Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003011.1 Kokia drynarioides strain JFW-HI SEQ_115519, 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: 423923
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 46 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:316498 original size:6 final size:6
Alignment explanation
Indices: 316487--316519 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
316477 ACATAAAAAG
316487 AAAGAA AAAG-A AAAGAA AAAGAGA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGA-A AAAGAA AAA
316520 AATAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:316501 original size:11 final size:11
Alignment explanation
Indices: 316481--316519 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
316471 TCAGTCACAT
316481 AAAAAG-AAAG
1 AAAAAGAAAAG
316491 AAAAAGAAAAG
1 AAAAAGAAAAG
316502 AAAAAGAGAAAAG
1 -AAAA-AGAAAAG
316515 AAAAA
1 AAAAA
316520 AATAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.23
11 5 0.19
12 8 0.31
13 7 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:316513 original size:13 final size:12
Alignment explanation
Indices: 316481--316520 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
316471 TCAGTCACAT
316481 AAAAAG-AAAG-
1 AAAAAGAAAAGA
316491 AAAAAGAAAAGA
1 AAAAAGAAAAGA
316503 AAAAGAGAAAAGA
1 AAAA-AGAAAAGA
316516 AAAAA
1 AAAAA
316521 ATAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.22
11 4 0.15
12 5 0.19
13 12 0.44
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:319279 original size:22 final size:22
Alignment explanation
Indices: 319253--319300 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
319243 TGATTCTATT
319253 AATATATGTAATAACTTTAGGC
1 AATATATGTAATAACTTTAGGC
319275 AATATATGTAATAACTTTAGGC
1 AATATATGTAATAACTTTAGGC
319297 AATA
1 AATA
319301 ACAAATTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (22 bp):
AATATATGTAATAACTTTAGGC
Found at i:320374 original size:56 final size:56
Alignment explanation
Indices: 320283--320393 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 56
320273 AGGTGTAAGG
* * *
320283 GACATATGGGCTGGGCACACGGGCGTGTGTCAGACCGTGTGTGCATACTATTTTGT
1 GACACATGGGCTAGGCACACGGGCGTGTGCCAGACCGTGTGTGCATACTATTTTGT
*
320339 GACACATGGGCTAGGTACACGGGCGTGTGCCAGACCGTGTGTGCATACTATTTTG
1 GACACATGGGCTAGGCACACGGGCGTGTGCCAGACCGTGTGTGCATACTATTTTG
320394 GAAATAGCGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (56 bp):
GACACATGGGCTAGGCACACGGGCGTGTGCCAGACCGTGTGTGCATACTATTTTGT
Found at i:320952 original size:40 final size:40
Alignment explanation
Indices: 320898--321006 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
320888 GAGAATATTT
* * *
320898 ACTAAACTGGCAGTGACACTGTAAACCCTACAAGATTACA
1 ACTAAACTGGCAGTGACACTGTAAACACTACAAAATAACA
* *
320938 ACTGAACTGACAGTGACACTGTAAACACTACAAAATAACA
1 ACTAAACTGGCAGTGACACTGTAAACACTACAAAATAACA
* * *
320978 ACTAAATTGGCAGTGAAATTGTAAACACT
1 ACTAAACTGGCAGTGACACTGTAAACACT
321007 GCAATGTGTC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (40 bp):
ACTAAACTGGCAGTGACACTGTAAACACTACAAAATAACA
Found at i:323897 original size:19 final size:19
Alignment explanation
Indices: 323861--323897 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
323851 CTAAGTATAA
