Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001361.1 Hibiscus syriacus cultivar Beakdansim tig00002653_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: 50588
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:757 original size:11 final size:10
Alignment explanation
Indices: 728--768 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
718 CTCATTCAGC
728 AAAGAAAAAGA
1 AAAGAAAAA-A
*
739 AAAAAAAAAA
1 AAAGAAAAAA
749 AAAGGAAAAAA
1 AAA-GAAAAAA
760 AAAGAAAAA
1 AAAGAAAAA
769 GGAAAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:760 original size:17 final size:17
Alignment explanation
Indices: 738--774 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
728 AAAGAAAAAG
738 AAAAAAAAAAAAAAGGA
1 AAAAAAAAAAAAAAGGA
*
755 AAAAAAAAGAAAAAGGA
1 AAAAAAAAAAAAAAGGA
772 AAA
1 AAA
775 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAGGA
Found at i:2991 original size:80 final size:81
Alignment explanation
Indices: 2889--3082 Score: 269
Period size: 76 Copynumber: 2.5 Consensus size: 81
2879 TGCAATATAC
*
2889 TCATAGCATC-TCTGGAAGTGTTCATTGAGTTATCTGATCTGGTTTGGT-AAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCA-TGAA
* *
2952 TTTG-AGATGAATGTGA
65 TTGGAAGAGGAATGTGA
2968 TCATAGCATCTTCTGGAAGTGTTCTTTGAG---T-T-ATCTGGTTTGGTAAAACCAATCATGAAT
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATGAAT
*
3028 TGGAAGAGGAATGTGC
66 TGGAAGAGGAATGTGA
* *
3044 TAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
3083 TTGATTTGAT
Statistics
Matches: 101, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
75 19 0.19
76 49 0.49
77 1 0.01
79 11 0.11
80 19 0.19
81 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (81 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATGAAT
TGGAAGAGGAATGTGA
Found at i:5367 original size:51 final size:52
Alignment explanation
Indices: 5254--5375 Score: 151
Period size: 51 Copynumber: 2.4 Consensus size: 52
5244 CCAGCATAAG
* * *
5254 CCACATGAGAGGATGAA--TGTTGTCAAATGTTTTACGAACATCTGAGCAGAAA
1 CCACAGGAAAGGATGAATGTGTTGTCAAAGGTTTTACG-A-ATCTGAGCAGAAA
* *
5306 CTACAGGAAAGGATGAATGTGTTGTCAAAGGTTTTACG-ATCTGAGCAGAAG
1 CCACAGGAAAGGATGAATGTGTTGTCAAAGGTTTTACGAATCTGAGCAGAAA
*
5357 CCATAGGAAAGGATGAATG
1 CCACAGGAAAGGATGAATG
5376 CACTGTCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
51 29 0.48
52 14 0.23
54 18 0.30
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (52 bp):
CCACAGGAAAGGATGAATGTGTTGTCAAAGGTTTTACGAATCTGAGCAGAAA
Found at i:5383 original size:51 final size:51
Alignment explanation
Indices: 5274--5395 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 51
5264 GGATGAATGT
* ***
5274 TGTCAAATGTTTTACGAACATCTGAGCAGAAACTACAGGAAAGGATGAATGTGT
1 TGTCAAATGTTTTACG---ATCTGAGCAGAAACCACAGGAAAGGATGAATGCAC
* * *
5328 TGTCAAAGGTTTTACGATCTGAGCAGAAGCCATAGGAAAGGATGAATGCAC
1 TGTCAAATGTTTTACGATCTGAGCAGAAACCACAGGAAAGGATGAATGCAC
*
5379 TGTCAAATTTTTTACGA
1 TGTCAAATGTTTTACGA
5396 ACCTGCTATT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 44 0.75
54 15 0.25
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (51 bp):
TGTCAAATGTTTTACGATCTGAGCAGAAACCACAGGAAAGGATGAATGCAC
Found at i:5788 original size:21 final size:22
Alignment explanation
Indices: 5744--5797 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
5734 ATCTACATTC
* *
5744 TTCAAAGATGATAGATTTTCTT
1 TTCAAAGATGACAGATTCTCTT
*
5766 TTTAAAGATGACAG-TTCTCTT
1 TTCAAAGATGACAGATTCTCTT
5787 TTCAAAGATGA
1 TTCAAAGATGA
5798 AACTTTATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:6778 original size:76 final size:76
Alignment explanation
Indices: 6465--7279 Score: 1438
