Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:618843 original size:25 final size:24
Alignment explanation
Indices: 618809--618869 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
618799 CCTGTGATTT
**
618809 ATATACGTGGTAAGGCCACGGGTTG
1 ATATACGTGGT-AGGCCACAAGTTG
618834 ATATACGTGGCTAGGCCACAAGTTG
1 ATATACGTGG-TAGGCCACAAGTTG
*
618859 ATGTACGTGGT
1 ATATACGTGGT
618870 TGTGACCACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (24 bp):
ATATACGTGGTAGGCCACAAGTTG
Found at i:620021 original size:67 final size:67
Alignment explanation
Indices: 619938--620073 Score: 173
Period size: 67 Copynumber: 2.0 Consensus size: 67
619928 GAAAAGTTAG
* * * * * * * *
619938 TTTTGGGTTTTGGTTGATCCCAAGAAAACCCATTGTTGAAGGTTGTGGCTGAGCTTGTGAAAAGC
1 TTTTGAGTTTAGGTTGATCCCAAGAAAAACCATTGCTAAAGGTTGAGACTGAGCCTGTGAAAAGC
620003 CA
66 CA
* * *
620005 TTTTGAGTTTAGGTTGATCCTATGAAAAACCATTGCTAAAGGTTGAGACTGAGCCTGTGAAATGC
1 TTTTGAGTTTAGGTTGATCCCAAGAAAAACCATTGCTAAAGGTTGAGACTGAGCCTGTGAAAAGC
620070 CA
66 CA
620072 TT
1 TT
620074 GTAAAAACTT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (67 bp):
TTTTGAGTTTAGGTTGATCCCAAGAAAAACCATTGCTAAAGGTTGAGACTGAGCCTGTGAAAAGC
CA
Found at i:626040 original size:13 final size:14
Alignment explanation
Indices: 626024--626067 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
626014 CCTTTTGCTG
626024 TTTCTTTTTTCT-T
1 TTTCTTTTTTCTCT
626037 TTTCTTTTTT-TCT
1 TTTCTTTTTTCTCT
*
626050 TTTCTTTCTTTCTGT
1 TTTCTTT-TTTCTCT
626065 TTT
1 TTT
626068 TCCTTCCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 18 0.67
14 3 0.11
15 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTTCTCT
Found at i:626061 original size:8 final size:7
Alignment explanation
Indices: 626024--626069 Score: 51
Period size: 6 Copynumber: 6.6 Consensus size: 7
626014 CCTTTTGCTG
626024 TTTCTTT
1 TTTCTTT
626031 TTTC-TT
1 TTTCTTT
626037 TTTCTTT
1 TTTCTTT
*
626044 TTT-TCT
1 TTTCTTT
626050 TTTCTTT
1 TTTCTTT
626057 CTTTCTGTT
1 -TTTCT-TT
626066 TTTC
1 TTTC
626070 CTTCCAAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
6 11 0.33
7 11 0.33
8 9 0.27
9 2 0.06
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTCTTT
Found at i:627739 original size:31 final size:29
Alignment explanation
Indices: 627680--627739 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
627670 ATTGGTATTC
*
627680 ATTCATGATTGAATGTTCACTTTGAATAT
1 ATTCATGATTGAATGTTCACTTTCAATAT
* *
627709 ATTCATGAGTTGAGTGTTTTACTTTCAATAT
1 ATTCATGA-TTGAATG-TTCACTTTCAATAT
627740 TCTATAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 6 0.23
31 12 0.46
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (29 bp):
ATTCATGATTGAATGTTCACTTTCAATAT
Found at i:631209 original size:35 final size:34
Alignment explanation
Indices: 631170--631268 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 34
631160 TTGATATTAG
631170 GAAAAACCATTGTTGAAGTTTGTGGCTGAGCCAGT
1 GAAAAACCATTGTTGAAGTTTGTGGCTGAGCC-GT
* * * *
631205 GAAAAGCCATT-TTGGA-TTT-TGGTTGATCTCGT
1 GAAAAACCATTGTTGAAGTTTGTGGCTGAGC-CGT
* * *
631237 GAAAAACCATTGTTAAAGGTTGTGGCTAAGCC
1 GAAAAACCATTGTTGAAGTTTGTGGCTGAGCC
631269 TATAAAAAGC
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
32 19 0.39
33 7 0.14
34 7 0.14
35 16 0.33
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31
Consensus pattern (34 bp):
GAAAAACCATTGTTGAAGTTTGTGGCTGAGCCGT
Found at i:633070 original size:29 final size:28
Alignment explanation
Indices: 633013--633269 Score: 183
Period size: 29 Copynumber: 8.9 Consensus size: 28
633003 GGTAGCTTTT
* *
633013 ACATGTTTGTCTTAATTTATAAAAAAAA
1 ACATGTTTGTCTTAATTTAGACAAAAAA
* * *
633041 ATATGTTTGGTCTAAATTTAGACAATAAA
1 ACATGTTT-GTCTTAATTTAGACAAAAAA
* * *
633070 ACATGCTTTGCCTTAATTTGGACAAGAAA
1 ACATG-TTTGTCTTAATTTAGACAAAAAA
*
633099 ACATGTTTGTCTTAATTTAAGATAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAA-AAAA
* * * *
633129 CCATGTTTTGACTTAATCTA-AGCAAGAAA
1 ACATG-TTTGTCTTAATTTAGA-CAAAAAA
* * * ***
633158 TCATGTTTGTCTCAATTTACACAAGGTA
1 ACATGTTTGTCTTAATTTAGACAAAAAA
* * *
633186 ACATGTTTTGGCTTAATCTAGACAAGAAA
1 ACATG-TTTGTCTTAATTTAGACAAAAAA
* * *
633215 ACATGTTTGTCTCAATTTAAACAAAATA
1 ACATGTTTGTCTTAATTTAGACAAAAAA
* *
633243 ACATATTTTGTCTTAATTAAAGACAAA
1 ACAT-GTTTGTCTTAATT-TAGACAAA
633270 GTTGTCTTAA
Statistics
Matches: 177, Mismatches: 42, Indels: 18
0.75 0.18 0.08
Matches are distributed among these distances:
28 60 0.34
29 87 0.49
30 19 0.11
31 11 0.06
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAAAAA
Found at i:633213 original size:57 final size:57
Alignment explanation
Indices: 633038--633259 Score: 230
Period size: 57 Copynumber: 3.8 Consensus size: 57
633028 TTTATAAAAA
* * * * * * * * *
633038 AAAATATGTTTGGTCTAAATTTAGACAATAAAACATGCTTTGCCTTAATTTGGACAAG
1 AAAACATGTTT-GTCTCAATTTAAACAAGATAACATGTTTTGACTTAATCTAGACAAG
* * *
633096 AAAACATGTTTGTCTTAATTTAAGATAAGAAAACCATGTTTTGACTTAATCTA-AGCAAG
1 AAAACATGTTTGTCTCAATTTAA-ACAAGATAA-CATGTTTTGACTTAATCTAGA-CAAG
* * * *
633155 AAATCATGTTTGTCTCAATTTACACAAGGTAACATGTTTTGGCTTAATCTAGACAAG
1 AAAACATGTTTGTCTCAATTTAAACAAGATAACATGTTTTGACTTAATCTAGACAAG
* * *
633212 AAAACATGTTTGTCTCAATTTAAACAAAATAACATATTTTGTCTTAAT
1 AAAACATGTTTGTCTCAATTTAAACAAGATAACATGTTTTGACTTAAT
633260 TAAAGACAAA
Statistics
Matches: 138, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
57 74 0.54
58 25 0.18
59 39 0.28
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (57 bp):
AAAACATGTTTGTCTCAATTTAAACAAGATAACATGTTTTGACTTAATCTAGACAAG
Found at i:633262 original size:28 final size:28
Alignment explanation
Indices: 633091--633263 Score: 97
Period size: 28 Copynumber: 6.0 Consensus size: 28
633081 CTTAATTTGG
*
633091 ACAAGAA-AACATGTTTGTCTTAATTTAA
1 ACAAGAATAACATTTTTGTCTTAA-TTAA
* *
633119 GATAAGAA-AACCATGTTTTGACTTAATCTAA
1 -ACAAGAATAA-CAT-TTTTGTCTTAAT-TAA
* * * * *
633150 GCAAGAA-ATCATGTTTGTCTCAATTTAC
1 ACAAGAATAACATTTTTGTCTTAA-TTAA
* * *
633178 ACAAG-GTAACATGTTTTGGCTTAATCTAG
1 ACAAGAATAACAT-TTTTGTCTTAAT-TAA
* *
633207 ACAAGAA-AACATGTTTGTCTCAATTTAA
1 ACAAGAATAACATTTTTGTCTTAA-TTAA
633235 ACAA-AATAACATATTTTGTCTTAATTAA
1 ACAAGAATAACAT-TTTTGTCTTAATTAA
633263 A
1 A
633264 GACAAAGTTG
Statistics
Matches: 109, Mismatches: 24, Indels: 23
0.70 0.15 0.15
Matches are distributed among these distances:
27 2 0.02
28 43 0.39
29 42 0.39
30 10 0.09
31 12 0.11
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (28 bp):
ACAAGAATAACATTTTTGTCTTAATTAA
Found at i:633431 original size:17 final size:17
Alignment explanation
Indices: 633409--633441 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
633399 ATAATAATGA
633409 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
633426 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
633442 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:638938 original size:29 final size:29
Alignment explanation
Indices: 638897--639110 Score: 225
Period size: 29 Copynumber: 7.3 Consensus size: 29
638887 CTTTTATATG
* *
638897 TTTGTATTAATTTAGACCAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* * *
638926 TTTGTCTTCATTTAGATAAGAAAATATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* *
638955 TATGTCTTAATTTAGAACAAGAAAATATGT
1 TTTGTCTTAATTTAG-ACAAGAAAACATGT
* **
638985 TTTGTCTTAATTTAGACAAGATAACA-CA
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* *
639013 TTTCTCTTAATGTAAGACAAGAAAAACATGT
1 TTTGTCTTAAT-TTAGACAAG-AAAACATGT
* *
639044 TTTGTCTTAATTTAGGCAAGAAAACAT-A
1 TTTGTCTTAATTTAGACAAGAAAACATGT
** *
639072 TTTGTCTTAATTTAGACAAGGTAACAAGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
*
639101 TTTATCTTAA
1 TTTGTCTTAA
639111 CTAAAACCAA
Statistics
Matches: 152, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
28 33 0.22
29 70 0.46
30 39 0.26
31 10 0.07
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (29 bp):
TTTGTCTTAATTTAGACAAGAAAACATGT
Found at i:638978 original size:59 final size:57
Alignment explanation
Indices: 638897--639110 Score: 248
Period size: 59 Copynumber: 3.7 Consensus size: 57
638887 CTTTTATATG
* * * * * *
638897 TTTGTATTAATTTAGACCAGAAAACATGTTTTGTCTTCATTTAGATAAGAAAATATG
1 TTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAAACATA
* * *
638954 TTATGTCTTAATTTAGAACAAGAAAATATGTTTTGTCTTAATTTAGACAAGATAACACA
1 TT-TGTCTTAATTTAG-ACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAAACATA
* * *
639013 TTTCTCTTAATGTAAGACAAGAAAAACATGTTTTGTCTTAATTTAGGCAAGAAAACATA
1 TTTGTCTTAAT-TTAGACAAG-AAAACATGTTTTGTCTTAATTTAGACAAGAAAACATA
** * *
639072 TTTGTCTTAATTTAGACAAGGTAACAAGTTTTATCTTAA
1 TTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAA
639111 CTAAAACCAA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
57 17 0.13
58 33 0.25
59 82 0.62
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (57 bp):
TTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAAACATA
Found at i:641246 original size:43 final size:46
Alignment explanation
Indices: 641155--641318 Score: 176
Period size: 49 Copynumber: 3.5 Consensus size: 46
641145 ATTTCTTTTA
* * *
641155 AATTTAAACAAATTAAATTAAAATGTAAT---TA-CTCT-TTATTT
1 AATTTAAACAAATTAAATTTAAATATAATGGATAGATCTATTATTT
641196 AAATTTAAACAAATTAAATTTAAATATAATGGATAGATCATTATTATTT
1 -AATTTAAACAAATTAAATTTAAATATAATGGATAGATC--TATTATTT
* *
641245 AAATTTAAACAAATTAAATTTAAATATAATGGATAGATCATTCTTAATTA
1 -AATTTAAACAAATTAAATTTAAATATAATGGATAGATC--TATT-ATTT
*
641295 AATTTAAGCAAATTAAATTTAAAT
1 AATTTAAACAAATTAAATTTAAAT
641319 TTATATCCTA
