Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2678122 original size:30 final size:29
Alignment explanation
Indices: 2678086--2678157 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
2678076 TTTCCCCCTG
* *
2678086 CAATTTGACCCTGAATTTAGCTTTGATATA
1 CAATTTGGCCCTGAATTTAGATTT-ATATA
* * *
2678116 CAATTTGGCACTTGAATTTGGATTTATCTA
1 CAATTTGGC-CCTGAATTTAGATTTATATA
2678146 CAATTTGGCCCT
1 CAATTTGGCCCT
2678158 TAACTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 2 0.06
30 21 0.60
31 12 0.34
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (29 bp):
CAATTTGGCCCTGAATTTAGATTTATATA
Found at i:2679130 original size:2 final size:2
Alignment explanation
Indices: 2679123--2679193 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
2679113 TTACAAAATA
2679123 AT AT 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 AT AT
2679165 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 A
2679194 ATGTACTTAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2679548 original size:10 final size:10
Alignment explanation
Indices: 2679533--2679577 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
2679523 TTTAAACACA
2679533 TCAAATCCTC
1 TCAAATCCTC
2679543 TCAAATCCTC
1 TCAAATCCTC
**
2679553 TCAAATTATC
1 TCAAATCCTC
* *
2679563 TTAAATCCTT
1 TCAAATCCTC
2679573 TCAAA
1 TCAAA
2679578 CCATATCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (10 bp):
TCAAATCCTC
Found at i:2679558 original size:20 final size:20
Alignment explanation
Indices: 2679533--2679587 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
2679523 TTTAAACACA
*
2679533 TCAAATCCTCTCAAATCCTC
1 TCAAATCATCTCAAATCCTC
* * *
2679553 TCAAATTATCTTAAATCCTT
1 TCAAATCATCTCAAATCCTC
* *
2679573 TCAAACCATATCAAA
1 TCAAATCATCTCAAA
2679588 ATCCAAAACC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAATCATCTCAAATCCTC
Found at i:2681773 original size:3 final size:3
Alignment explanation
Indices: 2681767--2681811 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
2681757 ATGATGACAT
* *
2681767 TGA TGA TGA TGA TGG TGA TGA TGA TGA TAA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2681812 GAGTTAGGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:2681777 original size:15 final size:15
Alignment explanation
Indices: 2681757--2681809 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
2681747 AATGATGACA
* *
2681757 ATGATGACATTGATG
1 ATGATGATAATGATG
**
2681772 ATGATGATGGTGATG
1 ATGATGATAATGATG
2681787 ATGATGATAATGATG
1 ATGATGATAATGATG
2681802 ATGATGAT
1 ATGATGAT
2681810 GAGAGTTAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (15 bp):
ATGATGATAATGATG
Found at i:2682152 original size:47 final size:47
Alignment explanation
Indices: 2682096--2682194 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
2682086 TGACTTAATT
*
2682096 TATTTTGTTTATTTTGTTTATTACTTAATTCAAGCGAATGATTTTAG
1 TATTTTGTTTATTTTGTTTATTACTTAATTCAAGCGAATGAGTTTAG
* *
2682143 TATTTTGTTTATTTTGTTTATTACTTAATTGAAGCGAATGAGTTTAT
1 TATTTTGTTTATTTTGTTTATTACTTAATTCAAGCGAATGAGTTTAG
2682190 TATTT
1 TATTT
2682195 ACTGAATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (47 bp):
TATTTTGTTTATTTTGTTTATTACTTAATTCAAGCGAATGAGTTTAG
Found at i:2682204 original size:47 final size:47
Alignment explanation
Indices: 2682106--2682204 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 47
2682096 TATTTTGTTT
* ** **
2682106 ATTTTGTTTATTACTTAATTCAAGCGAATGATTTTAGTATTTTGTTT
1 ATTTTGTTTATTACTTAATTCAAGCGAATGAGTTTAGTATTTACTGA
* *
2682153 ATTTTGTTTATTACTTAATTGAAGCGAATGAGTTTATTATTTACTGA
1 ATTTTGTTTATTACTTAATTCAAGCGAATGAGTTTAGTATTTACTGA
2682200 ATTTT
1 ATTTT
2682205 AATCCTTTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.54
Consensus pattern (47 bp):
ATTTTGTTTATTACTTAATTCAAGCGAATGAGTTTAGTATTTACTGA
Found at i:2687148 original size:16 final size:15
Alignment explanation
Indices: 2687117--2687150 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2687107 TTTTTATAAA
*
2687117 AAATTATAAAAATAT
1 AAATTAAAAAAATAT
2687132 AAATTAAAAATAATAT
1 AAATTAAAAA-AATAT
2687148 AAA
1 AAA
2687151 GAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAAAAAATAT
Found at i:2689243 original size:30 final size:30
Alignment explanation
Indices: 2689207--2689286 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
2689197 GAAAAGAAAC
*
2689207 ATGTTGAAGTGAGTGAAGATAGTGGTGAGG
1 ATGTTGAAGTGAGTGAAGATAGTGGCGAGG
* *
2689237 ATGTTGAAGTGGGTAAAGATAGTGGCGAGG
1 ATGTTGAAGTGAGTGAAGATAGTGGCGAGG
*
2689267 ATGTTGAAGTCAGTGAAGAT
1 ATGTTGAAGTGAGTGAAGAT
2689287 GATAGTGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.31, C:0.03, G:0.40, T:0.26
Consensus pattern (30 bp):
ATGTTGAAGTGAGTGAAGATAGTGGCGAGG
Found at i:2695569 original size:3 final size:3
Alignment explanation
Indices: 2695561--2695593 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2695551 ATTTAAGTTA
2695561 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2695594 GCAAGAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2698248 original size:45 final size:45
Alignment explanation
Indices: 2698205--2698297 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
2698195 TTTAATATTT
* *
2698205 TTAATAAAG-A-GTTATTTAAAATGTTA-TTTTTTATTGTAAATA
1 TTAATAAAGAACGTTACTTAAAATGTTATTTTTTTATTGAAAATA
** *
2698247 TTAATATCGAACGTTACTTAAAATGTTATTTTTTTATTGAAAATG
1 TTAATAAAGAACGTTACTTAAAATGTTATTTTTTTATTGAAAATA
2698292 TTAATA
1 TTAATA
2698298 TCAAAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 7 0.16
43 1 0.02
44 15 0.35
45 20 0.47
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (45 bp):
TTAATAAAGAACGTTACTTAAAATGTTATTTTTTTATTGAAAATA
Found at i:2698269 original size:44 final size:45
Alignment explanation
Indices: 2698215--2698299 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
2698205 TTAATAAAGA
* *
2698215 GTTATTTAAAATGTTA-TTTTTTATTGTAAATATTAATATCGAAC
1 GTTACTTAAAATGTTATTTTTTTATTGAAAATATTAATATCGAAC
*
2698259 GTTACTTAAAATGTTATTTTTTTATTGAAAATGTTAATATC
1 GTTACTTAAAATGTTATTTTTTTATTGAAAATATTAATATC
2698300 AAAAATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 15 0.41
45 22 0.59
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (45 bp):
GTTACTTAAAATGTTATTTTTTTATTGAAAATATTAATATCGAAC
Found at i:2698341 original size:21 final size:20
Alignment explanation
Indices: 2698309--2698365 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
2698299 CAAAAATATT
*
2698309 TATTTTAGGTAGTGAAACTAA
1 TATTTTA-GTAGTGAAAATAA
**
2698330 TATTTTCAGTAGAAAAAATAA
1 TATTTT-AGTAGTGAAAATAA
*
2698351 CATTTTAAGTAGTGA
1 TATTTT-AGTAGTGA
2698366 TCTAGGGGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (20 bp):
TATTTTAGTAGTGAAAATAA
Found at i:2701076 original size:3 final size:3
Alignment explanation
Indices: 2701070--2701143 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
2701060 ATATTATAAA
* *
2701070 TAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2701118 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2701144 AATTTTGTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2701087 original size:21 final size:21
Alignment explanation
Indices: 2701061--2701143 Score: 130
Period size: 21 Copynumber: 4.0 Consensus size: 21
2701051 TTTAAAAAAA
2701061 TATTATAAATATTATTATTAT
1 TATTATAAATATTATTATTAT
2701082 TATTATAAATATTATTATTAT
1 TATTATAAATATTATTATTAT
* *
2701103 TATTATTATTATTATTATTAT
1 TATTATAAATATTATTATTAT
* *
2701124 TATTATTATTATTATTATTA
1 TATTATAAATATTATTATTA
2701144 AATTTTGTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATAAATATTATTATTAT
Found at i:2701435 original size:19 final size:19
Alignment explanation
Indices: 2701388--2701442 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
2701378 CGCCACTGAG
2701388 CCACCAACGCCGAGCCATC
1 CCACCAACGCCGAGCCATC
** * *
2701407 TTATCGACGCCGAGCCATC
1 CCACCAACGCCGAGCCATC
*
2701426 CCACCAACGCTGAGCCA
1 CCACCAACGCCGAGCCA
2701443 CTGAATGTCC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.25, C:0.45, G:0.18, T:0.11
Consensus pattern (19 bp):
CCACCAACGCCGAGCCATC
Found at i:2702909 original size:30 final size:30
Alignment explanation
Indices: 2702875--2702939 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
2702865 ATTTTAGCTT
*
2702875 TTTAATTTTCAATTAATACCATTTTAGTCC
1 TTTAACTTTCAATTAATACCATTTTAGTCC
** * * *
2702905 TTTAACTTTCTGTTTATACTATTTTGGTCC
1 TTTAACTTTCAATTAATACCATTTTAGTCC
2702935 TTTAA
1 TTTAA
2702940 GTTTACGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTAACTTTCAATTAATACCATTTTAGTCC
Found at i:2703045 original size:401 final size:401
Alignment explanation
Indices: 2702302--2703103 Score: 1478
Period size: 401 Copynumber: 2.0 Consensus size: 401
2702292 ATGAAATTTG
* *
2702302 CATTTTAGTCATTATTTTGTATTTTAGGTTAAATCTTAAATTAGATTGTATGTTTTAATTTCATC
1 CATTTTAGTCACTATTTTGTATTTTAGGTTAAATCTTAAATTAGACTGTATGTTTTAATTTCATC
2702367 ACATTTTAGCCCTTAATATTATTAATGGATTATTTACATTTCCAATACTTACATTATTTAATAAT
66 ACATTTTAGCCCTTAATATTATTAATGGATTATTTACATTTCCAATACTTACATTATTTAATAAT
* *
2702432 TTTAATCTTGGTTTTGGTTTATTATATTTACTATTTTAGCTTTTAAATTTTCAATTAATATCATT
131 TTTAATCTTAGTTTTGGTTTATTATATTTACTATTTTAGCTTTTAAATTTTCAATTAATACCATT
*
2702497 TTAGTCCTTCAACTTTATGTTTGTACTATTTTGGTCCTTTAAGTTTACGTTTTTGCCATTGTGGT
196 TTAGTCCTTCAACTTTATGTTTATACTATTTTGGTCCTTTAAGTTTACGTTTTTGCCATTGTGGT
* *
2702562 CTTTTAAATTTCTATTTGTGTTATTTTGTTATTTTAAATTTCTGTTTTTACTGTTTTAGTCTCTT
261 CTTTTAAATTTCTATTAGTGTTATTTTGTTATTTTAAATTTATGTTTTTACTGTTTTAGTCTCTT
2702627 AACTTTACGTTTATGTTATTTTAATCCTTTAATTCCACGTTTTTAAAGATTTATTATCATGTTAA
326 AACTTTACGTTTATGTTATTTTAATCCTTTAATTCCACGTTTTTAAAGATTTATTATCATGTTAA
2702692 AGGATTTTCTT
391 AGGATTTTCTT
*
2702703 CATTTTAGTCACTATTTTGTATTTTAGGTTAAATCTTAAATTAGACTGTATGTTTTAATTTCATT
1 CATTTTAGTCACTATTTTGTATTTTAGGTTAAATCTTAAATTAGACTGTATGTTTTAATTTCATC
* *
2702768 ATATTTTAGTCCTTAATATTATTAATGGATTATTTACATTTCCAATACTTACATTATTTAATAAT
66 ACATTTTAGCCCTTAATATTATTAATGGATTATTTACATTTCCAATACTTACATTATTTAATAAT
*
2702833 TTTAATCTTAGTTTTGGTTTATTATATTTACTATTTTAGCTTTTTAATTTTCAATTAATACCATT
131 TTTAATCTTAGTTTTGGTTTATTATATTTACTATTTTAGCTTTTAAATTTTCAATTAATACCATT
* *
2702898 TTAGTCCTTTAACTTTCTGTTTATACTATTTTGGTCCTTTAAGTTTACGTTTTTGCCATTGTGGT
196 TTAGTCCTTCAACTTTATGTTTATACTATTTTGGTCCTTTAAGTTTACGTTTTTGCCATTGTGGT
2702963 CTTTTAAATTTCTATTAGTGTTATTTTGTTATTTTAAATTTATGTTTTTACTGTTTTAGTCTCTT