Period size: 75 Copynumber: 10.9 Consensus size: 76
6455 CTATTTCCCA
6465 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
6529 AGCCTTAGGGT
66 AGCCTTAGGGT
6540 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
6604 AGCCTTAGGGT
66 AGCCTTAGGGT
6615 CATCTGTAAGTCCTTCA--GCATGATGTTTCCAAAAAGCCTTC-GGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
6677 AGCCTTAGGGT
66 AGCCTTAGGGT
6688 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
6753 AGCCTTAGGGT
66 AGCCTTAGGGT
6764 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
6829 AGCC-TAGGGT
66 AGCCTTAGGGT
* * *
6839 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
6904 AGCCTTCGGGT
66 AGCCTTAGGGT
6915 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
6980 AGCCTTCGGGT
66 AGCCTTAGGGT
*
6991 CATCTGTAAGTCCTTCAGTGC---ATGTTTCAAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* * *
7053 AGCATTCGAGT
66 AGCCTTAGGGT
7064 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGAT-TTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
7128 AGCCTTAGGGT
66 AGCCTTAGGGT
*
7139 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
7202 AGCCTTCGGGT
66 AGCCTTAGGGT
*
7213 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
7278 AG
66 AG
7280 ATCAAGTCCT
Statistics
Matches: 710, Mismatches: 18, Indels: 23
0.95 0.02 0.03
Matches are distributed among these distances:
73 132 0.19
74 91 0.13
75 247 0.35
76 240 0.34
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:7308 original size:149 final size:151
Alignment explanation
Indices: 6465--7279 Score: 1400
Period size: 149 Copynumber: 5.4 Consensus size: 151
6455 CTATTTCCCA
6465 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
6529 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGATCTTTTTG
66 AGCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGATCTTTTTG
*
6594 ATGTTTTCAAAGCCTTAGGGT
131 ATGTTTTCAAAGCCTTCGGGT
6615 CATCTGTAAGTCCTTCA--GCATGATGTTTCCAAAAAGCCTTC-GGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
6677 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
66 AGCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATCTTTTT
*
6742 GATGTTTTCAAAGCCTTAGGGT
130 GATGTTTTCAAAGCCTTCGGGT
6764 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* *
6829 AGCCT-AGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTT
66 AGCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATCTTTTT
*
6893 GATGTTTTTAAAGCCTTCGGGT
130 GATGTTTTCAAAGCCTTCGGGT
6915 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
6980 AGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGC---ATGTTTCAAAAAAGCCTTCGGGATCTTTT
66 AGCC-TCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC-CAAAAGCCTTCGGGATCTTTT
* *
7041 TGATGTTTTCAAAGCATTCGAGT
129 TGATGTTTTCAAAGCCTTCGGGT
7064 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGAT-TTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* *
7128 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTTG
66 AGCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGATCTTTTTG
7193 ATG-TTTCAAAGCCTTCGGGT
131 ATGTTTTCAAAGCCTTCGGGT
*
7213 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
7278 AG
66 AG
7280 ATCAAGTCCT
Statistics
Matches: 637, Mismatches: 16, Indels: 24
0.94 0.02 0.04
Matches are distributed among these distances:
147 1 0.00
148 124 0.19
149 233 0.37
150 50 0.08
151 177 0.28
152 52 0.08
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (151 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGATCTTTTTG
ATGTTTTCAAAGCCTTCGGGT
Found at i:7510 original size:3 final size:3
