Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005765.1 Hibiscus syriacus cultivar Beakdansim tig00013497_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: 269056
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:14125 original size:48 final size:48
Alignment explanation
Indices: 14054--14147 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
14044 TCGCTTCATT
* * * *
14054 GATTCAGCCTTTGGGACTGATGGGGTACTGGCAACCTCCTGCTTTACC
1 GATTCAACCTTTGAGACTGATGGGATACTAGCAACCTCCTGCTTTACC
*
14102 GATTCAACCTTTGAGACTGATGGGATACTAGTAACCTCCTGCTTTA
1 GATTCAACCTTTGAGACTGATGGGATACTAGCAACCTCCTGCTTTA
14148 TAGATTCAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (48 bp):
GATTCAACCTTTGAGACTGATGGGATACTAGCAACCTCCTGCTTTACC
Found at i:16678 original size:7 final size:7
Alignment explanation
Indices: 16666--16731 Score: 123
Period size: 7 Copynumber: 9.4 Consensus size: 7
16656 TGTCTTTGGT
16666 TGGAGGC
1 TGGAGGC
16673 TGGAGGC
1 TGGAGGC
16680 TGGAGGC
1 TGGAGGC
16687 TGGAGGC
1 TGGAGGC
16694 TGGAGGC
1 TGGAGGC
16701 TGGAGGC
1 TGGAGGC
16708 TGGAGGC
1 TGGAGGC
16715 TGGAGGC
1 TGGAGGC
*
16722 TGGATGC
1 TGGAGGC
16729 TGG
1 TGG
16732 CTGGCGTGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.14, C:0.14, G:0.56, T:0.17
Consensus pattern (7 bp):
TGGAGGC
Found at i:18774 original size:22 final size:22
Alignment explanation
Indices: 18746--18806 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
18736 TCCTATTGAC
18746 ACGTTTTCAAAGTATAAATCAA
1 ACGTTTTCAAAGTATAAATCAA
18768 ACGTTTTCAAAGTATAAATCAA
1 ACGTTTTCAAAGTATAAATCAA
18790 ACGTTTTCAAAGTATAA
1 ACGTTTTCAAAGTATAA
18807 TAATTGCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (22 bp):
ACGTTTTCAAAGTATAAATCAA
Found at i:30148 original size:14 final size:15
Alignment explanation
Indices: 30129--30161 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30119 AATTGAAAAG
30129 ATAATATGT-AATAT
1 ATAATATGTAAATAT
*
30143 ATAATATTTAAATAT
1 ATAATATGTAAATAT
30158 ATAA
1 ATAA
30162 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAATATGTAAATAT
Found at i:30171 original size:24 final size:24
Alignment explanation
Indices: 30144--30189 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
30134 ATGTAATATA
*
30144 TAATATTTAAATATATAAAAAAAT
1 TAATATTTAAATAGATAAAAAAAT
* * *
30168 TAATTTTTCATTAGATAAAAAA
1 TAATATTTAAATAGATAAAAAA
30190 TCGAGAGGAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
TAATATTTAAATAGATAAAAAAAT
Found at i:30584 original size:21 final size:21
Alignment explanation
Indices: 30560--30654 Score: 102
Period size: 21 Copynumber: 4.6 Consensus size: 21
30550 TATCGCAAAT
* *
30560 TCGCGTTGCGATAATTGGAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
30581 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
30601 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
30622 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
30643 TCGCATTGCGAT
1 TCGCGTTGCGAT
30655 TTTCCATTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:30729 original size:19 final size:19
Alignment explanation
Indices: 30707--30746 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30697 TTCCAAATTC
* *
30707 GTTGCGATAGTCTACGGTT
1 GTTGCGAAAGTCTACAGTT
30726 GTTGCGAAAGTCTACAGTT
1 GTTGCGAAAGTCTACAGTT
30745 GT
1 GT
30747 CGTTGCGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (19 bp):
GTTGCGAAAGTCTACAGTT
Found at i:30754 original size:22 final size:19
Alignment explanation
Indices: 30705--30754 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
30695 TTTTCCAAAT
*
30705 TCGTTGCGATAGTCTACGG
1 TCGTTGCGAAAGTCTACGG
*
30724 TTGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGAAAGTCTAC-G--G
30746 TCGTTGCGA
1 TCGTTGCGA
30755 TTTTCCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
22 9 0.36
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (19 bp):
TCGTTGCGAAAGTCTACGG
Found at i:30882 original size:10 final size:11
Alignment explanation
Indices: 30853--30886 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
30843 GACACGTATT
30853 ACCACGACCACG
1 ACCACGA-CACG
30865 ACCACGACACG
1 ACCACGACACG
30876 A-CACGACACG
1 ACCACGACACG
30886 A
1 A
30887 TACAACCCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 5 0.23
12 7 0.32
ACGTcount: A:0.38, C:0.44, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACACG
Found at i:31393 original size:6 final size:6
Alignment explanation
Indices: 31384--31438 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
31374 GCCGTCCGTC
31384 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
31432 TCGTGG T
1 TCGTGG T
31439 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:31577 original size:41 final size:41
Alignment explanation
Indices: 31532--31621 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
31522 CAACGAATTT
* *
31532 TCGCAACGAATTTGGAAAATCACAACGATAACTGTAGACTA
1 TCGCAACGAATTTGAAAAATCACAACGACAACTGTAGACTA
*
31573 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGAAAAATCACAACGACAACTGTAGACTA
31614 TCGCAACG
1 TCGCAACG
31622 CGATTTTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTGAAAAATCACAACGACAACTGTAGACTA
Found at i:31658 original size:41 final size:40
Alignment explanation
Indices: 31613--31787 Score: 133
Period size: 41 Copynumber: 4.3 Consensus size: 40
31603 ACTGTAGACT
* *
31613 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGACTTT-AACTATCGCAACGCGAATTGGAAA
** * **
31654 ATCGCAACGCGAAATGAAAAATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGACTTTAACTATCGCAACGCGAA-TTGGAAA
* *
31693 ATCGCAACGACAACTGTAGACTATCGCAA--CGAATTTGGAAA
1 ATCGCAACG-CGACTTTA-ACTATCGCAACGCGAA-TTGGAAA
* * * * *
31734 ATCGCAACGACAACTGTAGACTATCGCAACGTGAACTCGAAA
1 ATCGCAACG-CGACTTTA-ACTATCGCAACGCGAATTGGAAA
31776 ATCGCAACGCGA
1 ATCGCAACGCGA
31788 AATGGAAAAT
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 4 0.04
39 15 0.13
40 12 0.11
41 64 0.57
42 14 0.12
43 3 0.03
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (40 bp):
ATCGCAACGCGACTTTAACTATCGCAACGCGAATTGGAAA
Found at i:31659 original size:20 final size:20
