Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 17
Found at i:3480538 original size:52 final size:52
Alignment explanation
Indices: 3480481--3480584 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
3480471 AGCTTTTTGA
*
3480481 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCC
*
3480533 TGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
1 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCC
3480585 AAAAAGCCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (52 bp):
TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCC
Found at i:3480617 original size:76 final size:76
Alignment explanation
Indices: 3480533--3480740 Score: 380
Period size: 76 Copynumber: 2.7 Consensus size: 76
3480523 TGATGTTTCC
*
3480533 TGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
3480598 GAGCTTTTTGA
66 GAGCTTTTTGA
*
3480609 TGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
3480674 GAGCTTTTTGA
66 GAGCTTTTTGA
* *
3480685 TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAA
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAA
3480741 CCTTCGAGTC
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 127 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAGCTTTTTGA
Found at i:3480648 original size:128 final size:129
Alignment explanation
Indices: 3480356--3480903 Score: 461
Period size: 122 Copynumber: 4.4 Consensus size: 129
3480346 CTTCAGTGCA
* * * **
3480356 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGA-------TGTTTTCAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
* *
3480414 GCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
* * *
3480478 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCTGTTTTCAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
*
3480543 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTT
66 ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
* *
3480606 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCC------AAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
* * * * ** * ** * * ** ***
3480665 AGCCTTCGGGAGC-TTTTTGATG-TTTTCAAAGCCTTA-GGGT-CATCTGTAAGTCCTTC---AG
66 A-CCTTCGGG-TCATCTGT-AAGCCCTACAGTGCATGATGTTTCCA--AAAAAG-CCTTCGGGAG
***
3480723 -TGCA
125 CTTTT
* * * * *
3480727 TGATGTTTCCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTT-C------CAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
* *
3480785 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTT
66 ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
* * *
3480849 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCC
3480904 AAAAAGCATT
Statistics
Matches: 347, Mismatches: 56, Indels: 45
0.77 0.12 0.10
Matches are distributed among these distances:
118 8 0.02
119 22 0.06
120 7 0.02
121 53 0.15
122 106 0.31
123 19 0.05
124 6 0.02
125 5 0.01
128 72 0.21
129 49 0.14
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (129 bp):
TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
Found at i:3480752 original size:45 final size:45
Alignment explanation
Indices: 3480682--3480830 Score: 244
Period size: 45 Copynumber: 3.3 Consensus size: 45
3480672 GGGAGCTTTT
* * * *
3480682 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
3480727 TGATGTTTCCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
3480772 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
3480817 TGATGTTTTCAAAA
1 TGATGTTTCCAAAA
3480831 AAGCCTTCGG
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 97 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:3480757 original size:371 final size:374
Alignment explanation
Indices: 3480311--3481085 Score: 1142
Period size: 371 Copynumber: 2.0 Consensus size: 374
3480301 CTTCAGTGCA
* *
3480311 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCG
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCG
* * * *
3480376 GGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCA
66 AGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
3480441 GTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCT
131 GTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCT
*
3480506 GTAAGCCCTTCAGTGCATGATGTTT-C-C-TGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTA
196 GTAAGCCCTTCAGTGCATGATGTTTACTCTTGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTA
3480568 CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGACATC
261 CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGACATC
* *
3480633 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
326 TGTAAGCCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* *
3480682 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTCG
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCG
3480747 AGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
66 AGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
*
3480812 GTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCT
131 GTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCT
*
3480877 GTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCATTTGGGATCTTTTTGATGTTTTCAAAGCCT
196 GTAAGCCCTTCAGTGCATGATGTTT------A-C--------TC----T--TGTTTTCAAAACCT
*
3480942 TAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
240 TAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
* * * ** * *
3481007 TTTCAAAGCCTTAGGGTCATTTGTAAGCCCTTTAATGCATGATGTTTCCAAAAAGCCTTCTGGAT
305 TTTCAAAACCTTAGGGACATCTGTAAGCCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAG
3481072 CTTTT
370 CTTTT
*
3481077 CGATGTTTT
1 TGATGTTTT
3481086 TAAACTCTCG
