Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002334.1 Hibiscus syriacus cultivar Beakdansim tig00004770_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: 102405
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:5076 original size:15 final size:15
Alignment explanation
Indices: 5041--5085 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
5031 CTCTATTTTA
5041 ATTAATAAAATAATATT
1 ATTAAT-AAAT-ATATT
5058 -TTAATAAATATATT
1 ATTAATAAATATATT
*
5072 ATTAAAAAATATAT
1 ATTAATAAATATAT
5086 AAACTCTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 5 0.19
15 16 0.62
16 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAATAAATATATT
Found at i:5743 original size:20 final size:20
Alignment explanation
Indices: 5715--5772 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
5705 TAACTTATCC
*
5715 AAATAATTATCAAAATTATT
1 AAATTATTATCAAAATTATT
* *
5735 AAATTATTATAAATAATTGTT
1 AAATTATTATCAA-AATTATT
5756 AAA-T-TTATCAAATATTA
1 AAATTATTATCAAA-ATTA
5773 ATATTGTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 9 0.29
20 12 0.39
21 9 0.29
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATTATTATCAAAATTATT
Found at i:11874 original size:18 final size:18
Alignment explanation
Indices: 11851--11909 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
11841 CGCAAATTCG
11851 CGTTGCGATTTTCCATTT
1 CGTTGCGATTTTCCATTT
* * *
11869 CGTTGCGATAGTGTACAGTGT
1 CGTTGCGAT--TTTCCA-TTT
11890 CGTTGCGATTTTCCATTT
1 CGTTGCGATTTTCCATTT
11908 CG
1 CG
11910 CGTTGCGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 13 0.41
19 4 0.12
20 4 0.12
21 11 0.34
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (18 bp):
CGTTGCGATTTTCCATTT
Found at i:12066 original size:21 final size:21
Alignment explanation
Indices: 12040--12159 Score: 85
Period size: 21 Copynumber: 5.9 Consensus size: 21
12030 TTTTTAATTT
*
12040 ACTGTAGATTATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
12061 ACTGT--ACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
12079 GA--GATGGAAAATCGCAACGAC
1 -ACTG-TAGACTATCGCAACGAC
12100 ACTGTAGACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
12120 GAAATG--GAAAATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
12141 ACTGTAGACTATCGCAACG
1 ACTGTAGACTATCGCAACG
12160 CGATTTTCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 24
0.68 0.11 0.22
Matches are distributed among these distances:
17 1 0.01
18 2 0.03
19 15 0.20
20 23 0.31
21 30 0.40
22 4 0.05
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
ACTGTAGACTATCGCAACGAC
Found at i:12094 original size:20 final size:20
Alignment explanation
Indices: 12069--12138 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
12059 ACACTGTACT
12069 ATCGCAACGCGAGATGGAAA
1 ATCGCAACGCGAGATGGAAA
* **
12089 ATCGCAACGAC-ACTG-TAGACT
1 ATCGCAACG-CGA--GATGGAAA
*
12110 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAGATGGAAA
12130 ATCGCAACG
1 ATCGCAACG
12139 ACACTGTAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
20 23 0.61
21 14 0.37
22 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAGATGGAAA
Found at i:12127 original size:41 final size:41
Alignment explanation
Indices: 12050--12162 Score: 203
Period size: 41 Copynumber: 2.8 Consensus size: 41
12040 ACTGTAGATT
*
12050 ATCGCAACGACACTGT--ACTATCGCAACGCGAGATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
12089 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
12130 ATCGCAACGACACTGTAGACTATCGCAACGCGA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGA
12163 TTTTCAACTA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
39 16 0.23
41 55 0.77
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:12191 original size:21 final size:21
Alignment explanation
Indices: 12107--12191 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
12097 GACACTGTAG
*
12107 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * *
12128 A-AATCGCAA--CGACACTGTA
1 ACTATCGCAACGCGA-AATGCA
** *
12147 GACTATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGCA
12169 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
12190 AC
1 AC
12192 GTGAATTTGC
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 3 0.06
19 4 0.08
20 8 0.17
21 28 0.58
22 2 0.04
23 3 0.06
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:18063 original size:60 final size:60
Alignment explanation
Indices: 17995--18110 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
17985 ACCATTTCGT
* * *
17995 ATTTTTAATAGTCGTGGTACTCAACAAAGCAACATCCTATAGTCG-AGTGATTATTTTGTA
1 ATTTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAG-GATTATTTTGTA
18055 ATTTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAGGATTATTT
1 ATTTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAGGATTATTT
18111 GTATACTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 50 0.96
61 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (60 bp):
ATTTTTAATAATCGGGGTACTCAACAAAACAACATCCTATAGTCGAAGGATTATTTTGTA
Found at i:18654 original size:21 final size:19
Alignment explanation
Indices: 18616--18681 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
18606 GTAAATGTTA
* *
18616 ATATCAAAAATATTTATTTT
1 ATATAAAAAATA-ATATTTT
18636 ATATAATAAAATTAATATTTT
1 ATATAA-AAAA-TAATATTTT
18657 -TGATAAAAAATAATATTTT
1 AT-ATAAAAAATAATATTTT
*
18676 AAATAA
1 ATATAA
18682 CGCTATACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 13 0.33
20 10 0.26
21 14 0.36
22 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATAAAAAATAATATTTT
Found at i:18681 original size:19 final size:21
Alignment explanation
Indices: 18630--18681 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
18620 CAAAAATATT
