Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 22 of 25
Found at i:3346107 original size:32 final size:29
Alignment explanation
Indices: 3346071--3346155 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
3346061 AAATAATATT
3346071 ATATTAATATTTATTTAATAATATTATTATAA
1 ATATTAATATTTATTTAATAA-A--ATTATAA
*
3346103 ATATT--TATATATTTAATAAAATTATAA
1 ATATTAATATTTATTTAATAAAATTATAA
*
3346130 AT-TAAATATTTATTTAAGTTAAAATT
1 ATATTAATATTTATTTAA--TAAAATT
3346156 TTTTAATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.02
27 9 0.20
28 10 0.22
29 1 0.02
30 20 0.43
32 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
ATATTAATATTTATTTAATAAAATTATAA
Found at i:3346118 original size:30 final size:32
Alignment explanation
Indices: 3346082--3346142 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
3346072 TATTAATATT
* *
3346082 TATTTAATAATATTAT-TA-TAAATATTTATA
1 TATTTAATAAAATTATAAATTAAATATTTATA
3346112 TATTTAATAAAATTATAAATTAAATATTTAT
1 TATTTAATAAAATTATAAATTAAATATTTAT
3346143 TTAAGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 15 0.56
31 1 0.04
32 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TATTTAATAAAATTATAAATTAAATATTTATA
Found at i:3346322 original size:12 final size:12
Alignment explanation
Indices: 3346305--3346352 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3346295 ATAGTGTTTA
3346305 TATATTTTATAT
1 TATATTTTATAT
3346317 TATATTTTATAT
1 TATATTTTATAT
* *
3346329 AAAATTTTATAT
1 TATATTTTATAT
* *
3346341 TTTATATTATAT
1 TATATTTTATAT
3346353 AAATTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:3346340 original size:24 final size:24
Alignment explanation
Indices: 3346308--3346424 Score: 87
Period size: 24 Copynumber: 4.7 Consensus size: 24
3346298 GTGTTTATAT
3346308 ATTTTATATTATATTTTATATAAA
1 ATTTTATATTATATTTTATATAAA
* *
3346332 ATTTTATATTTTATATTATAT-AA
1 ATTTTATATTATATTTTATATAAA
*
3346355 ATTTTAAAATATTTATATTTTA-ATAAT
1 ATTTT---ATA-TTATATTTTATATAAA
* * *
3346382 GTATTTATATTTTCTTATTAT-TAAA
1 AT-TTTATATTATATT-TTATATAAA
*
3346407 ATTTTTTATTAATATTTT
1 ATTTTATATT-ATATTTT
3346425 CCGTTCAACT
Statistics
Matches: 71, Mismatches: 13, Indels: 18
0.70 0.13 0.18
Matches are distributed among these distances:
23 7 0.10
24 33 0.46
25 13 0.18
26 5 0.07
27 10 0.14
28 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTTATATTATATTTTATATAAA
Found at i:3346363 original size:31 final size:32
Alignment explanation
Indices: 3346305--3346376 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
3346295 ATAGTGTTTA
*
3346305 TATATTTTATATTATATTTTATATAAAAT-TT
1 TATATTTTATATTATATATTATATAAAATATT
3346336 TATATTTTATATTATATAAATT-T-TAAAATATT
1 TATATTTTATATTATAT--ATTATATAAAATATT
3346368 TATATTTTA
1 TATATTTTA
3346377 ATAATGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 23 0.62
32 12 0.32
33 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TATATTTTATATTATATATTATATAAAATATT
Found at i:3346380 original size:26 final size:24
Alignment explanation
Indices: 3346316--3346380 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 24
3346306 ATATTTTATA
*
3346316 TTATATTTTATATAAAATTTTATATT
1 TTATATTTTA-AT-AAATTTTAAATT
*
3346342 TTATATTAT-ATAAATTTTAAAATAT
1 TTATATTTTAATAAATTTT-AAAT-T
3346367 TTATATTTTAATAA
1 TTATATTTTAATAA
3346381 TGTATTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 7 0.21
24 5 0.15
25 9 0.27
26 12 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATTTTAATAAATTTTAAATT
Found at i:3346386 original size:19 final size:18
Alignment explanation
Indices: 3346311--3346394 Score: 70
Period size: 19 Copynumber: 4.7 Consensus size: 18
3346301 TTTATATATT
3346311 TTATATTATATTTTATATAA
1 TTAT-TTATATTTTA-ATAA
*
3346331 -AATTTTATATTTT-AT-A
1 TTA-TTTATATTTTAATAA
* *
3346347 TTATATAAATTTTAA-AA
1 TTATTTATATTTTAATAA
3346364 -TATTTATATTTTAATAA
1 TTATTTATATTTTAATAA
3346381 TGTATTTATATTTT
1 T-TATTTATATTTT
3346395 CTTATTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
16 21 0.41
17 7 0.14
19 22 0.43
20 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TTATTTATATTTTAATAA
Found at i:3346727 original size:2 final size:2
Alignment explanation
Indices: 3346720--3346760 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3346710 GTTAGTGCAT
*
3346720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3346761 TTCTTAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3351326 original size:27 final size:27
Alignment explanation
Indices: 3351293--3351372 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
3351283 ATTATATTTT
3351293 TAAAATATAAATATGTATAATAATATTC
1 TAAAATATAAATAT-TATAATAATATTC
* *
3351321 -AAAATATAAATATTAAAAATTATATTC
1 TAAAATATAAATATT-ATAATAATATTC
* *
3351348 TTAAA-ATAAATTTTATAATAATATT
1 TAAAATATAAATATTATAATAATATT
3351373 TAATATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 10 0.23
27 31 0.70
28 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (27 bp):
TAAAATATAAATATTATAATAATATTC
Found at i:3351383 original size:22 final size:22
Alignment explanation
Indices: 3351358--3351417 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
3351348 TTAAAATAAA
*
3351358 TTTTATAATAATATTTAA-TAT
1 TTTTATAATAATAATTAAGTAT
*
3351379 TTTT-TAAATTAAAAATTAAGTAT
1 TTTTAT-AA-TAATAATTAAGTAT
3351402 TTTTATTAATAATAAT
1 TTTTA-TAATAATAAT
3351418 GTGTAACTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.03
21 6 0.19
22 8 0.26
23 13 0.42
24 2 0.06
25 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTATAATAATAATTAAGTAT
Found at i:3352168 original size:2 final size:2
Alignment explanation
Indices: 3352156--3352189 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3352146 CCCTTTGCTT
* *
3352156 TA TA TA AA TA TA TA TG 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
3352190 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3352619 original size:15 final size:13
Alignment explanation
Indices: 3352583--3352615 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3352573 AAGTAACCCA
3352583 ATAATATT-AAAT
1 ATAATATTAAAAT
3352595 ATAATATTAAAAT
1 ATAATATTAAAAT
3352608 ATAATATT
1 ATAATATT
3352616 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATATTAAAAT
Found at i:3352644 original size:31 final size:33
Alignment explanation
Indices: 3352593--3352673 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
3352583 ATAATATTAA
*
3352593 ATAT-AATATTAAAATA-TAATAT-TTTAAATTT
1 ATATAAATA-TAAAATATTAATATATTAAAATTT
*
3352624 -TATAAATATAAATTATTAATATATTAAAATTT
1 ATATAAATATAAAATATTAATATATTAAAATTT
3352656 ATATAAATATAAAATATT
1 ATATAAATATAAAATATT
3352674 TTAAATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 9 0.21
31 10 0.23
32 8 0.19
33 16 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAAATATAAAATATTAATATATTAAAATTT
Found at i:3352661 original size:33 final size:33
Alignment explanation
Indices: 3352593--3352723 Score: 103
Period size: 33 Copynumber: 3.9 Consensus size: 33
3352583 ATAATATTAA
* *
3352593 ATAT-AATATTAAAATA-TAATAT-TTTAAATTT
1 ATATAAATA-TAAATTATTAATATATTAAAATTT
3352624 -TATAAATATAAATTATTAATATATTAAAATTT
1 ATATAAATATAAATTATTAATATATTAAAATTT
* * *
3352656 ATATAAATATAAAATATTTTAAATATAATTATAATATA
1 ATATAAATAT-AAAT-TATT-AATAT-ATTAAAAT-TT
*
3352694 ATAAAATATATAAATTATTAA-A-ATTAAAAT
1 ATATAA-ATATAAATTATTAATATATTAAAAT
3352724 CAAAGTGTCG
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
30 9 0.11
31 10 0.12
32 8 0.10
