Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold475
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: 172351
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 2183 characters in sequence are not A, C, G, or T
Found at i:2939 original size:13 final size:13
Alignment explanation
Indices: 2921--2945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2911 TATATGCAAA
2921 TTTTGTGTATTTT
1 TTTTGTGTATTTT
2934 TTTTGTGTATTT
1 TTTTGTGTATTT
2946 GTGTTTTATG
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:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (13 bp):
TTTTGTGTATTTT
Found at i:3441 original size:43 final size:43
Alignment explanation
Indices: 3380--3542 Score: 222
Period size: 43 Copynumber: 3.8 Consensus size: 43
3370 TTTCTAACAA
3380 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
*
3423 GTGTTTTCGTGTAAGACCACGTCTGAGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
* *
3466 GTGTTTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATTGATTT
1 GTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACTT
* * * * *
3509 GTGATTACATGTAAGACCACGTCTAGGACATTGG
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGG
3543 TATTGTATGA
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
42 1 0.01
43 104 0.97
44 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (43 bp):
GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
Found at i:5831 original size:63 final size:63
Alignment explanation
Indices: 5696--5816 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 63
5686 AAGGGAAGCA
* * * **
5696 TGCTTGAAAACGCATTTCAGAATACGCATTTTCATCGAATAATAATAATGAAAGCTTCAGAGG
1 TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTCAGAGG
* *
5759 TGCTTGAAAATGCATTTCAGCAGACACATTTTCATCAAATAATAATAATGAAAGAGTC
1 TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTC
5817 TTCTGTGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (63 bp):
TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTCAGAGG
Found at i:7620 original size:51 final size:51
Alignment explanation
Indices: 7537--7653 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
7527 CGGATCACAT
*
7537 TTATCACTTGTCACTTGTCACTGATCCAATAAGTGTACCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTAATCCAATAAGTGTACCTAAAGCTACCAC
* *
7588 TTATCACTTATCACTTGTCACTAAT-CAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTAATCCA-ATAAGTGTACCTAAAGCTACCAC
7639 TTATCACTTGTCACT
1 TTATCACTTGTCACT
7654 GATCAGAAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 2 0.03
51 59 0.97
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTAATCCAATAAGTGTACCTAAAGCTACCAC
Found at i:14858 original size:18 final size:18
Alignment explanation
Indices: 14822--14865 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
14812 CATTAAAAAC
*
14822 TTTGGTAAAGTGACAAAT
1 TTTGGTAAAGTAACAAAT
14840 TTTGGTAAAGGTAAC-AAT
1 TTTGGTAAA-GTAACAAAT
*
14858 TTTAGTAA
1 TTTGGTAA
14866 TTGTTAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (18 bp):
TTTGGTAAAGTAACAAAT
Found at i:15040 original size:40 final size:38
Alignment explanation
Indices: 14913--15119 Score: 136
Period size: 40 Copynumber: 5.2 Consensus size: 38
14903 TATCTTATAA
* *
14913 ATTTTGGTAAAGT-TTTATAAATATTGATAATCGATAGAA
1 ATTTTGGTAAA-TCTTTAAAAATATTGATAATCG-TAGAT
*
14952 ATTTTGGTAAATCTTTAAAAAAAATTG-TAAAT-GTTAGAT
1 ATTTTGGTAAATCTTT-AAAAATATTGAT-AATCG-TAGAT
** **
14991 ATAATGGTAAATCTTTGGAAATATTGAATAATCGTCAGAT
1 ATTTTGGTAAATCTTTAAAAATATTG-ATAATCGT-AGAT
*
15031 ATTTTGGTAAAT-TCTTAAAAATTTTGATAAATCGTTAGAT
1 ATTTTGGTAAATCT-TTAAAAATATTGAT-AATCG-TAGAT
* ** * * *
15071 ATATTAATAAATCGTTAAATATATT-AGTAAGTCCTTAGAT
1 ATTTTGGTAAATCTTTAAAAATATTGA-TAA-T-CGTAGAT
15111 ATTTTGGTA
1 ATTTTGGTA
15120 GAGTCATAGA
Statistics
Matches: 130, Mismatches: 24, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
38 8 0.06
39 44 0.34
40 76 0.58
41 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (38 bp):
ATTTTGGTAAATCTTTAAAAATATTGATAATCGTAGAT
Found at i:15080 original size:20 final size:20
Alignment explanation
Indices: 15057--15112 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
15047 AAAAATTTTG
15057 ATAAATCGTTAGATATATTA
1 ATAAATCGTTAGATATATTA
*
15077 ATAAATCGTTAAATATATTA
1 ATAAATCGTTAGATATATTA
* * *
15097 GTAAGTCCTTAGATAT
1 ATAAATCGTTAGATAT
15113 TTTGGTAGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
ATAAATCGTTAGATATATTA
Found at i:15239 original size:20 final size:20
Alignment explanation
Indices: 15195--15350 Score: 141
Period size: 20 Copynumber: 7.8 Consensus size: 20
15185 TAAAAACTTG
* * *
15195 GAAATTTTGGTAAAGTCTCA
1 GAAATTTTGGTAAATTGTTA
* * *
15215 TAAATATTGGTAAATTGATA
1 GAAATTTTGGTAAATTGTTA
* ***
15235 GAAATTTTAGTAAAACATTA
1 GAAATTTTGGTAAATTGTTA
15255 GAAATTTTGGTAAATTGTTA
1 GAAATTTTGGTAAATTGTTA
* * * *
15275 GATATCTTGATAAATTCTTA
1 GAAATTTTGGTAAATTGTTA
*
15295 GAAATTTTGATAAATTGTTA
1 GAAATTTTGGTAAATTGTTA
* *
15315 GATATATTGGTAAATTGTTA
1 GAAATTTTGGTAAATTGTTA
* *
15335 GATATTTTGATAAATT
1 GAAATTTTGGTAAATT
15351 CTTTAAAATA
Statistics
Matches: 107, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 107 1.00
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (20 bp):
GAAATTTTGGTAAATTGTTA
Found at i:15289 original size:60 final size:58
Alignment explanation
Indices: 15173--15351 Score: 169
Period size: 60 Copynumber: 3.0 Consensus size: 58
15163 TTAGAAAATT
* * * * * * * *
15173 TAGAAATATTTGTAAAAACTTGGAAATTTTGGTAAAGTCTCATAAATATTGGTAAATTGA
1 TAGAAAT-TTTGTAAAAA-TTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTCA
* *
15233 TAGAAATTTTAGTAAAACATTAGAAATTTTGGTAAATTGTTAGATATCTTGATAAATTCT
1 TAGAAATTTT-GTAAAA-ATTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTCA
** * * *
15293 TAGAAATTTTGATAAATTGTTAGATATATTGGTAAATTGTTAGATATTTTGATAAATTC
1 TAGAAATTTTG-TAAA-AATTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTC
15352 TTTAAAATAC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.04
60 95 0.95
61 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (58 bp):
TAGAAATTTTGTAAAAATTAGAAATTTTGGTAAATTGTTAGATATATTGATAAATTCA
Found at i:15408 original size:20 final size:20
Alignment explanation
Indices: 15221--15548 Score: 171
Period size: 20 Copynumber: 16.4 Consensus size: 20
15211 CTCATAAATA
* * *
15221 TTGGTAAATTGATAGAAATT
1 TTGGTAAATCGTTAGATATT
* * * *
15241 TTAGTAAAACATTAGAAATT
1 TTGGTAAATCGTTAGATATT
* *
15261 TTGGTAAATTGTTAGATATC
