Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009841.1 Kokia drynarioides strain JFW-HI SEQ_124565, 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: 30689
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:830 original size:62 final size:62
Alignment explanation
Indices: 733--1083 Score: 435
Period size: 62 Copynumber: 5.8 Consensus size: 62
723 AATAAAAAGT
* * * * * **
733 AAAAAAATTTGCAATTTTTTTATCTGAGAATAGGAGGTATTGGCCATTGCATAACCAACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGGCCATTGCATGGCCAACACC
*
795 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGACCATTGCATGGCCAACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGGCCATTGCATGGCCAACACC
* * * * *
857 -AAAAAA--TGCAATTTTTTTATCAGAAAAAAAG-GGTGTCGGCCATTGTATGGCCAACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGGCCATTGCATGGCCAACACC
* * * *
915 AAAAAAATTTGAAAATTTTTTATCCGAAAAAAGGGGGTGTCGGCCATTACATGGCCAACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGGCCATTGCATGGCCAACACC
* * * * *
977 AAAAAAATTTGAAAATTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCAAGACCAACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGGCCATTGCATGGCCAACACC
* * *
1039 AAAAAAATTTGAAA-TTTTTTATCTGA-AAAAGGGGGTGTCGACCAT
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGGCCAT
1084 GCACCCAAAA
Statistics
Matches: 259, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
58 25 0.10
59 27 0.10
60 19 0.07
61 38 0.15
62 150 0.58
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (62 bp):
AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGGCCATTGCATGGCCAACACC
Found at i:1040 original size:182 final size:174
Alignment explanation
Indices: 733--1179 Score: 510
Period size: 182 Copynumber: 2.5 Consensus size: 174
723 AATAAAAAGT
* * * * * * **
733 AAAAAAATTTGCAATTTTTTTATCTGAGAATAGGAGGTATTGGCCATTGCATAACCAACACCAAA
1 AAAAAAATTTGCAATTTTTTTATCAGAAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCAAA
* * *
798 AAAATTTGAAATTTTTTTATCCGAGAAAAGGAGGTGTCGACCATTGCATGGCCAACACC-AAAAA
66 AAAATTTGAAAATTTTTTATCCGAGAAAAGGAGGTGTCGACCATTGCAAGACCAACACCAAAAAA
* *
862 A-TGCAATTTTTTTATCAGAAAAAAAGGGTGTCGGCCATTGTATGGCCAACACC
131 ATTG-AAATTTTTTATCAGAAAAAAAGGGTGTCGACC-----AT-G-C-AC-CC
* * * *
915 AAAAAAATTTGAAAATTTTTTATCCGAAAAAAGGGGGTGTCGGCCATTACATGGCCAACACCAAA
1 AAAAAAATTTGCAATTTTTTTATCAGAAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCAAA
*
980 AAAATTTGAAAATTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCAAGACCAACACCAAAAAA
66 AAAATTTGAAAATTTTTTATCCGAGAAAAGGAGGTGTCGACCATTGCAAGACCAACACCAAAAAA
* **
1045 ATTTGAAATTTTTTATCTGAAAAAGGGGGTGTCGACCATGCACCC
131 A-TTGAAATTTTTTATCAGAAAAAAAGGGTGTCGACCATGCACCC
* * * *
1090 --AAAAA--TGCAATTTTTTTATCAGAAAAAAGAGGATGTCGGTCATTGCATGGTCAACACCAAA
1 AAAAAAATTTGCAATTTTTTTATCAGAAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCAAA
* *
1151 ACAATTTGAAAATTTTTTATCCAAGAAAA
66 AAAATTTGAAAATTTTTTATCCGAGAAAA
1180 AGGGCATGGC
Statistics
Matches: 232, Mismatches: 30, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
171 75 0.32
173 5 0.02
175 2 0.01
176 2 0.01
177 1 0.00
178 1 0.00
179 2 0.01
182 109 0.47
183 6 0.03
184 27 0.12
185 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (174 bp):
AAAAAAATTTGCAATTTTTTTATCAGAAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCAAA
AAAATTTGAAAATTTTTTATCCGAGAAAAGGAGGTGTCGACCATTGCAAGACCAACACCAAAAAA
