Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012535.1 Kokia drynarioides strain JFW-HI SEQ_127543, 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: 115541
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:8207 original size:19 final size:20
Alignment explanation
Indices: 8175--8214 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
8165 ATTTAAGTTC
8175 ATTTAAAATAAAAAAAATAA
1 ATTTAAAATAAAAAAAATAA
*
8195 ATTT-AAATTAAAAAAATAA
1 ATTTAAAATAAAAAAAATAA
8214 A
1 A
8215 AATATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATTTAAAATAAAAAAAATAA
Found at i:29179 original size:22 final size:22
Alignment explanation
Indices: 29154--29220 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 22
29144 ATCAAACAAT
29154 TCAATTTTATCATTTTTGGTCA
1 TCAATTTTATCATTTTTGGTCA
* * **
29176 TCAA-TTGA-C--TATTGAACA
1 TCAATTTTATCATTTTTGGTCA
29194 -CAATTTTATCATTTTTGGTCA
1 TCAATTTTATCATTTTTGGTCA
29215 TCAATT
1 TCAATT
29221 GACTATTGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
17 3 0.09
18 9 0.28
19 1 0.03
20 1 0.03
21 9 0.28
22 9 0.28
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (22 bp):
TCAATTTTATCATTTTTGGTCA
Found at i:29209 original size:39 final size:39
Alignment explanation
Indices: 29155--29231 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
29145 TCAAACAATT
29155 CAATTTTATCATTTTTGGTCATCAATTGACTATTGAACA
1 CAATTTTATCATTTTTGGTCATCAATTGACTATTGAACA
29194 CAATTTTATCATTTTTGGTCATCAATTGACTATTGAAC
1 CAATTTTATCATTTTTGGTCATCAATTGACTATTGAAC
29232 GTACTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (39 bp):
CAATTTTATCATTTTTGGTCATCAATTGACTATTGAACA
Found at i:32890 original size:4 final size:4
Alignment explanation
Indices: 32883--32913 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
32873 CTTGCTCTCT
*
32883 CTCC CTCC CACC CTCC CTCC CTCC CTCC CTC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC
32914 GAATATCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.03, C:0.74, G:0.00, T:0.23
Consensus pattern (4 bp):
CTCC
Found at i:38074 original size:16 final size:19
Alignment explanation
Indices: 38044--38081 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
38034 CACTTGTCTC
38044 CTTTCTTTTATATA-TTTA
1 CTTTCTTTTATATATTTTA
38062 CTTT-TTTTA-ATATTTTA
1 CTTTCTTTTATATATTTTA
38079 CTT
1 CTT
38082 GTCATCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 12 0.63
18 4 0.21
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTCTTTTATATATTTTA
Found at i:40120 original size:13 final size:14
Alignment explanation
Indices: 40102--40130 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40092 GTGGTGTTCT
40102 TTAGTTAATTT-AA
1 TTAGTTAATTTCAA
40115 TTAGTTAATTTCAA
1 TTAGTTAATTTCAA
40129 TT
1 TT
40131 TTTAATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (14 bp):
TTAGTTAATTTCAA
Found at i:41429 original size:28 final size:28
Alignment explanation
Indices: 41326--41609 Score: 211
Period size: 29 Copynumber: 9.7 Consensus size: 28
41316 TAAAATAGTA
* *
41326 ATTTTTGGATGTTTCGGGGTCAAAAATGAG
1 ATTTTTGGAAG-TTCGGGGTC-AAAATGGG
**
41356 ATTTTTTGG-AGTTCGGGGGGT-AAAATAGTA
1 A-TTTTTGGAAGTTC--GGGGTCAAAAT-GGG
41386 ATTTTTGGAAGGTTCGGGGTCAAAATGGG
1 ATTTTTGGAA-GTTCGGGGTCAAAATGGG
**
41415 ATTTTTGGAAGTTCGAGGGT-AAAATGAT
1 ATTTTTGGAAGTTCG-GGGTCAAAATGGG
* *
41443 ATTATTTGGAAGGTTTGGGGTCAAGAATGAG
1 ATT-TTTGGAA-GTTCGGGGTCAA-AATGGG
* * * *
41474 ATTTTTTGAAATTTAGGGGT-AAAATGGTA
1 A-TTTTTGGAAGTTCGGGGTCAAAATGG-G
41503 ATTTTTGGAAGGTTCGGGGTCAAAAATGGG
1 ATTTTTGGAA-GTTCGGGGTC-AAAATGGG
* *
41533 ATTTTTGGAACTT-TGGGTCAAAAATGGG
1 ATTTTTGGAAGTTCGGGGTC-AAAATGGG
* *
41561 ATTTTTGGAAGTTTGGGGT-AAAATGGTA
1 ATTTTTGGAAGTTCGGGGTCAAAATGG-G
*
