Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013719.1 Kokia drynarioides strain JFW-HI SEQ_128747, 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: 65587
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Found at i:8768 original size:26 final size:26
Alignment explanation
Indices: 8706--8771 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
8696 AATTTAACAT
* *
8706 TGTTTTTAAAAAATATTTTTAAAAAG
1 TGTTTTTGAAAAATACTTTTAAAAAG
** * *
8732 TGTGGTAGAAAAATACTTTTGAAAAG
1 TGTTTTTGAAAAATACTTTTAAAAAG
8758 TGTTTTTGAAAAAT
1 TGTTTTTGAAAAAT
8772 TTAATTTAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41
Consensus pattern (26 bp):
TGTTTTTGAAAAATACTTTTAAAAAG
Found at i:8968 original size:23 final size:24
Alignment explanation
Indices: 8942--8998 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
8932 TATAATTTTT
*
8942 TATTAATATTTTAATATAT-GAAA
1 TATTAATATTTAAATATATCGAAA
* *
8965 TATTAAT-TTTAAATATTTCTAAA
1 TATTAATATTTAAATATATCGAAA
8988 TAATTAATATT
1 T-ATTAATATT
8999 AATTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 11 0.39
24 6 0.21
25 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTAATATTTAAATATATCGAAA
Found at i:9000 original size:24 final size:24
Alignment explanation
Indices: 8962--9019 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
8952 TTAATATATG
* *
8962 AAAT-ATTAATTTTAAATATTTCT
1 AAATAATTAATATTAAATATTTAT
*
8985 AAATAATTAATATTAATTATTTAT
1 AAATAATTAATATTAAATATTTAT
*
9009 AAA-ATTTAATA
1 AAATAATTAATA
9020 AAATTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATAATTAATATTAAATATTTAT
Found at i:17944 original size:34 final size:33
Alignment explanation
Indices: 17906--18003 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 33
17896 ACACGGTTAA
* *
17906 CCATCCAACACATCATATGCTCGTATGAGTAAAT
1 CCATCCAACACACCAAATGCTCGTATGAGT-AAT
*
17940 CCATCCAACACACCAAATGCTCATATGAGCTAAT
1 CCATCCAACACACCAAATGCTCGTATGAG-TAAT
* *
17974 CCATCCAGCACACCAAATGCTCGTAAGAGT
1 CCATCCAACACACCAAATGCTCGTATGAGT
18004 TAGTACAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 1 0.02
34 55 0.96
35 1 0.02
ACGTcount: A:0.36, C:0.31, G:0.12, T:0.21
Consensus pattern (33 bp):
CCATCCAACACACCAAATGCTCGTATGAGTAAT
Found at i:18020 original size:34 final size:34
Alignment explanation
Indices: 17908--18024 Score: 103
Period size: 34 Copynumber: 3.4 Consensus size: 34
17898 ACGGTTAACC
* * * * *
17908 ATCCAACACATCATATGCTCGTATGAG-TAAATCC
1 ATCCAACACACCAAATGCTCATAAGAGCT-AATCA
* *
17942 ATCCAACACACCAAATGCTCATATGAGCTAATCC
1 ATCCAACACACCAAATGCTCATAAGAGCTAATCA
* * * *
17976 ATCCAGCACACCAAATGCTCGTAAGAGTTAGTACA
1 ATCCAACACACCAAATGCTCATAAGAGCTAAT-CA
18011 AT-CAACACACCAAA
1 ATCCAACACACCAAA
18025 ACGCTGTAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
34 67 0.94
35 4 0.06
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (34 bp):
ATCCAACACACCAAATGCTCATAAGAGCTAATCA
Found at i:18647 original size:10 final size:10
Alignment explanation
Indices: 18632--18656 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18622 AAACTTGATA
18632 TTTAACCAAT
1 TTTAACCAAT
18642 TTTAACCAAT
1 TTTAACCAAT
18652 TTTAA
1 TTTAA
18657 GTATAGTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAACCAAT
Found at i:23981 original size:34 final size:34
Alignment explanation
Indices: 23938--24014 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
23928 ATCCATCTAG
*
23938 CACACCAAATGCTCGTAAGAGCTAGTCCAACCAA
1 CACACCAAATGCTCGTAAGAGATAGTCCAACCAA
* * *
23972 CACACCAAATGTTCGTAAGATATAGTCCATCCAA
1 CACACCAAATGCTCGTAAGAGATAGTCCAACCAA
24006 CACACCAAA
1 CACACCAAA
24015 ACACTATAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17
Consensus pattern (34 bp):
CACACCAAATGCTCGTAAGAGATAGTCCAACCAA
Found at i:25088 original size:16 final size:16
Alignment explanation
Indices: 25063--25093 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25053 AAGATGATAA
*
