Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold45
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: 1408018
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 441 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:122780 original size:79 final size:78
Alignment explanation
Indices: 122622--122808 Score: 214
Period size: 78 Copynumber: 2.4 Consensus size: 78
122612 GTCAGACTAC
* * * * * * * *
122622 GGTTGACTAGGGTGAAATCAATAAGTTAACGAGTTATAGAGGTTGACCAGGATGAAACGAGAAGT
1 GGTTGACT-GGATGAAATCAACAAGTCAACAAGTTAAAAAGGTTGACCAGGATAAAACGACAAGT
122687 CAACAAGTTAAAAA
65 CAACAAGTTAAAAA
* *
122701 GGTTGACTGGATGAAATCGACAAGTCAACAAGTTAAAAAGGTTGACTAGGATAAAACTGACAAGT
1 GGTTGACTGGATGAAATCAACAAGTCAACAAGTTAAAAAGGTTGACCAGGATAAAAC-GACAAGT
* *
122766 CAATAAGTTGAAAA
65 CAACAAGTTAAAAA
*
122780 GGTTGACTGAGAT-AAAACTAACAAGTCAA
1 GGTTGACTG-GATGAAATC-AACAAGTCAA
122809 TAAAGAGTGA
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
78 40 0.44
79 39 0.43
80 12 0.13
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.21
Consensus pattern (78 bp):
GGTTGACTGGATGAAATCAACAAGTCAACAAGTTAAAAAGGTTGACCAGGATAAAACGACAAGTC
AACAAGTTAAAAA
Found at i:127385 original size:25 final size:21
Alignment explanation
Indices: 127339--127462 Score: 101
Period size: 20 Copynumber: 5.6 Consensus size: 21
127329 AAAATTAACT
127339 AAATGTATCGATACATTGAAA
1 AAATGTATCGATACATTGAAA
127360 AAATGTATCGATACATCTGGGTAAAAAAA
1 AAATGTATCGATACAT-T--G----A-AA
127389 CATAATGTATCGATACATTG-AA
1 -A-AATGTATCGATACATTGAAA
* *
127411 AAATGTATCGATACATT-CAT
1 AAATGTATCGATACATTGAAA
* *
127431 ACATGTATCGATATATTG-AA
1 AAATGTATCGATACATTGAAA
127451 AAATGTATCGAT
1 AAATGTATCGAT
127463 GCATCAAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
20 44 0.51
21 17 0.20
22 3 0.03
24 1 0.01
28 2 0.02
29 2 0.02
30 2 0.02
31 15 0.17
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (21 bp):
AAATGTATCGATACATTGAAA
Found at i:127417 original size:20 final size:20
Alignment explanation
Indices: 127392--127462 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
127382 AAAAAAACAT
127392 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* *
127412 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
127432 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
127452 AATGTATCGAT
1 AATGTATCGAT
127463 GCATCAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:127472 original size:20 final size:20
Alignment explanation
Indices: 127392--127474 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
127382 AAAAAAACAT
*
127392 AATGTATCGATACATTGAAA
1 AATGTATCGATACATCGAAA
*
127412 AATGTATCGATACATTC-ATA
1 AATGTATCGATACA-TCGAAA
* * *
127432 CATGTATCGATATATTGAAA
1 AATGTATCGATACATCGAAA
* *
127452 AATGTATCGATGCATCAAAA
1 AATGTATCGATACATCGAAA
127472 AAT
1 AAT
127475 ATATAGAAAC
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATCGAAA
Found at i:127530 original size:21 final size:21
Alignment explanation
Indices: 127504--127556 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
127494 AAAATAGAAT
*
127504 ATATCGATACCTGTACTATTC
1 ATATCGATACATGTACTATTC
*
127525 ATATCGATACATGTACTGTTC
1 ATATCGATACATGTACTATTC
127546 ATATCGATACA
1 ATATCGATACA
127557 AATTATGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (21 bp):
ATATCGATACATGTACTATTC
Found at i:131035 original size:42 final size:44
Alignment explanation
Indices: 130976--131073 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 44
130966 ATACGTTACT
* * * *
130976 TAATGTATCGAAACATTGCATTTGAAA-ATCTAGTTGTTGGG-C
1 TAATGTATCGATACATTGCATTTAAAAGAACTAGCTGTTGGGCC
*
131018 TAATGTATCGATACATTGCTTTTAAAAGAACTAGCTGTTGGGCC
1 TAATGTATCGATACATTGCATTTAAAAGAACTAGCTGTTGGGCC
*
131062 AAATGTATCGAT
1 TAATGTATCGAT
131074 CCAATATTGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 24 0.50
43 12 0.25
44 12 0.25
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (44 bp):
TAATGTATCGATACATTGCATTTAAAAGAACTAGCTGTTGGGCC
Found at i:131212 original size:20 final size:21
Alignment explanation
Indices: 131169--131213 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
131159 CAATGACTTG
*
131169 TATCGATACATTTAAATAATT
1 TATCGATACATTGAAATAATT
*
131190 TATCGATACATTGCAAT-ATT
1 TATCGATACATTGAAATAATT
131210 TATC
1 TATC
131214 TTACATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (21 bp):
TATCGATACATTGAAATAATT
Found at i:131891 original size:16 final size:16
Alignment explanation
Indices: 131866--131896 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
131856 GTAAAAGTAT
131866 AAGCACAATTTCATAA
1 AAGCACAATTTCATAA
*
131882 AAGCATAATTTCATA
1 AAGCACAATTTCATA
131897 GATCATGAAA
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:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (16 bp):
AAGCACAATTTCATAA
Found at i:133612 original size:20 final size:21
Alignment explanation
Indices: 133570--133621 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
133560 ATAGGATGAA
*
133570 TGTATCGATAC--ATTAGTAT
1 TGTATCGATACAAATTAGCAT
133589 TGTATCGATACAAATT-GCAT
1 TGTATCGATACAAATTAGCAT
*
133609 TGTATCAATACAA
1 TGTATCGATACAA
133622 TCTGGAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.38
20 15 0.52
21 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (21 bp):
TGTATCGATACAAATTAGCAT
Found at i:133667 original size:48 final size:49
Alignment explanation
Indices: 133589--133696 Score: 112
Period size: 48 Copynumber: 2.2 Consensus size: 49
133579 ACATTAGTAT
* *
133589 TGTATCGATACAAATTGCATTGTATCAATACAATCTGG-AAAGCCCAGA
1 TGTATCGATACAAATTGCACTATATCAATACAATCTGGAAAAGCCCAGA
* * * * * *
133637 TGTATCGATAC-ATTATGCACTATATTAATACAGTTTGGAAAAGTCTAGA
1 TGTATCGATACAAAT-TGCACTATATCAATACAATCTGGAAAAGCCCAGA
*
133686 TGTATTGATAC
1 TGTATCGATAC
133697 TTTGAACAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
47 2 0.04
48 29 0.59
49 18 0.37
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (49 bp):
TGTATCGATACAAATTGCACTATATCAATACAATCTGGAAAAGCCCAGA
Found at i:139628 original size:43 final size:43
Alignment explanation
Indices: 139552--139649 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
139542 TACATTACTT
* * *
139552 AATGTATCGATACATTGCATTTGAAAATATAGCCGTTGGGCTA
1 AATGTATCGATACATTGCATTTGAAAAAATAGCCATTGGGCCA
* *
139595 ATTGTATTGATACATTGC-TTT-AAAAGAACTAGCCATTGGGCCA
1 AATGTATCGATACATTGCATTTGAAAA-AA-TAGCCATTGGGCCA
139638 AATGTATCGATA
1 AATGTATCGATA
139650 TAATATTGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.09
42 4 0.09
43 38 0.83
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (43 bp):
AATGTATCGATACATTGCATTTGAAAAAATAGCCATTGGGCCA
Found at i:139785 original size:20 final size:21
Alignment explanation
Indices: 139742--139812 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 21
139732 GCCAATGACT
139742 TGTATCGATATATTTACATAA
1 TGTATCGATATATTTACATAA
139763 TGTATCGATATA-TTACA-ATA
1 TGTATCGATATATTTACATA-A
* * *
139783 TGTATCGATACATTTTCAT-G
1 TGTATCGATATATTTACATAA
139803 TGTATCGATA
1 TGTATCGATA
139813 GAAATGAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.02
20 27 0.61
21 16 0.36
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (21 bp):
TGTATCGATATATTTACATAA
Found at i:141483 original size:57 final size:57
Alignment explanation
Indices: 141395--141508 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
141385 CCCAAAATCA
141395 GTACCTTACTAGCTACATTGTGACTTGACATTGGTTTCATTGGTTTTGAATCGATAT
1 GTACCTTACTAGCTACATTGTGACTTGACATTGGTTTCATTGGTTTTGAATCGATAT
141452 GTACCTTACTAGCTACATTGTGACTTGACATTGGTTTCATTGGTTTTGAATCGATAT
1 GTACCTTACTAGCTACATTGTGACTTGACATTGGTTTCATTGGTTTTGAATCGATAT
141509 TATTTCAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (57 bp):
GTACCTTACTAGCTACATTGTGACTTGACATTGGTTTCATTGGTTTTGAATCGATAT
Found at i:142291 original size:37 final size:37
Alignment explanation
Indices: 142217--142291 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
142207 ACATGAAGGA
* *
142217 AAGGATGTGTCAAGCTTTGAAAAATCACCTTGGCCTC
1 AAGGATGTGTCAAGCTTTGAAAAATCACCTCGACCTC
* *
142254 AAGGATGTGTTAGGCTTTGAAAAATCACCTCGACCTC
1 AAGGATGTGTCAAGCTTTGAAAAATCACCTCGACCTC
142291 A
1 A
142292 TTTAGTATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (37 bp):
AAGGATGTGTCAAGCTTTGAAAAATCACCTCGACCTC
Found at i:144790 original size:28 final size:28
Alignment explanation
Indices: 144726--145197 Score: 567
Period size: 28 Copynumber: 16.8 Consensus size: 28
144716 GTTGCCACCA
* **
144726 ACTTGTGTGGCTTTAGAGAAGGTTGCCACCA
1 ACTTGTG-GGCTTT-GA-AAGGATGCCACTG
* *
144757 ACTTGTGGGCTTTAAAAGGATGCCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
144785 ATTTGTGGGATTTGAAAGG-TGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
144812 ACTTGTGGGCTTTAAAAGGGTGCCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
144840 ACTTGTAGGCTTCGAAAGGGA-GCCA-TA
1 ACTTGTGGGCTTTGAAA-GGATGCCACTG
*
144867 ACTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
144895 ACTTGTATGGGC-TT-AAAGGGGTGCCACTG
1 ACTTG--TGGGCTTTGAAA-GGATGCCACTG
*
144924 ACTTGTGGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
144952 ACATGTGGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
144980 ACTTGTGGGCTTTGAAAGGATGCTACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
145008 ACTTGTGGGCTTTGAAAGGTTGCCAATG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
145036 ACATATGGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
145064 ACTTGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
145092 ACTTGTGGGCTTTGGAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
145120 ACATGTGGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
145148 ACTTGTGGGCTTTGAAAGGATACCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
145176 ACTTGTGGGCTTTGAAAAGGAT
1 ACTTGTGGGCTTTG-AAAGGAT
145198 CGTATTGATG
Statistics
Matches: 384, Mismatches: 47, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.01
27 47 0.12
28 286 0.74
29 31 0.08
30 11 0.03
31 7 0.02
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAAGGATGCCACTG
Found at i:151567 original size:13 final size:13
Alignment explanation
Indices: 151549--151574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
151539 ACAATATTCT
151549 TTGTATCGATACA
1 TTGTATCGATACA
151562 TTGTATCGATACA
1 TTGTATCGATACA
151575 AGGGTTACTA
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):
TTGTATCGATACA
Found at i:153519 original size:23 final size:23
Alignment explanation
Indices: 153476--153520 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
153466 TTGTAACCGA
*
153476 TTATCAAGGGGGAAAAATTTTTT
1 TTATCAAGAGGGAAAAATTTTTT
153499 TTATCAA-AGGG-AAAATTTTTT
1 TTATCAAGAGGGAAAAATTTTTT
153520 T
1 T
153521 GAACGAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 3 0.14
23 7 0.33
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (23 bp):
TTATCAAGAGGGAAAAATTTTTT
Found at i:153529 original size:22 final size:21
Alignment explanation
Indices: 153489--153529 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
153479 TCAAGGGGGA
* *
153489 AAAATTTTTTTTATCAAAGGG
1 AAAATTTTTTTGAACAAAGGG
153510 AAAATTTTTTTGAACGAAAG
1 AAAATTTTTTTGAAC-AAAG
153530 CCTTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (21 bp):
AAAATTTTTTTGAACAAAGGG
Found at i:154092 original size:13 final size:13
Alignment explanation
Indices: 154074--154098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
