Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009382.1 Kokia drynarioides strain JFW-HI SEQ_124089, 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: 35114
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:641 original size:29 final size:28
Alignment explanation
Indices: 593--1202 Score: 449
Period size: 29 Copynumber: 20.9 Consensus size: 28
583 GTCCCTAAAC
*
593 CTTCCAAAAGTTACCATTTTACCCCCGAA
1 CTTCCAAAA-ATACCATTTTACCCCCGAA
* *
622 CTTCCAAAAATCCCATTTTTGA-CTCCGAA
1 CTTCCAAAAATACCA-TTTT-ACCCCCGAA
651 TCTTCCAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAA-TACCATTTTACCCCCGAA
* *
681 CTTCCAAAAATCCCATTTTTAGCCCCGAA
1 CTTCCAAAAATACCA-TTTTACCCCCGAA
*
710 CCTTCTAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAA-TACCATTTTACCCCCGAA
* **
740 CTTCCAAAAATTCCATTTTTGGCCCCGAA
1 CTTCCAAAAATACCA-TTTTACCCCCGAA
*
769 CCTTCCAAAAATTACCATTTTACCCCCG-N
1 -CTTCCAAAAA-TACCATTTTACCCCCGAA
***** **
798 NNNNNAAAAAT-CTCATTTTTGGCCCCGAA
1 CTTCCAAAAATAC-CA-TTTTACCCCCGAA
827 CCTTCCAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAA-TACCATTTTACCCCCGAA
* * *
857 CTTCCAAAAATCCCATTTTAGCCCCAAA
1 CTTCCAAAAATACCATTTTACCCCCGAA
*
885 CCTTCCAAAAATTACCATTTTACCCCCAAA
1 -CTTCCAAAAA-TACCATTTTACCCCCGAA
* * * *
915 CTCCCAAAAATCCCATTTTTAGCCCCAAA
1 CTTCCAAAAATACCA-TTTTACCCCCGAA
* *
944 CTTTCAAAATTACCATTTTACCCCCGAA
1 CTTCCAAAAATACCATTTTACCCCCGAA
* * * * * *
972 CTTCTAGAAATCCCATTTTTAACCACTAA
1 CTTCCAAAAATACCA-TTTTACCCCCGAA
1001 CTTTCCAAAAATTACCATTTTACCCCCGAA
1 C-TTCCAAAAA-TACCATTTTACCCCCGAA
1031 CTTCCAAAAAT-CACATTTTTGA-CCCCGAA
1 CTTCCAAAAATAC-CA-TTTT-ACCCCCGAA
*
1060 TCTTCCAAAAATTACCATTTTACCCCTGAA
1 -CTTCCAAAAA-TACCATTTTACCCCCGAA
* * **** *
1090 CTTCCAGAAATTCCATTTTTGATCAGAA
1 CTTCCAAAAATACCATTTTACCCCCGAA
* * * *
1118 CCTTTCGAAAATTACCATTTTACCCTCAAA
1 -C-TTCCAAAAATACCATTTTACCCCCGAA
* **
1148 CTTCCAAAAATCCCATTTTTGA-TTCCGAA
1 CTTCCAAAAATACCA-TTTT-ACCCCCGAA
* *
1177 CCTTCCAAAACTACCATTTTGCCCCC
1 -CTTCCAAAAATACCATTTTACCCCC
1203 CCGTGCATCC
Statistics
Matches: 453, Mismatches: 92, Indels: 72
0.73 0.15 0.12
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 92 0.20
29 170 0.38
30 162 0.36
31 22 0.05
32 2 0.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.30
Consensus pattern (28 bp):
CTTCCAAAAATACCATTTTACCCCCGAA
Found at i:685 original size:59 final size:59
Alignment explanation
Indices: 590--1202 Score: 783
Period size: 59 Copynumber: 10.5 Consensus size: 59
580 GAGGTCCCTA
* *
590 AACCTTCCAAAAGTTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
649 AATCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-AGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCCG
* * *
708 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
****** * *
767 AACCTTCCAAAAATTACCATTTTACCCCCG-NNNNNNAAAAATCTCATTTTTGGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
825 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTAG-CCCCA
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
883 AACCTTCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCATTTTT-AGCCCC-
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCCG
* * * * * * *
941 AAACTTTC-AAAATTACCATTTTACCCCCGAACTTCTAGAAATCCCATTTTTAACCACT
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
999 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCACATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * *
1058 AATCTTCCAAAAATTACCATTTTACCCCTGAACTTCCAGAAATTCCATTTTTGA-TCAG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * **
1116 AACCTTTCGAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGATTCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
1175 AACCTTCC-AAAACTACCATTTTGCCCCC
1 AACCTTCCAAAAATTACCATTTTACCCCC
1203 CCGTGCATCC
Statistics
Matches: 480, Mismatches: 65, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
57 42 0.09
58 181 0.38
59 257 0.54
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.29
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:3935 original size:72 final size:72
Alignment explanation
Indices: 3818--3951 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
3808 GGATATCATG
* * *
3818 ATCGATGGCTTGAGATCCATCATGTGTTGTGAATTCTCTGAAGCTTGTGTGAGCAGCATCGAATC
1 ATCGATGGCTTGAGATCCAGCATGAGATGTGAATTCTCTGAAGCTTGTGTGAGCAGCATCGAATC
3883 ATTGATT
66 ATTGATT
* * *
3890 ATCGATGGCTTGAGATCTAGCACT-AGATGTGAATTTTTTGAAGCTTGTGTGAGCAGCATCGA
1 ATCGATGGCTTGAGATCCAGCA-TGAGATGTGAATTCTCTGAAGCTTGTGTGAGCAGCATCGA
3952 GTAAAGCTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 54 0.98
73 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (72 bp):
ATCGATGGCTTGAGATCCAGCATGAGATGTGAATTCTCTGAAGCTTGTGTGAGCAGCATCGAATC
ATTGATT
Found at i:6014 original size:11 final size:10
Alignment explanation
Indices: 5981--6083 Score: 67
Period size: 9 Copynumber: 10.6 Consensus size: 10
5971 TTATTTTTGC
5981 AATTTTT-AT
1 AATTTTTAAT
*
5990 AATTTAT-AT
1 AATTTTTAAT
5999 AATTTTTAAGT
1 AATTTTTAA-T
* *
6010 CATTTGTAAT
1 AATTTTTAAT
6020 AATTTTT-AT
1 AATTTTTAAT
6029 AATTTGTATAAT
1 AATTT-T-TAAT
*
6041 -ATTTTTTAT
1 AATTTTTAAT
6050 AATTTTTTAA-
1 AA-TTTTTAAT
*
6060 ATTTTTTAA-
1 AATTTTTAAT
*
6069 ATTTTTTAA-
1 AATTTTTAAT
6078 AATTTT
1 AATTTT
6084 AACATTTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
9 45 0.58
10 11 0.14
11 19 0.25
12 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:6040 original size:21 final size:21
Alignment explanation
Indices: 5981--6054 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
5971 TTATTTTTGC
5981 AATTTTTATAA-TT-TAT-AT
1 AATTTTTATAATTTGTATAAT
*
5999 AATTTTTAAGTCATTTG--TAAT
1 AATTTTT-A-TAATTTGTATAAT
6020 AATTTTTATAATTTGTATAAT
1 AATTTTTATAATTTGTATAAT
*
6041 ATTTTTTATAATTT
1 AATTTTTATAATTT
6055 TTTAAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 7 0.15
19 7 0.15
20 4 0.09
21 28 0.61
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (21 bp):
AATTTTTATAATTTGTATAAT
Found at i:6052 original size:30 final size:28
Alignment explanation
Indices: 5983--6083 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 28
5973 ATTTTTGCAA
*
5983 TTTTTATAATTTATATAATTTTTAAGTCAT
1 TTTTTATAATTTTTATAATTTTTAA-T-AT
* *
6013 TTGTAATAATTTTTATAATTTGTATAATAT
1 TTTTTATAATTTTTATAATTT-T-TAATAT
6043 TTTTTATAATTTTT-TAAATTTTTTAA-AT
1 TTTTTATAATTTTTAT-AA-TTTTTAATAT
*
6071 TTTTTAAAATTTT
1 TTTTTATAATTTT
6084 AACATTTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
28 14 0.23
29 4 0.07
30 35 0.57
31 5 0.08
32 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTTATAATTTTTATAATTTTTAATAT
Found at i:6063 original size:19 final size:19
Alignment explanation
Indices: 6022--6083 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
6012 TTTGTAATAA
*
6022 TTTTTATAATTTGTATAATAT
1 TTTTTATAATTT-TTTAA-AT
6043 TTTTTATAATTTTTTAAAT
1 TTTTTATAATTTTTTAAAT
6062 TTTTTA-AATTTTTTAAAAT
1 TTTTTATAATTTTTT-AAAT
6081 TTT
1 TTT
6084 AACATTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 8 0.21
