Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004676.1 Kokia drynarioides strain JFW-HI SEQ_118226, 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: 66340
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1421 original size:21 final size:20
Alignment explanation
Indices: 1374--1424 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1364 ATAAGCACGC
*
1374 TCAGATGCATCCACAATAAA
1 TCAGATGCATCCACAACAAA
* *
1394 GCTAGATGCATCCACACCAGAA
1 TC-AGATGCATCCACAACA-AA
1416 TCAGATGCA
1 TCAGATGCA
1425 GTCATAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (20 bp):
TCAGATGCATCCACAACAAA
Found at i:3212 original size:28 final size:27
Alignment explanation
Indices: 3181--3342 Score: 146
Period size: 28 Copynumber: 5.9 Consensus size: 27
3171 CGATACTCTG
*
3181 TTTATAGCTTGGGTAGAGCTTTGATCCA
1 TTTATAGCTCGGGTAGAGCTTTGAT-CA
* *
3209 TTTACAGTTCGGGTAGAGCTTTGATTCA
1 TTTATAGCTCGGGTAGAGCTTTGA-TCA
* *
3237 CTTATAGCTCGGGTATAGCTTTGATC-
1 TTTATAGCTCGGGTAGAGCTTTGATCA
** **
3263 TGTTGCAGCTCGGGTACTGCTTTGAATCA
1 T-TTATAGCTCGGGTAGAGCTTTG-ATCA
* * *
3292 TTTATAGCTCGGGTAGAGCTTTCACCTG
1 TTTATAGCTCGGGTAGAGCTTTGATC-A
* *
3320 TTTATAGCTCGAGTAGAGTTTTG
1 TTTATAGCTCGGGTAGAGCTTTG
3343 GTCTGCTTAC
Statistics
Matches: 107, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
27 22 0.21
28 83 0.78
29 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (27 bp):
TTTATAGCTCGGGTAGAGCTTTGATCA
Found at i:3301 original size:55 final size:56
Alignment explanation
Indices: 3181--3313 Score: 171
Period size: 55 Copynumber: 2.4 Consensus size: 56
3171 CGATACTCTG
* * * *
3181 TTTATAGCTTGGGTAGAGCTTTGATCCATTTACAGTTCGGGTAGAGCTTTGATTCA
1 TTTATAGCTCGGGTAGAGCTTTGATCCATTTACAGCTCGGGTACAGCTTTGAATCA
* * * *
3237 CTTATAGCTCGGGTATAGCTTTGAT-C-TGTTGCAGCTCGGGTACTGCTTTGAATCA
1 TTTATAGCTCGGGTAGAGCTTTGATCCAT-TTACAGCTCGGGTACAGCTTTGAATCA
3292 TTTATAGCTCGGGTAGAGCTTT
1 TTTATAGCTCGGGTAGAGCTTT
3314 CACCTGTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
54 1 0.02
55 43 0.65
56 22 0.33
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (56 bp):
TTTATAGCTCGGGTAGAGCTTTGATCCATTTACAGCTCGGGTACAGCTTTGAATCA
Found at i:3321 original size:55 final size:55
Alignment explanation
Indices: 3181--3330 Score: 167
Period size: 55 Copynumber: 2.7 Consensus size: 55
3171 CGATACTCTG
* * * *
3181 TTTATAGCTTGGGTAGAGCTTTGATCCAT-TTACAGTTCGGGTAGAGCTTTGATTCA
1 TTTATAGCTCGGGTAGAGCTTTGA-CC-TGTTACAGCTCGGGTACAGCTTTGAATCA
* * * * *
3237 CTTATAGCTCGGGTATAGCTTTGATCTGTTGCAGCTCGGGTACTGCTTTGAATCA
1 TTTATAGCTCGGGTAGAGCTTTGACCTGTTACAGCTCGGGTACAGCTTTGAATCA
* *
3292 TTTATAGCTCGGGTAGAGCTTTCACCTGTTTATAGCTCG
1 TTTATAGCTCGGGTAGAGCTTTGACCTG-TTACAGCTCG
3331 AGTAGAGTTT
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 1 0.01
55 47 0.61
56 29 0.38
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (55 bp):
TTTATAGCTCGGGTAGAGCTTTGACCTGTTACAGCTCGGGTACAGCTTTGAATCA
Found at i:10223 original size:12 final size:12
Alignment explanation
Indices: 10208--10250 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
10198 AAGGAACAAG
*
10208 AGAAGAAAAGAA
1 AGAAGAAAAGGA
10220 AGAAGAAAAGGA
1 AGAAGAAAAGGA
* *
10232 AGAGGAGAAGGA
1 AGAAGAAAAGGA
10244 AGAAGAA
