Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012460.1 Kokia drynarioides strain JFW-HI SEQ_127464, 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: 151180
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:11184 original size:2 final size:2
Alignment explanation
Indices: 11177--11201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11167 GAGCTCTAAT
11177 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11202 TTAGTAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18584 original size:17 final size:17
Alignment explanation
Indices: 18562--18596 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18552 TACTTTAATT
18562 AAACTCTTTCGATCAAA
1 AAACTCTTTCGATCAAA
18579 AAACTCTTTCGATCAAA
1 AAACTCTTTCGATCAAA
18596 A
1 A
18597 CCCCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (17 bp):
AAACTCTTTCGATCAAA
Found at i:25039 original size:52 final size:52
Alignment explanation
Indices: 24963--25132 Score: 166
Period size: 52 Copynumber: 3.3 Consensus size: 52
24953 GCCATAAATG
* * * *
24963 AAGAGGTCCGATGATTATGAGTCATCATGAGTATATGAATCCTTTACAGATT
1 AAGAGGTCCGATGACTAAGTGTCATCATGAGTATATGAATCCTTTACAGATC
*
25015 AA-ACGGTCCGATGACTAAGTGTCATCATGAGTATATCG-ATCCTTTACGGATC
1 AAGA-GGTCCGATGACTAAGTGTCATCATGAGTATAT-GAATCCTTTACAGATC
* * * * * * * *
25067 AAGAGGTCTGATGGCTTTA-TGTCATCGTGAGTATATGAATCCCTTGCGGATA
1 AAGAGGTCCGATGAC-TAAGTGTCATCATGAGTATATGAATCCTTTACAGATC
*
25119 AAGAGGTTCGATGA
1 AAGAGGTCCGATGA
25133 TTGACAAGCG
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
51 2 0.02
52 92 0.94
53 4 0.04
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (52 bp):
AAGAGGTCCGATGACTAAGTGTCATCATGAGTATATGAATCCTTTACAGATC
Found at i:27918 original size:16 final size:15
Alignment explanation
Indices: 27890--27935 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
27880 TCGCGTACCT
*
27890 AAAATACTAAAAATA
1 AAAATAATAAAAATA
27905 AAAATAAGTAAAAAT-
1 AAAATAA-TAAAAATA
*
27920 AAAATAATATAAATA
1 AAAATAATAAAAATA
27935 A
1 A
27936 TCGAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 14 0.52
16 7 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAATAAAAATA
Found at i:30296 original size:13 final size:13
Alignment explanation
Indices: 30278--30307 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30268 CCACTAGCAG
30278 CATCGACCATCTT
1 CATCGACCATCTT
*
30291 CATCGATCATCTT
1 CATCGACCATCTT
30304 CATC
1 CATC
30308 TCCAAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.37, G:0.07, T:0.33
Consensus pattern (13 bp):
CATCGACCATCTT
Found at i:35742 original size:36 final size:36
Alignment explanation
Indices: 35695--35769 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
35685 GTGTATAGAC
35695 TACAAACAACTAAACAAGGTAACAATCAAGAATAAA
1 TACAAACAACTAAACAAGGTAACAATCAAGAATAAA
35731 TACAAACAACTAAACAAGGTAACAATCAAGAATAAA
1 TACAAACAACTAAACAAGGTAACAATCAAGAATAAA
35767 TAC
1 TAC
35770 CTGCTGCCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.60, C:0.17, G:0.08, T:0.15
Consensus pattern (36 bp):
TACAAACAACTAAACAAGGTAACAATCAAGAATAAA
Found at i:39591 original size:52 final size:52
Alignment explanation
Indices: 39509--39704 Score: 223
