Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013946.1 Kokia drynarioides strain JFW-HI SEQ_128976, 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: 92706
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:3013 original size:18 final size:19
Alignment explanation
Indices: 2990--3027 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2980 TATTTTTATT
*
2990 AATTT-AAAATTTTAAAAA
1 AATTTAAAAAGTTTAAAAA
3008 AATTTAAAAAGTTTAAAAA
1 AATTTAAAAAGTTTAAAAA
3027 A
1 A
3028 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AATTTAAAAAGTTTAAAAA
Found at i:4617 original size:25 final size:25
Alignment explanation
Indices: 4589--4639 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
4579 TAATCGAAAC
4589 AAACTTAAAAATCTAATAAATATAA
1 AAACTTAAAAATCTAATAAATATAA
*
4614 AAACTTAAAAATCTAATAATTATAA
1 AAACTTAAAAATCTAATAAATATAA
4639 A
1 A
4640 CATAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
AAACTTAAAAATCTAATAAATATAA
Found at i:7506 original size:24 final size:24
Alignment explanation
Indices: 7485--7549 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
7475 CTGGGTCGAA
*
7485 TTCTGTCAACGGGTTTAGGTCGGG
1 TTCTGTCAACGGGTTCAGGTCGGG
7509 TT-TGGTCAACGGGTTCAGGTCGGG
1 TTCT-GTCAACGGGTTCAGGTCGGG
*
7533 TTCGGTCAACGGGTTCA
1 TTCTGTCAACGGGTTCA
7550 AGTCAGGCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.14, C:0.18, G:0.37, T:0.31
Consensus pattern (24 bp):
TTCTGTCAACGGGTTCAGGTCGGG
Found at i:25619 original size:43 final size:42
Alignment explanation
Indices: 25566--25660 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 42
25556 TGACGATGGC
25566 ATTGGAAAATGTAGGTTTGTCGAGGAATATTTTTTTAAAGCAT
1 ATTGG-AAATGTAGGTTTGTCGAGGAATATTTTTTTAAAGCAT
*
25609 ATTGGCAAATGTAGGTTTGTCGAGGAATATTTTTTTGAAGCAT
1 ATTGG-AAATGTAGGTTTGTCGAGGAATATTTTTTTAAAGCAT
25652 ATTGGAAAT
1 ATTGGAAAT
25661 ATGTTTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 4 0.08
43 46 0.92
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (42 bp):
ATTGGAAATGTAGGTTTGTCGAGGAATATTTTTTTAAAGCAT
Found at i:26312 original size:59 final size:59
Alignment explanation
Indices: 26224--26386 Score: 186
Period size: 59 Copynumber: 2.7 Consensus size: 59
26214 AAATAAGAAT
* * * * * *
26224 AAAAAAATATTTTTTTGGGTGTCTATCAAGCCATGGTCGACACCCTCTTTTTTAGATACC
1 AAAAAAA-ATATTTTTGGGTGTTTGTCAAGCCATGGTCGACACCCCCTTTTTCAAATACC
*
26284 AAAAAAAATATTTTTGGGTGTTTGTCAAGCTATGGTCGACACCCCCTTTTTCAAATACC
1 AAAAAAAATATTTTTGGGTGTTTGTCAAGCCATGGTCGACACCCCCTTTTTCAAATACC
* * * *
26343 -ATAAATATATTTTTTGGGTGTTTGCCAACCCATGG-CTGACACCC
1 AAAAAAAATA-TTTTTGGGTGTTTGTCAAGCCATGGTC-GACACCC
26387 AAAAATAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 8 0.09
59 74 0.83
60 7 0.08
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (59 bp):
AAAAAAAATATTTTTGGGTGTTTGTCAAGCCATGGTCGACACCCCCTTTTTCAAATACC
Found at i:30624 original size:25 final size:25
Alignment explanation
Indices: 30596--30686 Score: 130
Period size: 25 Copynumber: 3.6 Consensus size: 25
30586 AAAATCTAGC
*
30596 TTGAAATTAAATTTATAGTTTAAAA
1 TTGAAATTAAATTTATAGTTTAAAT
30621 TTGAAATTACAA-TTATAGTTTAAAT
1 TTGAAATTA-AATTTATAGTTTAAAT
*
30646 TTGAAATTAAAATTATAGTTTAAAT
1 TTGAAATTAAATTTATAGTTTAAAT
*
30671 TTGAAACTAAAATTTA
1 TTGAAA-TTAAATTTA
30687 ATTTTGGGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
24 2 0.03
25 49 0.82
26 9 0.15
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (25 bp):
TTGAAATTAAATTTATAGTTTAAAT
Found at i:30880 original size:6 final size:6
Alignment explanation
