Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009524.1 Kokia drynarioides strain JFW-HI SEQ_124235, 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: 161173
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:5061 original size:17 final size:16
Alignment explanation
Indices: 5014--5063 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
5004 CATTGACATT
5014 TATAAAATATATTTT-
1 TATAAAATATATTTTC
*
5029 TATTAAAT-TAATTTTC
1 TATAAAATAT-ATTTTC
5045 TATAATAATATATTTTC
1 TATAA-AATATATTTTC
5062 TA
1 TA
5064 AATTTCGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.41
16 4 0.14
17 11 0.38
18 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
TATAAAATATATTTTC
Found at i:5714 original size:18 final size:19
Alignment explanation
Indices: 5693--5734 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
5683 TGATTGTTTC
*
5693 AAATTATTAAATAT-ATTA
1 AAATTATTAAATATAAATA
*
5711 AAA-TCTTAAATATAAATA
1 AAATTATTAAATATAAATA
5729 AAATTA
1 AAATTA
5735 ATGTATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
17 9 0.47
18 9 0.47
19 1 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTATTAAATATAAATA
Found at i:7349 original size:17 final size:17
Alignment explanation
Indices: 7327--7360 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
7317 TTATCATTAG
7327 ATTTTATTTTTAGTTTT
1 ATTTTATTTTTAGTTTT
7344 ATTTTATTTTTAGTTTT
1 ATTTTATTTTTAGTTTT
7361 TACTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
ATTTTATTTTTAGTTTT
Found at i:10607 original size:15 final size:17
Alignment explanation
Indices: 10587--10620 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
10577 ATAATTCAAA
10587 ATTTTA-AAATAT-TAT
1 ATTTTATAAATATATAT
10602 ATTTTATAAATATATAT
1 ATTTTATAAATATATAT
10619 AT
1 AT
10621 AAAATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTATAAATATATAT
Found at i:15143 original size:48 final size:49
Alignment explanation
Indices: 15059--15159 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 49
15049 AAAATAGAAA
* ** * *
15059 AAAACTTAATGAATTTTAACAATTATCATTTGGTTAGGATTAAAATTTC
1 AAAACTAAATGAATTTTAACAATTATCATTAAGTTAGAACTAAAATTTC
* **
15108 AAAACTAAATG-ATTTTAACAATTTTTGTTAAGTTAGAACTAAAATTTC
1 AAAACTAAATGAATTTTAACAATTATCATTAAGTTAGAACTAAAATTTC
15156 AAAA
1 AAAA
15160 TACCATAGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 34 0.77
49 10 0.23
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (49 bp):
AAAACTAAATGAATTTTAACAATTATCATTAAGTTAGAACTAAAATTTC
Found at i:15423 original size:32 final size:32
Alignment explanation
Indices: 15360--15423 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
15350 TAAGTGACAT
** *
15360 AATTTAAAATAAAAATTTAAATAAAACTGAAA
1 AATTTAAAATAAAAATAGAAAGAAAACTGAAA
*
15392 AATTTAAAACTAAAAATAGAACGAAAA-TGAAA
1 AATTTAAAA-TAAAAATAGAAAGAAAACTGAAA
15424 GAAAAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.66, C:0.05, G:0.06, T:0.23
Consensus pattern (32 bp):
AATTTAAAATAAAAATAGAAAGAAAACTGAAA
Found at i:19208 original size:21 final size:21
Alignment explanation
Indices: 19183--19244 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
19173 TTTTTTGTTT
19183 AATTAGGGTTTATGGTTTTTA
1 AATTAGGGTTTATGGTTTTTA
*
19204 AATTAAGGTTTA-GGTTTTTA
1 AATTAGGGTTTATGGTTTTTA
*
19224 ATTATTTAGGGTTTATTGTTT
1 A--A-TTAGGGTTTATGGTTT
19245 AAAGGTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.26
21 11 0.32
