Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014642.1 Kokia drynarioides strain JFW-HI SEQ_129681, 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: 86763
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:5098 original size:15 final size:15
Alignment explanation
Indices: 5080--5109 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5070 TAATCTATAA
5080 TATAATAATACTTAT
1 TATAATAATACTTAT
*
5095 TATATTAATACTTAT
1 TATAATAATACTTAT
5110 AAAATTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATAATACTTAT
Found at i:5414 original size:17 final size:17
Alignment explanation
Indices: 5392--5428 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5382 ATAGTAGTAC
5392 ATTATATATTACATATT
1 ATTATATATTACATATT
*
5409 ATTATATATTATATATT
1 ATTATATATTACATATT
5426 ATT
1 ATT
5429 GTTTATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATATATTACATATT
Found at i:5757 original size:16 final size:17
Alignment explanation
Indices: 5736--5768 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5726 AATTTGATAG
5736 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
5752 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
5769 TATGTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Found at i:6686 original size:29 final size:28
Alignment explanation
Indices: 6642--6702 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 28
6632 GTAATTCACC
*
6642 AAAAAAAAAAAGTAAAAT-AAATTTAAA
1 AAAAAAAAAAAGTAAAATGAAATTCAAA
*
6669 AAAAAAAAAAAGACTAAATTGAAATTCAAA
1 AAAAAAAAAAAG--TAAAATGAAATTCAAA
6699 AAAA
1 AAAA
6703 TTTAAGGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
29 5 0.17
30 12 0.41
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (28 bp):
AAAAAAAAAAAGTAAAATGAAATTCAAA
Found at i:8631 original size:13 final size:13
Alignment explanation
Indices: 8605--8642 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
8595 TAGCACACAT
*
8605 AAAACATAGCTTTA
1 AAAACATA-ATTTA
8619 AAAACATAATTTA
1 AAAACATAATTTA
8632 AAAACATAATT
1 AAAACATAATT
8643 GGAAAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAACATAATTTA
Found at i:8710 original size:44 final size:44
Alignment explanation
Indices: 8647--8733 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
8637 ATAATTGGAA
8647 AATAGAGTCTCAAAACTTGAAAATGGAGTTTTGTAGAAAAACAC
1 AATAGAGTCTCAAAACTTGAAAATGGAGTTTTGTAGAAAAACAC
*
8691 AATAGAGTCTCAAAACTTGAAAATGGAGTTTTGTAGAAGAACA
1 AATAGAGTCTCAAAACTTGAAAATGGAGTTTTGTAGAAAAACA
8734 TAATTTTGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (44 bp):
AATAGAGTCTCAAAACTTGAAAATGGAGTTTTGTAGAAAAACAC
Found at i:14085 original size:73 final size:72
Alignment explanation
Indices: 13963--14121 Score: 214
Period size: 73 Copynumber: 2.2 Consensus size: 72
13953 TAGAAGAATA
* * * * *
13963 GACAGTGAGTTACACGGTCTAGGTACACGGGCGTGTCTTCGACCATGTGTACCTATTATTTTAGA
1 GACAGTGAGTTACACGGTCTAGCTACACGAGAGTGTCTTCGACCATGTGTACATACTATTTT-GA
14028 AATCAA-TG
65 AA-CAATTG
* *
14036 GACAGTGAGTTACACGGT-TTGACTACACGAGAGTGTCTTCGACCGTGTGTACATACTATTTTGA
1 GACAGTGAGTTACACGGTCTAG-CTACACGAGAGTGTCTTCGACCATGTGTACATACTATTTTGA
14100 AACAATTG
65 AACAATTG
14108 GACAGTGAGTTACA
1 GACAGTGAGTTACA
14122 AGAGCTAGAC
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
71 3 0.04
72 22 0.29
73 52 0.68
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (72 bp):
GACAGTGAGTTACACGGTCTAGCTACACGAGAGTGTCTTCGACCATGTGTACATACTATTTTGAA
ACAATTG
Found at i:14151 original size:72 final size:73
