Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004596.1 Kokia drynarioides strain JFW-HI SEQ_118091, 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: 34062
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 46 characters in sequence are not A, C, G, or T
Found at i:647 original size:49 final size:49
Alignment explanation
Indices: 514--1082 Score: 444
Period size: 49 Copynumber: 11.6 Consensus size: 49
504 CATGAATGTT
* **
514 TGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCAATACCATAGAAGATG
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCAT-GAAGATG
* * * ** * *
564 TGATAAGAAAAGGTTGAGGTCGTAACGATGAACCCAGTACCATGAAGATT
1 TGA-AGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATG
* * * *
614 TGAAAGGAAAGGTTGAGGCCGTAACGGCAAACCCAGTACCTTAGAAGATG
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCAT-GAAGATG
* * ** * *
664 TGATGGGAAAGGTTGATGCCGTAACGGCGAACATGATACCATGAAGATT
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATG
* * * *
713 TGAAGGGAAAGGTTGAGGCCGTAACGGTGAACTCGGTACCTTAAAAGATG
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCAT-GAAGATG
* * * * * * * **
763 TGATGGGAGAGATTGAGGTCATAACAGCGAATCCGGTACCATGAA-ACA
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATG
* * * * * *
811 TGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCATGAAGATT
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATG
* * * * * *
860 TAAAGGGAAAGATTGAGGCCGTAACGGTGAACCTGGTACCTTAGAAGACG
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCAT-GAAGATG
* * * ** *
910 TGATGGG-AAGGATTGAGGCTGTAACGGTGAATTCGGTACCAAGAA-ATG
1 TGAAGGGAAAGG-TTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATG
* * * * * * * *
958 TGATGGGAAAGGTTGAGGCTGCAATGACAAACCCGATACCATGAAGATA
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATG
* * * *
1007 TGAAGGGAAAGGTTGAGGTCGTAACGACGAACCCGGTACCTTAGAAG-CG
1 TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCAT-GAAGATG
* * **
1056 TGACGGGAAAGATTGAAACCGTAACGG
1 TGAAGGGAAAGGTTGAGGCCGTAACGG
1083 TGAATTTTCT
Statistics
Matches: 405, Mismatches: 105, Indels: 19
0.77 0.20 0.04
Matches are distributed among these distances:
48 69 0.17
49 176 0.43
50 126 0.31
51 34 0.08
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (49 bp):
TGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCATGAAGATG
Found at i:725 original size:99 final size:99
Alignment explanation
Indices: 504--1082 Score: 476
Period size: 99 Copynumber: 5.9 Consensus size: 99
494 ACCAAGGAAA
* ** *
504 CATGAATG-TTTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCAATACCATAGAAGATGTGAT
1 CATGAA-GATTTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * ** *
568 AAGAAAAGGTTGAGGTCGTAACGATGAAC-CCAGTAC
65 -GGGAAAGATTGAGGCCGTAACGGCGAACACGA-TAC
* * *
604 CATGAAGATTTGAAAGGAAAGGTTGAGGCCGTAACGGCAAACCCAGTACCTTAGAAGATGTGATG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATG
* * *
669 GGAAAGGTTGATGCCGTAACGGCGAACATGATAC
66 GGAAAGATTGAGGCCGTAACGGCGAACACGATAC
* * *
703 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACTCGGTACCTTAAAAGATGTGATG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATG
* * * * *
768 GGAGAGATTGAGGTCATAACAGCGAATC-CGGTAC
66 GGAAAGATTGAGGCCGTAACGGCGAA-CACGATAC
