Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 10 of 117
Found at i:2745527 original size:63 final size:62
Alignment explanation
Indices: 2745442--2745678 Score: 182
Period size: 62 Copynumber: 3.8 Consensus size: 62
2745432 ACCAAAAACG
* * *
2745442 CCTTAAATAAT-TACCT-TCATTTTTTTAAAGGACATTATTTAAGGTGTTTTTGGTCCAAAATA
1 CCTTAAATAATCT-CTTATCATTTTTTAAAAGG-CATTATTTAAGGTATTTTTGGTCCAAAATA
* * * * * *
2745504 CCTTAAATAGTCTCTTGAT-ATTTTTTAAAATGCATTATTTAATGTATTTTCGGTCAAAAAATG
1 CCTTAAATAATCTCTT-ATCATTTTTTAAAAGGCATTATTTAAGGTATTTTTGGTC-CAAAATA
* * * * * ***
2745567 TCTTAAATAAT-AC-AATCATTTTTTAAAAGGAGATTATTAAAGGTATTTTT-AAACAAAATTA
1 CCTTAAATAATCTCTTATCATTTTTTAAAAGG-CATTATTTAAGGTATTTTTGGTCCAAAA-TA
* * *
2745628 CTTTAAATAATCTCTT-TCATTTTTTTAAAAGGTATTATTTAAGGTGTTTTT
1 CCTTAAATAATCTCTTATCA-TTTTTTAAAAGGCATTATTTAAGGTATTTTT
2745679 AGATAAAAAA
Statistics
Matches: 135, Mismatches: 30, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
60 6 0.04
61 22 0.16
62 68 0.50
63 38 0.28
64 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (62 bp):
CCTTAAATAATCTCTTATCATTTTTTAAAAGGCATTATTTAAGGTATTTTTGGTCCAAAATA
Found at i:2745687 original size:124 final size:125
Alignment explanation
Indices: 2745414--2745688 Score: 290
Period size: 124 Copynumber: 2.2 Consensus size: 125
2745404 ATAAGGGAAC
* ** ** *
2745414 TATTTAAGGCGTTTTTAGACCAAAAACGCCTTAAATAATTACCTTCATTTTTTTAAAGGACATTA
1 TATTTAAGGTGTTTTTAGATAAAAAACGCCTTAAATAATTACAATCATTTTTTAAAAGGACATTA
* * *** * * *
2745479 TTTAAGGTGTTTTTGGTCCAAAATACCTTAAATAGTCTCTTGATATTTTTTAAAATGCAT
66 TTAAAGGTATTTTTGAAACAAAATACCTTAAATAATCTCTTCATATTTTTTAAAAGGCAT
* * * * *
2745539 TATTTAA--TGTATTTTCGGTCAAAAAATGTCTTAAATAA-TACAATCATTTTTTAAAAGGAGAT
1 TATTTAAGGTGT-TTTTAGAT-AAAAAACGCCTTAAATAATTACAATCATTTTTTAAAAGGACAT
* *
2745601 TATTAAAGGTATTTTT-AAACAAAATTACTTTAAATAATCTCTTTCAT-TTTTTTAAAAGGTAT
64 TATTAAAGGTATTTTTGAAACAAAA-TACCTTAAATAATCTC-TTCATATTTTTTAAAAGGCAT
2745663 TATTTAAGGTGTTTTTAGATAAAAAA
1 TATTTAAGGTGTTTTTAGATAAAAAA
2745689 AGCTTTGAAT
Statistics
Matches: 121, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
123 7 0.06
124 79 0.65
125 32 0.26
126 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (125 bp):
TATTTAAGGTGTTTTTAGATAAAAAACGCCTTAAATAATTACAATCATTTTTTAAAAGGACATTA
TTAAAGGTATTTTTGAAACAAAATACCTTAAATAATCTCTTCATATTTTTTAAAAGGCAT
Found at i:2748797 original size:13 final size:14
Alignment explanation
Indices: 2748770--2748801 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2748760 TTTAGTGATG
2748770 AAAATTATCAAAAT
1 AAAATTATCAAAAT
2748784 AAAATTAT-AAAAT
1 AAAATTATCAAAAT
2748797 AAAAT
1 AAAAT
2748802 AAAAGATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTATCAAAAT
Found at i:2767606 original size:15 final size:15
Alignment explanation
Indices: 2767558--2767607 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2767548 ACATTTATAT
2767558 AATTAATTAAATAATC
1 AATTAATT-AATAATC
*
2767574 AATT-ATTACATCAT-
1 AATTAATTA-ATAATC
*
2767588 AATTAATTAATGATC
1 AATTAATTAATAATC
2767603 AATTA
1 AATTA
2767608 TAATTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 9 0.31
15 16 0.55
16 4 0.14
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (15 bp):
AATTAATTAATAATC
Found at i:2795090 original size:34 final size:35
Alignment explanation
Indices: 2795037--2795104 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
2795027 TACCAAATGC
**
2795037 ATTTTTTAGAAAACAAAAAATTGAAAATAAAAACT
1 ATTTTTTAGAAAACAAAAAATAAAAAATAAAAACT
*
2795072 ATTTTTTAGAAAA-TAAAAATAAAAAATAAAAAC
1 ATTTTTTAGAAAACAAAAAATAAAAAATAAAAAC
2795105 AAAAAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (35 bp):
ATTTTTTAGAAAACAAAAAATAAAAAATAAAAACT
Found at i:2795099 original size:13 final size:13
Alignment explanation
Indices: 2795081--2795110 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2795071 TATTTTTTAG
*
2795081 AAAATAAAAATAA
1 AAAATAAAAACAA
2795094 AAAATAAAAACAA
1 AAAATAAAAACAA
2795107 AAAA
1 AAAA
2795111 CATTTTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAATAAAAACAA
Found at i:2798936 original size:26 final size:27
Alignment explanation
Indices: 2798868--2798937 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 27
2798858 ATTCAGTTAC
* *
2798868 ATCCATTTTTAGCTCAAATACTATGAT
1 ATCCATTTTTAGCTCAAAAACCATGAT
*
2798895 ATTCATTTTT--CTTCAAAAACCA-GAT
1 ATCCATTTTTAGC-TCAAAAACCATGAT
2798920 ATCCATTTTTAGCTCAAA
1 ATCCATTTTTAGCTCAAA
2798938 TAACTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 13 0.36
26 13 0.36
27 10 0.28
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (27 bp):
ATCCATTTTTAGCTCAAAAACCATGAT
Found at i:2800130 original size:156 final size:156
Alignment explanation
Indices: 2799846--2800158 Score: 608
Period size: 156 Copynumber: 2.0 Consensus size: 156
2799836 TCTCAATATC
2799846 AACCTATTTCTTGATGATCTGTTGAAAGACACAGCCATGTGATCTTGAGCTTCTTATGTCTTCCA
1 AACCTATTTCTTGATGATCTGTTGAAAGACACAGCCATGTGATCTTGAGCTTCTTATGTCTTCCA
*
2799911 ACCAAACCCCACCAGAATGCATCGTAACCAATTAGTCTGCAAGCCATTAGTTTCCTATATACATT
66 ACCAAACCCCACCAGAATGCATCGTAACCAATCAGTCTGCAAGCCATTAGTTTCCTATATACATT
2799976 CTTCCATCTATATATACAAGTGCATT
131 CTTCCATCTATATATACAAGTGCATT
*
2800002 AACCTATTTCTTGATGATCTGTTGAAGGACACAGCCATGTGATCTTGAGCTTCTTATGTCTTCCA
1 AACCTATTTCTTGATGATCTGTTGAAAGACACAGCCATGTGATCTTGAGCTTCTTATGTCTTCCA
2800067 ACCAAACCCCACCAGAATGCATCGTAACCAATCAGTCTGCAAGCCATTAGTTTCCTATATACATT
66 ACCAAACCCCACCAGAATGCATCGTAACCAATCAGTCTGCAAGCCATTAGTTTCCTATATACATT
2800132 CTTCCATCTATATATACAAGTGCATT
131 CTTCCATCTATATATACAAGTGCATT
2800158 A
1 A
2800159 TCCACACCAG
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (156 bp):
AACCTATTTCTTGATGATCTGTTGAAAGACACAGCCATGTGATCTTGAGCTTCTTATGTCTTCCA
ACCAAACCCCACCAGAATGCATCGTAACCAATCAGTCTGCAAGCCATTAGTTTCCTATATACATT
CTTCCATCTATATATACAAGTGCATT
Found at i:2801304 original size:24 final size:24
Alignment explanation
Indices: 2801277--2801323 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2801267 ATTTCGTATC
*
2801277 TATATTTTACATATAAATTTTTTT
1 TATATTTAACATATAAATTTTTTT
*
2801301 TATATTTAATATATAAATTTTTT
1 TATATTTAACATATAAATTTTTT
2801324 ATTAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTTAACATATAAATTTTTTT
Found at i:2801326 original size:20 final size:22
Alignment explanation
Indices: 2801297--2801360 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
2801287 ATATAAATTT
*
2801297 TTTTTATATTTAAT-ATATAAA
1 TTTTTATATTAAATAATATAAA
2801318 TTTTT-TATTAAATAATATAAA
1 TTTTTATATTAAATAATATAAA
* *
2801339 TTATTATTTTAAATTAAT-TAAA
1 TTTTTATATTAAA-TAATATAAA
2801361 ATTAATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.19
21 16 0.43
22 10 0.27
23 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTTATATTAAATAATATAAA
Found at i:2801333 original size:23 final size:24
Alignment explanation
Indices: 2801287--2801336 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2801277 TATATTTTAC
*
2801287 ATATAAATTTTTTTTATATTTAAT
1 ATATAAATTTTTTTTATATATAAT
2801311 ATATAAATTTTTTATTA-A-ATAAT
1 ATATAAATTTTTT-TTATATATAAT
2801334 ATA
1 ATA
2801337 AATTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 14 0.58
25 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATAAATTTTTTTTATATATAAT
Found at i:2814710 original size:2 final size:2
Alignment explanation
Indices: 2814703--2814736 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2814693 TTGATTTCTT
2814703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2814737 TCCTTAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2822297 original size:534 final size:531
Alignment explanation
Indices: 2821290--2822354 Score: 1735
Period size: 534 Copynumber: 2.0 Consensus size: 531
2821280 TTCTCTCGAA
*
2821290 CTCCAACATTGCATACGCTGATAGTGGACGAATTGTAAAAAGGCAAAATGCTGACCTCTTGAGCT