Period size: 52 Copynumber: 3.8 Consensus size: 52
39499 GCCATAAACG
* * * * * * *
39509 AAGAGGTCCGATGATTATGAGTCATTATGAGTATCTGAATTCTTTACGGATT
1 AAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCCTTACGGATT
* *
39561 AAGAGGTTCGATGACTCTGTGTCATCATGAGTATATGAATCCCTTGCGGATT
1 AAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCCTTACGGATT
* *
39613 AAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCCTTGCGGATT
1 AAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCCTTACGGATT
* * ** * *
39665 ATA-AGGTCTGGTGGTTATGTGTCATCGTGAGTATATGAAT
1 A-AGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAAT
39705 GAAGTGAAAT
Statistics
Matches: 127, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
52 126 0.99
53 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (52 bp):
AAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCCTTACGGATT
Found at i:44041 original size:22 final size:22
Alignment explanation
Indices: 44013--44056 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
44003 CAAAATGAAG
44013 AGCCTGTTAAGGGAATTAAAGT
1 AGCCTGTTAAGGGAATTAAAGT
44035 AGCCTGTTAAGGGAATTAAAGT
1 AGCCTGTTAAGGGAATTAAAGT
44057 CTCAAAGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (22 bp):
AGCCTGTTAAGGGAATTAAAGT
Found at i:44556 original size:17 final size:17
Alignment explanation
Indices: 44534--44572 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
44524 CTCCACCTTG
* *
44534 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
*
44551 ACAAGAACTCTCAATGA
1 ACAAGAACTCTCAACGA
44568 ACAAG
1 ACAAG
44573 TTCTACACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:53910 original size:6 final size:6
Alignment explanation
Indices: 53899--53924 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53889 TCGGAGAAAA
53899 CTGAGG CTGAGG CTGAGG CTGAGG CT
1 CTGAGG CTGAGG CTGAGG CTGAGG CT
53925 AAGCTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.46, T:0.19
Consensus pattern (6 bp):
CTGAGG
Found at i:54625 original size:22 final size:22
Alignment explanation
Indices: 54583--54626 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54573 TTTCAAAGAA
* *
54583 AATAGAATTTAACTAATTTTTC
1 AATAGAATTTAACAAAGTTTTC
54605 AATA-AATTTCAACAAAGTTTTC
1 AATAGAATTT-AACAAAGTTTTC
54627 TCTTAGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (22 bp):
AATAGAATTTAACAAAGTTTTC
Found at i:60489 original size:22 final size:22
Alignment explanation
Indices: 60447--60490 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
60437 GTTCAAAGAA
* *
60447 AATAGAATTTAACTAATTTTTC
1 AATAGAATTTAACAAAGTTTTC
60469 AATA-AATTTCAACAAAGTTTTC
1 AATAGAATTT-AACAAAGTTTTC
60491 TCTTAGTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (22 bp):
AATAGAATTTAACAAAGTTTTC
Found at i:68518 original size:28 final size:28
Alignment explanation
Indices: 68474--68549 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
68464 TTTTAACAAG
68474 ATTCTAATTAAAATAAAATAGATGACTT
1 ATTCTAATTAAAATAAAATAGATGACTT
*
68502 ATTTTAATTAAAATAAAATAGATGACTT
1 ATTCTAATTAAAATAAAATAGATGACTT
68530 ATTCTAATTAAAATAAAATA
1 ATTCTAATTAAAATAAAATA
