Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014471.1 Kokia drynarioides strain JFW-HI SEQ_129510, 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: 69893
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Warning! 90 characters in sequence are not A, C, G, or T
Found at i:538 original size:29 final size:29
Alignment explanation
Indices: 506--787 Score: 246
Period size: 29 Copynumber: 9.6 Consensus size: 29
496 AAAATTTTTA
* *
506 TTTTACCCCCAAACTTCCAAAAATCCCCT
1 TTTTACCCCCAAACTTTCAAAAATCCCAT
* * *
535 TTTTAACCCCAAACTTTCAAAAATTCTAT
1 TTTTACCCCCAAACTTTCAAAAATCCCAT
* * *
564 TTTTACCCACGAACTTCCAAAAATCCCAT
1 TTTTACCCCCAAACTTTCAAAAATCCCAT
** * *
593 TTTTAACCCTGAAACTTTCAAAAATTCTAT
1 TTTT-ACCCCCAAACTTTCAAAAATCCCAT
* * *
623 TTTTACCCTCGAACTTTCAAAAATCTCAT
1 TTTTACCCCCAAACTTTCAAAAATCCCAT
* * * *
652 TCTTAACCCCAAAACTTTCAAAAATTCTAT
1 T-TTTACCCCCAAACTTTCAAAAATCCCAT
* *
682 TTTTACCCTCGAAC-TTCAAAAAAT-CCATT
1 TTTTACCCCCAAACTTTC-AAAAATCCCA-T
* ***
711 TTTTAACCCCAAAACTTTCAAAAATTATAT
1 TTTT-ACCCCCAAACTTTCAAAAATCCCAT
*
741 TTTTACCCCCAAACTTTAAAAAATCCCAT
1 TTTTACCCCCAAACTTTCAAAAATCCCAT
*
770 TTTTGA-CCCCAAAATTTC
1 TTTT-ACCCCCAAACTTTC
788 CCAAAATTAC
Statistics
Matches: 199, Mismatches: 46, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
28 5 0.03
29 126 0.63
30 64 0.32
31 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
TTTTACCCCCAAACTTTCAAAAATCCCAT
Found at i:629 original size:59 final size:59
Alignment explanation
Indices: 487--787 Score: 396
Period size: 59 Copynumber: 5.2 Consensus size: 59
477 CATAGGCCCT
* * *
487 AAAACTTT-AAAAATT-TTTATTTTACCCCCAAACTTCCAAAAATCCCCTTTTTAACCCC
1 AAAACTTTCAAAAATTCTAT-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* *
545 -AAACTTTCAAAAATTCTATTTTTACCCACGAACTTCCAAAAATCCCATTTTTAACCCT
1 AAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* * * * *
603 GAAACTTTCAAAAATTCTATTTTTACCCTCGAACTTTCAAAAATCTCATTCTTAACCCC
1 AAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* *
662 AAAACTTTCAAAAATTCTATTTTTACCCTCGAACTTCAAAAAAT-CCATTTTTTAACCCC
1 AAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTAACCCC
* * ** *
721 AAAACTTTCAAAAATTATATTTTTACCCCCAAACTTTAAAAAATCCCATTTTTGACCCC
1 AAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
780 AAAA-TTTC
1 AAAACTTTC
788 CCAAAATTAC
Statistics
Matches: 218, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
57 7 0.03
58 48 0.22
59 160 0.73
60 3 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (59 bp):
AAAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
Found at i:832 original size:118 final size:114
Alignment explanation
Indices: 487--832 Score: 365
Period size: 118 Copynumber: 2.9 Consensus size: 114
477 CATAGGCCCT
* * * *
487 AAAACTTT-AAAAATTTTTATTTTACCCCCAAACTTCCAAAAATCCCCTTTTTAACCCCAAACTT
1 AAAACTTTCAAAAATTTAT-TTTTACCCCCAAACTTTCAAAAATCCCATTTTTAACCCCAAAATT
* *
551 TCAAAAATTCTATTTTTACCCACGAACTTCCAAAA-ATCCCATTTTTAACCCT
65 TCAAAAATTCTATTTTTACCCACGAA-ATCCAAAATAT--CATTTTTAACCCC
* * * * *
603 GAAACTTTCAAAAATTCTATTTTTACCCTCGAACTTTCAAAAATCTCATTCTTAACCCCAAAACT
1 AAAACTTTCAAAAATT-TATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTAACCCCAAAA-T
* * * *
668 TTCAAAAATTCTATTTTTACCCTCGAACTTCAAAAAATCCATTTTTTAACCCC
64 TTCAAAAATTCTATTTTTACCCACGAAATCCAAAATAT-CA-TTTTTAACCCC
* *
721 AAAACTTTCAAAAATTATATTTTTACCCCCAAACTTTAAAAAATCCCATTTTTGACCCCAAAATT
1 AAAACTTTCAAAAATT-TATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTAACCCCAAAATT
* * * *
786 TCCCAAAATTACCA-TTTCACCCCCGATAATCCAAAATTATCATTTTT
65 T-CAAAAATT-CTATTTTTACCCACGA-AATCCAAAA-TATCATTTTT
833 GCCCCCGGGA
Statistics
Matches: 193, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
116 7 0.04
117 55 0.28
118 118 0.61
119 11 0.06
120 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (114 bp):
AAAACTTTCAAAAATTTATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTAACCCCAAAATTT
CAAAAATTCTATTTTTACCCACGAAATCCAAAATATCATTTTTAACCCC
Found at i:4140 original size:27 final size:27
Alignment explanation
Indices: 4057--4187 Score: 104
Period size: 27 Copynumber: 4.9 Consensus size: 27
4047 ATAAGGTGGG
*
4057 GCCTATCTGACAGGCAGCACCAAAGGT
1 GCCTATCTGACAGGCGGCACCAAAGGT
* ** * * * **
4084 GCCTACCACATAGGCGGCACTAGATAT
1 GCCTATCTGACAGGCGGCACCAAAGGT
4111 GCCTATCTGACAGGCGGCACCAAAGGT
1 GCCTATCTGACAGGCGGCACCAAAGGT
* * *
4138 GCCT-TCCTGGCAAGCTGCACCAAAGGT
1 GCCTAT-CTGACAGGCGGCACCAAAGGT
* *
4165 GCCT-TCCTGGCAGGCTGCACCAA
1 GCCTAT-CTGACAGGCGGCACCAA
4188 CCCTATATTG
Statistics
Matches: 82, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
26 1 0.01
27 81 0.99
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (27 bp):
GCCTATCTGACAGGCGGCACCAAAGGT
Found at i:4270 original size:18 final size:17
Alignment explanation
Indices: 4232--4278 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
4222 GATTTTTTAC
4232 ATAAATAATACAAAAAA
1 ATAAATAATACAAAAAA
**
4249 ATAAAT-ATACACCAAA
1 ATAAATAATACAAAAAA
4265 AT--ATAATACAAAAA
1 ATAAATAATACAAAAA
4279 TTAAAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 7 0.28
16 10 0.40
17 6 0.24
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (17 bp):
ATAAATAATACAAAAAA
Found at i:4306 original size:9 final size:8
Alignment explanation
Indices: 4294--4336 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
4284 ATTAATAACT
4294 TAAATAGTA
1 TAAATA-TA
4303 TAAATATA
1 TAAATATA
*
4311 TATATATA
1 TAAATATA
*
4319 TATATATA
1 TAAATATA
*
4327 TATATATA
1 TAAATATA
4335 TA
1 TA
4337 TTTATCCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 27 0.82
9 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (8 bp):
TAAATATA
Found at i:4313 original size:2 final size:2
Alignment explanation
Indices: 4301--4337 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4291 ACTTAAATAG
*
4301 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4338 TTATCCATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4566 original size:8 final size:9
