Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004834.1 Kokia drynarioides strain JFW-HI SEQ_118477, 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: 141300
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:11627 original size:43 final size:43
Alignment explanation
Indices: 11302--11692 Score: 173
Period size: 43 Copynumber: 9.1 Consensus size: 43
11292 TTTCCTCGTA
* ** * * *
11302 AGTGCATTATCGAATAAACCGAAGCAACCATAATGGCACAAAC
1 AGTGCATCATCGAATAAACTAAAGCAACTATATTGGCACACAC
* * * * * * * *
11345 AATGCATCATAGGATATA-TCGAAGTAACTATATTGGCACATAT
1 AGTGCATCATCGAATAAACT-AAAGCAACTATATTGGCACACAC
* ** * * * * *
11388 AGTGCATCATCGGATCTACCAAAGCATCTATACTAGTACACAC
1 AGTGCATCATCGAATAAACTAAAGCAACTATATTGGCACACAC
* * * * ** *
11431 AGTGCATCATAGGATAAATCGAAA-CATCTATGCTAGCACACA-
1 AGTGCATCATCGAATAAA-CTAAAGCAACTATATTGGCACACAC
* * * * * * * *
11473 TGATGCATCACCGGATAAATTGAAGCAACTATATTGACATACAA
1 AG-TGCATCATCGAATAAACTAAAGCAACTATATTGGCACACAC
* * **
11517 AGAGCATCATCGGATAAAC-AAAGCAACTATACGGGCACACAC
1 AGTGCATCATCGAATAAACTAAAGCAACTATATTGGCACACAC
* * * ** * * * *
11559 AATGCATAAAT-GGATAGGCCAAAGCATA-TATGTTGGCACATAT
1 AGTGCAT-CATCGAATAAACTAAAGCA-ACTATATTGGCACACAC
*
11602 AGTGCATCATCGAATAAACTGAAGCAACTATATTGGCACACAC
1 AGTGCATCATCGAATAAACTAAAGCAACTATATTGGCACACAC
* * * * * * *
11645 AGTGTATCATCGTATATACTAAAGCAACTAAACTAGCACACAT
1 AGTGCATCATCGAATAAACTAAAGCAACTATATTGGCACACAC
11688 AGTGC
1 AGTGC
11693 TTAATAGCAT
Statistics
Matches: 257, Mismatches: 80, Indels: 22
0.72 0.22 0.06
Matches are distributed among these distances:
42 34 0.13
43 217 0.84
44 6 0.02
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (43 bp):
AGTGCATCATCGAATAAACTAAAGCAACTATATTGGCACACAC
Found at i:13727 original size:46 final size:46
Alignment explanation
Indices: 13659--13750 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
13649 GCTTAACTCG
*
13659 AATGGACAATATATGGGTTTACCTCATAAAGATAAAAGAGAGCATA
1 AATGGACAATATATGGGCTTACCTCATAAAGATAAAAGAGAGCATA
* *
13705 AATGGGCAATATATGGGCTTACCTCATGAAGATAAAAGAGAGCATA
1 AATGGACAATATATGGGCTTACCTCATAAAGATAAAAGAGAGCATA
13751 TTAAGTCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (46 bp):
AATGGACAATATATGGGCTTACCTCATAAAGATAAAAGAGAGCATA
Found at i:21400 original size:42 final size:41
Alignment explanation
Indices: 21241--21400 Score: 149
Period size: 41 Copynumber: 3.8 Consensus size: 41
21231 CGGGTTGAAC
* * * * *
21241 ATGAGAATTTGTATAAATGGAAGACTCATGACTCGAAATGAGC
1 ATGAGAATATG-ATTAA-GGAAGACTCATAACTCGAGATGAGA
* * * * ** *
21284 ATTAGATTATGAATAAGCAAGACTCATGTCTCGAGATGGGA
1 ATGAGAATATGATTAAGGAAGACTCATAACTCGAGATGAGA
* *
21325 ATGAGATTATGATTAAGGAAGACTCATATCTCGAGATGAGA
1 ATGAGAATATGATTAAGGAAGACTCATAACTCGAGATGAGA
* *
21366 ATGAGAATATGGTTAAAGGAAGACTTATAACTCGA
1 ATGAGAATATGATT-AAGGAAGACTCATAACTCGA
21401 TAGAGCAGAA
Statistics
Matches: 97, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
41 68 0.70
42 21 0.22
43 8 0.08
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (41 bp):
ATGAGAATATGATTAAGGAAGACTCATAACTCGAGATGAGA
Found at i:29763 original size:8 final size:7
Alignment explanation
Indices: 29742--29798 Score: 51
Period size: 7 Copynumber: 7.4 Consensus size: 7
29732 AGTCATTTAT
*
29742 AAAAAAA
1 AAAAAAG
29749 AAAAAAG
1 AAAAAAG
29756 AAAGAAAG
1 AAA-AAAG
29764 AAAGAAGAGG
1 AAA-AA-A-G
*
29774 AAAAGAG
1 AAAAAAG
29781 AAAAGAAG
1 AAAA-AAG
29789 AAAAAAG
1 AAAAAAG
