Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 20 of 21
Found at i:2539756 original size:28 final size:28
Alignment explanation
Indices: 2539711--2540247 Score: 455
Period size: 28 Copynumber: 19.0 Consensus size: 28
2539701 TACCTATTTA
*
2539711 GAGTCAGTGACACCCTTCCAAAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
* * *
2539739 GAATTAGTGGCACCCTTCCAAAACCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
*
2539767 GAGTCAGTGGCATCCTTCCAAAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
** *
2539795 GAGTCAGTGGCATCTTTTCAAAAGCCCAC
1 GAGTCAGTGGCA-CCCTTCCAAAGCCCAC
* * * *
2539824 GAGTCAATGGCATCCTTTCAAAATCCCAC
1 GAGTCAGTGGCA-CCCTTCCAAAGCCCAC
* * * *
2539853 GACTTAGTGGCACCCTTTCAAAAGCCCAT
1 GAGTCAGTGGCACCC-TTCCAAAGCCCAC
* * * **
2539882 AAGTCAATGACA-TTTTCTCAAAGCCCAC
1 GAGTCAGTGGCACCCTTC-CAAAGCCCAC
* * *
2539910 GAGTCAATGGCACCTTTTCAAAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
**
2539938 GAGTCAGTGGCACCCTTTAAAAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
* * * *
2539966 AAGTCAGTGGCAACCTTCTAAAGCCCAT
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
* * *
2539994 GAGTTAGTGGCATCCTTCTAAAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
* * * *
2540022 GAGTCAATGGCATCTTTCCAGAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
*
2540050 GAGTCAGTGGCATCCTTCCAAAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
* * *
2540078 AAGTCAGTGGCATCCTTCCAAAATCCCAC
1 GAGTCAGTGGCACCCTTCC-AAAGCCCAC
* * * * *
2540107 AAGTCATTAGCATCCTTTCAAAAGCCCAC
1 GAGTCAGTGGCA-CCCTTCCAAAGCCCAC
* * ** * *
2540136 AAGTCAGTGGCACCATTTTAAAGCTCTC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
* * * * *
2540164 AAGTCAATGGCACCTTTTCAAAGCTCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
* * * *
2540192 AAGTCAGTGGTACCCTTTCAAAGTCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
*
2540220 GAGTCAGTGGCACCCTTCTAAAGCCCAC
1 GAGTCAGTGGCACCCTTCCAAAGCCCAC
2540248 ACAAGTAGGT
Statistics
Matches: 420, Mismatches: 83, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
27 3 0.01
28 309 0.74
29 104 0.25
30 4 0.01
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
GAGTCAGTGGCACCCTTCCAAAGCCCAC
Found at i:2540183 original size:254 final size:255
Alignment explanation
Indices: 2539712--2540247 Score: 720
Period size: 254 Copynumber: 2.1 Consensus size: 255
2539702 ACCTATTTAG
* * *
2539712 AGTCAGTGACACCCTTCCAAAGCCCACGAATTAGTGGCACCCTTCCAAAACCCACGAGTCAGTGG
1 AGTCAGTGGCACCCTTCTAAAGCCCACGAATTAGTGGCACCCTTCCAAAACCCACGAGTCAATGG
* * *
2539777 CATCCTTCCAAAGCCCACGAGTCAGTGGCATCTTTTCAAAAGCCCACGAGTCAATGGCATCCTTT
66 CATCCTTCCAAAGCCCACGAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCAATGGCATCCTTC
* * * *
2539842 CAAAATCCCACGACTTAGTGGCACCCTTTCAAAAGCCCATAAGTCAATGACATTTTCTCAAAGCC
131 CAAAATCCCACAACTCAGTAGCACCCTTTCAAAAGCCCACAAGTCAATGACATTTTCTCAAAGCC
* *
2539907 CACGAGTCAATGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTAAAAGCCCACA
196 CACAAGTCAATGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACA
* * * * * *
2539967 AGTCAGTGGCAACCTTCTAAAGCCCATGAGTTAGTGGCATCCTTCTAAAGCCCACGAGTCAATGG
1 AGTCAGTGGCACCCTTCTAAAGCCCACGAATTAGTGGCACCCTTCCAAAACCCACGAGTCAATGG
* * * *
2540032 CATCTTTCCAGAGCCCACGAGTCAGTGGCATC-CTTCCAAAGCCCACAAGTCAGTGGCATCCTTC
66 CATCCTTCCAAAGCCCACGAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCAATGGCATCCTTC
* * * *
2540096 CAAAATCCCACAAGTCATTAGCATCCTTTCAAAAGCCCACAAGTCAGTGGCACCA-TTT-T-AAA
131 CAAAATCCCACAACTCAGTAGCACCCTTTCAAAAGCCCACAAGTCAAT-G-A-CATTTTCTCAAA
* * * * * * *
2540158 GCTCTCAAGTCAATGGCACCTTTTCAAAGCTCACAAGTCAGTGGTACCCTTTCAAAGTCCACG
193 GCCCACAAGTCAATGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACA
2540221 AGTCAGTGGCACCCTTCTAAAGCCCAC
1 AGTCAGTGGCACCCTTCTAAAGCCCAC
2540248 ACAAGTAGGT
Statistics
Matches: 243, Mismatches: 35, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
254 149 0.61
255 88 0.36
256 4 0.02
257 2 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (255 bp):
AGTCAGTGGCACCCTTCTAAAGCCCACGAATTAGTGGCACCCTTCCAAAACCCACGAGTCAATGG
CATCCTTCCAAAGCCCACGAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCAATGGCATCCTTC
CAAAATCCCACAACTCAGTAGCACCCTTTCAAAAGCCCACAAGTCAATGACATTTTCTCAAAGCC
CACAAGTCAATGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACA
Found at i:2540295 original size:29 final size:30
Alignment explanation
Indices: 2540226--2540292 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
2540216 CCACGAGTCA
*
2540226 GTGGCACCCTTCTAAAGCCCACACAAGTAG
1 GTGGCACCCTTTTAAAGCCCACACAAGTAG
* * *
2540256 GT-GAACCCTTTTAAAGTCCACACAAGTTG
1 GTGGCACCCTTTTAAAGCCCACACAAGTAG
2540285 GTGGCACC
1 GTGGCACC
2540293 TTTCAGTCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (30 bp):
GTGGCACCCTTTTAAAGCCCACACAAGTAG
Found at i:2541026 original size:62 final size:62
Alignment explanation
Indices: 2540950--2541095 Score: 184
Period size: 62 Copynumber: 2.4 Consensus size: 62
2540940 CTGAAAGGTG
* * ** * *
2540950 CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAAAACGCCTTTTCTTTTTTAAAGCC
1 CACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAACAAAACACCTTTTCCTTTTTAAAGCC
* ** *
2541012 CACACAAGTTGGTGGCACCTTTCAATTCTCAAAGAACAGGACACGTTTTCCTTTTTAAAGCC
1 CACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAACAAAACACCTTTTCCTTTTTAAAGCC
* *
2541074 CACACAAATTGTTGGCACCTTT
1 CACACAAGTTGGTGGCACCTTT
2541096 GTCATCTTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (62 bp):
CACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAACAAAACACCTTTTCCTTTTTAAAGCC
Found at i:2541289 original size:103 final size:104
Alignment explanation
Indices: 2541135--2541371 Score: 296
Period size: 103 Copynumber: 2.3 Consensus size: 104
2541125 TGAATTAGTG
* *
2541135 CATTGGCACTCTTCTCATTTTTAAGCCCAATGTTGCTGTCCTTGAATCAGTACATTAGCACCCTT
1 CATTGGCACTCTTCTCATTTTTAAGCCCAATGTCGCTGACCTTGAATCAGTACATTAGCACCCTT
* * **
2541200 ATCAAGTTTAAGTCTAACGTCGTTGGCCTTGAATCAACA
66 ATCAACTTTAAGTCCAACGTAATTGGCCTTGAATCAACA
* * * * *
2541239 CATTGGCAC-CTTTTCATTTTTAATCCCAATGTCGCTGACCTTGAATCAGTACGTTGGCACTCTT
1 CATTGGCACTCTTCTCATTTTTAAGCCCAATGTCGCTGACCTTGAATCAGTACATTAGCACCCTT
* * * *
2541303 CTCATCTTTAAGTCCAATGTAATTGGTCTTGAATCAACA
66 ATCAACTTTAAGTCCAACGTAATTGGCCTTGAATCAACA
* * * *
2541342 CATTGGCATTCTTTTTATCTTTAAGCCCAA
1 CATTGGCACTCTTCTCATTTTTAAGCCCAA
2541372 GCCTTGAATC
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
103 87 0.77
104 26 0.23
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (104 bp):
CATTGGCACTCTTCTCATTTTTAAGCCCAATGTCGCTGACCTTGAATCAGTACATTAGCACCCTT
ATCAACTTTAAGTCCAACGTAATTGGCCTTGAATCAACA
Found at i:2541334 original size:52 final size:52
Alignment explanation
Indices: 2541097--2541371 Score: 239
Period size: 52 Copynumber: 5.3 Consensus size: 52
2541087 GGCACCTTTG
* * * *
2541097 TCATCTTTAAGTCCGATGTCGCTCGCCTTGAATTAGTGCATTGGCACTCTTC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACTCTTC
* * * * * * *
2541149 TCATTTTTAAGCCCAATGTTGCTGTCCTTGAATCAGTACATTAGCACCCTTA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACTCTTC
** * * * ** *
2541201 TCAAGTTTAAGTCTAACGTCGTTGGCCTTGAATCAACACATTGGCAC-CTTT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACTCTTC
* * *
2541252 TCATTTTTAA-TCCCAATGTCGCTGACCTTGAATCAGTACGTTGGCACTCTTC
1 TCATCTTTAAGT-CCAATGTCGCTGGCCTTGAATCAGTACATTGGCACTCTTC
*** * ** * *
2541304 TCATCTTTAAGTCCAATGTAATTGGTCTTGAATCAACACATTGGCATTCTTT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACTCTTC
* *
2541356 TTATCTTTAAGCCCAA
1 TCATCTTTAAGTCCAA
2541372 GCCTTGAATC
Statistics
Matches: 174, Mismatches: 46, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
50 1 0.01
51 39 0.22
52 133 0.76
53 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (52 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACTCTTC
Found at i:2555643 original size:2 final size:2
Alignment explanation
Indices: 2555638--2555664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2555628 ATAATGTGTG
2555638 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
2555665 TTAAGACTAA
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:2558429 original size:20 final size:20
Alignment explanation
Indices: 2558404--2558476 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2558394 CAACTTTTTT
2558404 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2558424 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2558445 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2558465 ATGTATCGATAC
1 ATGTATCGATAC
2558477 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2558442 original size:41 final size:41
Alignment explanation
Indices: 2558383--2558476 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2558373 CAACCAAGAA
*
2558383 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
2558424 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
2558465 ATGTATCGATAC
1 ATGTATCGATAC
2558477 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:2558458 original size:21 final size:21
Alignment explanation
Indices: 2558383--2558458 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2558373 CAACCAAGAA
* *
2558383 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2558404 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2558424 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2558445 ATGTATCGATACAT
1 ATGTATCGATACAT
2558459 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2559143 original size:23 final size:23
Alignment explanation
Indices: 2559113--2559159 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2559103 ATCTCCCCCT
*
2559113 TAATCAAGTGATTCATATCAAAA
1 TAATCAAGTAATTCATATCAAAA
2559136 TAATCAAGTAATTCATATCAAAA
1 TAATCAAGTAATTCATATCAAAA
2559159 T
1 T
2559160 TTATTTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (23 bp):
TAATCAAGTAATTCATATCAAAA
Found at i:2560962 original size:13 final size:13
Alignment explanation
Indices: 2560944--2560982 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2560934 ATAATCACCC
*
2560944 TGTATCGATACAG
1 TGTATCGATACAA
2560957 TGTATCGATACAA
1 TGTATCGATACAA
2560970 TGTATCGATACAA
1 TGTATCGATACAA
2560983 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2560993 original size:20 final size:20
Alignment explanation
Indices: 2560968--2561046 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
2560958 GTATCGATAC
2560968 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
2560988 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
2561013 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
2561033 CATGTATCGATACA
1 AATGTATCGATACA
2561047 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2567172 original size:13 final size:13
Alignment explanation
Indices: 2567154--2567179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2567144 CAATTTTTTG
2567154 TGTATCGATACAT
1 TGTATCGATACAT
2567167 TGTATCGATACAT
1 TGTATCGATACAT
2567180 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2567264 original size:20 final size:20
Alignment explanation
Indices: 2567239--2567311 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2567229 CAACTTTTTT
2567239 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2567259 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2567280 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2567300 ATGTATCGATAC
1 ATGTATCGATAC
2567312 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2567277 original size:41 final size:41
Alignment explanation
Indices: 2567218--2567311 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2567208 CTGCCAAGAA
*
2567218 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
2567259 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
2567300 ATGTATCGATAC
1 ATGTATCGATAC
2567312 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:2567293 original size:21 final size:21
Alignment explanation
Indices: 2567218--2567293 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2567208 CTGCCAAGAA
* *
2567218 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2567239 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2567259 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2567280 ATGTATCGATACAT
1 ATGTATCGATACAT
2567294 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2571155 original size:52 final size:51
Alignment explanation
Indices: 2571077--2571225 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
2571067 CGAAATATGA
*
2571077 AAATTTGCCTGCATGCATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
