Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012242.1 Kokia drynarioides strain JFW-HI SEQ_127243, 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: 105331
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:300 original size:6 final size:6
Alignment explanation
Indices: 289--318 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
279 CAAGTCCATG
289 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA
319 TGGGTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:8904 original size:21 final size:21
Alignment explanation
Indices: 8880--8931 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
8870 TTAGAAAATA
*
8880 CTACCGATACAAGTGA-GACTT
1 CTACCGATACAAGTCATG-CTT
* * *
8901 CTACCAAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
8922 CTACCGATAC
1 CTACCGATAC
8932 TAAAAACTCC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:9670 original size:24 final size:24
Alignment explanation
Indices: 9639--9689 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
9629 TTAGAAAACA
**
9639 TTAGCTCTCACGAGCCCAGGATGG
1 TTAGCTCTCACGAGCCCAAAATGG
* *
9663 TTAGCTCTTATGAGCCCAAAATGG
1 TTAGCTCTCACGAGCCCAAAATGG
9687 TTA
1 TTA
9690 ACCAGTATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
TTAGCTCTCACGAGCCCAAAATGG
Found at i:13199 original size:34 final size:34
Alignment explanation
Indices: 13156--13222 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
13146 ATGAATGTAT
13156 ATATGCTTTGTGTTGTATTAGGTGCAATGCATTA
1 ATATGCTTTGTGTTGTATTAGGTGCAATGCATTA
13190 ATATGCTTTGTGTTGTATTAGGTGCAATGCATT
1 ATATGCTTTGTGTTGTATTAGGTGCAATGCATT
13223 GGTGAGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (34 bp):
ATATGCTTTGTGTTGTATTAGGTGCAATGCATTA
Found at i:15391 original size:26 final size:26
Alignment explanation
Indices: 15342--15392 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
15332 TTTATTGAAA
*
15342 TAATTAATAATATTAAACATTTAGAC
1 TAATTAATAATATTAAACAATTAGAC
*
15368 TAATTAATGATATTATAA-AATTAGA
1 TAATTAATAATATTA-AACAATTAGA
15393 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (26 bp):
TAATTAATAATATTAAACAATTAGAC
Found at i:15398 original size:26 final size:26
Alignment explanation
Indices: 15338--15400 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
15328 CAAATTTATT
*
15338 GAAATAATTAATAATATTAAACATTTA
1 GAAA-AATTAATAATATTAAACAATTA
** *
15365 GACTAATTAATGATATTATAA-AATTA
1 GAAAAATTAATAATATTA-AACAATTA
15391 GAAAAATTAA
1 GAAAAATTAA
15401 ATTATGTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (26 bp):
GAAAAATTAATAATATTAAACAATTA
Found at i:17205 original size:37 final size:37
Alignment explanation
Indices: 17167--17246 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
17157 CAACAAAATT
* * *
17167 AAAAAATATATAATATATAAATACACTTAAAA-ACATTA
1 AAAAAATAT-TAA-AAATAAACAAACTTAAAATACATTA
*
17205 AAACAAATATTAAAAATAAACAAATTTAAAATACATTA
1 AAA-AAATATTAAAAATAAACAAACTTAAAATACATTA
17243 AAAA
1 AAAA
17247 TTATTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
37 15 0.42
38 15 0.42
39 6 0.17
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.26
Consensus pattern (37 bp):
AAAAAATATTAAAAATAAACAAACTTAAAATACATTA
Found at i:17465 original size:12 final size:12
Alignment explanation
Indices: 17427--17466 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
17417 AACAACAACA
*
17427 AAAAATAACAGC
1 AAAAATAACAGT
*
17439 AAAAATAACAAT
1 AAAAATAACAGT
17451 AAAAATAACAGT
1 AAAAATAACAGT
17463 AAAA
1 AAAA
17467 GCAACACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.72, C:0.10, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAAATAACAGT
Found at i:17478 original size:24 final size:24
Alignment explanation
Indices: 17373--17478 Score: 79
Period size: 24 Copynumber: 4.4 Consensus size: 24
17363 ATAACATCTA
* * *
17373 AACAACAAAAACAACAACCAAAAC
1 AACAACAAAAATAACAGCAAAAAC
** * **
17397 AGTAGCAAAAATATTAGC-AAAAC
1 AACAACAAAAATAACAGCAAAAAC
*
17420 AACAACAAAAAATAACAGCAAAAAT
1 AACAAC-AAAAATAACAGCAAAAAC
* * *
17445 AACAATAAAAATAACAGTAAAAGC
1 AACAACAAAAATAACAGCAAAAAC
*
17469 AACACCAAAA
1 AACAACAAAA
17479 TAGTAAAAAA
Statistics
Matches: 61, Mismatches: 19, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
23 8 0.13
24 44 0.72
25 9 0.15
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (24 bp):
AACAACAAAAATAACAGCAAAAAC
Found at i:17495 original size:21 final size:21
Alignment explanation
Indices: 17471--17520 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
17461 GTAAAAGCAA
17471 CACCAAAATAGTAAAAAATAG
1 CACCAAAATAGTAAAAAATAG
17492 CACCAAAATAGTAAAAAATAG
