Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011528.1 Kokia drynarioides strain JFW-HI SEQ_126514, 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: 54389
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:1767 original size:116 final size:116
Alignment explanation
Indices: 1564--1777 Score: 259
Period size: 116 Copynumber: 1.8 Consensus size: 116
1554 ATCCAGGGAA
* * * * * * * *
1564 GTATCAATAGAAGTACAGGGTAGGAGAGAGATTGTTCTCTGATTTGGGTTGTATCGGTAGTTGAA
1 GTATCAATAGAAGTACAGGGTAAGAGAGAGATTGATATCTGACTTAGGTTGTACCGCTAGATGAA
* * * *
1629 TAGCAAGTGTCAGTAGTTATGTAATTAGAAATATCGGTATTTTGCATGTTT
66 TACCAAGTATCAATAGTCATGTAATTAGAAATATCGGTATTTTGCATGTTT
* * *
1680 GTATCGATAGAAGTATAGGGTAAGAGAGAGGTTGCATAT-TGACTTAGGTTGTACCGCTAGATGA
1 GTATCAATAGAAGTACAGGGTAAGAGAGAGATTG-ATATCTGACTTAGGTTGTACCGCTAGATGA
* *
1744 ATACCCAGTATCAATAGTCATGTATTTAGAAATA
65 ATACCAAGTATCAATAGTCATGTAATTAGAAATA
1778 CTGGTAGTTC
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
116 78 0.98
117 2 0.03
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.33
Consensus pattern (116 bp):
GTATCAATAGAAGTACAGGGTAAGAGAGAGATTGATATCTGACTTAGGTTGTACCGCTAGATGAA
TACCAAGTATCAATAGTCATGTAATTAGAAATATCGGTATTTTGCATGTTT
Found at i:7075 original size:21 final size:20
Alignment explanation
Indices: 7051--7108 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
7041 TAGAGGTGAA
*
7051 ACTTGTATCGATAGAAGAGTC
1 ACTTGTATCGGTAGAAGA-TC
**
7072 ACTTGTATCGGTAGGACTATC
1 ACTTGTATCGGTA-GAAGATC
7093 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
7109 ATCTGTGCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.06
21 27 0.84
22 3 0.09
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (20 bp):
ACTTGTATCGGTAGAAGATC
Found at i:16187 original size:144 final size:144
Alignment explanation
Indices: 16005--16432 Score: 721
Period size: 145 Copynumber: 3.0 Consensus size: 144
15995 TATTTGTCAT
16005 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
1 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
*
16070 ATAATAAAAAATAATTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
66 ATAATAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
16135 ATTAGATTAAACAA
131 ATTAGATTAAACAA
* * * *
16149 TCCAGATATGATTTGAATTTGAGTCACGTTAATCACATTTATTATTTGAGCTTTATTTTATTATT
1 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
* *
16214 ATAATAAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATTATTGGGAATGTTTTAAAGGGG
66 ATAAT-AAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGG
*
16279 CATTAGATTAAGCAA
130 CATTAGATTAAACAA
* * *
16294 TCCAGATATGATTTAAATTCGAATCACGTTAATCATATTTATTATTCGAGTTTTATTCTATTATT
1 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
* **
16359 ATAATAAAAAATAACTCTAAAAGATAAAAAAAAAAAATTCATCATTGGGAATGTTTTGAAGGGGC
66 ATAATAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
16424 ATTAGATTA
131 ATTAGATTA
16433 GGCAATTCGA
Statistics
Matches: 263, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
144 130 0.49
145 133 0.51
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (144 bp):
TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
ATAATAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
ATTAGATTAAACAA
Found at i:16295 original size:145 final size:144
Alignment explanation
Indices: 16005--16438 Score: 724
Period size: 144 Copynumber: 3.0 Consensus size: 144
15995 TATTTGTCAT
16005 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
1 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
*
16070 ATAATAAAAAATAATTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
66 ATAATAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
*
16135 ATTAGATTAAACAA
131 ATTAGATTAAGCAA
* * * *
16149 TCCAGATATGATTTGAATTTGAGTCACGTTAATCACATTTATTATTTGAGCTTTATTTTATTATT
1 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
* *
16214 ATAATAAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATTATTGGGAATGTTTTAAAGGGG
66 ATAAT-AAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGG
16279 CATTAGATTAAGCAA
130 CATTAGATTAAGCAA
* * *
16294 TCCAGATATGATTTAAATTCGAATCACGTTAATCATATTTATTATTCGAGTTTTATTCTATTATT
1 TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
* **
16359 ATAATAAAAAATAACTCTAAAAGATAAAAAAAAAAAATTCATCATTGGGAATGTTTTGAAGGGGC
66 ATAATAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
*
16424 ATTAGATTAGGCAA
131 ATTAGATTAAGCAA
16438 T
1 T
16439 TCGAGGGGCC
Statistics
Matches: 268, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
144 135 0.50
145 133 0.50
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (144 bp):
TCCAGATATGATTTGAATTTGAATCACGTTAATCACATTTATTATTCGAGTTTTATTCTATTATT
ATAATAAAAAATAACTCTAAAAGATAAAAAGAAAATTTTCATCATTGGGAATGTTTTGAAGGGGC
ATTAGATTAAGCAA
Found at i:17326 original size:23 final size:23
Alignment explanation
Indices: 17301--17343 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17291 CACGTTAATA
17301 AAAATT-TAAAAAAATAAATATG
1 AAAATTATAAAAAAATAAATATG
* *
17323 AAAATTATCAAAATATAAATA
1 AAAATTATAAAAAAATAAATA
17344 ATACGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATTATAAAAAAATAAATATG
Found at i:17551 original size:15 final size:15
Alignment explanation
Indices: 17531--17560 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17521 TGTAAAATAA
17531 ATTAAATATTAAAAT
1 ATTAAATATTAAAAT
17546 ATTAAATATTAAAAT
1 ATTAAATATTAAAAT
17561 TATTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAAATATTAAAAT
Found at i:17819 original size:16 final size:16
Alignment explanation
Indices: 17787--17816 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17777 TATTTTGAGA
17787 TTAAAAATTATATAAT
1 TTAAAAATTATATAAT
17803 TTAAAAA-TATATAA
1 TTAAAAATTATATAA
17817 ATTACTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAAATTATATAAT
Found at i:24770 original size:24 final size:22
Alignment explanation
Indices: 24743--24791 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
24733 TAATATAACA
24743 TTTTATATTT-GAATTTGATATTTT
1 TTTTA-ATTTAGAATTT--TATTTT
*
24767 TTTTAATTTAGCATTTTATTTT
1 TTTTAATTTAGAATTTTATTTT
24789 TTT
1 TTT
24792 ACTTAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.39
23 4 0.17
24 10 0.43
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTTAATTTAGAATTTTATTTT
Found at i:25096 original size:93 final size:92
Alignment explanation
Indices: 24989--25162 Score: 231
Period size: 93 Copynumber: 1.9 Consensus size: 92
24979 TTAAAAAATG
* * * * *
24989 TTAGGTATCAAATTAGGAAAAAAATGAAGTTCAAGTACCAAATTGGACCCCAAAAAGTTTAAATA
1 TTAGATATCAAATTAGGAAAAAAATCAAGTTCAAGTACCAAATTGAACCCAAAAAAATTTAAATA
25054 TCAAACTTAAAAAAAAAAAGTGTCAAGT
66 TCAAA-TTAAAAAAAAAAAGTGTCAAGT
*** ** *
25082 TTAGATATCAAATTAGGAAAACTGTCAAGTTTTAGTATCAAATTGAACCCAAAAAAATTTAAATA
1 TTAGATATCAAATTAGGAAAAAAATCAAGTTCAAGTACCAAATTGAACCCAAAAAAATTTAAATA
*
25147 TCAAATTAAGAAAAAA
66 TCAAATTAAAAAAAAA
25163 TATCAAGTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
92 10 0.14
93 59 0.86
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (92 bp):
TTAGATATCAAATTAGGAAAAAAATCAAGTTCAAGTACCAAATTGAACCCAAAAAAATTTAAATA
TCAAATTAAAAAAAAAAAGTGTCAAGT
Found at i:25110 original size:30 final size:30
Alignment explanation
Indices: 25069--25125 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
25059 CTTAAAAAAA
*
25069 AAAAGTGTCAAG-TTTAGATATCAAATTAGG
1 AAAACTGTCAAGTTTTAG-TATCAAATTAGG
25099 AAAACTGTCAAGTTTTAGTATCAAATT
1 AAAACTGTCAAGTTTTAGTATCAAATT
25126 GAACCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (30 bp):
AAAACTGTCAAGTTTTAGTATCAAATTAGG
Found at i:26461 original size:18 final size:19
Alignment explanation
Indices: 26426--26463 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
26416 TAATGGAAAA
26426 ATAATAAAAATAAATTAAT
1 ATAATAAAAATAAATTAAT
*
26445 ATAATAAACAT-AATTAAT
1 ATAATAAAAATAAATTAAT
26463 A
1 A
26464 ACACAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAAAAATAAATTAAT
Found at i:26703 original size:18 final size:17
Alignment explanation