Alignment explanation
Indices: 31634--31807 Score: 135
Period size: 20 Copynumber: 8.6 Consensus size: 20
31624 ATTTTCAACT
31634 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
* *
31654 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAACTGGAAA
*
31674 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
31693 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
*
31715 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
31734 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
* *
31756 ATCGCAACGTGAACTCGAAA
1 ATCGCAACGCGAACTGGAAA
*
31776 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
31796 ATCGCAACGCGA
1 ATCGCAACGCGA
31808 TTTTCAACTA
Statistics
Matches: 120, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
18 4 0.03
19 22 0.18
20 62 0.52
21 6 0.05
22 26 0.22
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:31694 original size:102 final size:102
Alignment explanation
Indices: 31572--31850 Score: 311
Period size: 102 Copynumber: 2.7 Consensus size: 102
31562 ACTGTAGACT
*
31572 ATCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAACTATC
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAA-TATC
31637 GCAACGCGAACTG-GAAAATCGCAACGCGAAAT-GAAAA
65 GCAACGCGAACTGAGAAAATCGCAACGCGAAATCG-AAA
* ** *
31674 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG-AATTTGGAAAATCG
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAATATCG
** * *
31738 CAACGAC-AACTGTAGACTATCGCAACGTGAACTCGAAA
66 CAACG-CGAACTG-AGAAAATCGCAACGCGAAATCGAAA
* * * * *
31776 ATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAATGCGATTTTCAATT
1 ATCGCAA--CGAATTTGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGATTTTCAA-T
31838 ATCGCAACGCGAA
62 ATCGCAACGCGAA
31851 ATGCAACGCG
Statistics
Matches: 149, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
100 14 0.09
101 7 0.05
102 89 0.60
103 24 0.16
104 15 0.10
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (102 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAATATCG
CAACGCGAACTGAGAAAATCGCAACGCGAAATCGAAA
Found at i:31695 original size:19 final size:19
Alignment explanation
Indices: 31648--31743 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
31638 CAACGCGAAC
*
31648 TGGAAAATCGCAACGCGAA-A
1 TGGAAAATCGCAA--CGAATT
*
31668 TGAAAAATCGCAACGAATT
1 TGGAAAATCGCAACGAATT
*
31687 TGGAAAATCGCAACGACAACTG
1 TGGAAAATCGCAACG--AA-TT
* **
31709 TAGACTATCGCAACGAATT
1 TGGAAAATCGCAACGAATT
31728 TGGAAAATCGCAACGA
1 TGGAAAATCGCAACGA
31744 CAACTGTAGA
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.07
19 28 0.46
20 14 0.23
21 2 0.03
22 13 0.21
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (19 bp):
TGGAAAATCGCAACGAATT
Found at i:31770 original size:22 final size:22
Alignment explanation
Indices: 31554--31764 Score: 87
Period size: 22 Copynumber: 10.2 Consensus size: 22
31544 TGGAAAATCA
*
31554 CAACGATAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
** **
31576 CAACGA-ATTTG-A-AAAATCG
1 CAACGACAACTGTAGACTATCG
31595 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * *
31617 CAACG-CGATTTTCA-ACTATCG
1 CAACGACAACTGT-AGACTATCG
**
31638 CAACG-CGAACTG--GAAAATCG
1 CAACGAC-AACTGTAGACTATCG
* **
31658 CAACG-CGAAATG-A-AAAATCG
1 CAACGAC-AACTGTAGACTATCG
* * **
31678 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
31697 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * **
31719 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
31738 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
31760 CAACG
1 CAACG
31765 TGAACTCGAA
Statistics
Matches: 143, Mismatches: 31, Indels: 30
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.01
18 2 0.01
19 36 0.25
20 34 0.24
21 25 0.17
22 45 0.31
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (22 bp):
CAACGACAACTGTAGACTATCG
Found at i:31822 original size:21 final size:21
Alignment explanation
Indices: 31796--31849 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
31786 GAAATGGAAA
31796 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
31817 ATCGCAATGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
31838 ATCGCAACGCGA
1 ATCGCAACGCGA
31850 AATGCAACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:31823 original size:143 final size:143
Alignment explanation
Indices: 31532--31807 Score: 448
Period size: 143 Copynumber: 1.9 Consensus size: 143
31522 CAACGAATTT
*
31532 TCGCAACGAATTTGGAAAATCACAACGATAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
1 TCGCAACGAATTTGGAAAATCACAACGACAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
** * *
31597 ACGACAACTGTAGACTATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAAC
66 ACGACAACTGTAGACTATCGCAACGCGATACTCAACAATCGCAACGCGAAATGGAAAATCGCAAC
*
31662 GCGAAATGAAAAA
131 GCGAAATCAAAAA
* *
31675 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCA
1 TCGCAACGAATTTGGAAAATCACAACGACAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
*
31740 ACGACAACTGTAGACTATCGCAACGTGA-ACTCGAA-AATCGCAACGCGAAATGGAAAATCGCAA
66 ACGACAACTGTAGACTATCGCAACGCGATACTC-AACAATCGCAACGCGAAATGGAAAATCGCAA
31803 CGCGA
130 CGCGA
31808 TTTTCAACTA
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
142 33 0.27
143 91 0.73
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (143 bp):
TCGCAACGAATTTGGAAAATCACAACGACAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
ACGACAACTGTAGACTATCGCAACGCGATACTCAACAATCGCAACGCGAAATGGAAAATCGCAAC
GCGAAATCAAAAA
Found at i:38153 original size:2 final size:2
Alignment explanation
Indices: 38146--38215 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
38136 AATACTACCC
38146 AT AT 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 AT AT
38188 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
38216 TCACGGCTAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39799 original size:2 final size:2
Alignment explanation
Indices: 39794--39840 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
39784 CGCGCGCGCG
39794 CA CA CA CA CA CA CA CA CA CA CA C- CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39835 CA CA CA
