Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013426.1 Kokia drynarioides strain JFW-HI SEQ_128452, 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: 208157
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8026 original size:26 final size:26
Alignment explanation
Indices: 7964--8032 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
7954 AGAATTTCAA
*
7964 CCAAAATTGTCACTGCATGACGATGT
1 CCAAAATTGTCACTGCATGACGATGC
* *
7990 CTAGAAA-TGTCGCTGCATGA-GCATGC
1 CCA-AAATTGTCACTGCATGACG-ATGC
8016 CCAAAATTGTCACTGCA
1 CCAAAATTGTCACTGCA
8033 GGAACTCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 4 0.11
26 28 0.80
27 3 0.09
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (26 bp):
CCAAAATTGTCACTGCATGACGATGC
Found at i:24908 original size:51 final size:51
Alignment explanation
Indices: 24830--25122 Score: 451
Period size: 51 Copynumber: 5.7 Consensus size: 51
24820 TGGATCTCTT
* * * ** * *
24830 TTCATATACTCACGATGACACTGAGTCATCGGAACTTTAATCTATCATGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
*
24881 TTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
*
24932 TTCTTTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
* * *
24983 TGCATTTACTCATGATGACACTTAGTCAACGGACCTTTAATCCGTAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
*
25034 TTCATTTACTCACGATAACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
* *
25085 TTCATTTACTCACAATGACACTTAGTCATCAGACCTTT
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTT
25123 TCGTTTATAG
Statistics
Matches: 221, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 221 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
Found at i:34175 original size:15 final size:16
Alignment explanation
Indices: 34149--34179 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
34139 AGAAAAAATG
34149 AGAAAAAGGAAGAAAA
1 AGAAAAAGGAAGAAAA
34165 AGAAAAA-GAAGAAAA
1 AGAAAAAGGAAGAAAA
34180 CATTTATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAAGGAAGAAAA
Found at i:38915 original size:26 final size:26
Alignment explanation
Indices: 38881--38935 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
38871 CACCTAGGAA
*
38881 TGTCGCTGCATGAACATGTCCAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
* *
38907 TGTCACTGCATGAACGTGTCTAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
38933 TGT
1 TGT
38936 GCCTAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (26 bp):
TGTCACTGCATGAACATGTCCAGAAT
Found at i:39753 original size:16 final size:16
Alignment explanation
Indices: 39732--39762 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39722 TTATGGATCC
39732 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
39748 CATTTTATCTTTATT
1 CATTTTACCTTTATT
39763 TTCACATTAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:52385 original size:21 final size:21
Alignment explanation
Indices: 52359--52409 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
52349 TACAAATTTG
52359 TACCGATACAAGTGAC-T-CCTC
1 TACCGATACAAGT--CTTACCTC
52380 TACCGATACAAGTCTTACCTC
1 TACCGATACAAGTCTTACCTC
