Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold201
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: 841227
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 75646 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:265042 original size:26 final size:24
Alignment explanation
Indices: 264986--265043 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
264976 AAATATACAT
264986 AAAATA-AATTATTAATACATAAA
1 AAAATATAATTATTAATACATAAA
**
265009 AATTTATAATTATTTAAATACATAAA
1 AAAATATAATTA-TT-AATACATAAA
265035 AAAATATAA
1 AAAATATAA
265044 ATACAAACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.14
24 5 0.18
25 2 0.07
26 17 0.61
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAATATAATTATTAATACATAAA
Found at i:272809 original size:97 final size:97
Alignment explanation
Indices: 272658--272891 Score: 362
Period size: 97 Copynumber: 2.4 Consensus size: 97
272648 TTTATTCCTC
* * * * ** *
272658 GGGATACTCCAACCCCATTCCTCCGAGGAGATACTCCAACTCTGCTTTTAAACTTGTCAAGATTC
1 GGGACACTCCAACCCCATTCCTCCAAGGGGATACTCCAACCCCACTTTCAAACTTGTCAAGATTC
*
272723 AAATCTTATTCTCGCTTAAATTGTCATCATCG
66 AAATCTTATTCTCGCTTAAATTGTCATCAACG
*
272755 GGGACACTCCAACCCCATTCCTTCAAGGGGATACTCCAACCCCACTTTCAAACTTGTCAAGATTC
1 GGGACACTCCAACCCCATTCCTCCAAGGGGATACTCCAACCCCACTTTCAAACTTGTCAAGATTC
272820 AAATCTTATTCTCGCTTAAATTGTCATCAACG
66 AAATCTTATTCTCGCTTAAATTGTCATCAACG
*
272852 GGGACACTCCAACCCCATTACTCCGAA-GGGATACTCCAAC
1 GGGACACTCCAACCCCATTCCTCC-AAGGGGATACTCCAAC
272892 TCTATTTTTT
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
97 123 0.98
98 2 0.02
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.27
Consensus pattern (97 bp):
GGGACACTCCAACCCCATTCCTCCAAGGGGATACTCCAACCCCACTTTCAAACTTGTCAAGATTC
AAATCTTATTCTCGCTTAAATTGTCATCAACG
Found at i:280041 original size:26 final size:26
Alignment explanation
Indices: 280012--280062 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
280002 ATAGTTGAAT
*
280012 GAGTGATATTAGAATAACATTTTCTA
1 GAGTGATATTAGAAGAACATTTTCTA
280038 GAGTGATATTAGAAGAACATTTTCT
1 GAGTGATATTAGAAGAACATTTTCT
280063 TCAACACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (26 bp):
GAGTGATATTAGAAGAACATTTTCTA
Found at i:281577 original size:169 final size:170
Alignment explanation
Indices: 281289--281625 Score: 495
Period size: 169 Copynumber: 2.0 Consensus size: 170
281279 AAAAGAGAAG
* *
281289 GTGATACAATAGTAATGTAAAAAAAAACTTATATTATTATCTTAATAAATTTCAAAACATCAAAC
1 GTGAAACAATAGTAATGT--AAAAAAACTTATAGTATTATCTTAATAAATTTCAAAACATCAAAC
*
281354 ATCAATCCATGATTTGTAATGAATTGTCAATTTTGCCTATATTCGAGTAATCAACCCTAGAAAGC
64 ATCAATCCATGATTTGTAATGAATTGTCAATTTTGCCTATATTCGAGCAATCAACCCTAGAAAGC
* * *
281419 TAACTTAATACACAATCACAATATCCAATCATAATACACAAT
129 CAACTAAATACACAATCACAATACCCAATCATAATACACAAT
*
281461 GTGAAACAATAGTAATGT-AAAAAACTTATAGTATTTTCTTAATAAATTTCAAAACATCAAACAT
1 GTGAAACAATAGTAATGTAAAAAAACTTATAGTATTATCTTAATAAATTTCAAAACATCAAACAT
* *
281525 -TATGCCATGATTTGTAATGAATTGTCAATTTCACT-CCTGT-TT-GAGCAATCAACCCTAGAAA
66 CAAT-CCATGATTTGTAATGAATTGTCAATTT---TGCCTATATTCGAGCAATCAACCCTAGAAA
*
281586 GCCAACTAAATACATAATCACAATACCCAATCATAATACA
127 GCCAACTAAATACACAATCACAATACCCAATCATAATACA
281626 AAATCATAAT
Statistics
Matches: 151, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
168 2 0.01
169 125 0.83
170 2 0.01
171 4 0.03
172 18 0.12
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (170 bp):
GTGAAACAATAGTAATGTAAAAAAACTTATAGTATTATCTTAATAAATTTCAAAACATCAAACAT
CAATCCATGATTTGTAATGAATTGTCAATTTTGCCTATATTCGAGCAATCAACCCTAGAAAGCCA
ACTAAATACACAATCACAATACCCAATCATAATACACAAT
Found at i:281630 original size:13 final size:13
Alignment explanation
Indices: 281594--281636 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
281584 AAGCCAACTA
* *
281594 AATACATAATCAC
1 AATACAAAATCAT
**
281607 AATACCCAATCAT
1 AATACAAAATCAT
281620 AATACAAAATCAT
1 AATACAAAATCAT
281633 AATA
1 AATA
281637 TATATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (13 bp):
AATACAAAATCAT
Found at i:281992 original size:16 final size:16
Alignment explanation
Indices: 281960--282004 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
281950 CCTAGCAACG
*
281960 ATTACTATAAT-AAAT
1 ATTATTATAATAAAAT
281975 A-TATTAATAATAAAAT
1 ATTATT-ATAATAAAAT
281991 ATTATTATAATAAA
1 ATTATTATAATAAA
282005 TTAATCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 6 0.23
16 13 0.50
17 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATTATAATAAAAT
Found at i:288031 original size:1 final size:1
Alignment explanation
Indices: 288025--288103 Score: 68
Period size: 1 Copynumber: 79.0 Consensus size: 1
288015 CCTTCTCTTC
** * * * * * *
288025 AAAAAAAAAGCAAAAAAAAAAAAACAAAAAAAAAAAAAACAAAACAAAGAAAAAGAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
288090 AATAAAAATAAAAA
1 AAAAAAAAAAAAAA
288104 TCTGCTTAAG
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.87, C:0.05, G:0.05, T:0.03
Consensus pattern (1 bp):
A
Found at i:288045 original size:15 final size:15
Alignment explanation
Indices: 288025--288091 Score: 84
Period size: 15 Copynumber: 4.5 Consensus size: 15
288015 CCTTCTCTTC
288025 AAAAAAAAAGCAAAA
1 AAAAAAAAAGCAAAA
288040 AAAAAAAAA-CAAAA
1 AAAAAAAAAGCAAAA
*
288054 AAAAAAAAAACAAAA
1 AAAAAAAAAGCAAAA
*
288069 CAAAGAAAAAG-AGAAA
1 -AAAAAAAAAGCA-AAA
288085 AAAAAAA
1 AAAAAAA
288092 TAAAAATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
14 14 0.30
15 21 0.46
16 11 0.24
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGCAAAA
Found at i:288057 original size:29 final size:30
Alignment explanation
Indices: 288025--288096 Score: 92
Period size: 29 Copynumber: 2.3 Consensus size: 30
288015 CCTTCTCTTC
*
288025 AAAAAAAAAGCAAAA-AAAAAAAAACAAAA
1 AAAAAAAAAACAAAACAAAAAAAAACAAAA
*
288054 AAAAAAAAAACAAAACAAAGAAAAAGAGAAAA
1 AAAAAAAAAACAAAACAAA-AAAAA-ACAAAA
288086 AAAAAATAAAA
1 AAAAAA-AAAA
288097 ATAAAAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 14 0.38
30 3 0.08
31 5 0.14
32 11 0.30
33 4 0.11
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.01
Consensus pattern (30 bp):
AAAAAAAAAACAAAACAAAAAAAAACAAAA
Found at i:288077 original size:20 final size:19
Alignment explanation
Indices: 288025--288103 Score: 81
Period size: 19 Copynumber: 4.1 Consensus size: 19
288015 CCTTCTCTTC
*
288025 AAAAAA-AAAGCAAAAAAA
1 AAAAAACAAAGAAAAAAAA
*
288043 AAAAAACAAAAAAAAAAAA
1 AAAAAACAAAGAAAAAAAA
*
288062 AACAAAACAAAGAAAAAGAGA
1 AA-AAAACAAAGAAAAA-AAA
*
288083 AAAAAA-AAATAAAAATAAA
1 AAAAAACAAAGAAAAA-AAA
288102 AA
1 AA
288104 TCTGCTTAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.12
19 24 0.47
20 17 0.33
21 4 0.08
ACGTcount: A:0.87, C:0.05, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAAACAAAGAAAAAAAA
Found at i:289148 original size:26 final size:26
Alignment explanation
Indices: 289118--289372 Score: 88
Period size: 26 Copynumber: 9.3 Consensus size: 26
289108 AAGTTGGTGG
*
289118 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
289144 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
289173 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
289199 CACCTTTCAAAGCCCACCCAAGTTGGTGG-
1 CACCTTTC--AGTCCA-CAAAG-AGCAGGA
* *
289228 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
289254 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
289283 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
289309 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
289338 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
289364 CACCTTTCA
1 CACCTTTCA
289373 AAGCCCACAC
Statistics
Matches: 157, Mismatches: 51, Indels: 42
0.63 0.20 0.17
Matches are distributed among these distances:
25 12 0.08
26 42 0.27
27 27 0.17
28 33 0.21
29 31 0.20
30 12 0.08
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:289155 original size:55 final size:55
Alignment explanation
Indices: 289065--289980 Score: 1206
Period size: 55 Copynumber: 16.4 Consensus size: 55
289055 TCTCCTTCCG
* *
289065 CTTTTTAGTCCTCAAAGAGTAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
289120 CCTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * *
289175 CCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
289230 -TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
289285 CCTTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
289340 CCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
289395 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCATATAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
289450 -TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
289505 -TTTTCCAGTCCTCAAAAAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
289560 -TTTTCCAATCCTCAAAGAGCAGGGCACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
289615 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
289676 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
289731 -TTTTCCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
289786 TTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
289847 CCTTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * *
289902 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
289957 CTTTTTACTCCTCAATGAGAAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
289981 TACACTTTAT
Statistics
Matches: 782, Mismatches: 56, Indels: 46
0.88 0.06 0.05
Matches are distributed among these distances:
54 15 0.02
55 654 0.84