1 TTGGTAAATCGTTAGATATT
* *
15281 TTGATAAATTC-TTAGAAATT
1 TTGGTAAA-TCGTTAGATATT
* * *
15301 TTGATAAATTGTTAGATATA
1 TTGGTAAATCGTTAGATATT
*
15321 TTGGTAAATTGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* * * *
15341 TTGATAAATTCTTTA-AAATA
1 TTGGTAAA-TCGTTAGATATT
* * * *
15361 CTGGTAAACCGTTATATATA
1 TTGGTAAATCGTTAGATATT
**
15381 TTATTAAATCGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* *
15401 TTGGTAAACCGATAG-T-TT
1 TTGGTAAATCGTTAGATATT
* * *
15419 TCCTCGAAAATCGATAGATATTT
1 T--TGGTAAATCGTTAGATA-TT
* * * *
15442 TTGATAAATCCTTAGAAATA
1 TTGGTAAATCGTTAGATATT
* * * *
15462 TTAGCAAGTCGTTAGATATA
1 TTGGTAAATCGTTAGATATT
* * *
15482 TTGGTAAATCCTTAAATTTT
1 TTGGTAAATCGTTAGATATT
*
15502 TTGATAAATCGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* *
15522 TTGGTAAAGTC-ATAGAAATT
1 TTGGTAAA-TCGTTAGATATT
15542 TTGGTAA
1 TTGGTAA
15549 TTGTTAAGAC
Statistics
Matches: 228, Mismatches: 70, Indels: 20
0.72 0.22 0.06
Matches are distributed among these distances:
18 3 0.01
19 6 0.03
20 197 0.86
21 19 0.08
23 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (20 bp):
TTGGTAAATCGTTAGATATT
Found at i:15635 original size:20 final size:20
Alignment explanation
Indices: 15612--15693 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
15602 CTAAATATTA
15612 GTAAAACGATAGAAATTTTG
1 GTAAAACGATAGAAATTTTG
** *
15632 GTAACTC-ATTAGACATTTTG
1 GTAAAACGA-TAGAAATTTTG
* **
15652 GTAAATCTTTAGAAATTTTG
1 GTAAAACGATAGAAATTTTG
* * *
15672 GTAAGATGATAAAAATTTTG
1 GTAAAACGATAGAAATTTTG
15692 GT
1 GT
15694 GTTTGTCAAG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.02
20 47 0.98
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (20 bp):
GTAAAACGATAGAAATTTTG
Found at i:15811 original size:20 final size:20
Alignment explanation
Indices: 15788--15904 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
15778 AGTAAATAGA
* *
15788 TAGAAATTTTGGTAACTTAT
1 TAGAAATTTTGGTAAATCAT
* * *
15808 TAGATATTTTGATAAATCCT
1 TAGAAATTTTGGTAAATCAT
* *
15828 TAGAAATATTGGTAAATCGT
1 TAGAAATTTTGGTAAATCAT
* *
15848 TAGATATATTGGTAAATGC-T
1 TAGAAATTTTGGTAAAT-CAT
* *
15868 TATAAATTTTGATAAAGTC-T
1 TAGAAATTTTGGTAAA-TCAT
* *
15888 TATAAATATTGGTAAAT
1 TAGAAATTTTGGTAAAT
15905 TGATATATTT
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.01
20 76 0.96
21 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
TAGAAATTTTGGTAAATCAT
Found at i:15843 original size:60 final size:60
Alignment explanation
Indices: 15731--15909 Score: 166
Period size: 60 Copynumber: 3.0 Consensus size: 60
15721 GAAAATTTAA
* * * * *
15731 AAATATCGGTAAAATCA-TAGAAATTTTGGTAAAGT-TTCATAAATATTAGTAAATAGATAG
1 AAATATTGGT-AAATGATTAGAAATTTTGATAAAGTCTT-AGAAATATTGGTAAATAGATAG
* * * * * *
15791 AAATTTTGGTAACTTATTAGATATTTTGATAAA-TCCTTAGAAATATTGGTAAATCGTTAG
1 AAATATTGGTAAATGATTAGAAATTTTGATAAAGT-CTTAGAAATATTGGTAAATAGATAG
* * * * *
15851 ATATATTGGTAAATGCTTATAAATTTTGATAAAGTCTTATAAATATTGGTAAATTGATA
1 AAATATTGGTAAATGATTAGAAATTTTGATAAAGTCTTAGAAATATTGGTAAATAGATA
15910 TATTTGTTTA
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
59 5 0.05
60 87 0.92
61 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (60 bp):
AAATATTGGTAAATGATTAGAAATTTTGATAAAGTCTTAGAAATATTGGTAAATAGATAG
Found at i:15851 original size:40 final size:40
Alignment explanation
Indices: 15788--15883 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
15778 AGTAAATAGA
* * *
15788 TAGAAATTTTGGTAACTTATTAGATATTTTGATAAATCCT
1 TAGAAATTTTGGTAAATCATTAGATATATTGATAAATCCT
* * * *
15828 TAGAAATATTGGTAAATCGTTAGATATATTGGTAAATGCT
1 TAGAAATTTTGGTAAATCATTAGATATATTGATAAATCCT
* *
15868 TATAAATTTTGATAAA
1 TAGAAATTTTGGTAAA
15884 GTCTTATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.42
Consensus pattern (40 bp):
TAGAAATTTTGGTAAATCATTAGATATATTGATAAATCCT
Found at i:22261 original size:46 final size:46
Alignment explanation
Indices: 22193--22439 Score: 367
Period size: 46 Copynumber: 5.5 Consensus size: 46
22183 TGATCAGTGA
22193 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
22239 CAAGTGACAAAGTGATAGGTGGTAGCTTTAGCTACACTTATCTAAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
22285 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATTTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
22330 CAAGTGACAAAGTGAGAAGTGGTAGCTTTAGCTACTCTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* * * *
22376 CAAGTGACAAAGTGATAAGTGGTAGC-CTAACTACATTTATCTAAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
22421 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
22440 ATCATACGTA
Statistics
Matches: 183, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
43 12 0.07
44 5 0.03
45 56 0.31
46 110 0.60
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:22352 original size:91 final size:91
Alignment explanation
Indices: 22193--22439 Score: 372
Period size: 91 Copynumber: 2.7 Consensus size: 91
22183 TGATCAGTGA
* * *
22193 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAGG
1 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATCAAGTGACAAAGTGAGAAG
22258 TGGTAGCTTTAGCTACACTTATCTAAT
65 TGGTAGCTTTAGCTACACTTATCTAAT
*
22285 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATTTGATCAAGTGACAAAGTGAGAAGT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGAGAAGT
* *
22350 GGTAGCTTTAGCTACTCTTATCTGAT
66 GGTAGCTTTAGCTACACTTATCTAAT
* * * * *
22376 CAAGTGACAAAGTGATAAGTGGTAGCCTAACTACATTTATCTAATC-AGGGAC-AAGTGATAAGT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGAGAAGT
22439 G
66 G
22440 ATCATACGTA
Statistics
Matches: 143, Mismatches: 12, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
89 11 0.08
90 5 0.03
91 101 0.71
92 26 0.18
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (91 bp):
CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGAGAAGT
GGTAGCTTTAGCTACACTTATCTAAT
Found at i:22486 original size:137 final size:136
Alignment explanation
Indices: 22193--22441 Score: 369
Period size: 137 Copynumber: 1.8 Consensus size: 136
22183 TGATCAGTGA
* *
22193 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAGG
1 CAAGTGACAAAGTGAGAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
* * * * * *
22258 TGGTAGCTTTAGCTACACTTATCTAATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTT
66 TGGTAGCTCTAACTACACTTATCTAATCAAGGGACAAAGTGATAAGTGATAACCTAGC-ACACAT
*
22323 ATTTGAT
130 AGTTGAT
*
22330 CAAGTGACAAAGTGAGAAGTGGTAGCTTTAGCTACTCTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGAGAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
