Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014382.1 Kokia drynarioides strain JFW-HI SEQ_129420, 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: 63793
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:933 original size:13 final size:12
Alignment explanation
Indices: 906--950 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
896 ATATTTAATT
*
906 ATATGTTCATGA
1 ATATGTTCTTGA
918 ATATGTTCTTTGA
1 ATATGTTC-TTGA
931 ATATGTTCTTGA
1 ATATGTTCTTGA
*
943 ACATGTTC
1 ATATGTTC
951 GATTAAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.47
Consensus pattern (12 bp):
ATATGTTCTTGA
Found at i:1613 original size:20 final size:20
Alignment explanation
Indices: 1567--1613 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1557 ACATTATTCA
1567 AAATAATATTTAATTAACAT
1 AAATAATATTTAATTAACAT
* * *
1587 AATTAATTTTTATATTAA-TT
1 AAATAATATTTA-ATTAACAT
1607 AAATAAT
1 AAATAAT
1614 GATTAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATATTTAATTAACAT
Found at i:4062 original size:23 final size:22
Alignment explanation
Indices: 4028--4108 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
4018 ACGCTAGCGC
*
4028 GCTTACTGTTTCGCACTTGGTGT
1 GCTTACTATTTCGCACTT-GTGT
*
4051 GCTTACTATTTCGTACTTCGTGT
1 GCTTACTATTTCGCACTT-GTGT
** *
4074 ATTTACTGTTTCGCACCTTGTGT
1 GCTTACTATTTCGCA-CTTGTGT
*
4097 GCCTACTGATTT
1 GCTTACT-ATTT
4109 GCGCTATGTG
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
23 39 0.87
24 6 0.13
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (22 bp):
GCTTACTATTTCGCACTTGTGT
Found at i:4118 original size:23 final size:22
Alignment explanation
Indices: 4092--4149 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
4082 TTTCGCACCT
*
4092 TGTGTGCCTACTGATTTGCGCTA
1 TGTGTGCCTACTGA-TTGCACTA
** *
4115 TGTGCACCTACTGATTGCACTG
1 TGTGTGCCTACTGATTGCACTA
*
4137 TGTGTGCTTACTG
1 TGTGTGCCTACTG
4150 TTTCCTCAGC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTA
Found at i:5736 original size:59 final size:57
Alignment explanation
Indices: 5673--5806 Score: 164
Period size: 57 Copynumber: 2.3 Consensus size: 57
5663 AATAAGAATA
* * *
5673 AAAAATTATTATTTTTTGA-TGTCTGTCAAGCT-ATGATCAACACCCCATTTTTCATATACA
1 AAAAA-TA-TATTTTTTGATTGTCTGTCAA-CTCATGATCAACACCCC--TTTCCAAATACC
* *
5733 AAAAAAATATTTTTTGATTGTCTGTCAACTCATGATCGACACCCCTTTCCAAATACC
1 AAAAATATATTTTTTGATTGTCTGTCAACTCATGATCAACACCCCTTTCCAAATACC
5790 AAAAATATATTTTTTGA
1 AAAAATATATTTTTTGA
5807 GTATTTACCA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
57 25 0.38
58 12 0.18
59 24 0.36
60 5 0.08
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (57 bp):
AAAAATATATTTTTTGATTGTCTGTCAACTCATGATCAACACCCCTTTCCAAATACC
Found at i:5940 original size:61 final size:58
Alignment explanation
Indices: 5833--5995 Score: 186
Period size: 61 Copynumber: 2.8 Consensus size: 58
5823 GACTGACACT
* * * * *
5833 CAAAAATA-AAATAAAAAAATTATATTTTGGTGTTTGCCATCTAATGGTCGACACCCA
1 CAAAAATACGAATAAAAAAATTATTTTTTGGTGTTTGACAACCAATGGTCGACACCCA
* *
5890 CAAATAATACGAATAAAAAAATTTATTTTTTTGGTGTTTGACAAGCAATGGTCGACACCTA
1 CAAA-AATACGAATAAAAAAA-TTA-TTTTTTGGTGTTTGACAACCAATGGTCGACACCCA
* * * *
5951 TAAAAATATGAAT-AAAAAATAATTTTTTGGTATTTGACAACCAAT
1 CAAAAATACGAATAAAAAAATTATTTTTTGGTGTTTGACAACCAAT
5996 AATCGACAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 25 0.28
58 6 0.07
59 16 0.18
60 11 0.12
61 32 0.36
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (58 bp):
CAAAAATACGAATAAAAAAATTATTTTTTGGTGTTTGACAACCAATGGTCGACACCCA
Found at i:20329 original size:20 final size:22
Alignment explanation
Indices: 20288--20332 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
20278 TAAAATATAA
20288 TAATCTAACTTTTTATATATTTT
1 TAATCTAAC-TTTTATATATTTT
20311 TAATCTAA-TTTTA-ATATTTT
1 TAATCTAACTTTTATATATTTT
20331 TA
1 TA
20333 TTTGAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
23 8 0.36
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATCTAACTTTTATATATTTT
Found at i:25832 original size:33 final size:33
Alignment explanation
