Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 115 of 172
Found at i:38438428 original size:7 final size:7
Alignment explanation
Indices: 38438383--38438471 Score: 61
Period size: 7 Copynumber: 12.6 Consensus size: 7
38438373 GAGTTACTAT
*
38438383 TTTAAGG
1 TTTATGG
38438390 TTTATGG
1 TTTATGG
*
38438397 ATTATGAG
1 TTTATG-G
*
38438405 TTTAGGG
1 TTTATGG
*
38438412 GTTATGG
1 TTTATGG
*
38438419 TTTATAG
1 TTTATGG
38438426 TTTATGG
1 TTTATGG
* *
38438433 TTTAAGA
1 TTTATGG
*
38438440 TTTAGGG
1 TTTATGG
*
38438447 TTTAAGG
1 TTTATGG
* **
38438454 GTTGCGG
1 TTTATGG
38438461 TTTATGG
1 TTTATGG
38438468 TTTA
1 TTTA
38438472 ATGTTATAGG
Statistics
Matches: 61, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
7 56 0.92
8 5 0.08
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:38438510 original size:21 final size:21
Alignment explanation
Indices: 38438486--38438549 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
38438476 TATAGGTTAA
38438486 GGGTTGAGGTTTAAGGTTTAG
1 GGGTTGAGGTTTAAGGTTTAG
38438507 GGGTTGAGAG-TTAAGAG-TTAG
1 GGGTTGAG-GTTTAAG-GTTTAG
* *
38438528 GGGTTTAGGATTTAGGGTTTAG
1 GGGTTGAGG-TTTAAGGTTTAG
38438550 ATTAATTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 1 0.03
21 25 0.69
22 10 0.28
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (21 bp):
GGGTTGAGGTTTAAGGTTTAG
Found at i:38438548 original size:7 final size:7
Alignment explanation
Indices: 38438404--38438549 Score: 50
Period size: 7 Copynumber: 20.9 Consensus size: 7
38438394 TGGATTATGA
38438404 GTTTAGG
1 GTTTAGG
* *
38438411 GGTTATG
1 GTTTAGG
**
38438418 GTTTATA
1 GTTTAGG
*
38438425 GTTTATG
1 GTTTAGG
*
38438432 GTTTAAG
1 GTTTAGG
*
38438439 ATTTAGG
1 GTTTAGG
38438446 GTTTAAGG
1 GTTT-AGG
38438454 G-TT-GCG
1 GTTTAG-G
*
38438460 GTTTATG
1 GTTTAGG
**
38438467 GTTTAAT
1 GTTTAGG
38438474 GTTATA-G
1 GTT-TAGG
*
38438481 GTTAAGG
1 GTTTAGG
*
38438488 GTTGA-G
1 GTTTAGG
*
38438494 GTTTAAG
1 GTTTAGG
38438501 GTTTAGGG
1 GTTTA-GG
* *
38438509 GTTGAGA
1 GTTTAGG
* *
38438516 GTTAAGA
1 GTTTAGG
38438523 G-TTAGGG
1 GTTTA-GG
38438530 GTTTAGG
1 GTTTAGG
*
38438537 ATTTAGG
1 GTTTAGG
38438544 GTTTAG
1 GTTTAG
38438550 ATTAATTAGT
Statistics
Matches: 105, Mismatches: 24, Indels: 20
0.70 0.16 0.13
Matches are distributed among these distances:
5 1 0.01
6 10 0.10
7 80 0.76
8 14 0.13
ACGTcount: A:0.22, C:0.01, G:0.36, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:38438676 original size:16 final size:17
Alignment explanation
Indices: 38438657--38438698 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
38438647 AAATTCTTTA
38438657 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
38438673 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
38438690 TAAAATAAT
1 T-AAATAAT
38438699 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:38438915 original size:21 final size:22
Alignment explanation
Indices: 38438891--38438931 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38438881 ATGGTTTATT
38438891 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
*
38438912 GTTTAGGGGTTAGGGATTTA
1 GTTTAAGGGTTAGGGATTTA
38438932 GGGTTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:38439321 original size:22 final size:22
Alignment explanation
Indices: 38439295--38439339 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
38439285 ACTAATAATT
38439295 TTTAACAAATAAAATAAA-AAAA
1 TTTAACAAAT-AAATAAATAAAA
38439317 TTTAACAAATAAATAAATAAAA
1 TTTAACAAATAAATAAATAAAA
38439339 T
1 T
38439340 CACTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
TTTAACAAATAAATAAATAAAA
Found at i:38439425 original size:38 final size:39
Alignment explanation
Indices: 38439342--38439426 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
38439332 AATAAAATCA
*
38439342 CTAAAAATAAGCATTAGCGGCGCTTTTCGGAAAACGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
* * *
38439381 CTAAAAATGAGCATTAGTGGCG-TTTTTAGAAAAGCGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAA-CGCCG
*
38439420 CAAAAAA
1 CTAAAAA
38439427 ACTAGGCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.22
39 31 0.77
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
Found at i:38440299 original size:38 final size:38
Alignment explanation
Indices: 38440219--38440300 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
38440209 GGTTACAAAC
* * * *
38440219 TTTATCTGTTTTTTATATGTTTATCTCACAAATTTTCT
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
38440257 TTTATCTGCTTTTTACATGTTTATCTCACAAA-GTTCGG
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTC-G
38440295 TTTATC
1 TTTATC
38440301 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (38 bp):
TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
Found at i:38444507 original size:43 final size:43
Alignment explanation
Indices: 38444460--38444547 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
38444450 GTTTGTTTTT
* *
38444460 AAAGCGTCGCTAAAGGTCAGGGTCTTTAGCGACGTTTGTTGGA
1 AAAGCGTCGCTAAAGGTCAGCGTCTTTAGCGACGTTTGTGGGA
* *
38444503 AAAGCGTCGCTAAAGGTCATCGTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGTCGCTAAAGGTCAGCGTCTTTAGCGACGTTTGTGGGA
38444546 AA
1 AA
38444548 GCGCCACTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (43 bp):
AAAGCGTCGCTAAAGGTCAGCGTCTTTAGCGACGTTTGTGGGA
Found at i:38446349 original size:12 final size:11
Alignment explanation
Indices: 38446290--38446349 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
38446280 TTTTTATAAA
*
38446290 AAATAAAATTT
1 AAATAAAATAT
* *
38446301 ATATAAAATCT
1 AAATAAAATAT
38446312 -AATAAAATAT
1 AAATAAAATAT
*
38446322 AAATTAAAAAATT
1 AAA-TAAAATA-T
38446335 AAATAAAATTAT
1 AAATAAAA-TAT
38446347 AAA
1 AAA
38446350 AAAGTAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
10 8 0.21
11 11 0.28
12 15 0.38
13 5 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:38446545 original size:26 final size:26
Alignment explanation
Indices: 38446516--38446586 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
38446506 GTTATACATC
38446516 ATTAATAAATAATAAAATTAT-ATCTT
1 ATTAATAAATAATAAAATTATGA-CTT
* *
38446542 ATTATTAAATAA-AAAAATATGACTT
1 ATTAATAAATAATAAAATTATGACTT
* *
38446567 ATAAATAAATACTAATAATT
1 ATTAATAAATAATAA-AATT
38446587 TTATTTAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
25 19 0.53
26 14 0.39
27 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (26 bp):
ATTAATAAATAATAAAATTATGACTT
Found at i:38446851 original size:18 final size:19
Alignment explanation
Indices: 38446818--38446853 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38446808 AAAGTTAACT
*
38446818 TTTTAGTGTGTAATTTGGG
1 TTTTAGGGTGTAATTTGGG
38446837 TTTTAGGGT-TAATTTGG
1 TTTTAGGGTGTAATTTGG
38446854 TGAAAGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.53
Consensus pattern (19 bp):
TTTTAGGGTGTAATTTGGG
Found at i:38452594 original size:42 final size:42
Alignment explanation
Indices: 38452546--38452626 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
38452536 GAAGGGTAAA
38452546 TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTTAAG
1 TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTTAAG
*
38452588 TTTATGTTTGAATTTATATGAGCTTACTAAACACTAGTT
1 TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTT
38452627 GCTTACATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (42 bp):
TTTATGTTTGAATTTATACGAGCTTACTAAACACTAGTTAAG
Found at i:38456409 original size:24 final size:24
Alignment explanation
Indices: 38456382--38456429 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
38456372 CCCTCACTAT
38456382 CAACAT-TGTCCCCACCCTCAGTCC
1 CAACATCT-TCCCCACCCTCAGTCC
* *
38456406 CAACATCTTCTCCACCTTCAGTCC
1 CAACATCTTCCCCACCCTCAGTCC
38456430 TAGAATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.21, C:0.48, G:0.06, T:0.25
Consensus pattern (24 bp):
CAACATCTTCCCCACCCTCAGTCC
Found at i:38459598 original size:20 final size:20
Alignment explanation
Indices: 38459573--38459614 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
38459563 AGAGGAGATT
38459573 AATCTGGATCTTAGGTGAAA
1 AATCTGGATCTTAGGTGAAA
38459593 AATCTGGATCTTAGGTGAAA
1 AATCTGGATCTTAGGTGAAA
38459613 AA
1 AA
38459615 GTAAGGCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (20 bp):
AATCTGGATCTTAGGTGAAA
Found at i:38461706 original size:48 final size:50
Alignment explanation