Statistics
Matches: 358, Mismatches: 22, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
371 211 0.59
379 1 0.00
388 1 0.00
395 145 0.41
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (374 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCG
AGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
GTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCT
GTAAGCCCTTCAGTGCATGATGTTTACTCTTGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTA
CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGACATC
TGTAAGCCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:3480900 original size:416 final size:409
Alignment explanation
Indices: 3479696--3481085 Score: 1492
Period size: 416 Copynumber: 3.4 Consensus size: 409
3479686 ATCTTTTTGA
*
3479696 TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
* * *
3479761 GAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-A
66 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAA
* * *
3479825 AAA-CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGT
131 AAAGCCTTC-GG------G--AG--CTT---T--TTGATGTTTTCAAAGCCTTAGGGTCATCTGT
* * * *
3479889 AAGCCCTTCAGTGCATGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTAT-AGTGCATGAT
180 AAGTCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCT-TCAGTGCATGAT
* * * * ** ** * * * * **
3479953 GTTTCCAAAAAGTCTTCGGAAG-C-TTTTTGATG-TTTTCAAAGCCTTAGGGTCATCTGTAAGTC
244 GTTTCC-AAAA-CCTTCGG--GTCATCTGT-AAGCCCTTCAGTGCATGA-TGT--TTTCAAAG-C
**
3480015 CTTC---AG-TGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGT
300 CTTCGGGAGCTATATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG-CCTTCAGTGCATGATGT
*
3480076 TTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGA----
364 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATTTT
*
3480118 TGTTTTC-AAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
3480182 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAA
66 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAA
*
3480247 AAAGCTTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
131 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
3480312 GATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGG
196 GATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGG
* * * * **
3480377 GTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGCCTTCGGG-TC-ATCTGTAAGCCCTTC
261 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGAGCTATATG-ATG-TTTTC
*** * * * *** ***
3480440 -AGTGCAT-GATGT-TTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTC
324 AAAACCTTCG-GGTCAT-C-TGTAAGCCTTC---AG-TGCATGATGTTTTCAAAACCTTCGGGTC
3480502 ATCTGTAAGCCCTTCAGTGCATGATGTTT
382 ATCTGTAAGCCCTTCAGTGCATGAT-TTT
*
3480531 CCTGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
1 --TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
3480596 GGGAGCTTTTTGATGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCC
64 GGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
3480661 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGC
129 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGC
*
3480726 ATGATGTTTCCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTC
194 ATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTC
* *
3480791 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTT
259 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC---AAAGCCTTCGGGAGCTATATGATGTT
* * *
3480856 TTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCATTTGGG--A
321 TTCAAAACCTTCGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCA
3480919 TC--T------TT---T---TGA----
383 TCTGTAAGCCCTTCAGTGCATGATTTT
* *
3480928 TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
* * * ** *
3480993 GAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATTTGTAAGCCCTTTAATGCATGATGTTTCCAA
66 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAA
* * *
3481058 AAAGCCTTCTGGATCTTTTCGATGTTTT
131 AAAGCCTTCGGGAGCTTTTTGATGTTTT
3481086 TAAACTCTCG
Statistics
Matches: 844, Mismatches: 86, Indels: 103
0.82 0.08 0.10
Matches are distributed among these distances:
395 145 0.17
401 5 0.01
402 8 0.01
403 5 0.01
404 18 0.02
405 23 0.03
406 5 0.01
407 94 0.11
408 50 0.06
409 1 0.00
412 3 0.00
414 3 0.00
415 7 0.01
416 296 0.35
417 6 0.01
418 6 0.01
419 18 0.02
420 14 0.02
421 120 0.14
422 13 0.02
423 4 0.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (409 bp):
TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAA
AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
GATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGG
GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGAGCTATATGATGTTTTCAA
AACCTTCGGGTCATCTGTAAGCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
CCCTTCAGTGCATGATTTT
Found at i:3480954 original size:76 final size:76
Alignment explanation
Indices: 3480772--3481085 Score: 475
Period size: 76 Copynumber: 4.1 Consensus size: 76
3480762 CTTCAGTGCA
* * *
3480772 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAGCCT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTCCAAAAAGCCT
3480837 TCGGGAGCTTTT
65 TCGGGAGCTTTT
* *
3480849 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCATT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* *
3480914 TGGGATCTTTT
66 CGGGAGCTTTT
* *
3480925 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
3480990 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * *
3481001 TGATGTTTTCAAAGCCTTAGGGTCATTTGTAAGCCCTTTAATGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* *
