Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 131 of 198
Found at i:41702842 original size:5 final size:5
Alignment explanation
Indices: 41702832--41702913 Score: 53
Period size: 5 Copynumber: 16.0 Consensus size: 5
41702822 AATTGAAAAG
* * * * *
41702832 TTTAA TTTAA TTAAA TTCATC TTTATA GTTTAA TTTAA -TTAA ATTCA
1 TTTAA TTTAA TTTAA TTTA-A TTTA-A -TTTAA TTTAA TTTAA TTTAA
41702879 TTT-- TTATAA TTTAA TTTAA TTTAA TTTTAA TTTAA
1 TTTAA TT-TAA TTTAA TTTAA TTTAA -TTTAA TTTAA
41702914 AAGTATCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
3 2 0.03
4 5 0.08
5 40 0.63
6 12 0.19
7 4 0.06
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (5 bp):
TTTAA
Found at i:41702863 original size:28 final size:28
Alignment explanation
Indices: 41702830--41702904 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
41702820 AAAATTGAAA
41702830 AGTTTAATTTAATTAAATTCATCTTTAT
1 AGTTTAATTTAATTAAATTCATCTTTAT
*
41702858 AGTTTAATTTAATTAAATTCATTTTTAT
1 AGTTTAATTTAATTAAATTCATCTTTAT
* *
41702886 AATTTAATTTAATTTAATT
1 AGTTTAATTTAATTAAATT
41702905 TTAATTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (28 bp):
AGTTTAATTTAATTAAATTCATCTTTAT
Found at i:41702906 original size:23 final size:23
Alignment explanation
Indices: 41702834--41702907 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
41702824 TTGAAAAGTT
*
41702834 TAATTTAATTAAATTCATCTTTATA
1 TAATTTAATTAAATTCA-ATTT-TA
*
41702859 GTTTAATTTAATTAAATTCATTTTTA
1 ---TAATTTAATTAAATTCAATTTTA
* *
41702885 TAATTTAATTTAATTTAATTTTA
1 TAATTTAATTAAATTCAATTTTA
41702908 ATTTAAAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 20 0.48
26 2 0.05
27 3 0.07
28 17 0.40
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (23 bp):
TAATTTAATTAAATTCAATTTTA
Found at i:41703277 original size:19 final size:20
Alignment explanation
Indices: 41703239--41703280 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
41703229 CGATCTGATC
*
41703239 AATTCAAAAAATTAATTAAA
1 AATTCAAAAAATTAAATAAA
*
41703259 AATTCAAAATA-TAAATAAA
1 AATTCAAAAAATTAAATAAA
41703278 AAT
1 AAT
41703281 ATATTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AATTCAAAAAATTAAATAAA
Found at i:41707735 original size:42 final size:42
Alignment explanation
Indices: 41707683--41707782 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
41707673 GATCTTGGTA
* **
41707683 TCGCACACTTAGTGCCCGTTATTCGACATCGTCATTTTTGTT
1 TCGCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAATT
41707725 TCGCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAATT
41707767 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
41707783 ATTCGTATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAATT
Found at i:41709540 original size:24 final size:24
Alignment explanation
Indices: 41709503--41709566 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
41709493 AAAGGAAGGC
* *
41709503 GATGAAGATGAAGATGAAAACGAG
1 GATGGAGATAAAGATGAAAACGAG
* * * *
41709527 GGTGGAGATAAAGATAAAAATGAT
1 GATGGAGATAAAGATGAAAACGAG
*
41709551 GATTGAGATAAAGATG
1 GATGGAGATAAAGATG
41709567 TGTACAAGAG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.48, C:0.02, G:0.31, T:0.19
Consensus pattern (24 bp):
GATGGAGATAAAGATGAAAACGAG
Found at i:41714437 original size:45 final size:45
Alignment explanation
Indices: 41714334--41714440 Score: 153
Period size: 46 Copynumber: 2.4 Consensus size: 45
41714324 TATGTGCCGA
*
41714334 TTACTGTTACTGTTACCAATTCGGCACTTTGTGTGTCGAAATACTG
1 TTACTGTTACTGTTA-CAATTCAGCACTTTGTGTGTCGAAATACTG
* *
41714380 TTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTG-AATACTG
1 TTACTGTTACTGTTACA-ATTCAGCACTTTGTGTGTCGAAATACTG
*
41714425 TTACTTTTACTGTTAC
1 TTACTGTTACTGTTAC
41714441 TGTTACCGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 23 0.42
46 32 0.58
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (45 bp):
TTACTGTTACTGTTACAATTCAGCACTTTGTGTGTCGAAATACTG
Found at i:41714461 original size:7 final size:6
Alignment explanation
Indices: 41714420--41714468 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
41714410 GTGTGTTGAA
* *
41714420 TACTGT TACTTT TACTGT TACTGT TACCGT TACTGAT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG-T TACTG
41714469 GTGTGTTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
6 25 0.68
7 12 0.32
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:41722663 original size:27 final size:27
Alignment explanation
Indices: 41722623--41722683 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
41722613 TGCGTATCTG
41722623 CAAAAACATGCAAATCATTCATACAAA
1 CAAAAACATGCAAATCATTCATACAAA
*
41722650 CGAAAACATGCAAATCATTCATACAAA
1 CAAAAACATGCAAATCATTCATACAAA
41722677 CAAAAAC
1 CAAAAAC
41722684 CAAGTTGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (27 bp):
CAAAAACATGCAAATCATTCATACAAA
Found at i:41726443 original size:87 final size:85
Alignment explanation
Indices: 41726160--41726466 Score: 272
Period size: 83 Copynumber: 3.6 Consensus size: 85
41726150 AATTAAATCA
* * * * *
41726160 AAATAAAATCTGTTAGACGACGAAAATAAATCCCGAAATAGA-ATTATTTGA--TTAAGTCTTCG
1 AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAGATTTTATTTAATTTTAAGTCTT-G
*
41726222 TTTGGAAACAAATC-AAGATC
65 TTTGGAAACAAATCAAAGATG
** * * * **
41726242 AAATAAAATCTGTTAAGTGACAGAAATAAATCCCAAAACAGATTTTATTTAATTTTAATTTCTCA
1 AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAGATTTTATTTAATTTTAA-GTCTTG
*
41726307 TTTGGCAACAAA--AAA-ATG
65 TTTGGAAACAAATCAAAGATG
* * ** *
41726325 GAATAAAAT-TCGTTGAACGGGGGGAATAAATCCCGAAACAGATTTTATTTTAATTTTAA-TACT
1 AAATAAAATCT-GTTAAACGACGGAAATAAATCCCGAAACAGATTTTA-TTTAATTTTAAGT-CT
*
41726388 TGTTTGGAAATAAAATCAAAGATG
63 TGTTTGGAAA-CAAATCAAAGATG
* * * * *
41726412 AAATAAAATTTGTTAAACGACGGGAATAAATCTCGGAACAGATTTTATTCAATTT
1 AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAGATTTTATTTAATTT
41726467 AAAATTTTGT
Statistics
Matches: 178, Mismatches: 34, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
82 37 0.21
83 54 0.30
84 16 0.09
85 15 0.08
86 13 0.07
87 42 0.24
88 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (85 bp):
AAATAAAATCTGTTAAACGACGGAAATAAATCCCGAAACAGATTTTATTTAATTTTAAGTCTTGT
TTGGAAACAAATCAAAGATG
Found at i:41726615 original size:6 final size:6
Alignment explanation
Indices: 41726604--41726692 Score: 119
Period size: 6 Copynumber: 14.8 Consensus size: 6
41726594 GCGAACAAAA
41726604 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
** *
41726652 AAATAT AAATAAAT AAATAT TTATAT ATATA- AAATA- AAATA
1 AAATAT AAAT--AT AAATAT AAATAT AAATAT AAATAT AAATA
41726693 AGTTGAATAT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
5 9 0.12
6 62 0.81
8 6 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATAT
Found at i:41736277 original size:2 final size:2
Alignment explanation
Indices: 41736270--41736306 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41736260 TGAATTAAAT
41736270 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
41736307 GCTTTTCACA
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:41736710 original size:13 final size:13
Alignment explanation
Indices: 41736692--41736754 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
41736682 TCTTCATTGT
41736692 TTTTGAAAAGTAC
1 TTTTGAAAAGTAC
41736705 TTTTGAAAAGTAC
1 TTTTGAAAAGTAC
** * *
41736718 AGTGGAAAAGTGC
1 TTTTGAAAAGTAC
* *
41736731 TTTTGAAAACTGC
1 TTTTGAAAAGTAC
41736744 TTTTGAAAAGT
1 TTTTGAAAAGT
41736755 TTGGTTTAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (13 bp):
TTTTGAAAAGTAC
Found at i:41740678 original size:4 final size:4
Alignment explanation
Indices: 41740669--41740933 Score: 530
Period size: 4 Copynumber: 66.2 Consensus size: 4
41740659 ACTAGATTAC
41740669 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41740717 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41740765 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41740813 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41740861 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41740909 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
41740934 TGTTCTTTTA
Statistics
Matches: 261, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 261 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:41745173 original size:38 final size:38
Alignment explanation
Indices: 41745128--41745206 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
41745118 CCAATTTAAA
41745128 ATATTGGAATTTTGTACCAATTAAGTAAAATATAAAAT
1 ATATTGGAATTTTGTACCAATTAAGTAAAATATAAAAT
41745166 ATATTGGAATTTTGTACCAATTAAGTAAAATATAAAAT
1 ATATTGGAATTTTGTACCAATTAAGTAAAATATAAAAT
41745204 ATA
1 ATA
41745207 CTTTTCTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (38 bp):
ATATTGGAATTTTGTACCAATTAAGTAAAATATAAAAT
Found at i:41750192 original size:13 final size:11
Alignment explanation
Indices: 41750147--41750195 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
41750137 AATTTGAGGC
41750147 AAATTA-TTAA
1 AAATTAGTTAA
*
41750157 AAATTACTT-A
1 AAATTAGTTAA
41750167 AAATTAGTTAA
1 AAATTAGTTAA
41750178 AAATTAGTATTAA
1 AAATTAG--TTAA
41750191 AAATT
1 AAATT
41750196 TCAAATACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 15 0.44
11 10 0.29
13 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (11 bp):
AAATTAGTTAA
Found at i:41751595 original size:27 final size:27
Alignment explanation
Indices: 41751552--41751614 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
41751542 ATCTAGGTAT
*
41751552 GCCACAAAGGCAGTTCTTTCAGAGTTC
1 GCCACAAAGCCAGTTCTTTCAGAGTTC
41751579 GCCACAAAGCCTA-TTCTTTCAGAGTTC
1 GCCACAAAGCC-AGTTCTTTCAGAGTTC
*
41751606 GTCACAAAG
1 GCCACAAAG
41751615 GCTTACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (27 bp):
GCCACAAAGCCAGTTCTTTCAGAGTTC
Found at i:41755144 original size:25 final size:26
Alignment explanation
Indices: 41755102--41755155 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
41755092 TTTCTCCTAA
*
41755102 TTTCAATTTTATTTAATTATTTAAT-T
1 TTTCAATTTTATTGAATTA-TTAATAT
41755128 TTTCAA-TTTATTGAATTATTAATAT
1 TTTCAATTTTATTGAATTATTAATAT
41755153 TTT
1 TTT
41755156 ATACTAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAATAT
Found at i:41759524 original size:13 final size:13
