Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014062.1 Kokia drynarioides strain JFW-HI SEQ_129093, 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: 131825
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:407 original size:23 final size:23
Alignment explanation
Indices: 381--536 Score: 135
Period size: 23 Copynumber: 6.8 Consensus size: 23
371 TTACTGTTCA
381 GCACTGTGTGTGCTTACT-ATTT
1 GCACTGTGTGTGCTTACTGATTT
403 CGCACT-TCGTGTGCTTACTG-TTT
1 -GCACTGT-GTGTGCTTACTGATTT
*
426 CGCACT-TCGTGTGCCTACTGATTT
1 -GCACTGT-GTGTGCTTACTGATTT
* * * *
450 GCGCTATGTGCGCCTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
* * * *
473 GCGCTATGTGCGCCTACTGA-TT
1 GCACTGTGTGTGCTTACTGATTT
*
495 GCACTGTGTGCGCTTACTGGA-TT
1 GCACTGTGTGTGCTTACT-GATTT
518 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
537 TTTCCCCAGC
Statistics
Matches: 121, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
22 19 0.16
23 98 0.81
24 4 0.03
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (23 bp):
GCACTGTGTGTGCTTACTGATTT
Found at i:468 original size:46 final size:45
Alignment explanation
Indices: 438--536 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
428 CACTTCGTGT
* *
438 GCCTACTGATTTGCGCTATGTGCGCCTACTGATTTGCGCTATGTGC
1 GCCTACTGA-TTGCACTATGTGCGCCTACTGATTTGCACTATGTGC
* * * *
484 GCCTACTGATTGCACTGTGTGCGCTTACTGGA-TTGCACTGTGTGT
1 GCCTACTGATTGCACTATGTGCGCCTACT-GATTTGCACTATGTGC
*
529 GCTTACTG
1 GCCTACTG
537 TTTCCCCAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 34 0.76
46 11 0.24
ACGTcount: A:0.13, C:0.24, G:0.27, T:0.35
Consensus pattern (45 bp):
GCCTACTGATTGCACTATGTGCGCCTACTGATTTGCACTATGTGC
Found at i:24728 original size:19 final size:19
Alignment explanation
Indices: 24686--24736 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
24676 CAAAAGAAAA
* *
24686 AAAAATCAAAATAAATTTC
1 AAAAATTAAAATTAATTTC
*
24705 AAAAATTAAAATTAATTTT
1 AAAAATTAAAATTAATTTC
* *
24724 TAAAATTTAAATT
1 AAAAATTAAAATT
24737 TTTTTATAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTAAAATTAATTTC
Found at i:24797 original size:16 final size:17
Alignment explanation
Indices: 24762--24811 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
24752 TAATTTAAAA
*
24762 AAAATCTAAAAATATTTG
1 AAAATTTAAAAAT-TTTG
24780 AAAATTT-AAAATTTTG
1 AAAATTTAAAAATTTTG
24796 AAAATTTAAAAATTTT
1 AAAATTTAAAAATTTT
24812 ATAAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.37
17 13 0.43
18 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (17 bp):
AAAATTTAAAAATTTTG
Found at i:24877 original size:2 final size:2
Alignment explanation
Indices: 24870--24901 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24860 TATCCTACTA
24870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24902 TATTTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35474 original size:3 final size:3
Alignment explanation
Indices: 35468--35501 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35458 TAGTTGTTTG
35468 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
35502 TCATTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:36710 original size:29 final size:30
Alignment explanation
Indices: 36641--36917 Score: 139
Period size: 29 Copynumber: 9.7 Consensus size: 30
36631 GAGGTCCCTG
* *
36641 AACTTCCCAAAATCCCATTTTGT--CCCCAA
1 AACTTCCAAAAATCTCATTTT-TAACCCCAA
* **
36670 AACTTCCAAAAATTTTGTTTTT-ACCCCAA
1 AACTTCCAAAAATCTCATTTTTAACCCCAA
36699 AAC-TCCAAAAAATCTCATTTTTAACCCCAA
1 AACTTCC-AAAAATCTCATTTTTAACCCCAA
* *
36729 AAATT-C------CT--TTTTT-ACCCCCA
1 AACTTCCAAAAATCTCATTTTTAACCCCAA
* *
36749 AATTTCCAAAAATC-C-TATTTTAACCCTAA
1 AACTTCCAAAAATCTCAT-TTTTAACCCCAA
* *
36778 AAC-TCCAAAAAATCTCATTTTTGACCCTAA
1 AACTTCC-AAAAATCTCATTTTTAACCCCAA
* *
