Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001270.1 Hibiscus syriacus cultivar Beakdansim tig00002491_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: 60079
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1006 original size:18 final size:19
Alignment explanation
Indices: 979--1015 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
969 CATTTCTTAG
979 CAGTACTTGTTTGG-TTTT
1 CAGTACTTGTTTGGATTTT
*
997 CAGTATTTGTTTGGATTTT
1 CAGTACTTGTTTGGATTTT
1016 TGTGATGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.14, C:0.08, G:0.22, T:0.57
Consensus pattern (19 bp):
CAGTACTTGTTTGGATTTT
Found at i:6442 original size:89 final size:89
Alignment explanation
Indices: 6291--6468 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
6281 CGATCCCATG
6291 CTCCTGAACTCACAGCAGGGTACTATAACACAAGGTACCGAGACGGTTACCTCTCGATTGCTCAA
1 CTCCTGAACTCACAGCAGGGTACTATAACACAAGGTACCGAGACGGTTACCTCTCGATTGCTCAA
6356 ATGCTAGCACGTCATGGAGCCGTT
66 ATGCTAGCACGTCATGGAGCCGTT
6380 CTCCTGAACTCACAGCAGGGTACTATAACACAAGGTACCGAGACGGTTACCTCTCGATTGCTCAA
1 CTCCTGAACTCACAGCAGGGTACTATAACACAAGGTACCGAGACGGTTACCTCTCGATTGCTCAA
6445 ATGCTAGCACGTCATGGAGCCGTT
66 ATGCTAGCACGTCATGGAGCCGTT
6469 TTCAATTTCA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (89 bp):
CTCCTGAACTCACAGCAGGGTACTATAACACAAGGTACCGAGACGGTTACCTCTCGATTGCTCAA
ATGCTAGCACGTCATGGAGCCGTT
Found at i:11033 original size:23 final size:23
Alignment explanation
Indices: 11007--11075 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
10997 CACCACAGCT
*
11007 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
11030 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
11053 CTTAGAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
11076 TATAAGATTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:12678 original size:24 final size:20
Alignment explanation
Indices: 12621--12683 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
12611 TTTCCCTTGA
*
12621 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
12641 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
12664 ATGTGCATCGATGCACTCCT
1 A-GTGCATCGATGCA-TCCT
12684 TATTAGAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 1 0.03
23 4 0.11
24 14 0.40
25 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:12684 original size:24 final size:22
Alignment explanation
Indices: 12621--12685 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
12611 TTTCCCTTGA
*
12621 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATCCTTAAC
*
12641 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CCTTAAC
12664 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCA-TCCTTA
12686 TTAGAGATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.46
25 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTAAC
Found at i:12752 original size:15 final size:14
Alignment explanation
Indices: 12734--12763 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
12724 GCGGGTTTTG
12734 ACGGTGCGGGCTTAA
1 ACGGTGCGGG-TTAA
12749 ACGGTGCGGGTTAA
1 ACGGTGCGGGTTAA
12763 A
1 A
12764 AAGCCCGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (14 bp):
ACGGTGCGGGTTAA
Found at i:13044 original size:2 final size:2
Alignment explanation
Indices: 13037--13075 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13027 TTAATCATTA
13037 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
13076 ATGATATAAT
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:17714 original size:14 final size:13
Alignment explanation
Indices: 17681--17723 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
17671 AAATAATTAA
*
17681 ATTTATAAAATAT
1 ATTTTTAAAATAT
17694 A--TTTAAAATAT
1 ATTTTTAAAATAT
17705 AGTTTTTAAAATAT
1 A-TTTTTAAAATAT
17719 ATTTT
1 ATTTT
17724 CATAACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 10 0.38
13 5 0.19
14 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
ATTTTTAAAATAT
Found at i:18657 original size:18 final size:19
Alignment explanation
Indices: 18616--18657 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
18606 ATTGTTCACC
18616 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAG-GA
*
18636 GAATGTAAGATTATCA-GA
1 GAATGTAAGATTACCAGGA
18654 GAAT
1 GAAT
18658 AGGATTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGA
Found at i:19312 original size:27 final size:27
Alignment explanation
Indices: 19274--19328 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
19264 GCAGTAGCTA
*
19274 TGGGCCTCCAATTTTTATATTTATAAT
1 TGGGCCTCCAATTTCTATATTTATAAT
19301 TGGG-CTCTCAATTTCTATATTTATAAT
1 TGGGCCTC-CAATTTCTATATTTATAAT
19328 T
1 T
19329 AGGTCCCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (27 bp):
