Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002015.1 Hibiscus syriacus cultivar Beakdansim tig00004115_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: 67836
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:120 original size:22 final size:23
Alignment explanation
Indices: 59--130 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
49 ATACTTTACA
* *
59 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
82 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* * *
105 ATAT-AGCTCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
127 ATAT
1 ATAT
131 TTTACCTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 18 0.43
23 24 0.57
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:541 original size:22 final size:22
Alignment explanation
Indices: 483--546 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 22
473 GATACTTTAC
*
483 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
506 ATATAAACGATACCTATTACATT
1 ATAT-AACGCTACCTATTACATT
529 ATATAACGCTACCTATTA
1 ATATAACGCTACCTATTA
547 TATCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.35
23 22 0.59
24 2 0.05
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:554 original size:22 final size:22
Alignment explanation
Indices: 482--554 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
472 AGATACTTTA
*
482 CATATAACCACTACCTATTACAT
1 CATATAA-CGCTACCTATTACAT
* *
505 TATATAAACGATACCTATTACAT
1 CATAT-AACGCTACCTATTACAT
* *
528 TATATAACGCTACCTATTATAT
1 CATATAACGCTACCTATTACAT
550 CATAT
1 CATAT
555 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 19 0.44
23 22 0.51
24 2 0.05
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.36
Consensus pattern (22 bp):
CATATAACGCTACCTATTACAT
Found at i:968 original size:23 final size:22
Alignment explanation
Indices: 902--973 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
892 ATACTTTACA
*
902 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
* *
925 ATATAACGATACATATTACATT
1 ATATAACGCTACCTATTACATT
*
947 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
970 ATAT
1 ATAT
974 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1243 original size:420 final size:424
Alignment explanation
Indices: 1--1585 Score: 2639
Period size: 419 Copynumber: 3.8 Consensus size: 424
1 TAATGTTTTCCACAGTGAAAAAAG--TAGAC-CTTTTATAAAAAAGGATAGATACTTTACAATAT
1 TAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTAT-AAAAAGGATAGATACTTTACAATAT
*
63 AACCACTACCTATTACATTATATAAACGATACCTATTACATTATAT-AGCTCTACCTATTACATC
65 AACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATC
127 ATA-TTTTACCTATTATATTG-AAGTGTCCATACTTTTTTATAAAAAAGGATCGATACTTTGTTT
130 ATATTTTTACCTATTATATTGAAAGTGTCCATAC-TTTTTAT--AAAAGGATCGATACTTTGTTT
190 -AAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGGTTTCATGTTTTCCACCTACAATATT
192 AAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGT-GTTTCATGTTTTCCACCTACAATATT
254 AATTTAATAATTTCATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAATAATATTTAG
255 AATTTAATAATTTCATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAATAATATTTAG
* *
319 AATTTAAATTTAACAATAATATATCGTAACGT-AAAAATAAATCATTAGACGTCTATATATTACT
320 AATTTAAATTTAATAATAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATA-ATTACT
383 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAAT
384 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAAT
*
424 TAATGTTTTCCACAGTGGAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTAC-ATATA
1 TAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATA
*
488 ACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA-CGCTACCTATTATATCA
66 ACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCA
552 TATTTTTACCTATTATATTGAAAGTGTCCATAC-TTTTATAAAAGGATCGATACTTTGGTTTAAA
131 TATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAGGATCGATACTTT-GTTTAAA
*
616 GTAATGTAATTT-T-TTTCAATTTTTTTAATAGTG-TTCATGTTTTCCA-CTACAATATTAATTT
195 GTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTT
*
677 AATAATTTCATTTACAGAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAAT
260 AATAATTTCATTTACA-CAAAAATTATTTGATTGTTTTGATATTTTAT-AAATAATATTTAGAAT
742 TTAAATTTAATAATAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
323 TTAAATTTAATAATAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
807 TAATATCTTAAAACTCACTC-AAAGATAACCTTAAAT
388 TAATATCTTAAAACTCACTCAAAAGATAACCTTAAAT
843 TAATGTTTTCCAC-GTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATA
1 TAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATA
*
907 ACCACTACCTATTACATTATAT-AACGATACATATTACATTATATAAGCGCTACCTATTACATCA
66 ACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCA
971 TATTTTTACCTATTATA-TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAA
131 TATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTTGTTTAAA
1035 GTTATGTAATTTATGTTTCAA-TTTTTTAATAGTG-TTCATGTTTTCCACCTACAATATTAATTT
195 GTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTT
*
1098 AATAATATCA-TTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAG-ATT
260 AATAATTTCATTTACACAAAAATTATTTGATTGTTTTGATATTTTAT-AAATAATATTTAGAATT
*
1161 TAAATTTAATAATAAGATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTATTAAA
324 TAAATTTAATAAT-A-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAA
1226 TTAATATCTTAAAACTCACTCAAAAGATAA-CTTAAAT
387 TTAATATCTTAAAACTCACTCAAAAGATAACCTTAAAT
*
1263 TAATGTTTTCCACAGTGAATAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATA
1 TAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATA
*
1328 ACCACTACC--TTACATTATAT--ACGATACCTATATACATTATATAAGCTCTACCTATTACATC
66 ACCACTACCTATTACATTATATAAACGATACCTAT-TACATTATATAAGCGCTACCTATTACATC
*
1389 ATATTTTTCCCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAGGATCGATACTTTGTTTAAA
130 ATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAGGATCGATACTTTGTTTAAA
*
1453 GTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATG-TTTCTACCTAC-A-A-T-ATT
195 GTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATT
1513 T-ATAATTTCATTTACACAAAAAATTATTTGATTG-TTTGATATTTTATAAATAATATTTAGAAT
259 TAATAATTTCATTTACAC-AAAAATTATTTGATTGTTTTGATATTTTATAAATAATATTTAGAAT
1576 TTAAATTTAA
323 TTAAATTTAA
1586 CAACATTAAC
Statistics
Matches: 1112, Mismatches: 20, Indels: 67
0.93 0.02 0.06
Matches are distributed among these distances:
415 21 0.02
416 35 0.03
417 17 0.02
418 184 0.17
419 258 0.23
420 258 0.23
421 140 0.13
422 23 0.02
423 28 0.03
424 86 0.08
425 43 0.04
426 19 0.02
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (424 bp):
TAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATA
ACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCA
TATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAGGATCGATACTTTGTTTAAAG
TTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTA
ATAATTTCATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAATAATATTTAGAATTTA
AATTTAATAATAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
TATCTTAAAACTCACTCAAAAGATAACCTTAAAT
Found at i:4626 original size:180 final size:183
Alignment explanation
Indices: 4191--4667 Score: 800
Period size: 180 Copynumber: 2.6 Consensus size: 183
4181 ACACTTTTTT
*
4191 AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGATACAATATTAGAAAGTGTC
1 AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATATTAGAAAGTGTC
4256 GATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTTATACCGGTTATATTACAAAATT
66 GATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTTATACCGGTTATATTACAAAATT
* * *
4321 ATCTATTACATTATAAATCTAGGTTCCTAAGTGTAAATGTCGACACTTTTTTA
131 ATCTATTACATTATAAATCTAGGTTCCGAAGTGTAAATGTCGACACGTTTTGA
*
4374 AATGGTATCGACACATTTTTCTTCCAATCTGGACATTAAGTACCGACACAATATTAGAAAGTGTC
1 AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATATTAGAAAGTGTC
*
4439 GATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATA-TAC-AAATT
66 GATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTTATACCGGTTATATTACAAAATT
* * * * *
4502 ATCTATTACATTAT-ATTCTGGGTTCCGATGTGTAACTGTCGACGCGTTTTGA
131 ATCTATTACATTATAAATCTAGGTTCCGAAGTGTAAATGTCGACACGTTTTGA
* *
4554 CAAT-GTATCGACACATTTTTCTTTCAATCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 -AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATATTAGAAAGTGT
4618 CGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTTATACCG
65 CGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTTATACCG
4668 ATAGCATTGC
Statistics
Matches: 278, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
180 136 0.49
181 22 0.08
182 3 0.01
183 117 0.42
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (183 bp):
AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATATTAGAAAGTGTC
GATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTTATACCGGTTATATTACAAAATT
ATCTATTACATTATAAATCTAGGTTCCGAAGTGTAAATGTCGACACGTTTTGA
Found at i:6564 original size:3 final size:3
Alignment explanation
Indices: 6556--6612 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
6546 ACTTGTTTGG
* * * * * *
6556 ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
6604 ATC ATC ATC
1 ATC ATC ATC
6613 GTCAGCTTCA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.07, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:6605 original size:24 final size:24
Alignment explanation
Indices: 6578--6629 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
6568 ATCATCGTCA
*
6578 TCATCTTCATCGTCAGCTTCATCG
1 TCATCATCATCGTCAGCTTCATCG
*
6602 TCATCATCATCGTCAGCTTCATCT
1 TCATCATCATCGTCAGCTTCATCG
6626 TCAT
1 TCAT
6630 TGACCGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (24 bp):
TCATCATCATCGTCAGCTTCATCG
Found at i:6613 original size:12 final size:12
Alignment explanation
Indices: 6556--6616 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
6546 ACTTGTTTGG
*
6556 ATCATCATCATC
1 ATCATCATCGTC
* *
6568 ATCATCGTCATC
1 ATCATCATCGTC
*
6580 ATCTTCATCGTC
1 ATCATCATCGTC
* *
6592 AGCTTCATCGTC
1 ATCATCATCGTC
6604 ATCATCATCGTC
1 ATCATCATCGTC
6616 A
1 A
6617 GCTTCATCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.08, T:0.34
Consensus pattern (12 bp):
ATCATCATCGTC
Found at i:6623 original size:12 final size:12
Alignment explanation
Indices: 6582--6624 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
6572 TCGTCATCAT
6582 CTTCATCGTCAG
1 CTTCATCGTCAG
*
6594 CTTCATCGTCAT
1 CTTCATCGTCAG
*
6606 CATCATCGTCAG
1 CTTCATCGTCAG
6618 CTTCATC
1 CTTCATC
6625 TTCATTGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.19, C:0.35, G:0.12, T:0.35
Consensus pattern (12 bp):
CTTCATCGTCAG
Found at i:6627 original size:6 final size:6
Alignment explanation
Indices: 6578--6629 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
6568 ATCATCGTCA
* * * * * *
6578 TCATCT TCATCG TCAGCT TCATCG TCATCA TCATCG TCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
