Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold326
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: 618170
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.30
Warning! 48140 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4774 original size:141 final size:143
Alignment explanation
Indices: 4605--4889 Score: 540
Period size: 141 Copynumber: 2.0 Consensus size: 143
4595 CAATTTTTTA
4605 TCATAAATAAATAAAATTACTAAAACAAGCACTTTTAGATTGAATATGAACAAATTGTTGTCCAG
1 TCATAAATAAATAAAATTACTAAAACAAGCACTTTTAGATTGAATATGAACAAATTGTTGTCCAG
4670 GTTAATCTAATTCTAGACAACCATTT-GTCTAAGTTC-TTTTTTTTATATATGAAATAATTTTAA
66 GTTAATCTAATTCTAGACAACCATTTGGT-TAAGTTCTTTTTTTTTATATATGAAATAATTTTAA
4733 TAAATTTATATATT
130 TAAATTTATATATT
4747 TCATAAATAAA-AAAATTACTAAAACAAGCACTTTTAGATTGAATATGAACAAATTGTTGTCCAG
1 TCATAAATAAATAAAATTACTAAAACAAGCACTTTTAGATTGAATATGAACAAATTGTTGTCCAG
4811 GTTAATCTAATTCTAGACAACCATTTGGTTAAGTTCTTTTTTTTTATATATGAAATAATTTTAAT
66 GTTAATCTAATTCTAGACAACCATTTGGTTAAGTTCTTTTTTTTTATATATGAAATAATTTTAAT
4876 AAATTTATATATT
131 AAATTTATATATT
4889 T
1 T
4890 TTTTAATTTT
Statistics
Matches: 141, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
141 86 0.61
142 55 0.39
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (143 bp):
TCATAAATAAATAAAATTACTAAAACAAGCACTTTTAGATTGAATATGAACAAATTGTTGTCCAG
GTTAATCTAATTCTAGACAACCATTTGGTTAAGTTCTTTTTTTTTATATATGAAATAATTTTAAT
AAATTTATATATT
Found at i:11408 original size:66 final size:65
Alignment explanation
Indices: 11320--11473 Score: 159
Period size: 66 Copynumber: 2.4 Consensus size: 65
11310 GTACCGACAC
* * * *
11320 AAAA-AAAAAATCA-TTTTTTTAAAGTTTTAAACCGGTGCCAACCACTTCAACATCGGCACCCAG
1 AAAACAAAAAATTATTTTTTTTAAAGCTTTAAACCGGTGCCAACCACTTCAACACCGGCA-CCAA
11383 A
65 A
* * ** * ***
11384 AAAGCAAAAAATTATTTTTTTTAAAGCTTTGAAGTGGTGTCGGTCACTTCAACACCGGCACCAAA
1 AAAACAAAAAATTATTTTTTTTAAAGCTTTAAACCGGTGCCAACCACTTCAACACCGGCACCAAA
* *
11449 AAAATAAAAAATTATTTTTATTAAA
1 AAAACAAAAAATTATTTTTTTTAAA
11474 ATATTATTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
64 3 0.04
65 34 0.47
66 36 0.49
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29
Consensus pattern (65 bp):
AAAACAAAAAATTATTTTTTTTAAAGCTTTAAACCGGTGCCAACCACTTCAACACCGGCACCAAA
Found at i:15213 original size:5 final size:5
Alignment explanation
Indices: 15203--15261 Score: 118
Period size: 5 Copynumber: 11.8 Consensus size: 5
15193 TTTGCTTTAT
15203 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
15253 TATAA TATA
1 TATAA TATA
15262 CTTAATAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:21564 original size:3 final size:3
Alignment explanation
Indices: 21556--21606 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
21546 ATGTTAACAA
*
21556 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21604 ATT
1 ATT
21607 GCAGTCCGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:24107 original size:17 final size:18
Alignment explanation
Indices: 24087--24126 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
24077 GTGGCAAAAG
*
24087 GAAAATCT-TTGGAATCT
1 GAAAATCTCTTGGAAGCT
*
24104 GAAAATGTCTTGGAAGCT
1 GAAAATCTCTTGGAAGCT
24122 GAAAA
1 GAAAA
24127 GAAACGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (18 bp):
GAAAATCTCTTGGAAGCT
Found at i:26238 original size:32 final size:33
Alignment explanation
Indices: 26202--26267 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
26192 ATTAGCCATT
*
26202 TGCTGTTACATGCAT-TTTGCAATGTTTTCCTG
1 TGCTGTTACATGCATGTTTACAATGTTTTCCTG
* * *
26234 TGCTGTTACTTGCATGTTTATAATGTTTTGCTG
1 TGCTGTTACATGCATGTTTACAATGTTTTCCTG
26267 T
1 T
26268 TGGCTTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (33 bp):
TGCTGTTACATGCATGTTTACAATGTTTTCCTG
Found at i:26281 original size:35 final size:34
Alignment explanation
Indices: 26201--26303 Score: 113
Period size: 35 Copynumber: 3.1 Consensus size: 34
26191 TATTAGCCAT
* * *
26201 TTGCTGTTACATGCAT-TTTGCAATGTTTTCCTG
1 TTGCTGTTACTTGCATATTTGAAATGTTTTGCTG
*
26234 -TGCTGTTACTTGCATGTTT-ATAATGTTTTGCTG
1 TTGCTGTTACTTGCATATTTGA-AATGTTTTGCTG
* *
26267 TTGGCTTTTACTTGCATATTTGAAATGCTTTGCTG
1 TT-GCTGTTACTTGCATATTTGAAATGTTTTGCTG
26302 TT
1 TT
26304 TATTTGGATT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
32 14 0.24
33 14 0.24
34 1 0.02
35 29 0.49
36 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.19, T:0.50
Consensus pattern (34 bp):
TTGCTGTTACTTGCATATTTGAAATGTTTTGCTG
Found at i:31041 original size:108 final size:105
Alignment explanation
Indices: 30851--31049 Score: 281
Period size: 108 Copynumber: 1.9 Consensus size: 105
30841 TGGATTAAGA
* * * *
30851 TTTAAGAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAACCCAGCACATTAGGGCACATTTC
1 TTTAAAAGGATATTTGGCTATTTGATCAAAAGAAAAATCGAACCCAGCACATTAGGGCACATTTC
* * * *
30916 CTTGAATTTTCAAACGCAAAATATTGTCTTACTTCGAAAT
66 CTCGAATCTCCAAACGCAAAACATTGTCTTACTTCGAAAT
*
30956 TTTAAAAGGATATTTGGCTATTTGATCGAACAAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGATC-AA-AAGAAAAATCG-AACCCAGCACATTAGGGCACAT
*
31021 TTTCTCGAATCTCCAAACGCAAAACATTG
63 TTCCTCGAATCTCCAAACGCAAAACATTG
31050 CCTGATAGAG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 25 0.31
106 2 0.02
107 9 0.11
108 45 0.56
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (105 bp):
TTTAAAAGGATATTTGGCTATTTGATCAAAAGAAAAATCGAACCCAGCACATTAGGGCACATTTC
CTCGAATCTCCAAACGCAAAACATTGTCTTACTTCGAAAT
Found at i:35186 original size:87 final size:87
Alignment explanation
Indices: 35076--35574 Score: 836
Period size: 87 Copynumber: 5.7 Consensus size: 87
35066 TAGGGAAGAT
35076 AAGATTCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 AAGA-TCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
35141 CTTCGCTGTTAACGCAAGAAGGC
65 CTTCGCTGTTAACGCAGGAAGGC
* * *
35164 AAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATAGAGGCAAGGCTTTGTTTTCGGTCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
*
35229 TTCGCTGTTAACGCAGGAAGGT
66 TTCGCTGTTAACGCAGGAAGGC
* *
35251 AAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGA
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
35316 TTCGCTGTTAACGCAGGAAGGC
66 TTCGCTGTTAACGCAGGAAGGC
* * * ** *
35338 AAGATCTGCTATCTTTAACCAGCCCCACTACAATCGATGGAGGCAATACTTTGTTTTCAATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
*
35403 TTCGCTATTAACGCAGGAAGGC
66 TTCGCTGTTAACGCAGGAAGGC
*
35425 AAGATATGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
*
35490 TTCGCTATTAACGCAGGAAGGC
66 TTCGCTGTTAACGCAGGAAGGC
*
35512 AAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
35575 TCACTGATCT
Statistics
Matches: 384, Mismatches: 27, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
87 380 0.99
88 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (87 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTGTTAACGCAGGAAGGC
Found at i:42874 original size:154 final size:154
Alignment explanation
Indices: 42594--42902 Score: 618
Period size: 154 Copynumber: 2.0 Consensus size: 154
42584 TCCTTTAATC
42594 TGTTTTTTTTCTACTTTTTATTTCTTGAAATCGTTCCCCCCTTTACAATGGTTTTTCAATCGGTT
1 TGTTTTTTTTCTACTTTTTATTTCTTGAAATCGTTCCCCCCTTTACAATGGTTTTTCAATCGGTT
42659 TTGTATCGAAAATAATATCCCCCTTTTTAGATCTGTTTGAATGGTTTTTAAATTGCCATTTTACA
66 TTGTATCGAAAATAATATCCCCCTTTTTAGATCTGTTTGAATGGTTTTTAAATTGCCATTTTACA
42724 ATTTTTCTATTATTTCTACTACTG
131 ATTTTTCTATTATTTCTACTACTG
42748 TGTTTTTTTTCTACTTTTTATTTCTTGAAATCGTTCCCCCCTTTACAATGGTTTTTCAATCGGTT
1 TGTTTTTTTTCTACTTTTTATTTCTTGAAATCGTTCCCCCCTTTACAATGGTTTTTCAATCGGTT
42813 TTGTATCGAAAATAATATCCCCCTTTTTAGATCTGTTTGAATGGTTTTTAAATTGCCATTTTACA
66 TTGTATCGAAAATAATATCCCCCTTTTTAGATCTGTTTGAATGGTTTTTAAATTGCCATTTTACA
42878 ATTTTTCTATTATTTCTACTACTG
131 ATTTTTCTATTATTTCTACTACTG
42902 T
1 T
42903 TTTGTTCTTC
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.51
Consensus pattern (154 bp):
TGTTTTTTTTCTACTTTTTATTTCTTGAAATCGTTCCCCCCTTTACAATGGTTTTTCAATCGGTT
TTGTATCGAAAATAATATCCCCCTTTTTAGATCTGTTTGAATGGTTTTTAAATTGCCATTTTACA
ATTTTTCTATTATTTCTACTACTG
Found at i:44753 original size:20 final size:20
Alignment explanation
Indices: 44728--44794 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
44718 ATATACTATT
*
44728 ACTATTTATGACATGACCTC
1 ACTATTCATGACATGACCTC
* *
44748 ACTATTCATGACTTGACCCC
1 ACTATTCATGACATGACCTC
* * ** *
44768 GCTGTTCATGATTTGACCCC
1 ACTATTCATGACATGACCTC
44788 ACTATTC
1 ACTATTC
44795 CTAGGACTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.34
Consensus pattern (20 bp):
ACTATTCATGACATGACCTC
Found at i:48343 original size:70 final size:70
Alignment explanation
Indices: 47923--48345 Score: 494
Period size: 70 Copynumber: 6.0 Consensus size: 70
47913 CCTGAAGATT
* * ** * *
47923 ATAGCTAGGAGCTTTTAACTCTCGCTAATTATTTAAAGGTTGCGGTATTAAACTTGCGAGCCTTA
1 ATAGCTTGGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGCGGTATTAAACCTGCGAGCCTTA
47988 AAATG
66 AAATG
* ** * * *
47993 -TCAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTTTGGAATTAAACCTGCAAGCCTC
1 AT-AGCTTGGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGCGGTATTAAACCTGCGAGCCTT
48057 AAAATG
65 AAAATG
** * *
48063 GCAG-TTGGGAGCTTTTAACTCTCGCTAACCATTTGGAGGCTGTGGTATTAAACCTGCGAGCCTT
1 ATAGCTT-GGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGCGGTATTAAACCTGCGAGCCTT
*
48127 AAAATT
65 AAAATG
* * * * *
48133 ACAGCTGGGAGCTTTTAACTCTCGCTAACTATTTAGAGGCTG-GGATATTAAATCTGCAAGCCTT
1 ATAGCTTGGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGCGG-TATTAAACCTGCGAGCCTT
48197 AAAATG
65 AAAATG
* * *
48203 ATAG-TTGGGAGCTTTTAACTCTTGCTAACTATTTGGAGGCTGCGATATTAAACTTGCGAGCCTT
1 ATAGCTT-GGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGCGGTATTAAACCTGCGAGCCTT
48267 AAAATG
65 AAAATG
** * * ** *
48273 ATAGCTTAAAGCTTTTAACTCTCACTAACTGTTTGGAGGCCACAGTATTAAACCTGCGAGCCTTA
1 ATAGCTTGGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGCGGTATTAAACCTGCGAGCCTTA
48338 AAATG
66 AAATG
48343 ATA
1 ATA
48346 AATACAAATA
Statistics