56 15 0.02
57 2 0.00
59 2 0.00
61 94 0.12
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (55 bp):
CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:289298 original size:29 final size:29
Alignment explanation
Indices: 289266--289353 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
289256 CCTCTTAAAG
289266 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
289295 CCCA-A-AGAG-CAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
289321 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
289350 CCCA
1 CCCA
289354 AAGAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:289904 original size:29 final size:28
Alignment explanation
Indices: 289824--289906 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 28
289814 TTTTCTTTTC
289824 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
* * **
289852 -CAGTCCC-CA-AAG-AGCAGGACACCTCTT
1 AAAG-CCCACACAAGTTGGTGG-CACCT-TT
289879 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
289907 CAGTCCTCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
25 3 0.08
26 8 0.20
27 9 0.22
28 9 0.22
29 8 0.20
30 3 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.19
Consensus pattern (28 bp):
AAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:290887 original size:13 final size:13
Alignment explanation
Indices: 290869--290894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
290859 CATTTTTCTG
290869 TGTATCGATACAT
1 TGTATCGATACAT
290882 TGTATCGATACAT
1 TGTATCGATACAT
290895 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:290891 original size:33 final size:33
Alignment explanation
Indices: 290849--290915 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
290839 GCCAAGGAAA
***
290849 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
290882 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
290915 T
1 T
290916 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:293432 original size:28 final size:27
Alignment explanation
Indices: 293368--293436 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
293358 CTTCACAATC
* *
293368 GGGGATACTCTAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
293395 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
293423 GGGGATACTCCAAC
1 GGGGATACTCCAAC
293437 TCAGGTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:293484 original size:52 final size:51
Alignment explanation
Indices: 293423--293592 Score: 157
Period size: 52 Copynumber: 3.3 Consensus size: 51
293413 TTATTTCTGA
*
293423 GGGGATACTCCAACTCAGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCAGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
* ** * **
293475 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACT-CAGGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * * *
293527 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCAGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
293579 GAGGATACTCCAAC
1 GGGGATACTCCAAC
293593 CTCGTTATTC
Statistics
Matches: 94, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
51 8 0.09
52 71 0.76
53 10 0.11
54 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCAGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:293612 original size:28 final size:28
Alignment explanation
Indices: 293576--293652 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
293566 ATTTTTCACA
* *
293576 ATCGAGGATACTCCAACCTCGTTA-TTCC
1 ATCGGGGATACTCCAACCCCGTTACTT-C
293604 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
293632 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
293653 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 41 0.93
29 2 0.05
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:293621 original size:212 final size:212
Alignment explanation
Indices: 293254--293648 Score: 625
Period size: 212 Copynumber: 1.9 Consensus size: 212
293244 TTATCAATTC
* *
293254 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
293319 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCTAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
293384 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCAGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCTGAGGGGATACTCCAACTCAGGTTTTATC
293449 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
293466 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
293530 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
293593 CTCGTTATTCCATCGGGGATACTCCAACCCCGTTACTTCTGAGGGGATACTCCAAC
129 CCCGTTAAT-CATCGGGGATACTCCAACCCCGTTACTTCTGAGGGGATACTCCAAC
293649 CCCGGCTTTA
Statistics
Matches: 167, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 31 0.19
212 101 0.60
213 35 0.21
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCTGAGGGGATACTCCAACTCAGGTTTTATC
GCTAAAACACTAATTTT
Found at i:296782 original size:22 final size:20
Alignment explanation
Indices: 296743--296784 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
296733 GCATGATCTA
*
296743 GGTGCTTATATTTGATTTTT
1 GGTGCTTATATTTAATTTTT
296763 GGTGCTTATATATATAATTTTT
1 GGTGCTTATAT-T-TAATTTTT
296785 TTTCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.21, C:0.05, G:0.17, T:0.57
Consensus pattern (20 bp):
GGTGCTTATATTTAATTTTT
Found at i:297760 original size:20 final size:20
Alignment explanation
Indices: 297735--297782 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
297725 AATTTCATGC
297735 ATCGATACATTTCAAGGTGT
1 ATCGATACATTTCAAGGTGT
297755 ATCGATACATTTCAAGGTGT
1 ATCGATACATTTCAAGGTGT
297775 ATCGATAC
1 ATCGATAC
297783 TATGAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (20 bp):
ATCGATACATTTCAAGGTGT
Found at i:300224 original size:33 final size:33
Alignment explanation
Indices: 300187--300253 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
300177 GTTACAAGCT
300187 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
300220 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
300253 A
1 A
300254 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:300225 original size:13 final size:13
Alignment explanation
Indices: 300207--300237 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
300197 ACATTTCTTC
300207 ATGTATCGATACA
1 ATGTATCGATACA
300220 ATGTATCGATACA
1 ATGTATCGATACA
*
300233 TTGTA
1 ATGTA
300238 CCATGTATCG
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:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:300368 original size:33 final size:32
Alignment explanation
Indices: 300304--300368 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
300294 CAATTTGTCC
* *
300304 ATGTATCGATGCAATGAACATATATCGATACA
1 ATGTATCGATACAAAGAACATATATCGATACA
* *
300336 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATATATCGATACA
300369 TCTGGGTGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATATATCGATACA
Found at i:304986 original size:13 final size:13
Alignment explanation
Indices: 304968--304994 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
304958 TACAATAAAC
304968 ATGTATCGATACA
1 ATGTATCGATACA
304981 ATGTATCGATACA
1 ATGTATCGATACA
304994 A
1 A
304995 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:307013 original size:52 final size:52
Alignment explanation
Indices: 306934--307032 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
306924 TTCACTGTTC
** *
306934 ATCACTATTCATCGTTGTTCATGTATCGATACATTGTGAATAGTATCAATAT
1 ATCACTATTCATCACTGTTCATATATCGATACATTGTGAATAGTATCAATAT
*
306986 ATCACTGTTCATCACTGTTCATATATCGATACATTGTGAATAGTATC
1 ATCACTATTCATCACTGTTCATATATCGATACATTGTGAATAGTATC
307033 GATACATTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (52 bp):
ATCACTATTCATCACTGTTCATATATCGATACATTGTGAATAGTATCAATAT
Found at i:307938 original size:20 final size:19
Alignment explanation
Indices: 307913--307984 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 19
307903 GTTACAAGCA
* *
307913 ATGTATCGAGACAATTCATC
1 ATGTATCGATACAATT-AAC
*
307933 ATGTATCGATACAATGTACC
1 ATGTATCGATACAAT-TAAC
*
307953 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATTAAC
307972 ATGTATCGATACA
1 ATGTATCGATACA
307985 GTGTATCGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 15 0.32
20 31 0.66
21 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAATTAAC
Found at i:307984 original size:39 final size:40
Alignment explanation
Indices: 307913--307989 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
307903 GTTACAAGCA
*
307913 ATGTATCGAGACAATTCATCATGTATCGATACAATGTACC
1 ATGTATCGAGACAATTCAACATGTATCGATACAATGTACC
* * *
307953 ATGTATCGATACAA-TGAACATGTATCGATACAGTGTA
1 ATGTATCGAGACAATTCAACATGTATCGATACAATGTA
307990 TCGATACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 20 0.61
40 13 0.39
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGTATCGAGACAATTCAACATGTATCGATACAATGTACC
Found at i:307991 original size:13 final size:13
Alignment explanation
Indices: 307973--307997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
307963 ACAATGAACA
307973 TGTATCGATACAG
1 TGTATCGATACAG
307986 TGTATCGATACA
1 TGTATCGATACA
307998 AAGCATAATG
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:309132 original size:14 final size:14
Alignment explanation
Indices: 309113--309139 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
309103 ATACTTTAAA
309113 GTATCGATACATTT
1 GTATCGATACATTT
309127 GTATCGATACATT
1 GTATCGATACATT
309140 ATGGTTGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (14 bp):
