Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014798.1 Kokia drynarioides strain JFW-HI SEQ_129840, 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: 141526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 319 characters in sequence are not A, C, G, or T
Found at i:3456 original size:16 final size:16
Alignment explanation
Indices: 3431--3471 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3421 TAAAACGTGC
3431 TTCTTCTTTTCTTT-TT
1 TTCTTCTTTT-TTTGTT
*
3447 TTCTTTTTTTTTTGTT
1 TTCTTCTTTTTTTGTT
3463 TTCTTCTTT
1 TTCTTCTTT
3472 GTATTAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (16 bp):
TTCTTCTTTTTTTGTT
Found at i:5524 original size:6 final size:6
Alignment explanation
Indices: 5515--5557 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
5505 AATCCAACTT
*
5515 CAACAC CAACAC CAACAC CAACAT CAACAC CAACAC CAACAC C
1 CAACAC CAACAC CAACAC CAACAC CAACAC CAACAC CAACAC C
5558 CATGCTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.02
Consensus pattern (6 bp):
CAACAC
Found at i:5536 original size:24 final size:24
Alignment explanation
Indices: 5508--5557 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5498 TACAAGTAAT
*
5508 CCAACTTCAACACCAACACCAACA
1 CCAACATCAACACCAACACCAACA
5532 CCAACATCAACACCAACACCAACA
1 CCAACATCAACACCAACACCAACA
5556 CC
1 CC
5558 CATGCTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.48, G:0.00, T:0.06
Consensus pattern (24 bp):
CCAACATCAACACCAACACCAACA
Found at i:7021 original size:1 final size:1
Alignment explanation
Indices: 6975--7001 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6965 CTAAAAAAGT
6975 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
7002 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10034 original size:29 final size:31
Alignment explanation
Indices: 9994--10280 Score: 193
Period size: 29 Copynumber: 9.8 Consensus size: 31
9984 ATAAAGATAA
* *
9994 AAAAAT-GAAATTTTTGGACA-TTTGGGGGT
1 AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
* *
10023 -AAAATGGTAA-TTTT-GAAAGTTTCGAGGT
1 AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
* * *
10051 CAAAAATGG-AGTTTTTGGACA-TATGGGGGT
1 -AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
* * *
10081 -AAAATGGTAATTTTT-GAAAGTCTCGAGGT
1 AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
*
10110 CAAAAATGG-AA-TTTTGG-AAGTTTAGGGGT
1 -AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
**
10139 -AAAATGGTAATTTTT-GAAAGTTTTAGGGT
1 AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
10168 CAAAAATGG-AATTTTTGG-AAGTTTGGGGGT
1 -AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
* * *
10198 AAAAAT-ATAATTTTTGG-AAGTTTTGAGGT
1 AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
* *
10227 CAAAAATGG-ATTTTTTAGAAA-TTTGGGGGT
1 -AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
* * * *
10257 CAAAAT-ATAATTTTTAGATAGTTT
1 AAAAATGGTAATTTTTGGAAAGTTT
10281 AAGGACCTCC
Statistics
Matches: 202, Mismatches: 33, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
27 10 0.05
28 29 0.14
29 83 0.41
30 60 0.30
31 20 0.10
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (31 bp):
AAAAATGGTAATTTTTGGAAAGTTTGGGGGT
Found at i:10035 original size:59 final size:58
Alignment explanation
Indices: 9936--10271 Score: 220
Period size: 59 Copynumber: 5.8 Consensus size: 58
9926 TTTTGGGATT
* * * *
9936 AAAAATGGAA-TTTTAGACATTAGAGGGTAAAAAGGTAATTTTTAGAAA-ATAAAGATAA
1 AAAAATGGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTT-GAAAGATAAAGAT-A
* * ** * *
9994 AAAAATGAAATTTTTGGACATTTGGGGGTAAAATGGTAA-TTTTGAAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAG-ATAAAGATA
* * * ** * *
10052 AAAAATGGAGTTTTTGGACATATGGGGGTAAAATGGTAATTTTTGAAAGTCTCGAGGTC
1 AAAAATGGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAG-ATAAAGATA
* * * * * *
10111 AAAAATGGAA-TTTTGGA-AGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTC
1 AAAAATGGAATTTTTGGACA-TTTGGGGGTAAAATGGTAATTTTTGAAAG-ATAAAGATA
* * * ** * *
10169 AAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAAT-ATAATTTTTGGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGACA-TTTGGGGGT-AAAATGGTAATTTTTGAAAG-ATAAAGATA
* * * *
10228 AAAAATGGATTTTTTAGAAATTTGGGGGTCAAAAT-ATAATTTTT
1 AAAAATGGAATTTTTGGACATTTGGGGGT-AAAATGGTAATTTTT
10272 AGATAGTTTA
Statistics
Matches: 241, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
57 5 0.02
58 99 0.41
59 131 0.54
60 6 0.02
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGATAAAGATA
Found at i:10056 original size:58 final size:58
Alignment explanation
Indices: 9994--10280 Score: 341
Period size: 59 Copynumber: 4.9 Consensus size: 58
9984 ATAAAGATAA
*
9994 AAAAATGAAATTTTTGGACATTTGGGGGTAAAATGGTAA-TTTTGAAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGA-ATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTC
* * *
10052 AAAAATGGAGTTTTTGGACATATGGGGGTAAAATGGTAATTTTTGAAAGTCTCGAGGTC
1 AAAAATGGAATTTTTGGA-ATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTC
* *
10111 AAAAATGGAA-TTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTT-TAGGGTC
1 AAAAATGGAATTTTTGGAA-TTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGA-GGTC
* * *
10169 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAAT-ATAATTTTTGGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAA-TTTGGGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTC
* * * *
10228 AAAAATGGATTTTTTAGAAATTTGGGGGTCAAAAT-ATAATTTTTAGATAGTTT
1 AAAAATGGAATTTTT-GGAATTTGGGGGT-AAAATGGTAATTTTT-GAAAGTTT
10281 AAGGACCTCC
Statistics
Matches: 203, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
57 2 0.01
58 86 0.42
59 100 0.49
60 15 0.07
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTC
Found at i:10084 original size:117 final size:112
Alignment explanation
Indices: 9900--10213 Score: 294
Period size: 117 Copynumber: 2.7 Consensus size: 112
9890 TTGGACTCTC
* * * * * *
9900 GGGGGCAAAATGGTAATTTTGGGAAATTTTG-GGATTAAAAATGGAATTTTAGACATTAGAGGGT
1 GGGGGTAAAATGGTAATTTT--GAAAGTTTGAGG-TCAAAAATGGATTTTTGGACATT-GGGGGT