Matches: 302, Mismatches: 43, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
69 5 0.02
70 293 0.97
71 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (70 bp):
ATAGCTTGGAGCTTTTAACTCTCGCTAACTATTTGGAGGCTGCGGTATTAAACCTGCGAGCCTTA
AAATG
Found at i:57181 original size:18 final size:18
Alignment explanation
Indices: 57158--57195 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
57148 GAAAGAACGA
57158 GTGAGTTCCATCAGTGAT
1 GTGAGTTCCATCAGTGAT
57176 GTGAGTTCCATCAGTGAT
1 GTGAGTTCCATCAGTGAT
57194 GT
1 GT
57196 TTCCGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (18 bp):
GTGAGTTCCATCAGTGAT
Found at i:58596 original size:149 final size:152
Alignment explanation
Indices: 58322--58600 Score: 374
Period size: 149 Copynumber: 1.8 Consensus size: 152
58312 GAACTATAAG
58322 CCCTCCAAATCACCCAATTGCTCCCCTTCTGCACCTTTTGCAAACACCAAATTTGCCTTTTCTTT
1 CCCTCCAAATCACCCAATTGCTCCCC-TCTGCACCTTTTGCAAACACCAAATTTGCCTTTTCTTT
* * *
58387 TAAGAGGGATTAGAATCGCCTACCCCAATCAACTAAAACCTAGCAACTGCATGTACACACAAGCT
65 TAACAGGGATTAGAATCGCCTACCCCAATCAACTAAAACCTAGCAACTGCAAGCACACACAAGCT
58452 CTCATGTTTAGGGGTCATGGGGC
130 CTCATGTTTAGGGGTCATGGGGC
* *
58475 CCCTCCCAATC-CCCTAATTGCTCCCC-CATGCACCTTTTGCAAACA-CAAGATTTGGCTCTTT-
1 CCCTCCAAATCACCC-AATTGCTCCCCTC-TGCACCTTTTGCAAACACCAA-ATTTGCCT-TTTC
* * * * *
58536 TTTT-ACA-GGATTAGAATCGCCTA-TCCAGTCAACTGAAAGCTAGCAGCTGCAAGCACACACAA
62 TTTTAACAGGGATTAGAATCGCCTACCCCAATCAACTAAAACCTAGCAACTGCAAGCACACACAA
58598 GCT
127 GCT
58601 ATTTTACTCA
Statistics
Matches: 112, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
149 35 0.31
150 16 0.14
151 6 0.05
152 31 0.28
153 24 0.21
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.26
Consensus pattern (152 bp):
CCCTCCAAATCACCCAATTGCTCCCCTCTGCACCTTTTGCAAACACCAAATTTGCCTTTTCTTTT
AACAGGGATTAGAATCGCCTACCCCAATCAACTAAAACCTAGCAACTGCAAGCACACACAAGCTC
TCATGTTTAGGGGTCATGGGGC
Found at i:59531 original size:63 final size:63
Alignment explanation
Indices: 59409--59531 Score: 147
Period size: 63 Copynumber: 2.0 Consensus size: 63
59399 CTACAATCCA
* *
59409 GACAATCAAACAAAACTTAGTTTAATCAATTGAAACAAAAAAATATTTGTCATTAGATGACCG
1 GACAATCAAACAAAACTTAGTTTAATCAATAGAAACAAAAAAATATTTGTCATCAGATGACCG
* * * * * * * * *
59472 GACATTCAAACAAAACTTGGTTTCATCTATAGAAATATACAAATCTTTGTCATCCGATGA
1 GACAATCAAACAAAACTTAGTTTAATCAATAGAAACAAAAAAATATTTGTCATCAGATGA
59532 ACCAGACTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.29
Consensus pattern (63 bp):
GACAATCAAACAAAACTTAGTTTAATCAATAGAAACAAAAAAATATTTGTCATCAGATGACCG
Found at i:60944 original size:27 final size:28
Alignment explanation
Indices: 60881--60953 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
60871 TTTATTTTAA
* * *
60881 TTTAGGTTTTTAATTATTAAACTTATTAT
1 TTTAAGTTTTTAATTAATAAAC-TATGAT
*
60910 TTTCAAGTTTTTAATTAATAAAC-ATGCT
1 TTT-AAGTTTTTAATTAATAAACTATGAT
60938 TTTAAGTTTTTTAATT
1 TTTAAG-TTTTTAATT
60954 TATTTTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 3 0.08
28 15 0.39
29 3 0.08
30 17 0.45
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (28 bp):
TTTAAGTTTTTAATTAATAAACTATGAT
Found at i:61406 original size:13 final size:13
Alignment explanation
Indices: 61388--61412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61378 CAATATATTT
61388 ATTAATTAAAAAC
1 ATTAATTAAAAAC
61401 ATTAATTAAAAA
1 ATTAATTAAAAA
61413 TAAAAAATAT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:69295 original size:16 final size:15
Alignment explanation
Indices: 69270--69312 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
69260 TAAACAAGTA
* *
69270 AATAAAAACTAGCTAT
1 AATAATAACTAACT-T
69286 AATAATAACTAACTT
1 AATAATAACTAACTT
69301 AACTAATAACTA
1 AA-TAATAACTA
69313 TGGAAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAATAACTAACTT
Found at i:99660 original size:42 final size:43
Alignment explanation
Indices: 99567--99732 Score: 151
Period size: 43 Copynumber: 3.9 Consensus size: 43
99557 CAATGACAAC
* * *
99567 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCAAT
*
99610 GTCCCAGACA-GCGTCTTACATGAAATCATATA-CGATGCCAAT
1 GTCCCAGACATG-GTCTTACATGAAATCAAATATCGATGCCAAT
* * * *
99652 GTCTCAGACATGGTCTTACACGTAAATCTCAAATA--GATGCTAAC
1 GTCCCAGACATGGTCTTACATG-AAA--TCAAATATCGATGCCAAT
* * * * *
99696 GTCCCAGACGTGATCTTACACGAGATCACATATCGAT
1 GTCCCAGACATGGTCTTACATGAAATCAAATATCGAT
99733 ATCCTATGTC
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
41 6 0.06
42 28 0.27
43 36 0.35
44 26 0.25
45 6 0.06
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCAAT
Found at i:107384 original size:42 final size:43
Alignment explanation
Indices: 107318--107459 Score: 155
Period size: 42 Copynumber: 3.3 Consensus size: 43
107308 TCTTATATGT
* * *
107318 AATCAAATATCGATGTCACTGTCCCAGACAGGGTCTTACACGA
1 AATCATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGA
*
107361 AATCATATA-CGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCATATATCGATGCCAATGTCCCAGACAGGGTCTTACACG-A
* * *
107404 AATC-TCAAATCGATGCCAACGTCCCAGAC-GTGATCTTACACGA
1 AATCAT-ATATCGATGCCAATGTCCCAGACAG-GGTCTTACACGA
* *
107447 GATCACATATCGA
1 AATCATATATCGA
107460 AATCCTATGT
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
42 30 0.36
43 25 0.30
44 28 0.34
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
AATCATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGA
Found at i:107431 original size:44 final size:42
Alignment explanation
Indices: 107318--107451 Score: 146
Period size: 44 Copynumber: 3.1 Consensus size: 42
107308 TCTTATATGT
* *
107318 AATCAAATATCGATGTC-ACTGTCCCAGACAGGGTCTTACACGA
1 AATCAAATA-CGATGCCAAC-GTCCCAGACATGGTCTTACACGA
* *
107361 AATCATATACGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCAAATACGATGCCAACGTCCCAGACATGGTCTTACACG-A
* *
107404 AATCTCAAAT-CGATGCCAACGTCCCAGACGTGATCTTACACGA
1 AA--TCAAATACGATGCCAACGTCCCAGACATGGTCTTACACGA
*
107447 GATCA
1 AATCA
107452 CATATCGAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
41 3 0.04
42 27 0.35
43 14 0.18
44 29 0.37
45 5 0.06
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
AATCAAATACGATGCCAACGTCCCAGACATGGTCTTACACGA
Found at i:111781 original size:31 final size:31
Alignment explanation
Indices: 111716--111785 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
111706 GGGATCAAGT
* * *
111716 AAAAATTTTAAAAATTTTAGGAGTTTAATGA
1 AAAAATTTTAAAAAATTAAGGAGTCTAATGA
*
111747 AAAAATTTTAAAAAAATTAAGG-GTCTAATTA
1 AAAAATTTT-AAAAAATTAAGGAGTCTAATGA
111778 AAAAATTT
1 AAAAATTT
111786 AAATTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.36
Consensus pattern (31 bp):
AAAAATTTTAAAAAATTAAGGAGTCTAATGA
Found at i:113329 original size:21 final size:21
Alignment explanation
Indices: 113303--113355 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
113293 AGCGGTGGCG
*
113303 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
113324 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
113345 GTGAGATTAGA
1 GTGAGATTAGA
113356 AACAGCGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:114202 original size:11 final size:12
Alignment explanation
Indices: 114173--114205 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
114163 TTCAGCTTGG
*
114173 ATGCTGGTCTGC
1 ATGCTGGTTTGC
114185 ATGCTGGTTTGC
1 ATGCTGGTTTGC
114197 -TGCTGGTTT
1 ATGCTGGTTT
114206 CCTGTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.06, C:0.18, G:0.33, T:0.42
Consensus pattern (12 bp):
ATGCTGGTTTGC
Found at i:117478 original size:12 final size:13
Alignment explanation
Indices: 117461--117495 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
117451 GCAACCCAAG
117461 GGGAAGGGGAA-A
1 GGGAAGGGGAAGA
117473 GGGAAGGGGAAGA
1 GGGAAGGGGAAGA
*
117486 GGAAAGGGGA
1 GGGAAGGGGA
117496 GAAGAAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (13 bp):
GGGAAGGGGAAGA
Found at i:117481 original size:18 final size:18
Alignment explanation
Indices: 117458--117493 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
117448 TTTGCAACCC
*
117458 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGAGGAAAGGG
117476 AAGGGGAAGAGGAAAGGG
1 AAGGGGAAGAGGAAAGGG
117494 GAGAAGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGAGGAAAGGG
Found at i:122519 original size:16 final size:16
Alignment explanation
Indices: 122494--122541 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
122484 TACATAGATT
122494 TTATTATATTATTATTA
1 TTATT-TATTATTATTA
122511 TTATTTATTATTA-TA
1 TTATTTATTATTATTA
*
122526 TT-TTT-TTATTTTTA
1 TTATTTATTATTATTA
122540 TT
1 TT
122542 TATGCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.17
14 7 0.24
15 4 0.14
16 8 0.28
17 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTATTATTATTA
Found at i:122905 original size:112 final size:108
Alignment explanation
Indices: 122775--123073 Score: 415
Period size: 108 Copynumber: 2.7 Consensus size: 108
122765 ATATTTAGCA
* * *
122775 TTTGGAAACTCGAAAAAACGTCCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
1 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTTCTCGTTCAACCAAATAG
*
122840 CTAAGA-ATCCGTTTAAAAAAAATTTCAAAATAAGACAATGTTTTGCG
65 CCAA-ATATCC-TTT--AAAAAATTTCAAAATAAGACAATGTTTTGCG
122887 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTCTCGTTCAACCAAATAGC
1 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTCTCGTTCAACCAAATAGC
* * * *
122952 CAAATATCCTTTCAAAAATTTTACAATAAGGCAATGTTTTGCG
66 CAAATATCCTTTAAAAAATTTCAAAATAAGACAATGTTTTGCG
* * **
122995 TTTGGAAATTCGAG-GAACATGCCCTAATGTGCTGGGTTTCGA-TTTCTCGTTGGACCAAATAGC
1 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTCTCGTTCAACCAAATAGC
123058 CAAATATCCTCTTAAA
66 CAAATATCCT-TTAAA
123074 TTTTAATTCA
Statistics
Matches: 172, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
106 29 0.17
107 30 0.17
108 41 0.24
110 4 0.02
111 28 0.16
112 40 0.23
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (108 bp):
TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTCTCGTTCAACCAAATAGC
CAAATATCCTTTAAAAAATTTCAAAATAAGACAATGTTTTGCG
Found at i:123006 original size:108 final size:109
Alignment explanation
Indices: 122750--123073 Score: 422
Period size: 112 Copynumber: 3.0 Consensus size: 109
122740 AAAATAAATT
* * * * * * * *
122750 TTTCTAAATGAGGCAATATTTAGCATTTGGAAACTCGAAAAAACGTCCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
122815 CGATTTTTCTCGTTCAACCAAATAGCTAAGA-ATCCGTTTAAAAAAAA
66 CGA-TTTTCTCGTTCAACCAAATAGCCAA-ATATCC-TTT-AAAAAAA
*
122862 TTTCAAAATAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
122927 CGATTTTCTCGTTCAACCAAATAGCCAAATATCCTTT-CAAAAA
66 CGATTTTCTCGTTCAACCAAATAGCCAAATATCCTTTAAAAAAA
* * * *
122970 TTTTACAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACATGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
**
123034 CGA-TTTCTCGTTGGACCAAATAGCCAAATATCCTCTTAAA
66 CGATTTTCTCGTTCAACCAAATAGCCAAATATCCT-TTAAA
123074 TTTTAATTCA
Statistics
Matches: 190, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
106 29 0.15
107 28 0.15
108 42 0.22
110 4 0.02
111 28 0.15
112 59 0.31
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTCTCGTTCAACCAAATAGCCAAATATCCTTTAAAAAAA
Found at i:129417 original size:29 final size:29
Alignment explanation
Indices: 129346--129417 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
129336 ATTGATATTG
* * *
129346 ATAAAAAAT-ATTTAAATATTTAAATATT
1 ATAAAAAATCATTTAAATATGTAAAAACT
129374 ATAAAAAATGC-TTTAAAT-TGTAAAAACT
1 ATAAAAAAT-CATTTAAATATGTAAAAACT
129402 AGTAAAAAATCATTTA
1 A-TAAAAAATCATTTA
129418 TTTTTTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 18 0.49
29 19 0.51
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (29 bp):
ATAAAAAATCATTTAAATATGTAAAAACT
Found at i:129771 original size:20 final size:20
Alignment explanation
Indices: 129746--129785 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
129736 CGTAAAATGA
* *
129746 TTTCTGGAAACTGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
129766 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
129786 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:132897 original size:15 final size:16
Alignment explanation
Indices: 132872--132904 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
132862 TCATATCTCT
*
132872 TTTTTTAAATAATTTA
1 TTTTTTAAATAAATTA
132888 TTTTTT-AATAAATTA
1 TTTTTTAAATAAATTA
132903 TT
1 TT
132905 GTATTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTAAATAAATTA
Found at i:138535 original size:105 final size:105
Alignment explanation
Indices: 138424--138650 Score: 296
Period size: 105 Copynumber: 2.2 Consensus size: 105
138414 ATTAATGCAT
* * * *
138424 TATATGTGACAACATCAGGCTCAATGCCTTTCTTTCTCATTGTATCAACAATATCTTCAGCTTTA
1 TATATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTGCATCAACAATATCTACAGCTTCA
138489 GAAACCATTCC-C-TCTTTGCAATGTGCATCAACCAATATAC
66 GAAACCA-TCCTCTTC-TTGCAATGTGCATCAACCAATATAC
* * * *
138529 TGTATGTGACAACATTAGGTTCAATGCCTTGCTTTCTCATTGCATCAACAGTATCTACAGCTTCA
1 TATATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTGCATCAACAATATCTACAGCTTCA
* * * *
138594 GAAATCATCCTCTTCTTGCAATGTGCATCTATCAATATAT
66 GAAACCATCCTCTTCTTGCAATGTGCATCAACCAATATAC
* *
138634 TATACGTGACAATATCA
1 TATATGTGACAACATCA
138651 AGAGAAATAT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
104 3 0.03
105 99 0.95
106 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (105 bp):
TATATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTGCATCAACAATATCTACAGCTTCA
GAAACCATCCTCTTCTTGCAATGTGCATCAACCAATATAC
Found at i:140913 original size:27 final size:24
Alignment explanation
Indices: 140879--140932 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 24
140869 ATATTTTTCA
140879 TAATTTTTGAAAATTTTAAAATTTATT
1 TAATTTTTGAAAA--TTAAAA-TTATT
*
140906 TAATTTTTTAAAATTAAAATTATT
1 TAATTTTTGAAAATTAAAATTATT
140930 TAA
1 TAA
140933 AAAAAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.31
25 6 0.23
27 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TAATTTTTGAAAATTAAAATTATT
Found at i:141451 original size:2 final size:2
Alignment explanation
Indices: 141444--141472 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
141434 TTTGTTGAAT
141444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
141473 GAATCCGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:141989 original size:293 final size:294
Alignment explanation
Indices: 141451--142037 Score: 1167
Period size: 293 Copynumber: 2.0 Consensus size: 294
141441 AATTATATAT
141451 ATATATATATATATATATATATGAATCCGATTAATTTAGTTTTAAAGAAGAATTGTTGTAGTAAC
1 ATATATATATATATATATATATGAATCCGATTAATTTAGTTTTAAAGAAGAATTGTTGTAGTAAC
141516 AAGTGGTTGAAAAAAGCGATAGACCAAAAGATTAAGTTGAAAGGTTAGAATTATGATTGTTTAGA
66 AAGTGGTTGAAAAAAGCGATAGACCAAAAGATTAAGTTGAAAGGTTAGAATTATGATTGTTTAGA
141581 AAGTTTTTATTTAAATACCACACTGCTCTAATTTTGTTGGATGTGGGTAAGGTAGATTTTGGCAG
131 AAGTTTTTATTTAAATACCACACTGCTCTAATTTTGTTGGATGTGGGTAAGGTAGATTTTGGCAG
141646 AAGACTACACGTAAAACCTAAGGGTAGATTCCCGGTGGCACCTTTAGCACCAAACGAGCTTAAGC
196 AAGACTACACGTAAAACCTAAGGGTAGATTCCCGGTGGCACCTTTAGCACCAAACGAGCTTAAGC
141711 TGGAAATCAAATTGCTTCATCATTTTGCAGTAAG
261 TGGAAATCAAATTGCTTCATCATTTTGCAGTAAG
141745 ATATATATAT-TATATATATATGAATCCGATTAATTTAGTTTTAAAGAAGAATTGTTGTAGTAAC
1 ATATATATATATATATATATATGAATCCGATTAATTTAGTTTTAAAGAAGAATTGTTGTAGTAAC
141809 AAGTGGTTGAAAAAAGCGATAGACCAAAAGATTAAGTTGAAAGGTTAGAATTATGATTGTTTAGA
66 AAGTGGTTGAAAAAAGCGATAGACCAAAAGATTAAGTTGAAAGGTTAGAATTATGATTGTTTAGA
141874 AAGTTTTTATTTAAATACCACACTGCTCTAATTTTGTTGGATGTGGGTAAGGTAGATTTTGGCAG
131 AAGTTTTTATTTAAATACCACACTGCTCTAATTTTGTTGGATGTGGGTAAGGTAGATTTTGGCAG
141939 AAGACTACACGTAAAACCTAAGGGTAGATTCCCGGTGGCACCTTTAGCACCAAACGAGCTTAAGC
196 AAGACTACACGTAAAACCTAAGGGTAGATTCCCGGTGGCACCTTTAGCACCAAACGAGCTTAAGC
142004 TGGAAATCAAATTGCTTCATCATTTTGCAGTAAG
261 TGGAAATCAAATTGCTTCATCATTTTGCAGTAAG
142038 GGTTGATCCT
Statistics
Matches: 293, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
293 283 0.97
294 10 0.03
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (294 bp):
ATATATATATATATATATATATGAATCCGATTAATTTAGTTTTAAAGAAGAATTGTTGTAGTAAC
AAGTGGTTGAAAAAAGCGATAGACCAAAAGATTAAGTTGAAAGGTTAGAATTATGATTGTTTAGA
AAGTTTTTATTTAAATACCACACTGCTCTAATTTTGTTGGATGTGGGTAAGGTAGATTTTGGCAG
AAGACTACACGTAAAACCTAAGGGTAGATTCCCGGTGGCACCTTTAGCACCAAACGAGCTTAAGC
TGGAAATCAAATTGCTTCATCATTTTGCAGTAAG
Found at i:151341 original size:39 final size:41
Alignment explanation
Indices: 151271--151360 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 41
151261 AAAAAGTATT
* *
151271 TATATTAAAAAAACACTACCATAAATATAATAAATGTTTTAC
1 TATATT-AAAAAACACTACAATAAATATAATAAATATTTTAC
* *
151313 TATATTAAAAAACAC-A-AATAAATATAATATATATTTTAT
1 TATATTAAAAAACACTACAATAAATATAATAAATATTTTAC
*
151352 TGTATTAAA
1 TATATTAAA
151361 TATAAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 27 0.63
40 1 0.02
41 9 0.21
42 6 0.14
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (41 bp):
TATATTAAAAAACACTACAATAAATATAATAAATATTTTAC
Found at i:155072 original size:131 final size:131
Alignment explanation
Indices: 154824--155111 Score: 407
Period size: 131 Copynumber: 2.2 Consensus size: 131
154814 TATTGTTTAC
* **
154824 TTTATATATCATGAACAATCTTATTTGAGTTAGCTGATTTAAGATCACTACTTCAAACAGCTTGT
1 TTTAT-TATCATGAACAATCTTATTTGAGTTAGCTGATTTAAGATCACTACTCCAAACAGCTCAT
* * * *
154889 TGATTTAATATCGCAGTTGATATCGTTAAGGTTTGCTGATTTGAATTCGCAATCTAAGTTCATTC
65 TGATTTAATATCGCAGCTGATATCGTTAAAGTTAGCTAATTTGAATTCGCAATCTAAGTTCATTC
154954 AA
130 AA
*
154956 TTTATTATCATGAACAATCTTATTTGAGTTAGCTGATTTAAGATCGCTACTCCAAACAGCTCATT
1 TTTATTATCATGAACAATCTTATTTGAGTTAGCTGATTTAAGATCACTACTCCAAACAGCTCATT
* * * *
155021 TATTTAATATCGCGGCTGATATTGTTAAAGTTAGCTAATTT-AATATTGCAATCTAAGTTCATTC
66 GATTTAATATCGCAGCTGATATCGTTAAAGTTAGCTAATTTGAAT-TCGCAATCTAAGTTCATTC
*
155085 GA
130 AA
* * *
155087 TTCAATATCATGAACAATCTCATTT
1 TTTATTATCATGAACAATCTTATTT
155112 TTGTTACCTA
Statistics
Matches: 139, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
130 3 0.02
131 131 0.94
132 5 0.04
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (131 bp):
TTTATTATCATGAACAATCTTATTTGAGTTAGCTGATTTAAGATCACTACTCCAAACAGCTCATT
GATTTAATATCGCAGCTGATATCGTTAAAGTTAGCTAATTTGAATTCGCAATCTAAGTTCATTCA
A
Found at i:163167 original size:103 final size:104
Alignment explanation
Indices: 162919--163224 Score: 398
Period size: 103 Copynumber: 2.9 Consensus size: 104
162909 TTATGACTTA
* * * * * ** *
162919 AGCTGGATTTTAGTAATTGATAATGGGTTAATGAAATGGGGATATTGTTGATGGTTAAATTATGT
1 AGCTGGATTTTAGTAATTGCTAGTGGATTAATGAAATGGGGTTATTGTTGATTGTTAAACAATGG
* *
162984 AGGAATTTTGTGGGTTTACAACTTAAAAAATTGGTGGTTTC
66 AGGAAATTTATGGGTTTACAACTT--AAAATTGGTGGTTTC
* *
163025 AGCTAGATTTTAGTAATTGCTAGTGGATTTATGAAATGGGGTTATTGTTGATTGTTAAACAATGG
1 AGCTGGATTTTAGTAATTGCTAGTGGATTAATGAAATGGGGTTATTGTTGATTGTTAAACAATGG
* * *
163090 AGGAAATTTATGGGTTTATAGCTT-AAATTGGTGGTTTT
66 AGGAAATTTATGGGTTTACAACTTAAAATTGGTGGTTTC
* * *
163128 AGTTGGATTTTAGTATTTGCTAGTGGATTAATGAAATGGGGTGATTGTTGATTGTTAAACAATGG
1 AGCTGGATTTTAGTAATTGCTAGTGGATTAATGAAATGGGGTTATTGTTGATTGTTAAACAATGG
* * *
163193 AAGAAATTTATGCGTTTACCACTTAAAATTGG
66 AGGAAATTTATGGGTTTACAACTTAAAATTGG
163225 CAACTTTTAG
Statistics
Matches: 174, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
103 92 0.53
104 7 0.04
106 75 0.43
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.40
Consensus pattern (104 bp):
AGCTGGATTTTAGTAATTGCTAGTGGATTAATGAAATGGGGTTATTGTTGATTGTTAAACAATGG
AGGAAATTTATGGGTTTACAACTTAAAATTGGTGGTTTC
Found at i:166498 original size:27 final size:27
Alignment explanation
Indices: 166465--166537 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
166455 TATGTCGAAT
166465 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
*
166492 TTGTTAGATATTGAATTTATTATGTTTTAATC
1 TTGTTAGATATTG-----ATTATGTTTTAAGC
*
166524 TTGTTGGATATTGA
1 TTGTTAGATATTGA
166538 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:166517 original size:32 final size:32