1 CTCCAACATTGCATACGCTGATAATGGACGAATTGTAAAAAGGCAAAATGCTGACCTCTTGAGCT
* *
2821355 GTTGCAGGTTATTTTCATGAATACCAAGTACCAACGACCAAACTGCTTAACAAATTAAGGGAGTA
66 GCTGCAGGTTATTTTCATGAATACCAAGTACCAACGACCAAAATGCTTAACAAATTAAGGGAGTA
* * *
2821420 TTTGAGTGATGATGAAAATATTGAAGGTCGTTCAGCAATCAAATTTAGAAAAAAATTAAAGATTA
131 ATTGAGTGATGATG--AACATTGAAGGTCGTTCAGCAATCAAATATAGAAAAAAATTAAAGATTA
* * *
2821485 AACATGCCCCATAAATTATTAAATACATGTCCCAGCTCAGGTTTTTTCTGGCCTCAATATTTGCA
194 AACATGCCCCACAAATTATTAAATACATGTACCAGCTCAGGTTTTTTCCGGCCTCAATATTTGCA
* *
2821550 TATCACTTTCAAGCATGCATCCAACAGTAAAAGGGGAGGACATGAATGACATGTTGATTTCTCTT
259 TATCACTTTCAAGCATGCATCCAACAGCAAAAGGGAAGGACATGAATGACATGTTGATTTCTCTT
*
2821615 TGCACAAATATATACATGTATCTGGGAACAAGTTGACACAATTTGATAATCATTGTTCGTATTCA
324 TGCACAAATATATACATCTATCTGGGAACAAGTTGACACAATTTGATAATCATTGTTCGTATTCA
*
2821680 GACAAAAGCAAGCTAGCATAAAGCTTTCAGGTTACCTGCATATTTTTACAAGCTCACCTATAGCT
389 GACAAAAGCAAGCTAGCATAAAACTTTCAGGTTACCTGCATATTTTTACAAGCTCACCTATAGCT
* *
2821745 TGCTAGCTAGAAAATTTAGTCTGACATCTGAACAAATTAATATTTTGAAGGAATTGATAAATTGA
454 AGCTAGCTAGAAAATTTAGTCTGACATCTGAACAAATTAATATTTTGAAGAAATTGATAAATTGA
2821810 GATGTGAATGATC
519 GATGTGAATGATC
* * * *
2821823 CTCCAACATTGCATATGCTGATAATGGACGAATTGTCAAAATGCAAACTGCTGACCTCTTGAGCT
1 CTCCAACATTGCATACGCTGATAATGGACGAATTGTAAAAAGGCAAAATGCTGACCTCTTGAGCT
2821888 GCTGCAGGTTATTTTCATGAATACCAAGTACCAACGACCAAAATGCTTAACAAATTAAGGG-G-A
66 GCTGCAGGTTATTTTCATGAATACCAAGTACCAACGACCAAAATGCTTAACAAATTAAGGGAGTA
*
2821951 ATTGAAGTGATGATG-GCATTGAAGGTCGTTCAGCAATCAAATATAGAAAAAAATTTAAAGATTA
131 ATTG-AGTGATGATGAACATTGAAGGTCGTTCAGCAATCAAATATAGAAAAAAA-TTAAAGATTA
* *
2822015 AACATGCCCCACAAATTATT-AATACCTGTACCAGCTCGGGTTTTTTCCGGCCTCAAACTCAATA
194 AACATGCCCCACAAATTATTAAATACATGTACCAGCTCAGGTTTTTTCCGG---C---CTCAATA
* *
2822079 TTTGCATATCACTTTCCAGCATGCATCC-ACAGCAAAAGGGAAGGACATTAATGACATGTTGATT
253 TTTGCATATCACTTTCAAGCATGCATCCAACAGCAAAAGGGAAGGACATGAATGACATGTTGATT
*
2822143 TCTCTTTGCACAAATATATACATCTATCTGGGAACAAGTTGACACAATTTGATAATCATTGTTCT
318 TCTCTTTGCACAAATATATACATCTATCTGGGAACAAGTTGACACAATTTGATAATCATTGTTCG
* * *
2822208 TATTCAGACAAATGCAAGCTAGTATAAAACTTTCAGGTTACCTGCATATTTTTACAAGGTCACCT
383 TATTCAGACAAAAGCAAGCTAGCATAAAACTTTCAGGTTACCTGCATATTTTTACAAGCTCACCT
* *
2822273 TTAGCTAGCTAGCTAGAAAATTTAGTCTGACATCTGAACAAATTAATATTTTGAAGAAATTGATT
448 ATAGCTAGCTAGCTAGAAAATTTAGTCTGACATCTGAACAAATTAATATTTTGAAGAAATTGATA
2822338 AATTGAGATGTGAATGA
513 AATTGAGATGTGAATGA
2822355 ACCTTTTAAC
Statistics
Matches: 494, Mismatches: 30, Indels: 15
0.92 0.06 0.03
Matches are distributed among these distances:
529 61 0.12
530 29 0.06
531 4 0.01
532 12 0.02
533 119 0.24
534 235 0.48
535 34 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (531 bp):
CTCCAACATTGCATACGCTGATAATGGACGAATTGTAAAAAGGCAAAATGCTGACCTCTTGAGCT
GCTGCAGGTTATTTTCATGAATACCAAGTACCAACGACCAAAATGCTTAACAAATTAAGGGAGTA
ATTGAGTGATGATGAACATTGAAGGTCGTTCAGCAATCAAATATAGAAAAAAATTAAAGATTAAA
CATGCCCCACAAATTATTAAATACATGTACCAGCTCAGGTTTTTTCCGGCCTCAATATTTGCATA
TCACTTTCAAGCATGCATCCAACAGCAAAAGGGAAGGACATGAATGACATGTTGATTTCTCTTTG
CACAAATATATACATCTATCTGGGAACAAGTTGACACAATTTGATAATCATTGTTCGTATTCAGA
CAAAAGCAAGCTAGCATAAAACTTTCAGGTTACCTGCATATTTTTACAAGCTCACCTATAGCTAG
CTAGCTAGAAAATTTAGTCTGACATCTGAACAAATTAATATTTTGAAGAAATTGATAAATTGAGA
TGTGAATGATC
Found at i:2829747 original size:2 final size:2
Alignment explanation
Indices: 2829740--2829776 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2829730 CCATAACAAT
2829740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2829777 CCATTTCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2837060 original size:4 final size:4
Alignment explanation
Indices: 2837051--2837101 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
2837041 AAAGTGTGTC
* * * *
2837051 TATA TATA TATA TATA TATA TATA TATA TATG TATG TATG TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
2837099 TAT
1 TAT
2837102 CTGCTTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:2846931 original size:2 final size:2
Alignment explanation
Indices: 2846924--2846948 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2846914 TGAACTAAAT
2846924 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2846949 TTCATTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2849513 original size:1 final size:1
Alignment explanation
Indices: 2849507--2849532 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2849497 TTATATCTCT
2849507 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2849533 CCAATTAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2856354 original size:16 final size:16
Alignment explanation
Indices: 2856342--2856402 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
2856332 AAATTATAAG
2856342 AATTTAAATTTATTAA
1 AATTTAAATTTATTAA
** *
2856358 CTTTTAAATTTAATTTA
1 AATTTAAATTT-ATTAA
*
2856375 AATTTAAATTTACTAA
1 AATTTAAATTTATTAA
*
2856391 AATTCAAATTTA
1 AATTTAAATTTA
2856403 ATTGAATCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
16 23 0.64
17 13 0.36
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAAATTTATTAA
Found at i:2856379 original size:33 final size:33
Alignment explanation
Indices: 2856342--2856405 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2856332 AAATTATAAG
* ** *
2856342 AATTTAAATTTATTAACTTTTAAATTTAATTTA
1 AATTTAAATTTACTAAAATTCAAATTTAATTTA
2856375 AATTTAAATTTACTAAAATTCAAATTTAATT
1 AATTTAAATTTACTAAAATTCAAATTTAATT
2856406 GAATCGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (33 bp):
AATTTAAATTTACTAAAATTCAAATTTAATTTA
Found at i:2856611 original size:24 final size:24
Alignment explanation
Indices: 2856583--2856646 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
2856573 AAAATTTTAA
**
2856583 ATTATATTAATTTTATATTTTATT
1 ATTATATTAATTTTATATCATATT
* *
2856607 TTTATACT-ATATTTATATCATATT
1 ATTATATTAAT-TTTATATCATATT
2856631 ATTATATTATATTTTA
1 ATTATATTA-ATTTTA
2856647 AATTATCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 2 0.06
24 23 0.74
25 4 0.13
26 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATATTAATTTTATATCATATT
Found at i:2860358 original size:15 final size:15
Alignment explanation
Indices: 2860313--2860360 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2860303 TTTATATTTT
2860313 TATAT-TAATATAAA
1 TATATATAATATAAA
2860327 TTATAATATAA-A-AAA
1 -TAT-ATATAATATAAA
2860342 TATATATAATATAAA
1 TATATATAATATAAA
2860357 TATA
1 TATA
2860361 CAAATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.21
14 4 0.14
15 13 0.45
16 3 0.10
17 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATATAATATAAA
Found at i:2860958 original size:101 final size:100
Alignment explanation
Indices: 2860779--2860968 Score: 321
Period size: 101 Copynumber: 1.9 Consensus size: 100
2860769 ATTGTATATG
* *
2860779 ATTAATATTTTATATTTTTATGTTAAAAATTAAAAAAATGAAAAATAATTTTGAAATATATTAAG
1 ATTAATATTTTATATTTTTATGTCAAAAATTAAAAAAATGAAAAATAATTTTGAAATAGATTAAG
2860844 AAAATACAGAGAAAATGAGATGTATGTTTTATAAT
66 AAAATACAGAGAAAATGAGATGTATGTTTTATAAT
2860879 ATTAATATTTT-TATTTTTATGTCAAAAATTAGAAAAAGATGAAAAATAATTTTGAAATAGATTA
1 ATTAATATTTTATATTTTTATGTCAAAAATTA-AAAAA-ATGAAAAATAATTTTGAAATAGATTA
2860943 AGAAAATACTA-AGAAAATGAGATGTA
64 AGAAAATAC-AGAGAAAATGAGATGTA
2860969 CGTAAATTGT
Statistics
Matches: 85, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
99 19 0.22
100 16 0.19
101 49 0.58
102 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (100 bp):
ATTAATATTTTATATTTTTATGTCAAAAATTAAAAAAATGAAAAATAATTTTGAAATAGATTAAG
AAAATACAGAGAAAATGAGATGTATGTTTTATAAT
Found at i:2865871 original size:21 final size:21
Alignment explanation
Indices: 2865834--2865873 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2865824 AGAAATAAGC
*