Statistics
Matches: 108, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
42 27 0.25
45 2 0.02
46 2 0.02
48 1 0.01
49 73 0.68
50 3 0.03
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (46 bp):
AATTTAAACAAATTAAATTTAAATATAATGGATAGATCTATTATTT
Found at i:641247 original size:28 final size:28
Alignment explanation
Indices: 641213--641297 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 28
641203 AACAAATTAA
641213 ATTTAAATATAATGGATAGATCATTATT
1 ATTTAAATATAATGGATAGATCATTATT
* * *
641241 ATTTAAATTTAA---ACA-A--ATTA-A
1 ATTTAAATATAATGGATAGATCATTATT
*
641262 ATTTAAATATAATGGATAGATCATTCTT
1 ATTTAAATATAATGGATAGATCATTATT
*
641290 AATTAAAT
1 ATTTAAAT
641298 TTAAGCAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
21 11 0.26
22 4 0.10
24 3 0.07
25 3 0.07
27 3 0.07
28 18 0.43
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (28 bp):
ATTTAAATATAATGGATAGATCATTATT
Found at i:641250 original size:49 final size:49
Alignment explanation
Indices: 641190--641318 Score: 231
Period size: 49 Copynumber: 2.6 Consensus size: 49
641180 TAATTACTCT
641190 TTATTTAAATTTAAACAAATTAAATTTAAATATAATGGATAGATCATTA
1 TTATTTAAATTTAAACAAATTAAATTTAAATATAATGGATAGATCATTA
*
641239 TTATTTAAATTTAAACAAATTAAATTTAAATATAATGGATAGATCATTC
1 TTATTTAAATTTAAACAAATTAAATTTAAATATAATGGATAGATCATTA
* *
641288 TTAATTAAATTTAAGCAAATTAAATTTAAAT
1 TTATTTAAATTTAAACAAATTAAATTTAAAT
641319 TTATATCCTA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 77 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (49 bp):
TTATTTAAATTTAAACAAATTAAATTTAAATATAATGGATAGATCATTA
Found at i:642845 original size:21 final size:21
Alignment explanation
Indices: 642809--642859 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
642799 ACTTGTTAAG
642809 TAGTT-AA-TTTAAGTTATTT
1 TAGTTAAATTTTAAGTTATTT
*
642828 TAGTTAAATTTTAGGTTATTT
1 TAGTTAAATTTTAAGTTATTT
*
642849 TATTTTAAATT
1 TA-GTTAAATT
642860 ACTGTAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 2 0.07
21 13 0.48
22 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
TAGTTAAATTTTAAGTTATTT
Found at i:651732 original size:18 final size:19
Alignment explanation
Indices: 651709--651744 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
651699 AGATTTGATA
651709 TTTTAACACTCAA-AGAGT
1 TTTTAACACTCAAGAGAGT
*
651727 TTTTAACATTCAAGAGAG
1 TTTTAACACTCAAGAGAG
651745 AAACTGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (19 bp):
TTTTAACACTCAAGAGAGT
Found at i:658989 original size:60 final size:60
Alignment explanation
Indices: 658892--659007 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
658882 GGAGAAGAAG
* **
658892 TAAGAAGAATTTTGAAGAAAATAACATAAGTGTGGGCTCGTTGCCTTCATTAAATAGAGC
1 TAAGAAGAATTTTGAAGAAAATAACATAAGTGAGGGCTCAATGCCTTCATTAAATAGAGC
*
658952 TAAGAAAGAA-TTTGAAGAAAA-ACGACATAAGT-AGGGCTCAATGCCTTTATTAAATA
1 TAAG-AAGAATTTTGAAGAAAATA--ACATAAGTGAGGGCTCAATGCCTTCATTAAATA
659008 TTATGGTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 1 0.02
60 35 0.71
61 13 0.27
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (60 bp):
TAAGAAGAATTTTGAAGAAAATAACATAAGTGAGGGCTCAATGCCTTCATTAAATAGAGC
Found at i:663344 original size:25 final size:25
Alignment explanation
Indices: 663293--663344 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
663283 ATATCAACTT
* *
663293 GTGGCCTAGCCACATATATCAATCC
1 GTGGCCTAGCCACATATAACAACCC
** *
663318 GTGGCCTAGCCATGTCTAACAACCC
1 GTGGCCTAGCCACATATAACAACCC
663343 GT
1 GT
663345 CGATGACCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (25 bp):
GTGGCCTAGCCACATATAACAACCC
Found at i:670674 original size:23 final size:24
Alignment explanation
Indices: 670648--670711 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
670638 GTGTGACTAG
670648 TTGATAGGTCATTGCATGT-GCAA
1 TTGATAGGTCATTGCATGTAGCAA
*
670671 TTGATAGGTCATT--ATGTGAGCAG
1 TTGATAGGTCATTGCATGT-AGCAA
*
670694 TTAATAGGTCATTGCATG
1 TTGATAGGTCATTGCATG
670712 AATATTGTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.11
23 28 0.80
25 3 0.09
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (24 bp):
TTGATAGGTCATTGCATGTAGCAA
Found at i:670777 original size:23 final size:23
Alignment explanation
Indices: 670746--670797 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
670736 TTTGGGTTAA
* * *
670746 CATTACGTGACTGGTCGATATGT
1 CATTGCGTGACTGGTCGATAGGC
* *
670769 CATTGCGTGAGTGGTTGATAGGC
1 CATTGCGTGACTGGTCGATAGGC
670792 CATTGC
1 CATTGC
670798 ATGAATATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (23 bp):
CATTGCGTGACTGGTCGATAGGC
Found at i:670895 original size:23 final size:23
Alignment explanation
Indices: 670869--670926 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
670859 TATGTGACTA
* * *
670869 GTTGATATGTCGTTGCGTGAGTG
1 GTTGATAGGTCATTGCATGAGTG
*
670892 GTTGACAGGTCATTGCATGAGTG
1 GTTGATAGGTCATTGCATGAGTG
670915 GTTGATAGGTCA
1 GTTGATAGGTCA
670927 CTACGTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.10, G:0.36, T:0.34
Consensus pattern (23 bp):
GTTGATAGGTCATTGCATGAGTG
Found at i:676144 original size:16 final size:17
Alignment explanation
Indices: 676121--676166 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
676111 TTCAACCACA
676121 TATAAAATATTAAT-ATT
1 TATAAAATATT-ATCATT
676138 T-TAAAATTATT-TCATT
1 TATAAAA-TATTATCATT
676154 TATAAAATATTAT
1 TATAAAATATTAT
676167 TTTATTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
17 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAAAATATTATCATT
Found at i:680014 original size:23 final size:23
Alignment explanation
Indices: 679960--680083 Score: 104
Period size: 23 Copynumber: 5.4 Consensus size: 23
679950 TGAGTATTTG
* *
679960 ATATGGAATCACGCGACTAGTAA
1 ATATGGAATTACGTGACTAGTAA
*
679983 ATACGGAATTACGTGACTAGTAA
1 ATATGGAATTACGTGACTAGTAA
* ** * **
680006 ATATAGAATCGCGTGACTAATCG
1 ATATGGAATTACGTGACTAGTAA
* * * **
680029 ATTTGGAATTGCATGACTAGTTG
1 ATATGGAATTACGTGACTAGTAA
* *
680052 ATATTGAATTACGTGAATAGTAA
1 ATATGGAATTACGTGACTAGTAA
680075 ATATGGAAT
1 ATATGGAAT
680084 CGCGTAAACC
Statistics
Matches: 77, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 77 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (23 bp):
ATATGGAATTACGTGACTAGTAA
Found at i:680036 original size:69 final size:69
Alignment explanation
Indices: 679920--680088 Score: 167
Period size: 69 Copynumber: 2.4 Consensus size: 69
679910 GTGTGTATGA
* * * * * * * * *
679920 AATTGCGTGACTAGTTAATATTGAATAGCATGAGTATTTGATATGGAATCACGCGACTAGTAAAT
1 AATTACGTGACTAGTAAATATAGAATCGCGTGACTAATCGATATGGAATCACACGACTAGTAAAT
679985 ACGG
66 ACGG
* ** * **
679989 AATTACGTGACTAGTAAATATAGAATCGCGTGACTAATCGATTTGGAATTGCATGACTAGTTGAT
1 AATTACGTGACTAGTAAATATAGAATCGCGTGACTAATCGATATGGAATCACACGACTAGTAAAT
**
680054 ATTG
66 ACGG
* *
680058 AATTACGTGAATAGTAAATATGGAATCGCGT
1 AATTACGTGACTAGTAAATATAGAATCGCGT
680089 AAACCGTTAA
Statistics
Matches: 81, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (69 bp):
AATTACGTGACTAGTAAATATAGAATCGCGTGACTAATCGATATGGAATCACACGACTAGTAAAT
ACGG
Found at i:680082 original size:46 final size:46
Alignment explanation
Indices: 679925--680083 Score: 138
Period size: 46 Copynumber: 3.5 Consensus size: 46
679915 TATGAAATTG
* * * * * *
679925 CGTGACTAGTTAATATTGAATAGCATGAGTATTTGATATGGAATCA
1 CGTGACTAGTAAATATGGAATTGCATGACTAGTTGATATAGAATCA
* * * * ** *
679971 CGCGACTAGTAAATACGGAATTACGTGACTAGTAAATATAGAATCG
1 CGTGACTAGTAAATATGGAATTGCATGACTAGTTGATATAGAATCA
* ** * * *
680017 CGTGACTAATCGATTTGGAATTGCATGACTAGTTGATATTGAATTA
1 CGTGACTAGTAAATATGGAATTGCATGACTAGTTGATATAGAATCA
*
680063 CGTGAATAGTAAATATGGAAT
1 CGTGACTAGTAAATATGGAAT
680084 CGCGTAAACC
Statistics
Matches: 82, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
46 82 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (46 bp):
CGTGACTAGTAAATATGGAATTGCATGACTAGTTGATATAGAATCA
Found at i:680103 original size:23 final size:23
Alignment explanation
Indices: 680077--680134 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
680067 AATAGTAAAT
680077 ATGGAATCGCGTAAACCGTTAAG
1 ATGGAATCGCGTAAACCGTTAAG
680100 ATGGAATCGCGTAAACCGTTAAG
1 ATGGAATCGCGTAAACCGTTAAG
680123 ATGGAATCGCGT
1 ATGGAATCGCGT
680135 GACTATTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (23 bp):
ATGGAATCGCGTAAACCGTTAAG
Found at i:680152 original size:23 final size:23
Alignment explanation
Indices: 680126--680187 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
680116 CGTTAAGATG
*
680126 GAATCGCGTGACTATTTGAT-TT
1 GAATCGCGTGACTAGTTGATATT
*
680148 AGAATTGCGTGACTAGTTGATATT
1 -GAATCGCGTGACTAGTTGATATT
* *
680172 GAATCGCATGAGTAGT
1 GAATCGCGTGACTAGT
680188 AAATATGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 31 0.94
24 2 0.06
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (23 bp):
GAATCGCGTGACTAGTTGATATT
Found at i:680210 original size:23 final size:23
Alignment explanation
Indices: 680178--680267 Score: 63
Period size: 23 Copynumber: 3.9 Consensus size: 23
680168 TATTGAATCG
*
680178 CATGAGTAGTAAATATGGAATAA
1 CATGACTAGTAAATATGGAATAA
* * * *
680201 CATTACTAGTTATTATGGAATCA
1 CATGACTAGTAAATATGGAATAA
* *** * *
680224 CATGACTATTTGTTCTGGAATTA
1 CATGACTAGTAAATATGGAATAA
**
680247 CATGACTAGTTGATATGGAAT
1 CATGACTAGTAAATATGGAAT
680268 CAAGTAACTT
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (23 bp):
CATGACTAGTAAATATGGAATAA
Found at i:683802 original size:13 final size:13
Alignment explanation
Indices: 683738--683794 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
