Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011647.1 Kokia drynarioides strain JFW-HI SEQ_126639, 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: 417821
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 115 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:284428 original size:12 final size:12
Alignment explanation
Indices: 284413--284451 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
284403 TAAATTTTTA
284413 TTTTTATTTTGG
1 TTTTTATTTTGG
284425 TTTTTATTTT-G
1 TTTTTATTTTGG
*
284436 TTTTT-TGTTGG
1 TTTTTATTTTGG
284447 TTTTT
1 TTTTT
284452 TTATCGGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 3 0.12
11 12 0.48
12 10 0.40
ACGTcount: A:0.05, C:0.00, G:0.15, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTGG
Found at i:290360 original size:14 final size:13
Alignment explanation
Indices: 290333--290357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290323 ACTTGTAACG
290333 AAAAATTAATTTA
1 AAAAATTAATTTA
290346 AAAAATTAATTT
1 AAAAATTAATTT
290358 TAAGGAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATTAATTTA
Found at i:294764 original size:21 final size:23
Alignment explanation
Indices: 294724--294772 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
294714 TAATTTTATT
*
294724 ATTATTAATATTTTAACAATTTA
1 ATTATTAATATTTTAACAATGTA
*
294747 ATTATTAA-A-TTTATCAATGTA
1 ATTATTAATATTTTAACAATGTA
294768 ATTAT
1 ATTAT
294773 AATTATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
22 1 0.04
23 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTATTAATATTTTAACAATGTA
Found at i:298184 original size:21 final size:21
Alignment explanation
Indices: 298158--298199 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
298148 TTTTCCTCAA
298158 AGCTTATTTTTTTCCAATTCT
1 AGCTTATTTTTTTCCAATTCT
298179 AGCTTATTTTTTTCCAATTCT
1 AGCTTATTTTTTTCCAATTCT
298200 GTTTGGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.57
Consensus pattern (21 bp):
AGCTTATTTTTTTCCAATTCT
Found at i:307967 original size:19 final size:18
Alignment explanation
Indices: 307945--308009 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
307935 AAATTTTGAA
307945 AATTTTTATAAATATTTTG
1 AATTTTTA-AAATATTTTG
**
307964 AATTTCAAAAATTATTTTG
1 AATTTTTAAAA-TATTTTG
* *
307983 AAAATTTGAAAATAATTTTG
1 -AATTTTTAAAAT-ATTTTG
308003 AATTTTT
1 AATTTTT
308010 TTATAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 3 0.08
19 19 0.53
20 14 0.39
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (18 bp):
AATTTTTAAAATATTTTG
Found at i:308000 original size:20 final size:20
Alignment explanation
Indices: 307936--308004 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
307926 AAAATATATA
*
307936 AATTTTGAAAATTTTTATAAAT
1 AATTTTGAAAA--TTTAAAAAT
307958 -ATTTTG--AATTTCAAAAAT
1 AATTTTGAAAATTT-AAAAAT
* *
307976 TATTTTGAAAATTTGAAAAT
1 AATTTTGAAAATTTAAAAAT
307996 AATTTTGAA
1 AATTTTGAA
308005 TTTTTTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.08
18 5 0.12
19 8 0.20
20 13 0.32
21 11 0.28
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (20 bp):
AATTTTGAAAATTTAAAAAT
Found at i:312781 original size:21 final size:23
Alignment explanation
Indices: 312756--312798 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
312746 AAAATTGATT
312756 TCACC-AAA-ATTTGAAAAAGAC
1 TCACCAAAATATTTGAAAAAGAC
312777 TCACCAAAATATTTGAAAAAGA
1 TCACCAAAATATTTGAAAAAGA
312799 TTTATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.21
Consensus pattern (23 bp):
TCACCAAAATATTTGAAAAAGAC
Found at i:314775 original size:19 final size:18
Alignment explanation
Indices: 314747--314789 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
314737 AATGGAATGT
*
314747 AAAAATTAAATTAAAAAC
1 AAAAATTAAAATAAAAAC