2865834 AAAATAAAATGAAAAAATGAT
1 AAAATAAAATAAAAAAATGAT
2865855 AAAA-AAAATAAAGAAAATG
1 AAAATAAAATAAA-AAAATG
2865874 TTCGAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATAAAATAAAAAAATGAT
Found at i:2872828 original size:2 final size:2
Alignment explanation
Indices: 2872823--2872858 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2872813 TATAAAAAAA
2872823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2872859 GAATGCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2873702 original size:18 final size:19
Alignment explanation
Indices: 2873679--2873741 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
2873669 TTAATTAAAA
2873679 TAATTAAAATATAAA-ATT
1 TAATTAAAATATAAATATT
*
2873697 TAATTAAATTCATAAATTATT
1 TAATTAAAAT-ATAAA-TATT
2873718 TGAATT-AAATATAAGAATATT
1 T-AATTAAAATAT-A-AATATT
2873739 TAA
1 TAA
2873742 ATTTAAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 9 0.24
19 5 0.14
20 4 0.11
21 13 0.35
22 6 0.16
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (19 bp):
TAATTAAAATATAAATATT
Found at i:2874020 original size:18 final size:17
Alignment explanation
Indices: 2873984--2874019 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2873974 TTTGAAATAC
2873984 ATATTATAAAAAATAAAA
1 ATATTA-AAAAAATAAAA
*
2874002 ATATTAAAAAGATAAAA
1 ATATTAAAAAAATAAAA
2874019 A
1 A
2874020 ACTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
ATATTAAAAAAATAAAA
Found at i:2874848 original size:19 final size:20
Alignment explanation
Indices: 2874803--2874848 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
2874793 ATTTTTAAGT
* *
2874803 AATAATATAAATAAAACTTT
1 AATAAAATAAATAAAACTTA
*
2874823 TAT-AAATAAATAAAA-TTA
1 AATAAAATAAATAAAACTTA
2874841 AATAAAAT
1 AATAAAAT
2874849 TCGTAAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.19
19 15 0.71
20 2 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAATAAATAAAACTTA
Found at i:2889741 original size:16 final size:13
Alignment explanation
Indices: 2889716--2889763 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 13
2889706 AATATTATCT
2889716 TTTTTAATTAATTCA
1 TTTTTAATT-ATT-A
2889731 TTTTTATATTATTA
1 TTTTTA-ATTATTA
2889745 TTTTTAAATATATTA
1 TTTTT-AAT-TATTA
2889760 TTTT
1 TTTT
2889764 ATGAGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.27
15 19 0.63
16 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTAATTATTA
Found at i:2889762 original size:29 final size:29
Alignment explanation
Indices: 2889707--2889763 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2889697 TTGGTAAATA
*
2889707 ATATTATCTTTTTTAATTAATTCATTTTT
1 ATATTATCTTTTTTAAATAATTCATTTTT
2889736 ATATTAT-TATTTTTAAATATATT-ATTTT
1 ATATTATCT-TTTTTAAATA-ATTCATTTT
2889764 ATGAGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 21 0.84
30 3 0.12
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (29 bp):
ATATTATCTTTTTTAAATAATTCATTTTT
Found at i:2890930 original size:21 final size:20
Alignment explanation
Indices: 2890890--2890930 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2890880 ATAATTATTT
*
2890890 TATATTAAAATTTATTTAAA
1 TATATTAAAATTTATATAAA
2890910 TATATTAAAATTTTATATAAA
1 TATATTAAAA-TTTATATAAA
2890931 AATAGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATTAAAATTTATATAAA
Found at i:2897151 original size:2 final size:2
Alignment explanation
Indices: 2897144--2897169 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2897134 ATCTATCAAA
2897144 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2897170 CCCGCACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2903687 original size:36 final size:36
Alignment explanation
Indices: 2903640--2903713 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
2903630 GCAAGACCTT
2903640 ATCAGTAATAACCAACTATTGTGATCAAATAAAAAA
1 ATCAGTAATAACCAACTATTGTGATCAAATAAAAAA
2903676 ATCAGTAATAACCAACTATTGTGATCAAATAAAAAA
1 ATCAGTAATAACCAACTATTGTGATCAAATAAAAAA
2903712 AT
1 AT
2903714 GTAAGTGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.26
Consensus pattern (36 bp):
ATCAGTAATAACCAACTATTGTGATCAAATAAAAAA
Found at i:2905175 original size:18 final size:19
Alignment explanation
Indices: 2905152--2905190 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2905142 CGATATATTT
*
2905152 TTTATTTT-TAAAATTTAA
1 TTTATTTTATAAAATTAAA
2905170 TTTATTTTATAAAATTAAA
1 TTTATTTTATAAAATTAAA
2905189 TT
1 TT
2905191 AATTAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATTTTATAAAATTAAA
Found at i:2905637 original size:21 final size:20
Alignment explanation
Indices: 2905578--2905637 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2905568 TACTTTTTAT
*
2905578 TTATAATAATAATTTTTACG
1 TTATAATAATATTTTTTACG
* *
2905598 TTATCAAT-TTAATTATTTACG
1 TTAT-AATAAT-ATTTTTTACG
2905619 TTATAATAATATGTTTTTA
1 TTATAATAATAT-TTTTTA
2905638 TATTTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
TTATAATAATATTTTTTACG
Found at i:2906717 original size:35 final size:36
Alignment explanation
Indices: 2906678--2906757 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
2906668 TTCCACACTT
*
2906678 ATTTTTTTAT-TTATAAATTT-TTATGTAT-AATACTA
1 ATTTTTTTATATTACAAATTTATTATGTATCAATA--A
* *
2906713 A-TTTTTTATATTACAGATTTATTATGTTTCAATAA
1 ATTTTTTTATATTACAAATTTATTATGTATCAATAA
2906748 ATTTTTTTAT
1 ATTTTTTTAT
2906758 GTTTATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 8 0.21
35 11 0.29
36 15 0.39
37 4 0.11
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (36 bp):
ATTTTTTTATATTACAAATTTATTATGTATCAATAA
Found at i:2906789 original size:21 final size:20
Alignment explanation
Indices: 2906748--2906791 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2906738 GTTTCAATAA
* **
2906748 ATTTTTTTATGTTTATTATT
1 ATTTTTTTACGTTTAAAATT
2906768 ATTTTTATTACGTTTAAAATT
1 ATTTTT-TTACGTTTAAAATT
2906789 ATT
1 ATT
2906792 ACAAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTTTTTACGTTTAAAATT
Found at i:2907119 original size:17 final size:18
Alignment explanation
Indices: 2907082--2907146 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
2907072 ATTAGTCTCA
*
2907082 ATTTTTTATATTAATACTT
1 ATTTTTTAT-TTAATAATT
2907101 ATTTTTTATTTAA-AATT
1 ATTTTTTATTTAATAATT
*
2907118 ATTATTTATTTATAATAATT
1 ATTTTTTA-TT-TAATAATT
2907138 ATTCTTTTA
1 ATT-TTTTA
2907147 AGTGCCAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 10 0.26
18 6 0.15
19 12 0.31
20 7 0.18
21 4 0.10
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTATTTAATAATT
Found at i:2907137 original size:20 final size:18
Alignment explanation
Indices: 2907086--2907140 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
2907076 GTCTCAATTT
* *
2907086 TTTATATTAATACTTATTT
1 TTTAT-TTAATAATTATTA
2907105 TTTATTTAA-AATTATTA
1 TTTATTTAATAATTATTA
*
2907122 TTTATTT-ATAATAATTA
1 TTTATTTAATAATTATTA
2907139 TT
1 TT
2907141 CTTTTAAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 22 0.69
18 4 0.12
19 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATTTAATAATTATTA
Found at i:2907464 original size:18 final size:19
Alignment explanation
Indices: 2907424--2907469 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
2907414 TATTCTCATA
*
2907424 TTTTTACTTTAACATGTAT
1 TTTTTACTTTAAAATGTAT
2907443 TTTTTAC-TTAAAAT-TAT
1 TTTTTACTTTAAAATGTAT
2907460 TTTTTA-TTTA
1 TTTTTACTTTA
2907470 TAATAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 6 0.24
19 7 0.28
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTACTTTAAAATGTAT
Found at i:2907662 original size:18 final size:18
Alignment explanation
Indices: 2907641--2907699 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
2907631 TATTTATATT
2907641 TTTTTATATTAATACTTA
1 TTTTTATATTAATACTTA
*
2907659 TTTTTAGTA-T-ATAATTA
1 TTTTTA-TATTAATACTTA
* *
2907676 TTTTTATTTATAATACTAA