GTATCGATACATTT
Found at i:309234 original size:13 final size:13
Alignment explanation
Indices: 309216--309242 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
309206 ACATACTGCT
309216 TTGTATCGATACA
1 TTGTATCGATACA
309229 TTGTATCGATACA
1 TTGTATCGATACA
309242 T
1 T
309243 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:309239 original size:33 final size:32
Alignment explanation
Indices: 309197--309261 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
309187 CACTCCCAGA
*
309197 TGTATCGATACATACTGCTTTGTATCGATACAT
1 TGTATCGATACATACT-CATTGTATCGATACAT
*
309230 TGTATCGATACATGCTCATTGTATCGATACAT
1 TGTATCGATACATACTCATTGTATCGATACAT
309262 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATACTCATTGTATCGATACAT
Found at i:309272 original size:20 final size:19
Alignment explanation
Indices: 309226--309282 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
309216 TTGTATCGAT
309226 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
309245 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
*
309264 ACAATTGTATCAATACATG
1 AC-ATTGTATCGATACATG
309283 AAACTGACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:309339 original size:20 final size:21
Alignment explanation
Indices: 309314--309363 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
309304 TCACTATTTA
309314 TATCGATACATG-GGACAA-TG
1 TATCGATACATGAGGA-AATTG
*
309334 TATCGATACATGATGAAATTG
1 TATCGATACATGAGGAAATTG
309355 TATCGATAC
1 TATCGATAC
309364 GTTGCTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (21 bp):
TATCGATACATGAGGAAATTG
Found at i:312508 original size:13 final size:13
Alignment explanation
Indices: 312490--312515 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312480 CAATTTTTTG
312490 TGTATCGATACAT
1 TGTATCGATACAT
312503 TGTATCGATACAT
1 TGTATCGATACAT
312516 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:312527 original size:32 final size:33
Alignment explanation
Indices: 312470--312533 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
312460 TACAAGCCAA
**
312470 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
312503 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
312534 AGTTTGGCTA
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:313206 original size:40 final size:41
Alignment explanation
Indices: 313160--313250 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 41
313150 TTTTCTTTCT
*
313160 CCCTTAATTAAAG-TAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTCATACATTCTCC
* * *
313200 CCCTTAA-T-AAGATAATTTTAGCAAATTTATGCATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTCATACATTCTCC
* *
313239 CCTTTTATTAAA
1 CCCTTAATTAAA
313251 AAAAAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 3 0.07
39 29 0.69
40 8 0.19
41 2 0.05
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (41 bp):
CCCTTAATTAAAGATAATTTTAACAAATTCATACATTCTCC
Found at i:314641 original size:21 final size:20
Alignment explanation
Indices: 314612--314654 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
314602 GGCTAGTGTG
* *
314612 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
314633 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
314653 GG
1 GG
314655 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:315113 original size:13 final size:12
Alignment explanation
Indices: 315095--315132 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
315085 ATAATCCCCC
315095 TGTATCGATACA
1 TGTATCGATACA
315107 GTGTATCGATACCA
1 -TGTATCGATA-CA
315121 TGTATCGATACA
1 TGTATCGATACA
315133 AAGAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:321325 original size:13 final size:13
Alignment explanation
Indices: 321307--321332 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
321297 CAATTTTTTG
321307 TGTATCGATACAT
1 TGTATCGATACAT
321320 TGTATCGATACAT
1 TGTATCGATACAT
321333 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:321344 original size:32 final size:33
Alignment explanation
Indices: 321287--321348 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
321277 TACAAGCCAA
**
321287 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
321320 TGTATCGATAC-ATACTTTGTGTATCGATA
1 TGTATCGATACAATACTTTGTGTATCGATA
321349 TAAGTTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:327436 original size:22 final size:20
Alignment explanation
Indices: 327410--327472 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
327400 TTGACAAAAA
327410 GGGAGAAATTCTTTGATTAAG
1 GGGAGAAATTCTTT-ATTAAG
*
327431 GCGGAG-AATT-TTTA-AAAG
1 G-GGAGAAATTCTTTATTAAG
*
327449 GAGAGAAATTCTTTAATTAAG
1 GGGAGAAATTCTTT-ATTAAG
327470 GGG
1 GGG
327473 GAGTTAAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.09
18 8 0.24
19 4 0.12
20 4 0.12
21 10 0.30
22 4 0.12
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.30
Consensus pattern (20 bp):
GGGAGAAATTCTTTATTAAG
Found at i:328109 original size:21 final size:21
Alignment explanation
Indices: 328062--328116 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
328052 CTATCACTAT
328062 TTGTATCGATACATGGGACAA
1 TTGTATCGATACATGGGACAA
* *
328083 -TGTATCGATCCATGATGA-AA
1 TTGTATCGATACATG-GGACAA
*
328103 TTGTATCAATACAT
1 TTGTATCGATACAT
328117 TGCTTGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACATGGGACAA
Found at i:330169 original size:15 final size:15
Alignment explanation
Indices: 330149--330178 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
330139 ACAATTTTTG
330149 ACCTGTTTAAATGGA
1 ACCTGTTTAAATGGA
330164 ACCTGTTTAAATGGA
1 ACCTGTTTAAATGGA
330179 TATAGGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
ACCTGTTTAAATGGA
Found at i:330430 original size:34 final size:34
Alignment explanation
Indices: 330288--330693 Score: 225
Period size: 34 Copynumber: 11.9 Consensus size: 34
330278 ATACAAGAAG
** *
330288 GACTCTTTTAACTTGTTTAGAAAGATGCAATTTT
1 GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
* * * * * **
330322 GACGC-TTGATC-TGTTTAGAAGGATACAAGCCT
1 GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
* * * * *
330354 AACTCTTTTTAAACTCGTTCA-ATAGGATACAAGTTT
1 GACTC-TTTT-AACTTGTTTAGA-AAGACACAAGTTT
* *
330390 AACTCTTTTAACTT-TCTTAGAAAGACATAAGTTT
1 GACTCTTTTAACTTGT-TTAGAAAGACACAAGTTT
* * * *
330424 GTCTCTTTCAACTTGTTT-GAGAGGATACAAGTTT
1 GACTCTTTTAACTTGTTTAGA-AAGACACAAGTTT
* *
330458 GACTTTTTTAACTTGTTTACAAAGACACAAGTTT
1 GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
* * * * * *
330492 AATTTTTTTTGACTTGTTCAAGAAA-ATA-AATGTTT
1 GA-CTCTTTTAACTTGTT-TAGAAAGACACAA-GTTT
* * *
330527 GACTCTTTTAACTTGTTCAGCAAGACATAAGTTT
1 GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
** * *
330561 GACTCTTTTAACTTGTTTAGATGGGCATAAGTTT
1 GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
* * ** * *
330595 TACTTTTTTAACTCATTTAGAAGGAGACAAGTTT
1 GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
* * * * * *
330629 GGCACTTTTAATTTGTTTAGAAAAATACATGTTT
1 GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
*
330663 GACTTTTTTTAACTTGTTTA-AAAGGACACAA
1 GAC-TCTTTTAACTTGTTTAGAAA-GACACAA
330694 ATTAGCGCCA
Statistics
Matches: 278, Mismatches: 77, Indels: 33
0.72 0.20 0.09
Matches are distributed among these distances:
32 19 0.07
33 11 0.04
34 175 0.63
35 49 0.18
36 24 0.09
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (34 bp):
GACTCTTTTAACTTGTTTAGAAAGACACAAGTTT
Found at i:330858 original size:53 final size:53
Alignment explanation
Indices: 330800--330902 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 53
330790 CTTAAATAAC
*
330800 TATATGCCAACTTCGCCTA-AGTAAACCAACTAGCTAAGTTAGGCTTTCTCATT
1 TATATGCCAACTTC-ACTATAGTAAACCAACTAGCTAAGTTAGGCTTTCTCATT
* * * * *
330853 TATATGCCAACTTCACTATTGTAAATCTACTAGCTACGTTGGGCTTTCTC
1 TATATGCCAACTTCACTATAGTAAACCAACTAGCTAAGTTAGGCTTTCTC
330903 TTGTAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 3 0.07
53 40 0.93
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (53 bp):
TATATGCCAACTTCACTATAGTAAACCAACTAGCTAAGTTAGGCTTTCTCATT
Found at i:332475 original size:9 final size:9
Alignment explanation
Indices: 332447--332502 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
332437 ACTTTGCTTC
332447 TTTTTCCTT
1 TTTTTCCTT
*
332456 TTTCTCC--
1 TTTTTCCTT
332463 TTTTTCCTT
1 TTTTTCCTT
*
332472 TTTTTTCTT
1 TTTTTCCTT
332481 TTTTT-CTT
1 TTTTTCCTT
*
332489 TTTTTTCTT
1 TTTTTCCTT
332498 TTTTT
1 TTTTT
332503 TTGTTTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 8 0.20
9 27 0.66
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:332501 original size:16 final size:16
Alignment explanation
Indices: 332444--332500 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
332434 ATTACTTTGC
*
332444 TTCTTTTTCCTTTTTC
1 TTCTTTTTCCTTTTTT
*
332460 TCCTTTTTCCTTTTTT
1 TTCTTTTTCCTTTTTT
*
332476 TTCTTTTTTTCTTTTTT
1 TTC-TTTTTCCTTTTTT
332493 TTCTTTTT
1 TTCTTTTT
332501 TTTTGTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
16 21 0.58
17 15 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTTTCCTTTTTT
Found at i:332509 original size:9 final size:9
Alignment explanation
Indices: 332463--332503 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
332453 CTTTTTCTCC
*
332463 TTTTTCCTT
1 TTTTTTCTT
332472 TTTTTTC-T
1 TTTTTTCTT
332480 TTTTTTCTT
1 TTTTTTCTT
332489 TTTTTTCTT
1 TTTTTTCTT
332498 TTTTTT
1 TTTTTT
332504 TGTTTTGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:332509 original size:17 final size:17