33 16 0.20
34 4 0.05
35 4 0.05
36 7 0.09
37 10 0.12
38 10 0.12
39 4 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATAAATATAAATTATTAATATATTAAAATTT
Found at i:3352671 original size:27 final size:29
Alignment explanation
Indices: 3352586--3352713 Score: 78
Period size: 27 Copynumber: 4.5 Consensus size: 29
3352576 TAACCCAATA
*
3352586 ATATTAAATATAATATTAAAAT-AT--AAT
1 ATATTAAATATATTA-TAAAATAATAAAAT
* *
3352613 ATTTTAAAT-T-TTATAAATATAAATTATTAAT
1 ATATTAAATATATTATAAA-AT-AA-TA-AAAT
3352644 ATATTAAA-AT-TTATATAAAT-ATAAAAT
1 ATATTAAATATATTATA-AAATAATAAAAT
* *
3352671 ATTTTAAATATAATTATAATATAATAAAAT
1 ATATTAAATAT-ATTATAAAATAATAAAAT
3352701 ATA-TAAAT-TATTA
1 ATATTAAATATATTA
3352714 AAATTAAAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
24 4 0.05
25 4 0.05
26 1 0.01
27 23 0.28
28 6 0.07
29 9 0.11
30 14 0.17
31 18 0.22
32 2 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATTAAATATATTATAAAATAATAAAAT
Found at i:3354474 original size:84 final size:84
Alignment explanation
Indices: 3354333--3354501 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
3354323 AGCCCTGTCC
3354333 GGTCCAACCAAAGATGGGTCTAATTTCAAGCATAATACCTTTTCTGACTTGGCTTTTCACATTCT
1 GGTCCAACCAAAGATGGGTCTAATTTCAAGCATAATACCTTTTCTGACTTGGCTTTTCACATTCT
3354398 TTGAGTTCAACACTTATTT
66 TTGAGTTCAACACTTATTT
3354417 GGTCCAACCAAAGATGGGTCTAATTTCAAGCATAATACCTTTTCTGACTTGGCTTTTCACATTCT
1 GGTCCAACCAAAGATGGGTCTAATTTCAAGCATAATACCTTTTCTGACTTGGCTTTTCACATTCT
3354482 TTGAGTTCAACACTTATTT
66 TTGAGTTCAACACTTATTT
3354501 G
1 G
3354502 AACATGAATA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (84 bp):
GGTCCAACCAAAGATGGGTCTAATTTCAAGCATAATACCTTTTCTGACTTGGCTTTTCACATTCT
TTGAGTTCAACACTTATTT
Found at i:3358936 original size:24 final size:23
Alignment explanation
Indices: 3358900--3358949 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3358890 TTATTTTTAA
3358900 AATATTAAAATATTATTT-TATATT
1 AATATTAAAATATT-TTTATA-ATT
* *
3358924 AATATTTATATATTTTTATAATT
1 AATATTAAAATATTTTTATAATT
3358947 AAT
1 AAT
3358950 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTAAAATATTTTTATAATT
Found at i:3359723 original size:4 final size:4
Alignment explanation
Indices: 3359714--3359738 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3359704 GTCAATTTGC
3359714 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
3359739 TATATCTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:3359905 original size:2 final size:2
Alignment explanation
Indices: 3359900--3359939 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3359890 ATATATATAT
*
3359900 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3359940 TTCTTCTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3361457 original size:11 final size:11
Alignment explanation
Indices: 3361441--3361473 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3361431 TATACATTAT
3361441 TTAAAAATAAA
1 TTAAAAATAAA
3361452 TTAAAAAT-AA
1 TTAAAAATAAA
3361462 TTATAAAATAAA
1 TTA-AAAATAAA
3361474 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 13 0.65
12 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TTAAAAATAAA
Found at i:3361896 original size:31 final size:31
Alignment explanation
Indices: 3361854--3361916 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3361844 TATTTTTACG
* * *
3361854 TTTATCTTAATTCATTTTATATTTTTTA-TAA
1 TTTATCATAATT-AATTAATATTTTTTAGTAA
3361885 TTTATCATAATTAATTAATATTTTTTAGTAA
1 TTTATCATAATTAATTAATATTTTTTAGTAA
3361916 T
1 T
3361917 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (31 bp):
TTTATCATAATTAATTAATATTTTTTAGTAA
Found at i:3362419 original size:20 final size:20
Alignment explanation
Indices: 3362373--3362419 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3362363 AAATAATATT
* *
3362373 TTTAAAATATTTATTTAAAA
1 TTTAAATTATATATTTAAAA
*
3362393 TTTAAATTATATATTTAATA
1 TTTAAATTATATATTTAAAA
3362413 TTTAAAT
1 TTTAAAT
3362420 CATTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATTATATATTTAAAA
Found at i:3362439 original size:9 final size:9
Alignment explanation
Indices: 3362427--3362463 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3362417 AATCATTTTT
3362427 ATTAAATTA
1 ATTAAATTA
*
3362436 ATT-AATAA
1 ATTAAATTA
3362444 ATTAAATTA
1 ATTAAATTA
3362453 ATTAAATTA
1 ATTAAATTA
3362462 AT
1 AT
3362464 AATAAATTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATTAAATTA
Found at i:3362483 original size:26 final size:26
Alignment explanation
Indices: 3362427--3362485 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
3362417 AATCATTTTT
**
3362427 ATTAAATTAATTAATAAATTAAATTA
1 ATTAAATTAATTAATAAATTAAACCA
**
3362453 ATTAAATTAA-TAATAAATTCGACCA
1 ATTAAATTAATTAATAAATTAAACCA
*
3362478 ATTTAATT
1 ATTAAATT
3362486 GGTCGTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTAAATTAATTAATAAATTAAACCA
Found at i:3362875 original size:14 final size:16
Alignment explanation
Indices: 3362837--3362937 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 16
3362827 ATGTAGGGTA
3362837 TTTATATTTATAAATAT
1 TTTATA-TTATAAATAT
*
3362854 TTTATATTATATATAT
1 TTTATATTATAAATAT
*
3362870 TTTATTATTTTTAAATAT
1 TTTA-TA-TTATAAATAT
3362888 TTT-TATTATAATTATAT
1 TTTATATTATAA--ATAT
* *
3362905 TTTATTTTTATATTATAT
1 TTTA-TATTATA-AATAT
*
3362923 TTAATATTATTAAAT
1 TTTATATTA-TAAAT
3362938 TTATTTAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
15 5 0.07
16 15 0.22
17 21 0.31
18 20 0.30
19 6 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATATTATAAATAT
Found at i:3362878 original size:24 final size:24
Alignment explanation
Indices: 3362854--3362932 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
3362844 TTATAAATAT
3362854 TTTATATTATATATATTTTATTAT-
1 TTTATATTATATAT-TTTTATTATA
3362878 TTT-TA--A-ATATTTTTATTATA
1 TTTATATTATATATTTTTATTATA
* *
3362898 ATTATATTTTAT-TTTTATATTATA
1 TTTATATTATATATTTT-TATTATA
3362922 TTTAATATTAT
1 TTT-ATATTAT
3362933 TAAATTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
19 9 0.20
20 6 0.14
21 3 0.07
23 6 0.14
24 14 0.32
25 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATATTATATATTTTTATTATA
Found at i:3362879 original size:40 final size:37
Alignment explanation
Indices: 3362835--3362911 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 37
3362825 TAATGTAGGG
3362835 TATTTATATTTATAAATATTTTATATTAT-A-TATATTT
1 TATTTATATTT-TAAATATTTT-TATTATAATTATATTT
3362872 TA-TTAT-TTTTAAATATTTTTATTATAATTATATTT
1 TATTTATATTTTAAATATTTTTATTATAATTATATTT
3362907 TATTT
1 TATTT
3362912 TTATATTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
33 6 0.16
34 11 0.30
35 12 0.32
36 6 0.16
37 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (37 bp):
TATTTATATTTTAAATATTTTTATTATAATTATATTT
Found at i:3362904 original size:35 final size:34
Alignment explanation
Indices: 3362837--3362932 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
3362827 ATGTAGGGTA
3362837 TTTA-TATTTATAAATATTTTATATTATATATAT
1 TTTATTATTTATAAATATTTTATATTATATATAT
*
3362870 TTTATTATTTTTAAATATTTT-TATTATAATTATAT
1 TTTATTATTTATAAATATTTTATATTAT-A-TATAT
* *
3362905 TTTATT-TTTATATTATATTTAATATTAT
1 TTTATTATTTATA-AATATTTTATATTAT
3362933 TAAATTTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
33 10 0.19
34 21 0.39
35 17 0.31
36 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (34 bp):
TTTATTATTTATAAATATTTTATATTATATATAT
Found at i:3362953 original size:52 final size:51
