Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 1 of 18
Found at i:11154 original size:42 final size:42
Alignment explanation
Indices: 11095--11503 Score: 271
Period size: 42 Copynumber: 9.7 Consensus size: 42
11085 TCCTACCCTC
* * * *
11095 AGTCTGCCTGTCAGCTTTGACCTTTGAGACTGCTTCATCTAA
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCTTCATCTAA
* * * * *
11137 AGTCTGTATGTCGGCTTTAACCTTGGAGACT--TTCCTACCCTCA
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCTT-C-A-TCTAA
* * * * * * * *
11180 A-TCAGTCTGTCGACTTTAACCTTGAAAACTACCTCATCTAA
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCTTCATCTAA
* * * * *
11221 AATCTGCCTGTCGGCTTTGACCCTGGAGGCTTTCCTTC-TCT-C
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGAC--TGCTTCATCTAA
* * * *
11263 AGTCTGCCTGTCGACTTTGACCCTAGAGACTGCTCCATCTAA
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCTTCATCTAA
* *
11305 AGTCTGTCTGTCGGCTTTGACCCTAGAAACTG-TCTCATCTAA
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCT-TCATCTAA
* * ** * * * *
11347 AATTTACCTGTCGGCTTTGATCTTGGAGACT--TTCCTACTATC
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCTTCAT-CTA-A
* *
11389 AGTCT-ACTTGTCGACTTTGACCCTGGAGACTG-TCTCATCTAA
1 AGTCTGTC-TGTCGGCTTTGACCCTGGAGACTGCT-TCATCTAA
** *
11431 AGTCTACCTGTCGGCTTTGACCTTGGAGACTGCTTCATCTAA
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCTTCATCTAA
* *
11473 AGTCTGTCAGTCGGCTTTGACCCTAGAGACT
1 AGTCTGTCTGTCGGCTTTGACCCTGGAGACT
11504 TTCTTACCCT
Statistics
Matches: 286, Mismatches: 63, Indels: 36
0.74 0.16 0.09
Matches are distributed among these distances:
40 9 0.03
41 14 0.05
42 241 0.84
43 14 0.05
44 8 0.03
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (42 bp):
AGTCTGTCTGTCGGCTTTGACCCTGGAGACTGCTTCATCTAA
Found at i:11335 original size:126 final size:126
Alignment explanation
Indices: 11205--11560 Score: 421
Period size: 126 Copynumber: 2.8 Consensus size: 126
11195 TTAACCTTGA
* * *
11205 AAACTACCTCATCTAAAATCTGCCTGTCGGCTTTGACCCTGGAGGCTTTCCTTCTCTCAGTCTGC
1 AAACTGCCTCATCTAAAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCTCTCAGTCTAC
**
11270 CTGTCGACTTTGACCCTAGAGACTG-CTCCATCTAAAGTCTGTCTGTCGGCTTTGACCCTAG
66 CTGTCGACTTTGACCCTAGAGACTGTCT-CATCTAAAGTCTACCTGTCGGCTTTGACCCTAG
* * * * * * *
11331 AAACTGTCTCATCTAAAATTTACCTGTCGGCTTTGATCTTGGAGACTTTCCTACTATCAGTCTAC
1 AAACTGCCTCATCTAAAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCTCTCAGTCTAC
* * * *
11396 TTGTCGACTTTGACCCTGGAGACTGTCTCATCTAAAGTCTACCTGTCGGCTTTGACCTTGG
66 CTGTCGACTTTGACCCTAGAGACTGTCTCATCTAAAGTCTACCTGTCGGCTTTGACCCTAG
* * * * * * *
11457 AGACTGCTTCATCTAAAGTCTGTCAGTCGGCTTTGACCCTAGAGACTTT-CTTACCCTCAGTCTA
1 AAACTGCCTCATCTAAAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT-CTCTCAGTCTA
* * **
11521 CCTGTCGACTTTAACCCT-GAAGATTACCTCATCTAAAGTC
65 CCTGTCGACTTTGACCCTAG-AGACTGTCTCATCTAAAGTC
11561 AGTGAGTCTC
Statistics
Matches: 192, Mismatches: 35, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
125 3 0.02
126 187 0.97
127 2 0.01
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (126 bp):
AAACTGCCTCATCTAAAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCTCTCAGTCTAC
CTGTCGACTTTGACCCTAGAGACTGTCTCATCTAAAGTCTACCTGTCGGCTTTGACCCTAG
Found at i:11519 original size:84 final size:84
Alignment explanation
Indices: 11081--11560 Score: 391
Period size: 84 Copynumber: 5.7 Consensus size: 84
11071 AACCATATGA
* * * *
11081 ACTTTCCTACCCTCAGTCTGCCTGTC-AGCTTTGACCTTTGAGACTGCTTCATCTAAAGTCTGTA
1 ACTTTCTTACCCTCAGTCTACCTGTCGA-CTTTGACCTTGGAGACTGCTTCATCTAAAGTCTGTC
* *
11145 TGTCGGCTTTAACCTTGGAG
65 TGTCGGCTTTGACCCTGGAG
* * * * * * * * * *
11165 ACTTTCCTACCCTCAATC-AGTCTGTCGACTTTAACCTTGAAAACTACCTCATCTAAAATCTGCC
1 ACTTTCTTACCCTCAGTCTA-CCTGTCGACTTTGACCTTGGAGACTGCTTCATCTAAAGTCTGTC
11229 TGTCGGCTTTGACCCTGGAG
65 TGTCGGCTTTGACCCTGGAG
* * * * * *
11249 GCTTTCCTT-CTCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCTCCATCTAAAGTCTGTC
1 ACTTT-CTTACCCTCAGTCTACCTGTCGACTTTGACCTTGGAGACTGCTTCATCTAAAGTCTGTC
* *
11313 TGTCGGCTTTGACCCTAGAA
65 TGTCGGCTTTGACCCTGGAG
* * * * * * * * * *
11333 ACTGTCTCA-TCTAAAATTTACCTGTCGGCTTTGATCTTGGAGACT--TTCCTACTATCAGTCT-
1 ACTTTCTTACCCT-CAGTCTACCTGTCGACTTTGACCTTGGAGACTGCTTCAT-CTA-AAGTCTG
* *
11394 ACTTGTCGACTTTGACCCTGGAG
63 TC-TGTCGGCTTTGACCCTGGAG
* * * * *
11417 ACTGTCTCA-TCTAAAGTCTACCTGTCGGCTTTGACCTTGGAGACTGCTTCATCTAAAGTCTGTC
1 ACTTTCTTACCCT-CAGTCTACCTGTCGACTTTGACCTTGGAGACTGCTTCATCTAAAGTCTGTC
* *
11481 AGTCGGCTTTGACCCTAGAG
65 TGTCGGCTTTGACCCTGGAG
* * * * * *
11501 ACTTTCTTACCCTCAGTCTACCTGTCGACTTTAACCCTGAAGATTACCTCATCTAAAGTC
1 ACTTTCTTACCCTCAGTCTACCTGTCGACTTTGACCTTGGAGACTGCTTCATCTAAAGTC
11561 AGTGAGTCTC
Statistics
Matches: 313, Mismatches: 70, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
82 3 0.01
83 9 0.03
84 288 0.92
85 9 0.03
86 4 0.01
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (84 bp):
ACTTTCTTACCCTCAGTCTACCTGTCGACTTTGACCTTGGAGACTGCTTCATCTAAAGTCTGTCT
GTCGGCTTTGACCCTGGAG
Found at i:13211 original size:16 final size:15
Alignment explanation
Indices: 13185--13215 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
13175 ATAAAAAAGA
13185 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
13200 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
13216 TATGGAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:14579 original size:5 final size:5
Alignment explanation
Indices: 14569--14643 Score: 78
Period size: 5 Copynumber: 15.0 Consensus size: 5
14559 ATGCATGAAA
* * * * * *
14569 GCAAT GCAAT GAAAT GCAAT GTAAT GAAAT GCAAT GAAAT GTAAT GAAAT
1 GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT
* *
14619 GCAAT GAAAT GCAAT GAAAT GCAAT
1 GCAAT GCAAT GCAAT GCAAT GCAAT
14644 AAAATGTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (5 bp):
GCAAT
Found at i:14586 original size:10 final size:10
Alignment explanation
Indices: 14563--14649 Score: 113
Period size: 10 Copynumber: 8.8 Consensus size: 10
14553 CATTTCATGC
14563 ATGAAA-GCA
1 ATGAAATGCA
* *
14572 ATGCAATGAA
1 ATGAAATGCA
* *
14582 ATGCAATGTA
1 ATGAAATGCA
14592 ATGAAATGCA
1 ATGAAATGCA
*
14602 ATGAAATGTA
1 ATGAAATGCA
14612 ATGAAATGCA
1 ATGAAATGCA
14622 ATGAAATGCA
1 ATGAAATGCA
14632 ATGAAATGCA
1 ATGAAATGCA
*
14642 ATAAAATG
1 ATGAAATG
14650 TTTTTGAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
9 5 0.07
10 64 0.93
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.22
Consensus pattern (10 bp):
ATGAAATGCA
Found at i:14716 original size:14 final size:15
Alignment explanation
Indices: 14697--14731 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
14687 GAATGTTACG
*
14697 TGAAAA-GCATGATA
1 TGAAAATGCATGAAA
14711 TGAAAATGCATGAAA
1 TGAAAATGCATGAAA
14726 TGAAAA
1 TGAAAA
14732 AATGTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (15 bp):
TGAAAATGCATGAAA
Found at i:15387 original size:42 final size:41
Alignment explanation
Indices: 15335--15826 Score: 330
Period size: 42 Copynumber: 11.6 Consensus size: 41
15325 AAGCCGCTAG
* * *
15335 GGTCAAAGCCGACAAGCAGAATAAGGAAATAAAAATCTCCA
1 GGTCAAAGCCGACAAGCAGACTAAGGAAAGAAAAGTCTCCA
* *
15376 GGATCAAAGCCGACAAGCAGATTAA-GAGATGAAAAGTCTCCA
1 GG-TCAAAGCCGACAAGCAGACTAAGGA-AAGAAAAGTCTCCA
* * * *
15418 GGGTCAAATCCAACAGGCAGACTAAGGAAAGAAAAGTCTCTAA
1 -GGTCAAAGCCGACAAGCAGACTAAGGAAAGAAAAGTCTC-CA
* * **
15461 GGTCAAAGCCGACAGGCAGACTAAAGAAAGAAAAGTCTTTA
1 GGTCAAAGCCGACAAGCAGACTAAGGAAAGAAAAGTCTCCA
* * * *** *
15502 GGGTTAAAACAGAC-AGACAGACTAAGGGTTGAAAAGTCTCTA
1 -GGTCAAAGCCGACAAG-CAGACTAAGGAAAGAAAAGTCTCCA
* * * * *
15544 GGTACGAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCTA
1 GGT-CAAAGCCGACAAGCAGACTAAGGAAAGAAAAGTCTCCA
* * * * * *
15586 GGGGCAAAACCGATAGGCAAACTAAAGAAAGAAAAGTCTCCA
