Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012161.1 Kokia drynarioides strain JFW-HI SEQ_127162, 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: 58718
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Warning! 360 characters in sequence are not A, C, G, or T
Found at i:4581 original size:22 final size:23
Alignment explanation
Indices: 4538--4582 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4528 TACAATTTTA
4538 AAATATTTAATTATAAAATATAT
1 AAATATTTAATTATAAAATATAT
4561 AAATA-TTAATT-TAAAATTATAT
1 AAATATTTAATTATAAAA-TATAT
4583 TTTTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATATTTAATTATAAAATATAT
Found at i:6219 original size:15 final size:17
Alignment explanation
Indices: 6185--6222 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
6175 AGTAAAAATG
6185 TAATTTCATCATTTTAA
1 TAATTTCATCATTTTAA
*
6202 TAATTT-AT-ATTTTTA
1 TAATTTCATCATTTTAA
6217 TAATTT
1 TAATTT
6223 TTAAAAGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTCATCATTTTAA
Found at i:7247 original size:22 final size:22
Alignment explanation
Indices: 7222--7289 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 22
7212 ATTCAGATTT
7222 GATTTAAAAAAAAAAATAAACA
1 GATTTAAAAAAAAAAATAAACA
* *
7244 GATTTAGAAAAAAATTAAATTAAGA
1 GATTTA-AAAAAAA--AAATAAACA
* *
7269 AATTTAAAAACAAAGAATAAA
1 GATTTAAAAA-AAAAAATAAA
7290 TGTTTAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 4 0.11
25 15 0.41
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (22 bp):
GATTTAAAAAAAAAAATAAACA
Found at i:7483 original size:31 final size:28
Alignment explanation
Indices: 7445--7510 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
7435 ATATCAAAAC
7445 TATACATGAACTATGATTTTATGTGTAATTG
1 TATACATG-ACTATGA-TTT-TGTGTAATTG
* * *
7476 TATACATGATTTTGATTTTGTGTAATTT
1 TATACATGACTATGATTTTGTGTAATTG
7504 TATACAT
1 TATACAT
7511 TAAAATCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 16 0.50
29 3 0.09
30 5 0.16
31 8 0.25
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (28 bp):
TATACATGACTATGATTTTGTGTAATTG
Found at i:7744 original size:29 final size:29
Alignment explanation
Indices: 7698--7778 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
7688 TTTGAACAAT
*
7698 AATTAGAGTTTCACATGTATAATG-ACACTA
1 AATTAAAG-TTCA-ATGTATAATGCACACTA
* *
7728 AATTAAAGTTCATATGTACAATTGCACATTA
1 AATTAAAGTTCA-ATGTATAA-TGCACACTA
*
7759 AATCAAAGTTC-ATGTATAAT
1 AATTAAAGTTCAATGTATAAT
7779 TTTGAGATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 18 0.42
30 9 0.21
31 15 0.35
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (29 bp):
AATTAAAGTTCAATGTATAATGCACACTA
Found at i:11025 original size:17 final size:17
Alignment explanation
Indices: 11003--11037 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10993 TTAGATCATG
11003 ATATTAAAAGATAATTT
1 ATATTAAAAGATAATTT
*
11020 ATATTAACAGATAATTT
1 ATATTAAAAGATAATTT
11037 A
1 A
11038 AATAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (17 bp):
ATATTAAAAGATAATTT
Found at i:13137 original size:3 final size:3
Alignment explanation
Indices: 13124--13176 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
