Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008973.1 Hibiscus syriacus cultivar Beakdansim tig00112319_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: 2070395
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2024933 original size:20 final size:20
Alignment explanation
Indices: 2024908--2025000 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
2024898 TTTTCCCAAT
2024908 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
2024928 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
2024948 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
2024969 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
2024990 TCGCAATGCGA
1 TCGCAATGCGA
2025001 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:2024950 original size:41 final size:41
Alignment explanation
Indices: 2024905--2025000 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2024895 CGATTTTCCC
2024905 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
2024946 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
2024987 AAATCGCAATGCGA
1 AATTCGCAATGCGA
2025001 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:2024954 original size:21 final size:20
Alignment explanation
Indices: 2024908--2025000 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2024898 TTTTCCCAAT
*
2024908 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
2024928 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
2024948 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
2024969 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
2024990 TCGCAATGCGA
1 TCGCAATGCGA
2025001 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:2025013 original size:41 final size:41
Alignment explanation
Indices: 2024927--2025061 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
2024917 GAATAAGTAA
* * *
2024927 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
2024968 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
2025009 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
2025050 TTCGCAACGCGA
1 ATCGCAACGCGA
2025062 TACTGATTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:2025014 original size:20 final size:20
Alignment explanation
Indices: 2024989--2025082 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
2024979 AATTGGGAAA
*
2024989 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2025009 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2025030 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
2025050 TTCGCAACGCGATACTGATT
1 ATCGCAACGCGATACTGACT
*
2025070 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2025083 TTACATAGCG
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2025661 original size:19 final size:19
Alignment explanation
Indices: 2025601--2025681 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
2025591 TTCGAGAATG
2025601 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
2025621 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
2025637 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
2025654 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
2025673 AAAATCGCA
1 AAAATCGCA
2025682 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2025699 original size:19 final size:19
Alignment explanation
Indices: 2025677--2025861 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
2025667 GAAACCAAAA
*
2025677 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2025696 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2025715 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
2025734 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
2025754 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2025770 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2025787 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
** **
2025801 TCTAGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
2025820 TCCACGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2025840 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2025860 TC
1 TC
2025862 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 48 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2025754 original size:39 final size:38
Alignment explanation
Indices: 2025677--2025861 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
2025667 GAAACCAAAA
*
2025677 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
2025715 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
2025754 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
** **
2025787 TCGCGTTGCGA--TTC---TCTAGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
2025820 TCCACGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
2025860 TC
1 TC
2025862 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 9 0.07
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.25
40 17 0.14
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:2025838 original size:20 final size:20
Alignment explanation
Indices: 2025805--2025861 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2025795 CGATTCTCTA
**
2025805 GTTGCGATAGTCATTTCCAC
1 GTTGCGATTCTCATTTCCAC
*
2025825 GTTGCGATTCTCATTAT-CTC
1 GTTGCGATTCTCATT-TCCAC
*
2025845 GTTGCGATTTTCATTTC
1 GTTGCGATTCTCATTTC
2025862 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (20 bp):
GTTGCGATTCTCATTTCCAC
Found at i:2027944 original size:21 final size:21
Alignment explanation
Indices: 2027920--2027986 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2027910 TCATTCCTCG
2027920 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2027941 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2027962 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2027983 AGAG
1 AGAG
2027987 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2027944 original size:42 final size:42
Alignment explanation
Indices: 2027864--2027986 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