1 -GGTCAAAGCCGACAAGCAGACTAAGGAAAGAAAAGTCTCCA
* ***
15628 GGGTCAAAGCCGAC-AGACAGACTGAGGGTTGAAAAGTCTCCA
1 -GGTCAAAGCCGACAAG-CAGACTAAGGAAAGAAAAGTCTCCA
* * * *
15670 GGGACGAAGCCGACAGGCAGACTAAGGGAAGTAAAGAAAAGTATCCA
1 -GGTCAAAGCCGACAAGCAGACTAA--G--G-AAAGAAAAGTCTCCA
** * * *
15717 GGGTCAAAATCGACAGGCAGACTAAAGG-AAGAAAAATCTCGAA
1 -GGTCAAAGCCGACAAGCAGACT-AAGGAAAGAAAAGTCTC-CA
* *
15760 GGTCAAAGCCGACAAGCAGACTGAAGG-AAGGAAAGTCTCCCG
1 GGTCAAAGCCGACAAGCAGACT-AAGGAAAGAAAAGTCT-CCA
*
15802 GGTCAAAGCCGACGA-CAGACTAAGG
1 GGTCAAAGCCGACAAGCAGACTAAGG
15827 GGAAAATAGA
Statistics
Matches: 356, Mismatches: 75, Indels: 41
0.75 0.16 0.09
Matches are distributed among these distances:
40 4 0.01
41 16 0.04
42 289 0.81
43 11 0.03
44 2 0.01
46 2 0.01
47 30 0.08
48 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.12
Consensus pattern (41 bp):
GGTCAAAGCCGACAAGCAGACTAAGGAAAGAAAAGTCTCCA
Found at i:15438 original size:84 final size:83
Alignment explanation
Indices: 15333--15825 Score: 393
Period size: 84 Copynumber: 5.8 Consensus size: 83
15323 AAAAGCCGCT
* * * * *
15333 AGGGTCAAAGCCGACAAGCAGAATAAGGAAATAAAAATCTCCAGGATCAAAGCCGACAAGCAGAT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG-TCAAAGCCGACAAGCAGAC
*
15398 TAAGAGATGAAAAGTCTCC
65 TAAGAGAAGAAAAGTCTCC
* * * *
15417 AGGGTCAAATCCAACAGGCAGACTAAGGAAAGAAAAGTCTCTAAGGTCAAAGCCGACAGGCAGAC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTC-CAGGTCAAAGCCGACAAGCAGAC
**
15482 TAA-AGAAAGAAAAGTCTTT
65 TAAGAG-AAGAAAAGTCTCC
* * * * *** * * *
15501 AGGGTTAAAACAGACAGACAGACTAAGGGTTGAAAAGTCTCTAGGTACGAAGCCGACAGGCAGAC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGT-CAAAGCCGACAAGCAGAC
* * *
15566 TAAGGGAAGGAAAGTCTCT
65 TAAGAGAAGAAAAGTCTCC
* * * * *
15585 AGGGGCAAAACCGATAGGCAAACTAAAGAAAGAAAAGTCTCCAGGGTCAAAGCCGAC-AGACAGA
1 AGGGTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGTCAAAGCCGACAAG-CAGA
* * **
15649 CTGAGGGTTGAAAAGTCTCC
64 CTAAGAGAAGAAAAGTCTCC
* * * ** *
15669 AGGGACGAAGCCGACAGGCAGACTAAGGGAAGTAAAGAAAAGTATCCAGGGTCAAAATCGACAGG
1 AGGGTCAAAGCCGACAGGCAGACTAA--G--G-AAAGAAAAGTCTCCA-GGTCAAAGCCGACAAG
* *
15734 CAGACTAA-AGGAAGAAAAATCTCG
60 CAGACTAAGA-GAAGAAAAGTCTCC
* * * * *
15758 AAGGTCAAAGCCGACAAGCAGACTGAAGG-AAGGAAAGTCTCCCGGGTCAAAGCCGACGA-CAGA
1 AGGGTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCT-CCAGGTCAAAGCCGACAAGCAGA
15821 CTAAG
64 CTAAG
15826 GGGAAAATAG
Statistics
Matches: 323, Mismatches: 70, Indels: 32
0.76 0.16 0.08
Matches are distributed among these distances:
83 15 0.05
84 230 0.71
85 9 0.03
86 1 0.00
88 2 0.01
89 63 0.20
90 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.12
Consensus pattern (83 bp):
AGGGTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGTCAAAGCCGACAAGCAGACT
AAGAGAAGAAAAGTCTCC
Found at i:15535 original size:126 final size:127
Alignment explanation
Indices: 15293--15826 Score: 515
Period size: 126 Copynumber: 4.2 Consensus size: 127
15283 ATTCTCCCGA
* * * * * * * *
15293 GTCAAAGCCAACGGGCAAACTTAGGAAAAGAAAAGCCGCTAGGGTCAAAGCCGACAAGCAGAATA
1 GTCAAAGCCAACAGGCAGACTAAGGAAAAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAGACTA
* * * * * * *
15358 AGGAAATAAAAATCTCCAGGATCAAAGCCGACA-AGCAGATTAAGAGATGAAAAGTCTCCAGG
66 AAGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGA-CAGACTAAGGGTTGAAAAGTCTCCAGG
* * *
15420 GTCAAATCCAACAGGCAGACTAAGG-AAAGAAAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTA
1 GTCAAAGCCAACAGGCAGACTAAGGAAAAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAGACTA
** * * * *
15484 AAGAAAGAAAAGTCTTTAGGGTTAAAACAGACAGACAGACTAAGGGTTGAAAAGTCTCTA-G
66 AAGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGACAGACTAAGGGTTGAAAAGTCTCCAGG
* * * * * * *
15545 GTACGAAGCCGACAGGCAGACTAAGG-GAAGGAAAGTCTCTAGGGGCAAAACCGATAGGCAAACT
1 GT-CAAAGCCAACAGGCAGACTAAGGAAAAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAGACT
*
15609 AAAGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGACAGACTGAGGGTTGAAAAGTCTCCAGG
65 AAAGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGACAGACTAAGGGTTGAAAAGTCTCCAGG
* * * * * *
15672 GACGAAGCCGACAGGCAGACTAAGGGAAGTAAAGAAAAGTATCCAGGGTCAAAATCGACAGGCAG
1 GTCAAAGCCAACAGGCAGACTAA-GG-A--AAAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAG
* * * * ** *
15737 ACTAAAGGAAGAAAAATCTCGAAGGTCAAAGCCGACA-AGCAGACTGAA-GGAAGGAAAGTCTCC
62 ACTAAAGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGA-CAGACT-AAGGGTTGAAAAGTCTCC
*
15800 CGG
125 AGG
* *
15803 GTCAAAGCCGAC-GACAGACTAAGG
1 GTCAAAGCCAACAGGCAGACTAAGG
15827 GGAAAATAGA
Statistics
Matches: 337, Mismatches: 60, Indels: 18
0.81 0.14 0.04
Matches are distributed among these distances:
125 3 0.01
126 205 0.61
127 26 0.08
129 2 0.01
130 10 0.03
131 90 0.27
132 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.12
Consensus pattern (127 bp):
GTCAAAGCCAACAGGCAGACTAAGGAAAAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAGACTA
AAGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGACAGACTAAGGGTTGAAAAGTCTCCAGG
Found at i:20442 original size:26 final size:25
Alignment explanation
Indices: 20383--20447 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
20373 AAAAATTTTA
*
20383 AATATGTATATATATTTAATGAAATT
1 AATAT-TATATAAATTTAATGAAATT
*
20409 AATAATTATATAAATTTTAATTAAATT
1 AAT-ATTATATAAA-TTTAATGAAATT
* *
20436 TATATTAAATAA
1 AATATTATATAA
20448 TTATCATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (25 bp):
AATATTATATAAATTTAATGAAATT
Found at i:21406 original size:23 final size:23
Alignment explanation
Indices: 21337--21406 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
21327 CATACAAAAA
*
21337 ATAACACGAATAATAA-ATGCAAC
1 ATAACACAAATAATAATATG-AAC
* * *
21360 ATATATA-AAAAAATAAT-TAAAAC
1 ATA-ACACAAATAATAATAT-GAAC
21383 ATAACACAAATAATAATATGAAC
1 ATAACACAAATAATAATATGAAC
21406 A
1 A
21407 CGATATGAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
22 2 0.06
23 30 0.86
24 3 0.09
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.21
Consensus pattern (23 bp):
ATAACACAAATAATAATATGAAC
Found at i:22414 original size:17 final size:17
Alignment explanation
Indices: 22394--22429 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
22384 TTTGCAAACA
22394 TGCAATCTCCAAGAATT
1 TGCAATCTCCAAGAATT
*
22411 TGCAATCTCTAAGAATT
1 TGCAATCTCCAAGAATT
22428 TG
1 TG
22430 ACTAACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (17 bp):
TGCAATCTCCAAGAATT
Found at i:27295 original size:2 final size:2
Alignment explanation
Indices: 27288--27324 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
27278 AGTAAGTTAT
* *
27288 TC TC TC TC TC TC TC TA TA TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
27325 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:27899 original size:18 final size:19
Alignment explanation
Indices: 27866--27906 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
27856 AAAATTAAAA
**
27866 ATATTTTTATTTAA-TTTT
1 ATATTTTTATAAAATTTTT
27884 ATATTTTTATAAAATTTTT
1 ATATTTTTATAAAATTTTT
27903 ATAT
1 ATAT
27907 ATAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATATTTTTATAAAATTTTT
Found at i:28118 original size:18 final size:18
Alignment explanation
Indices: 28066--28131 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 18
28056 AGTAAAATTG
*
28066 ATCTA-TTTTTAAA-TAA
1 ATCTATTTTTTAAATTTA
**
28082 ATCTATTTTTT-AACCTA
1 ATCTATTTTTTAAATTTA
28099 ATCTATTTTTTAAATTTA
1 ATCTATTTTTTAAATTTA
* *
28117 ATATATTTGTTAAAT
1 ATCTATTTTTTAAAT
28132 GAAATAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 7 0.17
17 17 0.41
18 17 0.41
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.55
Consensus pattern (18 bp):
ATCTATTTTTTAAATTTA
Found at i:29817 original size:78 final size:78
Alignment explanation