261 CTTTTAAATTTCTATTAGTGTTATTTTGTTATTTTAAATTTATGTTTTTACTGTTTTAGTCTCTT
*
2703028 AACTTTACGTTTATGTTATTTTAATCCTTTAATTCCATGTTTTTAAAGATTTATTATCATGTTAA
326 AACTTTACGTTTATGTTATTTTAATCCTTTAATTCCACGTTTTTAAAGATTTATTATCATGTTAA
2703093 AGGATTTTCTT
391 AGGATTTTCTT
2703104 TAAGTAATTA
Statistics
Matches: 387, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
401 387 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (401 bp):
CATTTTAGTCACTATTTTGTATTTTAGGTTAAATCTTAAATTAGACTGTATGTTTTAATTTCATC
ACATTTTAGCCCTTAATATTATTAATGGATTATTTACATTTCCAATACTTACATTATTTAATAAT
TTTAATCTTAGTTTTGGTTTATTATATTTACTATTTTAGCTTTTAAATTTTCAATTAATACCATT
TTAGTCCTTCAACTTTATGTTTATACTATTTTGGTCCTTTAAGTTTACGTTTTTGCCATTGTGGT
CTTTTAAATTTCTATTAGTGTTATTTTGTTATTTTAAATTTATGTTTTTACTGTTTTAGTCTCTT
AACTTTACGTTTATGTTATTTTAATCCTTTAATTCCACGTTTTTAAAGATTTATTATCATGTTAA
AGGATTTTCTT
Found at i:2706281 original size:29 final size:29
Alignment explanation
Indices: 2706239--2706441 Score: 130
Period size: 29 Copynumber: 7.2 Consensus size: 29
2706229 ACACATTTAT
* * *
2706239 CACCTTTTTTAAAAAAATTAAAAAAATAG
1 CACCATTTTAAAAAAAATTACAAAAATAG
* * *
2706268 CACCATTTTAAAAATAATTAGC-AAACTAT
1 CACCATTTTAAAAAAAATTA-CAAAAATAG
* * * *
2706297 CACCATTTTAAAAATATTTACTAAAATAT
1 CACCATTTTAAAAAAAATTACAAAAATAG
*** *
2706326 CACCATTTTTTCAAAAATTACTAAAATAG
1 CACCATTTTAAAAAAAATTACAAAAATAG
2706355 CA--ATTTT-AAAAAAA--ACAAAAATAG
1 CACCATTTTAAAAAAAATTACAAAAATAG
* * * * * *
2706379 CACCCTTTTCAAAATAATTACCAGAATAC
1 CACCATTTTAAAAAAAATTACAAAAATAG
* * * * *
2706408 CACCAGTTTCAAAATAATTACCAAAATAC
1 CACCATTTTAAAAAAAATTACAAAAATAG
2706437 CACCA
1 CACCA
2706442 GGTCAACGGT
Statistics
Matches: 142, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
24 11 0.08
26 9 0.06
27 11 0.08
28 1 0.01
29 110 0.77
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (29 bp):
CACCATTTTAAAAAAAATTACAAAAATAG
Found at i:2706366 original size:24 final size:25
Alignment explanation
Indices: 2706333--2706380 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2706323 TATCACCATT
** *
2706333 TTTTCAAAAATTACTAAAATAGCAA
1 TTTTCAAAAAAAACAAAAATAGCAA
2706358 TTTT-AAAAAAAACAAAAATAGCA
1 TTTTCAAAAAAAACAAAAATAGCA
2706381 CCCTTTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.27
Consensus pattern (25 bp):
TTTTCAAAAAAAACAAAAATAGCAA
Found at i:2706442 original size:29 final size:29
Alignment explanation
Indices: 2706261--2706441 Score: 151
Period size: 29 Copynumber: 6.4 Consensus size: 29
2706251 AAAAATTAAA
* *
2706261 AAAATAGCACCATTTTAAAAATAATTAGC
1 AAAATAGCACCATTTTCAAAATAATTACC
* * * * *
2706290 AAACTATCACCATTTTAAAAATATTTACT
1 AAAATAGCACCATTTTCAAAATAATTACC
* *
2706319 AAAATATCACCATTTTTTC-AAA-AATTACT
1 AAAATAGCACCA--TTTTCAAAATAATTACC
* *
2706348 AAAATAGCA--ATTTT-AAAA-AA-AACA
1 AAAATAGCACCATTTTCAAAATAATTACC
*
2706372 AAAATAGCACCCTTTTCAAAATAATTACC
1 AAAATAGCACCATTTTCAAAATAATTACC
* * *
2706401 AGAATACCACCAGTTTCAAAATAATTACC
1 AAAATAGCACCATTTTCAAAATAATTACC
*
2706430 AAAATACCACCA
1 AAAATAGCACCA
2706442 GGTCAACGGT
Statistics
Matches: 125, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
24 11 0.09
25 9 0.07
26 4 0.03
27 5 0.04
28 2 0.02
29 87 0.70
30 3 0.02
31 4 0.03
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAATAGCACCATTTTCAAAATAATTACC
Found at i:2713607 original size:29 final size:28
Alignment explanation
Indices: 2713566--2713723 Score: 110
Period size: 29 Copynumber: 5.6 Consensus size: 28
2713556 ATCACATTTT
* *
2713566 TTTTACAAA-AATTACAAACATAGCAACA
1 TTTTAAAAATAATTACAAA-ATATCAACA
2713594 TTTTAAAAATAATTAGCAAAATATC-ACA
1 TTTTAAAAATAATTA-CAAAATATCAACA
*
2713622 CTTTTAAAAATATTTACTAAAATATC-ACTA
1 -TTTTAAAAATAATTAC-AAAATATCAAC-A
** * **
2713652 TTTTTCAAA-AATTACGAAAAT-TGAATT
1 TTTTAAAAATAATTAC-AAAATATCAACA
* * *
2713679 TTTTAAAAAAAATTACAAAAATATCACCC
1 TTTTAAAAATAATTAC-AAAATATCAACA
*
2713708 TTTTCAAAATAATTAC
1 TTTTAAAAATAATTAC
2713724 CAGAATACCA
Statistics
Matches: 103, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
27 8 0.08
28 34 0.33
29 56 0.54
30 5 0.05
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (28 bp):
TTTTAAAAATAATTACAAAATATCAACA
Found at i:2713730 original size:29 final size:29
Alignment explanation
Indices: 2713575--2713764 Score: 93
Period size: 29 Copynumber: 6.6 Consensus size: 29
2713565 TTTTTACAAA
* * *
2713575 AATTA-CAAACATAGCAACATTTTAAAAAT
1 AATTACCAAA-ATACCACCATTTTCAAAAT
* * *
2713604 AATTAGCAAAATATCA-CACTTTTAAAAAT
1 AATTACCAAAATACCACCA-TTTTCAAAAT
* * * *
2713633 ATTTACTAAAATATCACTATTTTTC-AAA-
1 AATTACCAAAATACCACCA-TTTTCAAAAT
* ** *** * *
2713661 AATTACGAAAAT-TGAATTTTTTAAAAAA
1 AATTACCAAAATACCACCATTTTCAAAAT
* * *
2713689 AATTACAAAAATATCACCCTTTTCAAAAT
1 AATTACCAAAATACCACCATTTTCAAAAT
* * *
2713718 AATTACCAGAATACCACTAGTTTCAAAAT
1 AATTACCAAAATACCACCATTTTCAAAAT
*
2713747 AATTACCAAATTACCACC
1 AATTACCAAAATACCACC
2713765 CGGTCAATGG
Statistics
Matches: 126, Mismatches: 29, Indels: 12
0.75 0.17 0.07
Matches are distributed among these distances:
26 4 0.03
27 6 0.05
28 23 0.18
29 84 0.67
30 9 0.07
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (29 bp):
AATTACCAAAATACCACCATTTTCAAAAT
Found at i:2716831 original size:32 final size:32
Alignment explanation
Indices: 2716747--2716822 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
2716737 AGGAACAATG
2716747 GGGGCATCTTTGAAGATTCAACATCAAATATT
1 GGGGCATCTTTGAAGATTCAACATCAAATATT
* **
2716779 GGGGCATTTTTTTAGATTCAACATCAAATATT
1 GGGGCATCTTTGAAGATTCAACATCAAATATT
2716811 GGGGCATCTTTG
1 GGGGCATCTTTG
2716823 GGAATTCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (32 bp):
GGGGCATCTTTGAAGATTCAACATCAAATATT
Found at i:2717564 original size:64 final size:63
Alignment explanation
Indices: 2717414--2717677 Score: 361
Period size: 64 Copynumber: 4.1 Consensus size: 63
2717404 AAGCTGTCTG
* * *
2717414 TCAACAAACAACTTTCCAGTTTCATGCAGAGTCAATTTCAA-TTCATAGCGAAGGATATTGGAC
1 TCAAC-AACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
* * *
2717477 TCAACATACAAATTTCCAGTTTCATTCAGAGTCAAATTCAACTTCACAATGAAGGATATTGGAC
1 TCAACA-ACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
2717541 TCAACGAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGAC
1 TCAAC-AACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** *
2717605 TCAA-AATAACTTTTTAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGAC
1 TCAACAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
2717667 TCGAAACAACA
1 TC--AACAACA
2717678 CAATTTACTC
Statistics
Matches: 179, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
62 57 0.32
63 36 0.20
64 82 0.46
65 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (63 bp):
TCAACAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
Found at i:2717663 original size:126 final size:127
Alignment explanation
Indices: 2717414--2717668 Score: 379
Period size: 126 Copynumber: 2.0 Consensus size: 127
2717404 AAGCTGTCTG
*
2717414 TCAACAAACAACTTTCCAGTTTCATGCAGAGTCAATTTCAATTCATAGCGAAGGATATTGGACTC
1 TCAACAAACAACTTTCCAGTTTCATGCAGAGTCAATTTCAATTCACAGCGAAGGATATTGGACTC
*
2717479 AACATACAAATTTCCAGTTTCATTCAGAGTCAAATTCAACTTCACAATGAAGGATATTGGAC
66 AACATACAAATTTCCAGTTTCATTCAGAGTCAAATTCAACTTCACAACGAAGGATATTGGAC
* * * *
2717541 TCAACGAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACT
1 TCAACAAACAACTTTCCAGTTTCATGCAGAGTCAATTTCAA-TTCACAGCGAAGGATATTGGACT
* * ** * *
2717606 CAA-A-ATAACTTTTTAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGAC
65 CAACATACAAATTTCCAGTTTCATTCAGAGTCAAATTCAACTTCACAACGAAGGATATTGGAC
2717667 TC
1 TC
2717669 GAAACAACAC
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
126 52 0.45
127 39 0.34
128 24 0.21
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (127 bp):
TCAACAAACAACTTTCCAGTTTCATGCAGAGTCAATTTCAATTCACAGCGAAGGATATTGGACTC
AACATACAAATTTCCAGTTTCATTCAGAGTCAAATTCAACTTCACAACGAAGGATATTGGAC
Found at i:2718054 original size:124 final size:121
Alignment explanation
Indices: 2717751--2718098 Score: 464
Period size: 121 Copynumber: 2.9 Consensus size: 121
2717741 GAAACAATAC
* *
2717751 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCTAT
1 TTGGATTTCAACTTCACGATGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * * * *
2717816 CCAAGATTTCAACTTCACGACGAATGATATCGTGACCACAAGCAGCAATACAACCC
66 CCACGATTTCAACTTCACGACGAAAGATATCGTGCCCACAAGCAACAATACAACCA
* *
2717872 TTGGATTTTAACTTCACGATGAAAGATATCCAATTTAAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACGATGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * * *
2717937 CCACGATTTCAACTTTACGACGAAAGATATCGTGCCCACAAGCAAC-CTCCATCTCTAGA
66 CCACGATTTCAACTTCACGACGAAAGATATCGTGCCCACAAGCAACAATACAAC-C---A
* * * * * *
2717996 TTGGATTTCAACTTCACAACGAATGATATCCAATTCAAAACTCAACTTCACAGCGAATGAACCAT
1 TTGGATTTCAACTTCACGATGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* *
2718061 CCACGATTTCAACTTCACAACGAAGGATATCGTGCCCA
66 CCACGATTTCAACTTCACGACGAAAGATATCGTGCCCA
2718099 AAAGATCAAC
Statistics
Matches: 199, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
120 4 0.02
121 103 0.52
124 92 0.46
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (121 bp):
TTGGATTTCAACTTCACGATGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
CCACGATTTCAACTTCACGACGAAAGATATCGTGCCCACAAGCAACAATACAACCA
Found at i:2722731 original size:24 final size:24
Alignment explanation
Indices: 2722704--2722752 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2722694 AAGCTTTTCC
2722704 AAATTACAATTATTGAAGATCTAT
1 AAATTACAATTATTGAAGATCTAT
*
2722728 AAATTGCAATTATTGAAGATCTAT
1 AAATTACAATTATTGAAGATCTAT
2722752 A
1 A
2722753 TGTGATCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (24 bp):
AAATTACAATTATTGAAGATCTAT
Found at i:2733969 original size:20 final size:20
Alignment explanation
Indices: 2733944--2733995 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2733934 CATTGATGGT
*
2733944 ATTATCGGTACTACCTAGTG
1 ATTATCGATACTACCTAGTG
2733964 ATTATCGATACTACCTAGTG
1 ATTATCGATACTACCTAGTG
*
2733984 AGTATCGATACT
1 ATTATCGATACT
2733996 TCCCTTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (20 bp):
ATTATCGATACTACCTAGTG
Found at i:2736720 original size:16 final size:16
Alignment explanation
Indices: 2736701--2736745 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2736691 GTTAGTTTAG
2736701 ATTATTTTTAGATTAA
