Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003363.1 Hibiscus syriacus cultivar Beakdansim tig00007074_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: 77222
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:69 original size:21 final size:20
Alignment explanation
Indices: 9--60 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1 TGCGATTC
9 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATAGTCATTT
* *
29 CCGCGTTGCGATAGTCATTT
1 TCTCGTTGCGATAGTCATTT
49 TCTCGTTGCGAT
1 TCTCGTTGCGAT
61 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
TCTCGTTGCGATAGTCATTT
Found at i:1374 original size:41 final size:41
Alignment explanation
Indices: 1328--1422 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
1318 CACCTCACCC
1328 AGAGCCATCACCTGATCGACCCGACTATACACCTCTAC-ACG
1 AGAGCCATCACCTGATCGACCCG-CTATACACCTCTACAACG
* *
1369 AGAGCCATCACCTGATCGACTCGCTATACACTTCTACAACG
1 AGAGCCATCACCTGATCGACCCGCTATACACCTCTACAACG
1410 AGAGCCATCACCT
1 AGAGCCATCACCT
1423 ATCCCGTCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 13 0.25
41 38 0.75
ACGTcount: A:0.29, C:0.37, G:0.15, T:0.19
Consensus pattern (41 bp):
AGAGCCATCACCTGATCGACCCGCTATACACCTCTACAACG
Found at i:1987 original size:21 final size:21
Alignment explanation
Indices: 1963--2029 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1953 TCATTCCTCG
1963 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
1984 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
2005 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
2026 AGAG
1 AGAG
2030 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:3547 original size:14 final size:14
Alignment explanation
Indices: 3528--3582 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3518 TGTGAATGAA
3528 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3542 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3561 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3575 AATCGCAA
1 AATCGCAA
3583 TGCGAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3563 original size:33 final size:33
Alignment explanation
Indices: 3511--3603 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
3501 AAAAATGACT
*
3511 ATCGCAATGTG-AATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3543 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3576 ATCGCAATGCGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
3604 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
32 10 0.17
33 47 0.81
34 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3566 original size:19 final size:18
Alignment explanation
Indices: 3511--3607 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 18
3501 AAAAATGACT
*
3511 ATCGCAATGTGAATGAAA
1 ATCGCAATGCGAATGAAA
*
3529 ATCGCAA--CG-A-GAGA
1 ATCGCAATGCGAATGAAA
3543 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCG-AATGAAA
*
3562 ATCGCAA--CG-A-GAGA
1 ATCGCAATGCGAATGAAA
3576 ATCGCAATGCGAAACT-AAA
1 ATCGCAATGCG-AA-TGAAA
*
3595 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3608 ACTAAATTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 5 0.08
17 2 0.03
18 11 0.18
19 22 0.35
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAATGCGAATGAAA
Found at i:3608 original size:19 final size:19
Alignment explanation
Indices: 3575--3613 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3565 GCAACGAGAG
*
3575 AATCGCAATGCGAAACTAA
1 AATCGCAACGCGAAACTAA
3594 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
3613 A
1 A
3614 TTCGTGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:3636 original size:19 final size:19
Alignment explanation
Indices: 3614--3789 Score: 138
Period size: 19 Copynumber: 9.7 Consensus size: 19
3604 CGAAACTAAA
*
3614 TTCGTGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3633 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
3648 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3666 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
3681 -TCTCGTTGCGATCTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
3699 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
**
3718 TTCTGCGTTGCGATTTTTGT
1 TTC-GCGTTGCGATTTTCAT
*
3738 TTCGCGTTACGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
3757 TTCGCATTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
3776 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
3790 AGACATTAAG
Statistics
Matches: 121, Mismatches: 24, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
14 18 0.15
16 6 0.05
17 6 0.05
19 67 0.55
20 24 0.20
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3658 original size:14 final size:14
Alignment explanation
Indices: 3639--3692 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
3629 TCATTTCGCT
3639 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
3653 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
3670 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
3686 TTGCGAT
1 TTGCGAT
3693 CTTCATTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:3661 original size:33 final size:33
Alignment explanation
Indices: 3619--3711 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3609 CTAAATTCGT
*
3619 GTTGCGATTTTCATTTCGCTTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
3652 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
3685 GTTGCGATCTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
3712 AGTCATTTCT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:3741 original size:39 final size:39
Alignment explanation
Indices: 3619--3796 Score: 148
Period size: 33 Copynumber: 4.9 Consensus size: 39
3609 CTAAATTCGT
*
3619 GTTGCGATTTTCATTTCGCTTTGCGAT--TC---TCT-C
1 GTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCTGC
3652 GTTGCGATTTTCATTTCGCATTGCGAT--TC---TCT-C
1 GTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCTGC
*
3685 GTTGCGATCTTCATTTCGCATTGCGATAGTCATTTCTGC
1 GTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCTGC
** * * **
3724 GTTGCGATTTTTGTTTCGCGTTACGATTTTCATTTC-GC
1 GTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCTGC
* * * *
3762 ATTGCGATTTTTATTTCCGCGTTGCGATAGACATT
1 GTTGCGATTTTCATTT-CGCATTGCGATAGTCATT
3797 AAGATGATTG
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
33 58 0.47
35 2 0.02
38 19 0.15
39 44 0.36
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (39 bp):
GTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCTGC
Found at i:5145 original size:11 final size:11
Alignment explanation
Indices: 5129--5154 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5119 GCTAATAGGA
5129 CCTATGCAATC
1 CCTATGCAATC
5140 CCTATGCAATC
1 CCTATGCAATC
5151 CCTA
1 CCTA
5155 AGATGCCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.38, G:0.08, T:0.27
Consensus pattern (11 bp):
CCTATGCAATC
Found at i:7258 original size:20 final size:20
Alignment explanation
Indices: 7234--7360 Score: 89
Period size: 20 Copynumber: 6.3 Consensus size: 20
7224 AGAATCTCGT
7234 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
* *
7254 CGCGATTACGTAAATCGTAA
1 TGCGATTACGTAAATCGCAA
*
7274 TGCGATTACGT-AATCGCAT
1 TGCGATTACGTAAATCGCAA
* *
7293 TGCGATTTACGT-ATTCGCAT
1 TGCGA-TTACGTAAATCGCAA
* * *
7313 TGCGAATTAGGAAAATTGCAA
1 TGCG-ATTACGTAAATCGCAA
* ** *
7334 CGCGAATTTGGGAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
7355 TGCGAT
1 TGCGAT
7361 AGTCAGAATC
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
19 15 0.17
20 46 0.53
21 26 0.30
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:7340 original size:21 final size:21
Alignment explanation
Indices: 7314--7359 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
7304 TATTCGCATT
*
7314 GCGAATTAGGAAAATTGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
7335 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
7356 GCGA
1 GCGA
7360 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:8309 original size:24 final size:24
Alignment explanation
