Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004905.1 Kokia drynarioides strain JFW-HI SEQ_118598, 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: 169261
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1518 original size:31 final size:28
Alignment explanation
Indices: 1483--1539 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
1473 TTCATCTTTT
*
1483 TCTTTTCTCTCTTTCTTCTCACTTTCTTTGC
1 TCTTTTCTCTCATT-TT-TC-CTTTCTTTGC
1514 TCTTTTCTCTCATTTTTCCTTTCTTT
1 TCTTTTCTCTCATTTTTCCTTTCTTT
1540 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 2 0.08
30 2 0.08
31 13 0.52
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.65
Consensus pattern (28 bp):
TCTTTTCTCTCATTTTTCCTTTCTTTGC
Found at i:1540 original size:21 final size:20
Alignment explanation
Indices: 1514--1562 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1504 CTTTCTTTGC
*
1514 TCTTTTCTCTCATTTTTCCTT
1 TCTTTT-TCTCAATTTTCCTT
* *
1535 TCTTTTTTTCAATTTTCTTT
1 TCTTTTTCTCAATTTTCCTT
1555 TCTTTTTC
1 TCTTTTTC
1563 ATTCTCACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTTCTCAATTTTCCTT
Found at i:9502 original size:18 final size:19
Alignment explanation
Indices: 9467--9527 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
9457 AGGCACAACT
*
9467 AAGAAGGCAGAACCTGAGGAG
1 AAGAAGGAAGAA--TGAGGAG
9488 AAGAAGGAA-AATGAGGA-
1 AAGAAGGAAGAATGAGGAG
9505 AGAGAAGGAAGAA-GAGGAG
1 A-AGAAGGAAGAATGAGGAG
9524 AAGA
1 AAGA
9528 TTGAAGAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 1 0.03
18 22 0.61
19 3 0.08
20 2 0.06
21 8 0.22
ACGTcount: A:0.52, C:0.05, G:0.39, T:0.03
Consensus pattern (19 bp):
AAGAAGGAAGAATGAGGAG
Found at i:10149 original size:70 final size:67
Alignment explanation
Indices: 10022--10154 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
10012 ATAAACAATA
* * *
10022 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
10087 CT
66 CT
* * * *
10089 TAATGGTTTTTACTTTTAACTTTAGAAAGGGTAAACATTTATTAAAACGACGTAGTTTTACCTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTT
10154 T
63 T
10155 CTTATTCGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 18 0.32
68 2 0.04
70 36 0.64
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:14916 original size:20 final size:20
Alignment explanation
Indices: 14883--14921 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
14873 GAGGATTTTG
*
14883 ATAGAGGTGAGAGAGGAAAA
1 ATAGAAGTGAGAGAGGAAAA
* *
14903 ATAGAAGTGGGAGATGAAA
1 ATAGAAGTGAGAGAGGAAA
14922 GGGTTTGGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (20 bp):
ATAGAAGTGAGAGAGGAAAA
Found at i:15017 original size:30 final size:29
Alignment explanation
Indices: 14981--15037 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
14971 ATTGTTACTC
*
14981 AAATTAGTCCCTAAACTTTACTAAAATTAT
1 AAATTAGACCCTAAACTTTAC-AAAATTAT
*
15011 AAATTAGACCTTAAACTTTACAAAATT
1 AAATTAGACCCTAAACTTTACAAAATT
15038 TCTAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATTAGACCCTAAACTTTACAAAATTAT
Found at i:24195 original size:17 final size:17
Alignment explanation
Indices: 24138--24206 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
24128 CAATGATACG
24138 TGGAAATGCAATGACAA
1 TGGAAATGCAATGACAA
* * *
24155 TGTAGATGCAGTGACAA
1 TGGAAATGCAATGACAA
**
24172 TCAAAATGCAATGACAA
1 TGGAAATGCAATGACAA
* **
24189 AGGAAATGTGATGACAA
1 TGGAAATGCAATGACAA
24206 T
1 T
24207 TACATTACAG
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (17 bp):
TGGAAATGCAATGACAA
Found at i:29814 original size:20 final size:19
Alignment explanation
Indices: 29789--30007 Score: 186