Indices: 38461647--38461742 Score: 133
Period size: 48 Copynumber: 1.9 Consensus size: 50
38461637 TTCCAAAAAA
* *
38461647 TAATAATATTTTAATAGTTTGATATTAAATTAA-AT-TTAATATTAATCT
1 TAATAATATTTTAATAATTTAATATTAAATTAATATCTTAATATTAATCT
* *
38461695 TAATAGTATTTTATTAATTTAATATTAAATTAATTATCTTAATATTAA
1 TAATAATATTTTAATAATTTAATATTAAATTAA-TATCTTAATATTAA
38461743 GTCTAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 29 0.71
50 2 0.05
51 10 0.24
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (50 bp):
TAATAATATTTTAATAATTTAATATTAAATTAATATCTTAATATTAATCT
Found at i:38461722 original size:11 final size:11
Alignment explanation
Indices: 38461679--38461728 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
38461669 TATTAAATTA
38461679 AATTTAATATT
1 AATTTAATATT
*
38461690 AATCTTAATAGT
1 AAT-TTAATATT
38461702 -ATTT--TATT
1 AATTTAATATT
38461710 AATTTAATATT
1 AATTTAATATT
*
38461721 AAATTAAT
1 AATTTAAT
38461729 TATCTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
8 3 0.09
9 4 0.12
10 2 0.06
11 16 0.50
12 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AATTTAATATT
Found at i:38466224 original size:200 final size:200
Alignment explanation
Indices: 38465881--38466281 Score: 714
Period size: 200 Copynumber: 2.0 Consensus size: 200
38465871 GATGACTTGA
* * *
38465881 TTACTATTTGATGGTAGTTGGCTTTTCATGAATGAAGATGTAATGATTACCATGAGATAAAATAG
1 TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGAGATAAAATAA
*
38465946 AATCATATAAGGAGAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
66 AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
*
38466011 TATGATAAGGTCATTGAA-AGAGCATTGATTGAGTTGATTTAGTACTGGTATGCTATTGGGGAGA
131 TATGATAAGGTCATTGAACA-AGCATTGATTGAGTTGATTTAGTAATGGTATGCTATTGGGGAGA
38466075 GCTCGG
195 GCTCGG
*
38466081 TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGGGATAAAATAA
1 TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGAGATAAAATAA
*
38466146 AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTGAGGATATCCTATGAGGATAACACACT
66 AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
*
38466211 TATGATAAGGTCATTGAACAAGCATTGATTGAGTTGATTTAGTAATGGTATGCTGTTGGGGAGAG
131 TATGATAAGGTCATTGAACAAGCATTGATTGAGTTGATTTAGTAATGGTATGCTATTGGGGAGAG
38466276 CTCGG
196 CTCGG
38466281 T
1 T
38466282 CATGATACTA
Statistics
Matches: 192, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
200 191 0.99
201 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (200 bp):
TTACTATTTGATGGTAGTTGGCTTTTCATAAATGAAGATGCAATGATTACCATGAGATAAAATAA
AATCATATAAGGAAAAAGGATATTATCCCAAAGAAATTAAGGATATCCTATGAGGATAACACACT
TATGATAAGGTCATTGAACAAGCATTGATTGAGTTGATTTAGTAATGGTATGCTATTGGGGAGAG
CTCGG
Found at i:38470214 original size:27 final size:27
Alignment explanation
Indices: 38470162--38470223 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
38470152 GGAATACATA
* * *
38470162 ATGTATGTGTGTATATGTAATATATTT
1 ATGTATTTCTGTATATGTAATATATTC
*
38470189 ATGTATTTCTGTATATGTTAA-GTATTC
1 ATGTATTTCTGTATATG-TAATATATTC
*
38470216 ATGCATTT
1 ATGTATTT
38470224 GCCCATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (27 bp):
ATGTATTTCTGTATATGTAATATATTC
Found at i:38470364 original size:30 final size:30
Alignment explanation
Indices: 38470328--38470385 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
38470318 ATGTGTATAT
*
38470328 ATATGCATATCCGTATGTGTATATATATGC
1 ATATGCATATACGTATGTGTATATATATGC
*
38470358 ATATGCATATACGTATGTGTATGTATAT
1 ATATGCATATACGTATGTGTATATATAT
38470386 ATTAAGCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
ATATGCATATACGTATGTGTATATATATGC
Found at i:38470373 original size:24 final size:24
Alignment explanation
Indices: 38470322--38470373 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38470312 GTAGGAATGT
* **
38470322 GTATATATATGCATATCCGTATGT
1 GTATATATATGCATATCCATATAC
*
38470346 GTATATATATGCATATGCATATAC
1 GTATATATATGCATATCCATATAC
38470370 GTAT
1 GTAT
38470374 GTGTATGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (24 bp):
GTATATATATGCATATCCATATAC
Found at i:38471119 original size:12 final size:12
Alignment explanation
Indices: 38471082--38471127 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
38471072 TTTATCTGTG
38471082 TGTGTATATATA
1 TGTGTATATATA
** *
38471094 TGTGTGCATCTA
1 TGTGTATATATA
38471106 TGTGTATATATA
1 TGTGTATATATA
*
38471118 TGTATATATA
1 TGTGTATATA
38471128 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.48
Consensus pattern (12 bp):
TGTGTATATATA
Found at i:38473159 original size:20 final size:21
Alignment explanation
Indices: 38473136--38473180 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
38473126 TTTCTTTGTC
*
38473136 ATAATCATA-TTTAA-ATGTTT
1 ATAAT-ATATTTTAATATGTTG
38473156 ATAA-ATATTTTAATATGTTG
1 ATAATATATTTTAATATGTTG
38473176 ATAAT
1 ATAAT
38473181 TAATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 3 0.14
19 5 0.24
20 13 0.62
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
ATAATATATTTTAATATGTTG
Found at i:38474549 original size:22 final size:22
Alignment explanation
Indices: 38474523--38474570 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
38474513 GATTTGTGAG
* *
38474523 TATAAATGAATTTGGCTTTTTA
1 TATAAACGAATTTGCCTTTTTA
38474545 TATAAACGAATTTGCCTTTTTA
1 TATAAACGAATTTGCCTTTTTA
38474567 TATA
1 TATA
38474571 GACAAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (22 bp):
TATAAACGAATTTGCCTTTTTA
Found at i:38477610 original size:43 final size:43
Alignment explanation
Indices: 38477562--38477644 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
38477552 AAAAAAGCGT
38477562 CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAACGC
1 CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAACGC
* * * *
38477605 CGCTAAAGAACATGGCTTTTAGCGGCGCTTTTGTCACAAA
1 CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAA
38477645 AGCCATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (43 bp):
CGCTAAAGAACATGACATTTAGCGGCACTTTTATCACAAACGC
Found at i:38478423 original size:13 final size:14
Alignment explanation
Indices: 38478396--38478425 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
38478386 TACTAATGAC
38478396 TAATTAAACCATTA
1 TAATTAAACCATTA
38478410 TAATTAAA-CATTA
1 TAATTAAACCATTA
38478423 TAA
1 TAA
38478426 ATATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTAAACCATTA
Found at i:38482679 original size:40 final size:40
Alignment explanation
Indices: 38482624--38482759 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 40
38482614 TTTGGTCAAC
* **
38482624 CTATAGCGGCGTTTTTTAAAAAGTACCGCTAATGCTCGAT
1 CTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
* * *
38482664 CTATAGTGGCATTTTTCAAAAAGCGCCGCTGATGCTCGA-
1 CTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
*
38482703 CTTATAGCGGTGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
1 C-TATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
*
38482744 CTATAGTGGCGTTTTT
1 CTATAGCGGCGTTTTT
38482760 GGTCCTAGTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 80 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (40 bp):
CTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGAT
Found at i:38487849 original size:6 final size:6
Alignment explanation
Indices: 38487838--38487867 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
38487828 CGACGAAAAA
*
38487838 GACGGG GACGGG GACGGT GACGGG GACGGG
1 GACGGG GACGGG GACGGG GACGGG GACGGG
38487868 TCGGATATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.63, T:0.03
Consensus pattern (6 bp):
GACGGG
Found at i:38493294 original size:20 final size:20
Alignment explanation
Indices: 38493265--38493304 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38493255 AGTGATATGA
38493265 TAAAAAAAAATTAA-AAATAT
1 TAAAAAAAAA-TAATAAATAT
*
38493285 TAAAATAAAATAATAAATAT
1 TAAAAAAAAATAATAAATAT
38493305 ACCATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAAAAATAATAAATAT
Found at i:38496082 original size:10 final size:10
Alignment explanation
Indices: 38496067--38496096 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
38496057 AAAGCCTAAT
38496067 CCAAAATAAA
1 CCAAAATAAA
38496077 CCAAAATAAA
1 CCAAAATAAA
38496087 CCAAAATAAA
1 CCAAAATAAA
38496097 AATAAACCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (10 bp):
CCAAAATAAA
Found at i:38499995 original size:15 final size:14
