Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold130
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: 730134
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:371207 original size:32 final size:32
Alignment explanation
Indices: 371166--371228 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
371156 TAGCTAATTA
*
371166 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
371198 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
371229 AATTGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:371310 original size:21 final size:21
Alignment explanation
Indices: 371286--371342 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
371276 CATTTGTAGG
371286 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
371307 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
*
371328 ATGTATTGATACATT
1 ATGTATCGATACATT
371343 TGGATAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:374533 original size:11 final size:11
Alignment explanation
Indices: 374517--374548 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
374507 CTTCTTTTAA
374517 AAAAAAACAAC
1 AAAAAAACAAC
374528 AAAAAAACAAC
1 AAAAAAACAAC
374539 AAAAAAACAA
1 AAAAAAACAA
374549 AAAGGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:375961 original size:56 final size:56
Alignment explanation
Indices: 375649--376079 Score: 478
Period size: 61 Copynumber: 7.5 Consensus size: 56
375639 TTTCACCCTT
* * *
375649 TAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
375705 -AGTCTTCACAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
375759 TAGTCCTCAAAGAGCATGATGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 TAGTCCTCAAAGAGCAGGACG-C----C-TTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
375820 CAGTCCTCAAAGAGCATGACGCCTTTTCTTTTTAAAGCTCACACAAGTTGGTGGCA-TTTTC
1 TAGTCCTCAAAGAGCAGGACG-C----C-TTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
375881 -AGTCCTCAAAGAGCAGGACGCCTTTTAAAGACCACACAAATTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
375936 TAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
375992 TAGTCCTCAAAGGGCAGGACACCTTTTCTTTTCAAAGCCTACACAAGTTAGTGGCACTTTT-
1 TAGTCCTCAAAGAGCAGGAC-GC----CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
376053 TAGTCCTCAAAGAGCAGGACGCCTTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTT
376080 CTCTTTTATC
Statistics
Matches: 334, Mismatches: 26, Indels: 30
0.86 0.07 0.08
Matches are distributed among these distances:
54 28 0.08
55 69 0.21
56 75 0.22
57 1 0.00
59 1 0.00
60 21 0.06
61 113 0.34
62 26 0.08
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (56 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:376063 original size:233 final size:232
Alignment explanation
Indices: 375650--376087 Score: 655
Period size: 233 Copynumber: 1.9 Consensus size: 232
375640 TTCACCCTTT
* * * *
375650 AGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCACA
1 AGTCCTCAAAGAGCAAGACGCCTTTCAAAGACCACACAAATTGGTGGCACCTTTCAGTCCTCAAA
* **
375715 GAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCATGATG
66 GAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
* * *
375780 CCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCATGACGCCTT
131 CCTTTTCTTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTT
375845 TTCT-TTTTAAAGCTCACACAAGTTGGTGGCATTTTC
196 TTCTCTTTTAAAGCTCACACAAGTTGGTGGCATTTTC
* * *
375881 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGACCACACAAATTGGTGGCACTTTTCTAGTCCTCAA
1 AGTCCTCAAAGAGCAAGACGCCTTTCAAAGACCACACAAATTGGTGGCACCTTTC-AGTCCTCAA
* * * * *
375946 AGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGGGCAGGA
65 AGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGA
* *
376011 CACCTTTTCTTTTCAAAGCCTACACAAGTTAGTGGCACTTTT-TAGTCCTCAAAGAGCAGGACGC
129 CACCTTTTCTTTTCAAAGCCCACACAAGTTAGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGC
376075 CTTTTCTCTTTTA
193 CTTTTCTCTTTTA
376088 TCCTCAAAGA
Statistics
Matches: 183, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
231 50 0.27
232 44 0.24
233 80 0.44
234 9 0.05
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (232 bp):
AGTCCTCAAAGAGCAAGACGCCTTTCAAAGACCACACAAATTGGTGGCACCTTTCAGTCCTCAAA
GAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
CCTTTTCTTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTT
TTCTCTTTTAAAGCTCACACAAGTTGGTGGCATTTTC
Found at i:376187 original size:42 final size:43
Alignment explanation
Indices: 376081--376194 Score: 142
Period size: 45 Copynumber: 2.6 Consensus size: 43
376071 ACGCCTTTTC
* *
376081 TCTTTTATCCTCAAAGAGCAGGACACACTTCATTCCCTTCTTT
1 TCTTTTGTCCTCAAAGAGCAGGACGCACTTCATTCCCTTCTTT
* * *
376124 TCCCTTTTGTCCTCAAAGAGCAGGACGTACTTTATTTTCC-TCTTT
1 T--CTTTTGTCCTCAAAGAGCAGGACGCACTTCA-TTCCCTTCTTT
376169 T-TTTTGTCCTCAAAGAGCAGGACGCA
1 TCTTTTGTCCTCAAAGAGCAGGACGCA
376195 TTTTTCCTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
42 24 0.39
43 1 0.02
45 33 0.53
46 4 0.06
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (43 bp):
TCTTTTGTCCTCAAAGAGCAGGACGCACTTCATTCCCTTCTTT
Found at i:376210 original size:31 final size:34
Alignment explanation
Indices: 376175--376257 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 34
376165 CTTTTTTTTG
376175 TCCTCAAAGAGCAGGACG-C-ATTTTTC-CTTTA
1 TCCTCAAAGAGCAGGACGACTATTTTTCACTTTA
* *
376206 TCCTCGAAA-AGCAGGACGTACTCTTTTTCACTTTG
1 TCCTC-AAAGAGCAGGACG-ACTATTTTTCACTTTA
*
376241 TCCTCAAGGAGCAGGAC
1 TCCTCAAAGAGCAGGAC
376258 ACTTTCCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
31 14 0.33
32 3 0.07
33 1 0.02
34 8 0.19
35 17 0.40
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (34 bp):
TCCTCAAAGAGCAGGACGACTATTTTTCACTTTA
Found at i:376254 original size:35 final size:30
Alignment explanation
Indices: 376171--376257 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 30
376161 TCCTCTTTTT
376171 TTTGTCCTCAAAGAGCAGGACGCATTTTTCC
1 TTTGTCCTC-AAGAGCAGGACGCATTTTTCC
* * *
376202 TTTATCCTCGAAAAGCAGGACGTACTCTTTTTCAC
1 TTTGTCCTC-AAGAGCAGGACG--C-ATTTTTC-C
376237 TTTGTCCTCAAGGAGCAGGAC
1 TTTGTCCTCAA-GAGCAGGAC
376258 ACTTTCCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
31 19 0.42
33 1 0.02
34 8 0.18
35 17 0.38
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (30 bp):
TTTGTCCTCAAGAGCAGGACGCATTTTTCC
Found at i:376327 original size:40 final size:41
Alignment explanation
Indices: 376230--376328 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 41
376220 GACGTACTCT
* * *
376230 TTTTCACTTTGTCCTCAAGGAGCAGGACACTTTCCTTTTCTT
1 TTTTC-CTTTGTCCTCAAGGAGCAAGACACTTTCCTATTCTC
*
376272 TTTTCCTTTGTCCTCAAGGAGCAAGAC-CTATTTC-ATTCTC
1 TTTTCCTTTGTCCTCAAGGAGCAAGACACT-TTCCTATTCTC
376312 TTTTCCTTTGTCCTCAA
1 TTTTCCTTTGTCCTCAA
376329 AAAATGGGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
40 23 0.44
41 24 0.46
42 5 0.10
ACGTcount: A:0.17, C:0.27, G:0.12, T:0.43
Consensus pattern (41 bp):
TTTTCCTTTGTCCTCAAGGAGCAAGACACTTTCCTATTCTC
Found at i:376907 original size:13 final size:13
Alignment explanation
Indices: 376891--376920 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
376881 ATACATTGTT
376891 CATTGTATCGATA
1 CATTGTATCGATA
376904 CATTGTATCGATA
1 CATTGTATCGATA
376917 CATT
1 CATT
376921 CTAGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:376967 original size:19 final size:19
Alignment explanation
Indices: 376936--377008 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
376926 TTTACCCAGA
376936 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
376956 TGTATC-ATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
376975 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
*
376995 TGTATTGATACATT
1 TGTATCGATACATT
377009 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 17 0.37
20 29 0.63
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:379445 original size:78 final size:78
Alignment explanation
Indices: 379308--379530 Score: 227
Period size: 78 Copynumber: 2.8 Consensus size: 78
379298 TCTTCATCTC
* * *
379308 GGGGATACTCCAACCCCCGATATTATTTT-CAAAACATCAATTTTTCATAATCGGGGATACTCCA
1 GGGGATACTCCAA-CCCTGAT-TT-TTTTCCAAAACACCAATTTTTCATAATCGGAGATACTCCA
* *
379372 ATCCCGTTA-TTTCTAA
63 ACCCCGTCATTTTC-AA
* * *
379388 GGGGATACTCCAACTCTGATTTTTTTCCAAAACACCAGTTTTTCATAATTGGAGATACTCCAACC
1 GGGGATACTCCAACCCTGATTTTTTTCCAAAACACCAATTTTTCATAATCGGAGATACTCCAACC
*
379453 CCGTCATTTTCGA
66 CCGTCATTTTCAA
* * * * * * *
379466 GAGAATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTTCCACAATC-GAGGATACTCCAA
1 GGGGATACTCCAACCCTGATTTT-TTTCCAAAACACCAATTTTTCATAATCGGA-GATACTCCAA
379530 C
64 C
379531 TCTGATTTTA
Statistics
Matches: 120, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
77 4 0.03
78 62 0.52
79 41 0.34
80 13 0.11
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCTGATTTTTTTCCAAAACACCAATTTTTCATAATCGGAGATACTCCAACC
CCGTCATTTTCAA
Found at i:379529 original size:51 final size:51
Alignment explanation
Indices: 379470--379582 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
379460 TTTCGAGAGA
* * *
379470 ATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTTCCACAATCGAGG
1 ATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGG
* * *
379521 ATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGG
1 ATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGG
379572 ATACTCCAACC
1 ATACTCCAACC
379583 TCGTTATTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (51 bp):
ATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGG
Found at i:379593 original size:31 final size:29
Alignment explanation
Indices: 379565--379654 Score: 96
Period size: 28 Copynumber: 3.1 Consensus size: 29
379555 ATTTTTCACA
*
379565 ATCGGGGATACTCCAACCTCGTTATTT-C
1 ATCGGGGATACTCCAACCCCGTTATTTCC
379593 ATCGGGGATACTCCAACCCCGTTATTT-C
1 ATCGGGGATACTCCAACCCCGTTATTTCC
* *
379621 -TGAGGGGATACTCCAATCCCAGCTTTATTTCC
1 AT-CGGGGATACTCCAA-CCC--CGTTATTTCC
379653 AT
1 AT
379655 AATATTGATT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.02
28 40 0.75
29 3 0.06
31 7 0.13
32 1 0.02
33 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATTTCC
Found at i:379597 original size:28 final size:28
Alignment explanation
Indices: 379565--379636 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
379555 ATTTTTCACA
*
379565 ATCGGGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
379593 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