2027854 GCCCGACTCG
* * * * * * *
2027864 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
2027906 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
2027948 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2027987 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:2029364 original size:14 final size:14
Alignment explanation
Indices: 2029345--2029380 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2029335 ATTGTTTAAT
2029345 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2029359 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2029373 TGATTTGT
1 TGATTTGT
2029381 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2029563 original size:19 final size:20
Alignment explanation
Indices: 2029519--2029563 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2029509 GCAACGAGAG
2029519 AATT-GCAACGCGAAAATGA
1 AATTCGCAACGCGAAAATGA
* *
2029538 AAATCGCAACGCG-AAATTA
1 AATTCGCAACGCGAAAATGA
2029557 AATTCGC
1 AATTCGC
2029564 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (20 bp):
AATTCGCAACGCGAAAATGA
Found at i:2029605 original size:33 final size:32
Alignment explanation
Indices: 2029563--2029755 Score: 255
Period size: 33 Copynumber: 5.9 Consensus size: 32
2029553 ATTAAATTCG
2029563 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
2029596 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
2029629 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
2029662 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2029695 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
* *
2029728 TGTTGCGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2029756 AGTAATTTCC
Statistics
Matches: 142, Mismatches: 10, Indels: 16
0.85 0.06 0.10
Matches are distributed among these distances:
31 6 0.04
33 130 0.92
35 6 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2029638 original size:66 final size:66
Alignment explanation
Indices: 2029556--2029754 Score: 353
Period size: 66 Copynumber: 3.0 Consensus size: 66
2029546 ACGCGAAATT
2029556 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2029621 G
66 G
*
2029622 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2029687 G
66 G
* * * *
2029688 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTTGTTGCGATTTTCATTTCGTATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2029753 G
66 G
2029754 A
1 A
2029755 TAGTAATTTC
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 127 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:2032065 original size:12 final size:12
Alignment explanation
Indices: 2032048--2032072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2032038 TCTTCGGAGA
2032048 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2032060 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2032072 C
1 C
2032073 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2032281 original size:24 final size:24
Alignment explanation
Indices: 2032247--2032300 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2032237 CTGAAACATC
* *
2032247 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
2032271 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
2032295 ATCAAA
1 ATCAAA
2032301 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:2033385 original size:20 final size:20
Alignment explanation
Indices: 2033360--2033417 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2033350 ATTCATTTGA
2033360 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
2033380 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
2033400 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
2033418 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:2033477 original size:19 final size:19
Alignment explanation
Indices: 2033436--2033522 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
2033426 GAAATGAAAA
2033436 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2033452 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2033469 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2033488 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2033507 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
2033523 TCGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2033506 original size:38 final size:33
Alignment explanation
Indices: 2033436--2033551 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
2033426 GAAATGAAAA
2033436 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
2033469 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
***
2033507 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
2033540 TCGCGTTGCGAT
1 TCGCATTGCGAT
2033552 AGTCTGTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
35 3 0.04
36 3 0.04
38 30 0.41
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:2035575 original size:20 final size:19
Alignment explanation
Indices: 2035540--2035606 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2035530 GAAACTTAAA
2035540 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
2035559 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
2035579 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2035598 ATCGCAACG
1 ATCGCAACG
2035607 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2035614 original size:14 final size:14
Alignment explanation
Indices: 2035595--2035652 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2035585 ATGCGAAATG
2035595 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2035609 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2035625 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2035641 AAAATCGCAACG
1 AAAATCGCAACG
2035653 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2035637 original size:32 final size:33
Alignment explanation
Indices: 2035579--2035657 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2035569 GGAAATGGCT
*