*
22395 TGGTAGC-CTAACTACATTTATCTAATC-AGGGAC-AAGTGATAAGTGAT
66 TGGTAGCTCTAACTACACTTATCTAATCAAGGGACAAAGTGATAAGTGAT
22442 CATACGTAAG
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
134 13 0.12
135 5 0.05
136 17 0.16
137 69 0.66
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (136 bp):
CAAGTGACAAAGTGAGAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
TGGTAGCTCTAACTACACTTATCTAATCAAGGGACAAAGTGATAAGTGATAACCTAGCACACATA
GTTGAT
Found at i:24565 original size:17 final size:17
Alignment explanation
Indices: 24543--24583 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
24533 AATCATAATT
24543 ATTTAATGTATAACCAA
1 ATTTAATGTATAACCAA
24560 ATTTAATGTATAACCAA
1 ATTTAATGTATAACCAA
24577 ATTTAAT
1 ATTTAAT
24584 TCCATGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (17 bp):
ATTTAATGTATAACCAA
Found at i:25287 original size:95 final size:91
Alignment explanation
Indices: 25056--25271 Score: 279
Period size: 91 Copynumber: 2.3 Consensus size: 91
25046 TGAACATTTC
* * *
25056 AGTTTGTGGATGAACCACCAGTGTTTGTAGGTTAATACGCTGCTAGTAGGTTATGAATGCACAAC
1 AGTTTGTGGATGAACCACCAGTGTTTGCAGGTTAATACGTTGCCAGTAGGTTATGAATGCACAAC
* * *
25121 CTCTTTGCACATAAAAGTTGTCAGTA
66 CTATTTGCACATAAAAGCTGCCAGTA
* * * *
25147 AGTTTATGGATGAACCACTAGCGTTTGCAGGTTAATACGTTGCCAGTAGGTTGTGAATGCACAGC
1 AGTTTGTGGATGAACCACCAGTGTTTGCAGGTTAATACGTTGCCAGTAGGTTATGAATG--CA-C
* *
25212 ATACGTATTTGCAGATAAAAGCTGCCAGTA
63 A-ACCTATTTGCACATAAAAGCTGCCAGTA
*
25242 AGTTTGTGGATAAACCACCAGTGTTTGCAG
1 AGTTTGTGGATGAACCACCAGTGTTTGCAG
25272 ATTGTTAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
91 52 0.50
93 2 0.02
94 2 0.02
95 49 0.47
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (91 bp):
AGTTTGTGGATGAACCACCAGTGTTTGCAGGTTAATACGTTGCCAGTAGGTTATGAATGCACAAC
CTATTTGCACATAAAAGCTGCCAGTA
Found at i:25479 original size:38 final size:38
Alignment explanation
Indices: 25360--25485 Score: 128
Period size: 38 Copynumber: 3.3 Consensus size: 38
25350 TACATAAAAC
* ** *
25360 AGTAGACATGCTTTAATATGTATTATGTTCAACAATAAT
1 AGTAGACATGC-TTAACATGTATTCGGTTCAACAGTAAT
* * **
25399 AGTAAACATGCTTAACATGTA-TCTGGTTCAATAGTAGC
1 AGTAGACATGCTTAACATGTATTC-GGTTCAACAGTAAT
* *
25437 AGTAGACATGCTTAACATGTATTCGGTTCCACGGTAAT
1 AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAT
*
25475 AGTAGGCATGC
1 AGTAGACATGC
25486 AATCGATAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
37 1 0.01
38 57 0.81
39 12 0.17
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCGGTTCAACAGTAAT
Found at i:29057 original size:7 final size:7
Alignment explanation
Indices: 29034--29073 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
29024 TTACTCCATA
29034 TTTTTAT
1 TTTTTAT
*
29041 TTTTAAAT
1 TTTT-TAT
29049 TTTTTAT
1 TTTTTAT
29056 TTTTTAT
1 TTTTTAT
29063 TTTTTAT
1 TTTTTAT
29070 TTTT
1 TTTT
29074 CGAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:29584 original size:29 final size:28
Alignment explanation
Indices: 29551--29608 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
29541 TTTTTAAGAT
*
29551 TTACATCAACATTTTATTTCAAAAAAAAA
1 TTACATCAACATTTTA-ATCAAAAAAAAA
* *
29580 TTACATCAATATTTTAATCAAAATAAAA
1 TTACATCAACATTTTAATCAAAAAAAAA
29608 T
1 T
29609 ATTTGAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (28 bp):
TTACATCAACATTTTAATCAAAAAAAAA
Found at i:33360 original size:52 final size:52
Alignment explanation
Indices: 33303--33406 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
33293 ATAAATAAGA
33303 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
1 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
33355 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
1 GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
33407 ACCCATACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
GGATAATGAGTTTCAATGCACTCGAACTCACATCCCCTGTATTGACAACAAT
Found at i:33763 original size:31 final size:30
Alignment explanation
Indices: 33724--33787 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
33714 TTTTCATAAA
*
33724 TTTAGAATTTAGT-CTTTGTACTTTTTTATT
1 TTTAGAATTTAGTCCTTT-TACTTTTTTAGT
*
33754 TTTAGGAATTTTGTCCTTTTACTTTTTTAGT
1 TTTA-GAATTTAGTCCTTTTACTTTTTTAGT
33785 TTT
1 TTT
33788 CAAAATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 4 0.13
31 22 0.73
32 4 0.13
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (30 bp):
TTTAGAATTTAGTCCTTTTACTTTTTTAGT
Found at i:38363 original size:10 final size:10
Alignment explanation
Indices: 38345--38385 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
38335 AAATATTTAA
38345 AATAATTTTT
1 AATAATTTTT
38355 -ATAATTTTT
1 AATAATTTTT
38364 AATAA-TTTT
1 AATAATTTTT
*
38373 AATGATTTTT
1 AATAATTTTT
38383 AAT
1 AAT
38386 TTTTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 17 0.61
10 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
AATAATTTTT
Found at i:38367 original size:19 final size:19
Alignment explanation
Indices: 38345--38385 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
38335 AAATATTTAA
*
38345 AATAATTTTTATAATTTTT
1 AATAATTTTAATAATTTTT
*
38364 AATAATTTTAATGATTTTT
1 AATAATTTTAATAATTTTT
38383 AAT
1 AAT
38386 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
AATAATTTTAATAATTTTT
Found at i:40659 original size:21 final size:21
Alignment explanation
Indices: 40614--40660 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40604 TATATCTCTC
*
40614 GCAAAAATATTAATAATAATG
1 GCAAAAATATTAATAATAATA
*
40635 GCAAGAATATTAATAACTAA-A
1 GCAAAAATATTAATAA-TAATA
40656 GCAAA
1 GCAAA
40661 TTAATAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (21 bp):
GCAAAAATATTAATAATAATA
Found at i:50430 original size:24 final size:24
Alignment explanation
Indices: 50398--50446 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
50388 GATCTTGAAA
50398 ACTTAGGTTTAAGGGTAAGTTTGG
1 ACTTAGGTTTAAGGGTAAGTTTGG
*
50422 ACTTAGGTTTAAGGGTAGGTTTGG
1 ACTTAGGTTTAAGGGTAAGTTTGG
50446 A
1 A
50447 TGGATGGCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.35, T:0.37
Consensus pattern (24 bp):
ACTTAGGTTTAAGGGTAAGTTTGG
Found at i:52826 original size:32 final size:33
Alignment explanation
Indices: 52771--52837 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
52761 CTTAATACTT
** *
52771 TTTTTAATTTTTATATATTATTTACATT-TTTA
1 TTTTTAATTTTTATATAAAATTTAAATTATTTA
52803 TTTTTAATATTTT-TATAAAATTTAAATTATTTA
1 TTTTTAAT-TTTTATATAAAATTTAAATTATTTA