1 CACCAAAATAGTAAAAAATAG
17513 CACCAAAA
1 CACCAAAA
17521 CACAAGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.12
Consensus pattern (21 bp):
CACCAAAATAGTAAAAAATAG
Found at i:17501 original size:11 final size:11
Alignment explanation
Indices: 17471--17520 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
17461 GTAAAAGCAA
17471 CACCAAAATAG
1 CACCAAAATAG
* *
17482 TA-AAAAATAG
1 CACCAAAATAG
17492 CACCAAAATAG
1 CACCAAAATAG
* *
17503 TA-AAAAATAG
1 CACCAAAATAG
17513 CACCAAAA
1 CACCAAAA
17521 CACAAGAAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
10 16 0.55
11 13 0.45
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.12
Consensus pattern (11 bp):
CACCAAAATAG
Found at i:18010 original size:29 final size:28
Alignment explanation
Indices: 17914--18102 Score: 170
Period size: 29 Copynumber: 6.8 Consensus size: 28
17904 TATACTTTTG
*
17914 GTTTTCCATATTTTACAATTTTGCCACT
1 GTTTTCCATATTTTACAGTTTTGCCACT
* **
17942 G--TTCTATATTTTACAGTTTTATCACT
1 GTTTTCCATATTTTACAGTTTTGCCACT
*
17968 GTTTTCCATATTTTACAGTTTTGCCATT
1 GTTTTCCATATTTTACAGTTTTGCCACT
**
17996 GGTTTTCCATATTTTGTAGTTTTGCCACT
1 -GTTTTCCATATTTTACAGTTTTGCCACT
* * * *
18025 AGTTTTCTAGATTTAATAGTTTTGCCA-T
1 -GTTTTCCATATTTTACAGTTTTGCCACT
* * * *
18053 -TTTTGCATATTTTATAGTTTTTCTACT
1 GTTTTCCATATTTTACAGTTTTGCCACT
* *
18080 GGTTTTCCAAATTTTACAATTTT
1 -GTTTTCCATATTTTACAGTTTT
18103 TGTAACGCCC
Statistics
Matches: 129, Mismatches: 26, Indels: 11
0.78 0.16 0.07
Matches are distributed among these distances:
26 41 0.32
27 1 0.01
28 23 0.18
29 64 0.50
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (28 bp):
GTTTTCCATATTTTACAGTTTTGCCACT
Found at i:18690 original size:20 final size:20
Alignment explanation
Indices: 18665--18704 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18655 CTAGTTAAGT
18665 GTTGAAATGGAATTAGTGGA
1 GTTGAAATGGAATTAGTGGA
18685 GTTGAAATGGAATTAGTGGA
1 GTTGAAATGGAATTAGTGGA
18705 ATGACTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (20 bp):
GTTGAAATGGAATTAGTGGA
Found at i:19210 original size:63 final size:64
Alignment explanation
Indices: 19110--19232 Score: 194
Period size: 63 Copynumber: 1.9 Consensus size: 64
19100 ATGCTATACC
*
19110 ATGGAATACAAAAACAGTGAGTTACACGGCCTGGACACACAGGCGTGGGCTAGACCGTGTAACG
1 ATGGAATACAAAAACAGTGAGTTACACGACCTGGACACACAGGCGTGGGCTAGACCGTGTAACG
* * * *
19174 ATGGAAT-CGAAAACAGTGAGTTACACGATCTGGACACACGGGCGTGGGCTAGATCGTGT
1 ATGGAATACAAAAACAGTGAGTTACACGACCTGGACACACAGGCGTGGGCTAGACCGTGT
19233 GACGCCCACG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
63 47 0.87
64 7 0.13
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (64 bp):
ATGGAATACAAAAACAGTGAGTTACACGACCTGGACACACAGGCGTGGGCTAGACCGTGTAACG
Found at i:19402 original size:39 final size:39
Alignment explanation
Indices: 19369--19465 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 39
19359 CAATACTGAG
19369 CTGACGGTAACAATGTAAATACCATAAGGCAATACAAAA
1 CTGACGGTAACAATGTAAATACCATAAGGCAATACAAAA
* * * ** * *
19408 TTGACGGTTACACTGTAAATACCATACTGAAATACTAAA
1 CTGACGGTAACAATGTAAATACCATAAGGCAATACAAAA
* * *
19447 CTGATGGTGACACTGTAAA
1 CTGACGGTAACAATGTAAA
19466 CACCGTAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (39 bp):
CTGACGGTAACAATGTAAATACCATAAGGCAATACAAAA
Found at i:20453 original size:36 final size:36
Alignment explanation
Indices: 20413--20545 Score: 212
Period size: 36 Copynumber: 3.7 Consensus size: 36
20403 TACGATATGC
* *
20413 ATGATATGGTAAATTTTATTTGATTGATTATGCTAT
1 ATGATATGGTAAATATTATTTGATTAATTATGCTAT
20449 ATGATATGGTAAATATTATTTGATTAATTATGCTAT
1 ATGATATGGTAAATATTATTTGATTAATTATGCTAT
20485 ATGATATGGTAAATATTATTTGATTAATTATGCTAT
1 ATGATATGGTAAATATTATTTGATTAATTATGCTAT
* * * *
20521 ACGGTACGGTAAATGTTATTTGATT
1 ATGATATGGTAAATATTATTTGATT
20546 GACTGTGCTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.47
Consensus pattern (36 bp):
ATGATATGGTAAATATTATTTGATTAATTATGCTAT
Found at i:20555 original size:36 final size:36
Alignment explanation
Indices: 20415--20654 Score: 201
Period size: 36 Copynumber: 6.2 Consensus size: 36
20405 CGATATGCAT
* * *
20415 GATATGGTAAATTTTATTTGATTGATTATGCTATAT
1 GATATGGTAAATATTATTTGATTAATTATGCTATAC
*
20451 GATATGGTAAATATTATTTGATTAATTATGCTATAT
1 GATATGGTAAATATTATTTGATTAATTATGCTATAC
20487 GATATGGTAAATATTATTTGATTAATTATGCTATAC
1 GATATGGTAAATATTATTTGATTAATTATGCTATAC
* * * * * *
20523 GGTACGGTAAATGTTATTTGATTGACTGTGCTATAC
1 GATATGGTAAATATTATTTGATTAATTATGCTATAC
* *
20559 AGTATGCATGATATGATAAATATTATTTGATTAAGTATTCTATAC
1 -G-AT--ATG----G-TAAATATTATTTGATTAATTATGCTATAC
*
