Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012299.1 Kokia drynarioides strain JFW-HI SEQ_127300, 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: 196525
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 183 characters in sequence are not A, C, G, or T
Found at i:285 original size:13 final size:13
Alignment explanation
Indices: 257--295 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 13
247 CCCTTCTTCC
257 TTCTTCTTTCTTTCT
1 TTCTT-TTT-TTTCT
272 TTCTTTTTTTTCT
1 TTCTTTTTTTTCT
285 TTCTTTTTTTT
1 TTCTTTTTTTT
296 TTCAGTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 16 0.67
14 3 0.12
15 5 0.21
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:285 original size:17 final size:16
Alignment explanation
Indices: 263--297 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
253 TTCCTTCTTC
263 TTTCTTTCTTTCTTTTT
1 TTTCTTTCTTT-TTTTT
280 TTTCTTTCTTTTTTTT
1 TTTCTTTCTTTTTTTT
296 TT
1 TT
298 CAGTTTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTCTTTCTTTTTTTT
Found at i:1349 original size:32 final size:32
Alignment explanation
Indices: 1308--1393 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
1298 AAAATATTAG
*
1308 AAACACTACATAAGTCTTGAAAGTTAACAACC
1 AAACACTACATAAGTCTTGAAAGGTAACAACC
*
1340 AAACACTACATAAGTCTTAAAAGGTAACAACC
1 AAACACTACATAAGTCTTGAAAGGTAACAACC
* *
1372 AAACGCTACATAAATCTTGAAA
1 AAACACTACATAAGTCTTGAAA
1394 ACAACAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (32 bp):
AAACACTACATAAGTCTTGAAAGGTAACAACC
Found at i:1835 original size:21 final size:21
Alignment explanation
Indices: 1809--1848 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1799 ACCTTTTTTA
1809 AAGTTAAA-AGTCAAAACTATC
1 AAGTTAAATAG-CAAAACTATC
1830 AAGTTAAATAGCAAAACTA
1 AAGTTAAATAGCAAAACTA
1849 CATCATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.23
Consensus pattern (21 bp):
AAGTTAAATAGCAAAACTATC
Found at i:2741 original size:29 final size:27
Alignment explanation
Indices: 2697--2752 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 27
2687 ACTTTTCACA
2697 ATTTTTAAATTTAATTTTTATACTTTT
1 ATTTTTAAATTTAATTTTTATACTTTT
*
2724 ATTTTTAAGGATTTAATTTTTCTACTTTT
1 ATTTTTAA--ATTTAATTTTTATACTTTT
2753 TAAATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 8 0.31
29 18 0.69
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (27 bp):
ATTTTTAAATTTAATTTTTATACTTTT
Found at i:2742 original size:15 final size:13
Alignment explanation
Indices: 2696--2744 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
2686 TACTTTTCAC
2696 AATTTTTAAATTT
1 AATTTTTAAATTT
*
2709 AATTTTTATACTTT
1 AATTTTTA-AATTT
*
2723 TATTTTTAAGGATTT
1 AATTTTTAA--ATTT
2738 AATTTTT
1 AATTTTT
2745 CTACTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 9 0.31
14 11 0.38
15 9 0.31
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (13 bp):
AATTTTTAAATTT
Found at i:3869 original size:19 final size:17
Alignment explanation
Indices: 3813--3862 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
3803 AAACTTGTAA
*
3813 AAAGAAAATTAAAAATT
1 AAAGAAAATGAAAAATT
3830 -AAGAAAATAGAAAAATAT
1 AAAGAAAAT-GAAAAAT-T
3848 AAAGAAAATGAAAAA
1 AAAGAAAATGAAAAA
3863 GTCTAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 7 0.24
19 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (17 bp):
AAAGAAAATGAAAAATT
Found at i:3879 original size:19 final size:19
Alignment explanation
Indices: 3813--3880 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
3803 AAACTTGTAA
*
3813 AAAGAAAAT-TAAAAAT-T
1 AAAGAAAATAGAAAAATAT
3830 -AAGAAAATAGAAAAATAT
1 AAAGAAAATAGAAAAATAT
*
3848 AAAGAAAAT-GAAAAAGTCT
1 AAAGAAAATAGAAAAA-TAT
*
3867 AAA-AATATAGAAAA
1 AAAGAAAATAGAAAA
3881 TTACAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
16 8 0.19
17 6 0.14
18 11 0.26
19 18 0.42
ACGTcount: A:0.71, C:0.01, G:0.10, T:0.18
Consensus pattern (19 bp):
AAAGAAAATAGAAAAATAT
Found at i:3987 original size:29 final size:30
Alignment explanation
Indices: 3948--4010 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
3938 ACTTATCCTT
3948 TCAACCCATTTTCCCACCTTAGTTTGCATA
1 TCAACCCATTTTCCCACCTTAGTTTGCATA
* *
3978 TCAA-CCATTTTCCTATCTTAGTTTGCATA
1 TCAACCCATTTTCCCACCTTAGTTTGCATA
4007 TCAA
1 TCAA
4011 AACATTCCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.25, C:0.29, G:0.06, T:0.40
Consensus pattern (30 bp):
TCAACCCATTTTCCCACCTTAGTTTGCATA
Found at i:11530 original size:33 final size:34
Alignment explanation
Indices: 11486--11574 Score: 91
Period size: 33 Copynumber: 2.7 Consensus size: 34
11476 ATGTAAAAAA
*
11486 AAATTAATAATAAAATAAAAATTAT-ACAATATCT
1 AAATTAATAATAAAA-AAAAATAATAACAATATCT
*
11520 AAATT-ATAATAAAAAATAATAATAACAATA--T
1 AAATTAATAATAAAAAAAAATAATAACAATATCT
*
11551 -AA-TAACAATAACAAAAAAATAATA
1 AAATTAATAATAA-AAAAAAATAATA
11575 TTTTTTTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