154064 CATTATGCTT
154074 TGTATCGATACAA
1 TGTATCGATACAA
154087 TGTATCGATACA
1 TGTATCGATACA
154099 TATTCATTGT
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:154111 original size:19 final size:20
Alignment explanation
Indices: 154087--154138 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
154077 ATCGATACAA
**
154087 TGTATCGATACATATTC-AT
1 TGTATCGATACATAGGCAAT
*
154106 TGTATCGATACATGGGCAAT
1 TGTATCGATACATAGGCAAT
154126 TGTATCGATACAT
1 TGTATCGATACAT
154139 GAAACTAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATAGGCAAT
Found at i:154114 original size:32 final size:33
Alignment explanation
Indices: 154053--154117 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
154043 AAACACCTAG
*
154053 ATGTATCAATACATTATGCTTTGTATCGATACA
1 ATGTATCAATACATTATGCATTGTATCGATACA
* *
154086 ATGTATCGATACA-TATTCATTGTATCGATACA
1 ATGTATCAATACATTATGCATTGTATCGATACA
154118 TGGGCAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (33 bp):
ATGTATCAATACATTATGCATTGTATCGATACA
Found at i:154211 original size:33 final size:33
Alignment explanation
Indices: 154169--154247 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
154159 TACCACTGTT
154169 TGTATCGATACATG-GGACATTGTATCAATACAA
1 TGTATCGATACATGAGGA-ATTGTATCAATACAA
* *
154202 TGTATCGATACATGATGAATTGTATCGATACAA
1 TGTATCGATACATGAGGAATTGTATCAATACAA
154235 TGTATCGATACAT
1 TGTATCGATACAT
154248 TGCTTCAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGAGGAATTGTATCAATACAA
Found at i:154240 original size:13 final size:13
Alignment explanation
Indices: 154189--154246 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
154179 CATGGGACAT
*
154189 TGTATCAATACAA
1 TGTATCGATACAA
154202 TGTATCGATAC-A
1 TGTATCGATACAA
*
154214 TG-AT-G--A-AT
1 TGTATCGATACAA
154222 TGTATCGATACAA
1 TGTATCGATACAA
154235 TGTATCGATACA
1 TGTATCGATACA
154247 TTGCTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
8 3 0.08
9 2 0.06
10 2 0.06
11 2 0.06
12 4 0.11
13 23 0.64
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:154551 original size:21 final size:21
Alignment explanation
Indices: 154527--154596 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 21
154517 TCATTGTTGT
*
154527 TATTTTTCGAAAGCTCTTTTG
1 TATTTTTTGAAAGCTCTTTTG
154548 TATTTGTTTTG--AG-TCATTGTTG
1 TA-TT-TTTTGAAAGCTC-TT-TTG
154570 TTATTTTTTGAAAGCTCTTTTG
1 -TATTTTTTGAAAGCTCTTTTG
154592 TATTT
1 TATTT
154597 GTTCTGAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 16
0.70 0.02 0.28
Matches are distributed among these distances:
20 2 0.05
21 16 0.40
22 10 0.25
23 10 0.25
24 2 0.05
ACGTcount: A:0.17, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TATTTTTTGAAAGCTCTTTTG
Found at i:154583 original size:44 final size:45
Alignment explanation
Indices: 154517--154610 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 45
154507 GCCTTTGCAT
*
154517 TCATTGTTGTTATTTTTCGAAAGCTCTTTTGTATTTGTTTTGAG-
1 TCATTGTTGTTATTTTTCGAAAGCTCTTTTGTATTTGTTCTGAGC
*
154561 TCATTGTTGTTATTTTTTGAAAGCTCTTTTGTATTTGTTCTGAGC
1 TCATTGTTGTTATTTTTCGAAAGCTCTTTTGTATTTGTTCTGAGC
154606 TCATT
1 TCATT
154611 CTTTCACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 42 0.89
45 5 0.11
ACGTcount: A:0.16, C:0.11, G:0.17, T:0.56
Consensus pattern (45 bp):
TCATTGTTGTTATTTTTCGAAAGCTCTTTTGTATTTGTTCTGAGC
Found at i:154606 original size:21 final size:20
Alignment explanation
Indices: 154538--154607 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 20
154528 ATTTTTCGAA
154538 AGCTCTTTTGTATTTGTTTTG
1 AGCTCTTTTGTATTTG-TTTG
154559 AG-TCATTGTTGTTATTT-TTTG
1 AGCTC-TT-TTG-TATTTGTTTG
154580 AAAGCTCTTTTGTATTTGTTCTG
1 --AGCTCTTTTGTATTTGTT-TG
154603 AGCTC
1 AGCTC
154608 ATTCTTTCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
20 2 0.05
21 18 0.44
22 8 0.20
23 11 0.27
24 2 0.05
ACGTcount: A:0.14, C:0.11, G:0.19, T:0.56
Consensus pattern (20 bp):
AGCTCTTTTGTATTTGTTTG
Found at i:169185 original size:50 final size:51
Alignment explanation
Indices: 169128--169282 Score: 161
Period size: 50 Copynumber: 2.9 Consensus size: 51
169118 TTTTAACTAG
169128 ATGTATCGATACATTG-AAAACGTATCGATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAACGTATCGATACATCTGGGTAAAAAGACAGA
* *
169178 ATGTATCGATACATCTAGGTAAAAGACAAAATGTATCAATACATCTAGGT-AAAAGACAGA
1 ATGTATCGATACAT-T--G-AAAA-AC-----GTATCGATACATCTGGGTAAAAAGACAGA
* * *
169238 ATGCATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAA
1 ATGTATCGATACATTGAAAAACGTATCGATACATCTGGGTAAAAA
169283 TGTGACTTGT
Statistics
Matches: 86, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
50 29 0.34
51 5 0.06
53 1 0.01
55 4 0.05
56 6 0.07
57 1 0.01
59 1 0.01
60 23 0.27
61 16 0.19
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAACGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:169204 original size:30 final size:30
Alignment explanation
Indices: 169149--169251 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
169139 CATTGAAAAC
*
169149 GTATCGATACATCTGGGTAAAAAGACAGAAT
1 GTATCGATACATCTAGGT-AAAAGACAGAAT
*
169180 GTATCGATACATCTAGGTAAAAGACAAAAT
1 GTATCGATACATCTAGGTAAAAGACAGAAT
*
169210 GTATCAATACATCTAGGTAAAAGACAGAAT
1 GTATCGATACATCTAGGTAAAAGACAGAAT
*
169240 GCATCGATACAT
1 GTATCGATACAT
169252 TGAAAAATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
30 49 0.74
31 17 0.26
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (30 bp):
GTATCGATACATCTAGGTAAAAGACAGAAT
Found at i:171166 original size:92 final size:92
Alignment explanation
Indices: 171009--171528 Score: 589
Period size: 92 Copynumber: 5.7 Consensus size: 92
170999 AGAAGTGCAA
* * * *
171009 ACCACATATTCCCAATCATATCCCTTTCATCCAACTACTAGATGGTACTGATGCATCACATAGCC
1 ACCACACATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCC
* * **
171074 TATTTTCCTTAGGGCAAGGATATCCCA
66 TAGTTTCCTTAGGGCAAGGACATCCTG
* *
171101 ACCACACATTCCCAATCATATCTCC-TTCATCCAACCACTAAATGGTATTAATGCATCACAAAGC
1 ACCACACATTCCCAATCATATC-CCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGC
* * * * * *
171165 CTAATTTCCTAAAGGTAGGGACATCTTG
65 CTAGTTTCCTTAGGGCAAGGACATCCTG
* * * *
171193 ACCACATATTCCCAATCATAACCCTTTCATCCAACCACTAGATGGTATTGATGCATCATAGAGCC
1 ACCACACATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCC
171258 T-GATTT-CTTAGGGCCAAGGACATCCTG
66 TAG-TTTCCTTAGGG-CAAGGACATCCTG
* * * * * * *
171285 ACCACACATTCCCAATCATATACTTTTCATCAAACCACTATATGGTATTGATGTATTACAAAGCT
1 ACCACACATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCC
* *
171350 TGGTTTCCTTAGGGCAAAGACATCCTG
66 TAGTTTCCTTAGGGCAAGGACATCCTG
* *
171377 ACCACACATTCCCAATCATATCCCTTTCATCCAATCACTAGATGGTATTGATGCATCATAAAGCC
1 ACCACACATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCC
* * * * * *
171442 TGGTTTCCATGGGGTAAAGATATCCTG
66 TAGTTTCCTTAGGGCAAGGACATCCTG
* * ** * *
171469 GCCACACATTCCTAATCATATCCC-TTCATTTTAGCCATTAGATGGTATTGATGCATCACA
1 ACCACACATTCCCAATCATATCCCTTTCA-TCCAACCACTAGATGGTATTGATGCATCACA
171529 TCACCACAAA
Statistics
Matches: 361, Mismatches: 60, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
91 11 0.03
92 340 0.94
93 10 0.03
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.29
Consensus pattern (92 bp):
ACCACACATTCCCAATCATATCCCTTTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCC
TAGTTTCCTTAGGGCAAGGACATCCTG
Found at i:171513 original size:276 final size:276
Alignment explanation
Indices: 171009--171526 Score: 655
Period size: 276 Copynumber: 1.9 Consensus size: 276
170999 AGAAGTGCAA
* * * * *
171009 ACCACATATTCCCAATCATATCCCTTTCATCCAACTACTAGATGGTACTGATGCATCACATAGCC
1 ACCACACATTCCCAATCATATACCTTTCATCAAACCACTAGATGGTACTGATGCATCACAAAGCC
* * *
171074 TATTTTCCTTAGGGCAAGGATATCCCAACCACACATTCCCAATCATATCTCCTTCATCCAACCAC
66 TAGTTTCCTTAGGGCAAAGACATCCCAACCACACATTCCCAATCATATCTCCTTCATCCAACCAC
** * *
171139 TAAATGGTATTAATGCATCACAAAGCCTAATTTCCTAAAGGTAGGGACATCTTGACCACATATTC
131 TAAATGGTATTAATGCATCACAAAGCCTAATTTCCTAAAGGTAAAGACATCCTGACCACACATTC
171204 CCAATCATAACCCTTTCATCCAACCACTAGATGGTATTGATGCATCATAGAGCCTGATTTCTTAG
196 CCAATCATAACCCTTTCATCCAACCACTAGATGGTATTGATGCATCATAGAGCCTGATTTCTTAG
171269 GGCCAAGGACATCCTG
261 GGCCAAGGACATCCTG
* * * * * *
171285 ACCACACATTCCCAATCATATACTTTTCATCAAACCACTATATGGTATTGATGTATTACAAAGCT
1 ACCACACATTCCCAATCATATACCTTTCATCAAACCACTAGATGGTACTGATGCATCACAAAGCC
* ** *
171350 TGGTTTCCTTAGGGCAAAGACATCCTGACCACACATTCCCAATCATATC-CCTTTCATCCAATCA
66 TAGTTTCCTTAGGGCAAAGACATCCCAACCACACATTCCCAATCATATCTCC-TTCATCCAACCA
* * * ** ** * *
171414 CTAGATGGTATTGATGCATCATAAAGCCTGGTTTCC-ATGGGGTAAAGATATCCTGGCCACACAT
130 CTAAATGGTATTAATGCATCACAAAGCCTAATTTCCTA-AAGGTAAAGACATCCTGACCACACAT
* * ** * *
171478 TCCTAATCATATCCC-TTCATTTTAGCCATTAGATGGTATTGATGCATCA
194 TCCCAATCATAACCCTTTCA-TCCAACCACTAGATGGTATTGATGCATCA
171527 CATCACCACA
Statistics
Matches: 202, Mismatches: 37, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
275 7 0.03
276 195 0.97
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (276 bp):
ACCACACATTCCCAATCATATACCTTTCATCAAACCACTAGATGGTACTGATGCATCACAAAGCC
TAGTTTCCTTAGGGCAAAGACATCCCAACCACACATTCCCAATCATATCTCCTTCATCCAACCAC
TAAATGGTATTAATGCATCACAAAGCCTAATTTCCTAAAGGTAAAGACATCCTGACCACACATTC
CCAATCATAACCCTTTCATCCAACCACTAGATGGTATTGATGCATCATAGAGCCTGATTTCTTAG
GGCCAAGGACATCCTG
Found at i:172199 original size:91 final size:91
Alignment explanation
Indices: 172104--172274 Score: 218
Period size: 91 Copynumber: 1.9 Consensus size: 91
172094 CTATTTGACA
* * * * * **
172104 TGATGGTTCTTGCACTAGTTAAACTCTTTTC-TTCCTTGTTTGACGTGATGGTTCTTATTATGGT
1 TGATGGTTCTTGCACTAGTCAAACTCTTTTCACTAC-TATTTGACGTGATAGTTCTTACCATGGT
*
172168 TAAACATCTTTTCATTCCGATTTGATG
65 CAAACATCTTTTCATTCCGATTTGATG
* * * *
172195 TGATGGTTCTTGCCCTAGTCAAGCTCTTTTCACTACTATTTGACGTGATAGTTCTTGCCATTGTC
1 TGATGGTTCTTGCACTAGTCAAACTCTTTTCACTACTATTTGACGTGATAGTTCTTACCATGGTC
172260 AAACATCTTTTCATT
66 AAACATCTTTTCATT
172275 ATTGTTTAAC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
91 65 0.97
92 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (91 bp):
TGATGGTTCTTGCACTAGTCAAACTCTTTTCACTACTATTTGACGTGATAGTTCTTACCATGGTC
AAACATCTTTTCATTCCGATTTGATG
Found at i:172253 original size:45 final size:46
Alignment explanation
Indices: 172085--172272 Score: 168
Period size: 45 Copynumber: 4.1 Consensus size: 46
172075 GATAAAACTA
* *
172085 TTTTCACTACTATTTGACATGATGGTTCTTG-CACTAGTTAAAC-TC
1 TTTTCACTACTATTTGACGTGATGGTTCTTGCCA-TAGTCAAACATC
* * * *** * *
172130 TTTTC-TTCCTTGTTTGACGTGATGGTTCTTATTATGGTTAAACATC
1 TTTTCACTAC-TATTTGACGTGATGGTTCTTGCCATAGTCAAACATC
* * * * * *
172176 TTTTCATTCCGATTTGATGTGATGGTTCTTGCCCTAGTCAAGC-TC
1 TTTTCACTACTATTTGACGTGATGGTTCTTGCCATAGTCAAACATC
* *
172221 TTTTCACTACTATTTGACGTGATAGTTCTTGCCATTGTCAAACATC
1 TTTTCACTACTATTTGACGTGATGGTTCTTGCCATAGTCAAACATC
172267 TTTTCA
1 TTTTCA
172273 TTATTGTTTA
Statistics
Matches: 113, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
44 2 0.02
45 68 0.60
46 39 0.35
47 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (46 bp):
TTTTCACTACTATTTGACGTGATGGTTCTTGCCATAGTCAAACATC
Found at i:172428 original size:82 final size:82
Alignment explanation
Indices: 172212--172549 Score: 256
Period size: 81 Copynumber: 4.2 Consensus size: 82
172202 TCTTGCCCTA
* * * * * * *
172212 GTCAAGCTC-TTTTCACTACTATTTGACGTGATAGTTCTTGCCATT-GTCAAACATCTTTTCATT
1 GTCAAACTCTTTTTCATTACTGTTTGACATAATAGTTATTGCC-TTGGTCAAACATCTTTTCATC