22 1 0.03
23 9 0.26
24 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (21 bp):
AATTAGGGTTTATGGTTTTTA
Found at i:31021 original size:73 final size:73
Alignment explanation
Indices: 30939--31085 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
30929 AATTAAAAAA
30939 ATTAAAACAACTTTAAAAAATTATTCTAATGATCATTTTTGATAAAAATATATAAGATTTTATAA
1 ATTAAAACAACTTTAAAAAATTATTCTAATGATCATTTTTGATAAAAATATATAAGATTTTATAA
31004 AAATACAT
66 AAATACAT
31012 ATTAAAACAACTTTAAAAAATTATTCTAATGATCATTTTTGATAAAAATATATAAGATTTTATAA
1 ATTAAAACAACTTTAAAAAATTATTCTAATGATCATTTTTGATAAAAATATATAAGATTTTATAA
31077 AAATACAT
66 AAATACAT
31085 A
1 A
31086 CAATGTTGTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (73 bp):
ATTAAAACAACTTTAAAAAATTATTCTAATGATCATTTTTGATAAAAATATATAAGATTTTATAA
AAATACAT
Found at i:36468 original size:21 final size:21
Alignment explanation
Indices: 36442--36489 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
36432 GTTGCAACAA
*
36442 AGCTTCTCTCGTTTTCCATTC
1 AGCTTCTCTCGTTTTCCATGC
* *
36463 AGCTTCTTTCTTTTTCCATGC
1 AGCTTCTCTCGTTTTCCATGC
36484 AGCTTC
1 AGCTTC
36490 GTTTTTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.48
Consensus pattern (21 bp):
AGCTTCTCTCGTTTTCCATGC
Found at i:65694 original size:14 final size:13
Alignment explanation
Indices: 65675--65721 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
65665 CAAACAAGTG
65675 AAAAATTAGAATAT
1 AAAAATTA-AATAT
65689 AAAAATTAAAT-T
1 AAAAATTAAATAT
*
65701 AAAAATAAAAATATT
1 AAAAAT-TAAATA-T
65716 AAAAAT
1 AAAAAT
65722 GACTAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 7 0.24
13 7 0.24
14 8 0.28
15 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:65701 original size:19 final size:18
Alignment explanation
Indices: 65677--65712 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65667 AACAAGTGAA
*
65677 AAATTAGAATATAAAAATT
1 AAATTA-AAAATAAAAATT
65696 AAATTAAAAATAAAAAT
1 AAATTAAAAATAAAAAT
65713 ATTAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATTAAAAATAAAAATT
Found at i:65705 original size:13 final size:14
Alignment explanation
Indices: 65675--65721 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 14
65665 CAAACAAGTG
65675 AAAAATTAGAATAT
1 AAAAATTAGAATAT
65689 AAAAATTA-AAT-T
1 AAAAATTAGAATAT
* *
65701 AAAAATAAAAATATT
1 AAAAATTAGAATA-T
65716 AAAAAT
1 AAAAAT
65722 GACTAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 8 0.28
13 6 0.21
14 8 0.28
15 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATAT
Found at i:70188 original size:16 final size:16
Alignment explanation
Indices: 70156--70189 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
70146 TAGAAAATAA
*
70156 ATATAATATGTAAATG
1 ATATAATATATAAATG
*
70172 ATATAATATATAGATG
1 ATATAATATATAAATG
70188 AT
1 AT
70190 TAAATATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
ATATAATATATAAATG
Found at i:70468 original size:17 final size:16
Alignment explanation
Indices: 70446--70489 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
70436 CCATGTTAAT
70446 GGGAAAGTAACTCCGAA
1 GGGAAAGTAACTCC-AA
70463 GGGAAAGTTAGACTCCAA
1 GGGAAAG-TA-ACTCCAA
70481 -GGAAAGTAA
1 GGGAAAGTAA
70490 ATAAAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 2 0.08
17 13 0.52
18 4 0.16
19 5 0.20
ACGTcount: A:0.43, C:0.14, G:0.30, T:0.14
Consensus pattern (16 bp):
GGGAAAGTAACTCCAA
Found at i:76720 original size:21 final size:19