19 15 0.38
20 4 0.10
21 12 0.31
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTATAATTTTTTAAAT
Found at i:6075 original size:9 final size:9
Alignment explanation
Indices: 6022--6083 Score: 70
Period size: 10 Copynumber: 6.3 Consensus size: 9
6012 TTTGTAATAA
6022 TTTTTATAAT
1 TTTTTA-AAT
*
6032 TTGTATAATAT
1 TT-TTTAA-AT
6043 TTTTTATAAT
1 TTTTTA-AAT
6053 TTTTTAAAT
1 TTTTTAAAT
6062 TTTTTAAAT
1 TTTTTAAAT
6071 TTTTTAAAAT
1 TTTTT-AAAT
6081 TTT
1 TTT
6084 AACATTTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
9 17 0.37
10 21 0.46
11 8 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:6090 original size:18 final size:18
Alignment explanation
Indices: 6044--6091 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
6034 GTATAATATT
*
6044 TTTTATAATTTTTTAAATT
1 TTTTA-AATTTTTTAAATA
6063 TTTTAAATTTTTTAAA-A
1 TTTTAAATTTTTTAAATA
6080 TTTTAACATTTT
1 TTTTAA-ATTTT
6092 AACAATTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAAATTTTTTAAATA
Found at i:7020 original size:29 final size:29
Alignment explanation
Indices: 6988--7135 Score: 100
Period size: 30 Copynumber: 5.0 Consensus size: 29
6978 TAAGGAAAAA
*
6988 TGGGGTTAAAAATGAAATTTTGGAAAGTT
1 TGGGGTTAAAAATGAATTTTTGGAAAGTT
** ** * * *
7017 TGGGGGCCAAATTTGATTTTTTAGAAAGTG
1 T-GGGGTTAAAAATGAATTTTTGGAAAGTT
* * *
7047 TGGGGGT-CAAATCCAAATTTTTGGAAAGTT
1 TGGGGTTAAAAAT--GAATTTTTGGAAAGTT
* * * *
7077 TAGGGTCAAATATGAATTTTTAGAAAGTT
1 TGGGGTTAAAAATGAATTTTTGGAAAGTT
* *
7106 TAGGGGTTAAAACTTAATTTTTGGAAAGTT
1 T-GGGGTTAAAAATGAATTTTTGGAAAGTT
7136 CAAGGGAAAA
Statistics
Matches: 84, Mismatches: 30, Indels: 9
0.68 0.24 0.07
Matches are distributed among these distances:
28 2 0.02
29 20 0.24
30 59 0.70
31 3 0.04
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
TGGGGTTAAAAATGAATTTTTGGAAAGTT
Found at i:7068 original size:30 final size:29
Alignment explanation
Indices: 7034--7110 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
7024 CAAATTTGAT
* *
7034 TTTTTAGAAAGTGTGGGGGTCAAATCCAAA
1 TTTTTAGAAAGT-TGAGGGTCAAATACAAA
* * **
7064 TTTTTGGAAAGTTTAGGGTCAAATATGAA
1 TTTTTAGAAAGTTGAGGGTCAAATACAAA
*
7093 TTTTTAGAAAGTTTAGGG
1 TTTTTAGAAAGTTGAGGG
7111 GTTAAAACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 29 0.73
30 11 0.28
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTTTAGAAAGTTGAGGGTCAAATACAAA
Found at i:7112 original size:59 final size:60
Alignment explanation
Indices: 7005--7135 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 60
6995 AAAAATGAAA
* * * * *
7005 TTTTGGAAAGTTTGGGGGCCAAATTTGATTTTTTAGAAAGTGTGGGGGTCAAATCCAAAT
1 TTTTGGAAAGTTTGAGGGCCAAATATGAATTTTTAGAAAGTGTAGGGGTCAAAACCAAAT
* * * **
7065 TTTTGGAAAGTTT-AGGGTCAAATATGAATTTTTAGAAAGTTTAGGGGTTAAAACTTAAT
1 TTTTGGAAAGTTTGAGGGCCAAATATGAATTTTTAGAAAGTGTAGGGGTCAAAACCAAAT
7124 TTTTGGAAAGTT
1 TTTTGGAAAGTT
7136 CAAGGGAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 48 0.79
60 13 0.21
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.38
Consensus pattern (60 bp):
TTTTGGAAAGTTTGAGGGCCAAATATGAATTTTTAGAAAGTGTAGGGGTCAAAACCAAAT
Found at i:7127 original size:30 final size:30
Alignment explanation
Indices: 7034--7208 Score: 95
Period size: 30 Copynumber: 5.9 Consensus size: 30
7024 CAAATTTGAT
* * * * **
7034 TTTTTAGAAAGTGTGGGGGTCAAATCCAAA
1 TTTTTAGAAAGTTTAGGGGTTAAAACTTAA
* * *
7064 TTTTTGGAAAGTTTA-GGGTCAAATA-TGAA
1 TTTTTAGAAAGTTTAGGGGTTAAA-ACTTAA
7093 TTTTTAGAAAGTTTAGGGGTTAAAACTTAA