41589 ACTTTTGGAAGGTTCGGGGTC
1 ATTTTTGGAA-GTTCGGGGTC
41610 TTTCGGTGTA
Statistics
Matches: 208, Mismatches: 25, Indels: 42
0.76 0.09 0.15
Matches are distributed among these distances:
27 7 0.03
28 61 0.29
29 70 0.34
30 33 0.16
31 35 0.17
32 2 0.01
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.35
Consensus pattern (28 bp):
ATTTTTGGAAGTTCGGGGTCAAAATGGG
Found at i:41478 original size:59 final size:59
Alignment explanation
Indices: 41315--41542 Score: 261
Period size: 59 Copynumber: 3.9 Consensus size: 59
41305 ACATCCGGGA
* * *
41315 GTAAAAT-AGTAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTTTGG-AGTTCGGGGG
1 GTAAAATGA-TAATTTTTGGAAGGTTCGGGGTCAAAAATGAGA-TTTTTGGAAGTTC-GAGG
*
41375 GTAAAAT-AGTAATTTTTGGAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGAGG
1 GTAAAATGA-TAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
* * * * *
41433 GTAAAATGAT-ATTATTTGGAAGGTTTGGGGTCAAGAATGAGATTTTTTGAAATT-TAGGG
1 GTAAAATGATAATT-TTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGA-GG
* *
41492 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAA
1 GTAAAATGATAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAA
41543 CTTTGGGTCA
Statistics
Matches: 147, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
57 3 0.02
58 36 0.24
59 75 0.51
60 33 0.22
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (59 bp):
GTAAAATGATAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
Found at i:41557 original size:59 final size:58
Alignment explanation
Indices: 41315--41583 Score: 257
Period size: 59 Copynumber: 4.6 Consensus size: 58
41305 ACATCCGGGA
* * * *
41315 GTAAAATAGTAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTTTGG-AGTTCGGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGA-TTTTTGGAAGTTC--TGG
* * *
41375 GTAAAATAGTAATTTTTGGAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTC-TGG
* * * * *
41433 GTAAAATGAT-ATTATTTGGAAGGTTTGGGGTCAAGAATGAGATTTTTTGAAATT-TAGGG
1 GTAAAATGGTAATT-TTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCT--GG
* *
41492 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAACTT-TGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCTGG
* *
41549 GTCAAAAATGG-GATTTTTGGAA-GTTTGGGGT-AAAA
1 GT--AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAA
41584 TGGTAACTTT
Statistics
Matches: 181, Mismatches: 20, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
56 4 0.02
57 15 0.08
58 45 0.25
59 84 0.46
60 33 0.18
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (58 bp):
GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCTGG
Found at i:43389 original size:5 final size:5
Alignment explanation
Indices: 43373--43411 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
43363 TTAATTTTAT
*
43373 AATTA AATTTA AATTA AATTTA AAATA AATTA AATTA AA
1 AATTA AA-TTA AATTA AA-TTA AATTA AATTA AATTA AA
43412 AAAAAGGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 20 0.67
6 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:43389 original size:11 final size:11
Alignment explanation
Indices: 43363--43411 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
43353 TTTAGACTTT
*
43363 TTAATTTTATAA
1 TTAAATTTA-AA
43375 TTAAATTTAAA
1 TTAAATTTAAA
43386 TTAAATTTAAA
1 TTAAATTTAAA
*
43397 ATAAA-TTAAA
1 TTAAATTTAAA
43407 TTAAA
1 TTAAA
43412 AAAAAGGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 9 0.26
11 17 0.50
12 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:43413 original size:16 final size:16
Alignment explanation
Indices: 43382--43413 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43372 TAATTAAATT
*
43382 TAAATTAAATTTAAAA
1 TAAATTAAATTAAAAA
43398 TAAATTAAATTAAAAA