Alignment explanation
Indices: 3362850--3362955 Score: 119
Period size: 52 Copynumber: 2.1 Consensus size: 51
3362840 ATATTTATAA
* * *
3362850 ATATTTTATATTATATATATTTTATTATTTTTAAATATTTTTATTATAATT
1 ATATTTTATATTATATATATTTTAATATTATTAAATATTTTTAATATAATT
*
3362901 ATATTTTAT-TTTTATATTATATTTAATATTATTAAAT-TTATTTAA-ATAAATT
1 ATATTTTATATTATATA-TAT-TTTAATATTATTAAATATT-TTTAATAT-AATT
3362953 ATA
1 ATA
3362956 AAAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
50 6 0.13
51 16 0.34
52 25 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (51 bp):
ATATTTTATATTATATATATTTTAATATTATTAAATATTTTTAATATAATT
Found at i:3363443 original size:48 final size:49
Alignment explanation
Indices: 3363374--3363484 Score: 115
Period size: 49 Copynumber: 2.3 Consensus size: 49
3363364 TTAAATATTT
* *
3363374 ATATTTATAT-TTTAATTTTAAAATAT-AAAAA-ATTATATTTATAA-TA
1 ATATTTATATATTTTATATTAAAATATAAAAAATATTAT-TTTATAATTA
* * *
3363420 ATATTTATATATTTTATAATTAAATTTTAAAAAATATTATTTTTTAATTA
1 ATATTTATATATTTTAT-ATTAAAATATAAAAAATATTATTTTATAATTA
*
3363470 AAATTTAT-TATTTTA
1 ATATTTATATATTTTA
3363485 AACTAATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
46 10 0.19
47 5 0.09
48 7 0.13
49 18 0.33
50 14 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (49 bp):
ATATTTATATATTTTATATTAAAATATAAAAAATATTATTTTATAATTA
Found at i:3364324 original size:13 final size:13
Alignment explanation
Indices: 3364308--3364332 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3364298 TATTTAAAAA
3364308 TAAATTAAAAATT
1 TAAATTAAAAATT
3364321 TAAATTAAAAAT
1 TAAATTAAAAAT
3364333 AATTAATAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATTAAAAATT
Found at i:3364831 original size:12 final size:11
Alignment explanation
Indices: 3364814--3364869 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
3364804 TGTTGTTGTA
3364814 ATTATTTTTCAT
1 ATTATTTTT-AT
3364826 ATTATTTTTAT
1 ATTATTTTTAT
*
3364837 ATTATATCTTA-
1 ATTAT-TTTTAT
3364848 ATT-TATTTTAT
1 ATTAT-TTTTAT
3364859 ATT-TTTTTAT
1 ATTATTTTTAT
3364869 A
1 A
3364870 ATTTATCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
10 13 0.32
11 14 0.35
12 13 0.32
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTTTTAT
Found at i:3364868 original size:32 final size:31
Alignment explanation
Indices: 3364812--3364895 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
3364802 AATGTTGTTG
*
3364812 TAATTATTTTTCATATTATTTTTAT-ATTATATCT
1 TAATTA-TTTT-ATATT-TTTTTATAATT-TATCA
3364846 TAATTTATTTTATATTTTTTTATAATTTATCA
1 TAA-TTATTTTATATTTTTTTATAATTTATCA
* *
3364878 TAATTAATTAATATTTTT
1 TAATTATTTTATATTTTT
3364896 AATAATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
31 13 0.29
32 14 0.31
33 8 0.18
34 7 0.16
35 3 0.07
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (31 bp):
TAATTATTTTATATTTTTTTATAATTTATCA
Found at i:3365570 original size:59 final size:59
Alignment explanation
Indices: 3365497--3365615 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 59
3365487 TATGTTTAAG
* * **
3365497 ATTTATTTATATATAATTAAAATTTAAGAA-TTTATTTAAATATAAATTA-AAAATTAAAA
1 ATTTATTTATATATAATAAAAATATAA-AAGTTTAACTAAATA-AAATTATAAAATTAAAA
3365556 ATTTATTTGA-ATATAATAAAAATATAAAAGTTTAACTAAATAAAATTATAAAATTAAAA
1 ATTTATTT-ATATATAATAAAAATATAAAAGTTTAACTAAATAAAATTATAAAATTAAAA
3365615 A
1 A
3365616 GATTTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
58 8 0.15
59 44 0.83
60 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (59 bp):
ATTTATTTATATATAATAAAAATATAAAAGTTTAACTAAATAAAATTATAAAATTAAAA
Found at i:3365597 original size:29 final size:28
Alignment explanation
Indices: 3365492--3365614 Score: 122
Period size: 30 Copynumber: 4.2 Consensus size: 28
3365482 TAAATTATGT
* * *
3365492 TTAAGATTTATTTATATATAATTAAAAT
1 TTAAAATTTATTTAAATATAATTAAAAA
3365520 TTAAGAATTTATTTAAATATAAATTAAAAA
1 TTAA-AATTTATTTAAATAT-AATTAAAAA
*
3365550 TTAAAAATTTATTTGAATATAA-TAAAAA
1 TT-AAAATTTATTTAAATATAATTAAAAA
** *
3365578 TATAAAAGTTTAACTAAATAAAATTATAAAA
1 T-TAAAA-TTTATTTAAATATAATTA-AAAA
3365609 TTAAAA
1 TTAAAA
3365615 AGATTTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
28 15 0.19
29 27 0.34
30 31 0.39
31 7 0.09
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (28 bp):
TTAAAATTTATTTAAATATAATTAAAAA
Found at i:3366465 original size:22 final size:23
Alignment explanation
Indices: 3366419--3366470 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3366409 ACATGAATTA
*
3366419 TTAATTTTAAAAATATTAATTATT
1 TTAA-TTTAAAAATATTAATGATT
*
3366443 TTAATTTAAAAATTTTAA-GATT
1 TTAATTTAAAAATATTAATGATT
3366465 TTAATT
1 TTAATT
3366471 ATGGAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
23 13 0.50
24 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAATTTAAAAATATTAATGATT
Found at i:3374090 original size:2 final size:2
Alignment explanation
Indices: 3374069--3374125 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
3374059 CACACATGCA
* * *
3374069 CT CT CA CT CA CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3374111 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
3374126 ACAGAAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.05, C:0.51, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:3380236 original size:2 final size:2
Alignment explanation
Indices: 3380231--3380265 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3380221 GCAAAAAAAA
3380231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3380266 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:3387920 original size:11 final size:11
Alignment explanation
Indices: 3387906--3387930 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3387896 AAAAGAAATG
3387906 AAAAGAAAAAA
1 AAAAGAAAAAA
3387917 AAAAGAAAAAA
1 AAAAGAAAAAA
3387928 AAA
1 AAA
3387931 TTGACCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:3390974 original size:3 final size:3
Alignment explanation
Indices: 3390966--3390999 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3390956 TTAAAAGAGC
3390966 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
3391000 ATAAATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:3393301 original size:7 final size:7
Alignment explanation
Indices: 3393289--3393315 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3393279 ATATAAATTT
3393289 AATTAAA
1 AATTAAA
3393296 AATTAAA
1 AATTAAA
3393303 AATTAAA
1 AATTAAA
3393310 AATTAA
1 AATTAA
3393316 TAAACATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATTAAA
Found at i:3393508 original size:28 final size:29
Alignment explanation
Indices: 3393463--3393527 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
3393453 TTAATACAAT
*
3393463 TAATTAATATACAGTTAAGAAAATTCATA
1 TAATTAATATACAGTTAAAAAAATTCATA
3393492 TAATTATATATA-A-TTAAAAAAATTCATA
1 TAATTA-ATATACAGTTAAAAAAATTCATA
3393520 T--TTAATAT
1 TAATTAATAT
3393528 GAATTTGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
28 15 0.44
29 7 0.21
30 5 0.15
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (29 bp):
TAATTAATATACAGTTAAAAAAATTCATA
Found at i:3394261 original size:13 final size:13
Alignment explanation
Indices: 3394230--3394264 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3394220 CGGACACAGG
*
3394230 TAAGGCCATTCTC
1 TAAGGCCATCCTC
3394243 -AAGGCCATCCTC
1 TAAGGCCATCCTC
3394255 TAAGGCCATC
1 TAAGGCCATC
3394265 AGCTCCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (13 bp):