9964 AAAAAGGTAATTTTTAGAAA-ATAAAGATAAAAAAATGAAATTTTTGGACA-TTT
62 AAAAAGGTAATTTTT-GAAAGATAAAGAT-AAAAAATGAAA-TTTTGGA-AGTTT
10017 GGGGGTAAAATGGTAATTTTGAAAGTTTCGAGGTCAAAAATGGAGTTTTTGGACATATGGGGGTA
1 GGGGGTAAAATGGTAATTTTGAAAGTTT-GAGGTCAAAAATGGA-TTTTTGGACAT-TGGGGGTA
* * ** * * *
10082 AAATGGTAATTTTTGAAAGTCTCGAGGTCAAAAATGGAATTTTGGAAGTTT
63 AAAAGGTAATTTTTGAAAG-ATAAAGATAAAAAATGAAATTTTGGAAGTTT
* *
10133 AGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTTGGGGG
1 GGGGGTAAAATGGTAA-TTTTGAAAGTTTGA-GGTCAAAAATGG-ATTTTTGGACA--TTGGGGG
**
10197 TAAAAATATAATTTTTG
61 TAAAAAGGTAATTTTTG
10214 GAAGTTTTGA
Statistics
Matches: 167, Mismatches: 18, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
115 8 0.05
116 42 0.25
117 110 0.66
118 7 0.04
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (112 bp):
GGGGGTAAAATGGTAATTTTGAAAGTTTGAGGTCAAAAATGGATTTTTGGACATTGGGGGTAAAA
AGGTAATTTTTGAAAGATAAAGATAAAAAATGAAATTTTGGAAGTTT
Found at i:10226 original size:117 final size:116
Alignment explanation
Indices: 9994--10241 Score: 324
Period size: 117 Copynumber: 2.1 Consensus size: 116
9984 ATAAAGATAA
* * *
9994 AAAAATGAAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTGAAAGTTTCGAGGTCAAAAATG
1 AAAAATGGAA-TTTTGGACATTTAGGGGTAAAATGGTAATTTTGAAAGTTTAGAGGTCAAAAATG
* *
10059 GAGTTTTTGGACATATGGGGGTAAAATGGTAATTTTTGAAAGTCTCGAGGTC
65 GAATTTTTGGACATATGGGGGTAAAATGATAATTTTTGAAAGTCTCGAGGTC
10111 AAAAATGGAATTTTGGA-AGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAG-GGTCAAAAA
1 AAAAATGGAATTTTGGACA-TTTAGGGGTAAAATGGTAA-TTTTGAAAG-TTTAGAGGTCAAAAA
* * * *
10174 TGGAATTTTTGGA-AGTTTGGGGGTAAAAAT-ATAATTTTTGGAAGTTTTGAGGTC
63 TGGAATTTTTGGACA-TATGGGGGT-AAAATGATAATTTTTGAAAGTCTCGAGGTC
*
10228 AAAAATGGATTTTT
1 AAAAATGGAATTTT
10242 TAGAAATTTG
Statistics
Matches: 116, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
115 1 0.01
116 26 0.22
117 80 0.69
118 9 0.08
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (116 bp):
AAAAATGGAATTTTGGACATTTAGGGGTAAAATGGTAATTTTGAAAGTTTAGAGGTCAAAAATGG
AATTTTTGGACATATGGGGGTAAAATGATAATTTTTGAAAGTCTCGAGGTC
Found at i:10270 original size:30 final size:30
Alignment explanation
Indices: 10121--10271 Score: 125
Period size: 30 Copynumber: 5.1 Consensus size: 30
10111 AAAAATGGAA
* *
10121 TTTTGGAAGTTTAGGGGT-AAAATGGTAA-T
1 TTTTGGAAGTTTGGGGGTCAAAAT-ATAATT
* **
10150 TTTTGAAAGTTTTAGGGTCAAAA-ATGGAA-T
1 TTTTGGAAGTTTGGGGGTCAAAATAT--AATT
*
10180 TTTTGGAAGTTTGGGGGTAAAAATATAA-T
1 TTTTGGAAGTTTGGGGGTCAAAATATAATT
* * *
10209 TTTTGGAAGTTTTGAGGTCAAAA-ATGGATT
1 TTTTGGAAGTTTGGGGGTCAAAATAT-AATT
* *
10239 TTTTAGAAATTTGGGGGTCAAAATATAATT
1 TTTTGGAAGTTTGGGGGTCAAAATATAATT
10269 TTT
1 TTT
10272 AGATAGTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
28 3 0.03
29 39 0.40
30 52 0.53
31 4 0.04
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (30 bp):
TTTTGGAAGTTTGGGGGTCAAAATATAATT
Found at i:11387 original size:12 final size:12
Alignment explanation
Indices: 11372--11406 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11362 TTACGATGTT
11372 TATTATTATTAA
1 TATTATTATTAA
*
11384 TATTATTACTAA
1 TATTATTATTAA
*
11396 CATTATTATTA
1 TATTATTATTA
11407 TTAAGAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:11389 original size:9 final size:9
Alignment explanation
Indices: 11375--11440 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
11365 CGATGTTTAT
11375 TATTATTAA
1 TATTATTAA
*
11384 TATTATTAC
1 TATTATTAA
** *
11393 TAACATTAT
1 TATTATTAA
11402 TATTATTAA
1 TATTATTAA
* * *
11411 GAAGTAGTTAT
1 -TATTA-TTAA
11422 TATTATTAA
1 TATTATTAA
11431 TATTATTAA
1 TATTATTAA
11440 T
1 T
11441 GTCATTAATG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
9 33 0.79
10 6 0.14
11 3 0.07
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (9 bp):
TATTATTAA
Found at i:12174 original size:17 final size:17
Alignment explanation
Indices: 12152--12190 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
12142 TTTTTTAATT
12152 AATTTTAATTTACAA-TA
1 AATTTTAATTTA-AAGTA
12169 AATTTTAATTTAAAGTA
1 AATTTTAATTTAAAGTA
12186 AATTT
1 AATTT
12191 AAACTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTTAATTTAAAGTA
Found at i:13924 original size:75 final size:75
Alignment explanation
Indices: 13801--14479 Score: 912
Period size: 75 Copynumber: 9.1 Consensus size: 75
13791 GCGGATAGCT
* * * * *
13801 AGGAGGAGTAGGAGAGCTCTGAGAAGGGTTTGGTCCGGTCGGTACTTTTCTCTTTACATTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
13866 TATAATTGGA
66 TATAACTGGA
* *
13876 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTTCGGTCGGTACTTTTCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
13941 TATAAGTGGA
66 TATAACTGGA
* * *
13951 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTTGGTGCTTTTCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
14016 TATAATTGGA
66 TATAACTGGA
* *
14026 AGGATGG-GTAGGAGAACTTTGAGAAGGATTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAA
1 AGGA-GGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAA
*
14090 TTATAAGTGGA
65 TTATAACTGGA
* * * *
14101 AGGAGGATTAGGAGAACTTTGAGAAGGGTTAGGTCCGATCGGTACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
14166 TATAATTGGA
66 TATAACTGGA
* * * *
14176 AGGTGGGGTAGGAGAACTCTAAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCATGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
14241 TATAACTGGA
66 TATAACTGGA
* * * *
14251 AGGAGGAGTAGGAGAACTCTGCGTAGGGCTCGGTCCGGTTGGTACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
* *
14316 AATAACTAGA
66 TATAACTGGA
* * * * * *
14326 AGGAGGAGTAGGAGAACTTTGCGTAGGGCTCGGTCCGATCGATACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
14391 TATAACTAGA
66 TATAACTGGA
* ** * * * *
14401 AGGAGGAGTAAGAGAACTCTGAGAAGGGCTT-GGTCCACTTGGTACTTTTCTCTTTACGATGAAA
1 AGGAGGAGTAGGAGAACTCTGAGAAGGG-TTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAA
*
14465 TTATCACTGGA
65 TTATAACTGGA
14476 AGGA
1 AGGA
14480 TCATGAAGTA
Statistics
Matches: 542, Mismatches: 59, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