Alignment explanation
Indices: 166478--166538 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
166468 TTAGATATTG
166478 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
* *
166510 ATTATGTTTTAATCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
166539 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:169180 original size:33 final size:33
Alignment explanation
Indices: 169116--169515 Score: 206
Period size: 33 Copynumber: 11.8 Consensus size: 33
169106 NNNNNAAGGG
*
169116 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
169143 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
169176 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
* * *
169218 GGCTGCTAAGTGCTGATTCCCTGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
169251 GGTTGCTAAGTTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAG-TGCTGATTCC-CCG-A--TT-CAT-T---GGT
*
169294 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
169321 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
169354 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A---TT-CAT-T---GGT
*
169397 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
169424 GGTTGCTAAGTGCTGATTCACAGAATGATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
169457 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
169490 GGTCGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
169516 AACGCTTAAC
Statistics
Matches: 290, Mismatches: 35, Indels: 89
0.70 0.08 0.21
Matches are distributed among these distances:
27 62 0.21
28 4 0.01
31 5 0.02
32 6 0.02
33 97 0.33
34 20 0.07
35 4 0.01
36 3 0.01
37 4 0.01
38 6 0.02
39 6 0.02
40 3 0.01
41 4 0.01
42 32 0.11
43 34 0.12
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:169304 original size:76 final size:75
Alignment explanation
Indices: 169139--169315 Score: 300
Period size: 76 Copynumber: 2.3 Consensus size: 75
169129 TGATTCCCCC
* *
169139 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
169204 TTAAATGTGA
66 TTAAATGTGA
* *
169214 AAGGGGCTGCTAAGTGCTGATTCCCTGACTCATTGGTGGTTGCTAAGTTGCTGATTCCACCGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAG-TGCTGATTCCACCGTAT
169279 CTTAAATGTGA
65 CTTAAATGTGA
*
169290 AGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
169316 CAAGGGGTTG
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 43 0.46
76 51 0.54
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:169338 original size:103 final size:103
Alignment explanation
Indices: 169214--169476 Score: 438
Period size: 103 Copynumber: 2.6 Consensus size: 103
169204 TTAAATGTGA
* * *
169214 AAGGGGCTGCTAAGTGCTGATTCCCTGACTCATTGGTGGTTGCTAAGTTGCTGATTCCACCGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAG-TGCTGATTCCACCGTAT
169279 C-TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
65 CTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
169317 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
169382 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
169420 AAGGGGTTGCTAAGTGCTGATTCACAGAATGATTGGTGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTGATTCC
169477 CCGAATCACT
Statistics
Matches: 150, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
102 18 0.12
103 132 0.88
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:182061 original size:19 final size:20
Alignment explanation
Indices: 182036--182092 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
182026 ATCCAAACAC
182036 CAGAAAAGTAAATCATTTCT
1 CAGAAAAGTAAATCATTTCT
*
182056 -AGAAAAGTAAATCATTTTT
1 CAGAAAAGTAAATCATTTCT
* *
182075 CAGAAAAGAAAATTATTT
1 CAGAAAAGTAAATCATTT
182093 TCCAGAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (20 bp):
CAGAAAAGTAAATCATTTCT
Found at i:182081 original size:20 final size:20
Alignment explanation
Indices: 182036--182100 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
182026 ATCCAAACAC
*
182036 CAGAAAAGTAAATCATTTCT
1 CAGAAAAGTAAATCATTTTT
182056 -AGAAAAGTAAATCATTTTT
1 CAGAAAAGTAAATCATTTTT
* * *
182075 CAGAAAAGAAAATTATTTTC
1 CAGAAAAGTAAATCATTTTT
182095 CAGAAA
1 CAGAAA
182101 TTATTTTCCG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 18 0.45
20 22 0.55
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (20 bp):
CAGAAAAGTAAATCATTTTT
Found at i:182116 original size:15 final size:15
Alignment explanation
Indices: 182081--182121 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
182071 TTTTCAGAAA
182081 AGAAAATTATTTTCC
1 AGAAAATTATTTTCC
182096 AG-AAATTATTTTCC
1 AGAAAATTATTTTCC
*
182110 GGAAAA-TATTTT
1 AGAAAATTATTTT
182122 ACTAACAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (15 bp):
AGAAAATTATTTTCC
Found at i:183484 original size:105 final size:105
Alignment explanation
Indices: 183160--183580 Score: 474
Period size: 104 Copynumber: 4.0 Consensus size: 105
183150 TCCCTACTTG
* * ***
183160 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACAATATCTGGTGCTTCA-A
1 TATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTCTGTCAACAATATCTTCAGCTTCAGA
* *
183224 AACCATCCCCTTCTTGCAATGTGCATCAACCAATATACTA
66 AACCATTCCCTCCTTGCAATGTGCATCAACCAATATACTA
* * * *
183264 TGA-GTGTCAACGTCAGGTTCAATACCTTGCTTTCTCA-TCGTGTCAACAATATCTTCAGCTT-A
1 T-ATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTC-TGTCAACAATATCTTCAGCTTCA
* * * * **
183326 GGAACCATTCCCTCCTTGCAATGCGCATTAACCAACATGTTA
64 GAAACCATTCCCTCCTTGCAATGTGCATCAACCAATATACTA
* * * *
183368 TATGTGACAACATCAGGCTCAATGCCTAGCTTTTTCATACTGTCAACAATATCTTCAGCTTTAGA
1 TATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTCTGTCAACAATATCTTCAGCTTCAGA
* * *
183433 AATCATTCCCTTCTTGCAATATGCATCAACCAATATACTA
66 AACCATTCCCTCCTTGCAATGTGCATCAACCAATATACTA
* * ** * *
183473 TATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTTAACAATATCTAGAACTTCAAA
1 TATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTCTGTCAACAATATCTTCAGCTTCAGA
* * * *
183538 AATCATTCCCTCCTTG-AAGTGTGCATCAATCAATCTATTA
66 AACCATTCCCTCCTTGCAA-TGTGCATCAACCAATATACTA
183578 TAT
1 TAT
183581 ATAAAAATAT
Statistics
Matches: 262, Mismatches: 48, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
103 3 0.01
104 133 0.51
105 126 0.48
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (105 bp):
TATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTCTGTCAACAATATCTTCAGCTTCAGA
AACCATTCCCTCCTTGCAATGTGCATCAACCAATATACTA
Found at i:199542 original size:12 final size:12
Alignment explanation
Indices: 199525--199554 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
199515 CCTCACACGC
199525 TCGTGTGCTAGG
1 TCGTGTGCTAGG
199537 TCGTGTGCTAGG
1 TCGTGTGCTAGG
*
199549 CCGTGT
1 TCGTGT
199555 AACTGCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.40, T:0.33
Consensus pattern (12 bp):
TCGTGTGCTAGG
Found at i:203709 original size:85 final size:85
Alignment explanation
Indices: 203573--203736 Score: 202
Period size: 85 Copynumber: 1.9 Consensus size: 85
203563 CACTTTCACC
* * * * *
203573 ATAAGTAAGATACTGTCAAAGATCATGTAAAAATCCAATTTGAGATGATCCTGTGACATACTTGC
1 ATAACTAAGATAATGTCAAAGATCATGTAAAAATCCAATTTGAGATAATCCTATGACATACCTGC
203638 AACAACACAAGTATTTCAAA
66 AACAACACAAGTATTTCAAA
* * * * * ** *
203658 ATAACTAAGATAATGTCAGAGATCATGTCAGAATCTAATTTTAGATAATCCTATGATGTGCCTGC
1 ATAACTAAGATAATGTCAAAGATCATGTAAAAATCCAATTTGAGATAATCCTATGACATACCTGC
*
203723 AACAACATAAGTAT
66 AACAACACAAGTAT
203737 GTAGAGCATT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (85 bp):
ATAACTAAGATAATGTCAAAGATCATGTAAAAATCCAATTTGAGATAATCCTATGACATACCTGC
AACAACACAAGTATTTCAAA
Found at i:205567 original size:28 final size:28
Alignment explanation
Indices: 205536--205682 Score: 133
Period size: 28 Copynumber: 5.2 Consensus size: 28
205526 AGACTTATTC
**
205536 TTTCATATTACGCCACAAAGAAATTTCT
1 TTTCATATTACGCCACAAAGGCATTTCT
* * *
205564 TTTCATA-AATCGTCACAAAGGCTTATTC-
1 TTTCATATTA-CGCCACAAAGGCAT-TTCT
205592 TTTCATATTACGCCACAAAGGCATTTCT
1 TTTCATATTACGCCACAAAGGCATTTCT
* *
205620 TTTCATGAAT-CGCCACAGAGG-ATTAT-T
1 TTTCAT-ATTACGCCACAAAGGCATT-TCT
* *
205647 CTTTCATATTATGCCACAAAGACATTTCT
1 -TTTCATATTACGCCACAAAGGCATTTCT
205676 TTTCATA
1 TTTCATA
205683 AATTGCCACA
Statistics
Matches: 95, Mismatches: 14, Indels: 20
0.74 0.11 0.16
Matches are distributed among these distances:
27 10 0.11
28 75 0.79
29 10 0.11
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (28 bp):
TTTCATATTACGCCACAAAGGCATTTCT
Found at i:205589 original size:56 final size:56
Alignment explanation
Indices: 205506--205695 Score: 272
Period size: 56 Copynumber: 3.4 Consensus size: 56
205496 CAAGGTTATC
* * * * *
205506 CTTTTCATGAATCGCTACAGAGACTTATTCTTTCATATTACGCCACAAAGAAATTT
1 CTTTTCATAAATCGCCACAAAGGCTTATTCTTTCATATTACGCCACAAAGACATTT
* *
205562 CTTTTCATAAATCGTCACAAAGGCTTATTCTTTCATATTACGCCACAAAGGCATTT
1 CTTTTCATAAATCGCCACAAAGGCTTATTCTTTCATATTACGCCACAAAGACATTT
* * * *
205618 CTTTTCATGAATCGCCACAGAGGATTATTCTTTCATATTATGCCACAAAGACATTT
1 CTTTTCATAAATCGCCACAAAGGCTTATTCTTTCATATTACGCCACAAAGACATTT
*
205674 CTTTTCATAAATTGCCACAAAG
1 CTTTTCATAAATCGCCACAAAG
205696 TCTTCCATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 118 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (56 bp):
CTTTTCATAAATCGCCACAAAGGCTTATTCTTTCATATTACGCCACAAAGACATTT
Found at i:210180 original size:21 final size:22
Alignment explanation
Indices: 210156--210200 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
210146 GTTGAGAAGG
*
210156 AAGTTGCTACTGTAGAA-AAAA
1 AAGTTGCTACTGAAGAAGAAAA
* *
210177 AAGTTGTTGCTGAAGAAGAAAA
1 AAGTTGCTACTGAAGAAGAAAA
210199 AA
1 AA
210201 TTACTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (22 bp):
AAGTTGCTACTGAAGAAGAAAA
Found at i:216590 original size:39 final size:39
Alignment explanation
Indices: 216547--216718 Score: 213
Period size: 39 Copynumber: 4.4 Consensus size: 39
216537 ATAGAAATAT
216547 GGTGATTATTC-GAGCTATATGCCTAGCAGGCTTTGTGCC
1 GGTGATTATTCAG-GCTATATGCCTAGCAGGCTTTGTGCC
* * * *