683728 AGCAATTGCT
683738 TGACTAGCTATTA
1 TGACTAGCTATTA
* * *
683751 TGTATTTGCAATTGA
1 TG-ACTAGCTATT-A
683766 CTGACTAGCTATTA
1 -TGACTAGCTATTA
683780 TGACTAGCTATTA
1 TGACTAGCTATTA
683793 TG
1 TG
683795 TATGGCTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 17 0.49
14 8 0.23
15 8 0.23
16 2 0.06
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (13 bp):
TGACTAGCTATTA
Found at i:684157 original size:17 final size:17
Alignment explanation
Indices: 684135--684168 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
684125 TTCATCAAAA
*
684135 GCTCACAACCATTACTT
1 GCTCACAACCACTACTT
684152 GCTCACAACCACTACTT
1 GCTCACAACCACTACTT
684169 TATCTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.38, G:0.06, T:0.26
Consensus pattern (17 bp):
GCTCACAACCACTACTT
Found at i:688326 original size:22 final size:22
Alignment explanation
Indices: 688298--688342 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
688288 TCCCAACATA
**
688298 ATGCAATATGTAAAAACTAGTC
1 ATGCAATACCTAAAAACTAGTC
*
688320 ATGCAATACCTAAAAAGTAGTC
1 ATGCAATACCTAAAAACTAGTC
688342 A
1 A
688343 AGAAATGTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (22 bp):
ATGCAATACCTAAAAACTAGTC
Found at i:688516 original size:22 final size:22
Alignment explanation
Indices: 688490--688545 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
688480 CAACATCACA
*
688490 CAATACATAACAACAAGT-AACG
1 CAATACATAAAAACAAGTCAA-G
*
688512 CAATACATAAAAACCAGTCAAG
1 CAATACATAAAAACAAGTCAAG
*
688534 CAATACCTAAAA
1 CAATACATAAAA
688546 GGTAGTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.14
Consensus pattern (22 bp):
CAATACATAAAAACAAGTCAAG
Found at i:688647 original size:197 final size:193
Alignment explanation
Indices: 688404--688783 Score: 503
Period size: 197 Copynumber: 1.9 Consensus size: 193
688394 AGTTAGTCTC
* * * * * ** *
688404 GCAATACTTAATAATAAGTTACTCAATGTCTAATATCCATTCACGTTATGCTAACATAGTCAGTC
1 GCAAAACTTAATAATAAGTCACTCAATGCCTAATATCCACTCACGTTATGCCAACATAACCAATC
688469 ACATATTAGCCCAACATCACACAATACATAACAACAAGTAACGCAATACATAAAAACC-AGTCA-
66 ACATATTAGCCCAACATCACACAATACAT---AACAAGTAACGCAATACAT--AAACCTAGTCAC
* *
688532 AGCAATACCTAAAAGGTAGTCAAAAAATGTCTCAAAATAAGACATGCATTCCACAATTCCACAAT
126 A-CAATACCTAAAAAGTAGTCAAAAAATGTCTCAAAACAAGACATGCATTCCACAATTCCACAAT
688597 TCAT
190 TCAT
688601 GCAAAACTTAATAATAAGTCACTCAATGCCTAATATCCACTCACGTTATGCCAACATAACCAATC
1 GCAAAACTTAATAATAAGTCACTCAATGCCTAATATCCACTCACGTTATGCCAACATAACCAATC
* * ** *
688666 ACGTATTGGCCCAACATCATGCAATACATAACAAGTCACGCAATACATAAACCTAGTCACACAAT
66 ACATATTAGCCCAACATCACACAATACATAACAAGTAACGCAATACATAAACCTAGTCACACAAT
* * * * * *
688731 GCCTAAAAAGTAGTCAAGAAATGTTTCAACACAAGATATGCATTGCACAATTC
131 ACCTAAAAAGTAGTCAAAAAATGTCTCAAAACAAGACATGCATTCCACAATTC
688784 ACGTAGCGCC
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
192 5 0.03
193 54 0.34
194 19 0.12
197 82 0.51
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (193 bp):
GCAAAACTTAATAATAAGTCACTCAATGCCTAATATCCACTCACGTTATGCCAACATAACCAATC
ACATATTAGCCCAACATCACACAATACATAACAAGTAACGCAATACATAAACCTAGTCACACAAT
ACCTAAAAAGTAGTCAAAAAATGTCTCAAAACAAGACATGCATTCCACAATTCCACAATTCAT
Found at i:688730 original size:21 final size:19
Alignment explanation
Indices: 688687--688730 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
688677 CAACATCATG
*
688687 CAATACATAACAAGTCACG
1 CAATACATAACAAGTCACA
*
688706 CAATACATAAACCTAGTCACA
1 CAATACAT-AA-CAAGTCACA
688727 CAAT
1 CAAT
688731 GCCTAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.48, C:0.27, G:0.07, T:0.18
Consensus pattern (19 bp):
CAATACATAACAAGTCACA
Found at i:688986 original size:22 final size:22
Alignment explanation
Indices: 688961--689002 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
688951 CCATTTAGAA
* *
688961 AATGAATAATATCCCTTCACAC
1 AATGAATAAGATCCATTCACAC
*
688983 AATGCATAAGATCCATTCAC
1 AATGAATAAGATCCATTCAC
689003 TTAATGCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (22 bp):
AATGAATAAGATCCATTCACAC
Found at i:700427 original size:18 final size:18
Alignment explanation
Indices: 700404--700482 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
700394 ATATTTTAAT
700404 TTAATCATTTTAATCATG
1 TTAATCATTTTAATCATG
* **
700422 TTAATCATATTAATTGTG
1 TTAATCATTTTAATCATG
* *
700440 TAAATAATTTATAA--ATTG
1 TTAATCATTT-TAATCA-TG
700458 TATAA--ATTTTAATCATG
1 T-TAATCATTTTAATCATG
700475 TTAATCAT
1 TTAATCAT
700483 GTCGTATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
16 6 0.13
17 7 0.15
18 28 0.61
19 5 0.11
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (18 bp):
TTAATCATTTTAATCATG
Found at i:702876 original size:2 final size:2
Alignment explanation
Indices: 702869--702902 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
702859 ATTCACATGA
*
702869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
702903 TTGACTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:703051 original size:17 final size:18
Alignment explanation
Indices: 703025--703064 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
703015 TACCCATTTT
703025 AAAAATTAAAATAAATAC
1 AAAAATTAAAATAAATAC
703043 AAAAA-TAAAATAAATAC
1 AAAAATTAAAATAAATAC
703060 AAAAA
1 AAAAA
703065 ATATTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATTAAAATAAATAC
Found at i:703797 original size:70 final size:69
Alignment explanation
Indices: 703717--703846 Score: 163
Period size: 70 Copynumber: 1.9 Consensus size: 69
703707 AAGTCTTAAC
* * *
703717 TTTTGCCAAAGTGCTGGAAAAATTCAAGAAAAGTTT-TAAACAAAAAATAATAATAATAAAAATT
1 TTTTGCCAAAGGGCTGGAAAAATTCAAGAAAAGTTTCCAAAAAAAAAATAA-AA-AATAAAAATT
703781 CTTAGT
64 CTTAGT
* * * * *
703787 TTTTGTCAAAGGGTTGGGAAAATTTAAGACAAGTTTCCAAAAAAAAAATAAAAAATAAAA
1 TTTTGCCAAAGGGCTGGAAAAATTCAAGAAAAGTTTCCAAAAAAAAAATAAAAAATAAAA
703847 TCAATTGAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
69 7 0.14
70 32 0.63
71 12 0.24
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.28
Consensus pattern (69 bp):
TTTTGCCAAAGGGCTGGAAAAATTCAAGAAAAGTTTCCAAAAAAAAAATAAAAAATAAAAATTCT
TAGT
Found at i:711073 original size:30 final size:30
Alignment explanation
Indices: 711000--711081 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
710990 GAGTTAAGGT
* ** *
711000 GGTTATACCTTAGCCTTGAAAAGGTATAGA
1 GGTTATATCTTAGCCTTGAAAACATAGAGA
* * *
711030 TGTTCTATTTTAGCCTTGAAAACATAGAGA
1 GGTTATATCTTAGCCTTGAAAACATAGAGA
*
711060 GGTTATATCTTAGCCTTTAAAA
1 GGTTATATCTTAGCCTTGAAAA
711082 GAAAAAAGGC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (30 bp):
GGTTATATCTTAGCCTTGAAAACATAGAGA
Found at i:721526 original size:25 final size:25
Alignment explanation
Indices: 721497--721555 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
721487 TGGTCGCAAA
**
721497 CCACATATATCAACTTGTGGCCTAG
1 CCACATATATCAACCCGTGGCCTAG
* * *
721522 CCACATAAATTAACCCGTGGCCTTG
1 CCACATATATCAACCCGTGGCCTAG
*
721547 CCACGTATA
1 CCACATATA
721556 ATCACAAATC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (25 bp):
CCACATATATCAACCCGTGGCCTAG
Found at i:722156 original size:2 final size:2
Alignment explanation
Indices: 722149--722174 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
722139 CAGATAATAC
722149 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
722175 CTTTGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:747102 original size:22 final size:20
Alignment explanation
Indices: 747072--747115 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
747062 TGAAACAAAC
*
747072 TTAAAAATAAATATAATTATT
1 TTAAAAATAAAAATAATT-TT
747093 TTAAATAATAAAAATAATTTT
1 TTAAA-AATAAAAATAATTTT
747114 TT
1 TT
747116 CTCTCTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAAATAAAAATAATTTT
Found at i:749394 original size:22 final size:23
Alignment explanation
Indices: 749349--749394 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
749339 TCTACAAGCT
*
749349 AGTACTTCTGCTTTCATCTCACAC
1 AGTACATCTGCTTTCA-CTCACAC
749373 AGTACATCTGCTTTC-CTCACAC
1 AGTACATCTGCTTTCACTCACAC
749395 GATGATAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.22, C:0.35, G:0.09, T:0.35
Consensus pattern (23 bp):
AGTACATCTGCTTTCACTCACAC
Found at i:753773 original size:14 final size:15
Alignment explanation
Indices: 753742--753774 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
753732 TATAGAACGA
*
753742 TTTAAAATAGAAAGT
1 TTTAAAATAGAAAAT
753757 TTTAAAAT-GAAAAT
1 TTTAAAATAGAAAAT
753771 TTTA
1 TTTA
753775 TTTCAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (15 bp):
TTTAAAATAGAAAAT
Found at i:759125 original size:25 final size:24
Alignment explanation
Indices: 759084--759147 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
759074 GAAAAAGGGT
759084 AGCATTGGACCCCTTGAAGGGGAC
1 AGCATTGGACCCCTTGAAGGGGAC
* *
759108 AGCATTGGACCTCGTTGAAGGGGGC
1 AGCATTGGACC-CCTTGAAGGGGAC
*
759133 AGCATTGTACCCCTT
1 AGCATTGGACCCCTT
759148 TTAAAAGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 14 0.40
25 21 0.60
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (24 bp):
AGCATTGGACCCCTTGAAGGGGAC
Found at i:762909 original size:2 final size:2
Alignment explanation
Indices: 762904--762932 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
762894 CCTCTCTCTA
762904 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
762933 CAAACTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:763175 original size:28 final size:28
Alignment explanation
Indices: 763135--763190 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
