Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015177.1 Kokia drynarioides strain JFW-HI SEQ_130221, 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: 368428
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 552 characters in sequence are not A, C, G, or T
Found at i:23 original size:16 final size:16
Alignment explanation
Indices: 2--51 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1 T
2 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
18 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
33 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
48 ATTA
1 ATTA
52 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:502 original size:12 final size:12
Alignment explanation
Indices: 485--509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
475 AACTTAAAAT
485 ATTTTAAAATTA
1 ATTTTAAAATTA
497 ATTTTAAAATTA
1 ATTTTAAAATTA
509 A
1 A
510 CCATACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:6119 original size:31 final size:32
Alignment explanation
Indices: 6083--6144 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
6073 AATAAACCAT
* *
6083 ATATAAAATTATTAAATAT-TAAAATAATATA
1 ATATAAAATTATTAAAAATAAAAAATAATATA
* *
6114 ATATAAATTTTTTAAAAATAAAAAATAATAT
1 ATATAAAATTATTAAAAATAAAAAATAATAT
6145 GAACGAGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
ATATAAAATTATTAAAAATAAAAAATAATATA
Found at i:6682 original size:18 final size:19
Alignment explanation
Indices: 6650--6688 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6640 TATTTTTAAT
**
6650 AATTTAAAATTTTAAA-AA
1 AATTTAAAAGATTAAATAA
6668 AATTTAAAAGATTAAATAA
1 AATTTAAAAGATTAAATAA
6687 AA
1 AA
6689 AAAAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATTTAAAAGATTAAATAA
Found at i:23450 original size:5 final size:5
Alignment explanation
Indices: 23440--23481 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
23430 AATAAAGCAG
23440 TGGAT TGGAT TGGAT TGGAT TGGAT TGGAT TGGAT TGGAT TG
1 TGGAT TGGAT TGGAT TGGAT TGGAT TGGAT TGGAT TGGAT TG
23482 CTCAATGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TGGAT
Found at i:24362 original size:50 final size:50
Alignment explanation
Indices: 24287--24386 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
24277 ATGTGCTCGT
*
24287 GGTTTTCTTTTCTCTGGGCGGGTGGGGTTGGATGCACTTGACGACAACAA
1 GGTTTTCTTTCCTCTGGGCGGGTGGGGTTGGATGCACTTGACGACAACAA
24337 GGTTTTCTTTCCTCTGGGCGGGTGGGGTTGGATGCACTTGACGACAACAA
1 GGTTTTCTTTCCTCTGGGCGGGTGGGGTTGGATGCACTTGACGACAACAA
24387 TTAGATATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (50 bp):
GGTTTTCTTTCCTCTGGGCGGGTGGGGTTGGATGCACTTGACGACAACAA
Found at i:26444 original size:7 final size:7
Alignment explanation
Indices: 26432--26464 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
26422 ATTTATAGGT
26432 TAGGAGA
1 TAGGAGA
26439 TAGGAGA
1 TAGGAGA
26446 TAGGAGA
1 TAGGAGA
26453 TAGGAGA
1 TAGGAGA
26460 TAGGA
1 TAGGA
26465 ATGGATCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.15
Consensus pattern (7 bp):
TAGGAGA
Found at i:27116 original size:26 final size:29
Alignment explanation
Indices: 27086--27144 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
27076 CATAGAGACT
*
27086 AAATTATA-CTAAAATTTAAA-ATATA-A
1 AAATTAAATCTAAAATTTAAATATATATA
* *
27112 AAATTAAATTTCAAATTTAAATATATATA
1 AAATTAAATCTAAAATTTAAATATATATA
27141 AAAT
1 AAAT
27145 CAAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.26
27 10 0.37
28 5 0.19
29 5 0.19
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATTAAATCTAAAATTTAAATATATATA
Found at i:30058 original size:18 final size:17
Alignment explanation
Indices: 30032--30065 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30022 AATATATATT
30032 TATCAAACAATCTAATTA
1 TATCAAACAAT-TAATTA
*
30050 TATCCAACAATTAATT
1 TATCAAACAATTAATT
30066 TTAAGTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (17 bp):
TATCAAACAATTAATTA
Found at i:30125 original size:13 final size:13
Alignment explanation
Indices: 30093--30127 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
30083 CAATTTTATA
*
30093 ACTTAAATTCAAT
1 ACTTAATTTCAAT
30106 ACTTAATTTCAAT
1 ACTTAATTTCAAT
*
30119 ATTTAATTT
