Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015204.1 Kokia drynarioides strain JFW-HI SEQ_130248, 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: 184191
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 455 characters in sequence are not A, C, G, or T
Found at i:2396 original size:17 final size:17
Alignment explanation
Indices: 2374--2406 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2364 ATTTGGTTCG
*
2374 AAATTTAGTAATTAATC
1 AAATTTAATAATTAATC
2391 AAATTTAATAATTAAT
1 AAATTTAATAATTAAT
2407 AATACAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATTTAATAATTAATC
Found at i:8297 original size:21 final size:21
Alignment explanation
Indices: 8270--8320 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
8260 AATAATTTTT
8270 AACCCTAAATCTC-AAACCTTA
1 AACCCTAAATC-CAAAACCTTA
* *
8291 AATCCTAAATCCAAAACTTTA
1 AACCCTAAATCCAAAACCTTA
8312 AACCCTAAA
1 AACCCTAAA
8321 CATTAAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCCTAAATCCAAAACCTTA
Found at i:12722 original size:14 final size:14
Alignment explanation
Indices: 12705--12742 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
12695 TTAAACCCTA
*
12705 AACCATAAACTATG
1 AACCCTAAACTATG
*
12719 AACCCTAAACTTTG
1 AACCCTAAACTATG
12733 AACCCTAAAC
1 AACCCTAAAC
12743 CTAAATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.29, G:0.05, T:0.21
Consensus pattern (14 bp):
AACCCTAAACTATG
Found at i:14211 original size:18 final size:19
Alignment explanation
Indices: 14171--14212 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
14161 TTATATTTAA
14171 AAAAATATATAAAAATTCT
1 AAAAATATATAAAAATTCT
14190 -AAAATAGT-TAAAAATT-T
1 AAAAATA-TATAAAAATTCT
14207 AAAAAT
1 AAAAAT
14213 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAATATATAAAAATTCT
Found at i:20279 original size:65 final size:65
Alignment explanation
Indices: 20175--20303 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 65
20165 CCACAGCTTC
* *
20175 AGGTTGGATTTCTTGTCAATTTCAACATTATTTTATGACTTCAAATTTCTAGATGTAAGATTCTG
1 AGGTTGGATTTCATGTCAATTTCAACATTATCTTATGACTTCAAATTTCTAGATGTAAGATTCTG
20240 AGGTTGGATTTCATGTCAATTTCAACATTATCTTATGACTTCAAATTTCTAGATGTAAGATTCT
1 AGGTTGGATTTCATGTCAATTTCAACATTATCTTATGACTTCAAATTTCTAGATGTAAGATTCT
20304 TACTGATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (65 bp):
AGGTTGGATTTCATGTCAATTTCAACATTATCTTATGACTTCAAATTTCTAGATGTAAGATTCTG
Found at i:25486 original size:3 final size:3
Alignment explanation
Indices: 25478--25522 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
25468 AATGTCATTT
* *
25478 ATC ATC ATC ATC GTC ATC ATC ATC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
25523 CAGCACCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:25498 original size:15 final size:15
Alignment explanation
Indices: 25478--25519 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
25468 AATGTCATTT
25478 ATCATCATCATCGTC
1 ATCATCATCATCGTC
25493 ATCATCATCATCGTC
1 ATCATCATCATCGTC
25508 ATCATCATCATC
1 ATCATCATCATC
25520 ATCCAGCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.29, C:0.33, G:0.05, T:0.33
Consensus pattern (15 bp):
ATCATCATCATCGTC
Found at i:38151 original size:19 final size:19
Alignment explanation
Indices: 38116--38193 Score: 81
Period size: 18 Copynumber: 4.1 Consensus size: 19
38106 TTTTTAAAAA
*
38116 TATAAATA-TTAGAATTTT
1 TATAAATATTTTGAATTTT
38134 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
38152 TAAAAATTATTTTGAATTTT
1 TATAAA-TATTTTGAATTTT
38172 T-TAAAATAATTTTGAACTTTT
1 TAT-AAAT-ATTTTGAA-TTTT
38193 T
1 T
38194 TTTTTGTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
18 16 0.31
19 15 0.29
20 15 0.29
21 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:38177 original size:20 final size:20
Alignment explanation
Indices: 38086--38194 Score: 84
Period size: 19 Copynumber: 5.3 Consensus size: 20
38076 TCTTTAGATT
38086 TTTTTTAAAATT-TTTAT-AA
1 TTTTTTAAAATTATTT-TGAA
*
38105 TTTTTTAAAAATATAAATATTAGAA
1 TTTTTT-AAAAT-T--AT-TTTGAA