20604 GATATGCATGACATGGTAAATATTATTTGATTGATTATGCTATAC
1 -----G-AT---ATGGTAAATATTATTTGATTAATTATGCTATAC
20649 GATATG
1 GATATG
20655 TATGATATGG
Statistics
Matches: 168, Mismatches: 22, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
36 102 0.61
37 1 0.01
38 1 0.01
39 2 0.01
40 3 0.02
44 1 0.01
45 50 0.30
46 1 0.01
49 3 0.02
50 4 0.02
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.43
Consensus pattern (36 bp):
GATATGGTAAATATTATTTGATTAATTATGCTATAC
Found at i:20585 original size:45 final size:45
Alignment explanation
Indices: 20528--20692 Score: 206
Period size: 45 Copynumber: 3.7 Consensus size: 45
20518 TATACGGTAC
* *
20528 GGTAAATGTTATTTGATTGACTGTGCTATAC-AGTATGCATGATAT
1 GGTAAATATTATTTGATTGACTATGCTATACGA-TATGCATGATAT
* * * * *
20573 GATAAATATTATTTGATTAAGTATTCTATACGATATGCATGACAT
1 GGTAAATATTATTTGATTGACTATGCTATACGATATGCATGATAT
* *
20618 GGTAAATATTATTTGATTGATTATGCTATACGATATGTATGATAT
1 GGTAAATATTATTTGATTGACTATGCTATACGATATGCATGATAT
* * *
20663 GGTAAATATTATTTAATTGATTATACTATA
1 GGTAAATATTATTTGATTGACTATGCTATA
20693 TGACACATAT
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 103 0.99
46 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (45 bp):
GGTAAATATTATTTGATTGACTATGCTATACGATATGCATGATAT
Found at i:20692 original size:90 final size:90
Alignment explanation
Indices: 20528--20692 Score: 233
Period size: 90 Copynumber: 1.8 Consensus size: 90
20518 TATACGGTAC
* * *
20528 GGTAAATGTTATTTGATTGACTGTGCTATACAGTATGCATGATATGATAAATATTATTTGATTAA
1 GGTAAATATTATTTGATTGACTATGCTATACAGTATGCATGATATGATAAATATTATTTAATTAA
*
20593 GTATTCTATACGATATGCATGACAT
66 GTATACTATACGATATGCATGACAT
* * * *
20618 GGTAAATATTATTTGATTGATTATGCTATAC-GATATGTATGATATGGTAAATATTATTTAATTG
1 GGTAAATATTATTTGATTGACTATGCTATACAG-TATGCATGATATGATAAATATTATTTAATTA
*
20682 ATTATACTATA
65 AGTATACTATA
20693 TGACACATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
89 1 0.02
90 64 0.98
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (90 bp):
GGTAAATATTATTTGATTGACTATGCTATACAGTATGCATGATATGATAAATATTATTTAATTAA
GTATACTATACGATATGCATGACAT
Found at i:20930 original size:36 final size:36
Alignment explanation
Indices: 20885--20957 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
20875 ATATACGTGG
* * * * *
20885 TATGATAAATGTTATTTGATTGATTATGCTATATGA
1 TATGATAAATATTATCTAATTAATTAAGCTATATGA
*
20921 TATGGTAAATATTATCTAATTAATTAAGCTATATGA
1 TATGATAAATATTATCTAATTAATTAAGCTATATGA
20957 T
1 T
20958 TTGCTTGATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (36 bp):
TATGATAAATATTATCTAATTAATTAAGCTATATGA
Found at i:23155 original size:16 final size:16
Alignment explanation
Indices: 23130--23171 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
23120 AAGTTAAATT
*
23130 TTTTATTTTTCTTAAA
1 TTTTAATTTTCTTAAA
*
23146 TTTTAATTTT-TTTAA
1 TTTTAATTTTCTTAAA
23161 TTTT-ATTTTCT
1 TTTTAATTTTCT
23172 ATTTATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 9 0.39
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATTTTCTTAAA
Found at i:24096 original size:23 final size:23
Alignment explanation
Indices: 24070--24124 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
24060 CAATGGCATT
*
24070 TATTGTAATTAGTGATTTAATAA
1 TATTTTAATTAGTGATTTAATAA
*
24093 TATTTTAATTAGTGATTTAATAT
1 TATTTTAATTAGTGATTTAATAA
24116 TATTTTAAT
1 TATTTTAAT
24125 ATTTGAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (23 bp):
TATTTTAATTAGTGATTTAATAA
Found at i:31110 original size:29 final size:30
Alignment explanation
Indices: 31068--31149 Score: 112
Period size: 29 Copynumber: 2.7 Consensus size: 30
31058 TAATTGAATC
*
31068 AAATCAGAATTTCATATATAATATTACACA-
1 AAATCA-AAATTCATATATAATATTACACAT
*
31098 AAATCAAAATTCATATATAACATTACACATT
1 AAATCAAAATTCATATATAATATTACACA-T
*
31129 AAATCATAATTCATATATAAT
1 AAATCAAAATTCATATATAAT
31150 TTTGAGATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 21 0.46
30 6 0.13
31 19 0.41
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTCATATATAATATTACACAT
Found at i:32025 original size:24 final size:24
Alignment explanation
Indices: 31991--32038 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31981 ATTGATGTTC
*
31991 AACCTTTCATCTCCTTTAACCTTT
1 AACCTTCCATCTCCTTTAACCTTT
**
32015 AACCTTCCATCTTTTTTAACCTTT
1 AACCTTCCATCTCCTTTAACCTTT
32039 CATATTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (24 bp):
AACCTTCCATCTCCTTTAACCTTT
Found at i:38209 original size:16 final size:17
Alignment explanation
Indices: 38168--38210 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
38158 AAGAAACGGC
*
38168 ATTTTAAAATATAAAAG