Alignment explanation
Indices: 4548--4580 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
4538 GTAGTACACA
4548 TATATTTTT
1 TATATTTTT
4557 T-TAATTTTT
1 TAT-ATTTTT
4566 TATATTTTT
1 TATATTTTT
4575 TATATT
1 TATATT
4581 AAAAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TATATTTTT
Found at i:4649 original size:27 final size:27
Alignment explanation
Indices: 4611--4685 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
4601 AATTTGATGG
4611 ATGGTGCTTTTGGGGTAGGCGACACCA
1 ATGGTGCTTTTGGGGTAGGCGACACCA
4638 ATGGTGCTTTTGGGGTAGGCGACACCA
1 ATGGTGCTTTTGGGGTAGGCGACACCA
*
4665 ATGGTGCCTATT-GGGTAGGCG
1 ATGGTG-CTTTTGGGGTAGGCG
4686 GCACTAGTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 42 0.91
28 4 0.09
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.27
Consensus pattern (27 bp):
ATGGTGCTTTTGGGGTAGGCGACACCA
Found at i:7705 original size:7 final size:7
Alignment explanation
Indices: 7651--7738 Score: 54
Period size: 7 Copynumber: 11.9 Consensus size: 7
7641 AAGGTGATTA
*
7651 GTTTATG
1 GTTTAAG
*
7658 GTTTAAA
1 GTTTAAG
7665 GTCTTAAG
1 GT-TTAAG
7673 GATTTAAG
1 G-TTTAAG
*
7681 GTTTAAA
1 GTTTAAG
*
7688 GTGATAA-
1 GT-TTAAG
7695 GTTTAAG
1 GTTTAAG
7702 GTTTAATG
1 GTTTAA-G
*
7710 ATTTTAAG
1 -GTTTAAG
7718 GTTTTAAGG
1 G-TTTAA-G
7727 GTTT-AG
1 GTTTAAG
7733 GTTTAA
1 GTTTAA
7739 AGTGATTATT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
6 8 0.12
7 24 0.38
8 24 0.38
9 8 0.12
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.44
Consensus pattern (7 bp):
GTTTAAG
Found at i:7741 original size:52 final size:51
Alignment explanation
Indices: 7651--7786 Score: 143
Period size: 52 Copynumber: 2.6 Consensus size: 51
7641 AAGGTGATTA
* * * *
7651 GTTTATG-GTTTAAAGTCTTAAGGATTTAAGGTTTAAAGTGATAAGTTTAAG
1 GTTTATGATTTTAAGGTTTTAAGGGTTT-AGGTTTAAAGTGATAAGTTTAAG
* * *
7702 GTTTAATGATTTTAAGGTTTTAAGGGTTTAGGTTTAAAGTGATTATTTTAGG
1 GTTT-ATGATTTTAAGGTTTTAAGGGTTTAGGTTTAAAGTGATAAGTTTAAG
*
7754 GTTTATGTTTTTAATGG-TTT-AGGGTTTATGGTT
1 GTTTATGATTTTAA-GGTTTTAAGGGTTTA-GGTT
7787 GAATATTTAG
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
50 8 0.11
51 20 0.27
52 29 0.40
53 16 0.22
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.48
Consensus pattern (51 bp):
GTTTATGATTTTAAGGTTTTAAGGGTTTAGGTTTAAAGTGATAAGTTTAAG
Found at i:7837 original size:14 final size:14
Alignment explanation
Indices: 7820--7883 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
7810 GGGTATTATA
7820 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
* **
7834 TTTAGGATTTTTGG
1 TTTAGGGTTTAAGG
*
7848 TATTA--ATATTAAGG
1 T-TTAGGGT-TTAAGG
7862 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
7876 -TTAGGGTT
1 TTTAGGGTT
7884 ATCTAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 13 0.32
14 23 0.57
15 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:7864 original size:35 final size:35
Alignment explanation
Indices: 7806--7872 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
7796 GGGGTTAGAG
*
7806 TTTTGGGTATTATATTTAGGGTTTAAGGTTTAGGA
1 TTTTGGGTATTATATTTAAGGTTTAAGGTTTAGGA
* *
7841 TTTTTGGTATTA-ATATTAAGGTTTAGGGTTTA
1 TTTTGGGTATTATAT-TTAAGGTTTAAGGTTTA
7873 AGGTTAGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.07
35 26 0.93
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (35 bp):
TTTTGGGTATTATATTTAAGGTTTAAGGTTTAGGA
Found at i:8309 original size:6 final size:6
Alignment explanation
Indices: 8300--8329 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
8290 AATAAATAAG
*
8300 AACATA AACATA AACAAA AACATA AACATA
1 AACATA AACATA AACATA AACATA AACATA
8330 TTTAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.70, C:0.17, G:0.00, T:0.13
Consensus pattern (6 bp):
AACATA
Found at i:8321 original size:18 final size:18
Alignment explanation
Indices: 8287--8329 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
8277 TCATTAAATG
* *
8287 TAAA-ATAAATAAGAACA
1 TAAACATAAACAAAAACA
8304 TAAACATAAACAAAAACA
1 TAAACATAAACAAAAACA
8322 TAAACATA
1 TAAACATA
8330 TTTAATTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.70, C:0.12, G:0.02, T:0.16
Consensus pattern (18 bp):
TAAACATAAACAAAAACA
Found at i:11973 original size:27 final size:28
Alignment explanation
Indices: 11932--11986 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
11922 TGGGGAACAA
11932 CATTAGGTGCCGCCTGTC-AGATAGGCAC
1 CATTAGGTGCCGCCTGTCAAG-TAGGCAC
*
11960 CATT-GGTGCGGCCTGTCAAGTAGGCAC
1 CATTAGGTGCCGCCTGTCAAGTAGGCAC
11987 TACCCAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (28 bp):
CATTAGGTGCCGCCTGTCAAGTAGGCAC
Found at i:13365 original size:23 final size:23
Alignment explanation
Indices: 13337--13381 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13327 AAGATATCAT
* *
13337 TATAATGACAATTATAATTAATA
1 TATAATGACAATCACAATTAATA
*
13360 TATAATTACAATCACAATTAAT
1 TATAATGACAATCACAATTAAT
13382 CAGTACGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (23 bp):
TATAATGACAATCACAATTAATA
Found at i:14253 original size:17 final size:17
Alignment explanation
Indices: 14233--14303 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
14223 TTTTGGGGTT
*
14233 AAATTTAGTTTAAGTTA
1 AAATTTAATTTAAGTTA
* *
14250 AAATTTAAATTAAGTTT
1 AAATTTAATTTAAGTTA
* *
14267 AAATCTAATTTGAATTTA
1 AAATTTAATTT-AAGTTA
*
14285 AAATTTAAATTAA-TTA
1 AAATTTAATTTAAGTTA
14301 AAA
1 AAA
14304 GTCCAGTTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
16 6 0.14
17 25 0.57
18 13 0.30
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
AAATTTAATTTAAGTTA
Found at i:16199 original size:29 final size:29
Alignment explanation
Indices: 16148--16409 Score: 187
Period size: 30 Copynumber: 8.9 Consensus size: 29
16138 GGTGGTCCCT
* *
16148 AAACTGTCTAAAAATTACATTTTGACCCCC
1 AAACT-TCCAAAAATTCCATTTTGACCCCC
* * * * * *
16178 GAACTTTCAAAAATTCTATTTTTAACCTCG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
* *
16208 AAACCTCCAAAAA-TCACATTTT-ACCCCT