1 ACTTAATTT
30128 TACCATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (13 bp):
ACTTAATTTCAAT
Found at i:51386 original size:2 final size:2
Alignment explanation
Indices: 51379--51405 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51369 TTATACAAAC
51379 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 A
51406 GGGTATACCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62521 original size:7 final size:7
Alignment explanation
Indices: 62509--62544 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
62499 TCCAGTGTAG
62509 AAGACCT
1 AAGACCT
62516 AAGACCT
1 AAGACCT
62523 AAGACCT
1 AAGACCT
62530 AAGACCT
1 AAGACCT
62537 AAGACCT
1 AAGACCT
62544 A
1 A
62545 CAAGTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.44, C:0.28, G:0.14, T:0.14
Consensus pattern (7 bp):
AAGACCT
Found at i:69857 original size:40 final size:40
Alignment explanation
Indices: 69790--69870 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
69780 TTGTGTGGAT
*
69790 TTGATGTATTGTATTTTGACAAATGATGCAACGGAATTTA
1 TTGAAGTATTGTATTTTGACAAATGATGCAACGGAATTTA
* * **
69830 TTGAAGTATTGTATTTTGATAAGTGATGCAGGGGAATTTA
1 TTGAAGTATTGTATTTTGACAAATGATGCAACGGAATTTA
69870 T
1 T
69871 CTTATTATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (40 bp):
TTGAAGTATTGTATTTTGACAAATGATGCAACGGAATTTA
Found at i:74989 original size:10 final size:10
Alignment explanation
Indices: 74974--75003 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
74964 CACCAAAAGG
74974 AAAACCAAAA
1 AAAACCAAAA
74984 AAAACCAAAA
1 AAAACCAAAA
74994 AAAACCAAAA
1 AAAACCAAAA
75004 TACACAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACCAAAA
Found at i:85018 original size:31 final size:29
Alignment explanation
Indices: 84983--85068 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 29
84973 ACAACCCAAT
84983 AACTTGACCAAAAACTTTCAAATAGTTCAAC
1 AACTTGA--AAAAACTTTCAAATAGTTCAAC
* *
85014 AACTTAAATAAAAACTTTCGAATAGTTCAAC
1 AACTT-GA-AAAAACTTTCAAATAGTTCAAC
*
85045 AA-ATG--AAAACTTTCAAATAGTTCA
1 AACTTGAAAAAACTTTCAAATAGTTCA
85069 GTGATCATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
26 18 0.38
30 1 0.02
31 28 0.58
32 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (29 bp):
AACTTGAAAAAACTTTCAAATAGTTCAAC
Found at i:85053 original size:26 final size:26
Alignment explanation
Indices: 84992--85068 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 26
84982 TAACTTGACC
84992 AAAAACTTTCAAATAGTTCAACAACTTAAAT
1 AAAAACTTTCAAATAGTT---CAAC--AAAT
*
85023 AAAAACTTTCGAATAGTTCAACAAAT
1 AAAAACTTTCAAATAGTTCAACAAAT
*
85049 GAAAACTTTCAAATAGTTCA
1 AAAAACTTTCAAATAGTTCA
85069 GTGATCATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 22 0.51
28 4 0.09
31 17 0.40
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (26 bp):
AAAAACTTTCAAATAGTTCAACAAAT
Found at i:92961 original size:2 final size:2
Alignment explanation
Indices: 92954--93006 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
92944 ACTCAAATAG
92954 TA TA TA TA TA 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 TA TA TA TA TA
92996 T- TA TA TA TA TA
1 TA TA TA TA TA TA
93007 AAAGGGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:94588 original size:30 final size:29
Alignment explanation
Indices: 94547--94867 Score: 226
Period size: 29 Copynumber: 11.0 Consensus size: 29
94537 ATTTAAGATT
* *
94547 AAAATGCAATTTTGGAAAAGTTTAAGGGTA
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTC
*
94577 AAAATGTAATTTTGG-GAAGTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGTC
*
94605 AAAATGTGATTTTAGG-AAAG-TTAGAGGTC
1 AAAATGTAATTTT-GGAAAAGTTTAG-GGTC
** * *
94634 AAAATGTGGTTTTAGGAATA-TTGAGGGGTC
1 AAAATGTAATTTT-GGAAAAGTTTA-GGGTC
* * * * *
94664 AAAATGCAATTTTGG-GAAGTTCAATGGTT
1 AAAATGTAATTTTGGAAAAGTT-TAGGGTC
* *
94693 AAAATGTGATTTT-GAGAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGA-AAAGTTT-AGGGTC
* * * *
94723 AAAATATAATTTTAGAAAAGTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTC
*
94752 AAAATGTAACTTTGGAAAAGTTTAGGAGT-
1 AAAATGTAATTTTGGAAAAGTTTAGG-GTC
* * * *
94781 TAAATGCAATTTTAGAAAAGTTTAGGATC
1 AAAATGTAATTTTGGAAAAGTTTAGGGTC
* * * *