2571129 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
2571181 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
2571226 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:2571321 original size:13 final size:13
Alignment explanation
Indices: 2571303--2571327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2571293 AAAAAAAATA
2571303 TGTATCGATACAT
1 TGTATCGATACAT
2571316 TGTATCGATACA
1 TGTATCGATACA
2571328 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2578264 original size:18 final size:18
Alignment explanation
Indices: 2578241--2578276 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2578231 TTTAAAGGGA
2578241 AGTTCGGACAAAATTAAG
1 AGTTCGGACAAAATTAAG
2578259 AGTTCGGACAAAATTAAG
1 AGTTCGGACAAAATTAAG
2578277 TATTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
AGTTCGGACAAAATTAAG
Found at i:2579531 original size:19 final size:19
Alignment explanation
Indices: 2579507--2579574 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2579497 AATTCAACAA
2579507 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2579526 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2579541 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2579558 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2579575 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2579546 original size:13 final size:13
Alignment explanation
Indices: 2579528--2579552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2579518 ACATAAGTTT
2579528 TGTATCGATACAA
1 TGTATCGATACAA
2579541 TGTATCGATACA
1 TGTATCGATACA
2579553 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2579550 original size:32 final size:32
Alignment explanation
Indices: 2579509--2579571 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2579499 TTCAACAATT
*
2579509 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2579541 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2579572 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2579632 original size:13 final size:13
Alignment explanation
Indices: 2579614--2579639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2579604 CATTTTTCTG
2579614 TGTATCGATACAT
1 TGTATCGATACAT
2579627 TGTATCGATACAT
1 TGTATCGATACAT
2579640 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2579636 original size:33 final size:33
Alignment explanation
Indices: 2579594--2579660 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2579584 GCCAAGGAAA
***
2579594 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2579627 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2579660 T
1 T
2579661 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2582142 original size:27 final size:28
Alignment explanation
Indices: 2582112--2582187 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
2582102 TTTCTTCACA
*
2582112 ATCGGGGATACTCCAACCCTGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
2582139 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
2582167 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2582188 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.53
28 20 0.47
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:2582296 original size:52 final size:51
Alignment explanation
Indices: 2582170--2582339 Score: 205
Period size: 52 Copynumber: 3.3 Consensus size: 51
2582160 TTATTTCCGA
* *** *
2582170 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAGTC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * *
2582221 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTC-ATAATC
* *
2582273 GGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
*
2582325 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2582340 TCGTTATTTC
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
51 37 0.38
52 47 0.48
53 14 0.14
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:2582350 original size:31 final size:28
Alignment explanation
Indices: 2582324--2582403 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
2582314 TTTTCACAAT
*
2582324 CGAGGATACTCCAACCTCGTTATTTCAC
1 CGAGGATACTCCAACCCCGTTATTTCAC
* *
2582352 CGGGGATACTCCAACCCCGTTACTT--C
1 CGAGGATACTCCAACCCCGTTATTTCAC
* *
2582378 CGAGGGAACACTCCAACCCCATTATT
1 CGA-GG-ATACTCCAACCCCGTTATT
2582404 ATCTCCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 38 0.88
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (28 bp):
CGAGGATACTCCAACCCCGTTATTTCAC
Found at i:2582372 original size:211 final size:211
Alignment explanation
Indices: 2582008--2582397 Score: 597
Period size: 211 Copynumber: 1.8 Consensus size: 211
2581998 TTCTCCACAA
* * **
2582008 TCGGGGACATTCCAACTCCGATTTTATTTTCAAAACATTAATTTTCTATAATCGGGGATACTCCA
1 TCGGGGACACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCA
* *
2582073 ACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCTGTTAAT
66 ACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCTGTTAAT
* * * *
2582138 CATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAA
131 CACCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAAAA
2582203 TATTGATTTTTCATAG
196 TATTGATTTTTCATAG
* * *
2582219 TCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCC
1 TCGGGGACACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCC
*
2582284 AACACCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAA-CCTCGTTA
65 AACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCT-GTTA
*
2582346 TTTCACCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCC
129 -ATCACCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCC
2582398 ATTATTATCT
Statistics
Matches: 161, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
209 3 0.02
210 25 0.16
211 98 0.61
212 35 0.22
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (211 bp):
TCGGGGACACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCA
ACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCTGTTAAT
CACCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAAAA
TATTGATTTTTCATAG
Found at i:2586899 original size:22 final size:22
Alignment explanation
Indices: 2586874--2586939 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 22
2586864 CATTCGTATA
2586874 TTCATATTATGTTTATATTA-TT
1 TTCATATTAT-TTTATATTATTT
*
2586896 TTCATGATAAATTTTA-ATTATTT
1 TTCAT-AT-TATTTTATATTATTT
*
2586919 TGTCATATTATATTTGTATTA
1 T-TCATATTAT-TTTATATTA
2586940 GATATCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
22 11 0.31
23 14 0.40
24 10 0.29
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (22 bp):
TTCATATTATTTTATATTATTT
Found at i:2595318 original size:22 final size:22
Alignment explanation
Indices: 2595292--2595339 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2595282 CAATCTTTTT
**
2595292 TATTTTAATATTACCTTTTAAA
1 TATTTTAATATTACAATTTAAA
2595314 TATTTTAATATTACAATTTAAA
1 TATTTTAATATTACAATTTAAA
2595336 TATT
1 TATT
2595340 GTTGAGTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTTAATATTACAATTTAAA
Found at i:2604161 original size:23 final size:23
Alignment explanation
Indices: 2604109--2604191 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
2604099 TGATTTTTTT
* *
2604109 TCCTAAAATTAAGCACTCATGTCC
1 TCCTAAAATCAAGCACTTATG-CC
2604133 TCCTAAAATCAAGCACTTATGCC
1 TCCTAAAATCAAGCACTTATGCC
2604156 TCCTAAAATCAAGCACTTATG--
1 TCCTAAAATCAAGCACTTATGCC
*
2604177 TCGTAAAATCAAGCA
1 TCCTAAAATCAAGCA
2604192 TACTAATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.25
23 23 0.41
24 19 0.34
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (23 bp):
TCCTAAAATCAAGCACTTATGCC
Found at i:2604227 original size:12 final size:12
Alignment explanation
Indices: 2604210--2604240 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2604200 TACAACTAAT
2604210 CTCCTATAATTA
1 CTCCTATAATTA
2604222 CTCCTATAATTA
1 CTCCTATAATTA
*
2604234 CTACTAT
1 CTCCTAT
2604241 TTCACAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCCTATAATTA
Found at i:2604660 original size:32 final size:32
Alignment explanation
Indices: 2604619--2604683 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2604609 TAAATAATAG
2604619 ATGAATTAAATTGATACATGGAGCAAAACATT
1 ATGAATTAAATTGATACATGGAGCAAAACATT
2604651 ATGAATTAAATTGATACATGGAGCAAAACATT
1 ATGAATTAAATTGATACATGGAGCAAAACATT
2604683 A
1 A
2604684 CTATTAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (32 bp):
ATGAATTAAATTGATACATGGAGCAAAACATT
Found at i:2605826 original size:13 final size:13
Alignment explanation
Indices: 2605808--2605835 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2605798 GCTTGTTTTT
2605808 GTATGGGACATTA
1 GTATGGGACATTA
2605821 GTATGGGACATTA
1 GTATGGGACATTA
2605834 GT
1 GT
2605836 CACATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (13 bp):
GTATGGGACATTA
Found at i:2611581 original size:42 final size:42
Alignment explanation
Indices: 2611503--2611593 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
2611493 GTTCAGGTCT
* * *
2611503 GGTTACAGGTGTAGGAACGGGTTCAGACATAGGTTCAAACACA
1 GGTT-CAGGTGTAGAAACGGGTTCAGACACAAGTTCAAACACA
* * * *
2611546 GGTTCAGGTGTAGAAACGGGTTTAGGCACAAGTTCAGACACG
1 GGTTCAGGTGTAGAAACGGGTTCAGACACAAGTTCAAACACA
2611588 GGTTCA
1 GGTTCA
2611594 AATAGATTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (42 bp):
GGTTCAGGTGTAGAAACGGGTTCAGACACAAGTTCAAACACA
Found at i:2615186 original size:13 final size:13
Alignment explanation
Indices: 2615168--2615192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2615158 GTTGCTCCTC
2615168 TTTTATATCACTA
1 TTTTATATCACTA
2615181 TTTTATATCACT
1 TTTTATATCACT
2615193 GTCAAATGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTATATCACTA
Found at i:2616775 original size:38 final size:38
Alignment explanation
Indices: 2616733--2616810 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2616723 GATTATGGTT
2616733 ATAAAATAGGAAGTTAAAATCTAATCAAATCTCCTATA
1 ATAAAATAGGAAGTTAAAATCTAATCAAATCTCCTATA
2616771 ATAAAATAGGAAGTTAAAATCTAATCAAATCTCCTATA
1 ATAAAATAGGAAGTTAAAATCTAATCAAATCTCCTATA
2616809 AT
1 AT
2616811 CAAGCGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (38 bp):
ATAAAATAGGAAGTTAAAATCTAATCAAATCTCCTATA
Found at i:2616827 original size:38 final size:38
Alignment explanation
Indices: 2616747--2616878 Score: 151
Period size: 38 Copynumber: 3.5 Consensus size: 38
2616737 AATAGGAAGT
* * *
2616747 TAAAATCTAATCAAATCTCCTATAAT-AA-AATAGGAAGT
1 TAAAATCTAATCAAATCTCCTATAATCAAGCATA-TAA-A
*
2616785 TAAAATCTAATCAAATCTCCTATAATCAAGCGTATAAA
1 TAAAATCTAATCAAATCTCCTATAATCAAGCATATAAA
* * * *
2616823 TAAAATTTAATCAAATCTCCTATAATCAGGCCTATATA
1 TAAAATCTAATCAAATCTCCTATAATCAAGCATATAAA
*
2616861 TAAAATCTAATCGAATCT
1 TAAAATCTAATCAAATCT
2616879 AATCAAATCT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
38 76 0.93
39 4 0.05
40 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (38 bp):
TAAAATCTAATCAAATCTCCTATAATCAAGCATATAAA
Found at i:2618495 original size:17 final size:17
Alignment explanation
Indices: 2618473--2618507 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2618463 AGACACAAAA
2618473 GAAGAAATAGGCTAAGT
1 GAAGAAATAGGCTAAGT
2618490 GAAGAAATAGGCTAAGT
1 GAAGAAATAGGCTAAGT
2618507 G
1 G
2618508 CACTGACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.31, T:0.17
Consensus pattern (17 bp):
GAAGAAATAGGCTAAGT
Found at i:2626373 original size:38 final size:38
Alignment explanation
Indices: 2626330--2626428 Score: 144
Period size: 38 Copynumber: 2.6 Consensus size: 38
2626320 AATAGGAAGT
*
2626330 TAAAATCTAATCAAATCTCTTATAATCAAGCATATATA
1 TAAAATCTAATCAAATCTCCTATAATCAAGCATATATA
* *
2626368 TAAAATCTAATCAAATTTCCTATAATCAAGCCTATATA
1 TAAAATCTAATCAAATCTCCTATAATCAAGCATATATA
* * *
2626406 TAAAATCCAATCAAGTTTCCTAT
1 TAAAATCTAATCAAATCTCCTAT
2626429 TCTGTAACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.34
Consensus pattern (38 bp):
TAAAATCTAATCAAATCTCCTATAATCAAGCATATATA
Found at i:2628685 original size:33 final size:35
Alignment explanation
Indices: 2628648--2628713 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
2628638 TTTTTATTAA
*
2628648 TAATATATTTATAA-T-CATGTGTATCATAATTGG
1 TAATATATTTATAATTACAAGTGTATCATAATTGG
2628681 TAATATATTTATAATTACCAAGTGTATCATAAT
1 TAATATATTTATAATTA-CAAGTGTATCATAAT
2628714 CATGTATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 14 0.48
34 1 0.03
36 14 0.48
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (35 bp):
TAATATATTTATAATTACAAGTGTATCATAATTGG
Found at i:2630701 original size:53 final size:53
Alignment explanation
Indices: 2630635--2630736 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