74 2 0.00
75 537 0.99
76 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (75 bp):
AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
TATAACTGGA
Found at i:14900 original size:127 final size:126
Alignment explanation
Indices: 14658--15548 Score: 1130
Period size: 126 Copynumber: 7.0 Consensus size: 126
14648 TTGAAGTAAA
* * * *
14658 AATATGATTGATGGTAGGAAACAGAGTACAATACATTATATTTATATGAACATATTTTCAAATAG
1 AATATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * **
14723 AATCCAAGAATCGAACATTTTTAAGAAAATATTTTGTGCAGATTTCTATTTCCATTTTTGAT
66 AATCCAAGAATAG-ACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* * * *
14785 AATATGTTTGATGATAGGAAAAAGAGTACAATACATTATATTTATATGAATAAATTTTCAATTAG
1 AATATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* *
14850 AATCCAAGAATATGACATTTTTTAGAAAATATTTAATGCAAATTTTTATTTCCATTTTTGAT
66 AATCCAAGAATA-GACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* *
14912 AATATGTTTGATGGTAAGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAA
1 AATATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * * *
14977 AATCCAAGAATCAGACATTTTTGAGAAAATA-TTAATGTAGATTTTTGTTTCCATTTTTGAT
66 AATCCAAGAAT-AGACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* * *
15038 AATATGTTT-ATGGTAGGAAAGAGAGTACAATATATTATATTTATATGAACGGATTTTCAATTAA
1 AATATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * * ** *
15102 AATCCAAGAATCAAACATTTTTAAGAAAATATTTAATGCAGATTTTTATTTTTATTTTCGAT
66 AATCCAAGAAT-AGACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
*
15164 AATATGTTT-ATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAAATTTTCAATTAG
1 AATATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * *
15228 AATCCAAAAATCAGACATTTTTTTTAGAAAATATTTAATGTAGATTCCTATTTCCATTTTTGAT
66 AATCCAAGAAT-AGACA--TTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* * * * *
15292 AATATGATTGATGGTAGG-AAGTAGAGTATAATACATTATATTTTTATGAACATATTTTCGATTA
1 AATATGTTTGATGGTAGGAAAG-AGAGTACAATACATTATATTTATATGAACAGATTTTCAATTA
* * * *
15356 AAATCTAAGAATA-AGATATTTTTAGAAAATATTTAATGCAGATTTCTATTTCTATTTTTGAT
65 GAATCCAAGAATAGACAT-TTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* * * * **
15418 AATATGTTTGATGGTAGAAAATAGAATAGAATATGTTATATTTATATGAACAGA-TTTCAATTAG
1 AATATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * * * * ** *
15482 AATCTAAAAATCTA-ACATTTTTGAAAAAATATTTAATGGAGATTTCTATTAACATTTTTGAC
66 AATCCAAGAA--TAGACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
15544 AATAT
1 AATAT
15549 TGATATCAAG
Statistics
Matches: 676, Mismatches: 77, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
125 99 0.15
126 261 0.39
127 209 0.31
128 52 0.08
129 55 0.08
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (126 bp):
AATATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
AATCCAAGAATAGACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
Found at i:25381 original size:75 final size:75
Alignment explanation
Indices: 25297--26049 Score: 1114
Period size: 75 Copynumber: 10.0 Consensus size: 75
25287 CGGATTGCTG
** * *
25297 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCAATCGGTACTTTTCTCTTTACATTGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
25362 ATAACTGGAA
66 ATAACTGGAA
* * *
25372 GGAGGAGTAGGAGAGCTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTTACATTGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
25437 ATAACTGGAA
66 ATAACTGGAA
*
25447 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTTC-GTATTTTTCTCTTCACGTTGAAAT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGG-TCGGTACTTTTCTCTTCACGTTGAAAT
*
25511 TATAAATGGAA
65 TATAACTGGAA
* *
25522 GGAGGAGTAGGAGAACTCTGAGAAGGGTTTGGTCCGGTCCGTACTTTTCTCTTCACGTTGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
*
25587 ATAATTGGAA
66 ATAACTGGAA
* * * * *
25597 GGAGGGGTAGGAGAACTTTGGGAAGGGTTCGGTCCGGTTGGTACTTTCCTCTTCACGTTGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
*
25662 ATAATTGGAA
66 ATAACTGGAA
25672 GGACGG-GTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
1 GGA-GGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
*
25736 TATAACTAGAA
65 TATAACTGGAA
* * * * *
25747 GGAGAAGTAGGAGAACTCTGCGTAGGGCTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
25812 ATAACTGGAA
66 ATAACTGGAA
* *
25822 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCAGTCCGGTCGGTACTTTCCTCTTCACGTTGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
*
25887 ATAACTAGAA
66 ATAACTGGAA
* * * *
25897 GGAGGAGTAGGAGAACTCTGCGTAGGGCTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
*
25962 ATAACTAGAA
66 ATAACTGGAA
* ** * * *
25972 GGAGGAGTAGGAGAACTCTGAGAAGGGCTCGGTCCACTTGGTACTTTTCTCTTTACGATGAAATT
1 GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
* *
26037 ATCACTAGAA
66 ATAACTGGAA
26047 GGA
1 GGA
26050 TCATGAAGTA
Statistics
Matches: 625, Mismatches: 49, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
74 3 0.00
75 618 0.99
76 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (75 bp):
GGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAATT
ATAACTGGAA
Found at i:26470 original size:127 final size:127
Alignment explanation
Indices: 26228--27113 Score: 1095
Period size: 127 Copynumber: 7.0 Consensus size: 127
26218 TTGAAGTAAA
*
26228 AATATGATTT-ATGGTAGGAAACAA-AGTACAATACATTATATTTATATGAACAGATTTTCAAAT
1 AATATG-TTTGATGGTAGGAAA-AAGAGTACAATACATTATATTTATATGAACAGATTTTCAATT
* * ** *
26291 AGAATCCAAGAATCAAACATTTCTAAGAAAATATTTTGTGCAAATTTCTATTTCCATTTTTGAT
64 AGAATCCAAGAATCAAACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* * * *
26355 AATATGTTTGATGATAGGAAAAAGAGCACAATACATTATATTTATATGAACAAATTTCCAATTAG
1 AATATGTTTGATGGTAGGAAAAAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* *
26420 AATCCAAGAAT-AGGACATTTTTTAGAAAATATTTAATGCAGATTTTTATTTCCATTTTTGAT
66 AATCCAAGAATCA-AACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* *
26482 AATATGTTTGATGGTAAGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
1 AATATGTTTGATGGTAGGAAAAAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * * * * * *
26547 AATCTAGGAATCAAACATTTTTGAGAAAATGTTTAATGTAGATTTTTATTTCTATTTTTGAT
66 AATCCAAGAATCAAACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* *
26609 AATATGTTT-ATGGTAGGAAAGAGAGTACAATACATTATATTAATATGAACAGATTTTCAATTAG
1 AATATGTTTGATGGTAGGAAAAAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* *
26673 AATCCAAGAATCAAACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTTCATTTTCGAT
66 AATCCAAGAATCAAACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* * * *
26735 AATATGTTT-ATGGTAGGAAAGAGAGTACAATACGTTATATTTATAT-AACAAATTTTTAATTAG
1 AATATGTTTGATGGTAGGAAAAAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* ** * ** * *
26798 AATCCAAAAATCGGACATTTTTTTAGAAAATATTTAATGTAGATCCCAATTTTCATTTTTGAT
66 AATCCAAGAATCAAACA-TTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* ** * * * *
26861 AATATGATTGATGGTAGGAAGTAGAGTATAATACATTATATTTTTATGAACATATTTTCAATTAA
1 AATATGTTTGATGGTAGGAAAAAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * * ** * *
26926 AATCTAAGAATCAGATATTTTTTAGAAAATATTTAATATAGATTTTTATTTCTATTTTTGAT
66 AATCCAAGAATCAAACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
* * * * *
26988 AATATGTTTGATGATAGGAAATAA-AATATAATACATTATATTTATATGGACAGATTTTTAATTA
1 AATATGTTTGATGGTAGGAAA-AAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTA
* * * * *
27052 GAATCCAAAAATCAAATATTTTTGAAAAAAAATATTTAATAG-AAATTTCTATTTCCATTTTT
65 GAATCCAAGAATCAAACATTTTT--TAGAAAATATTTAAT-GCAGATTTCTATTTCCATTTTT
27114 TTGACAATAT
Statistics
Matches: 661, Mismatches: 87, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
125 29 0.04
126 204 0.31
127 369 0.56
128 29 0.04
129 30 0.05
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (127 bp):
AATATGTTTGATGGTAGGAAAAAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
AATCCAAGAATCAAACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGAT
Found at i:26738 original size:253 final size:252
Alignment explanation
Indices: 26228--27113 Score: 1109
Period size: 253 Copynumber: 3.5 Consensus size: 252
26218 TTGAAGTAAA
* *
26228 AATATGATTTATGGTAGGAAACAAAGTACAATACATTATATTTATATGAACAGATTTTCAAATAG
1 AATATG-TTTATGGTAGGAAAGAAAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * * ** * * *
26293 AATCCAAGAATCAAACATTTCTAAGAAAATATTTTGTGCAAATTTCTATTTCCATTTTTGATAAT
65 AATCCAAAAATCAAACATTTTTGAGAAAATATTTAATGTAGATTTCTATTTCTATTTTTGATAAT
* * * *
26358 ATGTTTGATGATAGGAAAAAGAGCACAATACATTATATTTATATGAACAAATTTCCAATTAGAAT
130 ATGTTT-ATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAAATTTTCAATTAGAAT
*
26423 CCAAGAAT-AGGACATTTTTTAGAAAATATTTAATGCAGATTTTTATTTCCATTTTTGAT
194 CCAAGAATCA-GACATTTTTTAGAAAATATTTAATGCAGATTTTTATTTTCATTTTTGAT
* *
26482 AATATGTTTGATGGTAAGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
1 AATATGTTT-ATGGTAGGAAAGAAAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* ** * *
26547 AATCTAGGAATCAAACATTTTTGAGAAAATGTTTAATGTAGATTTTTATTTCTATTTTTGATAAT
65 AATCCAAAAATCAAACATTTTTGAGAAAATATTTAATGTAGATTTCTATTTCTATTTTTGATAAT
* *
26612 ATGTTTATGGTAGGAAAGAGAGTACAATACATTATATTAATATGAACAGATTTTCAATTAGAATC
130 ATGTTTATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAAATTTTCAATTAGAATC
* * *
26677 CAAGAATCAAACATTTTTTAGAAAATATTTAATGCAGATTTCTATTTTCATTTTCGAT
195 CAAGAATCAGACATTTTTTAGAAAATATTTAATGCAGATTTTTATTTTCATTTTTGAT
* * * *
26735 AATATGTTTATGGTAGGAAAGAGAGTACAATACGTTATATTTATAT-AACAAATTTTTAATTAGA
1 AATATGTTTATGGTAGGAAAGAAAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGA
** * ** *
26799 ATCCAAAAATCGGACATTTTTTTAGAAAATATTTAATGTAGATCCCAATTT-TCATTTTTGATAA
66 ATCCAAAAATCAAACA-TTTTTGAGAAAATATTTAATGTAGATTTCTATTTCT-ATTTTTGATAA
* * * * *
26863 TATGATTGATGGTAGG-AAGTAGAGTATAATACATTATATTTTTATGAACATATTTTCAATTAAA
129 TATG-TTTATGGTAGGAAAG-AGAGTACAATACATTATATTTATATGAACAAATTTTCAATTAGA
* * **
26927 ATCTAAGAATCAGATATTTTTTAGAAAATATTTAATATAGATTTTTA-TTTCTATTTTTGAT
192 ATCCAAGAATCAGACATTTTTTAGAAAATATTTAATGCAGATTTTTATTTTC-ATTTTTGAT
* * * * * *
26988 AATATGTTTGATGATAGGAAATAAAATATAATACATTATATTTATATGGACAGATTTTTAATTAG
1 AATATGTTT-ATGGTAGGAAAGAAAGTACAATACATTATATTTATATGAACAGATTTTCAATTAG
* * * *
27053 AATCCAAAAATCAAATATTTTTGAAAAAAAATATTTAATAG-AAATTTCTATTTCCATTTTT
65 AATCCAAAAATCAAACATTTTTG--AGAAAATATTTAAT-GTAGATTTCTATTTCTATTTTT
27114 TTGACAATAT
Statistics
Matches: 548, Mismatches: 71, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
251 28 0.05
252 85 0.16
253 224 0.41
254 154 0.28
255 29 0.05
256 27 0.05
257 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (252 bp):
AATATGTTTATGGTAGGAAAGAAAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGA
ATCCAAAAATCAAACATTTTTGAGAAAATATTTAATGTAGATTTCTATTTCTATTTTTGATAATA
TGTTTATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAAATTTTCAATTAGAATCC
AAGAATCAGACATTTTTTAGAAAATATTTAATGCAGATTTTTATTTTCATTTTTGAT
Found at i:27979 original size:134 final size:134
Alignment explanation
Indices: 27739--28007 Score: 511
Period size: 134 Copynumber: 2.0 Consensus size: 134
27729 AAGGATAATA
*
27739 GGGATGACTAGAATCACACTTTCATACAATTCCTTCTCATGTTAGAATTGGTAATCAGTGACTAC
1 GGGATGACTAGAATCACACTTTCATACAATTCATTCTCATGTTAGAATTGGTAATCAGTGACTAC
27804 TATTCTATCACCTTATAATAAATTATACTATTCCCATTTGGGTCATACCATTAGTGGTCTCGTCT
66 TATTCTATCACCTTATAATAAATTATACTATTCCCATTTGGGTCATACCATTAGTGGTCTCGTCT
27869 TGTT
131 TGTT
* *
27873 GGGATGATTAGAATCACACTTTCATACAATTCATTCTCATGTTAGAATTGGTAATTAGTGACTAC
1 GGGATGACTAGAATCACACTTTCATACAATTCATTCTCATGTTAGAATTGGTAATCAGTGACTAC
27938 TATTCTATCACCTTATAATAAATTATACTATTCCCATTTGGGTCATACCATTAGTGGTCTCGTCT
66 TATTCTATCACCTTATAATAAATTATACTATTCCCATTTGGGTCATACCATTAGTGGTCTCGTCT
28003 TGTT
131 TGTT
28007 G
1 G
28008 TTAAGCCTAA
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (134 bp):
GGGATGACTAGAATCACACTTTCATACAATTCATTCTCATGTTAGAATTGGTAATCAGTGACTAC
TATTCTATCACCTTATAATAAATTATACTATTCCCATTTGGGTCATACCATTAGTGGTCTCGTCT
TGTT
Found at i:28982 original size:14 final size:14
Alignment explanation
Indices: 28963--28993 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28953 CAATGAACAC
28963 CAACCAAGTCCAAG