25063 TTTTACTTTAACATTC
1 TTTTAATTTAACATTC
25079 TTTTAATTTAACATT
1 TTTTAATTTAACATT
25094 ATTTACCTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAATTTAACATTC
Found at i:28139 original size:6 final size:6
Alignment explanation
Indices: 28128--28152 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28118 TCTATGTATG
28128 TATCTA TATCTA TATCTA TATCTA T
1 TATCTA TATCTA TATCTA TATCTA T
28153 GTCTGTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:31602 original size:18 final size:17
Alignment explanation
Indices: 31566--31610 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
31556 ATAATGGCAA
*
31566 AATAAAA-AAATACATG
1 AATAAAATAAATAAATG
31582 AATAAAATAAATTAAATG
1 AATAAAATAAA-TAAATG
*
31600 AATACAATAAA
1 AATAAAATAAA
31611 ATAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.28
17 3 0.12
18 15 0.60
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (17 bp):
AATAAAATAAATAAATG
Found at i:31814 original size:16 final size:16
Alignment explanation
Indices: 31790--31820 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31780 AAAATATGGC
31790 ATATAAATAAATAAAA
1 ATATAAATAAATAAAA
*
31806 ATATCAATAAATAAA
1 ATATAAATAAATAAA
31821 TGAAGGCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
ATATAAATAAATAAAA
Found at i:32045 original size:4 final size:4
Alignment explanation
Indices: 32036--32099 Score: 59
Period size: 4 Copynumber: 17.2 Consensus size: 4
32026 AAATTTAATG
* *
32036 ATAA ATAA ATAA ATAA ATAA ACAA GAT-A AT-A ACAA A-AA ATAA A-AA
1 ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA
32081 ATAA ATAA A-AA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA A
32100 AGAGATAACA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
3 16 0.31
4 34 0.67
5 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.19
Consensus pattern (4 bp):
ATAA
Found at i:32047 original size:8 final size:8
Alignment explanation
Indices: 32036--32099 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 8
32026 AAATTTAATG
32036 ATAAATAA
1 ATAAATAA
32044 ATAAATAA
1 ATAAATAA
*
32052 ATAAACAA
1 ATAAATAA
32060 GAT-AAT-A
1 -ATAAATAA
*
32067 ACAAA-AA
1 ATAAATAA
32074 ATAAA-AA
1 ATAAATAA
32081 ATAAATAA
1 ATAAATAA
32089 A-AAAT-A
1 ATAAATAA
32095 ATAAA
1 ATAAA
32100 AGAGATAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
6 3 0.06
7 22 0.47
8 20 0.43
9 2 0.04
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.19
Consensus pattern (8 bp):
ATAAATAA
Found at i:32086 original size:11 final size:11
Alignment explanation
Indices: 32036--32100 Score: 73
Period size: 10 Copynumber: 5.9 Consensus size: 11
32026 AAATTTAATG
32036 ATAAATAAATAA
1 ATAAATAAA-AA
32048 ATAAATAAACAA
1 ATAAATAAA-AA
*
32060 GAT-AATAACAA
1 -ATAAATAAAAA
32071 A-AAATAAAAA
1 ATAAATAAAAA
32081 ATAAATAAAAA
1 ATAAATAAAAA
32092 AT-AATAAAA
1 ATAAATAAAA
32101 GAGATAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 16 0.34
11 13 0.28
12 16 0.34
13 2 0.04
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (11 bp):
ATAAATAAAAA
Found at i:32108 original size:40 final size:42
Alignment explanation
Indices: 32038--32116 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
32028 ATTTAATGAT
*
32038 AAATAAATAAATAAATAAACAAGATAATAACAA-AAAATAAA
1 AAATAAATAAATAAATAAAAAAGATAATAACAATAAAATAAA
*
32079 AAATAAATAAA-AAATAATAAAAGA-GATAACAATAAAAT
1 AAATAAATAAATAAATAA-AAAAGATAATAACAATAAAAT
32117 GGTATGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 13 0.38
41 21 0.62
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (42 bp):
AAATAAATAAATAAATAAAAAAGATAATAACAATAAAATAAA
Found at i:32215 original size:13 final size:13
Alignment explanation
Indices: 32143--32215 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
32133 ACAACTAGAT
*
32143 AAATAAACAAAAAA
1 AAATAAAC-AATAA
32157 TAAATAAA-AATAA
1 -AAATAAACAATAA
**
32170 AAATTAAATGAT-A
1 AAA-TAAACAATAA
32183 AAATAAACAAATAA
1 AAATAAAC-AATAA