*
18630 TATTTTATATAATAAAATTAA
1 TATTTTAAATAATAAAATTAA
**
18651 TATTTTTGATAA-AAAA-TAA
1 TATTTTAAATAATAAAATTAA
18670 TATTTTAAATAA
1 TATTTTAAATAA
18682 CGCTATACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.48
20 4 0.15
21 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTTTAAATAATAAAATTAA
Found at i:19837 original size:19 final size:20
Alignment explanation
Indices: 19798--19849 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
19788 GTTCAATTCA
19798 GGTCAACCTTTAGATTTTTC
1 GGTCAACCTTTAGATTTTTC
*
19818 GGTCATCCTTTAGA-TTTTC
1 GGTCAACCTTTAGATTTTTC
19837 GGATCAACCTTTA
1 GG-TCAACCTTTA
19850 AAATTTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (20 bp):
GGTCAACCTTTAGATTTTTC
Found at i:31352 original size:21 final size:22
Alignment explanation
Indices: 31310--31352 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
31300 TTTAAACATC
* *
31310 TTAGATTTTATTATTTATTTAA
1 TTAGAATTTATTATTTACTTAA
*
31332 TTAGAATTT-TTATTTGCTTAA
1 TTAGAATTTATTATTTACTTAA
31353 AATTTCGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TTAGAATTTATTATTTACTTAA
Found at i:38084 original size:31 final size:32
Alignment explanation
Indices: 38040--38103 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
38030 ATAGATGGAC
*
38040 TTATTGCGACTTTT-TTAAAAAAACGCCACTA
1 TTATTACGACTTTTATTAAAAAAACGCCACTA
* * *
38071 TTATTACGGCTTTTATTGAAAAAACGCTACTA
1 TTATTACGACTTTTATTAAAAAAACGCCACTA
38103 T
1 T
38104 AGATGGACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (32 bp):
TTATTACGACTTTTATTAAAAAAACGCCACTA
Found at i:38301 original size:50 final size:50
Alignment explanation
Indices: 38225--38451 Score: 402
Period size: 50 Copynumber: 4.5 Consensus size: 50
38215 ACCTAGCCTG
38225 ATGTCAGCAAGGGTGACTGA-TCGCCCATATAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGT-GCCCATATAGAGATTGCATGTCATGATA
*
38275 ATGTCAGCAAGGGTGACTGAGTGCCCATTTAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
*
38325 ATGTCAGCAAGGGTGACTGAGCGCCCATATAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
38375 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
1 ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
**
38425 ATGTCAATAAGGGTGACTGAGTGCCCA
1 ATGTCAGCAAGGGTGACTGAGTGCCCA
38452 ACCAGGTAGG
Statistics
Matches: 170, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
50 169 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (50 bp):
ATGTCAGCAAGGGTGACTGAGTGCCCATATAGAGATTGCATGTCATGATA
Found at i:46664 original size:14 final size:14
Alignment explanation
Indices: 46645--46688 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
46635 CGATAATCTA
46645 TTTGTTTATGTTTG
1 TTTGTTTATGTTTG
**
46659 TTTGTTTATGTTCA
1 TTTGTTTATGTTTG
46673 TTTGTTTATGTTTG
1 TTTGTTTATGTTTG
46687 TT
1 TT
46689 CATGTTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.09, C:0.02, G:0.18, T:0.70
Consensus pattern (14 bp):
TTTGTTTATGTTTG
Found at i:46685 original size:24 final size:24
Alignment explanation
Indices: 46657--46719 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
46647 TGTTTATGTT
*
46657 TGTTTGTTTATGTTCATTTGTTTA
1 TGTTTGTTTATGTTCATTCGTTTA
*
46681 TGTTTGTTCATGTTCATTCGTTTA
1 TGTTTGTTTATGTTCATTCGTTTA
* *
46705 TATTCGTTTATGTTC
1 TGTTTGTTTATGTTC
46720 TCCAGACCCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.62
Consensus pattern (24 bp):
TGTTTGTTTATGTTCATTCGTTTA
Found at i:47129 original size:2 final size:2
Alignment explanation
Indices: 47122--47159 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47112 TTACATGCCA
47122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47160 CGAGAGTGAC
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):
AT
Found at i:53577 original size:21 final size:20
Alignment explanation
Indices: 53550--53647 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
53540 AATCAGTGTC
53550 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
53571 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
53591 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
53611 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
53632 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
53648 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:53600 original size:41 final size:41
Alignment explanation
Indices: 53491--53647 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
53481 AAATGACCAA
* **
53491 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
53530 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
53571 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
53612 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
53648 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:53657 original size:20 final size:20
Alignment explanation
Indices: 53634--53804 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
53624 GCGAATATGA
53634 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
53654 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
53674 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
53694 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
53714 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
53734 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
53754 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
53774 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
53794 AAATCGCAACG
1 AAATCGCAACG
53805 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:53699 original size:60 final size:58
Alignment explanation
Indices: 53614--53823 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
53604 CGATTTTCCA
* ** * *
53614 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
