Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013268.1 Kokia drynarioides strain JFW-HI SEQ_128289, 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: 58122
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 272 characters in sequence are not A, C, G, or T
Found at i:11751 original size:16 final size:16
Alignment explanation
Indices: 11730--11760 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11720 CAAGTTGCTC
11730 AACAAATTGATGTCCT
1 AACAAATTGATGTCCT
11746 AACAAATTGATGTCC
1 AACAAATTGATGTCC
11761 CTACATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (16 bp):
AACAAATTGATGTCCT
Found at i:13457 original size:26 final size:26
Alignment explanation
Indices: 13421--13473 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
13411 TAATCTAAAG
13421 TATGTTTTTCTTAGCAACAATAACAC
1 TATGTTTTTCTTAGCAACAATAACAC
*
13447 TATGTTTTTCTTAGCAATAATAACAC
1 TATGTTTTTCTTAGCAACAATAACAC
13473 T
1 T
13474 CTGCCAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (26 bp):
TATGTTTTTCTTAGCAACAATAACAC
Found at i:19087 original size:120 final size:120
Alignment explanation
Indices: 18872--19114 Score: 387
Period size: 120 Copynumber: 2.0 Consensus size: 120
18862 GCTACAATCA
* *
18872 TATTACAATTGCACCGGAAGGCCAATCTAAAATGACTTTCACTTGTCCGTTTGATACCTTTGCTT
1 TATTACAATTGCACCGGAAGACCAATCTAAAACGACTTTCACTTGTCCGTTTGATACCTTTGCTT
*
18937 TTCGTCGAATGCCATTTGATCTATGAAACGCACCAACCATATTTCAAAGGTGCAT
66 TTCGTCGAATGCCATTTGATCTATGAAACGCACCAACCACATTTCAAAGGTGCAT
* * * *
18992 TATTACAATTGCATCGGAAGACCAATCTAAAACGACTTTTACTTGTCCGTTTGGTACCTTTTCTT
1 TATTACAATTGCACCGGAAGACCAATCTAAAACGACTTTCACTTGTCCGTTTGATACCTTTGCTT
* * * *
19057 TTCGTCGAATGCCATTTGGTGTATGCAACGCACCAACCACATTTCGAAGGTGCAT
66 TTCGTCGAATGCCATTTGATCTATGAAACGCACCAACCACATTTCAAAGGTGCAT
19112 TAT
1 TAT
19115 GGCGATTTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (120 bp):
TATTACAATTGCACCGGAAGACCAATCTAAAACGACTTTCACTTGTCCGTTTGATACCTTTGCTT
TTCGTCGAATGCCATTTGATCTATGAAACGCACCAACCACATTTCAAAGGTGCAT
Found at i:21373 original size:34 final size:36
Alignment explanation
Indices: 21335--21429 Score: 86
Period size: 38 Copynumber: 2.6 Consensus size: 36
21325 TTACATGTTC
21335 ATGCAGCGACATTCCTGGGTGCAA-TTG-AATACTT
1 ATGCAGCGACATTCCTGGGTGCAATTTGAAATACTT
* * * * * *
21369 ATGCAGTGAAATTTCTGGATACAATTTGAATAATATTT
1 ATGCAGCGACATTCCTGGGTGCAATTTG-A-AATACTT
* *
21407 ATGCAGCGACAGTCTTGGGTGCA
1 ATGCAGCGACATTCCTGGGTGCA
21430 TTCTAGAAAT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
34 19 0.43
35 3 0.07
38 22 0.50
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (36 bp):
ATGCAGCGACATTCCTGGGTGCAATTTGAAATACTT
Found at i:24227 original size:18 final size:15
Alignment explanation
Indices: 24195--24241 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
24185 GTGACGTTAG
*
24195 TAAAAAAAATTAAAT
1 TAAAAAAAATAAAAT
24210 TGAAAACATAAATAAAAT
1 T-AAAA-A-AAATAAAAT
24228 TAAAAAAAATAAAA
1 TAAAAAAAATAAAA
24242 GACACTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
17 5 0.18
18 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
TAAAAAAAATAAAAT
