Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004109.1 Kokia drynarioides strain JFW-HI SEQ_117287, 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: 5640
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:940 original size:45 final size:45
Alignment explanation
Indices: 891--996 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
881 ACAATCAATA
* *
891 AAATAATATTTACCATATCACACATATTGTGTAACATAATG-ACTC
1 AAATAATATTTACCATATCACACATATCGTATAACAT-ATGTACTC
** *
936 AAATAATATTTACCATATCATGCATATCGTATAGCATATGTACTC
1 AAATAATATTTACCATATCACACATATCGTATAACATATGTACTC
*
981 AAATAATACTTACCAT
1 AAATAATATTTACCAT
997 TTTATAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 3 0.06
45 51 0.94
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (45 bp):
AAATAATATTTACCATATCACACATATCGTATAACATATGTACTC
Found at i:1393 original size:74 final size:74
Alignment explanation
Indices: 1265--1828 Score: 488
Period size: 74 Copynumber: 7.6 Consensus size: 74
1255 GGGTTGGAAA
* * * *
1265 AGACCTAGTC-AAGGCCACCCTTTAAAATAGGTTGGGTTAGGTC-TTGTCTAAGGCAACCTTTTA
1 AGACCT-GTCTAAGG-CAACCTTTAAAAAAGGTTGGGATA-GACATTGTCTAAGGCAACC-TTTA
1328 AAAATGGTTGAGAT
62 AAAA-GGTTGAGAT
* *
1342 AGACCCGTCTAAGGCAACC-TT-AAAAAGGTTGGGATAGACATTGTTTAAGGCAACCTTTAAAAA
1 AGACCTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACATTGTCTAAGGCAACCTTT-AAAA
*
1405 AGGTTGGGAT
65 AGGTTGAGAT
* ** * * *
1415 AAATATGTCTAAAGCAACC-TT-GAAAAGGTTGGGATAGATC-TTGTCTAAGACAACCTTTTAGA
1 AGACCTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGA-CATTGTCTAAGGCAACC-TTTA-A
*
1477 AAAGGTTGGGAT
63 AAAGGTTGAGAT
* * * * * *
1489 AGATCTTGTTTAAGACAACCTTTTAAAAAAGGTTGGGATAGACA-TGTCTAAAGCAACC-TTGAG
1 AGA-CCTGTCTAAGGCAACC-TTTAAAAAAGGTTGGGATAGACATTGTCTAAGGCAACCTTTAAA
1552 AAGGTT-AGGAT
64 AAGGTTGA-GAT
* ** * * * * *
1563 AAATTTTATCTAAGGCAACCTTTTAAAAAAGGTTAGGATAGA-GTCGTCTAAGGTAACC-TTAAA
1 AGA-CCTGTCTAAGGCAACC-TTTAAAAAAGGTTGGGATAGACATTGTCTAAGGCAACCTTTAAA
1626 AAGGTTGAGAT
64 AAGGTTGAGAT
** * * *
1637 AGACCTTGTCTAAGGCAACCTTTAAAAAATATTAGGATAGACATTATTTAAGGCAA-CTTTAAAA
1 AGACC-TGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACATTGTCTAAGGCAACCTTTAAAA
*
1701 AGGTTGGGAT
65 AGGTTGAGAT
* * * * *
1711 AGACCTTGTTTAAGGAAACCTTTAAAAAAGGTTGGGATAAACCTTGTTTAAGGCAACCTTTTAAA
1 AGACC-TGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACATTGTCTAAGGCAACC-TTTAAA
1776 AAGGTTGAGAT
64 AAGGTTGAGAT
* * * *
1787 AGACCTTGTCTAAGGTAACCTTTAAAAAGGGTTTGAATAGAC
1 AGACC-TGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGAC
1829 CCGTCTAAGG
Statistics
Matches: 402, Mismatches: 66, Indels: 39
0.79 0.13 0.08
Matches are distributed among these distances:
73 79 0.20
74 207 0.51
75 17 0.04
76 59 0.15
77 24 0.06
78 16 0.04
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (74 bp):
AGACCTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACATTGTCTAAGGCAACCTTTAAAAA
GGTTGAGAT
Found at i:1772 original size:260 final size:260
Alignment explanation
Indices: 1311--1808 Score: 693
Period size: 260 Copynumber: 1.9 Consensus size: 260
1301 TTAGGTCTTG
* *
1311 TCTAAGGCAACCTTTTAAAAATGGTTGAGATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGGGA
1 TCTAAGGCAACCTTTTAAAAAAGGTTGAGATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGAGA
* * * *
1376 TAGACATTGTTTAAGGCAACCTTTAAAAAAGGTTGGGATAAATATGTCTAAAGCAACCTTGAAAA
66 TAGACATTGTCTAAGGCAACCTTTAAAAAAGATTAGGATAAATATGTCTAAAGCAACCTTAAAAA
* * * *
1441 GGTTGGGATAGATCTTGTCTAAGACAACCTTTTAGAAAAGGTTGGGATAGATCTTGTTTAAGACA
131 GGTTGGGATAGACCTTGTCTAAGACAACCTTTTAAAAAAGGTTGGGATAAACCTTGTTTAAGACA
*
1506 ACCTTTTAAAAAAGGTTGGGATAGA-CATGTCTAAAGCAACCTTGAGAAGGTTAGGATAAATTTT
196 ACCTTTT-AAAAAGGTTGAGATAGACCATGTCTAAAGCAACCTTGAGAAGGTTAGGATAAATTTT
1570 A
260 A
** *
1571 TCTAAGGCAACCTTTTAAAAAAGGTT-AGGATAGAGTCGTCTAAGGTAACCTTAAAAAGGTTGAG
1 TCTAAGGCAACCTTTTAAAAAAGGTTGA-GATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGAG
* * * *
1635 ATAGACCTTGTCTAAGGCAACCTTTAAAAAATATTAGGATAGACATTAT-T-TAAGGCAACTTTA
65 ATAGACATTGTCTAAGGCAACCTTTAAAAAAGATTAGGATA-A-A-TATGTCTAAAGCAACCTTA
*
1698 AAAAGGTTGGGATAGACCTTGTTTAAGGA-AACC-TTTAAAAAAGGTTGGGATAAACCTTGTTTA
127 AAAAGGTTGGGATAGACCTTGTCTAA-GACAACCTTTTAAAAAAGGTTGGGATAAACCTTGTTTA
* * * *
1761 AGGCAACCTTTTAAAAAGGTTGAGATAGACCTTGTCTAAGGTAACCTT
191 AGACAACCTTTTAAAAAGGTTGAGATAGACCATGTCTAAAGCAACCTT
1809 TAAAAAGGGT
Statistics
Matches: 209, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
259 17 0.08
260 146 0.70
261 39 0.19
262 4 0.02
263 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (260 bp):
TCTAAGGCAACCTTTTAAAAAAGGTTGAGATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGAGA
TAGACATTGTCTAAGGCAACCTTTAAAAAAGATTAGGATAAATATGTCTAAAGCAACCTTAAAAA
GGTTGGGATAGACCTTGTCTAAGACAACCTTTTAAAAAAGGTTGGGATAAACCTTGTTTAAGACA
ACCTTTTAAAAAGGTTGAGATAGACCATGTCTAAAGCAACCTTGAGAAGGTTAGGATAAATTTTA
Found at i:1827 original size:38 final size:37
Alignment explanation
Indices: 1256--1838 Score: 506
Period size: 38 Copynumber: 15.6 Consensus size: 37
1246 TTTATTGAAG
* * * *
1256 GGTTGGAAAAGACCTAGTC-AAGGCCACCCTTTAAAATA
1 GGTTGGGATAGACCTTGTCTAAGG-CAACCTTTAAAA-A
* **
1294 GGTTGGGTTAGGTCTTGTCTAAGGCAACCTTTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACC-TTTAAAAA
* *
1332 TGGTTGAGATAGACC-CGTCTAAGGCAACC-TTAAAAA
1 -GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAA
* *
1368 GGTTGGGATAGACATTGTTTAAGGCAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTT-AAAAA
* * *
1406 GGTTGGGATA-A-ATATGTCTAAAGCAACC-TTGAAAA
1 GGTTGGGATAGACCT-TGTCTAAGGCAACCTTTAAAAA
* *
1441 GGTTGGGATAGATCTTGTCTAAGACAACCTTTTAGAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACC-TTTA-AAAA
* * *