1 TAAATTAAATTAAAAA
43414 AAAGGCCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAATTAAATTAAAAA
Found at i:44771 original size:21 final size:21
Alignment explanation
Indices: 44747--44800 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
44737 TTCATGAATT
44747 TTAATATAATTTTGATAATCA
1 TTAATATAATTTTGATAATCA
* * * *
44768 TTAATGTAATATTGGTAGTCA
1 TTAATATAATTTTGATAATCA
* *
44789 TTCATACAATTT
1 TTAATATAATTT
44801 GGGCAACAGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.46
Consensus pattern (21 bp):
TTAATATAATTTTGATAATCA
Found at i:54779 original size:19 final size:19
Alignment explanation
Indices: 54757--54799 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
54747 TAAATTTTAT
* *
54757 TAAAAATTAGACAAAATTA
1 TAAAAATCAGAAAAAATTA
*
54776 TAAAAATCATAAAAAATTA
1 TAAAAATCAGAAAAAATTA
54795 TAAAA
1 TAAAA
54800 TATATAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAAATCAGAAAAAATTA
Found at i:54805 original size:28 final size:27
Alignment explanation
Indices: 54769--54865 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 27
54759 AAAATTAGAC
54769 AAAATTATAAAAATCAT-AAAAAATTAT
1 AAAATTATAAAAAT-ATAAAAAAATTAT
*
54796 AAAATATATAGAAATATAAAAAAATTAT
1 AAAAT-TATAAAAATATAAAAAAATTAT
* * * *
54824 AAAATTTTATAAAATGGTAAGAAAATATAA
1 AAAATTATA-AAAAT-ATAAAAAAAT-TAT
*
54854 AAAAATATAAAA
1 AAAATTATAAAA
54866 TTCACAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
27 10 0.18
28 27 0.47
29 11 0.19
30 9 0.16
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAATTATAAAAATATAAAAAAATTAT
Found at i:54865 original size:8 final size:9
Alignment explanation
Indices: 54769--54866 Score: 51
Period size: 10 Copynumber: 10.6 Consensus size: 9
54759 AAAATTAGAC
54769 AAAAT-TAT
1 AAAATATAT
54777 AAAA-ATCAT
1 AAAATAT-AT
*
54786 AAAAAATTAT
1 AAAATA-TAT
54796 AAAATATAT
1 AAAATATAT
54805 AGAAATATA-
1 A-AAATATAT
*
54814 AAAAAATTAT
1 AAAATA-TAT
*
54824 AAAATTTTAT
1 AAAA-TATAT
* *
54834 AAAATGGTAAG
1 AAAAT-AT-AT
54845 AAAATATA-
1 AAAATATAT
*
54853 AAAAAATAT
1 AAAATATAT
54862 AAAAT
1 AAAAT
54867 TCACAAAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
8 16 0.23
9 19 0.27
10 28 0.40
11 7 0.10
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAATATAT
Found at i:54866 original size:38 final size:38
Alignment explanation
Indices: 54738--54867 Score: 117
Period size: 38 Copynumber: 3.4 Consensus size: 38
54728 AAAAAGCTAT
* *
54738 AAAAATATTTAAATTTTATTAAAA-AT-TAGACAAA-ATTAT
1 AAAAATA-TAAAATTTTA-TAAAATATATAGA-AAATA-TAA
**
54777 AAAAATCATAAAAAATTATAAAATATATAG-AAATATAA
1 AAAAAT-ATAAAATTTTATAAAATATATAGAAAATATAA
*
54815 AAAAATTATAAAATTTTATAAAATGGTA-AGAAAATATAA
1 AAAAA-TATAAAATTTTATAAAAT-ATATAGAAAATATAA
54854 AAAAATATAAAATT
1 AAAAATATAAAATT
54868 CACAAAAATA
Statistics
Matches: 77, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
38 41 0.53
39 32 0.42
40 4 0.05
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (38 bp):
AAAAATATAAAATTTTATAAAATATATAGAAAATATAA
Found at i:61795 original size:20 final size:21
Alignment explanation
Indices: 61772--61813 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
61762 TTCTTTTTAA
*
61772 TTTTTTATA-TTTAGTTTTTT
1 TTTTTTATATTTTAATTTTTT
61792 TTTTTTATATTTTAATTTTTT
1 TTTTTTATATTTTAATTTTTT
61813 T
1 T
61814 CTAGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTTTATATTTTAATTTTTT
Found at i:61857 original size:23 final size:23
Alignment explanation
Indices: 61831--61878 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
61821 TTATCTGTTT
**
61831 TTGTGACACGTTTTTCCTCTGTC
1 TTGTGACACACTTTTCCTCTGTC
* *
61854 TTGTGATACACTTTTCTTCTGTC
1 TTGTGACACACTTTTCCTCTGTC
61877 TT
1 TT