Indices: 30871--30904 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
30861 ATTGAAATCG
*
30871 AAATTA AAATTG AAATTA AAATTA AAATATA AAA
1 AAATTA AAATTA AAATTA AAATTA AAAT-TA AAA
30905 AATAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (6 bp):
AAATTA
Found at i:30883 original size:18 final size:18
Alignment explanation
Indices: 30860--30898 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
30850 AGTTTAGAAT
*
30860 AATTGAAATCGAAATTAA
1 AATTGAAATCAAAATTAA
*
30878 AATTGAAATTAAAATTAA
1 AATTGAAATCAAAATTAA
30896 AAT
1 AAT
30899 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (18 bp):
AATTGAAATCAAAATTAA
Found at i:30893 original size:12 final size:12
Alignment explanation
Indices: 30860--30904 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
30850 AGTTTAGAAT
* *
30860 AATTGAAATCGA
1 AATTAAAATTGA
30872 AATTAAAATTGA
1 AATTAAAATTGA
*
30884 AATTAAAATTAA
1 AATTAAAATTGA
30896 AATATAAAA
1 AAT-TAAAA
30905 AATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 24 0.83
13 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (12 bp):
AATTAAAATTGA
Found at i:31167 original size:20 final size:19
Alignment explanation
Indices: 31124--31167 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
31114 AGGAGAAAAA
*
31124 AAATATTTAAAAATATATT
1 AAATATTTAAAAATATAAT
31143 AAATATTTAATTAAA-ATAAT
1 AAATATTTAA--AAATATAAT
31163 AAATA
1 AAATA
31168 AATTACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 9 0.41
21 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATTTAAAAATATAAT
Found at i:32129 original size:173 final size:173
Alignment explanation
Indices: 31840--32179 Score: 653
Period size: 173 Copynumber: 2.0 Consensus size: 173
31830 GTTTGGGTTG
31840 ATTTAATAACAGCCTTAGTCGAAAGATGGTGGCCCAAGACCCACACGTTCCACCTCCCATGTGGG
1 ATTTAATAACAGCCTTAGTCGAAAGATGGTGGCCCAAGACCCACACGTTCCACCTCCCATGTGGG
*
31905 GAGACGACTATTACGCTATAAGATGTAGCAATCCAACTCGGGCTGCCCATTGACGGTACTACAGT
66 GAGACGACTATTACGCTATAAGATGTAACAATCCAACTCGGGCTGCCCATTGACGGTACTACAGT
*
31970 GATGGGTTTGAGTACATTAGCAGATCCTTGAGGCACTGGGCTA
131 GATGGGTCTGAGTACATTAGCAGATCCTTGAGGCACTGGGCTA
32013 ATTTAATAACAGCCTTAGTCGAAAGATGGTGGCCCAAGACCCACACGTTCCACCTCCCATGTGGG
1 ATTTAATAACAGCCTTAGTCGAAAGATGGTGGCCCAAGACCCACACGTTCCACCTCCCATGTGGG
32078 GAGACGACTATTACGCTATAAGATGTAACAATCCAACTCGGGCTGCCCATTGACGGTACTACAGT
66 GAGACGACTATTACGCTATAAGATGTAACAATCCAACTCGGGCTGCCCATTGACGGTACTACAGT
*
32143 GATGGGTCTGAGTACATTAGCAGATCCTTGGGGCACT
131 GATGGGTCTGAGTACATTAGCAGATCCTTGAGGCACT
32180 TGCTTACGGC
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 164 1.00
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (173 bp):
ATTTAATAACAGCCTTAGTCGAAAGATGGTGGCCCAAGACCCACACGTTCCACCTCCCATGTGGG
GAGACGACTATTACGCTATAAGATGTAACAATCCAACTCGGGCTGCCCATTGACGGTACTACAGT
GATGGGTCTGAGTACATTAGCAGATCCTTGAGGCACTGGGCTA
Found at i:32827 original size:22 final size:20
Alignment explanation
Indices: 32802--32847 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
32792 ATTTCTAAAT
32802 TTTTAAAAATATATTTTTTATA
1 TTTT-AAAA-ATATTTTTTATA
**
32824 TTTTCGAAATATTTTTTATA
1 TTTTAAAAATATTTTTTATA
32844 TTTT
1 TTTT
32848 CGAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.73
21 2 0.09
22 4 0.18
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAAAAATATTTTTTATA
Found at i:32837 original size:20 final size:20
Alignment explanation
Indices: 32812--32851 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
32802 TTTTAAAAAT
32812 ATATTTTTTATATTTTCGAA