Found at i:25037 original size:17 final size:17
Alignment explanation
Indices: 24992--25039 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
24982 TGATGATGTT
24992 AATAATTTTATATTTTAA
1 AATAATTTTA-ATTTTAA
* *
25010 AAAACAATTTAATTTTAA
1 AATA-ATTTTAATTTTAA
25028 AATAATTTTAAT
1 AATAATTTTAAT
25040 AATTTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 7 0.28
18 13 0.52
19 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATTTTAATTTTAA
Found at i:26216 original size:131 final size:130
Alignment explanation
Indices: 25982--26240 Score: 500
Period size: 131 Copynumber: 2.0 Consensus size: 130
25972 TTCTTGAATA
25982 CATTTTCAAAGCTTGCATCCATGGCAGCTTAACTTTTTGAAGGGCGACCTGACGTGAAGGAGGAG
1 CATTTTCAAAGCTTGCATCCATGGCAGCTTAACTTTTTGAAGGGCGACCTGACGTGAAGGAGGAG
26047 GCAGATCTGCTCTTGACGAGGAGCTCCTAACTGCGACTCAAGAGGAGAGTAAGGGAGCAAGTTNT
66 GCAGATCTGCTCTTGACGAGGAGCTCCTAACTGCGACTCAAGAGGAGAGTAAGGGAGCAAGTT-T
26112 C
130 C
26113 CATTTTCAAAGCTTGCATCCATGGCAGCTTAACTTTTTGAAGGGCGACCTGACGTGAAGGAGGAG
1 CATTTTCAAAGCTTGCATCCATGGCAGCTTAACTTTTTGAAGGGCGACCTGACGTGAAGGAGGAG
*
26178 TCAGATCTGCTCTTGACGAGGAGCTCCTAACTGCGACTCAAGAGGAGAGTAAGGGAGCAAGTT
66 GCAGATCTGCTCTTGACGAGGAGCTCCTAACTGCGACTCAAGAGGAGAGTAAGGGAGCAAGTT
26241 GAGTAGCCTA
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 127 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (130 bp):
CATTTTCAAAGCTTGCATCCATGGCAGCTTAACTTTTTGAAGGGCGACCTGACGTGAAGGAGGAG
GCAGATCTGCTCTTGACGAGGAGCTCCTAACTGCGACTCAAGAGGAGAGTAAGGGAGCAAGTTTC
Found at i:27217 original size:37 final size:37
Alignment explanation
Indices: 27176--27353 Score: 214
Period size: 37 Copynumber: 4.8 Consensus size: 37
27166 AACCTACTAG
* * *
27176 GCACATAGACTACTAGGCACATAGCCTGAACATACCA
1 GCACAAAGCCTACTAGGCACATAGCCTGAACACACCA
*
27213 GCACAAAGCCTACTAGGCACATAGCCTGAATACA-CA
1 GCACAAAGCCTACTAGGCACATAGCCTGAACACACCA
* * * *
27249 GACACAAAGCCTACCAGGCACATAGCCCGAATACACCG
1 G-CACAAAGCCTACTAGGCACATAGCCTGAACACACCA
** * *
27287 GCATGAAGCCTACTAGGCACATAGCTTGAACACACCT
1 GCACAAAGCCTACTAGGCACATAGCCTGAACACACCA
* *
27324 GCACAAAGCCTTCTAGGCACATAGCTTGAA
1 GCACAAAGCCTACTAGGCACATAGCCTGAA
27354 TGCACTGGCA
Statistics
Matches: 122, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
36 3 0.02
37 117 0.96
38 2 0.02
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (37 bp):
GCACAAAGCCTACTAGGCACATAGCCTGAACACACCA
Found at i:27238 original size:16 final size:16
Alignment explanation
Indices: 27168--27239 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 16
27158 CAGCACAAAA
27168 CCTACTAGGCACATAG
1 CCTACTAGGCACATAG
*
27184 ACTACTAGGCACATAG
1 CCTACTAGGCACATAG
* *
27200 CCTGAACATACCAGCACAAAG
1 CCT--AC-TA--GGCACATAG
27221 CCTACTAGGCACATAG
1 CCTACTAGGCACATAG
27237 CCT
1 CCT
27240 GAATACACAG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
16 27 0.60
18 4 0.09
19 4 0.09
21 10 0.22
ACGTcount: A:0.35, C:0.32, G:0.17, T:0.17
Consensus pattern (16 bp):
CCTACTAGGCACATAG
Found at i:27376 original size:95 final size:95
Alignment explanation
Indices: 27265--27442 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 95