Alignment explanation
Indices: 76687--76729 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
76677 TGTTATAATT
* *
76687 ATTTATTTTTTAACATTAA
1 ATTTATTTTTTAAAAATAA
76706 ATTTATTTGTTTTAAAAATAA
1 ATTTA-TT-TTTTAAAAATAA
76727 ATT
1 ATT
76730 ATTACACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTATTTTTTAAAAATAA
Found at i:89985 original size:142 final size:142
Alignment explanation
Indices: 89729--90012 Score: 550
Period size: 142 Copynumber: 2.0 Consensus size: 142
89719 AACAAAGCTT
*
89729 AACTGGAAGACTATTTCTCAAATTTGACTGAAATATGAGTCATACTTAACACTGACAAATGAACC
1 AACTGGAAGACTATTTATCAAATTTGACTGAAATATGAGTCATACTTAACACTGACAAATGAACC
89794 TCGAGGATAAAATAAAGTCTAATAACTATTTACGTCTTGCATTGACGGAAACAATCTGCTGAGCT
66 TCGAGGATAAAATAAAGTCTAATAACTATTTACGTCTTGCATTGACGGAAACAATCTGCTGAGCT
89859 TTAAGTGAAACG
131 TTAAGTGAAACG
89871 AACTGGAAGACTATTTATCAAATTTGACTGAAATATGAGTCATACTTAACACTGACAAATGAACC
1 AACTGGAAGACTATTTATCAAATTTGACTGAAATATGAGTCATACTTAACACTGACAAATGAACC
*
89936 TCGAGGATAAAATAAAGTCTAATAACTATTTACGTCTTGCATTGACGGAAATAATCTGCTGAGCT
66 TCGAGGATAAAATAAAGTCTAATAACTATTTACGTCTTGCATTGACGGAAACAATCTGCTGAGCT
90001 TTAAGTGAAACG
131 TTAAGTGAAACG
90013 TAGCAATAAT
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 140 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (142 bp):
AACTGGAAGACTATTTATCAAATTTGACTGAAATATGAGTCATACTTAACACTGACAAATGAACC
TCGAGGATAAAATAAAGTCTAATAACTATTTACGTCTTGCATTGACGGAAACAATCTGCTGAGCT
TTAAGTGAAACG
Found at i:93100 original size:7 final size:7
Alignment explanation
Indices: 93088--93117 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
93078 CACCGCTTTT
93088 TGCAACC
1 TGCAACC
93095 TGCAACC
1 TGCAACC
93102 TGCAACC
1 TGCAACC
93109 TGCAACC
1 TGCAACC
93116 TG
1 TG
93118 GGAACGCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.40, G:0.17, T:0.17
Consensus pattern (7 bp):
TGCAACC
Found at i:96236 original size:23 final size:24
Alignment explanation
Indices: 96186--96236 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
96176 AGTGGATGAG
*
96186 GATGTGGTGGAATAAAATGAGCCA
1 GATGTGGTGGAATAAAACGAGCCA
* *
96210 -ATGT-GTGGAATAGAACGAGCTA
1 GATGTGGTGGAATAAAACGAGCCA
96232 GATGT
1 GATGT
96237 TTCATTCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.33, T:0.24
Consensus pattern (24 bp):
GATGTGGTGGAATAAAACGAGCCA
Found at i:97630 original size:18 final size:19
Alignment explanation
Indices: 97599--97636 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
97589 TCTTTCAACA
97599 AAAAATTTAAAAAATTTAT
1 AAAAATTTAAAAAATTTAT
*
97618 AAAAATTT-CAAAATTTAT
1 AAAAATTTAAAAAATTTAT
97636 A
1 A
97637 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTTAAAAAATTTAT
Found at i:97703 original size:30 final size:30
Alignment explanation
Indices: 97641--97696 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
97631 TTTATATTTT
*
97641 AAAAAAATATAAAAATTCTAAATATATATA
1 AAAAAAATATAAAAATTCTAAAAATATATA
97671 AAAAAAAGT-TAAAAATT-TAAAAATAT
1 AAAAAAA-TATAAAAATTCTAAAAATAT
97697 TCTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
29 8 0.33
30 15 0.62
31 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAAAATATAAAAATTCTAAAAATATATA
Found at i:102065 original size:32 final size:32
Alignment explanation
Indices: 102029--102091 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
102019 TCATAAACTT
* *
102029 ATAAATTGATTACTTGAATTTAATAACTCATG