TAAGGCCATCCTC
Found at i:3394659 original size:2 final size:2
Alignment explanation
Indices: 3394654--3394684 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3394644 ATATATATAT
3394654 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3394685 CGCACAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3396780 original size:20 final size:21
Alignment explanation
Indices: 3396732--3396780 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
3396722 TTTTAAGATC
3396732 AATAATTA-ATGTATTTTTAT
1 AATAATTATATGTATTTTTAT
* *
3396752 AGTATTTATAT-TATTTTTAT
1 AATAATTATATGTATTTTTAT
3396772 AATAATTAT
1 AATAATTAT
3396781 CTTAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
AATAATTATATGTATTTTTAT
Found at i:3398199 original size:21 final size:22
Alignment explanation
Indices: 3398166--3398210 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3398156 AATATTATGT
* * *
3398166 AATATATTGTAATTATTATAAA
1 AATAAATTGTAATAATAATAAA
3398188 AATAAATT-TAATAATAATAAA
1 AATAAATTGTAATAATAATAAA
3398209 AA
1 AA
3398211 CATTATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AATAAATTGTAATAATAATAAA
Found at i:3399248 original size:13 final size:13
Alignment explanation
Indices: 3399230--3399257 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3399220 TTTAATTAGT
3399230 TTTTCATTTTTAA
1 TTTTCATTTTTAA
3399243 TTTTCATTTTTAA
1 TTTTCATTTTTAA
3399256 TT
1 TT
3399258 AGTTCATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTAA
Found at i:3401441 original size:29 final size:30
Alignment explanation
Indices: 3401408--3401477 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
3401398 TTTTTTTAGG
*
3401408 TAAGCACTTATA-CTTCT-TTTGTACCCAAA
1 TAAGCCCTTATACCTT-TATTTGTACCCAAA
*
3401437 TAAGCCCTTA-ACCTTTAATTTGTACCCAAC
1 TAAGCCCTTATACCTTT-ATTTGTACCCAAA
3401467 TAAGCCCTTAT
1 TAAGCCCTTAT
3401478 TCCAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.06
29 12 0.34
30 21 0.60
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (30 bp):
TAAGCCCTTATACCTTTATTTGTACCCAAA
Found at i:3403932 original size:25 final size:25
Alignment explanation
Indices: 3403904--3403955 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3403894 TCCAAAAAAC
3403904 TGATAACCAGATATGACAATTAAAG
1 TGATAACCAGATATGACAATTAAAG
3403929 TGATAACCAGATATGACAATTAAAG
1 TGATAACCAGATATGACAATTAAAG
3403954 TG
1 TG
3403956 CAGCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (25 bp):
TGATAACCAGATATGACAATTAAAG
Found at i:3404954 original size:20 final size:21
Alignment explanation
Indices: 3404929--3404971 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3404919 ATCATCTATA
3404929 ATTTAAT-TTTAAAATTTTTT
1 ATTTAATATTTAAAATTTTTT
3404949 ATTTAATATTTAAAATTTTTT
1 ATTTAATATTTAAAATTTTTT
3404970 AT
1 AT
3404972 ATATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTAATATTTAAAATTTTTT
Found at i:3404982 original size:22 final size:21
Alignment explanation
Indices: 3404935--3404989 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3404925 TATAATTTAA
*
3404935 TTTTAAAATTTTTTATTTAAT
1 TTTTAAAATTTTTTATATAAT
* *
3404956 ATTTAAAATTTTTTATATATTT
1 TTTTAAAATTTTTTATATA-AT
*
3404978 TTTTATAATTTT
1 TTTTAAAATTTT
3404990 AATAAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTAAAATTTTTTATATAAT
Found at i:3405558 original size:9 final size:9
Alignment explanation
Indices: 3405530--3405689 Score: 70
Period size: 10 Copynumber: 16.2 Consensus size: 9
3405520 CAATGGACAT
3405530 TTTTAATAA
1 TTTTAATAA
3405539 TTTTTATATAA
1 -TTTTA-ATAA
3405550 TTTTAATAA
1 TTTTAATAA
* *
3405559 TGCATGATATAA
1 T--TTTA-ATAA
* *
3405571 TATTAATTAT
1 TTTTAA-TAA
3405581 TTTTAATAA
1 TTTTAATAA
*
3405590 -TTTAAAAA
1 TTTTAATAA
3405598 TTTTAATATTA
1 TTTTAATA--A
3405609 TTTTAATAA
1 TTTTAATAA
*
3405618 TATTAATAAA
1 TTTTAAT-AA
* *
3405628 TCTTATTAA
1 TTTTAATAA
**
3405637 TTTTTGTTTAA
1 -TTTT-AATAA
*
3405648 TTTTGATAA
1 TTTTAATAA
3405657 TTTTTAATAAA
1 -TTTTAAT-AA
*
3405668 TTTAAATATAA
1 TTT-TA-ATAA
3405679 TTTTAATAA
1 TTTTAATAA
3405688 TT
1 TT
3405690 AAATTTATAA
Statistics
Matches: 117, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
8 7 0.06
9 32 0.27
10 44 0.38
11 27 0.23
12 7 0.06
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (9 bp):
TTTTAATAA
Found at i:3405647 original size:33 final size:28
Alignment explanation
Indices: 3405571--3405648 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 28
3405561 CATGATATAA
*
3405571 TATTAATTATTTTTAATAATTTAAAAAT
1 TATTAATTTTTTTTAATAATTTAAAAAT
*
3405599 T-TTAATATTATTTTAATAATATTAATAAATCT
1 TATTAAT-TTTTTTTAATAAT-TTAA-AAA--T
3405631 TATTAATTTTTGTTTAAT
1 TATTAATTTTT-TTTAAT
3405649 TTTGATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 5 0.12
28 12 0.30
29 4 0.10
30 3 0.08
32 5 0.12
33 11 0.28
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTAATTTTTTTTAATAATTTAAAAAT
Found at i:3405698 original size:21 final size:24
Alignment explanation
Indices: 3405643--3405699 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 24
3405633 TTAATTTTTG
*
3405643 TTTAATTTTGATAATTTTTAATAAA
1 TTTAAATTT-ATAATTTTTAATAAA
3405668 TTTAAA--TATAA-TTTTAAT-AA
1 TTTAAATTTATAATTTTTAATAAA
3405688 -TTAAATTTATAA
1 TTTAAATTTATAA
3405700 AAAAATACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 5 0.17
20 2 0.07
21 12 0.41
22 4 0.14
23 1 0.03
25 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAAATTTATAATTTTTAATAAA
Found at i:3413577 original size:19 final size:19
Alignment explanation
Indices: 3413542--3413579 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3413532 TTAATTAAAT
**
3413542 TTAATTTAATTTTAATCAA
1 TTAATTTAATTAAAATCAA
3413561 TTAATTTAATTAAAATCAA
1 TTAATTTAATTAAAATCAA
3413580 ATTATGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATTTAATTAAAATCAA
Found at i:3413954 original size:21 final size:21
Alignment explanation
Indices: 3413925--3413987 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
3413915 GTATTTAAAA
*
3413925 ATTTTAATTAATTTTATTTAT
1 ATTTAAATTAATTTTATTTAT
* * *
3413946 ATTTAAATTAAATCTATTTAA
1 ATTTAAATTAATTTTATTTAT
*
3413967 ATGTAAATT--TTATTATTTAT
1 ATTTAAATTAATT-TTATTTAT
3413987 A
1 A
3413988 ATATTATTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.03
20 7 0.21
21 25 0.76
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTAAATTAATTTTATTTAT
Found at i:3413965 original size:15 final size:16
Alignment explanation
Indices: 3413945--3413974 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3413935 ATTTTATTTA
3413945 TATTTAAAT-TAAATC
1 TATTTAAATGTAAATC
3413960 TATTTAAATGTAAAT
1 TATTTAAATGTAAAT
3413975 TTTATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TATTTAAATGTAAATC
Found at i:3414336 original size:24 final size:27
Alignment explanation
Indices: 3414304--3414368 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 27
3414294 AAAAATTAAA
3414304 ATATT-TAAATGATTT-TTAATTAG-T
1 ATATTATAAATGATTTATTAATTAGAT
3414328 AT-TTATAAAT-ATTTATTAATTAGATT
1 ATATTATAAATGATTTATTAATTAGA-T
3414354 ATATTATATAATGAT
1 ATATTATA-AATGAT
3414369 ATCTTCGCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
23 6 0.18
24 15 0.44
26 3 0.09
27 5 0.15
28 3 0.09
29 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (27 bp):
ATATTATAAATGATTTATTAATTAGAT
Found at i:3414751 original size:17 final size:17
Alignment explanation
