Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013383.1 Kokia drynarioides strain JFW-HI SEQ_128406, 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: 71338
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:322 original size:186 final size:186
Alignment explanation
Indices: 5--362 Score: 619
Period size: 186 Copynumber: 1.9 Consensus size: 186
1 ATAT
5 AATTACATATTTATAAGTTAATTTTATAAATAAAAGAATTATTAAAAAACTTGAAAATAATATAT
1 AATTACATATTTATAAGTTAATTTTATAAATAAAAGAATTATTAAAAAACTTGAAAATAATATAT
* *
70 AAAAGAAATTAGTTGATATTTTTTAAAAAATAAAATATAATTAAAATGATGATATATAAAAAAAA
66 AAAAGAAATTAGTTGATATTTTTTAAAAAATAAAATATAATTAAAATAATGATAAATAAAAAAAA
135 TTATATATTATTATTATACAATTATTAATTTAATTATATAAAAATTAGATATATAC
131 TTATATATTATTATTATACAATTATTAATTTAATTATATAAAAATTAGATATATAC
*
191 AATTACATATTTATAAGTTAATTTTATAAATAAAAGAATTATTAAAAAAACTTGAAAATGATATA
1 AATTACATATTTATAAGTTAATTTTATAAATAAAAGAATTATT-AAAAAACTTGAAAATAATATA
* * * *
256 TAAAAGAAATTAGTTGATATTTTTTTAAAAATAAAATATATTTAACATAATGATAAAT-ACAAAA
65 TAAAAGAAATTAGTTGATATTTTTTAAAAAATAAAATATAATTAAAATAATGATAAATAAAAAAA
* *
320 ATTATATATTTTTATTATATAATTATTAATTTAATTATATAAA
130 ATTATATATTATTATTATACAATTATTAATTTAATTATATAAA
363 GAAGGAATTA
Statistics
Matches: 162, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
186 89 0.55
187 73 0.45
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (186 bp):
AATTACATATTTATAAGTTAATTTTATAAATAAAAGAATTATTAAAAAACTTGAAAATAATATAT
AAAAGAAATTAGTTGATATTTTTTAAAAAATAAAATATAATTAAAATAATGATAAATAAAAAAAA
TTATATATTATTATTATACAATTATTAATTTAATTATATAAAAATTAGATATATAC
Found at i:358 original size:20 final size:21
Alignment explanation
Indices: 319--361 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
309 TAAATACAAA
* *
319 AATTATATATTTTTATTATAT
1 AATTATATAATTTAATTATAT
340 AATTAT-TAATTTAATTATAT
1 AATTATATAATTTAATTATAT
360 AA
1 AA
362 AGAAGGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTATATAATTTAATTATAT
Found at i:8763 original size:96 final size:98
Alignment explanation
Indices: 8635--8820 Score: 252
Period size: 96 Copynumber: 1.9 Consensus size: 98
8625 TATTTGTATG
* *
8635 TATTTTAACAAATTCAATAACTAAATGAAGGAATGCGA-T-A-TAAATGAAAAAGAAAATATTTG
1 TATTTTAACAAATTCAATAACTAAACGAAGGAATGCGAGTGATTAAATGAAAAA-AAAATATTTA
8697 TTGAGAAATAATGTAGAAAGCATAAATGCATATT
65 TTGAGAAATAATGTAGAAAGCATAAATGCATATT
* * * * * *
8731 TATTTTAATAAATTTAATAATTAAACGAAGGAATGTGATGTGATTTACATGAAAAAAACATATTT
1 TATTTTAACAAATTCAATAACTAAACGAAGGAATGCGA-GTGA-TTAAATGAAAAAAAAATATTT
8796 ATTGAGAAATAATGTAGAAAGCATA
64 ATTGAGAAATAATGTAGAAAGCATA
8821 GTTTAGTAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
96 33 0.43
98 1 0.01
99 1 0.01
100 32 0.42
101 10 0.13
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (98 bp):
TATTTTAACAAATTCAATAACTAAACGAAGGAATGCGAGTGATTAAATGAAAAAAAAATATTTAT
TGAGAAATAATGTAGAAAGCATAAATGCATATT
Found at i:11627 original size:20 final size:20
Alignment explanation
Indices: 11585--11623 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
11575 AAATTTTGAT
*
11585 TTAATTTGTAATTTGATATA
1 TTAATTTGTAATTTAATATA
*
11605 TTAATTT-TGATTTAATATA
1 TTAATTTGTAATTTAATATA
11624 ATTATACGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
TTAATTTGTAATTTAATATA
Found at i:11901 original size:19 final size:19
Alignment explanation
