Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011819.1 Kokia drynarioides strain JFW-HI SEQ_126814, 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: 75162
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 68 characters in sequence are not A, C, G, or T
Found at i:575 original size:30 final size:30
Alignment explanation
Indices: 541--640 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
531 ATTTTTTTTC
*
541 CGTTTACT-TTTTAAATTTAATTTGTAATTT
1 CGTTTA-TATTTTAAATTTAATTTCTAATTT
*
571 CGTTTTTATTTTAAATTTAATTTCTAATTT
1 CGTTTATATTTTAAATTTAATTTCTAATTT
* * **
601 CCTGTATATTTTAAATTTTTTTTCTAATTT
1 CGTTTATATTTTAAATTTAATTTCTAATTT
* *
631 CCTGTATATT
1 CGTTTATATT
641 CTAATTATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 1 0.02
30 61 0.98
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (30 bp):
CGTTTATATTTTAAATTTAATTTCTAATTT
Found at i:644 original size:17 final size:17
Alignment explanation
Indices: 592--646 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
582 TAAATTTAAT
592 TTCTAATTTCCTGTATA
1 TTCTAATTTCCTGTATA
*
609 TTTTAAATTT--T-T-T-
1 TTCT-AATTTCCTGTATA
622 TTCTAATTTCCTGTATA
1 TTCTAATTTCCTGTATA
639 TTCTAATT
1 TTCTAATT
647 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 2 0.07
15 2 0.07
16 2 0.07
17 11 0.37
18 5 0.17
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.60
Consensus pattern (17 bp):
TTCTAATTTCCTGTATA
Found at i:1729 original size:61 final size:61
Alignment explanation
Indices: 1541--1902 Score: 309
Period size: 62 Copynumber: 6.1 Consensus size: 61
1531 TCGGCCATGT
* * *
1541 GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTCAAATTTTTTT-TCTCAAAAA-GAG
1 GTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCTGAAAAAGGAG
** * * *
1600 AGTGTCGGCCATTGCATGATCAACACAAAAAAAATTTAAAATTTTTTTATCCGAGAATAGGGG
1 -GTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCTGA-AAAAGGAG
* * *
1663 GTGTCGACCATTGCATGGCCAACACAAAAAAAAATTAAAATTTTTTTATTTGAAAAAGGAG
1 GTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCTGAAAAAGGAG
* ** * *
1724 GTGTCGGCTATTGCATGGCCAACAC-TTAAAAATGT--AA-TTTTTT-TCTCAAAAAGG-G
1 GTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCTGAAAAAGGAG
* ** * * * * * * *
1779 GTATCGATCATTACATAGCCAACACCAAAAAAATTT-GAATTTTTTT-TCTCAAAATGGGG
1 GTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCTGAAAAAGGAG
* ** ** * *
1838 GTGTCGGCCATTACATGATCAACAC-AAAAAAATTT-TGATTTTTTT-TCCTCAAAAAGGGG
1 GTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTAAAATTTTTTTAT-CTGAAAAAGGAG
1897 GTGTCG
1 GTGTCG
1903 ATAAAAAATG
Statistics
Matches: 251, Mismatches: 43, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
55 20 0.08
56 16 0.06
57 8 0.03
58 37 0.15
59 37 0.15
60 49 0.20
61 32 0.13
62 50 0.20
63 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (61 bp):
GTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCTGAAAAAGGAG
Found at i:1852 original size:59 final size:59
Alignment explanation
Indices: 1541--1902 Score: 358
Period size: 59 Copynumber: 6.1 Consensus size: 59