Alignment explanation
Indices: 13963--14162 Score: 201
Period size: 73 Copynumber: 2.8 Consensus size: 73
13953 TAGAAGAATA
* * ** * * *
13963 GACAGTGAGTTACACGGTCTAG-GTACACGGGCGTGTCTTCGACCATGTGTACCTATTATTTTAG
1 GACAGTGAGTTACAAGG-CTAGACTACACAAGCGTGTCTTCGACCGTGTGTACATACTATTTTAG
14027 AAATCAATG
65 AAATCAATG
* * * * *
14036 GACAGTGAGTTACACGGTTTGACTACACGAGAGTGTCTTCGACCGTGTGTACATACTATTTT-GA
1 GACAGTGAGTTACAAGGCTAGACTACACAAGCGTGTCTTCGACCGTGTGTACATACTATTTTAGA
14100 AA-CAATTG
66 AATCAA-TG
* * * *
14108 GACAGTGAGTTACAAGAGCTAGAC-CCACAATCGTGTCTCCGACCGTGTGTGCATA
1 GACAGTGAGTTACAAG-GCTAGACTACACAAGCGTGTCTTCGACCGTGTGTACATA
14163 ATGGTTGGTG
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
71 3 0.03
72 48 0.45
73 56 0.52
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (73 bp):
GACAGTGAGTTACAAGGCTAGACTACACAAGCGTGTCTTCGACCGTGTGTACATACTATTTTAGA
AATCAATG
Found at i:18713 original size:69 final size:68
Alignment explanation
Indices: 18600--18739 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 68
18590 GAATTCGGGC
*
18600 TGAATAGCGAGGGAGTTTTGTGCTTCAAAGGCTAAATCTGTACTGGTGGCCTGAGTTGAAACGAG
1 TGAATAGCGAGGGAGTTTTATGCTTCAAAGGCTAAATCTGTACTGGTGGCCTGAGTTGAAACGAG
18665 ACG
66 ACG
18668 TGNAATAGCGAGGGAGTTTTATGCTTCAAAGGCTAAATCTGTACTGGTGGCCTGAGTTGAAACGA
1 TG-AATAGCGAGGGAGTTTTATGCTTCAAAGGCTAAATCTGTACTGGTGGCCTGAGTTGAAACGA
18733 GACG
65 GACG
18737 TGA
1 TGA
18740 CTACCTACGT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 3 0.04
69 67 0.96
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.26
Consensus pattern (68 bp):
TGAATAGCGAGGGAGTTTTATGCTTCAAAGGCTAAATCTGTACTGGTGGCCTGAGTTGAAACGAG
ACG
Found at i:23506 original size:18 final size:18
Alignment explanation
Indices: 23485--23521 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
23475 TCATAATGGG
23485 GTTCACATACATACATGA
1 GTTCACATACATACATGA
*
23503 GTTCACATACATATATGA
1 GTTCACATACATACATGA
23521 G
1 G
23522 GTTACACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (18 bp):
GTTCACATACATACATGA
Found at i:23551 original size:106 final size:106
Alignment explanation
Indices: 23428--23634 Score: 396
Period size: 106 Copynumber: 2.0 Consensus size: 106
23418 TACATATATG
23428 ACCTGGGTTCGCTAAGTAGCAAGACTATTGCCAACATCAAACTTTATTCATAATGGGGTTCACAT
1 ACCTGGGTTCGCTAAGTAGCAAGACTATTGCCAACATCAAACTTTATTCATAATGGGGTTCACAT
*
23493 ACATACATGAGTTCACATACATATATGAGGTTACACAATTT
66 ACATACATGAGTTCACATACATATATGAGGTCACACAATTT
23534 ACCTGGGTTCGCTAAGTAGCAAGACTATTGCCAACATCAAACTTTATTCATAATGGGGTTCACAT
1 ACCTGGGTTCGCTAAGTAGCAAGACTATTGCCAACATCAAACTTTATTCATAATGGGGTTCACAT
*
23599 ACATACATGAGTTCACATACATATATGGGGTCACAC
66 ACATACATGAGTTCACATACATATATGAGGTCACAC
23635 TCATATGTGA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (106 bp):
ACCTGGGTTCGCTAAGTAGCAAGACTATTGCCAACATCAAACTTTATTCATAATGGGGTTCACAT
ACATACATGAGTTCACATACATATATGAGGTCACACAATTT
Found at i:23632 original size:18 final size:17
Alignment explanation
Indices: 23582--23633 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
23572 AAACTTTATT
23582 CATAATGGGGTTCACATA
1 CATAATGGGG-TCACATA
* *
23600 CATACATGAGTTCACATA
1 CATA-ATGGGGTCACATA
23618 CATATATGGGGTCACA
1 CATA-ATGGGGTCACA
23634 CTCATATGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (17 bp):
CATAATGGGGTCACATA
Found at i:26277 original size:14 final size:14
Alignment explanation
Indices: 26255--26298 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
26245 GCACAGGTGC