763125 CTATGACAGG
763135 TAAACAATTCAGCACAAGAGGCATCAGA
1 TAAACAATTCAGCACAAGAGGCATCAGA
763163 TAAACAATTCAGCACAAGAGGCATCAGA
1 TAAACAATTCAGCACAAGAGGCATCAGA
763191 AGAGTGGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.14
Consensus pattern (28 bp):
TAAACAATTCAGCACAAGAGGCATCAGA
Found at i:770324 original size:16 final size:16
Alignment explanation
Indices: 770300--770331 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
770290 AAAGTGGAAA
*
770300 GAAAGATTAAAGAAGG
1 GAAAAATTAAAGAAGG
770316 GAAAAATTAAAGAAGG
1 GAAAAATTAAAGAAGG
770332 CGGTGGGTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.12
Consensus pattern (16 bp):
GAAAAATTAAAGAAGG
Found at i:773344 original size:363 final size:362
Alignment explanation
Indices: 772679--773399 Score: 1300
Period size: 363 Copynumber: 2.0 Consensus size: 362
772669 TGTCAAAAAA
772679 TTGCATTCAGCTATAACAAAGACATGCTGCAAGACCCATTGGTCATATTTAATAAGTTGTCAAGG
1 TTGCATTCAGCTATAACAAAGACATGCTGCAAGACCCATTGGTCATATTTAATAAGTTGTCAAGG
772744 GCTCATAGACAAGACAAGACAACTTCGCATTCAACACAACTCTGGATGATTATGTTATTTTTAAA
66 GCTCATAGACAAGACAAGACAACTTCGCATTCAACACAACTCTGGATGATTATGTTATTTTTAAA
*
772809 TCATATACTCCATTTTGATAATACTATTTTTTCCTACAAATAGGGGCATTCTGCATTTGAATGAT
131 TCATATACTCCATTTTGATAATAATATTTTTTCCTACAAATAGGGGCATTCTGCATTTGAATGAT
*
772874 ACCTATTTGAGACACTGATTTTCTAGAATACCAACACCTGAGGCTTTTCATCTTAAAAAAAGACA
196 ACCTATTTAAGACACTGATTTTCTAGAATACCAACACCTGAGGCTTTTCATCTTAAAAAAAGACA
*
772939 TCAAGGACTTCAAGCACAGATGTTGCCCCTCTCCACTTTCAACCATCCAAGATCAAGTTTTTTCA
261 TCAAGGACATCAAGCACAGATGTTGCCCCTCTCCACTTTCAACCATCCAAGATCAAGTTTTTTCA
* *
773004 TGGAACACCTCTTTTTAAGAACAGTCCAAGAAGATATC
326 TGGAACACCTC-CTTTAAGAACAGTACAAGAAGATATC
*
773042 TTGCATTCAGCTATAACAAAGACGTGCTGCAAGACCCATTGGTCATATTTAATAAGTTGTCAAGG
1 TTGCATTCAGCTATAACAAAGACATGCTGCAAGACCCATTGGTCATATTTAATAAGTTGTCAAGG
* *
773107 GCTCATAGACAAGACAAGACAACTTCGCATTCAACACAACTCTGGATGGTTATTTTATTTTTAAA
66 GCTCATAGACAAGACAAGACAACTTCGCATTCAACACAACTCTGGATGATTATGTTATTTTTAAA
*
773172 TCATATGCTCCATTTTGATAATAATATTTTTTCCTACAAATAGGGGCATTCTGCATTTGAATGAT
131 TCATATACTCCATTTTGATAATAATATTTTTTCCTACAAATAGGGGCATTCTGCATTTGAATGAT
*
773237 ACCTTTTTAAGACACTGATTTTCTAGAATACCAACACCTGAGGCTTTTCATC-TAAGAAAAAGAC
196 ACCTATTTAAGACACTGATTTTCTAGAATACCAACACCTGAGGCTTTTCATCTTAA-AAAAAGAC
* * *
773301 ATCAAGGACATCAAGCATAGATGTTGCGCCTCTCCACTTTCAACCATCCAGGATCAAGTTTTTTC
260 ATCAAGGACATCAAGCACAGATGTTGCCCCTCTCCACTTTCAACCATCCAAGATCAAGTTTTTTC
773366 ATGGAACACCTCCTTTAAGAACAGTACAAGAAGA
325 ATGGAACACCTCCTTTAAGAACAGTACAAGAAGA
773400 AGATATCTGG
Statistics
Matches: 344, Mismatches: 13, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
362 23 0.07
363 321 0.93
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (362 bp):
TTGCATTCAGCTATAACAAAGACATGCTGCAAGACCCATTGGTCATATTTAATAAGTTGTCAAGG
GCTCATAGACAAGACAAGACAACTTCGCATTCAACACAACTCTGGATGATTATGTTATTTTTAAA
TCATATACTCCATTTTGATAATAATATTTTTTCCTACAAATAGGGGCATTCTGCATTTGAATGAT
ACCTATTTAAGACACTGATTTTCTAGAATACCAACACCTGAGGCTTTTCATCTTAAAAAAAGACA
TCAAGGACATCAAGCACAGATGTTGCCCCTCTCCACTTTCAACCATCCAAGATCAAGTTTTTTCA
TGGAACACCTCCTTTAAGAACAGTACAAGAAGATATC
Found at i:777376 original size:45 final size:43
Alignment explanation
Indices: 777319--777412 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 43
777309 ATAAAAAAAA
*
777319 TATTTAAATATTATTT-AACTATAATAAATATTATAAAGAATAT
1 TATTTAAATATTATTTGAA-TATAATAAATATAATAAAGAATAT
* *
777362 TATTTAATATTATTATTTGAATATAATAACTGTAATAAAGAATAT
1 TATTTAA-A-TATTATTTGAATATAATAAATATAATAAAGAATAT
777407 TATTTA
1 TATTTA
777413 GAACTATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
43 7 0.16
44 1 0.02
45 35 0.78
46 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (43 bp):
TATTTAAATATTATTTGAATATAATAAATATAATAAAGAATAT
Found at i:780272 original size:479 final size:479
Alignment explanation
Indices: 779375--780340 Score: 1864
Period size: 479 Copynumber: 2.0 Consensus size: 479
779365 AATTGATAGA
*
779375 GGTGACGAAAGCTCTTGAACTATCGAGCGGTACGGCTCAACCGTACAGTCTGAATGAGCCATCGG
1 GGTGACGAAAGCTCTTGAACGATCGAGCGGTACGGCTCAACCGTACAGTCTGAATGAGCCATCGG
779440 TAAGGAAATAAAAATTATAACGATTAAGTTCAACGATGATTATTGAATAGCACAGTAATAACAGT
66 TAAGGAAATAAAAATTATAACGATTAAGTTCAACGATGATTATTGAATAGCACAGTAATAACAGT
779505 ATATGGTCTTGCAGTATAACCCATGCGAGAAAGTCAATGTCGGAGTAGTCACGATACGTGAGCTA
131 ATATGGTCTTGCAGTATAACCCATGCGAGAAAGTCAATGTCGGAGTAGTCACGATACGTGAGCTA
779570 CGACAGGTCATGCGCAGGCATGAAAAGGAGATGTGGGAGCTGAAGGCTTCAATTTAGTCATTGAC
196 CGACAGGTCATGCGCAGGCATGAAAAGGAGATGTGGGAGCTGAAGGCTTCAATTTAGTCATTGAC
*
779635 TCTAGCAATGCAGATGATGGAGGACCATATTGTTTGTCGAATTCTAGACGGCCTAAAATCACAAG
261 TCTAGCAATGCAGATGATGGAGGACCATATCGTTTGTCGAATTCTAGACGGCCTAAAATCACAAG
779700 TACGTTATTCTATCTTTGCTCATATAAAATTGACTTACTTTAAGCAAGTGTAGTCTAATATTTTA
326 TACGTTATTCTATCTTTGCTCATATAAAATTGACTTACTTTAAGCAAGTGTAGTCTAATATTTTA
*
779765 TTACCTGTTTATGGTTTATGGTATTTTTGGATCTAACAGAATTTCCTATTTGACTCTTTCTATAG
391 TTACCTGTTTATGGTTTATGGTATTTTTGGATCTAACAGAATTTCATATTTGACTCTTTCTATAG
779830 GGTGGTGCTTCATCGCATGCTGAT
456 GGTGGTGCTTCATCGCATGCTGAT
779854 GGTGACGAAAGCTCTTGAACGATCGAGCGGTACGGCTCAACCGTACAGTCTGAATGAGCCATCGG
1 GGTGACGAAAGCTCTTGAACGATCGAGCGGTACGGCTCAACCGTACAGTCTGAATGAGCCATCGG
*
779919 TAAGGAAATTAAAATTATAACGATTAATGTTCAACGATGATTATTGAATAGCACAGTAATAACAG
66 TAAGGAAATAAAAATTATAACGATTAA-GTTCAACGATGATTATTGAATAGCACAGTAATAACAG
779984 TATATGGTCTTGCAGT-TAACCCATGCGAGAAAAGTCAATGTCGGAGTAGTCACGATACGTGAGC
130 TATATGGTCTTGCAGTATAACCCATGCGAG-AAAGTCAATGTCGGAGTAGTCACGATACGTGAGC
780048 TACGACAGGTCATGCGCAGGCATGAAAAGGAGATGTGGGAGCTGAAGGCTTCAATTTAGTCATTG
194 TACGACAGGTCATGCGCAGGCATGAAAAGGAGATGTGGGAGCTGAAGGCTTCAATTTAGTCATTG
780113 ACTCTAGCAATGCAGATGATGGA-GACCATATCGTTTGTCGAATTCTAGACGGCCTAAAATCACA
259 ACTCTAGCAATGCAGATGATGGAGGACCATATCGTTTGTCGAATTCTAGACGGCCTAAAATCACA
780177 AGTACGTTATTCTATCTTTGCTCATATAAAATTGACTTACTTTAAGCAAGTGTAGTCTAATATTT
324 AGTACGTTATTCTATCTTTGCTCATATAAAATTGACTTACTTTAAGCAAGTGTAGTCTAATATTT
780242 TATTACCTGTTTATGGTTTATGGTATTTTTGGATCTAACAGAATTTCATATTTGACTCTTTCTAT
389 TATTACCTGTTTATGGTTTATGGTATTTTTGGATCTAACAGAATTTCATATTTGACTCTTTCTAT
780307 AGGGTGGTGCTTCATCGCATGCTGAT
454 AGGGTGGTGCTTCATCGCATGCTGAT
780333 GGTGACGA
1 GGTGACGA
780341 CCACAATGGT
Statistics
Matches: 481, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
479 306 0.64
480 175 0.36
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (479 bp):
GGTGACGAAAGCTCTTGAACGATCGAGCGGTACGGCTCAACCGTACAGTCTGAATGAGCCATCGG
TAAGGAAATAAAAATTATAACGATTAAGTTCAACGATGATTATTGAATAGCACAGTAATAACAGT
ATATGGTCTTGCAGTATAACCCATGCGAGAAAGTCAATGTCGGAGTAGTCACGATACGTGAGCTA
CGACAGGTCATGCGCAGGCATGAAAAGGAGATGTGGGAGCTGAAGGCTTCAATTTAGTCATTGAC
TCTAGCAATGCAGATGATGGAGGACCATATCGTTTGTCGAATTCTAGACGGCCTAAAATCACAAG
TACGTTATTCTATCTTTGCTCATATAAAATTGACTTACTTTAAGCAAGTGTAGTCTAATATTTTA
TTACCTGTTTATGGTTTATGGTATTTTTGGATCTAACAGAATTTCATATTTGACTCTTTCTATAG
GGTGGTGCTTCATCGCATGCTGAT
Found at i:782082 original size:23 final size:23
Alignment explanation
Indices: 782039--782672 Score: 470
Period size: 23 Copynumber: 27.7 Consensus size: 23
782029 CACACAACTA
**
782039 GGCATGGCGTGTCACTACATTGG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782062 GGCATAGAGTGTCACCGCATTCG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782085 AGCATGGCTTGTCACCTATCATTGG
1 GGCATGGCGTGTCACC--GCATTGG
* * *
782110 GGCATGGCTTGTCACTGCA-TGA
1 GGCATGGCGTGTCACCGCATTGG
*
782132 GACATGGCGTGTCACCGCATTGG
1 GGCATGGCGTGTCACCGCATTGG
* *
782155 AGCATGACGTGTCACCGCATTGG
1 GGCATGGCGTGTCACCGCATTGG
* * * *
782178 GGTATGGC-TGTCACTGCACTAG
1 GGCATGGCGTGTCACCGCATTGG
*
782200 GGCATGGCGTGTCACCGCATTAG
1 GGCATGGCGTGTCACCGCATTGG
* * * *
782223 GGCATGACTTGTTACCGCATTCG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782246 GGCATGGCTTGTCATCGCACT-G
1 GGCATGGCGTGTCACCGCATTGG
* * *
782268 GGCATGACGTGTCACCTGTATTTG
1 GGCATGGCGTGTCACC-GCATTGG
* * * *
782292 GGCATGGCTTGTCACCCCACTAG
1 GGCATGGCGTGTCACCGCATTGG
* * * *
782315 GGCATGGCTTGTCACTGCACTAG
1 GGCATGGCGTGTCACCGCATTGG
* *
782338 GGCATGGTGTGTCACCCCATTGG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782361 GGCATGGGGTGTCATCGCATTCG
1 GGCATGGCGTGTCACCGCATTGG
* * * * * **
782384 AGCATGGCTTGTTACCCCACTAA
1 GGCATGGCGTGTCACCGCATTGG
* * *
782407 GGCATGGCTTGTCACCGTATTGA
1 GGCATGGCGTGTCACCGCATTGG
* *
782430 GGCATCGCGTGTCACCGCATTAG
1 GGCATGGCGTGTCACCGCATTGG
** *
782453 GGCATGAAGTGTCACAGCATTGG
1 GGCATGGCGTGTCACCGCATTGG
* *
782476 GGCATGGCGTGTCAACGCATTAG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782499 GGCATGGCATGTCACCCCACTGG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782522 GGCATGGCTTGTCACCACACTGG
1 GGCATGGCGTGTCACCGCATTGG
* * * * *
782545 GGCATGGCTTGTCATCGTACTAG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782568 GG-TTAGGCGTGTCACCACAATGG
1 GGCAT-GGCGTGTCACCGCATTGG
*
782591 GGCATGGCATGTCACCGCATTGG
1 GGCATGGCGTGTCACCGCATTGG
* * *
782614 GGCATGGCTTATCACCACA-T-G
1 GGCATGGCGTGTCACCGCATTGG
* *
782635 GGCATGGCTTGTCACCCCATTGG
1 GGCATGGCGTGTCACCGCATTGG
*
782658 GGCATGGCATGTCAC
1 GGCATGGCGTGTCAC
782673 TGCACTAGGC
Statistics
Matches: 481, Mismatches: 120, Indels: 20
0.77 0.19 0.03
Matches are distributed among these distances:
21 18 0.04
22 53 0.11
23 375 0.78
24 16 0.03
25 19 0.04
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (23 bp):
GGCATGGCGTGTCACCGCATTGG
Found at i:782328 original size:138 final size:135
Alignment explanation
Indices: 782016--782685 Score: 578
Period size: 138 Copynumber: 4.9 Consensus size: 135
