Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013040.1 Kokia drynarioides strain JFW-HI SEQ_128058, 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: 36922
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Warning! 191 characters in sequence are not A, C, G, or T
Found at i:1060 original size:20 final size:19
Alignment explanation
Indices: 1003--1074 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
993 TAGATCCGAT
1003 CAAAATATTTTAAAATTTAC
1 CAAAAT-TTTTAAAATTTAC
* ** *
1023 CAATATTTTTATTGATTTAT
1 CAAAATTTTTA-AAATTTAC
1043 CAAAATATTTTAAAATTTAC
1 CAAAAT-TTTTAAAATTTAC
1063 CAAAATTTTTAA
1 CAAAATTTTTAA
1075 GTTCATACGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 11 0.26
20 26 0.62
21 5 0.12
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (19 bp):
CAAAATTTTTAAAATTTAC
Found at i:1405 original size:20 final size:20
Alignment explanation
Indices: 1382--1434 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1372 TGGTAAACAA
1382 TTAGAAATATTAATATAA-CC
1 TTAGAAATATTAATA-AATCC
* *
1402 TTAGAAATTTTGATAAATCC
1 TTAGAAATATTAATAAATCC
*
1422 TTATAAATATTAA
1 TTAGAAATATTAA
1435 AATTTTGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (20 bp):
TTAGAAATATTAATAAATCC
Found at i:1457 original size:28 final size:27
Alignment explanation
Indices: 1406--1461 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
1396 ATAACCTTAG
1406 AAATTTTGATAAATCCTTATAAATATTA
1 AAATTTTGATAAATCCTTATAAAT-TTA
*
1434 AAATTTTGGTAAATCCTTGA-AAATTTA
1 AAATTTTGATAAATCCTT-ATAAATTTA
1461 A
1 A
1462 TAAATCCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 21 0.81
29 1 0.04
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (27 bp):
AAATTTTGATAAATCCTTATAAATTTA
Found at i:1484 original size:19 final size:20
Alignment explanation
Indices: 1433--1511 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 20
1423 TATAAATATT
*
1433 AAAATTTTGGTAAATCCTTG
1 AAAATTTTGGTAAATCCTTA
**
1453 AAAA-TTTAATAAATCC-TA
1 AAAATTTTGGTAAATCCTTA
*
1471 AAAATTTTGGTAAA-CATTTA
1 AAAATTTTGGTAAATC-CTTA
*
1491 AGAAATATTGGTAAATCCTTA
1 A-AAATTTTGGTAAATCCTTA
1512 CATTATTGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
18 6 0.13
19 17 0.37
20 7 0.15
21 15 0.33
22 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (20 bp):
AAAATTTTGGTAAATCCTTA
Found at i:2014 original size:30 final size:31
Alignment explanation
Indices: 1971--2036 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
1961 CAACTTAACA
* * *
1971 AACAAATATCTCTAAAATAATAACAAAA-TT
1 AACAAAAACCTCTAAAATAATAAAAAAATTT
2001 AACAAAAACCTCTAAAATAATAAAAAAATTT
1 AACAAAAACCTCTAAAATAATAAAAAAATTT
2032 AACAA
1 AACAA
2037 CAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (31 bp):
AACAAAAACCTCTAAAATAATAAAAAAATTT
Found at i:2039 original size:34 final size:33
Alignment explanation
Indices: 1965--2041 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 33
1955 TAGATGCAAC
* * *
1965 TTAACAAACAAATATCTCTAAAATAATAACAAAA
1 TTAAC-AACAAAAACCTCTAAAATAATAAAAAAA
1999 TT---AACAAAAACCTCTAAAATAATAAAAAAA