94810 AAATTGCAATTTTAGAAAAATTTAGAGGTC
1 AAAATGTAATTTTGGAAAAGTTTAG-GGTC
*
94840 AAAATATAATTTTGG-AAAGTTTAAGGGT
1 AAAATGTAATTTTGGAAAAGTTT-AGGGT
94868 TAAAGTTAAA
Statistics
Matches: 234, Mismatches: 42, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
28 24 0.10
29 128 0.55
30 79 0.34
31 3 0.01
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTC
Found at i:94697 original size:59 final size:55
Alignment explanation
Indices: 94547--94865 Score: 158
Period size: 59 Copynumber: 5.5 Consensus size: 55
94537 ATTTAAGATT
* *
94547 AAAATGCAATTTTGGAAAAGTTTAAGGGTAAAAATGTAATTTTGGGAAGTTTAGGGTC
1 AAAATGCAATTTTGG-AAAG-TTAA-GGTAAAAATGTGATTTTAGGAAGTTTAGGGTC
** * *
94605 AAAATGTGATTTTAGGAAAGTTAGAGGTCAAAATGTGGTTTTAGGAA-TATTGAGGGGTC
1 AAAATGCAATTTT-GGAAAGTTA-AGGTAAAAATGTGATTTTAGGAAGT-TT-A-GGGTC
* * * *
94664 AAAATGCAATTTTGGGAAGTTCAATGGTTAAAATGTGATTTTGAGAAAGTTTAAGGGTT
1 AAAATGCAATTTTGGAAAGTT-AA-GGTAAAAATGTGATTTT-AGGAAGTTT-AGGGTC
** * ** * * *
94723 AAAATATAATTTTAGAAAAGTTTGGGGTTAAAATGTAACTTT-GGAAAAGTTTAGGAGT-
1 AAAATGCAATTTT-GGAAAG-TTAAGGTAAAAATGTGATTTTAGG--AAGTTTAGG-GTC
* * * * * ** * *
94781 TAAATGCAATTTTAGAAAAGTTTAGGATCAAATTGCAATTTTAGAAAAATTTAGAGGTC
1 AAAATGCAATTTT-GGAAAGTTAAGG-TAAAAATGTGATTTTAG-GAAGTTTAG-GGTC
**
94840 AAAATATAATTTTGGAAAGTTTAAGG
1 AAAATGCAATTTTGGAAAG-TTAAGG
94866 GTTAAAGTTA
Statistics
Matches: 202, Mismatches: 39, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
56 1 0.00
57 28 0.14
58 70 0.35
59 89 0.44
60 11 0.05
61 3 0.01
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (55 bp):
AAAATGCAATTTTGGAAAGTTAAGGTAAAAATGTGATTTTAGGAAGTTTAGGGTC
Found at i:95549 original size:2 final size:2
Alignment explanation
Indices: 95542--95585 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
95532 TGGATATGTG
* *
95542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95584 TA
1 TA
95586 ACGGAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119786 original size:16 final size:16
Alignment explanation
Indices: 119765--119796 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
119755 AAATTAAGGT
119765 GGGGCTTGATGTTAGG
1 GGGGCTTGATGTTAGG
119781 GGGGCTTGATGTTAGG
1 GGGGCTTGATGTTAGG
119797 CCCTTGTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.50, T:0.31
Consensus pattern (16 bp):
GGGGCTTGATGTTAGG
Found at i:123387 original size:224 final size:225
Alignment explanation
Indices: 122997--123448 Score: 834
Period size: 224 Copynumber: 2.0 Consensus size: 225
122987 ACTTACTGTT
* *
122997 TAACACAGATTATGATACATGAACAAAGGGATATTGAACAAATGAAAATGAGACGATACTATAAT
1 TAACACAGATTATGATACATGAACAAAGGGATATTGAACAAATGAAAATGAAACGATACTAAAAT
* *
123062 GTAATATTTAAAAAATACAATAATATATTTATAAGAAAAGATAATTGAAGGTTTGGAACAAAAAA
66 GTAATATTTAAAAAATACAATAATATATATATAAGAAAAGATAATTAAAGGTTTGGAACAAAAAA
* *
123127 GAAAAGACAAAGTAATTAAAGGGAAAAAAACAACCAAAAAAAACATTA-TTTTTTTTTTCTTAAA
131 GAAAAGAAAAAGTAATTAAAGGGAAAAAAACAACCAAAAAAAACATTAGATTTTTTTTTCTTAAA
123191 GAAGAAGGAACTCCAAAAAGAAAATCCTTG
196 GAAGAAGGAACTCCAAAAAGAAAATCCTTG
123221 TAACACAGATTATGATACATGAACAAAGGGATATTGAACAAATGAAAATGAAACGATACTAAAAT
1 TAACACAGATTATGATACATGAACAAAGGGATATTGAACAAATGAAAATGAAACGATACTAAAAT
123286 GTAATATTTAAAAAATACAATAATATATATATAAGAAAAGATAATTAAAGGTTTGGAACAAAAAA
66 GTAATATTTAAAAAATACAATAATATATATATAAGAAAAGATAATTAAAGGTTTGGAACAAAAAA
*
123351 GAAAATAAAAAGTAATTAAAGGGAAAAAAACAACCAAAAAAAACATTAGATTTTTTTTTCTTAAA
131 GAAAAGAAAAAGTAATTAAAGGGAAAAAAACAACCAAAAAAAACATTAGATTTTTTTTTCTTAAA
123416 GAAGAAGGAACTCCAAAAAGAAAATCCTTG
196 GAAGAAGGAACTCCAAAAAGAAAATCCTTG
123446 TAA
1 TAA
123449 AATGAAGTGA
Statistics
Matches: 220, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
224 172 0.78
225 48 0.22
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (225 bp):
TAACACAGATTATGATACATGAACAAAGGGATATTGAACAAATGAAAATGAAACGATACTAAAAT
GTAATATTTAAAAAATACAATAATATATATATAAGAAAAGATAATTAAAGGTTTGGAACAAAAAA
GAAAAGAAAAAGTAATTAAAGGGAAAAAAACAACCAAAAAAAACATTAGATTTTTTTTTCTTAAA
GAAGAAGGAACTCCAAAAAGAAAATCCTTG
Found at i:123910 original size:5 final size:5
Alignment explanation
Indices: 123900--123925 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
