Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002811.1 Hibiscus syriacus cultivar Beakdansim tig00005782_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: 102569
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1155 original size:146 final size:145
Alignment explanation
Indices: 932--1232 Score: 468
Period size: 146 Copynumber: 2.1 Consensus size: 145
922 TTTGTCCACT
* *
932 TTTGGTCACCGATTTCAAAAAAATAAGATATTTTCAGTTTTCGTTTTTATTTGATAAGATATGGT
1 TTTGGTCACCGATTTCAAAAAAATAAGATATTTTCAGCTTTCGTTTTTATTTGATAAGA-ATGAT
*
997 CACCTTCGTTTTATTTAATTAAGATGTGGTTATCCCGAGTTAACTGTCGTTAACGACAGTTAAAT
65 CACCTTCGTTTTATTTAATAAAGATGTGGTTAT-CCGAGTTAACTGTCGTTAACGACAGTTAAAT
1062 A-TTTGATATAATCACACA
129 ATTTTGATATAAT--CACA
*
1080 TTTGGTC-CTGATTTCAAAAAAATAAGATATTTTCA-CTTTCGTTTTTA-TTGATTAAG-ATGAT
1 TTTGGTCACCGATTTCAAAAAAATAAGATATTTTCAGCTTTCGTTTTTATTTGA-TAAGAATGAT
1141 CACCTTCGTTTTTTATTTAATAAAGATGTGGTTATCCGAGTTAACTGTCGTTAACGACAGTTAAA
65 CACCTTCG--TTTTATTTAATAAAGATGTGGTTATCCGAGTTAACTGTCGTTAACGACAGTTAAA
1206 TATTTTGATATAATCACA
128 TATTTTGATATAATCACA
1224 TTTGGTCAC
1 TTTGGTCAC
1233 TGTCATTTAC
Statistics
Matches: 144, Mismatches: 4, Indels: 13
0.89 0.02 0.08
Matches are distributed among these distances:
144 23 0.16
145 37 0.26
146 50 0.35
147 27 0.19
148 7 0.05
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (145 bp):
TTTGGTCACCGATTTCAAAAAAATAAGATATTTTCAGCTTTCGTTTTTATTTGATAAGAATGATC
ACCTTCGTTTTATTTAATAAAGATGTGGTTATCCGAGTTAACTGTCGTTAACGACAGTTAAATAT
TTTGATATAATCACA
Found at i:1526 original size:16 final size:17
Alignment explanation
Indices: 1505--1543 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1495 ACTCGGTACC
*
1505 TTATTTTTA-TATATTT
1 TTATTTTTATTAAATTT
1521 TTATTTTTATTAAATTT
1 TTATTTTTATTAAATTT
1538 TTATTT
1 TTATTT
1544 ATAATTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTTTATTAAATTT
Found at i:1800 original size:24 final size:25
Alignment explanation
Indices: 1744--1808 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 25
1734 ATTATATATA
1744 TTATTTTAAAATATTTTTATATTAAC
1 TTATTTT-AAATATTTTTATATTAAC
1770 TTA--TTAAATA-TTTTAT-TATAAC
1 TTATTTTAAATATTTTTATAT-TAAC
1792 TTATTTTAAATATTTTT
1 TTATTTTAAATATTTTT
1809 TTTATTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 1 0.03
22 13 0.37
23 5 0.14
24 9 0.26
25 4 0.11
26 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATTTTAAATATTTTTATATTAAC
Found at i:9004 original size:14 final size:14
Alignment explanation
Indices: 8976--9016 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
8966 ACCCGACTAT
8976 GGAAGAGGGAAGGG
1 GGAAGAGGGAAGGG
*
8990 GGAAG-GGGAATGG
1 GGAAGAGGGAAGGG
*
9003 GG-AGAGGGGAGGG
1 GGAAGAGGGAAGGG
9016 G
1 G
9017 ACCACGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 2 0.09
13 16 0.70
14 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.68, T:0.02
Consensus pattern (14 bp):
GGAAGAGGGAAGGG
Found at i:18622 original size:36 final size:36
Alignment explanation
Indices: 18582--18720 Score: 242
Period size: 36 Copynumber: 3.9 Consensus size: 36
18572 AGTTGAGTAT
18582 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* * *
18618 TATCAACTTCGGTACATTCGTGTATCAATATTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
18654 TATCAGCTTTGGTACATTCGTGTATCAATTTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
18690 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
18721 CCAGTACCAT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 96 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:26020 original size:36 final size:36
Alignment explanation
Indices: 25976--26115 Score: 235
Period size: 36 Copynumber: 3.9 Consensus size: 36
25966 AGTTGAGTAT
25976 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
26012 TTTCAGCTTTGGTACATTCGTGTATCAAAGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
26048 TATCCGCTTTGGTACATTCGTGTATCAATATTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
26084 TATCAGCTTTGATACATTCGTGTATCAATGTT
1 TATCAGCTTTGGTACATTCGTGTATCAATGTT
26116 CAGTACCGTC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:30885 original size:12 final size:13
Alignment explanation
Indices: 30863--30896 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
30853 GCTACATCAA
30863 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
30876 AAAA-AAAAAAAG
1 AAAAGAAAAAAAG
30888 AAACAGAAA
1 AAA-AGAAA
30897 CATCCAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.58
13 5 0.26
14 3 0.16
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:42871 original size:27 final size:27
Alignment explanation
Indices: 42833--42896 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
42823 AACAGTGCTG
*
42833 AATGATTCAGCACAGAAGTACATTCTA
1 AATGATTCAGCACAGAAGTACATTATA
*
42860 AATGATTTAGCACAGAAGTACATTATA
1 AATGATTCAGCACAGAAGTACATTATA
42887 AATGATTCAG
1 AATGATTCAG
42897 AGTCATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (27 bp):
AATGATTCAGCACAGAAGTACATTATA
Found at i:42973 original size:16 final size:16
Alignment explanation
Indices: 42948--42988 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
42938 ACAGAATCTC
42948 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
42964 TGAATTATTCAGCATT
1 TGAATCATTCAGCATT
42980 TGAATCATT
1 TGAATCATT
42989 AAGTGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:47069 original size:2 final size:2
Alignment explanation
Indices: 47062--47112 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
47052 ATTTAAACTA
47062 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
47104 AT AT AT AT A
1 AT AT AT AT A
47113 CACACACATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49569 original size:21 final size:20
Alignment explanation
Indices: 49543--49596 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
49533 TGATGTTGTT
49543 TTATTTTAATTTAG-TCACTG
1 TTATTTTAATTTAGCT-ACTG
*
49563 TTAATTTTTGATTTAGCTACTG
1 TT-A-TTTTAATTTAGCTACTG
49585 TTATTTTAATTT
1 TTATTTTAATTT
49597 TTTTCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 16 0.55
23 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.59
Consensus pattern (20 bp):
TTATTTTAATTTAGCTACTG
Found at i:53828 original size:54 final size:54