782006 CAGCCCATTG
* * * * * *
782016 GGGCATGGCTTGTCACACAACTA-GGCATGGCGTGTCACTACATTGGGGCATAGAGTGTCACCGC
1 GGGCATGGCGTGTCACCCCACTAGGGCATGGCGTGTCACTGCATTGGGGCATGGCGTGTCACCGC
* * * *
782080 ATTCGAGCATGGCTTGTCACCTATCATTGGGGCATGGCTTGTCACTGCA-TGAGACATGGCGTGT
66 ATTAGGGCATGGCTTGTCACC--CCATTGGGGCATGGCTTGTCAC-GCACTG-GGCATGGCGTGT
*
782144 CACCGCATT
127 CACCGTATT
* * * * * * *
782153 GGAGCATGACGTGTCACCGCATTGGGGTATGGC-TGTCACTGCACTAGGGCATGGCGTGTCACCG
1 GG-GCATGGCGTGTCACCCCACTAGGGCATGGCGTGTCACTGCATTGGGGCATGGCGTGTCACCG
* * * * *
782217 CATTAGGGCATGACTTGTTACCGCATTCGGGCATGGCTTGTCATCGCACTGGGCATGACGTGTCA
65 CATTAGGGCATGGCTTGTCACCCCATTGGGGCATGGCTTGTCA-CGCACTGGGCATGGCGTGTCA
782282 CCTGTATTT
129 CC-GTA-TT
* * * * * *
782291 GGGCATGGCTTGTCACCCCACTAGGGCATGGCTTGTCACTGCACTAGGGCATGGTGTGTCACCCC
1 GGGCATGGCGTGTCACCCCACTAGGGCATGGCGTGTCACTGCATTGGGGCATGGCGTGTCACCGC
* ** * * * * * * * *
782356 ATTGGGGCATGGGGTGTCATCGCATTCGAGCATGGCTTGTTACCCCACTAAGGCATGGCTTGTCA
66 ATTAGGGCATGGCTTGTCACCCCATTGGGGCATGGCTTGTCA-CGCACT-GGGCATGGCGTGTCA
782421 CCGTATT
129 CCGTATT
* * * ** * *
782428 GAGGCATCGCGTGTCACCGCATTAGGGCATGAAGTGTCACAGCATTGGGGCATGGCGTGTCAACG
1 G-GGCATGGCGTGTCACCCCACTAGGGCATGGCGTGTCACTGCATTGGGGCATGGCGTGTCACCG
* * * *
782493 CATTAGGGCATGGCATGTCACCCCACTGGGGCATGGCTTGTCACCACACTGGGGCATGGCTTGTC
65 CATTAGGGCATGGCTTGTCACCCCATTGGGGCATGGCTTGTCA-CGCACT-GGGCATGGCGTGTC
* *
782558 ATCGTACTA
128 ACCGTA-TT
* * * * * * * * *
782567 GGG-TTAGGCGTGTCACCACAATGGGGCATGGCATGTCACCGCATTGGGGCATGGCTTATCACCA
1 GGGCAT-GGCGTGTCACCCCACTAGGGCATGGCGTGTCACTGCATTGGGGCATGGCGTGTCACCG
* *
782631 CA-T-GGGCATGGCTTGTCACCCCATTGGGGCATGGCATGTCACTGCACTAGGCATG
65 CATTAGGGCATGGCTTGTCACCCCATTGGGGCATGGCTTGTCAC-GCACTGGGCATG
782686 CATATCACCC
Statistics
Matches: 433, Mismatches: 88, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
135 7 0.02
136 75 0.17
137 36 0.08
138 292 0.67
139 23 0.05
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.25
Consensus pattern (135 bp):
GGGCATGGCGTGTCACCCCACTAGGGCATGGCGTGTCACTGCATTGGGGCATGGCGTGTCACCGC
ATTAGGGCATGGCTTGTCACCCCATTGGGGCATGGCTTGTCACGCACTGGGCATGGCGTGTCACC
GTATT
Found at i:782694 original size:44 final size:44
Alignment explanation
Indices: 782470--782695 Score: 134
Period size: 46 Copynumber: 5.0 Consensus size: 44
782460 AGTGTCACAG
* * * *
782470 CATTGGGGCATGGCGTGTCAACGCATTAGGGCATGGCATGTCACCC
1 CATTGGGGCATGGCATATCACCACA-TA-GGCATGGCATGTCACCC
* * * * * * *
782516 CACTGGGGCATGGCTTGTCACCACACTGGGGCATGGCTTGTCATCG
1 CATTGGGGCATGGCATATCACCACA-T-AGGCATGGCATGTCACCC
* * * * * * * *
782562 TACTAGGG-TTAGGCGTGTCACCACAATGGGGCATGGCATGTCACCG
1 CATTGGGGCAT-GGCATATCACCAC-AT-AGGCATGGCATGTCACCC
* * *
782608 CATTGGGGCATGGCTTATCACCACATGGGCATGGCTTGTCACCC
1 CATTGGGGCATGGCATATCACCACATAGGCATGGCATGTCACCC
* *
782652 CATTGGGGCATGGCATGTCACTGCAC-TAGGCAT-GCATATCACCC
1 CATTGGGGCATGGCATATCAC--CACATAGGCATGGCATGTCACCC
782696 TGACTAACAT
Statistics
Matches: 146, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
44 44 0.30
45 9 0.06
46 91 0.62
47 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.23
Consensus pattern (44 bp):
CATTGGGGCATGGCATATCACCACATAGGCATGGCATGTCACCC
Found at i:784224 original size:22 final size:22
Alignment explanation
Indices: 784196--784252 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
784186 TTTTTCAACT
* *
784196 ATGTTACACGCCACGCTGAAAA
1 ATGTTACACGCCAAGCTCAAAA
*
784218 ATGTTACACG-CAAGTTCAAAA
1 ATGTTACACGCCAAGCTCAAAA
784239 ATTGTTACACGCCA
1 A-TGTTACACGCCA
784253 TGTTCACTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.30
22 19 0.63
23 2 0.07
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (22 bp):
ATGTTACACGCCAAGCTCAAAA
Found at i:785580 original size:3 final size:3
Alignment explanation
Indices: 785574--785620 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
785564 TTTTAAAAGG
785574 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
785621 AGTAACATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:786789 original size:18 final size:17
Alignment explanation
Indices: 786753--786796 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
786743 ACTCTTTAAA
786753 TTTTCT-CATCAAATAC
1 TTTTCTACATCAAATAC
*
786769 TTTTCTACATCTAATTAC
1 TTTTCTACATC-AAATAC
786787 TTTTCTACAT
1 TTTTCTACAT
786797 ATATCTCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 15 0.60
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTCTACATCAAATAC
Found at i:788015 original size:27 final size:27
Alignment explanation
Indices: 787940--788015 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
787930 ATGCCTAGAT
* *
787940 GTGTTTCAAGAGTGGAAGCACCCAAGG
1 GTGTTCCAAGAGTGAAAGCACCCAAGG
* *
787967 GTGTTCCAAGCACT-AAAGCACCTAAGG
1 GTGTTCCAAG-AGTGAAAGCACCCAAGG
* *
787994 GTGTTCCAAGTGTGAAAACACC
1 GTGTTCCAAGAGTGAAAGCACC
788016 AAAGAACAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.03
27 37 0.93
28 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (27 bp):
GTGTTCCAAGAGTGAAAGCACCCAAGG
Found at i:794483 original size:21 final size:20
Alignment explanation
Indices: 794457--794499 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
794447 GTATTCTTGA
794457 AAACTAAACCTCATTTTA-CCT
1 AAACTAAA-CT-ATTTTAGCCT
794478 AAACTAAACTATTTTAGCCT
1 AAACTAAACTATTTTAGCCT
794498 AA
1 AA
794500 TAACTCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (20 bp):
AAACTAAACTATTTTAGCCT
Found at i:808890 original size:7 final size:7
Alignment explanation
Indices: 808878--808919 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
808868 GCAAAAGAGG
808878 GAAGAAA
1 GAAGAAA
*
808885 GGAGAAA
1 GAAGAAA
808892 GAAGAAA
1 GAAGAAA
*
808899 AAAGAAA
1 GAAGAAA
*
808906 GGAGAAA
1 GAAGAAA
808913 GAAGAAA
1 GAAGAAA
808920 AAGGCTTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:808903 original size:21 final size:21
Alignment explanation
Indices: 808879--808921 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
808869 CAAAAGAGGG
808879 AAGAAAGGAGAAAGAAGAAAA
1 AAGAAAGGAGAAAGAAGAAAA
808900 AAGAAAGGAGAAAGAAGAAAA
1 AAGAAAGGAGAAAGAAGAAAA
808921 A
1 A
808922 GGCTTGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGAAAGGAGAAAGAAGAAAA
Found at i:814472 original size:31 final size:32
Alignment explanation
Indices: 814411--814476 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
814401 GTTTCAATAT
814411 TTTTTTTTATTTCTCTTTCATATATATTTATA
1 TTTTTTTTATTTCTCTTTCATATATATTTATA
* * *
814443 TTTTTTTTCTTT-TC-TTCATCATTTTTTTATA
1 TTTTTTTTATTTCTCTTTCAT-ATATATTTATA
814474 TTT
1 TTT
814477 AGAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
31 14 0.47
32 11 0.37
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTTTTTATTTCTCTTTCATATATATTTATA
Found at i:818656 original size:22 final size:22
Alignment explanation
Indices: 818631--818672 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
818621 AGTTATTTGG
818631 GCTTAATT-TTGATAGTAATTTA
1 GCTTAATTCTT-ATAGTAATTTA
*
818653 GCTTAGTTCTTATAGTAATT
1 GCTTAATTCTTATAGTAATT
818673 CATAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (22 bp):
GCTTAATTCTTATAGTAATTTA
Found at i:825187 original size:23 final size:23
Alignment explanation
Indices: 825157--825283 Score: 114
Period size: 23 Copynumber: 5.6 Consensus size: 23
825147 CAAGGTTGAT
*
825157 ACGCCATGCCCGAATGCGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
*
825180 ACGCCATGCCCCAATGCAGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * *
825203 ACGTCATGCCCCAGTGGGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * * *
825226 AAC-CCATGCTCCAGTGGGGCGAC
1 -ACGCCATGCCCCAATGCGGTGAC
* *
825249 ACGTCATGCCCTAATGC-GTGAC
1 ACGCCATGCCCCAATGCGGTGAC
**
825271 ACAACATGCCCCA
1 ACGCCATGCCCCA
825284 TGTTGGTCCC
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
22 16 0.19
23 66 0.79
24 2 0.02
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (23 bp):
ACGCCATGCCCCAATGCGGTGAC
Found at i:828160 original size:15 final size:16
Alignment explanation
Indices: 828142--828174 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
828132 ATCTCCCTAA
828142 ATTAAAAGCAAA-TGC
1 ATTAAAAGCAAATTGC
828157 ATTAAAAGCAAATTGC
1 ATTAAAAGCAAATTGC
828173 AT
1 AT
828175 CATCCACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (16 bp):
ATTAAAAGCAAATTGC
Found at i:840658 original size:20 final size:21
Alignment explanation
Indices: 840625--840663 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
840615 ATTGCCTTCT
* *
840625 TTCATTTTTTTTTTCAATTAA
1 TTCATTTTTATTTTAAATTAA
840646 TTCA-TTTTATTTTAAATT
1 TTCATTTTTATTTTAAATT
840664 TGGTATTACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCATTTTTATTTTAAATTAA
Found at i:849231 original size:14 final size:14
Alignment explanation
Indices: 849212--849242 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
849202 TCTAGATTTA
849212 ATTATTATATTATT
1 ATTATTATATTATT
*
849226 ATTATTATTTTATT
1 ATTATTATATTATT
849240 ATT
1 ATT
849243 TATAATTATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTATATTATT
Found at i:851310 original size:54 final size:54
Alignment explanation
Indices: 851237--851345 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
851227 AAGGAATTTT
*
851237 CAATCCACTAAAAGAATTCTTGCTTTTTAACAAGATAAAACGATAACTCTTACA
1 CAATCCACTAAAAGAATTCTTGCTTTTTAACAAGATAAAACGATAACCCTTACA
* *
851291 CAATCCA-TAAAAGAGATTCTTGCTTTTTAACAAGATCAAGCGATAACCCTTACA
1 CAATCCACTAAAAGA-ATTCTTGCTTTTTAACAAGATAAAACGATAACCCTTACA
851345 C
1 C
