Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015344.1 Kokia drynarioides strain JFW-HI SEQ_130391, 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: 296268
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 363 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:181288 original size:114 final size:112
Alignment explanation
Indices: 181076--181389 Score: 333
Period size: 114 Copynumber: 2.8 Consensus size: 112
181066 GTTTCATATA
* * * *
181076 GGTGTCTATCGGGCTTTGTGCCTAGCAAGCTTTATG-TCGGTGTTTATTAGGCTTCGTGCCTAAC
1 GGTGTTTATC-GGCTTTGTGCCTAGCAGGCTTTATGCT-GGTGTTTA-TCGGCTTCGTGCCTAGC
* * * *
181140 AGGCTTTATGCCGGTGTTTATAGAGATTCATGCCTAACAGGTTTTGTGCT
63 AGGCTTTATGCCGGTGTTTATAGAGATTCATGCCTAACAGGCTATATGCC
* *
181190 GGTGTTTATCAGGCTTTGTGCCTAGCAGGCTTTCTGCTGGTGTTTATCGGACTTCGTGTCTAGCA
1 GGTGTTTATC-GGCTTTGTGCCTAGCAGGCTTTATGCTGGTGTTTATCGG-CTTCGTGCCTAGCA
* * * **
181255 GGCTTTATGCCGGTGTTTATCGAGCTTCGTGCCTGGCAGGCTATATGCC
64 GGCTTTATGCCGGTGTTTATAGAGATTCATGCCTAACAGGCTATATGCC
* * * * * * * *
181304 AGTGTTTATCGAGCTTCGTACCTAACAGGCTTTATGCCGATGTTTATCAGGTTTCGTGCCTAGAA
1 GGTGTTTATCG-GCTTTGTGCCTAGCAGGCTTTATGCTGGTGTTTATC-GGCTTCGTGCCTAGCA
* *
181369 GGCTTTGTGCCAGTGTTTATA
64 GGCTTTATGCCGGTGTTTATA
181390 CTTGTTTGGT
Statistics
Matches: 167, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
113 4 0.02
114 160 0.96
115 3 0.02
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (112 bp):
GGTGTTTATCGGCTTTGTGCCTAGCAGGCTTTATGCTGGTGTTTATCGGCTTCGTGCCTAGCAGG
CTTTATGCCGGTGTTTATAGAGATTCATGCCTAACAGGCTATATGCC
Found at i:186598 original size:40 final size:40
Alignment explanation
Indices: 186521--186599 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
186511 ATCTAAGAAT
* * *
186521 TAATAGTTCAACAATTTATATGTAATTAATTAACAAAAAA
1 TAATAGTTCAACAATTTATATATAATAAAGTAACAAAAAA
* *
186561 TAATATTTCAACAATTTATATATAATAAAGTAGCAAAAA
1 TAATAGTTCAACAATTTATATATAATAAAGTAACAAAAA
186600 TCAGAAGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (40 bp):
TAATAGTTCAACAATTTATATATAATAAAGTAACAAAAAA
Found at i:191012 original size:26 final size:27
Alignment explanation
Indices: 190976--191028 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
190966 CTTAGTCTTT
*
190976 CAAAAATTTAGCTCACACGGGCCCAGA
1 CAAAAATTTAGCTCACACGAGCCCAGA
*
191003 CAAAAA-TTAGCTCATACGAGCCCAGA
1 CAAAAATTTAGCTCACACGAGCCCAGA
191029 ATGCTTAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (27 bp):
CAAAAATTTAGCTCACACGAGCCCAGA
Found at i:195699 original size:18 final size:17
Alignment explanation
Indices: 195659--195699 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
195649 TTTAAGTTTA
*
195659 TAATATTTTATATTATG
1 TAATTTTTTATATTATG
*
195676 TTATTTTTTATATTAATG
1 TAATTTTTTATATT-ATG
195694 TAATTT
1 TAATTT
195700 AAAACACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TAATTTTTTATATTATG
Found at i:198991 original size:32 final size:32
Alignment explanation
Indices: 198950--199012 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
198940 ACACTGGGTG
198950 AGTCATTATTAAGCGCGACTTTTCTCCCTTTT
1 AGTCATTATTAAGCGCGACTTTTCTCCCTTTT
198982 AGTCATTATTAAGCGCGACTTTTCTCCCTTT
1 AGTCATTATTAAGCGCGACTTTTCTCCCTTT