1 ATTTAAAAATATAAAAG
*
38185 TTTTAAAAAATATAAAA-
1 ATTT-AAAAATATAAAAG
38202 ATTTAAAAA
1 ATTTAAAAA
38211 AAATGTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
ATTTAAAAATATAAAAG
Found at i:38214 original size:19 final size:18
Alignment explanation
Indices: 38173--38212 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38163 ACGGCATTTT
* *
38173 AAAATATAAAAGTTTTAA
1 AAAATATAAAAATTTAAA
38191 AAAATATAAAAATTTAAA
1 AAAATATAAAAATTTAAA
38209 AAAA
1 AAAA
38213 ATGTAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATATAAAAATTTAAA
Found at i:41780 original size:21 final size:21
Alignment explanation
Indices: 41741--41780 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41731 TTTTTAGTAC
*
41741 CGGTAAAAGCATGATTTGTTT
1 CGGTAAAAGCATGACTTGTTT
* *
41762 CGGTAAAAGCTTTACTTGT
1 CGGTAAAAGCATGACTTGT
41781 ATCTGTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (21 bp):
CGGTAAAAGCATGACTTGTTT
Found at i:42921 original size:10 final size:10
Alignment explanation
Indices: 42906--42930 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42896 TTTTCAGCTT
42906 AAAAAATTTA
1 AAAAAATTTA
42916 AAAAAATTTA
1 AAAAAATTTA
42926 AAAAA
1 AAAAA
42931 TTAACTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:43855 original size:24 final size:24
Alignment explanation
Indices: 43820--43876 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
43810 AATCTTTCAG
*
43820 TTAAACTCTGTTTATTTATTTTAA
1 TTAAACTCTGTTTATTTATTTGAA
* * *
43844 TTAAACTTTGTTTATTTGTTTGAG
1 TTAAACTCTGTTTATTTATTTGAA
43868 TTAAACTCT
1 TTAAACTCT
43877 TATTAGTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTATTTGAA
Found at i:45861 original size:24 final size:24
Alignment explanation
Indices: 45810--45864 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
45800 TCTTTCAGTT
* * *
45810 AAACTTTGTTTATTTGTTTTAATT
1 AAACTCTGTTTATTTGTTTGAATC
*
45834 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTGAATC
45858 AAACTCT
1 AAACTCT
45865 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTGAATC
Found at i:49754 original size:29 final size:29
Alignment explanation
Indices: 49721--49776 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
49711 ATAATTGAAT
49721 CAAA-TAAAAATTTCATATATAAAATTATA
1 CAAATTAAAAA-TTCATATATAAAATTATA
*
49750 CAAATTCAAAATTCATATATAAAATTA
1 CAAATTAAAAATTCATATATAAAATTA
49777 CACATTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (29 bp):
CAAATTAAAAATTCATATATAAAATTATA
Found at i:49794 original size:31 final size:29
Alignment explanation
Indices: 49727--49802 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
49717 GAATCAAATA
* **
49727 AAAATTTCATATATAAAATTATACAAATTC
1 AAAA-TTCATATATAAAATTACACAAAACC
49757 AAAATTCATATATAAAATTACACATTAAACC
1 AAAATTCATATATAAAATTACACA--AAACC
*
49788 ATAATTCATATATAA
1 AAAATTCATATATAA
49803 TTTTGAGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.47
30 4 0.10
31 17 0.43
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAATTCATATATAAAATTACACAAAACC
Found at i:64215 original size:29 final size:27
Alignment explanation
Indices: 64169--64474 Score: 141
Period size: 29 Copynumber: 10.7 Consensus size: 27
64159 AAAGTTTTAG
* *
64169 GGGT-AAAATGTCATTTTGGGAAAGTTT
1 GGGTAAAAATGTGATTTTTGG-AAGTTT
*
64196 GGGTAAAAATGTGATTTTTGGAAGTTCCA
1 GGGTAAAAATGTGATTTTTGGAAGTT--T
* * * *
64225 AGGTCAAATTGTGATTTTTAGAAGTTT
1 GGGTAAAAATGTGATTTTTGGAAGTTT
* *
64252 AGGGGAAAAATGTGATTTTTGGAAGTTCGG
1 -GGGTAAAAATGTGATTTTTGGAAGTT--T
* * * *
64282 GGGCAAAAATG-AATATTTGATAAGTTT
1 GGGTAAAAATGTGATTTTTG-GAAGTTT
*
64309 AGAGGTAAAAATGTAATTTTTGAGAAGTTT
1 -G-GGTAAAAATGTGATTTTTG-GAAGTTT
* * * *
64339 GGGGTCAAAATGTGGTATTTGGAAGTTC
1 -GGGTAAAAATGTGATTTTTGGAAGTTT
** **
64367 GAGGGCAAAATGT-ATTTTTTTAAAAGTTT
1 G-GGTAAAAATGTGA--TTTTTGGAAGTTT
* *
64396 GAGGGTAAAAATGTAATTTTTGAGAAGTTCAA
1 --GGGTAAAAATGTGATTTTTG-GAAGTT--T
* * *
64428 GGGTCAAAATGTGATTTTAGGAAAGTTA
1 GGGTAAAAATGTGATTTTTGG-AAGTTT
* *
64456 GGTGTCAAAATGTAATTTT
1 GG-GTAAAAATGTGATTTT
64475 AAAAAAGTTT
Statistics
Matches: 215, Mismatches: 43, Indels: 40
0.72 0.14 0.13
Matches are distributed among these distances:
27 10 0.05
28 61 0.28
29 91 0.42
30 51 0.24
31 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (27 bp):
GGGTAAAAATGTGATTTTTGGAAGTTT
Found at i:64221 original size:57 final size:57
Alignment explanation
Indices: 64173--64337 Score: 156
Period size: 57 Copynumber: 2.9 Consensus size: 57
64163 TTTTAGGGGT
* *
64173 AAAATGTCATTTTGGGAAAGTTT-GGGTAAAAATGTGATTTTTGGAAGTTCCAAGGTC
1 AAAATGTCATTTTGAG-AAGTTTAGGGGAAAAATGTGATTTTTGGAAGTTCCAAGGTC