1 TTAACAACAAAAACCTCTAAAATAATAAAAAAA
2029 TTTAACAACAAAA
1 -TTAACAACAAAA
2042 TAAGTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
30 25 0.69
31 2 0.06
34 9 0.25
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (33 bp):
TTAACAACAAAAACCTCTAAAATAATAAAAAAA
Found at i:3109 original size:20 final size:20
Alignment explanation
Indices: 3000--3111 Score: 61
Period size: 20 Copynumber: 5.5 Consensus size: 20
2990 AAATCCTTGA
*
3000 AAATTTTGGTATAAC-CTTA-
1 AAATTTTGGTA-AACTTTTAG
*
3019 AAATTTTGGTAAA-TACATTAG
1 AAATTTTGGTAAACT--TTTAG
* *
3040 AAATTATGGTAAATTTTTAG
1 AAATTTTGGTAAACTTTTAG
** * *
3060 TTATTTTGGTATGACCTTATA-
1 AAATTTTGGTA--AACTTTTAG
**
3081 ATTTTTTGGTAAACTTTTAG
1 AAATTTTGGTAAACTTTTAG
3101 AAATTTTGGTA
1 AAATTTTGGTA
3112 TGTCAAAATA
Statistics
Matches: 70, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.03
19 17 0.24
20 24 0.34
21 21 0.30
22 6 0.09
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (20 bp):
AAATTTTGGTAAACTTTTAG
Found at i:3174 original size:20 final size:20
Alignment explanation
Indices: 3151--3215 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
3141 GGTACTAAGG
3151 AAATCTTTAGAAATATTGGT
1 AAATCTTTAGAAATATTGGT
** *
3171 AAATCTTTAGAAGCATTGGA
1 AAATCTTTAGAAATATTGGT
3191 AAAT-TCTTAGAAATATTGGT
1 AAATCT-TTAGAAATATTGGT
3211 AAATC
1 AAATC
3216 GTTGGATGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (20 bp):
AAATCTTTAGAAATATTGGT
Found at i:3267 original size:20 final size:19
Alignment explanation
Indices: 3151--3273 Score: 66
Period size: 20 Copynumber: 6.1 Consensus size: 19
3141 GGTACTAAGG
*
3151 AAATCTTTAGAAATATTGGT
1 AAATC-TTAGAAATTTTGGT
*** *
3171 AAATCTTTAGAAGCATTGGA
1 AAATC-TTAGAAATTTTGGT
*
3191 AAATTCTTAGAAATATTGGT
1 AAA-TCTTAGAAATTTTGGT
* **
3211 AAATCGTTGGATGTTTTTGGT
1 AAATC-TTAGA-AATTTTGGT
* *
3232 ATAACCTTAAAAATTTTGGT
1 A-AATCTTAGAAATTTTGGT
* *
3252 AAATTCTTAGATATTTTTGT
1 AAA-TCTTAGAAATTTTGGT
3272 AA
1 AA
3274 GGAATAATAT
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.05
20 60 0.76
21 12 0.15
22 3 0.04
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (19 bp):
AAATCTTAGAAATTTTGGT
Found at i:5472 original size:14 final size:14
Alignment explanation
Indices: 5437--5473 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5427 ATTAATTTTA
5437 TATTGAATTTAAAT
1 TATTGAATTTAAAT
**
5451 TAAAGAATTTAAAT
1 TATTGAATTTAAAT
5465 TATTGAATT
1 TATTGAATT
5474 AAACGTTAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (14 bp):
TATTGAATTTAAAT
Found at i:7133 original size:24 final size:24
Alignment explanation
Indices: 7101--7160 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
7091 ACTTTGTCTA
7101 GGCTTGTAAGAGCTAACCTATCTG
1 GGCTTGTAAGAGCTAACCTATCTG
*
7125 GGCTTGTAAGGGCTAACCTATCTG
1 GGCTTGTAAGAGCTAACCTATCTG
*
7149 GGCTCGTAAGAG
1 GGCTTGTAAGAG
7161 TTAATTTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (24 bp):
GGCTTGTAAGAGCTAACCTATCTG
Found at i:24391 original size:24 final size:24
Alignment explanation