851346 CGACTTTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 7 0.14
54 44 0.86
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (54 bp):
CAATCCACTAAAAGAATTCTTGCTTTTTAACAAGATAAAACGATAACCCTTACA
Found at i:853327 original size:31 final size:30
Alignment explanation
Indices: 853281--853367 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
853271 GAGTTTCGCG
* *
853281 TATGCGTGGCATGTCACGACATTTGACTTGA
1 TATGCATGGCGTGTCAC-ACATTTGACTTGA
* *
853312 TATGCATGGCGTGTCATCACATTTTACTTGT
1 TATGCATGGCGTGTCA-CACATTTGACTTGA
*
853343 TATGCATGGCGTGTAACCACATTTG
1 TATGCATGGCGTGTCA-CACATTTG
853368 TGCCATGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 47 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (30 bp):
TATGCATGGCGTGTCACACATTTGACTTGA
Found at i:859222 original size:23 final size:23
Alignment explanation
Indices: 859172--859222 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
859162 CGACCGCCCA
* *
859172 CCCCCCCCGCGGTGCCCGACGCC
1 CCCCCCCCGCCGCGCCCGACGCC
* *
859195 TCCCCCCCGCCGCGCCCG-CGCG
1 CCCCCCCCGCCGCGCCCGACGCC
859217 CCCCCC
1 CCCCCC
859223 TGCAGCCCCG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.02, C:0.71, G:0.24, T:0.04
Consensus pattern (23 bp):
CCCCCCCCGCCGCGCCCGACGCC
Found at i:859248 original size:18 final size:18
Alignment explanation
Indices: 859196--859249 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
859186 CCCGACGCCT
*
859196 CCCCCCCGCCGCGCCCGCG
1 CCCCCCCGGCGC-CCCGCG
* *
859215 CGCCCCCCTGCAGCCCCGGG
1 C-CCCCCCGGC-GCCCCGCG
859235 CCCCCCCGGCGCCCC
1 CCCCCCCGGCGCCCC
859250 CCCGGGGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 13 0.45
21 2 0.07
ACGTcount: A:0.02, C:0.70, G:0.26, T:0.02
Consensus pattern (18 bp):
CCCCCCCGGCGCCCCGCG
Found at i:867407 original size:13 final size:13
Alignment explanation
Indices: 867389--867413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
867379 AGATAATTAG
867389 GAGATTATGAAAT
1 GAGATTATGAAAT
867402 GAGATTATGAAA
1 GAGATTATGAAA
867414 CAAGTTGAAT
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:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (13 bp):
GAGATTATGAAAT
Found at i:872405 original size:13 final size:13
Alignment explanation
Indices: 872387--872411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
872377 ATTCAAAATC
872387 TATCAATACATTG
1 TATCAATACATTG
872400 TATCAATACATT
1 TATCAATACATT
872412 TGGATAGTGT
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:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
TATCAATACATTG
Found at i:904723 original size:12 final size:12
Alignment explanation
Indices: 904691--904732 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
904681 CTTTTTTTTT
904691 TAAA-AAAA-AA
1 TAAATAAAATAA
904701 TAAAT-AAATAA
1 TAAATAAAATAA
904712 TAAATAAAATAA
1 TAAATAAAATAA
904724 TAAATAAAA
1 TAAATAAAA
904733 AATTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.24
11 7 0.24
12 15 0.52
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAATAAAATAA
Found at i:904739 original size:12 final size:10
Alignment explanation
Indices: 904691--904757 Score: 62
Period size: 12 Copynumber: 6.0 Consensus size: 10
904681 CTTTTTTTTT
904691 TAAAAAAAAA
1 TAAAAAAAAA
*
904701 TAAATAAATAA
1 TAAA-AAAAAA
904712 TAAATAAAATAA
1 TAAA-AAAA-AA
904724 TAAATAAAAAA
1 TAAA-AAAAAA
904735 TTAAAAAAAAA
1 -TAAAAAAAAA
904746 GTTAAAAAAAAA
1 --TAAAAAAAAA
904758 GAGCTGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
10 4 0.08
11 21 0.41
12 26 0.51
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.19
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:904745 original size:11 final size:11
Alignment explanation
Indices: 904691--904745 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
904681 CTTTTTTTTT
904691 TAAA-AAAAAA
1 TAAATAAAAAA
*
904701 TAAATAAATAA
1 TAAATAAAAAA
904712 TAAATAAAATAA
1 TAAATAAAA-AA
904724 TAAATAAAAAA
1 TAAATAAAAAA
904735 TTAAA-AAAAAA
1 -TAAATAAAAAA
904746 GTTAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
10 4 0.10
11 21 0.52
12 15 0.38
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAATAAAAAA
Found at i:914550 original size:2 final size:2
Alignment explanation
Indices: 914545--914581 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
914535 CAACATTCTA
914545 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 A
914582 ATTGTAGTTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:915150 original size:4 final size:4
Alignment explanation
Indices: 915105--915141 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
915095 TTATGTGTCC
*
915105 ATGT TTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
915142 CATGTATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:915155 original size:2 final size:2
Alignment explanation
Indices: 915148--915174 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
915138 TGTACATGTA
915148 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
915175 AAGGACGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:918118 original size:18 final size:18
Alignment explanation
Indices: 918089--918132 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
918079 AGCGAGCAGA
*
918089 ATCAACTTTAAAACTTGAT
1 ATCAA-TTTAAAACTAGAT
* *
918108 GTCAATTTAAAGCTAGAT
1 ATCAATTTAAAACTAGAT
918126 ATCAATT
1 ATCAATT
918133 GACAAGCTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (18 bp):
ATCAATTTAAAACTAGAT
Found at i:923239 original size:15 final size:16
Alignment explanation
Indices: 923208--923250 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
923198 TTATTTTGTG
923208 TTAACGTTATAAAAATTA
1 TTAAC-TTAT-AAAATTA
923226 -TAACTTATAAAATTA
1 TTAACTTATAAAATTA
923241 TTAA-TTATAA
1 TTAACTTATAA
923251 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAACTTATAAAATTA
Found at i:924608 original size:23 final size:23
Alignment explanation
Indices: 924582--924625 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
924572 ATTTCTTACA
*
924582 ATAAAAAAATAGAAAATATATGC
1 ATAAAAAAATAAAAAATATATGC
* *
924605 ATAAGAGAATAAAAAATATAT
1 ATAAAAAAATAAAAAATATAT
924626 AAAAATATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (23 bp):
ATAAAAAAATAAAAAATATATGC
Found at i:932718 original size:15 final size:15
Alignment explanation
Indices: 932684--932722 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
932674 CTAATTAAAC
*
932684 TAAAAATTACTCAAT
1 TAAAAATTAATCAAT
*
932699 T-AAAATTAATTAAT
1 TAAAAATTAATCAAT
932713 TAAAAATTAA
1 TAAAAATTAA
932723 AGCAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAAATTAATCAAT
Found at i:939238 original size:80 final size:80
Alignment explanation
Indices: 939123--939404 Score: 369
Period size: 80 Copynumber: 3.6 Consensus size: 80
939113 ATCCTTAACC
*
939123 CATAGTGTATATGACTATCTCCACACATATC-TCTCATGGCATACATTTCATAATCTCATAAATC
1 CATAGTGTATATGACTATCTCAACACATA-CATCTCATGGCATACATTTCATAATCTCATAAATC
*
939187 ACTTGCATGCTTAGCT
65 ACTTACATGCTTAGCT
* * * *
939203 GATAATGTATATGACTATCTCAACACATAGATCTCATGGCATACATTTCATATTCTCATAAATCA
1 CATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAATCTCATAAATCA
*
939268 CTTACATGCTTAGCC
66 CTTACATGCTTAGCT
* * **
939283 CATAGTGTATATGATTATCTCAACATATACATCTCATGGCATAC----CATAGCCTCATAAATCA
1 CATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAATCTCATAAATCA
939344 CTTACATGCTTAGCT
66 CTTACATGCTTAGCT
* * * *
939359 TATAGTGTACATGA-TATTCTTAACAAATACATCTCATGGCATACAT
1 CATAGTGTATATGACTA-TCTCAACACATACATCTCATGGCATACAT
939405 GTTACAATCT
Statistics
Matches: 179, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
75 2 0.01
76 66 0.37
80 111 0.62
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (80 bp):
CATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAATCTCATAAATCA
CTTACATGCTTAGCT
Found at i:939399 original size:156 final size:157
Alignment explanation
Indices: 939116--939404 Score: 397
Period size: 156 Copynumber: 1.8 Consensus size: 157
939106 CATCATCATC
*
939116 CTTAACCCATAGTGTATATGACTATCTCCACACATATCTCTCATGGCATACATTTCATAATCTCA
1 CTTAACCCATAGTGTATATGACTATCTCCACACATATCTCTCATGGCATAC---TCATAACCTCA
* * * *
939181 TAAATCACTTGCATGCTTAGCTGATAATGTATATGACTATCTCAACACATAGATCTCATGGCATA
63 TAAATCACTTACATGCTTAGCTGATAATGTACATGACTATCTCAACAAATACATCTCATGGCATA
939246 CATTTCATATTCTCATAAATCACTTACATG
128 CATTTCATATTCTCATAAATCACTTACATG
* * *
939276 CTTAGCCCATAGTGTATATGATTATCT-CA-ACATATACATCTCATGGCATAC-CATAGCCTCAT
1 CTTAACCCATAGTGTATATGACTATCTCCACACATAT-C-TCTCATGGCATACTCATAACCTCAT
* * *
939338 AAATCACTTACATGCTTAGCTTATAGTGTACATGA-TATTCTTAACAAATACATCTCATGGCATA
64 AAATCACTTACATGCTTAGCTGATAATGTACATGACTA-TCTCAACAAATACATCTCATGGCATA
939402 CAT
128 CAT
939405 GTTACAATCT
Statistics
Matches: 115, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
155 2 0.02
156 66 0.57
158 6 0.05
159 3 0.03
160 38 0.33
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (157 bp):
CTTAACCCATAGTGTATATGACTATCTCCACACATATCTCTCATGGCATACTCATAACCTCATAA
ATCACTTACATGCTTAGCTGATAATGTACATGACTATCTCAACAAATACATCTCATGGCATACAT
TTCATATTCTCATAAATCACTTACATG
Found at i:940725 original size:16 final size:17
Alignment explanation
Indices: 940691--940733 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
940681 GGATTCAATA
940691 AAAATATAAAAAAACTC
1 AAAATATAAAAAAACTC
* *
940708 AAAATCTAAAATAA-TC
1 AAAATATAAAAAAACTC
*
940724 AAAATTTAAA
1 AAAATATAAA
940734 GTTTGGTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATATAAAAAAACTC
Found at i:948574 original size:30 final size:30
