Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012834.1 Kokia drynarioides strain JFW-HI SEQ_127847, 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: 108200
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31 ATTTGAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:105 original size:12 final size:13
Alignment explanation
Indices: 90--118 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
80 TGTTTTTCCT
90 TTTTTATTTT-AA
1 TTTTTATTTTCAA
102 TTTTTATTTTCAA
1 TTTTTATTTTCAA
115 TTTT
1 TTTT
119 CCAATGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTCAA
Found at i:2162 original size:27 final size:26
Alignment explanation
Indices: 2116--2175 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
2106 TGCCTTTTTC
*
2116 ATTTTAATATTTTTGAATTTTTATGA
1 ATTTTAATATTTTTGAATTTATATGA
*
2142 ATTTTAATTTATTTTT-CATTTATATGA
1 ATTTTAA--TATTTTTGAATTTATATGA
*
2169 TTTTTAA
1 ATTTTAA
2176 CGTAACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 7 0.24
27 15 0.52
28 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTAATATTTTTGAATTTATATGA
Found at i:3073 original size:23 final size:23
Alignment explanation
Indices: 3022--3078 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
3012 CCTTTCTCTC
3022 AATTTTT-TATTTTAAAATCTTG
1 AATTTTTATATTTTAAAATCTTG
*
3044 ACTATTTTTATATTTTAAAA-CTTTT
1 A--ATTTTTATATTTTAAAATC-TTG
3069 AATTTTTATA
1 AATTTTTATA
3079 AAAATAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.03
23 9 0.30
24 7 0.23
25 13 0.43
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (23 bp):
AATTTTTATATTTTAAAATCTTG
Found at i:10850 original size:56 final size:56
Alignment explanation
Indices: 10780--10921 Score: 176
Period size: 56 Copynumber: 2.5 Consensus size: 56
10770 ATTTTTTGTA
* * * * * *
10780 ACTTAATTATGAAAAGTTAGAAAATGATCACTCAACTATTATTAAAATTATTGGTT
1 ACTTAATTAAGAAAAATTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTT
*
10836 ACTTAATTAAGAAAAATTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTC
1 ACTTAATTAAGAAAAATTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTT
*** * *
10892 ACCCGACTATGAAAAATTACAAAATGATCA
1 ACTTAATTAAGAAAAATTACAAAATGATCA
10922 TTCAATTATT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (56 bp):
ACTTAATTAAGAAAAATTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTT
Found at i:11786 original size:23 final size:23
Alignment explanation
Indices: 11760--11805 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
11750 AATTTTTGTA
*
11760 TTTAAAAATAAATAAATTAAATT
1 TTTAAAAATAAAAAAATTAAATT
11783 TTTAAAAATAAAAAAATTAAATT
1 TTTAAAAATAAAAAAATTAAATT
11806 CTAAACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TTTAAAAATAAAAAAATTAAATT
Found at i:11810 original size:22 final size:23
Alignment explanation
Indices: 11762--11819 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
11752 TTTTTGTATT
* *
11762 TAAAAATAAATAAATTAAATTTT
1 TAAAAATAAAAAAATTAAATTTC
11785 TAAAAATAAAAAAATTAAA-TTC
1 TAAAAATAAAAAAATTAAATTTC
**
11807 TAAACTTAAAAAA
1 TAAAAATAAAAAA
11820 TATATAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAAATAAAAAAATTAAATTTC
Found at i:19399 original size:5 final size:5
Alignment explanation
Indices: 19389--19423 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
19379 AGACACCACC
* *
19389 TGCTT TGCTT TGCTG TGCTG TGCTG TGCTG TGCTG
1 TGCTG TGCTG TGCTG TGCTG TGCTG TGCTG TGCTG
19424 AGCCTGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.20, G:0.34, T:0.46
Consensus pattern (5 bp):
TGCTG
Found at i:21503 original size:17 final size:18
Alignment explanation
Indices: 21481--21518 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
21471 AAAAGACTCG
21481 AGAAAAGCGAGGAAGA-A
1 AGAAAAGCGAGGAAGAGA
*