29 1 0.02
30 8 0.17
31 12 0.25
32 7 0.15
33 15 0.31
34 5 0.10
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (34 bp):
AAATTAATAATAAAAAAAAATAATAACAATATCT
Found at i:11571 original size:17 final size:17
Alignment explanation
Indices: 11530--11572 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
11520 AAATTATAAT
*
11530 AAAAAATAATAATAACA
1 AAAAAATAACAATAACA
* *
11547 ATATAATAACAATAACA
1 AAAAAATAACAATAACA
11564 AAAAAATAA
1 AAAAAATAA
11573 TATTTTTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAAATAACAATAACA
Found at i:21575 original size:35 final size:35
Alignment explanation
Indices: 21536--21607 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
21526 ATTTTTTAGA
* *
21536 ATAT-ATTTTTTGAAAATTTATAAATTTTTAAAAAT
1 ATATAATTTGTTG-AAATTTATAAATATTTAAAAAT
* *
21571 ATATAATTTGTTGAATTTTATAAATATTTATAAAT
1 ATATAATTTGTTGAAATTTATAAATATTTAAAAAT
21606 AT
1 AT
21608 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 25 0.78
36 7 0.22
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (35 bp):
ATATAATTTGTTGAAATTTATAAATATTTAAAAAT
Found at i:21602 original size:10 final size:10
Alignment explanation
Indices: 21587--21620 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
21577 TTTGTTGAAT
21587 TTTATAAATA
1 TTTATAAATA
21597 TTTATAAATA
1 TTTATAAATA
*
21607 TTTAAAAATTA
1 TTTATAAA-TA
21618 TTT
1 TTT
21621 TGAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTATAAATA
Found at i:21609 original size:21 final size:21
Alignment explanation
Indices: 21585--21634 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
21575 AATTTGTTGA
21585 ATTTTATAAA-TATTTATAAAT
1 ATTTTATAAATTATTT-TAAAT
* *
21606 A-TTTAAAAATTATTTTGAAT
1 ATTTTATAAATTATTTTAAAT
*
21626 TTTTTATAA
1 ATTTTATAA
21635 TTTTTGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTTATAAATTATTTTAAAT
Found at i:21717 original size:18 final size:18
Alignment explanation
Indices: 21694--21731 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21684 ACCCCAATAT
*
21694 GTTATTCGAATGATTCAA
1 GTTATTCGAATAATTCAA
21712 GTTATTCGAATAATTCAA
1 GTTATTCGAATAATTCAA
21730 GT
1 GT
21732 ACTCGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (18 bp):
GTTATTCGAATAATTCAA
Found at i:21739 original size:17 final size:18
Alignment explanation
Indices: 21694--21739 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
21684 ACCCCAATAT
* *
21694 GTTATTCGAATGATTCAA
1 GTTACTCGAATAATTCAA
*
21712 GTTATTCGAATAATTCAA
1 GTTACTCGAATAATTCAA
21730 G-TACTCGAAT
1 GTTACTCGAAT
21740 TGTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (18 bp):
GTTACTCGAATAATTCAA
Found at i:31258 original size:24 final size:24
Alignment explanation
Indices: 31231--31294 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
31221 CTAAGTATAT
31231 GAGCATAAACATATAGTGCCTGAA
1 GAGCATAAACATATAGTGCCTGAA
** *
31255 GAGCATAAACATATAGTGGTTGAC
1 GAGCATAAACATATAGTGCCTGAA
*
31279 GAGCATAAACGTATAG
1 GAGCATAAACATATAG
31295 CGAATGACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (24 bp):
GAGCATAAACATATAGTGCCTGAA
Found at i:31302 original size:24 final size:24
Alignment explanation
Indices: 31231--31308 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
31221 CTAAGTATAT
** *
31231 GAGCATAAACATATAGTGCCTGAA
1 GAGCATAAACATATAGTGAATGAC
**
31255 GAGCATAAACATATAGTGGTTGAC
1 GAGCATAAACATATAGTGAATGAC
* *
31279 GAGCATAAACGTATAGCGAATGAC
1 GAGCATAAACATATAGTGAATGAC
*
31303 AAGCAT
1 GAGCAT
31309 GTTATACGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (24 bp):
GAGCATAAACATATAGTGAATGAC
Found at i:38099 original size:26 final size:29
Alignment explanation
Indices: 38050--38102 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
38040 TTTTCTATTT
*
38050 TCTAAATTAAATATTATTTGCTCAATTGA
1 TCTAAATTAAATATAATTTGCTCAATTGA
38079 TCTAAA-TAAAT-TAATTT-CTCAATT
1 TCTAAATTAAATATAATTTGCTCAATT
38103 AAATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 5 0.22
28 5 0.22
29 6 0.26
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (29 bp):
TCTAAATTAAATATAATTTGCTCAATTGA
Found at i:38111 original size:16 final size:18
Alignment explanation
Indices: 38085--38117 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38075 TTGATCTAAA
38085 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
38102 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
38118 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:43425 original size:52 final size:52
Alignment explanation
Indices: 43342--43580 Score: 336
Period size: 52 Copynumber: 4.6 Consensus size: 52
43332 ATTTCATTTA
** *
43342 ATACTCACGATGACACATAGTCATCAAACCTCTTAATCCGTATAA-GATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTA-AAGGATTCAT
* * *
43394 ATACTAACGATTACACATAGTTATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
43446 ATACTCACGATGATACATAATCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * **
43498 ATACACACGATGACATATAGTTATCGAACCTCATAATTTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
43550 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
43581 TTTTCATTTA
Statistics
Matches: 163, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
51 2 0.01
52 161 0.99
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:50707 original size:52 final size:51
Alignment explanation
Indices: 50597--50772 Score: 271
Period size: 52 Copynumber: 3.4 Consensus size: 51
50587 ATTTCATTTA
* *
50597 ATACTCACGATGACACATAGTCATCGGACCTTTAATCCGTATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTATAATCCGTAAAGGATTCAT
* * * *
50648 ATACTCACGATAACACATAGTAATCAGACCTAATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCT-ATAATCCGTAAAGGATTCAT
*
50700 ATACTCACGATGACACATAATCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCT-ATAATCCGTAAAGGATTCAT
50752 ATACTCACGATGACACATAGT
1 ATACTCACGATGACACATAGT
50773 GACATTTTCA
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 28 0.25
52 83 0.75
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTATAATCCGTAAAGGATTCAT
Found at i:62249 original size:32 final size:32
Alignment explanation
Indices: 62212--62306 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 32
62202 AAAAATTTAA
62212 GTACCAAATTAGGGAAAAAAATGTAAGTTCAG
1 GTACCAAATTAGGGAAAAAAATGTAAGTTCAG
**
62244 GTACCAAATT-GGGTTAAAAA---AAGTTCAG
1 GTACCAAATTAGGGAAAAAAATGTAAGTTCAG
* *
62272 GTACCAAATTA---AAAAAAGTGTTAAGTTTAG
1 GTACCAAATTAGGGAAAAAAATG-TAAGTTCAG
62302 GTACC
1 GTACC
62307 CAACATTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
26 4 0.08
28 18 0.35
30 12 0.23
31 8 0.15
32 10 0.19
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (32 bp):
GTACCAAATTAGGGAAAAAAATGTAAGTTCAG
Found at i:65109 original size:57 final size:58
Alignment explanation
Indices: 65006--65114 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 58
64996 TTTTCAGATA
* **
65006 CCCAAAAATATTTTTTTGAGTGATTACCATCCCATGGTTGAAACCCACTTTTGTAGGT
1 CCCAAAAATATTTTTTTGAGTGATTACCATCCAATGGCCGAAACCCACTTTTGTAGGT
* * *
65064 CCCAAAAATA-TTTTTTGGGTGATTATCATCCAATGGCCGAGACCCACTTTT
1 CCCAAAAATATTTTTTTGAGTGATTACCATCCAATGGCCGAAACCCACTTTT
65115 AACCTCAGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 35 0.78
58 10 0.22
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (58 bp):
CCCAAAAATATTTTTTTGAGTGATTACCATCCAATGGCCGAAACCCACTTTTGTAGGT
Found at i:67814 original size:40 final size:40
Alignment explanation
Indices: 67728--67831 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
67718 TCGACCTTGA
* *
67728 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGCTAC
1 GTCGATGAGACACTGGGTGTCATTATATTACTTCGACTAC
* *
67768 GCCGATGAGACACTGGGTGTCACTT-TATTGCTTCGAACTA-
1 GTCGATGAGACACTGGGTGTCA-TTATATTACTTCG-ACTAC
* * * *
67808 TTCGATGAGGCATTGGGTGCCATT
1 GTCGATGAGACACTGGGTGTCATT
67832 CTGGTGTGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
39 2 0.04
40 46 0.87
41 5 0.09
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCATTATATTACTTCGACTAC
Found at i:81133 original size:32 final size:32
Alignment explanation
Indices: 81070--81136 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
81060 AAATTTCTAT
* *
81070 TCAATCCTAATTTCTTCAGGGGTTTCTATTAA
1 TCAATCCTAATTTCTTCAAGGATTTCTATTAA
* *
81102 TCAATTCTAATTTCTTTAAGGATTTGC-ATTAA
1 TCAATCCTAATTTCTTCAAGGATTT-CTATTAA
81134 TCA
1 TCA
81137 TCGTCTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (32 bp):
TCAATCCTAATTTCTTCAAGGATTTCTATTAA
Found at i:81485 original size:2 final size:2
Alignment explanation
Indices: 81478--81502 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
81468 GGGGAGAGTT
81478 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 T
81503 TAAAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83964 original size:12 final size:12
Alignment explanation
Indices: 83949--83973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83939 TGTAAAGATG
83949 AAGAAGAAGAAA
1 AAGAAGAAGAAA
83961 AAGAAGAAGAAA
1 AAGAAGAAGAAA
83973 A
1 A
83974 TATATGAAAA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:86659 original size:132 final size:132
Alignment explanation
Indices: 86439--86700 Score: 355
Period size: 132 Copynumber: 2.0 Consensus size: 132
86429 TATCATGTAG
* * * * * *
86439 TGCTTACACGAGCTGTGGGTTGAGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
1 TGCTCACACGAGCTATAGGTTAAGATGTTAGGCTACACGATGCTACTCACACGAGCTGTGAAGAA
* * * * * *
86504 TCTACGACGTATGCCAAACCTCAGCCATCTGTAGGACATCTAGGACCAA-CACCCATATAACATG
66 TCCACAACATATACCAAACCTCAGCCATCGGTAGGACATCTAAGA-CAAGCACCCATATAACATG
86568 TGA
130 TGA
*
86571 TGCTCACACGAGCTATAGGTTAAGATGTTAGGCTACACTATGCTACTCACACGAGCTGTGAAGAA
1 TGCTCACACGAGCTATAGGTTAAGATGTTAGGCTACACGATGCTACTCACACGAGCTGTGAAGAA
* ** *
