Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013071.1 Kokia drynarioides strain JFW-HI SEQ_128089, 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: 52890
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:1183 original size:16 final size:16
Alignment explanation
Indices: 1139--1187 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
1129 AGGTCAAGCG
*
1139 AAAATAATT-TTTTTA
1 AAAATAATTAATTTTA
*
1154 AAATTAA--AATTTTTA
1 AAAATAATTAA-TTTTA
1169 AAAATAATTAATTTTA
1 AAAATAATTAATTTTA
1185 AAA
1 AAA
1188 TAGACAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 17 0.63
16 8 0.30
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAATTAATTTTA
Found at i:13207 original size:19 final size:20
Alignment explanation
Indices: 13168--13208 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13158 AGCAATATAA
*
13168 TATAAACAAATATCTATATT
1 TATAAACAAACATCTATATT
*
13188 TATATACAAACATC-ATATT
1 TATAAACAAACATCTATATT
13207 TA
1 TA
13209 AACAAATCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAACAAACATCTATATT
Found at i:13728 original size:15 final size:16
Alignment explanation
Indices: 13698--13731 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13688 GATAGAATCA
13698 AATTAAATTGGGAAAC
1 AATTAAATTGGGAAAC
*
13714 AATTTAATT-GGAAAC
1 AATTAAATTGGGAAAC
13729 AAT
1 AAT
13732 ATCAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (16 bp):
AATTAAATTGGGAAAC
Found at i:16836 original size:30 final size:30
Alignment explanation
Indices: 16800--16862 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
16790 ACTTAACAAG
* *
16800 CAAATGCCTCTAAAATAGTAACAAATTTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
16830 CAAATGCCTCTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
16860 CAA
1 CAA
16863 TACAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:16981 original size:24 final size:25
Alignment explanation
Indices: 16943--16990 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
16933 AAAATAGGAG
* * *
16943 AAAACAACAAGAAAATAA-CATTTA
1 AAAACAAAAAAAAAAAAAGCATTTA
16967 AAAACAAAAAAAAAAAAAGCATTT
1 AAAACAAAAAAAAAAAAAGCATTT
16991 TTTTGTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.71, C:0.10, G:0.04, T:0.15
Consensus pattern (25 bp):
AAAACAAAAAAAAAAAAAGCATTTA
Found at i:19543 original size:90 final size:90
Alignment explanation
Indices: 19365--19543 Score: 218
Period size: 90 Copynumber: 2.0 Consensus size: 90
19355 ACCTTTATAA
* ** * *
19365 TACACAAATTTATAGTTCATGTATCATATTGAATATTTTCAAAGTATGAATACTACATTGGATAT
1 TACACAAATTGATAGTTCAAATACCATATTGAATATTTTCAAAGTATG-ATACTACATTGAATAT
* * **
19430 TTTATAAAAGTACATGTTCCAAATAG
65 TTTATAAAAATACAGGTAACAAATAG
*
19456 TACACAAATTGATGGTTCAAATACCATATTGAATA-TTTCAAAGTACATG-TACTACATTGAATA
1 TACACAAATTGATAGTTCAAATACCATATTGAATATTTTCAAAGT--ATGATACTACATTGAATA
*
19519 TTTTATAAAAATATAGGTAACAAAT
64 TTTTATAAAAATACAGGTAACAAAT
19544 GTGATATTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
90 42 0.56
91 30 0.40
92 3 0.04
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (90 bp):
TACACAAATTGATAGTTCAAATACCATATTGAATATTTTCAAAGTATGATACTACATTGAATATT