1 TTTTTAGAAAGTTTAGGGGTTAAAACTTAA
* * * ** * *
7123 TTTTTGGAAAGTTCAAGGGAAAAAATTTATT
1 TTTTTAGAAAGTTTAGGGGTTAAAACTTA-A
* * * *
7154 TTTTTAAAAAATTT-GGGGGTAAAACATAA
1 TTTTTAGAAAGTTTAGGGGTTAAAACTTAA
* ** *
7183 TTTTTGGTTAGTTTAGAGGTTAAAAC
1 TTTTTAGAAAGTTTAGGGGTTAAAAC
7209 GCAATTTCTA
Statistics
Matches: 107, Mismatches: 33, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
29 34 0.32
30 63 0.59
31 10 0.09
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (30 bp):
TTTTTAGAAAGTTTAGGGGTTAAAACTTAA
Found at i:7155 original size:59 final size:59
Alignment explanation
Indices: 7025--7189 Score: 147
Period size: 59 Copynumber: 2.7 Consensus size: 59
7015 TTTGGGGGCC
* * * * *
7025 AAATTTGATTTTTTAGAAAGTGTGGGGGTCAAATCCA-AATTTTTGGAAAGTTTAGGGTCAA
1 AAATTT-ATTTTTTAGAAAGT-TTGGGGTTAAA-ACATAATTTTTGGAAAGTTAAGGGTAAA
* * * *
7086 ATA-TGAATTTTTAGAAAGTTTAGGGGTTAAAACTTAATTTTTGGAAAGTTCAAGGG-AAA
1 AAATTTATTTTTTAGAAAGTTT-GGGGTTAAAACATAATTTTTGGAAAGTT-AAGGGTAAA
* * *
7145 AAATTTATTTTTTTAAAAAATTTGGGGGTAAAACATAATTTTTGG
1 AAATTTA-TTTTTTAGAAAGTTTGGGGTTAAAACATAATTTTTGG
7190 TTAGTTTAGA
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
58 2 0.02
59 40 0.48
60 27 0.33
61 14 0.17
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (59 bp):
AAATTTATTTTTTAGAAAGTTTGGGGTTAAAACATAATTTTTGGAAAGTTAAGGGTAAA
Found at i:9160 original size:34 final size:34
Alignment explanation
Indices: 9113--9180 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
9103 TTTCACTCAC
* * *
9113 ATTGAGCTTCGCTTGATTATTTTGGTCCACTTCT
1 ATTGAGCTGCGCTTCATTATTTTGATCCACTTCT
9147 ATTGAGCTGCGCTTCATTATTTTGATCCACTTCT
1 ATTGAGCTGCGCTTCATTATTTTGATCCACTTCT
9181 TTGTATCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (34 bp):
ATTGAGCTGCGCTTCATTATTTTGATCCACTTCT
Found at i:9250 original size:110 final size:110
Alignment explanation
Indices: 9057--9256 Score: 337
Period size: 110 Copynumber: 1.8 Consensus size: 110
9047 CGCTTCGTTG
*
9057 TTTGATCTACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTT
1 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTT
*
9122 CGCTTGATTATTTTGGTCCACTTCTATTGAGCTGCGCTTCATTAT
66 CGCTTCATTATTTTGGTCCACTTCTATTGAGCTGCGCTTCATTAT
* * * *
9167 TTTGATCCACTTCTTTGTATCTCATTAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTT
1 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTT
*
9232 CGCTTCATTGTTTTGGTCCACTTCT
66 CGCTTCATTATTTTGGTCCACTTCT
9257 CTGTATCTCA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 83 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (110 bp):
TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTT
CGCTTCATTATTTTGGTCCACTTCTATTGAGCTGCGCTTCATTAT
Found at i:9343 original size:77 final size:76
Alignment explanation
Indices: 9147--9355 Score: 319
Period size: 76 Copynumber: 2.7 Consensus size: 76
9137 GTCCACTTCT
* * * * * * *
9147 ATTGAGCTGCGCTTCATTATTTTGATCCACTTCTTTGTATCTCATTAGGAAGATGGGGGTTTGAA
1 ATTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAGAGTTTGAA
9212 GTTTCACTCAC
66 GTTTCACTCAC
9223 ATTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAGAGTTTGAA
1 ATTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAGAGTTTGAA
9288 GTTTCACTCAC
66 GTTTCACTCAC
* * *
9299 GTTGAGTTTTCGCTTTATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGA
1 ATTGAG-CTTCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGA
9356 CCGCTTTGTT
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
76 74 0.61
77 48 0.39
