Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014797.1 Kokia drynarioides strain JFW-HI SEQ_129839, 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: 194488
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:678 original size:29 final size:29
Alignment explanation
Indices: 644--854 Score: 204
Period size: 29 Copynumber: 7.2 Consensus size: 29
634 TAAACTTTCT
644 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
* *
673 AAAAA-TCCCATTTTTGA-CCCCGAACCTTCT
1 AAAAATTACCA-TTTT-ACCCCCGAA-CTTCC
703 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
* * *
732 AAAAA-TCCCATTTTTGA-CTCCGAACCTTCT
1 AAAAATTACCA-TTTT-ACCCCCGAA-CTTCC
762 AAAAATTACCATCTTT-CCCCCGAACTTCC
1 AAAAATTACCAT-TTTACCCCCGAACTTCC
* *
791 AATAA-T-CTCATTTTGA-CCCCGAACCTTCT
1 AAAAATTAC-CATTTT-ACCCCCGAA-CTTCC
*
820 AAAAATTACCATCTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
849 AAAAAT
1 AAAAAT
855 CTCATTTTTG
Statistics
Matches: 149, Mismatches: 15, Indels: 36
0.75 0.08 0.18
Matches are distributed among these distances:
27 4 0.03
28 19 0.13
29 63 0.42
30 51 0.34
31 12 0.08
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAACTTCC
Found at i:832 original size:58 final size:59
Alignment explanation
Indices: 640--865 Score: 384
Period size: 59 Copynumber: 3.8 Consensus size: 59
630 TCCCTAAACT
640 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
*
699 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
758 TTCTAAAAATTACCATCTTT-CCCCCGAACTTCCAATAATCTCA-TTTTGACCCCGAACC
1 TTCTAAAAATTACCAT-TTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
816 TTCTAAAAATTACCATCTTACCCCCGAACTTCCAAAAATCTCATTTTTGA
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
866 ATTTTTGACT
Statistics
Matches: 158, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
57 2 0.01
58 52 0.33
59 101 0.64
60 3 0.02
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:847 original size:117 final size:118
Alignment explanation
Indices: 640--865 Score: 393
Period size: 117 Copynumber: 1.9 Consensus size: 118
630 TCCCTAAACT
640 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
*
705 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC
66 AAATTACCATCTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC
* *
758 TTCTAAAAATTACCATCTTT-CCCCCGAACTTCCAATAATCTCA-TTTTGACCCCGAACCTTCTA
1 TTCTAAAAATTACCAT-TTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
*
821 AAAATTACCATCTTACCCCCGAACTTCCAAAAATCTCATTTTTGA
65 AAAATTACCATCTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
866 ATTTTTGACT
Statistics
Matches: 103, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
117 63 0.61
118 37 0.36
119 3 0.03
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (118 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAA
AAATTACCATCTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC
Found at i:9593 original size:20 final size:21
Alignment explanation
Indices: 9554--9619 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
9544 AAAAATTCTC
*
9554 TAAAGGAAGTTTTTTGAATTTTT
1 TAAAAGAA-TTTTTT-AATTTTT
*
9577 TAAAA-TATTTTTTAA-TTTT
1 TAAAAGAATTTTTTAATTTTT
9596 TAAAAGAATGTTTTTAGATTTTT
1 TAAAAGAAT-TTTTTA-ATTTTT
9619 T
1 T
9620 TTTTCGAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.25
20 4 0.11
21 12 0.33
22 2 0.06
23 9 0.25
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (21 bp):
TAAAAGAATTTTTTAATTTTT
Found at i:10504 original size:15 final size:15
Alignment explanation
Indices: 10471--10504 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10461 GATGTTACAA
* *
10471 TTCCTTTCTTTTACT
1 TTCCTTTCTTTAACC
10486 TTCCTTTCTTTAACC
1 TTCCTTTCTTTAACC
10501 TTCC
1 TTCC
10505 CCTATTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (15 bp):
TTCCTTTCTTTAACC
Found at i:10596 original size:22 final size:22
Alignment explanation
Indices: 10571--10639 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
10561 CTTAACTCTA
*
10571 TTTATTAAAAATAATAATTAAT
1 TTTATAAAAAATAATAATTAAT
* * *
10593 TTTA-AAAAAATTAAGATTTATT
1 TTTATAAAAAA-TAATAATTAAT
*
10615 TTTATGAAATAAT-ATAATTATAT
1 TTTAT-AAAAAATAATAATTA-AT
10638 TT
1 TT
10640 GATACTTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
21 5 0.14
22 21 0.60
23 4 0.11
24 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTATAAAAAATAATAATTAAT
Found at i:12536 original size:16 final size:15
Alignment explanation
Indices: 12499--12557 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
12489 ATCTAAGAAA
*
12499 AAATAAAAGA-AACAG
1 AAATAAAA-ATAAAAG
*
12514 AATTAAAAATAAAAG
1 AAATAAAAATAAAAG
*
12529 AAAATAAAATTAAAAG
1 -AAATAAAAATAAAAG
12545 AAATAGAAAATAA
1 AAATA-AAAATAA
12558 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 16 0.44
16 19 0.53