**** * * *
172275 ATTGTTTAACTGTATCTA
65 CCCATTTGACTATATCTG
* * ** * *** * *
172293 GTCAAACTC-TTTTCATTACCGTTTGACTTGGTGGTCCCTACCTTGGTCGAACATCTTTTCATCC
1 GTCAAACTCTTTTTCATTACTGTTTGACATAATAGTTATTGCCTTGGTCAAACATCTTTTCATCC
* *
172357 CCATTTGACTGTATTTG
66 CCATTTGACTATATCTG
* * *
172374 GTTAAACTCCTTTTT-ATTACT-TCTTGACATAATGGTTATTGCCTTGGTCAAACATCTATTCAT
1 GTCAAACT-CTTTTTCATTACTGT-TTGACATAATAGTTATTGCCTTGGTCAAACATCTTTTCAT
*** * *
172437 TATCGTTTGACTATATCTA
64 CCCCATTTGACTATATCTG
* * * *
172456 GTCAAACT-TTTTTCATTACTGTTTGAGATAATAGTTCTTGCCCTGGTCAAACATCATTTCATCC
1 GTCAAACTCTTTTTCATTACTGTTTGACATAATAGTTATTGCCTTGGTCAAACATCTTTTCATCC
*
172520 CCATTTAACTATATCTG
66 CCATTTGACTATATCTG
172537 GTCAAACTCTTTT
1 GTCAAACTCTTTT
172550 CATCCTCGTT
Statistics
Matches: 200, Mismatches: 50, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
80 7 0.04
81 128 0.64
82 61 0.31
83 4 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (82 bp):
GTCAAACTCTTTTTCATTACTGTTTGACATAATAGTTATTGCCTTGGTCAAACATCTTTTCATCC
CCATTTGACTATATCTG
Found at i:174022 original size:165 final size:163
Alignment explanation
Indices: 173837--174146 Score: 365
Period size: 165 Copynumber: 1.9 Consensus size: 163
173827 TTATCGGACT
* * * * * * *
173837 AAAATTTTTAAAATTCATCAAATATTATTATCT-AATCACCATTTAATCAGCTTTAAAAAATTGA
1 AAAATTTTTAAAACTCATCAAATATCATCAT-TAAATCACC-GTAAATCAACTTTAAAAAATTCA
*
173901 TTTA-TTTT-TGAGTTTTTCATTTTTTTCCTTGAAATTCTCATATTTATAAAAAATCGAGTTTTC
64 TTTATTTTTATGAG-TTTTCA-TTTTTTCCTTGAAATTCTCATATTTATAAAAAATCGAATTTTC
*
173964 TTATTCCATAAATGTTTTCAAGGGGTTTTTCTCGGTTC
127 -TATTCAATAAATGTTTTCAAGGGGTTTTTCTCGGTTC
* * * * *
174002 AAAATTTTTAATACTCATCAAATATCATCATTGAAATCATCGTAAATTAATTTTGAAAAATTCAT
1 AAAATTTTTAAAACTCATCAAATATCATCATT-AAATCACCGTAAATCAACTTTAAAAAATTCAT
* * * * *
174067 TTATTTTTCATGAGTTTTCATTTTTTCTTTGAAATTCTCCTATTTTTGAAAAATTGAATTTTCTA
65 TTATTTTT-ATGAGTTTTCATTTTTTCCTTGAAATTCTCATATTTATAAAAAATCGAATTTTCTA
174132 TTCAATAAATGTTTT
129 TTCAATAAATGTTTT
174147 TGAGGTAATT
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
164 1 0.01
165 63 0.52
166 47 0.39
167 6 0.05
168 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (163 bp):
AAAATTTTTAAAACTCATCAAATATCATCATTAAATCACCGTAAATCAACTTTAAAAAATTCATT
TATTTTTATGAGTTTTCATTTTTTCCTTGAAATTCTCATATTTATAAAAAATCGAATTTTCTATT
CAATAAATGTTTTCAAGGGGTTTTTCTCGGTTC
Found at i:174201 original size:166 final size:164
Alignment explanation
Indices: 173892--174258 Score: 416
Period size: 166 Copynumber: 2.2 Consensus size: 164
173882 ATCAGCTTTA
*
173892 AAAAATTGATTTA-TTTTTGAGTTTTTCATTTTTTTCCTTGAAATTCTCATATTTATAAAAAATC
1 AAAAATTCATTTATTTTTTGAG-TTTTCA-TTTTTTCCTTGAAATTCTCATATTTATAAAAAATC
* * ** **
173956 GAGTTTTCTTATTCCATAAATGTTTTCAAGGGGTTTTTCTCGGTTCAAAATTTTTAATACTCATC
64 GAATTTTCTTATTCAATAAATGTTTTCAAGGAATTTTTCTCAATTCAAAATTTTTAATACTCATC
*
174021 AAATATCATCATTGAAATCATCGTAAATTAATTTTG
129 AAATATCATCATTGAAATCATAGTAAATTAATTTTG
* * * * *
174057 AAAAATTCATTTATTTTTCATGAGTTTTCATTTTTTCTTTGAAATTCTCCTATTTTTGAAAAATT
1 AAAAATTCATTTATTTTT--TGAGTTTTCATTTTTTCCTTGAAATTCTCATATTTATAAAAAATC
** * *
174122 GAATTTTC-TATTCAATAAATGTTTTTGAGGTAATTTTTCTCAATTTAAAATTTTTACA-ATTCA
64 GAATTTTCTTATTCAATAAATGTTTTCAAGG-AATTTTTCTCAATTCAAAATTTTTA-ATACTCA
* ** * * * *
174185 TCTAATATTGTCATTGAATTCTTATTAAATTACTTTTG
127 TCAAATATCATCATTGAAATCATAGTAAATTAATTTTG
*
174223 AAAAATTCAATTTATTTTTTGAGTTTTGAATTTTTT
1 AAAAATTC-ATTTATTTTTTGAGTTTT-CATTTTTT
174259 TGTATTTATT
Statistics
Matches: 170, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
165 39 0.23
166 110 0.65
167 17 0.10
168 4 0.02
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (164 bp):
AAAAATTCATTTATTTTTTGAGTTTTCATTTTTTCCTTGAAATTCTCATATTTATAAAAAATCGA
ATTTTCTTATTCAATAAATGTTTTCAAGGAATTTTTCTCAATTCAAAATTTTTAATACTCATCAA
ATATCATCATTGAAATCATAGTAAATTAATTTTG
Found at i:174768 original size:25 final size:25
Alignment explanation
Indices: 174722--174787 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
174712 TTTGGCAAGT
**
174722 AGAAAGAAAAAAGAGTAGAAAA-AAA
1 AGAAAG-AAAAAGAAAAGAAAATAAA
*
174747 AGAAAGAAAAAGAAAAGAAAAATAAG
1 AGAAAGAAAAAGAAAAG-AAAATAAA
*
174773 AGAAA-AATAAGAAAA
1 AGAAAGAAAAAGAAAA
174788 AAAGGCTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 9 0.26
25 19 0.54
26 7 0.20
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (25 bp):
AGAAAGAAAAAGAAAAGAAAATAAA
Found at i:174768 original size:35 final size:35
Alignment explanation
Indices: 174724--174790 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
174714 TGGCAAGTAG
*
174724 AAAGAAAAAA-GAGTAGAAAAAAAAGAAAGAAAAAGA
1 AAAGAAAAAATAAG-AGAAAAAAAAGAAA-AAAAAGA
*
174760 AAAG-AAAAATAAGAGAAAAATAAGAAAAAAA
1 AAAGAAAAAATAAGAGAAAAAAAAGAAAAAAA
174791 GGCTAAACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 18 0.64
36 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (35 bp):
AAAGAAAAAATAAGAGAAAAAAAAGAAAAAAAAGA
Found at i:174773 original size:20 final size:20
Alignment explanation
Indices: 174738--174791 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
174728 AAAAAAGAGT
174738 AGAAAA-AAAAGAAAGA-AAA
1 AGAAAAGAAAA-AAAGAGAAA
174757 AGAAAAGAAAAATAAGAGAAA
1 AGAAAAGAAAAA-AAGAGAAA
*
174778 A-ATAAGAAAAAAAG
1 AGAAAAGAAAAAAAG
174792 GCTAAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 10 0.32
20 17 0.55
21 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (20 bp):
AGAAAAGAAAAAAAGAGAAA
Found at i:174776 original size:11 final size:11
Alignment explanation
Indices: 174751--174789 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
174741 AAAAAAAGAA
* *
174751 AGAAAAAGAAA
1 AGAAAAATAAG
174762 AGAAAAATAAG
1 AGAAAAATAAG
174773 AGAAAAATAAG
1 AGAAAAATAAG
174784 A-AAAAA
1 AGAAAAA
174790 AGGCTAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (11 bp):
AGAAAAATAAG
Found at i:174789 original size:22 final size:20
Alignment explanation
Indices: 174740--174791 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
174730 AAAAGAGTAG
174740 AAAAAAAAGAAAGAAAAAGA
1 AAAAAAAAGAAAGAAAAAGA
* *
174760 AAAGAAAAATAAGAGAAAAATA
1 AAA-AAAAAGAA-AGAAAAAGA
174782 AGAAAAAAAG
1 A-AAAAAAAG
174792 GCTAAACTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 14 0.54
23 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAAAAAGAAAGAAAAAGA
Found at i:176503 original size:3 final size:3
Alignment explanation
Indices: 176495--176540 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
176485 CCAAATAGAA
176495 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
176541 GAAAAGCAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:180386 original size:167 final size:166
Alignment explanation
Indices: 180211--180512 Score: 416
Period size: 167 Copynumber: 1.8 Consensus size: 166
180201 AGCAAAATTG
*
180211 AATTTTAATCAT-TCTTTTTAATCTTTTATATT-CTTATGGGAGTCCGTAGGGGTATAAAAGATT
1 AATTTTAATCATCT-TTTTTAATCTTTTATATTGC-TATAGGAGTCCGTAGGGGTATAAAAGATT
* *
180274 TCCAAAACTTTTCGCATATTTTCGAGCT-TCCATTAAGGTACGAAATGATATTTTTC-GAAA-TT
64 TCCAAAACTTTTCACATATTTTCG-GCTCTCCATTAAGGT-CGAAATGA-ATTTTTCAAAAATTT
180336 AAATAAATAAATAACTAAATTAACACTTTTATAACCAGAATA
126 AAA-AAATAAATAACTAAATTAACACTTTTATAACCAGAATA
*** * *
180378 AATTTTAATCATCTTTTTTAATCTTTTATATTGCTATAGTTTTCTGTAGGGGTATAAAAGATTTT
1 AATTTTAATCATCTTTTTTAATCTTTTATATTGCTATAGGAGTCCGTAGGGGTATAAAAGATTTC
* * *
180443 CAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTCGAAATGAATTTTTCAAAAATTTAAAAA
66 CAAAACTTTTCACATATTTTCGGCTCTCCATTAAGGTCGAAATGAATTTTTCAAAAATTTAAAAA
180508 ATAAA
131 ATAAA
180513 AATAAAAATT
Statistics
Matches: 119, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
165 7 0.06
166 20 0.17
167 90 0.76
168 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (166 bp):
AATTTTAATCATCTTTTTTAATCTTTTATATTGCTATAGGAGTCCGTAGGGGTATAAAAGATTTC
CAAAACTTTTCACATATTTTCGGCTCTCCATTAAGGTCGAAATGAATTTTTCAAAAATTTAAAAA
ATAAATAACTAAATTAACACTTTTATAACCAGAATA
Found at i:181749 original size:13 final size:13
Alignment explanation
Indices: 181730--181768 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
181720 ACTATTTATG
181730 ATGTATCGATACA
1 ATGTATCGATACA
*
181743 CTGTATCGATACA
1 ATGTATCGATACA
181756 ATGTATCGATACA
1 ATGTATCGATACA
181769 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:181855 original size:21 final size:22
Alignment explanation
Indices: 181826--181878 Score: 99
Period size: 21 Copynumber: 2.5 Consensus size: 22
181816 GTGAATAGTG
181826 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
181848 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
181869 TGAACAGTGA
1 TGAACAGTGA
181879 CGAATAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:181986 original size:53 final size:53
Alignment explanation
Indices: 181922--182058 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
181912 CTACTACCAA
181922 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * * *
181975 TGTATCGATACATATTATGTTTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
182028 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
182059 TATGCAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 65 0.84
54 12 0.16
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:182091 original size:20 final size:20
Alignment explanation
Indices: 182028--182098 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
182018 GCCAATGTCT
**
182028 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
182048 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
182068 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
182088 TGTATCGATAC
1 TGTATCGATAC
182099 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:182164 original size:21 final size:21
Alignment explanation
Indices: 182138--182178 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
182128 GTCAACCTTG
182138 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
182159 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
182179 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:183841 original size:13 final size:13
Alignment explanation
Indices: 183823--183847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183813 ACTGAAGCAA
183823 TGTATCGATACAT
1 TGTATCGATACAT
183836 TGTATCGATACA
1 TGTATCGATACA
183848 ATTTGAAAAA
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:187592 original size:13 final size:13
Alignment explanation
Indices: 187573--187611 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
187563 ACTATTTATG
187573 ATGTATCGATACA
1 ATGTATCGATACA
*
187586 CTGTATCGATACA
1 ATGTATCGATACA
187599 ATGTATCGATACA
1 ATGTATCGATACA
187612 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:187723 original size:22 final size:22
Alignment explanation
Indices: 187669--187723 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
187659 GTGAATAGTG
187669 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
187691 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
187712 TGAACAGTGATG
1 TGAACAGTGATG
187724 AATAGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:187832 original size:53 final size:53
Alignment explanation
Indices: 187767--187901 Score: 225
Period size: 53 Copynumber: 2.5 Consensus size: 53
187757 ACTACCAATG
187767 TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACCTA
1 TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACCTA
* * * *