Alignment explanation
Indices: 41759508--41759532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41759498 TTACCTTTTA
41759508 ATTTTCTTAGTTC
1 ATTTTCTTAGTTC
41759521 ATTTTCTTAGTT
1 ATTTTCTTAGTT
41759533 AAAATCTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (13 bp):
ATTTTCTTAGTTC
Found at i:41759983 original size:9 final size:9
Alignment explanation
Indices: 41759969--41759993 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41759959 ATTCTTATTA
41759969 ATTTTTAAT
1 ATTTTTAAT
41759978 ATTTTTAAT
1 ATTTTTAAT
41759987 ATTTTTA
1 ATTTTTA
41759994 CAATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:41762453 original size:3 final size:3
Alignment explanation
Indices: 41762445--41762473 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41762435 ATTAAGTTGC
41762445 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
41762474 GAAACATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41772492 original size:80 final size:81
Alignment explanation
Indices: 41772407--41772572 Score: 325
Period size: 81 Copynumber: 2.1 Consensus size: 81
41772397 AAATATAATG
41772407 TTCAAAGTTATATCTTAAATATACAAATTATTATTACAATAT-AAAAAACATACACTAATCAAAC
1 TTCAAAGTTATATCTTAAATATACAAATTATTATTACAATATAAAAAAACATACACTAATCAAAC
41772471 CAATCTTAGTATTACT
66 CAATCTTAGTATTACT
41772487 TTCAAAGTTATATCTTAAATATACAAATTATTATTACAATATAAAAAAACATACACTAATCAAAC
1 TTCAAAGTTATATCTTAAATATACAAATTATTATTACAATATAAAAAAACATACACTAATCAAAC
41772552 CAATCTTAGTATTACT
66 CAATCTTAGTATTACT
41772568 TTCAA
1 TTCAA
41772573 CACAAATCTA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 42 0.49
81 43 0.51
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (81 bp):
TTCAAAGTTATATCTTAAATATACAAATTATTATTACAATATAAAAAAACATACACTAATCAAAC
CAATCTTAGTATTACT
Found at i:41772727 original size:111 final size:111
Alignment explanation
Indices: 41772529--41772750 Score: 324
Period size: 111 Copynumber: 2.0 Consensus size: 111
41772519 ATTACAATAT
* ** * *
41772529 AAAAAAACATACACTAATCAAACCAATCTTAGTATTACTTTCAACACAAATCTAATCATTCAAAC
1 AAAAAAACATACACTAATCAAACCAATCTTAATATTACTTAAAAAAAAAATCTAATCATTCAAAC
41772594 AAAAATATAATGTTCAAAGTTATATATT-AAAATATAAAAATTATTA
66 AAAAATATAATGTTCAAAGTTATAT-TTAAAAATATAAAAATTATTA
* *
41772640 AAAAAAACATGCACTAGTCAAACCAATCTTAATATTACTTAAAAAAAAAATCTAATCATTCAAAC
1 AAAAAAACATACACTAATCAAACCAATCTTAATATTACTTAAAAAAAAAATCTAATCATTCAAAC
*
41772705 AAAAATATAAAT-TT-AAATGTTATATTTAAAAATATACAAATTATTA
66 AAAAATAT-AATGTTCAAA-GTTATATTTAAAAATATAAAAATTATTA
41772751 TTTAAAATTA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
110 5 0.05
111 92 0.92
112 3 0.03
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (111 bp):
AAAAAAACATACACTAATCAAACCAATCTTAATATTACTTAAAAAAAAAATCTAATCATTCAAAC
AAAAATATAATGTTCAAAGTTATATTTAAAAATATAAAAATTATTA
Found at i:41778297 original size:16 final size:17
Alignment explanation
Indices: 41778263--41778307 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
41778253 ATCCACATAA
*
41778263 TATTTTCTTATTTTTTG
1 TATTTTCTTATTTTCTG
41778280 TATTTTCTT-TTTTCTG
1 TATTTTCTTATTTTCTG
*
41778296 TACTTTTTTTAT
1 TA-TTTTCTTAT
41778308 CACTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.33
17 15 0.62
18 1 0.04
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (17 bp):
TATTTTCTTATTTTCTG
Found at i:41789645 original size:13 final size:13
Alignment explanation
Indices: 41789627--41789655 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41789617 GAATTAACTT
41789627 AATTTGATAGTTA
1 AATTTGATAGTTA
41789640 AATTTGATAGTTA
1 AATTTGATAGTTA
41789653 AAT
1 AAT
41789656 ATTAAACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (13 bp):
AATTTGATAGTTA
Found at i:41789863 original size:138 final size:138
Alignment explanation
Indices: 41789706--41790126 Score: 641
Period size: 138 Copynumber: 3.1 Consensus size: 138
41789696 GAGAATATAG
41789706 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * *
41789771 AATATAAATAGTTATATTAATTACTTTCAGCCAAAATATAAAAG-CCTTGAAAATTAATATTCTT
66 AATATAAATAATTATATTAATTAATTTCAGCCAAAATATAAAAGACATAG-AAATTAATATTCTT
41789835 TTGGAAAGA
130 TTGGAAAGA
** *
41789844 ATATAATTAATATATGAATTTGATTCATGTAAAATATTAATTGTATATATTTCACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * * *
41789909 AATATAAACAATTATATTAATTAATTT-TGATCAAAATATAGAAGACATAGACATTAATATTCTT
66 AATATAAATAATTATATTAATTAATTTCAG-CCAAAATATAAAAGACATAGAAATTAATATTCTT
41789973 TTGGAAAGA
130 TTGGAAAGA
* * *
41789982 ATATAATTAAT-TATGTATTTGATTCACACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * *
41790046 AATATAAATAATTATATTAATTAATTTCGGGCAAAATATAAAAGGCATAGAAATTAATATTCTTT
66 AATATAAATAATTATATTAATTAATTTCAGCCAAAATATAAAAGACATAGAAATTAATATTCTTT
41790111 TGGAAAGA
131 TGGAAAGA
41790119 ATATAATT
1 ATATAATT
41790127 TCTTTTTCTA
Statistics
Matches: 256, Mismatches: 24, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
137 121 0.47
138 132 0.52
139 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAATAATTATATTAATTAATTTCAGCCAAAATATAAAAGACATAGAAATTAATATTCTTT
TGGAAAGA
Found at i:41799133 original size:22 final size:22
Alignment explanation
Indices: 41799088--41799150 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 22
41799078 TATGTATATG
41799088 TTTATAAAATGTATTATAATTTATAA
1 TTTATAAAAT-T-TTAT-ATTTAT-A
*
41799114 TTTATAAAATTTTAT-TTTATG
1 TTTATAAAATTTTATATTTATA
41799135 TTT-TAAAATTTT-TATT
1 TTTATAAAATTTTATATT
41799151 CATTTTGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 3 0.09
22 5 0.14
24 4 0.11
25 1 0.03
26 10 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (22 bp):
TTTATAAAATTTTATATTTATA
Found at i:41811358 original size:45 final size:44
Alignment explanation
Indices: 41811303--41811399 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
41811293 CCTGAGCAAT
** *
41811303 AGCGGAGCAGATCGAAGATGGTGAATCTTATCTCCCAGAGATTAC
1 AGCGGAGCAGATCGAAGACAGT-AATCCTATCTCCCAGAGATTAC
* * * *
41811348 AGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 AGCGGAGCAGATCGAAGACAGTAATCCTATCTCCCAGAGATTAC
*
41811392 AGTGGAGC
1 AGCGGAGC
41811400 GGATTAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 26 0.59
45 18 0.41
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (44 bp):
AGCGGAGCAGATCGAAGACAGTAATCCTATCTCCCAGAGATTAC
Found at i:41811529 original size:46 final size:46
Alignment explanation
Indices: 41811457--41811562 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
41811447 TCGCATTAGG
*
41811457 TCTTATCTCCCAGAGATTACAATGGAATAGACCGAAGAATTTCAGA
1 TCTTATCTCCCAGAGATTACAATGGAATAGACCAAAGAATTTCAGA
** *
41811503 TCTTATCTCCTTGAGATTACAGTGGAATAGACCAAAGAATTTCAGA
1 TCTTATCTCCCAGAGATTACAATGGAATAGACCAAAGAATTTCAGA
*
41811549 CCTTATCTCCCAGA
1 TCTTATCTCCCAGA
41811563 TAATGTAGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (46 bp):
TCTTATCTCCCAGAGATTACAATGGAATAGACCAAAGAATTTCAGA
Found at i:41818326 original size:26 final size:27
Alignment explanation
Indices: 41818297--41818349 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
41818287 ATGATCGTAA
*
41818297 TGCCCCTAGAGGGTAAATGACT-ATTT
1 TGCCCCTAGAAGGTAAATGACTGATTT
** *
41818323 TGCCGTTCGAAGGTAAATGACTGATTT
1 TGCCCCTAGAAGGTAAATGACTGATTT
41818350 GTGCTATGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (27 bp):
TGCCCCTAGAAGGTAAATGACTGATTT
Found at i:41824789 original size:187 final size:187
Alignment explanation
Indices: 41824466--41824839 Score: 498
Period size: 187 Copynumber: 2.0 Consensus size: 187
41824456 ACTGAAACTT
** * *
41824466 TTACAAATTATATCGTGATCCAAAATTTATTGCGGAGCATAGAGTATTGAATATCTTTACGGAAA
1 TTACAAATTATATAATGATCCAAAATTTATTGCGGACCATAGAGTATTGAATATCTTTACGAAAA
* ** * * *
41824531 CCCTAGTGTGGTGGAAAGACATATTGTTATATGATTTTACAAATGATTGTCTACGGGCTTGGCAG
66 CCCTAGTGTGGTCGAAAGACATATTGTTATACAATTTTACAAATGATTGCCTACAGGCTTGGCAC
*
41824596 TTTGGTGCCTTAGTGTGGTGTAGTTACTACTCTAACGAGCAACCTGATGTGGTCTAG
131 TTTGGTGCCCTAGTGTGGTGTAGTTACTACTCTAACGAGCAACCTGATGTGGTCTAG
* * * *
41824653 TTACAAATTATATAATGATCCAACATTTGTTGTGGACCATCGAGTATTGAATATCTTTAC-AAAG
1 TTACAAATTATATAATGATCCAAAATTTATTGCGGACCATAGAGTATTGAATATCTTTACGAAA-
** * ** * * * *
41824717 ATGCTAGTGTGGTCTAGGGACGTATTGTTATACAATTTTACAGATGGTTGCCTACAGGCTTTGCA
65 ACCCTAGTGTGGTCGAAAGACATATTGTTATACAATTTTACAAATGATTGCCTACAGGCTTGGCA
* *
41824782 CTTTGGTGCCCTAGTGTGGTGTAGTTACTACTCTAATGAGCAACCTGGTGTGGTCTAG
130 CTTTGGTGCCCTAGTGTGGTGTAGTTACTACTCTAACGAGCAACCTGATGTGGTCTAG
41824840 ATACCTATGT
Statistics
Matches: 160, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
186 2 0.01
187 158 0.99
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (187 bp):
TTACAAATTATATAATGATCCAAAATTTATTGCGGACCATAGAGTATTGAATATCTTTACGAAAA
CCCTAGTGTGGTCGAAAGACATATTGTTATACAATTTTACAAATGATTGCCTACAGGCTTGGCAC
TTTGGTGCCCTAGTGTGGTGTAGTTACTACTCTAACGAGCAACCTGATGTGGTCTAG
Found at i:41828875 original size:20 final size:20
Alignment explanation
Indices: 41828850--41828889 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41828840 ATTTTATATT
41828850 TTGAATTTATGAA-TGTTTTG
1 TTGAATTT-TGAATTGTTTTG
41828870 TTGAATTTTGAATTGTTTTG
1 TTGAATTTTGAATTGTTTTG
41828890 CAATTTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (20 bp):
TTGAATTTTGAATTGTTTTG
Found at i:41842149 original size:19 final size:20
Alignment explanation
Indices: 41842101--41842157 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
41842091 GAAGTCTAGG
*
41842101 CAGAGGCA-CAAATGTGCAAT
1 CAGAGGCACCAAA-GTGCAAA
41842121 CAGAGGCACCAAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
*
41842141 CAG-GGCACCGAAGTGCA
1 CAGAGGCACCAAAGTGCA
41842158 TACTCGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 13 0.38
20 17 0.50
21 4 0.12
ACGTcount: A:0.39, C:0.25, G:0.28, T:0.09
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAA
Found at i:41846862 original size:13 final size:13
Alignment explanation
Indices: 41846844--41846874 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41846834 TAATTTTTAG
41846844 GGTTTGATTCTTA
1 GGTTTGATTCTTA
41846857 GGTTTGATTCTTA
1 GGTTTGATTCTTA
*
41846870 AGTTT
1 GGTTT
41846875 TTCTTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55
Consensus pattern (13 bp):
GGTTTGATTCTTA
Found at i:41847919 original size:17 final size:17
