Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015334.1 Kokia drynarioides strain JFW-HI SEQ_130381, 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: 402212
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 161 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:344276 original size:25 final size:26
Alignment explanation
Indices: 344208--344281 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 26
344198 GAAAAATCGA
* *
344208 GGTAAAAAATGGAATTTTGGAAAGTTCGG
1 GGTAAAAAATGGAATTTTTG---GTTCAG
*
344237 GGT-AAAAATGTAATTTTTGGTT-AG
1 GGTAAAAAATGGAATTTTTGGTTCAG
344261 GGTAAAAAATGGAATTTTTGG
1 GGTAAAAAATGGAATTTTTGG
344282 AAGTTCGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 4 0.10
25 19 0.47
28 14 0.35
29 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.34
Consensus pattern (26 bp):
GGTAAAAAATGGAATTTTTGGTTCAG
Found at i:344333 original size:112 final size:111
Alignment explanation
Indices: 344061--344484 Score: 313
Period size: 112 Copynumber: 3.7 Consensus size: 111
344051 GCAAGTTCGA
* * * * *
344061 GGGTAATATGGTCATTTTTGG-AAAATCGGGGTCAAAAAATGGAATTTTTGGAAGTTTAGAGGTA
1 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGT-AAAAAATGGAATTTTTGGAAG-TTCGGGGTA
* * ** *
344125 AGATG-ATATTTTTGGAAAAACTAGACTCAAAAATGGAATTTTTAAAAGTCTGG
64 AAATGTA-ATTTTTGG-----TTAGGGTAAAAAATGGAATTTTTAAAAGTCTGG
344178 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAA-TTTTGGAAAGTTCGGGGTAA
1 GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAATTTTTGG-AAGTTCGGGGT-A
**
344242 AAATGTAATTTTTGGTTAGGGTAAAAAATGGAATTTTTGGAAGT-TCGG
64 AAATGTAATTTTTGGTTAGGGTAAAAAATGGAATTTTTAAAAGTCT-GG
* * * * *
344290 GGGTAAAAAT-GTATTTTTTGGGAAAATCGGGGTCAAAAGTGGAATTTTTGGAAGTTCGGGGTAA
1 GGGT-AAAATGGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAATTTTTGGAAGTTCGGGGTAA
* ** * * ** * *
344354 ATTGTAATTTTTTGAAAAATCGAGGTCAAAAATGGAATTTTTGGAA-TTTAG
65 AATGTAA-TTTTTG---GTTAG-GGTAAAAAATGGAATTTTTAAAAGTCTGG
* * * * * * *
344405 AGGTAAAA-GTGTAATTTTTTGAAAATTAGAGGTCAAAAATGGAATTTTTAGAAGGTCGGGTGTA
1 GGGTAAAATG-GTAATTTTTGGAAAAATCGAGGTAAAAAATGGAATTTTTGGAAGTTCGGG-GTA
*
344469 CAAATATAATTTTTGG
64 -AAATGTAATTTTTGG
344485 AAAAAAATCG
Statistics
Matches: 254, Mismatches: 36, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
111 9 0.04
112 75 0.30
113 11 0.04
114 4 0.02
115 48 0.19
116 44 0.17
117 52 0.20
118 11 0.04
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (111 bp):
GGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAATTTTTGGAAGTTCGGGGTAAA
ATGTAATTTTTGGTTAGGGTAAAAAATGGAATTTTTAAAAGTCTGG
Found at i:344407 original size:29 final size:28
Alignment explanation
Indices: 344095--344453 Score: 173
Period size: 29 Copynumber: 12.5 Consensus size: 28
344085 ATCGGGGTCA
*
344095 AAAAATGGAATTTTTGGAAGTTTAGAGGT
1 AAAAATGGAATTTTTGGAA-ATTAGAGGT
* * *
344124 -AAGAT-GATATTTTTGGAAAAACTAGA-CT
1 AAAAATGGA-ATTTTTGG--AAATTAGAGGT
* * *
344152 CAAAAATGGAATTTTT-AAAAGTCTGGGGGT
1 -AAAAATGGAATTTTTGGAAA-T-TAGAGGT
* *
344182 -AAAATGGTAATTTTTGGAAAAATCGAGGT
1 AAAAATGG-AATTTTTGG-AAATTAGAGGT
* *
344211 AAAAAATGGAA-TTTTGGAAAGTTCGGGGT
1 -AAAAATGGAATTTTTGGAAA-TTAGAGGT
*
344240 AAAAATGTAATTTTTGG---TTAG-GGT
1 AAAAATGGAATTTTTGGAAATTAGAGGT
* * *
344264 AAAAAATGGAATTTTTGGAAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAATT-AGAGGT