1 ATATTTTTTATATTTTCGAA
32832 ATATTTTTTATATTTTCGAA
1 ATATTTTTTATATTTTCGAA
32852 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
ATATTTTTTATATTTTCGAA
Found at i:35106 original size:58 final size:59
Alignment explanation
Indices: 35035--35174 Score: 187
Period size: 58 Copynumber: 2.4 Consensus size: 59
35025 ATAAACACCC
* * *
35035 AAAAAATATTTTTTTTTGTATTTGGAAAGAGAGATGTCAACCATGGCTTGGCAGA-A-CA
1 AAAAAATAATTTTTTTTGTATTT-GAAAAAGAGATGTCAACCATGGCTTGACAGACATCA
* **
35093 AAAAAATAATTTTTTTTGTATTTGAAAAAGAGGTGTCGCCCATGGCTTGACAGACATCA
1 AAAAAATAATTTTTTTTGTATTTGAAAAAGAGATGTCAACCATGGCTTGACAGACATCA
35152 AAAAAA-AATTTTTATTTGTATTT
1 AAAAAATAATTTTT-TTTGTATTT
35175 TTTTGGGTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
57 26 0.36
58 30 0.41
59 17 0.23
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (59 bp):
AAAAAATAATTTTTTTTGTATTTGAAAAAGAGATGTCAACCATGGCTTGACAGACATCA
Found at i:39411 original size:14 final size:15
Alignment explanation
Indices: 39392--39429 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
39382 AACATAATAG
39392 AATAGAACAAAACA-
1 AATAGAACAAAACAT
*
39406 AATAGAGCAAAACAT
1 AATAGAACAAAACAT
39421 AATAGAACA
1 AATAGAACA
39430 GGGTAGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.66, C:0.13, G:0.11, T:0.11
Consensus pattern (15 bp):
AATAGAACAAAACAT
Found at i:39419 original size:19 final size:20
Alignment explanation
Indices: 39370--39419 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39360 ACAACAGTAC
39370 AGAACAAAACAAAACATAAT
1 AGAACAAAACAAAACATAAT
* *
39390 AGAATAGAACAAAACA-AAT
1 AGAACAAAACAAAACATAAT
*
39409 AGAGCAAAACA
1 AGAACAAAACA
39420 TAATAGAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.68, C:0.14, G:0.10, T:0.08
Consensus pattern (20 bp):
AGAACAAAACAAAACATAAT
Found at i:43695 original size:21 final size:20
Alignment explanation
Indices: 43671--43727 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
43661 TGATGAGTGT
*
43671 TGTGGCTGCATCTGATTCTGG
1 TGTGGATGCATCTGATT-TGG
* * *
43692 TGTGGTTGCATCTAGCTTTGT
1 TGTGGATGCATCT-GATTTGG
43713 TGTGGATGCATCTGA
1 TGTGGATGCATCTGA
43728 GTATGATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.87
22 3 0.10
ACGTcount: A:0.12, C:0.16, G:0.32, T:0.40
Consensus pattern (20 bp):
TGTGGATGCATCTGATTTGG
Found at i:47609 original size:18 final size:19
Alignment explanation
Indices: 47574--47612 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
47564 AATAAATATA
47574 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
47593 AATA-AATTGTAAA-TTAAT
1 AATACAATT-TAAATTTAAT
47611 AA
1 AA
47613 AAAAACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:48006 original size:30 final size:30
Alignment explanation
Indices: 47970--48051 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
47960 TTTAGGTAAA
*
47970 TTAACAATGTGGGGTATGAGGTAAACCCTT
1 TTAACAATGTGGGATATGAGGTAAACCCTT
* * *
48000 TTAACAATGCGGGATATGAGTTCAACCCTT
1 TTAACAATGTGGGATATGAGGTAAACCCTT
*
48030 TTAACAATGTGAGATATGAGGT
1 TTAACAATGTGGGATATGAGGT
48052 TTTAAGTTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (30 bp):
TTAACAATGTGGGATATGAGGTAAACCCTT
Found at i:54956 original size:18 final size:18
Alignment explanation
Indices: 54933--54969 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54923 TTTGTGATAA
54933 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
54951 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
54969 A
1 A
54970 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:57865 original size:19 final size:19
