Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010407.1 Kokia drynarioides strain JFW-HI SEQ_125292, 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: 32293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:108 original size:17 final size:15
Alignment explanation
Indices: 70--111 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
60 AACACATTAC
70 CTTTCTTTCCTTCTT
1 CTTTCTTTCCTTCTT
*
85 GTTTCTTTCCTCTCCTT
1 CTTTCTTTCCT-T-CTT
102 CTTTCTTTCC
1 CTTTCTTTCC
112 CGTTTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 1 0.04
17 12 0.52
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:3735 original size:30 final size:30
Alignment explanation
Indices: 3701--3823 Score: 124
Period size: 30 Copynumber: 4.1 Consensus size: 30
3691 AAAAAGATCA
* *
3701 AGGGTTAAAAATTAAATTTTAGAAAGTTCG
1 AGGGTCAAAAATTAAATTTTAGAAAATTCG
* * *
3731 AGGGTGAAAAAATGAAATTTTAGAAAGTTCG
1 AGGGT-CAAAAATTAAATTTTAGAAAATTCG
3762 -GAGGTCAAAAA-TAAATTTTAGAAAATTCG
1 AG-GGTCAAAAATTAAATTTTAGAAAATTCG
* * * * *
3791 AGAGTCAAACATGAATTTTTAGAAAACTCG
1 AGGGTCAAAAATTAAATTTTAGAAAATTCG
3821 AGG
1 AGG
3824 TTAAATTTAA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
29 23 0.29
30 29 0.37
31 26 0.33
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (30 bp):
AGGGTCAAAAATTAAATTTTAGAAAATTCG
Found at i:3742 original size:31 final size:31
Alignment explanation
Indices: 3707--3794 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
3697 ATCAAGGGTT
3707 AAAAATTAAATTTTAGAAAGTTCGAG-GGTGA
1 AAAAATTAAATTTTAGAAAGTTCGAGAGGT-A
* *
3738 AAAAATGAAATTTTAGAAAGTTCG-GAGGTC
1 AAAAATTAAATTTTAGAAAGTTCGAGAGGTA
*
3768 AAAAA-TAAATTTTAGAAAATTCGAGAG
1 AAAAATTAAATTTTAGAAAGTTCGAGAG
3795 TCAAACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
29 16 0.31
30 9 0.18
31 26 0.51
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
AAAAATTAAATTTTAGAAAGTTCGAGAGGTA
Found at i:3781 original size:29 final size:29
Alignment explanation
Indices: 3707--3824 Score: 130
Period size: 29 Copynumber: 4.0 Consensus size: 29
3697 ATCAAGGGTT
* *
3707 AAAAATTAAATTTTAGAAAGTTCGAGGGTGA
1 AAAAATGAAATTTTAGAAAGTTCGA-GGT-C
3738 AAAAATGAAATTTTAGAAAGTTCGGAGGTC
1 AAAAATGAAATTTTAGAAAGTTC-GAGGTC
*
3768 AAAAAT-AAATTTTAGAAAATTCGAGAGTC
1 AAAAATGAAATTTTAGAAAGTTCGAG-GTC
* * **
3797 AAACATGAATTTTTAGAAAACTCGAGGT
1 AAAAATGAAATTTTAGAAAGTTCGAGGT
3825 TAAATTTAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
28 3 0.04
29 25 0.32
30 23 0.29
31 25 0.32
32 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (29 bp):
AAAAATGAAATTTTAGAAAGTTCGAGGTC
Found at i:5705 original size:118 final size:115
Alignment explanation
Indices: 5480--6024 Score: 472
Period size: 118 Copynumber: 4.7 Consensus size: 115
5470 TAGGATGATA
* * * * * * * *
5480 GCTTCAATCTACCCTATGATTGGGGTAAGAGAATGGTGTGTTTTCATTCTGCCCTCTAATTAGGG
1 GCTTCAATCTACCCCATGATTGGGGTAAGAG-ATTGTATGTCTTCAATCTGCCTTCTGATTAAGG