52401 TACCGATAC
1 TACCGATAC
52410 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 26 0.93
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.25
Consensus pattern (21 bp):
TACCGATACAAGTCTTACCTC
Found at i:53982 original size:262 final size:260
Alignment explanation
Indices: 53517--54045 Score: 907
Period size: 262 Copynumber: 2.0 Consensus size: 260
53507 AAAACGACTA
*
53517 TCATTTGCTCACCCAAATTAAAGCTCAAACATGGAAATGGAAAACCCTAATTTCTTCTCCTCTTG
1 TCATTTGCTCACCCAAATCAAAGCTCAAACATGGAAATGGAAAACCCTAATTTCTTCTCCTCTTG
* * * *
53582 GACGAAATTGTGAAGAAGATGAAGTGGAATTTCTCATTTTCTCTTTTTAATTTAATTTATATACC
66 GACAAAAATGTGAAGAAGATGAAGCGAAATTTCTCATTTTCTCTTTTTAATTTAATTTATATACC
** *
53647 TAATGGTATTTTTGTAAATAATTGGACTTTCTTAATTAACTTAATCAATCATTGTTTAACTTTAA
131 TAATGACATTTTTGTAAATAATTAGACTTTCTTAATTAACTTAATCAATCATTGTTTAACTTTAA
* *
53712 TTAATCTCACTTATCTTTAATATTTTCCATTATAATGCACCAACTAAAATACTGTAGGTCTATTC
196 TTAATCTCACTTATCTTTAATATTTTACATCATAATGCA-C-ACTAAAATACTGTAGGTCTATTC
53777 AT
259 AT
* *
53779 TCATTTGCTCACCCAAATCAAAGCTCAAACTTGGTAATGGAAAACCCTAATTTCTTCTCCTCTTG
1 TCATTTGCTCACCCAAATCAAAGCTCAAACATGGAAATGGAAAACCCTAATTTCTTCTCCTCTTG
53844 G-CTAAAAATGTGAAGAAGATGAAGCGAAATTTCTCATTTTCTCTTTTTAATTTAATTTATATAC
66 GAC-AAAAATGTGAAGAAGATGAAGCGAAATTTCTCATTTTCTCTTTTTAATTTAATTTATATAC
53908 CTAATGACATTTTTGTAAATAATTAGACTTTCTTAATTAACTTAATCAATCATTGTTTAACTTTA
130 CTAATGACATTTTTGTAAATAATTAGACTTTCTTAATTAACTTAATCAATCATTGTTTAACTTTA
*
53973 ATTAATCTCACTTATCTTTAATATTTTACATCATAATGCACACTAAAATACTTTAGGTCTATTCA
195 ATTAATCTCACTTATCTTTAATATTTTACATCATAATGCACACTAAAATACTGTAGGTCTATTCA
54038 T
260 T
54039 TCATTTG
1 TCATTTG
54046 ATCCCTCTAG
Statistics
Matches: 253, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
260 31 0.12
261 2 0.01
262 220 0.87
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (260 bp):
TCATTTGCTCACCCAAATCAAAGCTCAAACATGGAAATGGAAAACCCTAATTTCTTCTCCTCTTG
GACAAAAATGTGAAGAAGATGAAGCGAAATTTCTCATTTTCTCTTTTTAATTTAATTTATATACC
TAATGACATTTTTGTAAATAATTAGACTTTCTTAATTAACTTAATCAATCATTGTTTAACTTTAA
TTAATCTCACTTATCTTTAATATTTTACATCATAATGCACACTAAAATACTGTAGGTCTATTCAT
Found at i:55892 original size:21 final size:22
Alignment explanation
Indices: 55863--55903 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
55853 CTACCTTCCA
* *
55863 TGTCGCAACATGAA-TCTTGTG
1 TGTCACAACATCAACTCTTGTG
55884 TGTCACAACATCAACTCTTG
1 TGTCACAACATCAACTCTTG
55904 AACCTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (22 bp):
TGTCACAACATCAACTCTTGTG
Found at i:56122 original size:23 final size:22
Alignment explanation
Indices: 56077--56123 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
56067 TTCTTGTAAT
*
56077 TTAGGTTTAGTTTTTTTCTTTC
1 TTAGGTTTAGTTTTTTTCATTC
56099 TTAGGTTTTAGTTATTTTT-ATTC
1 TTAGG-TTTAGTT-TTTTTCATTC
56122 TT
1 TT
56124 GTTTTACGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 12 0.55
24 5 0.23
ACGTcount: A:0.13, C:0.06, G:0.13, T:0.68
Consensus pattern (22 bp):
TTAGGTTTAGTTTTTTTCATTC
Found at i:60581 original size:5 final size:5
Alignment explanation