1 AAACTTCCAAAAATTC-CATTTTGACCCCC
* ***
16236 AAACTTCCAAAAATTCCATTTTTAACCTTA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
*
16266 AAACTTCCAAAAATTCCATTTTTGA-CTCC
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
* * *
16295 GAACTTCC-AAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
*
16324 AAACTTCCAAAAATTACATTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTGACCCCC
* *
16352 GAA-TGTCCAAAAACTCCAATTTTGACCCCC
1 AAACT-TCCAAAAATTCC-ATTTTGACCCCC
*
16382 AAAACTTTCAAAAATTACCATTTT-ACCC
1 -AAACTTCCAAAAATT-CCATTTTGACCC
16410 TTAAATGTCT
Statistics
Matches: 185, Mismatches: 34, Indels: 26
0.76 0.14 0.11
Matches are distributed among these distances:
27 1 0.01
28 50 0.27
29 48 0.26
30 68 0.37
31 15 0.08
32 3 0.02
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCCCC
Found at i:16221 original size:30 final size:30
Alignment explanation
Indices: 16179--16405 Score: 182
Period size: 28 Copynumber: 7.7 Consensus size: 30
16169 TTGACCCCCG
* * *
16179 AACTTTCAAAAATTCTATTTTTAACCTCGA
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
* * *
16209 AACCTCCAAAAA-TCACA-TTTT-ACCCCTA
1 AACTTCCAAAAATTC-CATTTTTAACCTCAA
*
16237 AACTTCCAAAAATTCCATTTTTAACCTTAA
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
* **
16267 AACTTCCAAAAATTCCATTTTTGA-CTCCG
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
*
16296 AACTTCC-AAAATTCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
* * **
16325 AACTTCCAAAAATTACA-TTTT-ACCCCCG
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
* * * *
16353 AA-TGTCCAAAAACTCCAATTTTGACCCCCAA
1 AACT-TCCAAAAATTCC-ATTTTTAACCTCAA
*
16384 AACTTTCAAAAATTACCATTTT
1 AACTTCCAAAAATT-CCATTTT
16406 ACCCTTAAAT
Statistics
Matches: 157, Mismatches: 28, Indels: 23
0.75 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 50 0.32
29 35 0.22
30 49 0.31
31 19 0.12
32 3 0.02
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTAACCTCAA
Found at i:16248 original size:58 final size:58
Alignment explanation
Indices: 16148--16409 Score: 248
Period size: 58 Copynumber: 4.5 Consensus size: 58
16138 GGTGGTCCCT
* * * * *
16148 AAACTGTCTAAAAATTACATTTTGACCCCCGAACTTTCAAAAATTCTATTTTTAACCTCG
1 AAACT-TCCAAAAATCACATTTTGA-CCCCGAACTTCCAAAAATTCCATTTTTAACCTCA
* * *
16208 AAACCTCCAAAAATCACATTTT-ACCCCTAAACTTCCAAAAATTCCATTTTTAACCTTA
1 AAACTTCCAAAAATCACATTTTGACCCC-GAACTTCCAAAAATTCCATTTTTAACCTCA
* *
16266 AAACTTCCAAAAATTC-CATTTTTGACTCCGAACTTCC-AAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAA-TCACA-TTTTGACCCCGAACTTCCAAAAATTCCATTTTTAACCTCA
* * * * *
16324 AAACTTCCAAAAATTACATTTT-ACCCCCGAA-TGTCCAAAAACTCCAATTTTGACCCCCA
1 AAACTTCCAAAAATCACATTTTGA-CCCCGAACT-TCCAAAAATTCC-ATTTTTAACCTCA
* *
16383 AAACTTTCAAAAATTACCATTTT-ACCC
1 AAACTTCCAAAAATCA-CATTTTGACCC
16410 TTAAATGTCT
Statistics
Matches: 173, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
56 2 0.01
57 18 0.10
58 81 0.47
59 57 0.33
60 15 0.09
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (58 bp):
AAACTTCCAAAAATCACATTTTGACCCCGAACTTCCAAAAATTCCATTTTTAACCTCA
Found at i:16467 original size:29 final size:28
Alignment explanation
Indices: 16392--16492 Score: 73
Period size: 29 Copynumber: 3.5 Consensus size: 28
16382 AAAACTTTCA
*
16392 AAAATTACCATTTTACCCTTAAATGTCT
1 AAAATTACCATTTTACCCTTAAATGTCC
* * *
16420 AAAATT-TCATTTTTAACCC-TAAGTTTTCCC
1 AAAATTACCA-TTTT-ACCCTTAA-ATGT-CC
* *
16450 AAAATTACCATTTTACCCCTCGAGA-GTCC
1 AAAATTACCATTTTA-CCCT-TAAATGTCC
16479 AAAATTACCATTTT
1 AAAATTACCATTTT
16493 GCCCCCGAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
27 2 0.04
28 13 0.23
29 23 0.41
30 15 0.27
31 2 0.04
32 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTTAAATGTCC
Found at i:16511 original size:29 final size:29
Alignment explanation
Indices: 16448--16510 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
16438 CTAAGTTTTC
16448 CCAAAATTACCATTTTACCCCTCGAGAGT
1 CCAAAATTACCATTTTACCCCTCGAGAGT
*
16477 CCAAAATTACCATTTTGCCCC-CGAGCA-T
1 CCAAAATTACCATTTTACCCCTCGAG-AGT
16505 CCAAAA
1 CCAAAA
16511 AGTCTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCCTCGAGAGT
Found at i:28420 original size:115 final size:115
Alignment explanation
Indices: 28091--28413 Score: 522
Period size: 115 Copynumber: 2.8 Consensus size: 115
28081 GGCTCAAAGC
* *
28091 GAGCAAATCTTAGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTAGAAGTAATAAAATGG
1 GAGCAAATCTTAGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGG
* **
28156 TTAGCTTCCTGATGAGATACAAAGAAGTATACCAACTTGAGGCTCGATGT
66 TTAGCTTCCTGATGAGATACAGAGAAGTATACCAACCAGAGGCTCGATGT
* *
28206 GAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGTAATAAAATGG
1 GAGCAAATCTTAGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGG
28271 TTAGCTTCCTGATGAGATACAGAGAAGTATACCAACCCAG-GGCTCGATGT
66 TTAGCTTCCTGATGAGATACAGAGAAGTATACCAA-CCAGAGGCTCGATGT
* * *
28321 GAGCAAATCTTTGAATCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGG
1 GAGCAAATCTTAGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGG
* *
28386 TTAGTTTCCTGATGAGATACTGAGAAGT
66 TTAGCTTCCTGATGAGATACAGAGAAGT
28414 GGACCAAATT
Statistics
Matches: 194, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
115 192 0.99
116 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (115 bp):
GAGCAAATCTTAGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGG
TTAGCTTCCTGATGAGATACAGAGAAGTATACCAACCAGAGGCTCGATGT
Found at i:28620 original size:201 final size:201
Alignment explanation
Indices: 28275--28897 Score: 861
Period size: 201 Copynumber: 3.1 Consensus size: 201
28265 AAATGGTTAG
* *
28275 CTTCCTGATGAGATACAGAGAAGTATACCAACCCAGGGCTCGATGTGAGCAAATCTTTGAATCCT
1 CTTCCTGATGAGATACAGAGAAGTATACCAACCCAGGGCTCGATGTGAGCAAATCTTCGAACCCT
* * * *
28340 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGGTTAGTTTCCTGATGAGATA
66 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATA
* * *
28405 CTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACATAGAAGCGGATGGAAACAAGTGAGGC
