Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014817.1 Kokia drynarioides strain JFW-HI SEQ_129859, 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: 179261
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:1365 original size:3 final size:3
Alignment explanation
Indices: 1357--1381 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1347 TTCAAATAGT
1357 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
1382 ACAATGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1479 original size:31 final size:31
Alignment explanation
Indices: 1438--1504 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1428 TCATTATAAC
* *
1438 CCGTTTGATGTCCATCATGAA-GATATCAAAG
1 CCGTTAGATGTCCATCA-CAAGGATATCAAAG
*
1469 CCGTTAGATGTCCATCACAAGGATATCAGAG
1 CCGTTAGATGTCCATCACAAGGATATCAAAG
1500 CCGTT
1 CCGTT
1505 GATCTTGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (31 bp):
CCGTTAGATGTCCATCACAAGGATATCAAAG
Found at i:3956 original size:16 final size:17
Alignment explanation
Indices: 3925--3958 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3915 TTTAGATCTT
*
3925 TTTAAATTTTATAAAAA
1 TTTAAATTTAATAAAAA
3942 TTTAAA-TTAATAAAAA
1 TTTAAATTTAATAAAAA
3958 T
1 T
3959 AAATTTACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAATAAAAA
Found at i:6784 original size:13 final size:14
Alignment explanation
Indices: 6768--6796 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6758 CAAAATGAAA
6768 AAAAAAAATTA-TG
1 AAAAAAAATTAGTG
6781 AAAAAAAATTAGTG
1 AAAAAAAATTAGTG
6795 AA
1 AA
6797 TTGGCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (14 bp):
AAAAAAAATTAGTG
Found at i:7554 original size:15 final size:15
Alignment explanation
Indices: 7519--7555 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
7509 TTAAGATGAC
*
7519 TATATAAA-AAAAAT
1 TATATAAATAAAAAA
7533 TAT-TAAATAAAAAA
1 TATATAAATAAAAAA
7547 TATATAAAT
1 TATATAAAT
7556 TTATTAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TATATAAATAAAAAA
Found at i:14032 original size:15 final size:15
Alignment explanation
Indices: 13991--14050 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
13981 AATTTTCAAT
13991 AAATAAAAAATTATTA
1 AAATAAAAAA-TATTA
* **
14007 AATTACTAAATATTA
1 AAATAAAAAATATTA
14022 AAATAAAAAATA-TA
1 AAATAAAAAATATTA
14036 AACATTAAAAAATAT
1 AA-A-TAAAAAATAT
14051 ATATATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 4 0.11
15 15 0.43
16 16 0.46
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:14049 original size:31 final size:31
Alignment explanation
Indices: 13991--14050 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
13981 AATTTTCAAT
* **
13991 AAATAAAAAATTATTAAATTACTAAATATTA
1 AAATAAAAAATTATAAAATTAAAAAATATTA
14022 AAATAAAAAA-TATAAACATTAAAAAATAT
1 AAATAAAAAATTATAAA-ATTAAAAAATAT
14051 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (31 bp):
AAATAAAAAATTATAAAATTAAAAAATATTA
Found at i:20273 original size:21 final size:20
Alignment explanation
Indices: 20233--20276 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
20223 ATATTTATTA
*
20233 TAAAAAGGATTGATTAAAGT
1 TAAAAAGGATTAATTAAAGT
20253 TAAAAAGATGATTAATT-AAGT
1 TAAAAAG--GATTAATTAAAGT
20274 TAA
1 TAA
20277 TTATGAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (20 bp):
TAAAAAGGATTAATTAAAGT
Found at i:21137 original size:43 final size:43
Alignment explanation
Indices: 21060--21290 Score: 224
Period size: 42 Copynumber: 5.4 Consensus size: 43
21050 GAAACACTTG
* * *
21060 ATGTATAAATGGAAGAGTCATGTCTCAGG-TTGAGCATGAGAATT
1 ATGTTTAAA-GGAAGACTCATGTCTC-GGAATGAGCATGAGAATT
* * *
21104 -TGTATAAATGGAAGACTCGTGACTCGGAATGAGCATGAGAA-T