6626 TCAT
1 TCAT
6630 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:9006 original size:200 final size:200
Alignment explanation
Indices: 8057--9424 Score: 2560
Period size: 200 Copynumber: 6.9 Consensus size: 200
8047 TTTAAATTAA
8057 TATCGACACAAACTAAAAAAAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTAT
1 TATCGACACAAACT-AAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
8120 AC-TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGG
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGG
*
8184 ATCTACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC
8249 AAAAA-
195 AAAAAC
8254 TATCGACACAAACT--AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
8317 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
8382 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC-
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
8446 AAAAC
196 AAAAC
8451 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
8515 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTTGGGTTTCGATGTTTTTGGG
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTTGGGTTTCGATGTTTTTGGG
8580 ATCGACACTTTTTATATATGGATCG--ACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC
8643 AAAAAC
195 AAAAAC
*
8649 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACTGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
8713 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
8778 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGTACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
8843 AAAAC
196 AAAAC
8848 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
8913 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
8978 TCTACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
9043 AAAAC
196 AAAAC
9048 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
9113 CTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
9178 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
*
9243 AAAAA
196 AAAAC
9248 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
9313 CTTGTACCGGTTAGATTGGAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
* *
9378 TCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
9425 GGCCATATTG
Statistics
Matches: 1149, Mismatches: 11, Indels: 19
0.97 0.01 0.02
Matches are distributed among these distances:
194 28 0.02
195 1 0.00
196 23 0.02
197 240 0.21
198 161 0.14
199 181 0.16
200 515 0.45
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
AAAAC
Found at i:11393 original size:33 final size:33
Alignment explanation
Indices: 11356--11421 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
11346 CATCTTAATA
*
11356 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
11389 TCACCCCTCAACACCTCTATTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
11422 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:11480 original size:21 final size:21
Alignment explanation
Indices: 11455--11519 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
11445 CCCCTTATGC
* *
11455 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
11476 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
11497 CTATCAAGTTTCTCTTTGACT
1 CTCTCAAGTTTCTCTTCGACT
11518 CT
1 CT
11520 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:13569 original size:24 final size:24
Alignment explanation
Indices: 13533--13584 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
13523 CGTTCTATCA
13533 ATTTTCAGAGGATAT-TTAGCTTAT
1 ATTTTCAGAGGATATGTTA-CTTAT
** *
13557 ATTTTCATCGGATATGTTATTTAT
1 ATTTTCAGAGGATATGTTACTTAT
13581 ATTT
1 ATTT
13585 AATCGATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (24 bp):
ATTTTCAGAGGATATGTTACTTAT
Found at i:13746 original size:17 final size:18
Alignment explanation
Indices: 13724--13766 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
13714 ATATATCCGG
13724 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
13741 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
13761 TATCAT
1 TATCAT
13767 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:13775 original size:20 final size:19
Alignment explanation
Indices: 13729--13789 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
13719 TCCGGTATCA
13729 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
13748 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
* * *
13769 TTTTACCTGTTATATCGTT
1 TTTTACCGGTTTTATCATT
13788 TT
1 TT
13790 GGATCGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.14
20 27 0.77
21 3 0.09
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:13937 original size:20 final size:20
Alignment explanation
Indices: 13910--13956 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
13900 TCCGGTAACG
13910 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
13929 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
13950 TTTTACC
1 TTTTACC
13957 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:14009 original size:181 final size:182
Alignment explanation
Indices: 13696--14168 Score: 734
Period size: 181 Copynumber: 2.6 Consensus size: 182
13686 CGTACTTACG
* *
13696 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
13761 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATAGACACATTAT
*
13826 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
13877 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