Indices: 29688--29844 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
29678 TGGATTTGAG
29688 TAAAGAAAATTAGCAACTTTTGATATAACTTATGAGTCCTGAGGTTTAGTTTTCCTCAGGCAAGG
1 TAAAGAAAATTAGCAACTTTTGATATAACTTATGAGTCCTGAGGTTTAGTTTTCCTCAGGCAAGG
29753 TTATTTTTTTTTC
66 TTATTTTTTTTTC
29766 TAAAGAAAATTAGCAACTTTTGATATAACTTATGAGTCCTGAGGTTTAGTTTTCCTCAGGCAAGG
1 TAAAGAAAATTAGCAACTTTTGATATAACTTATGAGTCCTGAGGTTTAGTTTTCCTCAGGCAAGG
29831 TTATTTTTTTTTC
66 TTATTTTTTTTTC
29844 T
1 T
29845 TTCTTTCCTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.43
Consensus pattern (78 bp):
TAAAGAAAATTAGCAACTTTTGATATAACTTATGAGTCCTGAGGTTTAGTTTTCCTCAGGCAAGG
TTATTTTTTTTTC
Found at i:34972 original size:23 final size:23
Alignment explanation
Indices: 34945--34988 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34935 TGATTGTAGA
34945 TATTAAA-ATTAAAATTTTAAATT
1 TATTAAATATT-AAATTTTAAATT
*
34968 TATTAAATATTAATTTTTAAA
1 TATTAAATATTAAATTTTAAA
34989 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAAATATTAAATTTTAAATT
Found at i:35694 original size:24 final size:26
Alignment explanation
Indices: 35670--35719 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
35660 ATTAATAATA
* *
35670 CTAAATAAATTATTAT-TATATATAC
1 CTAAATAAATAAATATATATATATAC
*
35695 CTAAATTAATAAATATATATATATA
1 CTAAATAAATAAATATATATATATA
35720 TATACTAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
CTAAATAAATAAATATATATATATAC
Found at i:35911 original size:14 final size:14
Alignment explanation
Indices: 35888--35917 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35878 ATTTAAGTCC
*
35888 TACCTGCATCAACT
1 TACCTACATCAACT
35902 TACCTACATCAACT
1 TACCTACATCAACT
35916 TA
1 TA
35918 AAATTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (14 bp):
TACCTACATCAACT
Found at i:36207 original size:121 final size:121
Alignment explanation
Indices: 35993--36213 Score: 397
Period size: 121 Copynumber: 1.8 Consensus size: 121
35983 ATATGTACCT
* *
35993 TCATCTTTTACCCACATTCAGTCATGAGTTTATTTTTTCACTGAAAATGAAAGATATAGGGCAGC
1 TCATCTTTAACCCACATTCACTCATGAGTTTATTTTTTCACTGAAAATGAAAGATATAGGGCAGC
*
36058 CTATAGCTATTTTCTGCATGGTTATATATATATATGTGTGTGTGTGTGTGTGTGTG
66 CAATAGCTATTTTCTGCATGGTTATATATATATATGTGTGTGTGTGTGTGTGTGTG
*
36114 TCATCTTTAACCCACATTCACTCATTAGTTTATTTTTTCACTGAAAATGAAAGATATAGGGCAGC
1 TCATCTTTAACCCACATTCACTCATGAGTTTATTTTTTCACTGAAAATGAAAGATATAGGGCAGC
*
36179 CAATAGCTATTTTCTGCATGGTTTTATATATATAT
66 CAATAGCTATTTTCTGCATGGTTATATATATATAT
36214 ATATACACAC
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 95 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (121 bp):
TCATCTTTAACCCACATTCACTCATGAGTTTATTTTTTCACTGAAAATGAAAGATATAGGGCAGC
CAATAGCTATTTTCTGCATGGTTATATATATATATGTGTGTGTGTGTGTGTGTGTG
Found at i:37403 original size:2 final size:2
Alignment explanation
Indices: 37396--37424 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37386 CGGATCTTGC
37396 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 A
37425 AACCTTTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43433 original size:25 final size:25
Alignment explanation
Indices: 43404--43452 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
43394 TAAATACGAT
43404 TATGATATAATAAAAATAATTAAAA
1 TATGATATAATAAAAATAATTAAAA
* * *
43429 TATGATATGATATAAATATTTAAA
1 TATGATATAATAAAAATAATTAAA
43453 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
TATGATATAATAAAAATAATTAAAA
Found at i:43480 original size:34 final size:34
Alignment explanation
Indices: 43423--43489 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
43413 ATAAAAATAA
* *
43423 TTAAAATATGATATGATATAAATATTTAAATATT
1 TTAAAATATGATATAATATAAATATATAAATATT
*
43457 TTAAAAT-TTATATAATATAAAATATATAAATAT
1 TTAAAATATGATATAATAT-AAATATATAAATAT
43490 AATATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 9 0.31
34 20 0.69
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
TTAAAATATGATATAATATAAATATATAAATATT
Found at i:53382 original size:21 final size:21
Alignment explanation
Indices: 53331--53412 Score: 53
Period size: 23 Copynumber: 3.8 Consensus size: 21
53321 CTACTTTTCA
* *
53331 ATTATAAATATATATTTATAT
1 ATTATAAATATATATATATAC
53352 ATTATGTAAAT-TATATCATATAC
1 ATTA--TAAATATATAT-ATATAC
* *
53375 ATTATAAAGAATAAATATATA-
1 ATTATAAA-TATATATATATAC
*
53396 AATATATAATA-ATATAT
1 ATTATA-AATATATATAT
53413 TGTAAATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.10
21 14 0.29
22 12 0.25
23 17 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTATAAATATATATATATAC
Found at i:53433 original size:21 final size:21
Alignment explanation
Indices: 53394--53433 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53384 AATAAATATA
* *
53394 TAAATATATAATAATATATTG
1 TAAATATATAAAAAAATATTG
*
53415 TAAATATTTAAAAAAATAT
1 TAAATATATAAAAAAATAT
53434 GTTAAGTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAATATATAAAAAAATATTG
Found at i:56551 original size:2 final size:2
Alignment explanation
Indices: 56544--56578 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56534 ATTATTAAAT
56544 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 T
56579 TGGTATGATC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58818 original size:21 final size:21
Alignment explanation
Indices: 58794--58833 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
58784 TTTAAAAAAT
58794 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
58815 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
58834 AATAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:59083 original size:14 final size:15
Alignment explanation
Indices: 59064--59099 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
59054 ATTATATATT
*
59064 ATTTAATTTTT-TTA
1 ATTTAATTTTTAATA
59078 ATTTAATTTTTAATA
1 ATTTAATTTTTAATA
59093 ATTTAAT
1 ATTTAAT
59100 AATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTAATTTTTAATA
Found at i:64088 original size:2 final size:2
Alignment explanation
Indices: 64081--64112 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
64071 TCCCCTTGCC
64081 CT CT 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
64113 GAGTAGCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:65189 original size:3 final size:3
Alignment explanation
Indices: 65181--65220 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
65171 TAGTTTTAAT
65181 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
65221 GTTTTAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:66938 original size:20 final size:19
Alignment explanation
Indices: 66909--66962 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
66899 ATGGATTTAT
66909 ATAT-ATTGATATTAACTA
1 ATATGATTGATATTAACTA
* *
66927 ATACTGATTGATATAAATTA
1 ATA-TGATTGATATTAACTA
66947 ATATGATTGATATTAA
1 ATATGATTGATATTAA
66963 TCGATTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.10
19 13 0.42
20 15 0.48
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (19 bp):
ATATGATTGATATTAACTA
Found at i:67115 original size:2 final size:2
Alignment explanation
Indices: 67108--67159 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
67098 AATTATCTTC
67108 AT AT 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 AT AT
67150 AT AT AT AT AT
1 AT AT AT AT AT
67160 CGTTTGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67512 original size:22 final size:23
Alignment explanation
Indices: 67457--67513 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
67447 ATATTTATGT
*
67457 AATTAAATTTAAATAATAATTTTT
1 AATTAAA-TTAAATAATAATTTTA
* *
67481 TATT-ATTTAAATAATAA-TTTA
1 AATTAAATTAAATAATAATTTTA
67502 AATTAAATTAAA
1 AATTAAATTAAA
67514 ATATAATATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 6 0.22
22 17 0.63
23 1 0.04