* * * * *
344294 AAAAATGTATTTTTTGGGAAAATCGGGGT
1 AAAAATGGAATTTTT-GGAAATTAGAGGT
* * * *
344323 CAAAAGTGGAATTTTTGGAAGTTCGGGGT
1 -AAAAATGGAATTTTTGGAAATTAGAGGT
* * * * *
344352 -AAATTGTAATTTTTTGAAAAATCGAGGT
1 AAAAATGGAA-TTTTTGGAAATTAGAGGT
*
344380 CAAAAATGGAATTTTTGGAATTTAGAGGT
1 -AAAAATGGAATTTTTGGAAATTAGAGGT
* * *
344409 AAAAGTGTAATTTTTTGAAAATTAGAGGT
1 AAAAATGGAA-TTTTTGGAAATTAGAGGT
344438 CAAAAATGGAATTTTT
1 -AAAAATGGAATTTTT
344454 AGAAGGTCGG
Statistics
Matches: 253, Mismatches: 48, Indels: 58
0.70 0.13 0.16
Matches are distributed among these distances:
24 3 0.01
25 19 0.08
27 12 0.05
28 56 0.22
29 101 0.40
30 50 0.20
31 12 0.05
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAATTAGAGGT
Found at i:344482 original size:58 final size:57
Alignment explanation
Indices: 344003--344513 Score: 459
Period size: 58 Copynumber: 8.8 Consensus size: 57
343993 TAGACATCTA
* * * * *
344003 GGGGTAAAATGGTACTTTTTGGAAGAATCGGGGTC-AAAATAGAA-TTTTGCAAGTTC
1 GGGGTAAAAT-GTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* * * *
344059 GAGGGTAATATGGTCATTTTTGG-AAAATCGGGGTCAAAAAATGGAATTTTTGGAAGTTTA
1 G-GGGTAAAAT-GTAATTTTTGGAAAAATCGAGGTC-AAAAATGGAATTTTTGGAAG-TTC
* * * * ** *
344119 GAGGTAAGATG-ATATTTTTGGAAAAA-CTAGACTCAAAAATGGAATTTTTAAAAGTCTG
1 GGGGTAAAATGTA-ATTTTTGGAAAAATCGAG-GTCAAAAATGGAATTTTTGGAAGT-TC
*
344177 GGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAA-TTTTGGAAAGTTC
1 GGGGTAAAAT-GTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGG-AAGTTC
* * *
344235 GGGGTAAAAATGTAATTTTTGG----TTAG-GGTAAAAAATGGAATTTTTGGAAGTTC
1 GGGGT-AAAATGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* * * *
344288 GGGGGTAAAAATGTATTTTTTGGGAAAATCGGGGTCAAAAGTGGAATTTTTGGAAGTTC
1 -GGGGT-AAAATGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* * * *
344347 GGGGTAAATTGTAATTTTTTGAAAAATCGAGGTCAAAAATGGAATTTTTGGAATTTA
1 GGGGTAAAATGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* * * * * *
344404 GAGGTAAAAGTGTAATTTTTTGAAAATTAGAGGTCAAAAATGGAATTTTTAGAAGGTC
1 GGGGTAAAA-TGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* *
344462 GGGTGTACAAATATAATTTTTGGAAAAAAATCGAGGTCAAAAATAGAATTTT
1 GGG-GTA-AAATGTAATTTTTGG--AAAAATCGAGGTCAAAAATGGAATTTT
344514 AGAAAAGTTT
Statistics
Matches: 376, Mismatches: 53, Indels: 47
0.79 0.11 0.10
Matches are distributed among these distances:
53 20 0.05
54 29 0.08
56 12 0.03
57 70 0.19
58 118 0.31
59 93 0.25
60 10 0.03
61 24 0.06
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (57 bp):
GGGGTAAAATGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC
Found at i:345634 original size:3 final size:3
Alignment explanation
Indices: 345626--345762 Score: 57
Period size: 3 Copynumber: 45.0 Consensus size: 3
345616 AATTTCCTTT
* * * *
345626 TTA TTA TTA -TA TTA ATA ATA ATA ATA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
* * * * * * *
345671 CTA ATA TCA TTA TT- TTT TTA -AA ATA GTTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * *
345715 TTTA TTA TGGT- TTA TTA ATA ATA TCA TTA GTA TTA TTA TGTA TTA TTA
1 -TTA TTA T--TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
345763 CTGTCACTTG
Statistics
Matches: 105, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
2 6 0.06
3 87 0.83
4 11 0.10