TTATAAAAATACAGGTAACAAATAG
Found at i:26904 original size:41 final size:41
Alignment explanation
Indices: 26841--26937 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 41
26831 GTAGAGCAAT
* * * * *
26841 AGCGTCGCTAAAGATCATAGCAATAGCGGCGCTTATGGGCAA
1 AGCGCCGCTAAAGATCAGAGCAATAACGACGCTTAT-GACAA
* *
26883 A-CGCCGCTAAAGGTCAGAGCAATAACGACGCTTATGATAA
1 AGCGCCGCTAAAGATCAGAGCAATAACGACGCTTATGACAA
26923 AGCGCCGCTAAAGAT
1 AGCGCCGCTAAAGAT
26938 TAAAACAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 4 0.09
41 41 0.89
42 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.18
Consensus pattern (41 bp):
AGCGCCGCTAAAGATCAGAGCAATAACGACGCTTATGACAA
Found at i:29968 original size:16 final size:16
Alignment explanation
Indices: 29947--29978 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29937 CAGAGCAATA
29947 TAACTTCGTGCTTATT
1 TAACTTCGTGCTTATT
29963 TAACTTCGTGCTTATT
1 TAACTTCGTGCTTATT
29979 ACGGTGAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (16 bp):
TAACTTCGTGCTTATT
Found at i:30726 original size:43 final size:43
Alignment explanation
Indices: 30623--30800 Score: 164
Period size: 43 Copynumber: 4.2 Consensus size: 43
30613 GGCGTTCGTG
* *
30623 GGAAAAGTGTCGCTAAAGACCATGGTCTTTAGC-AGCGTTTG-T
1 GGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCGA-CGTTTGTT
* * * * *
30665 GAGAGAAGAGCCGTTAAAGACTATGTTCTTTAGCGACGTTTGTT
1 G-GAAAAGCGTCGCTAAAGACCATGTTCTTTAGCGACGTTTGTT
* * ** *
30709 GGAAAAGCGTCGCTAAAGACCATGTTTTTTAACGGGGTTTGTG
1 GGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCGACGTTTGTT
* * * **
30752 GGAAAAGCGTCGTTAAAGACTATGTTTTTTAGCGGGGTTT-TT
1 GGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCGACGTTTGTT
30794 GGAAAAG
1 GGAAAAG
30801 TTCCTTTAGC
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
42 9 0.08
43 101 0.89
44 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (43 bp):
GGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCGACGTTTGTT
Found at i:30768 original size:86 final size:85
Alignment explanation
Indices: 30623--30800 Score: 230
Period size: 86 Copynumber: 2.1 Consensus size: 85
30613 GGCGTTCGTG
* * *
30623 GGAAAAGTGTCGCTAAAGACCATGGTCTTTAGCAGCGTTTGTGAGAGAAGAGCCGTTAAAGACTA
1 GGAAAAGCGTCGCTAAAGACCATGGTCTTTAACAGCGTTTGTGAGAAAAGAGCCGTTAAAGACTA
30688 TGTTCTTTAGCGACGTTTGTT
66 TGTTCTTTAGCGACGTTT-TT
* * * * * * *
30709 GGAAAAGCGTCGCTAAAGACCATGTTTTTTAACGGGGTTTGTGGGAAAAGCGTCGTTAAAGACTA
1 GGAAAAGCGTCGCTAAAGACCATGGTCTTTAACAGCGTTTGTGAGAAAAGAGCCGTTAAAGACTA
* **
30774 TGTTTTTTAGCGGGGTTTTT
66 TGTTCTTTAGCGACGTTTTT
30794 GGAAAAG
1 GGAAAAG
30801 TTCCTTTAGC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 9 0.11
86 70 0.89
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (85 bp):
GGAAAAGCGTCGCTAAAGACCATGGTCTTTAACAGCGTTTGTGAGAAAAGAGCCGTTAAAGACTA
TGTTCTTTAGCGACGTTTTT
Found at i:37077 original size:26 final size:26
Alignment explanation
Indices: 37048--37128 Score: 144
Period size: 26 Copynumber: 3.1 Consensus size: 26
37038 TTTAGTTGTT
* *
37048 ATATTTGGGTTTTATTTAATAATTAA
1 ATATTTGAGTTGTATTTAATAATTAA