24 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTAAATTAAATAATAATTTTA
Found at i:68744 original size:21 final size:22
Alignment explanation
Indices: 68720--68777 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
68710 AATTAAATAA
68720 AAATAAAATTTAATTAATTT-T
1 AAATAAAATTTAATTAATTTAT
* **
68741 AAATAATTATTTTTTTAATTTAT
1 AAATAA-AATTTAATTAATTTAT
*
68764 AAA-AAAATTAAATT
1 AAATAAAATTTAATT
68778 TAATCATATA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAAAATTTAATTAATTTAT
Found at i:69041 original size:15 final size:15
Alignment explanation
Indices: 69021--69056 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
69011 GACCCCAACC
69021 CCACCACCACCGCCA
1 CCACCACCACCGCCA
*
69036 CCACCACCGCCGCCA
1 CCACCACCACCGCCA
*
69051 GCACCA
1 CCACCA
69057 ACCATCCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.64, G:0.11, T:0.00
Consensus pattern (15 bp):
CCACCACCACCGCCA
Found at i:69055 original size:12 final size:12
Alignment explanation
Indices: 69021--69046 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
69011 GACCCCAACC
69021 CCACCACCACCG
1 CCACCACCACCG
69033 CCACCACCACCG
1 CCACCACCACCG
69045 CC
1 CC
69047 GCCAGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.69, G:0.08, T:0.00
Consensus pattern (12 bp):
CCACCACCACCG
Found at i:69352 original size:3 final size:3
Alignment explanation
Indices: 69344--69396 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
69334 ACCTCAACTT
69344 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
69392 TTA TT
1 TTA TT
69397 TAAAGTGGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:69834 original size:17 final size:17
Alignment explanation
Indices: 69812--69848 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
69802 ATGAGTTTAC
69812 AATATTTCAATTCATTA
1 AATATTTCAATTCATTA
* *
69829 AATATTTGAATTTATTA
1 AATATTTCAATTCATTA
69846 AAT
1 AAT
69849 TAATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (17 bp):
AATATTTCAATTCATTA
Found at i:70057 original size:15 final size:16
Alignment explanation
Indices: 70026--70063 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
70016 CTTGTATCTA
70026 AAATTTAAAATTATTT
1 AAATTTAAAATTATTT
*
70042 AAATTTATAA-TATTT
1 AAATTTAAAATTATTT
70057 AAATTTA
1 AAATTTA
70064 CGTAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTAAAATTATTT
Found at i:71752 original size:18 final size:18
Alignment explanation
Indices: 71729--71788 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
71719 TTTATATTTA
71729 AAAAAACTATTAAAGTTT
1 AAAAAACTATTAAAGTTT
* * * *
71747 AAAAAATTACTCACGTTT
1 AAAAAACTATTAAAGTTT
* *
71765 TAGAAACTATTCAAA-TTT
1 AAAAAACTATT-AAAGTTT
71783 AAAAAA
1 AAAAAA
71789 GTACAAACTC
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAAACTATTAAAGTTT
Found at i:72563 original size:20 final size:21
Alignment explanation
Indices: 72529--72574 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
72519 GATATTGATT
**
72529 TTAT-ATCATATTTTATTATA
1 TTATAATCATATTTTAAAATA
72549 TTATAATCATA-TTTAAAATA
1 TTATAATCATATTTTAAAATA
72569 TTATAA
1 TTATAA
72575 ATTTTGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAATCATATTTTAAAATA
Found at i:73081 original size:2 final size:2
Alignment explanation
Indices: 73074--73117 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
73064 AACGTGTATG
73074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
73117 T
1 T
73118 TATGATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73121 original size:8 final size:9
Alignment explanation
Indices: 73070--73123 Score: 66
Period size: 8 Copynumber: 6.7 Consensus size: 9
73060 TAGTAACGTG
73070 TATG-TATA
1 TATGATATA
73078 TAT-ATATA
1 TATGATATA
73086 TAT-ATATA
1 TATGATATA
73094 TAT-ATATA
1 TATGATATA
73102 TAT-ATATA
1 TATGATATA
73110 TATGATAT-
1 TATGATATA
73118 TATGAT
1 TATGAT
73124 TTTTTTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
8 40 0.91
9 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (9 bp):
TATGATATA
Found at i:74777 original size:2 final size:2
Alignment explanation
Indices: 74770--74795 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74760 TATGTAAAGC
74770 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
74796 TGACAGCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75728 original size:21 final size:21
Alignment explanation
Indices: 75704--75743 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
75694 ATTAAATTCG
*
75704 AATAACTCGAATCTAAAATTA
1 AATAACTCAAATCTAAAATTA
* *
75725 AATAAGTCAAATTTAAAAT
1 AATAACTCAAATCTAAAAT
75744 AATTTAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (21 bp):
AATAACTCAAATCTAAAATTA
Found at i:77163 original size:13 final size:13
Alignment explanation
Indices: 77145--77184 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
77135 TTTTAAGTTT
77145 AAATATAAATATC
1 AAATATAAATATC
*
77158 AAATATAAATATTT
1 AAATATAAATA-TC
77172 ATAATATAAATAT
1 A-AATATAAATAT
77185 ATTTTATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 11 0.46
14 3 0.12
15 10 0.42
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:81345 original size:16 final size:16
Alignment explanation
Indices: 81324--81367 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
81314 AAATAATAAA
81324 TATATTTAT-TTATATT
1 TATATTTATATTA-ATT
81340 TATATTTATATTAATT
1 TATATTTATATTAATT
*
81356 TA-ATTTAAATTA
1 TATATTTATATTA
81368 TTATTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 14 0.54
17 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTATATTAATT
Found at i:81378 original size:20 final size:19
Alignment explanation
Indices: 81354--81403 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
81344 TTTATATTAA
*
81354 TTTAATTTAAATTATTATT
1 TTTAATTTAAATTAATATT
*
81373 TATTAA-TTAAAATAATATT
1 T-TTAATTTAAATTAATATT
81392 TTT-ATTTAAATT
1 TTTAATTTAAATT
81404 TAATTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.04
18 8 0.31
19 13 0.50
20 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATTTAAATTAATATT
Found at i:81412 original size:25 final size:24
Alignment explanation
Indices: 81344--81413 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 24
81334 TATATTTATA
81344 TTTATATT-AATTTAATT-TAAATT
1 TTTAT-TTAAATTTAATTATAAATT
* *
81367 ATTATTTATTAA-TTAA-AATAATATT
1 TTTATTTA--AATTTAATTATAA-ATT
81392 TTTATTTAAATTTAATTATAAA
1 TTTATTTAAATTTAATTATAAA
81414 AATATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
22 2 0.06
23 6 0.17
24 12 0.33
25 16 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATTTAAATTTAATTATAAATT
Found at i:81447 original size:11 final size:11
Alignment explanation
Indices: 81426--81455 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
81416 TATAAAAATA
81426 TTAATATATTTT
1 TTAA-ATATTTT
81438 TTAAATATTTT
1 TTAAATATTTT
81449 TTAAATA
1 TTAAATA
81456 ATAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTAAATATTTT
Found at i:86441 original size:2 final size:2
Alignment explanation
Indices: 86434--86465 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
86424 AAGCATTATT
86434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86466 ACAACTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:87355 original size:17 final size:16
Alignment explanation
Indices: 87335--87402 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
87325 GTATTATTAC
*
87335 TTTATTTTTTTGAACTA
1 TTTATTTTTTT-AAATA
*
87352 TTTAATTTTTTAAATA
1 TTTATTTTTTTAAATA
**
87368 TTTATATTTAATAAATA
1 TTTAT-TTTTTTAAATA
87385 TTT-TTATTATTTAAATA
1 TTTATT-TT-TTTAAATA
87402 T
1 T
87403 AATTATAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
15 1 0.02
16 11 0.27
17 29 0.71
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (16 bp):
TTTATTTTTTTAAATA