* *
5545 TAAAAGATTGGATTGTCTTTAATCTGACCTTTGATTAGGGTAAAAGATTGGAT
65 TAAAAGATTGG-TTGTCTTCAATCTG-CCTTTGATTAAGGTAAAAGATTGGAT
* * * * * *
5598 GTTTTAATCTGCCCCATGATCGGGGTAAGAGATTAGTTTGTCTTCAATCTACCTTCTGATTAAGG
1 GCTTCAATCTACCCCATGATTGGGGTAAGAGATT-GTATGTCTTCAATCTGCCTTCTGATTAAGG
* * *
5663 TAAGAGATTGGTGTGTCTTCAATCTTCCTTCTTATTAAGGTAAAAGATTGGAT
65 TAAAAGATTGGT-TGTCTTCAATCTGCCTT-TGATTAAGGTAAAAGATTGGAT
* *** * * * * *
5716 GCTTCAATCTACCTTC-TGATCAAGGTAAAAGATTGAATTATCTTAAATCTGCCTTCTAATTAAG
1 GCTTCAATCTACC-CCATGATTGGGGTAAGAGATTGTA-TGTCTTCAATCTGCCTTCTGATTAAG
* * *
5780 GTAAAAGATTGGATG-CTTCAATCTGCCTTCTGATCAAGGTAAAAGATTGAATT
64 GTAAAAGATTGGTTGTCTTCAATCTGCCTT-TGATTAAGGTAAAAGATTGGA-T
* * ** * * * * ***
5833 GTCTTCAATCTGCCTTC-TGATTAAGGTAAAAGATTGGATG-CTTCAATCTTCC-CCATGATCGG
1 G-CTTCAATCTACC-CCATGATTGGGGTAAGAGATTGTATGTCTTCAATCTGCCTTC-TGATTAA
* * *
5895 GGTAAGAGATTGAATTATCTTCAATCTGCCTTTTGATTAAGGTAAAAGATTGGAT
63 GGTAAAAGATTG-GTTGTCTTCAATCTGCC-TTTGATTAAGGTAAAAGATTGGAT
* *
5950 GCTTCAATCTACCCCATAATTGGGGTAAGAGATTAG-ATGTCTTCAATCTGCCTTTTGATTAAGG
1 GCTTCAATCTACCCCATGATTGGGGTAAGAGATT-GTATGTCTTCAATCTGCCTTCTGATTAAGG
*
6014 TAAAAAATTGG
65 TAAAAGATTGG
6025 ATGCTTTAAT
Statistics
Matches: 343, Mismatches: 69, Indels: 32
0.77 0.16 0.07
Matches are distributed among these distances:
115 2 0.01
116 84 0.24
117 42 0.12
118 212 0.62
119 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (115 bp):
GCTTCAATCTACCCCATGATTGGGGTAAGAGATTGTATGTCTTCAATCTGCCTTCTGATTAAGGT
AAAAGATTGGTTGTCTTCAATCTGCCTTTGATTAAGGTAAAAGATTGGAT
Found at i:6126 original size:78 final size:77
Alignment explanation
Indices: 5480--6136 Score: 543
Period size: 78 Copynumber: 8.4 Consensus size: 77
5470 TAGGATGATA
* * * * * * * * *
5480 GCTTCAATCTACCCTATGATTGGGGTAAGAGAATGGTGTGTTTTCATTCTGCCCTCTAATTAGGG
1 GCTTCAATCTACCCCATGATCGGGGTAAGAGATTGG-ATGTCTTCAATCTGCCTTCTGATTAAGG
5545 TAAAAGATTGGATT
65 TAAAAGATTGGA-T
* ** ** * * * ***
5559 GTCTTTAATCTGA-CCTTTGATTAGGGTAAAAGATTGGATGT-TTTAATCTGCC-CCATGATCGG
1 G-CTTCAATCT-ACCCCATGATCGGGGTAAGAGATTGGATGTCTTCAATCTGCCTTC-TGATTAA
* **
5621 GGTAAGAGATTAGTTT
63 GGTAAAAGATT-GGAT
* *** * * *
5637 GTCTTCAATCTACCTTC-TGATTAAGGTAAGAGATTGGTGTGTCTTCAATCTTCCTTCTTATTAA
1 G-CTTCAATCTACC-CCATGATCGGGGTAAGAGATTGG-ATGTCTTCAATCTGCCTTCTGATTAA
5701 GGTAAAAGATTGGAT
63 GGTAAAAGATTGGAT
* ** * * * * *
5716 GCTTCAATCTACCTTC-TGATCAAGGTAAAAGATTGAATTATCTTAAATCTGCCTTCTAATTAAG
1 GCTTCAATCTACC-CCATGATCGGGGTAAGAGATTGGA-TGTCTTCAATCTGCCTTCTGATTAAG
5780 GTAAAAGATTGGAT
64 GTAAAAGATTGGAT
* * ** * *
5794 GCTTCAATCTGCCTTC-TGATCAAGGTAAAAGATTGAATTGTCTTCAATCTGCCTTCTGATTAAG
1 GCTTCAATCTACC-CCATGATCGGGGTAAGAGATTGGA-TGTCTTCAATCTGCCTTCTGATTAAG
5858 GTAAAAGATTGGAT
64 GTAAAAGATTGGAT
* * * *
5872 GCTTCAATCTTCCCCATGATCGGGGTAAGAGATTGAATTATCTTCAATCTGCCTTTTGATTAAGG
1 GCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGA-TGTCTTCAATCTGCCTTCTGATTAAGG