* *
323861 TATTTTCGTTCAAGTACAG
1 TATTTTCGTCCAAATACAG
323880 TATTTTCGTCCAAATACA
1 TATTTTCGTCCAAATACA
323898 TTTGTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (19 bp):
TATTTTCGTCCAAATACAG
Found at i:330981 original size:21 final size:21
Alignment explanation
Indices: 330934--330987 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
330924 CCTTTGACAA
* *
330934 TTCTACCGATACAAGTAAGGG
1 TTCTACCGATACAACTAAGGC
** *
330955 AACTACCGATACAACTCAGGC
1 TTCTACCGATACAACTAAGGC
330976 TTCTACCGATAC
1 TTCTACCGATAC
330988 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (21 bp):
TTCTACCGATACAACTAAGGC
Found at i:331738 original size:53 final size:52
Alignment explanation
Indices: 331627--331809 Score: 253
Period size: 51 Copynumber: 3.5 Consensus size: 52
331617 TTCACATTTG
* *
331627 ATAACTCACGATGACACACAGTTATCAGACCTTTTAAT-TCGTAATAGGATTCAT
1 ATAACTCACGATGACACA-AGTCATTAGACC-TTTAATCT-GTAATAGGATTCAT
*
331681 ATAACTCACAATGACACATAGTCATTAGACCTTTAATCTGTAATAGGATTCAT
1 ATAACTCACGATGACACA-AGTCATTAGACCTTTAATCTGTAATAGGATTCAT
* * *
331734 ATAACTCATGATGACAC-AGTCATTGGACCTTTAATCTGTAACAGGATTCAT
1 ATAACTCACGATGACACAAGTCATTAGACCTTTAATCTGTAATAGGATTCAT
331785 ATAACTCACGATGACACAGAGTCAT
1 ATAACTCACGATGACACA-AGTCAT
331810 CGAACATTTT
Statistics
Matches: 117, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
51 48 0.41
53 41 0.35
54 28 0.24
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (52 bp):
ATAACTCACGATGACACAAGTCATTAGACCTTTAATCTGTAATAGGATTCAT
Found at i:333065 original size:19 final size:19
Alignment explanation
Indices: 333023--333066 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
333013 TTTGTTACAA
*
333023 AATAAATTAAATAAGATAT
1 AATAAATTAAAGAAGATAT
*
333042 AATAAATTAGAGAA-ATAT
1 AATAAATTAAAGAAGATAT
333060 ATATAAA
1 A-ATAAA
333067 ATCTTAGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
AATAAATTAAAGAAGATAT
Found at i:335248 original size:19 final size:19
Alignment explanation
Indices: 335197--335254 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
335187 ATGATCCAAC
*
335197 ATTGCTCTTACGAGCTAGT
1 ATTGCTCTTACGAGCCAGT
* *
335216 ATTACTC-AACGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
335234 ATTGCTCTTACGAGCCAGT
1 ATTGCTCTTACGAGCCAGT
335253 AT
1 AT
335255 GTTATTCCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (19 bp):
ATTGCTCTTACGAGCCAGT
Found at i:340550 original size:19 final size:19
Alignment explanation
Indices: 340526--340568 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
340516 AGGTTGGCGA
340526 GTTTGCATGGACTACTGTG
1 GTTTGCATGGACTACTGTG
340545 GTTTGCATGGACTACTGTG
1 GTTTGCATGGACTACTGTG
340564 GTTTG
1 GTTTG
340569 AATGCTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.40
Consensus pattern (19 bp):
GTTTGCATGGACTACTGTG
Found at i:340797 original size:22 final size:22
Alignment explanation
Indices: 340769--340812 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
340759 CATTTGGTCA
340769 ATGCAACACACCGACCACATTT
1 ATGCAACACACCGACCACATTT
340791 ATGCAACACACCGACCACATTT
1 ATGCAACACACCGACCACATTT
340813 CAAAGGTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.18
Consensus pattern (22 bp):
ATGCAACACACCGACCACATTT
Found at i:354759 original size:31 final size:31