36808 AACTTTCAAAAAT-TCCATTTTT-ACCCCCA
1 AACTTCCAAAAATCT-CATTTTTAACCCCAA
* * * *
36837 AACTTCCCAAAATCTCACTTTTGACCCTAAA
1 AACTTCCAAAAATCTCATTTTTAACCC-CAA
* *
36868 AACTTCCAAAAAAT-TC-TTTTTTACCCTC-G
1 AACTTCC-AAAAATCTCATTTTTAACCC-CAA
* *
36897 AATTTCCAAAAATCCCATTTT
1 AACTTCCAAAAATCTCATTTT
36918 CGACCTCAAA
Statistics
Matches: 193, Mismatches: 30, Indels: 49
0.71 0.11 0.18
Matches are distributed among these distances:
20 10 0.05
21 6 0.03
23 2 0.01
27 2 0.01
28 17 0.09
29 81 0.42
30 56 0.29
31 14 0.07
32 5 0.03
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (30 bp):
AACTTCCAAAAATCTCATTTTTAACCCCAA
Found at i:36739 original size:20 final size:21
Alignment explanation
Indices: 36706--36746 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
36696 CAAAACTCCA
36706 AAAAATCTCATTTTTAACCCC
1 AAAAATCTCATTTTTAACCCC
* *
36727 AAAAAT-TCCTTTTTTACCCC
1 AAAAATCTCATTTTTAACCCC
36747 CAAATTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATCTCATTTTTAACCCC
Found at i:36756 original size:79 final size:79
Alignment explanation
Indices: 36664--36809 Score: 211
Period size: 79 Copynumber: 1.8 Consensus size: 79
36654 CCCATTTTGT
** * *
36664 CCCCAAAACTTCCAAAAATTTTGTTTTTACCCCAAAACTCCAAAAAATCTCATTTTTAACCCCAA
1 CCCCAAAACTTCCAAAAATCCTATTTTAACCCCAAAACTCCAAAAAATCTCATTTTTAACCCCAA
36729 AAATTCCTTTTTTA
66 AAATTCCTTTTTTA
* * * * *
36743 CCCCCAAATTTCCAAAAATCCTATTTTAACCCTAAAACTCCAAAAAATCTCATTTTTGACCCTAA
1 CCCCAAAACTTCCAAAAATCCTATTTTAACCCCAAAACTCCAAAAAATCTCATTTTTAACCCCAA
36808 AA
66 AA
36810 CTTTCAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 58 1.00
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.32
Consensus pattern (79 bp):
CCCCAAAACTTCCAAAAATCCTATTTTAACCCCAAAACTCCAAAAAATCTCATTTTTAACCCCAA
AAATTCCTTTTTTA
Found at i:36906 original size:59 final size:59
Alignment explanation
Indices: 36752--36956 Score: 165
Period size: 59 Copynumber: 3.5 Consensus size: 59
36742 ACCCCCAAAT
* ** * *
36752 TTCCAAAAA-TCCTATTTTAACCCTAAAAC-TCCAAAAAATCTCATTTTTGACCCTAAAAC
1 TTCCAAAAATTCC-ATTTTTACCCCCAAACTTCC-CAAAATCTCACTTTTGACCCTAAAAC
*
36811 TTTCAAAAATTCCATTTTTACCCCCAAACTTCCCAAAATCTCACTTTTGACCCTAAAAAC
1 TTCCAAAAATTCCATTTTTACCCCCAAACTTCCCAAAATCTCACTTTTGACCCT-AAAAC
* * * * * *
36871 TTCCAAAAAATT-CTTTTTTACCCTCGAATTTCCAAAAATCCCA-TTTTCGA-CCTCAAAAC
1 TTCC-AAAAATTCCATTTTTACCCCCAAACTTCCCAAAATCTCACTTTT-GACCCT-AAAAC
*
36930 -TCTC-AAAATTACC-CTTTTACCCCCAAA
1 TTC-CAAAAATT-CCATTTTTACCCCCAAA
36957 TGTCTAAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
57 6 0.05
58 13 0.11
59 54 0.45
60 41 0.34
61 7 0.06
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTACCCCCAAACTTCCCAAAATCTCACTTTTGACCCTAAAAC
Found at i:42023 original size:6 final size:6
Alignment explanation
Indices: 41980--42068 Score: 55
Period size: 6 Copynumber: 15.3 Consensus size: 6
41970 CTGGACCCAA
* * * *
41980 TAAACT TAAATT T-ATTT TAAAAT TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
* *
42026 T-GATT GAAATT TAAATT T--ATT ATAAATT TAAATT TAAAATT TA
1 TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT T-AAATT TA
42069 TTTTAAATGT
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
4 5 0.08
5 9 0.14
6 37 0.59
7 12 0.19
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:42070 original size:24 final size:23
Alignment explanation
Indices: 42032--42076 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
42022 AATTTGATTG
42032 AAATTTAAATTTATTATAAATTT
1 AAATTTAAATTTATTATAAATTT
*
42055 AAATTTAAAATTTATTTTAAAT
1 AAATTT-AAATTTATTATAAAT
42077 GTCCAAGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATTTATTATAAATTT
Found at i:42071 original size:17 final size:17
Alignment explanation
Indices: 41979--42061 Score: 96
Period size: 17 Copynumber: 4.9 Consensus size: 17