ATTGAAATTTTTTATCAGAAAAAAAGGGTGTCGACCATGCACCC
Found at i:1255 original size:110 final size:107
Alignment explanation
Indices: 964--1263 Score: 275
Period size: 109 Copynumber: 2.7 Consensus size: 107
954 TCGGCCATTA
* * * * * * * *
964 CATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCAA
1 CATGGCCGACACAAAAAAAATTTGAAATTTTTTTATCAGA-AAAAGGAGGTGTCGGCTATTGCAT
*
1029 GACCAACACCAAAAAAATTTGAAATTTTTTATCTGAAAAAGGG
65 GACCAACACCAAAAAAATTTGAAATTTTTTATCAGAAAAAGGG
** * ** * *
1072 GGT-GTCGACCATGCACCCAAAAA--TGCAATTTTTTTATCAGAAAAAAGAGGATGTCGG-TCAT
1 CATGGCCGA-CA--CA-AAAAAAATTTGAAATTTTTTTATCAGAAAAAGGAGG-TGTCGGCT-AT
** *
1133 TGCATGGTCAACACCAAAACAATTTGAAAATTTTTTATCCAAGAAAAAGGG
60 TGCATGACCAACACCAAAAAAATTTG-AAATTTTTTAT-C-AGAAAAAGGG
* * *
1184 CATGGCCGACACAAAAAAAATTTTAAATTTTTTTATCTGAAAATGGAGGTGTCGGCTATTGCATG
1 CATGGCCGACACAAAAAAAATTTGAAATTTTTTTATCAGAAAAAGGAGGTGTCGGCTATTGCATG
*
1249 ACCAACACCCAAAAA
66 ACCAACACCAAAAAA
1264 TGCAATTTTT
Statistics
Matches: 146, Mismatches: 33, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
107 3 0.02
108 10 0.07
109 49 0.34
110 39 0.27
111 29 0.20
112 12 0.08
113 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (107 bp):
CATGGCCGACACAAAAAAAATTTGAAATTTTTTTATCAGAAAAAGGAGGTGTCGGCTATTGCATG
ACCAACACCAAAAAAATTTGAAATTTTTTATCAGAAAAAGGG
Found at i:1336 original size:60 final size:59
Alignment explanation
Indices: 1211--1449 Score: 206
Period size: 59 Copynumber: 4.1 Consensus size: 59
1201 AAATTTTAAA
* * * * ** *
1211 TTTTTTTATCTG---AAAATGGAGGTGTCGGCTATTGCATGACCAACACCCAAAAATGCAA
1 TTTTTTTATCTGACAAAAAAGGA-GTGTCGACCATTGCATGGCCAACA-CCAAAAATTTAT
*
1269 TTTTTTTATCTGA-AAAAAAGGAGTGCCGACCATTGCATGGCCAACATCCAAAAACTTTAT
1 TTTTTTTATCTGACAAAAAAGGAGTGTCGACCATTGCATGGCCAACA-CCAAAAA-TTTAT
* * * * * *
1329 TTTTTTTATCAGATAAATAA-GAGTGTC-AGCCATTGTATGGCCAACACAAAAAAATTAT
1 TTTTTTTATCTGACAAAAAAGGAGTGTCGA-CCATTGCATGGCCAACACCAAAAATTTAT
* * ** *
1387 ATTTTTTATCTGACAAAAAAGGAGTGTCGGCCATTGCATGAACAACACC-TAAATTT-T
1 TTTTTTTATCTGACAAAAAAGGAGTGTCGACCATTGCATGGCCAACACCAAAAATTTAT
1444 TTTTTT
1 TTTTTT
1450 CAAATTCTCG
Statistics
Matches: 147, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
57 6 0.04
58 37 0.25
59 56 0.38
60 43 0.29
61 5 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (59 bp):
TTTTTTTATCTGACAAAAAAGGAGTGTCGACCATTGCATGGCCAACACCAAAAATTTAT
Found at i:1373 original size:119 final size:118
Alignment explanation
Indices: 1211--1426 Score: 276
Period size: 119 Copynumber: 1.8 Consensus size: 118
1201 AAATTTTAAA
* * * * **
1211 TTTTTTTATCTGAAAATGGAGGTGTCGGCTATTGCATGACCAACACCCAAAAATGCAAT-TTTTT
1 TTTTTTTATCAGAAAATAGAGGTGTCAGCCATTGCATGACCAACACAAAAAAAT--AATATTTTT
1275 TATCTGA-AAAAAAGGAGTGCCGACCATTGCATGGCCAACATCCAAAAACTTTAT
64 TATCTGACAAAAAAGGAGTGCCGACCATTGCATGGCCAACATCCAAAAACTTTAT
* * *
1329 TTTTTTTATCAGATAAATA-AGAGTGTCAGCCATTGTATGGCCAACACAAAAAAATTATATTTTT
1 TTTTTTTATCAGA-AAATAGAG-GTGTCAGCCATTGCATGACCAACACAAAAAAATAATATTTTT
* *
1393 TATCTGACAAAAAAGGAGTGTCGGCCATTGCATG
64 TATCTGACAAAAAAGGAGTGCCGACCATTGCATG
1427 AACAACACCT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
117 2 0.02
118 26 0.31
119 55 0.66
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (118 bp):
TTTTTTTATCAGAAAATAGAGGTGTCAGCCATTGCATGACCAACACAAAAAAATAATATTTTTTA
TCTGACAAAAAAGGAGTGCCGACCATTGCATGGCCAACATCCAAAAACTTTAT