TGGGCCTCCAATTTCTATATTTATAAT
Found at i:19340 original size:27 final size:27
Alignment explanation
Indices: 19274--19341 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
19264 GCAGTAGCTA
*
19274 TGGG-CCTCCAATTTTTATATTTATAAT
1 TGGGCCCT-CAATTTCTATATTTATAAT
*
19301 TGGGCTCTCAATTTCTATATTTATAAT
1 TGGGCCCTCAATTTCTATATTTATAAT
*
19328 TAGGTCCCT-AATTT
1 T-GGGCCCTCAATTT
19342 TACTCAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 28 0.80
28 7 0.20
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (27 bp):
TGGGCCCTCAATTTCTATATTTATAAT
Found at i:22801 original size:59 final size:59
Alignment explanation
Indices: 22706--22819 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
22696 GGTCCTCCGA
* * * *
22706 CTATAAGAAATTATTTTGTTGAGTCTCATGATTATTAAAAGCTATAAAATGATCATTGG
1 CTATAAGAAATTATTTTATTAAGTCTCATGACTATTAAAAACTATAAAATGATCATTGG
* * * * *
22765 CTATAGGACATTATTTTATTAAGTTTCCTGACTATTAAAAATTATAAAATGATCA
1 CTATAAGAAATTATTTTATTAAGTCTCATGACTATTAAAAACTATAAAATGATCA
22820 CCCAACTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (59 bp):
CTATAAGAAATTATTTTATTAAGTCTCATGACTATTAAAAACTATAAAATGATCATTGG
Found at i:25183 original size:24 final size:25
Alignment explanation
Indices: 25156--25203 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
25146 TTTAATTAAA
* *
25156 TAGT-TTTTTTTATTTTATTTTTTG
1 TAGTATTTTGTTATTTAATTTTTTG
*
25180 TAGTATTTTGTTCTTTAATTTTTT
1 TAGTATTTTGTTATTTAATTTTTT
25204 TAGATCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (25 bp):
TAGTATTTTGTTATTTAATTTTTTG
Found at i:27334 original size:21 final size:21
Alignment explanation
Indices: 27308--27464 Score: 169
Period size: 21 Copynumber: 7.5 Consensus size: 21
27298 GTTTCCAGAT
**
27308 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAACTTGGACTA
27329 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
27350 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
27370 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
27391 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
27412 TCGCATTGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
27433 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
27454 TCGCATTGCGA
1 TCGCAATGCGA
27465 TAGTCCAAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.15
21 95 0.84
22 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:27374 original size:62 final size:62
Alignment explanation
Indices: 27308--27464 Score: 203
Period size: 62 Copynumber: 2.5 Consensus size: 62
27298 GTTTCCAGAT
*
27308 TCGCAATGCGATTTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGT-A-AA
1 TCGCAATGCGATATTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCG-ATA-GTCACAA
* * * *
27370 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCATTGCGATAGTCGACTA
1 TCGCAATGCGATATTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTC-ACAA
*
27433 TCGCAATGCGA-ACTTGGACTATCGCATTGCGA
1 TCGCAATGCGATA-TTGGACTATCGCAATGCGA
27465 TAGTCCAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
60 2 0.02
61 3 0.04
62 50 0.60
63 28 0.34
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (62 bp):
TCGCAATGCGATATTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCACAA
Found at i:27480 original size:42 final size:42
Alignment explanation
Indices: 27308--27469 Score: 213
Period size: 42 Copynumber: 3.9 Consensus size: 42
27298 GTTTCCAGAT
** * * *
27308 TCGCAATGCGATTTTGGACTATCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGAACTTGGACTATCGCATTGCGATA-GTCGACTA
* * *
27350 TCGCAATGCGAA-TATGTA-AATCGCAATGCGATAGTCGACTA
1 TCGCAATGCGAACT-TGGACTATCGCATTGCGATAGTCGACTA
27391 TCGCAATGCGAACTTGGACTATCGCATTGCGATAGTCGACTA
1 TCGCAATGCGAACTTGGACTATCGCATTGCGATAGTCGACTA
27433 TCGCAATGCGAACTTGGACTATCGCATTGCGATAGTC
1 TCGCAATGCGAACTTGGACTATCGCATTGCGATAGTC
27470 CAAAATCGCA
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
41 34 0.31
42 74 0.69
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (42 bp):
TCGCAATGCGAACTTGGACTATCGCATTGCGATAGTCGACTA
Found at i:45143 original size:21 final size:21
Alignment explanation
Indices: 45092--45144 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
45082 ATTATGACTA
45092 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
45113 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
45134 TCGCAATGCGA
1 TCGCAATGCGA
45145 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:45177 original size:21 final size:20
Alignment explanation
Indices: 45134--45180 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
45124 TTTTCCCAAT
*
45134 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
45154 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
45175 TCGCAA