*
314765 AAAATATTAAAATAAAAAT
1 AAAA-ATTAAAATAAAAAC
314784 AAAAAT
1 AAAAAT
314790 GACTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATTAAAATAAAAAC
Found at i:318244 original size:40 final size:40
Alignment explanation
Indices: 318195--318282 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
318185 AAATTAATCG
* * * *
318195 AACCGAAATTTTTTGGTTAATTTGGTTGATTAACTGAACT
1 AACCAAAATTTTTTGGTTAATTCGATCGATTAACTGAACT
*
318235 AACCAAAATTTTTTGGTTAATTCGATCGATTAACTGAATT
1 AACCAAAATTTTTTGGTTAATTCGATCGATTAACTGAACT
*
318275 AACAAAAA
1 AACCAAAA
318283 ATTATATGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (40 bp):
AACCAAAATTTTTTGGTTAATTCGATCGATTAACTGAACT
Found at i:318324 original size:9 final size:9
Alignment explanation
Indices: 318310--318361 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
318300 TTTGGTATAA
*
318310 AAATTATCC
1 AAATTAACC
318319 AAATTAACC
1 AAATTAACC
* *
318328 GAATTACCC
1 AAATTAACC
*
318337 AAATTACCC
1 AAATTAACC
*
318346 GAATTAACC
1 AAATTAACC
*
318355 GAATTAA
1 AAATTAA
318362 AGTATTGGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (9 bp):
AAATTAACC
Found at i:318332 original size:18 final size:18
Alignment explanation
Indices: 318311--318361 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
318301 TTGGTATAAA
*
318311 AATTATCCAAATTAACCG
1 AATTAACCAAATTAACCG
* *
318329 AATTACCCAAATTACCCG
1 AATTAACCAAATTAACCG
*
318347 AATTAACCGAATTAA
1 AATTAACCAAATTAA
318362 AGTATTGGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (18 bp):
AATTAACCAAATTAACCG
Found at i:325436 original size:22 final size:22
Alignment explanation
Indices: 325408--325462 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
325398 GATTGGGATT
*
325408 TTTTAGTTTTAATCTTTTAGAC
1 TTTTAGTTTTAACCTTTTAGAC
* *
325430 TTTTAGTTTTAGCCTTTTAGAT
1 TTTTAGTTTTAACCTTTTAGAC
*
325452 TTTTATTTTTA
1 TTTTAGTTTTA
325463 TTTATTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTAGTTTTAACCTTTTAGAC
Found at i:325439 original size:14 final size:15
Alignment explanation
Indices: 325422--325454 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
325412 AGTTTTAATC
325422 TTTTAGACTTTTAG-
1 TTTTAGACTTTTAGA
*
325436 TTTTAGCCTTTTAGA
1 TTTTAGACTTTTAGA
325451 TTTT
1 TTTT
325455 TATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTTAGACTTTTAGA
Found at i:325579 original size:15 final size:15
Alignment explanation
Indices: 325559--325588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
325549 GGTAGTAGGC
325559 TAATATTATATATTA
1 TAATATTATATATTA
*
325574 TAATATTATTTATTA
1 TAATATTATATATTA
325589 ATTTGGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATTATATATTA
Found at i:332187 original size:17 final size:18
Alignment explanation
Indices: 332167--332203 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
332157 ACAACAATGC
332167 AAATGCTAAA-AC-AAATA
1 AAATGC-AAAGACAAAATA
332184 AAATGCAAAGACAAAATA
1 AAATGCAAAGACAAAATA
332202 AA
1 AA
332204 TGTAATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 8 0.44
18 7 0.39
ACGTcount: A:0.68, C:0.11, G:0.08, T:0.14
Consensus pattern (18 bp):
AAATGCAAAGACAAAATA
Found at i:347705 original size:35 final size:35
Alignment explanation
Indices: 347666--347733 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
347656 TTGTTAACCA
347666 TAAATCCCTAAAATCTCAATTATGTTA-TTATTTTT
1 TAAATCCCTAAAATCTCAATTAT-TTATTTATTTTT
* * *
347701 TAAATCCTTAAAATCTTATTTATTTATTTATTT
1 TAAATCCCTAAAATCTCAATTATTTATTTATTT
347734 CATTTGTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 3 0.10
35 26 0.90
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (35 bp):
TAAATCCCTAAAATCTCAATTATTTATTTATTTTT
Found at i:348949 original size:23 final size:24