1 CA CA CA
39841 AGGGTCGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:41581 original size:17 final size:17
Alignment explanation
Indices: 41561--41593 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41551 ATTAGCTGCT
41561 GAAGATAAGGCTGGAAA
1 GAAGATAAGGCTGGAAA
*
41578 GAAGCTAAGGCTGGAA
1 GAAGATAAGGCTGGAA
41594 TTTGAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.36, T:0.12
Consensus pattern (17 bp):
GAAGATAAGGCTGGAAA
Found at i:48112 original size:14 final size:12
Alignment explanation
Indices: 48093--48124 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
48083 TAACCTTCTT
48093 GAGAGAGAAGCG
1 GAGAGAGAAGCG
48105 GAGAGAGAAGCG
1 GAGAGAGAAGCG
48117 GAGAGAGA
1 GAGAGAGA
48125 TTCTTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.50, T:0.00
Consensus pattern (12 bp):
GAGAGAGAAGCG
Found at i:48543 original size:7 final size:7
Alignment explanation
Indices: 48531--48596 Score: 125
Period size: 7 Copynumber: 9.6 Consensus size: 7
48521 ATAAGTCAGT
48531 GCCATTA
1 GCCATTA
48538 GCCATTA
1 GCCATTA
48545 GCCATTA
1 GCCATTA
48552 GCCATTA
1 GCCATTA
48559 GCCATTA
1 GCCATTA
48566 GCCATTA
1 GCCATTA
48573 GCCATTA
1 GCCATTA
48580 -CCATTA
1 GCCATTA
48586 GCCATTA
1 GCCATTA
48593 GCCA
1 GCCA
48597 AAACCATATG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.10
7 52 0.90
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (7 bp):
GCCATTA
Found at i:48602 original size:20 final size:20
Alignment explanation
Indices: 48539--48603 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
48529 GTGCCATTAG
*
48539 CCATTAGCCATTAGCCATTAG
1 CCATTAGCCATTAGCCA-TAA
*
48560 CCATTAGCCATTAGCCATTA
1 CCATTAGCCATTAGCCATAA
*
48580 CCATTAGCCATTAGCCAAAA
1 CCATTAGCCATTAGCCATAA
48600 CCAT
1 CCAT
48604 ATGCACCGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.32, C:0.31, G:0.11, T:0.26
Consensus pattern (20 bp):
CCATTAGCCATTAGCCATAA
Found at i:49296 original size:19 final size:19
Alignment explanation
Indices: 49272--49309 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49262 TCAAAATAGA
*
49272 AAATATCTTA-AATTATAAT
1 AAATAT-TTACAATCATAAT
49291 AAATATTTACAATCATAAT
1 AAATATTTACAATCATAAT
49310 CATAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATTTACAATCATAAT
Found at i:51565 original size:14 final size:14
Alignment explanation
Indices: 51529--51567 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
51519 CCAAAAAGTT
*
51529 TTTGGCGTGACTTG
1 TTTGGCGTGATTTG
51543 TTT-G-GTGATTTG
1 TTTGGCGTGATTTG
51555 TTTGGCGTGATTT
1 TTTGGCGTGATTT
51568 ATGGTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 10 0.45
13 2 0.09
14 10 0.45
ACGTcount: A:0.08, C:0.08, G:0.33, T:0.51
Consensus pattern (14 bp):
TTTGGCGTGATTTG
Found at i:63417 original size:16 final size:17
Alignment explanation
Indices: 63396--63430 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
63386 GCGACTTTCC
*
63396 AAATATA-TCATAAATT
1 AAATATATTAATAAATT
63412 AAATATATTAATAAATT
1 AAATATATTAATAAATT
63429 AA
1 AA
63431 TTCTTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATATTAATAAATT
Found at i:67084 original size:24 final size:24
Alignment explanation
Indices: 67005--67077 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
66995 TCACCATTTC
* * *
67005 CATCACCGTTGCGATCACCAGCAG
1 CATCACCATTGCGACCACCAACAG
67029 CATCACCATTGCGACCACCAACAG
1 CATCACCATTGCGACCACCAACAG
* *
67053 CATCACCATTGTGACCACCATCAG
1 CATCACCATTGCGACCACCAACAG
67077 C
1 C
67078 TGCACCACCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.29, C:0.40, G:0.15, T:0.16
Consensus pattern (24 bp):
CATCACCATTGCGACCACCAACAG
Found at i:67703 original size:36 final size:35
Alignment explanation
Indices: 67657--67877 Score: 229
Period size: 36 Copynumber: 6.3 Consensus size: 35
67647 ACCACCACCA
*
67657 CCTCCTCCTGGAACAGCATCAACAATGCCACAACAT
1 CCTCCTCCTGGAACAGCATCCACAATGCCAC-ACAT
* *
67693 CCTCCTCCTGGAACAGCATCAACAATGCCAC-C-G
1 CCTCCTCCTGGAACAGCATCCACAATGCCACACAT
* * *
67726 CATCCTCCTGGCACAGCATCCACAATGCCACCACCT
1 CCTCCTCCTGGAACAGCATCCACAATGCCA-CACAT
* * *
67762 CCTCCTCCTTGCACAGCATCCACAATGCCACCACCT
1 CCTCCTCCTGGAACAGCATCCACAATGCCA-CACAT
*
67798 CCTCTTCCTGGAACAGCATCCACAATGCCAC-CAATT
1 CCTCCTCCTGGAACAGCATCCACAATGCCACAC-A-T
* * *
67834 CC-CACTCCAGGAACAGCGTCCATAATGCCAC-CAT
1 CCTC-CTCCTGGAACAGCATCCACAATGCCACACAT
67868 -CTCCTCCTGG
1 CCTCCTCCTGG
67878 TGCAACAAAA
Statistics
Matches: 162, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
33 34 0.21
34 5 0.03
35 4 0.02
36 119 0.73
ACGTcount: A:0.26, C:0.43, G:0.12, T:0.18
Consensus pattern (35 bp):
CCTCCTCCTGGAACAGCATCCACAATGCCACACAT
Found at i:67732 original size:69 final size:69
Alignment explanation
Indices: 67651--67877 Score: 244
Period size: 69 Copynumber: 3.2 Consensus size: 69
67641 AGTTCCACCA
* *
67651 CCACCACCTCCTCCTGGAACAGCATCAACAATGCCACAACATCCTCCTCCTGGAACAGCATCAAC
1 CCACCACATCCTCCTGGAACAGCATCCACAATGCCACAACATCCTCCTCCTGGAACAGCATCAAC
67716 AATG
66 AATG
* * * * * * *
67720 CCACCGCATCCTCCTGGCACAGCATCCACAATGCCACCACCTCCTCCTCCTTGCACAGCATCCAC
1 CCACCACATCCTCCTGGAACAGCATCCACAATGCCACAACATCCTCCTCCTGGAACAGCATCAAC
67785 AATG
66 AATG
* * * *
67789 CCACCACCTCCTCTTCCTGGAACAGCATCCACAATGCCACCAA-TTCC-CACTCCAGGAACAGCG
1 CCACCACAT-C-C-TCCTGGAACAGCATCCACAATGCCA-CAACATCCTC-CTCCTGGAACAGCA
* *
67852 TCCATAATG
61 TCAACAATG
67861 CCACCATC-TCCTCCTGG
1 CCACCA-CATCCTCCTGG
67878 TGCAACAAAA
Statistics
Matches: 133, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
69 73 0.55
70 2 0.02
71 3 0.02
72 52 0.39
73 3 0.02
ACGTcount: A:0.26, C:0.44, G:0.12, T:0.18
Consensus pattern (69 bp):
CCACCACATCCTCCTGGAACAGCATCCACAATGCCACAACATCCTCCTCCTGGAACAGCATCAAC
AATG
Found at i:67850 original size:72 final size:71
Alignment explanation
Indices: 67648--67873 Score: 253
Period size: 72 Copynumber: 3.2 Consensus size: 71
67638 TCCAGTTCCA
* *
67648 CCACCACCACCTCCTCCTGGAACAGCATCAACAATGCCA-CAACATCCTCCTCCTGGAACAGCAT
1 CCACCACCTCCT-CTCCTGGAACAGCATCCACAATGCCACCAA-ATCCTCCTCCTGGAACAGCAT
*