53674 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
53734 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
53794 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
53824 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:53805 original size:20 final size:20
Alignment explanation
Indices: 53668--53823 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
53658 CGCAATGCGT
*
53668 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
53688 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
53708 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
53728 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
53748 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
53768 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
53788 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
53808 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
53824 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:53805 original size:40 final size:40
Alignment explanation
Indices: 53634--53823 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
53624 GCGAATATGA
* *
53634 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
53674 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
53714 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
53754 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
53794 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
53824 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:54544 original size:24 final size:24
Alignment explanation
Indices: 54505--54551 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54495 AAATTTGGTC
54505 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
54529 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
54552 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:57046 original size:19 final size:19
Alignment explanation
Indices: 57024--57401 Score: 483
Period size: 19 Copynumber: 21.4 Consensus size: 19
57014 CGGAAATTAC
*
57024 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57043 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
57057 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
57077 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
57091 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57110 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57129 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
57143 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57162 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57181 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
57195 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57214 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57233 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57252 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57271 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
57285 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57304 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57323 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57342 AATCGCAA--CGAAAT---
1 AATCGCAATGCGAAATGAA
57356 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57375 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57394 AATCGCAA
1 AATCGCAA
57402 CGAGAGAATC
Statistics
Matches: 318, Mismatches: 10, Indels: 62
0.82 0.03 0.16
Matches are distributed among these distances:
14 56 0.18
15 2 0.01
16 21 0.07
17 20 0.06
18 3 0.01
19 203 0.64
20 13 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:57175 original size:71 final size:71
Alignment explanation
Indices: 57091--57401 Score: 497
Period size: 71 Copynumber: 4.4 Consensus size: 71
57081 GCAACGAGAG
57091 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
57156 AATGAA
66 AATGAA
* *
57162 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAA
57222 TGCGAAATGAA
61 TGCGAAATGAA
*
57233 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
57298 AATGAA
66 AATGAA
* *
57304 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
57369 AATGAA
66 AATGAA
57375 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
57402 CGAGAGAATC
Statistics
Matches: 223, Mismatches: 7, Indels: 20
0.89 0.03 0.08
Matches are distributed among these distances:
66 8 0.04
68 3 0.01
69 4 0.02
70 1 0.00
71 191 0.86
72 1 0.00
73 4 0.02
74 3 0.01
76 8 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:57439 original size:52 final size:52
Alignment explanation
Indices: 57052--57423 Score: 556
Period size: 52 Copynumber: 7.0 Consensus size: 52
57042 AAATCCCAAC
57052 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
57105 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
57157 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
57209 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
* *
57266 ATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
* *
57318 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
57370 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
57422 AT
1 AT
57424 TATAAACGCA
Statistics
Matches: 300, Mismatches: 9, Indels: 21
0.91 0.03 0.06
Matches are distributed among these distances:
52 232 0.77
53 17 0.06
54 7 0.02
55 7 0.02
56 1 0.00
57 36 0.12
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:57439 original size:71 final size:69
Alignment explanation
Indices: 57024--57423 Score: 413
Period size: 71 Copynumber: 5.7 Consensus size: 69
57014 CGGAAATTAC
* *
57024 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAACGA-G-AAATCGCAAT-C-GAAATGAAAATCGCAATGC
*
57086 G--A-GAG
62 GAAATGAA
* * * * *