187820 TATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCCTG
1 TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACCTA
187873 TATCGATACATATTTGTGTGTATCGATAC
1 TATCGATACATATTT-TGTGTATCGATAC
187902 TATGCAATTT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 63 0.83
54 13 0.17
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (53 bp):
TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACCTA
Found at i:187934 original size:20 final size:20
Alignment explanation
Indices: 187871--187940 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
187861 GCCAATGTCC
**
187871 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
187891 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
187911 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
187931 TGTATCGATA
1 TGTATCGATA
187941 TTTTTTAGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 37 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:188007 original size:21 final size:21
Alignment explanation
Indices: 187981--188021 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
187971 GTCAACCTTG
187981 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
188002 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
188022 TTTTACGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:188510 original size:156 final size:156
Alignment explanation
Indices: 188222--188806 Score: 762
Period size: 156 Copynumber: 3.8 Consensus size: 156
188212 AAATCCTAAC
** * ** * * * * *
188222 AGTATCCTTTAGGGGTATTTTTGTAACTTTTTAGAACCAACTCCTACA-TCATCACTGGGTCTGC
1 AGTATCCCCTAGGGGCATTTTCATAATTTTTTAGAATCAACTCCTA-AGTTATAACTGGGTCCGC
* * * * * * *
188286 TTTTATGCCGAAGATGGTTATTTAGGATAGGTTCATCTAATTTCTAGTCCTTTTTAAGTCCATAA
65 TTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCATTTTCTAGTCCTTTTTAAGTCCTTTA
* * *
188351 GGGGTACCGAGATACTTTCACGTCGAA
130 GGGGTACCGGGATACTTTCATGTTGAA
* * * ** * *
188378 GGTATCCCTTAGGGGTATTTTTGTAATTTTTTAGAATCAAGTCCTAAGTTATAACT-GATACCGC
1 AGTATCCCCTAGGGGCATTTTCATAATTTTTTAGAATCAACTCCTAAGTTATAACTGGGT-CCGC
*
188442 TTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCCTTTTCTAGTCCTTTTTAAGTCCTTTA
65 TTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCATTTTCTAGTCCTTTTTAAGTCCTTTA
188507 GGGGTACCGGGATACTTTCATGTTGAA
130 GGGGTACCGGGATACTTTCATGTTGAA
* * * *
188534 AGTATCCCCCAGGGGCATTTTCATAATTTTTTAGAATCGAGTCCTAAGTTATAGCTGGGTCCGCT
1 AGTATCCCCTAGGGGCATTTTCATAATTTTTTAGAATCAACTCCTAAGTTATAACTGGGTCCGCT
** * *
188599 TTTATGCCGAAGGTAAGTATTTAGAATAGGTTCACCCCTTTTCTAGTCCTTTTTAAGTCCTTTAG
66 TTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCATTTTCTAGTCCTTTTTAAGTCCTTTAG
*
188664 GGGTACCGGGATACTTTCGTGTTGAA
131 GGGTACCGGGATACTTTCATGTTGAA
* * *
188690 AGTATCCCCTAGGGGCATTTTCATAATTTTTTAGAATCGACTTCTAAGTTATAACTAGGTCCGCT
1 AGTATCCCCTAGGGGCATTTTCATAATTTTTTAGAATCAACTCCTAAGTTATAACTGGGTCCGCT
*
188755 TTTATGCCGAAGGTGGGTATTTAGGATAGGTTCTCCCATTTTCTAGT-CTTTT
66 TTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCATTTTCTAGTCCTTTT
188807 AGGGGCATCG
Statistics
Matches: 383, Mismatches: 43, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
155 8 0.02
156 373 0.97
157 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (156 bp):
AGTATCCCCTAGGGGCATTTTCATAATTTTTTAGAATCAACTCCTAAGTTATAACTGGGTCCGCT
TTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCATTTTCTAGTCCTTTTTAAGTCCTTTAG
GGGTACCGGGATACTTTCATGTTGAA
Found at i:189134 original size:156 final size:156
Alignment explanation
Indices: 188836--189677 Score: 862
Period size: 156 Copynumber: 5.4 Consensus size: 156
188826 CATGTCGAAA
* * * * *
188836 GTATTTAGGATAGGTTCATCCCATTTCTAGTCCTTTTTAAGTCTTTTAGGTGTA-CTGAGATACT
1 GTATTTAGGATAGGTTCACCCCTTTTATAGTCATTTTTAAGTCTTTTAGGGGTATC-GAGATACT
* * * * *
188900 TTCACGTCGAAA-GTATCCCTTAGGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTGTC
65 TTCACATC-AAAGGTATCTCTTAGGGGCATTTTCGTAATTTTTTAGAATCGAGTCCTAGGTTATC
*** *
188964 GTTGGGTCCGCTTTTATGCCGAAAGTGG
129 ACCGGGTCCGCTTTTATGCTGAAAGTGG
* * * *
188992 GTATTTAGGATAGGTTCACCCCTGTTATAGTCATTTTTATGTCCTTTAGGGGTACCGAGATACTT
1 GTATTTAGGATAGGTTCACCCCTTTTATAGTCATTTTTAAGTCTTTTAGGGGTATCGAGATACTT
** * * *
189057 TCATGTCGAAGGTATCTCTTATGGGCATTTTTGTAATTTTTTAGAATCGAGTCCTAGGTTATCAC
66 TCACATCAAAGGTATCTCTTAGGGGCATTTTCGTAATTTTTTAGAATCGAGTCCTAGGTTATCAC
** * *
189122 CGAATCCACTTTTATGTTGAAAGTGG
131 CGGGTCCGCTTTTATGCTGAAAGTGG
* * *
189148 ATATTGAGGATAGGTTCGCCCCTTTTATAGTCCA-TTTTAAGTCTTTTAGGGGTATCGAGATACT
1 GTATTTAGGATAGGTTCACCCCTTTTATAGT-CATTTTTAAGTCTTTTAGGGGTATCGAGATACT
* * *** * * * * * *
189212 TTCATATTAAAAAAATC-CTCTAAGAGTATTTTCGTAATTTTTCA-AAACTGA-TTCTAGGTTAT
65 TTCACATCAAAGGTATCTCT-TAGGGGCATTTTCGTAATTTTTTAGAATC-GAGTCCTAGGTTAT
* * *
189274 AACCGGGTCCGTTTTTATGCTGAAGGTGG
128 CACCGGGTCCGCTTTTATGCTGAAAGTGG
* * *
189303 GTATTTAGGATAGGTTCATCCCTTTTATAGTCATTTTTAAGTGTTTTAGGGGTAT-GAGGTACTT
1 GTATTTAGGATAGGTTCACCCCTTTTATAGTCATTTTTAAGTCTTTTAGGGGTATCGAGATACTT
* * * * * * *
189367 TTACATCAAAGATATATTTTAGGGGGTATTTTTGTAATTTTTTAGAATCGAGTCCTACGTTATCA
66 TCACATCAAAGGTATCTCTTA-GGGGCATTTTCGTAATTTTTTAGAATCGAGTCCTAGGTTATCA
**
189432 CCGGGTCCGCTTTTATGCTGATGGTGG
130 CCGGGTCCGCTTTTATGCTGAAAGTGG
* * *
189459 GTATTGAGGATAGGTTCACCCCTTTTATAGTCCTTTTTAAGTCATTTAGGGGTATC-AGGATACT
1 GTATTTAGGATAGGTTCACCCCTTTTATAGTCATTTTTAAGTCTTTTAGGGGTATCGA-GATACT
* * * * * *
189523 TTCACATCAAAGGTATTCTCTGA-AGGCATTTTCATAATTTTTTAGAATC--GTCTTAAGTTATA
65 TTCACATCAAAGGTA-TCTCTTAGGGGCATTTTCGTAATTTTTTAGAATCGAGTCCTAGGTTATC
* * *
189585 ACCGAGTCTGCTTTTATGCCGAAAGTGG
129 ACCGGGTCCGCTTTTATGCTGAAAGTGG
* * * * * *
189613 GTATTTAGGATAAGTTCATCCCTTTTATAGTCATTTCTAAGTCCTTTAGGCGTATC-AGGTACTT
1 GTATTTAGGATAGGTTCACCCCTTTTATAGTCATTTTTAAGTCTTTTAGGGGTATCGAGATACTT
189677 T
66 T
189678 TATGTCGAAG
Statistics
Matches: 568, Mismatches: 105, Indels: 29
0.81 0.15 0.04
Matches are distributed among these distances:
153 7 0.01
154 105 0.18
155 107 0.19
156 324 0.57
157 21 0.04
158 4 0.01
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (156 bp):
GTATTTAGGATAGGTTCACCCCTTTTATAGTCATTTTTAAGTCTTTTAGGGGTATCGAGATACTT
TCACATCAAAGGTATCTCTTAGGGGCATTTTCGTAATTTTTTAGAATCGAGTCCTAGGTTATCAC
CGGGTCCGCTTTTATGCTGAAAGTGG
Found at i:189160 original size:377 final size:377
Alignment explanation
Indices: 188459--189179 Score: 1003
Period size: 377 Copynumber: 1.9 Consensus size: 377
188449 CCGAAGGTGG
* *
188459 GTATTTAGGATAGGTTCACCCCTTTTCTAGTCCTTTTTAAGTCCTTTAGGGGTACCGGGATACTT
1 GTATTTAGGATAGGTTCACCCCATTTCTAGTCCTTTTTAAGTCCTTTAGGGGTACCGAGATACTT
* * *
188524 TCATGTTGAAAGTATCCCCCAGGGGCATTTTCATAATTTTTTAGAATCGAGTCCTAAGTTATAGC
66 TCACGTCGAAAGTATCCCCCAGGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAAGTTATAGC
* * * *
188589 TGGGTCCGCTTTTATGCCGAAGGTAAGTATTTAGAATAGGTTCACCCCTTTTCTAGTCCTTTTTA
131 TGGGTCCGCTTTTATGCCGAAAGTAAGTATTTAGAATAGGTTCACCCCTGTTATAGTCATTTTTA
* * *
188654 AGTCCTTTAGGGGTACCGGGATACTTTCGTGTTGAAAGTATCCCCTAGGGGCATTTTCATAATTT
196 AGTCCTTTAGGGGTACCGAGATACTTTCATGTCGAAAGTATCCCCTAGGGGCATTTTCATAATTT
* * * * * * *
188719 TTTAGAATCGACTTCTAAGTTATAACTAGGTCCGCTTTTATGCCGAAGGTGGGTATTTAGGATAG
261 TTTAGAATCGACTCCTAAGTTATAACGAGATCCACTTTTATGCCGAAAGTGGATATTGAGGATAG
* *
188784 GTTCTCCCATTTTCTAGTCTTTTAGGGGCATCGAGAAACTTTCATGTCGAAA
326 GTTCGCCCATTTTATAGTCTTTTAGGGGCATCGAGAAACTTTCATGTCGAAA
* * * *
188836 GTATTTAGGATAGGTTCATCCCATTTCTAGTCCTTTTTAAGTCTTTTAGGTGTACTGAGATACTT
1 GTATTTAGGATAGGTTCACCCCATTTCTAGTCCTTTTTAAGTCCTTTAGGGGTACCGAGATACTT
** * * * *
188901 TCACGTCGAAAGTATCCCTTAGGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTGTCGT
66 TCACGTCGAAAGTATCCCCCAGGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAAGTTATAGC
** *
188966 TGGGTCCGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCACCCCTGTTATAGTCATTTTTA
131 TGGGTCCGCTTTTATGCCGAAAGTAAGTATTTAGAATAGGTTCACCCCTGTTATAGTCATTTTTA
* * * * * **
189031 TGTCCTTTAGGGGTACCGAGATACTTTCATGTCGAAGGTATCTCTTATGGGCATTTTTGTAATTT
196 AGTCCTTTAGGGGTACCGAGATACTTTCATGTCGAAAGTATCCCCTAGGGGCATTTTCATAATTT
* * * **
189096 TTTAGAATCGAGTCCTAGGTTATCACCGA-ATCCACTTTTATGTTGAAAGTGGATATTGAGGATA
261 TTTAGAATCGACTCCTAAGTTAT-AACGAGATCCACTTTTATGCCGAAAGTGGATATTGAGGATA
*
189160 GGTTCGCCCCTTTTATAGTC
325 GGTTCGCCCATTTTATAGTC
189180 CATTTTAAGT
Statistics
Matches: 296, Mismatches: 47, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
377 293 0.99
378 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (377 bp):
GTATTTAGGATAGGTTCACCCCATTTCTAGTCCTTTTTAAGTCCTTTAGGGGTACCGAGATACTT
TCACGTCGAAAGTATCCCCCAGGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAAGTTATAGC
TGGGTCCGCTTTTATGCCGAAAGTAAGTATTTAGAATAGGTTCACCCCTGTTATAGTCATTTTTA
AGTCCTTTAGGGGTACCGAGATACTTTCATGTCGAAAGTATCCCCTAGGGGCATTTTCATAATTT
TTTAGAATCGACTCCTAAGTTATAACGAGATCCACTTTTATGCCGAAAGTGGATATTGAGGATAG
GTTCGCCCATTTTATAGTCTTTTAGGGGCATCGAGAAACTTTCATGTCGAAA
Found at i:189406 original size:311 final size:309
Alignment explanation
Indices: 188967--189679 Score: 912
Period size: 311 Copynumber: 2.3 Consensus size: 309
188957 GGTTGTCGTT
* * *
188967 GGGTCCGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCACCCCTGTTATAGTCATTTTTAT
1 GGGTCCGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCATTTTTAA
* * * ** * * * *
189032 GTCCTTTAGGGGTACCGAGATACTTTCATGTCGAAGGTATCTCTTATGGGCATTTTTGTAATTTT
66 GTCCTTTAGGGGTA-TGAGGTACTTTTACATCAAAGATATATCTTAGGGGCATTTTTGTAATTTT
* *
189097 TTAGAATCGAGTCCTAGGTTATCACCGAATCCACTTTTATGTTGAAAGTGGATATTGAGGATAGG
130 TTAGAATCGAGTCCTACGTTATCACCGAATCCACTTTTATGCTGAAAGTGGATATTGAGGATAGG
* * * *
189162 TTCGCCCCTTTTATAGTCCATTTTAAGTCTTTTAGGGGTATC-GAGATACTTTCATATTAAAAAA
195 TTCACCCCTTTTATAGTCCATTTTAAGTCATTTAGGGGTATCAG-GATACTTTCACATCAAAAAA
* * *
189226 ATCCTCT-AAGAGTATTTTCGTAATTTTTCAAAA-CTGAT-TCTAGGTTATAACC
259 ATCCTCTGAAG-GCATTTTCATAATTTTTCAAAATC-G-TCT-TAAGTTATAACC
* * *
189278 GGGTCCGTTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCATTTTTAA
1 GGGTCCGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCATTTTTAA
** * *
189343 GTGTTTTAGGGGTATGAGGTACTTTTACATCAAAGATATATTTTAGGGGGTATTTTTGTAATTTT
66 GTCCTTTAGGGGTATGAGGTACTTTTACATCAAAGATATATCTTA-GGGGCATTTTTGTAATTTT
** * ** *
189408 TTAGAATCGAGTCCTACGTTATCACCGGGTCCGCTTTTATGCTGATGGTGGGTATTGAGGATAGG
130 TTAGAATCGAGTCCTACGTTATCACCGAATCCACTTTTATGCTGAAAGTGGATATTGAGGATAGG
* ***
189473 TTCACCCCTTTTATAGTCCTTTTTAAGTCATTTAGGGGTATCAGGATACTTTCACATCAAAGGTA
195 TTCACCCCTTTTATAGTCCATTTTAAGTCATTTAGGGGTATCAGGATACTTTCACATCAAAAAAA
* * *
189538 TTCTCTGAAGGCATTTTCATAATTTTTTAGAATCGTCTTAAGTTATAACC
260 TCCTCTGAAGGCATTTTCATAATTTTTCAAAATCGTCTTAAGTTATAACC
* * * *
189588 GAGTCTGCTTTTATGCCGAAAGTGGGTATTTAGGATAAGTTCATCCCTTTTATAGTCATTTCTAA
1 GGGTCCGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCATTTTTAA
* *
189653 GTCCTTTAGGCGTATCAGGTACTTTTA
66 GTCCTTTAGGGGTATGAGGTACTTTTA
189680 TGTCGAAGGT
Statistics
Matches: 345, Mismatches: 52, Indels: 11
0.85 0.13 0.03
Matches are distributed among these distances:
310 115 0.33
311 225 0.65
312 5 0.01
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (309 bp):
GGGTCCGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCATTTTTAA
GTCCTTTAGGGGTATGAGGTACTTTTACATCAAAGATATATCTTAGGGGCATTTTTGTAATTTTT
TAGAATCGAGTCCTACGTTATCACCGAATCCACTTTTATGCTGAAAGTGGATATTGAGGATAGGT
TCACCCCTTTTATAGTCCATTTTAAGTCATTTAGGGGTATCAGGATACTTTCACATCAAAAAAAT
CCTCTGAAGGCATTTTCATAATTTTTCAAAATCGTCTTAAGTTATAACC