Found at i:1489 original size:18 final size:18
Alignment explanation
Indices: 1466--1501 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1456 CTCGTATTTT
* *
1466 CGTATTTCAATAAAATAC
1 CGTATTTAAAAAAAATAC
1484 CGTATTTAAAAAAAATAC
1 CGTATTTAAAAAAAATAC
1502 ATAGATGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.31
Consensus pattern (18 bp):
CGTATTTAAAAAAAATAC
Found at i:2849 original size:11 final size:11
Alignment explanation
Indices: 2835--2873 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2825 GTTTTGCTAC
2835 TATTTTTTCAT
1 TATTTTTTCAT
**
2846 TATTTTTTTGT
1 TATTTTTTCAT
*
2857 TATTTTTTCAC
1 TATTTTTTCAT
2868 TATTTT
1 TATTTT
2874 GCTGTCATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTTTTCAT
Found at i:2883 original size:22 final size:22
Alignment explanation
Indices: 2836--2883 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2826 TTTTGCTACT
* ** *
2836 ATTTTTTCATTATTTTTTTGTT
1 ATTTTTTCACTATTTTGCTGTC
2858 ATTTTTTCACTATTTTGCTGTC
1 ATTTTTTCACTATTTTGCTGTC
2880 ATTT
1 ATTT
2884 CACAATTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.06, T:0.69
Consensus pattern (22 bp):
ATTTTTTCACTATTTTGCTGTC
Found at i:3547 original size:22 final size:21
Alignment explanation
Indices: 3502--3549 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3492 CCTTAAAAAT
*
3502 TATA-AAAAAAATAGAAATAA
1 TATATAAAAAAATACAAATAA
*
3522 -ATATAAAAAAATTCAAATATA
1 TATATAAAAAAATACAAATA-A
3543 TATATAA
1 TATATAA
3550 TCTAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 1 0.04
22 6 0.26
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TATATAAAAAAATACAAATAA
Found at i:3556 original size:57 final size:59
Alignment explanation
Indices: 3478--3589 Score: 142
Period size: 57 Copynumber: 1.9 Consensus size: 59
3468 TTTCTTCTGC
*
3478 CAAACATATATAAACCTTAAAAAT-TATAAAAAAAATA-GAAATAAA-TATAAAAAAATT
1 CAAACATATATAAACCTTAAAAATATAT-AAAAAAATAGGAAACAAACTATAAAAAAATT
* * *
3535 CAAATATATATATAATC-TAAAAATATATATAAAAATAGGAAACAAACTATAAAAA
1 CAAACATATATA-AACCTTAAAAATATATAAAAAAATAGGAAACAAACTATAAAAA
3590 GTATATATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 26 0.55
58 13 0.28
59 8 0.17
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (59 bp):
CAAACATATATAAACCTTAAAAATATATAAAAAAATAGGAAACAAACTATAAAAAAATT
Found at i:7470 original size:2 final size:2
Alignment explanation
Indices: 7463--7499 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7453 TTGAATATTG
7463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7500 ATTTTATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8078 original size:35 final size:35
Alignment explanation
Indices: 8032--8103 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
8022 ATAAGGTACT
8032 TTATGTGAGCAATAAGTTCAAAGATTGATTCATTG
1 TTATGTGAGCAATAAGTTCAAAGATTGATTCATTG
8067 TTATGTGAGCAATAAGTTCAAAGATTGATTCATTG
1 TTATGTGAGCAATAAGTTCAAAGATTGATTCATTG
8102 TT
1 TT
8104 TAACATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (35 bp):
TTATGTGAGCAATAAGTTCAAAGATTGATTCATTG
Found at i:12885 original size:25 final size:23
Alignment explanation
Indices: 12836--12888 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
12826 TTTAATTTTT
*
12836 TTTTTGTAACTCTTTAGCCATTA
1 TTTTTGTAACTCTTCAGCCATTA
12859 TTTTTGTAACTCTTCAGCCATTA
1 TTTTTGTAACTCTTCAGCCATTA
*
12882 TATTTGT
1 TTTTTGT