1531 TCGGCCATGT
* *
1541 GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTCAAATTTTTTTTCTCAAAAAGAGA
1 GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTT-AAATTTTTTTTCTCAAAAAGGGG
** * *
1601 GTGTCGGCCATTGCATGATCAACACAAAAAAAATTTAAAATTTTTTTATC-CGAGAATAGGGG
1 GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTT-AAATTTTTTT-TCTC-A-AAAAGGGG
* * * * * *
1663 GTGTCGACCATTGCATGGCCAACACAAAAAAAAATTAAAATTTTTTTATTTGAAAAAGGAG
1 GTGTCGGCCATTGCATGGCCAACAC-CAAAAAAATTTAAATTTTTTT-TCTCAAAAAGGGG
* ** *
1724 GTGTCGGCTATTGCATGGCCAACA-CTTAAAAATGT-AA-TTTTTTTCTCAAAAA-GGG
1 GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTCAAAAAGGGG
* ** * * * *
1779 GTATCGATCATTACATAGCCAACACCAAAAAAATTTGAATTTTTTTTCTCAAAATGGGG
1 GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTCAAAAAGGGG
* ** **
1838 GTGTCGGCCATTACATGATCAACA-CAAAAAAATTTTGATTTTTTTTCCTCAAAAAGGGG
1 GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTAAATTTTTTTT-CTCAAAAAGGGG
1897 GTGTCG
1 GTGTCG
1903 ATAAAAAATG
Statistics
Matches: 248, Mismatches: 44, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
55 20 0.08
56 15 0.06
57 8 0.03
58 36 0.15
59 44 0.18
60 44 0.18
61 31 0.12
62 40 0.16
63 10 0.04
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (59 bp):
GTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTCAAAAAGGGG
Found at i:2248 original size:30 final size:30
Alignment explanation
Indices: 2190--2250 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2180 ATTTTTAAAC
* *
2190 TTAAATTATTTTTATAAATAATCAAAAAAT
1 TTAAATTATTTTAATAAATAACCAAAAAAT
* *
2220 TTAAATTATTTTAATAAATTACCCAAAAAT
1 TTAAATTATTTTAATAAATAACCAAAAAAT
2250 T
1 T
2251 CAACTAACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAATTATTTTAATAAATAACCAAAAAAT
Found at i:6267 original size:21 final size:22
Alignment explanation
Indices: 6236--6279 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6226 ACACAAGTGA
6236 ATTGAGTTTTCTTCAATATTAG
1 ATTGAGTTTTCTTCAATATTAG
**
6258 ATTGA-TTTTCTTGGATATTAG
1 ATTGAGTTTTCTTCAATATTAG
6279 A
1 A
6280 ACACTGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (22 bp):
ATTGAGTTTTCTTCAATATTAG
Found at i:29209 original size:11 final size:11
Alignment explanation
Indices: 29196--29243 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
29186 TTTTTAATCT
*
29196 TTTCTTTTTTT
1 TTTCTTTTTTC
*
29207 TTTCTTATTTCC
1 TTTCTT-TTTTC
*
29219 TTACTTTTTTC
1 TTTCTTTTTTC
29230 TTTCTTTTCTTC
1 TTTCTTTT-TTC
29242 TT
1 TT
29244 ATCAATTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 17 0.57
12 13 0.43
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:29663 original size:20 final size:19
Alignment explanation
Indices: 29630--29667 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
29620 TAGATGAAAA
29630 GAAAAGAAGAGGAAGAAATG
1 GAAAAGAAGAGGAA-AAATG
29650 GAAAAG-AGAGGGAAAAAT
1 GAAAAGAAGA-GGAAAAAT
29668 AAGGGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (19 bp):
GAAAAGAAGAGGAAAAATG
Found at i:33574 original size:22 final size:21