Indices: 60559--60592 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
60549 TCAGTCACAT
60559 AAAA- AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
60593 ATAAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:60973 original size:21 final size:21
Alignment explanation
Indices: 60949--60989 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
60939 TGCCTTTTTA
* *
60949 GCATTTTTTAACTTAGTGATT
1 GCATTTTCTAACTCAGTGATT
60970 GCATTTTCTAACTCAGTGAT
1 GCATTTTCTAACTCAGTGAT
60990 GCTTGGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGATT
Found at i:70375 original size:24 final size:22
Alignment explanation
Indices: 70322--70375 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 22
70312 ACAATTCATA
70322 TTTTATTAATTTTCATTAGCAT
1 TTTTATTAATTTTCATTAGCAT
*
70344 TTTATATTATTTTTGCATT-GACAAT
1 TTT-TATTAATTTT-CATTAG-C-AT
70369 TTTTATT
1 TTTTATT
70376 CTTAACCTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.11
23 10 0.37
24 9 0.33
25 5 0.19
ACGTcount: A:0.26, C:0.07, G:0.06, T:0.61
Consensus pattern (22 bp):
TTTTATTAATTTTCATTAGCAT
Found at i:89418 original size:3 final size:3
Alignment explanation
Indices: 89410--89490 Score: 91
Period size: 3 Copynumber: 27.7 Consensus size: 3
89400 TGAGGCAAAG
89410 GAA GAA GAA GGAA -AA GAA GAA GAA -AA -AA GAA GAA GAAA GAA -AA
1 GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA
*
89453 GAA GAA GAA GAA GAA G-A GAA GGAA GAA AAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GA
89491 TATTGCCCCG
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
2 10 0.14
3 50 0.72
4 9 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:89462 original size:21 final size:22
Alignment explanation
Indices: 89411--89488 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
89401 GAGGCAAAGG
*
89411 AAGAAGAAGGAAAAGAAGAAGA
1 AAGAAGAAGAAAAAGAAGAAGA
*
89433 AAAAAGAAGAAGAAAGAA-AAG-
1 AAGAAGAAGAA-AAAGAAGAAGA
89454 AAGAAGAAGAAGAAGAGAAGGAAGA
1 AAGAAGAAGAA-AA-AGAA-GAAGA
89479 AA-AAGAAGAA
1 AAGAAGAAGAA
89489 GATATTGCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 13 0.27
22 16 0.33
23 6 0.12
24 11 0.23
25 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAAAAGAAGAAGA
Found at i:102103 original size:23 final size:23
Alignment explanation
Indices: 102064--102108 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
102054 TTCTTGTAAT
102064 TTAGGTTTAGT--TGTTTTATTTC
1 TTAGGTTTAGTCAT-TTTTATTTC
102086 TTAGGTTTTAGTCATTTTTATTT
1 TTAGG-TTTAGTCATTTTTATTT
102109 TTTTTTTACG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 8 0.40
25 1 0.05
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (23 bp):
TTAGGTTTAGTCATTTTTATTTC
Found at i:102989 original size:3 final size:3
Alignment explanation
Indices: 102981--103009 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
102971 TGGGTTGATG
102981 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
103010 GACGATAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:106199 original size:22 final size:21
Alignment explanation
Indices: 106174--106215 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