Indices: 3414684--3414751 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 17
3414674 ATTTTAATAC
3414684 ATATTATATTTATTTTT
1 ATATTATATTTATTTTT
3414701 -TATTATATTTTATATTAAATT
1 ATATTATA-TTTAT-TT---TT
* *
3414722 ATATTTTAATTATTTTT
1 ATATTATATTTATTTTT
3414739 ATATTATATTTAT
1 ATATTATATTTAT
3414752 AATATATATC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
16 7 0.17
17 18 0.44
18 2 0.05
20 2 0.05
21 6 0.15
22 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTATTTTT
Found at i:3415388 original size:15 final size:15
Alignment explanation
Indices: 3415368--3415396 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3415358 TTCATTACTT
3415368 AAAATTAATATCAAC
1 AAAATTAATATCAAC
3415383 AAAATTAATATCAA
1 AAAATTAATATCAA
3415397 AACTAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATTAATATCAAC
Found at i:3416008 original size:33 final size:32
Alignment explanation
Indices: 3415941--3416009 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
3415931 TATATATTTT
** **
3415941 TATAAATTTTGATATGTTAATAATTCGTGTTA
1 TATAAATTTTGATACATTAATAATTCGTAATA
3415973 TATAAATTTTGATACATTAATATATTCGTAATA
1 TATAAATTTTGATACATTAATA-ATTCGTAATA
3416006 TATA
1 TATA
3416010 TTTATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (32 bp):
TATAAATTTTGATACATTAATAATTCGTAATA
Found at i:3417099 original size:20 final size:20
Alignment explanation
Indices: 3417076--3417115 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3417066 TTATATATTG
3417076 AAAATAATATTTATTTAAAT
1 AAAATAATATTTATTTAAAT
*
3417096 AAAATATTATTTATTTAAAT
1 AAAATAATATTTATTTAAAT
3417116 TTTTTAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATAATATTTATTTAAAT
Found at i:3418077 original size:17 final size:18
Alignment explanation
Indices: 3418039--3418076 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3418029 TATTATGTAT
3418039 AAATAATTTTTTTTTAAA
1 AAATAATTTTTTTTTAAA
3418057 AAATAATTTTTTTTTAAA
1 AAATAATTTTTTTTTAAA
3418075 AA
1 AA
3418077 TTATCGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATAATTTTTTTTTAAA
Found at i:3418624 original size:22 final size:22
Alignment explanation
Indices: 3418599--3418640 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3418589 ATATATAAAA
3418599 ATAATTTTAT-ATTAATATTTTT
1 ATAATTTTATAATTAA-ATTTTT
3418621 ATAATTTTATAATTAAATTT
1 ATAATTTTATAATTAAATTT
3418641 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAATTTTATAATTAAATTTTT
Found at i:3418646 original size:22 final size:22
Alignment explanation
Indices: 3418597--3418646 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3418587 AAATATATAA
3418597 AAATAATTTTATATTAATATTT
1 AAATAATTTTATATTAATATTT
**
3418619 TTATAATTTTATAATTAA-ATTT
1 AAATAATTTTAT-ATTAATATTT
3418641 AAATAA
1 AAATAA
3418647 AAATATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATAATTTTATATTAATATTT
Found at i:3428700 original size:29 final size:29
Alignment explanation
Indices: 3428640--3428703 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
3428630 TCGAATCACT
*
3428640 ATTTAATTAATAAAAAATATTTTTATTAA
1 ATTTAATTAATAAAAAATATTTTTATAAA
3428669 ATTTAATT-AT-AAAAATATTTTTAATAACA
1 ATTTAATTAATAAAAAATATTTTT-ATAA-A
3428698 ATTTAA
1 ATTTAA
3428704 AGTTTATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 12 0.38
28 5 0.16
29 15 0.47
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTAATTAATAAAAAATATTTTTATAAA
Found at i:3431209 original size:23 final size:23
Alignment explanation
Indices: 3431165--3431210 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3431155 TCAATAAATT
* * *
3431165 TAATTTATATTTAATTATTTTAA
1 TAATTTAAATTGAATTAATTTAA
*
3431188 TAATTTAAATTGATTTAATTTAA
1 TAATTTAAATTGAATTAATTTAA
3431211 ATTATTAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATTTAAATTGAATTAATTTAA
Found at i:3431237 original size:33 final size:35
Alignment explanation
Indices: 3431194--3431279 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 35
3431184 TTAATAATTT
*
3431194 AAATTGATTTAATTTAAATTATTAATAAT-ATA-AA
1 AAATT-ATTTAATTTAAATTATAAATAATAATATAA
* *
3431228 AAATTATTTAA-ATATAATTATAAATATTAATATAA
1 AAATTATTTAATTTA-AATTATAAATAATAATATAA
3431263 AAATTATTT-ATTTAAAT
1 AAATTATTTAATTTAAAT
3431280 AATGAGTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 2 0.05
33 17 0.39
34 12 0.27
35 13 0.30
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (35 bp):
AAATTATTTAATTTAAATTATAAATAATAATATAA
Found at i:3431256 original size:39 final size:38
Alignment explanation
Indices: 3431203--3431280 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 38
3431193 TAAATTGATT
3431203 TAATTTAAATTATTAATAATATAAAA-AATTATTTAAATA
1 TAATTTAAATTATTAAT-ATA-AAAATAATTATTTAAATA
*
3431242 TAATTATAAA-TATTAATATAAAAATTATTTATTTAAATA
1 TAATT-TAAATTATTAATATAAAAA-TAATTATTTAAATA
3431281 ATGAGTTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
37 4 0.11
38 3 0.09
39 24 0.69
40 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (38 bp):
TAATTTAAATTATTAATATAAAAATAATTATTTAAATA
Found at i:3431745 original size:20 final size:21
Alignment explanation
Indices: 3431722--3431897 Score: 103
Period size: 20 Copynumber: 8.9 Consensus size: 21
3431712 AAATTAAATT
3431722 TAATAATAT-TAAATATATTA
1 TAATAATATATAAATATATTA
*
3431742 TAAT--TATAT--ATATATGA
1 TAATAATATATAAATATATTA
*
3431759 TAA-AAAATATAAATATATAATA
1 TAATAATATATAAATATAT--TA
*
3431781 TAA-AAAATATAAATATA--A
1 TAATAATATATAAATATATTA
**
3431799 TACGAATATATAAATATATTA
1 TAATAATATATAAATATATTA
* * *
3431820 AAAT-TTATATAACATAAATTA
1 TAATAATATATAA-ATATATTA
*
3431841 T--TAATATATAAAAAT-TTA
1 TAATAATATATAAATATATTA
*
3431859 T-ATAAAATATATAATATAATTA
1 TAATAATATATA-AATAT-ATTA
*
3431881 TAATATTATA-AAATATA
1 TAATAATATATAAATATA
3431898 AAAATTTATA
Statistics
Matches: 121, Mismatches: 18, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
17 10 0.08
18 14 0.12
19 25 0.21
20 29 0.24
21 14 0.12
22 23 0.19
23 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
TAATAATATATAAATATATTA
Found at i:3431777 original size:22 final size:22
Alignment explanation
Indices: 3431747--3431797 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 22
3431737 TATTATAATT
3431747 ATATATATATGATAAAAAATATAA
1 ATATATA-AT-ATAAAAAATATAA
3431771 ATATATAATATAAAAAATATAA
1 ATATATAATATAAAAAATATAA
3431793 ATATA
1 ATATA
3431798 ATACGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 18 0.67
23 2 0.07
24 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATATATAATATAAAAAATATAA
Found at i:3431797 original size:15 final size:16
Alignment explanation
Indices: 3431769--3431877 Score: 58
Period size: 14 Copynumber: 6.9 Consensus size: 16
3431759 TAAAAAATAT
3431769 AAATATATAATATAAA
1 AAATATATAATATAAA
3431785 AAATATA-AATATAATA
1 AAATATATAATATAA-A
* *
3431801 CGAATATATAAATATATTA
1 -AAATATAT-AATATA-AA
3431820 AAAT-T-T-ATATAACA
1 AAATATATAATATAA-A
3431834 TAAAT-TATTAATATATAA
1 -AAATATA-TAATATA-AA
3431852 AAAT-T-T-ATAT--A
1 AAATATATAATATAAA
3431863 AAATATATAATATAA
1 AAATATATAATATAA
3431878 TTATAATATT
Statistics
Matches: 73, Mismatches: 4, Indels: 32
0.67 0.04 0.29
Matches are distributed among these distances:
11 5 0.07
12 1 0.01
13 1 0.01
14 14 0.19
15 13 0.18
16 9 0.12
17 13 0.18
18 9 0.12
19 8 0.11
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (16 bp):
AAATATATAATATAAA
Found at i:3431883 original size:32 final size:32
Alignment explanation
Indices: 3431803--3431883 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