57091 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAT-GAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCG-CAATCGAAATGA-A-AATCGCAATGCG
57155 AAATGAA
63 AAATGAA
*
57162 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGA-AATCGCAAT-CGAAATGAAAATCGCAATGCGA
57227 AATGAA
64 AATGAA
* * * * *
57233 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAT-GAAAATCGCAACGACAGAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCG-CAATCGAAATGA-A-AATCGCAATGCG
57297 AAATGAA
63 AAATGAA
* * * * *
57304 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAT-GAAAATCGCAACGAAATAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCG-CAATCGAAATG-AA-AATCGCAATGCG
57368 AAATGAA
63 AAATGAA
57375 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGA-AATCGCAAT-CGAAAT
57424 TATAAACGCA
Statistics
Matches: 288, Mismatches: 26, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
64 5 0.02
65 3 0.01
66 15 0.05
67 26 0.09
68 2 0.01
69 7 0.02
70 8 0.03
71 196 0.68
72 14 0.05
73 12 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (69 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCGCAATCGAAATGAAAATCGCAATGCGAAA
TGAA
Found at i:57538 original size:19 final size:19
Alignment explanation
Indices: 57430--57530 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
57420 AAATTATAAA
57430 CGCATTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
57448 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
57468 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
57484 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
57501 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
57520 CGCATTGCGAT
1 CGCATTGCGAT
57531 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 46 0.62
20 8 0.11
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:57656 original size:14 final size:14
Alignment explanation
Indices: 57637--57673 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
57627 CATCAATTAC
57637 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
57651 ACAAATCATCTTTT
1 ACAAATCAACTTTT
57665 ACAAATCAA
1 ACAAATCAA
57674 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:59671 original size:14 final size:14
Alignment explanation
Indices: 59652--59708 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
59642 GCGAAATGAA
*
59652 AATCGCAACGACAG
1 AATCGCAACGAAAG
59666 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
59683 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
59699 AATCGCAACG
1 AATCGCAACG
59709 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:59679 original size:33 final size:33
Alignment explanation
Indices: 59633--59725 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
59623 GCGAAACCAA
*
59633 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
59666 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
59699 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
59726 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:59690 original size:19 final size:19
Alignment explanation
Indices: 59612--59730 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
59602 CACGAAACTT
**
59612 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
59631 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
59650 AAAATCGCAA--CGACA-G
1 AAAATCGCAACGCGAAATG
*
59666 --AATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
59683 AAAATCGCAA--CGAAA-G
1 AAAATCGCAACGCGAAATG
59699 --AATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
59716 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
59731 TTTTGGTTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.19
16 11 0.13
17 11 0.13
19 47 0.55
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:59748 original size:19 final size:19
Alignment explanation
Indices: 59726--59838 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
59716 AAAATCGCAA
59726 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
59745 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
59759 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
59778 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
59792 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
59811 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
59830 TGCGATTTT
1 TGCGATTTT
59839 AACTTTCGTG
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 48 0.62
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:59768 original size:33 final size:33
Alignment explanation
Indices: 59726--59817 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
59716 AAAATCGCAA
59726 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
59759 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
59792 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
59818 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:59851 original size:20 final size:18
Alignment explanation
Indices: 59756--59854 Score: 80
Period size: 19 Copynumber: 5.4 Consensus size: 18
59746 GCGATCTTGT
*
59756 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
* *
59775 CGTTGCGA--TTCTGT--
1 CGTTGCGATTTTATTTCG
59789 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTT-ATTTCG
*
59808 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
59827 CGTTGCGATTTTAACTTTCG
1 CGTTGCGATTTT-A-TTTCG
*
59847 TGTTGCGA
1 CGTTGCGA
59855 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 8 0.12
16 4 0.06
17 4 0.06
19 37 0.57
20 12 0.18
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTATTTCG
Found at i:60018 original size:93 final size:93
Alignment explanation
Indices: 59902--60370 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
59892 ATGGATTGCA
*
59902 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