68550 AAAGAAGTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (28 bp):
ATTCTAATTAAAATAAAATAGATGACTT
Found at i:68519 original size:142 final size:143
Alignment explanation
Indices: 68357--68622 Score: 507
Period size: 142 Copynumber: 1.9 Consensus size: 143
68347 GTTGAAACAC
68357 CTTATTCTAATTAAAATAAAATAGATGACTTATTCTAATTAAAATAAAATAAAAGAAGCCTAGTT
1 CTTATTCTAATTAAAATAAAATAGATGACTTATTCTAATTAAAATAAAATAAAAGAAGCCTAGTT
68422 TATTTGGACTTTACTTTTATTTTATTTTACCATTGTATTTTATTTTAACAAG-ATTCTAATTAAA
66 TATTTGGACTTTACTTTTATTTTATTTTACCATTGTATTTTATTTTAACAAGAATTCTAATTAAA
68486 ATAAAATAGATGA
131 ATAAAATAGATGA
* *
68499 CTTATTTTAATTAAAATAAAATAGATGACTTATTCTAATTAAAATAAAATAAAAGAAGTCTAGTT
1 CTTATTCTAATTAAAATAAAATAGATGACTTATTCTAATTAAAATAAAATAAAAGAAGCCTAGTT
68564 TATTTGGACTTTACTTTTATTTTATTTTACCATTGTATTTTATTTTAACAAGAATTCTA
66 TATTTGGACTTTACTTTTATTTTATTTTACCATTGTATTTTATTTTAACAAGAATTCTA
68623 GTCACCCAAT
Statistics
Matches: 121, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
142 115 0.95
143 6 0.05
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (143 bp):
CTTATTCTAATTAAAATAAAATAGATGACTTATTCTAATTAAAATAAAATAAAAGAAGCCTAGTT
TATTTGGACTTTACTTTTATTTTATTTTACCATTGTATTTTATTTTAACAAGAATTCTAATTAAA
ATAAAATAGATGA
Found at i:81237 original size:18 final size:18
Alignment explanation
Indices: 81203--81357 Score: 134
Period size: 18 Copynumber: 8.6 Consensus size: 18
81193 TATGCTTAAA
* *
81203 GAGCCAGTATACCCTATC
1 GAGCCAGTATGCTCTATC
*
81221 GACCCAGTATGCTCTATC
1 GAGCCAGTATGCTCTATC
* *
81239 AAGCCAGTATGCT-TAAAC
1 GAGCCAGTATGCTCT-ATC
* * *
81257 AAGCCAGTATGCTCAAAC
1 GAGCCAGTATGCTCTATC
*
81275 AAGCCAGTATGCTCTATC
1 GAGCCAGTATGCTCTATC
* *
81293 GAGCTAGTATGCTCAAAT-
1 GAGCCAGTATGCTC-TATC
*
81311 GAGCCAGTATCCTCTATC
1 GAGCCAGTATGCTCTATC
* * *
81329 GAGCTAGTATGCTCAAAC
1 GAGCCAGTATGCTCTATC
*
81347 GAGCCGGTATG
1 GAGCCAGTATG
81358 ATATTCCTTC
Statistics
Matches: 112, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
17 3 0.03
18 107 0.96
19 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (18 bp):
GAGCCAGTATGCTCTATC
Found at i:81345 original size:36 final size:36
Alignment explanation
Indices: 81185--81356 Score: 170
Period size: 36 Copynumber: 4.8 Consensus size: 36
81175 AATACTCTTA
* *
81185 CGAGTTAGTATGCTTAAA-GAGCCAGTATACC-CTAT
1 CGAGCTAGTATGCTCAAACGAGCCAGTAT-CCTCTAT
* * * * * * *
81220 CGACCCAGTATGCTCTATCAAGCCAGTATGCT-TAAA
1 CGAGCTAGTATGCTCAAACGAGCCAGTATCCTCT-AT
* * * *
81256 CAAGCCAGTATGCTCAAACAAGCCAGTATGCTCTAT
1 CGAGCTAGTATGCTCAAACGAGCCAGTATCCTCTAT
*
81292 CGAGCTAGTATGCTCAAATGAGCCAGTATCCTCTAT
1 CGAGCTAGTATGCTCAAACGAGCCAGTATCCTCTAT
*
81328 CGAGCTAGTATGCTCAAACGAGCCGGTAT
1 CGAGCTAGTATGCTCAAACGAGCCAGTAT
81357 GATATTCCTT
Statistics
Matches: 112, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
35 14 0.12
36 97 0.87
37 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (36 bp):
CGAGCTAGTATGCTCAAACGAGCCAGTATCCTCTAT
Found at i:81357 original size:54 final size:53
Alignment explanation
Indices: 81191--81357 Score: 183
Period size: 54 Copynumber: 3.1 Consensus size: 53
81181 CTTACGAGTT
* *
81191 AGTATGCTTAAAGAGCCAGTATACC-CTATCGACCCAGTATGCTCTATCAAGCC