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (15 bp):
AAATAAAAATAAAAG
Found at i:12543 original size:21 final size:22
Alignment explanation
Indices: 12497--12557 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
12487 CGATCTAAGA
* *
12497 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAAAATT
12518 AAAAATAAAAGAAAATAAAATT
1 AAAAATAAAAGAAAATAAAATT
*
12540 AAAAGA-AATAGAAAATAA
1 AAAA-ATAAAAGAAAATAA
12558 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAAAATT
Found at i:13341 original size:14 final size:14
Alignment explanation
Indices: 13324--13353 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13314 TTTAAACTCT
*
13324 AAAAGATAAATATA
1 AAAAGATAAACATA
13338 AAAAGATAAACATA
1 AAAAGATAAACATA
13352 AA
1 AA
13354 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAGATAAACATA
Found at i:13377 original size:19 final size:19
Alignment explanation
Indices: 13355--13397 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13345 AAACATAAAT
13355 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
13374 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
13393 TAAAT
1 TAAAT
13398 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:14880 original size:13 final size:13
Alignment explanation
Indices: 14857--14883 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14847 AATAAGATAG
14857 AAAAATAAAAATA
1 AAAAATAAAAATA
14870 AAAAATAAAAATA
1 AAAAATAAAAATA
14883 A
1 A
14884 TTGGGTTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:16619 original size:14 final size:14
Alignment explanation
Indices: 16600--16630 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
16590 TATTTAAAAA
16600 TTAAAAAAATATTT
1 TTAAAAAAATATTT
16614 TTAAAAAAATATTT
1 TTAAAAAAATATTT
16628 TTA
1 TTA
16631 GTTTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAAAAATATTT
Found at i:17315 original size:2 final size:2
Alignment explanation
Indices: 17308--17332 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17298 GTGCATGGTG
17308 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
17333 ATTATCTGGT
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:18024 original size:44 final size:44
Alignment explanation
Indices: 17986--18072 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
17976 TTTGTGTAAT
*
17986 ACAATTCGT-GTTCTTACATAAAAATTGGACTAACTTTGTTATG
1 ACAATTCATGGTTCTTACATAAAAATTGGACTAACTTTGTTATG
****
18029 TTGTTTCATGGTTCTTACATAAAAATTGGACTAACTTTGTTATG
1 ACAATTCATGGTTCTTACATAAAAATTGGACTAACTTTGTTATG
18073 TTGTTTCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 4 0.11
44 34 0.89
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (44 bp):
ACAATTCATGGTTCTTACATAAAAATTGGACTAACTTTGTTATG
Found at i:18073 original size:44 final size:44
Alignment explanation
Indices: 17995--18084 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
17985 TACAATTCGT
17995 GTTCTTACATAAAAATTGGACTAACTTTGTTATGTTGTTTCATG
1 GTTCTTACATAAAAATTGGACTAACTTTGTTATGTTGTTTCATG
18039 GTTCTTACATAAAAATTGGACTAACTTTGTTATGTTGTTTCATG
1 GTTCTTACATAAAAATTGGACTAACTTTGTTATGTTGTTTCATG
18083 GT
1 GT
18085 AGGTTAAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.46
Consensus pattern (44 bp):
GTTCTTACATAAAAATTGGACTAACTTTGTTATGTTGTTTCATG
Found at i:21085 original size:2 final size:2
Alignment explanation
Indices: 21078--21104 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21068 TTGTATTAAA
21078 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 A
21105 ATCAAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36350 original size:20 final size:19
Alignment explanation
Indices: 36305--36355 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
36295 AAAAATATAA
* *
36305 ATTTTGACATTTTTATAAAT
1 ATTTTGA-ATTTTCAAAAAT
*
36325 AATTTGAATTTTCAAAAATT
1 ATTTTGAATTTTCAAAAA-T
36345 ATTTTG-ATTTT
1 ATTTTGAATTTT
36356 TTTTTTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTCAAAAAT
Found at i:44864 original size:3 final size:3
Alignment explanation
Indices: 44844--44892 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
44834 TGACATTAAT
* *
44844 TAA TAA TAG TAA TTA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
44890 TAA
1 TAA
44893 CAAAAAATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:46117 original size:58 final size:59
Alignment explanation
Indices: 46012--46147 Score: 136
Period size: 58 Copynumber: 2.3 Consensus size: 59
46002 CAGCTAAAAT
* * * * *
46012 TTTCCAAAATAATATTTTGACCCTTAAACTTTATAAAAATTACATTTT-ATCTCCAAAC
1 TTTCCAAAATTACATTTTTACCCTCAAACTTTATAAAAATTACATTTTAACCTCCAAAC
* * *
46070 TTTCCAAAATTACATTTTTACCCTCGACCTTT-TAAAAATCT-CGATTTTAACCTCGAAAC
1 TTTCCAAAATTACATTTTTACCCTCAAACTTTATAAAAAT-TAC-ATTTTAACCTCCAAAC
*
46129 -TTCCAAAAATTCCATTTTT
1 TTTCC-AAAATTACATTTTT