1 ATGTTTAAA-GGAAGACTCATGTCTCGGAATGAGCATGAGAATT
* * *
21146 ATGTTTAAAGAAAGACTCATGTCTCGGGATGAGAATGAG-ATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGAATT
* *
21188 ATGTTTAAAAGAAGACTCATGTCTC-GAGATGAGAATGA-AATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGA-ATGAGCATGAGAATT
* * *
21230 ATGTTTAAAGGAAAACTCATGTTTCGGAATGAGCGTGAG-ATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGAATT
*
21272 ATATTTGAAAAGGAAGACT
1 ATGTTT--AAAGGAAGACT
21291 TATGGCTCTA
Statistics
Matches: 158, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
41 2 0.01
42 103 0.65
43 43 0.27
44 10 0.06
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.28
Consensus pattern (43 bp):
ATGTTTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGAATT
Found at i:30207 original size:14 final size:16
Alignment explanation
Indices: 30162--30205 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
30152 AATAGAATGA
*
30162 AAATAGATTTTTAATT
1 AAATAAATTTTTAATT
30178 AAATAAATTTAATTAATT
1 AAATAAATTT--TTAATT
30196 AAA-AAATTTT
1 AAATAAATTTT
30206 AAACCCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 6 0.24
18 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATAAATTTTTAATT
Found at i:30291 original size:35 final size:34
Alignment explanation
Indices: 30235--30315 Score: 126
Period size: 35 Copynumber: 2.4 Consensus size: 34
30225 AAAAACTCAT
* *
30235 TCGTCTCTCTTTTTTTTTTAGTTTTCTTTTCGTA
1 TCGTCTTTTTTTTTTTTTTAGTTTTCTTTTCGTA
*
30269 TCTTCTTTTTTTTTTTTGTTAGTTTTCTTTTCGTA
1 TCGTCTTTTTTTTTTTT-TTAGTTTTCTTTTCGTA
30304 TCGTCTTTTTTT
1 TCGTCTTTTTTT
30316 AGTTTTCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 14 0.33
35 28 0.67
ACGTcount: A:0.05, C:0.15, G:0.09, T:0.72
Consensus pattern (34 bp):
TCGTCTTTTTTTTTTTTTTAGTTTTCTTTTCGTA
Found at i:30616 original size:13 final size:13
Alignment explanation
Indices: 30573--30617 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
30563 CGGTCAAAGG
30573 AAAAAGAAAACTA
1 AAAAAGAAAACTA
*
30586 AAAAA-AAAAGATA
1 AAAAAGAAAA-CTA
30599 CAAAAAGAAAACTA
1 -AAAAAGAAAACTA
30613 AAAAA
1 AAAAA
30618 AGAGAGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 4 0.15
13 12 0.44
14 7 0.26
15 4 0.15
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAAGAAAACTA
Found at i:30617 original size:14 final size:14
Alignment explanation
Indices: 30573--30620 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
30563 CGGTCAAAGG
30573 AAAAAGAAAACTAA
1 AAAAAGAAAACTAA
*
30587 AAAAA-AAAGA-TAC
1 AAAAAGAAA-ACTAA
30600 AAAAAGAAAACTAA
1 AAAAAGAAAACTAA
30614 AAAAAGA
1 AAAAAGA
30621 GAGAGAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.79, C:0.06, G:0.08, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAACTAA
Found at i:34681 original size:31 final size:31
Alignment explanation
Indices: 34646--34708 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
34636 TTAACAGTCC
34646 AGTGACTTAAATAAAAACTTTCAAATAATTT
1 AGTGACTTAAATAAAAACTTTCAAATAATTT
* *
34677 AGTGACTTAAATGAAAATTTTCAAATAATTT
1 AGTGACTTAAATAAAAACTTTCAAATAATTT
34708 A
1 A
34709 ATGATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTCAAATAATTT
Found at i:35047 original size:17 final size:17
Alignment explanation
Indices: 35025--35064 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
35015 TAACAAAAGA
35025 AAGAAATCGACGTCAA-G
1 AAGAAATCGACGT-AATG
*
35042 AAGAAATCTACGTAATG
1 AAGAAATCGACGTAATG
35059 AAGAAA
1 AAGAAA
35065 AGTCAAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.15
Consensus pattern (17 bp):
AAGAAATCGACGTAATG
Found at i:37488 original size:25 final size:25
Alignment explanation