1 TTTTTATAT-TAATACTTA
2907695 TTTTT
1 TTTTT
2907700 TTACGTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.03
17 12 0.36
18 8 0.24
19 12 0.36
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTTATATTAATACTTA
Found at i:2907687 original size:16 final size:16
Alignment explanation
Indices: 2907630--2907689 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
2907620 AATTTTACGA
2907630 TTATTTAT-ATT-TTT
1 TTATTTATAATTATTT
*
2907644 TTATATTAATACTTATTT
1 TTAT-TT-ATAATTATTT
*
2907662 TTAGTATATAATTATTT
1 TTA-TTTATAATTATTT
2907679 TTATTTATAAT
1 TTATTTATAAT
2907690 ACTAATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.11
15 2 0.05
16 9 0.24
17 14 0.38
18 7 0.19
19 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTATAATTATTT
Found at i:2907934 original size:21 final size:20
Alignment explanation
Indices: 2907867--2907936 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 20
2907857 TGTTAATTTT
2907867 TTTTTAT-TTATAATAATAA
1 TTTTTATGTTATAATAATAA
* *
2907886 TTTTTTATATTGT--TAACCTAA
1 -TTTTTATGTTATAATAA--TAA
2907907 TTATTTATGTTATAATAATAA
1 TT-TTTATGTTATAATAATAA
2907928 CTTTTTATG
1 -TTTTTATG
2907937 ATTGTTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
19 3 0.08
20 9 0.22
21 23 0.57
22 2 0.05
23 3 0.08
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTTTATGTTATAATAATAA
Found at i:2908256 original size:21 final size:20
Alignment explanation
Indices: 2908231--2908275 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
2908221 GTAAAGAAAC
2908231 AAAACGTAAA-AAATAAAAATA
1 AAAAC-TAAAGAAA-AAAAATA
2908252 AAAACTAAAGGAAAAAAAATA
1 AAAACTAAA-GAAAAAAAATA
2908273 AAA
1 AAA
2908276 GAAGTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (20 bp):
AAAACTAAAGAAAAAAAATA
Found at i:2908381 original size:19 final size:21
Alignment explanation
Indices: 2908338--2908390 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
2908328 TTTATTTTAT
*
2908338 TTAATAAA-TAATATTTAATG
1 TTAATAAATTAATAATTAATG
2908358 TTAATAAATTAA-AATTAA-G
1 TTAATAAATTAATAATTAATG
2908377 TTAATAAATTAATA
1 TTAATAAATTAATA
2908391 GGTAATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 14 0.47
21 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
TTAATAAATTAATAATTAATG
Found at i:2926658 original size:7 final size:7
Alignment explanation
Indices: 2926646--2926688 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
2926636 TTGAAATCTG
2926646 GATTCTA
1 GATTCTA
2926653 GATTCTA
1 GATTCTA
2926660 GATTCTA
1 GATTCTA
2926667 GATTCTA
1 GATTCTA
2926674 GATTCTA
1 GATTCTA
2926681 GATTCTA
1 GATTCTA
2926688 G
1 G
2926689 CTTTAGCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (7 bp):
GATTCTA
Found at i:2941193 original size:23 final size:25
Alignment explanation
Indices: 2941166--2941226 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 25
2941156 TCTATTCGAA
2941166 AAAAATTAAATTT-TTATTAAATAT
1 AAAAATTAAATTTATTATTAAATAT
*
2941190 AAAAATTAAATTTATT-TT-TATAT
1 AAAAATTAAATTTATTATTAAATAT
**
2941213 ATTAATTAAATTTA
1 AAAAATTAAATTTA
2941227 ATAAAATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.48
24 15 0.45
25 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAAATTAAATTTATTATTAAATAT
Found at i:2941294 original size:46 final size:47
Alignment explanation
Indices: 2941193--2941296 Score: 112
Period size: 46 Copynumber: 2.3 Consensus size: 47
2941183 TAAATATAAA
*
2941193 AATTAAATTT-ATTTTTATATATTAATTAAATTTAATAAAATGAATTT
1 AATTAAATTTAATTTTTATATATTAATCAAATTTAATAAAA-GAATTT
*
2941240 AAGT-AATTTAATTTTTAT-T-TTGAATCAAATTTAAATTAAAA-AA-TT
1 AATTAAATTTAATTTTTATATATT-AATCAAATTT-AA-TAAAAGAATTT
2941285 AATTAAATTTAA
1 AATTAAATTTAA
2941297 ATTTAAATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
45 7 0.14
46 24 0.49
47 13 0.27
48 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (47 bp):
AATTAAATTTAATTTTTATATATTAATCAAATTTAATAAAAGAATTT
Found at i:2941305 original size:17 final size:17
Alignment explanation
Indices: 2941266--2941313 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2941256 ATTTTGAATC
2941266 AAATTTAAATTAAA---
1 AAATTTAAATTAAATTT
2941280 AAA-TT-AATTAAATTT
1 AAATTTAAATTAAATTT
2941295 AAATTTAAATTAAATTT
1 AAATTTAAATTAAATTT
2941312 AA
1 AA
2941314 TACTTAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.24
13 2 0.07
14 3 0.10
15 3 0.10
16 2 0.07
17 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAAATTAAATTT
Found at i:2941313 original size:23 final size:22
Alignment explanation
Indices: 2941266--2941307 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2941256 ATTTTGAATC
2941266 AAATTTAAATTAAAAAATTAATT
1 AAATTTAAATT-AAAAATTAATT
*
2941289 AAATTTAAATT-TAAATTAA
1 AAATTTAAATTAAAAATTAA
2941308 ATTTAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTTAAATTAAAAATTAATT
Found at i:2941322 original size:17 final size:16
Alignment explanation
Indices: 2941283--2941336 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
2941273 AATTAAAAAA
*
2941283 TTAATTAAATTTAAAT
1 TTAATTAAATTTAAAC
2941299 TTAAATTAAATTTAATAC
1 TT-AATTAAATTTAA-AC
*
2941317 TTAATT-GATTTAAAC
1 TTAATTAAATTTAAAC
2941332 TTAAT
1 TTAAT
2941337 AGATTACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 7 0.21
16 8 0.24
17 16 0.47
18 3 0.09
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (16 bp):
TTAATTAAATTTAAAC
Found at i:2941335 original size:15 final size:16
Alignment explanation
Indices: 2941308--2941341 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2941298 TTTAAATTAA
*
2941308 ATTTAATACTTAATTG
1 ATTTAATACTTAATAG
2941324 ATTTAA-ACTTAATAG
1 ATTTAATACTTAATAG
2941339 ATT
1 ATT
2941342 ACAAAGACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTTAATACTTAATAG
Found at i:2953334 original size:22 final size:20
Alignment explanation
Indices: 2953292--2953337 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2953282 AATTAATTAA
* *
2953292 TTATATATATTTATATAATT
1 TTATATATATTAAAATAATT
2953312 TTATATATATTAAAAATATATT
1 TTATATATATT-AAAATA-ATT
2953334 TTAT
1 TTAT
2953338 TTATTTCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 4 0.18
22 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATATATTAAAATAATT
Found at i:2960055 original size:53 final size:54
Alignment explanation
Indices: 2959997--2960105 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
2959987 TTTCCCTTAC
* * * *
2959997 GTCCCTTTAATATTT-ATTTTTTTAATAAATTATTTATTTTTTAATATTCGATA
1 GTCCCTCTAATATTTCATTTTTTTAATAAAATATTAATTTTTAAATATTCGATA
2960050 GTCCCTCTAATATTTCATTTTTTTAATAAAATATTAATTTTTAAATATTCGATA
1 GTCCCTCTAATATTTCATTTTTTTAATAAAATATTAATTTTTAAATATTCGATA
2960104 GT
1 GT
2960106 AAAATATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 14 0.27
54 37 0.73
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (54 bp):
GTCCCTCTAATATTTCATTTTTTTAATAAAATATTAATTTTTAAATATTCGATA
Found at i:2966921 original size:2 final size:2
Alignment explanation
Indices: 2966914--2966939 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2966904 TTTTGGCCCC
2966914 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2966940 AATCTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2971353 original size:23 final size:24
Alignment explanation
Indices: 2971309--2971362 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
2971299 TTTGATCTAA
* * *
2971309 TTTTATATATTATATATTTATTTT
1 TTTTATATAATATACATGTATTTT
*
2971333 TTTTAT-TAATATACATGTATTAT
1 TTTTATATAATATACATGTATTTT
*
2971356 ATTTATA
1 TTTTATA
2971363 AAATTATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTATATAATATACATGTATTTT
Found at i:2972765 original size:12 final size:12
Alignment explanation
Indices: 2972748--2972772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2972738 AAATTAATTT
