Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015172.1 Kokia drynarioides strain JFW-HI SEQ_130216, 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: 48503
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:7694 original size:109 final size:109
Alignment explanation
Indices: 7503--7720 Score: 391
Period size: 109 Copynumber: 2.0 Consensus size: 109
7493 TAGTTGATGT
** *
7503 TTGATTGACTTGTGATTTCAATTAAATTGCGAGTTTTGTTATAGTAAGTATAGCTATAGGTATAA
1 TTGATTGACTTGTGACATCAATTAAATTGCGAATTTTGTTATAGTAAGTATAGCTATAGGTATAA
7568 ATAATAAATTAAGTTGACTTTCGTTTTACTTGTGACATCAATTC
66 ATAATAAATTAAGTTGACTTTCGTTTTACTTGTGACATCAATTC
*
7612 TTGATTGACTTGTGACATCAATTTAATTGCGAATTTTGTTATAGTAAGTATAGCTATAGGTATAA
1 TTGATTGACTTGTGACATCAATTAAATTGCGAATTTTGTTATAGTAAGTATAGCTATAGGTATAA
*
7677 ATAATAAATTAAGTTGACTTTCGTTTTACTTGTGATATCAATTC
66 ATAATAAATTAAGTTGACTTTCGTTTTACTTGTGACATCAATTC
7721 ACATAAAAAT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (109 bp):
TTGATTGACTTGTGACATCAATTAAATTGCGAATTTTGTTATAGTAAGTATAGCTATAGGTATAA
ATAATAAATTAAGTTGACTTTCGTTTTACTTGTGACATCAATTC
Found at i:21428 original size:14 final size:14
Alignment explanation
Indices: 21409--21454 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
21399 TGTGAACCCG
21409 TGTGCAAACCCTTT
1 TGTGCAAACCCTTT
* *
21423 TGTGC-AAGCCTCT
1 TGTGCAAACCCTTT
*
21436 TGTGCAAACCCCTT
1 TGTGCAAACCCTTT
21450 TGTGC
1 TGTGC
21455 GAGCTCCTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (14 bp):
TGTGCAAACCCTTT
Found at i:21845 original size:29 final size:28
Alignment explanation
Indices: 21803--21892 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
21793 TCTCGTATGC
21803 ATGTGAATCCTAGGAATATGCGAGCCTAT
1 ATGTGAA-CCTAGGAATATGCGAGCCTAT
*
21832 ATGTGAACCTTAGGAATTTGCGAGCCTAT
1 ATGTGAACC-TAGGAATATGCGAGCCTAT
* * * * *
21861 ATGCGAACTCTAGGTACATGTGAGCTTAT
1 ATGTGAAC-CTAGGAATATGCGAGCCTAT
21890 ATG
1 ATG
21893 ATAATGCGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.04
29 49 0.94
30 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (28 bp):
ATGTGAACCTAGGAATATGCGAGCCTAT
Found at i:26800 original size:17 final size:17
Alignment explanation
Indices: 26778--26824 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
26768 CCAATTTTAG
*
26778 ATTTTAAATTTTAATTC
1 ATTTTAAATTTAAATTC
* *
26795 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTC
*
26812 ATTGTAAATTTAA
1 ATTTTAAATTTAA
26825 GCTTATTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTC
Found at i:26820 original size:34 final size:33
Alignment explanation
Indices: 26782--26848 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
26772 TTTTAGATTT
*
26782 TAAATTTTAA-TTCATTTTAAGTTTAAATTTATTG
1 TAAA-TTTAACTT-ATTTGAAGTTTAAATTTATTG
*
26816 TAAATTTAAGCTTATTTGGAGTTTAAATTTATT
1 TAAATTTAA-CTTATTTGAAGTTTAAATTTATT
26849 TTGAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 22 0.76
35 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (33 bp):
TAAATTTAACTTATTTGAAGTTTAAATTTATTG
Found at i:27572 original size:3 final size:3
Alignment explanation
Indices: 27552--27603 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
27542 ATATTAAATA
* **