1 AGAAGAA
10251 GAAAGTATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAGGA
Found at i:10673 original size:17 final size:17
Alignment explanation
Indices: 10647--10691 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
10637 GCGTGCATTT
10647 ATTTTAATTGTCAT-TGC
1 ATTTTAATTGTC-TCTGC
*
10664 ATTTTTATTGTCTCTGC
1 ATTTTAATTGTCTCTGC
*
10681 ATTTTATTTGT
1 ATTTTAATTGT
10692 TTTAGCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (17 bp):
ATTTTAATTGTCTCTGC
Found at i:14269 original size:28 final size:28
Alignment explanation
Indices: 14236--14338 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 28
14226 AATAGAGACA
* *
14236 ACCACAAAGGCTTTCCTTT-GAAAGGTTT
1 ACCACAAAGGCTTTCCTTTCCAAA-GATT
* *
14264 ACCACAAAGACTTACCTTTCCAAAGATT
1 ACCACAAAGGCTTTCCTTTCCAAAGATT
* * *
14292 AGCCACAAAGGC-TTCCTTTAACTAAGATA
1 A-CCACAAAGGCTTTCCTTT-CCAAAGATT
*
14321 ATCACAAAGGC-TTCCTTT
1 ACCACAAAGGCTTTCCTTT
14339 GAGAGGCTCC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 43 0.69
29 19 0.31
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (28 bp):
ACCACAAAGGCTTTCCTTTCCAAAGATT
Found at i:14758 original size:21 final size:21
Alignment explanation
Indices: 14733--14787 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
14723 TACCTTGTAA
*
14733 CTTCTACCTATACAAGTAAA-
1 CTTCTACCAATACAAGTAAAT
*
14753 CGTTCTACCAATGCAAGTAAAT
1 C-TTCTACCAATACAAGTAAAT
*
14775 CTTCTACCGATAC
1 CTTCTACCAATAC
14788 GTCAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (21 bp):
CTTCTACCAATACAAGTAAAT
Found at i:15336 original size:19 final size:19
Alignment explanation
Indices: 15314--15368 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
15304 ATGCTCTTAT
15314 GAGCCAGTATTGCTCAAAC
1 GAGCCAGTATTGCTCAAAC
* *
15333 GAGCCAATATT-CTTAAAC
1 GAGCCAGTATTGCTCAAAC
* *
15351 AAGCCAGT-GTGCTCAAAC
1 GAGCCAGTATTGCTCAAAC
15369 TTTCGCATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 1 0.03
18 18 0.62
19 10 0.34
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (19 bp):
GAGCCAGTATTGCTCAAAC
Found at i:16507 original size:55 final size:53
Alignment explanation
Indices: 16449--16623 Score: 154
Period size: 55 Copynumber: 3.2 Consensus size: 53
16439 AGATTAGAAT
* * *
16449 AAAGGCTTCCTTTAATTGAAATAGACACAAAGGCTTCCTTTGAGAGGTTTGCCAT
1 AAAGGCTTCCTTTAA-TGAAATAG-CACAAAGACTTCCTTTGAGAGGTTAGCCAC
* * ** *
16504 AAAGGCTAGCCTTTTAA-GAGATTAGCACAAAGACTTACCTTACAAGAGATTAGCCAC
1 AAAGGCT-TCC-TTTAATGA-AATAGCACAAAGACTT-CCTT-TGAGAGGTTAGCCAC
* ** *
16561 AAAGGCTTCCTTTAACTAAAATAGCCACAAATTCTTCCTTTGAGAGGTTCGCCAC
1 AAAGGCTTCCTTTAA-TGAAATAG-CACAAAGACTTCCTTTGAGAGGTTAGCCAC
16616 AAAGGCTT
1 AAAGGCTT
16624 TCGTATGAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 16
0.74 0.13 0.12
Matches are distributed among these distances:
55 43 0.45
56 20 0.21
57 32 0.34
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (53 bp):
AAAGGCTTCCTTTAATGAAATAGCACAAAGACTTCCTTTGAGAGGTTAGCCAC
Found at i:16535 original size:28 final size:28
Alignment explanation
Indices: 16499--16572 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
16489 TGAGAGGTTT
* **
16499 GCCATAAAGGCTAGCCTTTTAAGAGATTA
1 GCCACAAAGGCTA-CCTTACAAGAGATTA
*
16528 G-CACAAAGACTTACCTTACAAGAGATTA