Alignment explanation
Indices: 348923--348967 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
348913 GTAGAACAGA
348923 AATTAC-TTGAAGAGAA-AAAAGAT
1 AATTACGTTGAAGA-AATAAAAGAT
*
348946 AATTTCGTTGAAGAAATAAAAG
1 AATTACGTTGAAGAAATAAAAG
348968 TGGGATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.24
Consensus pattern (24 bp):
AATTACGTTGAAGAAATAAAAGAT
Found at i:356478 original size:16 final size:17
Alignment explanation
Indices: 356444--356482 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
356434 GATTTTGAGG
*
356444 AAGAAGCAGGGGAATTA
1 AAGAAGCAGGGGAAGTA
*
356461 AAGAAGC-GTGGAAGTA
1 AAGAAGCAGGGGAAGTA
356477 AAGAAG
1 AAGAAG
356483 TGTTGGTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.49, C:0.05, G:0.36, T:0.10
Consensus pattern (17 bp):
AAGAAGCAGGGGAAGTA
Found at i:359538 original size:28 final size:27
Alignment explanation
Indices: 359477--359537 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
359467 AAAATATATA
359477 TTTTTCCATTTTACTTTTCTTTACTTC
1 TTTTTCCATTTTACTTTTCTTTACTTC
*
359504 TTATTTCC-TTTTCACTTTTCATTTTATTTC
1 TT-TTTCCATTTT-ACTTTTC--TTTACTTC
359534 TTTT
1 TTTT
359538 CTGTTTGGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 6 0.21
28 12 0.41
29 2 0.07
30 9 0.31
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTCCATTTTACTTTTCTTTACTTC
Found at i:361248 original size:23 final size:23
Alignment explanation
Indices: 361222--361271 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
361212 TGGCTTTTGA
361222 TTTTTTAAGGT-TAAAGTTTAAGG
1 TTTTTT-AGGTATAAAGTTTAAGG
* *
361245 TTTTTTGGGTATAAAGTTTAGGG
1 TTTTTTAGGTATAAAGTTTAAGG
361268 TTTT
1 TTTT
361272 CGATTGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (23 bp):
TTTTTTAGGTATAAAGTTTAAGG
Found at i:364085 original size:42 final size:42
Alignment explanation
Indices: 364037--364162 Score: 128
Period size: 43 Copynumber: 3.0 Consensus size: 42
364027 GAGTCATAAA
* * *
364037 TCTTCCTTTAAACGTAATCTTATGCTCA-TCCCGAGTCACGAG
1 TCTTCCTTTAAACATAACCTCATGCT-ATTCCCGAGTCACGAG
* **
364079 TTTTCCTTTAAAACATAACCTCATGCTATTTTCGAGTCACGAG
1 TCTTCCTTT-AAACATAACCTCATGCTATTCCCGAGTCACGAG
* * * *
364122 TCTTCCTTTAAAACATAACATCATGCTCTTTCTGAGTCACG
1 TCTTCCTTT-AAACATAACCTCATGCTATTCCCGAGTCACG
364163 GATGTTCCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
42 9 0.13
43 62 0.87
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (42 bp):
TCTTCCTTTAAACATAACCTCATGCTATTCCCGAGTCACGAG
Found at i:364182 original size:43 final size:43
Alignment explanation
Indices: 364068--364162 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
364058 ATGCTCATCC
* *
364068 CGAGTCACGAGTTTTCCTTTAAAACATAACCTCATGCTATTTT
1 CGAGTCACGAGTCTTCCTTTAAAACATAACATCATGCTATTTT
*
364111 CGAGTCACGAGTCTTCCTTTAAAACATAACATCATGCT-CTTT
1 CGAGTCACGAGTCTTCCTTTAAAACATAACATCATGCTATTTT
364153 CTGAGTCACG
1 C-GAGTCACG
364163 GATGTTCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (43 bp):
CGAGTCACGAGTCTTCCTTTAAAACATAACATCATGCTATTTT
Found at i:368206 original size:16 final size:16
Alignment explanation
Indices: 368179--368237 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
368169 AATCAAAGAC
*
368179 AATAATAACAATAAAA
1 AATAATTACAATAAAA
*
368195 AATAATTGCAATAATGATA
1 AATAATTACAATAA--A-A
* *
368214 AAAAATTAAAATAAAA
1 AATAATTACAATAAAA
368230 AATAATTA
1 AATAATTA
368238 AGGGGTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 20 0.59
17 1 0.03
18 1 0.03
19 12 0.35
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (16 bp):
AATAATTACAATAAAA
Found at i:384115 original size:10 final size:10
Alignment explanation
Indices: 384100--384125 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
384090 GATTTTTCTT
384100 TTTGTCCCGC
1 TTTGTCCCGC