27552 AAT ATT AAT AAT GCT AAT AAT AAT AAT AAT AATT AAT AAT AA- AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AA-T
27598 AAT AAT
1 AAT AAT
27604 TTTAATAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:27832 original size:22 final size:21
Alignment explanation
Indices: 27798--27845 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
27788 AGCATATTAG
27798 AAACAAATGAAAATAAAAAAAA
1 AAACAAATGAAAA-AAAAAAAA
* * * *
27820 AAACAATTTAAAAAAAATAAT
1 AAACAAATGAAAAAAAAAAAA
27841 AAACA
1 AAACA
27846 GTTTTGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (21 bp):
AAACAAATGAAAAAAAAAAAA
Found at i:28757 original size:29 final size:29
Alignment explanation
Indices: 28706--28928 Score: 103
Period size: 29 Copynumber: 7.8 Consensus size: 29
28696 CCCTGAATTA
* *
28706 TTCCAAAAATCCATTTTTAACCC-CAAACT
1 TTCCAAAATTACATTTTT-ACCCTCAAACT
** *
28735 TTTTAGAAATTACATTTTTACCCTCGAACT
1 TTCCA-AAATTACATTTTTACCCTCAAACT
*
28765 TTCCAAAATTCCATTTTTA-CC-C-AA-T
1 TTCCAAAATTACATTTTTACCCTCAAACT
*
28790 TTCTCTGAAAATTACCA-TTTTACCCTCGAAC-
1 TTC-C--AAAATTA-CATTTTTACCCTCAAACT
* * * *
28821 TTCCAAAAATTCCATTTTGA-CCTC-GATT
1 TTCC-AAAATTACATTTTTACCCTCAAACT
* *
28849 TCTCCAAAATTACCA-TTTTACCCACGAAC-
1 T-TCCAAAATTA-CATTTTTACCCTCAAACT
* * **
28878 TTCCAAAACTTCCATTTTTACCCT-GATTT
1 TTCCAAAA-TTACATTTTTACCCTCAAACT
28907 TTCCAAAATTACCA-TTTTACCC
1 TTCCAAAATTA-CATTTTTACCC
28929 CTAGATGTCT
Statistics
Matches: 150, Mismatches: 24, Indels: 41
0.70 0.11 0.19
Matches are distributed among these distances:
25 4 0.03
26 3 0.02
27 2 0.01
28 51 0.34
29 63 0.42
30 22 0.15
31 5 0.03
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.37
Consensus pattern (29 bp):
TTCCAAAATTACATTTTTACCCTCAAACT
Found at i:28765 original size:30 final size:28
Alignment explanation
Indices: 28706--28983 Score: 99
Period size: 29 Copynumber: 9.6 Consensus size: 28
28696 CCCTGAATTA
* *
28706 TTCCAAAAATCCATTTTTAACCCCAAACT
1 TTCCAAAATTACATTTTT-ACCCCAAACT
** *
28735 TTTTAGAAATTACATTTTTACCCTCGAACT
1 TTCCA-AAATTACATTTTTACCC-CAAACT
*
28765 TTCCAAAATTCCATTTTTA-CCC-AA-T
1 TTCCAAAATTACATTTTTACCCCAAACT
*
28790 TTCTCTGAAAATTACCA-TTTTACCCTCGAAC-
1 TTC-C--AAAATTA-CATTTTTACCC-CAAACT
* * * * *
28821 TTCCAAAAATTCCATTTTGACCTC-GATT
1 TTCC-AAAATTACATTTTTACCCCAAACT
*
28849 TCTCCAAAATTACCA-TTTTACCCACGAAC-
1 T-TCCAAAATTA-CATTTTTACCC-CAAACT
* ** **
28878 TTCCAAAACTTCCATTTTTACCCTGATTT
1 TTCCAAAA-TTACATTTTTACCCCAAACT
*
28907 TTCCAAAATTACCA-TTTTACCCCTAGA-T
1 TTCCAAAATTA-CATTTTTACCCC-AAACT
* * * *
28935 GTCTAAAAATTCCATTTTAGACCCCAAACTT
1 TTC-CAAAATTACATTTT-TACCCCAAAC-T
*
28966 TTTCAAAATTACCATTTT
1 TTCCAAAATTA-CATTTT
28984 GCTCCCGAGT
Statistics
Matches: 184, Mismatches: 38, Indels: 52
0.67 0.14 0.19
Matches are distributed among these distances:
25 4 0.02
26 3 0.02
27 2 0.01
28 55 0.30
29 74 0.40
30 33 0.18
31 13 0.07
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (28 bp):
TTCCAAAATTACATTTTTACCCCAAACT
Found at i:28812 original size:57 final size:55
Alignment explanation
Indices: 28741--28928 Score: 261
Period size: 57 Copynumber: 3.3 Consensus size: 55
28731 AACTTTTTAG
* *
28741 AAATTA-CATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTACCCAATTTCTCTGA
1 AAATTACCA-TTTTACCCTCGAAC-TTCCAAAATTCCATTTTTACCCGATTTCTC-CA