1480 GGTTGGGATAGATCTTGTTTAAGACAACCTTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACC-TTT-AAAAA
* * * *
1519 GGTTGGGATAGA-CATGTCTAAAGCAACC-TTGAGAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAA
* * ** *
1554 GGTTAGGATAAATTTTATCTAAGGCAACCTTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACC-TTT-AAAAA
* * * *
1593 GGTTAGGATAGA-GTCGTCTAAGGTAACC-TTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAA
*
1628 GGTTGAGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTT-AAAAA
** * * * *
1666 TATTAGGATAGACATTATTTAAGGCAA-CTTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAA
* *
1702 GGTTGGGATAGACCTTGTTTAAGGAAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTT-AAAAA
* *
1740 GGTTGGGATAAACCTTGTTTAAGGCAACCTTTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACC-TTTAAAAA
* *
1778 GGTTGAGATAGACCTTGTCTAAGGTAACCTTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAA
* * *
1815 GGGTTTGAATAGACC-CGTCTAAGG
1 -GGTTGGGATAGACCTTGTCTAAGG
1839 TAACTTTTTT
Statistics
Matches: 450, Mismatches: 71, Indels: 49
0.79 0.12 0.09
Matches are distributed among these distances:
35 54 0.12
36 91 0.20
37 42 0.09
38 172 0.38
39 90 0.20
40 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (37 bp):
GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAA
Found at i:2536 original size:140 final size:139
Alignment explanation
Indices: 2282--2977 Score: 799
Period size: 140 Copynumber: 5.1 Consensus size: 139
2272 AACACTTTAG
* * * * *
2282 AAAGTGTCGTCATAGTATTGGACAAAGCAAACTCTTATTTAAGTGTTACCTTAGGCATGCATATT
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * ** ** *
2347 CAAACTCTTATACAAAGAGTTGGCCAAAGCGTATGCCAAAAAGTTTATCCCAACACTTAGGAAAG
66 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTAGCAAGTCTATCCCAACACTTAGGAAAG
*
2412 TGTCAACCCA
131 TGTC-GCCCA
* * * * *
2422 AAAGTATTGGCATAGTGTTGGACAAAGCCGACTCTTATATAAGTATTGCCTTAGGCATGCATATC
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * * * *
2487 CCAACCCTTATATAAAGAGTTGGCCAAAGCATATGTTTGTAACTCTATCCCAACACTTAGGAAA-
66 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTAGCAAGTCTATCCCAACACTTAGGAAAG
2551 -GT------
131 TGTCGCCCA
* *
2553 ---GT-T-GGCATAGTGTTGGACAAAGCCAACTTTTATTTAAGCGTTGCCTTAGGCATGCATATC
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * * *
2613 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGCTAACAAGTCTATCCCAATACTTAAGAAAG
66 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTAGCAAGTCTATCCCAACACTTAGGAAAG
*
2678 CGTCGGCCCA
131 TGTC-GCCCA
* * *
2688 AAAGTGTCGTCATAGTGTTGGACAAAGCCTACTCTTATTTAAGTGTTTCCTTAGGTCATGCATAT
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGG-CATGCATAT
* * * *
2753 CCCAACCCTTATACAAAAGAGTTGGCAAAAACGTATGTTGGCAAGTCTATCCCAACACTAAGGAA
65 CCCAACCCTTATAC-AAAGAGTTGGCCAAAGCGTATGTTAGCAAGTCTATCCCAACACTTAGGAA
2818 AGTGTCGCCCCA
129 AGTGTCG-CCCA