29796 AAA
1 AAA
29799 TATATGATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
7 20 0.47
8 17 0.40
9 2 0.05
10 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:29783 original size:25 final size:25
Alignment explanation
Indices: 29749--29796 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
29739 TATAAAAAAA
*
29749 AAAAAAG-AAAGAAAGAAAGAAGAGG
1 AAAAAAGAAAAG-AAGAAAAAAGAGG
*
29774 AAAAGAGAAAAGAAGAAAAAAGA
1 AAAAAAGAAAAGAAGAAAAAAGA
29797 AATATATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAAGAAGAAAAAAGAGG
Found at i:31797 original size:127 final size:126
Alignment explanation
Indices: 31607--31840 Score: 342
Period size: 127 Copynumber: 1.8 Consensus size: 126
31597 AACCGTAGTT
* * * * *
31607 CATCACTAGATATACCAAAGCATCTATACTGGTACACACAGTGCATCATCGGATGAATTGAAGCA
1 CATCACTAGATATACCAAAGCATCTATACTAGCACACACAGTGCATCAACGGATAAATCGAAGCA
* ** *
31672 ACTATATTGGCATACACAGTGCATCATCGAATTAATCGAAGCAACTATACTAGCACACAGTA
66 ACTATACTAACATACACAGTGCATCATCGAA-TAATCAAAGCAACTATACTAGCACACAGTA
* *
31734 CATCATTAGATATACCAAAGCATCTATACTAGCACACACGGTGCATCAACGGATAAATCGAAGCA
1 CATCACTAGATATACCAAAGCATCTATACTAGCACACACAGTGCATCAACGGATAAATCGAAGCA
* *
31799 ACTATACTAACATACACAGTGTATCATCGGATAATCAAAGCA
66 ACTATACTAACATACACAGTGCATCATCGAATAATCAAAGCA
31841 TCACATGTAC
Statistics
Matches: 94, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
126 10 0.11
127 84 0.89
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (126 bp):
CATCACTAGATATACCAAAGCATCTATACTAGCACACACAGTGCATCAACGGATAAATCGAAGCA
ACTATACTAACATACACAGTGCATCATCGAATAATCAAAGCAACTATACTAGCACACAGTA
Found at i:31830 original size:43 final size:43
Alignment explanation
Indices: 31560--31840 Score: 207
Period size: 43 Copynumber: 6.6 Consensus size: 43
31550 AGGCCGATCA
* *
31560 AGTGCATCATTGGATAAATCGAAGCATA-TATATTAGCA-AC-C
1 AGTGCATCATCGGATAAATCGAAGCA-ACTATACTAGCATACAC
* * * * * * * * *
31601 GTAGTTCATCA-CTAGATATACCAAAGCATCTATACTGGTACACAC
1 --AGTGCATCATC-GGATAAATCGAAGCAACTATACTAGCATACAC
* * * *
31646 AGTGCATCATCGGATGAATTGAAGCAACTATATTGGCATACAC
1 AGTGCATCATCGGATAAATCGAAGCAACTATACTAGCATACAC
* *
31689 AGTGCATCATCGAATTAATCGAAGCAACTATACTAGC--ACAC
1 AGTGCATCATCGGATAAATCGAAGCAACTATACTAGCATACAC
* ** * * * * *
31730 AGTACATCATTAGATATACCAAAGCATCTATACTAGCACACAC
1 AGTGCATCATCGGATAAATCGAAGCAACTATACTAGCATACAC
* * *
31773 GGTGCATCAACGGATAAATCGAAGCAACTATACTAACATACAC
1 AGTGCATCATCGGATAAATCGAAGCAACTATACTAGCATACAC
* *
31816 AGTGTATCATCGGAT-AATCAAAGCA
1 AGTGCATCATCGGATAAATCGAAGCA
31841 TCACATGTAC
Statistics
Matches: 181, Mismatches: 50, Indels: 15
0.74 0.20 0.06
Matches are distributed among these distances:
41 32 0.18
42 9 0.05
43 136 0.75
44 3 0.02
45 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (43 bp):
AGTGCATCATCGGATAAATCGAAGCAACTATACTAGCATACAC
Found at i:35546 original size:46 final size:46
Alignment explanation
Indices: 35465--35557 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
35455 ATCTATTTAA
** * * *
35465 AAGGTTGAAAAACCTTATTTTAATCAATGTCAAATAGATGAAGTGT
1 AAGGTTGAAAAACCTTATTTTAATCAAAATAAAATAAAAGAAGTGT
*
35511 AAGGTTGAAAAA-CTTTTTTCTAATCAAAATAAAATAAAAGAAGTGT
1 AAGGTTGAAAAACCTTATTT-TAATCAAAATAAAATAAAAGAAGTGT
35557 A
1 A
35558 GTTCTATATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
45 6 0.15
46 34 0.85
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (46 bp):
AAGGTTGAAAAACCTTATTTTAATCAAAATAAAATAAAAGAAGTGT
