Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012015.1 Kokia drynarioides strain JFW-HI SEQ_127013, 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: 144775
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1819 original size:25 final size:23
Alignment explanation
Indices: 1781--1833 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
1771 TATTAGAGAT
1781 AGTTAGTTGTTAAG-TCAATTAGC
1 AGTTAGTTGTTAAGAT-AATTAGC
1804 AGTTAGCTTAGTTAAGATAATTAGC
1 AGTTAG-TT-GTTAAGATAATTAGC
*
1829 TGTTA
1 AGTTA
1834 AGTCAGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.23
24 2 0.08
25 17 0.65
26 1 0.04
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (23 bp):
AGTTAGTTGTTAAGATAATTAGC
Found at i:9402 original size:108 final size:108
Alignment explanation
Indices: 9213--9427 Score: 394
Period size: 108 Copynumber: 2.0 Consensus size: 108
9203 ATGGGAAGGC
*
9213 ATTCTTACTTACTTTAAACATTGATAGCATTAGAAATGATACCTATTTTCTCCCTAAATTTTTGT
1 ATTCTTACTTACTTTAAACATTGATAGCATTAGAAATGATACCTATTTTCTCCCTAAATTTGTGT
9278 ATTATTTGTCTCTTTTGTACCATATTTAGCATGCATGTTAGGT
66 ATTATTTGTCTCTTTTGTACCATATTTAGCATGCATGTTAGGT
*
9321 ATTCTTACTTACTTTAAACATTGATATCATTAGAAATGATACCTATTTTCTCCCTAAATTTGTGT
1 ATTCTTACTTACTTTAAACATTGATAGCATTAGAAATGATACCTATTTTCTCCCTAAATTTGTGT
* *
9386 ATTTTTTTTCTCTTTTGTACCATATTTAGCATGCATGTTAGG
66 ATTATTTGTCTCTTTTGTACCATATTTAGCATGCATGTTAGG
9428 CATTTCATAC
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (108 bp):
ATTCTTACTTACTTTAAACATTGATAGCATTAGAAATGATACCTATTTTCTCCCTAAATTTGTGT
ATTATTTGTCTCTTTTGTACCATATTTAGCATGCATGTTAGGT
Found at i:19530 original size:19 final size:18
Alignment explanation
Indices: 19508--19549 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
19498 AATGTTGAAT
19508 GAGAAAAAGAAAAGAAAAA
1 GAGAAAAAG-AAAGAAAAA
*
19527 GAGAAAAAGAGAGAAAAA
1 GAGAAAAAGAAAGAAAAA
19545 -AGAAA
1 GAGAAA
19550 TATCGCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 9 0.41
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
GAGAAAAAGAAAGAAAAA
Found at i:21091 original size:79 final size:79
Alignment explanation
Indices: 20960--21116 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
20950 TATAATTTAT
20960 ATTAGTAGATATTGTGGCAGTAGAAGATGAATTAGCTGAATATATAACAAAATAAATAAAAACAA
1 ATTAGTAGATATTGTGGCAGTAGAAGATGAATTAGCTGAATATATAACAAAATAAATAAAAACAA
21025 GCTCACATCAATAC
66 GCTCACATCAATAC
21039 ATTAGTAGAGT-TTGTGGCAGTAGAAGATGAATTAGCTGAATATATAACAAAATAAATAAAAACA
1 ATTAGTAGA-TATTGTGGCAGTAGAAGATGAATTAGCTGAATATATAACAAAATAAATAAAAACA
21103 AGCTCACATCAATA
65 AGCTCACATCAATA
21117 TTCATAAGTA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
79 76 0.99
80 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (79 bp):
ATTAGTAGATATTGTGGCAGTAGAAGATGAATTAGCTGAATATATAACAAAATAAATAAAAACAA
GCTCACATCAATAC
Found at i:25155 original size:22 final size:23
Alignment explanation
Indices: 25115--25157 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
25105 TTTATTGGGG
*
25115 ATTAATTTAACTTAAATTTAAAT
1 ATTAATTTAAATTAAATTTAAAT
*
25138 ATTAA-TTAAATTAGATTTAA
1 ATTAATTTAAATTAAATTTAA
25158 TTGTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAATTTAAATTAAATTTAAAT
Found at i:34743 original size:109 final size:108
Alignment explanation
Indices: 34546--34771 Score: 321