*
28798 AAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCTCGATTTCTCCA
1 AAATTACCATTTTACCCTCGAACTTCC-AAAATTCCATTTTTACC-CGATTTCTCCA
* *
28855 AAATTACCATTTTACCCACGAACTTCCAAAACTTCCATTTTTACCCTGATTTTTCCA
1 AAATTACCATTTTACCCTCGAACTTCCAAAA-TTCCATTTTTACCC-GATTTCTCCA
28912 AAATTACCATTTTACCC
1 AAATTACCATTTTACCC
28929 CTAGATGTCT
Statistics
Matches: 120, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
56 9 0.08
57 101 0.84
58 10 0.08
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (55 bp):
AAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTACCCGATTTCTCCA
Found at i:28828 original size:28 final size:28
Alignment explanation
Indices: 28741--28928 Score: 151
Period size: 29 Copynumber: 6.6 Consensus size: 28
28731 AACTTTTTAG
28741 AAATTA-CATTTTTACCCTCGAACTTTCCA
1 AAATTACCA-TTTTACCCTCGAAC-TTCCA
*
28770 AAATT-CCATTTTTA-CC-C-AATTTCTCTGA
1 AAATTACCA-TTTTACCCTCGAACTTC-C--A
28798 AAATTACCATTTTACCCTCGAACTTCCAA
1 AAATTACCATTTTACCCTCGAACTTCC-A
**
28827 AAATT-CCATTTTGA-CCTCGATTTCTCCA
1 AAATTACCATTTT-ACCCTCGAACT-TCCA
*
28855 AAATTACCATTTTACCCACGAACTTCCA
1 AAATTACCATTTTACCCTCGAACTTCCA
**
28883 AAACTT-CCATTTTTACCCT-GATTTTTCCA
1 AAA-TTACCA-TTTTACCCTCGA-ACTTCCA
28912 AAATTACCATTTTACCC
1 AAATTACCATTTTACCC
28929 CTAGATGTCT
Statistics
Matches: 132, Mismatches: 11, Indels: 33
0.75 0.06 0.19
Matches are distributed among these distances:
25 3 0.02
26 3 0.02
27 1 0.01
28 56 0.42
29 62 0.47
30 2 0.02
31 5 0.04
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (28 bp):
AAATTACCATTTTACCCTCGAACTTCCA
Found at i:28948 original size:57 final size:57
Alignment explanation
Indices: 28765--28983 Score: 209
Period size: 57 Copynumber: 3.8 Consensus size: 57
28755 CCCTCGAACT
* * *
28765 TTCC-AAAATTCCATTTTTACCC-AATTTCTCTGAAAATTACCATTTTA-CCCTCGAAC
1 TTCCAAAAATTCCATTTTGACCCTAATTTCTC-CAAAATTACCATTTTACCCCTAG-AC
* *
28821 TTCCAAAAATTCCATTTTGA-CCTCGATTTCTCCAAAATTACCATTTTACCCACGA-AC
1 TTCCAAAAATTCCATTTTGACCCT-AATTTCTCCAAAATTACCATTTTACCC-CTAGAC
* * * *
28878 TTCCAAAACTTCCATTTTTACCCTGATTTTTCCAAAATTACCATTTTACCCCTAGA-
1 TTCCAAAAATTCCATTTTGACCCTAATTTCTCCAAAATTACCATTTTACCCCTAGAC
* * *
28934 TGTCTAAAAATTCCATTTTAGACCCCAAACTTT-TTCAAAATTACCATTTT
1 T-TCCAAAAATTCCATTTT-GA-CCCTAA-TTTCTCCAAAATTACCATTTT
28984 GCTCCCGAGT
Statistics
Matches: 137, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
56 9 0.07
57 91 0.66
58 13 0.09
59 21 0.15
60 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.37
Consensus pattern (57 bp):
TTCCAAAAATTCCATTTTGACCCTAATTTCTCCAAAATTACCATTTTACCCCTAGAC
Found at i:29029 original size:28 final size:28
Alignment explanation
Indices: 28970--29029 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
28960 AAACTTTTTC
* *
28970 AAAATTACCATTTTGCTCCCGAGTGTCC
1 AAAATTACCATTTTGCTCCCGAGTATCA
* *
28998 AAAATTACTATTTTGC-CCTCGGGTATCA
1 AAAATTACCATTTTGCTCC-CGAGTATCA
29026 AAAA
1 AAAA
29030 ATCACATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (28 bp):
AAAATTACCATTTTGCTCCCGAGTATCA
Found at i:35805 original size:18 final size:19
Alignment explanation
Indices: 35779--35821 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
35769 AGATATGAAG
35779 GAAAAGAAGAAAGAGAT-A