41969 TCTGGACCCA
*
41979 ATAAACTTAAATTTATT
1 ATAAATTTAAATTTATT
* * *
41996 TTAAAATTAAGTTTATT
1 ATAAATTTAAATTTATT
*
42013 CTAAATTTAAATTTGATT
1 ATAAATTTAAATTT-ATT
*
42031 -GAAATTTAAATTTATT
1 ATAAATTTAAATTTATT
42047 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
42062 AAATTTATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 3 0.05
17 50 0.89
18 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:42823 original size:15 final size:15
Alignment explanation
Indices: 42805--42846 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
42795 ATAAAATTAT
42805 TATTATTAATAAAGG
1 TATTATTAATAAAGG
* *
42820 TATTAATAATAAATG
1 TATTATTAATAAAGG
42835 T-TATATTAATAA
1 TAT-TATTAATAA
42847 TAATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TATTATTAATAAAGG
Found at i:42823 original size:18 final size:18
Alignment explanation
Indices: 42790--42824 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42780 TATTAATAGG
*
42790 TATTAATAAAATTATTAT
1 TATTAATAAAAGTATTAT
*
42808 TATTAATAAAGGTATTA
1 TATTAATAAAAGTATTA
42825 ATAATAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TATTAATAAAAGTATTAT
Found at i:43933 original size:29 final size:28
Alignment explanation
Indices: 43873--44097 Score: 181
Period size: 30 Copynumber: 7.7 Consensus size: 28
43863 CACTTTACCC
* *
43873 CCCG-AACTTCTAATAATCTCATTTTTGAA
1 CCCGAAACTTCCAAAAAT-TCATTTTTG-A
*
43902 CCCGAAACTTCCAAAAAATTCATTTATGA
1 CCCGAAACTTCC-AAAAATTCATTTTTGA
* *
43931 CCCCAAAACTTCCAAAAATTCCATTTTTACA
1 -CCCGAAACTTCCAAAAATT-CATTTTT-GA
*
43962 CCCG-AACTTCCAAAAATCCCATTTTTGA
1 CCCGAAACTTCCAAAAAT-TCATTTTTGA
* * *
43990 CCCTAAAACTTCAAAAAATTCCATTTTTGC
1 CCC-GAAACTTCCAAAAATT-CATTTTTGA
*
44020 CCTCG-AACTTCCAAAAATCCTATTTTTGA
1 CC-CGAAACTTCCAAAAATTC-ATTTTTGA
*
44049 CCCCAAAACTTCCAAAAATTCCATTTTT-A
1 -CCCGAAACTTCCAAAAATT-CATTTTTGA
44078 CCCCCG-AACTTCCAAAAATT
1 --CCCGAAACTTCCAAAAATT
44098 ACCATTTTGC
Statistics
Matches: 161, Mismatches: 20, Indels: 30
0.76 0.09 0.14
Matches are distributed among these distances:
28 5 0.03
29 67 0.42
30 81 0.50
31 8 0.05
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (28 bp):
CCCGAAACTTCCAAAAATTCATTTTTGA
Found at i:44007 original size:89 final size:86
Alignment explanation
Indices: 43842--44109 Score: 253
Period size: 89 Copynumber: 3.0 Consensus size: 86
43832 CCTTGGAGGT
* * * *
43842 CCCT-AAACTGTCCAAAAATTCCA-CTTTACCCCCCGAACTTCTAATAATCTCATTTTTGAACCC
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA--CCCCGAACTTCCAAAAATCCCATTTTTG-ACCC
*
43905 GAAACTTCCAAAAAATT-CATTTATG
62 AAAACTT-CAAAAAATTCCATTTATG
43930 ACCC-CAAAACTTCCAAAAATTCCATTTTTACACCCGAACTTCCAAAAATCCCATTTTTGACCCT
1 -CCCTC-AAACTTCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAATCCCATTTTTGACCC-
*
43994 AAAACTTCAAAAAATTCCATTTTTG
62 AAAACTTCAAAAAATTCCATTTATG
* * *
44019 CCCTCGAACTTCCAAAAA-TCCTATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCC
1 CCCTCAAACTTCCAAAAATTCC-ATTTTT-ACCCC-GAACTTCCAAAAATCCCATTTTTGA-CCC
** *
44082 CGAACTTCCAAAAATTACCATTT-TG
62 AAAACTTCAAAAAATT-CCATTTATG
44107 CCC
1 CCC
44110 CCGTGTATCC
Statistics
Matches: 155, Mismatches: 12, Indels: 25
0.81 0.06 0.13
Matches are distributed among these distances:
87 3 0.02
88 57 0.37
89 86 0.55
90 9 0.06
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30
Consensus pattern (86 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCAAAA
CTTCAAAAAATTCCATTTATG
Found at i:44106 original size:59 final size:58
Alignment explanation
Indices: 43902--44105 Score: 291
Period size: 59 Copynumber: 3.4 Consensus size: 58
43892 CATTTTTGAA
* * *
43902 CCCGAAACTTCCAAAAAATTCATTTATGACCCCAAAACTTCCAAAAATTCCATTTTTACA
1 CCCG-AACTTCC-AAAAATCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACC
* * *
43962 CCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCAAAAAATTCCATTTTTGCC
1 CCCGAACTTCCAAAAAT-CCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACC
*
44021 CTCGAACTTCCAAAAATCCTATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACC
1 CCCGAACTTCCAAAAATCC-ATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACC
44080 CCCGAACTTCCAAAAATTACCATTTT
1 CCCGAACTTCCAAAAA-T-CCATTTT
44106 GCCCCCGTGT
Statistics
Matches: 129, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
58 8 0.06
59 109 0.84
60 10 0.08
61 2 0.02
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (58 bp):
CCCGAACTTCCAAAAATCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACC
Found at i:44110 original size:29 final size:29
Alignment explanation
Indices: 43847--44112 Score: 234
Period size: 29 Copynumber: 9.0 Consensus size: 29
43837 GAGGTCCCTA
* **
43847 AACTGTCCAAAAATTCCACTTTACCCCCCG
1 AACT-TCCAAAAATTCCATTTTTGCCCCCG
* * **
43877 AACTTCTAATAA-TCTCATTTTTGAACCCG
1 AACTTCCAAAAATTC-CATTTTTGCCCCCG
* **
43906 AAACTTCCAAAAAATT-CATTTATGACCCCAA
1 -AACTTCC-AAAAATTCCATTTTTG-CCCCCG
* *
43937 AACTTCCAAAAATTCCATTTTTACACCCG
1 AACTTCCAAAAATTCCATTTTTGCCCCCG
* ***
43966 AACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTTG-CCCCCG
* *
43996 AACTTCAAAAAATTCCATTTTTGCCCTCG
1 AACTTCCAAAAATTCCATTTTTGCCCCCG
**
44025 AACTTCCAAAAA-TCCTATTTTTGACCCCAA
1 AACTTCCAAAAATTCC-ATTTTTG-CCCCCG
*
44055 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTGCCCCCG
44084 AACTTCCAAAAATTACCA-TTTTGCCCCCG
1 AACTTCCAAAAATT-CCATTTTTGCCCCCG
44113 TGTATCCGAA
Statistics
Matches: 188, Mismatches: 37, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
28 5 0.03
29 96 0.51
30 77 0.41
31 9 0.05
32 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTGCCCCCG
Found at i:47184 original size:25 final size:23
Alignment explanation
Indices: 47156--47201 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
47146 GTTTGATCCA
47156 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
47181 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
47202 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:47656 original size:21 final size:22
Alignment explanation
Indices: 47613--47657 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
47603 AAATAGATAC
*
47613 AAAATATTTTTCATTATTGAAA
1 AAAATATTTTTCATTATTCAAA
*
47635 AAAATATTTTT-ATTTTTCAAA
1 AAAATATTTTTCATTATTCAAA
47656 AA
1 AA
47658 TGTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAATATTTTTCATTATTCAAA
Found at i:47658 original size:19 final size:18
Alignment explanation
Indices: 47634--47669 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
47624 CATTATTGAA
47634 AAAAATATTTTTATTTTTC
1 AAAAATATTTTT-TTTTTC
*
47653 AAAAATGTTTTTTTTTT
1 AAAAATATTTTTTTTTT
47670 AATTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
AAAAATATTTTTTTTTTC
Found at i:50123 original size:58 final size:56
Alignment explanation
Indices: 50037--50159 Score: 185
Period size: 58 Copynumber: 2.2 Consensus size: 56
50027 ATTTAGGTGT
* * *
50037 CAAATTAGACCAAAAAATTAGATATCAAATTATG-AAAAAATGTTAAGTTGAGGTAC
1 CAAATTAGACCAAAAAATTAGACATCAAATTA-GAAAAAAATATCAAGTTGAGGTAC
50093 CAAATTAGACCCAAAAAACTTAGACATCAAATTAGAAAAAAATATCAAGTTGAGGTAC
1 CAAATTAGA-CCAAAAAA-TTAGACATCAAATTAGAAAAAAATATCAAGTTGAGGTAC
50151 CAAATTAGA
1 CAAATTAGA
50160 TAAAATAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 9 0.15
57 9 0.15
58 43 0.70
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (56 bp):
CAAATTAGACCAAAAAATTAGACATCAAATTAGAAAAAAATATCAAGTTGAGGTAC
Found at i:50158 original size:31 final size:30
Alignment explanation
Indices: 50120--50227 Score: 81
Period size: 31 Copynumber: 3.3 Consensus size: 30
50110 ACTTAGACAT