13114 TAACTCCTTA
13124 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13170 AAT AAT A
1 AAT AAT A
13177 CCACTGACTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:15994 original size:24 final size:24
Alignment explanation
Indices: 15955--16007 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
15945 TTGATAATAA
* * *
15955 TGTTGGTAAGGGTTATATTGTGTT
1 TGTTGGTAAGGATTATATCGAGTT
*
15979 TGTTGGTATGGATTATATCGAGTT
1 TGTTGGTAAGGATTATATCGAGTT
16003 TGTTG
1 TGTTG
16008 ATAGGGGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.32, T:0.49
Consensus pattern (24 bp):
TGTTGGTAAGGATTATATCGAGTT
Found at i:17738 original size:37 final size:36
Alignment explanation
Indices: 17696--17799 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
17686 TGATCATTAT
*
17696 TCGTTTTACTCCCTATTGACCCCAAAGATCATAATGC
1 TCGTTTTACTCCCTATTGA-CCCAAAGGTCATAATGC
* *
17733 TCGTTTTACTCCCTGTTGACCCAAAGGTCATTATGC
1 TCGTTTTACTCCCTATTGACCCAAAGGTCATAATGC
* * * *
17769 TCATTTTTCTTCCTATTGGCCCAAAGGTCAT
1 TCGTTTTACTCCCTATTGACCCAAAGGTCAT
17800 GCTTGTTACC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 41 0.69
37 18 0.31
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (36 bp):
TCGTTTTACTCCCTATTGACCCAAAGGTCATAATGC
Found at i:21398 original size:17 final size:17
Alignment explanation
Indices: 21376--21410 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21366 ATGGTACTAT
21376 AGTTTTATGACTCCATG
1 AGTTTTATGACTCCATG
21393 AGTTTTATGACTCCATG
1 AGTTTTATGACTCCATG
21410 A
1 A
21411 TTAAATGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (17 bp):
AGTTTTATGACTCCATG
Found at i:27348 original size:20 final size:20
Alignment explanation
Indices: 27247--27350 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
27237 TGTATTTGGT
*
27247 TGTTTGCACTTTGGTGCCCT
1 TGTTTGCACTTTGGTGCCCC
* * *
27267 TATTTGCACTTTGGTACCTC
1 TGTTTGCACTTTGGTGCCCC
** * **
27287 TGAATGCACGTCAGTGCCCC
1 TGTTTGCACTTTGGTGCCCC
* *
27307 TATATGCACTTTGGTGCCCC
1 TGTTTGCACTTTGGTGCCCC
*
27327 TGTTTGCACTTTGGTGTCCC
1 TGTTTGCACTTTGGTGCCCC
27347 TGTT
1 TGTT
27351 AGTATAAATG
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTTTGCACTTTGGTGCCCC
Found at i:31904 original size:21 final size:21
Alignment explanation
Indices: 31856--31923 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
31846 TTAGTATCGA
* *
31856 TAGAAGCATGACTTGTTTCGG
1 TAGAAGTATGACTTGTTTTGG
31877 TAGAAGTATGACTTGTTTTGG
1 TAGAAGTATGACTTGTTTTGG
* * * *
31898 TAGAAGTTTCACTTGTATTAG
1 TAGAAGTATGACTTGTTTTGG
31919 TAGAA
1 TAGAA
31924 TTGTTAGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (21 bp):
TAGAAGTATGACTTGTTTTGG
Found at i:34086 original size:17 final size:16
Alignment explanation
Indices: 34053--34107 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
34043 CCCAACTTGC
34053 ATTTCAAATTGATTTTAA
1 ATTT-AAATT-ATTTTAA
*
34071 GTTTACAATTATTTTAA
1 ATTTA-AATTATTTTAA
34088 ATTTAAATTTATTTTAA
1 ATTTAAA-TTATTTTAA
34105 ATT
1 ATT
34108 AAAAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 2 0.06
17 24 0.73
18 7 0.21
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:34762 original size:3 final size:3