12889 TTTAAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (23 bp):
TTTTTGTAACTCTTCAGCCATTA
Found at i:13270 original size:18 final size:18
Alignment explanation
Indices: 13243--13285 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
13233 ATGTTCATTT
13243 ATTT-TTATT-AATTTATA
1 ATTTATTATTAAATTTA-A
13260 ATTTATTATTAAATTTAA
1 ATTTATTATTAAATTTAA
13278 ATTGTATT
1 ATT-TATT
13286 TATATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTATTATTAAATTTAA
Found at i:18599 original size:25 final size:24
Alignment explanation
Indices: 18547--18595 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
18537 TTGCTTTAAT
*
18547 TTTTTTTGTAACTCTTCAACCATTA
1 TTTTTTTG-AACTCTTCAAACATTA
18572 TTTTTTTG-ACTCTTCAAACATTA
1 TTTTTTTGAACTCTTCAAACATTA
18595 T
1 T
18596 ATTTGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTTTTGAACTCTTCAAACATTA
Found at i:18982 original size:18 final size:19
Alignment explanation
Indices: 18959--18997 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
18949 TCATTTCTTT
18959 TTATT-AATTTACAATT-TA
1 TTATTAAATTTA-AATTATA
18977 TTATTAAATTTAAATTATA
1 TTATTAAATTTAAATTATA
18996 TT
1 TT
18998 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTATA
Found at i:19436 original size:45 final size:44
Alignment explanation
Indices: 19373--19463 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
19363 TCTGGCATGC
*
19373 TTTCACATGATGCCATAACATCTTTCAACTGTGATCTTACTCAT
1 TTTCACATGATGCCATAACATCTTTCAACTATGATCTTACTCAT
* *
19417 TTTCATCATGATGCCATAACATCTTTCAATTATGGTCTTACTCAT
1 TTTCA-CATGATGCCATAACATCTTTCAACTATGATCTTACTCAT
19462 TT
1 TT
19464 AGGCGTATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
44 5 0.12
45 38 0.88
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (44 bp):
TTTCACATGATGCCATAACATCTTTCAACTATGATCTTACTCAT
Found at i:19443 original size:23 final size:22
Alignment explanation
Indices: 19372--19444 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
19362 TTCTGGCATG
19372 CTTTCACATGATGCCATAACAT
1 CTTTCACATGATGCCATAACAT
* * *
19394 CTTTCA-ACTG-TGATCTTACTCAT
1 CTTTCACA-TGATG-CCATA-ACAT
19417 -TTTCATCATGATGCCATAACAT
1 CTTTCA-CATGATGCCATAACAT
19439 CTTTCA
1 CTTTCA
19445 ATTATGGTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 13
0.67 0.11 0.23
Matches are distributed among these distances:
21 3 0.08
22 19 0.50
23 13 0.34
24 3 0.08
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.38
Consensus pattern (22 bp):
CTTTCACATGATGCCATAACAT
Found at i:21787 original size:43 final size:43
Alignment explanation
Indices: 21704--21793 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
21694 GAATCACCAG
* ** *
21704 ATGTATAAATGGAAAACTCATGTCTCGGGATGAGCGTGAGATT
1 ATGTATAAATGGAAAACTCATGACTCGAAATGAGCATGAGATT
* *
21747 ATGTATAAATGGAATACTTATGACTCGAAATTG-GCATGAGATT
1 ATGTATAAATGGAAAACTCATGACTCGAAA-TGAGCATGAGATT
21790 ATGT
1 ATGT
21794 TTTAAGACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
43 38 0.95
44 2 0.05
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (43 bp):
ATGTATAAATGGAAAACTCATGACTCGAAATGAGCATGAGATT
Found at i:26304 original size:36 final size:37
Alignment explanation
Indices: 26256--26325 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
26246 CAGTGGATTC
26256 GAGAGTTTGCAGAGAGATGATCCAAAGCTTATAATTT
1 GAGAGTTTGCAGAGAGATGATCCAAAGCTTATAATTT
26293 GAGAG-TTGCAGAGAGATGATCCAAAGCTTATAA
1 GAGAGTTTGCAGAGAGATGATCCAAAGCTTATAA