* * * ** *
64230 AAATTGTGATTTTTAGAAGTTTAGGGGAAAAATGTGATTTTTGGAAGTT-CGGGGGC
1 AAAATGTCATTTTGAGAAGTTTAGGGGAAAAATGTGATTTTTGGAAGTTCCAAGGTC
* * * *
64286 AAAAATG-AATATTTGATAAGTTTAGAGGTAAAAATGTAATTTTTGAGAAGTT
1 -AAAATGTCAT-TTTGAGAAGTTTAG-GGGAAAAATGTGATTTTTG-GAAGTT
64338 TGGGGTCAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
56 12 0.13
57 54 0.61
58 17 0.19
59 6 0.07
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
AAAATGTCATTTTGAGAAGTTTAGGGGAAAAATGTGATTTTTGGAAGTTCCAAGGTC
Found at i:64360 original size:87 final size:87
Alignment explanation
Indices: 64238--64484 Score: 258
Period size: 87 Copynumber: 2.8 Consensus size: 87
64228 TCAAATTGTG
* * *
64238 ATTTTT-AGAAGTTTAGGGG-AAAAATGTGATTTTTGGAAGTTCGGGGGCAAAAATG-AATATTT
1 ATTTTTGAGAAGTTT-GGGGTCAAAATGTGATATTTGGAAGTTCGAGGGC-AAAATGTAATATTT
*
64300 GATAAGTTT-AGAGGTAAAAATGTA
64 GAAAAGTTTGAG-GGTAAAAATGTA
* * * *
64324 ATTTTTGAGAAGTTTGGGGTCAAAATGTGGTATTTGGAAGTTCGAGGGCAAAATGTATTTTTTTA
1 ATTTTTGAGAAGTTTGGGGTCAAAATGTGATATTTGGAAGTTCGAGGGCAAAATGTAATATTTGA
64389 AAAGTTTGAGGGTAAAAATGTA
66 AAAGTTTGAGGGTAAAAATGTA
**
64411 ATTTTTGAGAAGTTCAAGGGTCAAAATGTGAT-TTTAGGAAAGTT--AGGTGTCAAAATGTAAT-
1 ATTTTTGAGAAGTT-TGGGGTCAAAATGTGATATTT-GG-AAGTTCGAGG-G-CAAAATGTAATA
*
64472 TTTAAAAAAGTTT
61 TTT-GAAAAGTTT
64485 ACGGGTCAAA
Statistics
Matches: 138, Mismatches: 13, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
86 16 0.12
87 77 0.56
88 22 0.16
89 23 0.17
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (87 bp):
ATTTTTGAGAAGTTTGGGGTCAAAATGTGATATTTGGAAGTTCGAGGGCAAAATGTAATATTTGA
AAAGTTTGAGGGTAAAAATGTA
Found at i:64495 original size:30 final size:29
Alignment explanation
Indices: 64287--64496 Score: 135
Period size: 30 Copynumber: 7.2 Consensus size: 29
64277 TTCGGGGGCA
* *
64287 AAAATG-AATATTT-GATAAGTTTAGAGGTA
1 AAAATGTAAT-TTTAGAAAAGTTTAG-GGTC
* * *
64316 AAAATGTAATTTTTGAGAAGTTTGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGTC
** * *
64345 AAAATGTGGTATTT-G-GAAGTTCGAGGG-C
1 AAAATGTAAT-TTTAGAAAAGTT-TAGGGTC
* ** *
64373 AAAATGTATTTTTTTAAAAGTTTGAGGGTA
1 AAAATGTAATTTTAGAAAAGTTT-AGGGTC
* * *
64403 AAAATGTAATTTTTGAGAAGTTCAAGGGTC
1 AAAATGTAATTTTAGAAAAGTT-TAGGGTC
* *
64433 AAAATGTGATTTTAGGAAAG-TTAGGTGTC
1 AAAATGTAATTTTAGAAAAGTTTAGG-GTC
*
64462 AAAATGTAATTTTAAAAAAGTTTACGGGTC
1 AAAATGTAATTTTAGAAAAGTTTA-GGGTC
64492 AAAAT
1 AAAAT
64497 ATGATTCCTG
Statistics
Matches: 143, Mismatches: 26, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
27 3 0.02
28 18 0.13
29 54 0.38
30 66 0.46
31 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGTC
Found at i:66040 original size:18 final size:19
Alignment explanation
Indices: 66005--66041 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
65995 TTGGGCCCAA
*
66005 TTGGGTTTGTATTTTGGAC
1 TTGGGATTGTATTTTGGAC
66024 TTGGGATTGTA-TTTGGAC
1 TTGGGATTGTATTTTGGAC
66042 ATTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.14, C:0.05, G:0.32, T:0.49
Consensus pattern (19 bp):
TTGGGATTGTATTTTGGAC
Found at i:66094 original size:34 final size:33
Alignment explanation
Indices: 66053--66136 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 33
66043 TTTAAAATTA
66053 AAATTTAAATTTAAAATAAATTCAAACTCAAAAT
1 AAATTTAAATTTAAAATAAATTCAAACT-AAAAT
* *
66087 AAGTTTAAATTTAAAATAAATTCAAACTTAAAT
1 AAATTTAAATTTAAAATAAATTCAAACTAAAAT
*
66120 AAATTAAAATTTAAAAT
1 AAATTTAAATTTAAAAT
66137 TTAAAACTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 19 0.41
34 27 0.59
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (33 bp):
AAATTTAAATTTAAAATAAATTCAAACTAAAAT
Found at i:66136 original size:17 final size:17
Alignment explanation
Indices: 66042--66136 Score: 102
Period size: 17 Copynumber: 5.5 Consensus size: 17
66032 GTATTTGGAC
*
66042 ATTTAAAATTAAAATTTAA
1 ATTTAAAA-T-AAATTCAA
66061 ATTTAAAATAAATTCAA
1 ATTTAAAATAAATTCAA
* * * *
66078 ACTCAAAATAAGTTTAA
1 ATTTAAAATAAATTCAA
66095 ATTTAAAATAAATTCAA
1 ATTTAAAATAAATTCAA
* *
66112 ACTT-AAATAAATTAAA
1 ATTTAAAATAAATTCAA
66128 ATTTAAAAT
1 ATTTAAAAT
66137 TTAAAACTGT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
16 14 0.22
17 40 0.63
18 1 0.02
19 8 0.13
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (17 bp):
ATTTAAAATAAATTCAA
Found at i:66610 original size:39 final size:39
Alignment explanation
Indices: 66565--67123 Score: 303
Period size: 39 Copynumber: 14.4 Consensus size: 39
66555 GACCCCATGA
*
66565 TCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
* ** * * *
66604 TCGGGGTAAGAGATCGATTGATGGTGATTTGTCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