216586 GGTGATTATTCAGGCCATGTGCCTATCAGGCTTTATGCC
1 GGTGATTATTCAGGCTATATGCCTAGCAGGCTTTGTGCC
* * *
216625 GGTGGTTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCC
1 GGTGATTATTCAGGCTATATGCCTAGCAGGCTTTGTGCC
**
216664 GGTGATTATTCAGGCTA-AGTGCCTAGCAGGCTTTGTGTT
1 GGTGATTATTCAGGCTATA-TGCCTAGCAGGCTTTGTGCC
* *
216703 GTTGATTATTCCGGCT
1 GGTGATTATTCAGGCT
216719 TTGTACCGGT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 114 0.99
40 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.35
Consensus pattern (39 bp):
GGTGATTATTCAGGCTATATGCCTAGCAGGCTTTGTGCC
Found at i:216713 original size:78 final size:78
Alignment explanation
Indices: 216547--216697 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
216537 ATAGAAATAT
* * *
216547 GGTGATTATTCGAGCTATATGCCTAGCAGGCTTTGTGCCGGTGATTATTCAGGCCATGTGCCTAT
1 GGTGATTATTCGGGCTATATGCCTAGCAGGCTTTGTGCCGGTGATTATTCAGGCCAAGTGCCTAG
216612 CAGGCTTTATGCC
66 CAGGCTTTATGCC
* * *
216625 GGTGGTTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTATTCAGGCTAAGTGCCTAG
1 GGTGATTATTCGGGCTATATGCCTAGCAGGCTTTGTGCCGGTGATTATTCAGGCCAAGTGCCTAG
216690 CAGGCTTT
66 CAGGCTTT
216698 GTGTTGTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.33
Consensus pattern (78 bp):
GGTGATTATTCGGGCTATATGCCTAGCAGGCTTTGTGCCGGTGATTATTCAGGCCAAGTGCCTAG
CAGGCTTTATGCC
Found at i:216760 original size:16 final size:16
Alignment explanation
Indices: 216736--216779 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
216726 GGTGATTATT
216736 CAAGCTATGTGCCTAG
1 CAAGCTATGTGCCTAG
*
216752 CAGGCTATGTGCCTAG
1 CAAGCTATGTGCCTAG
*
216768 CAAGCTTTGTGC
1 CAAGCTATGTGC
216780 TGGTGATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (16 bp):
CAAGCTATGTGCCTAG
Found at i:216801 original size:23 final size:23
Alignment explanation
Indices: 216771--216814 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
216761 TGCCTAGCAA
216771 GCTTTGTGCTGG-TGATTATTCAG
1 GCTTTGTGC-GGATGATTATTCAG
216794 GCTTTGTGCGGATGATTATTC
1 GCTTTGTGCGGATGATTATTC
216815 GGGTCATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.43
Consensus pattern (23 bp):
GCTTTGTGCGGATGATTATTCAG
Found at i:216827 original size:78 final size:78
Alignment explanation
Indices: 216674--216842 Score: 216
Period size: 78 Copynumber: 2.2 Consensus size: 78
216664 GGTGATTATT
* * * * *
216674 CAGGCTAAGTGCCTAGCAGGCTTTGTGTTGTTGATTATTCCGGCTTTGTACCGGTGATTATTCAA
1 CAGGCTATGTGCCTAGCAAGCTTTGTGCTGGTGATTATTCAGGCTTTGTACCGGTGATTATTCAA
*
216739 GCTATGTGCCTAG
66 GCTATATGCCTAG
*
216752 CAGGCTATGTGCCTAGCAAGCTTTGTGCTGGTGATTATTCAGGCTTTGT-GCGGATGATTATTC-
1 CAGGCTATGTGCCTAGCAAGCTTTGTGCTGGTGATTATTCAGGCTTTGTACCGG-TGATTATTCA
* *
216815 GGGTCATATGCCTAG
65 AGCT-ATATGCCTAG
*
216830 CAGGCTTTGTGCC
1 CAGGCTATGTGCC
216843 GGTGATTATT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 5 0.06
78 74 0.94
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (78 bp):
CAGGCTATGTGCCTAGCAAGCTTTGTGCTGGTGATTATTCAGGCTTTGTACCGGTGATTATTCAA
GCTATATGCCTAG
Found at i:216834 original size:39 final size:39
Alignment explanation
Indices: 216791--216874 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
216781 GGTGATTATT
216791 CAGGCTTTGTG-CGGATGATTATTCGGG-TCATATGCCTAG
1 CAGGCTTTGTGCCGG-TGATTATTCGGGCT-ATATGCCTAG
*
216830 CAGGCTTTGTGCCGGTGATTATTCGGGCTATGTGCCTAG
1 CAGGCTTTGTGCCGGTGATTATTCGGGCTATATGCCTAG
216869 CAGGCT
1 CAGGCT
216875 ATATGCCGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
39 38 0.90
40 4 0.10
ACGTcount: A:0.15, C:0.20, G:0.32, T:0.32
Consensus pattern (39 bp):
CAGGCTTTGTGCCGGTGATTATTCGGGCTATATGCCTAG
Found at i:216882 original size:39 final size:39
Alignment explanation
Indices: 216806--216882 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
216796 TTTGTGCGGA
* *
216806 TGATTATTCGGGTCATATGCCTAGCAGGCTTTGTGCCGG
1 TGATTATTCGGGTCATATGCCTAGCAGGCTATATGCCGG
*
216845 TGATTATTCGGG-CTATGTGCCTAGCAGGCTATATGCCG
1 TGATTATTCGGGTC-ATATGCCTAGCAGGCTATATGCCG
216883 ATGTATTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (39 bp):
TGATTATTCGGGTCATATGCCTAGCAGGCTATATGCCGG
Found at i:222970 original size:6 final size:6
Alignment explanation
Indices: 222961--222988 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
222951 ATGTCTACCT
222961 CAAACA CAAACA CAAACA CAAACA CAAA
1 CAAACA CAAACA CAAACA CAAACA CAAA
222989 TAAATCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACA
Found at i:224899 original size:15 final size:15
Alignment explanation
Indices: 224872--224909 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
224862 ATTCATTGCT
224872 TTTAGGG-TTTAAGA
1 TTTAGGGTTTTAAGA
*
224886 TTTAGGGTTTTAAGG
1 TTTAGGGTTTTAAGA
224901 TTTAGGGTT
1 TTTAGGGTT
224910 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (15 bp):
TTTAGGGTTTTAAGA
Found at i:225198 original size:29 final size:28
Alignment explanation
Indices: 225131--225189 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
225121 AATAAACACC
225131 AAAAAATATTTTAAAAATAAAAATAATA
1 AAAAAATATTTTAAAAATAAAAATAATA
*
225159 AAAAAATATTTTAAAATTAAAGAATAA-A
1 AAAAAATATTTTAAAAATAAA-AATAATA
225187 AAA
1 AAA
225190 TATTTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAATATTTTAAAAATAAAAATAATA
Found at i:226165 original size:18 final size:18
Alignment explanation
Indices: 226139--226181 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
226129 GACTCGAAAA
* * *
226139 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
226157 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
226175 AGGATAC
1 AGGATAC
226182 GCACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:226840 original size:7 final size:7
Alignment explanation
Indices: 226828--226853 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
226818 TTATATATAT
226828 AATACTA
1 AATACTA
226835 AATACTA
1 AATACTA
226842 AATACTA
1 AATACTA
226849 AATAC
1 AATAC
226854 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:228029 original size:11 final size:10
Alignment explanation
Indices: 228015--228126 Score: 97
Period size: 11 Copynumber: 10.6 Consensus size: 10
228005 TAGGGATTTA
228015 AGAGAAATTTG
1 AGAGAAA-TTG
228026 AGAGCAAATTG
1 AGAG-AAATTG
228037 AGAGCAAATTG
1 AGAG-AAATTG
228048 AGAGCAAATT-
1 AGAG-AAATTG
*
228058 -GAG-ATTTG
1 AGAGAAATTG
228066 AGAGAAATTTG
1 AGAGAAA-TTG
228077 -GAAGGAAATTG
1 AG-A-GAAATTG
228088 AGAGCAAATTG
1 AGAG-AAATTG
228099 AGAGGAAATTG
1 AGA-GAAATTG
228110 AGAGGAAATTG
1 AGA-GAAATTG
228121 AGAGAA
1 AGAGAA
228127 TAATTGAGAA
Statistics
Matches: 89, Mismatches: 2, Indels: 21
0.79 0.02 0.19
Matches are distributed among these distances:
7 3 0.03
9 6 0.07
10 6 0.07
11 65 0.73
12 9 0.10
ACGTcount: A:0.46, C:0.04, G:0.30, T:0.21
Consensus pattern (10 bp):
AGAGAAATTG
Found at i:228040 original size:22 final size:21
Alignment explanation
Indices: 228015--228135 Score: 117
Period size: 22 Copynumber: 5.6 Consensus size: 21
228005 TAGGGATTTA
228015 AGAGAAATTTGAGAGCAAATTG
1 AGAGAAA-TTGAGAGCAAATTG
228037 AGAGCAAATTGAGAGCAAATT-
1 AGAG-AAATTGAGAGCAAATTG
*
228058 -GAG-ATTTGAGAG-AAATTTG
1 AGAGAAATTGAGAGCAAA-TTG
228077 -GAAGGAAATTGAGAGCAAATTG
1 AG-A-GAAATTGAGAGCAAATTG
*
228099 AGAGGAAATTGAGAGGAAATTG
1 AGA-GAAATTGAGAGCAAATTG
228121 AGAGAATAATTGAGA
1 AGAG-A-AATTGAGA
228136 AAGGATTAAT
Statistics
Matches: 86, Mismatches: 3, Indels: 19
0.80 0.03 0.18
Matches are distributed among these distances:
17 3 0.03
18 10 0.12
19 1 0.01
20 4 0.05
21 2 0.02
22 51 0.59
23 15 0.17
ACGTcount: A:0.45, C:0.03, G:0.30, T:0.21
Consensus pattern (21 bp):
AGAGAAATTGAGAGCAAATTG
Found at i:228070 original size:51 final size:51
Alignment explanation
Indices: 228009--228112 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 51
227999 TAAAAATAGG
228009 GATTTAAGAGAAATTT-GAGAGCAAATTGAGAGCAAATTGAGAGCAAATTGA
1 GATTTAAGAGAAATTTGGA-AGCAAATTGAGAGCAAATTGAGAGCAAATTGA
* * *
228060 GATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGAGAGGAAATTGA
1 GATTTAAGAGAAATTTGGAAGCAAATTGAGAGCAAATTGAGAGCAAATTGA
228111 GA
1 GA
228113 GGAAATTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 47 0.96
52 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.29, T:0.23
Consensus pattern (51 bp):
GATTTAAGAGAAATTTGGAAGCAAATTGAGAGCAAATTGAGAGCAAATTGA
Found at i:228086 original size:40 final size:40
Alignment explanation
Indices: 228021--228101 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
228011 TTTAAGAGAA
228021 ATTTGAGAGCAAATTGAGAGCAAATTGAGAGCAAATTGAG
1 ATTTGAGAGCAAATTGAGAGCAAATTGAGAGCAAATTGAG
*
228061 ATTTGAGAG-AAATTTG-GAAGGAAATTGAGAGCAAATTGAG
1 ATTTGAGAGCAAA-TTGAG-AGCAAATTGAGAGCAAATTGAG
228101 A
1 A
228102 GGAAATTGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
39 4 0.11
40 34 0.89
ACGTcount: A:0.43, C:0.05, G:0.28, T:0.23
Consensus pattern (40 bp):
ATTTGAGAGCAAATTGAGAGCAAATTGAGAGCAAATTGAG
Found at i:229094 original size:25 final size:25
Alignment explanation
Indices: 229066--229113 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
229056 GTTCGGGTAC
229066 CAATCAGGGACAAAAAAATAAGTAT
1 CAATCAGGGACAAAAAAATAAGTAT
* * *
229091 CAATCTGGGAGAAATAAATAAGT
1 CAATCAGGGACAAAAAAATAAGT
229114 TCAGGTACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (25 bp):
CAATCAGGGACAAAAAAATAAGTAT
Found at i:233598 original size:10 final size:9
Alignment explanation
Indices: 233540--233599 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
233530 GACTAAAGTG
233540 ATTTTTATA
1 ATTTTTATA
*
233549 ATCTTTA-A
1 ATTTTTATA
*
233557 ATATATTTATT
1 AT-T-TTTATA
233568 ATTTTT-TA
1 ATTTTTATA
233576 ATTTTTATGA
1 ATTTTTAT-A
233586 ATTTTTAATA
1 ATTTTT-ATA
233596 ATTT
1 ATTT
233600 ATTTACTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 10 0.24
9 10 0.24
10 17 0.41
11 4 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:234542 original size:38 final size:38
Alignment explanation
Indices: 234496--234571 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
234486 CTTGAATCAA
