Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010862.1 Kokia drynarioides strain JFW-HI SEQ_125830, 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: 24271
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Warning! 64 characters in sequence are not A, C, G, or T
Found at i:182 original size:22 final size:22
Alignment explanation
Indices: 142--202 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
132 TGAGCTAAGG
*
142 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
163 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
185 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
203 GGAAGTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:193 original size:15 final size:16
Alignment explanation
Indices: 168--197 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
158 GAATTAAAAA
168 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
184 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
198 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:1023 original size:19 final size:19
Alignment explanation
Indices: 999--1041 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
989 AAACATAAAT
999 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
1018 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
1037 TAAAT
1 TAAAT
1042 CCTAATGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:3895 original size:21 final size:21
Alignment explanation
Indices: 3861--3917 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
3851 ATAGATGCCT
*
3861 CAGTTTTC-TTTGAAAATCCA
1 CAGTTTGCTTTTGAAAATCCA
*
3881 CAGTTTGCTTTTGAAAATCTA
1 CAGTTTGCTTTTGAAAATCCA
* * *
3902 TAGATTGCTATTGAAA
1 CAGTTTGCTTTTGAAA
3918 TTTTAAGAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 7 0.23
21 24 0.77
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCCA
Found at i:5493 original size:22 final size:22
Alignment explanation
Indices: 5453--5513 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
5443 CGATCTAAGG
*
5453 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
5474 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
5496 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
5514 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:5504 original size:15 final size:16
Alignment explanation
Indices: 5479--5508 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5469 GAATTAAAAA
5479 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
5495 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
5509 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:6555 original size:10 final size:10
Alignment explanation
Indices: 6540--6568 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6530 ACTCCAAATT
6540 TATTTATTTC
1 TATTTATTTC
6550 TATTTATTTC
1 TATTTATTTC
6560 TATTT-TTTC
1 TATTTATTTC
6569 GGGTTAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTATTTC
Found at i:8078 original size:18 final size:19
Alignment explanation
Indices: 8055--8095 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
8045 TCTCACCAAC
*
8055 ATTTACCTTTT-GTTGGAT
1 ATTTACCTTTTCATTGGAT
8073 ATTTACCTTTTCATTGGAT
1 ATTTACCTTTTCATTGGAT
8092 ATTT
1 ATTT
8096 TCTAGTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (19 bp):