Alignment explanation
Indices: 7504--7562 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
7494 TTAATTTTTT
* * * *
7504 TTA TTA TTA TTT TTGT TTA TTA -TA TTA TTTA TTA ATA TTA GTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
7550 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
7563 AATAACAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:9131 original size:18 final size:17
Alignment explanation
Indices: 9110--9143 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9100 TTACTATATT
* *
9110 AAAATAAATTTTTGTCA
1 AAAAAAAATGTTTGTCA
9127 AAAAAAAATGTTTGTCA
1 AAAAAAAATGTTTGTCA
9144 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (17 bp):
AAAAAAAATGTTTGTCA
Found at i:9596 original size:3 final size:3
Alignment explanation
Indices: 9588--9626 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
9578 GGTGACGACA
9588 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TCT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
9627 CGTATGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:10661 original size:43 final size:42
Alignment explanation
Indices: 10559--10724 Score: 208
Period size: 43 Copynumber: 3.9 Consensus size: 42
10549 TTGATCATTT
** * *
10559 TCCTAATTCTACATGCAATCCTCTGCGGAGGG-ATCATCCCA
1 TCCTAATTCTACATGGGATCCTCTACGGAGGGCATCATCCCG
*
10600 TCCTGATTCTACATGGGATCCTCTACGGAGGGCATCATCCACG
1 TCCTAATTCTACATGGGATCCTCTACGGAGGGCATCATCC-CG
*
10643 TCCTAATTCTACATGGGATCCTCTACGGATGGCATCATCCTCG
1 TCCTAATTCTACATGGGATCCTCTACGGAGGGCATCATCC-CG
* * * * *
10686 TCTTGATTCTGCATGGGATACTCTACGGAGGACATCATC
1 TCCTAATTCTACATGGGATCCTCTACGGAGGGCATCATC
10725 GTTCTGATTA
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 28 0.26
42 7 0.06
43 74 0.68
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (42 bp):
TCCTAATTCTACATGGGATCCTCTACGGAGGGCATCATCCCG
Found at i:10712 original size:86 final size:84
Alignment explanation
Indices: 10559--10724 Score: 233
Period size: 86 Copynumber: 2.0 Consensus size: 84
10549 TTGATCATTT
* * *
10559 TCCTAATTCTACATGCAATCCTCTGCGGAGGGATCATCCCATCCTGATTCTACATGGGATCCTCT
1 TCCTAATTCTACATGCAATCCTCTACGGAGGCATCATCCCATCCTGATTCTACATGGGATACTCT
*
10624 ACGGAGGGCATCATCCACG
66 ACGGAGGACATCATCCACG
** * * *
10643 TCCTAATTCTACATGGGATCCTCTACGGATGGCATCATCCTCGTCTTGATTCTGCATGGGATACT
1 TCCTAATTCTACATGCAATCCTCTACGGA-GGCATCATCC-CATCCTGATTCTACATGGGATACT
10708 CTACGGAGGACATCATC
64 CTACGGAGGACATCATC
10725 GTTCTGATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 26 0.37
85 9 0.13
86 36 0.51
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (84 bp):
TCCTAATTCTACATGCAATCCTCTACGGAGGCATCATCCCATCCTGATTCTACATGGGATACTCT
ACGGAGGACATCATCCACG
Found at i:13763 original size:24 final size:23
Alignment explanation
Indices: 13707--13765 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
13697 CAGTCGAAAC
*
13707 TGCCACATAGAATTGCACCGAAG
1 TGCCACGTAGAATTGCACCGAAG
**
13730 TGCCGTGTAGAATATGCACCGAAG
1 TGCCACGTAGAAT-TGCACCGAAG
13754 TGCCACGTAGAA
1 TGCCACGTAGAA
13766 ATTGTCTCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (23 bp):
TGCCACGTAGAATTGCACCGAAG
Found at i:13801 original size:23 final size:23
Alignment explanation
Indices: 13748--13845 Score: 117
Period size: 23 Copynumber: 4.2 Consensus size: 23
13738 AGAATATGCA
13748 CCGAAGTG-CCACGTAGAAATTGTC
1 CCGAAG-GACCACGTAGAAA-TGTC
* *
13772 TCGAAGGACCACATAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
* * *
13795 CCAAAGGACCGCGTAGATATGTC
1 CCGAAGGACCACGTAGAAATGTC
*
13818 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTC
13841 CCGAA
1 CCGAA