Alignment explanation
Indices: 948540--948597 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
948530 CGCCGCTAAG
948540 TTCTCTCTACGTTCCCCT-TTCCCCTATTGT
1 TTCTCT-TACGTTCCCCTCTTCCCCTATTGT
* * *
948570 TTCTCTTACTTTCCTCTCTTCCCTTATT
1 TTCTCTTACGTTCCCCTCTTCCCCTATT
948598 CATAGTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.07, C:0.38, G:0.03, T:0.52
Consensus pattern (30 bp):
TTCTCTTACGTTCCCCTCTTCCCCTATTGT
Found at i:948799 original size:17 final size:17
Alignment explanation
Indices: 948748--948792 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
948738 TAAATTTATC
*
948748 TATTTTATTTTAAATAT
1 TATTTTATTTTAAATTT
** *
948765 TATTTTATTTGCATTTT
1 TATTTTATTTTAAATTT
948782 TATTTTATTTT
1 TATTTTATTTT
948793 TTATTTTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TATTTTATTTTAAATTT
Found at i:949550 original size:252 final size:252
Alignment explanation
Indices: 949097--950111 Score: 1100
Period size: 252 Copynumber: 4.0 Consensus size: 252
949087 TAATTGTAAA
* * * * * * * * *
949097 TTTTCACTGTATTTATTTTTATCTTTACTGTAATTTATTTATAGAGTAAAATTTATAAACCATTA
1 TTTTCACTATAATTATTTTTATCCTTACTATTATTCATTTATAAATTAAAATTTATAAAACATTA
** * * * *
949162 AATACTTTTAAACTTGAGAATAAAAATATAAATGTTTAGTTTTTCAAAAAATTATATTTATTTGA
66 AATAC-TTTAAACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAAATTATGTTTATTTGA
* * * * * * *
949227 CTTACTTGACCTGTTATGTTAAATCTCACATGTTTACGT-AATATTTTAACAATTCTTGTTCCAC
130 CATAATTGACTTGTTACGTTAAATCTCACATATTTACATCAATATTTTAACAATACTTGTTCCAC
* * ** *
949291 TTTTATAATTTTTTATGTTAATTCTTACAAGTTTAGGGGT-AAGTTTTTTCAATTGCTAT
195 CTTTATAATTTTTTATATTAATTCTTACAAGTTTA-GCATCAAG-TTTTTCAATTACTAT
* * * *
949350 TTTTCACAATAATTATTTTTATCCTTACTATTATTCATCTATAAATTAATATTTTTAAAACATTA
1 TTTTCACTATAATTATTTTTATCCTTACTATTATTCATTTATAAATTAAAATTTATAAAACATTA
* * *
949415 AATACTTTAAACTCAAGAACATAAATTTAAGTGTTTAATTTTTCAAAATATTATGTTTATTTGAC
66 AATACTTTAAACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAAATTATGTTTATTTGAC
* * * * * * **
949480 ATAATT-AGCTTGTAACGTTAAATCTCATAT-TTTACGTTAATAATTTAGCAATGTTTGTTCCAC
131 ATAATTGA-CTTGTTACGTTAAATCTCACATATTTACATCAATATTTTAACAATACTTGTTCCAC
* * * *
949543 CTTTATAATTTATTTATATTAATTATTATAGGTTT-GCATCAAAGTTTGTCAATTACTAT
195 CTTTATAATTT-TTTATATTAATTCTTACAAGTTTAGCATC-AAGTTTTTCAATTACTAT
* *
949602 TTTTCACTATAATTATTTTTATCCTTACTATTATTCATTTATAAATTAAAATTTATAAACCGTTA
1 TTTTCACTATAATTATTTTTATCCTTACTATTATTCATTTATAAATTAAAATTTATAAAACATTA
* * *
949667 AAAACTTTAAACTCAAGAATATAAATTTCAATGTTTAA-TTTTCTAAAAAATTTTGTTTATTTGA
66 AATACTTTAAACTCAAGAATATAAATTTAAATGTTTAATTTTTC-AAAAAATTATGTTTATTTGA
* * * * * ** * *
949731 CATAATTAACGTATTATGTTAAATGTCACACGTTTACATCAATATTTTAACAATACTTATTCTAC
130 CATAATTGACTTGTTACGTTAAATCTCACATATTTACATCAATATTTTAACAATACTTGTTCCAC
* * *
949796 CTTTATAATTTTTTATATTAATTCTTACAGGCTTA-CATCAAGATTTTTCAATTAATAAT
195 CTTTATAATTTTTTATATTAATTCTTACAAGTTTAGCATCAAG-TTTTTCAATTACT-AT
* * * * * *
949855 TTTT-ATTATAATTATTTTTATCTTTAATATTGTTTATTTATAAATTAAAATTTAT-ATACTATT
1 TTTTCACTATAATTATTTTTATCCTTACTATTATTCATTTATAAATTAAAATTTATAAAAC-ATT
* * * *
949918 AAATACTTTAAACTCGAGAATATAAATTTAAATATTTAATTTTTCAAAAACTTATGTTTATTTAA
65 AAATACTTTAAACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAAATTATGTTTATTTGA
* * * *
949983 TATAATTGACTTGTTACATTAAATTTCACATATTTACATCAATATTTTAACAATACTTGTTCTAC
130 CATAATTGACTTGTTACGTTAAATCTCACATATTTACATCAATATTTTAACAATACTTGTTCCAC
* * * * * *
950048 CTTTATAA--TTTTATGTTAATTTTTACAAGTTCA-CGTCAAGCTTTTTCAACTACTAA
195 CTTTATAATTTTTTATATTAATTCTTACAAGTTTAGCATCAAG-TTTTTCAATTACTAT
950104 TTTTCACT
1 TTTTCACT
950112 TTTCCTTTTA
Statistics
Matches: 639, Mismatches: 109, Indels: 31
0.82 0.14 0.04
Matches are distributed among these distances:
249 5 0.01
250 39 0.06
251 20 0.03
252 448 0.70
253 127 0.20
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.47
Consensus pattern (252 bp):
TTTTCACTATAATTATTTTTATCCTTACTATTATTCATTTATAAATTAAAATTTATAAAACATTA
AATACTTTAAACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAAATTATGTTTATTTGAC
ATAATTGACTTGTTACGTTAAATCTCACATATTTACATCAATATTTTAACAATACTTGTTCCACC
TTTATAATTTTTTATATTAATTCTTACAAGTTTAGCATCAAGTTTTTCAATTACTAT
Found at i:957660 original size:24 final size:25
Alignment explanation
Indices: 957628--957694 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 25
957618 CTATTGTACT
*
957628 TGGTTTGTTGATGA-CATTTTGATA
1 TGGTCTGTTGATGATCATTTTGATA
957652 TGGTCTGTTGATGATAATCATTTTGATA
1 TGGTCTGTTGATG---ATCATTTTGATA
* *
957680 AGATCTGTTGATGAT
1 TGGTCTGTTGATGAT
957695 AATCATTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 12 0.33
25 2 0.06
27 1 0.03
28 21 0.58
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (25 bp):
TGGTCTGTTGATGATCATTTTGATA
Found at i:957675 original size:28 final size:28
Alignment explanation
Indices: 957642--957704 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
957632 TTGTTGATGA
* *
957642 CATTTTGATATGGTCTGTTGATGATAAT
1 CATTTTGATAAGATCTGTTGATGATAAT
957670 CATTTTGATAAGATCTGTTGATGATAAT
1 CATTTTGATAAGATCTGTTGATGATAAT
957698 CATTTTG
1 CATTTTG
957705 TTGAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (28 bp):
CATTTTGATAAGATCTGTTGATGATAAT
Found at i:959937 original size:35 final size:34
Alignment explanation
Indices: 959857--959974 Score: 128
Period size: 34 Copynumber: 3.4 Consensus size: 34
959847 AAGTTATTCC
* *
959857 TAATTAATTAAATTGTTTAATTAAGTTAAAGGCA
1 TAATTAATTAAATTATTTAATTAAATTAAAGGCA
*** *
959891 TAATTAATTAAATTATTTAATTAAATTGTTGGGCT
1 TAATTAATTAAATTATTTAATTAAATT-AAAGGCA
* ** * *
959926 TAATTAATTAAATTATTTAATTAAGTTATCGACC
1 TAATTAATTAAATTATTTAATTAAATTAAAGGCA
959960 TAATTAATTAAATTA
1 TAATTAATTAAATTA
959975 AACAATTAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 43 0.60
35 29 0.40
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (34 bp):
TAATTAATTAAATTATTTAATTAAATTAAAGGCA
Found at i:961797 original size:16 final size:16
Alignment explanation
Indices: 961776--961808 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
961766 CAATGAATGA
961776 AGAATAAGT-TAAATTG
1 AGAATAA-TATAAATTG
961792 AGAATAATATAAATTG
1 AGAATAATATAAATTG
961808 A
1 A
961809 CGCCAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (16 bp):
AGAATAATATAAATTG
Found at i:975822 original size:19 final size:19
Alignment explanation
Indices: 975795--975842 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
975785 AAACAATTAT
* *
975795 TAAAAAATATGACAAATAC
1 TAAATAATATAACAAATAC
* * *
975814 TGAATAATATAACTAATAG
1 TAAATAATATAACAAATAC
975833 TAAATAATAT
1 TAAATAATAT
975843 TCTTACTCAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (19 bp):
TAAATAATATAACAAATAC
Found at i:986087 original size:1 final size:1
Alignment explanation
Indices: 986076--986118 Score: 68
Period size: 1 Copynumber: 43.0 Consensus size: 1
986066 TCAACGGCCT
* *
986076 CCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
986119 GATACCAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.95, G:0.02, T:0.02
Consensus pattern (1 bp):
C
Found at i:997898 original size:59 final size:58
Alignment explanation
Indices: 997791--997955 Score: 199
Period size: 57 Copynumber: 2.9 Consensus size: 58
997781 TCCTATCTTT
* * * * * **
997791 AATTAAGAAAAAACATATTATGTTGTC-TAAATTGAGACAAATAAGTTTTTTTATGTA
1 AATTAAGACAAAACATATTTTCTTGTCTTAAATTAAGACAAATATGTTTTTTTATCAA
* * *
997848 GATTAAGACAAAACATATTTTTCTTGTCTTAAATTAAGACAAGTATGTTTTTTTGTCAA
1 AATTAAGACAAAACATA-TTTTCTTGTCTTAAATTAAGACAAATATGTTTTTTTATCAA
* *
997907 AATTAAGACAAAGCATA-TTTCTTGTCTTAAATTAAGACAAACATGTTTT
1 AATTAAGACAAAACATATTTTCTTGTCTTAAATTAAGACAAATATGTTTT
997956 CTTGTTTAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
57 45 0.49
58 8 0.09
59 39 0.42
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (58 bp):
AATTAAGACAAAACATATTTTCTTGTCTTAAATTAAGACAAATATGTTTTTTTATCAA
Found at i:997899 original size:57 final size:57
Alignment explanation
Indices: 997791--997980 Score: 183
Period size: 57 Copynumber: 3.3 Consensus size: 57
997781 TCCTATCTTT
* * * * *
997791 AATTAAGAAAAAACATATTATGTTGTC-TAAATTGAGACAAATAAGTTTTTTTATGT-A
1 AATTAAGACAAAACATATTTTCTTGTCTTAAATTAAGACAAAT-A-TGTTTTTATGTAA
* * *
997848 GATTAAGACAAAACATATTTTTCTTGTCTTAAATTAAGACAAGTATGTTTTTTTGTCAA
1 AATTAAGACAAAACATA-TTTTCTTGTCTTAAATTAAGACAAATATGTTTTTATGT-AA
* * *
997907 AATTAAGACAAAGCATA-TTTCTTGTCTTAAATTAAGACAAACATGTTTTCT-TGTTTA
1 AATTAAGACAAAACATATTTTCTTGTCTTAAATTAAGACAAATATGTTTT-TATG-TAA
*
997964 AATAAAGA-AAAACATAT
1 AATTAAGACAAAACATAT
997981 AAAAGCTATC
Statistics
Matches: 111, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
56 7 0.06
57 64 0.58
58 11 0.10
59 29 0.26
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (57 bp):
AATTAAGACAAAACATATTTTCTTGTCTTAAATTAAGACAAATATGTTTTTATGTAA
Found at i:997931 original size:28 final size:30
Alignment explanation
Indices: 997849--997971 Score: 123
Period size: 29 Copynumber: 4.2 Consensus size: 30
997839 TTTTATGTAG
*
997849 ATTAAGACAAAACAT-ATTTTTCTTGTCTTAA
1 ATTAAGACAAAGCATGA--TTTCTTGTCTTAA
* * * *
997880 ATTAAGAC-AAGTATGTTTTTTTGTC-AAA
1 ATTAAGACAAAGCATGATTTCTTGTCTTAA
997908 ATTAAGACAAAGCAT-ATTTCTTGTCTTAA
1 ATTAAGACAAAGCATGATTTCTTGTCTTAA
*
997937 ATTAAGACAAA-CATGTTTTCTTGT-TTAA
1 ATTAAGACAAAGCATGATTTCTTGTCTTAA
*
997965 ATAAAGA
1 ATTAAGA
997972 AAAACATATA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
28 31 0.40
29 34 0.44
30 4 0.05
31 8 0.10
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (30 bp):