123890 TGAAAATTGT
123900 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
123926 GTTGGAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:135585 original size:28 final size:28
Alignment explanation
Indices: 135554--135611 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
135544 TAGGAAATAT
* *
135554 TAATCA-AAAAATTATATTTTTAATGAAA
1 TAATCACAAAAATTAT-GTGTTAATGAAA
* *
135582 TAATTACCAAAATTATGTGTTAATGAAA
1 TAATCACAAAAATTATGTGTTAATGAAA
135610 TA
1 TA
135612 GAAAATTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (28 bp):
TAATCACAAAAATTATGTGTTAATGAAA
Found at i:140030 original size:2 final size:2
Alignment explanation
Indices: 140023--140056 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
140013 CACATGATCG
140023 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
140057 NNNNNNNNNT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:140071 original size:2 final size:2
Alignment explanation
Indices: 140066--140098 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
140056 ANNNNNNNNN
*
140066 TA TA TA TA CA 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 TA TA TA T
140099 CATTTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:148481 original size:10 final size:11
Alignment explanation
Indices: 148466--148498 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
148456 GAATTGGATT
148466 TATATA-ATTA
1 TATATATATTA
148476 TATATATATTA
1 TATATATATTA
148487 T-TATATATTA
1 TATATATATTA
148497 TA
1 TA
148499 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATATATTA
Found at i:148483 original size:14 final size:14
Alignment explanation
Indices: 148466--148499 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
148456 GAATTGGATT
148466 TATATAATTATATA
1 TATATAATTATATA
*
148480 TATATTATTATATA
1 TATATAATTATATA
148494 T-TATAA
1 TATATAA
148500 AAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATAATTATATA
Found at i:148905 original size:13 final size:12
Alignment explanation
Indices: 148887--148917 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
148877 AAACAACACT
148887 ATAAAAAATAAAA
1 ATAAAAAAT-AAA
148900 ATAAAAAATAAA
1 ATAAAAAATAAA
148912 ATAAAA
1 ATAAAA
148918 CCTAGTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:163288 original size:61 final size:61
Alignment explanation
Indices: 163193--163315 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
163183 ATCAACCAGT
163193 TCCCTTGATCTTGTTATGGATAATCCACTTTCACAAAACCCAGGTAATTATCATGTTTTGC
1 TCCCTTGATCTTGTTATGGATAATCCACTTTCACAAAACCCAGGTAATTATCATGTTTTGC
163254 TCCCTTGATCTTGTTATGGATAATCCACTTTCACAAAACCCAGGTAATTATCATGTTTTGC
1 TCCCTTGATCTTGTTATGGATAATCCACTTTCACAAAACCCAGGTAATTATCATGTTTTGC
163315 T
1 T
163316 TTCTTTTTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (61 bp):
TCCCTTGATCTTGTTATGGATAATCCACTTTCACAAAACCCAGGTAATTATCATGTTTTGC
Found at i:167823 original size:18 final size:18
Alignment explanation
Indices: 167802--167836 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
167792 AATTTTTATT
*
167802 AATTTTTAATATTTTAAG
1 AATTTTTAATAATTTAAG
167820 AATTTTTAATAATTTAA
1 AATTTTTAATAATTTAA
167837 TGGACTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTTTTAATAATTTAAG
Found at i:167826 original size:10 final size:10
Alignment explanation
Indices: 167792--167834 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
167782 CGATTGAACC
*
167792 AATTTTTATT
1 AATTTTTAAT
167802 AATTTTTAAT
1 AATTTTTAAT
*
167812 -A-TTTTAAG
1 AATTTTTAAT
167820 AATTTTTAAT
1 AATTTTTAAT
167830 AATTT
1 AATTT
167835 AATGGACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.21
9 2 0.07
10 20 0.71
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:170786 original size:3 final size:3
Alignment explanation
Indices: 170778--170820 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
170768 ATTAGGTTTT
*
170778 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
170821 CACATACTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:186491 original size:31 final size:31
Alignment explanation
Indices: 186455--186513 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
186445 ATTATCAATC
* *