199013 CTTTTCCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (32 bp):
AGTCATTATTAAGCGCGACTTTTCTCCCTTTT
Found at i:222547 original size:2 final size:2
Alignment explanation
Indices: 222542--222567 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
222532 TGTGTGTGAC
222542 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
222568 GGACATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:228542 original size:2 final size:2
Alignment explanation
Indices: 228535--228563 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
228525 ATAATTCTAT
228535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
228564 TTGCTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:228778 original size:15 final size:14
Alignment explanation
Indices: 228751--228808 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
228741 CACTCTTGTG
*
228751 TTTTTAGTGTTATA
1 TTTTTAGTTTTATA
228765 TTTCTTAGTTTTATAA
1 TTT-TTAGTTTTAT-A
228781 TTTTATAGTTTT-TA
1 TTTT-TAGTTTTATA
*
228795 TTATTTAATTTTAT
1 TT-TTTAGTTTTAT
228809 TTCATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 12 0.32
15 14 0.38
16 11 0.30
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTAGTTTTATA
Found at i:229378 original size:28 final size:28
Alignment explanation
Indices: 229324--229378 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
229314 TACAAATTTA
* * * *
229324 TAAAAATTATAAGATATAAATATAAAAT
1 TAAAAATTAAAAAATAGAAATAGAAAAT
*
229352 TAAAAATTAAAAAATAGAAGTAGAAAA
1 TAAAAATTAAAAAATAGAAATAGAAAA
229379 AGGAGTGTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.25
Consensus pattern (28 bp):
TAAAAATTAAAAAATAGAAATAGAAAAT
Found at i:230382 original size:10 final size:10
Alignment explanation
Indices: 230355--230389 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
230345 ACAAAAAACA
230355 AAAAGAAGAAG
1 AAAAGAAG-AG
230366 AAAAGAAGAG
1 AAAAGAAGAG
*
230376 AAGAGAAGAG
1 AAAAGAAGAG
230386 AAAA
1 AAAA
230390 ATGAAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AAAAGAAGAG
Found at i:233175 original size:2 final size:2
Alignment explanation
Indices: 233168--233199 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
233158 GGTATAATTC
233168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233200 GAATATTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253324 original size:15 final size:15
Alignment explanation
Indices: 253282--253327 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
253272 GTAAGATATA
253282 TTTTAATTATTTATG
1 TTTTAATTATTTATG
* *
253297 TTTGAAATA-TTATG
1 TTTTAATTATTTATG
*
253311 TTTTAGTTATTTATG
1 TTTTAATTATTTATG
253326 TT
1 TT
253328 ATTGTTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (15 bp):
TTTTAATTATTTATG
Found at i:253488 original size:30 final size:29
Alignment explanation
Indices: 253443--253499 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
253433 CAACCAAGTA
*
253443 AATTAATTGATTTTTTAATTTAATTAATT
1 AATTAATTGATTTTTTAAATTAATTAATT
253472 AATTAATTGAATTTTTTAAATTAATTAA
1 AATTAATTG-ATTTTTTAAATTAATTAA
253500 AAGAAAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
AATTAATTGATTTTTTAAATTAATTAATT
Found at i:253490 original size:17 final size:17
Alignment explanation