379621 -TGAGGGGATACTCCAA
1 AT-CGGGGATACTCCAA
379637 TCCCAGCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:379633 original size:158 final size:158
Alignment explanation
Indices: 379441--379749 Score: 365
Period size: 158 Copynumber: 2.0 Consensus size: 158
379431 CATAATTGGA
* * *
379441 GATACTCCAACCCCGTCATTTTCGAGAGAATACTCCAA-CCCTGGTTTTATTTCTAAAACACTAA
1 GATACTCCAACCCCGTCATTTTCGAGAGAATACTCCAATCCC-AGCTTTATTTCCAAAACACTAA
* * **
379505 TTT-TCCACAATCGAGGATAC-TCCAACTCTGATTTTATTTCCAAAACACCAATTTTTCACAATC
65 TTTCT-CACAATCGAGGAAACTTCAAAC-CTGACCTTATTTCCAAAACACCAATTTTTCACAATC
*
379568 GGGGATACTCCAACCTCGTTATTTCATCGGG
128 GGGGATACTCCAACCCCGTTATTTCATCGGG
* * * * * * *
379599 GATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAATCCCAGCTTTATTTCCATAATATTGA
1 GATACTCCAACCCCGTCATTTTC-GAGAGAATACTCCAATCCCAGCTTTATTTCCAAAACACTAA
* * * * * *
379663 TTTCTCACAATCGGGGAAACTTTAAACCTGACCTTATTTCTAAATCATCGATTTTTCACAATCGG
65 TTTCTCACAATCGAGGAAACTTCAAACCTGACCTTATTTCCAAAACACCAATTTTTCACAATCGG
379728 GGATACTCCAACCCCGTTATTT
130 GGATACTCCAACCCCGTTATTT
379750 TTGAGGGAAT
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
157 4 0.03
158 114 0.90
159 8 0.06
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (158 bp):
GATACTCCAACCCCGTCATTTTCGAGAGAATACTCCAATCCCAGCTTTATTTCCAAAACACTAAT
TTCTCACAATCGAGGAAACTTCAAACCTGACCTTATTTCCAAAACACCAATTTTTCACAATCGGG
GATACTCCAACCCCGTTATTTCATCGGG
Found at i:381911 original size:21 final size:21
Alignment explanation
Indices: 381887--381928 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
381877 GGAGAGAATT
* *
381887 TTTTAATCTATGGGGAGAAAA
1 TTTTAATCTAAGGCGAGAAAA
381908 TTTTAATCTAAGGCGAGAAAA
1 TTTTAATCTAAGGCGAGAAAA
381929 ACTTGTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (21 bp):
TTTTAATCTAAGGCGAGAAAA
Found at i:382511 original size:20 final size:19
Alignment explanation
Indices: 382488--382539 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
382478 CACACCCAGA
*
382488 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
382508 TGTATCAATAC-TGTTCAT
1 TGTATCGATACATGTTCAT
382526 TGTATCGATACATG
1 TGTATCGATACATG
382540 AAACTGGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 12 0.44
19 4 0.15
20 11 0.41
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:382602 original size:13 final size:13
Alignment explanation
Indices: 382584--382614 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
382574 CGATACATGG
382584 TACATTGTATAGA
1 TACATTGTATAGA
*
382597 TACATTGTATCGA
1 TACATTGTATAGA
382610 TACAT
1 TACAT
382615 GATGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (13 bp):
TACATTGTATAGA
Found at i:382632 original size:33 final size:33
Alignment explanation
Indices: 382568--382636 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
382558 CTACCACTAT
* *
382568 TTGTATCGATACATGGTACATTGTATAGATACA
1 TTGTATCGATACATGATACATTATATAGATACA
*
382601 TTGTATCGATACATGATGA-ATTATATCGATACA
1 TTGTATCGATACATGAT-ACATTATATAGATACA
382634 TTG
1 TTG
382637 CTTGTAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATACATTATATAGATACA
Found at i:384573 original size:17 final size:17
Alignment explanation
Indices: 384551--384589 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
384541 TTAATTTTTT
384551 AATAATTA-ATTATATAA
1 AATAATTATA-TATATAA
*
384568 AATAATTTTATATATAA
1 AATAATTATATATATAA
384585 AATAA
1 AATAA
384590 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATTATATATATAA
Found at i:396664 original size:13 final size:13
Alignment explanation
Indices: 396646--396682 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
396636 GTACCCCTTA
*
396646 TATCGATACAGTG
1 TATCGATACAATG
*
396659 TATCGATATAATG
1 TATCGATACAATG
396672 TATCGATACAA
1 TATCGATACAA
396683 AGATCTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:402942 original size:19 final size:20
Alignment explanation
Indices: 402897--402947 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
402887 ACTGCACTTT
*
402897 CATGTATCGATAAAATTGAG
1 CATGTATCGATAAAATTGAA
* *
402917 TATGTATCGATATAA-TGAA
1 CATGTATCGATAAAATTGAA
*
402936 CATGTATTGATA
1 CATGTATCGATA
402948 CAAAGTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (20 bp):
CATGTATCGATAAAATTGAA
Found at i:403593 original size:8 final size:8
Alignment explanation
Indices: 403572--403616 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
403562 GCTAGCAAAT
403572 TTTTTTTAC
1 TTTTTTT-C
403581 ATTTTTTTC
1 -TTTTTTTC
403590 TTTTTTTC
1 TTTTTTTC
403598 TTTTTTGTTC
1 -TTTTT-TTC
403608 TTTTTTTC
1 TTTTTTTC
403616 T
1 T
403617 CTACTTTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 12 0.36
9 11 0.33
10 10 0.30
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:403616 original size:18 final size:17
Alignment explanation
Indices: 403572--403616 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
403562 GCTAGCAAAT
*
403572 TTTTTTTACATTTTTTTC
1 TTTTTTT-CTTTTTTTTC
403590 TTTTTTTCTTTTTTGTTC
1 TTTTTTTCTTTTTT-TTC
403608 TTTTTTTCT
1 TTTTTTTCT
403617 CTACTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTTC
Found at i:404337 original size:165 final size:166
Alignment explanation
Indices: 404016--404338 Score: 454
Period size: 165 Copynumber: 2.0 Consensus size: 166
404006 TTTTAAATTG
* * * * * *
404016 AGAAAAATCTCCCTGAAAACATTTATAGAATAGAAAACTCAGTTTTTCAGAAATAAAGGAATTTC
1 AGAAAAATCCCCCTGAAAACATTTATAGAATAGAAAACTCAGTATTGCAAAAACAAAAGAATTTC
* *
404081 AAAGAAAAAATGAAAAACTTATGAAAATAAATGAATTTTTCAAAACTGATTTACTATGAATTAAA
66 AAAGAAAAAATGAAAAACTTATGAAAATAAATCAATTTTTCAAAACTGATTTAATATGAATTAAA
* *
404146 TTATGATATTTGATAAATTTTAAAAATTATAAACCA
131 TAATGATATTTGATAAATATTAAAAATTATAAACCA
* *
404182 AGAAAAATCCCCCTGAAAACATTTATAGAGTAGAAAACTCCGTATTGCAAAAACAAAAGAATTT-
1 AGAAAAATCCCCCTGAAAACATTTATAGAATAGAAAACTCAGTATTGCAAAAACAAAAGAATTTC
* * *
404246 TAAGGAAAAATGAAAAACTTAT-AAAAGTAAATCAATTTTTCAAAACTGATTTAATATGAGTTAA
66 AAAGAAAAAATGAAAAACTTATGAAAA-TAAATCAATTTTTCAAAACTGATTTAATATGAATTAA
* *
404310 ATAAT-AGTATTTTATGAATATTAAAAATT
130 ATAATGA-TATTTGATAAATATTAAAAATT
404339 TTGAAGGGAT
Statistics
Matches: 138, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
164 5 0.04
165 77 0.56
166 56 0.41
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (166 bp):
AGAAAAATCCCCCTGAAAACATTTATAGAATAGAAAACTCAGTATTGCAAAAACAAAAGAATTTC
AAAGAAAAAATGAAAAACTTATGAAAATAAATCAATTTTTCAAAACTGATTTAATATGAATTAAA
TAATGATATTTGATAAATATTAAAAATTATAAACCA
Found at i:410039 original size:20 final size:20
Alignment explanation
Indices: 410014--410078 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
410004 AAAACTCAGA
410014 TGTATCGATACAGCATTCTC
1 TGTATCGATACAGCATTCTC
410034 TGTATCGAT--A-CA---T-
1 TGTATCGATACAGCATTCTC
410047 TGTATCGATACAGCATTCTC
1 TGTATCGATACAGCATTCTC
410067 TGTATCGATACA
1 TGTATCGATACA
410079 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 1 0.03
20 21 0.55
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAGCATTCTC
Found at i:410052 original size:13 final size:13
Alignment explanation
Indices: 410034--410104 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 13
410024 CAGCATTCTC
410034 TGTATCGATACAT
1 TGTATCGATACAT
410047 TGTATCGATACAGCATTCT
1 TGTATCGAT--A-CA---T
410066 CTGTATCGATACAT
1 -TGTATCGATACAT
*
410080 TGTATCGATACAG
1 TGTATCGATACAT
*
410093 TGTATTGATACA
1 TGTATCGATACA
410105 AAGGGTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 32 0.65
14 1 0.02
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 1 0.02
20 9 0.18
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:410056 original size:33 final size:33
Alignment explanation
Indices: 410014--410092 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
410004 AAAACTCAGA
410014 TGTATCGATACAGCATTCTCTGTATCGATACAT
1 TGTATCGATACAGCATTCTCTGTATCGATACAT
410047 TGTATCGATACAGCATTCTCTGTATCGATACAT
1 TGTATCGATACAGCATTCTCTGTATCGATACAT
410080 TGTATCGATACAG
1 TGTATCGATACAG
410093 TGTATTGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAGCATTCTCTGTATCGATACAT
Found at i:410571 original size:20 final size:22
Alignment explanation
Indices: 410546--410590 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
410536 GCAGCACTCA
410546 CCAGGTCGCAACC-GGCA-CCC
1 CCAGGTCGCAACCGGGCAGCCC
410566 CCAGGTCGCAACCGGGCAGCCC
1 CCAGGTCGCAACCGGGCAGCCC
410588 CCA
1 CCA
410591 CACTCACAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.57
21 4 0.17
22 6 0.26
ACGTcount: A:0.20, C:0.49, G:0.27, T:0.04
Consensus pattern (22 bp):
CCAGGTCGCAACCGGGCAGCCC
Found at i:412584 original size:13 final size:13
Alignment explanation
Indices: 412566--412590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
412556 ATAATGCACA
412566 GTATCGATACATT
1 GTATCGATACATT
412579 GTATCGATACAT
1 GTATCGATACAT
412591 GACCAAATGT
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):
GTATCGATACATT
Found at i:412690 original size:13 final size:13
Alignment explanation
Indices: 412672--412696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
412662 CTTAACTGTT
412672 TGTATCGATACAA
1 TGTATCGATACAA
412685 TGTATCGATACA
1 TGTATCGATACA
412697 TGACCAAATT
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:414185 original size:4 final size:4
Alignment explanation
Indices: 414176--414216 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
414166 TAATTTAATT
* *
414176 ATAA ATAA ATAA ATAA ATATA ATAC ATCA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA
414217 TAATTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:415157 original size:41 final size:41
Alignment explanation
Indices: 415112--415244 Score: 126
Period size: 41 Copynumber: 3.2 Consensus size: 41
415102 AACATGTTAG
* *
415112 TAATAAAAGATATATTGAAGAAAAGCAATAGATATGAAATA
1 TAATAAAAGATATATTGAAGAAAAGCAGTAGATATAAAATA
* * * * *
415153 TAATAAAATGGATAAATTCACAAAATAAG-TGTA-AAATAAAATA
1 TAATAAAA--GATATATTGA-AGAA-AAGCAGTAGATATAAAATA
* * *
415196 TAATAAAGGATATATTGAAGAAAAGCGGTAGATATTAAATA
1 TAATAAAAGATATATTGAAGAAAAGCAGTAGATATAAAATA
415237 TAATAAAA
1 TAATAAAA
415245 TAGATGAATT
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
39 3 0.04
40 6 0.08
41 31 0.44
43 23 0.32
44 5 0.07
45 3 0.04
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.26
Consensus pattern (41 bp):
TAATAAAAGATATATTGAAGAAAAGCAGTAGATATAAAATA
Found at i:415198 original size:43 final size:43
Alignment explanation
Indices: 415148--415273 Score: 116