Indices: 37460--37525 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
37450 AAATTACATA
*
37460 TTTAAGCTATGTATTTTAATTTGTT
1 TTTAAACTATGTATTTTAATTTGTT
*
37485 TTTAAATTATGTATTTTAATTTGTT
1 TTTAAACTATGTATTTTAATTTGTT
*
37510 TTTAAA-TTTGTATTTT
1 TTTAAACTATGTATTTT
37526 TCGAGTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
24 9 0.24
25 29 0.76
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (25 bp):
TTTAAACTATGTATTTTAATTTGTT
Found at i:37519 original size:12 final size:12
Alignment explanation
Indices: 37469--37525 Score: 73
Period size: 12 Copynumber: 4.7 Consensus size: 12
37459 ATTTAAGCTA
37469 TGTATTTTAATT
1 TGTATTTTAATT
37481 TGT-TTTTAAATT
1 TGTATTTT-AATT
37493 ATGTATTTTAATT
1 -TGTATTTTAATT
37506 TGT-TTTTAAATT
1 TGTATTTT-AATT
37518 TGTATTTT
1 TGTATTTT
37526 TCGAGTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.20
12 17 0.43
13 11 0.28
14 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.67
Consensus pattern (12 bp):
TGTATTTTAATT
Found at i:37526 original size:25 final size:25
Alignment explanation
Indices: 37467--37525 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
37457 ATATTTAAGC
37467 TATGTATTTTAATTTGTTTTTAAAT
1 TATGTATTTTAATTTGTTTTTAAAT
37492 TATGTATTTTAATTTGTTTTTAAAT
1 TATGTATTTTAATTTGTTTTTAAAT
37517 T-TGTATTTT
1 TATGTATTTT
37526 TCGAGTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 8 0.24
25 26 0.76
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.66
Consensus pattern (25 bp):
TATGTATTTTAATTTGTTTTTAAAT
Found at i:41558 original size:21 final size:21
Alignment explanation
Indices: 41502--41569 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
41492 ACATAATAGT
*
41502 AAAATGACAACAAAATATGAA
1 AAAATAACAACAAAATATGAA
*
41523 AAAACAA-AAGCAAAATAGTGAA
1 AAAATAACAA-CAAAATA-TGAA
* * *
41545 AAAATAACAAAAAAAAATGAG
1 AAAATAACAACAAAATATGAA
41566 AAAA
1 AAAA
41570 CAATAGTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 15 0.39
23 2 0.05
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAATAACAACAAAATATGAA
Found at i:42427 original size:2 final size:2
Alignment explanation
Indices: 42420--42450 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42410 AAATTTGATA
42420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42451 AAATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43799 original size:30 final size:30
Alignment explanation
Indices: 43741--43848 Score: 139
Period size: 30 Copynumber: 3.6 Consensus size: 30
43731 TGTCAAAACA
* *
43741 TAATTTTGAAAAAGTTT-GGGGGTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
*
43770 TAATTTTGGGAAAGTTTAGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* *
43800 TAATTTTGGAGAAGTTTTA-GGGTCAAAATG
1 TAATTTTGGAAAAG-TTTAGGGGTTAAAATG
*
43830 TAATTTTGGAAAATTTTAG
1 TAATTTTGGAAAAGTTTAG
43849 TGTGAAAATG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
29 19 0.28
30 45 0.66
31 4 0.06
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.38
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTAGGGGTTAAAATG
Found at i:43856 original size:29 final size:29
Alignment explanation
Indices: 43732--43859 Score: 123
Period size: 30 Copynumber: 4.3 Consensus size: 29
43722 AGAATACAAT
** * **
43732 GTCAAAACATAATTTTGAAAAAGTTTGGGG
1 GTCAAAATGTAATTTTGGAAAA-TTTTAGG
* *
43762 GT-AAAATGTAATTTTGGGAAAGTTTAGGG
1 GTCAAAATGTAATTTTGGAAAATTTTA-GG
* *
43791 GTTAAAATGTAATTTTGGAGAAGTTTTAGG
1 GTCAAAATGTAATTTTGGA-AAATTTTAGG
*
43821 GTCAAAATGTAATTTTGGAAAATTTTAGT
1 GTCAAAATGTAATTTTGGAAAATTTTAGG
*
43850 GTGAAAATGT
1 GTCAAAATGT
43860 GGTCAAAATG
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.02
29 36 0.44