3431793 ATATAATACG
*
3431803 AATATATAA-AT-A-TATTAAAATTTATATAA
1 AATATATAATATAATTATAAAAATTTATATAA
* * *
3431832 CATAAATTAT-TAATATATAAAAATTTATATAA
1 AATATATAATATAAT-TATAAAAATTTATATAA
3431864 AATATATAATATAATTATAA
1 AATATATAATATAATTATAA
3431884 TATTATAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
29 7 0.17
30 1 0.03
32 28 0.70
33 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
AATATATAATATAATTATAAAAATTTATATAA
Found at i:3431941 original size:47 final size:46
Alignment explanation
Indices: 3431846--3431955 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 46
3431836 AATTATTAAT
* * *
3431846 ATATAAAAATTTATATAAAATATATAATATAATTATAATATTATAAA
1 ATATAAAAATTTATAT-TAATATATAATATAATTAGAATATTAAAAA
* *
3431893 ATATAAAAATTTATATTAATATATAA-ATTATTCAGACTATTTAAAAA
1 ATATAAAAATTTATATTAATATATAATATAATT-AGAATA-TTAAAAA
* *
3431940 AT-TAATATTTTATATT
1 ATATAAAAATTTATATT
3431956 TACCTAAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
45 5 0.09
46 25 0.46
47 24 0.44
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (46 bp):
ATATAAAAATTTATATTAATATATAATATAATTAGAATATTAAAAA
Found at i:3432598 original size:33 final size:32
Alignment explanation
Indices: 3432541--3432610 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
3432531 GTTTGATGCA
*
3432541 ATTTAAATTATTATTTAATAATAAAAAT-TTT
1 ATTTAAATTATTATTTAAAAATAAAAATATTT
3432572 ATTTAAATT-TTATTATAAAAATATAAAAATATTT
1 ATTTAAATTATTATT-T-AAAA-ATAAAAATATTT
3432606 -TTTAA
1 ATTTAA
3432611 CATCATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 5 0.15
31 10 0.29
32 3 0.09
33 13 0.38
34 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
ATTTAAATTATTATTTAAAAATAAAAATATTT
Found at i:3432901 original size:18 final size:18
Alignment explanation
Indices: 3432874--3432917 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3432864 TGCATCAATT
* *
3432874 ATATATATTTATATGTAA
1 ATATAAATTTAAATGTAA
3432892 ATATAAATTTTAAATGTAA
1 ATATAAA-TTTAAATGTAA
3432911 A-ATAAAT
1 ATATAAAT
3432918 AAGTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
ATATAAATTTAAATGTAA
Found at i:3432908 original size:19 final size:18
Alignment explanation
Indices: 3432881--3432917 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3432871 ATTATATATA
*
3432881 TTTATATGTAAATATAAAT
1 TTTAAATGTAAA-ATAAAT
3432900 TTTAAATGTAAAATAAAT
1 TTTAAATGTAAAATAAAT
3432918 AAGTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
TTTAAATGTAAAATAAAT
Found at i:3433382 original size:23 final size:21
Alignment explanation
Indices: 3433351--3433412 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
3433341 ACCAATTTTT
*
3433351 TTTTCATTTTCTTTTATAAAATA
1 TTTTGATTTT-TTTTAT-AAATA
* *
3433374 TTTTGATTTTTTATATAATTA
1 TTTTGATTTTTTTTATAAATA
3433395 TTGTTCGATTTTTTTTAT
1 TT-TT-GATTTTTTTTAT
3433413 TTTCACTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.18
22 7 0.21
23 20 0.61
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTGATTTTTTTTATAAATA
Found at i:3433387 original size:20 final size:23
Alignment explanation
Indices: 3433362--3433408 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3433352 TTTCATTTTC
3433362 TTTTATA-AAATATT-TT-GATT
1 TTTTATATAAATATTGTTCGATT
*
3433382 TTTTATATAATTATTGTTCGATT
1 TTTTATATAAATATTGTTCGATT
3433405 TTTT
1 TTTT
3433409 TTATTTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 2 0.09
23 8 0.35
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTTATATAAATATTGTTCGATT
Found at i:3434153 original size:27 final size:26
Alignment explanation
Indices: 3434123--3434207 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
3434113 TTATTAAAAA
3434123 AATTAAAAATTTTAAAATATATTTAAT
1 AATTAAAAATTTT-AAATATATTTAAT
* * * *
3434150 AATTAAAATATTTTATATAAAATAAAT
1 AATTAAAA-ATTTTAAATATATTTAAT
* *
3434177 AATTAAATATTTT-AATTTATTTAAT
1 AATTAAAAATTTTAAATATATTTAAT
*
3434202 ATTTAA
1 AATTAA
3434208 TATATATAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
25 12 0.26
26 5 0.11
27 24 0.52
28 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTAAAAATTTTAAATATATTTAAT
Found at i:3434155 original size:18 final size:18
Alignment explanation
Indices: 3434134--3434169 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3434124 ATTAAAAATT
3434134 TTAAAATATATTTA-ATAA
1 TTAAAATAT-TTTATATAA
3434152 TTAAAATATTTTATATAA
1 TTAAAATATTTTATATAA
3434170 AATAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATATTTTATATAA
Found at i:3434189 original size:54 final size:54
Alignment explanation
Indices: 3434119--3434237 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
3434109 ATTATTATTA
3434119 AAAAAATTAAAAATTTTAAAATATATTTAATAATTAA-A-ATAT-TTTATATAAAAT
1 AAAAAATTAAAAATTTT--AATATATTTAATAATTAATATATATATTTATAT-AAAT
* * * *
3434173 AAATAATTAAATATTTTAATTTATTTAATATTTAATATATATAATTTATATAAAT
1 AAAAAATTAAAAATTTTAATATATTTAATAATTAATATATAT-ATTTATATAAAT
3434228 AAAAAATTAA
1 AAAAAATTAA
3434238 TATAAAAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
52 16 0.29
53 1 0.02
54 19 0.34
55 13 0.23
56 7 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (54 bp):
AAAAAATTAAAAATTTTAATATATTTAATAATTAATATATATATTTATATAAAT
Found at i:3434240 original size:17 final size:17
Alignment explanation
Indices: 3434215--3434274 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
3434205 TAATATATAT
* *
3434215 AATTTATATAAATAAAA
1 AATTAATATAAATAATA
3434232 AATTAATATAAA-AATTA
1 AATTAATATAAATAA-TA
3434249 AATTAAT-TAAAT-ATA
1 AATTAATATAAATAATA
3434264 AATT-ATATAAA
1 AATTAATATAAA
3434275 AAATTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 7 0.18
17 19 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTAATATAAATAATA
Found at i:3434267 original size:15 final size:17
Alignment explanation
Indices: 3434231--3434276 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 17
3434221 TATAAATAAA
3434231 AAATTAATATAAAAATT
1 AAATTAATATAAAAATT
*
3434248 AAATTAAT-TAAATA-T
1 AAATTAATATAAAAATT
3434263 AAATT-ATATAAAAA
1 AAATTAATATAAAAA
3434277 ATTATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 5 0.19
17 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTAATATAAAAATT
Found at i:3434341 original size:2 final size:2
Alignment explanation
Indices: 3434334--3434363 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3434324 ACCTCTTTTA
3434334 AT AT 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 AT AT
3434364 GAAAAACTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3434719 original size:2 final size:2
Alignment explanation
Indices: 3434712--3434756 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3434702 AAAATTCACA
3434712 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3434754 TC T
1 TC T
3434757 TTTTTGTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3440368 original size:2 final size:2
Alignment explanation
Indices: 3440361--3440399 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3440351 TTGATAATCC
3440361 TA TA TA TA 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 TA T
3440400 TATCAATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3442032 original size:77 final size:77
Alignment explanation
Indices: 3441905--3442049 Score: 256
Period size: 77 Copynumber: 1.9 Consensus size: 77
3441895 ATTACAAATT
* *
3441905 CATTTTTCTCTATTAAAGGAATAATGTTCCTCTAGAAGAGCCTTTCAAGGGTGGAGCAGTATGTT