50120 CAAATTAGAAAAAAATATCAAGTTGAGGTAC
1 CAAATTAGAAAAAAATATCAAGTT-AGGTAC
** *
50151 CAAATTAGATAAAATAAAATAAAAAAAGCTTATGTAC
1 CAAATTAG---AAA-AAAAT--ATCAAG-TTAGGTAC
* * *
50188 CAAATTAGAAAAAATTGTCAACTTAAGGTAC
1 CAAATTAGAAAAAAATATCAAGTT-AGGTAC
50219 CAAATTAGA
1 CAAATTAGA
50228 CAAATTTAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
30 2 0.03
31 24 0.40
33 4 0.07
34 6 0.10
35 5 0.08
37 17 0.28
38 2 0.03
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (30 bp):
CAAATTAGAAAAAAATATCAAGTTAGGTAC
Found at i:52841 original size:13 final size:13
Alignment explanation
Indices: 52806--52848 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
52796 TGCTTTTTAG
* *
52806 AAGTGCTTTTAAA
1 AAGTGATTTTGAA
52819 AAGTGATTTTGAA
1 AAGTGATTTTGAA
52832 AAGT-ATTTTTGAA
1 AAGTGA-TTTTGAA
52845 AAGT
1 AAGT
52849 TTGGTTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 1 0.04
13 26 0.96
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (13 bp):
AAGTGATTTTGAA
Found at i:55654 original size:17 final size:18
Alignment explanation
Indices: 55632--55668 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55622 GCTTGAAGAG
*
55632 ATTAATTTCA-AGTTTGC
1 ATTAATTTCACAATTTGC
55649 ATTAATTTCACAATTTGC
1 ATTAATTTCACAATTTGC
55667 AT
1 AT
55669 GAACCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (18 bp):
ATTAATTTCACAATTTGC
Found at i:58281 original size:30 final size:32
Alignment explanation
Indices: 58230--58291 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
58220 AATCTTGTGT
58230 TTTGTTCTCTAATGATTTAT-AAAAAATATTTA
1 TTTGTTCTCTAAT-ATTTATAAAAAAATATTTA
58262 TTTGTTCTCTAAT-TTTATAAAAAAATATTT
1 TTTGTTCTCTAATATTTATAAAAAAATATTT
58292 TAATTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 5 0.17
31 11 0.38
32 13 0.45
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTGTTCTCTAATATTTATAAAAAAATATTTA
Found at i:59239 original size:28 final size:28
Alignment explanation
Indices: 59203--59263 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
59193 TTACAAAATA
*
59203 TTAACACAATCATCAATATAAAATCATT
1 TTAAGACAATCATCAATATAAAATCATT
59231 TTAAGACAATCATCAATATAAAATCATT
1 TTAAGACAATCATCAATATAAAATCATT
59259 TTAAG
1 TTAAG
59264 TTCACATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (28 bp):
TTAAGACAATCATCAATATAAAATCATT
Found at i:68437 original size:20 final size:20
Alignment explanation
Indices: 68396--68437 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
68386 TCATTATTTC
* *
68396 ATTTAAATTCTTTATCATAA
1 ATTTAAATTCATTATCAAAA
68416 ATTTCAAATTCATTAT-AAAA
1 ATTT-AAATTCATTATCAAAA
68436 AT
1 AT
68438 GATATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAATTCATTATCAAAA
Found at i:78027 original size:18 final size:18
Alignment explanation
Indices: 78004--78039 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
77994 ACCTGAGAAT
78004 ACCATTTCGCGACCAAAC
1 ACCATTTCGCGACCAAAC
78022 ACCATTTCGCGACCAAAC
1 ACCATTTCGCGACCAAAC
78040 GCCCTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.39, G:0.11, T:0.17
Consensus pattern (18 bp):
ACCATTTCGCGACCAAAC
Found at i:78497 original size:24 final size:24
Alignment explanation
Indices: 78470--78516 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
78460 GTTAACTAAC
* *
78470 TGAGAAGGAACATGCTCAACTGTT
1 TGAGAAGAAACAGGCTCAACTGTT
* *
78494 TGAGACGAAATAGGCTCAACTGT
1 TGAGAAGAAACAGGCTCAACTGT
78517 CGAAGACGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (24 bp):
TGAGAAGAAACAGGCTCAACTGTT
Found at i:82744 original size:17 final size:17
Alignment explanation
Indices: 82722--82762 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
82712 AAGTGCAAAT
82722 AATATTTCTATTAAAAC
1 AATATTTCTATTAAAAC
82739 AATATTTCTATTAAAAC
1 AATATTTCTATTAAAAC
82756 AATATTT
1 AATATTT
