Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010686.1 Kokia drynarioides strain JFW-HI SEQ_125632, 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: 51302
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2592 original size:41 final size:41
Alignment explanation
Indices: 2535--2998 Score: 435
Period size: 41 Copynumber: 11.1 Consensus size: 41
2525 ATTCAGTCTT
* * *
2535 TTACCCTTAATCAAGAAGGTCAAATTGAAGATTCCAATCTC
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
* *
2576 TTACCCTTAATTAAGAAGGGCAGATTGAGGATTCCAATCTT
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
* * * * *
2617 TTACCCTTAATCAAAAAAGGCAGATTGAAGATTTCAGTCTC
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
* * * * * * *
2658 TTACCCTTAATAAAGAATGGTAGATTAAAGATTCTAATATT
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
* *
2699 TTACCCTTAATCAAGAAGGGCAGATTGATGATTCAAGATTCCAGTCTC
1 TTACCCTTAATTAAGAAGGGCAGA-T--TG----AAGATTCCAATCTC
* * *
2747 TTACCTTTAATTAAGAAGGGCA-ATTTGAAGATCCCAATCTT
1 TTACCCTTAATTAAGAAGGGCAGA-TTGAAGATTCCAATCTC
* * * *
2788 TTACCCTTAATTAAGAATGACAGATTGAATATTTCAATCTC
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
* * * * * *
2829 TTACCCTTAATTAAGAATGACAGATTGAAAATCCCAATTTT
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
* * * * * * * *
2870 TTACGCTTAATCAATAAAGGCAGATTAAAAATTTCAGTCTC
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
* * * * *
2911 TTACCCTTAATTAAAAAGGGCAAATTGAAGATTTCAGTCGC
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
*
2952 TTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCAATCTC
1 TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
2993 TTACCC
1 TTACCC
2999 CGATAATGGA
Statistics
Matches: 343, Mismatches: 72, Indels: 16
0.80 0.17 0.04
Matches are distributed among these distances:
41 305 0.89
42 2 0.01
44 1 0.00
45 2 0.01
47 3 0.01
48 30 0.09
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (41 bp):
TTACCCTTAATTAAGAAGGGCAGATTGAAGATTCCAATCTC
Found at i:2668 original size:82 final size:82
Alignment explanation
Indices: 2531--2998 Score: 499
Period size: 82 Copynumber: 5.6 Consensus size: 82
2521 CATCATTCAG
*
2531 TCTTTTACCCTTAATCAAG-AAGGTCAAATTGAAGATTCCAATCTCTTACCCTTAATTAAGAAGG
1 TCTTTTACCCTTAATCAAGAAAGG-CAGATTGAAGATTCCAATCTCTTACCCTTAATTAAGAAGG
*
2595 GCAGATTGAGGATTCCAA
65 GCAGATTGAAGATTCCAA
* * * * *
2613 TCTTTTACCCTTAATCAAAAAAGGCAGATTGAAGATTTCAGTCTCTTACCCTTAATAAAGAATGG
1 TCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTCCAATCTCTTACCCTTAATTAAGAAGGG
* * *
2678 TAGATTAAAGATTCTAA
66 CAGATTGAAGATTCCAA
* * * *
2695 TATTTTACCCTTAATCAAGAAGGGCAGATTGATGATTCAAGATTCCAGTCTCTTACCTTTAATTA
1 TCTTTTACCCTTAATCAAGAAAGGCAGA-T--TG----AAGATTCCAATCTCTTACCCTTAATTA
*
2760 AGAAGGGCA-ATTTGAAGATCCCAA
59 AGAAGGGCAGA-TTGAAGATTCCAA
* * * * * * *
2784 TCTTTTACCCTTAATTAAGAATGACAGATTGAATATTTCAATCTCTTACCCTTAATTAAGAATGA
1 TCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTCCAATCTCTTACCCTTAATTAAGAAGGG
* *
2849 CAGATTGAAAATCCCAA
66 CAGATTGAAGATTCCAA
* * * * * * * *
2866 TTTTTTACGCTTAATCAATAAAGGCAGATTAAAAATTTCAGTCTCTTACCCTTAATTAAAAAGGG
1 TCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTCCAATCTCTTACCCTTAATTAAGAAGGG