13846 TGACAGCATA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 47 0.76
24 15 0.24
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:13857 original size:23 final size:23
Alignment explanation
Indices: 13748--13858 Score: 93
Period size: 23 Copynumber: 4.8 Consensus size: 23
13738 AGAATATGCA
*
13748 CCGAAGTG-CCACGTAGAAATTGTC
1 CCGAAG-GACCACATAG-AATTGTC
* *
13772 TCGAAGGACCACATAGAAATGTC
1 CCGAAGGACCACATAGAATTGTC
* * *
13795 CCAAAGGACCGCGTAG-ATATGTC
1 CCGAAGGACCACATAGAAT-TGTC
*
13818 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACATAGAATTGTC
*
13841 CCGAATGA-CAGCATAGAA
1 CCGAAGGACCA-CATAGAA
13859 CCATTGACTC
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.04
23 54 0.76
24 14 0.20
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACATAGAATTGTC
Found at i:19301 original size:29 final size:28
Alignment explanation
Indices: 19269--19424 Score: 181
Period size: 30 Copynumber: 5.4 Consensus size: 28
19259 TTAACATAAC
*
19269 AAAATAGAAATTTAAAGGAATAAAATAG
1 AAAATAGAAATTTAAAGGACTAAAATAG
* *
19297 TAAAAATAGAAAATTAAAGGACTAAACTAG
1 --AAAATAGAAATTTAAAGGACTAAAATAG
*
19327 CAAATAGAAATTTAAAGGACT-AAATAG
1 AAAATAGAAATTTAAAGGACTAAAATAG
*
19354 AAAAAATATAAATTTAAAGGACT-AAATAG
1 --AAAATAGAAATTTAAAGGACTAAAATAG
* *
19383 AAAAAATAAATTTAAAGGACTAAAATAG
1 AAAATAGAAATTTAAAGGACTAAAATAG
19411 CAAAAATAGAAATT
1 --AAAATAGAAATT
19425 GGAAAGGCTA
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
27 25 0.23
28 25 0.23
29 25 0.23
30 35 0.32
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.22
Consensus pattern (28 bp):
AAAATAGAAATTTAAAGGACTAAAATAG
Found at i:19371 original size:57 final size:58
Alignment explanation
Indices: 19269--19437 Score: 227
Period size: 57 Copynumber: 2.9 Consensus size: 58
19259 TTAACATAAC
* * *
19269 AAAATAGAAATTTAAAGGAATAAAATAGTAAAAATAGAAAATTAAAGGACTAAACTAG
1 AAAATAGAAATTTAAAGGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAACTAG
* *
19327 CAAATAGAAATTTAAAGGACT-AAATAGAAAAAATATAAATTTAAAGGACTAAA-TAG
1 AAAATAGAAATTTAAAGGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAACTAG
* * * *
19383 AAAAAATAAATTTAAAGGACTAAAATAGCAAAAATAGAAATTGGAAAGG-CTAAAC
1 AAAATAGAAATTTAAAGGACTAAAATAGAAAAAATAGAAATT-TAAAGGACTAAAC
19438 AGTAATTACA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
56 21 0.22
57 52 0.54
58 24 0.25
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (58 bp):
AAAATAGAAATTTAAAGGACTAAAATAGAAAAAATAGAAATTTAAAGGACTAAACTAG
Found at i:21192 original size:43 final size:43
Alignment explanation
Indices: 21145--21276 Score: 132
Period size: 43 Copynumber: 3.2 Consensus size: 43
21135 TTCCTACACA
* *
21145 ATGAGGACGGCTAGTTATCTAAGGGTGAAATGGCTCCTACGTG
1 ATGAGGACGGCTAGTTATCTAAGGGTGACACGGCTCCTACGTG
* ** * *
21188 ATGAGGA--GATATGGTT-GGT-A-GATGACACGGTTCCTACGTG
1 ATGAGGACGGCTA--GTTATCTAAGGGTGACACGGCTCCTACGTG
*
21228 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGT-
1 ATGAGGACGGCTAGTTATCTAAGGGTGACACGGCTCCTACGTG
21270 ATGAGGA
1 ATGAGGA
21277 GGTCTGGTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
40 26 0.38
41 5 0.07
42 11 0.16
43 27 0.39
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (43 bp):
ATGAGGACGGCTAGTTATCTAAGGGTGACACGGCTCCTACGTG
Found at i:21243 original size:40 final size:40
Alignment explanation
Indices: 21179--21310 Score: 119
Period size: 40 Copynumber: 3.3 Consensus size: 40
21169 GTGAAATGGC
**
21179 TCCTACGTGATGAGGAGATATGGTT-GGTAGATGACACGGT
1 TCCTACGTGATGAGGAG-GCTGGTTAGGTAGATGACACGGT
** * *
21219 TCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGC
1 TCCTACGTGATGAGGA-GGCTGGTTAGGT-A-GATGACACGGT
*