Alignment explanation
Indices: 354724--354789 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
354714 GACCAATTTA
* * *
354724 TGGTATGCGTTCGGTGTGATGGTCAGTTATC
1 TGGTATGCGTTCAGAGTGATGGTCAATTATC
*
354755 TGGTATGCGTTTAGAGTGATGGTCAATTATC
1 TGGTATGCGTTCAGAGTGATGGTCAATTATC
354786 TGGT
1 TGGT
354790 TGTGTCATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.39
Consensus pattern (31 bp):
TGGTATGCGTTCAGAGTGATGGTCAATTATC
Found at i:360985 original size:47 final size:47
Alignment explanation
Indices: 360932--361043 Score: 122
Period size: 47 Copynumber: 2.4 Consensus size: 47
360922 GTTATTTTGT
*
360932 GTTTATTCGAATTTGATGTCG-ATATTGATTGTGATTTTTAATTTAGG
1 GTTTATTCGAATTTGAT-TCGAATATTGATTGTCATTTTTAATTTAGG
* * * *
360979 GTTTATTC-AATTTTGATTCGAATTTTGATTTTCATTTTTGATTTAGT
1 GTTTATTCGAA-TTTGATTCGAATATTGATTGTCATTTTTAATTTAGG
*
361026 G-TTATTTCGATTTTGATT
1 GTTTA-TTCGAATTTGATT
361044 GGATTATGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
46 8 0.15
47 46 0.84
48 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.17, T:0.56
Consensus pattern (47 bp):
GTTTATTCGAATTTGATTCGAATATTGATTGTCATTTTTAATTTAGG
Found at i:361231 original size:30 final size:31
Alignment explanation
Indices: 361165--361232 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
361155 GTTAATCAGT
* * *
361165 GACTATTTTGTCACTTTTTGATAATGTTAAC
1 GACTGTTTTGTCACATTTTCATAATGTTAAC
361196 GACTGTTTTGTCACATTTTCA-AA-GTTAAGC
1 GACTGTTTTGTCACATTTTCATAATGTTAA-C
361226 GACTGTT
1 GACTGTT
361233 GTGTTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 10 0.30
31 18 0.55
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (31 bp):
GACTGTTTTGTCACATTTTCATAATGTTAAC
Found at i:361690 original size:60 final size:59
Alignment explanation
Indices: 361512--361694 Score: 190
Period size: 60 Copynumber: 3.0 Consensus size: 59
361502 CTTAATCACT
* *
361512 TTAACATAATATTGAATTAATATAATACTTATCAAGATAAATA-TTAGATTAAATTTAATA
1 TTAA-ATAATATTAAATTAATATAATACTTATTAAGATAAATATTTA-ATTAAATTTAATA
* ** * *
361572 TTAATTCTTATTAAATTAATATAATATTTTATCTACCAGATAAATATTAAATTAAATTTAATA
1 TTAAATAATATTAAATTAATATAATA-CTTAT-TA--AGATAAATATTTAATTAAATTTAATA
* * *
361635 TTAAGATAATCATTAAATTAATACAATACTT-TTAAGATAAGTATTTAATTTAATTTAATA
1 TTAA-ATAAT-ATTAAATTAATATAATACTTATTAAGATAAATATTTAATTAAATTTAATA
361695 CTTTTAAGAT
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
59 18 0.18
60 31 0.31
61 1 0.01
62 2 0.02
63 27 0.27
64 6 0.06
65 16 0.16
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (59 bp):
TTAAATAATATTAAATTAATATAATACTTATTAAGATAAATATTTAATTAAATTTAATA
Found at i:361695 original size:32 final size:32
Alignment explanation
Indices: 361609--361709 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
361599 TTTATCTACC
* * *
361609 AGATAAATATTAAATTAAATTTAATA---TTA
1 AGATAAGTATTTAATTTAATTTAATACTTTTA
* **
361638 AGATAA-TCA-TTAAATTAATACAATACTTTTA
1 AGATAAGT-ATTTAATTTAATTTAATACTTTTA
361669 AGATAAGTATTTAATTTAATTTAATACTTTTA
1 AGATAAGTATTTAATTTAATTTAATACTTTTA
361701 AGATAAGTA
1 AGATAAGTA
361710 GAGTCCCAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
28 12 0.21
29 7 0.12
31 10 0.17
32 29 0.50
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (32 bp):