82763 TAAGTGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTTCTATTAAAAC
Found at i:84474 original size:17 final size:17
Alignment explanation
Indices: 84444--84477 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
84434 CATGACCTGA
*
84444 CACATGGCCGTGTGGCT
1 CACATGGCCATGTGGCT
*
84461 CACATGGCTATGTGGCT
1 CACATGGCCATGTGGCT
84478 AACTCGTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (17 bp):
CACATGGCCATGTGGCT
Found at i:91628 original size:3 final size:3
Alignment explanation
Indices: 91620--91649 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
91610 CTTAAGAAAT
91620 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
91650 AAAGGCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:92016 original size:29 final size:29
Alignment explanation
Indices: 91970--92030 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
91960 AGTTTATAGT
*
91970 TTTATAATTTTTAAAGAAT-TAAATAACAA
1 TTTATAATTTTTAAAGAATCAAAAT-ACAA
* **
91999 TTTATTATTTTTTGAGAATCAAAATACAA
1 TTTATAATTTTTAAAGAATCAAAATACAA
92028 TTT
1 TTT
92031 TACCATGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTATAATTTTTAAAGAATCAAAATACAA
Found at i:102276 original size:24 final size:23
Alignment explanation
Indices: 102244--102357 Score: 72
Period size: 23 Copynumber: 4.7 Consensus size: 23
102234 TAATTTTTTA
102244 AAATTATAAAAATATAAACTATTT
1 AAATTATAAAAAT-TAAACTATTT
* *
102268 AAATGAT-AAAATTAAA-TTTTT
1 AAATTATAAAAATTAAACTATTT
* * *
102289 ACTATCATAAAAATTACAATTTAATTT
1 A-AATTATAAAAATTA-AA-CT-ATTT
*
102316 CGAACTTATAAAAATATAAACTATTT
1 --AAATTATAAAAAT-TAAACTATTT
*
102342 AAATAAT-AAAATTAAA
1 AAATTATAAAAATTAAA
102358 TTTTTACTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
21 5 0.07
22 12 0.17
23 17 0.24
24 13 0.19
26 5 0.07
27 4 0.06
28 11 0.16
29 3 0.04
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATTATAAAAATTAAACTATTT
Found at i:102298 original size:22 final size:22
Alignment explanation
Indices: 102233--102374 Score: 63
Period size: 22 Copynumber: 6.0 Consensus size: 22
102223 AAAATTCGAT
* * *
102233 TTAATTTTTTAAAATTATAAAAA
1 TTAAATTTTTACAATCAT-AAAA
* *
102256 TATAAACTATTTA-AATGATAAAA
1 T-TAAA-TTTTTACAATCATAAAA
*
102279 TTAAATTTTTACTATCATAAAAA
1 TTAAATTTTTACAATCAT-AAAA
* *
102302 TTACAATTTAATTTCGAACTTATAAAAA
1 TTA-AATTT--TTAC-AA-TCAT-AAAA
* *
102330 TATAAACTATTTA-AATAATAAAA
1 T-TAAA-TTTTTACAATCATAAAA
*
102353 TTAAATTTTTACTATCATAAAA
1 TTAAATTTTTACAATCATAAAA
102375 ATTACAGTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
21 10 0.11
22 20 0.22
23 18 0.20
24 16 0.17
25 7 0.08
26 3 0.03
27 3 0.03
28 11 0.12
29 4 0.04
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (22 bp):
TTAAATTTTTACAATCATAAAA
Found at i:102329 original size:74 final size:74
Alignment explanation
Indices: 102247--102395 Score: 280
Period size: 74 Copynumber: 2.0 Consensus size: 74
102237 TTTTTTAAAA
*
102247 TTATAAAAATATAAACTATTTAAATGATAAAATTAAATTTTTACTATCATAAAAATTACAATTTA
1 TTATAAAAATATAAACTATTTAAATAATAAAATTAAATTTTTACTATCATAAAAATTACAATTTA
102312 ATTTCGAAC
66 ATTTCGAAC
*
102321 TTATAAAAATATAAACTATTTAAATAATAAAATTAAATTTTTACTATCATAAAAATTACAGTTTA
1 TTATAAAAATATAAACTATTTAAATAATAAAATTAAATTTTTACTATCATAAAAATTACAATTTA
102386 ATTTCGAAC
66 ATTTCGAAC
102395 T
1 T
102396 CCTTAAACAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.40
Consensus pattern (74 bp):
TTATAAAAATATAAACTATTTAAATAATAAAATTAAATTTTTACTATCATAAAAATTACAATTTA
ATTTCGAAC
Found at i:103577 original size:30 final size:29
Alignment explanation
Indices: 103458--103828 Score: 332
Period size: 29 Copynumber: 12.8 Consensus size: 29
103448 AATCGAGGTT
*
103458 AAAAATGGAA-TTTTAGATA-TTCGGGGT-
1 AAAAATGGAATTTTTGGA-AGTTCGGGGTC
* *
103485 -AAAATGAAATTTTTGG-AGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAAG-TTCGGGGTC