5937 TAAAAGATTGGAT
65 TAAAAGATTGGAT
* * * *
5950 GCTTCAATCTACCCCATAATTGGGGTAAGAGATTAGATGTCTTCAATCTGCCTTTTGATTAAGGT
1 GCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGTCTTCAATCTGCCTTCTGATTAAGGT
*
6015 AAAAAATTGGAT
66 AAAAGATTGGAT
* * * ** ** * * *
6027 GCTTTAATCTATCCCATGATCGGGGAAAGAGATTGGCGGTCTTTGATCTACCCTCTGATTAGGGT
1 GCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGTCTTCAATCTGCCTTCTGATTAAGGT
*
6092 AAGAGATCTGGAT
66 AAAAGAT-TGGAT
* *
6105 GCTTCAATCTGCCCCATGATCGAGGTAAGAGA
1 GCTTCAATCTACCCCATGATCGGGGTAAGAGA
6137 CCTACAAAAT
Statistics
Matches: 488, Mismatches: 78, Indels: 25
0.83 0.13 0.04
Matches are distributed among these distances:
77 97 0.20
78 328 0.67
79 11 0.02
80 50 0.10
81 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (77 bp):
GCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGTCTTCAATCTGCCTTCTGATTAAGGT
AAAAGATTGGAT
Found at i:11254 original size:23 final size:23
Alignment explanation
Indices: 11224--11271 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
11214 AGTTTACTTC
11224 GTATGAGTTTGGACCGATCAACA
1 GTATGAGTTTGGACCGATCAACA
11247 GTATGAGTTTGGACCGATCAACA
1 GTATGAGTTTGGACCGATCAACA
11270 GT
1 GT
11272 GGTATCTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (23 bp):
GTATGAGTTTGGACCGATCAACA
Found at i:14518 original size:21 final size:21
Alignment explanation
Indices: 14494--14535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14484 TTCTAGCTCC
14494 ACTATTCT-AGCTTCTAATTCA
1 ACTATT-TGAGCTTCTAATTCA
*
14515 ACTATTTGAGCTTTTAATTCA
1 ACTATTTGAGCTTCTAATTCA
14536 GCCTTCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (21 bp):
ACTATTTGAGCTTCTAATTCA
Found at i:17823 original size:16 final size:16
Alignment explanation
Indices: 17802--17836 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
17792 GAAAGATAAT
*
17802 AAAAAAACAA-AAAAC
1 AAAAAAAAAACAAAAC
17817 AAAAAAAAAACAAAAC
1 AAAAAAAAAACAAAAC
17833 AAAA
1 AAAA
17837 CAAAGGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAAC
Found at i:18150 original size:30 final size:29
Alignment explanation
Indices: 18067--18272 Score: 161
Period size: 30 Copynumber: 6.9 Consensus size: 29
18057 AAGGAAAATG
* *
18067 AGGGT-AAAATAAAAATTTTAGAAAGTTTT
1 AGGGTCAAAATGAAATTTTTAGAAAG-TTT
* *
18096 AGGGGCTAAAAT-ATAATTTTTTTAGAGAGTTT
1 AGGGTC-AAAATGA-AA--TTTTTAGAAAGTTT
18128 AGGAGTCAAAATGAAATTTTTAGAAAGTTT
1 AGG-GTCAAAATGAAATTTTTAGAAAGTTT
* * * * *
18158 AGGGGTCAAAATGAAACTTCTAAAAACATTG
1 A-GGGTCAAAATGAAATTTTTAGAAA-GTTT
* *
18189 GGGGTTAAAAATGAAA-TTTTAGAAAGTTT
1 AGGG-TCAAAATGAAATTTTTAGAAAGTTT
18218 GAGGGTCAAAAATGAAA-TTTTAGAAAGTTT
1 -AGGGTC-AAAATGAAATTTTTAGAAAGTTT
*
18248 AAGGGCCAAAATG-AATTTTTAGAAA
1 -AGGGTCAAAATGAAATTTTTAGAAA
18273 ACTCGAGGTT
Statistics
Matches: 144, Mismatches: 20, Indels: 26
0.76 0.11 0.14
Matches are distributed among these distances:
28 2 0.01
29 22 0.15
