Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006086.1 Kokia drynarioides strain JFW-HI SEQ_120580, 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: 136613
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30 TAATCATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:620 original size:24 final size:25
Alignment explanation
Indices: 549--621 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 25
539 TATATGATAA
549 AACACATGTAAGTTACAAATATAAATTAG
1 AACACATGTAAG-T-C-AATA-AAATTAG
** **
578 AGGACATGTAAGTTGATAAAA-TAG
1 AACACATGTAAGTCAATAAAATTAG
602 AACACATGTAAGTCAATAAA
1 AACACATGTAAGTCAATAAA
622 CTGCTACAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
24 19 0.53
25 3 0.08
26 3 0.08
28 1 0.03
29 10 0.28
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.25
Consensus pattern (25 bp):
AACACATGTAAGTCAATAAAATTAG
Found at i:6115 original size:49 final size:49
Alignment explanation
Indices: 6056--6151 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
6046 TATTTTTTTC
*
6056 TAGTCATCATCTAATCTCTCACTCTCTCACTCTCCATATATATTAATCA
1 TAGTCATCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
* *
6105 TAGTCTTCATCTAATCTCACACTCTCTCACTCTCCCTATATATTAAT
1 TAGTCATCATCTAATCTCACACTCTCTCACTCTCCATATATATTAAT
6152 TATTTGGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (49 bp):
TAGTCATCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
Found at i:7446 original size:43 final size:41
Alignment explanation
Indices: 7359--7444 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
7349 ACTCTTTAAA
* * * *
7359 TCTCCATATATATCAGTCATAGTTTTCATCTACTCTCTCAC
1 TCTCCATATATATCAATCATACTCTTCATCTAATCTCTCAC
*
7400 TCTCCATATATATTAATCATACTCTTCATCTAATCTCTCAC
1 TCTCCATATATATCAATCATACTCTTCATCTAATCTCTCAC
7441 TCTC
1 TCTC
7445 TCAATGTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.42
Consensus pattern (41 bp):
TCTCCATATATATCAATCATACTCTTCATCTAATCTCTCAC
Found at i:8868 original size:30 final size:30
Alignment explanation
Indices: 8829--8895 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
8819 TGTCCATGAA
* *
8829 TATTTTTGGTGAAAAGAATACCATAAGTGG
1 TATTCTTGGTGAAAAGAAGACCATAAGTGG
* *
8859 TATTCTTGGTGAATAGAAGACCATAATTGG
1 TATTCTTGGTGAAAAGAAGACCATAAGTGG
8889 TATTCTT
1 TATTCTT
8896 AGACTAGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (30 bp):
TATTCTTGGTGAAAAGAAGACCATAAGTGG
Found at i:11347 original size:28 final size:28
Alignment explanation
Indices: 11315--11376 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
11305 TTGACTCCCT
* **
11315 TTGACCTAAAGGTCATGCTTACTCCTTA
1 TTGACCCAAAGGTCACACTTACTCCTTA
*
11343 TTGACCCAAAGGTCACACTTACTCCTTG
1 TTGACCCAAAGGTCACACTTACTCCTTA
11371 TTGACC
1 TTGACC
11377 ATGCCTGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (28 bp):
TTGACCCAAAGGTCACACTTACTCCTTA
Found at i:18578 original size:21 final size:21
Alignment explanation
Indices: 18554--18593 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18544 GTAAACGATT
**
18554 TTGATGTGGCTGCATCTGATC
1 TTGATGTGAATGCATCTGATC
18575 TTGATGTGAATGCATCTGA
1 TTGATGTGAATGCATCTGA
18594 GTATTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (21 bp):
TTGATGTGAATGCATCTGATC
Found at i:20652 original size:85 final size:86
Alignment explanation
Indices: 20509--20681 Score: 294
Period size: 85 Copynumber: 2.0 Consensus size: 86
20499 CCAAAGATTA
*
20509 AACAGTAAAAGAAAGCTTGAATAATATATCATTTAGTCTTAAAATCAAATGTACTTTCATA-AAA
1 AACAGTAAAAGAAAGCTTGAATAAAATATCATTTAGTCTTAAAATCAAATGTACTTTCATACAAA
*
20573 CTTGAAATAACATGAATCACC
66 CTTGAAATAACACGAATCACC
* * *
20594 AACAGTAAAGGCAAGCTTGAATAAAATATCATTTAGTCTTAATATCAAATGTACTTTCATACAAA
1 AACAGTAAAAGAAAGCTTGAATAAAATATCATTTAGTCTTAAAATCAAATGTACTTTCATACAAA
20659 CTTGAAATAACACGAATCACC
66 CTTGAAATAACACGAATCACC
20680 AA
1 AA
20682 TGTTTAAGAA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 57 0.70
86 25 0.30
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (86 bp):
AACAGTAAAAGAAAGCTTGAATAAAATATCATTTAGTCTTAAAATCAAATGTACTTTCATACAAA
CTTGAAATAACACGAATCACC
Found at i:28200 original size:82 final size:82
Alignment explanation
Indices: 28010--28607 Score: 683
Period size: 82 Copynumber: 7.4 Consensus size: 82
28000 TAAACAATAA
** * *
28010 GAATAAATCCTAAAACATAACTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATA-AAT--
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
** ** *
28072 --TCTAATGAATGACAG
66 AATCTGTTGAACAACGG
* * * *
28087 GAATAAATCTCGAAAAAGAATTAATCAATTAATTCTTGTTTGGAAACAAAATCAGAATAGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
28152 AATCTGTTGAACAACGG
66 AATCTGTTGAACAACGG
* * *
28169 GAATAAATCTCGAAACAGAATTATTCTATTAATTCTTGTTTGGAAACAAAATCATAATAGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
* * * **
28234 AATCTATTGTACGATAG
66 AATCTGTTGAACAACGG
* * * *
28251 GAATAAATCCTGAAACAGAATTATTCAACTAA-TCGTTGTTTGGAAGCAAAATTAAAATAGAATA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTC-TTGTTTGGAAACAAAATCAAAATAGAATA
* * *
28315 AAATCTGCTGAACAGCAG
65 AAATCTGTTGAACAACGG
* * *
28333 GAATAAATCCCGAAAAAAAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
* **
28398 AATTTGTTGAACAGTGG
66 AATCTGTTGAACAACGG
* *
28415 GAATAAATCTCGAAACAGAATTATTCAATTAATCCTTGTTTGGAAACAAAATCAAAATAGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
* * **
28480 ATTCTATTGAACGGCGG
66 AATCTGTTGAACAACGG
* * * * *
28497 GAATAAATCCCGAGACAGATTTATT-AACTTAATTCTT-TTTGAAAATAAAATCACAATAGAATA
1 GAATAAATCCCGAAACAGAATTATTCAA-TTAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
28560 AAATCTGTTGAA-AGACGG
65 AAATCTGTTGAACA-ACGG
* *
28578 GAATAAATCCCGAAATAGATTTATTCAATT
1 GAATAAATCCCGAAACAGAATTATTCAATT
28608 TTAACTTTTA
Statistics
Matches: 444, Mismatches: 67, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
77 51 0.11
78 3 0.01
81 65 0.15
82 324 0.73
83 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (82 bp):
GAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
AATCTGTTGAACAACGG
Found at i:28439 original size:246 final size:246
Alignment explanation
Indices: 28010--28607 Score: 791
Period size: 246 Copynumber: 2.5 Consensus size: 246
28000 TAAACAATAA
* * * *
28010 GAATAAATCCTAAAACATAACTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATA-AAT--
1 GAATAAATCCTGAAACAGAATTATTCAACTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
* * * * *
28072 --TCTAATGAATGACAGGAATAAATCTCGAAAAAGAATTAATCAATTAATTCTTGTTTGGAAACA
66 AATCTGATGAAAGACAGGAATAAATCCCGAAAAAGAATTATTCAATTAATCCTTGTTTGGAAACA
* *
28135 AAATCAGAATAGAATAAAATCTGTTGAACAACGGGAATAAATCTCGAAACAGAATTATTCTATTA
131 AAATCAAAATAGAATAAAATCTGTTGAACAACGGGAATAAATCTCGAAACAGAATTATTCAATTA
* * * *
28200 ATTCTTGTTTGGAAACAAAATCATAATAGAATAAAATCTATTGTACGATAG
196 ATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAACGACAG
* *
28251 GAATAAATCCTGAAACAGAATTATTCAACTAA-TCGTTGTTTGGAAGCAAAATTAAAATAGAATA
1 GAATAAATCCTGAAACAGAATTATTCAACTAATTC-TTGTTTGGAAACAAAATCAAAATAGAATA
* *
28315 AAATCTGCTGAACAG-CAGGAATAAATCCCGAAAAAAAATTATTCAATTAATCCTTGTTTGGAAA
65 AAATCTGATGAA-AGACAGGAATAAATCCCGAAAAAGAATTATTCAATTAATCCTTGTTTGGAAA
* **
28379 CAAAATCAAAATAGAATAAAATTTGTTGAACAGTGGGAATAAATCTCGAAACAGAATTATTCAAT
129 CAAAATCAAAATAGAATAAAATCTGTTGAACAACGGGAATAAATCTCGAAACAGAATTATTCAAT
* * *
28444 TAATCCTTGTTTGGAAACAAAATCAAAATAGAATAAATTCTATTGAACGGCGG
194 TAATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAACGACAG
* * * * * *
28497 GAATAAATCCCGAGACAGATTTATT-AACTTAATTCTT-TTTGAAAATAAAATCACAATAGAATA
1 GAATAAATCCTGAAACAGAATTATTCAAC-TAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
* * * *
28560 AAATCTGTTGAAAGACGGGAATAAATCCCGAAATAGATTTATTCAATT
65 AAATCTGATGAAAGACAGGAATAAATCCCGAAAAAGAATTATTCAATT
28608 TTAACTTTTA
Statistics
Matches: 309, Mismatches: 38, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
240 2 0.01
241 50 0.16
242 3 0.01
244 2 0.01
245 64 0.21
246 185 0.60
247 3 0.01
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (246 bp):
GAATAAATCCTGAAACAGAATTATTCAACTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAA
AATCTGATGAAAGACAGGAATAAATCCCGAAAAAGAATTATTCAATTAATCCTTGTTTGGAAACA
AAATCAAAATAGAATAAAATCTGTTGAACAACGGGAATAAATCTCGAAACAGAATTATTCAATTA
ATCCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTATTGAACGACAG
Found at i:29171 original size:50 final size:51
Alignment explanation
Indices: 29085--29355 Score: 331
Period size: 50 Copynumber: 5.4 Consensus size: 51
29075 ACAAGATCTA
* * * *
29085 AAAAATAATATAAATAAATATTTATATTTATGTAAAACATAAGATTTGAAC
1 AAAAACAATTTAAATAAATATTTATATTTATATAAAACATAAGATCTGAAC
* * *
29136 AAAAA-AATTTAAATAAATATTTATACTTATATAAAACACT-AGATCCGAGC
1 AAAAACAATTTAAATAAATATTTATATTTATATAAAACA-TAAGATCTGAAC
* * *
29186 AAAAAACAATTTAAATAAATATTTATATTTATGTAAAACACAAGATCTAAAC
1 -AAAAACAATTTAAATAAATATTTATATTTATATAAAACATAAGATCTGAAC
*
29238 AAAAA-AATTTAAATAAATATTTATATTTATATAAAACACT-AGATCCGGAA-
1 AAAAACAATTTAAATAAATATTTATATTTATATAAAACA-TAAGAT-CTGAAC
*
29288 AAAAACAATTTAAATAAATATTTATTTTTATATAAAACATCAA-ATCTGAAC
1 AAAAACAATTTAAATAAATATTTATATTTATATAAAACAT-AAGATCTGAAC
*
29339 -AAAACAATTTAGATAAA
1 AAAAACAATTTAAATAAA
29356 CAAGTTCTAA
Statistics
Matches: 191, Mismatches: 19, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
50 99 0.52
51 53 0.28
52 39 0.20
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (51 bp):
AAAAACAATTTAAATAAATATTTATATTTATATAAAACATAAGATCTGAAC
Found at i:29324 original size:101 final size:102
Alignment explanation
Indices: 29084--29355 Score: 422
Period size: 102 Copynumber: 2.7 Consensus size: 102
29074 TACAAGATCT
* * * *
29084 AAAAAATAATATAAATAAATATTTATATTTATGTAAAACATAAGATTTGAACAAAAAAATTTAAA
1 AAAAAACAATTTAAATAAATATTTATATTTATGTAAAACACAAGATCTGAACAAAAAAATTTAAA
*
29149 TAAATATTTATACTTATATAAAACACTAGATCCGAGC
66 TAAATATTTATACTTATATAAAACACTAGATCCGAGA
*
29186 AAAAAACAATTTAAATAAATATTTATATTTATGTAAAACACAAGATCTAAACAAAAAAATTTAAA
1 AAAAAACAATTTAAATAAATATTTATATTTATGTAAAACACAAGATCTGAACAAAAAAATTTAAA
*
29251 TAAATATTTATATTTATATAAAACACTAGATCCG-GA
66 TAAATATTTATACTTATATAAAACACTAGATCCGAGA
* * * *
29287 AAAAAACAATTTAAATAAATATTTATTTTTATATAAAACATCAA-ATCTGAACAAAACAATTTAG
1 AAAAAACAATTTAAATAAATATTTATATTTATGTAAAACA-CAAGATCTGAACAAAAAAATTTAA
29351 ATAAA
65 ATAAA
29356 CAAGTTCTAA
Statistics
Matches: 157, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 61 0.39
102 96 0.61
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (102 bp):
AAAAAACAATTTAAATAAATATTTATATTTATGTAAAACACAAGATCTGAACAAAAAAATTTAAA
TAAATATTTATACTTATATAAAACACTAGATCCGAGA
Found at i:31758 original size:51 final size:51
Alignment explanation
Indices: 31677--31914 Score: 289
Period size: 51 Copynumber: 4.6 Consensus size: 51
31667 CTATAAATGA
*
31677 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
31728 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
31779 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGACT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * * * * **
31830 AAAGGTTCGATGACTCAGTGTCATCGTAAGGATACGAATTCTTATAAGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTT-TACGGATT
*
31882 AAGAGGTCCGACGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
31915 TTAAATGAAA
Statistics
Matches: 160, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
51 130 0.81
52 6 0.04
53 23 0.14
54 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:34758 original size:51 final size:51
Alignment explanation
Indices: 34677--34914 Score: 300
Period size: 51 Copynumber: 4.6 Consensus size: 51
34667 CTATAAATGA
34677 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
34728 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGATTTCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
34779 AAAGGTCCGATGATTAAGTGTCATCGTGAGTAAATGAATCCATGATGGACT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * **
34830 AAAGGTCCGATGACTCAA-TGTCATCGTGAGTATATGAATTCCTATACGGAAC
1 AAAGGTCCGATGACT-AAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
34882 AAGAGGTCCGATGACTATA-TGTCATAGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
34915 TTAAATAAAA
Statistics
Matches: 163, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
51 124 0.76
52 12 0.07
53 27 0.17
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:39004 original size:49 final size:49
Alignment explanation
Indices: 38928--39091 Score: 260
Period size: 49 Copynumber: 3.4 Consensus size: 49
38918 TTGTTTTTAC
*
38928 TAGT-TTCATCTAATCTCTCAGC-CTCTCACTCTCCATATATATTAATCA