Alignment explanation
Indices: 33549--33589 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33539 TTTAAAATAA
* *
33549 ATAAGTGAAATTAAGATTAATT
1 ATAAGT-AAAATAAAATTAATT
33571 ATAAGTAAAATAAAATTAA
1 ATAAGTAAAATAAAATTAA
33590 CCAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (21 bp):
ATAAGTAAAATAAAATTAATT
Found at i:37075 original size:30 final size:29
Alignment explanation
Indices: 37000--37182 Score: 113
Period size: 30 Copynumber: 6.3 Consensus size: 29
36990 CTCTGTTTTA
* * **
37000 TTTAAAAATTATATTTTGACCTTGTACTT
1 TTTAAAAATTATATTTTAACCCTAAACTT
** * **
37029 TCCAAAACTTCGATTTTAACTCCTAAACTT
1 TTTAAAAATTATATTTTAAC-CCTAAACTT
* * *
37059 TTTAAAAATCATATTTTGACCCCAAAC--
1 TTTAAAAATTATATTTTAACCCTAAACTT
* * * *
37086 TCTAAAAATTATATTTTAACTCTTGAATTT
1 TTTAAAAATTATATTTTAAC-CCTAAACTT
37116 TTTAAAAATTATATTTTAACCCTCAAACTT
1 TTTAAAAATTATATTTTAACCCT-AAACTT
* * * *
37146 TTTCAAACTT-TAATTTTGACCC-ATACTT
1 TTTAAAAATTAT-ATTTTAACCCTAAACTT
*
37174 TCTAAAAAT
1 TTTAAAAAT
37183 CACATTTTGA
Statistics
Matches: 113, Mismatches: 35, Indels: 13
0.70 0.22 0.08
Matches are distributed among these distances:
27 17 0.15
28 14 0.12
29 23 0.20
30 59 0.52
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTAAAAATTATATTTTAACCCTAAACTT
Found at i:42520 original size:50 final size:49
Alignment explanation
Indices: 42445--42545 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 49
42435 ATAAACTTTA
42445 AATTAATTCCTCACATCCTTTTCTTGCGTTCGCATACGCAACATATTCGG
1 AATTAATTCCTCACATCCTTTTCTTGCGTTCGCATACGCAACATA-TCGG
*
42495 AATTAATTCCTCACATCCTTTTCTTGCTTTCGCATACGCAACATATCGG
1 AATTAATTCCTCACATCCTTTTCTTGCGTTCGCATACGCAACATATCGG
42544 AA
1 AA
42546 GCTCCAAGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 6 0.12
50 44 0.88
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.36
Consensus pattern (49 bp):
AATTAATTCCTCACATCCTTTTCTTGCGTTCGCATACGCAACATATCGG
Found at i:43760 original size:15 final size:16
Alignment explanation
Indices: 43740--43777 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
43730 TCATATTCTC
*
43740 TCTTTTCTTTTC-GTT
1 TCTTTTCTTCTCTGTT
*
43755 TCTTTTCTTCTCTTTT
1 TCTTTTCTTCTCTGTT
43771 TCTTTTC
1 TCTTTTC
43778 CCTCATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (16 bp):
TCTTTTCTTCTCTGTT
Found at i:44500 original size:17 final size:17
Alignment explanation
Indices: 44478--44514 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
44468 AGTTGAAAGA
44478 TGGTGCGGACCGATGTG
1 TGGTGCGGACCGATGTG
44495 TGGTGCGGACCGATGTG
1 TGGTGCGGACCGATGTG
44512 TGG
1 TGG
44515 CAATACTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (17 bp):
TGGTGCGGACCGATGTG
Found at i:48246 original size:30 final size:29
Alignment explanation
Indices: 48177--48237 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
48167 TTTAAGTTTG
* * *
48177 AAAAATAGATAGATTAAATTTCTAAAATA
1 AAAAATATAAAGATTAAAATTCTAAAATA
48206 AAAAATATAAAGATTAAAATT-T-AAATA
1 AAAAATATAAAGATTAAAATTCTAAAATA
48233 AAAAA
1 AAAAA
48238 ATACATAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.34