30 74 0.51
31 21 0.15
32 13 0.09
33 12 0.08
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (29 bp):
AGGGTCAAAATGAAATTTTTAGAAAGTTT
Found at i:21094 original size:16 final size:17
Alignment explanation
Indices: 21064--21098 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
21054 AAAACAACAT
*
21064 AAATATAATAGATATGA
1 AAATATAATAAATATGA
21081 AAATA-AATAAATATGA
1 AAATATAATAAATATGA
21097 AA
1 AA
21099 TAAGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AAATATAATAAATATGA
Found at i:21970 original size:51 final size:51
Alignment explanation
Indices: 21758--22132 Score: 155
Period size: 51 Copynumber: 7.5 Consensus size: 51
21748 AAAAACTTTG
* *
21758 TTTAAAAATGTAAA-TTTTTCTTTAAAATGACTAAAAAAACATATTTTTATTT
1 TTTAAAAATCTAAATTTTTTCTTTAAAATGA-TTAAAAAACATATTTTTA-TT
* * **
21810 TTTAAAAATCTAAACTTCTTTTTTTTTTAAATGA--AAATCAC-TA-TTTTA--
1 TTTAAAAATCTAAA--T-TTTTTCTTTAAAATGATTAAAAAACATATTTTTATT
* * * * ** *
21858 CTTAAAAAT-TCAAA-TTTTTATTTCAAA-GTAGTTAAAAAAAAATCAAAGTTT-TG
1 TTTAAAAATCT-AAATTTTTTCTTTAAAATG-A-TT-AAAAAACAT--ATTTTTATT
*
21911 TTTAAAAATTTAAATTTTTTCTTTAAAATGATTAAAAAACATATTTTTATT
1 TTTAAAAATCTAAATTTTTTCTTTAAAATGATTAAAAAACATATTTTTATT
* * ** *
21962 TTTAAAAATCTAAACTTTCTCTTT--TTTGA--AGAAAATCACTA-TTTTA--
1 TTTAAAAATCTAAATTTTTTCTTTAAAATGATTA-AAAAACA-TATTTTTATT
* * ** *** *
22008 CTTAAAAATCCAAATTTTTAT-TTCGAAAT-AGTTAAAAAA-ATAAAACTT-TG
1 TTTAAAAATCTAAATTTTT-TCTTTAAAATGA-TTAAAAAACAT-ATTTTTATT
* * * * *
22058 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACCATATTTTTATT
1 TTTAAAAATCTAAATTTTTTCTTTAAAATGATTAAAAAACATATTTTTATT
*
22109 TTTAAAAATCTAATTTTTTTCTTT
1 TTTAAAAATCTAAATTTTTTCTTT
22133 TTTAAAGAAA
Statistics
Matches: 237, Mismatches: 50, Indels: 73
0.66 0.14 0.20
Matches are distributed among these distances:
43 1 0.00
44 12 0.05
46 17 0.07
47 5 0.02
48 29 0.12
49 13 0.05
50 35 0.15
51 53 0.22
52 26 0.11
53 18 0.08
54 13 0.05
55 1 0.00
56 14 0.06
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (51 bp):
TTTAAAAATCTAAATTTTTTCTTTAAAATGATTAAAAAACATATTTTTATT
Found at i:22101 original size:147 final size:146
Alignment explanation
Indices: 21676--22204 Score: 679
Period size: 147 Copynumber: 3.5 Consensus size: 146
21666 AAATCAAAAG
* * * *
21676 TTTTCTTTTAATTAAAACAAAATCATTATATTACTTCAAAATCAAAACTTTTATTTCGAAATAGT
1 TTTTCTTTT--TT-AAAGAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGT
* *
21741 TTAAAAAA-AAAACTTTGTTTAAAAATGTAAATTTTTCTTTAAAATGACTAAAAAAACATATTTT
63 TAAAAAAATAAAACTTTGTTTAAAAATTTAAATTTTTCTTTAAAATGACT-AAAAAACATATTTT
21805 TATTTTTTAAAAATCTAAACT
127 TA-TTTTTAAAAATCTAAACT
* *
21826 TCTTTTTTTTTTAAATGAAAATCACTATTTTACTTAAAAATTC-AAATTTTTATTTC-AAAGTAG
1 T-TTTCTTTTTTAAA-GAAAATCACTATTTTACTTAAAAA-TCAAAACTTTTATTTCGAAA-TAG
** *
21889 TTAAAAAAAAATCAAAGTTTTGTTTAAAAATTTAAATTTTTTCTTTAAAATGATTAAAAAACATA
62 TT--AAAAAAAT-AAAACTTTGTTTAAAAATTTAAA-TTTTTCTTTAAAATGACTAAAAAACATA