5 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:346501 original size:17 final size:17
Alignment explanation
Indices: 346474--346560 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 17
346464 AATTCTAGGG
* *
346474 TTAAGTTTAAAAT-CAT
1 TTAAATTTAAAATAAAT
*
346490 TTCAAATTTAAACTAAAT
1 TT-AAATTTAAAATAAAT
346508 TTAAATTT--AA-AAA-
1 TTAAATTTAAAATAAAT
* *
346521 -CAAATTTAAAGTAAAT
1 TTAAATTTAAAATAAAT
346537 TTAAATTTAAAAAATAAAT
1 TTAAATTT--AAAATAAAT
346556 TTAAA
1 TTAAA
346561 ACCAATCTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
12 6 0.11
14 4 0.07
15 4 0.07
16 2 0.04
17 21 0.39
18 4 0.07
19 13 0.24
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:346526 original size:29 final size:30
Alignment explanation
Indices: 346492--346560 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
346482 AAAATCATTT
346492 CAAATTTAAACTAAATTTAAATTT-AAAAA
1 CAAATTTAAACTAAATTTAAATTTAAAAAA
*
346521 CAAATTTAAAGTAAATTTAAATTTAAAAAA
1 CAAATTTAAACTAAATTTAAATTTAAAAAA
*
346551 TAAATTTAAA
1 CAAATTTAAA
346561 ACCAATCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (30 bp):
CAAATTTAAACTAAATTTAAATTTAAAAAA
Found at i:346560 original size:6 final size:6
Alignment explanation
Indices: 346488--346547 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
346478 GTTTAAAATC
* *** *
346488 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA AAACAA ATTTAA A-GTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
346535 ATTTAA ATTTAA A
1 ATTTAA ATTTAA A
346548 AAATAAATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
5 8 0.20
6 29 0.71
7 4 0.10
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (6 bp):
ATTTAA
Found at i:346561 original size:12 final size:13
Alignment explanation
Indices: 346509--346561 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
346499 AAACTAAATT
346509 TAAATTT-AAAAA
1 TAAATTTAAAAAA
*
346521 CAAATTTAAAGTAAA
1 TAAATTTAAA--AAA
346536 TTTAAATTTAAAAAA
1 --TAAATTTAAAAAA
346551 TAAATTTAAAA
1 TAAATTTAAAA
346562 CCAATCTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 6 0.18
13 13 0.38
15 6 0.18
17 9 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
TAAATTTAAAAAA
Found at i:346656 original size:6 final size:6
Alignment explanation
Indices: 346629--346715 Score: 83
Period size: 6 Copynumber: 15.0 Consensus size: 6
346619 GCTTTTATTT
* ** *
346629 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA AAATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
346676 A-TTAA ATTTAA ATTTAA ATTTAA A-ATAA ATCTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
346716 GACAAATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
4 1 0.02
5 11 0.17
6 52 0.79
7 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:346665 original size:29 final size:27
Alignment explanation
Indices: 346632--346715 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 27
346622 TTTATTTATT
346632 TAAATTTATAATAATTTTAAATTTAAAAA
1 TAAATTTA-AATAA-TTTAAATTTAAAAA
* **
346661 TAAATTTAAACTTAAATTAAATTTAAATT
1 TAAATTTAAA--TAATTTAAATTTAAAAA
*
346690 TAAATTTAAAATAAATCTAAATTTAA
1 TAAATTT-AAAT-AATTTAAATTTAA
346716 GACAAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 3 0.07
29 37 0.80
30 6 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATTTAAATAATTTAAATTTAAAAA