30 37 0.46
31 6 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (29 bp):
GTCAAAATGTAATTTTGGAAAATTTTAGG
Found at i:43857 original size:59 final size:59
Alignment explanation
Indices: 43741--43859 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 59
43731 TGTCAAAACA
* * *
43741 TAATTTTGAAAAAGTTTGGGGGTAAAATGTAATTTTGGGAAAGTTTAGGGGTTAAAATG
1 TAATTTTGAAAAAGTTTGAGGGTAAAATGTAATTTTGGAAAAGTTTAGGGGTGAAAATG
* * * * *
43800 TAATTTTGGAGAAGTTTTAGGGTCAAAATGTAATTTTGGAAAATTTTA-GTGTGAAAATG
1 TAATTTTGAAAAAGTTTGAGGGT-AAAATGTAATTTTGGAAAAGTTTAGGGGTGAAAATG
43859 T
1 T
43860 GGTCAAAATG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 29 0.57
60 22 0.43
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.38
Consensus pattern (59 bp):
TAATTTTGAAAAAGTTTGAGGGTAAAATGTAATTTTGGAAAAGTTTAGGGGTGAAAATG
Found at i:43936 original size:30 final size:30
Alignment explanation
Indices: 43862--43936 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
43852 GAAAATGTGG
*
43862 TCAAAATGTAATTTTGGAAAAGTTTAGGGT
1 TCAAAATATAATTTTGGAAAAGTTTAGGGT
* * *
43892 TCAAAATGTTATTTTGGAAAAGTTTGGGAGT
1 TCAAAATATAATTTTGGAAAAGTTTAGG-GT
*
43923 T-AATATATAATTTT
1 TCAAAATATAATTTT
43937 CAAAGAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 36 0.92
31 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (30 bp):
TCAAAATATAATTTTGGAAAAGTTTAGGGT
Found at i:45061 original size:29 final size:30
Alignment explanation
Indices: 45016--45075 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
45006 GAAAATAATA
45016 AATAAACAATTAATAAATATATT-ATATAT
1 AATAAACAATTAATAAATATATTAATATAT
*
45045 AATAAATAA-TAAGTAAATATATTAATATAT
1 AATAAACAATTAA-TAAATATATTAATATAT
45075 A
1 A
45076 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 3 0.11
29 18 0.64
30 7 0.25
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
AATAAACAATTAATAAATATATTAATATAT
Found at i:45091 original size:37 final size:39
Alignment explanation
Indices: 45008--45093 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
44998 ATTTCGCAGA
* *
45008 AAATAATAAATAAACAATTAATAAATATATTATATATAAT
1 AAATAATAAATAAACAATTAAT-AATATATTATAAAAAAT
* *
45048 AAATAATAAGTAAATATATTAAT-ATATATT-TAAAAAAT
1 AAATAATAAATAAACA-ATTAATAATATATTATAAAAAAT
45086 -AATAATAA
1 AAATAATAA
45094 TAATAAATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 8 0.20
38 6 0.15
39 7 0.17
40 14 0.34
41 6 0.15
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (39 bp):
AAATAATAAATAAACAATTAATAATATATTATAAAAAAT
Found at i:50364 original size:25 final size:26
Alignment explanation
Indices: 50336--50394 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
50326 ATTACCTAAA
50336 TAATTTATAAGATGA-ATTTATTATT
1 TAATTTATAAGATGATATTTATTATT
* * *
50361 TAATGTATTAGATGATTTTTTATTATT
1 TAATTTATAAGATGA-TATTTATTATT
*
50388 TATTTTA
1 TAATTTA
50395 GATTGTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 13 0.48
27 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (26 bp):
TAATTTATAAGATGATATTTATTATT
Found at i:73748 original size:132 final size:132
Alignment explanation
Indices: 73555--73949 Score: 594
Period size: 132 Copynumber: 3.0 Consensus size: 132
73545 AGAAGAACAG
* * * *
73555 GCTAGGTCGGAGGAAGTTA-CCTGCGTGCCTACTTTATCAACCATAGAAAATCCTCAAGTTGTTG
1 GCTAGGTCGGAGGAAGTTACCCT-TGTGCCTACTTTATCAACCGTAGAAAACCCACAAGTTGTTG
* * *
73619 AAATTAACCCTGGCATGGGAGTAAATTTTGAAGAATGTTCTCAGCTTCATCCCTCTAATCAAGGA
65 AAATTAATCCTGGCGTGGGAGAAAATTTTGAAGAATGTTCTCAGCTTCATCCCTCTAATCAAGGA
73684 GAC
130 GAC
*
73687 GCTAGGTCGGAGGAAGGTACCCTTGTGCCTACTTTATCAACCGTAGAAAACCCACAAGTTGTTGA
1 GCTAGGTCGGAGGAAGTTACCCTTGTGCCTACTTTATCAACCGTAGAAAACCCACAAGTTGTTGA