Found at i:41359 original size:13 final size:11
Alignment explanation
Indices: 41329--41353 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41319 TTACAAATAA
41329 AATAATTTTTT
1 AATAATTTTTT
41340 AATAATTTTTT
1 AATAATTTTTT
41351 AAT
1 AAT
41354 TGAATTGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATAATTTTTT
Found at i:42031 original size:29 final size:28
Alignment explanation
Indices: 41985--42039 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
41975 ATTGAATCAA
* * *
41985 AATTTTATCATTTTTTAAAGTTAAAATAT
1 AATTTTATCATATATT-AACTTAAAATAT
*
42014 AATTTTATTATATATTAACTTAAAAT
1 AATTTTATCATATATTAACTTAAAAT
42040 TTATAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 9 0.41
29 13 0.59
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (28 bp):
AATTTTATCATATATTAACTTAAAATAT
Found at i:51038 original size:27 final size:27
Alignment explanation
Indices: 51007--51061 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
50997 AGTTGTGTTT
*
51007 GCCAACAAGTTTGGCGAGCTAGGGTTC
1 GCCAACAAGTTTGGCGAGCTACGGTTC
*
51034 GCCAACAGGTTTGGCGAGCTACGGTTC
1 GCCAACAAGTTTGGCGAGCTACGGTTC
51061 G
1 G
51062 TCAGTATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.22
Consensus pattern (27 bp):
GCCAACAAGTTTGGCGAGCTACGGTTC
Found at i:55938 original size:32 final size:27
Alignment explanation
Indices: 55879--55941 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
55869 ACAAGCAAGG
55879 GGAAGGAAAAAAAAGAAGGGAATGTAA
1 GGAAGGAAAAAAAAGAAGGGAATGTAA
*
55906 GGAAGGAAAAAAAAGAAGGGAAGGTAA
1 GGAAGGAAAAAAAAGAAGGGAATGTAA
55933 GGTAAGGAA
1 GG-AAGGAA
55942 CATAAGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 28 0.82
28 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.06
Consensus pattern (27 bp):
GGAAGGAAAAAAAAGAAGGGAATGTAA
Found at i:62433 original size:27 final size:27
Alignment explanation
Indices: 62403--62455 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
62393 AAAAAGAAGG
* *
62403 TTTTTTGAAATGTATGTTTATGTTTTA
1 TTTTTTGAAAGGTATGTTTATCTTTTA
62430 TTTTTTGAAAGGTATGTTTATCTTTT
1 TTTTTTGAAAGGTATGTTTATCTTTT
62456 TCCTTTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.02, G:0.15, T:0.62
Consensus pattern (27 bp):
TTTTTTGAAAGGTATGTTTATCTTTTA
Found at i:62662 original size:17 final size:17
Alignment explanation
Indices: 62640--62677 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
62630 TAATATTTTT
62640 TAATTT-ATTGAAAATAA
1 TAATTTAATT-AAAATAA
62657 TAATTTAATTAAAATAA
1 TAATTTAATTAAAATAA
62674 -AATT
1 TAATT
62678 AATGAATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 13 0.65
18 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAATTTAATTAAAATAA
Found at i:64596 original size:27 final size:27
Alignment explanation
Indices: 64566--64628 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
64556 TCATCCAGGG
64566 TGGTCAGGCAATGGATATCAAACGAGT
1 TGGTCAGGCAATGGATATCAAACGAGT
* * *
64593 TGGTCAGGCCATGGATATCATACGGGT
1 TGGTCAGGCAATGGATATCAAACGAGT
*
64620 TGGCCAGGC
1 TGGTCAGGC
64629 TAGGAGTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (27 bp):
TGGTCAGGCAATGGATATCAAACGAGT
Found at i:65023 original size:26 final size:26
Alignment explanation
Indices: 64991--65239 Score: 363
Period size: 26 Copynumber: 9.6 Consensus size: 26
64981 TTTCATTTGG
*
64991 AATTAATTATGTTTATATTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
*
65017 AATTAATAATGTTTATGTTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
*
65043 AATTAACTATGTTTATGTTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
** *
65069 AATTAACAATGTTTATGTTTTTATTT
1 AATTAATTATGTTTATGTTTGTATTT
* *
65095 AATCAATTATGTTTATGTTTTTATTT
1 AATTAATTATGTTTATGTTTGTATTT
* *
65121 AATCAATTATGTTTATATTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
* *
65147 CATTAATTATGTTTATATTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
*
65173 CATTAATTATGTTTATGTTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
* *
65199 AATTAATTATATTTATGTTTGCATTT
1 AATTAATTATGTTTATGTTTGTATTT
65225 AATTAATTATGTTTA
1 AATTAATTATGTTTA
65240 GGGTTTAAGG
Statistics
Matches: 205, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 205 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (26 bp):
AATTAATTATGTTTATGTTTGTATTT
Found at i:65252 original size:14 final size:15
Alignment explanation
Indices: 65234--65275 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
65224 TAATTAATTA
65234 TGTTTAGGGTTTAAG
1 TGTTTAGGGTTTAAG
*
65249 -GTTTAAGGTTT-AG
1 TGTTTAGGGTTTAAG
*
65262 TGTTAAGGGTTTAA
1 TGTTTAGGGTTTAA
65276 CCCTGATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
13 2 0.09
14 19 0.86
15 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (15 bp):
TGTTTAGGGTTTAAG
Found at i:65259 original size:21 final size:21
Alignment explanation
Indices: 65235--65275 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
65225 AATTAATTAT
65235 GTTTAGGGTTTAA-GGTTTAAG
1 GTTTAGGG-TTAAGGGTTTAAG
*
65256 GTTTAGTGTTAAGGGTTTAA
1 GTTTAGGGTTAAGGGTTTAA
65276 CCCTGATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
GTTTAGGGTTAAGGGTTTAAG
Found at i:92994 original size:26 final size:22
Alignment explanation
Indices: 92950--93030 Score: 135
Period size: 22 Copynumber: 3.7 Consensus size: 22
92940 AAAAAAATTT
*
92950 TCAATTAAATTGGCACAATCAA
1 TCAATTATATTGGCACAATCAA
*
92972 TCAATTATATTGGCGCAATCAA
1 TCAATTATATTGGCACAATCAA
92994 TCAATTATATTGGCACAATCAA
1 TCAATTATATTGGCACAATCAA
*
93016 TCAATTATATGGGCA
1 TCAATTATATTGGCA
93031 TATTACATCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (22 bp):
TCAATTATATTGGCACAATCAA
Found at i:95150 original size:19 final size:19
Alignment explanation
Indices: 95126--95171 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
95116 TACAAAATAA
95126 TCAAAATAATTT-TAAAAAT
1 TCAAAAT-ATTTATAAAAAT
*
95145 TCAAAATATTTATAGAAAT
1 TCAAAATATTTATAAAAAT
95164 TCTAAAAT
1 TC-AAAAT
95172 TATATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 15 0.62
20 5 0.21
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (19 bp):
TCAAAATATTTATAAAAAT
Found at i:95910 original size:17 final size:18
Alignment explanation
Indices: 95869--95910 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
95859 AGGTACATCC
95869 AACTAAAACTCTAAAGTA
1 AACTAAAACTCTAAAGTA
* * *
95887 TACTAAAATTCT-AATTA
1 AACTAAAACTCTAAAGTA
95904 AACTAAA
1 AACTAAA
95911 CAAGAAATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (18 bp):
AACTAAAACTCTAAAGTA
Found at i:104740 original size:5 final size:5
Alignment explanation
Indices: 104730--104756 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
104720 ATAAAAACCA
104730 AAATT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AA
104757 CTATAGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:123729 original size:2 final size:2
Alignment explanation