1 ATAAATTAATTAATTGAATTTAATAACTCATG
* * *
102061 ATAAATTAATTAATTTAATTTGATAATTCAT
1 ATAAATTAATTAATTGAATTTAATAACTCAT
102092 ACGGATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCATG
Found at i:105453 original size:28 final size:28
Alignment explanation
Indices: 105413--105474 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
105403 GTTCTGCACA
105413 AAGGAGTGTGGGTGCATATTTTAATAAT
1 AAGGAGTGTGGGTGCATATTTTAATAAT
105441 AAGGAGTGTGGGTGCATATTTTAATAAT
1 AAGGAGTGTGGGTGCATATTTTAATAAT
105469 AAGGAG
1 AAGGAG
105475 ATTATGCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (28 bp):
AAGGAGTGTGGGTGCATATTTTAATAAT
Found at i:111771 original size:41 final size:41
Alignment explanation
Indices: 111714--111855 Score: 194
Period size: 41 Copynumber: 3.4 Consensus size: 41
111704 GAAAAGCGGT
* *
111714 AATAAATACAACTCATCACAACATCGGTTGAGATAACAGAC
1 AATAAATACGACTCATCACAACATCGGTTGAGATAATAGAC
* *
111755 AATAAATATGACTCATCACAACATCGGTTGAGATAATAAAC
1 AATAAATACGACTCATCACAACATCGGTTGAGATAATAGAC
* * * *
111796 AATAAATATGACTCATCACAATATCGGTTGAGGTAATAGGC
1 AATAAATACGACTCATCACAACATCGGTTGAGATAATAGAC
*
111837 AACAAATACGACTACATCA
1 AATAAATACGACT-CATCA
111856 TACTGCAGCC
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 85 0.94
42 5 0.06
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (41 bp):
AATAAATACGACTCATCACAACATCGGTTGAGATAATAGAC
Found at i:125671 original size:30 final size:30
Alignment explanation
Indices: 125596--125671 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
125586 AAAATTCAGT
*
125596 TTTTAAGGGATC-AAATTTTTTTTTACCAA
1 TTTTAAAGGATCTAAATTTTTTTTTACCAA
**
125625 TTTTGAAAGGGCCTAAATTTTTTTTT-CCAA
1 TTTT-AAAGGATCTAAATTTTTTTTTACCAA
*
125655 CTTTTAATGGATCTAAA
1 -TTTTAAAGGATCTAAA
125672 ACTCCAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 4 0.11
30 18 0.47
31 16 0.42
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (30 bp):
TTTTAAAGGATCTAAATTTTTTTTTACCAA
Found at i:130292 original size:3 final size:3
Alignment explanation
Indices: 130286--130324 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
130276 AACTATTATT
130286 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
130325 GAGTGTAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:135349 original size:23 final size:23
Alignment explanation
Indices: 135323--135366 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
135313 AAATTTTTTA
135323 TTTAATCTTTTAAAAATTACATT
1 TTTAATCTTTTAAAAATTACATT
* *
135346 TTTACTGTTTTAAAAATTACA
1 TTTAATCTTTTAAAAATTACA
135367 ATTTAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAATCTTTTAAAAATTACATT
Found at i:140406 original size:21 final size:21
Alignment explanation
Indices: 140382--140444 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
140372 AAAAATTATA
140382 TTGCTGTTTTGGTGCTATTTT
1 TTGCTGTTTTGGTGCTATTTT
* *
140403 TTGCTGTTTTGATG-TTTTTT
1 TTGCTGTTTTGGTGCTATTTT
140423 TTGCTGTTTTGGTGCTATTTT
1 TTGCTGTTTTGGTGCTATTTT
140444 T
1 T
140445 ACTGTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.05, C:0.08, G:0.22, T:0.65
Consensus pattern (21 bp):
TTGCTGTTTTGGTGCTATTTT
Found at i:140449 original size:20 final size:20
Alignment explanation
Indices: 140382--140450 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
140372 AAAAATTATA
140382 TTGCTGTTTTGGTGCTATTTT
1 TTGCTGTTTTGGTGCTA-TTT
* * *
140403 TTGCTGTTTTGATGTTTTTT