38130 -TTTTTATAAA-TATTTTGAA
1 TTTTTTA-AAATTATTTTGAA
*
38149 -TTTTAAAAATTATTTTGAA
1 TTTTTTAAAATTATTTTGAA
*
38168 TTTTTTAAAATAATTTTGAA
1 TTTTTTAAAATTATTTTGAA
38188 CTTTTTT
1 -TTTTTT
38195 TTTTGTAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.04
19 25 0.34
20 24 0.32
21 7 0.09
22 1 0.01
23 1 0.01
24 9 0.12
25 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTAAAATTATTTTGAA
Found at i:38803 original size:19 final size:19
Alignment explanation
Indices: 38779--38817 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38769 TTATTTTAAC
*
38779 ATAATTTTTAATATTTTTA
1 ATAATTTATAATATTTTTA
*
38798 ATAATTTATATTATTTTTA
1 ATAATTTATAATATTTTTA
38817 A
1 A
38818 GTTTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATAATTTATAATATTTTTA
Found at i:42806 original size:220 final size:219
Alignment explanation
Indices: 42415--42857 Score: 690
Period size: 220 Copynumber: 2.0 Consensus size: 219
42405 GGTTCGACCA
* * *
42415 ATGGTTGCTGCTGCAACAGGGTTTGAAAATGGAGAAAAGGCGAAACCCAGAGTCAACGAGTGGCC
1 ATGGCTGCTACTGCAACAGGGTCTGAAAATGGAGAAAAGGCGAAACCCAGAGTCAACGAGTGGCC
* *
42480 AAACTCACGGAGGACATACAGAAGCAAAAGGATAGACATGGAACACGACAAAGGGAAAGTCGACA
66 AAACTCACGGACGACATACAGAAGCAAAAGGATAGACATGGAACACGACAAAGGGAAAGTCCACA
* ** *
42545 ATGTGGATGAAACAGAGGATTCCGGTGGCTTGACTAGGTTTCGATATAGAACAGCGACCAGCCGT
131 ATGTAGATGAAACAGAGGATTCCAATGACTTGACTAGGTTTCGATATAGAACAGCGACCAGCCGT
*
42610 CGAACGTTTAAGTCGATGAGGACG
196 CGAACGTTTAAGTCGATGAAGACG
* *
42634 ATGGCTGCTACTGCAACAGGGTCTGAAAATGGAGAAGAGGCGAAACCCCAGAGTCAATGAGTGGC
1 ATGGCTGCTACTGCAACAGGGTCTGAAAATGGAGAAAAGGCGAAA-CCCAGAGTCAACGAGTGGC
* * * *
42699 CAAACTCACGGCCGACATACAGAAGCGAAAGGATAGACATGGAA-ATGGACGAAGGGAAAGTCCA
65 CAAACTCACGGACGACATACAGAAGCAAAAGGATAGACATGGAACA-CGACAAAGGGAAAGTCCA
* *
42763 CAATGTAGTTGAAACAGAGGATTCCAATGACTTGCCTAGGTTTCGATATAGAACAGCGACCAGCC
129 CAATGTAGATGAAACAGAGGATTCCAATGACTTGACTAGGTTTCGATATAGAACAGCGACCAGCC
*
42828 GTCGAACGTTTAAGTCGATGAATACG
194 GTCGAACGTTTAAGTCGATGAAGACG
42854 ATGG
1 ATGG
42858 AAGGCGAGGA
Statistics
Matches: 203, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
219 42 0.21
220 161 0.79
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (219 bp):
ATGGCTGCTACTGCAACAGGGTCTGAAAATGGAGAAAAGGCGAAACCCAGAGTCAACGAGTGGCC
AAACTCACGGACGACATACAGAAGCAAAAGGATAGACATGGAACACGACAAAGGGAAAGTCCACA
ATGTAGATGAAACAGAGGATTCCAATGACTTGACTAGGTTTCGATATAGAACAGCGACCAGCCGT
CGAACGTTTAAGTCGATGAAGACG
Found at i:47563 original size:29 final size:28
Alignment explanation
Indices: 47538--47662 Score: 128
Period size: 30 Copynumber: 4.3 Consensus size: 28
47528 TCAAAATTGG
47538 AATTTTTG-AGGTTCGAGGGTAAAAATGT
1 AATTTTTGAAGGTTCG-GGGTAAAAATGT
* *
47566 AATTTTTGGAAGTTTTGGGGTCAAAAATGT
1 AATTTTT-GAAGGTTCGGGGT-AAAAATGT
47596 AATTTTTGGAA-GTTCGAGGGTAAAAATGT
1 AATTTTT-GAAGGTTCG-GGGTAAAAATGT
* * *
47625 AATTTTTGAAAGTTTTGGGGTAAAAAATGG
1 AATTTTTG-AAGGTTCGGGGT-AAAAATGT
47655 AATTTTTG
1 AATTTTTG
47663 GATGGTTTAG
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
28 8 0.10
29 29 0.35
30 46 0.55
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.38
Consensus pattern (28 bp):
AATTTTTGAAGGTTCGGGGTAAAAATGT
Found at i:47594 original size:30 final size:29
Alignment explanation
Indices: 47554--47664 Score: 161
Period size: 30 Copynumber: 3.8 Consensus size: 29
47544 TGAGGTTCGA
47554 GGGTAAAAATGTAATTTTTGGAAGTTTTG
1 GGGTAAAAATGTAATTTTTGGAAGTTTTG
*
47583 GGGTCAAAAATGTAATTTTTGGAAG-TTCG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTTG
*
47612 AGGGTAAAAATGTAATTTTTGAAAGTTTTG
1 -GGGTAAAAATGTAATTTTTGGAAGTTTTG
*
47642 GGGTAAAAAATGGAATTTTTGGA
1 GGGT-AAAAATGTAATTTTTGGA
47665 TGGTTTAGGG
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
29 30 0.41
30 43 0.59
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTTG
Found at i:47614 original size:59 final size:59
Alignment explanation
Indices: 47493--47664 Score: 231
Period size: 59 Copynumber: 2.9 Consensus size: 59
47483 TTTGGACATC
* * *** * *