Alignment explanation
Indices: 34756--34851 Score: 167
Period size: 3 Copynumber: 32.3 Consensus size: 3
34746 TAAATAGGTT
*
34756 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
34804 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34851 T
1 T
34852 TTTAATAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35064 original size:3 final size:3
Alignment explanation
Indices: 35056--35089 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
35046 CTAGTTTTCT
35056 TAA TAA TAA TAA TAA TAA TAA TAA TAA TACA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
35090 AAAGAACGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:35988 original size:30 final size:29
Alignment explanation
Indices: 35962--36177 Score: 88
Period size: 30 Copynumber: 7.3 Consensus size: 29
35952 TAAAAATCAT
35962 ATTTTGACCCCTAAACTTTTCCAAAATTCC
1 ATTTTGACCCC-AAACTTTTCCAAAATTCC
* * *
35992 ATTTTGACCTCAAACTTTT-GAAAATTAC
1 ATTTTGACCCCAAACTTTTCCAAAATTCC
* * * *
36020 ATTTTTACCCTCCGAACTTTT-TAAAATTCT
1 ATTTTGA-CC-CCAAACTTTTCCAAAATTCC
* * * * *
36050 ATTTTTGACCTC-GATTTTTCTAAAAATTAC
1 A-TTTTGACCCCAAACTTTTC-CAAAATTCC
* *
36080 ATTTTTACCCTCGAAC--TTCCTAAAATTCC
1 ATTTTGACCC-CAAACTTTTCC-AAAATTCC
* ** **
36109 ATTTTTTACCCTGATTTTTTCCAAAATTACC
1 A-TTTTGACCCCAAACTTTTCCAAAATT-CC
*
36140 ATTTT-ACCTCCAAACTTCTT--AATATTCC
1 ATTTTGACC-CCAAACTT-TTCCAAAATTCC
36168 ATTTTTGACC
1 A-TTTTGACC
36178 TTGAAATTTC
Statistics
Matches: 140, Mismatches: 30, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
28 21 0.15
29 43 0.31
30 61 0.44
31 15 0.11
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (29 bp):
ATTTTGACCCCAAACTTTTCCAAAATTCC
Found at i:36025 original size:29 final size:29
Alignment explanation
Indices: 35963--36085 Score: 90
Period size: 30 Copynumber: 4.1 Consensus size: 29
35953 AAAAATCATA
* * *
35963 TTTTGACCCCTAAACTTTTCCAAAATTCCA-
1 TTTTGACCTC-AAACTTTT-AAAAATTACAT
*
35993 TTTTGACCTCAAACTTTTGAAAATTACAT
1 TTTTGACCTCAAACTTTTAAAAATTACAT
* *
36022 TTTT-ACCCTCCGAACTTTTTAAAATT-CTAT
1 TTTTGA-CCT-CAAACTTTTAAAAATTAC-AT
* **
36052 TTTTGACCTCGATTTTTCTAAAAATTACAT
1 TTTTGACCTCAAACTTT-TAAAAATTACAT
36082 TTTT
1 TTTT
36086 ACCCTCGAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
28 9 0.12
29 22 0.28
30 45 0.58
31 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTGACCTCAAACTTTTAAAAATTACAT
Found at i:36038 original size:59 final size:59
Alignment explanation
Indices: 35944--36113 Score: 170
Period size: 59 Copynumber: 2.9 Consensus size: 59
35934 GGAGGTCCTT
* * * * *
35944 AAACTGTCTAAAAATCATATTTTGACCC-CTAAACTTTTCCAAAATTCCATTTTGACCTC
1 AAACTTTCTAAAAATTACATTTTTACCCTC-GAACTTTTCCAAAATTCCATTTTGACCTC
* * *
36003 AAACTTT-TGAAAATTACATTTTTACCCTCCGAACTTTT-TAAAATTCTATTTTTGACCTC
1 AAACTTTCTAAAAATTACATTTTTACCCT-CGAACTTTTCCAAAATTCCA-TTTTGACCTC
* **
36062 GATTTTTCTAAAAATTACATTTTTACCCTCGAAC--TTCCTAAAATTCCATTTT
1 AAACTTTCTAAAAATTACATTTTTACCCTCGAACTTTTCC-AAAATTCCATTTT
36114 TTACCCTGAT
Statistics
Matches: 91, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
57 2 0.02
58 28 0.31
59 40 0.44