234496 TGTTGAACAATTCAAGCGTAAATCTTATGAAATCAGTG
1 TGTTGAACAATTCAAGCGTAAATCTTATGAAATCAGTG
234534 TGTTGAACAATTCAAGCGTAAATCTTATGAAATCAGTG
1 TGTTGAACAATTCAAGCGTAAATCTTATGAAATCAGTG
234572 AAGGTTGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (38 bp):
TGTTGAACAATTCAAGCGTAAATCTTATGAAATCAGTG
Found at i:235945 original size:12 final size:12
Alignment explanation
Indices: 235928--235954 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
235918 AATAAATCAT
235928 ATATGTATATTA
1 ATATGTATATTA
235940 ATATGTATATTA
1 ATATGTATATTA
235952 ATA
1 ATA
235955 GAAAATTTAA
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:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:236175 original size:21 final size:21
Alignment explanation
Indices: 236127--236182 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
236117 CACCATTGTT
*
236127 TCTAATCTCATCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
236148 TCCAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
236169 GT-TAATCCCACCGC
1 -TCTAATCTCACCGC
236183 CACCGCTGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.36, G:0.11, T:0.27
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:240179 original size:33 final size:32
Alignment explanation
Indices: 240142--240229 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 32
240132 ATTTATTCAA
* *
240142 ATAAAATAATTACAAATGCTTCATTTTGAATAT
1 ATAAAATAATTA-AAATCCTTCATTTTGAAAAT
* *
240175 AT-AAAT-ATTAAAATCCTAGCCTTTTGAAAAT
1 ATAAAATAATTAAAATCCT-TCATTTTGAAAAT
*
240206 ATAAAA-AATTTAAAATTCTTCATT
1 ATAAAATAA-TTAAAATCCTTCATT
240230 CGAATAGATG
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
30 6 0.14
31 16 0.36
32 11 0.25
33 11 0.25
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (32 bp):
ATAAAATAATTAAAATCCTTCATTTTGAAAAT
Found at i:244003 original size:15 final size:14
Alignment explanation
Indices: 243979--244012 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
243969 TATTTTTCTA
243979 TTTATTTAATTTAG
1 TTTATTTAATTTAG
*
243993 TTTAGTTTAATTTAT
1 TTTA-TTTAATTTAG
244008 TTTAT
1 TTTAT
244013 GATTTTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTATTTAATTTAG
Found at i:245021 original size:16 final size:16
Alignment explanation
Indices: 245000--245034 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
244990 GATTGGGGTG
245000 AATGGAATAG-GACTGT
1 AATGGAATAGAG-CTGT
245016 AATGGAATAGAGCTGT
1 AATGGAATAGAGCTGT
245032 AAT
1 AAT
245035 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.40, C:0.06, G:0.29, T:0.26
Consensus pattern (16 bp):
AATGGAATAGAGCTGT
Found at i:253708 original size:57 final size:56
Alignment explanation
Indices: 253618--253750 Score: 194
Period size: 57 Copynumber: 2.3 Consensus size: 56
253608 TATTGTTATT
* * *
253618 AAATTTTAATAGAATTATTATTAAATATAATTTAATAAAAAAATAAATATTTTAATC
1 AAATTTTAATATAATTATTATTAAATATAATTTAAT-AAAAAATAAATAATTTAATA
* * *
253675 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAAAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAAATAATTTAATA
253731 AAATTCTTAATATAATTATT
1 AAATT-TTAATATAATTATT
253751 CTTATATGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 21 0.31
57 46 0.69
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (56 bp):
AAATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAAATAATTTAATA
Found at i:253763 original size:56 final size:55
Alignment explanation
Indices: 253618--253770 Score: 182
Period size: 57 Copynumber: 2.7 Consensus size: 55
253608 TATTGTTATT
* * *
253618 AAATTTTAATAGAATTATTATTAAATATAATTTAATAAAAAAATAAATATTTTAATC
1 AAATTTTAATATAATTATTATT-AATATAATTTAAT-AAAAAATAAATAATTTAATA
* * *
253675 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAAAATATATAATTTAATA
1 AAATTTTAATATAATTATTATT-AATATAATTTAATAAAAAATAAATAATTTAATA
* *
253731 AAATTCTTAATATAATTATTCTT-ATATGAATTTACTAAAA
1 AAATT-TTAATATAATTATTATTAATAT-AATTTAATAAAA
253771 TCATTTTAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
55 4 0.05
56 32 0.38
57 48 0.57
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (55 bp):
AAATTTTAATATAATTATTATTAATATAATTTAATAAAAAATAAATAATTTAATA
Found at i:254958 original size:56 final size:55
Alignment explanation
Indices: 254808--254969 Score: 168
Period size: 57 Copynumber: 2.9 Consensus size: 55
254798 CGATTGTGTG
* **
254808 TCCCTTATTTTTCAGATTTTATAGTTTTGCCCTTATTTAATTAGATTTTACAATTTT
1 TCCCTTATTTTTCAGATTTTATAGTTTTACCCTTATTT--TTAGATTTTACAATAGT
* * * * *
254865 TCCCTTATTTTTTAGATTTTACATTTTTACCCCTATTTTTCAAATTTTACAA-AGT
1 TCCCTTATTTTTCAGATTTTATAGTTTTACCCTTATTTTT-AGATTTTACAATAGT
254920 TCCCTT-TGTTTCTCAGATTTTATAGTTTT-CCCTTTATTTTTTAGATTTTA
1 TCCCTTAT-TTT-TCAGATTTTATAGTTTTACCC-TTA-TTTTTAGATTTTA
254970 TAATTTTTCC
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
54 1 0.01
55 15 0.17
56 33 0.38
57 38 0.44
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (55 bp):
TCCCTTATTTTTCAGATTTTATAGTTTTACCCTTATTTTTAGATTTTACAATAGT
Found at i:255059 original size:84 final size:85
Alignment explanation
Indices: 254861--255065 Score: 231
Period size: 84 Copynumber: 2.4 Consensus size: 85
254851 GATTTTACAA
* *
254861 TTTTTCCCTTATTTTTTAGATTTTAC-ATTTTTACCCCTATTTTTCAAATTTTACAAAGTTCCCT
1 TTTTTCCCTTATTTTTTAGATTTTACAATTTTTACCCCGATTTTTCAAATTTTACAAAGTTCCCC
** *
254925 TTGTTTCTCAGATTTTATAG
66 TAATTTCTCAGATTCTATAG
* * * *
254945 -TTTTCCCTTTATTTTTTAGATTTTATAATTTTT-CCTCGGTTTCTT-AAATTTTACAAATTTCC
1 TTTTTCCC-TTATTTTTTAGATTTTACAATTTTTACCCCGATTT-TTCAAATTTTACAAAGTTCC
*
255007 CCTAATTT-TTAGATTCTATAG
64 CCTAATTTCTCAGATTCTATAG
* * *
255028 TTTTTCCCTTATTTTTTCAAAGTTTACAATTTTGACCC
1 TTTTTCCCTTATTTTTT-AGATTTTACAATTTTTACCC
255066 TAAAGTTTAT
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
83 27 0.27
84 63 0.63
85 10 0.10
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.55
Consensus pattern (85 bp):
TTTTTCCCTTATTTTTTAGATTTTACAATTTTTACCCCGATTTTTCAAATTTTACAAAGTTCCCC
TAATTTCTCAGATTCTATAG
Found at i:255060 original size:28 final size:27
Alignment explanation
Indices: 254808--255060 Score: 166
Period size: 28 Copynumber: 9.0 Consensus size: 27
254798 CGATTGTGTG
* * *
254808 TCCCTTATTTTTCAGATTTTATAGTTT
1 TCCCTTATTTTTTAGATTTTACAATTT
*
254835 TGCCCTTATTTAATTAGATTTTACAATTTT
1 T-CCCTTATTT-TTTAGATTTTACAA-TTT
*
254865 TCCCTTATTTTTTAGATTTTACATTTT
1 TCCCTTATTTTTTAGATTTTACAATTT
* * * **
254892 TACCCCTATTTTTCAAATTTTACAAAGT
1 T-CCCTTATTTTTTAGATTTTACAATTT
* * *
254920 TCCCTT-TGTTTCTCAGATTTTATAGTTT
1 TCCCTTAT-TTT-TTAGATTTTACAATTT
*
254948 TCCCTTTATTTTTTAGATTTTATAATTT
1 TCCC-TTATTTTTTAGATTTTACAATTT
* ** * * *
254976 TTCCTCGGTTTCTTAAATTTTACAAATT
1 TCCCT-TATTTTTTAGATTTTACAATTT
* * * * *
255004 TCCCCTAATTTTTAGATTCTATAGTTTT
1 TCCCTTATTTTTTAGATTTTACA-ATTT
* *
255032 TCCCTTATTTTTTCAAAGTTTACAATTT
1 TCCCTTATTTTTT-AGATTTTACAATTT
255060 T
1 T
255061 GACCCTAAAG
Statistics
Matches: 170, Mismatches: 45, Indels: 21
0.72 0.19 0.09
Matches are distributed among these distances:
26 1 0.01
27 24 0.14
28 110 0.65
29 30 0.18
30 5 0.03
ACGTcount: A:0.23, C:0.16, G:0.06, T:0.55
Consensus pattern (27 bp):
TCCCTTATTTTTTAGATTTTACAATTT
Found at i:255741 original size:133 final size:133
Alignment explanation
Indices: 255500--255761 Score: 337
Period size: 133 Copynumber: 2.0 Consensus size: 133
255490 GTACCCAAAG
* * * * * * * **
255500 CACAGTAGCAGTGTTTATCCTTTAACTACAAATTTGGTGTACATCCACAACTTATCGATAGCTTT
1 CACAGTAGCAATGTTTATCCTTTAACTAAAAAATTGCTATACATCCACAACTCATCGACAAATTT
* * * * *
255565 TACCTGCAATAATGTTTTGCATTTACATCCTAGTGTCAAATTTTATCTGCGATATTTTGCTGTGT
66 TACCTGCAATAATGTTGTGCATCTACAGCCCAGTGTCAAATTTTATCTGCGATATTTTACTGTGT
255630 TCC
131 TCC
* *
255633 CACAGTGGCAATGTTTATCCTTTAACTAAAAAATTGCTATACATCCACAACTCATTGACAAATTT
1 CACAGTAGCAATGTTTATCCTTTAACTAAAAAATTGCTATACATCCACAACTCATCGACAAATTT
* * *
255698 TACTTGCAATAATGTTGTGCATCTACAGCCCAGTGAT-AGATTTTATTTGCGATATTTTACTGTG
66 TACCTGCAATAATGTTGTGCATCTACAGCCCAGTG-TCAAATTTTATCTGCGATATTTTACTGTG
255762 CACCCTCAGC
Statistics
Matches: 109, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
133 108 0.99
134 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (133 bp):
CACAGTAGCAATGTTTATCCTTTAACTAAAAAATTGCTATACATCCACAACTCATCGACAAATTT
TACCTGCAATAATGTTGTGCATCTACAGCCCAGTGTCAAATTTTATCTGCGATATTTTACTGTGT
TCC
Found at i:255806 original size:45 final size:45
Alignment explanation
Indices: 255713--255833 Score: 118
Period size: 45 Copynumber: 2.7 Consensus size: 45
255703 GCAATAATGT
* * * * *
255713 TGTGCATCTACAGCCCAGTGATAGATTTTATTTGCGATATTTTAC
1 TGTGCACCCACAGCCCAGTGGTAGATTTTATTTACAATATTTTAC
* * *
255758 TGTGCACCCTCAGCCCAGTGGTGGATTTTATTTACAA-ATTTTTGC
1 TGTGCACCCACAGCCCAGTGGTAGATTTTATTTACAATA-TTTTAC
* * * *
255803 TGTGTATCCACATCCCAGTGGCAGATTTTAT
1 TGTGCACCCACAGCCCAGTGGTAGATTTTAT
255834 CTGTGAAACC
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (45 bp):
TGTGCACCCACAGCCCAGTGGTAGATTTTATTTACAATATTTTAC
Found at i:258112 original size:26 final size:26
Alignment explanation
Indices: 258081--258157 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
258071 ATGAATTTTC
258081 TCAAAATTTTACTAGGGGTAAAATTA
1 TCAAAATTTTACTAGGGGTAAAATTA
* *
258107 TCAAAATTTTA-TTGGGAGATAAAATCA
1 TCAAAATTTTACTAGGG-G-TAAAATTA
* *
258134 TCAAACTTTTACTA-GAGTAAAATT
1 TCAAAATTTTACTAGGGGTAAAATT
258158 GGGATGAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 10 0.24
26 13 0.31
27 18 0.43
28 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATTA
Found at i:260332 original size:18 final size:18
Alignment explanation
Indices: 260300--260347 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
260290 TATGATGAAT
*
260300 TACCAAAAAATATGAGTGGA
1 TACC-AAAAA-ATGAGAGGA
* *
260320 TACGAAAAAATGAGAGTA
1 TACCAAAAAATGAGAGGA
260338 TACCAAAAAA
1 TACCAAAAAA
260348 AAAACATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 16 0.67
19 5 0.21
20 3 0.12
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17
Consensus pattern (18 bp):