ATTTACCTTTTCATTGGAT
Found at i:11077 original size:22 final size:22
Alignment explanation
Indices: 11028--11078 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
11018 TTTGACCTAG
* * * *
11028 CGTTGACTGACCGTTCATCGAG
1 CGTTGACTGACCATTAACCGAC
*
11050 CATTGACTGACCATTAACCGAC
1 CGTTGACTGACCATTAACCGAC
11072 CGTTGAC
1 CGTTGAC
11079 CATTGACTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (22 bp):
CGTTGACTGACCATTAACCGAC
Found at i:12201 original size:23 final size:22
Alignment explanation
Indices: 12150--12201 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
12140 TTACTTTATC
* *
12150 TTATTATTATTTTGATTTTTGG
1 TTATTATTATCTTGATTGTTGG
*
12172 TTTTTATTATACTTGATTAGTT-G
1 TTATTATTAT-CTTGATT-GTTGG
12195 TTATTAT
1 TTATTAT
12202 AATTAGGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 9 0.38
23 13 0.54
24 2 0.08
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (22 bp):
TTATTATTATCTTGATTGTTGG
Found at i:14640 original size:58 final size:57
Alignment explanation
Indices: 14564--14921 Score: 289
Period size: 58 Copynumber: 6.2 Consensus size: 57
14554 CACCCCGAAC
* * *
14564 TTTCCAAAAATTA-TATTTTTACCCCGAACTTTCTAAAATTCCATTTTTAACCTCGAT
1 TTTCCAAAAATTACCA-TTTTACCCCGAACTTCCAAAAATTCCATTTTTAACCTCGAT
* * * *
14621 TTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTTCGTTTTTACCCT-AAT
1 TTTCCAAAAATTACCATTTTACCC-CGAACTTCCAAAAATTCCATTTTTAACCTCGAT
* * *
14678 TTCTCCAAAAATTATCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAATT
1 TT-TCCAAAAATTACCATTTTACCC-CGAACTTCCAAAAATTCCATTTTTAACCTCGA-T
* * * *
14738 TTTCTAAAAA-AACCATTTTACCCCCGAACTTCCAAAAATTTCATTTTTTATCC-CGATT
1 TTTCCAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATTCCA-TTTTTAACCTCGA-T
** * * * * *
14796 CTTTCCAAAAATCCCCATTTTACTCTCGGA-TGT-CTAAAATTCCATTTTTAACCTTGAAC
1 -TTTCCAAAAATTACCATTTTAC-CCCGAACT-TCCAAAAATTCCATTTTTAACCTCG-AT
* * * * * *
14855 TTTCCAAAAATTACCATTTTGCCCCCAAATATCCAAAATTTACCA-TTTTACCCTCGAG
1 TTTCCAAAAATTACCATTTTACCCCGAACT-TCCAAAAATT-CCATTTTTAACCTCGAT
*
14913 TATCCAAAA
1 TTTCCAAAA
14922 TCACATTTTC
Statistics
Matches: 243, Mismatches: 42, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
57 28 0.12
58 140 0.58
59 55 0.23
60 20 0.08
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.37
Consensus pattern (57 bp):
TTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTAACCTCGAT
Found at i:14727 original size:29 final size:29
Alignment explanation
Indices: 14531--14874 Score: 194
Period size: 29 Copynumber: 11.7 Consensus size: 29
14521 GAGGTCCTTA
*
14531 AACTGTCCAAAAA-TCATATTTTTCACCC-CG
1 AACT-TCCAAAAATTC-CATTTTT-ACCCTCG
**
14561 AACTTTCCAAAAATTATATTTTTACCC-CG
1 AAC-TTCCAAAAATTCCATTTTTACCCTCG
* * *
14590 AACTTTCTAAAATTCCATTTTTAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
**
14619 ATTTTCCAAAAATTACCA-TTTTACCCTCG
1 AACTTCCAAAAATT-CCATTTTTACCCTCG
* *
14648 AACTTCCAAAAATTTCGTTTTTACCCT--
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
14675 AATTTCTCCAAAAATTATCA-TTTTACCCTCG
1 AA-CT-TCCAAAAATT-CCATTTTTACCCTCG
14706 AACTTCCAAAAATTCCATTTTTGA-CCTC-
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* * ** *
14734 AATTTTTCTAAAAAAACCA-TTTTACCCCCG
1 AA--CTTCCAAAAATTCCATTTTTACCCTCG
* *
14764 AACTTCCAAAAATTTCATTTTTTATCC-CG