Found at i:191365 original size:19 final size:20
Alignment explanation
Indices: 191320--191371 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
191310 TTACAAGCCA
*
191320 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
191340 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
191360 -TGTATCGATACA
1 ATGTATCGATACA
191372 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:191501 original size:20 final size:20
Alignment explanation
Indices: 191456--191507 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
191446 ATCGATACAA
*
191456 TGTATCGATACTGTGCAATC
1 TGTATCGATACTGTGCAAGC
* *
191476 TCTATCGATACATGTG-AAGG
1 TGTATCGATAC-TGTGCAAGC
191496 TGTATCGATACT
1 TGTATCGATACT
191508 TTTCAGGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.81
21 4 0.15
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (20 bp):
TGTATCGATACTGTGCAAGC
Found at i:193904 original size:13 final size:13
Alignment explanation
Indices: 193886--193923 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
193876 ATAAACCCTT
*
193886 TGTATCGATACAC
1 TGTATCGATACAA
193899 TGTATCGATACAA
1 TGTATCGATACAA
193912 TGTATCGATACA
1 TGTATCGATACA
193924 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:200076 original size:19 final size:20
Alignment explanation
Indices: 200027--200078 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
200017 TTACGAGCCA
*
200027 ATGTATCGATACATTTTGTG
1 ATGTATCGATACATCTTGTG
*
200047 ATGTATAGATACATCTTGTG
1 ATGTATCGATACATCTTGTG
200067 -TGTATCGATACA
1 ATGTATCGATACA
200079 AATAGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATCTTGTG
Found at i:200156 original size:20 final size:21
Alignment explanation
Indices: 200109--200161 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
200099 ACCAATGACC
*
200109 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
200130 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
200150 TGTATCGATACA
1 TGTATCGATACA
200162 ATATATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:202354 original size:22 final size:20
Alignment explanation
Indices: 202329--202380 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
202319 GTTTTAGAGT
202329 TAAATATAGAT-TTTTTCAAG
1 TAAATATA-ATGTTTTTCAAG
*
202349 CATAAAAATAATGTTTTTCAAG
1 --TAAATATAATGTTTTTCAAG
202371 TAAATATAAT
1 TAAATATAAT
202381 TCAAAGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.33
21 2 0.07
22 16 0.59
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (20 bp):
TAAATATAATGTTTTTCAAG
Found at i:202655 original size:114 final size:114
Alignment explanation
Indices: 202497--202719 Score: 322
Period size: 114 Copynumber: 2.0 Consensus size: 114
202487 ATTGTATCGA
* *
202497 TACATGTTCATTGTATCGATACACCTGGAAATATTTCAATACATAAAACTGGCAGTAACTAAAAC
1 TACATGTTCATTGTATCGATACACCTGGAAATATATCAATACATAAAACTGGCAATAACTAAAAC
*
202562 TCGCTATGTA-TCGATACATTGTATTGATACATGATGAATTGTATCTATC
66 TCACTATGTAGT-GATACATTGTATTGATACATGATGAATTGTATCTATC
* * * *
202611 TACATGTTCATTGTATCGATACACCTTGAAATATATCGATACATAAAACTGGTAATAGCTAAAAC
1 TACATGTTCATTGTATCGATACACCTGGAAATATATCAATACATAAAACTGGCAATAACTAAAAC
* * ** *
202676 TCACTCTGTAGTGATACGTTGTATTGATGTATGGTGAATTGTAT
66 TCACTATGTAGTGATACATTGTATTGATACATGATGAATTGTAT
202720 TGATACATTG
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
114 95 0.99
115 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (114 bp):
TACATGTTCATTGTATCGATACACCTGGAAATATATCAATACATAAAACTGGCAATAACTAAAAC
TCACTATGTAGTGATACATTGTATTGATACATGATGAATTGTATCTATC
Found at i:203218 original size:36 final size:35
Alignment explanation
Indices: 203157--203228 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
203147 CTAAGTAATT
*
203157 GAGAGGTTCTATCTTACCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTACCCTATG-AAAAGATAGGGA
* *
203193 GAGAGGTTCTATCTTA-GCTCATGAAAAGCTAGGGA
1 GAGAGGTTCTATCTTACCCT-ATGAAAAGATAGGGA
203228 G
1 G
203229 GTTTCTATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 14 0.44
36 18 0.56
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (35 bp):
GAGAGGTTCTATCTTACCCTATGAAAAGATAGGGA
Found at i:204279 original size:20 final size:20
Alignment explanation
Indices: 204254--204308 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
204244 TTTTCACAAT
204254 TTGTATCGATACATTGTT-CA
1 TTGTATCGATACATT-TTGCA
204274 TTGTATCGATACATTTTGCA
1 TTGTATCGATACATTTTGCA
*
204294 ATGTATCGATACATT
1 TTGTATCGATACATT
204309 CAGGCATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTTTGCA
Found at i:206877 original size:79 final size:78
Alignment explanation
Indices: 206635--206922 Score: 274
Period size: 79 Copynumber: 3.7 Consensus size: 78
206625 TCATTCATGT
* * * * *
206635 TTTTATTTCCAAAACATCAATTTTTTACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
* *
206700 TACTTCAACCCTG
66 TACTCCAACCCCG
* * * * * **
206713 GTTTATTT-TCAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCGCA-AA
1 TTTTATTTCT-AAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCG-AGGG
206776 GATACTCCAACCCCGG
64 GATACTCCAACCCC-G
** * * * * *
206792 CCTTATTTCTAAAGCAACGATTTTTCACAATTGGAGATGCTCCAACCCCGTTATTTCCGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
206857 TACTCCAACCCCG
66 TACTCCAACCCCG
* * * * * * *
206870 ATTTTATTTCCAGAACACCGACTTTTCATAATCAGGGATACTCCAGCCCCGTT
1 -TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTT
206923 GTTATCCCCA
Statistics
Matches: 164, Mismatches: 40, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
78 62 0.38
79 101 0.62
80 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (78 bp):
TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
TACTCCAACCCCG
Found at i:208690 original size:21 final size:21
Alignment explanation
Indices: 208666--208708 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
208656 AATATTCTTA
* *
208666 AAAAGAAATTAAGTAAATTAG
1 AAAAGAAAATAAATAAATTAG
*
208687 AAAAGAAAATAAATGAATTAG
1 AAAAGAAAATAAATAAATTAG
208708 A
1 A
208709 GGAGAAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.21
Consensus pattern (21 bp):
AAAAGAAAATAAATAAATTAG
Found at i:208714 original size:21 final size:21
Alignment explanation
Indices: 208681--208723 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
208671 AAATTAAGTA
*
208681 AATTAGAAAAGAAAATAAATG
1 AATTAGAAAAGAAAAGAAATG
**
208702 AATTAGAGGAGAAAAGAAATG
1 AATTAGAAAAGAAAAGAAATG
208723 A
1 A
208724 GTTGCAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (21 bp):
AATTAGAAAAGAAAAGAAATG
Found at i:211386 original size:45 final size:44
Alignment explanation
Indices: 211272--211436 Score: 188
Period size: 44 Copynumber: 3.7 Consensus size: 44
211262 ATAACAAAGC
* * *
211272 CTCCTTCCTATTTGACGTATGGTTACCACCCTGGTCAGATTCT-T
1 CTCCTTCCTATTTGACATATGGTTACCACCCTGGTTA-AATCTGT
* * * * * *
211316 TTCATTCCGATTTGACAAATGGTTACCATCCTGGTTTAATCTGT
1 CTCCTTCCTATTTGACATATGGTTACCACCCTGGTTAAATCTGT
* * *
211360 CTCCTTCCTGATTTGACGTATGGTTACCACCCTAGTTAAATCTGC
1 CTCCTTCCT-ATTTGACATATGGTTACCACCCTGGTTAAATCTGT
*
211405 CTCCTTCCTATTTGACATATAGTTACCACCCT
1 CTCCTTCCTATTTGACATATGGTTACCACCCT
211437 AGTCAAATGA
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
43 4 0.04
44 57 0.58
45 38 0.38
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (44 bp):
CTCCTTCCTATTTGACATATGGTTACCACCCTGGTTAAATCTGT
Found at i:214230 original size:85 final size:85
Alignment explanation
Indices: 214053--214596 Score: 432
Period size: 85 Copynumber: 6.4 Consensus size: 85
214043 AAGCAGTCAG
* * ** * * *
214053 GTCAACAAAGTATGAAAAAG-GTTACCT-GAGACTAAACCAACAGGTAAACAAGGGAT-ACAAAA
1 GTCAACAAAGGAT-AAAAAGATTTACCTAG-GACTAAGTCAACAGGTAGACAAAGGATGA-AAGA
* * *
214115 GTTGA-CTGAGATTGAACCGACAA
63 GTTAACCT-AGATTAAATCGACAA
* * * * * *
214138 GTTAACAAAGGATAAAAGGATTTACCTAGGACTAAGTCGACGGGTAGATAAGGGATGAAAGAGTT
1 GTCAACAAAGGATAAAAAGATTTACCTAGGACTAAGTCAACAGGTAGACAAAGGATGAAAGAGTT
* * * *
214203 AACCGAGAATAAATTGAGAA
66 AACCTAGATTAAATCGACAA
* * *
214223 GTCAACAAAGGATAAAAAGATTTACACGA-GACTAAGTCAACAAGTAGACAAAGGATGAAGGAGT
1 GTCAACAAAGGATAAAAAGATTTAC-CTAGGACTAAGTCAACAGGTAGACAAAGGATGAAAGAGT
*
214287 TAA-CTAGGATTGAATCGACAA
65 TAACCTA-GATTAAATCGACAA
* ** * * *
214308 GTCAACAAAGGAT-AAAAGATTTAGCGGGGACTAAGGT-GACAGGTAAACAAAGGATGAAGGAGT
1 GTCAACAAAGGATAAAAAGATTTACCTAGGACTAA-GTCAACAGGTAGACAAAGGATGAAAGAGT
* *
214371 TGA-CTAAGATTGAATCGACAA
65 TAACCT-AGATTAAATCGACAA
* * *
214392 GTCAACAAAGGATAAAAAGATTTATCT-GGAACTAAGCCAACAGGTA-ACAAAGGATAAAAGAGT
1 GTCAACAAAGGATAAAAAGATTTACCTAGG-ACTAAGTCAACAGGTAGACAAAGGATGAAAGAGT
*
214455 TGACCTAGATTAAA-CTGACAA
65 TAACCTAGATTAAATC-GACAA
* * * ** * *
214476 GTCAACAAAGGATAAAAGGATTTACTTAGGACTAA-ACAGGTAGGTAAACAAAGGATAAAAGAGT
1 GTCAACAAAGGATAAAAAGATTTACCTAGGACTAAGTCA-ACAGGTAGACAAAGGATGAAAGAGT
* * * *
214540 TGACC-AGGATTGAACCAACAA
65 TAACCTA-GATTAAATCGACAA
* * *
214561 GACAACAAAGGATAAAAGGATTTACCCAGGACTAAG
1 GTCAACAAAGGATAAAAAGATTTACCTAGGACTAAG
214597 GTCGGGATTA
Statistics
Matches: 383, Mismatches: 56, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
83 5 0.01
84 145 0.38
85 227 0.59
86 6 0.02
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (85 bp):
GTCAACAAAGGATAAAAAGATTTACCTAGGACTAAGTCAACAGGTAGACAAAGGATGAAAGAGTT
AACCTAGATTAAATCGACAA
Found at i:214412 original size:169 final size:166
Alignment explanation
Indices: 214053--214585 Score: 513
Period size: 169 Copynumber: 3.2 Consensus size: 166
214043 AAGCAGTCAG
* * * * *
214053 GTCAACAAAGTATGAAAAAG-GTTAC-CTGAGACTAAACCAACAGGTAAACAAGGGATACAAA-A
1 GTCAACAAAGGAT-AAAAAGATTTACAC-GA-ACTAAGCCAACAAGT-AACAAAGGATA-AAAGA
* *
214115 GTTG-ACTGAGATTGAACCGACAAGTTAACAAAGGATAAAAGGATTTACCTAGGACTAAGTCGAC
61 GTTGAACT-AGATTGAAACGACAAGTCAACAAAGGATAAAAGGATTTA-CTAGGACTAAGT-GAC
* * * * * * * * * *
214179 GGGTAGATAAGGGATGAAAGAGTTAACCGAGAATAAATTGAGAA
123 AGGTAAACAAAGGATGAAAGAGTTGACCAAGATTGAATCGACAA
* * *
214223 GTCAACAAAGGATAAAAAGATTTACACGAGACTAAGTCAACAAGTAGACAAAGGATGAAGGAGTT
1 GTCAACAAAGGATAAAAAGATTTACACGA-ACTAAGCCAACAAGTA-ACAAAGGATAAAAGAGTT
* **
214288 -AACTAGGATTGAATCGACAAGTCAACAAAGGATAAAA-GATTTAGCGGGGACTAAGGTGACAGG
64 GAACTA-GATTGAAACGACAAGTCAACAAAGGATAAAAGGATTTA-CTAGGACTAA-GTGACAGG
* *
214351 TAAACAAAGGATGAAGGAGTTGACTAAGATTGAATCGACAA
126 TAAACAAAGGATGAAAGAGTTGACCAAGATTGAATCGACAA
** *
214392 GTCAACAAAGGATAAAAAGATTTATCTGGAACTAAGCCAACAGGTAACAAAGGATAAAAGAGTTG
1 GTCAACAAAGGATAAAAAGATTTA-CACGAACTAAGCCAACAAGTAACAAAGGATAAAAGAGTTG
* ** **
214457 ACCTAGATT-AAACTGACAAGTCAACAAAGGATAAAAGGATTTACTTAGGACTAAACAGGTAGGT
65 AACTAGATTGAAAC-GACAAGTCAACAAAGGATAAAAGGATTTAC-TAGGACT-AAGTGACAGGT
* * * *
214521 AAACAAAGGATAAAAGAGTTGACCAGGATTGAACCAACAA
127 AAACAAAGGATGAAAGAGTTGACCAAGATTGAATCGACAA
* *
214561 GACAACAAAGGATAAAAGGATTTAC
1 GTCAACAAAGGATAAAAAGATTTAC
214586 CCAGGACTAA
Statistics
Matches: 303, Mismatches: 47, Indels: 28
0.80 0.12 0.07
Matches are distributed among these distances:
167 3 0.01
168 44 0.15
169 173 0.57
170 82 0.27
171 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (166 bp):
GTCAACAAAGGATAAAAAGATTTACACGAACTAAGCCAACAAGTAACAAAGGATAAAAGAGTTGA
ACTAGATTGAAACGACAAGTCAACAAAGGATAAAAGGATTTACTAGGACTAAGTGACAGGTAAAC
AAAGGATGAAAGAGTTGACCAAGATTGAATCGACAA
Found at i:214483 original size:42 final size:42
Alignment explanation
Indices: 214053--214595 Score: 161
Period size: 42 Copynumber: 12.8 Consensus size: 42
214043 AAGCAGTCAG
* * ** *