*
73752 AATTAATCCTAGCGTGGGAGAAAATTTTGAAGAATGTTCTCAGCTTCATCCCTCTAATCAAGGAG
66 AATTAATCCTGGCGTGGGAGAAAATTTTGAAGAATGTTCTCAGCTTCATCCCTCTAATCAAGGAG
*
73817 AG
131 AC
* * * * * * *
73819 GCTAGGTTGGATGAAGTTTCCCTTGCGGCTACTTTATCAACCGTAGAAACCCCACAAGTTGATGA
1 GCTAGGTCGGAGGAAGTTACCCTTGTGCCTACTTTATCAACCGTAGAAAACCCACAAGTTGTTGA
* * *
73884 AATTAATCCTGGTGTGGGAGAAAATTTTGAAGAATGTTCTCAGCTTAATCCCTCCAATCAAGGAG
66 AATTAATCCTGGCGTGGGAGAAAATTTTGAAGAATGTTCTCAGCTTCATCCCTCTAATCAAGGAG
73949 A
131 A
73950 TATGCTCGTG
Statistics
Matches: 240, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 237 0.99
133 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (132 bp):
GCTAGGTCGGAGGAAGTTACCCTTGTGCCTACTTTATCAACCGTAGAAAACCCACAAGTTGTTGA
AATTAATCCTGGCGTGGGAGAAAATTTTGAAGAATGTTCTCAGCTTCATCCCTCTAATCAAGGAG
AC
Found at i:79573 original size:9 final size:9
Alignment explanation
Indices: 79559--79584 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
79549 AAGACAAGAA
79559 GAAAACACT
1 GAAAACACT
79568 GAAAACACT
1 GAAAACACT
79577 GAAAACAC
1 GAAAACAC
79585 ATAGCATTTA
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:0.23, G:0.12, T:0.08
Consensus pattern (9 bp):
GAAAACACT
Found at i:80615 original size:4 final size:4
Alignment explanation
Indices: 80606--80690 Score: 66
Period size: 4 Copynumber: 21.0 Consensus size: 4
80596 AAATAAACGG
* * * *
80606 GAAA GAAA GAAAA GAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA AAAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * *
80656 G-AA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
80691 TGTAATGTGT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
3 6 0.09
4 48 0.73
5 12 0.18
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:80659 original size:20 final size:20
Alignment explanation
Indices: 80636--80684 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
80626 AGAAAGAAAG
80636 GAAGAAGGAGAGGAAAAAAA
1 GAAGAAGGAGAGGAAAAAAA
*
80656 GAAGAAGGAGAGGAAAGAAA
1 GAAGAAGGAGAGGAAAAAAA
80676 GAAGAAGGA
1 GAAGAAGGA
80685 AAGAAATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (20 bp):
GAAGAAGGAGAGGAAAAAAA
Found at i:92715 original size:18 final size:19
Alignment explanation
Indices: 92680--92715 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
92670 ACAAGAAAGA
92680 TGATAATAGGTGGCAATGG
1 TGATAATAGGTGGCAATGG
*
92699 TGATAAT-GGTGGTAATG
1 TGATAATAGGTGGCAATG
92716 AAAAACCACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.31
Consensus pattern (19 bp):
TGATAATAGGTGGCAATGG
Found at i:112562 original size:17 final size:17
Alignment explanation
Indices: 112521--112563 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
112511 TGAAATTATA
*
112521 TTTTTATATATAAAATT
1 TTTTTTTATATAAAATT
*
112538 TATTTTTAT-TAAAAGTT
1 TTTTTTTATATAAAA-TT
112555 TTTTTTTAT
1 TTTTTTTAT
112564 GTTTCGCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTTTATATAAAATT
Found at i:113284 original size:16 final size:16
Alignment explanation
Indices: 113255--113329 Score: 105
Period size: 16 Copynumber: 4.4 Consensus size: 16
113245 TTCAAATGGG
113255 ATTAGAATAGATTTTTA
1 ATTA-AATAGATTTTTA
*
113272 ATTAAATAAATTTAATTA
1 ATTAAATAGATTT--TTA
113290 ATTAAAATAGATTTTTA
1 ATT-AAATAGATTTTTA
113307 ATTAAATAGATTTTTA
1 ATTAAATAGATTTTTA
113323 ATTAAAT
1 ATTAAAT
113330 GGGATGAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
16 28 0.53
17 10 0.19
18 6 0.11
19 9 0.17
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
ATTAAATAGATTTTTA
Found at i:113306 original size:35 final size:33
Alignment explanation
Indices: 113255--113328 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 33