46148 TGACCCCAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
57 8 0.12
58 36 0.55
59 21 0.32
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
TTTCCAAAATTACATTTTTACCCTCAAACTTTATAAAAATTACATTTTAACCTCCAAAC
Found at i:46145 original size:29 final size:29
Alignment explanation
Indices: 46046--46238 Score: 76
Period size: 29 Copynumber: 6.5 Consensus size: 29
46036 TAAACTTTAT
* * *
46046 AAAAATTACATTTT-ATCTCCAAACTTTCC
1 AAAAATTCCATTTTAACCTCGAAAC-TTCC
* * * **
46075 -AAAATTACATTTTTACCCTCG-ACCTTTT
1 AAAAATTCCA-TTTTAACCTCGAAACTTCC
*
46103 AAAAATCTCGATTTTAACCTCGAAACTTCC
1 AAAAAT-TCCATTTTAACCTCGAAACTTCC
* * **
46133 AAAAATTCCATTTTTTGACC-CCAATTTTCCC
1 AAAAATTCCA--TTTTAACCTCGAAACTT-CC
* *
46164 AAAAA-TCACATTTTACCCCCG-AA-TGTCC
1 AAAAATTC-CATTTTAACCTCGAAACT-TCC
* * *
46192 AAAAATTCCATTTTTTACGTCGAAACTTTCT
1 AAAAATTCCA-TTTTAACCTCGAAAC-TTCC
46223 AAAAATTACCATTTTA
1 AAAAATT-CCATTTTA
46239 CCACCGGATG
Statistics
Matches: 120, Mismatches: 27, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
28 21 0.17
29 41 0.34
30 25 0.21
31 29 0.24
32 4 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTAACCTCGAAACTTCC
Found at i:46193 original size:59 final size:59
Alignment explanation
Indices: 46130--46383 Score: 198
Period size: 59 Copynumber: 4.3 Consensus size: 59
46120 CCTCGAAACT
* * *
46130 TCCAAAAATTCCATTTTTTGACCCCAATTTTCCCAAAAATCA-CATTTTACCCCCGAATG
1 TCCAAAAATTCCATTTTTTGACCCAAATTTT-CTAAAAATTACCATTTTACCCCCGAATG
* * * *
46189 TCCAAAAATTCCATTTTTT-ACGTCGAAACTTTCTAAAAATTACCATTTTACCACCGGATG
1 TCCAAAAATTCCATTTTTTGAC--CCAAATTTTCTAAAAATTACCATTTTACCCCCGAATG
* * *** * * *
46249 TCGAAAAATTCTA-TTTTTGATCTTGATTTTTCTAAAAATTATCATTTTACCCTCGAATG
1 TCCAAAAATTCCATTTTTTGA-CCCAAATTTTCTAAAAATTACCATTTTACCCCCGAATG
* * * * * *
46308 T-CTAAAATTCCA--TTTTAACCCCAAAATTTTCTCAAAATTACCATTTTGCCCCCCAAGAG
1 TCCAAAAATTCCATTTTTTGA-CCC-AAATTTTCTAAAAATTACCATTTTACCCCCGAA-TG
46367 TCC-AAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
46384 GCCCCCGGGT
Statistics
Matches: 151, Mismatches: 33, Indels: 19
0.74 0.16 0.09
Matches are distributed among these distances:
57 6 0.04
58 36 0.24
59 69 0.46
60 37 0.25
61 1 0.01
62 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTTGACCCAAATTTTCTAAAAATTACCATTTTACCCCCGAATG
Found at i:57436 original size:61 final size:58
Alignment explanation
Indices: 57349--57510 Score: 184
Period size: 61 Copynumber: 2.7 Consensus size: 58
57339 CAAAAATCAT
*
57349 ATTTTAACCACCAAACTTTTCCAAAATCACATTTTGACCCCTAAACTTTTCCAAAATTAA
1 ATTTTAACC-CCAAA-TTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTAA
* * * ** *
57409 ATTTTAACCCTCCAAATTTTTCTAAAATTATATTTTGACCCTTAAACTTTTTGAAAATTAC
1 ATTTTAA-CC-CCAAA-TTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTAA
* *
57470 ATTTTTACCCCAAACTTTCCAAAATTACATTTT-A-CCCTAAA
1 ATTTTAACCCCAAATTTTCCAAAATTACATTTTGACCCCTAAA
57511 GCTTCCAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
56 6 0.07
57 1 0.01
58 16 0.18
59 5 0.06
60 9 0.10
61 50 0.57
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (58 bp):
ATTTTAACCCCAAATTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTAA
Found at i:57550 original size:29 final size:29
Alignment explanation
Indices: 57472--57581 Score: 93
Period size: 29 Copynumber: 3.8 Consensus size: 29
57462 AAAATTACAT
* *
57472 TTTTACCCC-AAACTT-TCCAAAATTA-CA
1 TTTTACCCCGAAACTTCT-AAAAATCACCA
* * *
57499 TTTTA-CCCTAAAGCTTCCAAAAATCACGA
1 TTTTACCCCGAAA-CTTCTAAAAATCACCA
* *
57528 TTTTAACCTCGAAACTTCTAAAAATTACCA
1 TTTT-ACCCCGAAACTTCTAAAAATCACCA
*
57558 TTTTACCCCTAAACTTCTAAAAAT
1 TTTTACCCCGAAACTTCTAAAAAT
57582 TTCATTTTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.05
27 8 0.12
28 9 0.14
29 23 0.35
30 18 0.27
31 5 0.08
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
TTTTACCCCGAAACTTCTAAAAATCACCA
Found at i:57582 original size:29 final size:28
Alignment explanation
Indices: 57371--57712 Score: 167
Period size: 30 Copynumber: 11.6 Consensus size: 28
57361 AAACTTTTCC
* * *
57371 AAAATCACATTTTGACCCCTAAACTTTTCC
1 AAAATTACATTTT-ACCCCTAAACTTCT-A
* * *
57401 AAAATTAAATTTTAACCCTCCAAATTTTTCT-
1 AAAATTACATTTT-ACCC-CTAAA--CTTCTA
* * * *
57432 AAAATTATATTTTGACCCTTAAACTTTTTG
1 AAAATTACATTTT-ACCCCTAAAC-TTCTA
*
57462 AAAATTACATTTTTACCCC-AAACTT-TCC
1 AAAATTACA-TTTTACCCCTAAACTTCT-A
*
57490 AAAATTACATTTTA-CCCTAAAGCTTCCA
1 AAAATTACATTTTACCCCTAAA-CTTCTA
* * *
57518 AAAATCACGATTTTAACCTCGAAACTTCTA
1 AAAATTAC-ATTTT-ACCCCTAAACTTCTA
57548 AAAATTACCATTTTACCCCTAAACTTCTA
1 AAAATTA-CATTTTACCCCTAAACTTCTA
* * * **
57577 AAAATTTCATTTTTGACCTC-GATTTTCCTA
1 AAAATTACA-TTTT-ACCCCTAAACTT-CTA
* *
57607 AAATTTACATTTTACCCCCAAA-TGTCTA
1 AAAATTACATTTTACCCCTAAACT-TCTA
* * * *
57635 AAAATTACATTTTGCCCTTGAA-TGTCCA
1 AAAATTACATTTTACCCCTAAACT-TCTA
* *