2630625 GACAGGATAG
* *
2630635 ATGTGGGGAAAGCATCATATTGAAGAGAAAGGTTTTGTAAGGACACAATAAGA
1 ATGTGAGGAAAGCATCATATTGAAGAGAAAAGTTTTGTAAGGACACAATAAGA
* * *
2630688 ATGTGAGGAAAGCATTATATTGAAGAGAAAAGTTTTTTAAGGATACAAT
1 ATGTGAGGAAAGCATCATATTGAAGAGAAAAGTTTTGTAAGGACACAAT
2630737 GAGACATGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.26
Consensus pattern (53 bp):
ATGTGAGGAAAGCATCATATTGAAGAGAAAAGTTTTGTAAGGACACAATAAGA
Found at i:2636644 original size:25 final size:25
Alignment explanation
Indices: 2636616--2636665 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2636606 TGTCAAGGTG
*
2636616 TAGATGAGCTGTGAATAGATTAGGA
1 TAGATGAGCTGTAAATAGATTAGGA
*
2636641 TAGATGAGCTGTAAATATATTAGGA
1 TAGATGAGCTGTAAATAGATTAGGA
2636666 GAATTAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (25 bp):
TAGATGAGCTGTAAATAGATTAGGA
Found at i:2643059 original size:19 final size:20
Alignment explanation
Indices: 2643035--2643084 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2643025 ATTATGCTTC
**
2643035 ATCGATACATGTTC-ATTGT
1 ATCGATACATGGACAATTGT
2643054 ATCGATACATGGACAATTGT
1 ATCGATACATGGACAATTGT
*
2643074 ATTGATACATG
1 ATCGATACATG
2643085 AAATTGGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
ATCGATACATGGACAATTGT
Found at i:2643167 original size:30 final size:30
Alignment explanation
Indices: 2643116--2643176 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2643106 CCACTGTTTG
*
2643116 TATCGATACATGGTACATTGTATCAATACA
1 TATCGATACATGATACATTGTATCAATACA
* *
2643146 TATCGATACATTATA-ATTTGTATCGATACA
1 TATCGATACATGATACA-TTGTATCAATACA
2643176 T
1 T
2643177 TACTTCAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (30 bp):
TATCGATACATGATACATTGTATCAATACA
Found at i:2643361 original size:21 final size:21
Alignment explanation
Indices: 2643336--2643383 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2643326 TTCAAGCCTA
*
2643336 TAAATTTGAGTTTTCAACAGT
1 TAAATTTGAGTTTCCAACAGT
2643357 TAAATTTGAGTTTCCAACAGT
1 TAAATTTGAGTTTCCAACAGT
*
2643378 TGAATT
1 TAAATT
2643384 GCAAAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (21 bp):
TAAATTTGAGTTTCCAACAGT
Found at i:2651717 original size:19 final size:19
Alignment explanation
Indices: 2651692--2651764 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
2651682 TGTATCTATA
2651692 CATTGTATCGATACAAGTT
1 CATTGTATCGATACAAGTT
* *
2651711 TATTGTATCGATACATGTT
1 CATTGTATCGATACAAGTT
* * **
2651730 CATTGTATCAATACATGGA
1 CATTGTATCGATACAAGTT
2651749 CAATTGTATCGATACA
1 C-ATTGTATCGATACA
2651765 TGAAACTGGC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 33 0.72
20 13 0.28
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACAAGTT
Found at i:2652697 original size:31 final size:31
Alignment explanation
Indices: 2652644--2652702 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2652634 TTTAAAATTA
* *
2652644 TTCTTAAAGAATTCAATCTCTTTTTATAAAG
1 TTCTAAAAGAATTCAATCTCTTTATATAAAG
*
2652675 TTCTAAAAGAATCTCACT-TCTTTATATA
1 TTCTAAAAGAAT-TCAATCTCTTTATATA
2652703 TCTTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (31 bp):
TTCTAAAAGAATTCAATCTCTTTATATAAAG
Found at i:2653189 original size:31 final size:31
Alignment explanation
Indices: 2653147--2653218 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
2653137 TTTAAACTTG
* *
2653147 TGCTTAAGAGTAATATAACAACCTAAGCTCT
1 TGCTTAGGAGTAATATAACAACCTAAGCTCA
* * ** *
2653178 TGCTTAGGAGTAGTATGACAATTTTAGCTCA
1 TGCTTAGGAGTAATATAACAACCTAAGCTCA
2653209 TGCTTAGGAG
1 TGCTTAGGAG
2653219 CATCATTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (31 bp):
TGCTTAGGAGTAATATAACAACCTAAGCTCA
Found at i:2655471 original size:42 final size:43
Alignment explanation
Indices: 2655399--2655496 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
2655389 AGGTCTTCAA
*
2655399 ACTTAATCTAGAATCAACAAGGTCTACTTCAAAG-G-TTTTTAG
1 ACTTAATCTTGAATCAACAAGGTCTACTTC-AAGTGTTTTTTAG
* ** * *
2655441 ATTTAATCTTGAATCAATGAGGTTTGCTTCAAGTGTTTTTTTAG
1 ACTTAATCTTGAATCAACAAGGTCTACTTCAAGTG-TTTTTTAG
2655485 ACTTAATCTTGA
1 ACTTAATCTTGA
2655497 CTAATGGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.07
42 25 0.54
44 18 0.39
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (43 bp):
ACTTAATCTTGAATCAACAAGGTCTACTTCAAGTGTTTTTTAG
Found at i:2655846 original size:45 final size:44
Alignment explanation
Indices: 2655779--2655897 Score: 177
Period size: 45 Copynumber: 2.7 Consensus size: 44
2655769 AAAACTTATC
* *
2655779 TTTTGTATTTATCTTTAATTAATTTAATTTAATAATAGAT-AAT
1 TTTTTTATTTATCTTTAATTAATTTAATTTAATAAGAGATAAAT
*
2655822 ATTTTTTATTTATCTCTTAATTAATTTAATTTAATCAGAGATAAAT
1 -TTTTTTATTTATCT-TTAATTAATTTAATTTAATAAGAGATAAAT
2655868 TTTTTTATTTATCTTTTAATTAATTTAATT
1 TTTTTTATTTATC-TTTAATTAATTTAATT
2655898 AATTAGTTAA
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
44 13 0.19
45 52 0.75
46 4 0.06
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (44 bp):
TTTTTTATTTATCTTTAATTAATTTAATTTAATAAGAGATAAAT
Found at i:2659689 original size:481 final size:474
Alignment explanation
Indices: 2658713--2659692 Score: 1048
Period size: 481 Copynumber: 2.0 Consensus size: 474
2658703 CCTTATTTTC
* * *
2658713 ATTGTCATTGTAA-ATATTTTTTATTATTAATAATAATTATCTAATTTATAAGTAGAAATTTTAA
1 ATTGTCATTGTAATAT-TTTTTTATTATTAATAAGAATTATCCAATTTATAAGTAAAAATTTTAA
* * * * *
2658777 TTTTACTAAAAATCTTTCATTAAATATATTTCTATGATATACCTAAAATATAGTTGAATTTTACT
65 TTTTACTAAAAATCTTTCATTAAATATATTTATATGATATACATAAAATAAAATTAAATTTTACT
*
2658842 TTAATATTTTTTTTAGAGTTGTAATTTTCATAACCTTCAAAAGTAAATGAATTTATTTGATAAAA
130 TAAATATTTTTTTTAGAGTTGTAATTTTCATAACCTTCAAAAGTAAATGAATTTATTTGATAAAA
* *
2658907 TATAAAAAATTTAAATTTTATATGACTATTTTATTTTCATAAATTTTAATTTTATAATAAAACTA
195 TAAAAAAAATTTAAATTTTATATGAC---TTTATTTTCATAAATTATAATTTTATAATAAAACTA
* * * *
2658972 AACAAATTTATAAATTTAAACATTGAATAAACTTTACATGTTTATACAATTATTAATTTTAATTA
257 AACAAAATAATAAATTTAAACATTGAACAAACTTTACATGTTAATACAATTATTAATTTTAATTA
* * * **
2659037 TTTGTAACATATACAACTACATATTATTAATAAATAAAAGAATGAATATTCATGTATGACATATG
322 TTTGTAAAATATACAACTACATATTATTAATAAATAAAAGAATGAATATTCATGTATGAAACACA
* * * * * * *
2659102 TGACAACAAATATTAGCATATATAAAAGCACGAATGTGATAATTTTTTTATCTAACAAAAGTAGT
387 TAACAACAAATAATAGCATATATAAAAGAACGAATATGATAATCTTTTGAACTAACAAAAGTAGT
* *
2659167 CTTGTTGTTGACTAAATTTTTAA
452 CTTGTTGTTGACAAAATTTCTAA
* * *
2659190 GTTGTTATTGTAAATATTTTTTTATTATTAATAAGATTTATCCAATTTATAAGTAAAAATTTTAA
1 ATTGTCATTGT-AATATTTTTTTATTATTAATAAGAATTATCCAATTTATAAGTAAAAATTTTAA
* * *
2659255 TTTTATTAAAAATCTTTCATT-AATATATTTATTTGATGATAGATAAAA-AAAATTAAAGTTTAT
65 TTTTACTAAAAATCTTTCATTAAATATATTTATATGAT-ATACATAAAATAAAATTAAA-TTT-T
* * *
2659318 A-TTAAATTACTTTATTTTTTA-AGTTTTAATTTTTCATAACCTT-AAAATTTAAATGAATTTGT
127 ACTTAAA-TA--TT-TTTTTTAGAGTTGTAA-TTTTCATAACCTTCAAAA-GTAAATGAATTTAT
2659380 TTGATAAAAAATAAAAAAAACGTTTAAA-TTTATATTGAC-TT-TTTTCATAAATTATAATTTTA
186 TTGAT--AAAATAAAAAAAA--TTTAAATTTTATA-TGACTTTATTTTCATAAATTATAATTTTA
* * * * *
2659442 T-ATGAAAA-TAAA-AAAATAATAAATTTGAATATTGGACAAACTTTACATGTTAATATATTTAT
246 TAAT-AAAACTAAACAAAATAATAAATTTAAACATTGAACAAACTTTACATGTTAATACAATTAT
* * * * *
2659504 TAATTTTAATTATTTTTAAAATATATAATTATATATT-TTAA-AAATTAATAAAACGATGAATAT
310 TAATTTTAATTATTTGTAAAATATACAACTACATATTATTAATAAA-TAA-AAGA--ATGAATAT
* * *
2659567 TCAT-TGATGAAACACATAACAATAAATAATAGTATATATAAAAGAATGAATAT-ATAGAAACTC
371 TCATGT-ATGAAACACATAACAACAAATAATAGCATATATAAAAGAACGAATATGAT---AA-TC
*
2659630 TTTTGAACTAATGAAAA-T-GATCATTG-T-TT-ACAAAATTTCTAA
431 TTTTGAACTAA-CAAAAGTAG-TC-TTGTTGTTGACAAAATTTCTAA
*
2659672 ATTGTCAATGTAATATTTTTT
1 ATTGTCATTGTAATATTTTTT
2659693 GCTATTAACA
Statistics
Matches: 419, Mismatches: 55, Indels: 54
0.79 0.10 0.10
Matches are distributed among these distances:
477 32 0.08
478 88 0.21
479 82 0.20
480 9 0.02
481 96 0.23
482 58 0.14
483 5 0.01
484 26 0.06
485 13 0.03
486 10 0.02
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (474 bp):
ATTGTCATTGTAATATTTTTTTATTATTAATAAGAATTATCCAATTTATAAGTAAAAATTTTAAT
TTTACTAAAAATCTTTCATTAAATATATTTATATGATATACATAAAATAAAATTAAATTTTACTT
AAATATTTTTTTTAGAGTTGTAATTTTCATAACCTTCAAAAGTAAATGAATTTATTTGATAAAAT
AAAAAAAATTTAAATTTTATATGACTTTATTTTCATAAATTATAATTTTATAATAAAACTAAACA
AAATAATAAATTTAAACATTGAACAAACTTTACATGTTAATACAATTATTAATTTTAATTATTTG
TAAAATATACAACTACATATTATTAATAAATAAAAGAATGAATATTCATGTATGAAACACATAAC
AACAAATAATAGCATATATAAAAGAACGAATATGATAATCTTTTGAACTAACAAAAGTAGTCTTG
TTGTTGACAAAATTTCTAA
Found at i:2660310 original size:18 final size:18
Alignment explanation
Indices: 2660265--2660310 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2660255 TATATGGTAG
2660265 AAAG-GAAGAAAAATAAA
1 AAAGAGAAGAAAAATAAA
*
2660282 AAAGAGAAAGAAAGA-AAA
1 AAAGAG-AAGAAAAATAAA
2660300 AAAGATGAAGA
1 AAAGA-GAAGA
2660311 GAAGTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
18 13 0.52
19 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (18 bp):
AAAGAGAAGAAAAATAAA
Found at i:2661548 original size:20 final size:20
Alignment explanation
Indices: 2661523--2661599 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
2661513 TTTTACCTAG
2661523 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
2661543 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
2661563 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
2661583 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
2661600 GTCCTTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2667192 original size:58 final size:57
Alignment explanation
Indices: 2667101--2667224 Score: 203
Period size: 58 Copynumber: 2.2 Consensus size: 57
2667091 AGGTGAAGAC
* * *
2667101 TTTATATAATTGGTAATATTTTATGTAATTTTGATGAAAATTATTATTAGGTAATGT
1 TTTATGTAATTGCTAATATTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGT
*
2667158 TTTATGTAATGTGCTAATGTTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGT
1 TTTATGTAAT-TGCTAATATTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGT
2667216 TTTATGTAA
1 TTTATGTAA
2667225 CTAGCAATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
57 9 0.15
58 53 0.85
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (57 bp):
TTTATGTAATTGCTAATATTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGT
Found at i:2667239 original size:58 final size:58
Alignment explanation
Indices: 2667114--2667244 Score: 203
Period size: 58 Copynumber: 2.3 Consensus size: 58
2667104 ATATAATTGG
* * *
2667114 TAATATTTTATGTAATTTTGATGAAAATTATTATTAGGTAATGTTTTATGTAATGTGC
1 TAATGTTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGTTTTATGTAATGAGC
2667172 TAATGTTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGTTTTATGTAACT-AGC
1 TAATGTTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGTTTTATGTAA-TGAGC
2667230 -AATGTTTTTATGTAA
1 TAATG-TTTTATGTAA
2667245 TGTGATAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
57 4 0.06
58 63 0.93
59 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (58 bp):
TAATGTTTTATGTAACTTTGATGAAAATTATTATTAGGTAATGTTTTATGTAATGAGC
Found at i:2667420 original size:54 final size:56
Alignment explanation
Indices: 2667355--2667476 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 56
2667345 AAAGTAAATG
*
2667355 GTAATGTTTTATGTAATTAAGATG-AAA-ATTCTTA-AGTAATATTTTATGTAACTCA
1 GTAATGTTTTATGTAATTAAGATGAAAATATTCTTAGA-TAATATTTTATCTAACT-A
*
2667410 -TAATGTTTTATGTAATTATGATGAAAATTATTCTTAGATAATATTTTATCTAACTA
1 GTAATGTTTTATGTAATTAAGATGAAAA-TATTCTTAGATAATATTTTATCTAACTA
2667466 GTAAT-TTTTAT
1 GTAATGTTTTAT
2667477 ATATAACTAG
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
54 22 0.37
55 3 0.05
56 7 0.12
57 27 0.45
58 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.48
Consensus pattern (56 bp):
GTAATGTTTTATGTAATTAAGATGAAAATATTCTTAGATAATATTTTATCTAACTA
Found at i:2667796 original size:215 final size:215
Alignment explanation
Indices: 2667561--2668123 Score: 878
Period size: 215 Copynumber: 2.6 Consensus size: 215
2667551 TAATACTACT
2667561 TTGTATTACCTTTTGATAATATATTTATATAATTTACAAAATTTTATGTAAATATAAGATATTTA
1 TTGTATTACCTTTTGATAATATATTTATATAATTTACAAAATTTTATGTAAATATAAGATATTTA
**
2667626 TGTATTAGTACTTTTATTATCTTACATCATTTATGTTTTAAGTAATGTATATGTGTAATTATAAT
66 TGTATTACAACTTTTATTATCTTACATCATTTATGTTTTAAGTAATGTATATGTGTAATTATAAT
*
2667691 ATAAATATGTAATAACTTCCATCTATACTTTTGATAATAATTTATCTAATGGATAATATAATTTA
131 ATAAATATGTAATAACTTCCATCTATACTTTTGATAATAATTTATATAATGGATAATATAATTTA
* *
2667756 TGTAAATATAATGTTTTAAG
196 CGTAAATATAATATTTTAAG
*
2667776 TTGTATTACCTTTTGATAATATATTTACATAATTTACAAAATTTTATGTAAATATAAGATATTTA
1 TTGTATTACCTTTTGATAATATATTTATATAATTTACAAAATTTTATGTAAATATAAGATATTTA