TACCAAAAAATGAGAGGA
Found at i:260356 original size:24 final size:23
Alignment explanation
Indices: 260324--260380 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
260314 AGTGGATACG
*
260324 AAAAAATGAGAG-TATACCAAAAA
1 AAAAAATGAGGGAT-TACCAAAAA
*
260347 AAAAACATGAGGGATTACGAAAAA
1 AAAAA-ATGAGGGATTACCAAAAA
*
260371 AAAAGATGAG
1 AAAAAATGAG
260381 CATAAACCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 10 0.34
24 18 0.62
25 1 0.03
ACGTcount: A:0.61, C:0.07, G:0.19, T:0.12
Consensus pattern (23 bp):
AAAAAATGAGGGATTACCAAAAA
Found at i:264483 original size:19 final size:20
Alignment explanation
Indices: 264438--264482 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
264428 AGATTACTAG
*
264438 AAAACATGAGGGAATACCAA
1 AAAAAATGAGGGAATACCAA
264458 AAAAAATGA-GGATATACCAA
1 AAAAAATGAGGGA-ATACCAA
264478 AAAAA
1 AAAAA
264483 TATAATGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.62, C:0.11, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAAAATGAGGGAATACCAA
Found at i:264772 original size:20 final size:20
Alignment explanation
Indices: 264749--264817 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
264739 AACATGACGG
*
264749 GATACCAAAAATTATGAGAA
1 GATACCAAAAAATATGAGAA
* *
264769 GATACTAAAAAATCTGAG--
1 GATACCAAAAAATATGAGAA
*
264787 GTTACCAAAAAATATGAGTAA
1 GATACCAAAAAATATGAG-AA
264808 -ATACCAAAAA
1 GATACCAAAAA
264818 TTGTGAGGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 15 0.38
20 24 0.62
ACGTcount: A:0.55, C:0.12, G:0.13, T:0.20
Consensus pattern (20 bp):
GATACCAAAAAATATGAGAA
Found at i:264963 original size:20 final size:20
Alignment explanation
Indices: 264938--264998 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
264928 CCAACAATTT
264938 TGAGAGTATACTAAAAAATA
1 TGAGAGTATACTAAAAAATA
* * *
264958 TGAGAGAATA-TCGAAATATA
1 TGAGAGTATACT-AAAAAATA
*
264978 TGAGAGTATACAAAAAAATA
1 TGAGAGTATACTAAAAAATA
264998 T
1 T
264999 AAGGATATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.25
Consensus pattern (20 bp):
TGAGAGTATACTAAAAAATA
Found at i:264999 original size:22 final size:22
Alignment explanation
Indices: 264971--265025 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
264961 GAGAATATCG
264971 AAATATATGAGAGTATA-CAAAA
1 AAATATATGAGA-TATATCAAAA
*
264993 AAATATAAG-GATATATCAAAA
1 AAATATATGAGATATATCAAAA
*
265014 AAA-ACATGAGAT
1 AAATATATGAGAT
265026 GTACCAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.25
21 13 0.46
22 8 0.29
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (22 bp):
AAATATATGAGATATATCAAAA
Found at i:265642 original size:98 final size:99
Alignment explanation
Indices: 265524--265721 Score: 389
Period size: 98 Copynumber: 2.0 Consensus size: 99
265514 TACTTGAAAG
265524 TTCTTAATATTTATAATAATATATTTTTATATTAAAATTATTTCTCGTATGAGGAAATATTAAAA
1 TTCTTAATATTTATAATAATATATTTTTATATTAAAATTATTTCTCGTATGAGGAAATATTAAAA
265589 TATTTTATGGAATACCAAAATTAATGAGAAAATA
66 TATTTTATGGAATACCAAAATTAATGAGAAAATA
265623 TTCTTAATA-TTATAATAATATATTTTTATATTAAAATTATTTCTCGTATGAGGAAATATTAAAA
1 TTCTTAATATTTATAATAATATATTTTTATATTAAAATTATTTCTCGTATGAGGAAATATTAAAA
265687 TATTTTATGGAATACCAAAATTAATGAGAAAATA
66 TATTTTATGGAATACCAAAATTAATGAGAAAATA
265721 T
1 T
265722 AGGCTACCGA
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 90 0.91
99 9 0.09
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (99 bp):
TTCTTAATATTTATAATAATATATTTTTATATTAAAATTATTTCTCGTATGAGGAAATATTAAAA
TATTTTATGGAATACCAAAATTAATGAGAAAATA
Found at i:268116 original size:9 final size:9
Alignment explanation
Indices: 268099--268150 Score: 95
Period size: 9 Copynumber: 5.8 Consensus size: 9
268089 TGAGTTTTCG
268099 AATTCGAAT
1 AATTCGAAT
*
268108 AACTCGAAT
1 AATTCGAAT
268117 AATTCGAAT
1 AATTCGAAT
268126 AATTCGAAT
1 AATTCGAAT
268135 AATTCGAAT
1 AATTCGAAT
268144 AATTCGA
1 AATTCGA
268151 CTATCAAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:268439 original size:7 final size:7
Alignment explanation
Indices: 268427--268462 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
268417 TCCCTTTCCA
268427 TCCCACC
1 TCCCACC
268434 TCCCACC
1 TCCCACC
268441 TCCCACC
1 TCCCACC
*
268448 TCCCATC
1 TCCCACC
268455 TCCCACC
1 TCCCACC
268462 T
1 T
268463 ACCCCAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.67, G:0.00, T:0.19
Consensus pattern (7 bp):
TCCCACC
Found at i:283519 original size:20 final size:22
Alignment explanation
Indices: 283482--283528 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
283472 GCCATACAGC
*
283482 TGTGTGCCTCCTTTCACATGAG
1 TGTGTGCCTCCTTCCACATGAG
*
283504 TGTGTGCCT-C-TCCACATGGG
1 TGTGTGCCTCCTTCCACATGAG
283524 TGTGT
1 TGTGT
283529 TGACCCCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 9 0.39
ACGTcount: A:0.11, C:0.26, G:0.28, T:0.36
Consensus pattern (22 bp):
TGTGTGCCTCCTTCCACATGAG
Found at i:288022 original size:27 final size:28
Alignment explanation
Indices: 287992--288135 Score: 111
Period size: 27 Copynumber: 5.3 Consensus size: 28
287982 AGGGGCATAA
*
287992 CGGTCATTTTACCCCAT-GAGGGTATTT
1 CGGTAATTTTACCCCATCGAGGGTATTT
* ** *
288019 CGGTTATTTT-CCCTTTCGGGGGTATTT
1 CGGTAATTTTACCCCATCGAGGGTATTT
*
288046 CAGTAATTTTA--CCATTCGAGGGTATTT
1 CGGTAATTTTACCCCA-TCGAGGGTATTT
* * *
288073 TGGTAATTTTA-CCCTTCGAAGGTATTT
1 CGGTAATTTTACCCCATCGAGGGTATTT
*** *
288100 CAAAAATTTTA-CCCTTCGAGGGTATTT
1 CGGTAATTTTACCCCATCGAGGGTATTT
*
288127 TGGTAATTT
1 CGGTAATTT
288136 AACAACCTTT
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
26 5 0.05
27 84 0.92
28 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (28 bp):
CGGTAATTTTACCCCATCGAGGGTATTT
Found at i:288082 original size:54 final size:54
Alignment explanation
Indices: 288009--288135 Score: 175
Period size: 54 Copynumber: 2.4 Consensus size: 54
287999 TTTACCCCAT
* * ** **
288009 GAGGGTATTTCGGTTATTTT-CCCTTTCGGGGGTATTTCAGTAATTTTACCATTC
1 GAGGGTATTTTGGTAATTTTACCC-TTCGAAGGTATTTCAAAAATTTTACCATTC
*
288063 GAGGGTATTTTGGTAATTTTACCCTTCGAAGGTATTTCAAAAATTTTACCCTTC
1 GAGGGTATTTTGGTAATTTTACCCTTCGAAGGTATTTCAAAAATTTTACCATTC
288117 GAGGGTATTTTGGTAATTT
1 GAGGGTATTTTGGTAATTT
288136 AACAACCTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 62 0.95
55 3 0.05
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (54 bp):
GAGGGTATTTTGGTAATTTTACCCTTCGAAGGTATTTCAAAAATTTTACCATTC
Found at i:290508 original size:24 final size:24
Alignment explanation
Indices: 290477--290525 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
290467 CCAACTATAA
290477 AAAGTTACAAAATGATCACCCACT
1 AAAGTTACAAAATGATCACCCACT
290501 AAAGTTACAAAATGATCACCCACT
1 AAAGTTACAAAATGATCACCCACT
290525 A
1 A
290526 TTCTATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.20
Consensus pattern (24 bp):
AAAGTTACAAAATGATCACCCACT
Found at i:294694 original size:21 final size:21
Alignment explanation
Indices: 294669--294712 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
294659 CAAGGTTTCT
*
294669 TCCAGCTGCCAAGTGGCTTCC
1 TCCAGCTCCCAAGTGGCTTCC
294690 TCCAGCTCCCAAGTGGCTTCC
1 TCCAGCTCCCAAGTGGCTTCC
294711 TC
1 TC
294713 AATACCATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.41, G:0.20, T:0.25
Consensus pattern (21 bp):
TCCAGCTCCCAAGTGGCTTCC
Found at i:296643 original size:207 final size:207
Alignment explanation
Indices: 296277--296688 Score: 709
Period size: 207 Copynumber: 2.0 Consensus size: 207
296267 CAAGCTCTTA
* **
296277 TGATCAATGCGTATATGGAACTTTTCTGAATAAAAGTAATGTTTCAGGATTTTTAGAGCAAAGGT
1 TGATCAATGCATATATGGAACTTTTCAAAATAAAAGTAATGTTTCAGGATTTTTAGAGCAAAGGT
* * * *
296342 AACAGCTACCAATTCTAGATTGGGCATTAGATAGTTCTTCTCGTGTGAATTTAACTGTTGAGAAG
66 AACAACTACCAATTCTAGATCGGGCATTAGATAGTTCTTCTCATGTGAATTTAACTGTCGAGAAG
296407 CATAAGCAATCACCTTACCTTCTTGCACCGAAATGCAACCTAATCCACTGAGCGAAGCATTACTA
131 CATAAGCAATCACCTTACCTTCTTGCACCGAAATGCAACCTAATCCACTGAGCGAAGCATTACTA
296472 TAAACAACGACT
196 TAAACAACGACT
* * *
296484 TGATCAGTGCATATATGGAATTTTTCAAAATAAAAGTAATGTTTCCA-GATTTTTAGAGCAAATG
1 TGATCAATGCATATATGGAACTTTTCAAAATAAAAGTAATGTTT-CAGGATTTTTAGAGCAAAGG
*
296548 TAACAACTACCAATTCTAGATCGGGCGTTAGATAGTTCTTCTCATGTGAATTTAACTGTCGAGAA
65 TAACAACTACCAATTCTAGATCGGGCATTAGATAGTTCTTCTCATGTGAATTTAACTGTCGAGAA
296613 GCATAAGCAATCACCTTACCTTCTTGCACCGAAATGCAACCTAATCCACTGAGCGAAGCATTACT
130 GCATAAGCAATCACCTTACCTTCTTGCACCGAAATGCAACCTAATCCACTGAGCGAAGCATTACT
296678 ATAAACAACGA
195 ATAAACAACGA
296689 ATTCCTTTCC
Statistics
Matches: 193, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
207 191 0.99
208 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (207 bp):
TGATCAATGCATATATGGAACTTTTCAAAATAAAAGTAATGTTTCAGGATTTTTAGAGCAAAGGT
AACAACTACCAATTCTAGATCGGGCATTAGATAGTTCTTCTCATGTGAATTTAACTGTCGAGAAG
CATAAGCAATCACCTTACCTTCTTGCACCGAAATGCAACCTAATCCACTGAGCGAAGCATTACTA
TAAACAACGACT
Found at i:302381 original size:13 final size:14
Alignment explanation
Indices: 302316--302400 Score: 61
Period size: 13 Copynumber: 5.9 Consensus size: 14
302306 TAACATTACT
302316 GAAAATAATAATAA
1 GAAAATAATAATAA
302330 GATTGAAATAATCAATAA
1 GA---AAATAAT-AATAA
*
302348 -AAACTATAATACTAA
1 GAAA--ATAATAATAA
*
302363 G-TAATAA-AATAA
1 GAAAATAATAATAA
*
302375 GAAAATAATAA-AT
1 GAAAATAATAATAA
302388 GAAAATAATAATA
1 GAAAATAATAATA
302401 CTAACTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
12 5 0.09
13 21 0.38
14 7 0.12
15 5 0.09
16 5 0.09
17 8 0.14
18 5 0.09
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (14 bp):
GAAAATAATAATAA
Found at i:302503 original size:18 final size:18
Alignment explanation
Indices: 302482--302516 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
302472 AATAATAAAT
302482 GAATAAATAAAAA-CTAAG
1 GAATAAA-AAAAAGCTAAG
302500 GAATAAAAAAAAGCTAA
1 GAATAAAAAAAAGCTAA
302517 TAAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.69, C:0.06, G:0.11, T:0.14
Consensus pattern (18 bp):
GAATAAAAAAAAGCTAAG
Found at i:309529 original size:18 final size:18
Alignment explanation