3481066 CTGGATCTTTT
66 CGGGAGCTTTT
*
3481077 CGATGTTTT
1 TGATGTTTT
3481086 TAAACTCTCG
Statistics
Matches: 219, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
76 170 0.78
77 49 0.22
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:3481265 original size:3 final size:3
Alignment explanation
Indices: 3481259--3481303 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3481249 TTATTTTGTT
* *
3481259 TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3481304 AATAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3481465 original size:30 final size:30
Alignment explanation
Indices: 3481430--3481517 Score: 158
Period size: 30 Copynumber: 2.9 Consensus size: 30
3481420 CTTCCAACCG
3481430 CCGCCTCAAGCTTCCAGTGAGCTCCAGCTA
1 CCGCCTCAAGCTTCCAGTGAGCTCCAGCTA
*
3481460 CCGCCTCAAGCTTCCAGTGAGCTCCAGCTG
1 CCGCCTCAAGCTTCCAGTGAGCTCCAGCTA
*
3481490 CCGCCTCAAGCTTCCAGTGAGTTCCAGC
1 CCGCCTCAAGCTTCCAGTGAGCTCCAGC
3481518 CGCCGTTGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (30 bp):
CCGCCTCAAGCTTCCAGTGAGCTCCAGCTA
Found at i:3482935 original size:19 final size:19
Alignment explanation
Indices: 3482911--3482947 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3482901 GATATGTTTA
*
3482911 ATTTATATTTTAGATATTT
1 ATTTATATTTTAAATATTT
*
3482930 ATTTATTTTTTAAATATT
1 ATTTATATTTTAAATATT
3482948 GAAGGAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTATATTTTAAATATTT
Found at i:3487033 original size:21 final size:19
Alignment explanation
Indices: 3487005--3487050 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
3486995 TCATTGAATC
3487005 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
3487025 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
3487044 ACTTAGT
1 A-TTAGT
3487051 AAGATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:3497144 original size:12 final size:12
Alignment explanation
Indices: 3497127--3497152 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3497117 GTTGGGTGAT
3497127 GGCGCTTATCTC
1 GGCGCTTATCTC
3497139 GGCGCTTATCTC
1 GGCGCTTATCTC
3497151 GG
1 GG
3497153 ACCGGTCCGA
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:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (12 bp):
GGCGCTTATCTC
Found at i:3497479 original size:3 final size:3
Alignment explanation
Indices: 3497471--3497543 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
3497461 TTAATATATT
* *
3497471 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3497517 TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3497544 ATAAATCAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3497554 original size:18 final size:17
Alignment explanation
Indices: 3497478--3497554 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 17
3497468 ATTTAATAAT
3497478 AATAATAATAAT-AAT-
1 AATAATAATAATAAATA
* *
3497493 AATATTTATAATAATATA
1 AATAATAATAATAA-ATA
*
3497511 ATATAATAATAATAATTA
1 A-ATAATAATAATAAATA
3497529 TAATAATAATAATAAATA
1 -AATAATAATAATAAATA
3497547 AATCAATA
1 AAT-AATA
3497555 TGGGTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 10 0.20
16 1 0.02
17 5 0.10
18 22 0.44
19 12 0.24
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAATAATAAATA
Found at i:3497962 original size:18 final size:18
Alignment explanation
Indices: 3497905--3497962 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
3497895 GTTAAACAAG
3497905 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
* *
3497923 TTCTTTTC-TTCA-GATGA-G
1 TTCTTCTCATT-ATGA--ACT
3497941 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
3497959 TTCT
1 TTCT
3497963 CTGTAAAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
17 5 0.17
18 20 0.67
19 5 0.17
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.52
Consensus pattern (18 bp):
TTCTTCTCATTATGAACT
Found at i:3498200 original size:113 final size:112
Alignment explanation
Indices: 3497796--3498559 Score: 974
Period size: 113 Copynumber: 6.8 Consensus size: 112
3497786 TTGAATAAGC
* * * *
3497796 TCTTCTTATTATGAACTT-TCTT--TTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGTA
1 TCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGA
* * * *
3497858 AAGGTTGATCCATTAAGTGATGAATTTAAACAAAAGGGTTAAACAAGT
66 AAAGCTGATCCATCAAGTGATGAATTTAAAC-AAAGGGTTAAACAAAT
* *
3497906 TCTTCTCATTATGAACTT-TCTT--TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGTA
1 TCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGA
* * * * *
3497968 AAGGTTGATCCATTAAGTGATGAATTTGAACAAAAGGGTTAAACAAGT
66 AAAGCTGATCCATCAAGTGATGAATTTAAAC-AAAGGGTTAAACAAAT
* * * *
3498016 TCTTCTCATTATGAACTT-TCTT--TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTTTGGC
1 TCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGA
*** * * * *
3498078 GCTGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGT
66 AAAGCTGATCCATCAAGTGATGAATTTAAACAAAGGGTTAAACAAAT
**
3498125 TCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTAACTGG
1 TCTTCTCATTATGAACTTCT-CTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
* * * * * * *
3498190 AAAGGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
65 AAAAGCTGATCCATCAAGTGATGAATTTAAACAAAGGGTTAAACAAAT
*
3498238 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATTATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
* *
3498303 AAAAGCTGATCCATCAAGTGATGGATTTAAACATAA-GGTTGAACAAAT
65 AAAAGCTGATCCATCAAGTGATGAATTTAAACA-AAGGGTTAAACAAAT
* *
3498351 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
* *
3498416 AAAAGCTGATCCATCAAGTGATGGATTTAAACATAA-GGTTGAACAAAT