Indices: 26639--26776 Score: 72
Period size: 18 Copynumber: 7.9 Consensus size: 17
26629 TATGACATAC
*
26639 AAATAAATAACAAATCAAT
1 AAATAAATAAAAAAT--AT
*
26658 GAATAAAT--AAAAT-T
1 AAATAAATAAAAAATAT
**
26672 AAATGAAAGCAAAAATAT
1 AAAT-AAATAAAAAATAT
*
26690 AAATAACATAAAAAATAAC
1 AAATAA-ATAAAAAAT-AT
* *
26709 AAATAAATAAAATACAT
1 AAATAAATAAAAAATAT
26726 AAA-ACAATAAATAAA-ATT
1 AAATA-AATAAA-AAATA-T
* *
26744 AAATAAAAGAAAAAATGT
1 AAAT-AAATAAAAAATAT
26762 AAAT-AATAAAAAATA
1 AAATAAATAAAAAATA
26777 AAAACCAATA
Statistics
Matches: 92, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
14 4 0.04
15 3 0.03
16 10 0.11
17 22 0.24
18 33 0.36
19 19 0.21
20 1 0.01
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:26727 original size:9 final size:9
Alignment explanation
Indices: 26659--26779 Score: 50
Period size: 10 Copynumber: 12.2 Consensus size: 9
26649 CAAATCAATG
26659 AATAAATAA
1 AATAAATAA
26668 AATTAAATGAA
1 AA-TAAAT-AA
*
26679 AGCAAAAATATA
1 A--ATAAATA-A
26691 AATAACAT-A
1 AATAA-ATAA
26700 AA-AAATAACA
1 AATAAAT-A-A
26710 AATAAATAA
1 AATAAATAA
*
26719 AATACATAAAA
1 AATA-A-ATAA
26730 CAATAAATAA
1 -AATAAATAA
26740 AATTAAATAA
1 AA-TAAATAA
*
26750 AAGAAA-AA
1 AATAAATAA
*
26758 ATGTAAATAA
1 A-ATAAATAA
*
26768 TAAAAAATAA
1 -AATAAATAA
26778 AA
1 AA
26780 ACCAATAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 34
0.67 0.07 0.26
Matches are distributed among these distances:
7 2 0.02
8 5 0.06
9 20 0.23
10 33 0.38
11 15 0.17
12 10 0.12
13 1 0.01
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (9 bp):
AATAAATAA
Found at i:26736 original size:21 final size:19
Alignment explanation
Indices: 26690--26778 Score: 81
Period size: 21 Copynumber: 4.4 Consensus size: 19
26680 GCAAAAATAT
*
26690 AAATAACATAAAA-AATAAC
1 AAATAA-ATAAAATAATAAA
26709 AAATAAATAAAATACATAAA
1 AAATAAATAAAATA-ATAAA
26729 ACAATAAATAAAATTAAATAAA
1 A-AATAAATAAAA-T-AATAAA
* *
26751 AGAAAAAATGTAAATAATAAA
1 A-AATAAAT-AAAATAATAAA
26772 AAATAAA
1 AAATAAA
26779 AACCAATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
18 6 0.10
19 7 0.12
20 10 0.17
21 18 0.31
22 14 0.24
23 4 0.07
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (19 bp):
AAATAAATAAAATAATAAA
Found at i:26759 original size:22 final size:24
Alignment explanation
Indices: 26662--26751 Score: 71
Period size: 25 Copynumber: 3.8 Consensus size: 24
26652 ATCAATGAAT
* *
26662 AAATAAAATTAAAT-GAAAGCAA-
1 AAATAAAATTAAATAAAAAACAAC
*
26684 AAATATAAA-TAACATAAAAAATAAC
1 AAATA-AAATTAA-ATAAAAAACAAC
* *
26709 AAAT-AAATAAAATACATAAAACAAT
1 AAATAAAATTAAATA-A-AAAACAAC
26734 AAATAAAATTAAATAAAA
1 AAATAAAATTAAATAAAA
26752 GAAAAAATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
22 8 0.15
23 11 0.21
24 10 0.19
25 15 0.28
26 9 0.17
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (24 bp):
AAATAAAATTAAATAAAAAACAAC
Found at i:26922 original size:19 final size:19
Alignment explanation
Indices: 26898--26944 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
26888 AATGACATGA
*
26898 AAATAAATAACAAATAAAT
1 AAATAAATAAAAAATAAAT
* *
26917 AAATAAACAAAAAATCAAT
1 AAATAAATAAAAAATAAAT
26936 AAATTAAAT
1 AAA-TAAAT
26945 GTCAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.21
Consensus pattern (19 bp):
AAATAAATAAAAAATAAAT
Found at i:26938 original size:15 final size:15
Alignment explanation
Indices: 26897--26938 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
26887 AAATGACATG
26897 AAAATAAAT-AACAA
1 AAAATAAATAAACAA
26911 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
26927 AAAATCAATAAA
1 AAAATAAATAAA
26939 TTAAATGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.72
16 6 0.24
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:27542 original size:11 final size:11
Alignment explanation
Indices: 27526--27575 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
27516 ATTGTTAATT
27526 TTTTTTGAAAA
1 TTTTTTGAAAA
27537 TTTTTT-AAAA
1 TTTTTTGAAAA
*
27547 TATTTTTCTAACAA
1 T-TTTTT-GAA-AA