1 TTGCTGTTTTGGTGCTATTT
140423 TTGCTGTTTTGGTGCTATTT
1 TTGCTGTTTTGGTGCTATTT
*
140443 TTACTGTT
1 TTGCTGTT
140451 ATTTTTGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.06, C:0.09, G:0.22, T:0.64
Consensus pattern (20 bp):
TTGCTGTTTTGGTGCTATTT
Found at i:140486 original size:55 final size:54
Alignment explanation
Indices: 140415--140530 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 54
140405 GCTGTTTTGA
* **
140415 TGTT-TTTTTTGCTGTTTTGGTGCTATTTTTACT-GTTATTTTTGTTGTTGCTTT
1 TGTTCTTTTTTGCTGTTTTGCTGCTATTTTTACTACAT-TTTTTGTTGTTGCTTT
* * * *
140468 TGTTGCTTTTTTGTTGTTTTGCTGTTATTTTTGCTACATTTTTTGTTGTTGTTTT
1 TGTT-CTTTTTTGCTGTTTTGCTGCTATTTTTACTACATTTTTTGTTGTTGCTTT
140523 TGTTCTTT
1 TGTTCTTT
140531 GAATATTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
53 4 0.08
54 4 0.08
55 44 0.83
56 1 0.02
ACGTcount: A:0.05, C:0.08, G:0.18, T:0.69
Consensus pattern (54 bp):
TGTTCTTTTTTGCTGTTTTGCTGCTATTTTTACTACATTTTTTGTTGTTGCTTT
Found at i:140714 original size:26 final size:26
Alignment explanation
Indices: 140662--140714 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
140652 ATTATAAAGA
*
140662 ATTTTTAATGTATTTTAAATTTATTT
1 ATTTTTAATGTATTTTAAATATATTT
140688 ATTTTTAATGCTTATTTT-AATAT-TTT
1 ATTTTTAATG--TATTTTAAATATATTT
140714 A
1 A
140715 AGTGTATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 14 0.58
27 4 0.17
28 6 0.25
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (26 bp):
ATTTTTAATGTATTTTAAATATATTT
Found at i:155426 original size:23 final size:23
Alignment explanation
Indices: 155395--155438 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
155385 CTCGAATAAA
* *
155395 TTTCATTTGATTTTATCTCTTTT
1 TTTCATTTGATCTAATCTCTTTT
*
155418 TTTCTTTTGATCTAATCTCTT
1 TTTCATTTGATCTAATCTCTT
155439 CTTCTTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.16, G:0.05, T:0.66
Consensus pattern (23 bp):
TTTCATTTGATCTAATCTCTTTT
Found at i:156257 original size:23 final size:23
Alignment explanation
Indices: 156231--156357 Score: 130
Period size: 23 Copynumber: 5.4 Consensus size: 23
156221 AGTGCTGGGC
* *
156231 AACAGAGAGCACATACTGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
156254 AACAGAGAGCACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* * *
156277 ATCAGAGAGCACATAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
156300 ATCAGAGAGCACACACAGTACTAA
1 AACAGAGAGCACACACAGTGCT-A
*
156324 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
156348 AACAGAGAGC
1 AACAGAGAGC
156358 GCGCTAGTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 68 0.77
24 2 0.02
25 15 0.17
26 3 0.03
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:156283 original size:46 final size:46
Alignment explanation
Indices: 156232--156357 Score: 173
Period size: 46 Copynumber: 2.7 Consensus size: 46
156222 GTGCTGGGCA
156232 ACAGAGAGCACATACTGTGCTAAACAGAGAGCACACAAAGTACTAAT
1 ACAGAGAGCACATAC-GTGCTAAACAGAGAGCACACAAAGTACTAAT
* * *
156279 -CAGAGAGCACATAAAGTGCTAATCAGAGAGCACACACAGTACTAAT
1 ACAGAGAGCACAT-ACGTGCTAAACAGAGAGCACACAAAGTACTAAT
*
156325 AACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 -ACAGAGAGCAC-ATACGTGCTAAACAGAGAGC
156358 GCGCTAGTGT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
46 41 0.59
47 1 0.01
48 26 0.38
49 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (46 bp):
ACAGAGAGCACATACGTGCTAAACAGAGAGCACACAAAGTACTAAT
Done.