Alignment explanation
Indices: 332447--332502 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
332437 ACTTTGCTTC
* * *
332447 TTTTTCCTTTTTCTCCT
1 TTTTTCTTTTTTTTCTT
*
332464 TTTTCCTTTTTTTTCTT
1 TTTTTCTTTTTTTTCTT
332481 TTTTTCTTTTTTTTCTT
1 TTTTTCTTTTTTTTCTT
332498 TTTTT
1 TTTTT
332503 TTGTTTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTTTTTCTT
Found at i:334303 original size:27 final size:26
Alignment explanation
Indices: 334273--334327 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
334263 TGATTAATTT
*
334273 TTCAA-TTTTCCCTTTTTTTTATTCTCC
1 TTCAACTTTT-CCTTTTTTTCATT-TCC
*
334300 TTCAACTTTTTCTTTTTTTCATTTCC
1 TTCAACTTTTCCTTTTTTTCATTTCC
334326 TT
1 TT
334328 TTTTTCTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 16 0.64
28 4 0.16
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.65
Consensus pattern (26 bp):
TTCAACTTTTCCTTTTTTTCATTTCC
Found at i:335981 original size:20 final size:20
Alignment explanation
Indices: 335956--336008 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
335946 ATACCTTGAT
* *
335956 GTATCGATACATTTTTCAAC
1 GTATCGATACATTTATAAAC
* *
335976 GTATCGATACATGTATAAAT
1 GTATCGATACATTTATAAAC
335996 GTATCGATACATT
1 GTATCGATACATT
336009 CTATCTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTTATAAAC
Found at i:346387 original size:52 final size:52
Alignment explanation
Indices: 346302--346426 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
346292 ATATGAAAAG
* *
346302 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
346354 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
346406 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
346427 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:346439 original size:52 final size:51
Alignment explanation
Indices: 346302--346446 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
346292 ATATGAAAAG
*
346302 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
346354 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
346406 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
346447 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:346453 original size:13 final size:13
Alignment explanation
Indices: 346435--346459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
346425 CAAAGATCAG
346435 TGTATCGATACAA
1 TGTATCGATACAA
346448 TGTATCGATACA
1 TGTATCGATACA
346460 TGTGAGTAAT
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:346542 original size:13 final size:13
Alignment explanation
Indices: 346524--346548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
346514 CAAAAAAATA
346524 TGTATCGATACAT
1 TGTATCGATACAT
346537 TGTATCGATACA
1 TGTATCGATACA
346549 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:346544 original size:33 final size:33
Alignment explanation
Indices: 346502--346568 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
346492 AGTAGCTTAA
346502 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
346535 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
346568 A
1 A
346569 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:347450 original size:67 final size:68
Alignment explanation
Indices: 347324--347450 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
347314 ATTGGGTTTT
* * *
347324 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
347389 AGA
66 AGA
* * * * *
347392 AAAG-TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAATGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
347451 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:347672 original size:49 final size:49
Alignment explanation
Indices: 347463--348070 Score: 799
Period size: 49 Copynumber: 12.7 Consensus size: 49
347453 AAAAGGATGT
* * *
347463 CAATGTGTTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGAAAATGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
* *
347515 CAATATGCTGATTCAAGGCTAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
347558 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-AGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA-TGAAGGTGC
*
347606 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
347655 CAATGTGCTGAGTCAAGGCCAGCTACATTGGA-TGTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACT-TAAAGATGAAGGTGC
* * *
347704 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
347753 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
347802 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
347851 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
347894 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
347943 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
347986 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
348035 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
348071 GAAGGGTTGC
Statistics
Matches: 495, Mismatches: 39, Indels: 47
0.85 0.07 0.08
Matches are distributed among these distances:
43 116 0.23
45 2 0.00
46 1 0.00
47 2 0.00
48 48 0.10
49 294 0.59
50 1 0.00
52 31 0.06
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:347737 original size:98 final size:98
Alignment explanation
Indices: 347397--348070 Score: 814
Period size: 92 Copynumber: 7.0 Consensus size: 98
347387 TGAGAAAAGT
* * * * * * *
347397 GATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAATGATGAGAAAAAGGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TG
* * *
347462 TCAATGTGTTGATTCAAGGCCAGCTATATTGAACTTAAA
60 CCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
347501 GATGGAAAATGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
*
347560 ATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
63 ATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
347596 -AGT-GAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAAT
1 GA-TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
347659 GTGCTGAGTCAAGGCCAGCTACATTGGA-TGTAAA
65 GTGCTGATTCAAGGCCAGCTATATTGGACT-TAAA
* *
347693 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
* *
347758 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGATTCAAGGCCAGCTATATTGGACTTAAA
*
347791 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
347856 TGCTGATTCAAGGCCAGCGATATTGGAC-T---
66 TGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
347885 --TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
347948 TGCTGATTCAAGGCCAGCGATATTGGAC-T---
66 TGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
347977 --TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
348040 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
66 TGCTGATTCAAGGCCAGCTATATTGGACTTA
348071 GAAGGGTTGC
Statistics
Matches: 521, Mismatches: 33, Indels: 42
0.87 0.06 0.07
Matches are distributed among these distances:
91 37 0.07
92 179 0.34
93 1 0.00
94 1 0.00
95 39 0.07
96 5 0.01
97 44 0.08
98 175 0.34
99 1 0.00
103 1 0.00
104 3 0.01
107 35 0.07
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (98 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
TGCTGATTCAAGGCCAGCTATATTGGACTTAAA
Found at i:348114 original size:33 final size:33
Alignment explanation
Indices: 348070--348190 Score: 201
Period size: 33 Copynumber: 3.7 Consensus size: 33
348060 TATTGGGCTT
348070 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
348103 AGAACGGTTGCCACCGACTTGTGTGGGATTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
348135 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
348168 AAGAA-GGTTGCCACCGACTTGTG
1 -AGAAGGGTTGCCACCGACTTGTG
348191 GACTTAAAAG
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
32 30 0.37
33 48 0.59
34 4 0.05
ACGTcount: A:0.20, C:0.19, G:0.35, T:0.26
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:348213 original size:33 final size:34
Alignment explanation
Indices: 348176--348415 Score: 107
Period size: 27 Copynumber: 7.6 Consensus size: 34
348166 AGAAGAAGGT
*
348176 TGCCACCGACTTGTGGACTTAAAAGG-AAAAGAG
1 TGCCACCGAGTTGTGGACTTAAAAGGAAAAAGAG
* * *
348209 TGCCA-CGTAGTTGTGGGCTTTAAAGGAAAAAAGGG
1 TGCCACCG-AGTTGTGGACTTAAAAGG-AAAAAGAG
* *
348244 TGCCACAGAGTCGTGGACTTAAAA-G-----G-G
1 TGCCACCGAGTTGTGGACTTAAAAGGAAAAAGAG
* * *
348271 TGCCACGGAGTTGTGGGCTT-AAACG-----G-G
1 TGCCACCGAGTTGTGGACTTAAAAGGAAAAAGAG
* * *
348298 TGCCACGGAGTTGTGGACTTAGAAGGAAAACGAG
1 TGCCACCGAGTTGTGGACTTAAAAGGAAAAAGAG
*
348332 TGCCA-CGAAGTTGTGGGCTTTAAAA-G-----G-G
1 TGCCACCG-AGTTGTGGAC-TTAAAAGGAAAAAGAG
* *
348360 TGCCACGGAGTTGTGGACTTAAAGATGAAAAA-AG
1 TGCCACCGAGTTGTGGACTTAAA-AGGAAAAAGAG
* *
348394 TGCCACGGAGTTGTGGGCTTAA
1 TGCCACCGAGTTGTGGACTTAA
348416 TGGTGCCATG
Statistics
Matches: 164, Mismatches: 20, Indels: 45
0.72 0.09 0.20
Matches are distributed among these distances:
26 3 0.02
27 45 0.27
28 20 0.12
29 3 0.02
32 2 0.01
33 22 0.13
34 39 0.24
35 29 0.18
36 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (34 bp):
TGCCACCGAGTTGTGGACTTAAAAGGAAAAAGAG
Found at i:348269 original size:35 final size:33
Alignment explanation
Indices: 348188--348269 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 33
348178 CCACCGACTT
*
348188 GTGGACTTAAAAGGAAAAGAGTGCCACGTAGTT
1 GTGGACTTAAAAGGAAAAGAGTGCCACGTAGTC
* * *
348221 GTGGGCTTTAAAGGAAAAAAGGGTGCCACAG-AGTC
1 GTGGACTTAAAAGG--AAAAGAGTGCCAC-GTAGTC
348256 GTGGACTTAAAAGG
1 GTGGACTTAAAAGG
348270 GTGCCACGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 12 0.30