26255 ACTTATAAAACATA
1 ACTTATAAAACATA
*
26269 ACTTTTAAAACATA
1 ACTTATAAAACATA
* *
26283 GCTTA-GAAACATA
1 ACTTATAAAACATA
26296 ACT
1 ACT
26299 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.30
Consensus pattern (14 bp):
ACTTATAAAACATA
Found at i:26994 original size:63 final size:63
Alignment explanation
Indices: 26927--27050 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
26917 TTTGCAGTCA
* *
26927 CACGAACTACATTTACATGAATTGTAATT-GCATAAACTGCTACATTTACATGAACTGTAGTTG
1 CACGAACTACATTTACAAGAACTG-AATTCGCATAAACTGCTACATTTACATGAACTGTAGTTG
* * * * * * *
26990 CACGAGCTGCATTTGCAAGAACTGCATTCGCATAAATTGTTGCATTTACATGAACTGTAGT
1 CACGAACTACATTTACAAGAACTGAATTCGCATAAACTGCTACATTTACATGAACTGTAGT
27051 CACATAAACT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
CACGAACTACATTTACAAGAACTGAATTCGCATAAACTGCTACATTTACATGAACTGTAGTTG
Found at i:28142 original size:25 final size:26
Alignment explanation
Indices: 28093--28160 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
28083 GGACTTTGAT
* *
28093 TGGCGAACCCCTAGTTTGCAACTC-AC
1 TGGCGAACCTC-AGTTCGCAACTCAAC
*
28119 TGGCGAACCTCAGTTCGCAGCTCAAC
1 TGGCGAACCTCAGTTCGCAACTCAAC
* *
28145 TAGCAAACCTCCAGTT
1 TGGCGAACCT-CAGTT
28161 TGCTAAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 10 0.29
26 20 0.57
27 5 0.14
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (26 bp):
TGGCGAACCTCAGTTCGCAACTCAAC
Found at i:33688 original size:26 final size:25
Alignment explanation
Indices: 33648--33728 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 25
33638 AATTAAGTTT
33648 AAAAAAAATTAGATACCAAATTAAA
1 AAAAAAAATTAGATACCAAATTAAA
** *
33673 AAAATAAAATTAGATATTAAACTAAA
1 AAAA-AAAATTAGATACCAAATTAAA
*
33699 TAAAAAAAATTTAAATACCAAATTAAA
1 -AAAAAAAA-TTAGATACCAAATTAAA
33726 AAA
1 AAA
33729 TATTAAGTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.09
26 25 0.54
27 17 0.37
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (25 bp):
AAAAAAAATTAGATACCAAATTAAA
Found at i:36680 original size:25 final size:26
Alignment explanation
Indices: 36660--36708 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
36650 TAAAACCTAA
36660 GAAAAAGAGAAAAACTTAAACTAAAC
1 GAAAAAGAGAAAAACTTAAACTAAAC
* *
36686 TAAAAAGAGAAAAA-TTAATCTAA
1 GAAAAAGAGAAAAACTTAAACTAA
36709 TTCATTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.16
Consensus pattern (26 bp):
GAAAAAGAGAAAAACTTAAACTAAAC
Found at i:37452 original size:3 final size:3
Alignment explanation
Indices: 37444--37573 Score: 106
Period size: 3 Copynumber: 42.7 Consensus size: 3
37434 ACAAAATCAA
*
37444 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA- ACGA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT
* * * * * *
37489 AAT GAC AAA ACAT AA- AACA AAT AAA AAGGC AA- AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AA-T AAT AAT AA--T AAT AAT AAT AAT AAT AAT
*
37536 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37574 CAACAACAAC
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.06
3 92 0.87
4 6 0.06
5 2 0.02
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:37491 original size:83 final size:83
Alignment explanation
Indices: 37391--37567 Score: 295
Period size: 83 Copynumber: 2.1 Consensus size: 83
37381 ATTAGTTGCA
*
37391 AATAA-AAGTAAACGAAATGACAAAACATAAAATAAATAAAAAGACAAAATCAA-AATAATAATA
1 AATAATAA-TAAACGAAATGACAAAACATAAAACAAATAAAAAGACAAAAT-AATAATAATAATA
37454 ATAATAATAACAATAATAAT
64 ATAATAATAACAATAATAAT
*