Period size: 109 Copynumber: 2.1 Consensus size: 108
34536 TGAATCTTCG
* *
34546 AAAACATAGAACATTTATCGATTTTAAATAGGATATTCAATTATCTAGGTTCAAAGAAAAACCAT
1 AAAACATTGAACATTTATCGATTTTAAATAGGATATTCAATTATCTAGATTCAAAGAAAAACCAT
* * *
34611 ACCCAATACGTTAGGACACAATTTCTCAAGTTCCCTAAAATAAA
66 AACCAATACATTAAGACACAATTTCTCAAGTTCCCTAAAAT-AA
*
34655 AAAACATTGAATATTTATCGATTTTAAATAGGATATTCAATTA-CATAGATTCAAAGAAAAACCA
1 AAAACATTGAACATTTATCGATTTTAAATAGGATATTCAATTATC-TAGATTCAAAGAAAAACCA
* * *
34719 TAACCAGTACATTGAAG-CAGAATTTCTCGAGTTCCCTAAAATAA
65 TAACCAATACATT-AAGACACAATTTCTCAAGTTCCCTAAAATAA
*
34763 AGAACATTG
1 AAAACATTG
34772 TCTTGGTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
108 11 0.10
109 92 0.88
110 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (108 bp):
AAAACATTGAACATTTATCGATTTTAAATAGGATATTCAATTATCTAGATTCAAAGAAAAACCAT
AACCAATACATTAAGACACAATTTCTCAAGTTCCCTAAAATAA
Found at i:36789 original size:58 final size:59
Alignment explanation
Indices: 36699--36813 Score: 196
Period size: 58 Copynumber: 1.9 Consensus size: 59
36689 CAATTTCGTT
36699 CGGTCCTATTGATTTTGGCTTCTTTGGCG-CTTCTTCTTCAAGTAATATGCTTTTCATC
1 CGGTCCTATTGATTTTGGCTTCTTTGGCGTCTTCTTCTTCAAGTAATATGCTTTTCATC
*
36757 CGGTCCTATTGATTTTGGCTTCTTTGGTGCTTCTTCTTCTTCAAGTAATATGCTTTT
1 CGGTCCTATTGATTTTGGCTTCTTT-G-GCGTCTTCTTCTTCAAGTAATATGCTTTT
36814 TCACTTCATT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
58 25 0.47
59 1 0.02
60 2 0.04
61 25 0.47
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.49
Consensus pattern (59 bp):
CGGTCCTATTGATTTTGGCTTCTTTGGCGTCTTCTTCTTCAAGTAATATGCTTTTCATC
Found at i:37104 original size:47 final size:47
Alignment explanation
Indices: 36902--37775 Score: 679
Period size: 47 Copynumber: 18.9 Consensus size: 47
36892 AATTGGCCAC
* * * * * *
36902 TCTGGATTTAGGGGTATACGATTTGATCTGGTAGCTTCAATCTGCCTCA
1 TCTGGATTT-GGGGTATAAGATTGGATGTGATGGCTTCAATCTGCC-CT
* * *
36951 T-TGGATTTAGGGGTATAAGATTGGAT-AG-TGGCTTCAATTTGGCCT
1 TCTGGATTT-GGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* * *
36996 TCTGGATTTAGGGGTATAAGATTGGAT-AG-TGGCTTCAACCT-ACCT
1 TCTGGATTT-GGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
** ** * * *
37041 CTCTAAATTTAAGGTATAAGATTAGATAG-GATGGCTTCAATTTACCCT
1 -TCTGGATTTGGGGTATAAGATTGGAT-GTGATGGCTTCAATCTGCCCT
* *
37089 TCTGGATTTGGGGTATGAGATTGGATG-G-TGGCTTCAATTTG-CCT
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* * * *
37133 ATTTGGATTT-AGGTATAATATTGGATGTGATGG-TTGCAATCTGCCCC
1 -TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTT-CAATCTGCCCT
* * * * *
37180 TCTAGATTT-AGGTATAAGATTGGATGTAATGGTTTCAATTTG-CCT
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
*
37225 CTCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTTAATCTGCCCT
1 -TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* * * * * *
37273 TCTAGATTTGGGGTATAAGATTAGATGAGATGACTTTAATCTGCCCC
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* * ** * *
37320 TCTGGATTTGAGGTATAAGACTAAATGAGATGGC-TCTAATCT-ACCT
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTC-AATCTGCCCT
** * * * *
37366 CTCTAAATTTGAGGTATAAGATTGAATAG-GATGGC-TCTAATCTACCCC
1 -TCTGGATTTGGGGTATAAGATTGGAT-GTGATGGCTTC-AATCTGCCCT
* ** * *
37414 TCTAGATTTAAGGTATAAGATTAGAT-AG-TGGCTTCAATCTG-CCT
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* * *