Alignment explanation
Indices: 41847881--41847934 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
41847871 ATTTTATTAA
41847881 TTTATTATTTCAGCTTAATT
1 TTTATTATTTCA--TT-ATT
*
41847901 TTCATT-TTTCATTATT
1 TTTATTATTTCATTATT
*
41847917 TTTATTATTTTATTATT
1 TTTATTATTTCATTATT
41847934 T
1 T
41847935 CCCTTGTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.27
17 12 0.40
19 5 0.17
20 5 0.17
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTATTATTTCATTATT
Found at i:41848025 original size:27 final size:27
Alignment explanation
Indices: 41847987--41848042 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
41847977 ATGATTACAG
41847987 TTGGTATGAAGGAAGAAATGGGATAAT
1 TTGGTATGAAGGAAGAAATGGGATAAT
41848014 TTGGTATGAAGGAAGAAATGGGATAAT
1 TTGGTATGAAGGAAGAAATGGGATAAT
41848041 TT
1 TT
41848043 TTACAATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (27 bp):
TTGGTATGAAGGAAGAAATGGGATAAT
Found at i:41853155 original size:17 final size:17
Alignment explanation
Indices: 41853133--41853166 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41853123 AGGCTTTAGG
41853133 TTTATTTT-TAGTTCTTT
1 TTTATTTTGT-GTTCTTT
41853150 TTTATTTTGTGTTCTTT
1 TTTATTTTGTGTTCTTT
41853167 GGAGAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTATTTTGTGTTCTTT
Found at i:41855179 original size:24 final size:25
Alignment explanation
Indices: 41855152--41855199 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
41855142 TATTGACCAA
41855152 AAAAACAAACGAAAAAGTA-AAAAG
1 AAAAACAAACGAAAAAGTATAAAAG
*
41855176 AAAAATAAACGAAAAAGTATAAAA
1 AAAAACAAACGAAAAAGTATAAAA
41855200 ATAAAATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.75, C:0.06, G:0.10, T:0.08
Consensus pattern (25 bp):
AAAAACAAACGAAAAAGTATAAAAG
Found at i:41861663 original size:10 final size:11
Alignment explanation
Indices: 41861630--41861661 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
41861620 CATAGGAAAT
41861630 TTGTTTTTAAA
1 TTGTTTTTAAA
41861641 TTGTTTTTAAA
1 TTGTTTTTAAA
41861652 TTGTTTTTAA
1 TTGTTTTTAA
41861662 TTTTTATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (11 bp):
TTGTTTTTAAA
Found at i:41867187 original size:14 final size:14
Alignment explanation
Indices: 41867168--41867198 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41867158 GCATCTAATA
*
41867168 AATGAATTAACTAG
1 AATGAATTAACCAG
41867182 AATGAATTAACCAG
1 AATGAATTAACCAG
41867196 AAT
1 AAT
41867199 TTCTTCTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (14 bp):
AATGAATTAACCAG
Found at i:41868206 original size:49 final size:49
Alignment explanation
Indices: 41868129--41868278 Score: 246
Period size: 49 Copynumber: 3.1 Consensus size: 49
41868119 TGATTCATGC
* *
41868129 TATACAATGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATT
1 TATACATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATT
*
41868178 TATACATTGCTAAACTTAGTCTTTCACTGTCTACACTCTTATCACTATT
1 TATACATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATT
* * *
41868227 TATACATTGCTAAACTTAGTCTTCCACTGTCTATATTCTTATCAATATT
1 TATACATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATT
41868276 TAT
1 TAT
41868279 CCCTTCTTGA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 94 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (49 bp):
TATACATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATT
Found at i:41869404 original size:43 final size:43
Alignment explanation
Indices: 41869355--41869436 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
41869345 TCATATTTGA
** *
41869355 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
1 TTTCTCATCAAATAATCATTTCTCAAATTTTCCATTTCAATAT
* *
41869398 TTTCTCATCAAATATTCATTTCTCAAATTTTCTATTTCA
1 TTTCTCATCAAATAATCATTTCTCAAATTTTCCATTTCA
41869437 GTATCGATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (43 bp):
TTTCTCATCAAATAATCATTTCTCAAATTTTCCATTTCAATAT
Found at i:41870646 original size:16 final size:18
Alignment explanation
Indices: 41870625--41870657 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
41870615 CATCTCTTTT
41870625 TCTTTC-TTTT-ATTATA
1 TCTTTCATTTTAATTATA
41870641 TCTTTCATTTTAATTAT
1 TCTTTCATTTTAATTAT
41870658 TATAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTCATTTTAATTATA
Found at i:41870931 original size:15 final size:15
Alignment explanation
Indices: 41870913--41870943 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41870903 TAAATTCATA
41870913 AATATTTAATTAAAT
1 AATATTTAATTAAAT
41870928 AATATTTAATTAAAT
1 AATATTTAATTAAAT
41870943 A
1 A
41870944 TTTATGAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTTAATTAAAT
Found at i:41873119 original size:49 final size:49
Alignment explanation
Indices: 41873046--41873166 Score: 129
Period size: 49 Copynumber: 2.5 Consensus size: 49
41873036 TGAGCATCCA
* * *
41873046 GATATATGGCTC-TTTGGAGCTTCTCGATATTGGCTCACTTGAACCTTCCC
1 GATATATGGCTCATAT-GAGCTTCTCGATAATGGCTCAC-CGAACCTTCCC
* * * * *
41873096 GATAT-TGGCTCGTATGAGCTTCTCGTTAATGGCTCTCCGGAGCTTCCC
1 GATATATGGCTCATATGAGCTTCTCGATAATGGCTCACCGAACCTTCCC
*
41873144 GTTATATGGCTCATATGAGCTTC
1 GATATATGGCTCATATGAGCTTC
41873167 CCGTTTGTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
48 12 0.20
49 41 0.68
50 7 0.12
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (49 bp):
GATATATGGCTCATATGAGCTTCTCGATAATGGCTCACCGAACCTTCCC
Found at i:41873171 original size:25 final size:24
Alignment explanation
Indices: 41873029--41873169 Score: 92
Period size: 25 Copynumber: 5.7 Consensus size: 24
41873019 ACACACCGTA
* *
41873029 GCTCTTATGAGCATCCAGATATATG
1 GCTC-TATGAGCTTCCCGATATATG
* *
41873054 GCTCTTTGGAGCTTCTCGATAT-TG
1 GCTCTAT-GAGCTTCCCGATATATG
*
41873078 GCTC-ACTTGAACCTTCCCGATAT-TG
1 GCTCTA--TG-AGCTTCCCGATATATG
* *
41873103 GCTCGTATGAGCTTCTCGTTA-ATG
1 GCTC-TATGAGCTTCCCGATATATG
** *
41873127 GCTCTCCGGAGCTTCCCGTTATATG
1 GCTCT-ATGAGCTTCCCGATATATG
41873152 GCTCATATGAGCTTCCCG
1 GCTC-TATGAGCTTCCCG
41873170 TTTGTGTGCT
Statistics
Matches: 91, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
23 1 0.01
24 36 0.40
25 52 0.57
26 1 0.01
27 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (24 bp):
GCTCTATGAGCTTCCCGATATATG
Found at i:41874257 original size:27 final size:27
Alignment explanation
Indices: 41874195--41874257 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
41874185 TAACAGTAAC
*
41874195 AGTACAGTGTGGGCCTTAGCCCAATAT
1 AGTACAGTGTGGGCCTAAGCCCAATAT
**
41874222 AAAAACAGTGT-GGCCTAAGCCCAATAT
1 -AGTACAGTGTGGGCCTAAGCCCAATAT
41874249 AGTATCAGT
1 AGTA-CAGT
41874258 ATGGTGCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
AGTACAGTGTGGGCCTAAGCCCAATAT
Found at i:41874440 original size:22 final size:21
Alignment explanation
Indices: 41874386--41874450 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
41874376 TACCAGTAGC
41874386 CAGAATGGCTAAGAGCCATAAA
1 CAGAATGGCTAA-AGCCATAAA
* ** *
41874408 CAGGACAGCTATAAGCTATAAA
1 CAGAATGGCTA-AAGCCATAAA
41874430 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTA-AAGCCATAA
41874451 GTACAGTAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (21 bp):
CAGAATGGCTAAAGCCATAAA
Found at i:41874497 original size:32 final size:31
Alignment explanation
Indices: 41874442--41874612 Score: 164
Period size: 32 Copynumber: 5.4 Consensus size: 31
41874432 GAATGGCTAC
* *
41874442 AAGCCATAAGTACAGTAATATGATTGGCACA
1 AAGCCATCAGTACAGTAATATGATCGGCACA
* * * * *
41874473 AAGCCATTAGTAGCATTGATATGATCGACGCA
1 AAGCCATCAGTA-CAGTAATATGATCGGCACA
* * * *
41874505 CAGTCATTAGTA-ATGGTAATATGACCGGCACA
1 AAGCCATCAGTACA--GTAATATGATCGGCACA
* *
41874537 AAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGT-ACAGTAATATGATCGGCACA
*
41874569 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGT-ACAGTAATATGATCGGCACA
41874601 AAGCCATCAGTA
1 AAGCCATCAGTA
41874613 GCATCGCAGC
Statistics
Matches: 115, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
30 1 0.01
31 12 0.10
32 101 0.88
33 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (31 bp):
AAGCCATCAGTACAGTAATATGATCGGCACA
Found at i:41874559 original size:64 final size:64
Alignment explanation
Indices: 41874442--41874612 Score: 209
Period size: 64 Copynumber: 2.7 Consensus size: 64
41874432 GAATGGCTAC
* * * * * * * *
41874442 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATTAGTAGCATTGATATGATCGACGCA
1 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAACAGTAATATGATCGACACA
* * * * * *
41874505 CAGTCATTAGTAATGGTAATATGACCGGCACAAAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAACAGTAATATGATCGACACA
41874569 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTA
1 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTA
41874613 GCATCGCAGC
Statistics
Matches: 89, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
63 8 0.09
64 81 0.91
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (64 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAACAGTAATATGATCGACACA
Found at i:41874686 original size:27 final size:27
Alignment explanation
Indices: 41874656--41874715 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
41874646 AACAAAGCTG
41874656 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAATAGTGAT-TGTGG-CAGAGCCA
41874683 CCAGTAATAGTGATTGTGGCAGAGCCA
1 CCAGTAATAGTGATTGTGGCAGAGCCA
41874710 CCAGTA
1 CCAGTA
41874716 CAGTACATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.06
27 27 0.87
28 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (27 bp):
CCAGTAATAGTGATTGTGGCAGAGCCA
Found at i:41874816 original size:24 final size:24
Alignment explanation
Indices: 41874794--41874858 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
41874784 ATTAGTCATT
41874794 CAAATCACAAACAAATCAATCATAC
1 CAAA-CACAAACAAATCAATCATAC
*
41874819 CAAACACAGACAAATCAATCATAC
1 CAAACACAAACAAATCAATCATAC
41874843 CAAACACAAACAAATC
1 CAAACACAAACAAATC
41874859 TGCCATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 34 0.89
25 4 0.11
ACGTcount: A:0.57, C:0.29, G:0.02, T:0.12
Consensus pattern (24 bp):
CAAACACAAACAAATCAATCATAC
Found at i:41874961 original size:27 final size:27
Alignment explanation
Indices: 41874928--41875641 Score: 1076
Period size: 27 Copynumber: 26.6 Consensus size: 27
41874918 CCACTAGGGC