47493 CGAGGGT-AAAATGGCAATTTTTGAAACTTTCAAGGTCAAAATTGGAATTTTT-GAGGTT
1 CGAGGGTAAAAAT-GTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
* *
47551 CGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGTAATTTTTGGAAGTT
1 CGAGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
*
47610 CGAGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTAAAAAATGGAATTTTTGGA
1 CGAGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGA
47665 TGGTTTAGGG
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
58 38 0.38
59 62 0.62
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (59 bp):
CGAGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
Found at i:48786 original size:30 final size:30
Alignment explanation
Indices: 48718--48787 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
48708 CTTCTTTTTT
* * *
48718 TTATGTATTATCTATTATTTATTAAATATTA
1 TTAT-TATTATCTATTATTAATAAAATAATA
48749 -TAGTTATTATC-ATTATTAATAATAATAATA
1 TTA-TTATTATCTATTATTAATAA-AATAATA
48779 TTATTATTA
1 TTATTATTA
48788 AAACGTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 9 0.27
30 21 0.64
31 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (30 bp):
TTATTATTATCTATTATTAATAAAATAATA
Found at i:48801 original size:27 final size:23
Alignment explanation
Indices: 48774--48823 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
48764 TTAATAATAA
48774 TAATAT-TATTATTAAAACGTTATT
1 TAATATAT-TTATTAAAACGTT-TT
*
48798 TAATATATTTATTAATACGTTTT
1 TAATATATTTATTAAAACGTTTT
48821 TAA
1 TAA
48824 AAGAACGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 18 0.75
25 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
TAATATATTTATTAAAACGTTTT
Found at i:51935 original size:80 final size:79
Alignment explanation
Indices: 51802--52158 Score: 554
Period size: 80 Copynumber: 4.5 Consensus size: 79
51792 GAGTTCGTGA
* *
51802 ATCATGTGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGATCATC
1 ATCATG-GGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATC
51867 CGATCTTTTACCCCG
65 CGATCTTTTACCCCG
*
51882 ATCATAGGGCTA-ATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCAT
1 ATCAT-GGGC-AGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCAT
51946 CCGATCTTTTACCCCG
64 CCGATCTTTTACCCCG
* *
51962 ATCATGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAAGATTAAAGACCATCC
1 ATCATGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCC
52027 GATCTTTTACCCCG
66 GATCTTTTACCCCG
* * * * *
52041 ATCATGGGGCAGATTGAAAAAATCCAATCTTTTACCCTAACTAAAGGGCAAGATTGAAGACCATG
1 ATCAT-GGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATC
*
52106 CAATCTTTTACCCCG
65 CGATCTTTTACCCCG
*
52121 ATCATGAGGCAGATTGAAGAAATTCAATCTTTTACCCT
1 ATCATG-GGCAGATTGAAGAAATCCAATCTTTTACCCT
52159 GACTATGGGG
Statistics
Matches: 258, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
78 1 0.00
79 75 0.29
80 180 0.70
81 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (79 bp):
ATCATGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCC
GATCTTTTACCCCG
Found at i:52098 original size:159 final size:160
Alignment explanation
Indices: 51802--52163 Score: 595
Period size: 159 Copynumber: 2.3 Consensus size: 160
51792 GAGTTCGTGA
* * *
51802 ATCATGTGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTAAAGATCATC
1 ATCATGAGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAAGATTAAAGACCATC
* *
51867 CGATCTTTTACCCCGATCATAGGGCTAATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCA
66 CGATCTTTTACCCCGATCATAGGGCTAATTGAAAAAATCCAATCTTTTACCCTAACCAAAGGGCA
*
51932 AGATTGAAGACCATCCGATCTTTTACCCCG
131 AGATTGAAGACCATCCAATCTTTTACCCCG
51962 ATCATG-GGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAAGATTAAAGACCATC
1 ATCATGAGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAAGATTAAAGACCATC
* *
52026 CGATCTTTTACCCCGATCATGGGGC-AGATTGAAAAAATCCAATCTTTTACCCTAACTAAAGGGC
66 CGATCTTTTACCCCGATCATAGGGCTA-ATTGAAAAAATCCAATCTTTTACCCTAACCAAAGGGC
*
52090 AAGATTGAAGACCATGCAATCTTTTACCCCG
130 AAGATTGAAGACCATCCAATCTTTTACCCCG
*
52121 ATCATGAGGCAGATTGAAGAAAT-TCAATCTTTTACCCTGACTA