65 AAAAGCTGATCCATCAAGTGATGAATTTAAACA-AAGGGTTAAACAAAT
* *
3498464 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
*
3498529 AAAAGCTGATCCATCAAGTGATGGATTTAAA
65 AAAAGCTGATCCATCAAGTGATGAATTTAAA
3498560 TCTTTGCTAA
Statistics
Matches: 605, Mismatches: 43, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
109 34 0.06
110 188 0.31
111 3 0.00
113 377 0.62
114 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (112 bp):
TCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGA
AAAGCTGATCCATCAAGTGATGAATTTAAACAAAGGGTTAAACAAAT
Found at i:3499428 original size:83 final size:83
Alignment explanation
Indices: 3499286--3499749 Score: 867
Period size: 83 Copynumber: 5.6 Consensus size: 83
3499276 GGTTCCTACT
3499286 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATT-ACTCTTCCAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCA-TCTTCCAAA
3499350 TTCAATGATTGGTTCTGCC
65 TTCAATGATTGGTTCTGCC
*
3499369 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAAT
3499434 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
*
3499452 AAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAAT
3499517 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
3499535 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAAT
3499600 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
*
3499618 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAAT
3499683 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
3499701 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
3499750 CATTGCATTT
Statistics
Matches: 371, Mismatches: 9, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
83 370 1.00
84 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAAT
TCAATGATTGGTTCTGCC
Found at i:3500918 original size:7 final size:7
Alignment explanation
Indices: 3500901--3500996 Score: 88
Period size: 7 Copynumber: 12.7 Consensus size: 7
3500891 TTGACCCCCC
3500901 TTTTTCTT
1 TTTTTC-T
3500909 TTTTTCTTT
1 TTTTTC--T
3500918 TTTTTCT
1 TTTTTCT
3500925 TTTTTCTT
1 TTTTTC-T
3500933 TTTTCTCT
1 TTTT-TCT
3500941 TTTCCTTCT
1 TTT--TTCT
3500950 TTTTTCT
1 TTTTTCT
3500957 TTTTTCT
1 TTTTTCT
3500964 TTTTT-T
1 TTTTTCT
3500970 CTTTTTCT
1 -TTTTTCT
3500978 TTCTTTC-
1 TT-TTTCT
*
3500985 TTCTTCT
1 TTTTTCT
3500992 TTTTT
1 TTTTT
3500997 TTTGCAAGCA
Statistics
Matches: 77, Mismatches: 2, Indels: 19
0.79 0.02 0.19
Matches are distributed among these distances:
6 4 0.05
7 36 0.47
8 20 0.26
9 16 0.21
10 1 0.01
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:3500919 original size:14 final size:14
Alignment explanation
Indices: 3500900--3500997 Score: 99
Period size: 14 Copynumber: 6.6 Consensus size: 14
3500890 CTTGACCCCC
3500900 CTTTTTCTT-TTTTT
1 CTTTTT-TTCTTTTT
3500914 CTTTTTTTTCTTTTTT
1 C-TTTTTTTC-TTTTT
*
3500930 CTTTTTTCTCTTTTC
1 CTTTTTT-TCTTTTT
3500945 CTTCTTTTTTCTTTTTT
1 C-T-TTTTTTC-TTTTT
3500962 CTTTTTTTCTTTTT
1 CTTTTTTTCTTTTT
* *
3500976 CTTTCTTTCTTCTT
1 CTTTTTTTCTTTTT
3500990 CTTTTTTT
1 CTTTTTTT
3500998 TTGCAAGCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
14 27 0.38
15 23 0.32
16 12 0.17
17 10 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTTTTCTTTTT
Found at i:3500929 original size:25 final size:24
Alignment explanation
Indices: 3500901--3500998 Score: 117
Period size: 24 Copynumber: 3.9 Consensus size: 24
3500891 TTGACCCCCC
3500901 TTTTTCTTTTTTTCTTTTTTTTCT
1 TTTTTCTTTTTTTCTTTTTTTTCT
**
3500925 TTTTTCTTTTTTCTCTTTTCCTTCT
1 TTTTTCTTTTTT-TCTTTTTTTTCT
*
3500950 TTTTTC-TTTTTTCTTTTTTTCTTT
1 TTTTTCTTTTTTTCTTTTTTT-TCT
3500974 TTCTTTCTTTCTTCTTCTTTTTTTT
1 TT-TTTCTTT-TT-TTCTTTTTTTT
3500999 TGCAAGCATA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.11
24 21 0.33
25 20 0.32
26 2 0.03
27 3 0.05
28 10 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCTTTTTTTCTTTTTTTTCT
Found at i:3500958 original size:32 final size:32
Alignment explanation
Indices: 3500901--3500999 Score: 123
Period size: 32 Copynumber: 3.2 Consensus size: 32
3500891 TTGACCCCCC
* *
3500901 TTTTTCTTTTTTTCTT-TTTTTTCTTTTTTCT
1 TTTTTCTCTTTTCCTTCTTTTTTCTTTTTTCT
3500932 TTTTTCTCTTTTCCTTCTTTTTTCTTTTTTCT
1 TTTTTCTCTTTTCCTTCTTTTTTCTTTTTTCT
* * *
3500964 TTTTT-TCTTTTTCTTTCTTTCTTCTTCTTT-T
1 TTTTTCTC-TTTTCCTTCTTTTTTCTTTTTTCT
3500995 TTTTT
1 TTTTT
3501000 GCAAGCATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 22 0.36
32 39 0.64
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (32 bp):
TTTTTCTCTTTTCCTTCTTTTTTCTTTTTTCT
Found at i:3500999 original size:25 final size:24
Alignment explanation
Indices: 3500901--3500999 Score: 105
Period size: 25 Copynumber: 4.0 Consensus size: 24
3500891 TTGACCCCCC
*
3500901 TTTTTCTTTTTTTCTT-TTTTTTCT
1 TTTTTC-TTTTTTCTTCTTTTTTTT
*
3500925 TTTTTCTTTTTTC-TCTTTTCCTTCT
1 TTTTTCTTTTTTCTTCTTTT--TTTT
3500950 TTTTTCTTTTTTCTT-TTTTTCTTT
1 TTTTTCTTTTTTCTTCTTTTT-TTT
*
3500974 TTCTTTCTTTCTTCTTCTTTTTTTT
1 TT-TTTCTTTTTTCTTCTTTTTTTT
3500999 T
1 T
3501000 GCAAGCATAA
Statistics
Matches: 66, Mismatches: 2, Indels: 13
0.81 0.02 0.16
Matches are distributed among these distances:
22 1 0.02
23 12 0.18
24 10 0.15
25 37 0.56
26 6 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCTTTTTTCTTCTTTTTTTT
Found at i:3511626 original size:28 final size:27
Alignment explanation
Indices: 3511587--3511650 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
3511577 TTGCAAATAA
* *
3511587 AATGAAACATATAAATATTATGAAAAT
1 AATGAAAAATATAAATATTATGAAAAG
*
3511614 AATGAATAAATATGAAA-ATTTTGAAAAG
1 AATGAA-AAATAT-AAATATTATGAAAAG
*
3511642 AAAGAAAAA
1 AATGAAAAA