1 AACTTCCAAAAATTCCA-TTTTTACCCTCG
* * *
14793 ATTCTTTCCAAAAATCCCCA-TTTTACTCTCG
1 A-AC-TTCCAAAAAT-TCCATTTTTACCCTCG
* * * *
14824 GA-TGT-CTAAAATTCCATTTTTAACCTTG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
14852 AACTTTCCAAAAATTACCATTTT
1 AAC-TTCCAAAAATT-CCATTTT
14875 GCCCCCAAAT
Statistics
Matches: 242, Mismatches: 44, Indels: 55
0.71 0.13 0.16
Matches are distributed among these distances:
27 5 0.02
28 51 0.21
29 101 0.42
30 60 0.25
31 23 0.10
32 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:14864 original size:116 final size:115
Alignment explanation
Indices: 14580--14880 Score: 333
Period size: 116 Copynumber: 2.6 Consensus size: 115
14570 AAAATTATAT
*
14580 TTTTACCC-CGAACTTTCTAAAATTCCATTTTTAACCTCG-ATTTTCCAAAAATTACCATTTTAC
1 TTTTACCCTCGAAC-TTCTAAAATTCCATTTTTAACCTTGAATTTTCCAAAAA-TACCATTTTAC
* * *
14643 CCTCGAACTTCCAAAAATTTCGTTTTTACCCTAATTTCTCCAAAAATTATCA
64 CCCCGAACTTCCAAAAATTTCGTTTTTACCCTAATTTCTCCAAAAATCACCA
* * * * *
14695 TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACC-TCAATTTTTCTAAAAAAACCATTTTAC
1 TTTTACCCTCGAACTT-CTAAAATTCCATTTTTAACCTTGAA-TTTTCCAAAAATACCATTTTAC
* * * *
14759 CCCCGAACTTCCAAAAATTTCATTTTTTATCCC-GATTCTTTCCAAAAATCCCCA
64 CCCCGAACTTCCAAAAATTTC-GTTTTTA-CCCTAATT-TCTCCAAAAATCACCA
* * * *
14813 TTTTACTCTCGGA-TGTCTAAAATTCCATTTTTAACCTTGAACTTTCCAAAAATTACCATTTTGC
1 TTTTACCCTCGAACT-TCTAAAATTCCATTTTTAACCTTGAATTTTCCAAAAA-TACCATTTTAC
14877 CCCC
64 CCCC
14881 AAATATCCAA
Statistics
Matches: 154, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
115 10 0.06
116 54 0.35
117 47 0.31
118 43 0.28
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.38
Consensus pattern (115 bp):
TTTTACCCTCGAACTTCTAAAATTCCATTTTTAACCTTGAATTTTCCAAAAATACCATTTTACCC
CCGAACTTCCAAAAATTTCGTTTTTACCCTAATTTCTCCAAAAATCACCA
Found at i:14922 original size:29 final size:29
Alignment explanation
Indices: 14857--14922 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
14847 CCTTGAACTT
* *
14857 TCCAAAAATTACCATTTTGCCCCCAAATA
1 TCCAAAATTTACCATTTTACCCCCAAATA
* * *
14886 TCCAAAATTTACCATTTTACCCTCGAGTA
1 TCCAAAATTTACCATTTTACCCCCAAATA
14915 TCCAAAAT
1 TCCAAAAT
14923 CACATTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.30
Consensus pattern (29 bp):
TCCAAAATTTACCATTTTACCCCCAAATA
Found at i:19371 original size:11 final size:11
Alignment explanation
Indices: 19355--19388 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
19345 GATGTGTTAT
19355 AAAAAAAAAGG
1 AAAAAAAAAGG
*
19366 AAAAAAAAAAG
1 AAAAAAAAAGG
19377 AGAAAAAAAAGG
1 A-AAAAAAAAGG
19389 GATGGGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:19373 original size:13 final size:13
Alignment explanation
Indices: 19355--19386 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
19345 GATGTGTTAT
19355 AAAAAAAAAG-GA
1 AAAAAAAAAGAGA
19367 AAAAAAAAAGAGA
1 AAAAAAAAAGAGA
19380 AAAAAAA
1 AAAAAAA
19387 GGGATGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAGA
Found at i:20328 original size:11 final size:11
Alignment explanation
Indices: 20300--20368 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 11
20290 AGATACAATG
20300 AAGAAAAA-ATA
1 AAGAAAAAGA-A
*
20311 AATAAAAAGAA
1 AAGAAAAAGAA
20322 AAG-AAAAG-A
1 AAGAAAAAGAA
20331 AAGAAAAAAGAA
1 AAG-AAAAAGAA