67712 CAACAATG
64 CCACAATG
* * * ** * *
67720 CCACCGCAT-C-CTCCTGGCACAGCATCCACAATGCCACCACCTCCTCCTCCTTGCACAGCATCC
1 CCACCACCTCCTCTCCTGGAACAGCATCCACAATGCCACCAAATCCTCCTCCTGGAACAGCATCC
67783 ACAATG
66 ACAATG
* * *
67789 CCACCACCTCCTCTTCCTGGAACAGCATCCACAATGCCACCAATTCC-CACTCCAGGAACAGCGT
1 CCACCACCTCCTC-TCCTGGAACAGCATCCACAATGCCACCAAATCCTC-CTCCTGGAACAGCAT
*
67853 CCATAATG
64 CCACAATG
*
67861 CCACCATCTCCTC
1 CCACCACCTCCTC
67874 CTGGTGCAAC
Statistics
Matches: 128, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
69 56 0.44
70 3 0.02
71 3 0.02
72 66 0.52
ACGTcount: A:0.27, C:0.45, G:0.11, T:0.17
Consensus pattern (71 bp):
CCACCACCTCCTCTCCTGGAACAGCATCCACAATGCCACCAAATCCTCCTCCTGGAACAGCATCC
ACAATG
Found at i:73592 original size:29 final size:29
Alignment explanation
Indices: 73557--73638 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
73547 AAACTAAATT
*
73557 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
73586 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
73615 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
73639 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:78342 original size:29 final size:29
Alignment explanation
Indices: 78307--78388 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
78297 AAACTAAATT
*
78307 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
78336 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
78365 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
78389 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:93863 original size:21 final size:21
Alignment explanation
Indices: 93839--93886 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
93829 ATACTTACAT
93839 TGCAACTTGCAAATCAGTTTC
1 TGCAACTTGCAAATCAGTTTC
93860 TGCAACTTGCAAATCAGTTTC
1 TGCAACTTGCAAATCAGTTTC
93881 TGCAAC
1 TGCAAC
93887 GTATAAAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (21 bp):
TGCAACTTGCAAATCAGTTTC
Found at i:103367 original size:14 final size:14
Alignment explanation
Indices: 103348--103375 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
103338 ATCATAACAA
103348 AATTATATAACTAT
1 AATTATATAACTAT
103362 AATTATATAACTAT
1 AATTATATAACTAT
103376 CTTCACTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:104172 original size:22 final size:23
Alignment explanation
Indices: 104132--104185 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
104122 AAGAAAGGTG
*
104132 AAAAGGTGGCAGACAAAACCACA
1 AAAAGGAGGCAGACAAAACCACA
104155 AAAAGGAGGCAGAC-AAACCACA
1 AAAAGGAGGCAGACAAAACCACA
104177 AAAAGGAGG
1 AAAAGGAGG
104186 GGAAGATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.54, C:0.19, G:0.26, T:0.02
Consensus pattern (23 bp):
AAAAGGAGGCAGACAAAACCACA
Found at i:110855 original size:20 final size:19
Alignment explanation
Indices: 110822--110860 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
110812 TGTTTGTGTG
110822 CTTCATGTGATATAATATAA
1 CTTCATGTGATAT-ATATAA
110842 CTTCATGT-AGTATATATAA
1 CTTCATGTGA-TATATATAA
110861 TATACCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
CTTCATGTGATATATATAA
Found at i:115590 original size:200 final size:203
Alignment explanation
Indices: 115218--115621 Score: 787
Period size: 200 Copynumber: 2.0 Consensus size: 203
115208 GATAAATGAA
115218 TAATTTTAAACAGGAAATTTGAAAGTTTTGCAAGTATGTAATTGTAAATTCATAATACATAAGAG
1 TAATTTTAAACAGGAAATTTGAAAGTTTTGCAAGTATGTAATTGTAAATTCATAATACATAAGAG
115283 GCCAAAGTTTAGCCTGTTACATTTTGACAAGTGCAAAAGAAAAATAAGTATAGTATAAACTAACA
66 GCCAAAGTTTAGCCTGTTACATTTTGACAAGTGCAAAAGAAAAATAAGTATAGTATAAACTAACA
115348 AACAGGAAAACTTACCCATATATCAATGCTTCCGGAGACTAGTCTGAAATGTGGGATTTAACTTG
131 AACAGGAAAACTTACCCATATATCAATGCTTCCGGAGACTAGTCTGAAATGTGGGATTTAACTTG
115413 TAAGTTGT
196 TAAGTTGT
115421 TAATTTTAAACAGG-AATTTGAAAGTTTTGCAAGTATGT-ATTGTAAATTCATAATACATAAGAG
1 TAATTTTAAACAGGAAATTTGAAAGTTTTGCAAGTATGTAATTGTAAATTCATAATACATAAGAG
115484 GCCAAAGTTTAGCCTGTTACATTTTGACAAGTGCAAAAG-AAAATAAGTATAGTATAAACTAACA
66 GCCAAAGTTTAGCCTGTTACATTTTGACAAGTGCAAAAGAAAAATAAGTATAGTATAAACTAACA
115548 AACAGGAAAACTTACCCATATATCAATGCTTCCGGAGACTAGTCTGAAATGTGGGATTTAACTTG
131 AACAGGAAAACTTACCCATATATCAATGCTTCCGGAGACTAGTCTGAAATGTGGGATTTAACTTG
115613 TAAGTTGT
196 TAAGTTGT
115621 T
1 T
115622 TCCTTCTTCC
Statistics
Matches: 201, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
200 99 0.49
201 64 0.32
202 24 0.12
203 14 0.07
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (203 bp):
TAATTTTAAACAGGAAATTTGAAAGTTTTGCAAGTATGTAATTGTAAATTCATAATACATAAGAG
GCCAAAGTTTAGCCTGTTACATTTTGACAAGTGCAAAAGAAAAATAAGTATAGTATAAACTAACA
AACAGGAAAACTTACCCATATATCAATGCTTCCGGAGACTAGTCTGAAATGTGGGATTTAACTTG
TAAGTTGT
Found at i:126586 original size:18 final size:18
Alignment explanation
Indices: 126563--126600 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
126553 GCACAATATG
126563 TTTAATAATACATGTATC
1 TTTAATAATACATGTATC
126581 TTTAATAATACATGTATC
1 TTTAATAATACATGTATC
126599 TT
1 TT
126601 CCTTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (18 bp):
TTTAATAATACATGTATC
Found at i:127750 original size:17 final size:18
Alignment explanation
Indices: 127728--127761 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
127718 TCAGCCGATC
127728 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
127745 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
127762 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:140321 original size:22 final size:21
Alignment explanation
Indices: 140263--140322 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
140253 ACTAGTATTT
* * *
140263 AAAATATGTTTATATTTTAATC
1 AAAATAT-TTTATATATGAATA
*
140285 AAAATATTTCAATATATGAATA
1 AAAATATTT-TATATATGAATA
140307 AAAATATATTTATATA
1 AAAATAT-TTTATATA
140323 AATGTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
AAAATATTTTATATATGAATA
Found at i:140323 original size:16 final size:16
Alignment explanation
Indices: 140304--140337 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
140294 CAATATATGA
140304 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