AGATAAGTATTTAATTTAATTTAATACTTTTA
Found at i:362023 original size:24 final size:24
Alignment explanation
Indices: 361984--362066 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
361974 ATTAATATAA
361984 TGGTATCCTTTCTGACCTTTTCAT
1 TGGTATCCTTTCTGACCTTTTCAT
* *
362008 TGGTATCTTTTTTGACCTTTTCAT
1 TGGTATCCTTTCTGACCTTTTCAT
* * *
362032 TAGTGA-CCTTTCCGTCCTTTTCAT
1 TGGT-ATCCTTTCTGACCTTTTCAT
362056 TGGTATCCTTT
1 TGGTATCCTTT
362067 TTGGAAAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 47 0.96
25 1 0.02
ACGTcount: A:0.12, C:0.23, G:0.13, T:0.52
Consensus pattern (24 bp):
TGGTATCCTTTCTGACCTTTTCAT
Found at i:362169 original size:41 final size:41
Alignment explanation
Indices: 362047--362172 Score: 175
Period size: 40 Copynumber: 3.1 Consensus size: 41
362037 ACCTTTCCGT
* *
362047 CCTTTTCA-TTGGTATCCTTTTTGGAAAACATCCTTTTCAA
1 CCTTTTCATTTGGTATCCTTTTCGGATAACATCCTTTTCAA
* *
362087 CCTTTTCATTTGATATCC-TTTCAGATAACATCCTTTTCAA
1 CCTTTTCATTTGGTATCCTTTTCGGATAACATCCTTTTCAA
* * *
362127 CCTTTTCATTTGGTATCCTTTTCGGATAAGATTCTTTCCAA
1 CCTTTTCATTTGGTATCCTTTTCGGATAACATCCTTTTCAA
362168 CCTTT
1 CCTTT
362173 CCTGATTCAG
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
40 44 0.59
41 31 0.41
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.46
Consensus pattern (41 bp):
CCTTTTCATTTGGTATCCTTTTCGGATAACATCCTTTTCAA
Found at i:362375 original size:20 final size:20
Alignment explanation
Indices: 362337--362375 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
362327 ACATATCAAT
* *
362337 TAATCTTTTAAATTCAAATG
1 TAATATTTTAAAATCAAATG
*
362357 TAATATTTTAAAATGAAAT
1 TAATATTTTAAAATCAAAT
362376 ACGAACTTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
TAATATTTTAAAATCAAATG
Found at i:381719 original size:21 final size:21
Alignment explanation
Indices: 381678--381719 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
381668 GAGCAAACGG
*
381678 GCATGTGGAGTAGCTACACAA
1 GCATGTGGAGTAGCCACACAA
*
381699 GCATGTGG-GATAGCCATACAA
1 GCATGTGGAG-TAGCCACACAA
381720 CCATTTCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (21 bp):
GCATGTGGAGTAGCCACACAA
Found at i:393346 original size:15 final size:15
Alignment explanation
Indices: 393326--393364 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
393316 TACAATAAAT
393326 AACAAGATTATCCAC
1 AACAAGATTATCCAC
*
393341 AACAAGATTATCTAC
1 AACAAGATTATCCAC
393356 AACAAGATT
1 AACAAGATT
393365 TGAACAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.23
Consensus pattern (15 bp):
AACAAGATTATCCAC
Found at i:402205 original size:14 final size:14
Alignment explanation
Indices: 402170--402215 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
402160 CATATTCTTA
402170 AAAGTAATATATAT
1 AAAGTAATATATAT
402184 -AA--AA-ATATAT
1 AAAGTAATATATAT
402194 AAAGTAATATATAT
1 AAAGTAATATATAT
402208 AAAGTAAT
1 AAAGTAAT
402216 TACAAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 6 0.21
11 4 0.14
13 4 0.14
14 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAGTAATATATAT
Found at i:402208 original size:24 final size:24
Alignment explanation
Indices: 402133--402231 Score: 85
Period size: 24 Copynumber: 4.0 Consensus size: 24
402123 AAGGATGATG
402133 AAAAATATATAAAGTAATATATAT
1 AAAAATATATAAAGTAATATATAT