60 21 0.23
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (59 bp):
AAACTTTCTAAAAATTACATTTTTACCCTCGAACTTTTCCAAAATTCCATTTTGACCTC
Found at i:36088 original size:60 final size:60
Alignment explanation
Indices: 35984--36209 Score: 216
Period size: 59 Copynumber: 3.8 Consensus size: 60
35974 AAACTTTTCC
* ** * *
35984 AAAATTCCA-TTTTGACCTCAAACTTT-TGAAAATTA-CATTTTTACCCTCCGAACTTTTT
1 AAAATTCCATTTTTGACCTCGATTTTTCTAAAAATTACCA-TTTTACCCTCCGAACTTCTT
* *
36042 AAAATTCTATTTTTGACCTCGATTTTTCTAAAAATTA-CATTTTTACCCT-CGAACTTCCT
1 AAAATTCCATTTTTGACCTCGATTTTTCTAAAAATTACCA-TTTTACCCTCCGAACTTCTT
* * *
36101 AAAATTCCATTTTTTACC-CTGATTTTT-TCCAAAATTACCATTTTA-CCTCCAAACTTCTT
1 AAAATTCCATTTTTGACCTC-GATTTTTCT-AAAAATTACCATTTTACCCTCCGAACTTCTT
* * * * *
36160 AATATTCCATTTTTGACCTTGAAATTTCCCAAAAATTACCATTTTACCCT
1 AAAATTCCATTTTTGACCTCG-ATTTTTCTAAAAATTACCATTTTACCCT
36210 TGAGAATCCA
Statistics
Matches: 139, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
58 13 0.09
59 82 0.59
60 41 0.29
61 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.42
Consensus pattern (60 bp):
AAAATTCCATTTTTGACCTCGATTTTTCTAAAAATTACCATTTTACCCTCCGAACTTCTT
Found at i:36105 original size:29 final size:29
Alignment explanation
Indices: 35979--36120 Score: 121
Period size: 30 Copynumber: 4.8 Consensus size: 29
35969 CCCCTAAACT
* * * *
35979 TTTCCAAAATTCCATTTTGA-CCTCAAAC
1 TTTCTAAAATTACATTTTTACCCTCGAAC
36007 TTT-TGAAAATTACATTTTTACCCTCCGAAC
1 TTTCT-AAAATTACATTTTTACCCT-CGAAC
* **
36037 TTTTTAAAATT-CTATTTTTGA-CCTCGATT
1 TTTCTAAAATTAC-ATTTTT-ACCCTCGAAC
36066 TTTCTAAAAATTACATTTTTACCCTCGAAC
1 TTTCT-AAAATTACATTTTTACCCTCGAAC
* *
36096 TTCCTAAAATTCCATTTTTTACCCT
1 TTTCTAAAATTACA-TTTTTACCCT
36121 GATTTTTTCC
Statistics
Matches: 93, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
28 16 0.17
29 20 0.22
30 54 0.58
31 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTCTAAAATTACATTTTTACCCTCGAAC
Found at i:43272 original size:18 final size:19
Alignment explanation
Indices: 43246--43288 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
43236 AGATGTGAAG
43246 GAAAAGAAGAAAGAGAT-A
1 GAAAAGAAGAAAGAGATGA
* **
43264 GAAAGGAAGCGAGAGATGA
1 GAAAAGAAGAAAGAGATGA
43283 GAAAAG
1 GAAAAG
43289 CACGACTGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.58, C:0.02, G:0.35, T:0.05
Consensus pattern (19 bp):
GAAAAGAAGAAAGAGATGA
Found at i:49633 original size:29 final size:29
Alignment explanation
Indices: 49590--49871 Score: 268
Period size: 29 Copynumber: 9.6 Consensus size: 29
49580 AAGGTCCCAT
* *
49590 AAACTATCTAAAAATTCTATTTTTACCCCA
1 AAACT-TCTAAAAATTCCATTTTTACCCCG
* *
49620 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCTAAAAATTCCATTTTT-ACCCCG
* *
49650 AAACTTTTAAAAA-TGCATTTTTACCCTCG
1 AAACTTCTAAAAATTCCATTTTTACCC-CG
* *
49679 -AACTTCCAAAAA-TCCTATTTTTGACCTCG
1 AAACTTCTAAAAATTCC-ATTTTT-ACCCCG
* *
49708 AAACTTCTAAAAATGCCATTTTTACCCCC
1 AAACTTCTAAAAATTCCATTTTTACCCCG
* * * *
49737 AAACTTCCAAAAATCCCATTTTAACCTCG
1 AAACTTCTAAAAATTCCATTTTTACCCCG
* *
49766 AAACTTCTAAAAATTCTATTTTTACACTCG
1 AAACTTCTAAAAATTCCATTTTTAC-CCCG
** *
49796 -AACTTCTAAAAACCCCATTTTTGACCTCG