Indices: 253443--253497 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
253433 CAACCAAGTA
253443 AATTAATTG-ATTTTTT
1 AATTAATTGAATTTTTT
253459 AATTTAATT-AA----TT
1 AA-TTAATTGAATTTTTT
253472 AATTAATTGAATTTTTT
1 AATTAATTGAATTTTTT
253489 AAATTAATT
1 -AATTAATT
253498 AAAAGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
16 2 0.06
17 9 0.29
18 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
AATTAATTGAATTTTTT
Found at i:253997 original size:159 final size:159
Alignment explanation
Indices: 253826--254129 Score: 482
Period size: 159 Copynumber: 1.9 Consensus size: 159
253816 GGGTTTTTTT
* * *
253826 TTTTGTAAAAAGATGGTTCATCTTTTCATGTTTTTTTGTATATGTGAAAAATAAAAAAGACATGC
1 TTTTGCAAAAAGATGGTTCATCTTTTCATATTTTTTTATATATGTGAAAAATAAAAAAGACATGC
* * *
253891 TTCATTTTGTTTATTTGTATATTGTGGGCAACCACGATAACAAGCAAGTATAGAGGTTGGTGCGT
66 TTCATTTTGTTTATTTGTATATTATGGGCAACCACAATAACAAGCAAGTATAGAGGTTAGTGCGT
253956 TCATTTATTCTTCTTCTTTTTTTCTGTCG
131 TCATTTATTCTTCTTCTTTTTTTCTGTCG
* * * *
253985 TTTTGCAAAAAGATGGTTCATTTTTTTATATTTTTTTATATATGTGACAAATAAAAAAGACATGT
1 TTTTGCAAAAAGATGGTTCATCTTTTCATATTTTTTTATATATGTGAAAAATAAAAAAGACATGC
* * *
254050 TTCATTTTGTTTATTTGTGTATTATGGGCAACCACAATAACAAGCAGGTATAGAGGTTAGTGGGT
66 TTCATTTTGTTTATTTGTATATTATGGGCAACCACAATAACAAGCAAGTATAGAGGTTAGTGCGT
*
254115 TCATTTCTTCTTCTT
131 TCATTTATTCTTCTT
254130 TTTCTCTATG
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
159 131 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (159 bp):
TTTTGCAAAAAGATGGTTCATCTTTTCATATTTTTTTATATATGTGAAAAATAAAAAAGACATGC
TTCATTTTGTTTATTTGTATATTATGGGCAACCACAATAACAAGCAAGTATAGAGGTTAGTGCGT
TCATTTATTCTTCTTCTTTTTTTCTGTCG
Found at i:262468 original size:33 final size:33
Alignment explanation
Indices: 262392--262475 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 33
262382 CCTATTTACT
* * * ** *
262392 TAAAATAAATAATTTTAGTCAAAATGAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
262425 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
262457 TAAAATAAACAACTTTAAT
1 TAAAATAAACAAATTTAAT
262476 TAAGCTTATT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
32 25 0.61
33 16 0.39
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:268977 original size:59 final size:58
Alignment explanation
Indices: 268913--269026 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 58
268903 ACTCATCCAC
*
268913 AAACTAAATCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAAACACTTGT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTT-AAAAAACACTTGT
* * *
268972 AAACTAAACCCAAATATTTTTAAACCTAAATATAATTTTATTCTTAAATAACACT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACT
269027 CATAAACAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 9 0.18
59 42 0.82
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTTGT
Found at i:270375 original size:17 final size:17
Alignment explanation
Indices: 270313--270376 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
270303 CAATTATATC
*
270313 TTTAAAAATAATTATAA
1 TTTAAAAATAATTAAAA
270330 TTTAAAAATTATGATAATAACACA
1 TTTAAAAA-TA--AT--TAA-A-A
270354 TTTAAAAATAATTAAAA
1 TTTAAAAATAATTAAAA
270371 TTTAAA
1 TTTAAA