1 ATCATGAGGCAGATTGAAGAAATCT-AATCTTTTACCCTAACTA
52164 TGGGGTAAAT
Statistics
Matches: 190, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
158 1 0.01
159 150 0.79
160 39 0.21
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (160 bp):
ATCATGAGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAAGATTAAAGACCATC
CGATCTTTTACCCCGATCATAGGGCTAATTGAAAAAATCCAATCTTTTACCCTAACCAAAGGGCA
AGATTGAAGACCATCCAATCTTTTACCCCG
Found at i:52964 original size:63 final size:62
Alignment explanation
Indices: 52889--53020 Score: 153
Period size: 63 Copynumber: 2.1 Consensus size: 62
52879 TATAATTTTT
52889 ATAAATATAAATAAATATAAAATAAT-ATTTA-T-TTTATTTTATTATTGTATGAATATAAATAA
1 ATAAATATAAAT-AATAT-AAATAATGATTTATTATTTA-TTTATTATTGTATGAATATAAATAA
* * ** * *
52951 ATAAATGTAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTTTATGAATATAAATAA
1 ATAAATAT-AAATAATATAAATAATGATTTATTATTTATTTATTATTGTATGAATATAAATAA
53014 ATAAATA
1 ATAAATA
53021 AATAACAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
61 4 0.07
62 16 0.27
63 35 0.59
64 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (62 bp):
ATAAATATAAATAATATAAATAATGATTTATTATTTATTTATTATTGTATGAATATAAATAA
Found at i:54265 original size:42 final size:44
Alignment explanation
Indices: 54218--54305 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 44
54208 CAAGCAACCC
*
54218 AACTAAATAC-A-TTGCGCTTGAATGATATTTTAGAATTGATCT
1 AACTAAATACAAGTTGCGCTTGAATGATATTTTAAAATTGATCT
54260 AACTAAATACAAGTTTGCGCTTGAATGATATTTTAAAATTGATCT
1 AACTAAATACAAG-TTGCGCTTGAATGATATTTTAAAATTGATCT
54305 A
1 A
54306 TGGCTTAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 10 0.24
43 1 0.02
45 31 0.74
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (44 bp):
AACTAAATACAAGTTGCGCTTGAATGATATTTTAAAATTGATCT
Found at i:58722 original size:31 final size:31
Alignment explanation
Indices: 58686--58771 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
58676 TTAAAAGTCT
*
58686 AATGACTTAAATGAAAACTTTTGAATAGTTC
1 AATGACTTAAATGAAAACTTTTGAATAATTC
* **
58717 AATGACTTAAATAAAAACTTTCAAATAATTC
1 AATGACTTAAATGAAAACTTTTGAATAATTC
*
58748 AATAAC-TAAAGTG-AAACTTTTGAA
1 AATGACTTAAA-TGAAAACTTTTGAA
58772 GTTGAGTAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 13 0.28
31 33 0.72
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (31 bp):
AATGACTTAAATGAAAACTTTTGAATAATTC
Found at i:61224 original size:20 final size:20
Alignment explanation
Indices: 61195--61233 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61185 ATTTTTATAT
*
61195 TTTTATTTTTAAAAATTTAG
1 TTTTACTTTTAAAAATTTAG
*
61215 TTTTACTTTTAAAATTTTA
1 TTTTACTTTTAAAAATTTA
61234 AAATTCAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTACTTTTAAAAATTTAG
Found at i:63364 original size:21 final size:21
Alignment explanation
Indices: 63327--63366 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
63317 CTATGGATTG
*
63327 TATTTGTTGTGTAATGTAATT
1 TATTTGTTGTATAATGTAATT
63348 TATTTGTATGTAT-ATGTAA
1 TATTTGT-TGTATAATGTAA
63367 ATGGTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (21 bp):
TATTTGTTGTATAATGTAATT
Found at i:65482 original size:19 final size:19
Alignment explanation
Indices: 65455--65497 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
65445 CTGCTTGTTC
*
65455 ACTTGTCTCAAGCAACAAT
1 ACTTTTCTCAAGCAACAAT
65474 ACTTTTCTCAAGCAACAAT
1 ACTTTTCTCAAGCAACAAT
65493 ACTTT
1 ACTTT
65498 CTTCATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.33
Consensus pattern (19 bp):
ACTTTTCTCAAGCAACAAT
Found at i:76706 original size:62 final size:62
Alignment explanation
Indices: 76620--76742 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
76610 GGTTCATTGC
* * * *
76620 GTGATGGTTCTTAAGATTCTATTGCTTTTGAACTGAGTTATGATGATTTGGGATTAATGGTA
1 GTGATGGTACTTAAGATGCTATTGCATTTGAACTGAGTTATGAAGATTTGGGATTAATGGTA
* * *
76682 GTGATGGTACTTAGGATGCTATTGCATTTGAACTGAGTTTTGAAGATTTGTGATTAATGGT
1 GTGATGGTACTTAAGATGCTATTGCATTTGAACTGAGTTATGAAGATTTGGGATTAATGGT