1 AGTATGCTTAAAGAGCCAGTAT-CCTCTATCGAGCCAGTATGCTCTATCGAGCC
* * * * * *
81244 AGTATGCTTAAACAAGCCAGTATGCTCAAACAAGCCAGTATGCTCTATCGAGCT
1 AGTATGCTTAAA-GAGCCAGTATCCTCTATCGAGCCAGTATGCTCTATCGAGCC
* * * *
81298 AGTATGCTCAAATGAGCCAGTATCCTCTATCGAGCTAGTATGCTCAAACGAGCC
1 AGTATGCTTAAA-GAGCCAGTATCCTCTATCGAGCCAGTATGCTCTATCGAGCC
*
81352 GGTATG
1 AGTATG
81358 ATATTCCTTC
Statistics
Matches: 92, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
53 13 0.14
54 79 0.86
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (53 bp):
AGTATGCTTAAAGAGCCAGTATCCTCTATCGAGCCAGTATGCTCTATCGAGCC
Found at i:83605 original size:158 final size:158
Alignment explanation
Indices: 83317--83632 Score: 605
Period size: 158 Copynumber: 2.0 Consensus size: 158
83307 TTGTACTTCT
83317 ACCGACACGTGCTAGGGTTTTACCGAAACAAGTACACAGAATTCACAAAATCACACAAATTCATC
1 ACCGACACGTGCTAGGGTTTTACCGAAACAAGTACACAGAATTCACAAAATCACACAAATTCATC
83382 TACAAAACTTCATTTCATAGACATGTAGTGCAATTCAACAACACACTGTGTTCAAGTACAACACC
66 TACAAAACTTCATTTCATAGACATGTAGTGCAATTCAACAACACACTGTGTTCAAGTACAACACC
83447 TAGCATTACATTTAAGTACTAGATGCCA
131 TAGCATTACATTTAAGTACTAGATGCCA
* * *
83475 ACCGATACGTGCTAGGGTTTTACCGAAACGAGTACACATAATTCACAAAATCACACAAATTCATC
1 ACCGACACGTGCTAGGGTTTTACCGAAACAAGTACACAGAATTCACAAAATCACACAAATTCATC
83540 TACAAAACTTCATTTCATAGACATGTAGTGCAATTCAACAACACACTGTGTTCAAGTACAACACC
66 TACAAAACTTCATTTCATAGACATGTAGTGCAATTCAACAACACACTGTGTTCAAGTACAACACC
83605 TAGCATTACATTTAAGTACTAGATGCCA
131 TAGCATTACATTTAAGTACTAGATGCCA
83633 GTAACAACAT
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
158 155 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (158 bp):
ACCGACACGTGCTAGGGTTTTACCGAAACAAGTACACAGAATTCACAAAATCACACAAATTCATC
TACAAAACTTCATTTCATAGACATGTAGTGCAATTCAACAACACACTGTGTTCAAGTACAACACC
TAGCATTACATTTAAGTACTAGATGCCA
Found at i:93000 original size:40 final size:40
Alignment explanation
Indices: 92918--93027 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 40
92908 CTTCGTCGTG
* * *
92918 ACATAGCATGTCTATGTTGC-AACAAACCCCCTATGCCGCA
1 ACATAGAATGTCTATGTCGCGAA-AAACCCCCTATGCCACA
* *
92958 ACATAGAATGTCTATGTCACGAAAAACCCCCTATGTCACA
1 ACATAGAATGTCTATGTCGCGAAAAACCCCCTATGCCACA
* * *
92998 ACACA-ACATGTTTATGTCGTGAAAAACCCC
1 ACATAGA-ATGTCTATGTCGCGAAAAACCCC
93028 TAAAGATGTC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.02
40 56 0.95
41 2 0.03
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.23
Consensus pattern (40 bp):
ACATAGAATGTCTATGTCGCGAAAAACCCCCTATGCCACA
Found at i:101081 original size:18 final size:18
Alignment explanation
Indices: 101060--101097 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
101050 ACAAGTCTTG
*
101060 AAAT-AAATCAAAGTCTCA
1 AAATAAAATAAAAGT-TCA
101078 AAATAAAATAAAAGTTCA
1 AAATAAAATAAAAGTTCA
101096 AA
1 AA
101098 CTTCTCCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATAAAAGTTCA
Found at i:106851 original size:22 final size:23
Alignment explanation
Indices: 106821--106864 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
106811 AGAACAAAAT
106821 AAAACAACT-AAACCTAAGAAAG
1 AAAACAACTAAAACCTAAGAAAG
*
106843 AAAATAACTAAAACCTAAGAAA
1 AAAACAACTAAAACCTAAGAAA