2972748 TTTTAAATTAAA
1 TTTTAAATTAAA
2972760 TTTTAAATTAAA
1 TTTTAAATTAAA
2972772 T
1 T
2972773 CAAATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTAAATTAAA
Found at i:2972903 original size:16 final size:18
Alignment explanation
Indices: 2972869--2972904 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2972859 AATTATTTAT
2972869 TTATATATATTTATATAA
1 TTATATATATTTATATAA
2972887 TTATATAT-TTTAT-TAA
1 TTATATATATTTATATAA
2972903 TT
1 TT
2972905 TCAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATATATTTATATAA
Found at i:2972948 original size:21 final size:22
Alignment explanation
Indices: 2972924--2973005 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 22
2972914 ATTAAAATAT
2972924 AATTTAT-A-TAATATCAAATCA
1 AATTTATAATTAA-ATCAAATCA
*
2972945 AA-TTATAATTAAATCTAATCA
1 AATTTATAATTAAATCAAATCA
*
2972966 AATTTA-AATTTAAT-AAATACA
1 AATTTATAATTAAATCAAAT-CA
* *
2972987 AAATCA-AATTAAATTCAAA
1 AATTTATAATTAAA-TCAAA
2973006 ACAAGCAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 7 0.14
21 32 0.65
22 7 0.14
23 3 0.06
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
AATTTATAATTAAATCAAATCA
Found at i:2972948 original size:32 final size:31
Alignment explanation
Indices: 2972889--2972949 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
2972879 TTATATAATT
* * *
2972889 ATATATTTTATTAATTTCAAATTAAATTAAA
1 ATATAATTTATTAATATCAAATCAAATTAAA
2972920 ATATAATTTATATAATATCAAATCAAATTA
1 ATATAATTTAT-TAATATCAAATCAAATTA
2972950 TAATTAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATAATTTATTAATATCAAATCAAATTAAA
Found at i:2975722 original size:21 final size:20
Alignment explanation
Indices: 2975672--2975723 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2975662 TTATTTTAAA
**
2975672 GTTCATTTTATATTTATTTTT
1 GTTCA-TTTATATTTATTTGG
*
2975693 GTTCGTTTATATTTATTTAGG
1 GTTCATTTATATTTATTT-GG
2975714 GTTCATTTAT
1 GTTCATTTAT
2975724 TTAAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.63
Consensus pattern (20 bp):
GTTCATTTATATTTATTTGG
Found at i:2975754 original size:14 final size:15
Alignment explanation
Indices: 2975718--2975755 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2975708 TTTAGGGTTC
2975718 ATTTATT-TAAATTT
1 ATTTATTATAAATTT
2975732 ATTTGATTAT-AATTT
1 ATTT-ATTATAAATTT
2975747 ATTTATTAT
1 ATTTATTAT
2975756 TCATAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 12 0.55
16 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTTATTATAAATTT
Found at i:2977615 original size:2 final size:2
Alignment explanation
Indices: 2977608--2977634 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2977598 CATTCATTTT
2977608 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2977635 GGGTGTAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2979425 original size:21 final size:20
Alignment explanation
Indices: 2979399--2979443 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
2979389 AGATTTATTG
*
2979399 ATTTAATTTTATGTTAAATTT
1 ATTTAATTATATGTT-AATTT
2979420 ATTTAATTATATGTTAATTT
1 ATTTAATTATATGTTAATTT
2979440 ATTT
1 ATTT
2979444 GTTTGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTAATTATATGTTAATTT
Found at i:2986750 original size:20 final size:23
Alignment explanation
Indices: 2986725--2986766 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
2986715 GCACCACATG
2986725 GCCATGA-AGA-AGAA-AAAGAA
1 GCCATGAGAGAGAGAAGAAAGAA
2986745 GCCATGAGAGAGAGAAGAAAGA
1 GCCATGAGAGAGAGAAGAAAGA
2986767 CCTCAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 4 0.21
23 5 0.26
ACGTcount: A:0.55, C:0.10, G:0.31, T:0.05
Consensus pattern (23 bp):
GCCATGAGAGAGAGAAGAAAGAA
Found at i:2987548 original size:15 final size:15
Alignment explanation
Indices: 2987528--2987562 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2987518 TTAATAAAAA
* *
2987528 ATATAATTTTTTATT
1 ATATAATATATTATT
2987543 ATATAATATATTATT
1 ATATAATATATTATT
2987558 ATATA
1 ATATA
2987563 TTCATAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATAATATATTATT
Found at i:2989998 original size:17 final size:18
Alignment explanation
Indices: 2989947--2989998 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
2989937 GATTTGGTGC
2989947 ATAAAATTATGATAATATAAG
1 ATAAAATTA-GAT--TATAAG
*
2989968 ATAAAATTATATTATAA-
1 ATAAAATTAGATTATAAG
*
2989985 ATATAATTAGATTA
1 ATAAAATTAGATTA
2989999 AATAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.43
18 5 0.18
20 2 0.07
21 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAAAATTAGATTATAAG
Found at i:3001760 original size:24 final size:22
Alignment explanation
Indices: 3001722--3001788 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 22
3001712 AACGTAAAAA
3001722 TAAAATATAAAAATTATATTATT
1 TAAAATATAAAAATTATA-TATT
*
3001745 TAAAATTATAATAATTATATATT
1 TAAAA-TATAAAAATTATATATT
3001768 TAGTAAA-ATTAAAAATTATAT
1 TA--AAATA-TAAAAATTATAT
3001789 CTTATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 12 0.32
24 23 0.61
25 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (22 bp):
TAAAATATAAAAATTATATATT
Found at i:3003015 original size:18 final size:17
Alignment explanation
Indices: 3002989--3003040 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 17
3002979 TTAATGTCAA
3002989 AAAATTAAAAAAATTTT
1 AAAATTAAAAAAATTTT
3003006 AAAATATAAAAAAAGTTTT
1 AAAAT-TAAAAAAA-TTTT
*
3003025 AGATATTTAAAAAAAT
1 A-A-AATTAAAAAAAT
3003041 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.17
18 8 0.27
19 6 0.20
20 9 0.30
21 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAATTAAAAAAATTTT
Found at i:3003085 original size:25 final size:24
Alignment explanation
Indices: 3003032--3003090 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
3003022 TTTAGATATT
3003032 TAAAAAAATAATTTTAAAACATCC
1 TAAAAAAATAATTTTAAAACATCC
3003056 TAAAAAAATAATTTTAAAACATCC
1 TAAAAAAATAATTTTAAAACATCC
3003080 TAAAAAAATAA
1 TAAAAAAATAA
3003091 ATAAAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAAAAATAATTTTAAAACATCC
Found at i:3005033 original size:22 final size:23
Alignment explanation
Indices: 3004998--3005042 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3004988 TTAAAAAAAA
* *
3004998 TTTATATATTAATTAATTTGATT
1 TTTATATATAAATTAAATTGATT
3005021 TTTATA-ATAAATTAAATTGATT
1 TTTATATATAAATTAAATTGATT
3005043 AGTTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTATATATAAATTAAATTGATT
Found at i:3005049 original size:39 final size:36
Alignment explanation
Indices: 3004977--3005050 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
3004967 CCTTAATTTG
* *
3004977 ATTTGATTTTTTTAAAAAAAATTTATATATTAATTA
1 ATTTGATTTTTATAAAAAAAATTGATATATTAATTA
3005013 ATTTGATTTTTATAATAAATTAAATTGAT-TAGTTAATT
1 ATTTGATTTTTATAA-AAA--AAATTGATATA-TTAATT
3005051 TACGATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 14 0.44
37 3 0.09
38 2 0.06
39 13 0.41
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (36 bp):
ATTTGATTTTTATAAAAAAAATTGATATATTAATTA
Found at i:3010391 original size:30 final size:30
Alignment explanation
Indices: 3010317--3010405 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
3010307 TCTAAAACTA
* * ** *
3010317 AAACCCTAAACCCTTTCAACTTTAAAATTG
1 AAACTCTAAACCCTTTAAACCATAAAATCG
*
3010347 AAACTCTAAAACCCTTTAAACCCTAAAATCG
1 AAACTCT-AAACCCTTTAAACCATAAAATCG
*
3010378 AAACTCTAAACCCTTTAAATCATAAAAT
1 AAACTCTAAACCCTTTAAACCATAAAAT
3010406 TTAAAACCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.49
31 26 0.51
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (30 bp):
AAACTCTAAACCCTTTAAACCATAAAATCG
Found at i:3010418 original size:15 final size:15
Alignment explanation
Indices: 3010398--3010445 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3010388 CCCTTTAAAT
3010398 CATAAAATTTAAAAC