76743 TCATTGCGTG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (62 bp):
GTGATGGTACTTAAGATGCTATTGCATTTGAACTGAGTTATGAAGATTTGGGATTAATGGTA
Found at i:82445 original size:8 final size:8
Alignment explanation
Indices: 82413--82456 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
82403 CAAATATTTT
*
82413 ATAATAAT
1 ATAATAAA
*
82421 A-AATAAT
1 ATAATAAA
82428 ATATATAAA
1 ATA-ATAAA
82437 ATAATAAA
1 ATAATAAA
82445 ATAATAAA
1 ATAATAAA
82453 ATAA
1 ATAA
82457 GAAACAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 7 0.21
8 19 0.58
9 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
ATAATAAA
Found at i:82456 original size:21 final size:21
Alignment explanation
Indices: 82415--82456 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
82405 AATATTTTAT
*
82415 AATAATAAATAATATATATAA
1 AATAATAAATAATATAAATAA
82436 AATAATAAAATAATA-AAATAA
1 AATAAT-AAATAATATAAATAA
82457 GAAACAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAATAAATAATATAAATAA
Found at i:87236 original size:70 final size:71
Alignment explanation
Indices: 87110--87254 Score: 195
Period size: 70 Copynumber: 2.0 Consensus size: 71
87100 ATTCTTTTAC
* *
87110 TTTTATTTTGGTGAATGAACCTGAGAGGTCGTCTATTATAACGACCTAATCAAATTAGTCCCTGT
1 TTTTATTTTGGTGAATGAACCT--GAGGTCCTCTATTATAACGACCAAATCAAATTAGTCCCTGT
*
87175 GTTATTAA
64 ATTATTAA
* * *
87183 TTTTATTTTGGTGAATGAA-CT-AGGTCTCTCTATTATAAGGATCAAATCAAATTAGTCCCTTTA
1 TTTTATTTTGGTGAATGAACCTGAGGTC-CTCTATTATAACGACCAAATCAAATTAGTCCCTGTA
87246 TTATTAA
65 TTATTAA
87253 TT
1 TT
87255 AAATTAATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
69 5 0.08
70 39 0.60
72 2 0.03
73 19 0.29
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (71 bp):
TTTTATTTTGGTGAATGAACCTGAGGTCCTCTATTATAACGACCAAATCAAATTAGTCCCTGTAT
TATTAA
Found at i:88906 original size:14 final size:14
Alignment explanation
Indices: 88880--88912 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
88870 AGATTTTTTC
88880 TTTTCTTTCCTGGG
1 TTTTCTTTCCTGGG
88894 TTTT-TTTCTCTGGG
1 TTTTCTTTC-CTGGG
88908 TTTTC
1 TTTTC
88913 ATGCTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.00, C:0.18, G:0.18, T:0.64
Consensus pattern (14 bp):
TTTTCTTTCCTGGG
Found at i:89615 original size:76 final size:78
Alignment explanation
Indices: 89474--89625 Score: 227
Period size: 76 Copynumber: 2.0 Consensus size: 78
89464 ATGTAGTTAA
* * * **
89474 TTATATGATTTGATGATGATTCAAATTGAACCATGGAACTTGAAATAACATATGAAGTTGTTATG
1 TTATATGATTTAATGAGGATTCAAATGGAACCATGGAACTTGAAATAACATATGAAGTTACTATG
89539 TACATTCATATGG
66 TACATTCATATGG
* *
89552 TTATATGATTTAATGAGGATT-AAATGGAACCATGGAACTTGAAGT-ACATTTGAAGTTACTATG
1 TTATATGATTTAATGAGGATTCAAATGGAACCATGGAACTTGAAATAACATATGAAGTTACTATG
89615 TACATTCATAT
66 TACATTCATAT
89626 ATGGAACCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 26 0.39
77 22 0.33
78 19 0.28
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (78 bp):
TTATATGATTTAATGAGGATTCAAATGGAACCATGGAACTTGAAATAACATATGAAGTTACTATG
TACATTCATATGG
Found at i:96121 original size:24 final size:25
Alignment explanation
Indices: 96080--96127 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
96070 TGAATATTTT
96080 AATTAGTATTTTCATAAAAAAAAAC
1 AATTAGTATTTTCATAAAAAAAAAC
**
96105 AATTAG-ATTTTTTTAAAAAAAAA
1 AATTAGTATTTTCATAAAAAAAAA
96128 TTGATGATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTAGTATTTTCATAAAAAAAAAC
Found at i:96959 original size:51 final size:47
Alignment explanation
Indices: 96904--96997 Score: 107
Period size: 51 Copynumber: 1.9 Consensus size: 47
96894 TGATACATCA
** *
96904 ATATTTATATTATTTTTAATTTAATATTTAATAATTTTATATATTTTTCTG
1 ATATTTATACAATATTTAATTTAA-ATTT-ATAA--TTATATATTTTTCTG
* *
96955 ATATTTCTCCAATATTTAATTTAAATTTATAATTATATATTTT
1 ATATTTATACAATATTTAATTTAAATTTATAATTATATATTTT
96998 ATATTTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
47 11 0.29
49 4 0.11
50 4 0.11
51 19 0.50
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (47 bp):
ATATTTATACAATATTTAATTTAAATTTATAATTATATATTTTTCTG