214053 GTCAACAAAGTATGAAAA-AGGTTACCTGAGACTAAACCAACAG
1 GTCAACAAAGGAT-AAAAGAGTTTACCT-AGACTAAACTGACAA
* * * * * *
214096 GTAAACAAGGGATACAAA-AGTTGA-CTGAGATTGAACCGACAA
1 GTCAACAAAGGATA-AAAGAGTTTACCT-AGACTAAACTGACAA
* * **
214138 GTTAACAAAGGATAAAAG-GATTTACCTAGGACT-AAGTCGACGG
1 GTCAACAAAGGATAAAAGAG-TTTACCTA-GACTAAACT-GACAA
* * * * * * * *
214181 GT-AGATAAGGGATGAAAGAGTTAACCGAGAATAAATTGAGAA
1 GTCA-ACAAAGGATAAAAGAGTTTACCTAGACTAAACTGACAA
* * *
214223 GTCAACAAAGGATAAAA-AGATTTACACGAGACT-AAGTCAACAA
1 GTCAACAAAGGATAAAAGAG-TTTAC-CTAGACTAAACT-GACAA
* * * * *
214266 GT-AGACAAAGGATGAAGGAG-TTAACTAGGATTGAA-TCGACAA
1 GTCA-ACAAAGGATAAAAGAGTTTACCTA-GACTAAACT-GACAA
*** ** *
214308 GTCAACAAAGGATAAAAGA-TTTAGCGGGGACTAAGGTGACAG
1 GTCAACAAAGGATAAAAGAGTTTA-CCTAGACTAAACTGACAA
* * * * * *
214350 GTAAACAAAGGATGAAGGAGTTGA-CTAAGATTGAA-TCGACAA
1 GTCAACAAAGGATAAAAGAGTTTACCT-AGACTAAACT-GACAA
* * * ** *
214392 GTCAACAAAGGATAAAA-AGATTTATCTGGAACTAAGCCAACAG
1 GTCAACAAAGGATAAAAGAG-TTTACCTAG-ACTAAACTGACAA
* *
214435 GT-AACAAAGGATAAAAGAGTTGACCTAGATTAAACTGACAA
1 GTCAACAAAGGATAAAAGAGTTTACCTAGACTAAACTGACAA
* * ** *
214476 GTCAACAAAGGATAAAAG-GATTTACTTAGGACTAAACAGGTAG
1 GTCAACAAAGGATAAAAGAG-TTTACCTA-GACTAAACTGACAA
* * * * **
214519 GTAAACAAAGGATAAAAGAGTTGACC-AGGATTGAACCAACAA
1 GTCAACAAAGGATAAAAGAGTTTACCTA-GACTAAACTGACAA
* *
214561 GACAACAAAGGATAAAAG-GATTTACCCAGGACTAA
1 GTCAACAAAGGATAAAAGAG-TTTACCTA-GACTAA
214596 GGTCGGGATT
Statistics
Matches: 362, Mismatches: 103, Indels: 70
0.68 0.19 0.13
Matches are distributed among these distances:
41 23 0.06
42 210 0.58
43 125 0.35
44 4 0.01
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (42 bp):
GTCAACAAAGGATAAAAGAGTTTACCTAGACTAAACTGACAA
Found at i:214844 original size:47 final size:47
Alignment explanation
Indices: 214775--214938 Score: 204
Period size: 47 Copynumber: 3.5 Consensus size: 47
214765 GTTTGACTAG
* * *
214775 GTCCTAACACCAATACAATCAAATGAGGGTGAAAAGAGTTAGACCAA
1 GTCCTAACGCCAATATAGTCAAATGAGGGTGAAAAGAGTTAGACCAA
* * * * *
214822 GTCCTAACGCTAATATGGTCAAATGAGGGTGAAAAAAGTTTA-ACTAG
1 GTCCTAACGCCAATATAGTCAAATGAGGGTGAAAAGAG-TTAGACCAA
* * *
214869 GTCCTAATGCCAATATAGTCAAATGAGAGTGAAAAGAGTTTGACCAA
1 GTCCTAACGCCAATATAGTCAAATGAGGGTGAAAAGAGTTAGACCAA
*
214916 ATCCTAACGCCAATATAGTCAAA
1 GTCCTAACGCCAATATAGTCAAA
214939 AAAGGGAAGA
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
46 2 0.02
47 92 0.95
48 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (47 bp):
GTCCTAACGCCAATATAGTCAAATGAGGGTGAAAAGAGTTAGACCAA
Found at i:214873 original size:94 final size:92
Alignment explanation
Indices: 214761--214986 Score: 281
Period size: 94 Copynumber: 2.4 Consensus size: 92
214751 ACGAGAATAG
* * * *
214761 AAAAGTTTGACTAGGTCCTAACACCAATACAATCAAATGAGGGTGAAAAGAGTTAGACCAAGTCC
1 AAAAGTTTAACTAGGTCCTAACGCCAATACAATCAAATGAGAGTGAAAAGAGTTAGACCAAATCC
* * * *
214826 TAACGCTAATATGGTCAAATGAGGGTGAA
66 TAACGCCAATATAGTCAAA-AAAGG-GAA
* * * *
214855 AAAAGTTTAACTAGGTCCTAATGCCAATATAGTCAAATGAGAGTGAAAAGAGTTTGACCAAATCC
1 AAAAGTTTAACTAGGTCCTAACGCCAATACAATCAAATGAGAGTGAAAAGAGTTAGACCAAATCC
214920 TAACGCCAATATAGTCAAAAAAGGGAA
66 TAACGCCAATATAGTCAAAAAAGGGAA
* * ***
214947 GACAGTTTAACTAGGTCCTAACGTTGATACAATCAAATGA
1 AAAAGTTTAACTAGGTCCTAACGCCAATACAATCAAATGA
214987 AATTGAAAGA
Statistics
Matches: 112, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
92 35 0.31
93 3 0.03
94 74 0.66
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.23
Consensus pattern (92 bp):
AAAAGTTTAACTAGGTCCTAACGCCAATACAATCAAATGAGAGTGAAAAGAGTTAGACCAAATCC
TAACGCCAATATAGTCAAAAAAGGGAA
Found at i:220351 original size:52 final size:52
Alignment explanation
Indices: 220281--220401 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
220271 GAAAATTTAT
*
220281 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
220333 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
220385 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
220402 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:220414 original size:52 final size:51
Alignment explanation
Indices: 220281--220421 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
220271 GAAAATTTAT
220281 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
220333 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
220385 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
220422 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:220428 original size:13 final size:13
Alignment explanation
Indices: 220410--220434 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220400 CAAAGATCAG
220410 TGTATCGATACAA
1 TGTATCGATACAA
220423 TGTATCGATACA
1 TGTATCGATACA
220435 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:220519 original size:13 final size:13
Alignment explanation
Indices: 220501--220525 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220491 CAAAAAAATA
220501 TGTATCGATACAT
1 TGTATCGATACAT
220514 TGTATCGATACA
1 TGTATCGATACA
220526 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:220521 original size:33 final size:33
Alignment explanation
Indices: 220479--220545 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
220469 AGTAGCTTAA
220479 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
220512 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
220545 A
1 A
220546 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:223643 original size:31 final size:30
Alignment explanation
Indices: 223608--223672 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
223598 GGTGTTTTAG
*
223608 AAATAAAACTGGAGTTGGAGTATCCCCTCGA
1 AAATAAAAC-GGAGTTAGAGTATCCCCTCGA
* *
223639 AAAT--AACGGTGTTAGAGTATCCCTTCGA
1 AAATAAAACGGAGTTAGAGTATCCCCTCGA
223667 AAATAA
1 AAATAA
223673 TGGGGTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 22 0.76
29 3 0.10
31 4 0.14
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (30 bp):
AAATAAAACGGAGTTAGAGTATCCCCTCGA
Found at i:223685 original size:28 final size:28
Alignment explanation
Indices: 223625--223688 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
223615 ACTGGAGTTG
*
223625 GAGTATCCCCTCGAAAATAACGGTGTTA
1 GAGTATCCCCTCGAAAATAACGGGGTTA
* *
223653 GAGTATCCCTTCGAAAATAATGGGGTTTA
1 GAGTATCCCCTCGAAAATAACGGGG-TTA
223682 -AGTATCC
1 GAGTATCC
223689 TCGATTATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (28 bp):
GAGTATCCCCTCGAAAATAACGGGGTTA
Found at i:223865 original size:79 final size:78
Alignment explanation
Indices: 223653--224080 Score: 334
Period size: 79 Copynumber: 5.5 Consensus size: 78
223643 AACGGTGTTA
* * * *
223653 GAGTATCCCTTCGAAAATAATGGGGTTT-AAGTATCCTCGATTATGGAAAATTAGTGTTTTGGAA
1 GAGTATCCCTTCGAAAATAAT-GGGTTTGGAGTATCCTCAATTATGGAAAATCAATGTTTTGGAA
**
223717 ATAAAACCG-G--G
65 ATAAAATAGAGTTG
* * * * * *
223728 GTTGT-TGCCC-TCGAAAATAATGGGGTTAGAGAATCTTCAATTGTGGAAAATCAATGTTTTGGA
1 G-AGTAT-CCCTTCGAAAATAATGGGTTTGGAGTATCCTCAATTATGGAAAATCAATGTTTTGGA
223791 AATAAAACTAGAGTTG
64 AATAAAA-TAGAGTTG
* * * *
223807 GAGTATCCCTTCAAAAATAATGGGTTTGGAGTATCCTCGATTGT-GAAAACTCAGTGTTTTGGAA
1 GAGTATCCCTTCGAAAATAATGGGTTTGGAGTATCCTCAATTATGGAAAA-TCAATGTTTTGGAA
*
223871 ATAAAATCAGGGTTG
65 ATAAAAT-AGAGTTG
* * *
223886 GAGTATCCCTTTGAAAATAATGGGATTGGAGTATCC-CTAATTATGGAAAATTAATGTTTTGGAA
1 GAGTATCCCTTCGAAAATAATGGGTTTGGAGTATCCTC-AATTATGGAAAATCAATGTTTTGGAA
*
223950 ATAAAATCGAGGTTG
65 ATAAAATAGA-GTTG
* * ** * * * * * * * *
223965 GAGTATCCCCTCGGAAATAACAAGG-TTAGAGTATCCCCGATTACGGAAAATCGATATTTTAGAC
1 GAGTATCCCTTCGAAAATAA-TGGGTTTGGAGTATCCTCAATTATGGAAAATCAATGTTTTGGAA
* *
224029 ATAAAACTTGGGATTG
65 ATAAAA-TAGAG-TTG
* * * * *
224045 GAATATCCCCTCGAAAATAACGGGGTAGGAGTATCC
1 GAGTATCCCTTCGAAAATAATGGGTTTGGAGTATCC
224081 CTGATGGTGA
Statistics
Matches: 284, Mismatches: 50, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
74 5 0.02
75 48 0.17
76 6 0.02
77 1 0.00
78 13 0.05
79 171 0.60
80 40 0.14
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (78 bp):
GAGTATCCCTTCGAAAATAATGGGTTTGGAGTATCCTCAATTATGGAAAATCAATGTTTTGGAAA
TAAAATAGAGTTG
Found at i:223983 original size:158 final size:154
Alignment explanation
Indices: 223653--224016 Score: 407
Period size: 158 Copynumber: 2.3 Consensus size: 154
223643 AACGGTGTTA
*
223653 GAGTATCCCTTCGAAAATAATGGGGTTTAAGTATCCTCGATTATGGAAAATTAGTGTTTTGGAAA
1 GAGTATCCCTTCGAAAATAATGGGGTTTAAGTATCCTCGATTATGGAAAATCAGTGTTTTGGAAA
* * * *
223718 TAAAACCGGGGTTGTTGCCCTCGAAAATAATGGGGTTAGAGAATCTTCAATTGTGGAAAATCAAT
66 TAAAACCAGGGTTGTTGCCCTCGAAAATAATGGGATTAGAGAATCCTCAATTATGGAAAATCAAT
*
223783 GTTTTGGAAATAAAACTAGAGTTG
131 GTTTTGGAAATAAAACGAGAGTTG
* * *
223807 GAGTATCCCTTCAAAAATAAT-GGGTTTGGAGTATCCTCGATTGT-GAAAACTCAGTGTTTTGGA
1 GAGTATCCCTTCGAAAATAATGGGGTTT-AAGTATCCTCGATTATGGAAAA-TCAGTGTTTTGGA
* * * *
223870 AATAAAATCAGGGTTGGAGTAT-CCCTTTGAAAATAATGGGATTGGAGTATCC-CTAATTATGGA
64 AATAAAACCAGGGTT---GT-TGCCC-TCGAAAATAATGGGATTAGAGAATCCTC-AATTATGGA
*
223933 AAATTAATGTTTTGGAAATAAAATCGAG-GTTG
123 AAATCAATGTTTTGGAAATAAAA-CGAGAGTTG
* * *** * *
223965 GAGTATCCCCTCGGAAATAACAAGG-TTAGAGTATCCCCGATTACGGAAAATC
1 GAGTATCCCTTCGAAAATAATGGGGTTTA-AGTATCCTCGATTATGGAAAATC
224017 GATATTTTAG
Statistics
Matches: 175, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
153 11 0.06
154 59 0.34
157 6 0.03
158 89 0.51
159 10 0.06
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (154 bp):
GAGTATCCCTTCGAAAATAATGGGGTTTAAGTATCCTCGATTATGGAAAATCAGTGTTTTGGAAA
TAAAACCAGGGTTGTTGCCCTCGAAAATAATGGGATTAGAGAATCCTCAATTATGGAAAATCAAT
GTTTTGGAAATAAAACGAGAGTTG
Found at i:224033 original size:158 final size:158
Alignment explanation
Indices: 223735--224160 Score: 400
Period size: 158 Copynumber: 2.7 Consensus size: 158
223725 GGGGTTGTTG
* * * *
223735 CCCTCGAAAATAATGGGGTTAGAGAAT-CTTCAATTGTGGAAAATCAATGTTTTGGAAATAAAAC
1 CCCTCGAAAATAATGGGGTTGGAGTATCCCT-AATTGTGGAAAATTAATGTTTTGGAAATAAAAC
* * * * * * *
223799 TAGAGTTGGAGTATCCCTTCAAAAATAA-TGGGTTTGGAGTATCCTCGATTGTGAAAACTCAGTG
65 GAG-GTTGGAGTATCCCCTCGAAAATAACAGGG-TTAGAGTATCCCCGATTGTGAAAACTCAGTA
* *
223863 TTTTGGAAATAAAA-TCAGGG-TTGGAGTATC
128 TTTTAGAAATAAAACT-AGGGATTGGAATATC
* * * *
223893 CCTTTGAAAATAATGGGATTGGAGTATCCCTAATTATGGAAAATTAATGTTTTGGAAATAAAATC
1 CCCTCGAAAATAATGGGGTTGGAGTATCCCTAATTGTGGAAAATTAATGTTTTGGAAATAAAA-C
* *
223958 GAGGTTGGAGTATCCCCTCGGAAATAACAAGGTTAGAGTATCCCCGATTACG-GAAAA-TC-GAT
65 GAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATCCCCGATT--GTGAAAACTCAG-T
* *
224020 ATTTTAGACATAAAACTTGGGATTGGAATATC
127 ATTTTAGAAATAAAACTAGGGATTGGAATATC
* * * * ** * * **
224052 CCCTCGAAAATAACGGGGTAGGAGTATCCCTGATGGT-GAAAATTTGGTATTTTAGAAATAAGGC
1 CCCTCGAAAATAATGGGGTTGGAGTATCCCTAATTGTGGAAAA-TTAATGTTTTGGAAATAA-AA
* * *
224116 CGACGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTGTCCC
64 CGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATCCC
224161 TAATGATGGA
Statistics
Matches: 218, Mismatches: 40, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
157 1 0.00
158 111 0.51
159 105 0.48
160 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (158 bp):
CCCTCGAAAATAATGGGGTTGGAGTATCCCTAATTGTGGAAAATTAATGTTTTGGAAATAAAACG
AGGTTGGAGTATCCCCTCGAAAATAACAGGGTTAGAGTATCCCCGATTGTGAAAACTCAGTATTT
TAGAAATAAAACTAGGGATTGGAATATC
Found at i:224077 original size:80 final size:79
Alignment explanation
Indices: 223772--224192 Score: 250
Period size: 79 Copynumber: 5.3 Consensus size: 79