21954 TTTTTATTTTTAAAAATCTAAACT
123 TTTTTATTTTTAAAAATCTAAACT
* * * *
21978 TTCTCTTTTTTGAAGAAAATCACTATTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAA
1 TTTTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAA
* *
22043 AAAAATAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACCATATTTTTAT
66 AAAAATAAAACTTTGTTTAAAAATTTAAA-TTTTTCTTTAAAATGACTAAAAAACATATTTTTAT
**
22108 TTTTAAAAATCTAATTT
130 TTTTAAAAATCTAAACT
* * *
22125 TTTTCTTTTTTAAAGAAAATCACTAATTTT-CCTAAAAATCAAAACTTTTATTTCGAGATTATTT
1 TTTTCTTTTTTAAAGAAAATCACT-ATTTTACTTAAAAATCAAAACTTTTATTTCGA-AATAGTT
*
22189 AAAAAAACAAAACTTT
64 AAAAAAATAAAACTTT
22205 TTCCAGAATT
Statistics
Matches: 336, Mismatches: 30, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
147 113 0.34
148 39 0.12
149 41 0.12
150 45 0.13
151 26 0.08
152 19 0.06
153 36 0.11
154 17 0.05
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (146 bp):
TTTTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAA
AAAAATAAAACTTTGTTTAAAAATTTAAATTTTTCTTTAAAATGACTAAAAAACATATTTTTATT
TTTAAAAATCTAAACT
Found at i:22621 original size:3 final size:3
Alignment explanation
Indices: 22613--22648 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
22603 CCATGAAACT
22613 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22649 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23178 original size:18 final size:18
Alignment explanation
Indices: 23130--23180 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
23120 TTGGTATAAA
*
23130 AATTACCCAAATTAACTG
1 AATTACACAAATTAACTG
*
23148 AATTA-ACCGAATTAA-TCG
1 AATTACA-CAAATTAACT-G
23166 AATTACACAAATTAA
1 AATTACACAAATTAA
23181 AGTATTGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (18 bp):
AATTACACAAATTAACTG
Found at i:26771 original size:16 final size:16
Alignment explanation
Indices: 26731--26771 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
26721 TTGGGTTTAT
26731 ATTAGGTTTATATTAG
1 ATTAGGTTTATATTAG
26747 ATT-GAGTTTATATT-G
1 ATTAG-GTTTATATTAG
26762 AATTAGGTTT
1 -ATTAGGTTT
26772 GGATGGATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (16 bp):
ATTAGGTTTATATTAG
Found at i:28140 original size:21 final size:22
Alignment explanation
Indices: 28114--28175 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
28104 TTTTTTAGTT
28114 TAATTAGGGTTTAGGGTTTTAA
1 TAATTAGGGTTTAGGGTTTTAA
* ***
28136 -AATTAGGATTTATATTTTTAA
1 TAATTAGGGTTTAGGGTTTTAA
*
28157 TTATTAGGGTTTAAGGGTT
1 TAATTAGGGTTT-AGGGTT
28176 CAGAAAAATT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
21 17 0.59
22 9 0.31
23 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (22 bp):
TAATTAGGGTTTAGGGTTTTAA
Found at i:30061 original size:18 final size:18
Alignment explanation
Indices: 30019--30061 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
30009 AAAAATTATA
*
30019 AAAAATATTAATTAAAATT
1 AAAAA-ATTAAATAAAATT
* *