106164 TACAAGTCCA
106174 TTAAATAAATATAATTTCATGC
1 TTAAATAAAT-TAATTTCATGC
* *
106196 TTAATTAAATTTATTTCATG
1 TTAAATAAATTAATTTCATG
106216 GCCCACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (21 bp):
TTAAATAAATTAATTTCATGC
Found at i:113307 original size:22 final size:22
Alignment explanation
Indices: 113279--113323 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
113269 ACAACGGGGC
113279 ATGTGAGTACTCCGAGGATCAT
1 ATGTGAGTACTCCGAGGATCAT
113301 ATGTGAGTACTCCGAGGATCAT
1 ATGTGAGTACTCCGAGGATCAT
113323 A
1 A
113324 CTCAAGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (22 bp):
ATGTGAGTACTCCGAGGATCAT
Found at i:147795 original size:18 final size:18
Alignment explanation
Indices: 147772--147806 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
147762 TTTATTTGAT
147772 CGAATTAA-TCAAATTAAC
1 CGAATTAACT-AAATTAAC
147790 CGAATTAACTAAATTAA
1 CGAATTAACTAAATTAA
147807 AGCTACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (18 bp):
CGAATTAACTAAATTAAC
Found at i:150367 original size:13 final size:14
Alignment explanation
Indices: 150349--150378 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
150339 GTCAATGCAA
150349 TCAAA-GTTAAATG
1 TCAAAGGTTAAATG
150362 TCAAAGGTTAAATG
1 TCAAAGGTTAAATG
150376 TCA
1 TCA
150379 GAACAACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (14 bp):
TCAAAGGTTAAATG
Found at i:157835 original size:25 final size:25
Alignment explanation
Indices: 157801--157849 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
157791 TAAATGCGTC
157801 GGTAATGGCTTCAACTCCAAGGTAG
1 GGTAATGGCTTCAACTCCAAGGTAG
157826 GGTAATGGCTTCAACTCCAAGGTA
1 GGTAATGGCTTCAACTCCAAGGTA
157850 AGAGCTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (25 bp):
GGTAATGGCTTCAACTCCAAGGTAG
Found at i:172632 original size:38 final size:37
Alignment explanation
Indices: 172590--173009 Score: 367
Period size: 38 Copynumber: 11.2 Consensus size: 37
172580 ATTCCAACAT
* *
172590 TTTTTTAAAGGTTGTCTTAGACTAGGTGTATCCCAACC
1 TTTTTTAAAGGTTG-CTTAGACAAGGTCTATCCCAACC
* * *
172628 TTTTTTAAAGGTTGCTTTAGATAAGGTTTATCCCAACT
1 TTTTTTAAAGGTTGC-TTAGACAAGGTCTATCCCAACC
* *
172666 TTTTTTAAAGGTTGTCTTAGATAAGGTCTATTCCAA-C
1 TTTTTTAAAGGTTG-CTTAGACAAGGTCTATCCCAACC
* *
172703 TTTTTTAAAATGTTGCCTTAAACAAGGTCTATCCCAACC
1 TTTTTT-AAAGGTTG-CTTAGACAAGGTCTATCCCAACC
* * * * *
172742 TATTTAAAAGTTTAACTTAGACAAGTTCTATCCCAACC
1 TTTTTTAAAGGTT-GCTTAGACAAGGTCTATCCCAACC
* *
172780 -TTTTT-AAGGTTGCTTTAGAC--GGTTTTATACCAA-C
1 TTTTTTAAAGGTTGC-TTAGACAAGG-TCTATCCCAACC
* *
172814 TTTTTCTAAAAAGTTGCATTAGACAAGATCTATCCCAA--
1 TTTTT-T-AAAGGTTGC-TTAGACAAGGTCTATCCCAACC
* * *
172852 TCTTTTAAAGGTTGCTTTAGAC-ATGTCTATCCCAATC
1 TTTTTTAAAGGTTGC-TTAGACAAGGTCTATCCCAACC
* * *
172889 TTTTTTAAAGGTTTCCTTAGACAAGGTATATCCTAACC
1 TTTTTTAAAGG-TTGCTTAGACAAGGTCTATCCCAACC
* * *
172927 -TTTTT-AAGGTTGCTTTAAACAAGGTTTATCCCAATC
1 TTTTTTAAAGGTTGC-TTAGACAAGGTCTATCCCAACC
* *
172963 TTTTGTAAAGGTTGCCTTAGACAGGGTCTATCCCAACC
1 TTTTTTAAAGGTTG-CTTAGACAAGGTCTATCCCAACC
173001 TTTTTTAAA
1 TTTTTTAAA
173010 AGATTGCCTT
Statistics