57663 AAAATTCCATTTTTGACCCCGAAACTTCCTA
1 AAAATTACA-TTTT-ACCCCTAAACTT-CTA
*
57694 AAAAATACCATTTTACCCC
1 AAAATTA-CATTTTACCCC
57713 CGAATGTACA
Statistics
Matches: 240, Mismatches: 48, Indels: 48
0.71 0.14 0.14
Matches are distributed among these distances:
26 3 0.01
27 9 0.04
28 61 0.25
29 48 0.20
30 72 0.30
31 42 0.17
32 2 0.01
33 3 0.01
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTTACCCCTAAACTTCTA
Found at i:57624 original size:58 final size:56
Alignment explanation
Indices: 57365--57707 Score: 201
Period size: 58 Copynumber: 5.9 Consensus size: 56
57355 ACCACCAAAC
* * * * * *
57365 TTTTCC-AAAATCACATTTTGACCCCTAAACTTTTCCAAAATTAAATTTTAACCCTCCAAA
1 TTTTCCTAAAATTACATTTT-ACCCCTAAACTTCT-AAAAATTACATTTTTA-CCT-C-GA
* * * * * * *
57425 TTTTTCTAAAATTATATTTTGACCCTTAAACTTTTTGAAAATTACATTTTTACCCCAAA
1 TTTTCCTAAAATTACATTTT-ACCCCTAAAC-TTCTAAAAATTACATTTTTACCTC-GA
* * * *
57484 CTTTCC-AAAATTACATTTTA-CCCTAAAGCTTCCAAAAATCACGATTTTAACCTCGAA
1 TTTTCCTAAAATTACATTTTACCCCTAAA-CTTCTAAAAATTAC-ATTTTTACCTCG-A
** *
57541 ACTT-CTAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTTCATTTTTGACCTCGA
1 TTTTCCT-AAAATTA-CATTTTACCCCTAAACTTCTAAAAATTACATTTTT-ACCTCGA
* ** *
57599 TTTTCCTAAAATTTACATTTTACCCCCAAA-TGTCTAAAAATTACATTTTGCCCTTGA
1 TTTTCCTAAAA-TTACATTTTACCCCTAAACT-TCTAAAAATTACATTTTTACCTCGA
* * * * * *
57656 ATGTCCAAAAATTCCATTTTTGACCCCGAAACTTCCTAAAAAATACCATTTT
1 TTTTCCTAAAATTACA-TTTT-ACCCCTAAACTT-CTAAAAATTA-CATTTT
57708 ACCCCCGAAT
Statistics
Matches: 227, Mismatches: 38, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
56 20 0.09
57 32 0.14
58 70 0.31
59 47 0.21
60 20 0.09
61 34 0.15
62 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (56 bp):
TTTTCCTAAAATTACATTTTACCCCTAAACTTCTAAAAATTACATTTTTACCTCGA
Found at i:57658 original size:28 final size:28
Alignment explanation
Indices: 57462--57728 Score: 102
Period size: 28 Copynumber: 9.2 Consensus size: 28
57452 AAACTTTTTG
* *
57462 AAAATTACATTTTTA-CCCCAAACTTTC-C
1 AAAATTACA-TTTTACCCCCAAA-TGTCTA
* *
57490 AAAATTACATTTTA-CCCTAAA-GCTTCCA
1 AAAATTACATTTTACCCCCAAATG--TCTA
* * *
57518 AAAATCACGATTTTAACCTCGAAACT-TCTA
1 AAAATTAC-ATTTT-ACCCCCAAA-TGTCTA
*
57548 AAAATTACCATTTTACCCCTAAACT-TCTA
1 AAAATTA-CATTTTACCCCCAAA-TGTCTA
* * * * *
57577 AAAATTTCATTTTTGA-CCTCGATTTTCCTA
1 AAAATTACA-TTTT-ACCCCCAAATGT-CTA
*
57607 AAATTTACATTTTACCCCCAAATGTCTA
1 AAAATTACATTTTACCCCCAAATGTCTA
* *** *
57635 AAAATTACATTTTGCCCTTGAATGTCCA
1 AAAATTACATTTTACCCCCAAATGTCTA
* *
57663 AAAATTCCATTTTTGACCCCGAAACT-TCCTA
1 AAAATTACA-TTTT-ACCCCCAAA-TGT-CTA
* *
57694 AAAAATACCATTTTACCCCCGAATGTAC-A
1 AAAATTA-CATTTTACCCCCAAATGT-CTA
57723 AAAATT
1 AAAATT
57729 TTGGTTTTTA
Statistics
Matches: 180, Mismatches: 39, Indels: 39
0.70 0.15 0.15
Matches are distributed among these distances:
27 13 0.07
28 53 0.29
29 53 0.29
30 41 0.23
31 18 0.10
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAATTACATTTTACCCCCAAATGTCTA
Found at i:57767 original size:146 final size:144
Alignment explanation
Indices: 57462--57792 Score: 329
Period size: 145 Copynumber: 2.3 Consensus size: 144
57452 AAACTTTTTG
* * * *
57462 AAAATTACATTTTTA-CCCCAAACTTTCCAAAATTACATTTTACCC-T-AAAGCTTCCAAAAA-T
1 AAAATTACA-TTTTACCCCCAAA-TGTCTAAAATTACATTTTGCCCTTGAATG--TCCAAAAATT
* * *
57523 CACGA-TTTTAACCTCGAAACTTCTAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTTCAT
62 C-C-ATTTTTAACCCCGAAACTTCTAAAAAATACCATTTTACCCCCAAACTTCTAAAAATTTCAT
*
57587 TTTTGACCTCGATTTTCCTA
125 TTTTGACCACGATTTTCCTA
*
57607 AAATTTACATTTTACCCCCAAATGTCTAAAAATTACATTTTGCCCTTGAATGTCCAAAAATTCCA
1 AAAATTACATTTTACCCCCAAATGTCT-AAAATTACATTTTGCCCTTGAATGTCCAAAAATTCCA
* * **
57672 TTTTTGACCCCGAAACTTCCTAAAAAATACCATTTTACCCCCGAA-TGTAC-AAAAATTTTGGTT
65 TTTTTAACCCCGAAACTT-CTAAAAAATACCATTTTACCCCCAAACT-T-CTAAAAA-TTTCATT
* *
57735 TTT-ATCACGATTTTTCTA
126 TTTGACCACGATTTTCCTA
* * *
57753 AAAATTACCA-TTTACCCTCGAATGTCTAAAATTCCATTTT
1 AAAATTA-CATTTTACCCCCAAATGTCTAAAATTACATTTT
57793 AACCCTAAAA
Statistics
Matches: 156, Mismatches: 19, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
144 9 0.06
145 68 0.44
146 65 0.42
147 14 0.09
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (144 bp):
AAAATTACATTTTACCCCCAAATGTCTAAAATTACATTTTGCCCTTGAATGTCCAAAAATTCCAT
TTTTAACCCCGAAACTTCTAAAAAATACCATTTTACCCCCAAACTTCTAAAAATTTCATTTTTGA
CCACGATTTTCCTA
Found at i:57828 original size:146 final size:144
Alignment explanation
Indices: 57462--57829 Score: 347
Period size: 146 Copynumber: 2.5 Consensus size: 144
57452 AAACTTTTTG
* * * *
57462 AAAATTACATTTTTA-CCCCAAACTTTC-CAAAATTACATTTTACCCTAAAGCTTCCAAAAATCA
1 AAAATTACA-TTTTACCCCCAAA-TGTCTAAAAATTACATTTTACCCTAAA-TTTCCAAAAATTA
* * * *
57525 CGATTTTAACCTCGAAACTTCTAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTTCATTTT
63 CCATTTTAACCCCGAAACTTCTAAAAAATACCATTTTACCCCCAAACTTCTAAAAATTTCATTTT
*
57590 TGACCTCGATTTTCCTA
128 TGACCACGATTTTCCTA
* * * *
57607 AAATTTACATTTTACCCCCAAATGTCTAAAAATTACATTTTGCCCTTGAATGTCCAAAAATT-CC
1 AAAATTACATTTTACCCCCAAATGTCTAAAAATTACATTTTACCC-TAAATTTCCAAAAATTACC
* * **
57671 ATTTTTGACCCCGAAACTTCCTAAAAAATACCATTTTACCCCCGAA-TGTAC-AAAAATTTTGGT
65 A-TTTTAACCCCGAAACTT-CTAAAAAATACCATTTTACCCCCAAACT-T-CTAAAAA-TTTCAT
* *
57734 TTTT-ATCACGATTTTTCTA
125 TTTTGACCACGATTTTCCTA
* * * *
57753 AAAATTACCA-TTTACCCTCGAATGTCT-AAAATTCCATTTTAACCCTAAAATTTTCCCAAAATT
1 AAAATTA-CATTTTACCCCCAAATGTCTAAAAATTACATTTT-ACCCT-AAA-TTTCCAAAAATT
*
57816 ACCATTTTACCCCC
62 ACCATTTTAACCCC
57830 TAATAGTCCA
Statistics
Matches: 181, Mismatches: 29, Indels: 24
0.77 0.12 0.10
Matches are distributed among these distances:
144 10 0.06
145 69 0.38
146 70 0.39
147 29 0.16
148 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (144 bp):
AAAATTACATTTTACCCCCAAATGTCTAAAAATTACATTTTACCCTAAATTTCCAAAAATTACCA
TTTTAACCCCGAAACTTCTAAAAAATACCATTTTACCCCCAAACTTCTAAAAATTTCATTTTTGA
CCACGATTTTCCTA
Found at i:57871 original size:29 final size:29
Alignment explanation
Indices: 57753--57870 Score: 91
Period size: 29 Copynumber: 4.1 Consensus size: 29
57743 GATTTTTCTA
* *
57753 AAAATTACCA-TTTACCCTCGAAT-GTCT
1 AAAATTACCATTTTACCCCCGAATAGTCC
*** **
57780 AAAATT-CCATTTTAACCCTAAAATTTTCCC
1 AAAATTACCATTTT-ACCCCCGAATAGT-CC
*
57810 AAAATTACCATTTTACCCCCTAATAGTCC
1 AAAATTACCATTTTACCCCCGAATAGTCC
* * *
57839 AAAATTACCATTTTGCCCTCGGATA-TCC
1 AAAATTACCATTTTACCCCCGAATAGTCC
57867 AAAA
1 AAAA
57871 AGTCTCATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.04
27 9 0.12
28 15 0.21
29 24 0.33
30 15 0.21
31 7 0.10
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAATAGTCC
Found at i:61078 original size:3 final size:3
Alignment explanation
Indices: 61072--61099 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
61062 TCAAAACCCA
61072 TGC TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC T
61100 CATTTGAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:67772 original size:5 final size:5
Alignment explanation
Indices: 67762--67788 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
67752 ATTTACCCTA
67762 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
67789 AATCTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:71061 original size:2 final size:2
Alignment explanation
Indices: 71054--71087 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
71044 TGAAAATTTA
71054 AT AT 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 AT AT
71088 TGTATTAAAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72752 original size:21 final size:23
Alignment explanation
Indices: 72728--72777 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
72718 TTTCAATATA
72728 TAAAAATAT-TAAATAT-TAAAT
1 TAAAAATATATAAATATATAAAT
72749 TAAAAA-ATATAAATATATAAAT
1 TAAAAATATATAAATATATAAAT
*
72771 TTAAAAT
1 TAAAAAT
72778 TTTGTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAAATATATAAATATATAAAT
Found at i:72757 original size:22 final size:22
Alignment explanation
Indices: 72729--72776 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
72719 TTCAATATAT
72729 AAAAATATTAAATAT-TAAATTA
1 AAAAATA-TAAATATATAAATTA
*
72751 AAAAATATAAATATATAAATTT
1 AAAAATATAAATATATAAATTA
72773 AAAA
1 AAAA
72777 TTTTGTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATATAAATATATAAATTA
Found at i:72766 original size:8 final size:8
Alignment explanation
Indices: 72722--72770 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
72712 ATAACATTTC
72722 AATATATA
1 AATATATA
*
72730 AAAATATTA
1 AATATA-TA
72739 AATAT-TA
1 AATATATA
72746 AAT-TA-A
1 AATATATA
*
72752 AAAATATA
1 AATATATA
72760 AATATATA
1 AATATATA
72768 AAT
1 AAT
72771 TTAAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
6 4 0.12
7 7 0.21
8 16 0.48
9 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATATA
Found at i:80364 original size:3 final size:3
Alignment explanation
Indices: 80356--80406 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
80346 TTGATGTTTG
80356 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
80404 CTT
1 CTT
80407 TGGAGAAAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:81758 original size:18 final size:19
Alignment explanation
Indices: 81737--81774 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
81727 TTTTAAACAA
81737 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
* *
81755 TATAAATCTTTTGAATTTT
1 TATAAATATTTAGAATTTT
81774 T
1 T
81775 TTGTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:90459 original size:13 final size:12
Alignment explanation
Indices: 90432--90456 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90422 AAATTATATA