1 GCCACAAAGGC-TACCTTACAAGAGATTA
*
16556 GCCACAAAGGCTTCCTT
1 GCCACAAAGGCTACCTT
16573 TAACTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
28 26 0.70
29 11 0.30
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (28 bp):
GCCACAAAGGCTACCTTACAAGAGATTA
Found at i:16620 original size:112 final size:110
Alignment explanation
Indices: 16422--16622 Score: 285
Period size: 112 Copynumber: 1.8 Consensus size: 110
16412 ACACCCCACA
* * * * *
16422 AAAGCTTACCTTTCCAGAGATTAGAATAAAGGCTTCCTTTAATTGAAATAGACACAAAGGCTTCC
1 AAAGCTTACCTTACAAGAGATTAGAACAAAGGCTTCCTTTAACTAAAATAGACACAAAGGCTTCC
* *
16487 TTTGAGAGGTTTGCCATAAAGGCTAGCCTTTTAAGAGATTAGCAC
66 TTTGAGAGGTTCGCCACAAAGGCTAGCCTTTTAAGAGATTAGCAC
* * **
16532 AAAGACTTACCTTACAAGAGATTAGCCACAAAGGCTTCCTTTAACTAAAATAGCCACAAATTCTT
1 AAAG-CTTACCTTACAAGAGATTAG-AACAAAGGCTTCCTTTAACTAAAATAGACACAAAGGCTT
16597 CCTTTGAGAGGTTCGCCACAAAGGCT
64 CCTTTGAGAGGTTCGCCACAAAGGCT
16623 TTCGTATGAA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
110 4 0.05
111 18 0.23
112 56 0.72
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (110 bp):
AAAGCTTACCTTACAAGAGATTAGAACAAAGGCTTCCTTTAACTAAAATAGACACAAAGGCTTCC
TTTGAGAGGTTCGCCACAAAGGCTAGCCTTTTAAGAGATTAGCAC
Found at i:19394 original size:19 final size:19
Alignment explanation
Indices: 19370--19438 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
19360 CCACTTTTCT
19370 ATTAAAATCTAACATGTCA
1 ATTAAAATCTAACATGTCA
* * *
19389 ATTAAAATCATACCACTTTTCT
1 ATTAAAATC-TA--ACATGTCA
19411 ATTAAAATCTAACATGTCA
1 ATTAAAATCTAACATGTCA
19430 ATTAAAATC
1 ATTAAAATC
19439 ATAAAATAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 23 0.56
20 2 0.05
21 2 0.05
22 14 0.34
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (19 bp):
ATTAAAATCTAACATGTCA
Found at i:19417 original size:22 final size:21
Alignment explanation
Indices: 19360--19421 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 21
19350 TTTTCATGGC
19360 CCACTTTTCTATTAAAATCTA
1 CCACTTTTCTATTAAAATCTA
* * *
19381 --ACATGTCAATTAAAATCATA
1 CCACTTTTCTATTAAAATC-TA
19401 CCACTTTTCTATTAAAATCTA
1 CCACTTTTCTATTAAAATCTA
19422 ACATGTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 14 0.44
20 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.39
Consensus pattern (21 bp):
CCACTTTTCTATTAAAATCTA
Found at i:19417 original size:41 final size:41
Alignment explanation
Indices: 19360--19441 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
19350 TTTTCATGGC
19360 CCACTTTTCTATTAAAATCTAACATGTCAATTAAAATCATA
1 CCACTTTTCTATTAAAATCTAACATGTCAATTAAAATCATA
19401 CCACTTTTCTATTAAAATCTAACATGTCAATTAAAATCATA
1 CCACTTTTCTATTAAAATCTAACATGTCAATTAAAATCATA
19442 AAATAAGCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (41 bp):
CCACTTTTCTATTAAAATCTAACATGTCAATTAAAATCATA
Found at i:31043 original size:8 final size:8
Alignment explanation
Indices: 31032--31073 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
31022 TAAATTTTTA
31032 TTTAAATT
1 TTTAAATT
31040 TTTAAATT
1 TTTAAATT
31048 TTTAAATTTT
1 TTTAAA--TT
*
31058 TTTAAAAT
1 TTTAAATT
31066 TTTAAATT
1 TTTAAATT
31074 AGTAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 22 0.73