3511651 AAATTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 9 0.29
28 19 0.61
29 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (27 bp):
AATGAAAAATATAAATATTATGAAAAG
Found at i:3513705 original size:3 final size:3
Alignment explanation
Indices: 3513697--3513768 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
3513687 ATTTAATATT
* * * * *
3513697 TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3513745 TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
3513769 ATAAATCAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:3515650 original size:21 final size:19
Alignment explanation
Indices: 3515622--3515667 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
3515612 TCATTGAATC
3515622 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
3515642 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
3515661 ACTTAGT
1 A-TTAGT
3515668 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:3515858 original size:18 final size:18
Alignment explanation
Indices: 3515835--3515869 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3515825 GTCCATATTT
3515835 ATAATTT-TTTCATAAATA
1 ATAATTTATTT-ATAAATA
3515853 ATAATTTATTTATAAAT
1 ATAATTTATTTATAAAT
3515870 TAATCTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAATTTATTTATAAATA
Found at i:3516392 original size:32 final size:32
Alignment explanation
Indices: 3516351--3516420 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
3516341 GTTGTGCAAA
* *
3516351 TCATCTTCAATCTCTTACACAACACACTCTTT
1 TCATCTTCAATCTCTTACACAACAAACTCCTT
*
3516383 TCATCTTCAATCTTTTACACAACAAACTCCTT
1 TCATCTTCAATCTCTTACACAACAAACTCCTT
3516415 TCATCT
1 TCATCT
3516421 AACCAAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.39
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACACAACAAACTCCTT
Found at i:3520604 original size:5 final size:5
Alignment explanation
Indices: 3520594--3520640 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
3520584 AAAGATATAT
*
3520594 TAAAA TAAAA T-AAA TAAAA -AAGA -AAAA TAAAA TAAAA TAATAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAA
3520641 TATTAATAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 10 0.27
5 22 0.59
6 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:3520638 original size:11 final size:10
Alignment explanation
Indices: 3520594--3520640 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
3520584 AAAGATATAT
3520594 TAAAATAAAA
1 TAAAATAAAA
3520604 T-AAATAAAA
1 TAAAATAAAA
*
3520613 -AAGA-AAAA
1 TAAAATAAAA
3520621 TAAAATAAAA
1 TAAAATAAAA
3520631 TAATAATAAA
1 TAA-AATAAA
3520641 TATTAATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
8 4 0.13
9 13 0.42
10 8 0.26
11 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:3520638 original size:16 final size:17
Alignment explanation
Indices: 3520594--3520664 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 17
3520584 AAAGATATAT
3520594 TAAAATAA-AATAAATA
1 TAAAATAATAATAAATA
* * *
3520610 AAAAAGAAAAATAAA-A
1 TAAAATAATAATAAATA
3520626 TAAAATAATAATAAATA
1 TAAAATAATAATAAATA
* *
3520643 T-TAATAGTAATAAATA
1 TAAAATAATAATAAATA
3520659 TAAAAT
1 TAAAAT
3520665 GGGGATTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
16 33 0.75
17 11 0.25
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
TAAAATAATAATAAATA
Found at i:3520709 original size:19 final size:18
Alignment explanation
Indices: 3520690--3520738 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
3520680 GTTATTTTTA
3520690 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
3520708 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
3520727 AAATAAACAAAT
1 AAATAAA-AAAT
3520739 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:3521418 original size:19 final size:19
Alignment explanation
Indices: 3521362--3521424 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
3521352 CTATTTAAAC
**
3521362 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
3521382 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
3521402 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
3521421 TAAA
1 TAAA
3521425 CTAAAATACC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:3523807 original size:21 final size:21
Alignment explanation
Indices: 3523783--3523834 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
3523773 GTTTTGTAAA
3523783 CATCAAATTCAACGATCTAAC
1 CATCAAATTCAACGATCTAAC
3523804 CATCAAATTCAACGATCTAAC
1 CATCAAATTCAACGATCTAAC
3523825 CATCAAATTC
1 CATCAAATTC
3523835 CATTGTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (21 bp):
CATCAAATTCAACGATCTAAC
Found at i:3526232 original size:21 final size:20
Alignment explanation
Indices: 3526166--3526226 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
3526156 GATTAAGTTG
3526166 AAAA-AATATATATTA-AAAT
1 AAAATAATATA-ATTATAAAT
* *
3526185 AAAATAATATAATAAAAAAT
1 AAAATAATATAATTATAAAT
3526205 AAAAATAATATAATTATAAAT
1 -AAAATAATATAATTATAAAT
3526226 A
1 A
3526227 TTAATAGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 7 0.19
20 11 0.31
21 18 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAATATAATTATAAAT
Found at i:3529575 original size:19 final size:19
Alignment explanation
Indices: 3529551--3529589 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3529541 TATATTTTAA
3529551 ATTTTT-AGTAAAAAAGATT
1 ATTTTTAAGTAAAAAA-ATT
*
3529570 ATTTTTAATTAAAAAAATT
1 ATTTTTAAGTAAAAAAATT
3529589 A
1 A
3529590 AAAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTTTTAAGTAAAAAAATT
Found at i:3533670 original size:22 final size:24