Period size: 41 Copynumber: 3.0 Consensus size: 43
415138 AATAGATATG
415148 AAATATAATAAAATGGATAAATTCACAAAATAAGTGTAAAATA
1 AAATATAATAAAATGGATAAATTCACAAAATAAGTGTAAAATA
* * * * * *
415191 AAATATAAT-AAA-GGATATATTGA-AGAA-AAGCGGTAGATATT
1 AAATATAATAAAATGGATAAATTCACAAAATAAG-TGTA-AAATA
* * **
415232 AAATATAATAAAATAGATGAATTCACAAAATTGGTGTAAAAT
1 AAATATAATAAAATGGATAAATTCACAAAATAAGTGTAAAAT
415274 GAGCTTAGCA
Statistics
Matches: 62, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
39 3 0.05
40 6 0.10
41 21 0.34
42 6 0.10
43 19 0.31
44 6 0.10
45 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (43 bp):
AAATATAATAAAATGGATAAATTCACAAAATAAGTGTAAAATA
Found at i:415236 original size:84 final size:84
Alignment explanation
Indices: 415112--415273 Score: 252
Period size: 84 Copynumber: 1.9 Consensus size: 84
415102 AACATGTTAG
*
415112 TAATAAAAGATATATTGAAGAAAAGCAATAGATATGAAATATAATAAAATGGATAAATTCACAAA
1 TAATAAAAGATATATTGAAGAAAAGCAATAGATATGAAATATAATAAAATAGATAAATTCACAAA
415177 ATAAGTGTAAAATAAAATA
66 ATAAGTGTAAAATAAAATA
* ** * *
415196 TAATAAAGGATATATTGAAGAAAAGCGGTAGATATTAAATATAATAAAATAGATGAATTCACAAA
1 TAATAAAAGATATATTGAAGAAAAGCAATAGATATGAAATATAATAAAATAGATAAATTCACAAA
**
415261 ATTGGTGTAAAAT
66 ATAAGTGTAAAAT
415274 GAGCTTAGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.27
Consensus pattern (84 bp):
TAATAAAAGATATATTGAAGAAAAGCAATAGATATGAAATATAATAAAATAGATAAATTCACAAA
ATAAGTGTAAAATAAAATA
Found at i:417276 original size:155 final size:155
Alignment explanation
Indices: 417019--417569 Score: 486
Period size: 155 Copynumber: 3.5 Consensus size: 155
417009 GACAAATTAA
* * * * * ** * * * *
417019 GACTCGATTCTAAAAAATTATGAAAAGGCCCCTATGGGTATATTTTTGACATAAAAGTATCTCGG
1 GACTCGATTTTAAAAAATTAAGAAAATGCTCCTAAGGG-ATACCTTCGACTTAGAAGTA-CTCGA
* * * * *
417084 TAACCCTATAGGACTTAAAAAGGATTATAGATGGGATGAACCTATATTAAATACCCACATTTGGC
64 TAACCCTAAAGGACTTAAAAAGGATTATTGATGGGATGAACCTATCTTAAATACCCACCTTCGGC
*
417149 ATAAAAGTAGACTCGGTGACAACCTAG
129 ATAAAAGTAGACTCGGTAACAACCTAG
* * * * *
417176 GACTCAATTTTGAAAAATTACGAAAATGCTCCTAAGAGATACCTTCGACTTCGAAGTACTCGATA
1 GACTCGATTTTAAAAAATTAAGAAAATGCTCCTAAGGGATACCTTCGACTTAGAAGTACTCGATA
* * * * * *
417241 ACCCTAAAGGACTTAAAAATGATTATTGATAGGATGAACCTATCTTATATACCAACCTTCGACAA
66 ACCCTAAAGGACTTAAAAAGGATTATTGATGGGATGAACCTATCTTAAATACCCACCTTCGGCAT
* * * * *
417306 AAAAGTGGACCCGATTACAACTTAAG
131 AAAAGTAGACTCGGTAACAACCT-AG
* * * * * * *
417332 G-CTCGGTTCTAAAAAAATT-TGAAAATAC-CTTTATGGGATACCTTCGACTTAGAAGTGCTCGA
1 GACTCGATT-TTAAAAAATTAAGAAAATGCTC-CTAAGGGATACCTTCGACTTAGAAGTACTCGA
* * * * *
417394 TAACCTTAAAGTACTTAAAAGGGATTATTGATGGGATGAAACTATCCTAAATA-CCACCTTCGGC
64 TAACCCTAAAGGACTTAAAAAGGATTATTGATGGGATGAACCTATCTTAAATACCCACCTTCGGC
* *
417458 ATAAAAG-CGAACTCAGTAACAACCTAG
129 ATAAAAGTAG-ACTCGGTAACAACCTAG
* * * * *
417485 GACTCGCTTCTAAAAAAGTTAAGAAAATG-TCCCTAGGGGATACCTTCAACTTAGAAATAC-CTG
1 GACTCGATTTTAAAAAA-TTAAGAAAATGCT-CCTAAGGGATACCTTCGACTTAGAAGTACTC-G
* *
417548 ATAACCTTAAAAGACTTAAAAA
63 ATAACCCTAAAGGACTTAAAAA
417570 TGATAAGTAA
Statistics
Matches: 312, Mismatches: 72, Indels: 22
0.77 0.18 0.05
Matches are distributed among these distances:
153 10 0.03
154 35 0.11
155 211 0.68
156 26 0.08
157 30 0.10
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (155 bp):
GACTCGATTTTAAAAAATTAAGAAAATGCTCCTAAGGGATACCTTCGACTTAGAAGTACTCGATA
ACCCTAAAGGACTTAAAAAGGATTATTGATGGGATGAACCTATCTTAAATACCCACCTTCGGCAT
AAAAGTAGACTCGGTAACAACCTAG
Found at i:421038 original size:20 final size:20
Alignment explanation
Indices: 421013--421068 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
421003 AATTTACCTG
*
421013 CATGTATTGATACATTGAAT
1 CATGTATCGATACATTGAAT
421033 CATGTATCGATACATTGAAT
1 CATGTATCGATACATTGAAT
*
421053 AATGTATCGATACATT
1 CATGTATCGATACATT
421069 TGGGTCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:422061 original size:52 final size:52
Alignment explanation
Indices: 421977--422224 Score: 228
Period size: 52 Copynumber: 4.6 Consensus size: 52
421967 GTTACTAATT
* ** **
421977 TGCTAATTCAAGGCCAATGATATTGGGTTTAAAGATGACAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
* * * * *
422029 TGCTGATTCAAGGCCAACGACATTAGACTTAAAGATAAGAAGAGTGATAAAGGTGCCGATG
1 TGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A-AAGA-TGACAAAGGTGCCAATG
* *
422090 TGCTGATACAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
** * * *
422142 TGCTGATTCAAGGCCAGCGATATTATACTT-AAGAAAGAAAAAGGTGGCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-ATGACAAAGGTGCCAATG
* *
422194 TGCTAATTCAAGGCCAGCGACATTGGACTTA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTA
422225 GAAAAAGTTA
Statistics
Matches: 159, Mismatches: 26, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
51 3 0.02
52 103 0.65
53 5 0.03
54 1 0.01
55 1 0.01
58 1 0.01
59 1 0.01
60 5 0.03
61 39 0.25
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (52 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
Found at i:422079 original size:113 final size:112
Alignment explanation
Indices: 421912--422180 Score: 290
Period size: 113 Copynumber: 2.4 Consensus size: 112
421902 AGGATGCGAA
* * * * * * * *
421912 AATATGCTGATTCACGGCCAAC-ATTATCAGGCCTGAAGATGAGAAGAATCATAAAGTTACTAAT
1 AATATGCTGATTCAAGGCCAACGA-CATTA-GACTTAAGATAAGAAGAATCATAAAGGTACCAAT
* * * **
421976 TTGCTAATTCAAGGCCAATGATATTGGGTTTAAAGATGACAAAGGTGCC
64 GTGCTAATACAAGGCCAACGATATTGGACTTAAAGATGACAAAGGTGCC
* * * * *
422025 AATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATAAGAAGAGTGATAAAGGTGCCGATG
1 AATATGCTGATTCAAGGCCAACGACATTAGACTT-AAGATAAGAAGAATCATAAAGGTACCAATG
* *
422090 TGCTGATACAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGTGCC
65 TGCTAATACAAGGCCAACGATATTGGACTTAAAGATGACAAAGGTGCC
* * *
422138 AATATGCTGATTCAAGGCCAGCGATATTATACTTAAGA-AAGAA
1 AATATGCTGATTCAAGGCCAACGACATTAGACTTAAGATAAGAA
422181 AAAGGTGGCA
Statistics
Matches: 130, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
111 5 0.04
112 7 0.05
113 117 0.90
114 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (112 bp):
AATATGCTGATTCAAGGCCAACGACATTAGACTTAAGATAAGAAGAATCATAAAGGTACCAATGT
GCTAATACAAGGCCAACGATATTGGACTTAAAGATGACAAAGGTGCC
Found at i:422119 original size:61 final size:60
Alignment explanation
Indices: 422008--422125 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 60
421998 ATTGGGTTTA
*
422008 AAGATGACAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATAAG
1 AAGATGACAAAGGTGCCAATGTGCTGATACAAGGCCAACGACATTAGACTTAAAGATAAG
* * * * *
422068 AAGAGTGATAAAGGTGCCGATGTGCTGATACAAGGCCAGCGATATTGGACTTAAAGAT
1 AAGA-TGACAAAGGTGCCAATGTGCTGATACAAGGCCAACGACATTAGACTTAAAGAT
422126 GACAAAGGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 4 0.08
61 47 0.92
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.21
Consensus pattern (60 bp):
AAGATGACAAAGGTGCCAATGTGCTGATACAAGGCCAACGACATTAGACTTAAAGATAAG
Found at i:422485 original size:27 final size:27
Alignment explanation
Indices: 422446--422504 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
422436 ATACAGTAGA
* *
422446 TGCCATTGATTATGGACTTCAAAAAGT
1 TGCCATTGATTATGGACTCCAAAAAGG
*
422473 TGCCA-TGACTTATGGACTCCAAAGAGG
1 TGCCATTGA-TTATGGACTCCAAAAAGG
422500 TGCCA
1 TGCCA
422505 CTAACTAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (27 bp):
TGCCATTGATTATGGACTCCAAAAAGG
Found at i:422555 original size:14 final size:14
Alignment explanation
Indices: 422536--422622 Score: 65
Period size: 13 Copynumber: 6.5 Consensus size: 14
422526 GGGATTCGTG
422536 TTGACAAAAATTTC
1 TTGACAAAAATTTC
*
422550 TTGAC-AAAGTTT-
1 TTGACAAAAATTTC
* *
422562 TTAACAAACA-TTC
1 TTGACAAAAATTTC
* *
422575 TCGACAAAAA-TCC
1 TTGACAAAAATTTC
* * *
422588 TTGGCAATAATTTT
1 TTGACAAAAATTTC
*
422602 TTGACAACAATTTC
1 TTGACAAAAATTTC
422616 TTGACAA
1 TTGACAA
422623 TGGCAAATTA
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
12 6 0.11
13 24 0.44
14 24 0.44
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (14 bp):
TTGACAAAAATTTC
Found at i:423024 original size:29 final size:28
Alignment explanation
Indices: 422948--423033 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
422938 TAGGACCTTA
* * * * *
422948 ATTCCATTAGAGATTATAGGTTGTTCAA
1 ATTCCATTAGGGGTTATAGGCTGTGCAT
*
422976 ACTCCATTAGGGGTTATAGGCTGTGCAT
1 ATTCCATTAGGGGTTATAGGCTGTGCAT
423004 ATTCCATTAGGGGGTTATAGGCTGTGCAT
1 ATTCCATTA-GGGGTTATAGGCTGTGCAT
423033 A
1 A
423034 CTTTTACGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 30 0.60
29 20 0.40
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (28 bp):
ATTCCATTAGGGGTTATAGGCTGTGCAT
Found at i:426308 original size:20 final size:20
Alignment explanation
Indices: 426283--426334 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
426273 TACAAGCCAA
**
426283 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
426303 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
426322 TGTATCGATACAA
1 TGTATCGATACAA
426335 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:428409 original size:21 final size:20
Alignment explanation
Indices: 428380--428422 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
428370 GACTAGTGTG
* *
428380 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
428401 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
428421 GG
1 GG
428423 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:430955 original size:15 final size:15
Alignment explanation
Indices: 430935--430965 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
430925 ATTTCGTTTG
*
430935 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
430950 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
430965 G
1 G
430966 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:435040 original size:13 final size:13
Alignment explanation
Indices: 435022--435047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
435012 CAATTTTTTG
435022 TGTATCGATACAT
1 TGTATCGATACAT
435035 TGTATCGATACAT
1 TGTATCGATACAT
435048 ACTTTGTGTA
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:435059 original size:32 final size:33
Alignment explanation
Indices: 435002--435065 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
434992 TACAAGCCAA
**
435002 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
435035 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
435066 AGTTTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:438252 original size:20 final size:20