13942 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATAGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATAGACACATTAT
** *
14007 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * *
14059 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCAGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
14123 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
14169 AATTTGGATC
Statistics
Matches: 267, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
181 168 0.63
182 98 0.37
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATAGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:14883 original size:11 final size:11
Alignment explanation
Indices: 14867--14891 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14857 AGGAAATGCG
14867 GGTTAATATAC
1 GGTTAATATAC
14878 GGTTAATATAC
1 GGTTAATATAC
14889 GGT
1 GGT
14892 GTTACCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:15253 original size:182 final size:180
Alignment explanation
Indices: 15045--15596 Score: 811
Period size: 182 Copynumber: 3.0 Consensus size: 180
15035 CGATACAAAT
* * * * * *
15045 TAAAAATGTATCGATCCATAGCAATATAACATGTAAAAATATGATAAAACCGATATC-ATTATAA
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAA-CGATCTCGA-AATGA
* ** *
15109 TAAAATCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
64 TAAAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
15174 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
129 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTA
* *
15227 TAAAAATGTGTCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAAGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACGA-TCTCGAAATGAT
*
15292 AAAACCGGTAAAAAGTTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
65 AAAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
*
15357 TTGTAATTTAAAAGAGAATAAGTTATAGCGCCTGAAAAGTGTCGATACTTTA
130 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * *
15409 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGACAAAA-GAGGTCTCGAAATGA
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACGA--TCTCGAAATGA
* *
15473 TAAAACCGGTAAAAAGATATCGGATATGTTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
64 TAAAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
* *
15538 TTCGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTAA
129 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTT-A
15592 TAAAA
1 TAAAA
15597 CCGTTTAATT
Statistics
Matches: 338, Mismatches: 27, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
181 3 0.01
182 325 0.96
183 10 0.03
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (180 bp):
TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACGATCTCGAAATGATA
AAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTT
TGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTGTCGATACTTTA
Found at i:16160 original size:87 final size:87
Alignment explanation
Indices: 16057--16216 Score: 284
Period size: 87 Copynumber: 1.8 Consensus size: 87
16047 AAATAGGTCA
*
16057 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
16122 CCGGTTAATTGCCTATTTTATT
66 CCGGTTAATTGCCTATTTTATT
* * *
16144 ATATAAGCGCTACCTATTACATTATCTAAGCGCTACCTAATATGTTGTTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
16209 CCGGTTAA
66 CCGGTTAA
16217 ATGATATAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAATTGCCTATTTTATT
Found at i:17575 original size:23 final size:23
Alignment explanation
Indices: 17549--17594 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17539 GTTCGGTTTA
17549 AATTTATATATTTAATAAAATTT
1 AATTTATATATTTAATAAAATTT
* **
17572 AATTTTTATATTTTTTAAAATTT
1 AATTTATATATTTAATAAAATTT
17595 TCATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTATATATTTAATAAAATTT
Found at i:17693 original size:19 final size:19
Alignment explanation
Indices: 17652--17693 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
17642 TTGAAAATAG
* *
17652 AAATTTATTTCTATTTATT
1 AAATATATTTCTATTTATA
17671 AAATATATTTCTAATTT-TA
1 AAATATATTTCT-ATTTATA
17690 AAAT
1 AAAT
17694 TTTAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATATATTTCTATTTATA
Found at i:17895 original size:19 final size:19
Alignment explanation
Indices: 17854--17895 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17844 ATGACCAACA
* * *
17854 AATTCGCAACGCGATCTCG
1 AATTCGCAACGAGAACTCC
17873 AATTCGCAACGAGAACTCC
1 AATTCGCAACGAGAACTCC
17892 AATT
1 AATT
17896 TTGTAACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (19 bp):
AATTCGCAACGAGAACTCC
Found at i:17978 original size:20 final size:21
Alignment explanation
Indices: 17907--17993 Score: 122
Period size: 21 Copynumber: 4.1 Consensus size: 21
17897 TGTAACTTAG
17907 TTTCCAAATTCGCAACGCGAT
1 TTTCCAAATTCGCAACGCGAT
**
17928 TTTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCGCAACGCGAT
17949 TTTCCAAATTCGCAACGCGA-
1 TTTCCAAATTCGCAACGCGAT
**
17969 TTTCTGAATTCGCAACGCGAAT
1 TTTCCAAATTCGCAACGCG-AT
17991 TTT
1 TTT
17994 GTTTTCGCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 17 0.29
21 38 0.66
22 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (21 bp):
TTTCCAAATTCGCAACGCGAT
Found at i:18040 original size:20 final size:19
Alignment explanation
Indices: 17957--18063 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 19
17947 ATTTTCCAAA
*
17957 TTCGCAACGCGATTTCTGAA-