37458 CTCTAGATTTGAGGTATAAGATTGGATGTGATGACTTCAATCTGCCCAT
1 -TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCC-T
** * * *
37507 T-TGGATTTAAGGTATAAGATTGGATGTGATGGCTTTAATTTGTTCC-
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTG-CCCT
* * * *
37553 TATGGTTTTGGGGTATAAGATTAGATGTGATGGCTTCAACCTG-CCT
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* *
37599 TCTAGATTTGGAGTATAAGATTGGATGTGATGGCTTCAATCTGCCC-
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* * * * *
37645 TCT--AGTTAGGGAAAAAAATTGGATGTGATGGCTTCAATCTGCCCT
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* * * * * *
37690 TTTGGATTTGTGGTATAAGATTGGATGCGATGGTTTCAATCTTCCCC
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
* *
37737 T-TGGATATAGGGTATAAGATTGGATGTGATGGCTTCAAT
1 TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAAT
37776 TTGTCCTCTA
Statistics
Matches: 679, Mismatches: 113, Indels: 69
0.79 0.13 0.08
Matches are distributed among these distances:
44 54 0.08
45 81 0.12
46 191 0.28
47 314 0.46
48 37 0.05
49 2 0.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (47 bp):
TCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCCT
Found at i:37244 original size:184 final size:186
Alignment explanation
Indices: 36906--37784 Score: 774
Period size: 184 Copynumber: 4.7 Consensus size: 186
36896 GGCCACTCTG
* * * * * *
36906 GATTTAGGGGTATACGATTTGATCTGGTAGCTTCAATCTGCCTCA-TTGGATTTAGGGGTATAAG
1 GATTT-GGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCT-ATTTGGATTT-GAGGTATAAG
* * * * *
36970 ATTGGATAGTG--GCTTCAATTTGGCCTTCTGGATTTAGGGGTATAAGATTGGAT-AG-TGGCTT
63 ATTGGAT-GTGATGGTTCAATCTGCCCCTCTGGATTTA--GGTATAAGATTGGATGTGATGGCTT
* * * * * *
37031 CAACCTACCTCTCTAAATTTAAGGTATAAGATTAGATAG-GATGGCTTCAATTTACCCTTCTG
125 CAATCTGCCTCTCTAGATTTAAGGTATAAGATTAGAT-GTGATGGCTTCAATCTGCCCTTCTA
* * *
37093 GATTTGGGGTATGAGATTGGATG-G-TGGCTTCAATTTGCCTATTTGGATTT-AGGTATAATATT
1 GATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCTATTTGGATTTGAGGTATAAGATT
* * * *
37155 GGATGTGATGGTTGCAATCTGCCCCTCTAGATTTAGGTATAAGATTGGATGTAATGGTTTCAATT
66 GGATGTGATGGTT-CAATCTGCCCCTCTGGATTTAGGTATAAGATTGGATGTGATGGCTTCAATC
* ** * *
37220 TGCCTCTCTGGATTTGGGGTATAAGATTGGATGTGATGGCTTTAATCTGCCCTTCTA
130 TGCCTCTCTAGATTTAAGGTATAAGATTAGATGTGATGGCTTCAATCTGCCCTTCTA
* * * * ** * *
37277 GATTTGGGGTATAAGATTAGATGAGATGACTTTAATCTGCCCCTCTGGATTTGAGGTATAAGACT
1 GATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCTATTTGGATTTGAGGTATAAGATT
** * * * * ** *
37342 AAATGAGATGGCTCTAATCTACCTCTCTAAATTTGAGGTATAAGATTGAATAG-GATGGC-TCTA
66 GGATGTGATGGTTC-AATCTGCCCCTCTGGATTT-AGGTATAAGATTGGAT-GTGATGGCTTC-A
* * *
37405 ATCTACCCCTCTAGATTTAAGGTATAAGATTAGAT-AG-TGGCTTCAATCTG-CCTCTCTA
127 ATCTGCCTCTCTAGATTTAAGGTATAAGATTAGATGTGATGGCTTCAATCTGCCCT-TCTA
* * * *
37463 GATTTGAGGTATAAGATTGGATGTGATGACTTCAATCTGCCCATTTGGATTTAAGGTATAAGATT
1 GATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCTATTTGGATTTGAGGTATAAGATT
* * ** * * * * *
37528 GGATGTGATGGCTTTAATTTGTTCCTATGGTTTTGGGGTATAAGATTAGATGTGATGGCTTCAAC
66 GGATGTGATGG-TTCAATCTGCCCCTCTGGATTT-AGGTATAAGATTGGATGTGATGGCTTCAAT
* *
37593 CTGCCT-TCTAGATTT-GGAGTATAAGATTGGATGTGATGGCTTCAATCTGCCC-TCTA
129 CTGCCTCTCTAGATTTAAG-GTATAAGATTAGATGTGATGGCTTCAATCTGCCCTTCTA