28 1 0.03
29 18 0.62
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAAATATAAAGATTAAAATTCTAAAATA
Found at i:49785 original size:23 final size:25
Alignment explanation
Indices: 49745--49791 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
49735 TTTATATATT
*
49745 TTTAATAATATATTAAATTAATTTA
1 TTTAATAATATATAAAATTAATTTA
49770 TTTAATAATA-A-AAAATTAATTT
1 TTTAATAATATATAAAATTAATTT
49792 GATGTCTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAATAATATATAAAATTAATTTA
Found at i:50142 original size:13 final size:13
Alignment explanation
Indices: 50121--50163 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
50111 TTTTTGACAT
50121 AAATAATACAAAA
1 AAATAATACAAAA
*
50134 AAATTATACACCAAA
1 AAATAATACA--AAA
*
50149 ACATAATACAAAA
1 AAATAATACAAAA
50162 AA
1 AA
50164 TAAAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 13 0.54
15 11 0.46
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAATACAAAA
Found at i:53518 original size:26 final size:26
Alignment explanation
Indices: 53480--53536 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
53470 GAATTTGAAA
*
53480 TTAATTATATTTAAATTTGAATTTAT
1 TTAATAATATTTAAATTTGAATTTAT
* **
53506 TTAATAATTTTTATGTTTGAATTTAT
1 TTAATAATATTTAAATTTGAATTTAT
53532 TTAAT
1 TTAAT
53537 GAGGTTTAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (26 bp):
TTAATAATATTTAAATTTGAATTTAT
Found at i:53544 original size:26 final size:26
Alignment explanation
Indices: 53495--53544 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
53485 TATATTTAAA
**
53495 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
53521 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
53545 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:53621 original size:6 final size:6
Alignment explanation
Indices: 53610--53650 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
53600 ATATTTGCAT
*
53610 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
53651 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:56073 original size:9 final size:8
Alignment explanation
Indices: 56047--56072 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
56037 ATAATTACTA
56047 TTATTTTT
1 TTATTTTT
56055 TTATTTTT
1 TTATTTTT
56063 TTATTTTT
1 TTATTTTT
56071 TT
1 TT
56073 TCTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:56623 original size:13 final size:14
Alignment explanation
Indices: 56600--56628 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
56590 AACAACATAC
56600 CTTTCTTTTCTTTT
1 CTTTCTTTTCTTTT
56614 CTTT-TTTTCTTTT
1 CTTTCTTTTCTTTT
56627 CT
1 CT
56629 CTCCTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTCTTTTCTTTT
Found at i:58383 original size:24 final size:20
Alignment explanation
Indices: 58355--58412 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
58345 ATTAATATTA
58355 AATTTATTATTATATTTTTAACAT
1 AATTTATTATTATATTTTT----T
*
58379 AATTTTTTA-TATATTTTTT
1 AATTTATTATTATATTTTTT
58398 AATTTATTATTATAT
1 AATTTATTATTATAT
