Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001935.1 Kokia drynarioides strain JFW-HI SEQ_113745, 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: 138684
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 62 characters in sequence are not A, C, G, or T
Found at i:14497 original size:37 final size:40
Alignment explanation
Indices: 14416--14500 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 40
14406 ACTAAATTAC
*
14416 ATTTA-TTTTAGTGTTATTTAAGTGTGAATATATTTTTTA
1 ATTTATTTTTAGTGTTATTTAAGTGTGAATATATTTTTAA
* *
14455 A--TATTTTTAGTG-TATTTGA-TGT-ATTATATTTTTAA
1 ATTTATTTTTAGTGTTATTTAAGTGTGAATATATTTTTAA
14490 ATTTATTTTTA
1 ATTTATTTTTA
14501 TATAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
35 12 0.30
36 3 0.08
37 16 0.40
38 8 0.20
39 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (40 bp):
ATTTATTTTTAGTGTTATTTAAGTGTGAATATATTTTTAA
Found at i:15741 original size:941 final size:935
Alignment explanation
Indices: 14445--16251 Score: 3010
Period size: 941 Copynumber: 1.9 Consensus size: 935
14435 AAGTGTGAAT
14445 ATATTTTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTAAATTTATTTTTATATAAAAAT
1 ATATTTTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTAAATTTATTTTTATATAAAAAT
* * *
14510 AATATGTGAGAGTCAAGTCGAGCTCGAGTTTTAATATTTTTATCCAGTTCAAGCTTGGGTAAAAT
66 AATATGTGAGAGTCAAGTCAAGCTCAAGTTTTAACATTTTTATCCAGTTCAAGCTTGGGTAAAAT
** * * * * *
14575 TTTAAACTCATTTTCGAGTCGAGCTTAGCCCGGGCTTAAAAAATAGACCTAAAATTTTATTGAGG
131 TTTAAACTCATTTTCGAGTCGAGCCGAGCCCGAGCTTAAAAAAAAAACCTAAAATTCTATTGAGA
* * *
14640 CCCGACCTGACCCATAATCACCTTTAATTGGATCCTTCGAATGATGATGAGGATCTTTTAGGGTC
196 CCCGACCTGACCCATAATAACCTCTAATTGGATCCTCCGAATGATGATGAGGATCTTTTAGGGTC
14705 CAATTGCCTTATTATGCGATGCACCCTCAATATCCAAGCAAAGGATGATTCTGATGAACAACGAA
261 CAATTGCCTTATTATGCGATGCACCCTCAATATCCAAGCAAAGGATGATTCTGATGAACAACGAA
* * * *
14770 CTAACATCTTCCACTCTCGATGTCTGATCAAAGAGGAACTATGTTTACTCATAATTGATAACAGT
326 CTAACATCTTCCACTCTCGATATATGATCAAAGAGAAACTATGTTCACTCATAATTGATAACAGT
*
14835 AGTTGTGCTAATGTGGTAACCAATTTTTTGGTGGACTTCCTTTCATTACCTTGTCAAAACCACCC
391 AGTTGTGCTAATGTGGTAACCAATTTTTTGGTGGACTCCCTTTCATTACCTTGTCAAAACCACCC
*
14900 TAATGCATACAGTCTCTAGTGGCTAGCTTCACGAAAGATCTGAGGTAAAAGTGGTAAAATAATAT
456 TAATGCATACAGTCTCTAGTGGCTAGCTTCACGAAAGATCTGAGGTAAAAGTGGTAAAACAATAT
14965 CTCGTCACTTTTAAAATCGAAAATTATACTGATGATGTTTGGTGTGATGTAGTCTCAATGCATGT
521 CTCGTCACTTTTAAAATCGAAAATTATACTGATGATGTTTGGTGTGATGTAGTCTCAATGCATGT
* *
15030 CATTCATTTACTATTAAGGAGACCATGGCAGTTTGGTCGAGATGTC-TTCCCCTATGGCAGTCAT
586 CATTCATTTACTATTAAGGAGACCATAGCAGTTTGGTCGAGATGTCTTTCACC-ATGGCAGTCAT
*
15094 TCATATTTTCTAAGCTAGTTTTTAGGGATTTATTTCTCTC-TTTTTTTAGTTCCCTTCTTGTATA
650 TCATATTTTCTAAGCTAGTTTTTAGGGATTTATTTCTCTCTTTTTTTTAATTCCCTTCTTGTATA
* *
15158 AAGATAATCTTTGAGTTATTTTCCTTTGCAATAATTTTTTTTTTGTTTTGTTTTTTTAATAAGAG
715 AAGATAATCTTTGAGTTATTTTCCTTTGCAAGAA-----TTTTT-TTTTGTTTTTTTAAGAAGAG
* *
15223 TTTTTAACTCAATCCTCTATGAGATTGTTGATGAGAGTTATTCACCCTTCGGTTTTTCAAGTTAT