Indices: 8282--8339 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
8272 AAATCAAAGC
*
8282 AGAAATCAGAACAAAATTCAGAGT
1 AGAAATCAGAACAAAATTCAGAGA
8306 AGAAATCAGAACAAAATTCAGAGA
1 AGAAATCAGAACAAAATTCAGAGA
*
8330 AAAAATCAGA
1 AGAAATCAGA
8340 TAAAATATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.14
Consensus pattern (24 bp):
AGAAATCAGAACAAAATTCAGAGA
Found at i:13145 original size:10 final size:9
Alignment explanation
Indices: 13132--13157 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
13122 CTTTTTTGGC
13132 TTTTTTTAT
1 TTTTTTTAT
13141 TTTTTTTAT
1 TTTTTTTAT
13150 TTTTTTTA
1 TTTTTTTA
13158 AATAGCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:17046 original size:23 final size:23
Alignment explanation
Indices: 17016--17060 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
17006 ACTTAAGTGC
*
17016 TTAATAATTTT-CTTTTCTTTTT
1 TTAATAATTTTACTTTTATTTTT
17038 TTAATTAATTTTACTTTTATTTT
1 TTAA-TAATTTTACTTTTATTTT
17061 CACCCACGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (23 bp):
TTAATAATTTTACTTTTATTTTT
Found at i:18229 original size:70 final size:70
Alignment explanation
Indices: 18142--18320 Score: 313
Period size: 70 Copynumber: 2.6 Consensus size: 70
18132 TAATTTTAGA
*
18142 AAAAAAATCTCACATGGTTAAGAAATATAGAAGAGCATCATAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGTTAAGAAATATAGAAGAGCATCATAAAAGTCTAAAGAGTAAAAATATG
18207 AAAAC
66 AAAAC
*
18212 AAAACAATCTCATATGGTTAAGAAATATAGAAGAGCATCATAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGTTAAGAAATATAGAAGAGCATCATAAAAGTCTAAAGAGTAAAAATATG
18277 AAAAC
66 AAAAC
** *
18282 AAAACAATCTCACATGACTAAGAAACATAGAAGAGCATC
1 AAAACAATCTCACATGGTTAAGAAATATAGAAGAGCATC
18321 CCAACTGACT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 103 1.00
ACGTcount: A:0.54, C:0.12, G:0.14, T:0.20
Consensus pattern (70 bp):
AAAACAATCTCACATGGTTAAGAAATATAGAAGAGCATCATAAAAGTCTAAAGAGTAAAAATATG
AAAAC
Found at i:26432 original size:40 final size:40
Alignment explanation
Indices: 26368--26460 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
26358 ATCCCTAAAC
*
26368 GTAACGCTCCAATCCTTTTCCTTTGATTTGTTGGGTCATA
1 GTAACGCTCCAATCCTTTTCCTTTGATTTGTTGGGTAATA
* * * *
26408 GTAACGGTCCAACTCGTTTT-CTTTGGTTTGTTTGGTAATA
1 GTAACGCTCCAA-TCCTTTTCCTTTGATTTGTTGGGTAATA
* *
26448 GCAACGTTCCAAT
1 GTAACGCTCCAAT
26461 GAAGCGGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.02
40 38 0.84
41 6 0.13
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.41
Consensus pattern (40 bp):
GTAACGCTCCAATCCTTTTCCTTTGATTTGTTGGGTAATA
Found at i:27581 original size:21 final size:21
Alignment explanation
Indices: 27556--27596 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
27546 TAGCTCCACC
27556 TTCATTGGAGAATTTGTACCT
1 TTCATTGGAGAATTTGTACCT
27577 TTCATTGGAGAATTTGTACC
1 TTCATTGGAGAATTTGTACC
27597 CATTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (21 bp):
TTCATTGGAGAATTTGTACCT
Found at i:29955 original size:20 final size:20
Alignment explanation
Indices: 29905--29955 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
29895 AATTACGATG
* *
29905 GTATCGATACTGACATTTTA
1 GTATCAATACTGACACTTTA
* *
29925 GTAT-ATGTACTGACCCTTTA
1 GTATCA-ATACTGACACTTTA
29945 GTATCAATACT
1 GTATCAATACT
29956 TTGCCTTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
GTATCAATACTGACACTTTA
Found at i:29962 original size:20 final size:20
Alignment explanation
Indices: 29939--29976 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29929 ATGTACTGAC
*
29939 CCTTTAGTATCAATACTTTG
1 CCTTAAGTATCAATACTTTG
*
29959 CCTTAAGTATCGATACTT
1 CCTTAAGTATCAATACTT
29977 CACTCTATTA
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:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (20 bp):
CCTTAAGTATCAATACTTTG
Found at i:30682 original size:100 final size:100
Alignment explanation
Indices: 30509--30699 Score: 292
Period size: 100 Copynumber: 1.9 Consensus size: 100
30499 GAGCTTACAA
* * * *
30509 AGCTCAACAATATAATCATTAATCTAGAACAATATTAAGGGTTACATAAACATAAGTGTGCTAAT