Alignment explanation
Indices: 53757--53894 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 54
53747 CTTTAGATTT
*
53757 GATTTCAACTTCACGACGAAGGGA-ATCGTGCCCATCAA-CAAC-AT-TCATCTCCAC
1 GATTTCAACTTCACGACGAA-GGATATCGTGCCCA-CAAGCAACAATGCCA--TCCAC
* *
53811 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGTAGCAATGCCATCCAC
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCCATCCAC
53865 GATTTCAACTTCACGACGAAGGATATCGTG
1 GATTTCAACTTCACGACGAAGGATATCGTG
53895 TTCATTTGCA
Statistics
Matches: 77, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
53 6 0.08
54 67 0.87
55 2 0.03
56 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (54 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCCATCCAC
Found at i:54037 original size:84 final size:84
Alignment explanation
Indices: 53896--54270 Score: 525
Period size: 84 Copynumber: 4.4 Consensus size: 84
53886 GATATCGTGT
* * * * *
53896 TCATTTGCAACATTGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
53961 CGCTTAGCTCAAAGGCACA
66 CACTCAGCTCAAAGGCACA
* * *
53980 TCATTTGCAGCATAGCTCAAGGCAAAAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCCACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
**
54045 CGTTCAGCTCAAAGGCACA
66 CACTCAGCTCAAAGGCACA
* *
54064 TCATTTGCAGCATAGCTCAAGGCAATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
*
54129 CACTCGGCTCAAAGGCACA
66 CACTCAGCTCAAAGGCACA
* * * *
54148 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAAAAACCTTCGAGTTCGAT
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC--AAAAGACCTTCGAGTTCGAC
*
54213 TACACTCAGCTCAAAGGCGCA
64 TACACTCAGCTCAAAGGCACA
* * *
54234 TAATTTGCAGCATAGCTCAAGGCGATAAGGGTTATCT
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCT
54271 ATCAGCAAAA
Statistics
Matches: 263, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
84 193 0.73
86 70 0.27
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (84 bp):
TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
CACTCAGCTCAAAGGCACA
Found at i:54434 original size:83 final size:83
Alignment explanation
Indices: 54235--54440 Score: 277
Period size: 83 Copynumber: 2.5 Consensus size: 83
54225 AAAGGCGCAT
* * * * *
54235 AATTTGCAGCATAGCTCAAGGCGATAAGGGTTATCTATCAGCAAAACTTTGAGTTCGATTACATT
1 AATTTACAGCATAACTCAAGGCGATAAGGGCTATCTGTCAGCAAAACTTCGAGTTCGATTACATT
54300 CAACTCATGGACATATCA
66 CAACTCATGGACATATCA
* * * * * * * *
54318 AATTTACAGTATAACTTAAGGTGAGAAGAGCTATTTGTCAGTAAACCTTCGAGTTCGATTACATT
1 AATTTACAGCATAACTCAAGGCGATAAGGGCTATCTGTCAGCAAAACTTCGAGTTCGATTACATT
*
54383 CAACTCTTGGACATATCA
66 CAACTCATGGACATATCA
*
54401 AATTTACAGCATAACTCAAGACGATAAGGGCTATCTGTCA
1 AATTTACAGCATAACTCAAGGCGATAAGGGCTATCTGTCA
54441 ACAAGAATTT
Statistics
Matches: 102, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 102 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (83 bp):
AATTTACAGCATAACTCAAGGCGATAAGGGCTATCTGTCAGCAAAACTTCGAGTTCGATTACATT
CAACTCATGGACATATCA
Found at i:55792 original size:3 final size:3
Alignment explanation
Indices: 55784--55810 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55774 TAGAATAAAA
55784 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
55811 TCCTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:63244 original size:2 final size:2
Alignment explanation
Indices: 63237--63266 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
63227 TGCACAATTA
63237 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
63267 GTCATCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65923 original size:20 final size:20
Alignment explanation
Indices: 65900--65938 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
65890 CAAAATTCTG
65900 ATAACTCAATATAAATACTA
1 ATAACTCAATATAAATACTA
65920 ATAACTCAATATAAATACT
1 ATAACTCAATATAAATACT
65939 GGATACCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAACTCAATATAAATACTA
Found at i:66379 original size:7 final size:7
Alignment explanation
Indices: 66355--66388 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
66345 TAAAAACATG
66355 ATTTCTA
1 ATTTCTA
* *
66362 ATTTTTG
1 ATTTCTA
66369 ATTTCTA
1 ATTTCTA
66376 ATTTCTA
1 ATTTCTA
66383 ATTTCT
1 ATTTCT
66389 GATACAAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (7 bp):
ATTTCTA
Found at i:74721 original size:117 final size:117
Alignment explanation
Indices: 74515--74745 Score: 365
Period size: 117 Copynumber: 2.0 Consensus size: 117
74505 TTTAGCTTTG
* * *
74515 CCTTCTGAATTTCGGCTAATGTTTCCTTTCTGATCACTCGGAATTTGTTCCAGTCTTAATGGAGT
1 CCTTCTGAATTTCGGCTAATGTTGCCTTTCTGATCACTCAGAATTTGTTCCAGTCTTAATGGAGA
* * * *
74580 ATGACTCTTTTCAGTAGCACTAACAGTGTCAACCGTCAGACCTAAAGCATTT
66 ATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTAAAGCATTT
*
74632 CCTTCTGAATTTCGGCTATTGTTGCCTTTCTGATCACTCAG-ATGTTGTTCCAGTCTTAATGGAG
1 CCTTCTGAATTTCGGCTAATGTTGCCTTTCTGATCACTCAGAAT-TTGTTCCAGTCTTAATGGAG
*
74696 AATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTGAAGCA
65 AATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTAAAGCA
74746 CCAGTTTCCA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
116 2 0.02
117 102 0.98
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (117 bp):
CCTTCTGAATTTCGGCTAATGTTGCCTTTCTGATCACTCAGAATTTGTTCCAGTCTTAATGGAGA
ATGACTCTTCTCAGTAGCACTAACAGAGTCAACAGTCACACCTAAAGCATTT
Found at i:76921 original size:17 final size:17
Alignment explanation
Indices: 76879--76919 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
76869 TATTTTGAAT
*
76879 TTATTTTAAATGGTATA
1 TTATTTTAAATGGTACA
76896 TTATTTTAAATGGTACA
1 TTATTTTAAATGGTACA
76913 TATATTT
1 T-TATTT
76920 AATTTGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (17 bp):
TTATTTTAAATGGTACA
Found at i:77021 original size:15 final size:15
Alignment explanation
Indices: 77003--77031 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
76993 TTTTTTCTAT
77003 TCAATTTTTTAATAA
1 TCAATTTTTTAATAA
77018 TCAATTTTTTAATA
1 TCAATTTTTTAATA
77032 TTTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TCAATTTTTTAATAA
Found at i:79137 original size:35 final size:35
Alignment explanation
Indices: 79052--79145 Score: 134
Period size: 36 Copynumber: 2.7 Consensus size: 35