1 TAGTCTTCATCTAATCTCACA-CTCTCTCACTCTCCATATATATTAATCA
*
38976 TAATCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
1 TAGTCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
* *
39025 TAGTTTTCATCTAAACTCACACTCTCTCACTCTCCATATATATTAATCA
1 TAGTCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
*
39074 TAGTCTTCTTCTAATCTC
1 TAGTCTTCATCTAATCTC
39092 TCACCCTACA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
48 4 0.04
49 102 0.96
ACGTcount: A:0.28, C:0.29, G:0.02, T:0.40
Consensus pattern (49 bp):
TAGTCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
Found at i:40363 original size:49 final size:43
Alignment explanation
Indices: 40310--40486 Score: 173
Period size: 41 Copynumber: 3.9 Consensus size: 43
40300 ATTGTTTGTC
*
40310 TAGTCTTCATCTAATCTTTCACTCTCTAACTCTCCATATATATTAGTCA
1 TAGTCTTCATCTAA-C--TC-CTCTC--ACTCTCCATATATATTAATCA
**
40359 TAGTCTTCATCT-ACT-CTCTCACTCTCCATATATAAAAATCA
1 TAGTCTTCATCTAACTCCTCTCACTCTCCATATATATTAATCA
40400 TAGTCTTCATCTAA-TCC-CTCACTCTCCATATATATTAATCA
1 TAGTCTTCATCTAACTCCTCTCACTCTCCATATATATTAATCA
* *
40441 TAGCCTTTATCTAATCTCTCACTCTTTCACTCTCCATATATATTAA
1 TAGTCTTCATCTAA---CTC-CTC--TCACTCTCCATATATATTAA
40487 CCTTTTGACT
Statistics
Matches: 111, Mismatches: 7, Indels: 20
0.80 0.05 0.14
Matches are distributed among these distances:
41 65 0.59
42 2 0.02
43 5 0.05
45 3 0.03
46 1 0.01
47 2 0.02
48 1 0.01
49 32 0.29
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (43 bp):
TAGTCTTCATCTAACTCCTCTCACTCTCCATATATATTAATCA
Found at i:40375 original size:41 final size:41
Alignment explanation
Indices: 40332--40465 Score: 196
Period size: 41 Copynumber: 3.3 Consensus size: 41
40322 AATCTTTCAC
* * *
40332 TCTCTAACTCTCCATATATATTAGTCATAGTCTTCATCTAC
1 TCTCTCACTCTCCATATATATTAATCATAGTCTTCATCTAA
**
40373 TCTCTCACTCTCCATATATAAAAATCATAGTCTTCATCTAA
1 TCTCTCACTCTCCATATATATTAATCATAGTCTTCATCTAA
* * *
40414 TCCCTCACTCTCCATATATATTAATCATAGCCTTTATCTAA
1 TCTCTCACTCTCCATATATATTAATCATAGTCTTCATCTAA
40455 TCTCTCACTCT
1 TCTCTCACTCT
40466 TTCACTCTCC
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.28, C:0.29, G:0.03, T:0.40
Consensus pattern (41 bp):
TCTCTCACTCTCCATATATATTAATCATAGTCTTCATCTAA
Found at i:45799 original size:24 final size:24
Alignment explanation
Indices: 45743--45822 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
45733 CTTCATCTAA
*
45743 TCTCCCTCCCTCTCTCTCTTTGTCACTC
1 TCTCCCTCCATCTCTCTC-TT-T--CTC
* *
45771 CCTCCCTCCTTCTCTCTCTTTCTC
1 TCTCCCTCCATCTCTCTCTTTCTC
* *
45795 TCTCCCTCCATCCCTCTCTCTCTC
1 TCTCCCTCCATCTCTCTCTTTCTC
45819 TCTC
1 TCTC
45823 TCACACACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 27 0.59
26 1 0.02
27 2 0.04
28 16 0.35
ACGTcount: A:0.03, C:0.54, G:0.01, T:0.42
Consensus pattern (24 bp):
TCTCCCTCCATCTCTCTCTTTCTC
Found at i:45823 original size:28 final size:28
Alignment explanation
Indices: 45744--45824 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 28
45734 TTCATCTAAT
* *
45744 CTCCCTCCCTCTCTCTCTTTGTCACTCC
1 CTCCCTCCCTCTCTCTCTTTCTCTCTCC
*
45772 CTCCCTCCTTCTCTCTCTTTCTCTCTCC
1 CTCCCTCCCTCTCTCTCTTTCTCTCTCC
* *
45800 CTCCATCCCTCTCTCTCTCTCTCTC
1 CTCCCTCCCTCTCTCTCTTTCTCTC
45825 ACACACACAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.02, C:0.54, G:0.01, T:0.42
Consensus pattern (28 bp):
CTCCCTCCCTCTCTCTCTTTCTCTCTCC
Found at i:49162 original size:14 final size:16
Alignment explanation
Indices: 49144--49180 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
49134 CTAATCTCCG
49144 TCCCTCCCTCTCT-CC
1 TCCCTCCCTCTCTGCC
*
49159 -CCCTCTCTCTCTGCC
1 TCCCTCCCTCTCTGCC
49174 TCCCTCC
1 TCCCTCC
49181 TCCCTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 11 0.61
15 2 0.11
16 5 0.28
ACGTcount: A:0.00, C:0.65, G:0.03, T:0.32
Consensus pattern (16 bp):
TCCCTCCCTCTCTGCC
Found at i:49198 original size:23 final size:22
Alignment explanation
Indices: 49147--49202 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
49137 ATCTCCGTCC
* *
49147 CTCCCTCTCTCCCCCTCTCTCT
1 CTCCCTCCCTCCCCCTCTCTAT
* *
49169 CTGCCTCCCTCCTCCCTTTCTAT
1 CTCCCTCCCTCC-CCCTCTCTAT
49192 CTCCCTCCCTC
1 CTCCCTCCCTC
49203 TCACTCTCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.02, C:0.61, G:0.02, T:0.36
Consensus pattern (22 bp):
CTCCCTCCCTCCCCCTCTCTAT
Found at i:52982 original size:20 final size:18
Alignment explanation
Indices: 52943--52978 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52933 ATATTTTTAT
*
52943 AAAAATAATTTTTGGGTA
1 AAAAAAAATTTTTGGGTA
52961 AAAAAAAATATTTTGGGT
1 AAAAAAAAT-TTTTGGGT
52979 TAAATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (18 bp):
AAAAAAAATTTTTGGGTA
Found at i:54326 original size:42 final size:42
Alignment explanation
Indices: 54267--54350 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
54257 CAAATATTTT
* *
54267 TAAACTCAAATATAATTTCATTCTTAAAAAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
* **
54309 TAAACCCAAATATAATTTTATTCCTAATTAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
54351 AACTCTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
Found at i:54569 original size:25 final size:25
Alignment explanation
Indices: 54531--54581 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
54521 TTCCTTTTCT
*
54531 TTGTTGTGGTTGCTCTCGCATTGAA
1 TTGTTGTGGCTGCTCTCGCATTGAA
*
54556 TTGTTGTGGCTGCTCTTGCATTGAA
1 TTGTTGTGGCTGCTCTCGCATTGAA
54581 T
1 T
54582 CAGCAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.16, G:0.27, T:0.45
Consensus pattern (25 bp):
TTGTTGTGGCTGCTCTCGCATTGAA
Found at i:56462 original size:28 final size:28
Alignment explanation
Indices: 56422--56477 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
56412 AATACGCCAA
*
56422 ACTAAGGTTGCATTTATACTTGCATAAC
1 ACTAAGGTTGCATTTATACTTGAATAAC
56450 ACTAAGGTTGCATTTATACTTGAATAAC
1 ACTAAGGTTGCATTTATACTTGAATAAC
56478 CTTAGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (28 bp):
ACTAAGGTTGCATTTATACTTGAATAAC
Found at i:62019 original size:29 final size:29
Alignment explanation
Indices: 61972--62029 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
61962 GAGCTAATGG
*
61972 AAAAAGGGTATGCTCGAGAGAGCTTAAGT
1 AAAAAGGGTATACTCGAGAGAGCTTAAGT