86636 TCCACAACATATATCGGATCTCAGCCATCGGTAGGACATCTAAGACAAGCACCCATATAACATGT
66 TCCACAACATATACCAAACCTCAGCCATCGGTAGGACATCTAAGACAAGCACCCATATAACATGT
86701 AAATCTTAGT
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
131 3 0.03
132 109 0.97
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (132 bp):
TGCTCACACGAGCTATAGGTTAAGATGTTAGGCTACACGATGCTACTCACACGAGCTGTGAAGAA
TCCACAACATATACCAAACCTCAGCCATCGGTAGGACATCTAAGACAAGCACCCATATAACATGT
GA
Found at i:89957 original size:23 final size:23
Alignment explanation
Indices: 89931--89975 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
89921 TGATTGATTC
* *
89931 TTTAAATATCAAATTAAAAATAT
1 TTTAAATACCAAAATAAAAATAT
*
89954 TTTAGATACCAAAATAAAAATA
1 TTTAAATACCAAAATAAAAATA
89976 AATATATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
TTTAAATACCAAAATAAAAATAT
Found at i:96518 original size:59 final size:59
Alignment explanation
Indices: 96423--96584 Score: 173
Period size: 59 Copynumber: 2.7 Consensus size: 59
96413 TTGGTATAAA
* * * * * * **
96423 AACTTGACACTTTTTCCTAATTTGATACATACACTTTTTTTTACTCAATTTGATATTTG
1 AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTTAACCCAATTTGATACCTG
* *
96482 AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTGTTTGAACCCAATTTGGTACCTG
1 AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTT-TTTTAACCCAATTTGATACCTG
* * *
96542 AACTT-AGCATTTTTTTCCTAATTTGGCACCTAAGCTTTTTTTA
1 AACTTGA-CACTTTTTT-CTAATTTGGTACCTAAACTTTTTTTA
96585 GATTCAATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 34 0.40
60 33 0.38
61 19 0.22
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (59 bp):
AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTTAACCCAATTTGATACCTG
Found at i:99577 original size:45 final size:45
Alignment explanation
Indices: 99545--99640 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
99535 ATTATATAAT
99545 AACGTAA-ATAACTAAAATATAAAATTTTAAATATAAATAACTAA
1 AACGTAACATAACTAAAATATAAAATTTTAAATATAAATAACTAA
* * *
99589 AATGTAACTTAACTAAAATATAAAATTTTAAATATAAATAATTAA
1 AACGTAACATAACTAAAATATAAAATTTTAAATATAAATAACTAA
*
99634 AATGTAA
1 AACGTAA
99641 AGAAAAGTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 6 0.12
45 42 0.88
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (45 bp):
AACGTAACATAACTAAAATATAAAATTTTAAATATAAATAACTAA
Found at i:99589 original size:14 final size:15
Alignment explanation
Indices: 99549--99641 Score: 73
Period size: 15 Copynumber: 6.3 Consensus size: 15
99539 TATAATAACG
99549 TAAATAACTAAAATA
1 TAAATAACTAAAATA
** *
99564 TAAA-ATTTTAAATA
1 TAAATAACTAAAATA
*
99578 TAAATAACTAAAATG
1 TAAATAACTAAAATA
*
99593 TAACTTAACTAAAATA
1 TAA-ATAACTAAAATA
** *
99609 TAAA-ATTTTAAATA
1 TAAATAACTAAAATA
* *
99623 TAAATAATTAAAATG
1 TAAATAACTAAAATA
99638 TAAA
1 TAAA
99642 GAAAAGTTAT
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
14 22 0.37
15 24 0.41
16 13 0.22
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAATAACTAAAATA
Found at i:109106 original size:18 final size:18
Alignment explanation
Indices: 109085--109147 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
109075 TAAACAATCC
109085 TCTTCATCCGGAGTGAAT
1 TCTTCATCCGGAGTGAAT
***
109103 TCTTCATCC--AAACAAT
1 TCTTCATCCGGAGTGAAT
109119 CCTCTTCATCCGGAGTGAAT
1 --TCTTCATCCGGAGTGAAT
*
109139 TCCTCATCC
1 TCTTCATCC
109148 AAACAATCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
16 4 0.12
18 26 0.76
20 4 0.12
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.32
Consensus pattern (18 bp):
TCTTCATCCGGAGTGAAT
Found at i:109110 original size:36 final size:36
Alignment explanation
Indices: 109066--109182 Score: 180
Period size: 36 Copynumber: 3.2 Consensus size: 36
109056 TCAATTCCTC
*
109066 TTCCTCATCTAAACAATCCTCTTCATCCGGAGTGAA
1 TTCCTCATCCAAACAATCCTCTTCATCCGGAGTGAA
*
109102 TTCTTCATCCAAACAATCCTCTTCATCCGGAGTGAA
1 TTCCTCATCCAAACAATCCTCTTCATCCGGAGTGAA
* * *
109138 TTCCTCATCCAAACAATCTTCTACATCTGGAGTGAA
1 TTCCTCATCCAAACAATCCTCTTCATCCGGAGTGAA
*
109174 CTCCTCATC
1 TTCCTCATC
109183 GTCATCTTCC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.31
Consensus pattern (36 bp):
TTCCTCATCCAAACAATCCTCTTCATCCGGAGTGAA
Found at i:109362 original size:150 final size:150
Alignment explanation
Indices: 109187--109500 Score: 484
Period size: 150 Copynumber: 2.1 Consensus size: 150
109177 CTCATCGTCA
* * * *
109187 TCTTCCTTTTCTTCTTCTTCCTCCTCATAATCCTTGTCTTCATCTTCTTCAATAGACACGCTTTC
1 TCTTCCTCTTCCTCTTCTTCCTCCTCATAATCCTCGTCTTCATCTTCTTCAACAGACACGCTTTC
* * * * ** *
109252 TCGCTTTACAGATTTTTTATCTGCAATCTTCCTCTCCCTTACCGAAGATATCCGTTCTCTTTTCA
66 CCACTTCACAGAATTTTTATCCACAATCTTCCTCTCCCTTACCGAAGATATCCGTCCTCTTTTCA
*
109317 AGCTAACAACCTCCCTCACC
131 ACCTAACAACCTCCCTCACC
*
109337 TCTTCCTCTTCCTCTTCTTCCTCCTCATAATCCTCGTCTTCATCTTCTTCAACAGACACGGTTTC
1 TCTTCCTCTTCCTCTTCTTCCTCCTCATAATCCTCGTCTTCATCTTCTTCAACAGACACGCTTTC
*