*
41874928 ATTACGGTCATTTTACCCTACAGTGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41874955 ATTACGGTTATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41874982 ATTACGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875009 ATTACGGTCATTCTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41875036 ATTACGGTTATTTTACCCTACA-GGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41875062 ATTACGGTCATTTTACCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41875089 ATTATGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
41875116 ATTACGATCATTTTATCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875143 ATTACGGTTATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875170 ATTACGGTCATTCTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
41875197 ATTACGGTCATTTTACCCTACA-GGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875223 ATTACGGTTATTTTACCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
41875250 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875277 ATTACGGTCATTTTATCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41875304 ATTACGGTCATTTTACCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41875331 ATTATGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875358 ATTACGGTCATTTTATCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875385 ATTACGGTTATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875412 ATTACGGTCATTCTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
41875439 ATTACGGTCATTTTACCCTACA-GGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875465 ATTACGGTTATTTTACCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
41875492 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875519 ATTACGGTCATTTTATCCTACAGAGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41875546 ATTACGATCATTTTATCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41875573 ATTACGGTCAGTTTA-CCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41875599 GTTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
41875626 ATTACGGTCATTTTAC
1 ATTACGGTCATTTTAC
41875642 AACCTTTTCG
Statistics
Matches: 618, Mismatches: 65, Indels: 8
0.89 0.09 0.01
Matches are distributed among these distances:
26 99 0.16
27 519 0.84
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:41875199 original size:161 final size:162
Alignment explanation
Indices: 41874928--41875641 Score: 1094
Period size: 161 Copynumber: 4.4 Consensus size: 162
41874918 CCACTAGGGC
* * * *
41874928 ATTACGGTCATTTTACCCTACAGTGGTATTACGGTTATTTTACCCTATAGGGGTATTACGGTCAT
1 ATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGAGGTATTACGGTCAT
* * *
41874993 TTTACCCTACAGGGGCATTACGGTCATTCTACCCTACAAGGGTATTACGGTTATTTTACCCTACA
66 TTTACCCTACAGAGGCATTACGGTCATTCTACCCTACAGGGGTATTACGGTCATTTTACCCTACA
41875058 G-GGTATTACGGTCATTTTACCCTACAGAGGT
131 GAGGTATTACGGTCATTTTACCCTACAGAGGT
* * * *
41875089 ATTATGGTCATTTTACCCTACAGGGGTATTACGATCATTTTATCCTACAGAGGTATTACGGTTAT
1 ATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGAGGTATTACGGTCAT
* *
41875154 TTTACCCTACAGGGGCATTACGGTCATTCTACCCTATAGGGGTATTACGGTCATTTTACCCTACA
66 TTTACCCTACAGAGGCATTACGGTCATTCTACCCTACAGGGGTATTACGGTCATTTTACCCTACA
*
41875219 G-GGTATTACGGTTATTTTACCCTACAGAGGT
131 GAGGTATTACGGTCATTTTACCCTACAGAGGT
*
41875250 ATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTATCCTACAGAGGTATTACGGTCAT
1 ATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGAGGTATTACGGTCAT
* * * *
41875315 TTTACCCTACAGAGGTATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTATCCTACA
66 TTTACCCTACAGAGGCATTACGGTCATTCTACCCTACAGGGGTATTACGGTCATTTTACCCTACA
* * *
41875380 GAGGTATTACGGTTATTTTACCCTACAGGGGC
131 GAGGTATTACGGTCATTTTACCCTACAGAGGT
* * *
41875412 ATTACGGTCATTCTACCCTATAGGGGTATTACGGTCATTTTACCCTACAG-GGTATTACGGTTAT
1 ATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGAGGTATTACGGTCAT
* * *
41875476 TTTACCCTACAGAGGTATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTATCCTACA
66 TTTACCCTACAGAGGCATTACGGTCATTCTACCCTACAGGGGTATTACGGTCATTTTACCCTACA
* * *
41875541 GAGGTATTACGATCATTTTATCCTACAGGGGT
131 GAGGTATTACGGTCATTTTACCCTACAGAGGT
* * *
41875573 ATTACGGTCAGTTTA-CCTACAGGGGTGTTACGGTCATTTTACCCTACAGGGGTATTACGGTCAT
1 ATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGAGGTATTACGGTCAT
41875637 TTTAC
66 TTTAC
41875642 AACCTTTTCG
Statistics
Matches: 514, Mismatches: 37, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
160 32 0.06
161 407 0.79
162 75 0.15
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (162 bp):
ATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGAGGTATTACGGTCAT
TTTACCCTACAGAGGCATTACGGTCATTCTACCCTACAGGGGTATTACGGTCATTTTACCCTACA
GAGGTATTACGGTCATTTTACCCTACAGAGGT
Found at i:41878304 original size:37 final size:37
Alignment explanation
Indices: 41878246--41878321 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
41878236 CCTGGCCACA
41878246 ATGGCGTGTGTCCCCTACACCTTGGAAAAATTTTGAT
1 ATGGCGTGTGTCCCCTACACCTTGGAAAAATTTTGAT
* * *
41878283 ATGGTGTGTGTCCCCTGCACCTTGGAAAATTTTTGAT
1 ATGGCGTGTGTCCCCTACACCTTGGAAAAATTTTGAT
41878320 AT
1 AT
41878322 TTTGCGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (37 bp):
ATGGCGTGTGTCCCCTACACCTTGGAAAAATTTTGAT
Found at i:41879328 original size:14 final size:14
Alignment explanation
Indices: 41879309--41879336 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41879299 ACCAAAAAAT
41879309 AAATAATTAAATAA
1 AAATAATTAAATAA
41879323 AAATAATTAAATAA
1 AAATAATTAAATAA
41879337 TCCAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAATTAAATAA
Found at i:41886628 original size:50 final size:47
Alignment explanation
Indices: 41886532--41887021 Score: 174
Period size: 44 Copynumber: 10.8 Consensus size: 47
41886522 AACAGGTCAA
* * *
41886532 TGAAGCCACT--AATCCTATATCCCTGAAGTTGCAGTG--GGATGGAT
1 TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTGAAGCAT-GAT
*
41886576 TGAAGTCATCATAGTGAATCTTATCTCCCTGAAGTTGCAGTGAAGCAT-AT
1 TGAAGCCA-C-TA--GAATCTTATCTCCCTGAAGTTGCAGTGAAGCATGAT
* *
41886626 TGAAGCCACTAG--TCTTATCTCCCTAAAGTTGCAGTGAAGC--GAC
1 TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTGAAGCATGAT
* * * *
41886669 TGAAG--A-TAGCGAATCTTATTTCCCTAAAGTTGTAGTG--GAATAGAT
1 TGAAGCCACTA--GAATCTTATCTCCCTGAAGTTGCAGTGAAGCAT-GAT
* * * *
41886714 TAAAGCTA-TAAATTGCAAATCTTATCTCTCTGAAGTTGCAGT-AAGGCA-GAA
1 TGAAGCCACT--A--G--AATCTTATCTCCCTGAAGTTGCAGTGAA-GCATGAT
* * *
41886765 TAAAGCTA-TA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCATG-T
1 TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTGAAGCATGAT
** * * * *
41886809 AT-AAGTTAC-A-AGTCTTATCTCCCTGAAGTTGTAGTG--GAATAGAC
1 -TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTGAAGCAT-GAT
* *
41886853 TGAAG--A-TAGCAAATCTTATCTCTCTGAAGTTGCAGT-AGAGCA-GAA
1 TGAAGCCACTAG--AATCTTATCTCCCTGAAGTTGCAGTGA-AGCATGAT
* ** * *
41886898 TAAAGTTA-TA-AACCTTATCTCCCTGAAGTTGCAGTGGAGCATG-T
1 TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTGAAGCATGAT
** * * * *
41886942 TGAAGTTAC-A-AGTCTTATCTCCCTGAAGTTGTAGTGGAGCA-GAA
1 TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTGAAGCATGAT
* * * *
41886986 TAAAGCTA-TA-AACCTTATCTCCCTGAAGTTACAGTG
1 TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTG
41887022 GAGTAGGTTG
Statistics
Matches: 351, Mismatches: 49, Indels: 92
0.71 0.10 0.19
Matches are distributed among these distances:
40 2 0.01
41 1 0.00
42 7 0.02
43 9 0.03
44 208 0.59
45 39 0.11
46 2 0.01
47 7 0.02
48 2 0.01
49 4 0.01
50 33 0.09
51 32 0.09
52 3 0.01
53 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (47 bp):
TGAAGCCACTAGAATCTTATCTCCCTGAAGTTGCAGTGAAGCATGAT
Found at i:41886686 original size:44 final size:43
Alignment explanation
Indices: 41886592--41887382 Score: 338
Period size: 44 Copynumber: 17.6 Consensus size: 43
41886582 CATCATAGTG
* ** *
41886592 AATCTTATCTCCCTGAAGTTGCAGTGAAGCATATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGC-GATTGAAGATACA
* * * *
41886636 AGTCTTATCTCCCTAAAGTTGCAGTGAAGCGACTGAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCGATTGAAGATA-CA
* * * ** *
41886680 AATCTTATTTCCCTAAAGTTGTAGTGGAATAGATTAAAGCTATAAATTGCA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGCGATTGAAG--AT--A---CA
* * * * *
41886731 AATCTTATCTCTCTGAAGTTGCAGT-AAGGCAGAATAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGAA-GC-GATTGAAGATACA
* * *
41886775 AATCTTATCTCCCTGAAGTTGCAGTGGAGC-ATGTATAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCGAT-T-GAAGATACA
* * ** *
41886819 AGTCTTATCTCCCTGAAGTTGTAGTGGAATAGACTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGCGATTGAAGATA-CA
* * * * *
41886864 AATCTTATCTCTCTGAAGTTGCAGT-AGAGCAGAATAAAGTTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGA-AGC-GATTGAAGATACA
* * *
41886908 AACCTTATCTCCCTGAAGTTGCAGTGGAGC-ATGTTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCGA--TTGAAGATACA
* * * * * * *
41886952 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGC-GATTGAAGATACA
* * * * * *
41886996 AACCTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAG-CGATTGAAGATACA
* * * ** ** *
41887040 AGTCTTATCTCCCTAAATTTTTAGTGGAATAGACTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGCGATTGAAGATA-CA
* * * * * *
41887085 AATCTTATCTCTCTGAAGTTGCAGT-AGAGTAGAATAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGA-AG-CGATTGAAGATACA
* * * * * *
41887129 AACCTTATCTCTCTGAAGTTGCAATGGAGCAGGTTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGC-GATTGAAGATACA
* * * * * *
41887173 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGC-GATTGAAGATA-CA
* * * *
41887218 AATCTTATTTCCCTGAAGTTACAGTGCAA-CAGATT-AAGGTTGCA
1 AATCTTATCTCCCTGAAGTTGCAGTG-AAGC-GATTGAA-GATACA
* * **
41887262 AATTACAATCAGATCTCCCTGAAGTTGCAATGGGGCAGATTGAAGATACA
1 AA-T-C--T--TATCTCCCTGAAGTTGCAGTGAAGC-GATTGAAGATACA
* * * * * * *
41887312 AGTCTTATCTCTCTAAAGTTGTAGTGGAGTAGACTGAAGATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAG-CGATTGAAGAT-ACA
*
41887357 AATCTTATCTCTCC-AAAGTTGCAGTG
1 AATCTTATCTC-CCTGAAGTTGCAGTG
41887383 GAATAGATCG
Statistics
Matches: 563, Mismatches: 140, Indels: 87
0.71 0.18 0.11
Matches are distributed among these distances:
42 2 0.00
43 10 0.02