106865 AAGAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.66, C:0.16, G:0.07, T:0.11
Consensus pattern (23 bp):
AAAACAACTAAAACCTAAGAAAG
Found at i:110027 original size:53 final size:53
Alignment explanation
Indices: 109947--110047 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 53
109937 TAACTGTCTA
* *
109947 TTGCATGTGTGTTTATATGCTTGTTTCTTCTATGTTAAATGGTCTTTTATGCG
1 TTGCATATATGTTTATATGCTTGTTTCTTCTATGTTAAATGGTCTTTTATGCG
*
110000 TTGCATATATGTTTATATGTTTGTTTCTTCTATGTTAAATGGTCTTTT
1 TTGCATATATGTTTATATGCTTGTTTCTTCTATGTTAAATGGTCTTTT
110048 GTGCTATGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.10, G:0.18, T:0.55
Consensus pattern (53 bp):
TTGCATATATGTTTATATGCTTGTTTCTTCTATGTTAAATGGTCTTTTATGCG
Found at i:110371 original size:20 final size:20
Alignment explanation
Indices: 110346--110386 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
110336 CCTGCGATCA
110346 TTAAGGGCCAAATTTATAAT
1 TTAAGGGCCAAATTTATAAT
*
110366 TTAAGGGTCAAATTTATAAT
1 TTAAGGGCCAAATTTATAAT
110386 T
1 T
110387 AGGCCTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (20 bp):
TTAAGGGCCAAATTTATAAT
Found at i:118625 original size:6 final size:6
Alignment explanation
Indices: 118614--118682 Score: 66
Period size: 6 Copynumber: 11.5 Consensus size: 6
118604 GTGGAGATGC
* * * * **
118614 CTGTGG CTGTGG CTGTGA CTGTGA CTGTGA CTGTGG CTGCGA CTGCAA
1 CTGTGA CTGTGA CTGTGA CTGTGA CTGTGA CTGTGA CTGTGA CTGTGA
* *
118662 CTGTGA CTGAGA CTGAGA CTG
1 CTGTGA CTGTGA CTGTGA CTG
118683 AGGCTGCTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.16, C:0.20, G:0.36, T:0.28
Consensus pattern (6 bp):
CTGTGA
Found at i:118664 original size:24 final size:24
Alignment explanation
Indices: 118614--118670 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
118604 GTGGAGATGC
* * **
118614 CTGTGGCTGTGGCTGTGACTGTGA
1 CTGTGACTGTGGCTGCGACTGCAA
118638 CTGTGACTGTGGCTGCGACTGCAA
1 CTGTGACTGTGGCTGCGACTGCAA
118662 CTGTGACTG
1 CTGTGACTG
118671 AGACTGAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.21, G:0.37, T:0.30
Consensus pattern (24 bp):
CTGTGACTGTGGCTGCGACTGCAA
Found at i:123523 original size:6 final size:6
Alignment explanation
Indices: 123512--123550 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
123502 GAAATCACAG
123512 AGCCAA AGCCAA AGCCAA AGCCAA AGGCC-A AGCCAA AGC
1 AGCCAA AGCCAA AGCCAA AGCCAA A-GCCAA AGCCAA AGC
123551 AGAGCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 3 0.10
6 25 0.81
7 3 0.10
ACGTcount: A:0.46, C:0.33, G:0.21, T:0.00
Consensus pattern (6 bp):
AGCCAA
Found at i:124435 original size:14 final size:14
Alignment explanation
Indices: 124413--124442 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
124403 ATTACAACTG
*
124413 TTTATAGAAACTAC
1 TTTACAGAAACTAC
124427 TTTACAGAAACTAC
1 TTTACAGAAACTAC
124441 TT
1 TT
124443 AGTAACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (14 bp):
TTTACAGAAACTAC
Found at i:125980 original size:52 final size:52
Alignment explanation
Indices: 125891--126239 Score: 563
Period size: 52 Copynumber: 6.7 Consensus size: 52
125881 ATTTCATTTC
** *
125891 ATTCATATACTCACGATGACACATAACCACCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