* * *
2931 CAAATTGAAGATTTCAG
66 CAGATTGAAGATTCCAA
** *
2948 TCGCTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCAATCTCTTACCC
1 TCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTCCAATCTCTTACCC
2999 CGATAATGGA
Statistics
Matches: 317, Mismatches: 59, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
82 240 0.76
83 6 0.02
85 2 0.01
86 2 0.01
88 2 0.01
89 65 0.21
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (82 bp):
TCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTCCAATCTCTTACCCTTAATTAAGAAGGG
CAGATTGAAGATTCCAA
Found at i:2814 original size:171 final size:164
Alignment explanation
Indices: 2533--2998 Score: 544
Period size: 171 Copynumber: 2.8 Consensus size: 164
2523 TCATTCAGTC
* * *
2533 TTTTACCCTTAATCAAG-AAGGTCAAATT-GAAGATTCCAATCTCTTACCCTTAATTAAGAAGGG
1 TTTTACCCTTAATCAAGAAAGG-CAGATTAAAAGATTCCAGTCTCTTACCCTTAATTAAGAAGGG
* * *
2596 CAGATTGAGGATTCCAATCTTTTACCCTTAATCAAAAAAGGCAGATTGAAGATTTCAGTCTCTTA
65 CA-ATTGAAGATTCCAATCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTTCAATCTCTTA
** * *
2661 CCCTTAATAAAGAATGGTAGATT-AAAGATTCTAATA
129 CCCTTAATAAAGAATGACAGATTGAAA-ATCCCAATA
* *
2697 TTTTACCCTTAATCAAGAAGGGCAGATTGATGATTCAAGATTCCAGTCTCTTACCTTTAATTAAG
1 TTTTACCCTTAATCAAGAAAGGCAGATT-A--A---AAGATTCCAGTCTCTTACCCTTAATTAAG
* * * * *
2762 AAGGGCAATTTGAAGATCCCAATCTTTTACCCTTAATTAAGAATGACAGATTGAATATTTCAATC
60 AAGGGCAA-TTGAAGATTCCAATCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTTCAATC
* *
2827 TCTTACCCTTAATTAAGAATGACAGATTGAAAATCCCAATT
124 TCTTACCCTTAATAAAGAATGACAGATTGAAAATCCCAATA
* * * *
2868 TTTTACGCTTAATCAATAAAGGCAGATTAAAA-ATTTCAGTCTCTTACCCTTAATTAAAAAGGGC
1 TTTTACCCTTAATCAAGAAAGGCAGATTAAAAGATTCCAGTCTCTTACCCTTAATTAAGAAGGGC
* * ** * *
2932 AAATTGAAGATTTCAGTCGCTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCAATCTCTTAC
66 -AATTGAAGATTCCAATCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTTCAATCTCTTAC
2997 CC
130 CC
2999 CGATAATGGA
Statistics
Matches: 256, Mismatches: 35, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
164 105 0.41
165 7 0.03
168 1 0.00
170 2 0.01
171 138 0.54
172 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (164 bp):
TTTTACCCTTAATCAAGAAAGGCAGATTAAAAGATTCCAGTCTCTTACCCTTAATTAAGAAGGGC
AATTGAAGATTCCAATCTTTTACCCTTAATCAAGAAAGGCAGATTGAAGATTTCAATCTCTTACC
CTTAATAAAGAATGACAGATTGAAAATCCCAATA
Found at i:9366 original size:15 final size:15
Alignment explanation
Indices: 9334--9367 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
9324 ACATTATATT
9334 TATTTCTAAAAAATA
1 TATTTCTAAAAAATA
9349 TATTTACTAATAAAATA
1 TATTT-CTAA-AAAATA
9366 TA
1 TA
9368 AAATCATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTTCTAAAAAATA
Found at i:10151 original size:39 final size:42
Alignment explanation
Indices: 10105--10199 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 42
10095 GTGAGTATGA
10105 TATTTCAAATA-T-T-TTTATATGTGAAATATTTCAATTAAT
1 TATTTCAAATATTATGTTTATATGTGAAATATTTCAATTAAT
10144 TATTTCAAATATCATTATGTTTATATGTGAAATATTTCAATTAAT
1 TATTTC-AA-AT-ATTATGTTTATATGTGAAATATTTCAATTAAT
10189 TATTTCAAATA
1 TATTTCAAATA
10200 CACATACAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
39 6 0.12