Alignment explanation
Indices: 438229--438288 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
438219 AAGTACCCAG
* *
438229 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
438249 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
438269 ATGTATCGATACATTCTATC
1 ATGTATCGATACATT-TATC
438289 CTTTTGCCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:451767 original size:9 final size:9
Alignment explanation
Indices: 451753--451811 Score: 75
Period size: 9 Copynumber: 6.6 Consensus size: 9
451743 TTATACCCAA
*
451753 AAAAAAAAG
1 AAAAAAAAC
451762 AAAAAAAACC
1 AAAAAAAA-C
451772 AAAAAAAAC
1 AAAAAAAAC
*
451781 AAAAACAA-
1 AAAAAAAAC
451789 AAAAAAAAC
1 AAAAAAAAC
*
451798 AAAAAAAAG
1 AAAAAAAAC
451807 AAAAA
1 AAAAA
451812 TAGCATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.16
9 29 0.66
10 8 0.18
ACGTcount: A:0.88, C:0.08, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:451767 original size:11 final size:11
Alignment explanation
Indices: 451750--451805 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
451740 CATTTATACC
451750 CAAAAAAAAAA
1 CAAAAAAAAAA
*
451761 GAAAAAAAACCAA
1 CAAAAAAAA--AA
*
451774 AAAAAACAAAAA
1 CAAAAA-AAAAA
451786 CAAAAAAAAAA
1 CAAAAAAAAAA
451797 CAAAAAAAA
1 CAAAAAAAA
451806 GAAAAATAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 22 0.56
12 7 0.18
13 7 0.18
14 3 0.08
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:451822 original size:1 final size:1
Alignment explanation
Indices: 451751--451811 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
451741 ATTTATACCC
* ** * * * *
451751 AAAAAAAAAAGAAAAAAAACCAAAAAAAACAAAAACAAAAAAAAAACAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
451812 TAGCATAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:451824 original size:26 final size:26
Alignment explanation
Indices: 451762--451811 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
451752 AAAAAAAAAG
*
451762 AAAAAAAACCAAAAAAAACAAAAACA
1 AAAAAAAAACAAAAAAAACAAAAACA
*
451788 AAAAAAAAACAAAAAAAAGAAAAA
1 AAAAAAAAACAAAAAAAACAAAAA
451812 TAGCATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (26 bp):
AAAAAAAAACAAAAAAAACAAAAACA
Found at i:452354 original size:13 final size:13
Alignment explanation
Indices: 452336--452360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
452326 ATGATGAAAT
452336 TGTATCGATACAG
1 TGTATCGATACAG
452349 TGTATCGATACA
1 TGTATCGATACA
452361 TGATGAAATT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:452358 original size:34 final size:34
Alignment explanation
Indices: 452315--452381 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
452305 TATCACTATT
452315 TGTATCGATACATGATGAAATTGTATCGATACAG
1 TGTATCGATACATGATGAAATTGTATCGATACAG
452349 TGTATCGATACATGATGAAATTGTATCGATACA
1 TGTATCGATACATGATGAAATTGTATCGATACA
452382 TTGCTTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (34 bp):
TGTATCGATACATGATGAAATTGTATCGATACAG
Found at i:458526 original size:13 final size:13
Alignment explanation
Indices: 458508--458535 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
458498 ACAACATTCC
458508 TTGTATCGATACA
1 TTGTATCGATACA
458521 TTGTATCGATACA
1 TTGTATCGATACA
458534 TT
1 TT
458536 ATGTACTATT
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:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:460426 original size:22 final size:22
Alignment explanation
Indices: 460377--460428 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
460367 TTATTTGACA
*
460377 AAGGGGGAGAAATTCTTTGATT
1 AAGGGGGAGAAATTCTTTAATT
*
460399 AAGGGGGAG-AATTTTTTAATT
1 AAGGGGGAGAAATTCTTTAATT
460420 AAGGGGGAG
1 AAGGGGGAG
460429 TAAAACGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.33, C:0.02, G:0.37, T:0.29
Consensus pattern (22 bp):
AAGGGGGAGAAATTCTTTAATT
Found at i:461039 original size:20 final size:19
Alignment explanation
Indices: 460993--461049 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
460983 ATCTATCGAT
460993 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
461012 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
461031 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
461050 AAACTGACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:461117 original size:13 final size:13
Alignment explanation
Indices: 461099--461123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
461089 CATGGGACAA
461099 TGTATCGATACAG
1 TGTATCGATACAG
461112 TGTATCGATACA
1 TGTATCGATACA
461124 TGATGAAATT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:463068 original size:28 final size:28
Alignment explanation
Indices: 463015--463573 Score: 713
Period size: 28 Copynumber: 19.5 Consensus size: 28
463005 CGTTCATCTC
463015 TTCAAAGCCCACGTAAGTCAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
**
463045 TTCAAAGCCCACAAGTCAGTGGCACTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
463073 TGTCAAAGCCCACAAGTTAATGGCACTCTT
1 T-TCAAAGCCCACAAGTCAGTGGCAC-CCT
463103 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* **
463131 TTTAAAGCCCACAAGTCAGTGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
463160 TTCAAAGGCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
463188 TTCAAAGGCCACAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
463217 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
463245 TTCAAAGCCTACGCAAGTCAGTGGCACCCT
1 TTCAAAGCC--CACAAGTCAGTGGCACCCT
* *
463275 TTCAAAGCCCACAGGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
463304 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
463332 TTCAAAGCCCACAAGTCAGTGGCACCCA
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* **
463360 TTCAAAGCCCACAAGTCAGTTGCATTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
463388 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
463416 TTCAAAGCCCACGCAAGTTAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* *
463446 TTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
463475 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
463503 TTCAAAGCCCACAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* **
463531 TTCAAAGCCCACAAGTTAGTGGCACTATT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
463560 TTCAAAGCCCACAA
1 TTCAAAGCCCACAA
463574 ACTAATGGTA
Statistics
Matches: 467, Mismatches: 51, Indels: 23
0.86 0.09 0.04
Matches are distributed among these distances:
28 241 0.52
29 157 0.34
30 69 0.15
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:463145 original size:57 final size:57
Alignment explanation
Indices: 463018--463573 Score: 687
Period size: 57 Copynumber: 9.7 Consensus size: 57
463008 TCATCTCTTC
*
463018 AAAGCCCACGTAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA-CTTTTGT
1 AAAGCCCAC--AAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT-T
* * *
463076 CAAAGCCCACAAGTTAATGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
1 -AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
** * *
463134 AAAGCCCACAAGTCAGTGGCACTTTTTTCAAAGGCCACAAGTCAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
* * * *
463191 AAAGGCCACAAGTCAATGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
* * *
463248 AAAGCCTACGCAAGTCAGTGGCAC-CCTTTCAAAGCCCACAGGTCAGTGGCACTCTTTT
1 AAAGCC--CACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
* * *
463306 CAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCATTC
1 -AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
* * * * *
463363 AAAGCCCACAAGTCAGTTGCA-TTCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
* * *
463419 AAAGCCCACGCAAGTTAGTGGCAC-CCTTTCAAAGCCCATAAGTCAGTGGCACTCTTTT
1 AAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
*
463477 CAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTT
1 -AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
* **
463533 CAAAGCCCACAAGTTAGTGGCACTATTTTCAAAGCCCACAA
1 -AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAA
463574 ACTAATGGTA
Statistics
Matches: 441, Mismatches: 44, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
56 85 0.19
57 219 0.50
58 96 0.22
59 41 0.09
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
Found at i:463478 original size:143 final size:142
Alignment explanation
Indices: 463015--463648 Score: 738
Period size: 143 Copynumber: 4.4 Consensus size: 142
463005 CGTTCATCTC
**
463015 TTCAAAGCCCACGTAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTGTCAAA
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTT-TCAAA
* * * *
463080 GCCCACAAGTTAATGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAA
63 GCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
*
463145 GTCAGTGGCACTTTT
128 GTCAGTGGCACTCTT
* * * *
463160 TTCAAAGGCCACAAGTCAGTGGCACCCTTTCAAAGGCCACAAGTCAATGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGC
* *
463225 CCACAAGTCAGTGGCACCC-TTTCAAAGCCTACGCAAGTCAGTGGCACCCTTTCAAAGCCCACAG
65 CCACAAGTCAGTGGCACCCTTTTCAAAGCC--CACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
463289 GTCAGTGGCACTCTT
128 GTCAGTGGCACTCTT
* * *
463304 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCATTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* ** * *
463369 CACAAGTCAGTTGCATTC-TTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACGCAAG
66 CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAG
* *
463433 TTAGTGGCAC-CCT
129 TCAGTGGCACTCTT
* * * *
463446 TTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* **
463511 CCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTTAGTGGCACTATTTTCAAAGCCCACAA-
65 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAG
* * *
463574 ACTAATGGTAACTCTT
129 TC-AGTGG-CACTCTT
* * * *
463590 TTCAAAGCCTACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACATAAGTTAGTGGCAC
1 TTCAAAGCC--CACAAGTCAGTGGC-AC-CCTTTCAAAGCCCAC--AAGTCAGTGGCAC
463649 TTTTTAAAAA
Statistics
Matches: 425, Mismatches: 48, Indels: 28
0.85 0.10 0.06
Matches are distributed among these distances:
141 27 0.06
142 42 0.10
143 186 0.44
144 118 0.28
145 11 0.03
146 11 0.03
147 18 0.04
149 12 0.03
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (142 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
AGTGGCACTCTT
Found at i:473034 original size:32 final size:33
Alignment explanation
Indices: 472993--473056 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
472983 GCCAAACTTG
**
472993 TATCGATACA-CATAGTATGTATCGATACATTA
