Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007856.1 Kokia drynarioides strain JFW-HI SEQ_122495, 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: 49503
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:5058 original size:7 final size:7
Alignment explanation
Indices: 5041--5087 Score: 55
Period size: 6 Copynumber: 7.0 Consensus size: 7
5031 AACAACTTAT
5041 AAAAT-A
1 AAAATAA
5047 AAAATAA
1 AAAATAA
5054 AAAATAA
1 AAAATAA
5061 AAAAT-A
1 AAAATAA
*
5067 AAAA-CA
1 AAAATAA
5073 AAAATAA
1 AAAATAA
5080 GAAAATAA
1 -AAAATAA
5088 CAATTTTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 15 0.42
7 14 0.39
8 7 0.19
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:5059 original size:13 final size:13
Alignment explanation
Indices: 5041--5087 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
5031 AACAACTTAT
5041 AAAATAAAAATAA
1 AAAATAAAAATAA
5054 AAAATAAAAA-ATA
1 AAAATAAAAATA-A
*
5067 AAAACAAAAATAA
1 AAAATAAAAATAA
5080 GAAAATAA
1 -AAAATAA
5088 CAATTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 1 0.03
13 21 0.72
14 7 0.24
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:5064 original size:20 final size:20
Alignment explanation
Indices: 5041--5087 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5031 AACAACTTAT
5041 AAAATAAAAATAAAAAATAA-
1 AAAATAAAAA-AAAAAATAAG
*
5061 AAAATAAAAACAAAAATAAG
1 AAAATAAAAAAAAAAATAAG
5081 AAAATAA
1 AAAATAA
5088 CAATTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (20 bp):
AAAATAAAAAAAAAAATAAG
Found at i:5435 original size:17 final size:18
Alignment explanation
Indices: 5402--5436 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5392 AAACTAAAAA
5402 TTTAATCGATCAATTTAAT
1 TTTAATCGA-CAATTTAAT
5421 TTTAATCGA-AATTTAA
1 TTTAATCGACAATTTAA
5437 ACACTCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTAATCGACAATTTAAT
Found at i:13361 original size:31 final size:31
Alignment explanation
Indices: 13323--13385 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
13313 CTGGCTAGTT
*
13323 ACCATATTAGCTAAAAGGAGAGTTTCATCCA
1 ACCATATTAGCTAAAAGGAGAGCTTCATCCA
13354 ACCATATTAGCTAAAAGGAGAGCTTCATCCA
1 ACCATATTAGCTAAAAGGAGAGCTTCATCCA
13385 A
1 A
13386 TTGCTCATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (31 bp):
ACCATATTAGCTAAAAGGAGAGCTTCATCCA
Found at i:22967 original size:58 final size:59
Alignment explanation
Indices: 22897--23230 Score: 339
Period size: 58 Copynumber: 5.6 Consensus size: 59
22887 TTTTGTCTTA
*
22897 GCCATCAAATGGCCGACACCTCCTTTTCTCGAAAAAAAAATT-ACA-TTTTTTGGTGTTG
1 GCCATCAAATGGCCGACACC-CCTTTTCTCGAAAAAAAAATTCAAATTTTTTTGGTGTTG
*** * * * **
22955 GCCATTGCATGGCCGACGCCCTCTTAT-T-GAGAAAAAAATTCAAATTTTTTTTATGTTG