79042 AAAAGTTGAA
*
79052 CACTTAAATCGAAAGTGTCGATGCCTCCTTCCGTT
1 CACTTGAATCGAAAGTGTCGATGCCTCCTTCCGTT
* *
79087 CGACTTGAATCGAAAGTGTCGATGCTTCTTTCCGTT
1 C-ACTTGAATCGAAAGTGTCGATGCCTCCTTCCGTT
* *
79123 CACTTGAATTGAAAGTGTTGATG
1 CACTTGAATCGAAAGTGTCGATG
79146 TTTCCTTCTG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
35 21 0.40
36 32 0.60
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (35 bp):
CACTTGAATCGAAAGTGTCGATGCCTCCTTCCGTT
Found at i:83632 original size:22 final size:22
Alignment explanation
Indices: 83574--83625 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
83564 AAAATCATGG
83574 AAGTGCCTTTGCACTAATACTA
1 AAGTGCCTTTGCACTAATACTA
* *
83596 AAGTGCCTTTTCACTAATATTA
1 AAGTGCCTTTGCACTAATACTA
83618 AAGTGCCT
1 AAGTGCCT
83626 CAGCACTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (22 bp):
AAGTGCCTTTGCACTAATACTA
Found at i:83642 original size:22 final size:22
Alignment explanation
Indices: 83617--83666 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
83607 CACTAATATT
*
83617 AAAGTGC-CTCAGCACTGGTACA
1 AAAGTGCACTCA-CACTGATACA
*
83639 AAAGTGCATTCACACTGATACA
1 AAAGTGCACTCACACTGATACA
83661 AAAGTG
1 AAAGTG
83667 GTGTAACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (22 bp):
AAAGTGCACTCACACTGATACA
Found at i:84524 original size:2 final size:2
Alignment explanation
Indices: 84519--84552 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
84509 TCTATATAAC
84519 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
84553 TCGAATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96061 original size:68 final size:68
Alignment explanation
Indices: 95973--96241 Score: 325
Period size: 68 Copynumber: 4.0 Consensus size: 68
95963 TTAGGGATTT
* * *
95973 TTTATGGTAAACTACTTATTTGGTCACTTATATATTATCTAGTTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
96038 TTA
66 TTA
* * * * *
96041 TTTAGAGTAAACTACATATTTAGTCACATATATATTATCTAATTTATGTTTTGGTGACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
96106 TTA
66 TTA
* * ** *
96109 TTTAGGGTAAACTACCTATTTGATCACTTATATATTATCTAATATAAT-TCAT-AT-A-T--ATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTCACTCGATT
*
96168 TTTA
65 ATTA
* * **
96172 TTTAGGGTAAGCTACCTATTTGGTAACTTATATATTATCTAATTTATGTTTTGGTCACTTTATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
96237 TTA
66 TTA
96240 TT
1 TT
96242 ATTTTCAAAA
Statistics
Matches: 169, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
62 3 0.02
63 48 0.28
64 1 0.01
65 2 0.01
66 2 0.01
67 1 0.01
68 109 0.64
69 3 0.02
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:97407 original size:215 final size:216
Alignment explanation
Indices: 97060--98385 Score: 2107
Period size: 215 Copynumber: 6.3 Consensus size: 216
97050 ATTTAAGAAT
* * *
97060 TAAATTGAACAAATATGAAATTACAAATTAAAATGTAAATAAAGTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
97125 GGATCAAATCGATATAATTTT-AAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATGATA
66 GGATCAAATCGAAATAATTTTAAAATTGTGAGGTTGAAATTAATACAAAAAA-TACTAAATTATA
* * *
97189 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTTTGGATCAATTTTA-
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
97253 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
* * * *
97275 TACATTGAACAAATATGAAATTCCAAATAAAAATTTAAATAAATTAAAAAACACACATTGACGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
97340 GGATCAAATCGAAATAATTTT-AAATTGT-ATAGTTGGAATTAATACAAAAAAACACTAAATTAT
66 GGATCAAATCGAAATAATTTTAAAATTGTGA-GGTTGAAATTAATAC-AAAAAATACTAAATTAT
97403 ACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAG-----A--AATAAGTATGGGTCAATTTCA
129 ACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCA
*
97461 GATGCAAATAAAATTTGAAGGAC
194 GATGCAAATAAAATTTGGAGGAC
97484 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
97549 GGATCAAATCGAAATAATTTTAAAA-T-TGAGGTTGAAATTAATAC-AAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATAC
*
97611 TCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
97676 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
*
97697 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAA-AACACACATTGACGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * *
97761 GGATCAAATCGAAATAATTTT-AAATTGTAAAGTTGGAATTAATACAAAAAAACACTAAATTATA
66 GGATCAAATCGAAATAATTTTAAAATTGTGAGGTTGAAATTAATAC-AAAAAATACTAAATTATA
97825 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAG-----A--AATAAGTATGGGTCAATTTCAG
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
*
97883 ATGCAAATAAAATTTGGAGGAT
195 ATGCAAATAAAATTTGGAGGAC
97905 TAAA-TGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT-AAC-A-ACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
97966 GGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAATACAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATAC
*
98030 TCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
98095 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
98116 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
98181 GGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAATACAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATAC
* * *
98245 TCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATACGTATGGGTCAATTTCAAA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
* *
98310 AGAAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
*
98331 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
98386 AAGGGATCAA
Statistics
Matches: 1034, Mismatches: 48, Indels: 58
0.91 0.04 0.05
Matches are distributed among these distances:
204 50 0.05
205 48 0.05
206 57 0.06
207 40 0.04
208 79 0.08
209 106 0.10
210 5 0.00
211 51 0.05
212 77 0.07
213 109 0.11
214 2 0.00
215 404 0.39
216 6 0.01
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
TGCAAATAAAATTTGGAGGAC
Found at i:98158 original size:419 final size:423
Alignment explanation
Indices: 97060--98385 Score: 2240
Period size: 421 Copynumber: 3.1 Consensus size: 423
97050 ATTTAAGAAT
* * *
97060 TAAATTGAACAAATATGAAATTACAAATTAAAATGTAAATAAAGTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
97125 GGATCAAATCGATATAATTTT-AAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATGATA
66 GGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAAT-ACAAAAAGTACTAAATTATA
* * * *
97189 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTTTGGATCAATTTTA-
129 CTCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
* *
97253 ATGCAAATAAAATTTGGAGGACTACATTGAACAAATATGAAATTCCAAATAAAAATTTAAATAAA
194 ATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAA
*
97318 TTAAAAAACACACATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTATAGTTGGAATTAAT
259 TT-AAAAACACACATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGGAATTAAT
97383 ACAAAAAAACACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTA
323 ACAAAAAAACACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTA
*
97448 TGGGTCAATTTCAGATGCAAATAAAATTTGAAGGAC
388 TGGGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
97484 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
97549 GGATCAAATCGAAATAATTTTAAAA-TTGAGGTTGAAATTAATAC-AAAAGTACTAAATTATACT
66 GGATCAAATCGAAATAATTTTAAAATTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACT
97612 CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
131 CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
97677 GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
196 GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
97742 AAAAACACACATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGGAATTAATACA
261 AAAAACACACATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGGAATTAATACA
97807 AAAAAACACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTATGG
326 AAAAAACACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTATGG
*
97872 GTCAATTTCAGATGCAAATAAAATTTGGAGGAT
391 GTCAATTTCAGATGCAAATAAAATTTGGAGGAC
97905 TAAA-TGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT-AAC-A-ACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
97966 GGATCAAATCGAAATAATTTTAAAATTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACT
66 GGATCAAATCGAAATAATTTTAAAATTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACT
98031 CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
131 CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
98096 GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
196 GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
* * * *
98161 AAACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAAATT-TGAGGTTGAAATTAATA
261 AAA-AACACACATTGACGAGGGATCAAATCGAAATAATTTT-AAATTGTAAAGTTGGAATTAATA
** *
98225 C-AAAAAGTACTAAATTATACTCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAA
324 CAAAAAAACACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAG--A-AA-T-A
* * *
98289 TACGTATGGGTCAATTTCAAAAGAAAATAAAATTTGGAGGAC
384 -A-GTATGGGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
*
98331 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
98386 AAGGGATCAA
Statistics
Matches: 858, Mismatches: 27, Indels: 28
0.94 0.03 0.03
Matches are distributed among these distances:
417 38 0.04
418 20 0.02
419 205 0.24
420 91 0.11
421 246 0.29
422 68 0.08
423 17 0.02
424 84 0.10
425 4 0.00
426 39 0.05
427 39 0.05
428 3 0.00
429 1 0.00
430 3 0.00
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (423 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAAATTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACT
CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATT
AAAAACACACATTGACGAGGGATCAAATCGAAATAATTTTAAATTGTAAAGTTGGAATTAATACA
AAAAAACACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTATGG
GTCAATTTCAGATGCAAATAAAATTTGGAGGAC
Found at i:98473 original size:2 final size:2
Alignment explanation
Indices: 98466--98573 Score: 73
Period size: 2 Copynumber: 54.5 Consensus size: 2
98456 AAAACAACTA
* * * *
98466 AT AT AT AT AT AT A- AT AT AA ACT AG AT AGT TT AT AT AT AA AGT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T
* *
98508 AT AT GT AT -T AT AT AT AT AT AT AT AT AA ACT AT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* *
98548 AT AT AT AT AT GT AT AA AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
98574 CCATGTATAA
Statistics
Matches: 81, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
1 5 0.06
2 72 0.89
3 4 0.05
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:98556 original size:29 final size:29
Alignment explanation
Indices: 98496--98571 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
98486 CTAGATAGTT
* *
98496 TATATATAAAGTATATGTATTATATATATA
1 TATATATAAACTATAT-AATTATATATATA
98526 TATATATAAACTATATAATTATATATATA
1 TATATATAAACTATATAATTATATATATA
* *
98555 TATGTATAAATTATATA
1 TATATATAAACTATATA
98572 TACCATGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 27 0.64
30 15 0.36
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (29 bp):
TATATATAAACTATATAATTATATATATA
Found at i:98579 original size:20 final size:20
Alignment explanation
Indices: 98537--98593 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
98527 ATATATAAAC
**
98537 TATATAATTATATATATATATG
1 TATA-AATTATATATA-CCATG
98559 TATAAATTATATATACCATG
1 TATAAATTATATATACCATG
*
98579 TATAAACTATA-ATAC
1 TATAAATTATATATAC
98594 TATATAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.12
20 13 0.41
21 11 0.34
22 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (20 bp):
TATAAATTATATATACCATG
Found at i:98708 original size:25 final size:23
Alignment explanation
Indices: 98659--98719 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
98649 CAGTTCATAT
98659 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
98679 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
98704 ATATAGTATATAAATA
1 ATATAGTATATAAATA
98720 TAAATTCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:98711 original size:12 final size:13
Alignment explanation
Indices: 98672--98721 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
98662 TAGTATATAA
98672 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
98686 TTATATAA-ATAGT
1 ATATA-AATATAGT
98699 ATA-AAATATAGT
1 ATATAAATATAGT
98711 ATATAAATATA
1 ATATAAATATA
98722 AATTCTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:98732 original size:20 final size:20
Alignment explanation
Indices: 98659--98723 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 20