131 CTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATCGAAACAAGTGATGC
*
28470 GGTAAT
196 GGTCAT
* *
28476 CTTCCTGATGAGATACAGAGAAGTATACCAACTCGGGGCTCGATGTGAGCAAATCTTCGAACCCT
1 CTTCCTGATGAGATACAGAGAAGTATACCAACCCAGGGCTCGATGTGAGCAAATCTTCGAACCCT
*
28541 AGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATA
66 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATA
* * * *
28606 CTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAATGATGC
131 CTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATCGAAACAAGTGATGC
*
28671 AGTCAT
196 GGTCAT
* * * * *
28677 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA-CGCTCGATGTGAGCAAACCTTCG
1 CTTCCTGATGAGATAC--AG-AGAAG--TATA-CCAACCCAGGGCTCGATGTGAGCAAATCTTCG
* * * *
28741 AACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTTGAAGCAATAAAGTGGTTAGCTTCCTAAT
60 AACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAAT
* * ** * * * * *
28806 GAGATACGGAGAAGTGAACCAAATCCGTCTTCTTGATGAAACACAGAGAAGTGGATCAAAACAAG
125 GAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATCGAAACAAG
28871 TGATGCGGTCAT
190 TGATGCGGTCAT
28883 CTTCCTGATGAGATA
1 CTTCCTGATGAGATA
28898 TTGAGAAGAA
Statistics
Matches: 373, Mismatches: 43, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
201 200 0.54
203 2 0.01
204 5 0.01
206 161 0.43
207 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (201 bp):
CTTCCTGATGAGATACAGAGAAGTATACCAACCCAGGGCTCGATGTGAGCAAATCTTCGAACCCT
AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATA
CTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATCGAAACAAGTGATGC
GGTCAT
Found at i:29317 original size:17 final size:17
Alignment explanation
Indices: 29297--29367 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
29287 TTTTGGGTTT
*
29297 AAATTTAGTTTAAGTTA
1 AAATTTAATTTAAGTTA
* *
29314 AAATTTAAATTAAGTTT
1 AAATTTAATTTAAGTTA
* *
29331 AAATCTAATTTGAATTTA
1 AAATTTAATTT-AAGTTA
*
29349 AAATTTAAATTAA-TTA
1 AAATTTAATTTAAGTTA
29365 AAA
1 AAA
29368 GTTCAGTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
16 6 0.14
17 25 0.57
18 13 0.30
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
AAATTTAATTTAAGTTA
Found at i:31306 original size:29 final size:30
Alignment explanation
Indices: 31256--31570 Score: 173
Period size: 29 Copynumber: 10.7 Consensus size: 30
31246 AACTGTTTAG
* * *
31256 AAATTACA-TTTTGACCCACGAACTTTCAA
1 AAATTCCATTTTTGACCCTCGAACTTCCAA
* *
31285 AAATTCCATTTTTGA-CTTCGAAACCTT-CGA
1 AAATTCCATTTTTGACCCTCG-AA-CTTCCAA
* * *
31315 AAA-T-CATATTTTTACCCCCGAGCTTCCAA
1 AAATTCCAT-TTTTGACCCTCGAACTTCCAA
* *
31344 AAATTCCA-TTTTGA-CCGCGAAACATCCAA
1 AAATTCCATTTTTGACCCTCG-AACTTCCAA
*
31373 AAATTACATTTTT-ACCCTCGAACTTCCAA
1 AAATTCCATTTTTGACCCTCGAACTTCCAA
* *
31402 AAATTCCATTTTTAACCC-CAAAACTTCCAA
1 AAATTCCATTTTTGACCCTC-GAACTTCCAA
* *
31432 AAATTACATCTTT-ACCCTC-AGA-TGTCCAA
1 AAATTCCATTTTTGACCCTCGA-ACT-TCCAA
* *
31461 AAACTCCATTTTTGACCCT-GAAACTTTCAA
1 AAATTCCATTTTTGACCCTCG-AACTTCCAA
**
31491 AAATTGCCA-TTTT-ACCCTCAGATGTT--AA
1 AAATT-CCATTTTTGACCCTC-GAACTTCCAA
* * * *
31519 AAATTCCATTTTTAACCC-CAAATTTTCCCA
1 AAATTCCATTTTTGACCCTCGAA-CTTCCAA
*
31549 AAATTACC-TTTTTGCCCCTCGA
1 AAATT-CCATTTTTGACCCTCGA
31571 GAGTCTAAAA
Statistics
Matches: 222, Mismatches: 34, Indels: 58
0.71 0.11 0.18
Matches are distributed among these distances:
27 4 0.02
28 26 0.12
29 92 0.41
30 85 0.38
31 15 0.07
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (30 bp):
AAATTCCATTTTTGACCCTCGAACTTCCAA
Found at i:31447 original size:59 final size:58
Alignment explanation
Indices: 31256--31560 Score: 253
Period size: 59 Copynumber: 5.2 Consensus size: 58
31246 AACTGTTTAG
* * * * * *
31256 AAATTACATTTTGACCCACGAACTTTCAAAAATTCCATTTTTGACTTCGAAACCTT-CGA
1 AAATTACATTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGAC-CCCAAAACTTCCAA
* * * * * * *
31315 AAATCATATTTTTACCCCCGAGCTTCCAAAAATTCCA-TTTTGACCGCGAAACATCCAA
1 AAATTACA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAA
*
31373 AAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAA
1 AAATTACA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAA
* ** *
31432 AAATTACATCTTTACCCTC-AGA-TGTCCAAAAACTCCATTTTTGACCCTGAAACTTTCAA
1 AAATTACAT-TTTACCCTCGA-ACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAA
* ** * ** *
31491 AAATTGCCATTTTACCCTCAGATGTT--AAAAATTCCATTTTTAACCCCAAATTTTCCCA
1 AAATT-ACATTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAA
*
31549 AAATTACCTTTT
1 AAATTACATTTT
31561 TGCCCCTCGA
Statistics
Matches: 199, Mismatches: 37, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
57 9 0.05
58 74 0.37
59 106 0.53
60 8 0.04
61 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (58 bp):
AAATTACATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAA
Found at i:31462 original size:117 final size:117
Alignment explanation
Indices: 31256--31555 Score: 306
Period size: 117 Copynumber: 2.6 Consensus size: 117
31246 AACTGTTTAG
* * * * * * * *
31256 AAATTACATTTTGACCCACGAACTTTCAAAAATTCCATTTTTGACTTCGAAACCTT-CGAAAATC
1 AAATTACATTTTTACCCTCGAAC-TTCAAAAATTCCATTTTTAAC-CCCAAAACTTCCAAAAATT
* * * *
31320 ATATTTTTACCCCCGAGCTTCCAAAAATTCCA-TTTTGACCGC-GAAACATCCAA
64 ACATCTTTACCCCCGAGATTCCAAAAACTCCATTTTTGACC-CTGAAACATCCAA
31373 AAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTA
1 AAATTACATTTTTACCCTCGAACTT-CAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTA
* * *
31438 CATCTTTACCCTC-AGATGTCCAAAAACTCCATTTTTGACCCTGAAACTTTCAA
65 CATCTTTACCCCCGAGAT-TCCAAAAACTCCATTTTTGACCCTGAAACATCCAA
* ** ** *
31491 AAATTGCCA-TTTTACCCTCAGATGTT-AAAAATTCCATTTTTAACCCCAAATTTTCCCAAAATT
1 AAATT-ACATTTTTACCCTC-GAACTTCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATT
31554 AC
64 AC
31556 CTTTTTGCCC
Statistics
Matches: 155, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
116 12 0.08
117 105 0.68
118 32 0.21
119 6 0.04
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (117 bp):
AAATTACATTTTTACCCTCGAACTTCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTAC
ATCTTTACCCCCGAGATTCCAAAAACTCCATTTTTGACCCTGAAACATCCAA
Found at i:31568 original size:59 final size:59
Alignment explanation
Indices: 31342--31590 Score: 215
Period size: 59 Copynumber: 4.2 Consensus size: 59
31332 CCGAGCTTCC
* * * ** * *
31342 AAAAATTCCA-TTTTGACCGCGAAACATCCAAAAATTACATTTTTACCCTC-GAACT-TCC
1 AAAAATTCCATTTTTAACCCCAAAATTTCCAAAAATTACCTTTTTACCCTCAG-A-TGTCT
* * * *
31400 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACATCTTTACCCTCAGATGTCC
1 AAAAATTCCATTTTTAACCCCAAAATTTCCAAAAATTACCTTTTTACCCTCAGATGTCT
* * * * * *
31459 AAAAACTCCATTTTTGACCCTGAAACTTT-CAAAAATTGCCATTTTACCCTCAGATGT-T
1 AAAAATTCCATTTTTAACCC-CAAAATTTCCAAAAATTACCTTTTTACCCTCAGATGTCT
* * *
31517 AAAAATTCCATTTTTAACCCCAAATTTTCCCAAAATTACCTTTTTGCCCCTCGAGA-GTCT
1 AAAAATTCCATTTTTAACCCCAAAATTTCCAAAAATTACCTTTTT-ACCCTC-AGATGTCT
31577 -AAAATTACCATTTT
1 AAAAATT-CCATTTT
31591 GTCCCCTCGG
Statistics
Matches: 159, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
57 6 0.04
58 42 0.26
59 94 0.59
60 17 0.11
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.33
Consensus pattern (59 bp):
AAAAATTCCATTTTTAACCCCAAAATTTCCAAAAATTACCTTTTTACCCTCAGATGTCT
Found at i:32666 original size:6 final size:6
Alignment explanation
Indices: 32655--32724 Score: 79
Period size: 6 Copynumber: 11.5 Consensus size: 6
32645 TGGATCAAGC
** **
32655 TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTTAAA TTT-GC TTTAAA
1 TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
32704 TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
32725 TAATGGATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
5 3 0.06
6 46 0.87
8 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:32758 original size:20 final size:19
Alignment explanation
Indices: 32733--32776 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
32723 TTTAATGGAT
* *
32733 TTAAAAACTTAATATTAAAA
1 TTAAAAACTCAA-ATAAAAA
*
32753 TTAAAAGCTCAAATAAAAA
1 TTAAAAACTCAAATAAAAA
32772 TTAAA
1 TTAAA
32777 TTAAAGTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
TTAAAAACTCAAATAAAAA
Found at i:33473 original size:15 final size:16
Alignment explanation
Indices: 33453--33482 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33443 GATAATAATA
33453 ATAA-TTTTATTAAAG
1 ATAATTTTTATTAAAG
33468 ATAATTTTTATTAAA
1 ATAATTTTTATTAAA
33483 TAATTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATAATTTTTATTAAAG
Found at i:34592 original size:30 final size:29
Alignment explanation
Indices: 34528--34950 Score: 336
Period size: 29 Copynumber: 14.5 Consensus size: 29
34518 AAACTGTTTG
*
34528 AAAATCCCATTTTTACCCCG-AACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
* * *
34556 AAAATTCTATTTTTGACCCCGAAACCTCCC
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
*
34586 AAAATTCCA-TTTTACCCC-TAACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
*
34613 AAAATTCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
*
34643 AAAAATCCATTTTTACCCTCG-AACTTCCA
1 AAAATTCCATTTTTACCC-CGAAACTTCCA
*
34672 AAAATTCCATTCTTAACCCCGAAACTTCCA
1 AAAATTCCATT-TTTACCCCGAAACTTCCA
* *
34702 AAAATTCCATTTTTAACCTCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
* *
34732 AATATTCCATTTTTACCCTCG-AACTTTCA
1 AAAATTCCATTTTTACCC-CGAAACTTCCA
* ** *
34761 AAATTTCCATTTTTGACCTTGAAACTT-CT
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
34790 AAAATTCCATTTTTACCCTC-AAA-TCTCCA
1 AAAATTCCATTTTTACCC-CGAAACT-TCCA
* * * *
34819 AAATTTCCATTTTAAACCCCAAAACTTTCA
1 AAAATTCCATTTT-TACCCCGAAACTTCCA
** * *
34849 AAAATTACCATTTTGCCCCCG-GA-TGTCTA
1 AAAATT-CCATTTTTACCCCGAAACT-TCCA
* * *
34878 AAAACTCCATTTTCGACCTCGAAAC-TCTC-
1 AAAATTCCATTTT-TACCCCGAAACTTC-CA
*
34907 AAAATTACC-TTTTTACCCTCG-AA-TGTCTA
1 AAAATT-CCATTTTTACCC-CGAAACT-TCCA
34936 AAAATTCCATTTTTA
1 AAAATTCCATTTTTA
34951 ACCCTGAATT
Statistics
Matches: 316, Mismatches: 49, Indels: 59
0.75 0.12 0.14
Matches are distributed among these distances:
27 16 0.05
28 43 0.14
29 130 0.41
30 119 0.38
31 8 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCGAAACTTCCA
Found at i:34695 original size:59 final size:59
Alignment explanation
Indices: 34528--34862 Score: 332
Period size: 59 Copynumber: 5.7 Consensus size: 59
34518 AAACTGTTTG
* * * *
34528 AAAATCCCATTTTTACCC-CGAACTTCCAAAAATTCTATTTTTGACCCCGAAACCTCCC
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* *
34586 AAAATTCCA-TTTTACCC-CTAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* * *
34643 AAAAATCCATTTTTACCCTCGAACTTCCAAAAATTCCATTCTTAACCCCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* * * *
34702 AAAATTCCATTTTTAACCTCAAAACTTCCAAATATTCCATTTTT-ACCCTCG-AACTTTCA
1 AAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGACCC-CGAAACTTCCA
* * *
34761 AAATTTCCATTTTTGA-CCTTGAAACTT-CTAAAATTCCATTTTT-ACCCTC-AAA-TCTCCA
1 AAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTGACCC-CGAAACT-TCCA
* * * *
34819 AAATTTCCATTTTAAACCC-CAAAACTTTCAAAAATTACCATTTT
1 AAAATTCCATTTT-TACCCTC-GAACTTCCAAAAATT-CCATTTT
34863 GCCCCCGGAT
Statistics
Matches: 237, Mismatches: 27, Indels: 24
0.82 0.09 0.08
Matches are distributed among these distances:
57 52 0.22
58 60 0.25
59 95 0.40
60 30 0.13
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
Found at i:34980 original size:117 final size:117
Alignment explanation
Indices: 34556--34954 Score: 304
Period size: 117 Copynumber: 3.4 Consensus size: 117
34546 CGAACTTCCA
* * * * *
34556 AAAATTCTATTTTTGACCC-CGAAACCTCCCAAAATTCCATTTT--ACCCC-TAACTTCCAAAAA
1 AAAATTCCATTTTT-ACCCTC-AAATCTCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAAA
* * * * * * *
34617 TT-CCATTTTTGACCTCGAAACT-TCCAAAAAATCCATTTT-TACCCTCG-AACTTCCA
64 TTACCA-TTTTGCCCCCG-GA-TGTCTAAAAACTCCATTTTCGA-CCTCGAAACTT-CT
* * * * *
34672 AAAATTCCATTCTTAACCC-CGAAA-CTTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAT
1 AAAATTCCATT-TTTACCCTC-AAATC-TCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAA
* * * * ** * *
34735 ATT-CCATTTTTACCCTCGAACTTTC-AAAATTTCCATTTTTGACCTTGAAACTTCT
63 ATTACCA-TTTTGCCCCCGGA-TGTCTAAAAACTCCATTTTCGACCTCGAAACTTCT
*
34790 AAAATTCCATTTTTACCCTCAAATCTCCAAAATTTCCATTTTAAACCCCAAAACTTTCAAAAATT
1 AAAATTCCATTTTTACCCTCAAATCTCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAAATT
34855 ACCATTTTGCCCCCGGATGTCTAAAAACTCCATTTTCGACCTCGAAAC-TCT
66 ACCATTTTGCCCCCGGATGTCTAAAAACTCCATTTTCGACCTCGAAACTTCT
* * * *
34906 CAAAATTACC-TTTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCC
1 -AAAATT-CCATTTTTACCCTCAAATCTCCAAAAATTCCATTTTAAACCC
34955 TGAATTTTCC
Statistics
Matches: 237, Mismatches: 32, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
115 1 0.00
116 41 0.17
117 118 0.50
118 43 0.18
119 34 0.14
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (117 bp):
AAAATTCCATTTTTACCCTCAAATCTCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAAATT
ACCATTTTGCCCCCGGATGTCTAAAAACTCCATTTTCGACCTCGAAACTTCT
Found at i:34997 original size:28 final size:28
Alignment explanation
Indices: 34964--35025 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
34954 CTGAATTTTC
*
34964 CCAAAATTACTATTTTGGCCT-CGAGAAT
1 CCAAAATTACCATTTT-GCCTCCGAGAAT
*
34992 CCAAAATTACCATTTTGCCTCCGAGTAT
1 CCAAAATTACCATTTTGCCTCCGAGAAT
35020 CCAAAA
1 CCAAAA
35026 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCTCCGAGAAT
Found at i:35871 original size:6 final size:6
Alignment explanation
Indices: 35860--35929 Score: 79
Period size: 6 Copynumber: 11.5 Consensus size: 6
35850 TGGATCAAGC
** **
35860 TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTTAAA TTT-GC TTTAAA
1 TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35909 TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
35930 TAATGGATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
5 3 0.06
6 46 0.87
8 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:35963 original size:20 final size:19
Alignment explanation
Indices: 35938--35981 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
35928 TTTAATGGAT
* *
35938 TTAAAAACTTAATATTAAAA
1 TTAAAAACTCAA-ATAAAAA
*
35958 TTAAAAGCTCAAATAAAAA
1 TTAAAAACTCAAATAAAAA
35977 TTAAA
1 TTAAA
35982 TTAAAGTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
TTAAAAACTCAAATAAAAA
Found at i:36678 original size:15 final size:16
Alignment explanation
Indices: 36658--36687 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36648 GATAATAATA
36658 ATAA-TTTTATTAAAG
1 ATAATTTTTATTAAAG
36673 ATAATTTTTATTAAA
1 ATAATTTTTATTAAA
36688 TAATTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATAATTTTTATTAAAG
Found at i:37797 original size:30 final size:29
Alignment explanation
Indices: 37733--38155 Score: 336
Period size: 29 Copynumber: 14.5 Consensus size: 29
37723 AAACTGTTTG
*
37733 AAAATCCCATTTTTACCCCG-AACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
* * *
37761 AAAATTCTATTTTTGACCCCGAAACCTCCC
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
*
37791 AAAATTCCA-TTTTACCCC-TAACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
*
37818 AAAATTCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
*
37848 AAAAATCCATTTTTACCCTCG-AACTTCCA
1 AAAATTCCATTTTTACCC-CGAAACTTCCA
*
37877 AAAATTCCATTCTTAACCCCGAAACTTCCA
1 AAAATTCCATT-TTTACCCCGAAACTTCCA
* *
37907 AAAATTCCATTTTTAACCTCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
* *
37937 AATATTCCATTTTTACCCTCG-AACTTTCA
1 AAAATTCCATTTTTACCC-CGAAACTTCCA
* ** *
37966 AAATTTCCATTTTTGACCTTGAAACTT-CT
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
37995 AAAATTCCATTTTTACCCTC-AAA-TCTCCA
1 AAAATTCCATTTTTACCC-CGAAACT-TCCA
* * * *
38024 AAATTTCCATTTTAAACCCCAAAACTTTCA
1 AAAATTCCATTTT-TACCCCGAAACTTCCA
** * *
38054 AAAATTACCATTTTGCCCCCG-GA-TGTCTA
1 AAAATT-CCATTTTTACCCCGAAACT-TCCA
* * *
38083 AAAACTCCATTTTCGACCTCGAAAC-TCTC-
1 AAAATTCCATTTT-TACCCCGAAACTTC-CA
*
38112 AAAATTACC-TTTTTACCCTCG-AA-TGTCTA
1 AAAATT-CCATTTTTACCC-CGAAACT-TCCA
38141 AAAATTCCATTTTTA
1 AAAATTCCATTTTTA
38156 ACCCTGAATT
Statistics
Matches: 316, Mismatches: 49, Indels: 59
0.75 0.12 0.14
Matches are distributed among these distances:
27 16 0.05
28 43 0.14
29 130 0.41
30 119 0.38
31 8 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCGAAACTTCCA
Found at i:37900 original size:59 final size:59
Alignment explanation
Indices: 37733--38067 Score: 332
Period size: 59 Copynumber: 5.7 Consensus size: 59
37723 AAACTGTTTG
* * * *
37733 AAAATCCCATTTTTACCC-CGAACTTCCAAAAATTCTATTTTTGACCCCGAAACCTCCC
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* *
37791 AAAATTCCA-TTTTACCC-CTAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* * *
37848 AAAAATCCATTTTTACCCTCGAACTTCCAAAAATTCCATTCTTAACCCCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* * * *
37907 AAAATTCCATTTTTAACCTCAAAACTTCCAAATATTCCATTTTT-ACCCTCG-AACTTTCA
1 AAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGACCC-CGAAACTTCCA
* * *
37966 AAATTTCCATTTTTGA-CCTTGAAACTT-CTAAAATTCCATTTTT-ACCCTC-AAA-TCTCCA
1 AAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTGACCC-CGAAACT-TCCA
* * * *
38024 AAATTTCCATTTTAAACCC-CAAAACTTTCAAAAATTACCATTTT
1 AAAATTCCATTTT-TACCCTC-GAACTTCCAAAAATT-CCATTTT
38068 GCCCCCGGAT
Statistics
Matches: 237, Mismatches: 27, Indels: 24
0.82 0.09 0.08
Matches are distributed among these distances:
57 52 0.22
58 60 0.25
59 95 0.40
60 30 0.13
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
Found at i:38185 original size:117 final size:117
Alignment explanation
Indices: 37761--38159 Score: 304
Period size: 117 Copynumber: 3.4 Consensus size: 117
37751 CGAACTTCCA
* * * * *
37761 AAAATTCTATTTTTGACCC-CGAAACCTCCCAAAATTCCATTTT--ACCCC-TAACTTCCAAAAA
1 AAAATTCCATTTTT-ACCCTC-AAATCTCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAAA
* * * * * * *
37822 TT-CCATTTTTGACCTCGAAACT-TCCAAAAAATCCATTTT-TACCCTCG-AACTTCCA
