Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009547.1 Kokia drynarioides strain JFW-HI SEQ_124259, 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: 36048
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:811 original size:17 final size:17
Alignment explanation
Indices: 763--835 Score: 101
Period size: 17 Copynumber: 4.2 Consensus size: 17
753 AACTTTATTT
* *
763 ATTTTAAATAATTTTAA
1 ATTTAAAATAAATTTAA
780 ATTTGAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
* *
798 ACTTAAATTAAATTTAA
1 ATTTAAAATAAATTTAA
815 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
832 ATTT
1 ATTT
836 TTAGACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
17 35 0.71
18 14 0.29
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:814 original size:11 final size:11
Alignment explanation
Indices: 776--834 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
766 TTAAATAATT
776 TTAAATTTGAAA
1 TTAAATTT-AAA
*
788 ATAAATTTAAA
1 TTAAATTTAAA
799 CTTAAA-TTAAA
1 -TTAAATTTAAA
810 TTTAAATTTAAA
1 -TTAAATTTAAA
*
822 ATAAATTTAAA
1 TTAAATTTAAA
833 TT
1 TT
835 TTTAGACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:851 original size:6 final size:6
Alignment explanation
Indices: 775--835 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
765 TTTAAATAAT
* *
775 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
822 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
836 TTAGACAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.26
6 31 0.67
7 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:1303 original size:17 final size:17
Alignment explanation
Indices: 1259--1331 Score: 110
Period size: 17 Copynumber: 4.2 Consensus size: 17
1249 AACTTTATTT
* *
1259 ATTTTAAATAATTTTAA
1 ATTTAAAATAAATTTAA
1276 ATTTGAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
*
1294 ACTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
1311 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
1328 ATTT
1 ATTT
1332 TTAGACAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 37 0.73
18 14 0.27
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:1347 original size:6 final size:6
Alignment explanation
Indices: 1271--1331 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
1261 TTTAAATAAT
* * *
1271 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1318 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
1332 TTAGACAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
5 11 0.25
6 30 0.68
7 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:2248 original size:26 final size:26
Alignment explanation
Indices: 2200--2250 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2190 TTGTTATTAC
* * * *
2200 ATTTTAATAAGATTATTATTAAATAT
1 ATTTTAATAAAAATAATAATAAATAT
2226 ATTTTAATAAAAATAATAATAAATA
1 ATTTTAATAAAAATAATAATAAATA
2251 ATTAAATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTTAATAAAAATAATAATAAATAT
Found at i:2276 original size:61 final size:61
Alignment explanation
Indices: 2211--2372 Score: 190
Period size: 61 Copynumber: 2.7 Consensus size: 61
2201 TTTTAATAAG
* * *
2211 ATTATTATTAAATATATTTTAATAAAAATAATAATAAATAATTAAATCATATT-TTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAT-AATAATTAAATAACATTCTTAACATA
* *
2272 ATTATTATTAAATATAATTTAAT-AAAATAAT-AT-ATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTAAATAACATTCTTAACATA
* *
2330 ATTATTATTAAA-ATACGAATTAATAAAAATCATAATATATAAT
1 ATTATTATTAAATATA--ATTTAATAAAAATAATAATA-ATAAT
2373 GTCAAAACCT
Statistics
Matches: 87, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
57 16 0.18
58 19 0.22
59 8 0.09
60 15 0.17
61 24 0.28
63 5 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (61 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTAAATAACATTCTTAACATA
Found at i:2789 original size:17 final size:17
Alignment explanation
Indices: 2767--2821 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2757 AACTTTTCTT
*
2767 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAAATTAAA
*
2784 TTAAGTTTAAAATTAAT
1 TTAAGTTTAAAATTAAA
* *
2801 TTGAA-TTGAAAATTTAA
1 TT-AAGTTTAAAATTAAA
2818 TTAA
1 TTAA
2822 TTAAAAAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 2 0.06
17 28 0.88
18 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (17 bp):
TTAAGTTTAAAATTAAA
Found at i:4748 original size:29 final size:29
Alignment explanation
Indices: 4706--4939 Score: 205
Period size: 29 Copynumber: 8.0 Consensus size: 29
4696 CTTCCAAAAT
*
4706 TTCCAAATATTCCATTTTTACCTCCGAAC
1 TTCCAAAAATTCCATTTTTACCTCCGAAC
*
4735 TTCCAAAAATTCCATTTTTA-CTCCCAAAC
1 TTCCAAAAATTCCATTTTTACCT-CCGAAC
**
4764 TTCCAAAAATTCCATTTTTAACCTCAAAAC
1 TTCCAAAAATTCCATTTTT-ACCTCCGAAC
*
4794 TTCCAAAAATTTCATTTTTACC-CTCGAAAC
1 TTCCAAAAATTCCATTTTTACCTC-CG-AAC
*
4824 TTCCAAAAATCCCATTTTTTA--TCACGAAAC
1 TTCCAAAAATTCCA-TTTTTACCTC-CG-AAC
* *
4854 TTCCAAAAATTCCGTTTTTGTCCT-CGAAC
1 TTCCAAAAATTCCATTTTT-ACCTCCGAAC
* **
4883 TTCC-AAAATATCCATTTTCGACCTCAAAAC
1 TTCCAAAAAT-TCCATTTT-TACCTCCGAAC
*
4913 -TCCTAAAATTACCATTTTTACC-CCGAA
1 TTCCAAAAATT-CCATTTTTACCTCCGAA
4940 TGTCTAAAAA
Statistics
Matches: 170, Mismatches: 20, Indels: 31
0.77 0.09 0.14
Matches are distributed among these distances:
28 11 0.06
29 75 0.44
30 75 0.44
31 8 0.05
32 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCTCCGAAC
Found at i:4796 original size:30 final size:30
Alignment explanation
Indices: 4700--4932 Score: 217
Period size: 30 Copynumber: 7.9 Consensus size: 30
4690 TTCGAACTTC
* *
4700 CAAAATTTCCAAATATTCCATTTTT-ACCT
1 CAAAACTTCCAAAAATTCCATTTTTAACCT
**
4729 CCGAACTTCCAAAAATTCCATTTTT-A-CT
1 CAAAACTTCCAAAAATTCCATTTTTAACCT
*
4757 CCCAAACTTCCAAAAATTCCATTTTTAACCT
1 -CAAAACTTCCAAAAATTCCATTTTTAACCT
* *
4788 CAAAACTTCCAAAAATTTCATTTTTACCCT
1 CAAAACTTCCAAAAATTCCATTTTTAACCT
* * * * *
4818 CGAAACTTCCAAAAATCCCATTTTTTATCA
1 CAAAACTTCCAAAAATTCCATTTTTAACCT
* * **
4848 CGAAACTTCCAAAAATTCCGTTTTTGTCCT
1 CAAAACTTCCAAAAATTCCATTTTTAACCT
* **
4878 C-GAACTTCC-AAAATATCCATTTTCGACCT
1 CAAAACTTCCAAAAAT-TCCATTTTTAACCT
*
4907 CAAAAC-TCCTAAAATTACCATTTTTA
1 CAAAACTTCCAAAAATT-CCATTTTTA
4933 CCCCGAATGT
Statistics
Matches: 169, Mismatches: 28, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
28 7 0.04
29 69 0.41
30 91 0.54
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
CAAAACTTCCAAAAATTCCATTTTTAACCT
Found at i:4799 original size:59 final size:59
Alignment explanation
Indices: 4706--4935 Score: 252
Period size: 59 Copynumber: 3.9 Consensus size: 59
4696 CTTCCAAAAT
* **
4706 TTCCAAATATTCCATTTTT-ACCTCCGAACTTCCAAAAATTCCATTTTTACTCC-CAAAC
1 TTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTAC-CCTCAAAC
*