58413 ATACTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 9 0.29
20 5 0.16
23 9 0.29
24 8 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTTATTATTATATTTTTT
Found at i:61662 original size:13 final size:14
Alignment explanation
Indices: 61646--61679 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
61636 TGTTTAGTAT
61646 TATTTTTTAA-AAA
1 TATTTTTTAACAAA
61659 TA-TTTTTAACAAA
1 TATTTTTTAACAAA
61672 TATTTTTT
1 TATTTTTT
61680 TAGTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.37
13 7 0.37
14 5 0.26
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTTAACAAA
Found at i:61666 original size:12 final size:13
Alignment explanation
Indices: 61649--61678 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
61639 TTAGTATTAT
61649 TTTTTAA-AAATA
1 TTTTTAACAAATA
61661 TTTTTAACAAATA
1 TTTTTAACAAATA
61674 TTTTT
1 TTTTT
61679 TTAGTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAACAAATA
Found at i:65392 original size:30 final size:31
Alignment explanation
Indices: 65348--65863 Score: 216
Period size: 30 Copynumber: 17.3 Consensus size: 31
65338 AAAAAAACGA
**
65348 GGTCAAAACGTAATTTTAGAAAAGTTTAGGG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * * *
65379 GGT-AAATTATAATTTTGGAGAAGTTT-TGG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* *
65408 AGTCAAAATATGATTTTAGAAAAGTTTA-GG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
*** * * * *
65438 GGTCAAAATGCGATCTTGGAGAAGTTTA-AG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * * *
65468 GGTTAAAATGTGATTTTAGAGAAGTTTA-GG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * * * * *
65498 GGTTAAAATGTGATTTTGGAGAAGTTTA-AG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * **
65528 GGTCAAAATGTAATTTTAGAAAGGTTT-GAA
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * * * * * *
65558 GATTAAAATGTGA-TTTGGAGAAGTTTA-AG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* *
65587 GGTCAAAATGTAATTTTAGAAAGGTTT-GGG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * * *
65617 GGTTAAAATATGATTTTGGAAAGGTTTA-GG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * * *
65647 GGTTAAAATGTGATTTT-GAAAAAGTTTA-AG
1 GGTCAAAATATAATTTTAG-AAAAGTTTAGGG
* * * *
65677 GGTTAAAATGTAATTTTGGAAAA-TTTTGGG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * * *
65707 TGCCAATATGTAATTTTAGAAACA-TTTA-GG
1 GGTCAAAATATAATTTTAGAAA-AGTTTAGGG
* * *
65737 GGTCAAAATATGATTTT-GTGAAAGTTTA-GT
1 GGTCAAAATATAATTTTAG-AAAAGTTTAGGG
* * * * *
65767 GGTTAAAATGTTATTTT-GAAATGTTTA-AG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
* * *
65796 GGTTAAAATATGATTTT-GAAAAAGTTTA-GA
1 GGTCAAAATATAATTTTAG-AAAAGTTTAGGG
* *
65826 GGTCAAAATATGATTTTA-AAAAATTTA-GG
1 GGTCAAAATATAATTTTAGAAAAGTTTAGGG
*
65855 AGTCAAAAT
1 GGTCAAAAT
65864 GTGATTTAAA
Statistics
Matches: 386, Mismatches: 84, Indels: 32
0.77 0.17 0.06
Matches are distributed among these distances:
29 71 0.18
30 307 0.80
31 8 0.02
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (31 bp):
GGTCAAAATATAATTTTAGAAAAGTTTAGGG
Found at i:65457 original size:60 final size:59