1 AAACTTCTAAAAATTCCATTTTT-ACCCCG
49825 AAACTTCTAAAAATTCCATTTTTACCCTCG
1 AAACTTCTAAAAATTCCATTTTTACCC-CG
* *
49855 -AACTTCCAAAACTTCCA
1 AAACTTCTAAAAATTCCA
49872 AAATTCCATT
Statistics
Matches: 209, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
28 15 0.07
29 124 0.59
30 68 0.33
31 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTTCTAAAAATTCCATTTTTACCCCG
Found at i:49683 original size:58 final size:58
Alignment explanation
Indices: 49590--49871 Score: 354
Period size: 58 Copynumber: 4.8 Consensus size: 58
49580 AAGGTCCCAT
* *
49590 AAACTATCTAAAAATTCTATTTTTACCC-CAAAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACT-TCTAAAAATGC-ATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGACCTCG
*
49650 AAACTTTTAAAAATGCATTTTTACCCTCGAACTTCCAAAAA-TCCTATTTTTGACCTCG
1 AAACTTCTAAAAATGCATTTTTACCCTCGAACTTCCAAAAATTCC-ATTTTTGACCTCG
* * * *
49708 AAACTTCTAAAAATGCCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTAACCTCG
1 AAACTTCTAAAAATG-CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * **
49766 AAACTTCTAAAAATTCTATTTTTACACTCGAACTTCTAAAAACCCCATTTTTGACCTCG
1 AAACTTCTAAAAATGC-ATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* *
49825 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAACTTCCA
1 AAACTTCTAAAAA-TGCATTTTTACCCTCGAACTTCCAAAAATTCCA
49872 AAATTCCATT
Statistics
Matches: 194, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
57 4 0.02
58 98 0.51
59 83 0.43
60 9 0.05
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (58 bp):
AAACTTCTAAAAATGCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:49807 original size:117 final size:117
Alignment explanation
Indices: 49590--49865 Score: 410
Period size: 117 Copynumber: 2.4 Consensus size: 117
49580 AAGGTCCCAT
* * * *
49590 AAACTATCTAAAAATTCTATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGACCTCGAAACT
1 AAACT-TCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCGAAACT
* * * *
49655 TTTAAAAATGCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTGACCTCG
65 TCTAAAAATGCATTTTTACACTCGAACTTCCAAAAACCCCATTTTTGACCTCG
*
49708 AAACTTCTAAAAATGCCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTAACCTCGAAACTT
1 AAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTT
* *
49772 CTAAAAATTCTATTTTTACACTCGAACTTCTAAAAACCCCATTTTTGACCTCG
66 CTAAAAATGC-ATTTTTACACTCGAACTTCCAAAAACCCCATTTTTGACCTCG
* *
49825 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAA
1 AAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAA
49866 CTTCCAAAAT
Statistics
Matches: 143, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
116 24 0.17
117 114 0.80
118 5 0.03
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (117 bp):
AAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTT
CTAAAAATGCATTTTTACACTCGAACTTCCAAAAACCCCATTTTTGACCTCG
Found at i:49885 original size:38 final size:38
Alignment explanation
Indices: 49825--49903 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
49815 TTTGACCTCG
49825 AAACTTCTAAAAATTCCATTTTTACCCTCG-AACTTCCA
1 AAACTTCTAAAAATTCCATTTTTACCCT-GAAACTTCCA
* * *
49863 AAACTTC-CAAAATTCCATTTTTTATCCTGAAACTTTCA