186455 TATTTGAAAGTTTTTATTTAAGTTATTAAAT
1 TATTTGAAAGTTTTTATCTAAGCTATTAAAT
186486 TATTTGAAAGTTTTTATCTAAGCTATTA
1 TATTTGAAAGTTTTTATCTAAGCTATTA
186514 GGCTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTTGAAAGTTTTTATCTAAGCTATTAAAT
Found at i:196092 original size:2 final size:2
Alignment explanation
Indices: 196085--196114 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
196075 GCAAAGGTCT
*
196085 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
196115 GCACACACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:201177 original size:36 final size:37
Alignment explanation
Indices: 201130--201199 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
201120 CGGGTCAAGA
201130 TACTATTCAAGTAAAACTTTTTTAATAGT-ATCGAGC
1 TACTATTCAAGTAAAACTTTTTTAATAGTGATCGAGC
*
201166 TACTATTCAAGTAAAACTTTTTTATTAGTGATCG
1 TACTATTCAAGTAAAACTTTTTTAATAGTGATCG
201200 TTTAAAGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (37 bp):
TACTATTCAAGTAAAACTTTTTTAATAGTGATCGAGC
Found at i:207035 original size:31 final size:31
Alignment explanation
Indices: 206995--207057 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
206985 AGATATAATA
* *
206995 TAATTTATATTTGTTGTAAAACAAACTATTT
1 TAATGTATATTTATTGTAAAACAAACTATTT
207026 TAATGTATATTTATTGTAAAACAAACTATTT
1 TAATGTATATTTATTGTAAAACAAACTATTT
207057 T
1 T
207058 TTTTCTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (31 bp):
TAATGTATATTTATTGTAAAACAAACTATTT
Found at i:222639 original size:21 final size:20
Alignment explanation
Indices: 222615--222703 Score: 90
Period size: 20 Copynumber: 4.3 Consensus size: 20
222605 ATTATATTGT
*
222615 TGTTTTGGTGCTTCTTTTTAC
1 TGTTTTGGTG-TTTTTTTTAC
*
222636 TGTTTTGGTTATTGTTTTTTAC
1 TGTTTTGG-TGTT-TTTTTTAC
* *
222658 TGTTTTGATTTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
* *
222678 TCTTTTGGTG-TTTTTTTAT
1 TGTTTTGGTGTTTTTTTTAC
222697 TGTTTTG
1 TGTTTTG
222704 ATTATTGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 14 0.25
20 15 0.26
21 13 0.23
22 15 0.26
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.70
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:222714 original size:22 final size:20
Alignment explanation
Indices: 222629--222706 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 20
222619 TTGGTGCTTC
*
222629 TTTTTACTGTTTTGGTTATTGT
1 TTTTTACTGTTTTGATT-TT-T
222651 TTTTTACTGTTTTGATTTTT
1 TTTTTACTGTTTTGATTTTT
* * *
222671 TTTTTACTCTTTTG-GTGTT
1 TTTTTACTGTTTTGATTTTT
*
222690 TTTTTATTGTTTTGATT
1 TTTTTACTGTTTTGATT
222707 ATTGTTTTGG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.31
20 15 0.31
21 2 0.04
22 16 0.33
ACGTcount: A:0.09, C:0.05, G:0.14, T:0.72
Consensus pattern (20 bp):
TTTTTACTGTTTTGATTTTT
Found at i:222770 original size:32 final size:30
Alignment explanation
Indices: 222728--222786 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 30
222718 TTTTTTATAC
*
222728 TGTTTTGATGTTATTTTTGATGTTGTTTTGGT
1 TGTTTAGATGTTATTTTT-ATG-TGTTTTGGT
222760 TGTTTAGATGTTATTTTTATGTGTTTT
1 TGTTTAGATGTTATTTTTATGTGTTTT
222787 TACTATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
31 3 0.12
32 17 0.65
ACGTcount: A:0.12, C:0.00, G:0.22, T:0.66
Consensus pattern (30 bp):
TGTTTAGATGTTATTTTTATGTGTTTTGGT
Found at i:222957 original size:21 final size:21
Alignment explanation
Indices: 222913--222958 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
222903 TAAATTTGTT
* *
222913 TATTTTTAATGTTTGTTTTAA
1 TATTTTTAATGTTTATTTGAA
222934 TATTTTTAA-GTTTATTTGATA
1 TATTTTTAATGTTTATTTGA-A
222955 TATT
1 TATT
222959 ATATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (21 bp):
TATTTTTAATGTTTATTTGAA
Found at i:224307 original size:27 final size:27
Alignment explanation
Indices: 224246--224310 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
224236 ATTAATCTAA
* * *
224246 AAAATTAATTAATTATGTAAATAATTT
1 AAAATTTATTAAATATGAAAATAATTT
***
224273 ATTTTTTATTAAATATGAAAATAATTT
1 AAAATTTATTAAATATGAAAATAATTT
224300 AAAATTTATTA
1 AAAATTTATTA
224311 TTAAAGTTGA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (27 bp):
AAAATTTATTAAATATGAAAATAATTT
Found at i:225138 original size:22 final size:24