* * * * *
103513 GAAAATAGAGTTTTTGGACA-TCCGGGGGC
1 AAAAATGGAATTTTTGGA-AGTTCGGGGTC
*
103542 AAAAATGGAATTTTTGGGAGTTACGGGGTC
1 AAAAATGGAATTTTTGGAAGTT-CGGGGTC
* * *
103572 GAAAATGAAACTTTTGGAAGTTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTCG-GGGTC
* * **
103601 AAAAATAGAATTTTTTGAAGTTTCGATGTC
1 AAAAATGGAATTTTTGGAAG-TTCGGGGTC
103631 AAAAATTGGAATTTTTGGAAGTTCGAGGGT-
1 AAAAA-TGGAATTTTTGGAAGTTCG-GGGTC
*
103661 AAAAATGGAATTTTTAGAAGTTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTCG-GGGTC
*
103690 AAAAATGGAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAG-TTCGGGGTC
*
103720 AAAAATGGAATTTTTTGAAGTTCGGGGT-
1 AAAAATGGAATTTTTGGAAGTTCGGGGTC
* * *
103748 AAAAATAGAATTTTTGTAAGGTTCGAGGTC
1 AAAAATGGAATTTTTGGAA-GTTCGGGGTC
* * *
103778 GAAAATGGAATTTTTGGGAGTACGGGGGT-
1 AAAAATGGAATTTTTGGAAGTTC-GGGGTC
103807 AAAAATGGAATTTTTGGAAGTT
1 AAAAATGGAATTTTTGGAAGTT
103829 TAGGGACCTT
Statistics
Matches: 277, Mismatches: 48, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.00
26 8 0.03
27 12 0.04
28 17 0.06
29 136 0.49
30 87 0.31
31 16 0.06
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGTC
Found at i:103821 original size:59 final size:57
Alignment explanation
Indices: 103457--103828 Score: 328
Period size: 59 Copynumber: 6.4 Consensus size: 57
103447 AAATCGAGGT
* * *
103457 TAAAAATGGAA-TTTTAGATA-TTCG-GGGT-AAAATGAAATTTTTGG-AGTTTCGAGG
1 TAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTGGAAG-TTCGGGG
* * * * * * *
103511 TCGAAAATAGAGTTTTTGGACA-TCCGGGGGCAAAAATGGAATTTTTGGGAGTTACGGGG
1 T-AAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTGGAAGTT-CGGGG
* * * * * **
103570 TCGAAAATGAAACTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTTGAAGTTTCGATG
1 T-AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAG-TTCGGGG
*
103629 TCAAAAATTGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTCGAGGG
1 T-AAAAA-TGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCG-GGG
* *
103689 TAAAAATGGAATTTTTGGAAGTTTTG-GGGTCAAAAATGGAATTTTTTGAAGTTCGGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTCGGGG
* * * * *
103747 TAAAAATAGAATTTTTGTAAGGTTCGA-GGTCGAAAATGGAATTTTTGGGAGTACGGGGG
1 TAAAAATGGAATTTTTGGAA-GTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTC-GGGG
103806 TAAAAATGGAATTTTTGGAAGTT
1 TAAAAATGGAATTTTTGGAAGTT
103829 TAGGGACCTT
Statistics
Matches: 264, Mismatches: 39, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
54 1 0.00
55 7 0.03
56 10 0.04
57 3 0.01
58 87 0.33
59 112 0.42
60 44 0.17
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (57 bp):
TAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCGGGG
Found at i:104896 original size:3 final size:3
Alignment explanation
Indices: 104879--104989 Score: 62
Period size: 3 Copynumber: 35.0 Consensus size: 3
104869 TTTCACTTTT
** * * *
104879 TTA TTCA TT- TTA TTA TTA ACA TTT TTA TTA ATA TTTA TTA ATA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * *
104925 TTTA TTA TTA ATA ATA TTA TTA TTTA TTAA ATA GTTA TTA TTA TTA TTAA
1 -TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA -TTA TTA TTA TTA TT-A
* *
104975 CTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA
104990 ATGCTACTTA
Statistics
Matches: 82, Mismatches: 18, Indels: 16
0.71 0.16 0.14
Matches are distributed among these distances:
2 2 0.02
3 63 0.77
4 17 0.21
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:104932 original size:16 final size:18
Alignment explanation
Indices: 104903--104989 Score: 88
Period size: 19 Copynumber: 4.7 Consensus size: 18
104893 ATTAACATTT
*
104903 TTATTAATATTTATTAATA
1 TTATTATTA-TTATTAATA
104922 TTA-T-TTATTATTAATA
1 TTATTATTATTATTAATA
*
104938 ATATTATTATTTATTAAATA