40 2 0.04
41 2 0.04
42 2 0.04
43 3 0.06
44 3 0.06
45 32 0.64
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.49
Consensus pattern (42 bp):
TATTTCAAATATTATGTTTATATGTGAAATATTTCAATTAAT
Found at i:14889 original size:5 final size:5
Alignment explanation
Indices: 14872--14930 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
14862 GGAACCAGGG
* **
14872 TTTCT TTTCCT TTTCT TTTTT TTTCTT TGTTCT TTGGT TTTC- TTTCT
1 TTTCT TTT-CT TTTCT TTTCT TTTC-T T-TTCT TTTCT TTTCT TTTCT
14919 TTTCT TTT-T TTT
1 TTTCT TTTCT TTT
14931 ATCTTGTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
4 8 0.18
5 24 0.55
6 9 0.20
7 3 0.07
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:20167 original size:2 final size:2
Alignment explanation
Indices: 20162--20197 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20152 TAAAAATAGA
20162 AT AT 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 AT AT
20198 TTGAACAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20231 original size:23 final size:21
Alignment explanation
Indices: 20205--20272 Score: 52
Period size: 23 Copynumber: 3.2 Consensus size: 21
20195 TATTTGAACA
20205 ATCTCATTATAGGTTTTAATCGT
1 ATCTCATTATA-GTTTTAATC-T
* * *
20228 ATCT-ACTATA-TTTGAA-CA
1 ATCTCATTATAGTTTTAATCT
20246 ATCTCATTATAAGTTTTAATCAT
1 ATCTCATTAT-AGTTTTAATC-T
20269 ATCT
1 ATCT
20273 ACTCTTTCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 6 0.18
21 5 0.15
22 6 0.18
23 8 0.24
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (21 bp):
ATCTCATTATAGTTTTAATCT
Found at i:20250 original size:41 final size:41
Alignment explanation
Indices: 20193--20275 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
20183 TATATATATA
* *
20193 TATATTTGAACAATCTCATTATAGGTTTTAATCGTATCTAC
1 TATATTTGAACAATCTCATTATAAGTTTTAATCATATCTAC
20234 TATATTTGAACAATCTCATTATAAGTTTTAATCATATCTAC
1 TATATTTGAACAATCTCATTATAAGTTTTAATCATATCTAC
20275 T
1 T
20276 CTTTCTGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (41 bp):
TATATTTGAACAATCTCATTATAAGTTTTAATCATATCTAC
Found at i:31957 original size:16 final size:16
Alignment explanation
Indices: 31935--31982 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
31925 ATAAATTTAA
31935 AAATAATGATAAAAAAT
1 AAATAAT-ATAAAAAAT
*
31952 -AATAATTTATTAAAAAT
1 AAATAA--TATAAAAAAT
31969 AAATAATATAAAAA
1 AAATAATATAAAAA
31983 TATTCAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 12 0.46
17 8 0.31
18 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
AAATAATATAAAAAAT
Found at i:33976 original size:17 final size:18
Alignment explanation
Indices: 33954--33988 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33944 AAAAAGAATC
*
33954 ATTTTT-AAATATTATTT
1 ATTTTTCAAATATAATTT
33971 ATTTTTCAAATATAATTT
1 ATTTTTCAAATATAATTT
33989 TTTACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTCAAATATAATTT
Found at i:47089 original size:61 final size:61
Alignment explanation
Indices: 47023--47514 Score: 446
Period size: 61 Copynumber: 8.2 Consensus size: 61
47013 TTATATGATC
* * * * *
47023 GACACCCCTTTTTCTTGAGAAAAAAATTTCAAATTTTTTTTGTATTGGCCATCAAATGGCT
1 GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCT
* * *