Period size: 20 Copynumber: 11.0 Consensus size: 19
29779 CCTAAATCAC
**
29789 CGGCACAAAGCCCAATACA
1 CGGCACAAAGCCTGATACA
29808 TCGGCACAAAGCCTGATACA
1 -CGGCACAAAGCCTGATACA
*
29828 CTGACACAAAGCCTGATACA
1 C-GGCACAAAGCCTGATACA
*
29848 CCGGCTCAAAGCCTGATACA
1 -CGGCACAAAGCCTGATACA
** * *
29868 CCAACACGAAGCCTAATACA
1 -CGGCACAAAGCCTGATACA
** *
29888 CCAACACGAAGCCTGATACA
1 -CGGCACAAAGCCTGATACA
**
29908 CCGGCATGAAGCCTGATACA
1 -CGGCACAAAGCCTGATACA
*
29928 CTGGCACGAAGCCTGATACA
1 C-GGCACAAAGCCTGATACA
*
29948 CCGGCACGAAGCCTGATACA
1 -CGGCACAAAGCCTGATACA
* *
29968 CCAGCACGAAGCCTGATACA
1 -CGGCACAAAGCCTGATACA
*
29988 CCGGCATAAAGCCTGATACA
1 -CGGCACAAAGCCTGATACA
30008 TAGAATGCAC
Statistics
Matches: 176, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.12
Consensus pattern (19 bp):
CGGCACAAAGCCTGATACA
Found at i:29836 original size:40 final size:40
Alignment explanation
Indices: 29803--30007 Score: 248
Period size: 40 Copynumber: 5.1 Consensus size: 40
29793 ACAAAGCCCA
* * * *
29803 ATACATCGGCACAAAGCCTGATACACTGACACAAAGCCTG
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTG
* * * *
29843 ATACACCGGCTCAAAGCCTGATACACCAACACGAAGCCTA
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTG
** * *
29883 ATACACCAACACGAAGCCTGATACACCGGCATGAAGCCTG
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTG
* *
29923 ATACACTGGCACGAAGCCTGATACACCGGCACGAAGCCTG
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTG
* * **
29963 ATACACCAGCACGAAGCCTGATACACCGGCATAAAGCCTG
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTG
30003 ATACA
1 ATACA
30008 TAGAATGCAC
Statistics
Matches: 143, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 143 1.00
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.13
Consensus pattern (40 bp):
ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTG
Found at i:29880 original size:60 final size:60
Alignment explanation
Indices: 29803--30007 Score: 259
Period size: 60 Copynumber: 3.4 Consensus size: 60
29793 ACAAAGCCCA
* * * * *
29803 ATACATCGGCACAAAGCCTGATACACTGACACAAAGCCTGATACACCGGCTCAAAGCCTG
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTGATACACCGGCTCGAAGCCTG
** * *
29863 ATACACCAACACGAAGCCTAATACACCAACACGAAGCCTGATACACCGGCAT-GAAGCCTG
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTGATACACCGGC-TCGAAGCCTG
* * * *
29923 ATACACTGGCACGAAGCCTGATACACCGGCACGAAGCCTGATACACCAGCACGAAGCCTG
1 ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTGATACACCGGCTCGAAGCCTG
**
29983 ATACACCGGCATAAAGCCTGATACA
1 ATACACCGGCACGAAGCCTGATACA
30008 TAGAATGCAC
Statistics
Matches: 123, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
60 122 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.13
Consensus pattern (60 bp):
ATACACCGGCACGAAGCCTGATACACCGACACGAAGCCTGATACACCGGCTCGAAGCCTG
Found at i:47245 original size:17 final size:18
Alignment explanation
Indices: 47225--47265 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
47215 CTAAAAATGA
47225 TTTTTGAAAAATAAT-TT
1 TTTTTGAAAAATAATATT
*
47242 TTTTAGAAAAATAATATT
1 TTTTTGAAAAATAATATT
47260 TTTTTG
1 TTTTTG
47266 TGTTCGGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (18 bp):
TTTTTGAAAAATAATATT
Found at i:47715 original size:19 final size:19
Alignment explanation
Indices: 47691--47730 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
47681 GTTCAAGTGT
* *
47691 ATAATTAGTATTACATCAC
1 ATAATTAGTACTACACCAC
47710 ATAATTAGTACTACACCAC
1 ATAATTAGTACTACACCAC
47729 AT
1 AT
47731 TAAAGCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAATTAGTACTACACCAC
Found at i:48900 original size:138 final size:138
Alignment explanation
Indices: 48652--48934 Score: 485
Period size: 138 Copynumber: 2.1 Consensus size: 138
48642 TAGAAAAATG
*
48652 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATTGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
48717 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAATT
48782 CATATATT
131 CATATATT
* ** * *
48790 AATTATATTCTTTGTAACAGAATGTTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
* * *
48855 TATAATTGTTTATATTAATAAATTCGGTAAAATATATATAATTAATATTTTGTATGAATCAATTT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAATT
48920 CATATATT
131 CATATATT
48928 AATTATA
1 AATTATA
48935 CTTGTCTGCC
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 136 1.00
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.48
Consensus pattern (138 bp):
AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAATT
CATATATT
Found at i:51203 original size:8 final size:8
Alignment explanation
Indices: 51179--51228 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
51169 CCGTCTTAAC
51179 CATATA-A
1 CATATATA
*
51186 CATTTCATA
1 CATAT-ATA
51195 CATATATA
1 CATATATA
51203 CATATA-A
1 CATATATA
51210 CATGTATATA
1 CA--TATATA
51220 CATATATA
1 CATATATA
51228 C
1 C
51229 GTATTAACGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 7 0.19
8 17 0.47
9 9 0.25
10 3 0.08
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (8 bp):
CATATATA
Found at i:51226 original size:25 final size:24
Alignment explanation
Indices: 51179--51228 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
51169 CCGTCTTAAC
51179 CATATAACATTTCATACATATATA
1 CATATAACATTTCATACATATATA
51203 CATATAACATGTAT-ATACATATATA
1 CATATAACAT-T-TCATACATATATA
51228 C
1 C
51229 GTATTAACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 10 0.42
25 13 0.54
26 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (24 bp):
CATATAACATTTCATACATATATA
Found at i:52042 original size:26 final size:26
Alignment explanation
Indices: 52006--52071 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
51996 TAACCATATA
* *
52006 TGCTCACACGAGTTATGAAATTGGTC
1 TGCTCACACGAGCTATGAAATGGGTC
*
52032 TGCTCACACGAACTATGAAATGGGTC
1 TGCTCACACGAGCTATGAAATGGGTC
52058 TGCTCACACGAGCT
1 TGCTCACACGAGCT
52072 GTGGGTCGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (26 bp):
TGCTCACACGAGCTATGAAATGGGTC
Found at i:54251 original size:17 final size:16
Alignment explanation
Indices: 54229--54260 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54219 ATATAGAACA
54229 ACATACTCATCAATATC
1 ACATACTCAT-AATATC
54246 ACATACTCATAATAT
1 ACATACTCATAATAT
54261 TGTATATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
ACATACTCATAATATC
Found at i:54509 original size:48 final size:49
Alignment explanation
Indices: 54449--54555 Score: 121
Period size: 48 Copynumber: 2.2 Consensus size: 49
54439 ATCATATATT
* * ** *
54449 CACATATTCACTTTGTAG-TAAAAATGCCACATAATTGTCAT-AAATTGC
1 CACATAATCACTTTATAGAT-AAAATGCCACATAATTACCATAAAATGGC
* *
54497 CACATAATCACTTTATAGATAAACTGCCACATATTTACCATAAAATGGC
1 CACATAATCACTTTATAGATAAAATGCCACATAATTACCATAAAATGGC
54546 CACAT-ATCAC
1 CACATAATCAC
54556 ATATTTGCCA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 38 0.76
49 12 0.24
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.30
Consensus pattern (49 bp):
CACATAATCACTTTATAGATAAAATGCCACATAATTACCATAAAATGGC
Found at i:55080 original size:16 final size:16
Alignment explanation
Indices: 55049--55095 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