** * * * * * * * * *
802 CATGAA-ACATGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCAT-GAAGATTTAAAG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATG
* *
865 GGAAAGATTGAGGCCGTAACGGTGAAC-CTGGTAC
66 GGAAAGATTGAGGCCGTAACGGCGAACAC-GATAC
* ** * * * ** *
899 CTTAGAAGACGTGATGGG-AAGGATTGAGGCTGTAACGGTGAATTCGGTACC-AAGAA-ATGTGA
1 CAT-GAAGATTTGAAGGGAAAGG-TTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGA
* * * * * * *
961 TGGGAAAGGTTGAGGCTGCAATGACAAACCCGATAC
64 TGGGAAAGATTGAGGCCGTAACGGCGAACACGATAC
* * * * *
997 CATGAAGATATGAAGGGAAAGGTTGAGGTCGTAACGACGAACCCGGTACCTTAGAAG-CGTGACG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATG
**
1061 GGAAAGATTGAAACCGTAACGG
66 GGAAAGATTGAGGCCGTAACGG
1083 TGAATTTTCT
Statistics
Matches: 381, Mismatches: 86, Indels: 26
0.77 0.17 0.05
Matches are distributed among these distances:
96 2 0.01
97 69 0.18
98 101 0.27
99 150 0.39
100 59 0.15
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (99 bp):
CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATGTGATG
GGAAAGATTGAGGCCGTAACGGCGAACACGATAC
Found at i:851 original size:147 final size:145
Alignment explanation
Indices: 664--1071 Score: 523
Period size: 147 Copynumber: 2.8 Consensus size: 145
654 TTAGAAGATG
* * * * **
664 TGATGGGAAAGGTTGATGCCGTAACGGCGAACATGATACCATGAAGATTTGAAGGGAAAGGTTGA
1 TGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCATGAAGATTTGAAGGGAAAGGTTGA
* *
729 GGCCGTAACGGTGAACTCGGTACCTTAAAAGATGTGATGGGAGAGATTGAGG-TCATAACAGCGA
66 GGCCGTAACGGTGAAC-CGGTACCTTAGAAGACGTGATGGGA-AGATTGAGGCT-ATAACAGCGA
*
793 ATCCGGTACCATGAAACA
128 ATCCGGTACCAAGAAACA
* *
811 TGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCATGAAGATTTAAAGGGAAAGATTGA
1 TGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCATGAAGATTTGAAGGGAAAGGTTGA
* * *
876 GGCCGTAACGGTGAACCTGGTACCTTAGAAGACGTGATGGGAAGGATTGAGGCTGTAACGGTGAA
66 GGCCGTAACGGTGAACC-GGTACCTTAGAAGACGTGATGGGAA-GATTGAGGCTATAACAGCGAA
* **
941 TTCGGTACCAAGAAATG
129 TCCGGTACCAAGAAACA
* * *
958 TGATGGGAAAGGTTGAGGCTGCAATGACAAACCCGATACCATGAAGATATGAAGGGAAAGGTTGA
1 TGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCATGAAGATTTGAAGGGAAAGGTTGA
* ** *
1023 GGTCGTAACGACGAACCCGGTACCTTAGAAG-CGTGACGGGAAAGATTGA
66 GGCCGTAACGGTGAA-CCGGTACCTTAGAAGACGTGATGGG-AAGATTGA
1072 AACCGTAACG
Statistics
Matches: 230, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
146 16 0.07
147 211 0.92
148 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.19
Consensus pattern (145 bp):
TGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGATACCATGAAGATTTGAAGGGAAAGGTTGA
GGCCGTAACGGTGAACCGGTACCTTAGAAGACGTGATGGGAAGATTGAGGCTATAACAGCGAATC
CGGTACCAAGAAACA
Found at i:1532 original size:122 final size:121
Alignment explanation
Indices: 1292--1686 Score: 389
Period size: 122 Copynumber: 3.2 Consensus size: 121
1282 ACCAAATCCG
* * * * * * * *
1292 TCTTCCTAATGAAATACAGAGAAGTGGATCAAATAATGAAA-CGGTCATCTTCCTGATAAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTAGATAAT-AAAGCGGTCATCTTCCTGGTGAGGTAC
* * ** * *
1356 AGAGAAGTAGACCAAATTAATTAAGCGGAGCTTAATGTGAGTGAAACTTCAAACCCCA
65 AGAGAAGTAGACCAAATCAATGAAGCTAAGC-TCATATGAGTGAAACTTCAAACCCCA
1414 TCTTCCTGATGAGATACAGAGAAGTGGGTTAGATAATAAAGCGGTCATCTTCCTGGTGAGGTACA
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTAGATAATAAAGCGGTCATCTTCCTGGTGAGGTACA
* * * *
1479 AAAAAGTAGACCAAATCAATGAAGCTAAGCTCATATGAGTAAAACTTTGAAACCCCA