* * * *
2830 AAAGTGTCGACATAGTGTTCGACAAAGCCAACTCTTATTTAAGAGTTGTCTTAGGCATGCATATC
1 AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * * ** *
2895 CCAACCCTTATACAAAAAGTTGACGAAAATGTATGTTGGCAAGTCTATCCCAACACTTA-GAACA
66 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTAGCAAGTCTATCCCAACACTTAGGAA-A
*
2959 TTGTCGCCCCA
130 GTGTCG-CCCA
2970 AAAGTGTC
1 AAAGTGTC
2978 ATCTTACGAC
Statistics
Matches: 477, Mismatches: 61, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
126 107 0.22
127 1 0.00
128 4 0.01
138 4 0.01
139 4 0.01
140 210 0.44
141 47 0.10
142 100 0.21
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (139 bp):
AAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTAGCAAGTCTATCCCAACACTTAGGAAAG
TGTCGCCCA
Found at i:2660 original size:126 final size:126
Alignment explanation
Indices: 2422--2954 Score: 526
Period size: 126 Copynumber: 4.0 Consensus size: 126
2412 TGTCAACCCA
* * * *
2422 AAAGTATTGGCATAGTGTTGGACAAAGCCGACTCTTATATAAGTATTGCCTTAGGCATGCATATC
1 AAAGTGTTGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * * * * *
2487 CCAACCCTTATATAAAGAGTTGGCCAAAGCATATGTTTGTAACTCTATCCCAACACTTAGG
66 CCAACCCTTATACAAAGAGTTGGCCAAAACGTATGTTGGCAAGTCTATCCCAACACTTAGG
* *
2548 AAAGTGTTGGCATAGTGTTGGACAAAGCCAACTTTTATTTAAGCGTTGCCTTAGGCATGCATATC
1 AAAGTGTTGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * ** *
2613 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGCTAACAAGTCTATCCCAATACTTAAGAAAG
66 CCAACCCTTATACAAAGAGTTGGCCAAAACGTATGTTGGCAAGTCTATCCCAACACTT-----A-
2678 CGTCGG
125 ----GG
* * * *
2684 CCCAAAAGTGTCGTCATAGTGTTGGACAAAGCCTACTCTTATTTAAGTGTTTCCTTAGGTCATGC
1 ----AAAGTGTTGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGG-CATGC
* *
2749 ATATCCCAACCCTTATACAAAAGAGTTGGCAAAAACGTATGTTGGCAAGTCTATCCCAACACTAA
61 ATATCCCAACCCTTATAC-AAAGAGTTGGCCAAAACGTATGTTGGCAAGTCTATCCCAACACTTA
2814 GG
125 GG
* * *
2816 AAAGTGTCGCCCCAAAAGTGTCGACATAGTGTTCGACAAAGCCAACTCTTATTTAAGAGTTGTCT
1 AAAGTGT-----------TG--G-CATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCT
* * * *
2881 TAGGCATGCATATCCCAACCCTTATACAAAAAGTTGACGAAAATGTATGTTGGCAAGTCTATCCC
52 TAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAACGTATGTTGGCAAGTCTATCCC
2946 AACACTTAG
117 AACACTTAG
2955 AACATTGTCG
Statistics
Matches: 338, Mismatches: 39, Indels: 46
0.80 0.09 0.11
Matches are distributed among these distances:
126 109 0.32
128 7 0.02
131 1 0.00
132 2 0.01
136 2 0.01
137 1 0.00
139 1 0.00
140 91 0.27
141 46 0.14
142 78 0.23
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (126 bp):
AAAGTGTTGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
CCAACCCTTATACAAAGAGTTGGCCAAAACGTATGTTGGCAAGTCTATCCCAACACTTAGG
Found at i:2708 original size:266 final size:267
Alignment explanation
Indices: 2221--2977 Score: 881
Period size: 266 Copynumber: 2.8 Consensus size: 267