37074 ATATTTGAGTTGTATTTAATAATTAA
1 ATATTTGAGTTGTATTTAATAATTAA
37100 ATATTTGAGTTGTATTTAATAATTAA
1 ATATTTGAGTTGTATTTAATAATTAA
37126 ATA
1 ATA
37129 GTTCGATTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATATTTGAGTTGTATTTAATAATTAA
Found at i:37278 original size:122 final size:121
Alignment explanation
Indices: 37120--38014 Score: 1239
Period size: 122 Copynumber: 7.4 Consensus size: 121
37110 TGTATTTAAT
* * *
37120 AATTAAATAGTTCGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTCAATATTTG
1 AATTAAATA-TTTGATTTAGAGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTG
* * *
37185 TTATGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
65 TTCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
* * * * * *
37242 ATTTGAATATTTCGATTTAAAGTTTAATTAATAACTAATTCCAATAATCAATTATTTTAATATTT
1 AATTAAATATTT-GATTTAGAGTTTAATAAATAACTAATT-AAATAATTAATTATTTTAATATTT
37307 GTTCTATTTTTAATAATTGAATATTTA-TTAAATATAATTAAATAATTTAATATTTTG
64 GTTCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
* * * **
37364 AATTGAATATTTCGATATAAAGTTTAATAAATAACTAATGCCAATAATTAATTATTTTAATATTT
1 AATTAAATATTT-GATTTAGAGTTTAATAAATAACTAAT-TAAATAATTAATTATTTTAATATTT
*
37429 GTTCTATTTTTAATAATTGAATTTTTATTT-AATATAATTAAATAATTTAATATTTTG
64 GTTCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
* *
37486 AATTAAATATTTGAGCTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTG
1 AATTAAATATTTGA-TTTAGAGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTG
* *
37551 TTCTATTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAGTATTTTG
65 TTCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
* * ** *
37608 AATTAAATATTTTGATTTAGGGTTTGATAAATAACTAATGCCAATAATTAATTGTTTTAATATTT
1 AATTAAATA-TTTGATTTAGAGTTTAATAAATAACTAAT-TAAATAATTAATTATTTTAATATTT
37673 GTTCTATTTTTAATAATTGAATATTTATTT-AATATAATTAAATAATTTAATATTTTG
64 GTTCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
*
37730 AATTAAATATTTGAGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTG
1 AATTAAATATTTGA-TTTAGAGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTG
* * * *
37795 TTCTGTTTTTGATAATTTAGTATTTATTTAAATATAATTAAATAATTTAATATTTTG
65 TTCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
* **
37852 AA-T---TA---G-----G-GTGTAATAAATAACTAATGCCAATAATTAATTATTTTAATATTTG
1 AATTAAATATTTGATTTAGAGTTTAATAAATAACTAAT-TAAATAATTAATTATTTTAATATTTG
*
37904 TTCTATTTTAAATAATTGAATATTTATTT-AATATAATTAAATAATTTAATATTTTG
65 TTCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
*
37960 AATTGAATATTTGAGTTTAGAGTTTAATAAATAACTAATTAAATAATTAATTATT
1 AATTAAATATTTGA-TTTAGAGTTTAATAAATAACTAATTAAATAATTAATTATT
38015 GGCATTTTGA
Statistics
Matches: 694, Mismatches: 54, Indels: 51
0.87 0.07 0.06
Matches are distributed among these distances:
108 46 0.07
109 50 0.07
112 2 0.00
115 2 0.00
118 2 0.00
121 124 0.18
122 365 0.53
123 103 0.15
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (121 bp):
AATTAAATATTTGATTTAGAGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTGT
TCTATTTTTAATAATTGAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
Found at i:37298 original size:59 final size:59