270377 TTACAATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
17 15 0.38
18 3 0.08
19 3 0.08
20 2 0.05
21 2 0.05
22 2 0.05
23 3 0.08
24 9 0.23
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
TTTAAAAATAATTAAAA
Found at i:270823 original size:22 final size:24
Alignment explanation
Indices: 270771--270823 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 24
270761 TTTAATTTTT
270771 ATTATATTACTAAATTAATTTTAAA
1 ATTAT-TTACTAAATTAATTTTAAA
* * *
270796 AATATTTA-TAATTTAA-TTTAGA
1 ATTATTTACTAAATTAATTTTAAA
270818 ATTATT
1 ATTATT
270824 AGTTAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 10 0.42
23 7 0.29
24 3 0.12
25 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTATTTACTAAATTAATTTTAAA
Found at i:273301 original size:52 final size:52
Alignment explanation
Indices: 273245--273404 Score: 156
Period size: 52 Copynumber: 3.1 Consensus size: 52
273235 ATGATTATAT
273245 TTAAAATGAATTCAAATTATATAAAAAAAATTTAATTAAACAATTATTGTAA
1 TTAAAATGAATTCAAATTATATAAAAAAAATTTAATTAAACAATTATTGTAA
* * * * *
273297 TT-AAA--AATTCTAAA-TACTCCTCAAAATATATATTT--TT-AA-AATGATTATAT
1 TTAAAATGAATTC-AAATTA-T-AT-AAAA-A-AAATTTAATTAAACAATTATTGTAA
*
273347 TTAAAATGAATTCAAATTATATAAAAAAAAATTAATTAAACAATTATTGTAA
1 TTAAAATGAATTCAAATTATATAAAAAAAATTTAATTAAACAATTATTGTAA
273399 TTAAAA
1 TTAAAA
273405 ATTCTAAATA
Statistics
Matches: 83, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
48 4 0.05
49 8 0.10
50 20 0.24
51 12 0.14
52 26 0.31
53 8 0.10
54 5 0.06
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (52 bp):
TTAAAATGAATTCAAATTATATAAAAAAAATTTAATTAAACAATTATTGTAA
Found at i:273306 original size:49 final size:50
Alignment explanation
Indices: 273253--273413 Score: 147
Period size: 50 Copynumber: 3.2 Consensus size: 50
273243 ATTTAAAATG
273253 AATTC-AAATTATATAAAAAAAATTTAATTAAACAATTATTGTAATTAAA
1 AATTCTAAATTATATAAAAAAAATTTAATTAAACAATTATTGTAATTAAA
* * * * *
273302 AATTCTAAA-TACTCCTCAAAATATATATTT--TT-AA-AATGATTATATTTAAAA
1 AATTCTAAATTA-T-AT-AAAA-A-AAATTTAATTAAACAATTATTGTAATT-AAA
*
273353 TGAATTC-AAATTATATAAAAAAAAATTAATTAAACAATTATTGTAATTAAA
1 --AATTCTAAATTATATAAAAAAAATTTAATTAAACAATTATTGTAATTAAA
273404 AATTCTAAAT
1 AATTCTAAAT
273414 ACTCCTAATT
Statistics
Matches: 86, Mismatches: 11, Indels: 29
0.68 0.09 0.23
Matches are distributed among these distances:
48 4 0.05
49 13 0.15
50 24 0.28
51 12 0.14
52 20 0.23
53 8 0.09
54 5 0.06
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (50 bp):
AATTCTAAATTATATAAAAAAAATTTAATTAAACAATTATTGTAATTAAA
Found at i:273391 original size:102 final size:102
Alignment explanation
Indices: 273215--273419 Score: 401
Period size: 102 Copynumber: 2.0 Consensus size: 102
273205 ATTTTTTGGG
*
273215 TCAAAATATATATTTTTAAAATGATTATATTTAAAATGAATTCAAATTATATAAAAAAAATTTAA
1 TCAAAATATATATTTTTAAAATGATTATATTTAAAATGAATTCAAATTATATAAAAAAAAATTAA
273280 TTAAACAATTATTGTAATTAAAAATTCTAAATACTCC
66 TTAAACAATTATTGTAATTAAAAATTCTAAATACTCC
273317 TCAAAATATATATTTTTAAAATGATTATATTTAAAATGAATTCAAATTATATAAAAAAAAATTAA
1 TCAAAATATATATTTTTAAAATGATTATATTTAAAATGAATTCAAATTATATAAAAAAAAATTAA
273382 TTAAACAATTATTGTAATTAAAAATTCTAAATACTCC
66 TTAAACAATTATTGTAATTAAAAATTCTAAATACTCC
273419 T
1 T