1 TCGCAA
45181 CGCGGTACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:45200 original size:20 final size:20
Alignment explanation
Indices: 45175--45242 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
45165 ATTTGGAAAA
*
45175 TCGCAACGCGGTACTGACTT
1 TCGCAACGCGGTACTTACTT
* *
45195 TCGCAACTCGGTACTTAATT
1 TCGCAACGCGGTACTTACTT
* * **
45215 TCGTAACTCAATACTTACTT
1 TCGCAACGCGGTACTTACTT
45235 TCGCAACG
1 TCGCAACG
45243 AGATAATACA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (20 bp):
TCGCAACGCGGTACTTACTT
Found at i:45463 original size:22 final size:22
Alignment explanation
Indices: 45435--45478 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45425 ACTCTCTCAC
45435 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
45457 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
45479 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:45784 original size:20 final size:20
Alignment explanation
Indices: 45761--45798 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
45751 TCAAATTTGC
45761 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
45781 GTTGCGATTTTCATTTTC
1 GTTGCGATTTTCATTTTC
45799 AGAAACTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.55
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:45989 original size:25 final size:24
Alignment explanation
Indices: 45935--45989 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
45925 TGTTTATTAT
* *
45935 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
45959 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
45985 TGTTT
1 TGTTT
45990 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:47140 original size:18 final size:18
Alignment explanation
Indices: 47119--47166 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
47109 TCCACTTCGG
47119 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
47137 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
47155 GAGCCATCACCT
1 GAGCCATCACCT
47167 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:47738 original size:20 final size:19
Alignment explanation
Indices: 47726--47847 Score: 128
Period size: 19 Copynumber: 6.6 Consensus size: 19
47716 GAAAATGACT
***
47726 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCG-AAATGAAA
*
47746 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
47765 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
47784 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
47803 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
47817 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
47836 ATCGCAATGCGA
1 ATCGCAACGCGA
47848 TTTGTGTTTC
Statistics
Matches: 90, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 64 0.71
20 10 0.11
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:47768 original size:19 final size:19
Alignment explanation
Indices: 47746--47847 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
47736 GAAAATGGCT
47746 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47765 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47784 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
47803 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
47817 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47836 ATCGCAATGCGA
1 ATCGCAATGCGA
47848 TTTGTGTTTC
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 59 0.79
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:47789 original size:38 final size:36
Alignment explanation
Indices: 47746--47847 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 36
47736 GAAAATGGCT
*
47746 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCG-AA-CAAA
47784 ATCGCAATGCGAAATGAAAATCGCAA--CG-ACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAACAAA
*
47817 ATCGCAACGCGAAATGAAAATCGCAATGCGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGA
47848 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
33 28 0.47
34 1 0.02
35 2 0.03
36 2 0.03
38 26 0.44
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAACAAA
Found at i:47919 original size:20 final size:20
Alignment explanation
Indices: 47873--47959 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
47863 ACGATTTTGT
**
47873 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
47892 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
47912 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
47932 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
47952 CGTTGCGA
1 CGTTGCGA
47960 AAGTAAGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 13 0.22
20 45 0.78
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:47970 original size:20 final size:19