* * * * *
37649 G--TTAGGGAAAAAAATTGGATGTGATGGCTTCAATCTGCCCT-TTTGGATTTGTGGTATAAGAT
1 GATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTG-CCTATTTGGATTTGAGGTATAAGAT
* * *
37711 TGGATGCGATGGTTTCAATCTTCCCCT-TGGATATAGGGTATAAGATTGGATGTGATGGCTTCAA
65 TGGATGTGATGG-TTCAATCTGCCCCTCTGGATTTA-GGTATAAGATTGGATGTGATGGCTTCAA
*
37775 TTTGTCCTCT
128 TCTG-CCTCT
37785 AGTTAGAGTA
Statistics
Matches: 556, Mismatches: 110, Indels: 54
0.77 0.15 0.08
Matches are distributed among these distances:
181 3 0.01
182 29 0.05
183 39 0.07
184 186 0.33
185 31 0.06
186 158 0.28
187 59 0.11
188 50 0.09
189 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (186 bp):
GATTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTGCCTATTTGGATTTGAGGTATAAGATT
GGATGTGATGGTTCAATCTGCCCCTCTGGATTTAGGTATAAGATTGGATGTGATGGCTTCAATCT
GCCTCTCTAGATTTAAGGTATAAGATTAGATGTGATGGCTTCAATCTGCCCTTCTA
Found at i:37824 original size:40 final size:40
Alignment explanation
Indices: 37581--38096 Score: 365
Period size: 40 Copynumber: 12.2 Consensus size: 40
37571 GATTAGATGT
* * * *
37581 GATGG-CTTCAACCTGCCTTCTAGATTTGGAGTATAAGATTG
1 GATGGTCTTCAATCTGCCCTCTAG-TTAGG-GTAAAAGATTG
* *
37622 GATGTGATGGCTTCAATCTGCCCTCTAGTTAGGGAAAAAAATTG
1 GATG-G-T--CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
* * * *
37666 GATGTGATGGCTTCAATCTGCCCTTTTGGATTTGTGGTATAAGATTG
1 GATG-G-T--CTTCAATCTGCCC-TCTAG-TTAG-GGTAAAAGATTG
* * * *
37713 GATGCGATGGTTTCAATCTTCCC-CTTGGATATAGGGTATAAGATTG
1 GATG-G-T--CTTCAATCTGCCCTC-TAG-T-TAGGGTAAAAGATTG
* * * *
37759 GATGTGATGGCTTCAATTTGTCCTCTAGTTAGAGTAAAAGATTA
1 GATG-G-T--CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
* * * *
37803 GATGGTCTTCAATCTACCCTCTGGTTGGGGTAAAAGATTA
1 GATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
* * *
37843 GATGATGTCTTCAATCTACCCTCTGGTTAGGTTAAAAGATTG
1 GATG--GTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
* * *
37885 GATGGTCTTCAATCTTCCCACTAGTT-GGGTTAAAAGATTA
1 GATGGTCTTCAATCTGCCCTCTAGTTAGGG-TAAAAGATTG
* *
37925 GATGGTGTCTTCAATTTGCCCTCT-GCTTGGGGTAAAAGATTG
1 GAT-G-GTCTTCAATCTGCCCTCTAG-TTAGGGTAAAAGATTG
* *
37967 GATGGTGTCTTCAATCTGCCTTTTAGTTAGGGTAAAAGATTG
1 GAT-G-GTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
* * *
38009 GATGGTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTC
1 GATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
* * * *
38049 GATGGACTTTAATCTTCCCTCTAGTTGGGGTAAAAGATTG
1 GATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
38089 GATGGTCT
1 GATGGTCT
38097 AATGTAACTT
Statistics
Matches: 395, Mismatches: 61, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.01
40 134 0.34
41 7 0.02
42 104 0.26
43 5 0.01
44 47 0.12
45 8 0.02
46 56 0.14
47 32 0.08
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (40 bp):
GATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG
Found at i:37856 original size:82 final size:82
Alignment explanation
Indices: 37763--38092 Score: 412
Period size: 82 Copynumber: 4.0 Consensus size: 82
37753 AGATTGGATG
* * * * * * *
37763 TGATGGCTTCAATTTGTCCTCTAGTTAGAGTAAAAGATTAGATGGTCTTCAATCTACCCTCTGGT
1 TGATGTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAATCTTCCCTCTAGT
37828 TGGGGTAAAAGATTAGA
66 TGGGGTAAAAGATTAGA
* * * *
37845 TGATGTCTTCAATCTACCCTCTGGTTAGGTTAAAAGATTGGATGGTCTTCAATCTTCCCACTAGT