140320 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
140336 AT
1 AT
140338 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:140411 original size:16 final size:18
Alignment explanation
Indices: 140379--140412 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
140369 TACTAATGTA
140379 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
140397 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
140413 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:141057 original size:130 final size:130
Alignment explanation
Indices: 140853--141097 Score: 391
Period size: 130 Copynumber: 1.9 Consensus size: 130
140843 AATTTTCTTC
* *
140853 TAATTAGGTGCTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGCTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* ** * *
140918 TCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGCACCAAATTGATAGCATATATAAA
* * * *
140983 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGCTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
141048 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGCACCAAATT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGCACCAAATT
141098 AATTATATAA
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 104 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGCTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGCACCAAATTGATAGCATATATAAA
Found at i:141548 original size:35 final size:35
Alignment explanation
Indices: 141498--141573 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
141488 AATTGAATTT
* *
141498 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
141533 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
141568 AATTGA
1 AATTGA
141574 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:146385 original size:31 final size:31
Alignment explanation
Indices: 146347--146442 Score: 183
Period size: 31 Copynumber: 3.1 Consensus size: 31
146337 GAACCTCGGC
*
146347 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
146378 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
146409 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
146440 AAC
1 AAC
146443 CCTCTACTCT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:148195 original size:22 final size:22
Alignment explanation
Indices: 148155--148206 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
148145 TATATTAGTC
* *
148155 CTTCGAGACGTATCCAGTGG-T
1 CTTCGGGACGTATACAGTGGTT
*
148176 CATTCGGGACGTATATAGTGGTT
1 C-TTCGGGACGTATACAGTGGTT
148199 CTTCGGGA
1 CTTCGGGA
148207 TATAGTGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (22 bp):
CTTCGGGACGTATACAGTGGTT
Found at i:154134 original size:8 final size:8
Alignment explanation
Indices: 154121--154147 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
154111 TAACGGTGGA
154121 AAGAAGCC
1 AAGAAGCC
154129 AAGAAGCC
1 AAGAAGCC
154137 AAGAAGCC
1 AAGAAGCC
154145 AAG
1 AAG
154148 GAACTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.22, G:0.26, T:0.00
Consensus pattern (8 bp):
AAGAAGCC
Found at i:155350 original size:61 final size:59
Alignment explanation
Indices: 155285--155400 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 59
155275 CAGTTCCCAA
*
155285 ATTCGCAACTCGAACAT-GAAAATTTTCGCAA-TGCTAATTACCGATATAGGTAAAAACAACT
1 ATTCGCAACTCGAA-ATCGAAAATTTT-GCAACT-C-AATTACCGACATAGGTAAAAACAACT
* **
155346 ATTCGCAACTCGAATTCGCCAATTTTGCAACTCAATTACCGACATAGGTAAAAAC
1 ATTCGCAACTCGAAATCGAAAATTTTGCAACTCAATTACCGACATAGGTAAAAAC
155401 GGTAGAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 21 0.43
60 6 0.12
61 22 0.45
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (59 bp):
ATTCGCAACTCGAAATCGAAAATTTTGCAACTCAATTACCGACATAGGTAAAAACAACT
Found at i:160331 original size:18 final size:19
Alignment explanation
Indices: 160295--160332 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
160285 AATATTTTTA
* *
160295 TTTTAACTATTTTTTTAAT
1 TTTTAACTATATTTATAAT
160314 TTTTAACTA-ATTTATAAT
1 TTTTAACTATATTTATAAT
160332 T
1 T
160333 ATATATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAACTATATTTATAAT
Found at i:172496 original size:24 final size:24
Alignment explanation
Indices: 172464--172530 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
172454 TATATTCACG
172464 AATAT-TAAATAAATATGTTG-ACA
1 AATATATAAATAAATATGTTGTA-A
* *
172487 TATATATAAATGAATATGTTGTAA
1 AATATATAAATAAATATGTTGTAA
*
172511 AACATATAAATAAATATGTT
1 AATATATAAATAAATATGTT
172531 CACGAAGGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.11
24 32 0.86
25 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (24 bp):
AATATATAAATAAATATGTTGTAA
Found at i:172921 original size:16 final size:16
Alignment explanation
Indices: 172896--172941 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
172886 ATTCATACAA
*
172896 AACATCTGAATCATTC
1 AACATTTGAATCATTC
*
172912 AACATTTGAATTATTC
1 AACATTTGAATCATTC
*
172928 AACACTT-AATCATT
1 AACATTTGAATCATT
172942 TTAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (16 bp):
AACATTTGAATCATTC
Found at i:179207 original size:63 final size:63
Alignment explanation
Indices: 179103--179226 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
179093 AACCAAAGAT
* *
179103 GGTAAATGAATCTAATTTAAACGAATAAAATTATTTGTATGTTCATTTATTTAATTTAAAAGG
1 GGTAAATGAATCAAATTTAAACAAATAAAATTATTTGTATGTTCATTTATTTAATTTAAAAGG
* * * *
179166 GGTAAATGAATCAAATTTAAATAAATAAAATTATTTTTATGTTCATTTGTTTATTTTAAAA
1 GGTAAATGAATCAAATTTAAACAAATAAAATTATTTGTATGTTCATTTATTTAATTTAAAA
179227 TTATTAACGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (63 bp):
GGTAAATGAATCAAATTTAAACAAATAAAATTATTTGTATGTTCATTTATTTAATTTAAAAGG
Found at i:184756 original size:2 final size:2
Alignment explanation
Indices: 184739--184808 Score: 115
Period size: 2 Copynumber: 34.5 Consensus size: 2
184729 TAATCGATAC
184739 AT AT A- AT AT GAT AT AT AT AT AT AT GAT 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 AT AT
184782 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
184809 CACGTATTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 60 0.92