Indices: 309478--309536 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 18
309468 TAAATTACGA
309478 TTTTAACCCTCACAATGC
1 TTTTAACCCTCACAATGC
* *
309496 TTTTGTCACACTCACAATGC
1 -TTT-TAACCCTCACAATGC
309516 TTTTAACCCTCACAATG-
1 TTTTAACCCTCACAATGC
309533 TTTT
1 TTTT
309537 GCTCCCACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.11
18 12 0.34
19 6 0.17
20 13 0.37
ACGTcount: A:0.25, C:0.29, G:0.07, T:0.39
Consensus pattern (18 bp):
TTTTAACCCTCACAATGC
Found at i:314301 original size:50 final size:50
Alignment explanation
Indices: 314133--314320 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
314123 TATCGATGAA
* * *
314133 CACGCGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-TAAA-ACTTGGT
* * * * *
314184 CACATGTGTAGTACTAAGTGAAGGATACTATGTGTACTG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAA-C-TTGGT
* * *
314235 CACGTGTGTAGTACTATGTGAAGGCTAGTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGT
*
314285 CACGTTTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
314321 TCGAATGATA
Statistics
Matches: 114, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 37 0.32
51 69 0.61
52 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGT
Found at i:323419 original size:153 final size:153
Alignment explanation
Indices: 323141--323428 Score: 479
Period size: 153 Copynumber: 1.9 Consensus size: 153
323131 AATCAATCAA
* *
323141 TTGATGAGTACTTCAAGAAAAGATGGTCAAATGAAAGAAAGAGTACAATTGATCTTACACTTGTT
1 TTGATGAGTACTTCAAGAAAAGATGGTCAAATGAAAGAAAGAGTACAATTGATCTTACACCTATT
* * *
323206 GTGAAATGTTATTGGTGTAGTTCAAAAGATCATGAGGGTTTCCAATGTCCAATTAAATGTCCAAC
66 GTGAAATGTTATTGGTGTAGCTCAAAAGATCATGAGGGTATACAATGTCCAATTAAATGTCCAAC
323271 TAGAAAGTAATTATGACTTTCAG
131 TAGAAAGTAATTATGACTTTCAG
*
323294 TTGATGAGTACTTCAAGAAGAGATGGTCAAATGAAAGAAAGAGTACAATTGATCTCT-CACCTAT
1 TTGATGAGTACTTCAAGAAAAGATGGTCAAATGAAAGAAAGAGTACAATTGATCT-TACACCTAT
* **
323358 TGTGAAATGTTATTGGTGTAGCTCAAAAGATCATGCGGGTATACGGTGTCCAATTAAATGTCCAA
65 TGTGAAATGTTATTGGTGTAGCTCAAAAGATCATGAGGGTATACAATGTCCAATTAAATGTCCAA
323423 CTAGAA
130 CTAGAA
323429 GGTATGACTT
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
153 124 0.99
154 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (153 bp):
TTGATGAGTACTTCAAGAAAAGATGGTCAAATGAAAGAAAGAGTACAATTGATCTTACACCTATT
GTGAAATGTTATTGGTGTAGCTCAAAAGATCATGAGGGTATACAATGTCCAATTAAATGTCCAAC
TAGAAAGTAATTATGACTTTCAG
Found at i:323763 original size:22 final size:21
Alignment explanation
Indices: 323738--323779 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
323728 ACAAGACACT
*
323738 ACATCAACATCATAAATTTTAC
1 ACATCAAC-GCATAAATTTTAC
*
323760 ACATCTACGCATAAATTTTA
1 ACATCAACGCATAAATTTTA
323780 AGCAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.33
Consensus pattern (21 bp):
ACATCAACGCATAAATTTTAC
Found at i:324329 original size:30 final size:29
Alignment explanation
Indices: 324295--324383 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 29
324285 ATATTGTAAA
*
324295 TCCAATATCCGATACCCATATCTTTGACTT
1 TCCAATAT-TGATACCCATATCTTTGACTT
*
324325 TCCAATATTTGATACCCATATATTTGACTT
1 TCCAATA-TTGATACCCATATCTTTGACTT
324355 T---AT-TTGATACCCATATCTTTGACTT
1 TCCAATATTGATACCCATATCTTTGACTT
324380 TCCA
1 TCCA
324384 TAAATATGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
25 22 0.42
27 2 0.04
30 27 0.52
31 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.42
Consensus pattern (29 bp):
TCCAATATTGATACCCATATCTTTGACTT
Found at i:324347 original size:15 final size:15
Alignment explanation
Indices: 324305--324351 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
324295 TCCAATATCC
*
324305 GATACCCATATCTTT
1 GATACCCATATATTT
**
324320 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
324335 GATACCCATATATTT
1 GATACCCATATATTT
324350 GA
1 GA
324352 CTTTATTTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:324364 original size:25 final size:25
Alignment explanation
Indices: 324330--324380 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
324320 GACTTTCCAA
324330 TATTTGATACCCATATATTTGACTT
1 TATTTGATACCCATATATTTGACTT
*
324355 TATTTGATACCCATATCTTTGACTT
1 TATTTGATACCCATATATTTGACTT
324380 T
1 T
324381 CCATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (25 bp):
TATTTGATACCCATATATTTGACTT
Found at i:328898 original size:31 final size:30
Alignment explanation
Indices: 328863--328926 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
328853 ATTTCTTATG
* *
328863 CCAATATCTCGATACCCATATCTTTTACTTT
1 CCAATAT-TCAATACCCATATCTTTGACTTT
*
328894 CCAATATTTAATACCCATATCTTTGACTTT
1 CCAATATTCAATACCCATATCTTTGACTTT
328924 CCA
1 CCA
328927 TAAATATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (30 bp):
CCAATATTCAATACCCATATCTTTGACTTT
Found at i:339256 original size:40 final size:40
Alignment explanation
Indices: 339199--339337 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
339189 TTATTCTCTC
* *
339199 TGTCTGGTGTGTTTCGGTTGGATTAGCTTTTATGAGCTTA
1 TGTCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCTTA
* *
339239 TATCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCTTC
1 TGTCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCTTA
*
339279 TGTCTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGCTTA
1 TGTCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCTTA
339319 TGTCTGGTGTG-TTCGGTTG
1 TGTCTGGTGTGTTTCGGTTG
339338 ATCTGACGAT
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 7 0.08
40 84 0.92
ACGTcount: A:0.12, C:0.14, G:0.30, T:0.45
Consensus pattern (40 bp):
TGTCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCTTA
Found at i:340878 original size:20 final size:20
Alignment explanation
Indices: 340853--340900 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
340843 TCGATCCGGA
*
340853 ATCGATACT-TTTCTTAAGGT
1 ATCGATA-TATTTCCTAAGGT
340873 ATCGATATATTTCCTAAGGT
1 ATCGATATATTTCCTAAGGT
340893 ATCGATAT
1 ATCGATAT
340901 TCTTGCACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATCGATATATTTCCTAAGGT
Found at i:347380 original size:21 final size:21
Alignment explanation
Indices: 347355--347432 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
347345 ATTTTTGAGG
347355 ATATGTAATCTTAGATATGAT
1 ATATGTAATCTTAGATATGAT
*
347376 ATATGCAATCTTAGATATG--
1 ATATGTAATCTTAGATATGAT
347395 ATATGTAATCTTAGAAGATATGAT
1 ATATGTAATCTT---AGATATGAT
*
347419 -TTTGTAATCTTAGA
1 ATATGTAATCTTAGA
347433 GATTTAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 11 0.22
20 3 0.06
21 18 0.37
22 7 0.14
23 10 0.20
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.41
Consensus pattern (21 bp):
ATATGTAATCTTAGATATGAT
Found at i:347428 original size:23 final size:22
Alignment explanation
Indices: 347354--347432 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 22
347344 AATTTTTGAG
*
347354 GATATGTAATCTTAG-ATATGAT
1 GATATGTAATCTTAGAAGAT-AT
*
347376 -ATATGCAATCTT---AGATAT
1 GATATGTAATCTTAGAAGATAT
347394 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTTAGAAGATAT
*
347416 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
347433 GATTTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.29
21 11 0.23
22 8 0.17
23 13 0.27
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (22 bp):
GATATGTAATCTTAGAAGATAT
Found at i:347442 original size:22 final size:23
Alignment explanation
Indices: 347398--347442 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
347388 AGATATGATA
*
347398 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
347421 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
347443 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:348588 original size:98 final size:98
Alignment explanation
Indices: 348480--348671 Score: 348
Period size: 98 Copynumber: 2.0 Consensus size: 98
348470 TTAAAAATAA
* *
348480 TAAAGGAAATATTCCGAATTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
348545 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
348578 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
348643 TTAAATCTTGGATAAGTGGATGTTCTTTT
66 TTAAATCTTGGATAAGTGGATGTTCTTTT
348672 GAAATTTTAT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:351860 original size:16 final size:16
Alignment explanation
Indices: 351839--351870 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
351829 CAATTTTGAA
*
351839 ATTCAATCTATATTTT
1 ATTCAATATATATTTT
351855 ATTCAATATATATTTT
1 ATTCAATATATATTTT
351871 CCCAGTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTCAATATATATTTT
Found at i:353854 original size:18 final size:18
Alignment explanation
Indices: 353831--353875 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
353821 ACGCAATAAA
353831 ACACATATATCCATATAT
1 ACACATATATCCATATAT
353849 ACACATATATCCATATAT
1 ACACATATATCCATATAT
*
353867 ATACATATA
1 ACACATATA
353876 AATACCTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (18 bp):
ACACATATATCCATATAT
Found at i:353855 original size:10 final size:10
Alignment explanation
Indices: 353831--353875 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 10
353821 ACGCAATAAA
353831 ACACATATAT
1 ACACATATAT
353841 -C-CATATAT
1 ACACATATAT
353849 ACACATATAT
1 ACACATATAT
353859 -C-CATATAT
1 ACACATATAT
*
353867 ATACATATA
1 ACACATATA
353876 AATACCTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
8 14 0.47
9 3 0.10
10 13 0.43
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (10 bp):
ACACATATAT
Found at i:355709 original size:27 final size:29
Alignment explanation
Indices: 355671--355727 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 29
355661 AATAAACAAA
*
355671 AAAAAAGGAGAGAT-GA-GATGTTCTTAC
1 AAAAAAGAAGAGATGGATGATGTTCTTAC
355698 AAAAAAGAAGAGATGGATGATGTTCTTAC
1 AAAAAAGAAGAGATGGATGATGTTCTTAC
355727 A
1 A
355728 TCAAAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.48
28 2 0.07
29 12 0.44
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.23
Consensus pattern (29 bp):
AAAAAAGAAGAGATGGATGATGTTCTTAC
Done.