Alignment explanation
Indices: 65348--65870 Score: 488
Period size: 60 Copynumber: 8.8 Consensus size: 59
65338 AAAAAAACGA
* * * * * * *
65348 GGTCAAAACGTAATTTTAGAAAAGTTTAGGGGGTAAATTATAATTTTGGAGAAGTTTTG
1 GGTCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTTAG
* * * *
65407 GAGTCAAAATATGATTTTAGAAAAGTTTAGGGGTCAAAATGCGATCTTGGAGAAGTTTAAG
1 G-GTCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTT-AG
* *
65468 GGTTAAAATGTGATTTTAGAGAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTTAAG
1 GGTCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTT-AG
* * * *
65528 GGTCAAAATGTAATTTTAGAAAGGTTT-GAAGATTAAAATGTGA-TTTGGAGAAGTTTAAG
1 GGTCAAAATGTGATTTTAGAAAAGTTTAG-GGGTTAAAATGTGATTTTGGAGAAGTTT-AG
* * * *
65587 GGTCAAAATGTAATTTTAGAAAGGTTTGGGGGTTAAAATATGATTTTGGA-AAGGTTTAGG
1 GGTCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAGAA-GTTTA-G
* * * * *
65647 GGTTAAAATGTGATTTT-GAAAAAGTTTAAGGGTTAAAATGTAATTTTGGA-AAATTTTG
1 GGTCAAAATGTGATTTTAG-AAAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTTAG
* * * *
65705 GGTGCCAATATGTAATTTTAGAAACA-TTTAGGGGTCAAAATATGATTTTGTGA-AAGTTTAG
1 GGT--CAAAATGTGATTTTAGAAA-AGTTTAGGGGTTAAAATGTGATTTTG-GAGAAGTTTAG
* * * * * * *
65766 TGGTTAAAATGTTATTTT-GAAATGTTTAAGGGTTAAAATATGATTTTGAAAAAGTTTAG
1 -GGTCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTTAG
* * * *
65825 AGGTCAAAATATGATTTTA-AAAAATTTAGGAGTCAAAATGTGATTT
1 -GGTCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTT
65871 AAAAAAATAG
Statistics
Matches: 386, Mismatches: 61, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
58 5 0.01
59 132 0.34
60 234 0.61
61 12 0.03
62 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (59 bp):
GGTCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTTAG
Found at i:65652 original size:179 final size:177
Alignment explanation
Indices: 65351--65870 Score: 509
Period size: 179 Copynumber: 2.9 Consensus size: 177
65341 AAAACGAGGT
* * * * * *
65351 CAAAACGTAATTTTAGAAA-AGTTTAGGGGGT-AAATTATAATTTTGGAGAAGTTTTGGAGTCAA
1 CAAAATGTAATTTTAGAAACA-TTTA-GAGATCAAAATATGATTTTGGAGAAGTTTAGG-GTCAA
* * * ** * *
65414 AATATGATTTTAGAAAAGTTTAGGGGTCAAAATGCGATCTTGGAGAAGTTTAAGGGTTAAAATGT
63 AATGTAATTTTAGAAAAGTTTAGGGGTTAAAATATGATTTTGGA-AAGTTTAGGGGTTAAAATGT
* *
65479 GATTTTAGAGAAGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTTAAGGGT-
127 GATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGA-AAATTT-AGGGTC
** * *
65531 CAAAATGTAATTTTAGAAAGGTTT-GAAGATTAAAATGTGA-TTTGGAGAAGTTTAAGGGTCAAA
1 CAAAATGTAATTTTAGAAACATTTAG-AGATCAAAATATGATTTTGGAGAAGTTT-AGGGTCAAA
* *
65594 ATGTAATTTTAGAAAGGTTTGGGGGTTAAAATATGATTTTGGAAAGGTTTAGGGGTTAAAATGTG
64 ATGTAATTTTAGAAAAGTTTAGGGGTTAAAATATGATTTTGGAAA-GTTTAGGGGTTAAAATGTG
* * *
65659 ATTTT-GAAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAATTTTGGGTGC
128 ATTTTAG-AAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAATTTAGGGT-C
* * * *
65710 CAATATGTAATTTTAGAAACATTTAGGGGTCAAAATATGATTTTGTGA-AAGTTTAGTGGTTAAA