27255 AAGCCTACCA
** * * *
27265 GGCACATAGCCCGAATACACCGGCA-TGAAGCCTACTAGGCACATAGCTTGAACACACCTG-CAC
1 GGCACATAGCCCGAATACACAAGCACAG-AGCCTACTAGACACATAGCCTGAACACACC-GACAC
*
27328 AAAGCCTTCTAGGCACATAGCTTGAATGCACT
64 AAAGCCTACTAGGCACATAGCTTGAATGCACT
* *
27360 GGCACATAGCCTGAATACACAAGCACAGAGCCTACTAGACACATAGCCTGAATACACCGACACAA
1 GGCACATAGCCCGAATACACAAGCACAGAGCCTACTAGACACATAGCCTGAACACACCGACACAA
27425 AGCCTACTAGGCACATAG
66 AGCCTACTAGGCACATAG
27443 ACTGTATTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 1 0.01
95 71 0.97
96 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (95 bp):
GGCACATAGCCCGAATACACAAGCACAGAGCCTACTAGACACATAGCCTGAACACACCGACACAA
AGCCTACTAGGCACATAGCTTGAATGCACT
Found at i:27385 original size:21 final size:21
Alignment explanation
Indices: 27340--27392 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
27330 AGCCTTCTAG
* * **
27340 GCACATAGCTTGAATGCACTG
1 GCACATAGCCTGAATACACAA
27361 GCACATAGCCTGAATACACAA
1 GCACATAGCCTGAATACACAA
*
27382 GCACAGAGCCT
1 GCACATAGCCT
27393 ACTAGACACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (21 bp):
GCACATAGCCTGAATACACAA
Found at i:27392 original size:58 final size:58
Alignment explanation
Indices: 27302--27412 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
27292 AAGCCTACTA
* ** * * *
27302 GGCACATAGCTTGAACACACCTGCACAAAGCCTTCTAGGCACATAGCTTGAATGCACT
1 GGCACATAGCCTGAACACACAAGCACAAAGCCTACTAGACACATAGCCTGAATGCACT
* *
27360 GGCACATAGCCTGAATACACAAGCACAGAGCCTACTAGACACATAGCCTGAAT
1 GGCACATAGCCTGAACACACAAGCACAAAGCCTACTAGACACATAGCCTGAAT
27413 ACACCGACAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (58 bp):
GGCACATAGCCTGAACACACAAGCACAAAGCCTACTAGACACATAGCCTGAATGCACT
Found at i:27403 original size:37 final size:37
Alignment explanation
Indices: 27362--27442 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
27352 AATGCACTGG
*
27362 CACATAGCCTGAATACACA-AGCACAGAGCCTACTAGA
1 CACATAGCCTGAATACACAGA-CACAAAGCCTACTAGA
* *
27399 CACATAGCCTGAATACACCGACACAAAGCCTACTAGG
1 CACATAGCCTGAATACACAGACACAAAGCCTACTAGA
27436 CACATAG
1 CACATAG
27443 ACTGTATTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 39 0.98
38 1 0.03
ACGTcount: A:0.40, C:0.31, G:0.16, T:0.14
Consensus pattern (37 bp):
CACATAGCCTGAATACACAGACACAAAGCCTACTAGA
Found at i:27408 original size:111 final size:109
Alignment explanation
Indices: 27139--27408 Score: 258
Period size: 111 Copynumber: 2.4 Consensus size: 109
27129 AGCCTACTCA
* * * *
27139 ACACATAGCCCAATTACACCAGCACAAAACCTACTAGGCACATAGACTACTAGGCACATAGCCTG
1 ACACATAG-CCAA-TACACAAGCACAAAGCCTACTAGACACATAGCCTACTAGGCACATAGCCTG
*
27204 AACATACCAGCACAAAGCCTACTAGGCACATAGCCTGAATACACAG
64 AACACACCAGCACAAAGCCTACTAGGCACATAGCCTGAATACACAG
* * * * * * *
27250 ACACAAAGCC--TAC-CAGGCACATAGCCCGAATACACCGGCATGAAGCCTACTAGGCACATAGC
1 ACACATAGCCAATACACAAGCACAAAG-CCTACTAGA-C-ACAT--AGCCTACTAGGCACATAGC
* * * * * *
27312 TTGAACACACCTGCACAAAGCCTTCTAGGCACATAGCTTGAATGCACTG
61 CTGAACACACCAGCACAAAGCCTACTAGGCACATAGCCTGAATACACAG
* *
27361 GCACATAGCCTGAATACACAAGCACAGAGCCTACTAGACACATAGCCT