2211 AATTAATTTG
* * * * *
2221 CCAACTCTTATACAAAGAGTTGGCCAAAGCATTTGTCGGCAAGTCTATCCTAACACTTTA-GAAA
1 CCAACCCTTATAAAAAGAGTTGGCCAAAGCATATGTTGGCAAGTCTATCCCAACAC-TTAGGAAA
* * * * * * * *
2285 GTGTCGTCATAGTATTGGACAAAGCAAACTCTTATTTAAGTGTTACCTTAGGCATGCATATTCAA
65 GTGTTGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGAGTTGCCTTAGGCATGCATATCCCA
* * * * *
2350 ACTCTTATACAAAGAGTTGGCCAAAGCGTATGCCAAAAAGTTTATCCCAACACTTAGGAAAGTGT
130 ACCCTTATACAAAGAGTTGGCCAAAGCGTATGCTAACAAGTCTATCCCAACACTTAAGAAAGTGT
* * *
2415 CAACCCAAAAGTATTGGCATAGTGTTGGACAAAGCCGACTCTTATATAAGTATTGCCTTAGG-CA
195 CGACCCAAAAGTGTCGGCATAGTGTTGGACAAAGCCGACTCTTATATAAGTATTGCCTTAGGTCA
2479 TGCATATC
260 TGCATATC
* * * *
2487 CCAACCCTTATATAAAGAGTTGGCCAAAGCATATGTTTGTAACTCTATCCCAACACTTAGGAAAG
1 CCAACCCTTATAAAAAGAGTTGGCCAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAG
* *
2552 TGTTGGCATAGTGTTGGACAAAGCCAACTTTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAA
66 TGTTGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGAGTTGCCTTAGGCATGCATATCCCAA
* *
2617 CCCTTATACAAAGAGTTGGCCAAAGCGTATGCTAACAAGTCTATCCCAATACTTAAGAAAGCGTC
131 CCCTTATACAAAGAGTTGGCCAAAGCGTATGCTAACAAGTCTATCCCAACACTTAAGAAAGTGTC
* * * * * *
2682 GGCCCAAAAGTGTCGTCATAGTGTTGGACAAAGCCTACTCTTATTTAAGTGTTTCCTTAGGTCAT
196 GACCCAAAAGTGTCGGCATAGTGTTGGACAAAGCCGACTCTTATATAAGTATTGCCTTAGGTCAT
2747 GCATATC
261 GCATATC
* * * *
2754 CCAACCCTTATACAAAAGAGTTGGCAAAAACGTATGTTGGCAAGTCTATCCCAACACTAAGGAAA
1 CCAACCCTTATA-AAAAGAGTTGGCCAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAA
* *
2819 GTGTCGCCCCAAAAGTGTCGACATAGTGTTCGACAAAGCCAACTCTTATTTAAGAGTTGTCTTAG
65 GTGT-----------TG--G-CATAGTGTTGGACAAAGCCAACTCTTATTTAAGAGTTGCCTTAG
* * * ** * **
2884 GCATGCATATCCCAACCCTTATACAAAAAGTTGACGAAAATGTATGTTGGCAAGTCTATCCCAAC
116 GCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGCTAACAAGTCTATCCCAAC
* *
2949 ACTT-AGAACATTGTCGCCCCAAAAGTGTC
181 ACTTAAGAA-AGTGTCGACCCAAAAGTGTC
2978 ATCTTACGAC
Statistics
Matches: 416, Mismatches: 57, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
265 3 0.01
266 219 0.53
267 22 0.05
268 48 0.12
279 2 0.00
281 5 0.01
282 117 0.28
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (267 bp):
CCAACCCTTATAAAAAGAGTTGGCCAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAG
TGTTGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGAGTTGCCTTAGGCATGCATATCCCAA
CCCTTATACAAAGAGTTGGCCAAAGCGTATGCTAACAAGTCTATCCCAACACTTAAGAAAGTGTC
GACCCAAAAGTGTCGGCATAGTGTTGGACAAAGCCGACTCTTATATAAGTATTGCCTTAGGTCAT
GCATATC
Found at i:3424 original size:45 final size:45
Alignment explanation
Indices: 3005--3401 Score: 625
Period size: 45 Copynumber: 8.8 Consensus size: 45
2995 TTGTAGTGAT
*
3005 CATATCATACATGTCGTATAGCATAATCAATCAAATAATATTTAC
1 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