4764 TTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTTCATTTTTACCCTCGAAAC
1 TTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCTC-AAAC
* * * * * * ** *
4824 TTCCAAAAATCCCATTTTTTATCACGAAACTTCCAAAAATTCCGTTTTTGTCCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCAAAC
** *
4883 TTCC-AAAATATCCATTTTCGACCTCAAAAC-TCCTAAAATTACCATTTTTACCC
1 TTCCAAAAAT-TCCATTTTTAACCTCAAAACTTCCAAAAATT-CCATTTTTACCC
4936 CGAATGTCTA
Statistics
Matches: 143, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
58 34 0.24
59 59 0.41
60 50 0.35
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCAAAC
Found at i:4854 original size:60 final size:59
Alignment explanation
Indices: 4706--4982 Score: 228
Period size: 59 Copynumber: 4.7 Consensus size: 59
4696 CTTCCAAAAT
* * **
4706 TTCCAAATATTCCATTTTT-ACCTCCGAACTTCCAAAAATTCCATTTTTACTCC-C-AAAC
1 TTCCAAA-AATCCATTTTTAACCACAAAACTTCCAAAAATTCCATTTTTAC-CCTCGAAAC
* *
4764 TTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTTCATTTTTACCCTCGAAAC
1 TTCCAAAAA-TCCATTTTTAACCACAAAACTTCCAAAAATTCCATTTTTACCCTCGAAAC
* * * * **
4824 TTCCAAAAATCCCATTTTTTATCACGAAACTTCCAAAAATTCCGTTTTTGTCCTCG-AAC
1 TTCCAAAAAT-CCATTTTTAACCACAAAACTTCCAAAAATTCCATTTTTACCCTCGAAAC
** * *
4883 TTCCAAAATATCCATTTTCGACCTCAAAAC-TCCTAAAATTACCATTTTTACCC-CG-AA-
1 TTCCAAAA-ATCCATTTTTAACCACAAAACTTCCAAAAATT-CCATTTTTACCCTCGAAAC
* * * **
4940 TGTCTAAAAATACCCTTTTTAAACCCCAAATTTTCCAAAAATT
1 T-TCCAAAAAT-CCATTTTT-AACCACAAAACTTCCAAAAATT
4983 ACCAATTTGG
Statistics
Matches: 179, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
57 4 0.02
58 43 0.24
59 71 0.40
60 61 0.34
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (59 bp):
TTCCAAAAATCCATTTTTAACCACAAAACTTCCAAAAATTCCATTTTTACCCTCGAAAC
Found at i:9784 original size:52 final size:52
Alignment explanation
Indices: 9706--9897 Score: 215
Period size: 52 Copynumber: 3.7 Consensus size: 52
9696 TTTTCACTTC
* * *
9706 ATTCATATACTTACGATGACATATAGTCATCGGACCTCATAATCCATAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
* * * ** * * *
9758 ATTCATATACCCACGATGAAACATAGTTATTAGA-CTTATTAATCTGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCA-TAATCCGTAAGGG
* * *
9810 ATTCATATACTCACGATGACACATAGCCACCGGACCTCATAATTCGTAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
* * *
9862 ATTCATATAATCACAATGACACAGAGTCATCGGACC
1 ATTCATATACTCACGATGACACATAGTCATCGGACC
9898 ACTTCATTTA
Statistics
Matches: 111, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
51 3 0.03
52 105 0.95
53 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
Found at i:10790 original size:20 final size:20
Alignment explanation
Indices: 10761--10799 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
10751 TTTTATAATT
10761 AACCTAATTAATC-CACTTG
1 AACCTAATTAATCTCACTTG
10780 AACCTTAATTAATCTCACTT
1 AACC-TAATTAATCTCACTT
10800 TTAAGCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (20 bp):
AACCTAATTAATCTCACTTG
Found at i:18421 original size:30 final size:29
Alignment explanation
Indices: 18389--18638 Score: 181
Period size: 30 Copynumber: 8.5 Consensus size: 29
18379 AATCGAGATA
18389 AAAAATGGAATTTTTAGACA-TTCGAGGGT
1 AAAAATGGAATTTTTAGA-AGTTCGAGGGT
* ***
18418 -AAAATGGTAATTTTTTGAAAGTTTTTGGGTT
1 AAAAATGG-AATTTTTAG-AAGTTCGAGGG-T
* *
18449 AAAAATGGAATTTTTAGAGGTTTTG-GGGT
1 AAAAATGGAATTTTTAGAAG-TTCGAGGGT
* * *