1 TTCGCAACACGATTT-T-AAT
* **
17977 TTCGCAACGCGAATTTTGTT
1 TTCGCAACACG-ATTTTAAT
* * *
17997 TTCGCAACTCGGTTTTCAAA
1 TTCGCAACACGATTTT-AAT
18017 TTCGCAACACGAATTTTAAT
1 TTCGCAACACG-ATTTTAAT
*
18037 TTCGCAACA-G-TTTTAGT
1 TTCGCAACACGATTTTAAT
18054 TTCGCAACAC
1 TTCGCAACAC
18064 AAATGTTTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
17 15 0.21
19 5 0.07
20 43 0.61
21 8 0.11
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (19 bp):
TTCGCAACACGATTTTAAT
Found at i:18056 original size:17 final size:17
Alignment explanation
Indices: 18030--18062 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18020 GCAACACGAA
18030 TTTTAATTTCGCAACAG
1 TTTTAATTTCGCAACAG
*
18047 TTTTAGTTTCGCAACA
1 TTTTAATTTCGCAACA
18063 CAAATGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTTAATTTCGCAACAG
Found at i:18911 original size:22 final size:22
Alignment explanation
Indices: 18894--18960 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
18884 CTCGTATAAA
18894 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
18916 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
18938 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
18960 T
1 T
18961 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:19227 original size:30 final size:29
Alignment explanation
Indices: 19160--19237 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
19150 CCGTAGTTCA
* * *
19160 TATCACGTAGACATAGTATTTCCATAACTT
1 TATCACATAGGCATA-TATTTACATAACTT
* *
19190 TAACACATAGGCATATCATTTACATACCTT
1 TATCACATAGGCATAT-ATTTACATAACTT
19220 TATCACATAGTGCATATA
1 TATCACATAG-GCATATA
19238 ACTTTTTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (29 bp):
TATCACATAGGCATATATTTACATAACTT
Found at i:19293 original size:29 final size:29
Alignment explanation
Indices: 19251--19322 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
19241 TTTTCTGCAT
* **
19251 ATTCATGTCATGTAATACGTATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
19280 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
19309 ATTCATGTCATGTA
1 ATTCATGTCATGTA
19323 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:19766 original size:68 final size:67
Alignment explanation
Indices: 19625--19775 Score: 207
Period size: 68 Copynumber: 2.2 Consensus size: 67
19615 TTTTCTCATG
* *
19625 GGGGAATCGGTTCCCCCCCCTGGGGTATCGTTCCCCTATGGCATTCTGGAATTTCTTATACGATG
1 GGGGTATCGGTTCCCCCCCCTGGGGTATCGTTCCCCTATGGCATTCTGGAAATTCTTATACGATG
*
19690 AG
66 AA
* *
19692 GGGGTATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATT-T-CG
1 GGGGTATCGGTTCCCCCCCCT-GGGGTATCG-TTCCCCTATGGCATTCTGGAAATTC-TTATACG
*
19755 TTGAA
63 ATGAA
19760 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
19776 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
67 20 0.27
68 30 0.40
69 23 0.31
70 2 0.03
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.30
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCCTGGGGTATCGTTCCCCTATGGCATTCTGGAAATTCTTATACGATG
AA
Found at i:19785 original size:21 final size:21
Alignment explanation
Indices: 19755--19797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19745 ATTCATTTCG
* *
19755 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
19776 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
19797 T
1 T
19798 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:25850 original size:22 final size:22
Alignment explanation
Indices: 25833--25899 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
25823 CTCGTATAAA
25833 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
25855 TGCACCAAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
25877 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
25899 T
1 T
25900 ATGTCCATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:26167 original size:30 final size:29
Alignment explanation
Indices: 26100--26177 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
26090 CCGTAGTTCA
* * *
26100 TATCACGTAGACATAGTATTTCCATAACTT
1 TATCACATAGGCATA-TATTTACATAACTT
* *
26130 TAACACATAGGCATATCATTTACATACCTT
1 TATCACATAGGCATAT-ATTTACATAACTT
26160 TATCACATAGTGCATATA
1 TATCACATAG-GCATATA
26178 ACTTTTTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (29 bp):
TATCACATAGGCATATATTTACATAACTT
Found at i:26233 original size:29 final size:29
Alignment explanation
Indices: 26191--26262 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
26181 TTTTCTGCAT
* **
26191 ATTCATGTCATGTAATACGTATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
26220 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
26249 ATTCATGTCATGTA
1 ATTCATGTCATGTA
26263 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:26706 original size:68 final size:68
Alignment explanation
Indices: 26566--26717 Score: 209
Period size: 68 Copynumber: 2.2 Consensus size: 68
26556 TTTTCTCATG
* * *
26566 GGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTATGGCATTCTGGAATTTCTTATACGAT
1 GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTATGGCATTCTGGAAATTCTTATACGAT
*
26631 GAG
66 GAA
* *
26634 GGGGTATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATT-T-CG
1 GGGGTATCGGTTCCCCCCCCT-GGGGTATCGATTCCCCTATGGCATTCTGGAAATTC-TTATACG
*
26697 TTGAA
64 ATGAA
26702 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
26718 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
68 41 0.55
69 32 0.43
70 2 0.03