1 GCCATCAAATGGCCGACACCC-CTTTTCTCGAAAAAAAAATTCAAATTTTTTTGGTGTTG
23013 GCCATCAAATGGCCGACA--CCTTTTCTCGAGAAAAAAAATTCAAAATTTTTTTGTGTTTGTGTT
1 GCCATCAAATGGCCGACACCCCTTTTCTCGA-AAAAAAAATTC-AAA-TTTTTT-TG---GTGTT
23076 G
59 G
* *
23077 GCCATCAAATGGTCGACACCTCCTTTTCTCG-AAAAAAAATTCAAAATTTTTTGGTGTTG
1 GCCATCAAATGGCCGACACC-CCTTTTCTCGAAAAAAAAATTCAAATTTTTTTGGTGTTG
* **
23136 GCTATCAAATGGCCGACACCCCCTTTTCTCG---AAAAAATTC-AATTTTTTTTATGTTG
1 GCCATCAAATGGCCGACA-CCCCTTTTCTCGAAAAAAAAATTCAAATTTTTTTGGTGTTG
* *
23192 ACCATCAAATGGCCGACACCCCTTGTTCTCGTAAAAAAA
1 GCCATCAAATGGCCGACACCCCTT-TTCTCGAAAAAAAA
23231 TTGTATTTTT
Statistics
Matches: 230, Mismatches: 26, Indels: 39
0.78 0.09 0.13
Matches are distributed among these distances:
55 10 0.04
56 48 0.21
57 15 0.07
58 55 0.24
59 40 0.17
60 8 0.03
61 1 0.00
62 2 0.01
63 5 0.02
64 25 0.11
65 11 0.05
67 10 0.04
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (59 bp):
GCCATCAAATGGCCGACACCCCTTTTCTCGAAAAAAAAATTCAAATTTTTTTGGTGTTG
Found at i:23061 original size:59 final size:59
Alignment explanation
Indices: 22834--23230 Score: 304
Period size: 58 Copynumber: 6.7 Consensus size: 59
22824 AAAAATTGGG
* * * ** * * *
22834 GTGTTGGCCATGC-AATGGCCGAAACCCTTTTTTTGTCAAAAAATA-T-ATATATTTTTT
1 GTGTTGGCCAT-CAAATGGCCGACACCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTT
* * * *
22891 GTCTTAGCCATCAAATGGCCGACACCTCCTTTTCTCGA-AAAAAAAATT-ACA-TTTTTTG
1 GTGTTGGCCATCAAATGGCCGACA-C-CCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTT
*** * * * *
22949 GTGTTGGCCATTGCATGGCCGACGCCCTCTTATTGAG-AAAAAAATTCAAATTTTTTTT
1 GTGTTGGCCATCAAATGGCCGACACCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTT
*
23007 ATGTTGGCCATCAAATGGCCGACA-CCTTTTCTCGAGAAAAAAAATTCAAAATTTTTTTGTGTTT
1 GTGTTGGCCATCAAATGGCCGACACCCTTTTCTCGAGAAAAAAAATTC-AAA---TTTT-T-TTT
* * *
23071 GTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTC--GAAAAAAAATTCAAAATTTTTTG
1 GTGTTGGCCATCAAATGGCCGACA-C-CCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTT
*
23130 GTGTTGGCTATCAAATGGCCGACACCCCCTTTTCTC--G--AAAAAATTC-AATTTTTTTT
1 GTGTTGGCCATCAAATGGCCGACA--CCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTT
* * *
23186 ATGTTGACCATCAAATGGCCGACACCCCTTGTTCTCG-TAAAAAAA
1 GTGTTGGCCATCAAATGGCCGACA-CCCTT-TTCTCGAGAAAAAAA
23231 TTGTATTTTT
Statistics
Matches: 277, Mismatches: 41, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
55 6 0.02
56 52 0.19
57 40 0.14
58 66 0.24
59 53 0.19
60 3 0.01
61 3 0.01
62 4 0.01
63 1 0.00
64 28 0.10
65 12 0.04
67 9 0.03
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (59 bp):
GTGTTGGCCATCAAATGGCCGACACCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTT
Found at i:23103 original size:180 final size:178
Alignment explanation
Indices: 22888--23211 Score: 472
Period size: 180 Copynumber: 1.8 Consensus size: 178
22878 ATATATATTT
*
22888 TTTGTCTTAGCCATCAAATGGCCGACACCTCCTTTTCTCGAAAAAAAAATT-ACATTTTTTGGTG
1 TTTGTCTTAGCCATCAAATGGCCGACACCTCCTTTTCTCG-AAAAAAAATTAAAATTTTTTGGTG
*** * * *
22952 TTGGCCATTGCATGGCCGACGCCCTCTTATT-GAGAAAAAAATTCAAATTTTTTTTATGTTGGCC
65 TTGGCCATCAAATGGCCGACACCCCCTT-TTCGAG-AAAAAATTC-AATTTTTTTTATGTTGACC
23016 ATCAAATGGCCGACACCTTTTCTCGAGAAAAAAAATTCAAAATTTTTTTGTG
127 ATCAAATGGCCGACACCTTTTCTCGAGAAAAAAAATTCAAAATTTTTTTGTG
* * *
23068 TTTGTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTCGAAAAAAAATTCAAAATTTTTTGGTG
1 TTTGTCTTAGCCATCAAATGGCCGACACCTCCTTTTCTCGAAAAAAAATT-AAAATTTTTTGGTG
* **
23133 TTGGCTATCAAATGGCCGACACCCCCTTTTCTCGAAAAAATTCAATTTTTTTTATGTTGACCATC
65 TTGGCCATCAAATGGCCGACACCCCCTTTTCGAGAAAAAATTCAATTTTTTTTATGTTGACCATC
23198 AAATGGCCGACACC
130 AAATGGCCGACACC
23212 CCTTGTTCTC
Statistics
Matches: 128, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
179 45 0.35
180 48 0.38
181 35 0.27
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (178 bp):
TTTGTCTTAGCCATCAAATGGCCGACACCTCCTTTTCTCGAAAAAAAATTAAAATTTTTTGGTGT
TGGCCATCAAATGGCCGACACCCCCTTTTCGAGAAAAAATTCAATTTTTTTTATGTTGACCATCA
AATGGCCGACACCTTTTCTCGAGAAAAAAAATTCAAAATTTTTTTGTG
Found at i:23240 original size:56 final size:56
Alignment explanation
Indices: 23068--23240 Score: 192
Period size: 56 Copynumber: 3.0 Consensus size: 56
23058 TTTTTTTGTG
* *
23068 TTTG-TGTTGGCCATCAAATGGTCGACACCTCCTTTTCTCGAAAAAAAATTCAAAATTT
1 TTTGATGTTGGCCATCAAATGGCCGACACC-CCTTTTCTCG-AAAAAAATT-AATATTT
* *
23126 TTTGGTGTTGGCTATCAAATGGCCGACACCCCCTTTTCTCG-AAAAAATTCAAT-TTT
1 TTTGATGTTGGCCATCAAATGGCCGACA-CCCCTTTTCTCGAAAAAAATT-AATATTT
* * *
23182 TTTTATGTTGACCATCAAATGGCCGACACCCCTTGTTCTCGTAAAAAAATT-GTATTT
1 TTTGATGTTGGCCATCAAATGGCCGACACCCCTT-TTCTCG-AAAAAAATTAATATTT
23239 TT
1 TT
23241 GGGTGTACCT
Statistics
Matches: 101, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
55 6 0.06
56 34 0.34
57 16 0.16
58 12 0.12
59 31 0.31
60 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (56 bp):
TTTGATGTTGGCCATCAAATGGCCGACACCCCTTTTCTCGAAAAAAATTAATATTT
Found at i:27142 original size:22 final size:21
Alignment explanation
Indices: 27090--27142 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
27080 AATGAACATG
*
27090 TTTAAATTTAAATAATTTAAA
1 TTTAAAATTAAATAATTTAAA
* * *
27111 CTTAATAATTATATAAGTTTGAA
1 TTTAA-AATTAAATAA-TTTAAA
27134 TTTAAAATT
1 TTTAAAATT
27143 CTACTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.16
22 12 0.48