Alignment explanation
Indices: 38499960--38499996 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38499950 TTTCTGTCGC
38499960 GATTTTTAGTTTTA
1 GATTTTTAGTTTTA
*
38499974 GACTTTTAGTTTTA
1 GATTTTTAGTTTTA
38499988 GGATTTTTA
1 -GATTTTTA
38499997 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.22, C:0.03, G:0.16, T:0.59
Consensus pattern (14 bp):
GATTTTTAGTTTTA
Found at i:38501785 original size:8 final size:8
Alignment explanation
Indices: 38501774--38501818 Score: 58
Period size: 7 Copynumber: 5.8 Consensus size: 8
38501764 TATTATTTTG
38501774 AAATTTAA
1 AAATTTAA
38501782 AAATTT-A
1 AAATTTAA
38501789 AAATTT-A
1 AAATTTAA
38501796 AAATTTAA
1 AAATTTAA
*
38501804 AATTTTATA
1 AAATTTA-A
38501813 AAATTT
1 AAATTT
38501819 TAGTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 14 0.42
8 13 0.39
9 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTAA
Found at i:38501793 original size:7 final size:7
Alignment explanation
Indices: 38501774--38501808 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
38501764 TATTATTTTG
38501774 AAATTTAA
1 AAATTT-A
38501782 AAATTTA
1 AAATTTA
38501789 AAATTTA
1 AAATTTA
38501796 AAATTTA
1 AAATTTA
38501803 AAATTT
1 AAATTT
38501809 TATAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATTTA
Found at i:38501800 original size:14 final size:15
Alignment explanation
Indices: 38501774--38501818 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 15
38501764 TATTATTTTG
38501774 AAATTTAAAAATTTA
1 AAATTTAAAAATTTA
38501789 AAATTT-AAAATTTA
1 AAATTTAAAAATTTA
38501803 AAATTTTATAAAATTT
1 AAA-TTTA-AAAATTT
38501819 TAGTTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.41
15 9 0.33
17 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTAAAAATTTA
Found at i:38503975 original size:20 final size:18
Alignment explanation
Indices: 38503938--38503976 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
38503928 TATATAACTT
*
38503938 AATTTTTATAACAATTAG
1 AATTTTTATAAAAATTAG
38503956 AATTATTTATAAGAAATTAG
1 AATT-TTTATAA-AAATTAG
38503976 A
1 A
38503977 TGAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTTTTATAAAAATTAG
Found at i:38506329 original size:6 final size:6
Alignment explanation
Indices: 38506318--38506357 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
38506308 CAACCGAACA
*
38506318 TTCACC TTCACC TTCACC CTCACC TTCACC TTCACC TTCA
1 TTCACC TTCACC TTCACC TTCACC TTCACC TTCACC TTCA
38506358 AGGTAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TTCACC
Found at i:38510921 original size:33 final size:33
Alignment explanation
Indices: 38510879--38510978 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
38510869 CAAACCTTCC
**
38510879 ACGGAAACCGCTGATTCGGAACAGCCGGCGACG
1 ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
*
38510912 ACGGAAACCGCTGGTTCCAAACAGCCGGCGACG
1 ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
* * * *
38510945 ACGGAAACCGCCGACTCCAAGCAACCGGCGACG
1 ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
38510978 A
1 A
38510979 AACCTTCATC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.29, C:0.34, G:0.30, T:0.07
Consensus pattern (33 bp):
ACGGAAACCGCTGATTCCAAACAGCCGGCGACG
Found at i:38511006 original size:42 final size:42
Alignment explanation
Indices: 38510943--38511117 Score: 167
Period size: 42 Copynumber: 4.2 Consensus size: 42
38510933 CAGCCGGCGA
* * *
38510943 CGACGGAAACCGCCG-ACTCCAAGCAACCGGCGACGAAACCTT
1 CGACGGAAAAC-CCGAAATCCAAACAACCGGCGACGAAACCTT
* *
38510985 C-ATCGGAAAACCCGGAATCCAAAAAACCGGCGACGAAACCTT
1 CGA-CGGAAAACCCGAAATCCAAACAACCGGCGACGAAACCTT
*
38511027 CGACGGAAACCCCGAAATCCAAACAACCGGCGACGAAACCTT
1 CGACGGAAAACCCGAAATCCAAACAACCGGCGACGAAACCTT
* ** * * *** *
38511069 TGAAAG-AAACCTCGGAATCTAAACAATTAGCGACGAAACCGT
1 CGACGGAAAACC-CGAAATCCAAACAACCGGCGACGAAACCTT
38511111 CGACGGA
1 CGACGGA
38511118 CACATCAGAA
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
41 8 0.07
42 99 0.92
43 1 0.01
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (42 bp):
CGACGGAAAACCCGAAATCCAAACAACCGGCGACGAAACCTT
Found at i:38511085 original size:84 final size:83
Alignment explanation
Indices: 38510943--38511117 Score: 203
Period size: 84 Copynumber: 2.1 Consensus size: 83
38510933 CAGCCGGCGA
* * *
38510943 CGACGGAAACCGCCGACTCCAAGCAACCGGCGACGAAACCTTCATCGGAAAACCCGGAATCCAAA
1 CGACGGAAACCGCCGAATCCAAACAACCGGCGACGAAACCTT-ATCGAAAAACCCGGAATCCAAA
* *
38511008 AAACCGGCGACGAAACCTT
65 AAACCAGCGACGAAACCGT
*
38511027 CGACGGAAACC-CCGAAATCCAAACAACCGGCGACGAAACCTT-T-GAAAGAAACCTCGGAATCT
1 CGACGGAAACCGCCG-AATCCAAACAACCGGCGACGAAACCTTATCG-AA-AAACC-CGGAATCC
* **
38511089 AAACAATTAGCGACGAAACCGT
62 AAAAAACCAGCGACGAAACCGT
38511111 CGACGGA
1 CGACGGA
38511118 CACATCAGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
81 1 0.01
82 2 0.03
83 8 0.10
84 67 0.86
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (83 bp):
CGACGGAAACCGCCGAATCCAAACAACCGGCGACGAAACCTTATCGAAAAACCCGGAATCCAAAA
AACCAGCGACGAAACCGT
Found at i:38512372 original size:16 final size:16
Alignment explanation
Indices: 38512341--38512377 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
38512331 ATGTGAATAA
38512341 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
38512357 TATT-TTTAAAACTTAT
1 TATTATTTAAAA-TTAT
38512373 TATTA
1 TATTA
38512378 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:38512427 original size:22 final size:22
Alignment explanation
Indices: 38512401--38512444 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38512391 ATATTCAATA
38512401 ATTTATTAAAATAATAAATTAT
1 ATTTATTAAAATAATAAATTAT
* * *
38512423 ATTTATTATATTAATAATTTAT
1 ATTTATTAAAATAATAAATTAT
38512445 TATATGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTAAAATAATAAATTAT
Found at i:38512692 original size:16 final size:16
Alignment explanation
Indices: 38512661--38512697 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
38512651 ATGTGAATAA
38512661 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
38512677 TATT-TTTAAAACTTAT
1 TATTATTTAAAA-TTAT
38512693 TATTA
1 TATTA
38512698 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:38512747 original size:22 final size:22
Alignment explanation
Indices: 38512721--38512764 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38512711 ATATTCAATA
38512721 ATTTATTAAAATAATAAATTAT
1 ATTTATTAAAATAATAAATTAT
* * *
38512743 ATTTATTATATTAATAATTTAT
1 ATTTATTAAAATAATAAATTAT
38512765 TATATGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTAAAATAATAAATTAT
Found at i:38512808 original size:320 final size:320
Alignment explanation
Indices: 38512226--38512865 Score: 1280
Period size: 320 Copynumber: 2.0 Consensus size: 320
38512216 ACATAGACTT
38512226 ATGACATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATTTACAATTGTAATGAAT
1 ATGACATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATTTACAATTGTAATGAAT
38512291 ATTTATTATTAAAATATTAATATTGAATATTTTTAATAATATGTGAATAATATTATTTAAAATTA
66 ATTTATTATTAAAATATTAATATTGAATATTTTTAATAATATGTGAATAATATTATTTAAAATTA
38512356 TTATTTTTAAAACTTATTATTAAAATAAAATTGAAATATTCAATAATTTATTAAAATAATAAATT
131 TTATTTTTAAAACTTATTATTAAAATAAAATTGAAATATTCAATAATTTATTAAAATAATAAATT
38512421 ATATTTATTATATTAATAATTTATTATATGACTAAATATAAATAATCGTATGTTTAATAATATTA
196 ATATTTATTATATTAATAATTTATTATATGACTAAATATAAATAATCGTATGTTTAATAATATTA
38512486 AAAATATAATATTTTAAATATTTTTAAAAATAAAAAAAATTTATTATCAATATAATAATG
261 AAAATATAATATTTTAAATATTTTTAAAAATAAAAAAAATTTATTATCAATATAATAATG
38512546 ATGACATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATTTACAATTGTAATGAAT
1 ATGACATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATTTACAATTGTAATGAAT
38512611 ATTTATTATTAAAATATTAATATTGAATATTTTTAATAATATGTGAATAATATTATTTAAAATTA
66 ATTTATTATTAAAATATTAATATTGAATATTTTTAATAATATGTGAATAATATTATTTAAAATTA
38512676 TTATTTTTAAAACTTATTATTAAAATAAAATTGAAATATTCAATAATTTATTAAAATAATAAATT
131 TTATTTTTAAAACTTATTATTAAAATAAAATTGAAATATTCAATAATTTATTAAAATAATAAATT
38512741 ATATTTATTATATTAATAATTTATTATATGACTAAATATAAATAATCGTATGTTTAATAATATTA
196 ATATTTATTATATTAATAATTTATTATATGACTAAATATAAATAATCGTATGTTTAATAATATTA
38512806 AAAATATAATATTTTAAATATTTTTAAAAATAAAAAAAATTTATTATCAATATAATAATG
261 AAAATATAATATTTTAAATATTTTTAAAAATAAAAAAAATTTATTATCAATATAATAATG
38512866 TTAAGCTTGA
Statistics