109402 CCACTTCACAGAATTTTTATCCACAATCTTCCTCTCCCTTACCGAAGATATCTGTCCTCTTTTCA
66 CCACTTCACAGAATTTTTATCCACAATCTTCCTCTCCCTTACCGAAGATATCCGTCCTCTTTTCA
*
109467 ACCTAACAACCTCTCTCACC
131 ACCTAACAACCTCCCTCACC
*
109487 TCGTCCTCTTCCTC
1 TCTTCCTCTTCCTC
109501 CTCATTGTAA
Statistics
Matches: 148, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
150 148 1.00
ACGTcount: A:0.18, C:0.37, G:0.06, T:0.39
Consensus pattern (150 bp):
TCTTCCTCTTCCTCTTCTTCCTCCTCATAATCCTCGTCTTCATCTTCTTCAACAGACACGCTTTC
CCACTTCACAGAATTTTTATCCACAATCTTCCTCTCCCTTACCGAAGATATCCGTCCTCTTTTCA
ACCTAACAACCTCCCTCACC
Found at i:113586 original size:5 final size:5
Alignment explanation
Indices: 113576--113600 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
113566 GATAGTTACT
113576 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
113601 CAAGCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:123489 original size:16 final size:17
Alignment explanation
Indices: 123457--123490 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
123447 TCATAAAACG
123457 AAAATAAAAAATAACAA
1 AAAATAAAAAATAACAA
123474 AAAATAAAAAAT-ACAA
1 AAAATAAAAAATAACAA
123490 A
1 A
123491 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAATAAAAAATAACAA
Found at i:142472 original size:29 final size:30
Alignment explanation
Indices: 142420--142478 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
142410 ATCTCTTTAT
* * *
142420 TATATATTAATTTTGATTCATTGTGTAATTG
1 TATATATGAATTTTAATT-ATTGTGCAATTG
142451 TATATATGAATTTTAATT-TTGTGCAATT
1 TATATATGAATTTTAATTATTGTGCAATT
142479 ATACACGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (30 bp):
TATATATGAATTTTAATTATTGTGCAATTG
Found at i:146686 original size:3 final size:3
Alignment explanation
Indices: 146678--146727 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
146668 CTAGTTTGCC
146678 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
146726 AA
1 AA
146728 AGAATGGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:152994 original size:37 final size:37
Alignment explanation
Indices: 152944--153220 Score: 254
Period size: 37 Copynumber: 7.5 Consensus size: 37
152934 AGTAAATCGA
* * *
152944 GCTATGTGCCTAGCAGGCTTCATGTTGATGTATTCAG
1 GCTATGTGCCTAGCAGGCTTTATGTCGGTGTATTCAG
* **
152981 GCTATGTGCCTAGCAGGGTTTGGGTCGGTGTATTC-G
1 GCTATGTGCCTAGCAGGCTTTATGTCGGTGTATTCAG
* * * *
153017 AGCTATGTGCCTAGCAAGCTTTATGCCGGTGTAATCGG
1 -GCTATGTGCCTAGCAGGCTTTATGTCGGTGTATTCAG
* * * *
153055 GCTATGTGCCTAGCAAGCTTTGTGTCGGTGAATTCGG
1 GCTATGTGCCTAGCAGGCTTTATGTCGGTGTATTCAG
** *
153092 GCTATGTGCCTAGCAGGC-CAAGTGTCGGTGTACTCAG
1 GCTATGTGCCTAGCAGGCTTTA-TGTCGGTGTATTCAG
* * * * * *
153129 GCTATGTGCCTAACAAGCTTTGTGCCGGTGAATTCGG
1 GCTATGTGCCTAGCAGGCTTTATGTCGGTGTATTCAG
* ** *
153166 GCTATGTGCCTAGAAGGC-CAAGTGTCGGTGTACTCAG
1 GCTATGTGCCTAGCAGGCTTTA-TGTCGGTGTATTCAG
*
153203 GCTATATGCCTAGCAGGC
1 GCTATGTGCCTAGCAGGC
153221 CTTTGTGCCG
Statistics
Matches: 191, Mismatches: 44, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
36 1 0.01
37 189 0.99
38 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.29
Consensus pattern (37 bp):
GCTATGTGCCTAGCAGGCTTTATGTCGGTGTATTCAG
Found at i:153061 original size:74 final size:74
Alignment explanation
Indices: 152940--153234 Score: 333
Period size: 74 Copynumber: 4.0 Consensus size: 74
152930 TTTAAGTAAA
* * * * * * *
152940 TCGAGCTATGTGCCTAGCAGGCTTCATGTTGATGTATTCAGGCTATGTGCCTAGCAGGGTTTGGG
1 TCGAGCTATGTGCCTAGCAGGCTTAATGTCGGTGTAATCAGGCTATGTGCCTAGCAAGCTTTGTG
*
153005 TCGGTGTAT
66 TCGGTGAAT
* * * *
153014 TCGAGCTATGTGCCTAGCAAGCTTTATGCCGGTGTAATCGGGCTATGTGCCTAGCAAGCTTTGTG
1 TCGAGCTATGTGCCTAGCAGGCTTAATGTCGGTGTAATCAGGCTATGTGCCTAGCAAGCTTTGTG
153079 TCGGTGAAT
66 TCGGTGAAT
* * * *
153088 TCGGGCTATGTGCCTAGCAGGC-CAAGTGTCGGTGTACTCAGGCTATGTGCCTAACAAGCTTTGT
1 TCGAGCTATGTGCCTAGCAGGCTTAA-TGTCGGTGTAATCAGGCTATGTGCCTAGCAAGCTTTGT
*
153152 GCCGGTGAAT
65 GTCGGTGAAT
* * * * * *
153162 TCGGGCTATGTGCCTAGAAGGC-CAAGTGTCGGTGTACTCAGGCTATATGCCTAGCAGGCCTTTG
1 TCGAGCTATGTGCCTAGCAGGCTTAA-TGTCGGTGTAATCAGGCTATGTGCCTAGCAAG-CTTTG
*
153226 TGCCGGTGA
64 TGTCGGTGA
153235 TTAGAGAACT
Statistics
Matches: 195, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
73 1 0.01
74 180 0.92
75 14 0.07
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (74 bp):
TCGAGCTATGTGCCTAGCAGGCTTAATGTCGGTGTAATCAGGCTATGTGCCTAGCAAGCTTTGTG
TCGGTGAAT
Found at i:153133 original size:111 final size:110
Alignment explanation
Indices: 152938--153221 Score: 331
Period size: 111 Copynumber: 2.6 Consensus size: 110
152928 CATTTAAGTA
* * * * ****
152938 AATCGAGCTATGTGCCTAGCAGGCTTCA-TGTTGATGTATTCAGGCTATGTGCCTAGCAGGGTTT
1 AATCGGGCTATGTGCCTAGCAAGCTT-AGTGTCGGTGTATTCAGGCTATGTGCCTAGCAGGCCAA
* *
153002 GGGTCGGTGTATTCGAGCTATGTGCCTAGCAAGCTTTATGCCGGTG
65 GGGTCGGTGTACTCGAGCTATGTGCCTAACAAGCTTTATGCCGGTG
* * *