90432 TAAAAATTTAAT
1 TAAAAATTTAAT
90444 TAAAAATTTAAT
1 TAAAAATTTAAT
90456 T
1 T
90457 TAATTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATTTAAT
Found at i:91616 original size:2 final size:2
Alignment explanation
Indices: 91609--91640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
91599 TAATTTACTC
91609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91641 CAAACACGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:99869 original size:7 final size:7
Alignment explanation
Indices: 99837--99870 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
99827 TTCAATCGTA
*
99837 GGTTAGG
1 GGTTCGG
*
99844 GGTTAGG
1 GGTTCGG
99851 GGTTCGG
1 GGTTCGG
99858 GGTTCGG
1 GGTTCGG
99865 GGTTCG
1 GGTTCG
99871 AGATTCAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.06, C:0.09, G:0.56, T:0.29
Consensus pattern (7 bp):
GGTTCGG
Found at i:102581 original size:36 final size:35
Alignment explanation
Indices: 102506--102579 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
102496 AAGTTCGAGG
* *
102506 TTTATTATATGTAATTGTATGTATGGGTTTTCGAAT
1 TTTATTATATGCAATTGTATGTATGCGTTTTC-AAT
* *
102542 TTTATTATGTGCAATTGTTATGTGTGCGTTTT-AAT
1 TTTATTATATGCAATTG-TATGTATGCGTTTTCAAT
102577 TTT
1 TTT
102580 TAGTCTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 6 0.18
36 15 0.45
37 12 0.36
ACGTcount: A:0.22, C:0.04, G:0.19, T:0.55
Consensus pattern (35 bp):
TTTATTATATGCAATTGTATGTATGCGTTTTCAAT
Found at i:103120 original size:29 final size:29
Alignment explanation
Indices: 103066--103122 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
103056 AAACCGATAA
*
103066 TCAATTAAACCATTAATCGAAAATAATAC
1 TCAATTAAACCATTAATCAAAAATAATAC
*
103095 TCAATTAAACCCTTAAT-AAAATATAATA
1 TCAATTAAACCATTAATCAAAA-ATAATA
103123 ACTGGGGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.30
Consensus pattern (29 bp):
TCAATTAAACCATTAATCAAAAATAATAC
Found at i:104104 original size:60 final size:60
Alignment explanation
Indices: 103995--104123 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
103985 GTTTAATCTC
* * * * ** * *
103995 TTTTTTTTTTATCTAAGTTAATTTTTAAACTTGATAATTATTTTTACATTGCGATTTGAA
1 TTTTTTTTTTATCTAAGTTAATCTCTAAACTTAACAATTATTTGCACATTGCGACTTCAA
* *
104055 TTTTTTTTTTATCTAAGTTAATCTCTGAACTTAACAATTATTTGCACATTGGGACTTCAA
1 TTTTTTTTTTATCTAAGTTAATCTCTAAACTTAACAATTATTTGCACATTGCGACTTCAA
*
104115 CTTTTTTTT
1 TTTTTTTTT
104124 GGTCCAAGTT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (60 bp):
TTTTTTTTTTATCTAAGTTAATCTCTAAACTTAACAATTATTTGCACATTGCGACTTCAA
Found at i:104301 original size:2 final size:2
Alignment explanation
Indices: 104294--104327 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
104284 TCCCACTCTT
104294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
104328 ATTGTGTTAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:104581 original size:17 final size:18
Alignment explanation
Indices: 104548--104580 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
104538 ATTTTTATAT
104548 ATTTTCTTAAAAATTTTC
1 ATTTTCTTAAAAATTTTC
104566 ATTTT-TT-AAAATTTT
1 ATTTTCTTAAAAATTTT
104581 TAAAAGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 2 0.13
18 5 0.33
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTCTTAAAAATTTTC
Found at i:109884 original size:21 final size:23
Alignment explanation
Indices: 109860--109903 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
109850 TTCATCTTAA
*
109860 TTAATACTTT-ACTATA-ATTTT
1 TTAATAATTTCACTATAGATTTT
109881 TTAATAATTTCACTATAGATTTT
1 TTAATAATTTCACTATAGATTTT
109904 GATCATATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAATAATTTCACTATAGATTTT
Found at i:115086 original size:34 final size:32
Alignment explanation
Indices: 115047--115112 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
115037 AATTTTTAAA
* *
115047 TTTAAAATATTTATAAAAAATTCTAAATTTATAT
1 TTTAAAAGA-TTAT-AAAAATTCTAAATATATAT
*
115081 TTTAAAAGATTCTAAAAATTCTAAATATATAT
1 TTTAAAAGATTATAAAAATTCTAAATATATAT
115113 ATAAAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 18 0.62
33 3 0.10
34 8 0.28
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTAAAAGATTATAAAAATTCTAAATATATAT
Found at i:116801 original size:39 final size:38
Alignment explanation
Indices: 116729--116803 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 38
116719 AATTCGATAC
*
116729 TTAAATTAAATTAATTAATTTAAATAATAAAAATATTT
1 TTAAATTAAATTAATTAATTAAAATAATAAAAATATTT
*
116767 TTAAATTTAAATTTAATT-A-TAAAATTATATAAAATAT
1 TTAAA-TTAAA-TTAATTAATTAAAATAATA-AAAATAT
116804 AAATTAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 13 0.41
39 13 0.41
40 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (38 bp):
TTAAATTAAATTAATTAATTAAAATAATAAAAATATTT
Found at i:119874 original size:6 final size:6