1 GAAAAGAAGAAAGAGATGA
* **
35797 GAAAGGAAGCGAGAGATGA
1 GAAAAGAAGAAAGAGATGA
35816 GAAAAG
1 GAAAAG
35822 CACGACTGAT
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:37521 original size:297 final size:297
Alignment explanation
Indices: 36987--37581 Score: 1109
Period size: 297 Copynumber: 2.0 Consensus size: 297
36977 TCCTTTTTCT
36987 CTTTCATGGATGGCTTCTTTGGGTATAACCAAATAAAGATGGACCTTGAAGATATGACGAAAATT
1 CTTTCATGGATGGCTTCTTTGGGTATAACCAAATAAAGATGGACCTTGAAGATATGACGAAAATT
*
37052 ACATTCGTCACAATGTGGGGGACATTCTGTTATAAGGTGATGCCAGTCGAACTTAAAAATATAGG
66 ACATTCGTCACAATGTGGGGGACATTCTGTTATAAGGTGATGCCAGTCGAACTTAAAAATACAGG
*
37117 GGCAACGTATGAAAAAGCCATGGTGACATTGTTTCATGATACGATGCACAAGTATATCGAGGTCT
131 GGCAACGTATGAAAAAGCCATGGTGACATTGTTTCATGATACGATGCACAAGTATATAGAGGTCT
* ** *
37182 ATGTCGATGACATGATTGTAAAGTCTTGAACTGGGGAAGAACATGTAAAGGTCTTGAGAAAGTTA
196 ATGTCAATGACATGATTACAAAGTCTTGAACTAGGGAAGAACATGTAAAGGTCTTGAGAAAGTTA
37247 TTCTTGAGATTAAGGAAGTTCCAGCTAAAGTTGAACC
261 TTCTTGAGATTAAGGAAGTTCCAGCTAAAGTTGAACC
37284 CTTTCATGGATGGCTTCTTTGGGTATAACCAAATAAAGATGGACCTTGAAGATATGACGAAAATT
1 CTTTCATGGATGGCTTCTTTGGGTATAACCAAATAAAGATGGACCTTGAAGATATGACGAAAATT
*
37349 ACATTCGTCATAATGTGGGGGACATTCTGTTATAAGGTGATGCCAGTCGAACTTAAAAATACAGG
66 ACATTCGTCACAATGTGGGGGACATTCTGTTATAAGGTGATGCCAGTCGAACTTAAAAATACAGG
*
37414 GGCAACGTATGAGAAAGCCATGGTGACATTGTTTCATGATACGATGCACAAGTATATAGAGGTCT
131 GGCAACGTATGAAAAAGCCATGGTGACATTGTTTCATGATACGATGCACAAGTATATAGAGGTCT
*
37479 ATGTCAATGACATGATTACAAAGTCTTGAACTAGGGAAGAACATGTAAAGGTCTTGAGAAAGTTG
196 ATGTCAATGACATGATTACAAAGTCTTGAACTAGGGAAGAACATGTAAAGGTCTTGAGAAAGTTA
37544 TTCTTGAGATTAAGGAAGTTCCAGCTAAAGTTGAACC
261 TTCTTGAGATTAAGGAAGTTCCAGCTAAAGTTGAACC
37581 C
1 C
37582 AGCCAAATGT
Statistics
Matches: 289, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
297 289 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (297 bp):
CTTTCATGGATGGCTTCTTTGGGTATAACCAAATAAAGATGGACCTTGAAGATATGACGAAAATT
ACATTCGTCACAATGTGGGGGACATTCTGTTATAAGGTGATGCCAGTCGAACTTAAAAATACAGG
GGCAACGTATGAAAAAGCCATGGTGACATTGTTTCATGATACGATGCACAAGTATATAGAGGTCT
ATGTCAATGACATGATTACAAAGTCTTGAACTAGGGAAGAACATGTAAAGGTCTTGAGAAAGTTA
TTCTTGAGATTAAGGAAGTTCCAGCTAAAGTTGAACC
Found at i:41219 original size:96 final size:95
Alignment explanation
Indices: 41041--41222 Score: 210
Period size: 96 Copynumber: 1.9 Consensus size: 95
41031 AAGGATGTTT
* * * * *
41041 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAGATTACACCTAGTAAGTTAAGGCACAATATTTCGAAACCGAAGA
*
41106 TAAGGAAAAATTGCCTCGATTAAGGGTATTC
66 TAA-GAAAAATTACCTCGATTAAGGGTATTC
* *
41137 GATTATTTCGATTTGAAGGAAA-ATTACACCTAGTGAGTTAAGGCACAA-ATTTTCGAAACCTGA
1 GATTATCTCGATTTGAA-GAAAGATTACACCTAGTAAGTTAAGGCACAATA-TTTCGAAACC-GA
41200 A-ATAA-AAGAATATTACCTCGATT
63 AGATAAGAA-AA-ATTACCTCGATT
41223 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
94 2 0.03
95 3 0.04
96 61 0.84
97 7 0.10
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (95 bp):
GATTATCTCGATTTGAAGAAAGATTACACCTAGTAAGTTAAGGCACAATATTTCGAAACCGAAGA
TAAGAAAAATTACCTCGATTAAGGGTATTC
Found at i:41521 original size:29 final size:28
Alignment explanation
Indices: 41479--41688 Score: 154
Period size: 29 Copynumber: 7.1 Consensus size: 28