1 CATTTTTCCCTATTAAAGGAATAATGTTCCTCTAGAAGAGCCTTTCAAGGGTGGAGCAGTATGCT
3441970 ATAGATAATATG
66 ATAGATAATATG
3441982 CATTTTTCCCTATTAAAGGAATAATG-TCACTCTAGAAGAGCCTTTCAAGGGTGGAGCAGTATGC
1 CATTTTTCCCTATTAAAGGAATAATGTTC-CTCTAGAAGAGCCTTTCAAGGGTGGAGCAGTATGC
3442046 TATA
65 TATA
3442050 AATTATATCA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
76 2 0.03
77 63 0.97
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (77 bp):
CATTTTTCCCTATTAAAGGAATAATGTTCCTCTAGAAGAGCCTTTCAAGGGTGGAGCAGTATGCT
ATAGATAATATG
Found at i:3446301 original size:2 final size:2
Alignment explanation
Indices: 3446294--3446331 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3446284 AAACACTTGA
3446294 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3446332 TATTAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3446444 original size:17 final size:17
Alignment explanation
Indices: 3446399--3446444 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
3446389 TTATTCTAAG
3446399 TTTATTT-AAGTTTGAA
1 TTTATTTAAAGTTTGAA
**
3446415 TTTATTTTGAGTTTGAA
1 TTTATTTAAAGTTTGAA
3446432 TATT-TTTAAAGTT
1 T-TTATTTAAAGTT
3446445 AAATAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 7 0.28
17 16 0.64
18 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (17 bp):
TTTATTTAAAGTTTGAA
Found at i:3447791 original size:28 final size:29
Alignment explanation
Indices: 3447757--3447819 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3447747 TAATCATAAA
*
3447757 ATTAAATTA-TTAAAAT-ATTATAGTTAAT
1 ATTAAA-TACTTAAAATAATAATAGTTAAT
* *
3447785 ATTAAATACTTAAAATAATAATATTTATT
1 ATTAAATACTTAAAATAATAATAGTTAAT
3447814 ATTAAA
1 ATTAAA
3447820 AATAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.07
28 13 0.43
29 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTAAATACTTAAAATAATAATAGTTAAT
Found at i:3447842 original size:19 final size:19
Alignment explanation
Indices: 3447798--3447855 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
3447788 AAATACTTAA
**
3447798 AATAATAATATTTATTAT-T
1 AATAATAAT-TTTAAAATAT
*
3447817 AAAAATAATTTTAAAATAT
1 AATAATAATTTTAAAATAT
*
3447836 AATAATAATTATGAAAATAT
1 AATAATAATT-TTAAAATAT
3447856 TATTTCTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.19
19 18 0.56
20 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AATAATAATTTTAAAATAT
Found at i:3448060 original size:14 final size:15
Alignment explanation
Indices: 3448043--3448071 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3448033 AATAATATTG
3448043 TTTTATT-AAATAAT
1 TTTTATTAAAATAAT
3448057 TTTTATTAAAATAAT
1 TTTTATTAAAATAAT
3448072 GAATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTATTAAAATAAT
Found at i:3448366 original size:18 final size:19
Alignment explanation
Indices: 3448343--3448387 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3448333 TTTAAAAAAA
*
3448343 TTTTATTTAT-AAATTATT
1 TTTTATTGATCAAATTATT
3448361 TTTTATTGATCAAATTATT
1 TTTTATTGATCAAATTATT
3448380 TTATTATT
1 TT-TTATT
3448388 AAAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
19 10 0.42
20 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATTGATCAAATTATT
Found at i:3448394 original size:19 final size:19
Alignment explanation
Indices: 3448353--3448394 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3448343 TTTTATTTAT
**
3448353 AAATTATTTTTTATTGATC
1 AAATTATTTTTTATTGAAA
3448372 AAATTATTTTATTATT-AAA
1 AAATTATTTT-TTATTGAAA
3448391 AAAT
1 AAAT
3448395 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
AAATTATTTTTTATTGAAA
Found at i:3448476 original size:17 final size:19
Alignment explanation
Indices: 3448446--3448482 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
3448436 AATTTTTAAA
3448446 ATATTATATAAATTTATAT
1 ATATTATATAAATTTATAT
3448465 ATATTA-AT-AATTTATAT
1 ATATTATATAAATTTATAT
3448482 A
1 A
3448483 ATATAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTATATAAATTTATAT
Found at i:3454917 original size:32 final size:30
Alignment explanation
Indices: 3454846--3454917 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 30
3454836 ATAAAAATAT
* *
3454846 AATTTTATATATTCATAAAAGATTTATAAA
1 AATTTAATATATTCATAAAAGATATATAAA
* *
3454876 AATTAAATATATTTATATAAA-ATATATAACA
1 AATTTAATATATTCATA-AAAGATATATAA-A
3454907 ATATTTAATAT
1 A-ATTTAATAT
3454918 TTACGTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 21 0.62
31 5 0.15
32 8 0.24
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
AATTTAATATATTCATAAAAGATATATAAA
Found at i:3458230 original size:3 final size:3
Alignment explanation
Indices: 3458222--3458250 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3458212 TTCCTCCAAA
3458222 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3458251 GCCTTCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3459007 original size:33 final size:34
Alignment explanation
Indices: 3458959--3459035 Score: 131
Period size: 33 Copynumber: 2.3 Consensus size: 34
3458949 TATTCAATCA
*
3458959 ATTTAAA-TTATTATTTATATAATAAA-TTTTTT
1 ATTTAAATTTATTATTTATACAATAAATTTTTTT
3458991 ATTTAAATTTATTATTTATACAATAAATTTTTTT
1 ATTTAAATTTATTATTTATACAATAAATTTTTTT
3459025 ATTTAAATTTA
1 ATTTAAATTTA
3459036 ACTGTAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
32 7 0.17
33 18 0.43
34 17 0.40
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (34 bp):
ATTTAAATTTATTATTTATACAATAAATTTTTTT
Found at i:3459217 original size:23 final size:22
Alignment explanation
Indices: 3459187--3459233 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3459177 TGTAATAATT
3459187 TTTAAAATATAATATTT-AATAAA
1 TTTAAAATATAA-ATTTCAA-AAA
*
3459210 TTTAAAATTTAAATTTCAAAAA
1 TTTAAAATATAAATTTCAAAAA
3459232 TT
1 TT
3459234 ACAATTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAAATATAAATTTCAAAAA
Found at i:3464264 original size:2 final size:2
Alignment explanation
Indices: 3464257--3464286 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3464247 TGCAGAGGGG
3464257 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3464287 CGCACAGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3465496 original size:2 final size:2
Alignment explanation
Indices: 3465491--3465520 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3465481 ATATATATAT
3465491 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3465521 CCTGAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3465719 original size:18 final size:18
Alignment explanation
Indices: 3465696--3465732 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3465686 ATAGGTATTT
3465696 TTCTTTCCTTTTCTTTTC
1 TTCTTTCCTTTTCTTTTC
**
3465714 TTCTTTGTTTTTCTTTTC
1 TTCTTTCCTTTTCTTTTC
3465732 T
1 T
3465733 CTCCGTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.76
Consensus pattern (18 bp):
TTCTTTCCTTTTCTTTTC
Found at i:3465984 original size:20 final size:21
Alignment explanation
Indices: 3465946--3465992 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
3465936 TAATAATTTG
3465946 TTAATAATTAAAAAATTAAATT
1 TTAA-AATTAAAAAATTAAATT
* *
3465968 TTAAAATT-AAAAGTTAATTT
1 TTAAAATTAAAAAATTAAATT
3465988 TTAAA
1 TTAAA
3465993 TAAAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
21 4 0.17
22 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAAATTAAAAAATTAAATT
Found at i:3466136 original size:16 final size:15
Alignment explanation
Indices: 3466108--3466165 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