774 TTTTCAACTCAATCCTCTATGAGATTGTTGATGAGAGTTATTCACCCTTCGGTTTTTCAAATTAT
*
15288 ATAGTTTGGATGGTCGATTAAAGTAATATTTGTTTACTAAATTATATTTATTTTAGTGTTATTTA
839 ATAGTTTGAATGGTCGATTAAAGTAATATTTGTTTACTAAATTATATTTATTTTAGTGTTATTTA
15353 AGTATAAATATATTTTTTTAATTTATTGAAAA
904 AGTATAAATATATTTTTTTAATTTATTGAAAA
*
15385 ATATTTTTTAATATTTTTAGTGTATTTGATGTATTATATTCTTTAAATTTATTTTTTTATAAAAA
1 ATATTTTTTAATATTTTTAGTGTATTTGATGTATTATATT-TTTAAATTTATTTTTATATAAAAA
*
15450 TAATATG-GAAGAGTCAAGTCAAGCTCAAGTTTTAGCATTTTTATCCA-TATCAAGCTTGGGTAA
65 TAATATGTG-AGAGTCAAGTCAAGCTCAAGTTTTAACATTTTTATCCAGT-TCAAGCTTGGGTAA
*
15513 AATTTTAAACTCATTTTCGGGTCGAGCCGAGCCCGAGCTTAAAAAAAAAACCTAAAATTCTATTG
128 AATTTTAAACTCATTTTCGAGTCGAGCCGAGCCCGAGCTTAAAAAAAAAACCTAAAATTCTATTG
* *
15578 AGACCCGGCCTGACCCATAATAACCTCTAATTGGATCCTCCTAATGATGATGAGGATCTTTTAGG
193 AGACCCGACCTGACCCATAATAACCTCTAATTGGATCCTCCGAATGATGATGAGGATCTTTTAGG
* * * *
15643 GTCCAATTGCCTTATTATGTGGTGCACCCTCAATATCCAAGCAAGGGATGATTCTGATGAGCAAC
258 GTCCAATTGCCTTATTATGCGATGCACCCTCAATATCCAAGCAAAGGATGATTCTGATGAACAAC
* *
15708 GGACTAACATCTTCCACTCTCGATATATGATCAAAGAGAAACTATGTTCACTCATAATTGATAAT
323 GAACTAACATCTTCCACTCTCGATATATGATCAAAGAGAAACTATGTTCACTCATAATTGATAAC
* *
15773 GGTAGTTGTGCTAATGTGGTAACCAGTTTTTTGGTGGACTCCCTTTCATTACCTTGTCAAAACCA
388 AGTAGTTGTGCTAATGTGGTAACCAATTTTTTGGTGGACTCCCTTTCATTACCTTGTCAAAACCA
* *
15838 CCCTAATGCATACAGTCTCTAGTGGCTAGCTTCATGAAGGATCTGAGGTAAAAGTGGTAAAACAA
453 CCCTAATGCATACAGTCTCTAGTGGCTAGCTTCACGAAAGATCTGAGGTAAAAGTGGTAAAACAA
* * *
15903 TATCTTGTCACTTTTAAAATTGGAAATTATACTGATGATGTTTGGTGTGATGTAGTCTCAATGCA
518 TATCTCGTCACTTTTAAAATCGAAAATTATACTGATGATGTTTGGTGTGATGTAGTCTCAATGCA
* * *
15968 TGTCGTTCATTTACTATTAGGGAGACCATAGCAGTTTGGTCGAGATGTCTTTCACCATGGTAGTC
583 TGTCATTCATTTACTATTAAGGAGACCATAGCAGTTTGGTCGAGATGTCTTTCACCATGGCAGTC
*
16033 ATTCATATTTTCTGAGCTAGTTTTTAGGGATTTATTTCTCTCTTTTTTTTTAATTCCCTTCTTGT
648 ATTCATATTTTCTAAGCTAGTTTTTAGGGATTTATTTCTCTC-TTTTTTTTAATTCCCTTCTTGT
16098 ATAAAGATAATCTTTGAGTTATTTTCCTTTGCAAGAATTTTTTTTTGTTTTTTTAAGAAGAGTTT
712 ATAAAGATAATCTTTGAGTTATTTTCCTTTGCAAGAATTTTTTTTTGTTTTTTTAAGAAGAGTTT
* * * *
16163 TCAACTCAATCTTCTTTGAGATTGTTGGTGAGAGTTCTTCACCCTTCGGTTTTTCAAATTATATA
777 TCAACTCAATCCTCTATGAGATTGTTGATGAGAGTTATTCACCCTTCGGTTTTTCAAATTATATA
16228 GTTTGAATGGTCGATTAAAGTAAT
842 GTTTGAATGGTCGATTAAAGTAAT
16252 TAGTGAAATT
Statistics
Matches: 808, Mismatches: 53, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
937 104 0.13
938 5 0.01
940 42 0.05
941 596 0.74
942 5 0.01
943 56 0.07
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (935 bp):
ATATTTTTTAATATTTTTAGTGTATTTGATGTATTATATTTTTAAATTTATTTTTATATAAAAAT
AATATGTGAGAGTCAAGTCAAGCTCAAGTTTTAACATTTTTATCCAGTTCAAGCTTGGGTAAAAT
TTTAAACTCATTTTCGAGTCGAGCCGAGCCCGAGCTTAAAAAAAAAACCTAAAATTCTATTGAGA
CCCGACCTGACCCATAATAACCTCTAATTGGATCCTCCGAATGATGATGAGGATCTTTTAGGGTC
CAATTGCCTTATTATGCGATGCACCCTCAATATCCAAGCAAAGGATGATTCTGATGAACAACGAA
CTAACATCTTCCACTCTCGATATATGATCAAAGAGAAACTATGTTCACTCATAATTGATAACAGT
AGTTGTGCTAATGTGGTAACCAATTTTTTGGTGGACTCCCTTTCATTACCTTGTCAAAACCACCC