66 GAGAAGTAGACCAAATCAATGAAGCTAAGCTCATATGAGTGAAAC-TTCAAACCCCA
* * * * * ** * *
1536 TCTTTCTGATGAGATACAGATAAGTGGGGTAGACAATGAAGCTATCGTCTTCCTGGTGAGGCACA
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTAGATAATAAAGCGGTCATCTTCCTGGTGAGGTACA
* * * * * * *
1601 GAGAAGTGGACTAAAACAATG-AGGTGAAGCTCAATACGAGTGAAACTTCAAATCCTA
66 GAGAAGTAGACCAAATCAATGAAGCT-AAGCTC-ATATGAGTGAAACTTCAAACCCCA
* * * *
1658 TCTTCTTGGTGAGGTACAAAGAAGTGGGT
1 TCTTCCTGATGAGATACAGAGAAGTGGGT
1687 GCAAAATTGT
Statistics
Matches: 224, Mismatches: 45, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
121 18 0.08
122 195 0.87
123 11 0.05
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (121 bp):
TCTTCCTGATGAGATACAGAGAAGTGGGTTAGATAATAAAGCGGTCATCTTCCTGGTGAGGTACA
GAGAAGTAGACCAAATCAATGAAGCTAAGCTCATATGAGTGAAACTTCAAACCCCA
Found at i:2158 original size:16 final size:16
Alignment explanation
Indices: 2139--2176 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2129 AAACCAAAAA
2139 TAAAATAAATTTAAAT
1 TAAAATAAATTTAAAT
*
2155 TAAAATAAATTTTAAT
1 TAAAATAAATTTAAAT
*
2171 TTAAAT
1 TAAAAT
2177 GTCCATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATAAATTTAAAT
Found at i:2961 original size:114 final size:115
Alignment explanation
Indices: 2785--2994 Score: 359
Period size: 114 Copynumber: 1.8 Consensus size: 115
2775 CGTCGAATAG
* *
2785 CCAATGTTTGTTGAGGGACACTTTGAATAACCAAAAAAGAAGGGAAACCTTCTTTTAAAAAA-CC
1 CCAATGTTTGTTGAGGGACACTTCGAATAACCAAAAAAGAAGGGAAACCTTCTCTTAAAAAACCC
* * *
2849 TAGAAATCGAATGGGTTTCGGATTTTTTGGGGATTTACTCTCTTGAACAA
66 TAGAAACCAAATGGGTTTCAGATTTTTTGGGGATTTACTCTCTTGAACAA
2899 CCAATGTTTGTTGAGGGACACTTCGAATAACCAAAAAAGAAGGGAAACCTTCTCTTAAAAAACCC
1 CCAATGTTTGTTGAGGGACACTTCGAATAACCAAAAAAGAAGGGAAACCTTCTCTTAAAAAACCC
*
2964 TAGAAACCAAATGGGTTTTAGATTTTTTGGG
66 TAGAAACCAAATGGGTTTCAGATTTTTTGGG
2995 AAATTTTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 60 0.67
115 29 0.33
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (115 bp):
CCAATGTTTGTTGAGGGACACTTCGAATAACCAAAAAAGAAGGGAAACCTTCTCTTAAAAAACCC
TAGAAACCAAATGGGTTTCAGATTTTTTGGGGATTTACTCTCTTGAACAA
Found at i:3599 original size:17 final size:19
Alignment explanation
Indices: 3555--3602 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
3545 CCCCTAAATC
3555 TTCC-TTTT-ATTTTATAT
1 TTCCATTTTAATTTTATAT
*
3572 TTCCTTTTTAATTTTAT-T
1 TTCCATTTTAATTTTATAT
3590 TT-CATTTTAATTT
1 TTCCATTTTAATTT
3603 GGCCCTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 14 0.50
18 7 0.25
19 7 0.25
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCCATTTTAATTTTATAT
Found at i:3959 original size:10 final size:11
Alignment explanation
Indices: 3938--3963 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3928 TTTGCCATTG
3938 TTTTGGATTTT
1 TTTTGGATTTT
3949 TTTTGGATTTT
1 TTTTGGATTTT
3960 TTTT
1 TTTT
3964 AAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (11 bp):
TTTTGGATTTT
Found at i:7274 original size:25 final size:25
Alignment explanation
Indices: 7221--7268 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
7211 GTTGGATCCA
7221 AATTAAATTCTAAAAAGATAATTCG
1 AATTAAATTCTAAAAAGATAATTCG
*
7246 AATTAAA-TCTAAATA-ATAATTCG
1 AATTAAATTCTAAAAAGATAATTCG
7269 CTAATTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 7 0.32
25 7 0.32