* *
62001 AAAAAGGGTATATTTGAGAGAGCTTAAGT
1 AAAAAGGGTATACTCGAGAGAGCTTAAGT
62030 CCATGTGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (29 bp):
AAAAAGGGTATACTCGAGAGAGCTTAAGT
Found at i:66695 original size:195 final size:195
Alignment explanation
Indices: 66362--66725 Score: 520
Period size: 195 Copynumber: 1.9 Consensus size: 195
66352 ACGTAACTAA
* *
66362 GTTTTTAATTCAAAGACTAAAAGTTGTTGACATAATAACAAACTATTTAGACCAAATGAAGCGAT
1 GTTTTTAATTCAAAGACTAAAACTTGTTGACAAAATAACAAACTATTTAGACCAAATGAAGCGAT
* * * *
66427 TTCCCGAGCATGGAATATTCAGAAAATTGCTCGAAGCAATGTATCGTCATTAATACTTTAAGGAA
66 TTCCAGAGCATGGAATATTCAAAAAATTGCTCGAAGCAATGGATCGTCATTAATACTTTAAAGAA
* * *
66492 GTGAAGTTATAAAAA-ACCTTGTAAAAGTTTGACTAGTTCTGAATTTTGTCCAAGAACCAAAATA
131 GTGAAGTTA-AAAAATAACTCGTAAAAGTTTGACAAGTTCTGAATTTTGTCCAAGAACCAAAATA
66556 T
195 T
* * * *
66557 GTTTTTAATTCAAAGACTAAAACTCT-TTTACAAAATGACAAACTATTTAGACCAAATGATGTGA
1 GTTTTTAATTCAAAGACTAAAACT-TGTTGACAAAATAACAAACTATTTAGACCAAATGAAGCGA
* * *
66621 TTTCCAGAGCATGGAATGTTCAAAAAATTGCTCGAAGGAATGGATCTTC-TTGAATACTTTAAAG
65 TTTCCAGAGCATGGAATATTCAAAAAATTGCTCGAAGCAATGGATCGTCATT-AATACTTTAAAG
66685 AA-TCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTC
129 AAGT-GAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTC
66726 GAAAGTTCAT
Statistics
Matches: 149, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
194 8 0.05
195 140 0.94
196 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (195 bp):
GTTTTTAATTCAAAGACTAAAACTTGTTGACAAAATAACAAACTATTTAGACCAAATGAAGCGAT
TTCCAGAGCATGGAATATTCAAAAAATTGCTCGAAGCAATGGATCGTCATTAATACTTTAAAGAA
GTGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCTGAATTTTGTCCAAGAACCAAAATAT
Found at i:66935 original size:216 final size:216
Alignment explanation
Indices: 66551--67568 Score: 1472
Period size: 216 Copynumber: 4.7 Consensus size: 216
66541 CCAAGAACCA
*
66551 AAATATGTTTTTAATTCAAAGACTAAAACTCT-TTTACAAAATGACAAACTATTTAGACCAAATG
1 AAATAAGTTTTTAATTCAAAGACTAAAACT-TGTTTACAAAATGACAAACTATTTAGACCAAATG
* * *
66615 ATGTGATTT-CCAGAGCATGGAATGTTCAAAAAATTGCTCGAAGGAATGGATCTTCTTGAATACT
65 ATGCGATTTCCCA-AGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACT
* * *
66679 TTAAAGAATCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAAC
129 TTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAAC
66744 AAAGAGAGAAACAATTCTCACGT
194 AAAGAGAGAAACAATTCTCACGT
*
66767 AAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
1 AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
* * * *
66832 TGTGATTTCCCAAGCATGGAAAGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATTCTTT
66 TGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTT
* * * * * * * * *
66897 AAGGAAGCGAAGTTGTAAAAGAACTCGTTAATGTTTGACAAGTTCAAAAGTTCGTCCTTA-TACC
131 AAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCC-AAGAACA
*
66961 AAGAGAGAAAAAATTCTCACGT
195 AAGAGAGAAACAATTCTCACGT
*
66983 AAATAAGTTGTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
1 AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
*** ** * *
67048 TGCGATTTCCTTTGCATGGAACATTCGAAAAATTACTCGAAGGAATGGATCGTCTTAAATACTTT
66 TGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTT
* * * *
67113 AAGG-ATCCGAAGTTATAAAAGAACTCATAAAAGTTTGAGAAGTTCGGAAGTTCGTCCAAGAACA
131 AAGGAAT-CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACA
*
67177 AAGAGAGAAACTATTCTCACGT
195 AAGAGAGAAACAATTCTCACGT
* *
67199 AAATAAGTTTTTAATTCGAAGACCAAAACTTG-TTACAAAATGACAAACTATTTAGACCAAATGA
1 AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
*
67263 TGCGATTTCCCAAGCATGGAATGTTCGAAAAATAGCTCGAAGGAATGGATCGTCTTGAATACTTT
66 TGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTT
* * * *
67328 AAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTAACAAATTCGGAAGTTCATCCAAGAACCA
131 AAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACAA
* *
67393 AGAGAGAAACAATTCACATGT
196 AGAGAGAAACAATTCTCACGT
* * *
67414 AAATAAGTTTTTAATTCAAAGACTAAAACTTTTTTGCAAAATGACAAACTATTTAGATCAAATGA
1 AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
* * *
67479 TGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGGAATGGATCGCCTTGAATACTT
66 TGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCTCG-AAGGAATGGATCGTCTTGAATACTT
* *
67544 TAAGGAA-CCAATGTTATATAAGAAC
130 TAAGGAATCGAA-GTTATAAAAGAAC
67569 CAAGAGAGAA
Statistics
Matches: 718, Mismatches: 75, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
215 195 0.27
216 476 0.66
217 47 0.07
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (216 bp):
AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGA
TGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTT
AAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACAA
AGAGAGAAACAATTCTCACGT
Found at i:68371 original size:215 final size:216
Alignment explanation
Indices: 67563--69555 Score: 2223
Period size: 216 Copynumber: 9.2 Consensus size: 216
67553 AATGTTATAT
* **
67563 AAGAACCAAGAGAGAAACAATTCTCACGGAAATAAGTTTTTAATTCAAAGACCAAAACTTCATTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * * *
67628 TAAAATGACAAACTATTTAGACAAAACGATGCGATTTCCTGAGCGT-G---GTTCGGAAAATTGC
66 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC
* * * * * * *
67689 ACGAAGGAATGGATTGTGTAGAATACGTTAAGGATCCAA-AAAGCTATAAAAGAACTCGTAAAAG
131 TCGAAGGAATGGATCGTCTTGAATACTTTAAGGA---AACGAAGTTATAAAAGAACTCGTAAAAG
67753 TTTGACAAGTT-GGAAAGTTCATCC
193 TTTGACAAGTTCGG-AAGTTCATCC
* * * * * *
67777 ATGAACCAAGAGAGAAACAATTTTCAGGTTAATAAGATTTTAATTCAAAAACCAAAACTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
** * * * * *
67842 CAACTTGACAAACTGTTTAGACCAATTGAAGCAATTTCCTGAGCATGGAATGTTC-AGAAAATTG
66 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTG
* * * * * * *
67906 CTCGATGGAATAGATCGTCTTGAATAC-TTAACGCAACAAAAGTTATAAAATAATTCGTAAAAGT
130 CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAAC-GAAGTTATAAAAGAACTCGTAAAAGT
*
67970 TTGACAAGTTCGAAAGTTCATCC
194 TTGACAAGTTCGGAAGTTCATCC
* *
67993 AAGAACCAAGAGAAAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCACAAAAACTTAT
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-C-C-AAAACTTGT
* *
68058 TTACAAAATGACAAACTATTTAGACCAAATTATGCGATTTCCCAAGCATGGAATGTTC-AGAAAA