52836 TT
1 TT
52838 GATGTATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTTTAATTTTTATATAAAATTTAAATTATTTA
Found at i:58995 original size:7 final size:7
Alignment explanation
Indices: 58983--59007 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
58973 TCTAATAAAA
58983 ACATGCC
1 ACATGCC
58990 ACATGCC
1 ACATGCC
58997 ACATGCC
1 ACATGCC
59004 ACAT
1 ACAT
59008 TTTCATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.40, G:0.12, T:0.16
Consensus pattern (7 bp):
ACATGCC
Found at i:60422 original size:13 final size:13
Alignment explanation
Indices: 60386--60422 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
60376 CTCTTTCTAT
60386 TTTTTATTTTTTA
1 TTTTTATTTTTTA
* *
60399 TTTATAATTTTTA
1 TTTTTATTTTTTA
60412 TTTTTATTTTT
1 TTTTTATTTTT
60423 GGAAAGTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:61416 original size:2 final size:2
Alignment explanation
Indices: 61409--61456 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
61399 CGGTTTCGTT
61409 TA TA TA TA TA TA 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 TA TA TA TA TA TA
*
61451 CA TA TA
1 TA TA TA
61457 AAAAAAAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:61600 original size:2 final size:2
Alignment explanation
Indices: 61595--61628 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61585 TGTTTTTTTT
61595 TA TA 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 TA TA
61629 AACCTAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68854 original size:29 final size:29
Alignment explanation
Indices: 68802--68857 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
68792 ATAGAGATTA
* *
68802 GATTAAATTAGTCTTTTTACTATTAAATG
1 GATTAAATTAGTCTATGTACTATTAAATG
* *
68831 GATTAATTTAGTCTATGTATTATTAAA
1 GATTAAATTAGTCTATGTACTATTAAA
68858 AAAATCAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (29 bp):
GATTAAATTAGTCTATGTACTATTAAATG
Found at i:69455 original size:26 final size:26
Alignment explanation
Indices: 69408--69457 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
69398 AGGGGGAGCC
* *
69408 TCGCGCCGCAACCAGGATCTTCACGT
1 TCGCGCCGCAACCACGACCTTCACGT
* *
69434 TCGCGCCGCAGCCCCGACCTTCAC
1 TCGCGCCGCAACCACGACCTTCAC
69458 CTGCAGCAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (26 bp):
TCGCGCCGCAACCACGACCTTCACGT
Found at i:70867 original size:15 final size:15
Alignment explanation
Indices: 70844--70877 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
70834 GTTTATTGAC
* *
70844 TTATGTTTTTTTCAT
1 TTATATTTTGTTCAT
70859 TTATATTTTGTTCAT
1 TTATATTTTGTTCAT
70874 TTAT
1 TTAT
70878 TTGATATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATATTTTGTTCAT
Found at i:70999 original size:19 final size:20
Alignment explanation
Indices: 70958--70999 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
70948 ATTTCTATGC
* *
70958 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
70978 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
70997 CAT
1 CAT
71000 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:74812 original size:23 final size:22
Alignment explanation
Indices: 74752--74812 Score: 52
Period size: 23 Copynumber: 2.7 Consensus size: 22
74742 TTTTAATCTA
* * *
74752 ATCACTTTCATTTTGGGTTTTG
1 ATCAGTTTAATTTTGGGGTTTG
*
74774 ATCAGTTTAAGGTTTGGGGTTTG
1 ATCAGTTTAA-TTTTGGGGTTTG
74797 AATC-GTTTAGATTTTG
1 -ATCAGTTTA-ATTTTG
74813 ATTGTTTTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 8 0.26
23 19 0.61
24 4 0.13
ACGTcount: A:0.18, C:0.08, G:0.25, T:0.49
Consensus pattern (22 bp):
ATCAGTTTAATTTTGGGGTTTG
Found at i:77253 original size:15 final size:17
Alignment explanation
Indices: 77224--77255 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
77214 ATAAAGGGCT
77224 AAAAATGATATTTTTAA
1 AAAAATGATATTTTTAA
77241 AAAAAT-AT-TTTTTAA
1 AAAAATGATATTTTTAA
77256 TTTTTAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAAAATGATATTTTTAA
Found at i:77302 original size:31 final size:31
Alignment explanation
Indices: 77267--77359 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
77257 TTTTAGAGTT
*
77267 AGAACTAAATTGATAGATTTTGTAAATATTG
1 AGAACTAAATTGATAAATTTTGTAAATATTG
* * * * *
77298 AGAACCAAATTTATTACATTTTTTAGA-ATT-
1 AGAACTAAATTGA-TAAATTTTGTAAATATTG
*
77328 AGAACTACAA-TGACAAATTTTGTAAATATTG
1 AGAACTA-AATTGATAAATTTTGTAAATATTG
77359 A
1 A
77360 AGGCTAATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
29 9 0.19
30 11 0.23
31 17 0.36
32 10 0.21
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (31 bp):
AGAACTAAATTGATAAATTTTGTAAATATTG
Found at i:77372 original size:61 final size:61
Alignment explanation
Indices: 77256--77383 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 61
77246 TATTTTTTAA
* * *
77256 TTTTTAGAGTTAGAACTAAATTGATAGATTTTGTAAATATTGAGAACCAAATTTATT-ACAT
1 TTTTTAGAATTAGAACTAAATTGACAAATTTTGTAAATATTGAGAACCAAATTTATTGA-AT
* * *
77317 TTTTTAGAATTAGAACTACAA-TGACAAATTTTGTAAATATTGA-AGGCTAATTTTATTGAAT
1 TTTTTAGAATTAGAACTA-AATTGACAAATTTTGTAAATATTGAGA-ACCAAATTTATTGAAT
77378 TTTTTA
1 TTTTTA
77384 TATTTTATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
60 1 0.02
61 54 0.93
62 3 0.05
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.43
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAATTGACAAATTTTGTAAATATTGAGAACCAAATTTATTGAAT
Found at i:83568 original size:2 final size:2
Alignment explanation
Indices: 83561--83586 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
83551 CCTGTGTAAA
83561 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
83587 CTTTGGAACA
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):
AT
Found at i:85300 original size:32 final size:32
Alignment explanation
Indices: 85259--85322 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
85249 TCAATACTAG
*
85259 TCAGAACGATAAAGTGAAGTTGATAGATGCTA
1 TCAGAACGATAAAGTGAAGTTGACAGATGCTA
*
85291 TCAGAACGATAAAGTGAAGTTGGCAGATGCTA
1 TCAGAACGATAAAGTGAAGTTGACAGATGCTA
85323 ACTCTGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (32 bp):
TCAGAACGATAAAGTGAAGTTGACAGATGCTA
Found at i:94473 original size:44 final size:44
Alignment explanation
Indices: 94425--94549 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 44
94415 AAGACTTTCT
94425 TCTTCAACTTATTCCACTGCTGACCAGGGAGATAGGATTCACAA
1 TCTTCAACTTATTCCACTGCTGACCAGGGAGATAGGATTCACAA
* * * ***
94469 TCTTCAA-TCTATTCCACTACT-ACTTAGGGAGATAAGATTTGTAA
1 TCTTCAACT-TATTCCACTGCTGAC-CAGGGAGATAGGATTCACAA