Indices: 25795--25865 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
25785 TAATTATGAT
* *
25795 ATTATAAAAAAGAAACCATGGATTACAAATTTA
1 ATTATAAAAAAGAAACCATGGATTACAAAGTCA
*** **
25828 ATTATGGTAAATTAACCATGGATTACAAAGTCA
1 ATTATAAAAAAGAAACCATGGATTACAAAGTCA
25861 ATTAT
1 ATTAT
25866 GGTACTATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (33 bp):
ATTATAAAAAAGAAACCATGGATTACAAAGTCA
Found at i:26386 original size:4 final size:4
Alignment explanation
Indices: 26373--26411 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
26363 AAAATTGAAG
*
26373 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
26412 GAAGGAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:26403 original size:21 final size:20
Alignment explanation
Indices: 26373--26413 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
26363 AAAATTGAAG
26373 GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAGAAAGAAAAAAGA
*
26393 GAAAGAAAGAAAGAAAGAAGA
1 GAAA-AAAGAAAGAAAAAAGA
26414 AGGAAGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAGAAAAAAGA
Found at i:26421 original size:18 final size:17
Alignment explanation
Indices: 26377--26410 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
26367 TTGAAGGAAA
26377 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
26394 AAAGAAAGAAAGAAAGA
1 AAAGAAAGAAA-AAAGA
26411 AGAAGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Found at i:26837 original size:20 final size:21
Alignment explanation
Indices: 26796--26838 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
26786 TAATTTACTT
26796 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
26817 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
26837 TA
1 TA
26839 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:27143 original size:16 final size:16
Alignment explanation
Indices: 27098--27147 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
27088 TAAACCTAGC
*
27098 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
27114 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
27128 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
27144 TAAT
1 TAAT
27148 ATCCCATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:28540 original size:43 final size:42
Alignment explanation
Indices: 28458--28550 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 42
28448 ATTAACATGT
* *
28458 TAAATTATATTACTTGACTCGTGTTAATATGGATGCATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCATGCATGTTA
* * *
28500 CTAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 -TAAATTATATTACTTGACTCGTATTAATATGCATG-CATGTTA
*
28543 TTAATTAT
1 TAAATTAT
28551 GCAATTCATC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 9 0.21
43 34 0.79
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (42 bp):
TAAATTATATTACTTGACTCGTATTAATATGCATGCATGTTA
Found at i:29178 original size:45 final size:45
Alignment explanation
Indices: 29110--29247 Score: 168
Period size: 45 Copynumber: 3.0 Consensus size: 45
29100 GCATAGCTCA
29110 TCAAGCCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAG-CCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * * *
29156 TCAAGCCAATGATATCAACCTCAATTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * * * *
29201 TCAAGGAAAGGATATTAGGCTGAGTTTGACGAGCCACAGCGATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
29246 TC
1 TC
29248 TATTCCTCCC
Statistics
Matches: 77, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
45 72 0.94
46 5 0.06
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:29537 original size:28 final size:28
Alignment explanation
Indices: 29504--29581 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
29494 AACCCTAAAT
* *
29504 CCTAAATTATAAATC-CTAGACTTGAAAC
1 CCTAAATCATAAA-CACTAGACTTAAAAC
29532 CCTAAATCATAAACACTAGACTTAAAAC
1 CCTAAATCATAAACACTAGACTTAAAAC
* * *
29560 TCTAAACCGTAAACACTAGACT
1 CCTAAATCATAAACACTAGACT
29582 GATTAAAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (28 bp):
CCTAAATCATAAACACTAGACTTAAAAC