Indices: 11879--11917 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11869 AAATCAAAAT
11879 TTAAATATAAAATT-ATATA
1 TTAAA-ATAAAATTCATATA
*
11898 TTAAACTAAAATTCATATA
1 TTAAAATAAAATTCATATA
11917 T
1 T
11918 AATTTTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAAATAAAATTCATATA
Found at i:12462 original size:29 final size:29
Alignment explanation
Indices: 12408--12465 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12398 TTATAAAAAT
* *
12408 TGGATCAACTTAGTTTCCTTATTATTAAA
1 TGGATCAACTTAGTCTCCTTACTATTAAA
*
12437 TGGATCAATTTAGTCT-CTATACTATTAAA
1 TGGATCAACTTAGTCTCCT-TACTATTAAA
12466 ATTAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (29 bp):
TGGATCAACTTAGTCTCCTTACTATTAAA
Found at i:19607 original size:17 final size:18
Alignment explanation
Indices: 19585--19619 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19575 ATATATTAAT
19585 TTATTTT-AAAATAAATA
1 TTATTTTAAAAATAAATA
19602 TTATTTTAAAAATAAATA
1 TTATTTTAAAAATAAATA
19620 AATAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTTTAAAAATAAATA
Found at i:19958 original size:14 final size:14
Alignment explanation
Indices: 19939--19968 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19929 GCTTTGCGTA
19939 AAAAAAAATAAAAT
1 AAAAAAAATAAAAT
19953 AAAAAAAATAAAAT
1 AAAAAAAATAAAAT
19967 AA
1 AA
19969 GATAGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAAAATAAAAT
Found at i:27473 original size:57 final size:56
Alignment explanation
Indices: 27405--27550 Score: 197
Period size: 57 Copynumber: 2.6 Consensus size: 56
27395 ATTCCGCTAT
* * * * *
27405 AACCACCACCACCACCTGGACCCCCAGCTCCACCGCCTACACCAGCTGTATCTGGAC
1 AACCA-CACCACCACCTAGACCTCCAACTCCACCGCCTACACCAACTGTACCTGGAC
* *
27462 AACCACTACCACCACCTAGACCTCCACCTCCACTGCCTACACCAACTGTACCTGGAC
1 AACCAC-ACCACCACCTAGACCTCCAACTCCACCGCCTACACCAACTGTACCTGGAC
27519 AACCAC-CC-CCACCTAGACCTCCAACTCCACCG
1 AACCACACCACCACCTAGACCTCCAACTCCACCG
27551 GTCCCACCGC
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
54 22 0.28
55 2 0.03
56 1 0.01
57 55 0.69
ACGTcount: A:0.27, C:0.50, G:0.10, T:0.13
Consensus pattern (56 bp):
AACCACACCACCACCTAGACCTCCAACTCCACCGCCTACACCAACTGTACCTGGAC
Found at i:27606 original size:42 final size:42
Alignment explanation
Indices: 27560--27663 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
27550 GGTCCCACCG
*
27560 CCTAGACCTCCAACTCCACCACCGGTTCCACCCCCTAAACCA
1 CCTAGACCTCCAACTCCACCACCAGTTCCACCCCCTAAACCA
* * * *
27602 CCTAGACCTCCAGCTCCGCCAGCAGTTCCACCCCCTAACCCA
1 CCTAGACCTCCAACTCCACCACCAGTTCCACCCCCTAAACCA
* *
27644 CCTAGGCCTCCAATTCCACC
1 CCTAGACCTCCAACTCCACC
27664 GCCTAAACCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.23, C:0.52, G:0.10, T:0.15
Consensus pattern (42 bp):
CCTAGACCTCCAACTCCACCACCAGTTCCACCCCCTAAACCA
Found at i:27661 original size:30 final size:30
Alignment explanation
Indices: 27627--27687 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
27617 CCGCCAGCAG
* *
27627 TTCCACCCCCT-AACCCACCTAGGCCTCCAA
1 TTCCACCCCCTAAACCC-CCTAGCCCACCAA
*
27657 TTCCACCGCCTAAACCCCCTAGCCCACCAA
1 TTCCACCCCCTAAACCCCCTAGCCCACCAA
27687 T
1 T
27688 GCCTTTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.25, C:0.52, G:0.07, T:0.16
Consensus pattern (30 bp):
TTCCACCCCCTAAACCCCCTAGCCCACCAA
Found at i:29044 original size:60 final size:59
Alignment explanation
Indices: 28938--29125 Score: 211