113245 TTCAAATGGG
*
113255 ATTAGAATAGATTTTTAATTAAATAAATTTAATTA
1 ATTAAAATAGATTTTTAATTAAATAAATTT--TTA
*
113290 ATTAAAATAGATTTTTAATTAAATAGATTTTTA
1 ATTAAAATAGATTTTTAATTAAATAAATTTTTA
113323 ATTAAA
1 ATTAAA
113329 TGGGATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 9 0.24
35 28 0.76
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (33 bp):
ATTAAAATAGATTTTTAATTAAATAAATTTTTA
Found at i:121602 original size:28 final size:28
Alignment explanation
Indices: 121569--121625 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
121559 ATCTATCAAC
121569 AAATAAATAT-TT-ATATTAATAAAATTAA
1 AAATAAAT-TGTTAATATTAAT-AAATTAA
*
121597 AAATAAATTGTTAATATTGATAAATTAA
1 AAATAAATTGTTAATATTAATAAATTAA
121625 A
1 A
121626 CATATCTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 18 0.69
29 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (28 bp):
AAATAAATTGTTAATATTAATAAATTAA
Found at i:122339 original size:22 final size:22
Alignment explanation
Indices: 122314--122356 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
122304 TATTCAAACA
*
122314 ATAACAATAAAATAGTAGCAAT
1 ATAACAATAAAATAATAGCAAT
* *
122336 ATAATAATGAAATAATAGCAA
1 ATAACAATAAAATAATAGCAA
122357 AAACAGTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAATAGCAAT
Found at i:123767 original size:3 final size:3
Alignment explanation
Indices: 123754--123807 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
123744 GAAAAAGAAA
* *
123754 AAT AGT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
123801 AAT AAT A
1 AAT AAT A
123808 GGGAAAGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:126242 original size:14 final size:14
Alignment explanation
Indices: 126223--126256 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
126213 TACAAAATCC
126223 AAATAATAACAATA
1 AAATAATAACAATA
*
126237 AAATAATAGCAATA
1 AAATAATAACAATA
*
126251 TAATAA
1 AAATAA
126257 CGAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:128215 original size:17 final size:17
Alignment explanation
Indices: 128193--128226 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
128183 GAAAAAATTC
*
128193 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
128210 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
128227 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:131168 original size:6 final size:6
Alignment explanation
Indices: 131157--131197 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
131147 TAGAATTAAA
*
131157 TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
131198 ATGCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:131292 original size:26 final size:26
Alignment explanation
Indices: 131263--131312 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
131253 TGTCATTTGC
*
131263 TAAACATCATTAAATAAATTCAAACA
1 TAAAAATCATTAAATAAATTCAAACA
*
131289 TAAAAATTATTAAATAAATTCAAA
1 TAAAAATCATTAAATAAATTCAAA
131313 TTTAAACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (26 bp):
TAAAAATCATTAAATAAATTCAAACA
Found at i:131326 original size:26 final size:26
Alignment explanation
Indices: 131271--131327 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
131261 GCTAAACATC
**
131271 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
131297 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
131323 ATTAA
1 ATTAA
131328 TTCTAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:140452 original size:20 final size:16
Alignment explanation
Indices: 140408--140441 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
140398 AACAGAAATA
140408 AAGATATTAATTCATC
1 AAGATATTAATTCATC