Alignment explanation
Indices: 37225--37421 Score: 147
Period size: 59 Copynumber: 3.3 Consensus size: 59
37215 AATATAATTA
37225 AATAATTTAA-TATTTTGATTTGAATATTTCGATTTAAAGTTTAATTAATAACTAATTCC
1 AATAA-TTAATTATTTTGATTTGAATATTTCGATTTAAAGTTTAATTAATAACTAATTCC
* * ** **
37284 AATAATCAATTATTTTAATATTTGTTCTATTTTTAATAATTGAATA-TTT-ATTAA-ATA-TAAT
1 AATAATTAATTATTTT--GATTTG-AATA-TTTCGAT--TT-AA-AGTTTAATTAATA-ACTAAT
*
37345 T-A
57 TCC
* * * *
37347 AATAATTTAA-TATTTTGAATTGAATATTTCGATATAAAGTTTAATAAATAACTAATGCC
1 AATAA-TTAATTATTTTGATTTGAATATTTCGATTTAAAGTTTAATTAATAACTAATTCC
37406 AATAATTAATTATTTT
1 AATAATTAATTATTTT
37422 AATATTTGTT
Statistics
Matches: 103, Mismatches: 18, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
55 1 0.01
56 5 0.05
57 6 0.06
58 12 0.12
59 27 0.26
60 2 0.02
61 9 0.09
62 2 0.02
63 16 0.16
64 9 0.09
65 8 0.08
66 5 0.05
67 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (59 bp):
AATAATTAATTATTTTGATTTGAATATTTCGATTTAAAGTTTAATTAATAACTAATTCC
Found at i:37903 original size:109 final size:108
Alignment explanation
Indices: 37746--37963 Score: 348
Period size: 108 Copynumber: 2.0 Consensus size: 108
37736 ATATTTGAGT
** * *
37746 TTAGGGTTTAATAAATAACTAAT-TAAATAATTAATTATTTTAATATTTGTTCTGTTTTTGATAA
1 TTAGGGTTTAATAAATAACTAATGCCAATAATTAATTATTTTAATATTTGTTCTATTTTTAATAA
* *
37810 TTTAGTATTTATTTAAATATAATTAAATAATTTAATATTTTGAA
66 TTGAATATTTATTT-AATATAATTAAATAATTTAATATTTTGAA
* *
37854 TTAGGGTGTAATAAATAACTAATGCCAATAATTAATTATTTTAATATTTGTTCTATTTTAAATAA
1 TTAGGGTTTAATAAATAACTAATGCCAATAATTAATTATTTTAATATTTGTTCTATTTTTAATAA
37919 TTGAATATTTATTTAATATAATTAAATAATTTAATATTTTGAA
66 TTGAATATTTATTTAATATAATTAAATAATTTAATATTTTGAA
37962 TT
1 TT
37964 GAATATTTGA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 53 0.52
109 48 0.48
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (108 bp):
TTAGGGTTTAATAAATAACTAATGCCAATAATTAATTATTTTAATATTTGTTCTATTTTTAATAA
TTGAATATTTATTTAATATAATTAAATAATTTAATATTTTGAA
Found at i:37931 original size:21 final size:22
Alignment explanation
Indices: 37910--37951 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
37900 TTTGTTCTAT
*
37910 TTTAA-ATAATTGAAT-ATTTA
1 TTTAATATAATTAAATAATTTA
37930 TTTAATATAATTAAATAATTTA
1 TTTAATATAATTAAATAATTTA
37952 ATATTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAATATAATTAAATAATTTA
Found at i:38000 original size:109 final size:107
Alignment explanation
Indices: 37650--37963 Score: 353
Period size: 109 Copynumber: 2.8 Consensus size: 107
37640 AACTAATGCC
* *
37650 AATAATTAATTGTTTTAATATTTGTTCTATTTTTAATAATTGAATATTTATTT-AATATAATTAA
1 AATAATTAATTATTTTAATATTTGTTCTATTTTAAATAATTGAATATTTATTTAAATATAATTAA
*
37714 ATAATTTAATATTTTGAATTAAATATTTGAGTTTAGGGTTTAATAAATAACTAATTA
66 ATAATTTAATATTTTGAATT--A-A---GA---T---G--TAATAAAGAACTAA-TA
* ** * *
37771 AATAATTAATTATTTTAATATTTGTTCTGTTTTTGATAATTTAGTATTTATTTAAATATAATTAA
1 AATAATTAATTATTTTAATATTTGTTCTATTTTAAATAATTGAATATTTATTTAAATATAATTAA
* * * *
37836 ATAATTTAATATTTTGAATTAGGGTGTAATAAATAACTAATGCC
66 ATAATTTAATATTTTGAATTAAGATGTAATAAAGAACTAAT--A