1 AGCTCAACAATATAATCATTAATCTAGAACAACATTAAGAGTTACATAAACAAAAGCGTGCTAAT
30574 GACGAGGTACTAAGAAGTAAGTACATACATGATAT
66 GACGAGGTACTAAGAAGTAAGTACATACATGATAT
* * * * *
30609 AGCTCAGCAATATAATCGTTAATCTCGAGCAACATTAAGAGTTACATAAAGAAAAGCGTGCTAAT
1 AGCTCAACAATATAATCATTAATCTAGAACAACATTAAGAGTTACATAAACAAAAGCGTGCTAAT
*
30674 GACGAGGTACTAAGCAGTAAGTACAT
66 GACGAGGTACTAAGAAGTAAGTACAT
30700 GCATTATCTA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (100 bp):
AGCTCAACAATATAATCATTAATCTAGAACAACATTAAGAGTTACATAAACAAAAGCGTGCTAAT
GACGAGGTACTAAGAAGTAAGTACATACATGATAT
Found at i:33170 original size:45 final size:46
Alignment explanation
Indices: 33082--33172 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
33072 TTGAAAAAGC
* * * * *
33082 CTGAGTGTATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCAAGGTCATGTACATCGATGCATAAAATGCA
33128 CTGAGTGCATCGATGCAAGGT-ATGTACATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCAAGGTCATGTACATCGATGCATAAAATGCA
33173 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCAAGGTCATGTACATCGATGCATAAAATGCA
Found at i:41263 original size:45 final size:46
Alignment explanation
Indices: 41175--41265 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
41165 TTGAAAAAGC
* * *
41175 CTGAGTGCATTGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
41221 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
41266 TTCGATGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:43885 original size:23 final size:23
Alignment explanation
Indices: 43852--43919 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
43842 AATCTTATAT
43852 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
43875 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
43898 GGCACTTCGATGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
43920 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:44684 original size:21 final size:21
Alignment explanation
Indices: 44658--44697 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44648 GGACCCCGAT
*
44658 TATCGATACTTCTTTGATAAG
1 TATCGATACTCCTTTGATAAG
44679 TATCGATACTCCTTTGATA
1 TATCGATACTCCTTTGATA
44698 CTTAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
TATCGATACTCCTTTGATAAG
Found at i:46528 original size:21 final size:21
Alignment explanation
Indices: 46504--46569 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
46494 GGCATATGAA
*
46504 AATTGTCCCGAAGGACCTGTG
1 AATTGTCCCGAAGGACCTATG
46525 AATTTGTCCCGAAGGACCTATG
1 AA-TTGTCCCGAAGGACCTATG
* *
46547 AGTTGTCCCGAAGGACTTATG
1 AATTGTCCCGAAGGACCTATG
46568 AA
1 AA
46570 ACCCTCGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 21 0.52
22 19 0.47
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
AATTGTCCCGAAGGACCTATG
Found at i:48043 original size:64 final size:63
Alignment explanation
Indices: 47945--48105 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
47935 TAATGAAGGT
* * *
47945 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
48008 GG
62 GC
*
48010 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
48074 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
48106 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:49052 original size:2 final size:2
Alignment explanation
Indices: 49045--49082 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
49035 CTTTTTCCTT
49045 TA 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 TA
49083 AATTCATATC
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):
TA
Found at i:51547 original size:22 final size:22
Alignment explanation
Indices: 51516--51587 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
51506 CTGAGTGGCA
51516 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
51539 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
51561 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
51582 TATGAA
1 TATGAA
51588 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:51572 original size:21 final size:21
Alignment explanation