1 ACACATAGCC--AATACACAAGCACAAAGCCTACTAGACACATAGCCT
27409 GAATACACCG
Statistics
Matches: 123, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
106 7 0.06
107 8 0.07
108 1 0.01
109 3 0.02
110 2 0.02
111 80 0.65
113 3 0.02
114 1 0.01
115 9 0.07
116 9 0.07
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.15
Consensus pattern (109 bp):
ACACATAGCCAATACACAAGCACAAAGCCTACTAGACACATAGCCTACTAGGCACATAGCCTGAA
CACACCAGCACAAAGCCTACTAGGCACATAGCCTGAATACACAG
Found at i:34566 original size:21 final size:21
Alignment explanation
Indices: 34542--34605 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
34532 AAGCCTACTC
34542 AGCACATAGCCTGAATACACA
1 AGCACATAGCCTGAATACACA
* *
34563 AGCACAAAGCC----TAC-TA
1 AGCACATAGCCTGAATACACA
* *
34579 TGCACATAGCCTGAATACACC
1 AGCACATAGCCTGAATACACA
34600 AGCACA
1 AGCACA
34606 AGACCTACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
16 10 0.32
17 3 0.10
20 3 0.10
21 15 0.48
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.14
Consensus pattern (21 bp):
AGCACATAGCCTGAATACACA
Found at i:34573 original size:37 final size:36
Alignment explanation
Indices: 34532--34627 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 36
34522 CACCAGCTCG
34532 AAGCCTACTCA-GCACATAGCCTGAATACACAAGCAC
1 AAGCCTACT-AGGCACATAGCCTGAATACACAAGCAC
* *
34568 AAAGCCTACTATGCACATAGCCTGAATACACCAGCAC
1 -AAGCCTACTAGGCACATAGCCTGAATACACAAGCAC
34605 AAGACCTACTAGGCACATAGCCT
1 AAG-CCTACTAGGCACATAGCCT
34628 ATATTCTTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
36 4 0.07
37 51 0.93
ACGTcount: A:0.38, C:0.32, G:0.15, T:0.16
Consensus pattern (36 bp):
AAGCCTACTAGGCACATAGCCTGAATACACAAGCAC
Found at i:34809 original size:37 final size:37
Alignment explanation
Indices: 34768--34842 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
34758 TATTCAATCT
* * *
34768 TGAATGCACCAGCACGAAGCCTACTTA-GCACATAGCC
1 TGAATACACCAGCACAAAACCTAC-TAGGCACATAGCC
*
34805 TGAATACACCGGCACAAAACCTACTAGGCACATAGCC
1 TGAATACACCAGCACAAAACCTACTAGGCACATAGCC
34842 T
1 T
34843 ATATTCTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 2 0.06
37 31 0.94
ACGTcount: A:0.35, C:0.32, G:0.17, T:0.16
Consensus pattern (37 bp):
TGAATACACCAGCACAAAACCTACTAGGCACATAGCC
Found at i:34940 original size:215 final size:215
Alignment explanation
Indices: 34553--34975 Score: 767
Period size: 215 Copynumber: 2.0 Consensus size: 215
34543 GCACATAGCC
*
34553 TGAATACACAAGCACAAAGCCTACTATGCACATAGCCTGAATACACCAGCACAAGACCTACTAGG
1 TGAATACACAAGCACAAAGCCTACTATGCACATAGCCTGAATACACCAGCACAAAACCTACTAGG
* *
34618 CACATAGCCTATATTCTTAGATGCAAATATGGTTATCCACAAAGGATTATACATGTCAACAATAA
66 CACATAGCCTATATTCTTAGATGCAAATATAGTAATCCACAAAGGATTATACATGTCAACAATAA
34683 CCATTATTTATATAAATCAAGTTAGACATTTATAAAGTGAATTTTATAAATATTAGATAATGAAA
131 CCATTATTTATATAAATCAAGTTAGACATTTATAAAGTGAATTTTATAAATATTAGATAATGAAA
34748 CGAACTTACCTATTCAATCT
196 CGAACTTACCTATTCAATCT
* * * *
34768 TGAATGCACCAGCACGAAGCCTACT-TAGCACATAGCCTGAATACACCGGCACAAAACCTACTAG
1 TGAATACACAAGCACAAAGCCTACTAT-GCACATAGCCTGAATACACCAGCACAAAACCTACTAG