Alignment explanation
Indices: 3533645--3533691 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3533635 AGTTGTGGTA
3533645 TTTTG-ATTAACTGC-TTATTTCT
1 TTTTGAATTAACTGCTTTATTTCT
3533667 TTTTGAAAATTAACTGCTTTATTTC
1 TTTTG--AATTAACTGCTTTATTTC
3533692 ACTGATGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTTGAATTAACTGCTTTATTTCT
Found at i:3533832 original size:19 final size:19
Alignment explanation
Indices: 3533808--3533844 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3533798 ACGACCAACA
*
3533808 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
3533827 AAATCGTAACGCGATCTC
1 AAATCGCAACGCGATCTC
3533845 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:3533954 original size:20 final size:20
Alignment explanation
Indices: 3533929--3533980 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
3533919 CGATTTTAGA
*
3533929 AAATCGCAATGCGA-ATATGT
1 AAATCGCAATGCGATA-ATAT
*
3533949 AAATCGCAACGCGATAATAT
1 AAATCGCAATGCGATAATAT
3533969 ATAATCGCAATG
1 A-AATCGCAATG
3533981 AGATTCTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGCGATAATAT
Found at i:3533997 original size:41 final size:41
Alignment explanation
Indices: 3533951--3534045 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
3533941 GAATATGTAA
* * *
3533951 ATCGCAACGCGATAATATATAATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATAATACATAACCGCAACGAGATTCTGACT
* *
3533992 TTCGCAACGCGATAATACATAACCGCAACGTGATTCTGACT
1 ATCGCAACGCGATAATACATAACCGCAACGAGATTCTGACT
*
3534033 ATCGCAATGCGAT
1 ATCGCAACGCGAT
3534046 TCTGACTGTC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAACCGCAACGAGATTCTGACT
Found at i:3534046 original size:20 final size:20
Alignment explanation
Indices: 3533972--3534062 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
3533962 ATAATATATA
* *
3533972 ATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
3533992 TTCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
3534012 AACCGCAACGTGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
3534033 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3534053 GTCGCAACGC
1 ATCGCAACGC
3534063 TGAATTTCAA
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.04
20 37 0.70
21 12 0.23
22 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3534908 original size:24 final size:24
Alignment explanation
Indices: 3534881--3534934 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3534871 GTATTCTAAA
3534881 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3534905 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3534929 TTTGAT
1 TTTGAT
3534935 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3537215 original size:18 final size:18
Alignment explanation
Indices: 3537192--3537226 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3537182 AGAAAAAGGT
*
3537192 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
3537210 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
3537227 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:3537536 original size:140 final size:140
Alignment explanation
Indices: 3537284--3537566 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
3537274 GCAAACGTTG
3537284 TATTATGTGTATTTTATGTGTAAACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
3537349 TTGAACATTGCTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3537414 CGAATTTGAC
131 CGAATTTGAC
* *
3537424 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAGCTTGAGT
1 TATTATGTGTATTTTATGTGTAAACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
3537489 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3537554 CGAATTTGAC
131 CGAATTTGAC
3537564 TAT
1 TAT
3537567 CGCAACGCAA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:3537562 original size:20 final size:20
Alignment explanation
Indices: 3537537--3537667 Score: 148
Period size: 20 Copynumber: 6.8 Consensus size: 20
3537527 TTACACATTC
*
3537537 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
3537557 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
3537576 A----A-AATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
3537591 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3537611 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
3537631 ATTTTATTATCGCAATGGGA
1 ATTTGACTATCGCAACGCGA
3537651 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
3537668 AGAAAATCGC
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.11
15 3 0.03
19 3 0.03
20 77 0.83
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:3537584 original size:14 final size:14
Alignment explanation
Indices: 3537565--3537591 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3537555 GAATTTGACT
3537565 ATCGCAACGCAAAA
1 ATCGCAACGCAAAA
3537579 ATCGCAACGCAAA
1 ATCGCAACGCAAA
3537592 TTTGACTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
ATCGCAACGCAAAA
Found at i:3537905 original size:62 final size:63
Alignment explanation
Indices: 3537795--3537947 Score: 263
Period size: 62 Copynumber: 2.4 Consensus size: 63
3537785 GATTGAAATC
3537795 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
1 AACAAATCAACTTTTACA----AATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
3537860 TA
62 TA
3537862 AACAAATCAACTTTTACAAATCAATTAAA-AAGCACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATTA
3537924 AACAAATCAACTTTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
3537948 CTTTTACAAA
Statistics
Matches: 86, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
62 57 0.66
63 11 0.13
67 18 0.21