18478 -AAAATGTAATTTTTAGAAGTTTGGGGGT
1 AAAAATGGAATTTTTAGAAGTTCGAGGGT
* *
18506 AAAAAATGTAATTTTT-GAAAGTTTC-AAGGT
1 -AAAAATGGAATTTTTAG-AAG-TTCGAGGGT
*
18536 CAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTAGAAGTTCGAGGGT
** * *
18566 AAAAATATAATTTTTGGAAGTTTTG-GGGTT
1 AAAAATGGAATTTTTAGAAG-TTCGAGGG-T
* *
18596 ATAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTAGAAGTTCGAGGGT
*
18625 AAAAATGTAATTTT
1 AAAAATGGAATTTT
18639 CAAATAGTTT
Statistics
Matches: 181, Mismatches: 24, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
27 4 0.02
28 28 0.15
29 51 0.28
30 76 0.42
31 15 0.08
32 7 0.04
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (29 bp):
AAAAATGGAATTTTTAGAAGTTCGAGGGT
Found at i:18491 original size:88 final size:87
Alignment explanation
Indices: 18390--18551 Score: 211
Period size: 88 Copynumber: 1.8 Consensus size: 87
18380 ATCGAGATAA
*** *
18390 AAAATGGAATTTTTAGACA-TTCGAGGGT-AAAATGGTAATTTTTTGAAAGTTTTTGGGTTAAAA
1 AAAATGGAATTTTTAGA-AGTTCGAGGGTAAAAAT-GTAA-TTTTTGAAAGTTTCAAGGTCAAAA
18453 ATGGAATTTTTAGAGGTTTTGGGGT
63 ATGGAATTTTTAGAGGTTTTGGGGT
* * *
18478 AAAATGTAATTTTTAGAAGTTTGGGGGTAAAAAATGTAATTTTTGAAAGTTTCAAGGTCAAAAAT
1 AAAATGGAATTTTTAGAAGTTCGAGGGT-AAAAATGTAATTTTTGAAAGTTTCAAGGTCAAAAAT
18543 GGAATTTTT
65 GGAATTTTT
18552 GGAAGTTCGA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
87 1 0.02
88 54 0.84
89 4 0.06
90 5 0.08
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.39
Consensus pattern (87 bp):
AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCAAGGTCAAAAATG
GAATTTTTAGAGGTTTTGGGGT
Found at i:18602 original size:59 final size:58
Alignment explanation
Indices: 18448--18638 Score: 231
Period size: 59 Copynumber: 3.3 Consensus size: 58
18438 GTTTTTGGGT
* * * * * * *
18448 TAAAAATGGAATTTTTAGAGGTTTTGGGG-TAAAATGTAATTTTTAGAAGTTTGGGGG
1 TAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAAATGGAATTTTTGGAAGTTCGAGGG
* *** *
18505 TAAAAAATGTAATTTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGG
1 T-AAAAATGTAATTTTTGGAAGTTTTGGGGT-TAAAATGGAATTTTTGGAAGTTCGAGGG
*
18565 TAAAAATATAATTTTTGGAAGTTTTGGGGTTATAAATGGAATTTTTGGAAGTTCGAGGG
1 TAAAAATGTAATTTTTGGAAGTTTTGGGGTTA-AAATGGAATTTTTGGAAGTTCGAGGG
18624 TAAAAATGTAATTTT
1 TAAAAATGTAATTTT
18639 CAAATAGTTT
Statistics
Matches: 111, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
57 1 0.01
58 22 0.20
59 64 0.58
60 24 0.22
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (58 bp):
TAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAAATGGAATTTTTGGAAGTTCGAGGG
Found at i:20691 original size:6 final size:6
Alignment explanation
Indices: 20680--20746 Score: 61
Period size: 6 Copynumber: 11.7 Consensus size: 6
20670 ATTTTGAAAA
* * *
20680 TAAATT TAAATT TAAGA-T T-AATT TAAATT CAAATT TAAA-A TAAATC
1 TAAATT TAAATT TAA-ATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
20726 TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
20747 AGGGGCCCGG
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 1 0.02
5 11 0.22
6 36 0.73
7 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:20706 original size:23 final size:23
Alignment explanation
Indices: 20680--20735 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
20670 ATTTTGAAAA
* * *
20680 TAAATTTAAATTTAAGATTAATT
1 TAAATTTAAATTTAAAATAAATC
*
20703 TAAATTCAAATTTAAAATAAATC