TAATGCATACAGTCTCTAGTGGCTAGCTTCACGAAAGATCTGAGGTAAAAGTGGTAAAACAATAT
CTCGTCACTTTTAAAATCGAAAATTATACTGATGATGTTTGGTGTGATGTAGTCTCAATGCATGT
CATTCATTTACTATTAAGGAGACCATAGCAGTTTGGTCGAGATGTCTTTCACCATGGCAGTCATT
CATATTTTCTAAGCTAGTTTTTAGGGATTTATTTCTCTCTTTTTTTTAATTCCCTTCTTGTATAA
AGATAATCTTTGAGTTATTTTCCTTTGCAAGAATTTTTTTTTGTTTTTTTAAGAAGAGTTTTCAA
CTCAATCCTCTATGAGATTGTTGATGAGAGTTATTCACCCTTCGGTTTTTCAAATTATATAGTTT
GAATGGTCGATTAAAGTAATATTTGTTTACTAAATTATATTTATTTTAGTGTTATTTAAGTATAA
ATATATTTTTTTAATTTATTGAAAA
Found at i:18650 original size:22 final size:23
Alignment explanation
Indices: 18625--18674 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
18615 AAATCTACTT
* *
18625 ATATTTTTTTTTATTTTAA-AAA
1 ATATTTTATATTATTTTAATAAA
*
18647 ATA-TTTATATTATTTTAATTAA
1 ATATTTTATATTATTTTAATAAA
18669 ATATTT
1 ATATTT
18675 ATTAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.57
22 8 0.35
23 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTTTATATTATTTTAATAAA
Found at i:18661 original size:21 final size:22
Alignment explanation
Indices: 18635--18676 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18625 ATATTTTTTT
18635 TTATTTTAA-AAAATATTTATA
1 TTATTTTAATAAAATATTTATA
*
18656 TTATTTTAATTAAATATTTAT
1 TTATTTTAATAAAATATTTAT
18677 TAATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTTTAATAAAATATTTATA
Found at i:18682 original size:21 final size:22
Alignment explanation
Indices: 18637--18687 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
18627 ATTTTTTTTT
* *
18637 ATTTTAA-AAAATATTTATATT
1 ATTTTAATTAAATATTTATATA
18658 ATTTTAATTAAATATTTAT-TA
1 ATTTTAATTAAATATTTATATA
*
18679 ATTTAAATT
1 ATTTTAATT
18688 TTTTTCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTAATTAAATATTTATATA
Found at i:22071 original size:15 final size:16
Alignment explanation
Indices: 22045--22086 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
22035 CTAAAATTGT
* *
22045 AAATGATCTAAACTTA
1 AAATGATTTAAACCTA
*
22061 AAATG-TTTAAACCTG
1 AAATGATTTAAACCTA
22076 AAATGATTTAA
1 AAATGATTTAA
22087 GATGAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (16 bp):
AAATGATTTAAACCTA
Found at i:33485 original size:42 final size:42
Alignment explanation
Indices: 33368--33487 Score: 186
Period size: 42 Copynumber: 2.9 Consensus size: 42
33358 GTATCCATAC
* * * * *
33368 CAGATAAGATGAAGGAATCTCAACTCTCAGATGAAGATGTTG
1 CAGATAAGCTCAAGGAATCTCAAGTCTCAGATGTAGACGTTG
33410 CAGATAAGCTCAAGGAATCTCAAGTCTCAGATGTAGACGTTG
1 CAGATAAGCTCAAGGAATCTCAAGTCTCAGATGTAGACGTTG
*
33452 CAGATAAGCTCAAGGAATCTAAAGTCTCAGATGTAG
1 CAGATAAGCTCAAGGAATCTCAAGTCTCAGATGTAG
33488 TTCTTGTAAG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (42 bp):
CAGATAAGCTCAAGGAATCTCAAGTCTCAGATGTAGACGTTG
Found at i:35557 original size:25 final size:25
Alignment explanation
Indices: 35511--35558 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35501 CATATTGTAA
*
35511 TAGCTCAAATACCCTACTAGTACCC
1 TAGCTCAAATACCCTACGAGTACCC
* *
35536 TAGCTCAAATATCCTAGGAGTAC
1 TAGCTCAAATACCCTACGAGTAC