21498 AGAAAAGGGAGGAAGAGA
1 AGAAAAGCGAGGAAGAGA
21516 AGA
1 AGA
21519 GAAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (18 bp):
AGAAAAGCGAGGAAGAGA
Found at i:21626 original size:19 final size:19
Alignment explanation
Indices: 21570--21632 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
21560 TTAATTTTTA
21570 TTATTATTTTAAG-TTAA-
1 TTATTATTTTAAGTTTAAT
*
21587 TT-TTATCTTTAATTTTGTAAT
1 TTATTAT-TTTAA-GTT-TAAT
21608 TTATTATTTTAAGTTTAAT
1 TTATTATTTTAAGTTTAAT
*
21627 TAATTA
1 TTATTA
21633 GTAAAAGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 4 0.11
17 7 0.19
19 10 0.27
20 5 0.14
21 7 0.19
22 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATTATTTTAAGTTTAAT
Found at i:35878 original size:31 final size:31
Alignment explanation
Indices: 35833--35909 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
35823 TATATTGACT
* *
35833 TAAATAATCAATTAAA-CTTGGTAAAATAATAA
1 TAAA-AATCAATTAAATCCTAGTAAAATAAT-A
*
35865 TAAAAATAAATTAAATCCTAGTAAAATAATA
1 TAAAAATCAATTAAATCCTAGTAAAATAATA
*
35896 GAAAAATCAATTAA
1 TAAAAATCAATTAA
35910 GCCTTCCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 23 0.59
32 16 0.41
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (31 bp):
TAAAAATCAATTAAATCCTAGTAAAATAATA
Found at i:47522 original size:18 final size:18
Alignment explanation
Indices: 47495--47538 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
47485 CAGATGTGAA
47495 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
* **
47513 GGAAAGGAAGCGAGAGAT
1 GGAAAAGAAGAAAGAGAT
47531 GAGAAAAG
1 G-GAAAAG
47539 CACGACTGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.39, T:0.05
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:51527 original size:18 final size:18
Alignment explanation
Indices: 51504--51539 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51494 GCATCTAATA
*
51504 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAAATATT
51522 TTGTTCCTTGTAAATATT
1 TTGTTCCTTGTAAATATT
51540 CGGCATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (18 bp):
TTGTTCCTTGTAAATATT
Found at i:52251 original size:147 final size:147
Alignment explanation
Indices: 52020--52834 Score: 701
Period size: 147 Copynumber: 5.5 Consensus size: 147
52010 GTACCTTAGT
* * *
52020 GACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCTAGTACCACGAAGACATGAAGGGAAAGA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACGAAGACATGAAGGGAAAGA
* * * * * *
52085 TCCAAGCCGTAATGACGGATCTAGTATCACAAAGACACGAAAGGAAAGATTTAAGCCACCACGGC
66 TCTAAGCCGCAATGGCGGATCTAGTACCACAAAGACACGAAAGGAAAGATTTAAGCCGCAACGGC
*
52150 GAATCCAATACCACGAA
131 GAATCCAGTACCACGAA
* * * *
52167 GACACAAAGGGAAAGATTTAAGCCACAACGGCGAATCTAGTATCACGAAGACATGAAGGGAAAGA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACGAAGACATGAAGGGAAAGA
* * * * * *
52232 TCTAAGCCACAATGGCGGATCCAGTACCACAAAGACACGAAGGGAAAGATTTAAGTCGTAACGGT
66 TCTAAGCCGCAATGGCGGATCTAGTACCACAAAGACACGAAAGGAAAGATTTAAGCCGCAACGGC
**
52297 GAATTTAGTACCACGAA
131 GAATCCAGTACCACGAA
* * * *
52314 GACATGAAA-GGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATGAAGACATGAAGGGAAGG
1 GACAT-AAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACGAAGACATGAAGGGAAAG
* * * * ** * * * * ** * * * *
52378 GTTTAAGTCGTAACAGTGAACCTTGTACCTTAAAAACATGAAGGGAAAGATTTAAGTCGCAACGG
65 ATCTAAGCCGCAATGGCGGATCTAGTACCACAAAGACACGAAAGGAAAGATTTAAGCCGCAACGG
* *
52443 CAAATCTAGTACCACGAA
130 CGAATCCAGTACCACGAA
* * * *
52461 GACATAAAGGGAAAGATTTAAGCCGCAATGACGGATCTAGTACCACAAAGACATGAAGGGAAATA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACGAAGACATGAAGGGAAAGA
* * * * * * *
52526 TCTAAGCCGCAACGGCGGATCTAATACCGCAAAGATACAAAAGGGAAATATTTAAGCCGTAACGG
66 TCTAAGCCGCAATGGCGGATCTAGTACCACAAAGACACGAAA-GGAAAGATTTAAGCCGCAACGG