21262 TCCTACGT-ATGAGGAGGTCTGGTTAGG--GATGACATGGT
1 TCCTACGTGATGAGGAGG-CTGGTTAGGTAGATGACACGGT
*
21300 TCCTATGTGAT
1 TCCTACGTGAT
21311 AAGAACGGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
38 15 0.20
39 2 0.03
40 21 0.28
41 4 0.05
42 15 0.20
43 17 0.23
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGGCTGGTTAGGTAGATGACACGGT
Found at i:21268 original size:83 final size:81
Alignment explanation
Indices: 21129--21310 Score: 240
Period size: 83 Copynumber: 2.2 Consensus size: 81
21119 GAGGGTGATT
*** *
21129 ACACGGTTCCTACACAATGAGGACGGCTAGTTATCTAAGGGTGAAATGGCTCCTACGTGATGAGG
1 ACACGGTTCCTACGTGATGAGGACGGCTAGTTATCTAAGGGTGAAACGGCTCCTACGT-ATGAGG
21194 AGATATGGTT-GGTAGATG
65 AGATATGGTTAGG--GATG
* *
21212 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTATGAGGA
1 ACACGGTTCCTACGTGATGAGGACGGCTAGTTATCTAAGGGTGAAACGGCTCCTACGTATGAGGA
* *
21277 GGTCTGGTTAGGGATG
66 GATATGGTTAGGGATG
* *
21293 ACATGGTTCCTATGTGAT
1 ACACGGTTCCTACGTGAT
21311 AAGAACGGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 20 0.23
82 14 0.16
83 54 0.61
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.26
Consensus pattern (81 bp):
ACACGGTTCCTACGTGATGAGGACGGCTAGTTATCTAAGGGTGAAACGGCTCCTACGTATGAGGA
GATATGGTTAGGGATG
Found at i:27576 original size:30 final size:30
Alignment explanation
Indices: 27502--27694 Score: 151
Period size: 30 Copynumber: 6.5 Consensus size: 30
27492 ACATTTGATG
* * **
27502 ATTTAAGGGATTAAAATAAAACTAACAGAAA
1 ATTTAAAGGACTAAAATAAAAAAAACA-AAA
* * *
27533 CTTGAGAGG-CTAAAATAAAAAAAACAAAA
1 ATTTAAAGGACTAAAATAAAAAAAACAAAA
* * *
27562 ATTTAAAGGACTAAAATAACAAAAATAGAA
1 ATTTAAAGGACTAAAATAAAAAAAACAAAA
* ***
27592 ATTTAAAGGACTAAAAT-AGAAAAATTGAA
1 ATTTAAAGGACTAAAATAAAAAAAACAAAA
** *
27621 ATTTAAAGGACTAAAAT-AGCAAAACAAAC
1 ATTTAAAGGACTAAAATAAAAAAAACAAAA
** *
27650 ATTTAAAGGACTAAAATAGTAAAAATAGAAA
1 ATTTAAAGGACTAAAATAAAAAAAACA-AAA
*
27681 A-TTAAAGGGCTAAA
1 ATTTAAAGGACTAAA
27695 CAGTAATTAC
Statistics
Matches: 133, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
29 60 0.45
30 65 0.49
31 8 0.06
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAAAAAAAACAAAA
Found at i:27592 original size:60 final size:59
Alignment explanation
Indices: 27502--27694 Score: 162
Period size: 59 Copynumber: 3.3 Consensus size: 59
27492 ACATTTGATG
* * * *
27502 ATTTAAGGGATTAAAATAA-AACTAACAGAAACTTGAGAGG-CTAAAATAAAAAAAACAAAA
1 ATTTAAAGGACTAAAATAACAA-AAACAGAAA-TTGAAAGGACTAAAAT-AAAAAAACAAAA
* * * ***
27562 ATTTAAAGGACTAAAATAACAAAAATAGAAATTTAAAGGACTAAAATAGAAAAATTGAA
1 ATTTAAAGGACTAAAATAACAAAAACAGAAATTGAAAGGACTAAAATAAAAAAACAAAA
* * * *
27621 ATTTAAAGGACTAAAATAGC-AAAACA-AACATTTAAAGGACTAAAATAGTAAAAATAGAAA
1 ATTTAAAGGACTAAAATAACAAAAACAGAA-ATTGAAAGGACTAAAATA-AAAAAACA-AAA
*
27681 A-TTAAAGGGCTAAA
1 ATTTAAAGGACTAAA
27695 CAGTAATTAC
Statistics
Matches: 112, Mismatches: 16, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
57 2 0.02
58 23 0.21
59 51 0.46
60 34 0.30
61 2 0.02
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (59 bp):
ATTTAAAGGACTAAAATAACAAAAACAGAAATTGAAAGGACTAAAATAAAAAAACAAAA
Found at i:27624 original size:29 final size:29
Alignment explanation
Indices: 27542--27694 Score: 182
Period size: 29 Copynumber: 5.2 Consensus size: 29
27532 ACTTGAGAGG
* * *
27542 CTAAAATAAAAAAAACAAAAATTTAAAGGA
1 CTAAAAT-AGAAAAATAGAAATTTAAAGGA
*
27572 CTAAAATAACAAAAATAGAAATTTAAAGGA
1 CTAAAAT-AGAAAAATAGAAATTTAAAGGA
*
27602 CTAAAATAGAAAAATTGAAATTTAAAGGA
1 CTAAAATAGAAAAATAGAAATTTAAAGGA
* *
27631 CTAAAATAGCAAAACA-AACATTTAAAGGA
1 CTAAAATAGAAAAATAGAA-ATTTAAAGGA
* *
27660 CTAAAATAGTAAAAATAGAAAATTAAAGGG