64 TTACCA-TTTTGCCCCCG-GA-TGTCTAAAAACTCCATTTTCGA-CCTCGAAACTT-CT
* * * * *
37877 AAAATTCCATTCTTAACCC-CGAAA-CTTCCAAAAATTCCATTTTTAACCTCAAAACTTCCAAAT
1 AAAATTCCATT-TTTACCCTC-AAATC-TCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAA
* * * * ** * *
37940 ATT-CCATTTTTACCCTCGAACTTTC-AAAATTTCCATTTTTGACCTTGAAACTTCT
63 ATTACCA-TTTTGCCCCCGGA-TGTCTAAAAACTCCATTTTCGACCTCGAAACTTCT
*
37995 AAAATTCCATTTTTACCCTCAAATCTCCAAAATTTCCATTTTAAACCCCAAAACTTTCAAAAATT
1 AAAATTCCATTTTTACCCTCAAATCTCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAAATT
38060 ACCATTTTGCCCCCGGATGTCTAAAAACTCCATTTTCGACCTCGAAAC-TCT
66 ACCATTTTGCCCCCGGATGTCTAAAAACTCCATTTTCGACCTCGAAACTTCT
* * * *
38111 CAAAATTACC-TTTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCC
1 -AAAATT-CCATTTTTACCCTCAAATCTCCAAAAATTCCATTTTAAACCC
38160 TGAATTTTCC
Statistics
Matches: 237, Mismatches: 32, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
115 1 0.00
116 41 0.17
117 118 0.50
118 43 0.18
119 34 0.14
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (117 bp):
AAAATTCCATTTTTACCCTCAAATCTCCAAAAATTCCATTTTAAACCCCAAAACTTTCAAAAATT
ACCATTTTGCCCCCGGATGTCTAAAAACTCCATTTTCGACCTCGAAACTTCT
Found at i:38202 original size:28 final size:28
Alignment explanation
Indices: 38169--38230 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
38159 CTGAATTTTC
*
38169 CCAAAATTACTATTTTGGCCT-CGAGAAT
1 CCAAAATTACCATTTT-GCCTCCGAGAAT
*
38197 CCAAAATTACCATTTTGCCTCCGAGTAT
1 CCAAAATTACCATTTTGCCTCCGAGAAT
38225 CCAAAA
1 CCAAAA
38231 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCTCCGAGAAT
Found at i:42498 original size:22 final size:23
Alignment explanation
Indices: 42457--42507 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
42447 CCTAAACAAA
*
42457 TAGAGGA-AAAATACAGACGAT-
1 TAGAGGAGAAAATACACACGATG
42478 TAGAGGAGAAAAT-CGACACGATG
1 TAGAGGAGAAAATAC-ACACGATG
42501 TA-AGGAG
1 TAGAGGAG
42508 TTGAAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.47, C:0.10, G:0.29, T:0.14
Consensus pattern (23 bp):
TAGAGGAGAAAATACACACGATG
Found at i:51535 original size:22 final size:23
Alignment explanation
Indices: 51494--51544 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
51484 CCTAAACAAA
*
51494 TAGAGGA-AAAATACAGACGAT-
1 TAGAGGAGAAAATACACACGATG
51515 TAGAGGAGAAAAT-CGACACGATG
1 TAGAGGAGAAAATAC-ACACGATG
51538 TA-AGGAG
1 TAGAGGAG
51545 TTGAAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.47, C:0.10, G:0.29, T:0.14
Consensus pattern (23 bp):
TAGAGGAGAAAATACACACGATG
Found at i:59072 original size:110 final size:112
Alignment explanation
Indices: 58939--59195 Score: 272
Period size: 115 Copynumber: 2.3 Consensus size: 112
58929 ATGCGATCAT
* * **
58939 CTTCCTGATGAGATATTGAGAAGTAGACCAAATCAATGAAACGA-G-GCTCAAAGC-G-AGCAAA
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATC-AGGAAACGATGTGAGCAAAGCTGAAGCAAA
* * *
59000 TCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG-ACATAAAATGGTTAG
65 GCTTCCTGATGAGATACTGAGAAGCAAGACGAAGCA-ATAAAAT-GTTAG
* * * *** * * **
59049 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGAGCAAATCTTTGAATCCC
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAGGAAACGATGTGAGCAAAGC--TGAAGCAA
59114 AGCTTCCTGATGAGATACTGAGAAGCAAGACGAAGCAATAAAATGTTAG
64 AGCTTCCTGATGAGATACTGAGAAGCAAGACGAAGCAATAAAATGTTAG
*
59163 CTTCCTGATGAGATACTGAGAAGTGGACCAAAT
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAAT
59196 TCGTCTTCCT
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
109 5 0.04
110 31 0.26
111 6 0.05
114 35 0.29
115 41 0.34
116 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (112 bp):
CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAGGAAACGATGTGAGCAAAGCTGAAGCAAAG
CTTCCTGATGAGATACTGAGAAGCAAGACGAAGCAATAAAATGTTAG
Found at i:59355 original size:205 final size:205
Alignment explanation
Indices: 59086--59473 Score: 695
Period size: 205 Copynumber: 1.9 Consensus size: 205
59076 CCAACTCAGG
* * * *
59086 GCTCGATGTGAGCAAATCTTTGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAAGACGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGACACACTGAGAAGCAAGACGAAGCA
*
59151 ATAAAATGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC
59216 AGAGAAGCGGATTAAAGCAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGGATTAAAGCAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
59281 TCAAACCCAC
196 TCAAACCCAC
* * * *
59291 GCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTGATGACACACTGAGCAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGACACACTGAGAAGCAAGACGAAGCA
59356 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC
59421 AGAGAAGCGGATTAAAGCAAACGACGCGGTCATCTTCCTGATGAGATACTGAG
131 AGAGAAGCGGATTAAAGCAAACGACGCGGTCATCTTCCTGATGAGATACTGAG
59474 NNNNNNNNNN
Statistics
Matches: 174, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
205 174 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (205 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGACACACTGAGAAGCAAGACGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC
AGAGAAGCGGATTAAAGCAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:66970 original size:110 final size:112
Alignment explanation
Indices: 66837--67093 Score: 272
Period size: 115 Copynumber: 2.3 Consensus size: 112
66827 ATGCGATCAT
* * **
66837 CTTCCTGATGAGATATTGAGAAGTAGACCAAATCAATGAAACGA-G-GCTCAAAGC-G-AGCAAA
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATC-AGGAAACGATGTGAGCAAAGCTGAAGCAAA
* * *
66898 TCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG-ACATAAAATGGTTAG
65 GCTTCCTGATGAGATACTGAGAAGCAAGACGAAGCA-ATAAAAT-GTTAG
* * * *** * * **
66947 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGAGCAAATCTTTGAATCCC
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAGGAAACGATGTGAGCAAAGC--TGAAGCAA
67012 AGCTTCCTGATGAGATACTGAGAAGCAAGACGAAGCAATAAAATGTTAG
64 AGCTTCCTGATGAGATACTGAGAAGCAAGACGAAGCAATAAAATGTTAG
*
67061 CTTCCTGATGAGATACTGAGAAGTGGACCAAAT