3 4 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:189844 original size:2 final size:2
Alignment explanation
Indices: 189837--189875 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
189827 CAATCAATCA
189837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
189876 ACGATAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:192347 original size:31 final size:30
Alignment explanation
Indices: 192295--192352 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
192285 CACATAAAGA
*
192295 CTATTATAAAATGGTCATTAAAACTTATTGG
1 CTATTACAAAATGGTCATT-AAACTTATTGG
**
192326 CTATTACAAAATGGTGGTTAAACTTAT
1 CTATTACAAAATGGTCATTAAACTTAT
192353 CATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (30 bp):
CTATTACAAAATGGTCATTAAACTTATTGG
Found at i:192889 original size:29 final size:29
Alignment explanation
Indices: 192832--192889 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
192822 GAATTTTTTA
* **
192832 AAAATTATTTGTTGAAATAAGATTTAATT
1 AAAATTATTTGTTGAAATAAAATGAAATT
*
192861 AAAATTATTTGTTGAGATAAAATGAAATT
1 AAAATTATTTGTTGAAATAAAATGAAATT
192890 TATAGTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (29 bp):
AAAATTATTTGTTGAAATAAAATGAAATT
Found at i:199193 original size:24 final size:25
Alignment explanation
Indices: 199166--199220 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
199156 CGTTCATTTA
199166 CGTTCGTG-AACGTTCGGTTATGTT
1 CGTTCGTGTAACGTTCGGTTATGTT
* *
199190 CGTTCG-GTCACGTTCGTTTATGTT
1 CGTTCGTGTAACGTTCGGTTATGTT
199214 CGTTCGT
1 CGTTCGT
199221 TTATGTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.44
Consensus pattern (25 bp):
CGTTCGTGTAACGTTCGGTTATGTT
Found at i:203719 original size:22 final size:23
Alignment explanation
Indices: 203694--203743 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
203684 GTTCGTGAAC
* *
203694 GTTCGATT-ATATGTTCGTTTAT
1 GTTCGATTCATATATTCATTTAT
*
203716 GTTCG-TTCATTTATTCATTTAT
1 GTTCGATTCATATATTCATTTAT
203738 GTTCGA
1 GTTCGA
203744 ACAGAGGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.54
Consensus pattern (23 bp):
GTTCGATTCATATATTCATTTAT
Found at i:208570 original size:190 final size:189
Alignment explanation
Indices: 208246--208621 Score: 644
Period size: 190 Copynumber: 2.0 Consensus size: 189
208236 GCTTCAGTTT
*
208246 TTGCACTGGAAGTGAGTTATGAAGGAGAAGATATTTCATAGCTGCATATTTAGAGACTGATTTTC
1 TTGCACTGGAAGTGAGTTATGAAGGAGAAGATATGTCATAGCTGCATATTTAGAGACTGATTTTC
* *
208311 CAAGATGCAACTTTGGCATAAAAAGGGAGAAGTTCTGAAAAAGAAACCAAAGGAGAAACCTTGTT
66 CAAGATGCAACTTTGGCATAAAAAGGGAGAAGCTCTGAAAAAGAAACCAAAAGAGAAACCTTGTT
*
208376 TGTGTAATGGTTAATGGGGTTTAATCATAATTAAAAAATTGAAGAACAACATTAGATGTG
131 TGTGTAAGGGTTAATGGGGTTTAATCATAATT-AAAAATTGAAGAACAACATTAGATGTG
* * *
208436 TTGCACTGGAAGTGAGTTATGAAGGAGAAGATATGTCATGGCTGCATGTTTAGAGACTGGTTTTC
1 TTGCACTGGAAGTGAGTTATGAAGGAGAAGATATGTCATAGCTGCATATTTAGAGACTGATTTTC
* * *
208501 TAAGGTGCAACTTTGGCATAAAAAGGGAGAAGCTCTGAAAAAGAAACCAAAAGAGAAACCTTTTT
66 CAAGATGCAACTTTGGCATAAAAAGGGAGAAGCTCTGAAAAAGAAACCAAAAGAGAAACCTTGTT
*
208566 TGTGTAAGGGTTGATGGGGTTTAATCATAATTAAAAATTGAAGAACAACATTAGAT
131 TGTGTAAGGGTTAATGGGGTTTAATCATAATTAAAAATTGAAGAACAACATTAGAT
208622 TTGTAATTAC
Statistics
Matches: 175, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
189 24 0.14
190 151 0.86
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (189 bp):
TTGCACTGGAAGTGAGTTATGAAGGAGAAGATATGTCATAGCTGCATATTTAGAGACTGATTTTC
CAAGATGCAACTTTGGCATAAAAAGGGAGAAGCTCTGAAAAAGAAACCAAAAGAGAAACCTTGTT
TGTGTAAGGGTTAATGGGGTTTAATCATAATTAAAAATTGAAGAACAACATTAGATGTG
Found at i:208729 original size:17 final size:17
Alignment explanation
Indices: 208707--208746 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
208697 GACAAGTAAT
208707 AGGTTGTCCCTAACGTC
1 AGGTTGTCCCTAACGTC
208724 AGGTTGTCCCTAACGTC
1 AGGTTGTCCCTAACGTC
208741 AGGTTG
1 AGGTTG
208747 GGAGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (17 bp):
AGGTTGTCCCTAACGTC
Found at i:219750 original size:20 final size:20
Alignment explanation
Indices: 219697--219751 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
219687 ACTCCCTAGT
* *
219697 GGTACTGTTCACACAGTATC
1 GGTACTATTCATACAGTATC
219717 GGTACTATTCATACAGTATC
1 GGTACTATTCATACAGTATC
*
219737 GGTACTATTTATACA
1 GGTACTATTCATACA
219752 ATACAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (20 bp):
GGTACTATTCATACAGTATC
Found at i:220982 original size:19 final size:17
Alignment explanation
Indices: 220958--221007 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
220948 AATTTAAAAG
220958 AAATAAAGATTTTTTTAA
1 AAATAAA-ATTTTTTTAA
*
220976 TAAATAATAATTTATTTTTA
1 -AAATAA-AATTT-TTTTAA
220996 AAATAAAATTTT
1 AAATAAAATTTT
221008 AATAATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 5 0.18
19 16 0.57
20 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATAAAATTTTTTTAA
Found at i:221297 original size:19 final size:19
Alignment explanation
Indices: 221275--221315 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
221265 AAAAATAAAA
*
221275 TAATTACTAA-AAATATTAT
1 TAATTA-TAATAAATACTAT
221294 TAATTATAATAAATACTAT
1 TAATTATAATAAATACTAT
221313 TAA
1 TAA
221316 ACTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTATAATAAATACTAT
Found at i:223830 original size:214 final size:211
Alignment explanation
Indices: 223437--223857 Score: 815
Period size: 214 Copynumber: 2.0 Consensus size: 211
223427 AGAGAGGAAC
223437 TGTAAAATCATGTAAGAGTTTGATACCTCTGGTGATTCTAATAAAGGAAACTGAATTCGTTAGAC
1 TGTAAAATCATGTAAGAGTTTGATACCTCTGGTGATTCTAATAAAGGAAACTGAATTCGTTAGAC
223502 GAATCTCAAATTGGCTTAACAAGGCAAATAACGATGTAAAACTGTTCGCACTCGAGCCAGGGGCA
66 GAATCTCAAATTGGCTTAACAAGGCAAATAACGATGTAAAACTGTTCGCACTCGAGCCAGGGGCA
223567 AGGATAATCAGCCATGGTGGAATTACATCAAAGCTGCTTTTCTCGTCACTTTGGGGACTACCGCT
131 AGGATAATCAGCCATGGTGGAATTACATCAAAGCTGCTTTTCTCGTCACTTTGGGGACTACCGCT
223632 ACGATCATGCTCAACT
196 ACGATCATGCTCAACT
223648 TGTAAAATCATGTAAGAGTTTGATACCTCTGGTGATTCTAATATAAAGGAAACTGAATTCGTTAG
1 TGTAAAATCATGTAAGAGTTTGATACCTCTGGTGATTCT-A-ATAAAGGAAACTGAATTCGTTAG