* * *
94513 T-TCCTAACCTATTCCACTGCTGACCAGAGAGATAGGA
1 TCTTC-AACTTATTCCACTGCTGACCAGGGAGATAGGA
94550 CTTGTGGCTT
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
43 5 0.08
44 57 0.89
45 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (44 bp):
TCTTCAACTTATTCCACTGCTGACCAGGGAGATAGGATTCACAA
Found at i:94705 original size:129 final size:128
Alignment explanation
Indices: 94485--94936 Score: 724
Period size: 128 Copynumber: 3.5 Consensus size: 128
94475 ATCTATTCCA
* * * * * *
94485 CTACTACTTAGGGAGATAAGATTTGTAATTCCTAACCTATTCCACTGCTGACCAGAGAGATAGGA
1 CTACTGCTTAGGGAGACAAGATCTATAATTTCTAACCTATTCCACTGCTGACCAGGGAGATAGGA
* * *
94550 CTTGTGGCTTAAATCTGCTTCCCTACTCCTGAATATAAGATTCGCCGTCTTCGATTTGCTCCG
66 CTTGTGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCG
* * *
94613 CTGCTGCTTAGGGAGACAAGATCTATAATTTCTAACATATTCCACATGTTGACCAGGGAGATAGG
1 CTACTGCTTAGGGAGACAAGATCTATAATTTCTAACCTATTCCAC-TGCTGACCAGGGAGATAGG
94678 ACTTGTGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCG
65 ACTTGTGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCG
** *
94742 CTACTGCTTAGGGAGACAAGATCTGCAATTTTTAACCTATTCCACTGCTGACCAGGGAGATAGGA
1 CTACTGCTTAGGGAGACAAGATCTATAATTTCTAACCTATTCCACTGCTGACCAGGGAGATAGGA
* *
94807 CTTGTGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCACCATCTTCGATCTGCTCCG
66 CTTGTGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCG
* *
94870 CTACTACTTAGGGAGACAAGATCTATAATTTCTAACCTATTCCACTGCTGATCAGGGAGATAGGA
1 CTACTGCTTAGGGAGACAAGATCTATAATTTCTAACCTATTCCACTGCTGACCAGGGAGATAGGA
94935 CT
66 CT
94937 ACTGGCTTCA
Statistics
Matches: 298, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
128 180 0.60
129 118 0.40
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (128 bp):
CTACTGCTTAGGGAGACAAGATCTATAATTTCTAACCTATTCCACTGCTGACCAGGGAGATAGGA
CTTGTGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCG
Found at i:95059 original size:132 final size:132
Alignment explanation
Indices: 94852--95113 Score: 323
Period size: 132 Copynumber: 2.0 Consensus size: 132
94842 TAAGATTCAC
* * * * * *
94852 CATCTTCGATCTGCTCCGCTACTACTTAGGGAGACAAGATCTATAATTTCTAACCTATTCCACTG
1 CATCTTCGATCCGCTCCACCACTACTGAGGGAGACAAGATCTATAATTTCTAACATATTCCACTA
* * *
94917 CTGATCAGGGAGATAGGACTACTGGCTTCAATGTACTCCATTGTAACC-TCAAGGAGGTAAAATC
66 CTGACCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAACCAT-AAGGAGGTAAAATC
94981 CAT
130 CAT
* * * * *
94984 CATCTTTGATCCGCTCCACCACTGCTGAGGGAGATAAGATCTGTAATCTTC-AATATATTCCACT
1 CATCTTCGATCCGCTCCACCACTACTGAGGGAGACAAGATCTATAAT-TTCTAACATATTCCACT
* * *
95048 ACT-ACCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCGCTGTAACCATAGGGAGGTAAAAT
65 ACTGACC-AGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAACCATAAGGAGGTAAAAT
95112 CC
129 CC
95114 GCTATCAACC
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
131 2 0.02
132 104 0.95
133 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
CATCTTCGATCCGCTCCACCACTACTGAGGGAGACAAGATCTATAATTTCTAACATATTCCACTA
CTGACCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAACCATAAGGAGGTAAAATCC
AT
Found at i:95176 original size:43 final size:43
Alignment explanation
Indices: 95127--95264 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 43
95117 ATCAACCTGT
95127 TTCGCTGCAAACGAGGGAGGCAAGGCTTGTGTCTTCGATCTGC
1 TTCGCTGCAAACGAGGGAGGCAAGGCTTGTGTCTTCGATCTGC
* * * * * *
95170 TTCGCTGTCGATAC-AAGAAGGCAA-GATCTGCTGTCTTCAACCTGC
1 TTCGCTG-C-AAACGAGGGAGGCAAGGCT-TG-TGTCTTCGATCTGC
* * * * * *
95215 TCCACTACAACCGAGGGAGGCAAGACTTGTATCTTCGATCTGC
1 TTCGCTGCAAACGAGGGAGGCAAGGCTTGTGTCTTCGATCTGC
95258 TTCGCTG
1 TTCGCTG
95265 TCGATGCAGG
Statistics
Matches: 68, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
43 26 0.38
44 22 0.32
45 20 0.29
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (43 bp):
TTCGCTGCAAACGAGGGAGGCAAGGCTTGTGTCTTCGATCTGC
Found at i:95267 original size:88 final size:88
Alignment explanation
Indices: 95131--95645 Score: 676
Period size: 88 Copynumber: 5.9 Consensus size: 88
95121 ACCTGTTTCG
* * *
95131 CTGCAAACGAGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCGATACAAGAAGGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGA
* *
95196 TCTGCTGTCTTCAACCTGCTCCA
66 TCTGCTATCTTTAACCTGCTCCA
* * *
95219 CTACAACCGAGGGAGGCAAGACTTGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGA
** **
95284 TCTTTTATCTTTAACCTAATCCA
66 TCTGCTATCTTTAACCTGCTCCA
* * * *
95307 CTACAACTGTGGGAGGCAAGGCTTGTATCTTTGATCTGCTTCGCTGTCGATACAGGAAGGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGA
*
95372 TCTGCTATCTTTAACCTGCTCTA
66 TCTGCTATCTTTAACCTGCTCCA
* * * * *
95395 CTGTAACCGAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAATGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGA
95460 TCTGCTATCTTTAACCTGCTCCA
66 TCTGCTATCTTTAACCTGCTCCA
* * * *
95483 CTGCAACCGATGGAGGCAAGGCTGGTATCTTCGATCTGTTTCGTTGTC-AGTACAGGAAGGCAAG
1 CTGCAACCGAGGGAGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGA-TACAGGAAGGCAAG
* * *
95547 ATCTGTTGTCTTTAACCCGCTCCA
65 ATCTGCTATCTTTAACCTGCTCCA
* * * * * *
95571 CTGTAACCGATGGAGGCAAGACTTTGT-T-TTCGATTTGCTTCGTTGTCGATGCAGGAAGGCAAG
1 CTGCAACCGAGGGAGGCAAGGC-TTGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAG
95634 ATCTGCTATCTT
65 ATCTGCTATCTT
95646 CACTGATCTG
Statistics
Matches: 375, Mismatches: 49, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
87 41 0.11
88 331 0.88
89 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (88 bp):
CTGCAACCGAGGGAGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGA
TCTGCTATCTTTAACCTGCTCCA
Found at i:95368 original size:44 final size:44
Alignment explanation
Indices: 95144--95458 Score: 125
Period size: 44 Copynumber: 7.2 Consensus size: 44
95134 CAAACGAGGG
* *
95144 AGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCGATACAAGA
1 AGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGA
* * * * * * * *
95188 AGGCAA-GATCTGCTGTCTTCAACCTGCTCCACT-AC-A-ACCGAGGG
1 AGGCAAGGCT-TG-TATCTTCGATCTGCTTCGCTGTCGATA-C-AGGA
* *
95232 AGGCAAGACTTGTATCTTCGATCTGCTTCGCTGTCGATGCAGGA
1 AGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGA
* * ** * ** * * * * *
95276 AGGCAAGATCTTTTATCTTTAACCTAATCCACT-AC-A-ACTGTGGG
1 AGGCAAG-GCTTGTATCTTCGATCTGCTTCGCTGTCGATAC--AGGA
*
95320 AGGCAAGGCTTGTATCTTTGATCTGCTTCGCTGTCGATACAGGA
1 AGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGA
* ** * *
95364 AGGCAA-GATCTGCTATCTTTAACCTGC-TCTACTGT--A-ACCGAAGG-