1 CAACCAAGTCCAAG
28977 CAACCAAGTCCAAG
1 CAACCAAGTCCAAG
28991 CAA
1 CAA
28994 TACTCAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.35, G:0.13, T:0.06
Consensus pattern (14 bp):
CAACCAAGTCCAAG
Found at i:36939 original size:31 final size:31
Alignment explanation
Indices: 36904--36962 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
36894 CTTGTTTAGG
36904 TTCTTTCTTAGGGGAAACAATCAAGGAAGGA
1 TTCTTTCTTAGGGGAAACAATCAAGGAAGGA
*
36935 TTCTTTCTTAGGGGAAACAATCGAGGAA
1 TTCTTTCTTAGGGGAAACAATCAAGGAA
36963 TGAGCTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (31 bp):
TTCTTTCTTAGGGGAAACAATCAAGGAAGGA
Found at i:47244 original size:2 final size:2
Alignment explanation
Indices: 47237--47266 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47227 ATCAAAATTT
47237 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47267 ATTGCATCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69605 original size:15 final size:15
Alignment explanation
Indices: 69581--69624 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
69571 TGGTGGAGGC
*
69581 GGAGGCGGCGGTGGA
1 GGAGGTGGCGGTGGA
*
69596 GGAGGTGGCGGTGGT
1 GGAGGTGGCGGTGGA
*
69611 GGAGGTGGTGGTGG
1 GGAGGTGGCGGTGG
69625 GGGTAGCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.09, C:0.07, G:0.68, T:0.16
Consensus pattern (15 bp):
GGAGGTGGCGGTGGA
Found at i:69620 original size:18 final size:18
Alignment explanation
Indices: 69571--69621 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
69561 ACCCACCTTC
* *
69571 TGGTGGAGGCGGAGGCGG
1 TGGTGGAGGAGGTGGCGG
*
69589 CGGTGGAGGAGGTGGCGG
1 TGGTGGAGGAGGTGGCGG
*
69607 TGGTGGAGGTGGTGG
1 TGGTGGAGGAGGTGG
69622 TGGGGGTAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.10, C:0.08, G:0.67, T:0.16
Consensus pattern (18 bp):
TGGTGGAGGAGGTGGCGG
Found at i:72261 original size:2 final size:2
Alignment explanation
Indices: 72254--72279 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
72244 AAACATCTTT
72254 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
72280 GTGTTACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76042 original size:50 final size:49
Alignment explanation
Indices: 75934--76045 Score: 117
Period size: 50 Copynumber: 2.3 Consensus size: 49
75924 ATATTTTCCA
75934 AAATATATTAAA-AATATATATTTTAAAAATTTATTATGAAAATAAAATTG
1 AAATA-ATTAAATAATATATATTTTAAAAATTTATTATG-AAATAAAATTG
* *
75984 AAAT-ATTAAATAATTTATTATTTTAATAAATTATATTATG--ATTAAATAT-
1 AAATAATTAAATAATATA-TATTTTAA-AAATT-TATTATGAAATAAAAT-TG
76033 AAATAATTAAATA
1 AAATAATTAAATA
76046 TGTATGTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
48 6 0.11
49 15 0.28
50 21 0.39
51 5 0.09
52 7 0.13
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (49 bp):
AAATAATTAAATAATATATATTTTAAAAATTTATTATGAAATAAAATTG
Found at i:77865 original size:2 final size:2
Alignment explanation
Indices: 77858--77882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
77848 TCGAAGTAAA
77858 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
77883 AGGGTGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93737 original size:15 final size:15
Alignment explanation
Indices: 93714--93743 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
93704 AGCTCACCAA
93714 GAATCTTTCTTTGAT
1 GAATCTTTCTTTGAT
*
93729 GAATGTTTCTTTGAT
1 GAATCTTTCTTTGAT
93744 TTGAAGGAGC
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:0.20, C:0.10, G:0.17, T:0.53
Consensus pattern (15 bp):
GAATCTTTCTTTGAT
Found at i:97617 original size:3 final size:3
Alignment explanation
Indices: 97609--97647 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
97599 TTCATTTTTC
*
97609 TTA TTA TTA TTA TTA TTA TTTA TTTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA T
97648 AAATATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 26 0.79
4 7 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:97637 original size:17 final size:16
Alignment explanation
Indices: 97615--97647 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
97605 TTTCTTATTA
97615 TTATTATTATTATTTAT
1 TTATTATTATT-TTTAT
97632 TTATTATTATTTTTAT
1 TTATTATTATTTTTAT
97648 AAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATTATTTTTAT
Found at i:97716 original size:63 final size:66
Alignment explanation
Indices: 97615--97794 Score: 225
Period size: 63 Copynumber: 2.8 Consensus size: 66
97605 TTTCTTATTA
* *
97615 TTATTATTATTATTTATTTA-TTATTATTTTTATAAATATAAATGAAT-A-TAAAATAATATTAA
1 TTATT-TTATTATTTATTTATTTATTATTTGTATAAATATAAATAAATAAGTAAAATAATATTAA
97677 TT
65 TT
*
97679 TTATTTTATTATTTATTTATTTATTA-TTGTATGAATATAAATAAATAAATGTAAAATAATATTA
1 TTATTTTATTATTTATTTATTTATTATTTGTATAAATATAAATAAAT-AA-GTAAAATAATATTA
97743 A-T
64 ATT
* *
97745 TT-TGTT-TTA-TTATTTATTTATTATTT-TATAAATATAAATAAATAAATAAA
1 TTATTTTATTATTTATTTATTTATTATTTGTATAAATATAAATAAATAAGTAAA
97795 TAACAAACCA
Statistics
Matches: 104, Mismatches: 6, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
61 4 0.04
62 2 0.02
63 61 0.59
64 16 0.15
65 4 0.04
66 3 0.03
67 14 0.13
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (66 bp):
TTATTTTATTATTTATTTATTTATTATTTGTATAAATATAAATAAATAAGTAAAATAATATTAAT
T
Found at i:97723 original size:67 final size:66
Alignment explanation
Indices: 97615--97792 Score: 235
Period size: 67 Copynumber: 2.8 Consensus size: 66
97605 TTTCTTATTA
* *
97615 TTATTATTATTATTTATTTA-TTATTATTT-T-TATA-AATATAAATGAATATAAAATAATATTA
1 TTATT-TTATTATTTATTTATTTATTATTTATAAATATAA-ATAAATAAATATAAAATAATATTA
97676 ATT
64 ATT
* *
97679 TTATTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAA
1 TTATTTTATTATTTATTTATTTATTATT-TATAAATATAAATAAATAAATATAAAATAATATTAA
97744 TT
65 TT
*
97746 TTGTTTTATTATTTATTTA-TTA-T-TTTATAAATATAAATAAATAAATA
1 TTATTTTATTATTTATTTATTTATTATTTATAAATATAAATAAATAAATA
97793 AATAACAAAC
Statistics
Matches: 103, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
63 34 0.33
64 15 0.15
65 2 0.02
66 4 0.04
67 46 0.45
68 2 0.02
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (66 bp):