* * * *** * * *
66643 TCGGGGTAAGAGATCGGACGGCT-ACAATCTGCTCTAAGC
1 TCGGGGTAAGAGATTGG-CTGATGGTGATCTGCCCCAGGC
* *
66682 TCGAGGTAAAAGATTGGCTGATGGTGATCTGCCCTC-GGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-CAGGC
* * * ** * * * *
66721 TCAGGGTAAAAGATAGAATTG-TTGTAATCTGCCCTAAGC
1 TCGGGGTAAGAGATTG-GCTGATGGTGATCTGCCCCAGGC
* * * *
66760 TCAGGGTAAGAGATTGGCTGATGGTGATCTACCCTAAGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
* * * ** * *
66799 ACGAGGTAAAAGATTGAATTGCT-GTAATCTGCCCCAGGC
1 TCGGGGTAAGAGATTG-GCTGATGGTGATCTGCCCCAGGC
** *
66838 TCGGGGTAAGAGATTTACTGATGGTGATCTGCCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
* * * * ** * * *
66877 TCGGGATAAAAAATCGAAT--TGCTACAATCTGCCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGGT--GATCTGCCCCAGGC
* * * * *
66916 TCGAGGTAAGAAATTGGTTGATGGAGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
* * * * *
66955 TCGGGGTAAAAGATCGGATGACT-GTTATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAGGC
* *
66994 TTGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
* * * **
67033 TCGAGGTAAAAGACT-G--GATGGCTGCAATCCACCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAGGC
** *
67072 TCGGGAAAAGAGATTGGCTGATGGTGATCTGCCCTAGG-
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
* *
67110 TTGGGGTAAAAGAT
1 TCGGGGTAAGAGAT
67124 CGGATGGCTT
Statistics
Matches: 385, Mismatches: 115, Indels: 41
0.71 0.21 0.08
Matches are distributed among these distances:
36 5 0.01
37 5 0.01
38 21 0.05
39 336 0.87
40 9 0.02
41 4 0.01
42 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
Found at i:66704 original size:78 final size:78
Alignment explanation
Indices: 66622--67138 Score: 468
Period size: 78 Copynumber: 6.6 Consensus size: 78
66612 AGAGATCGAT
* * * * * * *
66622 TGATGGTGATTTGTCCTAGGCTCGGGGTAAGAGATCGGACGGCTACAATCTGCTCTAAGCTCGAG
1 TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGAG
66687 GTAAAAGATTGGC
66 GTAAAAGATTGGC
* * * * * * * *
66700 TGATGGTGATCTGCCCTCGGCTCAGGGTAAAAGATAGAATTGTTGTAATCTGCCCTAAGCTC-AG
1 TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGA-
*
66764 GGTAAGAGATTGGC
65 GGTAAAAGATTGGC
* * * * * * * * * *
66778 TGATGGTGATCTACCCTAAGCACGAGGTAAAAGATTGAATTGCTGTAATCTGCCCCAGGCTCGGG
1 TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGAG
* **
66843 GTAAGAGATTTAC
66 GTAAAAGATTGGC
* * * * * * *
66856 TGATGGTGATCTGCCCTAGGCTCGGGATAAAAAATCGAATTGCTACAATCTGCCCTAGGCTCGAG
1 TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGAG
*
66921 GTAAGAA-ATTGGT
66 GTAA-AAGATTGGC
* * * * ** * *
66934 TGATGGAGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTGTTATCTGCCCCAAGCTTGGG
1 TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGAG
* *
66999 GTAAGAGATTAGC
66 GTAAAAGATTGGC
* * ** *
67012 TGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGA-CTGGATGGCTGCAATCCACCCCAGGCTCG-
1 TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATC-GGATGGCTGCAATCTGCCCCAAGCTCGA
*
67075 GGAAAAGAGATTGGC
65 GGTAAA-AGATTGGC
* *
67090 TGATGGTGATCTGCCCTAGG-TTGGGGTAAAAGATCGGATGGCTTCAATC
1 TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATC
67139 CATCCTTCTT
Statistics
Matches: 355, Mismatches: 77, Indels: 15
0.79 0.17 0.03
Matches are distributed among these distances:
77 31 0.09
78 323 0.91
79 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (78 bp):
TGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGAG
GTAAAAGATTGGC
Found at i:77708 original size:16 final size:17
Alignment explanation
Indices: 77687--77721 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
77677 ATCTATACTA
*
77687 ATAGTATCA-ACATAAT
1 ATAGTATCACACAAAAT
77703 ATAGTATCACACAAAAT
1 ATAGTATCACACAAAAT
77720 AT
1 AT
77722 TTGAGGATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (17 bp):
ATAGTATCACACAAAAT
Found at i:78807 original size:57 final size:59
Alignment explanation
Indices: 78719--79003 Score: 218
Period size: 57 Copynumber: 4.9 Consensus size: 59
78709 CATTTTTGGA
* *
78719 AAGTTCGA-GGTAAAAATATGATTTTTGGAAGTTTGAGGGTCAAAATGTGATTTCT-AG
1 AAGTTCGAGGGTCAAAATATGATTTTTGGAAGTTTGAGGGTCAAAATGTGATTTTTAAG
* * *
78776 AAGTTCGAGGGTCAAAATATGA-TTTTGGAAG-TTCAGGGGT-AAAATGTAATTTTTGAG
1 AAGTTCGAGGGTCAAAATATGATTTTTGGAAGTTTGA-GGGTCAAAATGTGATTTTTAAG
* * * * *
78833 AAGTTTG-GAGG-CAAAATGTGATTTTTTGAAGTTCGAGGG-CAAAAATGT-AATTTTAAG
1 AAGTTCGAG-GGTCAAAATATGATTTTTGGAAGTTTGAGGGTC-AAAATGTGATTTTTAAG
* * * *
78890 AAGTT-TAGGGGCAAAA-ATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGATTTTT-GG
1 AAGTTCGAGGGTCAAAATATG--ATTTTTG-GAAGTTTGAGGGTCAAAATGTGATTTTTAAG