Alignment explanation
Indices: 57841--57883 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
57831 AATAAATATA
57841 AATAAAATT-TAAATTTAAT
1 AATAAAATTGTAAA-TTAAT
57860 AAT-AAATTGTAAATTAAT
1 AATAAAATTGTAAATTAAT
57878 AA-AAAA
1 AATAAAA
57884 AGCAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AATAAAATTGTAAATTAAT
Found at i:59981 original size:13 final size:13
Alignment explanation
Indices: 59963--59987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59953 ACTAAGCTTG
59963 TAAATATTTTTAT
1 TAAATATTTTTAT
59976 TAAATATTTTTA
1 TAAATATTTTTA
59988 GAGTTATTGT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:62560 original size:24 final size:24
Alignment explanation
Indices: 62542--62624 Score: 130
Period size: 24 Copynumber: 3.5 Consensus size: 24
62532 TTTAGCCCAC
62542 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
62566 ACGAGCCCAGAATGGCTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* *
62590 ACGAGCCTAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
62614 ATGAGCCCAGA
1 ACGAGCCCAGA
62625 CAGAGTTTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:64694 original size:10 final size:10
Alignment explanation
Indices: 64679--64758 Score: 70
Period size: 10 Copynumber: 8.0 Consensus size: 10
64669 TAATTGACAA
*
64679 ATATATATAC
1 ATATATATAT
* *
64689 ATATATGTAC
1 ATATATATAT
* *
64699 ATGTATATAC
1 ATATATATAT
*
64709 ATATATGTAT
1 ATATATATAT
*
64719 ATACATATAT
1 ATATATATAT
* *
64729 GTGTATATAT
1 ATATATATAT
64739 ATATATATAT
1 ATATATATAT
*
64749 GTATATATAT
1 ATATATATAT
64759 GGTATAAAGA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 56 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (10 bp):
ATATATATAT
Found at i:64721 original size:34 final size:34
Alignment explanation
Indices: 64682--64755 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
64672 TTGACAAATA
*
64682 TATATACATATATGTACATGTATATACATATATG
1 TATATACATATATGTACATATATATACATATATG
** *
64716 TATATACATATATGTGTATATATATATATATATG
1 TATATACATATATGTACATATATATACATATATG
64750 TATATA
1 TATATA
64756 TATGGTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (34 bp):
TATATACATATATGTACATATATATACATATATG
Found at i:64739 original size:20 final size:20
Alignment explanation
Indices: 64679--64758 Score: 82
Period size: 20 Copynumber: 4.3 Consensus size: 20
64669 TAATTGACAA
*
64679 ATATATATACATATATGTAC
1 ATATATATACATATATGTAT
*
64699 ATGTATATACATATATG---
1 ATATATATACATATATGTAT
*
64716 ---TATATACATATATGTGT
1 ATATATATACATATATGTAT
*
64733 ATATATATATATATATGTAT
1 ATATATATACATATATGTAT
64753 ATATAT
1 ATATAT
64759 GGTATAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
14 14 0.27
20 37 0.73
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATATATACATATATGTAT
Found at i:64758 original size:14 final size:14
Alignment explanation
Indices: 64679--64756 Score: 75
Period size: 14 Copynumber: 5.6 Consensus size: 14
64669 TAATTGACAA
**
64679 ATATATATACATAT
1 ATATATATGTATAT
* *
64693 ATGTACATGTATAT
1 ATATATATGTATAT
*
64707 ACATATATGTATAT
1 ATATATATGTATAT
* *
64721 ACATATATGTGTAT
1 ATATATATGTATAT
*
64735 ATATATATATATAT
1 ATATATATGTATAT
*
64749 GTATATAT
1 ATATATAT
64757 ATGGTATAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 52 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:64759 original size:10 final size:10
Alignment explanation
Indices: 64723--64764 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
64713 ATGTATATAC
*
64723 ATATATGTGT
1 ATATATGTAT
*