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (76 bp):
ATTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAGAGTTTGAA
GTTTCACTCAC
Found at i:9452 original size:122 final size:123
Alignment explanation
Indices: 9249--9545 Score: 416
Period size: 122 Copynumber: 2.4 Consensus size: 123
9239 TTGTTTTGGT
* * ** *
9249 CCACTTCTCTGTATCTCATCAGGAAGATGAGAGTTTGAAGTTTCACTCACGTTGAGTTTTCGCTT
1 CCACTTCTCTGTATCTCATCAGGAAGAT-AGGGTTTGAAGTTTTACTCATATGGAGTTTTCGCTT
* * * * *
9314 TATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTGTTGTTTGAC
65 CATTGTTTTGGTCCACTTCTCTGTACCTCATCAGGAAGATGACCACCTCGTTGTTTGAC
*
9373 CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTTTTACCCATATGGAG-TTTCGCTTC
1 CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTTTTACTCATATGGAGTTTTCGCTTC
* * * *
9437 ATTGTTTTGGTCCACTTCTCTGTACCTTATTATGAAGATGGCCACCTCGTTGTTTGAC
66 ATTGTTTTGGTCCACTTCTCTGTACCTCATCAGGAAGATGACCACCTCGTTGTTTGAC
* * *
9495 TCACTTCTCTGTATCTAATCAGGAAGATGGGGTTTGAAGTTTTACTCATAT
1 CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTTTTACTCATAT
9546 TAAGCTTCAG
Statistics
Matches: 154, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
122 105 0.68
123 21 0.14
124 28 0.18
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (123 bp):
CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTTTTACTCATATGGAGTTTTCGCTTC
ATTGTTTTGGTCCACTTCTCTGTACCTCATCAGGAAGATGACCACCTCGTTGTTTGAC
Found at i:10269 original size:42 final size:43
Alignment explanation
Indices: 10209--10292 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
10199 TTTGGTTTTA
*** *
10209 AGACACCCTTTGTTGGTTTTCATCTCTATCC-CTTTTTTTTCG
1 AGACACCCTTTACGGGTTTTCATCTCGATCCTCTTTTTTTTCG
10251 AGACACCCTTTACGGGTTTTCATCTCGATCCTTCTTTTTTTT
1 AGACACCCTTTACGGGTTTTCATCTCGATCC-TCTTTTTTTT
10293 TCTTTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 27 0.75
44 9 0.25
ACGTcount: A:0.13, C:0.26, G:0.12, T:0.49
Consensus pattern (43 bp):
AGACACCCTTTACGGGTTTTCATCTCGATCCTCTTTTTTTTCG
Found at i:17423 original size:12 final size:12
Alignment explanation
Indices: 17391--17425 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
17381 TCGTCATTTG
* *
17391 TTCTTGCAACTG
1 TTCTTGCATCTA
17403 TTCTTGCATCTA
1 TTCTTGCATCTA
17415 TTCTTGCATCT
1 TTCTTGCATCT
17426 CTCTTCGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.11, T:0.49
Consensus pattern (12 bp):
TTCTTGCATCTA
Found at i:21350 original size:30 final size:30
Alignment explanation
Indices: 21313--21561 Score: 182
Period size: 30 Copynumber: 8.3 Consensus size: 30
21303 TGAAATCTTA
* * *
21313 GAAAGTTTGGGGGCCAAATTTGAATTTTTG
1 GAAAGTTTGGGGGTCAAATATAAATTTTTG
* * * * * *
21343 AAAAGTTTAGGTGTAAAATCTAAACTTTTG
1 GAAAGTTTGGGGGTCAAATATAAATTTTTG
* *
21373 GAAAGTTTGTGGGTTAAATATAAATTTTTG
1 GAAAGTTTGGGGGTCAAATATAAATTTTTG
**
21403 GAAAGTTTGGGGGTCAAA-ACTTTATTTTTG
1 GAAAGTTTGGGGGTCAAATA-TAAATTTTTG
* * *
21433 G-AAGTTTAGGGGTATAAATAT-AATTTTTT
1 GAAAGTTTGGGGGT-CAAATATAAATTTTTG
* * *
21462 GAAATTTTGAGGGTCAAATCTAAATTTTTG
1 GAAAGTTTGGGGGTCAAATATAAATTTTTG
*** * *
21492 GAAAGTTCAAGGGT-AAAAACATAATTTTTG
1 GAAAGTTTGGGGGTCAAATATA-AATTTTTG
* * * * *
21522 GAAATTTTAGGGGTTAAATATGAATTTTTA
1 GAAAGTTTGGGGGTCAAATATAAATTTTTG
21552 GAAAGTTTGG
1 GAAAGTTTGG
21562 TGTCAAAAAA
Statistics
Matches: 168, Mismatches: 44, Indels: 14
0.74 0.19 0.06
Matches are distributed among these distances:
29 28 0.17
30 135 0.80
31 5 0.03
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (30 bp):