1 ATTATTTTTAGATTAA
* *
2736717 ATTATCTTT-GTTTAA
1 ATTATTTTTAGATTAA
2736732 ATTAATTTTTAGAT
1 ATT-ATTTTTAGAT
2736746 GATTTCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.35
16 13 0.57
17 2 0.09
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (16 bp):
ATTATTTTTAGATTAA
Found at i:2739203 original size:45 final size:43
Alignment explanation
Indices: 2739039--2739218 Score: 184
Period size: 43 Copynumber: 4.2 Consensus size: 43
2739029 CCTGTTGTTG
*** *
2739039 CATTTGTAT-AAAAATGTCGCTATAGAACCTGACCTGTTGCGA
1 CATTTGTATAAAAAACACCGCTATAGAACCTGACCTATTGCGA
* * * * *
2739081 CATTTGTATAAAAAACATCGCTAAAGATCCTGACCTATTGTGG
1 CATTTGTATAAAAAACACCGCTATAGAACCTGACCTATTGCGA
* * *
2739124 CGTTTGTATAAAAAACGCCGCTATAAAACCTGACCTATTGCGA
1 CATTTGTATAAAAAACACCGCTATAGAACCTGACCTATTGCGA
* *
2739167 CATTTGTGA-AAGTAAAACACCGCTATAGAACTTGACCTATTTCGA
1 CATTTGT-ATAA--AAAACACCGCTATAGAACCTGACCTATTGCGA
*
2739212 CACTTGT
1 CATTTGT
2739219 GAAAGTAAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
42 9 0.08
43 69 0.61
44 1 0.01
45 34 0.30
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (43 bp):
CATTTGTATAAAAAACACCGCTATAGAACCTGACCTATTGCGA
Found at i:2740948 original size:25 final size:26
Alignment explanation
Indices: 2740914--2740962 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
2740904 AGTTGCTATT
2740914 AAGAGAGATATTTGATTA-AATTGTC
1 AAGAGAGATATTTGATTAGAATTGTC
2740939 AAGAGAGATATTTGATTAGAATTG
1 AAGAGAGATATTTGATTAGAATTG
2740963 ATATCGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (26 bp):
AAGAGAGATATTTGATTAGAATTGTC
Found at i:2749526 original size:24 final size:24
Alignment explanation
Indices: 2749491--2749559 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
2749481 GATACATGAC
* *
2749491 CTGAATTTTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
2749515 CTGGATTCTGTTATGATATCTGTT
1 CTGAATTCTGTTATGATTTCTGAT
* *
2749539 CTGAATTCTTTTTTGATTTCT
1 CTGAATTCTGTTATGATTTCT
2749560 AATATCTCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:2751474 original size:22 final size:23
Alignment explanation
Indices: 2751436--2751481 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2751426 TTTATGTTTG
2751436 GGGTGCTATTTATGTAAA-ATTT
1 GGGTGCTATTTATGTAAATATTT
*
2751458 GGGTGTTAGTTTA-GTAAATATTT
1 GGGTGCTA-TTTATGTAAATATTT
2751481 G
1 G
2751482 TAGAATGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.46
Consensus pattern (23 bp):
GGGTGCTATTTATGTAAATATTT
Found at i:2754073 original size:24 final size:24
Alignment explanation
Indices: 2754046--2754157 Score: 100
Period size: 24 Copynumber: 4.7 Consensus size: 24
2754036 ATTTCCAACA
* *
2754046 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATACTTGATC
* * *
2754070 TGAATTATGTTTTGAT-TTCTGATC
1 TGAATTCTGTTCTGATACT-TGATC
* * *
2754094 TGGATTCTGTTCTGATATTTGTTC
1 TGAATTCTGTTCTGATACTTGATC
* * *
2754118 TGAATTATGTTCTGATATTTGTTC
1 TGAATTCTGTTCTGATACTTGATC
*
2754142 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
2754158 TTCTGATATC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
24 71 0.97
25 2 0.03
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATACTTGATC
Found at i:2754101 original size:48 final size:48
Alignment explanation
Indices: 2754046--2754157 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 48
2754036 ATTTCCAACA
*
2754046 TGAATTCTGTTCTGATACATGACCTGAATTATGTTTTGAT-TTCTGATC
1 TGAATTCTGTTCTGATACATGACCTGAATTATGTTCTGATATT-TGATC
* ** ** *
2754094 TGGATTCTGTTCTGATATTTGTTCTGAATTATGTTCTGATATTTGTTC
1 TGAATTCTGTTCTGATACATGACCTGAATTATGTTCTGATATTTGATC
*
2754142 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
2754158 TTCTGATATC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.51
Consensus pattern (48 bp):
TGAATTCTGTTCTGATACATGACCTGAATTATGTTCTGATATTTGATC
Found at i:2754161 original size:12 final size:12
Alignment explanation
Indices: 2754077--2754162 Score: 70
Period size: 12 Copynumber: 7.2 Consensus size: 12
2754067 ACCTGAATTA
*
2754077 TGTTTTGATTTC
1 TGTTCTGATTTC
*
2754089 TGATCTGGA-TTC
1 TGTTCT-GATTTC
2754101 TGTTCTGATATT-
1 TGTTCTGAT-TTC
* *
2754113 TGTTCTGAATTA
1 TGTTCTGATTTC
2754125 TGTTCTGATATT-
1 TGTTCTGAT-TTC
*
2754137 TGTTCTGAATTC
1 TGTTCTGATTTC
*
2754149 TGTTTTGATTTC
1 TGTTCTGATTTC
2754161 TG
1 TG
2754163 ATATCTCCGT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 6 0.10
12 48 0.80
13 6 0.10
ACGTcount: A:0.15, C:0.10, G:0.19, T:0.56
Consensus pattern (12 bp):
TGTTCTGATTTC
Found at i:2755106 original size:15 final size:15
Alignment explanation
Indices: 2755086--2755128 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
2755076 TAAAAAACAC
2755086 TTAAAATTATTATTT
1 TTAAAATTATTATTT
*
2755101 TTAAAAGTTCAATATTT
1 TTAAAA-TT-ATTATTT
2755118 TCTAAAATTAT
1 T-TAAAATTAT
2755129 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 9 0.39
18 5 0.22
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAAAATTATTATTT
Found at i:2757261 original size:27 final size:28
Alignment explanation
Indices: 2757226--2757280 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
2757216 AAGATTAGAA
2757226 GAAGAAGAAGA-AAA-AAAAGAAATGATT
1 GAAGAAGAAGACAAAGAAAA-AAATGATT
*
2757253 GAAGGAGAAGATCAAAGAAAAAAATGAT
1 GAAGAAGAAGA-CAAAGAAAAAAATGAT
2757281 GGAGAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.42
29 10 0.42
30 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.24, T:0.11
Consensus pattern (28 bp):
GAAGAAGAAGACAAAGAAAAAAATGATT
Found at i:2757878 original size:23 final size:23
Alignment explanation
Indices: 2757852--2757896 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2757842 TTTCTTCTTT
*
2757852 TTTTCATGTAATTT-TTTTTTACA
1 TTTT-ATGCAATTTATTTTTTACA
*
2757875 TTTTATGCATTTTATTTTTTAC
1 TTTTATGCAATTTATTTTTTAC
2757897 TTTAGTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATGCAATTTATTTTTTACA
Found at i:2757930 original size:25 final size:25
Alignment explanation
Indices: 2757884--2757933 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2757874 ATTTTATGCA
*
2757884 TTTTATTTTTTACTTTAGTATATAT
1 TTTTATTTTTTACATTAGTATATAT
*
2757909 TTTTATTTTTTTAGATTA-TATATAT
1 TTTTA-TTTTTTACATTAGTATATAT
2757934 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTATTTTTTACATTAGTATATAT
Found at i:2758037 original size:87 final size:84
Alignment explanation
Indices: 2757906--2758075 Score: 225
Period size: 85 Copynumber: 2.0 Consensus size: 84
2757896 CTTTAGTATA
*
2757906 TATTTTTATTTTTTTAGATTATATATATATATATATATTATTTTTTTATTATCAATTTTATTAAT
1 TATTTTTATTTATTTA-ATTATATATATATATATATATTATTTTTTTATTAT-AATTTTATTAAT
2757971 TTATATATATATATATATTTAC
64 TTAT-TATATATATATATTTAC
* * *
2757993 TATTTTTATTTATTT-ATTATATATATATATATATTTTTACTTTTTTTATTATTATTTTATTTAT
1 TATTTTTATTTATTTAATTATATATATATATATA-TATTA-TTTTTTTATTATAATTTTATTAAT
* * *
2758057 TTGTTTTATTTATATATTT
64 TTATTATATATATATATTT
2758076 TTTTCTCTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
85 31 0.42
86 17 0.23
87 26 0.35
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (84 bp):
TATTTTTATTTATTTAATTATATATATATATATATATTATTTTTTTATTATAATTTTATTAATTT
ATTATATATATATATTTAC
Found at i:2758055 original size:51 final size:49
Alignment explanation
Indices: 2757996--2758114 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 49
2757986 TATTTACTAT
2757996 TTTTATTTATTTATTATATATATATATATATTTTTACT-TTT-TTTATTATTA
1 TTTTATTTATTTATT-T-TATATATATAT-TTTTTACTCTTTCTTTATT-TTA
* * * *
2758047 TTTTATTTATTTGTTTTATTTATATATTTTTTTCTCTTTCTTTATTTTT
1 TTTTATTTATTTATTTTATATATATATTTTTTACTCTTTCTTTATTTTA
2758096 TTTTATTT-TTTATATTTAT
1 TTTTATTTATTTAT-TTTAT
2758115 TTTACTTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
48 11 0.18
49 28 0.47
50 7 0.12
51 14 0.23
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (49 bp):
TTTTATTTATTTATTTTATATATATATTTTTTACTCTTTCTTTATTTTA
Found at i:2758057 original size:4 final size:4
Alignment explanation
Indices: 2757997--2758161 Score: 55
Period size: 4 Copynumber: 42.0 Consensus size: 4
2757987 ATTTACTATT
* * * *
2757997 TTTA TTTA TTTA -TTA TATA TATA TATA TATT- TTTA CTTTT TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA -TTTA TTTA TTTA
* * * * *
2758044 -TTA TTTTA TTTA TTTGT TTTA TTTA TATA TTT- TTT- TCTC TTTC TTTA
1 TTTA -TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
2758091 TTT- TTT- TTTA TTTT TTATA TTTA TTTTA CTTA -TTA TTTTA TTT- TTTC
1 TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA
* *
2758138 TTTC TTTA TCTTA TCT- TTTA TTTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA
2758162 ATTTGTTTTT
Statistics
Matches: 128, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
3 30 0.23
4 74 0.58
5 24 0.19
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:2758067 original size:18 final size:17
Alignment explanation
Indices: 2757996--2758173 Score: 71
Period size: 17 Copynumber: 9.9 Consensus size: 17
2757986 TATTTACTAT
*
2757996 TTTTATTTATTTATTATA
1 TTTTATTTATTT-TTTTA
* * *
2758014 TATATATATATATTTTTA
1 T-TTTATTTATTTTTTTA
*
2758032 CTTTT-TTTA--TTATTA
1 -TTTTATTTATTTTTTTA
2758047 TTTTATTTATTTGTTTTA
1 TTTTATTTATTT-TTTTA
* *
2758065 -TTTATATATTTTTTTC
1 TTTTATTTATTTTTTTA
*
2758081 TCTTTCTTTATTTTTTTTTA
1 T-TTTATTTA--TTTTTTTA
2758101 TTTT-TTATATTTATTTTA
1 TTTTATT-TATTT-TTTTA
*
2758119 CTTATTATTTTATTTTTTCTT
1 -TT-TTA-TTTATTTTTT-TA
*
2758140 TCTTTATCTTA-TCTTTTA
1 T-TTTAT-TTATTTTTTTA
* *
2758158 TTTAATTTGTTTTTTT
1 TTTTATTTATTTTTTT
2758174 TCTTCATTTT
Statistics
Matches: 121, Mismatches: 19, Indels: 41
0.67 0.10 0.23
Matches are distributed among these distances:
14 4 0.03
15 9 0.07
16 6 0.05
17 26 0.21
18 26 0.21
19 21 0.17
20 20 0.17
21 7 0.06
22 2 0.02
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTTATTTATTTTTTTA
Found at i:2758067 original size:39 final size:36
Alignment explanation
Indices: 2758024--2758136 Score: 95
Period size: 40 Copynumber: 2.9 Consensus size: 36
2758014 TATATATATA
2758024 TATTTTTACTTTTTTTATTATTATTTTATTTATTTGTTT
1 TATTTTTA-TTTTTTTATTATTATTTTATTT-TTT-TTT
* *
2758063 TATTTATATATTTTTTTCTCT-TT-CTTTATTTTTTTTT
1 TATTT-T-TATTTTTTTAT-TATTATTTTATTTTTTTTT
*
2758100 ATTTTTTATATTTATTTTACTTATTATTTTATTTTTT
1 -TATTTT-TATTT-TTTTA-TTATTATTTTATTTTTT
2758137 CTTTCTTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
37 10 0.16
38 12 0.20