Found at i:346680 original size:23 final size:23
Alignment explanation
Indices: 346648--346715 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
346638 TATAATAATT
*
346648 TTAAATTTAAAAATAAATTTAAAC
1 TTAAA-TTAAATATAAATTTAAAC
* *
346672 TTAAATTAAATTTAAATTTAAAT
1 TTAAATTAAATATAAATTTAAAC
* *
346695 TTAAAATAAATCTAAATTTAA
1 TTAAATTAAATATAAATTTAA
346716 GACAAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 34 0.87
24 5 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAATTAAATATAAATTTAAAC
Found at i:346704 original size:17 final size:17
Alignment explanation
Indices: 346629--346744 Score: 90
Period size: 17 Copynumber: 6.4 Consensus size: 17
346619 GCTTTTATTT
*
346629 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
346646 TTTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
*
346664 ATTTAAACTTAAATTAAATTTAA
1 ATTTAAA--T---TTAAA-ATAA
346687 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* * *
346704 ATCTAAATTTAAGACAA
1 ATTTAAATTTAAAATAA
*
346721 ATTT-TATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
346738 ATTTAAA
1 ATTTAAA
346745 AATGGGTTTG
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
16 2 0.03
17 40 0.52
18 18 0.23
20 1 0.01
21 1 0.01
22 3 0.04
23 12 0.16
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:364943 original size:31 final size:31
Alignment explanation
Indices: 364908--364971 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
364898 CATTATAAAC
364908 TTTAGACAATTTAAGAAGGTTATTATGAATT
1 TTTAGACAATTTAAGAAGGTTATTATGAATT
364939 TTTAGACAATTTAAGAAGGTTATTATGAATT
1 TTTAGACAATTTAAGAAGGTTATTATGAATT
364970 TT
1 TT
364972 GTGTGTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.44
Consensus pattern (31 bp):
TTTAGACAATTTAAGAAGGTTATTATGAATT
Found at i:365202 original size:33 final size:34
Alignment explanation
Indices: 365165--365233 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
365155 TAAATAAAAT
* *
365165 TATGTA-TTCTTTTTATATTTCTAGGTTTTGAAA
1 TATGTATTTCTTTTTATATTACTAGATTTTGAAA
*
365198 TATGTATTTTTTTTTATATTACTAGATTTTGAAA
1 TATGTATTTCTTTTTATATTACTAGATTTTGAAA
365232 TA
1 TA
365234 CTCATAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 6 0.19
34 26 0.81
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (34 bp):
TATGTATTTCTTTTTATATTACTAGATTTTGAAA
Found at i:366016 original size:15 final size:17
Alignment explanation
Indices: 365986--366018 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
365976 ACCGCATTAG
365986 ACATTTTATGAAAGTAC
1 ACATTTTATGAAAGTAC
366003 ACATTTT-T-AAAGTAC
1 ACATTTTATGAAAGTAC
366018 A
1 A
366019 AGTATCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (17 bp):
ACATTTTATGAAAGTAC
Found at i:375399 original size:150 final size:146
Alignment explanation
Indices: 375111--375653 Score: 664
Period size: 147 Copynumber: 3.7 Consensus size: 146
375101 AATATATTAC
* * *
375111 AAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGAT--ATATAAGAAGAA-A
1 AAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAAAAAAAAAAAGAACA
* * *
375173 AAAAT-GATCAAATAAGAAATTTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGCAC
66 AAACTGGATCAAATAAAAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGCAC
375237 AAAGACTAATTTCTAG
131 AAAGACTAATTTCTAG
* *