2667841 TGTATTACAACTTTTATTATCTTACATCATTTATGTTTTAAGTAATGTATATGTGTAATTATAAT
66 TGTATTACAACTTTTATTATCTTACATCATTTATGTTTTAAGTAATGTATATGTGTAATTATAAT
* *
2667906 ATAAATATGTAATAACTTTCATCTATACTTTTGATAATAATTTATATCATGGATAATATAATTTA
131 ATAAATATGTAATAACTTCCATCTATACTTTTGATAATAATTTATATAATGGATAATATAATTTA
*
2667971 CGTAAGTATAATATTTTAAG
196 CGTAAATATAATATTTTAAG
* * * * ** * *
2667991 TTGTATTTCCTTTTCATAATATATTTATGTAACTTACATACCTTTTATGTAAATATAATAAATTT
1 TTGTATTACCTTTTGATAATATATTTATATAATTTACA-AAATTTTATGTAAATATAAGATATTT
* * * * *
2668056 ATGTATTACAACTTTTATTATCTTTTATCATAATTTAAGTTTTAGGTAAAG--TATGTGTAATTG
65 ATGTATTACAACTTTTATTATC--TTA-CATCATTTATGTTTTAAGTAATGTATATGTGTAATTA
2668119 TAATA
127 TAATA
2668124 AAAGCATGTG
Statistics
Matches: 321, Mismatches: 23, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
215 239 0.74
216 44 0.14
217 16 0.05
218 3 0.01
219 19 0.06
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (215 bp):
TTGTATTACCTTTTGATAATATATTTATATAATTTACAAAATTTTATGTAAATATAAGATATTTA
TGTATTACAACTTTTATTATCTTACATCATTTATGTTTTAAGTAATGTATATGTGTAATTATAAT
ATAAATATGTAATAACTTCCATCTATACTTTTGATAATAATTTATATAATGGATAATATAATTTA
CGTAAATATAATATTTTAAG
Found at i:2676640 original size:22 final size:22
Alignment explanation
Indices: 2676615--2676660 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2676605 ACGAGATACA
2676615 TTACGACCACTACGCTTTCTTC
1 TTACGACCACTACGCTTTCTTC
2676637 TTACGACCACTACGCTTTCTTC
1 TTACGACCACTACGCTTTCTTC
2676659 TT
1 TT
2676661 CCTTGTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.35, G:0.09, T:0.39
Consensus pattern (22 bp):
TTACGACCACTACGCTTTCTTC
Found at i:2681291 original size:14 final size:14
Alignment explanation
Indices: 2681274--2681311 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2681264 AGTCAAAAGT
*
2681274 AAACACAAAAAACA
1 AAACAAAAAAAACA
2681288 AAACAAAAAAAAC-
1 AAACAAAAAAAACA
*
2681301 ACACAAAAAAA
1 AAACAAAAAAA
2681312 GTGCAAAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (14 bp):
AAACAAAAAAAACA
Found at i:2682628 original size:31 final size:31
Alignment explanation
Indices: 2682580--2683469 Score: 962
Period size: 31 Copynumber: 28.2 Consensus size: 31
2682570 TTTTCAAATC
* *
2682580 TCTTTTC-TCAAAGTCCACAACTCAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
2682610 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
**
2682641 TCTTTT-TTCCCCAAAGTCCACGACTCAGTGGTG
1 TCTTTTCTT--CC-AAGTCCACGACTCAGTGGCA
2682674 TCTTTT-TTCCTCAAAGTCCACGACTCAGTGGCA
1 TCTTTTCTT-C-C-AAGTCCACGACTCAGTGGCA
* * * *
2682707 TCTCTTCTTCAAAGTCCACGGCTTAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
2682738 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
* *
2682769 TCTTTT-TTCCCCAAAGTCCACAACTTAGTGGCA
1 TCTTTTCTT--CC-AAGTCCACGACTCAGTGGCA
** *
2682802 TCTTTTCTTTAAAGTCCACGACTTAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
*
2682833 TCTTTTCTTCCAAGTCCACGACTCAGTGGCG
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
2682864 TCTTTT-TTCCCCAAAGTCCACGACTCAGTGGCA
1 TCTTTTCTT--CC-AAGTCCACGACTCAGTGGCA
* * * * *
2682897 TCTCTTCTTCAAAGTTCATGACTTAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
**
2682928 TCTTTTCTTCCAAGTCCACGACTCAGTGGTG
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
*
2682959 TCTTTT-TTCCTCAAAGTCCATGACTCAGTGGCA
1 TCTTTTCTT-C-C-AAGTCCACGACTCAGTGGCA
* * * *
2682992 TCTCTTCTTCAAAGTCCACGGCTTAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
2683023 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
* *
2683054 TCTTTTTTCTCCAAAGTCCACGACTTAGTGGCA
1 TCTTTTCT-TCC-AAGTCCACGACTCAGTGGCA
* *
2683087 TCTCTTCTTCAAAGTCCACGACTCAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
**
2683118 TCTTTTCTTCCAAGTCCACGACTCAGTGGTG
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
2683149 TCTTTT-TTCCCCAAAGTCCACGACTCAGTGGCA
1 TCTTTTCTT--CC-AAGTCCACGACTCAGTGGCA
* * *
2683182 TCTCTTCTTCAAAGTCCACGACTCAATGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
* * *
2683213 TCTTTTCTTCAAAGTCCACAACTTAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
* * *
2683244 TCCCTTTC--CAAAGTCCACGGCTCAGTGGCA
1 T-CTTTTCTTCCAAGTCCACGACTCAGTGGCA
*
2683274 TCTTCTT-TTCAAAGTCCACGACAT-AGTGGCA
1 TCTT-TTCTTCCAAGTCCACGAC-TCAGTGGCA
2683305 TCTTTT-TTCTCTAAAGTCCACGACTCAGTGGCA
1 TCTTTTCTTC-C--AAGTCCACGACTCAGTGGCA
* *
2683338 TCTTTTCTTCAAAGTCCACGACACAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
* * *
2683369 TCTTTTCTTCAAAGTCCATGACACAGTGGCA
1 TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
2683400 TCTTTTCTT-CAACGTCCACGACAT-AGTGGCA
1 TCTTTTCTTCCAA-GTCCACGAC-TCAGTGGCA
** *
2683431 TCTTTTTTCTTTAAAGTCCACGACTCAATGGCA
1 TC--TTTTCTTCCAAGTCCACGACTCAGTGGCA
2683464 TCTTTT
1 TCTTTT
2683470 TCAAAGCCCA
Statistics
Matches: 738, Mismatches: 82, Indels: 79
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.00
30 46 0.06
31 430 0.58
32 26 0.04
33 219 0.30
34 15 0.02
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.33
Consensus pattern (31 bp):
TCTTTTCTTCCAAGTCCACGACTCAGTGGCA
Found at i:2682799 original size:95 final size:95
Alignment explanation
Indices: 2682588--2683480 Score: 1209
Period size: 95 Copynumber: 9.4 Consensus size: 95
2682578 TCTCTTTTCT
* * * *
2682588 CAAAGTCCACAACTCAGTGGCATCTTTTCTTCCAAGTCCACGACTCAGTGGCATCTTTT-TTCCC
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTT--C
** *
2682652 CAAAGTCCACGACTCAGTGGTGTCTTTTTTCCT
64 C-AAGTCCACGACTCAGTGGCATCTTTTTTCCC
*
2682685 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGGCTTAGTGGCATCTTTTCTTCCA
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
2682750 AGTCCACGACTCAGTGGCATCTTTTTTCCC
66 AGTCCACGACTCAGTGGCATCTTTTTTCCC
* * * *
2682780 CAAAGTCCACAACTTAGTGGCATCTTTTCTTTAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
*
2682845 AGTCCACGACTCAGTGGCGTCTTTTTTCCC
66 AGTCCACGACTCAGTGGCATCTTTTTTCCC
* *
2682875 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTTCATGACTTAGTGGCATCTTTTCTTCCA
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
** *
2682940 AGTCCACGACTCAGTGGTGTCTTTTTTCCT
66 AGTCCACGACTCAGTGGCATCTTTTTTCCC
* *
2682970 CAAAGTCCATGACTCAGTGGCATCTCTTCTTCAAAGTCCACGGCTTAGTGGCATCTTTTCTTCCA
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
*
2683035 AGTCCACGACTCAGTGGCATCTTTTTTCTC
66 AGTCCACGACTCAGTGGCATCTTTTTTCCC
* *
2683065 CAAAGTCCACGACTTAGTGGCATCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCCA
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
**
2683130 AGTCCACGACTCAGTGGTGTCTTTTTTCCC
66 AGTCCACGACTCAGTGGCATCTTTTTTCCC
* * *
2683160 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTCAATGGCATCTTTTCTTCAA
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
* * **
2683225 AGTCCACAACTTAGTGGCATC-CCTTT--C
66 AGTCCACGACTCAGTGGCATCTTTTTTCCC
* *
2683252 CAAAGTCCACGGCTCAGTGGCATCTTCTT-TTCAAAGTCCACGACATAGTGGCATCTTTT-TTCT
1 CAAAGTCCACGACTCAGTGGCATC-TCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTC-
2683315 CTAAAGTCCACGACTCAGTGGCATCTTTTCTT---
64 C--AAGTCCACGACTCAGTGGCATCTTTT-TTCCC
* * * **
2683347 CAAAGTCCACGACACAGTGGCATCTTTTCTTCAAAGTCCATGACACAGTGGCATCTTTTCTT-CA
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
**
2683411 ACGTCCACGACAT-AGTGGCATCTTTTTTCTT
66 A-GTCCACGAC-TCAGTGGCATCTTTTTTCCC
* * *
2683442 TAAAGTCCACGACTCAATGGCATCT-TT-TTCAAAGCCCAC
1 CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCAC
2683481 AAGTCAGTGG
Statistics
Matches: 717, Mismatches: 65, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
91 3 0.00
92 55 0.08
93 36 0.05
94 30 0.04
95 531 0.74
96 6 0.01
97 54 0.08
98 2 0.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (95 bp):
CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTCTTCCA
AGTCCACGACTCAGTGGCATCTTTTTTCCC
Found at i:2683560 original size:27 final size:27
Alignment explanation
Indices: 2683528--2683587 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
2683518 GCATCTTTTT
*
2683528 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCATGGCAC
2683555 CCTTTTAAGTCCACAACTCCATGGCAC
1 CCTTTTAAGTCCACAACTCCATGGCAC
*
2683582 CTTTTT
1 CCTTTT
2683588 TCTTTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.32
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCATGGCAC
Found at i:2683621 original size:62 final size:62
Alignment explanation
Indices: 2683467--2683622 Score: 190
Period size: 60 Copynumber: 2.5 Consensus size: 62
2683457 AATGGCATCT
* * * ** * * *
2683467 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCCGTGGCATCTTTTTCC
1 TTTTCAAAGCCCACAACTCCGTGGCACCCTT-TTAAGCCCACAACTCCATGGCACCTTTTTCC
* * *
2683530 TTTT--AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCACCTTTTTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCACCTTTTTCC
2683590 TTTTCAAAGCCCACAACTCCGTGGCACCCTTTT
1 TTTTCAAAGCCCACAACTCCGTGGCACCCTTTT
2683623 CCTTTTTAAG
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
60 28 0.35
61 21 0.27
62 26 0.33
63 4 0.05
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.29
Consensus pattern (62 bp):
TTTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCACCTTTTTCC
Found at i:2683667 original size:34 final size:33
Alignment explanation
Indices: 2683501--2683670 Score: 129
Period size: 35 Copynumber: 5.2 Consensus size: 33
2683491 CAACCTTCAA
* * * *
2683501 AAGCCCACAAGTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACCCTTTTCCTTGT
*
2683534 AAGTCCACAACTCCGTGGCACCC---T--TT-T
1 AAGCCCACAACTCCGTGGCACCCTTTTCCTTGT
* * * * *
2683561 AAGTCCACAACTCCATGGCACCTTTTTTCTTTT
1 AAGCCCACAACTCCGTGGCACCCTTTTCCTTGT
*
2683594 CAAAGCCCACAACTCCGTGGCACCCTTTTCCTTTTT
1 --AAGCCCACAACTCCGTGGCACCCTTTTCC-TTGT
* *
2683630 AAGCCCACACCTCTGTGGCATCCCTTTTTCC-TGT
1 AAGCCCACAACTCCGTGGCA-CCC-TTTTCCTTGT
2683664 AAGCCCA
1 AAGCCCA
2683671 TAAGTTAGTG
Statistics
Matches: 113, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
27 22 0.19
28 2 0.02
30 2 0.02
32 2 0.02
33 20 0.18
34 27 0.24
35 28 0.25
36 10 0.09
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACCCTTTTCCTTGT
Found at i:2683759 original size:29 final size:29
Alignment explanation
Indices: 2683664--2683759 Score: 97
Period size: 28 Copynumber: 3.3 Consensus size: 29
2683654 TTTTTCCTGT
* * * *
2683664 AAGCCCATAAGTTAGTGGCACCTCTTTCAA
1 AAGCCCACAAGTCAATGGCAAC-CTTTCAA
2683694 AAGCCCACAAGTCAATGGCAACC-TTCAA
1 AAGCCCACAAGTCAATGGCAACCTTTCAA
* **
2683722 AAGCACACAAGTTGAT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAATGGCAA-CCTTTCAA
2683751 AAGCCCACA
1 AAGCCCACA
2683760 CAAGTTGGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 4 0.07
28 20 0.36
29 14 0.25
30 18 0.32
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.19
Consensus pattern (29 bp):
AAGCCCACAAGTCAATGGCAACCTTTCAA
Found at i:2683839 original size:49 final size:49
Alignment explanation
Indices: 2683779--2684620 Score: 574
Period size: 49 Copynumber: 17.8 Consensus size: 49
2683769 GGCATCTTCT
* * *
2683779 TCTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTAAC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * *
2683828 TCTAAGACCAATGTCACTGGCCTTGAATCAGTACATTGG---C---A--
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
2683869 -C-AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * *
2683916 TTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCA-CATTGTC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
2683964 TCTAAGACCAATGTCGCTGGCCTTGAATCAGTACATTGG---C---A--
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
2684005 -C-AAG-CCCA-ATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
2684050 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACT-TTGG---C---A--
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCA-TATTGGCACCTTTATC
*
2684091 --TAAG-CCAAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTC
1 TCTAAGACC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
2684137 TCTCAGACCAATGTCGCTGGCCTTGAATCAGCACATT-G-A-C---A--
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * *
2684178 -C-AAGCCCAGTATCGTTGGTCTTGAATCAGCATATTGGCACCTTTATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * * * * **
2684225 TTTAAGAACGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT---TTATC
* * *
2684277 TTTAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATC
* * * * * *
2684329 TTTAAGTCCAATGTCGCTGGCCTTGAAACAGCACATTGGCACCTTCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * * **
2684378 TTTAAGACCGATGA-CGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATC
1 TCTAAGACCAAT-ATCGCTGGCCTTGAATCAGCATATTGGCACCT---TTATC
* * *