1 CAAAATGTAATTTTAGAAACATTTAGAGATCAAAATATGATTTTG-GAGAAGTTTAG-GGTCAAA
* * * * * * *
65774 ATGTTATTTT-GAAATGTTTAAGGGTTAAAATATGATTTTGAAAAAGTTTAGAGGTCAAAATATG
64 ATGTAATTTTAGAAAAGTTTAGGGGTTAAAATATGATTTTG-GAAAGTTTAGGGGTTAAAATGTG
* * *
65838 ATTTTA-AAAAATTTAGGAGTCAAAATGTGATTT
128 ATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTT
65871 AAAAAAATAG
Statistics
Matches: 283, Mismatches: 43, Indels: 30
0.79 0.12 0.08
Matches are distributed among these distances:
177 4 0.01
178 31 0.11
179 188 0.66
180 58 0.20
181 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (177 bp):
CAAAATGTAATTTTAGAAACATTTAGAGATCAAAATATGATTTTGGAGAAGTTTAGGGTCAAAAT
GTAATTTTAGAAAAGTTTAGGGGTTAAAATATGATTTTGGAAAGTTTAGGGGTTAAAATGTGATT
TTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAATTTAGGGTC
Found at i:65834 original size:149 final size:145
Alignment explanation
Indices: 65388--65870 Score: 449
Period size: 149 Copynumber: 3.2 Consensus size: 145
65378 GGGTAAATTA
* * * * *
65388 TAATTTTGGAGAAGTTTTG-GAGTCAAAATATGATTTTAGAAAAGTTTAGGGGTCAAAATGCGAT
1 TAATTTTAGAAAAG-TTTGAGA-TCAAAATGTAATTTTAGAAAA-TTTAGGGGTCAAAATGTGAT
* *
65452 CTTGGAGAAGTTTAAGGGTTAAAATGTGATTTTAGAGAAGTTTAGGGGTTAAAATGTGATTTTGG
63 TTTGGA-AAGTTT-AGGGTTAAAATGTGATTTTAGA-AAGTTTAGGGGTTAAAATGTGATTTTGA
*
65517 AGAAGTTTAAGGGTCAAAATG
125 AAAAGTTTAAGGGTCAAAATG
* * * * * * *
65538 TAATTTTAGAAAGGTTTGAAGATTAAAATGTGA-TTTGGAGAAGTTTAAGGGTCAAAATGTAATT
1 TAATTTTAGAAAAGTTTG-AGATCAAAATGTAATTTTAGA-AAATTTAGGGGTCAAAATGTGATT
* * * *
65602 TTAGAAAGGTTTGGGGGTTAAAATATGATTTTGGAAAGGTTTAGGGGTTAAAATGTGATTTTGAA
64 TTGGAAA-GTTT-AGGGTTAAAATGTGATTTTAGAAA-GTTTAGGGGTTAAAATGTGATTTTGAA
*
65667 AAAGTTTAAGGGTTAAAATG
126 AAAGTTTAAGGGTCAAAATG
* * * * *
65687 TAATTTTGGAAAATTTTG-GGTGCCAATATGTAATTTTAGAAACATTTAGGGGTCAAAATATGAT
1 TAATTTTAGAAAAGTTTGAGAT--CAAAATGTAATTTTAGAAA-ATTTAGGGGTCAAAATGTGAT
* * *
65751 TTTGTGAAAGTTTAGTGGTTAAAATGTTATTTT-GAAATGTTTAAGGGTTAAAATATGATTTTGA
63 TTTG-GAAAGTTTAG-GGTTAAAATGTGATTTTAGAAA-GTTTAGGGGTTAAAATGTGATTTTGA
*
65815 AAAAGTTT-AGAGGTCAAAATA
125 AAAAGTTTAAG-GGTCAAAATG
* * *
65836 TGATTTTA-AAAAATTT-AGGAGTCAAAATGTGATTT
1 TAATTTTAGAAAAGTTTGA-GA-TCAAAATGTAATTT
65871 AAAAAAATAG
Statistics
Matches: 272, Mismatches: 46, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
147 2 0.01
148 24 0.09
149 173 0.64
150 67 0.25
151 6 0.02
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (145 bp):
TAATTTTAGAAAAGTTTGAGATCAAAATGTAATTTTAGAAAATTTAGGGGTCAAAATGTGATTTT
GGAAAGTTTAGGGTTAAAATGTGATTTTAGAAAGTTTAGGGGTTAAAATGTGATTTTGAAAAAGT
TTAAGGGTCAAAATG
Found at i:65877 original size:30 final size:29
Alignment explanation
Indices: 65800--65878 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
65790 TTTAAGGGTT
* *
65800 AAAATATGATTTTGAAAAAGTTTAGAGGTC
1 AAAATATGA-TTTAAAAAAATTTAGAGGTC
*
65830 AAAATATGATTTTAAAAAATTTAG-GAGTC
1 AAAATATGATTTAAAAAAATTTAGAG-GTC
*
65859 AAAATGTGATTTAAAAAAAT
1 AAAATATGATTTAAAAAAAT
65879 AGGGGTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.02
29 34 0.77
30 9 0.20