ATTAAGACAAAGCATGATTTCTTGTCTTAA
Found at i:997945 original size:29 final size:29
Alignment explanation
Indices: 997786--997980 Score: 122
Period size: 28 Copynumber: 6.8 Consensus size: 29
997776 ACAACTCCTA
* * *
997786 TCTTTAATTAAGAAAAAACATATTATGTTG
1 TCTTAAATTAAGACAAAACATATT-TCTTG
*
997816 TC-TAAATTGAGACAAATA-AGT-TTT-TT-
1 TCTTAAATTAAGACAAA-ACA-TATTTCTTG
* *
997842 TATGTAGATTAAGACAAAACATATTTTTCTTG
1 TCT-TAAATTAAGACAAAACATA--TTTCTTG
** * *
997874 TCTTAAATTAAGAC-AAGTATGTTTTTTTG
1 TCTTAAATTAAGACAAAACAT-ATTTCTTG
* *
997903 TC-AAAATTAAGACAAAGCATATTTCTTG
1 TCTTAAATTAAGACAAAACATATTTCTTG
*
997931 TCTTAAATTAAGAC-AAACATGTTTTCTTG
1 TCTTAAATTAAGACAAAACAT-ATTTCTTG
*
997960 T-TTAAATAAAGA-AAAACATAT
1 TCTTAAATTAAGACAAAACATAT
997981 AAAAGCTATC
Statistics
Matches: 129, Mismatches: 21, Indels: 33
0.70 0.11 0.18
Matches are distributed among these distances:
26 1 0.01
27 5 0.04
28 53 0.41
29 45 0.35
30 11 0.09
31 12 0.09
32 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (29 bp):
TCTTAAATTAAGACAAAACATATTTCTTG
Found at i:1001952 original size:15 final size:14
Alignment explanation
Indices: 1001934--1001987 Score: 63
Period size: 15 Copynumber: 3.7 Consensus size: 14
1001924 GCAAAGTGAG
1001934 AAAGAAAGGAGAAA
1 AAAGAAAGGAGAAA
1001948 GAAAGAAAGGAAGAAA
1 -AAAGAAAGG-AGAAA
* *
1001964 AAAGGAAGAAGAAA
1 AAAGAAAGGAGAAA
*
1001978 AAGGAAAGGA
1 AAAGAAAGGA
1001988 AAGATTGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 12 0.36
15 16 0.48
16 5 0.15
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AAAGAAAGGAGAAA
Found at i:1009761 original size:20 final size:20
Alignment explanation
Indices: 1009738--1009776 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1009728 AATTAGAAAA
1009738 TTTTT-AAAAAAATATATTTT
1 TTTTTGAAAAAAAT-TATTTT
1009758 TTTTTGAAAAAAATTATTT
1 TTTTTGAAAAAAATTATTT
1009777 ATTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTTGAAAAAAATTATTTT
Found at i:1010011 original size:33 final size:32
Alignment explanation
Indices: 1009963--1010027 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
1009953 ACAGAATTTT
* * *
1009963 AATATAAGAATAACTCTCTTTTTTTCAAAAAAA
1 AATACAAGAAAAACTCTCTTTTCTT-AAAAAAA
*
1009996 AATACAAGAAAAACTCTGTTTTCTTAAAAAAA
1 AATACAAGAAAAACTCTCTTTTCTTAAAAAAA
1010028 TATTAATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (32 bp):
AATACAAGAAAAACTCTCTTTTCTTAAAAAAA
Found at i:1013304 original size:18 final size:19
Alignment explanation
Indices: 1013278--1013325 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1013268 GTGATAGATA
*
1013278 AAAAGAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
1013296 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
*
1013315 AAAATATTATT
1 AAAATAATATT
1013326 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:1018041 original size:18 final size:19
Alignment explanation
Indices: 1018015--1018062 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1018005 ATGATAGGTA
*
1018015 AAAAAAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
1018033 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
*
1018052 AAAATATTATT
1 AAAATAATATT
1018063 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:1025076 original size:36 final size:36
Alignment explanation
Indices: 1024965--1025077 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
1024955 TGATCTTGTG
*
1024965 AAAAAG-CATTGTGAGAGTTATCGCTTGAT-CTCGTT
1 AAAAAGTCATTGTGAGAGTTATCGCTTAATCCT-GTT
* ** *
1025000 AAAAAGTCGTTGTGAGCA-TTATCGCTTAATCCAATG
1 AAAAAGTCATTGTGAG-AGTTATCGCTTAATCCTGTT
* * * *
1025036 AAAAAGTCATTGTAAGGGTTATCCCTTTATCCTGTT
1 AAAAAGTCATTGTGAGAGTTATCGCTTAATCCTGTT
1025072 AAAAAG
1 AAAAAG
1025078 CAAGAATCTT
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
35 6 0.10
36 53 0.87
37 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (36 bp):
AAAAAGTCATTGTGAGAGTTATCGCTTAATCCTGTT
Found at i:1026077 original size:21 final size:22
Alignment explanation
Indices: 1026048--1026090 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1026038 AATACCATTT
*
1026048 ATTACAATATTTAAT-TTTTAA
1 ATTAAAATATTTAATATTTTAA
*
1026069 ATTAAAATATTTATTATTTTAA
1 ATTAAAATATTTAATATTTTAA
1026091 TAATTCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTAAAATATTTAATATTTTAA
Found at i:1027773 original size:22 final size:22
Alignment explanation
Indices: 1027745--1027810 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
1027735 GTTACAATTT
1027745 TAATGGAATT-AGAGATTATAGG
1 TAATGGAATTGA-AGATTATAGG
*
1027767 TAATGGAATTGAAGATTTTAGG
1 TAATGGAATTGAAGATTATAGG
1027789 TAATGGAATTGAAGATTATAGG
1 TAATGGAATTGAAGATTATAGG
1027811 GTATAGCTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 40 0.98
23 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (22 bp):
TAATGGAATTGAAGATTATAGG
Found at i:1034628 original size:20 final size:21
Alignment explanation
Indices: 1034592--1034631 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1034582 AAAAACTAAT
*
1034592 AAATAACAATCAAATTAAAAG
1 AAATAACAATAAAATTAAAAG
1034613 AAATAAC-ATAAAATTAAAA
1 AAATAACAATAAAATTAAAA
1034632 TAACTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAACAATAAAATTAAAAG
Found at i:1034648 original size:15 final size:16
Alignment explanation
Indices: 1034628--1034666 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1034618 ACATAAAATT
*
1034628 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
1034643 AAAATAAACTAACTATA
1 AAAAT-AACTAACTATA
1034660 AAAATAA
1 AAAATAA
1034667 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 9 0.43
17 7 0.33
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:1034652 original size:16 final size:17
Alignment explanation
Indices: 1034628--1034666 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1034618 ACATAAAATT
*
1034628 AAAAT-AACTCACT-TA
1 AAAATAAACTAACTATA
1034643 AAAATAAACTAACTATA
1 AAAATAAACTAACTATA
1034660 AAAATAA
1 AAAATAA
1034667 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATAAACTAACTATA
Found at i:1040500 original size:17 final size:20
Alignment explanation
Indices: 1040460--1040500 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 20
1040450 AACACATTAT
*
1040460 TATTATTTTGCTATCTTTCT
1 TATTATTTTGCTATCTTTCA
1040480 TATTA-TTT-CTAT-TTTCA
1 TATTATTTTGCTATCTTTCA
1040497 TATT
1 TATT
1040501 TTCTGTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 3 0.15
20 5 0.25
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTATTTTGCTATCTTTCA
Found at i:1041171 original size:17 final size:17
Alignment explanation
Indices: 1041139--1041172 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1041129 GCTCTTTTAG
**
1041139 GTTTTTCTTTTTTATTT
1 GTTTTTCTTTGCTATTT
1041156 GTTTTTCTTTGCTATTT
1 GTTTTTCTTTGCTATTT
1041173 TATGTGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.76
Consensus pattern (17 bp):
GTTTTTCTTTGCTATTT
Found at i:1041853 original size:5 final size:5
Alignment explanation
Indices: 1041840--1041894 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
1041830 TACTTTGACT
*
1041840 ATAAA ATAAG AT-AA A-AAA ATATAA ATAAA ATAAA ATAATA A-AAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATA-AA ATAAA ATAAA ATAA-A ATAAA ATAAA
1041889 GATAAA
1 -ATAAA
1041895 TAACAAAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
4 7 0.17
5 23 0.55
6 12 0.29
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:1041867 original size:19 final size:20
Alignment explanation
Indices: 1041842--1041894 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1041832 CTTTGACTAT
1041842 AAAATAAGATAAAAAAAT-A
1 AAAATAAGATAAAAAAATAA
* * *
1041861 TAAATAAAATAAAATAATAA
1 AAAATAAGATAAAAAAATAA
1041881 AAAATAAAGATAAA
1 AAAAT-AAGATAAA
1041895 TAACAAAGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 15 0.56
20 5 0.19
21 7 0.26
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (20 bp):
AAAATAAGATAAAAAAATAA
Found at i:1041867 original size:24 final size:24
Alignment explanation
Indices: 1041840--1041897 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1041830 TACTTTGACT
*
1041840 ATAAAATAAGATAA-AAAAATATAA
1 ATAAAATAAAATAATAAAAA-ATAA
1041864 ATAAAATAAAATAATAAAAAATAA
1 ATAAAATAAAATAATAAAAAATAA
*
1041888 AGATAAATAA
1 ATA-AAATAA
1041898 CAAAGACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (24 bp):
ATAAAATAAAATAATAAAAAATAA
Found at i:1043498 original size:2 final size:2
Alignment explanation
Indices: 1043491--1043528 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1043481 ATTTAGTTAC
1043491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1043529 GCACATTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1043859 original size:20 final size:20
Alignment explanation
Indices: 1043831--1043868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1043821 CCATCCAATA
*
1043831 GCATTTGTATCAATACATAG
1 GCATATGTATCAATACATAG
*
1043851 GCATATGTATCGATACAT
1 GCATATGTATCAATACAT
1043869 GCAAGAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
GCATATGTATCAATACATAG
Found at i:1046155 original size:12 final size:13
Alignment explanation
Indices: 1046136--1046171 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1046126 CCAAATAGTT
1046136 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
1046149 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
1046160 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1046172 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Done.