59966 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
59994 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
60059 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
60087 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
60152 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
60180 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
60245 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
60273 TTACTTTCAACCAAAAGACAAAGCAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
60338 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
60366 TTACT
1 TTACT
60371 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 369 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:62095 original size:14 final size:14
Alignment explanation
Indices: 62076--62165 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
62066 TTGAAATGAA
62076 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
62090 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
62109 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
62123 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
62142 AATCGCAACGAGAG
1 AATCGCAACGAGAG
62156 AATCGCAACG
1 AATCGCAACG
62166 CGAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:62113 original size:33 final size:33
Alignment explanation
Indices: 62068--62182 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
62058 TCTTTTGGTT
62068 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
62101 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
62134 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
62167 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
62183 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:62114 original size:19 final size:19
Alignment explanation
Indices: 62090--62187 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
62080 GCAACGAGAG
*
62090 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
62109 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
62123 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
62142 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
62156 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
62175 AATCGCAATGCGA
1 AATCGCAACGCGA
62188 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:62218 original size:14 final size:14
Alignment explanation
Indices: 62199--62255 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
62189 TTTGGTTTCG
62199 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
62213 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
62232 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
62246 CGTTGCGATT
1 CGTTGCGATT
62256 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:62237 original size:19 final size:19
Alignment explanation
Indices: 62213--62301 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
62203 GCGATTCTCT
62213 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
62232 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
62246 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
62265 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
62285 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
62302 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:62293 original size:39 final size:33
Alignment explanation
Indices: 62183--62301 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
62173 AAAATCGCAA
**
62183 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
62216 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
62249 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
62288 TGCGATTTTCATTT
1 TGCGATTTTCATTT
62302 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:62434 original size:33 final size:33
Alignment explanation
Indices: 62392--62462 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
62382 AATACTAACT
62392 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
62425 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
62458 TGAAA
1 TGAAA
62463 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:62694 original size:22 final size:22
Alignment explanation
Indices: 62642--62696 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
62632 TGGTTGTGAG
**
62642 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
62664 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
62686 GGATTTCTTCG
1 GGATTTCTTCG
62697 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:62868 original size:20 final size:20
Alignment explanation
Indices: 62843--63036 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
62833 CTTTAAATAT
62843 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
62863 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
62885 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
62904 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
62924 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
62944 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
62964 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
62984 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
63004 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
63024 CGCGTTGCGATTT
1 CGCGTTGCGATTT
63037 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:63008 original size:60 final size:60
Alignment explanation
Indices: 62845--63016 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
62835 TTAAATATCG
* ** *
62845 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
62906 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
62966 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
63017 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:63030 original size:60 final size:60