Indices: 24355--24417 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
24345 CAAAAGGAGA
*
24355 TGGTGGAGA-AGGAGTTGTTGCGGT
1 TGGTGGA-ACAGGAGTTGTTGCGGC
*
24379 TGGTGGAACAGGAAG-TGTTGGGGC
1 TGGTGGAACAGG-AGTTGTTGCGGC
* *
24403 TGGTAGAGCAGGAGT
1 TGGTGGAACAGGAGT
24418 CGGTGAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 3 0.09
24 27 0.84
25 2 0.06
ACGTcount: A:0.21, C:0.06, G:0.49, T:0.24
Consensus pattern (24 bp):
TGGTGGAACAGGAGTTGTTGCGGC
Found at i:27184 original size:21 final size:23
Alignment explanation
Indices: 27160--27222 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
27150 AGTAAACAAC
*
27160 ACATAACAAACATACA-ACTA-T
1 ACATAACAAACATACATAATAGT
*
27181 ACATATA-TAACATACATAATAGT
1 ACATA-ACAAACATACATAATAGT
27204 ACATAACATAACATACATA
1 ACATAACA-AACATACATA
27223 CAAATATACA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 13 0.38
22 5 0.15
23 6 0.18
24 10 0.29
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.24
Consensus pattern (23 bp):
ACATAACAAACATACATAATAGT
Found at i:27199 original size:9 final size:9
Alignment explanation
Indices: 27160--27533 Score: 144
Period size: 9 Copynumber: 40.9 Consensus size: 9
27150 AGTAAACAAC
*
27160 ACATAACAA
1 ACATAACAT
27169 ACAT-ACA-
1 ACATAACAT
27176 AC-TATACAT
1 ACATA-ACAT
*
27185 ATATAACAT
1 ACATAACAT
*
27194 ACATAATAGT
1 ACATAACA-T
27204 ACATAACAT
1 ACATAACAT
27213 AACAT-ACAT
1 -ACATAACAT
*
27222 ACA-AATAT
1 ACATAACAT
*
27230 ACA-AATAT
1 ACATAACAT
27238 AACACT-A-A-
1 -ACA-TAACAT
27246 ACATAACAT
1 ACATAACAT
*
27255 ACATAATAT
1 ACATAACAT
*
27264 ACGTAACAT
1 ACATAACAT
27273 ACATAACAT
1 ACATAACAT
*
27282 AACAGT-ACGTT
1 -ACA-TAAC-AT
*
27293 ACA-AATAT
1 ACATAACAT
27301 ACA-AACAT
1 ACATAACAT
*
27309 AACAGTAAACAAC
1 -ACA-T-AAC-AT
*
27322 ACATAACAA
1 ACATAACAT
27331 ACAT-ACA-
1 ACATAACAT
*
27338 A-TTATACAT
1 ACATA-ACAT
*
27347 ACATAATAT
1 ACATAACAT
27356 ACATAACAGT
1 ACATAACA-T
27366 ACATAACAT
1 ACATAACAT
27375 ACAT-ACA-
1 ACATAACAT
*
27382 A-ATATACAA
1 ACATA-ACAT
27391 ACATAACAGT
1 ACATAACA-T
27401 AAACATAACAT
1 --ACATAACAT
*
27412 ACATAATAT
1 ACATAACAT
*
27421 ACGTAACAGTAT
1 ACATAAC---AT
27433 GGACCATAACAT
1 --A-CATAACAT
27445 ACAT-ACAT
1 ACATAACAT
27453 AACATAACAGT
1 -ACATAACA-T
27464 ACATAACAT
1 ACATAACAT
*
27473 ACAAAACA-
1 ACATAACAT
*
27481 ATA-AACAT
1 ACATAACAT
27489 AACAT-ACAT
1 -ACATAACAT
*
27498 ACATAATAGT
1 ACATAACA-T
* *
27508 ACATGACAA
1 ACATAACAT
*
27517 ACATAATAT
1 ACATAACAT
27526 ACATAACA
1 ACATAACA
27534 ATTTAAAAAC
Statistics
Matches: 282, Mismatches: 35, Indels: 96
0.68 0.08 0.23
Matches are distributed among these distances:
6 5 0.02
7 12 0.04
8 51 0.18
9 125 0.44
10 59 0.21
11 5 0.02
12 18 0.06
13 1 0.00
14 1 0.00
15 5 0.02
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.22
Consensus pattern (9 bp):
ACATAACAT
Found at i:27199 original size:51 final size:49
Alignment explanation
Indices: 27143--27260 Score: 132
Period size: 49 Copynumber: 2.3 Consensus size: 49
27133 AGTCATACAA
* *
27143 ACATAACAGTAAACA-ACACATAACAAACATACAACTATACATATATAACAT