Found at i:87772 original size:19 final size:19
Alignment explanation
Indices: 87739--87783 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
87729 ATTAATTTAG
*
87739 TTTTAAATATTTTTATAATT
1 TTTTAAATATATTTAT-ATT
87759 TTTTAAATA-ATTTATATT
1 TTTTAAATATATTTATATT
87777 TATTTAA
1 T-TTTAA
87784 TTCAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAATATATTTATATT
Found at i:87808 original size:20 final size:23
Alignment explanation
Indices: 87764--87808 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
87754 TAATTTTTTA
*
87764 AATAATTTATATTTATTTAATTC
1 AATAATTTATATTTACTTAATTC
87787 AATAA-TTATATTT-CTT-ATTC
1 AATAATTTATATTTACTTAATTC
87807 AA
1 AA
87809 GTGAATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 8 0.38
23 5 0.24
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
AATAATTTATATTTACTTAATTC
Found at i:88025 original size:18 final size:19
Alignment explanation
Indices: 88002--88059 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
87992 GATAAATTTA
*
88002 ATAAAAT-ATTAATCATAT
1 ATAAAATAATTAATAATAT
* *
88020 ATAAAATCA-TAAAAATAT
1 ATAAAATAATTAATAATAT
*
88038 ATAAAATTAATTAATTATAT
1 ATAAAA-TAATTAATAATAT
88058 AT
1 AT
88060 CAATATAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 20 0.62
19 3 0.09
20 9 0.28
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAATAATTAATAATAT
Found at i:89130 original size:17 final size:16
Alignment explanation
Indices: 89107--89153 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
89097 TTGAGTTAAG
89107 TTTAAATAATTTAAAT
1 TTTAAATAATTTAAAT
*
89123 TATTAAATAAATTAAA-
1 T-TTAAATAATTTAAAT
89139 TTTAAAT-ATTTAAAT
1 TTTAAATAATTTAAAT
89154 ATCTCATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.22
15 6 0.22
16 2 0.07
17 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAATAATTTAAAT
Found at i:89257 original size:26 final size:26
Alignment explanation
Indices: 89213--89269 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
89203 TTTTAATTTT
*
89213 AATTT-AAATTCAAATATAAATAATTA
1 AATTTAAAATTCAAAGATAAA-AATTA
89239 AATTTAAAATT-AAAGATAAAAATTA
1 AATTTAAAATTCAAAGATAAAAATTA
89264 AATTTA
1 AATTTA
89270 TTTTTATCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 11 0.38
26 13 0.45
27 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
AATTTAAAATTCAAAGATAAAAATTA
Found at i:89344 original size:12 final size:11
Alignment explanation
Indices: 89294--89399 Score: 51
Period size: 11 Copynumber: 9.6 Consensus size: 11
89284 TTAATTTTAA
89294 TTAAA-TAAAT
1 TTAAATTAAAT
89304 TTAAATT--AT
1 TTAAATTAAAT
* * * *
89313 TTTATTTTATT
1 TTAAATTAAAT
89324 TTAAATTAAAT
1 TTAAATTAAAT
89335 TTAAATTTAAATT
1 TTAAA-TTAAA-T
*
89348 TTAAAAATAAAAT
1 TT--AAATTAAAT
*
89361 TT-AATCAAA-
1 TTAAATTAAAT
*
89370 TTCAATTAAATT
1 TTAAATTAAA-T
* *
89382 TTAAATTTAAC
1 TTAAATTAAAT
89393 TTAAATT
1 TTAAATT
89400 TTTTACCGCT
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
9 9 0.12
10 17 0.23
11 21 0.29
12 13 0.18
13 6 0.08
14 4 0.05
15 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:91915 original size:9 final size:9
Alignment explanation
Indices: 91901--91946 Score: 65
Period size: 9 Copynumber: 4.9 Consensus size: 9
91891 ATTTAATAAG
91901 GAAAGAAAA
1 GAAAGAAAA
91910 GAAAGAAAA
1 GAAAGAAAA
*
91919 GGAAAGAAAG
1 -GAAAGAAAA
91929 GAAAGAAATA
1 GAAAGAAA-A
91939 GAAAGAAA
1 GAAAGAAA
91947 TTTATATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:91922 original size:19 final size:19
Alignment explanation
Indices: 91898--91946 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
91888 TTTATTTAAT
91898 AAGGAAAGAAAAGAAAGAA
1 AAGGAAAGAAAAGAAAGAA
*
91917 AAGGAAAGAAAGGAAAGAA
1 AAGGAAAGAAAAGAAAGAA
91936 ATA-GAAAGAAA
1 A-AGGAAAGAAA
91947 TTTATATTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (19 bp):
AAGGAAAGAAAAGAAAGAA
Found at i:92101 original size:21 final size:21
Alignment explanation
Indices: 92077--92118 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
92067 TTGATTTATT
92077 AAAGGAAA-TAAGAAGAAAAAA
1 AAAGGAAAGTAAGAA-AAAAAA
92098 AAAGGAAAGGTAAGAAAAAAA
1 AAAGGAAA-GTAAGAAAAAAA
92119 TATTTGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (21 bp):
AAAGGAAAGTAAGAAAAAAAA
Found at i:92279 original size:19 final size:18
Alignment explanation
Indices: 92255--92290 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
92245 GGAAAAGGAA
*
92255 AGGAAATAGAAAGTAAAAG
1 AGGAAATAAAAAG-AAAAG
92274 AGGAAATAAAAAGAAAA
1 AGGAAATAAAAAGAAAA
92291 TCAGTGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (18 bp):
AGGAAATAAAAAGAAAAG
Found at i:102531 original size:13 final size:13
Alignment explanation
Indices: 102492--102544 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 13
102482 TTCATATATC
102492 ATATTTTAT--TT
1 ATATTTTATAATT
*
102503 ATATTTT-TTATT
1 ATATTTTATAATT
102515 -TATTTTATAATT
1 ATATTTTATAATT
*
102527 ATATTTAATATATT
1 ATATTTTATA-ATT
102541 ATAT
1 ATAT
102545 AATTATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 13 0.37
12 6 0.17
13 8 0.23
14 7 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATATTTTATAATT
Found at i:102586 original size:32 final size:33
Alignment explanation
Indices: 102526--102610 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 33
102516 ATTTTATAAT
*
102526 TATATTTAATATATTATATAATT-ATATAAATTTTAA
1 TATA-TTAATATATT-TAT--TTCATATAAAATTTAA
*
102562 TATATTAAT-TATTTATTTCATATAAAATTTAG
1 TATATTAATATATTTATTTCATATAAAATTTAA
*
102594 TATATTTATATATTTAT
1 TATATTAATATATTTAT
102611 ATTTTTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 2 0.05
32 19 0.43
33 10 0.23
34 4 0.09
35 5 0.11
36 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
TATATTAATATATTTATTTCATATAAAATTTAA
Found at i:102607 original size:8 final size:8
Alignment explanation
Indices: 102498--102631 Score: 64
Period size: 7 Copynumber: 16.6 Consensus size: 8
102488 TATCATATTT
102498 TATTTATA
1 TATTTATA
* *
102506 TTTTTTATT
1 -TATTTATA
102515 TATTT-TA
1 TATTTATA
*
102522 TAATTATA
1 TATTTATA
*
102530 T-TTAATA
1 TATTTATA
102537 TA-TTATA
1 TATTTATA
102544 TAATTATATA
1 T-ATT-TATA
*
102554 AATTTTAATA
1 TA-TTT-ATA
*
102564 TATTAAT-
1 TATTTATA
*
102571 TATTTATT
1 TATTTATA
*
102579 TCATATA-A
1 T-ATTTATA
*
102587 AATTTAGTA
1 TATTTA-TA
102596 TATTTATA
1 TATTTATA
102604 TATTTATA
1 TATTTATA
* *
102612 TTTTTTTA
1 TATTTATA
102620 TATTT-TA
1 TATTTATA
102627 TATTT
1 TATTT
102632 TGTATTATAT
Statistics
Matches: 94, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
7 32 0.34
8 31 0.33
9 21 0.22
10 10 0.11
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.62
Consensus pattern (8 bp):
TATTTATA
Found at i:102626 original size:17 final size:17
Alignment explanation
Indices: 102598--102654 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 17
102588 ATTTAGTATA
102598 TTTATATATTTATATTTT
1 TTTATAT-TTTATATTTT
102616 TTTATATTTTATATTTT
1 TTTATATTTTATATTTT
102633 GTATTATATTTTA-ATTATT
1 -T-TTATATTTTATATT-TT
102652 TTT
1 TTT
102655 TATGCTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
17 12 0.33
18 12 0.33
19 12 0.33
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTATATTTTATATTTT
Found at i:103915 original size:2 final size:2
Alignment explanation
Indices: 103904--103934 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
103894 TTTTTGCTTT
103904 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
103935 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:103939 original size:2 final size:2
Alignment explanation
Indices: 103934--103959 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
103924 ATATATATAT
103934 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
103960 GTGAGGTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:104788 original size:48 final size:52