384110 TTTGTCCCGC
1 TTTGTCCCGC
384120 TTTGTC
1 TTTGTC
384126 TCCGACGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.35, G:0.19, T:0.46
Consensus pattern (10 bp):
TTTGTCCCGC
Found at i:385157 original size:19 final size:20
Alignment explanation
Indices: 385124--385161 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
385114 ATTTTTCGAG
385124 AGATTCATTTAAAAATTTTA
1 AGATTCATTTAAAAATTTTA
*
385144 AGATT-ATTTTAAAATTTT
1 AGATTCATTTAAAAATTTT
385162 TGAAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
AGATTCATTTAAAAATTTTA
Found at i:385581 original size:18 final size:18
Alignment explanation
Indices: 385533--385613 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 18
385523 ATAGAAAAAT
* *
385533 AATTCAAAATAATTTTCAA
1 AATTAAAAAT-ATTTTTAA
*
385552 AATTTTAAAATATTTTTAA
1 AA-TTAAAAATATTTTTAA
385571 AATTAAAAATATTTTTAAA
1 AATTAAAAATATTTTT-AA
385590 AATTACAAAACTTATATTTTAA
1 AATTA-AAAA--TAT-TTTTAA
385612 AA
1 AA
385614 AATTAAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
18 13 0.25
19 18 0.34
20 11 0.21
22 7 0.13
23 4 0.08
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTAAAAATATTTTTAA
Found at i:385630 original size:9 final size:8
Alignment explanation
Indices: 385608--385633 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
385598 AACTTATATT
385608 TTAAAAAA
1 TTAAAAAA
385616 TTAAAAAA
1 TTAAAAAA
385624 TTAAAAAA
1 TTAAAAAA
385632 TT
1 TT
385634 TCTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TTAAAAAA
Found at i:385640 original size:18 final size:17
Alignment explanation
Indices: 385533--385678 Score: 71
Period size: 16 Copynumber: 8.1 Consensus size: 17
385523 ATAGAAAAAT
385533 AATTCAAAATAATTTTCAAA
1 AATT-AAAA-AATTTT-AAA
* * *
385553 ATTTTAAAATATTTTTAA
1 A-ATTAAAAAATTTTAAA
385571 AATTAAAAATATTTTTAAA
1 AATTAAAAA-A-TTTTAAA
* * *
385590 AATTACAAAA-CTTATA
1 AATTAAAAAATTTTAAA
** *
385606 TTTTAAAAAA-TTAAAA
1 AATTAAAAAATTTTAAA
385622 AATTAAAAAATTTCTAAA
1 AATTAAAAAATTT-TAAA
*
385640 AATTATATTAAAAATTTAAA
1 AATTA-A--AAAATTTTAAA
**
385660 TTTTAAAAAATTTCTAAA
1 AATTAAAAAATTT-TAAA
385678 A
1 A
385679 TAATAATTTT
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
16 22 0.23
17 14 0.15
18 17 0.18
19 21 0.22
20 12 0.13
21 8 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTAAAAAATTTTAAA
Found at i:388119 original size:17 final size:17
Alignment explanation
Indices: 388097--388139 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
388087 TTAACGATAT
*
388097 TGTGTCGACGATTCATA
1 TGTGTCGACGATGCATA
**
388114 TGTGTCGGTGATGCATA
1 TGTGTCGACGATGCATA
*
388131 TGTCTCGAC
1 TGTGTCGAC
388140 TTACCATTAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (17 bp):
TGTGTCGACGATGCATA
Found at i:388459 original size:24 final size:24
Alignment explanation
Indices: 388408--388466 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
388398 TCAGGTTAAG
388408 AATA-AAAATTGTCAGTGCAAAAGC
1 AATATAAAA-TGTCAGTGCAAAAGC
** *
388432 AATATAAAATGTCAGTGCAACTGT
1 AATATAAAATGTCAGTGCAAAAGC
388456 AATATAAAATG
1 AATATAAAATG
388467 AATTGATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (24 bp):
AATATAAAATGTCAGTGCAAAAGC
Found at i:390005 original size:2 final size:2
Alignment explanation
Indices: 389998--390023 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
389988 TTGTATAATA
389998 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
390024 TCTTTTTATC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:398893 original size:24 final size:24
Alignment explanation
Indices: 398842--398900 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
398832 ACAGGTTAAG
398842 AATA-AAAATTGTCAGTGCAAAAGC
1 AATATAAAA-TGTCAGTGCAAAAGC
** *
398866 AATATAAAATGTCAGTGCAACTGT