Alignment explanation
Indices: 225098--225142 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
225088 TTATTACTTA
*
225098 TTGTTTATATGTTGGATTATTTGC
1 TTGTTTATATGTTGAATTATTTGC
225122 TTGTTTA-A-GTTGAATTATTTG
1 TTGTTTATATGTTGAATTATTTG
225143 TAGAGGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 1 0.05
24 7 0.35
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.58
Consensus pattern (24 bp):
TTGTTTATATGTTGAATTATTTGC
Found at i:240563 original size:28 final size:28
Alignment explanation
Indices: 240518--240580 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
240508 TCAAATTTGG
240518 TAATATTTTTGTCAATAAAATCACAAAAA
1 TAAT-TTTTTGTCAATAAAATCACAAAAA
* * *
240547 TAATTTTTTGTTAATAAAATTAGAAAAA
1 TAATTTTTTGTCAATAAAATCACAAAAA
*
240575 GAATTT
1 TAATTT
240581 CGATGAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (28 bp):
TAATTTTTTGTCAATAAAATCACAAAAA
Found at i:252388 original size:2 final size:2
Alignment explanation
Indices: 252378--252427 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
252368 TTTTGGGTTA
252378 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
252419 AT AT AT AT A
1 AT AT AT AT A
252428 GTCATTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:256354 original size:2 final size:2
Alignment explanation
Indices: 256347--256380 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
256337 AAATAAACTA
256347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256381 CAAATATGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:270518 original size:30 final size:30
Alignment explanation
Indices: 270463--270519 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
270453 TGATCTACGT
* * **
270463 ATAATAATTTCAAACTTCTTTTACAAAAAA
1 ATAATAATATCAAACTTATAATACAAAAAA
270493 ATAATAATATCAAACTTATAATACAAA
1 ATAATAATATCAAACTTATAATACAAA
270520 CATTTGTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (30 bp):
ATAATAATATCAAACTTATAATACAAAAAA
Found at i:270986 original size:13 final size:14
Alignment explanation
Indices: 270968--270996 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
270958 TATCCCTTAC
270968 TCCCATTTT-TTCT
1 TCCCATTTTGTTCT
270981 TCCCATTTTGTTCT
1 TCCCATTTTGTTCT
270995 TC
1 TC
270997 ATTCCCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.07, C:0.31, G:0.03, T:0.59
Consensus pattern (14 bp):
TCCCATTTTGTTCT
Found at i:272174 original size:14 final size:15
Alignment explanation
Indices: 272155--272189 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
272145 TCAAGTATAA
272155 TTATTAAAATTAT-T
1 TTATTAAAATTATGT
*
272169 TTATTAAATTTATGT
1 TTATTAAAATTATGT
272184 TTATTA
1 TTATTA
272190 TAACGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTAAAATTATGT
Found at i:272730 original size:5 final size:6
Alignment explanation
Indices: 272713--272737 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
272703 TCGTAAAGAG
272713 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
272738 TGGGTTACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:275481 original size:13 final size:13
Alignment explanation
Indices: 275463--275487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
275453 AATTTTTAAA
275463 TTTTTAATTAATG
1 TTTTTAATTAATG
275476 TTTTTAATTAAT
1 TTTTTAATTAAT
275488 AAATATATTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:275688 original size:28 final size:29
Alignment explanation
Indices: 275638--275699 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
275628 AAATATTTTT
* * *
275638 AATTAATAACTCATTTATTTATATAAAT-A
1 AATTAATAAATCATGTAATTATAT-AATGA
275667 AATTAATAAAT-ATGTAATTATATAATGA
1 AATTAATAAATCATGTAATTATATAATGA
275695 AATTA
1 AATTA
275700 TATATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.10
28 16 0.55
29 10 0.34
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
AATTAATAAATCATGTAATTATATAATGA
Found at i:275746 original size:102 final size:101
Alignment explanation
Indices: 275550--275738 Score: 274
Period size: 100 Copynumber: 1.9 Consensus size: 101
275540 AAATAATTAT
* *
275550 TTTATTTATATAATAAAATAATAAATATGTAATTATATAGTGTATATATATATATATATATATAT