153048 TAATCGGGCTATGTGCCTAGCAAGCTTTGTGTCGGTGAATTCGGGCTATGTGCCTAGCAGGCCAA
1 -AATCGGGCTATGTGCCTAGCAAGCTTAGTGTCGGTGTATTCAGGCTATGTGCCTAGCAGGCCAA
* *
153113 GTGTCGGTGTACTC-AGGCTATGTGCCTAACAAGCTTTGTGCCGGTG
65 GGGTCGGTGTACTCGA-GCTATGTGCCTAACAAGCTTTATGCCGGTG
** * *
153159 AATTCGGGCTATGTGCCTAG-AAGGCCAAGTGTCGGTGTACTCAGGCTATATGCCTAGCAGGCC
1 AA-TCGGGCTATGTGCCTAGCAA-GCTTAGTGTCGGTGTATTCAGGCTATGTGCCTAGCAGGCC
153222 TTTGTGCCGG
Statistics
Matches: 147, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
110 5 0.03
111 142 0.97
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (110 bp):
AATCGGGCTATGTGCCTAGCAAGCTTAGTGTCGGTGTATTCAGGCTATGTGCCTAGCAGGCCAAG
GGTCGGTGTACTCGAGCTATGTGCCTAACAAGCTTTATGCCGGTG
Found at i:156436 original size:50 final size:50
Alignment explanation
Indices: 156376--156484 Score: 200
Period size: 50 Copynumber: 2.2 Consensus size: 50
156366 TAAAAAATTT
*
156376 TATTTAAATTTTTTATTCAATTAGTAAAGGTTTTAATAGTTTAAATAGAA
1 TATTAAAATTTTTTATTCAATTAGTAAAGGTTTTAATAGTTTAAATAGAA
156426 TATTAAAATTTTTTATTCAATTAGTAAAGGTTTTAATAGTTTAAATAGAA
1 TATTAAAATTTTTTATTCAATTAGTAAAGGTTTTAATAGTTTAAATAGAA
156476 TATTTAAAA
1 TA-TTAAAA
156485 CTTATCGAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
50 51 0.89
51 6 0.11
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (50 bp):
TATTAAAATTTTTTATTCAATTAGTAAAGGTTTTAATAGTTTAAATAGAA
Found at i:158917 original size:41 final size:41
Alignment explanation
Indices: 158806--159032 Score: 267
Period size: 41 Copynumber: 5.4 Consensus size: 41
158796 GAGACACTTG
*
158806 ATGTATAAATGGAAGACTCATGTCTC-GAGTTGAGCATGAGAAT
1 ATGT-TAAA-GGAAGACTCATGTCTCGGA-ATGAGCATGAGAAT
* * * *
158849 TTCTATAAATGGAAGACTCGTGACTCGGAATGAGCATGAGAAT
1 ATGT-TAAA-GGAAGACTCATGTCTCGGAATGAGCATGAGAAT
* * *
158892 ATGTTAAAGGAAGACTCATGTCTCGGGATGAGAATGATAAT
1 ATGTTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGAAT
* * *
158933 ATGTTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATT
1 ATGTTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGAAT
* *
158974 ATGTTAAAGAAAGACTCATGTCTCGGAATGAGCATGAGATT
1 ATGTTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGAAT
159015 ATGTTTGAAAGGAAGACT
1 ATG-TT-AAAGGAAGACT
159033 TATCCTTCGG
Statistics
Matches: 163, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
41 108 0.66
42 6 0.04
43 47 0.29
44 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (41 bp):
ATGTTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGAAT
Found at i:159071 original size:125 final size:125
Alignment explanation
Indices: 158806--159032 Score: 307
Period size: 125 Copynumber: 1.8 Consensus size: 125
158796 GAGACACTTG
* * * *
158806 ATGTATAAATGGAAGACTCATGTCTCGAGTTGAGCATGAGAATTTCTATAAATGGAAGACTCGTG
1 ATGT-TAAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAATTTCTATAAATGAAAGACTCATG
*
158871 ACTCGGAATGAGCATGAGAATATGTTAAAGGAAGACTCATGTCTCGGGATGAGAATGATAAT
64 ACTCGGAATGAGCATGAGAATATGTTAAAGGAAGACTCATCTCTCGGGATGAGAATGATAAT
* * *
158933 ATGTTAAAGGAAGACTCATGTCTCGGGATGAGAATGAG-ATTATGT-TAAA-GAAAGACTCATGT
1 ATGTTAAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATT-TCTATAAATGAAAGACTCATGA
*
158995 CTCGGAATGAGCATGAGATTATGTTTGAAAGGAAGACT
65 CTCGGAATGAGCATGAGAATATG-TT-AAAGGAAGACT
159033 TATCCTTCGG
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
123 32 0.36
124 9 0.10
125 40 0.45
126 4 0.04
127 4 0.04
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (125 bp):
ATGTTAAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATTTCTATAAATGAAAGACTCATGAC
TCGGAATGAGCATGAGAATATGTTAAAGGAAGACTCATCTCTCGGGATGAGAATGATAAT
Found at i:161499 original size:19 final size:19
Alignment explanation
Indices: 161475--161517 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
161465 AAACATAAAT
161475 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
161494 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
161513 TAAAT
1 TAAAT
161518 TCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:162290 original size:109 final size:112
Alignment explanation
Indices: 162111--162316 Score: 280
Period size: 109 Copynumber: 1.9 Consensus size: 112
162101 ATATATTGGA
* **
162111 CCTTTTGACGCGAAATGAAATGACACCCAAGCACTTCATCCCGGTTACTCAGCCCAACATGCTCT
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTTCATCCCGGTTACTCAGCCCAACACACTCT
*
162176 CAATTT-TTT-TCTTCTCTTT-TTT-TTTTTTTGTAGAATGTGTTAGC
66 CAATTTATTTAT-TTCTATTTATTTCTTTTTTTGTAGAATGTGTTAGC
* * *
162220 CCTTTTGACGCGAAGTGAAATGACAACCAAGCACTTCA-CCTCGGTTACTCAGTCTAACACACTC
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTTCATCC-CGGTTACTCAGCCCAACACACTC
162284 -CGAATTTATTTATTTCTATTTATTTCTTTTTTT
65 TC-AATTTATTTATTTCTATTTATTTCTTTTTTT
162317 CAGTTTAACG
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
108 3 0.04
109 60 0.71
110 10 0.12
111 4 0.05
112 7 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (112 bp):