55039 TCGTTTGGCC
**
55049 CAAAATAAAACCAAAA
1 CAAAATAAAAATAAAA
55065 CAAAATAAAAATAAAA
1 CAAAATAAAAATAAAA
**
55081 -AAACCAAAAATAAAA
1 CAAAATAAAAATAAAA
55096 TTTTTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.09
Consensus pattern (16 bp):
CAAAATAAAAATAAAA
Found at i:55632 original size:21 final size:22
Alignment explanation
Indices: 55608--55649 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
55598 TCGAAACGCG
55608 AAGA-AAT-CAATAGAAAAAAAA
1 AAGAGAATACAATA-AAAAAAAA
55629 AAGAGAATAACAATAAAAAAA
1 AAGAGAAT-ACAATAAAAAAA
55650 GATTTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 6 0.33
24 5 0.28
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.10
Consensus pattern (22 bp):
AAGAGAATACAATAAAAAAAAA
Found at i:56638 original size:2 final size:2
Alignment explanation
Indices: 56631--56657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56621 TTTATTTGTC
56631 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
56658 TATTTATCCT
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:61423 original size:37 final size:37
Alignment explanation
Indices: 61373--61444 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
61363 CTAATGTCGC
* * *
61373 TGCATGAGCACTTTTAGTTTGCGCCCAAAATTGTCAT
1 TGCATGAGCACTTTTAGATTGCACCCAAAACTGTCAT
61410 TGCATGAGCACTTTTAGATTGCACCCAAAACTGTC
1 TGCATGAGCACTTTTAGATTGCACCCAAAACTGTC
61445 GTCGTAGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (37 bp):
TGCATGAGCACTTTTAGATTGCACCCAAAACTGTCAT
Found at i:61582 original size:26 final size:26
Alignment explanation
Indices: 61553--61606 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
61543 CACCCACGAA
*
61553 TGTTATTGCATGAACATGTCCAGAAT
1 TGTTACTGCATGAACATGTCCAGAAT
* * *
61579 TGTTGCTGCATGAACGTGTCTAGAAT
1 TGTTACTGCATGAACATGTCCAGAAT
61605 TG
1 TG
61607 CGCTCAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (26 bp):
TGTTACTGCATGAACATGTCCAGAAT
Found at i:65363 original size:11 final size:11
Alignment explanation
Indices: 65347--65379 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
65337 AGTCACATAA
65347 AAGAAAAGAAG
1 AAGAAAAGAAG
65358 AAGAAAAGAA-
1 AAGAAAAGAAG
65368 AAGAAAA-AAG
1 AAGAAAAGAAG
65378 AA
1 AA
65380 AAATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.10
10 9 0.43
11 10 0.48
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAAG
Found at i:65381 original size:5 final size:5
Alignment explanation
Indices: 65345--65374 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
65335 TCAGTCACAT
65345 AAAAG AAAAG AAGAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AA-AAG AAAAG AAAAG AAAA
65375 AAGAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:75916 original size:198 final size:197
Alignment explanation
Indices: 75578--75997 Score: 581
Period size: 198 Copynumber: 2.1 Consensus size: 197
75568 AATCGAGCAT
* * * *
75578 TGTTTGTTTTAAACAAAACTCGATTTCCGTACGGTTATAGAGATATAAGGCTCATTTCCTATTCT
1 TGTTTGTTCTAAACAAAACTAGACTTCCGTACGGTTATAGAGATATAAGGCTCACTTCCTATTCT
** *
75643 ATCTTGTGCAATTTTTGGTGAATTTTAAAAGTCACTACTAAATCTATTTTATAAGAATTCTGCTG
66 ATCTTAAGCAATTTTTGGTGAATTTTAAAAGTCACTACTAAATCTATTTTATAAGAATTCTACTG
* *
75708 CCAGATTTTTATAACCTTTCAACATTAAAAAATTCATAGATTTTAAAATACAAATCAAAATCAAT
131 CCAGATTTTTATAACCTTTCAACACTAAAAAATTCACAGATTTTAAAATACAAATCAAAAT-AAT
*
75773 CTC
195 CTA
* * * * *
75776 TGTTTGTTCTAAACAAAATTAGACTTCCGTAGGGTTATA-AGGATATAAGGCTCACTTCTTTTTT
1 TGTTTGTTCTAAACAAAACTAGACTTCCGTACGGTTATAGA-GATATAAGGCTCACTTCCTATTC
* * * * *