GAAAGTTTGGGGGTCAAATATAAATTTTTG
Found at i:21497 original size:89 final size:89
Alignment explanation
Indices: 21292--21593 Score: 253
Period size: 89 Copynumber: 3.4 Consensus size: 89
21282 TAAGGAAAAA
* * * *
21292 TGGGGTCAAA-ATGAAA-TCTTAGAAAGTTTGGGGG-CCAAA-TTTGAATTTTTGAAAAGTTTAG
1 TGGGGTCAAATAT-AAATTTTTGGAAAGTTTGGGGGTCAAAACTTT--ATTTTTG-GAAGTTTAG
* * * *
21353 GTGTA-AAATCTAAACTTTTGGAAAGTT
62 GGGTATAAATATAAATTTTTAGAAAGTT
*
21380 TGTGGGTTAAATATAAATTTTTGGAAAGTTTGGGGGTCAAAACTTTATTTTTGGAAGTTTAGGGG
1 TG-GGGTCAAATATAAATTTTTGGAAAGTTTGGGGGTCAAAACTTTATTTTTGGAAGTTTAGGGG
* *
21445 TATAAATAT-AATTTTTTGAAATTT
65 TATAAATATAAATTTTTAGAAAGTT
* *** * * * *
21469 TGAGGGTCAAATCTAAATTTTTGGAAAGTTCAAGGGTAAAAACATAATTTTTGGAAATTTTAGGG
1 TG-GGGTCAAATATAAATTTTTGGAAAGTTTGGGGGTCAAAACTTTATTTTTGG-AAGTTTAGGG
*
21534 GT-TAAATATGAATTTTTAGAAAGTT
64 GTATAAATATAAATTTTTAGAAAGTT
* * *
21559 TGGTGTCAAA-A-AATATTTTTTGGATAGTATGGGGG
1 TGGGGTCAAATATAA-A-TTTTTGGAAAGTTTGGGGG
21594 GGTTAAAACG
Statistics
Matches: 175, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
87 2 0.01
88 3 0.02
89 107 0.61
90 56 0.32
91 4 0.02
92 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (89 bp):
TGGGGTCAAATATAAATTTTTGGAAAGTTTGGGGGTCAAAACTTTATTTTTGGAAGTTTAGGGGT
ATAAATATAAATTTTTAGAAAGTT
Found at i:21506 original size:60 final size:60
Alignment explanation
Indices: 21335--21559 Score: 215
Period size: 60 Copynumber: 3.8 Consensus size: 60
21325 GCCAAATTTG
* * * * **
21335 AATTTTTGAAAAGTTT-AGGTGTAAAATCTAAACTTTTGGAAAGTTTGTGGGT-TAAATAT
1 AATTTTTGGAAATTTTGAGG-GTCAAATCTAAATTTTTGGAAAGTTTAAGGGTATAAATAT
* * * ** *
21394 AAATTTTTGGAAAGTTTGGGGGTCAAAACTTTATTTTTGG-AAGTTTAGGGGTATAAATAT
1 -AATTTTTGGAAATTTTGAGGGTCAAATCTAAATTTTTGGAAAGTTTAAGGGTATAAATAT
* * * *
21454 AATTTTTTGAAATTTTGAGGGTCAAATCTAAATTTTTGGAAAGTTCAAGGGTAAAAACAT
1 AATTTTTGGAAATTTTGAGGGTCAAATCTAAATTTTTGGAAAGTTTAAGGGTATAAATAT
* * * *
21514 AATTTTTGGAAATTTT-AGGGGTTAAATATGAATTTTTAGAAAGTTT
1 AATTTTTGGAAATTTTGA-GGGTCAAATCTAAATTTTTGGAAAGTTT
21560 GGTGTCAAAA
Statistics
Matches: 136, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
59 44 0.32
60 90 0.66
61 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (60 bp):
AATTTTTGGAAATTTTGAGGGTCAAATCTAAATTTTTGGAAAGTTTAAGGGTATAAATAT
Found at i:21570 original size:60 final size:58
Alignment explanation
Indices: 21395--21582 Score: 150
Period size: 60 Copynumber: 3.2 Consensus size: 58
21385 GTTAAATATA
* * ** * * *
21395 AATTTTTGGAAAGTTTGGGGGTCAAA-ACTTTATTTTT-GGAAGTTTAGGGGTATAAATAT
1 AATTTTTGGAAATTTTGAGGGTCAAATA-TAAATTTTTAGAAAG-TTAAGGGTA-AAAAAT
* * *
21454 AATTTTTTGAAATTTTGAGGGTCAAATCTAAATTTTTGGAAAGTTCAAGGGTAAAAACAT
1 AATTTTTGGAAATTTTGAGGGTCAAATATAAATTTTTAGAAAGTT-AAGGGTAAAAA-AT
* * *
21514 AATTTTTGGAAATTTT-AGGGGTTAAATATGAATTTTTAGAAAGTT-TGGTGTCAAAAAAT
1 AATTTTTGGAAATTTTGA-GGGTCAAATATAAATTTTTAGAAAGTTAAGG-GT-AAAAAAT
*
21573 ATTTTTTGGA
1 AATTTTTGGA
21583 TAGTATGGGG
Statistics
Matches: 106, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
58 2 0.02
59 49 0.46
60 55 0.52
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (58 bp):
AATTTTTGGAAATTTTGAGGGTCAAATATAAATTTTTAGAAAGTTAAGGGTAAAAAAT
Found at i:22769 original size:29 final size:28
Alignment explanation
Indices: 22736--22791 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
22726 ATTTCTAATA
* *
22736 ATTTTATATATTTTTAGTATTTTTCATAG
1 ATTTTAAATATTTTTA-AATTTTTCATAG
22765 ATTTTAAATATTTTTAAATTTTTCATA
1 ATTTTAAATATTTTTAAATTTTTCATA