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.33
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTCG
Found at i:8777 original size:15 final size:15
Alignment explanation
Indices: 8757--8788 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
8747 CGTTAAGCCG
8757 GTGAAGGCTTAATAA
1 GTGAAGGCTTAATAA
8772 GTGAAGGCTTAATAA
1 GTGAAGGCTTAATAA
8787 GT
1 GT
8789 ACTACAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (15 bp):
GTGAAGGCTTAATAA
Found at i:9060 original size:45 final size:46
Alignment explanation
Indices: 9008--9120 Score: 122
Period size: 45 Copynumber: 2.5 Consensus size: 46
8998 AGTGCTGGGG
* *
9008 AAACAGTAAGCACACACAGTGC-AATCCAGTAGGCTCACACAGTG-C
1 AAACAGTAAGCACACACAGTGCAAAT-CAGTAGGCACACAAAGTGTC
* * * * * * *
9053 AATCAGTAGGCGCACATAGCGCAAATCAGTAGGCACAGAAAGTGTG
1 AAACAGTAAGCACACACAGTGCAAATCAGTAGGCACACAAAGTGTC
9099 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
9121 TGAACAGTAA
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
45 32 0.62
46 20 0.38
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.13
Consensus pattern (46 bp):
AAACAGTAAGCACACACAGTGCAAATCAGTAGGCACACAAAGTGTC
Found at i:9062 original size:22 final size:22
Alignment explanation
Indices: 9011--9120 Score: 103
Period size: 23 Copynumber: 4.9 Consensus size: 22
9001 GCTGGGGAAA
*
9011 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
9033 CCAGTAGGCTCACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
9056 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
* * * *
9079 CAGTAGGCACAGAAAGTGTGAAA
1 CAGTAGGCACACACAGTG-CAAT
*
9102 CAGTAAGCACACACAGTGC
1 CAGTAGGCACACACAGTGC
9121 TGAACAGTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
22 16 0.23
23 54 0.77
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:9126 original size:23 final size:22
Alignment explanation
Indices: 8983--9132 Score: 81
Period size: 23 Copynumber: 6.5 Consensus size: 22
8973 CGAAGTACTT
8983 AACAGTAAGCACACA-AGTGCTGGGG
1 AACAGTAAGCACACACAGTGC----G
9008 AAACAGTAAGCACACACAGTGC-
1 -AACAGTAAGCACACACAGTGCG
* *
9030 AATCCAGTAGGCTCACACAGTGC-
1 AA--CAGTAAGCACACACAGTGCG
* * * * *
9053 AATCAGTAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACACAGTGCG
* * * *
9076 AATCAGTAGGCACAGAAAGTGTG
1 AA-CAGTAAGCACACACAGTGCG
9099 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACACAGTGC-G
9123 AACAGTAAGC
1 AACAGTAAGC
9133 GCGCTAGCGT
Statistics
Matches: 102, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
21 2 0.02
22 16 0.16
23 61 0.60
24 3 0.03
26 15 0.15
27 5 0.05
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (22 bp):
AACAGTAAGCACACACAGTGCG
Found at i:10068 original size:432 final size:432
Alignment explanation
Indices: 9265--10566 Score: 2469
Period size: 432 Copynumber: 3.0 Consensus size: 432
9255 ACATATACAT
9265 AATCATGTATTTTTCACCTTTATTTTCTCAAAAGCTTCCACAACATCACCATTTAGTCATATAAT
1 AATCATGTATTTTTCACCTTTATTTTCTCAAAAGCTTCCACAACATCACCATTTAGTCATATAAT
*
9330 CAATATTTATATTTAAACACATAATATCTCACACATATATTTTCTCATATATTCATCATCATATA
66 CAATATTTATATTTAAACACATAATATCTCACACATATATTTTCTCATATATTCATCATCATGTA
*
9395 CCTCTTACTTTTATTTTCACATTAATTTTCAAAACTGTCCACTTGCGTCACAGTCACTAAATTAT
131 CCTCTTACTTTTATTTTCACATTAATTTTCAAAACTGTCCACTTGTGTCACAGTCACTAAATTAT
* *
9460 TTATATCTTGTGCTACAGAACTCAAAATTATAATCCGCTTGATATTTCTGAAACTAGACTCAATC