44 343 0.61
45 132 0.23
46 6 0.01
47 3 0.01
48 2 0.00
49 5 0.01
50 28 0.05
51 32 0.06
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGAAGCGATTGAAGATACA
Found at i:41886989 original size:221 final size:221
Alignment explanation
Indices: 41886733--41887243 Score: 792
Period size: 221 Copynumber: 2.3 Consensus size: 221
41886723 AAATTGCAAA
* * *
41886733 TCTTATCTCTCTGAAGTTGCAGT-AAGGCAGAATAAAGCTATAAATCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGAATAAAGCTATAAATCTTATCTCCCTGAAGTTAC
* *
41886797 AGTGGAGCATGTAT-AAGTTACAAGTCTTATCTCCCTGAAGTTGTAGTGGAATAGACTGAAGATA
65 AGTGGAGCAGGT-TGAAGTTACAAGTCTTATCTCCCTAAAGTTGTAGTGGAATAGACTGAAGATA
*
41886861 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAATAAAGTTATAAACCTTATCTCCCTGAAG
129 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAATAAAGCTATAAACCTTATCTCCCTGAAG
* *
41886926 TTGCAGTGGAGCATGTTGAAGTTACAAG
194 TTGCAATGGAGCAGGTTGAAGTTACAAG
* *
41886954 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGCTATAAACCTTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAGCTATAAATCTTATCTCCCTGAAGTTACA
* * *
41887019 GTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCTAAATTTTTAGTGGAATAGACTGAAGATAGC
66 GTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGTAGTGGAATAGACTGAAGATAGC
* *
41887084 AAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAATAAAGCTATAAACCTTATCTCTCTGAAGTT
131 AAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAATAAAGCTATAAACCTTATCTCCCTGAAGTT
41887149 GCAATGGAGCAGGTTGAAGTTACAAG
196 GCAATGGAGCAGGTTGAAGTTACAAG
* * * ** *
41887175 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAGCTA-TAAATCTTATCTCCCTGAAGTTAC
41887240 AGTG
65 AGTG
41887244 CAACAGATTA
Statistics
Matches: 264, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
220 1 0.00
221 238 0.90
222 25 0.09
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (221 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAGCTATAAATCTTATCTCCCTGAAGTTACA
GTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGTAGTGGAATAGACTGAAGATAGC
AAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAATAAAGCTATAAACCTTATCTCCCTGAAGTT
GCAATGGAGCAGGTTGAAGTTACAAG
Found at i:41887207 original size:133 final size:133
Alignment explanation
Indices: 41886595--41887389 Score: 688
Period size: 133 Copynumber: 5.9 Consensus size: 133
41886585 CATAGTGAAT
* * ** *
41886595 CTTATCTCCCTGAAGTTGCAGTGAAGCATATTGAAGCCACTAGTCTTATCTCCCTAAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAG
* * * * * *
41886660 TGAAGC-GACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGTAGTGGAATAGATTAAAGCTATA
66 TGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGAATAAAGCTATA
41886724 AATTGC
131 AA---C
* * * * * * * *
41886730 AAATCTTATCTCTCTGAAGTTGCAGT-AAGGCAGAATAAAGCTATAAATCTTATCTCCCTGAAGT
1 ----CTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGT
* * * * *
41886794 TGCAGTGGAGCATGTA-T-AAGTTA-CAAGTCTTATCTCCCTGAAGTTGTAGTGGAATAGACTGA
61 TGCAGTGGAGCA-G-ACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGAATAA
* * *
41886856 AGATAGCAAAT
124 AGCTA-TAAAC
* * * * * ** *
41886867 CTTATCTCTCTGAAGTTGCAGTAGAGCAGAATAAAGTTATAAACCTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAG
* * * * **
41886932 TGGAGCATG-TTGAAGTTA-CAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGCTAT
66 TGGAGCA-GACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGAATAAAGCTAT
41886995 AAAC
130 AAAC
* * * * **
41886999 CTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCTAAATTTTTAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAG
** * * *
41887064 TGGAATAGACTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAATAAAGCTATA
66 TGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGAATAAAGCTATA
41887129 AAC
131 AAC
* * *
41887132 CTTATCTCTCTGAAGTTGCAATGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAG
* * * * * * * *
41887197 TGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGAAGTTACAGTGCAACAGATTAAGGTTGCA
66 TGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGAATAA---AGC-
* *
41887262 AATTACAAT
127 TA-TA-AAC
** * * * * *
41887271 CAGATCTCCCTGAAGTTGCAATGGGGCAGATTGAAGATACAAGTCTTATCTCTCTAAAGTTGTAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAG
* * *
41887336 TGGAGTAGACTGAAGATAACAAATCTTATCTCTCC-AAAGTTGCAGTGGAATAGA
66 TGGAGCAGACTGAAGATAGCAAATCTTATCTC-CCTGAAGTTGCAGTGGAATAGA
41887390 TCGAAGTGAC
Statistics
Matches: 547, Mismatches: 92, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
131 1 0.00
132 67 0.12
133 262 0.48
134 1 0.00
136 2 0.00
137 1 0.00
138 4 0.01
139 196 0.36
140 10 0.02
141 2 0.00
142 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (133 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAG
TGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGAATAAAGCTATA
AAC
Found at i:41890176 original size:30 final size:31
Alignment explanation
Indices: 41890142--41890201 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
41890132 AAAGCTTTTA
*
41890142 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
** *
41890172 TTTTCCCTTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
41890202 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:41892348 original size:29 final size:29
Alignment explanation
Indices: 41892316--41892547 Score: 250
Period size: 29 Copynumber: 8.0 Consensus size: 29
41892306 TTGATTATCG
*
41892316 ACTATGAAAAGGGATGGTGATGACCATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
41892345 ACTATGAAAAGGGATGGTGACGACCATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
* * ** *
41892374 AATATGAAAAGGGATAGTTTCGACTATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
*
41892403 ACTATGAAAAGGGATGGTGACAACCATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
* * *
41892432 ACTATTAAAAGGGATGGCGACGACCATCG
1 ACTATGAAAAGGGATGGTGACGACCATCA
* * **
41892461 ATTAATGAAAAGAGATGGTTTCGACCATCA
1 ACT-ATGAAAAGGGATGGTGACGACCATCA
* * * * *
41892491 AATATGAAAAAGGATTGTGACAATCATCGA
1 ACTATGAAAAGGGATGGTGACGACCATC-A
* *
41892521 A-TATGAAAAGGGATGCTTACGACCATC
1 ACTATGAAAAGGGATGGTGACGACCATC
41892548 GTTTAGCACA
Statistics
Matches: 164, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
29 140 0.85
30 24 0.15
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (29 bp):
ACTATGAAAAGGGATGGTGACGACCATCA
Found at i:41892442 original size:87 final size:88
Alignment explanation
Indices: 41892281--41892547 Score: 331
Period size: 87 Copynumber: 3.0 Consensus size: 88
41892271 TATCGACAAG
* * * * * **
41892281 CATCAATTAAAGAAAAGGGATAGTTTTGATTATCGACTATGAAAAGGGATGGTGATGACCATCAA
1 CATCAAATAATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGGTGACAACCATCAA
41892346 CTATGAAAAGGGATGGTGACGAC
66 CTATGAAAAGGGATGGTGACGAC
41892369 CATCAAAT-ATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGGTGACAACCATCAA
1 CATCAAATAATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGGTGACAACCATCAA
* *
41892433 CTATTAAAAGGGATGGCGACGAC
66 CTATGAAAAGGGATGGTGACGAC
* * * * * * * * *
41892456 CATCGATTAATGAAAAGAGATGGTTTCGACCATCAAATATGAAAAAGGATTGTGACAATCATCGA
1 CATCAAATAATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGGTGACAACCATC-A
* *
41892521 A-TATGAAAAGGGATGCTTACGAC
65 ACTATGAAAAGGGATGGTGACGAC
41892544 CATC
1 CATC
41892548 GTTTAGCACA
Statistics
Matches: 155, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
87 77 0.50
88 76 0.49
89 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (88 bp):
CATCAAATAATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGGTGACAACCATCAA
CTATGAAAAGGGATGGTGACGAC
Found at i:41892511 original size:88 final size:87
Alignment explanation
Indices: 41892318--41892548 Score: 295
Period size: 88 Copynumber: 2.6 Consensus size: 87
41892308 GATTATCGAC
** * *
41892318 TATGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGGATGGTGACGACCATCAAATATGAAA
1 TATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGATGGCGACGACCATCGAATATGAAA
* * *
41892383 AGGGATAGTTTCGACTATCAAC
66 AGAGATAGTTTCGACCATCAAA
* *
41892405 TATGAAAAGGGATGGTGACAACCATCAACTATTAAAAGGGATGGCGACGACCATCGATTAATGAA
1 TATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGATGGCGACGACCATCGAAT-ATGAA
*
41892470 AAGAGATGGTTTCGACCATCAAA
65 AAGAGATAGTTTCGACCATCAAA
* * * *
41892493 TATGAAAAAGGATTGTGACAATCATCGAA-TATGAAAAGGGAT-GCTTACGACCATCG
1 TATGAAAAGGGATGGTGACAACCATC-AACTATGAAAAGGGATGGC-GACGACCATCG
41892549 TTTAGCACAC
Statistics
Matches: 126, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
87 55 0.44
88 69 0.55
89 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (87 bp):
TATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGATGGCGACGACCATCGAATATGAAA
AGAGATAGTTTCGACCATCAAA
Found at i:41897096 original size:28 final size:27
Alignment explanation
Indices: 41897032--41897092 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
41897022 AAATATTAAT
*
41897032 TAAACTAATTATATTAATTATCCTAAAA
1 TAAA-TAATTAAATTAATTATCCTAAAA
*
41897060 TAACATAATTAAATTAATTAAT-GTAAAA
1 TAA-ATAATTAAATTAATT-ATCCTAAAA
41897088 TAAAT
1 TAAAT
41897093 TAATGGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 2 0.07
28 24 0.83
29 3 0.10
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATAATTAAATTAATTATCCTAAAA
Found at i:41902759 original size:18 final size:18
Alignment explanation
Indices: 41902736--41902778 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
41902726 AAAATTCAAA
41902736 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
41902754 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
41902772 ATGTAAA
1 ATATAAA
41902779 AACAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:41905943 original size:3 final size:3
Alignment explanation
Indices: 41905890--41905923 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
41905880 CAAGATATAG
41905890 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41905924 CTTATTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41916174 original size:18 final size:18
Alignment explanation
Indices: 41916153--41916212 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
41916143 TTGACGACCA
41916153 TGATGATGAGCTTGTATC
1 TGATGATGAGCTTGTATC
*
41916171 TGATGA--A-TTTGATGATC