23 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTAAAATTAAATAATTTAAA
Found at i:27265 original size:67 final size:72
Alignment explanation
Indices: 27193--27427 Score: 185
Period size: 83 Copynumber: 3.2 Consensus size: 72
27183 AATTAAGTTA
*
27193 ACATTATTTA-A-ATAAA-A-AATATTATTATTATATTACAA-TTATAT-AAATATTATGTTAAT
1 ACATTATTTATATATAAAGACAA-ATTATTATTATATTACAATTTATATCAAATAATATGTTAAT
* *
27252 TTGATAAT
65 TTAACAAT
* * * *
27260 ACATTATTTATTATTTAAAGTACAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGA
1 ACATTATTTA-TATATAAAG-ACAAATTATTATTATATTACAATTTATATCAAATAATATGTTAA
27325 TTTAACAAT
64 TTTAACAAT
* * *
27334 ACATTATTTATTAATTTTATATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATA
1 AC-------ATT-A-TTTATATA--TAAAGACAAATTATTATTATATTACAATTTATATCAAATA
* * *
27399 ATATGTTTATTTGATAAT
55 ATATGTTAATTTAACAAT
27417 ACATTATTTAT
1 ACATTATTTAT
27428 TAATTTTATA
Statistics
Matches: 135, Mismatches: 14, Indels: 31
0.75 0.08 0.17
Matches are distributed among these distances:
67 10 0.07
69 1 0.01
70 4 0.03
72 19 0.14
73 7 0.05
74 25 0.19
75 1 0.01
76 3 0.02
81 3 0.02
82 4 0.03
83 54 0.40
84 4 0.03
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (72 bp):
ACATTATTTATATATAAAGACAAATTATTATTATATTACAATTTATATCAAATAATATGTTAATT
TAACAAT
Found at i:27353 original size:83 final size:83
Alignment explanation
Indices: 27266--27478 Score: 338
Period size: 83 Copynumber: 2.5 Consensus size: 83
27256 TAATACATTA
* *
27266 TTTAT-TATTTAAAGTACAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAA
1 TTTATATATTTAAA-TAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAA
27330 CAATACATTATTTATTAAT
65 CAATACATTATTTATTAAT
* * *
27349 TTTATATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTTATTTGAT
1 TTTATATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAAC
27414 AATACATTATTTATTAAT
66 AATACATTATTTATTAAT
27432 TTTATATATTTAAATAAAAATTATTATTATTATATTACAATTTTTAT
1 TTTATATATTTAAAT-AAAA--ATTATTATTATATTACAATTTTTAT
27479 TATATTTTAA
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
83 84 0.69
84 12 0.10
86 25 0.21
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (83 bp):
TTTATATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAAC
AATACATTATTTATTAAT
Found at i:29943 original size:30 final size:30
Alignment explanation
Indices: 29909--30000 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
29899 TCTGTTTACT
* *
29909 TTTTAAATTTAATTTGTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCTAATTTC-TTGTATA
29939 TTTTAAATTTAATTTCTAATTTCTTGTATA
1 TTTTAAATTTAATTTCTAATTTCTTGTATA
* ** *
29969 TTTTAATTTTTCTTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCTTGTATA
29999 TT
1 TT