1 AGGCAAGGCT-TG-TATCTTCGATCTGCTTC-GCTGTCGATA-C--AGGA
* *
95408 AGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGA
1 AGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGA
*
95452 ATGCAAG
1 AGGCAAG
95459 ATCTGCTATC
Statistics
Matches: 191, Mismatches: 54, Indels: 52
0.64 0.18 0.18
Matches are distributed among these distances:
42 3 0.02
43 59 0.31
44 68 0.36
45 59 0.31
46 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (44 bp):
AGGCAAGGCTTGTATCTTCGATCTGCTTCGCTGTCGATACAGGA
Found at i:95434 original size:43 final size:43
Alignment explanation
Indices: 95387--95520 Score: 101
Period size: 43 Copynumber: 3.1 Consensus size: 43
95377 TATCTTTAAC
95387 CTGCTCTACTGTAACCGAAGGAGGCAAGGCTGGTATCTTCGAT
1 CTGCTCTACTGTAACCGAAGGAGGCAAGGCTGGTATCTTCGAT
* * * * * * * ** *
95430 CTGCT-TCGCTGTCGA-TGCAGGAATGCAAGATCTGCTATCTTTAAC
1 CTGCTCT-ACTGT-AACCGAAGG-AGGCAAG-GCTGGTATCTTCGAT
* * *
95475 CTGCTCCACTGCAACCGATGGAGGCAAGGCTGGTATCTTCGAT
1 CTGCTCTACTGTAACCGAAGGAGGCAAGGCTGGTATCTTCGAT
95518 CTG
1 CTG
95521 TTTCGTTGTC
Statistics
Matches: 62, Mismatches: 23, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
42 1 0.02
43 26 0.42
44 14 0.23
45 21 0.34
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (43 bp):
CTGCTCTACTGTAACCGAAGGAGGCAAGGCTGGTATCTTCGAT
Found at i:96899 original size:22 final size:20
Alignment explanation
Indices: 96873--96921 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
96863 TTAGCCTCTC
96873 CATTTTT-ACTTGTTCATTTTTT
1 CATTTTTCA-TTGTTCA--TTTT
*
96895 CATTTTTCATTTTTCATTTT
1 CATTTTTCATTGTTCATTTT
96915 CATTTTT
1 CATTTTT
96922 TTTACTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 11 0.44
22 13 0.52
23 1 0.04
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.69
Consensus pattern (20 bp):
CATTTTTCATTGTTCATTTT
Found at i:96907 original size:13 final size:14
Alignment explanation
Indices: 96885--96921 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
96875 TTTTTACTTG
96885 TTCATTTTTTCATTT
1 TTCA-TTTTTCATTT
96900 TTCATTTTTCA-TT
1 TTCATTTTTCATTT
96913 TTCATTTTT
1 TTCATTTTT
96922 TTTACTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.50
14 7 0.32
15 4 0.18
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCATTTTTCATTT
Found at i:96922 original size:8 final size:7
Alignment explanation
Indices: 96885--96921 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
96875 TTTTTACTTG
96885 TTCATTTT
1 TTCA-TTT
96893 TTCATTT
1 TTCATTT
96900 TTCATTT
1 TTCATTT
96907 TTCA-TT
1 TTCATTT
96913 TTCATTT
1 TTCATTT
96920 TT
1 TT
96922 TTTACTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.21
7 18 0.64
8 4 0.14
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCATTT
Found at i:103834 original size:2 final size:2
Alignment explanation
Indices: 103815--103863 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
103805 ATTTAGTTTT
* * *
103815 TA TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
103857 TA TA TA T
1 TA TA TA T
103864 TATTTTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:106592 original size:9 final size:9
Alignment explanation
Indices: 106574--106678 Score: 140
Period size: 9 Copynumber: 11.4 Consensus size: 9
106564 TTTGGTTAAA
106574 AATTACCCG
1 AATTACCCG
*
106583 AATTATCCG
1 AATTACCCG
106592 AATTACCCG
1 AATTACCCG
*
106601 ACTTACCCG
1 AATTACCCG
106610 AATTACCC-
1 AATTACCCG
106618 AACTTACCCG
1 AA-TTACCCG
*
106628 ACTTACCCG
1 AATTACCCG
*
106637 AATTAACCG
1 AATTACCCG
106646 AAAATTACCCG
1 --AATTACCCG
106657 AATTACCCG
1 AATTACCCG
106666 AATTACCCG
1 AATTACCCG
106675 AATT
1 AATT
106679 GACACTTTGA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
8 2 0.02
9 73 0.87
10 1 0.01
11 8 0.10
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:107459 original size:16 final size:16
Alignment explanation
Indices: 107438--107477 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
107428 GCCTAAGAGA
107438 AAATTGGGCTGGATTT
1 AAATTGGGCTGGATTT
*
107454 AAATTGGGCTGGGTTT
1 AAATTGGGCTGGATTT
107470 AAATTGGG
1 AAATTGGG
107478 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.05, G:0.35, T:0.35
Consensus pattern (16 bp):
AAATTGGGCTGGATTT
Found at i:117154 original size:31 final size:29
Alignment explanation
Indices: 117094--117161 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
117084 GTGATAGTTT
*
117094 AAGTACCACATTAGACATTTTCAAAGTAC
1 AAGTACCACATTAGACATTATCAAAGTAC
*
117123 AAGTACCACATTAGACATGTAATGAAAGTAC
1 AAGTACCACATTAGACAT-T-ATCAAAGTAC
*
117154 AGGTACCA
1 AAGTACCA
117162 AATAATATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 18 0.53
30 1 0.03
31 15 0.44
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (29 bp):
AAGTACCACATTAGACATTATCAAAGTAC
Found at i:117249 original size:91 final size:91
Alignment explanation
Indices: 116974--117255 Score: 266
Period size: 91 Copynumber: 3.1 Consensus size: 91
116964 TAACTCCAAA
* * * * * *
116974 TACCATAATAATACACATATTGATAGTTCAAGTACCACCTT-GAATATTTTCAAAGTATAAGTAT
1 TACCA-AATAATACACAAAGTGATAGTTCAAGTACCACATTAG-ACATTTTCAAAGTACAAGTAC
** * * *
117038 CATGTTGGACATTTCATGAAAGTACA--
64 CACATTAGACATGTAATGAAAGTACAGG
* *
117064 AACCTTAAATAATACACAAAGTGATAGTTTAAGTACCACATTAGACATTTTCAAAGTACAAGTAC
1 TACC--AAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACAAGTAC
117129 CACATTAGACATGTAATGAAAGTACAGG
64 CACATTAGACATGTAATGAAAGTACAGG
* * * ** * *
117157 TACCAAATAATATACAAATTGATGGTTCAAGTACGGCATTAGACATTTTTAAGGTACATA-TACC
1 TACCAAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACA-AGTACC
* * * * *
117221 ACATTGGATATTTTATGAAAGTATAGG
65 ACATTAGACATGTAATGAAAGTACAGG
117248 TACCAAAT
1 TACCAAAT
117256 GTGACATTAT
Statistics
Matches: 159, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
90 3 0.02
91 150 0.94
92 3 0.02
93 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (91 bp):
TACCAAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACAAGTACCA
CATTAGACATGTAATGAAAGTACAGG
Found at i:121850 original size:20 final size:20
Alignment explanation
Indices: 121827--121878 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
121817 TGCATGAAGT
*
121827 ATAAAATATTCACTAAATTA
1 ATAAAATATTCAATAAATTA
*
121847 AT-AAATTTATCAATAAATTA
1 ATAAAATAT-TCAATAAATTA
*
121867 ATAAAGTATTCA
1 ATAAAATATTCA
121879 TTCATCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAAATATTCAATAAATTA
Found at i:123058 original size:27 final size:28
Alignment explanation