35 27 0.68
36 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (33 bp):
GTGGACTTAAAAGGAAAAGAGTGCCACGTAGTC
Found at i:348275 original size:27 final size:27
Alignment explanation
Indices: 348237--348500 Score: 176
Period size: 27 Copynumber: 9.2 Consensus size: 27
348227 TTTAAAGGAA
* *
348237 AAAAGGGTGCCACAGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
348264 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
348291 AAACGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
348318 AGAAGGAAAACGAGTGCCACGAAGTTGTGGGCTTT
1 ------AAAA-GGGTGCCACGGAGTTGTGGAC-TT
348353 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
348380 AAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
1 AAA-A-G-----GGTGCCACGGAGTTGTGGACTT
* * *
348414 --AATGGTGCCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
348439 --AATGGTGCCATGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
348465 GAAAAGAAGGTGCCACGGAGTCGTGGACTT
1 -AAAAG--GGTGCCACGGAGTTGTGGACTT
*
348495 AGAAGG
1 AAAAGG
348501 AAAACGAGTG
Statistics
Matches: 194, Mismatches: 22, Indels: 42
0.75 0.09 0.16
Matches are distributed among these distances:
25 43 0.22
26 2 0.01
27 55 0.28
28 19 0.10
29 11 0.06
30 2 0.01
31 18 0.09
32 1 0.01
33 3 0.02
34 38 0.20
35 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.37, T:0.22
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:348335 original size:34 final size:32
Alignment explanation
Indices: 348176--348415 Score: 166
Period size: 34 Copynumber: 7.7 Consensus size: 32
348166 AGAAGAAGGT
* *
348176 TGCCACCGACTTGTGGACTTAAAAGGAAAAGAG
1 TGCCACGGAGTTGTGGACTT-AAAGGAAAAGAG
* * *
348209 TGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAGG--AAAAGAG
* * *
348244 TGCCACAGAGTCGTGGACTT-----AAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAGGAAAAGAG
* *
348271 TGCCACGGAGTTGTGGGCTTAAACG----G-G
1 TGCCACGGAGTTGTGGACTTAAAGGAAAAGAG
348298 TGCCACGGAGTTGTGGACTTAGAAGGAAAACGAG
1 TGCCACGGAGTTGTGGACTTA-AAGGAAAA-GAG
* * * *
348332 TGCCACGAAGTTGTGGGCTT----TAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAGGAAAAGAG
*
348360 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAG--GAAAAGAG
*
348394 TGCCACGGAGTTGTGGGCTTAA
1 TGCCACGGAGTTGTGGACTTAA
348416 TGGTGCCATG
Statistics
Matches: 162, Mismatches: 24, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
27 45 0.28
28 24 0.15
29 4 0.02
33 20 0.12
34 49 0.30
35 20 0.12
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (32 bp):
TGCCACGGAGTTGTGGACTTAAAGGAAAAGAG
Found at i:348428 original size:25 final size:25
Alignment explanation
Indices: 348393--348463 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
348383 GATGAAAAAA
*
348393 GTGCCACGGAGTTGTGGGCTTAATG
1 GTGCCATGGAGTTGTGGGCTTAATG
348418 GTGCCATGGAGTTGTGGGCTTAATG
1 GTGCCATGGAGTTGTGGGCTTAATG
348443 GTGCCATGGAGTTGTGGGCTT
1 GTGCCATGGAGTTGTGGGCTT
348464 TGAAAAGAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.14, C:0.14, G:0.41, T:0.31
Consensus pattern (25 bp):
GTGCCATGGAGTTGTGGGCTTAATG
Found at i:348620 original size:63 final size:61
Alignment explanation
Indices: 348536--348659 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 61
348526 CTTTGAAAGG
* * * *
348536 AAGGTGCCACAGAGTCATGGACTTTGAGCAG-AGATTGCCACTGAGTCGTGGACTTTGAAGAA
1 AAGGTGCCACAGAGTCATGGACTTTGAGAAGAAG-GTGCCACGGAGTCATGGACTTT-AAGAA
* *
348598 AAGGATGCCACTGAGTCGTGGACTTTGAGAAGAAGGTGCCACGGAGTCATGGACTTTAAGAA
1 AAGG-TGCCACAGAGTCATGGACTTTGAGAAGAAGGTGCCACGGAGTCATGGACTTTAAGAA
348660 GGTATTTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
62 9 0.17
63 43 0.80
64 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (61 bp):
AAGGTGCCACAGAGTCATGGACTTTGAGAAGAAGGTGCCACGGAGTCATGGACTTTAAGAA
Found at i:348645 original size:31 final size:31
Alignment explanation
Indices: 348442--348660 Score: 194
Period size: 31 Copynumber: 6.9 Consensus size: 31
348432 TGGGCTTAAT
* * * *
348442 GGTGCCATGGAGTTGTGGGCTTTGAAAAGAA
1 GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
*
348473 GGTGCCACGGAGTCGTGGACTTAGAAGGAA-AA
1 GGTGCCACGGAGTCGTGGACTTTG-A-GAAGAA
* * *
348505 CGAGTGCCACGAAGTTGTGGGCTTTGA-AAGGAA
1 -G-GTGCCACGGAGTCGTGGACTTTGAGAA-GAA
* * *
348538 GGTGCCACAGAGTCATGGACTTTGAGCAG-A
1 GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
* *
348568 GATTGCCACTGAGTCGTGGACTTTGAAGAA-AA
1 G-GTGCCACGGAGTCGTGGACTTTG-AGAAGAA
*
348600 GGATGCCACTGAGTCGTGGACTTTGAGAAGAA
1 GG-TGCCACGGAGTCGTGGACTTTGAGAAGAA
* *
348632 GGTGCCACGGAGTCATGGACTTTAAGAAG
1 GGTGCCACGGAGTCGTGGACTTTGAGAAG
348661 GTATTTGAAG
Statistics
Matches: 153, Mismatches: 23, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
30 2 0.01
31 90 0.59
32 36 0.24
33 6 0.04
34 19 0.12
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (31 bp):
GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
Found at i:348645 original size:94 final size:96
Alignment explanation
Indices: 348475--348654 Score: 260
Period size: 94 Copynumber: 1.9 Consensus size: 96
348465 GAAAAGAAGG
* *
348475 TGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGTTGTGGGCTTTGAAAGGAAGG
1 TGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGTCGTGGACTTTGAAAGGAAGG
348540 TGCCACAGAGTCATGGACTTTGAGCAGAGAT
66 TGCCACAGAGTCATGGACTTTGAGCAGAGAT
* * *
348571 TGCCACTGAGTCGTGGACTTTGAA-GAAAAGGA-TGCCACTG-AGTCGTGGACTTTGAGAA-GAA
1 TGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCAC-GAAGTCGTGGACTTTGA-AAGGAA
*
348632 GGTGCCACGGAGTCATGGACTTT
64 GGTGCCACAGAGTCATGGACTTT
348655 AAGAAGGTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
94 44 0.58
95 10 0.13
96 22 0.29
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (96 bp):
TGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGTCGTGGACTTTGAAAGGAAGG
TGCCACAGAGTCATGGACTTTGAGCAGAGAT
Found at i:352195 original size:20 final size:20
Alignment explanation
Indices: 352166--352223 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
352156 GCAGTAGCTT
352166 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
352185 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
352205 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
352224 TCATTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:359401 original size:28 final size:28
Alignment explanation
Indices: 359358--360308 Score: 1073
Period size: 28 Copynumber: 33.5 Consensus size: 28
359348 CGTTCATCTC
359358 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
359386 TTTAAAGCCCACAAGTTAATGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
359414 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
359442 TTCAAAGCCCATAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
359470 TTCAAACCCCACAAATCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
359498 TTCAAAGCCCACAAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
**
359528 TTCAAAGCCCACAAGTCAGTGGCATACT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
359556 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
359584 TTCATAGCTCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
359612 TTCAATGCCTAGAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
359641 TTCAAAGCCCACAAGTCAGTGGCACCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
359669 TT-AGATGCCCACAAGTTAGTGGCATCCT
1 TTCA-AAGCCCACAAGTCAGTGGCACCCT
* * *
359697 TTCAAAGCCCATAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
359725 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
359753 TTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
359781 TTCAAAGCCTACAAGTCAGTGGAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
359810 TTCAAAGCCCACAAGTGAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
359838 TTCAAAGCCCACTAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
359866 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
359894 TTCAAAGCCCACAAGTCAATAGAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * * *
359923 TTTAAAGCCCATAAGTCAGT--AACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
359950 TTTAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
359978 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * **
360006 TTCCAAGCCACGCAAGTCAGTGGCACATT
1 TTCAAAGCC-CACAAGTCAGTGGCACCCT
* * *
360035 TTCAAAGCCCATAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
360064 TTCAAAGCCCACAAGTCATTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
360092 TTCAAAGCCCACAAGCCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
360121 TTCAAAGCCCACAAATTAGTGGCATCCC-
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
* *
360149 TTCAAAGCCCACAAGTTAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
360177 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
360205 TTCAAAGCCCACAAGTCAGTCGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
360234 TTCAAAGCCCACAAGCCAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CAC-CCT
* *
360264 TTCAAAGCCCACATGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCT
360296 TTCAAAGCCCACA
1 TTCAAAGCCCACA
360309 CAAGTTAGTG
Statistics
Matches: 792, Mismatches: 112, Indels: 34
0.84 0.12 0.04
Matches are distributed among these distances:
27 31 0.04
28 525 0.66
29 164 0.21
30 46 0.06
32 26 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:359690 original size:113 final size:112
Alignment explanation
Indices: 359358--360328 Score: 1122