30001 CTAATTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 2 0.04
30 53 0.96
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCTTGTATA
Found at i:30004 original size:17 final size:16
Alignment explanation
Indices: 29952--30006 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
29942 TAAATTTAAT
29952 TTCTAATTTCTTGTATA
1 TTCTAATTTC-TGTATA
* *
29969 TTTTAATTT-T-TCT-
1 TTCTAATTTCTGTATA
29982 TTCTAATTTCCTGTATA
1 TTCTAATTT-CTGTATA
29999 TTCTAATT
1 TTCTAATT
30007 ATTATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 2 0.07
16 2 0.07
17 16 0.53
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.62
Consensus pattern (16 bp):
TTCTAATTTCTGTATA
Found at i:30909 original size:62 final size:59
Alignment explanation
Indices: 30824--31290 Score: 305
Period size: 62 Copynumber: 7.8 Consensus size: 59
30814 AGGGGAAGTT
* *
30824 GGTGTCGACCATTATATGACCAACACCAAAAAAATTTGTAATTTTTTTATCTAAGAAAAGGG
1 GGTGTCGACCATT-GATGGCCAACA-CAAAAAAATTTGTAATTTTTTTATC-AAGAAAAGGG
* * * *
30886 GGTGTCGATCATTGCCTGGCCAACACCAAAAAAATTTGCAATTTTTTTATCCAAGAAAAGAG
1 GGTGTCGACCATTG-ATGGCCAACA-CAAAAAAATTTGTAATTTTTTTAT-CAAGAAAAGGG
* * ** * * *
30948 GGTGTC-AGCCA-TGCAATGACCAATACTTAAAAA--TGCAATTTTCTTT-TCGAGAACAGGG
1 GGTGTCGA-CCATTG--ATGGCCAACACAAAAAAATTTGTAATTTT-TTTATCAAGAAAAGGG
** *
31006 GGTGTCGGTCATTTGATGGCCAACACAAAAAAATTT-TGAATTTTTTTTTTCGAA-AAAAGGG
1 GGTGTCGACCA-TTGATGGCCAACACAAAAAAATTTGT-AA-TTTTTTTATC-AAGAAAAGGG
* * * * *
31067 GAGTGTCGGCCATTTGATGGCTAACACCAAAAAATTT-TGAATTTTTTTTTCAAGAACAGGG
1 G-GTGTCGACCA-TTGATGGCCAACACAAAAAAATTTGT-AATTTTTTTATCAAGAAAAGGG
* * * ** *
31128 GGTGTCGACCGTTTGATGGCCAACACAAAAAAATTTTTAATTTTTTTTTTC-TCAAAAGAG
1 GGTGTCGACC-ATTGATGGCCAACACAAAAAAATTTGTAA-TTTTTTTATCAAGAAAAGGG
* * ** *
31188 GGTGTCGGCCA-TGCAATGACCAACACCCAAAAA--TGTAATTTTTTT-TCAAGAAAAAGG
1 GGTGTCGACCATTG--ATGGCCAACACAAAAAAATTTGTAATTTTTTTATCAAGAAAAGGG
* * * **
31245 GGTGTTGGCCATTTGATGGCCAACA-TAAAAAATTTGTTTTTTTTTT
1 GGTGTCGACCA-TTGATGGCCAACACAAAAAAATTTGTAATTTTTTT
31291 TACAAAAATG
Statistics
Matches: 326, Mismatches: 53, Indels: 56
0.75 0.12 0.13
Matches are distributed among these distances:
56 7 0.02
57 31 0.10
58 46 0.14
59 12 0.04
60 74 0.23
61 50 0.15
62 105 0.32
63 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (59 bp):
GGTGTCGACCATTGATGGCCAACACAAAAAAATTTGTAATTTTTTTATCAAGAAAAGGG
Found at i:31051 original size:120 final size:117
Alignment explanation
Indices: 30839--31298 Score: 441
Period size: 120 Copynumber: 3.8 Consensus size: 117
30829 CGACCATTAT
* *
30839 ATGACCAACACCAAAAAAATTTGTAATTTTTTTATCTAAGAAAAGGGGGTGTCGATCA-TTGCCT
1 ATGACCAACACC-AAAAAA--TG-AATTTTTTT-TC-AAGAAAAGGGGGTGTCGACCATTTG-AT
* *