140424 AAGATATTAATTCATC
1 AAGATATTAATTCATC
140440 AA
1 AA
140442 TCTGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (16 bp):
AAGATATTAATTCATC
Found at i:156869 original size:3 final size:3
Alignment explanation
Indices: 156855--156889 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
156845 AACCCATTTG
*
156855 CAC CAT CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
156890 GCAGTCATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.63, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:157211 original size:6 final size:6
Alignment explanation
Indices: 157200--157233 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
157190 GAATTTAAGG
* *
157200 TTGGAT TTGGAT TTGGAT TTGGCT TTGGTT TTGG
1 TTGGAT TTGGAT TTGGAT TTGGAT TTGGAT TTGG
157234 GTGGATATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.09, C:0.03, G:0.35, T:0.53
Consensus pattern (6 bp):
TTGGAT
Found at i:160945 original size:3 final size:3
Alignment explanation
Indices: 160937--160962 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
160927 CCACACTTAA
160937 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
160963 ATGTAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:165985 original size:21 final size:22
Alignment explanation
Indices: 165953--166002 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
165943 TTTGATTTCT
*
165953 TAATT-TTAAAA-TATTATAAAA
1 TAATTATTAAAATTAAT-TAAAA
165974 TAATTATT-AAATTAATTAAAA
1 TAATTATTAAAATTAATTAAAA
*
165995 TATTTATT
1 TAATTATT
166003 TAAGTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATTATTAAAATTAATTAAAA
Found at i:166010 original size:21 final size:21
Alignment explanation
Indices: 165969--166019 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
165959 TAAAATATTA
* *
165969 TAAAATAATTATTAAATTAAT
1 TAAAATATTTATTAAAGTAAT
*
165990 TAAAATATTTATTTAAGTAAT
1 TAAAATATTTATTAAAGTAAT
*
166011 TAAACTATT
1 TAAAATATT
166020 CAAATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAAATATTTATTAAAGTAAT
Found at i:169741 original size:35 final size:35
Alignment explanation
Indices: 169695--169766 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
169685 AACCCGTCAG
*
169695 CCAATTGAAGCTTTGGAAATATTACTCGTAACAGA
1 CCAATTGAAGCTTTGAAAATATTACTCGTAACAGA
169730 CCAATTGAAGCTTTGAAAATATTACTCGTAACAGA
1 CCAATTGAAGCTTTGAAAATATTACTCGTAACAGA
169765 CC
1 CC
169767 CATCCACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (35 bp):
CCAATTGAAGCTTTGAAAATATTACTCGTAACAGA
Found at i:170568 original size:29 final size:29
Alignment explanation
Indices: 170536--170628 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
170526 AGAGGTTCAA
*
170536 TTTTTTTAATTTTTATAGGTC-AAAATTTT
1 TTTTTTTAATTTTTA-AGGACTAAAATTTT
* **
170565 TTTTTATCAATTTTTAAGGACTTCAATTTT
1 TTTTT-TTAATTTTTAAGGACTAAAATTTT
* *
170595 TTTTTTTAATTTTTAAAGACCCCAAAATTTT
1 TTTTTTTAATTTTTAAGGA--CTAAAATTTT
170626 TTT
1 TTT
170629 ATCAACTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
29 21 0.41
30 20 0.39
31 10 0.20
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTTTTTAATTTTTAAGGACTAAAATTTT
Found at i:170593 original size:30 final size:30
Alignment explanation
Indices: 170559--170641 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
170549 TATAGGTCAA
* **
170559 AATTTTTTTTTATCAATTTTTAAGGACTTC
1 AATTTTTTTTTATCAATTTTTAAAGACCCC
*
170589 AATTTTTTTTT-TTAATTTTTAAAGACCCC
1 AATTTTTTTTTATCAATTTTTAAAGACCCC
** *
170618 AAAATTTTTTTATCAACTTTTAAA
1 AATTTTTTTTTATCAATTTTTAAA
170642 AGACTTAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.54
Consensus pattern (30 bp):
AATTTTTTTTTATCAATTTTTAAAGACCCC
Done.