1 TATCGATACACCATAAAATGTATCGATACATTA
*
473025 TATCGATACACCATAAAATGTATCTATACATT
1 TATCGATACACCATAAAATGTATCGATACATT
473057 GGCTTATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (33 bp):
TATCGATACACCATAAAATGTATCGATACATTA
Found at i:483599 original size:68 final size:68
Alignment explanation
Indices: 483516--483651 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
483506 TTTAAAAAAA
483516 TCTGCATTTATATTAAAAGGATCGATTTCTACACTTGAGGGATTGATCCTTTTGTTTTGTTTTGT
1 TCTGCATTTATATTAAAAGGATCGATTTCTACACTTGAGGGATTGATCCTTTTGTTTTGTTTTGT
483581 TTT
66 TTT
483584 TCTGCATTTATATTAAAAGGATCGATTTCTACACTTGAGGGATTGATCCTTTTGTTTTGTTTTGT
1 TCTGCATTTATATTAAAAGGATCGATTTCTACACTTGAGGGATTGATCCTTTTGTTTTGTTTTGT
483649 TTT
66 TTT
483652 AACTTCTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.50
Consensus pattern (68 bp):
TCTGCATTTATATTAAAAGGATCGATTTCTACACTTGAGGGATTGATCCTTTTGTTTTGTTTTGT
TTT
Found at i:488535 original size:2 final size:2
Alignment explanation
Indices: 488528--488562 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
488518 CATTGTTGGA
488528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
488563 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:494856 original size:21 final size:21
Alignment explanation
Indices: 494832--494908 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
494822 AAAAATTTTA
494832 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
494853 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* * *
494874 AATGTATCAATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
494895 AATGTATCGATACA
1 AATGTATCGATACA
494909 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:494968 original size:19 final size:19
Alignment explanation
Indices: 494944--494998 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
494934 AATTCAACAA
494944 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
494963 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
494982 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
494999 TTAGCTATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:495056 original size:13 final size:13
Alignment explanation
Indices: 495038--495063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
495028 CATTTTTCTG
495038 TGTATCGATACAT
1 TGTATCGATACAT
495051 TGTATCGATACAT
1 TGTATCGATACAT
495064 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:495060 original size:33 final size:33
Alignment explanation
Indices: 495018--495084 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
495008 GCCAAGGAAA
***
495018 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
495051 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
495084 T
1 T
495085 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:495614 original size:10 final size:10
Alignment explanation
Indices: 495599--495624 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
495589 AGCAAAAAAG
495599 AAAAAACAAA
1 AAAAAACAAA
495609 AAAAAACAAA
1 AAAAAACAAA
495619 AAAAAA
1 AAAAAA
495625 ACACTATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:495614 original size:17 final size:16
Alignment explanation
Indices: 495592--495625 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
495582 ATCCTTTAGC
*
495592 AAAAAAGAAAAAACAAA
1 AAAAAACAAAAAA-AAA
495609 AAAAAACAAAAAAAAA
1 AAAAAACAAAAAAAAA
495625 A
1 A
495626 CACTATTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAAAAA
Found at i:495620 original size:11 final size:11
Alignment explanation
Indices: 495594--495627 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
495584 CCTTTAGCAA
495594 AAAAGAAAAAAC
1 AAAA-AAAAAAC
495606 -AAAAAAAAAC
1 AAAAAAAAAAC
495616 AAAAAAAAAAC
1 AAAAAAAAAAC
495627 A
1 A
495628 CTATTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:497659 original size:51 final size:52
Alignment explanation
Indices: 497597--497766 Score: 175
Period size: 52 Copynumber: 3.3 Consensus size: 52
497587 TTATTTCCGA
* * ***
497597 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTCC-ATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCTATAATC
* * * *
497648 GGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCTATAATC
* * * *
497700 GGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAAATTTT-C-ACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACC-AATTTTCCTATAATC
*
497752 GAGGATACTCCAACC
1 GGGGATACTCCAACC
497767 TCGTTAATTC
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 37 0.38
52 46 0.47
53 8 0.08
54 6 0.06
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCTATAATC
Found at i:497713 original size:52 final size:50
Alignment explanation
Indices: 497423--497766 Score: 176
Period size: 51 Copynumber: 6.6 Consensus size: 50
497413 TTGAGTTTCT
* * * * * *
497423 CAATTCTCCACAATCGGGGATATTCTAGCTCCGATTTTATTTTCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAAC-CCGATTTTATTTCCAAAACAC
* *
497474 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAAC-CCGATTTTATTTCC--AAAACAC
* * * * **** * *
497527 CAATTTTTTCACAATC-GGGACACTCCAACCCCG-TTAATCATTGAGGATACTC
1 CAA-TTTTCCATAATCGGGGATACTCCAA-CCCGATT--TTATTTCCAAAACAC
** * * * * *
497579 CAA--CCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATAT
1 CAATTTTCC-ATA-AT-C--GGGGATACTCCAA-CCCGATTTTATTTCCAAAACAC
** * *
497633 TGATTTTCCATAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACC-CGATTTTATTTCCAAAACAC
* *
497684 CAATTTTCCTTTAATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ATAATCGGGGATACTCCAAC-CCGATTTTATTTCC-AAAACAC
* * *
497737 CAAATTTT-CACAATTGAGGATACTCCAACC
1 C-AATTTTCCATAATCGGGGATACTCCAACC
497767 TCGTTAATTC
Statistics
Matches: 215, Mismatches: 58, Indels: 40
0.69 0.19 0.13
Matches are distributed among these distances:
49 1 0.00
50 3 0.01
51 73 0.34
52 56 0.26
53 33 0.15
54 28 0.13
55 18 0.08
56 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (50 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCGATTTTATTTCCAAAACAC
Found at i:497840 original size:211 final size:210
Alignment explanation
Indices: 497457--497840 Score: 560
Period size: 211 Copynumber: 1.8 Consensus size: 210
497447 CTAGCTCCGA
* *
497457 TTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA
1 TTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACACCGATTTTATTTCCAAAA
* *
497522 AACACCAATTTTTTCACAATCGGGACACTCCAACCCCGTTAATCATTGAGGATACTCCAACCCCG
66 AACACCAATATTTTCACAATCGGGACACTCCAACCCCGTTAATCATAGAGGATACTCCAACCCCG
* * * *
497587 TTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTCCATAATCGGGG
131 TTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCAAAATATTGATTTTCCATAATCGGGG
497652 ATACTCCAACCTCGG
196 ATACTCCAACCTCGG
*
497667 TTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACACCGATTTTATTTCC-AA
1 TTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCCAACACCGATTTTATTTCCAAA
* * * *
497731 AAATACCAA-ATTTTCACAATTGAGGATACTCCAACCTCGTTAATTCATCAG-GGATACTCCAAC
65 AAACACCAATATTTTCACAATCG-GGACACTCCAACCCCGTTAA-TCAT-AGAGGATACTCCAAC
* *
497794 TCCGTTACTTCCGAGGGAACACTCCAACCCCG-TTATTATCTCCAAAA
127 CCCGTTACTTCCGAGGGAACACTCCAACCCCGACT-TTATCTCCAAAA
497841 CATTAAATTT
Statistics
Matches: 154, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
209 11 0.07
210 52 0.34
211 90 0.58
212 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (210 bp):
TTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACACCGATTTTATTTCCAAAA
AACACCAATATTTTCACAATCGGGACACTCCAACCCCGTTAATCATAGAGGATACTCCAACCCCG
TTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCAAAATATTGATTTTCCATAATCGGGG
ATACTCCAACCTCGG
Found at i:506509 original size:4 final size:4
Alignment explanation
Indices: 506500--506561 Score: 61
Period size: 4 Copynumber: 14.8 Consensus size: 4
506490 TTTATCTCTC
* * *
506500 CTTT CTTT CTTCT CTTT CTTT CTTTT CTTT CTCT CTCT CTTT CTTT CTCTC
1 CTTT CTTT CTT-T CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CT-TT
*
506551 CTTT CTCT CTT
1 CTTT CTTT CTT
506562 CACCATGGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 38 0.78
5 11 0.22
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:506518 original size:13 final size:13
Alignment explanation
Indices: 506486--506562 Score: 77
Period size: 13 Copynumber: 5.8 Consensus size: 13
506476 CTCATTTCCT
*
506486 TTTCTTTATCTCTCC
1 TTTCTTTCT-TCT-C
506501 TTTCTTTCTTCTC
1 TTTCTTTCTTCTC
*
506514 TTTCTTTCTTTTC
1 TTTCTTTCTTCTC
*
506527 TTTCTCTC-TCTC
1 TTTCTTTCTTCTC
506539 TTTCTTTC-TCTCC
1 TTTCTTTCTTCT-C
*
506552 TTTCTCTCTTC
1 TTTCTTTCTTC
506563 ACCATGGCCC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
12 13 0.24
13 28 0.52
14 5 0.09
15 8 0.15
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTCTTTCTTCTC
Found at i:506543 original size:21 final size:21
Alignment explanation
Indices: 506474--506545 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
506464 TTCTTCTTCC
*
506474 CTCTCATTTCCTTTTCTTTATCT
1 CTCTC-TTT-CTTTTCTTTCTCT
506497 CTC-CTTTC-TTTC-TTCTCT
1 CTCTCTTTCTTTTCTTTCTCT
506515 -T-TCTTTCTTTTCTTTCTCT
1 CTCTCTTTCTTTTCTTTCTCT
506534 CTCTCTTTCTTT
1 CTCTCTTTCTTT
506546 CTCTCCTTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
17 6 0.14
18 9 0.21
19 10 0.23
20 2 0.05
21 12 0.28
22 1 0.02
23 3 0.07
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (21 bp):
CTCTCTTTCTTTTCTTTCTCT
Found at i:506543 original size:25 final size:25
Alignment explanation
Indices: 506494--506560 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
506484 CTTTTCTTTA
*
506494 TCTCTCCTTTCTTTCTTCTCTTTCTT
1 TCTCTCCTTTCTCTC-TCTCTTTCTT
* *
506520 TCTTTTCTTTCTCTCTCTCTTTCTT
1 TCTCTCCTTTCTCTCTCTCTTTCTT
506545 TCTCTCCTTTCTCTCT
1 TCTCTCCTTTCTCTCT
506561 TCACCATGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (25 bp):
TCTCTCCTTTCTCTCTCTCTTTCTT
Found at i:506557 original size:21 final size:21
Alignment explanation
Indices: 506462--506561 Score: 77
Period size: 21 Copynumber: 4.9 Consensus size: 21
506452 CACAAATTTT
* *
506462 TTTTCTTCTTCCCTCTCATTTCC
1 TTTTCTTCCTCTCTCTC-TTT-C
**
506485 TTTTCTTTATCTCTC-CTTTC
1 TTTTCTTCCTCTCTCTCTTTC
506505 -TTTCTT-CTCT-T-TCTTTC
1 TTTTCTTCCTCTCTCTCTTTC
*
506522 TTTTCTTTCTCTCTCTCTTTC
1 TTTTCTTCCTCTCTCTCTTTC
*
506543 -TTTCTCTCCTTTCTCTCTT
1 TTTTCT-TCCTCTCTCTCTT
506562 CACCATGGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
17 6 0.09
18 9 0.14
19 10 0.15
20 7 0.11
21 20 0.31
22 1 0.02
23 12 0.18