1 CATAAAATTTAAAAC
3010413 CAT-AAATTTCAAAAC
1 CATAAAATTT-AAAAC
*
3010428 CTTAAAATCCTTAAAAC
1 CATAAAAT--TTAAAAC
3010445 C
1 C
3010446 CTTGAAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.21
15 10 0.36
16 4 0.14
17 6 0.21
18 2 0.07
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (15 bp):
CATAAAATTTAAAAC
Found at i:3010519 original size:17 final size:18
Alignment explanation
Indices: 3010492--3010525 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3010482 AATCTTAGAT
3010492 TTTCGAAACCCCAAAATC
1 TTTCGAAACCCCAAAATC
*
3010510 TTTC-AAACCCTAAAAT
1 TTTCGAAACCCCAAAAT
3010526 TTAAGCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.26
Consensus pattern (18 bp):
TTTCGAAACCCCAAAATC
Found at i:3022393 original size:23 final size:23
Alignment explanation
Indices: 3022362--3022406 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3022352 CAATAAATTG
*
3022362 ATATAATTATTTAAA-TGATTAT
1 ATATAATTATCTAAATTGATTAT
3022384 ATATCAATTATCTAAATTGATTA
1 ATAT-AATTATCTAAATTGATTA
3022407 ATTATGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 6 0.30
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
ATATAATTATCTAAATTGATTAT
Found at i:3027710 original size:11 final size:11
Alignment explanation
Indices: 3027694--3027727 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3027684 TATAGGTAAT
3027694 ATGATATAAAA
1 ATGATATAAAA
3027705 ATGATATAAAA
1 ATGATATAAAA
*
3027716 ATAATATAAAA
1 ATGATATAAAA
3027727 A
1 A
3027728 ATATTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (11 bp):
ATGATATAAAA
Found at i:3027808 original size:31 final size:30
Alignment explanation
Indices: 3027749--3027810 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
3027739 ATTTTATAAA
* * * *
3027749 AATATATTTTGTATTTATTTATTTTAATAT
1 AATATAATTCGTATTTATATATGTTAATAT
3027779 AATATAATTCGTATCTTATATATGTTAATAT
1 AATATAATTCGTAT-TTATATATGTTAATAT
3027810 A
1 A
3027811 TCTAAACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (30 bp):
AATATAATTCGTATTTATATATGTTAATAT
Found at i:3028351 original size:23 final size:23
Alignment explanation
Indices: 3028316--3028368 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3028306 TGATTATTTA
* *
3028316 TTATTTTATTTATATTTATATAT
1 TTATATTAATTATATTTATATAT
*
3028339 TTATATTAATTATATTTATTTAT
1 TTATATTAATTATATTTATATAT
*
3028362 ATATATT
1 TTATATT
3028369 CGTGTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATATTAATTATATTTATATAT
Found at i:3028364 original size:29 final size:30
Alignment explanation
Indices: 3028314--3028424 Score: 124
Period size: 29 Copynumber: 3.9 Consensus size: 30
3028304 TATGATTATT
* *
3028314 TATT-ATTTTATTTATATT-TATATATTTA
1 TATTAATTATATTTATATTATATATATTCA
*
3028342 TATTAATTATATTTAT-TTATATATATTCG
1 TATTAATTATATTTATATTATATATATTCA
* **
3028371 TGTTAATTATATTTAT-TCGTATATATTCA
1 TATTAATTATATTTATATTATATATATTCA
*
3028400 TATTAATTATA-TCATATTATATATA
1 TATTAATTATATTTATATTATATATA
3028425 ATAAATATAT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 9 0.13
29 60 0.87
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (30 bp):
TATTAATTATATTTATATTATATATATTCA
Found at i:3028416 original size:20 final size:20
Alignment explanation
Indices: 3028393--3028495 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 20
3028383 TTATTCGTAT
3028393 ATATTCATATTAAT-TATATC
1 ATATT-ATATTAATATATATC
3028413 ATATTATATATAATAAATATATC
1 ATATTATAT-TAAT--ATATATC
*
3028436 ATATTTATATTTAATATTTAAAT-
1 ATA-TTATA-TTAATA--TATATC
* *
3028459 ATATTTTA-TAATTTATATC
1 ATATTATATTAATATATATC
3028478 ATATTCATATCTAATATA
1 ATATT-ATAT-TAATATA
3028496 GTATAAAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
18 4 0.06
19 9 0.14
20 15 0.23
22 11 0.17
23 12 0.18
24 13 0.20
25 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATATTAATATATATC
Found at i:3028437 original size:23 final size:24
Alignment explanation
Indices: 3028407--3028451 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3028397 TCATATTAAT
3028407 TATATCATA-TTATATATAATAAA
1 TATATCATATTTATATATAATAAA
*
3028430 TATATCATATTTATATTTAATA
1 TATATCATATTTATATATAATA
3028452 TTTAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATCATATTTATATATAATAAA
Found at i:3030479 original size:11 final size:11
Alignment explanation
Indices: 3030459--3030489 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3030449 CCCCTTCCTT
3030459 AAAA-AAAAAA
1 AAAAGAAAAAA
3030469 AAAAGAAAAAA
1 AAAAGAAAAAA
3030480 AAAAGAAAAA
1 AAAAGAAAAA
3030490 CCAACGTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:3030824 original size:29 final size:30
Alignment explanation
Indices: 3030773--3030863 Score: 96
Period size: 29 Copynumber: 3.0 Consensus size: 30
3030763 GATTTACTCT
* *
3030773 TAAATTATAATAAAATATTTAATATAATATA
1 TAAATTATAA-ATATTATTTAATATAATATA
* *
3030804 TAAAATT-TAAA-ATTTTTTAATATGATATA
1 T-AAATTATAAATATTATTTAATATAATATA
3030833 TAAATTATAAATCTATTATTTAATATAATAT
1 TAAATTATAAA--TATTATTTAATATAATAT
3030864 TCATTATAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
28 5 0.10
29 20 0.40
30 1 0.02
31 4 0.08
32 20 0.40
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
TAAATTATAAATATTATTTAATATAATATA
Found at i:3048203 original size:28 final size:27
Alignment explanation
Indices: 3048126--3048208 Score: 69
Period size: 28 Copynumber: 3.0 Consensus size: 27
3048116 TAAGAGTTTG
*
3048126 ATTTTTTAAAATAAATTTTAAAATTTAAA
1 ATTTTTTAAAA-AAAATTT-AAATTTAAA
* * * *
3048155 ATTTATGAATAAAAAA-ATAAATGTTCAA
1 ATTTTTTAA-AAAAAATTTAAAT-TTAAA
*
3048183 ATTTTTTAAAAAAAATTTAAAATTAA
1 ATTTTTTAAAAAAAATTTAAATTTAA
3048209 TCAAAATTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
27 13 0.32
28 16 0.39
29 10 0.24
30 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTTTTAAAAAAAATTTAAATTTAAA
Found at i:3048208 original size:17 final size:17
Alignment explanation
Indices: 3048188--3048222 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3048178 TTCAAATTTT
3048188 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
**
3048205 TTAATCAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
3048222 T
1 T
3048223 AATTACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:3049194 original size:13 final size:13
Alignment explanation
Indices: 3049176--3049201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3049166 AATGCTGAGA
3049176 TTTAAAAATAATT
1 TTTAAAAATAATT
3049189 TTTAAAAATAATT
1 TTTAAAAATAATT
3049202 ATATTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAAATAATT
Found at i:3075423 original size:14 final size:15
Alignment explanation
Indices: 3075388--3075425 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
3075378 TAAATTTTTT
*
3075388 ATTAAAAATAATTAA
1 ATTAAAAATTATTAA
3075403 ATT-AAAATTA-TAA
1 ATTAAAAATTATTAA
3075416 ATTAAAAATT
1 ATTAAAAATT
3075426 TTCATTACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 12 0.57
15 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAAAATTATTAA
Found at i:3075556 original size:29 final size:29
Alignment explanation
Indices: 3075523--3075584 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
3075513 TATTGATAAT
*
3075523 ATTTT-TAATAAATTTT-TTACATATTATTA
1 ATTTTATAATAAATTTTATTA-AT-TTATCA
*
3075552 ATTTTATATTAAATTTTATTAATTTATCA
1 ATTTTATAATAAATTTTATTAATTTATCA
3075581 ATTT
1 ATTT
3075585 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.48
30 12 0.41
31 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTTTATAATAAATTTTATTAATTTATCA
Found at i:3075557 original size:28 final size:29
Alignment explanation
Indices: 3075523--3075601 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 29
3075513 TATTGATAAT
* *
3075523 ATTTT-TAATAAATTTT-TTACATATTATTA
1 ATTTTATATTAAATTTTATTA-AT-TTATCA
3075552 ATTTTATATTAAATTTTATTAATTTATCA