Indices: 123022--123078 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
123012 ACCAAAATGT
123022 TATAACTTTTTTTATTTACCAAAAAATA
1 TATAACTTTTTTTATTTACCAAAAAATA
*
123050 TATAA-TTTTTTTATTTACCAAAATATA
1 TATAACTTTTTTTATTTACCAAAAAATA
123077 TA
1 TA
123079 AAAAAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (28 bp):
TATAACTTTTTTTATTTACCAAAAAATA
Found at i:123101 original size:17 final size:17
Alignment explanation
Indices: 123079--123119 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
123069 AAAATATATA
123079 AAAAAAACAAAAAACAG
1 AAAAAAACAAAAAACAG
*
123096 AAAAAAATAAAAAACAG
1 AAAAAAACAAAAAACAG
123113 AAAAAAA
1 AAAAAAA
123120 AACCTGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.85, C:0.07, G:0.05, T:0.02
Consensus pattern (17 bp):
AAAAAAACAAAAAACAG
Found at i:124113 original size:154 final size:149
Alignment explanation
Indices: 123634--124210 Score: 757
Period size: 152 Copynumber: 3.8 Consensus size: 149
123624 NNNNNNNNNN
*
123634 ATTTCAAACATAATGTACTAAAATAATGTAAAATTATAAAA-TACGAAAATAATATATTTTTATT
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTA-GAAAATAATATA-TTTT-TT
* **
123698 GAAAGTAATAAAATTCGAGAAAAAATACGAGTAAAGGGCCGAAATAAGGGTTTTTTTTAAATATA
63 GAAAGTAATAAAATTCGGGAAAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTTTT-AAT-TA
123763 TTTAAAAAACACACTAAATTAATAA
125 TTTAAAAAACACACTAAATTAATAA
* * *
123788 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTATAAAATAGTATATTTTTTCAA
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTGAA
* *
123853 AGTAATAAAATTCGGGAAAAAATACGAACAAAGGTCCGAAATAAGAGTTTTTTACTAA--ATTTA
66 AGTAATAAAATTCGGGAAAAAATACGAACAAAGG-CCGAAATAAGGGTTTTTT-TTAATTATTT-
* * * * *
123916 AAAAAATAAAATTAATTAATAC
128 AAAAAACACACTAAATTAATAA
* * *
123938 ATTTCAAACATAATTTACTAAAATAAAGTAAAATGATAAAA-TACGAAAATAATATATTTTTATT
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTA-GAAAATAATATA-TTTT-TT
* **
124002 GAAAGTAATAAAATTCGGGAAAAAAATACGAGCAAAGGGAGAAATAAGGGGTTTTTTTTAATTTA
63 GAAAGTAATAAAATTCGGG-AAAAAATACGAACAAAGGCCGAAATAA-GGGTTTTTTTTAA-TTA
*
124067 TTTAAAAAACACACTAAAATAATAA
125 TTTAAAAAACACACTAAATTAATAA
* * *
124092 ATCTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTAAA
1 ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTGAA
124157 AGTAATAAAATTCGGGAAAAAAATACGAACAAATGGCCGAAATAAGGGTTTTTT
66 AGTAATAAAATTCGGG-AAAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTT
124211 ACTAATTTTT
Statistics
Matches: 369, Mismatches: 40, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
149 6 0.02
150 65 0.18
151 6 0.02
152 127 0.34
153 43 0.12
154 114 0.31
155 8 0.02
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.31
Consensus pattern (149 bp):
ATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTTGAA
AGTAATAAAATTCGGGAAAAAATACGAACAAAGGCCGAAATAAGGGTTTTTTTTAATTATTTAAA
AAACACACTAAATTAATAA
Found at i:125394 original size:3 final size:3
Alignment explanation
Indices: 125386--125792 Score: 814
Period size: 3 Copynumber: 135.7 Consensus size: 3
125376 AGTGACATCT
125386 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125434 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125482 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125530 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125578 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125626 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125674 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125722 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
125770 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
125793 TAAAATTTTT
Statistics
Matches: 404, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 404 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:126115 original size:27 final size:27
Alignment explanation
Indices: 126074--126141 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
126064 AACACGAGTA
* ** **
126074 GTGCCGCCAATCTGGTTGGCAGGACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
*
126101 GTGCCGCCAACCTGGTTCCCTCCACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
126128 GTGCCGCCAACCTG
1 GTGCCGCCAACCTG
126142 CTTCTCTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.13, C:0.37, G:0.29, T:0.21
Consensus pattern (27 bp):
GTGCCGCCAACCTGGTTCCCACCACTG
Found at i:126156 original size:27 final size:27
Alignment explanation
Indices: 126097--126179 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
126087 GGTTGGCAGG
*
126097 ACTGGTGCCGCCAACCTGGTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
* *
126124 ACTGGTGCCGCCAACCTGCTTCTCT-T
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
* **
126150 ATTTGGTGCCGCCAACCCACTTCCCTCC
1 A-CTGGTGCCGCCAACCTGCTTCCCTCC
126178 AC
1 AC
126180 CCAAGGAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
26 1 0.02
27 43 0.96
28 1 0.02
ACGTcount: A:0.13, C:0.43, G:0.18, T:0.25
Consensus pattern (27 bp):
ACTGGTGCCGCCAACCTGCTTCCCTCC
Found at i:126457 original size:3 final size:3
Alignment explanation
Indices: 126449--126488 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
126439 ATCCTATTCC
*
126449 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
126489 TGTTTTAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:127587 original size:13 final size:13
Alignment explanation
Indices: 127571--127623 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
127561 TTTAAACCAA
127571 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
127584 ACTTTTCCACAA-T
1 ACTTTT-CAAAAGC
*
127597 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
127610 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
127623 A
1 A
127624 ATGATAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 26 0.76
14 4 0.12
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:139077 original size:26 final size:26
Alignment explanation
Indices: 139048--139108 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
139038 TTTTTAAAAA
139048 TTTTAAAAGTTT-AT-ATTTTTATATTT
1 TTTTAAAA-TTTAATCATTTTT-TATTT
*
139074 TTTTATAATTTAATCATTTTTTATTT
1 TTTTAAAATTTAATCATTTTTTATTT
139100 TTTTAAAAT
1 TTTTAAAAT
139109 ATTTTGTCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 3 0.10
26 22 0.71
27 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTTAAAATTTAATCATTTTTTATTT
Found at i:139080 original size:18 final size:18
Alignment explanation
Indices: 139057--139104 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