63 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA-AAAA
** * **
68122 TTGCTCGAAGGAATGGATCAACTTGAACACTTTAAGGAAACGAAGTTATAAAAGAACTAATAAAA
127 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACGAAGTTATAAAAGAACTCGTAAAA
*
68187 GTTTGACAAGTTCGGAAGTTCGTCC
192 GTTTGACAAGTTCGGAAGTTCATCC
* * * *
68212 AAGAACCATGAGAGAAA-AATTCTCACGTAAATAAGTTTTTAATTTAAAGACTAAAACTTCTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * *
68276 CAAATTGACAAACTGTTTAAACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAATTAC
66 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC
* * * *
68341 TCGAAGAAATAGATCGTCTTGAATACTTTAAAGAAGCGAAGTTATAAATA-AACTCGTAAAAGTT
131 TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACGAAGTTATAAA-AGAACTCGTAAAAGTT
* * * *
68405 TAACAAGTGCGGACGTTCGTCC
195 TGACAAGTTCGGAAGTTCATCC
* * * *
68427 AAGAACCAAGAGATAAACAATTCTTATGTAAATAAGTTTTTAATTAAAAGACCAAAACTT-TGTT
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGT-TT
* * * * *
68491 ACAAAATGACAAACTATTTAGATCAAATGACGCGATTTCTCGAGCTTGGATTGTTCGAAAAATTG
65 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTG
* ** * *
68556 CTCGAAGGAATGGACCGTCTTGAATACTTTAAGGAATTGAAGTTATAAAAGAACTTGTAAAACTT
130 CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACGAAGTTATAAAAGAACTCGTAAAAGTT
*
68621 TGACAAGTTCGGAAGTTC-TTC
195 TGACAAGTTCGGAAGTTCATCC
* * * * * **
68642 AACAACCAAGAGAGAAATAATTCTCACGTAAATAACTTTTTAATTTAAAGTCCATGACTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* *
68707 CAAAATGACAAACTATTTAGACTAAATGATGCGATTTTCCGAGCATGGAATGTTCGAAAAAAATT
66 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCG--AAAAATT
* * ** * * *
68772 TCTCAAAAAAATGGATCATCTTGAATACTTTAAGGAAGCGAAGTTATAAAAGAACTCATAAAAGT
129 GCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACGAAGTTATAAAAGAACTCGTAAAAGT
* *
68837 TTGACAAGTGCGGAAGTTCTTCC
194 TTGACAAGTTCGGAAGTTCATCC
* * * *
68860 ACGAACCAAGAGAGAGATAATTCTCACAG-AAATAAGTTTTTGATTCAAA-AGCCAAAACTTGTT
1 AAGAACCAAGAGAGAAACAATTCTCAC-GTAAATAAGTTTTTAATTCAAAGA-CCAAAACTTGTT
* * *
68923 TACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCTCGAGCAT--AGT-TTCG-AAAATT
64 TACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATT
* * * * * * * *
68984 GCACGAAGCG-ATGGATCATCGTGAATACGTTAAGGAACCAAAGCTATAAAAGAACTTGTAAAAG
129 GCTCGAAG-GAATGGATCGTCTTGAATACTTTAAGGAAACGAAGTTATAAAAGAACTCGTAAAAG
*
69048 TTTGACAAGTTCGAAAGTTCATCC
193 TTTGACAAGTTCGGAAGTTCATCC
* * * *
69072 ATGAACCAAGAGAGAAACAATTCTCATGTTAATAAGATTTTAATTCAAAGACCAAAACTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * * ** * *
69137 CAAATTGACAAATTGTTTCGACCAAATGGTATGATTTCCCAAGCATGGAATGTTCGAAATATTGC
66 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC
* * * * *
69202 TTGATGGAATAGATCATCTTGAATACTTTATA--CAACAGAAGTTATAAAAGAACTCGTAAAAGT
131 TCGAAGGAATGGATCGTCTTGAATACTTTA-AGGAAAC-GAAGTTATAAAAGAACTCGTAAAAGT
*
69265 TTGACAAGTTTGGAAGTT-ACTCC
194 TTGACAAGTTCGGAAGTTCA-TCC
* * * * * * * * * * *
69288 AAGAACAAAGATACAAACATTTATCACGTAACTAAGTTTTTAATTAAAAAACTAAAAGTTTTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * *
69353 CATAATGACAAACTATTTAGATCGAATGATGCGACTTCCCGAGCATGAAATGTTCGAAAAATTGC
66 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC
* **
69418 CCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAGTGAAGTTATAAAAGAACTCGTAAAAGTTT
131 TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACGAAGTTATAAAAGAACTCGTAAAAGTTT
* ** *
69483 GACAGGTTCTAAAGTTCGTCC
196 GACAAGTTCGGAAGTTCATCC
* * *
69504 AAGAACTAAGAGATAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGAC
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
69556 TAAATGTCAA
Statistics
Matches: 1487, Mismatches: 255, Indels: 72
0.82 0.14 0.04
Matches are distributed among these distances:
211 1 0.00
212 168 0.11
213 1 0.00
214 96 0.06
215 274 0.18
216 541 0.36
217 89 0.06
218 163 0.11
219 146 0.10
220 8 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (216 bp):
AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC
TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAACGAAGTTATAAAAGAACTCGTAAAAGTTT
GACAAGTTCGGAAGTTCATCC
Found at i:69291 original size:861 final size:862
Alignment explanation
Indices: 67563--69555 Score: 2428
Period size: 861 Copynumber: 2.3 Consensus size: 862
67553 AATGTTATAT
* * * *
67563 AAGAACCAAGAGAGAAACAATTCTCACGGAAATAAGTTTTTAATTCAAAGACCAAAACTTCATTA
1 AAGAACCAAGAGACAAACAATTCTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTTATTA
* * * *
67628 TAAAATGACAAACTATTTAGA-CAAAACGATGCGATTTCCTGAGC--G-TGGTTCGGAAAATTGC
66 CAAAATGACAAACTATTTAGATC-AAATGATGCGATTTCC-GAGCTGGATTGTTCGAAAAATTGC
* * * * ** *
67689 ACGAAGGAATGGATTGTGTAGAATACGTTAAGG-ATCCAAAAAGCTATAAAAGAACTCGTAAAAG
129 ACGAAGGAATGGATCGTCTTGAATACTTTAAGGAAT---TGAAGTTATAAAAGAACTCGTAAAAG
* * * * *
67753 TTTGACAAGTT-GGAAAGTTCATCCATGAACCAAGAGAGAAACAATTTTCAGGTTAATAAGATTT
191 TTTGACAAGTTCGG-AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* * ** * *
67817 TAATTCAAAAACCAAAACTTGTTTACAACTTGACAAACTGTTTAGACCAATTGAAGCAATTTCCT
255 TAATTTAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAAGCAATTTCCT
* * *** *
67882 GAGCATGGAATGTTCAGAAAATTGCTCGATGGAATAGATCGTCTTGAATACTTAACGCAACAAAA
320 GAGCATGGAATGTTCAAAAAATTGCTCAAAAAAATAGATCATCTTGAATACTTAACGCAACAAAA
* * * *
67947 GTTATAAAATAATTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAAAAACA
385 GTTATAAAAGAACTCATAAAAGTTTGACAAGTGCGAAAGTTCATCCAAGAACCAAGAGAAAAACA
68012 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACCACAAAAACTTATTTACAAAATGACAAACTAT
450 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACCACAAAAACTTATTTACAAAATGACAAACTAT
* * *
68077 TTAGACCAAATTATGCGATTTCCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCA
515 TTAGACAAAATGATGCGATTTCCCAAGCAT-GAATGTTCAGAAAATTGCACGAAGGAATGGATCA
* * * * *
68142 ACTTGAACACTTTAAGGAAACGAAGTTATAAAAGAACTAATAAAAGTTTGACAAGTTCGGAAGTT
579 ACGTGAACACGTTAAGGAAACAAAGCTATAAAAGAACTAATAAAAGTTTGACAAGTTCGAAAGTT
* * * * *
68207 CGTCCAAGAACCATGAGAGAAAAATTCTCACGTAAATAAGTTTTTAATTTAAAGACTAAAACTTC
644 CATCCAAGAACCAAGAGAGAAAAATTCTCACGTAAATAAGATTTTAATTCAAAGACCAAAACTTC
*
68272 TTTACAAATTGACAAACTGTTTAAACCAAATGATGCAATTTCCCGAGCATGGAATGTTCGAAAAA