37880 AATAATTAATTATTTTAATATTTGTTCTATTTTAAATAATTGAATATTTATTT-AATATAATTAA
1 AATAATTAATTATTTTAATATTTGTTCTATTTTAAATAATTGAATATTTATTTAAATATAATTAA
37944 ATAATTTAATATTTTGAATT
66 ATAATTTAATATTTTGAATT
37964 GAATATTTGA
Statistics
Matches: 177, Mismatches: 13, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
107 1 0.01
108 45 0.25
109 48 0.27
110 1 0.01
113 1 0.01
116 1 0.01
120 1 0.01
121 48 0.27
122 31 0.18
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (107 bp):
AATAATTAATTATTTTAATATTTGTTCTATTTTAAATAATTGAATATTTATTTAAATATAATTAA
ATAATTTAATATTTTGAATTAAGATGTAATAAAGAACTAATA
Found at i:40396 original size:18 final size:18
Alignment explanation
Indices: 40370--40410 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40360 GAAATTAGGG
*
40370 ATTTAGAAATGATAA-AGA
1 ATTTTGAAATGA-AAGAGA
40388 ATTTTGAAATGAAAGAGA
1 ATTTTGAAATGAAAGAGA
40406 ATTTT
1 ATTTT
40411 TTTTTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (18 bp):
ATTTTGAAATGAAAGAGA
Found at i:40671 original size:112 final size:112
Alignment explanation
Indices: 40474--40686 Score: 381
Period size: 112 Copynumber: 1.9 Consensus size: 112
40464 AGGTATACTG
*
40474 TTGTAGTTTCAATAAAGTTAAATGATTTAGCGGCGTTTATGTAAAAATACCGTTATTGCAATATA
1 TTGTAGTTTCAATAAAGTTAAATGATTTAGCGGCGTTTATGTAAAAATACCGTTATTGCAATACA
*
40539 TTTAGCGGCGTTTATAATAAAAATACCGTTAATGCTTTTGTGATGTT
66 TCTAGCGGCGTTTATAATAAAAATACCGTTAATGCTTTTGTGATGTT
*
40586 TTGTAGTTTCAATAAAGTTAAATGATTTAGCGGCGTTTATGTAAAAATATCGTTATTGCAATACA
1 TTGTAGTTTCAATAAAGTTAAATGATTTAGCGGCGTTTATGTAAAAATACCGTTATTGCAATACA
**
40651 TCTAGCGGCGTTTATAATAAAAATGTCGTTAATGCT
66 TCTAGCGGCGTTTATAATAAAAATACCGTTAATGCT
40687 CTGGATCTTT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 96 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (112 bp):
TTGTAGTTTCAATAAAGTTAAATGATTTAGCGGCGTTTATGTAAAAATACCGTTATTGCAATACA
TCTAGCGGCGTTTATAATAAAAATACCGTTAATGCTTTTGTGATGTT
Found at i:42099 original size:41 final size:41
Alignment explanation
Indices: 42031--42228 Score: 216
Period size: 41 Copynumber: 4.8 Consensus size: 41
42021 GCGCTTTTCT
* * * *
42031 AAAAATGCCGCTAATGCTCTGACCTTTAGCGGCACTTCAAC
1 AAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTCTAC
* * * *
42072 ATAAACGCCACTAATGCTCTGATCTTTAGCAGTGCTTCTAC
1 AAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTCTAC
* * * *
42113 AAAAACGCCGCTAATGCTTTAACCTTTAGTGGCGCTTCTAC
1 AAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTCTAC
* * *
42154 AAAAACGCCACTAATGCTCTGACATTTAGCAGCGCTTATAC
1 AAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTCTAC
* * ** *
42195 AAGAATGCCGTTAATGCTCTGACATTTAGCGGCG
1 AAAAACGCCACTAATGCTCTGACCTTTAGCGGCG
42229 TTTATGGAAA
Statistics
Matches: 129, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 129 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (41 bp):
AAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTCTAC
Found at i:42168 original size:82 final size:82
Alignment explanation
Indices: 42031--42227 Score: 261
Period size: 82 Copynumber: 2.4 Consensus size: 82
42021 GCGCTTTTCT
* *
42031 AAAAATGCCGCTAATGCTCTGACCTTTAGCGGCACTTCAACATAAACGCCACTAATGCTCTGATC