98649 CAGTTCATAT
98659 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
98679 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
98704 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
98724 TTCTAGTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 7 0.18
23 7 0.18
24 1 0.03
25 11 0.29
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:98806 original size:28 final size:27
Alignment explanation
Indices: 98769--98824 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
98759 ACCCTAAACC
98769 ATATATATAGTTCATATGTAAACTATAT
1 ATATATATAGTTCATAT-TAAACTATAT
* *
98797 ATATATATAGTTTATATTAATCTATAT
1 ATATATATAGTTCATATTAAACTATAT
98824 A
1 A
98825 GTTTACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (27 bp):
ATATATATAGTTCATATTAAACTATAT
Found at i:98843 original size:20 final size:20
Alignment explanation
Indices: 98800--99012 Score: 101
Period size: 18 Copynumber: 11.3 Consensus size: 20
98790 ACTATATATA
*
98800 TATATAGTTT--ATATTAATC
1 TATATAGTTTACATATGAA-C
98819 TATATAGTTTACATATGAAC
1 TATATAGTTTACATATGAAC
*
98839 TATATA-TATATAC-TAT--AG
1 TATATAGT-T-TACATATGAAC
*
98857 T-TGATA-TTTATATATGAAC
1 TAT-ATAGTTTACATATGAAC
*
98876 --TATAGTTTACATATAAAC
1 TATATAGTTTACATATGAAC
*
98894 TATATAGTTTATATA-GTAA-
1 TATATAGTTTACATATG-AAC
* *
98913 T-TATATTTTACATATAAAC
1 TATATAGTTTACATATGAAC
*
98932 TATAGTTGATATTTACATATGAAC
1 TATA--T-A-GTTTACATATGAAC
*
98956 TATAT--TTTACATATAAAC
1 TATATAGTTTACATATGAAC
*
98974 TCTATA---T--ATA--AAC
1 TATATAGTTTACATATGAAC
98987 TATATAGTTTACATATGAAC
1 TATATAGTTTACATATGAAC
99007 TATATA
1 TATATA
99013 TATATAATAT
Statistics
Matches: 151, Mismatches: 16, Indels: 53
0.69 0.07 0.24
Matches are distributed among these distances:
13 8 0.05
15 3 0.02
16 3 0.02
17 9 0.06
18 50 0.33
19 14 0.09
20 36 0.24
21 9 0.06
22 2 0.01
23 1 0.01
24 16 0.11
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (20 bp):
TATATAGTTTACATATGAAC
Found at i:98884 original size:18 final size:18
Alignment explanation
Indices: 98863--99100 Score: 70
Period size: 18 Copynumber: 12.9 Consensus size: 18
98853 ATAGTTGATA
98863 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* *
98881 TTTACATATAAACTATATAG
1 TTTATATATGAAC--TATAG
* *
98901 TTTATATA-GTAATTATAT
1 TTTATATATG-AACTATAG
* *
98919 TTTACATATAAACTATAG
1 TTTATATATGAACTATAG
*
98937 TTGATATTTACATATGAACTATAT
1 TT--TA--T--ATATGAACTATAG
* * *
98961 TTTACATATAAACTCTA-
1 TTTATATATGAACTATAG
98978 --TATATA--AACTATATAG
1 TTTATATATGAAC--TATAG
*
98994 TTTACATATGAACTATA-
1 TTTATATATGAACTATAG
**
99011 TATATATAATAT-AGTTGATA-
1 T-T-TAT-ATATGAACT-ATAG
99031 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* * *
99049 TTTACATTTAAACTATA-
1 TTTATATATGAACTATAG
*
99066 TAGTATATACT-AACTATAG
1 T-TTATATA-TGAACTATAG
99085 TTTACTAT-T-AACTATA
1 TTTA-TATATGAACTATA
99101 TATAAACTAT
Statistics
Matches: 162, Mismatches: 31, Indels: 55
0.65 0.12 0.22
Matches are distributed among these distances:
13 3 0.02
15 8 0.05
17 17 0.10
18 82 0.51
19 10 0.06
20 27 0.17
22 2 0.01
24 13 0.08
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:98887 original size:55 final size:55
Alignment explanation
Indices: 98821--99077 Score: 226
Period size: 55 Copynumber: 4.6 Consensus size: 55
98811 TATTAATCTA
*
98821 TATAGTTTACATATGAACTATATATATATACTATAGTTGATA-TTTATATATGAAC
1 TATAGTTTACATATGAACTATATATATATACTATAGTT-ATACTTTATATATAAAC
* * * * *
98876 TATAGTTTACATATAAACTATATAGTTTATA-TAGTAATTATATTTTACATATAAAC
1 TATAGTTTACATATGAACTATATA-TATATACTA-TAGTTATACTTTATATATAAAC
* *
98932 TATAGTTGATATTTACATATGAACTATAT-T-T-TAC-ATA--TAAACTCTATATATAAAC
1 TATA---G---TTTACATATGAACTATATATATATACTATAGTTATACTTTATATATAAAC
* *
98987 TATATAGTTTACATATGAACTATATATATATAATATAGTTGATA-TTTATATATGAAC
1 --TATAGTTTACATATGAACTATATATATATACTATAGTT-ATACTTTATATATAAAC
* *
99044 TATAGTTTACATTTAAACTATATAGTATATACTA
1 TATAGTTTACATATGAACTATATA-TATATACTA
99078 ACTATAGTTT
Statistics
Matches: 165, Mismatches: 17, Indels: 39
0.75 0.08 0.18
Matches are distributed among these distances:
51 18 0.11
52 1 0.01
53 1 0.01
54 3 0.02
55 67 0.41
56 32 0.19
57 18 0.11
58 5 0.03
59 2 0.01
60 1 0.01
62 17 0.10
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (55 bp):
TATAGTTTACATATGAACTATATATATATACTATAGTTATACTTTATATATAAAC
Found at i:98897 original size:42 final size:42
Alignment explanation
Indices: 98844--98974 Score: 173
Period size: 42 Copynumber: 3.2 Consensus size: 42
98834 TGAACTATAT
* *
98844 ATATATACTATAGTTGATATTTATATATGAACTATAGTTTAC
1 ATATAAACTATAGTTGATATTTATATATGAACTATATTTTAC
* *
98886 ATATAAACTATA--T-A-GTTTATATA-GTAATTATATTTTAC
1 ATATAAACTATAGTTGATATTTATATATG-AACTATATTTTAC
*
98924 ATATAAACTATAGTTGATATTTACATATGAACTATATTTTAC
1 ATATAAACTATAGTTGATATTTATATATGAACTATATTTTAC
98966 ATATAAACT
1 ATATAAACT
98975 CTATATATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
37 1 0.01
38 31 0.41
39 1 0.01
40 2 0.03
41 1 0.01
42 39 0.51
43 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (42 bp):
ATATAAACTATAGTTGATATTTATATATGAACTATATTTTAC
Found at i:98923 original size:38 final size:39
Alignment explanation
Indices: 98860--98982 Score: 151
Period size: 38 Copynumber: 3.1 Consensus size: 39
98850 ACTATAGTTG
*
98860 ATATTTATATATGAACTATAGTTTACATATAAACTATAT
1 ATATTTATATATGAACTATATTTTACATATAAACTATAT
* *
98899 A-GTTTATATA-GTAATTATATTTTACATATAAACTATAGTT
1 ATATTTATATATG-AACTATATTTTACATATAAACTATA--T
* *
98939 GATATTTACATATGAACTATATTTTACATATAAACTCTAT
1 -ATATTTATATATGAACTATATTTTACATATAAACTATAT
98979 ATAT
1 ATAT
98983 AAACTATATA
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
37 1 0.01
38 31 0.44
39 5 0.07
40 2 0.03
41 1 0.01
42 30 0.42
43 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (39 bp):
ATATTTATATATGAACTATATTTTACATATAAACTATAT
Found at i:98988 original size:31 final size:32
Alignment explanation
Indices: 98948--99016 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 32
98938 TGATATTTAC
* *
98948 ATATGAACTATAT-TTTACATATAAACTCTAT
1 ATATAAACTATATATTTACATATAAACTATAT
*
98979 ATATAAACTATATAGTTTACATATGAACTATAT
1 ATATAAACTATATA-TTTACATATAAACTATAT
99012 ATATA
1 ATATA