1 TTTATTTATATAATAAAATAATAAATATGTAATTATATAATGTAAATATATATATATATATATAT
275615 AGCATCATGTTAAAAATATTTTTAATTAATAACTCA
66 AGCATCATGTTAAAAATATTTTTAATTAATAACTCA
* * * *
275651 TTTATTTATATAAATAAATTAATAAATATGTAATTATATAATG-AAAT-TATATATTTTTATATT
1 TTTATTTATAT-AATAAAATAATAAATATGTAATTATATAATGTAAATATATATATATATATATA
* * *
275714 TATCATTATGTTAAATATATTTTTA
65 TAGCATCATGTTAAAAATATTTTTA
275739 CTTTTAATTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 35 0.45
101 14 0.18
102 29 0.37
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (101 bp):
TTTATTTATATAATAAAATAATAAATATGTAATTATATAATGTAAATATATATATATATATATAT
AGCATCATGTTAAAAATATTTTTAATTAATAACTCA
Found at i:283286 original size:36 final size:37
Alignment explanation
Indices: 283246--283316 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
283236 AAAGAGAGAA
*
283246 GAATATA-GG-ATGTTGTATGCCTTTACCAGGCAAAAG
1 GAATATAGGGCAT-TTGTATGCCTTTACAAGGCAAAAG
283282 GAATATAGGGCATTTGTATGCCTTTACAAGGCAAA
1 GAATATAGGGCATTTGTATGCCTTTACAAGGCAAA
283317 CTTGGCAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 7 0.22
37 23 0.72
38 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (37 bp):
GAATATAGGGCATTTGTATGCCTTTACAAGGCAAAAG
Found at i:285857 original size:20 final size:19
Alignment explanation
Indices: 285811--285853 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
285801 TGTCTCCTAC
285811 TTTTCTTTCTCCTTCTCCTT
1 TTTTCTTTCT-CTTCTCCTT
* *
285831 TCTTCTTTCTCTTCTTCTT
1 TTTTCTTTCTCTTCTCCTT
285850 TTTT
1 TTTT
285854 TCTTCTCTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTCTTTCTCTTCTCCTT
Found at i:288993 original size:15 final size:15
Alignment explanation
Indices: 288950--288993 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
288940 AACCAAATAA
**
288950 AATTAATTGATTTTT
1 AATTAATTGAAATTT
*
288965 AATTAAAT-AAATTT
1 AATTAATTGAAATTT
288979 AATTAATTGAAATTT
1 AATTAATTGAAATTT
288994 CTAAATCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
AATTAATTGAAATTT
Found at i:290166 original size:27 final size:26
Alignment explanation
Indices: 290086--290172 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
290076 AATTAGGTCC
* * *
290086 AAAAAAAGTTTAGGAACCAAATTAAAA
1 AAAAAAAGTTCAAGTACCAAATT-AAA
290113 AAAATATCAAGTTCAAGTACCAAATTAAA
1 AAAA-A--AAGTTCAAGTACCAAATTAAA
* **
290142 TAAAAAAAGTTTAAGTACCGGATTAAA
1 -AAAAAAAGTTCAAGTACCAAATTAAA
290169 AAAA
1 AAAA
290173 TGTCAAATTC
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.08
27 22 0.44
28 1 0.02
29 4 0.08
30 19 0.38
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (26 bp):
AAAAAAAGTTCAAGTACCAAATTAAA
Found at i:290184 original size:56 final size:57
Alignment explanation
Indices: 290086--290193 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 57
290076 AATTAGGTCC
* * *
290086 AAAAAAAGTTTAGGAACCAAATTAAAAAAAATATCAAGTTCAAGTACCAAATTAAAT
1 AAAAAAAGTTTAAGAACCAAATTAAAAAAAATATCAAATTCAAATACCAAATTAAAT
* ** *
290143 AAAAAAAGTTTAAGTACCGGATT-AAAAAAATGTCAAATTCAAATACCAAAT
1 AAAAAAAGTTTAAGAACCAAATTAAAAAAAATATCAAATTCAAATACCAAAT
290194 ATTATATTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
56 25 0.57
57 19 0.43
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.23
Consensus pattern (57 bp):
AAAAAAAGTTTAAGAACCAAATTAAAAAAAATATCAAATTCAAATACCAAATTAAAT
Found at i:290584 original size:21 final size:21
Alignment explanation
Indices: 290538--290577 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
290528 AAGATTATAT
**
290538 AAAT-AATTTATTTAATTTTA
1 AAATAAATTTATTTAATTCCA
290558 AAATAAATTTATTTAATTCC
1 AAATAAATTTATTTAATTCC
290578 CACATAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATAAATTTATTTAATTCCA
Found at i:300914 original size:2 final size:2
Alignment explanation
Indices: 300909--300938 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
300899 ACACACGTGC
*
300909 AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
300939 GTGTGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:311324 original size:29 final size:29
Alignment explanation
Indices: 311290--311345 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
311280 TTGATTCTTT
*
311290 TTTAATAGTATAAG-GACTAAATTGATCCA
1 TTTAATAATA-AAGTGACTAAATTGATCCA