Alignment explanation
Indices: 104719--104821 Score: 119
Period size: 48 Copynumber: 2.1 Consensus size: 52
104709 GTAAAAAAAA
* * *
104719 TAAAAAATAATTACTTTAAATTTTA-ATTT-AA-TTA-ATTTATATAATTTT
1 TAAAAAATAATTACTTTAAATTTAATATTTAAATTTATATATATATAATGTT
104767 TAAAAAATAA-TA-TTTAAAAATTTAATATTTAAATTTATATATATATAATGTT
1 TAAAAAATAATTACTTT--AAATTTAATATTTAAATTTATATATATATAATGTT
104819 TAA
1 TAA
104822 TGTTTTTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
46 3 0.07
47 2 0.04
48 17 0.37
49 4 0.09
50 2 0.04
51 3 0.07
52 15 0.33
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TAAAAAATAATTACTTTAAATTTAATATTTAAATTTATATATATATAATGTT
Found at i:104792 original size:15 final size:14
Alignment explanation
Indices: 104759--104799 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
104749 ATTAATTTAT
*
104759 ATAATTTTTAAAAA
1 ATAATATTTAAAAA
104773 ATAATATTTAAAAA
1 ATAATATTTAAAAA
*
104787 TTTAATATTTAAA
1 -ATAATATTTAAA
104800 TTTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATATTTAAAAA
Found at i:105715 original size:27 final size:27
Alignment explanation
Indices: 105685--105750 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
105675 TTAATTTTAA
*
105685 TTTAAAAATATTTAAAATAT-TTTATTT
1 TTTAAAAAT-TTTAAAATATATATATTT
* *
105712 TTT-AATATTTTAATATATATATATTT
1 TTTAAAAATTTTAAAATATATATATTT
105738 TTTAAAAATTTTA
1 TTTAAAAATTTTA
105751 GACTTTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 9 0.27
26 13 0.39
27 11 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAAAAATTTTAAAATATATATATTT
Found at i:105839 original size:5 final size:5
Alignment explanation
Indices: 105829--105865 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
105819 AATATTTTAA
*
105829 AAAAT AAAAT AAATT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
105866 GAATCTCTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:110685 original size:16 final size:16
Alignment explanation
Indices: 110666--110696 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
110656 TTTTGGGTTT
110666 ATTAAAATAAAATAAA
1 ATTAAAATAAAATAAA
*
110682 ATTATAATAAAATAA
1 ATTAAAATAAAATAA
110697 TTTTAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTAAAATAAAATAAA
Found at i:110707 original size:17 final size:17
Alignment explanation
Indices: 110667--110718 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
110657 TTTGGGTTTA
**
110667 TTAA-AATAAAATAAAA
1 TTAATAATAAAATAATT
110683 TT-ATAATAAAATAATT
1 TTAATAATAAAATAATT
**
110699 TTAATAATAATTTAATT
1 TTAATAATAAAATAATT
110716 TTA
1 TTA
110719 TAAAGTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 1 0.03
16 14 0.47
17 15 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATAATAAAATAATT
Found at i:112430 original size:164 final size:165
Alignment explanation
Indices: 112125--112446 Score: 574
Period size: 164 Copynumber: 2.0 Consensus size: 165
112115 ATATCACTAC
*
112125 TTGCTAACTGCTTTCCAATTCAAACGCTTGAGAGAAATCAAACTACCACCCCAATTTTTACATTG
1 TTGCTAACTGCTTTCCAATTCAAACACTTGAGAGAAATCAAACTACCACCCCAATTTTTACATTG
* *
112190 CCCCCAAAAGAAAGCCGTTTCCTTTAGGCAAATTCTCCTCTACAATTTACATTCCTCTCCTAACA
66 CCCCCAAAAGAAAGCCATTTCCTTTAGGCAAATTATCCTCTACAATTTACATTCCTCTCCTAACA
112255 CTAATTAATTGACTTTCCAGGAACCAGTGTAGAGG
131 CTAATTAATTGACTTTCCAGGAACCAGTGTAGAGG
* *
112290 TTGCTAACTGCTTTCCAATTCAAACACTTGAGAGAAATCAAACTCCCACCCCCATTTTTACATTG
1 TTGCTAACTGCTTTCCAATTCAAACACTTGAGAGAAATCAAACTACCACCCCAATTTTTACATTG
**
112355 -CCCCAAAAGAAAGCCATTTCCTTTAGGCAAATTATCCTCTGGAATTTACATTCCTCTCCTAACA
66 CCCCCAAAAGAAAGCCATTTCCTTTAGGCAAATTATCCTCTACAATTTACATTCCTCTCCTAACA
112419 CTAATTAATTGACTTTCCAGGAACCAGT
131 CTAATTAATTGACTTTCCAGGAACCAGT
112447 TTAGCGGGTG
Statistics
Matches: 150, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
164 88 0.59
165 62 0.41
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (165 bp):
TTGCTAACTGCTTTCCAATTCAAACACTTGAGAGAAATCAAACTACCACCCCAATTTTTACATTG
CCCCCAAAAGAAAGCCATTTCCTTTAGGCAAATTATCCTCTACAATTTACATTCCTCTCCTAACA
CTAATTAATTGACTTTCCAGGAACCAGTGTAGAGG
Found at i:116332 original size:21 final size:21
Alignment explanation
Indices: 116308--116366 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
116298 AATTTTTTAT
116308 AATTTTATTTTTATAAAATCA
1 AATTTTATTTTTATAAAATCA
* *
116329 AATTTTATTTTGATTAAATCA
1 AATTTTATTTTTATAAAATCA
*
116350 ACATTTTACTTATTATA
1 A-ATTTTA-TTTTTATA
116367 TTATTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 20 0.65
22 6 0.19
23 5 0.16
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (21 bp):
AATTTTATTTTTATAAAATCA
Found at i:117388 original size:21 final size:21
Alignment explanation
Indices: 117342--117398 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
117332 AACTTAAATA
* * *
117342 ATATTTTTTTATTATAATTTT
1 ATATTTTTATAATATAATTAT
* *
117363 TTATTTTTGTAATATAATTAT
1 ATATTTTTATAATATAATTAT
117384 ATATTTATTATAATA
1 ATATTT-TTATAATA
117399 GTTATAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATATTTTTATAATATAATTAT
Found at i:123082 original size:3 final size:3
Alignment explanation
Indices: 123074--123119 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
123064 TTAAGACACA
123074 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
123120 GTTATGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:123352 original size:2 final size:2
Alignment explanation
Indices: 123345--123394 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
123335 TATTGCTGAA
*
123345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
123387 AT TT AT AT
1 AT AT AT AT
123395 GCACTGTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124136 original size:22 final size:21
Alignment explanation
Indices: 124090--124142 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
124080 TTATTTAAAA
*
124090 ATATTAAAATT-T-TATTTTT
1 ATATTAAATTTATATATTTTT
*
124109 GTATTAAATTTATATATTTTT
1 ATATTAAATTTATATATTTTT
124130 ATAATTAAATTTA
1 AT-ATTAAATTTA
124143 ACTTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.32
20 1 0.04
21 8 0.29
22 10 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTAAATTTATATATTTTT
Found at i:124158 original size:22 final size:22
Alignment explanation
Indices: 124104--124167 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
124094 TAAAATTTTA
124104 TTTT-TGTATTAAATTTATATAT
1 TTTTATGTATTAAATTTA-ATAT
*
124126 TTTTAT-AATTAAATTTAACT-T
1 TTTTATGTATTAAATTTAA-TAT
124147 TTTTATGTATTAAATATTAAT
1 TTTTATGTATTAAAT-TTAAT
124168 CATGACCTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
21 8 0.22
22 23 0.64
23 5 0.14
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (22 bp):
TTTTATGTATTAAATTTAATAT
Found at i:125969 original size:11 final size:11
Alignment explanation
Indices: 125949--125983 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
125939 ACGATTTATG
*
125949 AATTATTTTTT
1 AATTAATTTTT
*
125960 ATTTAATTTTT
1 AATTAATTTTT
125971 AATTAATTTTT
1 AATTAATTTTT
125982 AA
1 AA
125984 AAAATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
AATTAATTTTT
Found at i:129185 original size:29 final size:29
Alignment explanation
Indices: 129151--129217 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
129141 CGTGTTAATA
*
129151 ATATTA-ATTATTTTTAAAATATATTTTAT
1 ATATTATATTATTTTT-AAATATATTATAT
* *
129180 ATATTATATTATTTTTATATTTATTATAT
1 ATATTATATTATTTTTAAATATATTATAT
129209 ATATTATAT
1 ATATTATAT
129218 CCGTATCACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATTATATTATTTTTAAATATATTATAT
Found at i:129762 original size:18 final size:18
Alignment explanation
Indices: 129730--129764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
129720 TCATATATTA
**
129730 TTTTTAAAAGCTAAAATT
1 TTTTTAAAAAATAAAATT
129748 TTTTTAAAAAATAAAAT