223762 CTTCAATTGT
* * * * * * * *
223772 GGAAAATCAATGTTTTGGAAATAAAA-CTAGAGTTGGAGTATCCCTTCAAAAATAATGGGTTTGG
1 GGAAAATCAATATTTTAGAAATAAAATCGAG-GTTGGAGTATCCCCTCGAAAATAACGGGATAGG
* *
223836 AGTATCCTCGATT--
65 AGTATCCCCAATTAC
* * * * * * *
223849 GTGAAAACTCAGTGTTTTGGAAATAAAATC-AGGGTTGGAGTATCCCTTTGAAAATAATGGGATT
1 G-GAAAA-TCAATATTTTAGAAATAAAATCGA-GGTTGGAGTATCCCCTCGAAAATAACGGGATA
* *
223913 GGAGTATCCCTAATTAT
63 GGAGTATCCCCAATTAC
* * * * * *
223930 GGAAAATTAATGTTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCGGAAATAACAAGGTTA-G
1 GGAAAATCAATATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAAC-GGGATAGG
*
223994 AGTATCCCCGATTAC
65 AGTATCCCCAATTAC
* * * * *
224009 GGAAAATCGATATTTTAGACATAAAACTTG-GGATTGGAATATCCCCTCGAAAATAACGGGGTAG
1 GGAAAATCAATATTTTAGAAATAAAA-TCGAGG-TTGGAGTATCCCCTCGAAAATAACGGGATAG
** *
224073 GAGTATCCCTGA-T-G
64 GAGTATCCCCAATTAC
*** *** * *
224087 GTGAAAATTTGGTATTTTAGAAATAAGGCCGACGTTGGAGTATCCCCTCGAAAATAACGGGGTTA
1 G-GAAAA-TCAATATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAAC-GGGATA
* * * *
224152 -GAGTGTCCCTAATGAT
63 GGAGTATCCCCAATTAC
* *
224168 GGAAAAT-TATATTTTGGAAATAAAA
1 GGAAAATCAATATTTTAGAAATAAAA
224193 ACGTCGATGA
Statistics
Matches: 277, Mismatches: 50, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
77 1 0.00
78 19 0.07
79 183 0.66
80 72 0.26
81 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
GGAAAATCAATATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGATAGGA
GTATCCCCAATTAC
Found at i:228077 original size:26 final size:27
Alignment explanation
Indices: 228048--228106 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
228038 TATTTATTTC
228048 TTTTTTCTTCCTTTC-TTTTTTCTTT-T
1 TTTTTTCTTCCTTTCATTTTTT-TTTGT
** *
228074 TTTTTGGTTTCTTTCATTTTTTTTTGT
1 TTTTTTCTTCCTTTCATTTTTTTTTGT
228101 TTTTTT
1 TTTTTT
228107 ATGGCTCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (27 bp):
TTTTTTCTTCCTTTCATTTTTTTTTGT
Found at i:228093 original size:19 final size:19
Alignment explanation
Indices: 228066--228102 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
228056 TCCTTTCTTT
*
228066 TTTCTTTTTTTTTGGTTTC
1 TTTCATTTTTTTTGGTTTC
*
228085 TTTCATTTTTTTTTGTTT
1 TTTCATTTTTTTTGGTTT
228103 TTTTATGGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.81
Consensus pattern (19 bp):
TTTCATTTTTTTTGGTTTC
Found at i:229344 original size:17 final size:17
Alignment explanation
Indices: 229322--229364 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
229312 GGGTGCAAAA
229322 GTTTATGGTTATCATAG
1 GTTTATGGTTATCATAG
229339 GTTTATGGTTATCATAG
1 GTTTATGGTTATCATAG
*
229356 ATTTATGGT
1 GTTTATGGT
229365 AGAAAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (17 bp):
GTTTATGGTTATCATAG
Found at i:233199 original size:114 final size:114
Alignment explanation
Indices: 233055--233283 Score: 395
Period size: 114 Copynumber: 2.0 Consensus size: 114
233045 TGACTAGTCC
* * *
233055 TATTTTATGGGCCATGTTAATGTAAATATTTTGTATTTTTGAGGATTTGATCATCGAGATACCTT
1 TATTTTATGGGCCATGTTAATGTAAATATTTTGTATTTTTGAGGACTCGATCATCGAGATACCCT
**
233120 AAATAGTCATTATGAAATGACCATTTATTTGGAGTCACCACCAATCTAT
66 AAATAGTCATTACAAAATGACCATTTATTTGGAGTCACCACCAATCTAT
233169 TATTTTATGGGCCATGTTAATGTAAATATTTTGTATTTTTGAGGACTCGATCATCGAGATACCCT
1 TATTTTATGGGCCATGTTAATGTAAATATTTTGTATTTTTGAGGACTCGATCATCGAGATACCCT
* *
233234 AAATAGTCATTACAAAATGACCATTTATTTGGGGTCACTACCAATCTAT
66 AAATAGTCATTACAAAATGACCATTTATTTGGAGTCACCACCAATCTAT
233283 T
1 T
233284 TTGGCCAAGT
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (114 bp):
TATTTTATGGGCCATGTTAATGTAAATATTTTGTATTTTTGAGGACTCGATCATCGAGATACCCT
AAATAGTCATTACAAAATGACCATTTATTTGGAGTCACCACCAATCTAT
Found at i:237097 original size:20 final size:20
Alignment explanation
Indices: 237069--237145 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
237059 ATTTACCTGC
237069 ATGTATCGATACATTAAATA
1 ATGTATCGATACATTAAATA
* **
237089 ATATATCGATACAATTTAAAGC
1 ATGTATCGATAC-A-TTAAATA
*
237111 ATGTATTGATACATT-AATAA
1 ATGTATCGATACATTAAAT-A
237131 ATGTATCGATACATT
1 ATGTATCGATACATT
237146 TCCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 2 0.04
22 15 0.33
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTAAATA
Found at i:238418 original size:140 final size:142
Alignment explanation
Indices: 238230--238489 Score: 346
Period size: 140 Copynumber: 1.8 Consensus size: 142
238220 CGAAAATCTC
* ** * *
238230 ATTTTGTACCTTAATGGAGAGTTGAAAAAATACGAAAAGTTTTGAAGAT-TGCTATACCCCTATG
1 ATTTCGTACCTTAATGGAGAACTGAAAAAATACGAAAAGTTTTAAAGATAT-CTATACCCCTAGG
* *
238294 GAAAACCATAGGAATA-TATAAATCGTGAAAAACTAAGACAACAA-TTTTTATTTAATTTTTAAT
65 GAAAACCATAGGAATATTAGAAATCGTGAAAAACTAAGAAAACAATTTTTTATTTAATTTTTAAT
238357 TTCCAAAAAATTT
130 TTCCAAAAAATTT
** * * * *
238370 ATTTCGTACCTTAATGGAGAACTGAAAGGATATGACAAGTTTTAAAGATATCTATGCCCTTAGGG
1 ATTTCGTACCTTAATGGAGAACTGAAAAAATACGAAAAGTTTTAAAGATATCTATACCCCTAGGG
* * *
238435 AAAACCATAGGAATATTAGAAATCTTGAAAAATTAAGAAAATAATTTTTTATTTA
66 AAAACCATAGGAATATTAGAAATCGTGAAAAACTAAGAAAACAATTTTTTATTTA
238490 GTGATAAAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
140 67 0.66
141 24 0.24
142 10 0.10
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (142 bp):
ATTTCGTACCTTAATGGAGAACTGAAAAAATACGAAAAGTTTTAAAGATATCTATACCCCTAGGG
AAAACCATAGGAATATTAGAAATCGTGAAAAACTAAGAAAACAATTTTTTATTTAATTTTTAATT
TCCAAAAAATTT
Found at i:239307 original size:12 final size:12
Alignment explanation
Indices: 239290--239316 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
239280 AAGAAATGAA
239290 CAAGAAAGAAAG
1 CAAGAAAGAAAG
239302 CAAGAAAGAAAG
1 CAAGAAAGAAAG
239314 CAA
1 CAA
239317 AATAGGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.11, G:0.22, T:0.00
Consensus pattern (12 bp):
CAAGAAAGAAAG
Found at i:239401 original size:13 final size:15
Alignment explanation
Indices: 239367--239401 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
239357 TTTGGTTTTA
239367 TTTTTTTTCTCTCTC
1 TTTTTTTTCTCTCTC
239382 TTTTTTTT-T-TCTC
1 TTTTTTTTCTCTCTC
239395 TTTTTTT
1 TTTTTTT
239402 CTTCACTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 1 0.05
15 8 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTTCTCTCTC
Found at i:239721 original size:10 final size:10
Alignment explanation
Indices: 239706--239730 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
239696 TGGGAATAAA
239706 TAAATAAAAT
1 TAAATAAAAT
239716 TAAATAAAAT
1 TAAATAAAAT
239726 TAAAT
1 TAAAT
239731 TTTAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAATAAAAT
Found at i:240867 original size:13 final size:13
Alignment explanation
Indices: 240849--240874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
240839 TACACAAAGT
240849 ATGTATCGATACA
1 ATGTATCGATACA
240862 ATGTATCGATACA
1 ATGTATCGATACA
240875 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:240872 original size:32 final size:33
Alignment explanation
Indices: 240831--240894 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
240821 TAGCCAAACT
**
240831 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
240863 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
240895 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:246209 original size:32 final size:32
Alignment explanation
Indices: 246154--246216 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
246144 TAGCCAAACT
* *
246154 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACAAAAAATATGTATCGATACAA
246186 TGTATCGATCACAAAAAAT-TGTATCGATACA
1 TGTATCGAT-ACAAAAAATATGTATCGATACA
246217 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAAAAAATATGTATCGATACAA
Found at i:248734 original size:79 final size:77
Alignment explanation
Indices: 248596--249014 Score: 407
Period size: 79 Copynumber: 5.3 Consensus size: 77
248586 AGTGAAACTC
* * ** *
248596 GAGGTTTGAGTATCCCCTCAAAAATAGTGGGGTTGGAGTAT-CTCCGAGATGAAAATTTTAATAT
1 GAGGTTGGAGTAT-CTCTCAAAAATAACGAGGTT-GAGTATCCT-CGAGATGAAAATTTTAATAT
*
248660 TTTGGAAATAAAAAC
63 TTTGGAAATAAAAAT
* *
248675 GGGGTTGGAGTATCTACTCAAAAATAACGAGGTTAGAGTATCCTCGAGATAAAAATTTTAATATT
1 GAGGTTGGAGTATCT-CTCAAAAATAACGAGGTT-GAGTATCCTCGAGATGAAAATTTTAATATT
*
248740 TTGGAAAAAAAAAT
64 TTGGAAATAAAAAT
* *** * *
248754 GAGGTAGGAGTATCCTCTTGGAAATAACAAGGGTGAAGTATCCTCGAGATGAAAATTTTAATATT
1 GAGGTTGGAGTAT-CTCTCAAAAATAACGAGGTTG-AGTATCCTCGAGATGAAAATTTTAATATT
248819 TTGGAAATAAAAAT
64 TTGGAAATAAAAAT
* * * * * * * *
248833 GTGGTTGGAGTAGCCCTTCGAAAATAATGGGGTTTTTAGTATCCTCGTA-ATGAAAAATTTAATA
1 GAGGTTGGAGTATCTC-TCAAAAATAACGAGG--TTGAGTATCCTCG-AGATGAAAATTTTAATA
*
248897 CTTTGGAAATAAAAAT
62 TTTTGGAAATAAAAAT
* *
248913 -AGGGTTGGAGTATCCTCTCAAAAATAA-TAGGGTTGAAGTATTCC-CGAGATGAAAATTTTAAC
1 GA-GGTTGGAGTAT-CTCTCAAAAATAACGA-GGTTG-AGTA-TCCTCGAGATGAAAATTTTAAT
248975 ATTTTGGAAATAAAAAT
61 ATTTTGGAAATAAAAAT
* *
248992 GAGGTTGGAGTATCCCTCGAAAA
1 GAGGTTGGAGTATCTCTCAAAAA
249015 GAATAGGGTT
Statistics
Matches: 281, Mismatches: 44, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
78 15 0.05
79 194 0.69
80 68 0.24
81 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (77 bp):
GAGGTTGGAGTATCTCTCAAAAATAACGAGGTTGAGTATCCTCGAGATGAAAATTTTAATATTTT
GGAAATAAAAAT
Found at i:249038 original size:159 final size:156
Alignment explanation
Indices: 248596--249033 Score: 517
Period size: 159 Copynumber: 2.8 Consensus size: 156
248586 AGTGAAACTC
* * * * *
248596 GAGGTTTGAGTATCCCCTCAAAAATAGTGGGGTTGGAGTATCTCCGAGATGAAAATTTTAATATT
1 GAGGTTGGAGTATCCTCTCAAAAATAATAGGGTTGAAGTATC-CCGAGATGAAAATTTTAATATT
* * * * *
248661 TTGGAAATAAAAACGGGGTTGGAGTATCTACTCAAAAATAA-CGAGGTTAGAGTATCCTCGAGAT
65 TTGGAAATAAAAATGAGGTTGGAGTATC-CCTCGAAAATAATAG-GGTTAGAGTATCCTCGAGAT
*
248725 AAAAATTTTAATATTTTGGAAAAAAAAAT
128 AAAAATTTTAATACTTTGGAAAAAAAAAT
* *** *
248754 GAGGTAGGAGTATCCTCTTGGAAATAACAAGGG-TGAAGTATCCTCGAGATGAAAATTTTAATAT
1 GAGGTTGGAGTATCCTCTCAAAAATAA-TAGGGTTGAAGTATCC-CGAGATGAAAATTTTAATAT
* * * **
248818 TTTGGAAATAAAAATGTGGTTGGAGTAGCCCTTCGAAAATAATGGGGTTTTTAGTATCCTCGTA-
64 TTTGGAAATAAAAATGAGGTTGGAGTATCCC-TCGAAAATAATAGGG-TTAGAGTATCCTCG-AG
*
248882 ATGAAAAA-TTTAATACTTTGGAAATAAAAAT
126 AT-AAAAATTTTAATACTTTGGAAAAAAAAAT
*
248913 -AGGGTTGGAGTATCCTCTCAAAAATAATAGGGTTGAAGTATTCCCGAGATGAAAATTTTAACAT
1 GA-GGTTGGAGTATCCTCTCAAAAATAATAGGGTTGAAGTA-TCCCGAGATGAAAATTTTAATAT
* *
248977 TTTGGAAATAAAAATGAGGTTGGAGTATCCCTCGAAAAGAATAGGGTTGGAGTATCC
64 TTTGGAAATAAAAATGAGGTTGGAGTATCCCTCGAAAATAATAGGGTTAGAGTATCC
249034 CCTCGAAAGT
Statistics
Matches: 238, Mismatches: 32, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
157 11 0.05
158 103 0.43
159 115 0.48
160 9 0.04
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (156 bp):
GAGGTTGGAGTATCCTCTCAAAAATAATAGGGTTGAAGTATCCCGAGATGAAAATTTTAATATTT
TGGAAATAAAAATGAGGTTGGAGTATCCCTCGAAAATAATAGGGTTAGAGTATCCTCGAGATAAA
AATTTTAATACTTTGGAAAAAAAAAT
Found at i:251511 original size:51 final size:52
Alignment explanation
Indices: 251389--251527 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 52
251379 AATAGCCTAC
* * * * * *
251389 ATGTATCAATACATTGAAGAATGTATTGATACATTTGGGTTAAAAACCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTTAAAAACCCAGA
*
251441 ATGTATCGATACAAGGAAAAATGTATCGATACATTTAGGTT-AAAACCCAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTTAAAAACCCAGA
* * *
251492 ATGTATCGATATAATGAAAAAAGTATCAATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