99017 TAATATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 12 0.36
33 21 0.64
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (32 bp):
ATATAAACTATATATTTACATATAAACTATAT
Found at i:99023 original size:31 final size:32
Alignment explanation
Indices: 98948--99026 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
98938 TGATATTTAC
* * *
98948 ATATGAAC-TATATTTTACATATAAACTCTAT
1 ATATAAACATATAGTTTACATATAAACTATAT
*
98979 ATATAAACTATATAGTTTACATATGAACTATAT
1 ATATAAAC-ATATAGTTTACATATAAACTATAT
*
99012 ATATATA-ATATAGTT
1 ATATAAACATATAGTT
99027 GATATTTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 15 0.37
33 26 0.63
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (32 bp):
ATATAAACATATAGTTTACATATAAACTATAT
Found at i:99040 original size:88 final size:90
Alignment explanation
Indices: 98886--99104 Score: 266
Period size: 88 Copynumber: 2.4 Consensus size: 90
98876 TATAGTTTAC
* * *
98886 ATATAAACTATATAGTTTATATA-GTAATTATATTTTACATATAAACTATAGTTGATATTTACAT
1 ATATAAACTATATAGTTTACATATG-AACTATA---TATATATAAACTATAGTTGATATTTACAT
* *
98950 ATGAACTATATTTTACATATAAACTCTAT
62 ATGAACTATAGTTTACATATAAACTATAT
*
98979 ATATAAACTATATAGTTTACATATGAACTATATATATAT-AA-TATAGTTGATATTTATATATGA
1 ATATAAACTATATAGTTTACATATGAACTATATATATATAAACTATAGTTGATATTTACATATGA
*
99042 ACTATAGTTTACATTTAAACTATAT
66 ACTATAGTTTACATATAAACTATAT
* *
99067 AGTATATACTAACTATAGTTTAC-TATTAACTATATATA
1 A-TATAAACT-A-TATAGTTTACATATGAACTATATATA
99105 AACTATAAGT
Statistics
Matches: 113, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
88 44 0.39
89 9 0.08
90 21 0.19
91 10 0.09
93 28 0.25
94 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.43
Consensus pattern (90 bp):
ATATAAACTATATAGTTTACATATGAACTATATATATATAAACTATAGTTGATATTTACATATGA
ACTATAGTTTACATATAAACTATAT
Found at i:99057 original size:24 final size:22
Alignment explanation
Indices: 99011--99058 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
99001 ATGAACTATA
*
99011 TATATATAATATAGTTGATATT
1 TATATATAATATAGTTGACATT
*
99033 TATATATGAACTATAGTTTACATT
1 TATATAT-AA-TATAGTTGACATT
99057 TA
1 TA
99059 AACTATATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 2 0.09
24 13 0.59
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (22 bp):
TATATATAATATAGTTGACATT
Found at i:99081 original size:36 final size:35
Alignment explanation
Indices: 99033--99102 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
99023 AGTTGATATT
99033 TATATATGAACTATAGTTTAC-ATTTAAACTATATAG
1 TATATATGAACTATAGTTTACTA-TT-AACTATATAG
99069 TATATACT-AACTATAGTTTACTATTAACTATATA
1 TATATA-TGAACTATAGTTTACTATTAACTATATA
99103 TAAACTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 9 0.28
36 21 0.66
37 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (35 bp):
TATATATGAACTATAGTTTACTATTAACTATATAG
Found at i:99214 original size:23 final size:21
Alignment explanation
Indices: 99186--99248 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 21
99176 AAATATAAAC
99186 TATAGTTTATATTATACAATATA
1 TATAGTTTATATTAT--AATATA
99209 TATAGTTTATATT-T-ATATA
1 TATAGTTTATATTATAATATA
99228 TATA-TTATATATTATAATATA
1 TATAGTT-TATATTATAATATA
99249 AACTATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.05
19 15 0.41
20 1 0.03
21 5 0.14
22 1 0.03
23 13 0.35
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (21 bp):
TATAGTTTATATTATAATATA
Found at i:99227 original size:17 final size:18
Alignment explanation
Indices: 99193--99277 Score: 68
Period size: 19 Copynumber: 4.7 Consensus size: 18
99183 AACTATAGTT
* *
99193 TATATTATACAATATATA
1 TATATTATATATTATATA
99211 TAGT-TTATAT-TTATATA
1 TA-TATTATATATTATATA
99228 TATATTATATATTATAATA
1 TATATTATATATTAT-ATA
* *
99247 TAAACTATATATCCTATATA
1 TATATTATATAT--TATATA
*
99267 -ATATTACATAT
1 TATATTATATAT
99278 GAACTATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
16 1 0.02
17 14 0.26
18 11 0.20
19 22 0.41
20 3 0.06
21 3 0.06
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (18 bp):
TATATTATATATTATATA
Found at i:99379 original size:32 final size:33
Alignment explanation
Indices: 99320--99398 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 33
99310 AGTTTATATT
* * *
99320 TATATACTATATAAAAAATTTATACTATA-ATA
1 TATAAACTATATAAAAAATATAAACTATAGATA
* *
99352 TATAAACTATATAATACATATAAACTATATGGTATA
1 TATAAACTATATAAAAAATATAAACTATA--G-ATA
99388 TATAAACTATA
1 TATAAACTATA
99399 CATATATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 24 0.63
36 14 0.37
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (33 bp):
TATAAACTATATAAAAAATATAAACTATAGATA
Found at i:99421 original size:33 final size:33
Alignment explanation
Indices: 99383--99459 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 33
99373 AAACTATATG
*
99383 GTATATATAAACTATACA-TATATATTTCATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
*
99415 GT-TATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATACATTATATAGTTCATTA
99447 GTATATATAAACT
1 GTATATATAAACT
99460 CTATAGTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 14 0.34
32 17 0.41
33 10 0.24
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (33 bp):
GTATATATAAACTATACATTATATAGTTCATTA
Found at i:99438 original size:18 final size:18
Alignment explanation
Indices: 99349--99641 Score: 130
Period size: 18 Copynumber: 16.9 Consensus size: 18
99339 TTATACTATA
*
99349 ATATATAAACTATATAAT
1 ATATATAAACTATATAGT
* *
99367 ACATATAAACTATATGGT
1 ATATATAAACTATATAGT
*
99385 ATATATAAACTATACA-T
1 ATATATAAACTATATAGT
**
99402 ATATAT-TTC-AT-TAGT
1 ATATATAAACTATATAGT
99417 -TATATAAACTATATA-T
1 ATATATAAACTATATAGT
**
99433 -TATAT-AGTTCAT-TAGT
1 ATATATAAACT-ATATAGT
*
99449 ATATATAAACTCTATAGT
1 ATATATAAACTATATAGT
*
99467 ATATGTAAACTATATA-T
1 ATATATAAACTATATAGT
* * *
99484 -TAT-T-TAGT-T-CAGT
1 ATATATAAACTATATAGT
*
99497 ATATATAACCTATATAGT
1 ATATATAAACTATATAGT
99515 ATGTATATACAACTATATA-T
1 A--TATATA-AACTATATAGT
* *
99535 ATATAGT--GC-AT-TGGT
1 ATATA-TAAACTATATAGT
*
99550 ATATATAACCTATATAGT
1 ATATATAAACTATATAGT
* *
99568 ATATGGCATATAC-A-A-ACT
1 ATAT---ATAAACTATATAGT
99586 ATATATTAAA-TAGTTCATTAGT
1 ATATA-TAAACTA--T-A-TAGT
99608 ATATATAAACTATATAGT
1 ATATATAAACTATATAGT
99626 ATATATAAACTATATA
1 ATATATAAACTATATA