34832 GCACATAGCCTATATTCTTAGATGCAAATATAGTAATCCACAAAGGATTATACATGTCAACAATA
65 GCACATAGCCTATATTCTTAGATGCAAATATAGTAATCCACAAAGGATTATACATGTCAACAATA
34897 ACCATTATTTATATAAATCAAGTTAGACATTTATAAAGTGAATTTTATAAATATTAGATAATGAA
130 ACCATTATTTATATAAATCAAGTTAGACATTTATAAAGTGAATTTTATAAATATTAGATAATGAA
34962 ACGAACTTACCTAT
195 ACGAACTTACCTAT
34976 GCTATATCAC
Statistics
Matches: 200, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
214 1 0.00
215 199 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (215 bp):
TGAATACACAAGCACAAAGCCTACTATGCACATAGCCTGAATACACCAGCACAAAACCTACTAGG
CACATAGCCTATATTCTTAGATGCAAATATAGTAATCCACAAAGGATTATACATGTCAACAATAA
CCATTATTTATATAAATCAAGTTAGACATTTATAAAGTGAATTTTATAAATATTAGATAATGAAA
CGAACTTACCTATTCAATCT
Found at i:36301 original size:15 final size:16
Alignment explanation
Indices: 36282--36316 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
36272 TTTGAAAGCA
36282 TAAAAATAAAA-AG-G
1 TAAAAATAAAATAGAG
36296 TAAAAATAAAATAGAG
1 TAAAAATAAAATAGAG
36312 TAAAA
1 TAAAA
36317 GTGGAGTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 2 0.11
16 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (16 bp):
TAAAAATAAAATAGAG
Found at i:40473 original size:21 final size:22
Alignment explanation
Indices: 40447--40489 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40437 ATGTTTGTAC
40447 TCATTT-TCTTTTT-TTTTCTTT
1 TCATTTGT-TTTTTCTTTTCTTT
40468 TCATTTGTTTTTTCTTTTCTTT
1 TCATTTGTTTTTTCTTTTCTTT
40490 GGCTAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (22 bp):
TCATTTGTTTTTTCTTTTCTTT
Found at i:40480 original size:17 final size:16
Alignment explanation
Indices: 40450--40490 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
40440 TTTGTACTCA
40450 TTTTCTTT-TTTTTTC
1 TTTTCTTTGTTTTTTC
40465 TTTTCATTTGTTTTTTC
1 TTTTC-TTTGTTTTTTC
40482 TTTTCTTTG
1 TTTTCTTTG
40491 GCTAAATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.21
16 7 0.29
17 12 0.50
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTTCTTTGTTTTTTC
Found at i:47261 original size:21 final size:21
Alignment explanation
Indices: 47227--47279 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
47217 CAAAAAAGAG
*
47227 AGAAATAGAGAAAAAAATTAAAA
1 AGAAA-AGA-AAAAAAAGTAAAA
* *
47250 AGAAAAGAAAAATAAGTAGAA
1 AGAAAAGAAAAAAAAGTAAAA
*
47271 ACAAAAGAA
1 AGAAAAGAA
47280 TCATGAGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 3 0.12
23 5 0.19
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (21 bp):
AGAAAAGAAAAAAAAGTAAAA
Found at i:47359 original size:58 final size:58
Alignment explanation
Indices: 47291--47407 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
47281 CATGAGTAAG
47291 AAAATATGTGAATAGTGATAAAATTATAAAGTCACCAAAAAAAGAAAAAGAAAATCTT
1 AAAATATGTGAATAGTGATAAAATTATAAAGTCACCAAAAAAAGAAAAAGAAAATCTT
47349 AAAATATGTGAATAGTGATAAAATTATAAAGTCACCAAAAAAAGAAAAAGAAAATCTT
1 AAAATATGTGAATAGTGATAAAATTATAAAGTCACCAAAAAAAGAAAAAGAAAATCTT
47407 A
1 A
47408 CTCAAGAAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.22
Consensus pattern (58 bp):
AAAATATGTGAATAGTGATAAAATTATAAAGTCACCAAAAAAAGAAAAAGAAAATCTT
Done.