1 TTTTTAAAAAATAAAAT
129765 AAATGTCACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
TTTTTAAAAAATAAAATT
Found at i:130728 original size:2 final size:2
Alignment explanation
Indices: 130721--130764 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
130711 TTTTCATTCA
130721 AT AT 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 AT AT
130763 AT
1 AT
130765 TGTTTAGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:131060 original size:11 final size:10
Alignment explanation
Indices: 131044--131081 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
131034 TATTCAGCAC
131044 TATAAAGTAAA
1 TATAAA-TAAA
131055 TATAAATAAAA
1 TATAAAT-AAA
131066 TATAAA-AAA
1 TATAAATAAA
131075 TATAAAT
1 TATAAAT
131082 GAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.36
10 1 0.04
11 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
TATAAATAAA
Found at i:132080 original size:21 final size:20
Alignment explanation
Indices: 132048--132087 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
132038 TTAAATTATG
*
132048 AATTTTGGTTATTATATTGT
1 AATTTTGGTTATAATATTGT
*
132068 AATTGTTGTTTATAATATTG
1 AATT-TTGGTTATAATATTG
132088 AAATATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (20 bp):
AATTTTGGTTATAATATTGT
Found at i:132959 original size:2 final size:2
Alignment explanation
Indices: 132946--132985 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
132936 CATTGCTGAG
* *
132946 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132986 TTCTATGCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133662 original size:19 final size:21
Alignment explanation
Indices: 133638--133683 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
133628 TTAATTTTAT
*
133638 TTATTT-AAAAT-TTAAATTA
1 TTATTTAAAAATATTAAAATA
133657 TTATTTAAAAATATTAAAATA
1 TTATTTAAAAATATTAAAATA
133678 TTATTT
1 TTATTT
133684 TTATATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTAAAAATATTAAAATA
Found at i:135722 original size:25 final size:25
Alignment explanation
Indices: 135652--135711 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
135642 CGATAGGCTG
*
135652 TAAGCACTCGAAACAATAATGTCAT
1 TAAGCACTCGAAACAATAATGCCAT
135677 TAAGCACTCGAAACAATAATGCCAT
1 TAAGCACTCGAAACAATAATGCCAT
135702 TAAGCACTCG
1 TAAGCACTCG
135712 CTACATGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (25 bp):
TAAGCACTCGAAACAATAATGCCAT
Found at i:137429 original size:10 final size:11
Alignment explanation
Indices: 137400--137431 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
137390 GTCCTTGTGG
137400 ATATATAT-AT
1 ATATATATAAT
137410 ATATATATAAT
1 ATATATATAAT
137421 ATA-ATATAAT
1 ATATATATAAT
137431 A
1 A
137432 CTACTACTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATATATAAT
Found at i:137988 original size:17 final size:17
Alignment explanation
Indices: 137966--138061 Score: 51
Period size: 17 Copynumber: 5.7 Consensus size: 17
137956 TTATTTAAAT
137966 TTAAATTTAAAATAATA
1 TTAAATTTAAAATAATA
** * *
137983 TTAAATTTTTATTTATA
1 TTAAATTTAAAATAATA
*
138000 TTTAAATTTTAAAA-AAAA
1 -TTAAA-TTTAAAATAATA
138018 TT--ATTT-AAATAATAA
1 TTAAATTTAAAATAAT-A
*
138033 TTTAAA-TTAAATTAAT-
1 -TTAAATTTAAAATAATA
138049 TTAAATTATAAAA
1 TTAAATT-TAAAA
138062 ATTTATATTT
Statistics
Matches: 57, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
13 3 0.05
14 5 0.09
15 7 0.12
16 3 0.05
17 21 0.37
18 14 0.25
19 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAAATAATA
Found at i:138034 original size:27 final size:27
Alignment explanation
Indices: 138007--138059 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
137997 ATATTTAAAT
138007 TTTAAAAAAAATT-ATTTAAATAATAA
1 TTTAAAAAAAATTAATTTAAATAATAA
** *
138033 TTTAAATTAAATTAATTTAAATTATAA
1 TTTAAAAAAAATTAATTTAAATAATAA
138060 AAATTTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAAAAAAAATTAATTTAAATAATAA
Found at i:138048 original size:15 final size:15
Alignment explanation
Indices: 138015--138056 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
138005 ATTTTAAAAA
138015 AAATT-ATTTAAA-T
1 AAATTAATTTAAATT
138028 -AA-TAATTTAAATT
1 AAATTAATTTAAATT
138041 AAATTAATTTAAATT
1 AAATTAATTTAAATT
138056 A
1 A
138057 TAAAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.36
13 1 0.04
14 2 0.08
15 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTAATTTAAATT
Found at i:138064 original size:15 final size:15
Alignment explanation
Indices: 138026--138075 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
138016 AATTATTTAA
*
138026 ATAATAATTTAAATT
1 ATAAAAATTTAAATT
*
138041 A-AATTAATTTAAATT
1 ATAA-AAATTTAAATT
*
138056 ATAAAAATTTATATT
1 ATAAAAATTTAAATT
138071 -TAAAA
1 ATAAAA
138076 TTGATGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.23
15 22 0.71
16 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAAATTTAAATT
Found at i:140514 original size:4 final size:4
Alignment explanation
Indices: 140501--140537 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
140491 TATATATATA
* *
140501 TATG TGTG TATG TATG TATG CATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
140538 CTGACTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:141589 original size:2 final size:2
Alignment explanation
Indices: 141582--141611 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
141572 GGCTAAGCAG
141582 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
141612 TAAAAGAAAA
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:141819 original size:29 final size:29
Alignment explanation
Indices: 141785--141860 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
141775 TGTCCCATTG
*
141785 GCAGAACT-TGAATATTCCAAAATGCTACT
1 GCAGAA-TATGAATATTCCAAAATGCTACC
*
141814 GCAGAATATGAATATTCCAAGATGCTACC
1 GCAGAATATGAATATTCCAAAATGCTACC
*
141843 GCAGAATATCAATATTCC
1 GCAGAATATGAATATTCC
141861 CACAATGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 1 0.02
29 42 0.98
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.26
Consensus pattern (29 bp):
GCAGAATATGAATATTCCAAAATGCTACC
Found at i:141882 original size:2 final size:2
Alignment explanation
Indices: 141875--141911 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
141865 ATGTTTTTCC
141875 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 T
141912 CATTCTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:142221 original size:22 final size:23
Alignment explanation
Indices: 142175--142239 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
142165 GTTATATGAT
*
142175 ATATATAATT-TATCATATTTA-A
1 ATATATAATTATAT-ATTTTTATA
142197 ATATA-AATTATATATTTTTATA
1 ATATATAATTATATATTTTTATA
*
142219 ATATATGATTAT-TATTTTTAT
1 ATATATAATTATATATTTTTAT
142240 TAAATAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.26
22 23 0.61
23 5 0.13
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATATAATTATATATTTTTATA
Found at i:142253 original size:24 final size:25
Alignment explanation
Indices: 142193--142253 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 25
142183 TTTATCATAT
*
142193 TTAAAT-ATAAATTATATATTTTTA
1 TTAAATAAAAAATTATATATTTTTA
* **
142217 -T-AATATATGATTAT-TATTTTTA
1 TTAAATAAAAAATTATATATTTTTA
142239 TTAAATAAAAAATTA
1 TTAAATAAAAAATTA
142254 ATTTTATTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
22 11 0.41
23 7 0.26
24 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTAAATAAAAAATTATATATTTTTA
Found at i:142285 original size:29 final size:30
Alignment explanation
Indices: 142227--142285 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
142217 TAATATATGA
* *
142227 TTATTATTTTTATTAAATAAAAAATTAATT
1 TTATTATGTTCATTAAATAAAAAATTAATT
*
142257 TTATTATGTTCATTTAA-AAAAAATTAATT
1 TTATTATGTTCATTAAATAAAAAATTAATT