196 TTATATCTTGTGCTACAGAACTCAAAATTATAATCCGATTCATATTTCTGAAACTAGACTCAATC
*
9525 ATATTTTTACCATAAAATTTCCAGAATTTTTTTTTTAGCCAATTTGTACAGTAAATTCTTTCAAT
261 ATATTTTTACCATAAAATTTCCAGAATTTTTTATTTAGCCAATTTGTACAGTAAATTCTTTCAAT
9590 TTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTCTTTCACTAAAAATTATTTATCTTTTTGTA
326 TTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTCTTTCACTAAAAATTATTTATCTTTTTGTA
*
9655 CAGAGATCAAATGATGTCCCTACCTGTTTCCCTTGAAAATAG
391 CAGAGATCAAATGATGTCCCTGCCTGTTTCCCTTGAAAATAG
9697 AATCATGTATTTTTCACCTTTATTTTCTCAAAAGCTTCCACAACATCACCATTTAGTCATATAAT
1 AATCATGTATTTTTCACCTTTATTTTCTCAAAAGCTTCCACAACATCACCATTTAGTCATATAAT
9762 CAATATTTATATTTAAACACATAATATCTCACACATATATTTTCTCATATATTCATCATCATGTA
66 CAATATTTATATTTAAACACATAATATCTCACACATATATTTTCTCATATATTCATCATCATGTA
9827 CCTCTTACTTTTATTTTCACATTAATTTTCAAAACTGTCCACTTGTGTCACAGTCACTAAATTAT
131 CCTCTTACTTTTATTTTCACATTAATTTTCAAAACTGTCCACTTGTGTCACAGTCACTAAATTAT
*
9892 TTATATCTTGTGCTACAGAACTCAAAATTATAATCCAATTCATATTTCTGAAACTAGACTCAATC
196 TTATATCTTGTGCTACAGAACTCAAAATTATAATCCGATTCATATTTCTGAAACTAGACTCAATC
9957 ATATTTTTACCATAAAATTTCCAGAATTTTTTATTTAGCCAATTTGTACAGTAAATTCTTTCAAT
261 ATATTTTTACCATAAAATTTCCAGAATTTTTTATTTAGCCAATTTGTACAGTAAATTCTTTCAAT
*
10022 TTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTTTTTCACTAAAAATTATTTATCTTTTTGTA
326 TTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTCTTTCACTAAAAATTATTTATCTTTTTGTA
10087 CAGAGATCAAATGATGTCCCTGCCTGTTTCCCTTGAAAATAG
391 CAGAGATCAAATGATGTCCCTGCCTGTTTCCCTTGAAAATAG
10129 AATCATGTATTTTTCACCTTTATTTTCTCAAAAGCTTCCACAACATCACCATTTAGTCATATAAT
1 AATCATGTATTTTTCACCTTTATTTTCTCAAAAGCTTCCACAACATCACCATTTAGTCATATAAT
*
10194 CAATATTTATATTTAAACACATAATATCTCACAGATATATTTTCTCATATATTCATCATCATGTA
66 CAATATTTATATTTAAACACATAATATCTCACACATATATTTTCTCATATATTCATCATCATGTA
*
10259 CCTCTTACTTTTATTTTCACATTAATTTTCAAAACTGTCCAATTGTGTCACAGTCACTAAATTAT
131 CCTCTTACTTTTATTTTCACATTAATTTTCAAAACTGTCCACTTGTGTCACAGTCACTAAATTAT
*
10324 TTATATCTTGTGCTACGGAACTCAAAATTATAATCCGATTCATATTTCTGAAACTAGACTCAATC
196 TTATATCTTGTGCTACAGAACTCAAAATTATAATCCGATTCATATTTCTGAAACTAGACTCAATC
*
10389 ATATTTTTACCATAAAATTTCCAGAATTTTTTCTTTAGCCAATTTGTACAGTAAATTCTTTCAAT
261 ATATTTTTACCATAAAATTTCCAGAATTTTTTATTTAGCCAATTTGTACAGTAAATTCTTTCAAT
* *
10454 TTACCCCTTCGCTGCTGCCTGACAGTTTCGACATTCTTTCACTAAAAATTGTTTATCTTTTTGTA
326 TTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTCTTTCACTAAAAATTATTTATCTTTTTGTA
*
10519 CAGAGATCAAATGATGTCCCTGCCTATTTCCCTTGAAAATAG
391 CAGAGATCAAATGATGTCCCTGCCTGTTTCCCTTGAAAATAG
10561 AATCAT
1 AATCAT
10567 TAATGATTAA
Statistics
Matches: 853, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
432 853 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (432 bp):
AATCATGTATTTTTCACCTTTATTTTCTCAAAAGCTTCCACAACATCACCATTTAGTCATATAAT
CAATATTTATATTTAAACACATAATATCTCACACATATATTTTCTCATATATTCATCATCATGTA
CCTCTTACTTTTATTTTCACATTAATTTTCAAAACTGTCCACTTGTGTCACAGTCACTAAATTAT
TTATATCTTGTGCTACAGAACTCAAAATTATAATCCGATTCATATTTCTGAAACTAGACTCAATC
ATATTTTTACCATAAAATTTCCAGAATTTTTTATTTAGCCAATTTGTACAGTAAATTCTTTCAAT
TTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTCTTTCACTAAAAATTATTTATCTTTTTGTA
CAGAGATCAAATGATGTCCCTGCCTGTTTCCCTTGAAAATAG
Found at i:13109 original size:54 final size:54
Alignment explanation
Indices: 13051--13156 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
