Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009151.1 Kokia drynarioides strain JFW-HI SEQ_123855, 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: 78450
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:223 original size:19 final size:20
Alignment explanation
Indices: 194--235 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
184 TTTTAGAATT
*
194 TTTGGGTATTTTTTTTTTAA
1 TTTGGGTATTTTTTTTGTAA
214 TTTGGG-ATTTTTTTTGTAA
1 TTTGGGTATTTTTTTTGTAA
233 TTT
1 TTT
236 TATAGGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (20 bp):
TTTGGGTATTTTTTTTGTAA
Found at i:2025 original size:18 final size:17
Alignment explanation
Indices: 1994--2034 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1984 TAGTTCAAAA
1994 TTATA-ATTTTTTTTAT
1 TTATATATTTTTTTTAT
2010 TTATATATTTTATTTTAT
1 TTATATATTTT-TTTTAT
*
2028 TTCTATA
1 TTATATA
2035 CGCAATAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.23
17 5 0.23
18 12 0.55
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATATTTTTTTTAT
Found at i:11437 original size:14 final size:14
Alignment explanation
Indices: 11418--11444 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11408 ATTCTCTCTT
11418 AGATGAAAATGCTG
1 AGATGAAAATGCTG
11432 AGATGAAAATGCT
1 AGATGAAAATGCT
11445 TTTAGAAGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (14 bp):
AGATGAAAATGCTG
Found at i:25625 original size:17 final size:17
Alignment explanation
Indices: 25603--25635 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25593 TCATGTCAAT
25603 TTTTTATTTTTATGAAC
1 TTTTTATTTTTATGAAC
*
25620 TTTTTATTTTTTTGAA
1 TTTTTATTTTTATGAA
25636 TTTGAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTTTATTTTTATGAAC
Found at i:29944 original size:7 final size:7
Alignment explanation
Indices: 29914--29945 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
29904 TATAAGATCC
*
29914 TTTTCTC
1 TTTTCTT
29921 TTTTCTT
1 TTTTCTT
29928 TTTTCTT
1 TTTTCTT
29935 TTTTCTT
1 TTTTCTT
29942 TTTT
1 TTTT
29946 GCAGTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:35707 original size:15 final size:15
Alignment explanation
Indices: 35677--35764 Score: 62
Period size: 16 Copynumber: 6.1 Consensus size: 15
35667 ATAATTTTTA
*
35677 TTATTAATAAATATTT
1 TTATTAAT-TATATTT
35693 TTATTAATTATATTT
1 TTATTAATTATATTT
*
35708 TAATTAA-TA-A-TT
1 TTATTAATTATATTT
*
35720 TTATAAATTATCATTT
1 TTATTAATTAT-ATTT
*
35736 TAATTAA-TA-A-TT
1 TTATTAATTATATTT
*
35748 TTATAAATTATCATTT
1 TTATTAATTAT-ATTT
35764 T
1 T
35765 AATTTATAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
12 14 0.25
13 6 0.11
14 2 0.04
15 16 0.29
16 18 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTAATTATATTT
Found at i:35721 original size:28 final size:28
Alignment explanation
Indices: 35680--35778 Score: 155
Period size: 28 Copynumber: 3.6 Consensus size: 28
35670 ATTTTTATTA
* * *
35680 TTAATAAATATTTTTATTAATTAT-ATT
1 TTAATTAATAATTTTATAAATTATCATT
35707 TTAATTAATAATTTTATAAATTATCATT
1 TTAATTAATAATTTTATAAATTATCATT
35735 TTAATTAATAATTTTATAAATTATCATT
1 TTAATTAATAATTTTATAAATTATCATT
*
35763 TTAATTTATAATTTTA
1 TTAATTAATAATTTTA
35779 CTTGATCACA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
27 21 0.31
28 46 0.69
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAATTAATAATTTTATAAATTATCATT
Found at i:35722 original size:13 final size:13
Alignment explanation
Indices: 35680--35778 Score: 60
Period size: 15 Copynumber: 7.2 Consensus size: 13
35670 ATTTTTATTA
*
35680 TTAATAAAT-ATT
1 TTAATTAATAATT
*
35692 TTTATTAATTATATT
1 TTAATTAA-TA-ATT
35707 TTAATTAATAATTT
1 TTAATTAATAA-TT
*
35721 TATAAATT-ATCATT
1 T-T-AATTAATAATT
35735 TTAATTAATAATTT
1 TTAATTAATAA-TT
*
35749 TATAAATT-ATCATT
1 T-T-AATTAATAATT
*
35763 TTAATTTATAATT
1 TTAATTAATAATT
35776 TTA
1 TTA
35779 CTTGATCACA
Statistics
Matches: 69, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