47084 AACACCCCCTTTT-T-GAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCT
1 GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCT
* * * * * *
47143 GACACCCCCCTTTT-TTGAAAAAAAAATTGT----ATTTTTGGGTGTTGGTCATTACATGG-T
1 GACA-CCCCCTTTTCTCGAGAAAAAAATT-TCAAAATTTTTTGGTGTTGGCCATCAAATGGCT
* *
47200 CGACACCCCCTTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGG-T
1 -GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCT
** * *
47261 CGACACCCTTTTTTCTCG-G-AAAAAATTGT-AAAA--TTTTGGTGTTGGCCATTGCATA-GTC-
1 -GACACCCCCTTTTCTCGAGAAAAAAATT-TCAAAATTTTTTGGTGTTGGCCA-T-CAAATGGCT
* * * *
47319 GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCTATCAAATAGCC
1 GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCT
* * *
47380 GACACCCCCTTTTCTCGA-AAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAATTGTC-
1 GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT-CAAATGGCT
* * * * * * *
47440 GACACCTCCTTTTCTCGAATAAAAAAATTACAAATTTTTTTGGTGTTGGGCAT-ATTATGGCC
1 GACACCCCCTTTTCTCG-AGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCA-AATGGCT
*
47502 GACACCCCTTTTT
1 GACACCCCCTTTT
47515 TATTTGGTAA
Statistics
Matches: 358, Mismatches: 48, Indels: 49
0.79 0.11 0.11
Matches are distributed among these distances:
57 40 0.11
58 42 0.12
59 75 0.21
60 62 0.17
61 98 0.27
62 41 0.11
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (61 bp):
GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCT
Found at i:47120 original size:59 final size:59
Alignment explanation
Indices: 46902--47515 Score: 413
Period size: 61 Copynumber: 10.3 Consensus size: 59
46892 TGCATTTTTC
* * * *
46902 ATGGCCGACACCCCTTTTTTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCTATCAA
1 ATGGCTGACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
* ******* * * * * *
46961 ATGGTTGACACCCCCTTTTT-TTTTTTTAAATT--ACATTTTTGGGTGTTGGTCATTAT
1 ATGGCTGACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
* * * * * *
47017 AT-GATCGACACCCCTTTTTCTTGAGAAAAAAATTTCAAATTTTTTTTGTATTGGCCATCAA
1 ATGGCT-GACACCCC-CTTT-TTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
* *
47078 ATGGCTAACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAA
1 ATGGCTGACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
** * * * *
47137 ATGGCTGACACCCCCCTTTTTTGA-AAAAAAAATT--GTATTTTTGGGTGTTGGTCATTAC
1 ATGGCTGACA-CCCCC-TTTTTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
* *
47195 ATGG-TCGACACCCCCTTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAA
1 ATGGCT-GACACCCCC-TTT-TTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
** * *
47256 ATGG-TCGACACCCTTTTTTCTCG-G--AAAAAATTGTAAAA--TTTTGGTGTTGGCCATTGCAT
1 ATGGCT-GACACCCCCTTTT-T-GAGAAAAAAAATT-CAAAATTTTTTGGTGTTGGCCA-T-CAA
* * * *
47315 A-GTC-GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCTATCAA
1 ATGGCTGACACCCCCTTTT-T-GAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
* *
47374 ATAGCCGACACCCCCTTTTCTCGA-AAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAA
1 ATGGCTGACACCCCCTTTT-T-GAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCAT-CAA
* * * * * *
47435 TTGTC-GACACCTCCTTTTCTCGA-ATAAAAAAATTACAAATTTTTTTGGTGTTGGGCAT-ATT