709 TTTACAAATTGACAAACTGTTTAAACCAAATGATG-AATTTCCCAAGCATGGAATGTTCGAAAAA
* *
68337 TTACTCGAAGAAATAGATCGTCTTGAATACTTTAAAGAAGCGAAGTTATAAATAAACTCGTAAAA
773 TTACTCGAAGAAATAGATCATCTTGAATACTTTAAACAAGCGAAGTTATAAATAAACTCGTAAAA
*
68402 GTTTAACAAGTGCGGACGTTCGTCC
838 GTTTAACAAGTGCGGAAGTTCGTCC
* * * *
68427 AAGAACCAAGAGATAAACAATTCTTATGTAAATAAGTTTTTAATTAAAAGACCAAAACTTTGTTA
1 AAGAACCAAGAGACAAACAATTCTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTTATTA
*
68492 CAAAATGACAAACTATTTAGATCAAATGACGCGATTTCTCGAGCTTGGATTGTTCGAAAAATTGC
66 CAAAATGACAAACTATTTAGATCAAATGATGCGATTTC-CGAGC-TGGATTGTTCGAAAAATTGC
* * * *
68557 TCGAAGGAATGGACCGTCTTGAATACTTTAAGGAATTGAAGTTATAAAAGAACTTGTAAAACTTT
129 ACGAAGGAATGGATCGTCTTGAATACTTTAAGGAATTGAAGTTATAAAAGAACTCGTAAAAGTTT
* * * *
68622 GACAAGTTCGGAAGTTC-TTCAACAACCAAGAGAGAAATAATTCTCACGTAAATAACTTTTTAAT
194 GACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
* ** * * *
68686 TTAAAGTCCATGACTTGTTTACAAAATGACAAACTATTTAGACTAAATGATGCGATTTTCC-GAG
259 TTAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAAGC-AATTTCCTGAG
* * * *
68750 CATGGAATGTTCGAAAAAAATTTCTCAAAAAAATGGATCATCTTGAATACTTTAA-GGAAGC-GA
323 CATGGAATGTTC--AAAAAATTGCTCAAAAAAATAGATCATCTTGAATAC-TTAACGCAA-CAAA
* * * * * *
68813 AGTTATAAAAGAACTCATAAAAGTTTGACAAGTGCGGAAGTTCTTCCACGAACCAAGAGAGAGAT
384 AGTTATAAAAGAACTCATAAAAGTTTGACAAGTGCGAAAGTTCATCCAAGAACCAAGAGAAAAAC
* * *
68878 AATTCTCACAG-AAATAAGTTTTTGATTCAAA-AGC-C-AAAACTTGTTTACAAAATGACAAACT
449 AATTCTCAC-GTAAATAAGTTTTTAATTCAAAGACCACAAAAACTTATTTACAAAATGACAAACT
* * *
68939 ATTTAGACAAAATGATGCGATTTCTCGAGCAT-AGT-TTC-GAAAATTGCACGAAGCG-ATGGAT
513 ATTTAGACAAAATGATGCGATTTCCCAAGCATGAATGTTCAGAAAATTGCACGAAG-GAATGGAT
* * * **
69000 CATCGTGAATACGTTAAGGAACCAAAGCTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGAAAG
577 CAACGTGAACACGTTAAGGAAACAAAGCTATAAAAGAACTAATAAAAGTTTGACAAGTTCGAAAG
* * *
69065 TTCATCCATGAACCAAGAGAGAAACAATTCTCATGTTAATAAGATTTTAATTCAAAGACCAAAAC
642 TTCATCCAAGAACCAAGAGAGAAA-AATTCTCACGTAAATAAGATTTTAATTCAAAGACCAAAAC
* * **
69130 TTGTTTACAAATTGACAAATTGTTTCGACCAAATGGTATG-ATTTCCCAAGCATGGAATGTTCGA
706 TTCTTTACAAATTGACAAACTGTTTAAACCAAAT-G-ATGAATTTCCCAAGCATGGAATGTTCGA
* * * * * *
69194 AATATTGCTTGATGGAATAGATCATCTTGAATACTTTATACAA-CAGAAGTTATAAA-AGAACTC
769 AAAATTACTCGAAGAAATAGATCATCTTGAATACTTTAAACAAGC-GAAGTTATAAATA-AACTC
* **
69257 GTAAAAGTTTGACAAGTTTGGAAGTTAC-TCC
832 GTAAAAGTTTAACAAGTGCGGAAGTT-CGTCC
* * * * * * * * *
69288 AAGAACAAAGATACAAACATTTATCACGTAACTAAGTTTTTAATTAAAAAACTAAAAGTTTTTTA
1 AAGAACCAAGAGACAAACAATTCTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTTATTA
* * * * *
69353 CATAATGACAAACTATTTAGATCGAATGATGCGACTTCCCGAGCATGAAATGTTCGAAAAATTGC
66 CAAAATGACAAACTATTTAGATCAAATGATGCGA-TTTCCGAGC-TGGATTGTTCGAAAAATTGC
* *
69418 CCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAGTGAAGTTATAAAAGAACTCGTAAAAGTTT
129 ACGAAGGAATGGATCGTCTTGAATACTTTAAGGAATTGAAGTTATAAAAGAACTCGTAAAAGTTT
* ** * * *
69483 GACAGGTTCTAAAGTTCGTCCAAGAACTAAGAGATAAACAATTCTCACGTAAATAAGTTTTTAAT
194 GACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
69548 TTAAAGAC
259 TTAAAGAC
69556 TAAATGTCAA
Statistics
Matches: 964, Mismatches: 142, Indels: 48
0.84 0.12 0.04
Matches are distributed among these distances:
860 98 0.10
861 349 0.36
862 55 0.06
863 3 0.00
864 148 0.15
865 98 0.10
866 46 0.05
867 118 0.12
868 47 0.05
869 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (862 bp):
AAGAACCAAGAGACAAACAATTCTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTTATTA
CAAAATGACAAACTATTTAGATCAAATGATGCGATTTCCGAGCTGGATTGTTCGAAAAATTGCAC
GAAGGAATGGATCGTCTTGAATACTTTAAGGAATTGAAGTTATAAAAGAACTCGTAAAAGTTTGA
CAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTT
AAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAAGCAATTTCCTGAGCAT
GGAATGTTCAAAAAATTGCTCAAAAAAATAGATCATCTTGAATACTTAACGCAACAAAAGTTATA
AAAGAACTCATAAAAGTTTGACAAGTGCGAAAGTTCATCCAAGAACCAAGAGAAAAACAATTCTC
ACGTAAATAAGTTTTTAATTCAAAGACCACAAAAACTTATTTACAAAATGACAAACTATTTAGAC
AAAATGATGCGATTTCCCAAGCATGAATGTTCAGAAAATTGCACGAAGGAATGGATCAACGTGAA
CACGTTAAGGAAACAAAGCTATAAAAGAACTAATAAAAGTTTGACAAGTTCGAAAGTTCATCCAA
GAACCAAGAGAGAAAAATTCTCACGTAAATAAGATTTTAATTCAAAGACCAAAACTTCTTTACAA
ATTGACAAACTGTTTAAACCAAATGATGAATTTCCCAAGCATGGAATGTTCGAAAAATTACTCGA
AGAAATAGATCATCTTGAATACTTTAAACAAGCGAAGTTATAAATAAACTCGTAAAAGTTTAACA
AGTGCGGAAGTTCGTCC
Found at i:73686 original size:20 final size:20
Alignment explanation
Indices: 73661--73707 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
73651 ATTATTTTTT
*
73661 TATAAAATTTAATTTAAATA
1 TATAAAATATAATTTAAATA
* *
73681 TATAAACTATATTTTAAATA
1 TATAAAATATAATTTAAATA
73701 T-TAAAAT
1 TATAAAAT
73708 GTAACCAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAAATATAATTTAAATA
Found at i:74991 original size:30 final size:30
Alignment explanation
Indices: 74909--75019 Score: 84
Period size: 30 Copynumber: 3.7 Consensus size: 30
74899 ATGGGTTATA
* *
74909 TCTTGACT-AGCTACTTCTTGATCGG-ATACT
1 TCTTGA-TGAGCTACTTCATGATGGGAAT-CT
* * * * *
74939 TCTCGATAAGCAACATCGTGATGGGAATCT
1 TCTTGATGAGCTACTTCATGATGGGAATCT
*
74969 TCTTGATGAGCTACTTCATGATGGGAGA-CC
1 TCTTGATGAGCTACTTCATGATGGGA-ATCT
* *
74999 TCCTGAGGAGCTACTTCATGA
1 TCTTGATGAGCTACTTCATGA
75020 GTTTGTTCCT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
29 1 0.02
30 61 0.94
31 3 0.05
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (30 bp):
TCTTGATGAGCTACTTCATGATGGGAATCT
Found at i:81995 original size:28 final size:29
Alignment explanation
Indices: 81963--82021 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
81953 AATTAAAAAA
*
81963 ATTATTTAAAA-TATAA-AATTTATTATTT
1 ATTATTTAAAATTATAAGAATATA-TATTT
81991 ATTATTTAAAATTATAAGAATATATATTT
1 ATTATTTAAAATTATAAGAATATATATTT
82020 AT
1 AT
82022 AATCATGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 11 0.39
29 12 0.43
30 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
ATTATTTAAAATTATAAGAATATATATTT
Found at i:82969 original size:40 final size:40
Alignment explanation
Indices: 82924--83004 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
82914 TCAAAAATAT
*
82924 TTTTTTAACTCAAAAGCACTTTTAAATAGTATTACTAAAC
1 TTTTTTAACTCAAAAGCACTTTTAAATAATATTACTAAAC