** * * * ** *
78949 AAGTTTTAGGGTAAAAATGTAATTGTTAAGAAGTTTG-GGGTTAAAATGTGATTTT
1 AAGTTCGAGGGTCAAAATATGATT-TTTGGAAGTTTGAGGGTCAAAATGTGATTTT
79004 AGGAAAGTTT
Statistics
Matches: 186, Mismatches: 24, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
56 29 0.16
57 60 0.32
58 45 0.24
59 35 0.19
60 16 0.09
61 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (59 bp):
AAGTTCGAGGGTCAAAATATGATTTTTGGAAGTTTGAGGGTCAAAATGTGATTTTTAAG
Found at i:78945 original size:59 final size:59
Alignment explanation
Indices: 78653--79060 Score: 263
Period size: 59 Copynumber: 7.0 Consensus size: 59
78643 AAAAATGAAC
* * * * *
78653 TTTTAGAGAA-TTT-GGGGTAAAAATGTAA-TTTTGAAAAGTTTTAAGGGTAAAAATATCA
1 TTTTA-AGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAG-TTTGAGGGTTAAAATGTGA
** * * * * *
78711 TTTTTGGAAAG-TTCGAGGTAAAAATATGATTTTTG-GAAGTTTGAGGGTCAAAATGTGA
1 TTTTAAG-AAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
* * * * * * *
78769 TTTCT-AGAAG-TTCGAGGGTCAAAATATGA-TTTTG-GAAG-TTCAGGGGTAAAATGTAA
1 TTT-TAAGAAGTTTAG-GGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
* * * * * ** *
78825 TTTTTGAGAAGTTT-GGAGG-CAAAATGTGATTTTT-TGAAGTTCGAGGGCAAAAATGTAA
1 -TTTTAAGAAGTTTAGG-GGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
*
78883 TTTTAAGAAGTTTAGGGGCAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
1 TTTTAAGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
** * *
78942 TTTTTGGAAGTTTTA-GGGTAAAAATGTAATTGTTAAGAAGTTTG-GGGTTAAAATGTGA
1 TTTTAAGAAG-TTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
* * * * * * * *
79000 TTTTAGGAAAGTTTATGTGTTAAAATGTAATTTTGGAAAAGTTTG-GGGTCAAAATATGA
1 TTTTAAG-AAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
79059 TT
1 TT
79061 CCTAAAAAGT
Statistics
Matches: 287, Mismatches: 44, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
56 25 0.09
57 50 0.17
58 94 0.33
59 109 0.38
60 9 0.03
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (59 bp):
TTTTAAGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTGA
Found at i:78967 original size:29 final size:29
Alignment explanation
Indices: 78663--79060 Score: 264
Period size: 29 Copynumber: 13.7 Consensus size: 29
78653 TTTTAGAGAA
* *
78663 TTTG-GGGTAAAAATGT-AATTTTGAAAAG
1 TTTGAGGGTAAAAATGTGATTTTTG-GAAG
* * *
78691 TTTTAAGGGTAAAAATATCATTTTTGGAAAG
1 -TTTGAGGGTAAAAATGTGATTTTTGG-AAG
* *
78722 TTCGA-GGTAAAAATATGATTTTTGGAAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAG
* * *
78750 TTTGAGGGTCAAAATGTGATTTCTAGAAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAG
* * *
78779 TTCGAGGGTCAAAATATGA-TTTTGGAAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAG
* *
78807 -TTCAGGGGT-AAAATGTAATTTTTGAGAAG
1 TTTGA-GGGTAAAAATGTGATTTTTG-GAAG
* *
78836 TTTG-GAGG-CAAAATGTGATTTTTTGAAG
1 TTTGAG-GGTAAAAATGTGATTTTTGGAAG
* * * **
78864 TTCGAGGGCAAAAATGTAATTTTAAGAAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAG
* *
78893 TTT-AGGGGCAAAAATGTAATTTTTGAGAAG
1 TTTGA-GGGTAAAAATGTGATTTTTG-GAAG
*
78923 TTTGAGGGTTAAAATGTGATTTTTGGAAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAG
* * **
78952 TTTTAGGGTAAAAATGTAATTGTTAAGAAG
1 TTTGAGGGTAAAAATGTGATT-TTTGGAAG
* *
78982 TTTG-GGGTTAAAATGTGATTTTAGGAAAG
1 TTTGAGGGTAAAAATGTGATTTTTGG-AAG
* * *
79011 TTT-ATGTGTTAAAATGT-AATTTTGGAAAAG
1 TTTGA-GGGTAAAAATGTGATTTTTGG--AAG
* *
79041 TTTG-GGGTCAAAATATGATT
1 TTTGAGGGTAAAAATGTGATT
79061 CCTAAAAAGT
Statistics
Matches: 297, Mismatches: 50, Indels: 43
0.76 0.13 0.11
Matches are distributed among these distances:
27 9 0.03
28 38 0.13
29 171 0.58
30 69 0.23
31 10 0.03
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTGAGGGTAAAAATGTGATTTTTGGAAG
Found at i:80594 original size:20 final size:20
Alignment explanation
Indices: 80569--80610 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
80559 CCAATTGAAT
*
80569 TTGTATTTTGGAC-TTTAAAA
1 TTGTA-TTTGAACATTTAAAA
80589 TTGTATTTGAACATTTAAAA
1 TTGTATTTGAACATTTAAAA
80609 TT
1 TT
80611 TAAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (20 bp):
TTGTATTTGAACATTTAAAA
Found at i:80617 original size:6 final size:6
Alignment explanation
Indices: 80601--80698 Score: 66
Period size: 6 Copynumber: 17.2 Consensus size: 6
80591 GTATTTGAAC
*
80601 ATTTAAA ATTTAA ATTTAA A-TTAA A-TTAA ATTTAA ATTTAA A-AT-A
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * * *
80646 ATTTCAA ACTCAA A-ATAA CTTTAA ATTTAA ACTTAA A--TAA ATTAAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
80692 ATTTAA A
1 ATTTAA A
80699 ATTGATTTCC
Statistics