1 AATATAAAATGTCAGTGCAAAAGC
398890 AATATAAAATG
1 AATATAAAATG
398901 AATTGATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (24 bp):
AATATAAAATGTCAGTGCAAAAGC
Found at i:399887 original size:17 final size:17
Alignment explanation
Indices: 399865--399901 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
399855 TTAACGATAT
399865 TGTGTCGACGATGCATA
1 TGTGTCGACGATGCATA
*
399882 TGTGTCGATGATGCATA
1 TGTGTCGACGATGCATA
399899 TGT
1 TGT
399902 CTAAACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (17 bp):
TGTGTCGACGATGCATA
Found at i:400234 original size:24 final size:24
Alignment explanation
Indices: 400207--400254 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
400197 ATAAAAATTT
400207 TCAGTGCAAAAGCAATATAAAATG
1 TCAGTGCAAAAGCAATATAAAATG
** *
400231 TCAGTGCAACTGTAATATAAAATG
1 TCAGTGCAAAAGCAATATAAAATG
400255 AATTGATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (24 bp):
TCAGTGCAAAAGCAATATAAAATG
Found at i:404272 original size:75 final size:75
Alignment explanation
Indices: 404100--404369 Score: 290
Period size: 75 Copynumber: 3.5 Consensus size: 75
404090 ATCAATTTTG
* * **
404100 TTGAACAACAGGAATAAATCTTGAAACAAAATTATTTAATTAATTCTTAATTGGAAACCAAAAAT
1 TTGAACGACAAGAATAAATCTTGAAACAAAATTATTTAATTAATTCTTGTTTGGAAA--AAAAA-
404165 AGAATAAATTCTA
63 AGAATAAATTCTA
* * * * * * *
404178 TTGAACGATAGGAATAAATCCTAAAATATAATTATTTAATTAATTATTGTTTGGAAAAAAAAAGA
1 TTGAACGACAAGAATAAATCTTGAAACAAAATTATTTAATTAATTCTTGTTTGGAAAAAAAAAGA
404243 ATAAATTCTA
66 ATAAATTCTA
* * **
404253 TTGAACGGCAAGAATAAATCTTGAAACAAAATTATTTAATTAATTCTTGTTTTGAAAAACAATCG
1 TTGAACGACAAGAATAAATCTTGAAACAAAATTATTTAATTAATTCTTGTTTGGAAAAA-AAAAG
* *
404318 AATAAATTTTG
65 AATAAATTCTA
* ** * *
404329 TTGAACGAC-AGAAATATATCCCGAAACAGAATTATTCAATT
1 TTGAACGACAAG-AATAAATCTTGAAACAAAATTATTTAATT
404370 TTATTTTTTA
Statistics
Matches: 162, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
75 65 0.40
76 49 0.30
78 48 0.30
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.33
Consensus pattern (75 bp):
TTGAACGACAAGAATAAATCTTGAAACAAAATTATTTAATTAATTCTTGTTTGGAAAAAAAAAGA
ATAAATTCTA
Found at i:411296 original size:51 final size:51
Alignment explanation
Indices: 411219--411509 Score: 368
Period size: 51 Copynumber: 5.6 Consensus size: 51
411209 AGCTATAAAC
*
411219 TAAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAAT
1 TAAA-GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGAT
* *
411271 TAAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGAT
1 TAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGAT
* *
411322 TAAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGTT
1 TAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGAT
** * * * *
411373 TAAAGGTTTGATGACTAAGTGTCATCATGAGTAAATGAATCCATGATGGAT
1 TAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGAT
* * * * * * *
411424 TAGAGGTCCGATGACTCAGAGTCATCGTGAGTATATGAATTCCTATACGAAA
1 TAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGAT
*
411476 CAAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 TAA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
411510 TTAAATGAAA
Statistics
Matches: 208, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
51 170 0.82
52 11 0.05
53 26 0.12
54 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (51 bp):
TAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGAT
Found at i:413980 original size:12 final size:11
Alignment explanation
Indices: 413958--413987 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
413948 TATTCACCAA
413958 AAAAATATTTT
1 AAAAATATTTT
413969 AAAAATATTTT
1 AAAAATATTTT
*
413980 TAAAATAT
1 AAAAATAT
413988 AGTTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AAAAATATTTT
Done.