13041 ATGTGCTTAA
* *
13051 CTGTGTGTCAAACTATGTAACATACTGACTTGGGCCACACACCCGTGTCTCAGC
1 CTGTGTGCCAAACCATGTAACATACTGACTTGGGCCACACACCCGTGTCTCAGC
* * * **
13105 CTGTGTGCCAGACCGTGTGACATACTGACTTGGGCCACATTCCCGTGTCTCA
1 CTGTGTGCCAAACCATGTAACATACTGACTTGGGCCACACACCCGTGTCTCA
13157 ACTCGTGTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (54 bp):
CTGTGTGCCAAACCATGTAACATACTGACTTGGGCCACACACCCGTGTCTCAGC
Found at i:13177 original size:54 final size:54
Alignment explanation
Indices: 13070--13178 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
13060 AAACTATGTA
* *
13070 ACATACTGACTTGGGCCACACACCCGTGTCTCAGCCTGTGTGCCAGACCGTGTG
1 ACATACTGACTTGGGCCACACACCCGTGTCTCAACCTGTGTGCCAGACAGTGTG
** * *
13124 ACATACTGACTTGGGCCACATTCCCGTGTCTCAA-CTCGTGTGCTAGATAGTGTG
1 ACATACTGACTTGGGCCACACACCCGTGTCTCAACCT-GTGTGCCAGACAGTGTG
13178 A
1 A
13179 ACCTTGCACC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
53 2 0.04
54 46 0.96
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (54 bp):
ACATACTGACTTGGGCCACACACCCGTGTCTCAACCTGTGTGCCAGACAGTGTG
Found at i:13917 original size:33 final size:33
Alignment explanation
Indices: 13872--13978 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
13862 TATACACGTA
13872 AACACACCGTATGCTCGTAAGAGCTAACCAACC
1 AACACACCGTATGCTCGTAAGAGCTAACCAACC
*
13905 AACACACTGTATGCTCGTAAGAGCTAACCAACC
1 AACACACCGTATGCTCGTAAGAGCTAACCAACC
* * * *
13938 AATACACCATATACTCATAAGAGCTAACCAACC
1 AACACACCGTATGCTCGTAAGAGCTAACCAACC
13971 AACACACC
1 AACACACC
13979 AATACACAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.40, C:0.33, G:0.11, T:0.16
Consensus pattern (33 bp):
AACACACCGTATGCTCGTAAGAGCTAACCAACC
Found at i:17110 original size:5 final size:6
Alignment explanation
Indices: 17100--17139 Score: 50
Period size: 5 Copynumber: 7.0 Consensus size: 6
17090 ATAAATATTC
17100 TATTAA T-TTAA TATTAA GTATT-A TATTAA T-TTAA TATTAA
1 TATTAA TATTAA TATTAA -TATTAA TATTAA TATTAA TATTAA
17140 AATAATTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 14 0.47
6 12 0.40
7 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TATTAA
Found at i:17126 original size:23 final size:23
Alignment explanation
Indices: 17095--17139 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17085 TGTAGATAAA
*
17095 TATTCTATTAATTTAATATTAAG
1 TATTATATTAATTTAATATTAAG
17118 TATTATATTAATTTAATATTAA
1 TATTATATTAATTTAATATTAA
17140 AATAATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTATATTAATTTAATATTAAG
Found at i:17127 original size:12 final size:11
Alignment explanation
Indices: 17100--17195 Score: 51
Period size: 11 Copynumber: 8.5 Consensus size: 11
17090 ATAAATATTC
17100 TATTAA-TTTAA
1 TATTAAGTTT-A
17111 TATTAAGTATTA
1 TATTAAGT-TTA
17123 TATTAA-TTTAA
1 TATTAAGTTT-A
**
17134 TATTAA-AATA
1 TATTAAGTTTA
17144 -ATTAAGTTTA
1 TATTAAGTTTA
*
17154 -ATTATAGTTGAAA
1 TATTA-AGTT--TA
17167 TATTAAGTATTA
1 TATTAAGT-TTA
17179 TATTAA-TTTAA
1 TATTAAGTTT-A
17190 TATTAA
1 TATTAA
17196 AATAATTAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
9 5 0.07
10 11 0.16
11 27 0.39
12 15 0.22
13 6 0.09
14 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (11 bp):
TATTAAGTTTA
Found at i:17167 original size:25 final size:25
Alignment explanation
Indices: 17139--17221 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 25