*
311319 TTTAATAATAAAGTGACTAATTTGATC
1 TTTAATAATAAAGTGACTAAATTGATC
311346 TAGTCCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (29 bp):
TTTAATAATAAAGTGACTAAATTGATCCA
Found at i:319916 original size:4 final size:4
Alignment explanation
Indices: 319907--319933 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
319897 TAACAGATCC
319907 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
319934 AAGAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:328960 original size:2 final size:2
Alignment explanation
Indices: 328953--328984 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
328943 ATCAATCCTA
328953 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
328985 CAGATACAAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:331380 original size:19 final size:19
Alignment explanation
Indices: 331358--331404 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
331348 TTTAGTAGTC
* *
331358 ATTTTTCTATTCTATGTCT
1 ATTTTACTATTATATGTCT
331377 ATTTTACTA-TATATGTCT
1 ATTTTACTATTATATGTCT
331395 ATTTTACTAT
1 ATTTTACTAT
331405 ATAGTTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTTTACTATTATATGTCT
Found at i:331391 original size:18 final size:18
Alignment explanation
Indices: 331370--331407 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
331360 TTTTCTATTC
331370 TATGTCTATTTTACTATA
1 TATGTCTATTTTACTATA
331388 TATGTCTATTTTACTATA
1 TATGTCTATTTTACTATA
331406 TA
1 TA
331408 GTTTAGTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (18 bp):
TATGTCTATTTTACTATA
Found at i:337298 original size:31 final size:31
Alignment explanation
Indices: 337260--337326 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
337250 GAGGTACAAG
*
337260 TGACTTAAAT-AAGAACTTTCAAATAGTTTAA
1 TGACTTAAATGAA-AACTTTCAAATAGTTCAA
*
337291 TGACTTAAATGAAAACTTTCGAATAGTTCAA
1 TGACTTAAATGAAAACTTTCAAATAGTTCAA
337322 TGACT
1 TGACT
337327 ATTTTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAA
Found at i:337524 original size:42 final size:42
Alignment explanation
Indices: 337444--337524 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
337434 TTTGTCATTT
* * ** *
337444 TTTATCACATGCACCCTAACTTAAGAATGGAAATACCAATTG
1 TTTATCACATGCACCCTAACGTAAAAATAAAAACACCAATTG
* *
337486 TTTATCATATGCACGCTAACGTAAAAATAAAAACACCAA
1 TTTATCACATGCACCCTAACGTAAAAATAAAAACACCAA
337525 AGAATCCAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (42 bp):
TTTATCACATGCACCCTAACGTAAAAATAAAAACACCAATTG
Found at i:347280 original size:10 final size:10
Alignment explanation
Indices: 347264--347298 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
347254 AATTCAAAAT
347264 ATTAATTAAA
1 ATTAATTAAA
*
347274 GTTAATTAAA
1 ATTAATTAAA
*
347284 ATTAATTAAC
1 ATTAATTAAA
347294 ATTAA
1 ATTAA
347299 CGAATTGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (10 bp):
ATTAATTAAA
Found at i:352367 original size:11 final size:11
Alignment explanation
Indices: 352351--352377 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
352341 CAAACAAAGA
352351 GTTTCAACTCT
1 GTTTCAACTCT
352362 GTTTCAACTCT
1 GTTTCAACTCT
352373 GTTTC
1 GTTTC
352378 TTATAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.48
Consensus pattern (11 bp):
GTTTCAACTCT
Found at i:354983 original size:13 final size:13
Alignment explanation
Indices: 354952--355001 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
354942 CTTAAACTAA
354952 ACTTTTCAAAAAT-
1 ACTTTTC-AAAATC
*
354965 AATTTTCAAAATC
1 ACTTTTCAAAATC
354978 ACTTTTCCAAAA-C
1 ACTTTT-CAAAATC
*
354991 ACTTCTCAAAA
1 ACTTTTCAAAA
355002 GCAATGCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 10 0.31
13 17 0.53
14 5 0.16
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAATC
Found at i:354999 original size:26 final size:26
Alignment explanation
Indices: 354952--355001 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
354942 CTTAAACTAA
* *
354952 ACTTTTCAAAAATAATTTTCAAAATC
1 ACTTTTCAAAAACAATTCTCAAAATC
* *
354978 ACTTTTCCAAAACACTTCTCAAAA
1 ACTTTTCAAAAACAATTCTCAAAA
355002 GCAATGCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (26 bp):
ACTTTTCAAAAACAATTCTCAAAATC
Done.