATAAT
*
34640 TTAAATAAA-ATTAAATTATAAT
1 TT-AATAAATATTAAATAATAAT
*
34662 TTTATATAATATT
1 TTAATA-AATATT
34675 TAAAATACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 3 0.10
22 12 0.41
23 8 0.28
24 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATAAATATTAAATAATAAT
Found at i:36136 original size:3 final size:3
Alignment explanation
Indices: 36117--36181 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
36107 TTATAATATT
* *
36117 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
36164 TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
36182 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:36146 original size:12 final size:12
Alignment explanation
Indices: 36109--36179 Score: 74
Period size: 12 Copynumber: 5.7 Consensus size: 12
36099 ATTGGGCTTT
36109 ATAAT-ATT-TA
1 ATAATAATTATA
36119 ATAAATAATATATA
1 AT-AATAAT-TATA
36133 ATAATAATTATA
1 ATAATAATTATA
36145 ATAATAATACTAATA
1 ATAATAAT--T-ATA
*
36160 ATAATAATTTTA
1 ATAATAATTATA
36172 ATAATAAT
1 ATAATAAT
36180 AAATTTAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
10 2 0.04
11 3 0.06
12 24 0.45
13 8 0.15
14 5 0.09
15 11 0.21
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATAATTATA
Found at i:36186 original size:15 final size:14
Alignment explanation
Indices: 36109--36187 Score: 71
Period size: 15 Copynumber: 5.9 Consensus size: 14
36099 ATTGGGCTTT
36109 ATAAT-ATTTAAT-
1 ATAATAATTTAATA
*
36121 A-AATAATAT-ATA
1 ATAATAATTTAATA
36133 ATAATAA-TT-ATA
1 ATAATAATTTAATA
*
36145 ATAATAATACTAATA
1 ATAATAAT-TTAATA
36160 ATAATAATTTTAATA
1 ATAATAA-TTTAATA
36175 ATAATAAATTTAA
1 ATAAT-AATTTAA
36188 ATGAAAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.09
12 16 0.29
13 5 0.09
14 1 0.02
15 25 0.45
16 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATTTAATA
Found at i:41220 original size:54 final size:54
Alignment explanation
Indices: 41129--41238 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
41119 ATAATCATAT
* * * * *
41129 TCGTATGGCCTCGGTGGTGGTGATCGGAAATCGTCTCGTCCACCGTATCTATCA
1 TCGTAGGGCCTCGGTGGCGGTGACCGAAAATCATCTCGTCCACCGTATCTATCA
* **
41183 TCGTAGGGCCTCGGTGGCGGTGACCGAAAATTATCTCGTCTTCCGTATCTATCA
1 TCGTAGGGCCTCGGTGGCGGTGACCGAAAATCATCTCGTCCACCGTATCTATCA
41237 TC
1 TC
41239 ACCACTCCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (54 bp):
TCGTAGGGCCTCGGTGGCGGTGACCGAAAATCATCTCGTCCACCGTATCTATCA
Found at i:45661 original size:60 final size:60
Alignment explanation
Indices: 45582--45695 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
45572 TTGGGTGACC
* * *
45582 ATTTTGTAACTTTTGATAGTCGA-AGGACTCAATAAATTAACAATCTATAGTCAGAAGACA
1 ATTTTGTAACTTTTAATAGTCGAGA-GACTCAATAAAATAACAACCTATAGTCAGAAGACA
* * *
45642 ATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAATAATACCCTATAGTCAG
1 ATTTTGTAACTTTTAATAGTCGAGAGACTCAATAAAATAACAACCTATAGTCAG
45696 GGGACCATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAGAGACTCAATAAAATAACAACCTATAGTCAGAAGACA
Found at i:52479 original size:31 final size:31
Alignment explanation
Indices: 52441--52517 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
52431 AATTAGTGTG
*
52441 TTGATTTTAGTCCCTAACGTTATCGACCCGT
1 TTGATTTTAGTCCCTAACATTATCGACCCGT
* *
52472 TTGATTTTAGTCTCTAACATTATCGATCCGT
1 TTGATTTTAGTCCCTAACATTATCGACCCGT
*
52503 TCGATTTTAGTCCCT
1 TTGATTTTAGTCCCT
52518 CAACCATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.43
Consensus pattern (31 bp):
TTGATTTTAGTCCCTAACATTATCGACCCGT
Found at i:52549 original size:15 final size:15
Alignment explanation
Indices: 52529--52558 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52519 AACCATATTC
*
52529 GGGACTTAAATAAAA
1 GGGACTTAAACAAAA
52544 GGGACTTAAACAAAA
1 GGGACTTAAACAAAA
52559 TAGGTTAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.17
Consensus pattern (15 bp):
GGGACTTAAACAAAA
Done.