39 15 0.25
40 21 0.34
41 3 0.05
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (36 bp):
TATTTTTATTTTTTTATTATTATTTTATTTTTTTTT
Found at i:2758074 original size:17 final size:16
Alignment explanation
Indices: 2757912--2758079 Score: 50
Period size: 17 Copynumber: 10.6 Consensus size: 16
2757902 TATATATTTT
*
2757912 TATTTTTTTAGATTATA
1 TATTTTTTTA-TTTATA
* * * *
2757929 TATATATATATATAT-
1 TATTTTTTTATTTATA
2757944 TATTTTTTTA-TTATCA
1 TATTTTTTTATTTAT-A
*
2757960 -ATTTTATTAATTTATA
1 TATTTT-TTTATTTATA
* *
2757976 TATATATATATATTTACTA
1 TAT-T-TTTTTATTTA-TA
2757995 T-TTTTATTTATTTAT-
1 TATTTT-TTTATTTATA
* * * *
2758010 TATATATATATATATA
1 TATTTTTTTATTTATA
*
2758026 T-TTTTACTTTTTTTAT-
1 TATTTT--TTTATTTATA
*
2758042 TATTATTTTA-TT-TA
1 TATTTTTTTATTTATA
*
2758056 T-TTGTTTTATTTATA
1 TATTTTTTTATTTATA
2758071 TATTTTTTT
1 TATTTTTTT
2758080 CTCTTTCTTT
Statistics
Matches: 105, Mismatches: 28, Indels: 37
0.62 0.16 0.22
Matches are distributed among these distances:
13 8 0.08
14 8 0.08
15 28 0.27
16 19 0.18
17 30 0.29
18 8 0.08
19 4 0.04
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (16 bp):
TATTTTTTTATTTATA
Found at i:2758115 original size:13 final size:15
Alignment explanation
Indices: 2758096--2758136 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 15
2758086 CTTTATTTTT
2758096 TTTTATTTTTTA-TA
1 TTTTATTTTTTATTA
2758110 -TTTATTTTACTTATTA
1 TTTTATTTT--TTATTA
2758126 TTTTATTTTTT
1 TTTTATTTTTT
2758137 CTTTCTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 8 0.35
15 5 0.22
16 2 0.09
17 8 0.35
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTTATTA
Found at i:2763671 original size:32 final size:31
Alignment explanation
Indices: 2763635--2763739 Score: 120
Period size: 31 Copynumber: 3.3 Consensus size: 31
2763625 GGAACAATGA
*
2763635 GGGCATCTTTGAAGATTTAACATCAAATGTTG
1 GGGCAT-TTTGTAGATTTAACATCAAATGTTG
*
2763667 GGGCATTTTTTAGATTTAACATCAAATGTTG
1 GGGCATTTTGTAGATTTAACATCAAATGTTG
* * * ** *
2763698 GGGCATTTTTTATATTCAACATTGAATATTG
1 GGGCATTTTGTAGATTTAACATCAAATGTTG
2763729 GGGCATCTTTG
1 GGGCAT-TTTG
2763740 GGAATTCAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 55 0.86
32 9 0.14
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (31 bp):
GGGCATTTTGTAGATTTAACATCAAATGTTG
Found at i:2763683 original size:31 final size:31
Alignment explanation
Indices: 2763647--2763734 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
2763637 GCATCTTTGA
2763647 AGATTTAACATCAAATGTTGGGGCATTTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTT
2763678 AGATTTAACATCAAATGTTGGGGCATTTTTT
1 AGATTTAACATCAAATGTTGGGGCATTTTTT
* * ** *
2763709 ATATTCAACATTGAATATTGGGGCAT
1 AGATTTAACATCAAATGTTGGGGCAT
2763735 CTTTGGGAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (31 bp):
AGATTTAACATCAAATGTTGGGGCATTTTTT
Found at i:2764732 original size:36 final size:36
Alignment explanation
Indices: 2764685--2764910 Score: 225
Period size: 36 Copynumber: 6.4 Consensus size: 36
2764675 ATTGAAAACA
* *
2764685 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2764721 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2764757 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
2764786 TTTTATTTGAAACAAATTTTATCTCTCTTGAGAGAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * *
2764822 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* * *
2764859 TTTCTCTTGAAACAAATTTAGTCTCTCTAGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2764895 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
2764911 ATCTTTGAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 2 0.01
35 2 0.01
36 100 0.64
37 33 0.21
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2764755 original size:101 final size:101
Alignment explanation
Indices: 2764626--2764874 Score: 302
Period size: 101 Copynumber: 2.5 Consensus size: 101
2764616 TATGTTTTAT
** * *
2764626 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA-TTGAAAACATTTCC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAACATTTGAAAACATTTCA
* *
2764690 CTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCC
65 CTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
* * * ** * *
2764727 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTAT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACATTTGAAAACATTTCAC
* * **
2764792 TTGAAACAAATTTTATCTCTCTTGAGAGAGTTTCTT
66 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
* *
2764828 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
2764875 TTTAGTCTCT
Statistics
Matches: 126, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
100 4 0.03
101 85 0.67
102 37 0.29
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (101 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACATTTGAAAACATTTCAC
TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
Found at i:2764954 original size:138 final size:138
Alignment explanation
Indices: 2764705--2764964 Score: 394
Period size: 138 Copynumber: 1.9 Consensus size: 138
2764695 AATAAATTTC
* *
2764705 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTAGTCTCTCTAGAGACAGTTTCCCTTGAAAC
* * ** * * *
2764770 AAAATATTTGAATATGTTTTATTTGAAACAAATTTTATCTCTCTTGAGAGAGTTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTTATCTCCCTTGAGACAGTTTCTTTTGGAAC
2764835 TAAGTTTT
131 TAAGTTTT
*
2764843 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTAGTCTCTCTAGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTAGTCTCTCTAGAGACAGTTTCCCTTGAAAC
* * * *
2764908 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTTATCTCCCTTGAGACAGTTTCT
2764965 CTTGAAACAC
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 108 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTAGTCTCTCTAGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTTATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:2764972 original size:65 final size:67
Alignment explanation
Indices: 2764868--2765024 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 67
2764858 GTTTCTCTTG
* * * **
2764868 AAACAAATTTAGTCTCTCTAGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
2764931 TA
66 TA
* *
2764933 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
2764998 TA
66 TA
* *
2765000 AAACAAAATTTTATTTCCCTTGAGA
1 AAAC-AAATTTTGTCTCCCTTGAGA
2765025 TATATCTTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
65 32 0.40
66 2 0.03
67 28 0.35
68 18 0.22
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:2765919 original size:106 final size:106
Alignment explanation
Indices: 2765734--2766083 Score: 488
Period size: 106 Copynumber: 3.3 Consensus size: 106
2765724 AAGGGGCTTC
* *
2765734 CCAGTTTCAAAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACATAAGCTCAA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
*
2765799 CTTCACAACGAAGGGGC-AGCTGGCTGTCAACAAACATTTTT
66 CTTCACAACGAAGGGGCGA-CTGGCTGTCAACAAACAATTTT
2765840 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
* ** *
2765905 CTTCACAACGAAGGGGCGAATGATTGTCAACAAATAACTTTT
66 CTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAA-TTTT
* * * * *
2765947 -CAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGAACTCGAGACAACACAAGC
1 CCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGC
* * *
2766011 TCAACTTCACAGCGAAGGGGCGACTAGCTGTCAACAAACAATTTC
62 TCAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAATTTT
*
2766056 CCAGTTCCAGAGCCAATTTCAACTTCAC
1 CCAGTTTCAGAGCCAATTTCAACTTCAC
2766084 GACGGATGAT
Statistics
Matches: 216, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
106 117 0.54
107 5 0.02
108 2 0.01
109 3 0.01
110 89 0.41
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
CTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAATTTT
Found at i:2767043 original size:2 final size:2
Alignment explanation
Indices: 2767033--2767063 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2767023 TTTTTTAGAT
*
2767033 TA TA AA 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 T
2767064 TTTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2767114 original size:44 final size:44
Alignment explanation
Indices: 2767043--2767177 Score: 130
Period size: 44 Copynumber: 3.0 Consensus size: 44
2767033 TATAAATATA
* * * * * *
2767043 TATATATATATATATATATATTTTTTTATTATCAGTTTTATTAATT
1 TATATATATAT-TATTTTTACTATTTTATTATTATTTTTATT-ATT
* * *
2767089 TATGTATATA-TATTTTTACTATTTTATT-TTTTTATTTATTATA
1 TATATATATATTATTTTTACTATTTTATTATTATT-TTTATTATT
*
2767132 TATATATATATTATTTTTACTTTTTTATTATTATTTTTATTTATT
1 TATATATATATTATTTTTACTATTTTATTATTATTTTTA-TTATT
2767177 T
1 T
2767178 GTTTTATTTA
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
43 13 0.18
44 41 0.57
45 9 0.12
46 9 0.12
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (44 bp):
TATATATATATTATTTTTACTATTTTATTATTATTTTTATTATT
Found at i:2767126 original size:36 final size:35
Alignment explanation
Indices: 2767055--2767165 Score: 109
Period size: 35 Copynumber: 3.1 Consensus size: 35
2767045 TATATATATA
* *
2767055 TATATATATTTTT-TTATTATCAGTTTTATTAATTTAT
1 TATATATATTTTTATTATT-TTA-TTTT-TTTATTTAT
*
2767092 GTATATATATTTTTACTATTTTATTTTTTTATTTAT
1 -TATATATATTTTTATTATTTTATTTTTTTATTTAT
* * *
2767128 TATATATATATATATTATTTTTACTTTTTTA-TTAT
1 TATATATATTTTTATTA-TTTTATTTTTTTATTTAT
2767163 TAT
1 TAT
2767166 TTTTATTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
35 21 0.33
36 20 0.31
37 4 0.06
38 15 0.23
39 4 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (35 bp):
TATATATATTTTTATTATTTTATTTTTTTATTTAT
Found at i:2767128 original size:4 final size:4
Alignment explanation
Indices: 2767111--2767235 Score: 57
Period size: 4 Copynumber: 31.8 Consensus size: 4
2767101 TTTTTACTAT
* * *
2767111 TTTA TTTT TTTA TTTA TTATA TATA TATA TATTA -TT- TTTA CTTT- TTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA T-TTA TTTA TTTA -TTTA TTTA
* * * * * * *
2767159 -TTA TTATT TTTA TTTA TTTGT TTTA TTTA TATA TTTT TTTC TTTT TTTC
1 TTTA TT-TA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
2767208 TTTA TTT- TTTA TTT- TTT- TGTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2767236 TACTTACTAT
Statistics
Matches: 93, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
3 18 0.19
4 61 0.66
5 14 0.15
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2767157 original size:52 final size:48