Alignment explanation
Indices: 62842--63157 Score: 232
Period size: 60 Copynumber: 5.2 Consensus size: 60
62832 GCTTTAAATA
* ** * *
62842 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
62903 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
62963 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * * *
63023 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
63085 TCGCGTTGCGATTT-TGGACACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
63144 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
63158 TGTTGGTCAT
Statistics
Matches: 207, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
59 16 0.08
60 92 0.44
61 77 0.37
62 20 0.10
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:63053 original size:21 final size:20
Alignment explanation
Indices: 63003--63100 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
62993 ATTTATGTGT
* * * *
63003 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
63023 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
63044 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
63064 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
63085 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
63101 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:63095 original size:41 final size:41
Alignment explanation
Indices: 63003--63159 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
62993 ATTTATGTGT
* * *
63003 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
63044 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
63085 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
63125 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
63160 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:76856 original size:31 final size:31
Alignment explanation
Indices: 76821--76910 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
76811 CATACCTAAC
* * *
76821 GTTTACCTTTTGTTTTATTTTAGTACCCGGA-
1 GTTTACTTTTTGTTTCATTTTAGTACCC-CAT
*
76852 GTTTACTTTTTGTTTCATTTTAATACCCCATT
1 GTTTACTTTTTGTTTCATTTTAGTACCCCA-T
*
76884 GTTAACTTTTTGTTTCATTTTAGTACC
1 GTTTACTTTTTGTTTCATTTTAGTACC
76911 TAAATTTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.02
31 25 0.49
32 25 0.49
ACGTcount: A:0.18, C:0.17, G:0.11, T:0.54
Consensus pattern (31 bp):
GTTTACTTTTTGTTTCATTTTAGTACCCCAT
Found at i:77240 original size:21 final size:21
Alignment explanation
Indices: 77197--77280 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
77187 TAATAGTGGA
* *
77197 TTGTTACATAAATAC-AAATAC
1 TTGTTACATTAATACTATA-AC
* **
77218 TTGTTACGTTAATGTTATAAC
1 TTGTTACATTAATACTATAAC
77239 TTGTTACATTAATACTATAAC
1 TTGTTACATTAATACTATAAC
77260 TTGTTACATTAATACTATAAC
1 TTGTTACATTAATACTATAAC
77281 GATCAACAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 52 0.96
22 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (21 bp):
TTGTTACATTAATACTATAAC
Found at i:78175 original size:18 final size:18
Alignment explanation
Indices: 78152--78187 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
78142 CAAACCCCGT
78152 GGAAAGCGGCGCGTGTCC
1 GGAAAGCGGCGCGTGTCC
*
78170 GGAAAGTGGCGCGTGTCC
1 GGAAAGCGGCGCGTGTCC
78188 CTATACACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.44, T:0.14
Consensus pattern (18 bp):
GGAAAGCGGCGCGTGTCC
Found at i:78662 original size:4 final size:4
Alignment explanation
Indices: 78653--78690 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
78643 AGTAATTTTG
* *
78653 ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
78691 TTGGCTTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:78951 original size:4 final size:4
Alignment explanation
Indices: 78944--78971 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
78934 AAATGTATGT
78944 ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG
78972 CTTAAGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
ATGG
Found at i:78954 original size:99 final size:100
Alignment explanation
Indices: 78764--78971 Score: 296
Period size: 99 Copynumber: 2.1 Consensus size: 100
78754 ATTGGTAGTT
* * *
78764 CCTGGATGGTGTCTACTATGAGAAGAAAGAGCTAGTAGAATTCACCACATGTTTTAATTGCATTG
1 CCTGGATGGTGTCTACTATAAGAAGAAAGAGCTAGTAGAATT--CCACATGTTTGAATTCCATTG
78829 TTTTGAAAATGTATGGATGGATGGATGGAAGGATGGA
64 TTTTGAAAATGTATGGATGGATGGATGGAAGGATGGA
* * * *
78866 CCTGGCTGGTGTTTACTATAAGAAGACAGAGCTAGTAGAATT-CACTTGTTTGAATTCCATTGTT
1 CCTGGATGGTGTCTACTATAAGAAGAAAGAGCTAGTAGAATTCCACATGTTTGAATTCCATTGTT
* *
78930 TTGAAAATGTATGTATGGATGGATGGATGGATGGA
66 TTGAAAATGTATGGATGGATGGATGGAAGGATGGA
78965 --TGGATGG
1 CCTGGATGG
78972 CTTAAGAGAT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
97 6 0.06
99 52 0.54
102 38 0.40
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (100 bp):
CCTGGATGGTGTCTACTATAAGAAGAAAGAGCTAGTAGAATTCCACATGTTTGAATTCCATTGTT
TTGAAAATGTATGGATGGATGGATGGAAGGATGGA
Found at i:95159 original size:26 final size:26
Alignment explanation
Indices: 95130--95186 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
95120 TAGTTTTATT
* *
95130 ATATAGTTGGCCCTACCGCCTGATTG
1 ATATAGTCGGCCATACCGCCTGATTG
* **
95156 ATATGGTCGGTTATACCGCCTGATTG
1 ATATAGTCGGCCATACCGCCTGATTG
95182 ATATA
1 ATATA
95187 TGGTCGATCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (26 bp):
ATATAGTCGGCCATACCGCCTGATTG
Found at i:101193 original size:15 final size:15
Alignment explanation
Indices: 101170--101201 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
101160 TAGAATATTG
101170 TTTTACTTTTGTTTA
1 TTTTACTTTTGTTTA
*
101185 TTTTTCTTTTGTTTA
1 TTTTACTTTTGTTTA
101200 TT
1 TT
101202 ATTGGTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTACTTTTGTTTA
Done.