64733 ATATATATAT
1 ATATATGTAT
64743 ATATATGTAT
1 ATATATGTAT
64753 ATATATGGTAT
1 ATATAT-GTAT
64764 A
1 A
64765 AAGATGAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 23 0.82
11 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (10 bp):
ATATATGTAT
Found at i:67947 original size:4 final size:4
Alignment explanation
Indices: 67929--67969 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
67919 TTAGCACGAC
67929 TCTT T-TT TCCTT TCTT TCTT TC-T TCTTT TCTT TCTT TCTT T
1 TCTT TCTT T-CTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT T
67970 TCACAGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 6 0.18
4 21 0.64
5 6 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:67948 original size:16 final size:16
Alignment explanation
Indices: 67929--67968 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
67919 TTAGCACGAC
*
67929 TCTTTTTTCCTTTCTT
1 TCTTTCTTCCTTTCTT
*
67945 TCTTTCTTCTTTTCTT
1 TCTTTCTTCCTTTCTT
67961 TCTTTCTT
1 TCTTTCTT
67969 TTCACAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTTTCTTCCTTTCTT
Found at i:67958 original size:12 final size:13
Alignment explanation
Indices: 67929--67971 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
67919 TTAGCACGAC
*
67929 TCTTTT-TTCCTT
1 TCTTTTCTTTCTT
67941 TC-TTTCTTTC-T
1 TCTTTTCTTTCTT
67952 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
67965 TCTTTTC
1 TCTTTTC
67972 ACAGTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.22
12 13 0.48
13 8 0.30
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:70527 original size:29 final size:29
Alignment explanation
Indices: 70473--70781 Score: 271
Period size: 29 Copynumber: 10.6 Consensus size: 29
70463 TTCTCGGGGG
* * *
70473 AAAAATGGTAATTTTGGGAAAATTCGGGGTT
1 AAAAATGG-AATTTTTGG-AAGTTCGAGGTT
*
70504 AAAAATGGAATTTTTAGACA-TTCGAGG-T
1 AAAAATGGAATTTTTGGA-AGTTCGAGGTT
70532 AAAAA-GGTAA-TTTT-GAGAGTTTCGAGGTT
1 AAAAATGG-AATTTTTGGA-AG-TTCGAGGTT
*
70561 -AAAATGGAATTTTTGGACA-TCTGGAGG-T
1 AAAAATGGAATTTTTGGA-AGT-TCGAGGTT
* * *
70589 -AAAATGGTAATTTTTGAAAGTTTCGGGGTC
1 AAAAATGG-AATTTTTGGAAG-TTCGAGGTT
* *
70619 AAAAATGGAAATTTT-GAAGGTTCGAGGGGT
1 AAAAATGGAATTTTTGGAA-GTTCGA-GGTT
*
70649 AAAAATGGAATTTTTGGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGTT
* *
70679 AAAAATGGAATTTTTCGAAGTTCGAGGCT
1 AAAAATGGAATTTTTGGAAGTTCGAGGTT
*
70708 AAAAATGGAATTTTTGGAAGCTTCGAGGTA
1 AAAAATGGAATTTTTGGAAG-TTCGAGGTT
* *
70738 AAAAATGGAA-TTTTGGAAGTTCAAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGTT
70766 AAAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
70782 AACAGTTTAG
Statistics
Matches: 231, Mismatches: 27, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
26 3 0.01
27 6 0.03
28 47 0.20
29 78 0.34
30 75 0.32
31 22 0.10
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGTT
Found at i:70536 original size:59 final size:58
Alignment explanation
Indices: 70473--70779 Score: 299
Period size: 59 Copynumber: 5.3 Consensus size: 58
70463 TTCTCGGGGG
** *
70473 AAAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATGGAATTTTTAGACA-TTCGAGGT
1 AAAAATGGTAATTTTGGGAAGTTTCGAGGTTAAAAATGGAATTTTT-GA-AGTTCGAGGT
* *
70532 AAAAA-GGTAATTTTGAG-AGTTTCGAGGTT-AAAATGGAATTTTTGGACA-TCTGGAGGT
1 AAAAATGGTAATTTTGGGAAGTTTCGAGGTTAAAAATGGAATTTTT-GA-AGT-TCGAGGT
* * * * *
70589 -AAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAATTTTGAAGGTTCGAGGGGT
1 AAAAATGGTAATTTTGGGAAGTTTCGAGGTTAAAAATGGAATTTTTGAA-GTTCGA--GGT
* *
70649 AAAAATGG-AATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTCGAAGTTCGAGGCT
1 AAAAATGGTAATTTTGGGAAGTTTCGAGGTTAAAAATGGAATTTTT-GAAGTTCGAGG-T
* * * * *
70708 AAAAATGG-AATTTTTGGAAGCTTCGAGGTAAAAAATGGAATTTTGGAAGTTCAAGGGT
1 AAAAATGGTAATTTTGGGAAGTTTCGAGGTTAAAAATGGAATTTTTGAAGTTCGA-GGT
70766 AAAAATGG-AATTTT
1 AAAAATGGTAATTTT
70780 TGAACAGTTT
Statistics
Matches: 213, Mismatches: 23, Indels: 25
0.82 0.09 0.10
Matches are distributed among these distances:
56 23 0.11
57 25 0.12
58 51 0.24
59 63 0.30
60 41 0.19
61 10 0.05
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.32
Consensus pattern (58 bp):
AAAAATGGTAATTTTGGGAAGTTTCGAGGTTAAAAATGGAATTTTTGAAGTTCGAGGT
Found at i:70793 original size:29 final size:28
Alignment explanation
Indices: 70503--70793 Score: 166
Period size: 30 Copynumber: 10.0 Consensus size: 28
70493 AATTCGGGGT
* *
70503 TAAAAATGGAATTTTTAGACA--TTCGAGG
1 TAAAAATGGAATTTTT-GAAAGTTTAG-GG
* *
70531 TAAAAA-GGTAA-TTTTGAGAGTTTCGAGG
1 TAAAAATGG-AATTTTTGAAAGTTTAG-GG
* * * *
70559 TTAAAATGGAATTTTTGGACA-TCTGGAGG
1 TAAAAATGGAATTTTT-GAAAGTTTAG-GG
*
70588 T-AAAATGGTAATTTTTGAAAGTTTCGGGG
1 TAAAAATGG-AATTTTTGAAAGTTT-AGGG
* * *
70617 TCAAAAATGGAAATTTTGAAGGTTCGAGGGG
1 T-AAAAATGGAATTTTTGAAAGTT-TA-GGG
* *
70648 TAAAAATGGAATTTTTGGAAGTTTCAAGGT
1 TAAAAATGGAATTTTTGAAAGTTT--AGGG
* *
70678 TAAAAATGGAATTTTTCG-AAGTTCGAGGC
1 TAAAAATGGAATTTTT-GAAAGTT-TAGGG
* * *
70707 TAAAAATGGAATTTTTGGAAGCTTCGAGG
1 TAAAAATGGAATTTTTGAAAGTTTAG-GG
* *
70736 TAAAAAATGGAA-TTTTGGAAGTTCAAGGG
1 T-AAAAATGGAATTTTTGAAAGTT-TAGGG
70765 TAAAAATGGAATTTTTGAACAGTTTAGGG
1 TAAAAATGGAATTTTTGAA-AGTTTAGGG
70794 ACCTTCAAGG
Statistics
Matches: 213, Mismatches: 27, Indels: 45
0.75 0.09 0.16
Matches are distributed among these distances:
26 3 0.01
27 6 0.03
28 44 0.21
29 73 0.34
30 74 0.35
31 13 0.06
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.32
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGAAAGTTTAGGG
Found at i:71914 original size:22 final size:21
Alignment explanation
Indices: 71883--71936 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
71873 AATTAAAGCC
71883 TTATTAATATCATTAATAAAA
1 TTATTAATATCATTAATAAAA
*
71904 TTATTCAATATTATTAATAAAA
1 TTATT-AATATCATTAATAAAA
71926 TTATTTAATAT
1 TTA-TTAATAT
71937 GTTTAATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.17
22 23 0.77
23 2 0.07
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATTAATATCATTAATAAAA
Found at i:71942 original size:22 final size:21
Alignment explanation
Indices: 71886--71944 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
71876 TAAAGCCTTA
*
71886 TTAATATCATTAATAAAATTAT
1 TTAATAT-TTTAATAAAATTAT
*
71908 TCAATATTATTAATAAAATTAT
1 TTAATATT-TTAATAAAATTAT
71930 TTAATATGTTTAATA
1 TTAATAT-TTTAATA
71945 TGTATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAATATTTTAATAAAATTAT
Found at i:72766 original size:6 final size:6
Alignment explanation
Indices: 72755--72822 Score: 88
Period size: 6 Copynumber: 11.7 Consensus size: 6
72745 ATTTTGAAAA
72755 TAAATT TAAATT TAAATT TAAATT TAAATT TAAGA-T T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT
* *
72802 CAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
72823 AGAAGCCCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 45 0.83
7 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:72799 original size:23 final size:22
Alignment explanation
Indices: 72755--72822 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 22
72745 ATTTTGAAAA
72755 TAAATTTAAATTTAAATTTAAATT
1 TAAATTTAAA-TT-AATTTAAATT