Alignment explanation
Indices: 119863--119890 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
119853 CAATAGGAAA
119863 CCCAAC CCCAAC CCCAAC CCCAAC CCCA
1 CCCAAC CCCAAC CCCAAC CCCAAC CCCA
119891 TAAAAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAC
Found at i:135703 original size:93 final size:93
Alignment explanation
Indices: 135544--135728 Score: 370
Period size: 93 Copynumber: 2.0 Consensus size: 93
135534 ACCCTTTACC
135544 ATGCTGACTACAACAATCGTAGCCCTGATGCTAACCACAAGATTAATAGGACGACTACCATGAAA
1 ATGCTGACTACAACAATCGTAGCCCTGATGCTAACCACAAGATTAATAGGACGACTACCATGAAA
135609 TTCACTATCCAGTCATTCCTTTCGAGCT
66 TTCACTATCCAGTCATTCCTTTCGAGCT
135637 ATGCTGACTACAACAATCGTAGCCCTGATGCTAACCACAAGATTAATAGGACGACTACCATGAAA
1 ATGCTGACTACAACAATCGTAGCCCTGATGCTAACCACAAGATTAATAGGACGACTACCATGAAA
135702 TTCACTATCCAGTCATTCCTTTCGAGC
66 TTCACTATCCAGTCATTCCTTTCGAGC
135729 AAAGAGAATT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (93 bp):
ATGCTGACTACAACAATCGTAGCCCTGATGCTAACCACAAGATTAATAGGACGACTACCATGAAA
TTCACTATCCAGTCATTCCTTTCGAGCT
Found at i:141127 original size:76 final size:76
Alignment explanation
Indices: 140984--141127 Score: 200
Period size: 76 Copynumber: 1.9 Consensus size: 76
140974 AATAGAAACT
* * * * **
140984 TAGGGGGCCATGGTTCCCAAAGTTTAAAAGTTTTTCAATTTAGCCATTTGTAATATACCACGGCT
1 TAGGGAGCCATGGTTCCCAAAGTTTAAAAGTTTTTAAATTTAACCATTTATAATATACCACAACT
141049 CTCCTAATATC
66 CTCCTAATATC
* *
141060 TAGGGAGCCATGGCTT-CCAAAGTTTAAAAGTTTTTAAATTTAACCATTTATAATATACTATAAC
1 TAGGGAGCCATGG-TTCCCAAAGTTTAAAAGTTTTTAAATTTAACCATTTATAATATACCACAAC
141124 TCTC
65 TCTC
141128 TCGATAATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
76 57 0.97
77 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (76 bp):
TAGGGAGCCATGGTTCCCAAAGTTTAAAAGTTTTTAAATTTAACCATTTATAATATACCACAACT
CTCCTAATATC
Found at i:143749 original size:52 final size:52
Alignment explanation
Indices: 143641--143750 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 52
143631 GTGGAGGGGA
**********
143641 TTTTTTTTTTTGTAAAAAGTGGATGTAGAATGGGACGAGGTGNNNNNNNNNN
1 TTTTTTTTTTTGTAAAAAGTGGATGTAGAATGGGACGAGGTGGATTTTTTTT
143693 TTTTTTTTTTTGTAAAAAGTGGATGTAGAATGGGACGAGGTGGATTTTTTTT
1 TTTTTTTTTTTGTAAAAAGTGGATGTAGAATGGGACGAGGTGGATTTTTTTT
143745 TTTTTT
1 TTTTTT
143751 GAATAATGAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.21, C:0.02, G:0.25, T:0.44
Consensus pattern (52 bp):
TTTTTTTTTTTGTAAAAAGTGGATGTAGAATGGGACGAGGTGGATTTTTTTT
Found at i:147149 original size:20 final size:20
Alignment explanation
Indices: 147102--147149 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
147092 AAAATGAAAA
147102 TAAAATATTTAACAATTTAC
1 TAAAATATTTAACAATTTAC
* * ** *
147122 CAATATATTTAAGGATTTAT
1 TAAAATATTTAACAATTTAC
147142 TAAAATAT
1 TAAAATAT
147150 ACAACGATTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (20 bp):
TAAAATATTTAACAATTTAC
Found at i:147180 original size:20 final size:20
Alignment explanation
Indices: 147156--147209 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
147146 ATATACAACG
*
147156 ATTTATCAAAATTTCTATCA
1 ATTTATCAAAATTTATATCA
* * *
147176 TTTTATCAATATTTATATGA
1 ATTTATCAAAATTTATATCA
147196 ATTTATCAAAATTT
1 ATTTATCAAAATTT
147210 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTATCAAAATTTATATCA
Found at i:148141 original size:26 final size:26
Alignment explanation
Indices: 148098--148156 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
148088 CAATATATAT
*
148098 TTATCTATTAATTAAATACAACTTCAA
1 TTAT-TATTAATTAAATACAACTTAAA
*
148125 TTATTATTAATTGAATACAACTTAAA
1 TTATTATTAATTAAATACAACTTAAA
148151 TTATTA
1 TTATTA
148157 ATTCGATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
TTATTATTAATTAAATACAACTTAAA
Found at i:150899 original size:117 final size:117
Alignment explanation
Indices: 150685--150922 Score: 440
Period size: 117 Copynumber: 2.0 Consensus size: 117
150675 GTTAAAATCT
150685 ATGTCCTTTTCATGCCACTTATTCCTGGGAAGTTAACTTGATTGTTTCCCATTTTCATGTTGCTC
1 ATGTCCTTTTCATGCCACTTATTCCTGGGAAGTTAACTTGATTGTTTCCCATTTTCATGTTGCTC
* *
150750 AAAATTGAAAATTTCTTCCGTGAGTAGTTAATCCCTAATCAGTTGTCAGTGC
66 AAAATTGAAAATTTCTTCCGTGAGCAGCTAATCCCTAATCAGTTGTCAGTGC
150802 ATGTCCTTTTCATGCCACTTATTCCTGGGAAGTTAACTTGATTGTTTCCCATTTTCATGTTGCTC
1 ATGTCCTTTTCATGCCACTTATTCCTGGGAAGTTAACTTGATTGTTTCCCATTTTCATGTTGCTC
* *
150867 AAAATTGAAAATTTCTTTCGTGAGCAGCTAATCCCTAATCGGTTGTCAGTGC
66 AAAATTGAAAATTTCTTCCGTGAGCAGCTAATCCCTAATCAGTTGTCAGTGC
150919 ATGT
1 ATGT
150923 ATTTTGGAAT
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (117 bp):
ATGTCCTTTTCATGCCACTTATTCCTGGGAAGTTAACTTGATTGTTTCCCATTTTCATGTTGCTC
AAAATTGAAAATTTCTTCCGTGAGCAGCTAATCCCTAATCAGTTGTCAGTGC
Found at i:161882 original size:6 final size:6
Alignment explanation