75840 TATCTTAAGCATTTTTTTGTGATTTTTCAAAGTCACTACTAAATCTGTTTTATAAGAATTCTACT
65 TATCTTAAGCAATTTTTGGTGAATTTTAAAAGTCACTACTAAATCTATTTTATAAGAATTCTACT
* ** **
75905 GCCTGATTTTTATGTCCTTTCAACACTAAAAAATTCACATCTTTTAAAATACAAATCAAAATAAT
130 GCCAGATTTTTATAACCTTTCAACACTAAAAAATTCACAGATTTTAAAATACAAATCAAAATAAT
75970 CTA
195 CTA
*
75973 TATTTGTTCTAAACAAAACTAGACT
1 TGTTTGTTCTAAACAAAACTAGACT
75998 GACCCATAGT
Statistics
Matches: 194, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
197 29 0.15
198 165 0.85
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (197 bp):
TGTTTGTTCTAAACAAAACTAGACTTCCGTACGGTTATAGAGATATAAGGCTCACTTCCTATTCT
ATCTTAAGCAATTTTTGGTGAATTTTAAAAGTCACTACTAAATCTATTTTATAAGAATTCTACTG
CCAGATTTTTATAACCTTTCAACACTAAAAAATTCACAGATTTTAAAATACAAATCAAAATAATC
TA
Found at i:85191 original size:28 final size:27
Alignment explanation
Indices: 85160--85221 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 27
85150 TATCATTTTG
85160 ATTCTT-ATTTTACACTGCTTATCTATTT
1 ATTCTTGA-TTTA-ACTGCTTATCTATTT
85188 ATTCTTGGATTTAACTGCTTATCTATTT
1 ATTCTT-GATTTAACTGCTTATCTATTT
85216 ATTCTT
1 ATTCTT
85222 CTTAAACGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 27 0.84
29 4 0.12
30 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.06, T:0.56
Consensus pattern (27 bp):
ATTCTTGATTTAACTGCTTATCTATTT
Found at i:85667 original size:7 final size:7
Alignment explanation
Indices: 85617--85649 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
85607 ATAGAATATT
85617 TTTTTTA
1 TTTTTTA
85624 TTTTTTA
1 TTTTTTA
85631 TTTTTTA
1 TTTTTTA
*
85638 TTTTTCA
1 TTTTTTA
85645 TTTTT
1 TTTTT
85650 CTTGTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:107570 original size:12 final size:12
Alignment explanation
Indices: 107549--107578 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
107539 TGTAAATGGA
*
107549 GAGAACATAGGT
1 GAGAAAATAGGT
107561 GAGAAAATAGGT
1 GAGAAAATAGGT
107573 GAGAAA
1 GAGAAA
107579 TGAAGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.13
Consensus pattern (12 bp):
GAGAAAATAGGT
Found at i:120799 original size:13 final size:13
Alignment explanation
Indices: 120781--120805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120771 TATGTTAGTG
120781 ATTAAAAATTAAA
1 ATTAAAAATTAAA
120794 ATTAAAAATTAA
1 ATTAAAAATTAA
120806 GGGTTAGTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAAATTAAA
Found at i:122534 original size:43 final size:43
Alignment explanation
Indices: 122486--122576 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
122476 GTACAGTGGT
* *
122486 CACACAAGC-TGGCACACGACCGTGTGTCCCAAGTCAGTATAGA
1 CACAC-AGCTTGGCACACGACCGTGTGACCCAAGTCACTATAGA
* ** *
122529 CACACAGCTTGGCACATGGTCGTGTGACCCAATTCACTATAGA
1 CACACAGCTTGGCACACGACCGTGTGACCCAAGTCACTATAGA
122572 CACAC
1 CACAC
122577 GATCATGGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 3 0.07
43 38 0.93
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (43 bp):
CACACAGCTTGGCACACGACCGTGTGACCCAAGTCACTATAGA
Found at i:123110 original size:27 final size:26
Alignment explanation
Indices: 123060--123110 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
123050 AATGTCGGTC
*
123060 TTGCTTTGGCTTCTTCACTATGGAAT
1 TTGCTTTGGCTTCTTCAATATGGAAT
*
123086 TTGCTTTGTGCTTCTTCAATTTGGA
1 TTGCTTTG-GCTTCTTCAATATGGA
123111 CTGAGGCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.49
Consensus pattern (26 bp):
TTGCTTTGGCTTCTTCAATATGGAAT
Found at i:137798 original size:16 final size:18
Alignment explanation
Indices: 137777--137813 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
137767 TGGCGTTTGT