139047 ATTTTAAAAG
139057 TTTATATTTTTAT-ATTTT
1 TTTATATTTTTATCA-TTT
* *
139075 TTTATAATTTAATCATTT
1 TTTATATTTTTATCATTT
*
139093 TTTATTTTTTTA
1 TTTATATTTTTA
139105 AAATATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATATTTTTATCATTT
Found at i:139930 original size:22 final size:23
Alignment explanation
Indices: 139862--139945 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 23
139852 CTTAAAAATA
* *
139862 ATAAAAATT-TAATTTAATTCTC
1 ATAAAAATTATAATTTAACTATC
* *
139884 -TAAAATATAAATTATTTAA--ATC
1 ATAAAA-AT-TATAATTTAACTATC
*
139906 AT-AAAATTATATTTTAACTATC
1 ATAAAAATTATAATTTAACTATC
139928 ATAAAAATTATAATTTAA
1 ATAAAAATTATAATTTAA
139946 TTTTGATCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
20 7 0.15
21 7 0.15
22 12 0.25
23 15 0.31
24 7 0.15
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAAAATTATAATTTAACTATC
Found at i:144322 original size:14 final size:14
Alignment explanation
Indices: 144303--144332 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
144293 CCCTCGTAGG
*
144303 GTTATCGTATACTT
1 GTTATCATATACTT
144317 GTTATCATATACTT
1 GTTATCATATACTT
144331 GT
1 GT
144333 GCACATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (14 bp):
GTTATCATATACTT
Found at i:146379 original size:26 final size:26
Alignment explanation
Indices: 146343--146402 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
146333 GAAGCTTCGG
146343 AGAGCCATTAATC-AGAAAGCTCACAA
1 AGAGCCATTAATCGAG-AAGCTCACAA
* *
146369 AGAGCCTTTAATCGAGAAGCTCACGA
1 AGAGCCATTAATCGAGAAGCTCACAA
146395 AGAGCCAT
1 AGAGCCAT
146403 ATATTGGGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
AGAGCCATTAATCGAGAAGCTCACAA
Found at i:149913 original size:20 final size:19
Alignment explanation
Indices: 149874--149914 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
149864 AATTTGTTTG
* *
149874 TTTAGTTAATTAACCTTAA
1 TTTAGTTAAATAAACTTAA
149893 TTTAGTTAAATAATACTTAA
1 TTTAGTTAAATAA-ACTTAA
149913 TT
1 TT
149915 AATTAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTAGTTAAATAAACTTAA
Found at i:155811 original size:14 final size:15
Alignment explanation
Indices: 155792--155824 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
155782 AAATCGCAAC
155792 AAACC-ATTTTGCTA
1 AAACCAATTTTGCTA
155806 AAACCATATTTTGCTA
1 AAACCA-ATTTTGCTA
155822 AAA
1 AAA
155825 ATCAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
16 12 0.71
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (15 bp):
AAACCAATTTTGCTA
Found at i:157053 original size:76 final size:76
Alignment explanation
Indices: 156927--157079 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
156917 TCCATTTCGA
* *
156927 CGGATTTAGTCTCTCGTTTTAGAATACTTAAAGTATTCACATAAATCACAAATCAAATAATAATA
1 CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
156992 TTTTGTTTAGG
66 TTTTGTTTAGG
157003 CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
1 CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
157068 TTTTGTTTAGG
66 TTTTGTTTAGG
157079 C
1 C
157080 ATTATTAACG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (76 bp):
CGGATTTAGTCTCTCATTTTAGAATACTTAAAGTATTCACATAAATCACAAATAAAATAATAATA
TTTTGTTTAGG
Found at i:163516 original size:9 final size:9
Alignment explanation
Indices: 163502--163601 Score: 101
Period size: 9 Copynumber: 10.4 Consensus size: 9
163492 CTTCGGGGGA
163502 ATGGGCGGC
1 ATGGGCGGC
*
163511 ATGGGCGAC
1 ATGGGCGGC
163520 ATGATGGGCGGC
1 ---ATGGGCGGC
163532 ATGGGCGGC
1 ATGGGCGGC
163541 ATGGGCGGC
1 ATGGGCGGC
163550 ATGGGCGGC
1 ATGGGCGGC
* *
163559 ATGGGTGAC
1 ATGGGCGGC
*
163568 ATGATGGGTGGC
1 ---ATGGGCGGC
163580 ATGGGCGGC
1 ATGGGCGGC
*
163589 ATGGGTGGC
1 ATGGGCGGC
163598 ATGG
1 ATGG
163602 ATGAATTTGA
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
9 62 0.79
12 16 0.21
ACGTcount: A:0.15, C:0.17, G:0.52, T:0.16
Consensus pattern (9 bp):
ATGGGCGGC
Found at i:163558 original size:48 final size:48
Alignment explanation
Indices: 163502--163601 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
163492 CTTCGGGGGA
163502 ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
1 ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
* * *
163550 ATGGGCGGCATGGGTGACATGATGGGTGGCATGGGCGGCATGGGTGGC
1 ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
163598 ATGG
1 ATGG
163602 ATGAATTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.15, C:0.17, G:0.52, T:0.16
Consensus pattern (48 bp):
ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
Found at i:163575 original size:30 final size:30
Alignment explanation
Indices: 163541--163600 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
163531 CATGGGCGGC
163541 ATGGGCGGCATGGGCGGCATGGGTGACATG
1 ATGGGCGGCATGGGCGGCATGGGTGACATG
* *
163571 ATGGGTGGCATGGGCGGCATGGGTGGCATG
1 ATGGGCGGCATGGGCGGCATGGGTGACATG
163601 GATGAATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.18
Consensus pattern (30 bp):
ATGGGCGGCATGGGCGGCATGGGTGACATG
Found at i:164513 original size:60 final size:60
Alignment explanation
Indices: 164439--164560 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
164429 TTTGTCTCAT
*
164439 GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTGTTTTTACACTAACTGCAG
1 GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTATTTTTACACTAACTGCAG
* *
164499 GTTACAGTATTATTACAGTATTTAATTTTACAATTATTGTTATTTTTACACTAATTGCAG
1 GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTATTTTTACACTAACTGCAG
164559 GT
1 GT
164561 AAATATACCG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (60 bp):
GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTATTTTTACACTAACTGCAG
Found at i:165051 original size:20 final size:20
Alignment explanation
Indices: 165018--165070 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
165008 TTTTATACAG
165018 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
165037 ATTTTGAATTTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
165057 ATTTTGTAATTTTT
1 ATTTTG-AATTTTT
165071 GTTGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:165215 original size:23 final size:23
Alignment explanation
Indices: 165185--165228 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
165175 CAACTCGAAC
165185 TTATTCAAGTTGGCTT-GAATTGT
1 TTATTCAAGTTGG-TTCGAATTGT
165208 TTATTCAAGTTGGTTCGAATT
1 TTATTCAAGTTGGTTCGAATT
165229 ATTCGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.48
Consensus pattern (23 bp):
TTATTCAAGTTGGTTCGAATTGT
Done.