27561 -TTTTTGAAAA
1 TTTTTTGAAAA
27571 TTTTT
1 TTTTT
27576 ACAACTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
10 7 0.21
11 17 0.52
12 5 0.15
13 2 0.06
14 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (11 bp):
TTTTTTGAAAA
Found at i:27652 original size:33 final size:33
Alignment explanation
Indices: 27585--27659 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 33
27575 TACAACTTTT
* *
27585 AATTTTTTAAATAATTGTTTCACTAATTTTTTTG
1 AATTTTTTAAATAATTATTTCACTAA-TTGTTTG
27619 AATTTTTTAATATAATTATTATCACT-A-TGTTTG
1 AATTTTTTAA-ATAATTATT-TCACTAATTGTTTG
27652 AATTTTTT
1 AATTTTTT
27660 TTATTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 13 0.35
34 10 0.27
35 9 0.24
36 5 0.14
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (33 bp):
AATTTTTTAAATAATTATTTCACTAATTGTTTG
Found at i:28921 original size:60 final size:59
Alignment explanation
Indices: 28826--28965 Score: 192
Period size: 60 Copynumber: 2.4 Consensus size: 59
28816 CAAAAAAAAA
* *
28826 TTTTGGTGTTGACCATGCAATAACCAACATTCCCTTTTTTATCTGGTAAAAAATCAATAT
1 TTTTGGTGTTGGCCATGCAATAACCAACATCCCCTTTTTTATCTGGTAAAAAATCAAT-T
* **
28886 TTTTGGTGTTGGCCATTGC-ATGACTGACATCCCCTTTTTTATCTGGTAAAAAATCAATT
1 TTTTGGTGTTGGCCA-TGCAATAACCAACATCCCCTTTTTTATCTGGTAAAAAATCAATT
* *
28945 TTTTTGTGTTGGTCATGCAAT
1 TTTTGGTGTTGGCCATGCAAT
28966 GGTCGACACC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
58 3 0.04
59 16 0.23
60 49 0.69
61 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (59 bp):
TTTTGGTGTTGGCCATGCAATAACCAACATCCCCTTTTTTATCTGGTAAAAAATCAATT
Found at i:29797 original size:17 final size:17
Alignment explanation
Indices: 29777--29831 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
29767 AAAAAATAAT
29777 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
* *
29794 AATTATAA-AT-TA--A
1 AATTAGAATATACAGGA
*
29807 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
29824 AATTAGAA
1 AATTAGAA
29832 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 8 0.28
14 2 0.07
15 2 0.07
16 2 0.07
17 15 0.52
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:29811 original size:30 final size:30
Alignment explanation
Indices: 29777--29874 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 30
29767 AAAAAATAAT
* *
29777 AATTAGAATATACAGGAAATTATAAATTAA
1 AATTAAAATATACAGGAAATTACAAATTAA
*
29807 AATTAAAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTACAAATTAA
* * * *
29837 ATTTAAAATAAAAACGAAATTACAAATTAA
1 AATTAAAATATACAGGAAATTACAAATTAA
*
29867 ATTTAAAA
1 AATTAAAA
29875 AGTAAACGGA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (30 bp):
AATTAAAATATACAGGAAATTACAAATTAA
Found at i:30404 original size:24 final size:24
Alignment explanation
Indices: 30368--30419 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
30358 CGCGGGCTCN
*
30368 CTCGTCAACGGGCTCGTACTCGGG
1 CTCGTCAACGGGCTCATACTCGGG
** *
30392 CTCGTCATTGGGCTCATCCTCGGG
1 CTCGTCAACGGGCTCATACTCGGG
30416 CTCG
1 CTCG
30420 AAATCTGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.35, G:0.31, T:0.25
Consensus pattern (24 bp):
CTCGTCAACGGGCTCATACTCGGG
Found at i:30880 original size:24 final size:24
Alignment explanation
Indices: 30853--30908 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
30843 ACCTCGTCCG
*
30853 CGGGCTCGTCAACGGGCTCGTACT
1 CGGGCTCGTCAACGGGCTCATACT
** *
30877 CGGGCTCGTCATTGGGCTCATCCT
1 CGGGCTCGTCAACGGGCTCATACT
30901 CGGGCTCG
1 CGGGCTCG
30909 AAATCTGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.09, C:0.34, G:0.34, T:0.23
Consensus pattern (24 bp):
CGGGCTCGTCAACGGGCTCATACT
Found at i:30953 original size:489 final size:480
Alignment explanation
Indices: 30327--31299 Score: 1822
Period size: 489 Copynumber: 2.0 Consensus size: 480
30317 TGGTGCTCCA
30327 ACTGGTACTCGGACTGGTAATCGACCTCGTCCGCGGGCTCNCTCGTCAACGGGCTCGTACTCGGG
1 ACTGGTACTCGGACTGGTAATCGACCTCGTCCGCGGG--C-CTCGTCAACGGGCTCGTACTCGGG
30392 CTCGTCATTGGGCTCATCCTCGGGCTCGAAATCTGAACCGGGGATCCAATCACGACGTCCATATG