12 14 0.20
13 15 0.22
14 14 0.20
15 18 0.26
16 8 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAATTAATAATT
Found at i:37950 original size:21 final size:21
Alignment explanation
Indices: 37924--37975 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
37914 TGAGATAATA
37924 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
37945 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
37966 CTACCGATAC
1 CTACCGATAC
37976 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:42569 original size:18 final size:18
Alignment explanation
Indices: 42546--42585 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
42536 GTTAATATAA
*
42546 TTTA-TTTAATATTACAAT
1 TTTATTTTAATAATA-AAT
42564 TTTATTTTAATAATAAAT
1 TTTATTTTAATAATAAAT
42582 TTTA
1 TTTA
42586 ACAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATTTTAATAATAAAT
Found at i:42708 original size:13 final size:14
Alignment explanation
Indices: 42679--42708 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42669 ATTACAATTT
42679 ATAAATATTTGATA
1 ATAAATATTTGATA
42693 ATAAATATTT-ATA
1 ATAAATATTTGATA
42706 ATA
1 ATA
42709 TAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
ATAAATATTTGATA
Found at i:44148 original size:29 final size:30
Alignment explanation
Indices: 44092--44150 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
44082 TATCATCCAA
* **
44092 AACTCGTGCTTTTTGAACTATTACCAAAAG
1 AACTCGTGCTTTTTGAACCAAAACCAAAAG
*
44122 AACTCGTGC-TTTTGAACCAAAAGCAAAAG
1 AACTCGTGCTTTTTGAACCAAAACCAAAAG
44151 CTGTTAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (30 bp):
AACTCGTGCTTTTTGAACCAAAACCAAAAG
Found at i:52646 original size:3 final size:3
Alignment explanation
Indices: 52638--52681 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
52628 GTAATAAAAC
52638 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
52682 AGAGAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:52986 original size:19 final size:19
Alignment explanation
Indices: 52964--53023 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 19
52954 ACAAAAATAT
52964 TTCAAAATAATTTAAAAAA
1 TTCAAAATAATTTAAAAAA
*
52983 TTCAAAAT-ATTTATAAAA
1 TTCAAAATAATTTAAAAAA
53001 TTCTAAAATTTATATTTAAAAAA
1 TTC-AAAA--TA-ATTTAAAAAA
53024 AAACTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 12 0.35
19 12 0.35
21 1 0.03
23 9 0.26
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TTCAAAATAATTTAAAAAA
Found at i:53724 original size:21 final size:21
Alignment explanation
Indices: 53700--53743 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
53690 TTTCTCTTTC
* *
53700 GGGTTATAGATTTTGATTTTT
1 GGGTTATAGATTTTCAATTTT
*
53721 GGGTTTTAGATTTTCAATTTT
1 GGGTTATAGATTTTCAATTTT
53742 GG
1 GG
53744 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.02, G:0.25, T:0.55
Consensus pattern (21 bp):
GGGTTATAGATTTTCAATTTT
Found at i:53888 original size:30 final size:29
Alignment explanation
Indices: 53838--53894 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
53828 CCTTCAATAT
*
53838 TTTTATTTTACACTAATAATGATGTATCA
1 TTTTATTTTACACAAATAATGATGTATCA
*
53867 TTTTATTATTA-ACAAATTAATGGTGTAT
1 TTTTATT-TTACACAAA-TAATGATGTAT
53895 AAAACCTACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (29 bp):
TTTTATTTTACACAAATAATGATGTATCA
Found at i:65052 original size:18 final size:18
Alignment explanation
Indices: 65025--65067 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
65015 TTTAGAAATG
* *
65025 TTTTTGTCTCAAAAGAGT
1 TTTTTATCTCAAAAGAGC
*
65043 TTTTTATCTCAAAAGTGC
1 TTTTTATCTCAAAAGAGC
65061 TTTTTAT
1 TTTTTAT
65068 AAATAATGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (18 bp):
TTTTTATCTCAAAAGAGC
Found at i:65142 original size:18 final size:18
Alignment explanation
Indices: 65119--65153 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65109 TTCTCAGAAG
65119 CACTTTTGAGACAAAAAA
1 CACTTTTGAGACAAAAAA