10 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTAAATT
Found at i:31061 original size:18 final size:18
Alignment explanation
Indices: 31038--31073 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31028 TTTATTTAAA
*
31038 TTTTTAAATTTTTAAATT
1 TTTTTAAAATTTTAAATT
31056 TTTTTAAAATTTTAAATT
1 TTTTTAAAATTTTAAATT
31074 AGTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTAAAATTTTAAATT
Found at i:31068 original size:26 final size:28
Alignment explanation
Indices: 31021--31073 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
31011 TTTAAAATAG
*
31021 TTAAATTTTTATTTAAATTTTTAAATTT
1 TTAAATTTTTATTTAAAATTTTAAATTT
31049 TTAAA-TTTT-TTTAAAATTTTAAATT
1 TTAAATTTTTATTTAAAATTTTAAATT
31074 AGTAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.62
27 4 0.17
28 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTAAATTTTTATTTAAAATTTTAAATTT
Found at i:31079 original size:26 final size:28
Alignment explanation
Indices: 31011--31079 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 28
31001 GCCCTGACCC
* *
31011 TTTAAAATAGTTAAATTTTTATTTAAATT
1 TTTAAATTAG-TAAATTTTTATTTAAAAT
**
31040 TTTAAATTTTTAAA-TTTT-TTTAAAAT
1 TTTAAATTAGTAAATTTTTATTTAAAAT
31066 TTTAAATTAGTAAA
1 TTTAAATTAGTAAA
31080 AATAAAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 19 0.56
27 4 0.12
28 4 0.12
29 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
TTTAAATTAGTAAATTTTTATTTAAAAT
Found at i:34947 original size:17 final size:16
Alignment explanation
Indices: 34921--34956 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
34911 AAGTGATTTC
34921 ATTTAGTTTTATGTTTT
1 ATTTAGTTTTAT-TTTT
*
34938 ATTTATTTTTATTTTT
1 ATTTAGTTTTATTTTT
34954 ATT
1 ATT
34957 GCTAGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (16 bp):
ATTTAGTTTTATTTTT
Found at i:37188 original size:50 final size:50
Alignment explanation
Indices: 37075--37188 Score: 192
Period size: 50 Copynumber: 2.3 Consensus size: 50
37065 CAGATATTTG
**
37075 CAGATTTACTACCATATACAGATTTATATGGTCATGACACCAGAAAATTA
1 CAGATTTACTGTCATATACAGATTTATATGGTCATGACACCAGAAAATTA
*
37125 CAGATTTACTGTCATATACAGATTTATATGGTCATGCCACCAGAAAATTA
1 CAGATTTACTGTCATATACAGATTTATATGGTCATGACACCAGAAAATTA
*
37175 CAGATTTATTGTCA
1 CAGATTTACTGTCA
37189 GATATTCCCA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (50 bp):
CAGATTTACTGTCATATACAGATTTATATGGTCATGACACCAGAAAATTA
Found at i:41259 original size:14 final size:13
Alignment explanation
Indices: 41228--41266 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
41218 TTAAACTATT
41228 ATAATA-ATAAATA
1 ATAATATAT-AATA
41241 ATAATATATAATA
1 ATAATATATAATA
41254 AGTAATATATAAT
1 A-TAATATATAAT
41267 GTACTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (13 bp):
ATAATATATAATA
Found at i:41350 original size:9 final size:9
Alignment explanation
Indices: 41338--41363 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41328 TGAATGAGTG
41338 AGAAAATTT
1 AGAAAATTT
41347 AGAAAATTT
1 AGAAAATTT
41356 AGAAAATT
1 AGAAAATT
41364 AGTTGGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (9 bp):
AGAAAATTT
Found at i:44146 original size:20 final size:21
Alignment explanation
Indices: 44098--44166 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