TTATTTTATTATTTATTTATTTATTATTTATAAATATAAATAAATAAATATAAAATAATATTAAT
T
Found at i:102837 original size:12 final size:13
Alignment explanation
Indices: 102814--102842 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
102804 AAAAAAGGAA
102814 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
102827 AAAAG-GAAAAAG
1 AAAAGAGAAAAAG
102839 AAAA
1 AAAA
102843 ATGGGAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:103818 original size:50 final size:50
Alignment explanation
Indices: 103755--103863 Score: 173
Period size: 50 Copynumber: 2.2 Consensus size: 50
103745 ATTTTTTACC
* * *
103755 CCTAAAGCTGTGGAGGTGCAAATTGAAACTGCAATGGCAAATCTCATACA
1 CCTAAAGCTGTGGAGGTGCAAATTGAAACCGCAACGGCAAATATCATACA
* *
103805 CCTGAAGCTGTGGAGGTGCAGATTGAAACCGCAACGGCAAATATCATACA
1 CCTAAAGCTGTGGAGGTGCAAATTGAAACCGCAACGGCAAATATCATACA
103855 CCTAAAGCT
1 CCTAAAGCT
103864 TTAGTGGGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTGGAGGTGCAAATTGAAACCGCAACGGCAAATATCATACA
Found at i:103876 original size:50 final size:50
Alignment explanation
Indices: 103755--103931 Score: 147
Period size: 50 Copynumber: 3.5 Consensus size: 50
103745 ATTTTTTACC
* * * * * *
103755 CCTAAAGCTGTGGAGGTGCAAATTGAAACTGCAATGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAACGGCAAATATCATACA
* * *
103805 CCTGAAGCTGTGGAGGTGCAGATTGAAACCGCAACGGCAAATATCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAACGGCAAATATCATACA
* * * * * * * * * *
103855 CCTAAAGCTTTAGTGGGGCAGAATGAAGCTGTAATGACAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAACGGCAAATATCATACA
* * * *
103905 CTTAAAGCTGCAGAGGAGAAGATTGAA
1 CCTAAAGCTGTAGAGGGGCAGATTGAA
103932 GTCACAAGGA
Statistics
Matches: 102, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAACGGCAAATATCATACA
Found at i:104123 original size:80 final size:80
Alignment explanation
Indices: 103986--104432 Score: 696
Period size: 80 Copynumber: 5.6 Consensus size: 80
103976 AGTTACAACC
* *
103986 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* *
104051 GGCAGATTAAAAAAA
66 GGCAGATTGAAGAAA
* * * *
104066 TCTAATCTTTTATCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTGCCCCGGTCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
104131 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * * *
104146 TCCAATCTTTTATCCTAACCAGAGGGCATGATTGAAGATCATTCGATCTTTTATCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
104211 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * *
104226 TCCAATCTGTTACCCTAACTAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
104291 GGCAAATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
104306 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAATACCATTCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
104371 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
* *
104386 TCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCCGAT
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGAT
104433 TGAAGACAAT
Statistics
Matches: 332, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 332 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Found at i:104252 original size:160 final size:160
Alignment explanation
Indices: 103986--104574 Score: 743
Period size: 160 Copynumber: 3.6 Consensus size: 160
103976 AGTTACAACC
*
103986 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATTCGATCTTTTACCCCGATCATGG
* *
104051 GGCAGATTAAAAAAATCTAATCTTTTATCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTT
66 GGCAGATTAAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTT
* * *
104116 TTGCCCCGGTCATGGGGCAGATTGAAGAAA
131 TTACCCCGATCATGGGGCAAATTGAAGAAA
* * * *
104146 TCCAATCTTTTATCCTAACCAGAGGGCATGATTGAAGATCATTCGATCTTTTATCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATTCGATCTTTTACCCCGATCATGG
* * * * *
104211 GGCAGATTGAAGAAATCCAATCTGTTACCCTAACTAGAGGGCAAGATTGAAGACCATCTGATCTT
66 GGCAGATTAAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTT
104276 TTACCCCGATCATGGGGCAAATTGAAGAAA
131 TTACCCCGATCATGGGGCAAATTGAAGAAA
* *
104306 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAATACCATTCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATTCGATCTTTTACCCCGATCATGG
104371 GGCAGATTAAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCCGATTGA
66 GGCAGATTAAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAG---A--C------
* *
104436 AGACAATCCGATCTTTTACCCCGATCATGAGGCATATTGAAGAAA
120 ---C-ATCCGATCTTTTACCCCGATCATGGGGCAAATTGAAGAAA
* * * * * * *
104481 TCTAATCTTCTACCCTAACTAAAGGGCAAGATT-AAAGACCATCCGATCTTTTACCACGATCATG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAA-ATCATTCGATCTTTTACCCCGATCATG
* *
104545 AGACAGATTGAAA-AAAT-TCAATCTTTTACC
65 GGGCAGATT-AAAGAAATCT-AATCTTTTACC
104575 TCGACTATGG
Statistics
Matches: 375, Mismatches: 36, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
160 253 0.67
163 1 0.00
165 1 0.00
174 4 0.01
175 113 0.30
176 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (160 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATTCGATCTTTTACCCCGATCATGG
GGCAGATTAAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTT
TTACCCCGATCATGGGGCAAATTGAAGAAA
Found at i:104409 original size:240 final size:245
Alignment explanation
Indices: 103986--104574 Score: 785
Period size: 240 Copynumber: 2.4 Consensus size: 245
103976 AGTTACAACC
* * *
103986 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATC-TTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* * *
104051 GGCAGATTAAAAAAATCTAATCTTTTATCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTT
65 GGCAGATTGAAAAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTT
* * * * *
104116 TTGCCCCGGTCATGGGGCAGATTGAAGAAATCCAATCTTTTATCCTAACCAGAGGGCATGATTGA
130 TTACCCCGATCATGGGGCAGATTAAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGA
* *
104181 AG-AT-C-A-T-T-CGATCTTTTATCCCGATCATGGGGCAGATTGAAGAAA
195 AGAATCCGATTATCCGATCTTTTACCCCGATCATGAGGCAGATTGAAGAAA
*
104226 TCCAATCTGTTACCCTAACTAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGG
1 TCCAATCT-TTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* * * *