41469 TTTTGGGGAG
* *
41479 GTTCGGAGTCAAAAATGGGATTTATGGAA
1 GTTCGGGGT-AAAAATGGGATTTTTGGAA
* *
41508 GTTCGAGGGT-AAAATGGTAATTTTTGAAA
1 GTTCG-GGGTAAAAATGG-GATTTTTGGAA
* * *
41537 GGTTCAGGGTAAAAAATGAGACTTCTTGGAA
1 -GTTCGGGGT-AAAAATGGGA-TTTTTGGAA
* *
41568 GTTTGGGGGT-AAAATGGTAATTTTTGGAA
1 G-TTCGGGGTAAAAATGG-GATTTTTGGAA
*
41597 GGTTCGGGGTTAAAATTGGGATTTTTGGAA
1 -GTTCGGGG-TAAAAATGGGATTTTTGGAA
* * ***
41627 GTTTGGGGGTAAAATTATAATTTTTGGAA
1 G-TTCGGGGTAAAAATGGGATTTTTGGAA
41656 GGTTCGGGGTTAAAAATGGGATTTTTGGAA
1 -GTTCGGGG-TAAAAATGGGATTTTTGGAA
41686 GTT
1 GTT
41689 TAGGGACCTC
Statistics
Matches: 141, Mismatches: 26, Indels: 28
0.72 0.13 0.14
Matches are distributed among these distances:
28 7 0.05
29 64 0.45
30 45 0.32
31 25 0.18
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (28 bp):
GTTCGGGGTAAAAATGGGATTTTTGGAA
Found at i:41541 original size:59 final size:59
Alignment explanation
Indices: 41453--41689 Score: 303
Period size: 59 Copynumber: 4.0 Consensus size: 59
41443 CCGGATGCAC
* * * * * * * * *
41453 GGGGGCAAGATGGTAGTTTTGGGGAGGTTCGGAGTCAAAAATGGGATTTATGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
* * * * * *
41512 GAGGGTAAAATGGTAATTTTTGAAAGGTTCAGGGTAAAAAATGAGACTTCTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGA-TTTTTGGAAGTTT
*
41572 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAATTGGGATTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
**
41631 GGGGGTAAAATTATAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
41690 AGGGACCTCC
Statistics
Matches: 153, Mismatches: 24, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
59 103 0.67
60 50 0.33
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.33
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
Found at i:41621 original size:30 final size:30
Alignment explanation
Indices: 41477--41686 Score: 171
Period size: 30 Copynumber: 7.1 Consensus size: 30
41467 AGTTTTGGGG
* * *
41477 AGGTTCGGAGTCAAAAATGGGATTTATGGA
1 AGGTTCGGGGTTAAAAATGGGATTTTTGGA
* *
41507 A-GTTCGAGGG-T-AAAATGGTAATTTTTGAA
1 AGGTTCG-GGGTTAAAAATGG-GATTTTTGGA
* * * *
41536 AGGTTCAGGGTAAAAAATGAGACTTCTTGGA
1 AGGTTCGGGGTTAAAAATGGGA-TTTTTGGA
* * *
41567 A-GTTTGGGGGT-AAAATGGTAATTTTTGGA
1 AGGTTCGGGGTTAAAAATGG-GATTTTTGGA
*
41596 AGGTTCGGGGTTAAAATTGGGATTTTTGGA
1 AGGTTCGGGGTTAAAAATGGGATTTTTGGA
* * * ***
41626 A-GTTTGGGGGTAAAATTATAATTTTTGGA
1 AGGTTCGGGGTTAAAAATGGGATTTTTGGA
41655 AGGTTCGGGGTTAAAAATGGGATTTTTGGA
1 AGGTTCGGGGTTAAAAATGGGATTTTTGGA
41685 AG
1 AG
41687 TTTAGGGACC
Statistics
Matches: 137, Mismatches: 33, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
28 7 0.05
29 54 0.39
30 57 0.42
31 19 0.14
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (30 bp):
AGGTTCGGGGTTAAAAATGGGATTTTTGGA
Found at i:41641 original size:119 final size:118
Alignment explanation
Indices: 41453--41689 Score: 303
Period size: 119 Copynumber: 2.0 Consensus size: 118
41443 CCGGATGCAC
* * *
41453 GGGGGCAAGATGGTAGTTTTGGGGAGGTTCGGAGTCAAAAATGGGATTTATGGAAGTTCGAGGGT
1 GGGGGCAAAATGGTAATTTTGGGAAGGTTCGGAGTCAAAAATGGGATTTATGGAAGTTCGAGGGT
*
41518 AAAATGGTAATTTTTGAAAGGTTCAGGGTAAAAAATGAGACTTCTTGGAAGTTT
66 AAAATGATAATTTTTGAAAGGTTCAGGGTAAAAAATGAGA-TTCTTGGAAGTTT