Period size: 59 Copynumber: 3.2 Consensus size: 59
28928 ATAAAATTAG
** **
28938 GTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTCAAGTTC-A
1 GTATCAAATTGGGTC-AAAAAAAATTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
**
28997 GATATCAAATTGGGTCAAAAAAAATTTAGGTATTAAATTAGGAAAAAATGTCAAGTTCAA
1 G-TATCAAATTGGGTCAAAAAAAATTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
* ** *
29057 GTA-CAAAATTAGGTCAAAAAAAAGTTTAAATACCAAATTA-AAAAAAATTGTCAAGTTCAA
1 GTATC-AAATTGGGTCAAAAAAAA-TTTAGGTACCAAATTAGGAAAAAA-TGTCAAGTTCAA
*
29117 GTACCAAAT
1 GTATCAAAT
29126 GTTATATTAA
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.01
59 64 0.58
60 45 0.41
61 1 0.01
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (59 bp):
GTATCAAATTGGGTCAAAAAAAATTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
Found at i:29066 original size:31 final size:31
Alignment explanation
Indices: 28967--29125 Score: 97
Period size: 31 Copynumber: 5.3 Consensus size: 31
28957 AAAAGCTTAG
28967 GTACCAAATTAGGAAAAAATGTCAAGTTC-A
1 GTACCAAATTAGGAAAAAATGTCAAGTTCAA
* * * *
28997 GATATCAAATTGGGTCAAAAAA----AA-TTTAG
1 G-TACCAAATTAGG--AAAAAATGTCAAGTTCAA
**
29026 GTATTAAATTAGGAAAAAATGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAATGTCAAGTTCAA
* *
29057 GTACAAAATTAGGTCAAAAAA----AAGTTTAA
1 GTACCAAATTAGG--AAAAAATGTCAAGTTCAA
* *
29086 ATACCAAATTA-AAAAAAATTGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAA-TGTCAAGTTCAA
29117 GTACCAAAT
1 GTACCAAAT
29126 GTTATATTAA
Statistics
Matches: 97, Mismatches: 16, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
26 12 0.12
28 12 0.12
29 19 0.20
30 3 0.03
31 39 0.40
33 12 0.12
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAGGAAAAAATGTCAAGTTCAA
Found at i:31369 original size:3 final size:3
Alignment explanation
Indices: 31361--31385 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31351 ATTGTTTGTC
31361 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
31386 CTCCTGTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:41421 original size:21 final size:21
Alignment explanation
Indices: 41396--41435 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41386 AAGCAGTAAT
41396 AATAAAATTA-ATTATTATAGA
1 AATAAAATTAGA-TATTATAGA
41417 AATAAAATTAGATATTATA
1 AATAAAATTAGATATTATA
41436 ACAATGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AATAAAATTAGATATTATAGA
Found at i:48544 original size:20 final size:20
Alignment explanation
Indices: 48495--48542 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
48485 AATTTTTTTT
*
48495 ACCCTAAACATTGAACCTTAA
1 ACCC-AAACATTGAACCATAA
48516 ACCTCAAAC-TTGAACCATAA
1 ACC-CAAACATTGAACCATAA
48536 ACCCAAA
1 ACCCAAA
48543 ACCTTAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 7 0.28
22 1 0.04
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (20 bp):
ACCCAAACATTGAACCATAA
Found at i:48646 original size:20 final size:20
Alignment explanation
Indices: 48621--48659 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
48611 TAGGGTTTAG
48621 GGTTCAAGATTCAAAGTTTT
1 GGTTCAAGATTCAAAGTTTT
*
48641 GGTTCAAGATTCAGAGTTT
1 GGTTCAAGATTCAAAGTTT
48660 GAGTTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (20 bp):
GGTTCAAGATTCAAAGTTTT
Found at i:49607 original size:15 final size:16
Alignment explanation