*
82964 TTTTTTAACTCAAAAGCATTTTTAAATAATATTACTAAAC
1 TTTTTTAACTCAAAAGCACTTTTAAATAATATTACTAAAC
83004 T
1 T
83005 AACCCTAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.42
Consensus pattern (40 bp):
TTTTTTAACTCAAAAGCACTTTTAAATAATATTACTAAAC
Found at i:88225 original size:19 final size:19
Alignment explanation
Indices: 88201--88246 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
88191 AAAGCAGCAG
88201 AGGCATTAGTTAACCCAAA
1 AGGCATTAGTTAACCCAAA
88220 AGGCATTAGTTAACCCAAA
1 AGGCATTAGTTAACCCAAA
*
88239 GGGCATTA
1 AGGCATTA
88247 CCAAGAACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (19 bp):
AGGCATTAGTTAACCCAAA
Found at i:91043 original size:22 final size:24
Alignment explanation
Indices: 91000--91045 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
90990 CAAAGTATAT
91000 TAATAATCCAAAATCAAAATAATAA
1 TAATAAT-CAAAATCAAAATAATAA
*
91025 TAATAAT-AAAAT-AATATAATA
1 TAATAATCAAAATCAAAATAATA
91046 TAAATTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
25 7 0.35
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (24 bp):
TAATAATCAAAATCAAAATAATAA
Found at i:92106 original size:7 final size:7
Alignment explanation
Indices: 92094--92175 Score: 64
Period size: 7 Copynumber: 12.0 Consensus size: 7
92084 TCGAAAAAAA
92094 GTCAAAG
1 GTCAAAG
92101 GTCAAA-
1 GTCAAAG
*
92107 GTCAACG
1 GTCAAAG
*
92114 ATCAAA-
1 GTCAAAG
*
92120 GTTAAAG
1 GTCAAAG
92127 GTCAAAG
1 GTCAAAG
*
92134 GTCAACG
1 GTCAAAG
92141 GTCAAAG
1 GTCAAAG
*
92148 TTCAATA-
1 GTCAA-AG
92155 GTCAACA-
1 GTCAA-AG
*
92162 GTCAACG
1 GTCAAAG
92169 GTCAAAG
1 GTCAAAG
92176 ATTAACTATC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
6 9 0.16
7 48 0.83
8 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (7 bp):
GTCAAAG
Found at i:92120 original size:20 final size:20
Alignment explanation
Indices: 92091--92148 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
92081 TTTTCGAAAA
92091 AAAG-TCAAAGGTCAAAGTC
1 AAAGATCAAAGGTCAAAGTC
* *
92110 AACGATCAAA-GTTAAAGGTC
1 AAAGATCAAAGGTCAAA-GTC
* *
92130 AAAGGTCAACGGTCAAAGT
1 AAAGATCAAAGGTCAAAGT
92149 TCAATAGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 8 0.27
20 17 0.57
21 5 0.17
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAGATCAAAGGTCAAAGTC
Found at i:92145 original size:14 final size:13
Alignment explanation
Indices: 92091--92175 Score: 89
Period size: 14 Copynumber: 6.3 Consensus size: 13
92081 TTTTCGAAAA
*
92091 AAAGTCAAAGGTC
1 AAAGTCAACGGTC
*
92104 AAAGTCAACGATC
1 AAAGTCAACGGTC
* *
92117 AAAGTTAAAGGTC
1 AAAGTCAACGGTC
92130 AAAGGTCAACGGTC
1 AAA-GTCAACGGTC
**
92144 AAAGTTCAATAGTC
1 AAAG-TCAACGGTC
92158 AACAGTCAACGGTC
1 AA-AGTCAACGGTC
92172 AAAG
1 AAAG
92176 ATTAACTATC
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
13 27 0.47
14 29 0.50
15 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:93554 original size:58 final size:58
Alignment explanation
Indices: 93468--93589 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 58
93458 GAAAGGAGTT
* *
93468 GTTTATGAGTGCTATTTAGGAATAAAATTATATTTGGATTCAAAAATATTTGGGTTTA
1 GTTTATGAGTGCTATTTAAGAATAAAATTATATTTGGATTCAAAAATATTTGGATTTA
* * * *
93526 GTTTATGAGTG-TTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGATTTA
1 GTTTATGAGTGCTATTT-AAGAATAAAATTATATTTGGATTCAAAAATATTTGGATTTA
93584 GTTTAT
1 GTTTAT
93590 TGATGAGTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 4 0.07
58 53 0.93
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (58 bp):
GTTTATGAGTGCTATTTAAGAATAAAATTATATTTGGATTCAAAAATATTTGGATTTA
Found at i:93736 original size:9 final size:9
Alignment explanation
Indices: 93722--93748 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
93712 AAATAATATA
93722 GTTTATTCG
1 GTTTATTCG
93731 GTTTATTCG
1 GTTTATTCG
93740 GTTTATTCG
1 GTTTATTCG
93749 AATAATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (9 bp):
GTTTATTCG
Found at i:94528 original size:25 final size:23
Alignment explanation
Indices: 94500--94545 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
94490 TAAATAGTTT
94500 TAATAAAATAAAATTTAAAAATATA
1 TAATAAAATAAAA--TAAAAATATA
* *
94525 TAATATAATTAAATAAAAATA
1 TAATAAAATAAAATAAAAATA
94546 ATTTTTGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
25 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAATAAAATAAAATAAAAATATA
Found at i:96866 original size:17 final size:16
Alignment explanation
Indices: 96841--96888 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
96831 ATATTAAATA
96841 TTTTTATATTATTTAT
1 TTTTTATATTATTTAT
* *
96857 TTTTTAATATTCTTAAT
1 TTTTT-ATATTATTTAT
96874 TTTTTATAATTATTT
1 TTTTTAT-ATTATTT
96889 TTTAATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTATATTATTTAT
Found at i:96867 original size:14 final size:14
Alignment explanation
Indices: 96839--96894 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
96829 TCATATTAAA
*
96839 TATTTTTATATTATT
1 TATTTTT-TAATATT
96854 TATTTTTTAATATTCT
1 TATTTTTTAATA-T-T
*
96870 TAATTTTTT-ATAAT
1 T-ATTTTTTAATATT
96884 TATTTTTTAAT
1 TATTTTTTAAT
96895 TTGTAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 7 0.20
14 8 0.23
15 8 0.23
16 5 0.14
17 7 0.20
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTTTAATATT
Found at i:100527 original size:13 final size:14
Alignment explanation
Indices: 100504--100536 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
100494 TATAGAGATC
100504 AATATATATGTAAA
1 AATATATATGTAAA
*
100518 AATA-ATATGTATA
1 AATATATATGTAAA
100531 AATATA
1 AATATA
100537 AAATAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
AATATATATGTAAA
Found at i:100607 original size:16 final size:17
Alignment explanation
Indices: 100587--100636 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
100577 GACATAAGAT
100587 TGTATATATATAAAATA
1 TGTATATATATAAAATA
* *
100604 -GTATATATAAAAAAAA
1 TGTATATATATAAAATA
*
100620 TGTATAAAATATAAAAT
1 TGTAT-ATATATAAAAT
100637 TCAAAATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 14 0.54
17 4 0.15
18 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
TGTATATATATAAAATA
Found at i:100612 original size:18 final size:17
Alignment explanation
Indices: 100589--100636 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