2684430 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CGTTATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * *
2684478 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
2684527 TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATC
* * * *
2684579 TTTAAAACCCAATGTCGTTGGCCTTGAATCAGCATATTGGCA
1 TCTAAGA-CCAATATCGCTGGCCTTGAATCAGCATATTGGCA
2684621 TTCTTCTCAT
Statistics
Matches: 630, Mismatches: 102, Indels: 118
0.74 0.12 0.14
Matches are distributed among these distances:
37 23 0.04
38 6 0.01
39 91 0.14
40 5 0.01
41 1 0.00
42 3 0.00
43 3 0.00
45 3 0.00
46 4 0.01
47 4 0.01
48 110 0.17
49 214 0.34
50 1 0.00
51 2 0.00
52 129 0.20
53 31 0.05
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (49 bp):
TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
Found at i:2683936 original size:88 final size:88
Alignment explanation
Indices: 2683786--2683958 Score: 247
Period size: 88 Copynumber: 2.0 Consensus size: 88
2683776 TCTTCTAAGT
* *
2683786 CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTAACTCTAAGACCAATGTCACTGGCCT
1 CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCAACTCTAAGACCAATATCACTGGCCT
*
2683851 TGAATCAGTACATTGGCACAAGC
66 TGAATCAGCACATTGGCACAAGC
** * * * * *
2683874 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCGATATCGCTGGCCT
1 CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCAACTCTAAGACCAATATCACTGGCCT
*
2683939 TGAATCAGCATATTGGCACA
66 TGAATCAGCACATTGGCACA
2683959 TTGTCTCTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (88 bp):
CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTCAACTCTAAGACCAATATCACTGGCCT
TGAATCAGCACATTGGCACAAGC
Found at i:2684077 original size:134 final size:136
Alignment explanation
Indices: 2683776--2684566 Score: 507
Period size: 153 Copynumber: 5.7 Consensus size: 136
2683766 GGTGGCATCT
* *
2683776 TCTTCTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTAACTCTAAGACCAATG
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTT-ACTCTAAGACCAATG
* *
2683841 TCACTGGCCTTGAATCAGTACATTGGCACAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGG
64 TCACTGGCCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGG
2683906 CACCTTCA
129 CACCTTCA
*
2683914 TCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACATTGT-CTCTAAGACCAATGT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATT-TACTCTAAGACCAATGT
*
2683978 CGCTGGCCTTGAATCAGTACATTGGCACAAGCCC-A-ATCGCTAGCCTTGAATCAGCATATTGGC
65 CACTGGCCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGC
2684041 ACCTTCA
130 ACCTTCA
* * *
2684048 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACT-TTGG--C----A---TAAG-CCAAATA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA-TATTGGCACATTTACTCTAAGACC-AATG
* * * * * * *
2684102 TCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTCAGACCAATGTCGCTGGCCTTGAATCA
64 TCACTGGCCTTGAATCAG--TA----CA--TTGGCAC-AAGCCCAATATCGCTAGCCTTGAATCA
*
2684167 GCACATT-G-A----CA
120 GCATATTGGCACCTTCA
* * * * * * * *
2684178 -C---AAGCCCAGTATCGTTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGAACGATGT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTA-CTCTAAGACCAATGT
** * * * *
2684239 CGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGCCCAATATTGCTGGCCTTGAA
65 CACTGGCCTTGAATCAGTACATTGG---------CA-C---AAGCCCAATATCGCTAGCCTTGAA
2684304 TCAGCATATTGGCACCTTCGTCA
117 TCAGCATATTGGCACC-T--TCA
* * * * * * * *
2684327 TCTTTAAGTCCAATGTCGCTGGCCTTGAAACAGCACATTGGCACCTTCATCTTTAAGACCGATGA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTA-CTCTAAGACCAATGT
** * * *
2684392 CGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGCCCAATATCGCTGGCCTTGAA
65 CACTGGCCTTGAATCAGTACATTGG---------CA-C---AAGCCCAATATCGCTAGCCTTGAA
*
2684457 TCAGCATATTGGCACGTT-A
117 TCAGCATATTGGCACCTTCA
* * * * * *
2684476 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATAT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTA-CTCTAAGACCAATGT
* * *
2684541 CGCTGGCCTTGAATCAGCATATTGGC
65 CACTGGCCTTGAATCAGTACATTGGC
2684567 GCCTTCGTCA
Statistics
Matches: 547, Mismatches: 54, Indels: 102
0.78 0.08 0.15
Matches are distributed among these distances:
124 2 0.00
125 26 0.05
126 29 0.05
127 2 0.00
128 3 0.01
129 1 0.00
130 4 0.01
131 2 0.00
132 2 0.00
133 5 0.01
134 75 0.14
135 4 0.01
136 93 0.17
137 42 0.08
138 6 0.01
140 31 0.06
141 1 0.00
142 1 0.00
149 86 0.16
150 2 0.00
152 1 0.00
153 129 0.24
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (136 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTACTCTAAGACCAATGTC
ACTGGCCTTGAATCAGTACATTGGCACAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA
CCTTCA
Found at i:2684138 original size:173 final size:176
Alignment explanation
Indices: 2683926--2684566 Score: 581
Period size: 173 Copynumber: 3.4 Consensus size: 176
2683916 TTTAAGTCCG
*
2683926 ATATCGCTGGCCTTGAATCAGCATATTGGCACATTGTCTCTAAGACCAATGTCGCTGGCCTTGAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAA
*
2683991 TCAGTACATTGGCACAAGCCCA-ATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
66 TCAGCACATTGGCACAAGCCCAGATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
* * *
2684055 GACCAATGTCGCTGGCCTTGAATCAGCACTTTGG-CA-TAAGCCAA
131 GAACAATGTCGCTGGCCTTGAATCAGCACATCGGCCATTAAGCCAA
*
2684099 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTCAGACCAATGTCGCTGGCCTTGAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAA
* * * * *
2684164 TCAGCACATTGACACAAGCCCAGTATCGTTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTA
66 TCAGCACATTGGCACAAGCCCAG-ATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTA
* * *
2684229 AGAACGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTTAAGCCCA
130 AGAACAATGTCGCTGGCCTTGAATCAGCACATCGG--------CCA---TTAAGCCAA
* *
2684287 ATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCT
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTC-TC--TAAGACCAATGTCGCTGGCCT
* * * * * *
2684352 TGAAACAGCACATTGGCACCTTCATCTTTAAGACC-GATGACGTTGGCCTTGAATCAGCACATCG
62 TGAATCAGCACATTGG------CA-C---AAGCCCAGAT--CGCTAGCCTTGAATCAGCATATTG
* ** * * *
2684416 GCACCTCAACCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACGTTATCTTT
115 GCACCT---TCATCTTTAAGAACAATGTCGCTGGCCTTGAATCAGCACATCGGC-C---A---TT
2684481 AAGTCC-A
170 AAG-CCAA
* * * * *
2684488 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCGCTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTCTAAGACCAATGTCGCTGGCCTTGA
*
2684553 ATCAGCATATTGGC
65 ATCAGCACATTGGC
2684567 GCCTTCGTCA
Statistics
Matches: 388, Mismatches: 41, Indels: 59
0.80 0.08 0.12
Matches are distributed among these distances:
173 83 0.21
175 67 0.17
184 2 0.01
188 41 0.11
189 3 0.01
190 2 0.01
192 34 0.09
197 1 0.00
198 36 0.09
199 1 0.00
200 3 0.01
201 46 0.12
202 34 0.09
205 35 0.09
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (176 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAA
TCAGCACATTGGCACAAGCCCAGATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
GAACAATGTCGCTGGCCTTGAATCAGCACATCGGCCATTAAGCCAA
Found at i:2684183 original size:87 final size:86
Alignment explanation
Indices: 2683926--2684266 Score: 468
Period size: 87 Copynumber: 3.9 Consensus size: 86
2683916 TTTAAGTCCG
* *
2683926 ATATCGCTGGCCTTGAATCAGCATATTGGCACATTGTCTCTAAGACCAATGTCGCTGGCCTTGAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTCTAAGACCAATGTCGCTGGCCTTGAA
* *
2683991 TCAGTACATTGGCACAAGCCC
66 TCAGCACATTGGCACAAGCCA
* *
2684012 A-ATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTCTAAGACCAATGTCGCTGGCCTTGA
* *
2684076 ATCAGCACTTTGGCATAAGCCAA
65 ATCAGCACATTGGCACAAGCC-A
* *
2684099 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTCAGACCAATGTCGCTGGCCTTGAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTCTAAGACCAATGTCGCTGGCCTTGAA
*
2684164 TCAGCACATTGACACAAGCCCA
66 TCAGCACATTGGCACAAG-CCA
* * * * * * *
2684186 GTATCGTTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGAACGATGTCGTTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTCTAAGACCAATGTCGCTGGCCTTGA
*
2684251 ATCAGCACATCGGCAC
65 ATCAGCACATTGGCAC
2684267 CTCAACCATC
Statistics
Matches: 224, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
85 31 0.14
86 46 0.21
87 74 0.33
88 73 0.33
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (86 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTCTAAGACCAATGTCGCTGGCCTTGAA
TCAGCACATTGGCACAAGCCA
Found at i:2684300 original size:52 final size:50
Alignment explanation
Indices: 2684179--2684620 Score: 455
Period size: 52 Copynumber: 8.8 Consensus size: 50
2684169 ACATTGACAC
* * * * *
2684179 AAGCCCAGTATCGTTGGTCTTGAATCAGCATATTGGCACCT-TTATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCATCTTT
** * * * * *
2684228 AAGAACGATGTCGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTC--TCATCTTT
* *
2684280 AAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TCATCTTT
* * *
2684332 AAGTCCAATGTCGCTGGCCTTGAAACAGCACATTGGCACCT-TCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCATCTTT
* * * * *
2684381 AAGACCGATGA-CGTTGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTT
1 AAGCCCAAT-ATCGCTGGCCTTGAATCAGCACATTGGCACCTC--TCATCTTT
* *
2684433 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACGT-T-ATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCATCTTT
* *
2684481 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT-TCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCATCTTT
* * *
2684530 AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC-TCATCTTT
* * * *
2684582 AAAACCCAATGTCGTTGGCCTTGAATCAGCATATTGGCA
1 -AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
2684621 TTCTTCTCAT
Statistics
Matches: 327, Mismatches: 52, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
48 44 0.13
49 117 0.36
50 1 0.00
51 2 0.01
52 128 0.39
53 35 0.11
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (50 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCTCATCTTT
Found at i:2684381 original size:101 final size:101
Alignment explanation
Indices: 2684179--2684725 Score: 491
Period size: 101 Copynumber: 5.4 Consensus size: 101
2684169 ACATTGACAC
* * * * *
2684179 AAGCCCAGTATCGTTGGTCTTGAATCAGCATATTGGCACCTT-T-ATCTTTAAGAACGATGTCGT
1 AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCTCATCTTTAAGACCAATGTCGC
* *
2684242 TGGCCTTGAATCAGCACATCGGCACCTCAACCATCTTT
66 TGGCCTTGAATCAGCACATTGGCACCT--ATCATCTTT
* * *
2684280 AAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCCAATGTCG
1 AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTC-TCATCTTTAAGACCAATGTCG
*
2684345 CTGGCCTTGAAACAGCACATTGGCACCT-TCATCTTT
65 CTGGCCTTGAATCAGCACATTGGCACCTATCATCTTT
* * * * * * *
2684381 AAGACCGATGA-CGTTGGCCTTGAATCAGCACATCGGCACC-TCAACCATCTTTAAGCCCAATAT
1 AAGCCCAAT-ATCGTTGGCCTTGAATCAGCATATTGGCACCTTC--TCATCTTTAAGACCAATGT
* *
2684444 CGCTGGCCTTGAATCAGCATATTGGCACGT-T-ATCTTT
63 CGCTGGCCTTGAATCAGCACATTGGCACCTATCATCTTT
* * * * *
2684481 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTTTAAGACCAATATCGC
1 AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCTCATCTTTAAGACCAATGTCGC
* * *
2684544 TGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTT
66 TGGCCTTGAATCAGCACATTGGCACC-T-ATCATCTTT
* * * * * *
2684582 AAAACCCAATGTCGTTGGCCTTGAATCAGCATATTGGCATTCTTCTCATCTTCAAGTCTAATGTC
1 -AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCA-CCTTCTCATCTTTAAGACCAATGTC
* * * * ** *
2684647 GTTGACCGTGAATTAGCACATTAACATCCTTTTTCTCATCTTT
64 GCTGGCCTTGAATCAGCACATTGGCA-CC----TATCATCTTT
* * * *
2684690 AAACCCAATATCGTTGACCGTGAATCAGCGTATTGG
1 AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGG
2684726 TCCCTTTATC
Statistics
Matches: 373, Mismatches: 55, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
97 44 0.12
98 1 0.00
100 44 0.12
101 127 0.34
102 35 0.09
103 2 0.01
104 42 0.11
105 34 0.09
106 2 0.01
107 32 0.09
108 8 0.02
109 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (101 bp):
AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCTCATCTTTAAGACCAATGTCGC
TGGCCTTGAATCAGCACATTGGCACCTATCATCTTT
Found at i:2690596 original size:105 final size:104
Alignment explanation
Indices: 2690321--2690631 Score: 410
Period size: 105 Copynumber: 3.0 Consensus size: 104
2690311 ACATCAGATG
* * * * **
2690321 GTAAGAGTAAAAAGCATACTAG-TTCTATGGCCAAAATAT-AAGAAAGATCATGACTGCTCAAGG
1 GTAAGAGTAAAAAGCATACT-GTTTCCATGGCAAAAATATAAAAAAAGATCATGACTGTTCAAAA
* * * *
2690384 TAACAGCTAGTTCTCAATTATTGGTACAAATTCTAGCTTG
65 TAGCAGCTAGTTCTCAACTATTGGTACAAATTCTAGCCTA
* * *