Indices: 49579--49608 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49569 TCGCTTCAAT
49579 ATTATCCATCTCAAAA
1 ATTATCCATCTCAAAA
49595 ATTATCCAT-TCAAA
1 ATTATCCATCTCAAA
49609 CCCAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTATCCATCTCAAAA
Found at i:50113 original size:15 final size:15
Alignment explanation
Indices: 50068--50114 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
50058 AAAAAAATAA
*
50068 AAATATTTTAAAAAT
1 AAATATTTAAAAAAT
* **
50083 -AATAATTAAATTAT
1 AAATATTTAAAAAAT
50097 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
50112 AAA
1 AAA
50115 AATGTAATAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:50706 original size:21 final size:24
Alignment explanation
Indices: 50681--50724 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
50671 ATTTATATGG
50681 ATGTA-AT-TAAGATATA-TTTAC
1 ATGTATATATAAGATATACTTTAC
*
50702 ATGTATATATAATATATACTTTA
1 ATGTATATATAAGATATACTTTA
50725 TTTTTTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 8 0.42
24 4 0.21
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (24 bp):
ATGTATATATAAGATATACTTTAC
Found at i:51907 original size:29 final size:29
Alignment explanation
Indices: 51846--51907 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
51836 TCATTTTTTT
* *
51846 TTTTGAAATTTTCATAAAACCTTAAAATT
1 TTTTGAAATTTTCATAAAACCCTAAAATG
*
51875 TTTTGAAATTTTCACTAAAACCCTCAAA-G
1 TTTTGAAATTTTCA-TAAAACCCTAAAATG
51904 TTTT
1 TTTT
51908 AAAAAAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (29 bp):
TTTTGAAATTTTCATAAAACCCTAAAATG
Found at i:56985 original size:44 final size:44
Alignment explanation
Indices: 56922--57011 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 44
56912 ACCGAGCCTC
56922 AAGTAAGATTTTTTTGACTTAGCTTGACCCAA-CTCAAATTTGCA
1 AAGTAAGATTTTTTTGACTTAGCTTGACCCAATC-CAAATTTGCA
56966 AAGTAAGATTTTTTTGACTTAGCTTGACCCAATCCAAATTTGCA
1 AAGTAAGATTTTTTTGACTTAGCTTGACCCAATCCAAATTTGCA
57010 AA
1 AA
57012 AAGAAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (44 bp):
AAGTAAGATTTTTTTGACTTAGCTTGACCCAATCCAAATTTGCA
Found at i:62081 original size:59 final size:59
Alignment explanation
Indices: 62010--62151 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
62000 ACTTGGATAA
*** * *
62010 AAAAAAAGTTCAAGCCTTAATGTGGA-AACAATTGTCAAGTTCAGGGATTAACTTGAAC
1 AAAAAAAGTTCAAGCCTTAATGTGGAGAACAATCACCAAGTTCAAGGACTAACTTGAAC
* * ** *
62068 AAAAAATAGTTCAACCCATACCGT-GAGAACAATCACCAAGTTCAAGGACTAATTTGAAC
1 AAAAAA-AGTTCAAGCCTTAATGTGGAGAACAATCACCAAGTTCAAGGACTAACTTGAAC
* *
62127 AAAAAAAGTTCATGCCTCAATGTGG
1 AAAAAAAGTTCAAGCCTTAATGTGG
62152 GAGTGATTGC
Statistics
Matches: 65, Mismatches: 16, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
58 19 0.29
59 46 0.71
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (59 bp):
AAAAAAAGTTCAAGCCTTAATGTGGAGAACAATCACCAAGTTCAAGGACTAACTTGAAC
Found at i:64258 original size:5 final size:5
Alignment explanation
Indices: 64248--64272 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
64238 ATTTATAAAA
64248 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
64273 CACCTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:67482 original size:26 final size:27
Alignment explanation
Indices: 67443--67495 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
67433 CATTTATTAG
* *
67443 GTCAATTCTATATAGTTGT-TTTTTTTA