63 CTCGTCATTGGGCTCATCCTCGGGCTCGAAATCTGAACCGGGGATCCAATCACGACGTCCATATG
30457 CGTTATTCACCAGACCCCATCGGTTGCCTTCCGAAATAAATCTCTTCGGCGTATACTCCTCGGGA
128 CGTTATTCACCAGACCCCATCGGTTGCCTTCCGAAATAAATCTCTTCGGCGTATACTCCTCGGGA
30522 TCAACCACCGGCATCCCGTATGCCATATACCGTTGCTTGTAATATGGAGTAACGGAATAATCCCT
193 TCAACCACCGGCATCCCGTATGCCATATACCGTTGCTTGTAATATGGAGTAACGGAATAATCCCT
30587 GTTACACAAATACAAGGTTGAACACCCATTTGCCCGATCATTCCAAAGCATGATATATGCCTGAA
258 GTTACACAAATACAAGGTTGAACACCCATTTGCCCGATCATTCCAAAGCATGATATATGCCTGAA
30652 GATCATGAGTCCAATTTATTCTGTTTCTACCATGTCCTTTTTTGTCGATCTGGTGGACTTTATCG
323 GATCATGAGTCCAATTTATTCTGTTTCTACCATGTCCTTTTTTGTCGATCTGGTGGACTTTATCG
30717 AGTTGGAAGGAAGGGTTCGGGATATGTTATATAGCATCGAACTGTCGCAAAACCCGATCTCCAGC
388 AGTTGGAAGGAAGGGTTCGGGATATGTTATATAGCATCGAACTGTCGCAAAACCCGATCTCCAGC
30782 GTGCTATTCCATCATATGAAAATTGAAT
453 GTGCTATTCCATCATATGAAAATTGAAT
30810 ANNNNNNNNNNCTGGTACTCGGACTGGTAATCGACCTCGTCCGCGGG-CTCGTCAACGGGCTCGT
1 A----------CTGGTACTCGGACTGGTAATCGACCTCGTCCGCGGGCCTCGTCAACGGGCTCGT
30874 ACTCGGGCTCGTCATTGGGCTCATCCTCGGGCTCGAAATCTGAACCGGGGATCCAATCACGACGT
56 ACTCGGGCTCGTCATTGGGCTCATCCTCGGGCTCGAAATCTGAACCGGGGATCCAATCACGACGT
30939 CCATATGCGTTATTCACCAGACCCCATCGGTTGCCTTCCGAAATAAATCTCTTCGGCGTATACTC
121 CCATATGCGTTATTCACCAGACCCCATCGGTTGCCTTCCGAAATAAATCTCTTCGGCGTATACTC
31004 CTCGGGATCAACCACCGGCATCCCGTATGCCATATACCGTTGCTTGTAATATGGAGTAACGGAAT
186 CTCGGGATCAACCACCGGCATCCCGTATGCCATATACCGTTGCTTGTAATATGGAGTAACGGAAT
31069 AATCCCTGTTACACAAATACAAGGTTGAACACCCATTTGCCCGATCATTCCAAAGCATGATATAT
251 AATCCCTGTTACACAAATACAAGGTTGAACACCCATTTGCCCGATCATTCCAAAGCATGATATAT
31134 GCCTGAAGATCATGAGTCCAATTTATTCTGTTTCTACCATGTCCTTTTTTGTCGATCTGGTGGAC
316 GCCTGAAGATCATGAGTCCAATTTATTCTGTTTCTACCATGTCCTTTTTTGTCGATCTGGTGGAC
31199 TTTATCGAGTTGGAAGGAAGGGTTCGGGATATGTTATATAGCATCGAACTGTCGCAAAACCCGAT
381 TTTATCGAGTTGGAAGGAAGGGTTCGGGATATGTTATATAGCATCGAACTGTCGCAAAACCCGAT
31264 CTCCAGCGTGCTATTCCATCATATGAAAATTGAAT
446 CTCCAGCGTGCTATTCCATCATATGAAAATTGAAT
31299 A
1 A
31300 TCTCCAGCGT
Statistics
Matches: 480, Mismatches: 0, Indels: 14
0.97 0.00 0.03
Matches are distributed among these distances:
483 1 0.00
489 443 0.92
493 36 0.08
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.27
Consensus pattern (480 bp):
ACTGGTACTCGGACTGGTAATCGACCTCGTCCGCGGGCCTCGTCAACGGGCTCGTACTCGGGCTC
GTCATTGGGCTCATCCTCGGGCTCGAAATCTGAACCGGGGATCCAATCACGACGTCCATATGCGT
TATTCACCAGACCCCATCGGTTGCCTTCCGAAATAAATCTCTTCGGCGTATACTCCTCGGGATCA
ACCACCGGCATCCCGTATGCCATATACCGTTGCTTGTAATATGGAGTAACGGAATAATCCCTGTT
ACACAAATACAAGGTTGAACACCCATTTGCCCGATCATTCCAAAGCATGATATATGCCTGAAGAT
CATGAGTCCAATTTATTCTGTTTCTACCATGTCCTTTTTTGTCGATCTGGTGGACTTTATCGAGT
TGGAAGGAAGGGTTCGGGATATGTTATATAGCATCGAACTGTCGCAAAACCCGATCTCCAGCGTG
CTATTCCATCATATGAAAATTGAAT
Found at i:31312 original size:37 final size:37
Alignment explanation
Indices: 31262--31336 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
31252 GCAAAACCCG
31262 ATCTCCAGCGTGCTATTCCATCATATGAAAATTGAAT
1 ATCTCCAGCGTGCTATTCCATCATATGAAAATTGAAT
31299 ATCTCCAGCGTGCTATTCCATCATATGAAAATTGAAT
1 ATCTCCAGCGTGCTATTCCATCATATGAAAATTGAAT
31336 A
1 A
31337 CCGACACATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (37 bp):
ATCTCCAGCGTGCTATTCCATCATATGAAAATTGAAT
Found at i:32699 original size:22 final size:22
Alignment explanation
Indices: 32674--32734 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
32664 AATTGAGGTG
32674 TTGGTGAGCTGGAATTTCGATT
1 TTGGTGAGCTGGAATTTCGATT
*
32696 TTGGTGAGCTGGAACTTCGATT
1 TTGGTGAGCTGGAATTTCGATT
*
32718 TAGGTGAGCTGGAATTT
1 TTGGTGAGCTGGAATTT
32735 GGGTGGTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.38
Consensus pattern (22 bp):
TTGGTGAGCTGGAATTTCGATT
Found at i:32979 original size:86 final size:86
Alignment explanation
Indices: 32827--33042 Score: 339
Period size: 86 Copynumber: 2.5 Consensus size: 86
32817 TAAATTTAAA
*
32827 ATTTGATAAAAATTGAAATATAATAAT-AT-TTTTTAATTTAAATATTAAAATTTAGTAAATAAT
1 ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAATATTAAAATTTAGTAAATAAT
32890 GTATTGTCAAATCAACACATT
66 GTATTGTCAAATCAACACATT
* * *
32911 ATTTGATAAAAATTGTAATATAATAATAATCTTTTTTATTTAAATATT-AAATTTTGATAAATAG
1 ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAATATTAAAATTTAG-TAAATAA
* *
32975 TGTATTGTTAAATCAACGCATT
65 TGTATTGTCAAATCAACACATT
*
32997 ATTTGATATAAATTGAAATATAATAATAATCTTTTTTATTTAAATA
1 ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAATA
33043 ATGTTAAATT
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 26 0.21
85 9 0.07
86 86 0.71
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (86 bp):
ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAATATTAAAATTTAGTAAATAAT
GTATTGTCAAATCAACACATT
Found at i:33072 original size:86 final size:83
Alignment explanation
Indices: 32827--33073 Score: 270
Period size: 86 Copynumber: 2.9 Consensus size: 83
32817 TAAATTTAAA
* * * *
32827 ATTTGATAAAAATTGAAATATAATAAT-AT-TTTTTAATTTAAATATTAAAATTTAGTAAATAAT
1 ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAATATTTAAA-TTATTTAA-AAT
32890 GT-ATTGTCAAATCAACACATT
64 GTAATT-T-AAATCAACACATT
*
32911 ATTTGATAAAAATTGTAATATAATAATAATCTTTTTTATTTAAATA-TTAAATT-TTGATAAATA
1 ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAATATTTAAATTATT--TAAA-A
* *
32974 GTGTATTGTTAAATCAACGCATT
63 -TGTAAT-TTAAATCAACACATT
* *
32997 ATTTGATATAAATTGAAATATAATAATAATCTTTTTTATTTAAATAATGTTAAATTAATTTTAAA
1 ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAAT-AT-TTAAATT-ATTTAAAA
33062 TGTAATTTAAAT
63 TGTAATTTAAAT
33074 TTCAACTTCA
Statistics
Matches: 139, Mismatches: 11, Indels: 24
0.80 0.06 0.14
Matches are distributed among these distances:
83 1 0.01
84 29 0.21
85 9 0.06
86 78 0.56
87 8 0.06
88 2 0.01
89 10 0.07
91 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (83 bp):
ATTTGATAAAAATTGAAATATAATAATAATCTTTTTTATTTAAATATTTAAATTATTTAAAATGT
AATTTAAATCAACACATT
Found at i:36055 original size:2 final size:2
Alignment explanation
Indices: 36048--36074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36038 TACTGACAGT
36048 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 T
36075 CTGGTGCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37135 original size:58 final size:58
Alignment explanation
Indices: 37025--37257 Score: 204
Period size: 58 Copynumber: 3.9 Consensus size: 58
37015 TTTACCGAAT
* * *
37025 AAAAAAGAGGGTGTCAGCCA-TGCAATGGCCAACAC-CAAAATTTCGAA-TTTTTATTTGAC
1 AAAAAAG-GGGTGTCGGCCATTGC-ATGGCCAACACAAAAAAATT--AATTTTTTATTTGAC
* * * * * * *
37084 AAAAAAGGGGTGTCGACCATTGCATGACCAATACAAAAAAATTAATGTTTTACTAGAT
1 AAAAAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAATTAATTTTTTATTTGAC
* * * *
37142 AAAAAAGGAGTGTCGGCGA-TGACATGGCTAACACAAAAAAATTTTGAATTTTTTATCTGAC
1 AAAAAAGGGGTGTCGGCCATTG-CATGGCCAACACAAAAAAA--TT-AATTTTTTATTTGAC
* * *
37203 AAAAAAGGGGTGTCGGCCATAGTATGGCCAACATCAAAAAAATTGATTTTTTATT
1 AAAAAAGGGGTGTCGGCCATTGCATGGCCAACA-CAAAAAAATTAATTTTTTATT
37258 CAGATAAACA
Statistics
Matches: 137, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
57 4 0.03
58 59 0.43
59 25 0.18
60 4 0.03
61 36 0.26
62 9 0.07
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (58 bp):
AAAAAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAATTAATTTTTTATTTGAC
Found at i:39445 original size:20 final size:20
Alignment explanation
Indices: 39409--39447 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39399 ACTTTCTTTA
*
39409 TATATATTTTTAGAATATTT
1 TATATATTTTTAAAATATTT
39429 TATAT-TTTTTAAAAATATT
1 TATATATTTTT-AAAATATT
39448 AATTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATATATTTTTAAAATATTT
Found at i:39856 original size:77 final size:77
Alignment explanation
Indices: 39717--39861 Score: 202
Period size: 77 Copynumber: 1.9 Consensus size: 77
39707 TCGAATCAAG
* * *
39717 TTTTACTCACTCTAATGTAGATTTAACTTACCTCTTACAAATCAAATTGCATTAGAATAAATCCA
1 TTTTACTCACTCTAATGTAAATTTAACTTAACTCTTACAAATCAAATTGCATTAGAACAAATCCA
39782 TTATAAATCGAA
66 TTATAAATCGAA
* * * **