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTCTTCCTCTCTCTCTTTC
Found at i:506559 original size:9 final size:9
Alignment explanation
Indices: 506494--506558 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 9
506484 CTTTTCTTTA
*
506494 TCTCTCCTT
1 TCTCTTCTT
506503 TCT-TTC-T
1 TCTCTTCTT
506510 TCTCTTTCTT
1 TCTC-TTCTT
*
506520 TCTTTTCTT
1 TCTCTTCTT
*
506529 TCTC-TCTC
1 TCTCTTCTT
506537 TCT-TTCTT
1 TCTCTTCTT
*
506545 TCTCTCCTT
1 TCTCTTCTT
506554 TCTCT
1 TCTCT
506559 CTTCACCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
7 4 0.09
8 14 0.31
9 23 0.51
10 4 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (9 bp):
TCTCTTCTT
Found at i:509401 original size:23 final size:23
Alignment explanation
Indices: 509370--509414 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
509360 CGGTGGGCGA
* *
509370 AGGTGGCGAGTTCCCAATATATG
1 AGGTAGCGAGTTCCCAACATATG
509393 AGGTAGCGAGTTCCCAACATAT
1 AGGTAGCGAGTTCCCAACATAT
509415 ATTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (23 bp):
AGGTAGCGAGTTCCCAACATATG
Found at i:509672 original size:2 final size:2
Alignment explanation
Indices: 509665--509698 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
509655 AGCTCCCAAC
509665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
509699 TTTAGGTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513283 original size:88 final size:88
Alignment explanation
Indices: 513170--513844 Score: 696
Period size: 88 Copynumber: 7.7 Consensus size: 88
513160 ATTAGGCGAG
* * * * * *
513170 TATGCATCTATCACATCTTTCGGGTTCTAAAAAATTTATTAGGCATTTGTCAAATATTTTCTATC
1 TATGCATCTATCACTTCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTATC
* *
513235 GTGTTAGAAGAAATTTGATACCC
66 GTGTCAGAAGGAATTTGATACCC
* * *
513258 TATGCATCTGTCACTTTTTTTGGGTTCCAAAAAATTTATTACGCATTAGTCAAATATTTT-TATC
1 TATGCATCTATCACTTCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTATC
* *
513322 ATGTCAGAAGGAATCTGATACCC
66 GTGTCAGAAGGAATTTGATACCC
* * ** * *
513345 TATGCGTCTATCACGTCTTTTGGGTTTTAACAAATTTATTAGGCATTAGTCAAATATTTTCTATC
1 TATGCATCTATCACTTCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTATC
* *
513410 GTATCAGAAGGAATTTGATACCT
66 GTGTCAGAAGGAATTTGATACCC
* * *
513433 TATGCATCTATCA-TATTTTTTGGGTTTCAAGAAATTTATTACGCATTAGTCAAATATTTTTTAT
1 TATGCATCTATCACT-TCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTAT
* * * *
513497 TGTGTTAGAAGAAATTTGATATCC
65 CGTGTCAGAAGGAATTTGATACCC
* * * * *
513521 TATACATCTATCACATCTTTTGGGTTCCAAGAAATTTAATAGGCATTAGTGAAATATTTTCTATC
1 TATGCATCTATCACTTCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTATC
* * * **
513586 ATGTCAGAAGGAATCTGAAATTGC
66 GTGTCAGAAGGAATTTGATA-CCC
* * * * *
513610 -ATGCATTTGTCA-TATCTTTTGGATTCCAAGAAATTTATTACACATTAGTCAAATATTTTCTGT
1 TATGCATCTATCACT-TCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTAT
*
513673 CGTGTCAAAAGGAATTTGATACCC
65 CGTGTCAGAAGGAATTTGATACCC
** * * * ** * * * *
513697 TATATATCTATCGCATCTTTCGCTTTCCAAGAAATTTATTAGGCATTAGTTAAATAGTTTCTGTC
1 TATGCATCTATCACTTCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTATC
* * *
513762 ATGTCAGAAGGAATCTGATA-TC
66 GTGTCAGAAGGAATTTGATACCC
* * * * *
513784 TCATGCATCTGTTA-TATCTTTTGGGTTCCAGGAAATTTATTACGCATTAGTTAAATCTTTT
1 T-ATGCATCTATCACT-TCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTT
513845 GGGTTTTAAA
Statistics
Matches: 481, Mismatches: 97, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
87 78 0.16
88 401 0.83
89 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (88 bp):
TATGCATCTATCACTTCTTTTGGGTTCCAAGAAATTTATTACGCATTAGTCAAATATTTTCTATC
GTGTCAGAAGGAATTTGATACCC
Found at i:513595 original size:176 final size:176
Alignment explanation
Indices: 513174--513844 Score: 819
Period size: 176 Copynumber: 3.8 Consensus size: 176
513164 GGCGAGTATG
* * * *
513174 CATCTATCACATCTTTCGGGTTCTAAAAAATTTATTAGGCATTTGTCAAATATTTTCTATCGTGT
1 CATCTATCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGT
* * * * * *
513239 TAGAAGAAATTTGATACCCTATGCATCTGTCACT-TTTTTTGGGTTCCAAAAAATTTATTACGCA
66 CAGAAGGAATCTGATACCTTATGCATCTGTCA-TATCTTTTGGGTTCCAAGAAATTTATTACGCA
* * *
513303 TTAGTCAAATA-TTTTTATCATGTCAGAAGGAATCTGATACCCTATG
130 TTAGTCAAATATTTTTTATCGTGTCAGAAGGAATTTGATACCCTATA
* * * ** * * *
513349 CGTCTATCACGTCTTTTGGGTTTTAACAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTAT
1 CATCTATCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGT
* * * *
513414 CAGAAGGAATTTGATACCTTATGCATCTATCATATTTTTTGGGTTTCAAGAAATTTATTACGCAT
66 CAGAAGGAATCTGATACCTTATGCATCTGTCATATCTTTTGGGTTCCAAGAAATTTATTACGCAT
* * * *
513479 TAGTCAAATATTTTTTATTGTGTTAGAAGAAATTTGATATCCTATA
131 TAGTCAAATATTTTTTATCGTGTCAGAAGGAATTTGATACCCTATA
* * *
513525 CATCTATCACATCTTTTGGGTTCCAAGAAATTTAATAGGCATTAGTGAAATATTTTCTATCATGT
1 CATCTATCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGT
* * * *
513590 CAGAAGGAATCTGA-A-ATTGCATGCATTTGTCATATCTTTTGGATTCCAAGAAATTTATTACAC
66 CAGAAGGAATCTGATACCTT--ATGCATCTGTCATATCTTTTGGGTTCCAAGAAATTTATTACGC
* * *
513653 ATTAGTCAAATATTTTCTGTCGTGTCAAAAGGAATTTGATACCCTATA
129 ATTAGTCAAATATTTTTTATCGTGTCAGAAGGAATTTGATACCCTATA
* * ** * * *
513701 TATCTATCGCATCTTTCGCTTTCCAAGAAATTTATTAGGCATTAGTTAAATAGTTTCTGTCATGT
1 CATCTATCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGT
* * * *
513766 CAGAAGGAATCTGATATCTCATGCATCTGTTATATCTTTTGGGTTCCAGGAAATTTATTACGCAT
66 CAGAAGGAATCTGATACCTTATGCATCTGTCATATCTTTTGGGTTCCAAGAAATTTATTACGCAT
* *
513831 TAGTTAAATCTTTT
131 TAGTCAAATATTTT
513845 GGGTTTTAAA
Statistics
Matches: 428, Mismatches: 62, Indels: 11
0.85 0.12 0.02
Matches are distributed among these distances:
174 3 0.01
175 126 0.29
176 297 0.69
177 1 0.00
178 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (176 bp):
CATCTATCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGT
CAGAAGGAATCTGATACCTTATGCATCTGTCATATCTTTTGGGTTCCAAGAAATTTATTACGCAT
TAGTCAAATATTTTTTATCGTGTCAGAAGGAATTTGATACCCTATA
Found at i:513708 original size:264 final size:263
Alignment explanation
Indices: 513174--513844 Score: 792
Period size: 264 Copynumber: 2.5 Consensus size: 263
513164 GGCGAGTATG
* * * *
513174 CATCTATCACATCTTTCGGG-TTCTAAAAAATTTATTAGGCATTTGTCAAATATTTTCTATCGTG
1 CATCTATCACATTTTTTGGGTTTC-AAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTG
* * * *
513238 TTAGAAGAAATTTGATACCCTATGCATCTGTCACTTTTTTTGGGTTCCAAAAAATTTATTACGCA
65 TTAGAAGAAATTTGATATCCTATGCATCTGTCACATCTTTTGGGTTCCAAGAAATTTATTACGCA
* * *
513303 TTAGTCAAATATTTTTATCATGTCAGAAGGAATCTGATACCCTATGCGTCTATCACGTCTTTTGG
130 TTAGTCAAATATTTTTATCATGTCAGAAGGAATCTGAAACCCTATGCATCTATCACATCTTTTGG
* ** ** * *
513368 GTTTTAACAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTATCAGAAGGAATTTGATACCT
195 ATTCCAACAAATTTATTACACATTAGTCAAATATTTTCTATCGTATCAAAAGGAATTTGATACCC
*
513433 TATG
260 TATA
* * * *
513437 CATCTATCATATTTTTTGGGTTTCAAGAAATTTATTACGCATTAGTCAAATATTTTTTATTGTGT
1 CATCTATCACATTTTTTGGGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGT
* * * *
513502 TAGAAGAAATTTGATATCCTATACATCTATCACATCTTTTGGGTTCCAAGAAATTTAATAGGCAT
66 TAGAAGAAATTTGATATCCTATGCATCTGTCACATCTTTTGGGTTCCAAGAAATTTATTACGCAT
* ** * * *
513567 TAGTGAAATATTTTCTATCATGTCAGAAGGAATCTGAAATTGC-ATGCATTTGTCATATCTTTTG
131 TAGTCAAATATTTT-TATCATGTCAGAAGGAATCTGAAA-CCCTATGCATCTATCACATCTTTTG
* * *
513631 GATTCCAAGAAATTTATTACACATTAGTCAAATATTTTCTGTCGTGTCAAAAGGAATTTGATACC
194 GATTCCAACAAATTTATTACACATTAGTCAAATATTTTCTATCGTATCAAAAGGAATTTGATACC
513696 CTATA
259 CTATA
* * * * * * * * *
513701 TATCTATCGCA-TCTTTCGCTTTCCAAGAAATTTATTAGGCATTAGTTAAATAGTTTCTGTCATG
1 CATCTATCACATTTTTTGGGTTT-CAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTG
* * * * * *
513765 TCAGAAGGAATCTGATAT-CTCATGCATCTGTTATATCTTTTGGGTTCCAGGAAATTTATTACGC
65 TTAGAAGAAATTTGATATCCT-ATGCATCTGTCACATCTTTTGGGTTCCAAGAAATTTATTACGC
* *
513829 ATTAGTTAAATCTTTT
129 ATTAGTCAAATATTTT
513845 GGGTTTTAAA
Statistics
Matches: 342, Mismatches: 61, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
263 133 0.39
264 208 0.61
265 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (263 bp):
CATCTATCACATTTTTTGGGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGT
TAGAAGAAATTTGATATCCTATGCATCTGTCACATCTTTTGGGTTCCAAGAAATTTATTACGCAT
TAGTCAAATATTTTTATCATGTCAGAAGGAATCTGAAACCCTATGCATCTATCACATCTTTTGGA
TTCCAACAAATTTATTACACATTAGTCAAATATTTTCTATCGTATCAAAAGGAATTTGATACCCT
ATA
Found at i:517413 original size:8 final size:8
Alignment explanation
Indices: 517388--517433 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
517378 TATTTTCAAA
517388 TTTTTA-T
1 TTTTTATT
* *
517395 TTTGTACT
1 TTTTTATT
517403 TTTTTATT
1 TTTTTATT
517411 TTTTTGATT
1 TTTTT-ATT
517420 TTTTTATT
1 TTTTTATT
517428 TTTTTA
1 TTTTTA
517434 GAAAATGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 5 0.15
8 21 0.62
9 8 0.24
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:520406 original size:632 final size:628
Alignment explanation
Indices: 518799--521252 Score: 1956
Period size: 635 Copynumber: 3.9 Consensus size: 628
518789 GATACTTATA
* * * * ** * * *
518799 TTTGAAACCACATTGCATTAGTGAAATGAAACTACCAAATGCTTTGTTTATGAAGAACAAAAGTA
1 TTTGAAACCACTTTACACTAGTGAAATGAAACCA-TTAACGTTTTGTTTATG-AGGACAAAAGTA
* * * * *
518864 TCTTTCTTATAGTTAATTTTCTATAGCAAATGAAGTGCAAAAGACTTGCTTC-AATTTAGAATGA
64 TTTTTCTTCTAGTTAATTTTCTATAACAAATGAAGTACAAAAGACTT-C--CAAATTAAGAATGA
** *
518928 TAAAGAAAGAAGAATAATGCTATATATTTCTCATTGTT-TTTGTTGGAAAATTATGATCTCTATT
126 TAAAGAAA-AAGAGCAATGCTATATATTTCTCATT-TTCTTTATTGGAAAATTATGATCTCTATT
* * * *
518992 TATAGAA-ATTCAATCAAGAGTTATATTGTTTTTATCCAACCAACTTATATTTTCATTAAGTTTC
189 TATA-AAGATTCAATCAAAAGTTATGTTATTTTTATCCAACCAACTTATATTTACATTAAGTTTC
* ** * * ** * * * *
519056 CACCTTTTAGTACTTTATAGGTGCCATTGGCAACCTTTTATCGATGAAAAGATGTCACTTGAAAA
253 CACCTTTTAGTACTTAATAAATACCATTAGCAACCTTCCACCAATG-AAAGATGTCACCTAAAAA
* * * * *
519121 GGTATGAATGAAGCTAGAACAAACCT-AAACAAAGCTAATTGTTACAGATAAATCTATTA-AAAT
317 AGTATGAATAAAG-T--TA-AAA--TGAAAC-TAGCTAA---TTACAGATAAATCTAATAGAAAT
** * * * * *
519184 TTGAAA-TGTGAGAGTCAAATCCTTAACTC-AGGAGA-TCTA-GTATCTTTTTGTAAATTTTAAC
372 TT-AAACTACGAGATTCAAATCCTTAACTCAAGGA-ATTTTATTTTTCTTTTTATAAATTTTAAC
* * * * * * * *
519245 AAAACACATTCCAAAACTCGATATTTGAATCCTTCTAAATGAGTATACTAATCCTTTTATATAAT
435 AAAACACATTTCAAAACCCGGTATTCGAATCTTTCTATACGAGTATACGAATCCTTTTATATAAT
* * * * *
519310 TTATAACATAAGCTTATTTTTCATTCCAAAACTAATGAGATATTAATCCCAATTTCTTTTAGACT