Alignment explanation
Indices: 47886--47985 Score: 76
Period size: 20 Copynumber: 5.1 Consensus size: 19
47876 TGCGATTTTC
* * **
47886 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* *
47905 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
47925 ATTTCCGCGTTGC-AATAGTCA
1 ATTT-CGCGTTGCGAA-AGT-A
*
47946 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
47965 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
47985 A
1 A
47986 ATTATTCTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.09
20 58 0.84
21 5 0.07
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:47977 original size:40 final size:40
Alignment explanation
Indices: 47886--47970 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
47876 TGCGATTTTC
* * * *
47886 ATTT-CGCATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCAATAGCCATTTCCGCGTTGCGAAAGTA
* *
47925 ATTTCCGCGTTGCAATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCAATAGCCATTTCCGCGTTGCGAAAGTA
47965 AGTTTC
1 A-TTTC
47971 GTGTTGCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.11
40 30 0.79
41 4 0.11
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
ATTTCCGCGTTGCAATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:48360 original size:21 final size:20
Alignment explanation
Indices: 48334--48403 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
48324 CTGTCATTCC
48334 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
48355 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
48376 TCAAGAGTCCCCCCCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
48397 TCAAGAG
1 TCAAGAG
48404 GCCACTATCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:48418 original size:21 final size:21
Alignment explanation
Indices: 48350--48430 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
48340 GTCCCCTCCA
48350 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCCCTATC
** * ***
48371 ATCCCTCAAGAGTCCCCCCCC
1 ATCGTTCAAGAGGCCCCTATC
* *
48392 ACCGTTCAAGAGGCCACTATC
1 ATCGTTCAAGAGGCCCCTATC
* *
48413 ATCGTTGAAGAGGTCCCT
1 ATCGTTCAAGAGGCCCCT
48431 CCCACCATTC
Statistics
Matches: 42, Mismatches: 18, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTATC
Found at i:48436 original size:42 final size:42
Alignment explanation
Indices: 48327--48415 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
48317 GACTCACCTG
* * * *
48327 TCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
48369 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTA
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
48411 TCATC
1 TCATC
48416 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:49843 original size:14 final size:15
Alignment explanation
Indices: 49811--49847 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
49801 GATTGTTTAA
49811 TTGATTTGTAAAAAG
1 TTGATTTGTAAAAAG
*
49826 -TGATTTGT-AAATG
1 TTGATTTGTAAAAAG
49839 TTGATTTGT
1 TTGATTTGT
49848 TTAATTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (15 bp):
TTGATTTGTAAAAAG
Found at i:49990 original size:13 final size:13
Alignment explanation
Indices: 49972--50023 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 13
49962 CGAAATGACT
49972 ATCGCAACGAGAA
1 ATCGCAACGAGAA
49985 ATCGCAATGCGAAATGAA
1 ATCGCAA--CG--A-GAA
50003 ATCGCAACGAGAAA
1 ATCGCAACGAG-AA
50017 ATCGCAA
1 ATCGCAA
50024 TGCGATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 8 0.24
14 10 0.30
15 2 0.06
16 2 0.06
17 1 0.03
18 10 0.30
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (13 bp):
ATCGCAACGAGAA
Found at i:49998 original size:32 final size:32
Alignment explanation
Indices: 49953--50028 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
49943 CAAACAGACT
** *
49953 ATCGCAACACGAAATGACTATCGCAACGAG-AA
1 ATCGCAATGCGAAATGA-AATCGCAACGAGAAA
49985 ATCGCAATGCGAAATGAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAATCGCAACGAGAAA
50017 ATCGCAATGCGA
1 ATCGCAATGCGA
50029 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 11 0.28
32 29 0.73
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGAGAAA
Found at i:50005 original size:18 final size:17
Alignment explanation
Indices: 49981--50028 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
49971 TATCGCAACG
49981 AGAAATCGCAATGCGAA
1 AGAAATCGCAATGCGAA
*
49998 ATGAAATCGCAA--CGAG
1 A-GAAATCGCAATGCGAA
50014 A-AAATCGCAATGCGA
1 AGAAATCGCAATGCGA
50029 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 9 0.33
16 7 0.26
17 1 0.04
18 10 0.37
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (17 bp):
AGAAATCGCAATGCGAA
Found at i:50072 original size:20 final size:20
Alignment explanation
Indices: 50047--50142 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