1 ATGGCTGACACCCCCTTTT-T-GAGA-AAAAAAATT-CAAAATTTTTTGGTGTTGGCCATCA-A
* *
47496 ATGGCCGACACCCCTTTTTT
1 ATGGCTGACACCCCCTTTTT
47516 ATTTGGTAAA
Statistics
Matches: 436, Mismatches: 87, Indels: 62
0.75 0.15 0.11
Matches are distributed among these distances:
55 2 0.00
56 27 0.06
57 42 0.10
58 46 0.11
59 92 0.21
60 81 0.19
61 112 0.26
62 34 0.08
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (59 bp):
ATGGCTGACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAA
Found at i:47250 original size:178 final size:176
Alignment explanation
Indices: 46909--47259 Score: 540
Period size: 178 Copynumber: 2.0 Consensus size: 176
46899 TTCATGGCCG
* * *
46909 ACACCCCTTTTTTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCTATCAAATGGTTGACACCC
1 ACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCTGACACCC
****** * *
46974 CCTTTTTTTTTTTTAAATTACATTTTTGGGTGTTGGTCATTATATGATCGACACCCCTTTTTCTT
66 CCTTTTTTAAAAAAAAATTACATTTTTGGGTGTTGGTCATTACATGATCGACACCCCCTTTTCTT
* *
47039 GAGAAAAAAATTTCAAATTTTTTTTGTATTGGCCATCAAATGGCTA
131 GAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGGCTA
47085 ACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCTGACACCC
1 ACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCTGACA-CC
** *
47150 CCCTTTTTTGAAAAAAAAATTGTATTTTTGGGTGTTGGTCATTACATGGTCGACACCCCCTTTTC
65 CCCTTTTTT-AAAAAAAAATTACATTTTTGGGTGTTGGTCATTACATGATCGACACCCCCTTTTC
47215 TTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGG
129 TTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGG
47260 TCGACACCCT
Statistics
Matches: 157, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
176 59 0.38
177 11 0.07
178 87 0.55
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (176 bp):
ACACCCCCTTTTTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCTGACACCC
CCTTTTTTAAAAAAAAATTACATTTTTGGGTGTTGGTCATTACATGATCGACACCCCCTTTTCTT
GAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGGCTA
Found at i:47296 original size:178 final size:176
Alignment explanation
Indices: 46902--47515 Score: 535
Period size: 178 Copynumber: 3.5 Consensus size: 176
46892 TGCATTTTTC
* * *
46902 ATGGCCGACACCC-CTTTT-TTGAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCTATCAAATGG
1 ATGGTCGACACCCTCTTTTCTCGAG--AAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGG
* ****** * * *
46965 TTGACACCCCCTTTTTT-TTTTTTAAATTACATTTTTGGGTGTTGGTCATTATATGATCGACACC
64 CTGACACCCCCTTTTTTGAAAAAAAAATT-TATTTTTGGGTGTTGGTCATTAAATGGTCGACACC
* * *
47029 CCTTTTTCTTGAGAAAAAAATTTCAAATTTTTTTTGTATTGGCCATCAA
128 CCCTTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAA
* *
47078 ATGG-CTAACACCCCCTTTT-T-GAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATG
1 ATGGTC-GACACCCTCTTTTCTCGAG--AAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATG
*
47140 GCTGACACCCCCCTTTTTTGAAAAAAAAATTGTATTTTTGGGTGTTGGTCATTACATGGTCGACA
63 GCTGACA-CCCCCTTTTTTGAAAAAAAAATT-TATTTTTGGGTGTTGGTCATTAAATGGTCGACA
47205 CCCCCTTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAA
126 CCCCCTTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAA
* * * *
47256 ATGGTCGACACCCTTTTTTCTCG-GAAAAAATTGTAAAA--TTTTGGTGTTGGCCATTGCATA-G
1 ATGGTCGACACCCTCTTTTCTCGAGAAAAAATT-CAAAATTTTTTTGTGTTGGCCA-T-CAAATG