2690424 GTAAGAGTAAAAAGCATACTGTTTGCATGCCAAAAATATAAAAAAAGATCATGACTGTTTAAAAT
1 GTAAGAGTAAAAAGCATACTGTTTCCATGGCAAAAATATAAAAAAAGATCATGACTGTTCAAAAT
* *
2690489 AGCAACCAGTTCTCAACTATTGGTACAAATTCTAGCCTA
66 AGCAGCTAGTTCTCAACTATTGGTACAAATTCTAGCCTA
*** *
2690528 GTAAGAGTAAAAAAGCATACTGTTTCCATGGTTGAAATATAAAAAAAGATCATGACTATTCAAAA
1 GTAAGAGT-AAAAAGCATACTGTTTCCATGGCAAAAATATAAAAAAAGATCATGACTGTTCAAAA
*
2690593 TAGCAGCTAGTTCTCAGCTATTGGTACAAATTCTAGCCT
65 TAGCAGCTAGTTCTCAACTATTGGTACAAATTCTAGCCT
2690632 TTTCTTATAT
Statistics
Matches: 180, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
102 1 0.01
103 33 0.18
104 61 0.34
105 85 0.47
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (104 bp):
GTAAGAGTAAAAAGCATACTGTTTCCATGGCAAAAATATAAAAAAAGATCATGACTGTTCAAAAT
AGCAGCTAGTTCTCAACTATTGGTACAAATTCTAGCCTA
Found at i:2690782 original size:23 final size:26
Alignment explanation
Indices: 2690730--2690785 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 26
2690720 TAAATATAGC
2690730 AAAT-ATTAAGAAGAAAAAATGGTTAA
1 AAATAATTAAGAAGAAAAAAT-GTTAA
2690756 AAATAATTAA-AAG-AAAAAT-TTAA
1 AAATAATTAAGAAGAAAAAATGTTAA
2690779 AAATAAT
1 AAATAAT
2690786 GAATTTGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 11 0.38
25 6 0.21
26 7 0.24
27 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (26 bp):
AAATAATTAAGAAGAAAAAATGTTAA
Found at i:2691391 original size:72 final size:71
Alignment explanation
Indices: 2691275--2691410 Score: 209
Period size: 72 Copynumber: 1.9 Consensus size: 71
2691265 CTTGTAAAAA
* * *
2691275 AGAAATATAAATGAAAAACAAAAAGAAAACTTTATTTTTTAGTCGATGAGAATAAGAAAGAAATG
1 AGAAATAGAAATGAAAAACAAAAAGAAAACTTCATTTTGTAGTCGATGAGAATAAGAAAGAAATG
2691340 GAACAG
66 GAACAG
** *
2691346 AGAAATAGAAATGTAAAAACAAAACTAAAACTTCATTTTGTAGTCGATGAGAATGAGAAAGAAAT
1 AGAAATAGAAATG-AAAAACAAAAAGAAAACTTCATTTTGTAGTCGATGAGAATAAGAAAGAAAT
2691411 AGGTATGGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
71 12 0.21
72 46 0.79
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.23
Consensus pattern (71 bp):
AGAAATAGAAATGAAAAACAAAAAGAAAACTTCATTTTGTAGTCGATGAGAATAAGAAAGAAATG
GAACAG
Found at i:2691610 original size:20 final size:20
Alignment explanation
Indices: 2691585--2691626 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2691575 CTTTAACTTA
2691585 ATCTTTAACTAACAAATAAT
1 ATCTTTAACTAACAAATAAT
* *
2691605 ATCTTTCACTGACAAATAAT
1 ATCTTTAACTAACAAATAAT
2691625 AT
1 AT
2691627 GACCATGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (20 bp):
ATCTTTAACTAACAAATAAT
Found at i:2695880 original size:13 final size:13
Alignment explanation
Indices: 2695858--2695898 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
2695848 CAATGTAACC
2695858 AAAA-GAAATTTT
1 AAAACGAAATTTT
2695870 AAAACGAAATTTT
1 AAAACGAAATTTT
*
2695883 AAAAC-AAAATTT
1 AAAACGAAATTTT
2695895 AAAA
1 AAAA
2695899 GCCCAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 14 0.52
13 13 0.48
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (13 bp):
AAAACGAAATTTT
Found at i:2696837 original size:151 final size:150
Alignment explanation
Indices: 2696664--2697115 Score: 780
Period size: 150 Copynumber: 3.0 Consensus size: 150
2696654 TATCTTTTAT
2696664 GAGTAATTGCATCTATGATGATCGATTATACTAAAGACAGAAAAAAAAAGTAAATAAGCAAGGGT
1 GAGTAATTGCATCTATGATGATCGATTATACTAAAGACAG-AAAAAAAAGTAAATAAGCAAGGGT
2696729 TTAGTTTAGGTAACCAAGTTTTGAAAAAGTGAAACTCTTTTTTTGGAGAGATTGTTAAAGAAAAA
65 TTAGTTTAGGTAACCAAGTTTTGAAAAAGTGAAACTC-TTTTTTGGAGAGATTGTTAAAGAAAAA
*
2696794 -AAAGGTAATTTAGACCTAAAA
129 CAAAGGTAATTCAGACCTAAAA
*
2696815 GAGTAATTGCATCTATGATGATCGATTACACTAAAGACAGAAAAAAAAGTAAATAAGCAAGGGTT
1 GAGTAATTGCATCTATGATGATCGATTATACTAAAGACAGAAAAAAAAGTAAATAAGCAAGGGTT
*
2696880 TAGTTTAGGTAACCAAGTTTTGAAAAAGTGGAACTCTTTTTTGGAGAGATTGTTAAAGAAAAACA
66 TAGTTTAGGTAACCAAGTTTTGAAAAAGTGAAACTCTTTTTTGGAGAGATTGTTAAAGAAAAACA
2696945 AAGGTAATTCAGACCTAAAA
131 AAGGTAATTCAGACCTAAAA
* **
2696965 GAGTAATTGCATCTATGATGATCGATTATACTAAAAACAGAAAAAAAAGTAAATAAAAAAGGGTT
1 GAGTAATTGCATCTATGATGATCGATTATACTAAAGACAGAAAAAAAAGTAAATAAGCAAGGGTT
* * * *
2697030 TAGTTTAGGTAACCAAGTTTCGAAAAAGGGAAACTCTTTTTTAGAGAGATTGTTAAAAAAAAACA
66 TAGTTTAGGTAACCAAGTTTTGAAAAAGTGAAACTCTTTTTTGGAGAGATTGTTAAAGAAAAACA
*
2697095 AAGATAATTCAGACCTAAAA
131 AAGGTAATTCAGACCTAAAA
2697115 G
1 G
2697116 TTTCAATTAT
Statistics
Matches: 287, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
149 27 0.09
150 221 0.77
151 39 0.14
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (150 bp):
GAGTAATTGCATCTATGATGATCGATTATACTAAAGACAGAAAAAAAAGTAAATAAGCAAGGGTT
TAGTTTAGGTAACCAAGTTTTGAAAAAGTGAAACTCTTTTTTGGAGAGATTGTTAAAGAAAAACA
AAGGTAATTCAGACCTAAAA
Found at i:2700591 original size:37 final size:37
Alignment explanation
Indices: 2700500--2700629 Score: 115
Period size: 37 Copynumber: 3.5 Consensus size: 37
2700490 GGCATAAGTT
* * * *
2700500 AGAACAAAAACTACTATTCTAATA-TGGTGGCACGGTTC
1 AGAACAAAAACTACTATTCT--TACCGATGGCACAGATC
*
2700538 AGAACAAAAA-TCACTATTCTTACCGATGGTACAGATC
1 AGAACAAAAACT-ACTATTCTTACCGATGGCACAGATC
* *
2700575 AGAACAAAAACTACTATTTTTACC-AGTGGCACAGGTC
1 AGAACAAAAACTACTATTCTTACCGA-TGGCACAGATC
*
2700612 GGAAC-AAAACTTACTATT
1 AGAACAAAAAC-TACTATT
2700630 ATTAACTAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
36 8 0.10
37 51 0.65
38 19 0.24
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (37 bp):
AGAACAAAAACTACTATTCTTACCGATGGCACAGATC
Found at i:2704694 original size:14 final size:14
Alignment explanation
Indices: 2704675--2704722 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2704665 ATTATAAAAA
2704675 ATAAAAATATTAAT
1 ATAAAAATATTAAT
*
2704689 ATAAAAATAAT-AT
1 ATAAAAATATTAAT
*
2704702 GT-AAAA-ATTAAT
1 ATAAAAATATTAAT
2704714 ATAAAAATA
1 ATAAAAATA
2704723 ATACATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
11 2 0.07
12 7 0.26
13 7 0.26
14 11 0.41
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
ATAAAAATATTAAT
Found at i:2704701 original size:11 final size:11
Alignment explanation
Indices: 2704685--2704744 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 11
2704675 ATAAAAATAT
2704685 TAATATAAAAA
1 TAATATAAAAA
2704696 TAATATGTAAAAA
1 TAATA--TAAAAA
2704709 TTAATATAAAAA
1 -TAATATAAAAA
*
2704721 TAATACATAAAA
1 TAATATA-AAAA
*
2704733 TGACTATAAAAA
1 T-AATATAAAAA
2704745 GATATTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
11 11 0.27
12 15 0.37
13 10 0.24
14 5 0.12
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATATAAAAA
Found at i:2704730 original size:13 final size:13
Alignment explanation
Indices: 2704675--2704732 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
2704665 ATTATAAAAA
*
2704675 ATAAAAATATTAAT
1 ATAAAAATAAT-AT
2704689 ATAAAAATAATAT
1 ATAAAAATAATAT
* *
2704702 GTAAAAATTA-AT
1 ATAAAAATAATAT
*
2704714 ATAAAAATAATAC
1 ATAAAAATAATAT
2704727 ATAAAA
1 ATAAAA
2704733 TGACTATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.27
13 17 0.46
14 10 0.27
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (13 bp):
ATAAAAATAATAT
Found at i:2704731 original size:25 final size:26
Alignment explanation
Indices: 2704678--2704733 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
2704668 ATAAAAAATA
**
2704678 AAAATATTAATATAAAAATAATATGT
1 AAAATATTAATATAAAAATAATACAT
2704704 AAAA-ATTAATATAAAAATAATACAT
1 AAAATATTAATATAAAAATAATACAT
2704729 AAAAT
1 AAAAT
2704734 GACTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAATATTAATATAAAAATAATACAT
Found at i:2708770 original size:37 final size:37
Alignment explanation
Indices: 2708725--2708796 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
2708715 AGAAAGCAAG
* ** *
2708725 GAGTAAACTTTTGTGGAGAGAAAGATAATAAAAAAGC
1 GAGTAAACTTTAGTCAAGAGAAAGAAAATAAAAAAGC
2708762 GAGTAAACTTTAGTCAAGAGAAAGAAAATAAAAAA
1 GAGTAAACTTTAGTCAAGAGAAAGAAAATAAAAAA
2708797 TTGAGTGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (37 bp):
GAGTAAACTTTAGTCAAGAGAAAGAAAATAAAAAAGC
Found at i:2710360 original size:17 final size:16
Alignment explanation
Indices: 2710338--2710374 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
2710328 AAAGCTAATC
2710338 TTTAGCCATGATTATTT
1 TTTAGCCATGATT-TTT
2710355 TTTAGCCATGATTTTT
1 TTTAGCCATGATTTTT
2710371 TTTA
1 TTTA
2710375 AGAATACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTAGCCATGATTTTT
Found at i:2712476 original size:20 final size:19
Alignment explanation
Indices: 2712447--2712517 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
2712437 ACCCTGAAAA
*
2712447 GTATCAATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
2712467 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
2712486 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
2712507 GTATCGATACA
1 GTATCGATACA
2712518 AGACATTGGC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.10
20 34 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:2712569 original size:53 final size:53
Alignment explanation
Indices: 2712487--2712623 Score: 211
Period size: 53 Copynumber: 2.6 Consensus size: 53
2712477 AGATTGCATA
2712487 GTATCGATACACACAAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
* * ** *
2712541 GTATCAATACACACAATATGTATCGATACAGGTTATTGGTAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
*
2712594 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
2712624 TTGGTAGTAG
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
53 63 0.83
54 13 0.17
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
Found at i:2712666 original size:10 final size:10
Alignment explanation
Indices: 2712647--2712685 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2712637 AATCTCATTT
*
2712647 TCACTGTTCA
1 TCACTATTCA
2712657 TCACTATTCA
1 TCACTATTCA
*
2712667 TCACTGTTCA
1 TCACTATTCA
2712677 -CACTATTCA
1 TCACTATTCA
2712686 CGTATCACTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (10 bp):
TCACTATTCA
Found at i:2712682 original size:19 final size:20
Alignment explanation
Indices: 2712647--2712685 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2712637 AATCTCATTT
2712647 TCACTGTTCATCACTATTCA
1 TCACTGTTCATCACTATTCA
2712667 TCACTGTTCA-CACTATTCA
1 TCACTGTTCATCACTATTCA
2712686 CGTATCACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (20 bp):
TCACTGTTCATCACTATTCA
Found at i:2712752 original size:13 final size:13
Alignment explanation
Indices: 2712734--2712768 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2712724 TCACTATTCA
*
2712734 TGTATCGATACAT
1 TGTATCGATACAG
2712747 TGTATCGATACAG
1 TGTATCGATACAG
2712760 TGTATCGAT
1 TGTATCGAT
2712769 CCATCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2713305 original size:34 final size:35
Alignment explanation
Indices: 2713242--2713308 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2713232 CTAAGTGATT
2713242 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2713278 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2713309 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2716098 original size:96 final size:97
Alignment explanation
Indices: 2715966--2716145 Score: 218
Period size: 97 Copynumber: 1.9 Consensus size: 97
2715956 CGGAGGAATA
* ** ** * **
2715966 GGGTTGGAGTATCCCCGACGATGGTAATTTGGGC-AAAGTAAGATTTAAACCTTGGTAAGCTTAA
1 GGGTTGGAGCATCCCCGACGATGACAATTTAAGCAAAAATAAGATTTAAACCTTAATAAGCTTAA
*
2716030 AAATAGGGTTAGAGTATCCCCTCAAAAAAATG
66 AAACAGGGTTAGAGTATCCCCTCAAAAAAATG
* * * * * *
2716062 GGGTTGGAGCATCCCCGATGATGACCATTTAAGCAAAAATAAGATTTAAATCTTAATGAGTTTGA
1 GGGTTGGAGCATCCCCGACGATGACAATTTAAGCAAAAATAAGATTTAAACCTTAATAAGCTTAA
2716127 AAACAGGGTTAGAGTATCC
66 AAACAGGGTTAGAGTATCC
2716146 TCGATATATA
Statistics
Matches: 68, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
96 27 0.40
97 41 0.60
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (97 bp):
GGGTTGGAGCATCCCCGACGATGACAATTTAAGCAAAAATAAGATTTAAACCTTAATAAGCTTAA
AAACAGGGTTAGAGTATCCCCTCAAAAAAATG
Found at i:2724260 original size:13 final size:13
Alignment explanation
Indices: 2724242--2724267 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2724232 ACAAAGATCC
2724242 ATGTATCGATACA
1 ATGTATCGATACA
2724255 ATGTATCGATACA
1 ATGTATCGATACA
2724268 TTCTACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2724344 original size:19 final size:21
Alignment explanation
Indices: 2724320--2724371 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
2724310 AGCGATACAC
*
2724320 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
2724339 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
*
2724360 TATATCGATACA
1 TGTATCGATACA