Matches: 308, Mismatches: 53, Indels: 42
0.76 0.13 0.10
Matches are distributed among these distances:
34 2 0.01
35 27 0.09
36 48 0.16
37 36 0.12
38 179 0.58
39 15 0.05
40 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTTTTAAAGGTTGCTTAGACAAGGTCTATCCCAACC
Found at i:172838 original size:74 final size:72
Alignment explanation
Indices: 172590--173005 Score: 363
Period size: 74 Copynumber: 5.6 Consensus size: 72
172580 ATTCCAACAT
* * * *
172590 TTTTTTAAAGGTTGTCTTAGACTAGGTGTATCCCAACCTTTTTTAAAGGTTGCTTTAGATAAGG-
1 TTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTT-AAGGTTGCTTTAG--ACGGT
172654 TTTATCCCAAC
62 TTTATCCCAAC
* * * * * * *
172665 TTTTTTTAAAGGTTGTCTTAGATAAGGTCTATTCCAACTTTTTTAAAATGTTGCCTTAAACAAGG
1 -TTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTT--AAGGTTGCTTTAGAC--GG
*
172730 -TCTATCCCAACC
61 TTTTATCCCAA-C
* * * ** *
172742 TATTTAAAAGTTTAACTTAGACAAGTTCTATCCCAACCTTTTTAAGGTTGCTTTAGACGGTTTTA
1 TTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCTTTAGACGGTTTTA
*
172807 TACCAAC
66 TCCCAAC
* * * * * *
172814 TTTTTCTAAAAAGTTGCATTAGACAAGATCTATCCCAATCTTTTAAAGGTTGCTTTAGAC-ATGT
1 TTTTT-T-AAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCTTTAGACGGT-T
*
172878 CTATCCCAATC
63 TTATCCCAA-C
* * * *
172889 TTTTTTAAAGGTTTCCTTAGACAAGGTATATCCTAACCTTTTTAAGGTTGCTTTAAACAAGG-TT
1 TTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCTTTAGAC--GGTTT
172953 TATCCCAATC
64 TATCCCAA-C
* *
172963 TTTTGTAAAGGTTGCCTTAGACAGGGTCTATCCCAACCTTTTT
1 TTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTT
173006 TAAAAGATTG
Statistics
Matches: 275, Mismatches: 53, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
72 7 0.03
73 52 0.19
74 115 0.42
75 11 0.04
76 89 0.32
77 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (72 bp):
TTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCTTTAGACGGTTTTA
TCCCAAC
Found at i:172911 original size:147 final size:143
Alignment explanation
Indices: 172590--173020 Score: 434
Period size: 147 Copynumber: 2.9 Consensus size: 143
172580 ATTCCAACAT
* * *
172590 TTTTTTAAAGGTTGTCTTAGACTAGGTGTATCCCAACCTTTTTTAAAGGTTGCTTTAGATAAGGT
1 TTTTTTAAAGGTT-TCTTAGACAAGGTATATCCCAACC-TTTTT-AAGGTTGCTTTAG--ACGGT
* * * *
172655 TTATCCCAACTTTTTTTAAAGGTTGTCTTAGATAAGGTCTATTCCAACTTTTTTAAAATGTTGCC
61 TTATCCCAAC-TTTTTTAAAGGTTG-CTTAGACAAGGTCTATCCCAA-TCTTTTAAAAGGTTGCC
172720 TTAAACAAGGTCTATCCCAAC
123 TTAAACAAGGTCTATCCCAAC
* * * * *
172741 CTATTTAAAAGTTTAACTTAGACAAGTTCTATCCCAACCTTTTTAAGGTTGCTTTAGACGGTTTT
1 TTTTTTAAAGGTTT--CTTAGACAAGGTATATCCCAACCTTTTTAAGGTTGCTTTAGACGG-TTT
* * * *
172806 ATACCAACTTTTTCTAAAAAGTTGCATTAGACAAGATCTATCCCAATCTTTT-AAAGGTTGCTTT
63 ATCCCAACTTTTT-T-AAAGGTTGC-TTAGACAAGGTCTATCCCAATCTTTTAAAAGGTTGCCTT
* *
172870 AGAC-ATGTCTATCCCAATC
125 AAACAAGGTCTATCCCAA-C
* *
172889 TTTTTTAAAGGTTTCCTTAGACAAGGTATATCCTAACCTTTTTAAGGTTGCTTTAAACAAGGTTT
1 TTTTTTAAAGGTTT-CTTAGACAAGGTATATCCCAACCTTTTTAAGGTTGCTTTAGAC--GGTTT
* * * *
172954 ATCCCAATCTTTTGTAAAGGTTGCCTTAGACAGGGTCTATCCCAACCTTTTTTAAAAGATTGCCT