223713 ACGAATCTCAAATTGGCTTAACAAGGCAAATAACGATGTAAAACTGTTTCGCACTCGAGCCAGGG
64 ACGAATCTCAAATTGGCTTAACAAGGCAAATAACGATGTAAAACTG-TTCGCACTCGAGCCAGGG
223778 GCAAGGATAATCAGCCATGGTGGAATTACATCAAAGCTGCTTTTCTCGTCACTTTGGGGACTACC
128 GCAAGGATAATCAGCCATGGTGGAATTACATCAAAGCTGCTTTTCTCGTCACTTTGGGGACTACC
223843 GCTACGATCATGCTC
193 GCTACGATCATGCTC
223858 TCGAAGCCTC
Statistics
Matches: 207, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
211 39 0.19
212 1 0.00
213 69 0.33
214 98 0.47
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (211 bp):
TGTAAAATCATGTAAGAGTTTGATACCTCTGGTGATTCTAATAAAGGAAACTGAATTCGTTAGAC
GAATCTCAAATTGGCTTAACAAGGCAAATAACGATGTAAAACTGTTCGCACTCGAGCCAGGGGCA
AGGATAATCAGCCATGGTGGAATTACATCAAAGCTGCTTTTCTCGTCACTTTGGGGACTACCGCT
ACGATCATGCTCAACT
Found at i:231068 original size:2 final size:2
Alignment explanation
Indices: 231061--231091 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
231051 TTCCTAACAG
231061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
231092 CAATACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:235520 original size:25 final size:25
Alignment explanation
Indices: 235471--235521 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
235461 ATTTCACCCG
*
235471 ACCCGACCCAATATATAACTTAAAA
1 ACCCGACCCAATATATAACTAAAAA
235496 ACCCGACCCGAA-ATAATAA-TAAAAA
1 ACCCGACCC-AATAT-ATAACTAAAAA
235521 A
1 A
235522 GTATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.53, C:0.25, G:0.06, T:0.16
Consensus pattern (25 bp):
ACCCGACCCAATATATAACTAAAAA
Found at i:240456 original size:32 final size:31
Alignment explanation
Indices: 240419--240501 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
240409 TTTTGATGAG
*
240419 TTTAATGACTATTTTGTAATAGTTTGATAAAA
1 TTTAATGACTATTTTGTAATAATTTGA-AAAA
* * * *
240451 TTTAAT-AATAATTTTTATAATAATTTGAGAAG
1 TTTAATGACT-A-TTTTGTAATAATTTGAAAAA
240483 TTTAATGACTATTTTGTAA
1 TTTAATGACTATTTTGTAA
240502 CTTTTGAGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
31 9 0.22
32 16 0.39
33 16 0.39
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTAATGACTATTTTGTAATAATTTGAAAAA
Found at i:244928 original size:536 final size:536
Alignment explanation
Indices: 243916--244985 Score: 2131
Period size: 536 Copynumber: 2.0 Consensus size: 536
243906 AGAAGTTTTT
243916 ATTCAATGATATTTTAGGTCTAGGTTACATCTCTATTTATAATAGAAAACCCTGGTACATAATTA
1 ATTCAATGATATTTTAGGTCTAGGTTACATCTCTATTTATAATAGAAAACCCTGGTACATAATTA
243981 CAAAATCAACCCTGTACCGTACCGCGGGGGCTACGCCCCCACACCCCCAACCCACATAATTCGTA
66 CAAAATCAACCCTGTACCGTACCGCGGGGGCTACGCCCCCACACCCCCAACCCACATAATTCGTA
244046 ACCCCACAACGAGACTTTTTATGAGCCATACATAACAAATCTCCACCTTGGCGAATATCCTGCCC
131 ACCCCACAACGAGACTTTTTATGAGCCATACATAACAAATCTCCACCTTGGCGAATATCCTGCCC
244111 CTTGGAAACTTCAATGTGGGTTGGGTTACCTTGCTTCTTTAACAACTCGAAACATTCAACAAGTC
196 CTTGGAAACTTCAATGTGGGTTGGGTTACCTTGCTTCTTTAACAACTCGAAACATTCAACAAGTC
244176 CAAGCAATGCTTGAACTTGTCTGTCGTAACTGGCTTGGTGAACATATCAGCGGCATTCTCATCAG
261 CAAGCAATGCTTGAACTTGTCTGTCGTAACTGGCTTGGTGAACATATCAGCGGCATTCTCATCAG
244241 TATGTACCTTCTGAAACAAAACCTCTCCAGATGCAACCAACTCTCTGATCTTGTGGAACCTTACA
326 TATGTACCTTCTGAAACAAAACCTCTCCAGATGCAACCAACTCTCTGATCTTGTGGAACCTTACA
244306 TCAATATGTTTAGTTCTAGCACGATACACCTGATTCTTAGCCAAGTGAATAGCACTTTGATTATC
391 TCAATATGTTTAGTTCTAGCACGATACACCTGATTCTTAGCCAAGTGAATAGCACTTTGATTATC
244371 ACAAAGCAACTGAACTCCACCTTGTTGAACACCCAACTCCTTCACTAAACCAGTAAGCCATAAAG
456 ACAAAGCAACTGAACTCCACCTTGTTGAACACCCAACTCCTTCACTAAACCAGTAAGCCATAAAG
244436 CTTCTTTTGCAGCTGA
521 CTTCTTTTGCAGCTGA
244452 ATTCAATGATATTTTAGGTCTAGGTTACATCTCTATTTATAATAGAAAACCCTGGTACATAATTA
1 ATTCAATGATATTTTAGGTCTAGGTTACATCTCTATTTATAATAGAAAACCCTGGTACATAATTA
*
244517 CAAAATCAACCCTGTACCGTACCGCGGGGGCTGCGCCCCCACACCCCCAACCCACATAATTCGTA
66 CAAAATCAACCCTGTACCGTACCGCGGGGGCTACGCCCCCACACCCCCAACCCACATAATTCGTA
244582 ACCCCACAACGAGACTTTTTATGAGCCATACATAACAAATCTCCACCTTGGCGAATATCCTGCCC
131 ACCCCACAACGAGACTTTTTATGAGCCATACATAACAAATCTCCACCTTGGCGAATATCCTGCCC
244647 CTTGGAAACTTCAATGTGGGTTGGGTTACCTTGCTTCTTTAACAACTCGAAACATTCAACAAGTC
196 CTTGGAAACTTCAATGTGGGTTGGGTTACCTTGCTTCTTTAACAACTCGAAACATTCAACAAGTC
244712 CAAGCAATGCTTGAACTTGTCTGTCGTAACTGGCTTGGTGAACATATCAGCGGCATTCTCATCAG
261 CAAGCAATGCTTGAACTTGTCTGTCGTAACTGGCTTGGTGAACATATCAGCGGCATTCTCATCAG
244777 TATGTACCTTCTGAAACAAAACCTCTCCAGATGCAACCAACTCTCTGATCTTGTGGAACCTTACA
326 TATGTACCTTCTGAAACAAAACCTCTCCAGATGCAACCAACTCTCTGATCTTGTGGAACCTTACA
244842 TCAATATGTTTAGTTCTAGCACGATACACCTGATTCTTAGCCAAGTGAATAGCACTTTGATTATC
391 TCAATATGTTTAGTTCTAGCACGATACACCTGATTCTTAGCCAAGTGAATAGCACTTTGATTATC
244907 ACAAAGCAACTGAACTCCACCTTGTTGAACACCCAACTCCTTCACTAAACCAGTAAGCCATAAAG
456 ACAAAGCAACTGAACTCCACCTTGTTGAACACCCAACTCCTTCACTAAACCAGTAAGCCATAAAG
244972 CTTCTTTTGCAGCT
521 CTTCTTTTGCAGCT
244986 TCAGCCGCTG
Statistics
Matches: 533, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
536 533 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (536 bp):
ATTCAATGATATTTTAGGTCTAGGTTACATCTCTATTTATAATAGAAAACCCTGGTACATAATTA
CAAAATCAACCCTGTACCGTACCGCGGGGGCTACGCCCCCACACCCCCAACCCACATAATTCGTA
ACCCCACAACGAGACTTTTTATGAGCCATACATAACAAATCTCCACCTTGGCGAATATCCTGCCC
CTTGGAAACTTCAATGTGGGTTGGGTTACCTTGCTTCTTTAACAACTCGAAACATTCAACAAGTC
CAAGCAATGCTTGAACTTGTCTGTCGTAACTGGCTTGGTGAACATATCAGCGGCATTCTCATCAG
TATGTACCTTCTGAAACAAAACCTCTCCAGATGCAACCAACTCTCTGATCTTGTGGAACCTTACA
TCAATATGTTTAGTTCTAGCACGATACACCTGATTCTTAGCCAAGTGAATAGCACTTTGATTATC
ACAAAGCAACTGAACTCCACCTTGTTGAACACCCAACTCCTTCACTAAACCAGTAAGCCATAAAG
CTTCTTTTGCAGCTGA
Found at i:251728 original size:16 final size:16
Alignment explanation
Indices: 251698--251728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
251688 TAATATTGAA
*
251698 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
251714 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
251729 AAATAGAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:259246 original size:36 final size:36
Alignment explanation
Indices: 259172--259246 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
259162 TTTTTATATT
* *