Found at i:98703 original size:2 final size:2
Alignment explanation
Indices: 98696--98723 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
98686 AAAGAAAATA
98696 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
98724 GATTTATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99728 original size:2 final size:2
Alignment explanation
Indices: 99721--99746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
99711 ATACATACTT
99721 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
99747 GCATATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:103048 original size:19 final size:20
Alignment explanation
Indices: 103024--103066 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
103014 ATCACTTAAC
* *
103024 AACTAACTA-AACTAAAATT
1 AACTAACTATAAATAAAATA
103043 AACTAACTATAAATAAAATA
1 AACTAACTATAAATAAAATA
103063 AACT
1 AACT
103067 TGAAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (20 bp):
AACTAACTATAAATAAAATA
Found at i:103653 original size:16 final size:18
Alignment explanation
Indices: 103614--103647 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
103604 TAAGTTTATA
103614 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
103631 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
103648 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:106039 original size:23 final size:23
Alignment explanation
Indices: 106013--106056 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
106003 CGAATTTTAA
*
106013 AAATATAAAA-ACTAAAATTAATC
1 AAAT-TAAAATACAAAAATTAATC
106036 AAATTAAAATACAAAAATTAA
1 AAATTAAAATACAAAAATTAA
106057 ATCCATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (23 bp):
AAATTAAAATACAAAAATTAATC
Found at i:110391 original size:138 final size:138
Alignment explanation
Indices: 110138--110418 Score: 490
Period size: 138 Copynumber: 2.0 Consensus size: 138
110128 AAATGAAAAC
* *
110138 TTTAGAAGAAGAGGGAAAGTTTACCCCTTTGATGGGTGTTGGAGGTGAGAATAGAGAAGGACATA
1 TTTAAAAGAAGAGGGAAAGTTTACCCCTTTGATGGGTGCTGGAGGTGAGAATAGAGAAGGACATA
** * * *
110203 CAATGATTTTAACAATCTAATAACTTAAATGAAAACTTTCGAATATTTCAATGACCATTTGTAAC
66 CAACAATTTTAACAACCCAATAACTTAAATGAAAACTTTCGAATAGTTCAATGACCATTTGTAAC
110268 CTTTGAAG
131 CTTTGAAG
110276 TTTAAAAGAAGAGGGAAAGTTTACCCCTTTGATGGGTGCTGGAGGTGAGAATAGAGAAGGACATA
1 TTTAAAAGAAGAGGGAAAGTTTACCCCTTTGATGGGTGCTGGAGGTGAGAATAGAGAAGGACATA
*
110341 CAACAATTTTAACAACCCAATAACTTAAATGAAAACTTTCGAATAGTTCAATGATCATTTGTAAC
66 CAACAATTTTAACAACCCAATAACTTAAATGAAAACTTTCGAATAGTTCAATGACCATTTGTAAC
110406 CTTTGAAG
131 CTTTGAAG
110414 TTTAA
1 TTTAA
110419 TGACCAAAAC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (138 bp):
TTTAAAAGAAGAGGGAAAGTTTACCCCTTTGATGGGTGCTGGAGGTGAGAATAGAGAAGGACATA
CAACAATTTTAACAACCCAATAACTTAAATGAAAACTTTCGAATAGTTCAATGACCATTTGTAAC
CTTTGAAG
Found at i:115140 original size:16 final size:17
Alignment explanation
Indices: 115113--115144 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
115103 CCCAAGACTA
115113 AATAATATAATATAAAC
1 AATAATATAATATAAAC
115130 AATAA-ATAATATAAA
1 AATAATATAATATAAA
115145 TAAGAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATATAATATAAAC
Found at i:119902 original size:15 final size:16
Alignment explanation
Indices: 119882--119913 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
119872 ATATTAAATG
119882 ATTTAATTAA-AAGTA
1 ATTTAATTAATAAGTA
119897 ATTTAATTAATAAGTA
1 ATTTAATTAATAAGTA
119913 A
1 A
119914 AAAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTTAATTAATAAGTA
Found at i:120349 original size:13 final size:13
Alignment explanation
Indices: 120307--120342 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
120297 AAGATTAGAG
*
120307 GAAAAAAATTAAA
1 GAAAAAAATCAAA
*
120320 AAAAAAAATCAAA
1 GAAAAAAATCAAA
120333 GAAAAAAATC
1 GAAAAAAATC
120343 TGAGAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.11
Consensus pattern (13 bp):
GAAAAAAATCAAA
Found at i:125546 original size:14 final size:14
Alignment explanation