3466098 TTTTGTTACA
3466108 TTTTTAAATAAATAT
1 TTTTTAAATAAATAT
*
3466123 TTTTTAAATCAAAT-G
1 TTTTTAAAT-AAATAT
*
3466138 TTTTTAACCTAAATAT
1 TTTTTAA-ATAAATAT
*
3466154 ATTTTTTAATAA
1 -TTTTTAAATAA
3466166 CCATCTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 20 0.59
16 8 0.24
17 6 0.18
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTTTAAATAAATAT
Found at i:3472138 original size:40 final size:40
Alignment explanation
Indices: 3472092--3472172 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 40
3472082 GAATACGATA
*
3472092 TAAATATAAAAATATTATAATAAATATAATATA-A-TTTATT
1 TAAATAT--AAATAATATAATAAATATAATATATATTTTATT
* *
3472132 TAAATATAATTAATATAATAAATTTAATATATATTTTATT
1 TAAATATAAATAATATAATAAATATAATATATATTTTATT
3472172 T
1 T
3472173 TATTTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 21 0.58
39 1 0.03
40 14 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (40 bp):
TAAATATAAATAATATAATAAATATAATATATATTTTATT
Found at i:3472158 original size:14 final size:14
Alignment explanation
Indices: 3472107--3472162 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
3472097 ATAAAAATAT
*
3472107 TATAATAAATATAA
1 TATAATAAATTTAA
**
3472121 TATAATTTATTTAA
1 TATAATAAATTTAA
3472135 -AT-AT-AA-TTAA
1 TATAATAAATTTAA
3472145 TATAATAAATTTAA
1 TATAATAAATTTAA
3472159 TATA
1 TATA
3472163 TATTTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 4 0.12
11 3 0.09
12 4 0.12
13 4 0.12
14 19 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAATAAATTTAA
Found at i:3472203 original size:15 final size:16
Alignment explanation
Indices: 3472174--3472203 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3472164 ATTTTATTTT
3472174 ATTTAAAATTAAATAA
1 ATTTAAAATTAAATAA
3472190 ATTTAAAA-TAAATA
1 ATTTAAAATTAAATA
3472204 TGATATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTTAAAATTAAATAA
Found at i:3472652 original size:2 final size:2
Alignment explanation
Indices: 3472645--3472673 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3472635 GTGGGTCCTT
3472645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3472674 TTCAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3472976 original size:21 final size:21
Alignment explanation
Indices: 3472951--3472990 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3472941 TTTTTTTAAT
3472951 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
*
3472972 TAAATATTAATATAGAATA
1 TAAATATTAATATAAAATA
3472991 AGAGTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:3473281 original size:11 final size:10
Alignment explanation
Indices: 3473251--3473284 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3473241 TATAAAAATT
3473251 TATATATTTA
1 TATATATTTA
3473261 TATATATTTA
1 TATATATTTA
*
3473271 TATCGTATTTA
1 TAT-ATATTTA
3473282 TAT
1 TAT
3473285 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (10 bp):
TATATATTTA
Found at i:3473372 original size:66 final size:65
Alignment explanation
Indices: 3473245--3473378 Score: 155
Period size: 66 Copynumber: 2.0 Consensus size: 65
3473235 ATTAAATATA
* * * * *
3473245 AAAATTTATATATTTATATATATTTATATCGTATTTATATTAATTTTTTTATTATAATAATATTC
1 AAAATTTATATATTTATATAAATTTATAACATATTAATATTAATTTTTATATTATAATAATATTC
*
3473310 AAAATATTATATATTTATATAAATTT-TAACATATTAATAATTTATATTTTATATATTTTAAT-A
1 AAAAT-TTATATATTTATATAAATTTATAACATATTAAT-A-TTA-ATTTT-TATATTATAATAA
3473373 TATTC
61 TATTC
3473378 A
1 A
3473379 TATATTCATA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
65 14 0.24
66 20 0.34
67 3 0.05
68 12 0.21
69 9 0.16
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (65 bp):
AAAATTTATATATTTATATAAATTTATAACATATTAATATTAATTTTTATATTATAATAATATTC
Found at i:3473395 original size:27 final size:24
Alignment explanation
Indices: 3473343--3473395 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
3473333 TTTTAACATA
* *
3473343 TTAATAATTTATATTTTATATATT
1 TTAATAATTCATATTTCATATATT
3473367 TTAATATATTCATATATTCATATTATT
1 TTAATA-ATTCATAT-TTCATA-TATT
3473394 TT
1 TT
3473396 TCTCTTATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 7 0.29
26 5 0.21
27 6 0.25
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TTAATAATTCATATTTCATATATT
Found at i:3473906 original size:14 final size:16
Alignment explanation
Indices: 3473877--3473910 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
3473867 ATTAAATAAT
3473877 TATTAATTATTTTATA
1 TATTAATTATTTTATA
3473893 TATTAA-TA-TTTATA
1 TATTAATTATTTTATA
3473907 TATT
1 TATT
3473911 TTTATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 2 0.11
16 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTAATTATTTTATA
Found at i:3473963 original size:28 final size:29
Alignment explanation
Indices: 3473868--3473963 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 29
3473858 TTTAAAATAA
*
3473868 TTAAATAATTATTAATTATTTTATATATTAATAT
1 TTAAAT-ATT-TT-ATTA-TTTAAATATTAA-AT
* *
3473902 TTATATATTTT-TATAATTAAAT-TTAAAT
1 TTAAATATTTTAT-TATTTAAATATTAAAT
**
3473930 AAAAATATTTTATTATTTAAATATT-AAT
1 TTAAATATTTTATTATTTAAATATTAAAT
3473958 TTAAAT
1 TTAAAT
3473964 TGAATTAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 25 0.50
29 7 0.14
30 6 0.12
31 2 0.04
32 2 0.04
33 3 0.06
34 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTAAATATTTTATTATTTAAATATTAAAT
Found at i:3475051 original size:15 final size:16
Alignment explanation
Indices: 3475015--3475054 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3475005 TTTAATATTT
*
3475015 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
3475032 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
3475047 ATAAAATT
1 ATAAAATT
3475055 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:3475057 original size:16 final size:17
Alignment explanation
Indices: 3475015--3475057 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3475005 TTTAATATTT
*
3475015 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
3475032 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
3475047 ATAAAATTTAT
1 ATAAAATTTAT
3475058 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:3475600 original size:15 final size:14
Alignment explanation
Indices: 3475573--3475609 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
3475563 AATGCATAAA
3475573 TTTTTTCTCTTTTTC
1 TTTTTT-TCTTTTTC
3475588 TTTCTTTTCTTTTTC
1 TTT-TTTTCTTTTTC
3475603 TTTTTTT
1 TTTTTTT
3475610 ATCAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 14 0.67
16 3 0.14
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:3476492 original size:28 final size:28
Alignment explanation
Indices: 3476460--3476522 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3476450 TTATCAACAT
*
3476460 ATTAAAACTAAATGCATATATTTATTTA
1 ATTAAAACTAAATACATATATTTATTTA
* * * * *
3476488 ATTAATAGTATATATATTTATTTATTTA
1 ATTAAAACTAAATACATATATTTATTTA
3476516 ATTAAAA
1 ATTAAAA
3476523 ATATAATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (28 bp):
ATTAAAACTAAATACATATATTTATTTA
Found at i:3476535 original size:28 final size:28
Alignment explanation
Indices: 3476478--3476533 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3476468 TAAATGCATA
* *
3476478 TATTTATTTAATTAATAGTATATATATT
1 TATTTATTTAATTAAAAATATATATATT
3476506 TATTTATTTAATTAAAAATATA-ATATT
1 TATTTATTTAATTAAAAATATATATATT
3476533 T
1 T
3476534 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTTATTTAATTAAAAATATATATATT
Done.