Alignment explanation
Indices: 2767101--2767221 Score: 129
Period size: 52 Copynumber: 2.4 Consensus size: 48
2767091 TGTATATATA
*
2767101 TTTTTACTATT-TTATTTTTTTATTTATTATATATATATATATTATTTTTACT
1 TTTTTACTATTATT-TTTATTTATTTATT-T-TATATATATATT-TTTTT-CT
* * *
2767153 TTTTTATTATTATTTTTATTTATTTGTTTTATTTATATATTTTTTTCT
1 TTTTTACTATTATTTTTATTTATTTATTTTATATATATATTTTTTTCT
*
2767201 TTTTTTCT-TTATTTTTTATTT
1 TTTTTACTATTA-TTTTTATTT
2767222 TTTTGTATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
47 3 0.05
48 17 0.28
49 5 0.08
50 11 0.18
51 1 0.02
52 22 0.36
53 2 0.03
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (48 bp):
TTTTTACTATTATTTTTATTTATTTATTTTATATATATATTTTTTTCT
Found at i:2767190 original size:48 final size:47
Alignment explanation
Indices: 2767087--2767235 Score: 130
Period size: 48 Copynumber: 3.1 Consensus size: 47
2767077 GTTTTATTAA
* * *
2767087 TTTATGTATATATATTTTTAC--TATTTTATT-TTTTTATTTA-TT-A
1 TTTATTTATATAT-TTTTTACTTTTTTTTATTATTTTTATTTATTTGT
* *
2767130 TATATATATATATTATTTTTACTTTTTTATTATTATTTTTATTTATTTGT
1 TTTATTTATATA-T-TTTTTACTTTTTT-TTATTATTTTTATTTATTTGT
* *
2767180 TTTATTTATATATTTTTTTCTTTTTTTCT-TTATTTTTTATTTTTTTGT
1 TTTATTTATATATTTTTTACTTTTTTT-TATTA-TTTTTATTTATTTGT
2767228 ATTTATTT
1 -TTTATTT
2767236 TACTTACTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
43 10 0.11
44 9 0.10
46 3 0.03
47 9 0.10
48 37 0.42
49 10 0.11
50 10 0.11
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (47 bp):
TTTATTTATATATTTTTTACTTTTTTTTATTATTTTTATTTATTTGT
Found at i:2767236 original size:21 final size:19
Alignment explanation
Indices: 2767167--2767236 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 19
2767157 TATTATTATT
*
2767167 TTTATTTATTTGTTTTATTTA
1 TTTATTT-TTT-TTTTTTTTA
* *
2767188 TATATTTTTTTCTTTTTTTC
1 TTTATTTTTTT-TTTTTTTA
2767208 TTTATTTTTTATTTTTTTGTA
1 TTTATTTTTT-TTTTTTT-TA
2767229 TTTATTTT
1 TTTATTTT
2767237 ACTTACTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
19 1 0.02
20 24 0.59
21 16 0.39
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTATTTTTTTTTTTTTTA
Found at i:2767285 original size:53 final size:51
Alignment explanation
Indices: 2767115--2767289 Score: 144
Period size: 54 Copynumber: 3.3 Consensus size: 51
2767105 TACTATTTTA
*
2767115 TTTT-TTTATTTATTATA-TATATATATATTATTTTTACTTT-TTTATTATTAT
1 TTTTATTTATTTATTTTACT-TATATAT-TTATTTTTACTTTCTTTA-TATTAT
* * * ** *
2767166 TTTTATTTATTTGTTTTATTTATATATTTTTTTCTTTTTTTCTTTATTTTTTAT
1 TTTTATTTATTTATTTTACTTATATATTTATTT-TTACTTTCTTTA--TATTAT
* *
2767220 TTTT-TTGTATTTATTTTACTTACTAT-TTTATTTTTGCTTTCTTTATCTTAT
1 TTTTATT-TATTTATTTTACTTA-TATATTTATTTTTACTTTCTTTATATTAT
2767271 CTTTTATTTAATTTATTTT
1 -TTTTATTT-ATTTATTTT
2767290 TTTTCTTCAT
Statistics
Matches: 102, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
51 14 0.14
52 28 0.27
53 28 0.27
54 29 0.28
55 3 0.03
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (51 bp):
TTTTATTTATTTATTTTACTTATATATTTATTTTTACTTTCTTTATATTAT
Found at i:2767335 original size:32 final size:28
Alignment explanation
Indices: 2767272--2767326 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
2767262 TTATCTTATC
*
2767272 TTTT-ATTTAATTTATTTTTTTTCTTCA
1 TTTTAATTTAATTAATTTTTTTTCTTCA
2767299 TTTTAATTTAATTAATTATTTATTTCTT
1 TTTTAATTTAATTAATT-TTT-TTTCTT
2767327 ACTTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 3 0.12
30 6 0.25
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTAATTTAATTAATTTTTTTTCTTCA
Found at i:2770830 original size:2 final size:2
Alignment explanation
Indices: 2770817--2770853 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2770807 TGAATAACCT
*
2770817 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2770854 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2770858 original size:2 final size:2
Alignment explanation
Indices: 2770853--2770879 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2770843 TCTCTCTCTC
2770853 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2770880 GATTGGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2771862 original size:31 final size:30
Alignment explanation
Indices: 2771827--2771888 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
2771817 TTAAAATACA
2771827 TAAGATATAGTTACTTTCATTTTTATTTAAT
1 TAAGATATAGTTACTTTCATTTTTA-TTAAT
* *
2771858 TAAGATATATTTACTTTTATTTTTATTAAT
1 TAAGATATAGTTACTTTCATTTTTATTAAT
2771888 T
1 T
2771889 TAAAATGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (30 bp):
TAAGATATAGTTACTTTCATTTTTATTAAT
Found at i:2772872 original size:2 final size:2
Alignment explanation
Indices: 2772865--2772894 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2772855 CTTCAACTTA
2772865 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
2772895 TATGGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2777229 original size:31 final size:30
Alignment explanation
Indices: 2777190--2777255 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2777180 TGTCAAATGG
*
2777190 ATATTTTATATAAAGTTTGT-GGGTTAAATTA
1 ATATTTTATATAAA-TTT-TAAGGTTAAATTA
* *
2777221 GTATTTTATGTAAATTTTAAGGTTAAATTA
1 ATATTTTATATAAATTTTAAGGTTAAATTA
2777251 ATATT
1 ATATT
2777256 CTGTCTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 17 0.57
31 12 0.40
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (30 bp):
ATATTTTATATAAATTTTAAGGTTAAATTA
Found at i:2779453 original size:30 final size:29
Alignment explanation
Indices: 2779397--2779453 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
2779387 TGAGCAACTC
* *
2779397 GAAAAAATAATATATTAAGATTTTATTTT
1 GAAAAAATAATATATTAAAATGTTATTTT
2779426 GAAAAAATAAGT-TATTAATAATGTTATT
1 GAAAAAATAA-TATATTAA-AATGTTATT
2779454 ATTTATGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (29 bp):
GAAAAAATAATATATTAAAATGTTATTTT
Found at i:2780547 original size:21 final size:21
Alignment explanation
Indices: 2780505--2780550 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2780495 GTTTACTACG
* * *
2780505 ATTGCGGCCATAGCGGATGCT
1 ATTGCGGCCATAACGAACGCT
*
2780526 ATTGCGGTCATAACGAACGCT
1 ATTGCGGCCATAACGAACGCT
2780547 ATTG
1 ATTG
2780551 TAGGTTTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (21 bp):
ATTGCGGCCATAACGAACGCT
Found at i:2785784 original size:20 final size:20
Alignment explanation
Indices: 2785759--2785811 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2785749 ATTGGAGAGG
**
2785759 TTCTAGAAAATTCTAGAGCT
1 TTCTAGAAAATTCTAGAAAT
* *
2785779 TTCTAGAAAAGTGTAGAAAT
1 TTCTAGAAAATTCTAGAAAT
*
2785799 TTCTAGAACATTC
1 TTCTAGAAAATTC
2785812 CGGAGAACTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (20 bp):
TTCTAGAAAATTCTAGAAAT
Found at i:2792894 original size:22 final size:22
Alignment explanation
Indices: 2792866--2792922 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
2792856 TCTGGACAAG
2792866 GTGCATCGATGCACATTCATAA
1 GTGCATCGATGCACATTCATAA
2792888 GTGCATCGATGCACATTCATAA
1 GTGCATCGATGCACATTCATAA
2792910 GTGCATCGATGCA
1 GTGCATCGATGCA
2792923 TTCCTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCATAA
Found at i:2792995 original size:64 final size:64
Alignment explanation
Indices: 2792911--2793056 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 64
2792901 CATTCATAAG
* * * *
2792911 TGCATCGATGCATTCC-TTTAAAAGAAGAACATCAAATGCCTTTGATGCATCGATGCA-TAGCTA
1 TGCATCGATGCA-TCCTTTTAAAAGAAAAACATCAAATGCATTTGATGCACCGATGCACAAG-TA
2792974 A
64 A
* * * *
2792975 TGCATCGATGCATCCTTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAAAACATCAAATGCATTTGATGCACCGATGCACAAGTAA
2793039 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
2793057 CATTGAAAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
63 3 0.04
64 62 0.87
65 6 0.08
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAAAAGAAAAACATCAAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:2793742 original size:31 final size:31
Alignment explanation
Indices: 2793654--2793761 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
2793644 AGTCGAGGGT
* * *
2793654 TTTACCTATG-TCTTTCGAGACATATGGACAA
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
2793685 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
2793716 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
2793747 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
2793762 ATGACCTCTG
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
30 13 0.21
31 46 0.74
32 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:2793768 original size:30 final size:30
Alignment explanation
Indices: 2793707--2793781 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
2793697 CTAAGGAACA
* *
2793707 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
2793738 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
2793768 TCTGGATAGTTACC
1 TATGGACAGTTACC
2793782 AGGGTCTGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 28 0.76
31 9 0.24
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:2797120 original size:64 final size:64
Alignment explanation
Indices: 2797036--2797181 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 64
2797026 CATTCATAAG
* * * *
2797036 TGCATCGATGCATTCC-TTTAAAAGAAGAACATCAAATGCCTTTGATGCATCGATGCA-TAGCTA
1 TGCATCGATGCA-TCCTTTTAAAAGAAAAACATCAAATGCATTTGATGCACCGATGCACAAG-TA
2797099 A
64 A
* * * *
2797100 TGCATCGATGCATCCTTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAAAACATCAAATGCATTTGATGCACCGATGCACAAGTAA
2797164 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
2797182 CATTGAAAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
63 3 0.04
64 62 0.87
65 6 0.08
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAAAAGAAAAACATCAAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:2797872 original size:31 final size:31
Alignment explanation
Indices: 2797778--2797885 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
2797768 AGTCGAGGGT
* *
2797778 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
2797809 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
2797840 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
2797871 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
2797886 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:2797892 original size:30 final size:30