1 TGATGATGAGCTTG-T-ATC
41916188 TGGATGATGAGCTTGTATC
1 T-GATGATGAGCTTGTATC
41916207 TGATGA
1 TGATGA
41916213 ATTTGATGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 4 0.12
18 16 0.47
19 4 0.12
20 2 0.06
21 3 0.09
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.38
Consensus pattern (18 bp):
TGATGATGAGCTTGTATC
Found at i:41916176 original size:36 final size:36
Alignment explanation
Indices: 41916129--41916234 Score: 160
Period size: 36 Copynumber: 2.9 Consensus size: 36
41916119 CATTGGAAAG
* *
41916129 TGTATCTGATGAAGTTGACGACCATGATGATGAGCT
1 TGTATCTGATGAATTTGATGACCATGATGATGAGCT
*
41916165 TGTATCTGATGAATTTGATGATC-TGGATGATGAGCT
1 TGTATCTGATGAATTTGATGACCAT-GATGATGAGCT
*
41916201 TGTATCTGATGAATTTGATGACCAAGATGATGAG
1 TGTATCTGATGAATTTGATGACCATGATGATGAG
41916235 TTTGATGAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
35 1 0.02
36 62 0.98
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.34
Consensus pattern (36 bp):
TGTATCTGATGAATTTGATGACCATGATGATGAGCT
Found at i:41926424 original size:50 final size:50
Alignment explanation
Indices: 41926362--41926675 Score: 250
Period size: 50 Copynumber: 6.3 Consensus size: 50
41926352 GATCTGTAAT
* * *
41926362 CTTCAATTTGTTCAACTGCAATGTTGGGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
* * * * *** * *
41926412 CTTCAATCTGTTCCACCGCACTGTCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
* * * *
41926462 CTTCAATCTTTTAAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
* * * * * *** * * *
41926512 CTTCAATCTGTTCCACCGCACTGCTAAGGAAGTAAGATCCACCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
* * * * *
41926562 CTTCAATCTTTTAAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
* * * * *** * *
41926612 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
*
41926662 CTTCAATCTTTTCA
1 CTTCAATCTGTTCA
41926676 CTTTTCAACC
Statistics
Matches: 192, Mismatches: 72, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 192 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
Found at i:41926492 original size:100 final size:100
Alignment explanation
Indices: 41926378--41926673 Score: 513
Period size: 100 Copynumber: 3.0 Consensus size: 100
41926368 TTTGTTCAAC
* * * *
41926378 TGCAATGTTGGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACCGCACTG-TCAGGGA
1 TGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACTGCT-AAGGA
41926442 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
41926478 TGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACTGCTAAGGAA
1 TGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACTGCTAAGGAA
*
41926543 GTAAGATCCACCGTTGTGGCTTCAATCTTTTAAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
* *
41926578 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACTGCTAAGGAA
41926643 GTAAGATCCGCCGTTGTGGCTTCAATCTTTT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTT
41926674 CACTTTTCAA
Statistics
Matches: 187, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
100 186 0.99
101 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (100 bp):
TGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
Found at i:41934772 original size:20 final size:20
Alignment explanation
Indices: 41934733--41934772 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41934723 TAAAGGTCTT
**
41934733 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCAATGC
41934753 TAATGCATATGATGCAATGC
1 TAATGCATATGATGCAATGC
41934773 ATGAGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCAATGC
Found at i:41938270 original size:14 final size:15
Alignment explanation
Indices: 41938248--41938293 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
41938238 AATTTACAGC
41938248 ATATACAAATA-AAT
1 ATATACAAATACAAT
* *
41938262 ATTTACAAATATAA-
1 ATATACAAATACAAT
41938276 ATATACAAATACAAT
1 ATATACAAATACAAT
41938291 ATA
1 ATA
41938294 ACCGTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATACAAATACAAT
Found at i:41968232 original size:13 final size:13
Alignment explanation
Indices: 41968216--41968255 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
41968206 TTTAAACTAA
41968216 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
* *
41968229 ACTTCTCAAAAGC
1 ACTTTTCAAAAGT
41968242 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
41968255 A
1 A
41968256 ATGAAGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:41969105 original size:21 final size:20
Alignment explanation
Indices: 41969076--41969126 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
41969066 TATAGGTAGT
*
41969076 AATAGAATTTGTATTAAAATA
1 AATAAAATTT-TATTAAAATA
** *
41969097 AATAAAATTTTATTTTAATG
1 AATAAAATTTTATTAAAATA
41969117 AATAAAATTT
1 AATAAAATTT
41969127 CTTAATGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
AATAAAATTTTATTAAAATA
Found at i:41970904 original size:20 final size:20
Alignment explanation
Indices: 41970858--41970951 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
41970848 GTTAGTATGC
*
41970858 TTGCACCTCGGTG-CCTCTGT
1 TTGCACTTCGGTGCCCT-TGT
* *
41970878 ATACACTTCGGTGCCCTTGT
1 TTGCACTTCGGTGCCCTTGT
*
41970898 TTGCACTACGGTGCCCTTGT
1 TTGCACTTCGGTGCCCTTGT
* ** *
41970918 TTTCACATT-TATGCCCCTGT
1 TTGCAC-TTCGGTGCCCTTGT
*
41970938 CTGCACTTCGGTGC
1 TTGCACTTCGGTGC
41970952 TCCTGTTATA
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.04
20 50 0.89
21 4 0.07
ACGTcount: A:0.11, C:0.32, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCACTTCGGTGCCCTTGT
Found at i:41980799 original size:20 final size:22
Alignment explanation
Indices: 41980760--41980800 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41980750 TAGGTACCAA
*
41980760 GTTGTGACGTTGGACGTTTGTG
1 GTTGTGACGTAGGACGTTTGTG
41980782 GTTGTGACG-AGG-CGTTTGT
1 GTTGTGACGTAGGACGTTTGT
41980801 TTTTGGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.10, C:0.10, G:0.41, T:0.39
Consensus pattern (22 bp):
GTTGTGACGTAGGACGTTTGTG
Found at i:41982682 original size:14 final size:13
Alignment explanation
Indices: 41982667--41982719 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
41982657 TCTATTTTTC
41982667 TTTTCTTTAATTT
1 TTTTCTTTAATTT
*
41982680 CTTTACTTTAATTT
1 -TTTTCTTTAATTT
* *
41982694 TGTTCTTATTATTT
1 TTTTCTT-TAATTT
*
41982708 TTATCTTTAATT
1 TTTTCTTTAATT
41982720 ACTTAACATT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTCTTTAATTT
Found at i:41988391 original size:18 final size:18
Alignment explanation
Indices: 41988368--41988405 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
41988358 TACTAAAAAA
41988368 GAATGAGAAGTTTGTGTG
1 GAATGAGAAGTTTGTGTG
*
41988386 GAATGAGAATTTTGTGTG
1 GAATGAGAAGTTTGTGTG
41988404 GA
1 GA
41988406 GCAACAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (18 bp):
GAATGAGAAGTTTGTGTG
Found at i:41992888 original size:51 final size:51
Alignment explanation
Indices: 41992808--41992995 Score: 231
Period size: 51 Copynumber: 3.7 Consensus size: 51
41992798 TATCGATGAA
* * *
41992808 CACGTGTGTAGTACTATGTGAAGGCTACTACATGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* * *
41992859 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* * *
41992910 CACGTGTGTAGTACTATGTGGAGGCTACTACGTGGACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGGT
*
41992960 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
41992996 TCGAATGATA
Statistics
Matches: 117, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
50 40 0.34
51 76 0.65
52 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:41997063 original size:13 final size:13
Alignment explanation
Indices: 41997045--41997071 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41997035 AGCCTATCGT
41997045 ATGTGAATGTGCA
1 ATGTGAATGTGCA
41997058 ATGTGAATGTGCA
1 ATGTGAATGTGCA
41997071 A
1 A
41997072 GTATACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (13 bp):
ATGTGAATGTGCA
Found at i:42003738 original size:2 final size:2
Alignment explanation
Indices: 42003731--42003769 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42003721 TATAGTAGTA
42003731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42003770 AAAGTCAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42004079 original size:19 final size:18
Alignment explanation
Indices: 42004042--42004091 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
42004032 AAATGTATAA
42004042 AATAAAATAA-AAAGACT
1 AATAAAATAATAAAGACT
*
42004059 AATAATAATAATAATGACT
1 AATAA-AATAATAAAGACT
42004078 AATAAAAATAATAA
1 AAT-AAAATAATAA
42004092 CAATAAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 17 0.59
20 2 0.07
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (18 bp):
AATAAAATAATAAAGACT
Found at i:42005255 original size:5 final size:5
Alignment explanation
Indices: 42005247--42005277 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
42005237 ATTTGGTTTG
42005247 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
42005278 GTATGTGGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:42014704 original size:45 final size:45
Alignment explanation
Indices: 42014640--42014726 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
42014630 TTCTAACTCA
* * *
42014640 GTGGATTCAGCACATAGCAACCGCCTTATTAATCAATGATGTCTG
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTG
*
42014685 GTGGAATCTGCACATAGCAACCACCTTACTAATCAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
42014727 TCGGTTCACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTG
Found at i:42014796 original size:51 final size:50
Alignment explanation
Indices: 42014728--42014923 Score: 214
Period size: 51 Copynumber: 3.9 Consensus size: 50
42014718 CAATGATGTT
* * * *
42014728 CGGTTCACATAGTAGCCTGCACATACTACTACACATTTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATC
* * ** * *
42014779 CGATACACGTAGTAGCCTGCACATAGTACTACACAAGTGATTGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * * *
42014830 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
* *
42014880 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
42014924 CACTTTCACT
Statistics
Matches: 117, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.33
51 75 0.64
52 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:42014911 original size:101 final size:101