Indices: 123722--123753 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
123712 CTAAAATGAT
123722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123754 ATTGACTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:126577 original size:195 final size:194
Alignment explanation
Indices: 126173--126618 Score: 451
Period size: 195 Copynumber: 2.3 Consensus size: 194
126163 AATCGACGCA
* * * *
126173 ATGGCTTAGGTACCACATATGTTGCT-AGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGT
1 ATGGCTGAGGTACCGCATATGTT-ATGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGT
*
126237 GAAATGAAAAAAGAATCTAAAAATGGATTACAGACCCTACGATGGCTGACATTTATGCATAAGTG
65 GAAATGAAAAAAGAATCT-AAAATGGATTAAAGACCCTACGATGGCTGACATTTATGCATAAGTG
* * * *
126302 CATATTCTCGACAACTCATGTGAGCAGCATCGTTAAGGAATAGTTATATGCACAGAAATCGTATC
129 CATACTCTCGACAACTCATGTGAGCAGCAACATTAAGGAATAGTTATATGCACAGAAATCGTACC
126367 G
194 G
* *
126368 ATGGCTGAGGTACCGCATATGTTATGAGTACTCGACAGCTCGTGTGAGCAACATCGTGACTCAG-
1 ATGGCTGAGGTACCGCATATGTTATGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTC-GT
* * * * * ** * *
126432 GAAA-GAGATATGGATCCT-AAATGGATTATAAG-CCCTACGATGGTTGGGA-TTATGCTTTA-T
65 GAAATGAAAAAAGAAT-CTAAAATGGATTA-AAGACCCTACGATGGCTGACATTTATGCATAAGT
* * *
126492 GCATACTCTCGACAACTCGTGTGAGCAGCAACATTAGGGAATAGTT-TATAGTACAGACAGCCA-
128 GCATACTCTCGACAACTCATGTGAGCAGCAACATTAAGGAATAGTTATAT-GCACAGA-A---AT
126555 CTGTACCG
188 C-GTACCG
* * ** * * * *
126563 ATGGTTGGGGTACCGCATACATTGTGAGTCCCCGACAACTCATGTGAGCAGCATCG
1 ATGGCTGAGGTACCGCATATGTTATGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
126619 AGTACTGGTA
Statistics
Matches: 208, Mismatches: 33, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
190 3 0.01
191 48 0.23
192 9 0.04
193 24 0.12
194 11 0.05
195 112 0.54
196 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (194 bp):
ATGGCTGAGGTACCGCATATGTTATGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGTG
AAATGAAAAAAGAATCTAAAATGGATTAAAGACCCTACGATGGCTGACATTTATGCATAAGTGCA
TACTCTCGACAACTCATGTGAGCAGCAACATTAAGGAATAGTTATATGCACAGAAATCGTACCG
Found at i:131704 original size:52 final size:51
Alignment explanation
Indices: 131622--131816 Score: 230
Period size: 52 Copynumber: 3.8 Consensus size: 51
131612 CCATAAACAA
* * * * * *
131622 AAAGGTCCAATGATTATGAGCCATCGTGAGTATATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATT
* *
131673 AAACGGTCCGATGACTAAGTGTCATTGTGAGTATATGGATCCTTTATGGATT
1 AAA-GGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATT
* * * *
131725 AAGAGGTCCGATGACTCTGTGTCATTGTGAGTATATGAATCCCTTGTGGAAT
1 AA-AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATT
*
131777 ATAAGGTCC-AGTGGCTATGTGTCATTGTGAGTATATGAAT
1 A-AAGGTCCGA-TGACTATGTGTCATTGTGAGTATATGAAT
131817 GAAGTGAAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
51 4 0.03
52 118 0.95
53 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (51 bp):
AAAGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATT
Found at i:132339 original size:24 final size:24
Alignment explanation
Indices: 132307--132359 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
132297 TGAATTGTGA
132307 GTATCAGTAGTTATATGTATAGAT
1 GTATCAGTAGTTATATGTATAGAT
132331 GTATCAGTAGTTATATGTATAGAT
1 GTATCAGTAGTTATATGTATAGAT
132355 GTATC
1 GTATC
132360 GATAGGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.42
Consensus pattern (24 bp):
GTATCAGTAGTTATATGTATAGAT
Done.