104291 GGCAAATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAATACCATTCGATCTT
65 GGCAGATTGAAAAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTT
*
104356 TTACCCCGATCATGGGGCAGATTAAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGA
130 TTACCCCGATCATGGGGCAGATTAAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGA
*
104421 AGACAATCCGATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCATATTGAAGAAA
195 AG--AATCCGATT-------ATCCGATCTTTTACCCCGATCATGAGGCAGATTGAAGAAA
* * * * *
104481 TCTAATCTTCTACCCTAACTAAAGGGCAAGATTAAAGACCATCCGATCTTTTACCACGATCATGA
1 TCCAATCTT-TACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* *
104546 GACAGATTGAAAAAATTCAATCTTTTACC
65 GGCAGATTGAAAAAATCCAATCTTTTACC
104575 TCGACTATGG
Statistics
Matches: 302, Mismatches: 30, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
239 1 0.00
240 178 0.59
243 2 0.01
244 1 0.00
245 1 0.00
246 1 0.00
254 2 0.01
255 116 0.38
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (245 bp):
TCCAATCTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGG
GCAGATTGAAAAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTT
TACCCCGATCATGGGGCAGATTAAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAA
GAATCCGATTATCCGATCTTTTACCCCGATCATGAGGCAGATTGAAGAAA
Found at i:104435 original size:15 final size:15
Alignment explanation
Indices: 104415--104447 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
104405 CAGAGGGCAA
104415 GATTGAAGACAATCC
1 GATTGAAGACAATCC
104430 GATTGAAGACAATCC
1 GATTGAAGACAATCC
104445 GAT
1 GAT
104448 CTTTTACCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (15 bp):
GATTGAAGACAATCC
Found at i:104498 original size:95 final size:95
Alignment explanation
Indices: 104335--104527 Score: 287
Period size: 95 Copynumber: 2.0 Consensus size: 95
104325 CAGAGGGCAA
* * * * *
104335 GATTGAATACCATTCGATCTTTTACCCCGATCATGGGGCAGATTAAAGAAATCTAATCTTTTACC
1 GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCAGATTAAAGAAATCTAATCTTCTACC
* *
104400 CTAACCAGAGGGCAAGATTGAAGACAATCC
66 CTAACCAAAGGGCAAGATTAAAGACAATCC
* *
104430 GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCATATTGAAGAAATCTAATCTTCTACC
1 GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCAGATTAAAGAAATCTAATCTTCTACC
* *
104495 CTAACTAAAGGGCAAGATTAAAGACCATCC
66 CTAACCAAAGGGCAAGATTAAAGACAATCC
104525 GAT
1 GAT
104528 CTTTTACCAC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (95 bp):
GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCAGATTAAAGAAATCTAATCTTCTACC
CTAACCAAAGGGCAAGATTAAAGACAATCC
Found at i:104570 original size:175 final size:175
Alignment explanation
Indices: 104255--104574 Score: 482
Period size: 175 Copynumber: 1.8 Consensus size: 175
104245 TAGAGGGCAA
* * * *
104255 GATTGAAGACCATCTGATCTTTTACCCCGATCATGGGGCAAATTGAAGAAATCCAATCTTTTACC
1 GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCAAATTGAAGAAATCCAATCTTCTACC
* * * * * * *
104320 CTAACCAGAGGGCAAGATTGAATACCATTCGATCTTTTACCCCGATCATGGGGCAGATTAAAGAA
66 CTAACCAAAGGGCAAGATTAAAGACCATCCGATCTTTTACCACGATCATGAGACAGATTAAAGAA
104385 ATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCC
131 ATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCC
* *
104430 GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCATATTGAAGAAATCTAATCTTCTACC
1 GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCAAATTGAAGAAATCCAATCTTCTACC
*
104495 CTAACTAAAGGGCAAGATTAAAGACCATCCGATCTTTTACCACGATCATGAGACAGATTGAAA-A
66 CTAACCAAAGGGCAAGATTAAAGACCATCCGATCTTTTACCACGATCATGAGACAGATT-AAAGA
104559 AAT-TCAATCTTTTACC
130 AATCT-AATCTTTTACC
104575 TCGACTATGG
Statistics
Matches: 129, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
174 1 0.01
175 125 0.97
176 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (175 bp):
GATTGAAGACAATCCGATCTTTTACCCCGATCATGAGGCAAATTGAAGAAATCCAATCTTCTACC
CTAACCAAAGGGCAAGATTAAAGACCATCCGATCTTTTACCACGATCATGAGACAGATTAAAGAA
ATCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCC
Found at i:104631 original size:39 final size:41
Alignment explanation
Indices: 104430--104694 Score: 176
Period size: 39 Copynumber: 6.7 Consensus size: 41
104420 AAGACAATCC
* *
104430 GATTGAAGACAATCCGATCTTTTACCCCGATCATGA-GGCA
1 GATTGAAGACAATCCAATCTTTTACCCCAATCATGAGGGCA
* * * * *
104470 TATTGAAGA-AATCTAATCTTCTACCCTAA-C-TAAAGGGCAA
1 GATTGAAGACAATCCAATCTTTTACCCCAATCAT-GAGGGC-A
* * * * * *
104510 GATTAAAGACCATCCGATCTTTTACCACGATCATGA-GACA
1 GATTGAAGACAATCCAATCTTTTACCCCAATCATGAGGGCA
* * * * *
104550 GATTGAA-AAAATTCAATCTTTTACCTCGA-CTATG-GGGTA
1 GATTGAAGACAATCCAATCTTTTACCCCAATC-ATGAGGGCA
*
104589 GATTGAAGA-AATCCAATCTTTTACCCTAATCA-GAGGGCA
1 GATTGAAGACAATCCAATCTTTTACCCCAATCATGAGGGCA
* * * * * *
104628 GATTAAAGACCATCAAATCTCTTACCCCGACCATG-GGGCA
1 GATTGAAGACAATCCAATCTTTTACCCCAATCATGAGGGCA
* *
104668 GATTGAA-ATAATCTAATCTTTTACCCC
1 GATTGAAGACAATCCAATCTTTTACCCC
104695 TGAAACTATA
Statistics
Matches: 169, Mismatches: 43, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
37 1 0.01
38 4 0.02
39 92 0.54
40 53 0.31
41 16 0.09
42 2 0.01
43 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (41 bp):
GATTGAAGACAATCCAATCTTTTACCCCAATCATGAGGGCA
Found at i:105240 original size:17 final size:16
Alignment explanation
Indices: 105218--105250 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
105208 ATTTTTCTTA
105218 TTATTATTATTATTTAT
1 TTATTATTATT-TTTAT
105235 TTATTATTATTTTTAT
1 TTATTATTATTTTTAT
105251 AAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATTATTTTTAT
Found at i:105326 original size:67 final size:66
Alignment explanation
Indices: 105218--105402 Score: 253
Period size: 67 Copynumber: 2.9 Consensus size: 66
105208 ATTTTTCTTA
*
105218 TTATTATTATTATTTATTTA-TTATTATTT-T-TATA-AATATAAATAAATATAAAATAATATTA
1 TTATT-TTATTATTTATTTATTTATTATTTATGAATATAA-ATAAATAAATATAAAATAATATTA
105279 ATT
64 ATT
*
105282 TTATTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAA
1 TTATTTTATTATTTATTTATTTATTATT-TATGAATATAAATAAATAAATATAAAATAATATTAA
105347 TT