273420 AATTATATTT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (102 bp):
TCAAAATATATATTTTTAAAATGATTATATTTAAAATGAATTCAAATTATATAAAAAAAAATTAA
TTAAACAATTATTGTAATTAAAAATTCTAAATACTCC
Found at i:277032 original size:275 final size:275
Alignment explanation
Indices: 276541--277089 Score: 1008
Period size: 275 Copynumber: 2.0 Consensus size: 275
276531 TAACAATTGC
*
276541 TTCTCAAACACCCATGCCCAATACGTAGGTTAATTTGTTCATTGATGGTGTAATTACTAGCGGTG
1 TTCTCAAACACCCATGCCCAATACGTAGGTTAATTTGTTCATTGATGGTGTAATTACTAGCGATG
* *
276606 ATGGAAGTGCTTCTGCTAGGTATGTTTTACTTGATCAATATTAGAATTGGATCTTGGGGTTTAAT
66 ATGGAAGTGCTTCTGCTAGGTATGTTTTACTTGATCAACATTAGAATTGGATCTTGAGGTTTAAT
*
276671 CATTATTTGGGACGATGCTTAATTTTCGAAGTTAAATTATGAGGAATCTTAGATGGTTTACTCGT
131 CATTATTTGGGACGATGCTTAATCTTCGAAGTTAAATTATGAGGAATCTTAGATGGTTTACTCGT
*
276736 GATGCTTAGCGAAGATTTTAAAAGGATCACGATTTAGACAGATAATTTAAAGGTTGTCAGTGCTC
196 GATGCTTAGCGAAGATTTTAAAAGGATCACGATTTAGACAGATAATCTAAAGGTTGTCAGTGCTC
276801 TACAAGAAAATATGG
261 TACAAGAAAATATGG
276816 TTCTCAAACACCCATGCCCAATACGTAGGTTAATTTGTTCATTGATGGTGTAATTACTAGCGATG
1 TTCTCAAACACCCATGCCCAATACGTAGGTTAATTTGTTCATTGATGGTGTAATTACTAGCGATG
*
276881 ATGGAAGTGCTTTTGCTAGGTATGTTTTACTTGATCAACATTAGAATTGGATCTTGAGGTTTAAT
66 ATGGAAGTGCTTCTGCTAGGTATGTTTTACTTGATCAACATTAGAATTGGATCTTGAGGTTTAAT
*
276946 CATTATTTGGGATGATGCTTAATCTTCGAAGTTAAATTATGAGGAATCTTAGATGGTTTACTCGT
131 CATTATTTGGGACGATGCTTAATCTTCGAAGTTAAATTATGAGGAATCTTAGATGGTTTACTCGT
* * *
277011 GATGCTTAGCGAAGGTTTTAAAAGGATCACGATTTAGATAGATAATCTGAAGGTTGTCAGTGCTC
196 GATGCTTAGCGAAGATTTTAAAAGGATCACGATTTAGACAGATAATCTAAAGGTTGTCAGTGCTC
277076 TACAAGAAAATATG
261 TACAAGAAAATATG
277090 ATGACAGACT
Statistics
Matches: 264, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
275 264 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (275 bp):
TTCTCAAACACCCATGCCCAATACGTAGGTTAATTTGTTCATTGATGGTGTAATTACTAGCGATG
ATGGAAGTGCTTCTGCTAGGTATGTTTTACTTGATCAACATTAGAATTGGATCTTGAGGTTTAAT
CATTATTTGGGACGATGCTTAATCTTCGAAGTTAAATTATGAGGAATCTTAGATGGTTTACTCGT
GATGCTTAGCGAAGATTTTAAAAGGATCACGATTTAGACAGATAATCTAAAGGTTGTCAGTGCTC
TACAAGAAAATATGG
Found at i:277893 original size:11 final size:11
Alignment explanation
Indices: 277877--277946 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
277867 GTTTATTTTA
277877 TTTTTTTTA-T
1 TTTTTTTTATT
*
277887 TTTTTTTTATC
1 TTTTTTTTATT
*
277898 TTTTTCTTATT
1 TTTTTTTTATT
*
277909 TTTATTTT-TT
1 TTTTTTTTATT
* **
277919 TTGTAATTATT
1 TTTTTTTTATT
277930 TTTTTATTTCATT
1 TTTTT-TTT-ATT
277943 TTTT
1 TTTT
277947 CCTGATTAGT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
10 15 0.34
11 20 0.45
12 2 0.05
13 7 0.16
ACGTcount: A:0.13, C:0.04, G:0.01, T:0.81
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:295292 original size:26 final size:26
Alignment explanation
Indices: 295262--295315 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
295252 AAAAAAATTT
* * * *
295262 AAAGTCCAATTACATACAATAAACCC
1 AAAGTCCAAATACAAAAAAAAAACCC
295288 AAAGTCCAAATACAAAAAAAAAACCC
1 AAAGTCCAAATACAAAAAAAAAACCC
295314 AA
1 AA
295316 TTAACCTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.13
Consensus pattern (26 bp):
AAAGTCCAAATACAAAAAAAAAACCC
Done.