2035579 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2035612 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2035644 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2035658 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2035708 original size:14 final size:14
Alignment explanation
Indices: 2035686--2035743 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2035676 TTTCATTTCG
*
2035686 CGTTACGATTTTGT
1 CGTTGCGATTTTGT
*
2035700 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2035716 CGTGTTGCGATTTTGT
1 C--GTTGCGATTTTGT
2035732 CGTTGCGATTTT
1 CGTTGCGATTTT
2035744 TATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 6 0.16
18 10 0.27
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2035757 original size:33 final size:33
Alignment explanation
Indices: 2035669--2035759 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
2035659 ACAAATCGCA
*
2035669 TTGCGATTTTCATTTCGCGTTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
2035702 TTGCGA-TTTCATTTCGTGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
2035734 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
2035760 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:2035767 original size:19 final size:20
Alignment explanation
Indices: 2035745--2035787 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2035735 TGCGATTTTT
*
2035745 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCAATAGCC
* *
2035764 ATTTCCGCGTTGCAATAGTC
1 ATTTCCGCATTGCAATAGCC
2035784 ATTT
1 ATTT
2035788 TCGTGTTGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCAATAGCC
Found at i:2036297 original size:18 final size:18
Alignment explanation
Indices: 2036271--2036315 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2036261 GTCGATCAGA
*
2036271 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
2036289 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
2036307 TGATGGCTC
1 TGATGGCTC
2036316 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:2037678 original size:20 final size:20
Alignment explanation
Indices: 2037635--2037672 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2037625 AATAGTTTCT
2037635 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2037655 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2037673 GAGAAACTAA
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2037947 original size:22 final size:22
Alignment explanation
Indices: 2037922--2037965 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2037912 GATTTAGATA
*
2037922 GACGGATTTCGTCGGAGATGGG
1 GACGAATTTCGTCGGAGATGGG
2037944 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGTCGGAGATGGG
2037966 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGAATTTCGTCGGAGATGGG
Found at i:2038178 original size:20 final size:20
Alignment explanation
Indices: 2038153--2038246 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2038143 GATTATGTAT
2038153 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2038173 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
2038193 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
2038214 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2038234 TATCGCATTGCGA
1 TATCGCGTTGCGA
2038247 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2038247 original size:20 final size:20
Alignment explanation
Indices: 2038133--2038247 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
2038123 CGCTTTGAAA
*
2038133 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
2038154 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
2038174 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2038194 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
2038215 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2038235 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2038248 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2038266 original size:41 final size:41
Alignment explanation
Indices: 2038175--2038309 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
2038165 AAAGTCAGTA
* * * ** *
2038175 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2038215 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
2038257 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2038298 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2038310 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2038280 original size:20 final size:20
Alignment explanation
Indices: 2038236--2038328 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2038226 ATAGTCAGTA
* **
2038236 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2038257 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2038277 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
2038298 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2038318 TCGCATTGCGA
1 TCGCATTGCGA
2038329 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2038310 original size:41 final size:41
Alignment explanation
Indices: 2038236--2038331 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2038226 ATAGTCAGTA
*
2038236 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2038277 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2038318 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2038332 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2039174 original size:200 final size:198
Alignment explanation
Indices: 2038782--2039189 Score: 552
Period size: 200 Copynumber: 2.1 Consensus size: 198
2038772 TTTAAAATAA
* * *
2038782 ACATTGCAAATTTATCTATTACATTATAATTATAGGTTTTGATGTTTTTGGGATCGATACAATTT
1 ACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTT
*
2038847 TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACAC
66 TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACAC
*
2038912 AAACTTAAAACATGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACCG
131 AAACTTAAAACATGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCG
2038977 AG-T
196 -GTT
* * *