1 ATTTTATATTAAATTTTATTAATTTATCA
3075581 A-TTTATATT---TTTTATTAATTT
1 ATTTTATATTAAATTTTATTAATTT
3075602 TTTATTAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 12 0.26
28 8 0.17
29 11 0.24
30 12 0.26
31 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTATATTAAATTTTATTAATTTATCA
Found at i:3075568 original size:12 final size:11
Alignment explanation
Indices: 3075547--3075614 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
3075537 TTTTACATAT
3075547 TATTAATTTTA
1 TATTAATTTTA
*
3075558 TATTAAATTT-
1 TATTAATTTTA
3075568 TATTAA-TTTA
1 TATTAATTTTA
*
3075578 TCAATTTATATTTTT
1 T--A-TTA-ATTTTA
*
3075593 TATTAATTTTT
1 TATTAATTTTA
3075604 TATTAATTTTA
1 TATTAATTTTA
3075615 CAAACTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
9 3 0.06
10 7 0.15
11 25 0.52
12 4 0.08
13 4 0.08
14 1 0.02
15 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTAATTTTA
Found at i:3075645 original size:15 final size:15
Alignment explanation
Indices: 3075625--3075654 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3075615 CAAACTTTAT
3075625 TTAAAAAATTTTCCC
1 TTAAAAAATTTTCCC
3075640 TTAAAAAATTTTCCC
1 TTAAAAAATTTTCCC
3075655 GACGTAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAAATTTTCCC
Found at i:3076251 original size:25 final size:27
Alignment explanation
Indices: 3076207--3076257 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
3076197 AAAAAATTTA
*
3076207 AATAAAGTTTTTTAGATAAAATTAATT
1 AATAAAGTTTTTTAGATAAAAATAATT
*
3076234 AATAAA-TTTTTTA-TTAAAAATAAT
1 AATAAAGTTTTTTAGATAAAAATAAT
3076258 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
AATAAAGTTTTTTAGATAAAAATAATT
Found at i:3076263 original size:26 final size:27
Alignment explanation
Indices: 3076205--3076265 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
3076195 GAAAAAAATT
*
3076205 TAAATAAAGTTTTTTAGATAAAATTAA
1 TAAATAAAGTTTTTTAGATAAAAATAA
* *
3076232 TTAATAAA-TTTTTTA-TTAAAAATAA
1 TAAATAAAGTTTTTTAGATAAAAATAA
3076257 TAAAATAAA
1 T-AAATAAA
3076266 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 9 0.31
26 13 0.45
27 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAATAAAGTTTTTTAGATAAAAATAA
Found at i:3077909 original size:3 final size:3
Alignment explanation
Indices: 3077901--3077927 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3077891 TGTCAAAGCT
3077901 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
3077928 AAAACAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3083127 original size:30 final size:31
Alignment explanation
Indices: 3083082--3083146 Score: 123
Period size: 30 Copynumber: 2.1 Consensus size: 31
3083072 TGTTGTGATG
3083082 AACCCTAGTTTTTTTTAACAGTGGTAACTCT
1 AACCCTAGTTTTTTTTAACAGTGGTAACTCT
3083113 AACCCTAG-TTTTTTTAACAGTGGTAACTCT
1 AACCCTAGTTTTTTTTAACAGTGGTAACTCT
3083143 AACC
1 AACC
3083147 TACCCTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (31 bp):
AACCCTAGTTTTTTTTAACAGTGGTAACTCT
Found at i:3083304 original size:64 final size:64
Alignment explanation
Indices: 3083203--3083336 Score: 223
Period size: 64 Copynumber: 2.1 Consensus size: 64
3083193 ATTGTTGCCT
* *
3083203 TTTGCTATAGTAAATTTGGGTACTTGCTCTTAAGTATGTACATACTACCCAAATAGTTGCTTTG
1 TTTGCTATAGTAAATTTGGGTACATGCGCTTAAGTATGTACATACTACCCAAATAGTTGCTTTG
* * *
3083267 TTTGCTATAGTAAATTTGGGTACATGCGCTTAAGTATGTACCTACTACCCCAATAGTTGTTTTG
1 TTTGCTATAGTAAATTTGGGTACATGCGCTTAAGTATGTACATACTACCCAAATAGTTGCTTTG
3083331 TTTGCT
1 TTTGCT
3083337 TGATTCAGTG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (64 bp):
TTTGCTATAGTAAATTTGGGTACATGCGCTTAAGTATGTACATACTACCCAAATAGTTGCTTTG
Found at i:3090165 original size:28 final size:28
Alignment explanation
Indices: 3090093--3090171 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
3090083 TCAATAGGAT
**
3090093 AATAAATTTCAATAAAAAAATTATATGTA
1 AATAAATTT-AATAAAAATTTTATATGTA
* * *
3090122 AAAAAATATTATTAAAAATTTTATTTGTA
1 AATAAAT-TTAATAAAAATTTTATATGTA
*
3090151 ATTAAATTTAATAAAAATTTT
1 AATAAATTTAATAAAAATTTT
3090172 GTTAAAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 13 0.32
29 26 0.63
30 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
AATAAATTTAATAAAAATTTTATATGTA
Found at i:3090197 original size:13 final size:12
Alignment explanation
Indices: 3090123--3090207 Score: 64
Period size: 12 Copynumber: 6.6 Consensus size: 12
3090113 TTATATGTAA
*
3090123 AAAAATATTATT
1 AAAAATTTTATT
3090135 AAAAATTTTATTTGT
1 AAAAATTTTA--T-T
*
3090150 AATTAAA-TTTAAT
1 AA--AAATTTTATT
*
3090163 AAAAATTTTGTT
1 AAAAATTTTATT
*
3090175 AAAATTTTTATT
1 AAAAATTTTATT
3090187 AAAAATGTTTAATT
1 AAAAAT-TTT-ATT
3090201 AAAAATT
1 AAAAATT
3090208 GATTAACATT
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
11 3 0.05
12 28 0.48
13 7 0.12
14 10 0.17
15 3 0.05
16 4 0.07
17 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (12 bp):
AAAAATTTTATT
Found at i:3090203 original size:14 final size:13
Alignment explanation
Indices: 3090157--3090207 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 13
3090147 TGTAATTAAA
3090157 TTTAA-TAAAAAT
1 TTTAATTAAAAAT
*
3090169 TTT-GTT-AAAAT
1 TTTAATTAAAAAT
*
3090180 TTTTATTAAAAAT
1 TTTAATTAAAAAT
3090193 GTTTAATTAAAAAT
1 -TTTAATTAAAAAT
3090207 T
1 T
3090208 GATTAACATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 8 0.25
12 6 0.19
13 6 0.19
14 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (13 bp):
TTTAATTAAAAAT
Found at i:3090663 original size:25 final size:21
Alignment explanation
Indices: 3090612--3090665 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 21
3090602 TATAATTTTT
3090612 TTATTTTTTAAAATTTATATA
1 TTATTTTTTAAAATTTATATA
*
3090633 TGATTTTATTAAAATTTAAGTTATA
1 TTATTTT-TTAAAATTT-A--TATA
3090658 TTATTTTT
1 TTATTTTT
3090666 ATTTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.22
22 9 0.33
23 1 0.04
24 1 0.04
25 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
TTATTTTTTAAAATTTATATA
Found at i:3093790 original size:71 final size:72
Alignment explanation
Indices: 3093699--3093847 Score: 185
Period size: 72 Copynumber: 2.1 Consensus size: 72
3093689 CATCGTGAGC
* * * **
3093699 TGTGCAGACAATTAATCATTTA-TTTGAAGACC-TAGATTTTATGTTCTGAAAGAGTATCAAACA
1 TGTGCAGACAATGAACCATTTAGTTT-AAGACCTTAGATTTTATGCTCCAAAAGAGTATCAAACA
3093762 AAAATTAT
65 AAAATTAT
* * *
3093770 TGTGCAGACAATGCACCATTTAGTTTAAGACCTTAGATTTTATGCTCCAAAAGAGTGTCAAACAG
1 TGTGCAGACAATGAACCATTTAGTTTAAGACCTTAGATTTTATGCTCCAAAAGAGTATCAAACAA
*
3093835 AGATTAT
66 AAATTAT
*
3093842 TTTGCA
1 TGTGCA
3093848 TTTGTGCATA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
71 25 0.38
72 41 0.62
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (72 bp):
TGTGCAGACAATGAACCATTTAGTTTAAGACCTTAGATTTTATGCTCCAAAAGAGTATCAAACAA
AAATTAT
Found at i:3099323 original size:2 final size:2
Alignment explanation
Indices: 3099316--3099343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3099306 AAGTAAATAA
3099316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3099344 CAAGAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3103807 original size:91 final size:91
Alignment explanation
Indices: 3103652--3103837 Score: 336
Period size: 91 Copynumber: 2.0 Consensus size: 91
3103642 AAAAAGTGAG
* * *
3103652 CCTGAAGTGATAGCTCGCTAATCAGGGACCAACGATTTTGGGTCGGTCAACGAAGCGTTCTGGTC
1 CCTGAAGTGATAGCTCACTAATCAGGGACCAACCATTTTGGATCGGTCAACGAAGCGTTCTGGTC
*
3103717 CGGTGCTTGCTGCCCTTGCTCTCCTA
66 CGGTGCTTGCTGCCCTTGCTCTCCAA
3103743 CCTGAAGTGATAGCTCACTAATCAGGGACCAACCATTTTGGATCGGTCAACGAAGCGTTCTGGTC
1 CCTGAAGTGATAGCTCACTAATCAGGGACCAACCATTTTGGATCGGTCAACGAAGCGTTCTGGTC
3103808 CGGTGCTTGCTGCCCTTGCTCTCCAA
66 CGGTGCTTGCTGCCCTTGCTCTCCAA
3103834 CCTG
1 CCTG
3103838 CCCTTCTCAC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (91 bp):