30903 GGCCAACACCAAAAAAA-TTTGCAA-TTTTTTTATCCAAGAAAAGAGGGTGTCAGCCATGCA
59 GGCCAACA-CAAAAAAATTTTG-AATTTTTTTTTTCCAA-AAAAGAGGGTGTCGGCCATGCA
* ** * * **
30963 ATGACCAATACTTAAAAATGCAATTTTCTTTTCGAGAACAGGGGGTGTCGGTCATTTGATGGCCA
1 ATGACCAACACCAAAAAATG-AATTTT-TTTTCAAGAAAAGGGGGTGTCGACCATTTGATGGCCA
* * ***
31028 ACACAAAAAAATTTTGAATTTTTTTTTTCGAAAAAAGGGGAGTGTCGGCCATTTG
64 ACACAAAAAAATTTTGAATTTTTTTTTTCCAAAAAAGAGG-GTGTCGGCCATGCA
* * * *
31083 ATGGCTAACACCAAAAAATTTTGAATTTTTTTTTCAAGAACAGGGGGTGTCGACCGTTTGATGGC
1 ATGACCAACACCAAAAAA---TGAA-TTTTTTTTCAAGAAAAGGGGGTGTCGACCATTTGATGGC
*
31148 CAACACAAAAAAATTTTTAATTTTTTTTTTCTC--AAAAGAGGGTGTCGGCCATGCA
62 CAACACAAAAAAATTTTGAATTTTTTTTTTC-CAAAAAAGAGGGTGTCGGCCATGCA
* * * *
31203 ATGACCAACACCCAAAAATGTAATTTTTTTTCAAGAAAAAGGGGTGTTGGCCATTTGATGGCCAA
1 ATGACCAACACCAAAAAATG-AATTTTTTTTCAAGAAAAGGGGGTGTCGACCATTTGATGGCCAA
* * *
31268 CA-TAAAAAA-TTTG-TTTTTTTTTTTACAAAAA
65 CACAAAAAAATTTTGAATTTTTTTTTTCCAAAAA
31299 TGGCCAACAC
Statistics
Matches: 281, Mismatches: 42, Indels: 35
0.78 0.12 0.10
Matches are distributed among these distances:
113 1 0.00
114 10 0.04
115 6 0.02
116 6 0.02
117 41 0.15
118 2 0.01
119 17 0.06
120 91 0.32
121 20 0.07
122 66 0.23
123 11 0.04
124 10 0.04
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (117 bp):
ATGACCAACACCAAAAAATGAATTTTTTTTCAAGAAAAGGGGGTGTCGACCATTTGATGGCCAAC
ACAAAAAAATTTTGAATTTTTTTTTTCCAAAAAAGAGGGTGTCGGCCATGCA
Found at i:34402 original size:6 final size:6
Alignment explanation
Indices: 34391--34417 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34381 ATCTCACATG
34391 ATGGGA ATGGGA ATGGGA ATGGGA ATG
1 ATGGGA ATGGGA ATGGGA ATGGGA ATG
34418 TTGTCATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.19
Consensus pattern (6 bp):
ATGGGA
Found at i:38132 original size:26 final size:26
Alignment explanation
Indices: 38103--38173 Score: 106
Period size: 27 Copynumber: 2.7 Consensus size: 26
38093 GGTAGGAAAC
*
38103 TAATAATATAATTTTGTTTTTTAAGG
1 TAATAATATGATTTTGTTTTTTAAGG
* *
38129 TAATAATATGGTTTTGGGTTTTTAAGG
1 TAATAATATGATTTT-GTTTTTTAAGG
38156 TAATAATATGATTTTGTT
1 TAATAATATGATTTTGTT
38174 CAACCTTGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 15 0.38
27 24 0.62
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (26 bp):
TAATAATATGATTTTGTTTTTTAAGG
Found at i:43739 original size:22 final size:21
Alignment explanation
Indices: 43705--43752 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
43695 CTTTGATCTT
*
43705 TTTAATATGTTTAAATTTAAAA
1 TTTAATATATTT-AATTTAAAA
* * *
43727 TTTAATCTATTTATTTTAAAT
1 TTTAATATATTTAATTTAAAA
43748 TTTAA
1 TTTAA
43753 CCTAATTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAATATATTTAATTTAAAA
Done.