Found at i:32868 original size:4 final size:4
Alignment explanation
Indices: 32848--32913 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
32838 AACACATTAC
* * * *
32848 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CGTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
32896 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
32914 CCGTTTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.81
5 7 0.13
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:32887 original size:17 final size:15
Alignment explanation
Indices: 32852--32894 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
32842 CATTACCTTT
*
32852 CTTTCCTTCTTCTTT
1 CTTTCCTTCTTCTTC
32867 CTTTCCTCTCGTTCTTC
1 CTTTCCT-TC-TTCTTC
*
32884 CTTTCTTTCTT
1 CTTTCCTTCTT
32895 TCTTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.38
16 4 0.17
17 11 0.46
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (15 bp):
CTTTCCTTCTTCTTC
Found at i:32889 original size:21 final size:21
Alignment explanation
Indices: 32858--32914 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
32848 CTTTCTTTCC
32858 TTCTTCTTTCTTTCCTCTC-G
1 TTCTTCTTTCTTTCCTCTCTG
* *
32878 TTCTTCCTTTCTTT-CTTTCTT
1 TTCTT-CTTTCTTTCCTCTCTG
32899 TTCTTTCTTTCTTTCC
1 TTC-TTCTTTCTTTCC
32915 CGTTTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 9 0.29
21 19 0.61
22 3 0.10
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (21 bp):
TTCTTCTTTCTTTCCTCTCTG
Found at i:32906 original size:25 final size:24
Alignment explanation
Indices: 32847--32913 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
32837 AAACACATTA
32847 CCTTTCTTTCCTTC-TTCTTTCTTT
1 CCTTTCTTT-CTTCTTTCTTTCTTT
* *
32871 CCTCTCGTTCTTCCTTTCTTTCTTT
1 CCTTTCTTTCTT-CTTTCTTTCTTT
*
32896 CTTTTCTTTCTTTCTTTC
1 CCTTTCTTTC-TTCTTTC
32914 CCGTTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.09
24 8 0.23
25 22 0.63
26 2 0.06
ACGTcount: A:0.00, C:0.33, G:0.01, T:0.66
Consensus pattern (24 bp):
CCTTTCTTTCTTCTTTCTTTCTTT
Found at i:33079 original size:32 final size:32
Alignment explanation
Indices: 33038--33104 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
33028 AAATAAACAC
33038 ACACACACGGCACAATGGGGTGCTGCCAAGAG
1 ACACACACGGCACAATGGGGTGCTGCCAAGAG
*
33070 ACACACACGGCACAATGGGGTGCTGCCAAGTG
1 ACACACACGGCACAATGGGGTGCTGCCAAGAG
33102 ACA
1 ACA
33105 AAACATCTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.30, T:0.10
Consensus pattern (32 bp):
ACACACACGGCACAATGGGGTGCTGCCAAGAG
Found at i:35623 original size:31 final size:29
Alignment explanation
Indices: 35533--35627 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
35523 GAGAGTTTAG
* * ** *
35533 GTACTACATTGAACATTTTCAAAATATAA
1 GTACCACATTGAACATTTTTAACGTACAA
* *
35562 GTACCACATTGGACATTTTTAACGTGCAA
1 GTACCACATTGAACATTTTTAACGTACAA
*
35591 GTACCACATTGAATATTTTATGAACGTACAA
1 GTACCACATTGAACATTTT-T-AACGTACAA
35622 GTACCA
1 GTACCA
35628 ACTGTGATAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 39 0.72
30 1 0.02
31 14 0.26
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (29 bp):
GTACCACATTGAACATTTTTAACGTACAA
Found at i:40737 original size:18 final size:18
Alignment explanation
Indices: 40714--40751 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40704 GATCGAACAC
40714 GGTGAAC-CTACTAAGATT
1 GGTGAACACT-CTAAGATT
*
40732 GGTGAACACTCTGAGATT
1 GGTGAACACTCTAAGATT
40750 GG
1 GG
40752 CAAACTACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (18 bp):
GGTGAACACTCTAAGATT
Found at i:41642 original size:2 final size:2
Alignment explanation
Indices: 41635--41661 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41625 CAATTTCTCC
41635 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
41662 TTTCATGTTT
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:51270 original size:17 final size:17
Alignment explanation
Indices: 51250--51289 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
51240 ATTTCAAAAC
*
51250 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
*
51267 TTATGTAGTATTTTTAA
1 TTATGTAATATTTTTAA