1 TGATGTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAATCTTCCCTCTAGT
*
37910 TGGGTTAAAAGATTAGA
66 TGGGGTAAAAGATTAGA
* * * * * *
37927 TGGTGTCTTCAATTTGCCCTCTGCTTGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCTTTTA
1 TGATGTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTGGAT-G-GTCTTCAATCTTCCCTCTA
* *
37992 GTTAGGGTAAAAGATTGGA
64 GTTGGGGTAAAAGATTAGA
* * *
38011 TG--GTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTCGATGGACTTTAATCTTCCCTCTAGT
1 TGATGTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAATCTTCCCTCTAGT
*
38074 TGGGGTAAAAGATTGGA
66 TGGGGTAAAAGATTAGA
38091 TG
1 TG
38093 GTCTAATGTA
Statistics
Matches: 212, Mismatches: 34, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
80 34 0.16
81 1 0.00
82 143 0.67
83 1 0.00
84 33 0.16
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (82 bp):
TGATGTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAATCTTCCCTCTAGT
TGGGGTAAAAGATTAGA
Found at i:38295 original size:97 final size:99
Alignment explanation
Indices: 38102--38316 Score: 244
Period size: 98 Copynumber: 2.2 Consensus size: 99
38092 GGTCTAATGT
* * *
38102 AACTTCACTCCATTCCATTGTAACTTTAGGGAGATTGAGATTCGCTACTATAGTTTTAATCCGCT
1 AACTTCACTCCATTCCATTGCAACTTCAGGGAGATTGAGATTCGATACTATAGTTTTAATCCGCT
*
38167 TTATTACAACTTTAGGAAAATAGGATTTGGTG-TG
66 TTATTA-AACTTTAGGAAAATAGGAGTTGGTGTTG
*
38201 -ACTTCACTCCATTCCATTGCAACTTCAGTGGAGATTGAGATTCGATACT-T-GTTTTACTCCGC
1 AACTTCACTCCATTCCATTGCAACTTCAG-GGAGATTGAGATTCGATACTATAGTTTTAATCCGC
* * **
38263 TCTTCTGT-AATTTTAAGG-GTATAGGAGTTGGTGTTG
65 T-TTAT-TAAACTTT-AGGAAAATAGGAGTTGGTGTTG
*
38299 AAGCTTCACTTCATTCCA
1 AA-CTTCACTCCATTCCA
38317 CTATAACCTC
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
97 29 0.29
98 35 0.35
99 21 0.21
100 14 0.14
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (99 bp):
AACTTCACTCCATTCCATTGCAACTTCAGGGAGATTGAGATTCGATACTATAGTTTTAATCCGCT
TTATTAAACTTTAGGAAAATAGGAGTTGGTGTTG
Found at i:43211 original size:109 final size:108
Alignment explanation
Indices: 43071--43284 Score: 342
Period size: 109 Copynumber: 2.0 Consensus size: 108
43061 AACAGAGAAC
*
43071 ATTTATCGATTTTAAATAGGATATTCTATTACTTAGGTTCAAAGAAAAACCATACCCAATACGTT
1 ATTTATCGATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATACCCAATACGTT
*
43136 AGGGCACAATTTCTC-GAGTT-CTCTAAAATAAAAGAACATTGAAT
66 AGGACACAATTTCTCAG-GTTCCT-TAAAATAAAA-AACATTGAAT
* * *
43180 ATTTATCGATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATATCGAGTACGTT
1 ATTTATCGATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATACCCAATACGTT
43245 AGGACACAATTTCTCAGGTTCCTTAAAATAAAAAACATTG
66 AGGACACAATTTCTCAGGTTCCTTAAAATAAAAAACATTG
43285 CCTTTATTTT
Statistics
Matches: 98, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
108 7 0.07
109 88 0.90
110 3 0.03
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (108 bp):
ATTTATCGATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCATACCCAATACGTT
AGGACACAATTTCTCAGGTTCCTTAAAATAAAAAACATTGAAT
Found at i:43820 original size:30 final size:29
Alignment explanation
Indices: 43768--43824 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
43758 ATAAATAAAT
*
43768 AAAAAAGAATGGTGGGTAAAATTTAAAAGG
1 AAAAAAGAATGGAGGGTAAAA-TTAAAAGG
*
43798 AAAAAA-AATGGAGGGATTAAATTAAAA