72779 TAAATTTAAGATTAATTTAAATT
1 TAAATTTAA-ATTAATTTAAATT
* *
72802 CAAATTTAAAATAAATTTAAA
1 TAAATTT-AAATTAATTTAAA
72823 AGAAGCCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 26 0.65
24 13 0.32
25 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (22 bp):
TAAATTTAAATTAATTTAAATT
Found at i:75893 original size:18 final size:19
Alignment explanation
Indices: 75870--75905 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
75860 TTATTACTGT
*
75870 TAAAATT-TATTATTAAAA
1 TAAAATTGTAATATTAAAA
75888 TAAAATTGTAATATTAAA
1 TAAAATTGTAATATTAAA
75906 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATTGTAATATTAAAA
Found at i:79931 original size:12 final size:13
Alignment explanation
Indices: 79908--79934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
79898 AGTTTAGCAT
79908 TACTTTTAAAAAA
1 TACTTTTAAAAAA
79921 TACTTTTAAAAAA
1 TACTTTTAAAAAA
79934 T
1 T
79935 GTGATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TACTTTTAAAAAA
Found at i:81666 original size:48 final size:48
Alignment explanation
Indices: 81613--81710 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
81603 CCAAGATGTA
81613 CAAAAAAATTCCTAACATTTCACGAGAAGATACGTGTCTTGAAGTTTG
1 CAAAAAAATTCCTAACATTTCACGAGAAGATACGTGTCTTGAAGTTTG
*
81661 CAAAAAAATTCTTAACATTTCACGAGAAGATACGTGTCTTGAAGTTTG
1 CAAAAAAATTCCTAACATTTCACGAGAAGATACGTGTCTTGAAGTTTG
81709 CA
1 CA
81711 GGTTGTATCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (48 bp):
CAAAAAAATTCCTAACATTTCACGAGAAGATACGTGTCTTGAAGTTTG
Found at i:82129 original size:72 final size:72
Alignment explanation
Indices: 82020--82357 Score: 572
Period size: 72 Copynumber: 4.7 Consensus size: 72
82010 AACAAATTTT
* * *
82020 ATATCC-AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
82084 AAATTCA
66 AAATTCA
* * *
82091 ATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAGATTGCACATAAATAAGTAAAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
82156 AAATTCAAA
66 AAATTC--A
82165 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
82230 AAATTCA
66 AAATTCA
*
82237 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGGTTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
82302 AAATTCA
66 AAATTCA
*
82309 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGTTTA-ACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACAT
82358 TGCTGTTTAG
Statistics
Matches: 255, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
71 10 0.04
72 176 0.69
74 69 0.27
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.23
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
AAATTCA
Found at i:82301 original size:146 final size:144
Alignment explanation
Indices: 82020--82357 Score: 572
Period size: 146 Copynumber: 2.3 Consensus size: 144
82010 AACAAATTTT
* * *
82020 ATATCC-AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
* *
82084 AAATTCAATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAGATTGCACATAAATAAGT
66 AAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGT
82149 AAAACATAAATTCAAA
131 AAAACATAAATTC--A
82165 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
*
82230 AAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGGTTACACATAAATAAGT
66 AAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGT
*
82295 AGAACATAAATTCA
131 AAAACATAAATTCA
*
82309 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGTTTA-ACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACAT
82358 TGCTGTTTAG
Statistics
Matches: 184, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