Period size: 113 Copynumber: 8.5 Consensus size: 112
359348 CGTTCATCTC
* * *
359358 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTTAATGGCATCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* *
359423 CACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTTAGTGGCATCCT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
359470 TTCAAACCCCACAAATCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-A-TCCTTTCAAAG
**
359535 CCCACAAGTCAGTGGCATACTTTCAAAGCCCACAAGTCAGTGGCATCCT
64 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * * * * *
359584 TTCATAGCTCACAAGTTAGTGGCACCCTTTCAATGCCTAGAAATCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGC
* * *
359649 CCACAAGTCAGTGGCACCATTT-AGATGCCCACAAGTTAGTGGCATCCT
65 CCACAAGTCAGTGGCACCCTTTCA-AAGCCCACAAGTCAGTGGCATCCT
* * * *
359697 TTCAAAGCCCATAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* * *
359762 CACAAGTCAGTGGCACCCTTTCAAAGCCTACAAGTCAGTGGAACTCTT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
* *
359810 TTCAAAGCCCACAAGTGAGTGGCACCCTTTCAAAGCCCACTAGTCAGTGGCATCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* * * * *
359875 CATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATAGAACTCTT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * * * * *
359923 TTTAAAGCCCATAAGTCAGT--AACTCTTTTTAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
359986 CCACAAGTCAGTGGCACCCTTTCCAAGCCACGCAAGTCAGTGGCA-CATT
65 CCACAAGTCAGTGGCACCCTTTCAAAGCC-CACAAGTCAGTGGCATC-CT
* * * * *
360035 TTCAAAGCCCATAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCATTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
360100 CCACAAGCCAGTGGCACTCTTTTCAAAGCCCACAAATTAGTGGCATCCC
65 CCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
360149 TTCAAAGCCCACAAGTTAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* * * * *
360214 CACAAGTCAGTCGCACTCTTTTCAAAGCCCACAAGCCAGTGGTAACTCTT
66 CACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGG-CA-TCCT
* * * *
360264 TTCAAAGCCCACATGAGTCGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCATCTTTTC
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAG-CC-CACAAGTCAGTGGCATCCTTTC
360329 TAAAAAAACC
Statistics
Matches: 735, Mismatches: 104, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
111 3 0.00
112 174 0.24
113 308 0.42
114 185 0.25
115 26 0.04
117 7 0.01
118 2 0.00
119 9 0.01
120 2 0.00
121 19 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (112 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:361235 original size:20 final size:20
Alignment explanation
Indices: 361212--361262 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
361202 AAGTACCCAG
* * *
361212 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATAA
*
361232 ATGTATCAATACATGTATAA
1 ATGTATCGATACATGTATAA
361252 ATGTATCGATA
1 ATGTATCGATA
361263 TATTCTGTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATGTATAA
Found at i:367674 original size:58 final size:58
Alignment explanation
Indices: 367600--367715 Score: 157
Period size: 58 Copynumber: 2.0 Consensus size: 58
367590 GCATCTTTTT
367600 ATCATTTTCCATGACTTAAGGAC-TT-CTATGCAATTTTATAAATTTTGATAACATTTAG
1 ATCATTTTCCATGACTTAAGGACTTTACTAT--AATTTTATAAATTTTGATAACATTTAG
* * *
367658 ATCATGTTT-CATGACTTAGGGACTTTACTATAATTTTATATATTTTGATATCATTTAG
1 ATCAT-TTTCCATGACTTAAGGACTTTACTATAATTTTATAAATTTTGATAACATTTAG
367716 GTTGTTAGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
58 43 0.83
59 5 0.10
60 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (58 bp):
ATCATTTTCCATGACTTAAGGACTTTACTATAATTTTATAAATTTTGATAACATTTAG
Found at i:368045 original size:13 final size:13
Alignment explanation
Indices: 368027--368053 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
368017 ACATTATGCT
368027 TTGTATCGATACA
1 TTGTATCGATACA
368040 TTGTATCGATACA
1 TTGTATCGATACA
368053 T
1 T
368054 GAAACTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:369697 original size:15 final size:15
Alignment explanation
Indices: 369677--369711 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
369667 AACCATCAAA
369677 GATGATAAAGATAAT
1 GATGATAAAGATAAT
* *
369692 GATGATGATGATAAT
1 GATGATAAAGATAAT
369707 GATGA
1 GATGA
369712 AGTTGACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (15 bp):
GATGATAAAGATAAT
Found at i:370247 original size:20 final size:20
Alignment explanation
Indices: 370224--370296 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
370214 ACAATTCAAA
370224 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
370244 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
370265 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
370285 GTATCGATACAT
1 GTATCGATACAT
370297 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:370268 original size:21 final size:21
Alignment explanation
Indices: 370242--370317 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
370232 ACATGTTGCA
370242 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
370263 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
370283 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
370304 ATGTATCGATACAT
1 ATGTATCGATACAT
370318 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:370275 original size:41 final size:41
Alignment explanation
Indices: 370224--370317 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
370214 ACAATTCAAA
*
370224 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
370265 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
370306 GTATCGATACAT
1 GTATCGATACAT
370318 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:370374 original size:13 final size:13
Alignment explanation
Indices: 370356--370381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
370346 TACAGCAAGT
370356 ATGTATCGATACA
1 ATGTATCGATACA
370369 ATGTATCGATACA
1 ATGTATCGATACA
370382 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:374462 original size:15 final size:15
Alignment explanation
Indices: 374442--374472 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
374432 TAAAAATGTC
*
374442 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
374457 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
374472 C
1 C
374473 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:376568 original size:20 final size:21
Alignment explanation
Indices: 376489--376567 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
376479 AATGTCCAAA
*
376489 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
376509 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
376534 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
376554 TTGTATCGATACAT
1 ATGTATCGATACAT
376568 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:376572 original size:13 final size:13
Alignment explanation
Indices: 376554--376592 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
376544 ACATTTTTCT
376554 TTGTATCGATACA
1 TTGTATCGATACA
376567 TTGTATCGATACA
1 TTGTATCGATACA
*
376580 CTGTATCGATACA
1 TTGTATCGATACA
376593 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:378300 original size:36 final size:36
Alignment explanation
Indices: 378253--378324 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
378243 AGTGCAAATA
*
378253 AATTTTGATATGAATTACTTGATTAATGGGGAGATT
1 AATTTTGATATGAATTACTTGATTAAGGGGGAGATT
378289 AATTTTGATATGAATTACTTGATTAAGGGGGAGATT
1 AATTTTGATATGAATTACTTGATTAAGGGGGAGATT
378325 TATTAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (36 bp):
AATTTTGATATGAATTACTTGATTAAGGGGGAGATT
Found at i:378968 original size:20 final size:20
Alignment explanation
Indices: 378945--379017 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
378935 ACAATTCAAA
378945 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
378965 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
378986 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
379006 GTATCGATACAT
1 GTATCGATACAT
379018 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:378989 original size:21 final size:21
Alignment explanation
Indices: 378963--379038 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
378953 ACATGTTGCA
378963 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
378984 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
379004 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
379025 ATGTATCGATACAT
1 ATGTATCGATACAT
379039 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:378996 original size:41 final size:41
Alignment explanation
Indices: 378945--379038 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
378935 ACAATTCAAA
*
378945 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
378986 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
379027 GTATCGATACAT
1 GTATCGATACAT
379039 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:379095 original size:13 final size:13
Alignment explanation
Indices: 379077--379102 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
379067 TACAGCAAGT
379077 ATGTATCGATACA
1 ATGTATCGATACA
379090 ATGTATCGATACA
1 ATGTATCGATACA
379103 TAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:382766 original size:16 final size:16
Alignment explanation
Indices: 382742--382772 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
382732 AAAGGCTCTC
*
382742 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