Indices: 125527--125556 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
125517 AAACAACGAA
125527 AGGTGCTTTGAAAG
1 AGGTGCTTTGAAAG
125541 AGGTGCTTTGAAAG
1 AGGTGCTTTGAAAG
125555 AG
1 AG
125557 AGCAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.27
Consensus pattern (14 bp):
AGGTGCTTTGAAAG
Found at i:127435 original size:31 final size:29
Alignment explanation
Indices: 127365--127441 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 29
127355 AAATGATTAG
* *
127365 ATTTTTTTAGCAAAAATAATTAATTTATT
1 ATTTTTTTAACAAAAATAAATAATTTATT
*
127394 -TTTTGATTTAACATACAATAAATAATTTATCT
1 ATTTT--TTTAACA-AAAATAAATAATTTAT-T
*
127426 ATTTTTTTAATAAAAA
1 ATTTTTTTAACAAAAA
127442 GATAAAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
28 4 0.11
30 9 0.24
31 20 0.53
32 1 0.03
33 4 0.11
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTTTTTTAACAAAAATAAATAATTTATT
Found at i:134929 original size:14 final size:14
Alignment explanation
Indices: 134910--134951 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
134900 AATAATAATT
134910 AAATTTTAAATTTC
1 AAATTTTAAATTTC
* *
134924 AAATTTCAAATTAC
1 AAATTTTAAATTTC
*
134938 AAAATTTAAATTTC
1 AAATTTTAAATTTC
134952 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTTAAATTTC
Found at i:135803 original size:22 final size:23
Alignment explanation
Indices: 135770--135817 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
135760 ATACCACAAT
*
135770 TTTTAATT-AAAAATGTATAGAAA
1 TTTTAATTAAAAAAT-TATAAAAA
135793 TTTT-ATTAAAAAATTATAAAAA
1 TTTTAATTAAAAAATTATAAAAA
135815 TTT
1 TTT
135818 AAAATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TTTTAATTAAAAAATTATAAAAA
Found at i:142161 original size:18 final size:18
Alignment explanation
Indices: 142140--142197 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
142130 CGACGACGGT
142140 GTCGGAAGTTATGACGCC
1 GTCGGAAGTTATGACGCC
* * * **
142158 GTC-GATGGGTACGACGGT
1 GTCGGA-AGTTATGACGCC
142176 GTCGGAAGTTATGACGCC
1 GTCGGAAGTTATGACGCC
142194 GTCG
1 GTCG
142198 ATGGGTTGTT
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.22
Consensus pattern (18 bp):
GTCGGAAGTTATGACGCC
Found at i:142179 original size:36 final size:36
Alignment explanation
Indices: 142132--142203 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
142122 AGTGGCGTCG
142132 ACGACGGTGTCGGAAGTTATGACGCCGTCGATGGGT
1 ACGACGGTGTCGGAAGTTATGACGCCGTCGATGGGT
142168 ACGACGGTGTCGGAAGTTATGACGCCGTCGATGGGT
1 ACGACGGTGTCGGAAGTTATGACGCCGTCGATGGGT
142204 TGTTTGGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.22
Consensus pattern (36 bp):
ACGACGGTGTCGGAAGTTATGACGCCGTCGATGGGT
Found at i:142609 original size:13 final size:14
Alignment explanation
Indices: 142591--142619 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
142581 CCAAATTTTG
142591 AATTTTAAAT-TTA
1 AATTTTAAATATTA
142604 AATTTTAAATATTA
1 AATTTTAAATATTA
142618 AA
1 AA
142620 AATTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTAAATATTA
Found at i:142636 original size:28 final size:28
Alignment explanation
Indices: 142604--142657 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
142594 TTTAAATTTA
*
142604 AATTT-TAAATATTAAAAATTATTAAAAT
1 AATTTATAAATA-AAAAAATTATTAAAAT
*
142632 AATTTATTAATAAAAAAATTATTAAA
1 AATTTATAAATAAAAAAATTATTAAA
142658 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AATTTATAAATAAAAAAATTATTAAAAT
Found at i:148568 original size:24 final size:24
Alignment explanation
Indices: 148536--148584 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
148526 TGAATTGCAC
*
148536 TGTTGGTAGCTATCTTTTAAACCA
1 TGTTGGTAGCGATCTTTTAAACCA
148560 TGTTGGTAGCGATCTTTTAAACCA
1 TGTTGGTAGCGATCTTTTAAACCA
148584 T
1 T
148585 CAAATATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
TGTTGGTAGCGATCTTTTAAACCA
Found at i:150710 original size:13 final size:13
Alignment explanation
Indices: 150692--150720 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
150682 TTTATGACAT
150692 TGTATTAAGTAAA
1 TGTATTAAGTAAA
150705 TGTATTAAGTAAA
1 TGTATTAAGTAAA