* ** *
3050 CATATCATGCATATCGTATAGTGTAATCAATCAAATAATATTTAT
1 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
* *
3095 CATATCATACATATCGTATAACATAATCAATCAAATAATTTTTAC
1 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
* *
3140 CATATCATACATATCATATAACATAATCAATCAAATAATATTTAC
1 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
* * *
3185 CATGTCATGCATATCGGATAGCATAATCAATCAAATAATATTTAC
1 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
3230 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
1 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
*
3275 CATATCATGCATATCGTATTA-CATAATCAATCAAATAATATTTAC
1 CATATCATACATATCGTA-TAGCATAATCAATCAAATAATATTTAC
3320 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
1 CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
* * * *
3365 CATGTCATGCATATCGTATAGTATAATTAATCAAATA
1 CATATCATACATATCGTATAGCATAATCAATCAAATA
3402 CTAACCAACT
Statistics
Matches: 323, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
44 2 0.01
45 319 0.99
46 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (45 bp):
CATATCATACATATCGTATAGCATAATCAATCAAATAATATTTAC
Found at i:3430 original size:45 final size:45
Alignment explanation
Indices: 3007--3485 Score: 177
Period size: 45 Copynumber: 10.6 Consensus size: 45
2997 GTAGTGATCA
* * * * *** * *
3007 TATCATACATGTCGTATAGCATAATCAATCAAATAATATTTACCA
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * ** * *** * *
3052 TATCATGCATATCGTATAGTGTAATCAATCAAATAATATTTATCA
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * * * **** * *
3097 TATCATACATATCGTATAACATAATCAATCAAATAATTTTTACCA
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * * *** * *
3142 TATCATACATATCATATAACATAATCAATCAAATAATATTTACCA
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * ** * *** * *
3187 TGTCATGCATATCGGATAGCATAATCAATCAAATAATATTTACCA
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * * *** * *
3232 TATCATACATATCGTATAGCATAATCAATCAAATAATATTTACCA
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * * *** * *
3277 TATCATGCATATCGTATTA-CATAATCAATCAAATAATATTTACCA
1 TATCATTCATATCATA-TAGCATAATTAATCAAATAATAACCAACT
* * * *** * *
3322 TATCATACATATCGTATAGCATAATCAATCAAATAATATTTACCA
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * * * *
3367 TGTCATGCATATCGTATAGTATAATTAATCAAATACTAACCAACT
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
** * ** *
3412 TATCATTCATATCATATAGCATGCTTAACCAAATAATAGTCATCT
1 TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
* * *
3457 TATCATTCATGTTATATAGCATAGTTAAT
1 TATCATTCATATCATATAGCATAATTAAT
3486 GTAACAGCTC
Statistics
Matches: 383, Mismatches: 49, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
44 2 0.01
45 379 0.99
46 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (45 bp):
TATCATTCATATCATATAGCATAATTAATCAAATAATAACCAACT