1 CTAAAATAG-AAAAATAGAAATTTAAAGGA
27690 CTAAA
1 CTAAA
27695 CAGTAATTAC
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
28 2 0.02
29 52 0.48
30 52 0.48
31 2 0.02
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (29 bp):
CTAAAATAGAAAAATAGAAATTTAAAGGA
Found at i:27644 original size:59 final size:59
Alignment explanation
Indices: 27542--27694 Score: 193
Period size: 59 Copynumber: 2.6 Consensus size: 59
27532 ACTTGAGAGG
** * *
27542 CTAAAATAAAAAAAACAAAAATTTAAAGGACTAAAATAACAAAA-ATAGAAATTTAAAGGA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAAATAACAAAACA-A-AAATTTAAAGGA
* * *
27602 CTAAAATAG-AAAAATTGAAATTTAAAGGACTAAAATAGCAAAACAAACATTTAAAGGA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAAATAACAAAACAAAAATTTAAAGGA
* *
27660 CTAAAATAGTAAAAATAGAAAATTAAAGGGCTAAA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAA
27695 CAGTAATTAC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
58 20 0.24
59 53 0.65
60 9 0.11
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (59 bp):
CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAAATAACAAAACAAAAATTTAAAGGA
Found at i:29083 original size:3 final size:3
Alignment explanation
Indices: 29060--29100 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
29050 ATTAAATTGT
*
29060 TAA TAA -AA TGAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29101 TAAAATATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:30038 original size:18 final size:19
Alignment explanation
Indices: 30015--30052 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
30005 CTAAAACAAT
*
30015 AACAAAATAA-AAATCTTA
1 AACAAAATAAGAAATATTA
*
30033 AACAAAGTAAGAAATATTA
1 AACAAAATAAGAAATATTA
30052 A
1 A
30053 GTTGCAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (19 bp):
AACAAAATAAGAAATATTA
Found at i:31263 original size:12 final size:12
Alignment explanation
Indices: 31237--31291 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
31227 ATATACAAAT
31237 ACCTAACTC-TC
1 ACCTAACTCTTC
31248 ACCTAACTCTTC
1 ACCTAACTCTTC
*
31260 ACCTAATTCTTC
1 ACCTAACTCTTC
*
31272 GCCTAACTCTTC
1 ACCTAACTCTTC
31284 ACCTAACT
1 ACCTAACT
31292 AAATTGATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
11 9 0.23
12 30 0.77
ACGTcount: A:0.25, C:0.40, G:0.02, T:0.33
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:32914 original size:3 final size:3
Alignment explanation
Indices: 32894--32979 Score: 133
Period size: 3 Copynumber: 29.7 Consensus size: 3
32884 TTTTTACCCA
*
32894 TAT TAT AAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
32941 TAT TAT TAT TAT TAT GAT TAT TA- TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
32980 AATATATTAA
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 6 0.08
3 70 0.92
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:32997 original size:20 final size:20
Alignment explanation
Indices: 32973--33014 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
32963 ATATTATTAT
32973 TATATTAAATATATTAAATACA
1 TATA-TAAATAT-TTAAATACA
*
32995 TATATAAATATTTAATTACA
1 TATATAAATATTTAAATACA
33015 AAGCCCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATAAATATTTAAATACA
Found at i:35127 original size:15 final size:13
Alignment explanation
Indices: 35107--35144 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
35097 TTTATATGTT
35107 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
35122 TTATTTTATTTCA
1 TTATTTTATTTCA
35135 TTA-TTTATTT
1 TTATTTTATTT
35145 TGCTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:38376 original size:15 final size:16
Alignment explanation