2038980 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTT
* * *
2039044 AATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGACATTCATTCTGGACAAAATGTATCGA
66 --TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACATTCATTCTGGA-AAAAAGTATCGA
*** *** * * * *
2039109 CAC-TTTTTAAATTTGTGTTGATACATTATGTTGGCCTATTCTCTCATAAAATCGGTATATTTAT
128 CACAAACTTAAA-ACATGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTAT
2039173 ACCGGTT
192 ACCGGTT
*
2039180 ATATTGTAAA
1 ACATTGTAAA
2039190 ACAATAATTG
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
197 3 0.02
198 55 0.30
199 53 0.29
200 72 0.39
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (198 bp):
ACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATACAATTT
TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACAC
AAACTTAAAACATGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCG
GTT
Found at i:2039526 original size:24 final size:23
Alignment explanation
Indices: 2039499--2039554 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
2039489 TTACCAAGGA
2039499 TAACAATAAAATAATATTATTTAT
1 TAACAATAAAATAATATTATTT-T
2039523 TAACAA-AATAATAATATTATTTT
1 TAACAATAA-AATAATATTATTTT
2039546 TAA-AATAAA
1 TAACAATAAA
2039555 CATTGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.10
23 8 0.27
24 19 0.63
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
TAACAATAAAATAATATTATTTT
Found at i:2039939 original size:200 final size:198
Alignment explanation
Indices: 2039554--2039994 Score: 624
Period size: 200 Copynumber: 2.2 Consensus size: 198
2039544 TTTAAAATAA
* * *
2039554 ACATTGCAAATTTA--TCTTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACAATTT
*
2039617 TAAATGTATTGACACTTTATGCGTGCACCTCGTTGGACATTCATTATGGAAAAAAGTATCGACAC
66 TAAATGTATTAACACTTTATGCGTGCACCTCGTTGGACATTCATTATGGAAAAAAGTATCGACAC
* *
2039682 AAACTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACCG
131 AAACTTAAAATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCG
2039747 AG-T
196 -GTT
* *
2039750 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCAATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACAATTT
* *
2039814 AATAAATGTATTAACACTTTATGTGTGCACCTCGTTTGG-CATTCATTCTGGAAAAAATGTATCG
66 --TAAATGTATTAACACTTTATGCGTGCACCTCG-TTGGACATTCATTATGGAAAAAA-GTATCG
*** * * *
2039878 ACAC-TTTTTAAATTTGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATCAGTATATTTA
127 ACACAAACTTAAA-ATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCAGTATATTTA
2039942 TACCGGTT
191 TACCGGTT
* *
2039950 ATATTGTAATTTTACCTATTACATTATAATTATCGGTTTCGATGT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
2039995 AACATATGTG
Statistics
Matches: 218, Mismatches: 19, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
196 13 0.06
197 3 0.01
198 41 0.19
199 53 0.24
200 108 0.50
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (198 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACAATTT
TAAATGTATTAACACTTTATGCGTGCACCTCGTTGGACATTCATTATGGAAAAAAGTATCGACAC
AAACTTAAAATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCG
GTT
Found at i:2040161 original size:30 final size:29
Alignment explanation
Indices: 2040095--2040181 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 29
2040085 TTATAATAAA
2040095 TAAT-AAATATAATTTATAATAATTTTATTT
1 TAATAAAATATAA--TATAATAATTTTATTT
2040125 TAATAAAATATAATAATAATAATTTT-TTAT
1 TAATAAAATATAAT-ATAATAATTTTATT-T
*
2040155 TTATAAAATTATAGATATAAT-ATTTTA
1 TAATAAAA-TATA-ATATAATAATTTTA
2040182 ATAGTAATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
29 3 0.06
30 28 0.56
31 17 0.34
32 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAATAAAATATAATATAATAATTTTATTT
Found at i:2040275 original size:24 final size:25
Alignment explanation
Indices: 2040207--2040275 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
2040197 TAAATAATAT
*
2040207 TAAATAA-ATTATTCTAATATT-TTAA
1 TAAATAATATTA-T-TATTATTGTTAA
2040232 -AAATAATATTATTATT-TTGTTAA
1 TAAATAATATTATTATTATTGTTAA
2040255 TAAATAATATTATT-TTATTGT
1 TAAATAATATTATTATTATTGT
2040276 ATTTGATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.23
24 24 0.62
25 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTGTTAA
Found at i:2046846 original size:26 final size:24
Alignment explanation
Indices: 2046775--2046846 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
2046765 TTATATTTGT
2046775 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
2046800 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
2046822 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2046847 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:2057328 original size:18 final size:17
Alignment explanation
Indices: 2057288--2057329 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
2057278 ATAAAATACA
2057288 ACATTCCCAGTAATCTT
1 ACATTCCCAGTAATCTT
2057305 --ATTCCCTAGTAATCTT
1 ACATTCCC-AGTAATCTT
2057321 ACATTCCCA
1 ACATTCCCA
2057330 CTGATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.27
16 9 0.41
17 1 0.05
18 6 0.27
ACGTcount: A:0.29, C:0.31, G:0.05, T:0.36
Consensus pattern (17 bp):
ACATTCCCAGTAATCTT
Found at i:2061306 original size:20 final size:20
Alignment explanation
Indices: 2061281--2061319 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2061271 TTTTCAAGGG
2061281 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
2061301 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
2061320 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:2061388 original size:45 final size:46
Alignment explanation
Indices: 2061339--2061429 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
2061329 GAACATCGAA
* *
2061339 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
2061384 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
2061430 GATTTTTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 21 0.49
46 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Done.