1 AAACTTCTAAAAATTCCA-TTTTTACCCTGAAACTTCCA
49901 AAA
1 AAA
49904 ATTACCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 10 0.28
38 26 0.72
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (38 bp):
AAACTTCTAAAAATTCCATTTTTACCCTGAAACTTCCA
Found at i:49931 original size:29 final size:28
Alignment explanation
Indices: 49899--50035 Score: 100
Period size: 29 Copynumber: 4.7 Consensus size: 28
49889 CTGAAACTTT
49899 CAAAAATTACCATTTTACCCTAAAATGTC
1 CAAAAATTACCATTTTACCC-AAAATGTC
* **
49928 CAAAAACT-CCATTTTTGACCCAAAAACTC
1 CAAAAATTACCA-TTTT-ACCCAAAATGTC
* *
49957 TC-AAAATTACCCTTTTACCCCTAAATGTC
1 -CAAAAATTACCATTTTA-CCCAAAATGTC
* *
49986 CAAAAATT-CCATCTTTAATCCCAAATTTTC
1 CAAAAATTACCAT-TTT-A-CCCAAAATGTC
* *
50016 TAAAAATTACCATTTCACCC
1 CAAAAATTACCATTTTACCC
50036 CCGAGAATCC
Statistics
Matches: 84, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
28 11 0.13
29 44 0.52
30 25 0.30
31 4 0.05
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.31
Consensus pattern (28 bp):
CAAAAATTACCATTTTACCCAAAATGTC
Found at i:49941 original size:59 final size:57
Alignment explanation
Indices: 49871--50035 Score: 179
Period size: 58 Copynumber: 2.8 Consensus size: 57
49861 CAAAACTTCC
* *
49871 AAAATTCCATTTTTTATCCTGAAACTTTCAAAAATTACCATTTTACCCTAAAATGTCCA
1 AAAATTCCATTTTTAATCC-AAAACTTTCAAAAATTACCATTTTACCCT-AAATGTCCA
* * * * *
49930 AAAACTCCATTTTTGACCCAAAAACTCTC-AAAATTACCCTTTTACCCCTAAATGTCCA
1 AAAATTCCATTTTTAATCC-AAAACTTTCAAAAATTACCATTTTA-CCCTAAATGTCCA
* * * *
49988 AAAATTCCATCTTTAATCCCAAATTTTCTAAAAATTACCATTTCACCC
1 AAAATTCCATTTTTAATCCAAAACTTTC-AAAAATTACCATTTTACCC
50036 CCGAGAATCC
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
57 6 0.07
58 41 0.47
59 40 0.46
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (57 bp):
AAAATTCCATTTTTAATCCAAAACTTTCAAAAATTACCATTTTACCCTAAATGTCCA
Found at i:50036 original size:59 final size:60
Alignment explanation
Indices: 49871--50036 Score: 187
Period size: 59 Copynumber: 2.8 Consensus size: 60
49861 CAAAACTTCC
* * *
49871 AAAATTCCATTTTTTATCCTGAAACTTTC-AAAAATTACCATTTTA-CCCTAAAATGTCCA
1 AAAATTCCATTTTTAATCC-CAAAATTTCTAAAAATTACCATTTTACCCCTAAAATGTCCA
* * ** * *
49930 AAAACTCCATTTTTGA-CCCAAAAACTCTCAAAATTACCCTTTTACCCCT-AAATGTCCA
1 AAAATTCCATTTTTAATCCCAAAATTTCTAAAAATTACCATTTTACCCCTAAAATGTCCA
* * *
49988 AAAATTCCATCTTTAATCCCAAATTTTCTAAAAATTACCATTTCACCCC
1 AAAATTCCATTTTTAATCCCAAAATTTCTAAAAATTACCATTTTACCCC
50037 CGAGAATCCA
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
57 5 0.06
58 38 0.44
59 44 0.51
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (60 bp):
AAAATTCCATTTTTAATCCCAAAATTTCTAAAAATTACCATTTTACCCCTAAAATGTCCA
Found at i:50052 original size:28 final size:29
Alignment explanation
Indices: 50018--50078 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
50008 AAATTTTCTA
50018 AAAATTACCATTTCACCCCCGAGAATCC-
1 AAAATTACCATTTCACCCCCGAGAATCCG
* *
50046 AAAATTACCATTTTACCCCCGAGTATCCG
1 AAAATTACCATTTCACCCCCGAGAATCCG
50075 AAAA
1 AAAA
50079 GTCTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (29 bp):
AAAATTACCATTTCACCCCCGAGAATCCG
Done.