22792 ATTAATAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (28 bp):
ATTTTAAATATTTTTAAATTTTTCATAG
Found at i:22896 original size:20 final size:19
Alignment explanation
Indices: 22856--22893 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
22846 TATGATTTAT
22856 TTTTTTGCATTTTTATATA
1 TTTTTTGCATTTTTATATA
*
22875 TTTTTT-CATTTTAATATA
1 TTTTTTGCATTTTTATATA
22893 T
1 T
22894 ATTATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTTGCATTTTTATATA
Found at i:23255 original size:54 final size:54
Alignment explanation
Indices: 23167--23274 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
23157 CCCGAACAAC
* * * * *
23167 AAACGCGACTTGAACCTAGACCACACTTGGAACGATGAACACCTTTAACTATCA
1 AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAACACCCTTAACTATCA
*
23221 AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAATACCCTTAACTATCA
1 AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAACACCCTTAACTATCA
23275 GACCATCACA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.19
Consensus pattern (54 bp):
AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAACACCCTTAACTATCA
Found at i:24386 original size:91 final size:92
Alignment explanation
Indices: 24291--24469 Score: 234
Period size: 92 Copynumber: 2.0 Consensus size: 92
24281 TCAAATTTTT
** * *
24291 TTCAAAAAAAGCAATTAATTCTCT-CTTTTTTTTTTCCCACTCAATTGAGCACTTGAAATTTTAA
1 TTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTCTTCCCACTCAATTGAGCACTTGAAATTTCAA
* *
24355 AATGCATAAAAAAGGCCCTCAAACTTC
66 AATGCATAAAAAAGACCCCCAAACTTC
* * * ** *
24382 TTCAAAAAAAGCAATTAAGCCTTTGCTTTTTTTCTTCTCACTCAATTGGGTGCTTGAACTTTCAA
1 TTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTCTTCCCACTCAATTGAGCACTTGAAATTTCAA
*
24447 AATGCATCAAAAAGACCCCCAAA
66 AATGCATAAAAAAGACCCCCAAA
24470 ATTAAAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
91 21 0.28
92 53 0.72
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (92 bp):
TTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTCTTCCCACTCAATTGAGCACTTGAAATTTCAA
AATGCATAAAAAAGACCCCCAAACTTC
Found at i:24759 original size:54 final size:54
Alignment explanation
Indices: 24671--24778 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
24661 CCCGAACAAC
* * * * *
24671 AAACGCGACTTGAACCTAGACCACACTTGGAACGATGAACACCTTTAACTATCA
1 AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAACACCCTTAACTATCA
*
24725 AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAATACCCTTAACTATCA
1 AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAACACCCTTAACTATCA
24779 GACCATCACA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.19
Consensus pattern (54 bp):
AAACGCGACTTGAACCCAAACCACACCTGAAACGATGAACACCCTTAACTATCA
Found at i:25890 original size:91 final size:92
Alignment explanation
Indices: 25795--25973 Score: 234
Period size: 92 Copynumber: 2.0 Consensus size: 92
25785 TCAAATTTTT
** * *
25795 TTCAAAAAAAGCAATTAATTCTCT-CTTTTTTTTTTCCCACTCAATTGAGCACTTGAAATTTTAA
1 TTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTCTTCCCACTCAATTGAGCACTTGAAATTTCAA
* *
25859 AATGCATAAAAAAGGCCCTCAAACTTC
66 AATGCATAAAAAAGACCCCCAAACTTC
* * * ** *
25886 TTCAAAAAAAGCAATTAAGCCTTTGCTTTTTTTCTTCTCACTCAATTGGGTGCTTGAACTTTCAA
1 TTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTCTTCCCACTCAATTGAGCACTTGAAATTTCAA
*
25951 AATGCATCAAAAAGACCCCCAAA
66 AATGCATAAAAAAGACCCCCAAA
25974 ATTAAAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
91 21 0.28
92 53 0.72