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (29 bp):
AAAATATGATTTAAAAAAATTTAGAGGTC
Found at i:71559 original size:30 final size:28
Alignment explanation
Indices: 71491--71560 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
71481 TTTTCATAAA
*
71491 TTTAAAATTTAGTCTTTATATTTTTATT
1 TTTAAAATTTAGTCTTTATATTTTTAAT
*
71519 TTTAATAATTTAGTTCATTTA-CTTTTTAGAT
1 TTTAA-AATTTAG-TC-TTTATATTTTTA-AT
71550 TTTAAAATTTA
1 TTTAAAATTTA
71561 AGTTAAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 5 0.14
29 7 0.19
30 14 0.39
31 10 0.28
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTAAAATTTAGTCTTTATATTTTTAAT
Found at i:72157 original size:23 final size:22
Alignment explanation
Indices: 72096--72270 Score: 96
Period size: 23 Copynumber: 7.8 Consensus size: 22
72086 GAAAGTACCA
* * *
72096 AAGTACTAAACAGATAGCACAT
1 AAGTGCTAAACAGAGAGCACAC
*
72118 AAGTGCTGGGAACAGAGAGCACAC
1 AAGTGCT--AAACAGAGAGCACAC
*
72142 ATAGTGCTAAACAGAGAGTACAC
1 A-AGTGCTAAACAGAGAGCACAC
* *
72165 AA-AG-T--AC--TGAGCACAC
1 AAGTGCTAAACAGAGAGCACAC
*
72181 AAAGTGCTAATCAGAGAGCACAC
1 -AAGTGCTAAACAGAGAGCACAC
* *
72204 GAAGAGCTAATAACGGAGAGCACTAAAC
1 -AAGTGCT-A-AACAGAGAGCAC---AC
72232 AA--GCTAAACAGAGAGCACAC
1 AAGTGCTAAACAGAGAGCACAC
*
72252 AAAGTGCTAAACGGAGAGC
1 -AAGTGCTAAACAGAGAGC
72271 GCGCTAGTGT
Statistics
Matches: 117, Mismatches: 18, Indels: 35
0.69 0.11 0.21
Matches are distributed among these distances:
16 7 0.06
17 2 0.02
18 3 0.03
19 1 0.01
20 3 0.03
21 4 0.03
22 7 0.06
23 52 0.44
24 15 0.13
25 19 0.16
27 2 0.02
28 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (22 bp):
AAGTGCTAAACAGAGAGCACAC
Found at i:74670 original size:27 final size:26
Alignment explanation
Indices: 74623--74680 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 26
74613 TTAATAATAT
*
74623 TAAAAATTAAATCTAAA-TTTTAAAA
1 TAAAAATAAAATCTAAATTTTTAAAA
74648 TAAAAATAAATATACTAAATTTTTAAAA
1 TAAAAATAAA-AT-CTAAATTTTTAAAA
74676 TAAAA
1 TAAAA
74681 GTTGACCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 9 0.31
26 2 0.07
27 5 0.17
28 13 0.45
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAAAATAAAATCTAAATTTTTAAAA
Found at i:75132 original size:17 final size:17
Alignment explanation
Indices: 75104--75161 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
75094 TTGGAAATTG
75104 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
75120 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
75137 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
75154 AATTTATT
1 AATTTATT
75162 A
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
16 5 0.13
17 33 0.87
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:75152 original size:7 final size:6
Alignment explanation
Indices: 75109--75159 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
75099 AATTGAATTT
* *
75109 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
75155 ATTTA
1 ATTTA
75160 TTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 26 0.68
7 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
ATTTAA
Done.