50037 TCGTATTGCG
*
50047 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ** ***
50067 ATTTTCGCGTTATGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
50088 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
50107 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* *
50127 ATTTTTGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
50143 TTCCCCGTTG
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
19 3 0.05
20 51 0.89
21 3 0.05
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:50380 original size:20 final size:20
Alignment explanation
Indices: 50355--50466 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
50345 TTTGAAGATG
50355 ATTGCGATTTTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
***
50375 ATTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
* * **
50395 GTTGCGATTTTGTATTATCTC
1 ATTGCGATTTT-CAGAATCTC
* ** * *
50416 GTTGCGATAGTCAGTATCGC
1 ATTGCGATTTTCAGAATCTC
*
50436 ATTGCGATTTTCCA-AATTCGC
1 ATTGCGATTTT-CAGAA-TCTC
50457 ATTGCGATTT
1 ATTGCGATTT
50467 ACTTATTCGC
Statistics
Matches: 70, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
20 39 0.56
21 31 0.44
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTGCGATTTTCAGAATCTC
Found at i:50476 original size:20 final size:21
Alignment explanation
Indices: 50432--50483 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
50422 ATAGTCAGTA
*
50432 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
50453 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
50473 TCGCATTGCGA
1 TCGCATTGCGA
50484 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:51281 original size:24 final size:24
Alignment explanation
Indices: 51254--51307 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
51244 GTATTCGAAA
*
51254 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
51278 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
51302 TTTGAT
1 TTTGAT
51308 GTTGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:53075 original size:90 final size:92
Alignment explanation
Indices: 52900--53077 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 92
52890 ATTTCAAACT
*
52900 TTCAACCAAAAGACAAAATAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT-AAGAATACACAGTTTAGC
52965 AGAATTGGCAGCAACCGAATAAATTTAC
65 AGAATTGGCAGCAACCGAATAAATTTAC
52993 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-A-AA-A-ACAGTTTAG
1 TTCAACCAAAAGAC-AAA-AAAAAGACAAATACTAACTTCACAGTGTTAAGAATACACAGTTTAG
*
53054 CAGTATTGGCAGCAACCGAATAAA
64 CAGAATTGGCAGCAACCGAATAAA
53078 CTAAGCAATC
Statistics
Matches: 81, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
90 32 0.40
91 1 0.01
92 2 0.02
93 15 0.19
94 3 0.04
95 28 0.35
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.20
Consensus pattern (92 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAGAATACACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTTAC
Found at i:54799 original size:40 final size:39
Alignment explanation
Indices: 54755--54864 Score: 117
Period size: 34 Copynumber: 3.0 Consensus size: 39
54745 TTTTTTGGTT
**
54755 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGACTATCGCAACGAGATAATGAGAATCGCAACGC
*
54794 GGAAATGACTATCG---C-A-ATGA-GAGAATCGCAACGC
1 -GAAATGACTATCGCAACGAGATAATGAGAATCGCAACGC
* *
54828 GAAATGACTATCGCAACGCGA-AATGAAAATCGCAACG
1 GAAATGACTATCGCAACGAGATAATGAGAATCGCAACG
54865 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
33 13 0.22
34 14 0.24
35 3 0.05
36 2 0.03
37 2 0.03
38 13 0.22
40 11 0.19
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (39 bp):
GAAATGACTATCGCAACGAGATAATGAGAATCGCAACGC
Found at i:54837 original size:33 final size:34
Alignment explanation
Indices: 54780--54843 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
54770 ACGAGATAAT
54780 GAGAATCGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAATGA
54814 GAGAATCGCAACGC-GAAATGACTATCGCAA
1 GAGAATCGCAACGCGGAAATGACTATCGCAA
54844 CGCGAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAATGA
Found at i:54842 original size:19 final size:18
Alignment explanation
Indices: 54755--54900 Score: 101
Period size: 19 Copynumber: 8.1 Consensus size: 18
54745 TTTTTTGGTT
*
54755 GAAATGAAAATCGCAACGA
1 GAAATG-AAATCGCAACGC
54774 GATAATGAGAATCGCAACGC
1 GA-AATGA-AATCGCAACGC
* *
54794 GGAAATGACTATCGCAA--T
1 -GAAATGA-AATCGCAACGC
*
54812 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
54828 GAAATGACTATCGCAACGC
1 GAAATGA-AATCGCAACGC
54847 GAAATGAAAATCGCAA--C
1 GAAATG-AAATCGCAACGC
*
54864 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
54880 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAACGC
54899 GA
1 GA