259172 TTTAATTTTGTAAAAAAAATTTATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
* *
259208 TTTAATTTTTTAAAGAAAATATATAAATATT-TACAA
1 TTTAATTTTGTAAAAAAAATATATAAATATTAT-CAA
259244 TTT
1 TTT
259247 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
Found at i:260257 original size:15 final size:16
Alignment explanation
Indices: 260203--260261 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
260193 ACAGAGCCCC
* * *
260203 TGAATCAATCGACATT
1 TGAATCATTCAACACT
*
260219 TGAATCATTCAACATT
1 TGAATCATTCAACACT
260235 TGAATCATTCAACACT
1 TGAATCATTCAACACT
260251 T-AATCATTCAA
1 TGAATCATTCAA
260262 AAGTAAACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 10 0.25
16 30 0.75
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:262224 original size:42 final size:42
Alignment explanation
Indices: 262098--262614 Score: 395
Period size: 43 Copynumber: 12.2 Consensus size: 42
262088 TAGAATTGAA
* * *
262098 AAAAATT-AGGGACATCAATTGTAAAGGTAAGAAGTGAGATTG
1 AAAAATTAAGGGTC-TCAATTATAAAGGTAAAAAGTGAGATTG
* * * * *
262140 AAAAATTAAGAGTCTCGATTACAAAAGGTAAAAAATGGGATTG
1 AAAAATTAAGGGTCTCAATTA-TAAAGGTAAAAAGTGAGATTG
* *
262183 AAAAATTATGGGTCTCAGTTATAAAGGTAAAAAGTGAGATTG
1 AAAAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAGATTG
*
262225 ATAAAATT-AGGG--TC--TTATATAGGTAAAAAGTG-GAATTG
1 A-AAAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAG-ATTG
* * *
262263 AAAAAAATT-AGGAG-CTTCAATTACAAAAGGTAAAAAATAAGATTG
1 --AAAAATTAAGG-GTC-TCAATTA-TAAAGGTAAAAAGTGAGATTG
* * * *
262308 AAAAAGTTAAGAGCCTCAATTAAAAAAGGTAAAAAGTGAAATT-
1 AAAAA-TTAAGGGTCTCAATT-ATAAAGGTAAAAAGTGAGATTG
* *
262351 AGAAAGTTAAGGG-CATCAATTATAAAGGT-AAAAGTGAGATTAA
1 A-AAAATTAAGGGTC-TCAATTATAAAGGTAAAAAGTGAGATT-G
* * **
262394 AAAAATTAGGGGCCTCAATTATAAAGGTGGAAAGTGAGATTG
1 AAAAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAGATTG
*
262436 AAAAAAATTAAGGGTCTCAATTATAAAGGTTAGAAAAG-GGGATTG
1 --AAAAATTAAGGGTCTCAATTATAAAGG-TA-AAAAGTGAGATTG
* *
262481 AAAATATT-AGGGGC-C--TTATGAAGGTAAAAAGTGAGATTG
1 AAAA-ATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAGATTG
* *
262520 AAAAA-TATAGAGTCTCAATTATAAAGGTAAAAAGTGGGATTG
1 AAAAATTA-AGGGTCTCAATTATAAAGGTAAAAAGTGAGATTG
** * * * *
262562 AAAAAAAATAGGGGCTCAATTATAAAGTTAAAATGTGAGATTAT
1 AAAAATTA-AGGGTCTCAATTATAAAGGTAAAAAGTGAGATT-G
262606 AAAAATTAA
1 AAAAATTAA
262615 AAACCTTTAT
Statistics
Matches: 385, Mismatches: 54, Indels: 71
0.75 0.11 0.14
Matches are distributed among these distances:
37 2 0.01
38 27 0.07
39 25 0.06
40 13 0.03
41 11 0.03
42 95 0.25
43 115 0.30
44 66 0.17
45 26 0.07
46 5 0.01
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.25
Consensus pattern (42 bp):
AAAAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAGATTG
Found at i:262342 original size:169 final size:166
Alignment explanation
Indices: 262090--262404 Score: 402
Period size: 169 Copynumber: 1.9 Consensus size: 166
262080 GAATTTTATA
** * * * *
262090 GAATTGAAAAAAATTAGGGACATCAATTGTAAAGGTAAGAAGTGAGATTGAAAAATTAAGAGTCT
1 GAATTGAAAAAAATTAGGGACATCAATTCAAAAGGTAAAAAATAAGATTGAAAAATTAAGAGCCT
* * ** * *
262155 CGATTACAAAAGGTAAAAAATGGGATT-GAAAAATTATGGGTC-TCAGTTATAAAGGTAAAAAGT
66 CAATTAAAAAAGGTAAAAAATGAAATTAG-AAAATTAAGGG-CATCAATTATAAAGGT-AAAAGT
* *
262218 GAGATTGATAAAATTAGGGTCTTATATAGGTAAAAAGTG
128 GAGATTAAAAAAATTAGGGTCTTATATAGGTAAAAAGTG
*
262257 GAATTGAAAAAAATTA-GGAGCTTCAATTACAAAAGGTAAAAAATAAGATTGAAAAAGTTAAGAG
1 GAATTGAAAAAAATTAGGGA-CATCAATT-CAAAAGGTAAAAAATAAGATTGAAAAA-TTAAGAG
* *
262321 CCTCAATTAAAAAAGGTAAAAAGTGAAATTAGAAAGTTAAGGGCATCAATTATAAAGGTAAAAGT
63 CCTCAATTAAAAAAGGTAAAAAATGAAATTAGAAAATTAAGGGCATCAATTATAAAGGTAAAAGT
262386 GAGATTAAAAAAATTAGGG
128 GAGATTAAAAAAATTAGGG
262405 GCCTCAATTA
Statistics
Matches: 126, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
166 3 0.02
167 23 0.18
168 46 0.37
169 53 0.42
170 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (166 bp):
GAATTGAAAAAAATTAGGGACATCAATTCAAAAGGTAAAAAATAAGATTGAAAAATTAAGAGCCT
CAATTAAAAAAGGTAAAAAATGAAATTAGAAAATTAAGGGCATCAATTATAAAGGTAAAAGTGAG
ATTAAAAAAATTAGGGTCTTATATAGGTAAAAAGTG
Found at i:262398 original size:86 final size:85
Alignment explanation
Indices: 262091--262614 Score: 296
Period size: 85 Copynumber: 6.2 Consensus size: 85
262081 AATTTTATAG
* * * *
262091 AATTGAAAAAAATT-AGGGACATCAATTGTAAAGGTAAGAAGTGAGATT-GAAAAATTAAGAGTC
1 AATT-AAAAAAATTAAGGGTC-TCAATTATAAAGGTAA-AAGTGAGATTAAAAAAATTAAGAGCC
* * *
262154 TCGATTACAAAAGGTAAAAAATGG
63 TCAATTA-AAAAGGTAAAAAGTGA
* * * * * * *
262178 GATT-GAAAAATTATGGGTCTCAGTTATAAAGGTAAAAAGTGAGATTGATAAAATT-AG-G-GTC
1 AATTAAAAAAATTAAGGGTCTCAATTATAAAGGT-AAAAGTGAGATTAAAAAAATTAAGAGCCTC
* * *
262239 --TTATATAGGTAAAAAGTGG
65 AATTAAAAAGGTAAAAAGTGA
* * * * *
262258 AATTGAAAAAAATT-AGGAG-CTTCAATTACAAAAGGTAAAAAATAAGATTGAAAAAGTTAAGAG
1 AATT-AAAAAAATTAAGG-GTC-TCAATTA-TAAAGGT-AAAAGTGAGATTAAAAAAATTAAGAG
262321 CCTCAATTAAAAAAGGTAAAAAGTGA
61 CCTCAATT-AAAAAGGTAAAAAGTGA
* * * *
262347 AATT-AGAAAGTTAAGGG-CATCAATTATAAAGGTAAAAGTGAGATTAAAAAAATTAGGGGCCTC
1 AATTAAAAAAATTAAGGGTC-TCAATTATAAAGGTAAAAGTGAGATTAAAAAAATTAAGAGCCTC
* **
262410 AATTATAAAGGTGGAAAGTGA
65 AATTAAAAAGGTAAAAAGTGA
* * * * * *
262431 GATTGAAAAAAATTAAGGGTCTCAATTATAAAGGTTAGAAAAG-GGGATTGAAAATATT-AGGGG
1 AATT-AAAAAAATTAAGGGTCTCAATTATAAAGG-T--AAAAGTGAGATTAAAAAAATTAAGAGC
**
262494 C-C--TTATGAAGGTAAAAAGTGA
62 CTCAATTAAAAAGGTAAAAAGTGA
* * * * * * *
262515 GATT-GAAAAA-TATAGAGTCTCAATTATAAAGGTAAAAAGTGGGATTGAAAAAAAAT-AGGGGC
1 AATTAAAAAAATTA-AGGGTCTCAATTATAAAGGT-AAAAGTGAGATT-AAAAAAATTAAGAGCC
* * *
262577 TCAATTATAAAGTTAAAATGTGA
63 TCAATTAAAAAGGTAAAAAGTGA
* *
262600 GATTATAAAAATTAA
1 AATTAAAAAAATTAA
262615 AAACCTTTAT
Statistics
Matches: 349, Mismatches: 59, Indels: 59
0.75 0.13 0.13
Matches are distributed among these distances:
80 21 0.06
81 15 0.04
82 49 0.14
83 27 0.08
84 40 0.11
85 80 0.23
86 51 0.15
87 26 0.07
88 17 0.05
89 23 0.07
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.25
Consensus pattern (85 bp):
AATTAAAAAAATTAAGGGTCTCAATTATAAAGGTAAAAGTGAGATTAAAAAAATTAAGAGCCTCA
ATTAAAAAGGTAAAAAGTGA
Done.