251528 TTTTCTAGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 41 0.54
52 35 0.46
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTTAAAAACCCAGA
Found at i:251628 original size:19 final size:20
Alignment explanation
Indices: 251582--251634 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
251572 ACATTTTAGA
251582 CATGTATCGAA-ACATTCACT
1 CATGTATC-AATACATTCACT
251602 CATGTATCAATACATTCACT
1 CATGTATCAATACATTCACT
* *
251622 -TTGTATCCATACA
1 CATGTATCAATACA
251635 AATTGTGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.34
Consensus pattern (20 bp):
CATGTATCAATACATTCACT
Found at i:252470 original size:42 final size:41
Alignment explanation
Indices: 252380--252501 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
252370 ACATAAAGAT
* * * *
252380 GATGTCACCAACTGGTGTGGGTTTTAAAAAGAAAAAAGAAAG
1 GATGCCACTAACTTGTGTGGGCTTTAAAAAG-AAAAAGAAAG
* * * *
252422 GATGCCAC-CATTTGTGTGGGCTTAAAGAAAGAAAAAGCAAGG
1 GATGCCACTAACTTGTGTGGGCTTTAA-AAAGAAAAAG-AAAG
* *
252464 GGTGCCACTAACTTGTGTGGGCTTTAAAAAGGAAAAGA
1 GATGCCACTAACTTGTGTGGGCTTTAAAAAGAAAAAGA
252502 CGTCTTGCTC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
41 20 0.31
42 30 0.46
43 15 0.23
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (41 bp):
GATGCCACTAACTTGTGTGGGCTTTAAAAAGAAAAAGAAAG
Found at i:252499 original size:43 final size:41
Alignment explanation
Indices: 252388--252499 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 41
252378 ATGATGTCAC
* * *
252388 CAACTGGTGTGGGTTTTAAAAAGAAAAAAGAAAGGATGCCA
1 CAACTTGTGTGGGCTTTAAAAAGGAAAAAGAAAGGATGCCA
* * * * *
252429 CCATTTGTGTGGGC-TTAAAGAAAGAAAAAGCAAGGGGTGCCA
1 CAACTTGTGTGGGCTTTAAA-AAGGAAAAAG-AAAGGATGCCA
252471 CTAACTTGTGTGGGCTTTAAAAAGGAAAA
1 C-AACTTGTGTGGGCTTTAAAAAGGAAAA
252500 GACGTCTTGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
40 5 0.09
41 18 0.32
42 10 0.18
43 18 0.32
44 5 0.09
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (41 bp):
CAACTTGTGTGGGCTTTAAAAAGGAAAAAGAAAGGATGCCA
Found at i:252561 original size:62 final size:62
Alignment explanation
Indices: 252464--253052 Score: 668
Period size: 62 Copynumber: 9.5 Consensus size: 62
252454 AAAAGCAAGG
* * * * *
252464 GGTGCCACTAACTTGTGTGGGCTTTAAAAAGGAAAAGACGTCTTGCTCTTTAAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* * * * * * * *
252526 GGTGCTACCAACATGTATGGGCTTTAAAAAGGAAAATGCATCATGCTCTTTGAAGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* * *
252588 GGTGCCACCAACTTGTGTGGGCTTTAAAATGGAAAAGGCGTCCTACCCTTTGAGGATTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* * * *
252650 GGTGCCACCAACTTATGTGGTCTTT-AAAAGGAAAAGGAAAGGTGTCC-AGCTCTTTGAGGACCA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGG---A--AAAGGCGTCCTA-CTCTTTGAGGACTA
252713 AAA
60 AAA
* * * *
252716 GATGCCACTAACTTGTGTGGGCTTTGAAAAGGAAAAGGCATCCTACTCTTTGAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* * * *
252778 GGTGCCACCAACTTGTGTGAGCTTTAAAAAAGAAAAGGCATCCTACTCTTTGGGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* * * * * *
252840 AGTGCTACCAACGTGTGTGGACTTTAAAAAGGAAAAGGCGTCCTTCTCTTTGAGGACCAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* * * * * *
252902 GGTGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAAGCATCCTGCTCATGGAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* * * *
252964 TGTGCCACCAATTTGTGTGGGCTTT-AAAA--AAAA-GTGTCCTACTCTTTAAGGACTAAAA
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
* *
253022 AGTGCCACCAACTTGTGTGGGCTTGAAAAAG
1 GGTGCCACCAACTTGTGTGGGCTTTAAAAAG
253053 AGGTGCTAAG
Statistics
Matches: 443, Mismatches: 74, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
58 41 0.09
59 8 0.02
61 9 0.02
62 331 0.75
63 1 0.00
64 2 0.00
65 1 0.00
66 44 0.10
67 6 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (62 bp):
GGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAA
Found at i:252911 original size:252 final size:246
Alignment explanation
Indices: 252465--253051 Score: 734
Period size: 252 Copynumber: 2.4 Consensus size: 246
252455 AAAGCAAGGG
* * *
252465 GTGCCACTAACTTGTGTGGGCTTTAAAAAGGAAAAGACGTCTTGCTCTTTAAGGACTAAAAGGTG
1 GTGCCACTAACTTGTGTGGGCTTT-AAAAGGAAAAGGC-TCCTACTCTTTAAGGACTAAAAGGTG
* * * * * * *
252530 CTACCAACATGTATGGGCTTTAAAAAGGAAAATGCATCATGCTCTTTGAAGACTAAAAGGTGCCA
64 CCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAAGACTAAAAAGTGCCA
* * * **
252595 CCAACTTGTGTGGGCTTTAAAATGGAAAAGGCGTCCTACCCTTTGAGGATTAAAAGGTGCCACCA
129 CCAACGTGTGTGGACTTTAAAAAGGAAAAGGCGTCCTACCCTTTGAGGACCAAAAGGTGCCACCA
* ** * *
252660 ACTTATGTGGTCTTT-AAAAGGAAAAGGAAAGGTGTCCAGCTCTTTGAGGACCAAAA-
194 ACTTATGTGGGCTTTAAAAAGG--AA--AAA-GCATCCAGCTCATGGAGGACCAAAAT
*
252716 GATGCCACTAACTTGTGTGGGCTTTGAAAAGGAAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
1 G-TGCCACTAACTTGTGTGGGCTTT-AAAAGGAAAAGGC-TCCTACTCTTTAAGGACTAAAAGGT
* * ** *
252781 GCCACCAACTTGTGTGAGCTTTAAAAAAGAAAAGGCATCCTACTCTTTGGGGACTAAAAAGTGCT
63 GCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAAGACTAAAAAGTGCC
* *
252846 ACCAACGTGTGTGGACTTTAAAAAGGAAAAGGCGTCCTTCTCTTTGAGGACCAAAAGGTGCCACC
128 ACCAACGTGTGTGGACTTTAAAAAGGAAAAGGCGTCCTACCCTTTGAGGACCAAAAGGTGCCACC
* *
252911 AACTTATGTGGGCTTTAAAAAGGAAAAAGCATCCTGCTCATGGAGGACTAAAAT
193 AACTTATGTGGGCTTTAAAAAGGAAAAAGCATCCAGCTCATGGAGGACCAAAAT
* * *
252965 GTGCCACCAATTTGTGTGGGCTTTAAAA--AAAAGTG-TCCTACTCTTTAAGGACTAAAAAGTGC
1 GTGCCACTAACTTGTGTGGGCTTTAAAAGGAAAAG-GCTCCTACTCTTTAAGGACTAAAAGGTGC
*
253027 CACCAACTTGTGTGGGCTTGAAAAA
65 CACCAACTTGTGTGGGCTTTAAAAA
253052 GAGGTGCTAA
Statistics
Matches: 294, Mismatches: 38, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
244 48 0.16
245 5 0.02
246 1 0.00
247 4 0.01
248 40 0.14
249 4 0.01
251 3 0.01
252 183 0.62
253 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (246 bp):
GTGCCACTAACTTGTGTGGGCTTTAAAAGGAAAAGGCTCCTACTCTTTAAGGACTAAAAGGTGCC
ACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCATACTCTTTGAAGACTAAAAAGTGCCACC
AACGTGTGTGGACTTTAAAAAGGAAAAGGCGTCCTACCCTTTGAGGACCAAAAGGTGCCACCAAC
TTATGTGGGCTTTAAAAAGGAAAAAGCATCCAGCTCATGGAGGACCAAAAT
Found at i:253115 original size:32 final size:31
Alignment explanation
Indices: 253047--253117 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
253037 TGTGGGCTTG
* *
253047 AAAAAGAGGTGCTAAGAAGTTGTGGACGTTAG
1 AAAAAG-GGTGCCAAGAAGTTGTGGACGTTAA
*
253079 AAAAAGGGTGCCACAG-AGTTGTGGACTTTCAA
1 AAAAAGGGTGCCA-AGAAGTTGTGGACGTT-AA
253111 AAAAAGG
1 AAAAAGG
253118 TTTGAAGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.53
32 16 0.47
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.20
Consensus pattern (31 bp):
AAAAAGGGTGCCAAGAAGTTGTGGACGTTAA
Found at i:253977 original size:13 final size:13
Alignment explanation
Indices: 253959--253984 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
253949 CAATTTTTTG
253959 TGTATCGATACAT
1 TGTATCGATACAT
253972 TGTATCGATACAT
1 TGTATCGATACAT
253985 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:253996 original size:32 final size:33
Alignment explanation
Indices: 253939--254002 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
253929 TACAAGCCAA
** *
253939 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCAATACAT
253972 TGTATCGATAC-ATACTTTGTGTATCAATACA
1 TGTATCGATACAATACTTTGTGTATCAATACA
254003 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCAATACAT
Found at i:254908 original size:23 final size:21
Alignment explanation
Indices: 254882--254925 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
254872 TATTATAGAT
*
254882 TAAAATTCAAAGTACAATGCAAA
1 TAAAATACAAAGT-CAA-GCAAA
254905 TAAAATACAAAGTCAAGCAAA
1 TAAAATACAAAGTCAAGCAAA
254926 AACTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (21 bp):
TAAAATACAAAGTCAAGCAAA
Found at i:256525 original size:13 final size:13
Alignment explanation
Indices: 256507--256544 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
256497 ATAATCCCCC
256507 TGTATCGATACAG
1 TGTATCGATACAG
*
256520 TGTATCGATACAT
1 TGTATCGATACAG
256533 TGTATCGATACA
1 TGTATCGATACA
256545 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:258655 original size:15 final size:15
Alignment explanation
Indices: 258619--258656 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
258609 TTCATCGATT
* *
258619 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
258634 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
258649 TCATTTTG
1 TCATTTTG
258657 GACATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:263177 original size:13 final size:13
Alignment explanation
Indices: 263159--263184 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263149 CAATTTTTTG
263159 TGTATCGATACAT
1 TGTATCGATACAT
263172 TGTATCGATACAT
1 TGTATCGATACAT
263185 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:263933 original size:21 final size:21
Alignment explanation
Indices: 263892--263935 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
263882 CTCCCCTTTA
* *
263892 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
263913 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
263934 TC
1 TC
263936 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:267854 original size:15 final size:15
Alignment explanation
Indices: 267834--267864 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
267824 ATTTCGTTTG
*
267834 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
267849 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
267864 G
1 G
267865 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:269697 original size:21 final size:21
Alignment explanation
Indices: 269668--269712 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
269658 AAGTTTTCAT
*
269668 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
269688 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
269710 TTT
1 TTT
269713 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:271946 original size:13 final size:13
Alignment explanation
Indices: 271928--271952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
271918 CAATTTTTTG
271928 TGTATCGATACAT
1 TGTATCGATACAT
271941 TGTATCGATACA
1 TGTATCGATACA
271953 AGTTTGGCTA
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:272675 original size:32 final size:33
Alignment explanation
Indices: 272615--272678 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
272605 TACAAGCCAA
** *
272615 TGTATCGATACAATTTTTTGTGTGTCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
272648 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
272679 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:278970 original size:14 final size:15
Alignment explanation
Indices: 278941--278970 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
278931 AATAACAGAC
278941 AAATTTAGACAAAAT
1 AAATTTAGACAAAAT
278956 AAATTTAGA-AAAAT
1 AAATTTAGACAAAAT
278970 A
1 A
278971 CATATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (15 bp):
AAATTTAGACAAAAT
Found at i:280056 original size:13 final size:13
Alignment explanation
Indices: 280038--280068 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
280028 ACTTTTCACT
280038 ATGTATCGATACA
1 ATGTATCGATACA
*
280051 ATGTATCTATACA
1 ATGTATCGATACA
280064 ATGTA
1 ATGTA
280069 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:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Done.