*
20343 AAGCAAAAACAA
1 AAG-AAAAAGAA
*
20355 GAAGAAAAACAA
1 -AAGAAAAAGAA
20367 AA
1 AA
20369 ATAGAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
9 4 0.08
10 5 0.10
11 17 0.35
12 20 0.41
13 3 0.06
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.03
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:20356 original size:22 final size:21
Alignment explanation
Indices: 20314--20384 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
20304 AAAAATAAAT
20314 AAAAAGAAAAGAAAAGAAAGA
1 AAAAAGAAAAGAAAAGAAAGA
20335 AAAAAGAAAAGCAAAA-ACAAGA
1 AAAAAGAAAAG-AAAAGA-AAGA
* *
20357 AGAAAA-ACAAA-AATAGAAAAA
1 A-AAAAGA-AAAGAAAAGAAAGA
20378 AAAAAGA
1 AAAAAGA
20385 GGTCGAGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
20 4 0.10
21 20 0.48
22 11 0.26
23 7 0.17
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.01
Consensus pattern (21 bp):
AAAAAGAAAAGAAAAGAAAGA
Found at i:20361 original size:18 final size:16
Alignment explanation
Indices: 20314--20369 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
20304 AAAAATAAAT
20314 AAAAAGAAAAGAAAAG-
1 AAAAA-AAAAGAAAAGC
20330 AAAGAAAAAAGAAAAGC
1 AAA-AAAAAAGAAAAGC
*
20347 AAAAACAAGAAGAAAAAC
1 AAAAA-AA-AAGAAAAGC
20365 AAAAA
1 AAAAA
20370 TAGAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 15 0.43
17 7 0.20
18 13 0.37
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAGC
Found at i:20376 original size:26 final size:25
Alignment explanation
Indices: 20300--20380 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 25
20290 AGATACAATG
20300 AAGAAA-AAATAAATAAAAAGAAAAGAA
1 AAGAAAGAAA-AAA-AAAAAGAAAA-AA
* *
20327 AAGAAAGAAAAAAGAAAAGCAAAAAC
1 AAGAAAGAAAAAAAAAAAG-AAAAAA
20353 AAG-AAGAAAAACAAAAATAGAAAAAA
1 AAGAAAGAAAAA-AAAAA-AGAAAAAA
20379 AA
1 AA
20381 AAGAGGTCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
25 8 0.17
26 20 0.43
27 15 0.33
28 3 0.07
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (25 bp):
AAGAAAGAAAAAAAAAAAGAAAAAA
Found at i:20382 original size:31 final size:30
Alignment explanation
Indices: 20304--20382 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
20294 ACAATGAAGA
* *
20304 AAAAATA-AATAAAAAGAAAAGAAAAGAAAG
1 AAAAATAGAA-AAAAAAAAAAGAAAAGAAAC
*
20334 AAAAA-AGAAAAGCAAAAACAAGAAGAA-AAAC
1 AAAAATAGAAAA--AAAAAAAAGAA-AAGAAAC
20365 AAAAATAGAAAAAAAAAA
1 AAAAATAGAAAAAAAAAA
20383 GAGGTCGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
29 3 0.08
30 12 0.30
31 17 0.43
32 8 0.20
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (30 bp):
AAAAATAGAAAAAAAAAAAAGAAAAGAAAC
Found at i:21751 original size:48 final size:48
Alignment explanation
Indices: 21600--22526 Score: 471
Period size: 49 Copynumber: 19.1 Consensus size: 48
21590 CAGCGGATCC
* * * * * * *
21600 AGTACCATGAAGACATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCC-
1 AGTACCACGAAGACA-CAAGGGAAAGGTTTAAGTCGCAATGACGAA-CCT
* * ** * * *
21649 AGTACCATGAAGACATGAAGGGAAATATCTAAGCCGCAACT-ACGGATCC-
1 AGTACCACGAAGACA-CAAGGGAAAGGTTTAAGTCGCAA-TGAC-GAACCT
* * * **
21698 AGTACCACGAAAACACAAAGGAAAGGTTTTAGTCATAATGACGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * * * * *
21746 AGTACCTC-AGAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATCT
1 AGTACCACGA-AGACA-CAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* **
21795 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGTAATGGTGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * * ** *
21843 AGTACCTC-AGAGACATGAAGGGAAAGATCTAAGCCGCAATGGTGGATCC-
1 AGTACCACGA-AGACA-CAAGGGAAAGGTTTAAGTCGCAAT-GACGAACCT
* * *
21892 AGTACCACGAAAACACAAGGGAAAGGTTTTAGTCACAATGACGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * * * * *
21940 AGTACCTC-AGAGACATGAACGGAAAGATCTAAGCCGCAACGACAGATCC-
1 AGTACCACGA-AGACA-CAAGGGAAAGGTTTAAGTCGCAATGAC-GAACCT
*
21989 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCG-AATGGCGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * * * *
22036 AGTACTTCA-G-AGACATGAAAGGAAAGATTTAAGCCACAACGACGGATCC-
1 AGTAC--CACGAAGACA-CAAGGGAAAGGTTTAAGTCGCAATGAC-GAACCT
* *
22085 AGTACCACGAAAACATAAGGGAAAGGTTTAAGTCGCAAT-AGCGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGA-CGAACCT
* * * * * * ** *
22133 AGTACCTC-AGAGACATGAAGGGAAAGATCTAAG-CTACAACGGTGGATCC-
1 AGTACCACGA-AGACA-CAAGGGAAAGGTTTAAGTC-GCAA-TGACGAACCT
* *
22182 AGTACCATGAAAACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * * * *
22230 AGTACCTC-AGAGACATTAAGGGAAAGATCTAAGCCGCAATGGCAGATCC-
1 AGTACCACGA-AGACA-CAAGGGAAAGGTTTAAGTCGCAATGAC-GAACCT
**
22279 AGTACCACGAAGACATGAGGGAAAGGTTTAAGTCGCAATGACGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * * * *
22327 AGTACCTC-AGAGACATTAAGGGAAAGATCTAAGCCGCAACGGTA-GATCC-
1 AGTACCACGA-AGACA-CAAGGGAAAGGTTTAAGTCGCAA-TG-ACGAACCT
* *
22376 AGTACCACGAAGACACGAGGGAAAGGTTTAAGTCGCAATGGCGAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * * * * ** *
22424 AGTACCTC-AGAGACATGAAGGGAAAGATCTAGGCCGCAACGGTGGATCC-
1 AGTACCACGA-AGACA-CAAGGGAAAGGTTTAAGTCGCAA-TGACGAACCT
* * *
22473 AGTACCATGAAGACACAAGGGAAAGGTTTAAG-CTGCAATGGCAAACCT
1 AGTACCACGAAGACACAAGGGAAAGGTTTAAGTC-GCAATGACGAACCT
*
22521 GGTACC
1 AGTACC
22527 TCAGAAAAAG
Statistics
Matches: 654, Mismatches: 172, Indels: 105
0.70 0.18 0.11
Matches are distributed among these distances:
46 4 0.01
47 57 0.09
48 269 0.41
49 283 0.43
50 40 0.06
51 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.16
Consensus pattern (48 bp):
AGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
Found at i:21766 original size:97 final size:97
Alignment explanation
Indices: 21561--22632 Score: 1284
Period size: 97 Copynumber: 11.1 Consensus size: 97
21551 AGTACCACGA
* * * *
21561 AGACATGAAGCGAAAGATCTAAGCCACAAC-AGCGGATCCAGTACCATGAAGACATGAAGGGAAA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGA-CGGATCCAGTACCACGAAGACA-CAAGGGAAA
* * * * * *
21625 GATTTAAGCCGTAACGGCGAATCC-AGTACCATGA-
64 GGTTTAAGTCGCAATGACGAA-CCTAGTACC-TCAG
* * * *
21659 AGACATGAAGGGAAATATCTAAGCCGCAACTACGGATCCAGTACCACGAAAACACAAAGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
* **
21724 TTTTAGTCATAATGACGAACCTAGTACCTCAG
66 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
* * *
21756 AGACATGAAGGGAAAGATTTAAGCCGCAACGGCGGATCTAGTACCACGAAGACACAAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
* **
21821 TTTAAGTCGTAATGGTGAACCTAGTACCTCAG
66 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
* ** *
21853 AGACATGAAGGGAAAGATCTAAGCCGCAATGGTGGATCCAGTACCACGAAAACACAAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