2724372 AATTATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 5 0.17
21 12 0.41
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:2724367 original size:21 final size:19
Alignment explanation
Indices: 2724322--2724371 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
2724312 CGATACACTG
* *
2724322 TATCGATACATTACTTATG
1 TATCGATACATTACTAATA
2724341 TATCGATACATTTACTGAATA
1 TATCGATACA-TTACT-AATA
2724362 TATCGATACA
1 TATCGATACA
2724372 AATTATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 5 0.19
21 12 0.44
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
TATCGATACATTACTAATA
Found at i:2724847 original size:20 final size:20
Alignment explanation
Indices: 2724819--2724857 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2724809 AATGAGTTTG
2724819 TAGGGTTTGAGATTTTCTAC
1 TAGGGTTTGAGATTTTCTAC
*
2724839 TAGGTTTTGAGATTTTCTA
1 TAGGGTTTGAGATTTTCTA
2724858 AGGCTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (20 bp):
TAGGGTTTGAGATTTTCTAC
Found at i:2725039 original size:40 final size:41
Alignment explanation
Indices: 2724995--2725098 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
2724985 GTCCCACTTT
* *
2724995 TTGAGGACAAAGGAAAAGAG-AATGAAATAG-GTCTTGCTCC
1 TTGAGGACAAAGGAAAAGAGAAAAGAAA-AGTGTCCTGCTCC
* * *
2725035 TTGAGGACAAAGGAAGAGAAGAAAAGGAAAGTGTCCTGCTTC
1 TTGAGGACAAAGGAAAAG-AGAAAAGAAAAGTGTCCTGCTCC
2725077 TTGAGGACAAAGTGTAAAAGAG
1 TTGAGGACAAAG-G-AAAAGAG
2725099 TACGTCCCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 17 0.32
41 4 0.08
42 25 0.47
43 3 0.06
44 4 0.08
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.18
Consensus pattern (41 bp):
TTGAGGACAAAGGAAAAGAGAAAAGAAAAGTGTCCTGCTCC
Found at i:2725277 original size:61 final size:61
Alignment explanation
Indices: 2725187--2725949 Score: 751
Period size: 61 Copynumber: 12.9 Consensus size: 61
2725177 ATAAAGTGCA
* *
2725187 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
* * * ** * **
2725248 TCCTACTCTTTGAAGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG-GAAAGGTG
* *
2725309 TCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGG-TTT---AA-G--AGGCG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
* *
2725363 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---AA-G--AGGCG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
* * *
2725418 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGG-CA----
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
* *
2725473 TCCTGCTCTTTGAGGACTAGAAAATTGCCACCAACTTGTGTGGGCTTTACAAGGGAAAA-AAAAG
1 TCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTT------GAAAAGGAAAG
2725537 GTG
59 GTG
* *
2725540 TCCTGCTCTTTAAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGG-AAAGGTG
* * *
2725601 TCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-ACAAGGAAAAAAAGGT
1 TCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG----AAAGGT
2725665 G
61 G
* *
2725666 TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGG-CA----
1 TCCTGCTCTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
** * *
2725721 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
* * * **
2725782 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
* *
2725843 TCCTGCTCTTTGAGGACTGGAAAATGCCACC-ACTTGTGTGGGCTTTG-AAAGG-CA----
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
*
2725897 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG
2725950 CATCATGCTC
Statistics
Matches: 618, Mismatches: 44, Indels: 86
0.83 0.06 0.11
Matches are distributed among these distances:
53 1 0.00
54 74 0.12
55 136 0.22
56 35 0.06
57 5 0.01
58 2 0.00
59 9 0.01
60 20 0.03
61 191 0.31
62 34 0.06
63 13 0.02
64 29 0.05
65 29 0.05
66 23 0.04
67 17 0.03
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGTG
Found at i:2725752 original size:181 final size:175
Alignment explanation
Indices: 2725179--2725949 Score: 849
Period size: 176 Copynumber: 4.3 Consensus size: 175
2725169 AGAGGAAAAT
* * *
2725179 AAAGTGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGG-AA
1 AAAG-GCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAA
* * * * ** * * *
2725243 ATGTGTCCTACTCTTTGAAGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGC
64 AGGTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGC
*
2725308 ATCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGG-TTTA
129 ATCCTGCTCTTTGAGGACTG-AAAATGCCACC-ACTTGTGTGGGCTTTA
* * *
2725356 AGAGGCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT--AA-G---A
1 AAAGGCATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA
* * * *
2725414 GGCGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT------AAAAGGCA
65 GGTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGCA
2725473 TCCTGCTCTTTGAGGACTAGAAAATTGCCACCAACTTGTGTGGGCTTTACAAGGGAAAAA
130 TCCTGCTCTTTGAGGACT-GAAAA-TGCCACC-ACTTGTGTGGGCTTT-----------A
** * *
2725533 AAAGGTGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
1 AAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
*
2725598 GTGTCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-ACAAGGAAAAAAA
66 GTGTCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGA-AA--AAAAAAA
**
2725662 GGTGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTA
127 -GCATCCTGCTCTTTGAGGACTGAAAA--TGCCACC-ACTTGTGTGGGCTTTA
* *
2725714 AAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAG
1 AAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
* *
2725779 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCAT
66 GTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGCAT
*
2725844 CCTGCTCTTTGAGGACTGGAAAATGCCACCACTTGTGTGGGCTTTG
131 CCTGCTCTTTGAGGACT-GAAAATGCCACCACTTGTGTGGGCTTTA
* *
2725890 AAAGGCATCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAAGGCATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
2725950 CATCATGCTC
Statistics
Matches: 513, Mismatches: 44, Indels: 75
0.81 0.07 0.12
Matches are distributed among these distances:
164 27 0.05
165 20 0.04
166 3 0.01
170 45 0.09
172 1 0.00
173 2 0.00
176 111 0.22
177 82 0.16
178 6 0.01
179 6 0.01
180 26 0.05
181 86 0.17
183 25 0.05
184 23 0.04
191 4 0.01
192 27 0.05
193 19 0.04
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (175 bp):
AAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
GTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGCAT
CCTGCTCTTTGAGGACTGAAAATGCCACCACTTGTGTGGGCTTTA
Found at i:2726083 original size:61 final size:61
Alignment explanation
Indices: 2725988--2726167 Score: 263
Period size: 61 Copynumber: 2.9 Consensus size: 61
2725978 AAAAGAGAGT
*
2725988 GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AGAAG
1 GCGTCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAG
* *
2726049 GCGTCCTACTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAAG
1 GCGTCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GGAAAAAG
* **
2726112 GTGTCCTGCTCTTTGAGGACTAAAATGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 GCGTCCTGCTCTTTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGG
2726168 CATCCTGCTA
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
61 51 0.48
62 6 0.06
63 50 0.47
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAG
Found at i:2726150 original size:63 final size:61
Alignment explanation
Indices: 2725988--2726167 Score: 263
Period size: 63 Copynumber: 2.9 Consensus size: 61
2725978 AAAAGAGAGT
*
2725988 GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GGAGAAG
1 GCGTCCTGCTCTTTGAGGACTA-GAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAG
* * *
2726049 GCGTCCTACTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAAG
1 GCGTCCTGCTCTTTGAGGACT-AGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGG-AAAAG
* *
2726112 GTGTCCTGCTCTTTGAGGACTAAAATGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 GCGTCCTGCTCTTTGAGGACTAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGG
2726168 CATCCTGCTA
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
61 50 0.47
62 4 0.04
63 52 0.49
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAG
Found at i:2726198 original size:218 final size:207
Alignment explanation
Indices: 2725781--2726206 Score: 570
Period size: 218 Copynumber: 2.0 Consensus size: 207
2725771 AAGAAAAGGT
2725781 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* *
2725846 TGCTCTTTGAGGACTGGAAAATGCCACCACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAG
66 TACTCTTTAAGGACTGGAAAATGCCACCACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAG
* * *
2725911 GACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCATGCTCTTTGAGGACTAAAGGG
131 GACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCATGCTATTTGAGGACAAAAAGG
2725976 TGAAAAGAGAGTGC
195 TGAAAAGAG-GTGC
* * * *
2725990 GTCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCGT
1 GTCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAAGCAT
* * **
2726053 CCTACTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAAGGTGTCC
64 CCTACTCTTTAAGGACTGGAAAATGCCACC-ACTTGTGTGGGCTTT------G--AAAGGCATCC
*
2726118 TGCTCTTTGAGGACT-AAAATGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTATTTG
120 TGCTCTTTGAGGACTGAAAA--TGCCACCAACTTGTGTGGGCTTTAAAAGGCATCATGCTATTTG
2726182 AGGACAAAAAGGTGAAAAGAGGTGC
183 AGGACAAAAAGGTGAAAAGAGGTGC
2726207 CATAGAGTCG
Statistics
Matches: 190, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
208 4 0.02
209 77 0.41
210 17 0.09
216 5 0.03
217 4 0.02
218 83 0.44
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (207 bp):
GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
TACTCTTTAAGGACTGGAAAATGCCACCACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAG
GACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCATGCTATTTGAGGACAAAAAGGT
GAAAAGAGGTGC
Found at i:2736326 original size:164 final size:163
Alignment explanation
Indices: 2736055--2736378 Score: 549
Period size: 164 Copynumber: 2.0 Consensus size: 163
2736045 AGAACAGAAA
* * * *
2736055 TTGAAAGAAGCATAAAAAATAATAAAACTTGAATAGATTAGAAATGAAGGATGGCGCCACAATCA
1 TTGAAAGAAGCAAAAAAAATAACAAAACTGGAATAGATTAGAAATGAAGGATGGCACCACAATCA
*
2736120 CAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAA
66 CAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAAAAA
2736185 AATTGGCTCACACAAGAACCTAAGAATCACACTC
131 AATTGGCTCACACAAGAA-CTAAGAATCACACTC
* *
2736219 TTGAAAGAAGCAAAAAAAATAACAATACTGGAATAGATTAGAGATGAAGGATGGCACCACAATCA
1 TTGAAAGAAGCAAAAAAAATAACAAAACTGGAATAGATTAGAAATGAAGGATGGCACCACAATCA
*
2736284 CAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAAAAA
66 CAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAAAAA
* *
2736349 AATTGGCTCACTCAAGAACTTAGAATCACA
131 AATTGGCTCACACAAGAACTAAGAATCACA
2736379 TTCTCACATA
Statistics
Matches: 150, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
163 11 0.07
164 139 0.93
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.19
Consensus pattern (163 bp):
TTGAAAGAAGCAAAAAAAATAACAAAACTGGAATAGATTAGAAATGAAGGATGGCACCACAATCA
CAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAAAAA
AATTGGCTCACACAAGAACTAAGAATCACACTC
Found at i:2741146 original size:12 final size:12
Alignment explanation
Indices: 2741126--2741203 Score: 55
Period size: 12 Copynumber: 7.0 Consensus size: 12
2741116 CTCTATTATC
*
2741126 CCTCTTATCTCT
1 CCTCCTATCTCT
2741138 CCTCCTATCATC-
1 CCTCCTATC-TCT
2741150 CCTCCTA--TCT
1 CCTCCTATCTCT
*
2741160 -CTACTATCT-T
1 CCTCCTATCTCT
2741170 --TCCTATCTCT
1 CCTCCTATCTCT
2741180 CCTCCTATCATC-
1 CCTCCTATC-TCT
*
2741192 CCTCATATCTCT
1 CCTCCTATCTCT
2741204 TCTTTCTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
9 14 0.26
10 2 0.04
11 3 0.06
12 30 0.57
13 4 0.08
ACGTcount: A:0.14, C:0.44, G:0.00, T:0.42
Consensus pattern (12 bp):
CCTCCTATCTCT
Found at i:2741149 original size:42 final size:42
Alignment explanation
Indices: 2741094--2741203 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
2741084 TTTTTCTCTC
* * * *
2741094 CTCCTCCTGTCATCCCACCTCTCTCTATTATCCCTCTTATCT
1 CTCCTCCTATCATCCCACCTATCTCTACTATCCCTCCTATCT
* **
2741136 CTCCTCCTATCATCCCTCCTATCTCTACTATCTTTCCTATCT
1 CTCCTCCTATCATCCCACCTATCTCTACTATCCCTCCTATCT
* *
2741178 CTCCTCCTATCATCCCTCATATCTCT
1 CTCCTCCTATCATCCCACCTATCTCT
2741204 TCTTTCTCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.14, C:0.45, G:0.01, T:0.41
Consensus pattern (42 bp):
CTCCTCCTATCATCCCACCTATCTCTACTATCCCTCCTATCT
Found at i:2741150 original size:24 final size:24
Alignment explanation
Indices: 2741118--2741203 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