Indices: 161871--161902 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
161861 ATTGATAGTG
161871 AACTCA AACTCA AACTCA AACTCA AACTCA AA
1 AACTCA AACTCA AACTCA AACTCA AACTCA AA
161903 TACATGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.16
Consensus pattern (6 bp):
AACTCA
Found at i:169699 original size:17 final size:17
Alignment explanation
Indices: 169674--169719 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
169664 TAAATAAAAA
*
169674 AAATAGTTAAAGAAGATG
1 AAAT-GTTAAAGAAAATG
*
169692 AAATGTTAAAAAAAATG
1 AAATGTTAAAGAAAATG
*
169709 AAATATTAAAG
1 AAATGTTAAAG
169720 GTTAAGGGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (17 bp):
AAATGTTAAAGAAAATG
Found at i:170142 original size:104 final size:104
Alignment explanation
Indices: 169957--170159 Score: 291
Period size: 104 Copynumber: 2.0 Consensus size: 104
169947 AATCAATTGT
* * *
169957 CGAATGAGTTTTAGTTCAATTGGTATAAATATTGTTGTCAATGTAAGAGGACGTAAGTTCGAGTA
1 CGAATGAGTTTTAGTTCAATTGGTATAAATATTATTGTCAATATAAGAGGACGTAAGTTCGAATA
*
170022 CGCTGAAGCATATTATCCTCCTATTTATAAGTTGGTTAC
66 CGCTGAAACATATTATCCTCCTATTTATAAGTTGGTTAC
* *
170061 CGAATGAGTTTTAGTTCGATTGGTATAAATATTATTGTCAATATAAGAGGACGTGAGCTT-GAAT
1 CGAATGAGTTTTAGTTCAATTGGTATAAATATTATTGTCAATATAAGAGGACGTAAG-TTCGAAT
* ** * *
170125 GCGCTGAAATGTCTTATCCTCTTATTTATAAGTTG
65 ACGCTGAAACATATTATCCTCCTATTTATAAGTTG
170160 AGGAGAGACT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 85 0.98
105 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (104 bp):
CGAATGAGTTTTAGTTCAATTGGTATAAATATTATTGTCAATATAAGAGGACGTAAGTTCGAATA
CGCTGAAACATATTATCCTCCTATTTATAAGTTGGTTAC
Found at i:172855 original size:31 final size:31
Alignment explanation
Indices: 172819--172886 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
172809 AATTAATTTA
* *
172819 GTCACTAATGTTTTAGATAATTTTTATTTTG
1 GTCACTAACGTTTTAGATAATTTTTATTTCG
* **
172850 GTCACTCACGTTTTAGATCGTTTTTATTTCG
1 GTCACTAACGTTTTAGATAATTTTTATTTCG
172881 GTCACT
1 GTCACT
172887 TTTCTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.50
Consensus pattern (31 bp):
GTCACTAACGTTTTAGATAATTTTTATTTCG
Found at i:173071 original size:13 final size:13
Alignment explanation
Indices: 173040--173064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173030 TACATAATAT
173040 TATTTATATTAAA
1 TATTTATATTAAA
173053 TATTTATATTAA
1 TATTTATATTAA
173065 TGTTTTAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTATATTAAA
Found at i:188234 original size:20 final size:19
Alignment explanation
Indices: 188209--188248 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
188199 ATATTATTAA
188209 ATGTTTTTGTTTTTGTTTTT
1 ATGTTTTT-TTTTTGTTTTT
*
188229 ATGTTTTTTTTTTTTTTTT
1 ATGTTTTTTTTTTGTTTTT
188248 A
1 A
188249 GAATGAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.82
Consensus pattern (19 bp):
ATGTTTTTTTTTTGTTTTT
Found at i:193775 original size:16 final size:16
Alignment explanation
Indices: 193754--193808 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
193744 GTGAGCTGTA
193754 AGCTCAACAAGGTGCG
1 AGCTCAACAAGGTGCG
* *
193770 AGCTCAGCAAAAAGAATGCG
1 AGCT---CAACAAG-GTGCG
193790 AGCTCAACAAGGTGCG
1 AGCTCAACAAGGTGCG
193806 AGC
1 AGC
193809 CATCAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 11 0.35
17 6 0.19
19 6 0.19
20 8 0.26
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.11
Consensus pattern (16 bp):
AGCTCAACAAGGTGCG
Found at i:193855 original size:30 final size:30
Alignment explanation
Indices: 193814--193926 Score: 172
Period size: 30 Copynumber: 3.8 Consensus size: 30
193804 CGAGCCATCA
* * *
193814 AAAGTGCGAGCCTGTTAAAGATAGTAAGCT
1 AAAGTGCGAGCCTGTCAAAGACAGTAAGCC
*
193844 AAAGTGTGAGCCTGTCAAAGACAGTAAGCC
1 AAAGTGCGAGCCTGTCAAAGACAGTAAGCC
*
193874 AAAGTGTGAGCCTGTCAAAGACAGTAAGCC
1 AAAGTGCGAGCCTGTCAAAGACAGTAAGCC
*
193904 AAAGTGCGAGCCTGTTAAAGACA
1 AAAGTGCGAGCCTGTCAAAGACA
193927 ACAAGCAAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.19
Consensus pattern (30 bp):
AAAGTGCGAGCCTGTCAAAGACAGTAAGCC
Found at i:193908 original size:60 final size:59
Alignment explanation
Indices: 193814--193952 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
193804 CGAGCCATCA
* * * * * **
193814 AAAGTGCGAGCCTGTTAAAGATAGTAAGCTAAAGTGTGAGCCTGTCAAAGACAGTAAGCC
1 AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTCAAAGACAACAAG-C
*
193874 AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTTAAAGACAACAAGC
1 AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTCAAAGACAACAAGC
* * *
193933 AAATTATGAGTCTGTCAAAG
1 AAAGTGTGAGCCTGTCAAAG
193953 TGTGAGCCTG
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 18 0.26
60 50 0.74
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (59 bp):
AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTCAAAGACAACAAGC
Done.