* *
52591 TGAATTCAGTACCAC-AA
130 CGAATCCAGTACCACGAA
* * * * * * * *
52608 CGAAATAAAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTA-TACCCTCAGAAG-CATGAAAGGA
1 -GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATC-TAGTA-CCAC-GAAGACATGAAGGGA
* * ** * **
52671 AAGATCTAAGCCGCAATGGTGGATCCAGTACCGTAAAGACA-TAAAGGGAAA-AGTTTAAGTTGC
62 AAGATCTAAGCCGCAATGGCGGATCTAGTACCACAAAGACACGAAA-GGAAAGA-TTTAAGCCGC
* *
52734 AACGACGAA-CCTAGTACCTCGGAA
125 AACGGCGAATCC-AGTACCAC-GAA
* * * * * * * * ** *
52758 -ACATGAAGGGAAATATTTAAGCTGTAACGGCGAATCCAGTACCATGAAGGCACAAAGGGAAAGG
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACGAAGACATGAAGGGAAAGA
* *
52822 TTTAAGTCGCAAT
66 TCTAAGCCGCAAT
52835 AGTGAATCTT
Statistics
Matches: 529, Mismatches: 126, Indels: 26
0.78 0.19 0.04
Matches are distributed among these distances:
146 7 0.01
147 346 0.65
148 123 0.23
149 48 0.09
150 5 0.01
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (147 bp):
GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACGAAGACATGAAGGGAAAGA
TCTAAGCCGCAATGGCGGATCTAGTACCACAAAGACACGAAAGGAAAGATTTAAGCCGCAACGGC
GAATCCAGTACCACGAA
Found at i:52590 original size:50 final size:49
Alignment explanation
Indices: 52020--52833 Score: 548
Period size: 49 Copynumber: 16.6 Consensus size: 49
52010 GTACCTTAGT
* * * *
52020 GACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCTAGTACCACGAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* ** * * * *
52069 GACATGAAGGGAAAGATCCAAGCCGTAATGACGGATCTAGTATCACAAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * * * * *
52118 GACACGAAA-GGAAAGATTTAAGCCACCACGGCGAATCCAATACCACGAA
1 GACA-TAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * * *
52167 GACACAAAGGGAAAGATTTAAGCCACAACGGCGAATCTAGTATCACGAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * * *
52216 GACATGAAGGGAAAGATCTAAGCCACAATGGCGGATCCAGTACCACAAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
** * * * * * *
52265 GACACGAAGGGAAAGATTTAAGTCGTAACGGTGAATTTAGTACCACGAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * **
52314 GACATGAAA-GGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATGAA
1 GACAT-AAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * * * * * * * * **
52363 GACATGAAGGGAAGGGTTTAAGTCGTAACAGTGAACCTTGTACCTTAAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * ** *
52412 AACATGAAGGGAAAGATTTAAGTCGCAACGGCAAATCTAGTACCACGAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* *
52461 GACATAAAGGGAAAGATTTAAGCCGCAATGACGGATCTAGTACCACAAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * * *
52510 GACATGAAGGGAAATATCTAAGCCGCAACGGCGGATCTAATACCGCAAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * * *
52559 GATACA-AAAGGGAAATATTTAAGCCGTAACGGTGAAT-TCAGTACCACAAC
1 G--ACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCT-AGTACCACAAA
* * * * * * *
52609 GAAATAAAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTA-TACCCTCAGAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATC-TAGTA-CCACA-AA
* * * * **
52660 G-CATGAAA-GGAAAGATCTAAGCCGCAATGGTGGATCCAGTACCGTAAA
1 GACAT-AAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
** * * * * *
52708 GACATAAAGGGAAA-AGTTTAAGTTGCAACGACGAACCTAGTACCTCGGAA
1 GACATAAAGGGAAAGA-TTTAAGCCGCAACGGCGGATCTAGTACCAC-AAA
* * * * * * **
52758 -ACATGAAGGGAAATATTTAAGCTGTAACGGCGAATCCAGTACCATGAA
1 GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
* * * *
52806 GGCACAAAGGGAAAGGTTTAAGTCGCAA
1 GACATAAAGGGAAAGATTTAAGCCGCAA
52834 TAGTGAATCT
Statistics
Matches: 597, Mismatches: 148, Indels: 40
0.76 0.19 0.05
Matches are distributed among these distances:
48 17 0.03
49 498 0.83
50 73 0.12
51 9 0.02
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (49 bp):
GACATAAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACAAA
Found at i:53324 original size:16 final size:17
Alignment explanation
Indices: 53291--53325 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
53281 GAATGTAATG
53291 AGCTGAACGATCGACGA
1 AGCTGAACGATCGACGA
*
53308 AGCTGAA-GATCGTCGA
1 AGCTGAACGATCGACGA
53324 AG
1 AG
53326 AATTGAGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.34, C:0.20, G:0.31, T:0.14
Consensus pattern (17 bp):
AGCTGAACGATCGACGA
Found at i:54107 original size:19 final size:19
Alignment explanation
Indices: 54083--54121 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
54073 ATTTATAATG
* *
54083 ATAATAATACTAGTAATAA
1 ATAATAATAATAATAATAA
*
54102 ATAATATTAATAATAATAA
1 ATAATAATAATAATAATAA
54121 A
1 A
54122 AAAGAAAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAATAATAATAATAATAA
Found at i:58147 original size:60 final size:60
Alignment explanation
Indices: 58078--58199 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
58068 AAATAAAAAT
*
58078 AATAAAAAGTTTTAGTTCAACTGTTTACTAATTTGATACTAATCTCTAGAAAGATAAACC
1 AATAAAAAGTTTTAGTTCAACTGTTTACTAATTCGATACTAATCTCTAGAAAGATAAACC
*
58138 AATAAAAAGTTTTAGTTCAACTGTTTACTAATTCGATACTAATCTCTAGAAAGATAACCC
1 AATAAAAAGTTTTAGTTCAACTGTTTACTAATTCGATACTAATCTCTAGAAAGATAAACC
58198 AA
1 AA
58200 CTAATTCTCG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (60 bp):
AATAAAAAGTTTTAGTTCAACTGTTTACTAATTCGATACTAATCTCTAGAAAGATAAACC
Found at i:74789 original size:13 final size:13
Alignment explanation
Indices: 74771--74798 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
74761 TCTTAAATAA
74771 TTTTTACAAAATT
1 TTTTTACAAAATT
74784 TTTTTACAAAATT
1 TTTTTACAAAATT
74797 TT
1 TT
74799 CAACATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTACAAAATT
Found at i:78850 original size:12 final size:12
Alignment explanation
Indices: 78835--78867 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
78825 CTATGTCGAC
78835 GACTATGACCAT
1 GACTATGACCAT
78847 GACTATGACCAT
1 GACTATGACCAT
78859 GACTATGAC
1 GACTATGAC
78868 TATGGACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (12 bp):
GACTATGACCAT
Found at i:78854 original size:6 final size:6
Alignment explanation
Indices: 78835--78871 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
78825 CTATGTCGAC
* *
78835 GACTAT GACCAT GACTAT GACCAT GACTAT GACTAT G
1 GACTAT GACTAT GACTAT GACTAT GACTAT GACTAT G
78872 GACACCATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (6 bp):
GACTAT
Found at i:78973 original size:2 final size:2
Alignment explanation
Indices: 78966--78994 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
78956 TTGGCTTCTG
78966 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
78995 TTCCCTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:80660 original size:397 final size:387
Alignment explanation
Indices: 79927--80705 Score: 1405
Period size: 397 Copynumber: 2.0 Consensus size: 387
79917 AGATTAAGTA
79927 TTTTTTTTAAAATGATACATGTGAAGTAAATTTGTTCATGGACCAGATTATTTATTTAAGTCCAA
1 TTTTTTTTAAAATGATACATGTGAAGTAAATTTGTTCATGGACCAGATTATTTATTTAAGTCCAA
79992 AAATATATCTTAAATATGGTCTTAGGTAAAAATAGTTAAGCTCATTTAAATGTGTCAAACTCAAA
66 AAATATATCTTAAATATGGTCTTAGGTAAAAATAGTTAAGCTCATTTAAATGTGTCAAACTCAAA
80057 CTTAAACATTTAAGGTTCAAGTTCAATTCAATCCGACTTGTTTTTTAAGTTTGTAATGTAAGGAT
131 CTTAAACATTTAAGGTTCAAGTTCAATTCAATCCGACTTGTTTTTTAAGTTTGTAATGTAAGGAT
* *
80122 GATTGAGTAAAATTTTAAATCCATATTTTGAGTCGAGTCAAATTTGGATAATCACAATGTATGTT
196 GATTGAGTAAAAATTTAAATCCATATTTTGAGTCGAGTCAAATTTGAATAATCACAATGTATGTT
* *
80187 AATATCATGTTTAAACTCAGATTGACTTGACTCGTGAATACCTTTAATATGGAACATTTGAACGA
261 AATATCATGTTTAAAATCAGATTGACTTGACTCGTGAATACCTTTAATATGAAACATTTGAACGA