*
65137 CACTTTTGAGATAAAAA
1 CACTTTTGAGACAAAAA
65154 CATTACTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (18 bp):
CACTTTTGAGACAAAAAA
Found at i:65844 original size:41 final size:41
Alignment explanation
Indices: 65787--65870 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
65777 TTTGTTTTGG
65787 TATTGTGAGTTACATTTTATTTTTCTATTATCTAAAAATTT
1 TATTGTGAGTTACATTTTATTTTTCTATTATCTAAAAATTT
65828 TATTGTGAGTTACATTTTATTTTTCTATTATCTAAAAATTT
1 TATTGTGAGTTACATTTTATTTTTCTATTATCTAAAAATTT
65869 TA
1 TA
65871 CGATGTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (41 bp):
TATTGTGAGTTACATTTTATTTTTCTATTATCTAAAAATTT
Found at i:68642 original size:15 final size:15
Alignment explanation
Indices: 68622--68651 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68612 AATTTCATGC
68622 TTCAATCACCATGTT
1 TTCAATCACCATGTT
68637 TTCAATCACCATGTT
1 TTCAATCACCATGTT
68652 ACATTTAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCAATCACCATGTT
Found at i:70853 original size:68 final size:68
Alignment explanation
Indices: 70744--70880 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
70734 TTAAGTTGAA
* *
70744 AATCCCTACCTGATTTTCAAAAATTGTGGAATTTGCCATCAGACCACTCCCACAATTCCCTTGTT
1 AATCCCTACCTGATTTTAAAAAATTGGGGAATTTGCCATCAGACCACTCCCACAATTCCCTTGTT
70809 TTT
66 TTT
*
70812 AATCCTTACCTGATTTTAAAAAATTGGGGAATTTGCCATCAGACCACTCCCACAATTCCCTTGTT
1 AATCCCTACCTGATTTTAAAAAATTGGGGAATTTGCCATCAGACCACTCCCACAATTCCCTTGTT
70877 TTT
66 TTT
70880 A
1 A
70881 CAAAATAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (68 bp):
AATCCCTACCTGATTTTAAAAAATTGGGGAATTTGCCATCAGACCACTCCCACAATTCCCTTGTT
TTT
Found at i:71060 original size:18 final size:19
Alignment explanation
Indices: 71034--71070 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
71024 TTCAATTATG
71034 ATTTGACCCAAAA-TATTT
1 ATTTGACCCAAAATTATTT
*
71052 ATTTTACCCAAAATTATTT
1 ATTTGACCCAAAATTATTT
71071 TTTCTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTTGACCCAAAATTATTT
Found at i:73478 original size:20 final size:19
Alignment explanation
Indices: 73441--73479 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
73431 CTCACATGTC
*
73441 AAAGTGAAAAATTGTTTTT
1 AAAGTGAAAAAGTGTTTTT
73460 AAAGTGAAAAAGTGATTTTT
1 AAAGTGAAAAAGTG-TTTTT
73480 GTGACCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (19 bp):
AAAGTGAAAAAGTGTTTTT
Found at i:73592 original size:46 final size:44
Alignment explanation
Indices: 73524--73624 Score: 148
Period size: 46 Copynumber: 2.2 Consensus size: 44
73514 AAAGGTGGAA
* * *
73524 GATGTGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATT
1 GATGTGATAGTATATCTACAAAAGTGGTGGCTTGTCCACAAT-TT
*
73569 GAATGTGGTAGTATATCTACAAAAGTGGTGGCTTGTCCACAATTT
1 G-ATGTGATAGTATATCTACAAAAGTGGTGGCTTGTCCACAATTT
73614 GATGTGATAGT
1 GATGTGATAGT
73625 TTGTCAGCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 9 0.18
45 4 0.08
46 37 0.74
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (44 bp):
GATGTGATAGTATATCTACAAAAGTGGTGGCTTGTCCACAATTT
Found at i:73762 original size:19 final size:20
Alignment explanation
Indices: 73721--73763 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
73711 GATGGGTAGG
* *
73721 ATTGTTTTAATAAAATTTTC
1 ATTGTTTTAATAAAATGTGC
*
73741 ATTGTTTT-ATGAAATGTGC
1 ATTGTTTTAATAAAATGTGC
73760 ATTG
1 ATTG
73764 ACTTGATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (20 bp):
ATTGTTTTAATAAAATGTGC
Found at i:75158 original size:15 final size:16
Alignment explanation
Indices: 75138--75167 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
75128 CATGCCTGCA
75138 AAGACAAAA-AGAAAT
1 AAGACAAAAGAGAAAT
75153 AAGACAAAAGAGAAA
1 AAGACAAAAGAGAAA
75168 AACAATAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.07, G:0.17, T:0.03
Consensus pattern (16 bp):
AAGACAAAAGAGAAAT
Found at i:75736 original size:20 final size:20
Alignment explanation