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.30
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTATGGCATTCTGGAAATTCTTATACGAT
GAA
Found at i:26727 original size:21 final size:21
Alignment explanation
Indices: 26697--26739 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26687 ATTCATTTCG
* *
26697 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
26718 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
26739 T
1 T
26740 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:30465 original size:12 final size:12
Alignment explanation
Indices: 30448--30488 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
30438 AGCAAAAGGA
*
30448 AATCAAAATCGC
1 AATCAAAATCAC
*
30460 AATCAAAATCAA
1 AATCAAAATCAC
*
30472 AATCAAAATCTC
1 AATCAAAATCAC
30484 AATCA
1 AATCA
30489 CAACCGACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:30469 original size:6 final size:6
Alignment explanation
Indices: 30447--30481 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
30437 AAGCAAAAGG
* *
30447 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
30482 TCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:30723 original size:29 final size:29
Alignment explanation
Indices: 30690--30750 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
30680 AAATTCGAAA
*
30690 CGCAAAAATCGCAACGCGAATTTGACTTT
1 CGCAAAAATCGCAACACGAATTTGACTTT
**
30719 CGCAACCATCGCAACACGAATTTGACTTT
1 CGCAAAAATCGCAACACGAATTTGACTTT
30748 CGC
1 CGC
30751 GTTGCGAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (29 bp):
CGCAAAAATCGCAACACGAATTTGACTTT
Found at i:30758 original size:20 final size:20
Alignment explanation
Indices: 30734--30778 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
30724 CCATCGCAAC
30734 ACGAATTTGACTTTCGCGTT
1 ACGAATTTGACTTTCGCGTT
* *
30754 GCGAATTTGATTTTCGCGTT
1 ACGAATTTGACTTTCGCGTT
30774 ACGAA
1 ACGAA
30779 AGTATACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
ACGAATTTGACTTTCGCGTT
Found at i:30938 original size:64 final size:64
Alignment explanation
Indices: 30837--30987 Score: 241
Period size: 64 Copynumber: 2.4 Consensus size: 64
30827 AATTTAAAAC
30837 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
30901 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*
30965 AATAAATCAAC-TTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
30988 CTTTTACAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 12 0.15
64 69 0.85
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:30984 original size:13 final size:14
Alignment explanation
Indices: 30968--30998 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
30958 TCAATTAAAT
30968 AAATCAAC-TTTAC
1 AAATCAACTTTTAC
30981 AAATCAACTTTTAC
1 AAATCAACTTTTAC
30995 AAAT
1 AAAT
30999 ACATCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:32384 original size:21 final size:20
Alignment explanation
Indices: 32360--32430 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
32350 GTATGAGGAA
*
32360 CCTCTTGAATAATGACAGGGG
1 CCTCTTGAATGATGA-AGGGG
*
32381 CCTCTTGAATGGTGGAAGGGG
1 CCTCTTGAATGAT-GAAGGGG
*
32402 CCTCTTGAAGGATGATAGGGG
1 CCTCTTGAATGATGA-AGGGG
32423 -CTCTTGAA
1 CCTCTTGAA
32431 CGATAGGAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
20 10 0.23
21 32 0.73
22 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (20 bp):
CCTCTTGAATGATGAAGGGG
Found at i:32445 original size:41 final size:42
Alignment explanation
Indices: 32360--32461 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 42
32350 GTATGAGGAA
** * * *
32360 CCTCTTGAATAATGACAGGGGCCTCTTGAATGGTGGAAGGGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGAAGAGG
* *
32402 CCTCTTGAAGGATGATAGGGG-CTCTTGAACGATAGG-AGAGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAACGAT-GGAAGAGG
*
32443 CCTCTTAAACGATGACAGG
1 CCTCTTGAACGATGACAGG
32462 TGAATCGAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
41 30 0.60
42 20 0.40
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGAAGAGG
Found at i:32620 original size:12 final size:12
Alignment explanation
Indices: 32601--32642 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
32591 GGGCCGCTAA
*
32601 AAATAAATTAAT
1 AAATAAATCAAT
*
32613 ACATAAATCAAT
1 AAATAAATCAAT
32625 AAATAAA-CAATT
1 AAATAAATCAA-T
32637 AAATAA
1 AAATAA
32643 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:35025 original size:22 final size:22
Alignment explanation
Indices: 34980--35025 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
34970 GATGGAGATA
**
34980 GACGGATATCGCCGGAGATTGT
1 GACGGATATCGCCGGAGAGAGT
* *
35002 GACGGATGTCGCCGTAGAGAGT
1 GACGGATATCGCCGGAGAGAGT
35024 GA
1 GA
35026 GAGATGGAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (22 bp):
GACGGATATCGCCGGAGAGAGT
Found at i:35211 original size:20 final size:20
Alignment explanation
Indices: 35163--35211 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
35153 TAAACGCACT
*
35163 TTGCAAATTTGACTTCTGTG
1 TTGCAAATTTGACTTATGTG
* * *
35183 TTACGAATTTGTCTTATGTG
1 TTGCAAATTTGACTTATGTG
35203 TTGCAAATT
1 TTGCAAATT
35212 ATAAATTCGC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (20 bp):
TTGCAAATTTGACTTATGTG
Found at i:43680 original size:14 final size:14
Alignment explanation
Indices: 43628--43680 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
43618 GCCCTCTGTT
*
43628 CGAACATAAACAAA
1 CGAACATAAACGAA
*
43642 CGAACATAAATG-A
1 CGAACATAAACGAA