CCTTTTGACGCGAAATGAAATGACAACCAAGCACTTCATCCCGGTTACTCAGCCCAACACACTCT
CAATTTATTTATTTCTATTTATTTCTTTTTTTGTAGAATGTGTTAGC
Found at i:167214 original size:22 final size:21
Alignment explanation
Indices: 167178--167220 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
167168 CGATCTCAGG
* *
167178 AAAAATAAAAGAAACATAATT
1 AAAAATAAAAAAAACAGAATT
167199 AAAAATAAAATAAAACAGAATT
1 AAAAATAAAA-AAAACAGAATT
167221 GAAAGAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (21 bp):
AAAAATAAAAAAAACAGAATT
Found at i:168066 original size:19 final size:19
Alignment explanation
Indices: 168042--168084 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
168032 AAACATAAAT
168042 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
168061 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
168080 TAAAT
1 TAAAT
168085 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:182818 original size:17 final size:17
Alignment explanation
Indices: 182796--182849 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
182786 AACTTTTCTT
182796 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
*
182813 TTAAGTTTAAA-TTAAT
1 TTAAGTTTAAATTTAAA
*
182829 TTAACTTTAAAATTT-AA
1 TTAAGTTT-AAATTTAAA
182846 TTAA
1 TTAA
182850 TTAAAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 11 0.34
17 19 0.59
18 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:182838 original size:22 final size:21
Alignment explanation
Indices: 182805--182851 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
182795 TTTAAGTTTA
*
182805 AATTTAAATT-AAGTTTAAATT
1 AATTTAAATTAAAATTT-AATT
*
182826 AATTTAACTTTAAAATTTAATT
1 AATTTAA-ATTAAAATTTAATT
182848 AATT
1 AATT
182852 AAAAAAGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATTTAAATTAAAATTTAATT
Found at i:182919 original size:18 final size:17
Alignment explanation
Indices: 182896--182969 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
182886 CCCAAATTGG
182896 GCCCAAATGCTAACCTAA
1 GCCCAAATGCTAA-CTAA
*
182914 GCCCAAATTCTAA--AA
1 GCCCAAATGCTAACTAA
* * *
182929 GACCCAAA-CCTAAAT-G
1 G-CCCAAATGCTAACTAA
182945 GCCCAAATGCTAACCTAA
1 GCCCAAATGCTAA-CTAA
182963 GCCCAAA
1 GCCCAAA
182970 CCCTTTGCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
15 13 0.30
16 11 0.25
17 1 0.02
18 19 0.43
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.15
Consensus pattern (17 bp):
GCCCAAATGCTAACTAA
Found at i:184578 original size:30 final size:29
Alignment explanation
Indices: 184537--184883 Score: 322
Period size: 30 Copynumber: 11.7 Consensus size: 29
184527 TTTACACTCG
* * **
184537 AACTT-CAAAAATCCCATTTTGGACCCTAA
1 AACTTCCAAAAATTCCATTTT-TACCCCCA
*
184566 AACTTCCAAAAATTACATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCA
* * *
184595 AACTTCCAAAAAAATCCATTTTTCACCCTCG
1 AACTTCC-AAAAATTCCATTTTT-ACCCCCA
*
184626 AACTTCCAAAAATTTCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCA
* *
184655 AACTTTCAAAAA-TCCAATTTTTAACCCCAA
1 AACTTCCAAAAATTCC-ATTTTT-ACCCCCA
* *
184685 AACTTTCAAAAATTTCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCA
* * * *
184714 AACTTCCAAAAATCCCATTCTTGACCTCAA
1 AACTTCCAAAAATTCCATT-TTTACCCCCA
* *
184744 AACTTCCAAAATTTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCA
*
184773 AACTTCCAAAAA-TCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCA
** * * * *
184802 AACTTAAAAAAAAATCAATTTTTACCCTCG
1 AACTT-CCAAAAATTCCATTTTTACCCCCA
*
184832 AACTTCCAAAAATTCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCA
* *
184862 AACTTCAAAAAAGTACCATTTT
1 AACTTCCAAAAA-TTCCATTTT
184884 GCTCCCGGAT
Statistics
Matches: 258, Mismatches: 48, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
28 11 0.04
29 101 0.39
30 116 0.45
31 30 0.12
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCA
Found at i:184695 original size:59 final size:58
Alignment explanation
Indices: 184505--184873 Score: 404
Period size: 59 Copynumber: 6.3 Consensus size: 58
184495 TGGAGGTCCT
* * * * *
184505 CAAAACTTCCAAAAATTTTGA-TTTTACACTCGAACTT-CAAAAATCCCATTTTGGACCC
1 CAAAACTTCCAAAAA-TTTCATTTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCC
* * *
184563 TAAAACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAAAATCCATTTTTCACCC
1 CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCC--AAAAATCCATTTTTGACCC
* * *
184623 TC-GAACTTCCAAAAATTTCATTTTTACCCCCAAACTTTCAAAAATCCAATTTTTAACCC
1 -CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAATCC-ATTTTTGACCC
* * *
184682 CAAAACTTTCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAATCCCATTCTTGACCT
1 CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCC
* *
184741 CAAAACTTCC-AAAATTTCCATTTTTACCCCCGAACTTCCAAAAATCCATTTTTAACCC
1 CAAAACTTCCAAAAATTT-CATTTTTACCCCCAAACTTCCAAAAATCCATTTTTGACCC
** ** * *
184799 CAAAACTTAAAAAAAAATCAATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCC
1 CAAAACTTCCAAAAATTTC-ATTTTTACCCCCAAACTTCCAAAAA-TCCATTTTTGACCC
* *
184859 CGAAACTTCAAAAAA
1 CAAAACTTCCAAAAA
184874 GTACCATTTT
Statistics
Matches: 267, Mismatches: 32, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
57 3 0.01
58 62 0.23
59 123 0.46
60 73 0.27
61 6 0.02
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (58 bp):
CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAATCCATTTTTGACCC
Found at i:190693 original size:17 final size:17
Alignment explanation
Indices: 190671--190724 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
190661 AACTTTTCTT
190671 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
*
190688 TTAAGTTTAAA-TTAAT
1 TTAAGTTTAAATTTAAA
*
190704 TTAACTTTAAAATTT-AA
1 TTAAGTTT-AAATTTAAA
190721 TTAA
1 TTAA
190725 TTAAAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 11 0.34
17 19 0.59
18 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:190713 original size:22 final size:21
Alignment explanation
Indices: 190680--190726 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
190670 TTTAAGTTTA
*
190680 AATTTAAATT-AAGTTTAAATT
1 AATTTAAATTAAAATTT-AATT
*
190701 AATTTAACTTTAAAATTTAATT
1 AATTTAA-ATTAAAATTTAATT
190723 AATT
1 AATT
190727 AAAAAAGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATTTAAATTAAAATTTAATT
Found at i:190794 original size:18 final size:17
Alignment explanation
Indices: 190771--190844 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
190761 CCCAAATTGG
190771 GCCCAAATGCTAACCTAA
1 GCCCAAATGCTAA-CTAA
*
190789 GCCCAAATTCTAA--AA
1 GCCCAAATGCTAACTAA
* * *
190804 GACCCAAA-CCTAAAT-G
1 G-CCCAAATGCTAACTAA
190820 GCCCAAATGCTAACCTAA
1 GCCCAAATGCTAA-CTAA
190838 GCCCAAA
1 GCCCAAA
190845 CCCTTTGCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
15 13 0.30
16 11 0.25
17 1 0.02
18 19 0.43
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.15
Consensus pattern (17 bp):
GCCCAAATGCTAACTAA
Found at i:192453 original size:30 final size:29
Alignment explanation
Indices: 192412--192758 Score: 322
Period size: 30 Copynumber: 11.7 Consensus size: 29
192402 TTTACACTCG
* * **
192412 AACTT-CAAAAATCCCATTTTGGACCCTAA
1 AACTTCCAAAAATTCCATTTT-TACCCCCA
*
192441 AACTTCCAAAAATTACATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCA
* * *
192470 AACTTCCAAAAAAATCCATTTTTCACCCTCG
1 AACTTCC-AAAAATTCCATTTTT-ACCCCCA
*
192501 AACTTCCAAAAATTTCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCA
* *
192530 AACTTTCAAAAA-TCCAATTTTTAACCCCAA
1 AACTTCCAAAAATTCC-ATTTTT-ACCCCCA
* *
192560 AACTTTCAAAAATTTCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCA
* * * *
192589 AACTTCCAAAAATCCCATTCTTGACCTCAA
1 AACTTCCAAAAATTCCATT-TTTACCCCCA
* *
192619 AACTTCCAAAATTTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCA
*
192648 AACTTCCAAAAA-TCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCA
** * * * *
192677 AACTTAAAAAAAAATCAATTTTTACCCTCG
1 AACTT-CCAAAAATTCCATTTTTACCCCCA
*
192707 AACTTCCAAAAATTCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCA
* *
192737 AACTTCAAAAAAGTACCATTTT
1 AACTTCCAAAAA-TTCCATTTT
192759 GCTCCCGGAT
Statistics
Matches: 258, Mismatches: 48, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
28 11 0.04
29 101 0.39
30 116 0.45
31 30 0.12
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCA
Found at i:192570 original size:59 final size:58
Alignment explanation
Indices: 192380--192748 Score: 404
Period size: 59 Copynumber: 6.3 Consensus size: 58
192370 TGGAGGTCCT
* * * * *
192380 CAAAACTTCCAAAAATTTTGA-TTTTACACTCGAACTT-CAAAAATCCCATTTTGGACCC
1 CAAAACTTCCAAAAA-TTTCATTTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCC
* * *
192438 TAAAACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAAAATCCATTTTTCACCC
1 CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCC--AAAAATCCATTTTTGACCC
* * *
192498 TC-GAACTTCCAAAAATTTCATTTTTACCCCCAAACTTTCAAAAATCCAATTTTTAACCC
1 -CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAATCC-ATTTTTGACCC
* * *
192557 CAAAACTTTCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAATCCCATTCTTGACCT
1 CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCC
* *
192616 CAAAACTTCC-AAAATTTCCATTTTTACCCCCGAACTTCCAAAAATCCATTTTTAACCC
1 CAAAACTTCCAAAAATTT-CATTTTTACCCCCAAACTTCCAAAAATCCATTTTTGACCC
** ** * *
192674 CAAAACTTAAAAAAAAATCAATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCC
1 CAAAACTTCCAAAAATTTC-ATTTTTACCCCCAAACTTCCAAAAA-TCCATTTTTGACCC
* *
192734 CGAAACTTCAAAAAA
1 CAAAACTTCCAAAAA
192749 GTACCATTTT
Statistics
Matches: 267, Mismatches: 32, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
57 3 0.01
58 62 0.23
59 123 0.46
60 73 0.27
61 6 0.02
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (58 bp):
CAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTTCCAAAAATCCATTTTTGACCC
Done.