35559 AAGCGTACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.25
Consensus pattern (25 bp):
TAGCTCAAATACCCTACGAGTACCC
Found at i:40989 original size:26 final size:28
Alignment explanation
Indices: 40958--41023 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
40948 TTATGGGGAC
40958 TGGATCAAATTAATCC-TAT-TATTAAA
1 TGGATCAAATTAATCCTTATATATTAAA
* *
40984 TGGATCAATTTAGTCCTTATACTATTAAA
1 TGGATCAAATTAATCCTTATA-TATTAAA
*
41013 AGGAATCAAAT
1 TGG-ATCAAAT
41024 AAGTCTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 14 0.44
27 3 0.09
29 9 0.28
30 6 0.19
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (28 bp):
TGGATCAAATTAATCCTTATATATTAAA
Found at i:46554 original size:31 final size:31
Alignment explanation
Indices: 46519--46580 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
46509 TAAAAATTGA
46519 TATTG-ATCTATTC-AAATGTTTTCATTGAAGT
1 TATTGAAT-TATTCGAAA-GTTTTCATTGAAGT
* *
46550 TATTGAATTATTCGAAAGTTTTTATTTAAGT
1 TATTGAATTATTCGAAAGTTTTCATTGAAGT
46581 CACTGGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (31 bp):
TATTGAATTATTCGAAAGTTTTCATTGAAGT
Found at i:51955 original size:19 final size:19
Alignment explanation
Indices: 51931--51970 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51921 TATAATTTAA
* *
51931 ATTTTTAATTAAAAATTAT
1 ATTTTTAATAAAAAAATAT
*
51950 ATTTTTTATAAAAAAATAT
1 ATTTTTAATAAAAAAATAT
51969 AT
1 AT
51971 CTGGCTATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTAATAAAAAAATAT
Found at i:57077 original size:25 final size:24
Alignment explanation
Indices: 57031--57077 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
57021 TGAATAGGAT
*
57031 TTTATAATTTTTAAGATTTTAATC
1 TTTATAATTTTTAAGATCTTAATC
57055 TTTATGAATTTTTTAAG-TCTTAA
1 TTTAT-AA-TTTTTAAGATCTTAA
57078 GGTACAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 7 0.35
26 8 0.40
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTATAATTTTTAAGATCTTAATC
Found at i:58579 original size:29 final size:30
Alignment explanation
Indices: 58538--58618 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
58528 GAATTGGATC
58538 AAATCAAAAATTCATGTATAAAATTACACA-
1 AAATC-AAAATTCATGTATAAAATTACACAT
* *
58568 AAATCAAAATTCATGTATATAATTGCACATT
1 AAATCAAAATTCATGTATAAAATTACACA-T
* *
58599 AAACCATAATTCATGTATAA
1 AAATCAAAATTCATGTATAA
58619 TTTTAACATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 22 0.50
30 5 0.11
31 17 0.39
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTCATGTATAAAATTACACAT
Found at i:71140 original size:23 final size:22
Alignment explanation
Indices: 71106--71148 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
71096 TTAACGTTTT
*
71106 AATCGATATTTTCATAAAAAACA
1 AATCGATATTTT-AAAAAAAACA
71129 AATCGACT-TTTTAAAAAAAA
1 AATCGA-TATTTTAAAAAAAA
71149 TTGATAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 10 0.56
24 1 0.06
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (22 bp):
AATCGATATTTTAAAAAAAACA
Found at i:71214 original size:2 final size:2
Alignment explanation