Indices: 51524--51586 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
51514 CATATGAAAT
* *
51524 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
51546 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
51567 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
51587 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:53060 original size:64 final size:63
Alignment explanation
Indices: 52962--53122 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
52952 TAATGAAGGT
* * *
52962 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
53025 GG
62 GC
*
53027 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
53091 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
53123 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:54002 original size:38 final size:38
Alignment explanation
Indices: 53932--54014 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
53922 ATACAGGAAA
* * * *
53932 TAATTTTTCTATTCAAGACTCTGATACAATAAATTAAC
1 TAATCTTTCTATTCAAAACCCTAATACAATAAATTAAC
** * *
53970 TAATCTTTCTATTCAAAACCCTAATATTATAAATTCAT
1 TAATCTTTCTATTCAAAACCCTAATACAATAAATTAAC
54008 TAATCTT
1 TAATCTT
54015 CCTTAACACA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (38 bp):
TAATCTTTCTATTCAAAACCCTAATACAATAAATTAAC
Found at i:56273 original size:17 final size:17
Alignment explanation
Indices: 56265--56311 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
56255 TCAACGGTCG
56265 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
*
56282 GGTCAGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
56299 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
56312 TGGTCGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:56278 original size:22 final size:22
Alignment explanation
Indices: 56253--56295 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
56243 GAAAGTCAAC
*
56253 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCAGGTCGGGTCG
56275 GGTCAACGGTCAGGTCGGGTC
1 GGTCAACGGTCAGGTCGGGTC
56296 AACGGTCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCAGGTCGGGTCG
Found at i:63610 original size:9 final size:9
Alignment explanation
Indices: 63543--63642 Score: 74
Period size: 9 Copynumber: 10.3 Consensus size: 9
63533 GGGTCGGTCG
*
63543 GGTCAGACC
1 GGTCAAACC
63552 GGTCAAACC
1 GGTCAAACC
*
63561 GGTTCAGACC
1 GG-TCAAACC
63571 GGTCAGAACC
1 GGTCA-AACC
*
63581 GGTTCGAACC
1 GG-TCAAACC
* *
63591 GATTGAAACC
1 G-GTCAAACC
63601 GGTCAAACC
1 GGTCAAACC
63610 GGTCAGAACC
1 GGTCA-AACC
*
63620 GGTTGAAAACC
1 GG-T-CAAACC
*
63631 GGTTAAACC
1 GGTCAAACC
63640 GGT
1 GGT
63643 TTCCAGCAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
9 32 0.44
10 31 0.42
11 9 0.12
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:63639 original size:39 final size:38
Alignment explanation
Indices: 63549--63642 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 38
63539 GTCGGGTCAG
* *
63549 ACCGGTCAAACCGGTTCAGACCGGTCAGAACCGGTTCGA
1 ACCGGTTAAACCGG-TCAAACCGGTCAGAACCGGTTCGA
*
63588 ACCGATTGAAACCGGTCAAACCGGTCAGAACCGGTT-GAAA
1 ACCGGTT-AAACCGGTCAAACCGGTCAGAACCGGTTCG--A
63628 ACCGGTTAAACCGGT
1 ACCGGTTAAACCGGT
63643 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
38 1 0.02
39 33 0.69
40 14 0.29
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.16
Consensus pattern (38 bp):
ACCGGTTAAACCGGTCAAACCGGTCAGAACCGGTTCGA
Found at i:63643 original size:9 final size:9
Alignment explanation
Indices: 63549--63643 Score: 64
Period size: 10 Copynumber: 9.8 Consensus size: 9
63539 GTCGGGTCAG
*
63549 ACCGGTCAA
1 ACCGGTTAA
*
63558 ACCGGTTCAG
1 ACCGGTT-AA
*
63568 ACCGGTCAGA
1 ACCGGTTA-A
*
63578 ACCGGTTCGA
1 ACCGGTT-AA
*
63588 ACCGATTGAA
1 ACCGGTT-AA
*
63598 ACCGGTCAA
1 ACCGGTTAA
*
63607 ACCGGTCAGA
1 ACCGGTTA-A
63617 ACCGGTTGAAA
1 ACCGGTT--AA
63628 ACCGGTTAA
1 ACCGGTTAA
63637 ACCGGTT
1 ACCGGTT
63644 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
9 26 0.38
10 33 0.49
11 8 0.12
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Done.