39794 TTTTACTCA-TCCTAATGTAAATTTAACTTAATTCTTACAAATCATATTGGATTAGGGCAAATCC
1 TTTTACTCACT-CTAATGTAAATTTAACTTAACTCTTACAAATCAAATTGCATTAGAACAAATCC
39858 ATTA
65 ATTA
39862 CACTAATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
76 1 0.02
77 58 0.98
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (77 bp):
TTTTACTCACTCTAATGTAAATTTAACTTAACTCTTACAAATCAAATTGCATTAGAACAAATCCA
TTATAAATCGAA
Found at i:40230 original size:32 final size:34
Alignment explanation
Indices: 40147--40240 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 34
40137 TTATTTAAAA
* *
40147 TTTTAAAAA-ATAAAAATAA-AATTATATTTTAAT
1 TTTTAAAAATATAAAAAAAATAATTATAATTT-AT
40180 TTCTTAAAAATA-ATAAAAAAATAATTA-AATTT-T
1 TT-TTAAAAATATA-AAAAAAATAATTATAATTTAT
*
40213 TTTTAAAAATATAAAAAATATAAATTAT
1 TTTTAAAAATATAAAAAAAAT-AATTAT
40241 TAAAAATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
32 16 0.31
33 11 0.22
34 8 0.16
35 11 0.22
36 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
TTTTAAAAATATAAAAAAAATAATTATAATTTAT
Found at i:40795 original size:17 final size:17
Alignment explanation
Indices: 40773--40811 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
40763 TTAAAAATCA
40773 GTTAACCTTTTAAAATT
1 GTTAACCTTTTAAAATT
40790 GTTAACCTTTTAAAATT
1 GTTAACCTTTTAAAATT
*
40807 ATTAA
1 GTTAA
40812 AAATCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (17 bp):
GTTAACCTTTTAAAATT
Found at i:42194 original size:12 final size:12
Alignment explanation
Indices: 42164--42202 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42154 TCAGCCTCAG
42164 CTGCTTCACCTT
1 CTGCTTCACCTT
**
42176 CACCTTCACCTT
1 CTGCTTCACCTT
*
42188 CTGCTTCCCCTT
1 CTGCTTCACCTT
42200 CTG
1 CTG
42203 GTTCTGGCTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.08, C:0.46, G:0.08, T:0.38
Consensus pattern (12 bp):
CTGCTTCACCTT
Found at i:42449 original size:4 final size:4
Alignment explanation
Indices: 42442--42475 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
42432 CACATGCATG
42442 CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
42476 ATAGACATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:45710 original size:102 final size:102
Alignment explanation
Indices: 45533--45792 Score: 340
Period size: 102 Copynumber: 2.5 Consensus size: 102
45523 ATGGCCCCCG
* * * * *
45533 GTGCCTAGCGGATATACCGTGGTATGTGAGCCCAGCCCTAGTTGGATTATCCAACGATTTGCGCC
1 GTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTAGTTGGATTAACCAACGATTTGCGCC
* * *
45598 CAGCGTTAGTCGGATAAACCAACGGTTATAGCACCCA
66 CAGCGCTAGTCAGATAAACCAACAGTTATAGCACCCA
* * *
45635 GTGCCTAGCGGATAAACTGCGATATGTGAGCCCAGCTCTGGTTGGATTAACCAACGGTTTGCGCC
1 GTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTAGTTGGATTAACCAACGATTTGCGCC
* ** *
45700 CAGTGCTAGTCAGATAAACTGACAGTTATGGCACCCA
66 CAGCGCTAGTCAGATAAACCAACAGTTATAGCACCCA
* * * * *
45737 ATACCTAGCGGATAAACCGCAATATGTGAACCCATCTCTAGTTGGATTAACCAACG
1 GTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTAGTTGGATTAACCAACG
45793 TTTTTCTAGT
Statistics
Matches: 136, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 136 1.00
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (102 bp):
GTGCCTAGCGGATAAACCGCGATATGTGAGCCCAGCTCTAGTTGGATTAACCAACGATTTGCGCC
CAGCGCTAGTCAGATAAACCAACAGTTATAGCACCCA
Found at i:45805 original size:24 final size:24
Alignment explanation
Indices: 45773--45820 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
45763 TGAACCCATC
45773 TCTAGTTGGATTAACCAACGTTTT
1 TCTAGTTGGATTAACCAACGTTTT
45797 TCTAGTTGGATTAACCAACGTTTT
1 TCTAGTTGGATTAACCAACGTTTT
45821 GAGACCAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (24 bp):
TCTAGTTGGATTAACCAACGTTTT
Found at i:46326 original size:27 final size:27
Alignment explanation
Indices: 46259--46317 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
46249 ATCCTTTGTA
46259 TTCAACTCATTTCAACAATCCAAAATG
1 TTCAACTCATTTCAACAATCCAAAATG
46286 TTCAACTCATTTCAACAATCCAAAATG
1 TTCAACTCATTTCAACAATCCAAAATG
46313 TTCAA
1 TTCAA