Alignment explanation
Indices: 2797800--2797906 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
2797790 TTTCGAGACA
* * * *
2797800 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
2797831 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
2797862 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
2797892 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
2797907 GGGTCTGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:2804542 original size:40 final size:41
Alignment explanation
Indices: 2804439--2804545 Score: 103
Period size: 40 Copynumber: 2.7 Consensus size: 41
2804429 AAACGCCACT
* * *
2804439 AATATCATAACCTTTAGTGGCGTTTAG-AAAAAAAGTCGCTA
1 AATAACATAACCTTTAGCGGTGTTT-GTAAAAAAAGTCGCTA
* * ** * *
2804480 AATATCATTACCTCAAGC-GTGTTTGTAAAAAACGTTGCTA
1 AATAACATAACCTTTAGCGGTGTTTGTAAAAAAAGTCGCTA
2804520 AA-AACATAACCTTTAGCGGTGTTTGT
1 AATAACATAACCTTTAGCGGTGTTTGT
2804546 GGTTCACAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
39 12 0.23
40 27 0.51
41 14 0.26
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (41 bp):
AATAACATAACCTTTAGCGGTGTTTGTAAAAAAAGTCGCTA
Found at i:2804899 original size:21 final size:22
Alignment explanation
Indices: 2804873--2804921 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2804863 AGCACGTCAT
2804873 CAATGCCAG-AAAAAAACTTAA
1 CAATGCCAGAAAAAAAACTTAA
2804894 CAATGCCAGAAAAAAAACTTAA
1 CAATGCCAGAAAAAAAACTTAA
2804916 CAATGC
1 CAATGC
2804922 ATTACCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.55, C:0.20, G:0.10, T:0.14
Consensus pattern (22 bp):
CAATGCCAGAAAAAAAACTTAA
Found at i:2805490 original size:41 final size:41
Alignment explanation
Indices: 2805435--2805931 Score: 343
Period size: 41 Copynumber: 12.1 Consensus size: 41
2805425 AAAAATTGTT
*
2805435 ACTAAAGTACGAGTCTTTAGCGAAATTTGTATAAAAATGCC
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
* * * *
2805476 ACTAATGTATGAGTCTCTAGCGACATTTGTATAAAAACGCC
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
* * *
2805517 ACTAAAGTACGAGCCTTTAGCGGCATTTATATAAAACA--CC
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAA-ATGCC
* * * *
2805557 ACTAAAGTACGAGTCTTTAGTGGCGTTTGTATAAAAA-CCC
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
* * * *
2805597 TACTAAAGGT-TGAGTCTTTAACGGCGTTTGTATAAAAATGCC
1 -ACTAAA-GTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
* * * *
2805639 ACTAAAGTACAAGTCTATAGCGATTTTTTTATTT-TATAAAAACGCC
1 ACTAAAGTACGAGTCTTTAGCGA------CATTTGTATAAAAATGCC
* * *
2805685 ACTAAAGTATGAGTCTTTAGCGGCATTTGTACGAAAACAT--C
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTA-TAAAA-ATGCC
* * * * *
2805726 TCTAAAATATGAGTCTTTAGC-AGCGTTTGTATAAAAA-ACC
1 ACTAAAGTACGAGTCTTTAGCGA-CATTTGTATAAAAATGCC
* * **
2805766 ACTAAAATACGAGTCTATAGCGATGTTTGTAT-AAAATGCC
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
* * * * *
2805806 ACTAAAGTAC-AATCTTCAGCGGCGTTTGTATAAAAACGCC
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
* * *** * *
2805846 ACTAAAGTAC-AATCTTCAGCGGTGTTTATATAAAAATCCC
1 ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
* * * * * *
2805886 ACTAAAGTACTAGTATTTAGTGACGTTTGTTCTAAAAACGCC
1 ACTAAAGTACGAGTCTTTAGCGACATTTG-TATAAAAATGCC
2805928 ACTA
1 ACTA
2805932 TAAACCTATT
Statistics
Matches: 368, Mismatches: 65, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
39 22 0.06
40 137 0.37
41 153 0.42
42 22 0.06
43 1 0.00
46 30 0.08
47 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (41 bp):
ACTAAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCC
Found at i:2805602 original size:81 final size:81
Alignment explanation
Indices: 2805435--2805931 Score: 416
Period size: 81 Copynumber: 6.0 Consensus size: 81
2805425 AAAAATTGTT
** * * * *
2805435 ACTAAAGTACGAGTCTTTAGCGAAATTTGTATAAAAATGCCACTAATGTATGAGTCTCTAGCGAC
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTACGAGTCTTTAGCGGC
*
2805500 ATTTGTATAAAAACGCC
65 GTTTGTATAAAAACGCC
* * *
2805517 ACTAAAGTACGAGCCTTTAGCGGCATTTATATAAAACA-CCACTAAAGTACGAGTCTTTAGTGGC
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAA-ATCCACTAAAGTACGAGTCTTTAGCGGC
2805581 GTTTGTATAAAAAC-CC
65 GTTTGTATAAAAACGCC
* * * * *
2805597 TACTAAAGGT-TGAGTCTTTAACGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCG
1 -ACTAAA-GTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTACGAGTCTTTAGCG
*** *
2805661 ATTTTTTTATTTTATAAAAACGCC
63 ----GCGT-TTGTATAAAAACGCC
* * * * * *
2805685 ACTAAAGTATGAGTCTTTAGCGGCATTTGTACGAAAACAT-CTCTAAAATATGAGTCTTTAGCAG
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTA-TAAAA-ATCCACTAAAGTACGAGTCTTTAGCGG
*
2805749 CGTTTGTATAAAAA-ACC
64 CGTTTGTATAAAAACGCC
* * *** * *
2805766 ACTAAAATACGAGTCTATAGCGATGTTTGTAT-AAAATGCCACTAAAGTAC-AATCTTCAGCGGC
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTACGAGTCTTTAGCGGC
2805829 GTTTGTATAAAAACGCC
65 GTTTGTATAAAAACGCC
* * ** * * * * *
2805846 ACTAAAGTAC-AATCTTCAGCGGTGTTTATATAAAAATCCCACTAAAGTACTAGTATTTAGTGAC
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTACGAGTCTTTAGCGGC
*
2805910 GTTTGTTCTAAAAACGCC
65 GTTTG-TATAAAAACGCC
2805928 ACTA
1 ACTA
2805932 TAAACCTATT
Statistics
Matches: 332, Mismatches: 63, Indels: 40
0.76 0.14 0.09
Matches are distributed among these distances:
78 2 0.01
79 42 0.13
80 39 0.12
81 102 0.31
82 80 0.24
83 2 0.01
86 3 0.01
87 54 0.16
88 6 0.02
89 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (81 bp):
ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAATCCACTAAAGTACGAGTCTTTAGCGGCG
TTTGTATAAAAACGCC
Found at i:2805731 original size:128 final size:128
Alignment explanation
Indices: 2805542--2805789 Score: 331
Period size: 128 Copynumber: 1.9 Consensus size: 128
2805532 TTTAGCGGCA
* * * *
2805542 TTTATATAAAACACCACTAAAGTACGAGTCTTTAGTGGCGTTTGTATAAAAACCCTACTAAAGGT
1 TTTATATAAAACACCACTAAAGTACGAGTCTTTAGCGGCATTTGTACAAAAACCCTACTAAA-AT
* * *
2805607 -TGAGTCTTTAACGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCGATTTTTTTAT
65 ATGAGTCTTTAACAGCGTTTGTATAAAAA-ACCACTAAAATACAAGTCTATAGCGATTTTTTTAT
* * * *
2805671 TTTATA-AAAACGCCACTAAAGTATGAGTCTTTAGCGGCATTTGTACGAAAACATCT-CTAAAAT
1 TTTATATAAAACACCACTAAAGTACGAGTCTTTAGCGGCATTTGTACAAAAAC-CCTACTAAAAT
* *
2805734 ATGAGTCTTTAGCAGCGTTTGTATAAAAAACCACTAAAATACGAGTCTATAGCGAT
65 ATGAGTCTTTAACAGCGTTTGTATAAAAAACCACTAAAATACAAGTCTATAGCGAT
2805790 GTTTGTATAA
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
127 25 0.24
128 71 0.68
129 8 0.08
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (128 bp):
TTTATATAAAACACCACTAAAGTACGAGTCTTTAGCGGCATTTGTACAAAAACCCTACTAAAATA
TGAGTCTTTAACAGCGTTTGTATAAAAAACCACTAAAATACAAGTCTATAGCGATTTTTTTAT
Found at i:2806389 original size:19 final size:18
Alignment explanation
Indices: 2806365--2806403 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2806355 ATACTCAAAA
*
2806365 TAATATTAATTTATATATT
1 TAATATTAATATA-ATATT
2806384 TAATATTAATATAATATT
1 TAATATTAATATAATATT
2806402 TA
1 TA
2806404 GGTGCGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATATTAATATAATATT
Found at i:2807669 original size:41 final size:41
Alignment explanation
Indices: 2807617--2807847 Score: 223
Period size: 41 Copynumber: 5.5 Consensus size: 41
2807607 AAAAGTGTAT
*
2807617 GAGTCTCTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
* * *
2807658 GAGCCTTTAGCGACATTTGTATAAAAACACCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
* * *
2807699 GAGTCTTTAGTGGCGTTTGTATAAAAAC-CCTACTAAAGGT-T
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCC-ACTAAA-GTAC
* * *
2807740 GAGTCTTTAACGGCGTTTGTATAAAAATGCCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
* * ** * *
2807781 AAGTCTATAGCGATTTTTTTATTTTATAAAAACGCCACTAAAGTAT
1 GAGTCTTTAGCGA----CGT-TTGTATAAAAACGCCACTAAAGTAC
* *
2807827 GAGTCTTTAGCGGCATTTGTA
1 GAGTCTTTAGCGACGTTTGTA
2807848 AAATATGAGT
Statistics
Matches: 153, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
40 4 0.03
41 111 0.73
42 5 0.03
45 1 0.01
46 32 0.21
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (41 bp):
GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
Found at i:2807849 original size:27 final size:27
Alignment explanation
Indices: 2807819--2807874 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2807809 AAAACGCCAC
* *
2807819 TAAAGTATGAGTCTTTAGCGGCATTTG
1 TAAAATATGAGTCTTTAGCAGCATTTG
*
2807846 TAAAATATGAGTCTTTAGCAGCGTTTG
1 TAAAATATGAGTCTTTAGCAGCATTTG
2807873 TA
1 TA
2807875 TAAAAAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.38
Consensus pattern (27 bp):
TAAAATATGAGTCTTTAGCAGCATTTG
Found at i:2807968 original size:40 final size:41
Alignment explanation
Indices: 2807857--2808051 Score: 159
Period size: 40 Copynumber: 4.8 Consensus size: 41
2807847 AAAATATGAG
* * * * *
2807857 TCTTTAGCAGCGTTTGTATAAAAA-ACCACTAAAATACGAG
1 TCTTCAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAA
* * *
2807897 TCTAT-AGCGACGTTTGTAT-AAAATGCAACTAAAGTAC-AA
1 TCT-TCAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAA
*
2807936 TCTTCAGCGGCGTTTGTTTAAAAACGCCACTAAAGTAC-AA
1 TCTTCAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAA
* * * *
2807976 TCTTCAGCGGTGTTTATATAAAAATC-CCACTAAAGTACTAG
1 TCTTCAGCGGCGTTTGTATAAAAA-CGCCACTAAAGTACGAA
* * * * *
2808017 TATTTAGTGACGTTTGTTCTAAAAACGCCACTAAA
1 TCTTCAGCGGCGTTTG-TATAAAAACGCCACTAAA
2808052 AATGCCACTA
Statistics
Matches: 126, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.01
39 20 0.16
40 76 0.60
41 14 0.11
42 15 0.12
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (41 bp):
TCTTCAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAA
Found at i:2808518 original size:19 final size:18
Alignment explanation
Indices: 2808494--2808531 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2808484 ATACTCAAAA
*
2808494 TAATATTAATTTATATATT
1 TAATATTAATATA-ATATT
2808513 TAATATTAATATAATATT
1 TAATATTAATATAATATT
2808531 T
1 T
2808532 GGGTGCGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTAATATAATATT
Found at i:2809799 original size:41 final size:41
Alignment explanation
Indices: 2809747--2809977 Score: 214
Period size: 41 Copynumber: 5.5 Consensus size: 41
2809737 AAAAGTGTAT
*
2809747 GAGTCTCTAGCGACGTTTGTATAAAAACACCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACACCACTAAAGTAC
* **