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (92 bp):
TTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTCTTCCCACTCAATTGAGCACTTGAAATTTCAA
AATGCATAAAAAAGACCCCCAAACTTC
Found at i:28554 original size:17 final size:18
Alignment explanation
Indices: 28527--28560 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28517 GCTTCGGGGA
28527 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
28545 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
28561 TAATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:30967 original size:10 final size:9
Alignment explanation
Indices: 30913--31081 Score: 73
Period size: 9 Copynumber: 18.0 Consensus size: 9
30903 TTTTGATATG
30913 ATAATTTTT
1 ATAATTTTT
30922 ATAATTCTTT
1 ATAATT-TTT
30932 AACTAA-TTTT
1 -A-TAATTTTT
30942 ATAATTCTTT
1 ATAATT-TTT
30952 AT-ATTTTAT
1 ATAATTTT-T
30961 ATAATTTTCT
1 ATAATTTT-T
**
30971 -TACAACTTT
1 ATA-ATTTTT
*
30980 ATAAAATTTT
1 AT-AATTTTT
30990 ATAATTTTT
1 ATAATTTTT
* *
30999 TTACATTTCT
1 ATA-ATTTTT
31009 AT-ATATTTT
1 ATAAT-TTTT
31018 ATAATTTTT
1 ATAATTTTT
*
31027 A-AGAGTTTT
1 ATA-ATTTTT
* *
31036 ATAAAATGTT
1 AT-AATTTTT
*
31046 ATACTTTTT
1 ATAATTTTT
31055 -TATATTTCTT
1 ATA-ATTT-TT
*
31065 ACAATTTTT
1 ATAATTTTT
31074 AT-ATTTTT
1 ATAATTTTT
31082 TTTTTCTAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 39
0.68 0.10 0.22
Matches are distributed among these distances:
8 16 0.13
9 51 0.41
10 48 0.39
11 5 0.04
12 3 0.02
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (9 bp):
ATAATTTTT
Found at i:31025 original size:28 final size:28
Alignment explanation
Indices: 30948--31026 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
30938 TTTTATAATT
*
30948 CTTTATAT-TTTATATAATTTTCTTACAA
1 CTTTATATATTT-TATAATTTTTTTACAA
*
30976 CTTTATAAAATTTTATAATTTTTTTAC-A
1 CTTTAT-ATATTTTATAATTTTTTTACAA
*
31004 TTTCTATATATTTTATAATTTTT
1 CTT-TATATATTTTATAATTTTT
31027 AAGAGTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 24 0.55
29 17 0.39
30 3 0.07
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (28 bp):
CTTTATATATTTTATAATTTTTTTACAA
Found at i:31047 original size:28 final size:27
Alignment explanation
Indices: 30960--31083 Score: 90
Period size: 28 Copynumber: 4.4 Consensus size: 27
30950 TTATATTTTA
*
30960 TATAATTTTCTTACAACTTTATAAAATTT
1 TATAATTTT-TTAC-ATTTTATAAAATTT
*
30989 TATAATTTTTTTACATTTCTAT-ATATTT
1 TATAA-TTTTTTACATTT-TATAAAATTT
* * *
31017 TATAATTTTTAAGAGTTTTATAAAATGT
1 TATAATTTTTTACA-TTTTATAAAATTT
* * *
31045 TATACTTTTTTATATTTCT-TACAATTTT
1 TATAATTTTTTACATTT-TATA-AAATTT
*
31073 TATATTTTTTT
1 TATAATTTTTT
31084 TTTCTAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
27 15 0.19
28 46 0.60
29 12 0.16
30 4 0.05
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (27 bp):
TATAATTTTTTACATTTTATAAAATTT
Found at i:31074 original size:56 final size:56
Alignment explanation
Indices: 30977--31082 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
30967 TTCTTACAAC
* * *
30977 TTTATAAAATTTTATAATTTTTTTACATTTCTATATATTTTATAATTTTTAAGAGT
1 TTTATAAAATGTTATAACTTTTTTACATTTCTAAATATTTTATAATTTTTAAGAGT
* *
31033 TTTATAAAATGTTAT-ACTTTTTTATATTTCTTACAAT-TTTTATATTTTTT
1 TTTATAAAATGTTATAACTTTTTTACATTTC-TA-AATATTTTATAATTTTT
31083 TTTTCTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
55 13 0.30
56 28 0.65
57 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (56 bp):
TTTATAAAATGTTATAACTTTTTTACATTTCTAAATATTTTATAATTTTTAAGAGT
Done.