1 TAAATTTAAATTTAAAATAAATC
20726 TAAATTTAAA
1 TAAATTTAAA
20736 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATAAATC
Found at i:20723 original size:17 final size:18
Alignment explanation
Indices: 20703--20746 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
20693 AAGATTAATT
20703 TAAATTC-AAATTTAAAA
1 TAAATTCTAAATTTAAAA
20720 TAAA-TCTAAATTTAAAA
1 TAAATTCTAAATTTAAAA
20737 TAAATT-TAAA
1 TAAATTCTAAA
20747 AGGGGCCCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTCTAAATTTAAAA
Found at i:21888 original size:51 final size:51
Alignment explanation
Indices: 21832--21990 Score: 128
Period size: 51 Copynumber: 3.1 Consensus size: 51
21822 AAAAAACTCA
*
21832 AAAACTCAAAAAAATGTGTTATATACTTCTTGAATGCTAAAATGTCTATCT
1 AAAACTCAAAAAAATGTGTTATATACTTCTTGAATGATAAAATGTCTATCT
* * * * * ** * * * **
21883 AAAACTTCAAGAAATTCAT-TTA-AAAATTCAATAAAATTATAAAA-ATATA-AA
1 AAAAC-TCAAAAAAAT-GTGTTATATACTTC--TTGAATGATAAAATGTCTATCT
*
21934 AAAACTCAAAAAAATGTGTTATATACTTCTTGAATGGTAAAATGTCTATCT
1 AAAACTCAAAAAAATGTGTTATATACTTCTTGAATGATAAAATGTCTATCT
21985 AAAACT
1 AAAACT
21991 TTAATAAATT
Statistics
Matches: 74, Mismatches: 26, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
49 10 0.14
50 14 0.19
51 26 0.35
52 14 0.19
53 10 0.14
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (51 bp):
AAAACTCAAAAAAATGTGTTATATACTTCTTGAATGATAAAATGTCTATCT
Found at i:22244 original size:208 final size:209
Alignment explanation
Indices: 21839--22413 Score: 854
Period size: 208 Copynumber: 2.7 Consensus size: 209
21829 TCAAAAACTC
* *
21839 AAAAAAATGTGTT-ATATACTTCTTGAATGCTAAAATGTCTATCTAAAACTTCAAGAAATTCATT
1 AAAAAAATGTGTTAAT-TACTTCTTGAATGGTAAAATGTCTATCTAAAACTTTAAGAAATTCATT
** **
21903 TAAAAATTCAATAAAATTATAAAAA-TATAAAAAAACTC-AAAAAAATGTGTT-ATATACTTCTT
65 TAAAAATTCAATAAAATTATAAAAAGT-TACGAAATTTCAAAAAAAATGTGTTAAT-TACTTCTT
* *
21965 GAATGGTAAAATGTCTATCTAAAACTTTAATAAATTCATTTAAAAATTCAATAAAATTATAAAAA
128 GAATGGTAAAATGTCTATCTAAAACATTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAA
22030 GTTCCGAAATTTC-AAA
193 GTTCCGAAATTTCAAAA
* *
22046 AAAAAAATGTGTTAATTACTTCTTGAATGGTAAAATGTTTATCCAAAACTTTAAGAAATTCATTT
1 AAAAAAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCTAAAACTTTAAGAAATTCATTT
*
22111 AAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTCAAAAAAAATGTGTTAATTACTTCTTGAA
66 AAAAATTCAATAAAATTATAAAAAGTTACGAAATTTCAAAAAAAATGTGTTAATTACTTCTTGAA
22176 TGGTAAAATGTCTATCTAAAACATTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTT
131 TGGTAAAATGTCTATCTAAAACATTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTT
22241 CCGAAATTTCAAAAAAA
196 CCGAAATTTC---AAAA
* * * *
22258 AAAAAAAAGTGTTAATTACTTCTGGAACGGTCAAATGTCTATCTAAAACTTTAAGAAATTCATTT
1 AAAAAAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCTAAAACTTTAAGAAATTCATTT
* *
22323 AAAAATTCAATAAAATTATAAAAAGTTTCGAAATTTCAAAAAAAAAAAAAAAGTGTTAATTACTT
66 AAAAATTCAATAAAATTATAAAAAGTTACGAAATTTC------AAAAAAAATGTGTTAATTACTT
22388 CTTGAATGGTAAAATGTCTATCTAAA
125 CTTGAATGGTAAAATGTCTATCTAAA
22414 GTTTGAATGG
Statistics
Matches: 335, Mismatches: 19, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
207 88 0.26
208 100 0.30
209 2 0.01
212 98 0.29
218 47 0.14
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (209 bp):
AAAAAAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCTAAAACTTTAAGAAATTCATTT
AAAAATTCAATAAAATTATAAAAAGTTACGAAATTTCAAAAAAAATGTGTTAATTACTTCTTGAA
TGGTAAAATGTCTATCTAAAACATTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTT
CCGAAATTTCAAAA
Found at i:22327 original size:109 final size:105
Alignment explanation
Indices: 21580--22413 Score: 928
Period size: 109 Copynumber: 8.0 Consensus size: 105
21570 ATAAAAATAA
* ** **
21580 AAAATTTTAA-AAATTCATTT-AATTTTCAATAAAAATTATAAAAA-TAT-AAAAATTTCAAAAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAAT-AAAATTATAAAAAGT-TCCGAAATTTCAAAAA
* * *
21641 AAAAATTGTGTTATTTGCTTCTTCAATGGTAAAATGTCTATCT
64 AAAAA-TGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
* * * * *
21684 AAAATTTTAGGAAATTCATTTAAAAATT-AATTAAAATTAT-AAAA-CTCCAAAAATT-AAAAAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAA-TAAAATTATAAAAAGTTCCGAAATTTCAAAAAA
* * * *
21745 AAAA-GTGTTATTTGCTTCTTCAATGGTAAAATGTGCTATTT
65 AAAATGTGTTAATTACTTCTTGAATGGTAAAATGT-CTATCT
**** * * ** * **
21786 GTTTCTTTAA-AAATTCA-AT-AAAATT--ATAAAAATATAAAAA-AACTCAAAAACTC---AAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTC-CGAAATTTCAAAAAA
*
21842 AAAATGTGTT-ATATACTTCTTGAATGCTAAAATGTCTATCT
65 AAAATGTGTTAAT-TACTTCTTGAATGGTAAAATGTCTATCT
* *** **
21883 AAAACTTCAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAA-TATAAAAAAACTC---AAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGT-TCCGAAATTTCAAAAAA
21944 AAAATGTGTT-ATATACTTCTTGAATGGTAAAATGTCTATCT
65 AAAATGTGTTAAT-TACTTCTTGAATGGTAAAATGTCTATCT
*
21985 AAAACTTTAATAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTCAAAAAAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTCAAAAAAA
* *
22050 AAATGTGTTAATTACTTCTTGAATGGTAAAATGTTTATCC
66 AAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
22090 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTC--AAAAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTCAAAAAAA
22153 AAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
66 AAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
*
22193 AAAACATTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTCAAAAAAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTC----AAA
* * * *
22258 AAAAAAAAGTGTTAATTACTTCTGGAACGGTCAAATGTCTATCT
62 AAAAAAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
*
22302 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTTCGAAATTTCAAAAAAA
1 AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTC----AAA
*
22367 AAAAAAAAGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
62 AAAAAAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
22411 AAA
1 AAA
22414 GTTTGAATGG
Statistics
Matches: 646, Mismatches: 57, Indels: 49
0.86 0.08 0.07
Matches are distributed among these distances:
97 26 0.04
98 37 0.06
99 14 0.02
100 7 0.01
101 37 0.06
102 123 0.19
103 112 0.17
104 19 0.03
105 116 0.18
106 7 0.01
109 148 0.23
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (105 bp):
AAAACTTTAAGAAATTCATTTAAAAATTCAATAAAATTATAAAAAGTTCCGAAATTTCAAAAAAA
AAATGTGTTAATTACTTCTTGAATGGTAAAATGTCTATCT
Found at i:23952 original size:21 final size:19
Alignment explanation
Indices: 23926--23964 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
23916 TATTATTTTT
23926 AATTAAATTATATATTATAAA
1 AATT-AATT-TATATTATAAA
*
23947 AATTAATTTTTATTATAA
1 AATTAATTTATATTATAA