**** *
402157 TCTCATATTCTTAAAAGTAATATATAT
1 AAAAATA-T-AT-AAAGTAATATATAT
402184 AAAAATATATAAAGTAATATATAT
1 AAAAATATATAAAGTAATATATAT
*
402208 AAAGTAAT-TA-CAAGTAATATATAT
1 AAA--AATATATAAAGTAATATATAT
402232 TCTCATATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
24 33 0.56
25 4 0.07
26 5 0.08
27 17 0.29
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (24 bp):
AAAAATATATAAAGTAATATATAT
Found at i:407630 original size:20 final size:20
Alignment explanation
Indices: 407597--407651 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
407587 ATCTTTTATA
*
407597 TATATATATATATATATT-CTT
1 TATA-ATATTTATAT-TTACTT
407618 TATAATATTTATATTTACTT
1 TATAATATTTATATTTACTT
407638 TATAATATTTATAT
1 TATAATATTTATAT
407652 GTATAAAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 2 0.06
20 26 0.81
21 4 0.12
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TATAATATTTATATTTACTT
Found at i:408119 original size:23 final size:23
Alignment explanation
Indices: 408078--408121 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
408068 GAAATTAAAT
** *
408078 TGTAATTTTTACGATATTAAAAA
1 TGTAATTTTTAAAAGATTAAAAA
408101 TGTAATTTTTAAAAGATTAAA
1 TGTAATTTTTAAAAGATTAAA
408122 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TGTAATTTTTAAAAGATTAAAAA
Found at i:408882 original size:55 final size:55
Alignment explanation
Indices: 408779--408883 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 55
408769 TTTTGCCAGT
* * *
408779 CGTGTGTATACTCGAAATAGGGTGACACGATCGTGTTTTAGCCTGTGTGCTCGAC
1 CGTGTGTATACTCGAAATAGGGTCACACGATCGTGTATCAGCCTGTGTGCTCGAC
* *
408834 CGTGTGTATACTTGAAATTGGGTCACAC-AGTCGTGTATCAG-CTCGTGTGC
1 CGTGTGTATACTCGAAATAGGGTCACACGA-TCGTGTATCAGCCT-GTGTGC
408884 CTACTGCACC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
54 3 0.07
55 40 0.93
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (55 bp):
CGTGTGTATACTCGAAATAGGGTCACACGATCGTGTATCAGCCTGTGTGCTCGAC
Found at i:413392 original size:13 final size:13
Alignment explanation
Indices: 413369--413393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
413359 ATTAAACTTG
413369 AAAATTAAAAATT
1 AAAATTAAAAATT
413382 AAAATTAAAAAT
1 AAAATTAAAAAT
413394 GAATTTGGGT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:423113 original size:37 final size:37
Alignment explanation
Indices: 423055--423255 Score: 249
Period size: 37 Copynumber: 5.4 Consensus size: 37
423045 ATTCTTAGAT
* * *
423055 CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATA
* * * *
423092 CACCGGCATGAAGGCTGCTAGGCACACAGCTTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATA
* *
423129 CACCGGCACGAAGCCTGTTAGGCACACAGCCTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATA
* * * *
423166 CATCGGCACGAAGCCTGTTAGGAACATAGCCCGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATA
* *
423203 CATCGGCCCGAAGCCTGCTAGGCACATAGCCTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATA
* *
423240 CACCGACACAAAGCCT
1 CACCGGCACGAAGCCT
423256 CTTAGCCACA
Statistics
Matches: 141, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 141 1.00
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.14
Consensus pattern (37 bp):
CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATA
Found at i:423202 original size:74 final size:74
Alignment explanation
Indices: 423055--423279 Score: 252
Period size: 74 Copynumber: 3.0 Consensus size: 74
423045 ATTCTTAGAT
* * * * * * *
423055 CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATACACCGGCATGAAGGCTGCTAGGCACACA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTGTTAGGAACACA
**
423120 GCTTGAATA
66 GCCCGAATA
* * * *
423129 CACCGGCACGAAGCCTGTTAGGCACACAGCCTGAATACATCGGCACGAAGCCTGTTAGGAACATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTGTTAGGAACACA
423194 GCCCGAATA
66 GCCCGAATA
* * * * * **
423203 CATCGGCCCGAAGCCTGCTAGGCACATAGCCTGAATACACCGACACAAAGCCTCTTAGCCACACA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTGTTAGGAACACA
**
423268 ATCCGAATA
66 GCCCGAATA
423277 CAC
1 CAC
423280 TTGCGCGAAG
Statistics
Matches: 124, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
74 124 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.14
Consensus pattern (74 bp):
CACCGGCACGAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACGAAGCCTGTTAGGAACACA
GCCCGAATA
Found at i:423291 original size:111 final size:111
Alignment explanation
Indices: 423058--423267 Score: 294
Period size: 111 Copynumber: 1.9 Consensus size: 111
423048 CTTAGATCAC
* ** * * * *
423058 CGGCACAAAGCCTACTAGGCACATAGCCCGAATACACCGGCATGAAGGCTGCTAGGCACACAGCT
1 CGGCACGAAGCCTGTTAGGAACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAGCC
* * * *
423123 TGAATACACCGGCACGAAGCCTGTTAGGCACACAGCCTGAATACAT
66 TGAATACACCGACACAAAGCCTCTTAGCCACACAGCCTGAATACAT
* * *
423169 CGGCACGAAGCCTGTTAGGAACATAGCCCGAATACATCGGCCCGAAGCCTGCTAGGCACATAGCC
1 CGGCACGAAGCCTGTTAGGAACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAGCC
423234 TGAATACACCGACACAAAGCCTCTTAGCCACACA
66 TGAATACACCGACACAAAGCCTCTTAGCCACACA
423268 ATCCGAATAC
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
111 85 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.14
Consensus pattern (111 bp):
CGGCACGAAGCCTGTTAGGAACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAGCC
TGAATACACCGACACAAAGCCTCTTAGCCACACAGCCTGAATACAT
Found at i:423313 original size:111 final size:111
Alignment explanation
Indices: 423058--423298 Score: 279
Period size: 111 Copynumber: 2.2 Consensus size: 111
423048 CTTAGATCAC
* * * * * *
423058 CGGCACAAAGCCTACTAGGCACATAGCCCGAATACACCGGCATGAAGGCTGCTAGGCACACAGCT
1 CGGCACGAAGCCAACTAGGAACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAGCC
* * * *
423123 TGAATACACCGGCACGAAGCCTGTTAGGCACACAGCCTGAATACAT
66 TGAATACACCGACACAAAGCCTCTTAGCCACACAGCCTGAATACAT
*** * * *
423169 CGGCACGAAGCCTGTTAGGAACATAGCCCGAATACATCGGCCCGAAGCCTGCTAGGCACATAGCC
1 CGGCACGAAGCCAACTAGGAACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAGCC
*
423234 TGAATACACCGACACAAAGCCTCTTAGCCACACAATCC-GAATACA-
66 TGAATACACCGACACAAAGCCTCTTAGCCACAC-AGCCTGAATACAT
* *
423279 CTTGCGCGAAGCCAACTAGG
1 C-GGCACGAAGCCAACTAGG
423299 CATACAACCT
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
110 1 0.01
111 104 0.96
112 3 0.03
ACGTcount: A:0.32, C:0.32, G:0.22, T:0.15
Consensus pattern (111 bp):
CGGCACGAAGCCAACTAGGAACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAGCC
TGAATACACCGACACAAAGCCTCTTAGCCACACAGCCTGAATACAT
Done.