500 TTATAACAAAAGCTTATTTTTCATTCCAAAACTCATGAGATATAAAT-CCAATTTCCTTTAGGCT
* * *
519375 TATCCCTCTATTAGTAATGATATGTAATAGAGGTTATCTAATAGCC-A-CATAACATAATGCCTA
564 TATCCCTCTATTAGTAATGATATG-AATAGGGGTTATCGAATAGCCAAGCAT-ACATGATGCCTA
519438 TG
627 TG
** * * * * *
519440 TTTGAAACCACTTTGTACTAGTGAAATGAAGCTATTAAATGTTTTGTTTATGAAGGATAAAAGCA
1 TTTGAAACCACTTTACACTAGTGAAATGAAACCATT-AACGTTTTGTTTATG-AGGACAAAAGTA
* * ** * *
519505 TTTTTTTTCTCA-TTAATTTTTTGCAACAAATGAAGTACAAAAGACTTGCTCCAATTAAGAAAGA
64 TTTTTCTTCT-AGTTAATTTTCTATAACAAATGAAGTACAAAAGACTT-C-CAAATTAAGAATGA
* * * * *
519569 TAAGGGAAGGAAA-AACAATGCTATATATTTTTCATTTTCTTTGTTGGAAAATTATGATCTCTAG
126 TAA-AGAA--AAAGAGCAATGCTATATATTTCTCATTTTCTTTATTGGAAAATTATGATCTCTAT
* * * * * * *
519633 TTATAGAGATTTAATCAAAAATTGTGTCATTTTTATCCAACCAACTTATCTTTACATCAAGTTTC
188 TTATAAAGATTCAATCAAAAGTTATGTTATTTTTATCCAACCAACTTATATTTACATTAAGTTTC
* * ** * * **
519698 CACCTTTTCGTACTTAGTGGATGCCATTGGCAACCTTCCACCAATGGAAAGATGTCA-CTTGAAA
253 CACCTTTTAGTACTTAATAAATACCATTAGCAACCTTCCACCAAT-GAAAGATGTCACCTAAAAA
* * *
519762 AGATATGAATAAAGTTAAAATGAAACTAGCT-ATTATAGATGAATCTAATAG-AATTTAAACTAT
317 AG-TATGAATAAAGTTAAAATGAAACTAGCTAATTACAGATAAATCTAATAGAAATTTAAACTAC
* * * * *
519825 GAGATTCGAATCCTTAACTCAAGGAATTTTGATTTTTTTTTTTGTAAATTTTAACAGAATACATT
381 GAGATTCAAATCCTTAACTCAAGGAATTTT-ATTTTTCTTTTTATAAATTTTAACAAAACACATT
* *** * * * * ** *
519890 TTAAAATTTGGTATT-TAGATCATTCTATACGGGTATATGAATTTTTTTATATAATTTATAACAG
445 TCAAAACCCGGTATTCGA-ATCTTTCTATACGAGTATACGAATCCTTTTATATAATTTATAACAA
*
519954 AAGCTTATTTTTCATTCCAAAACTCATGAGATATAAATCCAACTTTCCTCTAGGCTTAT-CCTCT
509 AAGCTTATTTTTCATTCCAAAACTCATGAGATATAAATCCAA-TTTCCTTTAGGCTTATCCCTCT
* * * *
520018 ATTAATAATAATATGAGTAGGGGTTTTCGAATAGCCATAGCATACAGTGATGCCTATG
573 ATTAGTAATGATATGAATAGGGGTTATCGAATAGCCA-AGCATACA-TGATGCCTATG
* *
520076 TTTGAAACCACTTTACACTAAGTGAAATAAAACCATTGAACGTTTTGTTTATGAGGAACAAAATT
1 TTTGAAACCACTTTACACT-AGTGAAATGAAACCATT-AACGTTTTGTTTATGAGG-ACAAAAGT
* * * *
520141 ATTTTTCTTCTAGTTAATTTTCTATAATAAATGGAAGTACAAGAGACTT-C-ATTTAAGAATGCT
63 ATTTTTCTTCTAGTTAATTTTCTATAACAAAT-GAAGTACAAAAGACTTCCAAATTAAGAATGAT
*
520204 AGGAA-AAAAAGAGCAATGTTATATATTTCTCA-TTTCTTTATTAGG-AAATTATGATCTCTATT
127 A--AAGAAAAAGAGCAATGCTATATATTTCTCATTTTCTTTATT-GGAAAATTATGATCTCTATT
* * * * * * * *
520266 TATAAAGATTCAATTAAAAGTTATTTTGTTTCTATCTAACCAACTTATATTCACATTGATTTTCC
189 TATAAAGATTCAATCAAAAGTTATGTTATTTTTATCCAACCAACTTATATTTACATTAAGTTTCC
* * * ** *
520331 ACCTTTTAGTACTCAACAAATACCATTAGCAGCCTTTTACCAATGCAAAGATGTTACCTAAAAAA
254 ACCTTTTAGTACTTAATAAATACCATTAGCAACCTTCCACCAATG-AAAGATGTCACCTAAAAAA
* * ** * * * * * *
520396 GTATGAATAAATTTAAAA-GAAACTA-ATGGTTACAGATGAAT-TTATTGAAATTTGAATTGCGA
318 GTATGAATAAAGTTAAAATGAAACTAGCTAATTACAGATAAATCTAATAGAAATTTAAACTACGA
* ** * ** * *
520458 GATTCAAATCCTTGACTCAAAGG-ATTAAGATCCTTTTTTTTTTTATAAATTTTAGTAGAACATA
383 GATTCAAATCCTTAACTC-AAGGAATT----TTATTTTTCTTTTTATAAATTTTAACAAAACACA
** * * * *
520522 TTTCAAAACCCCTTATGCGAATCTTTCTATATGGGTATACGAATACTTTTATATAATTTATAACA
443 TTTCAAAACCCGGTATTCGAATCTTTCTATACGAGTATACGAATCCTTTTATATAATTTATAACA
* * * * * *
520587 AAAGCTTATTTTTCATTCAAAAACTCATGAGATGTCAATCCCATTTCCTTTAGGTTTATCCCTCC
508 AAAGCTTATTTTTCATTCCAAAACTCATGAGATATAAATCCAATTTCCTTTAGGCTTATCCCTCT
* * * *
520652 ACTAGTAATGATATTCAATAGGGATTATCGAATAGCCACAAG-ATACAATGATGCTTATG
573 ATTAGTAATGATA-TGAATAGGGGTTATCGAATAG-C-CAAGCATAC-ATGATGCCTATG
** * *
520711 TTTGAAATAACTTTACACTAGTGAAATGAAACCATTAAC-TACTTTG-TTA--ACGAAAAATAG-
1 TTTGAAACCACTTTACACTAGTGAAATGAAACCATTAACGT--TTTGTTTATGAGGACAAA-AGT
* * * * *
520771 ATCTTTT-TTCTAGTTAATTTT-TTTGCAACAAACGAAGTACAAAAAACTTGCTTAAATTGAGAA
63 AT-TTTTCTTCTAGTTAATTTTCTAT--AACAAATGAAGTACAAAAGACTT-C-CAAATTAAGAA
* * * *
520834 TGATAAAGAAGGAAGAGCAATGCTATATATTTTTCATTTTCTCTATTGGAAAATAATGATCTCTA
123 TGATAAAGAA-AAAGAGCAATGCTATATATTTCTCATTTTCTTTATTGGAAAATTATGATCTCTA
* * * *
520899 TTTATAGAGATTCAATCAAGAGTTATGTTATTTTTATCTAACCAA-TT-TA--T-C-TTGAGTTT
187 TTTATAAAGATTCAATCAAAAGTTATGTTATTTTTATCCAACCAACTTATATTTACATTAAGTTT
* * * * * * * * * *
520958 TCATCTTTTGGTACTGAATTAGTGA-TATTAGCAATCTTCCACTAATGAAAGGATGTCACTTAAA
252 CCACCTTTTAGTACTTAATAAAT-ACCATTAGCAACCTTCCACCAATGAAA-GATGTCACCTAAA
* * ** * * * * * *
521022 AAAGTATGAATGAAGTTAAAACGGCACTAG-TAATTATATATAAATAT-ATTGAAATTTGAACAA
315 AAAGTATGAATAAAGTTAAAATGAAACTAGCTAATTACAGATAAATCTAATAGAAATTTAAACTA
* * * *
521085 CGAGATTCGAATCCTTAACTCACGGAATTTTAATTTTCTTTTTATAAATTTTAACAAAAAACATT
380 CGAGATTCAAATCCTTAACTCAAGGAATTTTATTTTTCTTTTTATAAATTTTAACAAAACACATT
** * * * * * * *
521150 TCAAAACCTAGTATTCGAGTCTTTCTATCCAAATATACAAATCTTTTTATATAATTTACAACAAA
445 TCAAAACCCGGTATTCGAATCTTTCTATACGAGTATACGAATCCTTTTATATAATTTATAACAAA
* * *
521215 AGCATATTTCTCATAT-CAAAACTCATGAGATATGAATC
510 AGCTTATTTTTCAT-TCCAAAACTCATGAGATATAAATC
521253 TCACAAATGG
Statistics
Matches: 1468, Mismatches: 278, Indels: 149
0.77 0.15 0.08
Matches are distributed among these distances:
626 109 0.07
627 1 0.00
628 3 0.00
629 74 0.05
630 91 0.06
631 64 0.04
632 184 0.13
633 74 0.05
634 222 0.15
635 241 0.16
636 44 0.03
637 64 0.04
638 18 0.01
639 1 0.00
640 2 0.00
641 115 0.08
642 157 0.11
643 3 0.00
644 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (628 bp):
TTTGAAACCACTTTACACTAGTGAAATGAAACCATTAACGTTTTGTTTATGAGGACAAAAGTATT
TTTCTTCTAGTTAATTTTCTATAACAAATGAAGTACAAAAGACTTCCAAATTAAGAATGATAAAG
AAAAAGAGCAATGCTATATATTTCTCATTTTCTTTATTGGAAAATTATGATCTCTATTTATAAAG
ATTCAATCAAAAGTTATGTTATTTTTATCCAACCAACTTATATTTACATTAAGTTTCCACCTTTT
AGTACTTAATAAATACCATTAGCAACCTTCCACCAATGAAAGATGTCACCTAAAAAAGTATGAAT
AAAGTTAAAATGAAACTAGCTAATTACAGATAAATCTAATAGAAATTTAAACTACGAGATTCAAA
TCCTTAACTCAAGGAATTTTATTTTTCTTTTTATAAATTTTAACAAAACACATTTCAAAACCCGG
TATTCGAATCTTTCTATACGAGTATACGAATCCTTTTATATAATTTATAACAAAAGCTTATTTTT
CATTCCAAAACTCATGAGATATAAATCCAATTTCCTTTAGGCTTATCCCTCTATTAGTAATGATA
TGAATAGGGGTTATCGAATAGCCAAGCATACATGATGCCTATG
Found at i:521973 original size:53 final size:53
Alignment explanation
Indices: 521912--522013 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
521902 ATCATTTCAA
*
521912 GTTCGGGTCATT-TAATATTCGAGTCAATCGGGTTTAACACTCAGGTTAATCAG
1 GTTCGGGTCATTCT-AGATTCGAGTCAATCGGGTTTAACACTCAGGTTAATCAG
* * *
521965 GTTCGGGTCATTCTAGATTCGAGTCAATTGGGTTTAACATTCGGGTTAA
1 GTTCGGGTCATTCTAGATTCGAGTCAATCGGGTTTAACACTCAGGTTAA
522014 ATCAAGTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 43 0.98
54 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (53 bp):
GTTCGGGTCATTCTAGATTCGAGTCAATCGGGTTTAACACTCAGGTTAATCAG
Found at i:522802 original size:16 final size:16
Alignment explanation
Indices: 522781--522827 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
522771 AATATTTTTA
522781 TCAATTCAAATTAAAT
1 TCAATTCAAATTAAAT
*
522797 TCAATTAAAATTAATAT
1 TCAATTCAAATTAA-AT
522814 T-AA-TC-AATTAAAT
1 TCAATTCAAATTAAAT
522827 T
1 T
522828 TTTTAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 3 0.11
14 6 0.21
15 1 0.04
16 15 0.54
17 3 0.11
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (16 bp):
TCAATTCAAATTAAAT
Found at i:525387 original size:23 final size:21
Alignment explanation
Indices: 525360--525402 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
525350 CTTAAATTTA
*
525360 AATTTTAATATTTATATTTTTTT
1 AATTTTAA-A-TTATAATTTTTT
525383 AATTTTAAATTATAATTTTT
1 AATTTTAAATTATAATTTTT
525403 AATGTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTTTAAATTATAATTTTTT
Found at i:525517 original size:8 final size:8
Alignment explanation
Indices: 525504--525546 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
525494 ATAATTAAAA
525504 TTATATAT
1 TTATATAT
525512 TTATATAT
1 TTATATAT
* *
525520 ATAGATAT
1 TTATATAT
525528 ATTATAT-T
1 -TTATATAT
525536 TTATATAT
1 TTATATAT
525544 TTA
1 TTA
525547 AAATTTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 19 0.66
9 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TTATATAT
Found at i:525739 original size:6 final size:6
Alignment explanation
Indices: 525728--525772 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
525718 TTAAATATTT
525728 TAAATA TAAATA TAAATA TAAATA TAAATA T-AATA -AATATA TAAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAA-ATA TAAA
525773 ATATGTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.14
6 29 0.81
7 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:525774 original size:9 final size:10
Alignment explanation
Indices: 525719--525776 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 10
525709 ATTAATTATT
*
525719 TAAATAT-TT
1 TAAATATATA
525728 TAAATATAAATA
1 TAAATAT--ATA
525740 TAAATATAAATA
1 TAAATAT--ATA
525752 TAAATATA-A
1 TAAATATATA
525761 TAAATATATA
1 TAAATATATA
525771 -AAATAT
1 TAAATAT
525777 GTTTGATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 22 0.50
10 2 0.05
12 20 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAATATATA
Found at i:525824 original size:11 final size:11
Alignment explanation
Indices: 525798--525838 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
525788 TATATTTAAA
*
525798 TATATATTTA-
1 TATATTTTTAT
525808 TATATTTTTAT
1 TATATTTTTAT
525819 TATATTTATT-T
1 TATATTT-TTAT
525830 TATATTTTT
1 TATATTTTT
525839 TAAAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 11 0.39
11 15 0.54
12 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:525846 original size:23 final size:24
Alignment explanation
Indices: 525795--525853 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
525785 AATTATATTT
*
525795 AAATATATA-TTTATATATTTTTA
1 AAATATTTATTTTATATATTTTTA
**
525818 TTATATTTATTTTATAT-TTTTTA
1 AAATATTTATTTTATATATTTTTA
*
525841 AAATATTAATTTT
1 AAATATTTATTTT
525854 TTCATCAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
AAATATTTATTTTATATATTTTTA
Found at i:526306 original size:46 final size:46
Alignment explanation
Indices: 526248--526339 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
526238 CTATTCACCA
526248 AAATAAATTTTTATAGGTATTGTTAAGTCTCATCCAATGCTTGTAG
1 AAATAAATTTTTATAGGTATTGTTAAGTCTCATCCAATGCTTGTAG
* *
526294 AAATGAATTTTTATAGGTATTGTTAAGTGTCATCCAATGCTTGTAG
1 AAATAAATTTTTATAGGTATTGTTAAGTCTCATCCAATGCTTGTAG
526340 TGTATTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (46 bp):
AAATAAATTTTTATAGGTATTGTTAAGTCTCATCCAATGCTTGTAG
Found at i:526691 original size:17 final size:17
Alignment explanation
Indices: 526657--526693 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
526647 ATATTTTAAA
*
526657 AATAAAAAAGTTACAAT