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.29
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATTA
Found at i:3537944 original size:14 final size:14
Alignment explanation
Indices: 3537925--3537961 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
3537915 CATCAATTAA
3537925 ACAAATCAACTTTT
1 ACAAATCAACTTTT
3537939 ACAAATCAACTTTT
1 ACAAATCAACTTTT
3537953 ACAAATCAA
1 ACAAATCAA
3537962 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3539328 original size:184 final size:183
Alignment explanation
Indices: 3539021--3539390 Score: 634
Period size: 184 Copynumber: 2.0 Consensus size: 183
3539011 AATTAAATGT
*
3539021 TTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTCAG
1 TTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTCAG
3539086 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
* * *
3539151 GAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATTTAATA
131 GAGTTTTAAATAGTTTGGACTGAGCCCAAATGTTATATATAATATATTTAATA
*
3539204 TTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT
1 TTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTC
* *
3539268 ATATAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAA
64 AGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAA
* *
3539333 TTGGGTTTTAAATAGTTTGGACTGAGCCCATATGTTATATATAATATATTTAATA
129 TTGAGTTTTAAATAGTTTGGACTGAGCCCAAATGTTATATATAATATATTTAATA
3539388 TTT
1 TTT
3539391 AAAATTTAAT
Statistics
Matches: 176, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
182 6 0.03
183 47 0.27
184 123 0.70
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (183 bp):
TTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTTTAAATAGTTTGGACTGAGCCCAAATGTTATATATAATATATTTAATA
Found at i:3540167 original size:21 final size:21
Alignment explanation
Indices: 3540122--3540223 Score: 73
Period size: 21 Copynumber: 4.9 Consensus size: 21
3540112 TGGGAGAGAC
* * * *
3540122 CTCTTCAACGATGACAGAGGC
1 CTCTTGAAGGATGACAGGGGA
*
3540143 CTCTTGAACGG-TGAGAGGGGA
1 CTCTTGAA-GGATGACAGGGGA
*
3540164 CTCTTGAAGGATGACAGGGGC
1 CTCTTGAAGGATGACAGGGGA
* * * *
3540185 CTCTTGAATGAT-AGGAGAGGC
1 CTCTTGAAGGATGA-CAGGGGA
*
3540206 CTCTTGAATGATGACAGG
1 CTCTTGAAGGATGACAGG
3540224 TGAGTCGGGC
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
20 3 0.05
21 60 0.92
22 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (21 bp):
CTCTTGAAGGATGACAGGGGA
Found at i:3540210 original size:42 final size:41
Alignment explanation
Indices: 3540101--3540223 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 41
3540091 GTGAATCGGG
* * *
3540101 CTCTTGAATGGTGGGAGAGACCTCTTCAACGATGACAGAGGC
1 CTCTTGAATGGT-GGAGAGGCCTCTTGAACGATGACAGGGGC
* * * *
3540143 CTCTTGAACGGTGAGAGGGGACTCTTGAAGGATGACAGGGGC
1 CTCTTGAATGGTG-GAGAGGCCTCTTGAACGATGACAGGGGC
* *
3540185 CTCTTGAATGATAGGAGAGGCCTCTTGAATGATGACAGG
1 CTCTTGAATGGT-GGAGAGGCCTCTTGAACGATGACAGG
3540224 TGAGTCGGGC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 65 0.97
43 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (41 bp):
CTCTTGAATGGTGGAGAGGCCTCTTGAACGATGACAGGGGC
Found at i:3540723 original size:20 final size:20
Alignment explanation
Indices: 3540698--3540741 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3540688 AATAGTTTCT
3540698 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
3540718 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
3540738 GAAA
1 GAAA
3540742 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:3540751 original size:20 final size:20
Alignment explanation
Indices: 3540728--3540776 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3540718 GAAACTTAAA
3540728 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
3540748 ATCGCAACTCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3540768 ATCGCAACG
1 ATCGCAACG
3540777 GGATAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3540807 original size:33 final size:34
Alignment explanation
Indices: 3540768--3540833 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
3540758 GAATTTGACT
* * *
3540768 ATCGCAACGGGATAATCGCAATGCGAAA-TAAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACTAAAA
*
3540801 ATCGCAACGAGAAAATTGCAACGCGAAACTAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACTAAA
3540834 TTCGCGTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAACGCGAAACTAAAA
Found at i:3540863 original size:20 final size:20
Alignment explanation
Indices: 3540834--3540871 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3540824 CGAAACTAAA
*
3540834 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
3540854 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
3540872 CGTTGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:3540899 original size:33 final size:34
Alignment explanation
Indices: 3540838--3540922 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 34
3540828 ACTAAATTCG
*
3540838 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
3540872 CGTTGCGATTTTTATTTT-GCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
**
3540905 CGTTGCGATAATCATTTT
1 CGTTGCGATTTTCATTTT
3540923 TGCGTTGCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 28 0.62
34 17 0.38
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:3542856 original size:20 final size:20
Alignment explanation
Indices: 3542833--3542922 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
3542823 TCTGAAACTT
3542833 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
3542853 AAAATTGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
** * ***
3542873 ACTATCGCAACGCGACTTTG