54901 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 15 0.15
16 9 0.09
17 9 0.09
19 38 0.38
20 27 0.27
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:54860 original size:52 final size:52
Alignment explanation
Indices: 54763--54900 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 52
54753 TTGAAATGAA
* * ** *
54763 AATCGCAACGAGATAATGAGAATCGCAACGCGGAAATGACTATCGCAATGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
**
54817 AATCGCAACGCGAAATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
54869 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
54901 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
52 48 0.64
53 15 0.20
54 12 0.16
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:55512 original size:20 final size:20
Alignment explanation
Indices: 55487--55598 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
55477 GCTATGTAAA
55487 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
55507 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
55527 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* ** *
55548 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * * *
55568 TCGCGTTGCGATTTACGTAC
1 TCGCATTGCGATGTAAGTAT
55588 TCGCATTGCGA
1 TCGCATTGCGA
55599 ATTATGAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:55557 original size:41 final size:40
Alignment explanation
Indices: 55505--55598 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
55495 CGATAGTAAG
* *
55505 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
55545 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
*
55586 ACTCGCATTGCGA
1 ATTCGCATTGCGA
55599 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:55649 original size:20 final size:20
Alignment explanation
Indices: 55588--55659 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
55578 ATTTACGTAC
* *
55588 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAA-TACGAAAA
* *
55609 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGAAAA
*
55629 TCGCAATGCGAATAGGAAAA
1 TCGCAATGCGAATACGAAAA
* *
55649 TTGCATTGCGA
1 TCGCAATGCGA
55660 GTCAGTATCG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 32 0.76
21 10 0.24
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGAAAA
Found at i:55757 original size:21 final size:21
Alignment explanation
Indices: 55706--55757 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
55696 GATTACTTAT
55706 TCGCATTGCG-AATGGGAAAA
1 TCGCATTGCGAAATGGGAAAA
* ** *
55726 TCGTAACGCGAAATTGGAAAA
1 TCGCATTGCGAAATGGGAAAA
55747 TCGCATTGCGA
1 TCGCATTGCGA
55758 TAGTCATAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (21 bp):
TCGCATTGCGAAATGGGAAAA
Found at i:55776 original size:118 final size:119
Alignment explanation
Indices: 55548--55777 Score: 252
Period size: 118 Copynumber: 1.9 Consensus size: 119
55538 TTTTCCTAAT
** * *
55548 TCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGTACTCGCATTGCGAATTATGAAAATCGC
1 TCGCATTGCGATTTACCAAATCGCATTGCGATTTACGTACTCGCATTGCGAATTAGGAAAATCGC
* * **
55613 AACGCGAATACGTAAATCGCAATGCGAATAGGAAAATTGCATTGCGAGTCAGTA
66 AACGCGAATACGAAAATCGCAATGCGAATAGCAAAACCGCATTGCGAGTCAGTA
* * *
55667 TCGCATTGCGATTT-CCAAATTCGCATTGCGA-TTACTTATTCGCATTGCGAA-TGGGAAAATCG
1 TCGCATTGCGATTTACCAAA-TCGCATTGCGATTTACGTACTCGCATTGCGAATTAGGAAAATCG
* ** * * *
55729 TAACGCGAAATTGGAAAATCGCATTGCG-ATAGTCATAACCGCGTTGCGA
65 CAACGCG-AATACGAAAATCGCAATGCGAATAG-CAAAACCGCATTGCGA
55778 ATCTGGAAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
117 19 0.21
118 48 0.53
119 24 0.26
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (119 bp):
TCGCATTGCGATTTACCAAATCGCATTGCGATTTACGTACTCGCATTGCGAATTAGGAAAATCGC
AACGCGAATACGAAAATCGCAATGCGAATAGCAAAACCGCATTGCGAGTCAGTA
Found at i:57204 original size:29 final size:30
Alignment explanation
Indices: 57150--57213 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 30
57140 TCTCAAGTTA
**
57150 TTTTCATATTTCATATTTTTTCTTC-TATT
1 TTTTCATATAGCATATTTTTTCTTCTTATT
*
57179 TTTTCATATAGCAT-TTTGTTTTTTCTTTATT
1 TTTTCATATAGCATATTT-TTTCTTC-TTATT
57210 TTTT
1 TTTT
57214 TAATGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 3 0.10
29 18 0.62
31 8 0.28
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.70
Consensus pattern (30 bp):
TTTTCATATAGCATATTTTTTCTTCTTATT
Found at i:59951 original size:27 final size:28
Alignment explanation
Indices: 59914--59967 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
59904 CATATTAAAA
59914 TTAATAGGAATTACTTTTAGAATCTTCG
1 TTAATAGGAATTACTTTTAGAATCTTCG
**
59942 TTAAT-GGAATTGTTTTTAGAATCTTC
1 TTAATAGGAATTACTTTTAGAATCTTC
59968 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (28 bp):
TTAATAGGAATTACTTTTAGAATCTTCG
Done.