* * **
125943 ATTCATATACTCATGATGACATATAGTCATCAAACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
*
125995 ATTCATATACTCACGATGATACATAGTCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
* *
126047 ATTCATATACTCACAATAACACATAGTCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
* * *
126099 ATTCATATACTCACGATGACACGTAGTCATCGGACCTCATAATTCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
*
126151 ATTCATATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
*
126203 ATTCATATACTCACGATGACACATAGTCATTGGACCT
1 ATTCATATACTCACGATGACACATAGTCATCGGACCT
126240 TTTTCATTTA
Statistics
Matches: 273, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 273 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
Found at i:126007 original size:26 final size:26
Alignment explanation
Indices: 125926--126007 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
125916 ACCACCGGAC
125926 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCGTAAAGGATTCATATA
* * * * *
125952 CTCATGATGACATATA-G--TCATCAAA
1 CTCATAAT-CCGTAAAGGATTCAT-ATA
125977 CCTCATAATCCGTAAAGGATTCATATA
1 -CTCATAATCCGTAAAGGATTCATATA
126004 CTCA
1 CTCA
126008 CGATGATACA
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
24 4 0.10
25 6 0.15
26 20 0.50
27 6 0.15
28 4 0.10
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (26 bp):
CTCATAATCCGTAAAGGATTCATATA
Found at i:129366 original size:14 final size:14
Alignment explanation
Indices: 129342--129376 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
129332 AACAGATTAC
129342 AACTA-TTTATAAA
1 AACTACTTTATAAA
*
129355 AACTACTTTATAGA
1 AACTACTTTATAAA
129369 AACTACTT
1 AACTACTT
129377 AGTAACTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (14 bp):
AACTACTTTATAAA
Found at i:130339 original size:27 final size:26
Alignment explanation
Indices: 130285--130350 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
130275 AAATTAAATT
*
130285 ATAATTATTTTT--AATGTAATTACC
1 ATAATTATTTTTAAAATATAATTACC
*
130309 ATAATTATTTTTAAATATATAATTATC
1 ATAATTATTTTTAAA-ATATAATTACC
*
130336 ATAATTTTTATTTAA
1 ATAATTATT-TTTAA
130351 TTATTATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.34
26 1 0.03
27 17 0.49
28 5 0.14
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATAATTATTTTTAAAATATAATTACC
Found at i:131362 original size:31 final size:31
Alignment explanation
Indices: 131280--131368 Score: 115
Period size: 31 Copynumber: 2.8 Consensus size: 31
131270 ATTTTATATT
* *
131280 TTATTATATTTAATTAGTTAAATATCATTTA
1 TTATTATATTTAATTATTTAAATATTATTTA
** *
131311 TCGTTATATTAAATTATTTAAATATTATTTA
1 TTATTATATTTAATTATTTAAATATTATTTA
*
131342 TTATTATATTTAATTTTTTAAAATATT
1 TTATTATATTTAATTATTT-AAATATT
131369 TTATATATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
31 41 0.85
32 7 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
TTATTATATTTAATTATTTAAATATTATTTA
Found at i:132848 original size:17 final size:18
Alignment explanation
Indices: 132815--132851 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
132805 TATCACTTTC
132815 TTGAAATAAATTAAATAA
1 TTGAAATAAATTAAATAA