382758 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
382773 GGAAATGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:384242 original size:13 final size:13
Alignment explanation
Indices: 384224--384263 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
384214 GCAATATTCT
384224 TTGTATCGATACA
1 TTGTATCGATACA
384237 TTGTATCGATACA
1 TTGTATCGATACA
*
384250 ATGTATCGATACA
1 TTGTATCGATACA
384263 T
1 T
384264 GGGTTACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:386748 original size:13 final size:13
Alignment explanation
Indices: 386730--386756 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
386720 ACATTATGCT
386730 TTGTATCGATACA
1 TTGTATCGATACA
386743 TTGTATCGATACA
1 TTGTATCGATACA
386756 T
1 T
386757 GAAACTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:386825 original size:13 final size:13
Alignment explanation
Indices: 386807--386831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
386797 CGTGGCATAT
386807 TGTATCGATACAA
1 TGTATCGATACAA
386820 TGTATCGATACA
1 TGTATCGATACA
386832 TGAAGAATTG
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:396761 original size:37 final size:37
Alignment explanation
Indices: 396700--396785 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
396690 ACCGGTTTCA
396700 AACCATGCCACCGATTAAAAATAG-TAGTTTTTATTCT
1 AACCATGCCACCGATTAAAAATAGTTA-TTTTTATTCT
* * * *
396737 GAACCGTGCCACTG-TTAAGAATAGTTATTTTTGTTCT
1 -AACCATGCCACCGATTAAAAATAGTTATTTTTATTCT
396774 AACCTATGCCAC
1 AACC-ATGCCAC
396786 AGGGATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 4 0.10
37 24 0.59
38 13 0.32
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (37 bp):
AACCATGCCACCGATTAAAAATAGTTATTTTTATTCT
Found at i:397127 original size:226 final size:226
Alignment explanation
Indices: 396764--397174 Score: 698
Period size: 226 Copynumber: 1.8 Consensus size: 226
396754 AGAATAGTTA
**
396764 TTTTTGTTCTAACCTATGCCACAGGGATTAAATATGGTTTTAGTATGTTACGGGAGACTAATAAA
1 TTTTTGTTCTAACCTATGCCACAGGGATTAAATATGGTTTTAGTATGTTACAAGAGACTAATAAA
** *
396829 AATTAATAATTTGTGATCCTACATTGTTTTGGTTACATGATAAACTTGATTTTGTAAATAATATG
66 AACCAATAAATTGTGATCCTACATTGTTTTGGTTACATGATAAACTTGATTTTGTAAATAATATG
*
396894 ATTTCGAAAGTAATATGTTTATTGAATATGAGATTACCCAAATTTTTATCATTGAGTGGTTTTTG
131 ATTTCGAAAGTAATATGTTTATTGAATATGAAATTACCCAAATTTTTATCATTGAGTGGTTTTTG
396959 TTCTGAACCGTGCCATCAAATTAGACTGTAG
196 TTCTGAACCGTGCCATCAAATTAGACTGTAG
* * *
396990 TTTTTGTTCTAACCTGTGCCAC-GGGGTTAAATGTGGTTTTAGTATGTTACAAGAGACTAATAAA
1 TTTTTGTTCTAACCTATGCCACAGGGATTAAATATGGTTTTAGTATGTTACAAGAGACTAATAAA
* *
397054 AACCAATAAATTGTGATCTTACATTGTTTTGGTTACTTTGATAAACTTGATTTTGTAAATAATAT
66 AACCAATAAATTGTGATCCTACATTGTTTTGGTTAC-ATGATAAACTTGATTTTGTAAATAATAT
*
397119 GATTTCGAAAGTAATATGTTTATTGAATATGAAATTACTCAAATTTTTATCATTGA
130 GATTTCGAAAGTAATATGTTTATTGAATATGAAATTACCCAAATTTTTATCATTGA
397175 AATTACTGTT
Statistics
Matches: 172, Mismatches: 12, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
225 70 0.41
226 102 0.59
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (226 bp):
TTTTTGTTCTAACCTATGCCACAGGGATTAAATATGGTTTTAGTATGTTACAAGAGACTAATAAA
AACCAATAAATTGTGATCCTACATTGTTTTGGTTACATGATAAACTTGATTTTGTAAATAATATG
ATTTCGAAAGTAATATGTTTATTGAATATGAAATTACCCAAATTTTTATCATTGAGTGGTTTTTG
TTCTGAACCGTGCCATCAAATTAGACTGTAG
Found at i:400707 original size:61 final size:61
Alignment explanation
Indices: 400602--400991 Score: 350
Period size: 61 Copynumber: 6.3 Consensus size: 61
400592 ACCTTTTATC
* * *
400602 CTTT-CAGTCCTCGAAA-AGCAGGACACCTTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCA
1 CTTTCCAGTCCTC-AAAGAGCAGGACGCCTTCTT-CTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
400663 CTTTCCAGTCCTTAAAGAGCAGGATGCCTTCTTCTTTTACAGCCCACACTAGTTGGTGGCA
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
400724 CCTTCTAGTCC-CAAAGAGCAAGACACCTTCCCCTTTTCTTTTTAAAGCCCATACAAGTTGGTGG
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTT---C--TTC-TTTTAAAGCCCACACAAGTTGGTGG
400788 CA
60 CA
* * * *
400790 CCTTT-CAGTCTTCAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCATACAAGTTGGTGGCA
1 -CTTTCCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
400851 CCTTT-CAGTCCTCAAAGAGCAAGATGCTTTC-TCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 -CTTTCCAGTCCTCAAAGAGCAGGACGCCTTCTTC-TTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
400912 CCTTCTAATTCTCAAAGAGTAGGACG--TT-TTCTTTTCAAAGCCCACACAAGTTGGTAGCA
1 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTT-AAAGCCCACACAAGTTGGTGGCA
* *
400971 CCTTT-TAGTCCTCAAAAAGCA
1 -CTTTCCAGTCCTCAAAGAGCA
400992 AGACACACTT
Statistics
Matches: 271, Mismatches: 43, Indels: 32
0.78 0.12 0.09
Matches are distributed among these distances:
58 4 0.01
59 38 0.14
60 21 0.08
61 135 0.50
62 22 0.08
63 1 0.00
64 1 0.00
65 3 0.01
66 28 0.10
67 18 0.07
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (61 bp):
CTTTCCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:400861 original size:127 final size:123
Alignment explanation
Indices: 400601--400997 Score: 440
Period size: 127 Copynumber: 3.2 Consensus size: 123
400591 AACCTTTTAT
* * * *
400601 CCTTTCAGTCCTCGAAA-AGCAGGACAC-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCA-
1 CCTTTCAGTCCTC-AAAGAGCAAGACACTCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
400663 CTTTCCAGTCCTT-AAAGAGCAGGATGCCTTCTTCTTTTACAGCCCACACTAGTTGGTGGCA
65 CTTT-CAGT-CTTCAAAGAGCAGGACGTCTTC-TCTTTTAAAGCCCACACAAGTTGGTGGCA
*
400724 CC-TTCTAGTCC-CAAAGAGCAAGACACCTTCCCCTTTTCTTTTTAAAGCCCATACAAGTTGGTG
1 CCTTTC-AGTCCTCAAAGAGCAAGACA-C-T--CCTTTTCTTTTTAAAGCCCACACAAGTTGGTG
*
400787 GCACCTTTCAGTCTTCAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCATACAAGTTGGTGGCA
61 GCACCTTTCAGTCTTCAAAGAGCAGGACGTCTTCT-CTTTTAAAGCCCACACAAGTTGGTGGCA
*
400851 CCTTTCAGTCCTCAAAGAGCAAG--A-TGCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CCTTTCAGTCCTCAAAGAGCAAGACACTCCTTT-TCTTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
400913 CTTCTAATTC-TCAAAGAGTAGGACGT-TT-TCTTTTCAAAGCCCACACAAGTTGGTAGCA
65 CTT-TCAGTCTTCAAAGAGCAGGACGTCTTCTCTTTT-AAAGCCCACACAAGTTGGTGGCA
* *
400971 CCTTTTAGTCCTCAAAAAGCAAGACAC
1 CCTTTCAGTCCTCAAAGAGCAAGACAC
400998 ACTTTATTTC
Statistics
Matches: 237, Mismatches: 19, Indels: 36
0.81 0.07 0.12
Matches are distributed among these distances:
119 5 0.02
120 43 0.18
121 9 0.04
122 61 0.26
123 13 0.05
126 5 0.02
127 83 0.35
128 18 0.08
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (123 bp):
CCTTTCAGTCCTCAAAGAGCAAGACACTCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACC
TTTCAGTCTTCAAAGAGCAGGACGTCTTCTCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:401024 original size:42 final size:43
Alignment explanation
Indices: 400978--401071 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 43
400968 GCACCTTTTA
*
400978 GTCCTCAAAAAGCAAGACACACTTTATTTCCTT-TTCTCCTTT
1 GTCCTCAAAAAGCAAGACACACTTAATTTCCTTCTTCTCCTTT
* * *
401020 GTCCTCGAACAGCAAGACACACTTAATTTCCTTCTTTTCCTTT
1 GTCCTCAAAAAGCAAGACACACTTAATTTCCTTCTTCTCCTTT
401063 GTCCTCAAA
1 GTCCTCAAA
401072 GAGTAAGATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 30 0.65
43 16 0.35
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.36
Consensus pattern (43 bp):
GTCCTCAAAAAGCAAGACACACTTAATTTCCTTCTTCTCCTTT
Found at i:401168 original size:62 final size:62
Alignment explanation
Indices: 401101--401372 Score: 400
Period size: 62 Copynumber: 4.4 Consensus size: 62
401091 TCTTTTTTCC
* * * * *
401101 TTAGTCCTTAAAGACCATGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTT
1 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAACCAACACGAGTTGGTGGCACCTT
* * * * *
401163 TTAGTCCTCAAAGAGCAAGATGCTTTTTTCTTTTTAAAGCCAACACGAGTTGATGGCACCTT
1 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAACCAACACGAGTTGGTGGCACCTT
* *
401225 TTAGTCCTCAAAGAGCAGGATGTCTTTTTCTTTTCAAAACCCACACGAGTTGGTGGCACCTT
1 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAACCAACACGAGTTGGTGGCACCTT
* * *
401287 TTAGTCCTCAAAGAGCAGGATGTCTTTTTCTTTTCAAAACCAACATGAGTTGGTGGCACCCT
1 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAACCAACACGAGTTGGTGGCACCTT
*
401349 TTAGTCCTCAAAAAGCAGGATGCC
1 TTAGTCCTCAAAGAGCAGGATGCC
401373 CCCTTCCTTT
Statistics
Matches: 191, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 191 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (62 bp):
TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAACCAACACGAGTTGGTGGCACCTT
Found at i:402231 original size:13 final size:13
Alignment explanation
Indices: 402213--402282 Score: 77
Period size: 13 Copynumber: 4.9 Consensus size: 13
402203 TTCAACAATT
402213 TGTATCGATACAA
1 TGTATCGATACAA
402226 TGTATCGATACAA
1 TGTATCGATACAA
*
402239 TGTATCGATAAATAA
1 TGTATCGAT--ACAA
402254 CTGTTGTATCGATACAA
1 ----TGTATCGATACAA
402271 TGTATCGATACA
1 TGTATCGATACA
402283 TAAGTTTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
13 34 0.69
15 3 0.06
17 3 0.06
19 9 0.18
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:402262 original size:32 final size:32
Alignment explanation
Indices: 402226--402309 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
402216 ATCGATACAA
402226 TGTATCGATACAATGTATCGATAAATAACTGT
1 TGTATCGATACAATGTATCGATAAATAACTGT
* * *
402258 TGTATCGATACAATGTATCGATACATAAGTTT
1 TGTATCGATACAATGTATCGATAAATAACTGT
402290 TGTATCGATACAATGTATCG
1 TGTATCGATACAATGTATCG