80252 TGTGGAATTAAACTTTTTCAATGGTATTATGTCAAATACTAACTTTTTTTTTTTTTTTTTTT
326 TGTGGAATTAAACTTTTTCAATGGTATTATGTCAAATACTAACTTTTTTTTTTTTTTTTTTT
80314 NNNNNNNNNNTTTTTTTTAAAATGATACATGTGAAGTAAATTTGTTCATGGACCAGATTATTTAT
1 ----------TTTTTTTTAAAATGATACATGTGAAGTAAATTTGTTCATGGACCAGATTATTTAT
80379 TTAAGTCCAAAAATATATCTTAAATATGGTCTTAGGTAAAAATAGTTAAGCTCATTTAAATGTGT
56 TTAAGTCCAAAAATATATCTTAAATATGGTCTTAGGTAAAAATAGTTAAGCTCATTTAAATGTGT
80444 CAAACTCAAACTTAAACATTTAAGGTTCAAGTTCAATTCAATCCGACTTGTTTTTTAAGTTTGTA
121 CAAACTCAAACTTAAACATTTAAGGTTCAAGTTCAATTCAATCCGACTTGTTTTTTAAGTTTGTA
* *
80509 ATGTAAGGATGATTGAGTAAAAATTTAAATCTATATTTTTAGTCGAGTCAAATTTGAATAATCAC
186 ATGTAAGGATGATTGAGTAAAAATTTAAATCCATATTTTGAGTCGAGTCAAATTTGAATAATCAC
*
80574 AATGTATGTTAATATCATGTTTAAAATCAGTTTGACTTGACTCGTGAATACCTTTAATATGAAAC
251 AATGTATGTTAATATCATGTTTAAAATCAGATTGACTTGACTCGTGAATACCTTTAATATGAAAC
80639 ATTTGAACGATGTGGAATTAAACTTTTTCAATGGTATTATGTCAAATACTAACTTTTTTTTTTTT
316 ATTTGAACGATGTGGAATTAAACTTTTTCAATGGTATTATGTCAAATACTAACTTTTTTTTTTTT
80704 TT
381 TT
80706 AATTTTGCTA
Statistics
Matches: 375, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
397 375 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (387 bp):
TTTTTTTTAAAATGATACATGTGAAGTAAATTTGTTCATGGACCAGATTATTTATTTAAGTCCAA
AAATATATCTTAAATATGGTCTTAGGTAAAAATAGTTAAGCTCATTTAAATGTGTCAAACTCAAA
CTTAAACATTTAAGGTTCAAGTTCAATTCAATCCGACTTGTTTTTTAAGTTTGTAATGTAAGGAT
GATTGAGTAAAAATTTAAATCCATATTTTGAGTCGAGTCAAATTTGAATAATCACAATGTATGTT
AATATCATGTTTAAAATCAGATTGACTTGACTCGTGAATACCTTTAATATGAAACATTTGAACGA
TGTGGAATTAAACTTTTTCAATGGTATTATGTCAAATACTAACTTTTTTTTTTTTTTTTTTT
Found at i:82115 original size:14 final size:15
Alignment explanation
Indices: 82092--82125 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
82082 AATTGTCATG
82092 TATTTCTTTTT-TAA
1 TATTTCTTTTTCTAA
*
82106 TATTTGTTTTTCTAA
1 TATTTCTTTTTCTAA
82121 TATTT
1 TATTT
82126 TTCCATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTCTTTTTCTAA
Found at i:89986 original size:17 final size:17
Alignment explanation
Indices: 89964--89997 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
89954 CTCGTGTTTT
89964 GGGGGAAGATATGCCAC
1 GGGGGAAGATATGCCAC
89981 GGGGGAAGATATGCCAC
1 GGGGGAAGATATGCCAC
89998 AATAGCCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.41, T:0.12
Consensus pattern (17 bp):
GGGGGAAGATATGCCAC
Found at i:90995 original size:4 final size:4
Alignment explanation
Indices: 90986--91011 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
90976 CATTAACTCT
90986 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
91012 GAAGAAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:107141 original size:41 final size:38
Alignment explanation
Indices: 107040--107143 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
107030 TTTGAAGCAA
* * *
107040 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGATACCCAGTGTCTCATCGAACCTAGCCGAAG
* * ** * *
107077 TAAAATGGTACCCAATACCTCATCGAATCTATCCGAAG
1 TAAAATGATACCCAGTGTCTCATCGAACCTAGCCGAAG
107115 TAAAATAATGATACCCAGTGTCTCATCGA
1 T--AA-AATGATACCCAGTGTCTCATCGA
107144 CTCAAGGTTG
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 19 0.38
38 10 0.20
40 2 0.04
41 19 0.38
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (38 bp):
TAAAATGATACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:107269 original size:18 final size:18
Alignment explanation
Indices: 107246--107282 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
107236 ACAATTCATA
107246 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
107264 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
107282 T
1 T
107283 TGATCACAAA
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:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Done.