*
32197 ATATAAACAATAA
1 AAATAAACAATAA
32210 AAATAA
1 AAATAA
32216 TTGGGATTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
12 7 0.15
13 24 0.50
14 10 0.21
15 7 0.15
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (13 bp):
AAATAAACAATAA
Found at i:33340 original size:50 final size:50
Alignment explanation
Indices: 33269--34301 Score: 863
Period size: 50 Copynumber: 20.7 Consensus size: 50
33259 TATCAGTTTT
* * **
33269 AATTCGCCCCTCTACAACTTTAGGGGTATAAGATTTGCTTCTGTAGCTTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * **
33319 AATCTGCTCCTCTACAGCTTTAGGGGTATAAGATTTGCTTCTGTAGCTTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * *
33369 AATTTGCCCCTGTACAACTTTAGGGGTATAAGATTCAATTTTGTAGCTTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* ** * *
33419 AATCTT-CCCCTCTACAG-TTATAAGCTTATAAGATTCGCTTTTGTAGCTTC
1 AAT-TTGCCCCTCTACAGCTT-TAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * * * * *
33469 AGTATGTCCTTTTATAGCTTTAGGGGTATAAGATTCACTTTTGTAGCTTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * ** *
33519 AATATGTCCCTCTACAACTTTAAAGGTATAAGATTCGCTTCTGTAGCTTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * * * * *
33569 AATTTGCCCCTCAACAACTTTAGGAGTATAAGTTTCACTTTTGTAACTTT
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
** * * ** * *
33619 AACCTGCCCCTCTAAAACTTTAGGGGTATAAGATTTGCTTCTGTATCTTT
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * * * * *
33669 AATTTGCCCCTTTACAGCTTTAAGAGTATAAGATTCATTTTTATAGCTTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
** * * * * * *
33719 AAACTGCCCTTCTACAACTTTATGGGTATAAGATTCACTTTTGTAGATTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * * * * * * *
33769 AATCTACCCTTCTACAACTTTAAGGGTATAAGATTCACTTTTTTAACTTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * ** * *
33819 AATCTGCCCCTCTACAGCTTTAGGGGTCTAAGATTTGCTTCTGTACCTTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * ** *
33869 AATTTGCCCTTCTATAGCTTTAGGGGTATAAGATTTGCTTCTGTAGCTTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * ** ** * * *
33919 AATTTACCCCTCTATAATTTTAATGGTATAAGA-TCAACTTCTATTGATTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTC-ACTTCTGTAGCTTC
* * * * * *
33969 AATTTGCCCCTCTATAGCTTTAGAGGTATAACATTCGCTTCTATAGTTTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * *
34019 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGAATCTCTTCTGTAGCTTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * ** * *
34069 AATTTGCCTCTCTACAACTTTAGAAGTATAAGATTCACTTTTGTAGCTTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * * *
34119 AATTTGCCTCTTTATAGCTTTAGGGGTATAAGATTCACTTTTGTAGCTTG
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * * * * * *
34169 AATCTACCCCTCTACAGTTTTAAGGGTATAAGATTTACTTTTATAGCTTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
* * ** * * *
34219 AATCT-ACCC-CTACAATTTTAGGTGCATAAGATT-AGCTTCTGTAGATTC
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCA-CTTCTGTAGCTTC
* *
34267 AATTTGCCCCTTTAAAGCTTTAGGGGTATAAGATT
1 AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATT
34302 TGGTGTGACT
Statistics
Matches: 803, Mismatches: 171, Indels: 18
0.81 0.17 0.02
Matches are distributed among these distances:
47 1 0.00
48 34 0.04
49 10 0.01
50 752 0.94
51 6 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (50 bp):
AATTTGCCCCTCTACAGCTTTAGGGGTATAAGATTCACTTCTGTAGCTTC
Found at i:39069 original size:12 final size:12
Alignment explanation
Indices: 39051--39115 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
39041 TATGTGAGGA
39051 TTTTTATTTT-T
1 TTTTTATTTTAT
*
39062 TATTTTA-TATAT
1 T-TTTTATTTTAT
*
39074 TATTTTATTTCAT
1 T-TTTTATTTTAT
39087 TTTTTATTTTGAT
1 TTTTTATTTT-AT
*
39100 TTATTATTTT-T
1 TTTTTATTTTAT
39111 TTTTT
1 TTTTT
39116 GAAATTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
11 8 0.18
12 21 0.48
13 15 0.34