63 ATCCCAA-CTTTTTTAAAGGTTG-CTTAGACAAGGTCTATCCCAA--TCTTTTAAAAGGTTGCCT
173019 TA
124 TA
173021 GATAAGACCT
Statistics
Matches: 233, Mismatches: 33, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
147 76 0.33
148 44 0.19
149 29 0.12
150 49 0.21
151 15 0.06
152 20 0.09
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (143 bp):
TTTTTTAAAGGTTTCTTAGACAAGGTATATCCCAACCTTTTTAAGGTTGCTTTAGACGGTTTATC
CCAACTTTTTTAAAGGTTGCTTAGACAAGGTCTATCCCAATCTTTTAAAAGGTTGCCTTAAACAA
GGTCTATCCCAAC
Found at i:174235 original size:14 final size:14
Alignment explanation
Indices: 174216--174243 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
174206 GTGAGTAGTT
174216 TTTTTATATTTTAA
1 TTTTTATATTTTAA
174230 TTTTTATATTTTAA
1 TTTTTATATTTTAA
174244 ATGCGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTATATTTTAA
Found at i:178590 original size:21 final size:19
Alignment explanation
Indices: 178564--178614 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
178554 GGAGTTTTTG
*
178564 GTATCGGTAAATGTATGACTT
1 GTATCGGTAAAT-CAT-ACTT
178585 GTATCGGTAGAAATCATACTT
1 GTATCGGT--AAATCATACTT
178606 GTATCGGTA
1 GTATCGGTA
178615 GAGCTAGCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
21 20 0.74
22 2 0.07
23 4 0.15
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (19 bp):
GTATCGGTAAATCATACTT
Found at i:184754 original size:22 final size:24
Alignment explanation
Indices: 184724--184776 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
184714 AAAAAAATTA
184724 TTTTT-TTGTTTTG-GTGTT-TTT
1 TTTTTATTGTTTTGAGTGTTGTTT
*
184745 TTTTTATTGTTTTGATTGTTGTTT
1 TTTTTATTGTTTTGAGTGTTGTTT
*
184769 TTGTTATT
1 TTTTTATT
184777 TTGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 8 0.30
23 4 0.15
24 10 0.37
ACGTcount: A:0.06, C:0.00, G:0.17, T:0.77
Consensus pattern (24 bp):
TTTTTATTGTTTTGAGTGTTGTTT
Found at i:184795 original size:17 final size:17
Alignment explanation
Indices: 184773--184812 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
184763 TTGTTTTTGT
184773 TATTTTGAT-TTTTTTAC
1 TATTTTG-TGTTTTTTAC
*
184790 TGTTTTGTGTTTTTTAC
1 TATTTTGTGTTTTTTAC
184807 TATTTT
1 TATTTT
184813 AATTGTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.72
Consensus pattern (17 bp):
TATTTTGTGTTTTTTAC
Found at i:184852 original size:22 final size:23
Alignment explanation
Indices: 184819--184861 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
184809 TTTTAATTGT
184819 TGTTTTAGTGCTATT-TTTTTAC
1 TGTTTTAGTGCTATTATTTTTAC
*
184841 TGTTTT-GATGCTGTTATTTTT
1 TGTTTTAG-TGCTATTATTTTT
184862 GTTGCTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 1 0.06
22 12 0.67
23 5 0.28
ACGTcount: A:0.12, C:0.07, G:0.16, T:0.65
Consensus pattern (23 bp):
TGTTTTAGTGCTATTATTTTTAC
Found at i:184893 original size:12 final size:12
Alignment explanation
Indices: 184855--184905 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
184845 TTGATGCTGT
184855 TATTTTTGTTGC
1 TATTTTTGTTGC
* **
184867 T-GTTTTGTTAT
1 TATTTTTGTTGC
184878 TATTTTTGTTGC
1 TATTTTTGTTGC
*
184890 TATTTTTATTGC
1 TATTTTTGTTGC
184902 TATT
1 TATT