Matches: 320, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 320 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (320 bp):
ATGACATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATTTACAATTGTAATGAAT
ATTTATTATTAAAATATTAATATTGAATATTTTTAATAATATGTGAATAATATTATTTAAAATTA
TTATTTTTAAAACTTATTATTAAAATAAAATTGAAATATTCAATAATTTATTAAAATAATAAATT
ATATTTATTATATTAATAATTTATTATATGACTAAATATAAATAATCGTATGTTTAATAATATTA
AAAATATAATATTTTAAATATTTTTAAAAATAAAAAAAATTTATTATCAATATAATAATG
Found at i:38515669 original size:16 final size:17
Alignment explanation
Indices: 38515642--38515681 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
38515632 ATTTAATGTG
38515642 TAATTAATTTAAAATTC
1 TAATTAATTTAAAATTC
*
38515659 TAATTAA-TTAAAATTT
1 TAATTAATTTAAAATTC
38515675 TAATTAA
1 TAATTAA
38515682 AAATCTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTAATTTAAAATTC
Found at i:38518372 original size:14 final size:15
Alignment explanation
Indices: 38518353--38518385 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38518343 ACACTAAAAT
38518353 TTATTTTA-AAATAA
1 TTATTTTATAAATAA
*
38518367 TTATTTTATAGATAA
1 TTATTTTATAAATAA
38518382 TTAT
1 TTAT
38518386 ATGATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATTTTATAAATAA
Found at i:38526275 original size:15 final size:15
Alignment explanation
Indices: 38526255--38526309 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
38526245 ATATGATGTT
38526255 TTTTAGGGTTTAGAG
1 TTTTAGGGTTTAGAG
* *
38526270 TTTTAGGGGTTATAG
1 TTTTAGGGTTTAGAG
* *
38526285 -TTTAGTGTTTAGGAC
1 TTTTAGGGTTTA-GAG
38526300 TTTTAGGGTT
1 TTTTAGGGTT
38526310 CAAGGGTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 9 0.29
15 14 0.45
16 8 0.26
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.49
Consensus pattern (15 bp):
TTTTAGGGTTTAGAG
Found at i:38526371 original size:53 final size:52
Alignment explanation
Indices: 38526256--38526371 Score: 142
Period size: 53 Copynumber: 2.2 Consensus size: 52
38526246 TATGATGTTT
* *
38526256 TTTAGGGTTTAGAGTTTTAGGGGTTATAGTTTAGTGTTTAGGACTTTTAGGG
1 TTTAAGGTTTAGAGTTTTAGGGGTTATAGATTAGTGTTTAGGACTTTTAGGG
* * * * **
38526308 TTCAAGGGTTTAGTGTTTTAGGGGTTATAGATTAGTGTTTATGATTTTTTTTGG
1 TTTAA-GGTTTAGAGTTTTAGGGGTTATAGATTAGTGTTTAGGA-CTTTTAGGG
38526362 TTTAAGGTTT
1 TTTAAGGTTT
38526372 TACAGAAAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
52 3 0.06
53 40 0.75
54 10 0.19
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (52 bp):
TTTAAGGTTTAGAGTTTTAGGGGTTATAGATTAGTGTTTAGGACTTTTAGGG
Found at i:38526414 original size:41 final size:41
Alignment explanation
Indices: 38526368--38526521 Score: 181
Period size: 41 Copynumber: 3.8 Consensus size: 41
38526358 TTGGTTTAAG
*
38526368 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCAGC
1 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
* * **
38526409 GTTTTACCGAAAGCGCCGCTAATGCTCTAGTTTTTAATGGC
1 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
* *
38526450 GTTTTACCGAAAGCGCCGCTATTGCTCT-GTTTTTAGCGGC
1 GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
* * *
38526490 G--TTCCA-AAAACGCCGCTATTGCTCTGTGTTTT
1 GTTTTACAGAAAGCGCCGCTAATGCTCTG-GTTTT
38526522 ACAATTTTTG
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
37 18 0.18
38 3 0.03
39 5 0.05
40 11 0.11
41 63 0.63
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
GTTTTACAGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGC
Found at i:38530591 original size:26 final size:26
Alignment explanation
Indices: 38530542--38530591 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
38530532 AATTAACTTT
*
38530542 AATATTAAATTTAATCTAAAATTATA
1 AATATTAAATTAAATCTAAAATTATA
* * *
38530568 AATATTAGATTAAATTTAATATTA
1 AATATTAAATTAAATCTAAAATTA
38530592 AATCTTATTA
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:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATTAAATTAAATCTAAAATTATA
Found at i:38530871 original size:23 final size:23
Alignment explanation
Indices: 38530845--38530888 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
38530835 CTGGCCATTG
38530845 GGACACTATCTTA-CCAGCCACCA
1 GGACACTATC-TACCCAGCCACCA
38530868 GGACACTATCTACCCAGCCAC
1 GGACACTATCTACCCAGCCAC
38530889 TGGCATCACC
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:0.30, C:0.41, G:0.14, T:0.16
Consensus pattern (23 bp):
GGACACTATCTACCCAGCCACCA
Found at i:38532392 original size:15 final size:15
Alignment explanation
Indices: 38532368--38532397 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38532358 TATAAATGCA
*
38532368 AAATATAAAAGACAT
1 AAATACAAAAGACAT
38532383 AAATACAAAAGACAT
1 AAATACAAAAGACAT
38532398 TGTACAAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:38534702 original size:76 final size:76
Alignment explanation
Indices: 38534576--38534724 Score: 289
Period size: 76 Copynumber: 2.0 Consensus size: 76
38534566 ATCGTTTTAG
38534576 TAAATCTTAAATTTTATTAAAATGATTAATCAAGGGTGATCCGATCACACCTCATAAAAAAGGAT
1 TAAATCTTAAATTTTATTAAAATGATTAATCAAGGGTGATCCGATCACACCTCATAAAAAAGGAT
38534641 TGGTGGCGGAA
66 TGGTGGCGGAA
*
38534652 TAAATCTTAAATTTTATTAAAATGATTAATCAAGGGTGATCCGATCACACCTCATCAAAAAGGAT
1 TAAATCTTAAATTTTATTAAAATGATTAATCAAGGGTGATCCGATCACACCTCATAAAAAAGGAT
38534717 TGGTGGCG
66 TGGTGGCG
38534725 ACTCCAGTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (76 bp):
TAAATCTTAAATTTTATTAAAATGATTAATCAAGGGTGATCCGATCACACCTCATAAAAAAGGAT
TGGTGGCGGAA
Found at i:38538032 original size:23 final size:23
Alignment explanation
Indices: 38538002--38538047 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
38537992 AGGAATTAAG
38538002 TTTGGTTCCAGACCTGGTACTCC
1 TTTGGTTCCAGACCTGGTACTCC
*
38538025 TTTGGTTCCGGACCTGGTACTCC
1 TTTGGTTCCAGACCTGGTACTCC
38538048 CTCCCAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (23 bp):
TTTGGTTCCAGACCTGGTACTCC
Found at i:38550075 original size:88 final size:86
Alignment explanation
Indices: 38549912--38550120 Score: 240
Period size: 88 Copynumber: 2.4 Consensus size: 86
38549902 CTAGAATTAG
* * * **
38549912 TGAATTCACAGATCTTACCCCATAAGCAGTAGGGGAATAGATCGAAGGCAACGAGCTTTAACCCC
1 TGAATTCACAGATCTTACCCCATAAGCAGTAGGGAAACAGATCCAAAACAACGAGCTTTAACCCC
* *
38549977 CTAAGTAGTAGGGTAACAAGC
66 CGAAGCAGTAGGGTAACAAGC
* *
38549998 TGAAGTTCATAGATCTTATCACCC-TAAGCAGTAGGGAAACAGATCCAAAATAACGAGCTTTAAC
1 TGAA-TTCACAGATCTTA-C-CCCATAAGCAGTAGGGAAACAGATCCAAAACAACGAGCTTTAAC
38550062 CCCCGAAGCAGTAGGGTAACAAGC
63 CCCCGAAGCAGTAGGGTAACAAGC
** * * * *
38550086 CAAATTTACAGACCTTAACCCCAAAAGTAGTAGGG
1 TGAATTCACAGATCTT-ACCCCATAAGCAGTAGGG
38550121 TAATAGGCTG
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
86 7 0.07
87 32 0.31
88 60 0.59
89 3 0.03
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (86 bp):
TGAATTCACAGATCTTACCCCATAAGCAGTAGGGAAACAGATCCAAAACAACGAGCTTTAACCCC
CGAAGCAGTAGGGTAACAAGC
Found at i:38550105 original size:43 final size:43
Alignment explanation
Indices: 38549969--38550123 Score: 123
Period size: 44 Copynumber: 3.6 Consensus size: 43
38549959 GCAACGAGCT
* * * * * *
38549969 TTAACCCCCTAAGTAGTAGGGTAACAAGCTGAAGTTCATAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGC-CAAATTAACAGACC
* * * * * *
38550013 TTATCACCCTAAGCAGTAGGGAAACAGATCCAAAATAAC-GAGCT
1 TTAACCCCCTAAGCAGTAGGGTAACA-AGCCAAATTAACAGA-CC
* *
38550057 TTAACCCCCGAAGCAGTAGGGTAACAAGCCAAATTTACAGACC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTAACAGACC
** *
38550100 TTAACCCCAAAAGTAGTAGGGTAA
1 TTAACCCCCTAAGCAGTAGGGTAA
38550124 TAGGCTGAAA
Statistics
Matches: 85, Mismatches: 23, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
43 33 0.39
44 50 0.59
45 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (43 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTAACAGACC
Found at i:38550305 original size:44 final size:44
Alignment explanation
Indices: 38550240--38550391 Score: 143
Period size: 44 Copynumber: 3.5 Consensus size: 44
38550230 AGATCTCAAC
* * * *
38550240 CCCCTAAGCAGTAGGGAAACAGATTGAAGATGAT-GAG-TCTTAAA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAA-AT-ATACAGACCTTAAA
* *
38550284 CCCCTAAGTAGTAGGGTAACAGGTT-AAATTTACAGACCTTAAA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAAATATACAGACCTTAAA
* * * *
38550327 CCCCTAAGCAGTAGGGTAACAGGTTG-AAT-TCAAAGGGCTTTAAC
1 CCCCTAAGCAGTAGGGTAACAGGTTGAAATAT-ACA-GACCTTAAA
38550371 CCCCTAAGCAGTAGGGTAACA
1 CCCCTAAGCAGTAGGGTAACA
38550392 AGCAGAATTT