1 AAAAAAGAATGGAGGG-TAAAATTAAAA
43825 TTAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (29 bp):
AAAAAAGAATGGAGGGTAAAATTAAAAGG
Found at i:43830 original size:29 final size:29
Alignment explanation
Indices: 43767--43835 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
43757 AATAAATAAA
*
43767 TAAAAAAGAATGGTGGGTAAAATTTAAAAG
1 TAAAAAA-AATGGAGGGTAAAATTTAAAAG
* * *
43797 GAAAAAAAATGGAGGGATTAAA-TTAAAAT
1 TAAAAAAAATGGAGGG-TAAAATTTAAAAG
*
43826 TAAAATAAAT
1 TAAAAAAAAT
43836 TTCAAAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (29 bp):
TAAAAAAAATGGAGGGTAAAATTTAAAAG
Found at i:55629 original size:18 final size:18
Alignment explanation
Indices: 55606--55642 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55596 ACAATTCATA
55606 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
55624 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
55642 T
1 T
55643 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:55973 original size:17 final size:18
Alignment explanation
Indices: 55941--55974 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55931 AATTTCTATG
55941 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
55959 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
55975 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:64341 original size:18 final size:19
Alignment explanation
Indices: 64318--64354 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
64308 ATAAAAAGAC
*
64318 TAAAATAAAGC-AAGTAAA
1 TAAAATAAAACAAAGTAAA
64336 TAAAATAAAACAAAGTAAA
1 TAAAATAAAACAAAGTAAA
64355 GCGTAAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.16
Consensus pattern (19 bp):
TAAAATAAAACAAAGTAAA
Found at i:75184 original size:42 final size:42
Alignment explanation
Indices: 75125--75209 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
75115 ACCTAGTGAC
75125 ACTAAGAATCCAATTCAAAAGGGGAAGGAGCATTGCAAAGCT
1 ACTAAGAATCCAATTCAAAAGGGGAAGGAGCATTGCAAAGCT
*
75167 ACTAAGAATCCAATTCAAAAGGGGAAGGAGCTTTGCAAAGCT
1 ACTAAGAATCCAATTCAAAAGGGGAAGGAGCATTGCAAAGCT
75209 A
1 A
75210 TTACTCTTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (42 bp):
ACTAAGAATCCAATTCAAAAGGGGAAGGAGCATTGCAAAGCT
Found at i:86825 original size:17 final size:17
Alignment explanation
Indices: 86801--86842 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
86791 AATTTTAAAA
*
86801 ATATATTTATATTATTTT
1 ATATATTTA-ATAATTTT
86819 A-ATATTTAATAATTTT
1 ATATATTTAATAATTTT
86835 ATATATTT
1 ATATATTT
86843 TTTATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATTTAATAATTTT
Found at i:88193 original size:24 final size:26
Alignment explanation
Indices: 88146--88194 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
88136 AATATTGAGG
88146 GTCAAATTTAACTAAAAAAAATAAAA
1 GTCAAATTTAACTAAAAAAAATAAAA
*
88172 GTCAAA-TTAA-TAAAAAATATAAA
1 GTCAAATTTAACTAAAAAAAATAAA
88195 TATTAAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 4 0.18
26 6 0.27
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.24
Consensus pattern (26 bp):
GTCAAATTTAACTAAAAAAAATAAAA
Found at i:90274 original size:2 final size:2
Alignment explanation
Indices: 90262--90297 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
90252 TGATAAGTGA