402310 CTACGAAGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACAATGTATCGATAAATAACTGT
Found at i:402372 original size:13 final size:13
Alignment explanation
Indices: 402354--402381 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
402344 ATTACTCAAA
402354 TGTATCGATACAT
1 TGTATCGATACAT
402367 TGTATCGATACAT
1 TGTATCGATACAT
402380 TG
1 TG
402382 ATCTTTGTAT
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:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:481823 original size:50 final size:50
Alignment explanation
Indices: 481763--481897 Score: 173
Period size: 50 Copynumber: 2.7 Consensus size: 50
481753 TTTCACAATT
* *
481763 TGTATCGATACATTCTTCATTGTGTCAATACATTTTGGGTTTAACCCAAA
1 TGTATCGATACATTCTTCATTGTATCAATACATTCTGGGTTTAACCCAAA
* * *
481813 TGTATCGATACATTCTTCATTGTATCAATACATTCTGGGTTTTACCTAGA
1 TGTATCGATACATTCTTCATTGTATCAATACATTCTGGGTTTAACCCAAA
* * * *
481863 TGAATCGATACACTT-TTCAATGTATCGATATATTC
1 TGTATCGATACA-TTCTTCATTGTATCAATACATTC
481898 AAGCATTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
50 73 0.97
51 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (50 bp):
TGTATCGATACATTCTTCATTGTATCAATACATTCTGGGTTTAACCCAAA
Found at i:483092 original size:21 final size:21
Alignment explanation
Indices: 483066--483141 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
483056 CTGCCAAGAA
*
483066 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
483087 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
483107 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
483128 ATGTATCGATACAT
1 ATGTATCGATACAT
483142 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:483112 original size:20 final size:20
Alignment explanation
Indices: 483087--483159 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
483077 CATCTTTTTT
483087 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
483107 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
483128 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
483148 ATGTATCGATAC
1 ATGTATCGATAC
483160 TTTCAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:483123 original size:41 final size:41
Alignment explanation
Indices: 483066--483159 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
483056 CTGCCAAGAA
*
483066 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
483107 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
483148 ATGTATCGATAC
1 ATGTATCGATAC
483160 TTTCAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:485633 original size:13 final size:13
Alignment explanation
Indices: 485611--485649 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
485601 ATAATCACCC
*
485611 TGTATCGATACAG
1 TGTATCGATACAA
*
485624 TGTATTGATACAA
1 TGTATCGATACAA
485637 TGTATCGATACAA
1 TGTATCGATACAA
485650 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:485660 original size:20 final size:20
Alignment explanation
Indices: 485635--485713 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
485625 GTATTGATAC
485635 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
485655 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
485680 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
485700 CATGTATCGATACA
1 AATGTATCGATACA
485714 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:485864 original size:8 final size:8
Alignment explanation
Indices: 485851--485882 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
485841 CATCATTCAA
485851 CACAAAAT
1 CACAAAAT
485859 CACAAAAT
1 CACAAAAT
485867 CACAAAAT
1 CACAAAAT
485875 CACAAAAT
1 CACAAAAT
485883 TTAATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.12
Consensus pattern (8 bp):
CACAAAAT
Found at i:489599 original size:21 final size:21
Alignment explanation
Indices: 489570--489614 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
489560 AAGTTTTCAT
*
489570 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
489590 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
489612 TTT
1 TTT
489615 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:491846 original size:13 final size:13
Alignment explanation
Indices: 491828--491853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
491818 CAATTTTTTG
491828 TGTATCGATACAT
1 TGTATCGATACAT
491841 TGTATCGATACAT
1 TGTATCGATACAT
491854 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:491918 original size:21 final size:21
Alignment explanation
Indices: 491892--491967 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
491882 CTGCCAAGAA
*
491892 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
491913 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
491933 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
491954 ATGTATCGATACAT
1 ATGTATCGATACAT
491968 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:491938 original size:20 final size:20
Alignment explanation
Indices: 491913--491985 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
491903 CATCTTTTTT
491913 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
491933 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
491954 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
491974 ATGTATCGATAC
1 ATGTATCGATAC
491986 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:491949 original size:41 final size:41
Alignment explanation
Indices: 491892--491985 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
491882 CTGCCAAGAA
*
491892 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
491933 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
491974 ATGTATCGATAC
1 ATGTATCGATAC
491986 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:492855 original size:60 final size:60
Alignment explanation
Indices: 492788--492913 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 60
492778 ATGTAGCTTG
* * *
492788 CATCTTCATCACCATAATGGCCTCTGTTTTTGAATCCCTTGTTCATTCCTTCCATATCCA
1 CATCTTCAACACCATAATGACCTCTATTTTTGAATCCCTTGTTCATTCCTTCCATATCCA
* * *
492848 CATCTTCAACATCATAATGACCTCTATTTTTGCATCCCTTGTTCATTCCTTCTATATCCA
1 CATCTTCAACACCATAATGACCTCTATTTTTGAATCCCTTGTTCATTCCTTCCATATCCA
492908 CATCTT
1 CATCTT
492914 TATCTCATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.21, C:0.31, G:0.06, T:0.41
Consensus pattern (60 bp):
CATCTTCAACACCATAATGACCTCTATTTTTGAATCCCTTGTTCATTCCTTCCATATCCA
Found at i:494597 original size:79 final size:81
Alignment explanation
Indices: 494322--494603 Score: 319
Period size: 80 Copynumber: 3.5 Consensus size: 81
494312 TGTTTTTATT
* *
494322 TTTCTAAAAC-GCTGATTTTTCACAATCGGGGATACTCCAACCTTGTTATTTCTG-AGGGGATAC
1 TTTCTAAAACATCTAATTTTTCACAATCGGGGATACTCCAACCTTGTTATTTCTGAAGGGGATAC
*
494385 TCCAACCTCGATTTTTA
66 TCCAACC-CAATTTTTA
* * *
494402 TTT-TCAAAACA-CTAATTTTTCATAATCGAGGATACTCCAACCTTGTTATTT-TCAAGGGGATA
1 TTTCT-AAAACATCTAATTTTTCACAATCGGGGATACTCCAACCTTGTTATTTCTGAAGGGGATA
494464 CTCCAACCCTAATTTTTA
65 CTCCAACCC-AATTTTTA
* * * * *** *
494482 TTTCCAAAACATC-AATCTTCCATAATCGGGGATACTCCAACCCCATTATTTCTGAAGAGG-TAC
1 TTTCTAAAACATCTAATTTTTCACAATCGGGGATACTCCAACCTTGTTATTTCTGAAGGGGATAC
* **
494545 TCCAACCCCAGCTTTA
66 TCCAACCCAATTTTTA
*
494561 TTTCTAAAACATC-GATTTTTCACAATCGGGGATACTCCAACCT
1 TTTCTAAAACATCTAATTTTTCACAATCGGGGATACTCCAACCT
494604 CAGTTTTATT
Statistics
Matches: 172, Mismatches: 23, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
79 45 0.26
80 120 0.70
81 7 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (81 bp):
TTTCTAAAACATCTAATTTTTCACAATCGGGGATACTCCAACCTTGTTATTTCTGAAGGGGATAC
TCCAACCCAATTTTTA
Found at i:494625 original size:51 final size:51
Alignment explanation
Indices: 494542--494655 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
494532 TCTGAAGAGG
* * **
494542 TACTCCAACCCCAGCTTTATTTCTAAAACATCGATTTTTCACAATCGGGGA
1 TACTCCAACCCCAGCTTTATTTCCAAAACATCGATTTTCCACAATCAAGGA
* * * *
494593 TACTCCAACCTCAGTTTTATTTCCAAAGCATCGATTTTCCATAATCAAGGA
1 TACTCCAACCCCAGCTTTATTTCCAAAACATCGATTTTCCACAATCAAGGA
494644 TACTCCAACCCC
1 TACTCCAACCCC
494656 GTTATTTCTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.31
Consensus pattern (51 bp):
TACTCCAACCCCAGCTTTATTTCCAAAACATCGATTTTCCACAATCAAGGA
Found at i:497965 original size:20 final size:20
Alignment explanation
Indices: 497942--497995 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
497932 AAGTACCCAG
* *
497942 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
* *
497962 ATGTATCAATACATGTATGA
1 ATGTATCGATACATGTATCA
497982 ATGTATCGATACAT
1 ATGTATCGATACAT
497996 CTAGTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:511935 original size:1 final size:1
Alignment explanation
Indices: 511929--511980 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
511919 CCTTCATGCC
* * * * * *
511929 AAAAAAAAAACAAAAAAAACAAAAAAACAAAAAAAAACAAACAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
511981 GGGGTCCAGA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:511945 original size:8 final size:8
Alignment explanation
Indices: 511932--511980 Score: 62
Period size: 8 Copynumber: 5.8 Consensus size: 8
511922 TCATGCCAAA
511932 AAAAAAAC
1 AAAAAAAC
511940 AAAAAAAAC
1 -AAAAAAAC
511949 AAAAAAAC
1 AAAAAAAC
511957 AAAAAAAAAC
1 --AAAAAAAC
*
511967 AAACAAAC
1 AAAAAAAC
511975 AAAAAA
1 AAAAAA
511981 GGGGTCCAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 20 0.56
9 8 0.22
10 8 0.22
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Done.