132833 TTGAAATAAA-TAAATAA
1 TTGAAATAAATTAAATAA
132850 TT
1 TT
132852 CAAAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TTGAAATAAATTAAATAA
Found at i:132860 original size:17 final size:17
Alignment explanation
Indices: 132826--132860 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
132816 TGAAATAAAT
* *
132826 TAAATAATTGAAATAAA
1 TAAATAATTCAAAAAAA
132843 TAAATAATTCAAAAAAA
1 TAAATAATTCAAAAAAA
132860 T
1 T
132861 CTCAAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAATAATTCAAAAAAA
Found at i:134098 original size:13 final size:13
Alignment explanation
Indices: 134080--134104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
134070 TAAAAATATC
134080 ATAATTAATCATG
1 ATAATTAATCATG
134093 ATAATTAATCAT
1 ATAATTAATCAT
134105 CACGATCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
ATAATTAATCATG
Found at i:138679 original size:15 final size:15
Alignment explanation
Indices: 138661--138714 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
138651 GTCATTAAGC
*
138661 TTAATTAAATTAATA
1 TTAATTAAACTAATA
*
138676 TTAAAGTAAACTAATCA
1 TT-AATTAAACTAAT-A
138693 -TAATTAAACT-A-A
1 TTAATTAAACTAATA
138705 TTAATTAAAC
1 TTAATTAAAC
138715 ACTAATCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
12 1 0.03
13 9 0.27
14 1 0.03
15 10 0.30
16 11 0.33
17 1 0.03
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (15 bp):
TTAATTAAACTAATA
Found at i:138711 original size:13 final size:14
Alignment explanation
Indices: 138662--138714 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
138652 TCATTAAGCT
*
138662 TAATTAAATTAATA
1 TAATTAAACTAATA
*
138676 TTAAAGTAAACTAATCA
1 -T-AATTAAACTAAT-A
138693 TAATTAAACTAAT-
1 TAATTAAACTAATA
138706 TAATTAAAC
1 TAATTAAAC
138715 ACTAATCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.27
15 12 0.36
16 11 0.33
17 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (14 bp):
TAATTAAACTAATA
Found at i:142163 original size:14 final size:14
Alignment explanation
Indices: 142144--142171 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
142134 CATATGTTAC
142144 CATAACCCAACTAT
1 CATAACCCAACTAT
142158 CATAACCCAACTAT
1 CATAACCCAACTAT
142172 GGTCTTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (14 bp):
CATAACCCAACTAT
Found at i:144767 original size:46 final size:46
Alignment explanation
Indices: 144700--144792 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
144690 CCACACCCAA
*
144700 TTATCTTTCCTCTATAGTTACCCCCTTAGCTCCAAGGTAAACAAAG
1 TTATCTTTCCTCTATAGTTACCCCCTTAGCTCAAAGGTAAACAAAG
144746 TTATCTTTCCTCTATAGTTACCCCCTTAGCTCAAAGGTAAACAAAG
1 TTATCTTTCCTCTATAGTTACCCCCTTAGCTCAAAGGTAAACAAAG
144792 T
1 T
144793 GATCCATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (46 bp):
TTATCTTTCCTCTATAGTTACCCCCTTAGCTCAAAGGTAAACAAAG
Found at i:150178 original size:20 final size:21
Alignment explanation
Indices: 150139--150178 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
150129 ATTAAAAATA
*
150139 TTAAAATCATTATTAAATTAT
1 TTAAAATAATTATTAAATTAT
*
150160 TTAAAATAATT-TTATATTA
1 TTAAAATAATTATTAAATTA
150179 AATAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATAATTATTAAATTAT
Done.