1 AATAAAAAAGTGACAAT
*
526674 AATAAAAAAGTGATAAT
1 AATAAAAAAGTGACAAT
526691 AAT
1 AAT
526694 TATGGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (17 bp):
AATAAAAAAGTGACAAT
Found at i:527749 original size:16 final size:15
Alignment explanation
Indices: 527702--527740 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
527692 AATAAAATAT
527702 TAATTTCAATTTAAAA
1 TAATTT-AATTTAAAA
527718 T-ATTTAATTTAAAAA
1 TAATTTAATTT-AAAA
527733 TAATTTAA
1 TAATTTAA
527741 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.24
15 9 0.43
16 7 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATTTAATTTAAAA
Found at i:527755 original size:23 final size:23
Alignment explanation
Indices: 527709--527768 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 23
527699 TATTAATTTC
527709 AATTTAAAATATTTAATTTAAAAAT
1 AATTT-AAAT-TTTAATTTAAAAAT
527734 AATTTAAATTTTAAATTT-AAAAT
1 AATTTAAATTTT-AATTTAAAAAT
*
527757 AATTTTAATTTT
1 AATTTAAATTTT
527769 TTTATTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 19 0.58
24 9 0.27
25 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTTAAATTTTAATTTAAAAAT
Found at i:527763 original size:24 final size:24
Alignment explanation
Indices: 527709--527769 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
527699 TATTAATTTC
*
527709 AATTTAAAATATTTAATTTAAAAAT
1 AATTTTAAAT-TTTAATTTAAAAAT
527734 AA-TTTAAATTTTAAATTT-AAAAT
1 AATTTTAAATTTT-AATTTAAAAAT
*
527757 AATTTTAATTTTT
1 AATTTTAAATTTT
527770 TTATTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 10 0.31
24 20 0.62
25 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTTTAAATTTTAATTTAAAAAT
Found at i:527924 original size:15 final size:14
Alignment explanation
Indices: 527884--527925 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
527874 TTTAAATATT
*
527884 TTAAAATATTAATA
1 TTAAAATATTAAAA
527898 -TAAAATTATTAAAA
1 TTAAAA-TATTAAAA
527912 CTTAAAATATTAAA
1 -TTAAAATATTAAA
527926 CTATATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 5 0.21
14 7 0.29
15 7 0.29
16 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATATTAAAA
Found at i:528267 original size:15 final size:15
Alignment explanation
Indices: 528235--528303 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 15
528225 AAATTCGATA
528235 ATAT-TAAATATAAT
1 ATATATAAATATAAT
528249 -TATATAAATATATTAT
1 ATATATAAATATA--AT
*
528265 ATATAATAAAAATAA-
1 ATAT-ATAAATATAAT
528280 A-ATA-AAATATAAT
1 ATATATAAATATAAT
528293 A-ATATAAATAT
1 ATATATAAATAT
528304 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
12 7 0.15
13 8 0.17
14 16 0.35
15 1 0.02
16 3 0.07
17 3 0.07
18 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATAAATATAAT
Found at i:528349 original size:26 final size:27
Alignment explanation
Indices: 528286--528350 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
528276 ATAAAATAAA
*
528286 ATATAATAATAT-AAATATTTTAAAAT
1 ATATAAAAATATAAAATATTTTAAAAT
* *
528312 TTATATAAATATAAAATATTTT-AAAT
1 ATATAAAAATATAAAATATTTTAAAAT
528338 ATA-AAAATATATA
1 ATATAAAA-ATATA
528351 TTATCATCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 3 0.09
26 20 0.62
27 9 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAAAAATATAAAATATTTTAAAAT
Found at i:529360 original size:29 final size:30
Alignment explanation
Indices: 529328--529392 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
529318 TAAAATTTTA
529328 AATTGATTTAATATTTATATTATA-TTAAT
1 AATTGATTTAATATTTATATTATATTTAAT
** * * * *
529357 AATTTTTTTTATCTTTTTGTTATATTTAAT
1 AATTGATTTAATATTTATATTATATTTAAT
529387 AATTGA
1 AATTGA
529393 AACTTTACAT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (30 bp):
AATTGATTTAATATTTATATTATATTTAAT
Found at i:529915 original size:2 final size:2
Alignment explanation
Indices: 529908--529934 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
529898 ATTGGAGGAA
529908 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
529935 TAGAATACGG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:530838 original size:24 final size:26
Alignment explanation
Indices: 530797--530863 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
530787 AGGATTTTGC
530797 ATGA-ATAAATAAAGTA-TTTAAAAT
1 ATGATATAAATAAAGTATTTTAAAAT
*
530821 ATGATATAAATACA-TATTTTAAAAT
1 ATGATATAAATAAAGTATTTTAAAAT
* *
530846 -TTATATAAATAAATTATT
1 ATGATATAAATAAAGTATT
530864 AATATATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 17 0.46
25 20 0.54
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (26 bp):
ATGATATAAATAAAGTATTTTAAAAT
Found at i:530863 original size:25 final size:25
Alignment explanation
Indices: 530797--530859 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
530787 AGGATTTTGC
530797 ATGA-ATAAATAAAGTA-TTTAAAAT
1 ATGATATAAATAAA-TATTTTAAAAT
*
530821 ATGATATAAATACATATTTTAAAAT
1 ATGATATAAATAAATATTTTAAAAT
*
530846 -TTATATAAATAAAT
1 ATGATATAAATAAAT
530860 TATTAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 18 0.53
25 16 0.47
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (25 bp):
ATGATATAAATAAATATTTTAAAAT
Found at i:530891 original size:33 final size:31
Alignment explanation
Indices: 530834--530896 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
530824 ATATAAATAC
* *
530834 ATATTTTAAAATTTATATAAATAAATTATTA
1 ATATATTAAAATTTATATAAATAAAATATTA
530865 ATATATTAAAATTTATATAAATATAAAATATT
1 ATATATTAAAATTTATAT-AA-ATAAAATATT
530897 TTAAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 17 0.61
32 2 0.07
33 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATATTAAAATTTATATAAATAAAATATTA
Found at i:533072 original size:7 final size:7
Alignment explanation
Indices: 533063--533096 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
533053 GCACCTGCAC
*
533063 GTGCCAC
1 GTGCCAA
533070 GTGCCAA
1 GTGCCAA
533077 GTGCCAA
1 GTGCCAA
533084 GTGCCAA
1 GTGCCAA
533091 GTGCCA
1 GTGCCA
533097 TATAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.24, C:0.32, G:0.29, T:0.15
Consensus pattern (7 bp):
GTGCCAA
Found at i:538387 original size:7 final size:7
Alignment explanation
Indices: 538375--538401 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
538365 GCACCTGCAC
538375 GTGCCAA
1 GTGCCAA
538382 GTGCCAA
1 GTGCCAA
538389 GTGCCAA
1 GTGCCAA
538396 GTGCCA
1 GTGCCA
538402 TATAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (7 bp):
GTGCCAA
Found at i:544801 original size:18 final size:19
Alignment explanation
Indices: 544765--544803 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
544755 TAGACCTAAA
544765 TGTATTGATACATAAGTGAT
1 TGTATTGATACA-AAGTGAT
544785 TGTATTGATAC-AAGTGAT
1 TGTATTGATACAAAGTGAT
544803 T
1 T
544804 ATATCGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (19 bp):
TGTATTGATACAAAGTGAT
Found at i:546665 original size:13 final size:13
Alignment explanation
Indices: 546624--546710 Score: 79
Period size: 13 Copynumber: 7.5 Consensus size: 13
546614 CCGTTACAAG
546624 CAATGTATCGATA
1 CAATGTATCGATA
546637 CAAT-T-TC-AT-
1 CAATGTATCGATA
546646 C-ATGTATCGATA
1 CAATGTATCGATA
546658 CAATGTATCGATA
1 CAATGTATCGATA
546671 C-A--T-T-G-TA
1 CAATGTATCGATA
*
546678 CCATGTATCGATA
1 CAATGTATCGATA
546691 CAATGTATCGATA
1 CAATGTATCGATA
*
546704 CATTGTA
1 CAATGTA
546711 CCATGTATCG
Statistics
Matches: 61, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
7 3 0.05
8 4 0.07
9 3 0.05
10 6 0.10
11 5 0.08
12 4 0.07
13 36 0.59
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:546685 original size:20 final size:20
Alignment explanation
Indices: 546660--546725 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
546650 TATCGATACA
546660 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
546680 ATGTATCGATAC-----A--
1 ATGTATCGATACATTGTACC
546693 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
546713 ATGTATCGATACA
1 ATGTATCGATACA
546726 AACAGTGGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.31
15 1 0.03
18 1 0.03
20 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:546688 original size:33 final size:33
Alignment explanation
Indices: 546624--546726 Score: 172
Period size: 33 Copynumber: 3.1 Consensus size: 33
546614 CCGTTACAAG
*
546624 CAATGTATCGATACAATT-TCATCATGTATCGATA
1 CAATGTATCGATAC-ATTGT-ACCATGTATCGATA
546658 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
546691 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
546724 CAA
1 CAA
546727 ACAGTGGCAG
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
33 52 0.78
34 15 0.22
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGATA
Found at i:546799 original size:19 final size:19
Alignment explanation
Indices: 546756--546810 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
546746 TGCTAATCTT
*
546756 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGACC
*
546776 ATGTATCGATACAATGAGC
1 ATGTATCGATACAATGACC
546795 ATGTATCGATACAATG
1 ATGTATCGATACAATG
546811 TATCAATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGACC
Found at i:549357 original size:13 final size:13
Alignment explanation
Indices: 549323--549364 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
549313 AATAGTACCC
*
549323 CAATGTATTGATA
1 CAATGTATCGATA
* *
549336 TAATATATCGATA
1 CAATGTATCGATA
549349 CAATGTATCGATA
1 CAATGTATCGATA
549362 CAA
1 CAA
549365 GGAATGTTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:555574 original size:13 final size:13
Alignment explanation
Indices: 555533--555586 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
555523 CCGTTACAAG
555533 CAATGTATCGATA
1 CAATGTATCGATA
555546 CAAT-T-TC-AT-
1 CAATGTATCGATA
555555 C-ATGTATCGATA
1 CAATGTATCGATA
*
555567 CAATGTATCAATA
1 CAATGTATCGATA
*
555580 CATTGTA
1 CAATGTA
555587 CCATGTATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.12
11 4 0.12
12 2 0.06
13 20 0.59
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:555597 original size:33 final size:34
Alignment explanation
Indices: 555533--555603 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
555523 CCGTTACAAG
* *
555533 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCAATACAATTTCACCATGTATCGATA
555567 CAATGTATCAATAC-ATTGT-ACCATGTATCGATA
1 CAATGTATCAATACAATT-TCACCATGTATCGATA
555600 CAAT
1 CAAT
555604 AAGCATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 20 0.59
34 14 0.41
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (34 bp):
CAATGTATCAATACAATTTCACCATGTATCGATA
Done.