184906 ATTATTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.12, C:0.06, G:0.14, T:0.69
Consensus pattern (12 bp):
TATTTTTGTTGC
Found at i:190150 original size:24 final size:23
Alignment explanation
Indices: 190093--190155 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
190083 AGAGAAGAAG
* *
190093 AAACAACTTCTGTTCTCTCTCAA
1 AAACTACTTCTGTTTTCTCTCAA
**
190116 AAACTTTTTCTTGTTTTCTCTCAA
1 AAACTACTTC-TGTTTTCTCTCAA
*
190140 ATACTACTTCTGTTTT
1 AAACTACTTCTGTTTT
190156 TTTGGTGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (23 bp):
AAACTACTTCTGTTTTCTCTCAA
Found at i:194158 original size:36 final size:36
Alignment explanation
Indices: 194116--194187 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
194106 TAGTAACAAG
*
194116 CATGATCTATAGGTTAATAGGGAGTAAAACGAGCAT
1 CATGATCTATAGGTCAATAGGGAGTAAAACGAGCAT
* *
194152 CATGATCTTTGGGTCAATAGGGAGTAAAACGAGCAT
1 CATGATCTATAGGTCAATAGGGAGTAAAACGAGCAT
194188 TATAACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.25
Consensus pattern (36 bp):
CATGATCTATAGGTCAATAGGGAGTAAAACGAGCAT
Found at i:194199 original size:36 final size:36
Alignment explanation
Indices: 194131--194216 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
194121 TCTATAGGTT
*
194131 AATAGGGAGTAAAACGAGCATCATGATCTTTGGGTC
1 AATAGGGAGTAAAACGAGCATCATAATCTTTGGGTC
*
194167 AATAGGGAGTAAAACGAGCATTATAA-CTTTTGGGTC
1 AATAGGGAGTAAAACGAGCATCATAATC-TTTGGGTC
*
194203 AACAGGGAGTAAAA
1 AATAGGGAGTAAAA
194217 TGAATAACGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 1 0.02
36 45 0.98
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (36 bp):
AATAGGGAGTAAAACGAGCATCATAATCTTTGGGTC
Found at i:199266 original size:17 final size:17
Alignment explanation
Indices: 199246--199290 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
199236 GATAATGTAG
199246 ATGCAGCGACATTAAAA
1 ATGCAGCGACATTAAAA
* *
199263 ATGCAACGACATTAATA
1 ATGCAGCGACATTAAAA
*
199280 ATGCAGGGACA
1 ATGCAGCGACA
199291 ATTATACTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (17 bp):
ATGCAGCGACATTAAAA
Found at i:204480 original size:34 final size:34
Alignment explanation
Indices: 204429--204519 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 34
204419 TGGTCAACGA
*
204429 TCAAAGTCAA-CAGTCAAGGTCAACAATCAACGGG
1 TCAAAGTCAATGA-TCAAGGTCAACAATCAACGGG
* ** **
204463 TCAAAGTCAATGATCAAGGACAACGGTCATTGGG
1 TCAAAGTCAATGATCAAGGTCAACAATCAACGGG
* *
204497 TCAAAGTCAATGGTCAAGATCAA
1 TCAAAGTCAATGATCAAGGTCAA
204520 AGTCAAAGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 46 0.98
35 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.19
Consensus pattern (34 bp):
TCAAAGTCAATGATCAAGGTCAACAATCAACGGG
Found at i:204566 original size:20 final size:20
Alignment explanation
Indices: 204541--204580 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
204531 ATAGGTCAAC
204541 AGGTCAACGGGTCAATGGGT
1 AGGTCAACGGGTCAATGGGT
204561 AGGTCAACGGGTCAATGGGT
1 AGGTCAACGGGTCAATGGGT
204581 TGGGTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.20
Consensus pattern (20 bp):
AGGTCAACGGGTCAATGGGT
Done.