137777 TTGATG-TTTATT-TTTA
1 TTGATGATTTATTCTTTA
137793 TTGATGCATTTATTCTTTA
1 TTGATG-ATTTATTCTTTA
137812 TT
1 TT
137814 ATCTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (18 bp):
TTGATGATTTATTCTTTA
Found at i:139778 original size:17 final size:17
Alignment explanation
Indices: 139758--139813 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
139748 TTAATGTCAT
139758 TGCATTTTTATTGTTGC
1 TGCATTTTTATTGTTGC
* ** ***
139775 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTTGC
139792 TGCATTTTTATTGTTGC
1 TGCATTTTTATTGTTGC
139809 TGCAT
1 TGCAT
139814 CTACATTGTC
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (17 bp):
TGCATTTTTATTGTTGC
Found at i:139790 original size:34 final size:34
Alignment explanation
Indices: 139752--139832 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
139742 ACATTATTAA
139752 TGTCATTGCATTTTTATTGTTGCTGCATCTACAT
1 TGTCATTGCATTTTTATTGTTGCTGCATCTACAT
139786 TGTCATTGCATTTTTATTGTTGCTGCATCTACAT
1 TGTCATTGCATTTTTATTGTTGCTGCATCTACAT
139820 TGTCATTGCATTT
1 TGTCATTGCATTT
139833 CCATATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (34 bp):
TGTCATTGCATTTTTATTGTTGCTGCATCTACAT
Found at i:139821 original size:17 final size:17
Alignment explanation
Indices: 139767--139822 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
139757 TTGCATTTTT
139767 ATTGTTGCTGCATCTAC
1 ATTGTTGCTGCATCTAC
*** * **
139784 ATTGTCATTGCATTTTT
1 ATTGTTGCTGCATCTAC
139801 ATTGTTGCTGCATCTAC
1 ATTGTTGCTGCATCTAC
139818 ATTGT
1 ATTGT
139823 CATTGCATTT
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (17 bp):
ATTGTTGCTGCATCTAC
Found at i:139829 original size:17 final size:17
Alignment explanation
Indices: 139775--139830 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
139765 TTATTGTTGC
139775 TGCATCTACATTGTCAT
1 TGCATCTACATTGTCAT
* ** ***
139792 TGCATTTTTATTGTTGC
1 TGCATCTACATTGTCAT
139809 TGCATCTACATTGTCAT
1 TGCATCTACATTGTCAT
139826 TGCAT
1 TGCAT
139831 TTCCATATAT
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (17 bp):
TGCATCTACATTGTCAT
Found at i:142021 original size:85 final size:85
Alignment explanation
Indices: 141878--142044 Score: 316
Period size: 85 Copynumber: 2.0 Consensus size: 85
141868 GAGAGTTGCT
* *
141878 TGAGATTAAAAGAGATTTTGGTCACTTGTTCTTGAGTGCACAACGTTGCTCACACCAAGAGGTAG
1 TGAGATTAAAACAGATTCTGGTCACTTGTTCTTGAGTGCACAACGTTGCTCACACCAAGAGGTAG
141943 GGTAATTGTGGGTGCTTAAG
66 GGTAATTGTGGGTGCTTAAG
141963 TGAGATTAAAACAGATTCTGGTCACTTGTTCTTGAGTGCACAACGTTGCTCACACCAAGAGGTAG
1 TGAGATTAAAACAGATTCTGGTCACTTGTTCTTGAGTGCACAACGTTGCTCACACCAAGAGGTAG
142028 GGTAATTGTGGGTGCTT
66 GGTAATTGTGGGTGCTT
142045 TGAGTCTCGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (85 bp):
TGAGATTAAAACAGATTCTGGTCACTTGTTCTTGAGTGCACAACGTTGCTCACACCAAGAGGTAG
GGTAATTGTGGGTGCTTAAG
Found at i:146302 original size:18 final size:21
Alignment explanation
Indices: 146252--146294 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
146242 CTAAGCATAG
146252 CACTAGAAATTTGACTATAAC
1 CACTAGAAATTTGACTATAAC
146273 CACTAGAAATTTGACTATAAC
1 CACTAGAAATTTGACTATAAC
146294 C
1 C
146295 TTAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (21 bp):
CACTAGAAATTTGACTATAAC
Found at i:167061 original size:13 final size:13
Alignment explanation
Indices: 167043--167073 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
167033 GTCATCAAGG
167043 AAGGGAAAGGGGA
1 AAGGGAAAGGGGA
*
167056 AAGGGAAAGGGGG
1 AAGGGAAAGGGGA
167069 AAGGG
1 AAGGG
167074 GAATTGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (13 bp):