30038 ATAAAATTAAATAATATT
1 AAAAAATTAAATAAAATT
30056 AAAAAA
1 AAAAAA
30062 AAAAATTAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATTAAATAAAATT
Found at i:30240 original size:22 final size:22
Alignment explanation
Indices: 30215--30260 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
30205 AATTGTGTGT
30215 AATTTAAAGAGAAATTAAGTGA
1 AATTTAAAGAGAAATTAAGTGA
* *
30237 AATTTAGAGAGAAATTTAGTGA
1 AATTTAAAGAGAAATTAAGTGA
30259 AA
1 AA
30261 CTTGTGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (22 bp):
AATTTAAAGAGAAATTAAGTGA
Found at i:30252 original size:12 final size:12
Alignment explanation
Indices: 30188--30255 Score: 52
Period size: 12 Copynumber: 5.9 Consensus size: 12
30178 AAGGAACTTT
*
30188 GAGAGATTTAGA
1 GAGAAATTTAGA
* *
30200 GAGAAAATT-GT
1 GAGAAATTTAGA
* * *
30211 GTGTAATTTAAA
1 GAGAAATTTAGA
30223 GAGAAA-TTA-A
1 GAGAAATTTAGA
*
30233 GTGAAATTTAGA
1 GAGAAATTTAGA
30245 GAGAAATTTAG
1 GAGAAATTTAG
30256 TGAAACTTGT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
10 6 0.15
11 13 0.32
12 22 0.54
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (12 bp):
GAGAAATTTAGA
Found at i:31299 original size:4 final size:4
Alignment explanation
Indices: 31290--31376 Score: 77
Period size: 4 Copynumber: 21.2 Consensus size: 4
31280 AAATAAACGG
* * *
31290 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
** * *
31340 GAAA GAGG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
31377 GTAATATATT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
3 3 0.04
4 55 0.80
5 11 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:31312 original size:17 final size:17
Alignment explanation
Indices: 31290--31376 Score: 99
Period size: 17 Copynumber: 5.3 Consensus size: 17
31280 AAATAAACGG
31290 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
31307 GAAAGAAAGAAA-GAAA
1 GAAAGAAAGAAAGGAAA
* * *
31323 GGAAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
** *
31340 GAAAGAGGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
31357 GAAAG-AAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
31372 GAAAG
1 GAAAG
31377 GTAATATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
15 11 0.18
16 14 0.23
17 36 0.59
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:31316 original size:21 final size:21
Alignment explanation
Indices: 31290--31376 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 21
31280 AAATAAACGG
31290 GAAAGAAAGAAAGGA-AAGAAA
1 GAAAGAAAG-AAGGAGAAGAAA
*
31311 GAAAGAAAGAAAGGAAGAAGGAGAG
1 GAAAGAAAG-AAGG-AGAA-GA-AA
* *
31336 GAAAGAAAGAGGGAGAGGAAA
1 GAAAGAAAGAAGGAGAAGAAA
31357 GAAAG-AAGAAGGA-AAGAAA
1 GAAAGAAAGAAGGAGAAGAAA
31376 G
1 G
31377 GTAATATATT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
19 6 0.11
20 7 0.12
21 20 0.36
22 3 0.05
23 5 0.09
24 5 0.09
25 10 0.18
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAGGAGAAGAAA
Done.