37474 AATAATAATAAACGAAATGACAAAACATAAAACAAATAAAAAGGCAAAATAATAATAATAATAAT
1 AATAATAATAAACGAAATGACAAAACATAAAACAAATAAAAAGACAAAATAATAATAATAATAAT
*
37539 AATAATAATAATAATAAT
66 AATAATAACAATAATAAT
37557 AATAATAATAA
1 AATAATAATAA
37568 CAATAACAAC
Statistics
Matches: 89, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
82 2 0.02
83 85 0.96
84 2 0.02
ACGTcount: A:0.68, C:0.06, G:0.05, T:0.21
Consensus pattern (83 bp):
AATAATAATAAACGAAATGACAAAACATAAAACAAATAAAAAGACAAAATAATAATAATAATAAT
AATAATAACAATAATAAT
Found at i:37578 original size:3 final size:3
Alignment explanation
Indices: 37566--37693 Score: 222
Period size: 3 Copynumber: 42.7 Consensus size: 3
37556 TAATAATAAT
* *
37566 AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA- TAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
37613 TAAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 -AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
37659 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
37694 TAATAATAAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
2 1 0.01
3 116 0.97
4 2 0.02
ACGTcount: A:0.66, C:0.31, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:39410 original size:11 final size:11
Alignment explanation
Indices: 39392--39432 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
39382 ATCTACGAAA
39392 AAAATATAAAT
1 AAAATATAAAT
*
39403 ATAATATAAAT
1 AAAATATAAAT
*
39414 AAAATAAAAAT
1 AAAATATAAAT
39425 AAAA-ATAA
1 AAAATATAA
39433 GAAGAAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 3 0.12
11 23 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATATAAAT
Found at i:41222 original size:22 final size:22
Alignment explanation
Indices: 41171--41251 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
41161 AAGTACTTAA
* *
41171 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTACAAT
41193 CCAGTAGGCACACACAGTACAAT
1 -CAGTAGGCACACACAGTACAAT
*
41216 CAGTAGGCACACATAGCGTA-AAT
1 CAGTAGGCACACACA--GTACAAT
*
41239 TAGTAGGCACACA
1 CAGTAGGCACACA
41252 AGGTGTGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
22 14 0.27
23 35 0.67
24 3 0.06
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.15
Consensus pattern (22 bp):
CAGTAGGCACACACAGTACAAT
Found at i:41266 original size:23 final size:23
Alignment explanation
Indices: 41240--41338 Score: 137
Period size: 23 Copynumber: 4.3 Consensus size: 23
41230 AGCGTAAATT
* *
41240 AGTAGGCACACAAGGTGTGAAAC
1 AGTAAGCACACAAGGTGCGAAAC
*
41263 AGTAAGCACACAAGGTGCAAAAC
1 AGTAAGCACACAAGGTGCGAAAC
*
41286 AGTAAGCACACAAAGTGCGAAAC
1 AGTAAGCACACAAGGTGCGAAAC
*
41309 AGTAAGCACACGAA-GTGCGAAAT
1 AGTAAGCACAC-AAGGTGCGAAAC
41332 AGTAAGC
1 AGTAAGC
41339 GCGCTAGAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
23 67 0.97
24 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (23 bp):
AGTAAGCACACAAGGTGCGAAAC
Found at i:41336 original size:46 final size:46
Alignment explanation
Indices: 41169--41338 Score: 143
Period size: 46 Copynumber: 3.7 Consensus size: 46
41159 CGAAGTACTT
*** * * *
41169 AACAGTAAGCACACACA-GTGCAATCCAGTAGGCACACACAGTAC-A
1 AACAGTAAGCACACA-AGGTGCAAAATAGTAAGCACACAAAGTGCGA
* * * * * *
41214 ATCAGTAGGCACACATAGCGT--AAATTAGTAGGCACACAAGGTGTGA
1 AACAGTAAGCACACA-AG-GTGCAAAATAGTAAGCACACAAAGTGCGA
*
41260 AACAGTAAGCACACAAGGTGCAAAACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAGGTGCAAAATAGTAAGCACACAAAGTGCGA
*
41306 AACAGTAAGCACACGAA-GTGCGAAATAGTAAGC
1 AACAGTAAGCACAC-AAGGTGCAAAATAGTAAGC
41339 GCGCTAGAGT