142286 GATGATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
TTATTATGTTCATTAAATAAAAAATTAATT
Found at i:143759 original size:17 final size:18
Alignment explanation
Indices: 143739--143772 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
143729 TAAAGGATTT
*
143739 ATTTTTATA-AAATTAAA
1 ATTTTTAAATAAATTAAA
143756 ATTTTTAAATAAATTAA
1 ATTTTTAAATAAATTAA
143773 TAAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTTAAATAAATTAAA
Found at i:143796 original size:28 final size:26
Alignment explanation
Indices: 143745--143803 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
143735 ATTTATTTTT
143745 ATAAAATTAAAATTTTTAAATAAATTA
1 ATAAAATTAAAATTTTTAAATAAA-TA
* **
143772 ATAAAATTTAAATTTTTTATTTAAATA
1 ATAAAA-TTAAAATTTTTAAATAAATA
143799 ATAAA
1 ATAAA
143804 TAAATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAAAATTAAAATTTTTAAATAAATA
Found at i:144028 original size:2 final size:2
Alignment explanation
Indices: 144021--144052 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
144011 AAAATAATAC
*
144021 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144053 GCTAGAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146927 original size:19 final size:20
Alignment explanation
Indices: 146883--146929 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
146873 AAAGGAGATT
*
146883 TAAATATTATATTAATTAAA
1 TAAATATTATAATAATTAAA
146903 -ATAATATTA-AATAATTAAA
1 TA-AATATTATAATAATTAAA
146922 TAAATATT
1 TAAATATT
146930 TTTAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATTATAATAATTAAA
Found at i:146941 original size:27 final size:25
Alignment explanation
Indices: 146911--146973 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
146901 AAATAATATT
146911 AAATAATTAAATAAA-TATTTTTAATAA
1 AAATAATTAAA-AAATTA-TTTT-ATAA
*
146938 AAATAAAATAAAAAATTATTTTATAA
1 AAAT-AATTAAAAAATTATTTTATAA
146964 ATAATAATTA
1 A-AATAATTA
146974 TGATAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 9 0.29
27 14 0.45
28 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATAATTAAAAAATTATTTTATAA
Found at i:146955 original size:36 final size:39
Alignment explanation
Indices: 146883--146955 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
146873 AAAGGAGATT
* * *
146883 TAAATATTATATTAATTAAAATAATATTAAATAATTAAA
1 TAAATATTATATTAATAAAAATAATAATAAAAAATTAAA
146922 TAAATATT-T-TTAATAAAAATAA-AATAAAAAATTA
1 TAAATATTATATTAATAAAAATAATAATAAAAAATTA
146956 TTTTATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 10 0.32
37 12 0.39
38 1 0.03
39 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (39 bp):
TAAATATTATATTAATAAAAATAATAATAAAAAATTAAA
Found at i:148385 original size:16 final size:16
Alignment explanation
Indices: 148364--148413 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
148354 ATTATATTAT
148364 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
*
148380 ATTTAT-TAATAATTT-
1 ATTTATATAA-ATTTTA
*
148395 ATATTATATAAATGTTA
1 AT-TTATATAAATTTTA
148412 AT
1 AT
148414 ATACTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 5 0.19
16 17 0.63
17 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:149134 original size:27 final size:26
Alignment explanation
Indices: 149058--149141 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 26
149048 TTTTTTAATA
* *
149058 AATATAATTAAA-ATATAAAATATGTT
1 AATATAATTAAACATAT-AAATTTATT
149084 AAATATAATTATAACATAATAAATTTATT
1 -AATATAATTA-AACAT-ATAAATTTATT
149113 AATATAATATAAACATATAAA-TTATT
1 AATATAAT-TAAACATATAAATTTATT
149139 AAT
1 AAT
149142 TTTATATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
26 8 0.16
27 15 0.29
28 15 0.29
29 11 0.22
30 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (26 bp):
AATATAATTAAACATATAAATTTATT
Found at i:149148 original size:26 final size:28
Alignment explanation
Indices: 149085--149141 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
149075 AAATATGTTA
149085 AATATAAT-TATAACATAATAAATTTATT
1 AATATAATATA-AACATAATAAATTTATT
149113 AATATAATATAAACAT-ATAAA-TTATT
1 AATATAATATAAACATAATAAATTTATT
149139 AAT
1 AAT
149142 TTTATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 8 0.29
27 5 0.18
28 13 0.46
29 2 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
AATATAATATAAACATAATAAATTTATT
Found at i:152292 original size:30 final size:30
Alignment explanation
Indices: 152256--152313 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
152246 TCTTTTCACT
152256 AATCTGAAAAATTGAGGAGAATTAATTGCA
1 AATCTGAAAAATTGAGGAGAATTAATTGCA
152286 AATCTGAAAAATTGAGGAGAATTAATTG
1 AATCTGAAAAATTGAGGAGAATTAATTG
152314 TAGAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (30 bp):
AATCTGAAAAATTGAGGAGAATTAATTGCA
Found at i:154256 original size:22 final size:20
Alignment explanation
Indices: 154231--154270 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
154221 TTGTTTGTTT
154231 ATTGCTCATGAGCATATTTTTA
1 ATTGCTCATGA--ATATTTTTA
*
154253 ATTGTTCATGAATATTTT
1 ATTGCTCATGAATATTTT
154271 CGATTATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
ATTGCTCATGAATATTTTTA
Found at i:156603 original size:2 final size:2
Alignment explanation
Indices: 156596--156634 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
156586 TATATTGGAA
156596 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
156635 TTCGGTTTAA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:167168 original size:18 final size:18
Alignment explanation
Indices: 167145--167188 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
167135 CACTTCGACA
* *
167145 AACAACAGCAGCAGCAAC
1 AACAACAACAACAGCAAC
167163 AACAACAACAACAGCAAC
1 AACAACAACAACAGCAAC
*
167181 AATAACAA
1 AACAACAA
167189 ACAAAACTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.59, C:0.30, G:0.09, T:0.02
Consensus pattern (18 bp):
AACAACAACAACAGCAAC
Found at i:176646 original size:1 final size:1
Alignment explanation
Indices: 176640--176755 Score: 106
Period size: 1 Copynumber: 116.0 Consensus size: 1
176630 TGGCAATTGT
* * * * * ** *
176640 AAAAAAACAAAAAAAAAAAAAAAAACAAAAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * *
176705 AAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
176756 GTGAAGATTT
Statistics
Matches: 91, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:176695 original size:31 final size:30
Alignment explanation
Indices: 176640--176755 Score: 155
Period size: 31 Copynumber: 3.8 Consensus size: 30
176630 TGGCAATTGT
* *
176640 AAAAAAACAAAAA-AAAAAAAAAAAA-CAA
1 AAAAAAAAAAAAACAAAAAAAAAAAAGGAA
176668 AAAAAAGAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAA-AAAAAAACAAAA-AAAAAAAAGGAA
*
176700 AAAGAAAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAACAAAA-AAAAAAAAGGAA
176731 AAAGAAAAAAAAAACAAAAAAAAAA
1 AAA-AAAAAAAAAACAAAAAAAAAA
176756 GTGAAGATTT
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
28 6 0.08
29 6 0.08
30 4 0.05
31 42 0.53
32 21 0.27
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAAACAAAAAAAAAAAAGGAA
Found at i:178961 original size:2 final size:2
Alignment explanation
Indices: 178954--178979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
178944 AGTTTATAAA
178954 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
178980 GTAGGAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:183196 original size:19 final size:19
Alignment explanation
Indices: 183170--183219 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
183160 GACATAATAA
*
183170 AAATTTATTTTTTAT-ATT
1 AAATTTATATTTTATAATT
183188 AATATTTATATTTTATAATT
1 AA-ATTTATATTTTATAATT
*
183208 AAATTTAAATTT
1 AAATTTATATTT
183220 AAAAGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 21 0.75
20 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATTTATATTTTATAATT
Done.