99642 TTGAAAAGTT
Statistics
Matches: 204, Mismatches: 35, Indels: 72
0.66 0.11 0.23
Matches are distributed among these distances:
12 1 0.00
13 2 0.01
14 13 0.06
15 19 0.09
16 22 0.11
17 19 0.09
18 89 0.44
19 3 0.01
20 11 0.05
21 16 0.08
22 9 0.04
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.41
Consensus pattern (18 bp):
ATATATAAACTATATAGT
Found at i:99470 original size:33 final size:32
Alignment explanation
Indices: 99383--99470 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 32
99373 AAACTATATG
* *
99383 GTATATATAAACTATACATATATATTTCATTA
1 GTATATATAAACTATATATATATAGTTCATTA
99415 GT-TATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATA-TATATAGTTCATTA
*
99447 GTATATATAAACTCTATAGTATAT
1 GTATATATAAACTATATA-TATAT
99471 GTAAACTATA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 14 0.28
32 17 0.34
33 19 0.38
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (32 bp):
GTATATATAAACTATATATATATAGTTCATTA
Found at i:99571 original size:33 final size:31
Alignment explanation
Indices: 99516--99630 Score: 100
Period size: 33 Copynumber: 3.8 Consensus size: 31
99506 CTATATAGTA
*
99516 TGTATATACAACTATATA-TATATAGTGCAT
1 TGTATATATAACTATATAGTATATAGTGCAT
99546 TGGTATATATAACCTATATAGTATAT-G-GCA-
1 T-GTATATATAA-CTATATAGTATATAGTGCAT
* * * *
99576 --TATACA-AACTATATATTAAATAGTTCAT
1 TGTATATATAACTATATAGTATATAGTGCAT
99604 TAGTATATATAAACTATATAGTATATA
1 T-GTATATAT-AACTATATAGTATATA
99631 TAAACTATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
25 11 0.17
26 3 0.05
27 7 0.11
30 1 0.02
31 17 0.26
32 8 0.12
33 19 0.29
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (31 bp):
TGTATATATAACTATATAGTATATAGTGCAT
Found at i:99622 original size:58 final size:57
Alignment explanation
Indices: 99417--99629 Score: 245
Period size: 58 Copynumber: 3.9 Consensus size: 57
99407 TTTCATTAGT
* * *
99417 TATATAAACTATATATTATATAGTTCATTAGTATATATAAACTCTATAGTATATG--
1 TATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGCA
* *
99472 --T--AAACTATATATTATTTAGTTC---AGTATATATAACCTATATAG--TATGTA
1 TATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGCA
* *
99520 TATAC-AACTATATA-TATATAGTGCATTGGTATATATAACCTATATAGTATATGGCA
1 TATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATAT-GCA
* *
99576 TATACAAACTATATATTAAATAGTTCATTAGTATATATAAACTATATAGTATAT
1 TATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATAT
99630 ATAAACTATA
Statistics
Matches: 133, Mismatches: 11, Indels: 25
0.79 0.07 0.15
Matches are distributed among these distances:
46 4 0.03
48 18 0.14
50 9 0.07
51 29 0.22
53 20 0.15
55 3 0.02
56 7 0.05
57 9 0.07
58 34 0.26
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (57 bp):
TATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGCA
Found at i:99652 original size:51 final size:51
Alignment explanation
Indices: 99413--99672 Score: 275
Period size: 51 Copynumber: 5.0 Consensus size: 51
99403 TATATTTCAT
* *
99413 TAGT-TATATAAACTATATATTATATAGTTCATTAGTATATATAAACTCTA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATA
* *
99463 TAGTATATGTAAACTATATATTATTTAGTTC---AGTATATATAACCTATA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATA
* *
99511 TAGTATGTATATACAACTATATA-TATATAGTGCATTGGTATATATAACCTATA
1 TAGTA--TATATA-AACTATATATTATATAGTTCATTAGTATATATAACCTATA
* *
99564 TAGTATATGGCATATACAAACTATATATTAAATAGTTCATTAGTATATATAAACTATA
1 TAG--TAT---ATAT--AAACTATATATTATATAGTTCATTAGTATATATAACCTATA
* *
99622 TAGTATATATAAACTATATATTGA-AAAGTTCAGTA-TAT-TATAACCTATA
1 TAGTATATATAAACTATATATT-ATATAGTTCATTAGTATATATAACCTATA
99671 TA
1 TA
99673 ATTATTAATA
Statistics
Matches: 179, Mismatches: 15, Indels: 33
0.79 0.07 0.15
Matches are distributed among these distances:
48 20 0.11
49 12 0.07
50 20 0.11
51 54 0.30
52 1 0.01
53 24 0.13
55 2 0.01
56 7 0.04
57 9 0.05
58 30 0.17
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (51 bp):
TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATA
Found at i:100299 original size:123 final size:122
Alignment explanation
Indices: 100074--100452 Score: 482
Period size: 123 Copynumber: 3.1 Consensus size: 122
100064 AAAATCAACC
* * *
100074 GTGTTCTTCATTTATTCATCCCAGTTCTTCCCCAAAACCCTCGTTTGGTCTTCAAAAACACCAAA
1 GTGTTCTTCATTTGTTCAT-CCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACC-AA
* * *
100139 ACCAAAACATTTTCGTGTTTTTTTCGATCAAATACCCAAATATTCATCCG-TGTTCTTAT
64 ACCAAACCA-TTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGATGTTCATAT
100198 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAA-CCTCCTTTGATCTTCAAAAACACCTAAA
1 GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACC-AAA
* * *
100262 CACAAACCATTTCGTGTTTTTTTCAGATCAAACACCCAAATTTTC-TTCGATGTTCATCT
65 C-CAAACCATTTCGTGTTTTTTTC-GATCAAACACCCAAATATTCATCCGATGTTCATAT
* * *
100321 GTGTTCTTCATTAGTTCATCCTAGTTCTTCCCCAAAACCCTCCTTTGATCTTTAAAAACATCAAA
1 GTGTTCTTCATTTGTTCATCC-AGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACCAAA
* * **
100386 CCCAAACCATTTCGTG-TTTTTTCGATTAAACA-CCAACAAATTCATCC-ATTGTTCATCC
65 -CCAAACCATTTCGTGTTTTTTTCGATCAAACACCCAA-ATATTCATCCGA-TGTTCATAT
100444 GTGTTCTTC
1 GTGTTCTTC
100453 CCTAAATCCT
Statistics
Matches: 228, Mismatches: 18, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
121 4 0.02
122 57 0.25
123 94 0.41
124 50 0.22
125 23 0.10
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.37
Consensus pattern (122 bp):
GTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCCTTTGATCTTCAAAAACACCAAAC
CAAACCATTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGATGTTCATAT
Found at i:100559 original size:34 final size:33
Alignment explanation
Indices: 100521--100586 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
100511 CCAAAACCCA
*
100521 AACTATTCATCTTCTCTAACCCCTAACTCTAAAT
1 AACTATTCATCTTCCCTAACCCCTAACT-TAAAT
100555 AACTATTCATCTTCCCTAACCCCTAACTTAAA
1 AACTATTCATCTTCCCTAACCCCTAACTTAAA
100587 CCCAAACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (33 bp):
AACTATTCATCTTCCCTAACCCCTAACTTAAAT
Found at i:100595 original size:6 final size:6
Alignment explanation
Indices: 100584--100793 Score: 108
Period size: 6 Copynumber: 35.8 Consensus size: 6
100574 CCCCTAACTT
* * * ** *