61879 ATGGCAGGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.52
Consensus pattern (23 bp):
TTGTGACACACTTTTCCTCTGTC
Found at i:61938 original size:25 final size:25
Alignment explanation
Indices: 61909--61959 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
61899 TTTGTGATAG
61909 ATTTGCATTCATGGATAATTTTCTC
1 ATTTGCATTCATGGATAATTTTCTC
* * *
61934 ATTTGCGTTCGTGGATAGTTTTCTC
1 ATTTGCATTCATGGATAATTTTCTC
61959 A
1 A
61960 CAACGCTCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (25 bp):
ATTTGCATTCATGGATAATTTTCTC
Found at i:63374 original size:15 final size:14
Alignment explanation
Indices: 63354--63402 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
63344 TTTAAATGGG
63354 TTTAAGGTTTAAGAT
1 TTTAAGGTTTAA-AT
*
63369 TTTAAGATTTAAAT
1 TTTAAGGTTTAAAT
63383 TTTAAAGGTTTAGAAT
1 TTT-AAGGTTTA-AAT
63399 TTTA
1 TTTA
63403 TGAAAGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 19 0.63
16 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (14 bp):
TTTAAGGTTTAAAT
Found at i:74947 original size:10 final size:11
Alignment explanation
Indices: 74927--74951 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
74917 CGTTCTTCTC
74927 TTTCTTTTTTT
1 TTTCTTTTTTT
74938 TTTCTTTTTTT
1 TTTCTTTTTTT
74949 TTT
1 TTT
74952 TTAAGACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:74949 original size:15 final size:15
Alignment explanation
Indices: 74925--74953 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
74915 GTCGTTCTTC
74925 TCTTTCTTTTTTTTT
1 TCTTTCTTTTTTTTT
74940 TCTTT-TTTTTTTTT
1 TCTTTCTTTTTTTTT
74954 AAGACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TCTTTCTTTTTTTTT
Found at i:81610 original size:58 final size:58
Alignment explanation
Indices: 81546--81656 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 58
81536 CGAAAAGGAG
81546 TTGTTTATGAGTGTTATTT-AAGAATAAAATTATATTTAAGTTTAAAAATATTTAGGTT
1 TTGTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTAAGTTTAAAAATATTTAGGTT
* **
81604 TTGTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTT
1 TTGTTTATGAGTGTTTTTGAAGAATAAAATTATATTTAAGTTTAAAAATATTT
81657 GAGTTTAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 3 0.06
58 46 0.94
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (58 bp):
TTGTTTATGAGTGTTTTTGAAGAATAAAATTATATTTAAGTTTAAAAATATTTAGGTT
Found at i:84299 original size:32 final size:33
Alignment explanation
Indices: 84230--84299 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
84220 AAAATAGTTT
**** * *
84230 ATATATGTAATTAATTTACTTTTTTATTATTTT
1 ATATATGTAATTAATTTACAGGGTTAGTATTTG
84263 ATATATGTAATTAATTTA-AGGGTTAGTATTTG
1 ATATATGTAATTAATTTACAGGGTTAGTATTTG
84295 ATATA
1 ATATA
84300 CAAGTTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (33 bp):
ATATATGTAATTAATTTACAGGGTTAGTATTTG
Found at i:84408 original size:16 final size:14
Alignment explanation
Indices: 84387--84424 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
84377 TATTTTTTTT
84387 TTAATTTAAATATCAA
1 TTAATTTAAA-AT-AA
84403 TTAATTTAAAATAA
1 TTAATTTAAAATAA
84417 TT-ATTTAA
1 TTAATTTAA
84425 TACACTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 4 0.18
15 2 0.09
16 10 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAATTTAAAATAA
Found at i:84711 original size:24 final size:24
Alignment explanation
Indices: 84666--84713 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
84656 GTAATATATT
* *
84666 TAAATATTAATAAAAATTAAAAAG
1 TAAAAATTAATAAAAATAAAAAAG
*
84690 TAAAAATTAATATAAAAAAAAAAA
1 TAAAAATTAATA-AAAATAAAAAA
84714 AAACTAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (24 bp):
TAAAAATTAATAAAAATAAAAAAG
Found at i:85035 original size:48 final size:48
Alignment explanation
Indices: 84965--85072 Score: 200