2741108 CCACCTCTCT
* *
2741118 CTATTATCCCTCTTATCTCTCCTC
1 CTATCATCCCTCCTATCTCTCCTC
*
2741142 CTATCATCCCTCCTA--TCT-CTA
1 CTATCATCCCTCCTATCTCTCCTC
*
2741163 CTATC-T--TTCCTATCTCTCCTC
1 CTATCATCCCTCCTATCTCTCCTC
*
2741184 CTATCATCCCTCATATCTCT
1 CTATCATCCCTCCTATCTCT
2741204 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 5 0.10
20 4 0.08
21 14 0.29
22 4 0.08
24 22 0.45
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTATCTCTCCTC
Found at i:2742490 original size:164 final size:164
Alignment explanation
Indices: 2742212--2742540 Score: 532
Period size: 164 Copynumber: 2.0 Consensus size: 164
2742202 AGAACAGAAA
* * * *
2742212 TTGAAAGCAGCAGAAAAAATAACAAAACTGGAATATATTAGAGATGAAGGATGGCGCCACAATCA
1 TTGAAAGAAGCAGAAAAAATAACAAAACTAGAATAGATTAGAGATGAAGGATGCCGCCACAATCA
* * * *
2742277 CAAGATTGATAAGCCAAAAGGAATGATCGCCAAAAGAGTCTTGGCCTCTTGATAAGATCTAGAAA
66 CAAGATTGATAAGCCAAAAGGAATGATCGCCAAAAGAGTCTTAGCCTCTTAATAAGATCCAAAAA
*
2742342 AATTAGCTCACTCAGGAACCTAAGAATCACACTC
131 AATTAGCTCACTCAAGAACCTAAGAATCACACTC
* *
2742376 TTGAAAGAAGCAGAAAAAATAACAAAACTAGAATAGATTAGAGATGGAGGATGCCGCCATAATCA
1 TTGAAAGAAGCAGAAAAAATAACAAAACTAGAATAGATTAGAGATGAAGGATGCCGCCACAATCA
* *
2742441 CAAGATTGATAAGTCAAAAGGAATGATCGCCACAAGAGTCTTAGCCTCTTAATAAGATCCAAAAA
66 CAAGATTGATAAGCCAAAAGGAATGATCGCCAAAAGAGTCTTAGCCTCTTAATAAGATCCAAAAA
*
2742506 AATTGGCTCACTCAAGAACCTAAGAATCACACTC
131 AATTAGCTCACTCAAGAACCTAAGAATCACACTC
2742540 T
1 T
2742541 CACATAAAAT
Statistics
Matches: 151, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
164 151 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (164 bp):
TTGAAAGAAGCAGAAAAAATAACAAAACTAGAATAGATTAGAGATGAAGGATGCCGCCACAATCA
CAAGATTGATAAGCCAAAAGGAATGATCGCCAAAAGAGTCTTAGCCTCTTAATAAGATCCAAAAA
AATTAGCTCACTCAAGAACCTAAGAATCACACTC
Found at i:2743729 original size:210 final size:214
Alignment explanation
Indices: 2743502--2744091 Score: 689
Period size: 210 Copynumber: 2.8 Consensus size: 214
2743492 TCAATTAGTG
2743502 CAATCCACATTCATTAAAAACCAAGAAAAACATGTAAAAAGGAATTAAAAGAAAAATTAAAAAGA
1 CAATCCACATTCATTAAAAACCAAGAAAAACATGTAAAAAGGAATTAAAAGAAAAATTAAAAAGA
* *
2743567 ATGAAATTTACCAAAAAAAACTAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCCTG-
66 ATGAAATTGACCAAAAAAAACTAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCATGT
* * * *
2743631 TTC-CGTTT-TC-TCTTTTTTCTTAGTTTCCAACCACCTAGAGTT-TTTCTATTTGCTTCTTTCT
131 TTCTC-TTTCTCTTCTTTTTTCTCAATTTCCAACCACCTAGAGTTATTT-TATTTGCTTCTCTCC
* * *
2743692 TTAGCTTGTCTA-TCA-CGTTG
194 TCAGCTTGTC-AGTCAGCATTA
* * **
2743712 TAATCCACATTCATTAAAAACCAAGAAAAACAAGTAAAAAGGAATTAAAAG-AAAATTTGAAAGT
1 CAATCCACATTCATTAAAAACCAAGAAAAACATGTAAAAAGGAATTAAAAGAAAAATTAAAAAG-
* * * *
2743776 AATGAAATTGACCAAAAAAAACTATAAAGTCTTAGAAAAAACAAAGAAAAATATATTTCACTCAT
65 AATGAAATTGACCAAAAAAAACTA-AAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCAT
* *
2743841 GTTTCTCTTTCTCTTTTTTTTTTCTCAATTTCCAACCATCTAGAGTTACTTTTATTTGCTTCTCT
129 GTTTCTCTTTCTC-TTCTTTTTTCTCAATTTCCAACCACCTAGAGTTA-TTTTATTTGCTTCTCT
*
2743906 CCTCAGCTTGTCAGTTAGCATTA
192 CCTCAGCTTGTCAGTCAGCATTA
* * * * * *
2743929 CAATCCACGTTCATTAAAAACCAAGAAAAGCATATAAAAAGGAATTCAAAGAAAAATTGAAAATA
1 CAATCCACATTCATTAAAAACCAAGAAAAACATGTAAAAAGGAATTAAAAGAAAAATTAAAAAGA
* * * * * *
2743994 ATAAAATTGA-CAAAAAAATCCCAAAAAAAACTTGGAAAATATAAAGAAAAAAATATTTCGCTCA
66 ATGAAATTGACCAAAAAAA--AC-TAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCA
** * *
2744058 CATTTCTCTTTCT-TT-TTTTTCCTCAGTTTCCAAC
128 TGTTTCTCTTTCTCTTCTTTTTTCTCAATTTCCAAC
2744092 TAGAATCACT
Statistics
Matches: 322, Mismatches: 43, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
209 10 0.03
210 72 0.22
211 36 0.11
212 6 0.02
213 3 0.01
215 46 0.14
216 34 0.11
217 61 0.19
218 53 0.16
219 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (214 bp):
CAATCCACATTCATTAAAAACCAAGAAAAACATGTAAAAAGGAATTAAAAGAAAAATTAAAAAGA
ATGAAATTGACCAAAAAAAACTAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCATGT
TTCTCTTTCTCTTCTTTTTTCTCAATTTCCAACCACCTAGAGTTATTTTATTTGCTTCTCTCCTC
AGCTTGTCAGTCAGCATTA
Found at i:2744077 original size:217 final size:212
Alignment explanation
Indices: 2743502--2744077 Score: 680
Period size: 217 Copynumber: 2.7 Consensus size: 212
2743492 TCAATTAGTG
* * *
2743502 CAATCCACATTCATTAAAAACCAAGAAAAACATGTAAAAAGGAATTAAAAGAAAAATTAAAAAGA
1 CAATCCACATTCATTAAAAACCAAGAAAAACATATAAAAAGGAATTAAAAGAAAAATTGAAAATA
* *
2743567 ATGAAATTTACCAAAAAAAACTAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTC-CTG
66 ATGAAATTGACCAAAAAAAACAAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCACT-
* * * * * * * *
2743631 TTC-CGTT-TTCTCTTTTTTCTTAGTTTCCAACCACCTAGAGTTTTTCTATTTGCTTCTTTCTTT
130 TTCTCTTTCTTTTTTTTTTTCTCAATTTCCAACCACCTAGAGTTTTTCTATTTGCTTCTCTCCTC
* *
2743694 AGCTTGTCTATCACGTTG
195 AGCTTGTCTATCACATTA
* * *
2743712 TAATCCACATTCATTAAAAACCAAGAAAAACA-AGTAAAAAGGAATTAAAAGAAAATTTGAAAGT
1 CAATCCACATTCATTAAAAACCAAGAAAAACATA-TAAAAAGGAATTAAAAGAAAAATTGAAAAT
* * * * *
2743776 AATGAAATTGACCAAAAAAAACTATAAAGTCTTAGAAAAAACAAAGAAAAATATATTTCACTCAT
65 AATGAAATTGACCAAAAAAAAC-AAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCA-
* *
2743841 GTTTCTCTTTCTCTTTTTTTTTTCTCAATTTCCAACCATCTAGAGTTACTTT-TATTTGCTTCTC
128 CTTTCTCTTTCT-TTTTTTTTTTCTCAATTTCCAACCACCTAGAGTT--TTTCTATTTGCTTCTC
*
2743905 TCCTCAGCTTGTC-AGTTAGCATTA
190 TCCTCAGCTTGTCTA-TCA-CATTA
* * *
2743929 CAATCCACGTTCATTAAAAACCAAGAAAAGCATATAAAAAGGAATTCAAAGAAAAATTGAAAATA
1 CAATCCACATTCATTAAAAACCAAGAAAAACATATAAAAAGGAATTAAAAGAAAAATTGAAAATA
* * * * *
2743994 ATAAAATTGA-CAAAAAAATCCCAAAAAAAACTTGGAAAATATAAAGAAAAAAATATTTCGCTCA
66 ATGAAATTGACCAAAAAAA--AC-AAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCA
2744058 CATTTCTCTTTCTTTTTTTT
128 C-TTTCTCTTTCTTTTTTTT
2744078 CCTCAGTTTC
Statistics
Matches: 307, Mismatches: 44, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
210 78 0.25
211 34 0.11
212 3 0.01
213 4 0.01
214 1 0.00
215 30 0.10
216 32 0.10
217 79 0.26
218 46 0.15
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (212 bp):
CAATCCACATTCATTAAAAACCAAGAAAAACATATAAAAAGGAATTAAAAGAAAAATTGAAAATA
ATGAAATTGACCAAAAAAAACAAAAAATCTTGGAAAATATAAAGAAAAATATATTTCACTCACTT
TCTCTTTCTTTTTTTTTTTCTCAATTTCCAACCACCTAGAGTTTTTCTATTTGCTTCTCTCCTCA
GCTTGTCTATCACATTA
Found at i:2745125 original size:42 final size:42
Alignment explanation
Indices: 2745078--2745199 Score: 244
Period size: 42 Copynumber: 2.9 Consensus size: 42
2745068 CTTCTTTTTC
2745078 TTCCTTTTTAGTGGAGTTACGATGATTGACTTCTCCTAGCTT
1 TTCCTTTTTAGTGGAGTTACGATGATTGACTTCTCCTAGCTT
2745120 TTCCTTTTTAGTGGAGTTACGATGATTGACTTCTCCTAGCTT
1 TTCCTTTTTAGTGGAGTTACGATGATTGACTTCTCCTAGCTT
2745162 TTCCTTTTTAGTGGAGTTACGATGATTGACTTCTCCTA
1 TTCCTTTTTAGTGGAGTTACGATGATTGACTTCTCCTA
2745200 CCTTACTCTA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCTTTTTAGTGGAGTTACGATGATTGACTTCTCCTAGCTT
Found at i:2747907 original size:13 final size:13
Alignment explanation
Indices: 2747889--2747914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2747879 CAGTAACTGT
2747889 ATCGATACATAAG
1 ATCGATACATAAG
2747902 ATCGATACATAAG
1 ATCGATACATAAG
2747915 TGTTGTATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATCGATACATAAG
Found at i:2747936 original size:13 final size:13
Alignment explanation
Indices: 2747918--2747943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2747908 ACATAAGTGT
2747918 TGTATCGATACAA
1 TGTATCGATACAA
2747931 TGTATCGATACAA
1 TGTATCGATACAA
2747944 AGCTACTGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2747965 original size:30 final size:30
Alignment explanation
Indices: 2747929--2748034 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
2747919 GTATCGATAC
2747929 AATGTATCGATACAAAGCTACTGCCAAGGA
1 AATGTATCGATACAAAGCTACTGCCAAGGA
* ** * *
2747959 AATGTATCGATTCATAAG-TGTTGTACCGA-TA
1 AATGTATCGATACA-AAGCTACTG--CCAAGGA
2747990 CAATGTATC-ACTACAAAGCTACTGCCAAGGA
1 -AATGTATCGA-TACAAAGCTACTGCCAAGGA
2748021 AATGTATCGATACA
1 AATGTATCGATACA
2748035 TTACTCATTG
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
30 31 0.53
31 10 0.17
32 17 0.29
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (30 bp):
AATGTATCGATACAAAGCTACTGCCAAGGA
Found at i:2747977 original size:62 final size:62
Alignment explanation
Indices: 2747902--2748054 Score: 236
Period size: 62 Copynumber: 2.5 Consensus size: 62
2747892 GATACATAAG
2747902 ATCGATACATAAGTGTTGTATCGATACAATGTATCGA-TACAAAGCTACTGCCAAGGAAATGT
1 ATCGATACATAAGTGTTGTATCGATACAATGTATC-ACTACAAAGCTACTGCCAAGGAAATGT
* *
2747964 ATCGATTCATAAGTGTTGTACCGATACAATGTATCACTACAAAGCTACTGCCAAGGAAATGT
1 ATCGATACATAAGTGTTGTATCGATACAATGTATCACTACAAAGCTACTGCCAAGGAAATGT
* * *
2748026 ATCGATACATTACTCATTGTATCGATACA
1 ATCGATACATAAGT-GTTGTATCGATACA
2748055 TGGATCTTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
61 1 0.01
62 69 0.84
63 12 0.15
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (62 bp):
ATCGATACATAAGTGTTGTATCGATACAATGTATCACTACAAAGCTACTGCCAAGGAAATGT
Found at i:2748048 original size:20 final size:20
Alignment explanation
Indices: 2748023--2748075 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2748013 GCCAAGGAAA
*
2748023 TGTATCGATACAT-TACTCAT
1 TGTATCGATACATGGA-TCAT
*
2748043 TGTATCGATACATGGATCTT
1 TGTATCGATACATGGATCAT
2748063 TGTATCGATACAT
1 TGTATCGATACAT
2748076 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATGGATCAT
Found at i:2754348 original size:16 final size:16
Alignment explanation
Indices: 2754300--2754340 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2754290 GAGTTCCCTT
*
2754300 AAAAAAA-AGAACGAAA
1 AAAAAAACAAAAC-AAA
2754316 AAAAAAACAAAACAAA
1 AAAAAAACAAAACAAA
2754332 AAAAAAACA
1 AAAAAAACA
2754341 CAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAACAAA
Found at i:2755634 original size:32 final size:30
Alignment explanation
Indices: 2755593--2755902 Score: 229
Period size: 30 Copynumber: 9.9 Consensus size: 30
2755583 TCTCTTCTCC
2755593 AAGTCCACGATTCAGTGGCATCTTTTTTCCT
1 AAGTCCACGATT-AGTGGCATCTTTTTTCCT
* *
2755624 AAAGTTCACGAATTAGTGGCATCTCTTTT-CT
1 -AAGTCCACG-ATTAGTGGCATCTTTTTTCCT
*
2755655 AAGTCCACAACTTAGTGGCATCCTTTTCTTCC-
1 AAGTCCACGA-TTAGTGGCAT-CTTTT-TTCCT
** *
2755687 AAGTCCATAACTCAGTGGCATC-TTTTTCCTTTT
1 AAGTCCACGA-TTAGTGGCATCTTTTTTCC---T
* *
2755720 AAGTCCATGACTTAGTGGCATCTATTTT-CT
1 AAGTCCACGA-TTAGTGGCATCTTTTTTCCT
* *
2755750 AAGTCCACGACTCAGTGGCATCTTTTCTT-CA
1 AAGTCCACGA-TTAGTGGCATCTTTT-TTCCT
* * *
2755781 AAGTTCACGACTCAGTGGCATCTCTTTT-CT
1 AAGTCCACGA-TTAGTGGCATCTTTTTTCCT
2755811 AAGTCCACGACTTAGTGGCATCATTTTCTTCC-
1 AAGTCCACGA-TTAGTGGCATC-TTTT-TTCCT
* * * * *
2755843 AAGTCCACAACTCAGTGGCATCTCTTTCCCA
1 AAGTCCACGA-TTAGTGGCATCTTTTTTCCT
*
2755874 AAGTCCATGACTTAGTGGCATCTTTTTTC
1 AAGTCCACGA-TTAGTGGCATCTTTTTTC
2755903 TTCAAAAATC
Statistics
Matches: 234, Mismatches: 29, Indels: 31
0.80 0.10 0.11
Matches are distributed among these distances:
29 5 0.02
30 70 0.30
31 64 0.27
32 65 0.28
33 26 0.11
34 4 0.02
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.36
Consensus pattern (30 bp):
AAGTCCACGATTAGTGGCATCTTTTTTCCT
Found at i:2755936 original size:93 final size:92
Alignment explanation
Indices: 2755580--2755937 Score: 361
Period size: 93 Copynumber: 3.8 Consensus size: 92
2755570 AATTCTTCAA
* * * * *
2755580 ATCTCTCTTCTCC-AAGTCCACGATTCAGTGGCATCTTTTTTCCTAAAGTTCACGAATTAGTGGC
1 ATCTCT-TTCTCCAAAGTCCATGACTCAGTGGCATCTTTTTT-CTTAAGTCCACGACTTAGTGGC
* *
2755644 ATCTCTTTTCTAAGTCCACAACTTAGTGGC
64 ATCT-TTTTCCAAGTCCACAACTCAGTGGC
* * *
2755674 ATC-CTTTTCTTCC-AAGTCCATAACTCAGTGGCATCTTTTTCCTTTTAAGTCCATGACTTAGTG
1 ATCTC-TTTC-TCCAAAGTCCATGACTCAGTGGCATCTTTTT--TCTTAAGTCCACGACTTAGTG
* *
2755737 GCATCTATTTTCTAAGTCCACGACTCAGTGGC
62 GCATCT-TTTTCCAAGTCCACAACTCAGTGGC
* * * *
2755769 ATCT-TTTCTTCAAAGTTCACGACTCAGTGGCATCTCTTTTC-TAAGTCCACGACTTAGTGGCAT
1 ATCTCTTTCTCCAAAGTCCATGACTCAGTGGCATCTTTTTTCTTAAGTCCACGACTTAGTGGCAT
2755832 CATTTTCTTCCAAGTCCACAACTCAGTGGC
66 C--TTT-TTCCAAGTCCACAACTCAGTGGC
* * * *
2755862 ATCTCTTTC-CCAAAGTCCATGACTTAGTGGCATCTTTTTTCTTCAAAAATCCACGACTCAGTAG
1 ATCTCTTTCTCCAAAGTCCATGACTCAGTGGCATCTTTTTTCTT---AAGTCCACGACTTAGTGG
2755926 CATC-TTTTCCAA
63 CATCTTTTTCCAA
2755938 CAATCCACGA
Statistics
Matches: 222, Mismatches: 28, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
91 22 0.10
92 3 0.01
93 65 0.29
94 65 0.29
95 47 0.21
96 1 0.00
97 19 0.09
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (92 bp):
ATCTCTTTCTCCAAAGTCCATGACTCAGTGGCATCTTTTTTCTTAAGTCCACGACTTAGTGGCAT
CTTTTTCCAAGTCCACAACTCAGTGGC
Done.