* * * * * * * *
47317 TC-GACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGG-CTATCAAATAGCC
63 GCTGACACCCCCTTTT-TTGAAAAAAAAATTT----ATTTTTGGGTGTTGGTC-ATTAAATGGTC
* * *
47380 GACACCCCCTTTTCTCGA-AAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGC-A
122 GACACCCCCTTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCAT-CAA
* * * *
47434 ATTGTCGACA-CCTCCTTTTCTCGAATAAAAAAATT-ACAAATTTTTTTGGTGTTGGGCAT-ATT
1 ATGGTCGACACCCT-CTTTTCTCG-A-GAAAAAATTCA-AAATTTTTTT-GTGTTGGCCATCA-A
*
47496 ATGGCCGACA-CCCCTTTTTT
60 ATGGCTGACACCCCCTTTTTT
47516 ATTTGGTAAA
Statistics
Matches: 369, Mismatches: 41, Indels: 51
0.80 0.09 0.11
Matches are distributed among these distances:
175 11 0.03
176 87 0.24
177 31 0.08
178 154 0.42
179 42 0.11
180 5 0.01
181 11 0.03
182 15 0.04
183 13 0.04
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (176 bp):
ATGGTCGACACCCTCTTTTCTCGAGAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCT
GACACCCCCTTTTTTGAAAAAAAAATTTATTTTTGGGTGTTGGTCATTAAATGGTCGACACCCCC
TTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAA
Found at i:47333 original size:118 final size:120
Alignment explanation
Indices: 47085--47515 Score: 481
Period size: 118 Copynumber: 3.6 Consensus size: 120
47075 CAAATGGCTA
* * * *
47085 ACACCCCCTTTT-T-GAGAAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCTGACAC
1 ACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGGCCGACA-
* * * *
47148 CCCCCTTTTT-T-GAAAAAAAAATTGT--ATTTTTGGGTGTTGGTCATTACATGGTCG
65 CCCCCTTTTTCTCG-AAAAAAAATTGTAAAATTTT-GGTGTTGGCCATTGCATAGTCG
* *
47202 ACACCCCCTTTTCTTGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGGTCGACA-
1 ACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGGCCGACAC
* *
47266 CCCTTTTTTCTCG-GAAAAAATTGTAAAATTTTGGTGTTGGCCATTGCATAGTCG
66 CCCCTTTTTCTCGAAAAAAAATTGTAAAATTTTGGTGTTGGCCATTGCATAGTCG
* *
47320 ACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCTATCAAATAGCCGACAC
1 ACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGGCCGACAC
* *
47385 CCCC-TTTTCTCGAAAAAAAAATT-CAAAATTTTTTGGTGTTGGCCA-TGCAATTGTCG
66 CCCCTTTTTCTCG-AAAAAAAATTGTAAAA--TTTTGGTGTTGGCCATTGC-ATAGTCG
* * * * * * *
47441 ACACCTCCTTTTCTCGAATAAAAAAATTACAAATTTTTTTGGTGTTGGGCAT-ATTATGGCCGAC
1 ACACCCCCTTTTCTCG-AGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCA-AATGGCCGAC
*
47505 ACCCCTTTTTT
64 ACCCCCTTTTT
47516 ATTTGGTAAA
Statistics
Matches: 270, Mismatches: 29, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
117 30 0.11
118 89 0.33
119 57 0.21
120 11 0.04
121 37 0.14
122 42 0.16
123 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (120 bp):
ACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTATTGGCCATCAAATGGCCGACAC
CCCCTTTTTCTCGAAAAAAAATTGTAAAATTTTGGTGTTGGCCATTGCATAGTCG
Found at i:51280 original size:12 final size:12
Alignment explanation
Indices: 51238--51285 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
51228 ATTTGTGTAA
*
51238 AAATTAATTTGA
1 AAATTAATTTGG
51250 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
51266 AAATTAATTTGG
1 AAATTAATTTGG
51278 AAATTAAT
1 AAATTAAT
51286 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Done.