1 TTATTATTA-TTATT-AATA
104958 GTTATTATTATTATTAACTA
1 -TTATTATTATTATTAA-TA
*
104978 TTATTACTATTA
1 TTATTATTATTA
104990 ATGCTACTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
16 11 0.19
17 3 0.05
18 4 0.07
19 21 0.36
20 11 0.19
21 8 0.14
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (18 bp):
TTATTATTATTATTAATA
Found at i:104939 original size:19 final size:18
Alignment explanation
Indices: 104888--104991 Score: 86
Period size: 19 Copynumber: 5.6 Consensus size: 18
104878 TTTATTCATT
* * *
104888 TTATTATTAACATTTTTA
1 TTATTATTAATAATATTA
* *
104906 TTAATATTTATTAATATTA
1 TTATTA-TTAATAATATTA
104925 TTTATTATTAATAATATTA
1 -TTATTATTAATAATATTA
104944 TTATTTATT-A-AATAGTTA
1 TTA-TTATTAATAATA-TTA
*
104962 TTATTATTATTAACTATTA
1 TTATTATTAATAA-TATTA
*
104981 TTACTATTAAT
1 TTATTATTAAT
104992 GCTACTTATT
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
17 9 0.13
18 15 0.22
19 38 0.55
20 7 0.10
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (18 bp):
TTATTATTAATAATATTA
Found at i:104990 original size:16 final size:16
Alignment explanation
Indices: 104960--104990 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104950 ATTAAATAGT
*
104960 TATTATTATTATTAAC
1 TATTATTACTATTAAC
104976 TATTATTACTATTAA
1 TATTATTACTATTAA
104991 TGCTACTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTACTATTAAC
Found at i:105728 original size:17 final size:17
Alignment explanation
Indices: 105703--105773 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
105693 GACTTTTTAA
* **
105703 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
105720 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
* *
105737 TTAAATTTAAAACAAAT
1 TTAAATTTTAAATAAAT
*
105754 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
105772 TT
1 TT
105774 GAATCAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 35 0.78
18 10 0.22
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:105732 original size:6 final size:6
Alignment explanation
Indices: 105718--105764 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
105708 TTTTAAATCC
* **
105718 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
105764 A
1 A
105765 AATAAATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 26 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:105849 original size:2 final size:2
Alignment explanation
Indices: 105842--105872 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
105832 GGCTTCAATA
*
105842 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
105873 AATTTTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:110602 original size:2 final size:2
Alignment explanation
Indices: 110597--110621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
110587 TTTGTGTGTG
110597 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
110622 GAAGTTGGAT
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:116538 original size:8 final size:8
Alignment explanation
Indices: 116522--116563 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
116512 GATAGTAAAG
116522 TTATAATT
1 TTATAATT
*
116530 TTATCATT
1 TTATAATT
116538 TTAATAA-T
1 TT-ATAATT
*
116546 TTATATTT
1 TTATAATT
116554 TTATAATT
1 TTATAATT
116562 TT
1 TT
116564 TAAAAGGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 3 0.11
8 22 0.79
9 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATAATT
Found at i:116559 original size:15 final size:16
Alignment explanation
Indices: 116522--116562 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
116512 GATAGTAAAG
116522 TTATAATTTTATCATTT
1 TTATAA-TTTATCATTT
*
116539 TAATAATTTAT-ATTT
1 TTATAATTTATCATTT
116554 TTATAATTT
1 TTATAATTT
116563 TTAAAAGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATAATTTATCATTT
Done.