65 TT
105349 TT-TTTTATTATTTATTTA-TTA-T-TTTATGAATATAAATAAATAAATA-AATAATAA
1 TTATTTTATTATTTATTTATTTATTATTTATGAATATAAATAAATAAATATAA-AATAA
105403 ACCAAAATAA
Statistics
Matches: 112, Mismatches: 3, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
61 2 0.02
62 26 0.23
63 16 0.14
64 14 0.12
65 4 0.04
66 17 0.15
67 31 0.28
68 2 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (66 bp):
TTATTTTATTATTTATTTATTTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAAT
T
Found at i:105412 original size:13 final size:13
Alignment explanation
Indices: 105394--105418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105384 ATAAATAAAT
105394 AAATAATAAACCA
1 AAATAATAAACCA
105407 AAATAATAAACC
1 AAATAATAAACC
105419 TAAAGTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAATAAACCA
Found at i:110866 original size:14 final size:15
Alignment explanation
Indices: 110847--110875 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
110837 TTAAAAATTG
110847 ATTTTTTT-TTTTAT
1 ATTTTTTTATTTTAT
110861 ATTTTTTTATTTTAT
1 ATTTTTTTATTTTAT
110876 TTGTCAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTTTTTATTTTAT
Found at i:113058 original size:8 final size:8
Alignment explanation
Indices: 113045--113071 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
113035 TTAATCTTGC
113045 AAAATAAA
1 AAAATAAA
113053 AAAATAAA
1 AAAATAAA
113061 AAAATAAA
1 AAAATAAA
113069 AAA
1 AAA
113072 GAGGAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:124397 original size:18 final size:18
Alignment explanation
Indices: 124356--124397 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
124346 TAAAATTTTT
* *
124356 CAAAGAAAATAACTTCAT
1 CAAAGAAAATAACTTAAC
124374 CAAAGAAAATAACTTAAC
1 CAAAGAAAATAACTTAAC
*
124392 CCAAGA
1 CAAAGA
124398 TTCGAGCAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (18 bp):
CAAAGAAAATAACTTAAC
Found at i:133719 original size:4 final size:4
Alignment explanation
Indices: 133710--133735 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
133700 GCTGTTCTTG
133710 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
133736 CCTTTTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:137539 original size:14 final size:14
Alignment explanation
Indices: 137520--137566 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
137510 TAATCAAATG
137520 AAAAAGAAAACTAA
1 AAAAAGAAAACTAA
137534 AAAAAGAAAGAC---
1 AAAAAGAAA-ACTAA
137546 AAAAAGAAAACTAA
1 AAAAAGAAAACTAA
*
137560 GAAAAGA
1 AAAAAGA
137567 GAGGATATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
11 2 0.07
12 9 0.32
14 15 0.54
15 2 0.07
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAACTAA
Found at i:138480 original size:34 final size:37
Alignment explanation
Indices: 138405--138474 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
138395 AAGACTCACC
138405 AATTA-AAATAATTACACAAATATATAATTATTATAT
1 AATTACAAATAATTACACAAATATATAATTATTATAT
138441 AATTACAAATAATTACACTAAA-AT-TCAATTATTA
1 AATTACAAATAATTACAC-AAATATAT-AATTATTA
138475 AATTACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
36 6 0.19
37 22 0.71
38 3 0.10
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (37 bp):
AATTACAAATAATTACACAAATATATAATTATTATAT
Found at i:139031 original size:17 final size:16
Alignment explanation
Indices: 139011--139064 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
139001 TAAAAATAAT
139011 AATTAAAATATACAGGA
1 AATTAAAATATA-AGGA
*
139028 AATTAGAA-A-AA--A
1 AATTAAAATATAAGGA
139040 AATTAAAATATATAGGA
1 AATTAAAATATA-AGGA
139057 AATTAAAA
1 AATTAAAA
139065 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 2 0.07
15 2 0.07
16 1 0.03
17 16 0.53
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (16 bp):
AATTAAAATATAAGGA
Found at i:139044 original size:29 final size:29
Alignment explanation
Indices: 139000--139079 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
138990 ATATAAATTT
139000 TTAAAAATAATAATTAAAATATACAGGAAA
1 TTAAAAATAA-AATTAAAATATACAGGAAA
*
139030 TTAGAAAA-AAAATTAAAATATATAGGAAA
1 TTA-AAAATAAAATTAAAATATACAGGAAA
*
139059 TTAAAAATTAAATTTAAAATA
1 TTAAAAA-TAAAATTAAAATA
139080 AAAACAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 4 0.09
29 21 0.47
30 16 0.36
31 4 0.09
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (29 bp):
TTAAAAATAAAATTAAAATATACAGGAAA
Found at i:139078 original size:30 final size:29
Alignment explanation
Indices: 139000--139134 Score: 107
Period size: 30 Copynumber: 4.6 Consensus size: 29
138990 ATATAAATTT
*
139000 TTAAAAATAATAATTAAAATATACAGGAAA
1 TTAAAAATAA-AATTAAAATATAAAGGAAA
*
139030 TTAGAAAA-AAAATTAAAATATATAGGAAA
1 TTA-AAAATAAAATTAAAATATAAAGGAAA
* * **
139059 TTAAAAATTAAATTTAAAATAAAAACAAAA
1 TTAAAAA-TAAAATTAAAATATAAAGGAAA
* *
139089 TTACAAATTAAATTTAAAA-AGTAAATGGAAA
1 TTA-AAAATAAAATTAAAATA-TAAA-GGAAA
139120 -T-AAAATCAAAATTAA
1 TTAAAAAT-AAAATTAA
139135 GTAGATCCCG
Statistics
Matches: 86, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
28 8 0.09
29 29 0.34
30 39 0.45
31 10 0.12
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (29 bp):
TTAAAAATAAAATTAAAATATAAAGGAAA
Found at i:139640 original size:12 final size:12
Alignment explanation
Indices: 139623--139661 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
139613 ATCAGCCTTA
139623 TCAGCGGGCTCG
1 TCAGCGGGCTCG
139635 TCAGCGGGCTCG
1 TCAGCGGGCTCG
* *
139647 TCTGTGGGCTCG
1 TCAGCGGGCTCG
139659 TCA
1 TCA
139662 TTGGGCTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.31, G:0.38, T:0.23
Consensus pattern (12 bp):
TCAGCGGGCTCG
Found at i:139666 original size:12 final size:12
Alignment explanation
Indices: 139628--139669 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
139618 CCTTATCAGC
**
139628 GGGCTCGTCAGC
1 GGGCTCGTCATT
139640 GGGCTCGTC-TGT
1 GGGCTCGTCAT-T
139652 GGGCTCGTCATT
1 GGGCTCGTCATT
139664 GGGCTC
1 GGGCTC
139670 ATCCTCAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 25 0.96
13 1 0.04
ACGTcount: A:0.05, C:0.29, G:0.40, T:0.26
Consensus pattern (12 bp):
GGGCTCGTCATT
Done.