90262 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90298 GGTAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:97273 original size:24 final size:23
Alignment explanation
Indices: 97236--97282 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
97226 AAGAGTTAGT
*
97236 TTGTCAACGAAAATATAAAATAAA
1 TTGTCAAAGAAAAT-TAAAATAAA
* *
97260 TTGTCAAAGCAAATTAAGATAAA
1 TTGTCAAAGAAAATTAAAATAAA
97283 ATGAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.26
Consensus pattern (23 bp):
TTGTCAAAGAAAATTAAAATAAA
Found at i:97392 original size:128 final size:128
Alignment explanation
Indices: 97164--97420 Score: 514
Period size: 128 Copynumber: 2.0 Consensus size: 128
97154 GCAACTAAAG
97164 TTAAAATTAGAAGAATTGTTACTAATAATATCAACACAATTGAGTTAGATCTGCACAACTAAAAG
1 TTAAAATTAGAAGAATTGTTACTAATAATATCAACACAATTGAGTTAGATCTGCACAACTAAAAG
97229 AGTTAGTTTGTCAACGAAAATATAAAATAAATTGTCAAAGCAAATTAAGATAAAATGAATAGT
66 AGTTAGTTTGTCAACGAAAATATAAAATAAATTGTCAAAGCAAATTAAGATAAAATGAATAGT
97292 TTAAAATTAGAAGAATTGTTACTAATAATATCAACACAATTGAGTTAGATCTGCACAACTAAAAG
1 TTAAAATTAGAAGAATTGTTACTAATAATATCAACACAATTGAGTTAGATCTGCACAACTAAAAG
97357 AGTTAGTTTGTCAACGAAAATATAAAATAAATTGTCAAAGCAAATTAAGATAAAATGAATAGT
66 AGTTAGTTTGTCAACGAAAATATAAAATAAATTGTCAAAGCAAATTAAGATAAAATGAATAGT
97420 T
1 T
97421 GTTGGGATGT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.29
Consensus pattern (128 bp):
TTAAAATTAGAAGAATTGTTACTAATAATATCAACACAATTGAGTTAGATCTGCACAACTAAAAG
AGTTAGTTTGTCAACGAAAATATAAAATAAATTGTCAAAGCAAATTAAGATAAAATGAATAGT
Found at i:97401 original size:24 final size:23
Alignment explanation
Indices: 97364--97410 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
97354 AAGAGTTAGT
*
97364 TTGTCAACGAAAATATAAAATAAA
1 TTGTCAAAGAAAAT-TAAAATAAA
* *
97388 TTGTCAAAGCAAATTAAGATAAA
1 TTGTCAAAGAAAATTAAAATAAA
97411 ATGAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.26
Consensus pattern (23 bp):
TTGTCAAAGAAAATTAAAATAAA
Found at i:98303 original size:31 final size:31
Alignment explanation
Indices: 98265--98324 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
98255 GGTTGTCACC
98265 GCATCTATGGGCGCAATCTATGATTTTTAAT
1 GCATCTATGGGCGCAATCTATGATTTTTAAT
98296 GCATCTATGGGCGCAATCTATGATTTTTA
1 GCATCTATGGGCGCAATCTATGATTTTTA
98325 CTTGCGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (31 bp):
GCATCTATGGGCGCAATCTATGATTTTTAAT
Found at i:117334 original size:80 final size:78
Alignment explanation
Indices: 117205--117363 Score: 219
Period size: 80 Copynumber: 2.0 Consensus size: 78
117195 CAACCAATAA
* * * * *
117205 ACACATTAAGGTTACATAAGTATTCATTAATGAGAAATGCCATGTCTTTTCACCTACATCAGATC
1 ACACATTAAGGATACATAAATATTCATTAAGGAGAAATGCCATGCCTTTTCAACTACATCAGATC
*
117270 CTAATGAAGAGAC
66 CTAATGAACAGAC
* * *
117283 ACACATTAAGGATACAATAAATCTTCATTTAAGGAGAAATGTCATGCCTTTTCAACTACATTAGA
1 ACACATTAAGGATAC-ATAAATATTCA-TTAAGGAGAAATGCCATGCCTTTTCAACTACATCAGA
117348 TCCTAATGAACAGAC
64 TCCTAATGAACAGAC
117363 A
1 A
117364 TGACTCATTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
78 14 0.20
79 9 0.13
80 47 0.67
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (78 bp):
ACACATTAAGGATACATAAATATTCATTAAGGAGAAATGCCATGCCTTTTCAACTACATCAGATC
CTAATGAACAGAC
Found at i:119107 original size:12 final size:13
Alignment explanation
Indices: 119090--119136 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