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 37 0.40
44 49 0.53
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (44 bp):
CCCCTAAGCAGTAGGGTAACAGGTTGAAATATACAGACCTTAAA
Found at i:38550340 original size:43 final size:44
Alignment explanation
Indices: 38550278--38550391 Score: 158
Period size: 43 Copynumber: 2.6 Consensus size: 44
38550268 GATGATGAGT
* * *
38550278 CTTAAACCCCTAAGTAGTAGGGTAACAGGTTAAATTTACA-GAC
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTCAAAGGAC
* *
38550321 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGAATTCAAAGGGC
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTCAAAGGAC
* *
38550365 TTTAACCCCCTAAGCAGTAGGGTAACA
1 CTTAAACCCCTAAGCAGTAGGGTAACA
38550392 AGCAGAATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 36 0.57
44 27 0.43
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (44 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTCAAAGGAC
Found at i:38550457 original size:87 final size:87
Alignment explanation
Indices: 38550224--38550476 Score: 210
Period size: 87 Copynumber: 2.9 Consensus size: 87
38550214 CAGATTAAAG
* * * * * * * *
38550224 ATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGA-AGATGATGAGTCTTAAACCCC
1 ATTTACAGACCTTAAACCCCTAAGCAGTAGGGAAACAGA-TAATAGAAGATGGGCCTTAACCCCC
* * *
38550288 TAAGTAGTAGGGTAACAGGTTAA
65 TAAGCAGTAGGGTAACAAGTCAA
* * ** *
38550311 ATTTACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGAATTCAA-A-GGGCTTTAACCCC
1 ATTTACAGACCTTAAACCCCTAAGCAGTAGGGAAACA-GAT-AATAGAAGATGGGCCTTAACCCC
38550374 CTAAGCAGTAGGGTAACAAG-CAGA
64 CTAAGCAGTAGGGTAACAAGTCA-A
** * * * **
38550398 ATTTGTAGATCTT-ATCACCCTAAGCAGTAGGGAAACAGATCATAGAAGATGGGCCTTAACCCTT
1 ATTTACAGACCTTAAAC-CCCTAAGCAGTAGGGAAACAGATAATAGAAGATGGGCCTTAACCCCC
*
38550462 TACGCAGTAGGGTAA
65 TAAGCAGTAGGGTAA
38550477 TAGGCTGAAA
Statistics
Matches: 130, Mismatches: 29, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
85 4 0.03
86 6 0.05
87 116 0.89
88 3 0.02
89 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (87 bp):
ATTTACAGACCTTAAACCCCTAAGCAGTAGGGAAACAGATAATAGAAGATGGGCCTTAACCCCCT
AAGCAGTAGGGTAACAAGTCAA
Found at i:38550694 original size:43 final size:44
Alignment explanation
Indices: 38550585--38550695 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 44
38550575 CCATCAAGCT
* * * *
38550585 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAAATA
1 TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAATTTATAAACA
*** * * *
38550629 TTATTGCCTTAAGCAATAGGGTAACAAGC-CAAATTT-TCAAACC
1 TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAATTTAT-AAACA
38550672 TTAAACCCCTAAGCAGTAGGGTAA
1 TTAAACCCCTAAGCAGTAGGGTAA
38550696 TAGGTTGAGT
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
42 1 0.02
43 27 0.52
44 24 0.46
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (44 bp):
TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAATTTATAAACA
Found at i:38553249 original size:77 final size:77
Alignment explanation
Indices: 38553161--38553410 Score: 500
Period size: 77 Copynumber: 3.2 Consensus size: 77
38553151 ACGACGTGTT
38553161 GTGCCCTAACTTACTGGGTATCATACTTTTTGTTTTAAAATAAAGGTAATATTCGGTGTTTGAGA
1 GTGCCCTAACTTACTGGGTATCATACTTTTTGTTTTAAAATAAAGGTAATATTCGGTGTTTGAGA
38553226 ATTCGAGAAAAC
66 ATTCGAGAAAAC
38553238 GTGCCCTAACTTACTGGGTATCATACTTTTTGTTTTAAAATAAAGGTAATATTCGGTGTTTGAGA
1 GTGCCCTAACTTACTGGGTATCATACTTTTTGTTTTAAAATAAAGGTAATATTCGGTGTTTGAGA
38553303 ATTCGAGAAAAC
66 ATTCGAGAAAAC
38553315 GTGCCCTAACTTACTGGGTATCATACTTTTTGTTTTAAAATAAAGGTAATATTCGGTGTTTGAGA
1 GTGCCCTAACTTACTGGGTATCATACTTTTTGTTTTAAAATAAAGGTAATATTCGGTGTTTGAGA
38553380 ATTCGAGAAAAC
66 ATTCGAGAAAAC
38553392 GTGCCCTAACTTACTGGGT
1 GTGCCCTAACTTACTGGGT
38553411 TTCGATTTCC
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 173 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (77 bp):
GTGCCCTAACTTACTGGGTATCATACTTTTTGTTTTAAAATAAAGGTAATATTCGGTGTTTGAGA
ATTCGAGAAAAC
Found at i:38558947 original size:41 final size:41
Alignment explanation
Indices: 38558888--38558968 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
38558878 TCTCTTGTCT
38558888 ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAAA
1 ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAAA
*
38558929 ATCCCCAAATTTGCCCACCATAAGGTTGTATCTAACCCAA
1 ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAA
38558969 CCTAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.25
Consensus pattern (41 bp):
ATCCCCAAATTTGACCACCATAAGGTTGTATCTAACCCAAA
Found at i:38560702 original size:19 final size:19
Alignment explanation
Indices: 38560661--38560702 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
38560651 TTAATTAATT
*
38560661 ATTTAATTTTAATTTTAAT
1 ATTTAATTTTAATTTTAAG
*
38560680 ATTTAA-TTTAGTATTTAAG
1 ATTTAATTTTAAT-TTTAAG
38560699 ATTT
1 ATTT
38560703 TTTCTCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTTAATTTTAATTTTAAG
Found at i:38560782 original size:14 final size:14
Alignment explanation
Indices: 38560763--38560790 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38560753 TTCTTTATTC
38560763 CACATTATTGATTT
1 CACATTATTGATTT
38560777 CACATTATTGATTT
1 CACATTATTGATTT
38560791 GTGTACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
CACATTATTGATTT
Found at i:38561486 original size:16 final size:16
Alignment explanation
Indices: 38561465--38561497 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38561455 ATAATTGAAT
38561465 AAGTAAACCTTAATCA
1 AAGTAAACCTTAATCA
38561481 AAGTAAACCTTAATCA
1 AAGTAAACCTTAATCA
38561497 A
1 A
38561498 TGAACTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
AAGTAAACCTTAATCA
Found at i:38565843 original size:43 final size:42
Alignment explanation
Indices: 38565756--38565865 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 42
38565746 CAACTTTTGC
* *
38565756 TAAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATGAGACTTCATG
* * * *
38565798 TAAGACTATAGCTGGGCTATTGGCATCGATATGAGATTTTATG
1 TAAGACCATAGCTGGGATA-TGGCATCGATATGAGACTTCATG
**
38565841 TAAGACCATATTTGGGATATGGCAT
1 TAAGACCATAGCTGGGATATGGCAT
38565866 TGGTACAGCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 22 0.39
43 35 0.61
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (42 bp):
TAAGACCATAGCTGGGATATGGCATCGATATGAGACTTCATG
Found at i:38568621 original size:8 final size:8
Alignment explanation
Indices: 38568601--38568656 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
38568591 TTATTTGTTT
38568601 TATT-TTA
1 TATTATTA
*
38568608 TGTTATTA
1 TATTATTA
38568616 TATTATTA
1 TATTATTA
38568624 TATTATTA
1 TATTATTA
38568632 TATTA-TA
1 TATTATTA
*
38568639 TTATAATTA
1 -TATTATTA
38568648 TTATTATTA
1 -TATTATTA
38568657 CTTAAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 5 0.12
8 27 0.64
9 10 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATTATTA
Found at i:38568622 original size:3 final size:3
Alignment explanation
Indices: 38568610--38568656 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
38568600 TTATTTTATG
*
38568610 TTA TTA -TA TTA TTA -TA TTA TTA -TA TTA -TA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38568654 TTA
1 TTA
38568657 CTTAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 8 0.21
3 30 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:38570895 original size:39 final size:39
Alignment explanation
Indices: 38570841--38570918 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
38570831 AGAAGTTAAT
38570841 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
1 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
38570880 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
1 TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
38570919 CCCGCTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (39 bp):
TTCGAATGATGAAATCAAGAAGGCTCTATTTGATATGGC
Found at i:38574994 original size:26 final size:26
Alignment explanation
Indices: 38574965--38575018 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
38574955 TTGTGAAACA
38574965 TAGGTATGGTATCATCCATACTGAGT
1 TAGGTATGGTATCATCCATACTGAGT
*
38574991 TAGGTATGGTATTATCCATACTGAGT
1 TAGGTATGGTATCATCCATACTGAGT
38575017 TA
1 TA
38575019 AGAAACGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (26 bp):
TAGGTATGGTATCATCCATACTGAGT
Found at i:38575030 original size:35 final size:35