100584 AAACCC AAACCC AAACCC AAACCC TAA-TC GAACAT AAATCC AAA-CC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * * * * * *
100630 GAACCG AAATCC AATCCG AAACCC AAACCC AAACCT AAATCCT AAA-CC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAA-CCC AAACCC
* * *
100678 AAACCC CAACCT AAACCC AAACCC AAA-CC GAACCC AAACCC AAA-CC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * ** * * * * * *
100724 GAACCT AAACCC AAA-TT AAACCC AAACCT GAACCT AAATCC TAACCA
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * *
100771 AAACCT GAACCC AAACCC TAACC
1 AAACCC AAACCC AAACCC AAACC
100794 AGAATCGAAC
Statistics
Matches: 148, Mismatches: 49, Indels: 14
0.70 0.23 0.07
Matches are distributed among these distances:
5 22 0.15
6 120 0.81
7 6 0.04
ACGTcount: A:0.47, C:0.40, G:0.04, T:0.09
Consensus pattern (6 bp):
AAACCC
Found at i:100728 original size:11 final size:11
Alignment explanation
Indices: 100697--100787 Score: 56
Period size: 11 Copynumber: 7.9 Consensus size: 11
100687 CCTAAACCCA
100697 AACCCAAACCG
1 AACCCAAACCG
*
100708 AACCCAAACCC
1 AACCCAAACCG
* * *
100719 AAACCGAACCTA
1 AACCCAAACC-G
***
100731 AACCCAAATTA
1 AACCCAAACCG
100742 AACCCAAACCTG
1 AACCCAAACC-G
* *
100754 AACCTAAATCCT
1 AACCCAAA-CCG
*
100766 AACCAAAACCTG
1 AACCCAAACC-G
100778 AACCCAAACC
1 AACCCAAACC
100788 CTAACCAGAA
Statistics
Matches: 60, Mismatches: 16, Indels: 7
0.72 0.19 0.08
Matches are distributed among these distances:
11 29 0.48
12 29 0.48
13 2 0.03
ACGTcount: A:0.47, C:0.40, G:0.04, T:0.09
Consensus pattern (11 bp):
AACCCAAACCG
Found at i:100822 original size:93 final size:91
Alignment explanation
Indices: 100584--100808 Score: 222
Period size: 93 Copynumber: 2.4 Consensus size: 91
100574 CCCCTAACTT
* * * ** * * *
100584 AAACCCAAACCCAAACCCAAACCCTAATCGAACATAAATCCAAACCGAACCGAAATCC-AATCCG
1 AAACCCCAACCCAAACCCAAACCCAAACCGAACCCAAA--CAAACCGAACCTAAACCCAAAT--T
100648 AAACCCAAACCCAAACCTAAATCCTAAACC
62 AAACCCAAACCCAAACCTAAATCCTAAACC
*
100678 AAACCCCAACCTAAACCCAAACCCAAACCGAACCCAAACCCAAACCGAACCTAAACCCAAATTAA
1 AAACCCCAACCCAAACCCAAACCCAAACCGAACCCAAA--CAAACCGAACCTAAACCCAAATTAA
**
100743 ACCCAAACCTGAACCTAAATCCT-AACC
64 ACCCAAACCCAAACCTAAATCCTAAACC
** * *
100770 AAAACCTGAACCCAAACCCTAA-CCAGAATCGAACCCAAA
1 -AAACCCCAACCCAAACCCAAACCCA-AACCGAACCCAAA
100809 AATATTCGAA
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
92 7 0.06
93 52 0.47
94 49 0.44
95 3 0.03
ACGTcount: A:0.48, C:0.39, G:0.04, T:0.09
Consensus pattern (91 bp):
AAACCCCAACCCAAACCCAAACCCAAACCGAACCCAAACAAACCGAACCTAAACCCAAATTAAAC
CCAAACCCAAACCTAAATCCTAAACC
Found at i:101036 original size:2 final size:2
Alignment explanation
Indices: 101029--101069 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
101019 GATATGCTTG
101029 AT AT AT AT AT AT AT AT AT AT -T 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
101070 TGGTTTATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:101162 original size:31 final size:31
Alignment explanation
Indices: 101124--101484 Score: 484
Period size: 31 Copynumber: 11.8 Consensus size: 31
101114 TGTGTTGAAA
**
101124 TACTGGTTTATTACTGTTGATGTAAATGATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
*
101155 TACTGGTTTATTGTTGTTGATGT--ATGATA
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
*
101184 TACTGG-TTATT-ATG-TGATGTAAATGATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
* **
101212 TATTGGTTTATTACTGTTGATGTAAATGATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
101243 TACTGGTTTATTGTTGTTGATGTAAATGATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
* * *
101274 TACTGGTTTACTGCTGTTGATATAAATGATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
* *
101305 TATTGGTTTATTGTTGTTGATGTAAATAATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
*
101336 TACTGGTTTATTGTTGTTGATGTAAATGATA
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
101367 TACTGGTTTATTGTTGTTGATGTAAATGATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
* ** *
101398 TAATGGTTTATTGCCGTTAATGTAAATGATG
1 TACTGGTTTATTGTTGTTGATGTAAATGATG
* *
101429 TACTAGTTTATAT-TTGTTGATGTAAATGATA
1 TACTGGTTTAT-TGTTGTTGATGTAAATGATG
*
101460 TACTGGTTTATTGTTG-TAATGTAAA
1 TACTGGTTTATTGTTGTTGATGTAAA
101485 CTAACCATGA
Statistics
Matches: 289, Mismatches: 34, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
26 6 0.02
27 2 0.01
28 15 0.05
29 16 0.06
30 11 0.04
31 238 0.82
32 1 0.00
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (31 bp):
TACTGGTTTATTGTTGTTGATGTAAATGATG
Found at i:101174 original size:88 final size:87
Alignment explanation
Indices: 101070--101458 Score: 294
Period size: 93 Copynumber: 4.3 Consensus size: 87
101060 ATATATATAT
* * *
101070 TGGTTTATTGCTGTTGATGTAAATGATGTTATTGCTGTTGATAT-TGTGTTGAAATACTGGTTTA
1 TGGTTTATTGTTGTTGATGTAAATGATGTTACTGCTGTTGATATATGTGTTG--ATATTGGTTTA
101134 TTACTGTTGATGTAAATGATGTAC
64 TTACTGTTGATGTAAATGATGTAC
* *
101158 TGGTTTATTGTTGTTGATGT--ATGAT-ATACTG--GTT-ATTATGTGATGTAAATGATGTATTG
1 TGGTTTATTGTTGTTGATGTAAATGATGTTACTGCTGTTGA-TATATG-TGT---TGA--TATTG
101217 GTTTATTACTGTTGATGTAAATGATGTAC
59 GTTTATTACTGTTGATGTAAATGATGTAC
** *
101246 TGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTACTGCTGTTGATATAAATGATG-TATTG
1 TGGTTTATTGTTGTTGATGT-AA--ATG-A-T-G-TTACTGCTGTTGATATATGTGTTGATATTG
** *
101310 GTTTATTGTTGTTGATGTAAATAATGTAC
59 GTTTATTACTGTTGATGTAAATGATGTAC
* * * ** * *
101339 TGGTTTATTGTTGTTGATGTAAATGATATACTGGTTTATTGTTGTTGATGTAAATGATG-TAATG
1 TGGTTTATTGTTGTTGATGTAAATG----A-T-G-TTACTGCTGTTGATATATGTGTTGATATTG
* * *
101403 GTTTATTGCCGTTAATGTAAATGATGTAC
59 GTTTATTACTGTTGATGTAAATGATGTAC
*
101432 TAGTTTATAT-TTGTTGATGTAAATGAT
1 TGGTTTAT-TGTTGTTGATGTAAATGAT
101459 ATACTGGTTT
Statistics
Matches: 255, Mismatches: 21, Indels: 50
0.78 0.06 0.15
Matches are distributed among these distances:
82 1 0.00
83 6 0.02
84 2 0.01
85 7 0.03
86 6 0.02
88 75 0.29
89 1 0.00
90 3 0.01
92 2 0.01
93 133 0.52
94 2 0.01
95 1 0.00
96 2 0.01
98 5 0.02
99 2 0.01
100 6 0.02
101 1 0.00
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.47
Consensus pattern (87 bp):
TGGTTTATTGTTGTTGATGTAAATGATGTTACTGCTGTTGATATATGTGTTGATATTGGTTTATT
ACTGTTGATGTAAATGATGTAC
Done.