100579 CATAAGATTG
100589 TATATATATAAAATAGTA
1 TATATATATAAAAT-GTA
* *
100607 TATATAAAAAAAATGTA
1 TATATATATAAAATGTA
*
100624 TA-AAATATAAAAT
1 TATATATATAAAAT
100637 TCAAAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 8 0.32
17 5 0.20
18 12 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
TATATATATAAAATGTA
Found at i:108933 original size:12 final size:12
Alignment explanation
Indices: 108916--108945 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
108906 ATTATGATTA
108916 TTTAAATTTATT
1 TTTAAATTTATT
108928 TTTAAATTTATT
1 TTTAAATTTATT
*
108940 TGTAAA
1 TTTAAA
108946 AAGATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:108973 original size:16 final size:16
Alignment explanation
Indices: 108942--108991 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
108932 AATTTATTTG
*
108942 TAAAAAGATTTAAAATA
1 TAAAAATATTT-AAATA
108959 TAAAAATATTTAAATA
1 TAAAAATATTTAAATA
* *
108975 -ATAATTATTT-AATA
1 TAAAAATATTTAAATA
108989 TAA
1 TAA
108992 TTATAAAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 9 0.32
16 5 0.18
17 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAAAATATTTAAATA
Found at i:108992 original size:16 final size:16
Alignment explanation
Indices: 108955--108992 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
108945 AAAGATTTAA
108955 AATATAA-AAATATTT
1 AATATAATAAATATTT
*
108970 AA-ATAATAATTATTT
1 AATATAATAAATATTT
108985 AATATAAT
1 AATATAAT
108993 TATAAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 4 0.20
15 11 0.55
16 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAATAAATATTT
Found at i:112943 original size:20 final size:20
Alignment explanation
Indices: 112915--112996 Score: 112
Period size: 20 Copynumber: 4.2 Consensus size: 20
112905 ACGTAATGTA
*
112915 ACAGAGGCACCGAAGTGCAT
1 ACAGGGGCACCGAAGTGCAT
*
112935 ACAGGGGCACC-TAGTGCAT
1 ACAGGGGCACCGAAGTGCAT
* *
112954 ACAAGGGCATCGAAGTGCAT
1 ACAGGGGCACCGAAGTGCAT
*
112974 ACAGGGCCACCGAAGTGCAT
1 ACAGGGGCACCGAAGTGCAT
112994 ACA
1 ACA
112997 ATGTTATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.30
20 37 0.70
ACGTcount: A:0.33, C:0.26, G:0.29, T:0.12
Consensus pattern (20 bp):
ACAGGGGCACCGAAGTGCAT
Found at i:112979 original size:39 final size:40
Alignment explanation
Indices: 112920--112997 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
112910 ATGTAACAGA
* *
112920 GGCACCGAAGTGCATACAGGGGCACC-TAGTGCATACAAG
1 GGCACCGAAGTGCATACAGGGCCACCGAAGTGCATACAAG
*
112959 GGCATCGAAGTGCATACAGGGCCACCGAAGTGCATACAA
1 GGCACCGAAGTGCATACAGGGCCACCGAAGTGCATACAA
112998 TGTTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 24 0.69
40 11 0.31
ACGTcount: A:0.32, C:0.26, G:0.29, T:0.13
Consensus pattern (40 bp):
GGCACCGAAGTGCATACAGGGCCACCGAAGTGCATACAAG
Found at i:114915 original size:215 final size:212
Alignment explanation
Indices: 114547--114975 Score: 741
Period size: 215 Copynumber: 2.0 Consensus size: 212
114537 ACTAAGCTTC
*
114547 CCTTTCCTATCGAAATGCAACACTTTTTTCCAAGGAGAGACTTTTAAAAACACTTTCTCTCTAAC
1 CCTTTCCTATCGAAATGCAACACTTTTTTCCAAGGAGAGACTTTTAAAAACACTTTCTCTCCAAC
*
114612 AGAAAATTCAATATCTTTTCGCTTTAAATTTGCGTATGACTTCTGACGATCTGATGCTGCTTTTA
66 AGAAAATTCAATATCTTTTCGCTTTAAATTTGCGTATGACTTCTGACGATCGGATGCTGCTTTTA
**
114677 AATTATCTTTTATAATCTTAACTTTTTCCACTGTTTCACGAACTAAATCAACTCCGGTTAGCTTT
131 AATTATCTTGAATAATCTTAACTTTTTCCACTGTTTCACGAACTAAATCAACTCCGGTTAGCTTT
114742 CTTTCACTCAACTCTGA
196 CTTTCACTCAACTCTGA
*
114759 CCTTTCCTATCGAAATGCAACACTTTTTTTTTCTAAGGAGAGACTTTTAAAAACACTTTCTCTCC
1 CCTTTCCTATCGAAATGCAACAC---TTTTTTCCAAGGAGAGACTTTTAAAAACACTTTCTCTCC
*
114824 AATAGAAAATTCAATATCTTTTCGCTTTAAATTTGCGTATGACTTCTGACGATCGGATGCTGCTT
63 AACAGAAAATTCAATATCTTTTCGCTTTAAATTTGCGTATGACTTCTGACGATCGGATGCTGCTT
* * *
114889 TTAAATTATCTTGAATAATCTTAACTTTTTCCTCTGTTTCATGAACTAAATCAACTCGGGTTAGC
128 TTAAATTATCTTGAATAATCTTAACTTTTTCCACTGTTTCACGAACTAAATCAACTCCGGTTAGC
*
114954 TTTCTTTCACTTAACTCTGA
193 TTTCTTTCACTCAACTCTGA
114974 CC
1 CC
114976 AACACAACGA
Statistics
Matches: 204, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
212 23 0.11
215 181 0.89
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.40
Consensus pattern (212 bp):
CCTTTCCTATCGAAATGCAACACTTTTTTCCAAGGAGAGACTTTTAAAAACACTTTCTCTCCAAC
AGAAAATTCAATATCTTTTCGCTTTAAATTTGCGTATGACTTCTGACGATCGGATGCTGCTTTTA
AATTATCTTGAATAATCTTAACTTTTTCCACTGTTTCACGAACTAAATCAACTCCGGTTAGCTTT
CTTTCACTCAACTCTGA
Found at i:118681 original size:22 final size:22
Alignment explanation
Indices: 118663--118706 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
118653 TAAGATTTAG
*
118663 GTAGAAATCTTATGTGATTGTA
1 GTAGAAATCTTAAGTGATTGTA
118685 GTAGAAATCTTAAGTGATTGTA
1 GTAGAAATCTTAAGTGATTGTA
118707 AGGTTAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (22 bp):
GTAGAAATCTTAAGTGATTGTA
Found at i:131120 original size:17 final size:18
Alignment explanation
Indices: 131098--131137 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
131088 ATAGTTTTCA
*
131098 TGCATTTT-TATTGTCAT
1 TGCATTTTATATTGTCAC
*
131115 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
131133 TGCAT
1 TGCAT
131138 CCCTTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:131965 original size:15 final size:15
Alignment explanation
Indices: 131945--131974 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
131935 AATGATTGCG
*
131945 GTGACATTTTTAATT
1 GTGACATTGTTAATT
131960 GTGACATTGTTAATT
1 GTGACATTGTTAATT
131975 TTTGTTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (15 bp):
GTGACATTGTTAATT
Found at i:133305 original size:13 final size:14
Alignment explanation
Indices: 133276--133305 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
133266 TTCAGTACAT
133276 TGACATTTAACCTC
1 TGACATTTAACCTC
133290 TGACATTTAA-CTC
1 TGACATTTAACCTC
133303 TGA
1 TGA
133306 TTGCGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:134287 original size:3 final size:3
Alignment explanation
Indices: 134279--134307 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
134269 CGAGCGCCCA
134279 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
134308 AGCCAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Done.