CCTGAAGTGATAGCTCACTAATCAGGGACCAACCATTTTGGATCGGTCAACGAAGCGTTCTGGTC
CGGTGCTTGCTGCCCTTGCTCTCCAA
Found at i:3104579 original size:15 final size:15
Alignment explanation
Indices: 3104561--3104594 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3104551 ATAATTTTAT
*
3104561 AATTAATTATTTAAA
1 AATTAATCATTTAAA
*
3104576 AATTTATCATTTAAA
1 AATTAATCATTTAAA
3104591 AATT
1 AATT
3104595 TAAATTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAATCATTTAAA
Found at i:3104870 original size:6 final size:6
Alignment explanation
Indices: 3104859--3104884 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3104849 TTATAAAATT
3104859 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
3104885 TTATTTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:3104932 original size:29 final size:29
Alignment explanation
Indices: 3104893--3104978 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
3104883 TTTTATTTGA
3104893 TTTGA-AT-TAAATTTATTAATTTATAAT
1 TTTGATATATAAATTTATTAATTTATAAT
*
3104920 TTAT-ATATATAAATTTAATATATTTAAATAAAT
1 TT-TGATATATAAATTTATTA-ATTT--AT-AAT
*
3104953 TTTGATATA-AAA-TTATTATTTTATAA
1 TTTGATATATAAATTTATTAATTTATAA
3104979 AAATTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 10 0.21
30 7 0.15
31 5 0.10
32 6 0.12
33 10 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTGATATATAAATTTATTAATTTATAAT
Found at i:3108697 original size:52 final size:51
Alignment explanation
Indices: 3108632--3108729 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
3108622 TTTTCCATTT
*
3108632 TAAAATTTTTCTTGTAACCTTTTCAAAAAATAAAATACAGAATTACAATCAA
1 TAAAATTTGTCTTGTAACCTTTT-AAAAAATAAAATACAGAATTACAATCAA
* * *
3108684 TAAAATTTGTCTTGTACCCTTTTTAAAATTAAAATACAGAATTACA
1 TAAAATTTGTCTTGTAACCTTTTAAAAAATAAAATACAGAATTACA
3108730 GTCAGTAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 21 0.50
52 21 0.50
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (51 bp):
TAAAATTTGTCTTGTAACCTTTTAAAAAATAAAATACAGAATTACAATCAA
Found at i:3109508 original size:6 final size:6
Alignment explanation
Indices: 3109497--3109521 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3109487 TTTTCATGGA
3109497 CAACGC CAACGC CAACGC CAACGC C
1 CAACGC CAACGC CAACGC CAACGC C
3109522 GATTATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CAACGC
Found at i:3112156 original size:32 final size:32
Alignment explanation
Indices: 3112118--3112246 Score: 249
Period size: 32 Copynumber: 4.0 Consensus size: 32
3112108 ATCATCCACT
3112118 TAACCTAATCTTTAAACAATTAGTTTTACATA
1 TAACCTAATCTTTAAACAATTAGTTTTACATA
3112150 TAACCTAATCTTTAAACAATTAGTTTTACATA
1 TAACCTAATCTTTAAACAATTAGTTTTACATA
*
3112182 TAACCTAATCTTTAAACAAATAGTTTTACATA
1 TAACCTAATCTTTAAACAATTAGTTTTACATA
3112214 TAACCTAATCTTTAAACAATTAGTTTTACATA
1 TAACCTAATCTTTAAACAATTAGTTTTACATA
3112246 T
1 T
3112247 CCCTCTTGAT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 95 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (32 bp):
TAACCTAATCTTTAAACAATTAGTTTTACATA
Found at i:3113271 original size:2 final size:2
Alignment explanation
Indices: 3113264--3113294 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3113254 CAATGCACGC
3113264 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
3113295 AATTTTCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:3116733 original size:18 final size:18
Alignment explanation
Indices: 3116710--3116747 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3116700 AACAACTCTT
3116710 AAGAAATAAAAATTACCC
1 AAGAAATAAAAATTACCC
3116728 AAGAAATAAAAATTACCC
1 AAGAAATAAAAATTACCC
3116746 AA
1 AA
3116748 ACATTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AAGAAATAAAAATTACCC
Found at i:3121615 original size:22 final size:22
Alignment explanation
Indices: 3121587--3121668 Score: 64
Period size: 22 Copynumber: 3.7 Consensus size: 22
3121577 ATTTTTTTAA
3121587 ATATTTATATAATTAAATAAAT
1 ATATTTATATAATTAAATAAAT
* *
3121609 ATATTTA-ATTAAATAAATAATT
1 ATATTTATA-TAATTAAATAAAT
*
3121631 A-ATTATTATATAA-TAATTAAATT
1 ATA-T-TTATATAATTAAATAAA-T
*
3121654 ATAATTAT-TAATTAA
1 ATATTTATATAATTAA
3121669 TTAATAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
21 5 0.10
22 33 0.69
23 8 0.17
24 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTTATATAATTAAATAAAT
Found at i:3121619 original size:18 final size:16
Alignment explanation
Indices: 3121596--3121676 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 16
3121586 AATATTTATA
3121596 TAATTAAATAAATATATT
1 TAATTAAATAAATA-A-T
3121614 TAATTAAATAAATAAT
1 TAATTAAATAAATAAT
*
3121630 TAATTATTATATAATAAT
1 TAATTA-AATA-AATAAT
* *
3121648 TAAATTATAATTATTAAT
1 T-AATTA-AATAAATAAT
3121666 TAATT-AATAAA
1 TAATTAAATAAA
3121677 AATAAAATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
15 4 0.07
16 7 0.13
17 8 0.15
18 27 0.50
19 8 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTAAATAAATAAT
Found at i:3121676 original size:25 final size:25
Alignment explanation
Indices: 3121613--3121676 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
3121603 ATAAATATAT
3121613 TTAATTAAATAAATAATTAATTATTA
1 TTAATT-AATAAATAATTAATTATTA
*
3121639 TATAA-TAATTAAATTA-TAATTATTAA
1 T-TAATTAA-TAAATAATTAATTATT-A
3121665 TTAATTAATAAA
1 TTAATTAATAAA
3121677 AATAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
25 17 0.52
26 13 0.39
27 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAATTAATAAATAATTAATTATTA
Found at i:3122677 original size:2 final size:2
Alignment explanation
Indices: 3122670--3122703 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3122660 CAATGAACAG
*
3122670 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3122704 ACTTCATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3123404 original size:20 final size:20
Alignment explanation
Indices: 3123379--3123417 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3123369 AGTGTCAATG
*
3123379 TTTTTATACCTTAGTGACTA
1 TTTTTATACCCTAGTGACTA
3123399 TTTTTATACCCTAGTGACT
1 TTTTTATACCCTAGTGACT
3123418 CATCTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTTTATACCCTAGTGACTA
Found at i:3124481 original size:20 final size:20
Alignment explanation
Indices: 3124456--3124494 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3124446 AGTGTCAATG
*
3124456 TTTTTATACCTTAGTGACTA
1 TTTTTATACCCTAGTGACTA
3124476 TTTTTATACCCTAGTGACT
1 TTTTTATACCCTAGTGACT
3124495 CATATTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTTTATACCCTAGTGACTA
Found at i:3125102 original size:20 final size:20
Alignment explanation
Indices: 3125077--3125117 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3125067 GTAGTATCAA
*
3125077 TGTTTTTATACCTTAGTGAC
1 TGTTTTTATACCCTAGTGAC
3125097 TGTTTTTATACCCTAGTGAC
1 TGTTTTTATACCCTAGTGAC
3125117 T
1 T
3125118 CATCTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (20 bp):
TGTTTTTATACCCTAGTGAC
Found at i:3142701 original size:15 final size:16
Alignment explanation
Indices: 3142678--3142719 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
3142668 TTGATTTATG
*
3142678 TAATTTTTAA-AAAAA
1 TAATATTTAATAAAAA
*
3142693 TAATATTTAATAAAAT
1 TAATATTTAATAAAAA
*
3142709 TTATATTTAAT
1 TAATATTTAAT
3142720 TTTTAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATATTTAATAAAAA
Found at i:3148512 original size:6 final size:7
Alignment explanation
Indices: 3148493--3148533 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
3148483 TGCAATTATT
3148493 TTAAAAA
1 TTAAAAA
3148500 TTAAAAA
1 TTAAAAA
3148507 TTAAAAA
1 TTAAAAA
3148514 TTATAAAA
1 TTA-AAAA
*
3148522 CTTAAAAT
1 -TTAAAAA
3148530 TTAA
1 TTAA
3148534 TATTTACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 21 0.68
8 7 0.23
9 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (7 bp):
TTAAAAA
Done.