51284 TTATGT
1 TTATGT
51290 GATGGTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:53489 original size:32 final size:31
Alignment explanation
Indices: 53443--53516 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 31
53433 TGGAATTAAA
53443 TTATATATTTTTGTTACAGTAAAAATATAATT
1 TTATA-ATTTTTGTTACAGTAAAAATATAATT
53475 TTATAATTTATTGTTACAGTAAAAATATAATT
1 TTATAATTT-TTGTTACAGTAAAAATATAATT
*
53507 TTATTATTTT
1 TTATAATTTT
53517 AATAGTTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 5 0.12
32 35 0.88
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (31 bp):
TTATAATTTTTGTTACAGTAAAAATATAATT
Found at i:59529 original size:12 final size:12
Alignment explanation
Indices: 59512--59536 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59502 AAAAATTTGT
59512 TATGAAAAGATA
1 TATGAAAAGATA
59524 TATGAAAAGATA
1 TATGAAAAGATA
59536 T
1 T
59537 CATATTAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TATGAAAAGATA
Found at i:62072 original size:59 final size:58
Alignment explanation
Indices: 62009--62333 Score: 325
Period size: 58 Copynumber: 5.5 Consensus size: 58
61999 TCTTCAGACA
* * **
62009 TTCGGGAGTAAAATAGTAATTTTTGGATGTTTCGGGGTCAAAAACGGGATTTTTGGAAG
1 TTCGGG-GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAG
* ** *
62068 TTCGGGGGTAAAATGGTAATTTTTAGAAGTTTCATGGTCAAAAATAGGATTTTTGGGAG
1 TTC-GGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAG
** * * *
62127 TTTATGGGTAAAATGGTAATTTTTAGAAGTTTTGAGGTC-AAAATAGGATTTTT-GAGAG
1 -TTCGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGA-AG
* * * ***
62185 TTTGGGGGTAAAATGGTAATTTTAGGAAGTTTCGGGGT-TAAAAT-GAGATTTTCAAAAG
1 -TTCGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAG-GATTTTTGGAAG
* * * * *
62243 TTTGGGTGTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAATTAGGTTTTTTGGAAG
1 TTCGGG-GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAG
*
62302 TTCAGGGTAAAATGGTAATTTTTGGATAGTTT
1 TTCGGGGTAAAATGGTAATTTTTGGA-AGTTT
62334 AGGGACCTCC
Statistics
Matches: 223, Mismatches: 33, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
57 7 0.03
58 110 0.49
59 100 0.45
60 6 0.03
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.38
Consensus pattern (58 bp):
TTCGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAG
Found at i:62337 original size:29 final size:28
Alignment explanation
Indices: 62016--62333 Score: 188
Period size: 29 Copynumber: 10.9 Consensus size: 28
62006 ACATTCGGGA
* *
62016 GTAAAATAGTAATTTTTGGATGTTTCGGG
1 GTAAAATGGTAATTTTTGGAAGTTT-GGG
* * *
62045 GTCAAAAACGG-GATTTTTGGAAGTTCGGGG
1 GT--AAAATGGTAATTTTTGGAAGTT-TGGG
* **
62075 GTAAAATGGTAATTTTTAGAAGTTTCATG
1 GTAAAATGGTAATTTTTGGAAGTTT-GGG
* *
62104 GTCAAAAATAGG--ATTTTTGGGAGTTTATGG
1 GT--AAAAT-GGTAATTTTTGGAAGTTT-GGG
* *
62134 GTAAAATGGTAATTTTTAGAAGTTTTGAG
1 GTAAAATGGTAATTTTTGGAAG-TTTGGG
62163 GTCAAAATAGG--ATTTTT-GAGAGTTTGGGG
1 GT-AAAAT-GGTAATTTTTGGA-AGTTT-GGG
*
62192 GTAAAATGGTAATTTTAGGAAGTTTCGGG
1 GTAAAATGGTAATTTTTGGAAGTTT-GGG
***
62221 GTTAAAAT-G-AGATTTTCAAAAGTTTGGG
1 G-TAAAATGGTA-ATTTTTGGAAGTTTGGG
*
62249 TGTAAAATGGTAATTTTAGGAAGTTTTGGG
1 -GTAAAATGGTAATTTTTGGAAG-TTTGGG
**
62279 GTCAAAATTAGGT--TTTTTGGAAGTTCAGG
1 GT-AAAA-T-GGTAATTTTTGGAAGTTTGGG
62308 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
62334 AGGGACCTCC
Statistics
Matches: 226, Mismatches: 33, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
26 3 0.01
27 5 0.02
28 43 0.19
29 89 0.39
30 68 0.30
31 13 0.06
32 5 0.02
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (28 bp):
GTAAAATGGTAATTTTTGGAAGTTTGGG
Found at i:63476 original size:18 final size:17
Alignment explanation
Indices: 63453--63492 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
63443 TTCGGTTTTT
63453 TATTTTAATTAATAATAA
1 TATTTTAA-TAATAATAA
63471 TATTTTTAATAATAATAA
1 TA-TTTTAATAATAATAA
63489 -ATTT
1 TATTT
63493 CATTTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.14
17 1 0.05
18 11 0.52
19 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTAATAATAATAA
Done.