375253 AAAAGAAATGCAATTGGACAAGAACTATGAAAACACAATGAACAAAGATAAGAGGAAAAAAAATG
1 AAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAA-A--AAAAAAAA-G
* * * *
375318 AACAAAACTGGATCAAATAAAAAATCTATCTGATTTAGAAGAGTATGCCACAAGAAAAGTAAAAT
62 AACAAAACTGGATCAAATAAAAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGAT
* * *
375383 TCACAAAGATTCATTTCTAG
127 GCACAAAGACTAATTTCTAG
* * * * *
375403 AAAAGAAATGCAATTGAACAAGGACAATGAAAACACAATGAATAAAGA-AAAAAAAATATATGAG
1 AAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAAAAAAAA-A-AAGAA
* * * * * * *
375467 CAAGACTCGATCAAATAAGAAACCTATCTGATTTAGAAGAATATACTGCAACAAAAATAAGATGC
64 CAAAACTGGATCAAATAAAAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGC
375532 ACAAAGACTAATTTCTAG
129 ACAAAGACTAATTTCTAG
* * * * * *
375550 AAAAGAAATGAAATTGAGCAAGAACGATGAAAACATAATAAACAAAAATAAGAGAAAAAAAAAAA
1 AAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAA-A-AAAAAAAAGAA
*
375615 CAAGACTGGATCAAATAAAAAAATCTATCTGATTTAGAA
64 CAAAACTGGATCAAAT-AAAAAATCTATCTGATTTAGAA
375654 AAATTCTAAG
Statistics
Matches: 338, Mismatches: 49, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
142 47 0.14
145 1 0.00
146 5 0.01
147 117 0.35
148 24 0.07
149 29 0.09
150 115 0.34
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (146 bp):
AAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAAAAAAAAAAAGAACA
AAACTGGATCAAATAAAAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGCAC
AAAGACTAATTTCTAG
Found at i:380022 original size:18 final size:18
Alignment explanation
Indices: 379995--380029 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
379985 CTTTAGAAAC
*
379995 TTTTTAAAAAATTATAAT
1 TTTTTAAAAAAATATAAT
*
380013 TTTTTTAAAAAATATAA
1 TTTTTAAAAAAATATAA
380030 AATTTGACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTTAAAAAAATATAAT
Found at i:389371 original size:60 final size:60
Alignment explanation
Indices: 389278--389440 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
389268 GGTCTCAGTG
* *
389278 ATGCGACCAATTTTTCTCCATCACGTCTCTATTACAAGCTTTTCATGTAAATGAGGTTAT
1 ATGCGACCAATTTTTCTCCATCATGTCTCTATTACAAGCTTTTCATGTAAATGAGATTAT
*
389338 ATGCGACCAATTTTTCTCCATCATGTCTGTATTACAAGCTTTTCATGTAAATGAGATTAT
1 ATGCGACCAATTTTTCTCCATCATGTCTCTATTACAAGCTTTTCATGTAAATGAGATTAT
* * * *
389398 CTGCTGAACAAATTTTCTCCATCATGTCTCTATAACAAG-TTTT
1 ATGC-GACCAATTTTTCTCCATCATGTCTCTATTACAAGCTTTT
389441 ACAGTAACAT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 64 0.68
61 30 0.32
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (60 bp):
ATGCGACCAATTTTTCTCCATCATGTCTCTATTACAAGCTTTTCATGTAAATGAGATTAT
Found at i:393864 original size:18 final size:17
Alignment explanation
Indices: 393827--393860 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
393817 ACAAATGTCT
393827 TTAAAATAATAACAAAA
1 TTAAAATAATAACAAAA
393844 TTAATAATAA-AACAAAA
1 TTAA-AATAATAACAAAA
393861 ATTATACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAATAATAACAAAA
Found at i:401702 original size:19 final size:19
Alignment explanation
Indices: 401678--401714 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
401668 GCAGCGATGC
401678 TATTGCTGCCATAAATCTT
1 TATTGCTGCCATAAATCTT
*
401697 TATTGCTGCGATAAATCT
1 TATTGCTGCCATAAATCT
401715 CTCCTGCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (19 bp):
TATTGCTGCCATAAATCTT
Done.