Matches: 72, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
4 6 0.08
5 14 0.19
6 45 0.62
7 7 0.10
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (6 bp):
ATTTAA
Found at i:80641 original size:17 final size:17
Alignment explanation
Indices: 80610--80683 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
80600 CATTTAAAAT
80610 TTAAATTTAAA-TTAAA
1 TTAAATTTAAATTTAAA
80626 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
* * *
80643 AT-AATTTCAAACTCAAA
1 TTAAATTT-AAATTTAAA
* *
80660 ATAACTTTAAATTTAAA
1 TTAAATTTAAATTTAAA
80677 CTTAAAT
1 -TTAAAT
80684 AAATTAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
16 16 0.35
17 22 0.48
18 8 0.17
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:80688 original size:16 final size:16
Alignment explanation
Indices: 80611--80676 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 16
80601 ATTTAAAATT
80611 TAAATTTAAA-TTAAA
1 TAAATTTAAATTTAAA
80626 TTAAATTTAAATTTAAA
1 -TAAATTTAAATTTAAA
**
80643 -ATAATTTCAAACTCAAAA
1 TA-AATTT-AAA-TTTAAA
*
80661 TAACTTTAAATTTAAA
1 TAAATTTAAATTTAAA
80677 CTTAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 1 0.03
16 19 0.47
17 11 0.28
18 8 0.20
19 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:87637 original size:3 final size:3
Alignment explanation
Indices: 87622--87688 Score: 50
Period size: 3 Copynumber: 23.3 Consensus size: 3
87612 TCCATTTTTC
* * * * *
87622 TCT TCT CCT TCT TCT TCT TCT TC- TCC TAT TCT TTT TCT TTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
87669 T-T TCT GCT TTT TC- TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT T
87689 AAACCCTAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:87673 original size:20 final size:20
Alignment explanation
Indices: 87622--87665 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
87612 TCCATTTTTC
87622 TCTTCTCC--TTCTTCTTCT
1 TCTTCTCCTATTCTTCTTCT
*
87640 TCTTCTCCTATTCTTTTTCT
1 TCTTCTCCTATTCTTCTTCT
*
87660 TTTTCT
1 TCTTCT
87666 TCTTTTCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (20 bp):
TCTTCTCCTATTCTTCTTCT
Found at i:92382 original size:28 final size:28
Alignment explanation
Indices: 92342--92395 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
92332 GATATCTAAT
*
92342 TTACTCCTTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
* *
92370 TTACTCCCTGTTGATCTAAAGGTCAT
1 TTACTCCCTGTTGACCCAAAGGTCAT
92396 AATGCTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:96676 original size:28 final size:28
Alignment explanation
Indices: 96636--96718 Score: 139
Period size: 28 Copynumber: 3.0 Consensus size: 28
96626 AATATCTGAT
96636 TTACTCCTTGTTGACCCAAATGTCATGC
1 TTACTCCTTGTTGACCCAAATGTCATGC
*
96664 TTACACCTTGTTGACCCAAATGTCATGC
1 TTACTCCTTGTTGACCCAAATGTCATGC
* *
96692 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTCCTTGTTGACCCAAATGTCATG
96719 ATGCTCTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (28 bp):
TTACTCCTTGTTGACCCAAATGTCATGC
Found at i:96747 original size:36 final size:36
Alignment explanation
Indices: 96692--96790 Score: 144
Period size: 36 Copynumber: 2.8 Consensus size: 36
96682 AATGTCATGC
* * *
96692 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCTTT
1 TTACTCCCTATTGACCCAAAGGTCATGATACTCATT
* *
96728 TTACTCCCTATTAATCCAAAGGTCATGATACTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATACTCATT
*
96764 TTACTCCCTTTTGACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
96791 CTTGTTACCA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.35
Consensus pattern (36 bp):
TTACTCCCTATTGACCCAAAGGTCATGATACTCATT
Found at i:103812 original size:16 final size:16
Alignment explanation
Indices: 103791--103821 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
103781 TGACAATCAA
103791 TATATATATACATATC
1 TATATATATACATATC
103807 TATATATATACATAT
1 TATATATATACATAT
103822 ATCTACAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATATATACATATC
Found at i:105300 original size:7 final size:7
Alignment explanation
Indices: 105256--105323 Score: 70
Period size: 7 Copynumber: 10.1 Consensus size: 7
105246 AATTGAAAAC
105256 GAGAAAG
1 GAGAAAG
105263 G-GAAAG
1 GAGAAAG
*
105269 GACAAAG
1 GAGAAAG
* *
105276 GGGGAAG
1 GAGAAAG
105283 G-GAAA-
1 GAGAAAG
*
105288 GCGAAAG
1 GAGAAAG
105295 GAGAAAG
1 GAGAAAG
*
105302 GAGAAAA
1 GAGAAAG
105309 GAGAAAG
1 GAGAAAG
105316 GAGAAAG
1 GAGAAAG
105323 G
1 G
105324 GGGAAGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 1 0.02
6 13 0.26
7 36 0.72
ACGTcount: A:0.53, C:0.03, G:0.44, T:0.00
Consensus pattern (7 bp):
GAGAAAG
Done.