2809788 GAGCCTTTAGCGATATTTGTATAAAAACACCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACACCACTAAAGTAC
* * *
2809829 GAGTCTTTAGTGGCGTTTGTATAAAAAC-CCTACTAAAGGT-T
1 GAGTCTTTAGCGACGTTTGTATAAAAACACC-ACTAAA-GTAC
* * **
2809870 GAGTCTTTAACGGCGTTTGTATAAAAATGCCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACACCACTAAAGTAC
* * ** * * *
2809911 AAGTCTATAGCGATTTTTTTATTTTATAAAAACGCCACTAAAGTAT
1 GAGTCTTTAGCGA----CGT-TTGTATAAAAACACCACTAAAGTAC
*
2809957 GAGTCTTTAGCGACATTTGTA
1 GAGTCTTTAGCGACGTTTGTA
2809978 AAATATGAGT
Statistics
Matches: 153, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
40 4 0.03
41 110 0.72
42 5 0.03
45 1 0.01
46 33 0.22
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (41 bp):
GAGTCTTTAGCGACGTTTGTATAAAAACACCACTAAAGTAC
Found at i:2810041 original size:40 final size:39
Alignment explanation
Indices: 2809997--2810180 Score: 160
Period size: 40 Copynumber: 4.6 Consensus size: 39
2809987 TCTTTAGCAG
*
2809997 CGTTTGTATAAAAA-ACCACTAAAGTACGAGTCTATAGCGA
1 CGTTTGTATAAAAACGCCACTAAAGTAC-AGTCT-TAGCGA
* * *
2810037 CGTTTGTAT-AAAATGCCACTAAAGTACAATCTTCAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACAGTCTT-AGCGA
* * *
2810076 CGTTTGTTTAAAAACGCCACTAAAGTACAATCTTCAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACAGTCTT-AGCGA
* * * *
2810116 TGTTTATATAAAAATC-CCACTAAAGTACTAGTATTTAGTGA
1 CGTTTGTATAAAAA-CGCCACTAAAGTAC-AGT-CTTAGCGA
*
2810157 CGTTTGT-TCTAAAACGCCACTAAA
1 CGTTTGTAT-AAAAACGCCACTAAA
2810181 AATGCCACTA
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.01
39 20 0.17
40 75 0.62
41 23 0.19
42 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (39 bp):
CGTTTGTATAAAAACGCCACTAAAGTACAGTCTTAGCGA
Found at i:2810127 original size:79 final size:82
Alignment explanation
Indices: 2809987--2810180 Score: 211
Period size: 79 Copynumber: 2.4 Consensus size: 82
2809977 AAAATATGAG
* * * * *
2809987 TCTTTAGCAGCGTTTGTATAAAAA-ACCACTAAAGTACGAGTCTATAGCGACGTTTGTAT-AAAA
1 TCTTTAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGAATCTATAGCGACGTTTATATAAAAA
*
2810050 TGCCACTAAAGTAC-AA
66 TCCCACTAAAGTACTAA
* **
2810066 TCTTCAGCGGCGTTTGTTTAAAAACGCCACTAAAGTAC-AATCT-TCAGCGGTGTTTATATAAAA
1 TCTTTAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGAATCTAT-AGCGACGTTTATATAAAA
*
2810129 ATCCCACTAAAGTACTAG
65 ATCCCACTAAAGTACTAA
* * *
2810147 TATTTAGTGACGTTTGTTCT-AAAACGCCACTAAA
1 TCTTTAGCGGCGTTTGTT-TAAAAACGCCACTAAA
2810181 AATGCCACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 36 0.38
80 29 0.30
81 29 0.30
82 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (82 bp):
TCTTTAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGAATCTATAGCGACGTTTATATAAAAA
TCCCACTAAAGTACTAA
Found at i:2810649 original size:19 final size:18
Alignment explanation
Indices: 2810625--2810662 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2810615 ATACTCAAAA
*
2810625 TAATATTAATTTATATATT
1 TAATATTAATATA-ATATT
2810644 TAATATTAATATAATATT
1 TAATATTAATATAATATT
2810662 T
1 T
2810663 GGGTGCGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTAATATAATATT
Found at i:2817346 original size:22 final size:22
Alignment explanation
Indices: 2817269--2817349 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 22
2817259 ATTTAAATTT
* *
2817269 ATTATTATTATTAAATTTATTATT
1 ATTATTATTATTATA-TTATTA-A
*
2817293 ATTATTATTATTATTATTAAATAA
1 ATTATTATTATTA-TATT-ATTAA
2817317 TATTATTATTATTATATTATTAA
1 -ATTATTATTATTATATTATTAA
*
2817340 ATAATTATTA
1 ATTATTATTA
2817350 CAAGCCCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
22 9 0.18
23 4 0.08
24 19 0.39
25 17 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTATTATTATATTATTAA
Found at i:2817349 original size:3 final size:3
Alignment explanation
Indices: 2817267--2817338 Score: 85
Period size: 3 Copynumber: 24.0 Consensus size: 3
2817257 TCATTTAAAT
*
2817267 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
2817313 ATA ATA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2817339 AATAATTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.05
3 55 0.90
4 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2819477 original size:20 final size:21
Alignment explanation
Indices: 2819454--2819494 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2819444 AGAAATTAAA
2819454 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTCAATTTTT
* *
2819474 AATTCTTTTCTTTCAATTTTT
1 AATTCATTTATTTCAATTTTT
2819495 TTTATTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTCATTTATTTCAATTTTT
Found at i:2821745 original size:44 final size:44
Alignment explanation
Indices: 2821679--2821762 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
2821669 AATAGAGAAA
* * *
2821679 TTAGGAGTGAAAGTTATTCCCTATAATGTAA-AGTTTTGTTGAAG
1 TTAGGACTGAAAGTTATCCCCTA-AATATAAGAGTTTTGTTGAAG
* *
2821723 TTAGGACTGAAAGTTGTCCCCTACATATAAGAGTTTTGTT
1 TTAGGACTGAAAGTTATCCCCTAAATATAAGAGTTTTGTT
2821763 TGATGTACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 5 0.15
44 29 0.85
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (44 bp):
TTAGGACTGAAAGTTATCCCCTAAATATAAGAGTTTTGTTGAAG
Found at i:2821926 original size:14 final size:15
Alignment explanation
Indices: 2821909--2821947 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2821899 GAACTGCACA
2821909 TTTTGCATTCTT-AT
1 TTTTGCATTCTTCAT
*
2821923 TTTTGCATTTTTGCAT
1 TTTTGCATTCTT-CAT
2821939 TTTTGCATT
1 TTTTGCATT
2821948 TTTGCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
16 11 0.50
ACGTcount: A:0.13, C:0.13, G:0.10, T:0.64
Consensus pattern (15 bp):
TTTTGCATTCTTCAT
Found at i:2821934 original size:8 final size:8
Alignment explanation
Indices: 2821909--2821956 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
2821899 GAACTGCACA
2821909 TTTTGCAT
1 TTTTGCAT
*
2821917 TCTT--AT
1 TTTTGCAT
2821923 TTTTGCAT
1 TTTTGCAT
2821931 TTTTGCAT
1 TTTTGCAT
2821939 TTTTGCAT
1 TTTTGCAT
2821947 TTTTGCAT
1 TTTTGCAT
2821955 TT
1 TT
2821957 ACATTACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 5 0.14
8 31 0.86
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.65
Consensus pattern (8 bp):
TTTTGCAT
Found at i:2824153 original size:2 final size:2
Alignment explanation
Indices: 2824146--2824247 Score: 204
Period size: 2 Copynumber: 51.0 Consensus size: 2
2824136 TTATCCTTTA
2824146 AT AT 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 AT AT
2824188 AT AT 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 AT AT
2824230 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2824248 CCTTTGTTGT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2826906 original size:114 final size:114
Alignment explanation
Indices: 2826703--2826923 Score: 388
Period size: 114 Copynumber: 1.9 Consensus size: 114
2826693 AAGTGTCATG
*
2826703 TGCTCATAGTAGAAATAAGAAGACTAAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCAAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
2826768 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
* *
2826817 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCAAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
2826882 TGGTTTGGTATGAACCCCAGAACCAATCATTAGAATTGAAAG
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGAATTGAAAG
2826924 GTGATCTGCA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCAAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
Found at i:2829312 original size:22 final size:22
Alignment explanation
Indices: 2829283--2829337 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2829273 ATCTACACTC
* *
2829283 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
*
2829305 TTTAAAGATGACAAATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
2829327 TTCAAAGATGA
1 TTCAAAGATGA
2829338 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:2830143 original size:76 final size:76
Alignment explanation
Indices: 2830034--2830732 Score: 1184
Period size: 76 Copynumber: 9.2 Consensus size: 76
2830024 CTTCAGTGCA
* * * *
2830034 TGATGTTTCCAAAAAGCCTTCGGGTCATTTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCC
1 TGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCC
2830099 TTCGGGAGCTTTT
64 TTCGGGAGCTTTT
*
2830112 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
2830177 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
2830188 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
2830253 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
2830264 TGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
2830328 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
2830339 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
2830404 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
2830415 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
2830480 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
2830491 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCATGCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
2830556 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
2830567 TGATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
*
2830632 CAGGAGCTTTT
66 CGGGAGCTTTT
*
2830643 TGATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
2830708 CGGGAGCTTTT
66 CGGGAGCTTTT
2830719 TGATGTTTTCAAAA
1 TGATGTTTTCAAAA
2830733 ACCAAAAAGC
Statistics
Matches: 601, Mismatches: 19, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
75 75 0.12
76 513 0.85
77 4 0.01
78 9 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:2830723 original size:31 final size:31
Alignment explanation
Indices: 2830688--2830778 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 31
2830678 CTTCAGTGCA
2830688 TGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
2830719 TGATGTTTTCAAAAACCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTT-------CAAAAAGCCTTCGGGAGCTTTT
2830757 TGATGTTTTC-AAAA-CCTTCGGG
1 TGATGTTTTCAAAAAGCCTTCGGG
2830779 TCATCTGTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
29 8 0.15
30 4 0.08
31 10 0.19
38 31 0.58
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (31 bp):
TGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
Found at i:2830748 original size:38 final size:38
Alignment explanation
Indices: 2830697--2830770 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
2830687 ATGATGTTTT