Indices: 38350--38382 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
38340 GTTGGGATCA
38350 ATACATTTTTGCATAC
1 ATACATTTTTGCATAC
38366 ATACA-TTTTGCATAC
1 ATACATTTTTGCATAC
38381 AT
1 AT
38383 GCATCATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATACATTTTTGCATAC
Found at i:45650 original size:10 final size:10
Alignment explanation
Indices: 45635--45700 Score: 68
Period size: 10 Copynumber: 6.9 Consensus size: 10
45625 TGCTTGAAGA
45635 AAAAAGAAAG
1 AAAAAGAAAG
45645 AAAAAGAAAG
1 AAAAAGAAAG
45655 --AAAG--AG
1 AAAAAGAAAG
*
45661 AAAAAGAAAA
1 AAAAAGAAAG
*
45671 AAAAAGAAAA
1 AAAAAGAAAG
*
45681 AAAAAAAAGAG
1 AAAAAGAA-AG
45692 AAAAAGAAA
1 AAAAAGAAA
45701 AGGGAGTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
6 2 0.04
8 8 0.17
10 29 0.62
11 8 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:45652 original size:6 final size:6
Alignment explanation
Indices: 45631--45701 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
45621 ATTATGCTTG
* *
45631 AAGAAA AA-AGA AAGAAA AAG--A AAGAAA GAGAAA AAGAAA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
45675 AGAAAAA AAAAAA AGAGAAA AAGAAA A
1 A-AGAAA AAGAAA A-AGAAA AAGAAA A
45702 GGGAGTCAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.07
5 8 0.15
6 33 0.61
7 9 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:45664 original size:16 final size:16
Alignment explanation
Indices: 45631--45701 Score: 99
Period size: 16 Copynumber: 4.4 Consensus size: 16
45621 ATTATGCTTG
*
45631 AAGAAAAAAGAAAGAAA
1 AAGAAAAAA-AGAGAAA
*
45648 AAGAAAGAAAGAGAAA
1 AAGAAAAAAAGAGAAA
*
45664 AAGAAAAAAAAAGAAA
1 AAGAAAAAAAGAGAAA
45680 AA-AAAAAAAGAGAAA
1 AAGAAAAAAAGAGAAA
45695 AAGAAAA
1 AAGAAAA
45702 GGGAGTCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
15 14 0.29
16 26 0.54
17 8 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAGAGAAA
Found at i:45693 original size:31 final size:33
Alignment explanation
Indices: 45631--45701 Score: 119
Period size: 31 Copynumber: 2.2 Consensus size: 33
45621 ATTATGCTTG
*
45631 AAGAAAAAAGAAAGAAAAAGAAAGAAAGAGAAA
1 AAGAAAAAAGAAAGAAAAAGAAAAAAAGAGAAA
45664 AAGAAAAAA-AAAGAAAAA-AAAAAAAGAGAAA
1 AAGAAAAAAGAAAGAAAAAGAAAAAAAGAGAAA
45695 AAGAAAA
1 AAGAAAA
45702 GGGAGTCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 19 0.51
32 9 0.24
33 9 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (33 bp):
AAGAAAAAAGAAAGAAAAAGAAAAAAAGAGAAA
Found at i:46044 original size:16 final size:17
Alignment explanation
Indices: 46023--46063 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
46013 TTTCAAGTTC
*
46023 ATTTATTTG-AGATTCA
1 ATTTATTTGAAAATTCA
46039 ATTTATTTTGAAAATTCA
1 ATTTA-TTTGAAAATTCA
46057 ATTTATT
1 ATTTATT
46064 CTTCTATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 11 0.50
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (17 bp):
ATTTATTTGAAAATTCA
Found at i:48088 original size:220 final size:220
Alignment explanation
Indices: 47686--48342 Score: 858
Period size: 220 Copynumber: 2.9 Consensus size: 220
47676 ATTCGAATCT
* * * * * *
47686 ATCATTTGATAGATTAGCTTTTCCAAAGAAGGTTCATAATGAGAAGAACTCATATGAAGAAGGAA
1 ATCAATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
47751 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGAT-GATTA
66 GAAGAAGTTCATAAT--G-AGAATTTGTTCAACCTTTTACCTGAATTCATC-AATTGATGGATTA
47815 TCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
127 TCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
47880 AGAATTTGTTCAA-CCTTTACCTGAATTC
192 AGAACTTGTTCAATCCTTTACCTGAATTC
*