AAGGGAAAGGGGA
Found at i:167129 original size:9 final size:9
Alignment explanation
Indices: 167115--167199 Score: 79
Period size: 9 Copynumber: 9.1 Consensus size: 9
167105 TAAAATGATG
167115 ATAATTTTA
1 ATAATTTTA
167124 ATAATTTT-
1 ATAATTTTA
167132 AT-ATTTTAA
1 ATAATTTT-A
167141 ATTAATTTTAAA
1 A-TAATTTT--A
167153 ATAATTTTA
1 ATAATTTTA
167162 ATAATTTT-
1 ATAATTTTA
167170 AT-ATTTTAAAA
1 ATAATTTT---A
167181 ATAATTTTA
1 ATAATTTTA
167190 ATAATTTTA
1 ATAATTTTA
167199 A
1 A
167200 AATCATTTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 20
0.77 0.00 0.23
Matches are distributed among these distances:
7 10 0.15
8 4 0.06
9 29 0.44
10 1 0.02
11 14 0.21
12 8 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATAATTTTA
Found at i:167187 original size:28 final size:27
Alignment explanation
Indices: 167145--167198 Score: 99
Period size: 28 Copynumber: 2.0 Consensus size: 27
167135 TTTTAAATTA
167145 ATTTTAAAATAATTTTAATAATTTTAT
1 ATTTTAAAATAATTTTAATAATTTTAT
167172 ATTTTAAAAATAATTTTAATAATTTTA
1 ATTTT-AAAATAATTTTAATAATTTTA
167199 AAATCATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTTAAAATAATTTTAATAATTTTAT
Found at i:167209 original size:38 final size:37
Alignment explanation
Indices: 167115--167199 Score: 136
Period size: 38 Copynumber: 2.3 Consensus size: 37
167105 TAAAATGATG
*
167115 ATAATTTTAATAATTTTATATTTTAAATTAATTTTAAA
1 ATAATTTTAATAATTTTATATTTTAAAATAATTTT-AA
167153 ATAATTTTAATAATTTTATATTTTAAAAATAATTTT-A
1 ATAATTTTAATAATTTTATATTTT-AAAATAATTTTAA
167190 ATAATTTTAA
1 ATAATTTTAA
167200 AATCATTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
37 11 0.24
38 24 0.53
39 10 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
ATAATTTTAATAATTTTATATTTTAAAATAATTTTAA
Found at i:167390 original size:31 final size:31
Alignment explanation
Indices: 167348--167434 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 31
167338 ATGATCAATT
*
167348 TGACCAAAAAAACAAAGGTTAGGGGCCAAAG
1 TGACCAAAAAAACAAACGTTAGGGGCCAAAG
* * *
167379 TGAGCAAAAAAA-AAACGATAAGGGCCAAAG
1 TGACCAAAAAAACAAACGTTAGGGGCCAAAG
* **
167409 TGACCAAACACCCAAACGTTAGGGGC
1 TGACCAAAAAAACAAACGTTAGGGGC
167435 TAATTTTGCA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
30 23 0.51
31 22 0.49
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.09
Consensus pattern (31 bp):
TGACCAAAAAAACAAACGTTAGGGGCCAAAG
Found at i:167686 original size:17 final size:18
Alignment explanation
Indices: 167666--167699 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
167656 TTGAATATTA
167666 GGCCC-AATTATCAAAGT
1 GGCCCAAATTATCAAAGT
167683 GGCCCAAATTATCAAAG
1 GGCCCAAATTATCAAAG
167700 AAGCCCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (18 bp):
GGCCCAAATTATCAAAGT
Found at i:167705 original size:18 final size:18
Alignment explanation
Indices: 167667--167706 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
167657 TGAATATTAG
**
167667 GCCC-AATTATCAAAGTG
1 GCCCAAATTATCAAAGAA
167684 GCCCAAATTATCAAAGAA
1 GCCCAAATTATCAAAGAA
167702 GCCCA
1 GCCCA
167707 TTTAATCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (18 bp):
GCCCAAATTATCAAAGAA
Found at i:169041 original size:19 final size:18
Alignment explanation
Indices: 169013--169051 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
169003 TTACTTAGTT
169013 TTATCATTCTTTGATTTC
1 TTATCATTCTTTGATTTC
169031 TTATACATTCTTTGATTTC
1 TTAT-CATTCTTTGATTTC
169050 TT
1 TT
169052 TTTTCACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.18, C:0.15, G:0.05, T:0.62
Consensus pattern (18 bp):
TTATCATTCTTTGATTTC
Done.