1 ACATAACAGT--ACATA-ACATAACAAACATACAAATATACAAATATAACAT
* *
27194 ACATAATAGTACATAACATAACATACATACAAATATACAAATATAACACT
1 ACATAACAGTACATAACATAACAAACATACAAATATACAAATATAACA-T
27244 AAACATAACA-TACATAA
1 --ACATAACAGTACATAA
27261 TATACGTAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
49 33 0.57
50 2 0.03
51 16 0.28
52 7 0.12
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.21
Consensus pattern (49 bp):
ACATAACAGTACATAACATAACAAACATACAAATATACAAATATAACAT
Found at i:27214 original size:5 final size:5
Alignment explanation
Indices: 27187--27533 Score: 106
Period size: 5 Copynumber: 70.2 Consensus size: 5
27177 CTATACATAT
* *
27187 ATAAC AT-AC ATAAT AGT-AC ATAAC ATAAC AT-AC ATACAA ATATAC
1 ATAAC ATAAC ATAAC A-TAAC ATAAC ATAAC ATAAC ATA-AC ATA-AC
* * *
27232 A-AAT ATAAC ACTAAAC ATAAC AT-AC ATAAT AT-AC GTAAC AT-AC ATAAC
1 ATAAC ATAAC A-T-AAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * *
27280 ATAAC AGT-AC GTTAC A-AAT AT-AC A-AAC ATAAC AGTAAAC A-ACAC
1 ATAAC A-TAAC ATAAC ATAAC ATAAC ATAAC ATAAC A-T-AAC ATA-AC
*
27324 ATAAC A-AAC AT-AC AATTATAC AT-AC ATAAT AT-AC ATAAC AGT-AC
1 ATAAC ATAAC ATAAC -A-TA-AC ATAAC ATAAC ATAAC ATAAC A-TAAC
*
27368 ATAAC AT-AC ATACAA ATATAC A-AAC ATAAC AGTAAAC ATAAC AT-AC
1 ATAAC ATAAC ATA-AC ATA-AC ATAAC ATAAC A-T-AAC ATAAC ATAAC
* *
27414 ATAAT AT-AC GTAAC AGTATGGACC ATAAC AT-AC AT-AC ATAAC ATAAC
1 ATAAC ATAAC ATAAC A-TA---A-C ATAAC ATAAC ATAAC ATAAC ATAAC
* *
27461 AGT-AC ATAAC AT-AC AAAAC AATAAAC ATAAC AT-AC AT-AC ATAAT
1 A-TAAC ATAAC ATAAC ATAAC -AT-AAC ATAAC ATAAC ATAAC ATAAC
* *
27505 AGT-AC ATGAC A-AAC ATAAT AT-AC ATAAC A
1 A-TAAC ATAAC ATAAC ATAAC ATAAC ATAAC A
27534 ATTTAAAAAC
Statistics
Matches: 258, Mismatches: 32, Indels: 104
0.65 0.08 0.26
Matches are distributed among these distances:
4 84 0.33
5 120 0.47
6 31 0.12
7 16 0.06
8 2 0.01
9 3 0.01
10 2 0.01
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.22
Consensus pattern (5 bp):
ATAAC
Found at i:27326 original size:44 final size:42
Alignment explanation
Indices: 27278--27405 Score: 141
Period size: 44 Copynumber: 3.0 Consensus size: 42
27268 AACATACATA
*
27278 ACATAACAGTACGTTACAAATATACAAACATAACAGTAAACAAC
1 ACATAACA-TAC-ATACAAATATACAAACATAACAGTAAACAAC
* * * * **
27322 ACATAACAAACATACAATTATACATACATAATA-TACATAACAGT
1 ACATAACATACATACAAATATACAAACATAACAGT--A-AACAAC
27366 ACATAACATACATACAAATATACAAACATAACAGTAAACA
1 ACATAACATACATACAAATATACAAACATAACAGTAAACA
27406 TAACATACAT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 22 0.32
43 4 0.06
44 41 0.59
45 1 0.01
ACGTcount: A:0.56, C:0.20, G:0.04, T:0.20
Consensus pattern (42 bp):
ACATAACATACATACAAATATACAAACATAACAGTAAACAAC
Found at i:27361 original size:162 final size:157
Alignment explanation
Indices: 27137--27428 Score: 485
Period size: 162 Copynumber: 1.8 Consensus size: 157
27127 ATAAACAGTC
* *
27137 ATACAAACATAACAGTAAACAACACATAACAAACATACAACTATACATATATAACATACATAATA
1 ATACAAACATAACAGTAAACAACACATAACAAACATACAACTATACATACATAACATACATAACA
*