Statistics
Matches: 100, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
44 2 0.02
45 32 0.32
46 62 0.62
47 4 0.04
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (46 bp):
AACAGTAAGCACACAAGGTGCAAAATAGTAAGCACACAAAGTGCGA
Found at i:58027 original size:18 final size:18
Alignment explanation
Indices: 58004--58040 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
57994 ACAATTCATA
58004 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
58022 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
58040 T
1 T
58041 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
Found at i:61183 original size:18 final size:18
Alignment explanation
Indices: 61160--61196 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
61150 ACAATTCATA
61160 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
61178 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
61196 T
1 T
61197 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
Found at i:67191 original size:74 final size:74
Alignment explanation
Indices: 67070--67218 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
67060 GGAAGGTGAG
67070 AGAAGGAGAAATAAGGAGGTGAGAGGGAATGAAATACTAAAAGGGGAAGAATAGGGAACAATAAA
1 AGAAGGAGAAATAAGGAGGTGAGAGGGAATGAAATACTAAAAGGGGAAGAATAGGGAACAATAAA
67135 ATGTGCCAA
66 ATGTGCCAA
67144 AGAAGGAGAAATAAGGAGGTGAGAGGGAATGAAATACTAAAAGGGGAAGAATAGGGAACAATAAA
1 AGAAGGAGAAATAAGGAGGTGAGAGGGAATGAAATACTAAAAGGGGAAGAATAGGGAACAATAAA
67209 ATGTGCCAA
66 ATGTGCCAA
67218 A
1 A
67219 CTGTCTTCGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.50, C:0.05, G:0.32, T:0.12
Consensus pattern (74 bp):
AGAAGGAGAAATAAGGAGGTGAGAGGGAATGAAATACTAAAAGGGGAAGAATAGGGAACAATAAA
ATGTGCCAA
Found at i:70140 original size:12 final size:12
Alignment explanation
Indices: 70123--70162 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
70113 CCTTGATAGG
70123 TTCTTTTCTTCT
1 TTCTTTTCTTCT
70135 TTCTTTTCTTCCT
1 TTCTTTTCTT-CT
70148 TTCCTTCTTCTTCT
1 TT-CTT-TTCTTCT
70162 T
1 T
70163 CTTGATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 4 0.16
14 6 0.24
15 5 0.20
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:71955 original size:46 final size:46
Alignment explanation
Indices: 71888--71975 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
71878 GCTAGGAGAG
* *
71888 AAAGAAATCACTCGGTGTGATTCTTGCAGAAAAACTAATGCTAACT
1 AAAGAAATCAATCGGGGTGATTCTTGCAGAAAAACTAATGCTAACT
* *
71934 AAAGAAATCAATCGGGGTGATTCTTGCTGAAAAAGTAATGCT
1 AAAGAAATCAATCGGGGTGATTCTTGCAGAAAAACTAATGCT
71976 GACTCATCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (46 bp):
AAAGAAATCAATCGGGGTGATTCTTGCAGAAAAACTAATGCTAACT
Found at i:78293 original size:48 final size:48
Alignment explanation
Indices: 78238--78333 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
78228 TATAGATGGA
78238 ATGTCACTACAATGAAGTCCCTTTGAGTTCTTACCAACAACAACTCTC
1 ATGTCACTACAATGAAGTCCCTTTGAGTTCTTACCAACAACAACTCTC
78286 ATGTCACTACAATGAAGTCCCTTTGAGTTCTTACCAACAACAACTCTC
1 ATGTCACTACAATGAAGTCCCTTTGAGTTCTTACCAACAACAACTCTC
78334 TACTTAATCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (48 bp):
ATGTCACTACAATGAAGTCCCTTTGAGTTCTTACCAACAACAACTCTC
Found at i:86687 original size:2 final size:2
Alignment explanation
Indices: 86680--86710 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
86670 TATTAATGAA
86680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
86711 AATTAAAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.