26326 CTAAGAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 28 0.85
37 5 0.15
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (37 bp):
GAGAGTTTGCAGAGAGATGATCCAAAGCTTATAATTT
Found at i:27499 original size:49 final size:49
Alignment explanation
Indices: 27427--27524 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
27417 TGGCTTTACC
27427 ACCAAAACTGGAGAAGATTCATAATGTATTTCATGTGTCAATGCTGAGA
1 ACCAAAACTGGAGAAGATTCATAATGTATTTCATGTGTCAATGCTGAGA
*
27476 ACCAAAACTGGAGAAGATTCATAATGTATTTCATGTGTCTATGCTGAGA
1 ACCAAAACTGGAGAAGATTCATAATGTATTTCATGTGTCAATGCTGAGA
27525 CGGTATAGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (49 bp):
ACCAAAACTGGAGAAGATTCATAATGTATTTCATGTGTCAATGCTGAGA
Found at i:29015 original size:41 final size:41
Alignment explanation
Indices: 28903--29106 Score: 180
Period size: 42 Copynumber: 4.9 Consensus size: 41
28893 GTCTTGGGAT
* * * *
28903 GAGCATGAGATTATGTATAAATGAAAGACTCGTGACTCGGAAT
1 GAGCATGAGATTATGTTTAAA-GGAAGACTCATGACTC-GAAA
* *
28946 GAACATGAGATTATGTTTAAAGGAAGACTCATGTCTCGAAA
1 GAGCATGAGATTATGTTTAAAGGAAGACTCATGACTCGAAA
* * *
28987 GGAGCATGGGACTATG-TTAAAGGAAGACTCATGTCTCGGAAA
1 -GAGCATGAGATTATGTTTAAAGGAAGACTCATGACTC-GAAA
* * * * **
29029 GAGCGTGAGAATATGTTTAATGGAAGACTTATGACTCGGTA
1 GAGCATGAGATTATGTTTAAAGGAAGACTCATGACTCGAAA
* * *
29070 GAGCATAAGA-T-TGTTTGAAAGGAAGACTTATGGCTCG
1 GAGCATGAGATTATGTTT-AAAGGAAGACTCATGACTCG
29107 GTGTAGCATA
Statistics
Matches: 136, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
39 5 0.04
40 19 0.14
41 46 0.34
42 47 0.35
43 19 0.14
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (41 bp):
GAGCATGAGATTATGTTTAAAGGAAGACTCATGACTCGAAA
Found at i:29045 original size:83 final size:85
Alignment explanation
Indices: 28903--29066 Score: 206
Period size: 83 Copynumber: 2.0 Consensus size: 85
28893 GTCTTGGGAT
* * * *
28903 GAGCATGAGATTATGTATAAATGAAAGACTCGTGACTCGGAATGAACATGAGATTATGTTTAAAG
1 GAGCATGAGACTATGTATAAATGAAAGACTCATGACTCGGAAAGAACATGAGAATATGTTTAAAG
*
28968 GAAGACTCATGTCTCGAAAG
66 GAAGACTCATGACTCGAAAG
* * * * * *
28988 GAGCATGGGACTATGT-TAAA-GGAAGACTCATGTCTCGGAAAGAGCGTGAGAATATGTTTAATG
1 GAGCATGAGACTATGTATAAATGAAAGACTCATGACTCGGAAAGAACATGAGAATATGTTTAAAG
*
29051 GAAGACTTATGACTCG
66 GAAGACTCATGACTCG
29067 GTAGAGCATA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 49 0.73
84 4 0.06
85 14 0.21
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGAGACTATGTATAAATGAAAGACTCATGACTCGGAAAGAACATGAGAATATGTTTAAAG
GAAGACTCATGACTCGAAAG
Found at i:29099 original size:40 final size:39
Alignment explanation
Indices: 28959--29123 Score: 127
Period size: 41 Copynumber: 4.1 Consensus size: 39
28949 CATGAGATTA
* * ** **
28959 TGTTTAAAGGAAGACTCATGTCTCGAAAGGAGCATGGGACT
1 TGTTTAAAGGAAGACTTATGACTCGGTA-GAGCATAAGA-T
* * * * *
29000 ATG-TTAAAGGAAGACTCATGTCTCGGAAAGAGCGTGAGAAT
1 -TGTTTAAAGGAAGACTTATGACTCGG-TAGAGCATAAG-AT
*
29041 ATGTTTAATGGAAGACTTATGACTCGGTAGAGCATAAGAT
1 -TGTTTAAAGGAAGACTTATGACTCGGTAGAGCATAAGAT
*
29081 TGTTTGAAAGGAAGACTTATGGCTCGGT-GTAGCATAAGAT
1 TGTTT-AAAGGAAGACTTATGACTCGGTAG-AGCATAAGAT
29121 TGT
1 TGT
29124 CCAAAGAGGA
Statistics
Matches: 107, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
39 6 0.06
40 35 0.33
41 41 0.38
42 25 0.23
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (39 bp):
TGTTTAAAGGAAGACTTATGACTCGGTAGAGCATAAGAT
Done.