1 AAAATCGCAACACGAAAATG
** *
3542893 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
3542912 AAAATCGCAAC
1 AAAATCGCAAC
3542923 GAAAAAATCG
Statistics
Matches: 55, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
19 11 0.20
20 44 0.80
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:3542950 original size:19 final size:18
Alignment explanation
Indices: 3542896--3542950 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
3542886 GACTTTGACT
3542896 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAAT-AAA
3542915 ATCGCAA--CG-AA-AAA
1 ATCGCAACGCGAAATAAA
3542929 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAA-TAAA
3542948 ATC
1 ATC
3542951 ACGTTGCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 10 0.32
16 4 0.13
17 4 0.13
19 13 0.42
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (18 bp):
ATCGCAACGCGAAATAAA
Found at i:3543359 original size:22 final size:22
Alignment explanation
Indices: 3543332--3543378 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3543322 GAGATAGACA
*
3543332 GATTTCGTCGGAGATGGGGATG
1 GATTTCGTCGGAGATGGGGACG
3543354 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCGGAGATGGGGACG
3543376 GAT
1 GAT
3543379 GTCACTGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.11, G:0.45, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACG
Found at i:3543574 original size:20 final size:20
Alignment explanation
Indices: 3543545--3543718 Score: 165
Period size: 20 Copynumber: 8.6 Consensus size: 20
3543535 ATTTTGTATT
*
3543545 ATCGCATTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
3543565 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
3543585 ATCGAGTTGCGATTATGT-ATT
1 ATCGCGTTGCGA-TA-GTCAGA
*
3543606 ATCGTGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
3543626 ATCTCGTTGCGATTATGT-ATT
1 ATCGCGTTGCGA-TA-GTCAGA
3543647 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
3543667 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * *
3543687 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
3543707 ATCGCGTTGCGA
1 ATCGCGTTGCGA
3543719 ATCTGGAAAC
Statistics
Matches: 124, Mismatches: 22, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
19 5 0.04
20 86 0.69
21 29 0.23
22 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:3543614 original size:21 final size:21
Alignment explanation
Indices: 3543585--3543659 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
3543575 GATAGTCAGA
*
3543585 ATCGAGTTGCGATTATGTATT
1 ATCGTGTTGCGATTATGTATT
**
3543606 ATCGTGTTGCGA-TA-GTCAGA
1 ATCGTGTTGCGATTATGT-ATT
3543626 ATC-TCGTTGCGATTATGTATT
1 ATCGT-GTTGCGATTATGTATT
*
3543647 ATCGCGTTGCGAT
1 ATCGTGTTGCGAT
3543660 AGTCAGAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 25 0.58
22 2 0.05
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (21 bp):
ATCGTGTTGCGATTATGTATT
Found at i:3543617 original size:41 final size:41
Alignment explanation
Indices: 3543565--3543718 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
3543555 GATAGTCAGA
*
3543565 ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
* *
3543606 ATCGTGTTGCGATAGTCAGAATCTCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
**
3543647 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT-TACA-T
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
* *
3543686 ATTCGCATTGCGATAGTCAAAATCGCGTTGCGA
1 A-TCGCGTTGCGATAGTCAGAATCGCGTTGCGA
3543719 ATCTGGAAAC
Statistics
Matches: 103, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
39 2 0.02
40 31 0.30
41 70 0.68
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
Found at i:3543676 original size:61 final size:61
Alignment explanation
Indices: 3543545--3543718 Score: 158
Period size: 61 Copynumber: 2.9 Consensus size: 61
3543535 ATTTTGTATT
* **
3543545 ATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTAGA
* * ** *
3543606 ATCGTGTTGCGATAGTCAGAATCTCGTTGCGATTATGT-ATTATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGA-TA-GTCAGAATCGAGTTGCGATTATGT-AGA
* * * * * *
3543667 ATCGCGTTGCGAT-TTACATATTCGCATTGCGATAGTCAAAATCGCGTTGCGA
1 ATCGCGTTGCGATAGT-CAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGA
3543719 ATCTGGAAAC
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
59 2 0.02
60 18 0.20
61 56 0.61
62 14 0.15
63 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTAGA
Found at i:3543756 original size:20 final size:19
Alignment explanation
Indices: 3543733--3543778 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3543723 GGAAACTTAT
*
3543733 TTGCGATAGTAGAGATCGCG
1 TTGCGAT-GTAGAGATCGCA
*
3543753 TTGCGATTTAGAGATCGCA
1 TTGCGATGTAGAGATCGCA
3543772 TTGCGAT
1 TTGCGAT
3543779 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATGTAGAGATCGCA
Found at i:3543766 original size:19 final size:19
Alignment explanation
Indices: 3543742--3543780 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3543732 TTTGCGATAG
*
3543742 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
3543761 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCGATT
3543780 T
1 T
3543781 TGTTGGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:3545959 original size:15 final size:16
Alignment explanation
Indices: 3545941--3545977 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3545931 TATGAACATC
3545941 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
3545956 AAATAGAATAACAATA
1 AAATAAAATAACAATA
3545972 AAATAA
1 AAATAA
3545978 TTTCTATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAAAATAACAATA
Done.