Indices: 75711--75773 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
75701 AGGCGGTGAA
75711 CGACGGTCGATTGGGAATAG
1 CGACGGTCGATTGGGAATAG
75731 CGACGGTCGATTGGGAATAG
1 CGACGGTCGATTGGGAATAG
* *
75751 CGACGGTCGATGGGGAACAG
1 CGACGGTCGATTGGGAATAG
75771 CGA
1 CGA
75774 TGGTGGCGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.41, T:0.16
Consensus pattern (20 bp):
CGACGGTCGATTGGGAATAG
Found at i:76240 original size:30 final size:30
Alignment explanation
Indices: 76195--76331 Score: 161
Period size: 29 Copynumber: 4.6 Consensus size: 30
76185 AAATTTTTTA
* * *
76195 AAAATAACATTTTGACCCTCGAACTTTTCC
1 AAAATTACATATTGACCCTCAAACTTTTCC
*
76225 AAAATTACATATTGACCCTCAAA-TTTTTC
1 AAAATTACATATTGACCCTCAAACTTTTCC
* * *
76254 AAAATTACACATTGACCCTTAAAC-TTTCT
1 AAAATTACATATTGACCCTCAAACTTTTCC
* *
76283 AAAATTACATATTAACCCTCAAATTTTTCC
1 AAAATTACATATTGACCCTCAAACTTTTCC
* *
76313 AAAATTACATTTTAACCCT
1 AAAATTACATATTGACCCT
76332 AAATGCTCCG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 49 0.54
30 42 0.46
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATATTGACCCTCAAACTTTTCC
Found at i:76261 original size:29 final size:29
Alignment explanation
Indices: 76181--76335 Score: 154
Period size: 29 Copynumber: 5.3 Consensus size: 29
76171 GCTAAGAGAT
* * *
76181 CCCT-AAATTTTTTAAAAATAACATTTTGA
1 CCCTCAAA-TTTTTCAAAATTACATATTGA
* *
76210 CCCTCGAACTTTTCCAAAATTACATATTGA
1 CCCTC-AAATTTTTCAAAATTACATATTGA
*
76240 CCCTCAAATTTTTCAAAATTACACATTGA
1 CCCTCAAATTTTTCAAAATTACATATTGA
* * *
76269 CCCTTAAA-CTTTCTAAAATTACATATTAA
1 CCCTCAAATTTTTC-AAAATTACATATTGA
* *
76298 CCCTCAAATTTTTCCAAAATTACATTTTAA
1 CCCTCAAATTTTT-CAAAATTACATATTGA
76328 CCCT-AAAT
1 CCCTCAAAT
76336 GCTCCGAGAC
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.04
29 56 0.53
30 43 0.41
31 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCTCAAATTTTTCAAAATTACATATTGA
Found at i:76279 original size:59 final size:59
Alignment explanation
Indices: 76181--76321 Score: 180
Period size: 58 Copynumber: 2.4 Consensus size: 59
76171 GCTAAGAGAT
* * * *
76181 CCCT-AAATTTTTTAAAAATA-ACATTTTGACCCTCGAACTTTTCCAAAATTACATATTGA
1 CCCTCAAATTTTTCAAAATTACACA-TTTGACCCTCAAAC-TTTCCAAAATTACATATTAA
* *
76240 CCCTCAAATTTTTCAAAATTACACA-TTGACCCTTAAACTTTCTAAAATTACATATTAA
1 CCCTCAAATTTTTCAAAATTACACATTTGACCCTCAAACTTTCCAAAATTACATATTAA
76298 CCCTCAAATTTTTCCAAAATTACA
1 CCCTCAAATTTTT-CAAAATTACA
76322 TTTTAACCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
58 31 0.42
59 25 0.34
60 14 0.19
61 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (59 bp):
CCCTCAAATTTTTCAAAATTACACATTTGACCCTCAAACTTTCCAAAATTACATATTAA
Found at i:76331 original size:59 final size:59
Alignment explanation
Indices: 76181--76331 Score: 189
Period size: 59 Copynumber: 2.6 Consensus size: 59
76171 GCTAAGAGAT
* * * *
76181 CCCT-AAATTTTTTAAAAATAACATTTTGACCCTCGAACTTTTCCAAAATTACATATTGA
1 CCCTCAAA-TTTTTCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATATTAA
** * *
76240 CCCTCAAATTTTTCAAAATTACACATTGACCCTTAAAC-TTTCTAAAATTACATATTAA
1 CCCTCAAATTTTTCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATATTAA
*
76298 CCCTCAAATTTTTCCAAAATTACATTTTAACCCT
1 CCCTCAAATTTTT-CAAAATTACATTTTGACCCT
76332 AAATGCTCCG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 31 0.39
59 45 0.57
60 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (59 bp):
CCCTCAAATTTTTCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATATTAA
Found at i:76474 original size:13 final size:15
Alignment explanation
Indices: 76443--76475 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
76433 TTAATCCTTT
76443 TTTTTGTATTCGATG
1 TTTTTGTATTCGATG
76458 TTTTTG-ATTCG-TG
1 TTTTTGTATTCGATG
76471 TTTTT
1 TTTTT
76476 CGTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 5 0.28
15 6 0.33
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (15 bp):
TTTTTGTATTCGATG
Done.