17129 TTTAATATTA
17139 AAATAATTAAGTTTAATTATAGTTG
1 AAATAATTAAGTTTAATTATAGTTG
* *
17164 AAAT-ATTAAGTATTATATTAATTTAATATTA
1 AAATAATTAAGT-TTA-ATT-A--T-A-GTTG
17195 AAATAATTAAGTTTAATTATAGTTG
1 AAATAATTAAGTTTAATTATAGTTG
17220 AA
1 AA
17222 CTCTCTAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
24 7 0.15
25 11 0.24
26 4 0.09
27 2 0.04
29 2 0.04
30 4 0.09
31 9 0.20
32 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (25 bp):
AAATAATTAAGTTTAATTATAGTTG
Found at i:17176 original size:56 final size:56
Alignment explanation
Indices: 17109--17221 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
17099 CTATTAATTT
17109 AATATTAAGTATTATATTAATTTAATATTAAAATAATTAAGTTTAATTATAGTTGA
1 AATATTAAGTATTATATTAATTTAATATTAAAATAATTAAGTTTAATTATAGTTGA
17165 AATATTAAGTATTATATTAATTTAATATTAAAATAATTAAGTTTAATTATAGTTGA
1 AATATTAAGTATTATATTAATTTAATATTAAAATAATTAAGTTTAATTATAGTTGA
17221 A
1 A
17222 CTCTCTAAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (56 bp):
AATATTAAGTATTATATTAATTTAATATTAAAATAATTAAGTTTAATTATAGTTGA
Found at i:19312 original size:2 final size:2
Alignment explanation
Indices: 19305--19329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19295 ACTAAATTTA
19305 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19330 AATTACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22565 original size:31 final size:31
Alignment explanation
Indices: 22527--22586 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
22517 AATCAGGGAG
*
22527 TGAATAGAATATAAAACAAACATGGAGGGCC
1 TGAATAGAATATAAAACAAACACGGAGGGCC
22558 TGAATAGAATATAAAACAAACACGGAGGG
1 TGAATAGAATATAAAACAAACACGGAGGG
22587 ACTCGAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.50, C:0.12, G:0.23, T:0.15
Consensus pattern (31 bp):
TGAATAGAATATAAAACAAACACGGAGGGCC
Found at i:23566 original size:82 final size:82
Alignment explanation
Indices: 23437--23594 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 82
23427 AAAATGCCGC
* * * * *
23437 AAAAGGTAAAGCAATGGCGATGTTTTTGGAAAAACGCCGCTACAGGTAAAGAGAAATACCGGCGT
1 AAAAGGTAAAGCAATAGCGACGTTTTTGGAAAAACGCCACTAAAGGTAAAGAGAAATAACGGCGT
23502 TTATGGGAAAACGTCGA
66 TTATGGGAAAACGTCGA
* * * * * * *
23519 AAAAGGTAAAGCAATAGCGACGTTTTTGGAGAAATGTCATTAAAGGTAAAGAGTATTAACGGTGT
1 AAAAGGTAAAGCAATAGCGACGTTTTTGGAAAAACGCCACTAAAGGTAAAGAGAAATAACGGCGT
23584 TTATGGGAAAA
66 TTATGGGAAAA
23595 ACACCGTAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (82 bp):
AAAAGGTAAAGCAATAGCGACGTTTTTGGAAAAACGCCACTAAAGGTAAAGAGAAATAACGGCGT
TTATGGGAAAACGTCGA
Found at i:23621 original size:41 final size:41
Alignment explanation
Indices: 23570--23655 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
23560 AAAGGTAAAG
* *
23570 AGTATTAACGGTGTTTATGGGAAAAACACCG-TAAAAGGTTA
1 AGTAGTAACGGTGTTTATGGGAAAAACACCGCCAAAA-GTTA
* *
23611 AGTAGTAACGGTGTTTATGGGAATAACGCCGCCAAAAGTTA
1 AGTAGTAACGGTGTTTATGGGAAAAACACCGCCAAAAGTTA
23652 AGTA
1 AGTA
23656 ATAGCTGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 36 0.90
42 4 0.10
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (41 bp):
AGTAGTAACGGTGTTTATGGGAAAAACACCGCCAAAAGTTA
Found at i:23666 original size:41 final size:41
Alignment explanation
Indices: 23570--23667 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
23560 AAAGGTAAAG
* *