* *
21918 TTTTAGTCACAATGACGAACCTAGTACCTCAG
66 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
* *
21950 AGACATGAACGGAAAGATCTAAGCCGCAACGACAGATCCAGTACCACGAAGACACAAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
* *
22015 TTTAAGTCG-AATGGCGAACCTAGTACTTCAG
66 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
* * * * *
22046 AGACATGAAAGGAAAGATTTAAGCCACAACGACGGATCCAGTACCACGAAAACATAAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
22111 TTTAAGTCGCAAT-AGCGAACCTAGTACCTCAG
66 TTTAAGTCGCAATGA-CGAACCTAGTACCTCAG
** ** * *
22143 AGACATGAAGGGAAAGATCTAAGCTACAACGGTGGATCCAGTACCATGAAAACACAAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
22208 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
66 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
* * * * **
22240 AGACATTAAGGGAAAGATCTAAGCCGCAATGGCAGATCCAGTACCACGAAGACATGAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
22305 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
66 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
* *** *
22337 AGACATTAAGGGAAAGATCTAAGCCGCAACGGTAGATCCAGTACCACGAAGACACGAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
*
22402 TTTAAGTCGCAATGGCGAACCTAGTACCTCAG
66 TTTAAGTCGCAATGACGAACCTAGTACCTCAG
* ** *
22434 AGACATGAAGGGAAAGATCTAGGCCGCAACGGTGGATCCAGTACCATGAAGACACAAGGGAAAGG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
* * *
22499 TTTAAG-CTGCAATGGCAAACCTGGTACCTCAG
66 TTTAAGTC-GCAATGACGAACCTAGTACCTCAG
* * ** * * * * * *
22531 A-A-A--AAGGGAAGGATTTAAGCTACAACGACGAATCTAATACCACGAAGATTTA-AAAGGAAG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGA--CACAAGGGAAA
* * ** *
22591 GGTTTAAGTTGCAATGACAAACCCGGTACCTTAG
64 GGTTTAAGTCGCAATGACGAACCTAGTACCTCAG
*
22625 AAACATGA
1 AGACATGA
22633 CGAGAAAGGT
Statistics
Matches: 861, Mismatches: 99, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
93 34 0.04
94 36 0.04
95 3 0.00
96 95 0.11
97 643 0.75
98 49 0.06
99 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (97 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACGAAGACACAAGGGAAAGG
TTTAAGTCGCAATGACGAACCTAGTACCTCAG
Found at i:22891 original size:31 final size:32
Alignment explanation
Indices: 22848--22908 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
22838 CAAAATGAAG
*
22848 ATTCTGATCTCTTACCCCGGGCCTGGGGCATC
1 ATTCTGATCTCTTACCCCGAGCCTGGGGCATC
*
22880 ATTC-GATCTCTTACCCCGAGCTTGGGGCA
1 ATTCTGATCTCTTACCCCGAGCCTGGGGCA
22909 GATCATCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.15, C:0.33, G:0.25, T:0.28
Consensus pattern (32 bp):
ATTCTGATCTCTTACCCCGAGCCTGGGGCATC
Found at i:23536 original size:17 final size:16
Alignment explanation
Indices: 23489--23589 Score: 58
Period size: 17 Copynumber: 5.9 Consensus size: 16
23479 GAGTCCAATC
* *
23489 TTTAATTTTTAATTTA
1 TTTAAATTTAAATTTA
* *
23505 CTTTAAGTTTGAATTTA
1 -TTTAAATTTAAATTTA
*
23522 TTCTAAATTTAAATTCATTT
1 TT-TAAATTTAAA-T--TTA
** *
23542 TTTAGGTTTCAATTTA
1 TTTAAATTTAAATTTA
23558 CTTTAAATTTAAATTTA
1 -TTTAAATTTAAATTTA
*
23575 TTATAAATTAAAATT
1 TT-TAAATTTAAATT
23590 AAATCAAAAG
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
16 6 0.09
17 46 0.71
18 2 0.03
19 7 0.11
20 4 0.06
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Done.