1 AAAAATGCCGCTAATGCTCTAACCTTTAGCGGCACTTCAACAAAAACGCCACTAATGCTCTGA-C
* *
42096 -TTTAGCAGTGCTTCTAC
65 ATTTAGCAGCGCTTATAC
* * * * *
42113 AAAAACGCCGCTAATGCTTTAACCTTTAGTGGCGCTTCTACAAAAACGCCACTAATGCTCTGACA
1 AAAAATGCCGCTAATGCTCTAACCTTTAGCGGCACTTCAACAAAAACGCCACTAATGCTCTGACA
42178 TTTAGCAGCGCTTATAC
66 TTTAGCAGCGCTTATAC
* * * *
42195 AAGAATGCCGTTAATGCTCTGACATTTAGCGGC
1 AAAAATGCCGCTAATGCTCTAACCTTTAGCGGC
42228 GTTTATGGAA
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 1 0.01
82 97 0.99
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (82 bp):
AAAAATGCCGCTAATGCTCTAACCTTTAGCGGCACTTCAACAAAAACGCCACTAATGCTCTGACA
TTTAGCAGCGCTTATAC
Found at i:42243 original size:41 final size:40
Alignment explanation
Indices: 42083--42252 Score: 126
Period size: 41 Copynumber: 4.2 Consensus size: 40
42073 TAAACGCCAC
* * * *
42083 TAATGCTCTGATC-TTTAGCAGTGCTTCTACAAAAACGCCGC
1 TAATGCTCTGA-CATTTAGCAGCGCTTATACAAAAATG-CGT
* * * ** * * **
42124 TAATGCTTTAACCTTTAGTGGCGCTTCTACAAAAACGCCAC
1 TAATGCTCTGACATTTAGCAGCGCTTATACAAAAATG-CGT
*
42165 TAATGCTCTGACATTTAGCAGCGCTTATACAAGAATGCCGT
1 TAATGCTCTGACATTTAGCAGCGCTTATACAAAAATG-CGT
* * **
42206 TAATGCTCTGACATTTAGCGGCGTTTATGGAAAAATGCGT
1 TAATGCTCTGACATTTAGCAGCGCTTATACAAAAATGCGT
*
42246 TAGTGCT
1 TAATGCT
42253 TTACTTTTTA
Statistics
Matches: 106, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
40 10 0.09
41 96 0.91
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (40 bp):
TAATGCTCTGACATTTAGCAGCGCTTATACAAAAATGCGT
Found at i:42428 original size:18 final size:18
Alignment explanation
Indices: 42407--42465 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
42397 TGGACTTAGA
42407 GGTGGTGGTGGTGGGTTT
1 GGTGGTGGTGGTGGGTTT
* * *
42425 GGTGGCGATGGTGGAG-CT
1 GGTGGTGGTGGTGG-GTTT
42443 GGT-GTCGGTGGTGGGTTT
1 GGTGGT-GGTGGTGGGTTT
42461 GGTGG
1 GGTGG
42466 AGAAGCTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.03, C:0.05, G:0.59, T:0.32
Consensus pattern (18 bp):
GGTGGTGGTGGTGGGTTT
Found at i:44284 original size:22 final size:23
Alignment explanation
Indices: 44234--44285 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
44224 ATACAAGGTT
*
44234 AAGTCTCGATACATAAGGTTATC
1 AAGTCTCGATACATAAGGTTAGC
*
44257 AAGTCTGGATACATAAGG-TAGC
1 AAGTCTCGATACATAAGGTTAGC
44279 AAGTCTC
1 AAGTCTC
44286 AAGACTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (23 bp):
AAGTCTCGATACATAAGGTTAGC
Found at i:46609 original size:21 final size:20
Alignment explanation
Indices: 46584--46634 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
46574 TCTCTCTTTT
46584 TTTTCTTTTTTTTTTCCTCAAA
1 TTTTCTTTTTTTTTT--TCAAA
46606 -TTTCTCTTTTTTTTTTCAAA
1 TTTTCT-TTTTTTTTTTCAAA
46626 TTTTCTTTT
1 TTTTCTTTT
46635 CGACTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.30
21 10 0.37
22 9 0.33
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTCTTTTTTTTTTTCAAA
Found at i:46617 original size:20 final size:19
Alignment explanation
Indices: 46592--46634 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
46582 TTTTTTCTTT
46592 TTTTTTTCCTCAAATTTCTC
1 TTTTTTTCCTCAAATTT-TC