23570 AGTATTAACGGTGTTTATGGGAAAAACACCGTAAAAGGTTA
1 AGTAATAACGGTGTTTATGGGAAAAACACCGCAAAAGGTTA
* * *
23611 AGTAGTAACGGTGTTTATGGGAATAACGCCGCCAAAA-GTTA
1 AGTAATAACGGTGTTTATGGGAAAAACACCG-CAAAAGGTTA
* *
23652 AGTAATAGCTGTGTTT
1 AGTAATAACGGTGTTT
23668 TCTCATAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 45 0.92
42 4 0.08
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.29
Consensus pattern (41 bp):
AGTAATAACGGTGTTTATGGGAAAAACACCGCAAAAGGTTA
Found at i:27211 original size:66 final size:66
Alignment explanation
Indices: 27091--27215 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 66
27081 CTTAAATTGG
* * *
27091 AGGCAGCAGTGAGAGAAGCAGAGGCTTAAAGAAAATATGATGAACTTCAACTACAACTTGAAGCT
1 AGGCAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGACGAACTTCAACTACAACTTGAAGCT
27156 A
66 A
* * * *
27157 AGGCAGCAGCGA-AGGAAGCTGAGTCTCAAAGAAAGTATGACGAA-TTGCAGCTACAACTT
1 AGGCAGCAGCGAGA-GAAGCAGAGGCTCAAAGAAAATATGACGAACTT-CAACTACAACTT
27216 CAAAATATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
65 3 0.06
66 47 0.94
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.18
Consensus pattern (66 bp):
AGGCAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGACGAACTTCAACTACAACTTGAAGCT
A
Found at i:27531 original size:43 final size:43
Alignment explanation
Indices: 27483--27588 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
27473 TTGTTAGCGT
*
27483 TAGCGGCGTTTGTGGGTAAAAA-GCCACTAAAGA-ACATGTTCTA
1 TAGCGGCGTTTGTGAG-AAAAACGCCACTAAAGACA-ATGTTCTA
* *
27526 TAGCGGCGTTTGTGAGAAAAACGCCGCTAAAGACAATGTTCTT
1 TAGCGGCGTTTGTGAGAAAAACGCCACTAAAGACAATGTTCTA
27569 TAGCGGCGTTTGCTG-GAAAA
1 TAGCGGCGTTTG-TGAGAAAA
27589 GCTCCGCCAT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
42 5 0.09
43 49 0.86
44 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAACGCCACTAAAGACAATGTTCTA
Found at i:29545 original size:30 final size:30
Alignment explanation
Indices: 29489--29565 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
29479 CTTACGGGGA
* *
29489 CGTTTAGGAACTTGAGAAGACCTGATATCT
1 CGTTCAGGAACTTGGGAAGACCTGATATCT
* *
29519 CGTTCAGGAGCTTGGGAAGACTTGATATCT
1 CGTTCAGGAACTTGGGAAGACCTGATATCT
* * *
29549 CATTCAAGATCTTGGGA
1 CGTTCAGGAACTTGGGA
29566 TTGAAAAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (30 bp):
CGTTCAGGAACTTGGGAAGACCTGATATCT
Found at i:29667 original size:36 final size:36
Alignment explanation
Indices: 29500--29667 Score: 101
Period size: 36 Copynumber: 5.0 Consensus size: 36
29490 GTTTAGGAAC
29500 TTGAGAAGACCTGATATCTCGTTCAGGAGCTT--G-
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
* * * *
29533 --G-GAAGACTTGATATCTCATTCAAGATCTTGGGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
* * * ** *
29566 TTGAAAAGGCCTAATATCTCCATCAGAAGCTTGGGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
* * * *
29602 ---A-CACA-C-GATAAT-GCGTTTAGGAGCTTGGGA
1 TTGAGAAGACCTGAT-ATCTCGTTCAGGAGCTTGGGA
*
29632 TTGAGAAGACTTGATATCTCGTTCAGGAGCTTGGGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
29668 AGATTTGATA
Statistics
Matches: 94, Mismatches: 27, Indels: 25
0.64 0.18 0.17
Matches are distributed among these distances:
30 39 0.41
31 4 0.04
32 2 0.02
33 2 0.02
34 2 0.02
35 3 0.03
36 42 0.45
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (36 bp):
TTGAGAAGACCTGATATCTCGTTCAGGAGCTTGGGA
Done.