23965 TTATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAATTTATATTATAAA
Found at i:24734 original size:266 final size:266
Alignment explanation
Indices: 24256--24788 Score: 1048
Period size: 266 Copynumber: 2.0 Consensus size: 266
24246 CCTCCTATTT
24256 AAGGATTGAGAAAGATCTATGTGTAGTTCTAAGCATTGTATCGAAAAGAACAAATATGATAAGAA
1 AAGGATTGAGAAAGATCTATGTGTAGTTCTAAGCATTGTATCGAAAAGAACAAATATGATAAGAA
24321 CCTATACATTCAAATATGTACATATTTCAAATGTCATTATGATTAATTAGTTTCAAACCATATCT
66 CCTATACATTCAAATATGTACATATTTCAAATGTCATTATGATTAATTAGTTTCAAACCATATCT
24386 TTCATTAGTTATTGTGTGTTATTTTTAAAAACTCATTTTTGTTTTAAATCCGTGGTTTTCACACA
131 TTCATTAGTTATTGTGTGTTATTTTTAAAAACTCATTTTTGTTTTAAATCCGTGGTTTTCACACA
*
24451 CATATGCGTGTTGATAGGTTTTTTAGTATAACTTATTTTAATTACGTAAGGATATTTTTGTAATT
196 CATATGCGTGATGATAGGTTTTTTAGTATAACTTATTTTAATTACGTAAGGATATTTTTGTAATT
24516 TTTCTG
261 TTTCTG
*
24522 AAGGATTGAGAAAGATCTATGTGTAGTTTTAAGCATTGTATCGAAAAGAACAAATATGATAAGAA
1 AAGGATTGAGAAAGATCTATGTGTAGTTCTAAGCATTGTATCGAAAAGAACAAATATGATAAGAA
24587 CCTATACATTCAAATATGTACATATTTCAAATGTCATTATGATTAATTAGTTTCAAACCATATCT
66 CCTATACATTCAAATATGTACATATTTCAAATGTCATTATGATTAATTAGTTTCAAACCATATCT
24652 TTCATTAGTTATTGTGTGTTATTTTTAAAAACTCATTTTTGTTTTAAATCCGTGGTTTTCACACA
131 TTCATTAGTTATTGTGTGTTATTTTTAAAAACTCATTTTTGTTTTAAATCCGTGGTTTTCACACA
24717 CATATGCGTGATGATAGGTTTTTTAGTATAACTTATTTTAATTACGTAAGGATATTTTTGTAATT
196 CATATGCGTGATGATAGGTTTTTTAGTATAACTTATTTTAATTACGTAAGGATATTTTTGTAATT
24782 TTTCTG
261 TTTCTG
24788 A
1 A
24789 TCAAGTTGAT
Statistics
Matches: 265, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 265 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (266 bp):
AAGGATTGAGAAAGATCTATGTGTAGTTCTAAGCATTGTATCGAAAAGAACAAATATGATAAGAA
CCTATACATTCAAATATGTACATATTTCAAATGTCATTATGATTAATTAGTTTCAAACCATATCT
TTCATTAGTTATTGTGTGTTATTTTTAAAAACTCATTTTTGTTTTAAATCCGTGGTTTTCACACA
CATATGCGTGATGATAGGTTTTTTAGTATAACTTATTTTAATTACGTAAGGATATTTTTGTAATT
TTTCTG
Found at i:26548 original size:6 final size:6
Alignment explanation
Indices: 26531--26571 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
26521 CCCGAAACCC
* *
26531 CAGCCA CCGCCA CAGCCA CAGCCA CAGCCA CAGCTA CAGCC
1 CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCC
26572 CGAATTGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.29, C:0.51, G:0.17, T:0.02
Consensus pattern (6 bp):
CAGCCA
Found at i:34683 original size:23 final size:23
Alignment explanation
Indices: 34657--34766 Score: 111
Period size: 23 Copynumber: 4.8 Consensus size: 23
34647 GCTGGGGAAA
34657 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCAAAT
*
34679 CCAGTAAACACACACAGTGC-AAT
1 -CAGTAAGCACACACAGTGCAAAT
* * * *
34702 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
*
34725 CAGTAGGCACACGA-AGTGCGAAAT
1 CAGTAAGCACAC-ACAGTGC-AAAT
34749 -AGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
34767 TGAACAGTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
22 15 0.20
23 54 0.73
24 5 0.07
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:34879 original size:24 final size:26
Alignment explanation
Indices: 34841--34888 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
34831 TCTACATGTG
34841 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
34867 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
34889 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.