*
43655 --AA-ATAAATGAA
1 CGAACATAAACGAA
43666 CGAACATAAACGAA
1 CGAACATAAACGAA
43680 C
1 C
43681 ATATAATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.22
11 3 0.09
13 3 0.09
14 19 0.59
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.11
Consensus pattern (14 bp):
CGAACATAAACGAA
Found at i:44029 original size:20 final size:20
Alignment explanation
Indices: 43980--44246 Score: 198
Period size: 20 Copynumber: 12.9 Consensus size: 20
43970 AAAATGACCA
*
43980 ACAAAATCGCAACGCGATAT
1 ACAAAATCGCAACGCGATTT
*
44000 -CAAAACCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* * * **
44019 AGAAAAGCGCAACGTTGA-AA
1 ACAAAATCGCAACG-CGATTT
* *
44039 AGAAGATCGCAACGCGATCTT
1 ACAAAATCGCAACGCGAT-TT
* * *
44060 CCAAGAATCGCAATGCGATTC
1 ACAA-AATCGCAACGCGATTT
*
44081 ATAAAATCGCAACGCGATCTT
1 ACAAAATCGCAACGCGAT-TT
* * *
44102 CCAAGAATCGCAATGCGATTC
1 ACAA-AATCGCAACGCGATTT
*
44123 ATAAAATCGCAACGCGATCTT
1 ACAAAATCGCAACGCGAT-TT
* *
44144 CCAAGAATCGCAACGCGATTC
1 ACAA-AATCGCAACGCGATTT
*
44165 AGAAAATCGCAACGCGATCTT
1 ACAAAATCGCAACGCGAT-TT
* *
44186 CCAAGAATCGCAACGCGATTA
1 ACAA-AATCGCAACGCGATTT
*
44207 AGAAAATCGCAACGCGA-TT
1 ACAAAATCGCAACGCGATTT
*
44226 CCAAAGAATCGCAACGCGATT
1 AC-AA-AATCGCAACGCGATT
44247 CAGAAAATGA
Statistics
Matches: 190, Mismatches: 43, Indels: 26
0.73 0.17 0.10
Matches are distributed among these distances:
19 20 0.11
20 78 0.41
21 38 0.20
22 54 0.28
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ACAAAATCGCAACGCGATTT
Found at i:44091 original size:42 final size:42
Alignment explanation
Indices: 44039--44254 Score: 355
Period size: 42 Copynumber: 5.2 Consensus size: 42
44029 AACGTTGAAA
* *
44039 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
* *
44081 ATAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
44123 ATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
44165 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
44207 AGAAAATCGCAACGCGA--TTCCAAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCC-AAGAATCGCAACGCGATTC
44248 AGAAAAT
1 AGAAAAT
44255 GAGTAAATTC
Statistics
Matches: 167, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
40 4 0.02
41 25 0.15
42 138 0.83
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.18
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:44135 original size:84 final size:84
Alignment explanation
Indices: 43984--44254 Score: 358
Period size: 84 Copynumber: 3.3 Consensus size: 84
43974 TGACCAACAA
* ** * * * *
43984 AATCGCAACGCGATATC--AAAACCGCAACGCGAT-TTAGAA-AAGCGCAACGTTGA-AAAGAAG
1 AATCGCAACGCGAT-TCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACG-CGATTAAGAAA
44044 ATCGCAACGCGATCTTCCAAG
64 ATCGCAACGCGATCTTCCAAG
* * * * *
44065 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCATAAAAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
44130 CGCAACGCGATCTTCCAAG
66 CGCAACGCGATCTTCCAAG
44149 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
44214 CGCAACGCGA--TTCCAAAG
66 CGCAACGCGATCTTCC-AAG
44232 AATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGATTCAGAAAAT
44255 GAGTAAATTC
Statistics
Matches: 168, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
80 2 0.01
81 13 0.08
82 19 0.11
83 32 0.19
84 102 0.61
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (84 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
CGCAACGCGATCTTCCAAG
Found at i:44361 original size:6 final size:6
Alignment explanation
Indices: 44350--44417 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
44340 GACACGTATT
44350 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
44398 ACCACG ACCCCG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
44418 CGAGACGAGA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
5 5 0.08
6 56 0.92
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:44959 original size:6 final size:6
Alignment explanation
Indices: 44898--44959 Score: 87
Period size: 6 Copynumber: 11.0 Consensus size: 6
44888 TCTCGTCTCG
*
44898 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
44942 GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT
44960 AGTAATACGT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 20 0.36
6 35 0.64
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:45083 original size:20 final size:20
Alignment explanation
Indices: 45058--45222 Score: 138
Period size: 20 Copynumber: 8.2 Consensus size: 20
45048 GAATTTACTC
*
45058 ATTTTCTGAATCGCATTGTG
1 ATTTTCTGAATCGCATTGCG
* *
45078 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCATTGCG
* *
45098 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCATTGCG
* *
45118 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCATTGCG
* *
45138 ATTCTT-GGAATTGCATTGCG
1 ATT-TTCTGAATCGCATTGCG
*
45158 ATTTTCTAAATCGCATTGCG
1 ATTTTCTGAATCGCATTGCG
* *
45178 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCATTGCG
* *
45200 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCATTGCG
45220 ATT
1 ATT
45223 CTTGGAATAT
Statistics
Matches: 116, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.03
20 90 0.78
21 9 0.08
22 13 0.11
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCATTGCG
Found at i:45121 original size:40 final size:40
Alignment explanation
Indices: 45065--45325 Score: 284
Period size: 40 Copynumber: 6.5 Consensus size: 40
45055 CTCATTTTCT
* *