Alignment explanation
Indices: 38574991--38575075 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 35
38574981 CATACTGAGT
*
38574991 TAGGTATGGTATTAT-CCATACTGAGTT-AAGAAACG
1 TAGGTATGGTATT-TCCCATACCGAGTTGAA-AAACG
* * *
38575026 TAGGTATGGCATTTCCCATACCGAGTTGTAAAATG
1 TAGGTATGGTATTTCCCATACCGAGTTGAAAAACG
38575061 TAGGTATGGTATTTC
1 TAGGTATGGTATTTC
38575076 AATGAGGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 1 0.02
35 41 0.95
36 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (35 bp):
TAGGTATGGTATTTCCCATACCGAGTTGAAAAACG
Found at i:38576402 original size:14 final size:14
Alignment explanation
Indices: 38576383--38576414 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
38576373 ACGTATAATG
38576383 AACTCGAATCATAA
1 AACTCGAATCATAA
*
38576397 AACTCGAATCGTAA
1 AACTCGAATCATAA
38576411 AACT
1 AACT
38576415 ATTTATAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (14 bp):
AACTCGAATCATAA
Found at i:38576944 original size:17 final size:17
Alignment explanation
Indices: 38576922--38576954 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38576912 AGACTATGTA
*
38576922 ATGTTAGTTTTCTTAAC
1 ATGTTAATTTTCTTAAC
38576939 ATGTTAATTTTCTTAA
1 ATGTTAATTTTCTTAA
38576955 GTACCACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (17 bp):
ATGTTAATTTTCTTAAC
Found at i:38579278 original size:16 final size:15
Alignment explanation
Indices: 38579259--38579301 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
38579249 TGCATATAAT
*
38579259 TATTTTATTGTAATTA
1 TATTTTATTGTAA-AA
38579275 TATTTATATT-TAAAA
1 TATTT-TATTGTAAAA
38579290 TATTTTATTGTA
1 TATTTTATTGTA
38579302 TTTTTATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.17
15 8 0.33
16 8 0.33
17 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TATTTTATTGTAAAA
Found at i:38579429 original size:21 final size:22
Alignment explanation
Indices: 38579390--38579436 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
38579380 TTTTAACATT
**
38579390 TTTTTATTTGTGTGGTTTTATA
1 TTTTTATTTGTGTAATTTTATA
*
38579412 TTTTT-TTTGTGTAATTTTTTA
1 TTTTTATTTGTGTAATTTTATA
38579433 TTTT
1 TTTT
38579437 AATTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (22 bp):
TTTTTATTTGTGTAATTTTATA
Found at i:38580253 original size:128 final size:128
Alignment explanation
Indices: 38580025--38580281 Score: 451
Period size: 128 Copynumber: 2.0 Consensus size: 128
38580015 AACCAGTGGG
*
38580025 CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAATTAGGTTT
1 CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
* *
38580090 AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTTACTTAGGTTT
66 AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
* *
38580153 CCCACTACTAAATCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
1 CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
**
38580218 AGGGTAAATTACACCAACAGTCACCCAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
66 AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
38580281 C
1 C
38580282 ATTTCAATCA
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 122 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (128 bp):
CCCACTACCAAACCCATGTTTGGTTGATTGTAAAAGTTTATTATGTCTGCTTTGAAAATAGGTTT
AGGGTAAATTACACCAACAGTCACAAAACTTTGGGGTAGCTGACAAAACAGTCACCTAGGTTT
Found at i:38580863 original size:6 final size:6
Alignment explanation
Indices: 38580847--38581048 Score: 199
Period size: 6 Copynumber: 32.7 Consensus size: 6
38580837 TTCGATTTAA
* * *
38580847 ATTTAG ATTTTA ATTTTG ATTTTG ATTTCG ATTTTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
** ** *
38580895 ATTTTG ATTTTG ATTTCA ATTTTG AAACACTCACTG ATTCTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ----A-T-TTTG ATTTTG ATTTTG
** **
38580943 ATTTTG ATTTCA ATTTCA ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
* * *
38580991 ATTTTG ATTTCT- ATTTCG ATTTTG ATTTTG ATTTTG ATTTCG ATTTGG
1 ATTTTG ATTT-TG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
38581039 ATTTTG ATTT
1 ATTTTG ATTT
38581049 AAGGTTATTT
Statistics
Matches: 166, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
6 159 0.96
7 2 0.01
8 1 0.01
10 1 0.01
11 1 0.01
12 2 0.01
ACGTcount: A:0.21, C:0.06, G:0.14, T:0.59
Consensus pattern (6 bp):
ATTTTG
Found at i:38583406 original size:8 final size:8
Alignment explanation
Indices: 38583393--38583424 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
38583383 CTAGATCGGC
38583393 AAAAGCCG
1 AAAAGCCG
38583401 AAAAGCCG
1 AAAAGCCG
*
38583409 AAATGCCG
1 AAAAGCCG
38583417 AAAAGCCG
1 AAAAGCCG
38583425 GTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:38583711 original size:28 final size:28
Alignment explanation
Indices: 38583671--38583729 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
38583661 ATGTACTAGA
*
38583671 ATACCCCTATGTATACAAAATTACCATT
1 ATACCCCTATGTATACAAAATGACCATT
* *
38583699 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATACAAAATGACCATT
38583727 ATA
1 ATA
38583730 ACGCTAGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATACAAAATGACCATT
Found at i:38586056 original size:66 final size:66
Alignment explanation
Indices: 38585839--38586060 Score: 336
Period size: 67 Copynumber: 3.3 Consensus size: 66
38585829 TTTTAGTCAT
* * ** * *
38585839 TTTTTTAATATGCCTATAGTGATTGTTTTTGTGTGTGACTATTTTTTAATATACATGTTGTTGAC
1 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACT-GTTTTTAATATACATGTTGTTGAC
38585904 TA
65 TA
*
38585906 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTGTTTTTTAATATACATGATGTTGAC
1 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTG-TTTTTAATATACATGTTGTTGAC
38585971 TA
65 TA
* *
38585973 TTTTTTAATATGTATGCAGTGATTGTTGGTGTGTATGACTGTTTTTAATATACATGTTGTTGACT
1 TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTGTTTTTAATATACATGTTGTTGACT
38586038 A
66 A
*
38586039 TTTTTTAATATGCATGCAGTGA
1 TTTTTTAATATGCATACAGTGA
38586061 GTATTTTTTA
Statistics
Matches: 143, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
66 45 0.31
67 98 0.69
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (66 bp):
TTTTTTAATATGCATACAGTGATTGTTGGTGTGTATGACTGTTTTTAATATACATGTTGTTGACT
A
Found at i:38586065 original size:25 final size:26
Alignment explanation
Indices: 38586014--38586088 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
38586004 TGTATGACTG
* **
38586014 TTTTTAATATACATGTTGTTGACTA-T
1 TTTTTAATATGCATGCAG-TGACTATT
*
38586040 TTTTTAATATGCATGCAGTGAGTATT
1 TTTTTAATATGCATGCAGTGACTATT
38586066 TTTTAATAATATGCATGCAGTGA
1 TTTT--TAATATGCATGCAGTGA
38586089 TTGTTGGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.12
26 20 0.48
28 17 0.40
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (26 bp):
TTTTTAATATGCATGCAGTGACTATT
Found at i:38586146 original size:95 final size:94
Alignment explanation
Indices: 38585941--38586188 Score: 353
Period size: 95 Copynumber: 2.6 Consensus size: 94
38585931 TTGGTGTGTA
* * *
38585941 TGACTGTTTTTTAATATACATG-ATGTTGACTA-TTTTT--TAATATGTATGCAGTGATTGTTGG
1 TGACTATTTTTTAATATGCATGCA-G-TGACTATTTTTTAATAATATGCATGCAGTGATTGTTGG
38586002 TGTGTATGACTGTTTTTAATATACATGTTGT
64 TGTGTATGACTGTTTTTAATATACATGTTGT
*
38586033 TGACTATTTTTTAATATGCATGCAGTGAGTATTTTTTAATAATATGCATGCAGTGATTGTTGGTG
1 TGACTATTTTTTAATATGCATGCAGTGACTATTTTTTAATAATATGCATGCAGTGATTGTTGGTG
*
38586098 T-TATGACTGGTTTTTTAATGTACATGTTGT
66 TGTATGACT-G-TTTTTAATATACATGTTGT
* * *
38586128 TGACTATTTTTTAATATGCATGCAATGACTATTTTTTAATAATATGCATGTAGTTATTGTT
1 TGACTATTTTTTAATATGCATGCAGTGACTATTTTTTAATAATATGCATGCAGTGATTGTT
38586189 TTTAGGGGGG
Statistics
Matches: 141, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
91 5 0.04
92 26 0.18
93 8 0.06
94 27 0.19
95 75 0.53
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (94 bp):
TGACTATTTTTTAATATGCATGCAGTGACTATTTTTTAATAATATGCATGCAGTGATTGTTGGTG
TGTATGACTGTTTTTAATATACATGTTGT
Found at i:38588264 original size:17 final size:17
Alignment explanation
Indices: 38588242--38588274 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38588232 TAATTCACTT
38588242 TTCATATACAA-TCAATA
1 TTCATAT-CAATTCAATA
38588259 TTCATATCAATTCAAT
1 TTCATATCAATTCAAT
38588275 TAATCACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
TTCATATCAATTCAATA
Found at i:38588305 original size:10 final size:10
Alignment explanation
Indices: 38588293--38588344 Score: 77