Alignment explanation
Indices: 42014735--42014919 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
42014725 GTTCGGTTCA
** *
42014735 CATAGTAGCCTGCACATACTACTACACATTTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATACTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTACA
42014800 CATAGTACTACACAAGTGATTGAAACTATCCGGTACG
65 CATAGTACTACACAAGTGATTGAAACTATCCGGTACG
* * *
42014837 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTACA
1 CATAGTAGCCTGCACATACTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTACA
*
42014901 CATAGTACTACACACGTGA
65 CATAGTACTACACAAGTGA
42014920 CCATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.52
102 32 0.43
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATACTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTACAC
ATAGTACTACACAAGTGATTGAAACTATCCGGTACG
Found at i:42016835 original size:15 final size:15
Alignment explanation
Indices: 42016815--42016845 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42016805 TTTTACTTAG
*
42016815 TAGTTTTATTTAATT
1 TAGTTTAATTTAATT
42016830 TAGTTTAATTTAATT
1 TAGTTTAATTTAATT
42016845 T
1 T
42016846 TTACAGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TAGTTTAATTTAATT
Found at i:42033040 original size:4 final size:4
Alignment explanation
Indices: 42033031--42033055 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42033021 AGTACTCGTT
42033031 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
42033056 TTGCTAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:42033705 original size:22 final size:23
Alignment explanation
Indices: 42033680--42033727 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
42033670 TCTATTCTTA
42033680 TTTTA-TT-TTATTTTATTACACT
1 TTTTATTTCTTATTTTATTA-ACT
42033702 TTTTATTTCCTTATTTTATTAACT
1 TTTTATTT-CTTATTTTATTAACT
42033726 TT
1 TT
42033728 ATCAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.22
23 2 0.09
24 5 0.22
25 11 0.48
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATTTCTTATTTTATTAACT
Found at i:42034399 original size:36 final size:37
Alignment explanation
Indices: 42034327--42034399 Score: 130
Period size: 38 Copynumber: 2.0 Consensus size: 37
42034317 TTGGGATAAG
42034327 CACAATACTAGTAGTGTTTATAATGTCAATCTCCTTTA
1 CACAATACTAGTAGTGTTTATAA-GTCAATCTCCTTTA
42034365 CACAATACTAGTAGTGTTTATAA-TCAATCTCCTTT
1 CACAATACTAGTAGTGTTTATAAGTCAATCTCCTTT
42034400 CTTCTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 12 0.34
38 23 0.66
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (37 bp):
CACAATACTAGTAGTGTTTATAAGTCAATCTCCTTTA
Found at i:42040600 original size:13 final size:13
Alignment explanation
Indices: 42040584--42040647 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
42040574 TTTAAACCAA
42040584 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
42040597 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
42040610 ACTTTTC-CATGTC
1 ACTTTTCAAAAG-C
*
42040623 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
42040636 ACTTTTCAAAAG
1 ACTTTTCAAAAG
42040648 TATTGCCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.05
13 38 0.93
14 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:42044943 original size:4 final size:4
Alignment explanation
Indices: 42044934--42044975 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
42044924 TTTAATGTAC
* *
42044934 ATAA ATAA ATAA ATAAA ACAA AAAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA A
42044976 GGCTCAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 31 0.91
5 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (4 bp):
ATAA
Found at i:42046627 original size:17 final size:17
Alignment explanation
Indices: 42046599--42046639 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
42046589 GTAATTACAA
42046599 AATTTGAATTTAATTTCC
1 AATTT-AATTTAATTTCC
42046617 AATTTAATTTAATTTCC
1 AATTTAATTTAATTTCC
*
42046634 TATTTA
1 AATTTA
42046640 TGTTGTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTAATTTAATTTCC
Found at i:42047163 original size:31 final size:31
Alignment explanation
Indices: 42047124--42047189 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
42047114 ACATAATATT
* *
42047124 TATA-GGAAAGATATATGATATATTCCTAAA
1 TATATGGAAAGATACATAATATATTCCTAAA
42047154 TATATGGAAAGATACATAATATATTCCTAAA
1 TATATGGAAAGATACATAATATATTCCTAAA
42047185 TATAT
1 TATAT
42047190 ACCTAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (31 bp):
TATATGGAAAGATACATAATATATTCCTAAA
Found at i:42047254 original size:31 final size:28
Alignment explanation
Indices: 42047216--42047312 Score: 142
Period size: 28 Copynumber: 3.4 Consensus size: 28
42047206 ATATATGTAG
42047216 ATATTCCTAAAAGACAATATCTCATAATAAT
1 ATATTCCTAAAAG---ATATCTCATAATAAT
*
42047247 ATATTCCTAAAAGATATATCATAATAAT
1 ATATTCCTAAAAGATATCTCATAATAAT
42047275 ATATTCCTAAAAGATATCTCATAATAAT
1 ATATTCCTAAAAGATATCTCATAATAAT
42047303 A-ATATCCTAA
1 ATAT-TCCTAA
42047313 CACCCCGCTC
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.03
28 48 0.76
31 13 0.21
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.34
Consensus pattern (28 bp):
ATATTCCTAAAAGATATCTCATAATAAT
Found at i:42047263 original size:13 final size:13
Alignment explanation
Indices: 42047214--42047291 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 13
42047204 CAATATATGT
42047214 AGATATTCCTAAA
1 AGATATTCCTAAA
*
42047227 AGACAATATCTCATAATA
1 AG---ATAT-TCCTAA-A
*
42047245 ATATATTCCTAAA
1 AGATATTCCTAAA
*
42047258 AGATATATCATAATA
1 AGATAT-TCCTAA-A
*
42047273 ATATATTCCTAAA
1 AGATATTCCTAAA
42047286 AGATAT
1 AGATAT
42047292 CTCATAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
13 14 0.28
14 15 0.30
15 10 0.20
16 4 0.08
17 5 0.10
18 2 0.04
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (13 bp):
AGATATTCCTAAA
Found at i:42047272 original size:28 final size:28
Alignment explanation
Indices: 42047183--42047312 Score: 138
Period size: 28 Copynumber: 4.5 Consensus size: 28
42047173 TATATTCCTA
*
42047183 AATATATACCTAAAAGATATA-CAATATAT
1 AATATATTCCTAAAAGATATATC-ATA-AT
* * *
42047212 GTAGATATTCCTAAAAGACAATATCTCATAAT
1 -AATATATTCCTAAAAG---ATATATCATAAT
42047244 AATATATTCCTAAAAGATATATCATAAT
1 AATATATTCCTAAAAGATATATCATAAT
*
42047272 AATATATTCCTAAAAGATATCTCATAAT
1 AATATATTCCTAAAAGATATATCATAAT
42047300 AATA-ATATCCTAA
1 AATATAT-TCCTAA
42047313 CACCCCGCTC
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
27 2 0.02
28 48 0.55
30 13 0.15
31 14 0.16
32 2 0.02
33 7 0.08
34 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (28 bp):
AATATATTCCTAAAAGATATATCATAAT
Found at i:42047288 original size:59 final size:58
Alignment explanation
Indices: 42047183--42047312 Score: 160
Period size: 61 Copynumber: 2.2 Consensus size: 58
42047173 TATATTCCTA
* *
42047183 AATATATACCTAAAAGATATACAATATATGTAGATATTCCTAAAAGACAATATCTCATAAT
1 AATATATTCCTAAAAGATATACAATATATGAAGATATTCCTAAAAG---ATATCTCATAAT
*
42047244 AATATATTCCTAAAAGATATATC-ATA-AT-AATATATTCCTAAAAGATATCTCATAAT
1 AATATATTCCTAAAAGATATA-CAATATATGAAGATATTCCTAAAAGATATCTCATAAT
42047300 AATA-ATATCCTAA
1 AATATAT-TCCTAA
42047313 CACCCCGCTC
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
55 2 0.03
56 22 0.34
59 14 0.22
60 2 0.03
61 23 0.36
62 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (58 bp):
AATATATTCCTAAAAGATATACAATATATGAAGATATTCCTAAAAGATATCTCATAAT
Found at i:42051003 original size:24 final size:24
Alignment explanation
Indices: 42050959--42051004 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
42050949 TCATGTGAAA
*
42050959 ATATACTCATTCAAATTTAATTTC
1 ATATACTCACTCAAATTTAATTTC
*
42050983 ATAT-CTCACTCAGATTCTAATT
1 ATATACTCACTCAAATT-TAATT
42051005 CAATTTCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATACTCACTCAAATTTAATTTC
Found at i:42051998 original size:46 final size:45
Alignment explanation
Indices: 42051945--42052127 Score: 276
Period size: 46 Copynumber: 4.0 Consensus size: 45
42051935 ATGCTATAAT
* *
42051945 TCAGTATGGTTTCCTTCACTGAAATATCATACCTACTTTTCACAAC
1 TCAGTATGGTTT-CTTCACTGAAACACCATACCTACTTTTCACAAC
*
42051991 TCAGTATGGTTTTCTTCACTGAAACACCATACCTGCTTTTCACAAC
1 TCAGTATGG-TTTCTTCACTGAAACACCATACCTACTTTTCACAAC
*
42052037 TCAGTATGGTCTTCTTCACAGAAACACCATACCTACTTTTCACAAC
1 TCAGTATGGT-TTCTTCACTGAAACACCATACCTACTTTTCACAAC
* *
42052083 TTAGTATGGCTTTCTTCACTGAAATACCATACCTACTTTTCACAA
1 TCAGTATGG-TTTCTTCACTGAAACACCATACCTACTTTTCACAA
42052128 TTTTTCCATG
Statistics
Matches: 126, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
45 1 0.01
46 121 0.96
47 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.35
Consensus pattern (45 bp):
TCAGTATGGTTTCTTCACTGAAACACCATACCTACTTTTCACAAC
Found at i:42053374 original size:17 final size:17
Alignment explanation
Indices: 42053352--42053399 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
42053342 AAATTCTTTT
42053352 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
42053369 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
42053386 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
42053400 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:42059194 original size:29 final size:29
Alignment explanation
Indices: 42059131--42059223 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
42059121 GTTACACAGT
* * **
42059131 CGTGTGGTAGGTCATGTGGATCACACGGC
1 CGTGTGGTAGGCCATGTGGGTCACACAAC
*
42059160 CATGTGGTAGGCCATGTGGGTCACACAAC
1 CGTGTGGTAGGCCATGTGGGTCACACAAC
* * * * * * *
42059189 TGTGTGGCAAGCCGTGTAGGTCACACGAT
1 CGTGTGGTAGGCCATGTGGGTCACACAAC
42059218 CGTGTG
1 CGTGTG
42059224 CCAGGTCGTG
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.24
Consensus pattern (29 bp):
CGTGTGGTAGGCCATGTGGGTCACACAAC
Found at i:42059348 original size:29 final size:29
Alignment explanation
Indices: 42059287--42059348 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
42059277 CAAACGGCTG
** * *
42059287 TGTGGCAAACCATATGGGTCACATGGTCT
1 TGTGGCAAACCATATGGGTCACACAGCCA
* *
42059316 TGTGGCAAACCGTGTGGGTCACACAGCCA
1 TGTGGCAAACCATATGGGTCACACAGCCA
42059345 TGTG
1 TGTG
42059349 TCAGGCCTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.24
Consensus pattern (29 bp):
TGTGGCAAACCATATGGGTCACACAGCCA