2830697 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAAC
1 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAAC
2830735 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAA
1 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAA
2830771 CCTTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (38 bp):
CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAAC
Found at i:2830762 original size:190 final size:190
Alignment explanation
Indices: 2830544--2830921 Score: 704
Period size: 190 Copynumber: 2.0 Consensus size: 190
2830534 CATGATGTTT
*
2830544 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTACAGT
1 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGT
2830609 GCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
66 GCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
*
2830674 AGTCCT-TCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAA
131 AGTCCTAT-AGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAA
*
2830734 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTGCAGT
1 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGT
*
2830799 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
66 GCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
2830864 AGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
131 AGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
2830922 GCCTTCGGGT
Statistics
Matches: 183, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
190 182 0.99
191 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (190 bp):
CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGT
GCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
AGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAA
Found at i:2830767 original size:266 final size:266
Alignment explanation
Indices: 2830468--2830966 Score: 944
Period size: 266 Copynumber: 1.9 Consensus size: 266
2830458 CATGATGTTT
2830468 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCATGCAGT
1 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCATGCAGT
2830533 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
66 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
*
2830598 AGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAATCCTTCG
131 AGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCG
* *
2830663 GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
196 GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
2830728 CAAAAA
261 CAAAAA
*
2830734 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTGCAGT
1 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCATGCAGT
2830799 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
66 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
* *
2830864 AGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCG
131 AGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCG
2830929 GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAA
196 GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAA
2830967 CATTTCCATC
Statistics
Matches: 227, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
266 227 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (266 bp):
CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCATGCAGT
GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTA
AGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCG
GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
CAAAAA
Found at i:2830820 original size:114 final size:114
Alignment explanation
Indices: 2830620--2830845 Score: 416
Period size: 114 Copynumber: 2.0 Consensus size: 114
2830610 CATGATGTTT
* *
2830620 CCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTGCAGT
*
2830685 GCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAA
66 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAA
*
2830734 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTGCAGT
1 CCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTGCAGT
2830799 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
66 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
2830846 TCCTTCGGGT
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (114 bp):
CCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTGCAGT
GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAA
Found at i:2830860 original size:76 final size:76
Alignment explanation
Indices: 2830734--2830966 Score: 394
Period size: 76 Copynumber: 3.1 Consensus size: 76
2830724 TTTTCAAAAA
*
2830734 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTGCAGT
1 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGT
2830799 GCATGATGTTT
66 GCATGATGTTT
* *
2830810 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTATAGT
1 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGT
2830875 GCATGATGTTT
66 GCATGATGTTT
* * * *
2830886 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGT
1 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGT
2830951 GCATGATGTTT
66 GCATGATGTTT
*
2830962 TCAAA
1 CCAAA
2830967 CATTTCCATC
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 148 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGT
GCATGATGTTT
Found at i:2831110 original size:18 final size:18
Alignment explanation
Indices: 2831087--2831125 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2831077 TTTTTTTCAT
2831087 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
2831105 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
2831123 TTA
1 TTA
2831126 TTAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:2831119 original size:21 final size:21
Alignment explanation
Indices: 2831093--2831160 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
2831083 TCATTTAAAT
2831093 TTATTATTATTATTAAATTTA
1 TTATTATTATTATTAAATTTA
2831114 TTATTATTATTATTAAATATTA
1 TTATTATTATTATTAAAT-TTA
*
2831136 TTATTA-TATTATTAAA-TAA
1 TTATTATTATTATTAAATTTA
2831155 TTATTA
1 TTATTA
2831161 CAAGCCCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 8 0.18
21 28 0.62
22 9 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTATTATTATTAAATTTA
Found at i:2831160 original size:3 final size:3
Alignment explanation
Indices: 2831093--2831149 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
2831083 TCATTTAAAT
* *
2831093 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA
2831139 TTA -TA TTA TTA
1 TTA TTA TTA TTA
2831150 AATAATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 40 0.87
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2834561 original size:22 final size:23
Alignment explanation
Indices: 2834534--2834578 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2834524 GGTGAGAATA
*
2834534 TTATTAAT-TATTTAAAGTATAT
1 TTATTAATATATTTAAAATATAT
*
2834556 TTATTAATATTTTTAAAATATAT
1 TTATTAATATATTTAAAATATAT
2834579 ATAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATTAATATATTTAAAATATAT
Found at i:2834576 original size:21 final size:21
Alignment explanation
Indices: 2834530--2834590 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
2834520 TTTTGGTGAG
*
2834530 AATA-TTATTAAT-TATTTAA
1 AATATTTATTAATATTTTTAA
2834549 AGTATATTTATTAATATTTTTAA
1 A--ATATTTATTAATATTTTTAA
*
2834572 AATATATA-TAATATTTTTA
1 AATATTTATTAATATTTTTA
2834591 TTTGAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 9 0.25
22 8 0.22
23 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATATTTATTAATATTTTTAA
Found at i:2842039 original size:16 final size:16
Alignment explanation
Indices: 2842018--2842057 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2842008 TCTTCCATTT
2842018 TTGCCTCTTCCATCGC
1 TTGCCTCTTCCATCGC
2842034 TTGCCTCTTCCATCGC
1 TTGCCTCTTCCATCGC
2842050 TTGCCTCT
1 TTGCCTCT
2842058 ATTGAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.42, G:0.12, T:0.40
Consensus pattern (16 bp):
TTGCCTCTTCCATCGC
Found at i:2842271 original size:78 final size:78
Alignment explanation
Indices: 2842142--2842287 Score: 229
Period size: 78 Copynumber: 1.9 Consensus size: 78
2842132 AAGATAATGA
*
2842142 TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAATGAAATTAAT
1 TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAAGGAAATTAAT
2842207 GGTTGAGTTAGCG
66 GGTTGAGTTAGCG
* * * * * *
2842220 TATATTAAATGACCTTTGAGATGATACAATGAATATCGTCTATAACTGTTACCAAGGCAATTAAT
1 TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAAGGAAATTAAT
2842285 GGT
66 GGT
2842288 ATAGTCAGCA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (78 bp):
TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAAGGAAATTAAT
GGTTGAGTTAGCG
Found at i:2846826 original size:41 final size:42
Alignment explanation
Indices: 2846767--2846845 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
2846757 TCAAAAGCTT
*
2846767 TGATACCAATTAAGTGTAACCCCCTAGA-CCAGCCTATACTC
1 TGATACCAATTAAATGTAACCCCCTAGACCCAGCCTATACTC
* *
2846808 TGATACCAATTAAATGTAATCCCTTAGACCCAGCCTAT
1 TGATACCAATTAAATGTAACCCCCTAGACCCAGCCTAT
2846846 GCGTTTCGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 25 0.74
42 9 0.26
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.27
Consensus pattern (42 bp):
TGATACCAATTAAATGTAACCCCCTAGACCCAGCCTATACTC
Found at i:2850012 original size:25 final size:26
Alignment explanation
Indices: 2849984--2850033 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
2849974 TGTGATATTT
2849984 TGTAAATATTTTTAAAA-GGTGTTTG
1 TGTAAATATTTTTAAAAGGGTGTTTG
2850009 TGTAAATATTTTTAAAAGGGTGTTT
1 TGTAAATATTTTTAAAAGGGTGTTT
2850034 AATACGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (26 bp):
TGTAAATATTTTTAAAAGGGTGTTTG
Found at i:2850132 original size:59 final size:59
Alignment explanation
Indices: 2850005--2850132 Score: 184
Period size: 59 Copynumber: 2.2 Consensus size: 59
2849995 TTAAAAGGTG
** *
2850005 TTTGTGTAAATATTTTTAAAAGGGTGTTTAATACGTAATTAATTTATGGTAAGGTGTTA
1 TTTGTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTATGGTAAGGTGATA
* * * *
2850064 TTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAGGGTGATA
1 TTTGTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTATGGTAAGGTGATA
*
2850123 TTTGCGTAAA
1 TTTGTGTAAA
2850133 AGTTGACCGT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.45
Consensus pattern (59 bp):
TTTGTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTATGGTAAGGTGATA
Done.