150718 TGT
1 TGT
150721 TTAGAGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATTAAGTAAA
Found at i:151526 original size:95 final size:95
Alignment explanation
Indices: 151416--151662 Score: 316
Period size: 95 Copynumber: 2.6 Consensus size: 95
151406 TGTTTTTGTG
* * * * *
151416 AAATTGTGGGATTTGTGAAAACCAACCAATGCTTTAAGCATGTAGTCTCTTTTGAACACAAATTT
1 AAATTGAGGGATTTGTGAAGATCGACCAATGCTTTAAGCATGTAGTCCCTTTTGAACACAAATTT
** *
151481 CTTATGATATTGGTAATATATTTTTTTTT-T
66 CTTATGATATTGCCAATAT-TTTTTTTTTAA
* * *
151511 AAATTGAGGGTTTTGTGAAGATCGATCAATGCTTTAAGCATGTAGTCCCTTTTGAATACAAATTT
1 AAATTGAGGGATTTGTGAAGATCGACCAATGCTTTAAGCATGTAGTCCCTTTTGAACACAAATTT
*
151576 CTTCTGATATTGCCAATATTTTTTTTTTAA
66 CTTATGATATTGCCAATATTTTTTTTTTAA
* * * * * *
151606 AAATAGAGGGCTTTGTGAAGATCGACCAATGTTTTAAGTATGTAGTTCCTTATGAAC
1 AAATTGAGGGATTTGTGAAGATCGACCAATGCTTTAAGCATGTAGTCCCTTTTGAAC
151663 CATTCATGCC
Statistics
Matches: 131, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
94 9 0.07
95 122 0.93
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (95 bp):
AAATTGAGGGATTTGTGAAGATCGACCAATGCTTTAAGCATGTAGTCCCTTTTGAACACAAATTT
CTTATGATATTGCCAATATTTTTTTTTTAA
Found at i:164808 original size:29 final size:29
Alignment explanation
Indices: 164775--164832 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
164765 TTTTATTCTT
* * *
164775 TTTAATAGTATAGGGACTAAATTGGTCCA
1 TTTAATAATAGAGGGACTAAATTGATCCA
*
164804 TTTAATAATAGAGGGACTAATTTGATCCA
1 TTTAATAATAGAGGGACTAAATTGATCCA
164833 GCCTCTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (29 bp):
TTTAATAATAGAGGGACTAAATTGATCCA
Found at i:167671 original size:18 final size:17
Alignment explanation
Indices: 167626--167669 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
167616 ATAGTAAAAA
167626 TATAATTTTATTATTTT
1 TATAATTTTATTATTTT
*
167643 TAAAAATTTTA-TATATTT
1 T-ATAATTTTATTAT-TTT
167661 TATAATTTT
1 TATAATTTT
167670 TAAAAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATAATTTTATTATTTT
Found at i:167710 original size:37 final size:38
Alignment explanation
Indices: 167669--167740 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
167659 TTTATAATTT
*
167669 TTAAAAG-ATTAA-ATTAAATTTATTATTTTTAAAAAAG
1 TTAAAAGTA-TAATATTAAATTTATTAATTTTAAAAAAG
* *
167706 TTAAAAGTATAATTTTAATTTTATTAATTTTAAAA
1 TTAAAAGTATAATATTAAATTTATTAATTTTAAAA
167741 TTTTAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 10 0.33
38 20 0.67
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (38 bp):
TTAAAAGTATAATATTAAATTTATTAATTTTAAAAAAG
Found at i:167747 original size:37 final size:36
Alignment explanation
Indices: 167647--167747 Score: 89
Period size: 37 Copynumber: 2.7 Consensus size: 36
167637 TATTTTTAAA
*
167647 AATTTTA-TATATTTTATAATTTTTAAAAGATTAAATT
1 AATTTTATTA-ATTTTA-AAATTTTAAAAGATTAAATT
* * ** *
167684 AAATTTATTATTTTTAAAAAAGTTAAAAG-TATAATTTT
1 AATTTTATTAATTTT-AAAATTTTAAAAGAT-TAA-ATT
167722 AATTTTATTAATTTTAAAATTTTAAA
1 AATTTTATTAATTTTAAAATTTTAAA
167748 TAAATGGAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
36 1 0.02
37 31 0.62
38 18 0.36
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (36 bp):
AATTTTATTAATTTTAAAATTTTAAAAGATTAAATT
Found at i:179674 original size:18 final size:19
Alignment explanation
Indices: 179646--179681 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
179636 ATCGATCTTT
179646 GATCAAATTAAATTAATTC
1 GATCAAATTAAATTAATTC
*
179665 GATC-AATTAATTTAATT
1 GATCAAATTAAATTAATT
179682 TTAACCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (19 bp):
GATCAAATTAAATTAATTC
Found at i:184018 original size:12 final size:12
Alignment explanation
Indices: 184003--184045 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
183993 CAATCGCCAT
*
184003 CTCCACCCTTGC
1 CTCCACCCTTAC
*
184015 CTCCACCCCTAC
1 CTCCACCCTTAC
*
184027 CCCCACCCTTAC
1 CTCCACCCTTAC
*
184039 ATCCACC
1 CTCCACC
184046 ATCCTTCAGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.63, G:0.02, T:0.19
Consensus pattern (12 bp):
CTCCACCCTTAC
Done.