* * * * * * * *
41572 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAATTGGGATTTTTGGAAGTTTGGGGGT
1 GGGGGCAAAATGGTAATTTTGGGAAGGTTCGGAGTCAAAAATGGGATTTATGGAAGTTCGAGGGT
* * * * * *
41637 AAAATTATAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
66 AAAATGATAATTTTTGAAAGGTTCAGGGTAAAAAATGAGATTCTTGGAAGTTT
41690 AGGGACCTCC
Statistics
Matches: 100, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
118 12 0.12
119 88 0.88
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.33
Consensus pattern (118 bp):
GGGGGCAAAATGGTAATTTTGGGAAGGTTCGGAGTCAAAAATGGGATTTATGGAAGTTCGAGGGT
AAAATGATAATTTTTGAAAGGTTCAGGGTAAAAAATGAGATTCTTGGAAGTTT
Found at i:43509 original size:12 final size:11
Alignment explanation
Indices: 43484--43508 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43474 AGAAATGTAA
43484 TTTGGACTTTT
1 TTTGGACTTTT
43495 TTTGGACTTTT
1 TTTGGACTTTT
43506 TTT
1 TTT
43509 TTTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTGGACTTTT
Found at i:43557 original size:17 final size:17
Alignment explanation
Indices: 43536--43646 Score: 132
Period size: 17 Copynumber: 6.4 Consensus size: 17
43526 TTTTAGCTTC
*
43536 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
43553 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* *
43571 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
43588 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
* *
43605 ATTTAAATTTTTAAACAA
1 ATTTAAA-TTTAAAATAA
*
43623 ATTTAATTTTAAAATAA
1 ATTTAAATTTAAAATAA
43640 ATTTAAA
1 ATTTAAA
43647 GGGAATTTGG
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
17 50 0.65
18 27 0.35
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:43575 original size:35 final size:35
Alignment explanation
Indices: 43536--43646 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 35
43526 TTTTAGCTTC
* *
43536 ATTTAAATTTATAATAATTTTAAATTTGAAAATAA
1 ATTTAAATTTATAATAAATTTAAATTTCAAAATAA
*
43571 ATTTAAACTTA-AATTAAATTTAAA-TTCAAAATAA
1 ATTTAAATTTATAA-TAAATTTAAATTTCAAAATAA
* * *
43605 ATTTAAATTTTTAAACAAATTT-AATTTTAAAATAA
1 ATTTAAATTTAT-AATAAATTTAAATTTCAAAATAA
43640 ATTTAAA
1 ATTTAAA
43647 GGGAATTTGG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
34 22 0.34
35 41 0.63
36 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
ATTTAAATTTATAATAAATTTAAATTTCAAAATAA
Found at i:43593 original size:11 final size:11
Alignment explanation
Indices: 43555--43613 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
43545 TATAATAATT
43555 TTAAATTTGAAA
1 TTAAATTT-AAA
*
43567 ATAAATTTAAA
1 TTAAATTTAAA
43578 CTTAAA-TTAAA
1 -TTAAATTTAAA
*
43589 TTTAAATTCAAA
1 -TTAAATTTAAA
*
43601 ATAAATTTAAA
1 TTAAATTTAAA
43612 TT
1 TT
43614 TTTAAACAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 23 0.61
12 15 0.39
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:43593 original size:52 final size:52
Alignment explanation
Indices: 43536--43646 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 52
43526 TTTTAGCTTC
* * * * *
43536 ATTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAA
1 ATTTAAATTCAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAA
** **
43588 ATTTAAATTCAAAATAAATTTAAATTTTTAAACAAATTTAATTTTAAAATAA