1 GTCAACTCTATATAATT-TATTTTTTTA
67470 GTCAACTC-ATATAATTTATTTTTTTA
1 GTCAACTCTATATAATTTATTTTTTTA
67496 ATTAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.04
26 15 0.65
27 7 0.30
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.57
Consensus pattern (27 bp):
GTCAACTCTATATAATTTATTTTTTTA
Found at i:68650 original size:27 final size:27
Alignment explanation
Indices: 68620--68680 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
68610 GGTGCCTATT
68620 TGACAGGAGGCAACAAAGATGCCTACC
1 TGACAGGAGGCAACAAAGATGCCTACC
* * *
68647 TGACAGGCGGCACCAAAGGTGCCTACC
1 TGACAGGAGGCAACAAAGATGCCTACC
*
68674 TTACAGG
1 TGACAGG
68681 TAGACTGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.13
Consensus pattern (27 bp):
TGACAGGAGGCAACAAAGATGCCTACC
Found at i:69154 original size:27 final size:27
Alignment explanation
Indices: 69096--69155 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
69086 AATTTGACGG
*
69096 GTGGTGCCTTTGGGATAGGCGGCACCA
1 GTGGTGCCTCTGGGATAGGCGGCACCA
* * *
69123 ATGGTGCCTACTGGG-TAGGTGGCACTA
1 GTGGTGCCT-CTGGGATAGGCGGCACCA
69150 GTGGTG
1 GTGGTG
69156 TGTAACACCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.15, C:0.18, G:0.42, T:0.25
Consensus pattern (27 bp):
GTGGTGCCTCTGGGATAGGCGGCACCA
Found at i:69674 original size:31 final size:31
Alignment explanation
Indices: 69639--69703 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
69629 TAGTATATAG
69639 CTTGTATCTTACCACATTGACATTCATTTCA
1 CTTGTATCTTACCACATTGACATTCATTTCA
69670 CTTGTATCTTACCACATTGACATTCATTTCA
1 CTTGTATCTTACCACATTGACATTCATTTCA
69701 CTT
1 CTT
69704 TGGTGCACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.06, T:0.43
Consensus pattern (31 bp):
CTTGTATCTTACCACATTGACATTCATTTCA
Found at i:69915 original size:23 final size:23
Alignment explanation
Indices: 69793--69942 Score: 112
Period size: 23 Copynumber: 6.4 Consensus size: 23
69783 CGAAGTATTT
69793 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
69819 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
69841 ATTCAGTAGGCACACACAGTGC-A
1 A-ACAGTAAGCACACAAAGTGCGA
* * *
69864 ATCAGT-AGCCACACATAGCGC-A
1 AACAGTAAG-CACACAAAGTGCGA
* * *
69886 AATCAGTAGGCACACGAGGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
69910 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
69933 AACAGTAAGC
1 AACAGTAAGC
69943 GCGCTAGCGT
Statistics
Matches: 103, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.01
22 19 0.18
23 60 0.58
24 4 0.04
26 14 0.14
27 5 0.05
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:70802 original size:89 final size:89
Alignment explanation
Indices: 70651--70829 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
70641 CTGTCCAAAC
* *
70651 TGTTTTACTAAATCATATGTTAATCCCTTCATTTTATCATTGTAAACATTCAAATTATGTACCTA
1 TGTTTTACTAAATCATATATTAATCCCTTCATTTTATCATTATAAACATTCAAATTATGTACCTA
70716 TATAACAATTTTTATGCTAATAAT
66 TATAACAATTTTTATGCTAATAAT
70740 TGTTTTACTAAATCATATATTAATCCCTTCATTTTATCATTATAAACATTCAAATTATGTACCTA
1 TGTTTTACTAAATCATATATTAATCCCTTCATTTTATCATTATAAACATTCAAATTATGTACCTA
70805 TATAACAATTTTTATGCTAATAAT
66 TATAACAATTTTTATGCTAATAAT
70829 T
1 T
70830 CATATACCAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (89 bp):
TGTTTTACTAAATCATATATTAATCCCTTCATTTTATCATTATAAACATTCAAATTATGTACCTA
TATAACAATTTTTATGCTAATAAT
Done.