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:39093 original size:17 final size:16
Alignment explanation
Indices: 39053--39113 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
39043 TGTGAGGATT
39053 TTTATTTTTTATTTTA
1 TTTATTTTTTATTTTA
*
39069 --TA--TATTATTTTA
1 TTTATTTTTTATTTTA
39081 TTTCATTTTTTATTTTGA
1 TTT-ATTTTTTATTTT-A
39099 TTTATTATTTT-TTTT
1 TTTATT-TTTTATTTT
39114 TTGAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
12 9 0.25
14 3 0.08
15 1 0.03
17 15 0.42
18 8 0.22
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTATTTTTTATTTTA
Found at i:42894 original size:17 final size:17
Alignment explanation
Indices: 42874--42907 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42864 AAAAAATATG
42874 ATATATAAATAAATAAA
1 ATATATAAATAAATAAA
* *
42891 ATATATCAATGAATAAA
1 ATATATAAATAAATAAA
42908 TGAAGACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
ATATATAAATAAATAAA
Found at i:42958 original size:12 final size:11
Alignment explanation
Indices: 42935--42976 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
42925 ATAGCATAAA
42935 AAATAAAAAAT
1 AAATAAAAAAT
42946 AAATAAAACAAT
1 AAATAAAA-AAT
* *
42958 AAAT-TAAATT
1 AAATAAAAAAT
42968 AAATAAAAA
1 AAATAAAAA
42977 CGAGAATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.23
11 13 0.50
12 7 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:42973 original size:22 final size:18
Alignment explanation
Indices: 42930--42976 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 18
42920 TATAAATAGC
42930 ATAAAAAATAAAAAATAA
1 ATAAAAAATAAAAAATAA
42948 ATAAAACAATAAATTAAATTAA
1 ATAAAA-AATAAA--AAA-TAA
42970 ATAAAAA
1 ATAAAAA
42977 CGAGAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.24
19 6 0.24
21 4 0.16
22 9 0.36
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAAAAATAAAAAATAA
Found at i:51547 original size:24 final size:24
Alignment explanation
Indices: 51502--51547 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
51492 AGTCAATTAA
* *
51502 ATTATGCTAATAAATGCAAAATAT
1 ATTATACTAATAAATACAAAATAT
*
51526 ATTATACTAATAAATACTAAAT
1 ATTATACTAATAAATACAAAAT
51548 CTTCTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (24 bp):
ATTATACTAATAAATACAAAATAT
Found at i:54941 original size:19 final size:19
Alignment explanation
Indices: 54917--54969 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
54907 ATTTATATCC
*
54917 TTTTTAATTTTATTTATAA
1 TTTTTAATTTTATTAATAA
54936 TTTTTATGATTTT-TTAATAA
1 TTTTTA--ATTTTATTAATAA
54956 TTTTTAAATTTTAT
1 TTTTT-AATTTTAT
54970 AACTAACGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 11 0.38
20 12 0.41
21 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTAATTTTATTAATAA
Found at i:60072 original size:40 final size:40
Alignment explanation
Indices: 60017--60096 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
60007 AAAAGCATCC
60017 TTCCATTCAAGATCCAATCTAGATGACCCTTGGATCAAAG
1 TTCCATTCAAGATCCAATCTAGATGACCCTTGGATCAAAG
60057 TTCCATTCAAGATCCAATCTAGATGACCCTTGGATCAAAG
1 TTCCATTCAAGATCCAATCTAGATGACCCTTGGATCAAAG
60097 CTTTCCCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (40 bp):
TTCCATTCAAGATCCAATCTAGATGACCCTTGGATCAAAG
Found at i:63936 original size:18 final size:19
Alignment explanation
Indices: 63894--63936 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
63884 AAAAAAAATT
*
63894 TAAAAATAAAAAAATTACA
1 TAAAAATAAAAAAATTAAA
*
63913 TAAAAAT-AAATAATTAAA
1 TAAAAATAAAAAAATTAAA
63931 TGAAAA
1 T-AAAA
63937 GTTTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAAATAAAAAAATTAAA
Found at i:63936 original size:19 final size:19
Alignment explanation
Indices: 63894--63936 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
63884 AAAAAAAATT
*
63894 TAAAAATAAAAAAATTACA
1 TAAAAATAAAAAAATTAAA
*
63913 TAAAAAT-AAATAATTAAA
1 TAAAAATAAAAAAATTAAA
*
63931 TGAAAA
1 TAAAAA
63937 GTTTATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAAATAAAAAAATTAAA
Done.