119080 TGTTATTTTC
119090 TTATTTTT-GTTT
1 TTATTTTTAGTTT
*
119102 TTATTTTTATTTT
1 TTATTTTTAGTTT
*
119115 TTATTTTATAAGTTG
1 TTATTTT-T-AGTTT
119130 TTATTTT
1 TTATTTT
119137 CTTTTGACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.28
13 10 0.34
14 1 0.03
15 10 0.34
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (13 bp):
TTATTTTTAGTTT
Found at i:119115 original size:13 final size:13
Alignment explanation
Indices: 119082--119121 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
119072 TCAAAAATTG
119082 TTATTTTCTTATTT
1 TTATTTT-TTATTT
*
119096 TT-GTTTTTATTT
1 TTATTTTTTATTT
119108 TTATTTTTTATTT
1 TTATTTTTTATTT
119121 T
1 T
119122 ATAAGTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.35
13 13 0.57
14 2 0.09
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:132087 original size:22 final size:22
Alignment explanation
Indices: 132062--132105 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
132052 ATATTTAATA
132062 ATATTGAACATTAT-AATATTTT
1 ATATT-AACATTATAAATATTTT
* *
132084 ATATTAATATTTTAAATATTTT
1 ATATTAACATTATAAATATTTT
132106 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATTAACATTATAAATATTTT
Found at i:132146 original size:26 final size:25
Alignment explanation
Indices: 132100--132148 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
132090 ATATTTTAAA
*
132100 TATTTTTAAAAATTAAAATTAAAAT
1 TATTTTTAAAAAATAAAATTAAAAT
*
132125 TATTTTTAAAATAATAATATTAAA
1 TATTTTTAAAA-AATAAAATTAAA
132149 TTTGTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTTTTAAAAAATAAAATTAAAAT
Found at i:132149 original size:25 final size:24
Alignment explanation
Indices: 132095--132150 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
132085 TATTAATATT
*
132095 TTAAA-TATTTTTAAAAATTAAAA
1 TTAAATTATTTTTAAAAAATAAAA
*
132118 TTAAAATTATTTTTAAAATAATAATA
1 TT-AAATTATTTTTAAAA-AATAAAA
132144 TTAAATT
1 TTAAATT
132151 TGTTTCAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 3 0.11
25 16 0.57
26 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAAATTATTTTTAAAAAATAAAA
Found at i:136241 original size:22 final size:24
Alignment explanation
Indices: 136216--136264 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
136206 AGTTACAAAT
*
136216 TTATATT-ATTTT-ATTATTATTA
1 TTATATTGATTTTGATTATTAATA
*
136238 TTATTTTGATTTTGGATTATTAATA
1 TTATATTGATTTT-GATTATTAATA
136263 TT
1 TT
136265 CTTTGTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TTATATTGATTTTGATTATTAATA
Found at i:144352 original size:19 final size:21
Alignment explanation
Indices: 144328--144373 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
144318 CAAATTTATG
144328 TTATTTT-ATTTT-ATTATTA
1 TTATTTTGATTTTGATTATTA
144347 TTATTTTGATTTTGGATTATTA
1 TTATTTTGATTTT-GATTATTA
*
144369 ATATT
1 TTATT
144374 CTTTTTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 5 0.22
22 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
TTATTTTGATTTTGATTATTA
Found at i:144750 original size:2 final size:2
Alignment explanation
Indices: 144743--144775 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
144733 TAATTTATGT
144743 TA TA TA TA GT- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.93
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Done.