Period size: 10 Copynumber: 5.2 Consensus size: 10
38588283 CATAATCATA
*
38588293 ATTCAATTCA
1 ATTCAATTCT
*
38588303 ATTCTATTCT
1 ATTCAATTCT
38588313 ATTCAATTCT
1 ATTCAATTCT
38588323 ATTCAATTCT
1 ATTCAATTCT
*
38588333 ATTCTATTCT
1 ATTCAATTCT
38588343 AT
1 AT
38588345 ACCACAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTCAATTCT
Found at i:38588316 original size:15 final size:15
Alignment explanation
Indices: 38588293--38588341 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
38588283 CATAATCATA
38588293 ATTCAATTCAATTCT
1 ATTCAATTCAATTCT
*
38588308 ATTCTATTCAATTCT
1 ATTCAATTCAATTCT
*
38588323 ATTCAATTCTATTCT
1 ATTCAATTCAATTCT
38588338 ATTC
1 ATTC
38588342 TATACCACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTCAATTCAATTCT
Found at i:38588342 original size:5 final size:5
Alignment explanation
Indices: 38588293--38588344 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
38588283 CATAATCATA
* * * *
38588293 ATTCA ATTCA ATTCT ATTCT ATTCA ATTCT ATTCA ATTCT ATTCT ATTCT
1 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT
38588343 AT
1 AT
38588345 ACCACAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (5 bp):
ATTCT
Found at i:38589599 original size:27 final size:26
Alignment explanation
Indices: 38589569--38589630 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
38589559 AGATAATTAA
38589569 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
38589596 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
38589623 AATAAAAT
1 AATAAAAT
38589631 AGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:38591207 original size:15 final size:15
Alignment explanation
Indices: 38591187--38591243 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
38591177 TTAATATCTG
*
38591187 AAAATAATAAATAAT
1 AAAATAATAAATAAA
38591202 AAAATAATAAGATAAA
1 AAAATAATAA-ATAAA
38591218 ATAAATAA-AAATAAA
1 A-AAATAATAAATAAA
38591233 AATAA-AATAAA
1 AA-AATAATAAA
38591244 AATTGGGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 3 0.08
15 21 0.57
16 7 0.19
17 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAA
Found at i:38591241 original size:11 final size:11
Alignment explanation
Indices: 38591192--38591246 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
38591182 ATCTGAAAAT
38591192 AATAAATAATAA
1 AATAAA-AATAA
38591204 AATAATAAGATAA
1 AATAA-AA-ATAA
*
38591217 AATAAATA-AA
1 AATAAAAATAA
38591227 AATAAAAATAA
1 AATAAAAATAA
38591238 AATAAAAAT
1 AATAAAAAT
38591247 TGGGTTGCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.24
11 12 0.32
12 7 0.18
13 10 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:38591243 original size:21 final size:25
Alignment explanation
Indices: 38591192--38591243 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 25
38591182 ATCTGAAAAT
38591192 AATAAATAATAAAATAATAAGATAA
1 AATAAATAATAAAATAATAAGATAA
38591217 AATAAAT-A-AAAATAA-AA-ATAA
1 AATAAATAATAAAATAATAAGATAA
38591238 AATAAA
1 AATAAA
38591244 AATTGGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.37
22 2 0.07
23 7 0.26
24 1 0.04
25 7 0.26
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (25 bp):
AATAAATAATAAAATAATAAGATAA
Found at i:38597491 original size:27 final size:26
Alignment explanation
Indices: 38597461--38597522 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
38597451 AGATAATTAA
38597461 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
38597488 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
38597515 AATAAAAT
1 AATAAAAT
38597523 GGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:38598672 original size:21 final size:21
Alignment explanation
Indices: 38598646--38598697 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
38598636 CAAGTTGTTG
* **
38598646 CCCCAACTCAGCAATAGGCTA
1 CCCCAACTCAGCAAGAGAATA
* *
38598667 CCCCAAATTAGCAAGAGAATA
1 CCCCAACTCAGCAAGAGAATA
38598688 CCCCAACTCA
1 CCCCAACTCA
38598698 ACAGGCTGCC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.13
Consensus pattern (21 bp):
CCCCAACTCAGCAAGAGAATA
Found at i:38599788 original size:12 final size:12
Alignment explanation
Indices: 38599752--38599794 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
38599742 ACTTCAGGCA
*
38599752 TCTTCATTTTTCC
1 TCTTC-TTTTTCT
*
38599765 TCTTCTTCTTCT
1 TCTTCTTTTTCT
*
38599777 TCTTTTTTTTCT
1 TCTTCTTTTTCT
38599789 TCTTCT
1 TCTTCT
38599795 CCTTCGTCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTCTTTTTCT
Found at i:38601580 original size:15 final size:16
Alignment explanation
Indices: 38601560--38601594 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
38601550 TTGGCTAGGT
38601560 TTTTG-AGGTAAGCTA
1 TTTTGAAGGTAAGCTA
38601575 TTTTGAAGGTAAGCTA
1 TTTTGAAGGTAAGCTA
38601591 TTTT
1 TTTT
38601595 CAAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (16 bp):
TTTTGAAGGTAAGCTA
Found at i:38602910 original size:23 final size:24
Alignment explanation
Indices: 38602883--38602928 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38602873 TAAATTTTGT
38602883 TCTATTATT-TAAA-TTTTATTTTA
1 TCTA-TATTATAAATTTTTATTTTA
38602906 TCTATATTATAAATTTTTATTTT
1 TCTATATTATAAATTTTTATTTT
38602929 TATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 8 0.38
24 9 0.43
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TCTATATTATAAATTTTTATTTTA
Found at i:38602938 original size:25 final size:22
Alignment explanation
Indices: 38602887--38602939 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
38602877 TTTTGTTCTA
38602887 TTATTTAAATTTTATTTTATCT
1 TTATTTAAATTTTATTTTATCT
* *
38602909 ATATTATAAATTTTTATTTTTATTT
1 TTATT-TAAA-TTTTA-TTTTATCT
38602934 TTATTT
1 TTATTT
38602940 TGATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 4 0.16
23 4 0.16
24 6 0.24
25 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTAAATTTTATTTTATCT
Found at i:38602974 original size:25 final size:24
Alignment explanation
Indices: 38602946--38602994 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
38602936 ATTTTGATGT
38602946 ATATAAATACTTTTATTTAAAAAAA
1 ATAT-AATACTTTTATTTAAAAAAA
**
38602971 ATATTTTACTTTTATTTAAAAAAA
1 ATATAATACTTTTATTTAAAAAAA
38602995 TATTATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATAATACTTTTATTTAAAAAAA
Found at i:38602995 original size:23 final size:24
Alignment explanation
Indices: 38602953--38602998 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
38602943 TGTATATAAA
38602953 TACTTTTATTTAAAAAAAATATTT
1 TACTTTTATTTAAAAAAAATATTT
38602977 TACTTTTATTT-AAAAAAATATT
1 TACTTTTATTTAAAAAAAATATT
38602999 ATTTCTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TACTTTTATTTAAAAAAAATATTT
Found at i:38603007 original size:21 final size:23
Alignment explanation
Indices: 38602953--38602998 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
38602943 TGTATATAAA
38602953 TACTTTTATTTAAAAAAAATATTT
1 TACTTTTATTTAAAAAAAATA-TT
38602977 TACTTTTATTT-AAAAAAATATT
1 TACTTTTATTTAAAAAAAATATT
38602999 ATTTCTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 9 0.41
24 11 0.50
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TACTTTTATTTAAAAAAAATATT
Found at i:38606753 original size:3 final size:3
Alignment explanation
Indices: 38606747--38606774 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38606737 TATTAAAATT
38606747 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
38606775 CTACCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:38607787 original size:47 final size:47
Alignment explanation
Indices: 38607718--38607814 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 47
38607708 CCTATTTTTA
**
38607718 GGCTCAGCCCGGACCCAATAAATGGGCATGATTTTTTAGTTGAGCTC
1 GGCTCAGCCCGGACCCAATAAATGAACATGATTTTTTAGTTGAGCTC
* * *
38607765 GGCTCGGCCCGGGCCCAATAAATGAACATTATTTTTTAGTTGAGCTC
1 GGCTCAGCCCGGACCCAATAAATGAACATGATTTTTTAGTTGAGCTC
38607812 GGC
1 GGC
38607815 CCAAACCCGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.28
Consensus pattern (47 bp):
GGCTCAGCCCGGACCCAATAAATGAACATGATTTTTTAGTTGAGCTC
Found at i:38607827 original size:47 final size:46
Alignment explanation
Indices: 38607725--38607827 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 46
38607715 TTAGGCTCAG
** * **
38607725 CCCGGACCCAATAAATGGGCATGATTTTTTAGTTGAGCTCGGCTCGG
1 CCCGG-CCCAATAAATGAACATGATTTTTTAGTTGAGCTCGGCCCAA
*