1 ATTTAAATTCAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAA
43640 ATTTAAA
1 ATTTAAA
43647 GGGAATTTGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (52 bp):
ATTTAAATTCAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAA
Found at i:43646 original size:6 final size:6
Alignment explanation
Indices: 43536--43614 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
43526 TTTTAGCTTC
* * *
43536 ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* *
43583 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
43615 TTAAACAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
4 1 0.02
5 13 0.23
6 38 0.67
7 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:44354 original size:209 final size:209
Alignment explanation
Indices: 43990--44724 Score: 1308
Period size: 209 Copynumber: 3.5 Consensus size: 209
43980 TGCTTCGACC
** *
43990 TGCTTCTCAGTGCCTCATCAGGAAACTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
*
44055 TTTGGTTTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
* * *
44120 GTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCTGTACCTTATCGGGAAGATGGTTAGGAAG
131 GTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCTGTACCTCATCGGGAAGATGGTTAGGAAG
*
44185 TTAACAGTTTGACT
196 CTAACAGTTTGACT
44199 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
*
44264 TTTGGTCTTCTTCTCACTATCTCATCAGGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
** ** *
44329 AAATCTCATCAGGAAGATAAATTTGGTCCGCTTCTCTGCACCTCATCGGGAAGATGGTTAGGAAG
131 GTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCTGTACCTCATCGGGAAGATGGTTAGGAAG
44394 CTAACAGTTTGACT
196 CTAACAGTTTGACT
* *
44408 TGCTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAGATTTTCTCACATCGAGCGTGGGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
44473 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
*
44538 GTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCTGTACCTCATCGGGAAGATGGTCAGGAAG
131 GTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCTGTACCTCATCGGGAAGATGGTTAGGAAG
44603 CTAACAGTTTGACT
196 CTAACAGTTTGACT
*
44617 TGCTTCTTAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
1 TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
44682 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTC
66 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTC
44725 ATTTTGTTGG
Statistics
Matches: 500, Mismatches: 26, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 500 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.34
Consensus pattern (209 bp):
TGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGG
TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTCTGTTTCAATTCGCTTCTCT
GTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCTGTACCTCATCGGGAAGATGGTTAGGAAG
CTAACAGTTTGACT
Found at i:45233 original size:27 final size:27
Alignment explanation
Indices: 45203--45263 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
45193 CAAGAATTCT
*
45203 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
*
45230 TATTAAAAGGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
45257 TCATTAA
1 T-ATTAA
45264 TTGAAGATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Done.