Found at i:42066269 original size:87 final size:87
Alignment explanation
Indices: 42066129--42066602 Score: 714
Period size: 87 Copynumber: 5.4 Consensus size: 87
42066119 AAGATTTGTC
* * *
42066129 ATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGTTGTTA
1 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
***
42066194 ATATAGGAAGGCAAGATCTGCT
66 ACGCAGGAAGGCAAGATCTGCT
** * * * *
42066216 ATCTTTAACCAGCTCCACTGTAACCGATTGAGGCAAGGCTTTGTTTCCAATCTGCTTCGCTGTCA
1 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
*
42066281 ATGCAGGAAGGCAAGATCTGCT
66 ACGCAGGAAGGCAAGATCTGCT
*** * * *
42066303 ATCTTTAATTGGCTCCACTACAATCAATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTA
1 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
42066368 ACGCAGGAAGGCAAGATCTGCT
66 ACGCAGGAAGGCAAGATCTGCT
* *
42066390 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCCTTGTTTTCAATCTGCTTCGCTGTTA
1 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
*
42066455 ACGCAGGAAGGCAAGATCTGTT
66 ACGCAGGAAGGCAAGATCTGCT
* * * *
42066477 ATCTTTAACCAGCTCCACTACAACTGATGGAGGTAAGGCTTTGTTTTCGATCTGCGTCGCTGTTT
1 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
42066542 ACGCAGGAAGGCAAGATCTGCT
66 ACGCAGGAAGGCAAGATCTGCT
42066564 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGC
1 ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGC
42066603 CTGTATCTTC
Statistics
Matches: 347, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 347 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
ATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
ACGCAGGAAGGCAAGATCTGCT
Found at i:42067857 original size:7 final size:7
Alignment explanation
Indices: 42067840--42067874 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
42067830 TCTATTTTAC
42067840 TTTTCATT
1 TTTTCA-T
42067848 TTTTCAT
1 TTTTCAT
42067855 TTTTCA-
1 TTTTCAT
42067861 TTTTCAT
1 TTTTCAT
42067868 TTTTCAT
1 TTTTCAT
42067875 CTCTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.23
7 14 0.54
8 6 0.23
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:42067864 original size:13 final size:13
Alignment explanation
Indices: 42067848--42067874 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42067838 ACTTTTCATT
42067848 TTTTCATTTTTCA
1 TTTTCATTTTTCA
42067861 TTTTCATTTTTCA
1 TTTTCATTTTTCA
42067874 T
1 T
42067875 CTCTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:42068354 original size:12 final size:13
Alignment explanation
Indices: 42068320--42068354 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
42068310 CTGTCTTTCT
42068320 TTTTG-TTTTTGA
1 TTTTGATTTTTGA
42068332 TTTTGATTTTTGA
1 TTTTGATTTTTGA
42068345 -TTTGATTTTT
1 TTTTGATTTTT
42068355 TTTTTGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.74
Consensus pattern (13 bp):
TTTTGATTTTTGA
Found at i:42068355 original size:32 final size:31
Alignment explanation
Indices: 42068264--42068341 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
42068254 TCATATTTTA
* * *
42068264 TTTTGACTTTGATTGAT-T-TCTCTTTTTTGC
1 TTTTGACTTTGATT-TTCTGTCTTTTTTTTGT
42068294 TTTTGACTTTGATTTTCTGTCTTTCTTTTTGT
1 TTTTGACTTTGATTTTCTGTCTTT-TTTTTGT
*
42068326 TTTTGATTTTGATTTT
1 TTTTGACTTTGATTTT
42068342 TGATTTGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.02
30 15 0.37
31 4 0.10
32 21 0.51
ACGTcount: A:0.09, C:0.10, G:0.13, T:0.68
Consensus pattern (31 bp):
TTTTGACTTTGATTTTCTGTCTTTTTTTTGT
Found at i:42069019 original size:150 final size:150
Alignment explanation
Indices: 42068748--42069038 Score: 564
Period size: 150 Copynumber: 1.9 Consensus size: 150
42068738 ATCTTTGAGG
*
42068748 TCAGGTCAATTTTAATCTTTACCAAGCTCACAATTTTTTATAATTCCTTGAGAGGTAGGGTCTGT
1 TCAGGTCAATTTTAATCTTTACCAAGCTCACAATTTTTTATAATTCCTTGAGAGGTAGGATCTGT
42068813 TTATCCTCTTGTTCTACCATCCTCGACAAGTTCGGAGATAAGCTACGATCTATGTCATTTCCAAA
66 TTATCCTCTTGTTCTACCATCCTCGACAAGTTCGGAGATAAGCTACGATCTATGTCATTTCCAAA
42068878 GCCATGAGATCTGTTTATCC
131 GCCATGAGATCTGTTTATCC
*
42068898 TCAGGTCAATTTTAATCTTTACCAAGTTCACAATTTTTTATAATTCCTTGAGAGGTAGGATCTGT
1 TCAGGTCAATTTTAATCTTTACCAAGCTCACAATTTTTTATAATTCCTTGAGAGGTAGGATCTGT
42068963 TTATCCTCTTGTTCTACCATCCTCGACAAGTTCGGAGATAAGCTACGATCTATGTCATTTCCAAA
66 TTATCCTCTTGTTCTACCATCCTCGACAAGTTCGGAGATAAGCTACGATCTATGTCATTTCCAAA
42069028 GCCATGAGATC
131 GCCATGAGATC
42069039 CGTCTAAACA
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 139 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (150 bp):
TCAGGTCAATTTTAATCTTTACCAAGCTCACAATTTTTTATAATTCCTTGAGAGGTAGGATCTGT
TTATCCTCTTGTTCTACCATCCTCGACAAGTTCGGAGATAAGCTACGATCTATGTCATTTCCAAA
GCCATGAGATCTGTTTATCC
Found at i:42074451 original size:20 final size:20
Alignment explanation
Indices: 42074415--42074461 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
42074405 AAATATCTAT
42074415 TTTTCT-TTTATTCGTTGCTG
1 TTTTCTGTTTATTCGTTGC-G
*
42074435 TTTTCTGTTT-TTTGTTGCG
1 TTTTCTGTTTATTCGTTGCG
*
42074454 TTTGCTGT
1 TTTTCTGT
42074462 GTCTTTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
20 13 0.54
21 3 0.12
ACGTcount: A:0.02, C:0.13, G:0.19, T:0.66
Consensus pattern (20 bp):
TTTTCTGTTTATTCGTTGCG
Found at i:42075410 original size:37 final size:36
Alignment explanation
Indices: 42075310--42075431 Score: 122
Period size: 37 Copynumber: 3.3 Consensus size: 36
42075300 AATCCATCCA
* *
42075310 AAAACATGCCAAATGCTCATAAGAGCTAATCCAA-CTG
1 AAAACACGCCAATTGCTCA-AAGAGCTAATCCAATC-G
* *
42075347 -ATACACGCCAATTGCTCGGAAGAGCTAATCCAATCG
1 AAAACACGCCAATTGCTC-AAAGAGCTAATCCAATCG
* * * *
42075383 AAAACATGCCAATTGCTTCAAAAAGCTAGTCCAATTG
1 AAAACACGCCAATTGC-TCAAAGAGCTAATCCAATCG
42075420 AAAACACGCCAA
1 AAAACACGCCAA
42075432 AATAGGGAGT
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
36 29 0.41
37 39 0.56
38 2 0.03
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (36 bp):
AAAACACGCCAATTGCTCAAAGAGCTAATCCAATCG
Found at i:42076594 original size:26 final size:26
Alignment explanation
Indices: 42076574--42076627 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
42076564 AATTTAGTCC
42076574 TTTTTCTTTAATTAACTATTTAAACA
1 TTTTTCTTTAATTAACTATTTAAACA
42076600 TTTTTCTTTAATTAACTATTTAAACA
1 TTTTTCTTTAATTAACTATTTAAACA
42076626 TT
1 TT
42076628 AAAATTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTTCTTTAATTAACTATTTAAACA
Found at i:42077920 original size:31 final size:28
Alignment explanation
Indices: 42077885--42077941 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 28
42077875 ATATATTTAG
42077885 ATATTCCTAAAAGACAATATCCCATAATAGT
1 ATATTCCTAAAAG---ATATCCCATAATAGT
**
42077916 ATATTTTTAAAAGATATCCCATAATA
1 ATATTCCTAAAAGATATCCCATAATA
42077942 ATAAGATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
31 11 0.46
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (28 bp):
ATATTCCTAAAAGATATCCCATAATAGT
Found at i:42089223 original size:24 final size:24
Alignment explanation
Indices: 42089196--42089281 Score: 109
Period size: 24 Copynumber: 3.6 Consensus size: 24
42089186 AGAATTAATA
42089196 AAGATCATTCATGTATATTCAATC
1 AAGATCATTCATGTATATTCAATC
* * *
42089220 AAGACCAGTCATGTATATTCACTC
1 AAGATCATTCATGTATATTCAATC
* * *
42089244 AAGGTCATTCACGTATATTTAATC
1 AAGATCATTCATGTATATTCAATC
*
42089268 AAAATCATTCATGT
1 AAGATCATTCATGT
42089282 GTACTTGCAT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (24 bp):
AAGATCATTCATGTATATTCAATC
Found at i:42089488 original size:20 final size:20
Alignment explanation
Indices: 42089440--42089491 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
42089430 AGGCATTGAG
* *
42089440 GTGCAAAGAGAGACACCAAA
1 GTGCAAACAAAGACACCAAA
**
42089460 GTGTGAACAAAGACACCAAA
1 GTGCAAACAAAGACACCAAA
42089480 GTGCAAACAAAG
1 GTGCAAACAAAG
42089492 GAATCGAAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.23, T:0.08
Consensus pattern (20 bp):
GTGCAAACAAAGACACCAAA
Found at i:42093143 original size:38 final size:38
Alignment explanation
Indices: 42093100--42093223 Score: 176
Period size: 38 Copynumber: 3.3 Consensus size: 38
42093090 CAATGAGTCA
*
42093100 ATAACCATTTCCATGGTGTCGCTCCGTAGAGCCAGTAG
1 ATAACCATTTCCATGGTGTCGCTCCGAAGAGCCAGTAG
* * *
42093138 ATAACCATTTTCATGGTGTCGCTTCGAAGAGTCAGTAG
1 ATAACCATTTCCATGGTGTCGCTCCGAAGAGCCAGTAG
* * *
42093176 ATAACCATTTCTATGGTCTTGCTCCGAAGAGCCAGTAG
1 ATAACCATTTCCATGGTGTCGCTCCGAAGAGCCAGTAG
*
42093214 ATAAACATTT
1 ATAACCATTT
42093224 TCATCCAATC
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (38 bp):
ATAACCATTTCCATGGTGTCGCTCCGAAGAGCCAGTAG
Found at i:42095489 original size:56 final size:57
Alignment explanation
Indices: 42095416--42095531 Score: 155
Period size: 56 Copynumber: 2.1 Consensus size: 57
42095406 CTAGGTCATT
* * *
42095416 TTTCATTTTCATTTTGGACAAAACCA-AATTCATTTGCAAATGATTCT-ATTTCTCCA
1 TTTCATTTTCATTTTGGACAAAACAATAAAT-ATTTGCAAATCATTCTCATTTCTCCA
* * *
42095472 TTTCATTTTCATTTTGGAGAAAACAATAAATATTTTCAAATCTTTCTCATTTCTCCA
1 TTTCATTTTCATTTTGGACAAAACAATAAATATTTGCAAATCATTCTCATTTCTCCA
42095529 TTT
1 TTT
42095532 TCACCATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 37 0.71
57 15 0.29
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (57 bp):
TTTCATTTTCATTTTGGACAAAACAATAAATATTTGCAAATCATTCTCATTTCTCCA
Found at i:42100295 original size:17 final size:17
Alignment explanation
Indices: 42100275--42100310 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42100265 GATCAATGGT
42100275 CTCATGGGATCTATTAA
1 CTCATGGGATCTATTAA
42100292 CTCATGGGATCTATTAA
1 CTCATGGGATCTATTAA
42100309 CT
1 CT
42100311 ATGTAAGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (17 bp):
CTCATGGGATCTATTAA
Found at i:42108841 original size:36 final size:36
Alignment explanation
Indices: 42108801--42108890 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 36
42108791 TCAAAATCAA
*
42108801 CTTAAAAAAGGTTGGGATAGACCAT-TCTATGCAAAC
1 CTTAAAAAAGGTTGGGATAGA-CATGTCTAAGCAAAC
**
42108837 CTT-AAAAAGGTTGGGATAGACATGTCTAAGGTAAC
1 CTTAAAAAAGGTTGGGATAGACATGTCTAAGCAAAC
*
42108872 CTTAAAAAA-GTTAGGATAG
1 CTTAAAAAAGGTTGGGATAG
42108891 GCCTTTTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 3 0.06
35 37 0.77
36 8 0.17
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (36 bp):
CTTAAAAAAGGTTGGGATAGACATGTCTAAGCAAAC
Done.