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAAT
67094 TCGTCTTCCT
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
109 5 0.04
110 31 0.26
111 6 0.05
114 35 0.29
115 41 0.34
116 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (112 bp):
CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAGGAAACGATGTGAGCAAAGCTGAAGCAAAG
CTTCCTGATGAGATACTGAGAAGCAAGACGAAGCAATAAAATGTTAG
Found at i:67760 original size:6 final size:6
Alignment explanation
Indices: 67739--67801 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
67729 TTTAAATTGG
** **
67739 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
67785 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
67802 TCAAATTTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
4 2 0.04
5 5 0.11
6 36 0.80
7 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:67774 original size:17 final size:17
Alignment explanation
Indices: 67739--67800 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
67729 TTTAAATTGG
*
67739 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TCTTAAA
67757 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
67774 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATC-TTAAA
67791 TTTAAATTTA
1 TTTAAATTTA
67801 ATCAAATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.03
17 29 0.73
18 10 0.25
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:68934 original size:30 final size:28
Alignment explanation
Indices: 68890--69234 Score: 275
Period size: 30 Copynumber: 11.8 Consensus size: 28
68880 GAAGGTCTCT
* *
68890 AAACTATCCGAAAATCCCATTTTTACCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCC
* * *
68919 TGAACTTCCAAAAAATACATTTTTGACCCC
1 -AAACTTCCAAAAATTCCATTTTT-ACCCC
* * * *
68949 TAAACCTCCCAAAATTCTATTTTTACCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCC
* *
68978 GAACTTCCAAAAATTCCATTTTTGAACCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCC
* *
69007 AAATCTT-CAAAACAATCTATTTTTACCCCC
1 AAA-CTTCCAAAA-ATTCCATTTTTA-CCCC
* *
69037 GAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACC-CC
** * *
69067 AAACTTCCAAAAATTAAAATTTTGACCTCG
1 AAACTTCCAAAAATT-CCATTTTTACC-CC
*
69097 AAACTT-AAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCC-C
69125 AAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCC
* * *
69154 AAAAGTTCCAAAAGTTCCATTTTTAACCTCA
1 -AAACTTCCAAAAATTCCATTTTT-ACC-CC
69185 AAACTTCCAAAAATTCCA-TTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
*
69212 TAAA-TCTCCAAAATTTCCATTTT
1 -AAACT-TCCAAAAATTCCATTTT
69235 AACCTTGAAA
Statistics
Matches: 254, Mismatches: 44, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.01
28 51 0.20
29 73 0.29
30 121 0.48
31 6 0.02
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTTACCCC
Found at i:69130 original size:88 final size:87
Alignment explanation
Indices: 68921--69264 Score: 335
Period size: 88 Copynumber: 3.9 Consensus size: 87
68911 TTTACCCCTG
* * * *
68921 AACTTCCAAAAAATACATTTTTGACCCCTAAACCTCCCAAAATTCTATTTTT-ACCTCG-AACTT
1 AACTT-CAAAAAATCCATTTTT-ACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTT
*
68984 CCAAAAATTCCATTTTTGAACC-CA
64 CCAAAAATTACATTTTTG-ACCTCA
* **
69008 AATCTTCAAAACAATCTATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTT
1 AA-CTTCAAAA-AATCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTT
* *
69073 CCAAAAATTAAAATTTTGACCTCGA
64 CCAAAAATTACATTTTTGACCTC-A
* * *
69098 AACTT-AAAAAATTCCATTTTTA-CCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAAGTT
1 AACTTCAAAAAA-TCCATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTT
* * *
69161 CCAAAAGTTCCATTTTTAACCTCAA
64 CCAAAAATTACATTTTTGACCTC-A
* * * *
69186 AACTTCCAAAAATTCCA-TTTTACCCCTAAA-TCTCCAAAATTTCCA-TTTTAACCTTGAAACTT
1 AACTT-CAAAAAATCCATTTTTACCCCTAAACT-TCCAAAAATTCCATTTTTGACCTCGAAACTT
*
69248 TCAAAAATTATCATTTT
64 CCAAAAATTA-CATTTT
69265 GCCCCCGGAT
Statistics
Matches: 212, Mismatches: 32, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
87 56 0.26
88 116 0.55
89 32 0.15
90 8 0.04
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (87 bp):
AACTTCAAAAAATCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
AAAAATTACATTTTTGACCTCA
Found at i:69263 original size:58 final size:59
Alignment explanation
Indices: 68890--69386 Score: 263
Period size: 58 Copynumber: 8.5 Consensus size: 59
68880 GAAGGTCTCT
* * * ** * * * * *
68890 AAACTATCCGAAAATCCCATTTTTACCCCTGAA-CTTCCAAAAAATACATTTTTGACCCCT
1 AAACT-TCCAAAAATTCCATTTTGACCCCAAAATC-TCCAAAAATTCCATTTTTAACCTCG
* * * * * * *
68950 AAACCTCCCAAAATTCTATTTTTACCTCGAACT-TCCAAAAATTCCATTTTTGAACC-C-
1 AAACTTCCAAAAATTCCATTTTGACCCCAAAATCTCCAAAAATTCCATTTTT-AACCTCG
* * * ** *
69007 AAATCTT-CAAAACAATCTATTTTTACCCCCGAA-CTTCCAAAAATTCCATTTTTGACCTCG
1 AAA-CTTCCAAAA-ATTCCATTTTGACCCCAAAATC-TCCAAAAATTCCATTTTTAACCTCG
** * * ** *
69067 AAACTTCCAAAAATTAAAATTTTGACCTCGAAA-CTTAAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATT-CCATTTTGACCCCAAAATCTCCAAAAATTCCATTTTTAACCTCG
* *
69125 AAACTTCCAAAAATTCCATTTTTGACCCCAAAAGT-TCCAAAAGTTCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCAAAA-TCTCCAAAAATTCCATTTTTAACCTCG
* * *
69185 AAACTTCCAAAAATTCCATTTT-ACCCCTAAATCTCCAAAATTTCCA-TTTTAACCTTG
1 AAACTTCCAAAAATTCCATTTTGACCCCAAAATCTCCAAAAATTCCATTTTTAACCTCG
* * *** * * **
69242 AAACTTTCAAAAATTATCATTTTG-CCCCCGGATGTCCAAAAACTCCATTTTCGACCTCG
1 AAACTTCCAAAAATT-CCATTTTGACCCCAAAATCTCCAAAAATTCCATTTTTAACCTCG
** * * * * *
69301 AAAC-TCTTAAAATTACCCTTTT-ACCCTC-GAATGT-CTAAAATTCCATTTTTAACC-CC
1 AAACTTCCAAAAATT-CCATTTTGACCC-CAAAATCTCCAAAAATTCCATTTTTAACCTCG
* * *
69357 AAATTTTCACAAAATTACCATTTTGTCCCC
1 AAACTTCCA-AAAATT-CCATTTTGACCCC
69387 GAGAATCCAA
Statistics
Matches: 344, Mismatches: 70, Indels: 48
0.74 0.15 0.10
Matches are distributed among these distances:
56 4 0.01
57 49 0.14
58 142 0.41
59 107 0.31
60 42 0.12
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTGACCCCAAAATCTCCAAAAATTCCATTTTTAACCTCG
Done.