38607772 CCCGGGCCCAATAAATGAACATTATTTTTTAGTTGAGCTCGGCCCAAA
1 CCC-GGCCCAATAAATGAACATGATTTTTTAGTTGAGCTCGGCCC-AA
38607820 CCCGGCCC
1 CCCGGCCC
38607828 GACCCAGCCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 43 0.90
48 5 0.10
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (46 bp):
CCCGGCCCAATAAATGAACATGATTTTTTAGTTGAGCTCGGCCCAA
Found at i:38614210 original size:29 final size:28
Alignment explanation
Indices: 38614134--38614210 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 28
38614124 ATTGAACCTG
* *
38614134 AATTTTAAAATTTAAAAAATAGAGAGACTA
1 AATTTT-AAATTT-AAAAGTAGAAAGACTA
** * *
38614164 AATTTCTAAAAATAAAAGTATAAAGATTA
1 AATTT-TAAATTTAAAAGTAGAAAGACTA
38614193 AATTTTAAATTTATAAAG
1 AATTTTAAATTTA-AAAG
38614211 AAATAGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
28 6 0.16
29 21 0.57
30 9 0.24
31 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.34
Consensus pattern (28 bp):
AATTTTAAATTTAAAAGTAGAAAGACTA
Found at i:38626924 original size:24 final size:23
Alignment explanation
Indices: 38626847--38626931 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 23
38626837 CTTATTGTTA
38626847 ATATTTT-AATA--TATAAAATAT
1 ATATTTTAAATATTTATAAAAT-T
* *
38626868 AAATTTTAAATATTTTTAAGCAATT
1 ATATTTTAAATATTTATAA--AATT
* *
38626893 A-ATATTAATTATTTATAAAATGT
1 ATATTTTAAATATTTATAAAAT-T
38626916 ATATTTTAAATATTTA
1 ATATTTTAAATATTTA
38626932 AATATAACCA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 6 0.12
22 7 0.14
23 2 0.04
24 30 0.60
25 2 0.04
26 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAATATTTATAAAATT
Found at i:38626965 original size:21 final size:21
Alignment explanation
Indices: 38626889--38626966 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
38626879 ATTTTTAAGC
*
38626889 AATTA-ATATTAATTATTTAT
1 AATTATATATTAAATATTTAT
*
38626909 AAAATGTATATTTTAAATATTTA-
1 --AAT-TATATATTAAATATTTAT
*
38626932 AA-TATAACCATTAAATATTTAT
1 AATTAT-A-TATTAAATATTTAT
38626954 AATTATATATTAA
1 AATTATATATTAA
38626967 CACATTTGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 18 0.40
22 6 0.13
23 5 0.11
24 12 0.27
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (21 bp):
AATTATATATTAAATATTTAT
Found at i:38627490 original size:9 final size:9
Alignment explanation
Indices: 38627476--38627500 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38627466 TCATATGACG
38627476 TTTTTAAAT
1 TTTTTAAAT
38627485 TTTTTAAAT
1 TTTTTAAAT
38627494 TTTTTAA
1 TTTTTAA
38627501 TTCGTAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:38630139 original size:18 final size:17
Alignment explanation
Indices: 38630106--38630144 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38630096 TTGTATAAAT
38630106 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
38630124 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
38630141 TGTG
1 TGTG
38630145 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:38630397 original size:23 final size:23
Alignment explanation
Indices: 38630370--38630467 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
38630360 AGTGTTATTG
*
38630370 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
38630393 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
38630416 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
38630438 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
38630461 ATCAGTG
1 ATCAGTG
38630468 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:38630436 original size:45 final size:45
Alignment explanation
Indices: 38630372--38630460 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
38630362 TGTTATTGAT
* *
38630372 CAGTGGTAACTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
*
38630417 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
38630461 ATCAGTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (45 bp):
CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:38633146 original size:30 final size:30
Alignment explanation
Indices: 38633110--38633169 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
38633100 ACTACCAAAG
38633110 ATACTCTAAATACATGAGAAAACTTGAAAA
1 ATACTCTAAATACATGAGAAAACTTGAAAA
38633140 ATACTCTAAATACATGAGAAAACTTGAAAA
1 ATACTCTAAATACATGAGAAAACTTGAAAA
38633170 GATCTTACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.23
Consensus pattern (30 bp):
ATACTCTAAATACATGAGAAAACTTGAAAA
Found at i:38633767 original size:5 final size:6
Alignment explanation
Indices: 38633750--38633794 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
38633740 AGATAAGTCA
* * *
38633750 TATTTT TATTTT TATTTT TATTTT AATATC TATTTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TA-TTTT TATTTT TA
38633795 ATTAGTATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:38639336 original size:5 final size:5
Alignment explanation
Indices: 38639328--38639356 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
38639318 ATTAAATTAC
38639328 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
38639357 CTATCCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:38640614 original size:25 final size:22
Alignment explanation
Indices: 38640568--38640618 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
38640558 TTTATTTTAA
*
38640568 TATAATAATTTTTATTTAATTT
1 TATAATAATTTTTATATAATTT
38640590 TATAATAATTATTTATAATACATTT
1 TATAATAATT-TTTAT-ATA-ATTT
38640615 TATA
1 TATA
38640619 TTTTTAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 5 0.20
24 2 0.08
25 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAATAATTTTTATATAATTT
Found at i:38643242 original size:14 final size:14
Alignment explanation
Indices: 38643223--38643253 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38643213 AGTAACATGT
38643223 TTTCTGGAAAATAA
1 TTTCTGGAAAATAA
*
38643237 TTTCTGGAAAATGA
1 TTTCTGGAAAATAA
38643251 TTT
1 TTT
38643254 ACTTTTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (14 bp):
TTTCTGGAAAATAA
Found at i:38643280 original size:20 final size:20
Alignment explanation
Indices: 38643237--38643278 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
38643227 TGGAAAATAA
38643237 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
38643257 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
38643276 TTT
1 TTT
38643279 TCGGTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:38643388 original size:20 final size:20
Alignment explanation
Indices: 38643363--38643402 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38643353 CTATATTTAC
38643363 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
38643383 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
38643403 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:38643401 original size:18 final size:18
Alignment explanation
Indices: 38643357--38643402 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
38643347 GAAAAGCTAT
*
38643357 ATTTACATATATTAATAA
1 ATTTATATATATTAATAA
38643375 ATTTATATATATATTAATAA
1 A-TT-TATATATATTAATAA
38643395 ATTTATAT
1 ATTTATAT
38643403 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 4 0.16
20 15 0.60
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATATATATTAATAA
Found at i:38645973 original size:6 final size:6
Alignment explanation
Indices: 38645962--38645987 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38645952 GTTGATGGAC
38645962 CCGCTG CCGCTG CCGCTG CCGCTG CC
1 CCGCTG CCGCTG CCGCTG CCGCTG CC
38645988 ACGTCGGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.54, G:0.31, T:0.15
Consensus pattern (6 bp):
CCGCTG
Found at i:38646479 original size:14 final size:14
Alignment explanation
Indices: 38646460--38646498 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
38646450 TTGTTTCACT
*
38646460 GAAAATGACTTTC-G
1 GAAAATGA-TTTCTA
38646474 GAAAATGATTTCTA
1 GAAAATGATTTCTA
38646488 GAAAATGATTT
1 GAAAATGATTT
38646499 ACTTTTCTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:38646525 original size:20 final size:20
Alignment explanation
Indices: 38646482--38646523 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
38646472 CGGAAAATGA
38646482 TTTCTAGAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
38646502 TTTCT-GAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
38646521 TTT
1 TTT
38646524 TCGGTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTAGAAAATGATTTACT
Done.