45065 GAATCGCATTGTGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
45105 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* * * *
45145 GAATTGCATTGCGATTTTCTAAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
45185 GAAGATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
45227 GAATATCGCGTTGCGATTTTCTT--TTGACTGTTGCGATTTTCTTTT
1 G-A-ATCGCGTTGCGATTTTCTTAATCG-C-GTTGCGA--TTC-TTG
*
45272 G-A-C-CGTTGCGATTTTCTAAATCGCGTTGCGATT-TT-
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
45307 GATATCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
45326 GTTGGTCATT
Statistics
Matches: 191, Mismatches: 17, Indels: 27
0.81 0.07 0.11
Matches are distributed among these distances:
35 1 0.01
36 2 0.01
37 1 0.01
38 3 0.02
39 12 0.06
40 98 0.51
41 4 0.02
42 64 0.34
44 3 0.02
45 3 0.02
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (40 bp):
GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
Found at i:45261 original size:20 final size:20
Alignment explanation
Indices: 45235--45288 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
45225 TGGAATATCG
45235 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAC
*
45255 TGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAC
45275 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
45289 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.09, C:0.19, G:0.20, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAC
Found at i:45298 original size:20 final size:19
Alignment explanation
Indices: 45275--45326 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
45265 TTCTTTTGAC
*
45275 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
*
45295 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
45314 CGTTGCGATTTTG
1 CGTTGCGATTTTG
45327 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:50317 original size:117 final size:117
Alignment explanation
Indices: 50102--50321 Score: 280
Period size: 117 Copynumber: 1.9 Consensus size: 117
50092 AATACTATTT
* * * * * * * * *
50102 CCATCCAATTACTTCGATTACTATAATTTGTATGTTCTTCAGAACCATACACTCACCTGCACACC
1 CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAACCATACACCCACCTGCACACC
* * **
50167 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCGGTAATAACTTCC
66 AATAAGAACTTACCCTGAGCACAAAGCAAAGGAGCCTGCGGTAATAACTTCC
*
50219 CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAATCATACACCCACCTGCACACC
1 CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAACCATACACCCACCTGCACACC
* *
50284 AATGAGAACTTACCCTGAGCACACAA-TAAAGGAGCCTG
66 AATAAGAACTTACCCTGAGCACA-AAGCAAAGGAGCCTG
50322 AAATACTTCC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
117 84 0.98
118 2 0.02
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (117 bp):
CCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCCTCAGAACCATACACCCACCTGCACACC
AATAAGAACTTACCCTGAGCACAAAGCAAAGGAGCCTGCGGTAATAACTTCC
Found at i:51295 original size:28 final size:28
Alignment explanation
Indices: 51242--51449 Score: 125
Period size: 29 Copynumber: 7.2 Consensus size: 28
51232 TTTACACAAT
* *
51242 TATCACCATTTTAAGAAATATTTACTAAAA
1 TATCACC-TTTTCA-AAATAATTACTAAAA
*
51272 TATCATCTTTTCAAAATAATTACTAAAA
1 TATCACCTTTTCAAAATAATTACTAAAA
** *
51300 TATCACCCTTTTCAAAA-AAAAAATGAAAA
1 TATCA-CCTTTTCAAAATAATTACT-AAAA
* * * * *
51329 TATCACTTTTTTTAAAAAAAATA-TGAAAT
1 TATCAC-CTTTTCAAAATAATTACT-AAAA
* *
51358 TATCACCTTTTTAAAA-AATTACGAAAA
1 TATCACCTTTTCAAAATAATTACTAAAA
* * * *
51385 TAGCACCATTTTCAATATAATCACCAAAA
1 TATCACC-TTTTCAAAATAATTACTAAAA
* ** *
51414 TACCATCAATTTCAAAATAATTACAAAAA
1 TATCA-CCTTTTCAAAATAATTACTAAAA
*
51443 TACCACC
1 TATCACC
51450 CGGTCAACGG
Statistics
Matches: 143, Mismatches: 27, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
27 13 0.09
28 41 0.29
29 78 0.55
30 11 0.08
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (28 bp):
TATCACCTTTTCAAAATAATTACTAAAA
Found at i:51497 original size:18 final size:18
Alignment explanation
Indices: 51457--51499 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
51447 ACCCGGTCAA
**
51457 CGGTCAACGGGTCGGGTC
1 CGGTCAACGGGTCGGAAC
*
51475 GGGTCAACGGGTCGGAAC
1 CGGTCAACGGGTCGGAAC
51493 CGGTCAA
1 CGGTCAA
51500 ACTTGTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.42, T:0.14
Consensus pattern (18 bp):
CGGTCAACGGGTCGGAAC
Found at i:53894 original size:15 final size:15
Alignment explanation
Indices: 53874--53902 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53864 ACTGAAAGTA
53874 ATTCAAATTTGATTT
1 ATTCAAATTTGATTT
53889 ATTCAAATTTGATT
1 ATTCAAATTTGATT
53903 CAAATCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
ATTCAAATTTGATTT
Found at i:59160 original size:24 final size:24
Alignment explanation
Indices: 59133--59180 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
59123 TTTCGGAACC
59133 TATTGAGAGGCTTTAATGGTAAGA
1 TATTGAGAGGCTTTAATGGTAAGA
59157 TATTGAGAGGCTTTAATGGTAAGA
1 TATTGAGAGGCTTTAATGGTAAGA
59181 GAATTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (24 bp):
TATTGAGAGGCTTTAATGGTAAGA
Found at i:62124 original size:2 final size:2
Alignment explanation
Indices: 62117--62153 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
62107 AAATAAACAA
*
62117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62154 ATAAAAATAA
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:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.