Found at i:3475 original size:135 final size:135
Alignment explanation
Indices: 3026--3479 Score: 469
Period size: 135 Copynumber: 3.4 Consensus size: 135
3016 TGTCGTATAG
* * * * * **
3026 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGTGTAATCAATCAAATAATAT
1 CATAATCAACCAAATAATAGTCACCATATCATACATATCATATAGCATAATCAATCAAATAATAT
* * **** * *
3091 TTATCATATCATACATATCGTATAACATAATCAATCAAATAATTTTTACCATATCATACATATCA
66 TTACCATATCATACATATCGTATAGCATAATCAATCAAATAATAACCAACATATCATGCATATCA
*
3156 TATAA
131 TATTA
* * * * * **
3161 CATAATCAATCAAATAATATTTACCATGTCATGCATATCGGATAGCATAATCAATCAAATAATAT
1 CATAATCAACCAAATAATAGTCACCATATCATACATATCATATAGCATAATCAATCAAATAATAT
*** * *
3226 TTACCATATCATACATATCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCG
66 TTACCATATCATACATATCGTATAGCATAATCAATCAAATAATAACCAACATATCATGCATATCA
3291 TATTA
131 TATTA
* * * *
3296 CATAATCAATCAAATAATATTTACCATATCATACATATCGTATAGCATAATCAATCAAATAATAT
1 CATAATCAACCAAATAATAGTCACCATATCATACATATCATATAGCATAATCAATCAAATAATAT
* * * * * * *
3361 TTACCATGTCATGCATATCGTATAGTATAATTAATCAAATACTAACCAACTTATCATTCATATCA
66 TTACCATATCATACATATCGTATAGCATAATCAATCAAATAATAACCAACATATCATGCATATCA
3426 TA-TA
131 TATTA
** * * * * * *
3430 GCATGCTTAACCAAATAATAGTCATCTTATCATTCATGTTATATAGCATA
1 -CATAATCAACCAAATAATAGTCACCATATCATACATATCATATAGCATA
3480 GTTAATGTAA
Statistics
Matches: 281, Mismatches: 37, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
134 2 0.01
135 279 0.99
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.35
Consensus pattern (135 bp):
CATAATCAACCAAATAATAGTCACCATATCATACATATCATATAGCATAATCAATCAAATAATAT
TTACCATATCATACATATCGTATAGCATAATCAATCAAATAATAACCAACATATCATGCATATCA
TATTA
Found at i:4750 original size:52 final size:51
Alignment explanation
Indices: 4670--4959 Score: 321
Period size: 52 Copynumber: 5.6 Consensus size: 51
4660 TAAATGAAAA
* *
4670 AGGTCTGGTGACTACATGTCATCGTGAGTATATGAATCTATTACGAATTATG
1 AGGTCTGATGACTACATGTCATCATGAGTATATGAATCT-TTACGAATTATG
* * * * *
4722 AGGTCCGATGACTACGTGTCATCATGAGTATATGAATCCCTTACAAAGTATG
1 AGGTCTGATGACTACATGTCATCATGAGTATATGAAT-CTTTACGAATTATG
* * *
4774 AAGTCTGATGACTACATGTCATCATGAGTATATGAATCCCTTACGGATTATG
1 AGGTCTGATGACTACATGTCATCATGAGTATATGAAT-CTTTACGAATTATG
* *
4826 AGGTCTGATGACTACATGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCTGATGACTACATGTCATCATGAGTATATGAAT-CTTTACGAATTATG
* ** * * * *
4878 AGGTCCGATGACTAGGTGTCATCATGAGTATGTGATTCTTTAATGAATTA-A
1 AGGTCTGATGACTACATGTCATCATGAGTATATGAATCTTT-ACGAATTATG
*** *
4929 AGGTCTGATGACTTTGTGTCATCGTGAGTAT
1 AGGTCTGATGACTACATGTCATCATGAGTAT
4960 TAAATACCAA
Statistics
Matches: 207, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
51 31 0.15
52 175 0.85
53 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (51 bp):
AGGTCTGATGACTACATGTCATCATGAGTATATGAATCTTTACGAATTATG
Done.