Period size: 48 Copynumber: 2.3 Consensus size: 48
84955 AAAAGTGTAT
84965 TTAAA-AATAACATAAAATAAATTATAAAACATATTATTTGAAATTAA
1 TTAAATAATAACATAAAATAAATTATAAAACATATTATTTGAAATTAA
*
85012 TTAAATAATAACATAAAATAAATTATGAAACATATTATTTGAAATTAA
1 TTAAATAATAACATAAAATAAATTATAAAACATATTATTTGAAATTAA
85060 TTAAATAATAACA
1 TTAAATAATAACA
85073 AAGGAAATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
47 5 0.08
48 54 0.92
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (48 bp):
TTAAATAATAACATAAAATAAATTATAAAACATATTATTTGAAATTAA
Found at i:85056 original size:26 final size:25
Alignment explanation
Indices: 84979--85062 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 25
84969 AAATAACATA
84979 AAATAAATTATAAAACATATTATTTG
1 AAATAAATTAT-AAACATATTATTTG
* ** *
85005 AAATTAATTA-AATA-ATA--ACATA
1 AAATAAATTATAA-ACATATTATTTG
85027 AAATAAATTATGAAACATATTATTTG
1 AAATAAATTAT-AAACATATTATTTG
*
85053 AAATTAATTA
1 AAATAAATTA
85063 AATAATAACA
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
22 11 0.26
23 1 0.02
24 10 0.23
25 1 0.02
26 20 0.47
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
AAATAAATTATAAACATATTATTTG
Found at i:93882 original size:22 final size:22
Alignment explanation
Indices: 93857--93903 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
93847 CTAGTTTCTA
*
93857 TTTCGATT-AGTTCAATCAATTT
1 TTTCGATTCAATTCAAT-AATTT
*
93879 TTTCGATTCAATTGAATAATTT
1 TTTCGATTCAATTCAATAATTT
93901 TTT
1 TTT
93904 TTTAAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (22 bp):
TTTCGATTCAATTCAATAATTT
Found at i:94328 original size:30 final size:31
Alignment explanation
Indices: 94264--94358 Score: 108
Period size: 30 Copynumber: 3.1 Consensus size: 31
94254 TGTAAATTTA
94264 ATAATACATGAAAT-AT-TTTAAAAT-TTTAAAT
1 ATAATA-AT-AAATCATATTTAAAATATTT-AAT
*
94295 ATAATAATAAATTATATTT-AAATATTTAAT
1 ATAATAATAAATCATATTTAAAATATTTAAT
* *
94325 ATAATGATAAATCATATTTAAAAAATTTAAT
1 ATAATAATAAATCATATTTAAAATATTTAAT
94356 ATA
1 ATA
94359 TTGATACATA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
29 4 0.07
30 28 0.49
31 25 0.44
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
ATAATAATAAATCATATTTAAAATATTTAAT
Found at i:94353 original size:31 final size:30
Alignment explanation
Indices: 94257--94364 Score: 107
Period size: 31 Copynumber: 3.6 Consensus size: 30
94247 AATTATTTGT
94257 AAATTTAATAATACATG--AAAT-AT-TTTAA
1 AAATTTAAT-ATA-ATGATAAATCATATTTAA
* * *
94285 AATTTTAAATATAATAATAAATTATATTTAA
1 AAATTT-AATATAATGATAAATCATATTTAA
*
94316 ATATTTAATATAATGATAAATCATATTTAAA
1 AAATTTAATATAATGATAAATCATATTT-AA
*
94347 AAATTTAATATATTGATA
1 AAATTTAATATAATGATA
94365 CATATAATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
27 2 0.03
28 8 0.12
29 7 0.11
30 22 0.33
31 27 0.41
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTAATATAATGATAAATCATATTTAA
Found at i:101846 original size:5 final size:5
Alignment explanation
Indices: 101815--101845 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
101805 ACCGAGATGT
*
101815 AGGAA AGGAA AGGAA AGGAA AGGAA ATGAA A
1 AGGAA AGGAA AGGAA AGGAA AGGAA AGGAA A
101846 TAATAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.03
Consensus pattern (5 bp):
AGGAA
Found at i:105609 original size:18 final size:17
Alignment explanation
Indices: 105586--105629 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
105576 ACAAAAACGG
105586 ATAAAAACTAAAAAAAA
1 ATAAAAACTAAAAAAAA
*
105603 ATCAAAATA-TAAAAGAAA
1 AT-AAAA-ACTAAAAAAAA
105621 ATAAAAACT
1 ATAAAAACT
105630 GAATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 14 0.61
19 1 0.04
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (17 bp):
ATAAAAACTAAAAAAAA
Done.