47908 ATCAAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-AATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
47973 AGAAGAAGTTCATAATGAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCT
65 AGAAGAAGTTCATAATGAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCT
*
48038 TTTCCAGAGAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
130 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--GAA
* * *
48103 GAACTTGTTCAATCTTTTGCTTGAATTC
193 GAACTTGTTCAATCCTTTACCTGAATTC
* * * * *
48131 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCAATTGATGGATTAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * *** * *
48195 GGAAGAATAAGTTCATAATGAGAAGACTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGTAT
62 GGAAGAAGAAGTTCATAATGAG-A-ATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGAT
* * * *
48260 CAACATTGCCAG-GTAGAGTTCATAATGA-AAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
125 TATCTTTTCCAGAG-A-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTC
48323 ATAA-GAAGAACTTGTTCAAT
185 ATAATGAAGAACTTGTTCAAT
48343 AATTCTATCA
Statistics
Matches: 390, Mismatches: 29, Indels: 27
0.87 0.07 0.06
Matches are distributed among these distances:
219 7 0.02
220 99 0.25
221 2 0.01
222 54 0.14
223 86 0.22
224 1 0.00
225 33 0.08
226 2 0.01
227 64 0.16
228 11 0.03
229 1 0.00
230 30 0.08
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (220 bp):
ATCAATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCTT
TTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAA
CTTGTTCAATCCTTTACCTGAATTC
Found at i:48668 original size:3 final size:3
Alignment explanation
Indices: 48653--48729 Score: 106
Period size: 3 Copynumber: 26.7 Consensus size: 3
48643 TTTTTACCCA
* *
48653 TAT TAT AAT TAT TAT TA- TAT TAT TAT TAT TAT TAT CAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
48699 TAT TAT TAT TAT CAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
48730 AATATATATT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 6 0.09
3 59 0.91
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:48678 original size:20 final size:19
Alignment explanation
Indices: 48653--48729 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 19
48643 TTTTTACCCA
48653 TATTATAATTATTATTATAT
1 TATTAT-ATTATTATTATAT
*
48673 TATTATTATTATTATCATTAT
1 TATTA-TATTATTATTA-TAT
48694 TATTATATTATTATTATCAT
1 TATTATATTATTATTAT-AT
48714 TATTATATTATTATTA
1 TATTATATTATTATTA
48730 AATATATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.02
20 42 0.81
21 9 0.17
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTATATTATTATTATAT
Found at i:48681 original size:23 final size:23
Alignment explanation
Indices: 48653--48729 Score: 100
Period size: 23 Copynumber: 3.2 Consensus size: 23
48643 TTTTTACCCA
*
48653 TATTATAATTATTATTATATTAT
1 TATTATTATTATTATTATATTAT
*
48676 TATTATTATTATCATTATTATTATAT
1 TATTATTATTATTATTA-TA-T-TAT
*
48702 TATTATTATCATTATTATATTAT
1 TATTATTATTATTATTATATTAT
48725 TATTA
1 TATTA
48730 AATATATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 23 0.49
24 3 0.06
25 3 0.06
26 18 0.38
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATTATTATTATTATATTAT
Found at i:48754 original size:10 final size:10
Alignment explanation
Indices: 48725--48763 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
48715 ATTATATTAT
48725 TATTAAATATA
1 TATTAAATA-A
48736 TATTAAATACA
1 TATTAAATA-A
48747 TA-TAAATAA
1 TATTAAATAA
48756 TATTAAAT
1 TATTAAAT
48764 TACAAAGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 3 0.12
10 11 0.42
11 12 0.46
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Done.