143 4 0.02
144 45 0.24
145 6 0.03
146 129 0.70
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.23
Consensus pattern (144 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
AAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGT
AAAACATAAATTCA
Found at i:82792 original size:18 final size:18
Alignment explanation
Indices: 82744--82813 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
82734 CGTTTCCATC
82744 AATGTTAACATCATTTGA
1 AATGTTAACATCATTTGA
*
82762 AAT-TTGAATATCATTTGA
1 AATGTT-AACATCATTTGA
* *
82780 AGTGTTAACATCATTTAA
1 AATGTTAACATCATTTGA
82798 AATGTTAACATCATTT
1 AATGTTAACATCATTT
82814 CCTGCATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
17 2 0.04
18 41 0.91
19 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (18 bp):
AATGTTAACATCATTTGA
Found at i:84062 original size:91 final size:91
Alignment explanation
Indices: 83907--84088 Score: 328
Period size: 91 Copynumber: 2.0 Consensus size: 91
83897 CAGCACAGTA
* *
83907 AACTTCTTTTAGATTACGAGAATTTGTTGAGTACTTCAACCACAGTATAACATTGAAGCAACAAA
1 AACTTCTTTTAGATTACGAGAATTTGTTGAGTACTTCAACCACAATATAACATTGAACCAACAAA
83972 TAACACTTAAAAAATTGCTTCAGATT
66 TAACACTTAAAAAATTGCTTCAGATT
*
83998 AACTTCTTTTAGATTACGGGAATTTGTTGAGTACTTCAACCACAATATAACATTGAACCAACAAA
1 AACTTCTTTTAGATTACGAGAATTTGTTGAGTACTTCAACCACAATATAACATTGAACCAACAAA
*
84063 TAACACTTGAAAAATTGCTTCAGATT
66 TAACACTTAAAAAATTGCTTCAGATT
84089 TTCGATAGAT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (91 bp):
AACTTCTTTTAGATTACGAGAATTTGTTGAGTACTTCAACCACAATATAACATTGAACCAACAAA
TAACACTTAAAAAATTGCTTCAGATT
Found at i:84072 original size:19 final size:19
Alignment explanation
Indices: 84030--84073 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
84020 TTTGTTGAGT
*
84030 ACTTCAACCACAATATAAC
1 ACTTGAACCACAATATAAC
84049 A-TTGAACCAACAA-ATAAC
1 ACTTGAACC-ACAATATAAC
84067 ACTTGAA
1 ACTTGAA
84074 AAATTGCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.50, C:0.25, G:0.05, T:0.20
Consensus pattern (19 bp):
ACTTGAACCACAATATAAC
Found at i:88735 original size:61 final size:61
Alignment explanation
Indices: 88635--88751 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 61
88625 TTCACAGCTG
88635 CATCAACATTCCTGAGAAAACTTCCAAGGCTGTAGGCTGATGGTATTGAATGAGAGATTTA
1 CATCAACATTCCTGAGAAAACTTCCAAGGCTGTAGGCTGATGGTATTGAATGAGAGATTTA
* ***
88696 CATCCACATTCCTGAGAAAACTTGTGAGGCTGTAGGCTGATGGTATTGAATGAGAG
1 CATCAACATTCCTGAGAAAACTTCCAAGGCTGTAGGCTGATGGTATTGAATGAGAG
88752 TTTTTTTGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (61 bp):
CATCAACATTCCTGAGAAAACTTCCAAGGCTGTAGGCTGATGGTATTGAATGAGAGATTTA
Found at i:90357 original size:9 final size:9
Alignment explanation
Indices: 90343--90372 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
90333 ACACCAATTT
90343 ATTATTCGA
1 ATTATTCGA
90352 ATTATTCGA
1 ATTATTCGA
*
90361 GTTATTCGA
1 ATTATTCGA
90370 ATT
1 ATT
90373 GTGAGATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (9 bp):
ATTATTCGA
Found at i:92219 original size:21 final size:21
Alignment explanation
Indices: 92195--92252 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
92185 TTTGTTTCAG
92195 TAGAAGTCACACTTGTACCGA
1 TAGAAGTCACACTTGTACCGA
** *
92216 TAGAAGT-ATCACAAGTATCGA
1 TAGAAGTCA-CACTTGTACCGA
92237 TAGAAGTCTACA-TTGT
1 TAGAAGTC-ACACTTGT
92253 TTCTGAATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.03
21 25 0.86
22 2 0.07
23 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (21 bp):
TAGAAGTCACACTTGTACCGA
Done.