Indices: 71207--71235 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
71197 AACTAAATTG
71207 AT AT 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 AT AT A
71236 AATTCAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73920 original size:22 final size:22
Alignment explanation
Indices: 73880--73940 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
73870 CGATCTAAGG
*
73880 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
73901 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
73923 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
73941 GAAAGTCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:73931 original size:15 final size:16
Alignment explanation
Indices: 73906--73935 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
73896 GAATTAAAAA
73906 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
73922 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
73936 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:74764 original size:19 final size:19
Alignment explanation
Indices: 74740--74782 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
74730 AAACATAAAT
74740 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
74759 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
74778 TAAAT
1 TAAAT
74783 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:80333 original size:43 final size:42
Alignment explanation
Indices: 80282--80445 Score: 159
Period size: 43 Copynumber: 3.8 Consensus size: 42
80272 GGTGATTACA
** *
80282 AAAAGGAAGACTCGTGTCTCGGCTAGAGCATGAGATTATTCAT
1 AAAAGGAAGACTTATGTCTCGG-TAGAGCATAAGATTATTCAT
* * * * *
80325 AAAGGGAAGACTTATGTCTCAGTTAGAGCATAAAATTGTTTAT
1 AAAAGGAAGACTTATGTCTC-GGTAGAGCATAAGATTATTCAT
* **
80368 AAAAGGAAGACTTATGTCTCGGTAAGAGCATAAGGTTATTTGT
1 AAAAGGAAGACTTATGTCTCGGT-AGAGCATAAGATTATTCAT
*
80411 AAATGGAAGAACTTATGAT-TCGGTCAGAGCATAAG
1 AAAAGGAAG-ACTTATG-TCTCGGT-AGAGCATAAG
80446 GTTAATACAG
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.02
43 75 0.74
44 23 0.23
45 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (42 bp):
AAAAGGAAGACTTATGTCTCGGTAGAGCATAAGATTATTCAT
Found at i:88205 original size:114 final size:114
Alignment explanation
Indices: 88011--88315 Score: 434
Period size: 115 Copynumber: 2.6 Consensus size: 114
88001 TTAAATTTTT
* * * * * *
88011 TTTTTATAATAATCCTAATATAAATCAACTTGTTCATGCA-AACTAAATAAAAGATTTACTCAAA
1 TTTTTATAAGAATCCTAATATAAATCAACCTCTT-AT--ATATCCAAATAAGAGATTTACTCAAA
* *
88075 ATAAAAATCAATAAAATATAT-AAAAAAAAATTTGGAATTAATTAAAAACCC
63 ATAAAAATCAATAAAATATATAAAAAAAAAACTTAGAATTAATTAAAAACCC
*
88126 TTTTTATAAGAATCCTAATATAAATCAACCTCTCTATATATCCAAATAAGAGATTTACTCAAAGT
1 TTTTTATAAGAATCCTAATATAAATCAACCTCT-TATATATCCAAATAAGAGATTTACTCAAAAT
88191 AAAAATCAATAAAATATATAAAAAAAAAACTTAGAATTAATTAAAAACCC
65 AAAAATCAATAAAATATATAAAAAAAAAACTTAGAATTAATTAAAAACCC
* * *
88241 TTTTTATAAGAATCCTAATATAAATCAACCTCTTTATCTATCCAAATAAGAGATTTACTCGAAAC
1 TTTTTATAAGAATCCTAATATAAATCAACCTC-TTATATATCCAAATAAGAGATTTACTCAAAAT
88306 AAAAACTCAA