46318 TATAATTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.25, G:0.03, T:0.31
Consensus pattern (27 bp):
TTCAACTCATTTCAACAATCCAAAATG
Found at i:46514 original size:132 final size:132
Alignment explanation
Indices: 46286--46615 Score: 554
Period size: 132 Copynumber: 2.5 Consensus size: 132
46276 ATCCAAAATG
* *
46286 TTCAACTCATTTCAACAATCCAAAATGTTCAATATAATTCACATGGCAAAAATCATTTATTTATT
1 TTCAACTCATTTCAACAATCCAAAATGTTCAATATAATTCACATAGCAAAAAGCATTTATTTATT
*
46351 CATTTCCAGCCACCAAATATGCATATCAATATATATA-ATAATTCAAATATTTCATTAATCCTTT
66 TATTTCCAGCCACCAAATATGCATATCAATATATATACA-AATTCAAATATTTCATTAATCCTTT
46415 GTA
130 GTA
* *
46418 TTCAACTCATTTCAACAATCCAAAATGTTCAATACAATTCACATAACAAAAAGCATTTATTTATT
1 TTCAACTCATTTCAACAATCCAAAATGTTCAATATAATTCACATAGCAAAAAGCATTTATTTATT
* * * *
46483 TATTTCCAGCTACCAAATATGTATATTAATATATATACAAATTCAAATATTTCATTAATTCTTTG
66 TATTTCCAGCCACCAAATATGCATATCAATATATATACAAATTCAAATATTTCATTAATCCTTTG
46548 TA
131 TA
*
46550 TTCAACTCATTTCAACAATCCAAAATGTTCAACATAATTCACATAGCAAAAAGCATTTATTTATT
1 TTCAACTCATTTCAACAATCCAAAATGTTCAATATAATTCACATAGCAAAAAGCATTTATTTATT
46615 T
66 T
46616 TTCTTAATGG
Statistics
Matches: 185, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 184 0.99
133 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (132 bp):
TTCAACTCATTTCAACAATCCAAAATGTTCAATATAATTCACATAGCAAAAAGCATTTATTTATT
TATTTCCAGCCACCAAATATGCATATCAATATATATACAAATTCAAATATTTCATTAATCCTTTG
TA
Found at i:53562 original size:102 final size:102
Alignment explanation
Indices: 53418--53719 Score: 388
Period size: 102 Copynumber: 3.0 Consensus size: 102
53408 TCTACCGTGG
* * ** * * * * **
53418 TATGTGAGCCTAGCTCTAATTGGATTATCCAACAATTTGCGCCCAACGTTAGTCGGATAAACCAA
1 TATGTAAGCCCAGCTCTGGTTGGATTAACCAACAGTTTGCGCCCAACGCTAGTCAGATAAACTGA
53483 CGGTTATGGCACCCAGTGCCTAGCGGATAAACCACGA
66 CGGTTATGGCACCCAGTGCCTAGCGGATAAACCACGA
* * * * *
53520 TATGTGAGCCCAGCTTTGGTTGGATTAACTAACGGTTTGCGCCCAGCGCTAGTCAGATAAACTGA
1 TATGTAAGCCCAGCTCTGGTTGGATTAACCAACAGTTTGCGCCCAACGCTAGTCAGATAAACTGA
* * * **
53585 CAGTTATGACACCCAATGCCTAGCGGATAAACTGCGA
66 CGGTTATGGCACCCAGTGCCTAGCGGATAAACCACGA
* * * *
53622 TATGTAAGCCCAGCTCTGGTTGGATTAACCAACATTTTGCGCGCAATGCTAGTTAGATAAACTGA
1 TATGTAAGCCCAGCTCTGGTTGGATTAACCAACAGTTTGCGCCCAACGCTAGTCAGATAAACTGA
53687 CGGTTATGGCACCCAGTGCCTAGCGGATAAACC
66 CGGTTATGGCACCCAGTGCCTAGCGGATAAACC
53720 GTGAGAGTGA
Statistics
Matches: 169, Mismatches: 31, Indels: 0
0.85 0.16 0.00
Matches are distributed among these distances:
102 169 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (102 bp):
TATGTAAGCCCAGCTCTGGTTGGATTAACCAACAGTTTGCGCCCAACGCTAGTCAGATAAACTGA
CGGTTATGGCACCCAGTGCCTAGCGGATAAACCACGA
Found at i:54297 original size:132 final size:133
Alignment explanation
Indices: 54060--54389 Score: 518
Period size: 136 Copynumber: 2.5 Consensus size: 133
54050 TTGCTCTCTC
*
54060 TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCTAAAATG
1 TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAATG
* *
54125 GTCAATATAATTCACATGGCAAAAAGC-ATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
66 GTCAATATAATTCACATAGCAAAAAACTATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
54189 CAA
131 CAA
* *
54192 TATATATAACGATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAGCAATCCAAAATG
1 TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAATG
* * **
54257 TTGAATATAATTCACATAGCAAAAAACATTTATTTATTTATTTATTTTTAGCCACCAAATATGCA
66 GTCAATATAATTCACATAGCAAAAAAC---TATTTATTTATTTATTTCCAGCCACCAAATATGCA
*
54322 TATTAA
128 TATCAA
* *
54328 TATATATAAAAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAA
1 TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAA
Statistics
Matches: 180, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
132 85 0.47
136 95 0.53
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (133 bp):
TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAATG
GTCAATATAATTCACATAGCAAAAAACTATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
CAA
Done.