44088 CAAAACATTT
44098 TGTTTGTAACTCTCCTCATAA
1 TGTTTGTAACTCTCCTCATAA
44119 TGTTTGTAACTCTCCTCATAA
1 TGTTTGTAACTCTCCTCATAA
* * *
44140 T-TTTGTAACTATCATCATTA
1 TGTTTGTAACTCTCCTCATAA
44160 TGTTTGT
1 TGTTTGT
44167 TTTAAATTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (21 bp):
TGTTTGTAACTCTCCTCATAA
Found at i:44543 original size:19 final size:20
Alignment explanation
Indices: 44515--44565 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
44505 AGTATACTTG
*
44515 TTATTTATTTTTAAATT-TA
1 TTATTAATTTTTAAATTATA
44534 TTATTAA-TTTTAAATTATA
1 TTATTAATTTTTAAATTATA
* *
44553 TTTTTATTTTTTA
1 TTATTAATTTTTA
44566 TATACTGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.33
19 13 0.48
20 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTAATTTTTAAATTATA
Found at i:44561 original size:18 final size:18
Alignment explanation
Indices: 44515--44562 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
44505 AGTATACTTG
44515 TTATTTATTTTTAAATTTA
1 TTATTTA-TTTTAAATTTA
*
44534 TTATTAATTTTAAATTATA
1 TTATTTATTTTAAATT-TA
44553 TT-TTTATTTT
1 TTATTTATTTT
44563 TTATATACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATTTTAAATTTA
Found at i:50532 original size:86 final size:86
Alignment explanation
Indices: 50379--50553 Score: 314
Period size: 86 Copynumber: 2.0 Consensus size: 86
50369 GCGATGCTGC
*
50379 CAAATACCACTGGAATGAGCCATACCTATTCAAGGTATGCACCGACAATATCATTCGTCGCTATG
1 CAAATACCACTGGAATGAGCCATACCTATTCAAGGTATGCACCGACAATATCATTCATCGCTATG
*
50444 TACCTGAATAAGAAATGATGT
66 TACCTAAATAAGAAATGATGT
* *
50465 CAAATACCACTGGAATGAGCCATACCTATTCAAGGTATGCACCGACAATATCATTCATCGTTGTG
1 CAAATACCACTGGAATGAGCCATACCTATTCAAGGTATGCACCGACAATATCATTCATCGCTATG
50530 TACCTAAATAAGAAATGATGT
66 TACCTAAATAAGAAATGATGT
50551 CAA
1 CAA
50554 TCCTATGACA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (86 bp):
CAAATACCACTGGAATGAGCCATACCTATTCAAGGTATGCACCGACAATATCATTCATCGCTATG
TACCTAAATAAGAAATGATGT
Found at i:54634 original size:9 final size:9
Alignment explanation
Indices: 54598--54634 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
54588 TCAGTCAATT
54598 GAAAAAAAA
1 GAAAAAAAA
54607 TGAAAAAAAA
1 -GAAAAAAAA
*
54617 GAAAGAAAA
1 GAAAAAAAA
54626 GAAAAAAAA
1 GAAAAAAAA
54635 AGAAGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:58972 original size:21 final size:21
Alignment explanation
Indices: 58920--58973 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
58910 ACCTACAAAA
*
58920 CATTATGTTTGTAACTCTCCT
1 CATTATGTTTGTAACTCTCAT
*
58941 CA-TAAGTTTTGTAACTCTCAT
1 CATTATG-TTTGTAACTCTCAT
58962 CATTATGTTTGT
1 CATTATGTTTGT
58974 TTTAAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (21 bp):
CATTATGTTTGTAACTCTCAT
Found at i:62788 original size:23 final size:21
Alignment explanation
Indices: 62739--62790 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
62729 AAAGTATGTG
62739 ATATAGTATTATATAATGAAAT
1 ATATA-TATTATATAATGAAAT
*
62761 A-ATATATTTTATAAGTGTAAAT
1 ATATATATTATATAA-TG-AAAT
62783 ATATATAT
1 ATATATAT
62791 AACAATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.35
21 5 0.19
22 6 0.23
23 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (21 bp):
ATATATATTATATAATGAAAT
Done.