65 AAAAA-TCAA
88316 CCATAAGATA
Statistics
Matches: 172, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
113 1 0.01
114 41 0.24
115 124 0.72
116 6 0.03
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (114 bp):
TTTTTATAAGAATCCTAATATAAATCAACCTCTTATATATCCAAATAAGAGATTTACTCAAAATA
AAAATCAATAAAATATATAAAAAAAAAACTTAGAATTAATTAAAAACCC
Found at i:93352 original size:29 final size:30
Alignment explanation
Indices: 93319--93375 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
93309 TGATTTAATG
93319 TGTAATTGTATACATG-AACTTTGATTTTA
1 TGTAATTGTATACATGAAACTTTGATTTTA
* *
93348 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATTGTATACATGAAACTTTGATTT
93376 GATCCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (30 bp):
TGTAATTGTATACATGAAACTTTGATTTTA
Found at i:93385 original size:30 final size:29
Alignment explanation
Indices: 93322--93386 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
93312 TTTAATGTGT
* * **
93322 AATTGTATACATGAACTTTGATTTTATGT
1 AATTTTATACATGAACTTTGATTTGATCC
*
93351 AATTTTATACATGAAATTTTGATTTGATCC
1 AATTTTATACATG-AACTTTGATTTGATCC
93381 AATTTT
1 AATTTT
93387 TGTAAGTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (29 bp):
AATTTTATACATGAACTTTGATTTGATCC
Found at i:96806 original size:18 final size:17
Alignment explanation
Indices: 96770--96806 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
96760 TCTGTATTTT
*
96770 ATAAAATTATTATTTAA
1 ATAAAATTATTATTAAA
96787 ATAAAATTATTTATTAAA
1 ATAAAATTA-TTATTAAA
96805 AT
1 AT
96807 TATTGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAAATTATTATTAAA
Found at i:101030 original size:29 final size:30
Alignment explanation
Indices: 100989--101090 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
100979 GAGATCCCTA
* *
100989 AACTATCCAAAAATCATATTTTGACCCTCG
1 AACTTTCCAAAAATCATATTTTGACCCTTG
* *
101019 AACTTTCCAAAATTC-CATTTTGA-CCTTG
1 AACTTTCCAAAAATCATATTTTGACCCTTG
** * *
101047 ATTTTTTCCAAAAAATTATATTTTTACCCTTG
1 A-ACTTTCC-AAAAATCATATTTTGACCCTTG
101079 AACTTTCCAAAA
1 AACTTTCCAAAA
101091 TTTCATTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
28 5 0.09
29 12 0.21
30 22 0.39
31 11 0.20
32 6 0.11
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTCCAAAAATCATATTTTGACCCTTG
Found at i:101086 original size:60 final size:59
Alignment explanation
Indices: 100997--101151 Score: 188
Period size: 59 Copynumber: 2.6 Consensus size: 59
100987 TAAACTATCC
* * * *
100997 AAAAATCATATTTTGACCCTCGAACTTTCCAAAATTCCA-TTTTGA-CCTTGATTTTTTCCA
1 AAAAATTATATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGATCC--CA-ATTTTCCA
* *
101057 AAAAATTATATTTTTACCCTTGAACTTTCCAAAATTTCATTTTTGATCCCAATTTTCCA
1 AAAAATTATATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGATCCCAATTTTCCA
* * *
101116 AAAAATTACATTTTTACCCGCGAAATTTCCAAAATT
1 AAAAATTATATTTTTACCCTCGAACTTTCCAAAATT
101152 ACTATTTTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 39 0.47
60 36 0.43
61 6 0.07
62 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAAATTATATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGATCCCAATTTTCCA
Found at i:101100 original size:29 final size:29
Alignment explanation
Indices: 101006--101151 Score: 93
Period size: 29 Copynumber: 4.9 Consensus size: 29
100996 CAAAAATCAT
* *
101006 ATTTTGACCCTCGAACTTTCCAAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAATTTC
* * **
101035 ATTTTGA-CCTTGATTTTTTCCAAAAAATTAT-
1 ATTTTTACCCTCGA-ACTTTCC--AAAATT-TC
*
101066 ATTTTTACCCTTGAACTTTCCAAAATTTC
1 ATTTTTACCCTCGAACTTTCCAAAATTTC
* * *
101095 ATTTTTGATCC-C-AATTTTCCAAAAAATTAC
1 ATTTTT-ACCCTCGAACTTTCC--AAAATTTC
* *
101125 ATTTTTACCCGCGAAATTTCCAAAATT
1 ATTTTTACCCTCGAACTTTCCAAAATT
101152 ACTATTTTAC
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
28 13 0.14
29 33 0.35
30 17 0.18
31 24 0.26
32 6 0.06
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTTCCAAAATTTC
Found at i:101152 original size:29 final size:28
Alignment explanation
Indices: 101058--101193 Score: 98
Period size: 29 Copynumber: 4.7 Consensus size: 28
101048 TTTTTTCCAA
* * *
101058 AAAATTATATTTTTACCCTTGAACTTTCC
1 AAAATTACATTTTTACCC-CGAAATTTCC
* * *
101087 AAAATTTCATTTTTGATCCC-AATTTTCC
1 AAAATTACATTTTT-ACCCCGAAATTTCC
101115 AAAAAATTACATTTTTACCCGCGAAATTTCC
1 --AAAATTACATTTTTACCC-CGAAATTTCC
* *
101146 AAAATTAC-TATTTTACCCCTAAAGTGTCC
1 AAAATTACAT-TTTTACCCCGAAA-TTTCC
*
101175 AAATTTACCA-TTTTACCCC
1 AAAATTA-CATTTTTACCCC
101194 CGAGCATCCA
Statistics
Matches: 87, Mismatches: 11, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
28 12 0.14
29 50 0.57
30 18 0.21
31 7 0.08
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATTACATTTTTACCCCGAAATTTCC
Found at i:103041 original size:32 final size:33
Alignment explanation
Indices: 102999--103060 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
102989 NNNNNNNNAA
* *
102999 AGGTATCAAATTAAAA-AAAAAAAGTCTAAGTC
1 AGGTACCAAATTAAAATAAAAAAAGACTAAGTC
*
103031 AGGTACCAAATTAAAATAAAAGAAGACTAA
1 AGGTACCAAATTAAAATAAAAAAAGACTAA
103061 ATAAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (33 bp):
AGGTACCAAATTAAAATAAAAAAAGACTAAGTC
Found at i:104718 original size:6 final size:6
Alignment explanation
Indices: 104707--104740 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
104697 TCCTTTATGC
* *
104707 TATACA TATACA TATACA TATATA TATATA TATA
1 TATACA TATACA TATACA TATACA TATACA TATA
104741 AAAGATTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (6 bp):
TATACA
Found at i:110632 original size:2 final size:2
Alignment explanation
Indices: 110625--110654 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
110615 TTCACTTTAA
110625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110655 TTAAGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112771 original size:15 final size:13
Alignment explanation
Indices: 112750--112791 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
112740 AGAGTATGGG
112750 TTTTTCTTTTCTTT
1 TTTTTCTTTT-TTT
112764 TCTTTTCTTTTTTT
1 T-TTTTCTTTTTTT
112778 TTTTT-TTTTTTT
1 TTTTTCTTTTTTT
112790 TT
1 TT