**
46612 TTTTTTTTTTCAAATTTTC
1 TTTTTTTCCTCAAATTTTC
46631 TTTT
1 TTTT
46635 CGACTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTTCCTCAAATTTTC
Found at i:49095 original size:3 final size:3
Alignment explanation
Indices: 49087--49158 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
49077 CCATAGTAGA
49087 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49135 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
49159 GATGATGATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49163 original size:3 final size:3
Alignment explanation
Indices: 49157--49187 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
49147 AATAATAATA
*
49157 ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
49188 AGATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:49192 original size:9 final size:9
Alignment explanation
Indices: 49154--49194 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
49144 AATAATAATA
49154 ATAATGATG
1 ATAATGATG
*
49163 ATGATGATG
1 ATAATGATG
*
49172 ATGATGATG
1 ATAATGATG
*
49181 ATAATGAAG
1 ATAATGATG
49190 ATAAT
1 ATAAT
49195 AATAATAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (9 bp):
ATAATGATG
Found at i:49246 original size:14 final size:14
Alignment explanation
Indices: 49229--49271 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
49219 AAATCTAAAC
49229 AAATAATAAAAAAT
1 AAATAATAAAAAAT
*
49243 AAATAATAAAATA-
1 AAATAATAAAAAAT
*
49256 AAATAA-ACAAAAT
1 AAATAATAAAAAAT
49269 AAA
1 AAA
49272 GAAAAGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.16
13 9 0.36
14 12 0.48
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAATAAAAAAT
Found at i:49250 original size:17 final size:17
Alignment explanation
Indices: 49224--49271 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
49214 ATAATAAATC
49224 TAAACAAATAATAAAAAA
1 TAAAC-AATAATAAAAAA
*
49242 TAAATAATAA-AATAAAA
1 TAAACAATAATAA-AAAA
49259 TAAACAA-AATAAA
1 TAAACAATAATAAA
49272 GAAAAGGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 5 0.19
17 17 0.65
18 4 0.15
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAACAATAATAAAAAA
Found at i:49997 original size:118 final size:118
Alignment explanation
Indices: 49767--49986 Score: 334
Period size: 118 Copynumber: 1.9 Consensus size: 118
49757 TTGATATTTT
* * * *
49767 AGAAAATAAGGCTCTAGTGGTCACACAATCTTGGAACACGCCCGTGTATGGCGGTCGTGGTCCTA
1 AGAAAATAAGGCTCCAATGGTCACACAATCCTGGAACACGCCCGTGTATGGCGGCCGTGGTCCTA
*
49832 TCTTCGCCTCTCCCACGTCCGTGTCTATAAACCGTGTCCTATTTCGAAGTTTC
66 TCTTCGCCTCTCCCACGCCCGTGTCTATAAACCGTGTCCTATTTCGAAGTTTC
*
49885 AGAAAATAAGGCTCCAATGGTCACACAGTCCTGGAACACGCCCGTGTATGGCGGCCGTGAG-CCT
1 AGAAAATAAGGCTCCAATGGTCACACAATCCTGGAACACGCCCGTGTATGGCGGCCGTG-GTCCT
* * * *
49949 GTCTTCGCTTCTTCCATGCCCGTGTCTATAAACCGTGT
65 ATCTTCGCCTCTCCCACGCCCGTGTCTATAAACCGTGT
49987 ATCGTTTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
118 90 0.99
119 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (118 bp):
AGAAAATAAGGCTCCAATGGTCACACAATCCTGGAACACGCCCGTGTATGGCGGCCGTGGTCCTA
TCTTCGCCTCTCCCACGCCCGTGTCTATAAACCGTGTCCTATTTCGAAGTTTC
Done.