27202 GTACATAACATAACATACATACAAATATACAAATATAACACTAAACATAACATACATAATATACG
66 G----T-ACATAACATACATACAAATATACAAACATAACACTAAACATAACATACATAATATACG
27267 TAACATACATAACATAACAGTACGTTACAAAT
126 TAACATACATAACATAACAGTACGTTACAAAT
* *
27299 ATACAAACATAACAGTAAACAACACATAACAAACATACAATTATACATACATAATATACATAACA
1 ATACAAACATAACAGTAAACAACACATAACAAACATACAACTATACATACATAACATACATAACA
*
27364 GTACATAACATACATACAAATATACAAACATAACAGTAAACATAACATACATAATATACGTAACA
66 GTACATAACATACATACAAATATACAAACATAACACTAAACATAACATACATAATATACGTAACA
27429 GTATGGACCA
Statistics
Matches: 124, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
157 61 0.49
158 1 0.01
162 62 0.50
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.22
Consensus pattern (157 bp):
ATACAAACATAACAGTAAACAACACATAACAAACATACAACTATACATACATAACATACATAACA
GTACATAACATACATACAAATATACAAACATAACACTAAACATAACATACATAATATACGTAACA
TACATAACATAACAGTACGTTACAAAT
Found at i:27671 original size:30 final size:30
Alignment explanation
Indices: 27637--27696 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
27627 CCCTGTAACT
27637 CACGAATGCCAAC-AAAAAAAAAAAAGTTA
1 CACGAATGCCAACAAAAAAAAAAAAAGTTA
27666 NCACGAATGCCAACAAAAAAAAAAAAAGTTA
1 -CACGAATGCCAACAAAAAAAAAAAAAGTTA
27697 GATATAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.10
Consensus pattern (30 bp):
CACGAATGCCAACAAAAAAAAAAAAAGTTA
Found at i:27733 original size:27 final size:28
Alignment explanation
Indices: 27684--27743 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
27674 GCCAACAAAA
*
27684 AAAAAAAAAGTTAGATATAATACGAATT
1 AAAAAAAAAGTTAGATATAATACGAAAT
*
27712 AAAAAAAAAGTTAGTTAT-ATACGAAAT
1 AAAAAAAAAGTTAGATATAATACGAAAT
27739 AAAAA
1 AAAAA
27744 TTGGAAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.23
Consensus pattern (28 bp):
AAAAAAAAAGTTAGATATAATACGAAAT
Found at i:27915 original size:29 final size:29
Alignment explanation
Indices: 27883--27938 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
27873 ATCTTAATTC
*
27883 GATGATGAAAAATAACCCAGAAAAATAAA
1 GATGATGAAAAATAACCCAAAAAAATAAA
*
27912 GATGATGAAAAATAATCCAAAAAAATA
1 GATGATGAAAAATAACCCAAAAAAATA
27939 GAGTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.16
Consensus pattern (29 bp):
GATGATGAAAAATAACCCAAAAAAATAAA
Found at i:29995 original size:25 final size:25
Alignment explanation
Indices: 29966--30015 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
29956 AAGTTACAGC
29966 AATAGAAATTGAAGAAGTTCAGAAG
1 AATAGAAATTGAAGAAGTTCAGAAG
*
29991 AATAGAAATTGAAGAAGTTGAGAAG
1 AATAGAAATTGAAGAAGTTCAGAAG
30016 GTATAAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.20
Consensus pattern (25 bp):
AATAGAAATTGAAGAAGTTCAGAAG
Found at i:33376 original size:24 final size:24
Alignment explanation
Indices: 33338--33383 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
33328 CACCTTCAAA
33338 TGTCACACGGCCATGTGACAGCCCG
1 TGTCACACGGCCATGTG-CAGCCCG
33363 TGTCACA-GGCCATGTGCAGCC
1 TGTCACACGGCCATGTGCAGCC
33384 TAATTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (24 bp):
TGTCACACGGCCATGTGCAGCCCG
Done.