112792 ATAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.33
13 4 0.15
14 5 0.19
15 9 0.33
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:113171 original size:5 final size:5
Alignment explanation
Indices: 113156--113185 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
113146 ACTTTGATGA
113156 CTTTT CTTTTT CTTTT CTTTT CTTTT CTTT
1 CTTTT C-TTTT CTTTT CTTTT CTTTT CTTT
113186 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:113939 original size:15 final size:14
Alignment explanation
Indices: 113915--113967 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
113905 CTGAAATTTT
*
113915 AAAATGAAAAGTAAA
1 AAAATTAAAA-TAAA
*
113930 AAAATTAAAATTAAT
1 AAAATTAAAA-TAAA
* *
113945 CAAATTAAAATATA
1 AAAATTAAAATAAA
113959 AAAATTAAA
1 AAAATTAAA
113968 TCATCAACTT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (14 bp):
AAAATTAAAATAAA
Found at i:118770 original size:36 final size:36
Alignment explanation
Indices: 118730--118800 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
118720 AGCTCGATCC
118730 AGATAAAAATATTAAAATTCAGGCTCAACTCGGCCT
1 AGATAAAAATATTAAAATTCAGGCTCAACTCGGCCT
* * * *
118766 AGATAAAAATGTTGAAATTCGGGCTCATCTCGGCC
1 AGATAAAAATATTAAAATTCAGGCTCAACTCGGCC
118801 CACCCAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (36 bp):
AGATAAAAATATTAAAATTCAGGCTCAACTCGGCCT
Found at i:119105 original size:19 final size:19
Alignment explanation
Indices: 119065--119106 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
119055 AAACAGCGAG
* *
119065 AAAACAACAAGAAAGCAGC
1 AAAACAACAAGAAAACAAC
*
119084 AAAATAACAAGAAAACAAC
1 AAAACAACAAGAAAACAAC
119103 AAAA
1 AAAA
119107 ATTTTTGTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.71, C:0.17, G:0.10, T:0.02
Consensus pattern (19 bp):
AAAACAACAAGAAAACAAC
Found at i:130352 original size:2 final size:2
Alignment explanation
Indices: 130347--130380 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
130337 TCATACATAT
130347 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
130381 GCATGGTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:137022 original size:116 final size:116
Alignment explanation
Indices: 136818--137050 Score: 448
Period size: 116 Copynumber: 2.0 Consensus size: 116
136808 CATAAACCCA
136818 AACAAAGTCATAATCATCATAAGCTGAGCATCAAACTCCACTATCGAAACTCTAAAAGAATCACG
1 AACAAAGTCATAATCATCATAAGCTGAGCATCAAACTCCACTATCGAAACTCTAAAAGAATCACG
136883 GAAGCCCTTATACTAGTAGTCATTGTACATCATGGTATGCCATGTATCTCT
66 GAAGCCCTTATACTAGTAGTCATTGTACATCATGGTATGCCATGTATCTCT
* *
136934 AACAAAGTCATAATCATCATAAGCTGAGCATCAAACTCCACTATCGGAACTCTAAAAGTATCACG
1 AACAAAGTCATAATCATCATAAGCTGAGCATCAAACTCCACTATCGAAACTCTAAAAGAATCACG
136999 GAAGCCCTTATACTAGTAGTCATTGTACATCATGGTATGCCATGTATCTCT
66 GAAGCCCTTATACTAGTAGTCATTGTACATCATGGTATGCCATGTATCTCT
137050 A
1 A
137051 TTTGGTTATT
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (116 bp):
AACAAAGTCATAATCATCATAAGCTGAGCATCAAACTCCACTATCGAAACTCTAAAAGAATCACG
GAAGCCCTTATACTAGTAGTCATTGTACATCATGGTATGCCATGTATCTCT
Done.